Index: trunk/psModules/configure.ac =================================================================== --- trunk/psModules/configure.ac (revision 6529) +++ trunk/psModules/configure.ac (revision 6872) @@ -8,20 +8,8 @@ AM_MAINTAINER_MODE -dnl handle debug building -AC_ARG_ENABLE(optimize, - [AS_HELP_STRING(--enable-optimize,enable compiler optimization)], - [AC_MSG_RESULT(compile optimization enabled) - CFLAGS="${CFLAGS=} -O2"], - [AC_MSG_RESULT([compile optimization disabled]) - CFLAGS="${CFLAGS=} -O0 -g"] -) - -dnl handle profiler building -AC_ARG_ENABLE(profile, - [AS_HELP_STRING(--enable-profile,enable compiler profiler information inclusion)], - [AC_MSG_RESULT(compile optimization enabled) - CFLAGS="${CFLAGS=} -fprofile-arcs -ftest-coverage -pg"] -) - +dnl otherise AC_PROG_CC will default CFLAGS to "-g -02" +if test -z ${CFLAGS} ; then + CFLAGS="" +fi AC_SUBST([CFLAGS]) @@ -29,8 +17,7 @@ AC_PROG_CC dnl FIXME document why GNU_SOURCE is being set -dnl AC_GNU_SOURCE +AC_GNU_SOURCE AC_PROG_INSTALL AM_PROG_LIBTOOL -AC_SYS_LARGEFILE AC_PREFIX_DEFAULT([`pwd`]) @@ -62,12 +49,30 @@ SRCPATH='${top_srcdir}/src' -SRCDIRS="astrom camera config detrend imcombine imsubtract objects photom" +SRCDIRS="astrom config detrend imcombine imsubtract objects pslib" # escape two escapes at this level so \\ gets passed to the shell and \ to perl SRCINC=`echo "${SRCDIRS=}" | ${PERL} -pe "s|(\w+)|-I\\\\${SRCPATH=}/\1|g"` SRCINC="-I${SRCPATH=} ${SRCINC=}" SRCSUBLIBS=`echo "${SRCDIRS=}" | ${PERL} -pe "s|(\w+)|\1/libpsmodule\1.la|g"` -AC_SUBST([SRCSUBLIBS],${SRCSUBLIBS=}) -AC_SUBST([SRCINC],${SRCINC=}) +AC_SUBST(SRCSUBLIBS,${SRCSUBLIBS=}) +AC_SUBST(SRCINC,${SRCINC=}) AC_SUBST([SRCDIRS],${SRCDIRS=}) + +dnl handle debug building +AC_ARG_ENABLE(optimize, + [AS_HELP_STRING(--enable-optimize,enable compiler optimization)], + [AC_MSG_RESULT(compile optimization enabled) + CFLAGS="${CFLAGS=} -O2"], + [AC_MSG_RESULT([compile optimization disabled]) + CFLAGS="${CFLAGS=} -O0 -g"] +) + +dnl handle profiler building +AC_ARG_ENABLE(profile, + [AS_HELP_STRING(--enable-profile,enable compiler profiler information inclusion)], + [AC_MSG_RESULT(compile optimization enabled) + CFLAGS="${CFLAGS=} -pg"] +) + +dnl CFLAGS="${CFLAGS=} -fprofile-arcs -ftest-coverage -pg"] dnl doxygen ------------------------------------------------------------------- @@ -75,4 +80,8 @@ AC_CHECK_PROG([doxygen], [doxygen], [true], [false]) AM_CONDITIONAL(DOXYGEN, test x$doxygen = xtrue) + +dnl libjpeg ------------------------------------------------------------------- + +AC_CHECK_LIB(jpeg,jpeg_CreateCompress,[],[AC_MSG_ERROR([jpeg library not found.])]) dnl pslib --------------------------------------------------------------------- @@ -82,5 +91,5 @@ if test -z ${PSLIB_CONFIG} ; then - PKG_CHECK_MODULES([PSLIB], [pslib >= 0.10.0]) + PKG_CHECK_MODULES([PSLIB], [pslib >= 0.9.0]) else AC_CHECK_FILE($PSLIB_CONFIG,[], @@ -105,5 +114,4 @@ src/Makefile src/astrom/Makefile - src/camera/Makefile src/config/Makefile src/detrend/Makefile @@ -111,8 +119,7 @@ src/imsubtract/Makefile src/objects/Makefile - src/photom/Makefile + src/pslib/Makefile test/Makefile test/astrom/Makefile - test/camera/Makefile test/config/Makefile test/detrend/Makefile @@ -120,5 +127,5 @@ test/imsubtract/Makefile test/objects/Makefile - test/photom/Makefile + test/pslib/Makefile Doxyfile psmodule-config Index: trunk/psModules/src/Makefile.am =================================================================== --- trunk/psModules/src/Makefile.am (revision 6529) +++ trunk/psModules/src/Makefile.am (revision 6872) @@ -7,3 +7,6 @@ libpsmodule_la_DEPENDENCIES = $(SRCSUBLIBS) +include_HEADERS = \ + psmodules.h + EXTRA_DIST = psErrorCodes.dat Index: trunk/psModules/src/astrom/Makefile.am =================================================================== --- trunk/psModules/src/astrom/Makefile.am (revision 6529) +++ trunk/psModules/src/astrom/Makefile.am (revision 6872) @@ -1,12 +1,50 @@ noinst_LTLIBRARIES = libpsmoduleastrom.la -libpsmoduleastrom_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) +libpsmoduleastrom_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) -I../pslib/ libpsmoduleastrom_la_LDFLAGS = -release $(PACKAGE_VERSION) libpsmoduleastrom_la_SOURCES = \ - pmAstrometry.c \ - pmAstrometryObjects.c + pmFPA.c \ + pmFPAConstruct.c \ + pmFPACopy.c \ + pmFPAMaskWeight.c \ + pmFPARead.c \ + pmFPAUtils.c \ + pmFPAWrite.c \ + pmHDU.c \ + pmHDUUtils.c \ + pmReadout.c \ + pmConcepts.c \ + pmConceptsRead.c \ + pmConceptsWrite.c \ + pmConceptsStandard.c \ + pmFPA_JPEG.c \ + pmFPAview.c \ + pmFPAfile.c + +# pmFPAAstrometry.c +# pmAstrometryObjects.c +# pmChipMosaic.c psmoduleincludedir = $(includedir) psmoduleinclude_HEADERS = \ - pmAstrometry.h \ - pmAstrometryObjects.h + pmFPA.h \ + pmFPAConstruct.h \ + pmFPACopy.h \ + pmFPAMaskWeight.h \ + pmFPARead.h \ + pmFPAUtils.h \ + pmFPAWrite.h \ + pmHDU.h \ + pmHDUUtils.h \ + pmReadout.h \ + pmConcepts.h \ + pmConceptsRead.h \ + pmConceptsWrite.h \ + pmConceptsStandard.h \ + pmFPA_JPEG.h \ + pmFPAview.h \ + pmFPAfile.h + +# pmFPAAstrometry.h +# pmAstrometryObjects.h +# pmChipMosaic.h Index: trunk/psModules/src/astrom/pmAstrometry.c =================================================================== --- trunk/psModules/src/astrom/pmAstrometry.c (revision 6529) +++ trunk/psModules/src/astrom/pmAstrometry.c (revision 6872) @@ -10,9 +10,9 @@ * XXX: We should review the extent of the warning messages on these functions * when the transformations are not successful. -* +* * XXX: Should we implement non-linear cell->chip transforms? -* -* @version $Revision: 1.12 $ $Name: not supported by cvs2svn $ -* @date $Date: 2006-01-26 21:10:50 $ +* +* @version $Revision: 1.13 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ * * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii @@ -25,5 +25,7 @@ #include #include "pslib.h" + #include "pmAstrometry.h" +#include "pmConcepts.h" /***************************************************************************** @@ -60,21 +62,11 @@ psFree(readout->mask); psFree(readout->weight); - // - // XXX: Not sure if this is the right way to do things. Currently the psListAdd() - // increase the memory reference counter to the list data. So, we - // iterate through the list, and decrement the reference counters. - // - if (1) { - if ((readout->bias != NULL) && (readout->bias->head != NULL)) { - psListElem *tmpElem = (psListElem *) readout->bias->head; - while (NULL != tmpElem) { - psMemDecrRefCounter((psImage *) tmpElem->data); - tmpElem = tmpElem->next; - } - } - } - psFree(readout->bias); psFree(readout->analysis); + #if 0 + psFree(readout->parent); + #endif + + readout->parent = NULL; } } @@ -88,8 +80,11 @@ psFree(cell->concepts); psFree(cell->analysis); + psFree(cell->camera); // // Set the parent to NULL in all cell->readouts before psFree(cell->readouts) // in order to avoid memory reference counter problems. // + #if 0 + for (psS32 i = 0 ; i < cell->readouts->n ; i++) { pmReadout *tmpReadout = (pmReadout *) cell->readouts->data[i]; @@ -99,7 +94,12 @@ } } + psFree(cell->parent); + #endif + + cell->parent = NULL; + psFree(cell->readouts); - psFree(cell->parent); psFree(cell->hdu); + } } @@ -116,4 +116,6 @@ // in order to avoid memory reference counter problems. // + #if 0 + for (psS32 i = 0 ; i < chip->cells->n ; i++) { pmCell *tmpCell = (pmCell *) chip->cells->data[i]; @@ -123,6 +125,9 @@ } } + psFree(chip->parent); + #endif + + chip->parent = NULL; psFree(chip->cells); - psFree(chip->parent); psFree(chip->hdu); } @@ -143,4 +148,6 @@ // in order to avoid memory reference counter problems. // + #if 0 + for (psS32 i = 0 ; i < fpa->chips->n ; i++) { pmChip *tmpChip = (pmChip *) fpa->chips->data[i]; @@ -150,4 +157,5 @@ } } + #endif psFree(fpa->chips); psFree(fpa->hdu); @@ -156,17 +164,28 @@ } +void p_pmHDUFree(p_pmHDU *hdu) +{ + if (hdu) { + psFree(hdu->extname); + psFree(hdu->header); + psFree(hdu->images); + psFree(hdu->masks); + psFree(hdu->weights); + } +} + // XXX: Verify these default values for row0, col0, rowBins, colBins +// PAP: These values may disappear in the future in favour of values in parent->concepts? pmReadout *pmReadoutAlloc(pmCell *cell) { pmReadout *tmpReadout = (pmReadout *) psAlloc(sizeof(pmReadout)); - tmpReadout->col0 = -1; - tmpReadout->row0 = -1; - tmpReadout->colBins = -1; - tmpReadout->rowBins = -1; + tmpReadout->col0 = 0; + tmpReadout->row0 = 0; + tmpReadout->colBins = 0; + tmpReadout->rowBins = 0; tmpReadout->image = NULL; tmpReadout->mask = NULL; tmpReadout->weight = NULL; - tmpReadout->bias = NULL; tmpReadout->analysis = psMetadataAlloc(); tmpReadout->parent = cell; @@ -179,13 +198,14 @@ // XXX: Verify these default values for row0, col0. +// PAP: These values may disappear in the future in favour of values in the "concepts"? pmCell *pmCellAlloc( pmChip *chip, - psMetadata *cameradata, - psString name) + psMetadata *cameraData, + const char *name) { pmCell *tmpCell = (pmCell *) psAlloc(sizeof(pmCell)); - tmpCell->col0 = -1; - tmpCell->row0 = -1; + tmpCell->col0 = 0; + tmpCell->row0 = 0; tmpCell->toChip = NULL; tmpCell->toFPA = NULL; @@ -196,6 +216,6 @@ psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not add CELL.NAME to metadata.\n"); } - tmpCell->camera = cameradata; - tmpCell->analysis = NULL; + tmpCell->camera = psMemIncrRefCounter(cameraData); + tmpCell->analysis = psMetadataAlloc(); tmpCell->readouts = psArrayAlloc(0); tmpCell->parent = chip; @@ -203,6 +223,9 @@ chip->cells = psArrayAdd(chip->cells, 1, (psPtr) tmpCell); } - tmpCell->valid = false; + tmpCell->process = true; // All cells are processed by default + tmpCell->exists = false; // Not yet read in tmpCell->hdu = NULL; + + pmConceptsBlankCell(tmpCell); psMemSetDeallocator(tmpCell, (psFreeFunc) cellFree); @@ -211,12 +234,13 @@ // XXX: Verify these default values for row0, col0. +// PAP: row0, col0 may disappear in the future in favour of storing values in the "concepts". pmChip *pmChipAlloc( pmFPA *fpa, - psString name) + const char *name) { pmChip *tmpChip = (pmChip *) psAlloc(sizeof(pmChip)); - tmpChip->col0 = -1; - tmpChip->row0 = -1; + tmpChip->col0 = 0; + tmpChip->row0 = 0; tmpChip->toFPA = NULL; tmpChip->fromFPA = NULL; @@ -226,5 +250,5 @@ psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not add CHIP.NAME to metadata.\n"); } - tmpChip->analysis = NULL; + tmpChip->analysis = psMetadataAlloc(); tmpChip->cells = psArrayAlloc(0); tmpChip->parent = fpa; @@ -232,6 +256,9 @@ fpa->chips = psArrayAdd(fpa->chips, 1, (psPtr) tmpChip); } - tmpChip->valid = false; + tmpChip->process = true; // Work on all chips, by default + tmpChip->exists = false; // Not read in yet tmpChip->hdu = NULL; + + pmConceptsBlankChip(tmpChip); psMemSetDeallocator(tmpChip, (psFreeFunc) chipFree); @@ -248,11 +275,27 @@ tmpFPA->concepts = psMetadataAlloc(); tmpFPA->analysis = NULL; - tmpFPA->camera = camera; + tmpFPA->camera = psMemIncrRefCounter((psPtr)camera); tmpFPA->chips = psArrayAlloc(0); tmpFPA->hdu = NULL; tmpFPA->phu = NULL; + pmConceptsBlankFPA(tmpFPA); + psMemSetDeallocator(tmpFPA, (psFreeFunc) FPAFree); return(tmpFPA); +} + +p_pmHDU *p_pmHDUAlloc(const char *extname) +{ + p_pmHDU *hdu = psAlloc(sizeof(p_pmHDU)); + psMemSetDeallocator(hdu, (psFreeFunc)p_pmHDUFree); + + hdu->extname = psStringCopy(extname); + hdu->header = NULL; + hdu->images = NULL; + hdu->masks = NULL; + hdu->weights = NULL; + + return hdu; } @@ -317,485 +360,26 @@ -/*****************************************************************************/ -/* FUNCTION IMPLEMENTATION - PUBLIC */ -/*****************************************************************************/ - -pmCell* pmCellInFPA( - const psPlane* fpaCoord, - const pmFPA* FPA) -{ - PS_ASSERT_PTR_NON_NULL(fpaCoord, NULL); - PS_ASSERT_PTR_NON_NULL(FPA, NULL); - - pmChip* tmpChip = NULL; - psPlane chipCoord; - pmCell* outCell = NULL; - - // Determine which chip contains the fpaCoords. - tmpChip = pmChipInFPA(fpaCoord, FPA); - if (tmpChip == NULL) { - return(NULL); - } - - // Convert to those chip coordinates. - psPlane *rc = pmCoordFPAToChip(&chipCoord, fpaCoord, tmpChip); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine Chip coords.\n"); - return(NULL); - } - - // Determine which cell contains those chip coordinates. - outCell = pmCellInChip(&chipCoord, tmpChip); - if (outCell == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the cell.\n"); - return(NULL); - } - - return (outCell); -} - -pmChip* pmChipInFPA( - const psPlane* fpaCoord, - const pmFPA* FPA) -{ - PS_ASSERT_PTR_NON_NULL(fpaCoord, NULL); - PS_ASSERT_PTR_NON_NULL(FPA, NULL); - PS_ASSERT_PTR_NON_NULL(FPA->chips, NULL); - - psArray* chips = FPA->chips; - psS32 nChips = chips->n; - psPlane chipCoord; - pmCell *tmpCell = NULL; - - // - // Loop through every chip in this FPA. Convert the original FPA - // coordinates to chip coordinates for that chip. Then, determine if any - // cells in that chip contain those chip coordinates. - // XXX: Depending on the number of chips, and their topology, there may be - // a much more efficient way of doing this. - // - for (psS32 i = 0; i < nChips; i++) { - pmChip* tmpChip = chips->data[i]; - PS_ASSERT_PTR_NON_NULL(tmpChip, NULL); - PS_ASSERT_PTR_NON_NULL(tmpChip->fromFPA, NULL); - - psPlaneTransformApply(&chipCoord, tmpChip->fromFPA, fpaCoord); - - tmpCell = pmCellInChip(&chipCoord, tmpChip); - if (tmpCell != NULL) { - return(tmpChip); - } - } - - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the chip.\n"); - return (NULL); -} - - -pmCell* pmCellInChip( - const psPlane* chipCoord, - const pmChip* chip) -{ - PS_ASSERT_PTR_NON_NULL(chipCoord, NULL); - PS_ASSERT_PTR_NON_NULL(chip, NULL); - - psPlane cellCoord; - psArray* cells; - - cells = chip->cells; - if (cells == NULL) { - return NULL; - } - - // - // We loop over each cell in the chip. We transform the chipCoord into - // a cellCoord for that cell and determine if that cellCoord is valid. - // If so, then we return that cell. - // XXX: Depending on the number of cells, and their topology, there may be - // a much more efficient way of doing this. - // - for (psS32 i = 0; i < cells->n; i++) { - pmCell* tmpCell = (pmCell* ) cells->data[i]; - PS_ASSERT_PTR_NON_NULL(tmpCell, NULL); - - psPlaneTransform *chipToCell = NULL; - if (true == p_psIsProjectionLinear(tmpCell->toChip)) { - chipToCell = p_psPlaneTransformLinearInvert(tmpCell->toChip); - } else { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: non-linear cell->chip transforms are not yet implemented.\n"); - //chipToCell = psPlaneTransformInvert(NULL, tmpCell->toChip, NULL, -1); - chipToCell = NULL; - } - if (chipToCell == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not invert the Cell->toChip transform.\n"); - return(NULL); - } - psArray* readouts = tmpCell->readouts; - - if (readouts != NULL) { - for (psS32 j = 0; j < readouts->n; j++) { - pmReadout* tmpReadout = readouts->data[j]; - PS_ASSERT_READOUT_NON_NULL(tmpReadout, NULL); - - psPlaneTransformApply(&cellCoord, - chipToCell, - chipCoord); - - if (checkValidImageCoords(cellCoord.x, - cellCoord.y, - tmpReadout->image)) { - psFree(chipToCell); - return (tmpCell); - } - } - } - psFree(chipToCell); - } - - //psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the cell.\n"); - return (NULL); -} - - -psPlane* pmCoordCellToFPA( - psPlane* fpaCoord, - const psPlane* cellCoord, - const pmCell* cell) -{ - PS_ASSERT_PTR_NON_NULL(cellCoord, NULL); - PS_ASSERT_PTR_NON_NULL(cell, NULL); - - psPlane *rc = psPlaneTransformApply(fpaCoord, cell->toFPA, cellCoord); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform cell coords to FPA coords.\n"); - } - return(rc); -} - - -psPlane* pmCoordChipToFPA( - psPlane* outCoord, - const psPlane* inCoord, - const pmChip* chip) -{ - PS_ASSERT_PTR_NON_NULL(inCoord, NULL); - PS_ASSERT_PTR_NON_NULL(chip, NULL); - - psPlane *rc = psPlaneTransformApply(outCoord, chip->toFPA, inCoord); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform chip coords to FPA coords.\n"); - } - return(rc); -} - - -psPlane* pmCoordFPAToChip( - psPlane* chipCoord, - const psPlane* fpaCoord, - const pmChip* chip) -{ - PS_ASSERT_PTR_NON_NULL(fpaCoord, NULL); - PS_ASSERT_PTR_NON_NULL(chip, NULL); - PS_ASSERT_PTR_NON_NULL(chip->fromFPA, NULL); - - psPlane *rc = psPlaneTransformApply(chipCoord, chip->fromFPA, fpaCoord); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform FPA coords to Chip coords.\n"); - } - return(rc); -} - -psPlane* pmCoordCellToChip( - psPlane* outCoord, - const psPlane* inCoord, - const pmCell* cell) -{ - PS_ASSERT_PTR_NON_NULL(inCoord, NULL); - PS_ASSERT_PTR_NON_NULL(cell, NULL); - - psPlane *rc = psPlaneTransformApply(outCoord, cell->toChip, inCoord); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform Cell coords to Chip coords.\n"); - } - return(rc); -} - -psPlane* pmCoordChipToCell( - psPlane* cellCoord, - const psPlane* chipCoord, - const pmCell* cell) -{ - PS_ASSERT_PTR_NON_NULL(chipCoord, NULL); - PS_ASSERT_PTR_NON_NULL(cell, NULL); - PS_ASSERT_PTR_NON_NULL(cell->parent, NULL); - - pmCell *tmpCell = pmCellInChip(chipCoord, cell->parent); - if (tmpCell == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the proper cell.\n"); - return(NULL); - } - - psPlaneTransform *tmpChipToCell = NULL; - PS_ASSERT_PTR_NON_NULL(tmpCell->toChip, NULL); - if (true == p_psIsProjectionLinear(tmpCell->toChip)) { - tmpChipToCell = p_psPlaneTransformLinearInvert(tmpCell->toChip); - } else { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: non-linear cell->chip transforms are not yet implemented.\n"); - // XXX: tmpChipToCell = psPlaneTransformInvert(NULL, tmpCell->toChip, NULL, -1); - tmpChipToCell = NULL; - } - if (tmpChipToCell == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not invert the Cell->toChip transform.\n"); - return(NULL); - } - - psPlane *rc = psPlaneTransformApply(cellCoord, tmpChipToCell, chipCoord); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform Chip coords to Cell coords.\n"); - } - psFree(tmpChipToCell); - return(rc); -} - -psPlane* pmCoordFPAToTP( - psPlane* outCoord, - const psPlane* inCoord, - double color, - double magnitude, - const pmFPA* fpa) -{ - PS_ASSERT_PTR_NON_NULL(inCoord, NULL); - PS_ASSERT_PTR_NON_NULL(fpa, NULL); - - psPlane *rc = psPlaneDistortApply(outCoord, fpa->toTangentPlane, inCoord, color, magnitude); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform FPA coords to tangent plane coords.\n"); - } - return(rc); -} - -psPlane* pmCoordTPToFPA( - psPlane* fpaCoord, - const psPlane* tpCoord, - double color, - double magnitude, - const pmFPA* fpa) -{ - PS_ASSERT_PTR_NON_NULL(tpCoord, NULL); - PS_ASSERT_PTR_NON_NULL(fpa, NULL); - PS_ASSERT_PTR_NON_NULL(fpa->fromTangentPlane, NULL); - - psPlane *rc = psPlaneDistortApply(fpaCoord, fpa->fromTangentPlane, tpCoord, color, magnitude); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform tangent plane coords to FPA coords.\n"); - } - return(rc); -} - - -/***************************************************************************** -XXXDeproject(outSphere, coord, projection): This private routine is a wrapper -for p_psDeproject(). The reason: p_psDeproject() and p_psProject() combined -do not seem to produce the original coordinates when they even though they -should. XXXDeproject() simply negates the ->r and ->d members of the output -psSphere if the input ->y is larger than 0.0. I don't know why it works. - -I'm guessing the p_psProject() and p_psDeproject() functions have bugs. - -XXX: It appears that p_psProject() and p_psDeproject() have been fixed. -Remove this. - *****************************************************************************/ -psSphere* XXXDeproject( - psSphere *outSphere, - const psPlane* coord, - const psProjection* projection) -{ - psSphere *rc = p_psDeproject(outSphere, coord, projection); - - if (coord->y >= 0.0) { - rc->d = -rc->d; - rc->r = -rc->r; - } - - return(rc); -} - -/***************************************************************************** - *****************************************************************************/ -psSphere* pmCoordTPToSky( - psSphere* outSphere, - const psPlane* tpCoord, - const psProjection *projection) -{ - PS_ASSERT_PTR_NON_NULL(tpCoord, NULL); - PS_ASSERT_PTR_NON_NULL(projection, NULL); - - // psSphere *rc = XXXDeproject(outSphere, tpCoord, projection); - psSphere *rc = p_psDeproject(outSphere, tpCoord, projection); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform tangent plane coords to sky coords.\n"); - } - return(rc); -} - /***************************************************************************** *****************************************************************************/ -psPlane* pmCoordSkyToTP( - psPlane* tpCoord, - const psSphere* in, - const psProjection *projection) -{ - PS_ASSERT_PTR_NON_NULL(in, NULL); - PS_ASSERT_PTR_NON_NULL(projection, NULL); - - psPlane *rc = p_psProject(tpCoord, in, projection); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform sky to tangent plane coords.\n"); - } - return(rc); -} - -/***************************************************************************** - *****************************************************************************/ -psSphere* pmCoordCellToSky( - psSphere* skyCoord, - const psPlane* cellCoord, - double color, - double magnitude, - const pmCell* cell) -{ - PS_ASSERT_PTR_NON_NULL(cellCoord, NULL); - PS_ASSERT_PTR_NON_NULL(cell, NULL); - PS_ASSERT_PTR_NON_NULL(cell->toFPA, NULL); - PS_ASSERT_PTR_NON_NULL(cell->parent, NULL); - PS_ASSERT_PTR_NON_NULL(cell->parent->parent, NULL); - PS_ASSERT_PTR_NON_NULL(cell->parent->parent->toTangentPlane, NULL); - PS_ASSERT_PTR_NON_NULL(cell->parent->parent->projection, NULL); - psPlane fpaCoord; - psPlane tpCoord; - psPlane *rc; - pmFPA* parFPA = (cell->parent)->parent; - - // Convert the input cell coordinates to FPA coordinates. - rc = psPlaneTransformApply(&fpaCoord, cell->toFPA, cellCoord); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could transform cell coords to FPA coords.\n"); - return(NULL); - } - - // Convert the FPA coordinates to tangent plane Coordinates. - rc = psPlaneDistortApply(&tpCoord, parFPA->toTangentPlane, &fpaCoord, color, magnitude); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could transform FPA coords to tangent plane coords.\n"); - return(NULL); - } - - // Convert the tangent plane Coordinates to sky coordinates. - psSphere *rc2 = pmCoordTPToSky(skyCoord, &tpCoord, parFPA->projection); - if (rc2 == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform cell coords to sky coords.\n"); - } - - return(rc2); -} - -/***************************************************************************** - *****************************************************************************/ -psPlane* pmCoordSkyToCell( - psPlane* cellCoord, - const psSphere* skyCoord, - float color, - float magnitude, - const pmCell* cell) -{ - PS_ASSERT_PTR_NON_NULL(skyCoord, NULL); - PS_ASSERT_PTR_NON_NULL(cell, NULL); - PS_ASSERT_PTR_NON_NULL(cell->parent, NULL); - PS_ASSERT_PTR_NON_NULL(cell->parent->parent, NULL); - pmChip *parChip = cell->parent; - pmFPA *parFPA = parChip->parent; - psPlane tpCoord; - psPlane fpaCoord; - psPlane chipCoord; - psPlane *rc; - - // Convert the skyCoords to tangent plane coords. - rc = pmCoordSkyToTP(&tpCoord, skyCoord, parFPA->projection); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine tangent plane coords.\n"); - return(NULL); - } - - // Convert the tangent plane coords to FPA coords. - rc = pmCoordTPToFPA(&fpaCoord, &tpCoord, color, magnitude, parFPA); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine FPA coords.\n"); - return(NULL); - } - - // Convert the FPA coords to chip coords. - rc = pmCoordFPAToChip(&chipCoord, &fpaCoord, parChip); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine chip coords.\n"); - return(NULL); - } - - // Convert the chip coords to cell coords. - rc = pmCoordChipToCell(cellCoord, &chipCoord, cell); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine cell coords.\n"); - return(NULL); - } - - return (cellCoord); -} - -/***************************************************************************** - *****************************************************************************/ -psSphere* pmCoordCellToSkyQuick( - psSphere* outSphere, - const psPlane* cellCoord, - const pmCell* cell) -{ - PS_ASSERT_PTR_NON_NULL(cellCoord, NULL); - PS_ASSERT_PTR_NON_NULL(cell, NULL); - PS_ASSERT_PTR_NON_NULL(cell->toSky, NULL); - psPlane outPlane; - psPlane *rc; - rc = psPlaneTransformApply(&outPlane, cell->toSky, cellCoord); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could transform cell coords to sky coords.\n"); - return(NULL); - } - - psSphere *out = outSphere; - if (out == NULL) { - out = psSphereAlloc(); - } - out->r = outPlane.y; - out->d = outPlane.x; - - return(out); -} - -/***************************************************************************** - *****************************************************************************/ -psPlane* pmCoordSkyToCellQuick( - psPlane* cellCoord, - const psSphere* skyCoord, - const pmCell* cell) -{ - PS_ASSERT_PTR_NON_NULL(skyCoord, NULL); - PS_ASSERT_PTR_NON_NULL(cell, NULL); - PS_ASSERT_PTR_NON_NULL(cell->toSky, NULL); - psPlane skyPlane; - skyPlane.y = skyCoord->r; - skyPlane.x = skyCoord->d; - - psPlane *rc = psPlaneTransformApply(cellCoord, cell->toSky, &skyPlane); - if (rc == NULL) { - psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform sky to cell coords.\n"); - } - return(cellCoord); + +// Set cells within a chip to be processed or not +static bool setCellsProcess(const pmChip *chip, // Chip of interest + bool process // Process this chip? + ) +{ + PS_ASSERT_PTR_NON_NULL(chip, false); + + psArray *cells = chip->cells; // Component cells + if (! cells) { + return false; + } + for (int i = 0; i < cells->n; i++) { + pmCell *tmpCell = cells->data[i]; // Cell of interest + if (tmpCell) { + tmpCell->process = process; + } + } + + return true; } @@ -807,23 +391,26 @@ { PS_ASSERT_PTR_NON_NULL(fpa, false); - if ((fpa->chips == NULL) || (chipNum >= fpa->chips->n)) { + + psArray *chips = fpa->chips; // Component chips + if ((chips == NULL) || (chipNum >= chips->n)) { return(false); } - psBool rc = true; - - for (psS32 i = 0 ; i < fpa->chips->n ; i++) { - pmChip *tmpChip = (pmChip *) fpa->chips->data[i]; + + for (int i = 0 ; i < chips->n ; i++) { + pmChip *tmpChip = (pmChip *) chips->data[i]; if (tmpChip == NULL) { - rc = false; + continue; + } + if (i == chipNum) { + tmpChip->process = true; + setCellsProcess(tmpChip, true); } else { - if (i == chipNum) { - tmpChip->valid = true; - } else { - tmpChip->valid = false; - } - } - } - - return(rc); + tmpChip->process = false; + setCellsProcess(tmpChip, false); + } + + } + + return true; } @@ -831,15 +418,15 @@ /***************************************************************************** XXX: The SDRS is ambiguous on a few things: - Whether or not the other chips should be set valid=true. - Should we return the number of chip valid=true before or after they're set, + Whether or not the other chips should be set process=true. [PAP: No] + Should we return the number of chip process=true before or after they're set, [PAP: After] *****************************************************************************/ /** - * - * pmFPAExcludeChip shall set valid to false only for the specified chip + * + * pmFPAExcludeChip shall set process to false only for the specified chip * number (chipNum). In the event that the specified chip number does not exist * within the fpa, the function shall generate a warning, and perform no action. - * The function shall return the number of chips within the fpa that have valid + * The function shall return the number of chips within the fpa that have process * set to true. - * + * */ int pmFPAExcludeChip( @@ -849,21 +436,22 @@ PS_ASSERT_PTR_NON_NULL(fpa, false); - if (fpa->chips == NULL) { + psArray *chips = fpa->chips; // Component chips + if (chips == NULL) { psLogMsg(__func__, PS_LOG_WARN, "WARNING: fpa->chips == NULL\n"); return(0); } - if ((chipNum >= fpa->chips->n) || (NULL == (pmChip *) fpa->chips->data[chipNum])) { + if ((chipNum >= chips->n) || (NULL == (pmChip *) chips->data[chipNum])) { psLogMsg(__func__, PS_LOG_WARN, "WARNING: the specified chip (%d) does not exist.\n", chipNum); return(0); } - psS32 numChips = 0; - for (psS32 i = 0 ; i < fpa->chips->n ; i++) { - pmChip *tmpChip = (pmChip *) fpa->chips->data[i]; + int numChips = 0; // Number of chips to be processed + for (int i = 0 ; i < chips->n ; i++) { + pmChip *tmpChip = (pmChip *) chips->data[i]; // Chip of interest if (tmpChip != NULL) { if (i == chipNum) { - tmpChip->valid = false; - } else { - tmpChip->valid = true; + tmpChip->process = false; + setCellsProcess(tmpChip, false); // Wipe out the cell as well + } else if (tmpChip->process) { numChips++; } @@ -874,2 +462,73 @@ } + +bool pmCellSetWeights(pmCell *cell // Cell for which to set weights + ) +{ + float gain = psMetadataLookupF32(NULL, cell->concepts, "CELL.GAIN"); // Cell gain + float readnoise = psMetadataLookupF32(NULL, cell->concepts, "CELL.READNOISE"); // Cell read noise + psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); // Trim section + + p_pmHDU *hdu = cell->hdu; // The data unit, containing the weight and mask originals + if (!hdu) { + pmChip *chip = cell->parent; // The parent chip + if (chip->hdu) { + hdu = chip->hdu; + } else { + pmFPA *fpa = chip->parent; // The parent FPA + hdu = fpa->hdu; + if (!hdu) { + psError(PS_ERR_UNKNOWN, true, "Unable to find the HDU in the hierarchy!\n"); + return false; + } + } + } + + psArray *pixels = hdu->images; // Array of images + psArray *weights = hdu->weights; // Array of weight images + psArray *masks = hdu->masks; // Array of mask images + // Generate the weights and masks if required + if (! weights) { + weights = psArrayAlloc(pixels->n); + for (int i = 0; i < pixels->n; i++) { + psImage *image = pixels->data[i]; + weights->data[i] = psImageAlloc(image->numCols, image->numRows, PS_TYPE_F32); + psImageInit(weights->data[i], 0.0); + } + hdu->weights = weights; + } + if (! masks) { + masks = psArrayAlloc(pixels->n); + for (int i = 0; i < pixels->n; i++) { + psImage *image = pixels->data[i]; + masks->data[i] = psImageAlloc(image->numCols, image->numRows, PS_TYPE_U8); + psImageInit(masks->data[i], 0); + } + hdu->masks = masks; + } + + // Set the pixels + psArray *readouts = cell->readouts; // Array of readouts + for (int i = 0; i < readouts->n; i++) { + pmReadout *readout = readouts->data[i]; // The readout of interest + + if (! readout->weight) { + readout->weight = weights->data[i]; + } + if (! readout->mask) { + readout->mask = masks->data[i]; + } + + // Mask is already set to 0 + + // Set weight image to the variance = g*f + rn^2 + psImage *image = psImageSubset(readout->image, *trimsec); // The pixels + psImage *weight = psImageSubset(readout->weight, *trimsec); // The weight map + psBinaryOp(weight, image, "*", psScalarAlloc(gain, PS_TYPE_F32)); + psBinaryOp(weight, weight, "+", psScalarAlloc(readnoise*readnoise, PS_TYPE_F32)); + } + + return true; +} + + Index: trunk/psModules/src/astrom/pmAstrometry.h =================================================================== --- trunk/psModules/src/astrom/pmAstrometry.h (revision 6529) +++ trunk/psModules/src/astrom/pmAstrometry.h (revision 6872) @@ -8,6 +8,6 @@ * @author GLG, MHPCC * -* @version $Revision: 1.6 $ $Name: not supported by cvs2svn $ -* @date $Date: 2006-01-26 21:10:50 $ +* @version $Revision: 1.7 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ * * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii @@ -30,14 +30,13 @@ { const char *extname; // Extension name, if it corresponds to this level - psArray *pixels; // The pixel data, if it corresponds to this level psMetadata *header; // The FITS header, if it corresponds to this level + psArray *images; // The pixel data, if it corresponds to this level + psArray *masks; // The mask data, if it corresponds to this level + psArray *weights; // The weight data, if it corresponds to this level } p_pmHDU; -p_pmHDU *pmHDUAlloc(); -void *pmHDUFree(p_pmHDU *hdu); - /** Focal plane data structure - * + * * A focal plane consists of one or more chips (according to the number of * pieces of contiguous silicon). It contains metadata containers for the @@ -52,5 +51,5 @@ * transformation which will be derived from numerically inverting the forward * transformation. - * + * */ typedef struct @@ -71,5 +70,5 @@ /** Chip data structure - * + * * A chip consists of one or more cells (according to the number of amplifiers * on the device). The chip contains metadata containers for the concepts and @@ -82,5 +81,5 @@ * inverting the forward transformation. A boolean indicates whether the chip is * of interest, allowing it to be excluded from analysis. - * + * */ typedef struct @@ -97,5 +96,6 @@ psArray *cells; ///< The cells (referred to by name) pmFPA *parent; ///< Parent FPA - bool valid; ///< Do we bother about reading and working with this chip? + bool process; ///< Do we bother about reading and working with this chip? + bool exists; ///< Does the chip exist --- has it been read in? p_pmHDU *hdu; ///< FITS data } @@ -126,5 +126,6 @@ psArray *readouts; ///< The readouts (referred to by number) pmChip *parent; ///< Parent chip - bool valid; ///< Do we bother about reading and working with this cell? + bool process; ///< Do we bother about reading and working with this cell? + bool exists; ///< Does the cell exist --- has it been read in? p_pmHDU *hdu; ///< FITS data } @@ -144,4 +145,5 @@ { // Position on the cell + // XXX: These may be removed in the future; use parent->concepts instead? int col0; ///< Offset from the left of chip. int row0; ///< Offset from the bottom of chip. @@ -152,5 +154,4 @@ psImage *mask; ///< Mask of input image psImage *weight; ///< Weight of input image - psList *bias; ///< List of bias section (sub-)images psMetadata *analysis; ///< Readout-level analysis metadata pmCell *parent; ///< Parent cell @@ -183,11 +184,11 @@ */ pmCell *pmCellAlloc( - pmChip *chip, ///< Parent chip - psMetadata *cameradata, - psString name + pmChip *chip, ///< Parent chip + psMetadata *cameraData, ///< Camera data + const char *name ///< Name of cell ); /** Allocates a pmChip - * + * * The constructor shall make an empty pmChip. If the parent fpa is not NULL, * the parent link is made and the chip shall be placed in the parent's array @@ -199,16 +200,15 @@ */ pmChip *pmChipAlloc( - pmFPA *fpa, - psString name - + pmFPA *fpa, ///< FPA to which the chip belongs + const char *name ///< Name of chip ); /** Allocates a pmFPA - * + * * The constructor shall make an empty pmFPA. The chips array shall be * allocated with a zero size, the camera and db pointers set to the values * provided, and the concepts metadata constructed. All other pointers in the * structure shall be initialized to NULL. - * + * */ pmFPA *pmFPAAlloc( @@ -216,12 +216,21 @@ ); +/** Allocates a p_pmHDU + * + * XXX: More detailed description + * + * @return p_pmHDU* newly allocated p_pmHDU + */ +p_pmHDU *p_pmHDUAlloc(const char *extname // Extension name + ); + /** Verify parent links. - * + * * This function checks the validity of the parent links in the FPA hierarchy. * If a parent link is not set (or not set correctly), it is corrected, and the * function shall return false. If all the parent pointers were correct, the * function shall return true. - * + * */ bool pmFPACheckParents( @@ -232,10 +241,38 @@ /** FUNC DESC - * - * - * - * - */ - + * + * + * + * + */ + + + +/** + * + * pmFPASelectChip shall set valid to true for the specified chip number + * (chipNum), and all other chips shall have valid set to false. In the event + * that the specified chip number does not exist within the fpa, the function + * shall return false. + * + */ +bool pmFPASelectChip( + pmFPA *fpa, + int chipNum +); + +/** + * + * pmFPAExcludeChip shall set valid to false only for the specified chip + * number (chipNum). In the event that the specified chip number does not exist + * within the fpa, the function shall generate a warning, and perform no action. + * The function shall return the number of chips within the fpa that have valid + * set to true. + * + */ +int pmFPAExcludeChip( + pmFPA *fpa, + int chipNum +); @@ -426,47 +463,4 @@ ); -/** - * - * pmFPASelectChip shall set valid to true for the specified chip number - * (chipNum), and all other chips shall have valid set to false. In the event - * that the specified chip number does not exist within the fpa, the function - * shall return false. - * - */ -bool pmFPASelectChip( - pmFPA *fpa, - int chipNum -); - - -/** - * - * pmFPAExcludeChip shall set valid to false only for the specified chip - * number (chipNum). In the event that the specified chip number does not exist - * within the fpa, the function shall generate a warning, and perform no action. - * The function shall return the number of chips within the fpa that have valid - * set to true. - * - */ -int pmFPAExcludeChip( - pmFPA *fpa, - int chipNum -); - - -/** - * - * pmFPAConstruct shall construct a focal plane hierarchy from a camera - * configuration. A db handle is also provided so that may be set in the pmFPA. - * The resultant pmFPA and its lower-down components shall be ready for to read a - * FITS file into it by setting the extname pointers at the appropriate levels to - * the appropriate FITS extension name. - * - */ -pmFPA *pmFPAConstruct( - const psMetadata *camera, - psDB *db -); - #endif // #ifndef PS_ASTROMETRY_H Index: trunk/psModules/src/astrom/pmAstrometryObjects.c =================================================================== --- trunk/psModules/src/astrom/pmAstrometryObjects.c (revision 6529) +++ trunk/psModules/src/astrom/pmAstrometryObjects.c (revision 6872) @@ -8,6 +8,6 @@ * @author EAM, IfA * -* @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ -* @date $Date: 2006-03-04 01:01:33 $ +* @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ * * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii @@ -20,5 +20,5 @@ #include #include "pslib.h" -#include "pmAstrometry.h" +#include "pmFPA.h" #include "pmAstrometryObjects.h" @@ -540,5 +540,6 @@ psArray *rot; - pmAstromStats minStat, newStat; + pmAstromStats minStat; + pmAstromStats newStat = {{0, 0, 0, 0}, {0, 0, 0, 0}, 0, 0, 0, 0}; psPlane center; Index: trunk/psModules/src/astrom/pmAstrometryObjects.h =================================================================== --- trunk/psModules/src/astrom/pmAstrometryObjects.h (revision 6529) +++ trunk/psModules/src/astrom/pmAstrometryObjects.h (revision 6872) @@ -8,6 +8,6 @@ * @author EAM, IfA * -* @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ -* @date $Date: 2006-01-26 21:10:50 $ +* @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ * * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii @@ -21,8 +21,8 @@ # include // for unlink # include -# include - -/* - * +# include + +/* + * * This structure specifies the coordinate of the detection in each of the * four necessary coordinate frames: pix defines the position in the psReadout @@ -35,7 +35,7 @@ * coordinates, while the reference detections will be projected to the other * frames from the sky coordinates. - * + * * XXX: There are more members here than in the SDRS. - * + * */ typedef struct @@ -55,9 +55,9 @@ /* - * + * * The pmAstromMatch structure defines the cross-correlation between two * arrays. A single such data item specifies that item number pmAstromMatch.idx1 * in the first list corresponds to pmAstromMatch.idx2 in the second list. - * + * */ typedef struct @@ -70,7 +70,7 @@ /* - * + * * XXX: Not in SDRS. - * + * */ typedef struct @@ -88,5 +88,5 @@ /* - * + * * If the two sets of coordinates are expected to agree very well (ie, the * current best-guess astrometric solution is quite close to the radius. The @@ -97,5 +97,5 @@ * ASTROM.MATCH.RADIUS). The output consists an array of pmAstromMatch values, * defined below. - * + * */ psArray *pmAstromRadiusMatch( @@ -108,11 +108,11 @@ /* - * + * * This function accepts an array of pmAstromObj objects and rotates them by * the given angle about the given center coordinate pCenter,qCenter in the Focal * Plane Array coordinates. - * + * * XXX: This differs from the SDRS - * + * */ /* SDRS @@ -132,5 +132,5 @@ /* - * + * * If the two sets of coordinates are not known to agree well, but the * relative scale and approximate relative rotation is known, then a much faster @@ -147,7 +147,7 @@ * allowing the procedure to scan over a range of rotations. We define the * following function to apply this matching algorithm: - * + * * XXX: In the SDRS, this function is a pointer. - * + * */ pmAstromStats pmAstromGridMatch( @@ -159,5 +159,5 @@ /* - * + * * The result of a pmAstromGridMatch may be used to modify the astrometry * transformation information for a pmFPA image hierarchy structure. The result @@ -167,7 +167,7 @@ * the linear terms of the pmFPA.toTangentPlane transformation. These two * adjustments are made using the function: - * + * * XXX: This function name is different in the SDRS. - * + * */ psPlaneTransform *pmAstromGridApply( @@ -178,9 +178,11 @@ /* - * + * * This function is identical to pmAstromGridMatch, but is valid for only a * single relative rotation. The input config information need not contain any of * the GRID.*.ANGLE entries (they will be ignored). - * + * + * XXX: This function name is different in the SDRS. + * */ /* in pmAstromGrid.c */ @@ -193,5 +195,5 @@ /* - * + * * This function accepts the raw and reference source lists and the list of * matched entries. It uses the matched list to determine a polynomial @@ -207,7 +209,7 @@ * modifications to pmFPA.toTangentPlane incorporate the rotation component of * the linear terms and the higher-order terms of the polynomial fits. - * + * * XXX: No prototype code. - * + * */ bool pmAstromFitFPA( @@ -233,7 +235,7 @@ *ASTROM.ORDER). The result of this fit is a set of modifications of the *components of the pmChip.toFPA transformation. - * + * * XXX: No prototype code. - * + * */ bool pmAstromFitChip( @@ -247,5 +249,5 @@ /* - * + * * The following function determines the position residual, in the tangent * plane, as a function of position in the focal plane, for a collection of raw @@ -253,7 +255,7 @@ * the bin size over which the gradient is measured (keyword: ASTROM.GRAD.BOX). * The function returns an array of pmAstromGradient structures, defined below. - * + * * XXX: No prototype code. - * + * */ psArray pmAstromMeasureGradients( @@ -267,9 +269,9 @@ /* - * + * * The following data structure carries the information about the residual * gradient of source positions in the tangent plane (pmAstromObj.TP) as a * function of position in the focal plane (pmAstromObj.FP). - * + * */ typedef struct @@ -283,5 +285,5 @@ /* - * + * * The gradient set measured above can be fitted with a pair of 2D * polynomials. The resulting fits can then be related back to the implied @@ -290,7 +292,7 @@ * supplied pmFPA structure. The configuration variable supplies the polynomial * order (keyword: ASTROM.DISTORT.ORDER). - * + * * XXX: No prototype code. - * + * */ psArray pmAstromFitDistortion( @@ -308,15 +310,15 @@ ******************************************************************************/ /* - * - * - * - * - */ - - -/* - * + * + * + * + * + */ + + +/* + * * Allocates a pmAstromObj struct. - * + * */ pmAstromObj *pmAstromObjAlloc (void); @@ -325,7 +327,7 @@ /* - * + * * Copies a pmAstromObj struct. - * + * */ pmAstromObj *pmAstromObjCopy( @@ -336,7 +338,7 @@ /* - * - * - * + * + * + * */ pmAstromMatch *pmAstromMatchAlloc( @@ -349,7 +351,7 @@ /* - * - * - * + * + * + * */ psPlaneTransform *pmAstromMatchFit( @@ -364,7 +366,7 @@ /* - * - * - * + * + * + * */ int pmAstromObjSortByFPX( @@ -376,7 +378,7 @@ /* - * - * - * + * + * + * */ int pmAstromObjSortByMag( Index: trunk/psModules/src/astrom/pmChipMosaic.c =================================================================== --- trunk/psModules/src/astrom/pmChipMosaic.c (revision 6872) +++ trunk/psModules/src/astrom/pmChipMosaic.c (revision 6872) @@ -0,0 +1,367 @@ +#include +#include + +#include "pslib.h" +#include "pmFPA.h" +#include "pmChipMosaic.h" + +#define MEM_LEAKS 0 + +// Compare a value with a maximum and minimum +#define COMPARE(value,min,max) \ +if ((value) < (min)) { \ + (min) = (value); \ +} \ +if ((value) > (max)) { \ + (max) = (value); \ +} + +// Mosaic multiple images, with flips, binning and offsets +psImage *p_pmImageMosaic(const psArray *source, // Images to splice in + const psVector *xFlip, const psVector *yFlip, // Need to flip x and y? + const psVector *xBinSource, const psVector *yBinSource, // Binning in x and y of + // source images + int xBinTarget, int yBinTarget, // Binning in x and y of target images + const psVector *x0, const psVector *y0 // Offsets for source images on target + ) +{ + assert(source); + assert(xFlip && xFlip->type.type == PS_TYPE_U8); + assert(yFlip && yFlip->type.type == PS_TYPE_U8); + assert(xBinSource && xBinSource->type.type == PS_TYPE_S32); + assert(yBinSource && yBinSource->type.type == PS_TYPE_S32); + assert(x0 && x0->type.type == PS_TYPE_S32); + assert(y0 && y0->type.type == PS_TYPE_S32); + + // Get the maximum extent of the mosaic image + int xMin = INT_MAX; + int xMax = - INT_MAX; + int yMin = INT_MAX; + int yMax = - INT_MAX; + psElemType type = 0; + for (int i = 0; i < source->n; i++) { + psImage *image = source->data[i]; // The image of interest + if (!image) { + continue; + } + + // Only implemented for F32 and U8 images so far. + assert(image->type.type == PS_TYPE_F32 || image->type.type == PS_TYPE_U8); + // All input types must be the same + if (type == 0) { + type = image->type.type; + } + assert(type == image->type.type); + + // Size of cell in x and y + int xParity = xFlip->data.U8[i] ? -1 : 1; + int yParity = yFlip->data.U8[i] ? -1 : 1; + psTrace(__func__, 5, "Extent of cell %d: %d -> %d , %d -> %d\n", i, x0->data.S32[i], + x0->data.S32[i] + xParity * xBinSource->data.S32[i] * image->numCols, y0->data.S32[i], + y0->data.S32[i] + yParity * yBinSource->data.S32[i] * image->numRows); + + COMPARE(x0->data.S32[i], xMin, xMax); + COMPARE(y0->data.S32[i], yMin, yMax); + // Subtract the parity to get the inclusive limit (not exclusive) + COMPARE(x0->data.S32[i] + xParity * xBinSource->data.S32[i] * image->numCols - xParity, xMin, xMax); + COMPARE(y0->data.S32[i] + yParity * yBinSource->data.S32[i] * image->numRows - yParity, yMin, yMax); + } + + // Set up the image + // Since both upper and lower values are inclusive, we need to add one to the size + float xSize = (float)(xMax - xMin + 1) / (float)xBinTarget; + if (xSize - (int)xSize > 0) { + xSize += 1; + } + float ySize = (float)(yMax - yMin + 1) / (float)yBinTarget; + if (ySize - (int)ySize > 0) { + ySize += 1; + } + + psTrace(__func__, 3, "Spliced image will be %dx%d\n", (int)xSize, (int)ySize); + psImage *mosaic = psImageAlloc((int)xSize, (int)ySize, type); // The mosaic image + psImageInit(mosaic, 0.0); + + // Next pass through the images to do the mosaicking + for (int i = 0; i < source->n; i++) { + psImage *image = source->data[i]; // The image of interest + if (!image) { + continue; + } + if (xBinSource->data.S32[i] == xBinTarget && yBinSource->data.S32[i] == yBinTarget && + xFlip->data.U8[i] == 0 && yFlip->data.U8[i] == 0) { + // Let someone else do the hard work; useful to test psImageOverlaySection if no other reason + psImageOverlaySection(mosaic, image, x0->data.S32[i], y0->data.S32[i], "+"); + } else { + // We have to do the hard work ourself + for (int y = 0; y < image->numRows; y++) { + int yParity = yFlip->data.U8[i] ? -1 : 1; + float yTargetBase = (y0->data.S32[i] + yParity * yBinSource->data.S32[i] * y) / yBinTarget; + for (int x = 0; x < image->numCols; x++) { + int xParity = xFlip->data.U8[i] ? -1 : 1; + float xTargetBase = (x0->data.S32[i] + xParity * xBinSource->data.S32[i] * x) / + xBinTarget; + + // In case the original image is binned but the mosaic is not, we need to fill in the + // values in the mosaic. + #define FILL_IN(TYPE) \ + for (int j = 0; j < yBinSource->data.S32[i]; j++) { \ + int yTarget = (int)(yTargetBase + yParity * (float)j / (float)yBinTarget); \ + for (int i = 0; i < xBinSource->data.S32[i]; i++) { \ + int xTarget = (int)(xTargetBase + xParity * (float)i / (float)xBinTarget); \ + mosaic->data.TYPE[yTarget][xTarget] += image->data.TYPE[y][x]; \ + } \ + } + + switch (type) { + case PS_TYPE_F32: + FILL_IN(F32); + break; + case PS_TYPE_U8: + FILL_IN(U8); + break; + default: + psAbort(__func__, "Should never get here.\n"); + } + + } + } // Iterating over input image + } + } + + return mosaic; +} + + +// Set the concepts in the new cell, based on the values in the old one +static bool cellConcepts(pmCell *target,// Target cell + psArray *sources, // Source cells + int xBin, int yBin // Binning + ) +{ + bool success = true; // Result of setting everything + float gain = 0.0; // Gain + float readnoise = 0.0; // Read noise + float saturation = 0.0; // Saturation level + float bad = 0.0; // Bad level + float exposure = 0.0; // Exposure time + float darktime = 0.0; // Dark time + double time = 0.0; // Time of observation + psTimeType timeSys = 0; // Time system + + int nCells = 0; // Number of cells; + for (int i = 0; i < sources->n; i++) { + pmCell *cell = sources->data[i];// The cell of interest + if (!cell) { + continue; + } + + nCells++; + gain += psMetadataLookupF32(NULL, cell->concepts, "CELL.GAIN"); + readnoise += psMetadataLookupF32(NULL, cell->concepts, "CELL.READNOISE"); + saturation += psMetadataLookupF32(NULL, cell->concepts, "CELL.SATURATION"); + bad += psMetadataLookupF32(NULL, cell->concepts, "CELL.BAD"); + exposure += psMetadataLookupF32(NULL, cell->concepts, "CELL.EXPOSURE"); + darktime += psMetadataLookupF32(NULL, cell->concepts, "CELL.DARKTIME"); + time += psTimeToMJD(psMetadataLookupPtr(NULL, cell->concepts, "CELL.TIME")); + if (i == 0) { + timeSys = psMetadataLookupS32(NULL, cell->concepts, "CELL.TIMESYS"); + } else if (timeSys != psMetadataLookupS32(NULL, cell->concepts, "CELL.TIMESYS")) { + psLogMsg(__func__, PS_LOG_ERROR, "Differing time systems in use: %d vs %d\n", timeSys, + psMetadataLookupS32(NULL, cell->concepts, "CELL.TIMESYS")); + success = false; + } + } + gain /= (float)nCells; + readnoise /= (float)nCells; + saturation /= (float)nCells; + bad /= (float)nCells; + exposure /= (float)nCells; + darktime /= (float)nCells; + psTime *timePtr = psTimeFromMJD(time/(double)nCells); + timePtr = psTimeConvert(timePtr, timeSys); + + // XXX *REALLY* need a generic "concept update" function that handles the type and comments transparently. + psMetadataAddF32(target->concepts, PS_LIST_TAIL, "CELL.GAIN", PS_META_REPLACE, "Gain (e/ADU)", gain); + psMetadataAddF32(target->concepts, PS_LIST_TAIL, "CELL.READNOISE", PS_META_REPLACE, "Read noise (e)", readnoise); + psMetadataAddF32(target->concepts, PS_LIST_TAIL, "CELL.SATURATION", PS_META_REPLACE, "Saturation level (ADU)", saturation); + psMetadataAddF32(target->concepts, PS_LIST_TAIL, "CELL.BAD", PS_META_REPLACE, "Bad level (ADU)", bad); + psMetadataAddF32(target->concepts, PS_LIST_TAIL, "CELL.EXPOSURE", PS_META_REPLACE, "Exposure time (sec)", exposure); + psMetadataAddF32(target->concepts, PS_LIST_TAIL, "CELL.DARKTIME", PS_META_REPLACE, "Time since last CCD flush (sec)", darktime); + psMetadataAddPtr(target->concepts, PS_LIST_TAIL, "CELL.TIME", PS_DATA_TIME | PS_META_REPLACE, "Time of observation", timePtr); + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.TIMESYS", PS_META_REPLACE, "Time system", timeSys); + psFree(timePtr); + + // Now fill in the ones I know by other means + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.X0", PS_META_REPLACE, "Position of (0,0) on the chip", 0); + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.Y0", PS_META_REPLACE, "Position of (0,0) on the chip", 0); + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.XPARITY", PS_META_REPLACE, "Orientation in x compared to the rest of the FPA", 1); + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.YPARITY", PS_META_REPLACE, "Orientation in x compared to the rest of the FPA", 1); + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.XBIN", PS_META_REPLACE, "Binning in x", xBin); + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.YBIN", PS_META_REPLACE, "Binning in x", yBin); + psMetadataAddS32(target->concepts, PS_LIST_TAIL, "CELL.READDIR", PS_META_REPLACE, "Read direction (faked)", 1); + psRegion *trimsec = psMetadataLookupPtr(NULL, target->concepts, "CELL.TRIMSEC"); + trimsec->x0 = trimsec->x1 = trimsec->y0 = trimsec->y1 = 0.0; + + return success; +} + + + +// Mosaic a chip together into a single image +int pmChipMosaic(pmChip *chip,// Chip to mosaic + int xBinChip, int yBinChip // Binning of mosaic image in x and y + ) +{ + + psArray *cells = chip->cells; // The array of cells + psArray *images = psArrayAlloc(cells->n); // Array of images that will be mosaicked + psArray *weights = psArrayAlloc(cells->n); // Array of weight images to be mosaicked + psArray *masks = psArrayAlloc(cells->n); // Array of mask images to be mosaicked + psVector *x0 = psVectorAlloc(cells->n, PS_TYPE_S32); // Origin x coordinates + psVector *y0 = psVectorAlloc(cells->n, PS_TYPE_S32); // Origin y coordinates + psVector *xBin = psVectorAlloc(cells->n, PS_TYPE_S32); // Binning in x + psVector *yBin = psVectorAlloc(cells->n, PS_TYPE_S32); // Binning in y + psVector *xFlip = psVectorAlloc(cells->n, PS_TYPE_U8); // Flip in x? + psVector *yFlip = psVectorAlloc(cells->n, PS_TYPE_U8); // Flip in y? + + // Set up the required inputs + psTrace(__func__, 1, "Mosaicking %d cells...\n", cells->n); + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // The cell of interest + if (!cell) { + continue; + } + x0->data.S32[i] = psMetadataLookupS32(NULL, cell->concepts, "CELL.X0"); + y0->data.S32[i] = psMetadataLookupS32(NULL, cell->concepts, "CELL.Y0"); + psTrace(__func__, 5, "Cell %d: x0=%d y0=%d\n", i, x0->data.S32[i], y0->data.S32[i]); + xBin->data.S32[i] = psMetadataLookupS32(NULL, cell->concepts, "CELL.XBIN"); + yBin->data.S32[i] = psMetadataLookupS32(NULL, cell->concepts, "CELL.XBIN"); + int xParity = psMetadataLookupS32(NULL, cell->concepts, "CELL.XPARITY"); + int yParity = psMetadataLookupS32(NULL, cell->concepts, "CELL.YPARITY"); + if (xParity == 1) { + xFlip->data.U8[i] = 0; + } else if (xParity == -1) { + xFlip->data.U8[i] = 1; + } else { + psLogMsg(__func__, PS_LOG_WARN, "The x parity of cell %d is not +/- 1 (it's %d) --- " + "assuming +1.\n", i, xParity); + xFlip->data.U8[i] = 0; + } + if (yParity == 1) { + yFlip->data.U8[i] = 0; + } else if (yParity == -1) { + yFlip->data.U8[i] = 1; + } else { + psLogMsg(__func__, PS_LOG_WARN, "The y parity of cell %d is not +/- 1 (it's %d) --- " + "assuming +1.\n", i, yParity); + yFlip->data.U8[i] = 0; + } + + psArray *readouts = cell->readouts; // The array of readouts + if (readouts->n > 1) { + psLogMsg(__func__, PS_LOG_WARN, "Cell %d contains more than one readout --- only the first will " + "be mosaicked.\n", i); + } + pmReadout *readout = readouts->data[0]; // The only readout we'll bother with + + // The images to put into the mosaic + images->data[i] = psMemIncrRefCounter(readout->image); + weights->data[i] = psMemIncrRefCounter(readout->weight); + masks->data[i] = psMemIncrRefCounter(readout->mask); + } + // Mosaic the images together and we're done + psImage *image = p_pmImageMosaic(images, xFlip, yFlip, xBin, yBin, xBinChip, yBinChip, x0, y0); + psImage *weight = p_pmImageMosaic(weights, xFlip, yFlip, xBin, yBin, xBinChip, yBinChip, x0, y0); + psImage *mask = p_pmImageMosaic(masks, xFlip, yFlip, xBin, yBin, xBinChip, yBinChip, x0, y0); + + // Clean up + psFree(x0); + psFree(y0); + psFree(xBin); + psFree(yBin); + psFree(xFlip); + psFree(yFlip); + psFree(images); + psFree(weights); + psFree(masks); + int nCells = cells->n; + + // Fix up the HDU + if (chip->parent->hdu) { + psLogMsg(__func__, PS_LOG_WARN, "The original format has the entire FPA in a single extension. " + "The FPA hierarchy may be invalid following the pmChipMosaic.\n"); + } else { + if (! chip->hdu) { + psString chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); + chip->hdu = p_pmHDUAlloc(chipName); + } + p_pmHDU *hdu = chip->hdu; + psArrayElementsFree(hdu->images); + psArrayElementsFree(hdu->weights); + psArrayElementsFree(hdu->masks); + hdu->images = psArrayRealloc(hdu->images,1); + hdu->weights = psArrayRealloc(hdu->weights, 1); + hdu->masks = psArrayRealloc(hdu->masks, 1); + hdu->images->data[0] = image; + hdu->weights->data[0] = weight; + hdu->masks->data[0] = mask; + psMetadataAddS32(hdu->header, PS_LIST_TAIL, "NAXIS1", PS_META_REPLACE, "Number of columns", image->numCols); + psMetadataAddS32(hdu->header, PS_LIST_TAIL, "NAXIS2", PS_META_REPLACE, "Number of rows", image->numRows); + } + + // Chop off all the component cells, and construct a new one + pmCell *newCell = pmCellAlloc(NULL, NULL, __func__); // New cell + cellConcepts(newCell, cells, xBinChip, yBinChip); + pmChipFreeCells(chip); + // Have to put in the new cell manually, since we didn't want to put it in before blowing the cells away. + newCell->parent = chip; + psArrayAdd(chip->cells, 1, newCell); + newCell->exists = true; + newCell->process = true; + + // Now make a new readout to go in the new cell + pmReadout *newReadout = pmReadoutAlloc(newCell); // New readout + // Want the readouts to contain a subimage, but that subimage is the whole image. + // This preserves the relationship there was before, where freeing the parent frees the child. + psRegion entire = {0.0, 0.0, 0.0, 0.0}; + newReadout->image = psMemIncrRefCounter(psImageSubset(image, entire)); + newReadout->weight = psMemIncrRefCounter(psImageSubset(weight, entire)); + newReadout->mask = psMemIncrRefCounter(psImageSubset(mask, entire)); + // Drop references + psFree(newReadout); + psFree(newCell); + + // Well, we've stuffed around with the camera configuration, so it's no longer valid... + #if 0 + + psFree(chip->parent->camera); + chip->parent->camera = NULL; + #endif + + return nCells; +} + + +int pmFPAMosaicCells(pmFPA *fpa, // FPA + int xBinChip, int yBinChip // Binning of mosaic image in x and y + ) +{ + assert(fpa); + + int numChips = 0; + psArray *chips = fpa->chips; // Component chips + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // The chip of interest + if (! chip || ! chip->exists || ! chip->process) { + continue; + } + + if (pmChipMosaic(chip, xBinChip, yBinChip) > 0) { + numChips++; + } + } + + return numChips; + +} Index: trunk/psModules/src/astrom/pmChipMosaic.h =================================================================== --- trunk/psModules/src/astrom/pmChipMosaic.h (revision 6872) +++ trunk/psModules/src/astrom/pmChipMosaic.h (revision 6872) @@ -0,0 +1,26 @@ +#ifndef PM_CHIP_MOSAIC_H +#define PM_CHIP_MOSAIC_H + +#include "pslib.h" +#include "pmFPA.h" + +// Mosaic multiple images, with flips, binning and offsets +psImage *p_pmImageMosaic(const psArray *source, // Images to splice in + const psVector *xFlip, const psVector *yFlip, // Need to flip x and y? + const psVector *xBinSource, const psVector *yBinSource, // Binning in x and y of + // source images + int xBinTarget, int yBinTarget, // Binning in x and y of target images + const psVector *x0, const psVector *y0 // Offsets for source images on target + ); + +// Mosaic a chip together into a single cell with single readout +int pmChipMosaic(pmChip *chip,// Chip to mosaic + int xBinChip, int yBinChip // Binning of mosaic image in x and y + ); + +// Mosaic all the cells in all (valid) chips together (neglecting the overscans); return number of chips +int pmFPAMosaicCells(pmFPA *fpa, // FPA + int xBinChip, int yBinChip // Binning of mosaic image in x and y + ); + +#endif Index: trunk/psModules/src/astrom/pmConcepts.c =================================================================== --- trunk/psModules/src/astrom/pmConcepts.c (revision 6872) +++ trunk/psModules/src/astrom/pmConcepts.c (revision 6872) @@ -0,0 +1,563 @@ +// XXX *REALLY* need generic "concept update" and "concept read" functions that handles the type transparently + +#include +#include + +#include "pslib.h" +#include "pmConcepts.h" +#include "pmConceptsRead.h" +#include "pmConceptsWrite.h" +#include "pmConceptsStandard.h" +#include "psAdditionals.h" + +static bool conceptsInitialised = false;// Have concepts been read? +static psMetadata *conceptsFPA = NULL; // Known concepts for FPA +static psMetadata *conceptsChip = NULL; // Known concepts for chip +static psMetadata *conceptsCell = NULL; // Known concepts for cell + +// Free a concept +static void conceptSpecFree(pmConceptSpec *spec) +{ + psFree(spec->blank); +} + +pmConceptSpec *pmConceptSpecAlloc(psMetadataItem *blank, // Blank value; contains the name + pmConceptParseFunc parse, // Function to call to parse the concept + pmConceptFormatFunc format // Function to call to format the concept + ) +{ + pmConceptSpec *spec = psAlloc(sizeof(pmConceptSpec)); + psMemSetDeallocator(spec, (psFreeFunc)conceptSpecFree); + + spec->blank = psMemIncrRefCounter(blank); + spec->parse = parse; + spec->format = format; + + return spec; +} + + +bool pmConceptRegister(psMetadataItem *blank, // Blank value; contains the name + pmConceptParseFunc parse, // Function to call to parse the concept + pmConceptFormatFunc format, // Function to call to format the concept + pmConceptLevel level // Level at which to store concept in the FPA hierarchy + ) +{ + assert(blank); + if (!conceptsInitialised) { + pmConceptsInit(); + } + + pmConceptSpec *spec = pmConceptSpecAlloc(blank, parse, format); // The concept specification + psMetadata **target = NULL; // The metadata of known concepts to write to + switch (level) { + case PM_CONCEPT_LEVEL_FPA: + target = &conceptsFPA; + break; + case PM_CONCEPT_LEVEL_CHIP: + target = &conceptsChip; + break; + case PM_CONCEPT_LEVEL_CELL: + target = &conceptsCell; + break; + default: + psError(PS_ERR_IO, true, "Unknown concept level provided: %d\n", level); + psFree(spec); + return false; + } + + psMetadataAdd(*target, PS_LIST_TAIL, blank->name, PS_DATA_UNKNOWN | PS_META_REPLACE, + "Concepts specification", spec); + psFree(spec); // Drop reference + + return true; +} + + +// Set all registered concepts to blank value for the specified level +static bool conceptsBlank(psMetadata **specs, // One of the concepts specifications + psMetadata *target // Place to install the concepts + ) +{ + if (!conceptsInitialised) { + pmConceptsInit(); + } + psMetadataIterator *specsIter = psMetadataIteratorAlloc(*specs, PS_LIST_HEAD, NULL); // Iterator on specs + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + psTrace(__func__, 9, "Blanking %s...\n", specItem->name); + pmConceptSpec *spec = specItem->data.V; // The specification + psMetadataItem *blank = spec->blank; // The concept + psMetadataItem *copy = NULL; // Copy of the blank concept + // Trap the lists, which can't be copied in the ordinary way without a warning + if (blank->type == PS_DATA_LIST) { + copy = psMetadataItemAllocPtr(blank->name, PS_DATA_LIST, blank->comment, blank->data.V); + } else { + copy = psMetadataItemCopy(blank); + } + if (!psMetadataAddItem(target, copy, PS_LIST_TAIL, PS_META_REPLACE)) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to add blank version of concept %s\n", blank->name); + } + psFree(copy); // Drop reference + } + psFree(specsIter); + + return true; +} + + + +// Read all registered concepts for the specified level +static bool conceptsRead(psMetadata **specs, // One of the concepts specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + pmConceptSource source, // The source of the concepts to read + psDB *db, // Database handle + psMetadata *target // Place into which to read the concepts + ) +{ + if (!conceptsInitialised) { + pmConceptsInit(); + } + + if (source & PM_CONCEPT_SOURCE_CAMERA || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsReadFromCamera(*specs, cell, target); + } + if (source & PM_CONCEPT_SOURCE_DEFAULTS || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsReadFromDefaults(*specs, fpa, chip, cell, target); + } + if (source & PM_CONCEPT_SOURCE_HEADER || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsReadFromHeader(*specs, fpa, chip, cell, target); + } + if (source & PM_CONCEPT_SOURCE_DATABASE || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsReadFromDatabase(*specs, fpa, chip, cell, db, target); + } + + return true; +} + +// Write all registered concepts for the specified level +static bool conceptsWrite(psMetadata **specs, // One of the concepts specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + pmConceptSource source, // The source of the concepts to write + psDB *db, // Database handle + psMetadata *concepts // The concepts to write out + ) +{ + if (!conceptsInitialised) { + pmConceptsInit(); + } + + if (source & PM_CONCEPT_SOURCE_CAMERA || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsWriteToCamera(*specs, cell, concepts); + } + if (source & PM_CONCEPT_SOURCE_DEFAULTS || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsWriteToDefaults(*specs, fpa, chip, cell, concepts); + } + if (source & PM_CONCEPT_SOURCE_HEADER || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsWriteToHeader(*specs, fpa, chip, cell, concepts); + } + if (source & PM_CONCEPT_SOURCE_DATABASE || source == PM_CONCEPT_SOURCE_ALL) { + pmConceptsWriteToDatabase(*specs, fpa, chip, cell, db, concepts); + } + + return true; +} + +// Set the concepts for a given FPA to blanks +bool pmConceptsBlankFPA(pmFPA *fpa // FPA for which to set blank concepts + ) +{ + psTrace("psModule.concepts", 5, "Blanking FPA concepts: %x %x\n", conceptsFPA, fpa->concepts); + return conceptsBlank(&conceptsFPA, fpa->concepts); +} + + +// Read the concepts for a given FPA +bool pmConceptsReadFPA(pmFPA *fpa, // FPA for which to read concepts + pmConceptSource source, // The source of the concepts to read + psDB *db // Database handle + ) +{ + psTrace("psModule.concepts", 5, "Reading FPA concepts: %x %x\n", conceptsFPA, fpa->concepts); + return conceptsRead(&conceptsFPA, fpa, NULL, NULL, source, db, fpa->concepts); +} + +// Read the concepts for a given FPA +bool pmConceptsWriteFPA(pmFPA *fpa, // FPA for which to write concepts + pmConceptSource source, // The source of the concepts to read + psDB *db // Database handle + ) +{ + psTrace("psModule.concepts", 5, "Writing FPA concepts: %x %x\n", conceptsFPA, fpa->concepts); + return conceptsWrite(&conceptsFPA, fpa, NULL, NULL, source, db, fpa->concepts); +} + +// Set the concepts for a given chip to blanks +bool pmConceptsBlankChip(pmChip *chip // FPA for which to set blank concepts + ) +{ + psTrace("psModule.concepts", 5, "Blanking chip concepts: %x %x\n", conceptsChip, chip->concepts); + return conceptsBlank(&conceptsChip, chip->concepts); +} + +// Read the concepts for a given FPA +bool pmConceptsReadChip(pmChip *chip, // Chip for which to read concepts + pmConceptSource source, // The source of the concepts to read + bool propagate, // Propagate to higher levels as well? + psDB *db // Database handle + ) +{ + psTrace("psModule.concepts", 5, "Reading chip concepts: %x %x\n", conceptsChip, chip->concepts); + pmFPA *fpa = chip->parent; // FPA to which the chip belongs + return conceptsRead(&conceptsChip, fpa, chip, NULL, source, db, chip->concepts) && + ((propagate && conceptsRead(&conceptsFPA, fpa, chip, NULL, source, db, fpa->concepts)) || + !propagate); +} + +// Read the concepts for a given FPA +bool pmConceptsWriteChip(pmChip *chip, // Chip for which to write concepts + pmConceptSource source, // The source of the concepts to read + bool propagate,// Propagate to higher levels as well? + psDB *db // Database handle + ) +{ + psTrace("psModule.concepts", 5, "Writing chip concepts: %x %x\n", conceptsChip, chip->concepts); + pmFPA *fpa = chip->parent; // FPA to which the chip belongs + return conceptsWrite(&conceptsChip, fpa, chip, NULL, source, db, chip->concepts) && + ((propagate && conceptsWrite(&conceptsFPA, fpa, chip, NULL, source, db, fpa->concepts)) || + !propagate); +} + +// Set the concepts for a given chip to blanks +bool pmConceptsBlankCell(pmCell *cell // Cell for which to set blank concepts + ) +{ + psTrace("psModule.concepts", 5, "Blanking cell concepts: %x %x\n", conceptsCell, cell->concepts); + return conceptsBlank(&conceptsCell, cell->concepts); +} + +// Read the concepts for a given FPA +bool pmConceptsReadCell(pmCell *cell, // Cell for which to read concepts + pmConceptSource source, // The source of the concepts to read + bool propagate,// Propagate to higher levels as well? + psDB *db // Database handle + ) +{ + psTrace("psModule.concepts", 5, "Reading cell concepts: %x %x\n", conceptsCell, cell->concepts); + pmChip *chip = cell->parent; // Chip to which the cell belongs + pmFPA *fpa = chip->parent; // FPA to which the chip belongs + return conceptsRead(&conceptsCell, fpa, chip, cell, source, db, cell->concepts) && + ((propagate && conceptsRead(&conceptsChip, fpa, chip, cell, source, db, chip->concepts) && + conceptsRead(&conceptsFPA, fpa, chip, cell, source, db, fpa->concepts)) || !propagate); +} + +// Read the concepts for a given FPA +bool pmConceptsWriteCell(pmCell *cell, // FPA for which to write concepts + pmConceptSource source, // The source of the concepts to read + bool propagate,// Propagate to higher levels as well? + psDB *db // Database handle + ) +{ + psTrace("psModule.concepts", 5, "Writing cell concepts: %x %x\n", conceptsCell, cell->concepts); + pmChip *chip = cell->parent; // Chip to which the cell belongs + pmFPA *fpa = chip->parent; // FPA to which the chip belongs + return conceptsWrite(&conceptsCell, fpa, chip, cell, source, db, cell->concepts) && + ((propagate && conceptsWrite(&conceptsChip, fpa, chip, cell, source, db, chip->concepts) && + conceptsWrite(&conceptsFPA, fpa, chip, cell, source, db, fpa->concepts)) || !propagate); +} + + +bool pmConceptsInit(void) +{ + bool init = false; // Did we initialise anything? + if (! conceptsFPA) { + conceptsFPA = psMetadataAlloc(); + init = true; + + // Install the standard concepts + + #if 0 + // FPA.NAME + { + psMetadataItem *fpaName = psMetadataItemAllocStr("FPA.NAME", "Name of FPA", ""); + pmConceptRegister(fpaName, NULL, NULL, PM_CONCEPT_LEVEL_FPA); + psFree(fpaName); + } + #endif + + // FPA.AIRMASS + { + psMetadataItem *fpaAirmass = psMetadataItemAllocF32("FPA.AIRMASS", "Airmass at boresight", 0.0); + pmConceptRegister(fpaAirmass, NULL, NULL, PM_CONCEPT_LEVEL_FPA); + psFree(fpaAirmass); + } + + // FPA.FILTER + { + psMetadataItem *fpaFilter = psMetadataItemAllocStr("FPA.FILTER", "Filter used", ""); + pmConceptRegister(fpaFilter, NULL, NULL, PM_CONCEPT_LEVEL_FPA); + psFree(fpaFilter); + } + + // FPA.POSANGLE + { + psMetadataItem *fpaPosangle = psMetadataItemAllocF32("FPA.POSANGLE", + "Position angle of instrument", 0.0); + pmConceptRegister(fpaPosangle, NULL, NULL, PM_CONCEPT_LEVEL_FPA); + psFree(fpaPosangle); + } + + // FPA.RADECSYS + { + psMetadataItem *fpaRadecsys = psMetadataItemAllocStr("FPA.RADECSYS", + "Celestial coordinate system", ""); + pmConceptRegister(fpaRadecsys, NULL, NULL, PM_CONCEPT_LEVEL_FPA); + psFree(fpaRadecsys); + } + + // FPA.RA + { + psMetadataItem *fpaRa = psMetadataItemAllocF64("FPA.RA", "Right Ascension of boresight", NAN); + pmConceptRegister(fpaRa, (pmConceptParseFunc)pmConceptParse_FPA_Coords, + (pmConceptFormatFunc)pmConceptFormat_FPA_Coords, PM_CONCEPT_LEVEL_FPA); + psFree(fpaRa); + } + + // FPA.DEC + { + psMetadataItem *fpaDec = psMetadataItemAllocF64("FPA.DEC", "Declination of boresight", NAN); + pmConceptRegister(fpaDec, (pmConceptParseFunc)pmConceptParse_FPA_Coords, + (pmConceptFormatFunc)pmConceptFormat_FPA_Coords, PM_CONCEPT_LEVEL_FPA); + psFree(fpaDec); + } + + // Done with FPA level concepts + } + if (! conceptsChip) { + conceptsChip = psMetadataAlloc(); + init = true; + // There are no standard concepts at the chip level to be installed + } + if (! conceptsCell) { + conceptsCell = psMetadataAlloc(); + init = true; + + // Install the standard concepts + + // CELL.GAIN + { + psMetadataItem *cellGain = psMetadataItemAllocF32("CELL.GAIN", "CCD gain (e/count)", NAN); + pmConceptRegister(cellGain, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellGain); + } + + // CELL.READNOISE + { + psMetadataItem *cellReadnoise = psMetadataItemAllocF32("CELL.READNOISE", + "CCD read noise (e)", NAN); + pmConceptRegister(cellReadnoise, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellReadnoise); + } + + // CELL.SATURATION + { + psMetadataItem *cellSaturation = psMetadataItemAllocF32("CELL.SATURATION", + "Saturation level (counts)", NAN); + pmConceptRegister(cellSaturation, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellSaturation); + } + + // CELL.BAD + { + psMetadataItem *cellBad = psMetadataItemAllocF32("CELL.BAD", "Bad level (counts)", NAN); + pmConceptRegister(cellBad, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellBad); + } + + // CELL.XPARITY + { + psMetadataItem *cellXparity = psMetadataItemAllocS32("CELL.XPARITY", + "Orientation in x compared to the rest of the FPA", 0); + pmConceptRegister(cellXparity, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellXparity); + } + + // CELL.YPARITY + { + psMetadataItem *cellYparity = psMetadataItemAllocS32("CELL.YPARITY", + "Orientation in x compared to the rest of the FPA", 0); + pmConceptRegister(cellYparity, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellYparity); + } + + // CELL.READDIR + { + psMetadataItem *cellReaddir = psMetadataItemAllocS32("CELL.READDIR", + "Read direction, rows=1, cols=2", 0); + pmConceptRegister(cellReaddir, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellReaddir); + } + + + // These (CELL.EXPOSURE and CELL.DARKTIME) used to be READOUT.EXPOSURE and READOUT.DARKTIME, but that + // doesn't really make sense at the moment. Maybe we need to add a "parent" link to the readouts. + // But then how are the exposure times REALLY derived? They're not in the FITS headers, because a + // readout is a plane in a 3D image. We'll have to dream up some additional suffix to specify these, + // but for now.... + + // CELL.EXPOSURE + { + psMetadataItem *cellExposure = psMetadataItemAllocF32("CELL.EXPOSURE", + "Exposure time (sec)", NAN); + pmConceptRegister(cellExposure, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellExposure); + } + + // CELL.DARKTIME + { + psMetadataItem *cellDarktime = psMetadataItemAllocF32("CELL.DARKTIME", + "Time since flush (sec)", NAN); + pmConceptRegister(cellDarktime, NULL, NULL, PM_CONCEPT_LEVEL_CELL); + psFree(cellDarktime); + } + + // CELL.TRIMSEC + { + psRegion *trimsec = psAlloc(sizeof(psRegion)); // Blank trimsec + trimsec->x0 = trimsec->y0 = trimsec->x1 = trimsec->y1 = NAN; + psMetadataItem *cellTrimsec = psMetadataItemAllocPtr("CELL.TRIMSEC", PS_DATA_REGION, + "Trim section", trimsec); + psFree(trimsec); + pmConceptRegister(cellTrimsec, (pmConceptParseFunc)pmConceptParse_CELL_TRIMSEC, + (pmConceptFormatFunc)pmConceptFormat_CELL_TRIMSEC, PM_CONCEPT_LEVEL_CELL); + psFree(cellTrimsec); + } + + // CELL.BIASSEC + { + psList *biassecs = psListAlloc(NULL); // Blank biassecs + psMetadataItem *cellBiassec = psMetadataItemAllocPtr("CELL.BIASSEC", PS_DATA_LIST, + "Bias sections", biassecs); + psFree(biassecs); + pmConceptRegister(cellBiassec, (pmConceptParseFunc)pmConceptParse_CELL_BIASSEC, + (pmConceptFormatFunc)pmConceptFormat_CELL_BIASSEC, PM_CONCEPT_LEVEL_CELL); + psFree(cellBiassec); + } + + // CELL.XBIN + { + psMetadataItem *cellXbin = psMetadataItemAllocS32("CELL.XBIN", "Binning in x", 0); + pmConceptRegister(cellXbin, (pmConceptParseFunc)pmConceptParse_CELL_Binning, + (pmConceptFormatFunc)pmConceptFormat_CELL_XBIN, PM_CONCEPT_LEVEL_CELL); + psFree(cellXbin); + } + + // CELL.YBIN + { + psMetadataItem *cellYbin = psMetadataItemAllocS32("CELL.YBIN", "Binning in y", 0); + pmConceptRegister(cellYbin, (pmConceptParseFunc)pmConceptParse_CELL_Binning, + (pmConceptFormatFunc)pmConceptFormat_CELL_YBIN, PM_CONCEPT_LEVEL_CELL); + psFree(cellYbin); + } + + // CELL.TIMESYS + { + psMetadataItem *cellTimesys = psMetadataItemAllocS32("CELL.TIMESYS", "Time system", -1); + pmConceptRegister(cellTimesys, (pmConceptParseFunc)pmConceptParse_CELL_TIMESYS, + (pmConceptFormatFunc)pmConceptFormat_CELL_TIMESYS, PM_CONCEPT_LEVEL_CELL); + psFree(cellTimesys); + } + + // CELL.TIME + { + psTime *time = psTimeAlloc(PS_TIME_TAI); // Blank time + // Not particularly distinguishing, but should be good enough + time->sec = 0; + time->nsec = 0; + psMetadataItem *cellTime = psMetadataItemAlloc("CELL.TIME", PS_DATA_TIME, + "Time of exposure", time); + psFree(time); + pmConceptRegister(cellTime, (pmConceptParseFunc)pmConceptParse_CELL_TIME, + (pmConceptFormatFunc)pmConceptFormat_CELL_TIME, PM_CONCEPT_LEVEL_CELL); + psFree(cellTime); + } + + // CELL.X0 + { + psMetadataItem *cellX0 = psMetadataItemAllocS32("CELL.X0", "Position of (0,0) on the chip", 0); + pmConceptRegister(cellX0, (pmConceptParseFunc)pmConceptParse_CELL_Positions, + (pmConceptFormatFunc)pmConceptFormat_CELL_Positions, PM_CONCEPT_LEVEL_CELL); + psFree(cellX0); + } + + // CELL.Y0 + { + psMetadataItem *cellY0 = psMetadataItemAllocS32("CELL.Y0", "Position of (0,0) on the chip", 0); + pmConceptRegister(cellY0, (pmConceptParseFunc)pmConceptParse_CELL_Positions, + (pmConceptFormatFunc)pmConceptFormat_CELL_Positions, PM_CONCEPT_LEVEL_CELL); + psFree(cellY0); + } + + } + + conceptsInitialised = true; + + return init; +} + +void pmConceptsDone(void) +{ + psFree(conceptsFPA); + psFree(conceptsChip); + psFree(conceptsCell); +} + + +// Copy concepts from one FPA to another +bool pmFPACopyConcepts(pmFPA *target, // The target FPA + pmFPA *source // The target FPA + ) +{ + // Copy FPA concepts + target->concepts = psMetadataCopy(target->concepts, source->concepts); + + // Copy chip concepts + psArray *targetChips = target->chips; // Chips in target + psArray *sourceChips = source->chips; // Chips in source + if (targetChips->n != sourceChips->n) { + psError(PS_ERR_IO, true, "Number of chips in target (%d) and source (%d) differ --- unable to copy " + "concepts.\n", targetChips->n, sourceChips->n); + return false; + } + for (int i = 0; i < targetChips->n; i++) { + pmChip *targetChip = targetChips->data[i]; // Target chip of interest + pmChip *sourceChip = sourceChips->data[i]; // Source chip of interest + if (! targetChip || ! sourceChip) { + continue; + } + targetChip->concepts = psMetadataCopy(targetChip->concepts, sourceChip->concepts); + + // Copy cell concepts + psArray *targetCells = targetChip->cells; // Cells in target + psArray *sourceCells = sourceChip->cells; // Cells in source + if (targetCells->n != sourceCells->n) { + psError(PS_ERR_IO, true, "Number of cells in target (%d) and source (%d) differ for chip %d ---" + " unable to copy concepts.\n", targetCells->n, sourceCells->n, i); + return false; + } + for (int j = 0; j < targetCells->n; j++) { + pmCell *targetCell = targetCells->data[j]; // Target chip of interest + pmCell *sourceCell = sourceCells->data[j]; // Source chip of interest + if (! targetCell || ! sourceCell) { + continue; + } + targetCell->concepts = psMetadataCopy(targetCell->concepts, sourceCell->concepts); + } + } + + return true; +} Index: trunk/psModules/src/astrom/pmConcepts.h =================================================================== --- trunk/psModules/src/astrom/pmConcepts.h (revision 6872) +++ trunk/psModules/src/astrom/pmConcepts.h (revision 6872) @@ -0,0 +1,99 @@ +#ifndef PM_CONCEPTS_H +#define PM_CONCEPTS_H + +#include "pslib.h" + +#include "pmFPA.h" + + +// Function to call to parse a concept once it has been read +typedef psMetadataItem* (*pmConceptParseFunc)(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +// Function to call to format a concept for writing +typedef psMetadataItem* (*pmConceptFormatFunc)(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); + +// A "concept" specification +typedef struct +{ + psMetadataItem *blank; // Blank value of concept; also contains the name + pmConceptParseFunc parse; // Function to call to read the concept + pmConceptFormatFunc format; // Function to call to write the concept +} +pmConceptSpec; + +// Allocator +pmConceptSpec *pmConceptSpecAlloc(psMetadataItem *blank, // Blank value; contains the name + pmConceptParseFunc parse, // Function to call to parse the concept + pmConceptFormatFunc format // Function to call to format the concept + ); + +// Level at which to store a concept in the FPA hierarchy +typedef enum { + PM_CONCEPT_LEVEL_FPA, // Store in the FPA + PM_CONCEPT_LEVEL_CHIP, // Store in the chip + PM_CONCEPT_LEVEL_CELL // Store in the cell +} pmConceptLevel; + +// Register a new concept +bool pmConceptRegister(psMetadataItem *blank, // Blank value; contains the name + pmConceptParseFunc parse, // Function to call to parse the concept + pmConceptFormatFunc format, // Function to call to format the concept + pmConceptLevel level // Level at which to store concept in the FPA hierarchy + ); + +// Some specificity to reading and writing concepts +typedef enum { + PM_CONCEPT_SOURCE_ALL = 0x00, // All concepts + PM_CONCEPT_SOURCE_CAMERA = 0x01, // Concept comes from the camera information + PM_CONCEPT_SOURCE_DEFAULTS = 0x02, // Concept comes from defaults + PM_CONCEPT_SOURCE_HEADER = 0x04, // Concept comes from FITS header + PM_CONCEPT_SOURCE_DATABASE = 0x08 // Concept comes from database +} pmConceptSource; + +// Set blanks, read or write concepts at the appropriate level +bool pmConceptsBlankFPA(pmFPA *fpa // FPA for which to set blank concepts + ); +bool pmConceptsReadFPA(pmFPA *fpa, // FPA for which to read concepts + pmConceptSource source, // Source for concepts + psDB *db // Database handle + ); +bool pmConceptsWriteFPA(pmFPA *fpa, // FPA for which to write concepts + pmConceptSource source, // Source for concepts + psDB *db // Database handle + ); +bool pmConceptsBlankChip(pmChip *chip // FPA for which to set blank concepts + ); +bool pmConceptsReadChip(pmChip *chip, // Chip for which to read concepts + pmConceptSource source, // Source for concepts + bool propagate, // Propagate to higher levels as well? + psDB *db // Database handle + ); +bool pmConceptsWriteChip(pmChip *chip, // Chip for which to write concepts + pmConceptSource source, // Source for concepts + bool propagate,// Propagate to higher levels as well? + psDB *db // Database handle + ); +bool pmConceptsBlankCell(pmCell *cell // Cell for which to set blank concepts + ); +bool pmConceptsReadCell(pmCell *cell, // Cell for which to read concepts + pmConceptSource source, // Source for concepts + bool propagate, // Propagate to higher levels as well? + psDB *db // Database handle + ); +bool pmConceptsWriteCell(pmCell *cell, // FPA for which to write concepts + pmConceptSource source, // Source for concepts + bool propagate,// Propagate to higher levels as well? + psDB *db // Database handle + ); + +// Set up the blank concepts +bool pmConceptsInit(void); +// Free the concept specs so there's no memory leak +void pmConceptsDone(void); + +// Copy all the concepts within an FPA to another FPA +bool pmFPACopyConcepts(pmFPA *target, // The target FPA + pmFPA *source // The target FPA + ); + + +#endif Index: trunk/psModules/src/astrom/pmConceptsRead.c =================================================================== --- trunk/psModules/src/astrom/pmConceptsRead.c (revision 6872) +++ trunk/psModules/src/astrom/pmConceptsRead.c (revision 6872) @@ -0,0 +1,606 @@ +#include + +#include "pslib.h" +#include "psMetadataItemParse.h" + +#include "pmFPA.h" +#include "pmHDU.h" +#include "pmHDUUtils.h" +#include "pmConcepts.h" +#include "pmConceptsRead.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// This function gets called for the really boring concepts --- where all you have to do is parse from a +// header or database and you don't need to muck around with conversions. There is no similar "formatPlain", +// since the type is already known. +static psMetadataItem *parsePlain(psMetadataItem *concept, // The concept to parse + psMetadataItem *pattern // The concept pattern + ) +{ + switch (pattern->type) { + case PS_DATA_STRING: { + psString string = psMetadataItemParseString(concept); // Get the string, so I can free it after it + // goes on the MetadataItem + psMetadataItem *item = psMetadataItemAllocStr(pattern->name, pattern->comment, string); + psFree(string); + return item; + } + case PS_DATA_S32: + return psMetadataItemAllocS32(pattern->name, pattern->comment, psMetadataItemParseS32(concept)); + case PS_DATA_F32: + return psMetadataItemAllocF32(pattern->name, pattern->comment, psMetadataItemParseF32(concept)); + case PS_DATA_F64: + return psMetadataItemAllocF64(pattern->name, pattern->comment, psMetadataItemParseF64(concept)); + default: + psLogMsg(__func__, PS_LOG_WARN, "Concept %s (%s) is not of a standard type (%x)\n", + pattern->name, pattern->comment, pattern->type); + return NULL; + } +} + + +// Parse a single concept +static bool conceptParse(pmConceptSpec *spec, // The concept specification + psMetadataItem *concept, // The concept to parse + psMetadata *cameraFormat, // The camera format + psMetadata *target, // The target + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell // The cell + ) +{ + if (concept) { + psMetadataItem *parsed = NULL; // The parsed concept + if (spec->parse) { + parsed = spec->parse(concept, spec->blank, cameraFormat, fpa, chip, cell); + } else { + parsed = parsePlain(concept, spec->blank); + } + + // Reformat so that everything's clean + if (strcmp(spec->blank->name, parsed->name) != 0 || + strcmp(spec->blank->comment, parsed->comment) != 0) { + psMetadataItem *cleaned = NULL; // Item that's been cleaned up --- correct name and comment + switch (spec->blank->type) { + case PS_DATA_STRING: + cleaned = psMetadataItemAllocStr(spec->blank->name, spec->blank->comment, parsed->data.V); + break; + case PS_DATA_S32: + cleaned = psMetadataItemAllocS32(spec->blank->name, spec->blank->comment, parsed->data.S32); + break; + case PS_DATA_F32: + cleaned = psMetadataItemAllocF32(spec->blank->name, spec->blank->comment, parsed->data.F32); + break; + case PS_DATA_F64: + cleaned = psMetadataItemAllocF64(spec->blank->name, spec->blank->comment, parsed->data.F64); + break; + default: + cleaned = psMetadataItemAlloc(spec->blank->name, concept->type, spec->blank->comment, + parsed->data.V); + } + psFree(parsed); + parsed = cleaned; + } + psMetadataAddItem(target, parsed, PS_LIST_TAIL, PS_META_REPLACE); + psFree(parsed); // Drop reference + return true; + } + + return false; +} + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +bool pmConceptsReadFromCamera(psMetadata *specs, // The concept specifications + pmCell *cell, // The cell + psMetadata *target // Place into which to read the concepts + ) +{ + if (cell) { + pmHDU *hdu = pmHDUGetLowest(NULL, NULL, cell); // The HDU at the lowest level + if (! hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + psMetadata *cellConfig = cell->config; // The camera configuration for this cell + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + psMetadataItem *conceptItem = psMetadataLookup(cellConfig, name); // The concept, or NULL + psMetadataItem *value = NULL; // The value of the concept + if (conceptItem) { + if (conceptItem->type == PS_DATA_STRING) { + // Check the SOURCE + psString nameSource = NULL; // String with the concept name and ".SOURCE" added + psStringAppend(&nameSource, "%s.SOURCE", name); + bool mdok = true; // Status of MD lookup + psString source = psMetadataLookupStr(&mdok, cell->config, nameSource); // The source + psFree(nameSource); + if (mdok && strlen(source) > 0 && strcasecmp(source, "VALUE") == 0) { + value = conceptItem; + conceptParse(spec, value, cameraFormat, target, NULL, NULL, cell); + } else if (source && (strlen(source) == 0 || strcasecmp(source, "HEADER") != 0)) { + // We leave "HEADER" to pmConceptsReadFromHeader + psError(PS_ERR_IO, true, "%s isn't HEADER or VALUE --- can't read %s\n", source, + name); + continue; + } + } else { + // Another type --- should be OK + conceptParse(spec, conceptItem, cameraFormat, target, NULL, NULL, cell); + } + } + } + psFree(specsIter); + return true; + } + return false; +} + + +bool pmConceptsReadFromDefaults(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *target // Place into which to read the concepts + ) +{ + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + if (!hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + bool mdok = true; // Status of MD lookup + psMetadata *defaults = psMetadataLookupMD(&mdok, cameraFormat, "DEFAULTS"); // The DEFAULTS spec + if (mdok && defaults) { + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + psMetadata *cameraFormat = hdu->format; // The camera format + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + psMetadataItem *conceptItem = psMetadataLookup(defaults, name); // The concept, or NULL + conceptParse(spec, conceptItem, cameraFormat, target, fpa, chip, cell); + } + psFree(specsIter); + return true; + } + return false; +} + + +bool pmConceptsReadFromHeader(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *target // Place into which to read the concepts + ) +{ + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + if (!hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + bool mdok = true; // Status of MD lookup + psMetadata *transSpec = psMetadataLookupMD(&mdok, cameraFormat, "TRANSLATION"); // The TRANSLATION spec + if (mdok && transSpec) { + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + psMetadataItem *headerItem = NULL; // The value of the concept from the header + // First check the cell configuration + if (cell && cell->config) { + psMetadataItem *conceptItem = psMetadataLookup(cell->config, name); // The concept, or NULL + if (conceptItem) { + // Check the SOURCE + psString nameSource = NULL; // String with the concept name and ".SOURCE" added + psStringAppend(&nameSource, "%s.SOURCE", name); + psString source = psMetadataLookupStr(&mdok, cell->config, nameSource); // The source + psFree(nameSource); + if (mdok && strlen(source) && strcasecmp(source, "HEADER") == 0) { + headerItem = psMetadataLookup(hdu->header, conceptItem->data.V); + } + // Leave the error handling to pmConceptsFromCamera, which should already have been called + } + } + if (! headerItem) { + psString keywords = psMetadataLookupStr(&mdok, transSpec, name); // The FITS keywords + if (mdok && strlen(keywords) > 0) { + // In case there are multiple headers + psList *keys = psStringSplit(keywords, " ,;"); // List of keywords + if (keys->n == 1) { + // Only one key --- proceed as usual + headerItem = psMetadataLookup(hdu->header, keywords); + } else { + psListIterator *keysIter = psListIteratorAlloc(keys, PS_LIST_HEAD, false); // Iterator + psString key = NULL; // Item from iteration + psList *values = psListAlloc(NULL); // List containing the values + while ((key = psListGetAndIncrement(keysIter))) { + psMetadataItem *value = psMetadataLookup(hdu->header, key); + psListAdd(values, PS_LIST_TAIL, value); + } + psFree(keysIter); + headerItem = psMetadataItemAlloc(name, PS_DATA_LIST, specItem->comment, values); + psFree(values); + } + psFree(keys); + } + } + + // This will also clean up the name + conceptParse(spec, headerItem, cameraFormat, target, fpa, chip, cell); + } + psFree(specsIter); + return true; + } + return false; +} + + +// XXX --- the below code has NOT been tested! +bool pmConceptsReadFromDatabase(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // The database handle + psMetadata *target // Place into which to read the concepts + ) +{ + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + if (!hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + bool mdok = true; // Status of MD lookup + psMetadata *dbSpec = psMetadataLookupMD(&mdok, cameraFormat, "DATABSE"); // The DATABASE spec + if (mdok && dbSpec) { + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + psMetadata *cameraFormat = hdu->format; // The camera format + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + + psMetadata *dbLookup = psMetadataLookupMD(&mdok, dbSpec, name); + if (mdok && dbLookup) { + const char *tableName = psMetadataLookupStr(&mdok, dbLookup, "TABLE"); // Table name + // Names of the "where" columns + const char *givenCols = psMetadataLookupStr(&mdok, dbLookup, "GIVENDBCOL"); + // Values of the "where" columns + const char *givenPS = psMetadataLookupStr(&mdok, dbLookup, "GIVENPS"); + + // Now, need to get the "given"s + if (strlen(givenCols) > 0 || strlen(givenPS) > 0) { + psList *cols = psStringSplit(givenCols, ",;"); // List of column names + psList *values = psStringSplit(givenPS, ",;"); // List of value names for the columns + psMetadata *selection = psMetadataAlloc(); // The stuff to select in the DB + if (cols->n != values->n) { + psLogMsg(__func__, PS_LOG_WARN, + "The GIVENDBCOL and GIVENPS entries for %s do not have " + "the same number of entries --- ignored.