Index: /branches/haf_branches/videophot2010/ppImage/autogen.sh =================================================================== --- /branches/haf_branches/videophot2010/ppImage/autogen.sh (revision 29946) +++ /branches/haf_branches/videophot2010/ppImage/autogen.sh (revision 29947) @@ -8,5 +8,5 @@ cd $srcdir -PROJECT=ppImage +PROJECT=psvideophot TEST_TYPE=-f # change this to be a unique filename in the top level dir Index: /branches/haf_branches/videophot2010/ppImage/configure.ac =================================================================== --- /branches/haf_branches/videophot2010/ppImage/configure.ac (revision 29946) +++ /branches/haf_branches/videophot2010/ppImage/configure.ac (revision 29947) @@ -1,5 +1,5 @@ AC_PREREQ(2.61) -AC_INIT([ppImage], [1.1.0], [ipp-support@ifa.hawaii.edu]) +AC_INIT([psvideophot], [1.1.0], [ipp-support@ifa.hawaii.edu]) AC_CONFIG_SRCDIR([src]) @@ -28,6 +28,6 @@ IPP_VERSION -AC_SUBST([PPIMAGE_CFLAGS]) -AC_SUBST([PPIMAGE_LIBS]) +AC_SUBST([PSVIDEOPHOT_CFLAGS]) +AC_SUBST([PSVIDEOPHOT_LIBS]) AC_CONFIG_FILES([ Index: /branches/haf_branches/videophot2010/ppImage/src/Makefile.am =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/Makefile.am (revision 29946) +++ /branches/haf_branches/videophot2010/ppImage/src/Makefile.am (revision 29947) @@ -1,65 +1,42 @@ -bin_PROGRAMS = ppImage +bin_PROGRAMS = psvideophot noinst_HEADERS = \ - ppImage.h + psvideophot.h if HAVE_SVNVERSION -PPIMAGE_VERSION=`$(SVNVERSION) ..` +PSVIDEOPHOT_VERSION=`$(SVNVERSION) ..` else -PPIMAGE_VERSION="UNKNOWN" +PSVIDEOPHOT_VERSION="UNKNOWN" endif if HAVE_SVN -PPIMAGE_BRANCH=`$(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 }'` -PPIMAGE_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'` +PSVIDEOPHOT_BRANCH=`$(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 }'` +PSVIDEOPHOT_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'` else -PPIMAGE_BRANCH="UNKNOWN" -PPIMAGE_SOURCE="UNKNOWN" +PSVIDEOPHOT_BRANCH="UNKNOWN" +PSVIDEOPHOT_SOURCE="UNKNOWN" endif -# Force recompilation of ppImageVersion.c, since it gets the version information -ppImageVersion.c: ppImageVersionDefinitions.h -ppImageVersionDefinitions.h: ppImageVersionDefinitions.h.in FORCE - -$(RM) ppImageVersionDefinitions.h - $(SED) -e "s|@PPIMAGE_VERSION@|\"$(PPIMAGE_VERSION)\"|" -e "s|@PPIMAGE_BRANCH@|\"$(PPIMAGE_BRANCH)\"|" -e "s|@PPIMAGE_SOURCE@|\"$(PPIMAGE_SOURCE)\"|" ppImageVersionDefinitions.h.in > ppImageVersionDefinitions.h +# Force recompilation of psvideophotVersion.c, since it gets the version information +psvideophotVersion.c: psvideophotVersionDefinitions.h +psvideophotVersionDefinitions.h: psvideophotVersionDefinitions.h.in FORCE + -$(RM) psvideophotVersionDefinitions.h + $(SED) -e "s|@PSVIDEOPHOT_VERSION@|\"$(PSVIDEOPHOT_VERSION)\"|" -e "s|@PSVIDEOPHOT_BRANCH@|\"$(PSVIDEOPHOT_BRANCH)\"|" -e "s|@PSVIDEOPHOT_SOURCE@|\"$(PSVIDEOPHOT_SOURCE)\"|" psvideophotVersionDefinitions.h.in > psvideophotVersionDefinitions.h FORCE: ; -BUILT_SOURCES = ppImageVersionDefinitions.h +BUILT_SOURCES = psvideophotVersionDefinitions.h -ppImage_CFLAGS = $(PPIMAGE_CFLAGS) $(PPSTATS_CFLAGS) $(PSASTRO_CFLAGS) $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) -ppImage_LDFLAGS = $(PPIMAGE_LIBS) $(PSASTRO_LIBS) $(PPSTATS_LIBS) $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS) -ppImage_SOURCES = \ - ppImage.c \ - ppImageArguments.c \ - ppImageParseCamera.c \ - ppImageLoop.c \ - ppImageCleanup.c \ - ppImageOptions.c \ - ppImageDetrendReadout.c \ - ppImageDetrendRecord.c \ - ppImageDetrendNonLinear.c \ - ppImageDetrendFringe.c \ - ppImageDetrendFree.c \ - ppImageDetrendPattern.c \ - ppImageRebinReadout.c \ - ppImageMosaic.c \ - ppImageMaskStats.c \ - ppImagePhotom.c \ - ppImageAstrom.c \ - ppImageAddstar.c \ - ppImageStatsOutput.c \ - ppImagePixelStats.c \ - ppImageMetadataStats.c \ - ppImageReplaceBackground.c \ - ppImageMeasureCrosstalk.c \ - ppImageCorrectCrosstalk.c \ - ppImageDefineFile.c \ - ppImageSetMaskBits.c \ - ppImageBurntoolMask.c \ - ppImageParityFlip.c \ - ppImageCheckCTE.c \ - ppImageFileCheck.c \ - ppImageVersion.c \ - ppImageMemory.c +psvideophot_CFLAGS = $(PSVIDEOPHOT_CFLAGS) $(PPSTATS_CFLAGS) $(PSASTRO_CFLAGS) $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) +psvideophot_LDFLAGS = $(PSVIDEOPHOT_LIBS) $(PSASTRO_LIBS) $(PPSTATS_LIBS) $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS) +psvideophot_SOURCES = \ + psvideophot.c \ + psvideophotArguments.c \ + psvideophotParseCamera.c \ + psvideophotOptions.c \ + psvideophotCleanup.c \ + psvideophotDefineFile.c \ + psvideoLoop.c \ + psvideophotFileCheck.c \ + psvideophotVersion.c CLEANFILES = *~ Index: anches/haf_branches/videophot2010/ppImage/src/ppFocus.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppFocus.c (revision 29946) +++ (revision ) @@ -1,74 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -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 = ppFocusArguments(argc, argv); - if (config == NULL) { - psErrorStackPrint(stderr, " "); - exit(1); - } - - // we search the argument data for the named fileset (argname) - psArray *infiles = psMetadataLookupPtr(NULL, config->arguments, "INPUT"); - if (!infiles) { - psTrace("pmFPAfile", 5, "Failed to find INPUT in argument list"); - exit(1); - } - - // allocate vectors for analysis - psVector *focus = psVectorAllocEmpty(infiles->n, PS_TYPE_F32); - psVector *fwhm = psVectorAllocEmpty(infiles->n, PS_TYPE_F32); - - for (int i = 0; i < infiles->n; i++) { - - // define recipe options - // define the active I/O files - ppImageOptions *options = ppFocusParseCamera(config, i); - if (options == NULL) { - psErrorStackPrint(stderr, " "); - exit(1); - } - - // Image Arithmetic Loop - // XXX ppFocus REQUIRES photom: for it to be true? - // - if (!ppImageLoop(config, options)) { - psErrorStackPrint(stderr, " "); - exit(1); - } - - // determine FWHM at reference location in image - // (also removes PPIMAGE.INPUT from config->files) - ppFocusGetFWHM (config, focus, fwhm); - - ppFocusDropCamera (config); - psFree (options); - } - - ppFocusFitFWHM (config, focus, fwhm); - - psLogMsg ("ppFocus", 3, "complete ppFocus run: %f sec\n", psTimerMark (TIMER_TOTAL)); - - // Cleaning up - psFree (focus); - psFree (fwhm); - ppImageCleanup(config, NULL); - return EXIT_SUCCESS; -} - -// ppFocus is a lot like ppImage, but with a few important differences: -// - the input list is a set of independent images (not multiple files for a single image) -// - each pass to ppImageLoop performs the analysis on a different pmFPAfile -// - after each ppImageLoop, grap the input pmFPAfile and extract the FWHM stats Index: anches/haf_branches/videophot2010/ppImage/src/ppFocusArguments.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppFocusArguments.c (revision 29946) +++ (revision ) @@ -1,72 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -static void usage (void) { - fprintf (stderr, "USAGE: ppFocus [-file focus.*.fits] [-list INPUT.txt] OUTPUT\n"); - exit (2); -} - -pmConfig *ppFocusArguments(int argc, char **argv) { - - int N; - bool status; - - if (argc == 1) usage (); - - // load the site-wide configuration information - pmConfig *config = pmConfigRead(&argc, argv, RECIPE_NAME); - if (config == NULL) { - psErrorStackPrint(stderr, "Can't find site configuration!\n"); - exit(EXIT_FAILURE); - } - - // save the following additional recipe values based on command-line options - // these options override the PPIMAGE recipe values loaded from recipe files - psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); - - // save these recipe options until we have loaded the options - // psMetadata *options = psMetadataAlloc (); - // psMetadataAddPtr (config->arguments, PS_LIST_TAIL, "PPIMAGE.OPTIONS", PS_DATA_METADATA, "", options); - - // the following options override the PPIMAGE recipe options - - // recipe option: -usemask : override MASK setting in phase2.recipe - if ((N = psArgumentGet(argc, argv, "-usemask"))) { - psArgumentRemove (N, &argc, argv); - psMetadataAddBool (options, PS_LIST_TAIL, "MASK", PS_META_REPLACE, "", true); - psArgumentRemove (N, &argc, argv); - } - - // XXX add other PPIMAGE recipe options here - - // the input file is a required argument; if not found, we will exit - status = pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list"); - if (!status) { usage ();} - - // if these command-line options are supplied, load the file name lists into config->arguments - // override any configuration-specified source for these files - pmConfigFileSetsMD (config->arguments, &argc, argv, "BIAS", "-bias", "-biaslist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "DARK", "-dark", "-darklist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "FLAT", "-flat", "-flatlist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "MASK", "-mask", "-masklist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "FRINGE", "-fringe", "-fringelist"); - - // chip selection is used to limit chips to be processed - if ((N = psArgumentGet (argc, argv, "-chip"))) { - psArgumentRemove (N, &argc, argv); - psMetadataAddStr (config->arguments, PS_LIST_TAIL, "CHIP_SELECTIONS", PS_DATA_STRING, "", - argv[N]); - psArgumentRemove (N, &argc, argv); - } - - 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: anches/haf_branches/videophot2010/ppImage/src/ppFocusFitFWHM.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppFocusFitFWHM.c (revision 29946) +++ (revision ) @@ -1,30 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -bool ppFocusFitFWHM (pmConfig *config, psVector *focus, psVector *fwhm) { - - float minFocus; - - psPolynomial1D *poly = psPolynomial1DAlloc (PS_POLYNOMIAL_ORD, 2); - - if (!psVectorFitPolynomial1D (poly, NULL, 0, fwhm, NULL, focus)) { - psError (PS_ERR_UNKNOWN, false, "failed to fit focus/fwhm trend; invalid image data?"); - return false; - } - - if (poly->coeff[2] <= 0.0) { - psLogMsg ("ppFocus", 3, "poor focus fit: zero or negative curvature\n"); - psLogMsg ("ppFocus", 3, "fit coeffs: %f %f %f\n", - poly->coeff[0], poly->coeff[1], poly->coeff[2]); - } - - minFocus = -0.5 * poly->coeff[1] / poly->coeff[2]; - psLogMsg ("ppFocus", 3, "best fit focus: %f\n", minFocus); - psLogMsg ("ppFocus", 3, "fwhm @ min: %f\n", psPolynomial1DEval (poly, minFocus)); - - psFree (poly); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppFocusGetFWHM.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppFocusGetFWHM.c (revision 29946) +++ (revision ) @@ -1,79 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -bool ppFocusGetFWHM (pmConfig *config, psVector *focus, psVector *fwhm) { - - bool status; - pmChip *chip; - pmCell *cell; - pmReadout *readout; - psMetadata *header; - float FOCUS, FWHM, FWHM_X, FWHM_Y, FWHMsum; - int FWHMnum; - - pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSPHOT.OUTPUT"); - if (!status) { - psErrorStackPrint(stderr, "Can't find input data!\n"); - exit(EXIT_FAILURE); - } - - pmFPAview *view = pmFPAviewAlloc (0); - - // - find readouts with measured PSFs - // - measure the average central FWHM for each PSF - FWHMsum = 0.0; - FWHMnum = 0; - - while ((chip = pmFPAviewNextChip (view, input->fpa, 1)) != NULL) { - psLogMsg ("ppImageLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); - if (!chip->process || !chip->file_exists) { continue; } - - while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { - psLogMsg ("ppImageLoop", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); - if (!cell->process || !cell->file_exists) { continue; } - - // process each of the readouts - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (!readout->data_exists) { continue; } - - // get average FWHM - // psphotReadout writes the FWHM values into the PSPHOT.HEADER table - // the source of this value depends on the psphot options. - // - if breakPoint is set to PEAKS, the value will not be defined - // - if breakPoint is set to MOMENTS, the PSFSTAR moments are used - // - in all other cases, the psf model is used - header = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.HEADER"); - if (header == NULL) { - psError(PS_ERR_IO, false, "Missing header in ppFocus"); - continue; - } - - FWHM_X = psMetadataLookupF32 (&status, header, "FWHM_X"); - FWHM_Y = psMetadataLookupF32 (&status, header, "FWHM_Y"); - - FWHMsum += 0.5*(FWHM_X + FWHM_Y); - FWHMnum ++; - - psLogMsg ("ppFocus", 4, "focus pt: %f,%f, fwhm sum: %f, fwhm num: %d\n", FWHM_X, FWHM_Y, FWHMsum, FWHMnum); - } - } - } - - FWHM = FWHMsum / FWHMnum; - - FOCUS = psMetadataLookupF32 (&status, input->fpa->concepts, "FPA.FOCUS"); - - fwhm->data.F32[fwhm->n] = FWHM; - focus->data.F32[focus->n] = FOCUS; - - psVectorExtend (fwhm, 10, 1); - psVectorExtend (focus, 10, 1); - - psLogMsg ("ppFocus", 4, "focus: %f, fwhm: %f (%d)\n", FOCUS, FWHM, FWHMnum); - - psFree (view); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppFocusParseCamera.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppFocusParseCamera.c (revision 29946) +++ (revision ) @@ -1,133 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -// XXX clean up error checks: return NULL, not psAbort -ppImageOptions *ppFocusParseCamera (pmConfig *config, int entry) { - - bool status = false; - - // the first input image defines the camera, and all recipes and options that follow - // select only the first file from the INPUT array - pmFPAfile *input = pmFPAfileDefineSingleFromArgs (&status, config, "PPIMAGE.INPUT", "INPUT", entry); - if (!status) { - psError(PS_ERR_IO, false, "Failed to build FPA from PPIMAGE.INPUT"); - return NULL; - } - - // parse the options from the metadata format to the ppImageOptions structure - ppImageOptions *options = ppImageOptionsParse (config); - - // the following are defined from the argument list, if given, - // otherwise they revert to the config information or detrend database if specified - // not all input or output images are used in a given recipe - if (options->doBias) { - if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.BIAS", "BIAS", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_BIAS)) { - psError (PS_ERR_IO, false, "Can't find a bias image source"); - return NULL; - } - } - if (options->doDark) { - if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.DARK", "DARK", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_DARK)) { - psError (PS_ERR_IO, false, "Can't find a dark image source"); - return NULL; - } - } - if (options->doMask) { - if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.MASK", "MASK", PM_FPA_FILE_MASK, PM_DETREND_TYPE_MASK)) { - psError (PS_ERR_IO, false, "Can't find a mask image source"); - return NULL; - } - } - if (options->doFlat) { - if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.FLAT", "FLAT", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_FLAT)) { - psError (PS_ERR_IO, false, "Can't find a shutter image source"); - return NULL; - } - } - - // the following files are output targets - pmFPAfile *output = pmFPAfileDefineOutput (config, input->fpa, "PPIMAGE.OUTPUT"); - pmFPAfile *byChip = pmFPAfileDefineNewCamera (config, "PPIMAGE.OUTPUT.CHIP"); - pmFPAfile *byFPA1 = pmFPAfileDefineNewCamera (config, "PPIMAGE.OUTPUT.FPA1"); - pmFPAfile *byFPA2 = pmFPAfileDefineNewCamera (config, "PPIMAGE.OUTPUT.FPA2"); - - // save any of these files? - output->save = options->BaseFITS; - byChip->save = options->ChipFITS; - byFPA1->save = options->FPA1FITS; - byFPA2->save = options->FPA2FITS; - - // output is used as a carrier: input to byChip - output->freeLevel = PM_FPA_LEVEL_CHIP; - - // define the binned target files (which may just be carriers for some camera configurations) - pmFPAfile *bin1 = pmFPAfileDefineFromFPA (config, byChip->fpa, options->xBin1, options->yBin1, "PPIMAGE.BIN1"); - pmFPAfile *bin2 = pmFPAfileDefineFromFPA (config, byChip->fpa, options->xBin2, options->yBin2, "PPIMAGE.BIN2"); - - // bin1 and bin2 are used as carriers: input for byFPA1, byFPA2 - bin1->freeLevel = PM_FPA_LEVEL_FPA; - bin2->freeLevel = PM_FPA_LEVEL_FPA; - - pmFPAfile *jpg1 = pmFPAfileDefineOutput (config, byFPA1->fpa, "PPIMAGE.JPEG1"); - pmFPAfile *jpg2 = pmFPAfileDefineOutput (config, byFPA2->fpa, "PPIMAGE.JPEG2"); - - // XXX we could potentially not define these pmFPAfiles if no output is requested... - bin1->save = options->Bin1FITS; - bin2->save = options->Bin2FITS; - jpg1->save = options->Bin1JPEG; - jpg2->save = options->Bin2JPEG; - - // Chip selection: turn on only the chips specified (pass status to suppress missing-key log msg) - char *chipLine = psMetadataLookupStr(&status, config->arguments, "CHIP_SELECTIONS"); - psArray *chips = psStringSplitArray (chipLine, ",", false); - if (chips->n > 0) { - pmFPASelectChip (input->fpa, -1, true); // deselect all chips - for (int i = 0; i < chips->n; i++) { - int chipNum = atoi(chips->data[i]); - if (! pmFPASelectChip(input->fpa, chipNum, false)) { - psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum); - return false; - } - } - } - psFree (chips); - - return (options); -} - -// remove from config all pmFPAfiles which could have been added (ignore missing entries) -void ppFocusDropCamera (pmConfig *config) { - - psMetadataRemoveKey (config->files, "PPIMAGE.INPUT"); - - psMetadataRemoveKey (config->files, "PPIMAGE.BIAS"); - psMetadataRemoveKey (config->files, "PPIMAGE.DARK"); - psMetadataRemoveKey (config->files, "PPIMAGE.MASK"); - psMetadataRemoveKey (config->files, "PPIMAGE.FLAT"); - - psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT"); - psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT.CHIP"); - psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT.FPA1"); - psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT.FPA2"); - - psMetadataRemoveKey (config->files, "PPIMAGE.BIN1"); - psMetadataRemoveKey (config->files, "PPIMAGE.BIN2"); - - psMetadataRemoveKey (config->files, "PPIMAGE.JPEG1"); - psMetadataRemoveKey (config->files, "PPIMAGE.JPEG2"); - - psMetadataRemoveKey (config->files, "PSPHOT.INPUT"); - psMetadataRemoveKey (config->files, "PSPHOT.OUTPUT"); - psMetadataRemoveKey (config->files, "PSPHOT.RESID"); - psMetadataRemoveKey (config->files, "PSPHOT.BACKMDL"); - psMetadataRemoveKey (config->files, "PSPHOT.BACKGND"); - psMetadataRemoveKey (config->files, "PSPHOT.BACKSUB"); - psMetadataRemoveKey (config->files, "PSPHOT.PSF.LOAD"); - psMetadataRemoveKey (config->files, "PSPHOT.PSF.SAVE"); - - return; -} - Index: anches/haf_branches/videophot2010/ppImage/src/ppImage.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImage.c (revision 29946) +++ (revision ) @@ -1,48 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -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 = ppImageArguments(argc, argv); - if (config == NULL) { - psErrorStackPrint(stderr, "Unable to parse command-line arguments."); - ppImageCleanup(config, NULL); - exit(PS_EXIT_CONFIG_ERROR); - } - - ppImageVersionPrint(); - - // define recipe options - // define the active I/O files - ppImageOptions *options = ppImageParseCamera(config); - if (options == NULL) { - psErrorStackPrint(stderr, "Unable to parse camera."); - ppImageCleanup(config, options); - exit(PS_EXIT_CONFIG_ERROR); - } - - // Image Arithmetic Loop - if (!ppImageLoop(config, options)) { - psErrorStackPrint(stderr, "Unable to loop over input"); - ppImageCleanup(config, options); - exit(PS_EXIT_SYS_ERROR); - } - - psLogMsg("ppImage", PS_LOG_INFO, "Complete ppImage run: %f sec\n", psTimerMark(TIMER_TOTAL)); - - // Cleaning up - ppImageCleanup(config, options); - - return PS_EXIT_SUCCESS; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImage.h =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImage.h (revision 29946) +++ (revision ) @@ -1,293 +1,0 @@ -#ifndef PP_IMAGE_H -#define PP_IMAGE_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" - -#define RECIPE_NAME "PPIMAGE" // Name of the recipe to use -#define TIMER_TOTAL "PPIMAGE.TOTAL" // Name of timer for total time -#define TIMER_DETREND "PPIMAGE.DETREND" // Name of timer for detrend time -#define TIMER_PHOT "PPIMAGE.PHOT" // Name of timer for photometry time - -// Options for ppImage processing -typedef struct { - // actions which ppImage should perform - 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 doPatternRow; // Row pattern correction - bool doPatternCell; // Cell pattern correction - 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 doMaskStats; // Calculate mask statistics - - 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 correction - int patternRowOrder; // Polynomial order - int patternRowIter; // Clipping iterations - float patternRowRej; // Clipping threshold - float patternRowThresh; // Ignore threshold - psStatsOptions patternRowMean; // Statistic for mean - psStatsOptions patternRowStdev; // Statistic for stdev - psStatsOptions patternCellBG; // statistic for background - psStatsOptions patternCellMean; // Statistic for mean - - int remnanceSize; // Size for remnance detection - float remnanceThresh; // Threshold for remnance detection - - char *normClass; // class to use for per-class normalization - - psU16 maskstat_static; - psU16 maskstat_dynamic; - psU16 maskstat_magic; - psU16 maskstat_advisory; - -} ppImageOptions; - -// Cells to be used in the detrend -typedef struct { - pmCell *input; // The input cell, to be operated upon - pmCell *mask; // The bad pixel mask - pmCell *bias; // The bias correction - pmCell *dark; // The dark correction - pmCell *flat; // The flat-field correction -} ppImageDetrend; - -ppImageOptions *ppImageOptionsAlloc(void); - -// Determine the processing options -ppImageOptions *ppImageOptionsParse(pmConfig *config); - -// Get the configuration -pmConfig *ppImageArguments(int argc, char **argv); - -// Determine what type of camera, and initialise -ppImageOptions *ppImageParseCamera(pmConfig *config); -bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options); - -// apply the cell flips to the input data before analysis -bool ppImageParityFlip (pmConfig *config, const ppImageOptions *options, const pmFPAview *view, bool native); - -// Loop over the input -bool ppImageLoop(pmConfig *config, ppImageOptions *options); - -// free memory, check for leaks -void ppImageCleanup (pmConfig *config, ppImageOptions *options); - -// perform the detrend analysis on the current readout -bool ppImageDetrendReadout (pmConfig *config, ppImageOptions *options, pmFPAview *view); - -bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options); - -//bool ppImageDetrendNonLinear(pmReadout *input, ppImageOptions *options); -bool ppImageDetrendNonLinear(pmReadout *input, pmFPAview *linearity, pmConfig *config); -bool ppImageDetrendNonLinearLookup(pmReadout *input, psMetadataItem *dataItem); -bool ppImageDetrendNonLinearPolynomial(pmReadout *input, psMetadataItem *dataItem); - -bool ppImageDetrendCell(ppImageDetrend *detrend, ppImageOptions *options, pmConfig *config); -bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options); -pmReadout* ppImageDetrendSelectFirst(pmCell *cell, char *name, bool doThis); - -bool ppImageDetrendFree(pmConfig *config, pmFPAview *view); -bool ppImageFringeFree(pmConfig *config, pmFPAview *view); - -bool ppImageCheckCTE(pmConfig *config, ppImageOptions *options, pmFPAview *view); - -bool ppImageBurntoolMask(pmConfig *config, ppImageOptions *options, pmFPAview *view, pmReadout *mask); - -bool ppImageDetrendPatternApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, const ppImageOptions *options); - -// Record which detrend file was used for the detrending -bool ppImageDetrendRecord( - pmCell *cell, // Cell of interest - const pmConfig *config, // Configuration - const ppImageOptions *options, // Processing options - const pmFPAview *view // View to cell - ); - -bool ppImageRebinChip (pmConfig *config, pmFPAview *view, ppImageOptions *options, char *outName); - -bool ppImagePhotom(psMetadata *stats, pmConfig *config, pmFPAview *view); -bool ppImageAstrom(pmConfig *config, psMetadata *stats); -bool ppImageAddstar(pmConfig *config); - -// Subtract background from the chip-mosaicked image -bool ppImageSubtractBackground( - pmConfig *config, // Configuration - const pmFPAview *view, // View to chip of interest - const ppImageOptions *options // Processing options - ); - -bool ppImageMosaicChip (pmConfig *config, const ppImageOptions *options, const pmFPAview *view, - const char *outFile, const char *inFile); -bool ppImageMosaicFPA (pmConfig *config, const ppImageOptions *options, - const char *outFile, const char *inFile); - -bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options); - -void ppImageFileCheck (pmConfig *config); - -// functions used by ppFocus -pmConfig *ppFocusArguments(int argc, char **argv); -ppImageOptions *ppFocusParseCamera (pmConfig *config, int entry); -bool ppFocusGetFWHM (pmConfig *config, psVector *focus, psVector *fwhm); -bool ppFocusFitFWHM (pmConfig *config, psVector *focus, psVector *fwhm); - -void ppFocusDropCamera (pmConfig *config); - -bool ppImageDefineFile (pmConfig *config, pmFPA *input, char *filerule, char *argname, pmFPAfileType fileType, pmDetrendType detrendType); - -// write stats to output file -bool ppImageStatsOutput(pmConfig *config, // Configuration - psMetadata *stats, // Statistics output - const ppImageOptions *options // Options - ); - - -// measure the crosstalk signal -bool ppImageMeasureCrosstalk(pmConfig *config, ppImageOptions *options, pmFPAview *view); - -// correct the crosstalk signal -bool ppImageCorrectCrosstalk(pmConfig *config, ppImageOptions *options, pmFPAview *view); - -// Measure fringes -bool ppImageDetrendFringeMeasure(pmReadout *readout, // Readout to measure - pmCell *fringe, // Fringe cell (each readout is a different component) - const bool isResidual, - const ppImageOptions *options // Options - ); - -// Solve the fringe system -bool ppImageDetrendFringeSolve(pmChip *scienceChip, // Chip with science - const pmChip *refChip, // Chip with reference fringes - const bool isResidual, - const ppImageOptions *options // Options - ); - -// Generate fringe frame -bool ppImageDetrendFringeGenerate(pmCell *science, // Science cell - pmCell *fringes, // Fringe cell, one readout per fringe component - const ppImageOptions *options // Options - ); - - -bool ppImageDetrendFringeApply (pmConfig *config, // config - pmChip *chip, // science chip - const pmFPAview *inputView, // current view - const ppImageOptions *options // options - ); - -/// Return short version information -psString ppImageVersion(void); - -/// Return software source -psString ppImageSource(void); - -/// Return long version information -psString ppImageVersionLong(void); - -/// Populate the header with version information for all dependencies -bool ppImageVersionHeader(psMetadata *metadata ///< Header to populate - ); - -/// Print version information -void ppImageVersionPrint(void); - - -// calculate stats, including MD5 -bool ppImagePixelStats(pmConfig *config,// Configuration - psMetadata *stats, // Statistics output - const ppImageOptions *options, // Options - const pmFPAview *inputView // View to data - ); - -// Calculate Mask statistics -bool ppImageMaskStats(pmConfig *config, pmFPAview *view, psMetadata *stats); - -// calculate stats from headers and concepts -bool ppImageMetadataStats(pmConfig *config, // Configuration - psMetadata *stats, // Statistics output - const ppImageOptions *options // Options - ); - -void ppImageFileCheck(pmConfig *config); - -/// Dump memory summary to text file -void ppImageMemoryDump(const char *description); - -#endif Index: anches/haf_branches/videophot2010/ppImage/src/ppImageAddstar.