Index: trunk/ppSub/src/Makefile.am =================================================================== --- trunk/ppSub/src/Makefile.am (revision 23740) +++ trunk/ppSub/src/Makefile.am (revision 23753) @@ -32,7 +32,5 @@ ppSubReadoutStats.c \ ppSubReadoutSubtract.c \ - ppSubSetMasks.c \ - ppSubReadoutRenorm.c \ - ppSubVarianceFactors.c + ppSubSetMasks.c ppSubKernel_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(PPSUB_CFLAGS) Index: trunk/ppSub/src/ppSub.c =================================================================== --- trunk/ppSub/src/ppSub.c (revision 23740) +++ trunk/ppSub/src/ppSub.c (revision 23753) @@ -41,4 +41,5 @@ psErrorStackPrint(stderr, "Error initialising model classes.\n"); exitValue = PS_EXIT_PROG_ERROR; + psFree(config); goto die; } @@ -47,10 +48,11 @@ psErrorStackPrint(stderr, "Error initialising psphot.\n"); exitValue = PS_EXIT_PROG_ERROR; + psFree(config); goto die; } - data = ppSubDataAlloc(); // Processing data + data = ppSubDataAlloc(config); - if (!ppSubArguments(argc, argv, config, data)) { + if (!ppSubArguments(argc, argv, data)) { psErrorStackPrint(stderr, "Error reading arguments.\n"); exitValue = PS_EXIT_CONFIG_ERROR; @@ -58,5 +60,5 @@ } - if (!ppSubCamera(config, data)) { + if (!ppSubCamera(data)) { psErrorStackPrint(stderr, "Error setting up camera.\n"); exitValue = PS_EXIT_CONFIG_ERROR; @@ -64,5 +66,5 @@ } - if (!ppSubLoop(config, data)) { + if (!ppSubLoop(data)) { psErrorStackPrint(stderr, "Error performing subtraction.\n"); exitValue = PS_EXIT_SYS_ERROR; @@ -75,5 +77,4 @@ psFree(data); - psFree(config); pmVisualClose(); //close plot windows, if -visual is set Index: trunk/ppSub/src/ppSub.h =================================================================== --- trunk/ppSub/src/ppSub.h (revision 23740) +++ trunk/ppSub/src/ppSub.h (revision 23753) @@ -40,4 +40,5 @@ /// Data for processing typedef struct { + pmConfig *config; // Configuration psErrorCode quality; // Quality code; 0 for no problem bool photometry; // Perform photometry? @@ -45,4 +46,5 @@ psString stamps; // Stamps file pmPSF *psf; // Point Spread Function + psString statsName; // Name of statistics file FILE *statsFile; // Statistics file psMetadata *stats; // Statistics @@ -50,25 +52,18 @@ /// Constructor -ppSubData *ppSubDataAlloc(void); +ppSubData *ppSubDataAlloc(pmConfig *config ///< Configuration + ); /// Setup the arguments parsing bool ppSubArguments(int argc, char *argv[], ///< Command-line arguments - pmConfig *config, ///< Configuration ppSubData *data ///< Processing data ); /// Parse the camera input -bool ppSubCamera(pmConfig *config, ///< Configuration - ppSubData *data ///< Processing data +bool ppSubCamera(ppSubData *data ///< Processing data ); /// Loop over the FPA hierarchy -bool ppSubLoop(pmConfig *config, ///< Configuration - ppSubData *data ///< Processing data - ); - -/// Perform PSF-matched image subtraction on the readout -bool ppSubReadout(pmConfig *config, ///< Configuration - ppSubData *data ///< Processing data +bool ppSubLoop(ppSubData *data ///< Processing data ); @@ -79,6 +74,5 @@ /// Generate the PSF-matching kernel and convolve the images as needed. Most of this function involves /// looking up the parameters in the recipe and supplying them to the function pmSubtractionMatch() -bool ppSubMatchPSFs(pmConfig *config, ///< Configuration - ppSubData *data ///< Processing data +bool ppSubMatchPSFs(ppSubData *data ///< Processing data ); @@ -89,6 +83,5 @@ /// Photometry stage 