\n", name); + } else { + // Iterators for the lists + psListIterator *colsIter = psListIteratorAlloc(cols, PS_LIST_HEAD, false); + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); + char *column = NULL; // Name of the column + while ((column = psListGetAndIncrement(colsIter))) { + char *dependName = psListGetAndIncrement(valuesIter); // Name for the value + if (!strlen(column) || !strlen(name)) { + psLogMsg(__func__, PS_LOG_WARN, "One of the columns or value names for %s is " + " empty --- ignored.\n", name); + } else { + // Search for the value name + psMetadataItem *item = NULL; // The value + if (!item && cell) { + item = psMetadataLookup(cell->concepts, dependName); + } + if (!item && chip) { + item = psMetadataLookup(chip->concepts, dependName); + } + if (!item && fpa) { + item = psMetadataLookup(fpa->concepts, dependName); + } + if (! item) { + psLogMsg(__func__, PS_LOG_ERROR, "Unable to find the value name %s for DB" + " lookup on %s --- ignored.\n", dependName, name); + } else { + // We need to create a new psMetadataItem. I don't think we can't + // simply hack the existing one, since that could conceivably cause + // memory leaks + psMetadataItem *newItem = psMetadataItemAlloc(name, item->type, + item->comment, + item->data.V); + psMetadataAddItem(selection, newItem, PS_LIST_TAIL, PS_META_REPLACE); + psFree(newItem); + } + } + psFree(dependName); + psFree(column); + } // Iterating through the columns + psFree(colsIter); + psFree(valuesIter); + + psArray *dbResult = psDBSelectRows(db, tableName, selection, 2); // Lookup result + // Note that we use limit=2 in order to test if there are multiple rows returned + + psMetadataItem *conceptItem = NULL; // The final result of the DB lookup + if (dbResult->n == 0) { + psLogMsg(__func__, PS_LOG_WARN, + "Unable to find any rows in DB for %s --- ignored\n", name); + } else { + if (dbResult-> n > 1) { + psLogMsg(__func__, PS_LOG_WARN, + "Multiple rows returned in DB lookup for %s --- " + " using the first one only.\n", name); + } + conceptItem = (psMetadataItem*)dbResult->data[0]; + } + + // Now we have the result + conceptParse(spec, conceptItem, cameraFormat, target, fpa, chip, cell); + + } + psFree(cols); + psFree(values); + } + } // Doing the "given"s. + + } // Iterating through the concept specifications + psFree(specsIter); + + return true; + } + return false; +} + + + + +#ifdef OLD + +psMetadataItem *pmConceptReadFromCamera(pmCell *cell, // The cell + const char *concept // Name of concept + ) +{ + if (cell) { + psMetadata *camera = cell->config; // Camera configuration + psMetadataItem *item = psMetadataLookup(camera, concept); + return item; + } + return NULL; +} + +psMetadataItem *pmConceptReadFromHeader(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ) +{ + bool mdStatus = true; // Status of MD lookup + psMetadata *translation = psMetadataLookupMD(&mdStatus, fpa->camera, "TRANSLATION"); // FITS translation + if (! mdStatus) { + psError(PS_ERR_IO, false, "Unable to find TRANSLATION in camera configuration.\n"); + return NULL; + } + + // Look for how to translate the concept into a FITS header name + const char *keyword = psMetadataLookupStr(&mdStatus, translation, concept); + if (mdStatus && strlen(keyword) > 0) { + // We have a FITS header to look up --- search each level + if (cell && cell->hdu) { + psMetadataItem *cellItem = psMetadataLookup(cell->hdu->header, keyword); + if (cellItem) { + // XXX: Need to clean up before returning + return cellItem; + } + } + + if (chip && chip->hdu) { + psMetadataItem *chipItem = psMetadataLookup(chip->hdu->header, keyword); + if (chipItem) { + // XXX: Need to clean up before returning + return chipItem; + } + } + + if (fpa->hdu) { + psMetadataItem *fpaItem = psMetadataLookup(fpa->hdu->header, keyword); + if (fpaItem) { + // XXX: Need to clean up before returning + return fpaItem; + } + } + } + + // No header value + return NULL; +} + + +// Look for a default +psMetadataItem *pmConceptReadFromDefault(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ) +{ + bool mdOK = true; // Status of MD lookup + psMetadata *defaults = psMetadataLookupMD(&mdOK, fpa->camera, "DEFAULTS"); + if (! mdOK) { + psError(PS_ERR_IO, false, "Unable to find DEFAULTS in camera configuration.\n"); + return NULL; + } + + psMetadataItem *defItem = psMetadataLookup(defaults, concept); + if (defItem) { + if (defItem->type == PS_DATA_METADATA) { + // A dependent default + psTrace(__func__, 7, "Evaluating dependent default....\n"); + psMetadata *dependents = defItem->data.V; // The list of dependents + // Find out what it depends on + psString dependName = psStringCopy(concept); + psStringAppend(&dependName, ".DEPEND"); + psString dependsOn = psMetadataLookupStr(&mdOK, defaults, dependName); + if (! mdOK) { + psError(PS_ERR_IO, false, "Unable to find %s in camera configuration for dependent default" + " --- ignored\n", dependName); + // XXX: Need to clean up before returning + return NULL; + } + psFree(dependName); + // Find the value of the dependent concept + psMetadataItem *depItem = pmConceptReadFromHeader(fpa, chip, cell, dependsOn); + if (! depItem) { + psError(PS_ERR_IO, true, "Unable to find value for %s (required for %s)\n", dependsOn, + concept); + return NULL; + } + if (depItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "Value of %s is not of type string, as required for dependency" + " --- ignored.\n", dependsOn); + } + + defItem = psMetadataLookup(dependents, depItem->data.V); // This is now what we were after + } + } + + // XXX: Need to clean up before returning + return defItem; // defItem is either NULL or points to what was desired +} + + +// Look for a database lookup +// XXX: Not tested +psMetadataItem *pmConceptReadFromDB(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Name of concept + ) +{ + if (! db) { + // No database initialised + return NULL; + } + + bool mdStatus = true; // Status of MD lookup + psMetadata *database = psMetadataLookupMD(&mdStatus, fpa->camera, "DATABASE"); + if (! mdStatus) { + // No error, because not everyone needs to use the DB + return NULL; + } + + psMetadata *dbLookup = psMetadataLookupMD(&mdStatus, database, concept); + if (dbLookup) { + const char *tableName = psMetadataLookupStr(&mdStatus, dbLookup, "TABLE"); // Name of the table + // const char *colName = psMetadataLookupStr(&mdStatus, dbLookup, "COLUMN"); // Name of the column + const char *givenCols = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENDBCOL"); // Name of "where" + // columns + const char *givenPS = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENPS"); // Values for "where" + // columns + + // Now, need to get the "given"s + if (strlen(givenCols) || strlen(givenPS)) { + psList *cols = psStringSplit(givenCols, ",;"); // List of column names + psList *values = psStringSplit(givenPS, ",;"); // List of value names for the columns + psMetadata *selection = psMetadataAlloc(); // The stuff to select in the DB + if (cols->n != values->n) { + psLogMsg(__func__, PS_LOG_WARN, "The GIVENDBCOL and GIVENPS entries for %s do not have " + "the same number of entries --- ignored.\n", concept); + } else { + // Iterators for the lists + psListIterator *colsIter = psListIteratorAlloc(cols, PS_LIST_HEAD, false); + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); + char *column = NULL; // Name of the column + while ((column = psListGetAndIncrement(colsIter))) { + char *name = psListGetAndIncrement(valuesIter); // Name for the value + if (!strlen(column) || !strlen(name)) { + psLogMsg(__func__, PS_LOG_WARN, "One of the columns or value names for %s is " + " empty --- ignored.\n", concept); + } else { + // Search for the value name + psMetadataItem *item = pmConceptReadFromHeader(fpa, chip, cell, name); + if (! item) { + item = pmConceptReadFromDefault(fpa, chip, cell, name); + } + if (! item) { + psLogMsg(__func__, PS_LOG_ERROR, "Unable to find the value name %s for DB " + " lookup on %s --- ignored.\n", name, concept); + } else { + // We need to create a new psMetadataItem. I don't think we can't simply hack + // the existing one, since that could conceivably cause memory leaks + psMetadataItem *newItem = psMetadataItemAlloc(concept, item->type, + item->comment, item->data.V); + psMetadataAddItem(selection, newItem, PS_LIST_TAIL, PS_META_REPLACE); + psFree(newItem); + } + } + psFree(name); + psFree(column); + } // Iterating through the columns + psFree(colsIter); + psFree(valuesIter); + + psArray *dbResult = psDBSelectRows(db, tableName, selection, 2); // Lookup result + // Note that we use limit=2 in order to test if there are multiple rows returned + + psMetadataItem *result = NULL; // The final result of the DB lookup + if (dbResult->n == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find any rows in DB for %s --- ignored\n", + concept); + } else { + if (dbResult-> n > 1) { + psLogMsg(__func__, PS_LOG_WARN, "Multiple rows returned in DB lookup for %s --- " + " using the first one only.\n", concept); + } + result = (psMetadataItem*)dbResult->data[0]; + } + // XXX: Need to clean up before returning + return result; + } + psFree(cols); + psFree(values); + } + } // Doing the "given"s. + + psAbort(__func__, "Shouldn't ever get here.\n"); + return NULL; +} + + +// Concept lookup +psMetadataItem *pmConceptRead(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *name // Concept name + ) +{ + // Try headers, database, defaults in order + psMetadataItem *item = pmConceptReadFromCamera(cell, name); + if (! item) { + item = pmConceptReadFromHeader(fpa, chip, cell, name); + } + if (! item) { + item = pmConceptReadFromDB(fpa, chip, cell, db, name); + } + if (! item) { + item = pmConceptReadFromDefault(fpa, chip, cell, name); + } + return item; // item is either NULL, or points to what was desired +} + + +#endif Index: trunk/psModules/src/astrom/pmConceptsRead.h =================================================================== --- trunk/psModules/src/astrom/pmConceptsRead.h (revision 6872) +++ trunk/psModules/src/astrom/pmConceptsRead.h (revision 6872) @@ -0,0 +1,94 @@ +#ifndef PM_CONCEPTS_READ_H +#define PM_CONCEPTS_READ_H + +#include "pmFPA.h" + + +bool pmConceptsReadFromCamera(psMetadata *specs, // The concept specifications + pmCell *cell, // The cell + psMetadata *target // Place into which to read the concepts + ); +bool pmConceptsReadFromDefaults(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *target // Place into which to read the concepts + ); +bool pmConceptsReadFromHeader(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *target // Place into which to read the concepts + ); +bool pmConceptsReadFromDatabase(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // The database handle + psMetadata *target // Place into which to read the concepts + ); + + + + +#ifdef OLD +psMetadataItem *pmConceptReadFromCamera(pmCell *cell, // The cell + const char *concept // Name of concept + ); + +psMetadataItem *pmConceptReadFromHeader(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ); + +psMetadataItem *pmConceptReadFromDefault(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ); + +psMetadataItem *pmConceptReadFromDB(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Name of concept + ); + +psMetadataItem *pmConceptRead(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Concept name + ); + +float pmConceptReadF32(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *name // Name of the concept + ); + +double pmConceptReadF64(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *name // Name of the concept + ); + +int pmConceptReadS32(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *name // Name of the concept + ); + +psString pmConceptReadString(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *name // Name of the concept + ); +#endif + +#endif Index: trunk/psModules/src/astrom/pmConceptsStandard.c =================================================================== --- trunk/psModules/src/astrom/pmConceptsStandard.c (revision 6872) +++ trunk/psModules/src/astrom/pmConceptsStandard.c (revision 6872) @@ -0,0 +1,610 @@ +#include +#include + +#include "pslib.h" + +#include "pmFPA.h" +#include "pmConceptsRead.h" +#include "pmConceptsWrite.h" +#include "pmConceptsStandard.h" + + +#define COMPARE_REGIONS(a,b) (((a)->x0 == (b)->x0 && \ + (a)->x1 == (b)->x1 && \ + (a)->y0 == (b)->y0 && \ + (a)->y1 == (b)->y1) ? true : false) + + +static double defaultCoordScaling(psMetadataItem *pattern) +{ + if (strcmp(pattern->name, "FPA.RA") == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Assuming format for %s is HOURS.\n", pattern->name); + return M_PI / 12.0; + } + if (strcmp(pattern->name, "FPA.DEC") == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Assuming format for %s is DEGREES.\n", pattern->name); + return M_PI / 180.0; + } + psAbort(__func__, "Should never ever get here.\n"); + return NAN; +} + + +// FPA.RA and FPA.DEC +psMetadataItem *pmConceptParse_FPA_Coords(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(pattern); + assert(cameraFormat); + + double coords = NAN; // The coordinates + switch (concept->type) { + case PS_TYPE_F32: + coords = concept->data.F32; + break; + case PS_TYPE_F64: + coords = concept->data.F64; + break; + case PS_DATA_STRING: + // Sexagesimal format + { + int big, medium; + float small; + // XXX: Upgrade path is to allow dd:mm.mmm + if (sscanf(concept->data.V, "%d:%d:%f", &big, &medium, &small) != 3 && + sscanf(concept->data.V, "%d %d %f", &big, &medium, &small) != 3) + { + psError(PS_ERR_IO, true, "Cannot interpret FPA.RA: %s\n", concept->data.V); + break; + } + coords = abs(big) + (float)medium/60.0 + small/3600.0; + if (big < 0) + { + coords *= -1.0; + } + } + break; + default: + psError(PS_ERR_IO, true, "%s concept is of an unexpected type: %x\n", pattern->name, concept->type); + return NULL; + } + + // How to interpret the coordinates + bool mdok = true; // Status of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, cameraFormat, "FORMATS"); + if (mdok && formats) { + psString format = psMetadataLookupStr(&mdok, formats, pattern->name); + if (mdok && strlen(format) > 0) { + if (strcasecmp(format, "HOURS") == 0) { + coords *= M_PI / 12.0; + } else if (strcasecmp(format, "DEGREES") == 0) { + coords *= M_PI / 180.0; + } else if (strcasecmp(format, "RADIANS") == 0) { + // No action required + } else { + coords *= defaultCoordScaling(pattern); + } + } else { + coords *= defaultCoordScaling(pattern); + } + } else { + coords *= defaultCoordScaling(pattern); + } + + return psMetadataItemAllocF64(pattern->name, pattern->comment, coords); +} + +// FPA.RA and FPA.DEC +psMetadataItem *pmConceptFormat_FPA_Coords(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat) +{ + assert(concept); + assert(pattern); + assert(cameraFormat); + + double coords = concept->data.F64; // The coordinates + + // How to interpret the coordinates + bool mdok = true; // Status of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, cameraFormat, "FORMATS"); + if (mdok && formats) { + psString format = psMetadataLookupStr(&mdok, formats, pattern->name); + if (mdok && strlen(format) > 0) { + if (strcasecmp(format, "HOURS") == 0) { + coords /= M_PI / 12.0; + } else if (strcasecmp(format, "DEGREES") == 0) { + coords /= M_PI / 180.0; + } else if (strcasecmp(format, "RADIANS") == 0) { + // No action required + } else { + coords /= defaultCoordScaling(pattern); + } + } else { + coords /= defaultCoordScaling(pattern); + } + } else { + coords /= defaultCoordScaling(pattern); + } + + // We choose to write sexagesimal format + int big, medium; + float small; + big = (int)coords; + medium = (int)(60.0*(coords - (double)big)); + small = 3600.0*(coords - (double)big - 60.0 * (double)medium); + psString coordString = NULL; // String with the coordinates in sexagesimal format + psStringAppend(&coordString, "%d:%d:%.2f", big, medium, small); + psMetadataItem *coordItem = psMetadataItemAllocStr(pattern->name, pattern->comment, coordString); + psFree(coordString); + + return coordItem; +} + + +psMetadataItem *pmConceptParse_CELL_TRIMSEC(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(cell); + assert(pattern); + + psRegion *trimsec = psAlloc(sizeof(psRegion)); // Make space for a psRegion (usually passed by value) + + if (concept->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "CELL.TRIMSEC after read is not of type STR (%x)\n", concept->type); + *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0); + } else { + *trimsec = psRegionFromString(concept->data.V); + } + + psMetadataItem *item = psMetadataItemAllocPtr(pattern->name, PS_DATA_REGION, pattern->comment, trimsec); + psFree(trimsec); + return item; +} + +psMetadataItem *pmConceptParse_CELL_BIASSEC(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(cell); + assert(pattern); + + psList *biassecs = psListAlloc(NULL); // List of bias sections + + switch (concept->type) { + case PS_DATA_STRING: { + psList *regions = psStringSplit(concept->data.V, " ;"); // List of regions + psListIterator *regionsIter = psListIteratorAlloc(regions, PS_LIST_HEAD, false); // Iterator + psString regionString = NULL; // Region string from iteration + while ((regionString = psListGetAndIncrement(regionsIter))) { + psRegion *region = psAlloc(sizeof(psRegion)); // The region + *region = psRegionFromString(regionString); + psListAdd(biassecs, PS_LIST_TAIL, region); + psFree(region); // Drop reference + } + psFree(regionsIter); + psFree(regions); + break; + } + case PS_DATA_LIST: { + psList *regions = concept->data.V; // The list of regions + psListIterator *regionsIter = psListIteratorAlloc(regions, PS_LIST_HEAD, false); // Iterator + psMetadataItem *regionItem = NULL; // Item from list iteration + while ((regionItem = psListGetAndIncrement(regionsIter))) { + if (regionItem->type != PS_DATA_STRING) { + psLogMsg(__func__, PS_LOG_WARN, "CELL.BIASSEC member is not of type STR --- ignored.\n"); + continue; + } + psRegion *region = psAlloc(sizeof(psRegion)); // The region + *region = psRegionFromString(regionItem->data.V); + psListAdd(biassecs, PS_LIST_TAIL, region); + psFree(region); // Drop reference + } + psFree(regionsIter); + break; + } + default: + psError(PS_ERR_IO, true, "CELL.BIASSEC after read is not of type STRING or LIST --- assuming " + "blank.\n"); + } + + psMetadataItem *item = psMetadataItemAllocPtr(pattern->name, PS_DATA_LIST, pattern->comment, biassecs); + psFree(biassecs); // Drop reference + return item; +} + +// CELL.XBIN and CELL.YBIN +psMetadataItem *pmConceptParse_CELL_Binning(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(pattern); + + int binning = 1; // Binning factor in x + if (concept->type == PS_DATA_STRING) { + psString binString = concept->data.V; // The string containing the binning + if ((strcmp(pattern->name, "CELL.XBIN") == 0 && sscanf(binString, "%d %*d", &binning) != 1 && + sscanf(binString, "%d,%*d", &binning) != 1) || + (strcmp(pattern->name, "CELL.YBIN") == 0 && sscanf(binString, "%*d %d", &binning) != 1 && + sscanf(binString, "%*d,%d", &binning) != 1)) { + psError(PS_ERR_IO, true, "Unable to parse string to get %s: %s\n", pattern->name, binString); + } + } else if (concept->type == PS_TYPE_S32) { + binning = concept->data.S32; + } else { + psError(PS_ERR_IO, true, "Note sure how to parse %s of type %x --- assuming 1.\n", pattern->name, + concept->type); + } + + return psMetadataItemAllocS32(pattern->name, pattern->comment, binning); +} + + +psMetadataItem *pmConceptParse_CELL_TIMESYS(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(pattern); + + psTimeType timeSys = PS_TIME_UTC; // The time system + psString sys = concept->data.V; // The time system string + if (concept->type != PS_DATA_STRING || strlen(sys) <= 0) { + psError(PS_ERR_IO, true, "Can't interpret CELL.TIMESYS --- assuming UTC.\n"); + } else if (strcasecmp(sys, "TAI") == 0) { + timeSys = PS_TIME_TAI; + } else if (strcasecmp(sys, "UTC") == 0) { + timeSys = PS_TIME_UTC; + } else if (strcasecmp(sys, "UT1") == 0) { + timeSys = PS_TIME_UT1; + } else if (strcasecmp(sys, "TT") == 0) { + timeSys = PS_TIME_TT; + } else { + psError(PS_ERR_IO, true, "Can't interpret CELL.TIMESYS --- assuming UTC.\n"); + } + + return psMetadataItemAllocS32(pattern->name, pattern->comment, timeSys); +} + + +psMetadataItem *pmConceptParse_CELL_TIME(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(cameraFormat); + assert(cell); + + // Need CELL.TIMESYS first + bool mdok = true; // Result of MD lookup + psTimeType timeSys = psMetadataLookupS32(&mdok, cell->concepts, "CELL.TIMESYS"); // The time system + if (!mdok) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find CELL.TIMESYS in concepts --- assuming UTC.\n"); + timeSys = PS_TIME_UTC; + } + + // Get format + psMetadata *formats = psMetadataLookupMD(&mdok, cameraFormat, "FORMATS"); + if (!mdok || !formats) { + psError(PS_ERR_IO, false, "Unable to find FORMATS in camera configuration.\n"); + return NULL; + } + + psString timeFormat = psMetadataLookupStr(&mdok, formats, "CELL.TIME"); + if (!mdok || strlen(timeFormat) == 0) { + psError(PS_ERR_IO, false, "Unable to find CELL.TIME in FORMATS.\n"); + return NULL; + } + + psTime *time = NULL; // The time + switch (concept->type) { + case PS_DATA_LIST: { + // The date and time are stored separately + // Assume the date is first and the time second + psList *dateTime = concept->data.V; // The list containing items for date and time + psMetadataItem *dateItem = psListGet(dateTime, PS_LIST_HEAD); // Item containing the date + psMetadataItem *timeItem = psListGet(dateTime, PS_LIST_HEAD + 1); // Item containing the time + if (dateItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "Date is not of type STR.\n"); + return NULL; + } + psString dateString = dateItem->data.V; // The string with the date + int day = 0, month = 0, year = 0; + if (sscanf(dateString, "%d-%d-%d", &day, &month, &year) != 3 && + sscanf(dateString, "%d/%d/%d", &day, &month, &year) != 3) { + psError(PS_ERR_IO, true, "Unable to read date: %s\n", dateString); + return NULL; + } + if (strstr(timeFormat, "BACKWARDS")) { + int temp = day; + day = year; + year = temp; + } + if (strstr(timeFormat, "PRE2000") || year < 2000) { + year += 2000; + } + + psString timeString = NULL; // The string with the time + if (timeItem->type == PS_DATA_STRING) { + timeString = timeItem->data.V; + } else { + // Assume that time is specified in Second of Day (!) + double seconds = NAN; + switch (timeItem->type) { + case PS_TYPE_S32: + seconds = timeItem->data.S32; + break; + case PS_TYPE_F32: + seconds = timeItem->data.F32; + break; + case PS_TYPE_F64: + seconds = timeItem->data.F64; + break; + default: + psError(PS_ERR_IO, true, "Time is not of an expected type: %x\n", timeItem->type); + return NULL; + } + // Now print to timeString as "hh:mm:ss.ss" + int hours = seconds / 3600; + seconds -= (double)hours * 3600.0; + int minutes = seconds / 60; + seconds -= (double)minutes * 60.0; + psStringAppend(&timeString, "%02d:%02d:%02f", hours, minutes, seconds); + } + psString dateTimeString = NULL; + psStringAppend(&dateTimeString, "%sT%s", dateString, timeString); + time = psTimeFromISO(dateTimeString, timeSys); + break; + } + case PS_DATA_STRING: { + psString timeString = concept->data.V; // String with the time + if (strcasecmp(timeFormat, "ISO") == 0) { + // timeString contains an ISO time + time = psTimeFromISO(timeString, timeSys); + } else if (strcasecmp(timeFormat, "JD") == 0) { + double timeValue = strtod (timeString, NULL); + time = psTimeFromJD(timeValue); + } else if (strcasecmp(timeFormat, "MJD") == 0) { + double timeValue = strtod (timeString, NULL); + time = psTimeFromMJD(timeValue); + } else { + psError(PS_ERR_IO, true, "Not sure how to parse CELL.TIME (%s) --- trying " + "ISO\n", timeString); + time = psTimeFromISO(timeString, timeSys); + } // Interpreting the time string + break; + } + case PS_TYPE_F32: { + double timeValue = (double)concept->data.F32; + if (strcasecmp(timeFormat, "JD") == 0) { + time = psTimeFromJD(timeValue); + } else if (strcasecmp(timeFormat, "MJD") == 0) { + time = psTimeFromMJD(timeValue); + } else { + psError(PS_ERR_IO, true, "Not sure how to parse CELL.TIME (%f) --- trying " + "JD\n", timeValue); + time = psTimeFromJD(timeValue); + } + break; + } + case PS_TYPE_F64: { + double timeValue = (double)concept->data.F64; + if (strcasecmp(timeFormat, "JD") == 0) { + time = psTimeFromJD(timeValue); + } else if (strcasecmp(timeFormat, "MJD") == 0) { + time = psTimeFromMJD(timeValue); + } else { + psError(PS_ERR_IO, true, "Not sure how to parse CELL.TIME (%f) --- trying " + "JD\n", timeValue); + time = psTimeFromJD(timeValue); + } + break; + } + default: + psError(PS_ERR_IO, true, "Unable to parse CELL.TIME.\n"); + return NULL; + } + + psMetadataItem *item = psMetadataItemAllocPtr(pattern->name, PS_DATA_TIME, pattern->comment, time); + psFree(time); + return item; +} + +// Correct a position --- in case the user wants FORTRAN indexing (like the FITS standard...) +static int fortranCorr(psMetadata *cameraFormat, // The camera format description + const char *name // Name of concept to check for FORTRAN indexing + ) +{ + bool mdok = false; // Result of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, cameraFormat, "FORMATS"); + if (mdok && formats) { + psString format = psMetadataLookupStr(&mdok, formats, name); + if (mdok && strlen(format) > 0 && strcasecmp(format, "FORTRAN") == 0) { + return 1; + } + } + return 0; +} + +psMetadataItem *pmConceptParse_CELL_Positions(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(cameraFormat); + + if (concept->type != PS_TYPE_S32) { + psError(PS_ERR_IO, true, "Concept %s is not of type S32, as expected.\n", pattern->name); + return NULL; + } + int offset = concept->data.S32; + offset -= fortranCorr(cameraFormat, pattern->name); + return psMetadataItemAllocS32(pattern->name, pattern->comment, offset); +} + + +psMetadataItem *pmConceptFormat_CELL_TRIMSEC(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + + psRegion *trimsec = concept->data.V; // The trimsec region + psString trimsecString = psRegionToString(*trimsec); + psMetadataItem *formatted = psMetadataItemAllocStr(concept->name, concept->comment, + trimsecString); + psFree(trimsecString); + return formatted; +} + +psMetadataItem *pmConceptFormat_CELL_BIASSEC(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + // Return a metadata item containing a list of metadata items of region strings + psList *biassecs = concept->data.V; // The biassecs region list + psListIterator *biassecsIter = psListIteratorAlloc(biassecs, PS_LIST_HEAD, false); // Iterator + psRegion *region = NULL; // Region from iteration + psList *new = psListAlloc(NULL); // New list containing metadatas + while ((region = psListGetAndIncrement(biassecsIter))) { + psString regionString = psRegionToString(*region); // The string region "[x0:x1,y0:y1]" + psMetadataItem *item = psMetadataItemAllocStr(concept->name, concept->comment, regionString); + psFree(regionString); // Drop reference + psListAdd(new, PS_LIST_TAIL, item); + psFree(item); // Drop reference + } + psFree(biassecsIter); + psMetadataItem *formatted = psMetadataItemAllocPtr(concept->name, PS_DATA_LIST, concept->comment, new); + psFree(new); // Drop reference + return formatted; +} + +// This function actually does both CELL.XBIN and CELL.YBIN if CELL.XBIN and CELL.YBIN are specified by the +// same header. +psMetadataItem *pmConceptFormat_CELL_XBIN(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + + psMetadata *translation = psMetadataLookupMD(NULL, cameraFormat, "TRANSLATION"); + bool xBinOK = true, yBinOK = true; // Status of MD lookups + psString xKeyword = psMetadataLookupStr(&xBinOK, translation, "CELL.XBIN"); + psString yKeyword = psMetadataLookupStr(&yBinOK, translation, "CELL.YBIN"); + if (xBinOK && yBinOK && strlen(xKeyword) > 0 && strlen(yKeyword) > 0 && + strcasecmp(xKeyword, yKeyword) == 0) { + psMetadataItem *yBinItem = psMetadataLookup(cell->concepts, "CELL.YBIN"); // Binning factor in y + psString binString = psStringCopy(""); + psStringAppend(&binString, "%d %d", concept->data.S32, yBinItem->data.S32); + psMetadataItem *binItem = psMetadataItemAllocStr(concept->name, concept->comment, binString); + psFree(binString); + return binItem; + } + + // Otherwise, there's no formatting required + return psMemIncrRefCounter(concept); +} + +// Only need to format if both if CELL.XBIN and CELL.YBIN are not specified by the same header. +psMetadataItem *pmConceptFormat_CELL_YBIN(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + + psMetadata *translation = psMetadataLookupMD(NULL, cameraFormat, "TRANSLATION"); + bool xBinOK = true, yBinOK = true; // Status of MD lookups + psString xKeyword = psMetadataLookupStr(&xBinOK, translation, "CELL.XBIN"); + psString yKeyword = psMetadataLookupStr(&yBinOK, translation, "CELL.YBIN"); + if (xBinOK && yBinOK && strlen(xKeyword) > 0 && strlen(yKeyword) > 0 && + strcasecmp(xKeyword, yKeyword) == 0) { + // Censor this --- it's already done (though no harm if it's done twice + return NULL; + } + + // No formatting required + return psMemIncrRefCounter(concept); +} + + +psMetadataItem *pmConceptFormat_CELL_TIMESYS(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + psString sys = NULL; // String to store + switch (concept->data.S32) { + case PS_TIME_TAI: + sys = psStringCopy("TAI"); + break; + case PS_TIME_UTC: + sys = psStringCopy("UTC"); + break; + case PS_TIME_UT1: + sys = psStringCopy("UT1"); + break; + case PS_TIME_TT: + sys = psStringCopy("TT"); + break; + default: + sys = psStringCopy("Unknown"); + } + psMetadataItem *newItem = psMetadataItemAllocStr(concept->name, concept->comment, sys); + psFree(sys); + + return newItem; +} + +psMetadataItem *pmConceptFormat_CELL_TIME(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + psTime *time = concept->data.V; // The time + psMetadata *formats = psMetadataLookupMD(NULL, cameraFormat, "FORMATS"); + psString format = psMetadataLookupStr(NULL, formats, "CELL.TIME"); + + if (strlen(format) == 0 || strcasecmp(format, "ISO") == 0) { + psString dateTimeString = psTimeToISO(time); // String representation + psMetadataItem *item = psMetadataItemAllocStr(concept->name, concept->comment, dateTimeString); + psFree(dateTimeString); + return item; + } + if (strstr(format, "SEPARATE")) { + // We're working with two separate headers --- construct a list with the date and time separately + psString dateTimeString = psTimeToISO(time); // String representation + psList *dateTime = psStringSplit(dateTimeString, "T"); + psFree(dateTimeString); + psString dateString = psListGet(dateTime, PS_LIST_HEAD); // The date string + psString timeString = psListGet(dateTime, PS_LIST_TAIL); // The time string + + // Need to format the strings.... + // XXX: Couldn't be bothered doing these right now + if (strstr(format, "PRE2000")) { + psError(PS_ERR_IO, true, "Don't you realise it's the twenty-first century?\n"); + return NULL; + } + if (strstr(format, "BACKWARDS")) { + psError(PS_ERR_IO, true, "You want it BACKWARDS? Not right now, thanks.\n"); + return NULL; + } + + psMetadataItem *dateItem = psMetadataItemAllocStr(concept->name, "The date of observation", + dateString); + psMetadataItem *timeItem = psMetadataItemAllocStr(concept->name, "The time of observation", + timeString); + psFree(dateString); + psFree(timeString); + + psListRemove(dateTime, PS_LIST_HEAD); + psListRemove(dateTime, PS_LIST_HEAD); + psListAdd(dateTime, PS_LIST_HEAD, dateItem); + psListAdd(dateTime, PS_LIST_TAIL, timeItem); + + psMetadataItem *item = psMetadataItemAllocPtr(concept->name, PS_DATA_LIST, concept->comment, + dateTime); + return item; + } + if (strcasecmp(format, "MJD") == 0) { + double mjd = psTimeToMJD(time); + return psMetadataItemAllocF64(concept->name, concept->comment, mjd); + } + if (strcasecmp(format, "JD") == 0) { + double jd = psTimeToMJD(time); + return psMetadataItemAllocF64("CELL.TIME", "JD of observation", jd); + } + + psError(PS_ERR_IO, true, "Not sure how to format concept CELL.TIME\n"); + return NULL; +} + +psMetadataItem *pmConceptFormat_CELL_Positions(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell) +{ + assert(concept); + assert(cameraFormat); + + if (concept->type != PS_TYPE_S32) { + psError(PS_ERR_IO, true, "Concept %s is not of type S32, as expected.\n", concept->name); + return NULL; + } + int offset = concept->data.S32; + offset += fortranCorr(cameraFormat, concept->name); + return psMetadataItemAllocS32(concept->name, concept->comment, offset); +} + Index: trunk/psModules/src/astrom/pmConceptsStandard.h =================================================================== --- trunk/psModules/src/astrom/pmConceptsStandard.h (revision 6872) +++ trunk/psModules/src/astrom/pmConceptsStandard.h (revision 6872) @@ -0,0 +1,24 @@ +#ifndef PM_CONCEPTS_STANDARD_H +#define PM_CONCEPTS_STANDARD_H + +#include "pslib.h" +#include "pmFPA.h" + + +psMetadataItem *pmConceptParse_FPA_Coords(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_FPA_Coords(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat); +psMetadataItem *pmConceptParse_CELL_TRIMSEC(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptParse_CELL_BIASSEC(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptParse_CELL_Binning(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptParse_CELL_TIMESYS(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptParse_CELL_TIME(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptParse_CELL_Positions(psMetadataItem *concept, psMetadataItem *pattern, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_CELL_TRIMSEC(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_CELL_BIASSEC(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_CELL_XBIN(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_CELL_YBIN(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_CELL_TIMESYS(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_CELL_TIME(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); +psMetadataItem *pmConceptFormat_CELL_Positions(psMetadataItem *concept, psMetadata *cameraFormat, pmFPA *fpa, pmChip *chip, pmCell *cell); + +#endif Index: trunk/psModules/src/astrom/pmConceptsWrite.c =================================================================== --- trunk/psModules/src/astrom/pmConceptsWrite.c (revision 6872) +++ trunk/psModules/src/astrom/pmConceptsWrite.c (revision 6872) @@ -0,0 +1,870 @@ +#include +#include +#include "pslib.h" + +#include "pmFPA.h" +#include "pmHDU.h" +#include "pmHDUUtils.h" +#include "pmConcepts.h" +#include "pmConceptsRead.h" +#include "psAdditionals.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +static bool compareConcepts(psMetadataItem *compare, // Item to compare + psMetadataItem *standard // Standard for comparison + ) +{ + // First order checks + if (! compare || ! standard) { + return false; + } + if (strcasecmp(compare->name, standard->name) != 0) { + return false; + } + + // Check the more boring types + switch (compare->type) { + case PS_TYPE_S32: + switch (standard->type) { + case PS_TYPE_S32: + psTrace(__func__, 10, "Comparing %d and %d...\n", compare->data.S32, standard->data.S32); + return (compare->data.S32 == standard->data.S32) ? true : false; + case PS_TYPE_F32: + psTrace(__func__, 10, "Comparing %d and %d...\n", compare->data.S32, (int)standard->data.F32); + return (compare->data.S32 == (int)standard->data.F32) ? true : false; + case PS_TYPE_F64: + psTrace(__func__, 10, "Comparing %d and %d...\n", compare->data.S32, (int)standard->data.F64); + return (compare->data.S32 == (int)standard->data.F64) ? true : false; + default: + return false; + } + case PS_TYPE_F32: + switch (standard->type) { + case PS_TYPE_S32: + psTrace(__func__, 10, "Comparing %f and %f...\n", compare->data.F32, (float)standard->data.S32); + return (compare->data.F32 == (float)standard->data.S32) ? true : false; + case PS_TYPE_F32: + psTrace(__func__, 10, "Comparing %f and %f...\n", compare->data.F32, standard->data.F32); + return (compare->data.F32 == standard->data.F32) ? true : false; + case PS_TYPE_F64: + psTrace(__func__, 10, "Comparing %f and %f...\n", compare->data.F32, (float)standard->data.F64); + return (compare->data.F32 == (float)standard->data.F64) ? true : false; + default: + return false; + } + case PS_TYPE_F64: + switch (standard->type) { + case PS_TYPE_S32: + psTrace(__func__, 10, "Comparing %f and %f...\n", compare->data.F32, (double)standard->data.S32); + return (compare->data.F64 == (double)standard->data.S32) ? true : false; + case PS_TYPE_F32: + psTrace(__func__, 10, "Comparing %f and %f...\n", compare->data.F32, (double)standard->data.F32); + return (compare->data.F64 == (double)standard->data.F32) ? true : false; + case PS_TYPE_F64: + psTrace(__func__, 10, "Comparing %f and %f...\n", compare->data.F32, standard->data.F64); + return (compare->data.F64 == standard->data.F64) ? true : false; + default: + return false; + } + return (compare->data.F64 == standard->data.F64) ? true : false; + case PS_DATA_STRING: + if (standard->type != PS_DATA_STRING) { + return false; + } + psTrace(__func__, 10, "Comparing '%s' and '%s'\n", compare->data.V, standard->data.V); + return (strcasecmp(compare->data.V, standard->data.V) == 0) ? true : false; + case PS_DATA_LIST: { // A list of strings + // "compare" contains a list of psMetadataItems + // "standard" likely contains just a string (but it might possibly be a list of strings) + psList *cList = compare->data.V; // The list from comparison item + psList *sList = NULL; // The list from standard item + switch (standard->type) { + case PS_DATA_STRING: + sList = psStringSplit(standard->data.V, " ;"); + break; + case PS_DATA_LIST: + sList = psMemIncrRefCounter(standard->data.V); + break; + default: + return false; + } + if (cList->n != sList->n) { + psFree(sList); + return false; + } + psVector *match = psVectorAlloc(cList->n, PS_TYPE_U8); // Array indicating which values match + psVectorInit(match, 0); + psListIterator *cIter = psListIteratorAlloc(cList, PS_LIST_HEAD, false); // compare iterator + psListIterator *sIter = psListIteratorAlloc(sList, PS_LIST_HEAD, false); // standard iterator + psMetadataItem *cItem = NULL; // Item from compare list + while ((cItem = psListGetAndIncrement(cIter))) { + if (cItem->type != PS_DATA_STRING) { + psLogMsg(__func__, PS_LOG_WARN, "psMetadataItem from list is of type %x instead of " + "%x (PS_DATA_STRING) --- can't interpret.\n", cItem->type, PS_DATA_STRING); + psFree(cIter); + psFree(sIter); + psFree(match); + psFree(sList); + return false; + } + psString cString = cItem->data.V; // String from compare list + psListIteratorSet(sIter, PS_LIST_HEAD); + int index = 0; // Index for list + bool found = false; // Found a match? + for (psString sString = NULL; (sString = psListGetAndIncrement(sIter)) && !found; index++) { + if (strcasecmp(cString, sString) == 0) { + match->data.U8[index]++; + found = true; + } + } + if (! found) { + // Can give up immediately + psFree(cIter); + psFree(sIter); + psFree(match); + psFree(sList); + return false; + } + } + // Make sure we got 100% matches in both directions + bool allMatch = true; // Did all of them match? + for (int i = 0; i < match->n && allMatch; i++) { + if (!match->data.U8[i]) { + allMatch = false; + } + } + psFree(cIter); + psFree(sIter); + psFree(sList); + psFree(match); + return allMatch; + } + default: + return false; + } + psAbort(__func__, "Should never get here.\n"); +} + + +// Format a single concept +static psMetadataItem *conceptFormat(pmConceptSpec *spec, // The concept specification + psMetadataItem *concept, // The concept to parse + psMetadata *cameraFormat, // The camera format + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell // The cell + ) +{ + if (concept) { + psMetadataItem *formatted = NULL; // The formatted concept + if (spec->format) { + formatted = spec->format(concept, cameraFormat, fpa, chip, cell); + } else { + formatted = psMemIncrRefCounter(concept); + } + + return formatted; + } + return NULL; +} + +// Write a single value to a header +static bool writeSingleHeader(pmHDU *hdu, // HDU for which to add to the header + const char *keyword, // Keyword to add + psMetadataItem *item // Item to add to the header + ) +{ + switch (item->type) { + case PS_DATA_STRING: + return psMetadataAddStr(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, item->comment, + item->data.V); + case PS_DATA_S32: + return psMetadataAddS32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, item->comment, + item->data.S32); + case PS_DATA_F32: + return psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, item->comment, + item->data.F32); + case PS_DATA_F64: + return psMetadataAddF64(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, item->comment, + item->data.F64); + case PS_DATA_REGION: { + psString region = psRegionToString(*(psRegion*)item->data.V); + bool result = psMetadataAddStr(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, item->comment, + region); + psFree(region); + return result; + } + default: + psLogMsg(__func__, PS_LOG_WARN, "Type of %s is not suitable for a FITS header --- not added.\n", + item->name); + return false; + } +} + + +// Write potentially multiple values to a header +static bool writeHeader(pmHDU *hdu, // HDU for which to add to the header + const char *keywords, // Keywords to add + psMetadataItem *item // Item to add to the header + ) +{ + bool status = true; // Status of writing headers, to be returned + if (item->type == PS_DATA_LIST) { + psList *values = item->data.V; // List of outputs + psList *keys = psStringSplit(keywords, " ,;"); // List of keywords + if (keys->n != values->n) { + psLogMsg(__func__, PS_LOG_WARN, "Number of keywords (%d) does not match number of values (%d).\n", + keys->n, values->n); + } + psListIterator *keysIter = psListIteratorAlloc(keys, PS_LIST_HEAD, false); // Iterator for keywords + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); // Iterator for values + psString key = NULL; // Keyword from iteration + psMetadataItem *value = NULL; // Value from iteration + while ((key = psListGetAndIncrement(keysIter)) && (value = psListGetAndIncrement(valuesIter))) { + status |= writeSingleHeader(hdu, key, value); + } + psFree(keysIter); + psFree(valuesIter); + psFree(keys); + } else { + status = writeSingleHeader(hdu, keywords, item); + } + return status; +} + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +bool pmConceptsWriteToCamera(psMetadata *specs, // The concept specifications + pmCell *cell, // The cell + psMetadata *concepts // The concepts + ) +{ + if (cell) { + pmHDU *hdu = pmHDUGetLowest(NULL, NULL, cell); // The HDU at the lowest level + if (!hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + psMetadataItem *cameraItem = psMetadataLookup(cell->config, name); // The concept from the camera, + // or NULL + if (cameraItem) { + // Grab the concept + psMetadataItem *conceptItem = psMetadataLookup(concepts, name); // The concept + // Formatted version + psMetadataItem *formatted = conceptFormat(spec, conceptItem, cameraFormat, NULL, NULL, cell); + if (!formatted) { + continue; + } + psString nameSource = NULL; // String with the concept name and ".SOURCE" added + psStringAppend(&nameSource, "%s.SOURCE", name); + bool mdok = true; // Status of MD lookup + psString source = psMetadataLookupStr(&mdok, cell->config, nameSource); // The source + if (mdok && strlen(source) > 0) { + psTrace(__func__, 8, "%s is %s\n", nameSource, source); + if (strcasecmp(source, "HEADER") == 0) { + if (cameraItem->type != PS_DATA_STRING) { + psLogMsg(__func__, PS_LOG_WARN, "Concept %s is specified by header, but is not " + "of type STR --- ignored.\n", conceptItem->name); + continue; + } + psTrace(__func__, 8, "Writing %s to header %s\n", name, cameraItem->data.V); + writeHeader(hdu, cameraItem->data.V, formatted); + } else if (strcasecmp(source, "VALUE") == 0) { + psTrace(__func__, 8, "Checking %s against camera format.\n", name); + if (! compareConcepts(formatted, cameraItem)) { + psLogMsg(__func__, PS_LOG_WARN, "Concept %s is specified by value in the camera " + "format, but the values don't match.\n", name); + } + } else { + psLogMsg(__func__, PS_LOG_WARN, "Concept source %s isn't HEADER or VALUE --- can't " + "write\n", nameSource); + } + } else if (! compareConcepts(formatted, cameraItem)) { + // Assume it's specified by value + psLogMsg(__func__, PS_LOG_WARN, "Concept %s is specified by value in the camera " + "format, but the values don't match.\n", name); + } + psFree(formatted); + psFree(nameSource); + } + + } + psFree(specsIter); + return true; + } + return false; +} + +bool pmConceptsWriteToDefaults(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *concepts // The concepts + ) +{ + pmHDU *hdu = pmHDUGetLowest(NULL, NULL, cell); // The HDU at the lowest level + if (!hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + bool mdok = true; // Status of MD lookup + psMetadata *defaults = psMetadataLookupMD(&mdok, cameraFormat, "DEFAULTS"); // The DEFAULTS spec + if (mdok && defaults) { + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + psMetadata *cameraFormat = hdu->format; // The camera format + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + psMetadataItem *defaultItem = psMetadataLookup(defaults, name); // The item from the DEFAULTS + if (defaultItem) { + psMetadataItem *conceptItem = NULL; // The item from the concepts + if (defaultItem->type == PS_DATA_METADATA) { + // It's a menu --- need to look up the .DEPEND + psString dependName = NULL; // The concept name with ".DEPEND" on the end + psStringAppend(&dependName, ".DEPEND"); + psString dependKey = psMetadataLookupStr(&mdok, defaults, dependName); // The keyword + psFree(dependName); + if (!mdok || !dependKey || strlen(dependKey) == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Can't find %s in the DEFAULTS for %s --- ignored.\n", + dependName, name); + continue; + } + psString dependValue = psMetadataLookupStr(&mdok, concepts, dependName); // The value + if (!mdok || !dependKey || strlen(dependKey) == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Concept %s specified by %s isn't of type STR -- " + "ignored.\n", name, dependName); + continue; + } + conceptItem = psMetadataLookup(defaultItem->data.V, dependValue); + } else { + conceptItem = psMetadataLookup(concepts, name); // The item from the concepts + } + psMetadataItem *formatted = conceptFormat(spec, conceptItem, cameraFormat, fpa, chip, cell); + if (!formatted) { + continue; + } + if (! compareConcepts(formatted, defaultItem)) { + psLogMsg(__func__, PS_LOG_WARN, "Concept %s is specified by the DEFAULTS in the camera " + "format, but the values don't match.\n", name); + } + psFree(formatted); + } + } + psFree(specsIter); + return true; + } + return false; +} + + +bool pmConceptsWriteToHeader(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *concepts // The concepts + ) +{ + pmHDU *hdu = pmHDUGetLowest(NULL, NULL, cell); // The HDU at the lowest level + if (!hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + bool mdok = true; // Status of MD lookup + psMetadata *translation = psMetadataLookupMD(&mdok, cameraFormat, "TRANSLATION"); // The TRANSLATION spec + if (mdok && translation) { + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + psMetadata *cameraFormat = hdu->format; // The camera format + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + psMetadataItem *headerItem = psMetadataLookup(translation, name); // The item from the TRANSLATION + if (headerItem) { + if (headerItem->type != PS_DATA_STRING) { + psLogMsg(__func__, PS_LOG_WARN, "TRANSLATION keyword for concept %s isn't of type STR ---" + " ignored.", name); + continue; + } + psMetadataItem *conceptItem = psMetadataLookup(concepts, name); // The item from the concepts + psMetadataItem *formatted = conceptFormat(spec, conceptItem, cameraFormat, fpa, chip, cell); + if (!formatted) { + continue; + } + psList *keywords = psStringSplit(headerItem->data.V, " ,;"); // List of header keywords + if (formatted->type == PS_DATA_LIST) { + psList *values = formatted->data.V; // The values for the headers + if (values->n != keywords->n) { + psLogMsg(__func__, PS_LOG_WARN, "Number of headers specified does not match number " + "of values for concept %s.\n", name); + } + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); // Iterator + psListIterator *keywordsIter = psListIteratorAlloc(keywords, PS_LIST_HEAD, false); + psMetadataItem *valuesItem = NULL; // Item from list + while ((valuesItem = psListGetAndIncrement(valuesIter))) { + psString keyword = psListGetAndIncrement(keywordsIter); // Keyword from the list + if (strlen(keyword) > 0) { + writeHeader(hdu, keyword, formatted); + } + } + psFree(valuesIter); + psFree(keywordsIter); + } else { + psString keyword = psListGet(keywords, PS_LIST_HEAD); // The keyword + writeHeader(hdu, keyword, formatted); + } + psFree(formatted); + psFree(keywords); + } + } + psFree(specsIter); + return true; + } + return false; +} + +// XXX Warning: This code has not been tested at all +bool pmConceptsWriteToDatabase(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db,// The database handle + psMetadata *concepts // The concepts + ) +{ + pmHDU *hdu = pmHDUGetLowest(NULL, NULL, cell); // The HDU at the lowest level + if (!hdu) { + return false; + } + psMetadata *cameraFormat = hdu->format; // The camera format + bool mdok = true; // Status of MD lookup + psMetadata *database = psMetadataLookupMD(&mdok, cameraFormat, "DATABASE"); // The DATABASE spec + if (mdok && database) { + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // The HDU at the lowest level + psMetadata *cameraFormat = hdu->format; // The camera format + psMetadataIterator *specsIter = psMetadataIteratorAlloc(specs, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *specItem = NULL; // Item from the specs metadata + while ((specItem = psMetadataGetAndIncrement(specsIter))) { + pmConceptSpec *spec = specItem->data.V; // The specification + psString name = specItem->name; // The concept name + + psMetadataItem *dbItem = psMetadataLookup(database, name); // The item from the DATABASE + if (dbItem) { + if (dbItem->type != PS_DATA_METADATA) { + psLogMsg(__func__, PS_LOG_WARN, "DATABASE keyword for concept %s isn't of type METADATA " + "--- ignored.\n", name); + continue; + } + + psMetadataItem *conceptItem = psMetadataLookup(concepts, name); // The item from the concepts + psMetadataItem *formatted = conceptFormat(spec, conceptItem, cameraFormat, fpa, chip, cell); + if (!formatted) { + continue; + } + + psMetadata *dbLookup = dbItem->data.V; // How to look up the value of interest + // Name of the table + const char *tableName = psMetadataLookupStr(&mdok, dbLookup, "TABLE"); + // Name of "where" columns + const char *givenCols = psMetadataLookupStr(&mdok, dbLookup, "GIVENDBCOL"); + // Values for "where" columns + const char *givenPS = psMetadataLookupStr(&mdok, dbLookup, "GIVENPS"); + + // Now, need to get the "given"s + if (strlen(givenCols) || strlen(givenPS)) { + psList *cols = psStringSplit(givenCols, ",;"); // List of column names + psList *values = psStringSplit(givenPS, ",;"); // List of value names for the columns + psMetadata *selection = psMetadataAlloc(); // The stuff to select in the DB + if (cols->n != values->n) { + psLogMsg(__func__, PS_LOG_WARN, + "The GIVENDBCOL and GIVENPS entries for %s do not have " + "the same number of entries --- ignored.\n", name); + } else { + // Iterators for the lists + psListIterator *colsIter = psListIteratorAlloc(cols, PS_LIST_HEAD, false); + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); + char *column = NULL; // Name of the column + while ((column = psListGetAndIncrement(colsIter))) { + char *dependName = psListGetAndIncrement(valuesIter); // Name for the value + if (!strlen(column) || !strlen(name)) { + psLogMsg(__func__, PS_LOG_WARN, "One of the columns or value names for %s is " + " empty --- ignored.\n", name); + } else { + // Search for the value name + psMetadataItem *item = NULL; // The value + if (!item && cell) { + item = psMetadataLookup(cell->concepts, dependName); + } + if (!item && chip) { + item = psMetadataLookup(chip->concepts, dependName); + } + if (!item && fpa) { + item = psMetadataLookup(fpa->concepts, dependName); + } + if (! item) { + psLogMsg(__func__, PS_LOG_ERROR, + "Unable to find the value name %s for DB " + " lookup on %s --- ignored.\n", dependName, name); + } else { + // We need to create a new psMetadataItem. I don't think we can't simply + // hack the existing one, since that could conceivably cause memory leaks + psMetadataAddItem(selection, formatted, PS_LIST_TAIL, PS_META_REPLACE); + psFree(formatted); + } + } + psFree(dependName); + psFree(column); + } // Iterating through the columns + psFree(colsIter); + psFree(valuesIter); + + // Check first to make sure we're only going to touch one row + psArray *dbResult = psDBSelectRows(db, tableName, selection, 2); // Lookup result + // Note that we use limit=2 in order to test if there are multiple rows returned + if (! dbResult || dbResult->n == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find any rows in DB for %s --- " + "ignored\n", name); + return false; + } else { + if (dbResult->n > 1) { + psLogMsg(__func__, PS_LOG_WARN, "Multiple rows returned in DB lookup for %s " + "--- ignored.\n", name); + } + // Update the DB + psMetadata *update = psMetadataAlloc(); + psMetadataAddItem(update, conceptItem, PS_LIST_HEAD, 0); + psDBUpdateRows(db, tableName, selection, update); + psFree(update); + return true; + } + } + psFree(cols); + psFree(values); + } // Doing the "given"s. + } + } + psFree(specsIter); + return true; + } + return false; +} + + + + +#if 0 + +// Well, not really "write", but check to make sure it's there and matches +bool pmConceptWriteToCamera(pmCell *cell, // The cell + psMetadataItem *concept // Concept + ) +{ + if (! cell->config) { + return false; + } + if (cell) { + psMetadataItem *item = psMetadataLookup(cell->config, concept->name); // Info we want + return compareConcepts(item, concept); + } + + return false; +} + +// Write the concept to the header in the appropriate location +bool pmConceptWriteToHeader(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psMetadataItem *concept // Concept + ) +{ + bool mdok = true; // Status of MD lookup + bool status = false; // Status of setting header + if (! fpa->camera) { + return false; + } + psMetadata *translation = psMetadataLookupMD(&mdok, fpa->camera, "TRANSLATION"); // FITS translation + if (! mdok) { + psError(PS_ERR_IO, false, "Unable to find TRANSLATION in camera configuration.\n"); + return false; + } + + // Look for how to translate the concept into a FITS header name + const char *keyword = psMetadataLookupStr(&mdok, translation, concept->name); + if (mdok && strlen(keyword) > 0) { + psTrace(__func__, 6, "It's in keyword %s\n", keyword); + psMetadataItem *headerItem = NULL; // Item to add to header + // XXX: Need to expand range of types + switch (concept->type) { + case PS_DATA_STRING: + headerItem = psMetadataItemAllocStr(keyword, concept->comment, concept->data.V); + break; + case PS_DATA_S32: + headerItem = psMetadataItemAllocS32(keyword, concept->comment, concept->data.S32); + break; + case PS_DATA_F32: + headerItem = psMetadataItemAllocF32(keyword, concept->comment, concept->data.F32); + break; + case PS_DATA_F64: + headerItem = psMetadataItemAllocF64(keyword, concept->comment, concept->data.F64); + break; + default: + headerItem = psMetadataItemAlloc(keyword, concept->type, concept->comment, + concept->data.V); // Item for the header + } + + // We have a FITS header to look up --- search each level + if (cell && cell->hdu) { + psTrace(__func__, 7, "Adding to the cell level header...\n"); + psMetadataAddItem(cell->hdu->header, headerItem, PS_LIST_TAIL, PS_META_REPLACE); + status = true; + } else if (chip && chip->hdu) { + psTrace(__func__, 7, "Adding to the chip level header...\n"); + psMetadataAddItem(chip->hdu->header, headerItem, PS_LIST_TAIL, PS_META_REPLACE); + status = true; + } else if (fpa->hdu) { + psTrace(__func__, 7, "Adding to the FPA level header...\n"); + psMetadataAddItem(fpa->hdu->header, headerItem, PS_LIST_TAIL, PS_META_REPLACE); + status = true; + } + psFree(headerItem); + } + + // No header value + return status; +} + + +// Well, not really "write", but check to see if it's there, and matches +bool pmConceptWriteToDefault(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psMetadataItem *concept // Concept + ) +{ + bool mdOK = true; // Status of MD lookup + if (! fpa->camera) { + return false; + } + psMetadata *defaults = psMetadataLookupMD(&mdOK, fpa->camera, "DEFAULTS"); + if (! mdOK || ! defaults) { + psError(PS_ERR_IO, false, "Unable to find DEFAULTS in camera configuration.\n"); + return false; + } + + psMetadataItem *defItem = psMetadataLookup(defaults, concept->name); + bool status = false; // Result of checking the database + if (defItem) { + if (defItem->type == PS_DATA_METADATA) { + // A dependent default + psTrace(__func__, 7, "Evaluating dependent default....\n"); + psMetadata *dependents = defItem->data.V; // The list of dependents + // Find out what it depends on + psString dependName = psStringCopy(concept->name); + psStringAppend(&dependName, ".DEPEND"); + psString dependsOn = psMetadataLookupStr(&mdOK, defaults, dependName); + if (! mdOK) { + psError(PS_ERR_IO, false, "Unable to find %s in camera configuration for dependent default" + " --- ignored\n", dependName); + // XXX: Need to clean up before returning + return false; + } + psFree(dependName); + // Find the value of the dependent concept + psMetadataItem *depItem = pmConceptReadFromHeader(fpa, chip, cell, dependsOn); + if (! depItem) { + psError(PS_ERR_IO, true, "Unable to find value for %s (required for %s)\n", dependsOn, + concept->name); + return false; + } + if (depItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "Value of %s is not of type string, as required for dependency" + " --- ignored.\n", dependsOn); + } + + defItem = psMetadataLookup(dependents, depItem->data.V); // This is now what we were after + } + + status = compareConcepts(defItem, concept); + if (! status) { + psError(PS_ERR_IO, true, "Concept %s is specified by default in the camera configuration, " + "but doesn't match the actual value.\n", concept->name); + } + } + + // XXX: Need to clean up before returning + return status; +} + + +// XXX: Not tested at all +// XXX I WOULD NOT TRUST THIS FUNCTION IN THE SLIGHTEST YET! --- PAP +bool pmConceptWriteToDB(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadataItem *concept // Concept + ) +{ + if (! db) { + // No database initialised + return false; + } + + bool mdStatus = true; // Status of MD lookup + if (! fpa->camera) { + return false; + } + psMetadata *database = psMetadataLookupMD(&mdStatus, fpa->camera, "DATABASE"); + if (! mdStatus) { + // No error, because not everyone needs to use the DB + return NULL; + } + + psMetadata *dbLookup = psMetadataLookupMD(&mdStatus, database, concept->name); + if (dbLookup) { + const char *tableName = psMetadataLookupStr(&mdStatus, dbLookup, "TABLE"); // Name of the table + // const char *colName = psMetadataLookupStr(&mdStatus, dbLookup, "COLUMN"); // Name of the column + const char *givenCols = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENDBCOL"); // Name of "where" + // columns + const char *givenPS = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENPS"); // Values for "where" + // columns + + // Now, need to get the "given"s + if (strlen(givenCols) || strlen(givenPS)) { + psList *cols = psStringSplit(givenCols, ",;"); // List of column names + psList *values = psStringSplit(givenPS, ",;"); // List of value names for the columns + psMetadata *selection = psMetadataAlloc(); // The stuff to select in the DB + if (cols->n != values->n) { + psLogMsg(__func__, PS_LOG_WARN, "The GIVENDBCOL and GIVENPS entries for %s do not have " + "the same number of entries --- ignored.\n", concept); + } else { + // Iterators for the lists + psListIterator *colsIter = psListIteratorAlloc(cols, PS_LIST_HEAD, false); + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); + char *column = NULL; // Name of the column + while ((column = psListGetAndIncrement(colsIter))) { + char *name = psListGetAndIncrement(valuesIter); // Name for the value + if (!strlen(column) || !strlen(name)) { + psLogMsg(__func__, PS_LOG_WARN, "One of the columns or value names for %s is " + " empty --- ignored.\n", concept); + } else { + // Search for the value name + psMetadataItem *item = pmConceptReadFromHeader(fpa, chip, cell, name); + if (! item) { + item = pmConceptReadFromDefault(fpa, chip, cell, name); + } + if (! item) { + psLogMsg(__func__, PS_LOG_ERROR, "Unable to find the value name %s for DB " + " lookup on %s --- ignored.\n", name, concept); + } else { + // We need to create a new psMetadataItem. I don't think we can't simply hack + // the existing one, since that could conceivably cause memory leaks + psMetadataItem *newItem = psMetadataItemAlloc(concept->name, item->type, + item->comment, item->data.V); + psMetadataAddItem(selection, newItem, PS_LIST_TAIL, PS_META_REPLACE); + psFree(newItem); + } + } + psFree(name); + psFree(column); + } // Iterating through the columns + psFree(colsIter); + psFree(valuesIter); + + // Check first to make sure we're only going to touch one row + psArray *dbResult = psDBSelectRows(db, tableName, selection, 2); // Lookup result + // Note that we use limit=2 in order to test if there are multiple rows returned + if (! dbResult || dbResult->n == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find any rows in DB for %s --- ignored\n", + concept->name); + return false; + } else { + if (dbResult->n > 1) { + psLogMsg(__func__, PS_LOG_WARN, "Multiple rows returned in DB lookup for %s --- " + " ignored.\n", concept->name); + } + // Update the DB + psMetadata *update = psMetadataAlloc(); + psMetadataAddItem(update, concept, PS_LIST_HEAD, 0); + psDBUpdateRows(db, tableName, selection, update); + psFree(update); + return true; + } + } + psFree(cols); + psFree(values); + } + } // Doing the "given"s. + + psAbort(__func__, "Shouldn't ever get here?\n"); + return false; +} + + +// Concept write from item +bool pmConceptWriteItem(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadataItem *concept // Concept item + ) +{ + if (! fpa->camera) { + return false; + } + + // Try headers, database, defaults in order + psTrace(__func__, 3, "Trying to set concept %s...\n", concept->name); + bool status = pmConceptWriteToCamera(cell, concept); // Status for return + if (! status) { + psTrace(__func__, 5, "Trying header....\n"); + status = pmConceptWriteToHeader(fpa, chip, cell, concept); + } + if (! status) { + psTrace(__func__, 5, "Trying database....\n"); + status = pmConceptWriteToDB(fpa, chip, cell, db, concept); + } + if (! status) { + psTrace(__func__, 5, "Checking defaults....\n"); + status = pmConceptWriteToDefault(fpa, chip, cell, concept); + } + + if (! status) { + psError(PS_ERR_IO, true, "Unable to set %s (%s).\n", concept->name, concept->comment); + } + + return status; +} + + +// Concept write +bool pmConceptWrite(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // Concepts MD from which to set + const char *name // Name of the concept + ) +{ + psMetadataItem *concept = psMetadataLookup(concepts, name); + if (! concept) { + psError(PS_ERR_IO, true, "No such concept as %s\n", name); + return false; + } + return pmConceptWriteItem(fpa, chip, cell, db, concept); +} + +#endif Index: trunk/psModules/src/astrom/pmConceptsWrite.h =================================================================== --- trunk/psModules/src/astrom/pmConceptsWrite.h (revision 6872) +++ trunk/psModules/src/astrom/pmConceptsWrite.h (revision 6872) @@ -0,0 +1,80 @@ +#ifndef PM_CONCEPTS_WRITE_H +#define PM_CONCEPTS_WRITE_H + +#include "pslib.h" +#include "pmFPA.h" + + + +bool pmConceptsWriteToCamera(psMetadata *specs, // The concept specifications + pmCell *cell, // The cell + psMetadata *concepts // The concepts + ); +bool pmConceptsWriteToDefaults(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *concepts // The concepts + ); +bool pmConceptsWriteToHeader(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psMetadata *concepts // The concepts + ); +bool pmConceptsWriteToDatabase(psMetadata *specs, // The concept specifications + pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db,// The database handle + psMetadata *concepts // The concepts + ); + + +#ifdef OLD + +// Well, not really "write", but check to make sure it's there and matches +bool pmConceptWriteToCamera(pmCell *cell, // The cell + psMetadataItem *concept // Concept + ); + +// Write the concept to the header in the appropriate location +bool pmConceptWriteToHeader(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psMetadataItem *concept // Concept + ); + +// Well, not really "write", but check to see if it's there, and matches +bool pmConceptWriteToDefault(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psMetadataItem *concept // Concept + ); + +bool pmConceptWriteToDB(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadataItem *concept // Concept + ); + +// Concept write from item +bool pmConceptWriteItem(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadataItem *concept // Concept item + ); + +bool pmConceptWrite(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // Concepts MD from which to set + const char *name // Name of the concept + ); + +#endif + +#endif Index: trunk/psModules/src/astrom/pmFPA.c =================================================================== --- trunk/psModules/src/astrom/pmFPA.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPA.c (revision 6872) @@ -0,0 +1,649 @@ +/** @file pmFPA.c +* +* @brief This file defines the basic types for the FPA hierarchy +* +* @ingroup AstroImage +* +* @author GLG, MHPCC +* +* XXX: We should review the extent of the warning messages on these functions +* when the transformations are not successful. +* +* XXX: Should we implement non-linear cell->chip transforms? +* +* @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ +* +* Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii +*/ + +/******************************************************************************/ +/* INCLUDE FILES */ +/******************************************************************************/ +#include +#include +#include +#include "pslib.h" + +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmConcepts.h" +#include "pmMaskBadPixels.h" + +/****************************************************************************** + *****************************************************************************/ +#define PS_FREE_HIERARCHY 1 +#define PARENT_LINKS 0 + +static void readoutFree(pmReadout *readout) +{ + psTrace(__func__, 9, "Removing readout %lx from cell %lx...\n", (size_t) readout, (size_t) readout->parent); + if (readout->parent) { + psArray *readouts = readout->parent->readouts; + for (int i = 0; i < readouts->n; i++) { + if (readouts->data[i] == readout) { + // pmReadout *tmpReadout = readouts->data[i]; + readouts->data[i] = NULL; + #if PARENT_LINKS + + psFree(tmpReadout); + #endif + + break; + } + } + } + psTrace(__func__, 9, "Freeing readout %lx\n", (size_t) readout); + + #if PARENT_LINKS + + psFree(readout->parent); + #endif + + psFree(readout->image); + psFree(readout->mask); + psFree(readout->weight); + psFree(readout->analysis); + psFree(readout->bias); +} + +static void cellFree(pmCell *cell) +{ + psTrace(__func__, 9, "Removing cell %lx from chip %lx...\n", (size_t)cell, (size_t)cell->parent); + if (cell->parent) { + psArray *cells = cell->parent->cells; + for (int i = 0; i < cells->n; i++) { + if (cells->data[i] == cell) { + // pmCell *tmpCell = cells->data[i]; + cells->data[i] = NULL; + #if PARENT_LINKS + + psFree(tmpCell); + #endif + + break; + } + } + } + psTrace(__func__, 9, "Freeing cell %lx\n", (size_t)cell); + + pmCellFreeReadouts(cell); + psFree(cell->readouts); + #if PARENT_LINKS + + psFree(cell->parent); + #endif + + psFree(cell->concepts); + psFree(cell->analysis); + psFree(cell->config); + psFree(cell->hdu); +} + +static void chipFree(pmChip* chip) +{ + psTrace(__func__, 9, "Removing chip %lx from fpa %lx...\n", (size_t)chip, (size_t)chip->parent); + if (chip->parent) { + psArray *chips = chip->parent->chips; + for (int i = 0; i < chips->n; i++) { + if (chips->data[i] == chip) { + // pmChip *tmpChip = chips->data[i]; + chips->data[i] = NULL; + #if PARENT_LINKS + + psFree(tmpChip); + #endif + + break; + } + } + } + psTrace(__func__, 9, "Freeing chip %lx\n", (size_t)chip); + + pmChipFreeCells(chip); + psFree(chip->cells); + #if PARENT_LINKS + + psFree(chip->parent); + #endif + + #if 0 + + psFree(chip->toFPA); + psFree(chip->fromFPA); + #endif + + psFree(chip->concepts); + psFree(chip->analysis); + psFree(chip->hdu); +} + + +static void FPAFree(pmFPA *fpa) +{ + psTrace(__func__, 9, "Freeing fpa %lx\n", (size_t)fpa); + #if 0 + + psFree(fpa->fromTangentPlane); + psFree(fpa->toTangentPlane); + psFree(fpa->projection); + #endif + + psFree(fpa->concepts); + psFree(fpa->analysis); + psFree(fpa->camera); + // + // Set the parent to NULL in all fpa->chips before psFree(fpa->chips) + // in order to avoid memory reference counter problems. + // + psArray *chips = fpa->chips; + for (psS32 i = 0 ; i < chips->n ; i++) { + pmChip *tmpChip = chips->data[i]; + if (! tmpChip) { + continue; + } + chips->data[i] = NULL; + tmpChip->parent = NULL; + if (PS_FREE_HIERARCHY == 1) { + psFree(tmpChip); + } + } + psFree(fpa->chips); + psFree(fpa->hdu); +} + +void pmCellFreeReadouts(pmCell *cell) +{ + // + // Set the parent to NULL in all cell->readouts before psFree(cell->readouts) + // in order to avoid memory reference counter problems. + // + psArray *readouts = cell->readouts; + for (psS32 i = 0 ; i < readouts->n ; i++) { + pmReadout *tmpReadout = readouts->data[i]; + if (! tmpReadout) { + continue; + } + readouts->data[i] = NULL; + tmpReadout->parent = NULL; + psTrace(__func__, 9, "Will now free readout %lx...\n", (size_t)tmpReadout); + psFree(tmpReadout); // Drop the readout + #if PARENT_LINKS + + psFree(cell); // Decrement reference counter on cell, since readout->parent isn't held any more + #endif + + } + cell->readouts = psArrayRealloc(cell->readouts, 0); + cell->readouts->n = 0; +} + + +void pmChipFreeCells(pmChip *chip) +{ + // + // Set the parent to NULL in all chip->cells before psFree(chip->cells) + // in order to avoid memory reference counter problems. + // + psArray *cells = chip->cells; + for (int i = 0 ; i < cells->n ; i++) { + pmCell *tmpCell = cells->data[i]; + if (! tmpCell) { + continue; + } + cells->data[i] = NULL; + tmpCell->parent = NULL; + pmCellFreeReadouts(tmpCell);// Drop all readouts the cell holds + psFree(tmpCell); // Drop the cell + #if PARENT_LINKS + + psFree(chip); // Decrement reference counter on chip, since cell->parent isn't held any more + #endif + + } + chip->cells = psArrayRealloc(chip->cells, 0); + chip->cells->n = 0; +} + + +pmReadout *pmReadoutAlloc(pmCell *cell) +{ + pmReadout *tmpReadout = (pmReadout *) psAlloc(sizeof(pmReadout)); + tmpReadout->row0 = 0; + + tmpReadout->image = NULL; + tmpReadout->mask = NULL; + tmpReadout->weight = NULL; + tmpReadout->bias = psListAlloc(NULL); + tmpReadout->analysis = psMetadataAlloc(); + #if PARENT_LINKS + + tmpReadout->parent = psMemIncrRefCounter(cell); + #else + + tmpReadout->parent = cell; + #endif + + if (cell != NULL) { + cell->readouts = psArrayAdd(cell->readouts, 1, (psPtr) tmpReadout); + } + + tmpReadout->process = true; // All cells are processed by default + tmpReadout->file_exists = false; // file not yet identified + tmpReadout->data_exists = false; // data yet read in + + psMemSetDeallocator(tmpReadout, (psFreeFunc) readoutFree); + return(tmpReadout); +} + +// XXX: Verify these default values for row0, col0. +// PAP: These values may disappear in the future in favour of values in the "concepts"? +pmCell *pmCellAlloc( + pmChip *chip, + const char *name) +{ + pmCell *tmpCell = (pmCell *) psAlloc(sizeof(pmCell)); + + tmpCell->concepts = psMetadataAlloc(); + psBool rc = psMetadataAddStr(tmpCell->concepts, PS_LIST_HEAD, "CELL.NAME", 0, NULL, name); + if (rc == false) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not add CELL.NAME to metadata.\n"); + } + tmpCell->config = NULL; + tmpCell->analysis = psMetadataAlloc(); + tmpCell->readouts = psArrayAlloc(0); + #if PARENT_LINKS + + tmpCell->parent = psMemIncrRefCounter(chip); + #else + + tmpCell->parent = chip; + #endif + + if (chip != NULL) { + chip->cells = psArrayAdd(chip->cells, 1, (psPtr) tmpCell); + } + tmpCell->process = true; // All cells are processed by default + tmpCell->file_exists = false; // Not yet identified + tmpCell->data_exists = false; // Not yet read in + tmpCell->hdu = NULL; + + pmConceptsBlankCell(tmpCell); + + psMemSetDeallocator(tmpCell, (psFreeFunc) cellFree); + return(tmpCell); +} + +// XXX: Verify these default values for row0, col0. +// PAP: row0, col0 may disappear in the future in favour of storing values in the "concepts". +pmChip *pmChipAlloc( + pmFPA *fpa, + const char *name) +{ + pmChip *tmpChip = (pmChip *) psAlloc(sizeof(pmChip)); + + #if 0 + + tmpChip->col0 = 0; + tmpChip->row0 = 0; + tmpChip->toFPA = NULL; + tmpChip->fromFPA = NULL; + #endif + + tmpChip->concepts = psMetadataAlloc(); + psBool rc = psMetadataAddStr(tmpChip->concepts, PS_LIST_HEAD, "CHIP.NAME", 0, NULL, name); + if (rc == false) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not add CHIP.NAME to metadata.\n"); + } + tmpChip->analysis = psMetadataAlloc(); + tmpChip->cells = psArrayAlloc(0); + #if PARENT_LINKS + + tmpChip->parent = psMemIncrRefCounter(fpa); + #else + + tmpChip->parent = fpa; + #endif + + if (fpa != NULL) { + fpa->chips = psArrayAdd(fpa->chips, 1, (psPtr) tmpChip); + } + tmpChip->process = true; // Work on all chips, by default + tmpChip->file_exists = false; // Not yet identified + tmpChip->data_exists = false; // Not yet read in + tmpChip->hdu = NULL; + + pmConceptsBlankChip(tmpChip); + + psMemSetDeallocator(tmpChip, (psFreeFunc) chipFree); + return(tmpChip); +} + +pmFPA *pmFPAAlloc(const psMetadata *camera) +{ + pmFPA *tmpFPA = (pmFPA *) psAlloc(sizeof(pmFPA)); + + #if 0 + + tmpFPA->fromTangentPlane = NULL; + tmpFPA->toTangentPlane = NULL; + tmpFPA->projection = NULL; + #endif + + tmpFPA->concepts = psMetadataAlloc(); + tmpFPA->analysis = NULL; + tmpFPA->camera = psMemIncrRefCounter((psPtr)camera); + tmpFPA->chips = psArrayAlloc(0); + tmpFPA->hdu = NULL; + + pmConceptsBlankFPA(tmpFPA); + + psMemSetDeallocator(tmpFPA, (psFreeFunc) FPAFree); + return(tmpFPA); +} + +static psBool cellCheckParents(pmCell *cell) +{ + if (cell == NULL) { + return(true); + } + psBool flag = true; + + for (psS32 i = 0 ; i < cell->readouts->n ; i++) { + pmReadout *tmpReadout = (pmReadout *) cell->readouts->data[i]; + PS_ASSERT_PTR_NON_NULL(tmpReadout, false); + if (tmpReadout->parent != cell) { + tmpReadout->parent = cell; + flag = false; + } + } + return(flag); +} + +static psBool chipCheckParents(pmChip *chip) +{ + if (chip == NULL) { + return(true); + } + psBool flag = true; + + for (psS32 i = 0 ; i < chip->cells->n ; i++) { + pmCell *tmpCell = (pmCell *) chip->cells->data[i]; + PS_ASSERT_PTR_NON_NULL(tmpCell, false); + if (tmpCell->parent != chip) { + tmpCell->parent = chip; + flag = false; + } + + flag &= cellCheckParents(tmpCell); + } + return(flag); +} + +psBool pmFPACheckParents(pmFPA *fpa) +{ + if (fpa == NULL) { + return(true); + } + psBool flag = true; + + for (psS32 i = 0 ; i < fpa->chips->n ; i++) { + pmChip *tmpChip = (pmChip *) fpa->chips->data[i]; + PS_ASSERT_PTR_NON_NULL(tmpChip, false); + if (tmpChip->parent != fpa) { + tmpChip->parent = fpa; + flag = false; + } + + flag &= chipCheckParents(tmpChip); + } + return(flag); +} + +/** functions to turn on/off the file_exists flag **/ +bool pmFPASetFileStatus (pmFPA *fpa, bool status) +{ + + for (int i = 0; i < fpa->chips->n; i++) { + pmChip *chip = fpa->chips->data[i]; + pmChipSetFileStatus (chip, status); + } + return true; +} + +bool pmChipSetFileStatus (pmChip *chip, bool status) +{ + + chip->file_exists = status; + for (int i = 0; i < chip->cells->n; i++) { + pmCell *cell = chip->cells->data[i]; + pmCellSetFileStatus (cell, status); + } + return true; +} + +bool pmCellSetFileStatus (pmCell *cell, bool status) +{ + + cell->file_exists = status; + for (int i = 0; i < cell->readouts->n; i++) { + pmReadout *readout = cell->readouts->data[i]; + readout->file_exists = status; + } + return true; +} + +/** functions to turn on/off the data_exists flag **/ +bool pmFPASetDataStatus (pmFPA *fpa, bool status) +{ + + for (int i = 0; i < fpa->chips->n; i++) { + pmChip *chip = fpa->chips->data[i]; + pmChipSetDataStatus (chip, status); + } + return true; +} + +bool pmChipSetDataStatus (pmChip *chip, bool status) +{ + + chip->data_exists = status; + for (int i = 0; i < chip->cells->n; i++) { + pmCell *cell = chip->cells->data[i]; + pmCellSetDataStatus (cell, status); + } + return true; +} + +bool pmCellSetDataStatus (pmCell *cell, bool status) +{ + + cell->data_exists = status; + for (int i = 0; i < cell->readouts->n; i++) { + pmReadout *readout = cell->readouts->data[i]; + readout->data_exists = status; + } + return true; +} + +/***************************************************************************** + *****************************************************************************/ + +// Set cells within a chip to be processed or not +static bool setCellsProcess(const pmChip *chip, // Chip of interest + bool process // Process this chip? + ) +{ + PS_ASSERT_PTR_NON_NULL(chip, false); + + psArray *cells = chip->cells; // Component cells + if (! cells) { + return false; + } + for (int i = 0; i < cells->n; i++) { + pmCell *tmpCell = cells->data[i]; // Cell of interest + if (tmpCell) { + tmpCell->process = process; + } + } + + return true; +} + +/***************************************************************************** +XXX EAM : I've added the 'exclusive' option. if true all other chips are de-selected +XXX EAM : a negative value is valid and, in combinations with exclusive, de-selects all chips + *****************************************************************************/ +bool pmFPASelectChip(pmFPA *fpa, int chipNum, bool exclusive) +{ + PS_ASSERT_PTR_NON_NULL(fpa, false); + + psArray *chips = fpa->chips; // Component chips + if ((chips == NULL) || (chipNum >= chips->n)) { + return(false); + } + + for (int i = 0 ; i < chips->n ; i++) { + pmChip *tmpChip = (pmChip *) chips->data[i]; + if (tmpChip == NULL) { + continue; + } + if (i == chipNum) { + tmpChip->process = true; + setCellsProcess(tmpChip, true); + } else { + if (exclusive) { + tmpChip->process = false; + setCellsProcess(tmpChip, false); + } + } + + } + + return true; +} + +/***************************************************************************** +XXX EAM : I've added the 'exclusive' option. if true all other chips are de-selected +XXX EAM : a negative value is valid and, in combinations with exclusive, de-selects all cells +XXX this function should probably be re-defined to merge with 'setCellsProcess' + *****************************************************************************/ +bool pmChipSelectCell(pmChip *chip, int cellNum, bool exclusive) +{ + assert(chip); + + psArray *cells = chip->cells; // Component cells + if (!cells || cellNum > cells->n) { + return false; + } + + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; + if (!cell) { + continue; + } + if (i == cellNum) { + cell->process = true; + } else { + if (exclusive) { + cell->process = false; + } + } + } + return true; +} + +/***************************************************************************** +XXX: The SDRS is ambiguous on a few things: + Whether or not the other chips should be set process=true. [PAP: No] + Should we return the number of chip process=true before or after they're set, [PAP: After] + *****************************************************************************/ +/** + * + * pmFPAExcludeChip shall set process to false only for the specified chip + * number (chipNum). In the event that the specified chip number does not exist + * within the fpa, the function shall generate a warning, and perform no action. + * The function shall return the number of chips within the fpa that have process + * set to true. + * + */ +int pmFPAExcludeChip( + pmFPA *fpa, + int chipNum) +{ + PS_ASSERT_PTR_NON_NULL(fpa, false); + + psArray *chips = fpa->chips; // Component chips + if (chips == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: fpa->chips == NULL\n"); + return(0); + } + if ((chipNum >= chips->n) || (NULL == (pmChip *) chips->data[chipNum])) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: the specified chip (%d) does not exist.\n", chipNum); + return(0); + } + + int numChips = 0; // Number of chips to be processed + for (int i = 0 ; i < chips->n ; i++) { + pmChip *tmpChip = (pmChip *) chips->data[i]; // Chip of interest + if (tmpChip != NULL) { + if (i == chipNum) { + tmpChip->process = false; + setCellsProcess(tmpChip, false); // Wipe out the cell as well + } else if (tmpChip->process) { + numChips++; + } + } + } + + return(numChips); +} + +int pmChipExcludeCell(pmChip *chip, + int cellNum + ) +{ + assert(chip); + + psArray *cells = chip->cells; // The component cells + if (!cells || cellNum > cells->n) { + return 0; + } + + int numCells = 0; // Number of cells to be processed + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; + if (!cell) { + continue; + } + if (i == cellNum) { + cell->process = false; + } else { + numCells++; + } + } + + return numCells; +} + + Index: trunk/psModules/src/astrom/pmFPA.h =================================================================== --- trunk/psModules/src/astrom/pmFPA.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPA.h (revision 6872) @@ -0,0 +1,279 @@ +/** @file pmFPA.h +* +* @brief This file defines the basic types the focal plane hierarchy. +* +* @ingroup AstroImage +* +* @author GLG, MHPCC +* +* @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ +* +* Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii +*/ + +#ifndef PM_FPA_H +#define PM_FPA_H +#if HAVE_CONFIG_H +#include +#endif + +#include "pslib.h" +#include "pmHDU.h" + +/// @addtogroup AstroImage +/// @{ + +/** Focal plane data structure + * + * A focal plane consists of one or more chips (according to the number of + * pieces of contiguous silicon). It contains metadata containers for the + * concepts and analysis, a link to the parent, and pointers to the FITS header, + * if that corresponds to this level (the FPA may be the PHU, but will not ever + * contain pixels). For astrometry, it contains a transformation from the focal + * plane to the tangent plane and the fixed pattern residuals. It is expected + * that the transformation will consist of two 4D polynomials (i.e. a function + * of two coordinates in position, the magnitude of the object, and the color of + * the object) in order to correct for optical distortions and the effects of + * the atmosphere; hence we think that it is prudent to include a reverse + * transformation which will be derived from numerically inverting the forward + * transformation. + * + */ +typedef struct +{ + #if 0 + // Astrometric transformations + psPlaneDistort* fromTangentPlane; ///< Transformation from tangent plane to focal plane + psPlaneDistort* toTangentPlane; ///< Transformation from focal plane to tangent plane + psProjection *projection; ///< Projection from tangent plane to sky + #endif + // Information + psMetadata *concepts; ///< Cache for PS concepts + psMetadata *analysis; ///< FPA-level analysis metadata + const psMetadata *camera; ///< Camera configuration + psArray *chips; ///< The chips + pmHDU *hdu; ///< FITS data +} +pmFPA; + +/** Chip data structure + * + * A chip consists of one or more cells (according to the number of amplifiers + * on the device). The chip contains metadata containers for the concepts and + * analysis, a link to the parent, and pointers to the pointers to the various + * FITS data, if that corresponds to this level. For astrometry, in addition to + * the rough positioning information, it contains a coordinate transform from + * the chip to the focal plane. It is expected that this transform will consist + * of two second-order 2D polynomials; hence we think that it is prudent to + * include a reverse transformation which will be derived from numerically + * inverting the forward transformation. A boolean indicates whether the chip is + * of interest, allowing it to be excluded from analysis. + * + */ +typedef struct +{ + #if 0 + // Offset specifying position on focal plane + int col0; ///< Offset from the left of FPA. + int row0; ///< Offset from the bottom of FPA. + // Astrometric transformations + psPlaneTransform* toFPA; ///< Transformation from chip to FPA coordinates + psPlaneTransform* fromFPA; ///< Transformation from FPA to chip coordinates + #endif + // Information + psMetadata *concepts; ///< Cache for PS concepts + psMetadata *analysis; ///< Chip-level analysis metadata + psArray *cells; ///< The cells (referred to by name) + pmFPA *parent; ///< Parent FPA + bool process; ///< Do we bother about reading and working with this chip? + bool file_exists; ///< Does the file for this chip exist (read case only)? + bool data_exists; ///< Does the data for this chip exist (read case only)? + pmHDU *hdu; ///< FITS data +} +pmChip; + +/** Cell data structure + * + * A cell consists of one or more readouts. It also contains a pointer to the + * cell's metadata, and its parent chip. On the astrometry side, it also + * contains coordinate transforms from the cell to chip, from the cell to + * focal-plane, as well as a "quick and dirty" tranform from the cell to + * sky coordinates. + * + */ +typedef struct +{ + psMetadata *concepts; ///< Cache for PS concepts + psMetadata *config; ///< Cell configuration info + psMetadata *analysis; ///< Cell-level analysis metadata + psArray *readouts; ///< The readouts (referred to by number) + pmChip *parent; ///< Parent chip + bool process; ///< Do we bother about reading and working with this cell? + bool file_exists; ///< Does the file for this cell exist (read case only)? + bool data_exists; ///< Does the data for this cell exist (read case only)? + pmHDU *hdu; ///< FITS data +} +pmCell; + +/** Readout data structure. + * + * A readout is the result of a single read of a cell (or a portion thereof). + * It contains the offset from the lower-left corner of the chip, in the case + * that the CCD was windowed, as well as the binning factors and parity (if the + * binning value is negative, then the parity is reversed). It also contains the + * pixel data, metadata containers for the concepts and analysis, and a link to + * the parent. + * + */ +typedef struct +{ + int row0; ///< Row offset; non-zero if reading in bit by bit + psImage *image; ///< Imaging area of readout + psImage *mask; ///< Mask of input image + psImage *weight; ///< Weight of input image + psList *bias; ///< Overscan images + psMetadata *analysis; ///< Readout-level analysis metadata + pmCell *parent; ///< Parent cell + bool process; ///< Do we bother about reading and working with this readout? + bool file_exists; ///< Does the file for this readout exist (read case only)? + bool data_exists; ///< Does the data for this readout exist (read case only)? +} +pmReadout; + +void pmCellFreeReadouts(pmCell *cell); +void pmChipFreeCells(pmChip *chip); + +/** Allocates a pmReadout + * + * The constructor shall make an empty pmReadout. If the parent cell is not + * NULL, the parent link is made and the readout shall be placed in the + * parents array of readouts. The metadata containers shall be allocated. All + * other pointers in the structure shall be initialized to NULL. + * + * @return pmReadout* newly allocated pmReadout with all internal pointers set to NULL + */ +pmReadout *pmReadoutAlloc( + pmCell *cell ///< Parent cell +); + +/** Allocates a pmCell + * + * The constructor shall make an empty pmCell. If the parent chip is not NULL, + * the parent link is made and the cell shall be placed in the parents array of + * cells. The readouts array shall be allocated with a zero size, and the + * metadata containers constructed. All other pointers in the structure shall be + * initialized to NULL. + * + * @return pmCell* newly allocated pmCell + */ +pmCell *pmCellAlloc( + pmChip *chip, ///< Parent chip + const char *name ///< Name of cell +); + +/** Allocates a pmChip + * + * The constructor shall make an empty pmChip. If the parent fpa is not NULL, + * the parent link is made and the chip shall be placed in the parent's array + * of chips. The cells array shall be allocated with a zero size, and the + * metadata containers constructed. All other pointers in the structure shall be + * initialized to NULL. + * + * @return pmChip* newly allocated pmChip + */ +pmChip *pmChipAlloc( + pmFPA *fpa, ///< FPA to which the chip belongs + const char *name ///< Name of chip +); + +/** Allocates a pmFPA + * + * The constructor shall make an empty pmFPA. The chips array shall be + * allocated with a zero size, the camera and db pointers set to the values + * provided, and the concepts metadata constructed. All other pointers in the + * structure shall be initialized to NULL. + * + */ +pmFPA *pmFPAAlloc( + const psMetadata *camera ///< Camera configuration +); + + +/** Verify parent links. + * + * This function checks the validity of the parent links in the FPA hierarchy. + * If a parent link is not set (or not set correctly), it is corrected, and the + * function shall return false. If all the parent pointers were correct, the + * function shall return true. + * + */ +bool pmFPACheckParents( + pmFPA *fpa +); + +/* functions to turn on/off the file_exists flags */ +bool pmFPASetFileStatus (pmFPA *fpa, bool status); +bool pmChipSetFileStatus (pmChip *chip, bool status); +bool pmCellSetFileStatus (pmCell *cell, bool status); + +/* functions to turn on/off the data_exists flags */ +bool pmFPASetDataStatus (pmFPA *fpa, bool status); +bool pmChipSetDataStatus (pmChip *chip, bool status); +bool pmCellSetDataStatus (pmCell *cell, bool status); + +/** Specify the level for an operation. + */ +typedef enum { + PM_FPA_LEVEL_NONE, ///< No particular level specified + PM_FPA_LEVEL_FPA, ///< Level corresponds to an FPA + PM_FPA_LEVEL_CHIP, ///< Level corresponds to a Chip + PM_FPA_LEVEL_CELL, ///< Level corresponds to a Cell + PM_FPA_LEVEL_READOUT ///< Level corresponds to a Readout +} pmFPALevel; + + +/** + * + * pmFPASelectChip shall set valid to true for the specified chip number + * (chipNum), and all other chips shall have valid set to false. In the event + * that the specified chip number does not exist within the fpa, the function + * shall return false. + * + */ +bool pmFPASelectChip( + pmFPA *fpa, + int chipNum, + bool exclusive +); + +bool pmChipSelectCell(pmChip *chip, + int cellNum, + bool exclusive + ); + +/** + * + * pmFPAExcludeChip shall set valid to false only for the specified chip + * number (chipNum). In the event that the specified chip number does not exist + * within the fpa, the function shall generate a warning, and perform no action. + * The function shall return the number of chips within the fpa that have valid + * set to true. + * + */ +int pmFPAExcludeChip( + pmFPA *fpa, + int chipNum +); + +int pmChipExcludeCell(pmChip *chip, + int cellNum + ); + +// Set the weights and masks within a cell, based on the gain and RN +bool pmCellSetWeights(pmCell *cell // Cell for which to set weights + ); + + + +#endif // #ifndef PM_FPA_H Index: trunk/psModules/src/astrom/pmFPAAstrometry.c =================================================================== --- trunk/psModules/src/astrom/pmFPAAstrometry.