Index: anches/eam_branches/20091201/psModules/src/objects/pmObjects.c =================================================================== --- /branches/eam_branches/20091201/psModules/src/objects/pmObjects.c (revision 26522) +++ (revision ) @@ -1,25 +1,0 @@ -/** @file pmObjects.c - * - * This file will ... - * - * @author GLG, MHPCC - * @author EAM, IfA: significant modifications. - * - * @version $Revision: 1.13 $ $Name: not supported by cvs2svn $ - * @date $Date: 2006-09-15 09:49:01 $ - * - * Copyright 2004 Maui High Performance Computing Center, University of Hawaii - * - */ - -#ifdef HAVE_CONFIG_H -#include -#endif - -#include -#include -#include -#include -#include "pmObjects.h" -#include "pmModelGroup.h" - Index: anches/eam_branches/20091201/psModules/src/objects/pmObjects.h =================================================================== --- /branches/eam_branches/20091201/psModules/src/objects/pmObjects.h (revision 26522) +++ (revision ) @@ -1,68 +1,0 @@ -/* @file pmObjects.h - * - * The process of finding, measuring, and classifying astronomical sources on - * images is one of the critical tasks of the IPP or any astronomical software - * system. This file will define structures and functions related to the task - * of source detection and measurement. The elements defined in this section - * are generally low-level components which can be connected together to - * construct a complete object measurement suite. - * - * @author GLG, MHPCC - * - * @version $Revision: 1.8 $ $Name: not supported by cvs2svn $ - * @date $Date: 2007-01-24 02:54:15 $ - * Copyright 2004 Maui High Performance Computing Center, University of Hawaii - */ - -#ifndef PM_OBJECTS_H -#define PM_OBJECTS_H - -/// @addtogroup Objects Object Detection / Analysis Functions -/// @{ - -#include -#include -#include - -/** - * - * This function converts the source classification into the closest available - * approximation to the Dophot classification scheme: - * XXX EAM : fix this to use current source classification scheme - * - * PM_SOURCE_DEFECT: 8 - * PM_SOURCE_SATURATED: 8 - * PM_SOURCE_SATSTAR: 10 - * PM_SOURCE_PSFSTAR: 1 - * PM_SOURCE_GOODSTAR: 1 - * PM_SOURCE_POOR_FIT_PSF: 7 - * PM_SOURCE_FAIL_FIT_PSF: 4 - * PM_SOURCE_FAINTSTAR: 4 - * PM_SOURCE_GALAXY: 2 - * PM_SOURCE_FAINT_GALAXY: 2 - * PM_SOURCE_DROP_GALAXY: 2 - * PM_SOURCE_FAIL_FIT_GAL: 2 - * PM_SOURCE_POOR_FIT_GAL: 2 - * PM_SOURCE_OTHER: ? - * - */ -int pmSourceDophotType( - pmSource *source ///< Add comment. -); - - -/** pmSourceSextractType() - * - * This function converts the source classification into the closest available - * approximation to the Sextractor classification scheme. the correspondence is - * not yet defined (TBD) . - * - * XXX: Must code this. - * - */ -int pmSourceSextractType( - pmSource *source ///< Add comment. -); - -/// @} -#endif Index: /branches/eam_branches/20091201/psModules/src/objects/pmPhotObj.c =================================================================== --- /branches/eam_branches/20091201/psModules/src/objects/pmPhotObj.c (revision 26523) +++ /branches/eam_branches/20091201/psModules/src/objects/pmPhotObj.c (revision 26523) @@ -0,0 +1,39 @@ +/** @file pmPhotObj.c + * + * @author EAM, IfA + * + * @version $Revision: 1.13 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-09-15 09:49:01 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include +#include +#include +#include "pmPhotObj.h" + +static void pmPhotObjFree (pmPhotObj *tmp) +{ + if (!tmp) return; + psFree(tmp->sources); +} + + +pmPhotObj *pmPhotObjAlloc() +{ + static int id = 1; + pmPhotObj *obj = (pmPhotObj *) psAlloc(sizeof(pmPhotObj)); + psMemSetDeallocator(obj, (psFreeFunc) pmPhotObjFree); + + *(int *)&obj->id = id; // cast away the const to set the id. + id++; + + obj->sources = NULL; + return obj; +} + Index: /branches/eam_branches/20091201/psModules/src/objects/pmPhotObj.h =================================================================== --- /branches/eam_branches/20091201/psModules/src/objects/pmPhotObj.h (revision 26523) +++ /branches/eam_branches/20091201/psModules/src/objects/pmPhotObj.h (revision 26523) @@ -0,0 +1,41 @@ +/* @file pmPhotObj.h + * + * @author EAM, IfA + * + * @version $Revision: $ + * @date $Date: 2009-02-16 22:30:50 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# ifndef PM_PHOT_OBJ_H +# define PM_PHOT_OBJ_H + +#include +#include "pmPeaks.h" +#include "pmModel.h" +#include "pmMoments.h" + +/// @addtogroup Objects Object Detection / Analysis Functions +/// @{ + + +/** pmPhotObj data structure + * + * A Photometry Object is a connected set of source measurements with a common + * connection. Each source that comprises the object represents the detection of some + * astronomical object on a single image. The object represents the related collection + * of measurements. The fits are coupled in some way. For example, they may all have + * the same position, but independent fluxes. Or, they may have a common set of + * positions and shape parameters. Or the position in each image may be related by a + * function. + * + * XXX is thre any info that is neaded for each object beyond that carried by the sources + * (besides ID)? + */ +typedef struct { + int seq; ///< ID for output (generated on write OR set on read) + psArray *sources; +} pmPhotObj; + +/// @} +# endif /* PM_PHOT_OBJ_H */ Index: /branches/eam_branches/20091201/psModules/src/objects/pmSource.c =================================================================== --- /branches/eam_branches/20091201/psModules/src/objects/pmSource.c (revision 26522) +++ /branches/eam_branches/20091201/psModules/src/objects/pmSource.c (revision 26523) @@ -3,12 +3,10 @@ * Functions to define and manipulate sources on images * - * @author GLG, MHPCC - * @author EAM, IfA: significant modifications. + * @author EAM, IfA + * @author GLG, MHPCC (initial code base) * * @version $Revision: 1.70 $ $Name: not supported by cvs2svn $ * @date $Date: 2009-02-16 22:29:59 $ - * - * Copyright 2004 Maui High Performance Computing Center, University of Hawaii - * + * Copyright 2009 Institute for Astronomy, University of Hawaii */ Index: /branches/eam_branches/20091201/psphot/src/psphotMaskReadout.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotMaskReadout.c (revision 26522) +++ /branches/eam_branches/20091201/psphot/src/psphotMaskReadout.c (revision 26523) @@ -75,2 +75,25 @@ return true; } + +bool psphotStackSetMaskAndVariance (pmConfig *config, const pmFPAview *view, psMetadata *recipe) { + + int num = psMetadataAddS32 (&status, config->arguments, "INPUTS.NUM"); + psAbort (!status, "programming error: must define INPUTS.NUM"); + + // loop over the available readouts + for (int i = 0; i < num; i++) { + + pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PSPHOT.INPUT", i); // File of interest + + // find the currently selected readout + pmReadout *readout = pmFPAviewThisReadout (view, file->fpa); + PS_ASSERT_PTR_NON_NULL (readout, false); + + // Generate the mask and weight images, including the user-defined analysis region of interest + psphotSetMaskAndVariance (config, readout, recipe); + + // display the image, weight, mask (ch 1,2,3) + psphotVisualShowImage (readout); + } + +} Index: /branches/eam_branches/20091201/psphot/src/psphotModelBackground.