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageAddstar.c (revision 29946) +++ (revision ) @@ -1,120 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -bool setFilename (pmFPAfile *file, pmFPAview *view); -bool addstarFile (char *addstarCommand, char *filename); - -bool ppImageAddstar (pmConfig *config) { - - bool status; - pmChip *chip; - pmCell *cell; - pmReadout *readout; - - // select recipe options supplied on command line - psMetadata *recipe = psMetadataLookupPtr (&status, config->recipes, RECIPE_NAME); - - // find a pmFPAfile PSASTRO.OUTPUT - pmFPAfile *file = psMetadataLookupPtr (&status, config->files, "PSASTRO.OUTPUT"); - if (!status) { - psError (PS_ERR_IO, true, "no PSASTRO.OUTPUT file defined"); - return false; - } - - // find the addstar command: %s is replaced with name of output file - char *addstarCommand = psMetadataLookupStr (&status, recipe, "ADDSTAR.COMMAND"); - - pmFPAview *view = pmFPAviewAlloc (0); - if (file->fileLevel == PM_FPA_LEVEL_CHIP) { - // call addstar on this file - setFilename (file, view); - addstarFile (addstarCommand, file->filename); - return true; - } - - while ((chip = pmFPAviewNextChip (view, file->fpa, 1)) != NULL) { - psLogMsg ("ppImageAddstar", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); - if (!chip->process || !chip->file_exists) { continue; } - - if (file->fileLevel == PM_FPA_LEVEL_CHIP) { - // call addstar on this file - setFilename (file, view); - addstarFile (addstarCommand, file->filename); - continue; - } - - while ((cell = pmFPAviewNextCell (view, file->fpa, 1)) != NULL) { - psLogMsg ("ppImageAddstar", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); - if (! cell->process || ! cell->file_exists) { continue; } - - if (file->fileLevel == PM_FPA_LEVEL_CELL) { - // call addstar on this file - setFilename (file, view); - addstarFile (addstarCommand, file->filename); - continue; - } - - // process each of the readouts - while ((readout = pmFPAviewNextReadout (view, file->fpa, 1)) != NULL) { - if (! readout->data_exists) { continue; } - - if (file->fileLevel == PM_FPA_LEVEL_READOUT) { - // call addstar on this file - setFilename (file, view); - addstarFile (addstarCommand, file->filename); - continue; - } else { - psError (PS_ERR_IO, true, "inconsistent fileLevel for %s: %d\n", file->name, file->fileLevel); - return false; - } - } - } - } - return true; -} - -bool setFilename (pmFPAfile *file, pmFPAview *view) { - - // determine the file name - // free a name allocated earlier - psFree (file->filename); - file->filename = pmFPAfileNameFromRule (file->filerule, file, view); - if (file->filename == NULL) { - psError(PS_ERR_IO, true, "Filename is NULL"); - return false; - } - - // indirect filenames are not allowed for output - if (!strcasecmp (file->filename, "@FILES")) { - psError(PS_ERR_IO, true, "indirect filenames are not allowed for output : %s\n", file->name); - return false; - } - if (!strcasecmp (file->filename, "@DETDB")) { - psError(PS_ERR_IO, true, "detrend db filenames are not allowed for output : %s\n", file->name); - return false; - } - return true; -} - -bool addstarFile (char *addstarCommand, char *filename) { - - bool status; - char *addstarLine = psStringCopy(addstarCommand); - psStringSubstitute(&addstarCommand, filename, "%s"); - - // catch addstar stderr/stdout and do what? - psIOBuffer *buffer = psIOBufferAlloc (512); - psPipe *pipe = psPipeOpen (addstarLine); - status = psIOBufferReadEmpty (buffer, 100, pipe->fd_stdout); - if (!status) { - psError (PS_ERR_IO, false, "detselect is not responding"); - } - psFree (addstarLine); - psFree (buffer); - psPipeClose (pipe); - psFree (pipe); - return status; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageArguments.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageArguments.c (revision 29946) +++ (revision ) @@ -1,173 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -static void usage (void) { - fprintf(stderr, "USAGE: ppImage [-file INPUT.fits] [-list INPUT.txt] OUTPUT\n\n"); - fprintf(stderr, "Optional arguments:\n"); - fprintf(stderr, "\t-stats STATS.mdc: Output statistics into STATS.mdc\n"); - fprintf(stderr, "\t-isfringe: The input image contains fringe data.\n"); - fprintf(stderr, "\t-isdark: The input image contains dark data.\n"); - fprintf(stderr, "\t-usemask MASKVAL: Use this mask value (override recipe).\n"); - fprintf(stderr, "\t-chip CHIPNUM: Only process this chip number.\n"); - fprintf(stderr, "\t-norm VALUE: Divide through by this value when done.\n"); - fprintf(stderr, "\t-normlist file.mdc: normalizations by class_id.\n"); - fprintf(stderr, "\t-video: process video cells\n"); - fprintf(stderr, "\n"); - fprintf(stderr, "Input options (single file / file list):\n"); - fprintf(stderr, "\t-noisemap/-noisemaplist: Noise Map image.\n"); - fprintf(stderr, "\t-bias/-biaslist: Bias image.\n"); - fprintf(stderr, "\t-dark/-darklist: Dark image.\n"); - fprintf(stderr, "\t-shutter/-shutterlist: Shutter image.\n"); - fprintf(stderr, "\t-flat/-flatlist: Flat image.\n"); - fprintf(stderr, "\t-mask/-masklist: Mask image.\n"); - fprintf(stderr, "\t-fringe/-fringelist: Fringe image and data.\n"); - fprintf(stderr, "\t-linearity/-linearlist: linearity correction file.\n"); - fprintf(stderr, "\n"); - exit (2); -} - -pmConfig *ppImageArguments(int argc, char **argv) -{ - int argnum; // Argument number of interest - - if (argc == 1) { - usage(); - } - - if (psArgumentGet (argc, argv, "-version")) { - psString version; - version = ppImageVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); - version = ppStatsVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); - version = psphotVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); - version = psastroVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); - version = psModulesVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); - version = psLibVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); - exit (0); - } - - // load the site-wide configuration information - pmConfig *config = pmConfigRead(&argc, argv, RECIPE_NAME); - if (config == NULL) { - psErrorStackPrint(stderr, "Can't find site configuration!\n"); - exit(EXIT_FAILURE); - } - - // save the following additional recipe values based on command-line options - // these options override the PPIMAGE recipe values loaded from recipe files - psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); - - // save these recipe options until we have loaded the options - // psMetadata *options = psMetadataAlloc (); - // psMetadataAddPtr (config->arguments, PS_LIST_TAIL, "PPIMAGE.OPTIONS", PS_DATA_METADATA, "", options); - - if ((argnum = psArgumentGet(argc, argv, "-stats"))) { - psArgumentRemove(argnum, &argc, argv); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "STATS", PS_META_REPLACE, - "Filename for summary statistics", argv[argnum]); - psArgumentRemove(argnum, &argc, argv); - } - - if ((argnum = psArgumentGet(argc, argv, "-isfringe"))) { - psArgumentRemove(argnum, &argc, argv); - psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUT_IS_FRINGE", PS_META_REPLACE, - "Input is fringe image", true); - } - if ((argnum = psArgumentGet(argc, argv, "-isdark"))) { - psArgumentRemove(argnum, &argc, argv); - psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUT_IS_DARK", PS_META_REPLACE, - "Input is dark image", true); - } - - if ((argnum = psArgumentGet(argc, argv, "-video"))) { - psArgumentRemove(argnum, &argc, argv); - psMetadataAddBool(config->arguments, PS_LIST_TAIL, "PROCESS_VIDEO", PS_META_REPLACE, "process video cells", true); - } - - if ((argnum = psArgumentGet(argc, argv, "-visual"))) { - psArgumentRemove(argnum, &argc, argv); - pmVisualSetVisual(true); - } - - // Number of threads - if ((argnum = psArgumentGet(argc, argv, "-threads"))) { - psArgumentRemove(argnum, &argc, argv); - int nThreads = atoi(argv[argnum]); - psMetadataAddS32(config->arguments, PS_LIST_TAIL, "NTHREADS", 0, "number of warp threads", nThreads); - psArgumentRemove(argnum, &argc, argv); - - // create the thread pool with number of desired threads, supplying our thread launcher function - // XXX need to determine the number of threads from the config data - psThreadPoolInit (nThreads); - } - - // the following options override the PPIMAGE recipe options - - // recipe option: -usemask : override MASK setting in recipe - if ((argnum = psArgumentGet(argc, argv, "-usemask"))) { - psArgumentRemove(argnum, &argc, argv); - psMetadataAddBool(options, PS_LIST_TAIL, "MASK", PS_META_REPLACE, "", true); - psArgumentRemove(argnum, &argc, argv); - } - - // XXX add other PPIMAGE recipe options here - - // the input file is a required argument; if not found, we will exit - pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list"); - - // if these command-line options are supplied, load the file name lists into config->arguments - // override any configuration-specified source for these files - pmConfigFileSetsMD (config->arguments, &argc, argv, "NOISEMAP", "-noisemap", "-noisemaplist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "BIAS", "-bias", "-biaslist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "DARK", "-dark", "-darklist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "SHUTTER", "-shutter", "-shutterlist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "FLAT", "-flat", "-flatlist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "MASK", "-mask", "-masklist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "FRINGE", "-fringe", "-fringelist"); - pmConfigFileSetsMD (config->arguments, &argc, argv, "LINEARITY", "-linearity", "-linearlist"); - - // chip selection is used to limit chips to be processed - if ((argnum = psArgumentGet (argc, argv, "-chip"))) { - psArgumentRemove (argnum, &argc, argv); - psMetadataAddStr (config->arguments, PS_LIST_TAIL, "CHIP_SELECTIONS", PS_DATA_STRING, "", argv[argnum]); - psArgumentRemove (argnum, &argc, argv); - } - - // Optional normalization factor - if ((argnum = psArgumentGet(argc, argv, "-norm"))) { - psArgumentRemove(argnum, &argc, argv); - float norm = atof(argv[argnum]); - psMetadataAddF32(config->arguments, PS_LIST_TAIL, "NORMALIZATION", 0, - "Normalisation to apply", norm); - psArgumentRemove(argnum, &argc, argv); - } - - // Optional per-class normalization table - if ((argnum = psArgumentGet(argc, argv, "-normlist"))) { - psArgumentRemove(argnum, &argc, argv); - - unsigned int nFail = 0; - psMetadata *normlist = psMetadataConfigRead (NULL, &nFail, argv[argnum], false); - // XXX allow this file to be in nebulous? - - psMetadataAddMetadata(config->arguments, PS_LIST_TAIL, "NORMALIZATION.TABLE", 0, "Normalization to apply", normlist); - psFree (normlist); - psArgumentRemove(argnum, &argc, argv); - } - - if ((argnum = psArgumentGet(argc, argv, "-dumpconfig"))) { - psArgumentRemove(argnum, &argc, argv); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "DUMP_CONFIG", PS_META_REPLACE, - "Filename for configuration dump", argv[argnum]); - psArgumentRemove(argnum, &argc, argv); - } - - 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: anches/haf_branches/videophot2010/ppImage/src/ppImageAstrom.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageAstrom.c (revision 29946) +++ (revision ) @@ -1,66 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -// this function is mostly equivalent to the top-level of psastro, with some -// modifications since the data has already been loaded. -bool ppImageAstrom (pmConfig *config, psMetadata *stats) { - - bool status; - - // select recipe options supplied on command line - // XXX move these options to the "PSASTRO" recipe? - psMetadata *recipe = psMetadataLookupPtr (&status, config->recipes, PSASTRO_RECIPE); - - // find or define a pmFPAfile PSPHOT.INPUT - pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSASTRO.INPUT"); - PS_ASSERT (input, false); - - ppImageMemoryDump("astrom"); - - // convert the output sources created by psphot into astrometry objects - if (!psastroConvertFPA (input->fpa, recipe)) { - psError (PSASTRO_ERR_UNKNOWN, false, "error reading input data\n"); - return false; - } - - if (!psastroAnalysis(config, stats)) { - psError (PSASTRO_ERR_UNKNOWN, false, "failure in psastro analysis\n"); - return false; - } - - // deactivate the psastro files, reactive when needed - pmFPAfileActivate (config->files, false, NULL); - pmFPAfileActivate (config->files, true, "PSASTRO.OUTPUT"); - - // loop over all chips and perform IO needed - pmChip *chip = NULL; - pmFPAview *view = pmFPAviewAlloc(0);// View for level of interest - while ((chip = pmFPAviewNextChip(view, input->fpa, 1)) != NULL) { - psLogMsg ("ppImageLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); - - ppImageMemoryDump("astrom"); - - // Output and Close at Chip level - if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { - psFree(view); - return false; - } - } - - // Output and Close FPA - if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { - psFree(view); - return false; - } - - // deactivate the PSASTRO files, re-active all else - // XXX do we need a way to activate / deactivate other groups? - pmFPAfileActivate (config->files, true, NULL); - pmFPAfileActivate (config->files, false, "PSASTRO.OUTPUT"); - - psFree(view); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageBurntoolMask.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageBurntoolMask.c (revision 29946) +++ (revision ) @@ -1,96 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#define PPIMAGE_BURNTOOL_DEBUG 0 - -#include "ppImage.h" - -bool ppImageBurntoolMask (pmConfig *config, ppImageOptions *options, pmFPAview *view,pmReadout *mask) { - bool status = true; - int burntool_cell; - /* Find input filename */ - pmFPAfile *inputFile = psMetadataLookupPtr(&status , config->files, "PPIMAGE.INPUT"); - if (!status) { - psError(PS_ERR_IO,false, "Unable to identify inputFile"); - return(false); - } - psFits *fits = inputFile->fits; - - /* Read input header, and find the burntool data table. */ - if (!psFitsMoveExtName(fits,"burntool_areas")) { - psError(PS_ERR_IO,false, "Unable to find extension burntool_areas"); - return(false); - } - long Nrows = psFitsTableSize(fits); - - long row = 0; - - psLogMsg ("ppImageBurntoolMask", 4, "Inside burntool mask %ld", Nrows); - - /* Redirects and Memory juggling. */ - view->readout = 0; - psImage *image = mask->mask; - - - /* Set the maskValue from the recipes. */ - psImageMaskType maskValue = options->burntoolMask; -#if PPIMAGE_BURNTOOL_DEBUG - psLogMsg("ppImageBurntoolMask", 4, "Status: %ld %d\n",Nrows,maskValue); -#endif - - burntool_cell = view->cell; - burntool_cell = (view->cell % 8) * 8 + (view->cell - (view->cell % 8)) / 8; - psLogMsg("ppImageBurntoolMask", 4, "Cell mapping: %d %d %d\n",view->cell,burntool_cell,-1); - for (row = 0; row < Nrows; row++) { - psMetadata *rowMD = psFitsReadTableRow(fits,row); - - if (psMetadataLookupS32(&status,rowMD,"cell") == burntool_cell) { - if (((options->burntoolTrails & 0x01)&&(psMetadataLookupS32(&status,rowMD,"func") == 4))|| - (((options->burntoolTrails & 0x02)&&(psMetadataLookupS32(&status,rowMD,"up") == 1))|| - ((options->burntoolTrails & 0x04)&&(psMetadataLookupS32(&status,rowMD,"up") == 0)))) { - /* If the fit fails, burntool reports zero here. This - signifies that it expected to see a trail (else why - fit) but did not find it when it attempted to - correct. */ -#if PPIMAGE_BURNTOOL_DEBUG - psLogMsg ("ppImageBurntoolMask", 4, "Masking! %d (%d %d %d) %d %d", - psMetadataLookupS32(&status,rowMD,"cell"), - ((options->burntoolTrails & 0x0001)&&(psMetadataLookupS32(&status,rowMD,"nfit") == 0)), - ((options->burntoolTrails & 0x02)&&(psMetadataLookupS32(&status,rowMD,"up") == 1)), - ((options->burntoolTrails & 0x04)&&(psMetadataLookupS32(&status,rowMD,"up") == 0)), - options->burntoolTrails, - maskValue - ); -#endif - for (int i = psMetadataLookupS32(&status,rowMD,"sxfit"); - i <= psMetadataLookupS32(&status,rowMD,"exfit"); - i++) { - - if (psMetadataLookupS32(&status,rowMD,"up") == 0) { - for (int j = 0; j <= psMetadataLookupS32(&status,rowMD,"y1p"); j++) { -#if PPIMAGE_BURNTOOL_DEBUG - psLogMsg("ppImageBurntoolMask", 4, "Noisy!: %d %d %d %d\n", - i,j,image->data.PS_TYPE_IMAGE_MASK_DATA[j][i],maskValue); -#endif - image->data.PS_TYPE_IMAGE_MASK_DATA[j][i] |= maskValue; - } - } - else { - for (int j = psMetadataLookupS32(&status,rowMD,"y1m"); j < image->numRows ; j++) { -#if PPIMAGE_BURNTOOL_DEBUG - psLogMsg("ppImageBurntoolMask", 4, "Noisy!: %d %d %d %d\n", - i,j,image->data.PS_TYPE_IMAGE_MASK_DATA[j][i],maskValue); -#endif - image->data.PS_TYPE_IMAGE_MASK_DATA[j][i] |= maskValue; - } - } - } - - } - } - psFree(rowMD); - } - - return(status); -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageCheckCTE.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageCheckCTE.c (revision 29946) +++ (revision ) @@ -1,109 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -// XXX I originally coded this to create a new pmFPAfile, but in retrospect it makes more sense -// to treat this function as an operation on the input image - -// XXX make the choice of stats optional -bool ppImageCheckCTE(pmConfig *config, ppImageOptions *options, pmFPAview *view) -{ - bool status; - - // this step is complete optional. - if (!options->checkCTE) { - return true; - } - - // add recipe options supplied on command line - psMetadata *recipe = psMetadataLookupPtr(&status, config->recipes, RECIPE_NAME); - - // find the currently selected readout - pmReadout *inReadout = pmFPAfileThisReadout(config->files, view, "PPIMAGE.INPUT"); - - psImage *image = inReadout->image; - psImage *mask = inReadout->mask; - // psImage *variance = inReadout->variance; - - // I have the fine image size, I know the binning factor, determine the ruff image size - psImageBinning *binning = psImageBinningAlloc(); - binning->nXfine = image->numCols; - binning->nYfine = image->numRows; - binning->nXbin = psMetadataLookupS32 (&status, recipe, "CTE.XBIN"); - binning->nYbin = psMetadataLookupS32 (&status, recipe, "CTE.YBIN"); - - psImageBinningSetRuffSize(binning, PS_IMAGE_BINNING_CENTER); - psImageBinningSetSkip(binning, image); - - psStats *stats = psStatsAlloc (PS_STAT_ROBUST_MEDIAN); - psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS); - psImageBackground (stats, NULL, image, mask, 0xffff, rng); - float cellMedian = stats->robustMedian; - psFree (stats); - - // stats = psStatsAlloc (PS_STAT_SAMPLE_STDEV); - // psStats *statsDefaults = psStatsAlloc (PS_STAT_SAMPLE_STDEV); - - stats = psStatsAlloc (PS_STAT_ROBUST_STDEV); - psStats *statsDefaults = psStatsAlloc (PS_STAT_ROBUST_STDEV); - - // measure median and variance for subimages - psRegion ruffRegion = {0,0,0,0}; - psRegion fineRegion = {0,0,0,0}; - for (int iy = 0; iy < binning->nYruff; iy++) { - for (int ix = 0; ix < binning->nXruff; ix++) { - - // convert the ruff grid cell to the equivalent fine grid cell - ruffRegion = psRegionSet (ix, ix + 1, iy, iy + 1); - fineRegion = psImageBinningSetFineRegion (binning, ruffRegion); - fineRegion = psRegionForImage (image, fineRegion); - if (fineRegion.x0 >= image->numCols) continue; - if (fineRegion.y0 >= image->numRows) continue; - - psImage *subset = psImageSubset (image, fineRegion); - if (!subset->numCols || !subset->numRows) { - psFree (subset); - continue; - } - psImage *submask = NULL; - if (mask) { - submask = psImageSubset (mask, fineRegion); - } - - // reset the default values - statsDefaults->tmpData = stats->tmpData; // XXX this is fairly hackish: tmpData is internal storage for stats; the assign drops the reference... - *stats = *statsDefaults; - statsDefaults->tmpData = NULL; - - psImageStats (stats, subset, submask, 0xffff); - - // XXX need to apply the gain as well - float normVariance = PS_SQR(stats->robustStdev) / cellMedian; - // float normVariance = PS_SQR(stats->sampleStdev) / cellMedian; - // if (!isfinite(normVariance)) fprintf (stderr, "** normVariance is nan **\n"); - - // apply resulting value to the input pixels - for (int jy = fineRegion.y0; jy < fineRegion.y1; jy++) { - if (jy < 0) continue; - if (jy >= image->numRows) continue; - for (int jx = fineRegion.x0; jx < fineRegion.x1; jx++) { - if (jx < 0) continue; - if (jx >= image->numCols) continue; - image->data.F32[jy][jx] = normVariance; - } - } - - psFree (subset); - psFree (submask); - } - } - - psFree (rng); - psFree (binning); - psFree (stats); - psFree (statsDefaults); - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageCheckCTE.v1.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageCheckCTE.v1.c (revision 29946) +++ (revision ) @@ -1,101 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageCheckCTE(pmConfig *config, ppImageOptions *options, pmFPAview *view) -{ - bool status; - - // this step is complete optional. - if (!options->checkCTE) { - return true; - } - - // add recipe options supplied on command line - psMetadata *recipe = psMetadataLookupPtr(&status, config->recipes, RECIPE_NAME); - - // find the currently selected readout - pmReadout *inReadout = pmFPAfileThisReadout(config->files, view, "PPIMAGE.INPUT"); - - psImage *image = inReadout->image; - psImage *mask = inReadout->mask; - // psImage *variance = inReadout->variance; - - // I have the fine image size, I know the binning factor, determine the ruff image size - psImageBinning *binning = psImageBinningAlloc(); - binning->nXfine = image->numCols; - binning->nYfine = image->numRows; - binning->nXbin = psMetadataLookupS32 (&status, recipe, "CTE.XBIN"); - binning->nYbin = psMetadataLookupS32 (&status, recipe, "CTE.YBIN"); - - psImageBinningSetRuffSize(binning, PS_IMAGE_BINNING_CENTER); - psImageBinningSetSkip(binning, image); - - pmCell *inCell = pmFPAfileThisCell (config->files, view, "PPIMAGE.INPUT"); - pmCell *outCell = pmFPAfileThisCell (config->files, view, "PPIMAGE.CTEMAP"); - if (!pmCellCopyStructure(outCell, inCell, binning->nXbin, binning->nYbin)) { - psError(PS_ERR_UNKNOWN, false, "Unable to copy cell structure."); - return false; - } - - pmReadout *outRO = pmFPAfileThisReadout(config->files, view, "PPIMAGE.CTEMAP"); - psImage *output = outRO->image; - - // Don't care about the bias: get rid of it, if present - psFree(outRO->bias); - outRO->bias = psListAlloc(NULL); - psMetadataItem *biassec = psMetadataLookup(outCell->concepts, "CELL.BIASSEC"); - psFree(biassec->data.V); - biassec->data.V = psListAlloc(NULL); - - psStats *stats = psStatsAlloc (PS_STAT_SAMPLE_MEDIAN | PS_STAT_SAMPLE_STDEV); - psStats *statsDefaults = psStatsAlloc (PS_STAT_SAMPLE_MEDIAN | PS_STAT_SAMPLE_STDEV); - - // measure median and variance for subimages - psRegion ruffRegion = {0,0,0,0}; - psRegion fineRegion = {0,0,0,0}; - for (int iy = 0; iy < output->numRows; iy++) { - for (int ix = 0; ix < output->numCols; ix++) { - - // convert the ruff grid cell to the equivalent fine grid cell - ruffRegion = psRegionSet (ix, ix + 1, iy, iy + 1); - fineRegion = psImageBinningSetFineRegion (binning, ruffRegion); - fineRegion = psRegionForImage (image, fineRegion); - if (fineRegion.x0 >= image->numCols || fineRegion.x1 >= image->numCols || - fineRegion.y0 >= image->numRows || fineRegion.y1 >= image->numRows) { - continue; - } - - psImage *subset = psImageSubset (image, fineRegion); - if (!subset->numCols || !subset->numRows) { - psFree (subset); - continue; - } - psImage *submask = NULL; - if (mask) { - submask = psImageSubset (mask, fineRegion); - } - - // reset the default values - statsDefaults->tmpData = stats->tmpData; // XXX this is fairly hackish: tmpData is internal storage for stats; the assign drops the reference... - *stats = *statsDefaults; - statsDefaults->tmpData = NULL; - - psImageStats (stats, subset, submask, 0); - - // XXX need to apply the gain as well - output->data.F32[iy][ix] = PS_SQR(stats->sampleStdev) / stats->sampleMedian; - - psFree (subset); - psFree (submask); - } - } - - psFree (binning); - psFree (stats); - psFree (statsDefaults); - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageCleanup.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageCleanup.c (revision 29946) +++ (revision ) @@ -1,35 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -void ppImageCleanup (pmConfig *config, ppImageOptions *options) -{ - if (psErrorCodeLast() != PS_ERR_NONE) { - pmFPAfileFreeSetStrict(false); - } - - // Free memory used by ppImage - psFree(options); - psFree(config); - - // Free memory used by psModules - pmSourceFitSetDone (); - pmConceptsDone(); - pmConfigDone(); - pmModelClassCleanup(); - pmVisualCleanup (); - - // Free memory used by psLib - psLibFinalize(); - - // psMemBlock **memblocks; - // int Nleaks = psMemCheckLeaks (0, &memblocks, stderr, false); - // fprintf (stderr, "Found %d leaks at %s\n", Nleaks, "ppImage"); - - // fprintf(stderr, "Found %d leaks at %s\n", psMemCheckLeaks (0, NULL, NULL, false), "ppImage"); - psLogMsg("ppImage", PS_LOG_INFO, "Memory leaks: %d\n", psMemCheckLeaks(0, NULL, stdout, false)); - - return; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageCorrectCrosstalk.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageCorrectCrosstalk.c (revision 29946) +++ (revision ) @@ -1,18 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -#define ESCAPE(MESSAGE) { \ - psError(PS_ERR_UNKNOWN, false, MESSAGE); \ - psFree(view); \ - return false; \ -} - -// For the moment, this implementation is VERY GPC-specific - -bool ppImageCorrectCrosstalk(pmConfig *config, ppImageOptions *options, pmFPAview *view) -{ - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageDefineFile.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageDefineFile.c (revision 29946) +++ (revision ) @@ -1,56 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -bool ppImageDefineFile(pmConfig *config, pmFPA *input, char *filerule, char *argname, - pmFPAfileType fileType, pmDetrendType detrendType) -{ - bool status; - pmFPAfile *file = NULL; // File to be defined - - if (!file) { - // look for the file on the argument list - file = pmFPAfileDefineFromArgs(&status, config, filerule, argname); - if (!status) { - psError(PS_ERR_UNKNOWN, false, "failed to load file definition ARG LIST"); - return false; - } - } - if (!file) { - // look for the file on the RUN metadata - file = pmFPAfileDefineFromRun(&status, NULL, config, filerule); - if (!status) { - psError(PS_ERR_UNKNOWN, false, "failed to load file definition RUN"); - return false; - } - } - if (!file) { - // look for the file in the camera config table - file = pmFPAfileDefineFromConf(&status, config, filerule); - if (!status) { - psError(PS_ERR_UNKNOWN, false, "failed to load file definition CONFIG"); - return false; - } - } - if (!file) { - // look for the file to be loaded from the detrend database - file = pmFPAfileDefineFromDetDB(&status, config, filerule, input, detrendType); - if (!status) { - psError(PS_ERR_UNKNOWN, false, "failed to load file definition DETREND"); - return false; - } - } - - if (!file) { - return false; - } - - if (file->type != fileType) { - psError(PS_ERR_IO, true, "%s is not of type %s", filerule, pmFPAfileStringFromType(fileType)); - return false; - } - return true; -} - Index: anches/haf_branches/videophot2010/ppImage/src/ppImageDetrendFree.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageDetrendFree.c (revision 29946) +++ (revision ) @@ -1,72 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -// list of the detrend types to free -static char *detrendTypes[] = { - "PPIMAGE.MASK", - "PPIMAGE.NOISEMAP", - "PPIMAGE.BIAS", - "PPIMAGE.DARK", - "PPIMAGE.FLAT", - "PPIMAGE.SHUTTER", - "PPIMAGE.LINEARITY", - NULL -}; - -bool ppImageDetrendFree (pmConfig *config, pmFPAview *view) { - - bool status; - - for (int i = 0; detrendTypes[i] != NULL; i++) { - - pmFPAfile *file = psMetadataLookupPtr(&status, config->files, detrendTypes[i]); // File of interest - psTrace("pmFPAfileFree",1,"Working on %s\n",detrendTypes[i]); - if (!file) continue; // not all detrends are used in any given run - - // this only returns false on a failure. if we are not ready to write or close, it is not an error - if (!pmFPAfileWrite (file, view, config)) { - psError(PS_ERR_IO, false, "failed to WRITE %s", file->name); - return false; - } - if (!pmFPAfileClose(file, view)) { - psError(PS_ERR_IO, false, "failed to CLOSE for %s", file->name); - return false; - } - if (!pmFPAfileFreeData(file, view)) { - if (!psMetadataRemoveKey(config->files, file->name)) { - psError(PS_ERR_IO, false, "failed to remove %s in FPA_AFTER block", file->name); - return false; - } - } - } - return true; -} - -bool ppImageFringeFree (pmConfig *config, pmFPAview *view) { - - bool status; - - pmFPAfile *file = psMetadataLookupPtr(&status, config->files, "PPIMAGE.FRINGE"); // File of interest - if (!file) return true; - - // this only returns false on a failure. if we are not ready to write or close, it is not an error - if (!pmFPAfileWrite (file, view, config)) { - psError(PS_ERR_IO, false, "failed to WRITE %s", file->name); - return false; - } - if (!pmFPAfileClose(file, view)) { - psError(PS_ERR_IO, false, "failed to CLOSE for %s", file->name); - return false; - } - if (!pmFPAfileFreeData(file, view)) { - if (!psMetadataRemoveKey(config->files, file->name)) { - psError(PS_ERR_IO, false, "failed to remove %s in FPA_AFTER block", file->name); - return false; - } - } - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageDetrendFringe.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageDetrendFringe.c (revision 29946) +++ (revision ) @@ -1,390 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageDetrendFringeMeasure(pmReadout *readout, pmCell *fringe, const bool isResidual, const ppImageOptions *options) -{ - PS_ASSERT_PTR_NON_NULL(readout, false); - PS_ASSERT_PTR_NON_NULL(fringe, false); - PS_ASSERT_PTR_NON_NULL(options, false); - - // Reference fringe measurements (stored on the reference cell->analysis) - psArray *references = psMemIncrRefCounter(psMetadataLookupPtr(NULL, fringe->analysis, "FRINGE.MEASUREMENTS")); - if (!references) { - psError(PS_ERR_IO, false, "Unable to find fringe references.