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAAstrometry.c (revision 6872) @@ -0,0 +1,512 @@ +#include +#include "pslib.h" +#include "pmFPAAstrometry.h" +#include "pmFPA.h" + + +/***************************************************************************** +checkValidImageCoords(): this is a private function which simply determines if +the supplied x,y coordinates are in the range for the supplied psImage. + +XXX: What about col0 and row0 +XXX: This should return a psBool. +XXX: Macro this for speed. + *****************************************************************************/ +static psS32 checkValidImageCoords( + double x, + double y, + psImage* tmpImage) +{ + PS_ASSERT_IMAGE_NON_NULL(tmpImage, 0); + + // The FLT_EPSILON is because -0.0 was failing this. + if (((x+FLT_EPSILON) < 0.0) || (x > (double)tmpImage->numCols) || + ((y+FLT_EPSILON) < 0.0) || (y > (double)tmpImage->numRows)) { + return (0); + } + + return (1); +} + +/*****************************************************************************/ +/* FUNCTION IMPLEMENTATION - PUBLIC */ +/*****************************************************************************/ + +pmCell* pmCellInFPA( + const psPlane* fpaCoord, + const pmFPA* FPA) +{ + PS_ASSERT_PTR_NON_NULL(fpaCoord, NULL); + PS_ASSERT_PTR_NON_NULL(FPA, NULL); + + pmChip* tmpChip = NULL; + psPlane chipCoord; + pmCell* outCell = NULL; + + // Determine which chip contains the fpaCoords. + tmpChip = pmChipInFPA(fpaCoord, FPA); + if (tmpChip == NULL) { + return(NULL); + } + + // Convert to those chip coordinates. + psPlane *rc = pmCoordFPAToChip(&chipCoord, fpaCoord, tmpChip); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine Chip coords.\n"); + return(NULL); + } + + // Determine which cell contains those chip coordinates. + outCell = pmCellInChip(&chipCoord, tmpChip); + if (outCell == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the cell.\n"); + return(NULL); + } + + return (outCell); +} + +pmChip* pmChipInFPA( + const psPlane* fpaCoord, + const pmFPA* FPA) +{ + PS_ASSERT_PTR_NON_NULL(fpaCoord, NULL); + PS_ASSERT_PTR_NON_NULL(FPA, NULL); + PS_ASSERT_PTR_NON_NULL(FPA->chips, NULL); + + psArray* chips = FPA->chips; + psS32 nChips = chips->n; + psPlane chipCoord; + pmCell *tmpCell = NULL; + + // + // Loop through every chip in this FPA. Convert the original FPA + // coordinates to chip coordinates for that chip. Then, determine if any + // cells in that chip contain those chip coordinates. + // XXX: Depending on the number of chips, and their topology, there may be + // a much more efficient way of doing this. + // + for (psS32 i = 0; i < nChips; i++) { + pmChip* tmpChip = chips->data[i]; + PS_ASSERT_PTR_NON_NULL(tmpChip, NULL); + PS_ASSERT_PTR_NON_NULL(tmpChip->fromFPA, NULL); + + psPlaneTransformApply(&chipCoord, tmpChip->fromFPA, fpaCoord); + + tmpCell = pmCellInChip(&chipCoord, tmpChip); + if (tmpCell != NULL) { + return(tmpChip); + } + } + + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the chip.\n"); + return (NULL); +} + + +pmCell* pmCellInChip( + const psPlane* chipCoord, + const pmChip* chip) +{ + PS_ASSERT_PTR_NON_NULL(chipCoord, NULL); + PS_ASSERT_PTR_NON_NULL(chip, NULL); + + psPlane cellCoord; + psArray* cells; + + cells = chip->cells; + if (cells == NULL) { + return NULL; + } + + // + // We loop over each cell in the chip. We transform the chipCoord into + // a cellCoord for that cell and determine if that cellCoord is valid. + // If so, then we return that cell. + // XXX: Depending on the number of cells, and their topology, there may be + // a much more efficient way of doing this. + // + for (psS32 i = 0; i < cells->n; i++) { + pmCell* tmpCell = (pmCell* ) cells->data[i]; + PS_ASSERT_PTR_NON_NULL(tmpCell, NULL); + + psPlaneTransform *chipToCell = NULL; + if (true == p_psIsProjectionLinear(tmpCell->toChip)) { + chipToCell = p_psPlaneTransformLinearInvert(tmpCell->toChip); + } else { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: non-linear cell->chip transforms are not yet implemented.\n"); + //chipToCell = psPlaneTransformInvert(NULL, tmpCell->toChip, NULL, -1); + chipToCell = NULL; + } + if (chipToCell == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not invert the Cell->toChip transform.\n"); + return(NULL); + } + psArray* readouts = tmpCell->readouts; + + if (readouts != NULL) { + for (psS32 j = 0; j < readouts->n; j++) { + pmReadout* tmpReadout = readouts->data[j]; + PS_ASSERT_READOUT_NON_NULL(tmpReadout, NULL); + + psPlaneTransformApply(&cellCoord, + chipToCell, + chipCoord); + + if (checkValidImageCoords(cellCoord.x, + cellCoord.y, + tmpReadout->image)) { + psFree(chipToCell); + return (tmpCell); + } + } + } + psFree(chipToCell); + } + + //psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the cell.\n"); + return (NULL); +} + + +psPlane* pmCoordCellToFPA( + psPlane* fpaCoord, + const psPlane* cellCoord, + const pmCell* cell) +{ + PS_ASSERT_PTR_NON_NULL(cellCoord, NULL); + PS_ASSERT_PTR_NON_NULL(cell, NULL); + + psPlane *rc = psPlaneTransformApply(fpaCoord, cell->toFPA, cellCoord); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform cell coords to FPA coords.\n"); + } + return(rc); +} + + +psPlane* pmCoordChipToFPA( + psPlane* outCoord, + const psPlane* inCoord, + const pmChip* chip) +{ + PS_ASSERT_PTR_NON_NULL(inCoord, NULL); + PS_ASSERT_PTR_NON_NULL(chip, NULL); + + psPlane *rc = psPlaneTransformApply(outCoord, chip->toFPA, inCoord); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform chip coords to FPA coords.\n"); + } + return(rc); +} + + +psPlane* pmCoordFPAToChip( + psPlane* chipCoord, + const psPlane* fpaCoord, + const pmChip* chip) +{ + PS_ASSERT_PTR_NON_NULL(fpaCoord, NULL); + PS_ASSERT_PTR_NON_NULL(chip, NULL); + PS_ASSERT_PTR_NON_NULL(chip->fromFPA, NULL); + + psPlane *rc = psPlaneTransformApply(chipCoord, chip->fromFPA, fpaCoord); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform FPA coords to Chip coords.\n"); + } + return(rc); +} + +psPlane* pmCoordCellToChip( + psPlane* outCoord, + const psPlane* inCoord, + const pmCell* cell) +{ + PS_ASSERT_PTR_NON_NULL(inCoord, NULL); + PS_ASSERT_PTR_NON_NULL(cell, NULL); + + psPlane *rc = psPlaneTransformApply(outCoord, cell->toChip, inCoord); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform Cell coords to Chip coords.\n"); + } + return(rc); +} + +psPlane* pmCoordChipToCell( + psPlane* cellCoord, + const psPlane* chipCoord, + const pmCell* cell) +{ + PS_ASSERT_PTR_NON_NULL(chipCoord, NULL); + PS_ASSERT_PTR_NON_NULL(cell, NULL); + PS_ASSERT_PTR_NON_NULL(cell->parent, NULL); + + pmCell *tmpCell = pmCellInChip(chipCoord, cell->parent); + if (tmpCell == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine the proper cell.\n"); + return(NULL); + } + + psPlaneTransform *tmpChipToCell = NULL; + PS_ASSERT_PTR_NON_NULL(tmpCell->toChip, NULL); + if (true == p_psIsProjectionLinear(tmpCell->toChip)) { + tmpChipToCell = p_psPlaneTransformLinearInvert(tmpCell->toChip); + } else { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: non-linear cell->chip transforms are not yet implemented.\n"); + // XXX: tmpChipToCell = psPlaneTransformInvert(NULL, tmpCell->toChip, NULL, -1); + tmpChipToCell = NULL; + } + if (tmpChipToCell == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not invert the Cell->toChip transform.\n"); + return(NULL); + } + + psPlane *rc = psPlaneTransformApply(cellCoord, tmpChipToCell, chipCoord); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform Chip coords to Cell coords.\n"); + } + psFree(tmpChipToCell); + return(rc); +} + +psPlane* pmCoordFPAToTP( + psPlane* outCoord, + const psPlane* inCoord, + double color, + double magnitude, + const pmFPA* fpa) +{ + PS_ASSERT_PTR_NON_NULL(inCoord, NULL); + PS_ASSERT_PTR_NON_NULL(fpa, NULL); + + psPlane *rc = psPlaneDistortApply(outCoord, fpa->toTangentPlane, inCoord, color, magnitude); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform FPA coords to tangent plane coords.\n"); + } + return(rc); +} + +psPlane* pmCoordTPToFPA( + psPlane* fpaCoord, + const psPlane* tpCoord, + double color, + double magnitude, + const pmFPA* fpa) +{ + PS_ASSERT_PTR_NON_NULL(tpCoord, NULL); + PS_ASSERT_PTR_NON_NULL(fpa, NULL); + PS_ASSERT_PTR_NON_NULL(fpa->fromTangentPlane, NULL); + + psPlane *rc = psPlaneDistortApply(fpaCoord, fpa->fromTangentPlane, tpCoord, color, magnitude); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform tangent plane coords to FPA coords.\n"); + } + return(rc); +} + + +/***************************************************************************** +XXXDeproject(outSphere, coord, projection): This private routine is a wrapper +for p_psDeproject(). The reason: p_psDeproject() and p_psProject() combined +do not seem to produce the original coordinates when they even though they +should. XXXDeproject() simply negates the ->r and ->d members of the output +psSphere if the input ->y is larger than 0.0. I don't know why it works. + +I'm guessing the p_psProject() and p_psDeproject() functions have bugs. + +XXX: It appears that p_psProject() and p_psDeproject() have been fixed. +Remove this. + *****************************************************************************/ +psSphere* XXXDeproject( + psSphere *outSphere, + const psPlane* coord, + const psProjection* projection) +{ + psSphere *rc = p_psDeproject(outSphere, coord, projection); + + if (coord->y >= 0.0) { + rc->d = -rc->d; + rc->r = -rc->r; + } + + return(rc); +} + +/***************************************************************************** + *****************************************************************************/ +psSphere* pmCoordTPToSky( + psSphere* outSphere, + const psPlane* tpCoord, + const psProjection *projection) +{ + PS_ASSERT_PTR_NON_NULL(tpCoord, NULL); + PS_ASSERT_PTR_NON_NULL(projection, NULL); + + // psSphere *rc = XXXDeproject(outSphere, tpCoord, projection); + psSphere *rc = p_psDeproject(outSphere, tpCoord, projection); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform tangent plane coords to sky coords.\n"); + } + return(rc); +} + +/***************************************************************************** + *****************************************************************************/ +psPlane* pmCoordSkyToTP( + psPlane* tpCoord, + const psSphere* in, + const psProjection *projection) +{ + PS_ASSERT_PTR_NON_NULL(in, NULL); + PS_ASSERT_PTR_NON_NULL(projection, NULL); + + psPlane *rc = p_psProject(tpCoord, in, projection); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform sky to tangent plane coords.\n"); + } + return(rc); +} + +/***************************************************************************** + *****************************************************************************/ +psSphere* pmCoordCellToSky( + psSphere* skyCoord, + const psPlane* cellCoord, + double color, + double magnitude, + const pmCell* cell) +{ + PS_ASSERT_PTR_NON_NULL(cellCoord, NULL); + PS_ASSERT_PTR_NON_NULL(cell, NULL); + PS_ASSERT_PTR_NON_NULL(cell->toFPA, NULL); + PS_ASSERT_PTR_NON_NULL(cell->parent, NULL); + PS_ASSERT_PTR_NON_NULL(cell->parent->parent, NULL); + PS_ASSERT_PTR_NON_NULL(cell->parent->parent->toTangentPlane, NULL); + PS_ASSERT_PTR_NON_NULL(cell->parent->parent->projection, NULL); + psPlane fpaCoord; + psPlane tpCoord; + psPlane *rc; + pmFPA* parFPA = (cell->parent)->parent; + + // Convert the input cell coordinates to FPA coordinates. + rc = psPlaneTransformApply(&fpaCoord, cell->toFPA, cellCoord); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could transform cell coords to FPA coords.\n"); + return(NULL); + } + + // Convert the FPA coordinates to tangent plane Coordinates. + rc = psPlaneDistortApply(&tpCoord, parFPA->toTangentPlane, &fpaCoord, color, magnitude); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could transform FPA coords to tangent plane coords.\n"); + return(NULL); + } + + // Convert the tangent plane Coordinates to sky coordinates. + psSphere *rc2 = pmCoordTPToSky(skyCoord, &tpCoord, parFPA->projection); + if (rc2 == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform cell coords to sky coords.\n"); + } + + return(rc2); +} + +/***************************************************************************** + *****************************************************************************/ +psPlane* pmCoordSkyToCell( + psPlane* cellCoord, + const psSphere* skyCoord, + float color, + float magnitude, + const pmCell* cell) +{ + PS_ASSERT_PTR_NON_NULL(skyCoord, NULL); + PS_ASSERT_PTR_NON_NULL(cell, NULL); + PS_ASSERT_PTR_NON_NULL(cell->parent, NULL); + PS_ASSERT_PTR_NON_NULL(cell->parent->parent, NULL); + pmChip *parChip = cell->parent; + pmFPA *parFPA = parChip->parent; + psPlane tpCoord; + psPlane fpaCoord; + psPlane chipCoord; + psPlane *rc; + + // Convert the skyCoords to tangent plane coords. + rc = pmCoordSkyToTP(&tpCoord, skyCoord, parFPA->projection); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine tangent plane coords.\n"); + return(NULL); + } + + // Convert the tangent plane coords to FPA coords. + rc = pmCoordTPToFPA(&fpaCoord, &tpCoord, color, magnitude, parFPA); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine FPA coords.\n"); + return(NULL); + } + + // Convert the FPA coords to chip coords. + rc = pmCoordFPAToChip(&chipCoord, &fpaCoord, parChip); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine chip coords.\n"); + return(NULL); + } + + // Convert the chip coords to cell coords. + rc = pmCoordChipToCell(cellCoord, &chipCoord, cell); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not determine cell coords.\n"); + return(NULL); + } + + return (cellCoord); +} + +/***************************************************************************** + *****************************************************************************/ +psSphere* pmCoordCellToSkyQuick( + psSphere* outSphere, + const psPlane* cellCoord, + const pmCell* cell) +{ + PS_ASSERT_PTR_NON_NULL(cellCoord, NULL); + PS_ASSERT_PTR_NON_NULL(cell, NULL); + PS_ASSERT_PTR_NON_NULL(cell->toSky, NULL); + psPlane outPlane; + psPlane *rc; + rc = psPlaneTransformApply(&outPlane, cell->toSky, cellCoord); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could transform cell coords to sky coords.\n"); + return(NULL); + } + + psSphere *out = outSphere; + if (out == NULL) { + out = psSphereAlloc(); + } + out->r = outPlane.y; + out->d = outPlane.x; + + return(out); +} + +/***************************************************************************** + *****************************************************************************/ +psPlane* pmCoordSkyToCellQuick( + psPlane* cellCoord, + const psSphere* skyCoord, + const pmCell* cell) +{ + PS_ASSERT_PTR_NON_NULL(skyCoord, NULL); + PS_ASSERT_PTR_NON_NULL(cell, NULL); + PS_ASSERT_PTR_NON_NULL(cell->toSky, NULL); + psPlane skyPlane; + skyPlane.y = skyCoord->r; + skyPlane.x = skyCoord->d; + + psPlane *rc = psPlaneTransformApply(cellCoord, cell->toSky, &skyPlane); + if (rc == NULL) { + psLogMsg(__func__, PS_LOG_WARN, "WARNING: could not transform sky to cell coords.\n"); + } + return(cellCoord); +} Index: trunk/psModules/src/astrom/pmFPAAstrometry.h =================================================================== --- trunk/psModules/src/astrom/pmFPAAstrometry.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAAstrometry.h (revision 6872) @@ -0,0 +1,188 @@ +#ifndef PM_FPA_ASTROMETRY_H +#define PM_FPA_ASTROMETRY_H + +#include "pslib.h" +#include "pmFPA.h" + +/** Find cooresponding cell for given FPA coordinate + * + * @return pmCell* the cell cooresponding to the coord in FPA + */ +pmCell* pmCellInFPA( + const psPlane* coord, ///< the coordinate in FPA plane + const pmFPA* FPA ///< the FPA to search for the cell +); + + +/** Find cooresponding chip for given FPA coordinate + * + * @return pmChip* the chip cooresponding to coord + */ +pmChip* pmChipInFPA( + const psPlane* coord, ///< the coordinate in FPA plane + const pmFPA* FPA ///< the FPA to search for the cell +); + + +/** Find cooresponding cell for given Chip coordinate + * + * @return pmCell* the cell cooresponding to coord + */ +pmCell* pmCellInChip( + const psPlane* coord, ///< the coordinate in Chip plane + const pmChip* chip ///< the chip to search for the cell +); + + +/** Translate a cell coordinate into a chip coordinate + * + * @return psPlane* the resulting chip coordinate + */ +psPlane* pmCoordCellToChip( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within Cell + const pmCell* cell ///< the Cell in interest +); + + +/** Translate a chip coordinate into a FPA coordinate + * + * @return psPlane* the resulting FPA coordinate + */ +psPlane* pmCoordChipToFPA( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within Chip + const pmChip* chip ///< the chip in interest +); + + +/** Translate a FPA coordinate into a Tangent Plane coordinate + * + * @return psPlane* the resulting Tangent Plane coordinate + */ +psPlane* pmCoordFPAToTP( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within FPA + double color, ///< Color of source + double magnitude, ///< Magnitude of source + const pmFPA* fpa ///< the FPA in interest +); + + +/** Translate a Tangent Plane coordinate into a Sky coordinate + * + * @return psSphere* the resulting Sky coordinate + */ +psSphere* pmCoordTPToSky( + psSphere* out, ///< a sphere struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within Tangent Plane + const psProjection *projection +); + +/** Translate a cell coordinate into a FPA coordinate + * + * @return psPlane* the resulting FPA coordinate + */ +psPlane* pmCoordCellToFPA( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within cell + const pmCell* cell ///< the cell in interest +); + + +/** Translate a cell coordinate into a Sky coordinate + * + * @return psSphere* the resulting Sky coordinate + */ +psSphere* pmCoordCellToSky( + psSphere* out, ///< a sphere struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within cell + double color, ///< Color of source + double magnitude, ///< Magnitude of source + const pmCell* cell ///< the cell in interest +); + + +/** Translate a cell coordinate into a Sky coordinate using a 'quick and + * dirty' method + * + * @return psSphere* the resulting Sky coordinate + */ +psSphere* pmCoordCellToSkyQuick( + psSphere* out, ///< a sphere struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within cell + const pmCell* cell ///< the cell in interest +); + + +/** Translate a Sky coordinate into a Tangent Plane coordinate + * + * @return psPlane* the resulting Tangent Plane coordinate + */ +psPlane* pmCoordSkyToTP( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psSphere* in, ///< the sky coordinate + const psProjection *projection +); + +/** Translate a Tangent Plane coordinate into a FPA coordinate + * + * @return psPlane* the resulting FPA coordinate + */ +psPlane* pmCoordTPToFPA( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the coordinate within tangent plane + double color, ///< Color of source + double magnitude, ///< Magnitude of source + const pmFPA* fpa ///< the FPA of interest +); + + +/** Translate a FPA coordinate into a chip coordinate + * + * @return psPlane* the resulting chip coordinate + */ +psPlane* pmCoordFPAToChip( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the FPA coordinate + const pmChip* chip ///< the chip of interest +); + + +/** Translate a chip coordinate into a cell coordinate + * + * @return psPlane* the resulting cell coordinate + */ +psPlane* pmCoordChipToCell( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psPlane* in, ///< the Chip coordinate + const pmCell* cell ///< the cell of interest +); + + +/** Translate a sky coordinate into a cell coordinate + * + * @return psPlane* the resulting cell coordinate + */ +psPlane* pmCoordSkyToCell( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psSphere* in, ///< the Sky coordinate + float color, ///< Color of source + float magnitude, ///< Magnitude of source + const pmCell* cell ///< the cell of interest +); + + +/** Translate a sky coordinate into a cell coordinate using a 'quick and + * dirty' method + * + * @return psPlane* the resulting cell coordinate + */ +psPlane* pmCoordSkyToCellQuick( + psPlane* out, ///< a plane struct to recycle. If NULL, a new struct is created + const psSphere* in, ///< the Sky coordinate + const pmCell* cell ///< the cell of interest +); + + +#endif Index: trunk/psModules/src/astrom/pmFPAConceptsGet.c =================================================================== --- trunk/psModules/src/astrom/pmFPAConceptsGet.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAConceptsGet.c (revision 6872) @@ -0,0 +1,1197 @@ +#include +#include +#include +#include "pslib.h" + +#include "pmAstrometry.h" +#include "pmFPAConceptsGet.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Private functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +psMetadataItem *p_pmFPAConceptGetFromCamera(pmCell *cell, // The cell + const char *concept // Name of concept + ) +{ + if (cell) { + psMetadata *camera = cell->camera; // Camera data + psMetadataItem *item = psMetadataLookup(camera, concept); + return item; + } + return NULL; +} + + +psMetadataItem *p_pmFPAConceptGetFromHeader(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ) +{ + bool mdStatus = true; // Status of MD lookup + psMetadata *translation = psMetadataLookupMD(&mdStatus, fpa->camera, "TRANSLATION"); // FITS translation + if (! mdStatus) { + psError(PS_ERR_IO, false, "Unable to find TRANSLATION in camera configuration.\n"); + return NULL; + } + + // Look for how to translate the concept into a FITS header name + const char *keyword = psMetadataLookupStr(&mdStatus, translation, concept); + if (mdStatus && strlen(keyword) > 0) { + // We have a FITS header to look up --- search each level + if (cell && cell->hdu) { + psMetadataItem *cellItem = psMetadataLookup(cell->hdu->header, keyword); + if (cellItem) { + // XXX: Need to clean up before returning + return cellItem; + } + } + + if (chip && chip->hdu) { + psMetadataItem *chipItem = psMetadataLookup(chip->hdu->header, keyword); + if (chipItem) { + // XXX: Need to clean up before returning + return chipItem; + } + } + + if (fpa->hdu) { + psMetadataItem *fpaItem = psMetadataLookup(fpa->hdu->header, keyword); + if (fpaItem) { + // XXX: Need to clean up before returning + return fpaItem; + } + } + + if (fpa->phu) { + psMetadataItem *fpaItem = psMetadataLookup(fpa->phu, keyword); + if (fpaItem) { + // XXX: Need to clean up before returning + return fpaItem; + } + } + } + + // No header value + return NULL; +} + + +// Look for a default +psMetadataItem *p_pmFPAConceptGetFromDefault(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ) +{ + bool mdOK = true; // Status of MD lookup + psMetadata *defaults = psMetadataLookupMD(&mdOK, fpa->camera, "DEFAULTS"); + if (! mdOK) { + psError(PS_ERR_IO, false, "Unable to find DEFAULTS in camera configuration.\n"); + return NULL; + } + + psMetadataItem *defItem = psMetadataLookup(defaults, concept); + if (defItem) { + if (defItem->type == PS_DATA_METADATA) { + // A dependent default + psTrace(__func__, 7, "Evaluating dependent default....\n"); + psMetadata *dependents = defItem->data.V; // The list of dependents + // Find out what it depends on + psString dependName = psStringCopy(concept); + psStringAppend(&dependName, ".DEPEND"); + psString dependsOn = psMetadataLookupStr(&mdOK, defaults, dependName); + if (! mdOK) { + psError(PS_ERR_IO, false, "Unable to find %s in camera configuration for dependent default" + " --- ignored\n", dependName); + // XXX: Need to clean up before returning + return NULL; + } + psFree(dependName); + // Find the value of the dependent concept + psMetadataItem *depItem = p_pmFPAConceptGetFromHeader(fpa, chip, cell, dependsOn); + if (! depItem) { + psError(PS_ERR_IO, true, "Unable to find value for %s (required for %s)\n", dependsOn, + concept); + return NULL; + } + if (depItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "Value of %s is not of type string, as required for dependency" + " --- ignored.\n", dependsOn); + } + + defItem = psMetadataLookup(dependents, depItem->data.V); // This is now what we were after + } + } + + // XXX: Need to clean up before returning + return defItem; // defItem is either NULL or points to what was desired +} + + +// Look for a database lookup +// XXX: Not tested +psMetadataItem *p_pmFPAConceptGetFromDB(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Name of concept + ) +{ + if (! db) { + // No database initialised + return NULL; + } + + bool mdStatus = true; // Status of MD lookup + psMetadata *database = psMetadataLookupMD(&mdStatus, fpa->camera, "DATABASE"); + if (! mdStatus) { + // No error, because not everyone needs to use the DB + return NULL; + } + + psMetadata *dbLookup = psMetadataLookupMD(&mdStatus, database, concept); + if (dbLookup) { + const char *tableName = psMetadataLookupStr(&mdStatus, dbLookup, "TABLE"); // Name of the table + // const char *colName = psMetadataLookupStr(&mdStatus, dbLookup, "COLUMN"); // Name of the column + const char *givenCols = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENDBCOL"); // Name of "where" + // columns + const char *givenPS = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENPS"); // Values for "where" + // columns + + // Now, need to get the "given"s + if (strlen(givenCols) || strlen(givenPS)) { + psList *cols = psStringSplit(givenCols, ",;"); // List of column names + psList *values = psStringSplit(givenPS, ",;"); // List of value names for the columns + psMetadata *selection = psMetadataAlloc(); // The stuff to select in the DB + if (cols->n != values->n) { + psLogMsg(__func__, PS_LOG_WARN, "The GIVENDBCOL and GIVENPS entries for %s do not have " + "the same number of entries --- ignored.\n", concept); + } else { + // Iterators for the lists + psListIterator *colsIter = psListIteratorAlloc(cols, PS_LIST_HEAD, false); + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); + char *column = NULL; // Name of the column + while ((column = psListGetAndIncrement(colsIter))) { + char *name = psListGetAndIncrement(valuesIter); // Name for the value + if (!strlen(column) || !strlen(name)) { + psLogMsg(__func__, PS_LOG_WARN, "One of the columns or value names for %s is " + " empty --- ignored.\n", concept); + } else { + // Search for the value name + psMetadataItem *item = p_pmFPAConceptGetFromHeader(fpa, chip, cell, name); + if (! item) { + item = p_pmFPAConceptGetFromDefault(fpa, chip, cell, name); + } + if (! item) { + psLogMsg(__func__, PS_LOG_ERROR, "Unable to find the value name %s for DB " + " lookup on %s --- ignored.\n", name, concept); + } else { + // We need to create a new psMetadataItem. I don't think we can't simply hack + // the existing one, since that could conceivably cause memory leaks + psMetadataItem *newItem = psMetadataItemAlloc(concept, item->type, + item->comment, item->data.V); + psMetadataAddItem(selection, newItem, PS_LIST_TAIL, PS_META_REPLACE); + psFree(newItem); + } + } + psFree(name); + psFree(column); + } // Iterating through the columns + psFree(colsIter); + psFree(valuesIter); + + psArray *dbResult = psDBSelectRows(db, tableName, selection, 2); // Lookup result + // Note that we use limit=2 in order to test if there are multiple rows returned + + psMetadataItem *result = NULL; // The final result of the DB lookup + if (dbResult->n == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find any rows in DB for %s --- ignored\n", + concept); + } else { + if (dbResult-> n > 1) { + psLogMsg(__func__, PS_LOG_WARN, "Multiple rows returned in DB lookup for %s --- " + " using the first one only.\n", concept); + } + result = (psMetadataItem*)dbResult->data[0]; + } + // XXX: Need to clean up before returning + return result; + } + psFree(cols); + psFree(values); + } + } // Doing the "given"s. + + psAbort(__func__, "Shouldn't ever get here.\n"); + return NULL; +} + + +// Concept lookup +psMetadataItem *p_pmFPAConceptGet(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Concept name + ) +{ + // Try headers, database, defaults in order + psMetadataItem *item = p_pmFPAConceptGetFromCamera(cell, concept); + if (! item) { + item = p_pmFPAConceptGetFromHeader(fpa, chip, cell, concept); + } + if (! item) { + item = p_pmFPAConceptGetFromDB(fpa, chip, cell, db, concept); + } + if (! item) { + item = p_pmFPAConceptGetFromDefault(fpa, chip, cell, concept); + } + return item; // item is either NULL, or points to what was desired +} + + +void p_pmFPAConceptGetF32(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ) +{ + psMetadataItem *item = p_pmFPAConceptGet(fpa, chip, cell, db, name); + float value = NAN; + if (item) { + switch (item->type) { + case PS_DATA_F32: + value = item->data.F32; + break; + case PS_DATA_F64: + // Assume it's OK to truncate to floating point from double + value = (float)item->data.F64; + break; + case PS_DATA_S32: + // Promote to float + value = (float)item->data.S32; + break; + default: + psError(PS_ERR_IO, true, "Concept %s (%s) is not of floating point type (%x) --- treating as " + "undefined.\n", name, comment, item->type); + } + } else { + psError(PS_ERR_IO, true, "Concept %s (%s) is not defined.\n", name, comment); + } + psTrace(__func__, 7, "Adding %s (%s): %f\n", name, comment, value); + + psMetadataAdd(concepts, PS_LIST_TAIL, name, PS_TYPE_F32 | PS_META_REPLACE, comment, value); +} + +void p_pmFPAConceptGetF64(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ) +{ + psMetadataItem *item = p_pmFPAConceptGet(fpa, chip, cell, db, name); + double value = NAN; + if (item) { + switch (item->type) { + case PS_TYPE_F64: + value = item->data.F64; + break; + case PS_TYPE_F32: + // Promote to double + value = (double)item->data.F32; + break; + case PS_TYPE_S32: + // Promote to double + value = (double)item->data.S32; + break; + default: + psError(PS_ERR_IO, true, "Concept %s (%s) is not of double-precision floating point type (%x) " + "--- treating as undefined.\n", name, comment, item->type); + } + } else { + psError(PS_ERR_IO, true, "Concept %s (%s) is not defined.\n", name, comment); + } + psTrace(__func__, 7, "Adding %s (%s): %f\n", name, comment, value); + + psMetadataAdd(concepts, PS_LIST_TAIL, name, PS_TYPE_F64 | PS_META_REPLACE, comment, value); +} + +void p_pmFPAConceptGetS32(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ) +{ + psMetadataItem *item = p_pmFPAConceptGet(fpa, chip, cell, db, name); + int value = 0; + if (item) { + switch (item->type) { + case PS_TYPE_S32: + value = item->data.S32; + break; + case PS_TYPE_F32: + psLogMsg(__func__, PS_LOG_WARN, "Concept %s (%s) should be S32, but is F32 --- converting.\n", + name, comment); + value = (int)item->data.F32; + break; + case PS_TYPE_F64: + psLogMsg(__func__, PS_LOG_WARN, "Concept %s (%s) should be S32, but is F64 --- converting.\n", + name, comment); + value = (int)item->data.F64; + break; + default: + psError(PS_ERR_IO, true, "Concept %s (%s) is not of integer type (%x) --- treating as " + "undefined.\n", name, comment, item->type); + } + } else { + psError(PS_ERR_IO, true, "Concept %s (%s) is not defined.\n", name, comment); + } + psTrace(__func__, 7, "Adding %s (%s): %d\n", name, comment, value); + + psMetadataAdd(concepts, PS_LIST_TAIL, name, PS_TYPE_S32 | PS_META_REPLACE, comment, value); +} + +void p_pmFPAConceptGetString(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ) +{ + psMetadataItem *item = p_pmFPAConceptGet(fpa, chip, cell, db, name); + psString value = NULL; + if (item) { + switch (item->type) { + case PS_DATA_STRING: + value = psMemIncrRefCounter(item->data.V); + break; + case PS_DATA_F32: + psStringAppend(&value, "%f", item->data.F32); + break; + case PS_DATA_S32: + psStringAppend(&value, "%d", item->data.S32); + break; + default: + psError(PS_ERR_IO, true, "Concept %s (%s) is not of string type (%x) --- treating as " + "undefined.\n", name, comment, item->type); + } + } else { + psError(PS_ERR_IO, true, "Concept %s (%s) is not defined.\n", name, comment); + value = psStringCopy(""); + } + psTrace(__func__, 7, "Adding %s (%s): %s\n", name, comment, value); + + psMetadataAdd(concepts, PS_LIST_TAIL, name, PS_DATA_STRING | PS_META_REPLACE, comment, value); + psFree(value); +} + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Ingest concepts for the FPA +void pmFPAIngestConcepts(pmFPA *fpa, // The FPA + psDB *db // DB handle + ) +{ + if (! fpa->concepts) { + fpa->concepts = psMetadataAlloc(); + } + + // FPA.NAME + p_pmFPAConceptGetString(fpa, NULL, NULL, db, fpa->concepts, "FPA.NAME", "Name of FPA"); + + // FPA.AIRMASS + p_pmFPAConceptGetF32(fpa, NULL, NULL, db, fpa->concepts, "FPA.AIRMASS", "Airmass at boresight"); + + // FPA.FILTER + p_pmFPAConceptGetString(fpa, NULL, NULL, db, fpa->concepts, "FPA.FILTER", "Filter used"); + + // FPA.POSANGLE + p_pmFPAConceptGetF32(fpa, NULL, NULL, db, fpa->concepts, "FPA.POSANGLE", "Position angle for instrument"); + + // FPA.RADECSYS + p_pmFPAConceptGetString(fpa, NULL, NULL, db, fpa->concepts, "FPA.RADECSYS", "Celestial coordinate system"); + + // These take some extra work + + // FPA.RA + { + double ra = NAN; // The RA + psMetadataItem *raItem = p_pmFPAConceptGet(fpa, NULL, NULL, db, "FPA.RA"); // The FPA.RA item + if (raItem) + { + switch (raItem->type) { + case PS_TYPE_F32: + ra = raItem->data.F32; + break; + case PS_TYPE_F64: + ra = raItem->data.F64; + break; + case PS_DATA_STRING: + // Sexagesimal format + { + int big, medium; + float small; + // XXX: Upgrade path is to allow dd:mm.mmm + if (sscanf(raItem->data.V, "%d:%d:%f", &big, &medium, &small) != 3 && + sscanf(raItem->data.V, "%d %d %f", &big, &medium, &small) != 3) + { + psError(PS_ERR_IO, true, "Cannot interpret FPA.RA: %s\n", raItem->data.V); + break; + } + ra = abs(big) + (float)medium/60.0 + small/3600.0; + if (big < 0) + { + ra *= -1.0; + } + } + break; + default: + psError(PS_ERR_IO, true, "FPA.RA is of an unexpected type: %x\n", raItem->type); + } + + // How to interpret the RA + const psMetadata *camera = fpa->camera; // Camera configuration data + bool mdok = true; // Status of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, camera, "FORMATS"); + if (mdok && formats) { + psString raFormat = psMetadataLookupStr(&mdok, formats, "FPA.RA"); + if (mdok && strlen(raFormat) > 0) { + if (strcasecmp(raFormat, "HOURS") == 0) { + ra *= M_PI / 12.0; + } else if (strcasecmp(raFormat, "DEGREES") == 0) { + ra *= M_PI / 180.0; + } else if (strcasecmp(raFormat, "RADIANS") == 0) { + // No action required + } else { + psLogMsg(__func__, PS_LOG_WARN, "Don't understand FPA.RA in FORMATS (%s) --- assuming" + " HOURS.\n"); + ra *= M_PI / 12.0; + } + } else { + psError(PS_ERR_IO, false, "Unable to find FPA.RA in FORMATS --- assuming HOURS.\n"); + ra *= M_PI / 12.0; + } + } else { + psError(PS_ERR_IO, false, "Unable to find FORMAT metadata in camera configuration --- " + "assuming format for FPA.RA is HOURS.\n"); + ra *= M_PI / 12.0; + } + } else + { + psError(PS_ERR_IO, false, "Couldn't find FPA.RA.\n"); + } + + psMetadataAdd(fpa->concepts, PS_LIST_TAIL, "FPA.RA", PS_DATA_F64 | PS_META_REPLACE, + "Right Ascension of the boresight (radians)", ra); + + } + + // FPA.DEC + { + double dec = NAN; // The DEC + psMetadataItem *decItem = p_pmFPAConceptGet(fpa, NULL, NULL, db, "FPA.DEC"); // The FPA.DEC item + if (decItem) { + switch (decItem->type) { + case PS_TYPE_F32: + dec = decItem->data.F32; + break; + case PS_TYPE_F64: + dec = decItem->data.F64; + break; + case PS_DATA_STRING: + // Sexagesimal format + { + int big, medium; + float small; + // XXX: Upgrade path is to allow dd:mm.mmm + if (sscanf(decItem->data.V, "%d:%d:%f", &big, &medium, &small) != 3 && + sscanf(decItem->data.V, "%d %d %f", &big, &medium, &small) != 3) + { + psError(PS_ERR_IO, true, "Cannot interpret FPA.DEC: %s\n", decItem->data.V); + break; + } + dec = abs(big) + (float)medium/60.0 + small/3600.0; + if (big < 0) + { + dec *= -1.0; + } + } + break; + default: + psError(PS_ERR_IO, true, "FPA.DEC is of an unexpected type: %x\n", decItem->type); + } + + // How to interpret the DEC + const psMetadata *camera = fpa->camera; // Camera configuration data + bool mdok = true; // Status of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, camera, "FORMATS"); + if (mdok && formats) { + psString decFormat = psMetadataLookupStr(&mdok, formats, "FPA.DEC"); + if (mdok && strlen(decFormat) > 0) { + if (strcasecmp(decFormat, "HOURS") == 0) { + dec *= M_PI / 12.0; + } else if (strcasecmp(decFormat, "DEGREES") == 0) { + dec *= M_PI / 180.0; + } else if (strcasecmp(decFormat, "RADIANS") == 0) { + // No action required + } else { + psLogMsg(__func__, PS_LOG_WARN, "Don't understand FPA.DEC in FORMATS (%s) --- " + "assuming DEGREES.\n"); + dec *= M_PI / 180.0; + } + } else { + psError(PS_ERR_IO, false, "Unable to find FPA.DEC in FORMATS --- assuming DEGREES.\n"); + dec *= M_PI / 180.0; + } + } else { + psError(PS_ERR_IO, false, "Unable to find FORMATS metadata in camera configuration --- " + "assuming format for FPA.DEC is DEGREES.\n"); + dec *= M_PI / 180.0; + } + } else { + psError(PS_ERR_IO, false, "Couldn't find FPA.DEC.\n"); + } + + psMetadataAdd(fpa->concepts, PS_LIST_TAIL, "FPA.DEC", PS_DATA_F64 | PS_META_REPLACE, + "Declination of the boresight (radians)", dec); + + } + + // Pau. +} + + +// Ingest concepts for the chip +bool pmChipIngestConcepts(pmChip *chip, // The chip + psDB *db // DB handle + ) +{ + // pmFPA *fpa = chip->parent; // The parent FPA + + if (! chip->concepts) { + chip->concepts = psMetadataAlloc(); + } + + // CHIP.NAME --- added by pmFPAConstruct + + // Pau. + return true; +} + + +// Add corrective to a position --- in case the user wants FORTRAN indexing (like the FITS standard...) +static bool correctPosition(pmFPA *fpa, // FPA, contains the camera configuration + pmCell *cell, // Cell containing the concept to correct + const char *conceptName // Name of concept to correct + ) +{ + bool mdok = false; // Result of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, fpa->camera, "FORMATS"); + if (mdok && formats) { + psString format = psMetadataLookupStr(&mdok, formats, conceptName); + if (mdok && strlen(format) > 0 && strcasecmp(format, "FORTRAN") == 0) { + psMetadataItem *valueItem = psMetadataLookup(cell->concepts, conceptName); + valueItem->data.S32 -= 1; + } + } + return true; +} + +bool p_pmCellIngestConcept(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Name of the concept + ) +{ + if (strcmp(concept, "CELL.GAIN") == 0) { + p_pmFPAConceptGetF32(fpa, chip, cell, db, cell->concepts, "CELL.GAIN", "CCD gain (e/count)"); + } else if (strcmp(concept, "CELL.READNOISE") == 0) { + p_pmFPAConceptGetF32(fpa, chip, cell, db, cell->concepts, "CELL.READNOISE", "CCD read noise (e)"); + } else if (strcmp(concept, "CELL.SATURATION") == 0) { + p_pmFPAConceptGetF32(fpa, chip, cell, db, cell->concepts, "CELL.SATURATION", + "Saturation level (ADU)"); + } else if (strcmp(concept, "CELL.BAD") == 0) { + p_pmFPAConceptGetF32(fpa, chip, cell, db, cell->concepts, "CELL.BAD", "Bad level (ADU)"); + } else if (strcmp(concept, "CELL.XPARITY") == 0) { + p_pmFPAConceptGetS32(fpa, chip, cell, db, cell->concepts, "CELL.XPARITY", + "Orientation in x compared to the rest of the FPA"); + } else if (strcmp(concept, "CELL.YPARITY") == 0) { + p_pmFPAConceptGetS32(fpa, chip, cell, db, cell->concepts, "CELL.YPARITY", + "Orientation in y compared to the rest of the FPA"); + } else if (strcmp(concept, "CELL.READDIR") == 0) { + p_pmFPAConceptGetS32(fpa, chip, cell, db, cell->concepts, "CELL.READDIR", + "Read direction: 1=row, 2=col"); + } else if (strcmp(concept, "CELL.EXPOSURE") == 0) { // used to be READOUT.EXPOSURE + p_pmFPAConceptGetF32(fpa, chip, cell, db, cell->concepts, "CELL.EXPOSURE", "Exposure time (sec)"); + } else if (strcmp(concept, "CELL.DARKTIME") == 0) { // used to be READOUT.DARKTIME + p_pmFPAConceptGetF32(fpa, chip, cell, db, cell->concepts, "CELL.DARKTIME", + "Time since CCD flush (sec)"); + // These take some extra work + } else if (strcmp(concept, "CELL.TRIMSEC") == 0) { + psRegion *trimsec = psAlloc(sizeof(psRegion)); // Make space for a psRegion (usually passed by value) + + psMetadataItem *secItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.TRIMSEC"); + if (! secItem) { + psError(PS_ERR_IO, false, "Couldn't find CELL.TRIMSEC.\n"); + *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0); + } else if (secItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "CELL.TRIMSEC is not of type STR (%x)\n", secItem->type); + *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0); + } else { + psString section = secItem->data.V; // The section string + + psMetadataItem *sourceItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.TRIMSEC.SOURCE"); + if (! sourceItem) { + psError(PS_ERR_IO, false, "Couldn't find CELL.TRIMSEC.SOURCE.\n"); + *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0); + } else if (sourceItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "CELL.TRIMSEC.SOURCE is not of type STR (%x)\n", sourceItem->type); + *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0); + } else { + psString source = sourceItem->data.V; // The source string + + if (strcasecmp(source, "VALUE") == 0) { + *trimsec = psRegionFromString(section); + } else if (strcasecmp(source, "HEADER") == 0) { + psMetadata *header = NULL; // The FITS header + if (cell->hdu) { + header = cell->hdu->header; + } else if (chip->hdu) { + header = chip->hdu->header; + } else if (fpa->hdu) { + header = fpa->hdu->header; + } + if (! header) { + psError(PS_ERR_IO, true, "Unable to find FITS header!\n"); + *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0); + } else { + bool mdok = true; // Status of MD lookup + psString secValue = psMetadataLookupStr(&mdok, header, section); + if (! mdok || ! secValue) { + psError(PS_ERR_IO, false, "Unable to locate header %s\n", section); + *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0); + } else { + *trimsec = psRegionFromString(secValue); + } + } + } else { + psError(PS_ERR_IO, true, "CELL.TRIMSEC.SOURCE (%s) is not HEADER or VALUE --- trying " + "VALUE.\n", source); + *trimsec = psRegionFromString(section); + } // Value of CELL.TRIMSEC.SOURCE + } // Looking up CELL.TRIMSEC.SOURCE + } // Looking up CELL.TRIMSEC + + psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.TRIMSEC", PS_DATA_UNKNOWN | PS_META_REPLACE, + "Trim section", trimsec); + psFree(trimsec); + + } else if (strcmp(concept, "CELL.BIASSEC") == 0) { + psList *biassecs = psListAlloc(NULL); // List of bias sections + + psMetadataItem *secItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.BIASSEC"); + if (! secItem) { + psError(PS_ERR_IO, false, "Couldn't find CELL.BIASSEC.\n"); + } else if (secItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "CELL.BIASSEC is not of type STR (%x)\n", secItem->type); + } else { + psString sections = secItem->data.V; // The section string + + psMetadataItem *sourceItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.BIASSEC.SOURCE"); + if (! sourceItem) { + psError(PS_ERR_IO, false, "Couldn't find CELL.BIASSEC.SOURCE.\n"); + } else if (sourceItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "CELL.BIASSEC.SOURCE is not of type STR (%x)\n", sourceItem->type); + } else { + psString source = sourceItem->data.V; // The source string + + psList *secList = psStringSplit(sections, " ;"); // List of sections + psListIterator *secIter = psListIteratorAlloc(secList, PS_LIST_HEAD, false); // Iterator over + // sections + psString aSection = NULL; // A section from the list + while ((aSection = psListGetAndIncrement(secIter))) { + psRegion *region = psAlloc(sizeof(psRegion)); // Make space for a psRegion (usually passed + // by value) + + if (strcasecmp(source, "VALUE") == 0) { + *region = psRegionFromString(aSection); + } else if (strcasecmp(source, "HEADER") == 0) { + psMetadata *header = NULL; // The FITS header + if (cell->hdu) { + header = cell->hdu->header; + } else if (chip->hdu) { + header = chip->hdu->header; + } else if (fpa->hdu) { + header = fpa->hdu->header; + } + if (! header) { + psError(PS_ERR_IO, true, "Unable to find FITS header!\n"); + *region = psRegionSet(0.0,0.0,0.0,0.0); + } else { + bool mdok = true; // Status of MD lookup + psString secValue = psMetadataLookupStr(&mdok, header, aSection); + if (! mdok || ! secValue) { + psError(PS_ERR_IO, false, "Unable to locate header %s\n", aSection); + *region = psRegionSet(0.0,0.0,0.0,0.0); + } else { + *region = psRegionFromString(secValue); + } + } + } else { + psError(PS_ERR_IO, true, "CELL.BIASSEC.SOURCE (%s) is not HEADER or VALUE --- trying " + "VALUE.\n", source); + *region = psRegionFromString(aSection); + } // Value of CELL.BIASSEC.SOURCE + + psListAdd(biassecs, PS_LIST_TAIL, region); + psFree(region); + } // Iterating over multiple sections + psFree(secIter); + psFree(secList); + } // Looking up CELL.BIASSEC.SOURCE + } // Looking up CELL.BIASSEC + + psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.BIASSEC", PS_DATA_LIST | PS_META_REPLACE, + "Bias sections", biassecs); + psFree(biassecs); + + } else if (strcmp(concept, "CELL.XBIN") == 0) { + int xBin = 1; // Binning factor in x + psMetadataItem *binItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.XBIN"); + if (! binItem) { + psError(PS_ERR_IO, false, "Couldn't find CELL.XBIN.\n"); + } else if (binItem->type == PS_DATA_STRING) { + psString binString = binItem->data.V; // The string containing the binning + if (sscanf(binString, "%d %*d", &xBin) != 1 && + sscanf(binString, "%d,%*d", &xBin) != 1) { + psError(PS_ERR_IO, true, "Unable to read string to get x binning: %s\n", binString); + } + } else if (binItem->type == PS_TYPE_S32) { + xBin = binItem->data.S32; + } else { + psError(PS_ERR_IO, true, "Note sure how to interpret CELL.XBIN of type %x --- assuming 1.\n", + binItem->type); + } + + psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.XBIN", PS_TYPE_S32 | PS_META_REPLACE, + "Binning in x", xBin); + + } else if (strcmp(concept, "CELL.YBIN") == 0) { + int yBin = 1; // Binning factor in y + psMetadataItem *binItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.YBIN"); + if (! binItem) { + psError(PS_ERR_IO, false, "Couldn't find CELL.YBIN.\n"); + } else if (binItem->type == PS_DATA_STRING) { + psString binString = binItem->data.V; // The string containing the binning + if (sscanf(binString, "%*d %d", &yBin) != 1 && + sscanf(binString, "%*d,%d", &yBin) != 1) { + psError(PS_ERR_IO, true, "Unable to read string to get y binning: %s\n", binString); + } + } else if (binItem->type == PS_TYPE_S32) { + yBin = binItem->data.S32; + } else { + psError(PS_ERR_IO, true, "Note sure how to interpret CELL.YBIN of type %x --- assuming 1.\n", + binItem->type); + } + + psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.YBIN", PS_TYPE_S32 | PS_META_REPLACE, + "Binning in y", yBin); + + } else if (strcmp(concept, "CELL.TIME") == 0 || strcmp(concept, "CELL.TIMESYS") == 0) { + // Do CELL.TIME and CELL.TIMESYS together + psTime *time = NULL; // The time + psTimeType timeSys = PS_TIME_UTC; // The time system + + // CELL.TIMESYS + psMetadataItem *sysItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.TIMESYS"); + if (! sysItem) { + psError(PS_ERR_IO, true, "Couldn't find CELL.TIMESYS --- assuming UTC.\n"); + } else if (sysItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "CELL.TIMESYS isn't of type STRING --- assuming UTC.\n"); + } else { + psString sys = sysItem->data.V; // The time system string + if (strcasecmp(sys, "TAI") == 0) { + timeSys = PS_TIME_TAI; + } else if (strcasecmp(sys, "UTC") == 0) { + timeSys = PS_TIME_UTC; + } else if (strcasecmp(sys, "UT1") == 0) { + timeSys = PS_TIME_UT1; + } else if (strcasecmp(sys, "TT") == 0) { + timeSys = PS_TIME_TT; + } else { + psError(PS_ERR_IO, true, "Can't interpret CELL.TIMESYS --- assuming UTC.\n"); + } + } + psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.TIMESYS", PS_TYPE_S32 | PS_META_REPLACE, + "Time system", timeSys); + + psMetadataItem *timeItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.TIME"); + if (! timeItem) { + psError(PS_ERR_IO, false, "Couldn't find CELL.TIME.\n"); + } else { + // Get format + const psMetadata *camera = fpa->camera; // The camera configuration data + bool mdok = true; // Status of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, camera, "FORMATS"); + if (mdok && formats) { + psString timeFormat = psMetadataLookupStr(&mdok, formats, "CELL.TIME"); + if (mdok && strlen(timeFormat) > 0) { + switch (timeItem->type) { + case PS_DATA_STRING: { + psString timeString = timeItem->data.V; // String with the time + if (strcasecmp(timeFormat, "ISO") == 0) { + // timeString contains an ISO time + time = psTimeFromISO(timeString, timeSys); + } else if (strcasecmp(timeFormat, "JD") == 0) { + double timeValue = strtod (timeString, NULL); + time = psTimeFromJD(timeValue); + } else if (strcasecmp(timeFormat, "MJD") == 0) { + double timeValue = strtod (timeString, NULL); + time = psTimeFromMJD(timeValue); + } else if (strstr(timeFormat, "SEPARATE")) { + // timeString contains headers for the date and time + psMetadata *header = NULL; // The FITS header + if (cell->hdu) { + header = cell->hdu->header; + } else if (chip->hdu) { + header = chip->hdu->header; + } else if (fpa->hdu) { + header = fpa->hdu->header; + } + if (! header) { + psError(PS_ERR_IO, true, "Unable to find FITS header!\n"); + } else { + // Get the headers + char *stuff1 = strpbrk(timeString, " ,;"); + psString dateName = psStringNCopy(timeString, + strlen(timeString) - strlen(stuff1)); + char *stuff2 = strpbrk(stuff1, "abcdefghijklmnopqrstuvwxyz" + "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); + psString timeName = psStringCopy(stuff2); + + bool mdok = true; // Status of MD lookup + psString dateString = psMetadataLookupStr(&mdok, header, dateName); + psFree(dateName); + int day = 0, month = 0, year = 0; + if (sscanf(dateString, "%d-%d-%d", &day, &month, &year) != 3 && + sscanf(dateString, "%d/%d/%d", &day, &month, &year) != 3) { + psError(PS_ERR_IO, true, "Unable to read date: %s\n", dateString); + } else { + if (strstr(timeFormat, "BACKWARDS")) { + int temp = day; + day = year; + year = temp; + } + if (strstr(timeFormat, "PRE2000") || year < 2000) { + year += 2000; + } + + psMetadataItem *timeItem = psMetadataLookup(header, timeName); + if (! timeItem) { + psError(PS_ERR_IO, false, "Unable to find time header: %s\n", + timeName); + } else if (timeItem->type == PS_DATA_STRING) { + // Time is a string, in the usual way: + psStringAppend(&dateString, "T%s", timeItem->data.V); + } else { + // Assume that time is specified in Second of Day + double seconds = NAN; + switch (timeItem->type) { + case PS_TYPE_S32: + seconds = timeItem->data.S32; + break; + case PS_TYPE_F32: + seconds = timeItem->data.F32; + break; + case PS_TYPE_F64: + seconds = timeItem->data.F64; + break; + default: + psError(PS_ERR_IO, true, "Time header (%s) is not of an " + "expected type: %x\n", timeName, timeItem->type); + } + // Now print to timeString as "hh:mm:ss.ss" + int hours = seconds / 3600; + seconds -= (double)hours * 3600.0; + int minutes = seconds / 60; + seconds -= (double)minutes * 60.0; + psStringAppend(&dateString, "T%02d:%02d:%02f", hours, minutes, + seconds); + } + time = psTimeFromISO(dateString, timeSys); + } // Reading date and time + psFree(timeName); + } // Reading headers + } else { + psError(PS_ERR_IO, true, "Not sure how to parse CELL.TIME (%s) --- trying " + "ISO\n", timeString); + time = psTimeFromISO(timeString, timeSys); + } // Interpreting the time string + } + break; + case PS_TYPE_F32: { + double timeValue = (double)timeItem->data.F32; + if (strcasecmp(timeFormat, "JD") == 0) { + time = psTimeFromJD(timeValue); + } else if (strcasecmp(timeFormat, "MJD") == 0) { + time = psTimeFromMJD(timeValue); + } else { + psError(PS_ERR_IO, true, "Not sure how to parse CELL.TIME (%f) --- trying " + "JD\n", timeValue); + time = psTimeFromJD(timeValue); + } + } + break; + case PS_TYPE_F64: { + double timeValue = (double)timeItem->data.F64; + if (strcasecmp(timeFormat, "JD") == 0) { + time = psTimeFromJD(timeValue); + } else if (strcasecmp(timeFormat, "MJD") == 0) { + time = psTimeFromMJD(timeValue); + } else { + psError(PS_ERR_IO, true, "Not sure how to parse CELL.TIME (%f) --- trying " + "JD\n", timeValue); + time = psTimeFromJD(timeValue); + } + } + break; + default: + psError(PS_ERR_IO, true, "Unable to parse CELL.TIME.\n"); + } + } else { + psError(PS_ERR_IO, false, "Unable to find CELL.TIME in FORMATS.\n"); + } // Getting the format + } else { + psError(PS_ERR_IO, false, "Unable to find FORMATS in camera configuration.\n"); + } // Getting the formats + } // Getting CELL.TIME + + psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.TIME", PS_DATA_TIME | PS_META_REPLACE, + "Time of exposure", time); + psFree(time); + + // These are new and experimental concepts: CELL.X0 and CELL.Y0 + } else if (strcmp(concept, "CELL.X0") == 0) { + p_pmFPAConceptGetS32(fpa, chip, cell, db, cell->concepts, "CELL.X0", "Position of (0,0) on the chip"); + correctPosition(fpa, cell, "CELL.X0"); + } else if (strcmp(concept, "CELL.Y0") == 0) { + p_pmFPAConceptGetS32(fpa, chip, cell, db, cell->concepts, "CELL.Y0", "Position of (0,0) on the chip"); + correctPosition(fpa, cell, "CELL.Y0"); + } + + return true; +} + + + +// Ingest concepts for the cell +bool pmCellIngestConcepts(pmCell *cell, // The cell + psDB *db // DB handle + ) +{ + pmChip *chip = cell->parent; // The parent chip + pmFPA *fpa = chip->parent; // The parent FPA + + if (! cell->concepts) { + cell->concepts = psMetadataAlloc(); + } + + // CELL.NAME --- added by pmFPAConstruct + + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.GAIN"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.READNOISE"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.SATURATION"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.BAD"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.XPARITY"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.YPARITY"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.READDIR"); + + // These used to be pmReadoutGetExposure and pmReadoutGetDarkTime, but that doesn't really make sense at + // the moment. Maybe we need to add a "parent" link to the readouts. But then how are the exposure times + // REALLY derived? They're not in the FITS headers, because a readout is a plane in a 3D image. We'll + // have to dream up some additional suffix to specify these, but for now.... + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.EXPOSURE"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.DARKTIME"); + + + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.TRIMSEC"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.BIASSEC"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.TIME"); // This also does CELL.TIMESYS + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.XBIN"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.YBIN"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.X0"); + p_pmCellIngestConcept(fpa, chip, cell, db, "CELL.Y0"); + + return true; +} + + +// Retrieve a concept +psMetadataItem *pmCellGetConcept(pmCell *cell, // The cell + const char *concept // The concept + ) +{ + psMetadataItem *item = psMetadataLookup(cell->concepts, concept); + if (! item) { + pmChip *chip = cell->parent; + item = psMetadataLookup(chip->concepts, concept); + if (! item) { + pmFPA *fpa = chip->parent; + item = psMetadataLookup(fpa->concepts, concept); + } + } + return item; // item is either NULL or is what we want. +} + + +// Set up concepts for blank image +bool pmFPABlankConcepts(pmFPA *fpa // The FPA + ) +{ + assert(fpa); + + // FPA-level concepts + if (! fpa->concepts) { + fpa->concepts = psMetadataAlloc(); + } + psMetadataAddStr(fpa->concepts, PS_LIST_TAIL, "FPA.NAME", PS_META_REPLACE, "Name of FPA", ""); + psMetadataAddF32(fpa->concepts, PS_LIST_TAIL, "FPA.AIRMASS", PS_META_REPLACE, + "Airmass at boresight", NAN); + psMetadataAddStr(fpa->concepts, PS_LIST_TAIL, "FPA.FILTER", PS_META_REPLACE, "Filter used", ""); + psMetadataAddF32(fpa->concepts, PS_LIST_TAIL, "FPA.POSANGLE", PS_META_REPLACE, + "Position angle for instrument", NAN); + psMetadataAddStr(fpa->concepts, PS_LIST_TAIL, "FPA.RADECSYS", PS_META_REPLACE, + "Celestial coordinate system", ""); + psMetadataAddF64(fpa->concepts, PS_LIST_TAIL, "FPA.RA", PS_META_REPLACE, + "Right Ascension of the boresight (radians)", NAN); + psMetadataAddF64(fpa->concepts, PS_LIST_TAIL, "FPA.DEC", PS_META_REPLACE, + "Declination of the boresight (radians)", NAN); + + // Iterate through the chips + psArray *chips = fpa->chips; // Array of chips + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // The chip of interest + if (! chip) { + continue; + } + + // Chip-level concepts + if (! chip->concepts) { + chip->concepts = psMetadataAlloc(); + } + // CHIP.NAME *should* have been added by pmFPAConstruct --- make sure + psMetadataItem *chipNameItem = psMetadataLookup(chip->concepts, "CHIP.NAME"); + if (! chipNameItem) { + psMetadataAddStr(fpa->concepts, PS_LIST_TAIL, "CHIP.NAME", PS_META_REPLACE, "Name of Chip", ""); + } + + // Iterate through the cells + psArray *cells = chip->cells; // Array of cells + for (int j = 0; j < cells->n; j++) { + pmCell *cell = cells->data[i]; // The cell of interest + if (! cell) { + continue; + } + + // Cell-level concepts + if (! cell->concepts) { + cell->concepts = psMetadataAlloc(); + } + // CELL.NAME *should* have been added by pmFPAConstruct --- make sure + psMetadataItem *cellNameItem = psMetadataLookup(cell->concepts, "CELL.NAME"); + if (!cellNameItem) { + psMetadataAddStr(fpa->concepts, PS_LIST_TAIL, "CELL.NAME", PS_META_REPLACE, + "Name of Cell", ""); + } + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.GAIN", PS_META_REPLACE, "CCD gain (e/count)", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.READNOISE", PS_META_REPLACE, "CCD read noise (e)", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.SATURATION", PS_META_REPLACE, "Saturation level (ADU)", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.BAD", PS_META_REPLACE, "Bad level (ADU)", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.XPARITY", PS_META_REPLACE, "Orientation in x compared to the rest of the FPA", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.YPARITY", PS_META_REPLACE, "Orientation in x compared to the rest of the FPA", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.READDIR", PS_META_REPLACE, "Read direction: 1=row, 2=col", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.EXPOSURE", PS_META_REPLACE, "Exposure time (sec)", NAN); + psMetadataAddF32(cell->concepts, PS_LIST_TAIL, "CELL.DARKTIME", PS_META_REPLACE, "Time since CCD flush (sec)", NAN); + psMetadataAddS32(cell->concepts, PS_LIST_TAIL, "CELL.XBIN", PS_META_REPLACE, "Binning in x", 0); + psMetadataAddS32(cell->concepts, PS_LIST_TAIL, "CELL.YBIN", PS_META_REPLACE, "Binning in y", 0); + psMetadataAddS32(cell->concepts, PS_LIST_TAIL, "CELL.X0", PS_META_REPLACE, "Position of (0,0) on the chip", 0); + psMetadataAddS32(cell->concepts, PS_LIST_TAIL, "CELL.Y0", PS_META_REPLACE, "Position of (0,0) on the chip", 0); + + psRegion *trimsec = psAlloc(sizeof(psRegion)); // Dummy region + trimsec->x0 = NAN; + trimsec->x1 = NAN; + trimsec->y0 = NAN; + trimsec->y1 = NAN; + psMetadataAddPtr(cell->concepts, PS_LIST_TAIL, "CELL.TRIMSEC", PS_META_REPLACE, "Trim section", trimsec); + psList *biassecs = psListAlloc(NULL); // Dummy list + psMetadataAddPtr(cell->concepts, PS_LIST_TAIL, "CELL.BIASSEC", PS_META_REPLACE, "Bias section", biassecs); + psTime *time = psTimeAlloc(PS_TIME_TAI); // Dummy time + psMetadataAddPtr(cell->concepts, PS_LIST_TAIL, "CELL.TIME", PS_META_REPLACE, "Time of exposure", time); + psMetadataAddS32(cell->concepts, PS_LIST_TAIL, "CELL.TIMESYS", PS_META_REPLACE, "Time system", PS_TIME_TAI); + } + } + + return true; +} + +// Copy concepts from one FPA to another +bool pmFPACopyConcepts(pmFPA *target, // The target FPA + pmFPA *source // The target FPA + ) +{ + // Copy FPA concepts + target->concepts = pap_psMetadataCopy(target->concepts, source->concepts); + + // Copy chip concepts + psArray *targetChips = target->chips; // Chips in target + psArray *sourceChips = source->chips; // Chips in source + if (targetChips->n != sourceChips->n) { + psError(PS_ERR_IO, true, "Number of chips in target (%d) and source (%d) differ --- unable to copy " + "concepts.\n", targetChips->n, sourceChips->n); + return false; + } + for (int i = 0; i < targetChips->n; i++) { + pmChip *targetChip = targetChips->data[i]; // Target chip of interest + pmChip *sourceChip = sourceChips->data[i]; // Source chip of interest + if (! targetChip || ! sourceChip) { + continue; + } + targetChip->concepts = pap_psMetadataCopy(targetChip->concepts, sourceChip->concepts); + + // Copy cell concepts + psArray *targetCells = targetChip->cells; // Cells in target + psArray *sourceCells = sourceChip->cells; // Cells in source + if (targetCells->n != sourceCells->n) { + psError(PS_ERR_IO, true, "Number of cells in target (%d) and source (%d) differ for chip %d ---" + " unable to copy concepts.\n", targetCells->n, sourceCells->n, i); + return false; + } + for (int j = 0; j < targetCells->n; j++) { + pmCell *targetCell = targetCells->data[j]; // Target chip of interest + pmCell *sourceCell = sourceCells->data[j]; // Source chip of interest + if (! targetCell || ! sourceCell) { + continue; + } + targetCell->concepts = pap_psMetadataCopy(targetCell->concepts, sourceCell->concepts); + } + } + + return true; +} Index: trunk/psModules/src/astrom/pmFPAConceptsGet.h =================================================================== --- trunk/psModules/src/astrom/pmFPAConceptsGet.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAConceptsGet.h (revision 6872) @@ -0,0 +1,103 @@ +#ifndef PM_FPA_CONCEPTS_GET_H +#define PM_FPA_CONCEPTS_GET_H + +#include "pslib.h" +#include "pmAstrometry.h" +#include "psAdditionals.h" + +psMetadataItem *p_pmFPAConceptGetFromCamera(pmCell *cell, // The cell + const char *concept // Name of concept + ); +psMetadataItem *p_pmFPAConceptGetFromHeader(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ); +psMetadataItem *p_pmFPAConceptGetFromDefault(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + const char *concept // Name of concept + ); +psMetadataItem *p_pmFPAConceptGetFromDB(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Name of concept + ); +psMetadataItem *p_pmFPAConceptGet(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Concept name + ); +void p_pmFPAConceptGetF32(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ); +void p_pmFPAConceptGetF64(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ); +void p_pmFPAConceptGetS32(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ); +void p_pmFPAConceptGetString(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // The concepts MD + const char *name, // Name of the concept + const char *comment // Comment for concept + ); + + +// Ingest a single cell concept; this is the workhorse for ingesting cell concepts +bool p_pmCellIngestConcept(pmFPA *fpa, // The FPA + pmChip *chip, // The chip + pmCell *cell, // The cell + psDB *db, // DB handle + const char *concept // Name of the concept + ); + +// Ingest concepts for the FPA +void pmFPAIngestConcepts(pmFPA *fpa, // The FPA + psDB *db // DB handle + ); +// Ingest concepts for the chip +bool pmChipIngestConcepts(pmChip *chip, // The chip + psDB *db // DB handle + ); +// Ingest concepts for the cell +bool pmCellIngestConcepts(pmCell *cell, // The cell + psDB *db // DB handle + ); + +// Set up concepts for blank image +bool pmFPABlankConcepts(pmFPA *fpa // The FPA + ); + +// Copy concepts from one FPA to another +bool pmFPACopyConcepts(pmFPA *target, // The target FPA + pmFPA *source // The target FPA + ); + +// Retrieve a concept +psMetadataItem *pmCellGetConcept(pmCell *cell, // The cell + const char *concept // The concept + ); + + +#endif Index: trunk/psModules/src/astrom/pmFPAConceptsSet.c =================================================================== --- trunk/psModules/src/astrom/pmFPAConceptsSet.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAConceptsSet.c (revision 6872) @@ -0,0 +1,904 @@ +#include +#include +#include "pslib.h" + +#include "pmAstrometry.h" +#include "pmFPAConceptsGet.h" +#include "pmFPAConceptsSet.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +#define COMPARE_REGIONS(a,b) (((a)->x0 == (b)->x0 && \ + (a)->x1 == (b)->x1 && \ + (a)->y0 == (b)->y0 && \ + (a)->y1 == (b)->y1) ? true : false) + + +static bool compareConcepts(psMetadataItem *item1, // First item to compare + psMetadataItem *item2 // Second item to compare + ) +{ + // First order checks + if (! item1 || ! item2) { + return false; + } + if (strcasecmp(item1->name, item2->name) != 0) { + return false; + } + + // Check the more boring types + switch (item1->type) { + case PS_TYPE_S32: + switch (item2->type) { + case PS_TYPE_S32: + return (item1->data.S32 == item2->data.S32) ? true : false; + case PS_TYPE_F32: + return (item1->data.S32 == (int)item2->data.F32) ? true : false; + case PS_TYPE_F64: + return (item1->data.S32 == (int)item2->data.F64) ? true : false; + default: + return false; + } + case PS_TYPE_F32: + switch (item2->type) { + case PS_TYPE_S32: + return (item1->data.F32 == (float)item2->data.S32) ? true : false; + case PS_TYPE_F32: + return (item1->data.F32 == item2->data.F32) ? true : false; + case PS_TYPE_F64: + return (item1->data.F32 == (float)item2->data.F64) ? true : false; + default: + return false; + } + case PS_TYPE_F64: + switch (item2->type) { + case PS_TYPE_S32: + return (item1->data.F64 == (double)item2->data.S32) ? true : false; + case PS_TYPE_F32: + return (item1->data.F64 == (double)item2->data.F32) ? true : false; + case PS_TYPE_F64: + return (item1->data.F64 == item2->data.F64) ? true : false; + default: + return false; + } + return (item1->data.F64 == item2->data.F64) ? true : false; + case PS_DATA_STRING: + if (item2->type != PS_DATA_STRING) { + return false; + } + return (strcasecmp(item1->data.V, item2->data.V) == 0) ? true : false; + default: + return false; + } + psAbort(__func__, "Should never get here.\n"); +} + + +// Well, not really "set", but check to make sure it's there and matches +static bool setConceptInCamera(pmCell *cell, // The cell + psMetadataItem *concept // Concept + ) +{ + if (cell) { + psMetadataItem *item = psMetadataLookup(cell->camera, concept->name); // Info we want + return compareConcepts(item, concept); + } + + return false; +} + + +static bool setConceptInHeader(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psMetadataItem *concept // Concept + ) +{ + bool mdok = true; // Status of MD lookup + bool status = false; // Status of setting header + psMetadata *translation = psMetadataLookupMD(&mdok, fpa->camera, "TRANSLATION"); // FITS translation + if (! mdok) { + psError(PS_ERR_IO, false, "Unable to find TRANSLATION in camera configuration.\n"); + return false; + } + + // Look for how to translate the concept into a FITS header name + const char *keyword = psMetadataLookupStr(&mdok, translation, concept->name); + if (mdok && strlen(keyword) > 0) { + psTrace(__func__, 6, "It's in keyword %s\n", keyword); + psMetadataItem *headerItem = NULL; // Item to add to header + // XXX: Need to expand range of types + switch (concept->type) { + case PS_DATA_STRING: + headerItem = psMetadataItemAllocStr(keyword, concept->comment, concept->data.V); + break; + case PS_DATA_S32: + headerItem = psMetadataItemAllocS32(keyword, concept->comment, concept->data.S32); + break; + case PS_DATA_F32: + headerItem = psMetadataItemAllocF32(keyword, concept->comment, concept->data.F32); + break; + case PS_DATA_F64: + headerItem = psMetadataItemAllocF64(keyword, concept->comment, concept->data.F64); + break; + default: + headerItem = psMetadataItemAlloc(keyword, concept->type, concept->comment, + concept->data.V); // Item for the header + } + + // We have a FITS header to look up --- search each level + if (cell && cell->hdu) { + psTrace(__func__, 7, "Adding to the cell level header...\n"); + psMetadataAddItem(cell->hdu->header, headerItem, PS_LIST_TAIL, PS_META_REPLACE); + status = true; + } else if (chip && chip->hdu) { + psTrace(__func__, 7, "Adding to the chip level header...\n"); + psMetadataAddItem(chip->hdu->header, headerItem, PS_LIST_TAIL, PS_META_REPLACE); + status = true; + } else if (fpa->hdu) { + psTrace(__func__, 7, "Adding to the FPA level header...\n"); + psMetadataAddItem(fpa->hdu->header, headerItem, PS_LIST_TAIL, PS_META_REPLACE); + status = true; + } else { + // In desperation, add to the PHU --- it HAS to be in the header somewhere! + if (! fpa->phu) { + fpa->phu = psMetadataAlloc(); + } + psTrace(__func__, 7, "Adding to the PHU...\n"); + psMetadataAddItem(fpa->phu, headerItem, PS_LIST_TAIL, PS_META_REPLACE); + status = true; + } + psFree(headerItem); + } + + // No header value + return status; +} + + +// Well, not really "set", but check to see if it's there, and matches +static bool setConceptInDefault(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psMetadataItem *concept // Concept + ) +{ + bool mdOK = true; // Status of MD lookup + psMetadata *defaults = psMetadataLookupMD(&mdOK, fpa->camera, "DEFAULTS"); + if (! mdOK || ! defaults) { + psError(PS_ERR_IO, false, "Unable to find DEFAULTS in camera configuration.\n"); + return false; + } + + psMetadataItem *defItem = psMetadataLookup(defaults, concept->name); + bool status = false; // Result of checking the database + if (defItem) { + if (defItem->type == PS_DATA_METADATA) { + // A dependent default + psTrace(__func__, 7, "Evaluating dependent default....\n"); + psMetadata *dependents = defItem->data.V; // The list of dependents + // Find out what it depends on + psString dependName = psStringCopy(concept->name); + psStringAppend(&dependName, ".DEPEND"); + psString dependsOn = psMetadataLookupStr(&mdOK, defaults, dependName); + if (! mdOK) { + psError(PS_ERR_IO, false, "Unable to find %s in camera configuration for dependent default" + " --- ignored\n", dependName); + // XXX: Need to clean up before returning + return false; + } + psFree(dependName); + // Find the value of the dependent concept + psMetadataItem *depItem = p_pmFPAConceptGetFromHeader(fpa, chip, cell, dependsOn); + if (! depItem) { + psError(PS_ERR_IO, true, "Unable to find value for %s (required for %s)\n", dependsOn, + concept->name); + return false; + } + if (depItem->type != PS_DATA_STRING) { + psError(PS_ERR_IO, true, "Value of %s is not of type string, as required for dependency" + " --- ignored.\n", dependsOn); + } + + defItem = psMetadataLookup(dependents, depItem->data.V); // This is now what we were after + } + + status = compareConcepts(defItem, concept); + if (! status) { + psError(PS_ERR_IO, true, "Concept %s is specified by default in the camera configuration, " + "but doesn't match the actual value.\n", concept->name); + } + } + + // XXX: Need to clean up before returning + return status; +} + + +// XXX: Not tested at all +static bool setConceptInDB(pmFPA *fpa, // The FPA that contains the chip + pmChip *chip, // The chip that contains the cell + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadataItem *concept // Concept + ) +{ + if (! db) { + // No database initialised + return false; + } + + bool mdStatus = true; // Status of MD lookup + psMetadata *database = psMetadataLookupMD(&mdStatus, fpa->camera, "DATABASE"); + if (! mdStatus) { + // No error, because not everyone needs to use the DB + return NULL; + } + + psMetadata *dbLookup = psMetadataLookupMD(&mdStatus, database, concept->name); + if (dbLookup) { + const char *tableName = psMetadataLookupStr(&mdStatus, dbLookup, "TABLE"); // Name of the table + // const char *colName = psMetadataLookupStr(&mdStatus, dbLookup, "COLUMN"); // Name of the column + const char *givenCols = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENDBCOL"); // Name of "where" + // columns + const char *givenPS = psMetadataLookupStr(&mdStatus, dbLookup, "GIVENPS"); // Values for "where" + // columns + + // Now, need to get the "given"s + if (strlen(givenCols) || strlen(givenPS)) { + psList *cols = psStringSplit(givenCols, ",;"); // List of column names + psList *values = psStringSplit(givenPS, ",;"); // List of value names for the columns + psMetadata *selection = psMetadataAlloc(); // The stuff to select in the DB + if (cols->n != values->n) { + psLogMsg(__func__, PS_LOG_WARN, "The GIVENDBCOL and GIVENPS entries for %s do not have " + "the same number of entries --- ignored.\n", concept); + } else { + // Iterators for the lists + psListIterator *colsIter = psListIteratorAlloc(cols, PS_LIST_HEAD, false); + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); + char *column = NULL; // Name of the column + while ((column = psListGetAndIncrement(colsIter))) { + char *name = psListGetAndIncrement(valuesIter); // Name for the value + if (!strlen(column) || !strlen(name)) { + psLogMsg(__func__, PS_LOG_WARN, "One of the columns or value names for %s is " + " empty --- ignored.\n", concept); + } else { + // Search for the value name + psMetadataItem *item = p_pmFPAConceptGetFromHeader(fpa, chip, cell, name); + if (! item) { + item = p_pmFPAConceptGetFromDefault(fpa, chip, cell, name); + } + if (! item) { + psLogMsg(__func__, PS_LOG_ERROR, "Unable to find the value name %s for DB " + " lookup on %s --- ignored.\n", name, concept); + } else { + // We need to create a new psMetadataItem. I don't think we can't simply hack + // the existing one, since that could conceivably cause memory leaks + psMetadataItem *newItem = psMetadataItemAlloc(concept->name, item->type, + item->comment, item->data.V); + psMetadataAddItem(selection, newItem, PS_LIST_TAIL, PS_META_REPLACE); + psFree(newItem); + } + } + psFree(name); + psFree(column); + } // Iterating through the columns + psFree(colsIter); + psFree(valuesIter); + + // Check first to make sure we're only going to touch one row + psArray *dbResult = psDBSelectRows(db, tableName, selection, 2); // Lookup result + // Note that we use limit=2 in order to test if there are multiple rows returned + if (! dbResult || dbResult->n == 0) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find any rows in DB for %s --- ignored\n", + concept->name); + return false; + } else { + if (dbResult->n > 1) { + psLogMsg(__func__, PS_LOG_WARN, "Multiple rows returned in DB lookup for %s --- " + " ignored.\n", concept->name); + } + // Update the DB + psMetadata *update = psMetadataAlloc(); + psMetadataAddItem(update, concept, PS_LIST_HEAD, 0); + psDBUpdateRows(db, tableName, selection, update); + psFree(update); + return true; + } + } + psFree(cols); + psFree(values); + } + } // Doing the "given"s. + + psAbort(__func__, "Shouldn't ever get here?\n"); + return false; +} + + +// Concept set from item +static bool setConceptItem(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadataItem *concept // Concept item + ) +{ + // Try headers, database, defaults in order + psTrace(__func__, 3, "Trying to set concept %s...\n", concept->name); + bool status = setConceptInCamera(cell, concept); // Status for return + if (! status) { + psTrace(__func__, 5, "Trying header....\n"); + status = setConceptInHeader(fpa, chip, cell, concept); + } + if (! status) { + psTrace(__func__, 5, "Trying database....\n"); + status = setConceptInDB(fpa, chip, cell, db, concept); + } + if (! status) { + psTrace(__func__, 5, "Checking defaults....\n"); + status = setConceptInDefault(fpa, chip, cell, concept); + } + + if (! status) { + psError(PS_ERR_IO, true, "Unable to set %s (%s).\n", concept->name, concept->comment); + } + + return status; +} + + +// Concept set +static bool setConcept(pmFPA *fpa, // The FPA + pmChip *chip,// The chip + pmCell *cell, // The cell + psDB *db, // DB handle + psMetadata *concepts, // Concepts MD from which to set + const char *name // Name of the concept + ) +{ + psMetadataItem *concept = psMetadataLookup(concepts, name); + if (! concept) { + psError(PS_ERR_IO, true, "No such concept as %s\n", name); + return false; + } + return setConceptItem(fpa, chip, cell, db, concept); +} + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Outget concepts from the FPA +void pmFPAOutgestConcepts(pmFPA *fpa, // The FPA + psDB *db // DB handle + ) +{ + // FPA.NAME + setConcept(fpa, NULL, NULL, db, fpa->concepts, "FPA.NAME"); + + // FPA.AIRMASS + setConcept(fpa, NULL, NULL, db, fpa->concepts, "FPA.AIRMASS"); + + // FPA.FILTER + setConcept(fpa, NULL, NULL, db, fpa->concepts, "FPA.FILTER"); + + // FPA.POSANGLE + setConcept(fpa, NULL, NULL, db, fpa->concepts, "FPA.POSANGLE"); + + // FPA.RADECSYS + setConcept(fpa, NULL, NULL, db, fpa->concepts, "FPA.RADECSYS"); + + // These take some extra work + + // FPA.RA + { + double ra = psMetadataLookupF64(NULL, fpa->concepts, "FPA.RA"); // The RA + + // How to interpret the RA + const psMetadata *camera = fpa->camera; // Camera configuration data + bool mdok = true; // Status of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, camera, "FORMATS"); + if (mdok && formats) + { + psString raFormat = psMetadataLookupStr(&mdok, formats, "FPA.RA"); + if (mdok && strlen(raFormat) > 0) { + if (strcasecmp(raFormat, "HOURS") == 0) { + ra /= M_PI / 12.0; + } else if (strcasecmp(raFormat, "DEGREES") == 0) { + ra /= M_PI / 180.0; + } else if (strcasecmp(raFormat, "RADIANS") == 0) { + // No action required + } else { + psLogMsg(__func__, PS_LOG_WARN, "Don't understand FPA.RA in FORMATS (%s) --- assuming" + " HOURS.\n"); + ra /= M_PI / 12.0; + } + } else { + psError(PS_ERR_IO, false, "Unable to find FPA.RA in FORMATS --- assuming HOURS.\n"); + ra /= M_PI / 12.0; + } + } else + { + psError(PS_ERR_IO, false, "Unable to find FORMAT metadata in camera configuration --- " + "assuming format for FPA.RA is HOURS.\n"); + ra /= M_PI / 12.0; + } + + // We choose to write sexagesimal format + int big, medium; + float small; + big = (int)ra; + medium = (int)(60.0*(ra - (double)big)); + small = 3600.0*(ra - (double)big - 60.0 * (double)medium); + psString raString = psStringCopy(""); + psStringAppend(&raString, "%d:%d:%.2f", big, medium, small); + psMetadataItem *raItem = psMetadataItemAllocStr("FPA.RA", "Right Ascension of the boresight", + raString); + setConceptItem(fpa, NULL, NULL, db, raItem); + psFree(raItem); + psFree(raString); + } + + // FPA.DEC + { + double dec = psMetadataLookupF64(NULL, fpa->concepts, "FPA.DEC"); // The DEC + + // How to interpret the DEC + const psMetadata *camera = fpa->camera; // Camera configuration data + bool mdok = true; // Status of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, camera, "FORMATS"); + if (mdok && formats) + { + psString decFormat = psMetadataLookupStr(&mdok, formats, "FPA.DEC"); + if (mdok && strlen(decFormat) > 0) { + if (strcasecmp(decFormat, "HOURS") == 0) { + dec /= M_PI / 12.0; + } else if (strcasecmp(decFormat, "DEGREES") == 0) { + dec /= M_PI / 180.0; + } else if (strcasecmp(decFormat, "RADIANS") == 0) { + // No action required + } else { + psLogMsg(__func__, PS_LOG_WARN, "Don't understand FPA.DEC in FORMATS (%s) --- assuming" + " DEGREES.\n"); + dec /= M_PI / 180.0; + } + } else { + psError(PS_ERR_IO, false, "Unable to find FPA.DEC in FORMATS --- assuming DEGREES.\n"); + dec /= M_PI / 180.0; + } + } else + { + psError(PS_ERR_IO, false, "Unable to find FORMAT metadata in camera configuration --- " + "assuming format for FPA.DEC is HOURS.\n"); + dec /= M_PI / 12.0; + } + + // We choose to write sexagesimal format + int big, medium; + float small; + big = (int)dec; + medium = (int)(60.0*(dec - (double)big)); + small = 3600.0*(dec - (double)big - 60.0 * (double)medium); + psString decString = psStringCopy(""); + psStringAppend(&decString, "%d:%d:%.2f", big, medium, small); + psMetadataItem *decItem = psMetadataItemAllocStr("FPA.DEC", "Right Ascension of the boresight", + decString); + setConceptItem(fpa, NULL, NULL, db, decItem); + psFree(decItem); + psFree(decString); + + } + + // Pau. +} + + +// Outgest concepts for the chip +void pmChipOutgestConcepts(pmChip *chip, // The chip + psDB *db // DB handle + ) +{ + // pmFPA *fpa = chip->parent; // The parent FPA + + // CHIP.NAME --- no need to do anything + + // Pau. +} + + +// Outgest concepts for the cell +void pmCellOutgestConcepts(pmCell *cell, // The cell + psDB *db // DB handle + ) +{ + pmChip *chip = cell->parent; // The parent chip + pmFPA *fpa = chip->parent; // The parent FPA + + // CELL.NAME --- no need to do anything + + // CELL.GAIN + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.GAIN"); + + // CELL.READNOISE + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.READNOISE"); + + // CELL.SATURATION + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.SATURATION"); + + // CELL.BAD + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.BAD"); + + // CELL.XPARITY + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.XPARITY"); + + // CELL.YPARITY + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.YPARITY"); + + // CELL.READDIR + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.READDIR"); + + // These used to be pmReadoutGetExposure and pmReadoutGetDarkTime, but that doesn't really make sense at + // the moment. Maybe we need to add a "parent" link to the readouts. But then how are the exposure times + // REALLY derived? They're not in the FITS headers, because a readout is a plane in a 3D image. We'll + // have to dream up some additional suffix to specify these, but for now.... + + // CELL.EXPOSURE (used to be READOUT.EXPOSURE) + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.EXPOSURE"); + + // CELL.DARKTIME (used to be READOUT.DARKTIME) + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.DARKTIME"); + + // These take some extra work + + // CELL.TRIMSEC + { + psMetadataItem *trimsecItem = psMetadataLookup(cell->concepts, "CELL.TRIMSEC"); + psRegion *trimsec = trimsecItem->data.V; // The trimsec region + psMetadataItem *sourceItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.TRIMSEC.SOURCE"); + if (! sourceItem) + { + psError(PS_ERR_IO, false, "Couldn't find CELL.TRIMSEC.SOURCE.\n"); + } else if (sourceItem->type != PS_DATA_STRING) + { + psError(PS_ERR_IO, true, "CELL.TRIMSEC.SOURCE is not of type STR (%x)\n", sourceItem->type); + } else + { + psString source = sourceItem->data.V; // The source string + + if (strcasecmp(source, "VALUE") == 0) { + // Check that it's the same value as stored in the camera + psString checkString = psMetadataLookupStr(NULL, cell->camera, "CELL.TRIMSEC"); + psRegion checkRegion = psRegionFromString(checkString); + if (! COMPARE_REGIONS(&checkRegion, trimsec)) { + psError(PS_ERR_IO, true, "Target CELL.TRIMSEC is specified by value, and values don't " + "match.\n"); + } + } else if (strcasecmp(source, "HEADER") == 0) { + // psString keyword = psMetadataLookupStr(NULL, cell->camera, "CELL.TRIMSEC"); + psMetadata *header = NULL; // The FITS header + if (cell->hdu) { + header = cell->hdu->header; + } else if (chip->hdu) { + header = chip->hdu->header; + } else if (fpa->hdu) { + header = fpa->hdu->header; + } + if (! header) { + psError(PS_ERR_IO, true, "Unable to find FITS header!\n"); + } else { + psMetadataAddItem(header, trimsecItem, PS_LIST_TAIL, PS_META_REPLACE); + } + } else { + psError(PS_ERR_IO, true, "CELL.TRIMSEC.SOURCE (%s) is not HEADER or VALUE.\n", source); + } + } + } + + // CELL.BIASSEC + { + psMetadataItem *biassecItem = psMetadataLookup(cell->concepts, "CELL.BIASSEC"); + psList *biassecs = biassecItem->data.V; // The biassecs region list + psMetadataItem *sourceItem = p_pmFPAConceptGet(fpa, chip, cell, db, "CELL.BIASSEC.SOURCE"); + if (! sourceItem) + { + psError(PS_ERR_IO, false, "Couldn't find CELL.BIASSEC.SOURCE.\n"); + } else if (sourceItem->type != PS_DATA_STRING) + { + psError(PS_ERR_IO, true, "CELL.BIASSEC.SOURCE is not of type STR (%x)\n", sourceItem->type); + } else + { + psString source = sourceItem->data.V; // The source string + + if (strcasecmp(source, "VALUE") == 0) { + // Check that it's the same value as stored in the camera + psString checkString = psMetadataLookupStr(NULL, cell->camera, "CELL.BIASSEC"); + psList *checkList = psStringSplit(checkString, " ;"); + if (biassecs->n != checkList->n) { + psError(PS_ERR_IO, true, "Target CELL.BIASSEC is specified by value, but number of " + "entries doesn't match.\n"); + } else { + // We don't care if the order matches or not + psVector *check = psVectorAlloc(biassecs->n, PS_TYPE_U8); // Vector to mark regions off + for (int i = 0; i < check->n; i++) { + check->data.U8[i] = 0; + } + psListIterator *biassecsIter = psListIteratorAlloc(biassecs, PS_LIST_HEAD, + false); // Iterator + psListIterator *checkListIter = psListIteratorAlloc(checkList, PS_LIST_HEAD, false); + psRegion *biassec = NULL; // Region from iteration + while ((biassec = psListGetAndIncrement(biassecsIter))) { + psListIteratorSet(checkListIter, PS_LIST_HEAD); + psString checkRegionString = NULL; // Region string from iteration + int i = 0; // Counter + while ((checkRegionString = psListGetAndIncrement(checkListIter))) { + psRegion checkRegion = psRegionFromString(checkRegionString); + psTrace(__func__, 7, "Checking [%.0f:%.0f,%.0f:%.0f] against " + "[%.0f:%.0f,%.0f:%.0f]\n", biassec->x0, biassec->x1, biassec->y0, + biassec->y1, checkRegion.x0, checkRegion.x1, checkRegion.y0, + checkRegion.y1); + if (COMPARE_REGIONS(biassec, &checkRegion)) { + check->data.U8[i] = 1; + i++; + break; + } + i++; + } + } + for (int i = 0; i < check->n; i++) { + if (check->data.U8[i] == 0) { + psError(PS_ERR_IO, true, "Target CELL.BIASSEC is specified by value, but values " + "don't match.\n"); + break; + } + } + psFree(checkListIter); + psFree(biassecsIter); + psFree(check); + } + psFree(checkList); + } else if (strcasecmp(source, "HEADER") == 0) { + psString keywordsString = psMetadataLookupStr(NULL, cell->camera, "CELL.BIASSEC"); + psList *keywords = psStringSplit(keywordsString, " ,;"); + if (biassecs->n != keywords->n) { + psError(PS_ERR_IO, true, "Target CELL.BIASSEC is sepcified by headers, but the number " + "of headers doesn't match.\n"); + } else { + psMetadata *header = NULL; // The FITS header + if (cell->hdu) { + header = cell->hdu->header; + } else if (chip->hdu) { + header = chip->hdu->header; + } else if (fpa->hdu) { + header = fpa->hdu->header; + } + if (! header) { + psError(PS_ERR_IO, true, "Unable to find FITS header!\n"); + } else { + psListIterator *keywordsIter = psListIteratorAlloc(keywords, PS_LIST_HEAD, false); + psListIterator *biassecsIter = psListIteratorAlloc(biassecs, PS_LIST_HEAD, false); + psString keyword = NULL; // Header keyword from list + while ((keyword = psListGetAndIncrement(keywordsIter))) { + // Update the header + psRegion *biassec = psListGetAndIncrement(biassecsIter); + psString biassecString = psRegionToString(*biassec); + psMetadataAdd(header, PS_LIST_TAIL, keyword, PS_DATA_STRING | PS_META_REPLACE, + "Bias section", biassecString); + psFree(biassecString); + } + psFree(keywordsIter); + psFree(biassecsIter); + } + } + psFree(keywords); + } else { + psError(PS_ERR_IO, true, "CELL.BIASSEC.SOURCE (%s) is not HEADER or VALUE.\n", source); + } + } + } + + // CELL.XBIN and CELL.YBIN + { + psMetadataItem *xBinItem = psMetadataLookup(cell->concepts, "CELL.XBIN"); // Binning factor in x + psMetadataItem *yBinItem = psMetadataLookup(cell->concepts, "CELL.YBIN"); // Binning factor in y + + // If these are specified by the header, we need to check to see if it's the same header keyword + const psMetadata *camera = fpa->camera; + psMetadata *translation = psMetadataLookupMD(NULL, camera, "TRANSLATION"); + psString xKeyword = psMetadataLookupStr(NULL, translation, "CELL.XBIN"); + psString yKeyword = psMetadataLookupStr(NULL, translation, "CELL.YBIN"); + if (strlen(xKeyword) > 0 && strcasecmp(xKeyword, yKeyword) != 0) + { + setConceptInHeader(fpa, chip, cell, xBinItem); + xBinItem = NULL; + } + if (strlen(yKeyword) > 0 && strcasecmp(xKeyword, yKeyword) != 0) + { + setConceptInHeader(fpa, chip, cell, yBinItem); + yBinItem = NULL; + } + if (strlen(xKeyword) > 0 && strlen(yKeyword) > 0 && strcasecmp(xKeyword, yKeyword) == 0) + { + psString binString = psStringCopy(""); + psStringAppend(&binString, "%d,%d", xBinItem->data.S32, yBinItem->data.S32); + psMetadataItem *binItem = psMetadataItemAllocStr(xKeyword, "Binning factor in x and y", + binString); + psFree(binString); + psMetadata *header = NULL; // The FITS header + if (cell->hdu) { + header = cell->hdu->header; + } else if (chip->hdu) { + header = chip->hdu->header; + } else if (fpa->hdu) { + header = fpa->hdu->header; + } + if (! header) { + psError(PS_ERR_IO, true, "Unable to find FITS header!