1: measure the PSF from the minuend image -bool ppSubMakePSF(pmConfig *config, ///< Configuration - ppSubData *data ///< Processing data +bool ppSubMakePSF(ppSubData *data ///< Processing data ); @@ -100,11 +93,5 @@ /// Photometry stage 2: find and measure sources on the subtracted image bool ppSubReadoutPhotometry(const char *name, ///< Name of file to photometer - pmConfig *config, ///< Configuration ppSubData *data ///< Processing data - ); - -/// Renormalize, update headers and generate JPEGs -bool ppSubReadoutUpdate(pmConfig *config, ///< Configuration - ppSubData *data ///< Processing data ); @@ -121,6 +108,5 @@ /// Mark the data quality as bad and prepare to suspend processing -void ppSubDataQuality(pmConfig *config, ///< Configuration - ppSubData *data, ///< Processing data +void ppSubDataQuality(ppSubData *data, ///< Processing data psErrorCode error,///< Error code ppSubFiles files ///< Files to deactivate @@ -150,6 +136,5 @@ /// Collect statistics -bool ppSubReadoutStats(pmConfig *config,// Configuration - ppSubData *data // Processing data +bool ppSubReadoutStats(ppSubData *data // Processing data ); Index: trunk/ppSub/src/ppSubArguments.c =================================================================== --- trunk/ppSub/src/ppSubArguments.c (revision 23740) +++ trunk/ppSub/src/ppSubArguments.c (revision 23753) @@ -57,6 +57,8 @@ } -bool ppSubArguments(int argc, char *argv[], pmConfig *config, ppSubData *data) +bool ppSubArguments(int argc, char *argv[], ppSubData *data) { + assert(data); + pmConfig *config = data->config; assert(config); @@ -127,7 +129,7 @@ data->stamps = psMemIncrRefCounter(psMetadataLookupStr(NULL, arguments, "-stamps")); - const char *statsName = psMetadataLookupStr(NULL, arguments, "-stats"); // Filename for statistics - if (statsName && strlen(statsName) > 0) { - psString resolved = pmConfigConvertFilename(statsName, config, true, true); // Resolved filename + data->statsName = psMetadataLookupStr(NULL, arguments, "-stats"); // Filename for statistics + if (data->statsName && strlen(data->statsName) > 0) { + psString resolved = pmConfigConvertFilename(data->statsName, config, true, true); // Resolved filename data->statsFile = fopen(resolved, "w"); if (!data->statsFile) { Index: trunk/ppSub/src/ppSubCamera.c =================================================================== --- trunk/ppSub/src/ppSubCamera.c (revision 23740) +++ trunk/ppSub/src/ppSubCamera.c (revision 23753) @@ -134,6 +134,8 @@ -bool ppSubCamera(pmConfig *config, ppSubData *data) +bool ppSubCamera(ppSubData *data) { + psAssert(data, "Require processing data"); + pmConfig *config = data->config; psAssert(config, "Require configuration"); Index: trunk/ppSub/src/ppSubData.c =================================================================== --- trunk/ppSub/src/ppSubData.c (revision 23740) +++ trunk/ppSub/src/ppSubData.c (revision 23753) @@ -22,16 +22,26 @@ psFree(stats); fclose(data->statsFile); + pmConfigRunFilenameAddWrite(data->config, "STATS", data->statsName); } + psFree(data->statsName); psFree(data->stamps); psFree(data->psf); psFree(data->stats); + + psString dump_file = psMetadataLookupStr(NULL, data->config->arguments, "-dumpconfig"); + if (dump_file) { + pmConfigDump(data->config, dump_file); + } + psFree(data->config); + return; } -ppSubData *ppSubDataAlloc(void) +ppSubData *ppSubDataAlloc(pmConfig *config) { ppSubData *data = psAlloc(sizeof(ppSubData)); // Processing data, to return