Index: trunk/ppbgrestore/Makefile.am =================================================================== --- trunk/ppbgrestore/Makefile.am (revision 25972) +++ trunk/ppbgrestore/Makefile.am (revision 25972) @@ -0,0 +1,3 @@ +SUBDIRS = src + +CLEANFILES = *~ core core.* Index: trunk/ppbgrestore/autogen.sh =================================================================== --- trunk/ppbgrestore/autogen.sh (revision 25972) +++ trunk/ppbgrestore/autogen.sh (revision 25972) @@ -0,0 +1,103 @@ +#!/bin/sh +# Run this to generate all the initial makefiles, etc. + +srcdir=`dirname $0` +test -z "$srcdir" && srcdir=. + +ORIGDIR=`pwd` +cd $srcdir + +PROJECT=ppbgrestore +TEST_TYPE=-f +# change this to be a unique filename in the top level dir +FILE=autogen.sh + +DIE=0 + +LIBTOOLIZE=libtoolize +ACLOCAL="aclocal $ACLOCAL_FLAGS" +AUTOHEADER=autoheader +AUTOMAKE=automake +AUTOCONF=autoconf + +($LIBTOOLIZE --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $LIBTOOLIZE installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/libtool/" + DIE=1 +} + +($ACLOCAL --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $ACLOCAL installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/" + DIE=1 +} + +($AUTOHEADER --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOHEADER installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/" + DIE=1 +} + +($AUTOMAKE --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOMAKE installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/" + DIE=1 +} + +($AUTOCONF --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOCONF installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/" + DIE=1 +} + +if test "$DIE" -eq 1; then + exit 1 +fi + +test $TEST_TYPE $FILE || { + echo "You must run this script in the top-level $PROJECT directory" + exit 1 +} + +if test -z "$*"; then + echo "I am going to run ./configure with no arguments - if you wish " + echo "to pass any to it, please specify them on the $0 command line." +fi + +$LIBTOOLIZE --copy --force || echo "$LIBTOOLIZE failed" +$ACLOCAL || echo "$ACLOCAL failed" +$AUTOHEADER || echo "$AUTOHEADER failed" +$AUTOMAKE --add-missing --force-missing --copy || echo "$AUTOMAKE failed" +$AUTOCONF || echo "$AUTOCONF failed" + +cd $ORIGDIR + +run_configure=true +for arg in $*; do + case $arg in + --no-configure) + run_configure=false + ;; + *) + ;; + esac +done + +if $run_configure; then + $srcdir/configure --enable-maintainer-mode "$@" + echo + echo "Now type 'make' to compile $PROJECT." +else + echo + echo "Now run 'configure' and 'make' to compile $PROJECT." +fi Index: trunk/ppbgrestore/configure.ac =================================================================== --- trunk/ppbgrestore/configure.ac (revision 25972) +++ trunk/ppbgrestore/configure.ac (revision 25972) @@ -0,0 +1,46 @@ +dnl Process this file with autoconf to produce a configure script. +AC_PREREQ(2.61) + +AC_INIT([ppbgrestore], [0.1.1], [ipp-support@ifa.hawaii.edu]) +AC_CONFIG_SRCDIR([src]) + +AM_INIT_AUTOMAKE([1.6 foreign dist-bzip2]) +AM_CONFIG_HEADER([src/config.h]) +AM_MAINTAINER_MODE + +IPP_STDCFLAGS + +AC_LANG(C) +AC_GNU_SOURCE +AC_PROG_CC_C99 +AC_PROG_INSTALL +AC_PROG_LIBTOOL +AC_SYS_LARGEFILE + +dnl ------------------------------------------------------------ + +AC_PATH_PROG([ERRORCODES], [psParseErrorCodes], [missing]) +if test "$ERRORCODES" = "missing" ; then + AC_MSG_ERROR([psParseErrorCodes is required]) +fi + + +PKG_CHECK_MODULES([PSLIB], [pslib >= 1.0.0]) +PKG_CHECK_MODULES([PSMODULE], [psmodules >= 1.0.0]) +PKG_CHECK_MODULES([PSPHOT], [psphot >= 0.9.0]) + +dnl Set CFLAGS for build +IPP_STDOPTS +CFLAGS="${CFLAGS} -Wall -Werror" +# echo "PPSTAMP_CFLAGS: $PPSTAMP_CFLAGS" +# echo "PPSTAMP_LIBS: $PPSTAMP_LIBS" + +AC_SUBST([PPSTAMP_CFLAGS]) +AC_SUBST([PPSTAMP_LIBS]) + +AC_CONFIG_FILES([ + Makefile + src/Makefile +]) + +AC_OUTPUT Index: trunk/ppbgrestore/src/Makefile.am =================================================================== --- trunk/ppbgrestore/src/Makefile.am (revision 25972) +++ trunk/ppbgrestore/src/Makefile.am (revision 25972) @@ -0,0 +1,24 @@ +bin_PROGRAMS = ppbgrestore + + +noinst_HEADERS = \ + ppbgrestore.h + +ppbgrestore_CPPFLAGS = $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) + +ppbgrestore_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS) + +ppbgrestore_SOURCES = \ + ppbgrestore.c \ + ppbgrestoreArguments.c \ + ppbgrestoreCleanup.c \ + ppbgrestoreLoop.c \ + ppbgrestoreParseCamera.c \ + ppbgrestoreVersion.c + +clean-local: + -rm -f TAGS + +# Tags for emacs +tags: + etags `find . -name \*.[ch] -print` Index: trunk/ppbgrestore/src/ppbgrestore.c =================================================================== --- trunk/ppbgrestore/src/ppbgrestore.c (revision 25972) +++ trunk/ppbgrestore/src/ppbgrestore.c (revision 25972) @@ -0,0 +1,50 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppbgrestore.h" + +#define TIMER_TOTAL "PPBGRESTORE_TOTAL" + +int main(int argc, char **argv) { + + psLibInit(NULL); + + psTimerStart(TIMER_TOTAL); + + // Parse the configuration and arguments + // Open the input image(s) + // Determine camera, format from header if not already defined + // Construct camera in preparation for reading + pmConfig *config = ppbgrestoreArguments(argc, argv); + if (config == NULL) { + psErrorStackPrint(stderr, "Unable to parse command-line arguments."); + ppbgrestoreCleanup(config, NULL); + exit(PS_EXIT_CONFIG_ERROR); + } + + ppbgrestoreVersionPrint(); + + // define recipe options + // define the active I/O files + ppbgrestoreOptions *options = ppbgrestoreParseCamera(config); + if (options == NULL) { + psErrorStackPrint(stderr, "Unable to parse camera."); + ppbgrestoreCleanup(config, options); + exit(PS_EXIT_CONFIG_ERROR); + } + + // Image Arithmetic Loop + if (!ppbgrestoreLoop(config, options)) { + psErrorStackPrint(stderr, "Unable to loop over input"); + ppbgrestoreCleanup(config, options); + exit(PS_EXIT_SYS_ERROR); + } + + psLogMsg("ppbgrestore", PS_LOG_INFO, "Complete ppbgrestore run: %f sec\n", psTimerMark(TIMER_TOTAL)); + + // Cleaning up + ppbgrestoreCleanup(config, options); + + return PS_EXIT_SUCCESS; +} Index: trunk/ppbgrestore/src/ppbgrestore.h =================================================================== --- trunk/ppbgrestore/src/ppbgrestore.h (revision 25972) +++ trunk/ppbgrestore/src/ppbgrestore.h (revision 25972) @@ -0,0 +1,154 @@ +#ifndef PP_BG_RESTORE_H +#define PP_BG_RESTORE_H + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include +#include // for strcasecmp +#include // for unlink +#include "pslib.h" +#include "psmodules.h" +#include "psphot.h" +#include "psastro.h" +#include "ppStats.h" + +// Options for ppbgrestore processing +typedef struct { + // actions which ppbgrestore should perform + bool dummy; +#ifdef notdef + bool doMaskBuild; // Build internal mask + bool doVarianceBuild; // Build internal variance map + bool doMaskBurntool; // mask potential burntool trails + bool doMaskSat; // mask saturated pixels + bool doMaskLow; // mask low pixels + bool doMask; // Mask bad pixels + bool doNonLin; // Non-linearity correction + bool doOverscan; // Overscan subtraction + bool doNoiseMap; // Bias subtraction + bool doBias; // Bias subtraction + bool doDark; // Dark subtraction + bool doRemnance; // Remnance masking + bool doShutter; // Shutter correction + bool doFlat; // Flat-field normalisation + bool doPattern; // Pattern noise subtraction + bool doFringe; // Fringe subtraction + bool doPhotom; // Source identification and photometry + bool doBG; // Background subtraction + bool doAstromChip; // per-chip Astrometry + bool doAstromMosaic; // full-mosaic Astrometry + bool doStats; // call ppStats on the image + bool checkCTE; // measure pixel-based variance + bool applyParity; // Apply Cell parities + + bool doCrosstalkMeasure; // measure crosstalk signal + bool doCrosstalkCorrect; // apply crosstalk correction + + // output