\n"); + } else { + psMetadataAddItem(header, binItem, PS_LIST_TAIL, PS_META_REPLACE); + xBinItem = NULL; + yBinItem = NULL; + } + psFree(binItem); + } + + // Do it in the usual way if we have to + if (xBinItem) + { + setConceptItem(fpa, chip, cell, db, xBinItem); + } + if (yBinItem) + { + setConceptItem(fpa, chip, cell, db, yBinItem); + } + } + + // CELL.TIMESYS + { + psMetadataItem *sysItem = psMetadataLookup(cell->concepts, "CELL.TIMESYS"); + psString sys = NULL; // String to store + switch (sysItem->data.S32) + { + case PS_TIME_TAI: + sys = psStringCopy("TAI"); + break; + case PS_TIME_UTC: + sys = psStringCopy("UTC"); + break; + case PS_TIME_UT1: + sys = psStringCopy("UT1"); + break; + case PS_TIME_TT: + sys = psStringCopy("TT"); + break; + default: + sys = psStringCopy("Unknown"); + } + psMetadataItem *newItem = psMetadataItemAllocStr("CELL.TIMESYS", "Time system", sys); + setConceptItem(fpa, chip, cell, db, newItem); + psFree(newItem); + psFree(sys); + } + + // CELL.TIME + { + psMetadataItem *timeItem = psMetadataLookup(cell->concepts, "CELL.TIME"); + psTime *time = timeItem->data.V; // The time + psString dateTimeString = psTimeToISO(time); // String representation + + psMetadata *formats = psMetadataLookupMD(NULL, fpa->camera, "FORMATS"); + psString format = psMetadataLookupStr(NULL, formats, "CELL.TIME"); + + if (strlen(format) == 0) + { + // No format specified --> do it in the usual way (maybe it's a DB lookup) + psMetadataItem *newTimeItem = psMetadataItemAllocStr("CELL.TIME", "Time of observation", + dateTimeString); + setConceptItem(fpa, chip, cell, db, newTimeItem); + psFree(newTimeItem); + } else + { + if (strcasecmp(format, "ISO") == 0) { + // dateTimeString contains an ISO time + psMetadataItem *newTimeItem = psMetadataItemAllocStr("CELL.TIME", "Time of observation", + dateTimeString); + setConceptItem(fpa, chip, cell, db, newTimeItem); + psFree(newTimeItem); + } else if (strstr(format, "SEPARATE")) { + // We're working with two separate headers + psMetadata *header = NULL; // The FITS header + if (cell->hdu) { + header = cell->hdu->header; + } else if (chip->hdu) { + header = chip->hdu->header; + } else if (fpa->hdu) { + header = fpa->hdu->header; + } + if (! header) { + psError(PS_ERR_IO, true, "Unable to find FITS header!\n"); + } else { + // Get the headers + const psMetadata *camera = fpa->camera; + psMetadata *translation = psMetadataLookupMD(NULL, camera, "TRANSLATION"); + psString keywords = psMetadataLookupStr(NULL, translation, "CELL.TIME"); + psList *dateTimeKeywords = psStringSplit(keywords, " ,;"); + psString dateKeyword = psListGet(dateTimeKeywords, PS_LIST_HEAD); + psString timeKeyword = psListGet(dateTimeKeywords, PS_LIST_TAIL); + + psList *dateTime = psStringSplit(dateTimeString, " T"); // Find the middle T + psString dateString = psListGet(dateTime, PS_LIST_HEAD); + psString timeString = psListGet(dateTime, PS_LIST_TAIL); + + // XXX: Couldn't be bothered doing these right now + if (strstr(format, "PRE2000")) { + psError(PS_ERR_IO, true, "Don't you realise it's the twenty-first century?\n"); + } + if (strstr(format, "BACKWARDS")) { + psError(PS_ERR_IO, true, "You want it BACKWARDS? Not right now, thanks.\n"); + } + + psMetadataItem *dateItem = psMetadataItemAllocStr(dateKeyword, "Date of observation", + dateString); + psMetadataItem *timeItem = psMetadataItemAllocStr(timeKeyword, "Time of observation", + timeString); + psMetadataAddItem(header, dateItem, PS_LIST_TAIL, PS_META_REPLACE); + psMetadataAddItem(header, timeItem, PS_LIST_TAIL, PS_META_REPLACE); + + psFree(dateTimeKeywords); + psFree(dateTime); + psFree(dateItem); + psFree(timeItem); + } + } else if (strcasecmp(format, "MJD") == 0) { + double mjd = psTimeToMJD(time); + psMetadataItem *newTimeItem = psMetadataItemAllocF64("CELL.TIME", "MJD of observation", mjd); + setConceptItem(fpa, chip, cell, db, newTimeItem); + psFree(newTimeItem); + } else if (strcasecmp(format, "JD") == 0) { + double jd = psTimeToMJD(time); + psMetadataItem *newTimeItem = psMetadataItemAllocF64("CELL.TIME", "JD of observation", jd); + setConceptItem(fpa, chip, cell, db, newTimeItem); + psFree(newTimeItem); + } else { + psError(PS_ERR_IO, true, "Not sure how to outgest CELL.TIME (%s) --- trying " + "ISO\n", dateTimeString); + psMetadataItem *newTimeItem = psMetadataItemAllocStr("CELL.TIME", "Time of observation", + dateTimeString); + setConceptItem(fpa, chip, cell, db, newTimeItem); + psFree(newTimeItem); + } + } + + psFree(dateTimeString); + } + + // Remove corrective + { + const psMetadata *camera = fpa->camera; + bool mdok = false; // Result of MD lookup + psMetadata *formats = psMetadataLookupMD(&mdok, camera, "FORMATS"); + if (mdok && formats) + { + psString format = psMetadataLookupStr(&mdok, formats, "CELL.X0"); + if (mdok && strlen(format) > 0 && strcasecmp(format, "FORTRAN") == 0) { + psMetadataItem *cellx0 = psMetadataLookup(cell->concepts, "CELL.X0"); + cellx0->data.S32 += 1; + } + format = psMetadataLookupStr(&mdok, formats, "CELL.Y0"); + if (mdok && strlen(format) > 0 && strcasecmp(format, "FORTRAN") == 0) { + psMetadataItem *celly0 = psMetadataLookup(cell->concepts, "CELL.Y0"); + celly0->data.S32 += 1; + } + } + } + // CELL.X0 + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.X0"); + // CELL.Y0 + setConcept(fpa, chip, cell, db, cell->concepts, "CELL.Y0"); + + // Pau. +} + Index: trunk/psModules/src/astrom/pmFPAConceptsSet.h =================================================================== --- trunk/psModules/src/astrom/pmFPAConceptsSet.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAConceptsSet.h (revision 6872) @@ -0,0 +1,20 @@ +#ifndef PM_FPA_CONCEPTS_SET_H +#define PM_FPA_CONCEPTS_SET_H + +#include "pslib.h" +#include "pmAstrometry.h" + +void pmFPAOutgestConcepts(pmFPA *fpa, // The FPA + psDB *db // DB handle + ); +void pmChipOutgestConcepts(pmChip *chip, // The chip + psDB *db // DB handle + ); +void pmCellOutgestConcepts(pmCell *cell, // The cell + psDB *db // DB handle + ); + + + + +#endif Index: trunk/psModules/src/astrom/pmFPAConstruct.c =================================================================== --- trunk/psModules/src/astrom/pmFPAConstruct.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAConstruct.c (revision 6872) @@ -0,0 +1,777 @@ +#include +#include +#include +#include "pslib.h" +#include "psMetadataItemParse.h" + +#include "pmFPA.h" +#include "pmConcepts.h" +#include "pmFPAConstruct.h" +#include "pmFPAview.h" +#include "pmFPAUtils.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Read data for a particular cell from the camera format description +static psMetadata *getCellData(const psMetadata *format, // The camera format description + const char *cellName // The name of the cell + ) +{ + bool status = true; // Result of MD lookup + psMetadata *cells = psMetadataLookupMD(&status, format, "CELLS"); // The CELLS + if (! status) { + psError(PS_ERR_IO, false, "Unable to determine CELLS of camera.\n"); + return NULL; + } + + psMetadata *cellData = psMetadataLookupMD(&status, cells, cellName); // The data for the particular cell + if (!status || !cellData) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find specs for cell %s: ignored\n", cellName); + } + + return cellData; +} + +// Parse a list of first:second:third pairs in a string +static bool parseContent(psArray **first, // Array of the first values + psArray **second, // Array of the second values + psArray **third, // Array of the third values + const char *string // The string to parse + ) +{ + bool allOK = true; // Everything was OK? + psList *values = psStringSplit(string, " ,;"); // List of the parts + *first = psArrayAlloc(values->n); + *second = psArrayAlloc(values->n); + *third = psArrayAlloc(values->n); + int num = 0; + psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); // Iterator for values + psString value = NULL; // "first:second:third" string + while ((value = psListGetAndIncrement(valuesIter))) { + psList *firstSecondThird = psStringSplit(value, ":"); // List containing the first, second, third + psArray *fst = psListToArray(firstSecondThird); // An array representation + psFree(firstSecondThird); + psString firstPart = NULL; // The first part + psString secondPart = NULL; // The second part + psString thirdPart = NULL; // The third part + switch (firstSecondThird->n) { + case 1: + thirdPart = fst->data[0]; + break; + case 2: + secondPart = fst->data[0]; + thirdPart = fst->data[1]; + break; + case 3: + firstPart = fst->data[0]; + secondPart = fst->data[1]; + thirdPart = fst->data[2]; + break; + default: + psLogMsg(__func__, PS_LOG_WARN, "Badly formated specifier: %s --- ignored.\n", value); + allOK = false; + psFree(fst); + continue; + } + psArraySet(*first, num, firstPart); + psArraySet(*second, num, secondPart); + psArraySet(*third, num, thirdPart); + num++; + psFree(fst); + } + psFree(valuesIter); + psFree(values); + + return allOK; +} + +// Get the name of a PHU chip or cell from the header +static psString phuNameFromHeader(const char *name, // The name to lookup: "CELL.NAME" or "CHIP.NAME" + const psMetadata *fileInfo, // FILE within the camera format description + const psMetadata *header // Primary header + ) +{ + bool mdok = true; // Result of MD lookup + psString keyword = psMetadataLookupStr(&mdok, fileInfo, name); + if (!mdok || strlen(keyword) == 0) { + return false; + } + psMetadataItem *resultItem = psMetadataLookup(header, keyword); + if (! resultItem) { + psError(PS_ERR_IO, false, "Unable to find %s in primary header to identify %s.\n", keyword, name); + return NULL; + } + return psMetadataItemParseString(resultItem); +} + +// Add an HDU to the FPA +static bool addHDUtoFPA(pmFPA *fpa, // FPA to which to add + pmHDU *hdu // HDU to be added + ) +{ + assert(fpa); + assert(hdu); + + if (fpa->hdu) { + // Something's already here + if (fpa->hdu != hdu) { + psError(PS_ERR_IO, true, "Unable to add HDU since FPA already has one.\n"); + } + return false; + } + fpa->hdu = psMemIncrRefCounter(hdu); + if (hdu->header) { + pmConceptsReadFPA(fpa, PM_CONCEPT_SOURCE_HEADER, NULL); + } + pmFPASetFileStatus(fpa, true); + + return true; +} + +// Add an HDU to the chip +static bool addHDUtoChip(pmChip *chip, // Chip to which to add + pmHDU *hdu // HDU to be added + ) +{ + assert(chip); + assert(hdu); + + if (chip->hdu) { + // Something's already here + if (chip->hdu != hdu) { + psError(PS_ERR_IO, true, "Unable to add HDU since chip already has one.\n"); + } + return false; + } + chip->hdu = psMemIncrRefCounter(hdu); + if (hdu->header) { + pmConceptsReadChip(chip, PM_CONCEPT_SOURCE_HEADER, true, NULL); + } + pmChipSetFileStatus(chip, true); + + return true; +} + +// Add an HDU to the cell +static bool addHDUtoCell(pmCell *cell, // Cell to which to add + pmHDU *hdu // HDU to be added + ) +{ + assert(cell); + assert(hdu); + + if (cell->hdu) { + // Something's already here + if (cell->hdu != hdu) { + psError(PS_ERR_IO, true, "Unable to add HDU since cell already has one.\n"); + } + return false; + } + cell->hdu = psMemIncrRefCounter(hdu); + if (hdu->header) { + pmConceptsReadCell(cell, PM_CONCEPT_SOURCE_HEADER, true, NULL); + } + pmCellSetFileStatus(cell, true); + + return true; +} + + +// Looks up the particular content based on the header +static const char *getContent(psMetadata *fileInfo, // The FILE from the camera format configuration + psMetadata *contents, // The CONTENTS from the camera format configuration + psMetadata *header // The (primary) header + ) +{ + bool mdok = true; // Status of MD lookup + const char *contentHeaders = psMetadataLookupStr(&mdok, fileInfo, "CONTENT"); // Headers for content + if (!mdok || !contentHeaders || strlen(contentHeaders) == 0) { + psError(PS_ERR_IO, true, "Unable to find CONTENT in FILE within camera format configuration.\n"); + return NULL; + } + + psList *keywords = psStringSplit(contentHeaders, " ,;"); // List of keywords + psListIterator *keywordsIter = psListIteratorAlloc(keywords, PS_LIST_HEAD, false); // Iterator + psString keyword = NULL; // Keyword, from iteration + psString contentsKey = NULL; // Key to the CONTENTS menu + bool first = true; // Is it the first value? + while ((keyword = psListGetAndIncrement(keywordsIter))) { + const char *value = psMetadataLookupStr(&mdok, header, keyword); + if (first) { + psStringAppend(&contentsKey, "%s", value); + first = false; + } else { + psStringAppend(&contentsKey, "_%s", value); + } + } + psFree(keywordsIter); + psFree(keywords); + psTrace(__func__, 5, "Looking up %s in the CONTENTS.\n", contentsKey); + const char *content = psMetadataLookupStr(&mdok, contents, contentsKey); + if (!mdok || !content || strlen(content) == 0) { + psError(PS_ERR_IO, true, "Unable to find %s in the CONTENTS.\n", contentsKey); + return NULL; + } + psFree(contentsKey); + + return content; +} + + +// Given a (string) list of contents "chip:cell:type chip:cell:type", put the HDU in the correct place and +// plug in the cell configuration information +static int processContents(pmFPA *fpa, // The FPA + pmChip *chip, // The chip, or NULL + pmCell *cell, // The cell, or NULL + pmHDU *hdu, // The HDU to be added + pmFPALevel level, // The level at which to add the HDU + const char *contents, // The contents line, consisting of a list of chip:cell + psMetadata *format // Camera format configuration + ) +{ + assert(fpa); + assert(contents && strlen(contents) > 0); + assert(!cell || (cell && chip)); // Need both chip and cell if given a cell + + if (hdu && level == PM_FPA_LEVEL_FPA) { + addHDUtoFPA(fpa, hdu); + } + + // Parse the list of chip:cell:type + psArray *chips = NULL; // The chips (first bits) + psArray *cells = NULL; // The cells (second bits) + psArray *types = NULL; // The cell types (third bits) + int numCells = 0; // Number of cells processed + parseContent(&chips, &cells, &types, contents); + for (int i = 0; i < types->n; i++) { + psString chipName = chips->data[i]; // The name of the chip + psString cellName = cells->data[i]; // The name of the cell + psString cellType = types->data[i]; // The type of the cell + + // Get the chip + pmChip *newChip = NULL; // The chip specified + if (chip) { + newChip = chip; + } else if (chipName) { + // Find the chip + int chipNum = pmFPAFindChip(fpa, chipName); // The chip we're looking for + if (chipNum == -1) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find chip %s in fpa --- ignored.\n", chipName); + continue; + } + newChip = fpa->chips->data[chipNum]; + } + + if (!newChip) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to determine chip for entry %d of content (follows) --- " + "ignored.\n\t%s", i, contents); + continue; + } + + // Get the cell + pmCell *newCell = NULL; // The cell specified + if (cell) { + newCell = cell; + } else if (cellName) { + // Find the cell + int cellNum = pmChipFindCell(newChip, cellName); // The cell we're looking for + if (cellNum == -1) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find cell %s in chip %s --- ignored.\n", + cellName, chipName); + continue; + } + newCell = newChip->cells->data[cellNum]; + } + if (!newCell) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to determine cell for entry %d of content (follows) --- " + "ignored.\n\t%s", i, contents); + continue; + } + + // Get the type + if (!cellType) { + psLogMsg(__func__, PS_LOG_WARN, "Unable to determine cell type for entry %d of content (follows) " + "--- ignored.\n\t%s", i, contents); + continue; + } + psMetadata *cellData = getCellData(format, cellType); // Data for this cell + + // Put in the HDU + if (hdu && level == PM_FPA_LEVEL_CHIP) { + addHDUtoChip(newChip, hdu); + } + if (hdu && level == PM_FPA_LEVEL_CELL) { + addHDUtoCell(newCell, hdu); + } + + // Put in the cell data + if (newCell->config) { + psLogMsg(__func__, PS_LOG_WARN, "Overwriting cell data in chip %s, cell %s\n", chipName, + cellName); + psFree(newCell->config); // Make way! + } + newCell->config = psMemIncrRefCounter(cellData); + pmConceptsReadCell(newCell, PM_CONCEPT_SOURCE_CAMERA | PM_CONCEPT_SOURCE_DEFAULTS, false, NULL); + numCells++; + } + psFree(chips); + psFree(cells); + psFree(types); + + return numCells; +} + +static pmFPALevel hduLevel(psMetadata *format // The camera format configuration + ) +{ + bool mdok = true; // Status of MD lookup + psMetadata *file = psMetadataLookupMD(&mdok, format, "FILE"); // File information + if (!mdok || !file) { + psError(PS_ERR_IO, true, "Unable to find FILE information in camera format configuration.\n"); + return PM_FPA_LEVEL_NONE; + } + const char *extType = psMetadataLookupStr(&mdok, file, "EXTENSIONS"); + if (!mdok || !extType || strlen(extType) == 0) { + psError(PS_ERR_IO, true, "Unable to find EXTENSIONS in the FILE information in the camera format" + " configuration.\n"); + return PM_FPA_LEVEL_NONE; + } + + // Where do we stick in the HDUs? + pmFPALevel level = PM_FPA_LEVEL_NONE; // Level for HDU insertion + if (strcasecmp(extType, "CHIP") == 0) { + level = PM_FPA_LEVEL_CHIP; + } else if (strcasecmp(extType, "CELL") == 0) { + level = PM_FPA_LEVEL_CELL; + } else if (strcasecmp(extType, "NONE") != 0) { + psError(PS_ERR_IO, true, "EXTENSIONS is not CHIP or CELL or NONE.\n"); + } + + return level; +} + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Construct an FPA instance on the basis of a camera configuration +pmFPA *pmFPAConstruct(const psMetadata *camera // The camera configuration + ) +{ + pmFPA *fpa = pmFPAAlloc(camera); // The FPA to fill out + + bool mdok = true; // Status from MD lookups + psMetadata *components = psMetadataLookupMD(&mdok, camera, "FPA"); // FPA components + psMetadataIterator *componentsIter = psMetadataIteratorAlloc(components, PS_LIST_HEAD, NULL); + psMetadataItem *componentsItem = NULL; // Item from components + while ((componentsItem = psMetadataGetAndIncrement(componentsIter))) { + const char *chipName = componentsItem->name; // Name of the chip + if (componentsItem->type != PS_DATA_STRING) { + psLogMsg(__func__, PS_LOG_WARN, "Element %s in FPA within the camera configuration is not of " + "type STR (type=%x) --- ignored.\n", chipName, componentsItem->type); + continue; + } + pmChip *chip = pmChipAlloc(fpa, chipName); // The chip + psList *cellNames = psStringSplit(componentsItem->data.V, " ,;"); // List of cell names + psListIterator *cellNamesIter = psListIteratorAlloc(cellNames, PS_LIST_HEAD, false); // Iterator + psString cellName = NULL; // Name of cell + while ((cellName = psListGetAndIncrement(cellNamesIter))) { + pmCell *cell = pmCellAlloc(chip, cellName); // New cell + psFree(cell); // Drop reference + } + psFree(chip); // Drop reference + psFree(cellNamesIter); + psFree(cellNames); + } + psFree(componentsIter); + + return fpa; +} + +bool pmFPAAddSourceFromView(pmFPA *fpa, // The FPA + const pmFPAview *phuView, // The view, corresponding to the PHU + psMetadata *format // Format of file + ) +{ + assert(fpa); + assert(phuView); + assert(format); + + // Where does the PHU go? + bool mdok = true; // Status of MD lookup + psMetadata *fileInfo = psMetadataLookupMD(&mdok, format, "FILE"); // File information from the format + if (!mdok || !fileInfo) { + psError(PS_ERR_IO, false, "Unable to find FILE information in the camera format configuration.\n"); + return false; + } + const char *phuType = psMetadataLookupStr(&mdok, fileInfo, "PHU"); // What is the PHU? + if (!mdok || strlen(phuType) == 0) { + psError(PS_ERR_IO, false, "Unable to find PHU in the FILE information of the camera format.\n"); + return false; + } + + // Generate the PHU + pmHDU *phdu = pmHDUAlloc("PHU"); // The primary header data unit + phdu->format = psMemIncrRefCounter(format); + + // Put in the PHU + pmChip *chip = NULL; // The chip that corresponds to the PHU + pmCell *cell = NULL; // The cell that corresponds to the PHU + if (strcasecmp(phuType, "FPA") == 0) { + addHDUtoFPA(fpa, phdu); + psFree(phdu); + } else { + psArray *chips = fpa->chips; // Array of chips + if (phuView->chip < 0 || phuView->chip > chips->n) { + psError(PS_ERR_IO, true, "PHU specified by the camera format requires specification of a " + "particular chip, which cannot be determined from the view (%d).\n", phuView->chip); + psFree(phdu); + return false; + } + chip = chips->data[phuView->chip]; + if (strcasecmp(phuType, "CHIP") == 0) { + addHDUtoChip(chip, phdu); + psFree(phdu); + } else if (strcasecmp(phuType, "CELL") == 0) { + psArray *cells = chip->cells; // Array of cells + if (phuView->cell < 0 || phuView->cell > cells->n) { + psError(PS_ERR_IO, true, "PHU specified by the camera format requires specification of a " + "particular cell, which cannot be determined from the view (%d).\n", phuView->cell); + psFree(phdu); + return false; + } + addHDUtoCell(cell, phdu); + psFree(phdu); + } else { + psError(PS_ERR_IO, true, "PHU in the camera configuration format is not FPA, CHIP or CELL.\n"); + psFree(phdu); + return false; + } + } + + // Put in the extensions + pmFPALevel level = hduLevel(format);// The level for the HDUs to go + if (level == PM_FPA_LEVEL_NONE) { + // No extensions --- we're done + return true; + } + psMetadata *contents = psMetadataLookupMD(&mdok, format, "CONTENTS"); // The contents of the FITS file + if (!mdok || !contents) { + psError(PS_ERR_IO, false, "Unable to find CONTENTS in the camera format configuration.\n"); + return false; + } + + psMetadataIterator *contentsIter = psMetadataIteratorAlloc(contents, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *contentsItem = NULL;// Item from the contents iteration + while ((contentsItem = psMetadataGetAndIncrement(contentsIter))) { + if (contentsItem->type != PS_DATA_STRING) { + psLogMsg(__func__, PS_LOG_WARN, "Content item %s is not of type STR --- ignored.\n", + contentsItem->name); + continue; + } + pmHDU *hdu = pmHDUAlloc(contentsItem->name); // HDU to add + hdu->format = psMemIncrRefCounter(format); + const char *content = contentsItem->data.V; // The content data + processContents(fpa, chip, cell, hdu, level, content, format); + psFree(hdu); + } + psFree(contentsIter); + + return true; +} + + + +// Add an input file to the FPA +pmFPAview *pmFPAAddSourceFromHeader(pmFPA *fpa, // The FPA + psMetadata *phu, // Primary header of file + psMetadata *format // Format of file + ) +{ + assert(fpa); + assert(phu); + assert(format); + + bool mdok = true; // Status from metadata lookups + psMetadata *fileInfo = psMetadataLookupMD(&mdok, format, "FILE"); // The file information + if (!mdok || !fileInfo) { + psError(PS_ERR_IO, false, "Unable to find FILE in the camera format configuration.\n"); + return NULL; + } + + // Check the name of the FPA + psString newFPAname = phuNameFromHeader("FPA.NAME", fileInfo, phu); // New name for the FPA + const char *currentFPAname = psMetadataLookupStr(&mdok, fpa->concepts, "FPA.NAME"); // Current name + if (mdok && currentFPAname && strlen(currentFPAname) > 0 && strcmp(currentFPAname, newFPAname) != 0) { + psLogMsg(__func__, PS_LOG_WARN, "FPA.NAME for new source (%s) doesn't match FPA.NAME for current " + "fpa (%s).\n", newFPAname, currentFPAname); + } + psMetadataAddStr(fpa->concepts, PS_LIST_HEAD, "FPA.NAME", PS_META_REPLACE, "Name of FPA", newFPAname); + psFree(newFPAname); // Drop reference + + // Where does the PHU go? + const char *phuType = psMetadataLookupStr(&mdok, fileInfo, "PHU"); // What is the PHU? + if (!mdok || strlen(phuType) == 0) { + psError(PS_ERR_IO, false, "Unable to find PHU in the format specification.\n"); + return NULL; + } + pmHDU *phdu = pmHDUAlloc("PHU"); // The primary header data unit + phdu->header = psMemIncrRefCounter(phu); + phdu->format = psMemIncrRefCounter(format); + // Generate the view + pmFPAview *view = pmFPAviewAlloc(0); // The FPA view corresponding to the PHU, to be returned + view->chip = -1; + view->cell = -1; + view->readout = -1; + + // And what are the individual extensions? + const char *extType = psMetadataLookupStr(&mdok, fileInfo, "EXTENSIONS"); // What's in the extns? + if (!mdok || strlen(extType) == 0) { + psError(PS_ERR_IO, false, "Unable to find EXTENSIONS in the format specification.\n"); + psFree(view); + return NULL; + } + + + // This is a special case: PHU=FPA and EXTENSIONS=NONE. The only reason to do this is in the case of + // single CCD imagers, where the entire FPA is in the PHU image. In this case, the CONTENTS is of type + // STR (rather than METADATA), and has the usual chip:cell. + if (strcasecmp(phuType, "FPA") == 0 && strcasecmp(extType, "NONE") == 0) { + const char *contents = psMetadataLookupStr(&mdok, format, "CONTENTS"); // The contents of the file + if (!mdok || !contents || strlen(contents) == 0) { + psError(PS_ERR_IO, true, "Unable to find CONTENTS in the camera format configuration.\n"); + psFree(view); + return NULL; + } + + processContents(fpa, NULL, NULL, phdu, PM_FPA_LEVEL_FPA, contents, format); + psFree(phdu); + return view; + } + + // In all other cases, the CONTENTS is of type METADATA, and is either a menu if EXTENSIONS=NONE, or + // a list of extensions otherwise. + psMetadata *contents = psMetadataLookupMD(&mdok, format, "CONTENTS"); // The contents of the FITS file + if (!mdok || !contents) { + psError(PS_ERR_IO, false, "Unable to find CONTENTS in the camera format configuration.\n"); + psFree(view); + return NULL; + } + + // No extensions --- only have the PHU. In this case, the CONTENTS is a menu, with CONTENT indicating + // header keywords that provides a key to the CONTENTS menu. + if (strcasecmp(extType, "NONE") == 0) { + // We have already dealt with the case PHU=FPA, in a special case, above. + const char *content = getContent(fileInfo, contents, phu); // The content: string of chip:cell pairs + + // Need to look up what chip we have. + psString chipName = phuNameFromHeader("CHIP.NAME", fileInfo, phu); + psTrace(__func__, 5, "This is chip %s\n", chipName); + int chipNum = pmFPAFindChip(fpa, chipName); // Chip number + if (chipNum == -1) { + psError(PS_ERR_IO, true, "Unable to find chip %s in FPA.\n", chipName); + psFree(view); + return NULL; + } + pmChip *chip = fpa->chips->data[chipNum]; // Chip of interest + view->chip = chipNum; + + pmCell *cell = NULL; // Cell of interest + + pmFPALevel level = PM_FPA_LEVEL_NONE; // Level for HDU to be added + if (strcasecmp(phuType, "CHIP") == 0) { + level = PM_FPA_LEVEL_CHIP; + } else if (strcasecmp(phuType, "CELL") == 0) { + level = PM_FPA_LEVEL_CELL; + // Need to look up what cell we have. + psString cellName = phuNameFromHeader("CELL.NAME", fileInfo, phu); + int cellNum = pmChipFindCell(chip, cellName); // Cell number + if (cellNum == -1) { + psError(PS_ERR_IO, true, "Unable to find cell %s in chip %s.\n", cellName, chipName); + psFree(view); + return NULL; + } + cell = chip->cells->data[cellNum]; + view->cell = cellNum; + psFree(cellName); + } else { + psError(PS_ERR_IO, true, "PHU is not FPA, CHIP or CELL.\n"); + psFree(view); + return NULL; + } + psFree(chipName); + + processContents(fpa, chip, cell, phdu, level, content, format); + psFree(phdu); + return view; + } + + + // From here on, we have extensions that we iterate through. The CONTENTS is a list of extensions. + pmChip *chip = NULL; // The chip of interest + pmCell *cell = NULL; // The cell of interest + + // First, put in the PHU + if (strcasecmp(phuType, "FPA") == 0) { + addHDUtoFPA(fpa, phdu); + } else { + // Get the chip + psString chipName = phuNameFromHeader("CHIP.NAME", fileInfo, phu); // Name of the chip + int chipNum = pmFPAFindChip(fpa, chipName); // Chip number + if (chipNum == -1) { + psError(PS_ERR_IO, true, "Unable to find chip %s in FPA.\n", chipName); + psFree(view); + return NULL; + } + chip = fpa->chips->data[chipNum]; // The specified chip + view->chip = chipNum; + + if (strcasecmp(phuType, "CHIP") == 0) { + addHDUtoChip(chip, phdu); + } else if (strcasecmp(phuType, "CELL") == 0) { + psString cellName = phuNameFromHeader("CELL.NAME", fileInfo, phu); // Name of the cell + int cellNum = pmChipFindCell(chip, cellName); // Cell number + if (cellNum == -1) { + psError(PS_ERR_IO, true, "Unable to find cell %s in chip %s.\n", cellName, chipName); + psFree(view); + return NULL; + } + cell = chip->cells->data[cellNum]; // The specified cell + view->cell = cellNum; + psFree(cellName); + + addHDUtoCell(cell, phdu); + } else { + psError(PS_ERR_IO, true, "The format of the PHU (%s) is not FPA, CHIP or CELL.\n", phuType); + psFree(view); + return NULL; + } + psFree(chipName); + } + psFree(phdu); + + pmFPALevel level = hduLevel(format);// The level at which to plug in HDU + + // Now go through the contents + psMetadataIterator *contentsIter = psMetadataIteratorAlloc(contents, PS_LIST_HEAD, NULL); + psMetadataItem *contentsItem = NULL; // Item from contents + while ((contentsItem = psMetadataGetAndIncrement(contentsIter))) { + const char *extName = contentsItem->name; + if (contentsItem->type != PS_DATA_STRING) { + psLogMsg(__func__, PS_LOG_WARN, "CONTENTS item %s is not of type STR --- ignored.\n", extName); + continue; + } + + pmHDU *hdu = pmHDUAlloc(extName); // The extension + hdu->format = psMemIncrRefCounter(format); + + processContents(fpa, chip, cell, hdu, level, contentsItem->data.V, format); + psFree(hdu); + } + psFree(contentsIter); + + pmConceptsReadFPA(fpa, PM_CONCEPT_SOURCE_DEFAULTS, NULL); + + return view; +} + + +// Print out the focal plane structure +void pmFPAPrint(pmFPA *fpa, // FPA to print + bool header, // Print headers? + bool concepts // Print concepts? + ) +{ + psTrace(__func__, 1, "FPA:\n"); + if (fpa->hdu) { + psTrace(__func__, 2, "---> FPA is extension %s.\n", fpa->hdu->extname); + if (! fpa->hdu->images) { + psTrace(__func__, 2, "---> NO PIXELS read in for extension %s\n", fpa->hdu->extname); + } + if (header) { + if (fpa->hdu->header) { + psTrace(__func__, 2, "---> Header:\n"); + psMetadataPrint(fpa->hdu->header, 8); + } else { + psTrace(__func__, 2, "---> NO HEADER read in for extension %s\n", fpa->hdu->extname); + } + } + } + if (concepts) { + psMetadataPrint(fpa->concepts, 2); + } + + psArray *chips = fpa->chips; // Array of chips + // Iterate over the FPA + for (int i = 0; i < chips->n; i++) { + psTrace(__func__, 3, "Chip: %d\n", i); + pmChip *chip = chips->data[i]; // The chip + if (chip->hdu) { + psTrace(__func__, 4, "---> Chip is extension %s.\n", chip->hdu->extname); + if (header) { + if (chip->hdu->header) { + psTrace(__func__, 4, "---> Header:\n"); + psMetadataPrint(chip->hdu->header, 8); + } else { + psTrace(__func__, 4, "---> NO HEADER read in for extension %s\n", chip->hdu->extname); + } + } + if (! chip->hdu->images) { + psTrace(__func__, 4, "---> NO PIXELS read in for extension %s\n", chip->hdu->extname); + } + } + if (concepts) { + psMetadataPrint(chip->concepts, 4); + } + + // Iterate over the chip + psArray *cells = chip->cells; // Array of cells + for (int j = 0; j < cells->n; j++) { + psTrace(__func__, 5, "Cell: %d\n", j); + pmCell *cell = cells->data[j]; // The cell + if (cell->hdu) { + psTrace(__func__, 6, "---> Cell is extension %s.\n", cell->hdu->extname); + if (header) { + if (cell->hdu->header) { + psTrace(__func__, 6, "---> Header:\n"); + psMetadataPrint(cell->hdu->header, 8); + } else { + psTrace(__func__, 6, "---> NO HEADER read in for extension %s\n", cell->hdu->extname); + } + } + if (! cell->hdu->images) { + psTrace(__func__, 6, "---> NO PIXELS read in for extension %s\n", cell->hdu->extname); + } + } + if (concepts) { + psMetadataPrint(cell->concepts, 6); + } + + psTrace(__func__, 7, "Readouts:\n"); + psArray *readouts = cell->readouts; // Array of readouts + for (int k = 0; k < readouts->n; k++) { + pmReadout *readout = readouts->data[k]; // The readout + psImage *image = readout->image; // The image + psList *bias = readout->bias; // The list of bias images + if (image) { + psTrace(__func__, 8, "Image: [%d:%d,%d:%d] (%dx%d)\n", image->col0, image->col0 + + image->numCols, image->row0, image->row0 + image->numRows, image->numCols, + image->numRows); + } + if (bias) { + psListIterator *biasIter = psListIteratorAlloc(bias, PS_LIST_HEAD, false); // Iterator + psImage *biasImage = NULL; // Bias image from iteration + while ((biasImage = psListGetAndIncrement(biasIter))) { + psTrace(__func__, 8, "Bias: [%d:%d,%d:%d] (%dx%d)\n", biasImage->col0, + biasImage->col0 + biasImage->numCols, biasImage->row0, + biasImage->row0 + biasImage->numRows, biasImage->numCols, biasImage->numRows); + } + psFree(biasIter); + } + } // Iterating over cell + } // Iterating over chip + } // Iterating over FPA + +} Index: trunk/psModules/src/astrom/pmFPAConstruct.h =================================================================== --- trunk/psModules/src/astrom/pmFPAConstruct.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAConstruct.h (revision 6872) @@ -0,0 +1,28 @@ +#ifndef PM_FPA_CONSTRUCT_H +#define PM_FPA_CONSTRUCT_H + +#include "pslib.h" +#include "pmFPA.h" +#include "pmFPAview.h" + +// Construct an FPA instance on the basis of a camera configuration +pmFPA *pmFPAConstruct(const psMetadata *camera // The camera configuration + ); + +bool pmFPAAddSourceFromView(pmFPA *fpa, // The FPA + const pmFPAview *phuView, // The view, corresponding to the PHU + psMetadata *format // Format of file + ); + +pmFPAview *pmFPAAddSourceFromHeader(pmFPA *fpa, // The FPA + psMetadata *phu, // Primary header of file + psMetadata *format // Format of file + ); + +// Print out the FPA +void pmFPAPrint(pmFPA *fpa, // FPA to print + bool header, // Print headers? + bool concepts // Print concepts? + ); + +#endif Index: trunk/psModules/src/astrom/pmFPACopy.c =================================================================== --- trunk/psModules/src/astrom/pmFPACopy.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPACopy.c (revision 6872) @@ -0,0 +1,692 @@ +#include +#include + +#include "pslib.h" +#include "psImageFlip.h" +#include "psRegionIsBad.h" + +#include "pmFPA.h" +#include "pmFPAUtils.h" +#include "pmHDU.h" +#include "pmHDUUtils.h" +#include "pmFPACopy.h" + +#define MAX(x,y) ((x) > (y) ? (x) : (y)) + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Add cells in a chip to a list +static bool addCellsFromChip(psList *list, // List of cells + const pmChip *chip // The chip from which to add cells + ) +{ + assert(list); + assert(chip); + + psArray *cells = chip->cells; // Array of cells + bool result = true; // Result of adding cells + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // A cell + result |= psListAdd(list, PS_LIST_TAIL, cell); + } + + return result; +} + +// Add cells in an FPA to a list +static bool addCellsFromFPA(psList *list, // List of cells + const pmFPA *fpa // The FPA from which to add cells + ) +{ + assert(list); + assert(fpa); + + psArray *chips = fpa->chips; // Array of chips + bool result = true; // Result of adding cells + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // A chip + result |= addCellsFromChip(list, chip); + } + + return result; +} + +// Get a list of cells that share the HDU for the target cell +static bool cellList(psList *targets, // The list of target cells + psList *sources, // The list of source cells + pmCell *targetCell, // The target cell + pmCell *sourceCell // The source cell + ) +{ + assert(targetCell); + assert(sourceCell); + + if (targetCell->hdu) { + if (targets) { + psListAdd(targets, PS_LIST_TAIL, targetCell); + } + if (sources) { + psListAdd(sources, PS_LIST_TAIL, sourceCell); + } + } else { + pmChip *targetChip = targetCell->parent; // The target parent chip + pmChip *sourceChip = sourceCell->parent; // The source parent chip + if (targetChip->hdu) { + if (targets) { + addCellsFromChip(targets, targetChip); + } + if (sources) { + addCellsFromChip(sources, sourceChip); + } + } else { + pmFPA *targetFPA = targetChip->parent; // The target parent FPA + pmFPA *sourceFPA = sourceChip->parent; // The source parent FPA + if (targetFPA->hdu) { + if (targets) { + addCellsFromFPA(targets, targetFPA); + } + if (sources) { + addCellsFromFPA(sources, sourceFPA); + } + } else { + psError(PS_ERR_IO, true, "Unable to find HDU for cell to generate list!\n"); + return false; + } + } + } + + return true; +} + +// Get the maximum extent of the HDU from the trimsec and biassecs +static bool sizeHDU(int *xSize, int *ySize, // Size of HDU + psList *cells // List of cells + ) +{ + psListIterator *cellsIter = psListIteratorAlloc(cells, PS_LIST_HEAD, false); // Iterator for cells + pmCell *cell = NULL; // The cell from iteration + bool mdok = true; // Status of MD lookup + *xSize = 0; + *ySize = 0; + while ((cell = psListGetAndIncrement(cellsIter))) { + psRegion *trimsec = psMetadataLookupPtr(&mdok, cell->concepts, "CELL.TRIMSEC"); // Trim section + if (mdok && trimsec && !psRegionIsBad(*trimsec)) { + *xSize = MAX(trimsec->x1, *xSize); + *ySize = MAX(trimsec->y1, *ySize); + } else { + psFree(cellsIter); + return false; + } + psList *biassecs = psMetadataLookupPtr(&mdok, cell->concepts, "CELL.BIASSEC"); // Bias sections + if (mdok && biassecs) { + psListIterator *biassecsIter = psListIteratorAlloc(biassecs, PS_LIST_HEAD, false); // Iterator + psRegion *biassec = NULL; // The bias section + while ((biassec = psListGetAndIncrement(biassecsIter))) { + if (!psRegionIsBad(*trimsec)) { + *xSize = MAX(biassec->x1, *xSize); + *ySize = MAX(biassec->y1, *ySize); + } else { + psFree(biassecsIter); + psFree(cellsIter); + return false; + } + } + psFree(biassecsIter); + } + } + psFree(cellsIter); + + return (*xSize != 0 && *ySize != 0); +} + + +static psRegion sectionForImage(int *position, // Position on the output image, updated + const psImage *image, // Image containing the sizes and offsets + int readdir // Read direction, 1=rows, 2=cols + ) +{ + psRegion region; + switch (readdir) { + case 1: // Read direction is rows + region = psRegionSet(*position, *position + image->numCols, image->row0, + image->row0 + image->numRows); + *position += image->numCols; + break; + case 2: // Read direction is columns + region = psRegionSet(image->col0, image->col0 + image->numCols, *position, + *position + image->numRows); + *position += image->numRows; + break; + default: + psAbort(__func__, "Shouldn't ever get here!\n"); + } + + return region; +} + +static bool doBiasSections(int *position, // Position on the output image, updated + pmCell *target, // Target cell + const pmCell *source // Source cell + ) +{ + psMetadataItem *biassecItem = psMetadataLookup(target->concepts, "CELL.BIASSEC"); // Bias sections + if (!biassecItem) { + psLogMsg(__func__, PS_LOG_WARN, "CELL.BIASSEC has not been initialised in target cell --- " + "ignored.\n"); + return false; + } + psFree(biassecItem->data.V); // Blow away the old list + psList *biassecs = psListAlloc(NULL); + biassecItem->data.V = biassecs; + + bool mdok = true; // Status of MD lookup + int readdir = psMetadataLookupS32(&mdok, source->concepts, "CELL.READDIR"); // Read direction + if (!mdok || (readdir != 1 && readdir != 2)) { + // Probably unnecessary, but just in case.... + psLogMsg(__func__, PS_LOG_WARN, "CELL.READDIR is not set in source cell --- ignored.\n"); + return false; + } + + pmReadout *readout = source->readouts->data[0]; // The first source readout, as representative + psList *biases = readout->bias; // The bias images from the source readout + + psListIterator *biasIter = psListIteratorAlloc(biases, PS_LIST_HEAD, true); // Iterator for biases + psImage *bias = NULL; // Bias image from iteration + while ((bias = psListGetAndIncrement(biasIter))) { + // Construct a region + psRegion *biassec = psAlloc(sizeof(psRegion)); // The new region; need a psMemBlock + *biassec = sectionForImage(position, bias, readdir); + psListAdd(biassecs, PS_LIST_TAIL, biassec); + psFree(biassec); // Drop reference + } + psFree(biasIter); + + return true; +} + +// Generate CELL.TRIMSEC and CELL.BIASSEC for the target cells +static bool generateTrimBias(psList *targets, // List of target cells + psList *sources // List of source cells + ) +{ + pmCell *target = NULL, *source = NULL; // Cells from iteration + int numCells = targets->n; // Number of cells + int cellNum = 0; // The cell number + int position = 0; // Position on the image + bool mdok = true; // Status of MD lookup + + // First run through to do the LHS biases + psListIterator *targetsIter = psListIteratorAlloc(targets, PS_LIST_HEAD, false); // Iterator for targets + psListIterator *sourcesIter = psListIteratorAlloc(sources, PS_LIST_HEAD, false); // Iterator for sources + bool done = false; // Done with iteration? + while ((target = psListGetAndIncrement(targetsIter)) && (source = psListGetAndIncrement(sourcesIter)) && + !done) { + if (cellNum <= numCells/2 - 1) { + doBiasSections(&position, target, source); + cellNum++; + } else { + done = true; + } + } + + // Second run through to do the trim sections + psListIteratorSet(targetsIter, PS_LIST_HEAD); + psListIteratorSet(sourcesIter, PS_LIST_HEAD); + while ((target = psListGetAndIncrement(targetsIter)) && (source = psListGetAndIncrement(sourcesIter))) { + psRegion *trimsec = psMetadataLookupPtr(&mdok, target->concepts, "CELL.TRIMSEC"); // Trim section + if (!mdok || !trimsec) { + psLogMsg(__func__, PS_LOG_WARN, "CELL.TRIMSEC has not been initialised in target cell --- " + "ignored.\n"); + continue; + } + + int readdir = psMetadataLookupS32(&mdok, source->concepts, "CELL.READDIR"); // Read direction + if (!mdok || (readdir != 1 && readdir != 2)) { + // Probably unnecessary, but just in case.... + psLogMsg(__func__, PS_LOG_WARN, "CELL.READDIR is not set in source cell --- ignored.\n"); + continue; + } + + pmReadout *readout = source->readouts->data[0]; // The first source readout, as representative + psImage *image = readout->image;// The proper image + *trimsec = sectionForImage(&position, image, readdir); + } + + // A final run through to do the RHS biases + psListIteratorSet(targetsIter, cellNum); + psListIteratorSet(sourcesIter, cellNum); + while ((target = psListGetAndIncrement(targetsIter)) && (source = psListGetAndIncrement(sourcesIter))) { + doBiasSections(&position, target, source); + } + + // Clean up + psFree(targetsIter); + psFree(sourcesIter); + + return (position > 0); +} + + +// Generate an HDU with the pixels +static bool generateHDU(pmCell *target, // The target cell + pmCell *source, // The source cell + int xBin, int yBin // Binning in x and y + ) +{ + // Get the HDU and a list of cells below it + pmHDU *hdu = pmHDUFromCell(target); // The HDU in the target cell + psList *targetCells = psListAlloc(NULL); // List of target cells below the target HDU + psList *sourceCells = psListAlloc(NULL); // List of source cells below the target HDU + if (! cellList(targetCells, sourceCells, target, source)) { + psError(PS_ERR_IO, true, "Unable to find cells to generate HDU!\n"); + return false; + } + + // Check the number of readouts + int numReadouts = -1; // Number of readouts + { + psListIterator *iter = psListIteratorAlloc(sourceCells, PS_LIST_HEAD, false); // Iterator for cells + pmCell *cell = NULL; // The cell from iteration + while ((cell = psListGetAndIncrement(iter))) + { + psArray *readouts = cell->readouts; + if (numReadouts == -1) { + numReadouts = readouts->n; + } else if (readouts->n != numReadouts) { + psError(PS_ERR_IO, true, "Number of readouts doesn't match: %d vs %d\n", readouts->n, + numReadouts); + return false; + } + + } + psFree(iter); + } + + // Get the size of the HDU, either from existing trimsec and biassec, or generate these and try again + int xSize = 0, ySize = 0; // Size of HDU + if (!sizeHDU(&xSize, &ySize, targetCells) && !(generateTrimBias(targetCells, sourceCells) && + sizeHDU(&xSize, &ySize, targetCells))) { + psError(PS_ERR_IO, true, "Unable to determine size of HDU!\n"); + return false; + } + psFree(targetCells); + psFree(sourceCells); + + xSize = (int)ceilf((float)xSize/(float)xBin); + ySize = (int)ceilf((float)ySize/(float)yBin); + + hdu->images = psArrayAlloc(numReadouts); + for (int i = 0; i < numReadouts; i++) { + psImage *image = psImageAlloc(xSize, ySize, PS_TYPE_F32); + psImageInit(image, 0.0); + hdu->images->data[i] = image; + } + + return true; +} + +// Copy pixels from a target image to a source image, with flips +static bool copyPixels(psImage *target, // Target image (HDU pixels) + psImage *source, // Source image (from source cell) + psRegion region, // Region for pasting + bool xFlip, // Flip in x? + bool yFlip // Flip in y? + ) +{ + psImage *overlay = psMemIncrRefCounter(source); + if (xFlip) { + psImage *temp = psImageFlipX(overlay); + psFree(overlay); + overlay = temp; + } + if (yFlip) { + psImage *temp = psImageFlipY(overlay); + psFree(overlay); + overlay = temp; + } + int numPix = psImageOverlaySection(target, overlay, region.x0, region.y0, "="); + psFree(overlay); + return (numPix > 0); +} + +// Bin a region down by specified factors in x and y +static void binRegion(psRegion *region, // Region to be binned + int xBin, int yBin// Binning in x and y + ) +{ + // Want to include the lower bound: 1 binned by 4 --> 0; 3 binned by 4 --> 0; 4 binned by 4 --> 1 + region->x0 = (int)(region->x0 / xBin); + region->y0 = (int)(region->y0 / yBin); + // Want to exclude the upper bound: 4 binned by 4 --> 1; 5 binned by 4 --> 2; 7 binned by 4 --> 2 + region->x1 = (int)((region->x1 + xBin - 1) / xBin); + region->y1 = (int)((region->y1 + yBin - 1) / yBin); +} + + +static pmHDU *findPHU(const pmCell *cell// The cell for which to find the PHU + ) +{ + if (cell->hdu && cell->hdu->phu) { + return cell->hdu; + } + pmChip *chip = cell->parent; // The parent chip + if (chip->hdu && chip->hdu->phu) { + return chip->hdu; + } + pmFPA *fpa = chip->parent; // The parent FPA + if (fpa->hdu && fpa->hdu->phu) { + return fpa->hdu; + } + + psError(PS_ERR_IO, true, "Unable to find PHU for target cell.\n"); + return NULL; +} + + +static bool copyPHU(pmCell *targetCell, // The target cell + pmCell *sourceCell // The source cell + ) +{ + // Find the respective PHUs + pmHDU *targetPHU = findPHU(targetCell); // The target PHU + if (targetPHU->header) { + return false; // No work required + } + // Copy the header over + pmHDU *sourcePHU = findPHU(sourceCell); // The source PHU + targetPHU->header = psMetadataCopy(NULL, sourcePHU->header); + return true; +} + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static engine functions --- these do all the work. Actually, cellCopy does all the work; the others +// merely iterate on the higher-level components. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +static int cellCopy(pmCell *target, // The target cell + pmCell *source, // The source cell, to be copied + bool pixels, // Copy the pixels? + int xBin, int yBin // (Relative) binning factors in x and y + ) +{ + assert(target); + assert(source); + + psArray *sourceReadouts = source->readouts; // The source readouts + int numReadouts = sourceReadouts->n; // Number of readouts copied + + // Copy any headers + if (target->hdu && !target->hdu->phu) { + pmHDU *sourceHDU = pmHDUFromCell(source); + target->hdu->header = psMetadataCopy(target->hdu->header, sourceHDU->header); + } + + pmHDU *hdu = pmHDUFromCell(target); // The target HDU; we need to fix this up + if (!hdu->images) { + generateHDU(target, source, xBin, yBin); + } + if (!hdu->header) { + hdu->header = psMetadataAlloc(); + } + // Copy the PHU over as well, if required + copyPHU(target, source); + + // Need to check/change CELL.XPARITY and CELL.YPARITY + bool xFlip = (psMetadataLookupS32(NULL, target->concepts, "CELL.XPARITY") != + psMetadataLookupS32(NULL, source->concepts, "CELL.XPARITY")); // Switch parity in x? + bool yFlip = (psMetadataLookupS32(NULL, target->concepts, "CELL.YPARITY") != + psMetadataLookupS32(NULL, source->concepts, "CELL.YPARITY")); // Switch parity in y? + psTrace(__func__, 3, "xFlip: %d; yFlip: %d\n", xFlip, yFlip); + + bool mdok = true; // Status of MD lookup + psRegion *trimsec = psMetadataLookupPtr(&mdok, target->concepts, "CELL.TRIMSEC"); // The trim section + if (!mdok || !trimsec || psRegionIsBad(*trimsec)) { + psError(PS_ERR_IO, true, "CELL.TRIMSEC isn't set!\n"); + return 0; + } + psList *biassecs = psMetadataLookupPtr(&mdok, target->concepts, "CELL.BIASSEC"); // The bias sections + if (!mdok || !biassecs) { + psError(PS_ERR_IO, true, "CELL.BIASSEC isn't set!\n"); + return 0; + } + + for (int i = 0; i < numReadouts; i++) { + pmReadout *sourceReadout = sourceReadouts->data[i]; // The source readout + psImage *sourceImage = sourceReadout->image; // The source image + pmReadout *targetReadout = pmReadoutAlloc(target); // The target readout; this adds it to the cell + if (sourceImage->numCols != trimsec->x1 - trimsec->x0 || + sourceImage->numRows != trimsec->y1 - trimsec->y0) { + psString trimsecString = psRegionToString(*trimsec); // String with the trim section + psLogMsg(__func__, PS_LOG_WARN, "Source image size (%dx%d) for readout %d doesn't match " + "CELL.TRIMSEC for target (%s) -- ignored.\n", sourceImage->numCols, sourceImage->numRows, + i, trimsecString); + psFree(trimsecString); + } else { + binRegion(trimsec, xBin, yBin); + if (pixels) { + copyPixels(hdu->images->data[i], sourceImage, *trimsec, xFlip, yFlip); + } + targetReadout->image = psImageSubset(hdu->images->data[i], *trimsec); + } + + psListIterator *biassecsIter = psListIteratorAlloc(biassecs, PS_LIST_HEAD, false); // Iterator + psRegion *biassec = NULL; // Bias section from iteration + psListIterator *biasIter = psListIteratorAlloc(sourceReadout->bias, PS_LIST_HEAD, false); // Iterator + psImage *bias = NULL; // Bias image from iteration + while ((biassec = psListGetAndIncrement(biassecsIter)) && (bias = psListGetAndIncrement(biasIter))) { + if (psRegionIsBad(*biassec)) { + psString biassecString = psRegionToString(*biassec); // String for bias section + psLogMsg(__func__, PS_LOG_WARN, "Bias section (%s) isn't set --- ignored.\n", biassecString); + psFree(biassecString); + continue; + } + if (bias->numCols != biassec->x1 - biassec->x0 || + bias->numRows != biassec->y1 - biassec->y0) { + psString biassecString = psRegionToString(*biassec); // String with the bias section + psLogMsg(__func__, PS_LOG_WARN, "Source image size (%dx%d) for readout %d doesn't match " + "CELL.BIASSEC for target (%s) -- ignored.\n", bias->numCols, bias->numRows, i, + biassecString); + psFree(biassecString); + } else { + binRegion(biassec, xBin, yBin); + if (pixels) { + copyPixels(hdu->images->data[i], bias, *biassec, xFlip, yFlip); + } + psImage *newBias = psImageSubset(hdu->images->data[i], *biassec); + psListAdd(targetReadout->bias, PS_LIST_TAIL, newBias); + psFree(newBias); // Drop reference + } + } + psFree(targetReadout); // Drop reference + psFree(biassecsIter); + psFree(biasIter); + } + + // Copy the remaining "concepts" over + psMetadataIterator *conceptsIter = psMetadataIteratorAlloc(source->concepts, PS_LIST_HEAD, NULL); + psMetadataItem *conceptItem = NULL; // Item from iteration + while ((conceptItem = psMetadataGetAndIncrement(conceptsIter))) { + psString name = conceptItem->name; // Name of concept + if (strcmp(name, "CELL.TRIMSEC") != 0 && strcmp(name, "CELL.BIASSEC") != 0 && + strcmp(name, "CELL.XPARITY") != 0 && strcmp(name, "CELL.YPARITY") != 0 && + strcmp(name, "CELL.X0") != 0 && strcmp(name, "CELL.Y0") != 0) { + psMetadataAddItem(target->concepts, conceptItem, PS_LIST_TAIL, PS_META_REPLACE); + } + } + psFree(conceptsIter); + + // Need to update CELL.X0 and CELL.Y0 if we flipped + if (xFlip) { + int xZero = psMetadataLookupS32(NULL, source->concepts, "CELL.X0"); // CELL.X0 from source + int xParity = psMetadataLookupS32(NULL, target->concepts, "CELL.XPARITY"); // Parity in x + int xBin = psMetadataLookupS32(NULL, source->concepts, "CELL.XBIN"); // CELL.XBIN from source + pmReadout *readout = source->readouts->data[0]; // A representative readout + psTrace(__func__, 3, "CELL.X0: Before: %d After: %d\n", xZero, + xZero - (readout->image->numCols - 1) * xParity * xBin); + psTrace(__func__, 9, "(xParity: %d xBin: %d numCols: %d)\n", xParity, xBin, readout->image->numCols); + xZero -= (readout->image->numCols - 1) * xParity * xBin; // Change the parity on the X0 position + psMetadataItem *newItem = psMetadataLookup(target->concepts, "CELL.X0"); // CELL.X0 from target + newItem->data.S32 = xZero; + } + if (yFlip) { + int yZero = psMetadataLookupS32(NULL, source->concepts, "CELL.Y0"); // CELL.Y0 from source + int yParity = psMetadataLookupS32(NULL, target->concepts, "CELL.YPARITY"); // Parity in y + int yBin = psMetadataLookupS32(NULL, source->concepts, "CELL.YBIN"); // Parity in y + pmReadout *readout = source->readouts->data[0]; // A representative readout + psTrace(__func__, 3, "CELL.Y0: Before: %d After: %d\n", yZero, + yZero - (readout->image->numRows - 1) * yParity * yBin); + psTrace(__func__, 9, "(yParity: %d yBin: %d numRows: %d)\n", yParity, yBin, readout->image->numRows); + yZero -= (readout->image->numRows - 1) * yParity * yBin; // Change the parity on the Y0 position + psMetadataItem *newItem = psMetadataLookup(target->concepts, "CELL.Y0"); // CELL.Y0 from target + newItem->data.S32 = yZero; + } + + // Update the binning concepts + psMetadataItem *binItem = psMetadataLookup(target->concepts, "CELL.XBIN"); + binItem->data.S32 *= xBin; + binItem = psMetadataLookup(target->concepts, "CELL.YBIN"); + binItem->data.S32 *= yBin; + + return numReadouts; +} + +static int chipCopy(pmChip *target, // The target chip + pmChip *source, // The source chip, to be copied + bool pixels, // Copy the pixels? + int xBin, int yBin // (Relative) binning factors in x and y + ) +{ + assert(target); + assert(source); + + psArray *targetCells = target->cells; // The target cells + psArray *sourceCells = source->cells; // The source cells + if (targetCells->n != sourceCells->n) { + psError(PS_ERR_IO, true, "Number of source cells (%d) differs from the number of target cells (%d)\n", + sourceCells->n, targetCells->n); + return false; + } + + // Copy any headers + if (target->hdu && !target->hdu->phu) { + pmHDU *sourceHDU = pmHDUFromChip(source); + target->hdu->header = psMetadataCopy(target->hdu->header, sourceHDU->header); + } + + int numCells = 0; // Number of cells copied + for (int i = 0; i < targetCells->n; i++) { + pmCell *targetCell = targetCells->data[i]; // The target cell + const char *cellName = psMetadataLookupStr(NULL, targetCell->concepts, "CELL.NAME"); // Name of cell + int cellNum = pmChipFindCell(source, cellName); // Number of cell with that name + if (cellNum >= 0) { + pmCell *sourceCell = sourceCells->data[cellNum]; // The source cell + int numReadouts = cellCopy(targetCell, sourceCell, pixels, xBin, yBin); // Number of readouts + // copied + psTrace(__func__, 5, "Copied %d readouts for cell %s\n", numReadouts, cellName); + numCells++; + } + } + + // Update the concepts + psMetadataCopy(target->concepts, source->concepts); + + return numCells; + +} + +static int fpaCopy(pmFPA *target, // The target FPA + pmFPA *source, // The source FPA, to be copied + bool pixels, // Copy the pixels? + int xBin, int yBin // (Relative) binning factors in x and y + ) +{ + assert(target); + assert(source); + + psArray *targetChips = target->chips; // The target chips + psArray *sourceChips = source->chips; // The source chips + if (targetChips->n != sourceChips->n) { + psError(PS_ERR_IO, true, "Number of source chips (%d) differs from the number of target chips (%d)\n", + sourceChips->n, targetChips->n); + return false; + } + + // Copy any headers + if (target->hdu && !target->hdu->phu) { + pmHDU *sourceHDU = pmHDUFromFPA(source); + target->hdu->header = psMetadataCopy(target->hdu->header, sourceHDU->header); + } + + int numChips = 0; // Number of chips copied + for (int i = 0; i < targetChips->n; i++) { + pmChip *targetChip = targetChips->data[i]; // The target chip + const char *chipName = psMetadataLookupStr(NULL, targetChip->concepts, "CHIP.NAME"); // Name of chip + int chipNum = pmFPAFindChip(source, chipName); // Number of chip with that name + if (chipNum >= 0) { + pmChip *sourceChip = sourceChips->data[chipNum]; // The source chip + int numCells = chipCopy(targetChip, sourceChip, pixels, xBin, yBin); // Number of cells copied + psTrace(__func__, 5, "Copied %d cells for chip %s\n", numCells, chipName); + numChips++; + } + } + + // Update the concepts + psMetadataCopy(target->concepts, source->concepts); + + return numChips; +} + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + +int pmFPACopy(pmFPA *target, // The target FPA + pmFPA *source // The source FPA, to be copied + ) +{ + return fpaCopy(target, source, true, 1, 1); +} + +int pmChipCopy(pmChip *target, // The target chip + pmChip *source // The source chip, to be copied + ) +{ + return chipCopy(target, source, true, 1, 1); +} + +int pmCellCopy(pmCell *target, // The target cell + pmCell *source // The source cell, to be copied + ) +{ + return cellCopy(target, source, true, 1, 1); +} + + +int pmFPACopyStructure(pmFPA *target, // The target FPA + pmFPA *source, // The source FPA, to be copied + int xBin, int yBin // Binning factors in x and y + ) +{ + return fpaCopy(target, source, false, xBin, yBin); +} + +int pmChipCopyStructure(pmChip *target, // The target chip + pmChip *source, // The source chip, to be copied + int xBin, int yBin // Binning factors in x and y + ) +{ + return chipCopy(target, source, false, xBin, yBin); +} + +int pmCellCopyStructure(pmCell *target, // The target cell + pmCell *source, // The source cell, to be copied + int xBin, int yBin // Binning factors in x and y + ) +{ + return cellCopy(target, source, false, xBin, yBin); +} Index: trunk/psModules/src/astrom/pmFPACopy.h =================================================================== --- trunk/psModules/src/astrom/pmFPACopy.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPACopy.h (revision 6872) @@ -0,0 +1,30 @@ +#ifndef PM_FPA_COPY_H +#define PM_FPA_COPY_H + +// Copy the FPA components, including the pixels +int pmFPACopy(pmFPA *target, // The target FPA + pmFPA *source // The source FPA, to be copied + ); +int pmChipCopy(pmChip *target, // The target chip + pmChip *source // The source chip, to be copied + ); +int pmCellCopy(pmCell *target, // The target cell + pmCell *source // The source cell, to be copied + ); + +// Versions that copy the structure and not the pixels; they also allow binning +int pmFPACopyStructure(pmFPA *target, // The target FPA + pmFPA *source, // The source FPA, to be copied + int xBin, int yBin // Binning factors in x and y + ); +int pmChipCopyStructure(pmChip *target, // The target chip + pmChip *source, // The source chip, to be copied + int xBin, int yBin // Binning factors in x and y + ); +int pmCellCopyStructure(pmCell *target, // The target cell + pmCell *source, // The source cell, to be copied + int xBin, int yBin // Binning factors in x and y + ); + + +#endif Index: trunk/psModules/src/astrom/pmFPAMaskWeight.c =================================================================== --- trunk/psModules/src/astrom/pmFPAMaskWeight.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAMaskWeight.c (revision 6872) @@ -0,0 +1,101 @@ +#include +#include "pslib.h" +#include "pmFPA.h" +#include "pmFPAMaskWeight.h" + +bool pmReadoutSetMask(pmReadout *readout // Readout for which to set mask + ) +{ + PS_ASSERT_PTR_NON_NULL(readout, false); + + pmCell *cell = readout->parent; // The parent cell + bool mdok = true; // Status of MD lookup + + // Get the "concepts" of interest + float saturation = psMetadataLookupF32(&mdok, cell->concepts, "CELL.SATURATION"); // Saturation level + if (!mdok || isnan(saturation)) { + psError(PS_ERR_IO, true, "CELL.SATURATION is not set --- unable to set mask.\n"); + return false; + } + float bad = psMetadataLookupF32(NULL, cell->concepts, "CELL.BAD"); // Bad level + if (!mdok || isnan(bad)) { + psError(PS_ERR_IO, true, "CELL.BAD is not set --- unable to set mask.\n"); + return false; + } + + psImage *image = readout->image; // The image pixels + psImage *mask = readout->mask; // The mask pixels + if (!mask) { + mask = psImageAlloc(image->numCols, image->numRows, PS_TYPE_U8); + readout->mask = mask; + psImageInit(mask, 0); + } + + // Set up the mask + for (int i = 0; i < image->numRows; i++) { + for (int j = 0; j < image->numCols; j++) { + if (image->data.F32[i][j] > saturation) { + mask->data.U8[i][j] |= PM_MASK_SAT; + } + if (image->data.F32[i][j] < bad) { + mask->data.U8[i][j] |= PM_MASK_BAD; + } + } + } + + return true; +} + +bool pmReadoutSetWeight(pmReadout *readout // Readout for which to set weight + ) +{ + PS_ASSERT_PTR_NON_NULL(readout, false); + + pmCell *cell = readout->parent; // The parent cell + bool mdok = true; // Status of MD lookup + + // Get the "concepts" of interest + float gain = psMetadataLookupF32(&mdok, cell->concepts, "CELL.GAIN"); // Cell gain + if (!mdok || isnan(gain)) { + psError(PS_ERR_IO, true, "CELL.GAIN is not set --- unable to set weight.\n"); + return false; + } + float readnoise = psMetadataLookupF32(&mdok, cell->concepts, "CELL.READNOISE"); // Cell read noise + if (!mdok || isnan(readnoise)) { + psError(PS_ERR_IO, true, "CELL.READNOISE is not set --- unable to set weight.\n"); + return false; + } + + psImage *image = readout->image; // The image pixels + psImage *weight = readout->weight; // The weight pixels + if (!weight) { + weight = psImageAlloc(image->numCols, image->numRows, PS_TYPE_F32); + readout->weight = weight; + psImageInit(weight, 0.0); + } + + // Set weight image to the variance in ADU = f/g + rn^2 + psBinaryOp(readout->weight, image, "/", psScalarAlloc(gain, PS_TYPE_F32)); + psBinaryOp(readout->weight, readout->weight, "+", + psScalarAlloc(readnoise*readnoise/gain/gain, PS_TYPE_F32)); + + return true; +} + + + +bool pmCellSetMaskWeight(pmCell *cell // Cell for which to set weights + ) +{ + PS_ASSERT_PTR_NON_NULL(cell, false); + + bool success = true; // Was everything successful? + psArray *readouts = cell->readouts; // Array of readouts + for (int i = 0; i < readouts->n; i++) { + pmReadout *readout = readouts->data[i]; // The readout + success |= pmReadoutSetMask(readout); + success |= pmReadoutSetWeight(readout); + } + + return success; +} Index: trunk/psModules/src/astrom/pmFPAMaskWeight.h =================================================================== --- trunk/psModules/src/astrom/pmFPAMaskWeight.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAMaskWeight.h (revision 6872) @@ -0,0 +1,23 @@ +#ifndef PM_READOUT_MASK_WEIGHT_H +#define PM_READOUT_MASK_WEIGHT_H + +#include "pmFPA.h" + +/** Mask values */ +typedef enum { + PM_MASK_TRAP = 0x0001, ///< The pixel is a charge trap. + PM_MASK_BADCOL = 0x0002, ///< The pixel is a bad column. + PM_MASK_SAT = 0x0004, ///< The pixel is saturated. + PM_MASK_BAD = 0x0008, ///< The pixel is low + PM_MASK_FLAT = 0x0010 ///< The pixel is non-positive in the flat-field. +} pmMaskValue; + +bool pmReadoutSetMask(pmReadout *readout // Readout for which to set mask + ); +bool pmReadoutSetWeight(pmReadout *readout // Readout for which to set weight + ); +bool pmCellSetMaskWeight(pmCell *cell // Cell for which to set weights + ); + + +#endif Index: trunk/psModules/src/astrom/pmFPARead.c =================================================================== --- trunk/psModules/src/astrom/pmFPARead.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPARead.c (revision 6872) @@ -0,0 +1,242 @@ +#include +#include +#include +#include "pslib.h" + +#include "pmFPA.h" +#include "pmFPARead.h" +#include "pmHDU.h" +#include "pmHDUUtils.h" +#include "pmConcepts.h" +#include "psRegionIsBad.h" +#include "pmHDUUtils.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Carve a readout from the image pixels +static pmReadout *readoutCarve(pmCell *cell, // Cell into which the new readout will be placed + psImage *image, // Image that will be carved + const psRegion *trimsec, // Trim section + const psList *biassecs // Bias sections + ) +{ + pmReadout *readout = pmReadoutAlloc(cell); + + // The image corresponding to the trim region + if (psRegionIsBad(*trimsec)) { + psString regionString = psRegionToString(*trimsec); + psError(PS_ERR_IO, true, "Invalid trim section: %s\n", regionString); + psFree(regionString); + psFree(readout); + return NULL; + } + readout->image = psMemIncrRefCounter(psImageSubset(image, *trimsec)); + + // Get the list of overscans + psListIterator *iter = psListIteratorAlloc((psList*)biassecs, PS_LIST_HEAD, false); // Iterator + psRegion *biassec = NULL; // A BIASSEC region from the list + while ((biassec = psListGetAndIncrement(iter))) { + if (psRegionIsBad(*biassec)) { + psString regionString = psRegionToString(*biassec); + psError(PS_ERR_IO, true, "Invalid bias section: %s\n", regionString); + psFree(regionString); + psFree(readout); + return NULL; + } + psImage *overscan = psMemIncrRefCounter(psImageSubset(image, *biassec)); + psListAdd(readout->bias, PS_LIST_TAIL, overscan); + psFree(overscan); + } + psFree(iter); + + return readout; +} + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Read the next readout; return true if we read pixels in. +bool pmReadoutReadNext(pmReadout *readout, // Readout into which to read + psFits *fits, // FITS file from which to read + int z, // Readout number/plane; zero-offset indexing + int numRows // The number of rows to read + ) +{ + // Get the HDU and read the header + pmCell *cell = readout->parent; // The parent cell + pmHDU *hdu = pmHDUFromCell(cell); // The HDU + if (!hdu) { + return false; + } + + if (!pmHDUReadHeader(hdu, fits)) { + psError(PS_ERR_IO, false, "Unable to read HDU header!\n"); + return false; + } + + // Check the third dimension + bool mdok = true; // Status of MD lookup + int naxis = psMetadataLookupS32(&mdok, hdu->header, "NAXIS"); // The number of axes + if (!mdok) { + psError(PS_ERR_IO, true, "Unable to find NAXIS in header for extension %s\n", hdu->extname); + return false; + } + if (naxis == 0) { + // No pixels to read, as for a PHU. + return false; + } + if (naxis < 2 || naxis > 3) { + psError(PS_ERR_IO, true, "NAXIS in header of extension %s (= %d) is not valid.\n", + hdu->extname, naxis); + return false; + } + int naxis3 = 1; // The number of image planes + if (naxis == 3) { + naxis3 = psMetadataLookupS32(&mdok, hdu->header, "NAXIS3"); + if (!mdok) { + psError(PS_ERR_IO, true, "Unable to find NAXIS3 in header for extension %s\n", hdu->extname); + return false; + } + } + if (z >= naxis3) { + // Nothing to see here. Move along. + return false; + } + + // Get the size of the image plane + int naxis1 = psMetadataLookupS32(&mdok, hdu->header, "NAXIS1"); // The number of columns + if (!mdok) { + psError(PS_ERR_IO, true, "Unable to find NAXIS1 in header for extension %s\n", hdu->extname); + return false; + } + int naxis2 = psMetadataLookupS32(&mdok, hdu->header, "NAXIS2"); // The number of columns + if (!mdok) { + psError(PS_ERR_IO, true, "Unable to find NAXIS2 in header for extension %s\n", hdu->extname); + return false; + } + + // Read the FITS image + int offset = readout->row0; // The row number to read + if (readout->image) { + offset += readout->image->numRows; + } + if (offset >= naxis2) { + // We've read everything there is + return false; + } + int upper = offset + numRows; // The upper limit for the pixel read + if (upper > naxis2) { + upper = naxis2; + } + psRegion region = psRegionSet(0, naxis1, offset, upper); // Region to be read + psImage *image = psFitsReadImage(fits, region, z); // The image + if (readout->image) { + psFree(readout->image); + } + + // Stick the image into the HDU and the readout + if (!hdu->images) { + hdu->images = psArrayAlloc(naxis3); + } + if (hdu->images->n != naxis3) { + hdu->images = psArrayRealloc(hdu->images, naxis3); + } + if (hdu->images->data[z]) { + psFree(hdu->images->data[z]); + } + hdu->images->data[z] = image; + readout->image = psImageSubset(hdu->images->data[z], psRegionSet(0,0,0,0)); + readout->row0 = region.y0; + + return true; +} + + +// Read in the cell, and allocate the readouts +bool pmCellRead(pmCell *cell, // Cell to read into + psFits *fits, // FITS file from which to read + psDB *db // Database handle, for "concepts" ingest + ) +{ + pmHDU *hdu = pmHDUFromCell(cell); // The HDU + if (!hdu) { + return false; // Nothing to see here; move along + } + if (!hdu->images && !pmHDURead(hdu, fits)) { + psError(PS_ERR_IO, false, "Unable to read HDU for cell.\n"); + return false; + } + + pmConceptsReadCell(cell, PM_CONCEPT_SOURCE_HEADER, false, NULL); + + // Having read the cell, we now have to cut it up + psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); + psList *biassecs = psMetadataLookupPtr(NULL, cell->concepts, "CELL.BIASSEC"); + + // Iterate over each of the image planes + for (int i = 0; i < hdu->images->n; i++) { + psImage *image = hdu->images->data[i]; // The i-th plane + + // XXX: Type conversion here to support the modules, which don't have multiple type support yet + if (image->type.type != PS_TYPE_F32) { + psImage *temp = psImageCopy(NULL, image, PS_TYPE_F32); // Temporary image + psFree(hdu->images->data[i]); + hdu->images->data[i] = temp; + image = temp; + } + + pmReadout *readout = readoutCarve(cell, image, trimsec, biassecs); + readout->mask = NULL; + readout->weight = NULL; + psFree(readout); // Drop reference + } + + pmCellSetDataStatus (cell, true); + return true; +} + +// Read in the component cells +bool pmChipRead(pmChip *chip, // Chip to read into + psFits *fits, // FITS file from which to read + psDB *db // Database handle, for "concepts" ingest + ) +{ + bool success = false; // Were we able to read at least one HDU? + psArray *cells = chip->cells; // Array of cells + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // The cell of interest + success |= pmCellRead(cell, fits, db); + } + if (success) { + pmConceptsReadChip(chip, PM_CONCEPT_SOURCE_HEADER, false, NULL); + // XXX probably could just use chip->data_exists + pmChipSetDataStatus (chip, true); + } + + return success; +} + +// Read in the component chips +bool pmFPARead(pmFPA *fpa, // FPA to read into + psFits *fits, // FITS file from which to read + psDB *db // Database handle, for "concepts" ingest + ) +{ + bool success = false; // Were we able to read at least one HDU? + psArray *chips = fpa->chips; // Array of chips + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // The cell of interest + success |= pmChipRead(chip, fits, db); + } + if (success) { + pmConceptsReadFPA(fpa, PM_CONCEPT_SOURCE_HEADER, NULL); + } else { + psLogMsg(__func__, PS_LOG_WARN, "Unable to read any chips in FPA.\n"); + } + + return success; +} + Index: trunk/psModules/src/astrom/pmFPARead.h =================================================================== --- trunk/psModules/src/astrom/pmFPARead.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPARead.h (revision 6872) @@ -0,0 +1,67 @@ +#ifndef PM_FPA_READ_H +#define PM_FPA_READ_H + +#include "pslib.h" +#include "pmFPA.h" + + +bool pmReadoutReadNext(pmReadout *readout, // Readout into which to read + psFits *fits, // FITS file from which to read + int z, // Readout number/plane; zero-offset indexing + int numRows // The number of rows to read + ); + +bool pmCellRead(pmCell *cell, // Cell to read into + psFits *fits, // FITS file from which to read + psDB *db // Database handle, for "concepts" ingest + ); + +bool pmChipRead(pmChip *chip, // Chip to read into + psFits *fits, // FITS file from which to read + psDB *db // Database handle, for "concepts" ingest + ); + +bool pmFPARead(pmFPA *fpa, // FPA to read into + psFits *fits, // FITS file from which to read + psDB *db // Database handle, for "concepts" ingest + ); + +bool pmCellReadPHU(pmCell *cell, // Cell to read into + psFits *fits // FITS file from which to read + ); + +bool pmChipReadPHU(pmChip *chip, // Chip to read into + psFits *fits // FITS file from which to read + ); + +bool pmFPAReadPHU(pmFPA *fpa, // FPA to read into + psFits *fits // FITS file from which to read + ); + + +#if 0 +bool pmFPARead(pmFPA *fpa, // FPA to read into + psFits *fits, // FITS file from which to read + psMetadata *phu, // Primary header + psDB *db // Database handle, for concept ingest + ); + +psString p_pmFPATranslateName(const psString name, // The name to translate + const pmCell *cell // The cell for which to translate + ); + +psString p_pmFPATranslateFileExt(psString *extName, // Extension name, to be returned + const psString filenameExt, // The string to parse into filename and ext + const pmCell *cell // The cell + ); + +bool pmFPAReadMask(pmFPA *fpa, // FPA to read into + psFits *source // Source FITS file (for the original data) + ); + +bool pmFPAReadWeight(pmFPA *fpa, // FPA to read into + psFits *source // Source FITS file (for the original data) + ); +#endif + +#endif Index: trunk/psModules/src/astrom/pmFPAUtils.c =================================================================== --- trunk/psModules/src/astrom/pmFPAUtils.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAUtils.c (revision 6872) @@ -0,0 +1,41 @@ +#include +#include "pslib.h" +#include "pmFPA.h" +#include "pmFPAUtils.h" + +// Find a chip by name; return the index +int pmFPAFindChip(const pmFPA *fpa, // FPA in which to find the chip + const char *name // Name of the chip + ) +{ + psArray *chips = fpa->chips; // Array of chips + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // The chip of interest + psString testName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); // Name of this chip + if (strcmp(name, testName) == 0) { + return i; + } + } + + psError(PS_ERR_IO, true, "Unable to find chip %s\n", name); + return -1; +} + +// Find a cell by name; return the index +int pmChipFindCell(const pmChip *chip, // Chip in which to find the cell + const char *name // Name of the cell + ) +{ + psArray *cells = chip->cells; // Array of cells + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // The cell of interest + psString testName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of this cell + if (strcmp(name, testName) == 0) { + return i; + } + } + + psError(PS_ERR_IO, true, "Unable to find cell %s\n", name); + return -1; +} + Index: trunk/psModules/src/astrom/pmFPAUtils.h =================================================================== --- trunk/psModules/src/astrom/pmFPAUtils.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAUtils.h (revision 6872) @@ -0,0 +1,17 @@ +#ifndef PM_FPA_UTILS_H +#define PM_FPA_UTILS_H + +#include "pmFPA.h" + +// Find a chip by name; return the index +int pmFPAFindChip(const pmFPA *fpa, // FPA in which to find the chip + const char *name // Name of the chip + ); + +// Find a cell by name; return the index +int pmChipFindCell(const pmChip *chip, // Chip in which to find the cell + const char *name // Name of the cell + ); + + +#endif Index: trunk/psModules/src/astrom/pmFPAWrite.c =================================================================== --- trunk/psModules/src/astrom/pmFPAWrite.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAWrite.c (revision 6872) @@ -0,0 +1,78 @@ +#include +#include +#include "pslib.h" + +#include "pmFPA.h" +#include "pmHDU.h" +#include "pmConcepts.h" + + +bool pmCellWrite(pmCell *cell, // Cell to write + psFits *fits, // FITS file to which to write + psDB *db // Database handle for "concepts" update + ) +{ + pmConceptsWriteCell(cell, PM_CONCEPT_SOURCE_HEADER | PM_CONCEPT_SOURCE_CAMERA | PM_CONCEPT_SOURCE_DEFAULTS, + false, NULL); + + pmHDU *hdu = cell->hdu; // The HDU + if (hdu && !pmHDUWrite(hdu, fits)) { + psError(PS_ERR_IO, false, "Unable to write HDU for Chip.\n"); + return false; + } + + return true; +} + + +bool pmChipWrite(pmChip *chip, // Chip to write + psFits *fits, // FITS file to which to write + psDB *db // Database handle for "concepts" update + ) +{ + pmConceptsWriteChip(chip, PM_CONCEPT_SOURCE_HEADER | PM_CONCEPT_SOURCE_CAMERA | PM_CONCEPT_SOURCE_DEFAULTS, + false, NULL); + + pmHDU *hdu = chip->hdu; // The HDU + if (hdu && !pmHDUWrite(hdu, fits)) { + psError(PS_ERR_IO, false, "Unable to write HDU for Chip.\n"); + return false; + } + + bool success = true; // Success of writing + psArray *cells = chip->cells; // Array of cells + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // The cell of interest + success |= pmCellWrite(cell, fits, db); + } + + return success; +} + + + + +bool pmFPAWrite(pmFPA *fpa, // FPA to write + psFits *fits, // FITS file to which to write + psDB *db // Database handle for "concepts" update + ) +{ + pmConceptsWriteFPA(fpa, PM_CONCEPT_SOURCE_HEADER | PM_CONCEPT_SOURCE_CAMERA | PM_CONCEPT_SOURCE_DEFAULTS, + NULL); + + pmHDU *hdu = fpa->hdu; // The HDU + if (hdu && !pmHDUWrite(hdu, fits)) { + psError(PS_ERR_IO, false, "Unable to write HDU for FPA.\n"); + return false; + } + + bool success = true; // Success of writing + psArray *chips = fpa->chips; // Array of chips + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // The chip of interest + success |= pmChipWrite(chip, fits, db); + } + + return success; +} + Index: trunk/psModules/src/astrom/pmFPAWrite.h =================================================================== --- trunk/psModules/src/astrom/pmFPAWrite.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAWrite.h (revision 6872) @@ -0,0 +1,21 @@ +#ifndef PM_FPA_WRITE_H +#define PM_FPA_WRITE_H + +#include "pslib.h" +#include "pmFPA.h" + + +bool pmCellWrite(pmCell *cell, // Cell to write + psFits *fits, // FITS file to which to write + psDB *db // Database handle for "concepts" update + ); +bool pmChipWrite(pmChip *chip, // Chip to write + psFits *fits, // FITS file to which to write + psDB *db // Database handle for "concepts" update + ); +bool pmFPAWrite(pmFPA *fpa, // FPA to write + psFits *fits, // FITS file to which to write + psDB *db // Database handle for "concepts" update + ); + +#endif Index: trunk/psModules/src/astrom/pmFPA_JPEG.c =================================================================== --- trunk/psModules/src/astrom/pmFPA_JPEG.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPA_JPEG.c (revision 6872) @@ -0,0 +1,163 @@ +/** @file pmFPA_JPEG.c + * + * This file contains functions to write JPEG images. + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:04 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +/*****************************************************************************/ +/* INCLUDE FILES */ +/*****************************************************************************/ + +#include +# include "psImageJpeg.h" +# include "psImageUnbin.h" +# include "psAdditionals.h" + +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAfile.h" +#include "pmFPAview.h" +#include "pmFPA_JPEG.h" + + +bool pmFPAviewWriteJPEG (const pmFPAview *view, pmFPAfile *file) +{ + + pmFPA *fpa = file->fpa; + + if (view->chip == -1) { + pmFPAWriteJPEG (fpa, view, file); + return true; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + pmChipWriteJPEG (chip, view, file); + return true; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellWriteJPEG (cell, view, file); + return true; + } + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + pmReadoutWriteJPEG (readout, view, file); + return true; +} + +// read in all chip-level JPEG files for this FPA +bool pmFPAWriteJPEG (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < fpa->chips->n; i++) { + + pmChip *chip = fpa->chips->data[i]; + pmChipWriteJPEG (chip, view, file); + } + return true; +} + +// read in all cell-level JPEG files for this chip +bool pmChipWriteJPEG (pmChip *chip, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < chip->cells->n; i++) { + + pmCell *cell = chip->cells->data[i]; + pmCellWriteJPEG (cell, view, file); + } + return true; +} + +// read in all readout-level JPEG files for this cell +bool pmCellWriteJPEG (pmCell *cell, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < cell->readouts->n; i++) { + + pmReadout *readout = cell->readouts->data[i]; + pmReadoutWriteJPEG (readout, view, file); + } + return true; +} + +// read in all readout-level Objects files for this cell +bool pmReadoutWriteJPEG (pmReadout *readout, const pmFPAview *view, pmFPAfile *file) +{ + char *name, *mode, *word, *mapname; + psArray *range; + psImageJpegColormap *map; + + switch (file->type) { + case PM_FPA_FILE_JPEG: + + name = pmFPAfileNameFromRule (file->filerule, file, view); + + mapname = pmFPAfileNameFromRule (file->filextra, file, view); + map = psImageJpegColormapSet (NULL, mapname); + if (!map) { + map = psImageJpegColormapSet (NULL, "-greyscale"); + } + + mode = pmFPAfileNameFromRule (file->extrule, file, view); + word = pmFPAfileNameFromRule (file->extxtra, file, view); + range = psStringSplitArray (word, ":"); + + // XXX we need to decide where the scale will come from in the long term + psImageClippedStatsInit (10000); + + psStats *stats = psImageClippedStats (readout->image, NULL, 0, 0.25, 0.75); + float delta = stats->robustUQ - stats->robustLQ; + float min = stats->robustMedian - 3*delta; + float max = stats->robustMedian - 6*delta; + if (!strcasecmp (mode, "RANGE") && range) { + float fmin = atof(range->data[0]); + float fmax = atof(range->data[1]); + min = stats->robustMedian + fmin*delta; + max = stats->robustMedian + fmax*delta; + } + if (!strcasecmp (mode, "FRACTION")) { + float fmin = atof(range->data[0]); + float fmax = atof(range->data[1]); + min = fmin*stats->robustMedian; + max = fmax*stats->robustMedian; + } + psImageJpeg (map, readout->image, name, min, max); + + psFree (name); + psFree (mode); + psFree (word); + psFree (mapname); + psFree (map); + psFree (stats); + psImageClippedStatsCleanup (); + + return true; + + default: + fprintf (stderr, "warning: type mismatch\n"); + break; + } + return false; +} Index: trunk/psModules/src/astrom/pmFPA_JPEG.h =================================================================== --- trunk/psModules/src/astrom/pmFPA_JPEG.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPA_JPEG.h (revision 6872) @@ -0,0 +1,27 @@ +/** @file pmFPAview.h +* +* @brief Tools to manipulate the FPA structure elements. +* +* @ingroup AstroImage +* +* @author EAM, IfA +* +* @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ +* +* Copyright 2004-2005 Institute for Astronomy, University of Hawaii +*/ + +#ifndef PM_FPA_JPEG_H +#define PM_FPA_JPEG_H + +/// @addtogroup AstroImage +/// @{ + +bool pmFPAviewWriteJPEG (const pmFPAview *view, pmFPAfile *file); +bool pmFPAWriteJPEG (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file); +bool pmChipWriteJPEG (pmChip *chip, const pmFPAview *view, pmFPAfile *file); +bool pmCellWriteJPEG (pmCell *cell, const pmFPAview *view, pmFPAfile *file); +bool pmReadoutWriteJPEG (pmReadout *readout, const pmFPAview *view, pmFPAfile *file); + +# endif Index: trunk/psModules/src/astrom/pmFPAfile.c =================================================================== --- trunk/psModules/src/astrom/pmFPAfile.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAfile.c (revision 6872) @@ -0,0 +1,1092 @@ +#include +#include "pslib.h" +#include "psAdditionals.h" +#include "pmConfig.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAConstruct.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" +#include "pmFPACopy.h" +#include "pmFPARead.h" +#include "pmFPAWrite.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmModel.h" +#include "pmSource.h" +#include "pmSourceIO.h" +#include "pmGrowthCurve.h" +#include "pmPSF.h" +#include "pmPSF_IO.h" +#include "pmFPA_JPEG.h" + +static void pmFPAfileFree (pmFPAfile *file) +{ + + if (file == NULL) + return; + + psFree (file->fpa); + psFree (file->readout); + psFree (file->names); + + psFree (file->format); + psFree (file->name); + + if (file->fits != NULL) { + psFitsClose (file->fits); + } + + psFree (file->filerule); + psFree (file->filextra); + psFree (file->extrule); + psFree (file->extxtra); + + psFree (file->filename); + psFree (file->extname); + + // these are just views ?? + // psFree (file->phu); + // psFree (file->header); + + return; +} + +pmFPAfile *pmFPAfileAlloc () +{ + + pmFPAfile *file = psAlloc (sizeof(pmFPAfile)); + psMemSetDeallocator (file, (psFreeFunc) pmFPAfileFree); + + file->phu = NULL; + file->readout = NULL; + file->header = NULL; + + file->fpa = NULL; + file->fits = NULL; + file->names = psMetadataAlloc(); + + file->format = NULL; + file->name = NULL; + + file->filerule = NULL; + file->filextra = NULL; + file->extrule = NULL; + file->extxtra = NULL; + + file->filename = NULL; + file->extname = NULL; + + file->type = PM_FPA_FILE_NONE; + file->mode = PM_FPA_MODE_NONE; + file->state = PM_FPA_STATE_CLOSED; + + return (file); +} + +pmFPAfile *pmFPAfileDefine (psMetadata *files, psMetadata *camera, pmFPA *fpa, char *name) +{ + + bool status; + char *depth; + char *type; + + // select the FILERULES from the camera config + psMetadata *filerules = psMetadataLookupPtr (&status, camera, "FILERULES"); + if (filerules == NULL) { + psErrorStackPrint(stderr, "Can't find FILERULES in the CAMERA configuration!\n"); + return NULL; + } + + // select the name from the FILERULES + // check for alias name (type == STR, name is aliased name) + char *realname = psMetadataLookupStr (&status, filerules, name); + if (realname == NULL) + realname = name; + + psMetadata *data = psMetadataLookupPtr (&status, filerules, realname); + if (data == NULL) { + psErrorStackPrint(stderr, "Can't find file concept %s!