\n"); - return false; - } - - pmFringeStats *reference = references->data[0]; // Take the first as representative - pmFringeRegions *regions = reference->regions; // Regions to measure - pmFringeStats *measurements = pmFringeStatsMeasure(regions, readout, options->maskValue); // Fringe stats - - // Normalise measurements by the exposure time - bool mdok; // Status of MD lookup - float expTime = psMetadataLookupF32(&mdok, readout->parent->concepts, "CELL.EXPOSURE"); // Exp. time - if (!mdok || !isfinite(expTime)) { - psError(PS_ERR_UNKNOWN, false, "CELL.EXPOSURE is not set for --- can't normalise fringes\n"); - psFree(measurements); - return false; - } - if (expTime == 0) { - psWarning("Exposure time is zero --- are you sure you want fringe subtraction?\n"); - expTime = 1.0; - } - // normalize by exposure time : NOTE df is 1/sigma - psBinaryOp(measurements->f, measurements->f, "*", psScalarAlloc(1.0 / expTime, PS_TYPE_F32)); - psBinaryOp(measurements->df, measurements->df, "*", psScalarAlloc(expTime, PS_TYPE_F32)); - - char *scienceFringes = NULL; - if (isResidual) { - scienceFringes = psStringCopy ("FRINGE.RESIDUALS"); - } else { - scienceFringes = psStringCopy ("FRINGE.MEASUREMENTS"); - } - - // Science fringe measurements - pmFringeStats *previous = psMetadataLookupPtr(NULL, readout->parent->analysis, scienceFringes); - if (previous) { - // Multiple readouts: concatenate - psArray *concatenate = psArrayAlloc(2); // Array to hold fringes - - // Concatenate science measurements - concatenate->data[0] = previous; - concatenate->data[1] = measurements; - pmFringeStats *new = pmFringeStatsConcatenate(concatenate, NULL, NULL); // New measurements - psFree(measurements); - measurements = new; - - // Concatenate reference measurements (duplication, so the science and reference line up) - for (int i = 0; i < references->n; i++) { - concatenate->data[0] = concatenate->data[1] = references->data[i]; - pmFringeStats *refNew = pmFringeStatsConcatenate(concatenate, NULL, NULL); - psFree(references->data[i]); - references->data[i] = refNew; - } - concatenate->data[0] = concatenate->data[1] = NULL; - psFree(concatenate); - } - - psMetadataAdd(readout->parent->analysis, PS_LIST_TAIL, scienceFringes, PS_DATA_UNKNOWN | PS_META_REPLACE, "Fringe measurements", measurements); - psFree(measurements); - psFree(scienceFringes); - psFree(references); - - return true; -} - - -// Pull the fringes out of the cell analysis FRINGE.MEASUREMENTS for a chip -// XXX need some error checks -static psArray *getFringes(const pmChip *chip, const char *source) -{ - psArray *cells = chip->cells; // Component cells - psArray *fringes = psArrayAlloc(cells->n); // Fringes, to return - int video_cell_zero = 0; - - for (int i = 0; i < cells->n; i++) { - fringes->data[i] = NULL; - - pmCell *cell = cells->data[i]; // Cell of interest - - psTrace("psModules.detrend",7,"Readouts: Cell %d chip: %ld\n",i,cell->readouts->n); - // XXX for now, skip the video cells (cell->readouts->n > 1) - // CZW: This mess creates a fake set of fringe stats by stealing the previous one. - // We let the fitting code know that this is all lies by scaling the weights by a crazy amount. - - if ( (cell->readouts->n > 1) ) { - psTrace("psModules.detrend",7,"Should be skipping scichip: %d\n",i); - psWarning ("Skipping Video Cell (%d) for ppImageDetrendFringe.c:getFringes", i); - - if (i == 0) { - video_cell_zero = 1; - } - else { - pmFringeStats *prevFringe = fringes->data[i-1]; - pmFringeStats *fringe = pmFringeStatsAlloc(prevFringe->regions); - for (int j = 0; j < fringe->regions->nRequested; j++) { - fringe->f->data.F32[j] = prevFringe->f->data.F32[j]; - fringe->df->data.F32[j] = prevFringe->df->data.F32[j] / 1e6; - } - fringes->data[i] = fringe; - } - - continue; - } - - fringes->data[i] = psMemIncrRefCounter(psMetadataLookupPtr(NULL, cell->analysis, source)); - } - - if (video_cell_zero == 1) { - pmFringeStats *prevFringe = fringes->data[1]; - pmFringeStats *fringe = pmFringeStatsAlloc(prevFringe->regions); - for (int j = 0; j < fringe->regions->nRequested; j++) { - fringe->f->data.F32[j] = NAN; - fringe->df->data.F32[j] = 1.0; - } - fringes->data[0] = fringe; - } - - return fringes; -} - - -// Solve the fringe system: we have science fringe measurements for each cell, and an array of reference -// fringe measurements for each cell. Need to concatenate these together first, and then solve. -bool ppImageDetrendFringeSolve(pmChip *scienceChip, const pmChip *refChip, const bool isResidual, const ppImageOptions *options) -{ - PS_ASSERT_PTR_NON_NULL(scienceChip, NULL); - PS_ASSERT_PTR_NON_NULL(refChip, NULL); - PS_ASSERT_PTR_NON_NULL(options, NULL); - - psArray *science = NULL; - if (isResidual) { - science = getFringes(scienceChip, "FRINGE.RESIDUALS"); // Fringe residuals on science chip - } else { - science = getFringes(scienceChip, "FRINGE.MEASUREMENTS"); // Fringe measurements on science chip - } - - pmFringeStats *scienceCat = pmFringeStatsConcatenate(science, NULL, NULL); // Science fringes - psFree(science); - - // Need to transform the array of cells each with an array of fringes --> array of fringes for the chip as - // a whole - psArray *references = getFringes(refChip, "FRINGE.MEASUREMENTS"); // Fringe measurements on reference chip - int numRefs = ((psArray*)references->data[0])->n; // Number of reference fringes - psArray *referencesCat = psArrayAlloc(numRefs); // Reference fringes - for (int i = 0; i < numRefs; i++) { // Iterate over fringes - psArray *refs = psArrayAlloc(references->n); // Array of fringes for each cell - for (int j = 0; j < references->n; j++) { // Iterate over cells - psArray *ref = references->data[j]; // Array of references for this cell - - refs->data[j] = psMemIncrRefCounter(ref->data[i]); - } - referencesCat->data[i] = pmFringeStatsConcatenate(refs, NULL, NULL); - psFree(refs); - } - psFree(references); - - // Now we can solve - psTrace("ppImage", 3, "Solving fringe system...\n"); - pmFringeScale *solution = pmFringeScaleMeasure(scienceCat, referencesCat, options->fringeRej, - options->fringeIter, options->fringeKeep); - - if (isResidual) { - psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.RESIDUAL.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); - } else { - psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); - } - -# if (0) - // write the fringe amplitude or residual amplitude to the header - // XXX this is measured per cell, but we only have headers per chip - pmHDU *hdu = pmHDUFromCell(science);// HDU of interest - for (int i = 0; i < solution->nFringeFrames; i++) { - // write metadata header value - psString keyword = NULL; - if (isResidual) { - psStringAppend (&keyword, "FRES_%02dV", i); - } else { - psStringAppend (&keyword, "FRNG_%02dV", i); - } - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); - psFree (keyword); - - keyword = NULL; - if (isResidual) { - psStringAppend (&keyword, "FRES_%02dE", i); - } else { - psStringAppend (&keyword, "FRNG_%02dE", i); - } - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); - psFree (keyword); - } -# endif - - psFree(solution); - psFree(scienceCat); - psFree(referencesCat); - - return true; -} - - -bool ppImageDetrendFringeGenerate(pmCell *science, pmCell *fringes, const ppImageOptions *options) -{ - PS_ASSERT_PTR_NON_NULL(science, false); - PS_ASSERT_PTR_NON_NULL(fringes, false); - - pmFringeScale *solution = psMetadataLookupPtr(NULL, science->parent->analysis, "FRINGE.SOLUTION"); - if (!solution) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find fringe solution.\n"); - return false; - } - assert(fringes->readouts->n == solution->nFringeFrames); - - psImageMaskType maskVal = options->flatMask; - - bool mdok; // Status of MD lookup - float expTime = psMetadataLookupF32(&mdok, science->concepts, "CELL.EXPOSURE"); // Exp. time - if (!mdok || !isfinite(expTime)) { - psError(PS_ERR_UNKNOWN, true, "CELL.EXPOSURE is not set --- can't renormalise fringes\n"); - return false; - } - if (expTime == 0) { - psWarning("Exposure time is zero --- are you sure you want fringe subtraction?\n"); - expTime = 1.0; - } - - pmHDU *hdu = pmHDUFromCell(science);// HDU of interest - - // Construct the fringe image from the scale - psTrace("ppImage", 3, "Generating fringe correction...\n"); - psImage *sumFringe = NULL; // Sum of the fringes - for (int i = 0; i < solution->nFringeFrames; i++) { - pmReadout *fringeRO = fringes->readouts->data[i]; // Fringe readout - psImage *fringe = fringeRO->image; // Fringe image - psTrace("ppImage", 5, "Scale for fringe component %d is %f\n", - i, solution->coeff->data.F32[i + 1]); - psBinaryOp(fringe, fringe, "*", psScalarAlloc(solution->coeff->data.F32[i + 1], PS_TYPE_F32)); - if (!sumFringe) { - sumFringe = psImageCopy(NULL, fringe, PS_TYPE_F32); - } else { - psBinaryOp(sumFringe, sumFringe, "+", fringe); - } - - psVector *md5 = psImageMD5(fringe); // md5 hash - psString md5string = psMD5toString(md5); // String - psFree(md5); - psStringPrepend(&md5string, "Fringe image %d (scale %.3f) MD5: ", - i, solution->coeff->data.F32[i + 1]); - psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, - md5string, ""); - psFree(md5string); - -# if (0) - // write metadata header value - // XXX this is measured per cell, but we only have headers per chip - psString keyword = NULL; - psStringAppend (&keyword, "FRNG_%02dV", i); - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); - psFree (keyword); - - keyword = NULL; - psStringAppend (&keyword, "FRNG_%02dE", i); - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); - psFree (keyword); -# endif - - } - if (expTime != 1.0) { - psBinaryOp(sumFringe, sumFringe, "*", psScalarAlloc(expTime, PS_TYPE_F32)); - } - - // Apply the correction to all readouts - psArray *readouts = science->readouts; // Array of science readouts - for (int i = 0; i < readouts->n; i++) { - pmReadout *readout = readouts->data[i]; // Readout of interest - if (!readout || !readout->data_exists) { - continue; - } - - // subtract fringe and update mask if fringe value is NAN - for (int iy = 0; iy < readout->image->numRows; iy++) { - for (int ix = 0; ix < readout->image->numCols; ix++) { - readout->image->data.F32[iy][ix] -= sumFringe->data.F32[iy][ix]; - if (!isfinite(sumFringe->data.F32[iy][ix]) && readout->mask) { - readout->mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= maskVal; - } - } - } - - // XXX: Make generic, so subregions may be subtracted as well - // if (!psBinaryOp(readout->image, readout->image, "-", sumFringe)) { - // psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to subtract fringe.\n"); - // return false; - // } - - // measure residual fringe amplitude. results go to FRINGE.RESIDUALS - ppImageDetrendFringeMeasure (readout, fringes, true, options); - } - psFree(sumFringe); - - psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now, used for reporting - psString timeString = psTimeToISO(time); // String with time - psFree(time); - psStringPrepend(&timeString, "Fringe correction completed at "); - psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, - timeString, ""); - psFree(timeString); - - return true; -} - -bool ppImageDetrendFringeApply (pmConfig *config, pmChip *chip, const pmFPAview *inputView, const ppImageOptions *options) { - - pmCell *cell = NULL; - - assert (options->doFringe); // do not call if not needed - assert (inputView->chip != -1); - assert (inputView->cell == -1); - assert (inputView->readout == -1); - - pmFPAview *view = pmFPAviewAlloc(0); // View for local processing - *view = *inputView; - - // select the reference chip - pmChip *fringe = pmFPAfileThisChip(config->files, view, "PPIMAGE.FRINGE"); - if (!fringe) { - psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); - psFree (view); - return false; - } - - // Solve the fringe system - if (!ppImageDetrendFringeSolve(chip, fringe, false, options)) { - psError(PS_ERR_UNKNOWN, false, "failed to solve the fringe system.\n"); - psFree (view); - return false; - } - - // Go back over the cells to apply the fringe correction - view->cell = view->readout = -1; - while ((cell = pmFPAviewNextCell(view, chip->parent, 1)) != NULL) { - if (!cell->process || !cell->file_exists) { - continue; - } - - // Apply the fringe correction - psTrace("ppImage", 3, "Applying fringe correction...\n"); - pmCell *fringeCell = pmFPAfileThisCell(config->files, view, "PPIMAGE.FRINGE"); - if (!fringeCell) { - psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); - psFree (view); - return false; - } - - // XXX for now, skip the video cells (cell->readouts->n > 1) - if (cell->readouts->n > 1) { - psWarning ("Skipping Video Cell for ppImageDetrendFringeApply"); - continue; - } - - if (!ppImageDetrendFringeGenerate(cell, fringeCell, options)) { - psError(PS_ERR_UNKNOWN, false, "failed to apply fringe image.\n"); - psFree (view); - return false; - } - } - - // Solve the residual fringe system - if (!ppImageDetrendFringeSolve(chip, fringe, true, options)) { - psError(PS_ERR_UNKNOWN, false, "failed to solve the residual fringe system.\n"); - psFree (view); - return false; - } - - psFree (view); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageDetrendNonLinear.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageDetrendNonLinear.c (revision 29946) +++ (revision ) @@ -1,149 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageDetrendNonLinearPolynomial(pmReadout *input, psMetadataItem *dataItem) { - - // These are the polynomial coefficients - psVector *coeff = dataItem->data.V; // The coefficient vector - if (coeff->type.type != PS_TYPE_F64) { - psVector *temp = psVectorCopy(NULL, coeff, PS_TYPE_F64); // F64 version - psFree (coeff); - coeff = temp; - } - psPolynomial1D *correction = psPolynomial1DAlloc(coeff->n - 1, PS_POLYNOMIAL_ORD); - psFree(correction->coeff); - correction->coeff = psMemIncrRefCounter(coeff->data.F64); - pmNonLinearityPolynomial(input, correction); - psFree(coeff); - psFree(correction); - return true; -} - -bool ppImageDetrendNonLinearLookup(pmReadout *input, psMetadataItem *dataItem) { - - // This is a filename: lookup table - char *name = dataItem->data.V; // Filename - psLookupTable *table = psLookupTableAlloc(name, "%f %f", 0); - if (psLookupTableRead(table) <= 0) { - psErrorStackPrint(stderr, "Unable to read non-linearity correction file " - "%s --- ignored\n", name); - return false; - } -#ifdef PRODUCTION - pmNonLinearityLookup(input, table); -#else - psVector *influx = table->values->data[0]; - psVector *outflux = table->values->data[1]; - pmNonLinearityLookup(input, influx, outflux); -#endif - psFree(table); - return true; -} - - -bool ppImageDetrendNonLinear(pmReadout *input, pmFPAview *detview, pmConfig *config) { - bool status; - - pmFPAfile *linearity_file = psMetadataLookupPtr(&status,config->files,"PPIMAGE.LINEARITY"); - psFits *linearity_fits = linearity_file->fits; - - char *extname = psMetadataLookupStr(&status,input->parent->concepts,"CELL.NAME"); - if (!extname) { - psError(PS_ERR_IO, false, "missing CELL.NAME in concepts"); - return(false); - } - - if (!psFitsMoveExtName(linearity_fits,extname)) { - psError(PS_ERR_IO, false, "Unable to move to non-linearity table %s", extname); - return(false); - } - - psArray *table = psFitsReadTable(linearity_fits); - if (!table) { - psError(PS_ERR_IO, false, "Unable to read non-linearity table.\n"); - return(false); - } - - // It might be better to pack lookup table here... - // Why? I only use that lookup table once for the single cell it matches. - - if (!pmNonLinearityApply(input,table)) { - psError(PS_ERR_UNKNOWN, false, "Unable to apply non-linearity corrections.\n"); - psFree (table); - return(false); - } - psFree (table); - - return true; -} - -bool ppImageDetrendNonLinear_Original(pmReadout *input, ppImageOptions *options) { - - psMetadataItem *concept; - pmCell *cell = input->parent; - - switch (options->nonLinearType) { - case PS_DATA_VECTOR: - ppImageDetrendNonLinearPolynomial (input, options->nonLinearData); - return true; - - case PS_DATA_STRING: - ppImageDetrendNonLinearLookup (input, options->nonLinearData); - return true; - - case PS_DATA_METADATA: - // Go looking for the value in the hierarchy - concept = psMetadataLookup(cell->concepts, options->nonLinearSource); - if (! concept) { - pmChip *chip = cell->parent;// Parent chip - concept = psMetadataLookup(chip->concepts, options->nonLinearSource); - if (! concept) { - pmFPA *fpa = chip->parent; // Parent FPA - concept = psMetadataLookup(fpa->concepts, options->nonLinearSource); - if (! concept) { - psLogMsg("phase2", PS_LOG_WARN, "Unable to find value of concept %s " - "for non-linearity correction --- ignored.\n", (char *)options->nonLinearSource); - return false; - } - } - } - - if (concept->type != PS_DATA_STRING) { - psLogMsg("phase2", PS_LOG_WARN, "Type for concept %p isn't STRING, as" - " expected for non-linearity correction --- ignored.\n", - concept); - return false; - } - - // Get the value of the concept - psString conceptValue = concept->data.V; - psMetadata *folder = (psMetadata *)options->nonLinearData->data.V; - psMetadataItem *optionItem = psMetadataLookup(folder, conceptValue); - if (!optionItem) { - psLogMsg("phase2", PS_LOG_WARN, "Unable to find %s in NONLIN.DATA" - " --- ignored.\n", conceptValue); - return false; - } - - switch (optionItem->type) { - case PS_DATA_VECTOR: - ppImageDetrendNonLinearPolynomial (input, optionItem); - return true; - case PS_DATA_STRING: - ppImageDetrendNonLinearLookup (input, optionItem); - return true; - default: - psLogMsg("phase2", PS_LOG_WARN, "Non-linearity correction " - "desired but unable to interpret NONLIN.DATA for %s" - " --- ignored\n", conceptValue); - return false; - } - default: - psAbort("Invalid options->nonLinearType"); - } - return true; -} - Index: anches/haf_branches/videophot2010/ppImage/src/ppImageDetrendPattern.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageDetrendPattern.c (revision 29946) +++ (revision ) @@ -1,160 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -#define ESCAPE(STATUS,...) { \ - psError(PS_ERR_UNKNOWN, STATUS, __VA_ARGS__); \ - psFree(view); \ - return false; \ - } - -static bool doPatternForView (bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipename, const char *recipevalue); - -bool ppImageDetrendPatternApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, - const ppImageOptions *options) -{ - pmCell *cell = NULL; - - assert(options->doPatternRow || options->doPatternCell); // do not call if not needed - assert(inputView->chip != -1); - assert(inputView->cell == -1); - assert(inputView->readout == -1); - - if (options->doPatternRow) { - bool status; - pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT"); - pmFPAview *view = pmFPAviewAlloc(0); // View for local processing - *view = *inputView; - while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { - if (!cell->process || !cell->file_exists) { - continue; - } - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - ESCAPE(false, "load failure for Cell"); - } - - if (!cell->data_exists) { - continue; - } - - if (cell->readouts->n > 1) { - psWarning ("Skipping Video Cell for ppImageDetrendPatternApply"); - continue; - } - - bool doPattern = false; - if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.ROW.SUBSET")) { - ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); - } - if (!doPattern) continue; - - const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); - const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); - psLogMsg("ppImage", PS_LOG_INFO, "Performing row pattern correction for %s, %s\n", - chipName, cellName); - - // process each of the readouts - pmReadout *readout; // Readout from cell - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - ESCAPE(false, "load failure for Readout"); - } - if (!readout->data_exists) { - continue; - } - - // Perform pattern correction - if (!pmPatternRow(readout, options->patternRowOrder, options->patternRowIter, - options->patternRowRej, options->patternRowThresh, options->patternRowMean, - options->patternRowStdev, options->maskValue, options->darkMask)) { - psFree(view); - return(false); - } - } - } - psFree(view); - } - - if (options->doPatternCell) { - int numCells = chip->cells->n; // Number of cells - psVector *tweak = psVectorAlloc(numCells, PS_TYPE_U8); // Tweak cell? - pmFPAview *view = pmFPAviewAlloc(0); // View for local processing - *view = *inputView; - for (int i = 0; i < chip->cells->n; i++) { - view->cell = i; - - pmCell *cell = chip->cells->data[i]; // Cell of interest - if (cell->readouts->n > 1) { - psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction on video cell."); - continue; - } - - bool doPattern = false; - if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CELL.SUBSET")) { - ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); - } - if (doPattern) { - tweak->data.U8[i] = 0xFF; - } - } - - // Tweak the cells - if (!pmPatternCell(chip, tweak, options->patternCellBG, options->patternCellMean, - options->maskValue, options->darkMask)) { - psFree(tweak); - psFree(view); - return false; - } - psFree(tweak); - psFree(view); - } - - return(true); -} - -static bool doPatternForView (bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipeName, const char *recipeValue) { - - *doit = false; - - psMetadataItem *doPattern = pmConfigRecipeValueByView(config, recipeName, recipeValue, chip->parent, view); - if (!doPattern) { - psError(PS_ERR_UNKNOWN, false, "Unable to determine whether row pattern matching should be applied."); - return false; - } - if (doPattern->type == PS_DATA_BOOL) { - *doit = doPattern->data.B; - return true; - } - if (doPattern->type == PS_DATA_STRING) { - // expect a string of the form "000110001001" with at least view->cell entries - char *string = doPattern->data.str; - if (strlen(string) < view->cell) { - psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET chip string (too few elements %d)", (int) strlen(string)); - return false; - } - switch (string[view->cell]) { - case '0': - case 'f': - case 'F': - case 'n': - case 'N': - *doit = false; - return true; - case '1': - case 't': - case 'T': - case 'y': - case 'Y': - *doit = true; - return true; - default: - psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET chip string %s (unknown value %c))", string, string[view->cell]); - return false; - } - psAbort("imposible to reach here"); - } - psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET : invalid data type"); - return false; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageDetrendReadout.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageDetrendReadout.c (revision 29946) +++ (revision ) @@ -1,248 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageDetrendReadout(pmConfig *config, ppImageOptions *options, pmFPAview *view) -{ - // construct a view for the detrend images (which have only one readout) - pmFPAview *detview = pmFPAviewAlloc(0); - *detview = *view; - detview->readout = 0; - - // find the currently selected readout - pmReadout *input = pmFPAfileThisReadout(config->files, view, "PPIMAGE.INPUT"); - - // Check that the gain is set (this is used by both pmReadoutGenerateMask and pmReadoutGenerateVariance) - { - float gain = psMetadataLookupF32(NULL, input->parent->concepts, "CELL.GAIN"); // Gain for cell - if (!isfinite(gain)) { - psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, RECIPE_NAME); // Recipe - psAssert(recipe, "Should be there!"); - bool override = psMetadataLookupBool(NULL, recipe, "GAIN.OVERRIDE"); // Override the bad gain? - if (override) { - psWarning("CELL.GAIN is not set for readout (%d,%d,%d) --- setting to unity.", view->chip, view->cell, view->readout); - psMetadataItem *item = psMetadataLookup(input->parent->concepts, "CELL.GAIN"); // Gain item - psAssert(item, "Should be there!"); - item->data.F32 = 1.0; - - // for unity gain, there is no modification for the readnoise, note that it has (effectively) been updated - psMetadataRemoveKey(input->parent->concepts, "CELL.READNOISE.UPDATE"); - } else { - psWarning("CELL.GAIN is NAN for readout (%d,%d,%d), image will be masked.", view->chip, view->cell, view->readout); - } - } - } - - // Masking on the basis of pixel value needs to be done before anything else, so the values are pristine. - if (options->doMaskBuild) { - psImageMaskType satMask = options->doMaskSat ? options->satMask : 0; - psImageMaskType lowMask = options->doMaskLow ? options->lowMask : 0; - pmReadoutGenerateMask(input, satMask, lowMask); - } - // apply the externally supplied mask to the input->mask pixels - if (options->doMask) { - pmReadout *mask = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.MASK"); - pmMaskBadPixels(input, mask, options->maskValue); - } - if (options->doMaskBurntool) { - ppImageBurntoolMask(config,options,view,input); - } - - // Subtract the overscan - if (options->doOverscan) { - if (!pmOverscanSubtract (input, options->overscan)) { - psError(PS_ERR_UNKNOWN, false, "Unable to subtract overscan."); - psFree(detview); - return false; - } - } - - // Non-linearity correction - if (options->doNonLin) { - // linearity = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.LINEARITY"); - if (!ppImageDetrendNonLinear(input,detview,config)) { - psError(PS_ERR_UNKNOWN, false, "Unable to correct NonLinearity"); - psFree(detview); - return(false); - } - /* ppImageDetrendNonLinear(detrend->input, input, options); */ - } - - // set up the dark and bias - pmCell *dark = NULL; // Multi-dark - pmReadout *oldDark = NULL; // Old-fashioned dark - pmReadout *bias = NULL; - if (options->doBias) { - bias = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.BIAS"); - } - if (options->doDark) { - bool mdok; // Status of MD lookup - psMetadata *recipe = psMetadataLookupPtr (&mdok, config->recipes, RECIPE_NAME); - assert(mdok && recipe); - if (psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { - oldDark = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.DARK"); - } else { - dark = pmFPAfileThisCell(config->files, detview, "PPIMAGE.DARK"); - } - } - - // Bias and temperature-independent-dark subtraction are merged. - if (options->doBias) { - if (!pmBiasSubtract(input, bias, oldDark, view)) { - psError(PS_ERR_UNKNOWN, false, "Unable to subtract bias."); - psFree(detview); - return false; - } - } - - // Weight on the basis of pixel value needs to be done after the overscan has been subtracted - if (options->doVarianceBuild) { - // create the target mask and variance images - psImage *noiseImage = NULL; - if (options->doNoiseMap) { - // XXX convert the noiseMap image to a binned image - pmReadout *noiseMap = NULL; - noiseMap = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.NOISEMAP"); - noiseImage = psImageCopy (NULL, input->image, PS_TYPE_F32); - psImageInit (noiseImage, 0.0); - - // XXX this works, but is not really quite right: the model shoud include the - // offset information, we are not really getting exactly the right mapping from the - // original file. - psImageBinning *binning = psImageBinningAlloc(); - binning->nXruff = noiseMap->image->numCols; - binning->nYruff = noiseMap->image->numRows; - binning->nXfine = input->image->numCols; - binning->nYfine = input->image->numRows; - psImageBinningSetScale(binning, PS_IMAGE_BINNING_LEFT); - - psImageUnbin (noiseImage, noiseMap->image, binning); - psFree (binning); - } - - pmReadoutGenerateVariance(input, noiseImage, true); - psFree (noiseImage); - } - - if (options->doDark && dark) { - if (!pmDarkApply(input, dark, options->darkMask)) { - psError(PS_ERR_UNKNOWN, false, "Unable to subtract dark."); - psFree(detview); - return false; - } - } - - if (options->doRemnance) { - if (!pmRemnance(input, options->maskValue, options->lowMask, - options->remnanceSize, options->remnanceThresh)) { - psError(PS_ERR_UNKNOWN, false, "Unable to mask remnance."); - psFree(detview); - return false; - } - } - - // Shutter correction - if (options->doShutter) { - pmReadout *shutter = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.SHUTTER"); - if (!pmShutterCorrectionApply(input, shutter, pmConfigMaskGet("FLAT", config))) { - psFree(detview); - return false; - } - } - - // Flat-field correction (no options used?) - if (options->doFlat) { - pmReadout *flat = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.FLAT"); - if (!pmFlatField(input, flat, options->flatMask)) { - psFree(detview); - return false; - } - } - -/* // Pattern noise correction */ -/* if (options->doPattern) { */ -/* if (!pmPatternRow(input, options->patternOrder, options->patternIter, options->patternRej, */ -/* options->patternThresh, options->patternMean, options->patternStdev, */ -/* options->maskValue, options->darkMask)) { */ -/* psFree(detview); */ -/* return false; */ -/* } */ -/* } */ - - // Normalization by a single (known) constant - bool mdok; // Status of MD lookup - float norm = psMetadataLookupF32(&mdok, config->arguments, "NORMALIZATION"); - if (mdok && isfinite(norm) && norm != 1.0) { - pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest - psString comment = NULL; // Comment to add - psStringAppend(&comment, "Normalization: %f", norm); - psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, comment, ""); - psFree(comment); - - psBinaryOp(input->image, input->image, "*", psScalarAlloc(norm, PS_TYPE_F32)); - } - -# if (1) - // Normalization by per-class values - psMetadata *normlist = psMetadataLookupMetadata(&mdok, config->arguments, "NORMALIZATION.TABLE"); - if (normlist) { - pmFPAfile *inputFile = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.INPUT"); - - // get the menu of class IDs - psMetadata *menu = psMetadataLookupMetadata(&mdok, inputFile->camera, "CLASSID"); - if (!menu) { - psError(PS_ERR_IO, false, "Unable to find CLASSID metadata in camera configuration"); - psFree(detview); - return false; - } - // get the rule for class_id for the desired class - const char *rule = psMetadataLookupStr(&mdok, menu, options->normClass); - if (!rule) { - psError(PS_ERR_IO, false, "Unable to find NORM.CLASS value %s in CLASSID in camera configuration", options->normClass); - psFree(detview); - return false; - } - // get the class_id from the rule - char *classID = pmFPAfileNameFromRule(rule, inputFile, view); - if (!classID) { - psError(PS_ERR_IO, false, "error converting CLASSID rule %s to name\n", rule); - psFree(detview); - return false; - } - - // get normalization from the class_id - float norm = psMetadataLookupF32 (&mdok, normlist, classID); - if (!mdok) { - psError(PS_ERR_IO, false, "failed to find class ID %s in normalization table\n", classID); - psFree(detview); - return false; - } - - pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest - psString comment = NULL; // Comment to add - psStringAppend(&comment, "Normalization: %f", norm); - psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, comment, ""); - psFree(comment); - - // apply the normalization - psBinaryOp(input->image, input->image, "*", psScalarAlloc(norm, PS_TYPE_F32)); - - psFree (classID); - } -# endif - - if (options->doFringe) { - pmCell *fringe = pmFPAfileThisCell(config->files, detview, "PPIMAGE.FRINGE"); - if (!ppImageDetrendFringeMeasure(input, fringe, false, options)) { - psFree(detview); - return false; - } - } - - ppImageMemoryDump("detrend"); - - psFree(detview); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageDetrendRecord.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageDetrendRecord.c (revision 29946) +++ (revision ) @@ -1,79 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -static void detrendRecord( - bool doThis, // Are we supposed to do this? - psMetadata *target, // Target metadata - const pmConfig *config, // Configuration - const pmFPAview *view, // View to cell - const char *filename, // Name of file - const char *name, // Name in header - const char *desc // Description - ) -{ - psAssert(config, "Need configuration"); - psAssert(view, "Need view to cell"); - psAssert(name, "Need file name"); - - if (!doThis) { - return; - } - - pmFPAfile *file = psMetadataLookupPtr(NULL, config->files, filename); // File of interest - psAssert(file, "Should be there"); - - if (target) { - psMetadataAddStr(target, PS_LIST_TAIL, name, 0, desc, file->filename); - } - - pmCell *input = pmFPAfileThisCell(config->files, view, "PPIMAGE.INPUT"); // File we're processing - psAssert(input, "Should be there"); - pmHDU *hdu = pmHDUGetHighest(input->parent->parent, input->parent, input); // HDU for cell - - // Strip off path and Nebulous bits - char *base = file->filename; // Base name of file - for (char *new = base; (new = strpbrk(base, "/:")); base = new + 1); // No action - - // We don't want multiple listings in the header saying the same thing, so make sure we haven't put the - // same entry there. Usually (if the detrend and the image have the same file level) there'll only end up - // being one entry. - psString regexp = NULL; // Regular expression - psStringAppend(®exp, "^%s$", name); - psMetadataIterator *iter = psMetadataIteratorAlloc(hdu->header, PS_LIST_HEAD, regexp); // Iterator for hdr - psFree(regexp); - psMetadataItem *item; // Item from iteration - bool found = false; - while (!found && (item = psMetadataGetAndIncrement(iter))) { - if (item->type == PS_DATA_STRING && strcmp(item->data.str, base) == 0) { - found = true; - } - } - psFree(iter); - if (!found) { - psMetadataAddStr(hdu->header, PS_LIST_TAIL, name, PS_META_DUPLICATE_OK, desc, base); - } - - return; -} - - -bool ppImageDetrendRecord(pmCell *cell, const pmConfig *config, const ppImageOptions *options, - const pmFPAview *view) -{ - psMetadata *detrend = psMetadataAlloc(); // Detrend information - psMetadataAddMetadata(cell->analysis, PS_LIST_TAIL, "DETREND", 0, "Detrend information", detrend); - - detrendRecord(options->doMask, detrend, config, view, "PPIMAGE.MASK", "DETREND.MASK", "Mask filename"); - detrendRecord(options->doNoiseMap, detrend, config, view, "PPIMAGE.NOISEMAP", "DETREND.NOISEMAP", "Noise Map filename"); - detrendRecord(options->doBias, detrend, config, view, "PPIMAGE.BIAS", "DETREND.BIAS", "Bias filename"); - detrendRecord(options->doDark, detrend, config, view, "PPIMAGE.DARK", "DETREND.DARK", "Dark filename"); - detrendRecord(options->doShutter, detrend, config, view, "PPIMAGE.SHUTTER", "DETREND.SHUTTER", "Shutter correction filename"); - detrendRecord(options->doFlat, detrend, config, view, "PPIMAGE.FLAT", "DETREND.FLAT", "Flat filename"); - detrendRecord(options->doFringe, detrend, config, view, "PPIMAGE.FRINGE", "DETREND.FRINGE", "Fringe filename"); - - psFree (detrend); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageErrorCodes.c.in =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageErrorCodes.c.in (revision 29946) +++ (revision ) @@ -1,26 +1,0 @@ -/* - * The line - { PPIMAGE_ERR_$X{ErrorCode}, "$X{ErrorDescription}"}, - * (without the Xs) - * will be replaced by values from errorCodes.dat - */ -#include "pslib.h" -#include "ppImageErrorCodes.h" - -void ppImageErrorRegister(void) -{ - static psErrorDescription errors[] = { - { PPIMAGE_ERR_BASE, "First value we use; lower values belong to psLib" }, - { PPIMAGE_ERR_${ErrorCode}, "${ErrorDescription}"}, - }; - static int nerror = PPIMAGE_ERR_NERROR - PPIMAGE_ERR_BASE; // number of values in enum - - for (int i = 0; i < nerror; i++) { - psErrorDescription *tmp = psAlloc(sizeof(psErrorDescription)); - p_psMemSetPersistent(tmp, true); - *tmp = errors[i]; - psErrorRegister(tmp, 1); - psFree(tmp); /* it's on the internal list */ - } - nerror = 0; // don't register more than once -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageErrorCodes.dat =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageErrorCodes.dat (revision 29946) +++ (revision ) @@ -1,10 +1,0 @@ -# -# This file is used to generate ppImageErrorClasses.h - -BASE = 5000 First value we use; lower values belong to psLib -# these errors correspond to standard exit conditions -ARGUMENTS Incorrect arguments -SYS System error -CONFIG Problem in configure files -PROG Programming error -DATA invalid data Index: anches/haf_branches/videophot2010/ppImage/src/ppImageErrorCodes.h.in =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageErrorCodes.h.in (revision 29946) +++ (revision ) @@ -1,18 +1,0 @@ -#if !defined(PPIMAGE_ERROR_CODES_H) -#define PPIMAGE_ERROR_CODES_H -/* - * The line - * PPIMAGE_ERR_$X{ErrorCode}, - * (without the X) - * - * will be replaced by values from errorCodes.dat - */ -typedef enum { - PPIMAGE_ERR_BASE = 5000, - PPIMAGE_ERR_${ErrorCode}, - PPIMAGE_ERR_NERROR -} ppImageErrorCode; - -void ppImageErrorRegister(void); - -#endif Index: anches/haf_branches/videophot2010/ppImage/src/ppImageFileCheck.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageFileCheck.c (revision 29946) +++ (revision ) @@ -1,60 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -void ppImageFileCheck (pmConfig *config) { - - // add the output names to the output-type files - psMetadataItem *item = NULL; - psMetadataIterator *iter = psMetadataIteratorAlloc (config->files, PS_LIST_HEAD, NULL); - while ((item = psMetadataGetAndIncrement (iter)) != NULL) { - pmFPAfile *file = item->data.V; - pmFPA *fpa = file->fpa; - fprintf (stderr, "file %s\n", file->name); - if (!fpa) { - fprintf (stderr, " has no FPA\n"); - continue; - } - if (fpa->hdu) { - if (fpa->hdu->images) fprintf (stderr, " (%d,%d) images\n", -1, -1); - if (fpa->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", -1, -1); - if (fpa->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", -1, -1); - if (fpa->hdu->header) fprintf (stderr, " (%d,%d) header\n", -1, -1); - } else { - // fprintf (stderr, " has no fpa data (%d,%d)\n", -1, -1); - } - for (int i = 0; i < fpa->chips->n; i++) { - pmChip *chip = fpa->chips->data[i]; - if (chip->hdu) { - if (chip->hdu->images) fprintf (stderr, " (%d,%d) images\n", i, -1); - if (chip->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", i, -1); - if (chip->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", i, -1); - if (chip->hdu->header) fprintf (stderr, " (%d,%d) header\n", i, -1); - } else { - // fprintf (stderr, " has no chip data (%d,%d)\n", i, -1); - } - for (int j = 0; j < chip->cells->n; j++) { - pmCell *cell = chip->cells->data[j]; - if (cell->hdu) { - if (cell->hdu->images) fprintf (stderr, " (%d,%d) images\n", i, j); - if (cell->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", i, j); - if (cell->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", i, j); - if (cell->hdu->header) fprintf (stderr, " (%d,%d) header\n", i, j); - } else { - // fprintf (stderr, " has no cell data (%d,%d)\n", i, j); - } - for (int k = 0; k < cell->readouts->n; k++) { - pmReadout *readout = cell->readouts->data[k]; - if (readout) { - if (readout->image) fprintf (stderr, " (%d,%d,%d) image\n", i, j, k); - if (readout->variance) fprintf (stderr, " (%d,%d,%d) variance\n", i, j, k); - if (readout->mask) fprintf (stderr, " (%d,%d,%d) masks\n", i, j, k); - } - } - } - } - } - psFree (iter); -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageLoop.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageLoop.c (revision 29946) +++ (revision ) @@ -1,295 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -#define ESCAPE(MESSAGE) { \ - psError(PS_ERR_UNKNOWN, false, MESSAGE); \ - psFree(view); \ - pmFPAfileFreeSetStrict(false); \ - return false; \ -} - -bool ppImageLoop(pmConfig *config, ppImageOptions *options) -{ - psMetadata *stats = NULL; // Statistics to output - float timeDetrend = 0; // Amount of time spent in detrend - float timePhot = 0; // Amount of time spent in photometry - - if (options->doStats) { - stats = psMetadataAlloc(); - psMetadataAddS32(stats, PS_LIST_TAIL, "QUALITY", 0, "No problems", 0); - } - - bool status; // Status of MD lookup - pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT"); - if (!status) { - psErrorStackPrint(stderr, "Can't find input data!\n"); - ppImageCleanup(config, options); - exit(PS_EXIT_PROG_ERROR); - } - - pmConfigCamerasCull(config, NULL); - pmConfigRecipesCull(config, "PPIMAGE,PPSTATS,PSPHOT,MASKS,PSASTRO,JPEG"); - - 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 ("ppImageLoop", 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"); - } - - // crosstalk measurement needs to be done on the entire chip at once, and before - // signal levels are modified by the detrending. If crosstalk measurement is - // requested, the read-level for the images is set to CHIP. - if (!ppImageMeasureCrosstalk(config, options, view)) { - ESCAPE("Unable to perform crosstalk correction"); - } - - // crosstalk correction needs to be done on the entire chip at once, and before - // signal levels are modified by the detrending. If crosstalk correction is - // requested, the read-level for the images is set to CHIP. - if (!ppImageCorrectCrosstalk(config, options, view)) { - ESCAPE("Unable to perform crosstalk correction"); - } - - psTimerStart(TIMER_DETREND); - pmCell *cell; // Cell from chip - while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { - psLogMsg ("ppImageLoop", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); - if (!cell->process || !cell->file_exists) { - continue; - } - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - ESCAPE("load failure for Cell"); - } - - // Put version information into the header - pmHDU *hdu = pmHDUGetHighest(input->fpa, chip, cell); - if (hdu && hdu != lastHDU) { - ppImageVersionHeader(hdu->header); - lastHDU = hdu; - } - - // XXX for now, skip the video cells (cell->readouts->n > 1) - if (cell->readouts->n > 1) { - psWarning ("Skipping Video Cell for ppImageDetrendReadout"); - continue; - } - - // process each of the readouts - pmReadout *readout; // Readout from cell - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - ESCAPE("load failure for Readout"); - } - if (!readout->data_exists) { - continue; - } - - // flip the image to match the native detector orientation (to match bias, flat, etc) - if (!ppImageParityFlip(config, options, view, true)) { - ESCAPE("Unable to detrend readout"); - } - - // XXX set the options->*Mask values here (after the mask images have been loaded - // and before any of the value are used) - if (!ppImageSetMaskBits(config, options)) { - ESCAPE("Unable to set bit masks"); - } - - // perform the detrend analysis - if (!ppImageDetrendReadout(config, options, view)) { - ESCAPE("Unable to detrend readout"); - } - - // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT - if (!ppImageDetrendFree (config, view)) { - ESCAPE("Unable to free detrend images"); - } - - // optionally measure CTE by examining the variance in a box - if (!ppImageCheckCTE (config, options, view)) { - ESCAPE("Unable to measure CTE"); - } - } - - if (cell->data_exists) { - ppImageDetrendRecord(cell, config, options, view); - } - - // process each of the readouts - // XXX reset the view to the first readout? - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (!readout->data_exists) { - continue; - } - // flip the image to match the raw readout orientation - if (!ppImageParityFlip(config, options, view, false)) { - ESCAPE("Unable to detrend readout"); - } - } - - // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT - if (!ppImageDetrendFree (config, view)) { - ESCAPE("Unable to free detrend images"); - } - } - // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT - if (!ppImageDetrendFree (config, view)) { - ESCAPE("Unable to free detrend images"); - } - - // Apply the fringe correction - if (options->doFringe) { - if (!ppImageDetrendFringeApply(config, chip, view, options)) { - ESCAPE("Unable to defringe"); - } - } - // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT - if (!ppImageFringeFree (config, view)) { - ESCAPE("Unable to free fringe images"); - } - - // Apply the pattern correction - if (options->doPatternRow || options->doPatternCell) { - if (!ppImageDetrendPatternApply(config,chip,view,options)) { - ESCAPE("Unable to apply pattern corrections"); - } - } - - // measure various pixel-based statistics for this image - if (!ppImagePixelStats(config, stats, options, view)) { - ESCAPE("Unable to measures pixel stats for image"); - } - - if (!ppImageMosaicChip(config, options, view, "PPIMAGE.CHIP", "PPIMAGE.OUTPUT")) { - ESCAPE("Unable to mosaic chip"); - } - timeDetrend += psTimerClear(TIMER_DETREND); - - // we perform photometry on the readouts of this chip in the output - - psTimerStart(TIMER_PHOT); - if (options->doPhotom) { - if (!ppImagePhotom(stats, config, view)) { - ESCAPE("error running photometry."); - } - } - timePhot += psTimerClear(TIMER_PHOT); - - // replace the masked pixels with the background level - if (options->doBG) { - if (!ppImageSubtractBackground(config, view, options)) { - ESCAPE("Unable to subtract background"); - } - } - - if (options->doMaskStats) { - //if (!ppImageMaskStats(config, view, options)) { - if (!ppImageMaskStats(config, view, stats)) { - ESCAPE("Unable to do Mask stats"); - } - } - - // these may be used by ppImageSubtractBackground. - // if these are defined as internal files, drop them here - status = true; - status &= pmFPAfileDropInternal (config->files, "PSPHOT.BACKMDL"); - status &= pmFPAfileDropInternal (config->files, "PSPHOT.BACKMDL.STDEV"); - status &= pmFPAfileDropInternal (config->files, "PSPHOT.BACKGND"); - if (!status) { - psError(PSPHOT_ERR_PROG, false, "trouble dropping internal files"); - psFree (view); - return false; - } - - // binning (used for display) must take place after the background is replaced, if desired - if (!ppImageRebinChip(config, view, options, "PPIMAGE.BIN1")) { - ESCAPE("Unable to bin chip (level 1)."); - } - if (!ppImageRebinChip(config, view, options, "PPIMAGE.BIN2")) { - ESCAPE("Unable to bin chip (level 2)."); - } - - // Close cells (XXX shouldn't pmFPAfileClose iterate down as needed?) - view->cell = -1; - while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { - if (!cell->process || !cell->file_exists) { - continue; - } - if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { - ESCAPE("save failure for Cell"); - } - } - - // Close chip - if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { - ESCAPE("save failure for Chip"); - } - } - - // generate the full-scale FPA mosaic - if (!ppImageMosaicFPA(config, options, "PPIMAGE.OUTPUT.FPA1", "PPIMAGE.BIN1")) { - ESCAPE("failure in FPA Mosaic (level 1)"); - } - if (!ppImageMosaicFPA(config, options, "PPIMAGE.OUTPUT.FPA2", "PPIMAGE.BIN2")) { - ESCAPE("failure in FPA Mosaic (level 2)"); - } - - // we perform astrometry on all chips after sources have been detected - // this also performs the psastro file IO - if (options->doAstromChip || options->doAstromMosaic) { - if (!ppImageAstrom(config, stats)) { - ESCAPE("error running astrometry."); - } - } - - if (psTraceGetLevel("ppImage") >= 3) { - ppImageFileCheck(config); - } - - // Calculate summary statistics from FPA Metadata - if (!ppImageMetadataStats(config, stats, options)) { - ESCAPE("Unable to determine FPA-level metadata statistics."); - } - - // Output and Close FPA - if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { - ESCAPE("save failure for FPA"); - } - psFree(view); - - // Dump configuration - psString dump_file = psMetadataLookupStr(&status, config->arguments, "DUMP_CONFIG"); - if (dump_file) { - if (!pmConfigDump(config, dump_file)) { - ESCAPE("Unable to dump configuration."); - } - } - - // Write out summary statistics - if (options->doStats) { - psMetadataAddF32(stats, PS_LIST_TAIL, "DT_DET", 0, "Time spent detrending (sec)", timeDetrend); - psMetadataAddF32(stats, PS_LIST_TAIL, "DT_PHOT", 0, "Time spent photometering (sec)", timePhot); - psMetadataAddF32(stats, PS_LIST_TAIL, "DT_TOTAL", 0, "Total time (sec)", psTimerMark(TIMER_TOTAL)); - if (!ppImageStatsOutput(config, stats, options)) { - ESCAPE("Unable to write statistics file."); - } - } - psFree (stats); - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageMaskStats.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageMaskStats.c (revision 29946) +++ (revision ) @@ -1,92 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - - -bool ppImageMaskStats(pmConfig *config, pmFPAview *view, psMetadata *stats) -{ - PS_ASSERT_PTR_NON_NULL(view, false); - PS_ASSERT_PTR_NON_NULL(config, false); - - if (!stats) { - return true; - } - - bool status; - - pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.CHIP"); - if (!status) { - psError(PS_ERR_UNEXPECTED_NULL, true, "PPIMAGE.CHIP file is not defined"); - return(false); - } - - psMetadata *recipe = psMetadataLookupMetadata(&status, config->recipes, "PPIMAGE"); - - psU16 staticMaskVal = psMetadataLookupU32(&status, recipe, "MASKSTAT.STATIC"); - psU16 magicMaskVal = psMetadataLookupU32(&status, recipe, "MASKSTAT.MAGIC"); - psU16 dynamicMaskVal = psMetadataLookupU32(&status, recipe, "MASKSTAT.DYNAMIC"); - psU16 advisoryMaskVal = psMetadataLookupU32(&status, recipe, "MASKSTAT.ADVISORY"); - - psS32 Npix_valid = 0; - psS32 Npix_static = 0; - psS32 Npix_magic = 0; - psS32 Npix_dynamic = 0; - psS32 Npix_advisory = 0; - - pmChip *chip = pmFPAviewThisChip(view, input->fpa); // Chip of interest - if (!chip) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find chip"); - return(false); - } - if (chip->cells->n == 0) { - psWarning("Chip has no cells"); - return(true); - } - if (chip->cells->n > 1) { - psWarning("Chip has %ld cells; only the first will be processed", chip->cells->n); - } - pmCell *cell = chip->cells->data[0]; // Cell of interest - if (!cell || !cell->process || !cell->file_exists) { - // Nothing to process - return(true); - } - if (cell->readouts->n == 0) { - psWarning("Cell has no readouts"); - return(true); - } - if (cell->readouts->n > 1) { - psWarning("Cell has %ld readouts; only the first will be processed", cell->readouts->n); - } - pmReadout *readout = cell->readouts->data[0]; // Readout of interest; - if (!readout || !readout->data_exists) { - // Nothing to process - return(true); - } - - psImage *mask = readout->mask; // Mask of interest; - psWarning("In ppImageMaskStats: %d %ld\n",Npix_valid, (long) mask); - - if (!pmSingleImageMaskStats(mask,&Npix_valid,&Npix_static,&Npix_magic, - &Npix_dynamic,&Npix_advisory, - staticMaskVal,magicMaskVal, - dynamicMaskVal,advisoryMaskVal)) { - psError(PS_ERR_UNKNOWN, false, "Unable to calculate masks for readout."); - return(false); - } - psMetadataAddS32(stats, PS_LIST_TAIL,"MASKFRAC_NPIX", 0, - "Number of valid pixels", Npix_valid); - psMetadataAddF32(stats,PS_LIST_TAIL, "MASKFRAC_STATIC", 0, - "Fraction of pixels statically masked", (float) Npix_static / Npix_valid); - psMetadataAddF32(stats,PS_LIST_TAIL, "MASKFRAC_DYNAMIC", 0, - "Fraction of pixels dynamically masked", (float) Npix_dynamic / Npix_valid); - psMetadataAddF32(stats,PS_LIST_TAIL, "MASKFRAC_MAGIC", 0, - "Fraction of pixels magically masked", (float) Npix_magic / Npix_valid); - psMetadataAddF32(stats,PS_LIST_TAIL, "MASKFRAC_ADVISORY", 0, - "Fraction of pixels masked as an advisory", (float) Npix_advisory / Npix_valid); - psWarning("In ppImageMaskStats: %d %f %f %f %f\n",Npix_valid, (float) Npix_static / Npix_valid, - (float) Npix_dynamic / Npix_valid, (float) Npix_magic / Npix_valid, - (float) Npix_advisory / Npix_valid); - return(true); -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageMeasureCrosstalk.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageMeasureCrosstalk.c (revision 29946) +++ (revision ) @@ -1,187 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -#define ESCAPE(MESSAGE) { \ - psError(PS_ERR_UNKNOWN, false, MESSAGE); \ - psFree(view); \ - return false; \ - } - -// For the moment, this implementation is VERY GPC-specific - -bool ppImageMeasureCrosstalk(pmConfig *config, ppImageOptions *options, pmFPAview *view) -{ - bool status; - const float CUTOFF = 60000; - const int MIN_MATCHED_PIXELS = 500; // require a significant area of high signal - char name[64]; - - if (!options->doCrosstalkMeasure) return true; - - psTimerStart("crosstalk"); - - // confirm that this camera is GPC1 - - // find the currently selected chip - pmChip *chip = pmFPAfileThisChip(config->files, view, "PPIMAGE.INPUT"); - pmFPA *fpa = chip->parent; - if (chip->cells->n != 64) return true; - - // for each cell (xyNM), we want to find the pixels with values above a cutoff (40k, 60k, ?) - // for all of the other cells in the row (xyJM), we want to measure the (robust) median flux in the pixels - // corresponding to the high pixels in xyNM, and compare with the median flux for the cell - - psArray *vectorSet = psArrayAlloc(8); - psArray *cellRows = psArrayAlloc(8); - psArray *imageRows = psArrayAlloc(8); - for (int i = 0; i < 8; i++) { - psArray *cellRow = psArrayAlloc(8); - cellRows->data[i] = cellRow; - psArray *imageRow = psArrayAlloc(8); - imageRows->data[i] = imageRow; - psVector *vector = psVectorAllocEmpty(100, PS_TYPE_F32); - vectorSet->data[i] = vector; - } - - // assign the cells to arrays by row and column - for (int i = 0; i < chip->cells->n; i++) { - - pmCell *cell = chip->cells->data[i]; - - // skip the video cells and empty cells (cell->readouts->n != 1) - if (cell->readouts->n != 1) { - psWarning ("Skipping Empty and Video Cell for ppImageCrosstalk"); - continue; - } - - // place the image from this cell in the 2D array: - const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); - int row = cellName[3] - '0'; - int col = cellName[2] - '0'; - assert (row >= 0 && row < 8); - assert (col >= 0 && col < 8); - - pmReadout *readout = cell->readouts->data[0]; - psImage *image = readout->image; - - psArray *cellRow = cellRows->data[row]; - cellRow->data[col] = psMemIncrRefCounter(cell); - - psArray *imageRow = imageRows->data[row]; - imageRow->data[col] = psMemIncrRefCounter(image); - } - - psVector *sample = NULL; - psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS); - psStats *stats = psStatsAlloc (PS_STAT_ROBUST_MEDIAN); - - // measure the background for each cell - for (int row = 0; row < cellRows->n; row++) { - psArray *cellRow = cellRows->data[row]; - psArray *imageRow = imageRows->data[row]; - for (int col = 0; col < cellRow->n; col++) { - pmCell *cell = cellRow->data[col]; - if (!cell) continue; - psImage *image = imageRow->data[col]; - if (!image) continue; // XXX assert on this? - - psStatsInit (stats); - if (!psImageBackground (stats, &sample, image, NULL, 0, rng)) continue; - psMetadataAddF32 (cell->analysis, PS_LIST_TAIL, "XTALK.REF", PS_META_REPLACE, "crosstalk measurement", stats->robustMedian); - // fprintf (stderr, "xtalk.ref (xy%d%d) : %f\n", col, row, stats->robustMedian); - } - } - - for (int row = 0; row < cellRows->n; row++) { - psArray *cellRow = cellRows->data[row]; - psArray *imageRow = imageRows->data[row]; - for (int col = 0; col < cellRow->n; col++) { - psImage *image = imageRow->data[col]; - if (!image) continue; - - // initialize the storage vectors - for (int i = 0; i < 8; i++) { - psVector *vector = vectorSet->data[i]; - vector->n = 0; - } - - int nBright = 0; - - // generate a vector for each of the other cells in this row - // containing only the pixels for which this cell is > CUTOFF - for (int iy = 0; iy < image->numRows; iy++) { - for (int ix = 0; ix < image->numCols; ix++) { - - if (image->data.F32[iy][ix] < CUTOFF) continue; - nBright ++; - - // this is a pixel of interest in the target cell; extract the matched pixels - - for (int i = 0; i < 8; i++) { - if (i == col) continue; - - psImage *matchImage = imageRow->data[i]; - if (!matchImage) continue; - - psVector *vector = vectorSet->data[i]; - psVectorAppend (vector, matchImage->data.F32[iy][ix]); - } - } - } - // fprintf (stderr, "nBright for xy%d%d : %d\n", col, row, nBright); - if (nBright < MIN_MATCHED_PIXELS) continue; - - // pmCell *refCell = cellRow->data[col]; - // float refBackground = psMetadataLookupF32 (&status, refCell->analysis, "XTALK.REF"); - // float swing = CUTOFF - refBackground; - - // now we need to measure the median for these vectors - for (int i = 0; i < 8; i++) { - if (i == col) continue; - psVector *vector = vectorSet->data[i]; - if (vector->n < MIN_MATCHED_PIXELS) continue; - - pmCell *cell = cellRow->data[i]; - if (!cell) continue; // XXX assert on this? - - psStatsInit (stats); - if (!psVectorStats (stats, vector, NULL, NULL, 0)) { - psError(PS_ERR_UNKNOWN, false, "failure to measure stats"); - return false; - } - - float background = psMetadataLookupF32 (&status, cell->analysis, "XTALK.REF"); - float xtalk = (stats->robustMedian - background) / CUTOFF; - - // Put version information into the header - pmHDU *hdu = pmHDUGetHighest(fpa, chip, cell); - if (hdu) { - // add this to the PHU header - snprintf (name, 64, "XT_%d%d_%d%d", col, row, i, row); - psMetadataAddF32 (hdu->header, PS_LIST_TAIL, name, PS_META_REPLACE, "crosstalk measurement", xtalk); - } - - // keyword for resulting value: - snprintf (name, 64, "XTALK_%d%d", i, row); - - psMetadataAddF32 (cell->analysis, PS_LIST_TAIL, name, PS_META_REPLACE, "crosstalk measurement", xtalk); - // fprintf (stderr, "xtalk (xy%d%d on xy%d%d) : %f -> delta is %f, slope if %e\n", col, row, i, row, stats->robustMedian, stats->robustMedian - background, xtalk); - } - } - } - psLogMsg ("ppImage", 3, "crosstalk measurement: %f sec\n", psTimerMark ("crosstalk")); - - psFree (vectorSet); - psFree (cellRows); - psFree (imageRows); - psFree (stats); - psFree (rng); - psFree (sample); - - // need to free all sorts of things here.... - return true; -} - Index: anches/haf_branches/videophot2010/ppImage/src/ppImageMemory.