files requested + bool BaseFITS; + bool BaseMaskFITS; + bool BaseVarianceFITS; + + bool ChipFITS; + bool ChipMaskFITS; + bool ChipVarianceFITS; + + bool FPA1FITS; + bool FPA2FITS; + bool Bin1FITS; + bool Bin1JPEG; + bool Bin2FITS; + bool Bin2JPEG; + + // make values for abstract concepts of masking + psImageMaskType maskValue; // apply this bit-mask to choose masked bits + psImageMaskType markValue; // apply this bit-mask to choose masked bits + psImageMaskType satMask; // Mask value to give saturated pixels + psImageMaskType lowMask; // Mask value to give bad pixels + psImageMaskType flatMask; // Mask value to give bad flat pixels + psImageMaskType darkMask; // Mask value to give bad dark pixels + psImageMaskType blankMask; // Mask value to give blank pixels + psImageMaskType burntoolMask; // Suspect pixels that fall where a burntool trail is expected. + // non-linear correction parameters + psDataType nonLinearType; + psMetadataItem *nonLinearData; + void *nonLinearSource; + + // options for the analysis + pmOverscanOptions *overscan; // Overscan options + int burntoolTrails; + // binning parameters + int xBin1; // x-binning, scale 1 + int yBin1; // y-binning, scale 1 + int xBin2; // x-binning, scale 2 + int yBin2; // y-binning, scale 2 + + // parameters used by the fringe analysis + float fringeRej; // Fringe rejection limit + int fringeIter; // Fringe iterations + float fringeKeep; // Fringe keep fraction + + // Pattern noise subtraction + int patternOrder; // Polynomial order + int patternIter; // Clipping iterations + float patternRej; // Clipping threshold + float patternThresh; // Ignore threshold + psStatsOptions patternMean; // Statistic for mean + psStatsOptions patternStdev; // Statistic for stdev + + int remnanceSize; // Size for remnance detection + float remnanceThresh; // Threshold for remnance detection + + char *normClass; // class to use for per-class normalization +#endif +} ppbgrestoreOptions; + + +ppbgrestoreOptions *ppbgrestoreOptionsAlloc(void); + +// Determine the processing options +ppbgrestoreOptions *ppbgrestoreOptionsParse(pmConfig *config); + +// Get the configuration +pmConfig *ppbgrestoreArguments(int argc, char **argv); + +// Determine what type of camera, and initialise +ppbgrestoreOptions *ppbgrestoreParseCamera(pmConfig *config); + +// Loop over the input +bool ppbgrestoreLoop(pmConfig *config, ppbgrestoreOptions *options); + +// free memory, check for leaks +void ppbgrestoreCleanup (pmConfig *config, ppbgrestoreOptions *options); + +// Subtract background from the chip-mosaicked image +bool ppbgrestoreRestoreBackground( + pmConfig *config, // Configuration + const pmFPAview *view, // View to chip of interest + const ppbgrestoreOptions *options // Processing options + ); + + +/// Return short version information +psString ppbgrestoreVersion(void); + +/// Return software source +psString ppbgrestoreSource(void); + +/// Return long version information +psString ppbgrestoreVersionLong(void); + +/// Populate the header with version information for all dependencies +bool ppbgrestoreVersionHeader(psMetadata *metadata ///< Header to populate + ); + +/// Print version information +void ppbgrestoreVersionPrint(void); + + +void ppbgrestoreFileCheck(pmConfig *config); + +#endif Index: trunk/ppbgrestore/src/ppbgrestoreArguments.c =================================================================== --- trunk/ppbgrestore/src/ppbgrestoreArguments.c (revision 25972) +++ trunk/ppbgrestore/src/ppbgrestoreArguments.c (revision 25972) @@ -0,0 +1,31 @@ +#include "ppbgrestore.h" + +void usage() +{ + fprintf(stderr, "USAGE: ppbgrestore [-file INPUT.fits] | [-list INPUT.txt] [-backmdl BACKMDL.fits] | [-backmdllist BACKMDL.txt] OUTPUT\n\n"); + exit(2); +} +pmConfig *ppbgrestoreArguments(int argc, char *argv[]) +{ + pmConfig *config = pmConfigRead(&argc, argv, NULL); + if (config == NULL) { + psErrorStackPrint(stderr, "Can't find site configuration!