Index: trunk/ppBackground/configure.ac =================================================================== --- trunk/ppBackground/configure.ac (revision 28276) +++ trunk/ppBackground/configure.ac (revision 28280) @@ -20,5 +20,10 @@ PKG_CHECK_MODULES([PSLIB], [pslib >= 1.0.0]) PKG_CHECK_MODULES([PSMODULE], [psmodules >= 1.0.0]) -PKG_CHECK_MODULES([PSPHOT], [psphot >= 1.0.0]) +PKG_CHECK_MODULES([PSPHOT], [psphot]) + +AC_PATH_PROG([ERRORCODES], [psParseErrorCodes], [missing]) +if test "$ERRORCODES" = "missing" ; then + AC_MSG_ERROR([psParseErrorCodes is required]) +fi dnl Set CFLAGS for build Index: trunk/ppBackground/src/Makefile.am =================================================================== --- trunk/ppBackground/src/Makefile.am (revision 28276) +++ trunk/ppBackground/src/Makefile.am (revision 28280) @@ -2,15 +2,15 @@ if HAVE_SVNVERSION -PPVIZPATTERN_VERSION=`$(SVNVERSION) ..` +PPBACKGROUND_VERSION=`$(SVNVERSION) ..` else -PPVIZPATTERN_VERSION="UNKNOWN" +PPBACKGROUND_VERSION="UNKNOWN" endif if HAVE_SVN -PPVIZPATTERN_BRANCH=`$(SVN) info .. | $(SED) -n -e '/URL:/ h' -e '/Repository Root:/ { x; H; x; s|Repository Root: \(.*\)\nURL: \1\(.*\)|\2| ; s|^/|| ; s|/[a-zA-Z]*/src.*|| ; p }'` -PPVIZPATTERN_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'` +PPBACKGROUND_BRANCH=`$(SVN) info .. | $(SED) -n -e '/URL:/ h' -e '/Repository Root:/ { x; H; x; s|Repository Root: \(.*\)\nURL: \1\(.*\)|\2| ; s|^/|| ; s|/[a-zA-Z]*/src.*|| ; p }'` +PPBACKGROUND_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'` else -PPVIZPATTERN_BRANCH="UNKNOWN" -PPVIZPATTERN_SOURCE="UNKNOWN" +PPBACKGROUND_BRANCH="UNKNOWN" +PPBACKGROUND_SOURCE="UNKNOWN" endif @@ -19,5 +19,5 @@ ppBackgroundVersionDefinitions.h: ppBackgroundVersionDefinitions.h.in FORCE -$(RM) ppBackgroundVersionDefinitions.h - $(SED) -e "s|@PPVIZPATTERN_VERSION@|\"$(PPVIZPATTERN_VERSION)\"|" -e "s|@PPVIZPATTERN_BRANCH@|\"$(PPVIZPATTERN_BRANCH)\"|" -e "s|@PPVIZPATTERN_SOURCE@|\"$(PPVIZPATTERN_SOURCE)\"|" ppBackgroundVersionDefinitions.h.in > ppBackgroundVersionDefinitions.h + $(SED) -e "s|@PPBACKGROUND_VERSION@|\"$(PPBACKGROUND_VERSION)\"|" -e "s|@PPBACKGROUND_BRANCH@|\"$(PPBACKGROUND_BRANCH)\"|" -e "s|@PPBACKGROUND_SOURCE@|\"$(PPBACKGROUND_SOURCE)\"|" ppBackgroundVersionDefinitions.h.in > ppBackgroundVersionDefinitions.h FORCE: ; @@ -35,6 +35,7 @@ ppBackgroundLoop.c \ ppBackgroundVersion.c \ - ppBackgroundModel.c \ - ppBackgroundErrorCodes.c + ppBackgroundRestore.c \ + ppBackgroundErrorCodes.c \ + ppBackgroundExit.c noinst_HEADERS = \ Index: trunk/ppBackground/src/ppBackground.c =================================================================== --- trunk/ppBackground/src/ppBackground.c (revision 28276) +++ trunk/ppBackground/src/ppBackground.c (revision 28280) @@ -6,4 +6,5 @@ #include #include +#include #include "ppBackground.h" @@ -12,4 +13,8 @@ { ppBackgroundVersionPrint(); + + pmErrorRegister(); + psphotErrorRegister(); + ppBackgroundErrorRegister(); ppBackgroundData *data = ppBackgroundDataInit(&argc, argv); @@ -46,5 +51,4 @@ } data->statsFile = NULL; - pmConfigRunFilenameAddWrite(data->config, "STATS", data->statsName); exitValue = ppBackgroundExitCode(exitValue); } Index: trunk/ppBackground/src/ppBackground.h =================================================================== --- trunk/ppBackground/src/ppBackground.h (revision 