Index: /trunk/psphot/src/Makefile.am =================================================================== --- /trunk/psphot/src/Makefile.am (revision 6310) +++ /trunk/psphot/src/Makefile.am (revision 6311) @@ -1,16 +1,15 @@ -lib_LTLIBRARIES = libpsphot.la -bin_PROGRAMS = psphot psphotTest +# lib_LTLIBRARIES = libpsphot.la +# libpsphot_la_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(psphot_CFLAGS) +# libpsphot_la_LDFLAGS = $(PSMODULE_LIBS) $(PSLIB_LIBS) -libpsphot_la_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(psphot_CFLAGS) -libpsphot_la_LDFLAGS = $(PSLIB_LIBS) $(PSMODULE_LIBS) +bin_PROGRAMS = psphot +psphot_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(psphot_CFLAGS) +psphot_LDFLAGS = $(PSLIB_LIBS) $(PSMODULE_LIBS) -psphot_CPPFLAGS = $(libpsphot_la_CPPFLAGS) -psphot_LDADD = libpsphot.la +# psphot_CPPFLAGS = $(libpsphot_la_CPPFLAGS) +# psphot_LDFLAGS = $(PSMODULE_LIBS) $(PSLIB_LIBS) +# psphot_LDADD = libpsphot.la -psphotTest_CPPFLAGS = $(libpsphot_la_CPPFLAGS) -psphotTest_LDADD = libpsphot.la - - -libpsphot_la_SOURCES = \ +psphot_SOURCES = \ psphotReadout.c \ psphotImageStats.c \ @@ -46,20 +45,12 @@ pmModelFitSet.c \ pmCellSetMask.c \ - pmSourceFitSet.c - - -psphot_SOURCES = \ + pmSourceFitSet.c \ psphot.c \ psphotArguments.c \ psphotParseCamera.c \ - psphotImageLoop.c \ - psphotModelTest.c + psphotModelTest.c \ + psphotImageLoop.c -psphotTest_SOURCES = \ - psphotTest.c \ - psImageJpeg.c \ - psphotTestArguments.c - -include_HEADERS = \ +noinst_HEADERS = \ psLibUtils.h \ psModulesUtils.h \ Index: /trunk/psphot/src/pmCellSetMask.c =================================================================== --- /trunk/psphot/src/pmCellSetMask.c (revision 6310) +++ /trunk/psphot/src/pmCellSetMask.c (revision 6311) @@ -6,4 +6,7 @@ // mask the excluded outer pixels + // these coordinates refer to the parent image + // these bounds will saturate on the subimage + // negative upper bounds will subtract from the *subimage* float XMIN = psMetadataLookupF32 (&status, recipe, "XMIN"); float XMAX = psMetadataLookupF32 (&status, recipe, "XMAX"); @@ -17,5 +20,9 @@ pmReadout *readout = readouts->data[i]; // The readout of interest + // psRegionForImage creates a region for the subimage, not the parent + // XXX I propose that psRegionForImage treat the region as referring to the parent... psRegion keep = psRegionForImage (readout->image, valid); + + // psImageKeepRegion assumes the region refers to the parent coordinates psImageKeepRegion (readout->mask, keep, "OR", PSPHOT_MASK_INVALID); } Index: /trunk/psphot/src/psLibUtils.h =================================================================== --- /trunk/psphot/src/psLibUtils.h (revision 6310) +++ /trunk/psphot/src/psLibUtils.h (revision 6311) @@ -14,4 +14,5 @@ bool psLineInit (psLine *line); bool psLineAdd (psLine *line, char *format, ...); +int psStringStrip (char *string); # endif Index: /trunk/psphot/src/psLine.c =================================================================== --- /trunk/psphot/src/psLine.c (revision 6310) +++ /trunk/psphot/src/psLine.c (revision 6311) @@ -47,2 +47,20 @@ } +#ifndef whitespace +#define whitespace(c) (((c) == ' ') || ((c) == '\t')) +#endif + +/* Strip whitespace from the start and end of STRING. */ +int psStringStrip (char *string) { + + int i; + + if (string == (char *) NULL) return (FALSE); + + for (i = 0; whitespace (string[i]); i++); + if (i) memmove (string, string + i, strlen(string+i)+1); + for (i = strlen (string) - 1; (i > 0) && whitespace (string[i]); i--); + string[++i] = 0; + return (i); + +} Index: /trunk/psphot/src/psModulesUtils.c =================================================================== --- /trunk/psphot/src/psModulesUtils.c (revision 6310) +++ /trunk/psphot/src/psModulesUtils.c (revision 6311) @@ -193,4 +193,5 @@ config->recipe = NULL; config->arguments = NULL; + config->options = NULL; config->database = NULL; Index: /trunk/psphot/src/psModulesUtils.h =================================================================== --- /trunk/psphot/src/psModulesUtils.h (revision 6310) +++ /trunk/psphot/src/psModulesUtils.h (revision 6311) @@ -22,5 +22,6 @@ psMetadata *camera; // The camera configuration psMetadata *recipe; // The