Index: trunk/ippScripts/scripts/staticsky.pl =================================================================== --- trunk/ippScripts/scripts/staticsky.pl (revision 33689) +++ trunk/ippScripts/scripts/staticsky.pl (revision 33690) @@ -89,5 +89,5 @@ my $logDest = $ipprc->filename("LOG.EXP", $outroot); -$ipprc->redirect_output($logDest) or my_die( "Unable to redirect output", $sky_id, $PS_EXIT_SYS_ERROR ) if $redirect; +$ipprc->redirect_to_logfile($logDest) or my_die( "Unable to redirect output", $sky_id, $PS_EXIT_SYS_ERROR ) if $redirect; my $traceDest = $ipprc->filename("TRACE.EXP", $outroot); @@ -148,8 +148,10 @@ my $maskCnv = $ipprc->filename("PPSTACK.OUTPUT.MASK", $path_base ); # Mask name my $weightCnv = $ipprc->filename("PPSTACK.OUTPUT.VARIANCE", $path_base ); # Weight name + my $expnumCnv = $ipprc->filename("PPSTACK.OUTPUT.EXPNUM", $path_base ); # Expnum name my $imageRaw = $ipprc->filename("PPSTACK.UNCONV", $path_base ); # Image name my $maskRaw = $ipprc->filename("PPSTACK.UNCONV.MASK", $path_base ); # Mask name my $weightRaw = $ipprc->filename("PPSTACK.UNCONV.VARIANCE", $path_base ); # Weight name + my $expnumRaw = $ipprc->filename("PPSTACK.UNCONV.EXPNUM", $path_base ); # Expnum name my $sources = $ipprc->filename("PSPHOT.OUT.CMF.MEF", $path_base ); # Sources name @@ -162,7 +164,9 @@ &my_die("Couldn't find input: $maskRaw", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$maskRaw"); &my_die("Couldn't find input: $weightRaw", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$weightRaw"); + &my_die("Couldn't find input: $expnumRaw", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$expnumRaw"); &my_die("Couldn't find input: $imageCnv", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$imageCnv"); &my_die("Couldn't find input: $maskCnv", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$maskCnv"); &my_die("Couldn't find input: $weightCnv", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$weightCnv"); + &my_die("Couldn't find input: $expnumCnv", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$expnumCnv"); &my_die("Couldn't find input: $psfCnv", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$psfCnv"); &my_die("Couldn't find input: $sources", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$sources"); @@ -171,8 +175,10 @@ print $listFile " RAW:MASK STR " . $maskRaw . "\n"; print $listFile " RAW:VARIANCE STR " . $weightRaw . "\n"; + print $listFile " RAW:EXPNUM STR " . $expnumRaw . "\n"; print $listFile " CNV:IMAGE STR " . $imageCnv . "\n"; print $listFile " CNV:MASK STR " . $maskCnv . "\n"; print $listFile " CNV:VARIANCE STR " . $weightCnv . "\n"; + print $listFile " CNV:EXPNUM STR " . $expnumCnv . "\n"; print $listFile " CNV:PSF STR " . $psfCnv . "\n"; @@ -288,5 +294,5 @@ my $use_raw = metadataLookupBool($recipeData, 'PSPHOT.STACK.USE.RAW'); - my ($image, $mask, $variance); + my ($image, $mask, $variance, $expnum); if ($use_raw) { $image = $ipprc->filename("PPSTACK.UNCONV", $path_base ); # Image name @@ -297,4 +303,5 @@ $mask = $ipprc->filename("PPSTACK.OUTPUT.MASK", $path_base ); # Mask name $variance = $ipprc->filename("PPSTACK.OUTPUT.VARIANCE", $path_base ); # Weight name + $expnum = $ipprc->filename("PPSTACK.OUTPUT.EXPNUM", $path_base ); # Weight name } @@ -306,4 +313,5 @@ &my_die("Couldn't find input: $mask", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$mask"); &my_die("Couldn't find input: $variance", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$variance"); + &my_die("Couldn't find input: $expnum", $sky_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists("$expnum"); # Perform stack photometry analysis @@ -313,4 +321,5 @@ $command .= " -mask $mask"; $command .= " -variance $variance"; + $command .= " -expnum $expnum"; $command .= " -threads $threads" if defined $threads; $command .= " -recipe PSPHOT $recipe_psphot"; Index: trunk/ippconfig/recipes/filerules-split.mdc =================================================================== --- trunk/ippconfig/recipes/filerules-split.mdc (revision 33689) +++ trunk/ippconfig/recipes/filerules-split.mdc (revision 33690) @@ -74,5 +74,5 @@ PSPHOT.INPUT.CMF INPUT @FILES CHIP CMF PSPHOT.INPUT.TEXT INPUT @FILES CHIP SRCTEXT -PSPHOT.EXPNUM INPUT @FILES CHIP MASK +PSPHOT.EXPNUM INPUT @FILES CHIP EXPNUM ## files used by psphotStack @@ -80,8 +80,10 @@ PSPHOT.STACK.MASK.RAW INPUT @FILES CHIP MASK PSPHOT.STACK.VARIANCE.RAW INPUT @FILES CHIP VARIANCE +PSPHOT.STACK.EXPNUM.RAW INPUT @FILES CHIP EXPNUM PSPHOT.STACK.PSF.RAW INPUT @FILES CHIP PSF PSPHOT.STACK.INPUT.CNV INPUT @FILES CHIP IMAGE PSPHOT.STACK.MASK.CNV INPUT @FILES CHIP MASK PSPHOT.STACK.VARIANCE.CNV INPUT @FILES CHIP VARIANCE +PSPHOT.STACK.EXPNUM.CNV INPUT @FILES CHIP EXPNUM PSPHOT.STACK.PSF.CNV INPUT @FILES CHIP PSF PSPHOT.STACK.SOURCES INPUT @FILES FPA CMF Index: trunk/psModules/src/camera/Makefile.am =================================================================== --- trunk/psModules/src/camera/Makefile.am (revision 33689) +++ trunk/psModules/src/camera/Makefile.am (revision 33690) @@ -30,5 +30,6 @@ pmReadoutStack.c \ pmReadoutFake.c \ - pmFPABin.c + pmFPABin.c \ + pmFPAExpNumIO.c pkginclude_HEADERS = \ @@ -59,5 +60,6 @@ pmReadoutStack.h \ pmReadoutFake.h \ - pmFPABin.h + pmFPABin.h \ + pmFPAExpNumIO.h CLEANFILES = *~ Index: trunk/psModules/src/camera/pmFPAExpNumIO.c =================================================================== --- trunk/psModules/src/camera/pmFPAExpNumIO.c (revision 33690) +++ trunk/psModules/src/camera/pmFPAExpNumIO.c (revision 33690) @@ -0,0 +1,450 @@ +#include +#include +#include + +#include "pmHDU.h" +#include "pmHDUUtils.h" +#include "pmFPA.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" +#include "pmFPAfileFitsIO.h" +#include "pmFPAHeader.h" +#include "pmConceptsRead.h" +#include "pmConceptsWrite.h" + +#include "pmFPAExpNumIO.h" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + +static bool pmReadoutReadExpNum(pmReadout *ro, psFits *fits) +{ + PM_ASSERT_READOUT_NON_NULL(ro, false); + PS_ASSERT_FITS_NON_NULL(fits, false); + + pmCell *cell = ro->parent; // Cell of interest + if (!cell) { + psError(PS_ERR_UNEXPECTED_NULL, true, "No cell associated with readout."); + return false; + } + pmChip *chip = cell->parent; // Chip of interest + pmFPA *fpa = chip->parent; // FPA of interest + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // HDU for readout + if (!hdu) { + psError(PS_ERR_UNEXPECTED_NULL, true, "No HDU associated with readout."); + return false; + } + +#ifdef notdef + if (!psFitsMoveExtName(fits, hdu->extname)) { + psError(PS_ERR_IO, false, "Unable to move to EXPNUM image."); + return false; + } +#endif + psMetadata *header = psFitsReadHeader(NULL, fits); // Header + if (!header) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to read header for EXPNUM image."); + return false; + } + + bool data = false; // Did we find any data? + + int naxis = psMetadataLookupS32(NULL, header, "NAXIS"); // Number of axes + if (naxis > 0) { + psImage *expnum = psFitsReadImage(fits, psRegionSet(0, 0, 0, 0), 0); + psMetadataAddImage(ro->analysis, PS_LIST_TAIL, "EXPNUM", PS_META_REPLACE, + "EXPNUM", expnum); + psFree(expnum); + data = true; + } + + if (data) { + ro->data_exists = true; + ro->parent->data_exists = true; + ro->parent->parent->data_exists = true; + } + + psFree(header); + + return true; +} + +static bool pmCellReadExpNum(pmCell *cell, const pmFPAview *view, + pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(cell, false); + PS_ASSERT_PTR_NON_NULL(cell->readouts, false); + + pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view + *thisView = *view; + + // Create a readout if none exists + if (!cell->readouts || cell->readouts->n == 0) { + pmReadout *readout = pmReadoutAlloc(cell); // New readout + psFree(readout); // Drop reference + } + + cell->data_exists = false; + for (int i = 0; i < cell->readouts->n; i++) { + pmReadout *readout = cell->readouts->data[i]; + thisView->readout = i; + if (!pmReadoutReadExpNum(readout, file->fits)) { + psError(PS_ERR_IO, false, "Unable to read pattern correction."); + return false; + } + } + psFree(thisView); + + if (!pmCellReadHeader(cell, file->fits, config)) { + psError(PS_ERR_IO, false, "Unable to read header for cell."); + return false; + } + // load in the concept information for this cell + if (!pmConceptsReadCell(cell, PM_CONCEPT_SOURCE_HEADER, true, NULL)) { + psErrorClear(); + psWarning("Difficulty reading concepts for cell; attempting to proceed."); + } + + return true; +} + +static bool pmChipReadExpNum(pmChip *chip, const pmFPAview *view, + pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(chip, false); + PS_ASSERT_PTR_NON_NULL(chip->cells, false); + + pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view + *thisView = *view; + + chip->data_exists = false; + for (int i = 0; i < chip->cells->n; i++) { + pmCell *cell = chip->cells->data[i]; + thisView->cell = i; + pmCellReadExpNum(cell, thisView, file, config); + if (!cell->data_exists) { + continue; + } + chip->data_exists = true; + } + psFree(thisView); + + if (!pmChipReadHeader(chip, file->fits, config)) { + psError(PS_ERR_IO, false, "Unable to read header for cell."); + return false; + } + if (!pmConceptsReadChip(chip, PM_CONCEPT_SOURCE_HEADER, true, true, NULL)) { + psError(PS_ERR_IO, false, "Failed to read concepts for chip.