28276) +++ trunk/ppBackground/src/ppBackground.h (revision 28280) @@ -5,5 +5,5 @@ #include -#include +#include "ppBackgroundErrorCodes.h" #define PPBACKGROUND_RECIPE "PPBACKGROUND" // Recipe name @@ -37,4 +37,13 @@ ); +/// Restore the background to an image +bool ppBackgroundRestore( + pmChip *chip, // Input chip + const pmChip *background, // Chip with background model + const pmChip *pattern, // Chip with pattern + const pmFPAview *view, // View to data + pmConfig *config // Configuration + ); + /// Determine exit code psExit ppBackgroundExitCode( Index: trunk/ppBackground/src/ppBackgroundArguments.c =================================================================== --- trunk/ppBackground/src/ppBackgroundArguments.c (revision 28276) +++ trunk/ppBackground/src/ppBackgroundArguments.c (revision 28280) @@ -48,6 +48,7 @@ psMetadataAddStr(arguments, PS_LIST_TAIL, "-pattern", 0, "Filename of pattern correction", NULL); psMetadataAddStr(arguments, PS_LIST_TAIL, "-background", 0, "Filename of background model", NULL); - psMetadataAddStr(arguments, PS_LIST_TAIL, "-image", 0, "Filename of image", NULL); + psMetadataAddStr(arguments, PS_LIST_TAIL, "-image", 0, "Filename of image (required)", NULL); psMetadataAddStr(arguments, PS_LIST_TAIL, "-mask", 0, "Filename of mask", NULL); + psMetadataAddStr(arguments, PS_LIST_TAIL, "-stats", 0, "Output statistics file", NULL); if (argc == 1 || !psArgumentParse(arguments, &argc, argv) || argc != 2) { usage(argv[0], arguments, data); @@ -68,6 +69,21 @@ return false; } + if (!data->imageName) { + psError(PPBACKGROUND_ERR_CONFIG, true, "Must specify -image"); + return false; + } PS_ASSERT_STRING_NON_EMPTY(data->outRoot, false); + + const char *statsName = psMetadataLookupStr(NULL, arguments, "-stats"); + if (statsName) { + data->statsFile = fopen(statsName, "w"); + if (!data->statsFile) { + psError(PPBACKGROUND_ERR_IO, true, "Unable to open statistics file %s", statsName); + return false; + } + data->stats = psMetadataAlloc(); + pmConfigRunFilenameAddWrite(data->config, "STATS", statsName); + } return true; Index: trunk/ppBackground/src/ppBackgroundCamera.c =================================================================== --- trunk/ppBackground/src/ppBackgroundCamera.c (revision 28276) +++ trunk/ppBackground/src/ppBackgroundCamera.c (revision 28280) @@ -33,6 +33,5 @@ fileArguments("PATTERN", data->patternName, "Input pattern", data->config); - pmFPAfile *pattern = pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.PATTERN", - "PATTERN"); // File + pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.PATTERN", "PATTERN"); // File if (!status) { psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.PATTERN"); @@ -41,6 +40,5 @@ fileArguments("BACKGROUND", data->backgroundName, "Input background model", data->config); - pmFPAfile *background = pmFPAfileBindFromArgs(&status, data->config, "PPBACKGROUND.BACKGROUND", - "BACKGROUND"); // File + pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.BACKGROUND", "BACKGROUND"); // File if (!status) { psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.BACKGROUND"); @@ -49,7 +47,7 @@ fileArguments("IMAGE", data->backgroundName, "Input uncorrected image", data->config); - pmFPAfile *image = pmFPAfileBindFromArgs(&status, background, data->config, "PPBACKGROUND.IMAGE", - "IMAGE"); // File - if (!status) { + pmFPAfile *image = pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.IMAGE", + "IMAGE"); // File + if (!status || !image) { psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.IMAGE"); return false; @@ -57,6 +55,5 @@ fileArguments("MASK", data->backgroundName, "Input uncorrected mask", data->config); - pmFPAfile *mask = pmFPAfileBindFromArgs(&status, image, data->config, "PPBACKGROUND.MASK", - "MASK"); // File + pmFPAfileBindFromArgs(&status, image, data->config, "PPBACKGROUND.MASK", "MASK"); // File if (!status) { psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.MASK"); @@ -64,5 +61,5 @@ } - pmFPAfile *output = pmFPAfileDefineOutput(data->config, file->fpa, "PPBACKGROUND.OUTPUT"); + pmFPAfile *output = pmFPAfileDefineOutput(data->config, image->fpa, "PPBACKGROUND.OUTPUT"); if (!output) { psError(psErrorCodeLast(), false, "Unable to define output."); Index: trunk/ppBackground/src/ppBackgroundLoop.c =================================================================== --- trunk/ppBackground/src/ppBackgroundLoop.c (revision 28276) +++ trunk/ppBackground/src/ppBackgroundLoop.c (revision 28280) @@ -13,6 +13,7 @@ { pmConfig *config = data->config; // Configuration data - pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.BACKGROUND", 0); + pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.IMAGE", 0); pmFPAfile *patternFile = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.PATTERN", 0); // File with data + pmFPAfile *bgFile = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.BACKGROUND", 0); // File with bg pmFPA *patternMosaic = pmFPAConstruct(file->camera, file->cameraName); // Mosaicked FPA for pattern @@ -34,5 +35,5 @@ } - if (chip->cell->n > 1) { + if (chip->cells->n > 1) { psError(PPBACKGROUND_ERR_CONFIG, true, "Input image and background model should be chip-mosaicked"); @@ -44,7 +45,7 @@ pmFPAfileActivate(config->files, true, "PPBACKGROUND.PATTERN"); - pmCell *cell; // Cell with pattern data + pmCell *patternCell; // Cell with pattern data while ((patternCell = pmFPAviewNextCell(view, patternFile->fpa, 1))) { - if (!cell->process || !cell->file_exists) { + if (!patternCell->process || !patternCell->file_exists) { continue; } @@ -68,10 +69,10 @@ // Get size of image from concepts if (numCols == 0 || numRows == 0) { - numCols = psMetadataLookupS32(NULL, cell->concepts, "CELL.XSIZE"); - numRows = psMetadataLookupS32(NULL, cell->concepts, "CELL.YSIZE"); + numCols = psMetadataLookupS32(NULL, patternCell->concepts, "CELL.XSIZE"); + numRows = psMetadataLookupS32(NULL, patternCell->concepts, "CELL.YSIZE"); } // Get size of image from TRIMSEC if (numCols == 0 || numRows == 0) { - psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); + psRegion *trimsec = psMetadataLookupPtr(NULL, patternCell->concepts, "CELL.TRIMSEC"); numCols = trimsec->x1 - trimsec->x0; numRows = trimsec->y1 - trimsec->y0; @@ -91,5 +92,5 @@ // Remove bias sections to avoid warnings - psMetadataItem *biassec = psMetadataLookup(patternRO->parent->concepts, "CELL.BIASSEC"); + psMetadataItem *biassec = psMetadataLookup(patternCell->concepts, "CELL.BIASSEC"); if (psListLength(biassec->data.V)) { psFree(biassec->data.V); @@ -123,26 +124,21 @@ } + pmChip *patternChip = patternFile ? pmFPAviewThisChip(view, patternMosaic) : NULL; // Chip with pattern + pmChip *bgChip = bgFile ? pmFPAviewThisChip(view, bgFile->fpa) : NULL; // Chip with background model + if (!ppBackgroundRestore(chip, bgChip, patternChip, view, config)) { + psError(psErrorCodeLast(), false, "Unable to replace background"); + return false; + } + pmChipFreeData(patternChip); - - - - - - pmHDU *hdu = pmHDUGetLowest(file->fpa, chip, cell); // HDU for readout - if (!hdu) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find HDU for data."); - return false; - } - if (!hdu->header) { - hdu->header = psMetadataAlloc(); - } - ppBackgroundVersionHeader(hdu->header); - - - - - - - + pmHDU *hdu = pmHDUGetLowest(file->fpa, chip, NULL); // HDU for chip + if (!hdu) { + psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find HDU for data."); + return false; + } + if (!hdu->header) { + hdu->header = psMetadataAlloc(); + } + ppBackgroundVersionHeader(hdu->header); // Chip @@ -158,4 +154,7 @@ } + psFree(view); + psFree(patternMosaic); + return true; } Index: trunk/ppBackground/src/ppBackgroundModel.c =================================================================== --- trunk/ppBackground/src/ppBackgroundModel.c (revision 28276) +++ (revision ) @@ -1,92 +1,0 @@ -#include -#include -#include -#include - - -bool ppBackgroundModel( - 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; - background->save = save_background; - - psImageBinning *binning = psphotBackgroundBinning(image, config); - if (!binning) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find background binning"); - return false; - } - pmReadout *backgroundRO; -#define USE_CELL -#ifdef USE_CELL - pmCell *backgroundCell = pmFPAviewThisCell(&roView, background->fpa); - backgroundRO = pmReadoutAlloc(backgroundCell); -#else - backgroundRO = pmFPAviewThisReadout(&roView, background->fpa); -// backgroundRO = pmFPAfileDefineInternal (config->files, "PSPHOT.BACKGND", image->numCols, image->numRows, PS_TYPE_F32); -#endif - backgroundRO->image = psImageAlloc(image->numCols, image->numRows, PS_TYPE_F32); - backgroundRO->data_exists = true; - backgroundRO->parent->data_exists = true; - backgroundRO->parent->parent->data_exists = true; - - // linear interpolation to full-scale - if (!psImageUnbin (backgroundRO->image, modelRO->image, binning)) { - psError (PSPHOT_ERR_PROG, true, "inconsistent sizes for unbinning"); - psFree(binning); - return false; - } - psFree(binning); - psF32 **backData = backgroundRO->image->data.F32; - - // Undo the background subtraction - int numCols = image->numCols, numRows = image->numRows; // Size of image - long nancount = 0; - long naninputs = 0; - long finitecount = 0; - for (int y = 0; y < numRows; y++) { - for (int x = 0; x < numCols; x++) { - float imageval = image->data.F32[y][x] ; - float bgvalue = backData[y][x]; - if (!isfinite(bgvalue)) { - // if background is NAN leave the image unchanged - // According to ppImageSubtractBackground pixels where the background is not finite should be NAN - // experimentally - // for breakpoint - 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 if (isfinite(imageval)) { - // XXX: TODO:following ppImage we should not modify pixels that are masked. - image->data.F32[y][x] = imageval + bgvalue; - } else { - naninputs++; - } - } - } - if (naninputs) { - printf("%ld infinite pixels found in input image\n", naninputs); - } - if (nancount) { - psWarning("%ld infinite pixels found