recipe (i.e., specific setups) - psMetadata *arguments; // The command-line arguments + psMetadata *arguments; // Command-line arguments + psMetadata *options; // Command-line recipe options psDB *database; // Database handle } ppConfig; Index: /trunk/psphot/src/psphot.c =================================================================== --- /trunk/psphot/src/psphot.c (revision 6310) +++ /trunk/psphot/src/psphot.c (revision 6311) @@ -15,6 +15,6 @@ ppFile *input = psphotParseCamera (config); - // run a single-model test if desired - XXX push in psphotImageLoop? - // psphotModelTest (input, options); + // check on output mode,format, setup basic filename, etc + psphotOutputPrep (input, config); // call psphot for each readout Index: /trunk/psphot/src/psphot.h =================================================================== --- /trunk/psphot/src/psphot.h (revision 6310) +++ /trunk/psphot/src/psphot.h (revision 6311) @@ -24,5 +24,5 @@ bool psphotImageLoop (ppFile *input, ppConfig *config); -bool psphotModelTest (pmReadout *readout, psMetadata *config); +bool psphotModelTest (pmReadout *readout, psMetadata *arguments, psMetadata *recipe); bool psphotReadout (pmReadout *readout, psMetadata *config); bool ppImageLoadPixels (ppFile *input, psDB *db, int chipNum, int cellNum); @@ -36,5 +36,5 @@ bool psphotBasicDeblend (psArray *sources, psMetadata *config, psStats *sky); pmPSF *psphotChoosePSF (psMetadata *config, psArray *sources, psStats *sky); -void psphotOutput (pmReadout *readout, psMetadata *config); +void psphotOutput (pmReadout *readout, psMetadata *arguments); // optional object analysis steps @@ -80,5 +80,5 @@ bool pmMomentsWriteText (psArray *sources, char *filename); -bool psphotSamplePSFs (psMetadata *config, pmPSF *psf, psImage *image); +bool psphotSamplePSFs (pmPSF *psf, psImage *image, char *output); bool psphotDumpMoments (psMetadata *config, psArray *sources); int psphotSaveImage (psMetadata *header, psImage *image, char *filename); @@ -86,4 +86,8 @@ int pmSourcesDophotType (pmSource *source); bool psMetadataItemTransfer (psMetadata *out, psMetadata *in, char *key); + +char *psphotSplitName (psMetadata *header); +void psphotOutputPrep (ppFile *file, ppConfig *config); +char *psphotNameSubstitute (char *input, char *replace, char *key); bool psphotMagnitudes (psMetadata *config, psArray *sources, pmPSF *psf); Index: /trunk/psphot/src/psphotArguments.c =================================================================== --- /trunk/psphot/src/psphotArguments.c (revision 6310) +++ /trunk/psphot/src/psphotArguments.c (revision 6311) @@ -1,9 +1,11 @@ # include "psphot.h" -static void usage (psMetadata *arguments) ; +static void usage (void); ppConfig *psphotArguments (int *argc, char **argv) { int N; + + if (*argc == 1) usage (); // basic pslib options @@ -22,10 +24,32 @@ // arguments (must be supplied for each run, or not used) - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-psf", 0, "input psf file", ""); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-mask", 0, "Name of the mask image", ""); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-resid", 0, "Name of the output residual image", ""); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-weight", 0, "Name of the weight image", ""); - psMetadataAddS32(config->arguments, PS_LIST_TAIL, "-chip", 0, "Chip number to process (if positive)", -1); - + // mask image (input) is used by psphotImageLoop + if ((N = psArgumentGet (*argc, argv, "-mask"))) { + psArgumentRemove (N, argc, argv); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "MASK_IMAGE", PS_META_REPLACE, "", psStringCopy(argv[N])); + psArgumentRemove (N, argc, argv); + } + + // weight image (input) is used by psphotImageLoop + if ((N = psArgumentGet (*argc, argv, "-weight"))) { + psArgumentRemove (N, argc, argv); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "WEIGHT_IMAGE", PS_META_REPLACE, "", psStringCopy(argv[N])); + psArgumentRemove (N, argc, argv); + } + + // residual image (output) is used by psphotOutput + if ((N = psArgumentGet (*argc, argv, "-resid"))) { + psArgumentRemove (N, argc, argv); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "RESID_IMAGE", PS_META_REPLACE, "", psStringCopy(argv[N])); + psArgumentRemove (N, argc, argv); + } + + // 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_SELECTION", PS_META_REPLACE, "", psStringCopy(argv[N])); + psArgumentRemove (N, argc, argv); + } + // run the test model (requires X,Y coordinate) if ((N = psArgumentGet (*argc, argv, "-modeltest"))) { @@ -58,36 +82,39 @@ } - // Parse command-line overrides of recipe values - psMetadata *recipe = psMetadataAlloc (); + // these other options override the recipe options + config->options = psMetadataAlloc (); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-photcode", 0, "photometry code", "NONE"); - psMetadataAddStr (config->arguments, PS_LIST_TAIL, "-break", 0, "", "NONE"); - psMetadataAddS32 (config->arguments, PS_LIST_TAIL, "-fitmode", 0, "", 2); - - // analysis region : XXX override recipe - if ((N = psArgumentGet (*argc, argv, "-photcode"))) { + // PSF : optional psf file to be loaded + if ((N = psArgumentGet (*argc, argv, "-psf"))) { psArgumentRemove (N, argc, argv); - psMetadataAddStr (recipe, PS_LIST_TAIL, "PHOTCODE", PS_META_REPLACE, "", psStringCopy(argv[N])); + psMetadataAddStr (config->options, PS_LIST_TAIL, "PSF_INPUT_FILE", PS_META_REPLACE, "", psStringCopy(argv[N])); psArgumentRemove (N, argc, argv); } - // analysis region : XXX override recipe - if ((N = psArgumentGet (*argc, argv, "-break"))) { + // photcode : used in output to supplement header data (argument or recipe?) + if ((N = psArgumentGet (*argc, argv, "-photcode"))) { psArgumentRemove (N, argc, argv); - psMetadataAddStr (recipe, PS_LIST_TAIL, "BREAK_POINT", PS_META_REPLACE, "", psStringCopy(argv[N])); + psMetadataAddStr (config->options, PS_LIST_TAIL, "PHOTCODE", PS_META_REPLACE, "", psStringCopy(argv[N])); psArgumentRemove (N, argc, argv); } - // analysis region : XXX override recipe - if ((N = psArgumentGet (*argc, argv, "-fitmode"))) { + // break : used from recipe throughout psphotReadout + if ((N = psArgumentGet (*argc, argv, "-break"))) { psArgumentRemove (N, argc, argv); - psMetadataAddStr (recipe, PS_LIST_TAIL, "FITMODE", PS_META_REPLACE, "", psStringCopy(argv[N])); + psMetadataAddStr (config->options, PS_LIST_TAIL, "BREAK_POINT", PS_META_REPLACE, "", psStringCopy(argv[N])); psArgumentRemove (N, argc, argv); } - // analysis region : XXX override recipe + // fitmode : used from recipe throughout psphotReadout + if ((N = psArgumentGet (*argc, argv, "-fitmode"))) { + psArgumentRemove (N, argc, argv); + psMetadataAddStr (config->options, PS_LIST_TAIL, "FITMODE", PS_META_REPLACE, "", psStringCopy(argv[N])); + psArgumentRemove (N, argc, argv); + } + + // analysis region : overrides recipe value, used in psphotReadout/psphotEnsemblePSF if ((N = psArgumentGet (*argc, argv, "-region"))) { psArgumentRemove (N, argc, argv); - psMetadataAddStr (recipe, PS_LIST_TAIL, "ANALYSIS_REGION", 0, "", psStringCopy(argv[N])); + psMetadataAddStr (config->options, PS_LIST_TAIL, "ANALYSIS_REGION", 0, "", psStringCopy(argv[N])); psArgumentRemove (N, argc, argv); } @@ -96,5 +123,5 @@ while ((N = psArgumentGet (*argc, argv, "-D"))) { psArgumentRemove (N, argc, argv); - psMetadataAddStr (recipe, PS_LIST_TAIL, argv[N], 0, "", argv[N+1]); + psMetadataAddStr (config->options, PS_LIST_TAIL, argv[N], 0, "", argv[N+1]); psArgumentRemove (N, argc, argv); psArgumentRemove (N, argc, argv); @@ -104,5 +131,5 @@ while ((N = psArgumentGet (*argc, argv, "-Df"))) { psArgumentRemove (N, argc, argv); - psMetadataAddF32 (recipe, PS_LIST_TAIL, argv[N], 0, "", atof(argv[N+1])); + psMetadataAddF32 (config->options, PS_LIST_TAIL, argv[N], 0, "", atof(argv[N+1])); psArgumentRemove (N, argc, argv); psArgumentRemove (N, argc, argv); @@ -112,26 +139,22 @@ while ((N = psArgumentGet (*argc, argv, "-Di"))) { psArgumentRemove (N, argc, argv); - psMetadataAddS32 (recipe, PS_LIST_TAIL, argv[N], 0, "", atoi(argv[N+1])); + psMetadataAddS32 (config->options, PS_LIST_TAIL, argv[N], 0, "", atoi(argv[N+1])); psArgumentRemove (N, argc, argv); psArgumentRemove (N, argc, argv); } - // place the recipe options on the arguments stack - psMetadataAddPtr (config->arguments, PS_LIST_TAIL, "RECIPE.OPTIONS", PS_DATA_UNKNOWN, "", recipe); - - if (!psArgumentParse(config->arguments, argc, argv)) usage (config->arguments); - if (*argc != 3) usage (config->arguments); + if (*argc != 3) usage (); // input and output positions are fixed - psMetadataAddStr (config->arguments, PS_LIST_TAIL, "-input", PS_META_REPLACE, "", argv[1]); - psMetadataAddStr (config->arguments, PS_LIST_TAIL, "-output", PS_META_REPLACE, "", argv[2]); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "INPUT_FILE", PS_META_REPLACE, "", argv[1]); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "OUTPUT_ROOT", PS_META_REPLACE, "", argv[2]); + psTrace(__func__, 1, "Done with psphotArguments...