\n"); + exit(EXIT_FAILURE); + } + + // the input file is a required argument if not found we will exit + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "INPUT", "-file", "-list")) { + fprintf(stderr, "input file is required\n"); + usage(); + } + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "BACKMDL", "-backmdl", "-backmdllist")) { + fprintf(stderr, "backmdl file is required\n"); + usage(); + } + if (argc != 2) usage (); + + // Add the input and output images (which remain on the command-line) to the arguments list + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "Name of the output image", argv[1]); + + return config; +} Index: trunk/ppbgrestore/src/ppbgrestoreCleanup.c =================================================================== --- trunk/ppbgrestore/src/ppbgrestoreCleanup.c (revision 25972) +++ trunk/ppbgrestore/src/ppbgrestoreCleanup.c (revision 25972) @@ -0,0 +1,6 @@ +#include "ppbgrestore.h" + +void ppbgrestoreCleanup(pmConfig *config, ppbgrestoreOptions *options) +{ + // XXX: todo +} Index: trunk/ppbgrestore/src/ppbgrestoreLoop.c =================================================================== --- trunk/ppbgrestore/src/ppbgrestoreLoop.c (revision 25972) +++ trunk/ppbgrestore/src/ppbgrestoreLoop.c (revision 25972) @@ -0,0 +1,160 @@ +#include "ppbgrestore.h" +#include "psphot.h" + +#define ESCAPE(MESSAGE) { \ + psError(PS_ERR_UNKNOWN, false, MESSAGE); \ + psFree(view); \ + return false; \ +} + + +bool ppbgrestoreLoop(pmConfig *config, ppbgrestoreOptions *options) +{ + bool status; // Status of MD lookup + pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPBGRESTORE.INPUT"); + if (!status) { + psErrorStackPrint(stderr, "Can't find input data!\n"); + ppbgrestoreCleanup(config, options); + exit(PS_EXIT_PROG_ERROR); + } + pmFPAfile *backmdl = psMetadataLookupPtr(&status, config->files, "PPBGRESTORE.BACKMDL"); + if (!status) { + psErrorStackPrint(stderr, "Can't find background model data!\n"); + ppbgrestoreCleanup(config, options); + exit(PS_EXIT_PROG_ERROR); + } + pmFPAfile *output= psMetadataLookupPtr(&status, config->files, "PPBGRESTORE.OUTPUT"); + if (!status) { + psErrorStackPrint(stderr, "Can't find output data!\n"); + ppbgrestoreCleanup(config, options); + exit(PS_EXIT_PROG_ERROR); + } + + pmFPAview *view = pmFPAviewAlloc(0);// View for level of interest +// pmHDU *lastHDU = NULL; // Last HDU that was updated + + // files associated with the science image + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE("load failure for FPA"); + } + + pmChip *chip; // Chip from FPA + while ((chip = pmFPAviewNextChip(view, input->fpa, 1)) != NULL) { + psLogMsg ("ppbgrestoreLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); + if (!chip->process || !chip->file_exists) { + continue; + } + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE("load failure for Chip"); + } + + // much of the following is adapted from ppImageSubtractBackground + + if (chip->cells->n == 0) { + psError(PS_ERR_UNKNOWN, true, "Chip has no cells"); + return false; + } + + if (chip->cells->n > 1) { + psError(PS_ERR_UNKNOWN, true, "Chip has too many cells: %ld", chip->cells->n); + return false; + } + pmCell *cell = chip->cells->data[0]; // Cell of interest + if (!cell || !cell->process || !cell->file_exists) { + // Nothing to process + return false; + } + if (cell->readouts->n == 0) { + psError(PS_ERR_UNKNOWN, true, "Cell has no readouts"); + return false; + } + if (cell->readouts->n > 1) { + psWarning("Cell has %ld readouts; only the first will be processed", cell->readouts->n); + } + pmReadout *ro = cell->readouts->data[0]; // Readout of interest + if (!ro || !ro->data_exists) { + psError(PS_ERR_UNKNOWN, true, "readout has no data"); + return false; + } + psImage *image = ro->image; +// psImage *mask = NULL; +// psImageMaskType maskVal = 0; + + pmFPAview roView = *view; + roView.cell = 0; + roView.readout = 0; + pmReadout *modelRO = pmFPAviewThisReadout(&roView, backmdl->fpa); + if (!modelRO || !modelRO->data_exists) { + psError(PS_ERR_UNKNOWN, true, "model readout has no data"); + return false; + } + output->save = true; + +#ifdef notdef + psImageBinning *binning = psMetadataLookupPtr(&status, modelRO->analysis, + "PSPHOT.BACKGROUND.BINNING"); // Binning for model +#endif + psImageBinning *binning = psphotBackgroundBinning(image, config); + if (!binning) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find background binning"); + return false; + } + pmReadout *background = pmFPAfileDefineInternal (config->files, "PSPHOT.BACKGND", image->numCols, image->numRows, PS_TYPE_F32); + + // linear interpolation to full-scale + if (!psImageUnbin (background->image, modelRO->image, binning)) { + psError (PSPHOT_ERR_PROG, true, "inconsistent sizes for unbinning"); + return false; + } + psF32 **backData = background->image->data.F32; + + // Do the background subtraction + int numCols = image->numCols, numRows = image->numRows; // Size of image + long nancount = 0; + long finitecount = 0; + for (int y = 0; y < numRows; y++) { + for (int x = 0; x < numCols; x++) { + float value = backData[y][x]; + if (!isfinite(value)) { + // if background is NAN leave the image unchanged + // According to ppImageSubtractBackground pixels where the background is not finite should be NAN + // experimentally + // for breakpoint + float imageval = image->data.F32[y][x] ; + nancount++; + if (isfinite(imageval)) { + finitecount++; + // psWarning("unexpected finite image value %f found at %d %d background is infinite", imageval, x, y); + } + // Doing this is causes a lot of new NAN pixels to appear. + // NANS are appearing in the model for some reason. + // image->data.F32[y][x] = NAN; + } else { + // XXX: TODO:following ppImage we should not modify pixels that are masked. + image->data.F32[y][x] += value; + } + } + } + if (nancount) { + psWarning("%ld infinite pixels found in background %ld pixels were finite\n", nancount, finitecount); + } + pmFPAfileDropInternal(config->files, "PSPHOT.BACKGND"); + + // Close chip + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for Chip"); + } + } + + if (psTraceGetLevel("ppbgrestore") >= 3) { +// ppbgrestoreFileCheck(config); + } + + // Output and Close FPA + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for FPA"); + } + psFree(view); + + return true; +} Index: trunk/ppbgrestore/src/ppbgrestoreParseCamera.c =================================================================== --- trunk/ppbgrestore/src/ppbgrestoreParseCamera.c (revision 25972) +++ trunk/ppbgrestore/src/ppbgrestoreParseCamera.c (revision 25972) @@ -0,0 +1,31 @@ +#include "ppbgrestore.h" + +ppbgrestoreOptions *ppbgrestoreParseCamera(pmConfig *config) +{ + ppbgrestoreOptions *options = psAlloc(sizeof(*options)); + bool status; + + memset(options, 0, sizeof(*options)); + + pmFPAfile *input = pmFPAfileDefineFromArgs(&status, config, "PPBGRESTORE.INPUT", "INPUT"); + if (!input) { + psFree(options); + psError(PS_ERR_UNKNOWN, false, "failed to define input file"); + return NULL; + } + pmFPAfile *backmdl = pmFPAfileDefineFromArgs(&status, config, "PPBGRESTORE.BACKMDL", "BACKMDL"); + if (!backmdl) { + psFree(options); + psError(PS_ERR_UNKNOWN, false, "failed to define background model file"); + return NULL; + } + // pmFPAfile *outImage = pmFPAfileDefineOutput(config, input->fpa, "PPBGRESTORE.OUTPUT"); + pmFPAfile *outImage = pmFPAfileDefineOutput(config, input->fpa, "PPBGRESTORE.OUTPUT"); + if (!outImage) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.OUTPUT")); + psFree(options); + return NULL; + } + + return options; +} Index: trunk/ppbgrestore/src/ppbgrestoreVersion.c =================================================================== --- trunk/ppbgrestore/src/ppbgrestoreVersion.c (revision 25972) +++ trunk/ppbgrestore/src/ppbgrestoreVersion.c (revision 25972) @@ -0,0 +1,7 @@ +#include "ppbgrestore.h" + +void ppbgrestoreVersionPrint() +{ + // XXX: TODO + printf("version 0.0\n"); +}