\n"); + return false; + } + + return true; +} + +static bool pmFPAReadExpNum(pmFPA *fpa, const pmFPAview *view, + pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(file, false); + PS_ASSERT_PTR_NON_NULL(file->fpa, false); + PS_ASSERT_PTR_NON_NULL(file->fpa->chips, false); + + pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view + *thisView = *view; + + for (int i = 0; i < fpa->chips->n; i++) { + pmChip *chip = fpa->chips->data[i]; + thisView->chip = i; + pmChipReadExpNum(chip, thisView, file, config); + } + psFree(thisView); + + if (!pmFPAReadHeader(fpa, file->fits, config)) { + psError(PS_ERR_IO, false, "Unable to read header for cell."); + return false; + } + if (!pmConceptsReadFPA(fpa, PM_CONCEPT_SOURCE_HEADER, true, NULL)) { + psError(PS_ERR_IO, false, "Failed to read concepts for fpa.\n"); + return false; + } + + return true; +} + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +bool pmExpNumRead(const pmFPAview *view, pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(file, false); + PS_ASSERT_PTR_NON_NULL(file->fpa, false); + + pmFPA *fpa = file->fpa; + + if (view->chip == -1) { + pmFPAReadExpNum(fpa, view, file, config); + return true; + } + + if (view->chip >= fpa->chips->n) { + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + pmChipReadExpNum(chip, view, file, config); + return true; + } + + if (view->cell >= chip->cells->n) { + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + pmCellReadExpNum(cell, view, file, config); + return true; + } + + if (view->readout >= cell->readouts->n) { + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + return pmReadoutReadExpNum(readout, file->fits); +} +#ifdef notyet +// Currently only ppStack writes an EXPNUM image and it uses file type MASK +bool pmReadoutWriteExpNum(pmReadout *ro, psFits *fits) +{ + PM_ASSERT_READOUT_NON_NULL(ro, false); + PS_ASSERT_FITS_NON_NULL(fits, false); + + bool gotRow, gotCell; + psImage *rowCorr = psMetadataLookupPtr(&gotRow, ro->analysis, PM_PATTERN_ROW_CORRECTION); // Row correction + float cellCorr = psMetadataLookupF32(&gotCell, ro->analysis, PM_PATTERN_CELL_CORRECTION); // Cell corr. + + pmCell *cell = ro->parent; // Cell of interest + if (!cell) { + psError(PS_ERR_UNEXPECTED_NULL, true, "No cell associated with readout."); + return false; + } + pmChip *chip = cell->parent; // Chip of interest + pmFPA *fpa = chip->parent; // FPA of interest + pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // HDU for readout + if (!hdu) { + psError(PS_ERR_UNEXPECTED_NULL, true, "No HDU associated with readout."); + return false; + } + + psMetadata *header = psMetadataCopy(NULL, hdu->header); // Header for output + + if (gotCell) { + psMetadataAddF32(header, PS_LIST_TAIL, PM_PATTERN_CELL_CORRECTION, PS_META_REPLACE, + "ExpNum cell correction value", cellCorr); + } + + if (gotRow) { + if (!psFitsWriteImage(fits, header, rowCorr, 0, hdu->extname)) { + psError(PS_ERR_IO, false, "Unable to write pattern row correction."); + psFree(header); + return false; + } + } else { + if (!psFitsWriteBlank(fits, header, hdu->extname)) { + psError(PS_ERR_IO, false, "Unable to write pattern cell correction."); + psFree(header); + return false; + } + } + + psFree(header); + return true; +} + +static bool pmCellWriteExpNum(pmCell *cell, const pmFPAview *view, + pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(cell, false); + PS_ASSERT_PTR_NON_NULL(cell->readouts, false); + PS_ASSERT_PTR_NON_NULL(view, false); + + if (!pmConceptsWriteCell(cell, true, config)) { + psError(PS_ERR_IO, false, "Unable to write concepts for cell."); + return false; + } + + // Only do the FIRST readout --- don't want to write lots of headers + pmReadout *readout = cell->readouts->data[0]; + if (!pmReadoutWriteExpNum(readout, file->fits)) { + psError(PS_ERR_IO, false, "Failed to write readout"); + return false; + } + return true; +} + +static bool pmChipWriteExpNum(pmChip *chip, const pmFPAview *view, + pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(chip, false); + PS_ASSERT_PTR_NON_NULL(chip->cells, false); + PS_ASSERT_PTR_NON_NULL(view, false); + + if (!pmConceptsWriteChip(chip, true, true, config)) { + psError(PS_ERR_IO, false, "Unable to write concepts for chip.\n"); + return false; + } + + pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view + *thisView = *view; + + for (int i = 0; i < chip->cells->n; i++) { + pmCell *cell = chip->cells->data[i]; + thisView->cell = i; + if (!pmCellWriteExpNum(cell, thisView, file, config)) { + psError(PS_ERR_IO, false, "Failed to write %dth cell", i); + psFree(thisView); + return false; + } + } + psFree(thisView); + return true; +} + +static bool pmFPAWriteExpNum(pmFPA *fpa, const pmFPAview *view, + pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(fpa, false); + PS_ASSERT_PTR_NON_NULL(fpa->chips, false); + + if (!pmConceptsWriteFPA(fpa, true, config)) { + psError(PS_ERR_IO, false, "Unable to write concepts for FPA.