\n"); return (config); } -static void usage (psMetadata *arguments) { +static void usage (void) { fprintf (stderr, "USAGE: psphot (image) (output)\n"); - psArgumentHelp (arguments); exit (2); } Index: /trunk/psphot/src/psphotDefinePixels.c =================================================================== --- /trunk/psphot/src/psphotDefinePixels.c (revision 6310) +++ /trunk/psphot/src/psphotDefinePixels.c (revision 6311) @@ -1,4 +1,5 @@ # include "psphot.h" +// x,y are defined in the parent image coords of readout->image bool psphotDefinePixels(pmSource *mySource, const pmReadout *readout, Index: /trunk/psphot/src/psphotFindPeaks.c =================================================================== --- /trunk/psphot/src/psphotFindPeaks.c (revision 6310) +++ /trunk/psphot/src/psphotFindPeaks.c (revision 6311) @@ -16,6 +16,10 @@ psImage *smooth = psImageCopy (NULL, readout->image, PS_TYPE_F32); + psphotSaveImage (NULL, smooth, "presmooth.fits"); + psImageSmooth (smooth, SIGMA, NSIGMA); psLogMsg ("psphot", 4, "smooth: %f sec\n", psTimerMark ("psphot")); + + psphotSaveImage (NULL, smooth, "smooth.fits"); psTimerStart ("psphot"); Index: /trunk/psphot/src/psphotGrowthCurve.c =================================================================== --- /trunk/psphot/src/psphotGrowthCurve.c (revision 6310) +++ /trunk/psphot/src/psphotGrowthCurve.c (revision 6311) @@ -15,7 +15,7 @@ pmModel *modelRef = pmModelAlloc(psf->type); - // use this image region - xc = 0.5*readout->image->numCols; - yc = 0.5*readout->image->numRows; + // use center of the image + xc = 0.5*(readout->image->numCols + readout->image->col0); + yc = 0.5*(readout->image->numRows + readout->image->row0); dx = psf->growth->maxRadius + 1; dy = psf->growth->maxRadius + 1; Index: /trunk/psphot/src/psphotImageBackground.c =================================================================== --- /trunk/psphot/src/psphotImageBackground.c (revision 6310) +++ /trunk/psphot/src/psphotImageBackground.c (revision 6311) @@ -28,6 +28,6 @@ double frnd = psRandomUniform (rnd); int pixel = Npixels * frnd; - int ix = pixel / image->numCols; - int iy = pixel % image->numCols; + int ix = pixel % image->numCols; + int iy = pixel / image->numCols; float value = image->data.F32[iy][ix]; if (fabs(value - Sky) > dSky) continue; Index: /trunk/psphot/src/psphotImageLoop.c =================================================================== --- /trunk/psphot/src/psphotImageLoop.c (revision 6310) +++ /trunk/psphot/src/psphotImageLoop.c (revision 6311) @@ -5,5 +5,4 @@ bool status; ppImageLoadDepth imageLoadDepth; - char filename[1024]; // determine the load depth @@ -27,8 +26,4 @@ } - char *outputRoot = psMetadataLookupPtr (&status, config->arguments, "-output"); - if (!status) psAbort ("psphot", "output file not specified"); - - int Nout = 0; for (int i = 0; i < file->fpa->chips->n; i++) { pmChip *chip = file->fpa->chips->data[i]; // Chip of interest in input image @@ -53,4 +48,6 @@ } + // XXX optional mask and weight input image should be loaded here? + // this sets the weight map and basic mask applying CELL.BAD and CELL.SATURATION pmCellSetWeights(cell); @@ -58,23 +55,13 @@ pmCellSetMask (cell, config->recipe); - // process each of the readouts for (int k = 0; k < cell->readouts->n; k++) { pmReadout *readout = cell->readouts->data[k]; // Readout of interest in input image - // psphotSaveImage (NULL, readout->image, "image.fits"); - // psphotSaveImage (NULL, readout->weight, "weight.fits"); - // psphotSaveImage (NULL, readout->mask, "mask.fits"); + // run a single-model test if desired + psphotModelTest (readout, config->arguments, config->recipe); psphotReadout (readout, config->recipe); - - // XXX EAM : temporarily write out only CMF with fixed extension - sprintf (filename, "%s.