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageMemory.c (revision 29946) +++ (revision ) @@ -1,38 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include -#include - -#include "ppImage.h" - -//#define TESTING - -void ppImageMemoryDump(const char *description) -{ -#ifndef TESTING - return; -#else - psMemBlock **leaks = NULL; - int numLeaks = psMemCheckLeaks(0, &leaks, NULL, true); - - static int num = 0; - psString filename = NULL; - psStringAppend(&filename, "%s_%d.txt", description, num++); - FILE *fp = fopen(filename, "w"); - psFree(filename); - - for (int i = 0; i < numLeaks; i++) { - psMemBlock *memBlock = leaks[i]; - fprintf(fp, "%ld : %s at (%s:%d) ID: %lu Ref: %lu\n", - (unsigned long)memBlock->userMemorySize, memBlock->func, memBlock->file, - (int)memBlock->lineno, (unsigned long)memBlock->id, memBlock->refCounter); - } - psFree(leaks); - - fclose(fp); - - return; -#endif -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageMetadataStats.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageMetadataStats.c (revision 29946) +++ (revision ) @@ -1,46 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -// calculate stats from headers and concepts -bool ppImageMetadataStats(pmConfig *config, psMetadata *stats, const ppImageOptions *options) -{ - bool mdok; // Status of MD lookup - - if (!options->doStats) { - return true; - } - - // Extract statistics from the last output fpa - pmFPAfile *outImage = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.OUTPUT"); - pmFPAfile *outPhotom = psMetadataLookupPtr(&mdok, config->files, "PSPHOT.OUTPUT"); - pmFPAfile *outAstrom = psMetadataLookupPtr(&mdok, config->files, "PSASTRO.OUTPUT"); - - if (!outImage && !outPhotom && !outAstrom) { - psError(PS_ERR_UNEXPECTED_NULL, true, - "Unable to find any output file (PPIMAGE.OUTPUT, PSPHOT.OUTPUT, PSASTRO.OUTPUT)."); - return false; - } - - // get the latest output product available - pmFPAfile *output = outAstrom; - if (!output) { - output = outPhotom; - } - if (!output) { - output = outImage; - } - - // extract stats for the complete fpa - pmFPAview *view = pmFPAviewAlloc(0); - if (!ppStatsMetadata(stats, output->fpa, view, options->maskValue, config)) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to generate stats for image."); - psFree(view); - return false; - } - - psFree(view); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageMosaic.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageMosaic.c (revision 29946) +++ (revision ) @@ -1,103 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageMosaicChip(pmConfig *config, const ppImageOptions *options, const pmFPAview *view, - const char *outFile, const char *inFile) -{ - bool status; // Status of MD lookup - - pmFPAfile *in = psMetadataLookupPtr(&status, config->files, inFile); // Input file - if (!status) { - psErrorStackPrint(stderr, "Can't find required I/O file!\n"); - exit(EXIT_FAILURE); - } - - pmFPAfile *out = psMetadataLookupPtr(&status, config->files, outFile); // Output file - if (!status) { - psErrorStackPrint(stderr, "Can't find required I/O file!\n"); - exit(EXIT_FAILURE); - } - - pmChip *outChip = pmFPAviewThisChip(view, out->fpa); - pmChip *inChip = pmFPAviewThisChip(view, in->fpa); - if (!outChip->hdu && !outChip->parent->hdu) { - pmFPAAddSourceFromView(out->fpa, view, out->format); - } - - // If the input is a dark (normalising and mosaicking) then it looks like a video cell and will be ignored - // by pmChipMosaic. We therefore hack the structure so it doesn't look like a video cell. - psVector *darkNumbers = NULL; // Number of dark readouts for each cell - if (psMetadataLookupBool(&status, config->arguments, "INPUT_IS_DARK")) { - darkNumbers = psVectorAlloc(inChip->cells->n, PS_TYPE_S32); - psVectorInit(darkNumbers, 0); - for (int i = 0; i < inChip->cells->n; i++) { - pmCell *cell = inChip->cells->data[i]; - if (!cell) { - continue; - } - darkNumbers->data.S32[i] = cell->readouts->n; - cell->readouts->n = 1; - } - } - - psTrace("pmChipMosaic", 5, "mosaic chip %s to %s (xbin,ybin: %d,%d to %d,%d)\n", - in->name, out->name, in->xBin, in->yBin, out->xBin, out->yBin); - - // Mosaic the chip, making a deep copy. This has the side effect of making the output - // image products pure trimmed images, but also increases the memory footprint. - status = pmChipMosaic(outChip, inChip, true, options->blankMask); - - // Restore dark structure - if (darkNumbers) { - for (int i = 0; i < inChip->cells->n; i++) { - pmCell *cell = inChip->cells->data[i]; - if (!cell) { - continue; - } - cell->readouts->n = darkNumbers->data.S32[i]; - } - psFree(darkNumbers); - } - - return status; -} - -bool ppImageMosaicFPA (pmConfig *config, const ppImageOptions *options, const char *outFile, - const char *inFile) -{ - bool status; // Status of MD lookup - - pmFPAfile *in = psMetadataLookupPtr(&status, config->files, inFile); // Input file - if (!status) { - psErrorStackPrint(stderr, "Can't find required I/O file!\n"); - exit(EXIT_FAILURE); - } - - pmFPAfile *out = psMetadataLookupPtr(&status, config->files, outFile); // Output file - if (!status) { - psErrorStackPrint(stderr, "Can't find required I/O file!\n"); - exit(EXIT_FAILURE); - } - - // XXX test printing of all concepts - #if 0 - for (int i = 0; i < in->fpa->chips->n; i++) { - pmChip *chip = in->fpa->chips->data[i]; - for (int j = 0; j < chip->cells->n; j++) { - pmCell *cell = chip->cells->data[j]; - psMetadataPrint(stdout, cell->concepts, 2); - } - } - #endif - - pmFPAview *view = pmFPAviewAlloc(0); - pmFPAAddSourceFromView(out->fpa, view, out->format); - psFree(view); - - psTrace ("pmFPAMosaic", 5, "mosaic fpa %s to %s (xbin,ybin: %d,%d to %d,%d)\n", - in->name, out->name, in->xBin, in->yBin, out->xBin, out->yBin); - return pmFPAMosaic(out->fpa, in->fpa, false, options->blankMask); -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageOptions.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageOptions.c (revision 29946) +++ (revision ) @@ -1,346 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -static void imageOptionsFree(ppImageOptions *options) -{ - psFree(options->overscan); - // psFree(options->nonLinearData); - // psFree(options->nonLinearSource); -} - -ppImageOptions *ppImageOptionsAlloc(void) -{ - ppImageOptions *options = psAlloc(sizeof(ppImageOptions)); - psMemSetDeallocator(options, (psFreeFunc)imageOptionsFree); - - // actions which ppImage should perform - options->doMaskBuild = false; // Build internal mask - options->doMaskSat = false; // mask saturated pixels - options->doMaskLow = false; // mask low pixels - options->doMaskBurntool = false; // mask potential burntool trails - options->doVarianceBuild = false; // Build internal variance - options->doMask = false; // Mask bad pixels - options->doNonLin = false; // Non-linearity correction - options->doOverscan = false; // Overscan subtraction - options->doNoiseMap = false; // Apply Read Noise Map - options->doBias = false; // Bias subtraction - options->doDark = false; // Dark subtraction - options->doRemnance = false; // Remnance masking - options->doShutter = false; // Shutter correction - options->doFlat = false; // Flat-field normalisation - options->doPatternRow = false; // Row pattern correction - options->doPatternCell = false; // Cell pattern correction - options->doFringe = false; // Fringe subtraction - options->doPhotom = false; // Source identification and photometry - options->doAstromChip = false; // Astrometry (per-chip) - options->doAstromMosaic = false; // Astrometry (full-mosaic) - options->doStats = false; // Measure and save image statistics - options->checkCTE = false; // Measure pixel-based variance - options->applyParity = false; // Apply Cell parities - options->doMaskStats = false; // Calculate mask fractions - - // output files requested - options->BaseFITS = false; // create output image - options->BaseMaskFITS = false; // create output mask image - options->BaseVarianceFITS = false; // create output variance image - - options->ChipFITS = false; // create output chip-mosaic image - options->ChipMaskFITS = false; // create output chip-mosaic mask image - options->ChipVarianceFITS = false; // create output chip-mosaic variance image - - options->FPA1FITS = false; // create fpa-mosaic binned image (scale 1) - options->FPA2FITS = false; // create fpa-mosaic binned image (scale 2) - options->Bin1FITS = false; // create binned image (scale 1) - options->Bin2FITS = false; // create binned image (scale 2) - options->Bin1JPEG = false; // create jpeg of binned image (scale 1) - options->Bin2JPEG = false; // create jpeg of binned image (scale 2) - - // default flags for various activities - options->maskValue = 0x00; // Default mask value (used to skip / ignore pixels) - options->satMask = 0x00; // Saturated pixels (supplied to pmReadoutGenerateMask) - options->lowMask = 0x00; // out-of-bounds (low) pixels (supplied to pmReadoutGenerateMask) - options->flatMask = 0x00; // Bad flat pixels (supplied to pmFlatField) - options->darkMask = 0x00; // Bad dark pixels (supplied to pmDarkApply) - options->blankMask = 0x00; // Blank (no data, cell gap) pixels (supplied to pmChipMosaic, pmFPAMosaic) - options->markValue = 0x00; // A safe bit for internal marking - options->burntoolMask = 0x00; // Suspect pixels that fall where a burntool trail is expected. - options->burntoolTrails = 0x07; // Which types of burntool areas to mask. - // crosstalk options - options->doCrosstalkMeasure = false; // measure crosstalk - options->doCrosstalkCorrect = false; // correct crosstalk - - // Non-linearity default options - options->nonLinearType = 0; // Type of non-linearity data (vector, string or metadata) - options->nonLinearData = NULL; // The non-linearity data - options->nonLinearSource = NULL; // If the non-linearity data is a menu, this provides the key - - // Overscan defaults - options->overscan = NULL; // Overscan options - - // binning parameters - options->xBin1 = 16; // x-binning, scale 1 - options->yBin1 = 16; // y-binning, scale 1 - options->xBin2 = 16; // x-binning, scale 2 - options->yBin2 = 16; // y-binning, scale 2 - - // Fringe defaults - options->fringeRej = NAN; // Fringe rejection limit - options->fringeIter = 0; // Fringe iterations - options->fringeKeep = 1.0; // Fringe keep fraction - - // Pattern correction values - - options->patternRowOrder = 0; // Polynomial order - options->patternRowIter = 0; // Clipping iterations - options->patternRowRej = NAN; // Clipping rejection threshold - options->patternRowThresh = NAN; // Threshold for ignoring pixels - options->patternRowMean = PS_STAT_NONE; // Statistic for mean - options->patternRowStdev = PS_STAT_NONE; // Statistic for standard deviation - options->patternCellBG = PS_STAT_NONE; // Statistic for background - options->patternCellMean = PS_STAT_NONE; // Statistic for mean - - // Remnance values - options->remnanceSize = 30; // Size for remnance detection - options->remnanceThresh = 25.0; // Threshold for remnance detection - - // per-class normalization source - options->normClass = NULL; // per-class normalizations refer to this class - - return options; -} - -ppImageOptions *ppImageOptionsParse(pmConfig *config) -{ - bool status; - ppImageOptions *options = ppImageOptionsAlloc (); - - // select the recipe for this analysis - bool mdStatus = false; // Result of MD lookup - psMetadata *recipe = psMetadataLookupMetadata(&mdStatus, config->recipes, RECIPE_NAME); - if (! mdStatus || !recipe) { - psLogMsg("ppImage", PS_LOG_ERROR, "Can't find recipe %s in the RECIPES.\n", RECIPE_NAME); - exit(EXIT_FAILURE); - } - - // Non-linearity recipe options - if (psMetadataLookupBool(NULL, recipe, "NONLIN")) { - psMetadataItem *dataItem = psMetadataLookup(recipe, "NONLIN.DATA"); - if (! dataItem) { - psLogMsg("ppImage", PS_LOG_ERROR, "Non-linearity correction desired, but unable to find NONLIN.DATA in recipe %s.", RECIPE_NAME); - exit(EXIT_FAILURE); - } - - options->doNonLin = true; - options->nonLinearType = dataItem->type; - options->nonLinearData = dataItem; - - switch (dataItem->type) { - // No immediate action required - case PS_DATA_VECTOR: - case PS_DATA_STRING: - break; - - // This is a menu; we need the key - case PS_DATA_METADATA: - options->nonLinearSource = psMetadataLookupStr(&status, recipe, "NONLIN.SOURCE"); - if (! status || ! options->nonLinearSource) { - psLogMsg("ppImage", PS_LOG_ERROR, "Non-linearity correction desired, but unable to find NONLIN.SOURCE in recipe %s.", RECIPE_NAME); - exit(EXIT_FAILURE); - } - break; - default: - psLogMsg("ppImage", PS_LOG_ERROR, "Non-linearity correction desired, but NONLIN.DATA is of invalid type in recipe %s.", RECIPE_NAME); - exit(EXIT_FAILURE); - } - } - - // XXX PAP: The overscan stuff needs to be updated following the reworked API - - // Overscan recipe options - // XXX EAM : we should abort on invalid options. default options? - if (psMetadataLookupBool(NULL, recipe, "OVERSCAN")) { - options->doOverscan = true; - - // Do the overscan as a single value? - bool overscanSingle = psMetadataLookupBool(NULL, recipe, "OVERSCAN.SINGLE"); - - // How do we fit it? - pmFit overscanFit = PM_FIT_NONE; // Fit type for overscan - int overscanOrder = 0; // Order for overscan fit - psString fit = psMetadataLookupStr(NULL, recipe, "OVERSCAN.FIT"); - if (! strcasecmp(fit, "POLYNOMIAL")) { - overscanFit = PM_FIT_POLY_ORD; - overscanOrder = psMetadataLookupS32(NULL, recipe, "OVERSCAN.ORDER"); - } else if (! strcasecmp(fit, "CHEBYSHEV")) { - overscanFit = PM_FIT_POLY_CHEBY; - overscanOrder = psMetadataLookupS32(NULL, recipe, "OVERSCAN.ORDER"); - } else if (! strcasecmp(fit, "SPLINE")) { - overscanFit = PM_FIT_SPLINE; - } else if (strcasecmp(fit, "NONE")) { - psLogMsg(__func__, PS_LOG_WARN, - "OVERSCAN.FIT (%s) in recipe %s is not one of NONE, POLYNOMIAL, or SPLINE", - fit, RECIPE_NAME); - exit(EXIT_FAILURE); - } - - // What method do we use to measure the overscan statistics? - // XXX allow user to specify psStats types by name - psStats *overscanStats = NULL; // Statistics for overscan - psString stat = psMetadataLookupStr(NULL, recipe, "OVERSCAN.STAT"); - if (! strcasecmp(stat, "MEAN")) { - // overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN); - overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN); - } else if (! strcasecmp(stat, "MEDIAN")) { - overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEDIAN); - } else { - psErrorStackPrint(stderr, "OVERSCAN.STAT (%s) in recipe %s is not one of MEAN or MEDIAN", - stat, RECIPE_NAME); - exit(EXIT_FAILURE); - } - - int boxcar = psMetadataLookupS32(NULL, recipe, "OVERSCAN.BOXCAR"); - float gauss = psMetadataLookupF32(NULL, recipe, "OVERSCAN.GAUSS"); - - // Fill in the options - options->overscan = pmOverscanOptionsAlloc(overscanSingle, overscanFit, overscanOrder, - overscanStats, boxcar, gauss); - - options->overscan->constant = psMetadataLookupBool(NULL, recipe, "OVERSCAN.CONSTANT"); - options->overscan->value = psMetadataLookupF32(NULL, recipe, "OVERSCAN.VALUE"); - - psFree(overscanStats); - } - - // for these images, even if not required otherwise - options->doMaskBuild = psMetadataLookupBool(NULL, recipe, "MASK.BUILD"); - options->doMaskSat = psMetadataLookupBool(NULL, recipe, "MASK.SATURATED"); - options->doMaskLow = psMetadataLookupBool(NULL, recipe, "MASK.LOW"); - options->doMaskBurntool = psMetadataLookupBool(NULL, recipe, "MASK.BURNTOOL"); - options->doVarianceBuild = psMetadataLookupBool(NULL, recipe, "VARIANCE.BUILD"); - - // Mask recipe options (note that mask bit values are set in ppImageSetMaskBits.c) - options->doMask = psMetadataLookupBool(NULL, recipe, "MASK"); - - // Mask recipe options (note that mask bit values are set in ppImageSetMaskBits.c) - options->doCrosstalkMeasure = psMetadataLookupBool(NULL, recipe, "CROSSTALK.MEASURE"); - options->doCrosstalkCorrect = psMetadataLookupBool(NULL, recipe, "CROSSTALK.CORRECT"); - - options->doNoiseMap = psMetadataLookupBool(NULL, recipe, "NOISEMAP"); - options->doBias = psMetadataLookupBool(NULL, recipe, "BIAS"); - options->doDark = psMetadataLookupBool(NULL, recipe, "DARK"); - options->doRemnance = psMetadataLookupBool(NULL, recipe, "REMNANCE"); - options->doFlat = psMetadataLookupBool(NULL, recipe, "FLAT"); - options->doFringe = psMetadataLookupBool(NULL, recipe, "FRINGE"); - options->doShutter = psMetadataLookupBool(NULL, recipe, "SHUTTER"); - options->doPatternRow = psMetadataLookupBool(NULL, recipe, "PATTERN.ROW"); - options->doPatternCell = psMetadataLookupBool(NULL, recipe, "PATTERN.CELL"); - options->doMaskStats = psMetadataLookupBool(NULL, recipe, "MASK.STATS"); - - options->doStats = false; - char *statsName = psMetadataLookupStr(&status, config->arguments, "STATS"); // Filename for statistics - if (statsName) { - options->doStats = true; - } - - options->applyParity = psMetadataLookupBool(NULL, recipe, "APPLY.CELL.PARITY"); - - options->burntoolTrails = psMetadataLookupS32(&status, recipe, "BURNTOOL.TRAILS"); - psTrace("psModules.detrend", 7, "burntoolTrails: %d BURNTOOL.TRAILS: %d Status: %d\n", - options->burntoolTrails,psMetadataLookupS32(&status,recipe,"BURNTOOL.TRAILS"),status); - if (!status) { - psWarning("BURNTOOL.TRAILS not found in recipe: setting to default value.\n"); - } - - // binned image options - options->xBin1 = psMetadataLookupS32(&status, recipe, "BIN1.XBIN"); - if (!status) { - psWarning("BIN1.XBIN not found in recipe: setting to default value.\n"); - options->xBin1 = 4; - } - options->yBin1 = psMetadataLookupS32(&status, recipe, "BIN1.YBIN"); - if (!status) { - psWarning("BIN1.YBIN not found in recipe: setting to default value.\n"); - options->yBin1 = 4; - } - - options->xBin2 = psMetadataLookupS32(&status, recipe, "BIN2.XBIN"); - if (!status) { - psWarning("BIN2.XBIN not found in recipe: setting to default value.\n"); - options->xBin1 = 16; - } - options->yBin2 = psMetadataLookupS32(&status, recipe, "BIN2.YBIN"); - if (!status) { - psWarning("BIN2.YBIN not found in recipe: setting to default value.\n"); - options->yBin1 = 16; - } - - options->BaseFITS = psMetadataLookupBool(NULL, recipe, "BASE.FITS"); - options->BaseMaskFITS = psMetadataLookupBool(NULL, recipe, "BASE.MASK.FITS"); - options->BaseVarianceFITS = psMetadataLookupBool(NULL, recipe, "BASE.VARIANCE.FITS"); - - options->ChipFITS = psMetadataLookupBool(NULL, recipe, "CHIP.FITS"); - options->ChipMaskFITS = psMetadataLookupBool(NULL, recipe, "CHIP.MASK.FITS"); - options->ChipVarianceFITS = psMetadataLookupBool(NULL, recipe, "CHIP.VARIANCE.FITS"); - - options->FPA1FITS = psMetadataLookupBool(NULL, recipe, "FPA1.FITS"); - options->FPA2FITS = psMetadataLookupBool(NULL, recipe, "FPA2.FITS"); - - options->Bin1FITS = psMetadataLookupBool(NULL, recipe, "BIN1.FITS"); - options->Bin1JPEG = psMetadataLookupBool(NULL, recipe, "BIN1.JPEG"); - options->Bin2FITS = psMetadataLookupBool(NULL, recipe, "BIN2.FITS"); - options->Bin2JPEG = psMetadataLookupBool(NULL, recipe, "BIN2.JPEG"); - - options->doPhotom = psMetadataLookupBool(NULL, recipe, "PHOTOM"); - options->doAstromChip = psMetadataLookupBool(NULL, recipe, "ASTROM.CHIP"); - options->doAstromMosaic = psMetadataLookupBool(NULL, recipe, "ASTROM.MOSAIC"); - options->doBG = psMetadataLookupBool(NULL, recipe, "BACKGROUND"); - - options->checkCTE = psMetadataLookupBool(NULL, recipe, "CHECK.CTE"); - - // even if not requested explicitly, if any of these are set, build an internal mask and variance: - if (options->doNoiseMap || options->doBias || options->doOverscan || options->doDark || options->doShutter || options->doFlat || - options->doPhotom) { - options->doMaskBuild = true; - options->doVarianceBuild = true; - } else if (options->doMask || options->doBG) { - options->doMaskBuild = true; - } - - if ((options->doAstromChip || options->doAstromMosaic) && !options->doPhotom) { - psLogMsg(__func__, PS_LOG_ERROR, "Invalid PPIMAGE options: cannot do ASTROMetry without PHOTOMetry"); - exit(EXIT_FAILURE); - } - - // Fringe options - options->fringeRej = psMetadataLookupF32(NULL, recipe, "FRINGE.REJ"); - options->fringeIter = psMetadataLookupS32(NULL, recipe, "FRINGE.ITER"); - options->fringeKeep = psMetadataLookupF32(NULL, recipe, "FRINGE.KEEP"); - - // Pattern correction - options->patternRowOrder = psMetadataLookupS32(NULL, recipe, "PATTERN.ROW.ORDER"); - options->patternRowIter = psMetadataLookupS32(NULL, recipe, "PATTERN.ROW.ITER"); - options->patternRowRej = psMetadataLookupF32(NULL, recipe, "PATTERN.ROW.REJ"); - options->patternRowThresh = psMetadataLookupF32(NULL, recipe, "PATTERN.ROW.THRESH"); - options->patternRowMean = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.ROW.MEAN")); - options->patternRowStdev = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.ROW.STDEV")); - options->patternCellBG = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.CELL.BG")); - options->patternCellMean = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.CELL.MEAN")); - - // Remnance options - options->remnanceSize = psMetadataLookupF32(NULL, recipe, "REMNANCE.SIZE"); - options->remnanceThresh = psMetadataLookupS32(NULL, recipe, "REMNANCE.THRESH"); - - // per-class normalization source (just a reference; don't free) - options->normClass = psMetadataLookupStr(NULL, recipe, "NORM.CLASS"); - - options->maskstat_static = psMetadataLookupU16(NULL, recipe, "MASKSTAT.STATIC"); - options->maskstat_dynamic = psMetadataLookupU16(NULL, recipe, "MASKSTAT.DYNAMIC"); - options->maskstat_magic = psMetadataLookupU16(NULL, recipe, "MASKSTAT.MAGIC"); - options->maskstat_advisory = psMetadataLookupU16(NULL, recipe, "MASKSTAT.ADVISORY"); - - - return options; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageParityFlip.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageParityFlip.c (revision 29946) +++ (revision ) @@ -1,162 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -// Update a concept to the assumed value -#define FIX_CONCEPT(SOURCE, NAME, TYPE, VALUE) { \ -psMetadataItem *item = psMetadataLookup(SOURCE, NAME); \ -item->data.TYPE = VALUE; } - -// flip the image to have 'native' (detector) or 'raw' (readout) orientation -bool ppImageParityFlip (pmConfig *config, const ppImageOptions *options, const pmFPAview *view, bool native) { - - bool status; - int xParity, yParity; - int xParityRaw, yParityRaw; - int xParityTarget, yParityTarget; - - if (!options->applyParity) return true; - - // find the currently selected readout - pmReadout *readout = pmFPAfileThisReadout(config->files, view, "PPIMAGE.INPUT"); - - pmCell *cell = readout->parent; - - if (native) { - // find the current (raw) parity - xParity = psMetadataLookupS32(&status, cell->concepts, "CELL.XPARITY"); - if (!status || (xParity != -1 && xParity != 1)) { - psWarning("CELL.XPARITY is not set for the input cell; assuming 1.\n"); - FIX_CONCEPT(cell->concepts, "CELL.XPARITY", S32, 1); - xParity = 1; - } - yParity = psMetadataLookupS32(&status, cell->concepts, "CELL.YPARITY"); - if (!status || (yParity != -1 && yParity != 1)) { - psWarning("CELL.YPARITY is not set for the input cell; assuming 1.\n"); - FIX_CONCEPT(cell->concepts, "CELL.YPARITY", S32, 1); - yParity = 1; - } - - // save the raw parity - psMetadataAddS32 (cell->concepts, PS_LIST_TAIL, "CELL.XPARITY.RAW", PS_META_REPLACE, "original parity", xParity); - psMetadataAddS32 (cell->concepts, PS_LIST_TAIL, "CELL.YPARITY.RAW", PS_META_REPLACE, "original parity", yParity); - - xParityTarget = 1; - yParityTarget = 1; - } else { - // find the current (native) parity - xParity = psMetadataLookupS32(&status, cell->concepts, "CELL.XPARITY"); - psAssert (status, "CELL.XPARITY not set : cannot call ppImageParityFlip (native = false) without first calling it with native = true"); - - yParity = psMetadataLookupS32(&status, cell->concepts, "CELL.YPARITY"); - psAssert (status, "CELL.YPARITY not set : cannot call ppImageParityFlip (native = false) without first calling it with native = true"); - - // find the raw parity - xParityRaw = psMetadataLookupS32(&status, cell->concepts, "CELL.XPARITY.RAW"); - psAssert (status, "CELL.XPARITY not set : cannot call ppImageParityFlip (native = false) without first calling it with native = true"); - - yParityRaw = psMetadataLookupS32(&status, cell->concepts, "CELL.YPARITY.RAW"); - psAssert (status, "CELL.YPARITY not set : cannot call ppImageParityFlip (native = false) without first calling it with native = true"); - - xParityTarget = xParityRaw; - yParityTarget = yParityRaw; - } - - // for this case, nothing to be done: - if ((xParity == xParityTarget) && (yParity == yParityTarget)) return true; - - psImage *image = readout->image; - psImage *var = readout->variance; - psImage *mask = readout->mask; - - if (var) psAssert (image->numCols == var->numCols, "image and variance sizes are mismatched"); - if (var) psAssert (image->numRows == var->numRows, "image and variance sizes are mismatched"); - if (mask) psAssert (image->numCols == mask->numCols, "image and mask sizes are mismatched"); - if (mask) psAssert (image->numRows == mask->numRows, "image and mask sizes are mismatched"); - - int Nx = image->numCols; - int Ny = image->numRows; - - // we need working buffers for the image, variance, and mask: - psF32 *imrow = (psF32 *) psAlloc (Nx*sizeof(psF32)); - psF32 *wtrow = (psF32 *) psAlloc (Nx*sizeof(psF32)); - psImageMaskType *mkrow = (psImageMaskType *) psAlloc (Nx*sizeof(psImageMaskType)); - - // the three cases (+1,-1), (-1,+1), (-1,-1) should be handled independently - - // flip only in x-direction - if ((xParity != xParityTarget) && (yParity == yParityTarget)) { - for (int iy = 0; iy < Ny; iy++) { - for (int ix = 0; ix < Nx; ix++) { - imrow[Nx-1-ix] = image->data.F32[iy][ix]; - } - for (int ix = 0; (var != NULL) && (ix < Nx); ix++) { - wtrow[Nx-1-ix] = var->data.F32[iy][ix]; - } - for (int ix = 0; (mask != NULL) && (ix < Nx); ix++) { - mkrow[Nx-1-ix] = mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix]; - } - memcpy (image->data.F32[iy], imrow, Nx*sizeof(psF32)); - if (var) memcpy (var->data.F32[iy], wtrow, Nx*sizeof(psF32)); - if (mask) memcpy (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy], mkrow, Nx*sizeof(psImageMaskType)); - } - } - // flip only in y-direction - if ((xParity == xParityTarget) && (yParity != yParityTarget)) { - for (int iy = 0; iy < Ny/2; iy++) { - memcpy (imrow, image->data.F32[iy], Nx*sizeof(psF32)); - memcpy (image->data.F32[iy], image->data.F32[Ny-1-iy], Nx*sizeof(psF32)); - memcpy (image->data.F32[Ny-1-iy], imrow, Nx*sizeof(psF32)); - - if (var) { - memcpy (wtrow, var->data.F32[iy], Nx*sizeof(psF32)); - memcpy (var->data.F32[iy], var->data.F32[Ny-1-iy], Nx*sizeof(psF32)); - memcpy (var->data.F32[Ny-1-iy], wtrow, Nx*sizeof(psF32)); - } - - if (mask) { - memcpy (mkrow, mask->data.PS_TYPE_IMAGE_MASK_DATA[iy], Nx*sizeof(psImageMaskType)); - memcpy (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy], mask->data.PS_TYPE_IMAGE_MASK_DATA[Ny-1-iy], Nx*sizeof(psImageMaskType)); - memcpy (mask->data.PS_TYPE_IMAGE_MASK_DATA[Ny-1-iy], mkrow, Nx*sizeof(psImageMaskType)); - } - } - } - // flip in both directions - if ((xParity != xParityTarget) && (yParity != yParityTarget)) { - for (int iy = 0; iy < Ny/2; iy++) { - for (int ix = 0; ix < Nx; ix++) { - imrow[Nx-1-ix] = image->data.F32[iy][ix]; - } - for (int ix = 0; var && (ix < Nx); ix++) { - wtrow[Nx-1-ix] = var->data.F32[iy][ix]; - } - for (int ix = 0; mask && (ix < Nx); ix++) { - mkrow[Nx-1-ix] = mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix]; - } - - for (int ix = 0; ix < Nx; ix++) { - image->data.F32[iy][Nx-1-ix] = image->data.F32[Ny-1-iy][ix]; - } - for (int ix = 0; var && (ix < Nx); ix++) { - var->data.F32[iy][Nx-1-ix] = var->data.F32[Ny-1-iy][ix]; - } - for (int ix = 0; mask && (ix < Nx); ix++) { - mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][Nx-1-ix] = mask->data.PS_TYPE_IMAGE_MASK_DATA[Ny-1-iy][ix]; - } - - memcpy (image->data.F32[Ny-1-iy], imrow, Nx*sizeof(psF32)); - if (var) memcpy (var->data.F32[Ny-1-iy], wtrow, Nx*sizeof(psF32)); - if (mask) memcpy (mask->data.PS_TYPE_IMAGE_MASK_DATA[Ny-1-iy], mkrow, Nx*sizeof(psImageMaskType)); - } - } - - FIX_CONCEPT(cell->concepts, "CELL.XPARITY", S32, xParityTarget); - FIX_CONCEPT(cell->concepts, "CELL.YPARITY", S32, yParityTarget); - - psFree (imrow); - psFree (wtrow); - psFree (mkrow); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageParseCamera.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageParseCamera.c (revision 29946) +++ (revision ) @@ -1,480 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -ppImageOptions *ppImageParseCamera(pmConfig *config) -{ - bool status = false; - - if (!ppImageDefineFile(config, NULL, "PPIMAGE.INPUT", "INPUT", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_NONE)) { - psError(PS_ERR_IO, false, "Can't find an input image source"); - return NULL; - } - pmFPAfile *input = psMetadataLookupPtr(NULL, config->files, "PPIMAGE.INPUT"); // Input file - psAssert(input, "We just put it there!"); - - // add recipe options supplied on command line - psMetadata *recipe = psMetadataLookupPtr(&status, config->recipes, RECIPE_NAME); - - // parse the options from the metadata format to the ppImageOptions structure - ppImageOptions *options = ppImageOptionsParse(config); - - // the following are defined from the argument list, if given, - // otherwise they revert to the config information - // not all input or output images are used in a given recipe - if (options->doNoiseMap) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.NOISEMAP", "NOISEMAP", - PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_NOISEMAP)) { - psError(PS_ERR_IO, false, "Can't find a noise map image source"); - psFree(options); - return NULL; - } - } - if (options->doBias) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.BIAS", "BIAS", - PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_BIAS)) { - psError(PS_ERR_IO, false, "Can't find a bias image source"); - psFree(options); - return NULL; - } - } - if (options->doDark) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.DARK", "DARK", - PM_FPA_FILE_DARK, PM_DETREND_TYPE_DARK)) { - psError(PS_ERR_IO, false, "Can't find a dark image source"); - psFree(options); - return NULL; - } - } - if (options->doMask) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.MASK", "MASK", - PM_FPA_FILE_MASK, PM_DETREND_TYPE_MASK)) { - psError(PS_ERR_IO, false, "Can't find a mask image source"); - psFree(options); - return NULL; - } - } - if (options->doShutter) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.SHUTTER", "SHUTTER", - PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_SHUTTER)) { - psError(PS_ERR_IO, false, "Can't find a shutter image source"); - psFree(options); - return NULL; - } - } - - if (options->doFlat) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.FLAT", "FLAT", - PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_FLAT)) { - psError(PS_ERR_IO, false, "Can't find a flat image source"); - psFree(options); - return NULL; - } - } - - if (options->doNonLin) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.LINEARITY", "LINEARITY", - PM_FPA_FILE_LINEARITY, PM_DETREND_TYPE_LINEARITY)) { - psError(PS_ERR_IO, false, "Can't find a non-linearity correction source"); - psFree(options); - return NULL; - } - } - - int nThreads = psMetadataLookupS32(&status, config->arguments, "NTHREADS"); - if (nThreads > 0) { - int nScanRows = psMetadataLookupS32(&status, recipe, "SCAN.ROWS"); - pmDetrendSetThreadTasks(nScanRows); - } - - if (options->doPatternRow || options->doPatternCell) { - pmFPAfile *outPattern = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.PATTERN"); - if (!outPattern) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.PATTERN")); - psFree(options); - return NULL; - } - outPattern->save = true; - } - - // fringe frame are only applied for a subset of the filters. - // if the filter is one of those identified by a FRINGE.FILTERS metadata entry - // in ppImage.config, apply the fringe frame - if (options->doFringe) { - // determine filter from the concepts - const char *filter = psMetadataLookupStr(&status, input->fpa->concepts, "FPA.FILTER"); - if (!status || !filter || strlen(filter) == 0) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find FPA.FILTER.\n"); - psFree(options); - return NULL; - } - - // select FRINGE.FILTERS from the recipe and test if the filter matches - // is the mdi saved with psList or string? - psMetadataItem *mdi = psMetadataLookup (recipe, "FRINGE.FILTERS"); - if (mdi == NULL) { - // no valid filters for fringe data for this camera - options->doFringe = false; - goto skip_fringe; - } - // place entry on a list regardless of type - psList *filters = NULL; - if (mdi->type == PS_DATA_STRING) { - filters = psListAlloc(NULL); - psListAdd (filters, PS_LIST_HEAD, mdi); - } else if (mdi->type == PS_DATA_METADATA_MULTI) { - filters = psMemIncrRefCounter(mdi->data.list); - } else { - psError(PS_ERR_BAD_PARAMETER_TYPE, true, - "FRINGE.FILTERS in recipe %s is not of type METADATA", RECIPE_NAME); - psFree(options); - return NULL; - } - - // search through list to find the current filter - psListIterator *iter = psListIteratorAlloc (filters, PS_LIST_HEAD, FALSE); - options->doFringe = false; - for (int i = 0; !options->doFringe && (i < filters->n); i++) { - psMetadataItem *item = psListGetAndIncrement (iter); - char *validFilter = item->data.V; - if (strcmp (validFilter, filter)) continue; - options->doFringe = true; - } - psFree(iter); - psFree(filters); - } -skip_fringe: - if (options->doFringe) { - if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.FRINGE", "FRINGE", - PM_FPA_FILE_FRINGE, PM_DETREND_TYPE_FRINGE)) { - psError (PS_ERR_IO, false, "Can't find a fringe image source"); - return NULL; - } - } - - if (options->checkCTE && false) { - int DX = psMetadataLookupS32 (&status, recipe, "CTE.XBIN"); - int DY = psMetadataLookupS32 (&status, recipe, "CTE.YBIN"); - pmFPAfile *outCTE = pmFPAfileDefineFromFile (config, input, DX, DY, "PPIMAGE.CTEMAP"); - if (!outCTE) { - psError(PSPHOT_ERR_CONFIG, false, "Cannot find a rule for PPIMAGE.CTEMAP"); - return false; - } - outCTE->save = true; - } - - // the following files are output targets - pmFPAfile *outImage = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT"); - if (!outImage) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.OUTPUT")); - psFree(options); - return NULL; - } - if (outImage->type != PM_FPA_FILE_IMAGE) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT is not of type IMAGE"); - psFree(options); - return NULL; - } - pmFPAfile *outMask = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.MASK"); - if (!outMask) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.OUTPUT.MASK")); - psFree(options); - return NULL; - } - if (outMask->type != PM_FPA_FILE_MASK) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.MASK is not of type MASK"); - psFree(options); - return NULL; - } - pmFPAfile *outVariance = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.VARIANCE"); - if (!outVariance) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.OUTPUT.VARIANCE")); - psFree(options); - return NULL; - } - if (outVariance->type != PM_FPA_FILE_VARIANCE) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.VARIANCE is not of type VARIANCE"); - psFree(options); - return NULL; - } - - // XXX should these be bound explicitly to the outImage->fpa rather than the input->fpa? - pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, input->fpa, "PPIMAGE.CHIP"); - if (!chipImage) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.CHIP")); - psFree(options); - return NULL; - } - if (chipImage->type != PM_FPA_FILE_IMAGE) { - psError(PS_ERR_IO, true, "PPIMAGE.CHIP is not of type IMAGE"); - psFree(options); - return NULL; - } - pmFPAfile *chipMask = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.MASK"); - if (!chipMask) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.CHIP.MASK")); - psFree(options); - return NULL; - } - if (chipMask->type != PM_FPA_FILE_MASK) { - psError(PS_ERR_IO, true, "PPIMAGE.CHIP.MASK is not of type MASK"); - psFree(options); - return NULL; - } - pmFPAfile *chipVariance = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.VARIANCE"); - if (!chipVariance) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.CHIP.VARIANCE")); - psFree(options); - return NULL; - } - if (chipVariance->type != PM_FPA_FILE_VARIANCE) { - psError(PS_ERR_IO, true, "PPIMAGE.CHIP.VARIANCE is not of type VARIANCE"); - psFree(options); - return NULL; - } - - pmFPAfile *byFPA1 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA1"); - if (!byFPA1) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.OUTPUT.FPA1")); - psFree(options); - return NULL; - } - if (byFPA1->type != PM_FPA_FILE_IMAGE) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.FPA1 is not of type IMAGE"); - psFree(options); - return NULL; - } - pmFPAfile *byFPA2 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA2"); - if (!byFPA2) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.OUTPUT.FPA2")); - psFree(options); - return NULL; - } - if (byFPA2->type != PM_FPA_FILE_IMAGE) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.FPA2 is not of type IMAGE"); - psFree(options); - return NULL; - } - - // chipImage -> psphotInput (pmFPAfileDefineFromFile) : fpa is constructed - // psphotInput -> psphotOutput (pmFPAfileDefineOutputFromFile) : fpa is equated - // psphotOutput -> psastroInput (pmFPAfileDefineInput) : fpa is ref-copied - // psastroInput -> psastroModel (pmFPAfileDefineFromArgs : fpa is ref-copied - // psastroInput -> psastroModel (pmFPAfileDefineFromConf : fpa is constructed - // psastroInput -> psastroModel (pmFPAfileDefineFromDetDB : fpa is constructed (pmDetrendSelect uses input concepts ) - - // For photometry, we operate on the chip-mosaicked image - // we create a copy of the mosaicked image for psphot so we can write out a clean image - if (options->doPhotom || options->doBG) { - - // this file is just used as a carrier; output files (eg, PSPHOT.RESID) are defined by - // psphotDefineFiles - pmFPAfile *psphotInput = pmFPAfileDefineFromFile (config, chipImage, 1, 1, "PSPHOT.INPUT"); - PS_ASSERT (psphotInput, false); - - // specify the number of psphot input images - psMetadataAddS32 (config->arguments, PS_LIST_TAIL, "PSPHOT.INPUT.NUM", PS_META_REPLACE, "number of inputs", 1); - - // define associated psphot input/output files - if (!psphotDefineFiles (config, psphotInput)) { - psError(PSPHOT_ERR_CONFIG, false, - "Trouble defining the additional input/output files for psphot"); - return false; - } - } - - // For photometry, we operate on the chip-mosaicked image - if (options->doAstromChip || options->doAstromMosaic) { - if (!options->doPhotom) { - psError(PSASTRO_ERR_CONFIG, false, - "Photometry mode is not selected; it is required for astrometry"); - return false; - } - - pmFPAfile *psphotOutput = psMetadataLookupPtr(&status, config->files, "PSPHOT.OUTPUT"); - PS_ASSERT(psphotOutput, false); - - pmFPAfile *psastroInput = pmFPAfileDefineInput(config, psphotOutput->fpa, NULL, "PSASTRO.INPUT"); - PS_ASSERT(psastroInput, false); - psastroInput->mode = PM_FPA_MODE_REFERENCE; - - // define associated psphot input/output files - if (!psastroDefineFiles(config, psastroInput)) { - psError(PSPHOT_ERR_CONFIG, false, - "Trouble defining the additional input/output files for psastro"); - return false; - } - - // deactivate the psastro files, reactive when needed - pmFPAfileActivate(config->files, false, "PSASTRO.OUTPUT"); - } - - // save any of these files? - outImage->save = options->BaseFITS; - outMask->save = options->BaseMaskFITS; - outVariance->save = options->BaseVarianceFITS; - - chipImage->save = options->ChipFITS; - chipMask->save = options->ChipMaskFITS; - chipVariance->save = options->ChipVarianceFITS; - - byFPA1->save = options->FPA1FITS; - byFPA2->save = options->FPA2FITS; - - // outImage is used as a carrier: input to chipImage -> require the data to remain at the CHIP level - outImage->freeLevel = PS_MIN(outImage->freeLevel, PM_FPA_LEVEL_CHIP); - outImage->dataLevel = outImage->freeLevel; - outImage->fileLevel = PS_MIN(outImage->fileLevel, outImage->dataLevel); - - // outMask and outVariance must be freed at the same level as outImage (all freed by pmFPAFreeData) - outMask->freeLevel = outImage->freeLevel; - outVariance->freeLevel = outImage->freeLevel; - outMask->dataLevel = outImage->dataLevel; - outVariance->dataLevel = outImage->dataLevel; - - // Ditto for the chip-mosaicked version - chipMask->freeLevel = chipImage->freeLevel; - chipVariance->freeLevel = chipImage->freeLevel; - chipMask->dataLevel = chipImage->dataLevel; - chipVariance->dataLevel = chipImage->dataLevel; - - // the input data is the same as the outImage data : force the free levels to match - input->freeLevel = PS_MIN(outImage->freeLevel, input->freeLevel); - - // define the binned target files (which may just be carriers for some camera configurations) - pmFPAfile *bin1 = pmFPAfileDefineFromFPA(config, chipImage->fpa, options->xBin1, options->yBin1, - "PPIMAGE.BIN1"); - if (!bin1) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.BIN1")); - psFree(options); - return NULL; - } - if (bin1->type != PM_FPA_FILE_IMAGE) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.BIN1 is not of type IMAGE"); - psFree(options); - return NULL; - } - - pmFPAfile *bin2 = pmFPAfileDefineFromFPA(config, chipImage->fpa, options->xBin2, options->yBin2, - "PPIMAGE.BIN2"); - if (!bin2) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.BIN2")); - psFree(options); - return NULL; - } - if (bin2->type != PM_FPA_FILE_IMAGE) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.BIN2 is not of type IMAGE"); - psFree(options); - return NULL; - } - - // bin1 and bin2 are used as carriers: input for byFPA1, byFPA2 - bin1->freeLevel = PM_FPA_LEVEL_FPA; - bin2->freeLevel = PM_FPA_LEVEL_FPA; - - pmFPAfile *jpg1 = pmFPAfileDefineOutput(config, byFPA1->fpa, "PPIMAGE.JPEG1"); - if (!jpg1) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.JPEG1")); - psFree(options); - return NULL; - } - if (jpg1->type != PM_FPA_FILE_JPEG) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.JPEG1 is not of type JPEG"); - psFree(options); - return NULL; - } - pmFPAfile *jpg2 = pmFPAfileDefineOutput(config, byFPA2->fpa, "PPIMAGE.JPEG2"); - if (!jpg2) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.JPEG2")); - psFree(options); - return NULL; - } - if (jpg2->type != PM_FPA_FILE_JPEG) { - psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.JPEG2 is not of type JPEG"); - psFree(options); - return NULL; - } - - // XXX we could potentially not define these pmFPAfiles if no output is requested... - bin1->save = options->Bin1FITS; - bin2->save = options->Bin2FITS; - jpg1->save = options->Bin1JPEG; - jpg2->save = options->Bin2JPEG; - - // Chip selection: turn on only the chips specified (pass status to suppress missing-key log msg) - char *chipLine = psMetadataLookupStr(&status, config->arguments, "CHIP_SELECTIONS"); - psArray *chips = psStringSplitArray(chipLine, ",", false); - if (chips->n > 0) { - pmFPASelectChip (input->fpa, -1, true); // deselect all chips - for (int i = 0; i < chips->n; i++) { - int chipNum = atoi(chips->data[i]); - if (! pmFPASelectChip(input->fpa, chipNum, false)) { - psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum); - psFree(options); - return false; - } - } - } - psFree (chips); - - if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_FRINGE")) { - // It's a fringe file, so change the file type - input->type = PM_FPA_FILE_FRINGE; - outImage->type = PM_FPA_FILE_FRINGE; - } - if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_DARK")) { - // It's a dark file, so change the file type - input->type = PM_FPA_FILE_DARK; - outImage->type = PM_FPA_FILE_DARK; - // Turn off compression --- there are just too many nasties that can happen - psFree(outImage->compression); - outImage->compression = NULL; - psFree(outImage->options); - outImage->options = NULL; - } - - // Turn off mask and variance output if we're not doing anything interesting - if (!options->doMaskBuild && outMask->save) { - psWarning("output mask image (BASE.MASK.FITS) requested, but not generated: skipping.\n"); - outMask->save = false; - } - if (!options->doVarianceBuild && outVariance->save) { - psWarning("output variance image (BASE.VARIANCE.FITS) requested, but not generated: skipping.\n"); - outVariance->save = false; - } - if (!options->doMaskBuild && chipMask->save) { - psWarning("output mask image (CHIP.MASK.FITS) requested, but not generated: skipping.\n"); - chipMask->save = false; - } - if (!options->doVarianceBuild && chipVariance->save) { - psWarning("output variance image (CHIP.VARIANCE.FITS) requested, but not generated: skipping.\n"); - chipVariance->save = false; - } - - if (psTraceGetLevel("ppImage.config") > 0) { - // Get a look inside all the files. - psMetadataIterator *filesIter = psMetadataIteratorAlloc(config->files, PS_LIST_HEAD, NULL); - psMetadataItem *item; // Item from iteration - fprintf(stderr, "Files:\n"); - while ((item = psMetadataGetAndIncrement(filesIter))) { - pmFPAfile *file = item->data.V; // File of interest - fprintf(stderr, "%s: %p %p %p (%p) %p\n", file->name, - file->src, file->fpa, - file->camera, file->fpa->camera, file->format); - } - psFree(filesIter); - } - - // Change the input dark type between the old (IMAGE) and new (multi-DARK). - // Hopefully this is a temporary change until we all move over to using the new dark types - bool mdok; // Status of MD lookup - if (options->doDark && psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { - pmFPAfile *dark = psMetadataLookupPtr(NULL, config->files, "PPIMAGE.DARK"); - assert(dark); - dark->type = PM_FPA_FILE_IMAGE; - } - - return (options); -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImagePhotom.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImagePhotom.c (revision 29946) +++ (revision ) @@ -1,69 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -# include "ppImage.h" - -// In this function, we perform the psphot analysis routine for the chip-mosaicked images -bool ppImagePhotom(psMetadata *stats, pmConfig *config, pmFPAview *view) { - - bool status; - pmCell *cell; - pmReadout *readout; - printf("%x %s\n",psErrorCodeLast(),psErrorCodeString(psErrorCodeLast())); - psphotInit(); - printf("%x %s\n",psErrorCodeLast(),psErrorCodeString(psErrorCodeLast())); - // find or define a pmFPAfile PSPHOT.INPUT - pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSPHOT.INPUT"); - if (!status) { - psError(PSPHOT_ERR_CONFIG, false, "PSPHOT.INPUT I/O file is not defined"); - return false; - } - printf("%x %s\n",psErrorCodeLast(),psErrorCodeString(psErrorCodeLast())); - // we make a new copy of the output chip to keep psphot from modifying the output image - pmChip *oldChip = pmFPAviewThisChip (view, input->src); - pmChip *newChip = pmFPAviewThisChip (view, input->fpa); - pmChipCopy (newChip, oldChip); - printf("%x %s\n",psErrorCodeLast(),psErrorCodeString(psErrorCodeLast())); - // iterate over the cells and readout for this chip - while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { - psLogMsg ("ppImagePhotom", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); - if (! cell->process || ! cell->file_exists) { continue; } - - // process each of the readouts - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (! readout->data_exists) { continue; } - printf("%x %s\n",psErrorCodeLast(),psErrorCodeString(psErrorCodeLast())); - // run the actual photometry analysis - if (!psphotReadout (config, view)) { - // This is likely a data quality issue - // XXX Split into multiple cases using error codes? - psErrorStackPrint(stderr, "Unable to perform photometry on image"); - psWarning("Unable to perform photometry on image --- suspect bad data quality."); - if (stats && psMetadataLookupS32(NULL, stats, "QUALITY") == 0) { - psMetadataAddS32(stats, PS_LIST_TAIL, "QUALITY", PS_META_REPLACE, - "Unable to perform photometry on image", psErrorCodeLast()); - } - psErrorClear(); - psphotFilesActivate(config, false); - } - - // we want to save the MASK as modified by psphot, but not the data or weight - // free the old mask and replace with a memory copy of the new mask - pmReadout *oldReadout = pmFPAviewThisReadout(view, input->src); - pmReadout *newReadout = pmFPAviewThisReadout(view, input->fpa); - psFree (oldReadout->mask); - oldReadout->mask = psMemIncrRefCounter(newReadout->mask); - } - } - - ppImageMemoryDump("photom"); - - // the PSPHOT.INPUT file is a temporary file used to carry PPIMAGE.CHIP to psphotReadout - // XXX not sure that this is needed... -// pmFPAfileActivate (config->files, false, "PSPHOT.INPUT"); - - return true; -} - -// XXX do we need to deactivate all files and activate the psphot ones explicitly? Index: anches/haf_branches/videophot2010/ppImage/src/ppImagePixelStats.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImagePixelStats.c (revision 29946) +++ (revision ) @@ -1,85 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -// calculate stats, including MD5 -bool ppImagePixelStats(pmConfig *config, psMetadata *stats, const ppImageOptions *options, - const pmFPAview *inputView) -{ - bool mdok; // Status of MD lookup - - // loop over the cells/readouts for this chip - pmFPAview *view = pmFPAviewAlloc(0); // View for local processing - *view = *inputView; - - // perform the analysis of for this FPA - pmFPAfile *output = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.OUTPUT"); - if (!output) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find output file (PPIMAGE.OUTPUT)."); - psFree(view); - return false; - } - - // select the corresponding chip - pmChip *chip = pmFPAviewThisChip(view, output->fpa); - if (!chip) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find requested chip."); - psFree(view); - return false; - } - - // Perform statistics for this chip - if (options->doStats) { - if (!ppStatsPixels(stats, output->fpa, view, options->maskValue, config)) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to generate stats for image."); - psFree(view); - return false; - } - - // extract the fringe amplitude from the analysis - if (options->doFringe && !ppStatsFringe(stats, chip, "FRINGE", "FRINGE.SOLUTION")) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to extract fringe solution for image."); - psFree(view); - return false; - } - - // extract the fringe residual amplitude from the analysis - if (options->doFringe && !ppStatsFringe(stats, chip, "FRINGE_RESID", "FRINGE.RESIDUAL.SOLUTION")) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to extract fringe solution for image."); - psFree(view); - return false; - } - } - - - view->cell = view->readout = -1; - pmCell *cell = NULL; // Cell from iteration - while ((cell = pmFPAviewNextCell(view, output->fpa, 1)) != NULL) { - if (!cell->process || !cell->file_exists) { - continue; - } - - // Add MD5 information for cell - pmHDU *hdu = pmHDUFromCell(cell); // HDU that owns the cell - pmReadout *readout = NULL; // Readout from iteration - while ((readout = pmFPAviewNextReadout(view, output->fpa, 1)) != NULL) { - const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); - const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); - - psString headerName = NULL; // Header name for MD5 - psStringAppend(&headerName, "MD5_%s_%s_%d", chipName, cellName, view->readout); - - psVector *md5 = psImageMD5(readout->image); // md5 hash - psString md5string = psMD5toString(md5); // String - psFree(md5); - psMetadataAddStr(hdu->header, PS_LIST_TAIL, headerName, PS_META_REPLACE, "Image MD5", md5string); - psFree(md5string); - psFree(headerName); - } - } - - psFree (view); - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageRebinReadout.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageRebinReadout.c (revision 29946) +++ (revision ) @@ -1,44 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageRebinChip (pmConfig *config, pmFPAview *view, ppImageOptions *options, char *outName) { - - pmCell *cell; - pmReadout *inReadout, *outReadout; - - pmFPAfile *outFile = psMetadataLookupPtr(NULL, config->files, outName); - if (outFile == NULL) return false; - - // XXX double check that chip != -1? - - pmChip *inChip = pmFPAviewThisChip (view, outFile->src); - pmChip *outChip = pmFPAviewThisChip (view, outFile->fpa); - if (!pmChipCopyStructure (outChip, inChip, outFile->xBin, outFile->yBin)) { - psError(PS_ERR_UNKNOWN, false, "Unable to copy chip structure."); - return false; - } - - while ((cell = pmFPAviewNextCell (view, outFile->src, 1)) != NULL) { - psLogMsg ("ppImageRebinChip", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); - if (! cell->process || ! cell->file_exists) { continue; } - - // process each of the readouts - while ((inReadout = pmFPAviewNextReadout (view, outFile->src, 1)) != NULL) { - if (! inReadout->data_exists) { continue; } - - outReadout = pmFPAviewThisReadout (view, outFile->fpa); - - // run the rebin code - if (!pmReadoutRebin(outReadout, inReadout, options->maskValue, outFile->xBin, outFile->yBin)) { - psError(PS_ERR_UNKNOWN, false, "Unable to rebin readout."); - return false; - } - } - } - - return true; -} - Index: anches/haf_branches/videophot2010/ppImage/src/ppImageReplaceBackground.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageReplaceBackground.c (revision 29946) +++ (revision ) @@ -1,184 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -// In this function, we perform the psphot analysis routine for the chip-mosaicked images -bool ppImageSubtractBackground(pmConfig *config, const pmFPAview *view, const ppImageOptions *options) -{ - psAssert(config, "Need configuration"); - psAssert(view, "Need view to chip"); - psAssert(options, "Need options"); - - if (!options->doBG) { - return true; - } - - bool status; // Status of MD lookup - pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.CHIP"); // File to correct - if (!status) { - psError(PS_ERR_UNEXPECTED_NULL, true, "PPIMAGE.CHIP file is not defined"); - return false; - } - - psMetadata *ppImageRecipe = psMetadataLookupPtr(NULL, config->recipes, RECIPE_NAME); - psAssert(ppImageRecipe, "Need PPIMAGE recipe"); - psMetadata *psphotRecipe = psMetadataLookupPtr(NULL, config->recipes, PSPHOT_RECIPE); - psAssert(psphotRecipe, "Need PSPHOT recipe"); - - // XXX Should this be options->maskValue or options->maskValue & ~options->satMask? - // The latter will leave saturated pixels high - psImageMaskType maskVal = options->maskValue; - - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMetadataAddImageMask(psphotRecipe, PS_LIST_TAIL, "MASK.PSPHOT", PS_META_REPLACE, "user-defined mask", maskVal); - - // Since we are working on a chip-mosaicked image, there should only be a single cell and readout - pmChip *chip = pmFPAviewThisChip(view, input->fpa); // Chip of interest - if (!chip) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find chip"); - return false; - } - if (chip->cells->n == 0) { - psWarning("Chip has no cells"); - return true; - } - if (chip->cells->n > 1) { - psWarning("Chip has %ld cells; only the first will be processed", chip->cells->n); - } - pmCell *cell = chip->cells->data[0]; // Cell of interest - if (!cell || !cell->process || !cell->file_exists) { - // Nothing to process - return true; - } - if (cell->readouts->n == 0) { - psWarning("Cell has no readouts"); - return true; - } - 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) { - // Nothing to process - return true; - } - psImage *image = ro->image, *mask = ro->mask; // Image and mask of interest - - // View corresponding to this readout - pmFPAview roView = *view; - roView.cell = roView.readout = 0; - - // If the background model file has not been defined, psphotModelBackground will generate it - pmReadout *modelRO = NULL; - pmFPAfile *modelFile = psMetadataLookupPtr(&status, config->files, "PSPHOT.BACKMDL"); // Background model - if (modelFile && modelFile->fpa) { - modelRO = pmFPAviewThisReadout(&roView, modelFile->fpa); // Background model - } - - // the background model has not been defined, or at least not generated - if (!modelFile || !modelRO) { - if (!psphotModelBackgroundReadoutFileIndex(config, &roView, "PPIMAGE.CHIP", 0)) { - psError(PS_ERR_UNKNOWN, false, "Unable to model background"); - return false; - } - // the model file should now at least be defined - modelFile = psMetadataLookupPtr(&status, config->files, "PSPHOT.BACKMDL"); // Background model - if (!modelFile) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to define background model I/O file"); - return false; - } - // now grab the readout from the correct location: - if (modelFile->mode == PM_FPA_MODE_INTERNAL) { - modelRO = modelFile->readout; - } else { - modelRO = pmFPAviewThisReadout(&roView, modelFile->fpa); - } - if (!modelRO) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find background model"); - return false; - } - } - psImageBinning *binning = psMetadataLookupPtr(&status, modelRO->analysis, - "PSPHOT.BACKGROUND.BINNING"); // Binning for model - if (!binning) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find background binning"); - return false; - } - -# define USE_UNBIN 1 -# if (USE_UNBIN) - // select background pixels, from output background file, or create - pmReadout *background = NULL; - pmFPAfile *backfile = psMetadataLookupPtr (&status, config->files, "PSPHOT.BACKGND"); - if (backfile) { - // we are using PSPHOT.BACKGND as an I/O file: select readout or create - if (backfile->mode == PM_FPA_MODE_INTERNAL) { - background = backfile->readout; - } else { - background = pmFPAviewThisReadout (&roView, backfile->fpa); - } - if (background == NULL) { - // readout does not yet exist: create from input - pmFPAfileCopyStructureView (backfile->fpa, input->fpa, 1, 1, &roView); - background = pmFPAviewThisReadout (&roView, backfile->fpa); - if ((image->numCols != background->image->numCols) || (image->numRows != background->image->numRows)) { - psError (PSPHOT_ERR_PROG, true, "inconsistent sizes for background dimensions"); - return false; - } - } - } else { - background = pmFPAfileDefineInternal (config->files, "PSPHOT.BACKGND", image->numCols, image->numRows, PS_TYPE_F32); - } - psF32 **backData = background->image->data.F32; - - // linear interpolation to full-scale - if (!psImageUnbin (background->image, modelRO->image, binning)) { - psError (PSPHOT_ERR_PROG, true, "inconsistent sizes for unbinning"); - return false; - } - - // Do the background subtraction - int numCols = image->numCols, numRows = image->numRows; // Size of image - for (int y = 0; y < numRows; y++) { - for (int x = 0; x < numCols; x++) { - if (mask && mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & maskVal) { - image->data.F32[y][x] = 0.0; - } else { - float value = backData[y][x]; - if (!isfinite(value)) { - image->data.F32[y][x] = NAN; - mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= options->lowMask; - } else { - image->data.F32[y][x] -= value; - } - } - } - } -# else - // Do the background subtraction - int numCols = image->numCols, numRows = image->numRows; // Size of image - for (int y = 0; y < numRows; y++) { - for (int x = 0; x < numCols; x++) { - if (mask && mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & maskVal) { - image->data.F32[y][x] = 0.0; - } else { - float value = psImageUnbinPixel(x + 0.5, y + 0.5, modelRO->image, binning); // Background value - if (!isfinite(value)) { - image->data.F32[y][x] = NAN; - mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= options->lowMask; - } else { - image->data.F32[y][x] -= value; - } - } - } - } -# endif - - // XXX should these really be here?? (probably not...) - // pmFPAfileDropInternal(config->files, "PSPHOT.BACKMDL"); - // pmFPAfileDropInternal(config->files, "PSPHOT.BACKMDL.STDEV"); - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageSetMaskBits.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageSetMaskBits.c (revision 29946) +++ (revision ) @@ -1,60 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options) { - - if (!pmConfigMaskSetBits(&options->maskValue, &options->markValue, config)) { - psError (PS_ERR_UNKNOWN, true, "Unable to define the mask bit values"); - return false; - } - - // at this point we know we have valid values for required entries SAT, BAD, FLAT, BLANK: - - // mask for bad flat corrections - options->flatMask = pmConfigMaskGet("FLAT", config); - psAssert (options->flatMask, "flat mask not set"); - - // mask for bad dark corrections - options->darkMask = pmConfigMaskGet("DARK", config); - psAssert (options->darkMask, "dark mask not set"); - - // mask for non-existent data (default to DETECTOR if not defined) - options->blankMask = pmConfigMaskGet("BLANK", config); - psAssert (options->blankMask, "blank mask not set"); - - // mask for saturated data (default to RANGE if not defined) - options->satMask = pmConfigMaskGet("SAT", config); - psAssert (options->satMask, "sat mask not set"); - - // mask for below-range data (default to RANGE if not defined) - options->lowMask = pmConfigMaskGet("LOW", config); - if (!options->lowMask) { - // look up old name for backward compatability - options->lowMask = pmConfigMaskGet("BAD", config); - } - psAssert (options->lowMask, "low mask not set"); - - // mask for suspect regions due to burntool if we need to. - if (options->doMaskBurntool) { - options->burntoolMask = pmConfigMaskGet("BURNTOOL",config); - psAssert (options->burntoolMask, "burntool mask not set"); - } - - // save MASK and MARK on the PSPHOT recipe - psMetadata *recipe = psMetadataLookupPtr (NULL, config->recipes, PSPHOT_RECIPE); - if (!recipe) { - psError(PSPHOT_ERR_CONFIG, false, "missing recipe %s", PSPHOT_RECIPE); - return false; - } - - // set maskValue and markValue in the psphot recipe - psMetadataAddImageMask(recipe, PS_LIST_TAIL, "MASK.PSPHOT", PS_META_REPLACE, "user-defined mask", - options->maskValue); - psMetadataAddImageMask(recipe, PS_LIST_TAIL, "MARK.PSPHOT", PS_META_REPLACE, "user-defined mask", - options->markValue); - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageSetThreads.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageSetThreads.c (revision 29946) +++ (revision ) @@ -1,26 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -bool ppImageThread_ppImageDetrendReadout (psThreadJob *job) { - - pmConfig *config = job->args->data[0]; - ppImageOptions *options = job->args->data[1]; - pmFPAview *view = job->args->data[2]; - - bool status = ppImageDetrendReadout(config, options, view); - return status; -} - -bool ppImageSetThreads () { - - psThreadTask *task = NULL; - - task = psThreadTaskAlloc ("PPIMAGE_DETREND_READOUT", 3); - task->function = &ppImageThread_ppImageDetrendReadout; - psThreadTaskAdd (task); - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageStatsOutput.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageStatsOutput.c (revision 29946) +++ (revision ) @@ -1,40 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" - -// write stats to output file -bool ppImageStatsOutput(pmConfig *config, psMetadata *stats, const ppImageOptions *options) -{ - bool mdok; - - // measure statistics, or ignore? - if (!options->doStats) { - return true; - } - - // get the output stats filename - const char *statsName = psMetadataLookupStr(&mdok, config->arguments, "STATS"); // Filename for statistics - if (!statsName || !strlen(statsName)) { - psError(PS_ERR_UNEXPECTED_NULL, false, "missing STATS entry in arguments list."); - return false; - } - - // Write out - psString resolved = pmConfigConvertFilename(statsName, config, true, true); // Resolved filename - if (!resolved) { - psError(psErrorCodeLast(), false, "Unable to resolve statistics file name"); - return false; - } - if (!psMetadataConfigWrite(stats, resolved)) { - psError(psErrorCodeLast(), false, "Unable to serialize stats metadata.\n"); - psFree(resolved); - return false; - } - psFree(resolved); - - pmConfigRunFilenameAddWrite(config, "STATS", statsName); - - return true; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageVersion.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageVersion.c (revision 29946) +++ (revision ) @@ -1,115 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include "ppImage.h" -#include "ppImageVersionDefinitions.h" - -#ifndef PPIMAGE_VERSION -#error "PPIMAGE_VERSION is not set" -#endif -#ifndef PPIMAGE_BRANCH -#error "PPIMAGE_BRANCH is not set" -#endif -#ifndef PPIMAGE_SOURCE -#error "PPIMAGE_SOURCE is not set" -#endif - -psString ppImageVersion(void) -{ - char *value = NULL; - psStringAppend(&value, "%s@%s", PPIMAGE_BRANCH, PPIMAGE_VERSION); - return value; -} - -psString ppImageSource(void) -{ - return psStringCopy(PPIMAGE_SOURCE); -} - -psString ppImageVersionLong(void) -{ - psString version = ppImageVersion(); // Version, to return - psString source = ppImageSource(); // Source - - psStringPrepend(&version, "ppImage "); - psStringAppend(&version, " from %s, built %s, %s", source, __DATE__, __TIME__); - psFree(source); - -#ifdef __OPTIMIZE__ - psStringAppend(&version, " optimised"); -#else - psStringAppend(&version, " unoptimised"); -#endif - - return version; -}; - -bool ppImageVersionHeader(psMetadata *header) -{ - PS_ASSERT_METADATA_NON_NULL(header, false); - - psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now - psString timeString = psTimeToISO(time); // The time in an ISO string - psFree(time); - psString history = NULL; // History string - psStringAppend(&history, "ppImage at %s", timeString); - psFree(timeString); - psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, history); - psFree(history); - - psLibVersionHeader(header); - psModulesVersionHeader(header); - psphotVersionHeader(header); - psastroVersionHeader(header); - ppStatsVersionHeader(header); - - psString version = ppImageVersion(); // ppImage software version - psString source = ppImageSource(); // ppImage software source - - psMetadataAddStr(header, PS_LIST_TAIL, "IMAGE_V", PS_META_REPLACE, NULL, PPIMAGE_VERSION); - - psStringPrepend(&version, "ppImage version: "); - psStringPrepend(&source, "ppImage source: "); - - psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, version); - psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, source); - - psFree(version); - psFree(source); - - return true; -} - - -void ppImageVersionPrint(void) -{ - psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now - psString timeString = psTimeToISO(time); // The time in an ISO string - psFree(time); - psLogMsg("ppImage", PS_LOG_INFO, "ppImage at %s", timeString); - psFree(timeString); - - psString pslib = psLibVersionLong();// psLib version - psString psmodules = psModulesVersionLong(); // psModules version - psString psphot = psphotVersionLong(); // psphot version - psString psastro = psastroVersionLong(); // psastro version - psString ppStats = ppStatsVersionLong(); // ppStats version - psString ppImage = ppImageVersionLong(); // ppImage version - - psLogMsg("ppImage", PS_LOG_INFO, "%s", pslib); - psLogMsg("ppImage", PS_LOG_INFO, "%s", psmodules); - psLogMsg("ppImage", PS_LOG_INFO, "%s", psphot); - psLogMsg("ppImage", PS_LOG_INFO, "%s", psastro); - psLogMsg("ppImage", PS_LOG_INFO, "%s", ppStats); - psLogMsg("ppImage", PS_LOG_INFO, "%s", ppImage); - - psFree(pslib); - psFree(psmodules); - psFree(psphot); - psFree(psastro); - psFree(ppStats); - psFree(ppImage); - - return; -} Index: anches/haf_branches/videophot2010/ppImage/src/ppImageVersionDefinitions.h.in =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/ppImageVersionDefinitions.h.in (revision 29946) +++ (revision ) @@ -1,8 +1,0 @@ -#ifndef PPIMAGE_VERSION_DEFINITIONS_H -#define PPIMAGE_VERSION_DEFINITIONS_H - -#define PPIMAGE_VERSION @PPIMAGE_VERSION@ // SVN version -#define PPIMAGE_BRANCH @PPIMAGE_BRANCH@ // SVN branch -#define PPIMAGE_SOURCE @PPIMAGE_SOURCE@ // SVN source - -#endif Index: /branches/haf_branches/videophot2010/ppImage/src/psvideoLoop.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideoLoop.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideoLoop.c (revision 29947) @@ -0,0 +1,141 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "psvideophot.h" + +#define ESCAPE(MESSAGE) { \ + psError(PS_ERR_UNKNOWN, false, MESSAGE); \ + psFree(view); \ + pmFPAfileFreeSetStrict(false); \ + return false; \ +} + +bool psvideophotLoop(pmConfig *config, psvideophotOptions *options) +{ + psMetadata *stats = NULL; // Statistics to output + float timeDetrend = 0; // Amount of time spent in detrend + float timePhot = 0; // Amount of time spent in photometry + + if (options->doStats) { + stats = psMetadataAlloc(); + psMetadataAddS32(stats, PS_LIST_TAIL, "QUALITY", 0, "No problems", 0); + } + + bool status; // Status of MD lookup + + pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PSVIDEOPHOT.INPUT"); + + if (!status) { + psErrorStackPrint(stderr, "Can't find input data!\n"); + psvideophotCleanup(config, options); + exit(PS_EXIT_PROG_ERROR); + } + + pmConfigCamerasCull(config, NULL); + pmConfigRecipesCull(config, "PSVIDEOPHOT,PPSTATS,PSPHOT,MASKS,PSASTRO,JPEG"); + + 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 ("psvideophotLoop", 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"); + } + + + psTimerStart(TIMER_DETREND); + pmCell *cell; // Cell from chip + while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { + psLogMsg ("psvideophotLoop", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (!cell->process || !cell->file_exists) { + continue; + } + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE("load failure for Cell"); + } + + // Put version information into the header + pmHDU *hdu = pmHDUGetHighest(input->fpa, chip, cell); + if (hdu && hdu != lastHDU) { + psvideophotVersionHeader(hdu->header); + lastHDU = hdu; + } + + // XXX for now, skip the video cells (cell->readouts->n > 1) + if (cell->readouts->n <2) { + psWarning("Skipping Non-Video Cell for psvideophotDetrendReadout"); + continue; + } + + // process each of the readouts + pmReadout *readout; // Readout from cell + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE("load failure for Readout"); + } + if (!readout->data_exists) { + continue; + } + + } + + + + } + // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT + timeDetrend += psTimerClear(TIMER_DETREND); + + // we perform photometry on the readouts of this chip in the output + + psTimerStart(TIMER_PHOT); + timePhot += psTimerClear(TIMER_PHOT); + + view->cell = -1; + while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { + if (!cell->process || !cell->file_exists) { + continue; + } + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for Cell"); + } + } + + // Close chip + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for Chip"); + } + } + + if (psTraceGetLevel("psvideophot") >= 3) { + psvideophotFileCheck(config); + } + + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for FPA"); + } + psFree(view); + + // Dump configuration + psString dump_file = psMetadataLookupStr(&status, config->arguments, "DUMP_CONFIG"); + if (dump_file) { + if (!pmConfigDump(config, dump_file)) { + ESCAPE("Unable to dump configuration."); + } + } + + + psFree (stats); + + return true; +} Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophot.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophot.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophot.c (revision 29947) @@ -0,0 +1,48 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "psvideophot.h" + +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 = psvideophotArguments(argc, argv); + if (config == NULL) { + psErrorStackPrint(stderr, "Unable to parse command-line arguments."); + psvideophotCleanup(config, NULL); + exit(PS_EXIT_CONFIG_ERROR); + } + + psvideophotVersionPrint(); + + // define recipe options + // define the active I/O files + psvideophotOptions *options = psvideophotParseCamera(config); + if (options == NULL) { + psErrorStackPrint(stderr, "Unable to parse camera."); + psvideophotCleanup(config, options); + exit(PS_EXIT_CONFIG_ERROR); + } + + // Image Arithmetic Loop + if (!psvideophotLoop(config, options)) { + psErrorStackPrint(stderr, "Unable to loop over input"); + psvideophotCleanup(config, options); + exit(PS_EXIT_SYS_ERROR); + } + + psLogMsg("psvideophot", PS_LOG_INFO, "Complete psvideophot run: %f sec\n", psTimerMark(TIMER_TOTAL)); + + // Cleaning up + // psvideophotCleanup(config, options); + + return PS_EXIT_SUCCESS; +} Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophot.h =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophot.h (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophot.h (revision 29947) @@ -0,0 +1,293 @@ +#ifndef PS_VIDEOPHOT_H +#define PS_VIDEOPHOT_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" + +#define RECIPE_NAME "PSVIDEOPHOT" // Name of the recipe to use +#define TIMER_TOTAL "PSVIDEOPHOT.TOTAL" // Name of timer for total time +#define TIMER_DETREND "PSVIDEOPHOT.DETREND" // Name of timer for detrend time +#define TIMER_PHOT "PSVIDEOPHOT.PHOT" // Name of timer for photometry time + +// Options for psvideophot processing +typedef struct { + // actions which psvideophot should perform + 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 doPatternRow; // Row pattern correction + bool doPatternCell; // Cell pattern correction + 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 doMaskStats; // Calculate mask statistics + + 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 correction + int patternRowOrder; // Polynomial order + int patternRowIter; // Clipping iterations + float patternRowRej; // Clipping threshold + float patternRowThresh; // Ignore threshold + psStatsOptions patternRowMean; // Statistic for mean + psStatsOptions patternRowStdev; // Statistic for stdev + psStatsOptions patternCellBG; // statistic for background + psStatsOptions patternCellMean; // Statistic for mean + + int remnanceSize; // Size for remnance detection + float remnanceThresh; // Threshold for remnance detection + + char *normClass; // class to use for per-class normalization + + psU16 maskstat_static; + psU16 maskstat_dynamic; + psU16 maskstat_magic; + psU16 maskstat_advisory; + +} psvideophotOptions; + +// Cells to be used in the detrend +typedef struct { + pmCell *input; // The input cell, to be operated upon + pmCell *mask; // The bad pixel mask + pmCell *bias; // The bias correction + pmCell *dark; // The dark correction + pmCell *flat; // The flat-field correction +} psvideophotDetrend; + +psvideophotOptions *psvideophotOptionsAlloc(void); + +// Determine the processing options +psvideophotOptions *psvideophotOptionsParse(pmConfig *config); + +// Get the configuration +pmConfig *psvideophotArguments(int argc, char **argv); + +// Determine what type of camera, and initialise +psvideophotOptions *psvideophotParseCamera(pmConfig *config); +bool psvideophotSetMaskBits (pmConfig *config, psvideophotOptions *options); + +// apply the cell flips to the input data before analysis +bool psvideophotParityFlip (pmConfig *config, const psvideophotOptions *options, const pmFPAview *view, bool native); + +// Loop over the input +bool psvideophotLoop(pmConfig *config, psvideophotOptions *options); + +// free memory, check for leaks +void psvideophotCleanup (pmConfig *config, psvideophotOptions *options); + +// perform the detrend analysis on the current readout +bool psvideophotDetrendReadout (pmConfig *config, psvideophotOptions *options, pmFPAview *view); + +bool psvideophotDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, psvideophotOptions *options); + +//bool psvideophotDetrendNonLinear(pmReadout *input, psvideophotOptions *options); +bool psvideophotDetrendNonLinear(pmReadout *input, pmFPAview *linearity, pmConfig *config); +bool psvideophotDetrendNonLinearLookup(pmReadout *input, psMetadataItem *dataItem); +bool psvideophotDetrendNonLinearPolynomial(pmReadout *input, psMetadataItem *dataItem); + +bool psvideophotDetrendCell(psvideophotDetrend *detrend, psvideophotOptions *options, pmConfig *config); +bool psvideophotDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, psvideophotOptions *options); +pmReadout* psvideophotDetrendSelectFirst(pmCell *cell, char *name, bool doThis); + +bool psvideophotDetrendFree(pmConfig *config, pmFPAview *view); +bool psvideophotFringeFree(pmConfig *config, pmFPAview *view); + +bool psvideophotCheckCTE(pmConfig *config, psvideophotOptions *options, pmFPAview *view); + +bool psvideophotBurntoolMask(pmConfig *config, psvideophotOptions *options, pmFPAview *view, pmReadout *mask); + +bool psvideophotDetrendPatternApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, const psvideophotOptions *options); + +// Record which detrend file was used for the detrending +bool psvideophotDetrendRecord( + pmCell *cell, // Cell of interest + const pmConfig *config, // Configuration + const psvideophotOptions *options, // Processing options + const pmFPAview *view // View to cell + ); + +bool psvideophotRebinChip (pmConfig *config, pmFPAview *view, psvideophotOptions *options, char *outName); + +bool psvideophotPhotom(psMetadata *stats, pmConfig *config, pmFPAview *view); +bool psvideophotAstrom(pmConfig *config, psMetadata *stats); +bool psvideophotAddstar(pmConfig *config); + +// Subtract background from the chip-mosaicked image +bool psvideophotSubtractBackground( + pmConfig *config, // Configuration + const pmFPAview *view, // View to chip of interest + const psvideophotOptions *options // Processing options + ); + +bool psvideophotMosaicChip (pmConfig *config, const psvideophotOptions *options, const pmFPAview *view, + const char *outFile, const char *inFile); +bool psvideophotMosaicFPA (pmConfig *config, const psvideophotOptions *options, + const char *outFile, const char *inFile); + +bool psvideophotSetMaskBits (pmConfig *config, psvideophotOptions *options); + +void psvideophotFileCheck (pmConfig *config); + +// functions used by ppFocus +pmConfig *ppFocusArguments(int argc, char **argv); +psvideophotOptions *ppFocusParseCamera (pmConfig *config, int entry); +bool ppFocusGetFWHM (pmConfig *config, psVector *focus, psVector *fwhm); +bool ppFocusFitFWHM (pmConfig *config, psVector *focus, psVector *fwhm); + +void ppFocusDropCamera (pmConfig *config); + +bool psvideophotDefineFile (pmConfig *config, pmFPA *input, char *filerule, char *argname, pmFPAfileType fileType, pmDetrendType detrendType); + +// write stats to output file +bool psvideophotStatsOutput(pmConfig *config, // Configuration + psMetadata *stats, // Statistics output + const psvideophotOptions *options // Options + ); + + +// measure the crosstalk signal +bool psvideophotMeasureCrosstalk(pmConfig *config, psvideophotOptions *options, pmFPAview *view); + +// correct the crosstalk signal +bool psvideophotCorrectCrosstalk(pmConfig *config, psvideophotOptions *options, pmFPAview *view); + +// Measure fringes +bool psvideophotDetrendFringeMeasure(pmReadout *readout, // Readout to measure + pmCell *fringe, // Fringe cell (each readout is a different component) + const bool isResidual, + const psvideophotOptions *options // Options + ); + +// Solve the fringe system +bool psvideophotDetrendFringeSolve(pmChip *scienceChip, // Chip with science + const pmChip *refChip, // Chip with reference fringes + const bool isResidual, + const psvideophotOptions *options // Options + ); + +// Generate fringe frame +bool psvideophotDetrendFringeGenerate(pmCell *science, // Science cell + pmCell *fringes, // Fringe cell, one readout per fringe component + const psvideophotOptions *options // Options + ); + + +bool psvideophotDetrendFringeApply (pmConfig *config, // config + pmChip *chip, // science chip + const pmFPAview *inputView, // current view + const psvideophotOptions *options // options + ); + +/// Return short version information +psString psvideophotVersion(void); + +/// Return software source +psString psvideophotSource(void); + +/// Return long version information +psString psvideophotVersionLong(void); + +/// Populate the header with version information for all dependencies +bool psvideophotVersionHeader(psMetadata *metadata ///< Header to populate + ); + +/// Print version information +void psvideophotVersionPrint(void); + + +// calculate stats, including MD5 +bool psvideophotPixelStats(pmConfig *config,// Configuration + psMetadata *stats, // Statistics output + const psvideophotOptions *options, // Options + const pmFPAview *inputView // View to data + ); + +// Calculate Mask statistics +bool psvideophotMaskStats(pmConfig *config, pmFPAview *view, psMetadata *stats); + +// calculate stats from headers and concepts +bool psvideophotMetadataStats(pmConfig *config, // Configuration + psMetadata *stats, // Statistics output + const psvideophotOptions *options // Options + ); + +void psvideophotFileCheck(pmConfig *config); + +/// Dump memory summary to text file +void psvideophotMemoryDump(const char *description); + +#endif Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotArguments.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotArguments.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotArguments.c (revision 29947) @@ -0,0 +1,173 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "psvideophot.h" + +static void usage (void) { + fprintf(stderr, "USAGE: psvideophot [-file INPUT.fits] [-list INPUT.txt] OUTPUT\n\n"); + fprintf(stderr, "Optional arguments:\n"); + fprintf(stderr, "\t-stats STATS.mdc: Output statistics into STATS.mdc\n"); + fprintf(stderr, "\t-isfringe: The input image contains fringe data.\n"); + fprintf(stderr, "\t-isdark: The input image contains dark data.\n"); + fprintf(stderr, "\t-usemask MASKVAL: Use this mask value (override recipe).\n"); + fprintf(stderr, "\t-chip CHIPNUM: Only process this chip number.\n"); + fprintf(stderr, "\t-norm VALUE: Divide through by this value when done.\n"); + fprintf(stderr, "\t-normlist file.mdc: normalizations by class_id.\n"); + fprintf(stderr, "\t-video: process video cells\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "Input options (single file / file list):\n"); + fprintf(stderr, "\t-noisemap/-noisemaplist: Noise Map image.\n"); + fprintf(stderr, "\t-bias/-biaslist: Bias image.\n"); + fprintf(stderr, "\t-dark/-darklist: Dark image.\n"); + fprintf(stderr, "\t-shutter/-shutterlist: Shutter image.\n"); + fprintf(stderr, "\t-flat/-flatlist: Flat image.\n"); + fprintf(stderr, "\t-mask/-masklist: Mask image.\n"); + fprintf(stderr, "\t-fringe/-fringelist: Fringe image and data.\n"); + fprintf(stderr, "\t-linearity/-linearlist: linearity correction file.\n"); + fprintf(stderr, "\n"); + exit (2); +} + +pmConfig *psvideophotArguments(int argc, char **argv) +{ + int argnum; // Argument number of interest + + if (argc == 1) { + usage(); + } + + if (psArgumentGet (argc, argv, "-version")) { + psString version; + version = psvideophotVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = ppStatsVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psphotVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psastroVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psModulesVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psLibVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + exit (0); + } + + // load the site-wide configuration information + pmConfig *config = pmConfigRead(&argc, argv, RECIPE_NAME); + if (config == NULL) { + psErrorStackPrint(stderr, "Can't find site configuration!\n"); + exit(EXIT_FAILURE); + } + + // save the following additional recipe values based on command-line options + // these options override the PSVIDEOPHOT recipe values loaded from recipe files + psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); + + // save these recipe options until we have loaded the options + // psMetadata *options = psMetadataAlloc (); + // psMetadataAddPtr (config->arguments, PS_LIST_TAIL, "PSVIDEOPHOT.OPTIONS", PS_DATA_METADATA, "", options); + + if ((argnum = psArgumentGet(argc, argv, "-stats"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "STATS", PS_META_REPLACE, + "Filename for summary statistics", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-isfringe"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUT_IS_FRINGE", PS_META_REPLACE, + "Input is fringe image", true); + } + if ((argnum = psArgumentGet(argc, argv, "-isdark"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUT_IS_DARK", PS_META_REPLACE, + "Input is dark image", true); + } + + if ((argnum = psArgumentGet(argc, argv, "-video"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "PROCESS_VIDEO", PS_META_REPLACE, "process video cells", true); + } + + if ((argnum = psArgumentGet(argc, argv, "-visual"))) { + psArgumentRemove(argnum, &argc, argv); + pmVisualSetVisual(true); + } + + // Number of threads + if ((argnum = psArgumentGet(argc, argv, "-threads"))) { + psArgumentRemove(argnum, &argc, argv); + int nThreads = atoi(argv[argnum]); + psMetadataAddS32(config->arguments, PS_LIST_TAIL, "NTHREADS", 0, "number of warp threads", nThreads); + psArgumentRemove(argnum, &argc, argv); + + // create the thread pool with number of desired threads, supplying our thread launcher function + // XXX need to determine the number of threads from the config data + psThreadPoolInit (nThreads); + } + + // the following options override the PSVIDEOPHOT recipe options + + // recipe option: -usemask : override MASK setting in recipe + if ((argnum = psArgumentGet(argc, argv, "-usemask"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(options, PS_LIST_TAIL, "MASK", PS_META_REPLACE, "", true); + psArgumentRemove(argnum, &argc, argv); + } + + // XXX add other PSVIDEOPHOT recipe options here + + // the input file is a required argument; if not found, we will exit + pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list"); + + // if these command-line options are supplied, load the file name lists into config->arguments + // override any configuration-specified source for these files + pmConfigFileSetsMD (config->arguments, &argc, argv, "NOISEMAP", "-noisemap", "-noisemaplist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "BIAS", "-bias", "-biaslist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "DARK", "-dark", "-darklist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "SHUTTER", "-shutter", "-shutterlist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "FLAT", "-flat", "-flatlist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "MASK", "-mask", "-masklist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "FRINGE", "-fringe", "-fringelist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "LINEARITY", "-linearity", "-linearlist"); + + // chip selection is used to limit chips to be processed + if ((argnum = psArgumentGet (argc, argv, "-chip"))) { + psArgumentRemove (argnum, &argc, argv); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "CHIP_SELECTIONS", PS_DATA_STRING, "", argv[argnum]); + psArgumentRemove (argnum, &argc, argv); + } + + // Optional normalization factor + if ((argnum = psArgumentGet(argc, argv, "-norm"))) { + psArgumentRemove(argnum, &argc, argv); + float norm = atof(argv[argnum]); + psMetadataAddF32(config->arguments, PS_LIST_TAIL, "NORMALIZATION", 0, + "Normalisation to apply", norm); + psArgumentRemove(argnum, &argc, argv); + } + + // Optional per-class normalization table + if ((argnum = psArgumentGet(argc, argv, "-normlist"))) { + psArgumentRemove(argnum, &argc, argv); + + unsigned int nFail = 0; + psMetadata *normlist = psMetadataConfigRead (NULL, &nFail, argv[argnum], false); + // XXX allow this file to be in nebulous? + + psMetadataAddMetadata(config->arguments, PS_LIST_TAIL, "NORMALIZATION.TABLE", 0, "Normalization to apply", normlist); + psFree (normlist); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-dumpconfig"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "DUMP_CONFIG", PS_META_REPLACE, + "Filename for configuration dump", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + 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: /branches/haf_branches/videophot2010/ppImage/src/psvideophotCleanup.