\n", name); + return NULL; + } + + pmFPAfile *file = pmFPAfileAlloc (); + + // save the name of this pmFPAfile + file->name = psStringCopy (name); + + file->filerule = psMemIncrRefCounter(psMetadataLookupStr (&status, data, "FILENAME.RULE")); + file->filextra = psMemIncrRefCounter(psMetadataLookupStr (&status, data, "FILENAME.XTRA")); + file->extrule = psMemIncrRefCounter(psMetadataLookupStr (&status, data, "EXTNAME.RULE")); + file->extxtra = psMemIncrRefCounter(psMetadataLookupStr (&status, data, "EXTNAME.XTRA")); + + file->fileDepth = PM_FPA_DEPTH_NONE; + depth = psMetadataLookupStr (&status, data, "FILE.DEPTH"); + if (depth != NULL) { + if (!strcasecmp (depth, "FPA")) { + file->fileDepth = PM_FPA_DEPTH_FPA; + } + if (!strcasecmp (depth, "CHIP")) { + file->fileDepth = PM_FPA_DEPTH_CHIP; + } + if (!strcasecmp (depth, "CELL")) { + file->fileDepth = PM_FPA_DEPTH_CELL; + } + if (!strcasecmp (depth, "READOUT")) { + file->fileDepth = PM_FPA_DEPTH_READOUT; + } + } + if (file->fileDepth == PM_FPA_DEPTH_NONE) { + psLogMsg (__func__, 3, "warning: FILE.DEPTH is not set for %s\n", name); + } + + file->dataDepth = PM_FPA_DEPTH_NONE; + depth = psMetadataLookupStr (&status, data, "DATA.DEPTH"); + if (depth != NULL) { + if (!strcasecmp (depth, "FPA")) { + file->dataDepth = PM_FPA_DEPTH_FPA; + } + if (!strcasecmp (depth, "CHIP")) { + file->dataDepth = PM_FPA_DEPTH_CHIP; + } + if (!strcasecmp (depth, "CELL")) { + file->dataDepth = PM_FPA_DEPTH_CELL; + } + if (!strcasecmp (depth, "READOUT")) { + file->dataDepth = PM_FPA_DEPTH_READOUT; + } + } + if (file->dataDepth == PM_FPA_DEPTH_NONE) { + psLogMsg (__func__, 3, "warning: DATA.DEPTH is not set for %s\n", name); + } + + file->type = PM_FPA_FILE_NONE; + type = psMetadataLookupStr (&status, data, "FILE.TYPE"); + if (type != NULL) { + if (!strcasecmp (type, "SX")) { + file->type = PM_FPA_FILE_SX; + } + if (!strcasecmp (type, "OBJ")) { + file->type = PM_FPA_FILE_OBJ; + } + if (!strcasecmp (type, "CMP")) { + file->type = PM_FPA_FILE_CMP; + } + if (!strcasecmp (type, "CMF")) { + file->type = PM_FPA_FILE_CMF; + } + if (!strcasecmp (type, "RAW")) { + file->type = PM_FPA_FILE_RAW; + } + if (!strcasecmp (type, "IMAGE")) { + file->type = PM_FPA_FILE_IMAGE; + } + if (!strcasecmp (type, "PSF")) { + file->type = PM_FPA_FILE_PSF; + } + if (!strcasecmp (type, "JPEG")) { + file->type = PM_FPA_FILE_JPEG; + } + } + if (file->type == PM_FPA_FILE_NONE) { + psLogMsg (__func__, 3, "warning: FILE.TYPE is not defined for %s\n", name); + } + + file->mode = PM_FPA_MODE_NONE; + type = psMetadataLookupStr (&status, data, "FILE.MODE"); + if (type != NULL) { + if (!strcasecmp (type, "READ")) { + file->mode = PM_FPA_MODE_READ; + } + if (!strcasecmp (type, "WRITE")) { + file->mode = PM_FPA_MODE_WRITE; + } + } + if (file->mode == PM_FPA_MODE_NONE) { + psLogMsg (__func__, 3, "warning: FILE.MODE is not defined for %s\n", name); + } + + if (fpa != NULL) { + file->fpa = psMemIncrRefCounter(fpa); + } + + // for WRITE type of data, the output format needs to be determined + // this is only needed if the output file is not identical in structure to the input + char *formatName = psMetadataLookupStr (&status, data, "FILE.FORMAT"); + if (formatName && strcasecmp (formatName, "NONE")) { + psMetadata *formats = psMetadataLookupMD(&status, camera, "FORMATS"); // List of formats + char *formatFile = psMetadataLookupStr (&status, formats, formatName); + readConfig (&file->format, formatFile, formatName); + } + + psMetadataAddPtr (files, PS_LIST_TAIL, name, PS_DATA_UNKNOWN, "", file); + + // we free this copy of file, but 'files' still has a copy + psFree (file); + + // the returned value is a view into the version on 'files' + return (file); +} + +/* +pmFPAfile *pmFPAfileConstruct (psMetadata *files, psMetadata *format, psMetadata *camera, char *name) +{ + pmFPA *fpa = pmFPAConstruct (camera); + pmFPAfile *file = pmFPAfileDefine (files, format, fpa, name); + psFree (fpa); + return file; +} +*/ + +// open file (if not already opened) +bool pmFPAfileOpen (pmFPAfile *file, const pmFPAview *view) +{ + + bool status; + char *extra; + char *mode = NULL; + char *readMode = "r"; + char *writeMode = "w"; + + if (file->mode == PM_FPA_MODE_NONE) { + return false; + } + if (file->mode == PM_FPA_MODE_INTERNAL) { + return false; + } + if (file->mode == PM_FPA_MODE_READ) { + mode = readMode; + } + if (file->mode == PM_FPA_MODE_WRITE) { + mode = writeMode; + } + + if (file->state == PM_FPA_STATE_OPEN) { + return true; + } + + // determine the file name + file->filename = pmFPAfileNameFromRule (file->filerule, file, view); + if (file->filename == NULL) + return false; + + // indirect filenames + if (!strcasecmp (file->filename, "@FILES")) { + psFree (file->filename); + extra = pmFPAfileNameFromRule (file->filextra, file, view); + file->filename = psMetadataLookupStr (&status, file->names, extra); + psFree (extra); + if (file->filename == NULL) + return false; + // psMetadataLookupStr just returns a view, file->filename must be protected + psMemIncrRefCounter (file->filename); + } + if (!strcasecmp (file->filename, "@DETDB")) { + psFree (file->filename); + extra = pmFPAfileNameFromRule (file->filextra, file, view); + // file->filename = pmDetrendSelect (extra); + psFree (extra); + if (file->filename == NULL) + return false; + psMemIncrRefCounter (file->filename); + } + + switch (file->type) { + // open the FITS types: + case PM_FPA_FILE_IMAGE: + case PM_FPA_FILE_CMF: + psTrace ("pmFPAfile", 5, "opening %s (type: %d)\n", file->filename, file->type); + file->fits = psFitsOpen (file->filename, mode); + if (file->fits == NULL) + psAbort (__func__, "error opening file %s\n", file->filename); + file->state = PM_FPA_STATE_OPEN; + break; + + // defer opening TEXT types: + case PM_FPA_FILE_SX: + case PM_FPA_FILE_OBJ: + case PM_FPA_FILE_CMP: + case PM_FPA_FILE_RAW: + case PM_FPA_FILE_PSF: + case PM_FPA_FILE_JPEG: + psTrace ("pmFPAfile", 5, "not opening %s (type: %d)\n", file->filename, file->type); + break; + + default: + fprintf (stderr, "warning: type mismatch for %s : %d\n", file->filename, file->type); + return false; + } + return true; +} + +bool pmFPAfileRead (pmFPAfile *file, const pmFPAview *view) +{ + if (file->mode != PM_FPA_MODE_READ) + return false; + + // get the current depth + pmFPAdepth depth = pmFPAviewDepth (view); + + // do we need to open this file? + if (depth == file->fileDepth) { + pmFPAfileOpen (file, view); + } + + // do we need to read this file? + if (depth != file->dataDepth) + return false; + + switch (file->type) { + case PM_FPA_FILE_IMAGE: + if (pmFPAviewReadFitsImage (view, file)) { + psTrace ("pmFPAfile", 5, "reading %s (type: %d)\n", file->filename, file->type); + } else { + psTrace ("pmFPAfile", 5, "skipping %s (type: %d)\n", file->filename, file->type); + } + break; + + case PM_FPA_FILE_SX: + case PM_FPA_FILE_RAW: + case PM_FPA_FILE_OBJ: + case PM_FPA_FILE_CMP: + case PM_FPA_FILE_CMF: + pmFPAviewReadObjects (view, file); + psTrace ("pmFPAfile", 5, "reading %s (type: %d)\n", file->filename, file->type); + break; + + case PM_FPA_FILE_PSF: + pmFPAviewReadPSFmodel (view, file); + psTrace ("pmFPAfile", 5, "reading %s (type: %d)\n", file->filename, file->type); + break; + + case PM_FPA_FILE_JPEG: + break; + + default: + fprintf (stderr, "warning: type mismatch\n"); + return false; + } + return true; +} + +bool pmFPAfileWrite (pmFPAfile *file, const pmFPAview *view) +{ + if (file->mode != PM_FPA_MODE_WRITE) + return false; + + // get the current depth + pmFPAdepth depth = pmFPAviewDepth (view); + + // do we need to write this file? + if (depth != file->dataDepth) + return false; + + // do we need to open this file? + if (depth >= file->fileDepth) { + pmFPAfileOpen (file, view); + } + + switch (file->type) { + case PM_FPA_FILE_IMAGE: + pmFPAviewWriteFitsImage (view, file); + psTrace ("pmFPAfile", 5, "wrote image %s (fpa: %p)\n", file->filename, file->fpa); + break; + + case PM_FPA_FILE_SX: + case PM_FPA_FILE_RAW: + case PM_FPA_FILE_OBJ: + case PM_FPA_FILE_CMP: + case PM_FPA_FILE_CMF: + pmFPAviewWriteObjects (view, file); + psTrace ("pmFPAfile", 5, "wrote object %s (fpa: %p)\n", file->filename, file->fpa); + break; + + case PM_FPA_FILE_PSF: + pmFPAviewWritePSFmodel (view, file); + psTrace ("pmFPAfile", 5, "wrote PSF %s (fpa: %p)\n", file->filename, file->fpa); + break; + + case PM_FPA_FILE_JPEG: + pmFPAviewWriteJPEG (view, file); + psTrace ("pmFPAfile", 5, "wrote PSF %s (fpa: %p)\n", file->filename, file->fpa); + break; + + default: + fprintf (stderr, "warning: type mismatch\n"); + return false; + } + return true; +} + +// create the data elements (headers, images) appropriate for this view +bool pmFPAfileCreate (pmFPAfile *file, const pmFPAview *view) +{ + if (file->mode != PM_FPA_MODE_WRITE) + return false; + + // get the current depth + pmFPAdepth depth = pmFPAviewDepth (view); + + // do we need to write this file? + if (depth != file->dataDepth) + return false; + + // XXX is this a sufficient check to avoid creating elements? + if (file->src == NULL) + return false; + + switch (file->type) { + case PM_FPA_FILE_IMAGE: + /* create a PHU for thie file, if it does not exist */ + pmFPAfileCopyStructureView (file->fpa, file->src, file->format, file->xBin, file->yBin, view); + psTrace ("pmFPAfile", 5, "created fpa data elements for %s (fpa: %p)\n", file->filename, file->fpa); + break; + + case PM_FPA_FILE_SX: + case PM_FPA_FILE_RAW: + case PM_FPA_FILE_OBJ: + case PM_FPA_FILE_CMP: + case PM_FPA_FILE_CMF: + case PM_FPA_FILE_PSF: + case PM_FPA_FILE_JPEG: + break; + + default: + fprintf (stderr, "warning: type mismatch\n"); + return false; + } + return true; +} + +bool pmFPAfileClose (pmFPAfile *file, const pmFPAview *view) +{ + if (file->state == PM_FPA_STATE_CLOSED) { + return true; + } + + // is current depth == open depth? + pmFPAdepth depth = pmFPAviewDepth (view); + if (file->fileDepth != depth) { + return false; + } + + // check if we are actually open + switch (file->type) { + // check the FITS types + case PM_FPA_FILE_IMAGE: + case PM_FPA_FILE_CMF: + psFitsClose (file->fits); + psTrace ("pmFPAfile", 5, "closing %s (type: %d)\n", file->filename, file->type); + file->fits = NULL; + file->phu = NULL; + file->header = NULL; + file->state = PM_FPA_STATE_CLOSED; + break; + + // ignore the TEXT types + case PM_FPA_FILE_SX: + case PM_FPA_FILE_RAW: + case PM_FPA_FILE_OBJ: + case PM_FPA_FILE_CMP: + case PM_FPA_FILE_PSF: + case PM_FPA_FILE_JPEG: + break; + + default: + fprintf (stderr, "warning: type mismatch\n"); + return false; + } + return true; +} + +// attempt open, read, write, or close pmFPAfiles in files +bool pmFPAfileIOChecks (psMetadata *files, const pmFPAview *view, pmFPAfilePlace place) +{ + // recipe override values (command-line options): + psMetadataItem *item = NULL; + psMetadataIterator *iter = psMetadataIteratorAlloc (files, PS_LIST_HEAD, NULL); + while ((item = psMetadataGetAndIncrement (iter)) != NULL) { + pmFPAfile *file = item->data.V; + + if (place == PM_FPA_BEFORE) { + pmFPAfileRead (file, view); + pmFPAfileCreate (file, view); + } else { + pmFPAfileWrite (file, view); + pmFPAfileClose (file, view); + } + } + psFree (iter); + return true; +} + +// create a file with the given name, assign it type "INTERNAL", and supply it with an image +// of the requested dimensions. (image only, mask and weight are ignored) +pmReadout *pmFPAfileCreateInternal (psMetadata *files, char *name, int Nx, int Ny, int type) +{ + pmReadout *readout = pmReadoutAlloc (NULL); + readout->image = psImageAlloc (Nx, Ny, type); + + // I want an image from the + pmFPAfile *file = pmFPAfileAlloc(); + file->mode = PM_FPA_MODE_INTERNAL; + + file->readout = readout; + psMetadataAddPtr (files, PS_LIST_TAIL, name, PS_DATA_UNKNOWN, "", file); + psFree (file); + // we free this copy of file, but 'files' still has a copy + + return (readout); +} + +bool pmFPAfileDropInternal (psMetadata *files, char *name) +{ + bool status; + + pmFPAfile *file = psMetadataLookupPtr (&status, files, name); + if (file == NULL) + return false; + + if (file->mode != PM_FPA_MODE_INTERNAL) + return false; + + psMetadataRemoveKey (files, name); + return true; +} + +// select the readout from the named pmFPAfile; if the named file does not exist, +pmReadout *pmFPAfileThisReadout (psMetadata *files, const pmFPAview *view, const char *name) +{ + bool status; + + pmFPAfile *file = psMetadataLookupPtr (&status, files, name); + if (file == NULL) + return NULL; + + // internal files have the readout as a separate element: + if (file->mode == PM_FPA_MODE_INTERNAL) { + return file->readout; + } + + pmReadout *readout = pmFPAviewThisReadout (view, file->fpa); + return readout; +} + +// given an already-opened fits file, read the components corresponding +// to the specified view +bool pmFPAviewReadFitsImage (const pmFPAview *view, pmFPAfile *file) +{ + bool status; + pmFPA *fpa = file->fpa; + psFits *fits = file->fits; + + if (view->chip == -1) { + status = pmFPARead (fpa, fits, NULL); + return status; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + status = pmChipRead (chip, fits, NULL); + return status; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + status = pmCellRead (cell, fits, NULL); + return status; + } + return false; + + // XXX pmReadoutRead, pmReadoutReadSegement disabled for now + # if (0) + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + if (view->nRows == 0) { + pmReadoutRead (readout, fits, NULL); + } else { + pmReadoutReadSegment (readout, fits, view->nRows, view->iRows, NULL, NULL); + } + return true; + # endif +} + +// given an already-opened fits file, write the components corresponding +// to the specified view +bool pmFPAviewWriteFitsImage (const pmFPAview *view, pmFPAfile *file) +{ + + pmFPA *fpa = file->fpa; + psFits *fits = file->fits; + + // pmFPAWrite takes care of all PHUs as needed + if (view->chip == -1) { + pmFPAWrite (fpa, fits, NULL); + return true; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + // do we need to write out a PHU for this entry? + if (file->phu == NULL) { + pmHDU *hdu = pmFPAviewThisHDU (view, file->fpa); + pmHDU *phu = pmFPAviewThisPHU (view, file->fpa); + // if this hdu is the phu, the write function below will create the phu + if (hdu != phu) { + // we assume that the PHU is just a header + psMetadata *outhead = psMetadataCopy (NULL, phu->header); + psMetadataAdd (outhead, PS_LIST_TAIL, "EXTEND", PS_DATA_BOOL | PS_META_REPLACE, "this file has extensions", true); + psFitsWriteHeaderNotImage (file->fits, outhead); + file->phu = phu->header; + psTrace ("pmFPAfile", 5, "wrote phu %s (type: %d)\n", file->filename, file->type); + psFree (outhead); + } + } + + if (view->cell == -1) { + pmChipWrite (chip, fits, NULL); + return true; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellWrite (cell, fits, NULL); + return true; + } + return false; + + // XXX disable readout write for now + # if (0) + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + if (view->nRows == 0) { + pmReadoutWrite (readout, fits, NULL, NULL); + } else { + pmReadoutWriteSegment (readout, fits, view->nRows, view->iRows, NULL, NULL); + } + return true; + # endif +} + +// look for the given name on the argument list. +// returns the file (a view to the one saved on config->files) +pmFPAfile *pmFPAfileFromArgs (bool *found, pmConfig *config, char *filename, char *argname) +{ + bool status; + pmFPA *fpa = NULL; + psFits *fits = NULL; + pmFPAfile *file = NULL; + psMetadata *phu = NULL; + psMetadata *format = NULL; + + if (*found) + return NULL; + + // we search the argument data for the named fileset (argname) + psArray *infiles = psMetadataLookupPtr(&status, config->arguments, argname); + if (!status) + return NULL; + if (infiles->n < 1) + return NULL; + + // determine the current format from the header + // if no camera has been specified, use the first image as a template for the rest. + fits = psFitsOpen (infiles->data[0], "r"); + phu = psFitsReadHeader (NULL, fits); + format = pmConfigCameraFormatFromHeader (config, phu); + psFitsClose (fits); + + // build the template fpa, set up the basic view + fpa = pmFPAConstruct (config->camera); + + // load the given filerule (from config->camera) and associate it with the fpa + // the output file is just a view to the file on config->files + file = pmFPAfileDefine (config->files, config->camera, fpa, filename); + if (!file) { + psErrorStackPrint(stderr, "file %s not defined\n", filename); + psFree (fpa); + psFree (format); + return NULL; + } + + // this file is (by virtue of being supplied in the argument list) coming from the fileset + psFree (file->filerule); + psFree (file->filextra); + + // adjust the rules to identify these files in the file->names data + file->filerule = psStringCopy ("@FILES"); + // XXX this rule does not work in general + file->filextra = psStringCopy ("{CHIP.NAME}.{CELL.NAME}"); + + // examine the list of input files and validate their cameras + for (int i = 0; i < infiles->n; i++) { + if (i > 0) { + fits = psFitsOpen (infiles->data[i], "r"); + phu = psFitsReadHeader (NULL, fits); + pmConfigValidateCameraFormat (format, phu); + psFitsClose (fits); + } + + // set the view to the corresponding entry for this phu + pmFPAview *view = pmFPAAddSourceFromHeader (fpa, phu, format); + + // XXX is this the correct psMD to save the filename? + char *name = pmFPAfileNameFromRule (file->filextra, file, view); + psMetadataAddStr (file->names, PS_LIST_TAIL, name, 0, "", infiles->data[i]); + + psFree (view); + psFree (name); + psFree (phu); + } + psFree (fpa); + psFree (format); + *found = true; + + return file; +} + +// XXX this this function through, then finish +# if 0 +// look for the given name on the argument list. +// returns the file (a view to the one saved on config->files) +// in this case, each file should correspond to the same view +// (except at the readout level), of multiple FPAs +// XXX think this through a bit more: +// - do we create multiple input fpas, or assign the same files to the single fpa? +// - do we save the multiple pmFPAfiles in the config->files psMD? +// - do we save the multiple filenames in the file->names psMD? +// - if we have a single FPA and multiple names, we need a method to +// turn on a specific name for the I/O actions. probably true if we +// have multiple FPAs as well. +pmFPAfile *pmFPAfileSetFromArgs (bool *found, pmConfig *config, char *filename, char *argname) +{ + bool status; + pmFPA *fpa = NULL; + psFits *fits = NULL; + pmFPAfile *file = NULL; + psMetadata *phu = NULL; + psMetadata *format = NULL; + + if (*found) + return NULL; + + // we search the argument data for the named fileset (argname) + psArray *infiles = psMetadataLookupPtr(&status, config->arguments, argname); + if (!status) + return NULL; + if (infiles->n < 1) + return NULL; + + // determine the current format from the header + // if no camera has been specified, use the first image as a template for the rest. + fits = psFitsOpen (infiles->data[0], "r"); + phu = psFitsReadHeader (NULL, fits); + format = pmConfigCameraFormatFromHeader (config, phu); + psFitsClose (fits); + + // build the template fpa, set up the basic view + fpa = pmFPAConstruct (config->camera); + + // load the given filerule (from config->camera) and associate it with the fpa + // the output file is just a view to the file on config->files + // XXX the filenames placed on config->files should include the seq number + file = pmFPAfileDefine (config->files, config->camera, fpa, filename); + if (!file) { + psErrorStackPrint(stderr, "file %s not defined\n", filename); + psFree (fpa); + psFree (format); + return NULL; + } + + // this file is (by virtue of being supplied in the argument list) coming from the fileset + psFree (file->filerule); + psFree (file->filextra); + + // adjust the rules to identify these files in the file->names data + file->filerule = psStringCopy ("@FILES"); + // XXX this rule does not work in general + file->filextra = psStringCopy ("{CHIP.NAME}.{CELL.NAME}"); + + // examine the list of input files and validate their cameras + for (int i = 0; i < infiles->n; i++) { + if (i > 0) { + fits = psFitsOpen (infiles->data[i], "r"); + phu = psFitsReadHeader (NULL, fits); + pmConfigValidateCameraFormat (format, phu); + psFitsClose (fits); + } + + // set the view to the corresponding entry for this phu + pmFPAview *view = pmFPAAddSourceFromHeader (fpa, phu, format); + + // XXX is this the correct psMD to save the filename? + char *name = pmFPAfileNameFromRule (file->filextra, file, view); + psMetadataAddStr (file->names, PS_LIST_TAIL, name, 0, "", infiles->data[i]); + + psFree (view); + psFree (name); + psFree (phu); + } + psFree (fpa); + psFree (format); + *found = true; + + return file; +} +# endif + +// create a new output pmFPAfile based on an existing FPA +pmFPAfile *pmFPAfileFromFPA (pmConfig *config, pmFPA *src, int xBin, int yBin, char *filename) +{ + // XXX pmFPAConstruct has many leaks (6919) + pmFPA *fpa = pmFPAConstruct (config->camera); + pmFPAfile *file = pmFPAfileDefine (config->files, config->camera, fpa, filename); + file->src = src; // inherit output elements from this source pmFPA + file->xBin = xBin; + file->yBin = yBin; + + return file; +} + +// look for the given name on the argument list. +pmFPAfile *pmFPAfileFromConf (bool *found, pmConfig *config, char *filename, pmFPA *input) +{ + psFits *fits = NULL; + pmFPAfile *file = NULL; + psMetadata *phu = NULL; + psMetadata *format = NULL; + psArray *infiles = NULL; + + if (*found) + return NULL; + + // a camera config is needed (as source of file rule) + if (config->camera == NULL) { + psErrorStackPrint (stderr, "camera is not defined\n"); + return NULL; + } + + // expect @DETDB in the config filerule + file = pmFPAfileDefine (config->files, config->camera, NULL, filename); + if (!file) { + psErrorStackPrint(stderr, "file %s not defined\n", filename); + return NULL; + } + + // image names come from the file->name list? + if (!strcasecmp (file->filerule, "@FILES")) + psAbort ("pmFPAfileFromConfig", "programming error"); + + // image needs to come from the detrend database + if (!strcasecmp (file->filerule, "@DETDB")) { + // char *extra = pmFPAfileNameFromRule (file->filextra, file, view); + // psArray *infiles = pmDetrendSelect (extra, input); + psAbort ("pmFPAfileFromConfig", "@DETDB not yet defined"); + } else { + infiles = psArrayAlloc(1); + infiles->n = 1; + infiles->data[0] = psStringCopy (file->filerule); + } + if (infiles == NULL) + return NULL; + if (infiles->n < 1) { + psFree (infiles); + return NULL; + } + + // determine the current format from the header + // if no camera has been specified, use the first image as a template for the rest. + fits = psFitsOpen (infiles->data[0], "r"); + phu = psFitsReadHeader (NULL, fits); + format = pmConfigCameraFormatFromHeader (config, phu); + psFitsClose (fits); + + // build the template fpa, set up the basic view + file->fpa = pmFPAConstruct (config->camera); + + // this file is (by virtue of being supplied in the argument list) coming from the fileset + psFree (file->filerule); + psFree (file->filextra); + + // adjust the rules to identify these files in the file->names data + file->filerule = psStringCopy ("@FILES"); + // XXX this rule does not work in general + file->filextra = psStringCopy ("{CHIP.NAME}.{CELL.NAME}"); + + // examine the list of input files and validate their cameras + for (int i = 0; i < infiles->n; i++) { + if (i > 0) { + fits = psFitsOpen (infiles->data[i], "r"); + phu = psFitsReadHeader (NULL, fits); + pmConfigValidateCameraFormat (format, phu); + psFitsClose (fits); + } + + // set the view to the corresponding entry for this phu + pmFPAview *view = pmFPAAddSourceFromHeader (file->fpa, phu, format); + + // XXX is this the correct psMD to save the filename? + char *name = pmFPAfileNameFromRule (file->filextra, file, view); + psMetadataAddStr (file->names, PS_LIST_TAIL, name, 0, "", infiles->data[i]); + + psFree (view); + psFree (name); + psFree (phu); + } + psFree (format); + psFree (infiles); + *found = true; + return file; +} + +bool pmFPAfileAddFileNames (psMetadata *files, char *name, char *value, int mode) +{ + + // add the output names to the output-type files + psMetadataItem *item = NULL; + psMetadataIterator *iter = psMetadataIteratorAlloc (files, PS_LIST_HEAD, NULL); + while ((item = psMetadataGetAndIncrement (iter)) != NULL) { + pmFPAfile *file = item->data.V; + + if (file->mode == mode) { + psMetadataAddStr (file->names, PS_LIST_TAIL, name, 0, "", value); + } + } + psFree (iter); + return true; +} + +// select the rule from the camera configuration, perform substitutions as needed +char *pmFPAfileNameFromRule (char *rule, pmFPAfile *file, const pmFPAview *view) +{ + + char *newName = NULL; // destination for resulting name + + newName = psStringCopy (rule); + + if (strstr (newName, "{CHIP.NAME}") != NULL) { + pmChip *chip = pmFPAviewThisChip (view, file->fpa); + if (chip != NULL) { + char *name = psMetadataLookupStr (NULL, chip->concepts, "CHIP.NAME"); + if (name != NULL) { + newName = psStringSubstitute (newName, name, "{CHIP.NAME}"); + } + } + } + if (strstr (newName, "{CELL.NAME}") != NULL) { + pmCell *cell = pmFPAviewThisCell (view, file->fpa); + if (cell != NULL) { + char *name = psMetadataLookupStr (NULL, cell->concepts, "CELL.NAME"); + if (name != NULL) { + newName = psStringSubstitute (newName, name, "{CELL.NAME}"); + } + } + } + if (strstr (newName, "{EXTNAME}") != NULL) { + pmHDU *hdu = pmFPAviewThisHDU (view, file->fpa); + if (hdu->extname != NULL) { + newName = psStringSubstitute (newName, hdu->extname, "{EXTNAME}"); + } + } + if (strstr (newName, "{OUTPUT}") != NULL) { + char *name = psMetadataLookupStr (NULL, file->names, "OUTPUT"); + if (name != NULL) { + newName = psStringSubstitute (newName, name, "{OUTPUT}"); + } + } + return newName; +} + +// given an already-opened fits file, write the components corresponding +// to the specified view +bool pmFPAfileCopyView (pmFPA *out, pmFPA *in, const pmFPAview *view) +{ + // pmFPAWrite takes care of all PHUs as needed + if (view->chip == -1) { + pmFPACopy (out, in); + return true; + } + if (view->chip >= in->chips->n) { + return false; + } + pmChip *inChip = in->chips->data[view->chip]; + pmChip *outChip = out->chips->data[view->chip]; + + if (view->cell == -1) { + pmChipCopy (outChip, inChip); + return true; + } + if (view->cell >= inChip->cells->n) { + return false; + } + pmCell *inCell = inChip->cells->data[view->cell]; + pmCell *outCell = outChip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellCopy (outCell, inCell); + return true; + } + return false; + + // XXX add readout / segment equivalents +} + +// given an already-opened fits file, write the components corresponding +// to the specified view +bool pmFPAfileCopyStructureView (pmFPA *out, pmFPA *in, psMetadata *format, int xBin, int yBin, const pmFPAview *view) +{ + // pmFPAWrite takes care of all PHUs as needed + if (view->chip == -1) { + pmFPAAddSourceFromView (out, view, format); + pmFPACopyStructure (out, in, xBin, yBin); + return true; + } + if (view->chip >= in->chips->n) { + return false; + } + pmChip *inChip = in->chips->data[view->chip]; + pmChip *outChip = out->chips->data[view->chip]; + + if (view->cell == -1) { + pmFPAAddSourceFromView (out, view, format); + pmChipCopyStructure (outChip, inChip, xBin, yBin); + return true; + } + if (view->cell >= inChip->cells->n) { + return false; + } + pmCell *inCell = inChip->cells->data[view->cell]; + pmCell *outCell = outChip->cells->data[view->cell]; + + if (view->readout == -1) { + pmFPAAddSourceFromView (out, view, format); + pmCellCopyStructure (outCell, inCell, xBin, yBin); + return true; + } + return false; + + // XXX add readout / segment equivalents +} Index: trunk/psModules/src/astrom/pmFPAfile.h =================================================================== --- trunk/psModules/src/astrom/pmFPAfile.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAfile.h (revision 6872) @@ -0,0 +1,155 @@ +/** @file pmFPAview.h +* +* @brief Tools to manipulate the FPA structure elements. +* +* @ingroup AstroImage +* +* @author EAM, IfA +* +* @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ +* +* Copyright 2004-2005 Institute for Astronomy, University of Hawaii +*/ + +#ifndef PM_FPA_FILE_H +#define PM_FPA_FILE_H + +#include "pslib.h" +#include "pmConfig.h" +#include "pmFPA.h" +#include "pmFPAview.h" + +typedef enum { + PM_FPA_BEFORE, + PM_FPA_AFTER, +} pmFPAfilePlace; + +typedef enum { + PM_FPA_FILE_NONE, + PM_FPA_FILE_SX, + PM_FPA_FILE_OBJ, + PM_FPA_FILE_CMP, + PM_FPA_FILE_CMF, + PM_FPA_FILE_RAW, + PM_FPA_FILE_IMAGE, + PM_FPA_FILE_PSF, + PM_FPA_FILE_JPEG, +} pmFPAfileType; + +typedef enum { + PM_FPA_MODE_NONE, + PM_FPA_MODE_READ, + PM_FPA_MODE_WRITE, + PM_FPA_MODE_INTERNAL, +} pmFPAfileMode; + +typedef enum { + PM_FPA_STATE_OPEN, + PM_FPA_STATE_CLOSED, +} pmFPAfileState; + +typedef struct +{ + pmFPAfileMode mode; // is this file read, written, or only used internally? + pmFPAfileType type; // what type of data is read from / written to disk? + pmFPAfileState state; // have we opened the file, etc? + + pmFPAdepth fileDepth; // what depth in the FPA hierarchy represents a unique file? + pmFPAdepth dataDepth; // at what depth do we read/write the data segment? + + pmFPA *fpa; // for I/O files, we carry a pointer to the complete fpa + psFits *fits; // for I/O files of fits type (IMAGE, CMP, CMF), we carry a file handle + + psMetadata *phu; // pointer (view) to the current phu header + psMetadata *header; // pointer (view) to the current hdu header + + pmReadout *readout; // for internal files, we only carry a single readout + + psMetadata *names; // filenames supplied by the cmdline or detdb are saved here + + char *filerule; // rule for constructing a filename when needed + char *filextra; // additional information used to define filenames (context dependent) + char *extrule; // rule for constructing an extension name when needed + char *extxtra; // additional information used to define extension names (context dependent) + + char *name; // the name of the rule (useful for debugging / tracing) + char *filename; // the current name of an active file + char *extname; // the current name of an active file extension + + // the following elements are used for WRITE-mode IMAGE-type pmFPAfiles to inform + // the creation of a new image based on an existing image + pmFPA *src; // if an output FPA, inherit from this FPA + int xBin; // desired binning in x direction + int yBin; // desired binning in y direction + psMetadata *format; +} +pmFPAfile; + +// allocate an empty pmFPAfile structure +pmFPAfile *pmFPAfileAlloc (); + +// load the pmFPAfile information from the camera configuration data +pmFPAfile *pmFPAfileDefine (psMetadata *files, psMetadata *camera, pmFPA *fpa, char *name); + +// load the pmFPAfile information from the camera configuration data, constructing the needed fpa structure +// XXX deprecate this function? +// pmFPAfile *pmFPAfileConstruct (psMetadata *files, psMetadata *format, psMetadata *camera, char *name); + +// open the real file corresponding to the given pmFPAfile appropriate to the current view +bool pmFPAfileOpen (pmFPAfile *file, const pmFPAview *view); + +// read from the real file corresponding to the given pmFPAfile for the current view +bool pmFPAfileRead (pmFPAfile *file, const pmFPAview *view); + +bool pmFPAfileCreate (pmFPAfile *file, const pmFPAview *view); + +// write to the real file corresponding to the given pmFPAfile for the current view +bool pmFPAfileWrite (pmFPAfile *file, const pmFPAview *view); + +// close the real file corresponding to the given pmFPAfile appropriate to the current view +bool pmFPAfileClose (pmFPAfile *file, const pmFPAview *view); + +// examine all pmFPAfiles listed in the files and perform the needed I/O operations (open,read,write,close) +bool pmFPAfileIOChecks (psMetadata *files, const pmFPAview *view, pmFPAfilePlace place); + +// return an image corresponding to the current readout, from the specified file. if the pmFPAfile does not +// exist, construct the image using the given size and type (save it in a pmFPAfile??) +// psImage *pmFPAfileReadoutImage (psMetadata *files, const pmFPAview *view, char *name, int Nx, int Ny, int type); + +// select the readout from the named pmFPAfile; if the named file does not exist, +pmReadout *pmFPAfileThisReadout (psMetadata *files, const pmFPAview *view, const char *name); + +// create a file with the given name, assign it type "INTERNAL", and supply it with an image +// of the requested dimensions. (image only, mask and weight are ignored) +pmReadout *pmFPAfileCreateInternal (psMetadata *files, char *name, int Nx, int Ny, int type); + +// delete the INTERNAL file of the given name (if it exists) +bool pmFPAfileDropInternal (psMetadata *files, char *name); + +// read an image into the current view +bool pmFPAviewReadFitsImage (const pmFPAview *view, pmFPAfile *file); + +// write the components for the specified view +bool pmFPAviewWriteFitsImage (const pmFPAview *view, pmFPAfile *file); + +// look for the given argname on the argument list. find the give filename from the file rules +pmFPAfile *pmFPAfileFromArgs (bool *found, pmConfig *config, char *filename, char *argname); + +// look for the given argname on the argument list. find the give filename from the file rules +pmFPAfile *pmFPAfileFromConf (bool *found, pmConfig *config, char *filename, pmFPA *input); + +// create a new output pmFPAfile based on an existing FPA +pmFPAfile *pmFPAfileFromFPA (pmConfig *config, pmFPA *src, int xBin, int yBin, char *filename); + +// add the specified filename info (value) to the files of the given mode using the given reference name +bool pmFPAfileAddFileNames (psMetadata *files, char *name, char *value, int mode); + +// convert the rule to a name based on the current view +char *pmFPAfileNameFromRule (char *rule, pmFPAfile *file, const pmFPAview *view); + +bool pmFPAfileCopyView (pmFPA *out, pmFPA *in, const pmFPAview *view); + +bool pmFPAfileCopyStructureView (pmFPA *out, pmFPA *in, psMetadata *format, int xBin, int yBin, const pmFPAview *view); + +# endif Index: trunk/psModules/src/astrom/pmFPAview.c =================================================================== --- trunk/psModules/src/astrom/pmFPAview.c (revision 6872) +++ trunk/psModules/src/astrom/pmFPAview.c (revision 6872) @@ -0,0 +1,267 @@ +/** @file pmFPAview.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:04 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmHDU.h" +#include "pmHDUUtils.h" +#include "pmFPA.h" +#include "pmFPAview.h" + +static void pmFPAviewFree (pmFPAview *view) +{ + if (view == NULL) + return; + return; +} + +pmFPAview *pmFPAviewAlloc (int nRows) +{ + pmFPAview *view = psAlloc (sizeof(pmFPAview)); + psMemSetDeallocator (view, (psFreeFunc) pmFPAviewFree); + + view->chip = -1; + view->cell = -1; + view->readout = -1; + view->iRows = 0; + view->nRows = nRows; + return (view); +} + +pmFPAdepth pmFPAviewDepth (const pmFPAview *view) +{ + + if (view->chip < 0) { + return PM_FPA_DEPTH_FPA; + } + if (view->cell < 0) { + return PM_FPA_DEPTH_CHIP; + } + if (view->readout < 0) { + return PM_FPA_DEPTH_CELL; + } + return PM_FPA_DEPTH_READOUT; +} + +pmChip *pmFPAviewThisChip (const pmFPAview *view, pmFPA *fpa) +{ + + if (view->chip < 0) { + return NULL; + } + + if (view->chip >= fpa->chips->n) { + return NULL; + } + + pmChip *chip = fpa->chips->data[view->chip]; + return chip; +} + +pmChip *pmFPAviewNextChip (pmFPAview *view, pmFPA *fpa, int nStep) +{ + view->cell = -1; + view->readout = -1; + view->iRows = 0; + + // if there are no available chips, return NULL + if (fpa->chips->n <= 0) { + view->chip = -1; + return NULL; + } + + // clean up < -1 values + if (view->chip < -1) { + view->chip = -1; + } + + // increment to the next chip + view->chip += nStep; + + // if we are at the end of the stack, return NULL + if (view->chip >= fpa->chips->n) { + view->chip = -1; + return NULL; + } + + // get the correct chip pointer + pmChip *chip = fpa->chips->data[view->chip]; + return (chip); +} + +pmCell *pmFPAviewThisCell (const pmFPAview *view, pmFPA *fpa) +{ + + if (view->cell < 0) { + return NULL; + } + + pmChip *chip = pmFPAviewThisChip (view, fpa); + if (chip == NULL) { + return NULL; + } + + if (view->cell >= chip->cells->n) { + return NULL; + } + + pmCell *cell = chip->cells->data[view->cell]; + return cell; +} + +pmCell *pmFPAviewNextCell (pmFPAview *view, pmFPA *fpa, int nStep) +{ + + pmChip *chip = pmFPAviewThisChip (view, fpa); + if (chip == NULL) { + return NULL; + } + + view->readout = -1; + view->iRows = 0; + + // if there are no available cells, return NULL + if (chip->cells->n <= 0) { + view->cell = -1; + return NULL; + } + + // clean up < -1 values + if (view->cell < -1) { + view->cell = -1; + } + + // increment to the next cell + view->cell += nStep; + + // if we are at the end of the stack, return NULL + if (view->cell >= chip->cells->n) { + view->cell = -1; + return NULL; + } + + // get the correct cell pointer + pmCell *cell = chip->cells->data[view->cell]; + return (cell); +} + +pmReadout *pmFPAviewThisReadout (const pmFPAview *view, pmFPA *fpa) +{ + + if (view->readout < 0) { + return NULL; + } + + pmCell *cell = pmFPAviewThisCell (view, fpa); + if (cell == NULL) { + return NULL; + } + + if (view->readout >= cell->readouts->n) { + return NULL; + } + + pmReadout *readout = cell->readouts->data[view->readout]; + return readout; +} + +pmReadout *pmFPAviewNextReadout (pmFPAview *view, pmFPA *fpa, int nStep) +{ + + pmCell *cell = pmFPAviewThisCell (view, fpa); + if (cell == NULL) { + return NULL; + } + + view->iRows = 0; + + // if there are no available cells, return NULL + if (cell->readouts->n <= 0) { + view->readout = -1; + return NULL; + } + + // clean up < -1 values + if (view->readout < -1) { + view->readout = -1; + } + + // increment to the next cell + view->readout += nStep; + + // if we are at the end of the stack, return NULL + if (view->readout >= cell->readouts->n) { + view->readout = -1; + return NULL; + } + + // get the correct cell pointer + pmReadout *readout = cell->readouts->data[view->readout]; + return (readout); +} + +pmHDU *pmFPAviewThisHDU (const pmFPAview *view, pmFPA *fpa) +{ + // the HDU is attached to a cell, chip or fpa + // if this view has a -1 for the level which contains the hdu, + // there is no unambiguous HDU + + if (view->chip < 0) { + return pmHDUFromFPA (fpa); + } + if (view->cell < 0) { + return pmHDUFromChip (pmFPAviewThisChip (view, fpa)); + } + if (view->readout < 0) { + return pmHDUFromCell (pmFPAviewThisCell (view, fpa)); + } + return NULL; +} + +pmHDU *pmFPAviewThisPHU (const pmFPAview *view, pmFPA *fpa) +{ + // select the HDU which corresponds to the PHU containing this view + + pmHDU *hdu; + pmFPAview new; + pmChip *chip; + pmCell *cell; + + new = *view; + + if (view->chip < 0) { + hdu = pmHDUFromFPA (fpa); + if (hdu->phu) + return hdu; + return NULL; + } + if (view->cell < 0) { + chip = pmFPAviewThisChip (view, fpa); + hdu = pmHDUFromChip (chip); + if (hdu->phu) + return hdu; + new.chip = -1; + hdu = pmFPAviewThisPHU (&new, fpa); + return hdu; + } + if (view->readout < 0) { + cell = pmFPAviewThisCell (view, fpa); + hdu = pmHDUFromCell (cell); + if (hdu->phu) + return hdu; + new.cell = -1; + hdu = pmFPAviewThisPHU (&new, fpa); + return hdu; + } + return NULL; +} Index: trunk/psModules/src/astrom/pmFPAview.h =================================================================== --- trunk/psModules/src/astrom/pmFPAview.h (revision 6872) +++ trunk/psModules/src/astrom/pmFPAview.h (revision 6872) @@ -0,0 +1,70 @@ +/** @file pmFPAview.h +* +* @brief Tools to manipulate the FPA structure elements. +* +* @ingroup AstroImage +* +* @author EAM, IfA +* +* @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-04-17 18:01:04 $ +* +* Copyright 2004-2005 Institute for Astronomy, University of Hawaii +*/ + +#ifndef PM_FPA_VIEW_H +#define PM_FPA_VIEW_H + +#include "pmFPA.h" + +/// @addtogroup AstroImage +/// @{ + +// depth of interest +typedef enum { + PM_FPA_DEPTH_NONE, + PM_FPA_DEPTH_FPA, + PM_FPA_DEPTH_CHIP, + PM_FPA_DEPTH_CELL, + PM_FPA_DEPTH_READOUT, +} pmFPAdepth; + +typedef struct +{ + int chip; // Number of the chip, or -1 for all + int cell; // Number of the cell, or -1 for all + int readout; // Number of the readout, or -1 for all + int nRows; // Maximum number of rows per readout segment read, or 0 for all + int iRows; // Starting point for this read +} +pmFPAview; + +// allocate a pmFPAview structure for this fpa and camera +pmFPAview *pmFPAviewAlloc (int nRows); + +// determine the current view depth +pmFPAdepth pmFPAviewDepth (const pmFPAview *view); + +// return the currently selected chip for this view +pmChip *pmFPAviewThisChip (const pmFPAview *view, pmFPA *fpa); + +// advance view to the next chip +pmChip *pmFPAviewNextChip (pmFPAview *view, pmFPA *fpa, int nStep); + +// return the currently selected cell for this view +pmCell *pmFPAviewThisCell (const pmFPAview *view, pmFPA *fpa); + +// advance view to the next cell +pmCell *pmFPAviewNextCell (pmFPAview *view, pmFPA *fpa, int nStep); + +// return the currently selected readout for this view +pmReadout *pmFPAviewThisReadout (const pmFPAview *view, pmFPA *fpa); + +// advance view to the next readout +pmReadout *pmFPAviewNextReadout (pmFPAview *view, pmFPA *fpa, int nStep); + +// return the HDU corresponding to the current view +pmHDU *pmFPAviewThisHDU (const pmFPAview *view, pmFPA *fpa); +pmHDU *pmFPAviewThisPHU (const pmFPAview *view, pmFPA *fpa); + +# endif Index: trunk/psModules/src/astrom/pmHDU.c =================================================================== --- trunk/psModules/src/astrom/pmHDU.c (revision 6872) +++ trunk/psModules/src/astrom/pmHDU.c (revision 6872) @@ -0,0 +1,225 @@ +#include +#include + +#include "pslib.h" +#include "pmFPA.h" +#include "psAdditionals.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// File-static (private) functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Move to the appropriate extension in FITS file for HDU +static bool hduMove(pmHDU *hdu, // HDU with extname + psFits *fits // FITS file in which to move + ) +{ + // Deal with the PHU case + if (strcasecmp(hdu->extname, "PHU") == 0 || hdu->phu) { + if (! psFitsMoveExtNum(fits, 0, false)) { + psError(PS_ERR_IO, false, "Unable to move to primary header!\n"); + return false; + } + hdu->phu = true; + return true; + } + + if (! psFitsMoveExtName(fits, hdu->extname)) { + psError(PS_ERR_IO, false, "Unable to move to extension %s\n", hdu->extname); + return false; + } + // Now, just in case for some reason the PHU has an extension name that we've moved to.... + if (psFitsGetExtNum(fits) == 0) { + hdu->phu = true; + } else { + hdu->phu = false; + } + + return true; +} + +static void hduFree(pmHDU *hdu) +{ + psFree(hdu->extname); + psFree(hdu->format); + psFree(hdu->header); + psFree(hdu->images); + psFree(hdu->table); + psFree(hdu->weights); + psFree(hdu->masks); +} + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Public functions +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +pmHDU *pmHDUAlloc(const char *extname // Extension name + ) +{ + pmHDU *hdu = psAlloc(sizeof(pmHDU)); + psMemSetDeallocator(hdu, (psFreeFunc)hduFree); + + if (! extname || strlen(extname) == 0) { + hdu->phu = true; + hdu->extname = psStringCopy("PHU"); + } else { + if (strcasecmp(extname, "PHU") == 0) { + hdu->phu = true; + } else { + hdu->phu = false; + } + hdu->extname = psStringCopy(extname); + } + hdu->format = NULL; + hdu->header = NULL; + hdu->images = NULL; + hdu->table = NULL; + hdu->weights = NULL; + hdu->masks = NULL; + + return hdu; +} + +bool pmHDUReadHeader(pmHDU *hdu, // HDU for which to read header + psFits *fits // FITS file from which to read + ) +{ + assert(hdu); + assert(fits); + + // Move to the appropriate extension + psTrace(__func__, 5, "Moving to extension %s...\n", hdu->extname); + if (!hduMove(hdu, fits)) { + return false; + } + + if (!hdu->header) { + psTrace(__func__, 5, "Reading the header...\n"); + hdu->header = psFitsReadHeader(NULL, fits); + if (! hdu->header) { + psError(PS_ERR_IO, false, "Unable to read header for extension %s\n", hdu->extname); + return false; + } + } + + return true; +} + +// Read the HDU +// XXX: Add a region specifier? +bool pmHDURead(pmHDU *hdu, // HDU to read + psFits *fits // FITS file to read from + ) +{ + assert(hdu); + assert(fits); + + // Read the header; includes the move + if (!pmHDUReadHeader(hdu, fits)) { + return false; + } + + #ifdef FITS_TABLES + // What type is it? + if (psFitsIsImage(hdu->header)) { + #endif + if (hdu->images) { + psLogMsg(__func__, PS_LOG_WARN, "HDU %s has already been read --- overwriting.\n", hdu->extname); + psFree(hdu->images); // Blow away anything existing + } + psTrace(__func__, 5, "Reading the pixels...\n"); + hdu->images = psFitsReadImageCube(fits, psRegionSet(0,0,0,0)); + if (! hdu->images) { + psError(PS_ERR_IO, false, "Unable to read pixels for extension %s\n", hdu->extname); + return false; + } + return true; + #ifdef FITS_TABLES + + } + if (psFitsIsTable(hdu->table)) { + // Read the table + if (hdu->table) { + psFree(hdu->table); // Blow away anything existing + } + hdu->table = psFitsReadTable(fits); + return true; + } + + psError(PS_ERR_UNKNOWN, true, "No idea what this HDU consists of!\n"); + return false; + #endif +} + +// Write the HDU +// XXX: Add a region specifier? +bool pmHDUWrite(pmHDU *hdu, // HDU to write + psFits *fits // FITS file to write to + ) +{ + assert(hdu); + assert(fits); + + psTrace(__func__, 7, "Writing HDU %s\n", hdu->extname); + + if (hdu->images && hdu->table && !hdu->header) { + psError(PS_ERR_IO, true, "Both image and table data provided in HDU, but no header --- " + "don't know which to write!\n"); + return false; + } + + if (!hdu->images && !hdu->table && !hdu->header) { + psLogMsg(__func__, PS_LOG_WARN, "Nothing to write for HDU %s\n", hdu->extname); + return false; + } + + // Preserve the extension name, if it's the PHU + char *extname = hdu->extname; // The name of the extension + if (strcasecmp(extname, "PHU") == 0 && hdu->header) { + bool mdok = true; // Status of MD lookup + extname = psMetadataLookupStr(&mdok, hdu->header, "EXTNAME"); + if (!mdok || !extname || strlen(extname) == 0) { + extname = ""; + } + } + + // Only a header + if (!hdu->images && !hdu->table) { + // Tell CFITSIO there's nothing there + psMetadataItem *naxis = psMetadataLookup(hdu->header, "NAXIS"); + if (naxis) { + naxis->data.S32 = 0; + } + + if (!psFitsWriteHeader(hdu->header, fits)) { + psError(PS_ERR_IO, false, "Unable to write header for extension %s\n", extname); + } + } + + #ifdef FITS_TABLES + if (hdu->images && (!hdu->table || psFitsIsImage(hdu->header))) { + psFitsWriteImageCube(fits, hdu->header, hdu->images, extname); + return true; + } + + if (hdu->table && (!hdu->images || psFitsIsTable(hdu->header))) { + bool psFitsWriteTable(psFits* fits, const psMetadata *header, const psArray* table); + return true; + } + + psError(PS_ERR_IO, true, "No idea what this HDU consists of!\n"); + return false; + #else + + if (hdu->images) { + psTrace(__func__, 9, "Writing pixels for %s\n", hdu->extname); + if (!psFitsWriteImageCube(fits, hdu->header, hdu->images, extname)) { + psError(PS_ERR_IO, false, "Unable to write image to extension %s\n", hdu->extname); + return false; + } + } + return true; + #endif +} + Index: trunk/psModules/src/astrom/pmHDU.h =================================================================== --- trunk/psModules/src/astrom/pmHDU.h (revision 6872) +++ trunk/psModules/src/astrom/pmHDU.h (revision 6872) @@ -0,0 +1,37 @@ +#ifndef PM_HDU_H +#define PM_HDU_H + +// An instance of the FITS Header Data Unit +typedef struct +{ + psString extname; // The extension name + bool phu; // Is this the FITS Primary Header Unit + psMetadata *format; // The camera format + psMetadata *header; // The FITS header, or NULL if primary for FITS; or section info + psArray *images; // The pixel data + psArray *weights; // The pixel data + psArray *masks; // The pixel data + psArray *table; // The table data +} +pmHDU; + + +// Allocators +pmHDU *pmHDUAlloc(const char *extname); + +// Read the header +bool pmHDUReadHeader(pmHDU *hdu, // HDU for which to read header + psFits *fits // FITS file from which to read + ); + +// Read the HDU +bool pmHDURead(pmHDU *hdu, // HDU to read + psFits *fits // FITS file to read from + ); + +// Write the HDU +bool pmHDUWrite(pmHDU *hdu, // HDU to write + psFits *fits // FITS file to write to + ); + +#endif Index: trunk/psModules/src/astrom/pmHDUUtils.c =================================================================== --- trunk/psModules/src/astrom/pmHDUUtils.c (revision 6872) +++ trunk/psModules/src/astrom/pmHDUUtils.c (revision 6872) @@ -0,0 +1,60 @@ +#include +#include "pmFPA.h" +#include "pmHDU.h" +#include "pmHDUUtils.h" + + +pmHDU *pmHDUFromFPA(pmFPA *fpa // FPA for which to find HDU + ) +{ + return fpa->hdu; +} + +pmHDU *pmHDUFromChip(pmChip *chip // Chip for which to find HDU + ) +{ + pmHDU *hdu = chip->hdu; // The HDU information + if (!hdu) { + hdu = pmHDUFromFPA(chip->parent); // Grab HDU info from the FPA + } + + return hdu; +} + +pmHDU *pmHDUFromCell(pmCell *cell // Cell for which to find HDU + ) +{ + pmHDU *hdu = cell->hdu; // The HDU information + if (!hdu) { + hdu = pmHDUFromChip(cell->parent); // Grab HDU info from the chip + } + + return hdu; +} + +pmHDU *pmHDUFromReadout (pmReadout *readout) +{ + + pmCell *cell = readout->parent; // cell containing this readout; + pmHDU *hdu = pmHDUFromCell (cell); + return hdu; +} + +// Get the lowest HDU +pmHDU *pmHDUGetLowest(pmFPA *fpa, // The FPA + pmChip *chip, // The chip, or NULL + pmCell *cell // The cell, or NULL + ) +{ + pmHDU *hdu = NULL; // The HDU that's at the lowest level + if (cell) { + hdu = pmHDUFromCell(cell); + } else if (chip) { + hdu = pmHDUFromChip(chip); + } else if (fpa) { + hdu = pmHDUFromFPA(fpa); + } + + return hdu; +} + Index: trunk/psModules/src/astrom/pmHDUUtils.h =================================================================== --- trunk/psModules/src/astrom/pmHDUUtils.h (revision 6872) +++ trunk/psModules/src/astrom/pmHDUUtils.h (revision 6872) @@ -0,0 +1,24 @@ +#ifndef PM_HDU_UTILS_H +#define PM_HDU_UTILS_H + +#include "pmFPA.h" +#include "pmHDU.h" + +// Get the lowest HDU in the hierarchy, as supplied +pmHDU *pmHDUGetLowest(pmFPA *fpa, // The FPA + pmChip *chip, // The chip, or NULL + pmCell *cell // The cell, or NULL + ); + +// Find the HDU in the FPA hierarchy +pmHDU *pmHDUFromFPA(pmFPA *fpa // FPA for which to find HDU + ); +pmHDU *pmHDUFromChip(pmChip *chip // Chip for which to find HDU + ); +pmHDU *pmHDUFromCell(pmCell *cell // Cell for which to find HDU + ); + +pmHDU *pmHDUFromReadout (pmReadout *readout // Readout for which to find HDU + ); + +#endif Index: trunk/psModules/src/astrom/pmReadout.c =================================================================== --- trunk/psModules/src/astrom/pmReadout.c (revision 6872) +++ trunk/psModules/src/astrom/pmReadout.c (revision 6872) @@ -0,0 +1,109 @@ +#include +#include "pslib.h" +#include "pmFPA.h" +#include "pmHDUUtils.h" +#include "pmFPAMaskWeight.h" + +// Get the bias images for a readout, using the CELL.BIASSEC +psList *pmReadoutGetBias(pmReadout *readout // Readout for which to get the bias sections + ) +{ + pmCell *cell = readout->parent; // The parent cell + psList *sections = (psList*)psMetadataLookupPtr(NULL, cell->concepts, "CELL.BIASSEC"); // CELL.BIASSEC + + psImage *image = readout->image; // The image that contains both the biassec and the trimsec + + psList *images = psListAlloc(NULL); // List of images from bias sections + psListIterator *sectionsIter = psListIteratorAlloc(sections, PS_LIST_HEAD, true); // Iterator + psRegion *region = NULL; // Bias region from list + while ((region = psListGetAndIncrement(sectionsIter))) { + psImage *bias = psMemIncrRefCounter(psImageSubset(image, *region)); // Image from bias section + psListAdd(images, PS_LIST_TAIL, bias); + psFree(bias); + } + psFree(sectionsIter); + + return images; +} + +bool pmReadoutSetWeights(pmReadout *readout) +{ + + pmCell *cell = readout->parent; + + float gain = psMetadataLookupF32(NULL, cell->concepts, "CELL.GAIN"); // Cell gain + float readnoise = psMetadataLookupF32(NULL, cell->concepts, "CELL.READNOISE"); // Cell read noise + psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); // Trim section + float saturation = psMetadataLookupF32(NULL, cell->concepts, "CELL.SATURATION"); // Saturation level + float bad = psMetadataLookupF32(NULL, cell->concepts, "CELL.BAD"); // Bad level + + pmHDU *hdu = pmHDUFromCell (cell); + + psArray *pixels = hdu->images; // Array of images + psArray *weights = hdu->weights; // Array of weight images + psArray *masks = hdu->masks; // Array of mask images + // Generate the weights and masks if required + if (! weights) { + weights = psArrayAlloc(pixels->n); + for (int i = 0; i < pixels->n; i++) { + psImage *image = pixels->data[i]; + weights->data[i] = psImageAlloc(image->numCols, image->numRows, PS_TYPE_F32); + psImageInit(weights->data[i], 0.0); + } + hdu->weights = weights; + } + if (! masks) { + masks = psArrayAlloc(pixels->n); + for (int i = 0; i < pixels->n; i++) { + psImage *image = pixels->data[i]; + masks->data[i] = psImageAlloc(image->numCols, image->numRows, PS_TYPE_U8); + psImageInit(masks->data[i], 0); + } + hdu->masks = masks; + } + + // Set the pixels + psArray *readouts = cell->readouts; // Array of readouts + for (int i = 0; i < readouts->n; i++) { + pmReadout *readout = readouts->data[i]; // The readout of interest + + if (! readout->weight) { + readout->weight = psMemIncrRefCounter(psImageSubset(weights->data[i], *trimsec)); + } + if (! readout->mask) { + readout->mask = psMemIncrRefCounter(psImageSubset(masks->data[i], *trimsec)); + } + + // Set up the mask + psImage *image = readout->image;// Pixels + psImage *mask = readout->mask; // Mask image + for (int i = 0; i < image->numRows; i++) { + for (int j = 0; j < image->numCols; j++) { + if (image->data.F32[i][j] >= saturation) { + mask->data.U8[i][j] = PM_MASK_SAT; + } + if (image->data.F32[i][j] <= bad) { + mask->data.U8[i][j] = PM_MASK_BAD; + } + } + } + + psImage *weight = readout->weight; // Mask image + float rnoise = PS_SQR(readnoise/gain); + for (int i = 0; i < image->numRows; i++) { + for (int j = 0; j < image->numCols; j++) { + if (!mask->data.U8[i][j]) { + weight->data.F32[i][j] = image->data.F32[i][j]/ gain + rnoise; + } + } + } + + // Set weight image to the variance = g*f + rn^2 + // psBinaryOp(readout->weight, image, "/", psScalarAlloc(gain, PS_TYPE_F32)); + // psBinaryOp(readout->weight, readout->weight, "+", + // psScalarAlloc(readnoise*readnoise/gain/gain, PS_TYPE_F32)); + } + + return true; +} + Index: trunk/psModules/src/astrom/pmReadout.h =================================================================== --- trunk/psModules/src/astrom/pmReadout.h (revision 6872) +++ trunk/psModules/src/astrom/pmReadout.h (revision 6872) @@ -0,0 +1,13 @@ +#ifndef PM_READOUT_H +#define PM_READOUT_H + +#include "pslib.h" +#include "pmFPA.h" + +// Get the bias sections for a specific readout +psList *pmReadoutGetBias(pmReadout *readout // Readout for which to get the bias sections + ); + +bool pmReadoutSetWeights(pmReadout *readout); + +#endif Index: trunk/psModules/src/camera/Makefile.am =================================================================== --- trunk/psModules/src/camera/Makefile.am (revision 6529) +++ trunk/psModules/src/camera/Makefile.am (revision 6872) @@ -3,7 +3,20 @@ libpsmodulecamera_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) libpsmodulecamera_la_LDFLAGS = -release $(PACKAGE_VERSION) -libpsmodulecamera_la_SOURCES = +libpsmodulecamera_la_SOURCES = \ + pmChipMosaic.c \ + pmFPAConceptsGet.c \ + pmFPAConceptsSet.c \ + pmFPAConstruct.c \ + pmFPAMorph.c \ + pmFPARead.c \ + pmFPAWrite.c psmoduleincludedir = $(includedir) -psmoduleinclude_HEADERS = - +psmoduleinclude_HEADERS = \ + pmChipMosaic.h \ + pmFPAConceptsGet.h \ + pmFPAConceptsSet.h \ + pmFPAConstruct.h \ + pmFPAMorph.h \ + pmFPARead.h \ + pmFPAWrite.h Index: trunk/psModules/src/config/pmConfig.h =================================================================== --- trunk/psModules/src/config/pmConfig.h (revision 6529) +++ trunk/psModules/src/config/pmConfig.h (revision 6872) @@ -3,6 +3,6 @@ * @author PAP, IfA * - * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ - * @date $Date: 2006-02-02 04:51:14 $ + * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -15,7 +15,24 @@ +// Configuration information +typedef struct +{ + psMetadata *site; // Site configuration + psMetadata *camera; // Camera specification + psMetadata *recipes; // Recipes for processing + psMetadata *arguments; // Command-line arguments + psMetadata *files; // pmFPAfiles used for analysis + // psMetadata *format; // camera format for primary image + psDB *database; // Database handle +} +pmConfig; + +pmConfig *pmConfigAlloc(void); + +// Free static variables +void pmConfigDone(void); /** pmConfigRead - * + * * pmConfigRead shall load the site configuration (according to the above rule * for determining the source). The camera configuration shall also be loaded if @@ -32,62 +49,57 @@ * */ -bool pmConfigRead( - psMetadata **site, - psMetadata **camera, - psMetadata **recipe, +pmConfig *pmConfigRead( int *argc, - char **argv, - const char *recipeName + char **argv); + +/** we need this elsewhere; make it public **/ +bool readConfig( + psMetadata **config, // Config to output + const char *name, // Name of file + const char *description // Description of file ); - - /** pmConfigValidateCamera - * + * * This function, used by pmConfigCameraFromHeader, shall return true if the * FITS header matches the rule contained in the camera configuration (see * x2.2.2.3); otherwise it shall return false. - * + * */ -bool pmConfigValidateCamera( - const psMetadata *camera, - const psMetadata *header -); - +bool pmConfigValidateCameraFormat( + const psMetadata *cameraFormat, + const psMetadata *header); /** pmConfigCameraFromHeader - * + * * pmConfigCameraFromHeader shall load the camera configuration based on the * contents of the FITS header, using the list of known cameras contained in the * site configuration. If more than one camera matches the FITS header, a warning * shall be generated and the first matching camera returned. - * + * */ -psMetadata *pmConfigCameraFromHeader( - const psMetadata *site, - const psMetadata *header +psMetadata *pmConfigCameraFormatFromHeader( + pmConfig *config, // The configuration + const psMetadata *header // The FITS header ); - /** pmConfigRecipeFromCamera - * - * pmConfigRecipeFromCamera shall load the recipe configuration based on the - * recipeName and the list of known recipes contained in the camera + * + * pmConfigRecipeFromCamera shall load the recipes from the list of known recipes contained in the camera * configuration. - * + * */ -psMetadata *pmConfigRecipeFromCamera( - const psMetadata *camera, - const char *recipeName +bool pmConfigReadRecipes( + pmConfig *config ); /** pmConfigDB - * + * * pmConfigDB shall use the site configuration data to open a database handle. * This is fairly straightforward at the moment, but will change when we beef up * security. (TBD) - * + * */ #ifdef DOMIT_PSDB @@ -99,4 +111,16 @@ ); +/** pmConfigConformHeader + * + * Make the supplied header conform to the nominated camera format. + */ +bool pmConfigConformHeader(psMetadata *header, // Header to conform + const psMetadata *format // Camera format + ); + + +psArray *pmConfigFileSets (int *argc, char **argv, char *file, char *list); +bool pmConfigFileSetsMD (psMetadata *metadata, int *argc, char **argv, char *name, char *file, char *list); + #endif Index: trunk/psModules/src/detrend/Makefile.am =================================================================== --- trunk/psModules/src/detrend/Makefile.am (revision 6529) +++ trunk/psModules/src/detrend/Makefile.am (revision 6872) @@ -3,15 +3,18 @@ libpsmoduledetrend_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) libpsmoduledetrend_la_LDFLAGS = -release $(PACKAGE_VERSION) -libpsmoduledetrend_la_SOURCES = pmFlatField.c \ - pmMaskBadPixels.c \ - pmNonLinear.c +libpsmoduledetrend_la_SOURCES = \ + pmFlatField.c \ + pmFringeStats.c \ + pmMaskBadPixels.c \ + pmNonLinear.c psmoduleincludedir = $(includedir) psmoduleinclude_HEADERS = \ - pmFlatField.h \ - pmFlatFieldErrors.h \ - pmMaskBadPixelsErrors.h \ - pmMaskBadPixels.h \ - pmNonLinear.h + pmFlatField.h \ + pmFlatFieldErrors.h \ + pmFringeStats.h \ + pmMaskBadPixelsErrors.h \ + pmMaskBadPixels.h \ + pmNonLinear.h EXTRA_DIST = pmFlatFieldErrors.dat pmMaskBadPixelsErrors.dat Index: trunk/psModules/src/detrend/pmFlatField.c =================================================================== --- trunk/psModules/src/detrend/pmFlatField.c (revision 6529) +++ trunk/psModules/src/detrend/pmFlatField.c (revision 6872) @@ -1,2 +1,8 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + /** @file pmFlatField.c * @@ -18,6 +24,6 @@ * @author Ross Harman, MHPCC * - * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-11-18 19:43:14 $ + * @version $Revision: 1.5 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -30,5 +36,5 @@ #include #include -#include +#include #include "pslib.h" @@ -36,32 +42,8 @@ #include "pmMaskBadPixels.h" #include "pmFlatFieldErrors.h" -#include "pmSubtractBias.h" -// XXX: This should be removed when the autoconf stuff handles psConstants.h correctly. -#define PS_WARN_PTR_NON_NULL(NAME) \ -if ((NAME) == NULL) { \ - psLogMsg(__func__, PS_LOG_WARN, "WARNING: %s is NULL.", #NAME); \ -} \ -bool pmFlatField( - pmReadout *in, - const pmReadout *flat) +bool pmFlatField(pmReadout *in, const pmReadout *flat) { - // XXX: Use the proper image and readout asserts. - PS_ASSERT_PTR_NON_NULL(in, true); - PS_ASSERT_PTR_NON_NULL(in->image, false); - PS_ASSERT_PTR_NON_NULL(in->mask, false); - PS_ASSERT_PTR_NON_NULL(flat, false); - PS_ASSERT_PTR_NON_NULL(flat->image, false); - if (in == NULL) - printf("XXX: NULL\n"); - - // XXX: Not sure if this is correct. Must consult with IfA. - PS_ASSERT_PTR_NON_NULL(in->mask, false); - - PS_WARN_PTR_NON_NULL(in->parent); - if (in->parent != NULL) { - PS_WARN_PTR_NON_NULL(in->parent->concepts); - } int i = 0; int j = 0; @@ -71,28 +53,43 @@ psElemType flatType; psElemType maskType; - psImage *inMask = NULL; - psImage *flatImage = NULL; - // - // Determine trimmed image from metadata. - // - psImage *trimmedImg = p_psDetermineTrimmedImage(in); - flatImage = flat->image; - inMask = in->mask; + // Check for nulls + if (in == NULL) { + return true; // Readout may not have data in it + } else if(flat==NULL) { + psError( PS_ERR_BAD_PARAMETER_NULL, true, + PS_ERRORTEXT_pmFlatField_NULL_FLAT_READOUT); + return false; + } + + psImage *inImage = in->image; // Input image + psImage *inMask = in->mask; // Mask for input image + psImage *flatImage = flat->image; // Flat-field image + + // Offsets on the chip + int x0in = psMetadataLookupS32(NULL, in->parent->concepts, "CELL.X0"); + int y0in = psMetadataLookupS32(NULL, in->parent->concepts, "CELL.Y0"); + int x0flat = psMetadataLookupS32(NULL, flat->parent->concepts, "CELL.X0"); + int y0flat = psMetadataLookupS32(NULL, flat->parent->concepts, "CELL.Y0"); + + if (inImage == NULL) { + psError( PS_ERR_BAD_PARAMETER_NULL, true, + PS_ERRORTEXT_pmFlatField_NULL_INPUT_IMAGE); + return false; + } else if(flatImage == NULL) { + psError( PS_ERR_BAD_PARAMETER_NULL, true, + PS_ERRORTEXT_pmFlatField_NULL_FLAT_IMAGE); + return false; + } // Check input image and its mask are not larger than flat image - if (trimmedImg == NULL) - printf("XXX: 00\n"); - if (flatImage == NULL) - printf("XXX 01\n"); - - if (trimmedImg->numRows>flatImage->numRows || trimmedImg->numCols>flatImage->numCols) { + if (inImage->numRows>flatImage->numRows || inImage->numCols>flatImage->numCols) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmFlatField_SIZE_INPUT_IMAGE, - trimmedImg->numRows, trimmedImg->numCols, flatImage->numRows, flatImage->numCols); + inImage->numRows, inImage->numCols, flatImage->numRows, flatImage->numCols); return false; } - if (inMask->numRows > flatImage->numRows || inMask->numCols > flatImage->numCols) { + if (inMask && (inMask->numRows > flatImage->numRows || inMask->numCols > flatImage->numCols)) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmFlatField_SIZE_MASK_IMAGE, @@ -102,6 +99,6 @@ // Determine total offset based on image offset with chip offset - totOffCol = trimmedImg->col0 + in->col0; - totOffRow = trimmedImg->row0 + in->row0; + totOffCol = inImage->col0 + y0in - flatImage->col0 - y0flat; + totOffRow = inImage->row0 + x0in - flatImage->row0 - x0flat; // Check that offsets are within image limits @@ -111,10 +108,10 @@ totOffRow, totOffCol, flatImage->numRows, flatImage->numCols); return false; - } else if(totOffRow>=trimmedImg->numRows || totOffCol>=trimmedImg->numCols) { + } else if(totOffRow>=inImage->numRows || totOffCol>=inImage->numCols) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmFlatField_OFFSET_INPUT_IMAGE, - totOffRow, totOffCol, trimmedImg->numRows, trimmedImg->numCols); + totOffRow, totOffCol, inImage->numRows, inImage->numCols); return false; - } else if(totOffRow>=inMask->numRows || totOffCol>=inMask->numCols) { + } else if(inMask && (totOffRow>=inMask->numRows || totOffCol>=inMask->numCols)) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmFlatField_OFFSET_MASK_IMAGE, @@ -124,5 +121,5 @@ // Check for incorrect types - inType = trimmedImg->type.type; + inType = inImage->type.type; flatType = flatImage->type.type; maskType = inMask->type.type; @@ -137,5 +134,5 @@ flatType); return false; - } else if(maskType != PS_TYPE_MASK) { + } else if(inMask && inMask->type.type != PS_TYPE_MASK) { psError( PS_ERR_BAD_PARAMETER_TYPE, true, PS_ERRORTEXT_pmFlatField_TYPE_MASK_IMAGE, @@ -153,18 +150,20 @@ case PS_TYPE_##TYPE: \ /* Per Eugene's request, use two sets of loops: first to fill mask, second to avoid div with bad pix */ \ - for(j = totOffRow; j < trimmedImg->numRows; j++) { \ - for(i = totOffCol; i < trimmedImg->numCols; i++) { \ + for(j = totOffRow; j < inImage->numRows; j++) { \ + for(i = totOffCol; i < inImage->numCols; i++) { \ if(flatImage->data.TYPE[j][i] <= 0.0) { \ /* Negative or zero flat pixels shall be masked in input image as PM_MASK_FLAT */ \ - inMask->data.PS_TYPE_MASK_DATA[j][i] |= PM_MASK_FLAT; \ + if (inMask) { \ + inMask->data.PS_TYPE_MASK_DATA[j][i] |= PM_MASK_FLAT; \ + } \ flatImage->data.TYPE[j][i] = 0.0; \ } \ } \ } \ - for(j = totOffRow; j < trimmedImg->numRows; j++) { \ - for(i = totOffCol; i < trimmedImg->numCols; i++) { \ - if(!inMask->data.PS_TYPE_MASK_DATA[j][i]) { \ + for(j = totOffRow; j < inImage->numRows; j++) { \ + for(i = totOffCol; i < inImage->numCols; i++) { \ + if(inMask && !inMask->data.PS_TYPE_MASK_DATA[j][i]) { \ /* Module shall divide the input image by the flat-fielded image */ \ - trimmedImg->data.TYPE[j][i] /= flatImage->data.TYPE[j][i]; \ + inImage->data.TYPE[j][i] /= flatImage->data.TYPE[j][i]; \ } \ } \ Index: trunk/psModules/src/detrend/pmFlatField.h =================================================================== --- trunk/psModules/src/detrend/pmFlatField.h (revision 6529) +++ trunk/psModules/src/detrend/pmFlatField.h (revision 6872) @@ -1,2 +1,8 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + /** @file pmFlatField.h * @@ -18,6 +24,6 @@ * @author Ross Harman, MHPCC * - * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-10-20 23:06:24 $ + * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -25,5 +31,5 @@ #include "pslib.h" -#include "pmAstrometry.h" +#include "pmFPA.h" Index: trunk/psModules/src/detrend/pmFringeStats.c =================================================================== --- trunk/psModules/src/detrend/pmFringeStats.c (revision 6872) +++ trunk/psModules/src/detrend/pmFringeStats.c (revision 6872) @@ -0,0 +1,240 @@ +/** @file pmFringeStats.c + * + * @author Eugene Magnier, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 IfA + */ + +#include "pslib.h" +#include "pmFPA.h" +#include "pmFringeStats.h" + +static void fringeRegionsFree(pmFringeRegions *fringe) +{ + psFree(fringe->x); + psFree(fringe->y); + psFree(fringe->mask); + return; +} + +pmFringeRegions *pmFringeRegionsAlloc(int nPts, int dX, int dY, int nX, int nY) +{ + pmFringeRegions *fringe = psAlloc(sizeof(pmFringeRegions)); + (void)psMemSetDeallocator(fringe, (psFreeFunc)fringeRegionsFree); + + fringe->x = NULL; + fringe->y = NULL; + fringe->mask = NULL; + + fringe->nRequested = nPts; + fringe->nAccepted = 0; + + fringe->dX = dX; + fringe->dY = dY; + fringe->nX = nX; + fringe->nY = nY; + + return fringe; +} + + +static void fringeStatsFree(pmFringeStats *stats) +{ + psFree(stats->regions); + psFree(stats->f); + psFree(stats->df); +} + +pmFringeStats *pmFringeStatsAlloc(pmFringeRegions *regions) +{ + pmFringeStats *stats = psAlloc(sizeof(pmFringeStats)); + (void)psMemSetDeallocator(stats, (psFreeFunc)fringeStatsFree); + + stats->regions = psMemIncrRefCounter(regions); + stats->f = psVectorAlloc(regions->x->n, PS_TYPE_F32); + stats->df = psVectorAlloc(regions->x->n, PS_TYPE_F32); + + return stats; +} + + +static void fringeScaleFree(pmFringeScale *scale) +{ + psFree(scale->coeff); + psFree(scale->coeffErr); + return; +} + +pmFringeScale *pmFringeScaleAlloc(int nFringeFrames) +{ + pmFringeScale *scale = psAlloc(sizeof(pmFringeScale)); + (void)psMemSetDeallocator(scale, (psFreeFunc)fringeScaleFree); + + scale->nFringeFrames = nFringeFrames; + scale->coeff = psVectorAlloc(nFringeFrames + 1, PS_TYPE_F32); + scale->coeffErr = psVectorAlloc(nFringeFrames + 1, PS_TYPE_F32); + + return scale; +} + +bool pmFringeStatsCreatePoints(pmFringeRegions *fringe, psImage *image) +{ + + double frnd; + // create fringe->nRequested + + psRandom *rnd = psRandomAlloc(PS_RANDOM_TAUS, 0); + + fringe->x = psVectorRecycle(fringe->x, fringe->nRequested, PS_TYPE_F32); + fringe->y = psVectorRecycle(fringe->y, fringe->nRequested, PS_TYPE_F32); + fringe->mask = psVectorRecycle(fringe->mask, fringe->nRequested, PS_TYPE_U8); + + int nX = image->numCols; + int nY = image->numRows; + + psF32 *xPt = fringe->x->data.F32; + psF32 *yPt = fringe->y->data.F32; + + int dX = fringe->dX; + int dY = fringe->dY; + + // generate random points located within image bounds + for (int i = 0; i < fringe->nRequested; i++) { + frnd = psRandomUniform(rnd); + xPt[i] = (nX - 2*dX)* frnd + dX; + frnd = psRandomUniform(rnd); + yPt[i] = (nY - 2*dY)* frnd + dY; + } + return true; +} + +pmFringeStats *pmFringeStatsMeasure(pmFringeRegions *fringe, pmReadout *readout, psMaskType maskVal) +{ + if (!fringe->x || !fringe->y) { + // create the fringe vectors for this image + pmFringeStatsCreatePoints(fringe, readout->image); + } + + PS_ASSERT_PTR_NON_NULL(fringe->x, false); + PS_ASSERT_PTR_NON_NULL(fringe->y, false); + + pmFringeStats *measurements = pmFringeStatsAlloc(fringe); + + psF32 *xPt = fringe->x->data.F32; + psF32 *yPt = fringe->y->data.F32; + psF32 *fPt = measurements->f->data.F32; + psF32 *dfPt = measurements->df->data.F32; + + int dX = fringe->dX; + int dY = fringe->dY; + + psImage *image = readout->image; + psImage *mask = readout->mask; + + psStats *stats = psStatsAlloc(PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_STDEV); + + for (int i = 0; i < fringe->x->n; i++) { + psRegion region = psRegionSet(xPt[i] - dX, yPt[i] - dY, xPt[i] + dX + 1, yPt[i] + dY + 1); + region = psRegionForImage(image, region); + psImage *subImage = psImageSubset(image, region); + psImage *subMask = psImageSubset(mask, region); + psImageStats(stats, subImage, subMask, maskVal); + + fPt[i] = stats->sampleMedian; + dfPt[i] = stats->sampleStdev; + } + + return measurements; +} + +// XXX include the fringe error (fringe->df) in the fit? +pmFringeScale *pmFringeScaleMeasure(pmFringeStats *science, psArray *fringes) +{ + double sum; + psVector *v1; + psVector *v2; + + pmFringeScale *scale = pmFringeScaleAlloc(fringes->n); + + int nCof = fringes->n + 1; + int nPts = science->f->n; + + psImage *A = psImageAlloc(nCof, nCof, PS_TYPE_F64); + psVector *B = psVectorAlloc(nCof, PS_TYPE_F64); + + for (int i = 0; i < nCof; i++) { + psF32 *p1 = NULL; + if (i != 0) { + v1 = fringes->data[i - 1]; + p1 = v1->data.F32; + } + for (int j = 0; j < nCof; j++) { + psF32 *p2 = NULL; + if (j != 0) { + v2 = fringes->data[j - 1]; + p2 = v2->data.F32; + } + + sum = 0; + for (int k = 0; k < nPts; k++) { + psF32 f1 = (p1 == NULL) ? 1.0 : p1[k]; + psF32 f2 = (p2 == NULL) ? 1.0 : p2[k]; + sum += f1*f2; + } + A->data.F32[i][j] = sum; + } + + sum = 0; + psF32 *p2 = science->f->data.F32; + for (int j = 0; j < nPts; j++) { + psF32 f1 = (p1 == NULL) ? 1.0 : p1[j]; + psF32 f2 = p2[j]; + sum += f1*f2; + } + B->data.F32[i] = sum; + } + + if (! psGaussJordan(A, B)) { + psError(PS_ERR_UNKNOWN, false, "Could not solve linear equations. Returning NULL.\n"); + } + + + for (int i = 0; i < nCof; i++) { + scale->coeff->data.F32[i] = B->data.F32[i]; + scale->coeffErr->data.F32[i] = sqrt(A->data.F32[i][i]); + } + + return scale; +} + +// XXX note that this modifies the input fringe images +psImage *pmFringeCorrect(pmReadout *readout, pmFringeRegions *fringes, psArray *fringeImages, psArray *fringeStats, psMaskType maskVal) +{ + // measure the fringe stats for the science frame and solve for the scales + pmFringeStats *scienceStats = pmFringeStatsMeasure(fringes, readout, maskVal); + pmFringeScale *scale = pmFringeScaleMeasure(scienceStats, fringeStats); + psFree(scienceStats); + + // build the fringe correction image + // XXX we could save data space by making the first image the output image + psImage *sumFringe = NULL; + for (int i = 0; i < fringeImages->n; i++) { + + // rescale the fringe image + psBinaryOp(fringeImages->data[i], fringeImages->data[i], "*", + psScalarAlloc(scale->coeff->data.F32[i+1], PS_TYPE_F32)); + + // sum together + sumFringe = (psImage*)psBinaryOp(sumFringe, sumFringe, "+", fringeImages->data[i]); + } + psFree(scale); + + // subtract the resulting fringe frame + readout->image = (psImage*)psBinaryOp(readout->image, readout->image, "-", sumFringe); + + return sumFringe; +} + Index: trunk/psModules/src/detrend/pmFringeStats.h =================================================================== --- trunk/psModules/src/detrend/pmFringeStats.h (revision 6872) +++ trunk/psModules/src/detrend/pmFringeStats.h (revision 6872) @@ -0,0 +1,92 @@ +/** @file pmFringeStats.h + * + * @brief Measure Fringe statistics and apply correction + * + * @author Eugene Magnier, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 IfA, University of Hawaii + */ + +# ifndef PM_FRINGE_STATS +# define PM_FRINGE_STATS + +/** Structure to hold the fringe measurement regions. + */ +typedef struct +{ + psU32 nRequested; // number of fringe points selected + psU32 nAccepted; // number of fringe points not masked + psU32 dX; // median box half-width + psU32 dY; // median box half-height + psU32 nX; // large-scale smoothing in x (col) + psU32 nY; // large-scale smoothing in y (row) + psVector *x; // fringe point coordinates (col) + psVector *y; // fringe point coordinates (row) + psVector *mask; // fringe point on/off mask +} +pmFringeRegions; + +pmFringeRegions *pmFringeRegionsAlloc ( + int nPts, // number of points to create + int dX, // half-width of fringe boxes + int dY, // half-height of fringe boxes + int nX, // smoothing scale in x + int nY // smoothing scale in y +); + +/** Structure to hold the fringe measurements for a particular image + */ +typedef struct +{ + pmFringeRegions *regions; // Fringe regions + psVector *f; // fringe point median + psVector *df; // fringe point stdev +} +pmFringeStats; + +pmFringeStats *pmFringeStatsAlloc(pmFringeRegions *regions); + + +/** the pmFringeScale structure defines the relationship between two fringe measurements + */ +typedef struct +{ + int nFringeFrames; + psVector *coeff; + psVector *coeffErr; +} +pmFringeScale; + +/** Measure the fringe stats for an image + * + * Given an input image and a fringe stats structure, measure the statistics for each of the fringe points on + * the image. If the fringe vectors are NULL, new vectors are created. + * + * XXX should the structure carry the image dimensions for validation? + * + * @return bool: True or false for success or failure + */ +pmFringeStats *pmFringeStatsMeasure( + pmFringeRegions *fringe, ///< fringe regions + pmReadout *readout, ///< measure fringes on this readout + psMaskType maskVal ///< Mask value for statistics +); + +/** Fringe correct the science image + * + * Given a science image, a set of fringe stats and a matched set of fringe images, correct the science image + * for the fringe images. + * + * @return psImage: summed fringe image + */ +psImage *pmFringeCorrect(pmReadout *in, // place info about results here + pmFringeRegions *fringes, // The fringe regions used + psArray *fringeImages, // fringe images to use in correction + psArray *fringeStats, // fringe stats to use in correction + psMaskType maskVal // Value to mask + ); + +# endif Index: trunk/psModules/src/detrend/pmMaskBadPixels.c =================================================================== --- trunk/psModules/src/detrend/pmMaskBadPixels.c (revision 6529) +++ trunk/psModules/src/detrend/pmMaskBadPixels.c (revision 6872) @@ -1,2 +1,7 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /** @file pmMaskBadPixels.c * @@ -19,6 +24,6 @@ * @author Ross Harman, MHPCC * - * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-11-18 19:43:14 $ + * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -31,157 +36,77 @@ #include #include -#include +#include #include "pmMaskBadPixels.h" #include "pmMaskBadPixelsErrors.h" -#include "pmSubtractBias.h" -//XXX: REmove, autoconf is broken. -#define PS_WARN_PTR_NON_NULL(NAME) \ -if ((NAME) == NULL) { \ - psLogMsg(__func__, PS_LOG_WARN, "WARNING: %s is NULL.", #NAME); \ -} \ +bool pmMaskBadPixels(pmReadout *in, const psImage *mask, unsigned int maskVal, float sat, + unsigned int growVal, int grow) +{ + int i = 0; + int j = 0; + int jj = 0; + int ii = 0; + int rRound = 0; + int rowMin = 0; + int rowMax = 0; + int colMin = 0; + int colMax = 0; + int totOffCol = 0; + int totOffRow = 0; + float r = 0.0f; + psElemType inType; + psElemType maskType; + psImage *inImage = NULL; + psImage *inMask = NULL; -/****************************************************************************** -GrowPixel(inMask, row, col, radius, maskVal): This private routine takes an -input image mask and a pixel location, then sets (logical or) all pixels with -parameter radius if that pixel to maskVal parameter. -*****************************************************************************/ -psBool GrowPixel( - psImage *inMask, - psS32 col, - psS32 row, - psS32 radius, - psU32 maskVal) -{ - psS32 rowMin = PS_MAX(row-radius, 0); - psS32 rowMax = PS_MIN(row+radius+1, inMask->numRows); - psS32 colMin = PS_MAX(col-radius, 0); - psS32 colMax = PS_MIN(col+radius+1, inMask->numCols); - psF32 squareRadius = PS_SQR(radius); + // Check for nulls + if (in == NULL) { + return true; // Readout may not have data in it + } else if(mask==NULL) { + psError( PS_ERR_BAD_PARAMETER_NULL, true, + PS_ERRORTEXT_pmMaskBadPixels_NULL_MASK_IMAGE); + return false; + } - - for(psS32 i=rowMin; idata.U8[i][j] |= maskVal; - } - } - } - return(true); -} - -/****************************************************************************** -GetRadius(inImg, col, row, sat, growVal, grow): This private routine takes an -input image and pixel location and determines what radius that pixel must grow -by. - -//XXX: Inline this or macro it for speed. - *****************************************************************************/ -static psS32 GetRadius( - psImage *inImg, - psS32 col, - psS32 row, - psF32 sat, - psU32 growVal, - psS32 grow) -{ - psS32 growRadius = 0; - if (inImg->type.type == PS_TYPE_F32) { - if(inImg->data.F32[row][col] == growVal) { - growRadius = grow; - } - if (inImg->data.F32[row][col] > sat) { - growRadius = PS_MAX(growRadius+1, 2); - } - } else if (inImg->type.type == PS_TYPE_S32) { - if(inImg->data.S32[row][col] == growVal) { - growRadius = grow; - } - if (inImg->data.S32[row][col] > sat) { - growRadius = PS_MAX(growRadius+1, 2); - } - } else if (inImg->type.type == PS_TYPE_U16) { - if(inImg->data.U16[row][col] == growVal) { - growRadius = grow; - } - if (inImg->data.U16[row][col] > sat) { - growRadius = PS_MAX(growRadius+1, 2); - } - } else { - psError( PS_ERR_BAD_PARAMETER_TYPE, true, - PS_ERRORTEXT_pmMaskBadPixels_TYPE_MASK_IMAGE, - inImg->type.type); - } - return(growRadius); -} - - -bool pmMaskBadPixels( - pmReadout *in, - const pmReadout *mask, - unsigned int maskVal, - float sat, - unsigned int growVal, - int grow) -{ - // XXX: Review this code then put all asserts at the top. - PS_ASSERT_PTR_NON_NULL(in, true); - PS_ASSERT_PTR_NON_NULL(in->image, false); - PS_WARN_PTR_NON_NULL(in->parent); - if (in->parent != NULL) { - PS_WARN_PTR_NON_NULL(in->parent->concepts); - } - PS_ASSERT_PTR_NON_NULL(mask, false); - int i = 0; - int j = 0; - int totOffCol = 0; - int totOffRow = 0; - psElemType inType; - psElemType maskType; - psImage *inMask = NULL; - - // - // Determine trimmed image from metadata. - // - psImage *trimmedImg = p_psDetermineTrimmedImage(in); - if(in->mask == NULL) { - in->mask = psImageAlloc(trimmedImg->numCols, trimmedImg->numRows, PS_TYPE_MASK); - PS_IMAGE_SET_U8(in->mask, 0); + inImage = in->image; + if (inImage == NULL) { + psError( PS_ERR_BAD_PARAMETER_NULL, true, + PS_ERRORTEXT_pmMaskBadPixels_NULL_INPUT_IMAGE); + return false; + } else if(in->mask == NULL) { + in->mask = psImageAlloc(inImage->numCols, inImage->numRows, PS_TYPE_MASK); + memset(in->mask->data.V[0], 0, inImage->numCols*inImage->numRows*PSELEMTYPE_SIZEOF(PS_TYPE_MASK)); } inMask = in->mask; // Check input image and its mask are not larger than mask - if(trimmedImg->numRows > mask->image->numRows || trimmedImg->numCols > mask->image->numCols) { + if(inImage->numRows > mask->numRows || inImage->numCols > mask->numCols) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmMaskBadPixels_SIZE_INPUT_IMAGE, - trimmedImg->numRows, trimmedImg->numCols, mask->image->numRows, mask->image->numCols); + inImage->numRows, inImage->numCols, mask->numRows, mask->numCols); return false; - } else if(inMask->numRows > mask->image->numRows || inMask->numCols > mask->image->numCols) { + } else if(inMask->numRows>mask->numRows || inMask->numCols>mask->numCols) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmMaskBadPixels_SIZE_MASK_IMAGE, - inMask->numRows, inMask->numCols, mask->image->numRows, mask->image->numCols); + inMask->numRows, inMask->numCols, mask->numRows, mask->numCols); return false; } // Determine total offset based on image offset with chip offset - totOffCol = trimmedImg->col0 + in->col0; - totOffRow = trimmedImg->row0 + in->row0; + totOffCol = inImage->col0; // + in->col0; + totOffRow = inImage->row0; // + in->row0; // Check that offsets are within image limits - if(totOffRow>=mask->image->numRows || totOffCol>=mask->image->numCols) { + if(totOffRow>=mask->numRows || totOffCol>=mask->numCols) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmMaskBadPixels_OFFSET_MASK_IMAGE, - totOffRow, totOffCol, mask->image->numRows, mask->image->numCols); + totOffRow, totOffCol, mask->numRows, mask->numCols); return false; - } else if(totOffRow>=trimmedImg->numRows || totOffCol>=trimmedImg->numCols) { + } else if(totOffRow>=inImage->numRows || totOffCol>=inImage->numCols) { psError( PS_ERR_BAD_PARAMETER_SIZE, true, PS_ERRORTEXT_pmMaskBadPixels_OFFSET_INPUT_IMAGE, - totOffRow, totOffCol, trimmedImg->numRows, trimmedImg->numCols); + totOffRow, totOffCol, inImage->numRows, inImage->numCols); return false; } else if(totOffRow>=inMask->numRows || totOffCol>=inMask->numCols) { @@ -193,6 +118,6 @@ // Check for incorrect types - inType = trimmedImg->type.type; - maskType = mask->image->type.type; + inType = inImage->type.type; + maskType = mask->type.type; if(PS_IS_PSELEMTYPE_COMPLEX(inType)) { psError( PS_ERR_BAD_PARAMETER_TYPE, true, @@ -207,34 +132,57 @@ } - // - // This is the main loop which examines each pixel and masks pixels if - // A: The mask matches the maskValue - // B: The pixel is larger than the saturation value - // C: The pixel equals the grow value (in which case a circle is masked) - // - for(i=totOffRow; inumRows; i++) { - for(j=totOffCol; jnumCols; j++) { - // - // A: Pixels which satisfy maskVal shall be masked - // - if (mask->image->data.U8[i][j] == maskVal) { - in->mask->data.U8[i][j] |= maskVal; - } + // Macro for all PS types + #define PM_BAD_PIXELS(TYPE) \ +case PS_TYPE_##TYPE: \ + for(j=totOffRow; jnumRows; j++) { \ + for(i=totOffCol; inumCols; i++) { \ + \ + /* Pixels with flux greater than sat shall be masked */ \ + if(inImage->data.TYPE[j][i] > sat) { \ + inMask->data.PS_TYPE_MASK_DATA[j][i] |= PM_MASK_SAT; \ + } \ + \ + /* Pixels which satisfy maskVal shall be masked */ \ + inMask->data.PS_TYPE_MASK_DATA[j][i] |= (mask->data.PS_TYPE_MASK_DATA[j][i]&maskVal); \ + \ + /* Pixels which satisfy growVal and within the grow radius shall be masked */ \ + if(mask->data.PS_TYPE_MASK_DATA[j][i] & growVal) { \ + rowMin = MAX(j-grow, 0); \ + rowMax = MIN(j+grow+1, inImage->numRows); \ + colMin = MAX(i-grow, 0); \ + colMax = MIN(i+grow+1, inImage->numCols); \ + for(jj=rowMin; jjdata.PS_TYPE_MASK_DATA[jj][ii] |= \ + (mask->data.PS_TYPE_MASK_DATA[j][i]&growVal); \ + } \ + } \ + } \ + } \ + } \ + } \ + break; - // - // We first determine how much we need to grow by and store this in - // growRadius. - // - psS32 growRadius = GetRadius(trimmedImg, j, i, sat, growVal, grow); - - // - // Grow the pixel mask if necessary. - // - if (growRadius != 0) { - GrowPixel(in->mask, j, i, growRadius, maskVal); - } - } + // Switch to call bad pixel masking macro defined above + switch(inType) { + PM_BAD_PIXELS(U8); + PM_BAD_PIXELS(U16); + PM_BAD_PIXELS(U32); + PM_BAD_PIXELS(U64); + PM_BAD_PIXELS(S8); + PM_BAD_PIXELS(S16); + PM_BAD_PIXELS(S32); + PM_BAD_PIXELS(S64); + PM_BAD_PIXELS(F32); + PM_BAD_PIXELS(F64); + default: + psError( PS_ERR_BAD_PARAMETER_TYPE, true, + PS_ERRORTEXT_pmMaskBadPixels_TYPE_UNSUPPORTED, + inType); } - return true; + return false; } Index: trunk/psModules/src/detrend/pmMaskBadPixels.h =================================================================== --- trunk/psModules/src/detrend/pmMaskBadPixels.h (revision 6529) +++ trunk/psModules/src/detrend/pmMaskBadPixels.h (revision 6872) @@ -1,2 +1,7 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /** @file pmMaskBadPixels.h * @@ -19,6 +24,6 @@ * @author Ross Harman, MHPCC * - * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-11-15 20:09:03 $ + * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -26,5 +31,5 @@ #include "pslib.h" -#include "pmAstrometry.h" +#include "pmFPA.h" /** Mask values */ @@ -33,8 +38,8 @@ PM_MASK_BADCOL = 0x0002, ///< The pixel is a bad column. PM_MASK_SAT = 0x0004, ///< The pixel is saturated. - PM_MASK_FLAT = 0x0008 ///< The pixel is non-positive in the flat-field. + PM_MASK_BAD = 0x0008, ///< The pixel is low + PM_MASK_FLAT = 0x0010 ///< The pixel is non-positive in the flat-field. } pmMaskValue; -// XXX: Use PS_MIN, PS_MAX /** Macro to find maximum of two numbers */ #define MAX(A,B)((A)>=(B)?(A):(B)) @@ -54,5 +59,5 @@ bool pmMaskBadPixels( pmReadout *in, ///< Readout containing input image data. - const pmReadout *mask, ///< Mask data to be added to readout mask data. + const psImage *mask, ///< Mask data to be added to readout mask data. unsigned int maskVal, ///< Mask value to determine what to add to input mask. float sat, ///< Saturation limit to mask bad pixels. Index: trunk/psModules/src/detrend/pmMaskBadPixelsErrors.h =================================================================== --- trunk/psModules/src/detrend/pmMaskBadPixelsErrors.h (revision 6529) +++ trunk/psModules/src/detrend/pmMaskBadPixelsErrors.h (revision 6872) @@ -1,2 +1,7 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /** @file pmMaskBadPixelsErrors.h * @@ -7,6 +12,6 @@ * @author Ross Harman, MHPCC * - * @version $Revision: 1.1 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-09-28 20:43:52 $ + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -23,5 +28,5 @@ * $2 The error text (rest of the line in pmMaskBadPixelsErrors.h) * $n The order of the source line in pmMaskBadPixelsErrors.h (comments excluded) - * + * * DO NOT EDIT THE LINES BETWEEN //~Start and //~End! ANY CHANGES WILL BE OVERWRITTEN. */ Index: trunk/psModules/src/detrend/pmNonLinear.c =================================================================== --- trunk/psModules/src/detrend/pmNonLinear.c (revision 6529) +++ trunk/psModules/src/detrend/pmNonLinear.c (revision 6872) @@ -1,2 +1,7 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /** @file pmNonLinear.c * @@ -5,6 +10,6 @@ * @author GLG, MHPCC * - * @version $Revision: 1.5 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-12-05 20:49:40 $ + * @version $Revision: 1.6 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -22,22 +27,14 @@ #include "pmNonLinear.h" -#include "pmSubtractBias.h" -// XXX: Remove, autoconf must be -#define PS_WARN_PTR_NON_NULL(NAME) \ -if ((NAME) == NULL) { \ - psLogMsg(__func__, PS_LOG_WARN, "WARNING: %s is NULL.", #NAME); \ -} \ /****************************************************************************** pmNonLinearityLookup(): This routine will take an pmReadout image as input and a 1-D polynomial. For each pixel in the input image, the polynomial will -be evaluated at that pixels value, and the image pixel will then be set -to +be evaluated at that pixels value, and the image pixel will then be set to that value. -*****************************************************************************/ + *****************************************************************************/ -pmReadout *pmNonLinearityPolynomial( - pmReadout *inputReadout, - const psPolynomial1D *input1DPoly) +pmReadout *pmNonLinearityPolynomial(pmReadout *inputReadout, + const psPolynomial1D *input1DPoly) { PS_ASSERT_PTR_NON_NULL(inputReadout, NULL); @@ -45,18 +42,11 @@ PS_ASSERT_IMAGE_TYPE(inputReadout->image, PS_TYPE_F32, NULL); PS_ASSERT_PTR_NON_NULL(input1DPoly, NULL); - PS_WARN_PTR_NON_NULL(inputReadout->parent); - if (inputReadout->parent != NULL) { - PS_WARN_PTR_NON_NULL(inputReadout->parent->concepts); - } - // - // Determine trimmed image from metadata. - // - psImage *trimmedImg = p_psDetermineTrimmedImage(inputReadout); + psS32 i; + psS32 j; - for (psS32 i=0;inumRows;i++) { - for (psS32 j=0;jnumCols;j++) { - trimmedImg->data.F32[i][j] = psPolynomial1DEval(input1DPoly, - trimmedImg->data.F32[i][j]); + for (i=0;iimage->numRows;i++) { + for (j=0;jimage->numCols;j++) { + inputReadout->image->data.F32[i][j] = psPolynomial1DEval(input1DPoly, inputReadout->image->data.F32[i][j]); } } @@ -71,48 +61,68 @@ inFluxe, and the corresponding value in outFlux. The image pixel will then be set to the value from outFlux. - -XXX: Must assert that filename exists. This should probably happen in -the lookup files. *****************************************************************************/ -pmReadout *pmNonLinearityLookup( - pmReadout *inputReadout, - const char *filename -) +pmReadout *pmNonLinearityLookup(pmReadout *inputReadout, + const psVector *inFlux, + const psVector *outFlux) { PS_ASSERT_PTR_NON_NULL(inputReadout,NULL); PS_ASSERT_PTR_NON_NULL(inputReadout->image,NULL); PS_ASSERT_IMAGE_TYPE(inputReadout->image, PS_TYPE_F32, NULL); - PS_WARN_PTR_NON_NULL(inputReadout->parent); - if (inputReadout->parent != NULL) { - PS_WARN_PTR_NON_NULL(inputReadout->parent->concepts); + PS_ASSERT_PTR_NON_NULL(inFlux,NULL); + if (inFlux->n < 2) { + psError(PS_ERR_UNKNOWN,true, "pmNonLinearityLookup(): input vector less than 2 elements. Returning inputReadout image."); + return(inputReadout); } - // - // Determine trimmed image from metadata. - // - psImage *trimmedImg = p_psDetermineTrimmedImage(inputReadout); + PS_ASSERT_PTR_NON_NULL(outFlux,NULL); + psS32 tableSize = inFlux->n; + if (inFlux->n != outFlux->n) { + tableSize = PS_MIN(inFlux->n, outFlux->n); + psLogMsg(__func__, PS_LOG_WARN, + "WARNING: pmNonLinear.c: pmNonLinearityLookup(): input vectors have different sizes (%d, %d)\n", inFlux->n, outFlux->n); + } + PS_ASSERT_VECTOR_TYPE(inFlux, PS_TYPE_F32, NULL); + PS_ASSERT_VECTOR_TYPE(outFlux, PS_TYPE_F32, NULL); - psLookupTable *tmpLT = psLookupTableAlloc(filename, "%f %f", 0); - psS32 numLines = psLookupTableRead(tmpLT); + psS32 i; + psS32 j; + psS32 binNum; + psScalar x; psS32 numPixels = 0; - if (numLines < 2) { - psLogMsg(__func__, PS_LOG_WARN, - "WARNING: Lookup Table is too small. Returning original pmReadout.