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotModelBackground.c (revision 26522) +++ /branches/eam_branches/20091201/psphot/src/psphotModelBackground.c (revision 26523) @@ -328,5 +328,5 @@ } - +// XXX these two functions are absurdly-named and very similar -- fix! psImage *psphotBackgroundModel(pmReadout *ro, const pmConfig *config) @@ -376,2 +376,33 @@ return true; } + +// XXX supply filename or keep PSPHOT.INPUT fixed? +bool psphotStackModelBackground (pmConfig *config, const pmFPAview *view) +{ + bool status = true; + + int num = psMetadataAddS32 (&status, config->arguments, "INPUTS.NUM"); + psAbort (!status, "programming error: must define INPUTS.NUM"); + + // loop over the available readouts + for (int i = 0; i < num; i++) { + + pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PSPHOT.INPUT", i); // File of interest + + // find the currently selected readout + pmReadout *readout = pmFPAviewThisReadout (view, file->fpa); + PS_ASSERT_PTR_NON_NULL (readout, false); + + psImageBinning *binning = psphotBackgroundBinning(readout->image, config); // Image binning parameters + pmReadout *model = pmFPAGenerateReadout(config, view, "PSPHOT.BACKMDL", inFPA, binning); // this needs to be a MULTI like PSPHOT.INPUT + pmReadout *modelStdev = pmFPAGenerateReadout(config, view, "PSPHOT.BACKMDL.STDEV", inFPA, binning); // this needs to be a MULTI like PSPHOT.INPUT + + // XXX save results on model->analysis or readout->analysis?? + if (!backgroundModel(model->image, modelStdev->image, model->analysis, readout, binning, config)) { + psError(PS_ERR_UNKNOWN, false, "Unable to generate background model"); + return false; + } + npass ++; + } + return true; +} Index: /branches/eam_branches/20091201/psphot/src/psphotReadoutStack.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotReadoutStack.c (revision 26523) +++ /branches/eam_branches/20091201/psphot/src/psphotReadoutStack.c (revision 26523) @@ -0,0 +1,207 @@ +# include "psphotInternal.h" + +bool psphotReadoutStack (pmConfig *config, const pmFPAview *view) { + + psTimerStart ("psphotReadout"); + + pmModelClassSetLimits(PM_MODEL_LIMITS_LAX); // allow models to have ugly fits (eg, central cusp) + + // select the current recipe + psMetadata *recipe = psMetadataLookupPtr (NULL, config->recipes, PSPHOT_RECIPE); + if (!recipe) { + psError(PSPHOT_ERR_CONFIG, false, "missing recipe %s", PSPHOT_RECIPE); + return false; + } + + // set the photcode for this image + if (!psphotAddPhotcode (recipe, config, view, "PSPHOT.INPUT")) { + psError (PSPHOT_ERR_CONFIG, false, "trouble defining the photcode"); + return false; + } + + // generate a background model (median, smoothed image) + if (!psphotStackSetMaskAndVariance (config, view, recipe)) { + return psphotReadoutCleanupStack (config, recipe, NULL, NULL, NULL); + } + if (!strcasecmp (breakPt, "NOTHING")) { + return psphotReadoutCleanup(config, readout, recipe, NULL, NULL, NULL); + } + + // optional break-point for processing + char *breakPt = psMetadataLookupStr (NULL, recipe, "BREAK_POINT"); + PS_ASSERT_PTR_NON_NULL (breakPt, false); + + // generate a background model (median, smoothed image) + if (!psphotStackModelBackground (config, view)) { + return psphotReadoutCleanup (config, readout, recipe, NULL, NULL, NULL); + } + if (!psphotSubtractBackground (config, view, "PSPHOT.INPUT")) { + return psphotReadoutCleanup (config, readout, recipe, NULL, NULL, NULL); + } + if (!strcasecmp (breakPt, "BACKMDL")) { + return psphotReadoutCleanup (config, readout, recipe, NULL, NULL, NULL); + } + + // find the detections (by peak and/or footprint) in the image. + pmDetections *detections = psphotFindDetections (NULL, readout, recipe); + if (!detections) { + psLogMsg ("psphot", 3, "unable to find detections in this image"); + return psphotReadoutCleanup (config, readout, recipe, detections, psf, NULL); + } + + // construct sources and measure basic stats + psArray *sources = psphotSourceStats (config, readout, detections, true); + if (!sources) return false; + if (!strcasecmp (breakPt, "PEAKS")) { + return psphotReadoutCleanup(config, readout, recipe, detections, psf, sources); + } + + // find blended neighbors of very saturated stars + // XXX