psMemSetDeallocator(data, (psFreeFunc)subDataFree); + data->config = config; data->quality = 0; data->photometry = false; @@ -39,4 +49,5 @@ data->stamps = NULL; data->psf = NULL; + data->statsName = NULL; data->statsFile = NULL; data->stats = psMetadataAlloc(); @@ -47,7 +58,6 @@ -void ppSubDataQuality(pmConfig *config, ppSubData *data, psErrorCode error, ppSubFiles files) +void ppSubDataQuality(ppSubData *data, psErrorCode error, ppSubFiles files) { - psAssert(config, "Require configuration"); psAssert(data, "Require processing data"); @@ -57,5 +67,5 @@ } - ppSubFilesActivate(config, files, false); + ppSubFilesActivate(data->config, files, false); psErrorClear(); Index: trunk/ppSub/src/ppSubLoop.c =================================================================== --- trunk/ppSub/src/ppSubLoop.c (revision 23740) +++ trunk/ppSub/src/ppSubLoop.c (revision 23753) @@ -20,6 +20,8 @@ #include "ppSub.h" -bool ppSubLoop(pmConfig *config, ppSubData *data) +bool ppSubLoop(ppSubData *data) { + psAssert(data, "Require processing data"); + pmConfig *config = data->config; // Configuration psAssert(config, "Require configuration."); @@ -45,5 +47,5 @@ } - if (!ppSubMatchPSFs(config, data)) { + if (!ppSubMatchPSFs(data)) { psError(PS_ERR_UNKNOWN, false, "Unable to match PSFs."); return false; @@ -74,5 +76,5 @@ } - if (!data->quality && !ppSubMakePSF(config, data)) { + if (!data->quality && !ppSubMakePSF(data)) { psError(PS_ERR_UNKNOWN, false, "Unable to generate PSF."); return false; @@ -101,5 +103,5 @@ } - if (!data->quality && !ppSubReadoutPhotometry("PPSUB.OUTPUT", config, data)) { + if (!data->quality && !ppSubReadoutPhotometry("PPSUB.OUTPUT", data)) { psError(PS_ERR_UNKNOWN, false, "Unable to perform photometry."); return false; @@ -112,5 +114,5 @@ // Perform statistics on the cell - if (!ppSubReadoutStats(config, data)) { + if (!ppSubReadoutStats(data)) { psError(PS_ERR_UNKNOWN, false, "Unable to collect statistics"); return false; @@ -150,5 +152,5 @@ } - if (!data->quality && !ppSubReadoutPhotometry("PPSUB.INVERSE", config, data)) { + if (!data->quality && !ppSubReadoutPhotometry("PPSUB.INVERSE", data)) { psError(PS_ERR_UNKNOWN, false, "Unable to perform photometry."); return false; @@ -168,10 +170,4 @@ } - psString dump_file = psMetadataLookupStr(NULL, config->arguments, "-dumpconfig"); - if (dump_file) { - pmFPAfile *input = psMetadataLookupPtr(NULL, config->files, "PPSUB.INPUT"); // Input file - pmConfigDump(config, input->fpa, dump_file); - } - return true; } Index: trunk/ppSub/src/ppSubMakePSF.c =================================================================== --- trunk/ppSub/src/ppSubMakePSF.c (revision 23740) +++ trunk/ppSub/src/ppSubMakePSF.c (revision 23753) @@ -22,6 +22,8 @@ #include "ppSub.h" -bool ppSubMakePSF(pmConfig *config, ppSubData *data) +bool ppSubMakePSF(ppSubData *data) { + psAssert(data, "Require processing data"); + pmConfig *config = data->config; // Configuration psAssert(config, "Require configuration"); @@ -105,5 +107,5 @@ psErrorStackPrint(stderr, "Unable to determine PSF"); psWarning("Unable to determine PSF --- suspect bad data quality."); - ppSubDataQuality(config, data, PSPHOT_ERR_PSF, PPSUB_FILES_PHOT_SUB | PPSUB_FILES_PHOT_INV); + ppSubDataQuality(data, PSPHOT_ERR_PSF, PPSUB_FILES_PHOT_SUB | PPSUB_FILES_PHOT_INV); psFree(view); return true; Index: trunk/ppSub/src/ppSubMatchPSFs.c =================================================================== --- trunk/ppSub/src/ppSubMatchPSFs.c (revision 