\n"); - } else { - for (psS32 i=0;inumRows;i++) { - for (psS32 j=0;jnumCols;j++) { - psF64 tmpD = psLookupTableInterpolate(tmpLT, trimmedImg->data.F32[i][j], 1); - if (!isnan(tmpD)) { - trimmedImg->data.F32[i][j] = tmpD; - } else { - numPixels++; - } + psF32 slope; + + x.type.type = PS_TYPE_F32; + for (i=0;iimage->numRows;i++) { + for (j=0;jimage->numCols;j++) { + x.data.F32 = inputReadout->image->data.F32[i][j]; + binNum = p_psVectorBinDisect((psVector *)inFlux, &x); + + if (binNum == -2) { + // We get here if x is below the table lookup range. + inputReadout->image->data.F32[i][j] = outFlux->data.F32[0]; + numPixels++; + + } else if (binNum == -1) { + // We get here if x is above the table lookup range. + inputReadout->image->data.F32[i][j] = outFlux->data.F32[tableSize-1]; + numPixels++; + + } else if (binNum < -2) { + // We get here if there was some other problem. + psError(PS_ERR_UNKNOWN,true, "pmNonLinearityLookup(): Could not perform p_psVectorBinDisect(). Returning inputReadout image."); + return(inputReadout); + numPixels++; + } else { + // Perform linear interpolation. + slope = (outFlux->data.F32[binNum+1] - outFlux->data.F32[binNum]) / + (inFlux->data.F32[binNum+1] - inFlux->data.F32[binNum]); + inputReadout->image->data.F32[i][j] = outFlux->data.F32[binNum] + + ((x.data.F32 - inFlux->data.F32[binNum]) * slope); } } - if (numPixels > 0) { - psLogMsg(__func__, PS_LOG_WARN, - "WARNING: pmNonLinear.c: pmNonLinearityLookup(): %d pixels outside table.", numPixels); - } } - + if (numPixels > 0) { + psLogMsg(__func__, PS_LOG_WARN, + "WARNING: pmNonLinear.c: pmNonLinearityLookup(): %d pixels outside table.", numPixels); + } return(inputReadout); } Index: trunk/psModules/src/detrend/pmNonLinear.h =================================================================== --- trunk/psModules/src/detrend/pmNonLinear.h (revision 6529) +++ trunk/psModules/src/detrend/pmNonLinear.h (revision 6872) @@ -1,2 +1,7 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /** @file pmNonLinear.h * @@ -5,6 +10,6 @@ * @author GLG, MHPCC * - * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-10-20 23:06:24 $ + * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -16,15 +21,12 @@ #include "pslib.h" -#include "pmAstrometry.h" +#include "pmFPA.h" -pmReadout *pmNonLinearityPolynomial( - pmReadout *in, - const psPolynomial1D *coeff -); +pmReadout *pmNonLinearityPolynomial(pmReadout *in, + const psPolynomial1D *coeff); -pmReadout *pmNonLinearityLookup( - pmReadout *in, - const char *filename -); +pmReadout *pmNonLinearityLookup(pmReadout *in, + const psVector *inFlux, + const psVector *outFlux); #endif Index: trunk/psModules/src/imcombine/Makefile.am =================================================================== --- trunk/psModules/src/imcombine/Makefile.am (revision 6529) +++ trunk/psModules/src/imcombine/Makefile.am (revision 6872) @@ -3,9 +3,9 @@ libpsmoduleimcombine_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) libpsmoduleimcombine_la_LDFLAGS = -release $(PACKAGE_VERSION) -libpsmoduleimcombine_la_SOURCES = pmImageCombine.c \ - pmReadoutCombine.c +libpsmoduleimcombine_la_SOURCES = pmImageCombine.c +# pmReadoutCombine.c psmoduleincludedir = $(includedir) psmoduleinclude_HEADERS = \ - pmImageCombine.h \ - pmReadoutCombine.h + pmImageCombine.h +# pmReadoutCombine.h Index: trunk/psModules/src/imcombine/pmReadoutCombine.h =================================================================== --- trunk/psModules/src/imcombine/pmReadoutCombine.h (revision 6529) +++ trunk/psModules/src/imcombine/pmReadoutCombine.h (revision 6872) @@ -5,6 +5,6 @@ * @author GLG, MHPCC * - * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ - * @date $Date: 2006-01-26 21:10:50 $ + * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -23,5 +23,5 @@ #include "pslib.h" #include "psConstants.h" -#include "pmAstrometry.h" +#include "pmFPA.h" typedef struct @@ -33,11 +33,13 @@ int nKeep; } -psCombineParams; +pmCombineParams; + +pmCombineParams *pmCombineParamsAlloc (psStatsOptions statsOptions); psImage *pmReadoutCombine(psImage *output, - const psList *inputs, - psCombineParams *params, + const psArray *inputs, const psVector *zero, const psVector *scale, + pmCombineParams *params, bool applyZeroScale, float gain, @@ -72,29 +74,3 @@ pmFringePoint; - -/** - * - * The input array fluxLevels consists of Ni vectors, one per mosaic image. - * Each vector consists of Nj elements, each a measurement of the input - * flat-field image flux levels. All of these vectors must be constructed with - * the same number of elements, or the function will return an error. If a chip - * is missing from a particular image, that element should be set to NaN. The - * vector chipGains supplies initial guesses for the chip gains. If the vector - * contains the values 0.0 or NaN for any of the elements, the gain is set to the - * mean of the valid values. If the vector length does not match the number of - * chips, an warning is raised, all chip gain guesses will be set to 1.0, and the - * vector length modified to match the number of chips defined by the supplied - * fluxLevels. The sourceFlux input vector must be allocated (not NULL), but the - * routine will set the vector length to the number of source images regardless - * of the initial state of the vector. All vectors used by this function must be - * of type PS_DATA_F64. - * - */ -bool pmFlatNormalization( - psVector *sourceFlux, - psVector *chipGains, - psArray *fluxLevels -); - - #endif Index: trunk/psModules/src/imsubtract/Makefile.am =================================================================== --- trunk/psModules/src/imsubtract/Makefile.am (revision 6529) +++ trunk/psModules/src/imsubtract/Makefile.am (revision 6872) @@ -4,10 +4,10 @@ libpsmoduleimsubtract_la_LDFLAGS = -release $(PACKAGE_VERSION) libpsmoduleimsubtract_la_SOURCES = pmImageSubtract.c \ - pmSubtractBias.c \ - pmSubtractSky.c + pmSubtractBias.c +# pmSubtractSky.c psmoduleincludedir = $(includedir) psmoduleinclude_HEADERS = \ pmImageSubtract.h \ - pmSubtractBias.h \ - pmSubtractSky.h + pmSubtractBias.h +# pmSubtractSky.h Index: trunk/psModules/src/imsubtract/pmSubtractBias.h =================================================================== --- trunk/psModules/src/imsubtract/pmSubtractBias.h (revision 6529) +++ trunk/psModules/src/imsubtract/pmSubtractBias.h (revision 6872) @@ -1,2 +1,7 @@ +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// XXX WARNING: I have completely replaced this file with an OLD VERSION (that works) instead of the +// one that was being worked on. +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /** @file pmSubtractBias.h * @@ -6,6 +11,6 @@ * @author GLG, MHPCC * - * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-11-23 23:54:30 $ + * @version $Revision: 1.5 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -23,8 +28,10 @@ #include #include "pslib.h" -#include "pmAstrometry.h" + +#include "pmFPA.h" typedef enum { PM_OVERSCAN_NONE, ///< No overscan subtraction + PM_OVERSCAN_EDGE, ///< Subtract the statistic of pixels along the to-be-determined readout direction PM_OVERSCAN_ROWS, ///< Subtract rows PM_OVERSCAN_COLUMNS, ///< Subtract columns @@ -33,30 +40,38 @@ typedef enum { - PM_FIT_NONE, ///< No fit - PM_FIT_POLYNOMIAL, ///< Fit polynomial - PM_FIT_SPLINE ///< Fit cubic splines + PM_FIT_NONE, ///< No fit + PM_FIT_POLY_ORD, ///< Fit ordinary polynomial + PM_FIT_POLY_CHEBY, ///< Fit Chebyshev polynomial + PM_FIT_SPLINE ///< Fit cubic splines } pmFit; -pmReadout *pmSubtractBias( - pmReadout *in, ///< The input pmReadout image - void *fitSpec, ///< A polynomial or spline, defining the fit type. - pmFit fit, ///< PM_FIT_SPLINE, PM_FIT_POLYNOMIAL, or PM_FIT_NONE - bool overscan, - psStats *stat, ///< The statistic to be used in combining overscan data - int nBin, ///< The amount of binning to be done image pixels. - const pmReadout *bias, ///< A possibly NULL bias pmReadout which is to be subtracted - const pmReadout *dark ///< A possibly NULL bias pmReadout which is to be subtracted -); +typedef struct +{ + // Inputs + bool single; // Reduce all overscan regions to a single value? + pmFit fitType; // Type of fit to overscan + unsigned int order; // Order of polynomial, or number of spline pieces + psStats *stat; // Statistic to use when reducing the minor direction + // Outputs + psPolynomial1D *poly; // Result of polynomial fit + psSpline1D *spline; // Result of spline fit +} +pmOverscanOptions; -/****************************************************************************** -DetermineTrimmedImageg() This private routine determines the region of the -input pmReadout which will be operated on by the various detrend modules. It -does a metadata fetch on "CELL.TRIMSEC" for the parent cell of the pmReadout. - -XXX: Consider making a pmUtils.c file and put this routine there. - *****************************************************************************/ -psImage *p_psDetermineTrimmedImage( - pmReadout *in -); +pmOverscanOptions *pmOverscanOptionsAlloc(bool single, pmFit fitType, unsigned int order, psStats *stat); + +pmReadout *pmSubtractBias(pmReadout *in, pmOverscanOptions *overscanOpts, + const pmReadout *bias, const pmReadout *dark); + +#if 0 +pmReadout *pmSubtractBias(pmReadout *in, ///< The input pmReadout image + void *fitSpec, ///< A polynomial or spline, defining the fit type. + const psList *overscans, ///< A psList of overscan images + pmOverscanAxis overScanAxis, ///< Defines how overscans are applied + psStats *stat, ///< The statistic to be used in combining overscan data + int nBin, ///< The amount of binning to be done image pixels. + pmFit fit, ///< PM_FIT_SPLINE, PM_FIT_POLYNOMIAL, or PM_FIT_NONE + const pmReadout *bias); ///< A possibly NULL bias pmReadout which is to be subtracted +#endif #endif Index: trunk/psModules/src/imsubtract/pmSubtractSky.h =================================================================== --- trunk/psModules/src/imsubtract/pmSubtractSky.h (revision 6529) +++ trunk/psModules/src/imsubtract/pmSubtractSky.h (revision 6872) @@ -6,6 +6,6 @@ * @author GLG, MHPCC * - * @version $Revision: 1.1 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-09-28 20:43:52 $ + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -23,5 +23,5 @@ #include #include "pslib.h" -#include "pmAstrometry.h" +#include "pmFPA.h" // XXX: this is pmFit in pmSubtractBias.c, named psFit here. Index: trunk/psModules/src/objects/Makefile.am =================================================================== --- trunk/psModules/src/objects/Makefile.am (revision 6529) +++ trunk/psModules/src/objects/Makefile.am (revision 6872) @@ -1,12 +1,26 @@ noinst_LTLIBRARIES = libpsmoduleobjects.la -libpsmoduleobjects_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) +libpsmoduleobjects_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) -I../pslib/ libpsmoduleobjects_la_LDFLAGS = -release $(PACKAGE_VERSION) libpsmoduleobjects_la_SOURCES = \ - pmObjects.c \ - pmPSF.c \ - pmPSFtry.c \ - pmModelGroup.c \ - psEllipse.c + pmPeaks.c \ + pmMoments.c \ + pmModel.c \ + pmModelGroup.c \ + pmSource.c \ + pmSourceSky.c \ + pmSourceContour.c \ + pmSourceFitModel.c \ + pmSourcePhotometry.c \ + pmSourceIO.c \ + pmSourceIO_CMF.c \ + pmSourceIO_CMP.c \ + pmSourceIO_OBJ.c \ + pmSourceIO_SX.c \ + pmSourceIO_RAW.c \ + pmPSF.c \ + pmPSF_IO.c \ + pmPSFtry.c \ + pmGrowthCurve.c EXTRA_DIST = \ @@ -18,7 +32,16 @@ psmoduleincludedir = $(includedir) psmoduleinclude_HEADERS = \ - pmObjects.h \ - pmPSF.h \ - pmPSFtry.h \ - pmModelGroup.h \ - psEllipse.h + pmPeaks.h \ + pmMoments.h \ + pmModel.h \ + pmModelGroup.h \ + pmSource.h \ + pmSourceSky.h \ + pmSourceContour.h \ + pmSourceFitModel.h \ + pmSourcePhotometry.h \ + pmSourceIO.h \ + pmPSF.h \ + pmPSF_IO.h \ + pmPSFtry.h \ + pmGrowthCurve.h Index: trunk/psModules/src/objects/models/pmModel_PGAUSS.c =================================================================== --- trunk/psModules/src/objects/models/pmModel_PGAUSS.c (revision 6529) +++ trunk/psModules/src/objects/models/pmModel_PGAUSS.c (revision 6872) @@ -26,13 +26,13 @@ if (deriv != NULL) { - // note difference from a pure gaussian: q = PAR[1]*r + psF32 *dPAR = deriv->data.F32; psF32 q = PAR[1]*r*r*t; - deriv->data.F32[0] = +1.0; - deriv->data.F32[1] = +r; - deriv->data.F32[2] = q*(2.0*px*PAR[4] + PAR[6]*Y); - deriv->data.F32[3] = q*(2.0*py*PAR[5] + PAR[6]*X); - deriv->data.F32[4] = -2.0*q*px*X; - deriv->data.F32[5] = -2.0*q*py*Y; - deriv->data.F32[6] = -q*X*Y; + dPAR[0] = +1.0; + dPAR[1] = +r; + dPAR[2] = q*(2.0*px*PAR[4] + PAR[6]*Y); + dPAR[3] = q*(2.0*py*PAR[5] + PAR[6]*X); + dPAR[4] = -2.0*q*px*X; + dPAR[5] = -2.0*q*py*Y; + dPAR[6] = -q*X*Y; } return(f); @@ -50,5 +50,5 @@ beta_lim[0][0].data.F32[0] = 1000; - beta_lim[0][0].data.F32[1] = 10000; + beta_lim[0][0].data.F32[1] = 3e6; beta_lim[0][0].data.F32[2] = 5; beta_lim[0][0].data.F32[3] = 5; @@ -66,5 +66,5 @@ params_max[0][0].data.F32[0] = 1e5; - params_max[0][0].data.F32[1] = 1e6; + params_max[0][0].data.F32[1] = 1e8; params_max[0][0].data.F32[2] = 1e4; // this should be set by image dimensions! params_max[0][0].data.F32[3] = 1e4; // this should be set by image dimensions! @@ -133,4 +133,5 @@ params[5] = 1.2 / moments->Sy; params[6] = 0.0; + return(true); } Index: trunk/psModules/src/objects/models/pmModel_QGAUSS.c =================================================================== --- trunk/psModules/src/objects/models/pmModel_QGAUSS.c (revision 6529) +++ trunk/psModules/src/objects/models/pmModel_QGAUSS.c (revision 6872) @@ -26,21 +26,27 @@ psF32 py = PAR[5]*Y; psF32 z = 0.5*PS_SQR(px) + 0.5*PS_SQR(py) + PAR[6]*X*Y; - - psF32 r = 1.0 / (1 + PAR[7]*z + pow(z, 2.25)); - psF32 f = PAR[1]*r + PAR[0]; + psF32 zp = pow(z,1.25); + + psF32 r = 1.0 / (1 + PAR[7]*z + z*zp); + // test: psF32 r = 1.0 / (1 + PAR[7]*z + PS_SQR(z)); + psF32 r1 = PAR[1]*r; + psF32 f = r1 + PAR[0]; if (deriv != NULL) { + psF32 *dPAR = deriv->data.F32; + // note difference from a pure gaussian: q = params->data.F32[1]*r - psF32 t = PAR[1]*r*r; - psF32 q = t*(PAR[7] + 2.25*pow(z, 1.25)); - - deriv->data.F32[0] = +1.0; - deriv->data.F32[1] = +r; - deriv->data.F32[2] = q*(2.0*px*PAR[4] + PAR[6]*Y); - deriv->data.F32[3] = q*(2.0*py*PAR[5] + PAR[6]*X); - deriv->data.F32[4] = -2.0*q*px*X; - deriv->data.F32[5] = -2.0*q*py*Y; - deriv->data.F32[6] = -q*X*Y; - deriv->data.F32[7] = -t*z; + psF32 t = r1*r; + psF32 q = t*(PAR[7] + 2.25*zp); + // test: psF32 q = t*(PAR[7] + 2*z); + + dPAR[0] = +1.0; + dPAR[1] = +r; + dPAR[2] = q*(2.0*px*PAR[4] + PAR[6]*Y); + dPAR[3] = q*(2.0*py*PAR[5] + PAR[6]*X); + dPAR[4] = -2.0*q*px*X; + dPAR[5] = -2.0*q*py*Y; + dPAR[6] = -q*X*Y; + dPAR[7] = -t*z; } return(f); @@ -58,5 +64,5 @@ beta_lim[0][0].data.F32[0] = 1000; - beta_lim[0][0].data.F32[1] = 10000; + beta_lim[0][0].data.F32[1] = 3e6; beta_lim[0][0].data.F32[2] = 5; beta_lim[0][0].data.F32[3] = 5; @@ -76,5 +82,5 @@ params_max[0][0].data.F32[0] = 1e5; - params_max[0][0].data.F32[1] = 1e6; + params_max[0][0].data.F32[1] = 1e8; params_max[0][0].data.F32[2] = 1e4; // this should be set by image dimensions! params_max[0][0].data.F32[3] = 1e4; // this should be set by image dimensions! @@ -102,4 +108,5 @@ params[6] = 0.0; params[7] = 1.0; + return(true); } @@ -119,9 +126,10 @@ // the area needs to be multiplied by the integral of f(z) norm = 0.0; - for (z = 0.005; z < 50; z += 0.01) { + for (z = 0.05; z < 50; z += 0.1) { f = 1.0 / (1 + PAR[7]*z + pow(z, 2.25)); + // test: f = 1.0 / (1 + PAR[7]*z + PS_SQR(z)); norm += f; } - norm *= 0.01; + norm *= 0.1; psF64 Flux = PAR[1] * Area * norm; @@ -150,6 +158,7 @@ // we can do this much better with intelligent choices here - for (z = 0.0; z < 20.0; z += dz) { + for (z = 0.0; z < 30.0; z += dz) { f = 1.0 / (1 + PAR[7]*z + pow(z, 2.25)); + // test: f = 1.0 / (1 + PAR[7]*z + PS_SQR(z)); if (f < limit) break; @@ -201,6 +210,6 @@ status &= ((dPAR[1]/PAR[1]) < 0.5); - if (status) - return true; - return false; -} + if (!status) + return false; + return true; +} Index: trunk/psModules/src/objects/models/pmModel_RGAUSS.c =================================================================== --- trunk/psModules/src/objects/models/pmModel_RGAUSS.c (revision 6529) +++ trunk/psModules/src/objects/models/pmModel_RGAUSS.c (revision 6872) @@ -117,7 +117,7 @@ psVector *params = model->params; - EllipseAxes axes; - EllipseShape shape; - EllipseMoments moments; + psEllipseAxes axes; + psEllipseShape shape; + psEllipseMoments moments; moments.x2 = PS_SQR(source->moments->Sx); @@ -125,6 +125,6 @@ moments.xy = source->moments->Sxy; - axes = EllipseMomentsToAxes(moments); - shape = EllipseAxesToShape(axes); + axes = psEllipseMomentsToAxes(moments); + shape = psEllipseAxesToShape(axes); params->data.F32[0] = source->moments->Sky; Index: trunk/psModules/src/objects/models/pmModel_SGAUSS.c =================================================================== --- trunk/psModules/src/objects/models/pmModel_SGAUSS.c (revision 6529) +++ trunk/psModules/src/objects/models/pmModel_SGAUSS.c (revision 6872) @@ -17,5 +17,5 @@ # define SQ(A)((A)*(A)) -psF64 psImageEllipseContour (EllipseAxes axes, double xc, double yc, psImage *image); +psF64 psImageEllipseContour (psEllipseAxes axes, double xc, double yc, psImage *image); psF64 p_psImageGetElementF64(psImage *a, int i, int j); @@ -102,5 +102,5 @@ // measure the flux for the elliptical contour -psF64 psImageEllipseContour (EllipseAxes axes, double xc, double yc, psImage *image) +psF64 psImageEllipseContour (psEllipseAxes axes, double xc, double yc, psImage *image) { @@ -149,7 +149,7 @@ psF32 *params = model->params->data.F32; - EllipseAxes axes; - EllipseShape shape; - EllipseMoments moments; + psEllipseAxes axes; + psEllipseShape shape; + psEllipseMoments moments; moments.x2 = PS_SQR(sMoments->Sx); @@ -158,6 +158,6 @@ // solve the math to go from Moments To Shape - axes = EllipseMomentsToAxes(moments); - shape = EllipseAxesToShape(axes); + axes = psEllipseMomentsToAxes(moments); + shape = psEllipseAxesToShape(axes); params[0] = sMoments->Sky; @@ -199,7 +199,7 @@ float f1, f2; - EllipseAxes axes; - EllipseShape shape; - EllipseMoments moments; + psEllipseAxes axes; + psEllipseShape shape; + psEllipseMoments moments; moments.x2 = PS_SQR(sMoments->Sx); @@ -208,6 +208,6 @@ // solve the math to go from Moments To Shape - axes = EllipseMomentsToAxes(moments); - shape = EllipseAxesToShape(axes); + axes = psEllipseMomentsToAxes(moments); + shape = psEllipseAxesToShape(axes); params[0] = sMoments->Sky; @@ -265,9 +265,9 @@ psF64 pmModelRadius_SGAUSS (const psVector *params, psF64 flux) { - psF64 r, z, pr, f; + psF64 r, z = 0.0, pr, f; psF32 *PAR = params->data.F32; - EllipseAxes axes; - EllipseShape shape; + psEllipseAxes axes; + psEllipseShape shape; if (flux <= 0) @@ -283,5 +283,5 @@ shape.sxy = PAR[6]; - axes = EllipseShapeToAxes (shape); + axes = psEllipseShapeToAxes (shape); psF64 dr = 1.0 / axes.major; psF64 limit = flux / PAR[1]; @@ -327,6 +327,6 @@ psF32 dP; bool status; - EllipseAxes axes; - EllipseShape shape; + psEllipseAxes axes; + psEllipseShape shape; psF32 *PAR = model->params->data.F32; @@ -337,5 +337,5 @@ shape.sxy = PAR[6]; - axes = EllipseShapeToAxes (shape); + axes = psEllipseShapeToAxes (shape); dP = 0; Index: trunk/psModules/src/objects/models/pmModel_ZGAUSS.c =================================================================== --- trunk/psModules/src/objects/models/pmModel_ZGAUSS.c (revision 6529) +++ trunk/psModules/src/objects/models/pmModel_ZGAUSS.c (revision 6872) @@ -85,6 +85,6 @@ psF32 *PAR = params->data.F32; - EllipseAxes axes; - EllipseShape shape; + psEllipseAxes axes; + psEllipseShape shape; if (flux <= 0) @@ -100,5 +100,5 @@ shape.sxy = PAR[6]; - axes = EllipseShapeToAxes (shape); + axes = psEllipseShapeToAxes (shape); psF64 dr = 1.0 / axes.major; psF64 limit = flux / PAR[1]; @@ -124,7 +124,7 @@ psVector *params = model->params; - EllipseAxes axes; - EllipseShape shape; - EllipseMoments moments; + psEllipseAxes axes; + psEllipseShape shape; + psEllipseMoments moments; moments.x2 = PS_SQR(source->moments->Sx); @@ -132,6 +132,6 @@ moments.xy = source->moments->Sxy; - axes = EllipseMomentsToAxes(moments); - shape = EllipseAxesToShape(axes); + axes = psEllipseMomentsToAxes(moments); + shape = psEllipseAxesToShape(axes); params->data.F32[0] = source->moments->Sky; Index: trunk/psModules/src/objects/pmGrowthCurve.c =================================================================== --- trunk/psModules/src/objects/pmGrowthCurve.c (revision 6872) +++ trunk/psModules/src/objects/pmGrowthCurve.c (revision 6872) @@ -0,0 +1,130 @@ +/** @file pmGrowthCurve.c + * + * Measure the curve-of-growth for sources + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include "pmGrowthCurve.h" + +static void pmGrowthCurveFree (pmGrowthCurve *growth) +{ + + if (growth == NULL) + return; + + psFree (growth->radius); + psFree (growth->apMag); + return; +} + +pmGrowthCurve *pmGrowthCurveAlloc (psF32 minRadius, psF32 maxRadius, psF32 refRadius) +{ + + pmGrowthCurve *growth = psAlloc (sizeof(pmGrowthCurve)); + psMemSetDeallocator(growth, (psFreeFunc) pmGrowthCurveFree); + + // fractional pixel radii are not well defined; use integer steps + growth->radius = psVectorCreate (NULL, minRadius, maxRadius, 1.0, PS_TYPE_F32); + growth->apMag = psVectorAlloc (growth->radius->n, PS_TYPE_F32); + + // XXX may want to extend this to allow for a different refRadius; + growth->refRadius = refRadius; + growth->maxRadius = maxRadius; + growth->apLoss = 0.0; + growth->fitMag = 0.0; + return growth; +} + +psF32 pmGrowthCurveCorrect (pmGrowthCurve *growth, psF32 radius) +{ + + float apRad = psVectorInterpolate (growth->radius, growth->apMag, radius); + float apCor = growth->apRef - apRad; + return apCor; +} + +// return the last entry below or first entry above key value +int psVectorBracket (psVector *index, psF32 key, bool above) +{ + + int N; + int Nlo = 0; + int Nhi = index->n; + + if (above) { + while (Nhi - Nlo > 10) { + N = 0.5*(Nlo + Nhi); + if (index->data.F32[N] > key) { + Nhi = N; + } else { + Nlo = N - 1; + } + } + // at this point, index[Nhi] > key >= index[Nlo] + N = Nlo; + while ((index->data.F32[N] <= key) && (N < Nhi)) { + N++; + } + return (N); + } + while (Nhi - Nlo > 10) { + N = 0.5*(Nlo + Nhi); + if (index->data.F32[N] < key) { + Nlo = N; + } else { + Nhi = N + 1; + } + } + // at this point, index[Nhi] >= key > index[Nlo] + N = Nhi; + while ((index->data.F32[N] >= key) && (N > Nlo)) { + N--; + } + return (N); +} + +// search for the bins bounding key in index, interpolate the corresponding values +psF32 psVectorInterpolate (psVector *index, psVector *value, psF32 key) +{ + + int n0 = 0; + int n1 = 0; + + // extrapolate at ends + if (key < index->data.F32[0]) { + n0 = 0; + n1 = 1; + } + + // extrapolate at ends + if (key > index->data.F32[index->n-1]) { + n0 = index->n-2; + n1 = index->n-1; + } + + if (n1 == 0) { + n0 = psVectorBracket (index, key, FALSE); + n1 = n0 + 1; + } + + if (n0 == index->n-1) { + n1 = n0; + n0 = n1 - 1; + } + + float dy = value->data.F32[n1] - value->data.F32[n0]; + float dx = index->data.F32[n1] - index->data.F32[n0]; + float dX = key - index->data.F32[n0]; + float dY = dX * (dy/dx); + float result = value->data.F32[n0] + dY; + return result; +} + Index: trunk/psModules/src/objects/pmGrowthCurve.h =================================================================== --- trunk/psModules/src/objects/pmGrowthCurve.h (revision 6872) +++ trunk/psModules/src/objects/pmGrowthCurve.h (revision 6872) @@ -0,0 +1,24 @@ + +# ifndef PM_GROWTH_CURVE_H +# define PM_GROWTH_CURVE_H + +typedef struct +{ + psVector *radius; + psVector *apMag; + psF32 refRadius; + psF32 maxRadius; + psF32 fitMag; + psF32 apRef; // apMag[refRadius] + psF32 apLoss; // fitMag - apRef +} +pmGrowthCurve; + +pmGrowthCurve *pmGrowthCurveAlloc (psF32 minRadius, psF32 maxRadius, psF32 refRadius); +int psVectorBracket (psVector *index, psF32 key, bool above); +psF32 psVectorInterpolate (psVector *index, psVector *value, psF32 key); +psF32 pmGrowthCurveCorrect (pmGrowthCurve *growth, psF32 radius); + +// XXX psVectorBracket,Interpolate should be put in pslib + +# endif /* PM_GROWTH_CURVE_H */ Index: trunk/psModules/src/objects/pmModel.c =================================================================== --- trunk/psModules/src/objects/pmModel.c (revision 6872) +++ trunk/psModules/src/objects/pmModel.c (revision 6872) @@ -0,0 +1,225 @@ +/** @file pmModel.c + * + * Functions to define and manipulate object models + * + * @author GLG, MHPCC + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmModel.h" + +/* The following types and functions need to be known by pmModel.c and are defined in + pmModelGroup.h. The use of pmSource and other types in pmModelGroup.h prevent us from + directly including it here ***/ + +typedef psMinimizeLMChi2Func pmModelFunc; +typedef bool (*pmModelFitStatusFunc)(pmModel *model); +pmModelFunc pmModelFunc_GetFunction (pmModelType type); +pmModelFitStatusFunc pmModelFitStatusFunc_GetFunction (pmModelType type); +int pmModelParameterCount(pmModelType type); + +static void modelFree(pmModel *tmp) +{ + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + psFree(tmp->params); + psFree(tmp->dparams); + psTrace(__func__, 4, "---- %s() end ----\n", __func__); +} + +/****************************************************************************** +pmModelAlloc(): Allocate the pmModel structure, along with its parameters, +and initialize the type member. Initialize the params to 0.0. +XXX EAM: simplifying code with pmModelParameterCount +*****************************************************************************/ +pmModel *pmModelAlloc(pmModelType type) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + pmModel *tmp = (pmModel *) psAlloc(sizeof(pmModel)); + + tmp->type = type; + tmp->chisq = 0.0; + tmp->nIter = 0; + tmp->radiusTMP = 0; + tmp->status = PM_MODEL_UNTRIED; + + psS32 Nparams = pmModelParameterCount(type); + if (Nparams == 0) { + psError(PS_ERR_UNKNOWN, true, "Undefined pmModelType"); + return(NULL); + } + + tmp->params = psVectorAlloc(Nparams, PS_TYPE_F32); + tmp->dparams = psVectorAlloc(Nparams, PS_TYPE_F32); + + for (psS32 i = 0; i < tmp->params->n; i++) { + tmp->params->data.F32[i] = 0.0; + tmp->dparams->data.F32[i] = 0.0; + } + + psMemSetDeallocator(tmp, (psFreeFunc) modelFree); + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmp); +} + +// copy model to a new structure +pmModel *pmModelCopy (pmModel *model) +{ + + pmModel *new = pmModelAlloc (model->type); + + new->chisq = model->chisq; + new->nDOF = model->nDOF; + new->nIter = model->nIter; + new->status = model->status; + new->radiusTMP = model->radiusTMP; + + for (int i = 0; i < new->params->n; i++) { + new->params->data.F32[i] = model->params->data.F32[i]; + new->dparams->data.F32[i] = model->dparams->data.F32[i]; + } + + return (new); +} + +/****************************************************************************** + pmModelEval(source, level, row): evaluates the model function at the specified coords. + + NOTE: The coords are in subImage source->pixel coords, not image coords. + + XXX: Use static vectors for x (NO: needs to be thread safe) +*****************************************************************************/ +psF32 pmModelEval(pmModel *model, psImage *image, psS32 col, psS32 row) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(image, false); + PS_ASSERT_PTR_NON_NULL(model, false); + PS_ASSERT_PTR_NON_NULL(model->params, false); + + // Allocate the x coordinate structure and convert row/col to image space. + // + psVector *x = psVectorAlloc(2, PS_TYPE_F32); + x->data.F32[0] = (psF32) (col + image->col0); + x->data.F32[1] = (psF32) (row + image->row0); + psF32 tmpF; + pmModelFunc modelFunc; + + modelFunc = pmModelFunc_GetFunction (model->type); + tmpF = modelFunc (NULL, model->params, x); + psFree(x); + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmpF); +} + +bool AddOrSubModel(psImage *image, + psImage *mask, + pmModel *model, + bool center, + bool sky, + bool add + ) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + + PS_ASSERT_PTR_NON_NULL(model, false); + PS_ASSERT_IMAGE_NON_NULL(image, false); + PS_ASSERT_IMAGE_TYPE(image, PS_TYPE_F32, false); + + psVector *x = psVectorAlloc(2, PS_TYPE_F32); + psVector *params = model->params; + pmModelFunc modelFunc = pmModelFunc_GetFunction (model->type); + psS32 imageCol; + psS32 imageRow; + psF32 skyValue = params->data.F32[0]; + psF32 pixelValue; + + for (psS32 i = 0; i < image->numRows; i++) { + for (psS32 j = 0; j < image->numCols; j++) { + if ((mask != NULL) && mask->data.U8[i][j]) + continue; + + // Convert i/j to image coord space: + // 'center' option changes meaning of i,j: + if (center) { + imageCol = j - 0.5*image->numCols + model->params->data.F32[2]; + imageRow = i - 0.5*image->numRows + model->params->data.F32[3]; + } else { + imageCol = j + image->col0; + imageRow = i + image->row0; + } + + x->data.F32[0] = (float) imageCol; + x->data.F32[1] = (float) imageRow; + + // set the appropriate pixel value for this coordinate + if (sky) { + pixelValue = modelFunc (NULL, params, x); + } else { + pixelValue = modelFunc (NULL, params, x) - skyValue; + } + + + // add or subtract the value + if (add + ) { + image->data.F32[i][j] += pixelValue; + } + else { + image->data.F32[i][j] -= pixelValue; + } + } + } + psFree(x); + psTrace(__func__, 3, "---- %s(true) end ----\n", __func__); + return(true); +} + +/****************************************************************************** + *****************************************************************************/ +bool pmModelAdd(psImage *image, + psImage *mask, + pmModel *model, + bool center, + bool sky) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + psBool rc = AddOrSubModel(image, mask, model, center, sky, true); + psTrace(__func__, 3, "---- %s(%d) end ----\n", __func__, rc); + return(rc); +} + +/****************************************************************************** + *****************************************************************************/ +bool pmModelSub(psImage *image, + psImage *mask, + pmModel *model, + bool center, + bool sky) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + psBool rc = AddOrSubModel(image, mask, model, center, sky, false); + psTrace(__func__, 3, "---- %s(%d) end ----\n", __func__, rc); + return(rc); +} + +// check for success of model fit +bool pmModelFitStatus (pmModel *model) +{ + + bool status; + + pmModelFitStatusFunc statusFunc = pmModelFitStatusFunc_GetFunction (model->type); + status = statusFunc (model); + + return (status); +} + Index: trunk/psModules/src/objects/pmModel.h =================================================================== --- trunk/psModules/src/objects/pmModel.h (revision 6872) +++ trunk/psModules/src/objects/pmModel.h (revision 6872) @@ -0,0 +1,113 @@ +/** @file pmObjects.h + * + * Functions to define and manipulate object models + * + * @author GLG, MHPCC + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_MODEL_H +# define PM_MODEL_H + +// type of model carried by the pmModel structure +typedef int pmModelType; + +typedef enum { + PM_MODEL_UNTRIED, ///< model fit not yet attempted + PM_MODEL_SUCCESS, ///< model fit succeeded + PM_MODEL_NONCONVERGE, ///< model fit did not converge + PM_MODEL_OFFIMAGE, ///< model fit drove out of range + PM_MODEL_BADARGS ///< model fit called with invalid args +} pmModelStatus; + +/** pmModel data structure + * + * Every source may have two types of models: a PSF model and a EXT (extended-source) + * model. The PSF model represents the best fit of the image PSF to the specific + * object. In this case, the PSF-dependent parameters are specified for the + * object by the PSF, not by the fit. The EXT model represents the best fit of + * the given model to the object, with all shape parameters floating in the fit. + * + */ +typedef struct +{ + pmModelType type; ///< Model to be used. + psVector *params; ///< Paramater values. + psVector *dparams; ///< Parameter errors. + float chisq; ///< Fit chi-squared. + float chisqNorm; ///< re-normalized fit chi-squared. + int nDOF; ///< number of degrees of freedom + int nIter; ///< number of iterations to reach min + pmModelStatus status; ///< fit status + float radiusTMP; ///< fit radius actually used +} +pmModel; + +/** pmModelAlloc() + * + */ +pmModel *pmModelAlloc(pmModelType type); + +// copy model to a new structure +pmModel *pmModelCopy (pmModel *model); + +psF32 pmModelEval(pmModel *model, psImage *image, psS32 col, psS32 row); + +/** pmModelAdd() + * + * Add the given source model flux to/from the provided image. The boolean + * option center selects if the source is re-centered to the image center or if + * it is placed at its centroid location. The boolean option sky selects if the + * background sky is applied (TRUE) or not. The pixel range in the target image + * is at most the pixel range specified by the source.pixels image. The success + * status is returned. + * + */ +bool pmModelAdd( + psImage *image, ///< The output image (float) + psImage *mask, ///< The image pixel mask (valid == 0) + pmModel *model, ///< The input pmModel + bool center, ///< A boolean flag that determines whether pixels are centered + bool sky ///< A boolean flag that determines if the sky is subtracted +); + + +/** pmModelSub() + * + * Subtract the given source model flux to/from the provided image. The + * boolean option center selects if the source is re-centered to the image center + * or if it is placed at its centroid location. The boolean option sky selects if + * the background sky is applied (TRUE) or not. The pixel range in the target + * image is at most the pixel range specified by the source.pixels image. The + * success status is returned. + * + */ +bool pmModelSub( + psImage *image, ///< The output image (float) + psImage *mask, ///< The image pixel mask (valid == 0) + pmModel *model, ///< The input pmModel + bool center, ///< A boolean flag that determines whether pixels are centered + bool sky ///< A boolean flag that determines if the sky is subtracted +); + +/** pmModelFitStatus() + * + * This function wraps the call to the model-specific function returned by + * pmModelFitStatusFunc_GetFunction. The model-specific function examines the + * model parameters, parameter errors, Chisq, S/N, and other parameters available + * from model to decide if the particular fit was successful or not. + * + * XXX: Must code this. + * + */ +bool pmModelFitStatus( + pmModel *model ///< Model to be used +); + +# endif /* PM_MODEL_H */ Index: trunk/psModules/src/objects/pmModelGroup.c =================================================================== --- trunk/psModules/src/objects/pmModelGroup.c (revision 6529) +++ trunk/psModules/src/objects/pmModelGroup.c (revision 6872) @@ -1,8 +1,35 @@ -# include "pmModelGroup.h" - +/** @file pmModelGroup.c + * + * Functions to define and manipulate object model attributes + * + * @author GLG, MHPCC + * @author EAM, IfA + * + * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "psEllipse.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" + +// XXX shouldn't these be defined for us in pslib.h ??? double hypot(double x, double y); double sqrt (double x); -#include "psEllipse.h" #include "models/pmModel_GAUSS.c" #include "models/pmModel_PGAUSS.c" @@ -25,5 +52,4 @@ if (modelGroup == NULL) return; - psFree (modelGroup); return; } @@ -60,4 +86,11 @@ } Nmodels = Nnew; + return; +} + +void pmModelGroupCleanup (void) +{ + + psFree (models); return; } @@ -153,2 +186,28 @@ return (models[type].name); } + +/****************************************************************************** + pmSourceModelGuess(source, model): This function allocates a new + pmModel structure based on the given modelType specified in the argument list. + The corresponding pmModelGuess function is returned, and used to + supply the values of the params array in the pmModel structure. + + XXX: Many parameters are based on the src->moments structure, which is in + image, not subImage coords. Therefore, the calls to the model evaluation + functions will be in image, not subImage coords. Remember this. +*****************************************************************************/ +pmModel *pmSourceModelGuess(pmSource *source, + pmModelType modelType) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source->moments, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + + pmModel *model = pmModelAlloc(modelType); + + pmModelGuessFunc modelGuessFunc = pmModelGuessFunc_GetFunction(modelType); + modelGuessFunc(model, source); + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(model); +} + Index: trunk/psModules/src/objects/pmModelGroup.h =================================================================== --- trunk/psModules/src/objects/pmModelGroup.h (revision 6529) +++ trunk/psModules/src/objects/pmModelGroup.h (revision 6872) @@ -9,16 +9,84 @@ * @author EAM, IfA * - * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-12-24 01:24:32 $ + * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii * */ -#include "pmObjects.h" -#include "pmPSF.h" -/** - * - * This function returns the number of parameters used by the listed function. - * + +# ifndef PM_MODEL_GROUP_H +# define PM_MODEL_GROUP_H + +// This function is the model chi-square minimization function for this model. +typedef psMinimizeLMChi2Func pmModelFunc; + +// This function returns the integrated flux for the given model parameters. +typedef psF64 (*pmModelFlux)(const psVector *params); + + +// This function returns the radius at which the given model and parameters +// achieves the given flux. +typedef psF64 (*pmModelRadius)(const psVector *params, double flux); + +/* This function sets the model parameter limits vectors for the given model + */ +typedef bool (*pmModelLimits)(psVector **beta_lim, psVector **params_min, psVector **params_max); + +/* This function provides the model guess parameters based on the details of + * the given source. + */ +typedef bool (*pmModelGuessFunc)(pmModel *model, pmSource *source); + + +/* This function constructs the PSF model for the given source based on the + * supplied psf and the EXT model for the object. + */ +typedef bool (*pmModelFromPSFFunc)(pmModel *modelPSF, pmModel *modelEXT, pmPSF *psf); + +/* This function returns the success / failure status of the given model fit + */ +typedef bool (*pmModelFitStatusFunc)(pmModel *model); + +/* Every model instance belongs to a class of models, defined by the value of + * the pmModelType type entry. Various functions need access to information about + * each of the models. Some of this information varies from model to model, and + * may depend on the current parameter values or other data quantities. In order + * to keep the code from requiring the information about each model to be coded + * into the low-level fitting routines, we define a collection of functions which + * allow us to abstract this type of model-dependent information. These generic + * functions take the model type and return the corresponding function pointer + * for the specified model. Each model is defined by creating this collection of + * specific functions, and placing them in a single file for each model. We + * define the following structure to carry the collection of information about + * the models. + */ +typedef struct +{ + char *name; + int nParams; + pmModelFunc modelFunc; + pmModelFlux modelFlux; + pmModelRadius modelRadius; + pmModelLimits modelLimits; + pmModelGuessFunc modelGuessFunc; + pmModelFromPSFFunc modelFromPSFFunc; + pmModelFitStatusFunc modelFitStatusFunc; +} +pmModelGroup; + +// allocate a pmModelGroup to hold nModels entries +pmModelGroup *pmModelGroupAlloc (int nModels); + +// initialize the internal (static) model group with the default models +void pmModelGroupInit (void); + +// free the internal (static) model group +void pmModelGroupCleanup (void); + +// add a new model to the internal (static) model group +void pmModelGroupAdd (pmModelGroup *model); + +/* This function returns the number of parameters used by the listed function. */ int pmModelParameterCount( @@ -27,8 +95,5 @@ -/** - * - * This function returns the user-space model names for the specified model type. - * +/* This function returns the user-space model names for the specified model type. */ char *pmModelGetType( @@ -46,62 +111,4 @@ ); - -#ifndef PM_MODEL_GROUP_H -#define PM_MODEL_GROUP_H - -/** - * - * This function is the model chi-square minimization function for this model. - * - */ -typedef psMinimizeLMChi2Func pmModelFunc; - - -/** - * - * This function returns the integrated flux for the given model parameters. - */ -typedef psF64 (*pmModelFlux)(const psVector *params); - - -/** - * - * This function returns the radius at which the given model and parameters - * achieves the given flux. - * - */ -typedef psF64 (*pmModelRadius)(const psVector *params, double flux); - -/** - * - * This function sets the model parameter limits vectors for the given model - * - */ -typedef bool (*pmModelLimits)(psVector **beta_lim, psVector **params_min, psVector **params_max); - -/** - * - * This function provides the model guess parameters based on the details of - * the given source. - * - */ -typedef bool (*pmModelGuessFunc)(pmModel *model, pmSource *source); - - -/** - * - * This function constructs the PSF model for the given source based on the - * supplied psf and the FLT model for the object. - * - */ -typedef bool (*pmModelFromPSFFunc)(pmModel *modelPSF, pmModel *modelFLT, pmPSF *psf); - -/** - * - * This function returns the success / failure status of the given model fit - * - */ -typedef bool (*pmModelFitStatusFunc)(pmModel *model); - /** * @@ -110,5 +117,4 @@ * */ - /** @@ -177,44 +183,17 @@ +/** pmSourceModelGuess() + * + * Convert available data to an initial guess for the given model. This + * function allocates a pmModel entry for the pmSource structure based on the + * provided model selection. The method of defining the model parameter guesses + * are specified for each model below. The guess values are placed in the model + * parameters. The function returns TRUE on success or FALSE on failure. + * + */ +pmModel *pmSourceModelGuess( + pmSource *source, ///< The input pmSource + pmModelType model ///< The type of model to be created. +); - -/** - * - * Every model instance belongs to a class of models, defined by the value of - * the pmModelType type entry. Various functions need access to information about - * each of the models. Some of this information varies from model to model, and - * may depend on the current parameter values or other data quantities. In order - * to keep the code from requiring the information about each model to be coded - * into the low-level fitting routines, we define a collection of functions which - * allow us to abstract this type of model-dependent information. These generic - * functions take the model type and return the corresponding function pointer - * for the specified model. Each model is defined by creating this collection of - * specific functions, and placing them in a single file for each model. We - * define the following structure to carry the collection of information about - * the models. - * - */ -typedef struct -{ - char *name; - int nParams; - pmModelFunc modelFunc; - pmModelFlux modelFlux; - pmModelRadius modelRadius; - pmModelLimits modelLimits; - pmModelGuessFunc modelGuessFunc; - pmModelFromPSFFunc modelFromPSFFunc; - pmModelFitStatusFunc modelFitStatusFunc; -} -pmModelGroup; - -// allocate a pmModelGroup to hold nModels entries -pmModelGroup *pmModelGroupAlloc (int nModels); - -// initialize the internal (static) model group with the default models -void pmModelGroupInit (void); - -// add a new model to the internal (static) model group -void pmModelGroupAdd (pmModelGroup *model); - -# endif +# endif /* PM_MODEL_GROUP_H */ Index: trunk/psModules/src/objects/pmMoments.c =================================================================== --- trunk/psModules/src/objects/pmMoments.c (revision 6872) +++ trunk/psModules/src/objects/pmMoments.c (revision 6872) @@ -0,0 +1,39 @@ +/** @file pmMoments.c + * + * Functions defining the pmMoments structure + * + * @author GLG, MHPCC + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include "pslib.h" +#include "pmMoments.h" + +/****************************************************************************** +pmMomentsAlloc(): Allocate the pmMoments structure and initialize the members +to zero. +*****************************************************************************/ +pmMoments *pmMomentsAlloc() +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + pmMoments *tmp = (pmMoments *) psAlloc(sizeof(pmMoments)); + tmp->x = 0.0; + tmp->y = 0.0; + tmp->Sx = 0.0; + tmp->Sy = 0.0; + tmp->Sxy = 0.0; + tmp->Sum = 0.0; + tmp->Peak = 0.0; + tmp->Sky = 0.0; + tmp->nPixels = 0; + + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmp); +} + Index: trunk/psModules/src/objects/pmMoments.h =================================================================== --- trunk/psModules/src/objects/pmMoments.h (revision 6872) +++ trunk/psModules/src/objects/pmMoments.h (revision 6872) @@ -0,0 +1,45 @@ +/** @file pmMoments.h + * + * Definitions of the moments structure + * + * @author GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_MOMENTS_H +# define PM_MOMENTS_H + +/** pmMoments data structure + * + * One of the simplest measurements which can be made quickly for an object + * are the object moments. We specify a structure to carry the moment information + * for a specific source: + * + */ +typedef struct +{ + float x; ///< X-coord of centroid. + float y; ///< Y-coord of centroid. + float Sx; ///< x-second moment. + float Sy; ///< y-second moment. + float Sxy; ///< xy cross moment. + float Sum; ///< Pixel sum above sky (background). + float Peak; ///< Peak counts above sky. + float Sky; ///< Sky level (background). + float dSky; ///< local Sky variance + float SN; ///< approx signal-to-noise + int nPixels; ///< Number of pixels used. +} +pmMoments; + +/** pmMomentsAlloc() + * + */ +pmMoments *pmMomentsAlloc(); + +# endif Index: trunk/psModules/src/objects/pmObjects.h =================================================================== --- trunk/psModules/src/objects/pmObjects.h (revision 6529) +++ trunk/psModules/src/objects/pmObjects.h (revision 6872) @@ -10,6 +10,6 @@ * @author GLG, MHPCC * - * @version $Revision: 1.5 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-12-24 01:24:32 $ + * @version $Revision: 1.6 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -27,535 +27,4 @@ #include #include "pslib.h" -#include "pmAstrometry.h" -/** - * In the object analysis process, we will use specific mask values to mark the - * image pixels. The following structure defines the relevant mask values. - * - * XXX: This is probably a bad solution: we will want to set mask values - * outside of the PSPHOT code. Perhaps we can set up a registered set of mask - * values with specific meanings that other functions can add to or define? - */ -typedef enum { - PSPHOT_MASK_CLEAR = 0x00, - PSPHOT_MASK_INVALID = 0x01, - PSPHOT_MASK_SATURATED = 0x02, - PSPHOT_MASK_MARKED = 0x08, -} psphotMaskValues; - - -/** pmPeakType - * - * A peak pixel may have several features which may be determined when the - * peak is found or measured. These are specified by the pmPeakType enum. - * PM_PEAK_LONE represents a single pixel which is higher than its 8 immediate - * neighbors. The PM_PEAK_EDGE represents a peak pixel which touching the image - * edge. The PM_PEAK_FLAT represents a peak pixel which has more than a specific - * number of neighbors at the same value, within some tolarence: - * - */ -typedef enum { - PM_PEAK_LONE, ///< Isolated peak. - PM_PEAK_EDGE, ///< Peak on edge. - PM_PEAK_FLAT, ///< Peak has equal-value neighbors. - PM_PEAK_UNDEF ///< Undefined. -} pmPeakType; - - -/** pmPeak data structure - * - * A source has the capacity for several types of measurements. The - * simplest measurement of a source is the location and flux of the peak pixel - * associated with the source: - * - */ -typedef struct -{ - int x; ///< X-coordinate of peak pixel. - int y; ///< Y-coordinate of peak pixel. - float counts; ///< Value of peak pixel (above sky?). - pmPeakType class; ///< Description of peak. -} -pmPeak; - - -/** pmMoments data structure - * - * One of the simplest measurements which can be made quickly for an object - * are the object moments. We specify a structure to carry the moment information - * for a specific source: - * - */ -typedef struct -{ - float x; ///< X-coord of centroid. - float y; ///< Y-coord of centroid. - float Sx; ///< x-second moment. - float Sy; ///< y-second moment. - float Sxy; ///< xy cross moment. - float Sum; ///< Pixel sum above sky (background). - float Peak; ///< Peak counts above sky. - float Sky; ///< Sky level (background). - float SN; ///< approx signal-to-noise - int nPixels; ///< Number of pixels used. -} -pmMoments; - - -/** pmPSFClump data structure - * - * A collection of object moment measurements can be used to determine - * approximate object classes. The key to this analysis is the location and - * statistics (in the second-moment plane, - * - */ -typedef struct -{ - float X; - float dX; - float Y; - float dY; -} -pmPSFClump; - -// type of model carried by the pmModel structure -typedef int pmModelType; - -typedef enum { - PM_MODEL_UNTRIED, ///< model fit not yet attempted - PM_MODEL_SUCCESS, ///< model fit succeeded - PM_MODEL_NONCONVERGE, ///< model fit did not converge - PM_MODEL_OFFIMAGE, ///< model fit drove out of range - PM_MODEL_BADARGS ///< model fit called with invalid args -} pmModelStatus; - -/** pmModel data structure - * - * Every source may have two types of models: a PSF model and a FLT (floating) - * model. The PSF model represents the best fit of the image PSF to the specific - * object. In this case, the PSF-dependent parameters are specified for the - * object by the PSF, not by the fit. The FLT model represents the best fit of - * the given model to the object, with all parameters floating in the fit. - * - */ -typedef struct -{ - pmModelType type; ///< Model to be used. - psVector *params; ///< Paramater values. - psVector *dparams; ///< Parameter errors. - float chisq; ///< Fit chi-squared. - int nDOF; ///< number of degrees of freedom - int nIter; ///< number of iterations to reach min - int status; ///< fit status - float radius; ///< fit radius actually used -} -pmModel; - -/** pmSourceType enumeration - * - * A given source may be identified as most-likely to be one of several source - * types. The pmSource entry pmSourceType defines the current best-guess for this - * source. - * - * XXX: The values given below are currently illustrative and will require - * some modification as the source classification code is developed. (TBD) - * - */ -typedef enum { - PM_SOURCE_DEFECT, ///< a cosmic-ray - PM_SOURCE_SATURATED, ///< random saturated pixels - - PM_SOURCE_SATSTAR, ///< a saturated star - PM_SOURCE_PSFSTAR, ///< a PSF star - PM_SOURCE_GOODSTAR, ///< a good-quality star - - PM_SOURCE_POOR_FIT_PSF, ///< poor quality PSF fit - PM_SOURCE_FAIL_FIT_PSF, ///< failed to get a good PSF fit - PM_SOURCE_FAINTSTAR, ///< below S/N cutoff - - PM_SOURCE_GALAXY, ///< an extended object (galaxy) - PM_SOURCE_FAINT_GALAXY, ///< a galaxy below S/N cutoff - PM_SOURCE_DROP_GALAXY, ///< ? - PM_SOURCE_FAIL_FIT_GAL, ///< failed on the galaxy fit - PM_SOURCE_POOR_FIT_GAL, ///< poor quality galaxy fit - - PM_SOURCE_OTHER, ///< unidentified -} pmSourceType; - -/** pmSource data structure - * - * This source has the capacity for several types of measurements. The - * simplest measurement of a source is the location and flux of the peak pixel - * associated with the source: - * - */ -typedef struct -{ - pmPeak *peak; ///< Description of peak pixel. - psImage *pixels; ///< Rectangular region including object pixels. - psImage *weight; ///< Image variance. - psImage *mask; ///< Mask which marks pixels associated with objects. - pmMoments *moments; ///< Basic moments measure for the object. - pmModel *modelPSF; ///< PSF Model fit (parameters and type) - pmModel *modelFLT; ///< FLT (floating) Model fit (parameters and type). - pmSourceType type; ///< Best identification of object. - float apMag; - float fitMag; -} -pmSource; - - -/** pmPeakAlloc() - * - * @return pmPeak* newly allocated pmPeak with all internal pointers set to NULL - */ -pmPeak *pmPeakAlloc( - int x, ///< Row-coordinate in image space - int y, ///< Col-coordinate in image space - float counts, ///< The value of the peak pixel - pmPeakType class ///< The type of peak pixel -); - - -/** pmMomentsAlloc() - * - */ -pmMoments *pmMomentsAlloc(); - - -/** pmModelAlloc() - * - */ -pmModel *pmModelAlloc(pmModelType type); - - -/** pmSourceAlloc() - * - */ -pmSource *pmSourceAlloc(); - - -/** pmFindVectorPeaks() - * - * Find all local peaks in the given vector above the given threshold. A peak - * is defined as any element with a value greater than its two neighbors and with - * a value above the threshold. Two types of special cases must be addressed. - * Equal value elements: If an element has the same value as the following - * element, it is not considered a peak. If an element has the same value as the - * preceding element (but not the following), then it is considered a peak. Note - * that this rule (arbitrarily) identifies flat regions by their trailing edge. - * Edge cases: At start of the vector, the element must be higher than its - * neighbor. At the end of the vector, the element must be higher or equal to its - * neighbor. These two rules again places the peak associated with a flat region - * which touches the image edge at the image edge. The result of this function is - * a vector containing the coordinates (element number) of the detected peaks - * (type psU32). - * - */ -psVector *pmFindVectorPeaks( - const psVector *vector, ///< The input vector (float) - float threshold ///< Threshold above which to find a peak -); - - -/** pmFindImagePeaks() - * - * Find all local peaks in the given image above the given threshold. This - * function should find all row peaks using pmFindVectorPeaks, then test each row - * peak and exclude peaks which are not local peaks. A peak is a local peak if it - * has a higher value than all 8 neighbors. If the peak has the same value as its - * +y neighbor or +x neighbor, it is NOT a local peak. If any other neighbors - * have an equal value, the peak is considered a valid peak. Note two points: - * first, the +x neighbor condition is already enforced by pmFindVectorPeaks. - * Second, these rules have the effect of making flat-topped regions have single - * peaks at the (+x,+y) corner. When selecting the peaks, their type must also be - * set. The result of this function is an array of pmPeak entries. - * - */ -psArray *pmFindImagePeaks( - const psImage *image, ///< The input image where peaks will be found (float) - float threshold ///< Threshold above which to find a peak -); - - -/** pmCullPeaks() - * - * Eliminate peaks from the psList that have a peak value above the given - * maximum, or fall outside the valid region. - * - */ -psList *pmCullPeaks( - psList *peaks, ///< The psList of peaks to be culled - float maxValue, ///< Cull peaks above this value - const psRegion valid ///< Cull peaks otside this psRegion -); - - -/** pmPeaksSubset() - * - * Create a new peaks array, removing certain types of peaks from the input - * array of peaks based on the given criteria. Peaks should be eliminated if they - * have a peak value above the given maximum value limit or if the fall outside - * the valid region. The result of the function is a new array with a reduced - * number of peaks. - * - */ -psArray *pmPeaksSubset( - psArray *peaks, ///< Add comment. - float maxvalue, ///< Add comment. - const psRegion valid ///< Add comment. -); - - -/** pmSourceDefinePixels() - * - * Define psImage subarrays for the source located at coordinates x,y on the - * image set defined by readout. The pixels defined by this operation consist of - * a square window (of full width 2Radius+1) centered on the pixel which contains - * the given coordinate, in the frame of the readout. The window is defined to - * have limits which are valid within the boundary of the readout image, thus if - * the radius would fall outside the image pixels, the subimage is truncated to - * only consist of valid pixels. If readout->mask or readout->weight are not - * NULL, matching subimages are defined for those images as well. This function - * fails if no valid pixels can be defined (x or y less than Radius, for - * example). This function should be used to define a region of interest around a - * source, including both source and sky pixels. - * - * XXX: must code this. - * - */ -// XXX: Uncommenting the pmReadout causes compile errors. -bool pmSourceDefinePixels( - pmSource *mySource, ///< Add comment. - pmReadout *readout, ///< Add comment. - psF32 x, ///< Add comment. - psF32 y, ///< Add comment. - psF32 Radius ///< Add comment. -); - - -/** pmSourceLocalSky() - * - * Measure the local sky in the vicinity of the given source. The Radius - * defines the square aperture in which the moments will be measured. This - * function assumes the source pixels have been defined, and that the value of - * Radius here is smaller than the value of Radius used to define the pixels. The - * annular region not contained within the radius defined here is used to measure - * the local background in the vicinity of the source. The local background - * measurement uses the specified statistic passed in via the statsOptions entry. - * This function allocates the pmMoments structure. The resulting sky is used to - * set the value of the pmMoments.sky element of the provided pmSource structure. - * - */ -bool pmSourceLocalSky( - pmSource *source, ///< The input image (float) - psStatsOptions statsOptions, ///< The statistic used in calculating the background sky - float Radius ///< The inner radius of the square annulus to exclude -); - - -/** pmSourceMoments() - * - * Measure source moments for the given source, using the value of - * source.moments.sky provided as the local background value and the peak - * coordinates as the initial source location. The resulting moment values are - * applied to the source.moments entry, and the source is returned. The moments - * are measured within the given circular radius of the source.peak coordinates. - * The return value indicates the success (TRUE) of the operation. - * - */ -bool pmSourceMoments( - pmSource *source, ///< The input pmSource for which moments will be computed - float radius ///< Use a circle of pixels around the peak -); - - -/** pmSourcePSFClump() - * - * We use the source moments to make an initial, approximate source - * classification, and as part of the information needed to build a PSF model for - * the image. As long as the PSF shape does not vary excessively across the - * image, the sources which are represented by a PSF (the start) will have very - * similar second moments. The function pmSourcePSFClump searches a collection of - * sources with measured moments for a group with moments which are all very - * similar. The function returns a pmPSFClump structure, representing the - * centroid and size of the clump in the sigma_x, sigma_y second-moment plane. - * - * The goal is to identify and characterize the stellar clump within the - * sigma_x, sigma_y second-moment plane. To do this, an image is constructed to - * represent this plane. The units of sigma_x and sigma_y are in image pixels. A - * pixel in this analysis image represents 0.1 pixels in the input image. The - * dimensions of the image need only be 10 pixels. The peak pixel in this image - * (above a threshold of half of the image maximum) is found. The coordinates of - * this peak pixel represent the 2D mode of the sigma_x, sigma_y distribution. - * The sources with sigma_x, sigma_y within 0.2 pixels of this value are then - * * used to calculate the median and standard deviation of the sigma_x, sigma_y - * values. These resulting values are returned via the pmPSFClump structure. - * - * The return value indicates the success (TRUE) of the operation. - * - * XXX: Limit the S/N of the candidate sources (part of Metadata)? (TBD). - * XXX: Save the clump parameters on the Metadata (TBD) - * - */ -pmPSFClump pmSourcePSFClump( - psArray *source, ///< The input pmSource - psMetadata *metadata ///< Contains classification parameters -); - - -/** pmSourceRoughClass() - * - * Based on the specified data values, make a guess at the source - * classification. The sources are provides as a psArray of pmSource entries. - * Definable parameters needed to make the classification are provided to the - * routine with the psMetadata structure. The rules (in SDRS) refer to values which - * can be extracted from the metadata using the given keywords. Except as noted, - * the data type for these parameters are psF32. - * - */ -bool pmSourceRoughClass( - psArray *source, ///< The input pmSource - psMetadata *metadata, ///< Contains classification parameters - pmPSFClump clump ///< Statistics about the PSF clump -); - - -/** pmSourceModelGuess() - * - * Convert available data to an initial guess for the given model. This - * function allocates a pmModel entry for the pmSource structure based on the - * provided model selection. The method of defining the model parameter guesses - * are specified for each model below. The guess values are placed in the model - * parameters. The function returns TRUE on success or FALSE on failure. - * - */ -pmModel *pmSourceModelGuess( - pmSource *source, ///< The input pmSource - pmModelType model ///< The type of model to be created. -); - - -/** pmContourType - * - * Only one type is defined at present. - * - */ -typedef enum { - PS_CONTOUR_CRUDE, - PS_CONTOUR_UNKNOWN01, - PS_CONTOUR_UNKNOWN02 -} pmContourType; - - -/** pmSourceContour() - * - * Find points in a contour for the given source at the given level. If type - * is PM_CONTOUR_CRUDE, the contour is found by starting at the source peak, - * running along each pixel row until the level is crossed, then interpolating to - * the level coordinate for that row. This is done for each row, with the - * starting point determined by the midpoint of the previous row, until the - * starting point has a value below the contour level. The returned contour - * consists of two vectors giving the x and y coordinates of the contour levels. - * This function may be used as part of the model guess inputs. Other contour - * types may be specified in the future for more refined contours (TBD) - * - */ -psArray *pmSourceContour( - pmSource *source, ///< The input pmSource - const psImage *image, ///< The input image (float) (this arg should be removed) - float level, ///< The level of the contour - pmContourType mode ///< Currently this must be PS_CONTOUR_CRUDE -); - - -/** pmSourceFitModel() - * - * Fit the requested model to the specified source. The starting guess for the - * model is given by the input source.model parameter values. The pixels of - * interest are specified by the source.pixelsand source.maskentries. This - * function calls psMinimizeLMChi2() on the image data. The function returns TRUE - * on success or FALSE on failure. - * - */ -bool pmSourceFitModel( - pmSource *source, ///< The input pmSource - pmModel *model, ///< model to be fitted - const bool PSF ///< Treat model as PSF or FLT? -); - - -/** pmModelFitStatus() - * - * This function wraps the call to the model-specific function returned by - * pmModelFitStatusFunc_GetFunction. The model-specific function examines the - * model parameters, parameter errors, Chisq, S/N, and other parameters available - * from model to decide if the particular fit was successful or not. - * - * XXX: Must code this. - * - */ -bool pmModelFitStatus( - pmModel *model ///< Add comment. -); - - -/** pmSourceAddModel() - * - * Add the given source model flux to/from the provided image. The boolean - * option center selects if the source is re-centered to the image center or if - * it is placed at its centroid location. The boolean option sky selects if the - * background sky is applied (TRUE) or not. The pixel range in the target image - * is at most the pixel range specified by the source.pixels image. The success - * status is returned. - * - */ -bool pmSourceAddModel( - psImage *image, ///< The output image (float) - psImage *mask, ///< The image pixel mask (valid == 0) - pmModel *model, ///< The input pmModel - bool center, ///< A boolean flag that determines whether pixels are centered - bool sky ///< A boolean flag that determines if the sky is subtracted -); - - -/** pmSourceSubModel() - * - * Subtract the given source model flux to/from the provided image. The - * boolean option center selects if the source is re-centered to the image center - * or if it is placed at its centroid location. The boolean option sky selects if - * the background sky is applied (TRUE) or not. The pixel range in the target - * image is at most the pixel range specified by the source.pixels image. The - * success status is returned. - * - */ -bool pmSourceSubModel( - psImage *image, ///< The output image (float) - psImage *mask, ///< The image pixel mask (valid == 0) - pmModel *model, ///< The input pmModel - bool center, ///< A boolean flag that determines whether pixels are centered - bool sky ///< A boolean flag that determines if the sky is subtracted -); - - -/** - * - * The function returns both the magnitude of the fit, defined as -2.5log(flux), - * where the flux is integrated under the model, theoretically from a radius of 0 - * to infinity. In practice, we integrate the model beyond 50sigma. The aperture magnitude is - * defined as -2.5log(flux) , where the flux is summed for all pixels which are - * not excluded by the aperture mask. The model flux is calculated by calling the - * model-specific function provided by pmModelFlux_GetFunction. - * - * XXX: must code this. - * - */ -bool pmSourcePhotometry( - float *fitMag, ///< integrated fit magnitude - float *obsMag, ///< aperture flux magnitude - pmModel *model, ///< model used for photometry - psImage *image, ///< image pixels to be used - psImage *mask ///< mask of pixels to ignore -); - /** @@ -563,4 +32,5 @@ * This function converts the source classification into the closest available * approximation to the Dophot classification scheme: + * XXX EAM : fix this to use current source classification scheme * * PM_SOURCE_DEFECT: 8 @@ -598,60 +68,4 @@ ); -/** pmSourceFitModel_v5() - * - * Fit the requested model to the specified source. The starting guess for the - * model is given by the input source.model parameter values. The pixels of - * interest are specified by the source.pixelsand source.maskentries. This - * function calls psMinimizeLMChi2() on the image data. The function returns TRUE - * on success or FALSE on failure. - * - */ -bool pmSourceFitModel_v5( - pmSource *source, ///< The input pmSource - pmModel *model, ///< model to be fitted - const bool PSF ///< Treat model as PSF or FLT? -); - - -/** pmSourceFitModel_v7() - * - * Fit the requested model to the specified source. The starting guess for the - * model is given by the input source.model parameter values. The pixels of - * interest are specified by the source.pixelsand source.maskentries. This - * function calls psMinimizeLMChi2() on the image data. The function returns TRUE - * on success or FALSE on failure. - * - */ -bool pmSourceFitModel_v7( - pmSource *source, ///< The input pmSource - pmModel *model, ///< model to be fitted - const bool PSF ///< Treat model as PSF or FLT? -); - - -/** pmSourcePhotometry() - * - * XXX: Need descriptions - * - */ -bool pmSourcePhotometry( - float *fitMag, - float *obsMag, - pmModel *model, - psImage *image, - psImage *mask -); - -/** pmModelEval() - * - * XXX: Need descriptions - * - */ -psF32 pmModelEval( - pmModel *model, - psImage *image, - psS32 col, - psS32 row -); #endif Index: trunk/psModules/src/objects/pmPSF.h =================================================================== --- trunk/psModules/src/objects/pmPSF.h (revision 6529) +++ trunk/psModules/src/objects/pmPSF.h (revision 6872) @@ -6,6 +6,6 @@ * @author EAM, IfA * - * @version $Revision: 1.1 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-10-10 19:53:40 $ + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -15,5 +15,4 @@ # ifndef PM_PSF_H # define PM_PSF_H - /** pmPSF data structure @@ -33,12 +32,29 @@ pmModelType type; ///< PSF Model in use psArray *params; ///< Model parameters (psPolynomial2D) - float chisq; ///< PSF goodness statistic - float ApResid; ///< ??? - float dApResid; ///< ??? - float skyBias; ///< ??? + psPolynomial1D *ChiTrend; ///< Chisq vs flux fit (correction for systematic errors) + psPolynomial4D *ApTrend; ///< ApResid vs (x,y,rflux) (rflux = ten(0.4*mInst) + pmGrowthCurve *growth; ///< apMag vs Radius + float ApResid; ///< apMag - psfMag (for PSF stars) + float dApResid; ///< scatter of ApResid + float skyBias; ///< implied residual sky offset from ApResid fit + float skySat; ///< roll-over of ApResid fit + float chisq; ///< PSF goodness statistic (unused??) int nPSFstars; ///< number of stars used to measure PSF + int nApResid; ///< number of stars used to measure ApResid + bool poissonErrors; } pmPSF; +typedef enum { + PM_PSF_NONE, + PM_PSF_CONSTANT, + PM_PSF_SKYBIAS, + PM_PSF_SKYSAT, + PM_PSF_XY_LIN, + PM_PSF_XY_QUAD, + PM_PSF_SKY_XY_LIN, + PM_PSF_SKYSAT_XY_LIN, + PM_PSF_ALL +} pmPSF_ApTrendOptions; /** @@ -48,5 +64,6 @@ */ pmPSF *pmPSFAlloc( - pmModelType type ///< Add comment + pmModelType type, // type of model for PSF + bool poissonErrors ///< use poissonian errors or not? ); @@ -85,3 +102,5 @@ ); +bool pmPSF_MaskApTrend (pmPSF *psf, pmPSF_ApTrendOptions option); + # endif Index: trunk/psModules/src/objects/pmPSF_IO.c =================================================================== --- trunk/psModules/src/objects/pmPSF_IO.c (revision 6872) +++ trunk/psModules/src/objects/pmPSF_IO.c (revision 6872) @@ -0,0 +1,312 @@ +/** @file pmPSF_IO.c + * + * This file contains functions to read and write PSF models using the psMetadata Config file + * format. + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +/*****************************************************************************/ +/* INCLUDE FILES */ +/*****************************************************************************/ + +#include +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAfile.h" +#include "pmFPAfile.h" + +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmPSF_IO.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceIO.h" + +psMetadata *pmPSFtoMD (psMetadata *metadata, pmPSF *psf) +{ + + if (metadata == NULL) { + metadata = psMetadataAlloc (); + } + + char *modelName = pmModelGetType (psf->type); + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_MODEL_NAME", PS_DATA_STRING, "PSF model name", modelName); + + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_POISSON_ERRORS", PS_DATA_BOOL, "Poisson errors for fits", psf->poissonErrors); + + int nPar = pmModelParameterCount (psf->type) ; + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_MODEL_NPAR", PS_DATA_S32, "PSF model parameter count", nPar); + + for (int i = 0; i < nPar - 4; i++) { + psPolynomial2D *poly = psf->params->data[i]; + psPolynomial2DtoMD (metadata, poly, "PSF_PAR%02d", i); + } + psPolynomial4DtoMD (metadata, psf->ApTrend, "APTREND"); + + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_AP_RESID", PS_DATA_F32, "aperture residual", psf->ApResid); + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_dAP_RESID", PS_DATA_F32, "aperture residual scatter", psf->dApResid); + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_SKY_BIAS", PS_DATA_F32, "sky bias level", psf->skyBias); + + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_CHISQ", PS_DATA_F32, "chi-square for fit", psf->chisq); + psMetadataAdd (metadata, PS_LIST_TAIL, "PSF_NSTARS", PS_DATA_S32, "number of stars used to measure PSF", psf->nPSFstars); + + return metadata; +} + +pmPSF *pmPSFfromMD (psMetadata *metadata) +{ + + bool status; + char keyword[80]; + + char *modelName = psMetadataLookupPtr (&status, metadata, "PSF_MODEL_NAME"); + pmModelType type = pmModelSetType (modelName); + + bool poissonErrors = psMetadataLookupPtr (&status, metadata, "PSF_POISSON_ERRORS"); + if (!status) + poissonErrors = true; + + pmPSF *psf = pmPSFAlloc (type, poissonErrors); + + int nPar = psMetadataLookupS32 (&status, metadata, "PSF_MODEL_NPAR"); + if (nPar != pmModelParameterCount (psf->type)) + psAbort ("read PSF" , "mismatch model par count"); + + for (int i = 0; i < nPar - 4; i++) { + sprintf (keyword, "PSF_PAR%02d", i); + psMetadata *folder = psMetadataLookupPtr (&status, metadata, keyword); + psPolynomial2D *poly = psPolynomial2DfromMD (folder); + psFree (psf->params->data[i]); + psf->params->data[i] = poly; + } + sprintf (keyword, "APTREND"); + psMetadata *folder = psMetadataLookupPtr (&status, metadata, keyword); + psPolynomial4D *poly = psPolynomial4DfromMD (folder); + psFree (psf->ApTrend); + psf->ApTrend = poly; + + psf->ApResid = psMetadataLookupF32 (&status, metadata, "PSF_AP_RESID"); + psf->dApResid = psMetadataLookupF32 (&status, metadata, "PSF_dAP_RESID"); + psf->skyBias = psMetadataLookupF32 (&status, metadata, "PSF_SKY_BIAS"); + + psf->chisq = psMetadataLookupF32 (&status, metadata, "PSF_CHISQ"); + psf->nPSFstars = psMetadataLookupS32 (&status, metadata, "PSF_NSTARS"); + + psFree (metadata); + return (psf); +} + +bool pmFPAviewWritePSFmodel (const pmFPAview *view, pmFPAfile *file) +{ + + pmFPA *fpa = file->fpa; + + if (view->chip == -1) { + pmFPAWritePSFmodel (fpa, view, file); + return true; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + pmChipWritePSFmodel (chip, view, file); + return true; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellWritePSFmodel (cell, view, file); + return true; + } + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + pmReadoutWritePSFmodel (readout, view, file); + return true; +} + +// read in all chip-level PSFmodel files for this FPA +bool pmFPAWritePSFmodel (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < fpa->chips->n; i++) { + + pmChip *chip = fpa->chips->data[i]; + pmChipWritePSFmodel (chip, view, file); + } + return true; +} + +// read in all cell-level PSFmodel files for this chip +bool pmChipWritePSFmodel (pmChip *chip, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < chip->cells->n; i++) { + + pmCell *cell = chip->cells->data[i]; + pmCellWritePSFmodel (cell, view, file); + } + return true; +} + +// read in all readout-level PSFmodel files for this cell +bool pmCellWritePSFmodel (pmCell *cell, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < cell->readouts->n; i++) { + + pmReadout *readout = cell->readouts->data[i]; + pmReadoutWritePSFmodel (readout, view, file); + } + return true; +} + +// read in all readout-level Objects files for this cell +bool pmReadoutWritePSFmodel (pmReadout *readout, const pmFPAview *view, pmFPAfile *file) +{ + bool status; + char *filename; + + pmPSF *psf = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.PSF"); + + switch (file->type) { + case PM_FPA_FILE_PSF: + filename = pmFPAfileNameFromRule (file->filerule, file, view); + psMetadata *psfData = pmPSFtoMD (NULL, psf); + psMetadataConfigWrite (psfData, filename); + psFree (psfData); + psFree (filename); + return true; + + default: + fprintf (stderr, "warning: type mismatch\n"); + break; + } + return false; +} + + + +bool pmFPAviewReadPSFmodel (const pmFPAview *view, pmFPAfile *file) +{ + + pmFPA *fpa = file->fpa; + + if (view->chip == -1) { + pmFPAReadPSFmodel (fpa, view, file); + return true; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + pmChipReadPSFmodel (chip, view, file); + return true; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellReadPSFmodel (cell, view, file); + return true; + } + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + pmReadoutReadPSFmodel (readout, view, file); + return true; +} + +// read in all chip-level PSFmodel files for this FPA +bool pmFPAReadPSFmodel (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < fpa->chips->n; i++) { + + pmChip *chip = fpa->chips->data[i]; + pmChipReadPSFmodel (chip, view, file); + } + return true; +} + +// read in all cell-level PSFmodel files for this chip +bool pmChipReadPSFmodel (pmChip *chip, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < chip->cells->n; i++) { + + pmCell *cell = chip->cells->data[i]; + pmCellReadPSFmodel (cell, view, file); + } + return true; +} + +// read in all readout-level PSFmodel files for this cell +bool pmCellReadPSFmodel (pmCell *cell, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < cell->readouts->n; i++) { + + pmReadout *readout = cell->readouts->data[i]; + pmReadoutReadPSFmodel (readout, view, file); + } + return true; +} + +// read in all readout-level Objects files for this cell +bool pmReadoutReadPSFmodel (pmReadout *readout, const pmFPAview *view, pmFPAfile *file) +{ + + int Nfail; + char *filename; + + switch (file->type) { + case PM_FPA_FILE_PSF: + filename = pmFPAfileNameFromRule (file->filerule, file, view); + + psMetadata *psfData = psMetadataConfigParse (NULL, &Nfail, filename, FALSE); + pmPSF *psf = pmPSFfromMD (psfData); + psMetadataAdd (readout->analysis, PS_LIST_TAIL, "PSPHOT.PSF", PS_DATA_UNKNOWN, "psphot psf", psf); + + psFree (psf); + psFree (psfData); + psFree (filename); + + return true; + + default: + fprintf (stderr, "warning: type mismatch\n"); + break; + } + return false; +} + Index: trunk/psModules/src/objects/pmPSF_IO.h =================================================================== --- trunk/psModules/src/objects/pmPSF_IO.h (revision 6872) +++ trunk/psModules/src/objects/pmPSF_IO.h (revision 6872) @@ -0,0 +1,32 @@ +/** @file pmPSF.h + * + * This file contains typedefs for the Point-Spread Function and prototypes + * for functions that calculate the PSF. + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_PSF_IO_H +# define PM_PSF_IO_H + +psMetadata *pmPSFtoMD (psMetadata *metadata, pmPSF *psf); +pmPSF *pmPSFfromMD (psMetadata *metadata); +bool pmFPAviewWritePSFmodel (const pmFPAview *view, pmFPAfile *file); +bool pmFPAWritePSFmodel (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file); +bool pmChipWritePSFmodel (pmChip *chip, const pmFPAview *view, pmFPAfile *file); +bool pmCellWritePSFmodel (pmCell *cell, const pmFPAview *view, pmFPAfile *file); +bool pmReadoutWritePSFmodel (pmReadout *readout, const pmFPAview *view, pmFPAfile *file); + +bool pmFPAviewReadPSFmodel (const pmFPAview *view, pmFPAfile *file); +bool pmFPAReadPSFmodel (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file); +bool pmChipReadPSFmodel (pmChip *chip, const pmFPAview *view, pmFPAfile *file); +bool pmCellReadPSFmodel (pmCell *cell, const pmFPAview *view, pmFPAfile *file); +bool pmReadoutReadPSFmodel (pmReadout *readout, const pmFPAview *view, pmFPAfile *file); + +# endif Index: trunk/psModules/src/objects/pmPSFtry.h =================================================================== --- trunk/psModules/src/objects/pmPSFtry.h (revision 6529) +++ trunk/psModules/src/objects/pmPSFtry.h (revision 6872) @@ -6,6 +6,6 @@ * @author EAM, IfA * - * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ - * @date $Date: 2005-12-24 01:24:32 $ + * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -18,11 +18,11 @@ /** - * + * * This structure contains a pointer to the collection of sources which will * be used to test the PSF model form. It lists the pmModelType type of model * being tests, and contains an element to store the resulting psf * representation. In addition, this structure carries the complete collection of - * FLT (floating parameter) and PSF (fixed parameter) model fits to each of the - * sources modelFLT and modelPSF. It also contains a mask which is set by the + * EXT (floating parameter) and PSF (fixed parameter) model fits to each of the + * sources modelEXT and modelPSF. It also contains a mask which is set by the * model fitting and psf fitting steps. For each model, the value of the quality * metric is stored in the vector metric and the fitted instrumental magnitude is @@ -38,9 +38,9 @@ * ultimate metric to intercompare multiple types of PSF models is the value of * the aperture correction scatter. - * + * * XXX: There are many more members in the SDRS then in the prototype code. * I stuck with the prototype code. - * - * + * + * */ typedef struct @@ -48,5 +48,5 @@ pmPSF *psf; ///< Add comment. psArray *sources; ///< pointers to the original sources - psArray *modelFLT; ///< model fits, floating parameters + psArray *modelEXT; ///< model fits, floating parameters psArray *modelPSF; ///< model fits, PSF parameters psVector *mask; ///< Add comment. @@ -58,13 +58,13 @@ /** pmPSFtryMaskValues - * + * * The following datatype defines the masks used by the pmPSFtry analysis to * identify sources which should or should not be included in the analysis. - * + * */ -enum { +typedef enum { PSFTRY_MASK_CLEAR = 0x00, ///< Add comment. PSFTRY_MASK_OUTLIER = 0x01, ///< 1: outlier in psf polynomial fit (provided by psPolynomials) - PSFTRY_MASK_FLT_FAIL = 0x02, ///< 2: flt model failed to converge + PSFTRY_MASK_EXT_FAIL = 0x02, ///< 2: ext model failed to converge PSFTRY_MASK_PSF_FAIL = 0x04, ///< 3: psf model failed to converge PSFTRY_MASK_BAD_PHOT = 0x08, ///< 4: invalid source photometry @@ -74,33 +74,35 @@ /** pmPSFtryAlloc() - * + * * Allocate a pmPSFtry data structure. - * + * */ pmPSFtry *pmPSFtryAlloc( psArray *stars, ///< Add comment. - char *modelName ///< Add comment. + char *modelName, ///< Add comment. + bool poissonErrors // use poissonian or constant errors? ); /** pmPSFtryModel() - * + * * This function takes the input collection of sources and performs a complete * analysis to determine a PSF model of the given type (specified by model name). * The result is a pmPSFtry with the results of the analysis. - * + * */ pmPSFtry *pmPSFtryModel( psArray *sources, ///< Add comment. char *modelName, ///< Add comment. - float radius ///< Add comment. + float radius, ///< Add comment. + bool poissonErrors // use poissonian or constant errors? ); /** pmPSFtryMetric() - * + * * This function is used to measure the PSF model metric for the set of * results contained in the pmPSFtry structure. - * + * */ bool pmPSFtryMetric( Index: trunk/psModules/src/objects/pmPeaks.c =================================================================== --- trunk/psModules/src/objects/pmPeaks.c (revision 6872) +++ trunk/psModules/src/objects/pmPeaks.c (revision 6872) @@ -0,0 +1,542 @@ +/** @file pmPeaks.c + * + * This file defines functions to detect and manipulate peaks in images + * + * @author GLG, MHPCC + * @author EAM, IfA: significant modifications. + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmPeaks.h" + +/****************************************************************************** +myListAddPeak(): A private function which allocates a psArray, if the list +argument is NULL, otherwise it adds the peak to that list. +XXX EAM : changed the output to psArray +XXX EAM : Switched row, col args +XXX EAM : NOTE: this was changed in the call, so the new code is consistent +*****************************************************************************/ +static psArray *myListAddPeak(psArray *list, + psS32 row, + psS32 col, + psF32 counts, + pmPeakType type) +{ + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + pmPeak *tmpPeak = pmPeakAlloc(col, row, counts, type); + + if (list == NULL) { + list = psArrayAlloc(100); + list->n = 0; + } + psArrayAdd(list, 100, tmpPeak); + psFree (tmpPeak); + // XXX EAM : is this free appropriate? (does psArrayAdd increment memory counter?) + + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return(list); +} + +/****************************************************************************** +getRowVectorFromImage(): a private function which simply returns a +psVector containing the specified row of data from the psImage. + +XXX: Is there a better way to do this? +XXX EAM: does this really need to alloc a new vector??? +*****************************************************************************/ +static psVector *getRowVectorFromImage(psImage *image, + psU32 row) +{ + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + PS_ASSERT_IMAGE_NON_NULL(image, NULL); + PS_ASSERT_IMAGE_TYPE(image, PS_TYPE_F32, NULL); + + psVector *tmpVector = psVectorAlloc(image->numCols, PS_TYPE_F32); + for (psU32 col = 0; col < image->numCols ; col++) { + tmpVector->data.F32[col] = image->data.F32[row][col]; + } + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return(tmpVector); +} + +/****************************************************************************** +isItInThisRegion(): a private function which simply returns a +boolean denoting if specified coordinate is in the region. +XXX: Macro this. +*****************************************************************************/ +static bool isItInThisRegion(const psRegion valid, + psS32 x, + psS32 y) +{ + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + if ((x >= valid.x0) && + (x <= valid.x1) && + (y >= valid.y0) && + (y <= valid.y1)) { + psTrace(__func__, 4, "---- %s(true) end ----\n", __func__); + return(true); + } + psTrace(__func__, 4, "---- %s(false) end ----\n", __func__); + return(false); +} + +/****************************************************************************** +pmPeakAlloc(): Allocate the pmPeak data structure and set appropriate members. +*****************************************************************************/ +pmPeak *pmPeakAlloc(psS32 x, + psS32 y, + psF32 counts, + pmPeakType type) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + pmPeak *tmp = (pmPeak *) psAlloc(sizeof(pmPeak)); + tmp->x = x; + tmp->y = y; + tmp->counts = counts; + tmp->type = type; + + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmp); +} + +// psSort comparison function for peaks +int pmPeaksCompareAscend (const void **a, const void **b) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + pmPeak *A = *(pmPeak **)a; + pmPeak *B = *(pmPeak **)b; + + psF32 diff; + + diff = A->counts - B->counts; + if (diff < FLT_EPSILON) { + psTrace(__func__, 3, "---- %s(-1) end ----\n", __func__); + return (-1); + } else if (diff > FLT_EPSILON) { + psTrace(__func__, 3, "---- %s(+1) end ----\n", __func__); + return (+1); + } + psTrace(__func__, 3, "---- %s(0) end ----\n", __func__); + return (0); +} + +// psSort comparison function for peaks +int pmPeaksCompareDescend (const void **a, const void **b) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + pmPeak *A = *(pmPeak **)a; + pmPeak *B = *(pmPeak **)b; + + psF32 diff; + + diff = A->counts - B->counts; + if (diff < FLT_EPSILON) { + psTrace(__func__, 3, "---- %s(+1) end ----\n", __func__); + return (+1); + } else if (diff > FLT_EPSILON) { + psTrace(__func__, 3, "---- %s(-1) end ----\n", __func__); + return (-1); + } + psTrace(__func__, 3, "---- %s(0) end ----\n", __func__); + return (0); +} + +/****************************************************************************** +pmFindVectorPeaks(vector, threshold): Find all local peaks in the given vector +above the given threshold. Returns a vector of type PS_TYPE_U32 containing +the location (x value) of all peaks. + +XXX: What types should be supported? Only F32 is implemented. + +XXX: We currently step through the input vector twice; once to determine the +size of the output vector, then to set the values of the output vector. +Depending upon actual use, this may need to be optimized. +*****************************************************************************/ +psVector *pmFindVectorPeaks(const psVector *vector, + psF32 threshold) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_VECTOR_NON_NULL(vector, NULL); + PS_ASSERT_VECTOR_NON_EMPTY(vector, NULL); + PS_ASSERT_VECTOR_TYPE(vector, PS_TYPE_F32, NULL); + int count = 0; + int n = vector->n; + + // + // Special case: the input vector has a single element. + // + if (n == 1) { + psVector *tmpVector = NULL; + ; + if (vector->data.F32[0] > threshold) { + tmpVector = psVectorAlloc(1, PS_TYPE_U32); + tmpVector->data.U32[0] = 0; + } else { + tmpVector = psVectorAlloc(0, PS_TYPE_U32); + } + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmpVector); + } + + // + // Determine if first pixel is a peak + // + if ((vector->data.F32[0] > vector->data.F32[1]) && + (vector->data.F32[0] > threshold)) { + count++; + } + + // + // Determine if interior pixels are peaks + // + for (psU32 i = 1; i < n-1 ; i++) { + if ((vector->data.F32[i] > vector->data.F32[i-1]) && + (vector->data.F32[i] > vector->data.F32[i+1]) && + (vector->data.F32[i] > threshold)) { + count++; + } + } + + // + // Determine if last pixel is a peak + // + if ((vector->data.F32[n-1] > vector->data.F32[n-2]) && + (vector->data.F32[n-1] > threshold)) { + count++; + } + + // + // We know how many peaks exist, so we now allocate a psVector to store + // those peaks. + // + psVector *tmpVector = psVectorAlloc(count, PS_TYPE_U32); + count = 0; + + // + // Determine if first pixel is a peak + // + if ((vector->data.F32[0] > vector->data.F32[1]) && + (vector->data.F32[0] > threshold)) { + tmpVector->data.U32[count++] = 0; + } + + // + // Determine if interior pixels are peaks + // + for (psU32 i = 1; i < (n-1) ; i++) { + if ((vector->data.F32[i] > vector->data.F32[i-1]) && + (vector->data.F32[i] > vector->data.F32[i+1]) && + (vector->data.F32[i] > threshold)) { + tmpVector->data.U32[count++] = i; + } + } + + // + // Determine if last pixel is a peak + // + if ((vector->data.F32[n-1] > vector->data.F32[n-2]) && + (vector->data.F32[n-1] > threshold)) { + tmpVector->data.U32[count++] = n-1; + } + + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmpVector); +} + + +/****************************************************************************** +pmFindImagePeaks(image, threshold): Find all local peaks in the given psImage +above the given threshold. Returns a psArray containing location (x/y value) +of all peaks. + +XXX: I'm not convinced the peak type definition in the SDRS is mutually +exclusive. Some peaks can have multiple types. Edges for sure. Also, a +digonal line with the same value at each point will have a peak for every +point on that line. + +XXX: This does not work if image has either a single row, or a single column. + +XXX: In the output psArray elements, should we use the image row/column offsets? + Currently, we do not. +XXX EAM : this function needs to return peaks in *parent* coords + +XXX: Merge with CVS 1.20. This had the proper code for images with a single +row or column. + +*****************************************************************************/ +psArray *pmFindImagePeaks(const psImage *image, + psF32 threshold) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_IMAGE_NON_NULL(image, NULL); + PS_ASSERT_IMAGE_TYPE(image, PS_TYPE_F32, NULL); + if ((image->numRows == 1) || (image->numCols == 1)) { + psError(PS_ERR_UNKNOWN, true, "Currently, input image must have at least 2 rows and 2 columns."); + psTrace(__func__, 3, "---- %s(NULL) end ----\n", __func__); + return(NULL); + } + psVector *tmpRow = NULL; + psU32 col = 0; + psU32 row = 0; + psArray *list = NULL; + + psU32 col0 = image->col0; + psU32 row0 = image->row0; + + // + // Find peaks in row 0 only. + // + row = 0; + tmpRow = getRowVectorFromImage((psImage *) image, row); + psVector *row1 = pmFindVectorPeaks(tmpRow, threshold); + // pmFindVectorPeaks returns coords in the vector, not corrected for col0 + + for (psU32 i = 0 ; i < row1->n ; i++ ) { + col = row1->data.U32[i]; + // + // Determine if pixel (0,0) is a peak. + // + if (col == 0) { + if ( (image->data.F32[row][col] > image->data.F32[row][col+1]) && + (image->data.F32[row][col] > image->data.F32[row+1][col]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col+1])) { + + if (image->data.F32[row][col] > threshold) { + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], PM_PEAK_EDGE); + } + } + } else if (col < (image->numCols - 1)) { + if ( (image->data.F32[row][col] >= image->data.F32[row][col-1]) && + (image->data.F32[row][col] > image->data.F32[row][col+1]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col-1]) && + (image->data.F32[row][col] > image->data.F32[row+1][col]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col+1])) { + if (image->data.F32[row][col] > threshold) { + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], PM_PEAK_EDGE); + } + } + + } else if (col == (image->numCols - 1)) { + if ( (image->data.F32[row][col] >= image->data.F32[row][col-1]) && + (image->data.F32[row][col] > image->data.F32[row+1][col]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col-1])) { + if (image->data.F32[row][col] > threshold) { + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], PM_PEAK_EDGE); + } + } + + } else { + psError(PS_ERR_UNKNOWN, true, "peak specified valid column range."); + } + } + psFree (tmpRow); + psFree (row1); + + // + // Exit if this image has a single row. + // + if (image->numRows == 1) { + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(list); + } + + // + // Find peaks in interior rows only. + // + for (row = 1 ; row < (image->numRows - 1) ; row++) { + tmpRow = getRowVectorFromImage((psImage *) image, row); + row1 = pmFindVectorPeaks(tmpRow, threshold); + + // Step through all local peaks in this row. + for (psU32 i = 0 ; i < row1->n ; i++ ) { + pmPeakType myType = PM_PEAK_UNDEF; + col = row1->data.U32[i]; + + if (col == 0) { + // If col==0, then we can not read col-1 pixels + if ((image->data.F32[row][col] > image->data.F32[row-1][col]) && + (image->data.F32[row][col] >= image->data.F32[row-1][col+1]) && + (image->data.F32[row][col] >= image->data.F32[row][col+1]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col+1])) { + myType = PM_PEAK_EDGE; + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], myType); + } + } else if (col < (image->numCols - 1)) { + // This is an interior pixel + if ((image->data.F32[row][col] >= image->data.F32[row-1][col-1]) && + (image->data.F32[row][col] > image->data.F32[row-1][col]) && + (image->data.F32[row][col] >= image->data.F32[row-1][col+1]) && + (image->data.F32[row][col] > image->data.F32[row][col-1]) && + (image->data.F32[row][col] >= image->data.F32[row][col+1]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col-1]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col+1])) { + if (image->data.F32[row][col] > threshold) { + if ((image->data.F32[row][col] > image->data.F32[row-1][col-1]) && + (image->data.F32[row][col] > image->data.F32[row-1][col]) && + (image->data.F32[row][col] > image->data.F32[row-1][col+1]) && + (image->data.F32[row][col] > image->data.F32[row][col-1]) && + (image->data.F32[row][col] > image->data.F32[row][col+1]) && + (image->data.F32[row][col] > image->data.F32[row+1][col-1]) && + (image->data.F32[row][col] > image->data.F32[row+1][col]) && + (image->data.F32[row][col] > image->data.F32[row+1][col+1])) { + myType = PM_PEAK_LONE; + } + + if ((image->data.F32[row][col] == image->data.F32[row-1][col-1]) || + (image->data.F32[row][col] == image->data.F32[row-1][col]) || + (image->data.F32[row][col] == image->data.F32[row-1][col+1]) || + (image->data.F32[row][col] == image->data.F32[row][col-1]) || + (image->data.F32[row][col] == image->data.F32[row][col+1]) || + (image->data.F32[row][col] == image->data.F32[row+1][col-1]) || + (image->data.F32[row][col] == image->data.F32[row+1][col]) || + (image->data.F32[row][col] == image->data.F32[row+1][col+1])) { + myType = PM_PEAK_FLAT; + } + + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], myType); + } + } + } else if (col == (image->numCols - 1)) { + // If col==numCols - 1, then we can not read col+1 pixels + if ((image->data.F32[row][col] >= image->data.F32[row-1][col-1]) && + (image->data.F32[row][col] > image->data.F32[row-1][col]) && + (image->data.F32[row][col] > image->data.F32[row][col-1]) && + (image->data.F32[row][col] >= image->data.F32[row][col+1]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col-1]) && + (image->data.F32[row][col] >= image->data.F32[row+1][col])) { + myType = PM_PEAK_EDGE; + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], myType); + } + } else { + psError(PS_ERR_UNKNOWN, true, "peak specified outside valid column range."); + } + + } + psFree (tmpRow); + psFree (row1); + } + + // + // Find peaks in the last row only. + // + row = image->numRows - 1; + tmpRow = getRowVectorFromImage((psImage *) image, row); + row1 = pmFindVectorPeaks(tmpRow, threshold); + for (psU32 i = 0 ; i < row1->n ; i++ ) { + col = row1->data.U32[i]; + if (col == 0) { + if ( (image->data.F32[row][col] > image->data.F32[row-1][col]) && + (image->data.F32[row][col] >= image->data.F32[row-1][col+1]) && + (image->data.F32[row][col] > image->data.F32[row][col+1])) { + if (image->data.F32[row][col] > threshold) { + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], PM_PEAK_EDGE); + } + } + } else if (col < (image->numCols - 1)) { + if ( (image->data.F32[row][col] >= image->data.F32[row-1][col-1]) && + (image->data.F32[row][col] > image->data.F32[row-1][col]) && + (image->data.F32[row][col] >= image->data.F32[row-1][col+1]) && + (image->data.F32[row][col] > image->data.F32[row][col-1]) && + (image->data.F32[row][col] >= image->data.F32[row][col+1])) { + if (image->data.F32[row][col] > threshold) { + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], PM_PEAK_EDGE); + } + } + + } else if (col == (image->numCols - 1)) { + if ( (image->data.F32[row][col] >= image->data.F32[row-1][col-1]) && + (image->data.F32[row][col] > image->data.F32[row-1][col]) && + (image->data.F32[row][col] > image->data.F32[row][col-1])) { + if (image->data.F32[row][col] > threshold) { + list = myListAddPeak(list, row + row0, col + col0, image->data.F32[row][col], PM_PEAK_EDGE); + } + } + } else { + psError(PS_ERR_UNKNOWN, true, "peak specified outside valid column range."); + } + } + psFree (tmpRow); + psFree (row1); + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(list); +} + + +/****************************************************************************** +psCullPeaks(peaks, maxValue, valid): eliminate peaks from the psArray that have +a peak value above the given maximum, or fall outside the valid region. + +XXX: Should the sky value be used when comparing the maximum? + +XXX: warning message if valid is NULL? + +XXX: changed API to create a NEW output psArray (should change name as well) + +XXX: Do we free the psList elements of those culled peaks? + +XXX EAM : do we still need pmCullPeaks, or only pmPeaksSubset? +*****************************************************************************/ +psList *pmCullPeaks(psList *peaks, + psF32 maxValue, + const psRegion valid) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(peaks, NULL); + + psListElem *tmpListElem = (psListElem *) peaks->head; + psS32 indexNum = 0; + + // printf("pmCullPeaks(): list size is %d\n", peaks->size); + while (tmpListElem != NULL) { + pmPeak *tmpPeak = (pmPeak *) tmpListElem->data; + if ((tmpPeak->counts > maxValue) || + (true == isItInThisRegion(valid, tmpPeak->x, tmpPeak->y))) { + psListRemoveData(peaks, (psPtr) tmpPeak); + } + + indexNum++; + tmpListElem = tmpListElem->next; + } + + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(peaks); +} + +// XXX EAM: I changed this to return a new, subset array +// rather than alter the existing one +// XXX: Fix the *valid pointer. +psArray *pmPeaksSubset( + psArray *peaks, + psF32 maxValue, + const psRegion valid) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(peaks, NULL); + + psArray *output = psArrayAlloc (200); + output->n = 0; + + psTrace (".pmObjects.pmCullPeaks", 3, "list size is %d\n", peaks->n); + + for (int i = 0; i < peaks->n; i++) { + pmPeak *tmpPeak = (pmPeak *) peaks->data[i]; + if (tmpPeak->counts > maxValue) + continue; + if (isItInThisRegion(valid, tmpPeak->x, tmpPeak->y)) + continue; + psArrayAdd (output, 200, tmpPeak); + } + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(output); +} Index: trunk/psModules/src/objects/pmPeaks.h =================================================================== --- trunk/psModules/src/objects/pmPeaks.h (revision 6872) +++ trunk/psModules/src/objects/pmPeaks.h (revision 6872) @@ -0,0 +1,143 @@ +/** @file pmPeaks.h + * + * The process of finding, measuring, and classifying astronomical sources on + * images is one of the critical tasks of the IPP or any astronomical software + * system. This file will define structures and functions related to the task + * of source detection and measurement. The elements defined in this section + * are generally low-level components which can be connected together to + * construct a complete object measurement suite. + * + * @author GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_PEAKS_H +# define PM_PEAKS_H + +/** pmPeakType + * + * A peak pixel may have several features which may be determined when the + * peak is found or measured. These are specified by the pmPeakType enum. + * PM_PEAK_LONE represents a single pixel which is higher than its 8 immediate + * neighbors. The PM_PEAK_EDGE represents a peak pixel which touching the image + * edge. The PM_PEAK_FLAT represents a peak pixel which has more than a specific + * number of neighbors at the same value, within some tolarence: + * + */ +typedef enum { + PM_PEAK_LONE, ///< Isolated peak. + PM_PEAK_EDGE, ///< Peak on edge. + PM_PEAK_FLAT, ///< Peak has equal-value neighbors. + PM_PEAK_UNDEF ///< Undefined. +} pmPeakType; + + +/** pmPeak data structure + * + * A source has the capacity for several types of measurements. The + * simplest measurement of a source is the location and flux of the peak pixel + * associated with the source: + * + */ +typedef struct +{ + int x; ///< X-coordinate of peak pixel. + int y; ///< Y-coordinate of peak pixel. + float counts; ///< Value of peak pixel (above sky?). + pmPeakType type; ///< Description of peak. +} +pmPeak; + + +/** pmPeakAlloc() + * + * @return pmPeak* newly allocated pmPeak with all internal pointers set to NULL + */ +pmPeak *pmPeakAlloc( + int x, ///< Row-coordinate in image space + int y, ///< Col-coordinate in image space + float counts, ///< The value of the peak pixel + pmPeakType type ///< The type of peak pixel +); + + +/** pmFindVectorPeaks() + * + * Find all local peaks in the given vector above the given threshold. A peak + * is defined as any element with a value greater than its two neighbors and with + * a value above the threshold. Two types of special cases must be addressed. + * Equal value elements: If an element has the same value as the following + * element, it is not considered a peak. If an element has the same value as the + * preceding element (but not the following), then it is considered a peak. Note + * that this rule (arbitrarily) identifies flat regions by their trailing edge. + * Edge cases: At start of the vector, the element must be higher than its + * neighbor. At the end of the vector, the element must be higher or equal to its + * neighbor. These two rules again places the peak associated with a flat region + * which touches the image edge at the image edge. The result of this function is + * a vector containing the coordinates (element number) of the detected peaks + * (type psU32). + * + */ +psVector *pmFindVectorPeaks( + const psVector *vector, ///< The input vector (float) + float threshold ///< Threshold above which to find a peak +); + + +/** pmFindImagePeaks() + * + * Find all local peaks in the given image above the given threshold. This + * function should find all row peaks using pmFindVectorPeaks, then test each row + * peak and exclude peaks which are not local peaks. A peak is a local peak if it + * has a higher value than all 8 neighbors. If the peak has the same value as its + * +y neighbor or +x neighbor, it is NOT a local peak. If any other neighbors + * have an equal value, the peak is considered a valid peak. Note two points: + * first, the +x neighbor condition is already enforced by pmFindVectorPeaks. + * Second, these rules have the effect of making flat-topped regions have single + * peaks at the (+x,+y) corner. When selecting the peaks, their type must also be + * set. The result of this function is an array of pmPeak entries. + * + */ +psArray *pmFindImagePeaks( + const psImage *image, ///< The input image where peaks will be found (float) + float threshold ///< Threshold above which to find a peak +); + + +/** pmCullPeaks() + * + * Eliminate peaks from the psList that have a peak value above the given + * maximum, or fall outside the valid region. + * + */ +psList *pmCullPeaks( + psList *peaks, ///< The psList of peaks to be culled + float maxValue, ///< Cull peaks above this value + const psRegion valid ///< Cull peaks otside this psRegion +); + + +/** pmPeaksSubset() + * + * Create a new peaks array, removing certain types of peaks from the input + * array of peaks based on the given criteria. Peaks should be eliminated if they + * have a peak value above the given maximum value limit or if the fall outside + * the valid region. The result of the function is a new array with a reduced + * number of peaks. + * + */ +psArray *pmPeaksSubset( + psArray *peaks, ///< Add comment. + float maxvalue, ///< Add comment. + const psRegion valid ///< Add comment. +); + +int pmPeaksCompareAscend (const void **a, const void **b); +int pmPeaksCompareDescend (const void **a, const void **b); + +# endif /* PM_PEAKS_H */ Index: trunk/psModules/src/objects/pmSource.c =================================================================== --- trunk/psModules/src/objects/pmSource.c (revision 6872) +++ trunk/psModules/src/objects/pmSource.c (revision 6872) @@ -0,0 +1,609 @@ +/** @file pmSource.c + * + * Functions to define and manipulate sources on images + * + * @author GLG, MHPCC + * @author EAM, IfA: significant modifications. + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmModel.h" +#include "pmSource.h" + +static void sourceFree(pmSource *tmp) +{ + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + psFree(tmp->peak); + psFree(tmp->pixels); + psFree(tmp->weight); + psFree(tmp->mask); + psFree(tmp->moments); + psFree(tmp->modelPSF); + psFree(tmp->modelEXT); + psFree(tmp->blends); + psTrace(__func__, 4, "---- %s() end ----\n", __func__); +} + +/****************************************************************************** +pmSourceAlloc(): Allocate the pmSource structure and initialize its members +to NULL. +*****************************************************************************/ +pmSource *pmSourceAlloc() +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + pmSource *tmp = (pmSource *) psAlloc(sizeof(pmSource)); + tmp->peak = NULL; + tmp->pixels = NULL; + tmp->weight = NULL; + tmp->mask = NULL; + tmp->moments = NULL; + tmp->blends = NULL; + tmp->modelPSF = NULL; + tmp->modelEXT = NULL; + tmp->type = PM_SOURCE_TYPE_UNKNOWN; + tmp->mode = PM_SOURCE_MODE_DEFAULT; + psMemSetDeallocator(tmp, (psFreeFunc) sourceFree); + + tmp->psfMag = 32.0; + tmp->extMag = 32.0; + tmp->errMag = 32.0; + tmp->apMag = 32.0; + tmp->pixWeight = 0.0; + + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmp); +} + +// x,y are defined in the parent image coords of readout->image +bool pmSourceDefinePixels(pmSource *mySource, + const pmReadout *readout, + psF32 x, + psF32 y, + psF32 Radius) +{ + psRegion srcRegion; + + // Grab a subimage of the original image of size (2 * outerRadius). + srcRegion = psRegionForSquare (x, y, Radius); + srcRegion = psRegionForImage (readout->image, srcRegion); + + mySource->pixels = psImageSubset(readout->image, srcRegion); + mySource->weight = psImageSubset(readout->weight, srcRegion); + mySource->mask = psImageSubset(readout->mask, srcRegion); + mySource->region = srcRegion; + + return true; +} + +bool pmSourceRedefinePixels(pmSource *mySource, + const pmReadout *readout, + psF32 x, + psF32 y, + psF32 Radius) +{ + bool extend; + psRegion newRegion; + + if (Radius == 0) + return false; + + // check to see if new region is completely contained within old region + newRegion = psRegionForSquare (x, y, Radius); + newRegion = psRegionForImage (readout->image, newRegion); + + extend = false; + extend |= (int)(newRegion.x0) < (int)(mySource->region.x0); + extend |= (int)(newRegion.x1) > (int)(mySource->region.x1); + extend |= (int)(newRegion.y0) < (int)(mySource->region.y0); + extend |= (int)(newRegion.y1) > (int)(mySource->region.y1); + + extend |= (mySource->pixels == NULL); + extend |= (mySource->weight == NULL); + extend |= (mySource->mask == NULL); + + // extend = true; + if (extend) { + // Grab a new subimage + psFree (mySource->pixels); + psFree (mySource->weight); + psFree (mySource->mask); + + mySource->pixels = psImageSubset(readout->image, newRegion); + mySource->weight = psImageSubset(readout->weight, newRegion); + mySource->mask = psImageSubset(readout->mask, newRegion); + mySource->region = newRegion; + } + + return extend; +} + +/****************************************************************************** + pmSourcePSFClump(source, metadata): Find the likely PSF clump in the + sigma-x, sigma-y plane. return 0,0 clump in case of error. +*****************************************************************************/ + +// XXX EAM include a S/N cutoff in selecting the sources? +pmPSFClump pmSourcePSFClump(psArray *sources, psMetadata *metadata) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + + # define NPIX 10 + # define SCALE 0.1 + + psArray *peaks = NULL; + pmPSFClump emptyClump = {0.0, 0.0, 0.0, 0.0}; + pmPSFClump psfClump = emptyClump; + + PS_ASSERT_PTR_NON_NULL(sources, emptyClump); + PS_ASSERT_PTR_NON_NULL(metadata, emptyClump); + + // find the sigmaX, sigmaY clump + { + psStats *stats = NULL; + psImage *splane = NULL; + int binX, binY; + bool status; + + psF32 SX_MAX = psMetadataLookupF32 (&status, metadata, "MOMENTS_SX_MAX"); + if (!status) + SX_MAX = 10.0; + psF32 SY_MAX = psMetadataLookupF32 (&status, metadata, "MOMENTS_SY_MAX"); + if (!status) + SY_MAX = 10.0; + + // construct a sigma-plane image + // psImageAlloc does zero the data + splane = psImageAlloc (SX_MAX/SCALE, SY_MAX/SCALE, PS_TYPE_F32); + for (int i = 0; i < splane->numRows; i++) + { + memset (splane->data.F32[i], 0, splane->numCols*sizeof(PS_TYPE_F32)); + } + + // place the sources in the sigma-plane image (ignore 0,0 values?) + for (psS32 i = 0 ; i < sources->n ; i++) + { + pmSource *tmpSrc = (pmSource *) sources->data[i]; + if (tmpSrc == NULL) { + continue; + } + if (tmpSrc->moments == NULL) { + continue; + } + + // Sx,Sy are limited at 0. a peak at 0,0 is artificial + if ((fabs(tmpSrc->moments->Sx) < FLT_EPSILON) && (fabs(tmpSrc->moments->Sy) < FLT_EPSILON)) { + continue; + } + + // for the moment, force splane dimensions to be 10x10 image pix + binX = tmpSrc->moments->Sx/SCALE; + if (binX < 0) + continue; + if (binX >= splane->numCols) + continue; + + binY = tmpSrc->moments->Sy/SCALE; + if (binY < 0) + continue; + if (binY >= splane->numRows) + continue; + + splane->data.F32[binY][binX] += 1.0; + } + + // find the peak in this image + stats = psStatsAlloc (PS_STAT_MAX); + stats = psImageStats (stats, splane, NULL, 0); + peaks = pmFindImagePeaks (splane, stats[0].max / 2); + psTrace (".pmObjects.pmSourceRoughClass", 2, "clump threshold is %f\n", stats[0].max/2); + + psFree (splane); + psFree (stats); + + } + // XXX EAM : possible errors: + // 1) no peak in splane + // 2) no significant peak in splane + + // measure statistics on Sx, Sy if Sx, Sy within range of clump + { + pmPeak *clump; + psF32 minSx, maxSx; + psF32 minSy, maxSy; + psVector *tmpSx = NULL; + psVector *tmpSy = NULL; + psStats *stats = NULL; + + // XXX EAM : this lets us takes the single highest peak + psArraySort (peaks, pmPeaksCompareDescend); + clump = peaks->data[0]; + psTrace (".pmObjects.pmSourceRoughClass", 2, "clump is at %d, %d (%f)\n", clump->x, clump->y, clump->counts); + + // define section window for clump + minSx = clump->x * SCALE - 0.2; + maxSx = clump->x * SCALE + 0.2; + minSy = clump->y * SCALE - 0.2; + maxSy = clump->y * SCALE + 0.2; + + tmpSx = psVectorAlloc (sources->n, PS_TYPE_F32); + tmpSy = psVectorAlloc (sources->n, PS_TYPE_F32); + tmpSx->n = 0; + tmpSy->n = 0; + + // XXX clip sources based on flux? + // create vectors with Sx, Sy values in window + for (psS32 i = 0 ; i < sources->n ; i++) + { + pmSource *tmpSrc = (pmSource *) sources->data[i]; + + if (tmpSrc->moments->Sx < minSx) + continue; + if (tmpSrc->moments->Sx > maxSx) + continue; + if (tmpSrc->moments->Sy < minSy) + continue; + if (tmpSrc->moments->Sy > maxSy) + continue; + tmpSx->data.F32[tmpSx->n] = tmpSrc->moments->Sx; + tmpSy->data.F32[tmpSy->n] = tmpSrc->moments->Sy; + tmpSx->n++; + tmpSy->n++; + if (tmpSx->n == tmpSx->nalloc) { + psVectorRealloc (tmpSx, tmpSx->nalloc + 100); + psVectorRealloc (tmpSy, tmpSy->nalloc + 100); + } + } + + // measures stats of Sx, Sy + stats = psStatsAlloc (PS_STAT_CLIPPED_MEAN | PS_STAT_CLIPPED_STDEV); + + stats = psVectorStats (stats, tmpSx, NULL, NULL, 0); + psfClump.X = stats->clippedMean; + psfClump.dX = stats->clippedStdev; + + stats = psVectorStats (stats, tmpSy, NULL, NULL, 0); + psfClump.Y = stats->clippedMean; + psfClump.dY = stats->clippedStdev; + + psTrace (".pmObjects.pmSourceRoughClass", 2, "clump X, Y: %f, %f\n", psfClump.X, psfClump.Y); + psTrace (".pmObjects.pmSourceRoughClass", 2, "clump DX, DY: %f, %f\n", psfClump.dX, psfClump.dY); + // these values should be pushed on the metadata somewhere + + psFree (stats); + psFree (peaks); + psFree (tmpSx); + psFree (tmpSy); + } + + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return (psfClump); +} + +/****************************************************************************** + pmSourceRoughClass(source, metadata): make a guess at the source + classification. + + XXX: push the clump info into the metadata? + + XXX: How can this function ever return FALSE? + + EAM: I moved S/N calculation to pmSourceMoments, using weight image +*****************************************************************************/ + +bool pmSourceRoughClass(psArray *sources, psMetadata *metadata, pmPSFClump clump) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + + psBool rc = true; + + int Nsat = 0; + int Next = 0; + int Nstar = 0; + int Npsf = 0; + int Ncr = 0; + int Nsatstar = 0; + // psRegion allArray = psRegionSet (0, 0, 0, 0); + psRegion inner; + + // report stats on S/N values for star-like objects + psVector *starsn = psVectorAlloc (sources->n, PS_TYPE_F32); + starsn->n = 0; + + // check return status value (do these exist?) + bool status; + psF32 PSF_SN_LIM = psMetadataLookupF32 (&status, metadata, "PSF_SN_LIM"); + + // XXX allow clump size to be scaled relative to sigmas? + // make rough IDs based on clumpX,Y,DX,DY + for (psS32 i = 0 ; i < sources->n ; i++) { + + pmSource *tmpSrc = (pmSource *) sources->data[i]; + + tmpSrc->peak->type = 0; + + psF32 sigX = tmpSrc->moments->Sx; + psF32 sigY = tmpSrc->moments->Sy; + + // XXX EAM : can we use the value of SATURATE if mask is NULL? + // inner = psRegionForSquare (tmpSrc->peak->x - tmpSrc->mask->col0, tmpSrc->peak->y - tmpSrc->mask->row0, 2); + inner = psRegionForSquare (tmpSrc->peak->x, tmpSrc->peak->y, 2); + int Nsatpix = psImageCountPixelMask (tmpSrc->mask, inner, PM_SOURCE_MASK_SATURATED); + + // saturated star (size consistent with PSF or larger) + // Nsigma should be user-configured parameter + bool big = (sigX > (clump.X - clump.dX)) && (sigY > (clump.Y - clump.dY)); + big = true; + if ((Nsatpix > 1) && big) { + tmpSrc->type = PM_SOURCE_TYPE_STAR; + tmpSrc->mode = PM_SOURCE_MODE_SATSTAR; + Nsatstar ++; + continue; + } + + // saturated object (not a star, eg bleed trails, hot pixels) + if (Nsatpix > 1) { + tmpSrc->type = PM_SOURCE_TYPE_SATURATED; + tmpSrc->mode = PM_SOURCE_MODE_DEFAULT; + Nsat ++; + continue; + } + + // likely defect (too small to be stellar) (push out to 3 sigma) + // low S/N objects which are small are probably stellar + // only set candidate defects if + if ((sigX < 0.05) || (sigY < 0.05)) { + tmpSrc->type = PM_SOURCE_TYPE_DEFECT; + tmpSrc->mode = PM_SOURCE_MODE_DEFAULT; + Ncr ++; + continue; + } + + // likely unsaturated extended source (too large to be stellar) + if ((sigX > (clump.X + 3*clump.dX)) || (sigY > (clump.Y + 3*clump.dY))) { + tmpSrc->type = PM_SOURCE_TYPE_EXTENDED; + tmpSrc->mode = PM_SOURCE_MODE_DEFAULT; + Next ++; + continue; + } + + // the rest are probable stellar objects + starsn->data.F32[starsn->n] = tmpSrc->moments->SN; + starsn->n ++; + Nstar ++; + + // PSF star (within 1.5 sigma of clump center, S/N > limit) + psF32 radius = hypot ((sigX-clump.X)/clump.dX, (sigY-clump.Y)/clump.dY); + if ((tmpSrc->moments->SN > PSF_SN_LIM) && (radius < 1.5)) { + tmpSrc->type = PM_SOURCE_TYPE_STAR; + tmpSrc->mode = PM_SOURCE_MODE_PSFSTAR; + Npsf ++; + continue; + } + + // random type of star + tmpSrc->type = PM_SOURCE_TYPE_STAR; + tmpSrc->mode = PM_SOURCE_MODE_DEFAULT; + } + + { + psStats *stats = NULL; + stats = psStatsAlloc (PS_STAT_MIN | PS_STAT_MAX); + stats = psVectorStats (stats, starsn, NULL, NULL, 0); + psLogMsg ("pmObjects", 3, "SN range: %f - %f\n", stats[0].min, stats[0].max); + psFree (stats); + psFree (starsn); + } + + psTrace (".pmObjects.pmSourceRoughClass", 2, "Nstar: %3d\n", Nstar); + psTrace (".pmObjects.pmSourceRoughClass", 2, "Npsf: %3d\n", Npsf); + psTrace (".pmObjects.pmSourceRoughClass", 2, "Next: %3d\n", Next); + psTrace (".pmObjects.pmSourceRoughClass", 2, "Nsatstar: %3d\n", Nsatstar); + psTrace (".pmObjects.pmSourceRoughClass", 2, "Nsat: %3d\n", Nsat); + psTrace (".pmObjects.pmSourceRoughClass", 2, "Ncr: %3d\n", Ncr); + + psTrace(__func__, 3, "---- %s(%d) end ----\n", __func__, rc); + return(rc); +} + +/****************************************************************************** +pmSourceMoments(source, radius): this function takes a subImage defined in the +pmSource data structure, along with the peak location, and determines the +various moments associated with that peak. + +Requires the following to have been created: + pmSource + pmSource->peak + pmSource->pixels + pmSource->weight + pmSource->mask + +XXX: The peak calculations are done in image coords, not subImage coords. + +XXX EAM : this version clips input pixels on S/N +XXX EAM : this version returns false for several reasons +*****************************************************************************/ +# define VALID_RADIUS(X,Y,RAD2) (((RAD2) >= (PS_SQR(X) + PS_SQR(Y))) ? 1 : 0) + +bool pmSourceMoments(pmSource *source, + psF32 radius) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + PS_ASSERT_PTR_NON_NULL(source->pixels, false); + PS_ASSERT_PTR_NON_NULL(source->mask, false); + PS_ASSERT_FLOAT_LARGER_THAN(radius, 0.0, false); + + // + // XXX: Verify the setting for sky if source->moments == NULL. + // + psF32 sky = 0.0; + if (source->moments == NULL) { + source->moments = pmMomentsAlloc(); + } else { + sky = source->moments->Sky; + } + + // + // Sum = SUM (z - sky) + // X1 = SUM (x - xc)*(z - sky) + // X2 = SUM (x - xc)^2 * (z - sky) + // XY = SUM (x - xc)*(y - yc)*(z - sky) + // + psF32 peakPixel = -PS_MAX_F32; + psS32 numPixels = 0; + psF32 Sum = 0.0; + psF32 Var = 0.0; + psF32 X1 = 0.0; + psF32 Y1 = 0.0; + psF32 X2 = 0.0; + psF32 Y2 = 0.0; + psF32 XY = 0.0; + psF32 x = 0; + psF32 y = 0; + psF32 R2 = PS_SQR(radius); + + psF32 xPeak = source->peak->x; + psF32 yPeak = source->peak->y; + psF32 xOff = source->pixels->col0 - source->peak->x; + psF32 yOff = source->pixels->row0 - source->peak->y; + + // XXX why do I get different results for these two methods of finding Sx? + // XXX Sx, Sy would be better measured if we clip pixels close to sky + // XXX Sx, Sy can still be imaginary, so we probably need to keep Sx^2? + // We loop through all pixels in this subimage (source->pixels), and for each + // pixel that is not masked, AND within the radius of the peak pixel, we + // proceed with the moments calculation. need to do two loops for a + // numerically stable result. first loop: get the sums. + // XXX EAM : mask == 0 is valid + + for (psS32 row = 0; row < source->pixels->numRows ; row++) { + + psF32 *vPix = source->pixels->data.F32[row]; + psF32 *vWgt = source->weight->data.F32[row]; + psU8 *vMsk = (source->mask == NULL) ? NULL : source->mask->data.U8[row]; + + for (psS32 col = 0; col < source->pixels->numCols ; col++, vPix++, vWgt++) { + if ((vMsk != NULL) && *vMsk) { + vMsk++; + continue; + } + + psF32 xDiff = col + xOff; + psF32 yDiff = row + yOff; + + // radius is just a function of (xDiff, yDiff) + if (!VALID_RADIUS(xDiff, yDiff, R2)) { + if (vMsk != NULL) + vMsk++; + continue; + } + + psF32 pDiff = *vPix - sky; + psF32 wDiff = *vWgt; + + // XXX EAM : check for valid S/N in pixel + // XXX EAM : should this limit be user-defined? + if (PS_SQR(pDiff) < wDiff) { + if (vMsk != NULL) + vMsk++; + continue; + } + + Var += wDiff; + Sum += pDiff; + + psF32 xWght = xDiff * pDiff; + psF32 yWght = yDiff * pDiff; + + X1 += xWght; + Y1 += yWght; + + XY += xDiff * yWght; + X2 += xDiff * xWght; + Y2 += yDiff * yWght; + + peakPixel = PS_MAX (*vPix, peakPixel); + numPixels++; + if (vMsk != NULL) + vMsk++; + } + } + + // if we have less than (1/4) of the possible pixels, force a retry + // XXX EAM - the limit is a bit arbitrary. make it user defined? + if ((numPixels < 0.75*R2) || (Sum <= 0)) { + psTrace (".psModules.pmSourceMoments", 3, "no valid pixels for source\n"); + psTrace(__func__, 3, "---- %s(false) end ----\n", __func__); + return (false); + } + + psTrace (".psModules.pmSourceMoments", 5, + "sky: %f Sum: %f X1: %f Y1: %f X2: %f Y2: %f XY: %f Npix: %d\n", + sky, Sum, X1, Y1, X2, Y2, XY, numPixels); + + // + // first moment X = X1/Sum + xc + // second moment X = sqrt (X2/Sum - (X1/Sum)^2) + // Sxy = XY / Sum + // + x = X1/Sum; + y = Y1/Sum; + if ((fabs(x) > radius) || (fabs(y) > radius)) { + psTrace (".psModules.pmSourceMoments", 3, + "large centroid swing; invalid peak %d, %d\n", + source->peak->x, source->peak->y); + psTrace(__func__, 3, "---- %s(false) end ----\n", __func__); + return (false); + } + + source->moments->x = x + xPeak; + source->moments->y = y + yPeak; + + // XXX EAM : Sxy needs to have x*y subtracted + source->moments->Sxy = XY/Sum - x*y; + source->moments->Sum = Sum; + source->moments->SN = Sum / sqrt(Var); + source->moments->Peak = peakPixel; + source->moments->nPixels = numPixels; + + // XXX EAM : these values can be negative, so we need to limit the range + source->moments->Sx = sqrt(PS_MAX(X2/Sum - PS_SQR(x), 0)); + source->moments->Sy = sqrt(PS_MAX(Y2/Sum - PS_SQR(y), 0)); + + psTrace (".psModules.pmSourceMoments", 4, + "sky: %f Sum: %f x: %f y: %f Sx: %f Sy: %f Sxy: %f\n", + sky, Sum, source->moments->x, source->moments->y, + source->moments->Sx, source->moments->Sy, source->moments->Sxy); + + psTrace(__func__, 3, "---- %s(true) end ----\n", __func__); + return(true); +} + +pmModel *pmSourceSelectModel (pmSource *source) +{ + switch (source->type) { + case PM_SOURCE_TYPE_STAR: + return source->modelPSF; + + case PM_SOURCE_TYPE_EXTENDED: + return source->modelEXT; + + default: + return NULL; + } + return NULL; +} Index: trunk/psModules/src/objects/pmSource.h =================================================================== --- trunk/psModules/src/objects/pmSource.h (revision 6872) +++ trunk/psModules/src/objects/pmSource.h (revision 6872) @@ -0,0 +1,216 @@ +/** @file pmSource.h + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_SOURCE_H +# define PM_SOURCE_H + +/** + * In the object analysis process, we will use specific mask values to mark the + * image pixels. The following structure defines the relevant mask values. + * + * XXX: This is probably a bad solution: we will want to set mask values + * outside of the PSPHOT code. Perhaps we can set up a registered set of mask + * values with specific meanings that other functions can add to or define? + */ +typedef enum { + PM_SOURCE_MASK_CLEAR = 0x00, + PM_SOURCE_MASK_INVALID = 0x01, + PM_SOURCE_MASK_SATURATED = 0x02, + PM_SOURCE_MASK_MARKED = 0x08, +} psphotMaskValues; + +/** pmSourceType enumeration + * + * A given source may be identified as most-likely to be one of several source + * types. The pmSource entry pmSourceType defines the current best-guess for this + * source. + * + * XXX: The values given below are currently illustrative and will require + * some modification as the source classification code is developed. (TBD) + * + */ +typedef enum { + PM_SOURCE_TYPE_UNKNOWN, ///< a cosmic-ray + PM_SOURCE_TYPE_DEFECT, ///< a cosmic-ray + PM_SOURCE_TYPE_SATURATED, ///< random saturated pixels + PM_SOURCE_TYPE_STAR, ///< a good-quality star + PM_SOURCE_TYPE_EXTENDED, ///< an extended object (eg, galaxy) +} pmSourceType; + +typedef enum { + PM_SOURCE_MODE_DEFAULT = 0x0000, ///< + PM_SOURCE_MODE_PSFMODEL = 0x0001, ///< + PM_SOURCE_MODE_EXTMODEL = 0x0002, ///< + PM_SOURCE_MODE_SUBTRACTED = 0x0004, ///< + PM_SOURCE_MODE_FITTED = 0x0008, ///< + PM_SOURCE_MODE_FAIL = 0x0010, ///< + PM_SOURCE_MODE_POOR = 0x0020, ///< + PM_SOURCE_MODE_PAIR = 0x0040, ///< + PM_SOURCE_MODE_PSFSTAR = 0x0080, ///< + PM_SOURCE_MODE_SATSTAR = 0x0100, ///< + PM_SOURCE_MODE_BLEND = 0x0200, ///< + PM_SOURCE_MODE_LINEAR = 0x0400, ///< + PM_SOURCE_MODE_TEMPSUB = 0x0800, ///< XXX get me a better name! +} pmSourceMode; + +/** pmSource data structure + * + * This source has the capacity for several types of measurements. The + * simplest measurement of a source is the location and flux of the peak pixel + * associated with the source: + * + */ +typedef struct +{ + pmPeak *peak; ///< Description of peak pixel. + psImage *pixels; ///< Rectangular region including object pixels. + psImage *weight; ///< Image variance. + psImage *mask; ///< Mask which marks pixels associated with objects. + pmMoments *moments; ///< Basic moments measure for the object. + pmModel *modelPSF; ///< PSF Model fit (parameters and type) + pmModel *modelEXT; ///< EXT (floating) Model fit (parameters and type). + pmSourceType type; ///< Best identification of object. + pmSourceMode mode; ///< Best identification of object. + psArray *blends; + float psfMag; + float extMag; + float errMag; + float apMag; + float pixWeight; // model-weighted coverage of valid pixels + psRegion region; // area on image covered by selected pixels +} +pmSource; + +/** pmPSFClump data structure + * + * A collection of object moment measurements can be used to determine + * approximate object classes. The key to this analysis is the location and + * statistics (in the second-moment plane, + * + */ +typedef struct +{ + float X; + float dX; + float Y; + float dY; +} +pmPSFClump; + + +/** pmSourceAlloc() + * + */ +pmSource *pmSourceAlloc(); + + +/** pmSourceDefinePixels() + * + * Define psImage subarrays for the source located at coordinates x,y on the + * image set defined by readout. The pixels defined by this operation consist of + * a square window (of full width 2Radius+1) centered on the pixel which contains + * the given coordinate, in the frame of the readout. The window is defined to + * have limits which are valid within the boundary of the readout image, thus if + * the radius would fall outside the image pixels, the subimage is truncated to + * only consist of valid pixels. If readout->mask or readout->weight are not + * NULL, matching subimages are defined for those images as well. This function + * fails if no valid pixels can be defined (x or y less than Radius, for + * example). This function should be used to define a region of interest around a + * source, including both source and sky pixels. + * + */ +bool pmSourceDefinePixels( + pmSource *mySource, ///< source to be re-defined + const pmReadout *readout, ///< base the source on this readout + psF32 x, ///< center coords of source + psF32 y, ///< center coords of source + psF32 Radius ///< size of box on source +); + +bool pmSourceRedefinePixels ( + pmSource *mySource, ///< source to be re-defined + const pmReadout *readout, ///< base the source on this readout + psF32 x, ///< center coords of source + psF32 y, ///< center coords of source + psF32 Radius ///< size of box on source +); + +/** pmSourcePSFClump() + * + * We use the source moments to make an initial, approximate source + * classification, and as part of the information needed to build a PSF model for + * the image. As long as the PSF shape does not vary excessively across the + * image, the sources which are represented by a PSF (the start) will have very + * similar second moments. The function pmSourcePSFClump searches a collection of + * sources with measured moments for a group with moments which are all very + * similar. The function returns a pmPSFClump structure, representing the + * centroid and size of the clump in the sigma_x, sigma_y second-moment plane. + * + * The goal is to identify and characterize the stellar clump within the + * sigma_x, sigma_y second-moment plane. To do this, an image is constructed to + * represent this plane. The units of sigma_x and sigma_y are in image pixels. A + * pixel in this analysis image represents 0.1 pixels in the input image. The + * dimensions of the image need only be 10 pixels. The peak pixel in this image + * (above a threshold of half of the image maximum) is found. The coordinates of + * this peak pixel represent the 2D mode of the sigma_x, sigma_y distribution. + * The sources with sigma_x, sigma_y within 0.2 pixels of this value are then + * * used to calculate the median and standard deviation of the sigma_x, sigma_y + * values. These resulting values are returned via the pmPSFClump structure. + * + * The return value indicates the success (TRUE) of the operation. + * + * XXX: Limit the S/N of the candidate sources (part of Metadata)? (TBD). + * XXX: Save the clump parameters on the Metadata (TBD) + * + */ +pmPSFClump pmSourcePSFClump( + psArray *source, ///< The input pmSource + psMetadata *metadata ///< Contains classification parameters +); + + +/** pmSourceRoughClass() + * + * Based on the specified data values, make a guess at the source + * classification. The sources are provides as a psArray of pmSource entries. + * Definable parameters needed to make the classification are provided to the + * routine with the psMetadata structure. The rules (in SDRS) refer to values which + * can be extracted from the metadata using the given keywords. Except as noted, + * the data type for these parameters are psF32. + * + */ +bool pmSourceRoughClass( + psArray *source, ///< The input pmSource + psMetadata *metadata, ///< Contains classification parameters + pmPSFClump clump ///< Statistics about the PSF clump +); + + +/** pmSourceMoments() + * + * Measure source moments for the given source, using the value of + * source.moments.sky provided as the local background value and the peak + * coordinates as the initial source location. The resulting moment values are + * applied to the source.moments entry, and the source is returned. The moments + * are measured within the given circular radius of the source.peak coordinates. + * The return value indicates the success (TRUE) of the operation. + * + */ +bool pmSourceMoments( + pmSource *source, ///< The input pmSource for which moments will be computed + float radius ///< Use a circle of pixels around the peak +); + + +// select the model used for this source +pmModel *pmSourceSelectModel (pmSource *source); + +# endif /* PM_SOURCE_H */ Index: trunk/psModules/src/objects/pmSourceContour.c =================================================================== --- trunk/psModules/src/objects/pmSourceContour.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceContour.c (revision 6872) @@ -0,0 +1,446 @@ +/** @file pmSourceContour.c + * + * Functions to measure the local sky and sky variance for sources on images + * + * @author GLG, MHPCC + * @author EAM, IfA: significant modifications. + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmModel.h" +#include "pmSource.h" +#include "pmSourceContour.h" + +/****************************************************************************** +findValue(source, level, row, col, dir): a private function which determines +the column coordinate of the model function which has the value "level". If +dir equals 0, then you loop leftwards from the peak pixel, otherwise, +rightwards. + +XXX: reverse order of row,col args? + +XXX: Input row/col are in image coords. + +XXX: The result is returned in image coords. +*****************************************************************************/ +# define LEFT false +# define RIGHT true + +// return the first coordinate at or below the threshold in the requested direction +static int findContourNeg( + psImage *image, + float threshold, + int x, + int y, + bool right) +{ + + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + + // We define variables incr and lastColumn so that we can use the same loop + // whether we are stepping leftwards, or rightwards. + + int incr; + int subCol; + int lastColumn; + if (right) { + incr = 1; + lastColumn = image->numCols - 1; + } else { + incr = -1; + lastColumn = 0; + } + + subCol = x; + + while (subCol != lastColumn) { + float value = image->data.F32[y][subCol]; + if (value <= threshold) { + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return (subCol); + } + subCol += incr; + } + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return (lastColumn); +} + +// return the last coordinate at or below the threshold in the requested direction +static int findContourPos( + psImage *image, + float threshold, + int x, + int y, + bool right, + int xEnd) +{ + + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + + // We define variables incr and lastColumn so that we can use the same loop + // whether we are stepping leftwards, or rightwards. + + int incr; + int subCol; + int lastColumn; + if (right) { + incr = 1; + lastColumn = PS_MIN (image->numCols - 1, xEnd); + } else { + incr = -1; + lastColumn = PS_MAX (0, xEnd); + } + + subCol = x; + while (subCol != lastColumn) { + float value = image->data.F32[y][subCol]; + if (value >= threshold) { + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + if (subCol == x) { + return (subCol); + } + return (subCol); + } + subCol += incr; + } + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return (lastColumn); +} + +/****************************************************************************** +findValue(source, level, row, col, dir): a private function which determines +the column coordinate of the model function which has the value "level". If +dir equals 0, then you loop leftwards from the peak pixel, otherwise, +rightwards. + +XXX: reverse order of row,col args? + +XXX: Input row/col are in image coords. + +XXX: The result is returned in image coords. +*****************************************************************************/ +static psF32 findValue(pmSource *source, + psF32 level, + psU32 row, + psU32 col, + psU32 dir) +{ + psTrace(__func__, 4, "---- %s() begin ----\n", __func__); + // + // Convert coords to subImage space. + // + psU32 subRow = row - source->pixels->row0; + psU32 subCol = col - source->pixels->col0; + + // Ensure that the starting column is allowable. + if (!((0 <= subCol) && (subCol < source->pixels->numCols))) { + psError(PS_ERR_UNKNOWN, true, "Starting column outside subImage range"); + psTrace(__func__, 4, "---- %s(NAN) end ----\n", __func__); + return(NAN); + } + if (!((0 <= subRow) && (subRow < source->pixels->numRows))) { + psTrace(__func__, 4, "---- %s(NAN) end ----\n", __func__); + psError(PS_ERR_UNKNOWN, true, "Starting row outside subImage range"); + return(NAN); + } + + // XXX EAM : i changed this to match pmModelEval above, but see + // XXX EAM the note below in pmSourceContour + psF32 oldValue = pmModelEval(source->modelEXT, source->pixels, subCol, subRow); + if (oldValue == level) { + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return(((psF32) (subCol + source->pixels->col0))); + } + + // + // We define variables incr and lastColumn so that we can use the same loop + // whether we are stepping leftwards, or rightwards. + // + psS32 incr; + psS32 lastColumn; + if (dir == 0) { + incr = -1; + lastColumn = -1; + } else { + incr = 1; + lastColumn = source->pixels->numCols; + } + subCol+=incr; + + while (subCol != lastColumn) { + psF32 newValue = pmModelEval(source->modelEXT, source->pixels, subCol, subRow); + if (oldValue == level) { + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return((psF32) (subCol + source->pixels->col0)); + } + + if ((newValue <= level) && (level <= oldValue)) { + // This is simple linear interpolation. + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return( ((psF32) (subCol + source->pixels->col0)) + ((psF32) incr) * ((level - newValue) / (oldValue - newValue)) ); + } + + if ((oldValue <= level) && (level <= newValue)) { + // This is simple linear interpolation. + psTrace(__func__, 4, "---- %s() end ----\n", __func__); + return( ((psF32) (subCol + source->pixels->col0)) + ((psF32) incr) * ((level - oldValue) / (newValue - oldValue)) ); + } + + subCol+=incr; + } + + psTrace(__func__, 4, "---- %s(NAN) end ----\n", __func__); + return(NAN); +} + +/****************************************************************************** +new implementation of source contour function +*****************************************************************************/ +psArray *pmSourceContour (psImage *image, int xc, int yc, float threshold) +{ + + int xR, yR, x0, x1, x0s, x1s; + + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(image, false); + + int x = xc - image->col0; + int y = yc - image->row0; + + // the requested point must be within the contour + if (image->data.F32[y][x] < threshold) + return NULL; + + // Ensure that the starting column is allowable. + if (x < 0) + return NULL; + if (y < 0) + return NULL; + if (x >= image->numCols) + return NULL; + if (y >= image->numRows) + return NULL; + + // Allocate data for x/y pairs. + psVector *xVec = psVectorAlloc(100, PS_TYPE_F32); + psVector *yVec = psVectorAlloc(100, PS_TYPE_F32); + + // First row: find the left and right end-points + int Npt = 0; + + x0 = findContourNeg (image, threshold, x, y, LEFT); + x1 = findContourNeg (image, threshold, x, y, RIGHT); + xVec->data.F32[Npt + 0] = image->col0 + x0; + xVec->data.F32[Npt + 1] = image->col0 + x1; + yVec->data.F32[Npt + 0] = image->row0 + y; + yVec->data.F32[Npt + 1] = image->row0 + y; + Npt += 2; + + x0s = x0; + x1s = x1; + + // look for contour outline above row + xR = x0s; + yR = y + 1; + while (yR < image->numRows) { + if (image->data.F32[yR][xR] < threshold) { + x0 = findContourPos (image, threshold, xR, yR, RIGHT, x1); + if (x0 == x1) { + // fprintf (stderr, "top: %d (%d - %d)\n", yR, xR, x1); + goto pt1; + } + x1 = findContourNeg (image, threshold, x0, yR, RIGHT); + x0--; + } else { + x0 = findContourNeg (image, threshold, xR, yR, LEFT); + x1 = findContourNeg (image, threshold, xR, yR, RIGHT); + } + // fprintf (stderr, "pos: %d (%d - %d)\n", yR, x0, x1); + + xVec->data.F32[Npt + 0] = image->col0 + x0; + xVec->data.F32[Npt + 1] = image->col0 + x1; + yVec->data.F32[Npt + 0] = image->row0 + yR; + yVec->data.F32[Npt + 1] = image->row0 + yR; + Npt += 2; + + if (Npt >= xVec->nalloc - 1) { + psVectorRealloc (xVec, xVec->nalloc + 100); + psVectorRealloc (yVec, yVec->nalloc + 100); + } + yR ++; + xR = x0; + } + +pt1: + // look for contour outline below row + xR = x0s; + x1 = x1s; + yR = y - 1; + while (yR >= 0) { + if (image->data.F32[yR][xR] < threshold) { + x0 = findContourPos (image, threshold, xR, yR, RIGHT, x1); + if (x0 == x1) { + // fprintf (stderr, "top: %d (%d - %d)\n", yR, xR, x1); + goto pt2; + } + x1 = findContourNeg (image, threshold, x0, yR, RIGHT); + x0--; + } else { + x0 = findContourNeg (image, threshold, xR, yR, LEFT); + x1 = findContourNeg (image, threshold, xR, yR, RIGHT); + } + // fprintf (stderr, "neg: %d (%d - %d)\n", yR, x0, x1); + + xVec->data.F32[Npt + 0] = image->col0 + x0; + xVec->data.F32[Npt + 1] = image->col0 + x1; + yVec->data.F32[Npt + 0] = image->row0 + yR; + yVec->data.F32[Npt + 1] = image->row0 + yR; + Npt += 2; + + if (Npt >= xVec->nalloc - 1) { + psVectorRealloc (xVec, xVec->nalloc + 100); + psVectorRealloc (yVec, yVec->nalloc + 100); + } + yR --; + } +pt2: + xVec->n = Npt; + yVec->n = Npt; + + // fprintf (stderr, "done\n"); + psArray *tmpArray = psArrayAlloc(2); + tmpArray->data[0] = (psPtr *) xVec; + tmpArray->data[1] = (psPtr *) yVec; + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmpArray); +} + +/****************************************************************************** + pmSourceContour(src, img, level, mode): For an input subImage, and model, this + routine returns a psArray of coordinates that evaluate to the specified level. + + XXX: Probably should remove the "image" argument. + XXX: What type should the output coordinate vectors consist of? col,row? + XXX: Why a pmArray output? + XXX: doex x,y correspond with col,row or row/col? + XXX: What is mode? + XXX: The top, bottom of the contour is not correctly determined. + XXX EAM : this function is using the model for the contour, but it should + be using only the image counts +*****************************************************************************/ +psArray *pmSourceContour_Crude(pmSource *source, + const psImage *image, + psF32 level) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source, false); + PS_ASSERT_PTR_NON_NULL(image, false); + PS_ASSERT_PTR_NON_NULL(source->moments, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + PS_ASSERT_PTR_NON_NULL(source->pixels, false); + PS_ASSERT_PTR_NON_NULL(source->modelEXT, false); + // XXX EAM : what is the purpose of modelPSF/modelEXT? + + // + // Allocate data for x/y pairs. + // + psVector *xVec = psVectorAlloc(2 * source->pixels->numRows, PS_TYPE_F32); + psVector *yVec = psVectorAlloc(2 * source->pixels->numRows, PS_TYPE_F32); + + // + // Start at the row with peak pixel, then decrement. + // + psS32 col = source->peak->x; + for (psS32 row = source->peak->y; row>= 0 ; row--) { + // XXX: yVec contain no real information. Do we really need it? + yVec->data.F32[row] = (psF32) (source->pixels->row0 + row); + yVec->data.F32[row+yVec->n] = (psF32) (source->pixels->row0 + row); + + // Starting at peak pixel, search leftwards for the column intercept. + psF32 leftIntercept = findValue(source, level, row, col, 0); + if (isnan(leftIntercept)) { + psError(PS_ERR_UNKNOWN, true, "Could not find contour edge (NAN)"); + psFree(xVec); + psFree(yVec); + psTrace(__func__, 3, "---- %s(NULL) end ----\n", __func__); + return(NULL); + //psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not find contour edge (NAN)\n"); + } + xVec->data.F32[row] = ((psF32) source->pixels->col0) + leftIntercept; + + // Starting at peak pixel, search rightwards for the column intercept. + + psF32 rightIntercept = findValue(source, level, row, col, 1); + if (isnan(rightIntercept)) { + psError(PS_ERR_UNKNOWN, true, "Could not find contour edge (NAN)"); + psFree(xVec); + psFree(yVec); + psTrace(__func__, 3, "---- %s(NULL) end ----\n", __func__); + return(NULL); + //psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not find contour edge (NAN)\n"); + } + psTrace(__func__, 4, "The intercepts are (%.2f, %.2f)\n", leftIntercept, rightIntercept); + xVec->data.F32[row+xVec->n] = ((psF32) source->pixels->col0) + rightIntercept; + + // Set starting column for next row + col = (psS32) ((leftIntercept + rightIntercept) / 2.0); + } + // + // Start at the row (+1) with peak pixel, then increment. + // + col = source->peak->x; + for (psS32 row = 1 + source->peak->y; row < source->pixels->numRows ; row++) { + // XXX: yVec contain no real information. Do we really need it? + yVec->data.F32[row] = (psF32) (source->pixels->row0 + row); + yVec->data.F32[row+yVec->n] = (psF32) (source->pixels->row0 + row); + + // Starting at peak pixel, search leftwards for the column intercept. + psF32 leftIntercept = findValue(source, level, row, col, 0); + if (isnan(leftIntercept)) { + psError(PS_ERR_UNKNOWN, true, "Could not find contour edge (NAN)"); + psFree(xVec); + psFree(yVec); + psTrace(__func__, 3, "---- %s(NULL) end ----\n", __func__); + return(NULL); + //psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not find contour edge (NAN)\n"); + } + xVec->data.F32[row] = ((psF32) source->pixels->col0) + leftIntercept; + + // Starting at peak pixel, search rightwards for the column intercept. + psF32 rightIntercept = findValue(source, level, row, col, 1); + if (isnan(rightIntercept)) { + psError(PS_ERR_UNKNOWN, true, "Could not find contour edge (NAN)"); + psFree(xVec); + psFree(yVec); + psTrace(__func__, 3, "---- %s(NULL) end ----\n", __func__); + return(NULL); + //psLogMsg(__func__, PS_LOG_WARN, "WARNING: Could not find contour edge (NAN)\n"); + } + xVec->data.F32[row+xVec->n] = ((psF32) source->pixels->col0) + rightIntercept; + + // Set starting column for next row + col = (psS32) ((leftIntercept + rightIntercept) / 2.0); + } + + // + // Allocate an array for result, store coord vectors there. + // + psArray *tmpArray = psArrayAlloc(2); + tmpArray->data[0] = (psPtr *) yVec; + tmpArray->data[1] = (psPtr *) xVec; + psTrace(__func__, 3, "---- %s() end ----\n", __func__); + return(tmpArray); +} Index: trunk/psModules/src/objects/pmSourceContour.h =================================================================== --- trunk/psModules/src/objects/pmSourceContour.h (revision 6872) +++ trunk/psModules/src/objects/pmSourceContour.h (revision 6872) @@ -0,0 +1,37 @@ +/** @file pmSourceContour.h + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_SOURCE_CONTOUR_H +# define PM_SOURCE_CONTOUR_H + +psArray *pmSourceContour (psImage *image, int xc, int yc, float threshold); + + +/** pmSourceContour() + * + * Find points in a contour for the given source at the given level. If type + * is PM_CONTOUR_CRUDE, the contour is found by starting at the source peak, + * running along each pixel row until the level is crossed, then interpolating to + * the level coordinate for that row. This is done for each row, with the + * starting point determined by the midpoint of the previous row, until the + * starting point has a value below the contour level. The returned contour + * consists of two vectors giving the x and y coordinates of the contour levels. + * This function may be used as part of the model guess inputs. Other contour + * types may be specified in the future for more refined contours (TBD) + * + */ +psArray *pmSourceContour_Crude( + pmSource *source, ///< The input pmSource + const psImage *image, ///< The input image (float) (this arg should be removed) + float level ///< The level of the contour +); + +# endif /* PM_SOURCE_PHOTOMETRY_H */ Index: trunk/psModules/src/objects/pmSourceFitModel.c =================================================================== --- trunk/psModules/src/objects/pmSourceFitModel.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceFitModel.c (revision 6872) @@ -0,0 +1,559 @@ +/** @file pmSourceFitModel.c + * + * fit single source models to image pixels + * + * @author EAM, IfA + * @author GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceFitModel.h" + +// save as static values so they may be set externally +static psF32 PM_SOURCE_FIT_MODEL_NUM_ITERATIONS = 15; +static psF32 PM_SOURCE_FIT_MODEL_TOLERANCE = 0.1; +static bool PM_PSF_POISSON_WEIGHTS = true; + +bool pmSourceFitModelInit (float nIter, float tol, bool poissonErrors) +{ + + PM_SOURCE_FIT_MODEL_NUM_ITERATIONS = nIter; + PM_SOURCE_FIT_MODEL_TOLERANCE = tol; + PM_PSF_POISSON_WEIGHTS = poissonErrors; + + return true; +} + +bool pmSourceFitModel (pmSource *source, + pmModel *model, + pmSourceFitMode mode) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source, false); + PS_ASSERT_PTR_NON_NULL(source->moments, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + PS_ASSERT_PTR_NON_NULL(source->pixels, false); + PS_ASSERT_PTR_NON_NULL(source->mask, false); + PS_ASSERT_PTR_NON_NULL(source->weight, false); + + // XXX EAM : is it necessary for the mask & weight to exist? the + // tests below could be conditions (!NULL) + + psBool fitStatus = true; + psBool onPic = true; + psBool rc = true; + + psVector *params = model->params; + psVector *dparams = model->dparams; + psVector *paramMask = NULL; + + pmModelFunc modelFunc = pmModelFunc_GetFunction (model->type); + + psF32 dSky = source->moments->dSky; + + // maximum number of valid pixels + psS32 nPix = source->pixels->numRows * source->pixels->numCols; + + // construct the coordinate and value entries + psArray *x = psArrayAlloc(nPix); + psVector *y = psVectorAlloc(nPix, PS_TYPE_F32); + psVector *yErr = psVectorAlloc(nPix, PS_TYPE_F32); + + nPix = 0; + for (psS32 i = 0; i < source->pixels->numRows; i++) { + for (psS32 j = 0; j < source->pixels->numCols; j++) { + // skip masked points + if (source->mask->data.U8[i][j]) { + continue; + } + // skip zero-weight points + if (source->weight->data.F32[i][j] == 0) { + continue; + } + + psVector *coord = psVectorAlloc(2, PS_TYPE_F32); + + // Convert i/j to image space: + coord->data.F32[0] = (psF32) (j + source->pixels->col0); + coord->data.F32[1] = (psF32) (i + source->pixels->row0); + x->data[nPix] = (psPtr *) coord; + y->data.F32[nPix] = source->pixels->data.F32[i][j]; + // psMinimizeLMChi2 takes wt = 1/dY^2 + if (PM_PSF_POISSON_WEIGHTS) { + yErr->data.F32[nPix] = 1.0 / source->weight->data.F32[i][j]; + } else { + yErr->data.F32[nPix] = 1.0 / dSky; + } + // XXX EAM : suggestion from RHL is to use the local sky as weight + // to avoid the bias from systematic errors + // here we would just use the source sky variance + nPix++; + } + } + x->n = nPix; + y->n = nPix; + yErr->n = nPix; + + // XXX EAM : the new minimization API supplies the constraints as a struct + // XXX the chisq if a fcn of source flux. the minimization criterion should + // probably be scaled somehow by flux. measure the trend? it depends on + // the about of systematic error in the models themselves... + psMinimization *myMin = psMinimizationAlloc(PM_SOURCE_FIT_MODEL_NUM_ITERATIONS, + PM_SOURCE_FIT_MODEL_TOLERANCE); + psMinConstrain *constrain = psMinConstrainAlloc(); + + // set parameter mask based on fitting mode + paramMask = psVectorAlloc (params->n, PS_TYPE_U8); + psVectorInit (paramMask, 1); + + int nParams = 0; + switch (mode) { + case PM_SOURCE_FIT_NORM: + // NORM-only model fits only source normalization (Io) + nParams = 1; + paramMask->data.U8[1] = 0; + break; + case PM_SOURCE_FIT_PSF: + // PSF model only fits x,y,Io + nParams = 3; + paramMask->data.U8[1] = 0; + paramMask->data.U8[2] = 0; + paramMask->data.U8[3] = 0; + break; + case PM_SOURCE_FIT_EXT: + // EXT model fits all params (except sky) + nParams = params->n - 1; + psVectorInit (paramMask, 0); + paramMask->data.U8[0] = 1; + break; + case PM_SOURCE_FIT_PSF_AND_SKY: + nParams = 4; + psAbort ("pmSourceFitModel", "PSF + SKY not currently available"); + break; + case PM_SOURCE_FIT_EXT_AND_SKY: + nParams = params->n; + psAbort ("pmSourceFitModel", "EXT + SKY not currently available"); + break; + default: + psAbort ("pmSourceFitModel", "invalid fitting mode"); + } + constrain->paramMask = paramMask; + + if (nPix < nParams + 1) { + psTrace (".pmObjects.pmSourceFitModel", 4, "insufficient valid pixels\n"); + psTrace(__func__, 3, "---- %s(false) end ----\n", __func__); + model->status = PM_MODEL_BADARGS; + psFree (x); + psFree (y); + psFree (yErr); + psFree (myMin); + psFree (constrain); + psFree (paramMask); + return(false); + } + + // Set the parameter range checks + pmModelLimits modelLimits = pmModelLimits_GetFunction (model->type); + modelLimits (&constrain->paramDelta, &constrain->paramMin, &constrain->paramMax); + + psImage *covar = psImageAlloc (params->n, params->n, PS_TYPE_F64); + + psTrace (".pmObjects.pmSourceFitModel", 5, "fitting function\n"); + + fitStatus = psMinimizeLMChi2(myMin, covar, params, constrain, x, y, yErr, modelFunc); + for (int i = 0; i < dparams->n; i++) { + if ((paramMask != NULL) && paramMask->data.U8[i]) + continue; + dparams->data.F32[i] = sqrt(covar->data.F64[i][i]); + } + + // save the resulting chisq, nDOF, nIter + model->chisq = myMin->value; + model->nIter = myMin->iter; + model->nDOF = y->n - nParams; + + // get the Gauss-Newton distance for fixed model parameters + if (paramMask != NULL) { + psVector *delta = psVectorAlloc (params->n, PS_TYPE_F64); + psMinimizeGaussNewtonDelta(delta, params, NULL, x, y, yErr, modelFunc); + for (int i = 0; i < dparams->n; i++) { + if (!paramMask->data.U8[i]) + continue; + dparams->data.F32[i] = delta->data.F64[i]; + } + psFree (delta); + } + + // set the model success or failure status + if (!fitStatus) { + model->status = PM_MODEL_NONCONVERGE; + } else { + model->status = PM_MODEL_SUCCESS; + } + + // models can go insane: reject these + onPic &= (params->data.F32[2] >= source->pixels->col0); + onPic &= (params->data.F32[2] < source->pixels->col0 + source->pixels->numCols); + onPic &= (params->data.F32[3] >= source->pixels->row0); + onPic &= (params->data.F32[3] < source->pixels->row0 + source->pixels->numRows); + if (!onPic) { + model->status = PM_MODEL_OFFIMAGE; + } + + source->mode |= PM_SOURCE_MODE_FITTED; + + psFree(x); + psFree(y); + psFree(yErr); + psFree(myMin); + psFree(covar); + psFree(constrain->paramMask); + psFree(constrain->paramMin); + psFree(constrain->paramMax); + psFree(constrain->paramDelta); + psFree(constrain); + + rc = (onPic && fitStatus); + psTrace(__func__, 3, "---- %s(%d) end ----\n", __func__, rc); + return(rc); +} + +/********************* Source Model Set Functions ***************************/ + +// these static variables are used by one pass of pmSourceFitSet to store +// data for a model set. If we are going to make psphot thread-safe, these +// will have to go in a structure of their own. +// sky, p1.1, p1.2, p1.3,... p1.n, p2.1, p2.2, +// nPar = nSrc*(nOnePar - 1) + 1 +static pmModelFunc mFunc; +static int nPar; +static psVector *onePar; +static psVector *oneDeriv; + +bool pmModelFitSetInit (pmModelType type) +{ + + mFunc = pmModelFunc_GetFunction (type); + nPar = pmModelParameterCount (type); + + onePar = psVectorAlloc (nPar, PS_DATA_F32); + oneDeriv = psVectorAlloc (nPar, PS_DATA_F32); + + return true; +} + +void pmModelFitSetClear (void) +{ + + psFree (onePar); + psFree (oneDeriv); + return; +} + +psF32 pmModelFitSet(psVector *deriv, + const psVector *params, + const psVector *x) +{ + + psF32 value; + psF32 model; + + psF32 *PAR = onePar->data.F32; + psF32 *dPAR = oneDeriv->data.F32; + + psF32 *pars = params->data.F32; + psF32 *dpars = (deriv == NULL) ? NULL : deriv->data.F32; + + int nSrc = (params->n - 1) / (nPar - 1); + + PAR[0] = model = pars[0]; + for (int i = 0; i < nSrc; i++) { + int nOff = i*nPar - i; + for (int n = 1; n < nPar; n++) { + PAR[n] = pars[nOff + n]; + } + if (deriv == NULL) { + value = mFunc (NULL, onePar, x); + } else { + value = mFunc (oneDeriv, onePar, x); + for (int n = 1; n < nPar; n++) { + dpars[nOff + n] = dPAR[n]; + } + } + model += value; + } + if (deriv != NULL) { + dpars[0] = dPAR[0]*2.0; + } + return (model); +} + +/* +i: 0 1 2 +n: 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 +i*6 + n: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 +*/ + +bool pmSourceFitSet (pmSource *source, + psArray *modelSet, + pmSourceFitMode mode) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source, false); + PS_ASSERT_PTR_NON_NULL(source->moments, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + PS_ASSERT_PTR_NON_NULL(source->pixels, false); + PS_ASSERT_PTR_NON_NULL(source->mask, false); + PS_ASSERT_PTR_NON_NULL(source->weight, false); + + psBool fitStatus = true; + psBool onPic = true; + psBool rc = true; + + // base values on first model + pmModel *model = modelSet->data[0]; + + // set the static variables + pmModelFitSetInit (model->type); + + int nSrc = modelSet->n; + int nPar = model->params->n - 1; // number of object parameters (excluding sky) + + // define parameter vectors for source set + psVector *params = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + psVector *dparams = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + + pmModelLimits modelLimits = pmModelLimits_GetFunction (model->type); + + // define limits for a single-source model + psVector *oneDelta; + psVector *oneParMin; + psVector *oneParMax; + modelLimits (&oneDelta, &oneParMin, &oneParMax); + + psMinConstrain *constrain = psMinConstrainAlloc(); + constrain->paramMin = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + constrain->paramMax = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + constrain->paramMask = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_U8); + constrain->paramDelta = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + + // set the parameter guesses and constraints for the multiple models + // first the values for the single sky parameter + params->data.F32[0] = model->params->data.F32[0]; + constrain->paramMin->data.F32[0] = oneParMin->data.F32[0]; + constrain->paramMax->data.F32[0] = oneParMax->data.F32[0]; + constrain->paramDelta->data.F32[0] = oneDelta->data.F32[0]; + + // next, the values for the source parameters + for (int i = 0; i < nSrc; i++) { + model = modelSet->data[i]; + for (int n = 1; n < nPar + 1; n++) { + params->data.F32[i*nPar + n] = model->params->data.F32[n]; + constrain->paramDelta->data.F32[i*nPar + n] = oneDelta->data.F32[n]; + constrain->paramMin->data.F32[i*nPar + n] = oneParMin->data.F32[n]; + constrain->paramMax->data.F32[i*nPar + n] = oneParMax->data.F32[n]; + } + } + psFree (oneDelta); + psFree (oneParMin); + psFree (oneParMax); + + if (psTraceGetLevel(__func__) >= 5) { + for (int i = 0; i < params->n; i++) { + fprintf (stderr, "%d %f %d\n", i, params->data.F32[i], constrain->paramMask->data.U8[i]); + } + } + + // set the parameter masks based on the fitting mode + int nParams = 0; + switch (mode) { + case PM_SOURCE_FIT_NORM: + // NORM-only model fits only source normalization (Io) + nParams = nSrc; + psVectorInit (constrain->paramMask, 1); + for (int i = 0; i < nSrc; i++) { + constrain->paramMask->data.U8[1 + i*nPar] = 0; + } + break; + case PM_SOURCE_FIT_PSF: + // PSF model only fits x,y,Io + nParams = 3*nSrc; + psVectorInit (constrain->paramMask, 1); + for (int i = 0; i < nSrc; i++) { + constrain->paramMask->data.U8[1 + i*nPar] = 0; + constrain->paramMask->data.U8[2 + i*nPar] = 0; + constrain->paramMask->data.U8[3 + i*nPar] = 0; + } + break; + case PM_SOURCE_FIT_EXT: + // EXT model fits all params (except sky) + nParams = nPar*nSrc; + psVectorInit (constrain->paramMask, 0); + constrain->paramMask->data.U8[0] = 1; + break; + case PM_SOURCE_FIT_PSF_AND_SKY: + nParams = 1 + 3*nSrc; + psAbort ("pmSourceFitModel", "PSF + SKY not currently available"); + break; + case PM_SOURCE_FIT_EXT_AND_SKY: + nParams = 1 + nPar*nSrc; + psAbort ("pmSourceFitModel", "EXT + SKY not currently available"); + break; + default: + psAbort ("pmSourceFitModel", "invalid fitting mode"); + } + + // maximum number of valid pixels + psS32 nPix = source->pixels->numRows * source->pixels->numCols; + + // local sky variance + psF32 dSky = source->moments->dSky; + + // construct the coordinate and value entries + psArray *x = psArrayAlloc(nPix); + psVector *y = psVectorAlloc(nPix, PS_TYPE_F32); + psVector *yErr = psVectorAlloc(nPix, PS_TYPE_F32); + + nPix = 0; + for (psS32 i = 0; i < source->pixels->numRows; i++) { + for (psS32 j = 0; j < source->pixels->numCols; j++) { + // skip masked points + if (source->mask->data.U8[i][j]) { + continue; + } + // skip zero-weight points + if (source->weight->data.F32[i][j] == 0) { + continue; + } + psVector *coord = psVectorAlloc(2, PS_TYPE_F32); + + // Convert i/j to image space: + coord->data.F32[0] = (psF32) (j + source->pixels->col0); + coord->data.F32[1] = (psF32) (i + source->pixels->row0); + x->data[nPix] = (psPtr *) coord; + y->data.F32[nPix] = source->pixels->data.F32[i][j]; + // psMinimizeLMChi2 takes wt = 1/dY^2 + if (PM_PSF_POISSON_WEIGHTS) { + yErr->data.F32[nPix] = 1.0 / source->weight->data.F32[i][j]; + } else { + yErr->data.F32[nPix] = 1.0 / dSky; + } + nPix++; + } + } + if (nPix < nParams + 1) { + psTrace (__func__, 4, "insufficient valid pixels\n"); + psTrace(__func__, 3, "---- %s() end : fail pixels ----\n", __func__); + model->status = PM_MODEL_BADARGS; + psFree (x); + psFree (y); + psFree (yErr); + psFree (params); + psFree (dparams); + psFree(constrain->paramMask); + psFree(constrain->paramMin); + psFree(constrain->paramMax); + psFree(constrain->paramDelta); + psFree(constrain); + return(false); + } + x->n = nPix; + y->n = nPix; + yErr->n = nPix; + + psMinimization *myMin = psMinimizationAlloc(PM_SOURCE_FIT_MODEL_NUM_ITERATIONS, + PM_SOURCE_FIT_MODEL_TOLERANCE); + + psImage *covar = psImageAlloc (params->n, params->n, PS_TYPE_F64); + + psTrace (__func__, 5, "fitting function\n"); + fitStatus = psMinimizeLMChi2(myMin, covar, params, constrain, x, y, yErr, pmModelFitSet); + + // parameter errors from the covariance matrix + for (int i = 0; i < dparams->n; i++) { + if ((constrain->paramMask != NULL) && constrain->paramMask->data.U8[i]) + continue; + dparams->data.F32[i] = sqrt(covar->data.F64[i][i]); + } + + // get the Gauss-Newton distance for fixed model parameters + if (constrain->paramMask != NULL) { + psVector *delta = psVectorAlloc (params->n, PS_TYPE_F64); + psMinimizeGaussNewtonDelta(delta, params, NULL, x, y, yErr, pmModelFitSet); + for (int i = 0; i < dparams->n; i++) { + if (!constrain->paramMask->data.U8[i]) + continue; + dparams->data.F32[i] = delta->data.F64[i]; + } + psFree (delta); + } + + // assign back the parameters to the models + for (int i = 0; i < nSrc; i++) { + model = modelSet->data[i]; + model->params->data.F32[0] = params->data.F32[0]; + for (int n = 1; n < nPar + 1; n++) { + model->params->data.F32[n] = params->data.F32[i*nPar + n]; + model->dparams->data.F32[n] = dparams->data.F32[i*nPar + n]; + } + // save the resulting chisq, nDOF, nIter + // these are not unique for any one source + model->chisq = myMin->value; + model->nIter = myMin->iter; + model->nDOF = y->n - nParams; + + // set the model success or failure status + model->status = fitStatus ? PM_MODEL_SUCCESS : PM_MODEL_NONCONVERGE; + + // models can go insane: reject these + onPic &= (model->params->data.F32[2] >= source->pixels->col0); + onPic &= (model->params->data.F32[2] < source->pixels->col0 + source->pixels->numCols); + onPic &= (model->params->data.F32[3] >= source->pixels->row0); + onPic &= (model->params->data.F32[3] < source->pixels->row0 + source->pixels->numRows); + if (!onPic) { + model->status = PM_MODEL_OFFIMAGE; + } + } + + source->mode |= PM_SOURCE_MODE_FITTED; + + psFree(x); + psFree(y); + psFree(yErr); + psFree(myMin); + psFree(covar); + psFree(constrain->paramMask); + psFree(constrain->paramMin); + psFree(constrain->paramMax); + psFree(constrain->paramDelta); + psFree(constrain); + psFree(params); + psFree(dparams); + + // free static memory used by pmModelFitSet + pmModelFitSetClear (); + + rc = (onPic && fitStatus); + psTrace (__func__, 5, "onPic: %d, fitStatus: %d, nIter: %d, chisq: %f, nDof: %d\n", onPic, fitStatus, model->nIter, model->chisq, model->nDOF); + psTrace(__func__, 3, "---- %s end : status %d ----\n", __func__, rc); + return(rc); +} + Index: trunk/psModules/src/objects/pmSourceFitModel.h =================================================================== --- trunk/psModules/src/objects/pmSourceFitModel.h (revision 6872) +++ trunk/psModules/src/objects/pmSourceFitModel.h (revision 6872) @@ -0,0 +1,69 @@ +/** @file pmSourceFitModel.h + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_SOURCE_FIT_MODEL_H +# define PM_SOURCE_FIT_MODEL_H + +typedef enum { + PM_SOURCE_FIT_NORM, + PM_SOURCE_FIT_PSF, + PM_SOURCE_FIT_EXT, + PM_SOURCE_FIT_PSF_AND_SKY, + PM_SOURCE_FIT_EXT_AND_SKY +} pmSourceFitMode; + +bool pmSourceFitModelInit( + float nIter, ///< max number of allowed iterations + float tol, ///< convergence criterion + bool poissonErrors // use poisson errors for fits? +); + +/** pmSourceFitModel() + * + * Fit the requested model to the specified source. The starting guess for the model is given + * by the input source.model parameter values. The pixels of interest are specified by the + * source.pixels and source.mask entries. This function calls psMinimizeLMChi2() on the image + * data. The function returns TRUE on success or FALSE on failure. + * + */ +bool pmSourceFitModel( + pmSource *source, ///< The input pmSource + pmModel *model, ///< model to be fitted + pmSourceFitMode mode ///< define parameters to be fitted +); + + +// initialize data for a group of object models +bool pmModelFitSetInit (pmModelType type); + +// clear data for a group of object models +void pmModelFitSetClear (void); + +// function used to fit a group of object models +psF32 pmModelFitSet(psVector *deriv, + const psVector *params, + const psVector *x); + +/** pmSourceFitSet() + * + * Fit the requested model to the specified source. The starting guess for the model is given + * by the input source.model parameter values. The pixels of interest are specified by the + * source.pixels and source.mask entries. This function calls psMinimizeLMChi2() on the image + * data. The function returns TRUE on success or FALSE on failure. + * + */ +bool pmSourceFitSet( + pmSource *source, ///< The input pmSource + psArray *modelSet, ///< model to be fitted + pmSourceFitMode mode ///< define parameters to be fitted +); + +# endif /* PM_SOURCE_FIT_MODEL_H */ Index: trunk/psModules/src/objects/pmSourceFitSet.c =================================================================== --- trunk/psModules/src/objects/pmSourceFitSet.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceFitSet.c (revision 6872) @@ -0,0 +1,334 @@ +/** @file pmSourceFitSet.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceFitSet.h" + +// sky, p1.1, p1.2, p1.3,... p1.n, p2.1, p2.2, +// nPar = nSrc*(nOnePar - 1) + 1 + +static pmModelFunc mFunc; +static int nPar; +static psVector *onePar; +static psVector *oneDeriv; + +// save as static values so they may be set externally +static psF32 PM_SOURCE_FIT_MODEL_NUM_ITERATIONS = 15; +static psF32 PM_SOURCE_FIT_MODEL_TOLERANCE = 0.1; +static bool PM_PSF_POISSON_WEIGHTS = true; + +bool pmSourceFitSetInit (float nIter, float tol, bool poissonErrors) +{ + + PM_SOURCE_FIT_MODEL_NUM_ITERATIONS = nIter; + PM_SOURCE_FIT_MODEL_TOLERANCE = tol; + + PM_PSF_POISSON_WEIGHTS = poissonErrors; + + return true; +} + +bool pmModelFitSetInit (pmModelType type) +{ + + mFunc = pmModelFunc_GetFunction (type); + nPar = pmModelParameterCount (type); + + onePar = psVectorAlloc (nPar, PS_DATA_F32); + oneDeriv = psVectorAlloc (nPar, PS_DATA_F32); + + return true; +} + +void pmModelFitSetClear (void) +{ + + psFree (onePar); + psFree (oneDeriv); + return; +} + +psF32 pmModelFitSet(psVector *deriv, + const psVector *params, + const psVector *x) +{ + + psF32 value; + psF32 model; + + psF32 *PAR = onePar->data.F32; + psF32 *dPAR = oneDeriv->data.F32; + + psF32 *pars = params->data.F32; + psF32 *dpars = (deriv == NULL) ? NULL : deriv->data.F32; + + int nSrc = (params->n - 1) / (nPar - 1); + + PAR[0] = model = pars[0]; + for (int i = 0; i < nSrc; i++) { + int nOff = i*nPar - i; + for (int n = 1; n < nPar; n++) { + PAR[n] = pars[nOff + n]; + } + if (deriv == NULL) { + value = mFunc (NULL, onePar, x); + } else { + value = mFunc (oneDeriv, onePar, x); + for (int n = 1; n < nPar; n++) { + dpars[nOff + n] = dPAR[n]; + } + } + model += value; + } + if (deriv != NULL) { + dpars[0] = dPAR[0]*2.0; + } + return (model); +} + +/* +i: 0 1 2 +n: 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 +i*6 + n: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 +*/ + +/* +# define PM_SOURCE_FIT_MODEL_NUM_ITERATIONS 15 +# define PM_SOURCE_FIT_MODEL_TOLERANCE 0.1 +*/ + +bool pmSourceFitSet (pmSource *source, + psArray *modelSet, + const bool PSF) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source, false); + PS_ASSERT_PTR_NON_NULL(source->moments, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + PS_ASSERT_PTR_NON_NULL(source->pixels, false); + PS_ASSERT_PTR_NON_NULL(source->mask, false); + PS_ASSERT_PTR_NON_NULL(source->weight, false); + + psBool fitStatus = true; + psBool onPic = true; + psBool rc = true; + + // base values on first model + pmModel *model = modelSet->data[0]; + + // set the static variables + pmModelFitSetInit (model->type); + + int nSrc = modelSet->n; + int nPar = model->params->n - 1; // number of object parameters (excluding sky) + + // define parameter vectors for source set + psVector *params = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + psVector *dparams = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + + pmModelLimits modelLimits = pmModelLimits_GetFunction (model->type); + + // define limits for single-source model + psVector *oneDelta; + psVector *oneParMin; + psVector *oneParMax; + modelLimits (&oneDelta, &oneParMin, &oneParMax); + + psMinConstrain *constrain = psMinConstrainAlloc(); + constrain->paramDelta = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + constrain->paramMin = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + constrain->paramMax = psVectorAlloc (nSrc*nPar + 1, PS_TYPE_F32); + constrain->paramMask = PSF ? psVectorAlloc (nSrc*nPar + 1, PS_TYPE_U8) : NULL; + + // all but the sky are allowed to vary independently (subject to PSF) + // set the parameters from the multiple models + // also, set limits based on single-source limits + params->data.F32[0] = model->params->data.F32[0]; + constrain->paramDelta->data.F32[0] = oneDelta->data.F32[0]; + constrain->paramMin->data.F32[0] = oneParMin->data.F32[0]; + constrain->paramMax->data.F32[0] = oneParMax->data.F32[0]; + + // XXX all models skip the sky + constrain->paramMask->data.U8[0] = 1; + for (int i = 0; i < nSrc; i++) { + model = modelSet->data[i]; + for (int n = 1; n < nPar + 1; n++) { + params->data.F32[i*nPar + n] = model->params->data.F32[n]; + dparams->data.F32[i*nPar + n] = model->dparams->data.F32[n]; + constrain->paramDelta->data.F32[i*nPar + n] = oneDelta->data.F32[n]; + constrain->paramMin->data.F32[i*nPar + n] = oneParMin->data.F32[n]; + constrain->paramMax->data.F32[i*nPar + n] = oneParMax->data.F32[n]; + if (PSF) { + constrain->paramMask->data.U8[i*nPar + n] = (n < 4) ? 0 : 1; + } + } + } + psFree (oneDelta); + psFree (oneParMin); + psFree (oneParMax); + + if (psTraceGetLevel(__func__) >= 5) { + for (int i = 0; i < params->n; i++) { + fprintf (stderr, "%d %f %d\n", i, params->data.F32[i], constrain->paramMask->data.U8[i]); + } + } + + // PSF model only fits first 4 parameters, EXT model fits all + int nParams = PSF ? nSrc*3 + 1 : nSrc*nPar + 1; + + // maximum number of valid pixels + psS32 nPix = source->pixels->numRows * source->pixels->numCols; + + // local sky variance + psF32 dSky = source->moments->dSky; + + // construct the coordinate and value entries + psArray *x = psArrayAlloc(nPix); + psVector *y = psVectorAlloc(nPix, PS_TYPE_F32); + psVector *yErr = psVectorAlloc(nPix, PS_TYPE_F32); + + nPix = 0; + for (psS32 i = 0; i < source->pixels->numRows; i++) { + for (psS32 j = 0; j < source->pixels->numCols; j++) { + // skip masked points + if (source->mask->data.U8[i][j]) { + continue; + } + // skip zero-weight points + if (source->weight->data.F32[i][j] == 0) { + continue; + } + psVector *coord = psVectorAlloc(2, PS_TYPE_F32); + + // Convert i/j to image space: + coord->data.F32[0] = (psF32) (j + source->pixels->col0); + coord->data.F32[1] = (psF32) (i + source->pixels->row0); + x->data[nPix] = (psPtr *) coord; + y->data.F32[nPix] = source->pixels->data.F32[i][j]; + // psMinimizeLMChi2 takes wt = 1/dY^2 + if (PM_PSF_POISSON_WEIGHTS) { + yErr->data.F32[nPix] = 1.0 / source->weight->data.F32[i][j]; + } else { + yErr->data.F32[nPix] = 1.0 / dSky; + } + nPix++; + } + } + if (nPix < nParams + 1) { + psTrace (__func__, 4, "insufficient valid pixels\n"); + psTrace(__func__, 3, "---- %s() end : fail pixels ----\n", __func__); + model->status = PM_MODEL_BADARGS; + psFree (x); + psFree (y); + psFree (yErr); + psFree (params); + psFree (dparams); + psFree(constrain->paramMask); + psFree(constrain->paramMin); + psFree(constrain->paramMax); + psFree(constrain->paramDelta); + psFree(constrain); + return(false); + } + x->n = nPix; + y->n = nPix; + yErr->n = nPix; + + psMinimization *myMin = psMinimizationAlloc(PM_SOURCE_FIT_MODEL_NUM_ITERATIONS, + PM_SOURCE_FIT_MODEL_TOLERANCE); + + psImage *covar = psImageAlloc (params->n, params->n, PS_TYPE_F64); + + psTrace (__func__, 5, "fitting function\n"); + fitStatus = psMinimizeLMChi2(myMin, covar, params, constrain, x, y, yErr, pmModelFitSet); + + // parameter errors from the covariance matrix + for (int i = 0; i < dparams->n; i++) { + if ((constrain->paramMask != NULL) && constrain->paramMask->data.U8[i]) + continue; + dparams->data.F32[i] = sqrt(covar->data.F64[i][i]); + } + + // get the Gauss-Newton distance for fixed model parameters + if (constrain->paramMask != NULL) { + psVector *delta = psVectorAlloc (params->n, PS_TYPE_F64); + psMinimizeGaussNewtonDelta(delta, params, NULL, x, y, yErr, pmModelFitSet); + for (int i = 0; i < dparams->n; i++) { + if (!constrain->paramMask->data.U8[i]) + continue; + dparams->data.F32[i] = delta->data.F64[i]; + } + psFree (delta); + } + + // assign back the parameters to the models + for (int i = 0; i < nSrc; i++) { + model = modelSet->data[i]; + model->params->data.F32[0] = params->data.F32[0]; + for (int n = 1; n < nPar + 1; n++) { + model->params->data.F32[n] = params->data.F32[i*nPar + n]; + model->dparams->data.F32[n] = dparams->data.F32[i*nPar + n]; + } + // save the resulting chisq, nDOF, nIter + // these are not unique for any one source + model->chisq = myMin->value; + model->nIter = myMin->iter; + model->nDOF = y->n - nParams; + + // set the model success or failure status + model->status = fitStatus ? PM_MODEL_SUCCESS : PM_MODEL_NONCONVERGE; + + // models can go insane: reject these + onPic &= (model->params->data.F32[2] >= source->pixels->col0); + onPic &= (model->params->data.F32[2] < source->pixels->col0 + source->pixels->numCols); + onPic &= (model->params->data.F32[3] >= source->pixels->row0); + onPic &= (model->params->data.F32[3] < source->pixels->row0 + source->pixels->numRows); + if (!onPic) { + model->status = PM_MODEL_OFFIMAGE; + } + } + + source->mode |= PM_SOURCE_MODE_FITTED; + + psFree(x); + psFree(y); + psFree(yErr); + psFree(myMin); + psFree(covar); + psFree(constrain->paramMask); + psFree(constrain->paramMin); + psFree(constrain->paramMax); + psFree(constrain->paramDelta); + psFree(constrain); + psFree(params); + psFree(dparams); + + // free static memory used by pmModelFitSet + pmModelFitSetClear (); + + rc = (onPic && fitStatus); + psTrace (__func__, 5, "onPic: %d, fitStatus: %d, nIter: %d, chisq: %f, nDof: %d\n", onPic, fitStatus, model->nIter, model->chisq, model->nDOF); + psTrace(__func__, 3, "---- %s end : status %d ----\n", __func__, rc); + return(rc); +} + Index: trunk/psModules/src/objects/pmSourceFitSet.h =================================================================== --- trunk/psModules/src/objects/pmSourceFitSet.h (revision 6872) +++ trunk/psModules/src/objects/pmSourceFitSet.h (revision 6872) @@ -0,0 +1,40 @@ +/** @file pmSourceFitset.h + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_SOURCE_FIT_SET_H +# define PM_SOURCE_FIT_SET_H + +psF32 pmModelFitSet(psVector *deriv, + const psVector *params, + const psVector *x); + +bool pmModelFitSetInit (pmModelType type); + +void pmModelFitSetClear (void); + +bool pmSourceFitSetInit (float nIter, float tol, bool poissonErrors); + +/** pmSourceFitSet() + * + * Fit the requested model to the specified source. The starting guess for the + * model is given by the input source.model parameter values. The pixels of + * interest are specified by the source.pixelsand source.maskentries. This + * function calls psMinimizeLMChi2() on the image data. The function returns TRUE + * on success or FALSE on failure. + * + */ +bool pmSourceFitSet( + pmSource *source, ///< The input pmSource + psArray *modelSet, ///< model to be fitted + const bool PSF ///< Treat model as PSF or EXT? +); + +# endif /* PM_SOURCE_FIT_MODEL_H */ Index: trunk/psModules/src/objects/pmSourceIO.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceIO.c (revision 6872) @@ -0,0 +1,378 @@ +/** @file pmSourceIO.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "psAdditionals.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" + +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceIO.h" + +// translations between psphot object types and dophot object types +int pmSourceDophotType (pmSource *source) +{ + + switch (source->type) { + + case PM_SOURCE_TYPE_DEFECT: + case PM_SOURCE_TYPE_SATURATED: + return (8); + + case PM_SOURCE_TYPE_STAR: + if (source->mode & PM_SOURCE_MODE_SATSTAR) + return (10); + if (source->mode & PM_SOURCE_MODE_POOR) + return (7); + if (source->mode & PM_SOURCE_MODE_FAIL) + return (4); + return (1); + + case PM_SOURCE_TYPE_EXTENDED: + return (2); + + default: + return (0); + } + return (0); +} + +// Given a FITS file pointer, read the table of object data +bool pmFPAviewWriteObjects (const pmFPAview *view, pmFPAfile *file) +{ + + pmFPA *fpa = file->fpa; + + if (view->chip == -1) { + pmFPAWriteObjects (fpa, view, file); + return true; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + pmChipWriteObjects (chip, view, file); + return true; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellWriteObjects (cell, view, file); + return true; + } + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + pmReadoutWriteObjects (readout, view, file); + return true; +} + +// read in all chip-level Objects files for this FPA +bool pmFPAWriteObjects (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < fpa->chips->n; i++) { + + pmChip *chip = fpa->chips->data[i]; + pmChipWriteObjects (chip, view, file); + } + return true; +} + +// read in all cell-level Objects files for this chip +bool pmChipWriteObjects (pmChip *chip, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < chip->cells->n; i++) { + + pmCell *cell = chip->cells->data[i]; + pmCellWriteObjects (cell, view, file); + } + return true; +} + +// read in all readout-level Objects files for this cell +bool pmCellWriteObjects (pmCell *cell, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < cell->readouts->n; i++) { + + pmReadout *readout = cell->readouts->data[i]; + pmReadoutWriteObjects (readout, view, file); + } + return true; +} + +// read in all readout-level Objects files for this cell +bool pmReadoutWriteObjects (pmReadout *readout, const pmFPAview *view, pmFPAfile *file) +{ + + bool status; + char *filename; + char *dataname; + char *headname; + pmHDU *hdu; + pmHDU *phu; + psMetadata *updates; + psMetadata *outhead; + + psArray *sources = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.SOURCES"); + + switch (file->type) { + case PM_FPA_FILE_RAW: + filename = pmFPAfileNameFromRule (file->filerule, file, view); + pmSourcesWriteRAW (sources, filename); + psFree (filename); + break; + + case PM_FPA_FILE_OBJ: + filename = pmFPAfileNameFromRule (file->filerule, file, view); + pmSourcesWriteOBJ (sources, filename); + psFree (filename); + break; + + case PM_FPA_FILE_SX: + filename = pmFPAfileNameFromRule (file->filerule, file, view); + pmSourcesWriteSX (sources, filename); + psFree (filename); + break; + + case PM_FPA_FILE_CMP: + // a SPLIT format : only one header and object table per file + hdu = pmFPAviewThisHDU (view, file->fpa); + filename = pmFPAfileNameFromRule (file->filerule, file, view); + + // copy the header to an output header, add the output header data + outhead = psMetadataCopy (NULL, hdu->header); + + // check/fix first line (must be SIMPLE = F) + psMetadataItem *item = psMetadataGet (outhead, PS_LIST_HEAD); + if (strcmp (item->name, "SIMPLE") && strcmp (item->name, "XTENSION")) { + psErrorStackPrint(stderr, "invalid header: first line is neither SIMPLE nor XTENSION\n"); + exit(EXIT_FAILURE); + } + if (!strcmp (item->name, "XTENSION")) { + psMetadataRemoveIndex (outhead, PS_LIST_HEAD); + } + psMetadataAddBool (outhead, PS_LIST_HEAD, "SIMPLE", PS_META_REPLACE, "CMP file, not simple", false); + + // copy over the entries saved in the + updates = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.HEADER"); + psMetadataCopy (outhead, updates); + + pmSourcesWriteCMP (sources, filename, outhead); + psFree (outhead); + psFree (filename); + break; + + case PM_FPA_FILE_CMF: + // write a PHU? + // write a header? + // write the data + + // get the current header + hdu = pmFPAviewThisHDU (view, file->fpa); + + // if file does not yet have a PHU, write it to disk + if (file->phu == NULL) { + // get the corresponding phu + phu = pmFPAviewThisPHU (view, file->fpa); + + // CMF always has extensions + outhead = psMetadataCopy (NULL, phu->header); + psMetadataAdd (outhead, PS_LIST_TAIL, "EXTEND", PS_DATA_BOOL | PS_META_REPLACE, "this file has extensions", true); + psFitsWriteHeaderNotImage (file->fits, outhead); + file->phu = phu->header; + psTrace ("pmFPAfile", 5, "wrote phu %s (type: %d)\n", file->filename, file->type); + psFree (outhead); + } + + // this this header block is new, write it to disk, + if (hdu->header != file->header) { + // determine name for header extension + headname = pmFPAfileNameFromRule (file->extxtra, file, view); + outhead = psMetadataCopy (NULL, hdu->header); + psMetadataAddStr (outhead, PS_LIST_TAIL, "EXTNAME", PS_META_REPLACE, "extension name", headname); + psFitsWriteHeaderNotImage (file->fits, outhead); + psTrace ("pmFPAfile", 5, "wrote ext head %s (type: %d)\n", file->filename, file->type); + file->header = hdu->header; + psFree (outhead); + psFree (headname); + } + + // write this table to disk + dataname = pmFPAfileNameFromRule (file->extrule, file, view); + updates = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.HEADER"); + pmSourcesWriteCMF (file->fits, sources, updates, dataname); + psTrace ("pmFPAfile", 5, "wrote ext data %s (type: %d)\n", file->filename, file->type); + psFree (dataname); + break; + + default: + fprintf (stderr, "warning: type mismatch\n"); + break; + } + return true; +} +// a MEF CMF file has: PHU, CELL-HEAD, TABLE, CELL-HEAD, TABLE, TABLE, TABLE... + +// Given a FITS file pointer, read the table of object data +bool pmFPAviewReadObjects (const pmFPAview *view, pmFPAfile *file) +{ + pmFPA *fpa = file->fpa; + + if (view->chip == -1) { + pmFPAReadObjects (fpa, view, file); + return true; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + pmChipReadObjects (chip, view, file); + return true; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellReadObjects (cell, view, file); + return true; + } + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + pmReadoutReadObjects (readout, view, file); + return true; +} + +// read in all chip-level Objects files for this FPA +bool pmFPAReadObjects (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < fpa->chips->n; i++) { + + pmChip *chip = fpa->chips->data[i]; + pmChipReadObjects (chip, view, file); + } + return true; +} + +// read in all cell-level Objects files for this chip +bool pmChipReadObjects (pmChip *chip, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < chip->cells->n; i++) { + + pmCell *cell = chip->cells->data[i]; + pmCellReadObjects (cell, view, file); + } + return true; +} + +// read in all readout-level Objects files for this cell +bool pmCellReadObjects (pmCell *cell, const pmFPAview *view, pmFPAfile *file) +{ + + for (int i = 0; i < cell->readouts->n; i++) { + + pmReadout *readout = cell->readouts->data[i]; + pmReadoutReadObjects (readout, view, file); + } + return true; +} + +// read in all readout-level Objects files for this cell +bool pmReadoutReadObjects (pmReadout *readout, const pmFPAview *view, pmFPAfile *file) +{ + + bool status; + psArray *sources = NULL; + pmHDU *hdu; + + switch (file->type) { + case PM_FPA_FILE_OBJ: + fprintf (stderr, "warning: OBJ is not supported as an input object format\n"); + break; + + case PM_FPA_FILE_SX: + fprintf (stderr, "warning: SX is not supported as an input object format\n"); + break; + + case PM_FPA_FILE_CMP: + // a SPLIT format : only one header and object table per file + + // read in header, if not yet loaded + hdu = pmFPAviewThisHDU (view, file->fpa); + + char *filename = pmFPAfileNameFromRule (file->filerule, file, view); + file->fits = psFitsOpen (filename, "r"); + hdu->header = psFitsReadHeader (NULL, file->fits); + psFitsClose (file->fits); + sources = pmSourcesReadCMP (filename, hdu->header); + psFree (filename); + break; + + case PM_FPA_FILE_CMF: + // read in header, if not yet loaded + hdu = pmFPAviewThisHDU (view, file->fpa); + if (hdu->header == NULL) { + char *headname = pmFPAfileNameFromRule (file->extxtra, file, view); + psFitsMoveExtName (file->fits, headname); + hdu->header = psFitsReadHeader (NULL, file->fits); + psFree (headname); + } + + char *dataname = pmFPAfileNameFromRule (file->extrule, file, view); + psFitsMoveExtName (file->fits, dataname); + sources = pmSourcesReadCMF (file->fits, hdu->header); + psFree (dataname); + break; + + default: + fprintf (stderr, "warning: type mismatch\n"); + break; + } + status = psMetadataAdd (readout->analysis, PS_LIST_TAIL, "PSPHOT.SOURCES", PS_DATA_ARRAY, "psphot sources", sources); + return true; +} + + Index: trunk/psModules/src/objects/pmSourceIO.h =================================================================== --- trunk/psModules/src/objects/pmSourceIO.h (revision 6872) +++ trunk/psModules/src/objects/pmSourceIO.h (revision 6872) @@ -0,0 +1,44 @@ +/** @file pmSourceIO.h + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_SOURCE_IO_H +# define PM_SOURCE_IO_H + +int pmSourceDophotType (pmSource *source); + +bool pmSourcesWriteRAW (psArray *sources, char *filename); +bool pmSourcesWriteOBJ (psArray *sources, char *filename); +bool pmSourcesWriteSX (psArray *sources, char *filename); +bool pmSourcesWriteCMP (psArray *sources, char *filename, psMetadata *header); +bool pmSourcesWriteCMF (psFits *fits, psArray *sources, psMetadata *header, char *extname); + +psArray *pmSourcesReadCMP (char *filename, psMetadata *header); +psArray *pmSourcesReadCMF (psFits *fits, psMetadata *header); + +bool pmSourcesWritePSFs (psArray *sources, char *filename); +bool pmSourcesWriteEXTs (psArray *sources, char *filename); +bool pmSourcesWriteNULLs (psArray *sources, char *filename); +bool pmMomentsWriteText (psArray *sources, char *filename); +bool pmPeaksWriteText (psArray *peaks, char *filename); + +bool pmFPAviewReadObjects (const pmFPAview *view, pmFPAfile *file); +bool pmFPAReadObjects (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file); +bool pmChipReadObjects (pmChip *chip, const pmFPAview *view, pmFPAfile *file); +bool pmCellReadObjects (pmCell *cell, const pmFPAview *view, pmFPAfile *file); +bool pmReadoutReadObjects (pmReadout *readout, const pmFPAview *view, pmFPAfile *file); + +bool pmFPAviewWriteObjects (const pmFPAview *view, pmFPAfile *file); +bool pmFPAWriteObjects (pmFPA *fpa, const pmFPAview *view, pmFPAfile *file); +bool pmChipWriteObjects (pmChip *chip, const pmFPAview *view, pmFPAfile *file); +bool pmCellWriteObjects (pmCell *cell, const pmFPAview *view, pmFPAfile *file); +bool pmReadoutWriteObjects (pmReadout *readout, const pmFPAview *view, pmFPAfile *file); + +# endif /* PM_SOURCE_IO_H */ Index: trunk/psModules/src/objects/pmSourceIO_CMF.