\n"); + return false; + } + + pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view + *thisView = *view; + + for (int i = 0; i < fpa->chips->n; i++) { + pmChip *chip = fpa->chips->data[i]; + thisView->chip = i; + if (!pmChipWriteExpNum(chip, thisView, file, config)) { + psError(PS_ERR_IO, false, "Failed to write %dth chip", i); + psFree(thisView); + return false; + } + } + psFree(thisView); + return true; +} +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// Currently only ppStack writes an EXPNUM image and it uses file type MASK +bool pmExpNumWrite(const pmFPAview *view, pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(file, false); + PS_ASSERT_PTR_NON_NULL(file->fpa, false); + + pmFPA *fpa = pmFPAfileSuitableFPA(file, view, config, false); // Suitable FPA for writing + + if (view->chip == -1) { + if (!pmFPAWriteExpNum(fpa, view, file, config)) { + psError(PS_ERR_IO, false, "Failed to write pattern correction from fpa"); + psFree(fpa); + return false; + } + psFree(fpa); + return true; + } + + if (view->chip >= fpa->chips->n) { + psError(PS_ERR_UNKNOWN, false, "Writing chip == %d (>= chips->n == %ld)", view->chip, fpa->chips->n); + psFree(fpa); + return false; + } + pmChip *chip = fpa->chips->data[view->chip]; + + if (view->cell == -1) { + if (!pmChipWriteExpNum(chip, view, file, config)) { + psError(PS_ERR_IO, false, "Failed to write pattern correction from chip"); + psFree(fpa); + return false; + } + psFree(fpa); + return true; + } + + if (view->cell >= chip->cells->n) { + psError(PS_ERR_UNKNOWN, false, "Writing cell == %d (>= cells->n == %ld)", + view->cell, chip->cells->n); + psFree(fpa); + return false; + } + pmCell *cell = chip->cells->data[view->cell]; + + if (view->readout == -1) { + if (!pmCellWriteExpNum(cell, view, file, config)) { + psError(PS_ERR_IO, false, "Failed to write pattern correction from cell"); + psFree(fpa); + return false; + } + psFree(fpa); + return true; + } + + if (view->readout >= cell->readouts->n) { + psError(PS_ERR_UNKNOWN, false, "Writing readout == %d (>= readouts->n == %ld)", + view->readout, cell->readouts->n); + psFree(fpa); + return false; + } + pmReadout *readout = cell->readouts->data[view->readout]; + + if (!pmReadoutWriteExpNum(readout, file->fits)) { + psError(PS_ERR_IO, false, "Failed to write pattern correction from readout %d", view->readout); + psFree(fpa); + return false; + } + + psFree(fpa); + return true; +} + +bool pmExpNumWritePHU(const pmFPAview *view, pmFPAfile *file, pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(file, false); + + if (file->wrote_phu) { + return true; + } + + // find the FPA phu + pmFPA *fpa = pmFPAfileSuitableFPA(file, view, config, false); // Suitable FPA for writing + pmHDU *phu = psMemIncrRefCounter(pmFPAviewThisPHU(view, fpa)); + psFree(fpa); + + // if there is no PHU, this is a single header+image (extension-less) file. This could be the case for an + // input SPLIT set of files being written out as a MEF. if there is a PHU, write it out as a 'blank' + psMetadata *outhead = psMetadataAlloc(); + if (phu) { + psMetadataCopy (outhead, phu->header); + } + psFree(phu); + + pmConfigConformHeader(outhead, file->format); + + psFitsWriteBlank(file->fits, outhead, ""); + file->wrote_phu = true; + + psTrace("pmFPAfile", 5, "wrote phu %s (type: %d)\n", file->filename, file->type); + psFree(outhead); + + return true; +} +#endif // notyet + Index: trunk/psModules/src/camera/pmFPAExpNumIO.h =================================================================== --- trunk/psModules/src/camera/pmFPAExpNumIO.h (revision 33690) +++ trunk/psModules/src/camera/pmFPAExpNumIO.h (revision 33690) @@ -0,0 +1,36 @@ +#ifndef PM_EXPNUM_IO_H +#define PM_EXPNUM_IO_H + +#include + +#include +#include + + +bool pmExpNumRead(const pmFPAview *view, ///< View into which to read + pmFPAfile *file, ///< File from which to read + pmConfig *config ///< Configuration + ); + +#ifdef notyet +// Currently we don't need write functions for the EXPNUM images. +// Only ppStack creates them and it uses a MASK file type + +/// Write pattern correction within a readout to a FITS file +bool pmReadoutWritePattern( + pmReadout *readout, ///< Readout for which to write pattern correction (in analysis MD) + psFits *fits ///< FITS file to which to write + ); +bool pmPatternWrite(const pmFPAview *view, ///< View from which to write + pmFPAfile *file, ///< File to which to write + pmConfig *config ///< Configuration + ); + +bool pmPatternWritePHU(const pmFPAview *view, // View to PHU + pmFPAfile *file, ///< File to which to write + pmConfig *config ///< Configuration + ); + +#endif // notyet + +#endif Index: trunk/psModules/src/camera/pmFPAfile.c =================================================================== --- trunk/psModules/src/camera/pmFPAfile.c (revision 33689) +++ trunk/psModules/src/camera/pmFPAfile.c (revision 33690) @@ -543,4 +543,7 @@ if (!strcasecmp(type, "PATTERN")) { return PM_FPA_FILE_PATTERN; + } + if (!strcasecmp(type, "EXPNUM")) { + return PM_FPA_FILE_EXPNUM; } @@ -589,4 +592,6 @@ case PM_FPA_FILE_PATTERN: return "PATTERN"; + case PM_FPA_FILE_EXPNUM: + return "EXPNUM"; default: return ("NONE"); Index: trunk/psModules/src/camera/pmFPAfile.h =================================================================== --- trunk/psModules/src/camera/pmFPAfile.h (revision 33689) +++ trunk/psModules/src/camera/pmFPAfile.h (revision 33690) @@ -51,4 +51,5 @@ PM_FPA_FILE_PATTERN, PM_FPA_FILE_LINEARITY, + PM_FPA_FILE_EXPNUM, } pmFPAfileType; Index: trunk/psModules/src/camera/pmFPAfileIO.c =================================================================== --- trunk/psModules/src/camera/pmFPAfileIO.c (revision 33689) +++ trunk/psModules/src/camera/pmFPAfileIO.c (revision 33690) @@ -53,4 +53,5 @@ #include "pmSubtractionIO.h" #include "pmPatternIO.h" +#include "pmFPAExpNumIO.h" #include "pmConcepts.h" #include "pmConfigRun.h" @@ -231,4 +232,7 @@ status = pmAstromModelReadForView (view, file, config); break; + case PM_FPA_FILE_EXPNUM: + status = pmExpNumRead(view, file, config); + break; case PM_FPA_FILE_ASTROM_REFSTARS: case PM_FPA_FILE_JPEG: @@ -291,4 +295,5 @@ case PM_FPA_FILE_DARK: case PM_FPA_FILE_PATTERN: + case PM_FPA_FILE_EXPNUM: { // create FPA structure component based on view @@ -500,4 +505,9 @@ status = pmFPAviewWriteSourcePlot (view, file, config); break; + + case PM_FPA_FILE_EXPNUM: + // when ppStack output's EXPNUM file it uses a file rule where the file type is MASK + psError(PS_ERR_IO, true, "cannot write type EXPNUM (%s)", file->name); + return false; case PM_FPA_FILE_WCS: @@ -562,4 +572,5 @@ case PM_FPA_FILE_ASTROM_REFSTARS: case PM_FPA_FILE_LINEARITY: + case PM_FPA_FILE_EXPNUM: psTrace ("psModules.camera", 5, "closing %s (%s) (%d:%d:%d)\n", file->filename, file->name, view->chip, view->cell, view->readout); status = psFitsClose (file->fits); @@ -636,4 +647,5 @@ case PM_FPA_FILE_ASTROM_MODEL: case PM_FPA_FILE_ASTROM_REFSTARS: + case PM_FPA_FILE_EXPNUM: psTrace ("psModules.camera", 6, "NOT freeing %s (%s) : save for further analysis\n", file->filename, file->name); return true; @@ -797,4 +809,5 @@ case PM_FPA_FILE_ASTROM_REFSTARS: case PM_FPA_FILE_LINEARITY: + case PM_FPA_FILE_EXPNUM: psTrace ("psModules.camera", 5, "opening %s (%s) (%d:%d:%d)\n", file->filename, file->name, view->chip, view->cell, view->readout); @@ -996,4 +1009,5 @@ status = pmAstromRefstarsWritePHU (view, file, config); break; + case PM_FPA_FILE_EXPNUM: case PM_FPA_FILE_ASTROM_MODEL: case PM_FPA_FILE_SX: Index: trunk/psModules/src/objects/pmSource.c =================================================================== --- trunk/psModules/src/objects/pmSource.c (revision 33689) +++ trunk/psModules/src/objects/pmSource.c (revision 33690) @@ -160,4 +160,5 @@ source->parent = NULL; source->imageID = -1; + source->nFrames = 0; psMemSetDeallocator(source, (psFreeFunc) sourceFree); Index: trunk/psModules/src/objects/pmSource.h =================================================================== --- trunk/psModules/src/objects/pmSource.h (revision 33689) +++ trunk/psModules/src/objects/pmSource.h (revision 33690) @@ -118,4 +118,5 @@ pmSource *parent; ///< reference to the master source from which this is derived int imageID; + psU16 nFrames; }; Index: trunk/psModules/src/objects/pmSourceIO_CMF_PS1_DV1.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_CMF_PS1_DV1.c (revision 33689) +++ trunk/psModules/src/objects/pmSourceIO_CMF_PS1_DV1.c (revision 33690) @@ -81,10 +81,9 @@ } - short nImageOverlap; float magOffset; float zeroptErr; float fwhmMajor; float fwhmMinor; - pmSourceOutputsCommonValues (&nImageOverlap, &magOffset, &zeroptErr, &fwhmMajor, &fwhmMinor, readout, imageHeader); + pmSourceOutputsCommonValues (&magOffset, &zeroptErr, &fwhmMajor, &fwhmMinor, readout, imageHeader); table = psArrayAllocEmpty (sources->n); @@ -161,6 +160,5 @@ psMetadataAdd (row, PS_LIST_TAIL, "FLAGS", PS_DATA_U32, "psphot analysis flags", source->mode); - // XXX not sure how to get this : need to load Nimages with weight? - psMetadataAdd (row, PS_LIST_TAIL, "N_FRAMES", PS_DATA_U16, "Number of frames overlapping source center", nImageOverlap); + psMetadataAdd (row, PS_LIST_TAIL, "N_FRAMES", PS_DATA_U16, "Number of frames overlapping source center", source->nFrames); psMetadataAdd (row, PS_LIST_TAIL, "PADDING", PS_DATA_S16, "padding", 0); Index: trunk/psModules/src/objects/pmSourceIO_CMF_PS1_DV2.