merge this with Basic Deblend? + psphotDeblendSatstars (readout, sources, recipe); + + // mark blended peaks PS_SOURCE_BLEND + if (!psphotBasicDeblend (sources, recipe)) { + psLogMsg ("psphot", 3, "failed on deblend analysis"); + return psphotReadoutCleanup (config, readout, recipe, detections, psf, sources); + } + + // classify sources based on moments, brightness + if (!psphotRoughClass (readout, sources, recipe, havePSF)) { + psLogMsg ("psphot", 3, "failed to find a valid PSF clump for image"); + return psphotReadoutCleanup (config, readout, recipe, detections, psf, sources); + } + if (!strcasecmp (breakPt, "MOMENTS")) { + return psphotReadoutCleanup(config, readout, recipe, detections, psf, sources); + } + + if (!havePSF && !psphotImageQuality (recipe, sources)) { + psLogMsg("psphot", 3, "failed to measure image quality"); + return psphotReadoutCleanup(config, readout, recipe, detections, psf, sources); + } + + // if we were not supplied a PSF, choose one here + if (psf == NULL) { + // use bright stellar objects to measure PSF + // XXX if we do not have enough stars to generate the PSF, build one + // from the SEEING guess and model class + psf = psphotChoosePSF (readout, sources, recipe); + if (psf == NULL) { + psLogMsg ("psphot", 3, "failure to construct a psf model"); + return psphotReadoutCleanup (config, readout, recipe, detections, psf, sources); + } + havePSF = true; + } + if (!strcasecmp (breakPt, "PSFMODEL")) { + return psphotReadoutCleanup (config, readout, recipe, detections, psf, sources); + } + psphotVisualShowPSFModel (readout, psf); + + // include externally-supplied sources + psphotLoadExtSources (config, view, sources); + + // construct an initial model for each object, set the radius to fitRadius, set circular fit mask + psphotGuessModels (config, readout, sources, psf); + + // linear PSF fit to source peaks, subtract the models from the image (in PSF mask) + psphotFitSourcesLinear (readout, sources, recipe, psf, FALSE); + + // We have to place these visualizations here because the models are not realized until + // psphotGuessModels or fitted until psphotFitSourcesLinear. + psphotVisualShowPSFStars (recipe, psf, sources); + + // identify CRs and extended sources + psphotSourceSize (config, readout, sources, recipe, psf, 0); + if (!strcasecmp (breakPt, "ENSEMBLE")) { + goto finish; + } + psphotVisualShowSatStars (recipe, psf, sources); + + // non-linear PSF and EXT fit to brighter sources + // replace model flux, adjust mask as needed, fit, subtract the models (full stamp) + psphotBlendFit (config, readout, sources, psf); + + // replace all sources + psphotReplaceAllSources (sources, recipe); + + // linear fit to include all sources (subtract again) + psphotFitSourcesLinear (readout, sources, recipe, psf, TRUE); + + // if we only do one pass, skip to extended source analysis + if (!strcasecmp (breakPt, "PASS1")) { + goto pass1finish; + } + // NOTE: possibly re-measure background model here with objects subtracted + + // add noise for subtracted objects + psphotAddNoise (readout, sources, recipe); + + // find fainter sources (pass 2) + detections = psphotFindDetections (detections, readout, recipe); + + // remove noise for subtracted objects (ie, return to normal noise level) + psphotSubNoise (readout, sources, recipe); + + // define new sources based on only the new peaks + psArray *newSources = psphotSourceStats (config, readout, detections, false); + + // set source type + if (!psphotRoughClass (readout, newSources, recipe, havePSF)) { + psLogMsg ("psphot", 3, "failed to find a valid PSF clump for image"); + return psphotReadoutCleanup (config, readout, recipe, detections, psf, sources); + } + + // create full input models, set the radius to fitRadius, set circular fit mask + psphotGuessModels (config, readout, newSources, psf); + + // replace