23740) +++ trunk/ppSub/src/ppSubMatchPSFs.c (revision 23753) @@ -22,6 +22,8 @@ #include "ppSub.h" -bool ppSubMatchPSFs(pmConfig *config, ppSubData *data) +bool ppSubMatchPSFs(ppSubData *data) { + psAssert(data, "Require processing data"); + pmConfig *config = data->config; // Configuration psAssert(config, "Require configuration"); @@ -161,5 +163,5 @@ psErrorStackPrint(stderr, "Unable to find stamps"); psWarning("Unable to find stamps --- suspect bad data quality."); - ppSubDataQuality(config, data, error, PPSUB_FILES_ALL); + ppSubDataQuality(data, error, PPSUB_FILES_ALL); return true; } else { Index: trunk/ppSub/src/ppSubReadout.c =================================================================== --- trunk/ppSub/src/ppSubReadout.c (revision 23740) +++ trunk/ppSub/src/ppSubReadout.c (revision 23753) @@ -21,9 +21,11 @@ #include "ppSub.h" -bool ppSubReadout(const char *name, bool reverse, pmConfig *config, ppSubData *data, const pmFPAview *view) +bool ppSubReadout(const char *name, bool reverse, ppSubData *data, const pmFPAview *view) { + psAssert(data, "Require processing data"); + pmConfig *config = data->config; // Configuration + psAssert(config, "Require configuration"); + psAssert(name, "Require name"); - psAssert(config, "Require configuration"); - psAssert(data, "Require data"); psAssert(view, "Require view"); Index: trunk/ppSub/src/ppSubReadoutPhotometry.c =================================================================== --- trunk/ppSub/src/ppSubReadoutPhotometry.c (revision 23740) +++ trunk/ppSub/src/ppSubReadoutPhotometry.c (revision 23753) @@ -22,6 +22,8 @@ #include "ppSub.h" -bool ppSubReadoutPhotometry(const char *name, pmConfig *config, ppSubData *data) +bool ppSubReadoutPhotometry(const char *name, ppSubData *data) { + psAssert(data, "Require processing data"); + pmConfig *config = data->config; // Configuration psAssert(config, "Require configuration"); @@ -51,5 +53,5 @@ psErrorStackPrint(stderr, "No PSF available"); psWarning("No PSF available --- suspect bad data quality."); - ppSubDataQuality(config, data, psErrorCodeLast(), PPSUB_FILES_PHOT_SUB | PPSUB_FILES_PHOT_INV); + ppSubDataQuality(data, psErrorCodeLast(), PPSUB_FILES_PHOT_SUB | PPSUB_FILES_PHOT_INV); return true; } @@ -94,5 +96,5 @@ psErrorStackPrint(stderr, "Unable to perform photometry on image"); psWarning("Unable to perform photometry on image --- suspect bad data quality."); - ppSubDataQuality(config, data, psErrorCodeLast(), PPSUB_FILES_PHOT_SUB | PPSUB_FILES_PHOT_INV); + ppSubDataQuality(data, psErrorCodeLast(), PPSUB_FILES_PHOT_SUB | PPSUB_FILES_PHOT_INV); } Index: trunk/ppSub/src/ppSubReadoutRenorm.c =================================================================== --- trunk/ppSub/src/ppSubReadoutRenorm.c (revision 23740) +++ (revision ) @@ -1,65 +1,0 @@ -/** @file ppSubReadoutRenorm.c - * - * @brief - * - * @ingroup ppSub - * - * @author IfA - * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-06 03:20:02 $ - * Copyright 2009 Institute for Astronomy, University of Hawaii - */ - -#include "ppSub.h" - -bool ppSubReadoutRenormPixels (pmConfig *config, psMetadata *recipe, pmReadout *readout) { - - bool mdok = false; - - if (!psMetadataLookupBool(&mdok, recipe, "RENORM")) return true; - - // Statistics for renormalisation - psStatsOptions renormMean = psStatsOptionFromString(psMetadataLookupStr(&mdok, recipe, "RENORM.MEAN")); - psStatsOptions renormStdev = psStatsOptionFromString(psMetadataLookupStr(&mdok, recipe, "RENORM.STDEV")); - if (renormMean == PS_STAT_NONE || renormStdev == PS_STAT_NONE) { - psError(PS_ERR_BAD_PARAMETER_VALUE, false, - "Unable to parse renormalisation statistics from recipe."); - return false; - } - psImageMaskType maskValue = pmConfigMaskGet("BLANK", config); // Bits to mask - if (!pmReadoutVarianceRenormPixels(readout, maskValue, renormMean, renormStdev, NULL)) { - psError(PS_ERR_UNKNOWN, false, "Unable to renormalise variances."); - return false; - } - return true; -} - -/** - * old-style variance renormalization - */ -bool ppSubReadoutRenormPhot (pmConfig *config, psMetadata *recipe, pmReadout *readout) { - - bool mdok = false; - - if (!psMetadataLookupBool(&mdok, recipe, "RENORM")) return true; - - // Statistics for renormalisation - psStatsOptions renormMean = psStatsOptionFromString(psMetadataLookupStr(&mdok, recipe, "RENORM.MEAN")); - psStatsOptions renormStdev = psStatsOptionFromString(psMetadataLookupStr(&mdok, recipe, "RENORM.STDEV")); - if (renormMean == PS_STAT_NONE || renormStdev == PS_STAT_NONE) { - psError(PS_ERR_BAD_PARAMETER_VALUE, false, - "Unable to parse renormalisation statistics from recipe."); - return false; - } - - // other renorm parameters - int renormNum = psMetadataLookupS32(&mdok, recipe, "RENORM.NUM"); // Number of samples for renormalisation - float renormWidth = psMetadataLookupS32(&mdok, recipe, "RENORM.WIDTH"); // Width of Gaussian phot - - psImageMaskType maskValue = pmConfigMaskGet("BLANK", config); // Bits to mask - if (!pmReadoutVarianceRenormPhot(readout, maskValue, renormNum, renormWidth, renormMean, renormStdev, NULL)) { - psError(PS_ERR_UNKNOWN, false, "Unable to renormalise variances."); - return false; - } - return true; -} Index: trunk/ppSub/src/ppSubReadoutStats.c =================================================================== --- trunk/ppSub/src/ppSubReadoutStats.c (revision 23740) +++ trunk/ppSub/src/ppSubReadoutStats.c (revision 23753) @@ -10,8 +10,9 @@ -bool ppSubReadoutStats(pmConfig *config, ppSubData *data) +bool ppSubReadoutStats(ppSubData *data) { + psAssert(data, "Require processing data"); + pmConfig *config = data->config; // Configuration psAssert(config, "Require configuration"); - psAssert(data, "Require data"); if (!data->statsFile) { Index: trunk/ppSub/src/ppSubReadoutUpdate.c =================================================================== --- trunk/ppSub/src/ppSubReadoutUpdate.c (revision 23740) +++ (revision ) @@ -1,21 +1,0 @@ -/** @file ppSubReadoutUpdate.c - * - * @brief - * - * @ingroup ppSub - * - * @author IfA - * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-18 00:31:20 $ - * Copyright 2009 Institute for Astronomy, University of Hawaii - */ - -#ifdef HAVE_CONFIG_H -#include -#endif - -#include -#include -#include - -#include "ppSub.h" Index: trunk/ppSub/src/ppSubVarianceFactors.c =================================================================== --- trunk/ppSub/src/ppSubVarianceFactors.c (revision 23740) +++ (revision ) @@ -1,99 +1,0 @@ -/** @file ppSubVarianceFactors.c - * - * @brief - * - * @ingroup ppSub - * - * @author IfA - * @version $Revision: 1.4 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-18 00:31:20 $ - * Copyright 2009 Institute for Astronomy, University of Hawaii - */ - -#include "ppSub.h" - -/** - * Calculate the variance factor for the output image based on the input images - */ -bool ppSubVarianceFactors (pmConfig *config, psMetadata *stats, const pmFPAview *view) { - - // Look up