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_CMF_PS1_DV2.c (revision 33689) +++ trunk/psModules/src/objects/pmSourceIO_CMF_PS1_DV2.c (revision 33690) @@ -82,10 +82,9 @@ table = psArrayAllocEmpty (sources->n); - short nImageOverlap; float magOffset; float zeroptErr; float fwhmMajor; float fwhmMinor; - pmSourceOutputsCommonValues (&nImageOverlap, &magOffset, &zeroptErr, &fwhmMajor, &fwhmMinor, readout, imageHeader); + pmSourceOutputsCommonValues (&magOffset, &zeroptErr, &fwhmMajor, &fwhmMinor, readout, imageHeader); // we write out PSF-fits for all sources, regardless of quality. the source flags tell us the state @@ -180,5 +179,5 @@ // XXX not sure how to get this : need to load Nimages with weight? - psMetadataAdd (row, PS_LIST_TAIL, "N_FRAMES", PS_DATA_U16, "Number of frames overlapping source center", nImageOverlap); + psMetadataAdd (row, PS_LIST_TAIL, "N_FRAMES", PS_DATA_U16, "Number of frames overlapping source center", source->nFrames); psMetadataAdd (row, PS_LIST_TAIL, "PADDING", PS_DATA_S16, "padding", 0); Index: trunk/psModules/src/objects/pmSourceIO_CMF_PS1_SV1.c =================================================================== --- trunk/psModules/src/objects/pmSourceIO_CMF_PS1_SV1.c (revision 33689) +++ trunk/psModules/src/objects/pmSourceIO_CMF_PS1_SV1.c (revision 33690) @@ -84,10 +84,9 @@ table = psArrayAllocEmpty (sources->n); - short nImageOverlap; float magOffset; float zeroptErr; float fwhmMajor; float fwhmMinor; - pmSourceOutputsCommonValues (&nImageOverlap, &magOffset, &zeroptErr, &fwhmMajor, &fwhmMinor, readout, imageHeader); + pmSourceOutputsCommonValues (&magOffset, &zeroptErr, &fwhmMajor, &fwhmMinor, readout, imageHeader); // we write out PSF-fits for all sources, regardless of quality. the source flags tell us the state @@ -170,6 +169,5 @@ psMetadataAdd (row, PS_LIST_TAIL, "FLAGS2", PS_DATA_U32, "psphot analysis flags", source->mode2); - // XXX not sure how to get this : need to load Nimages with weight? - psMetadataAdd (row, PS_LIST_TAIL, "N_FRAMES", PS_DATA_U16, "Number of frames overlapping source center", nImageOverlap); + psMetadataAdd (row, PS_LIST_TAIL, "N_FRAMES", PS_DATA_U16, "Number of frames overlapping source center", source->nFrames); psMetadataAdd (row, PS_LIST_TAIL, "PADDING", PS_DATA_S16, "padding", 0); Index: trunk/psModules/src/objects/pmSourceOutputs.c =================================================================== --- trunk/psModules/src/objects/pmSourceOutputs.c (revision 33689) +++ trunk/psModules/src/objects/pmSourceOutputs.c (revision 33690) @@ -40,5 +40,5 @@ #include "pmSourceOutputs.h" -bool pmSourceOutputsCommonValues (short *nImageOverlap, float *magOffset, float *zeroptErr, float *fwhmMajor, float *fwhmMinor, pmReadout *readout, psMetadata *header) { +bool pmSourceOutputsCommonValues (float *magOffset, float *zeroptErr, float *fwhmMajor, float *fwhmMinor, pmReadout *readout, psMetadata *header) { pmFPA *fpa = readout->parent->parent->parent; @@ -72,5 +72,4 @@ } - *nImageOverlap = psMetadataLookupS32 (&status2, header, "NINPUTS"); return true; Index: trunk/psModules/src/objects/pmSourceOutputs.h =================================================================== --- trunk/psModules/src/objects/pmSourceOutputs.h (revision 33689) +++ trunk/psModules/src/objects/pmSourceOutputs.h (revision 33690) @@ -56,5 +56,5 @@ } pmSourceOutputsMoments; -bool pmSourceOutputsCommonValues (short *nImageOverlap, float *magOffset, float *zeroptErr, float *fwhmMajor, float *fwhmMinor, pmReadout *readout, psMetadata *header); +bool pmSourceOutputsCommonValues (float *magOffset, float *zeroptErr, float *fwhmMajor, float *fwhmMinor, pmReadout *readout, psMetadata *header); bool pmSourceOutputsSetValues (pmSourceOutputs *outputs, pmSource *source, pmChip *chip, float fwhmMajor, float fwhmMinor, float magOffset); Index: trunk/psphot/src/Makefile.am =================================================================== --- trunk/psphot/src/Makefile.am (revision 33689) +++ trunk/psphot/src/Makefile.am (revision 33690) @@ -206,5 +206,6 @@ psphotPetrosianStats.c \ psphotPetrosianVisual.c \ - psphotEfficiency.c + psphotEfficiency.c \ + psphotSetNFrames.c # re-instate these Index: trunk/psphot/src/psphot.h =================================================================== --- trunk/psphot/src/psphot.h (revision 33689) +++ trunk/psphot/src/psphot.h (revision 33690) @@ -481,3 +481,6 @@ bool