all sources so fit below applies to all at once + psphotReplaceAllSources (sources, recipe); + + // merge the newly selected sources into the existing list + psphotMergeSources (sources, newSources); + psFree (newSources); + + // linear fit to all sources + psphotFitSourcesLinear (readout, sources, recipe, psf, TRUE); + +pass1finish: + + // measure source size for the remaining sources + psphotSourceSize (config, readout, sources, recipe, psf, 0); + + psphotExtendedSourceAnalysis (readout, sources, recipe); + + psphotExtendedSourceFits (readout, sources, recipe); + +finish: + + // plot positive sources + // psphotSourcePlots (readout, sources, recipe); + + // measure aperture photometry corrections + if (!psphotApResid (config, readout, sources, psf)) { + psLogMsg ("psphot", 3, "failed on psphotApResid"); + return psphotReadoutCleanup (config, readout, recipe, detections, psf, sources); + } + + // calculate source magnitudes + psphotMagnitudes(config, readout, view, sources, psf); + + if (!psphotEfficiency(config, readout, view, psf, recipe, sources)) { + psErrorStackPrint(stderr, "Unable to determine detection efficiencies from fake sources"); + psErrorClear(); + } + + // replace failed sources? + // psphotReplaceUnfitSources (sources); + + // replace background in residual image + psphotSkyReplace (config, view); + + // drop the references to the image pixels held by each source + psphotSourceFreePixels (sources); + + // create the exported-metadata and free local data + return psphotReadoutCleanup(config, readout, recipe, detections, psf, sources); +} + Index: /branches/eam_branches/20091201/psphot/src/psphotStack.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotStack.c (revision 26523) +++ /branches/eam_branches/20091201/psphot/src/psphotStack.c (revision 26523) @@ -0,0 +1,35 @@ +# include "psphotStandAlone.h" + +int main (int argc, char **argv) { + + psTimerStart ("complete"); + pmErrorRegister(); // register psModule's error codes/messages + psphotInit(); + + // load command-line arguments, options, and system config data + pmConfig *config = psphotStackArguments (argc, argv); + assert(config); + + psphotVersionPrint(); + + // load input data (config and images (signal, noise, mask) + if (!psphotStackParseCamera (config)) { + psErrorStackPrint(stderr, "Error setting up the camera\n"); + exit (psphotGetExitStatus()); + } + + // call psphot for each readout + if (!psphotStacImageLoop (config)) { + psErrorStackPrint(stderr, "Error in the psphot image loop\n"); + exit (psphotGetExitStatus()); + } + + psLogMsg ("psphot", 3, "complete psphot run: %f sec\n", psTimerMark ("complete")); + + psErrorCode exit_status = psphotGetExitStatus(); + psphotCleanup (config); + exit (exit_status); +} + +// all functions which return to this level must raise one of the top-level error codes if they +// exit with an error. these error codes are used to specify the program exit status Index: /branches/eam_branches/20091201/psphot/src/psphotStackArguments.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotStackArguments.c (revision 26523) +++ /branches/eam_branches/20091201/psphot/src/psphotStackArguments.c (revision 26523) @@ -0,0 +1,159 @@ +# include "psphotStandAlone.h" + +static void usage(pmConfig *config, int exitCode); +static void writeHelpInfo(pmConfig* config, FILE* ofile); + +pmConfig *psphotStackArguments(int argc, char **argv) { + + int N; + bool status; + + // print help info + if (psArgumentGet(argc, argv, "-help")) writeHelpInfo(argv[0], config, stdout); + if (psArgumentGet(argc, argv, "-h")) writeHelpInfo(argv[0], config, stdout); + + // load config data from default locations + pmConfig *config = pmConfigRead(&argc, argv, PSPHOT_RECIPE); + if (config == NULL) { + psErrorStackPrint(stderr, "Can't read site