%02d.cmf", outputRoot, Nout); - psMetadata *header = pmReadoutGetHeader (readout); - - psArray *sources = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.SOURCES"); - - pmSourcesWriteCMF (sources, filename, header); - Nout++; + psphotOutput (readout, config->arguments); } } Index: /trunk/psphot/src/psphotModelTest.c =================================================================== --- /trunk/psphot/src/psphotModelTest.c (revision 6310) +++ /trunk/psphot/src/psphotModelTest.c (revision 6311) @@ -2,5 +2,5 @@ # include "psEllipse.h" -bool psphotModelTest (pmReadout *readout, psMetadata *config) { +bool psphotModelTest (pmReadout *readout, psMetadata *arguments, psMetadata *recipe) { bool status; @@ -14,8 +14,8 @@ // run model fitting tests on a single source - if (!psMetadataLookupBool (&status, config, "TEST_FIT")) return false; + if (!psMetadataLookupBool (&status, arguments, "TEST_FIT")) return false; // what fitting mode to use? - char *psfModeWord = psMetadataLookupPtr (&status, config, "TEST_FIT_MODE"); + char *psfModeWord = psMetadataLookupPtr (&status, arguments, "TEST_FIT_MODE"); if (!status) { psfModeWord = psStringCopy ("EXT"); @@ -25,5 +25,5 @@ // in psfMode, psf sets the model type if (psfMode) { - char *psfFile = psMetadataLookupPtr (&status, config, "PSF_INPUT_FILE"); + char *psfFile = psMetadataLookupPtr (&status, arguments, "PSF_INPUT_FILE"); if (!status) psAbort ("psphotModelTest", "PSF_INPUT_FILE not supplied"); psMetadata *psfData = psMetadataConfigParse (NULL, &Nfail, psfFile, FALSE); @@ -32,12 +32,20 @@ } else { // find the model: supplied by user or first in the PSF_MODEL list - char *modelName = psMetadataLookupPtr (&status, config, "TEST_FIT_MODEL"); + char *modelName = psMetadataLookupPtr (&status, arguments, "TEST_FIT_MODEL"); if (modelName == NULL) { // get the list pointers for the PSF_MODEL entries - psMetadataItem *mdi = psMetadataLookup (config, "PSF_MODEL"); - if (mdi == NULL) psAbort ("psphotChoosePSF", "missing PSF_MODEL selection"); + + psList *list = NULL; + psMetadataItem *mdi = psMetadataLookup (recipe, "PSF_MODEL"); + if (mdi == NULL) psAbort ("psphotModelTest", "missing PSF_MODEL selection"); + if (mdi->type == PS_DATA_STRING) { + list = psListAlloc(NULL); + psListAdd (list, PS_LIST_HEAD, mdi); + } else { + if (mdi->type != PS_DATA_METADATA_MULTI) psAbort ("psphotChoosePSF", "missing PSF_MODEL selection"); + list = psMemIncrRefCounter(mdi->data.list); + } // take the first list element - psList *list = (psList *) mdi->data.list; item = psListGet (list, PS_LIST_HEAD); modelName = item->data.V; @@ -48,27 +56,27 @@ // find the fitting parameters (try test values first) - float INNER = psMetadataLookupF32 (&status, config, "TEST_FIT_INNER_RADIUS"); + float INNER = psMetadataLookupF32 (&status, arguments, "TEST_FIT_INNER_RADIUS"); if (!status) { - INNER = psMetadataLookupF32 (&status, config, "SKY_INNER_RADIUS"); + INNER = psMetadataLookupF32 (&status, recipe, "SKY_INNER_RADIUS"); } - float OUTER = psMetadataLookupF32 (&status, config, "TEST_FIT_OUTER_RADIUS"); + float OUTER = psMetadataLookupF32 (&status, arguments, "TEST_FIT_OUTER_RADIUS"); if (!status) { - OUTER = psMetadataLookupF32 (&status, config, "SKY_OUTER_RADIUS"); + OUTER = psMetadataLookupF32 (&status, recipe, "SKY_OUTER_RADIUS"); } - float RADIUS = psMetadataLookupF32 (&status, config, "TEST_FIT_RADIUS"); + float RADIUS = psMetadataLookupF32 (&status, arguments, "TEST_FIT_RADIUS"); if (!status) { - RADIUS = psMetadataLookupF32 (&status, config, "PSF_FIT_RADIUS"); + RADIUS = psMetadataLookupF32 (&status, recipe, "PSF_FIT_RADIUS"); } - float mRADIUS = psMetadataLookupF32 (&status, config, "TEST_MOMENTS_RADIUS"); + float mRADIUS = psMetadataLookupF32 (&status, arguments, "TEST_MOMENTS_RADIUS"); if (!status) { - mRADIUS = psMetadataLookupF32 (&status, config, "PSF_MOMENTS_RADIUS"); + mRADIUS = psMetadataLookupF32 (&status, recipe, "PSF_MOMENTS_RADIUS"); } // define the source of interest - float xObj = psMetadataLookupF32 (&status, config, "TEST_FIT_X"); - float yObj = psMetadataLookupF32 (&status, config, "TEST_FIT_Y"); + float xObj = psMetadataLookupF32 (&status, arguments, "TEST_FIT_X"); + float yObj = psMetadataLookupF32 (&status, arguments, "TEST_FIT_Y"); // construct the source structures @@ -111,5 +119,5 @@ } sprintf (name, "TEST_FIT_PAR%d", i); - value = psMetadataLookupF32 (&status, config, name); + value = psMetadataLookupF32 (&status, arguments, name); if (status) { params[i] = value; @@ -145,5 +153,5 @@ psImageKeepCircle (source->mask, xObj, yObj, RADIUS, "OR", PSPHOT_MASK_MARKED); - char *fitset = psMetadataLookupPtr (&status, config, "TEST_FIT_SET"); + char *fitset = psMetadataLookupPtr (&status, arguments, "TEST_FIT_SET"); if (status) { status = psphotFitSet (source, model, fitset, psfMode); Index: /trunk/psphot/src/psphotOutput.c =================================================================== --- /trunk/psphot/src/psphotOutput.c (revision 6310) +++ /trunk/psphot/src/psphotOutput.c (revision 6311) @@ -1,8 +1,146 @@ # include "psphot.h" +static int extNumber = -1; + +static char *outputName = NULL; +static char *outputRoot = NULL; +static char *outputMode = NULL; +static char *outputFormat = NULL; + +static char *extNumberFormat = NULL; +static char *extNameKey = NULL; +static char *extRoot = NULL; + +void psphotOutputPrep (ppFile *file, ppConfig *config) { + + bool status; + + outputRoot = psMetadataLookupPtr (&status, config->arguments, "OUTPUT_ROOT"); + if (!status) psAbort ("psphot", "output file not specified"); + + outputName = psMetadataLookupPtr (&status, config->recipe, "OUTPUT_NAME"); + outputMode = psMetadataLookupPtr (&status, config->recipe, "OUTPUT_MODE"); + outputFormat = psMetadataLookupPtr (&status, config->recipe, "OUTPUT_FORMAT"); + + // rules to construct output names + extNumberFormat = psMetadataLookupPtr (&status, config->recipe, "EXTNUMBER_FORMAT"); + extNameKey = psMetadataLookupPtr (&status, config->recipe, "EXTNAME"); + extRoot = psMetadataLookupPtr (&status, config->recipe, "EXTROOT"); + + if (extNumberFormat == NULL) { + extNumberFormat = psStringCopy ("%02d"); + } + + psStringStrip (outputName); + psStringStrip (extNameKey); + psStringStrip (extRoot); + + // validate the outputMode and outputFormat + status = false; + status |= !strcasecmp (outputFormat, "TEXT"); + status |= !strcasecmp (outputFormat, "OBJ"); + status |= !strcasecmp (outputFormat, "SX"); + status |= !strcasecmp (outputFormat, "CMP"); + status |= !strcasecmp (outputFormat, "CMF"); + if (!status) { + psLogMsg ("psphot", PS_LOG_ERROR, "invalid output format %s", outputFormat); + exit (1); + } + + // validate the outputMode and outputFormat + status = false; + status |= !strcasecmp (outputMode, "MEF"); + status |= !strcasecmp (outputMode, "SPLIT"); + if (!status) { + psLogMsg ("psphot", PS_LOG_ERROR, "invalid output mode %s", outputMode); + exit (1); + } + + // for MEF output, we need to open a file up front + if (!strcasecmp (outputMode, "MEF")) { + psLogMsg ("psphot", PS_LOG_ERROR, "MEF output mode unavailable"); + exit (1); + } + + return; +} + +// generate the SPLIT filenames +char *psphotSplitName (psMetadata *header) { + + bool status; + + char *newName = NULL; // destination for resulting name + char *extNameWord = NULL; // this contains the per-extension word to add + char extNumberWord[16]; // this will store the string-formatted number + + // extNumberFormat must be set to a valid entry in psphotOutputPrep + sprintf (extNumberWord, extNumberFormat, extNumber); + + // find the extname: + char *extNameVal = psMetadataLookupPtr (&status, header, extNameKey); + + extNameWord = extNameVal; + if ((extRoot != NULL) && (extNameVal != NULL)) { + // check that the extNameVal matches the expected root + if (strncmp (extNameVal, extRoot, strlen(extRoot))) { + psLogMsg ("psphotSplitName", PS_LOG_WARN, "header entry does not match expected format"); + } + extNameWord = extNameVal + strlen(extRoot); + } + + if (extNameWord != NULL) { + psStringStrip (extNameWord); + } + + // note : if the user mis-specifies the output name, we will happily overwrite files + newName = psStringCopy (outputName); + newName = psphotNameSubstitute (newName, outputRoot, "%r"); + newName = psphotNameSubstitute (newName, extNameWord, "%x"); + newName = psphotNameSubstitute (newName, extNumberWord, "%n"); + + return newName; +} + + +// given the input string, search for the key, and replace with the replacement +// the input string may be freed if not needed +char *psphotNameSubstitute (char *input, char *replace, char *key) { + + char *p; + + if (key == NULL) return input; + if (strlen(key) == 0) return input; + + p = strstr (input, key); + if (p == NULL) return input; + + // we have input = xxxkeyxxx + // we want output = xxxreplacexxx + + // this is safe since we will subtract strlen(key) elements from input + char *output = psAlloc(strlen(input) + strlen(replace) + 1); + int Nc = p - input; + + // copy the first segement into 'output' + strncpy (output, input, Nc); + + // copy the key replacement to the start of the key + + strcpy (&output[Nc], replace); + Nc += strlen (replace); + + // copy the remainder to the end of the replacement + strcpy (&output[Nc], p + strlen(key)); + + psFree (input); + return output; +} + // output functions: we have several fixed modes (sx, obj, cmp) -void psphotOutput (pmReadout *readout, psMetadata *config) { +void psphotOutput (pmReadout *readout, psMetadata *arguments) { bool status; + char *outputFile; psTimerStart ("psphot"); @@ -13,11 +151,24 @@ pmPSF *psf = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.PSF"); - char *outputMode = psMetadataLookupPtr (&status, config, "OUTPUT_MODE"); - char *outputFile = psMetadataLookupPtr (&status, config, "OUTPUT_FILE"); - char *residImage = psMetadataLookupPtr (&status, config, "RESID_IMAGE"); - char *psfFile = psMetadataLookupPtr (&status, config, "PSF_OUTPUT_FILE"); - + // starting value is -1 + extNumber ++; + + // for SPLIT output, we need to open a file for each output call + if (!strcasecmp (outputMode, "SPLIT")) { + outputFile = psphotSplitName (header); + } else { + // construct appropriate extname + psAbort ("psphotOutput", "programming error"); + } + + fprintf (stderr, "output file: %s\n", outputFile); + return; + + char *psfFile = psMetadataLookupPtr (&status, arguments, "PSF_OUTPUT_FILE"); + char *psfSample = psMetadataLookupPtr (&status, arguments, "PSF_SAMPLE_FILE"); + char *residImage = psMetadataLookupPtr (&status, arguments, "RESID_IMAGE"); + + if (psfSample != NULL) psphotSamplePSFs (psf, readout->image, psfSample); if (residImage != NULL) psphotSaveImage (header, readout->image, residImage); - psphotSamplePSFs (config, psf, readout->image); if (psfFile != NULL) { @@ -30,30 +181,30 @@ return; } - if (outputMode == NULL) { - psLogMsg ("output", 3, "no data output mode selected"); + if (outputFormat == NULL) { + psLogMsg ("output", 3, "no data output format selected"); return; } - if (!strcasecmp (outputMode, "SX")) { + if (!strcasecmp (outputFormat, "SX")) { pmSourcesWriteSX (sources, outputFile); return; } - if (!strcasecmp (outputMode, "OBJ")) { + if (!strcasecmp (outputFormat, "OBJ")) { pmSourcesWriteOBJ (sources, outputFile); return; } - if (!strcasecmp (outputMode, "CMP")) { + if (!strcasecmp (outputFormat, "CMP")) { pmSourcesWriteCMP (sources, outputFile, header); return; } - if (!strcasecmp (outputMode, "CMF")) { + if (!strcasecmp (outputFormat, "CMF")) { pmSourcesWriteCMF (sources, outputFile, header); return; } - if (!strcasecmp (outputMode, "TEXT")) { + if (!strcasecmp (outputFormat, "TEXT")) { pmSourcesWriteText (sources, outputFile); return; } - psAbort ("psphot", "unknown output mode %s", outputMode); + psAbort ("psphot", "unknown output mode %s", outputFormat); } @@ -560,8 +711,5 @@ } - -bool psphotSamplePSFs (psMetadata *config, pmPSF *psf, psImage *image) { - - bool status; +bool psphotSamplePSFs (pmPSF *psf, psImage *image, char *output) { // make sample PSFs for 4 corners and the center @@ -569,7 +717,4 @@ // optional dump of all rough source data - char *output = psMetadataLookupPtr (&status, config, "PSF_SAMPLE_FILE"); - if (!status) return false; - if (output == NULL) return false; if (output[0] == 0) return false; @@ -580,4 +725,5 @@ psFits *fits = psFitsOpen (output, "w"); + // the centers are in parent coordinates; they do not need to correspond to valid pixels... sample = pmModelPSFatXY (image, modelEXT, psf, 25, 25, 25, 25); psFitsWriteImage (fits, NULL, sample, 