psphotStackObjectsSelectForAnalysis (pmConfig *config, const pmFPAview *view, const char *filerule, psArray *objects); +bool psphotSetNFrames (pmConfig *config, const pmFPAview *view, const char *filerule); +bool psphotSetNFramesReadout (pmConfig *config, const pmFPAview *view, const char *filerule, int index); + #endif Index: trunk/psphot/src/psphotArguments.c =================================================================== --- trunk/psphot/src/psphotArguments.c (revision 33689) +++ trunk/psphot/src/psphotArguments.c (revision 33690) @@ -217,4 +217,5 @@ pmConfigFileSetsMD (config->arguments, &argc, argv, "PSPHOT.PSF", "-psf", "-psflist"); pmConfigFileSetsMD (config->arguments, &argc, argv, "SRC", "-src", "-srclist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "EXPNUM", "-expnum", "-expnumlist"); if (argc == 1) { Index: trunk/psphot/src/psphotKronIterate.c =================================================================== --- trunk/psphot/src/psphotKronIterate.c (revision 33689) +++ trunk/psphot/src/psphotKronIterate.c (revision 33690) @@ -150,5 +150,5 @@ if (!psphotKronIterate_Threaded(job)) { psError(PS_ERR_UNKNOWN, false, "Unable to guess model."); - psFree(AnalysisRegion); + // psFree(AnalysisRegion); return false; } @@ -222,4 +222,8 @@ float windowRadius = PS_MAX(RADIUS, maxWindow); +#ifdef notdef + fprintf(stderr, "Redefining pixels for source: %d %4d %4d new radius: %f\n", + i, source->peak->x, source->peak->y, windowRadius+2); +#endif // re-allocate image, weight, mask arrays for each peak with box big enough to fit BIG_RADIUS pmSourceRedefinePixels (source, readout, source->peak->x, source->peak->y, windowRadius + 2); Index: trunk/psphot/src/psphotParseCamera.c =================================================================== --- trunk/psphot/src/psphotParseCamera.c (revision 33689) +++ trunk/psphot/src/psphotParseCamera.c (revision 33690) @@ -2,4 +2,6 @@ // define the needed / desired I/O files + + bool psphotParseCamera (pmConfig *config) { @@ -40,4 +42,11 @@ } + pmFPAfileBindFromArgs (&status, input, config, "PSPHOT.EXPNUM", "EXPNUM"); + if (!status) { + psError (PS_ERR_UNKNOWN, false, "failed to load find definition"); + return NULL; + } + + // define the additional input/output files associated with psphot if (!psphotDefineFiles (config, input)) { Index: trunk/psphot/src/psphotSetNFrames.c =================================================================== --- trunk/psphot/src/psphotSetNFrames.c (revision 33690) +++ trunk/psphot/src/psphotSetNFrames.c (revision 33690) @@ -0,0 +1,68 @@ +# include "psphotInternal.h" + +# define ESCAPE(MESSAGE) { \ + psError(PSPHOT_ERR_DATA, false, MESSAGE); \ + psFree (view); \ + return false; \ + } + + +// Set source->nFrames based on the values in the EXPNUM image at the coordinates of each source's peak + +bool psphotSetNFrames (pmConfig *config, const pmFPAview *view, const char *filerule) +{ + psLogMsg ("psphot", PS_LOG_INFO, "--- psphot Set N Frames ---"); + + int num = psphotFileruleCount(config, filerule); + + // loop over the inputs + for (int i = 0; i < num; i++) { + if (!psphotSetNFramesReadout (config, view, filerule, i)) { + psError (PSPHOT_ERR_CONFIG, false, "failed to set nFrames for %s entry %d", filerule, i); + return false; + } + } + + return true; +} + +bool psphotSetNFramesReadout (pmConfig *config, const pmFPAview *view, const char *filerule, int index) +{ + bool status; + // find the currently selected readout + pmFPAfile *file = pmFPAfileSelectSingle(config->files, filerule, index); // File of interest + psAssert (file, "missing file?"); + + pmReadout *readout = pmFPAviewThisReadout(view, file->fpa); + psAssert (readout, "missing readout?"); + + psImage *expnum = psMetadataLookupPtr(&status, readout->analysis, "EXPNUM"); + if (!status || !expnum) { + psLogMsg ("psphot", PS_LOG_INFO, "No EXPNUM image for input %d", index); + return true; + } + + pmDetections *detections = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.DETECTIONS"); + psAssert (detections, "missing detections?"); + psAssert (detections->allSources, "missing sources?"); + + psArray *sources = detections->allSources; + + int col0 = expnum->col0; + int row0 = expnum->row0; + int numCols = expnum->numCols; + int numRows = expnum->numRows; + + for (int i = 0; i < sources->n; i++) { + pmSource *source = sources->data[i]; + int x = source->peak->x; + int y = source->peak->y; + if (x >= col0 && x < numCols && y >= row0 && y < numRows) { + source->nFrames = expnum->data.PS_TYPE_IMAGE_MASK_DATA[y][x]; + } else { + source->nFrames = 0; + } + } + + return true; +} Index: trunk/psphot/src/psphotStackArguments.c =================================================================== --- trunk/psphot/src/psphotStackArguments.c (revision 33689) +++ trunk/psphot/src/psphotStackArguments.c (revision 33690) @@ -53,4 +53,8 @@ psMetadataAddStr (options, PS_LIST_TAIL, "BREAK_POINT", PS_META_REPLACE, "", argv[N]); psArgumentRemove (N, &argc, argv); + } + if ((N = psArgumentGet (argc, argv, "-ds9regions"))) { + psArgumentRemove (N, &argc, argv); + pmSubtractionRegions(true); } Index: trunk/psphot/src/psphotStackImageLoop.c =================================================================== --- trunk/psphot/src/psphotStackImageLoop.c (revision 33689) +++ trunk/psphot/src/psphotStackImageLoop.c (revision 33690) @@ -30,7 +30,16 @@ } + psMetadata *recipe = psMetadataLookupPtr (NULL, config->recipes, PSPHOT_RECIPE); + bool useRaw = psMetadataLookupBool (NULL, recipe, "PSPHOT.STACK.USE.RAW"); + if (useRaw && inputRaw == NULL) { + psLogMsg ("psphot", 1, "PSPHOT.STACK.USE.RAW set but no raw input."); + useRaw = false; + } + pmFPAview *view = pmFPAviewAlloc (0); - // XXX for now, just load the full set of images up front + + // XXX for now, just load the full set of images up front except for EXPNUM which we defer + pmFPAfileActivate (config->files, false, "PSPHOT.STACK.EXPNUM.RAW"); if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE ("failed input for fpa in psphot."); @@ -86,6 +95,9 @@ UpdateHeadersForChip(config, view); - // save output which is saved at the chip level - if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE ("failed output for Chip in psphot."); + // Defer output until we have performed psphotSetNFrames() + pmFPAfileActivate (config->files, false, NULL); + + // Iterate up + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE ("failed pmFPAfileIOChecks for Chip in psphot."); } psMemDump("doneloop"); @@ -93,5 +105,36 @@ UpdateHeadersForFPA(config, view); - // save output which is saved at the fpa level + // Iterate up output which is saved at the fpa level + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE ("failed ouput pmFPAfileIOChecks FPA in psphot."); + + // Load the appropriate EXPNUM image + pmFPAfileActivate (config->files, true, useRaw ? "PSPHOT.STACK.EXPNUM.RAW" : "PSPHOT.STACK.EXPNUM.CNV"); + + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE ("failed input for fpa EXPNUM in psphot."); + + // for psphot, we force data to be read at the chip level + while ((chip = pmFPAviewNextChip (view, input->fpa, 1)) != NULL) { + psLogMsg ("psphot", 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 ("failed input for Chip EXPNUM in psphotStack."); + + // there is now only a single chip (multiple readouts?). loop over it and process + while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { + psLogMsg ("psphot", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE ("failed input for Cell in psphotStack."); + + // process each of the readouts + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + psLogMsg ("psphot", 6, "Readout %d: %x %x\n", view->readout, cell->file_exists, cell->process); + if (! readout->data_exists) { continue; } + + if (!psphotSetNFrames (config, view, useRaw ? inputRaw->name : inputCnv->name)) ESCAPE ("failed to setNFrames."); + } + } + // now activate all files to trigger final output + pmFPAfileActivate (config->files, true, NULL); + + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE ("failed output for Chip in psphot."); + } if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE ("failed ouput for FPA in psphot."); Index: trunk/psphot/src/psphotStackParseCamera.c =================================================================== --- trunk/psphot/src/psphotStackParseCamera.c (revision 33689) +++ trunk/psphot/src/psphotStackParseCamera.c (revision 33690) @@ -59,4 +59,11 @@ } } + psString expnum = psMetadataLookupStr(&status, input, "RAW:EXPNUM"); // Name of expnum image + if (expnum && strlen(expnum) > 0) { + if (!defineFile(config, rawInputFile, "PSPHOT.STACK.EXPNUM.RAW", expnum, PM_FPA_FILE_EXPNUM)) { + psError(PS_ERR_UNKNOWN, false, "Unable to define file from expnum %d (%s)", i, expnum); + return false; + } + } nRaw ++; } @@ -81,4 +88,11 @@ if (!defineFile(config, cnvInputFile, "PSPHOT.STACK.VARIANCE.CNV", variance, PM_FPA_FILE_VARIANCE)) { psError(PS_ERR_UNKNOWN, false, "Unable to define file from variance %d (%s)", i, variance); + return false; + } + } + psString expnum = psMetadataLookupStr(&status, input, "CNV:EXPNUM"); // Name of EXPNUM image + if (expnum && strlen(expnum) > 0) { + if (!defineFile(config, cnvInputFile, "PSPHOT.STACK.EXPNUM.CNV", expnum, PM_FPA_FILE_EXPNUM)) { + psError(PS_ERR_UNKNOWN, false, "Unable to define file from expnum %d (%s)", i, expnum); return false; }