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_CMF.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceIO_CMF.c (revision 6872) @@ -0,0 +1,161 @@ +/** @file pmSourceIO.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "psEllipse.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" + +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceIO.h" + +// elixir-style FITS table output (header + table in 1st extension) +// this format consists of a header derived from the image header +// followed by a zero-size matrix, followed by the table data +bool pmSourcesWriteCMF (psFits *fits, psArray *sources, psMetadata *header, char *extname) +{ + + psArray *table; + psMetadata *row; + int i, type; + psF32 *PAR, *dPAR; + float lsky; + bool status; + psEllipseShape shape; + psEllipseAxes axes; + + // find config information for output header + float ZERO_POINT = psMetadataLookupF32 (&status, header, "ZERO_PT"); + + table = psArrayAlloc (sources->n); + table->n = 0; + + for (i = 0; i < sources->n; i++) { + pmSource *source = (pmSource *) sources->data[i]; + pmModel *model = pmSourceSelectModel (source); + if (model == NULL) + continue; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + type = pmSourceDophotType (source); + lsky = (PAR[0] < 1.0) ? 0.0 : log10(PAR[0]); + + shape.sx = PAR[4]; + shape.sy = PAR[5]; + shape.sxy = PAR[6]; + axes = psEllipseShapeToAxes (shape); + + row = psMetadataAlloc (); + psMetadataAdd (row, PS_LIST_TAIL, "X_PIX", PS_DATA_F32, "", PAR[2]); + psMetadataAdd (row, PS_LIST_TAIL, "Y_PIX", PS_DATA_F32, "", PAR[3]); + psMetadataAdd (row, PS_LIST_TAIL, "MAG_RAW", PS_DATA_F32, "", PS_MIN (99.0, source->psfMag + ZERO_POINT)); + psMetadataAdd (row, PS_LIST_TAIL, "MAG_GAL", PS_DATA_F32, "", PS_MIN (99.0, source->extMag + ZERO_POINT)); + psMetadataAdd (row, PS_LIST_TAIL, "MAG_AP", PS_DATA_F32, "", PS_MIN (99.0, source->apMag + ZERO_POINT)); + psMetadataAdd (row, PS_LIST_TAIL, "MAG_ERR", PS_DATA_F32, "", PS_MIN (999, 1000*source->errMag)); + psMetadataAdd (row, PS_LIST_TAIL, "LOG_SKY", PS_DATA_F32, "", lsky); + psMetadataAdd (row, PS_LIST_TAIL, "FWHM_X", PS_DATA_F32, "", axes.major); + psMetadataAdd (row, PS_LIST_TAIL, "FWHM_Y", PS_DATA_F32, "", axes.minor); + psMetadataAdd (row, PS_LIST_TAIL, "THETA", PS_DATA_F32, "", axes.theta); + psMetadataAdd (row, PS_LIST_TAIL, "DOPHOT", PS_DATA_U8, "", type); + psMetadataAdd (row, PS_LIST_TAIL, "WEIGHT", PS_DATA_U8, "", PS_MIN (255, PS_MAX(0, 255*source->pixWeight))); + psMetadataAdd (row, PS_LIST_TAIL, "DUMMY", PS_DATA_STRING, "", "12"); + + psArrayAdd (table, 100, row); + psFree (row); + } + + // create the basic table header + psMetadataAdd (header, PS_LIST_HEAD, "EXTNAME", PS_DATA_STRING | PS_META_REPLACE, "extension name", extname); + + // XXX this is broken : does not write the existing header elements except EXTNAME + psFitsWriteTable (fits, header, table); + psTrace ("pmFPAfile", 5, "wrote ext data %s\n", extname); + + psFree (table); + return true; +} + +// read in a readout from the fits file +psArray *pmSourcesReadCMF (psFits *fits, psMetadata *header) +{ + + bool status; + psF32 *PAR, *dPAR; + psEllipseShape shape; + psEllipseAxes axes; + float lsky; + + // define PSF model type + int modelType = pmModelSetType ("PS_MODEL_GAUSS"); + + char *PSF_NAME = psMetadataLookupStr (&status, header, "PSF_NAME"); + if (PSF_NAME != NULL) { + modelType = pmModelSetType (PSF_NAME); + } + + // find config information for output header + float ZERO_POINT = psMetadataLookupF32 (&status, header, "ZERO_PT"); + if (!status) + ZERO_POINT = 25.0; + + psArray *table = psFitsReadTable (fits); + // validate a single row of the table (must match SMP) + + psArray *sources = psArrayAlloc (table->n); + + // convert the table to the pmSource entries + // XXX need to chooose PSF vs EXT, based on type? + for (int i = 0; i < table->n; i++) { + pmSource *source = pmSourceAlloc (); + pmModel *model = pmModelAlloc (modelType); + source->modelPSF = model; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + psMetadata *row = table->data[i]; + + lsky = psMetadataLookupF32 (&status, row, "LOG_SKY"); + PAR[0] = pow(lsky, 10.0); + PAR[2] = psMetadataLookupF32 (&status, row, "X_PIX"); + PAR[3] = psMetadataLookupF32 (&status, row, "Y_PIX"); + axes.major = psMetadataLookupF32 (&status, row, "FWHM_X"); + axes.minor = psMetadataLookupF32 (&status, row, "FWHM_Y"); + axes.theta = psMetadataLookupF32 (&status, row, "THETA"); + + shape = psEllipseAxesToShape (axes); + + PAR[4] = shape.sx; + PAR[5] = shape.sy; + PAR[6] = shape.sxy; + + source->psfMag = psMetadataLookupF32 (&status, row, "MAG_RAW") - ZERO_POINT; + source->extMag = psMetadataLookupF32 (&status, row, "MAG_GAL") - ZERO_POINT; + source->errMag = psMetadataLookupF32 (&status, row, "MAG_ERR"); + source->apMag = psMetadataLookupF32 (&status, row, "MAG_AP") - ZERO_POINT; + + sources->data[i] = source; + } + return (sources); +} Index: trunk/psModules/src/objects/pmSourceIO_CMP.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_CMP.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceIO_CMP.c (revision 6872) @@ -0,0 +1,250 @@ +/** @file pmSourceIO.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "psLine.h" +#include "psEllipse.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" + +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceIO.h" + +// elixir-style pseudo FITS table (header + ascii list) +bool pmSourcesWriteCMP (psArray *sources, char *filename, psMetadata *header) +{ + + int i, type, nSrc; + psMetadataItem *mdi; + psF32 *PAR, *dPAR; + float lsky = 0; + bool status; + psEllipseShape shape; + psEllipseAxes axes; + + // find config information for output header + float ZERO_POINT = psMetadataLookupF32 (&status, header, "ZERO_PT"); + if (!status) + ZERO_POINT = 25.0; + + // count the number of sources which will be written + for (i = nSrc = 0; i < sources->n; i++) { + pmSource *source = (pmSource *) sources->data[i]; + pmModel *model = pmSourceSelectModel (source); + if (model == NULL) + continue; + nSrc ++; + } + psMetadataAdd (header, PS_LIST_TAIL, "NSTARS", PS_DATA_S32 | PS_META_REPLACE, "NUMBER OF STARS", nSrc); + + // set NAXIS to 0 : CFITSIO requires isolated header to have NAXIS = 0 + mdi = psMetadataLookup (header, "NAXIS"); + mdi->data.S32 = 0; + mdi->type = PS_DATA_S32; + + // create file, write-out header + psFits *fits = psFitsOpen (filename, "w"); + psFitsWriteHeader (header, fits); + psFitsClose (fits); + + // re-open, add data to end of file + FILE *f = fopen (filename, "a+"); + if (f == NULL) { + psLogMsg ("WriteSourceOBJ", 3, "can't open output file for output %s\n", filename); + return false; + } + fseek (f, 0, SEEK_END); + + psLine *line = psLineAlloc (67); // 66 is imclean-defined line length + + // write sources with models first + for (i = 0; i < sources->n; i++) { + pmSource *source = (pmSource *) sources->data[i]; + pmModel *model = pmSourceSelectModel (source); + if (model == NULL) + continue; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + type = pmSourceDophotType (source); + lsky = (PAR[0] < 1.0) ? 0.0 : log10(PAR[0]); + + shape.sx = PAR[4]; + shape.sy = PAR[5]; + shape.sxy = PAR[6]; + axes = psEllipseShapeToAxes (shape); + + psLineInit (line); + psLineAdd (line, "%6.1f ", PAR[2]); + psLineAdd (line, "%6.1f ", PAR[3]); + psLineAdd (line, "%6.3f ", PS_MIN (99.0, source->psfMag + ZERO_POINT)); + psLineAdd (line, "%03d ", PS_MIN (999, (int)(1000*source->errMag))); + psLineAdd (line, "%2d ", type); + psLineAdd (line, "%3.1f ", lsky); + psLineAdd (line, "%6.3f ", PS_MIN (99.0, source->extMag + ZERO_POINT)); + psLineAdd (line, "%6.3f ", PS_MIN (99.0, source->apMag + ZERO_POINT)); + psLineAdd (line, "%6.2f ", axes.major); + psLineAdd (line, "%6.2f ", axes.minor); + psLineAdd (line, "%5.1f\n", axes.theta); + fwrite (line->line, 1, line->Nline, f); + } + fclose (f); + psFree (line); + return true; +} + +# define BYTES_STAR 66 +# define BLOCK 1000 + +// elixir-style pseudo FITS table (header + ascii list) +psArray *pmSourcesReadCMP (char *filename, psMetadata *header) +{ + + int Ninstar; + psF32 *PAR, *dPAR; + bool status; + psEllipseShape shape; + psEllipseAxes axes; + + // define PSF model type + int modelType = pmModelSetType ("PS_MODEL_GAUSS"); + + char *PSF_NAME = psMetadataLookupStr (&status, header, "PSF_NAME"); + if (PSF_NAME != NULL) { + modelType = pmModelSetType (PSF_NAME); + } + + // find config information for output header + float ZERO_POINT = psMetadataLookupF32 (&status, header, "ZERO_PT"); + if (!status) + ZERO_POINT = 25.0; + + // how many lines in the header? + int nLines = header->list->n; + int nBytes = nLines * 80; + if (nBytes % 2880) { + int nBlock = 1 + (int)(nBytes / 2880); + nBytes = nBlock * 2880; + } + + // re-open, seek to end of header + FILE *f = fopen (filename, "r"); + if (f == NULL) { + psLogMsg ("pmSourcesReadCMP", 3, "can't open output file for input %s\n", filename); + return NULL; + } + fseek (f, nBytes, SEEK_SET); + + // prepare array to store data + int nStars = psMetadataLookupS32 (&status, header, "NSTARS"); + psArray *sources = psArrayAlloc (nStars); + sources->n = 0; + + // we have fixed bytes / line : use that info + char *buffer = psAlloc (BYTES_STAR*nStars); + + int Nextra = 0; + while (true) { + /* load next data block */ + int Nbytes = BYTES_STAR * BLOCK - Nextra; + int nbytes = fread (&buffer[Nextra], 1, Nbytes, f); + if (nbytes == 0) { + goto done_load; + } + nbytes += Nextra; + + /* check line-by-line integrity */ + char *c = buffer; + char *c2 = NULL; + while (c < buffer + nbytes) { + for (c2 = c; *c2 == '\n'; c2++) + ; + if (c2 > c) { /* extra return chars */ + memmove (c, c2, (int)(buffer + nbytes - c2)); + int Nskip = c2 - c; + nbytes -= Nskip; + bzero (buffer + nbytes, Nskip); + psLogMsg (__func__, 4, "deleted %d extra return chars\n", Nskip); + } + c2 = strchr (c, '\n'); + if (c2 == (char *) NULL) { + goto done_check; + } + c2++; + if ((c2 - c) != BYTES_STAR) { /* bad line, delete it */ + memmove (c, c2, (int)(buffer + nbytes - c2)); + int Nskip = c2 - c; + nbytes -= Nskip; + bzero (buffer + nbytes, Nskip); + psLogMsg (__func__, 4, "deleted line, %d extra chars\n", Nskip); + } else { + c = c2; + } + } +done_check: + + /* extract data for stars */ + Ninstar = nbytes / BYTES_STAR; + Nextra = nbytes % BYTES_STAR; + for (int j = 0; j < Ninstar; j++) { + psString line = psStringNCopy (&buffer[j*BYTES_STAR], BYTES_STAR); + psList *list = psStringSplit (line, " "); + psArray *array = psListToArray (list); + + pmSource *source = pmSourceAlloc (); + pmModel *model = pmModelAlloc (modelType); + source->modelPSF = model; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + PAR[0] = pow (atof (array->data[5]), 10.0); + PAR[2] = atof (array->data[0]); + PAR[3] = atof (array->data[1]); + source->psfMag = atof (array->data[2]); + source->extMag = atof (array->data[6]); + source->errMag = atof (array->data[3]) / 1000.0; + source->apMag = atof (array->data[7]); + axes.major = atof (array->data[8]); + axes.minor = atof (array->data[9]); + axes.theta = atof (array->data[10]); + + shape = psEllipseAxesToShape (axes); + + PAR[4] = shape.sx; + PAR[5] = shape.sy; + PAR[6] = shape.sxy; + + // source->type = atof (array->data[4]); + + psArrayAdd (sources, 100, source); + } + } +done_load: + + // XXX free up temp memory in this block + // XXX if sources->n != nStars, give an error? + + fclose (f); + return (sources); +} Index: trunk/psModules/src/objects/pmSourceIO_OBJ.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_OBJ.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceIO_OBJ.c (revision 6872) @@ -0,0 +1,94 @@ +/** @file pmSourceIO.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "psLine.h" +#include "psEllipse.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" + +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceIO.h" + +// dophot-style output list with fixed line width +bool pmSourcesWriteOBJ (psArray *sources, char *filename) +{ + + int type; + psF32 *PAR, *dPAR; + float dmag, apResid; + psEllipseShape shape; + psEllipseAxes axes; + + psTimerStart ("string"); + + psLine *line = psLineAlloc (104); // 104 is dophot-defined line length + + FILE *f = fopen (filename, "w"); + if (f == NULL) { + psLogMsg (__func__, 3, "can't open output file for output %s\n", filename); + return false; + } + + // write sources with models + for (int i = 0; i < sources->n; i++) { + pmSource *source = (pmSource *) sources->data[i]; + pmModel *model = pmSourceSelectModel (source); + if (model == NULL) + continue; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + dmag = dPAR[1] / PAR[1]; + type = pmSourceDophotType (source); + if ((source->apMag < 99.0) && (source->psfMag < 99.0)) { + apResid = source->apMag - source->psfMag; + } else { + apResid = 0.0; + } + + shape.sx = PAR[4]; + shape.sy = PAR[5]; + shape.sxy = PAR[6]; + axes = psEllipseShapeToAxes (shape); + + psLineInit (line); + psLineAdd (line, "%3d", type); + psLineAdd (line, "%8.2f", PAR[2]); + psLineAdd (line, "%8.2f", PAR[3]); + psLineAdd (line, "%8.3f", source->psfMag); + psLineAdd (line, "%6.3f", dmag); + psLineAdd (line, "%9.2f", PAR[0]); + psLineAdd (line, "%9.3f", axes.major); + psLineAdd (line, "%9.3f", axes.minor); + psLineAdd (line, "%7.2f", axes.theta); + psLineAdd (line, "%8.3f", source->extMag); + psLineAdd (line, "%8.3f", source->apMag); + psLineAdd (line, "%8.2f\n", apResid); + fwrite (line->line, 1, line->Nline, f); + } + fclose (f); + psFree (line); + fprintf (stderr, "%f seconds for %d objects\n", psTimerMark ("string"), (int)sources->n); + return true; +} Index: trunk/psModules/src/objects/pmSourceIO_RAW.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_RAW.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceIO_RAW.c (revision 6872) @@ -0,0 +1,268 @@ +/** @file pmSourceIO.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "psLine.h" +#include "psEllipse.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" + +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourcePhotometry.h" +#include "pmSourceIO.h" + +/***** Text Output Methods *****/ +bool pmSourcesWriteRAW (psArray *sources, char *filename) +{ + + char *name = (char *) psAlloc (strlen(filename) + 10); + + sprintf (name, "%s.psf.dat", filename); + pmSourcesWritePSFs (sources, name); + + sprintf (name, "%s.ext.dat", filename); + pmSourcesWriteEXTs (sources, name); + + sprintf (name, "%s.nul.dat", filename); + pmSourcesWriteNULLs (sources, name); + + sprintf (name, "%s.mnt.dat", filename); + pmMomentsWriteText (sources, name); + + psFree (name); + return true; +} + +// write the PSF sources to an output file +bool pmSourcesWritePSFs (psArray *sources, char *filename) +{ + + double dPos; + int i, j; + FILE *f; + psF32 *PAR, *dPAR; + pmModel *model; + + f = fopen (filename, "w"); + if (f == NULL) { + psLogMsg (__func__, 3, "can't open output file for PSFs: %s\n", filename); + return false; + } + + // write sources with models first + for (i = 0; i < sources->n; i++) { + pmSource *source = (pmSource *) sources->data[i]; + if (source->type != PM_SOURCE_TYPE_STAR) + continue; + model = source->modelPSF; + if (model == NULL) + continue; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + // dPos is positional error, dMag is mag error + dPos = hypot (dPAR[2], dPAR[3]); + + fprintf (f, "%7.1f %7.1f %7.1f %8.4f %7.4f %7.4f ", + PAR[2], PAR[3], PAR[0], source->psfMag, source->errMag, dPos); + + for (j = 4; j < model->params->n; j++) { + fprintf (f, "%9.6f ", PAR[j]); + } + fprintf (f, " : "); + for (j = 4; j < model->params->n; j++) { + fprintf (f, "%9.6f ", dPAR[j]); + } + fprintf (f, ": %8.4f %2d %#5x %7.3f %7.3f %7.1f %7.2f %4.2f %4d %2d\n", + source[0].apMag, source[0].type, source[0].mode, + log10(model[0].chisq/model[0].nDOF), + log10(model[0].chisqNorm/model[0].nDOF), + source[0].moments->SN, + model[0].radiusTMP, + source[0].pixWeight, + model[0].nDOF, + model[0].nIter); + } + fclose (f); + return true; +} + +// dump the sources to an output file +bool pmSourcesWriteEXTs (psArray *sources, char *filename) +{ + + double dPos; + int i, j; + FILE *f; + psF32 *PAR, *dPAR; + pmModel *model; + + f = fopen (filename, "w"); + if (f == NULL) { + psLogMsg ("pmModelWriteEXTs", 3, "can't open output file for moments%s\n", filename); + return false; + } + + // write sources with models first + for (i = 0; i < sources->n; i++) { + pmSource *source = (pmSource *) sources->data[i]; + + if (source->type != PM_SOURCE_TYPE_EXTENDED) + continue; + + model = source->modelEXT; + if (model == NULL) + continue; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + // dPos is shape error + // XXX these are hardwired for SGAUSS + dPos = hypot ((dPAR[4] / PAR[4]), (dPAR[5] / PAR[5])); + + fprintf (f, "%7.1f %7.1f %7.1f %8.4f %7.4f %7.4f ", + PAR[2], PAR[3], PAR[0], source->extMag, source->errMag, dPos); + + for (j = 4; j < model->params->n; j++) { + fprintf (f, "%9.6f ", PAR[j]); + } + fprintf (f, " : "); + for (j = 4; j < model->params->n; j++) { + fprintf (f, "%9.6f ", dPAR[j]); + } + fprintf (f, ": %7.4f %2d %#5x %7.3f %7.3f %7.1f %7.2f %4.2f %4d %2d\n", + source->apMag, + source[0].type, source[0].mode, + log10(model[0].chisq/model[0].nDOF), + log10(model[0].chisqNorm/model[0].nDOF), + source[0].moments->SN, + model[0].radiusTMP, + source[0].pixWeight, + model[0].nDOF, + model[0].nIter); + } + fclose (f); + return true; +} + +// dump the sources to an output file +bool pmSourcesWriteNULLs (psArray *sources, char *filename) +{ + + int i; + FILE *f; + pmMoments *moment = NULL; + pmSource *source = NULL; + + f = fopen (filename, "w"); + if (f == NULL) { + psLogMsg ("DumpObjects", 3, "can't open output file for moments%s\n", filename); + return false; + } + + pmMoments *empty = pmMomentsAlloc (); + + // write sources with models first + for (i = 0; i < sources->n; i++) { + source = sources->data[i]; + + // skip these sources (in PSF or EXT) + if (source->type == PM_SOURCE_TYPE_STAR) + continue; + if (source->type == PM_SOURCE_TYPE_EXTENDED) + continue; + + if (source->moments == NULL) { + moment = empty; + } else { + moment = source->moments; + } + + fprintf (f, "%5d %5d %7.1f %7.1f %7.1f %6.3f %6.3f %8.1f %7.1f %7.1f %7.1f %4d %2d\n", + source->peak->x, source->peak->y, source->peak->counts, + source->moments->x, source->moments->y, + source->moments->Sx, source->moments->Sy, + source->moments->Sum, source->moments->Peak, + source->moments->Sky, source->moments->SN, + source->moments->nPixels, source->type); + } + fclose (f); + psFree (empty); + return true; +} + +// write the moments to an output file +bool pmMomentsWriteText (psArray *sources, char *filename) +{ + + int i; + FILE *f; + pmSource *source = NULL; + + f = fopen (filename, "w"); + if (f == NULL) { + psLogMsg ("pmMomentsWriteText", 3, "can't open output file for moments%s\n", filename); + return false; + } + + for (i = 0; i < sources->n; i++) { + source = sources->data[i]; + if (source->moments == NULL) + continue; + fprintf (f, "%5d %5d %7.1f %7.1f %7.1f %6.3f %6.3f %10.1f %7.1f %7.1f %7.1f %4d %2d %#5x\n", + source->peak->x, source->peak->y, source->peak->counts, + source->moments->x, source->moments->y, + source->moments->Sx, source->moments->Sy, + source->moments->Sum, source->moments->Peak, + source->moments->Sky, source->moments->SN, + source->moments->nPixels, source->type, source->mode); + } + fclose (f); + return true; +} + +// write the peaks to an output file +bool pmPeaksWriteText (psArray *peaks, char *filename) +{ + + int i; + FILE *f; + + f = fopen (filename, "w"); + if (f == NULL) { + psLogMsg ("pmPeaksWriteText", 3, "can't open output file for peaks%s\n", filename); + return false; + } + + for (i = 0; i < peaks->n; i++) { + pmPeak *peak = peaks->data[i]; + if (peak == NULL) + continue; + fprintf (f, "%5d %5d %7.1f\n", + peak->x, peak->y, peak->counts); + } + fclose (f); + return true; +} + Index: trunk/psModules/src/objects/pmSourceIO_SX.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_SX.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceIO_SX.c (revision 6872) @@ -0,0 +1,86 @@ +/** @file pmSourceIO.c + * + * @author EAM, IfA + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "psLine.h" +#include "psEllipse.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" + +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourceIO.h" + +// elixir-mode / sextractor-style output list with fixed line width +bool pmSourcesWriteSX (psArray *sources, char *filename) +{ + + psF32 *PAR, *dPAR; + psEllipseShape shape; + psEllipseAxes axes; + + psLine *line = psLineAlloc (110); // 110 is sextractor line length + + FILE *f = fopen (filename, "w"); + if (f == NULL) { + psLogMsg (__func__, 3, "can't open output file for output %s\n", filename); + return false; + } + + // write sources with models + for (int i = 0; i < sources->n; i++) { + pmSource *source = (pmSource *) sources->data[i]; + pmModel *model = pmSourceSelectModel (source); + if (model == NULL) + continue; + + PAR = model->params->data.F32; + dPAR = model->dparams->data.F32; + + // pmSourceSextractType (source, &type, &flags); + + shape.sx = PAR[4]; + shape.sy = PAR[5]; + shape.sxy = PAR[6]; + axes = psEllipseShapeToAxes (shape); + + psLineInit (line); + psLineAdd (line, "%5.2f", 0.0); // should be type + psLineAdd (line, "%11.3f", PAR[2]); + psLineAdd (line, "%11.3f", PAR[3]); + psLineAdd (line, "%9.4f", source->psfMag); + psLineAdd (line, "%9.4f", source->errMag); + psLineAdd (line, "%13.4f", PAR[0]); + psLineAdd (line, "%9.2f", axes.major); + psLineAdd (line, "%9.2f", axes.minor); + psLineAdd (line, "%6.1f", axes.theta); + psLineAdd (line, "%9.4f", source->extMag); + psLineAdd (line, "%9.4f", source->apMag); + psLineAdd (line, "%4d\n", 0); // should be flags + fwrite (line->line, 1, line->Nline, f); + } + fclose (f); + psFree (line); + return true; +} + +// XXX need to fix the FWHM / shape stuff, +// XXX make sure we are using the correct mags, etc Index: trunk/psModules/src/objects/pmSourcePhotometry.c =================================================================== --- trunk/psModules/src/objects/pmSourcePhotometry.c (revision 6872) +++ trunk/psModules/src/objects/pmSourcePhotometry.c (revision 6872) @@ -0,0 +1,387 @@ +/** @file pmSourcePhotometry.c + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmGrowthCurve.h" +#include "pmModel.h" +#include "pmPSF.h" +#include "pmSource.h" +#include "pmModelGroup.h" +#include "pmSourcePhotometry.h" + +# define DO_SKY 0 + +static float AP_MIN_SN = 0.0; + +bool pmSourceMagnitudesInit (psMetadata *config) +{ + + bool status; + + float limit = psMetadataLookupF32 (&status, config, "AP_MIN_SN"); + if (status) { + AP_MIN_SN = limit; + } + return true; +} + +/** + this function is used to calculate the three defined source magnitudes: + - apMag : only if S/N > AP_MIN_SN + : is optionally corrected for curve-of-growth if: + - the source is a STAR (PSF) + - the option is selected (how??) + - psfMag : all sources with non-NULL modelPSF + : is optionally corrected for aperture residual if: + - the source is a STAR (PSF) + - the option is selected (how??) + + - extMag : all sources with non-NULL modelEXT +**/ + +// XXX EAM : masked region should be (optionally) elliptical +bool pmSourceMagnitudes (pmSource *source, pmPSF *psf, pmSourcePhotometryMode mode) +{ + + int status = false; + bool isPSF; + float x, y; + float rflux; + float SN; + pmModel *model; + + source->psfMag = 99.0; + source->extMag = 99.0; + source->errMag = 99.0; + source->apMag = 99.0; + + switch (source->type) { + case PM_SOURCE_TYPE_STAR: + model = source->modelPSF; + if (model == NULL) + return false; + isPSF = true; + break; + + case PM_SOURCE_TYPE_EXTENDED: + model = source->modelEXT; + if (model == NULL) + return false; + isPSF = false; + break; + + default: + return false; + } + + if (model->dparams->data.F32[1] > 0) { + SN = model->params->data.F32[1] / model->dparams->data.F32[1]; + source->errMag = 1.0 / SN; + } else { + SN = 0.0; + source->errMag = 0.0; + } + x = model->params->data.F32[2]; + y = model->params->data.F32[3]; + + // measure object model photometry + status = pmSourcePhotometryModel (&source->psfMag, source->modelPSF); + status = pmSourcePhotometryModel (&source->extMag, source->modelEXT); + // for PSFs, correct both apMag and psfMag to same system, consistent with infinite flux star in aperture RADIUS + if ((mode & PM_SOURCE_PHOT_APCORR) && isPSF && psf) { + // convert to the equivalent 2D model? + source->psfMag += psPolynomial4DEval (psf->ApTrend, x, y, 0.0, 0.0); + } + + if (SN < AP_MIN_SN) + return false; + + // replace source flux + // XXX test to see if source has been subtracted? + pmModelAdd (source->pixels, source->mask, model, false, false); + + // set aperture mask circle to model radius + psImageKeepCircle (source->mask, x, y, model->radiusTMP, "OR", PM_SOURCE_MASK_MARKED); + + // measure the weight of included pixels + if (mode & PM_SOURCE_PHOT_WEIGHT) { + pmSourcePixelWeight (&source->pixWeight, model, source->pixels, source->mask); + } + + // measure object aperture photometry + status = pmSourcePhotometryAper (&source->apMag, model, source->pixels, source->mask); + + // for PSFs, correct both apMag and psfMag to same system, consistent with infinite flux star in aperture RADIUS + if (status && isPSF && psf) { + if (psf->growth && (mode & PM_SOURCE_PHOT_GROWTH)) { + source->apMag += pmGrowthCurveCorrect (psf->growth, model->radiusTMP); + } + if (mode & PM_SOURCE_PHOT_APCORR) { + rflux = pow (10.0, 0.4*source->psfMag); + source->apMag -= PS_SQR(model->radiusTMP)*rflux * psf->skyBias + psf->skySat / rflux; + } + } + + // unmask aperture + psImageKeepCircle (source->mask, x, y, model->radiusTMP, "AND", ~PM_SOURCE_MASK_MARKED); + + // subtract object, leave local sky + pmModelSub (source->pixels, source->mask, model, false, false); + + return status; +} + +/* +aprMag' - fitMag = flux*skySat + r^2*rflux*skyBias + ApTrend(x,y) +(aprMag - flux*skySat - r^2*rflux*skyBias) - fitMAg = ApTrend(x,y) +(aprMag - flux*skySat - r^2*rflux*skyBias) = fitMAg + ApTrend(x,y) + +*/ + +// return source model magnitude +bool pmSourcePhotometryModel (float *fitMag, pmModel *model) +{ + + float fitSum = 0; + *fitMag = 99.0; + + if (model == NULL) { + return false; + } + + // measure fitMag + pmModelFlux modelFluxFunc = pmModelFlux_GetFunction (model->type); + fitSum = modelFluxFunc (model->params); + if (fitSum <= 0) + return false; + if (!isfinite(fitSum)) + return false; + *fitMag = -2.5*log10(fitSum); + + return (true); +} + +// return source aperture magnitude +bool pmSourcePhotometryAper (float *apMag, pmModel *model, psImage *image, psImage *mask) +{ + float apSum = 0; + float sky = 0; + *apMag = 99.0; + + if (model == NULL) { + return false; + } + + if (DO_SKY) { + sky = model->params->data.F32[0]; + } else { + sky = 0; + } + + // measure apMag + for (int ix = 0; ix < image->numCols; ix++) { + for (int iy = 0; iy < image->numRows; iy++) { + if (mask->data.U8[iy][ix]) + continue; + apSum += image->data.F32[iy][ix] - sky; + } + } + if (apSum <= 0) + return false; + + *apMag = -2.5*log10(apSum); + return (true); +} + +// return source aperture magnitude +bool pmSourcePixelWeight (float *pixWeight, pmModel *model, psImage *image, psImage *mask) +{ + float modelSum = 0; + float validSum = 0; + float sky = 0; + float value; + + int Xo, Yo, dP; + int dX, DX, NX; + int dY, DY, NY; + + *pixWeight = 0.0; + + if (model == NULL) + return false; + + // we only care about the value of the object model, not the local sky + if (DO_SKY) { + sky = model->params->data.F32[0]; + } else { + sky = 0; + } + + // the model function returns the source flux at a position + pmModelFunc modelFunc = pmModelFunc_GetFunction (model->type); + psVector *coord = psVectorAlloc(2, PS_TYPE_F32); + psVector *params = model->params; + + Xo = params->data.F32[2]; + Yo = params->data.F32[3]; + + dX = Xo - image->col0; + dP = image->numCols - dX; + DX = PS_MAX(dX, dP); + NX = image->numCols; + + dY = Yo - image->row0; + dP = image->numRows - dY; + DY = PS_MAX(dY, dP); + NY = image->numRows; + + // measure modelSum and validSum + // XXX this does not work for sources near the edge: we need to measure for + // a full square region + for (int ix = -DX; ix < DX + 1; ix++) { + int mx = ix + dX; + for (int iy = -DY; iy < DY + 1; iy++) { + int my = iy + dY; + + coord->data.F32[0] = (psF32) (ix + Xo); + coord->data.F32[1] = (psF32) (iy + Yo); + + // for the full model, add all points + value = modelFunc (NULL, params, coord) - sky; + modelSum += value; + + // include count only the unmasked pixels within the image area + if (mx < 0) + continue; + if (my < 0) + continue; + if (mx >= NX) + continue; + if (my >= NY) + continue; + if (mask->data.U8[my][mx]) + continue; + + validSum += value; + } + } + if (validSum <= 0) + return false; + + *pixWeight = validSum / modelSum; + return (true); +} + +float pmSourceCrossProduct (pmSource *Mi, pmSource *Mj) +{ + + int Xs, Xe, Ys, Ye; + int xi, xj, yi, yj; + int xIs, xJs, yIs, yJs; + int xIe, yIe; + float flux, wt; + + psImage *Pi = Mi->pixels; + psImage *Pj = Mj->pixels; + + psImage *Wi = Mi->weight; + + psImage *Ti = Mi->mask; + psImage *Tj = Mj->mask; + + Xs = PS_MAX (Pi->col0, Pj->col0); + Xe = PS_MIN (Pi->col0 + Pi->numCols, Pj->col0 + Pj->numCols); + + Ys = PS_MAX (Pi->row0, Pj->row0); + Ye = PS_MIN (Pi->row0 + Pi->numRows, Pj->row0 + Pj->numRows); + + xIs = Xs - Pi->col0; + xJs = Xs - Pj->col0; + yIs = Ys - Pi->row0; + yJs = Ys - Pj->row0; + + xIe = Xe - Pi->col0; + yIe = Ye - Pi->row0; + + // note that this is addressing the same image pixels, + // though only if both are source not model images + flux = 0; + for (yi = yIs, yj = yJs; yi < yIe; yi++, yj++) { + for (xi = xIs, xj = xJs; xi < xIe; xi++, xj++) { + if (Ti->data.U8[yi][xi]) + continue; + if (Tj->data.U8[yj][xj]) + continue; + wt = Wi->data.F32[yi][xi]; + if (wt > 0) { + flux += (Pi->data.F32[yi][xi] * Pj->data.F32[yj][xj]) / wt; + } + } + } + return (flux); +} + +float pmSourceCrossWeight (pmSource *Mi, pmSource *Mj) +{ + + int Xs, Xe, Ys, Ye; + int xi, xj, yi, yj; + int xIs, xJs, yIs, yJs; + int xIe, yIe; + float flux, wt; + + psImage *Pi = Mi->pixels; + psImage *Pj = Mj->pixels; + + psImage *Wi = Mi->weight; + + psImage *Ti = Mi->mask; + psImage *Tj = Mj->mask; + + Xs = PS_MAX (Pi->col0, Pj->col0); + Xe = PS_MIN (Pi->col0 + Pi->numCols, Pj->col0 + Pj->numCols); + + Ys = PS_MAX (Pi->row0, Pj->row0); + Ye = PS_MIN (Pi->row0 + Pi->numRows, Pj->row0 + Pj->numRows); + + xIs = Xs - Pi->col0; + xJs = Xs - Pj->col0; + yIs = Ys - Pi->row0; + yJs = Ys - Pj->row0; + + xIe = Xe - Pi->col0; + yIe = Ye - Pi->row0; + + // note that this is addressing the same image pixels, + // though only if both are source not model images + flux = 0; + for (yi = yIs, yj = yJs; yi < yIe; yi++, yj++) { + for (xi = xIs, xj = xJs; xi < xIe; xi++, xj++) { + if (Ti->data.U8[yi][xi]) + continue; + if (Tj->data.U8[yj][xj]) + continue; + wt = Wi->data.F32[yi][xi]; + if (wt > 0) { + flux += 1.0 / wt; + } + } + } + return (flux); +} + Index: trunk/psModules/src/objects/pmSourcePhotometry.h =================================================================== --- trunk/psModules/src/objects/pmSourcePhotometry.h (revision 6872) +++ trunk/psModules/src/objects/pmSourcePhotometry.h (revision 6872) @@ -0,0 +1,53 @@ +/** @file pmSourcePhotometry.h + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_SOURCE_PHOTOMETRY_H +# define PM_SOURCE_PHOTOMETRY_H + +/** + * + * The function returns both the magnitude of the fit, defined as -2.5log(flux), + * where the flux is integrated under the model, theoretically from a radius of 0 + * to infinity. In practice, we integrate the model beyond 50sigma. The aperture magnitude is + * defined as -2.5log(flux) , where the flux is summed for all pixels which are + * not excluded by the aperture mask. The model flux is calculated by calling the + * model-specific function provided by pmModelFlux_GetFunction. + * + * XXX: must code this. + * + */ + +typedef enum { + PM_SOURCE_PHOT_NONE = 0x0000, + PM_SOURCE_PHOT_GROWTH = 0x0001, + PM_SOURCE_PHOT_APCORR = 0x0002, + PM_SOURCE_PHOT_WEIGHT = 0x0004, +} pmSourcePhotometryMode; + +bool pmSourcePhotometryModel( + float *fitMag, ///< integrated fit magnitude + pmModel *model ///< model used for photometry +); + +bool pmSourcePhotometryAper( + float *apMag, ///< aperture flux magnitude + pmModel *model, ///< model used for photometry + psImage *image, ///< image pixels to be used + psImage *mask ///< mask of pixels to ignore +); + +bool pmSourceMagnitudesInit (psMetadata *config); +bool pmSourceMagnitudes (pmSource *source, pmPSF *psf, pmSourcePhotometryMode mode); +float pmSourceCrossProduct (pmSource *Mi, pmSource *Mj); +float pmSourceCrossWeight (pmSource *Mi, pmSource *Mj); +bool pmSourcePixelWeight (float *pixWeight, pmModel *model, psImage *image, psImage *mask); + +# endif /* PM_SOURCE_PHOTOMETRY_H */ Index: trunk/psModules/src/objects/pmSourceSky.c =================================================================== --- trunk/psModules/src/objects/pmSourceSky.c (revision 6872) +++ trunk/psModules/src/objects/pmSourceSky.c (revision 6872) @@ -0,0 +1,120 @@ +/** @file pmSourceSky.c + * + * Functions to measure the local sky and sky variance for sources on images + * + * @author GLG, MHPCC + * @author EAM, IfA: significant modifications. + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +#include +#include +#include +#include "pslib.h" +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmPeaks.h" +#include "pmMoments.h" +#include "pmModel.h" +#include "pmSource.h" +#include "pmSourceSky.h" + +/****************************************************************************** +pmSource *pmSourceLocalSky(source, statsOptions, Radius): this +routine creates a new pmSource.moments element if needed and sets pmSource.pmMoments.sky + +The sky value is set from the pixels in the square annulus surrounding the +peak pixel. + +The source.pixels and source.mask must already exist +*****************************************************************************/ + +bool pmSourceLocalSky( + pmSource *source, + psStatsOptions statsOptions, + psF32 Radius) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source, false); + PS_ASSERT_IMAGE_NON_NULL(source->pixels, false); + PS_ASSERT_IMAGE_NON_NULL(source->mask, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + PS_ASSERT_INT_POSITIVE(Radius, false); + PS_ASSERT_INT_NONNEGATIVE(Radius, false); + + psImage *image = source->pixels; + psImage *mask = source->mask; + pmPeak *peak = source->peak; + psRegion srcRegion; + + srcRegion = psRegionForSquare(peak->x, peak->y, Radius); + srcRegion = psRegionForImage(mask, srcRegion); + + psImageMaskRegion(mask, srcRegion, "OR", PM_SOURCE_MASK_MARKED); + psStats *myStats = psStatsAlloc(statsOptions); + myStats = psImageStats(myStats, image, mask, 0xff); + psImageMaskRegion(mask, srcRegion, "AND", ~PM_SOURCE_MASK_MARKED); + + psF64 tmpF64; + p_psGetStatValue(myStats, &tmpF64); + psFree(myStats); + + if (isnan(tmpF64)) { + psTrace(__func__, 3, "---- %s(false) end ----\n", __func__); + return(false); + } + if (source->moments == NULL) { + source->moments = pmMomentsAlloc(); + } + source->moments->Sky = (psF32) tmpF64; + psTrace(__func__, 3, "---- %s(true) end ----\n", __func__); + return (true); +} + +// A complementary function to pmSourceLocalSky: calculate the local median variance +bool pmSourceLocalSkyVariance( + pmSource *source, + psStatsOptions statsOptions, + psF32 Radius) +{ + psTrace(__func__, 3, "---- %s() begin ----\n", __func__); + PS_ASSERT_PTR_NON_NULL(source, false); + PS_ASSERT_IMAGE_NON_NULL(source->weight, false); + PS_ASSERT_IMAGE_NON_NULL(source->mask, false); + PS_ASSERT_PTR_NON_NULL(source->peak, false); + PS_ASSERT_INT_POSITIVE(Radius, false); + PS_ASSERT_INT_NONNEGATIVE(Radius, false); + + psImage *image = source->weight; + psImage *mask = source->mask; + pmPeak *peak = source->peak; + psRegion srcRegion; + + srcRegion = psRegionForSquare(peak->x, peak->y, Radius); + srcRegion = psRegionForImage(mask, srcRegion); + + psImageMaskRegion(mask, srcRegion, "OR", PM_SOURCE_MASK_MARKED); + psStats *myStats = psStatsAlloc(statsOptions); + myStats = psImageStats(myStats, image, mask, 0xff); + psImageMaskRegion(mask, srcRegion, "AND", ~PM_SOURCE_MASK_MARKED); + + psF64 tmpF64; + p_psGetStatValue(myStats, &tmpF64); + psFree(myStats); + + if (isnan(tmpF64)) { + psTrace(__func__, 3, "---- %s(false) end ----\n", __func__); + return(false); + } + if (source->moments == NULL) { + source->moments = pmMomentsAlloc(); + } + source->moments->dSky = (psF32) tmpF64; + psTrace(__func__, 3, "---- %s(true) end ----\n", __func__); + return (true); +} Index: trunk/psModules/src/objects/pmSourceSky.h =================================================================== --- trunk/psModules/src/objects/pmSourceSky.h (revision 6872) +++ trunk/psModules/src/objects/pmSourceSky.h (revision 6872) @@ -0,0 +1,42 @@ +/** @file pmSourceSky.h + * + * @author EAM, IfA; GLG, MHPCC + * + * @version $Revision: 1.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-04-17 18:01:05 $ + * + * Copyright 2004 Maui High Performance Computing Center, University of Hawaii + * + */ + +# ifndef PM_SOURCE_SKY_H +# define PM_SOURCE_SKY_H + +/** pmSourceLocalSky() + * + * Measure the local sky in the vicinity of the given source. The Radius + * defines the square aperture in which the moments will be measured. This + * function assumes the source pixels have been defined, and that the value of + * Radius here is smaller than the value of Radius used to define the pixels. The + * annular region not contained within the radius defined here is used to measure + * the local background in the vicinity of the source. The local background + * measurement uses the specified statistic passed in via the statsOptions entry. + * This function allocates the pmMoments structure. The resulting sky is used to + * set the value of the pmMoments.sky element of the provided pmSource structure. + * + */ +bool pmSourceLocalSky( + pmSource *source, ///< The input image (float) + psStatsOptions statsOptions, ///< The statistic used in calculating the background sky + float Radius ///< The inner radius of the square annulus to exclude +); + + +// A complementary function to pmSourceLocalSky: calculate the local sky variance +bool pmSourceLocalSkyVariance( + pmSource *source, ///< The input image (float) + psStatsOptions statsOptions, ///< The statistic used in calculating the background sky + float Radius ///< The inner radius of the square annulus to exclude +); + +# endif /* PM_SOURCE_PHOTOMETRY_H */ Index: trunk/psModules/src/pslib/.cvsignore =================================================================== --- trunk/psModules/src/pslib/.cvsignore (revision 6872) +++ trunk/psModules/src/pslib/.cvsignore (revision 6872) @@ -0,0 +1,6 @@ +.deps +.libs +Makefile +Makefile.in +*.la +*.lo Index: trunk/psModules/src/pslib/Makefile.am =================================================================== --- trunk/psModules/src/pslib/Makefile.am (revision 6872) +++ trunk/psModules/src/pslib/Makefile.am (revision 6872) @@ -0,0 +1,28 @@ +noinst_LTLIBRARIES = libpsmodulepslib.la + +libpsmodulepslib_la_CPPFLAGS = $(SRCINC) $(PSMODULE_CFLAGS) +libpsmodulepslib_la_LDFLAGS = -release $(PACKAGE_VERSION) +libpsmodulepslib_la_SOURCES = \ + psAdditionals.c \ + psEllipse.c \ + psImageJpeg.c \ + psImageFlip.c \ + psImageUnbin.c \ + psLine.c \ + psMetadataItemParse.c \ + psPolynomialUtils.c \ + psRegionIsBad.c \ + psSparse.c + +psmoduleincludedir = $(includedir) +psmoduleinclude_HEADERS = \ + psAdditionals.h \ + psEllipse.h \ + psImageJpeg.h \ + psImageFlip.h \ + psImageUnbin.h \ + psLine.h \ + psMetadataItemParse.h \ + psPolynomialUtils.h \ + psRegionIsBad.h \ + psSparse.h Index: trunk/psModules/src/pslib/psAdditionals.c =================================================================== --- trunk/psModules/src/pslib/psAdditionals.c (revision 6872) +++ trunk/psModules/src/pslib/psAdditionals.c (revision 6872) @@ -0,0 +1,238 @@ +#include +#include +#include "pslib.h" +#include "psAdditionals.h" + +psMetadata *pap_psMetadataCopy(psMetadata *out, + const psMetadata *in) +{ + PS_ASSERT_PTR_NON_NULL(in,NULL); + if (out == NULL) { + out = psMetadataAlloc(); + } + psMetadataItem *inItem = NULL; + psMetadataIterator *iter = psMetadataIteratorAlloc(*(psMetadata**)&in, PS_LIST_HEAD, NULL); + unsigned long numPointers = 0; // Number of pointers we were forced to copy + while ((inItem = psMetadataGetAndIncrement(iter))) { + // Need to look for MULTI, which won't be picked up using the iterator. + psMetadataItem *multiCheckItem = psMetadataLookup(in, inItem->name); + unsigned int flag = PS_META_REPLACE; // Flag to indicate MULTI; otherwise, replace + if (multiCheckItem->type == PS_DATA_METADATA_MULTI) { + psTrace(__func__, 10, "MULTI: %s (%s)\n", inItem->name, inItem->comment); + flag = PS_DATA_METADATA_MULTI; + } + + psTrace(__func__, 5, "Copying %s (%s)...\n", inItem->name, inItem->comment); + + #define PS_METADATA_COPY_CASE(NAME,TYPE) \ + case PS_TYPE_##NAME: \ + if (! psMetadataAdd(out, PS_LIST_TAIL, inItem->name, PS_TYPE_##NAME | flag, inItem->comment, \ + inItem->data.TYPE)) { \ + psErrorStackPrint(stderr, "Error copying %s (%s) in the metadata\n", inItem->name, \ + inItem->comment); \ + } \ + break; + + switch (inItem->type) { + // Numerical types + PS_METADATA_COPY_CASE(BOOL,B); + PS_METADATA_COPY_CASE(S8,S8); + PS_METADATA_COPY_CASE(S16,S16); + PS_METADATA_COPY_CASE(S32,S32); + PS_METADATA_COPY_CASE(U8,U8); + PS_METADATA_COPY_CASE(U16,U16); + PS_METADATA_COPY_CASE(U32,U32); + PS_METADATA_COPY_CASE(F32,F32); + PS_METADATA_COPY_CASE(F64,F64); + + // String: relying on the fact that this will copy the string, not point at it. + case PS_DATA_STRING: + psMetadataAdd(out, PS_LIST_TAIL, inItem->name, PS_DATA_STRING | flag, inItem->comment, + inItem->data.V); + break; + + // Metadata: copy the next level and stuff that in too + case PS_DATA_METADATA: { + psMetadata *metadata = pap_psMetadataCopy(NULL, inItem->data.md); + psMetadataAdd(out, PS_LIST_TAIL, inItem->name, PS_DATA_METADATA | flag, inItem->comment, + metadata); + break; + } + // Other kinds of pointers + default: + numPointers++; + psTrace(__func__, 10, "Copying a pointer in the metadata: %x\n", inItem->type); + psMetadataAdd(out, PS_LIST_TAIL, inItem->name, inItem->type | flag, inItem->comment, + inItem->data.V); + break; + } + } + psFree(iter); + + if (numPointers > 0) { + psLogMsg(__func__, PS_LOG_WARN, "Forced to copy %d pointers when copying metadata. Updating the " + "copied psMetadata will affect the original!\n", numPointers); + } + return out; +} + +// may need to extend this to change the keyname in the copy +bool psMetadataItemTransfer (psMetadata *out, psMetadata *in, char *key) +{ + + psMetadataItem *item = psMetadataLookup (in, key); + if (item == NULL) + return false; + + psMetadataAddItem (out, item, PS_LIST_TAIL, PS_META_REPLACE); + return true; +} + +void psMetadataPrint(psMetadata *md, int level) +{ + psMetadataIterator *iter = psMetadataIteratorAlloc(md, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *item = NULL; // Item from metadata + while ((item = psMetadataGetAndIncrement(iter))) { + // Indent... + for (int i = 0; i < level; i++) { + printf(" "); + } + printf("%s", item->name); + if (item->comment && strlen(item->comment) > 0) { + printf(" (%s)", item->comment); + } + printf(": "); + switch (item->type) { + case PS_DATA_STRING: + printf("%s", (char*)item->data.V); + break; + case PS_DATA_BOOL: + if (item->data.B) { + printf("True"); + } else { + printf("False"); + } + break; + case PS_DATA_S32: + printf("%d", item->data.S32); + break; + case PS_DATA_F32: + printf("%f", item->data.F32); + break; + case PS_DATA_F64: + printf("%f", item->data.F64); + break; + case PS_DATA_METADATA: + printf("\n"); + psMetadataPrint(item->data.V, level + 1); + break; + default: + printf("\n"); + psError(PS_ERR_IO, false, "Non-printable metadata type: %x\n", item->type); + } + printf("\n"); + } + psFree(iter); + + return; +} + +// XXX: This should probably be implemented using strpbrk +psList *psStringSplit(const char *string, + const char *splitters) +{ + psList *values = psListAlloc(NULL); // The list of values to return + if (string == NULL) + return values; // NULL string is not an error, just an empty list + + unsigned int length = strlen(string); // The length of the string + unsigned int numSplitters = strlen(splitters); // Number of characters that might split + unsigned int start = 0; // The position of the start of a word + for (int i = 1; i < length; i++) { + bool split = false; // Is this character a splitter? + for (int j = 0; j < numSplitters && ! split; j++) { + if (string[i] == splitters[j]) { + split = true; + } + } + if (split) { + if (i == start) { + // Some idiot put in two spaces, or two commas or something + start++; + } else { + // We're at the end of the word + psString word = psStringNCopy(&string[start], i - start); + (void)psListAdd(values, PS_LIST_TAIL, word); + start = i + 1; + psFree(word); + } + } + } + if (start < length) { + // Copy the last word + psString word = psStringNCopy(&string[start], length - start); + (void)psListAdd(values, PS_LIST_TAIL, word); + psFree(word); + } + + return values; +} + +psArray *psStringSplitArray (const char *string, const char *splitters) +{ + + psList *list = psStringSplit (string, splitters); + psArray *array = psListToArray (list); + psFree (list); + return array; +} + +#ifndef whitespace +#define whitespace(c) (((c) == ' ') || ((c) == '\t')) +#endif + +/* Strip whitespace from the start and end of STRING. */ +int psStringStrip (char *string) +{ + + int i; + + if (string == (char *) NULL) + return (FALSE); + + for (i = 0; whitespace (string[i]); i++) + ; + if (i) + memmove (string, string + i, strlen(string+i)+1); + for (i = strlen (string) - 1; (i > 0) && whitespace (string[i]); i--) + ; + string[++i] = 0; + return (i); + +} + +bool psFitsWriteHeaderNotImage (psFits *fits, psMetadata *header) +{ + + int status = 0; + char fitsErr[1024]; + + psMetadataItem *mdi = NULL; + mdi = psMetadataLookup (header, "NAXIS"); + if (mdi != NULL) { + mdi->data.S32 = 0; + mdi->type = PS_DATA_S32; + } + + fits_create_img (fits->fd, SHORT_IMG, 0, NULL, &status); + + if (status != 0) { + fits_get_errstatus (status, fitsErr); + psError (PS_ERR_IO, true, PS_ERRORTEXT_psFits_WRITE_FAILED, fitsErr); + exit (2); + } + + psFitsWriteHeader (header, fits); + + return true; +} Index: trunk/psModules/src/pslib/psAdditionals.h =================================================================== --- trunk/psModules/src/pslib/psAdditionals.h (revision 6872) +++ trunk/psModules/src/pslib/psAdditionals.h (revision 6872) @@ -0,0 +1,42 @@ +// Functions that should go into psLib. + + +#ifndef PS_ADDITIONALS_H +#define PS_ADDITIONALS_H + +#include "pslib.h" + +// Deep copy of metadata +// Corrected version of MHPCC code in psLib at the moment +psMetadata *pap_psMetadataCopy(psMetadata *out, // Target, to which the copy is made + const psMetadata *in // Source, from which the copy is made + ); + +// copy a metadata item from one psMetadata to another +bool psMetadataItemTransfer (psMetadata *out, // Destination: copy is placed here + psMetadata *in, // Source: item comes from here + char *key // key to identify the metadata item + ); + + +// Print out the metadata +void psMetadataPrint(psMetadata *md, // Metadata to print + int level // Indent level + ); + +// Split string on given characters +psList *psStringSplit(const char *string, // String to split + const char *splitters // Characters on which to split + ); + +// Split string on given characters +psArray *psStringSplitArray(const char *string, // String to split + const char *splitters // Characters on which to split + ); + +// strip whitespace from head and tail of string +int psStringStrip (char *string); + +// write out header with NAXIS=0 +bool psFitsWriteHeaderNotImage (psFits *fits, psMetadata *header); +#endif Index: trunk/psModules/src/pslib/psEllipse.c =================================================================== --- trunk/psModules/src/pslib/psEllipse.c (revision 6872) +++ trunk/psModules/src/pslib/psEllipse.c (revision 6872) @@ -0,0 +1,62 @@ +# include "pslib.h" +# include "psEllipse.h" + +psEllipseAxes psEllipseMomentsToAxes (psEllipseMoments moments) +{ + + psEllipseAxes axes; + + double f = sqrt (0.25*PS_SQR(moments.x2 - moments.y2) + PS_SQR(moments.xy)); + if (f > (moments.x2 + moments.y2) / 2.0) { + f = 0.98*(moments.x2 + moments.y2) / 2.0; + } + + axes.major = sqrt (0.5*(moments.x2 + moments.y2) + f); + axes.minor = sqrt (0.5*(moments.x2 + moments.y2) - f); + axes.theta = atan2 (2*moments.xy, moments.x2 - moments.y2) / 2; + // theta in radians + + return (axes); +} + +psEllipseShape psEllipseAxesToShape (psEllipseAxes axes) +{ + + psEllipseShape shape; + + double r1 = 1.0 / PS_SQR(axes.major) + 1.0 / PS_SQR(axes.minor); + double r2 = 1.0 / PS_SQR(axes.major) - 1.0 / PS_SQR(axes.minor); + + double sxr = r1 + r2*cos(2*axes.theta); + double syr = r1 - r2*cos(2*axes.theta); + + shape.sx = 1.0 / sqrt(sxr); + shape.sy = 1.0 / sqrt(syr); + shape.sxy = r2*sin(2*axes.theta); + + return (shape); +} + +psEllipseAxes psEllipseShapeToAxes (psEllipseShape shape) +{ + + psEllipseAxes axes; + + double f1 = 1.0 / PS_SQR(shape.sx) + 1.0 / PS_SQR(shape.sy); + double f2 = 1.0 / PS_SQR(shape.sx) - 1.0 / PS_SQR(shape.sy); + + // force the axis ratio to be less than 10 + double r1 = 0.5*0.95*sqrt (PS_SQR(f1) - PS_SQR(f2)); + + shape.sxy = PS_MIN(PS_MAX(shape.sxy, -r1), r1); + + axes.theta = atan2 (-2.0*shape.sxy, f2) / 2.0; + + double Ar = 0.25*f1 + 0.25*sqrt(PS_SQR(f2) + 4*PS_SQR(shape.sxy)); + double Br = 0.25*f1 - 0.25*sqrt(PS_SQR(f2) + 4*PS_SQR(shape.sxy)); + + axes.minor = 1.0 / sqrt (Ar); + axes.major = 1.0 / sqrt (Br); + + return (axes); +} Index: trunk/psModules/src/pslib/psEllipse.h =================================================================== --- trunk/psModules/src/pslib/psEllipse.h (revision 6872) +++ trunk/psModules/src/pslib/psEllipse.h (revision 6872) @@ -0,0 +1,30 @@ +// strucures to define elliptical shape parameters +typedef struct +{ + double major; + double minor; + double theta; +} +psEllipseAxes; + +typedef struct +{ + double x2; + double y2; + double xy; +} +psEllipseMoments; + +typedef struct +{ + double sx; + double sy; + double sxy; +} +psEllipseShape; + +// conversions between elliptical shape representations +psEllipseAxes psEllipseMomentsToAxes (psEllipseMoments moments); +psEllipseShape psEllipseAxesToShape (psEllipseAxes axes); +psEllipseAxes psEllipseShapeToAxes (psEllipseShape shape); + Index: trunk/psModules/src/pslib/psImageFlip.c =================================================================== --- trunk/psModules/src/pslib/psImageFlip.c (revision 6872) +++ trunk/psModules/src/pslib/psImageFlip.c (revision 6872) @@ -0,0 +1,76 @@ +#include +#include "pslib.h" + + +#define FLIP_X_CASE(TYPENAME,TYPE) \ +case TYPENAME: \ +for (int i = 0; i < image->numRows; i++) { \ + for (int j = 0; j < image->numCols; j++) { \ + output->data.TYPE[i][j] = image->data.TYPE[i][image->numCols - j - 1]; \ + } \ +} \ +break; + +// Return a flipped image in x +psImage *psImageFlipX(psImage *image // Image to flip + ) +{ + psImage *output = psImageAlloc(image->numCols, image->numRows, image->type.type); // Output image + switch(image->type.type) { + FLIP_X_CASE(PS_TYPE_U8, U8); + FLIP_X_CASE(PS_TYPE_U16, U16); + FLIP_X_CASE(PS_TYPE_U32, U32); + FLIP_X_CASE(PS_TYPE_U64, U64); + FLIP_X_CASE(PS_TYPE_S8, S8); + FLIP_X_CASE(PS_TYPE_S16, S16); + FLIP_X_CASE(PS_TYPE_S32, S32); + FLIP_X_CASE(PS_TYPE_S64, S64); + FLIP_X_CASE(PS_TYPE_F32, F32); + FLIP_X_CASE(PS_TYPE_F64, F64); + FLIP_X_CASE(PS_TYPE_C32, C32); + FLIP_X_CASE(PS_TYPE_C64, C64); + default: + psFree(output); + psError(PS_ERR_BAD_PARAMETER_TYPE, true, "Unknown type for input image: %x\n", image->type.type); + return NULL; + } + + return output; +} + + +#define FLIP_Y_CASE(TYPENAME,TYPE) \ +case TYPENAME: \ +for (int i = 0; i < image->numRows; i++) { \ + for (int j = 0; j < image->numCols; j++) { \ + output->data.TYPE[i][j] = image->data.TYPE[image->numRows - i - 1][j]; \ + } \ +} \ +break; + +// Return a flipped image in y +psImage *psImageFlipY(psImage *image // Image to flip + ) +{ + psImage *output = psImageAlloc(image->numCols, image->numRows, image->type.type); // Output image + switch(image->type.type) { + FLIP_Y_CASE(PS_TYPE_U8, U8); + FLIP_Y_CASE(PS_TYPE_U16, U16); + FLIP_Y_CASE(PS_TYPE_U32, U32); + FLIP_Y_CASE(PS_TYPE_U64, U64); + FLIP_Y_CASE(PS_TYPE_S8, S8); + FLIP_Y_CASE(PS_TYPE_S16, S16); + FLIP_Y_CASE(PS_TYPE_S32, S32); + FLIP_Y_CASE(PS_TYPE_S64, S64); + FLIP_Y_CASE(PS_TYPE_F32, F32); + FLIP_Y_CASE(PS_TYPE_F64, F64); + FLIP_Y_CASE(PS_TYPE_C32, C32); + FLIP_Y_CASE(PS_TYPE_C64, C64); + default: + psFree(output); + psError(PS_ERR_BAD_PARAMETER_TYPE, true, "Unknown type for input image: %x\n", image->type.type); + return NULL; + } + + return output; +} Index: trunk/psModules/src/pslib/psImageFlip.h =================================================================== --- trunk/psModules/src/pslib/psImageFlip.h (revision 6872) +++ trunk/psModules/src/pslib/psImageFlip.h (revision 6872) @@ -0,0 +1,13 @@ +#ifndef PS_IMAGE_FLIP_H +#define PS_IMAGE_FLIP_H + +#include "pslib.h" + +// Return a flipped image in x +psImage *psImageFlipX(psImage *image // Image to flip + ); +// Return a flipped image in y +psImage *psImageFlipY(psImage *image // Image to flip + ); + +#endif Index: trunk/psModules/src/pslib/psImageJpeg.c =================================================================== --- trunk/psModules/src/pslib/psImageJpeg.c (revision 6872) +++ trunk/psModules/src/pslib/psImageJpeg.c (revision 6872) @@ -0,0 +1,191 @@ +# include +# include // for strcasecmp +# include // for unlink +# include +# include "jpeglib.h" +# include "psImageJpeg.h" + +static void psImageJpegColormapFree (psImageJpegColormap *map) +{ + + if (map == NULL) + return; + + psFree (map->red); + psFree (map->green); + psFree (map->blue); + return; +} + +psImageJpegColormap *psImageJpegColormapAlloc () +{ + + psImageJpegColormap *map; + map = psAlloc (sizeof(psImageJpegColormap)); + psMemSetDeallocator(map, (psFreeFunc) psImageJpegColormapFree); + + map->red = psVectorAlloc (256, PS_TYPE_U8); + map->blue = psVectorAlloc (256, PS_TYPE_U8); + map->green = psVectorAlloc (256, PS_TYPE_U8); + + return (map); +} + +psImageJpegColormap *psImageJpegColormapSet (psImageJpegColormap *map, char *name) +{ + + if (map == NULL) { + map = psImageJpegColormapAlloc (); + } + + /* grayscale */ + if ((!strcasecmp (name, "grayscale")) || (!strcasecmp (name, "greyscale"))) { + for (int i = 0; i < map->red->n; i++) { + map->red->data.U8[i] = PS_JPEG_RANGELIM(i); + map->green->data.U8[i] = PS_JPEG_RANGELIM(i); + map->blue->data.U8[i] = PS_JPEG_RANGELIM(i); + } + return map; + } + + /* -grayscale */ + if ((!strcasecmp (name, "-grayscale")) || (!strcasecmp (name, "-greyscale"))) { + for (int i = 0; i < map->red->n; i++) { + map->red->data.U8[i] = PS_JPEG_RANGELIM(256 - i); + map->green->data.U8[i] = PS_JPEG_RANGELIM(256 - i); + map->blue->data.U8[i] = PS_JPEG_RANGELIM(256 - i); + } + return map; + } + + /* rainbow */ + if (!strcasecmp (name, "rainbow")) { + int I1 = 0.25*map->red->n; + int I2 = 0.50*map->red->n; + int I3 = 0.75*map->red->n; + for (int i = 0; i < I1; i++) { + map->red->data.U8[i] = 0; + map->green->data.U8[i] = 0; + map->blue->data.U8[i] = PS_JPEG_RANGELIM(4*i); + } + for (int i = I1; i < I2; i++) { + map->red->data.U8[i] = PS_JPEG_RANGELIM(4*(i - I1)); + map->green->data.U8[i] = 0; + map->blue->data.U8[i] = PS_JPEG_RANGELIM(4*(I2 - i)); + } + for (int i = I2; i < I3; i++) { + map->red->data.U8[i] = 255; + map->green->data.U8[i] = 4*(i - I2); + map->blue->data.U8[i] = 0; + } + for (int i = I3; i < map->red->n; i++) { + map->red->data.U8[i] = 255; + map->green->data.U8[i] = 255; + map->blue->data.U8[i] = PS_JPEG_RANGELIM(4*(i - I3)); + } + return map; + } + + /* heat */ + if (!strcasecmp (name, "heat")) { + int I1 = 0.25*map->red->n; + int I2 = 0.50*map->red->n; + int I3 = 0.75*map->red->n; + for (int i = 0; i < I1; i++) { + map->red->data.U8[i] = PS_JPEG_RANGELIM(2*i); + map->green->data.U8[i] = 0; + map->blue->data.U8[i] = 0; + } + for (int i = I1; i < I2; i++) { + map->red->data.U8[i] = PS_JPEG_RANGELIM(2*i); + map->green->data.U8[i] = PS_JPEG_RANGELIM(2*(i - I1)); + map->blue->data.U8[i] = 0; + } + for (int i = I2; i < I3; i++) { + map->red->data.U8[i] = 255; + map->green->data.U8[i] = PS_JPEG_RANGELIM(2*(i - I1)); + map->blue->data.U8[i] = PS_JPEG_RANGELIM(2*(i - I2)); + } + for (int i = I3; i < map->red->n; i++) { + map->red->data.U8[i] = 255; + map->green->data.U8[i] = 255; + map->blue->data.U8[i] = PS_JPEG_RANGELIM(2*(i - I2)); + } + return map; + } + + // invalid colormap : warn user + map = psImageJpegColormapSet (map, "greyscale"); + return map; +} + +bool psImageJpeg (psImageJpegColormap *map, psImage *image, char *filename, float min, float max) +{ + + struct jpeg_compress_struct cinfo; + struct jpeg_error_mgr jerr; + + int pixel; + JSAMPLE *jpegLine; // Points to data for current line + JSAMPROW jpegLineList[1]; // pointer to JSAMPLE row[s] + JSAMPLE *outPix; + + if (map->red == NULL) + return false; + if (map->green == NULL) + return false; + if (map->blue == NULL) + return false; + + /* JPEG init calls */ + cinfo.err = jpeg_std_error (&jerr); + jpeg_create_compress (&cinfo); + + /* open file, prep for jpeg */ + FILE *f = fopen (filename, "w"); + if (f == NULL) { + fprintf (stderr, "failed to open %s for output\n", filename); + return (TRUE); + } + jpeg_stdio_dest(&cinfo, f); + + /* set up color jpeg buffers */ + int quality = 75; + cinfo.image_width = image->numCols; // image width and height, in pixels + cinfo.image_height = image->numRows; + cinfo.input_components = 3; + cinfo.in_color_space = JCS_RGB; + jpeg_set_defaults (&cinfo); + jpeg_set_quality (&cinfo, quality, true); // limit to baseline-JPEG values + jpeg_start_compress (&cinfo, true); + + jpegLine = psAlloc (3*image->numCols*sizeof(JSAMPLE)); + jpegLineList[0] = jpegLine; + + psU8 *Rpix = map->red->data.U8; + psU8 *Gpix = map->green->data.U8; + psU8 *Bpix = map->blue->data.U8; + + float zero = min; + float scale = 256.0/(max - min); + + for (int j = 0; j < image->numRows; j++) { + psF32 *row = image->data.F32[j]; + + outPix = jpegLine; + for (int i = 0; i < image->numCols; i++, outPix += 3) { + pixel = PS_JPEG_SCALEVALUE(row[i],zero,scale); + outPix[0] = Rpix[pixel]; + outPix[1] = Gpix[pixel]; + outPix[2] = Bpix[pixel]; + } + jpeg_write_scanlines (&cinfo, jpegLineList, 1); + } + + jpeg_finish_compress (&cinfo); + fclose (f); + jpeg_destroy_compress (&cinfo); + + psFree (jpegLine); + return true; +} Index: trunk/psModules/src/pslib/psImageJpeg.h =================================================================== --- trunk/psModules/src/pslib/psImageJpeg.h (revision 6872) +++ trunk/psModules/src/pslib/psImageJpeg.h (revision 6872) @@ -0,0 +1,32 @@ +/** @file psImageJpeg.h + * + * the functions to generate JPEG images from psImage + */ + +# ifndef PS_IMAGE_JPEG_H +# define PS_IMAGE_JPEG_H + +typedef struct +{ + psString name; + psVector *red; + psVector *green; + psVector *blue; +} +psImageJpegColormap; + +# define PS_JPEG_RANGELIM(A)(PS_MAX(0,PS_MIN(255,(A)))) + +# define PS_JPEG_SCALEVALUE(VALUE,ZERO,SCALE)(PS_MAX(0,PS_MIN(255,(SCALE*(VALUE-ZERO))))) + +// allocate a colormap (does not define the map values) +psImageJpegColormap *psImageJpegColormapAlloc (); + +// set the colormap values using the supplied name +psImageJpegColormap *psImageJpegColormapSet (psImageJpegColormap *map, char *name); + +// write out a JPEG file using the supplied image and colormap +// output goes to the specified filename +bool psImageJpeg (psImageJpegColormap *map, psImage *image, char *filename, float min, float max); + +# endif /* PS_IMAGE_JPEG_H */ Index: trunk/psModules/src/pslib/psImageUnbin.c =================================================================== --- trunk/psModules/src/pslib/psImageUnbin.c (revision 6872) +++ trunk/psModules/src/pslib/psImageUnbin.c (revision 6872) @@ -0,0 +1,273 @@ +#include +#include "pslib.h" +#include "psImageUnbin.h" + +// interpolate from model to background (~bresenham linear interpolation) +// XXX this code skips the initial pixels? +psImage *psImageUnbin (psImage *out, psImage *in, int DX, int DY, int dx, int dy) +{ + + int nx = in->numCols; + int ny = in->numRows; + + if (out == NULL) + psAbort ("psImageUnbin", "please supply output image"); + + int Nx = out->numCols; + int Ny = out->numRows; + + psF32 **vIn = in->data.F32; + psF32 **vOut = out->data.F32; + + for (int Iy = 0; Iy < ny-1; Iy ++) { + for (int Ix = 0; Ix < nx-1; Ix ++) { + + float V00 = vIn[Iy+0][Ix+0]; + float V01 = vIn[Iy+0][Ix+1]; + float V10 = vIn[Iy+1][Ix+0]; + float V11 = vIn[Iy+1][Ix+1]; + + // a single binned pixel quad + // (Xs,Ys) : (Xe,Ye) : binned pixel centers in unbinned coords + // corresponding to (Ix,Iy), (Ix+1,Iy+1) + int Xs = (Ix + 1)*DX - dx; + int Ys = (Iy + 1)*DY - dy; + int Xe = Xs + DX; + int Ye = Ys + DY; + + for (int iy = Ys; (iy < Ye) && (iy < Ny); iy++) { + float Vxs = (V10 - V00)*(iy - Ys) / DY + V00; + float Vxe = (V11 - V01)*(iy - Ys) / DY + V01; + float dV = (Vxe - Vxs) / DX; + float V = Vxs; + for (int ix = Xs; (ix < Xe) && (ix < Nx); ix++) { + vOut[iy][ix] = V; + V += dV; + } + } + } + } + + // side pixels + int Xs = DX - dx; + int Xe = nx*DX - dx; + for (int Iy = 0; Iy < ny - 1; Iy++) { + + int Ys = (Iy + 1)*DY - dy; + int Ye = Ys + DY; + + // leading edge + float V0 = vIn[Iy+0][0]; + float V1 = vIn[Iy+1][0]; + float dV = (V1 - V0) / DY; + float V = V0; + for (int iy = Ys; (iy < Ye) && (iy < Ny); iy++) { + for (int ix = 0; ix < Xs; ix++) { + vOut[iy][ix] = V; + } + V += dV; + } + + // trailing edge + V0 = vIn[Iy+0][nx-1]; + V1 = vIn[Iy+1][nx-1]; + dV = (V1 - V0) / DY; + V = V0; + for (int iy = Ys; (iy < Ye) && (iy < Ny); iy++) { + for (int ix = Xe; ix < Nx; ix++) { + vOut[iy][ix] = V; + } + V += dV; + } + } + + // top and bottom pixels + int Ys = DY - dy; + int Ye = ny*DY - dy; + for (int Ix = 0; Ix < nx - 1; Ix++) { + + int Xs = (Ix + 1)*DX - dx; + int Xe = Xs + DX; + + // top edge + float V0 = vIn[0][Ix+0]; + float V1 = vIn[0][Ix+1]; + float dV = (V1 - V0) / DX; + for (int iy = 0; iy < Ys; iy++) { + float V = V0; + for (int ix = Xs; (ix < Xe) && (ix < Nx); ix++) { + vOut[iy][ix] = V; + V += dV; + } + } + + // bottom edge + V0 = vIn[ny-1][Ix+0]; + V1 = vIn[ny-1][Ix+1]; + dV = (V1 - V0) / DX; + for (int iy = Ye; iy < Ny; iy++) { + float V = V0; + for (int ix = Xs; (ix < Xe) && (ix < Nx); ix++) { + vOut[iy][ix] = V; + V += dV; + } + } + } + + // the four corners + { + float V; + // 0,0 + V = vIn[0][0]; + for (int iy = 0; iy < DY - dy; iy++) + { + for (int ix = 0; ix < DX - dx; ix++) { + vOut[iy][ix] = V; + } + } + // Nx,0 + V = vIn[0][nx-1]; + for (int iy = 0; iy < DY - dy; iy++) + { + for (int ix = nx*DX - dx; ix < Nx; ix++) { + vOut[iy][ix] = V; + } + } + // 0,Ny + V = vIn[ny-1][0]; + for (int iy = ny*DY - dy; iy < Ny; iy++) + { + for (int ix = 0; ix < DX - dx; ix++) { + vOut[iy][ix] = V; + } + } + // Nx,Ny + V = vIn[nx-1][ny-1]; + for (int iy = ny*DY - dy; iy < Ny; iy++) + { + for (int ix = nx*DX - dx; ix < Nx; ix++) { + vOut[iy][ix] = V; + } + } + } + + return out; +} + +// random number seed to select a fraction of the image pixels +static psRandom *rnd = NULL; + +// use no more than MAX_SAMPLE_PIXELS pixels for each median box +static int MAX_SAMPLE_PIXELS; + +void psImageClippedStatsInit (int nMax) +{ + + MAX_SAMPLE_PIXELS = nMax; + + if (!rnd) { + rnd = psRandomAlloc (PS_RANDOM_TAUS, 0); + } + return; +} + +void psImageClippedStatsCleanup () +{ + psFree (rnd); + rnd = NULL; + return; +} + +psStats *psImageClippedStats (psImage *image, psImage *mask, psU8 maskValue, double fmin, double fmax) +{ + double value; + int nx = image->numCols; + int ny = image->numRows; + + psStats *stats = psStatsAlloc (PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_QUARTILE); + if (nx*ny <= 0) + return stats; + + int Nsubset = PS_MIN (MAX_SAMPLE_PIXELS, nx*ny); + int Npixels = nx*ny; + + psVector *values = psVectorAlloc (Nsubset, PS_TYPE_F32); + + float min = values->data.F32[0]; + float max = values->data.F32[0]; + + int n = 0; + for (int i = 0; i < Nsubset; i++) { + double frnd = psRandomUniform (rnd); + int pixel = Npixels * frnd; + int ix = pixel % nx; + int iy = pixel / nx; + + if (mask && mask->data.U8[iy][ix] & maskValue) + continue; + + value = image->data.F32[iy][ix]; + min = PS_MIN (value, min); + max = PS_MIN (value, max); + values->data.F32[n] = value; + n++; + } + values->n = n; + + int imin = fmin * n; + int imax = fmax * n; + int npts = imax - imin + 1; + + fsort (values->data.F32, n); + + value = 0; + for (int i = imin; (i <= imax) && (i < n); i++) { + value += values->data.F32[i]; + } + value = value / npts; + + stats->robustMedian = value; + stats->robustUQ = values->data.F32[imax]; + stats->robustLQ = values->data.F32[imin]; + + psFree (values); + return stats; + // XXX correct for selection bias?? +} + +void fsort (float *value, int N) +{ + + int l,j,ir,i; + float temp; + + if (N < 2) + return; + l = N >> 1; + ir = N - 1; + for (;;) { + if (l > 0) { + temp = value[--l]; + } else { + temp = value[ir]; + value[ir] = value[0]; + if (--ir == 0) { + value[0] = temp; + return; + } + } + i = l; + j = (l << 1) + 1; + while (j <= ir) { + if (j < ir && value[j] < value[j+1]) + ++j; + if (temp < value[j]) { + value[i]=value[j]; + j += (i=j) + 1; + } else + j = ir + 1; + } + value[i] = temp; + } +} + Index: trunk/psModules/src/pslib/psImageUnbin.h =================================================================== --- trunk/psModules/src/pslib/psImageUnbin.h (revision 6872) +++ trunk/psModules/src/pslib/psImageUnbin.h (revision 6872) @@ -0,0 +1,18 @@ +#ifndef PS_IMAGE_UNBIN_H +#define PS_IMAGE_UNBIN_H + +#include "pslib.h" + +// This needs to be considered more carefully +psImage *psImageUnbin (psImage *out, psImage *in, int DX, int DY, int dx, int dy); + +void psImageClippedStatsInit (int nMax); +void psImageClippedStatsCleanup (); + +// my temporary image stats function; seems to be much faster than psLib??? +psStats *psImageClippedStats (psImage *image, psImage *mask, psU8 maskValue, double fmin, double fmax); + +// my temporary sort which is based on N.R.; seems to be faster than psLib sort??? +void fsort (float *value, int N); + +#endif Index: trunk/psModules/src/pslib/psLine.c =================================================================== --- trunk/psModules/src/pslib/psLine.c (revision 6872) +++ trunk/psModules/src/pslib/psLine.c (revision 6872) @@ -0,0 +1,55 @@ +# include +# include "psLine.h" + +static void psLineFree (psLine *line) +{ + + if (line == NULL) + return; + + psFree (line->line); + return; +} + +// allocate a psLine structrue +psLine *psLineAlloc (int Nline) +{ + + psLine *line; + line = psAlloc (sizeof(psLine)); + psMemSetDeallocator(line, (psFreeFunc) psLineFree); + + line->Nline = 0; + line->NLINE = Nline; + line->line = psAlloc (Nline); + return (line); +} + +bool psLineInit (psLine *line) +{ + if (line == NULL) + return (false); + line->Nline = 0; + return (true); +} + +bool psLineAdd (psLine *line, char *format, ...) +{ + + int Nchar; + va_list ap; + + if (line == NULL) + return (false); + + int nMax = line->NLINE - line->Nline; + + va_start (ap, format); + Nchar = vsnprintf (&line->line[line->Nline], nMax, format, ap); + line->Nline += PS_MIN (nMax - 1, Nchar); + va_end (ap); + + if (Nchar >= nMax) + return (false); + return (true); +} Index: trunk/psModules/src/pslib/psLine.h =================================================================== --- trunk/psModules/src/pslib/psLine.h (revision 6872) +++ trunk/psModules/src/pslib/psLine.h (revision 6872) @@ -0,0 +1,27 @@ +/** @file psLine.h + * + * the psLine functions allow manipulation of fixed-length lines + */ + +# ifndef PS_LINE_H +# define PS_LINE_H + +// structure to carry a dynamic string +typedef struct +{ + int NLINE; + int Nline; + char *line; +} +psLine; + +// allocate a line object of length Nline +psLine *psLineAlloc (int Nline); + +// (re-)init the line +bool psLineInit (psLine *line); + +// add the new string segment to the line +bool psLineAdd (psLine *line, char *format, ...); + +# endif /* PS_LINE_H */ Index: trunk/psModules/src/pslib/psMetadataItemParse.c =================================================================== --- trunk/psModules/src/pslib/psMetadataItemParse.c (revision 6872) +++ trunk/psModules/src/pslib/psMetadataItemParse.c (revision 6872) @@ -0,0 +1,85 @@ +#include +#include "pslib.h" + +psF32 psMetadataItemParseF32(psMetadataItem *item + ) +{ + switch (item->type) { + case PS_DATA_F32: + return item->data.F32; + case PS_DATA_F64: + // Assume it's OK to truncate to floating point from double + return (float)item->data.F64; + case PS_DATA_S32: + // Promote to float + return (float)item->data.S32; + default: + psError(PS_ERR_IO, true, "Item %s (%s) is not of floating point type (%x) --- treating as NaN.\n", + item->name, item->comment, item->type); + return NAN; + } +} + +psF64 psMetadataItemParseF64(psMetadataItem *item + ) +{ + switch (item->type) { + case PS_TYPE_F64: + return item->data.F64; + case PS_TYPE_F32: + // Promote to double + return (double)item->data.F32; + case PS_TYPE_S32: + // Promote to double + return (double)item->data.S32; + default: + psError(PS_ERR_IO, true, "Item %s (%s) is not of double-precision floating point type (%x) " + "--- treating as NaN.\n", item->name, item->comment, item->type); + return NAN; + } +} + +psS32 psMetadataItemParseS32(psMetadataItem *item + ) +{ + switch (item->type) { + case PS_TYPE_S32: + return item->data.S32; + case PS_TYPE_F32: + psLogMsg(__func__, PS_LOG_WARN, "Item %s (%s) should be S32, but is F32 --- converting.\n", + item->name, item->comment); + return (int)item->data.F32; + case PS_TYPE_F64: + psLogMsg(__func__, PS_LOG_WARN, "Item %s (%s) should be S32, but is F64 --- converting.\n", + item->name, item->comment); + return (int)item->data.F64; + default: + psError(PS_ERR_IO, true, "Item %s (%s) is not of integer type (%x) --- treating as zero.\n", + item->name, item->comment, item->type); + return 0; + } +} + +psString psMetadataItemParseString(psMetadataItem *item + ) +{ + switch (item->type) { + case PS_DATA_STRING: + return psMemIncrRefCounter(item->data.V); + case PS_DATA_F32: { + psString value = NULL; // String to return + psStringAppend(&value, "%f", item->data.F32); + return value; + } + case PS_DATA_S32: { + psString value = NULL; // String to return + psStringAppend(&value, "%d", item->data.S32); + return value; + } + default: + psError(PS_ERR_IO, true, "Item %s (%s) is not of string type (%x) --- treating as " + "undefined.\n", item->name, item->comment, item->type); + return psStringCopy(""); + } +} + Index: trunk/psModules/src/pslib/psMetadataItemParse.h =================================================================== --- trunk/psModules/src/pslib/psMetadataItemParse.h (revision 6872) +++ trunk/psModules/src/pslib/psMetadataItemParse.h (revision 6872) @@ -0,0 +1,15 @@ +#ifndef PS_METADATA_ITEM_PARSE_H +#define PS_METADATA_ITEM_PARSE_H + +#include "pslib.h" + +psF32 psMetadataItemParseF32(psMetadataItem *item + ); +psF64 psMetadataItemParseF64(psMetadataItem *item + ); +psS32 psMetadataItemParseS32(psMetadataItem *item + ); +psString psMetadataItemParseString(psMetadataItem *item + ); + +#endif Index: trunk/psModules/src/pslib/psPolynomialUtils.c =================================================================== --- trunk/psModules/src/pslib/psPolynomialUtils.c (revision 6872) +++ trunk/psModules/src/pslib/psPolynomialUtils.c (revision 6872) @@ -0,0 +1,161 @@ +# include +# include // for strcasecmp +# include // for unlink +# include +# include "psPolynomialUtils.h" + +psPolynomial4D *psVectorChiClipFitPolynomial4D( + psPolynomial4D *poly, + psStats *stats, + const psVector *mask, + psMaskType maskValue, + const psVector *f, + const psVector *fErr, + const psVector *x, + const psVector *y, + const psVector *z, + const psVector *t) +{ + PS_ASSERT_POLY_NON_NULL(poly, NULL); + PS_ASSERT_POLY_TYPE(poly, PS_POLYNOMIAL_ORD, NULL); + PS_ASSERT_PTR_NON_NULL(stats, NULL); + PS_ASSERT_VECTOR_NON_NULL(f, NULL); + PS_ASSERT_VECTOR_TYPE_F32_OR_F64(f, NULL); + if (mask != NULL) { + PS_ASSERT_VECTORS_SIZE_EQUAL(f, mask, NULL); + PS_ASSERT_VECTOR_TYPE(mask, PS_TYPE_U8, NULL); + } + PS_ASSERT_VECTOR_NON_NULL(x, NULL); + PS_ASSERT_VECTORS_SIZE_EQUAL(f, x, NULL); + PS_ASSERT_VECTOR_TYPE_F32_OR_F64(x, NULL); + PS_ASSERT_VECTOR_NON_NULL(y, NULL); + PS_ASSERT_VECTORS_SIZE_EQUAL(f, y, NULL); + PS_ASSERT_VECTOR_TYPE_F32_OR_F64(y, NULL); + PS_ASSERT_VECTOR_NON_NULL(z, NULL); + PS_ASSERT_VECTORS_SIZE_EQUAL(f, z, NULL); + PS_ASSERT_VECTOR_TYPE_F32_OR_F64(z, NULL); + PS_ASSERT_VECTOR_NON_NULL(t, NULL); + PS_ASSERT_VECTORS_SIZE_EQUAL(f, t, NULL); + PS_ASSERT_VECTOR_TYPE_F32_OR_F64(t, NULL); + PS_ASSERT_VECTOR_NON_NULL(fErr, NULL); + PS_ASSERT_VECTORS_SIZE_EQUAL(fErr, mask, NULL); + PS_ASSERT_VECTOR_TYPE_F32_OR_F64(fErr, NULL); + + // clipping range defined by min and max and/or clipSigma + float minClipSigma; + float maxClipSigma; + if (isfinite(stats->max)) { + maxClipSigma = +fabs(stats->max); + } else { + maxClipSigma = +fabs(stats->clipSigma); + } + if (isfinite(stats->min)) { + minClipSigma = -fabs(stats->min); + } else { + minClipSigma = -fabs(stats->clipSigma); + } + psVector *fit = NULL; + psVector *resid = psVectorAlloc (x->n, PS_TYPE_F64); + + // eventual expansion: user supplies one of various stats option pairs, + // eg (SAMPLE_MEAN | SAMPLE_STDEV) and the correct pair is used to + // evaluate the clipping sigma + // for now, for the SAMPLE_MEDIAN and SAMPLE_STDEV to be used + stats->options |= (PS_STAT_SAMPLE_MEDIAN | PS_STAT_SAMPLE_STDEV); + + for (int N = 0; N < stats->clipIter; N++) { + int Nkeep = 0; + + poly = psVectorFitPolynomial4D (poly, mask, maskValue, f, fErr, x, y, z, t); + fit = psPolynomial4DEvalVector (poly, x, y, z, t); + resid = (psVector *) psBinaryOp (resid, (void *) f, "-", (void *) fit); + + stats = psVectorStats (stats, resid, NULL, mask, maskValue); + psTrace (__func__, 5, "resid stats: %f +/- %f\n", stats->sampleMedian, stats->sampleStdev); + + // set mask if pts are not valid + // we are masking out any point which is out of range + // recovery is not allowed with this scheme + for (int i = 0; i < resid->n; i++) { + if ((mask != NULL) && (mask->data.U8[i] & maskValue)) { + continue; + } + float sigma = hypot (psVectorGet (fErr, i), stats->sampleStdev); + if (resid->data.F64[i] - stats->sampleMedian > sigma*maxClipSigma) { + if (mask != NULL) { + mask->data.U8[i] |= 0x01; + } + continue; + } + if (resid->data.F64[i] - stats->sampleMedian < sigma*minClipSigma) { + if (mask != NULL) { + mask->data.U8[i] |= 0x01; + } + continue; + } + Nkeep ++; + } + + psTrace (__func__, 4, "keeping %d of %d pts for fit\n", + Nkeep, x->n); + + stats->clippedNvalues = Nkeep; + psFree (fit); + } + // Free local temporary variables + psFree (resid); + + if (poly == NULL) { + psError(PS_ERR_UNKNOWN, true, "Could not fit a polynomial to the data. Returning NULL.\n"); + return(NULL); + } + return(poly); +} + +psPolynomial2D *psImageBicubeFit (psImage *image, int x, int y) +{ + + int ix = x - image->col0; + int iy = y - image->row0; + + psF32 *Fm = &image->data.F32[iy - 1][ix]; + psF32 *Fo = &image->data.F32[iy + 0][ix]; + psF32 *Fp = &image->data.F32[iy + 1][ix]; + + double Fxm = Fm[-1] + Fo[-1] + Fp[-1]; + double Fxp = Fm[+1] + Fo[+1] + Fp[+1]; + double Fym = Fm[-1] + Fm[+0] + Fm[+1]; + double Fyp = Fp[-1] + Fp[+0] + Fp[+1]; + double Foo = Fym + Fyp + Fo[-1] + Fo[+0] + Fo[+1]; + + psPolynomial2D *poly = psPolynomial2DAlloc (PS_POLYNOMIAL_ORD, 2, 2); + poly->mask[2][2] = 1; + poly->mask[1][2] = 1; + poly->mask[2][1] = 1; + + poly->coeff[0][0] = Foo*(5.0/9.0) - (Fxp + Fxm)/3.0 - (Fyp + Fym)/3.0 ; + + poly->coeff[1][0] = (Fxp - Fxm)/6.0; + poly->coeff[0][1] = (Fyp - Fym)/6.0; + + poly->coeff[2][0] = (Fxp + Fxm)/2.0 - Foo/3.0; + poly->coeff[0][2] = (Fyp + Fym)/2.0 - Foo/3.0; + + poly->coeff[1][1] = (Fp[+1] + Fm[-1] - Fm[+1] - Fp[-1])/4.0; + + return (poly); +} + +psPlane psImageBicubeMin (psPolynomial2D *poly) +{ + + psPlane min; + + min.xErr = min.yErr = 0; + + double det = 4*poly->coeff[2][0]*poly->coeff[0][2] - PS_SQR(poly->coeff[1][1]); + + min.x = (poly->coeff[1][1]*poly->coeff[0][1] - 2*poly->coeff[0][2]*poly->coeff[1][0]) / det; + min.y = (poly->coeff[1][1]*poly->coeff[1][0] - 2*poly->coeff[2][0]*poly->coeff[0][1]) / det; + return (min); +} Index: trunk/psModules/src/pslib/psPolynomialUtils.h =================================================================== --- trunk/psModules/src/pslib/psPolynomialUtils.h (revision 6872) +++ trunk/psModules/src/pslib/psPolynomialUtils.h (revision 6872) @@ -0,0 +1,28 @@ +/** @file psPolynomialUtils.h + * + * extra psPolynomial-related functions + */ + +# ifndef PS_POLY_UTILS_H +# define PS_POLY_UTILS_H + +// perform vector clip-fit based on significance of deviations +psPolynomial4D *psVectorChiClipFitPolynomial4D( + psPolynomial4D *poly, + psStats *stats, + const psVector *mask, + psMaskType maskValue, + const psVector *f, + const psVector *fErr, + const psVector *x, + const psVector *y, + const psVector *z, + const psVector *t); + +// fit a 2D 2nd order polynomial to the 9 pixels centered on (x,y) +psPolynomial2D *psImageBicubeFit (psImage *image, int x, int y); + +// detemine the min(max) of the special 2D 2nd order polynomial +psPlane psImageBicubeMin (psPolynomial2D *poly); + +# endif /* PS_POLY_UTILS_H */ Index: trunk/psModules/src/pslib/psRegionIsBad.c =================================================================== --- trunk/psModules/src/pslib/psRegionIsBad.c (revision 6872) +++ trunk/psModules/src/pslib/psRegionIsBad.c (revision 6872) @@ -0,0 +1,21 @@ +#include +#include "pslib.h" + +bool psRegionIsBad(const psRegion region) +{ + return isnan(region.x0) || isnan(region.x1) || isnan(region.y0) || isnan(region.y1); +} + +bool psRegionIsNaN (psRegion region) +{ + + if (!isfinite(region.x0)) + return true; + if (!isfinite(region.x1)) + return true; + if (!isfinite(region.y0)) + return true; + if (!isfinite(region.y1)) + return true; + return false; +} Index: trunk/psModules/src/pslib/psRegionIsBad.h =================================================================== --- trunk/psModules/src/pslib/psRegionIsBad.h (revision 6872) +++ trunk/psModules/src/pslib/psRegionIsBad.h (revision 6872) @@ -0,0 +1,12 @@ +#ifndef PS_REGION_IS_BAD_H +#define PS_REGION_IS_BAD_H + +#include "pslib.h" + +bool psRegionIsBad(const psRegion region); + +// test is any element of the region is not finite +bool psRegionIsNaN (psRegion region // test for this region + ); + +#endif Index: trunk/psModules/src/pslib/psSparse.c =================================================================== --- trunk/psModules/src/pslib/psSparse.c (revision 6872) +++ trunk/psModules/src/pslib/psSparse.c (revision 6872) @@ -0,0 +1,245 @@ +# include +# include "psSparse.h" + +static void psSparseFree (psSparse *sparse) +{ + if (sparse == NULL) + return; + psFree (sparse->Aij); + psFree (sparse->Bfj); + psFree (sparse->Qii); + psFree (sparse->Si); + psFree (sparse->Sj); + return; +} + +// allocate a sparse matrix container for Nrows, with Nelem slots allocated +psSparse *psSparseAlloc (int Nrows, int Nelem) +{ + + psSparse *sparse = (psSparse *) psAlloc (sizeof(psSparse)); + sparse->Aij = psVectorAlloc (Nelem, PS_DATA_F32); + sparse->Si = psVectorAlloc (Nelem, PS_DATA_S32); + sparse->Sj = psVectorAlloc (Nelem, PS_DATA_S32); + + sparse->Aij->n = 0; + sparse->Si->n = 0; + sparse->Sj->n = 0; + sparse->Nelem = 0; + + sparse->Bfj = psVectorAlloc (Nrows, PS_DATA_F32); + sparse->Qii = psVectorAlloc (Nrows, PS_DATA_F32); + + sparse->Nrows = Nrows; + psMemSetDeallocator(sparse, (psFreeFunc) psSparseFree); + return (sparse); +} + +// user should only add elements above the diagonal, but we don't check this +void psSparseMatrixElement (psSparse *sparse, int i, int j, float value) +{ + + int k; + + if (i < j) { + fprintf (stderr, "*** error: subdiagonal element ***\n"); + return; + } + + if (i == j) { + // add to the diagonal + sparse->Qii->data.F32[i] = value; + + // check vectors lengths and extend if needed + if (sparse->Nelem >= sparse->Aij->nalloc) { + psVectorRealloc (sparse->Aij, sparse->Aij->nalloc + 100); + psVectorRealloc (sparse->Si, sparse->Si->nalloc + 100); + psVectorRealloc (sparse->Sj, sparse->Sj->nalloc + 100); + } + + k = sparse->Nelem; + sparse->Aij->data.F32[k] = value; + sparse->Si->data.S32[k] = i; + sparse->Sj->data.S32[k] = j; + + sparse->Nelem ++; + sparse->Aij->n ++; + sparse->Si->n ++; + sparse->Sj->n ++; + } else { + // check vectors lengths and extend if needed + if (sparse->Nelem >= sparse->Aij->nalloc - 1) { + psVectorRealloc (sparse->Aij, sparse->Aij->nalloc + 100); + psVectorRealloc (sparse->Si, sparse->Si->nalloc + 100); + psVectorRealloc (sparse->Sj, sparse->Sj->nalloc + 100); + } + + k = sparse->Nelem; + sparse->Aij->data.F32[k] = value; + sparse->Si->data.S32[k] = i; + sparse->Sj->data.S32[k] = j; + k++; + + sparse->Aij->data.F32[k] = value; + sparse->Si->data.S32[k] = j; + sparse->Sj->data.S32[k] = i; + + sparse->Nelem += 2; + sparse->Aij->n += 2; + sparse->Si->n += 2; + sparse->Sj->n += 2; + } + return; +} + +void psSparseVectorElement (psSparse *sparse, int i, float value) +{ + + sparse->Bfj->data.F32[i] = value; + return; +} + +// multiple A * x +psVector *psSparseMatrixTimesVector (psVector *output, psSparse *matrix, psVector *vector) +{ + + int i, Nelem; + float F; + + if (output == NULL) { + output = psVectorAlloc (vector->n, PS_DATA_F32); + } + + Nelem = 0; + for (int j = 0; j < vector->n; j++) { + F = 0; + while (matrix->Sj->data.S32[Nelem] == j) { + i = matrix->Si->data.S32[Nelem]; + F += vector->data.F32[i] * matrix->Aij->data.F32[Nelem]; + Nelem++; + } + output->data.F32[j] = F; + } + return (output); +} + +psVector *psSparseSolve (psVector *guess, psSparseConstraint constraint, psSparse *sparse, int Niter) +{ + + psF32 dG; + + psVector *Qii = sparse->Qii; + psVector *Bfj = sparse->Bfj; + + guess = psVectorCopy (guess, Bfj, PS_DATA_F32); + + // temporary storage for intermediate results + psVector *dQ = psVectorAlloc (guess->n, PS_DATA_F32); + + for (int j = 0; j < Niter; j++) { + dQ = psSparseMatrixTimesVector (dQ, sparse, guess); + for (int i = 0; i < dQ->n; i++) { + dG = (dQ->data.F32[i] - Bfj->data.F32[i]) / Qii->data.F32[i]; + if (fabs (dG) > constraint.paramDelta) { + if (dG > 0) { + dG = +constraint.paramDelta; + } else { + dG = -constraint.paramDelta; + } + } + guess->data.F32[i] -= dG; + guess->data.F32[i] = PS_MAX (guess->data.F32[i], constraint.paramMin); + guess->data.F32[i] = PS_MIN (guess->data.F32[i], constraint.paramMax); + } + } + psFree (dQ); + return (guess); +} + +void psSparseResort (psSparse *sparse) +{ + + int Nelem = sparse->Nelem; + + psVector *index = psVectorSortIndex (NULL, sparse->Sj); + psVector *Aij = sparse->Aij; + psVector *Si = sparse->Si; + psVector *Sj = sparse->Sj; + + // allocate new temporary vectors + psVector *tAij = psVectorAlloc (Nelem, PS_DATA_F32); + psVector *tSi = psVectorAlloc (Nelem, PS_DATA_S32); + psVector *tSj = psVectorAlloc (Nelem, PS_DATA_S32); + for (int i = 0; i < Nelem; i++) { + int j = index->data.U32[i]; + tAij->data.F32[i] = Aij->data.F32[j]; + tSi->data.S32[i] = Si->data.S32[j]; + tSj->data.S32[i] = Sj->data.S32[j]; + } + psFree (index); + psFree (Aij); + psFree (Si); + psFree (Sj); + + sparse->Aij = tAij; + sparse->Si = tSi; + sparse->Sj = tSj; + return; +} + +void psSparseMatrixTest () +{ + + // build a sparse matrix + psSparse *sparse = psSparseAlloc (3, 9); + + psSparseMatrixElement (sparse, 0, 0, 3.0); + psSparseMatrixElement (sparse, 1, 1, 2.0); + psSparseMatrixElement (sparse, 2, 2, 1.0); + + psSparseMatrixElement (sparse, 1, 0, 0.1); + psSparseMatrixElement (sparse, 2, 0, -0.1); + + psSparseResort (sparse); + for (int i = 0; i < sparse->Nelem; i++) { + fprintf (stderr, "%d %d %f\n", + sparse->Si->data.S32[i], + sparse->Sj->data.S32[i], + sparse->Aij->data.F32[i]); + } + + psVector *x = psVectorAlloc (3, PS_DATA_F32); + x->data.F32[0] = 3; + x->data.F32[1] = 5; + x->data.F32[2] = 7; + fprintf (stderr, "x: %f %f %f\n", x->data.F32[0], x->data.F32[1], x->data.F32[2]); + + psVector *B = psSparseMatrixTimesVector (NULL, sparse, x); + fprintf (stderr, "B: %f %f %f\n", B->data.F32[0], B->data.F32[1], B->data.F32[2]); + + sparse->Bfj->data.F32[0] = B->data.F32[0]; + sparse->Bfj->data.F32[1] = B->data.F32[1]; + sparse->Bfj->data.F32[2] = B->data.F32[2]; + + psSparseConstraint constraint; + constraint.paramMin = -1e8; + constraint.paramMax = +1e8; + constraint.paramDelta = +1e8; + + x = psSparseSolve (x, constraint, sparse, 0); + fprintf (stderr, "x: %f %f %f\n", x->data.F32[0], x->data.F32[1], x->data.F32[2]); + + x = psSparseSolve (x, constraint, sparse, 1); + fprintf (stderr, "x: %f %f %f\n", x->data.F32[0], x->data.F32[1], x->data.F32[2]); + + x = psSparseSolve (x, constraint, sparse, 2); + fprintf (stderr, "x: %f %f %f\n", x->data.F32[0], x->data.F32[1], x->data.F32[2]); + + x = psSparseSolve (x, constraint, sparse, 3); + fprintf (stderr, "x: %f %f %f\n", x->data.F32[0], x->data.F32[1], x->data.F32[2]); + + x = psSparseSolve (x, constraint, sparse, 4); + fprintf (stderr, "x: %f %f %f\n", x->data.F32[0], x->data.F32[1], x->data.F32[2]); + return; +} + Index: trunk/psModules/src/pslib/psSparse.h =================================================================== --- trunk/psModules/src/pslib/psSparse.h (revision 6872) +++ trunk/psModules/src/pslib/psSparse.h (revision 6872) @@ -0,0 +1,62 @@ + +/** @file psSparse.h + * + * functions to manipulate sparse matrices equations + * + */ + +# ifndef PS_SPARSE_H +# define PS_SPARSE_H + +// constraints to limit the range of the matrix equation solution +typedef struct +{ + double paramDelta; + double paramMin; + double paramMax; +} +psSparseConstraint; + +// a sparse matrix equation: A x = Bf +// Aij contains the populated elements of the matrix +// Bfj contains the elements of the vector Bf +// Qii contains the diagonal elements of Aij +// Si contains the i-index values of Aij +// Sj contains the j-index values of Aij +typedef struct +{ + psVector *Aij; + psVector *Bfj; + psVector *Qii; + psVector *Si; + psVector *Sj; + int Nelem; + int Nrows; +} +psSparse; + +// allocate a sparse matrix structure +psSparse *psSparseAlloc (int Nrows, int Nelem); + +// add a new matrix element +// user should only add elements above the diagonal +void psSparseMatrixElement (psSparse *sparse, int i, int j, float value); + +// define a new sparse matrix equation vector element +void psSparseVectorElement (psSparse *sparse, int i, float value); + +// perform the operation matrix * vector on a sparse matrix and a vector +psVector *psSparseMatrixTimesVector (psVector *output, psSparse *matrix, psVector *vector); + +// re-sort a sparse matrix to have all elements in index order rather than insertion order +// call this before solving, but after populating matrix and vector +void psSparseResort (psSparse *sparse); + +// solve the equation A x = Bf for the value of x +// a good starting guess is the vector Bf +psVector *psSparseSolve (psVector *guess, psSparseConstraint constraint, psSparse *sparse, int Niter); + +// test of the sparse matrix solutions (move to test suite) +void psSparseMatrixTest (); + +# endif /* PS_SPARSE_H */ Index: trunk/psModules/src/psmodules.h =================================================================== --- trunk/psModules/src/psmodules.h (revision 6872) +++ trunk/psModules/src/psmodules.h (revision 6872) @@ -0,0 +1,75 @@ +#ifndef PS_MODULES_H +#define PS_MODULES_H + +// XXX should this be included explicitly? +#include + +// the following headers are from psModule:pslib +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +// the following headers are from psModule:config +#include + +// the following headers are from psModule:astrom +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +// #include +// #include + +// the following headers are from psModule:detrend +#include +#include +#include +#include +#include + +// the following headers are from psModule:imcombine +#include +// #include + +// the following headers are from psModule:detrend +#include +#include +// #include + +// the following headers are from psModule:objects +# include +# include +# include +# include +# include +# include +# include +# include +# include +# include +# include +# include +# include +# include + +#endif Index: trunk/psModules/test/pslib/.cvsignore =================================================================== --- trunk/psModules/test/pslib/.cvsignore (revision 6872) +++ trunk/psModules/test/pslib/.cvsignore (revision 6872) @@ -0,0 +1,5 @@ +.deps +.libs +Makefile +Makefile.in +temp Index: trunk/psModules/test/pslib/Makefile.am =================================================================== --- trunk/psModules/test/pslib/Makefile.am (revision 6872) +++ trunk/psModules/test/pslib/Makefile.am (revision 6872) @@ -0,0 +1,16 @@ +# Makefile for psModule tests + +AM_LDFLAGS = -L$(top_builddir)/src -lpsmodule $(PSMODULE_LIBS) +AM_CFLAGS = @AM_CFLAGS@ $(PSMODULE_CFLAGS) $(SRCINC) + +TESTS = + +check_PROGRAMS = $(TESTS) + +TESTS_ENVIRONMENT = perl $(top_srcdir)/test/runTest --verified=$(srcdir)/verified + +tests: $(TESTS) + +CLEANFILES = $(TESTS) temp/* + +test: check