in background %ld pixels were finite\n", nancount, finitecount); - } -// pmFPAfileDropInternal(config->files, "PSPHOT.BACKGND"); Index: trunk/ppBackground/src/ppBackgroundRestore.c =================================================================== --- trunk/ppBackground/src/ppBackgroundRestore.c (revision 28280) +++ trunk/ppBackground/src/ppBackgroundRestore.c (revision 28280) @@ -0,0 +1,71 @@ +#include +#include +#include +#include + +#include "ppBackground.h" + +bool ppBackgroundRestore(pmChip *chip, const pmChip *background, const pmChip *pattern, + const pmFPAview *oldView, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(chip, false); + PS_ASSERT_PTR_NON_NULL(oldView, false); + + pmFPAview *view = pmFPAviewAlloc(0); // View to readout + *view = *oldView; + view->cell = 0; + view->readout = 0; + + pmReadout *ro = pmFPAviewThisReadout(view, chip->parent); + if (!ro || !ro->data_exists) { + psError(PPBACKGROUND_ERR_CONFIG, true, "Readout has no data"); + return false; + } + psImage *image = ro->image; // Image to correct + int numCols = image->numCols, numRows = image->numRows; // Size of image + + if (background) { + pmReadout *bgRO = pmFPAviewThisReadout(view, background->parent); // Readout with background + psImageBinning *binning = psphotBackgroundBinning(bgRO->image, config); + if (!binning) { + psError(psErrorCodeLast(), false, "Unable to find background binning"); + return false; + } + if (binning->nXfine != numCols || binning->nYfine != numRows) { + psError(PPBACKGROUND_ERR_CONFIG, true, + "Unbinned background model and input don't match (%dx%d vs %dx%d)", + binning->nXfine, binning->nYfine, numCols, numRows); + return false; + } + + psImage *bgImage = psImageAlloc(numCols, numRows, PS_TYPE_F32); // Background + if (!psImageUnbin(bgImage, bgRO->image, binning)) { + psError(psErrorCodeLast(), false, "Unable to unbin background model"); + psFree(binning); + return false; + } + psFree(binning); + + for (int y = 0; y < numRows; y++) { + for (int x = 0; x < numCols; x++) { + image->data.F32[y][x] += bgImage->data.F32[y][x]; + } + } + psFree(bgImage); + } + + if (pattern) { + pmReadout *patternRO = pmFPAviewThisReadout(view, pattern->parent); // Readout with pattern + psImage *patternImage = patternRO->image; // Image with pattern + for (int y = 0; y < numRows; y++) { + for (int x = 0; x < numCols; x++) { + image->data.F32[y][x] += patternImage->data.F32[y][x]; + } + } + } + + return true; +} + + + Index: trunk/ppBackground/src/ppBackgroundVersionDefinitions.h.in =================================================================== --- trunk/ppBackground/src/ppBackgroundVersionDefinitions.h.in (revision 28276) +++ trunk/ppBackground/src/ppBackgroundVersionDefinitions.h.in (revision 28280) @@ -1,8 +1,8 @@ -#ifndef PPVIZPATTERN_VERSION_DEFINITIONS_H -#define PPVIZPATTERN_VERSION_DEFINITIONS_H +#ifndef PPBACKGROUND_VERSION_DEFINITIONS_H +#define PPBACKGROUND_VERSION_DEFINITIONS_H -#define PPVIZPATTERN_VERSION @PPVIZPATTERN_VERSION@ // SVN version -#define PPVIZPATTERN_BRANCH @PPVIZPATTERN_BRANCH@ // SVN branch -#define PPVIZPATTERN_SOURCE @PPVIZPATTERN_SOURCE@ // SVN source +#define PPBACKGROUND_VERSION @PPBACKGROUND_VERSION@ // SVN version +#define PPBACKGROUND_BRANCH @PPBACKGROUND_BRANCH@ // SVN branch +#define PPBACKGROUND_SOURCE @PPBACKGROUND_SOURCE@ // SVN source #endif