0); Index: /trunk/psphot/src/psphotParseCamera.c =================================================================== --- /trunk/psphot/src/psphotParseCamera.c (revision 6310) +++ /trunk/psphot/src/psphotParseCamera.c (revision 6311) @@ -1,11 +1,16 @@ # include "psphot.h" + +# define METADATA_ADD_DEFAULT(CONFIG, TYPE, NAME, VALUE, COMMENT)\ + { psMetadataItem *ITEM; \ + ITEM = psMetadataLookup (CONFIG, NAME); \ + if (ITEM == NULL) { \ + psMetadataAdd##TYPE (CONFIG, PS_LIST_TAIL, NAME, 0, COMMENT, VALUE); \ + } else { psFree (ITEM); } } ppFile *psphotParseCamera (ppConfig *config) { - bool status; - ppFile *input = ppFileAlloc (); - input->filename = psMemIncrRefCounter(psMetadataLookupStr(NULL, config->arguments, "-input")); + input->filename = psMemIncrRefCounter(psMetadataLookupStr(NULL, config->arguments, "INPUT_FILE")); // Open the input image @@ -33,8 +38,7 @@ } - // Determine the correct recipe to use - // if the user specifies a recipe, no default values are supplied + // Determine the correct recipe to use (from camera or from user) + // if config->recipe is not NULL, it is a user-supplied recipe if (!config->recipe) { - config->recipe = pmConfigRecipeFromCamera(config->camera, PSPHOT_RECIPE); if (config->recipe == NULL) { @@ -43,9 +47,8 @@ } } - - // recipe override values: - psMetadata *recipe = psMetadataLookupPtr (&status, config->arguments, "RECIPE.OPTIONS"); + + // recipe override values (command-line options): psMetadataItem *item = NULL; - psMetadataIterator *iter = psMetadataIteratorAlloc (recipe, PS_LIST_HEAD, NULL); + psMetadataIterator *iter = psMetadataIteratorAlloc (config->options, PS_LIST_HEAD, NULL); while ((item = psMetadataGetAndIncrement (iter)) != NULL) { psMetadataAddItem (config->recipe, item, PS_LIST_TAIL, PS_META_REPLACE); @@ -54,17 +57,33 @@ psFree (iter); - psMetadataAddStr (config->recipe, PS_LIST_TAIL, "FITMODE", 0, "", "NONE"); - psMetadataAddStr (config->recipe, PS_LIST_TAIL, "PHOTCODE", 0, "", "NONE"); - psMetadataAddStr (config->recipe, PS_LIST_TAIL, "BREAK_POINT", 0, "", "NONE"); + // set default recipe values here + METADATA_ADD_DEFAULT (config->recipe, Str, "FITMODE", "NONE", ""); + METADATA_ADD_DEFAULT (config->recipe, Str, "PHOTCODE", "NONE", ""); + METADATA_ADD_DEFAULT (config->recipe, Str, "BREAK_POINT", "NONE", ""); + METADATA_ADD_DEFAULT (config->recipe, Str, "OUTPUT_FORMAT", "CMP", ""); + METADATA_ADD_DEFAULT (config->recipe, Str, "OUTPUT_MODE", "SPLIT", ""); - // XXX EAM : extend this to allow an array of selected chips by name // Chip selection: if we are using a single chip, select it for each FPA - int chipNum = psMetadataLookupS32(NULL, config->arguments, "-chip"); // Chip number to work on - if (chipNum >= 0) { - if (! pmFPASelectChip(input->fpa, chipNum)) { - psErrorStackPrint(stderr, "Chip number %d doesn't exist in camera.\n", chipNum); - exit(EXIT_FAILURE); + // Chip numbers to work on: -chip 1,2,3,5,8,10 + char *chips = psMetadataLookupStr(NULL, config->arguments, "CHIP_SELECTIONS"); + if (chips != NULL) { + char *p = chips; + while (strlen(p)) { + char *q = strchr (p, ','); + if (q == NULL) { + q = p + strlen(p); + } else { + *q = 0; + q = q + 1; + } + int chipNum = atoi(p); + // XXX EAM : extend this to allow an array of selected chips (by name) + if (! pmFPASelectChip(input->fpa, chipNum)) { + psErrorStackPrint(stderr, "Chip number %d doesn't exist in camera.\n", chipNum); + exit(EXIT_FAILURE); + } + psLogMsg("psphot", PS_LOG_INFO, "Operating only on chip %d\n", chipNum); + p = q; } - psLogMsg("psphot", PS_LOG_INFO, "Operating only on chip %d\n", chipNum); } @@ -72,4 +91,5 @@ input->fpa = pmFPAConstruct(config->camera); + psTrace(__func__, 1, "Done with psphotParseCamera...\n"); return input; } Index: /trunk/psphot/src/psphotReadout.c =================================================================== --- /trunk/psphot/src/psphotReadout.c (revision 6310) +++ /trunk/psphot/src/psphotReadout.c (revision 6311) @@ -8,4 +8,8 @@ psStats *sky = NULL; bool status; + + psphotSaveImage (NULL, readout->mask, "mask.fits"); + psphotSaveImage (NULL, readout->image, "image.fits"); + psphotSaveImage (NULL, readout->weight, "weight.fits"); // measure image stats for initial guess