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotCleanup.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotCleanup.c (revision 29947) @@ -0,0 +1,35 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "psvideophot.h" + +void psvideophotCleanup (pmConfig *config, psvideophotOptions *options) +{ + if (psErrorCodeLast() != PS_ERR_NONE) { + pmFPAfileFreeSetStrict(false); + } + + // Free memory used by psvideophot + psFree(options); + psFree(config); + + // Free memory used by psModules + pmSourceFitSetDone (); + pmConceptsDone(); + pmConfigDone(); + pmModelClassCleanup(); + pmVisualCleanup (); + + // Free memory used by psLib + psLibFinalize(); + + // psMemBlock **memblocks; + // int Nleaks = psMemCheckLeaks (0, &memblocks, stderr, false); + // fprintf (stderr, "Found %d leaks at %s\n", Nleaks, "psvideophot"); + + // fprintf(stderr, "Found %d leaks at %s\n", psMemCheckLeaks (0, NULL, NULL, false), "psvideophot"); + psLogMsg("psvideophot", PS_LOG_INFO, "Memory leaks: %d\n", psMemCheckLeaks(0, NULL, stdout, false)); + + return; +} Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotDefineFile.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotDefineFile.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotDefineFile.c (revision 29947) @@ -0,0 +1,56 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "psvideophot.h" + +bool psvideophotDefineFile(pmConfig *config, pmFPA *input, char *filerule, char *argname, + pmFPAfileType fileType, pmDetrendType detrendType) +{ + bool status; + pmFPAfile *file = NULL; // File to be defined + + if (!file) { + // look for the file on the argument list + file = pmFPAfileDefineFromArgs(&status, config, filerule, argname); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition ARG LIST"); + return false; + } + } + if (!file) { + // look for the file on the RUN metadata + file = pmFPAfileDefineFromRun(&status, NULL, config, filerule); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition RUN"); + return false; + } + } + if (!file) { + // look for the file in the camera config table + file = pmFPAfileDefineFromConf(&status, config, filerule); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition CONFIG"); + return false; + } + } + if (!file) { + // look for the file to be loaded from the detrend database + file = pmFPAfileDefineFromDetDB(&status, config, filerule, input, detrendType); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition DETREND"); + return false; + } + } + + if (!file) { + return false; + } + + if (file->type != fileType) { + psError(PS_ERR_IO, true, "%s is not of type %s", filerule, pmFPAfileStringFromType(fileType)); + return false; + } + return true; +} + Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotFileCheck.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotFileCheck.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotFileCheck.c (revision 29947) @@ -0,0 +1,60 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "psvideophot.h" + +void psvideophotFileCheck (pmConfig *config) { + + // add the output names to the output-type files + psMetadataItem *item = NULL; + psMetadataIterator *iter = psMetadataIteratorAlloc (config->files, PS_LIST_HEAD, NULL); + while ((item = psMetadataGetAndIncrement (iter)) != NULL) { + pmFPAfile *file = item->data.V; + pmFPA *fpa = file->fpa; + fprintf (stderr, "file %s\n", file->name); + if (!fpa) { + fprintf (stderr, " has no FPA\n"); + continue; + } + if (fpa->hdu) { + if (fpa->hdu->images) fprintf (stderr, " (%d,%d) images\n", -1, -1); + if (fpa->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", -1, -1); + if (fpa->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", -1, -1); + if (fpa->hdu->header) fprintf (stderr, " (%d,%d) header\n", -1, -1); + } else { + // fprintf (stderr, " has no fpa data (%d,%d)\n", -1, -1); + } + for (int i = 0; i < fpa->chips->n; i++) { + pmChip *chip = fpa->chips->data[i]; + if (chip->hdu) { + if (chip->hdu->images) fprintf (stderr, " (%d,%d) images\n", i, -1); + if (chip->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", i, -1); + if (chip->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", i, -1); + if (chip->hdu->header) fprintf (stderr, " (%d,%d) header\n", i, -1); + } else { + // fprintf (stderr, " has no chip data (%d,%d)\n", i, -1); + } + for (int j = 0; j < chip->cells->n; j++) { + pmCell *cell = chip->cells->data[j]; + if (cell->hdu) { + if (cell->hdu->images) fprintf (stderr, " (%d,%d) images\n", i, j); + if (cell->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", i, j); + if (cell->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", i, j); + if (cell->hdu->header) fprintf (stderr, " (%d,%d) header\n", i, j); + } else { + // fprintf (stderr, " has no cell data (%d,%d)\n", i, j); + } + for (int k = 0; k < cell->readouts->n; k++) { + pmReadout *readout = cell->readouts->data[k]; + if (readout) { + if (readout->image) fprintf (stderr, " (%d,%d,%d) image\n", i, j, k); + if (readout->variance) fprintf (stderr, " (%d,%d,%d) variance\n", i, j, k); + if (readout->mask) fprintf (stderr, " (%d,%d,%d) masks\n", i, j, k); + } + } + } + } + } + psFree (iter); +} Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotOptions.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotOptions.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotOptions.c (revision 29947) @@ -0,0 +1,258 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "psvideophot.h" + +static void imageOptionsFree(psvideophotOptions *options) +{ + psFree(options->overscan); + // psFree(options->nonLinearData); + // psFree(options->nonLinearSource); +} + +psvideophotOptions *psvideophotOptionsAlloc(void) +{ + psvideophotOptions *options = psAlloc(sizeof(psvideophotOptions)); + psMemSetDeallocator(options, (psFreeFunc)imageOptionsFree); + + // actions which psvideophot should perform + options->doMaskBuild = false; // Build internal mask + options->doMaskSat = false; // mask saturated pixels + options->doMaskLow = false; // mask low pixels + options->doMaskBurntool = false; // mask potential burntool trails + options->doVarianceBuild = false; // Build internal variance + options->doMask = false; // Mask bad pixels + options->doNonLin = false; // Non-linearity correction + options->doOverscan = false; // Overscan subtraction + options->doNoiseMap = false; // Apply Read Noise Map + options->doBias = false; // Bias subtraction + options->doDark = false; // Dark subtraction + options->doRemnance = false; // Remnance masking + options->doShutter = false; // Shutter correction + options->doFlat = false; // Flat-field normalisation + options->doPatternRow = false; // Row pattern correction + options->doPatternCell = false; // Cell pattern correction + options->doFringe = false; // Fringe subtraction + options->doPhotom = false; // Source identification and photometry + options->doAstromChip = false; // Astrometry (per-chip) + options->doAstromMosaic = false; // Astrometry (full-mosaic) + options->doStats = false; // Measure and save image statistics + options->checkCTE = false; // Measure pixel-based variance + options->applyParity = false; // Apply Cell parities + options->doMaskStats = false; // Calculate mask fractions + + // output files requested + options->BaseFITS = false; // create output image + options->BaseMaskFITS = false; // create output mask image + options->BaseVarianceFITS = false; // create output variance image + + options->ChipFITS = false; // create output chip-mosaic image + options->ChipMaskFITS = false; // create output chip-mosaic mask image + options->ChipVarianceFITS = false; // create output chip-mosaic variance image + + options->FPA1FITS = false; // create fpa-mosaic binned image (scale 1) + options->FPA2FITS = false; // create fpa-mosaic binned image (scale 2) + options->Bin1FITS = false; // create binned image (scale 1) + options->Bin2FITS = false; // create binned image (scale 2) + options->Bin1JPEG = false; // create jpeg of binned image (scale 1) + options->Bin2JPEG = false; // create jpeg of binned image (scale 2) + + // default flags for various activities + options->maskValue = 0x00; // Default mask value (used to skip / ignore pixels) + options->satMask = 0x00; // Saturated pixels (supplied to pmReadoutGenerateMask) + options->lowMask = 0x00; // out-of-bounds (low) pixels (supplied to pmReadoutGenerateMask) + options->flatMask = 0x00; // Bad flat pixels (supplied to pmFlatField) + options->darkMask = 0x00; // Bad dark pixels (supplied to pmDarkApply) + options->blankMask = 0x00; // Blank (no data, cell gap) pixels (supplied to pmChipMosaic, pmFPAMosaic) + options->markValue = 0x00; // A safe bit for internal marking + options->burntoolMask = 0x00; // Suspect pixels that fall where a burntool trail is expected. + options->burntoolTrails = 0x07; // Which types of burntool areas to mask. + // crosstalk options + options->doCrosstalkMeasure = false; // measure crosstalk + options->doCrosstalkCorrect = false; // correct crosstalk + + // Non-linearity default options + options->nonLinearType = 0; // Type of non-linearity data (vector, string or metadata) + options->nonLinearData = NULL; // The non-linearity data + options->nonLinearSource = NULL; // If the non-linearity data is a menu, this provides the key + + // Overscan defaults + options->overscan = NULL; // Overscan options + + // binning parameters + options->xBin1 = 16; // x-binning, scale 1 + options->yBin1 = 16; // y-binning, scale 1 + options->xBin2 = 16; // x-binning, scale 2 + options->yBin2 = 16; // y-binning, scale 2 + + // Fringe defaults + options->fringeRej = NAN; // Fringe rejection limit + options->fringeIter = 0; // Fringe iterations + options->fringeKeep = 1.0; // Fringe keep fraction + + // Pattern correction values + + options->patternRowOrder = 0; // Polynomial order + options->patternRowIter = 0; // Clipping iterations + options->patternRowRej = NAN; // Clipping rejection threshold + options->patternRowThresh = NAN; // Threshold for ignoring pixels + options->patternRowMean = PS_STAT_NONE; // Statistic for mean + options->patternRowStdev = PS_STAT_NONE; // Statistic for standard deviation + options->patternCellBG = PS_STAT_NONE; // Statistic for background + options->patternCellMean = PS_STAT_NONE; // Statistic for mean + + // Remnance values + options->remnanceSize = 30; // Size for remnance detection + options->remnanceThresh = 25.0; // Threshold for remnance detection + + // per-class normalization source + options->normClass = NULL; // per-class normalizations refer to this class + + return options; +} + +psvideophotOptions *psvideophotOptionsParse(pmConfig *config) +{ + bool status; + psvideophotOptions *options = psvideophotOptionsAlloc (); + + // select the recipe for this analysis + bool mdStatus = false; // Result of MD lookup + psMetadata *recipe = psMetadataLookupMetadata(&mdStatus, config->recipes, RECIPE_NAME); + if (! mdStatus || !recipe) { + psLogMsg("psvideophot", PS_LOG_ERROR, "Can't find recipe %s in the RECIPES.\n", RECIPE_NAME); + exit(EXIT_FAILURE); + } + + // Non-linearity recipe options + if (psMetadataLookupBool(NULL, recipe, "NONLIN")) { + psMetadataItem *dataItem = psMetadataLookup(recipe, "NONLIN.DATA"); + if (! dataItem) { + psLogMsg("psvideophot", PS_LOG_ERROR, "Non-linearity correction desired, but unable to find NONLIN.DATA in recipe %s.", RECIPE_NAME); + exit(EXIT_FAILURE); + } + + options->doNonLin = true; + options->nonLinearType = dataItem->type; + options->nonLinearData = dataItem; + + switch (dataItem->type) { + // No immediate action required + case PS_DATA_VECTOR: + case PS_DATA_STRING: + break; + + // This is a menu; we need the key + case PS_DATA_METADATA: + options->nonLinearSource = psMetadataLookupStr(&status, recipe, "NONLIN.SOURCE"); + if (! status || ! options->nonLinearSource) { + psLogMsg("psvideophot", PS_LOG_ERROR, "Non-linearity correction desired, but unable to find NONLIN.SOURCE in recipe %s.", RECIPE_NAME); + exit(EXIT_FAILURE); + } + break; + default: + psLogMsg("psvideophot", PS_LOG_ERROR, "Non-linearity correction desired, but NONLIN.DATA is of invalid type in recipe %s.", RECIPE_NAME); + exit(EXIT_FAILURE); + } + } + + // XXX PAP: The overscan stuff needs to be updated following the reworked API + + // Overscan recipe options + // XXX EAM : we should abort on invalid options. default options? + if (psMetadataLookupBool(NULL, recipe, "OVERSCAN")) { + options->doOverscan = true; + + // Do the overscan as a single value? + bool overscanSingle = psMetadataLookupBool(NULL, recipe, "OVERSCAN.SINGLE"); + + // How do we fit it? + pmFit overscanFit = PM_FIT_NONE; // Fit type for overscan + int overscanOrder = 0; // Order for overscan fit + psString fit = psMetadataLookupStr(NULL, recipe, "OVERSCAN.FIT"); + if (! strcasecmp(fit, "POLYNOMIAL")) { + overscanFit = PM_FIT_POLY_ORD; + overscanOrder = psMetadataLookupS32(NULL, recipe, "OVERSCAN.ORDER"); + } else if (! strcasecmp(fit, "CHEBYSHEV")) { + overscanFit = PM_FIT_POLY_CHEBY; + overscanOrder = psMetadataLookupS32(NULL, recipe, "OVERSCAN.ORDER"); + } else if (! strcasecmp(fit, "SPLINE")) { + overscanFit = PM_FIT_SPLINE; + } else if (strcasecmp(fit, "NONE")) { + psLogMsg(__func__, PS_LOG_WARN, + "OVERSCAN.FIT (%s) in recipe %s is not one of NONE, POLYNOMIAL, or SPLINE", + fit, RECIPE_NAME); + exit(EXIT_FAILURE); + } + + // What method do we use to measure the overscan statistics? + // XXX allow user to specify psStats types by name + psStats *overscanStats = NULL; // Statistics for overscan + psString stat = psMetadataLookupStr(NULL, recipe, "OVERSCAN.STAT"); + if (! strcasecmp(stat, "MEAN")) { + // overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN); + overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN); + } else if (! strcasecmp(stat, "MEDIAN")) { + overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEDIAN); + } else { + psErrorStackPrint(stderr, "OVERSCAN.STAT (%s) in recipe %s is not one of MEAN or MEDIAN", + stat, RECIPE_NAME); + exit(EXIT_FAILURE); + } + + int boxcar = psMetadataLookupS32(NULL, recipe, "OVERSCAN.BOXCAR"); + float gauss = psMetadataLookupF32(NULL, recipe, "OVERSCAN.GAUSS"); + + // Fill in the options + options->overscan = pmOverscanOptionsAlloc(overscanSingle, overscanFit, overscanOrder, + overscanStats, boxcar, gauss); + + options->overscan->constant = psMetadataLookupBool(NULL, recipe, "OVERSCAN.CONSTANT"); + options->overscan->value = psMetadataLookupF32(NULL, recipe, "OVERSCAN.VALUE"); + + psFree(overscanStats); + } + + // for these images, even if not required otherwise + + options->doVarianceBuild = psMetadataLookupBool(NULL, recipe, "VARIANCE.BUILD"); + + // Mask recipe options (note that mask bit values are set in psvideophotSetMaskBits.c) + + + // Mask recipe options (note that mask bit values are set in psvideophotSetMaskBits.c) + + options->doStats = false; + char *statsName = psMetadataLookupStr(&status, config->arguments, "STATS"); // Filename for statistics + if (statsName) { + options->doStats = true; + } + + options->BaseFITS = psMetadataLookupBool(NULL, recipe, "BASE.FITS"); + options->BaseMaskFITS = psMetadataLookupBool(NULL, recipe, "BASE.MASK.FITS"); + options->BaseVarianceFITS = psMetadataLookupBool(NULL, recipe, "BASE.VARIANCE.FITS"); + + options->ChipFITS = psMetadataLookupBool(NULL, recipe, "CHIP.FITS"); + options->ChipMaskFITS = psMetadataLookupBool(NULL, recipe, "CHIP.MASK.FITS"); + options->ChipVarianceFITS = psMetadataLookupBool(NULL, recipe, "CHIP.VARIANCE.FITS"); + + + options->doPhotom = psMetadataLookupBool(NULL, recipe, "PHOTOM"); + options->doAstromChip = psMetadataLookupBool(NULL, recipe, "ASTROM.CHIP"); + options->doAstromMosaic = psMetadataLookupBool(NULL, recipe, "ASTROM.MOSAIC"); + options->doBG = psMetadataLookupBool(NULL, recipe, "BACKGROUND"); + + options->checkCTE = psMetadataLookupBool(NULL, recipe, "CHECK.CTE"); + + // even if not requested explicitly, if any of these are set, build an internal mask and variance: + if (options->doNoiseMap || options->doBias || options->doOverscan || options->doDark || options->doShutter || options->doFlat || + options->doPhotom) { + options->doMaskBuild = true; + options->doVarianceBuild = true; + } else if (options->doMask || options->doBG) { + options->doMaskBuild = true; + } + + return options; +} Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotParseCamera.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotParseCamera.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotParseCamera.c (revision 29947) @@ -0,0 +1,170 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "psvideophot.h" + +psvideophotOptions *psvideophotParseCamera(pmConfig *config) +{ + bool status = false; + + if (!psvideophotDefineFile(config, NULL, "PSVIDEOPHOT.INPUT", "INPUT", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_NONE)) { + psError(PS_ERR_IO, false, "Can't find an input image source"); + return NULL; + } + pmFPAfile *input = psMetadataLookupPtr(NULL, config->files, "PSVIDEOPHOT.INPUT"); // Input file + psAssert(input, "We just put it there!"); + + // add recipe options supplied on command line + psMetadata *recipe = psMetadataLookupPtr(&status, config->recipes, RECIPE_NAME); + + // parse the options from the metadata format to the psvideophotOptions structure + psvideophotOptions *options = psvideophotOptionsParse(config); + + // the following are defined from the argument list, if given, + // otherwise they revert to the config information + // not all input or output images are used in a given recipe + + int nThreads = psMetadataLookupS32(&status, config->arguments, "NTHREADS"); + if (nThreads > 0) { + int nScanRows = psMetadataLookupS32(&status, recipe, "SCAN.ROWS"); + pmDetrendSetThreadTasks(nScanRows); + } + + // the following files are output targets + pmFPAfile *outImage = pmFPAfileDefineOutput(config, input->fpa, "PSVIDEOPHOT.OUTPUT"); + if (!outImage) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PSVIDEOPHOT.OUTPUT")); + psFree(options); + return NULL; + } + if (outImage->type != PM_FPA_FILE_OBJ) { + psError(PS_ERR_IO, true, "PSVIDEOPHOT.OUTPUT is not of type OBJ"); + psFree(options); + return NULL; + } + + // XXX should these be bound explicitly to the outImage->fpa rather than the input->fpa? + pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, input->fpa, "PSVIDEOPHOT.CHIP"); + if (!chipImage) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PSVIDEOPHOT.CHIP")); + psFree(options); + return NULL; + } + if (chipImage->type != PM_FPA_FILE_OBJ) { + psError(PS_ERR_IO, true, "PSVIDEOPHOT.CHIP is not of type OBJ"); + psFree(options); + return NULL; + } + + + // chipImage -> psphotInput (pmFPAfileDefineFromFile) : fpa is constructed + // psphotInput -> psphotOutput (pmFPAfileDefineOutputFromFile) : fpa is equated + // psphotOutput -> psastroInput (pmFPAfileDefineInput) : fpa is ref-copied + // psastroInput -> psastroModel (pmFPAfileDefineFromArgs : fpa is ref-copied + // psastroInput -> psastroModel (pmFPAfileDefineFromConf : fpa is constructed + // psastroInput -> psastroModel (pmFPAfileDefineFromDetDB : fpa is constructed (pmDetrendSelect uses input concepts ) + + // For photometry, we operate on the chip-mosaicked image + // we create a copy of the mosaicked image for psphot so we can write out a clean image + + + // this file is just used as a carrier; output files (eg, PSPHOT.RESID) are defined by + // psphotDefineFiles + pmFPAfile *psphotInput = pmFPAfileDefineFromFile (config, chipImage, 1, 1, "PSPHOT.INPUT"); + PS_ASSERT (psphotInput, false); + + // specify the number of psphot input images + psMetadataAddS32 (config->arguments, PS_LIST_TAIL, "PSPHOT.INPUT.NUM", PS_META_REPLACE, "number of inputs", 1); + + // define associated psphot input/output files + if (!psphotDefineFiles (config, psphotInput)) { + psError(PSPHOT_ERR_CONFIG, false, + "Trouble defining the additional input/output files for psphot"); + return false; + } + + + // For photometry, we operate on the chip-mosaicked image + + + // save any of these files? + outImage->save = options->BaseFITS; + + + chipImage->save = options->ChipFITS; + + + + // outImage is used as a carrier: input to chipImage -> require the data to remain at the CHIP level + outImage->freeLevel = PS_MIN(outImage->freeLevel, PM_FPA_LEVEL_CHIP); + outImage->dataLevel = outImage->freeLevel; + outImage->fileLevel = PS_MIN(outImage->fileLevel, outImage->dataLevel); + + // outMask and outVariance must be freed at the same level as outImage (all freed by pmFPAFreeData) + + + // the input data is the same as the outImage data : force the free levels to match + input->freeLevel = PS_MIN(outImage->freeLevel, input->freeLevel); + + // define the binned target files (which may just be carriers for some camera configurations) + + // Chip selection: turn on only the chips specified (pass status to suppress missing-key log msg) + char *chipLine = psMetadataLookupStr(&status, config->arguments, "CHIP_SELECTIONS"); + psArray *chips = psStringSplitArray(chipLine, ",", false); + if (chips->n > 0) { + pmFPASelectChip (input->fpa, -1, true); // deselect all chips + for (int i = 0; i < chips->n; i++) { + int chipNum = atoi(chips->data[i]); + if (! pmFPASelectChip(input->fpa, chipNum, false)) { + psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum); + psFree(options); + return false; + } + } + } + psFree (chips); + + if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_FRINGE")) { + // It's a fringe file, so change the file type + input->type = PM_FPA_FILE_FRINGE; + outImage->type = PM_FPA_FILE_FRINGE; + } + if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_DARK")) { + // It's a dark file, so change the file type + input->type = PM_FPA_FILE_DARK; + outImage->type = PM_FPA_FILE_DARK; + // Turn off compression --- there are just too many nasties that can happen + psFree(outImage->compression); + outImage->compression = NULL; + psFree(outImage->options); + outImage->options = NULL; + } + + // Turn off mask and variance output if we're not doing anything interesting + + if (psTraceGetLevel("psvideophot.config") > 0) { + // Get a look inside all the files. + psMetadataIterator *filesIter = psMetadataIteratorAlloc(config->files, PS_LIST_HEAD, NULL); + psMetadataItem *item; // Item from iteration + fprintf(stderr, "Files:\n"); + while ((item = psMetadataGetAndIncrement(filesIter))) { + pmFPAfile *file = item->data.V; // File of interest + fprintf(stderr, "%s: %p %p %p (%p) %p\n", file->name, + file->src, file->fpa, + file->camera, file->fpa->camera, file->format); + } + psFree(filesIter); + } + + // Change the input dark type between the old (IMAGE) and new (multi-DARK). + // Hopefully this is a temporary change until we all move over to using the new dark types + bool mdok; // Status of MD lookup + if (options->doDark && psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { + pmFPAfile *dark = psMetadataLookupPtr(NULL, config->files, "PSVIDEOPHOT.DARK"); + assert(dark); + dark->type = PM_FPA_FILE_IMAGE; + } + + return (options); +} Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersion.c =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersion.c (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersion.c (revision 29947) @@ -0,0 +1,115 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "psvideophot.h" +#include "psvideophotVersionDefinitions.h" + +#ifndef PSVIDEOPHOT_VERSION +#error "PSVIDEOPHOT_VERSION is not set" +#endif +#ifndef PSVIDEOPHOT_BRANCH +#error "PSVIDEOPHOT_BRANCH is not set" +#endif +#ifndef PSVIDEOPHOT_SOURCE +#error "PSVIDEOPHOT_SOURCE is not set" +#endif + +psString psvideophotVersion(void) +{ + char *value = NULL; + psStringAppend(&value, "%s@%s", PSVIDEOPHOT_BRANCH, PSVIDEOPHOT_VERSION); + return value; +} + +psString psvideophotSource(void) +{ + return psStringCopy(PSVIDEOPHOT_SOURCE); +} + +psString psvideophotVersionLong(void) +{ + psString version = psvideophotVersion(); // Version, to return + psString source = psvideophotSource(); // Source + + psStringPrepend(&version, "psvideophot "); + psStringAppend(&version, " from %s, built %s, %s", source, __DATE__, __TIME__); + psFree(source); + +#ifdef __OPTIMIZE__ + psStringAppend(&version, " optimised"); +#else + psStringAppend(&version, " unoptimised"); +#endif + + return version; +}; + +bool psvideophotVersionHeader(psMetadata *header) +{ + PS_ASSERT_METADATA_NON_NULL(header, false); + + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now + psString timeString = psTimeToISO(time); // The time in an ISO string + psFree(time); + psString history = NULL; // History string + psStringAppend(&history, "psvideophot at %s", timeString); + psFree(timeString); + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, history); + psFree(history); + + psLibVersionHeader(header); + psModulesVersionHeader(header); + psphotVersionHeader(header); + psastroVersionHeader(header); + ppStatsVersionHeader(header); + + psString version = psvideophotVersion(); // psvideophot software version + psString source = psvideophotSource(); // psvideophot software source + + psMetadataAddStr(header, PS_LIST_TAIL, "IMAGE_V", PS_META_REPLACE, NULL, PSVIDEOPHOT_VERSION); + + psStringPrepend(&version, "psvideophot version: "); + psStringPrepend(&source, "psvideophot source: "); + + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, version); + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, source); + + psFree(version); + psFree(source); + + return true; +} + + +void psvideophotVersionPrint(void) +{ + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now + psString timeString = psTimeToISO(time); // The time in an ISO string + psFree(time); + psLogMsg("psvideophot", PS_LOG_INFO, "psvideophot at %s", timeString); + psFree(timeString); + + psString pslib = psLibVersionLong();// psLib version + psString psmodules = psModulesVersionLong(); // psModules version + psString psphot = psphotVersionLong(); // psphot version + psString psastro = psastroVersionLong(); // psastro version + psString ppStats = ppStatsVersionLong(); // ppStats version + psString psvideophot = psvideophotVersionLong(); // psvideophot version + + psLogMsg("psvideophot", PS_LOG_INFO, "%s", pslib); + psLogMsg("psvideophot", PS_LOG_INFO, "%s", psmodules); + psLogMsg("psvideophot", PS_LOG_INFO, "%s", psphot); + psLogMsg("psvideophot", PS_LOG_INFO, "%s", psastro); + psLogMsg("psvideophot", PS_LOG_INFO, "%s", ppStats); + psLogMsg("psvideophot", PS_LOG_INFO, "%s", psvideophot); + + psFree(pslib); + psFree(psmodules); + psFree(psphot); + psFree(psastro); + psFree(ppStats); + psFree(psvideophot); + + return; +} Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersionDefinitions.h =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersionDefinitions.h (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersionDefinitions.h (revision 29947) @@ -0,0 +1,8 @@ +#ifndef PSVIDEOPHOT_VERSION_DEFINITIONS_H +#define PSVIDEOPHOT_VERSION_DEFINITIONS_H + +#define PSVIDEOPHOT_VERSION "29871:29881M" // SVN version +#define PSVIDEOPHOT_BRANCH "branches/haf_branches/videophot2010/ppImage" // SVN branch +#define PSVIDEOPHOT_SOURCE "60eb6cdc-a59c-4636-a4e0-dba66a9721fd" // SVN source + +#endif Index: /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersionDefinitions.h.in =================================================================== --- /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersionDefinitions.h.in (revision 29947) +++ /branches/haf_branches/videophot2010/ppImage/src/psvideophotVersionDefinitions.h.in (revision 29947) @@ -0,0 +1,8 @@ +#ifndef PSVIDEOPHOT_VERSION_DEFINITIONS_H +#define PSVIDEOPHOT_VERSION_DEFINITIONS_H + +#define PSVIDEOPHOT_VERSION @PSVIDEOPHOT_VERSION@ // SVN version +#define PSVIDEOPHOT_BRANCH @PSVIDEOPHOT_BRANCH@ // SVN branch +#define PSVIDEOPHOT_SOURCE @PSVIDEOPHOT_SOURCE@ // SVN source + +#endif