recipe values - psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSUB_RECIPE); // Recipe for ppSim - psAssert(recipe, "We checked this earlier, so it should be here."); - - // convolved input images - pmCell *inCell = pmFPAfileThisCell(config->files, view, "PPSUB.INPUT.CONV"); // Input cell - pmCell *refCell = pmFPAfileThisCell(config->files, view, "PPSUB.REF.CONV"); // Reference cell - - pmReadout *inConv = pmFPAfileThisReadout(config->files, view, "PPSUB.INPUT.CONV"); // Input cell - pmReadout *refConv = pmFPAfileThisReadout(config->files, view, "PPSUB.REF.CONV"); // Reference cell - - pmReadout *outRO = pmFPAfileThisReadout(config->files, view, "PPSUB.OUTPUT"); // Output readout - - // Update variance factors - // It's not possible to do this perfectly, since we're combining different images: - // vf_sum sigma_sum^2 = vf_1 * sigma_1^2 + vf_2 * sigma_2^2 - // It's not possible to write vf_sum as a function of vf_1 and vf_2 with no reference to the sigmas. - // Instead, we're going to cheat. - - bool mdok; // Status of MD lookup - pmSubtractionKernels *kernels = psMetadataLookupPtr(&mdok, outRO->analysis, PM_SUBTRACTION_ANALYSIS_KERNEL); // Kernels - if (!mdok) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find subtraction kernels."); - return false; - } - - float vfIn = psMetadataLookupF32(NULL, inCell->concepts, "CELL.VARFACTOR"); // Variance factor for input - if (!isfinite(vfIn)) { - vfIn = 1.0; - } - float vfRef = psMetadataLookupF32(NULL, refCell->concepts, "CELL.VARFACTOR"); // Variance factor for ref - if (!isfinite(vfRef)) { - vfRef = 1.0; - } - - if (kernels->mode == PM_SUBTRACTION_MODE_1) { - vfIn *= pmSubtractionVarianceFactor(kernels, 0.0, 0.0, false); - } - if (kernels->mode == PM_SUBTRACTION_MODE_2) { - vfRef *= pmSubtractionVarianceFactor(kernels, 0.0, 0.0, false); - } - if (kernels->mode == PM_SUBTRACTION_MODE_DUAL) { - vfIn *= pmSubtractionVarianceFactor(kernels, 0.0, 0.0, false); - vfRef *= pmSubtractionVarianceFactor(kernels, 0.0, 0.0, true); - } - - psStats *vfStats = psStatsAlloc(PS_STAT_ROBUST_MEDIAN); // Statistics - psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS); // Random number generator - - // mask these values when examining the background - psImageMaskType maskVal = pmConfigMaskGet("MASK.VALUE", config); // Bits to mask going in to pmSubtractionMatch - psImageMaskType maskBad = pmConfigMaskGet("BLANK", config); // Bits to mask for bad pixels - - // measure the mean of the convolved input variance image - if (!psImageBackground(vfStats, NULL, inConv->variance, inConv->mask, maskVal | maskBad, rng)) { - psError(PS_ERR_UNKNOWN, false, "Unable to measure mean variance for convolved input"); - psFree(vfStats); - psFree(rng); - return false; - } - float inMeanVar = vfStats->robustMedian; // Mean variance of input - - // measure the mean of the convolved reference variance image - if (!psImageBackground(vfStats, NULL, refConv->variance, refConv->mask, maskVal | maskBad, rng)) { - psError(PS_ERR_UNKNOWN, false, "Unable to measure mean variance for convolved reference"); - psFree(vfStats); - psFree(rng); - return false; - } - float refMeanVar = vfStats->robustMedian; // Mean variance of reference - - psFree(rng); - psFree(vfStats); - - float vf = (vfIn * inMeanVar + vfRef * refMeanVar) / (inMeanVar + refMeanVar); // Resulting var factor - psMetadataItem *vfItem = psMetadataLookup(outRO->parent->concepts, "CELL.VARFACTOR"); - vfItem->data.F32 = vf; - - return true; -}