configuration"); + exit(PS_EXIT_CONFIG_ERROR); + } + + // -version and -dumpconfig arguments + PSARGUMENTS_INSTANTIATE_GENERICS( psphot, config, argc, argv ); + + // save the following additional recipe values based on command-line options + // these options override the PSPHOT recipe values loaded from recipe files + psMetadata *options = pmConfigRecipeOptions (config, PSPHOT_RECIPE); + + // Number of threads is handled + PSARGUMENTS_INSTANTIATE_THREADSARG( psphot, config, argc, argv ) + + // photcode : used in output to supplement header data (argument or recipe?) + if ((N = psArgumentGet (argc, argv, "-photcode"))) { + if (argc <= N+1) { + psErrorStackPrint(stderr, "Expected to see 1 more argument; saw %d", argc - 1); + exit(PS_EXIT_CONFIG_ERROR); + } + psArgumentRemove (N, &argc, argv); + psMetadataAddStr (options, PS_LIST_TAIL, "PHOTCODE", PS_META_REPLACE, "", argv[N]); + psArgumentRemove (N, &argc, argv); + } + + // visual : interactive display mode + if ((N = psArgumentGet (argc, argv, "-visual"))) { + psArgumentRemove (N, &argc, argv); + pmVisualSetVisual(true); + } + + // break : used from recipe throughout psphotReadout to stop processing early + if ((N = psArgumentGet (argc, argv, "-break"))) { + if (argc <= N+1) { + psErrorStackPrint(stderr, "Expected to see 1 more argument; saw %d", argc - 1); + exit(PS_EXIT_CONFIG_ERROR); + } + psArgumentRemove (N, &argc, argv); + psMetadataAddStr (options, PS_LIST_TAIL, "BREAK_POINT", PS_META_REPLACE, "", argv[N]); + psArgumentRemove (N, &argc, argv); + } + + // find the input data file (an mdc file) + if ((N = psArgumentGet(argc, argv, "-input"))) { + if (argc <= N+1) { + psErrorStackPrint(stderr, "Expected to see 1 more argument; saw %d", argc - 1); + exit(PS_EXIT_CONFIG_ERROR); + } + psArgumentRemove(N, &argc, argv); + + unsigned int numBad = 0; // Number of bad lines + psMetadata *inputs = psMetadataConfigRead(NULL, &numBad, argv[N], false); // Input file info + if (!inputs || numBad > 0) { + psErrorStackPrint(stderr, "Unable to cleanly read MDC file with inputs."); + exit(PS_EXIT_CONFIG_ERROR); + } + psMetadataAddMetadata(config->arguments, PS_LIST_TAIL, "INPUTS", 0, "Metadata with input details", inputs); + psFree(inputs); + + psArgumentRemove(N, &argc, argv); + } + + if (argc != 2) { + psError(PSPHOT_ERR_ARGUMENTS, true, "Expected to see one more argument; saw %d", argc - 1); + usage(config, PS_EXIT_CONFIG_ERROR); + } + + // output position is fixed + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "", argv[1]); + + psTrace("psphot", 1, "Done with psphotArguments...\n"); + return (config); +} + +static void writeHelpInfo(pmConfig* config, FILE* ofile) +{ + fprintf(ofile, + "Usage: psphotStack -input (input.mdc) outroot\n" + "\n" + "where:\n" + " FileNameList is a text file containing filenames, one per line\n" + " MaskFileNameList is a text file of mask filenames, one per line\n" + " VarFileNameList is a text file of variance filenames, one per line\n" + " OutFileBaseName is the 'root name' for output files\n" + "\n" + "additional options:\n" + " -chip nn[,nn,...]\n" + " select detector chips to process; default is all.\n" + " Indices correspond to zero-based offset in the FPA metadata table.\n" + " -photcode PhotoCodeName\n" + " specify photocode\n" + " -region RegionString\n" + " specify analysis region. String is of form '[x0:x1,y0:y1]'\n" + " To use this option you must define a default in psphot.config\n" + " -visual\n" + " turns on interactive display mode\n" + " -dumpconfig CfgFileName\n" + " causes config info to be dumped to the named file.\n" + " -break NOTHING|BACKMDL|PEAKS|MOMENTS|PSFMODEL|ENSEMBLE|PASS1\n" + " choose a point at which to exit processing early\n" + " -nthreads n\n" + " set number of parallel threads of execution\n" + " -F OldFileRule ReplacementFileRule\n" + " change file naming rule; e.g. '-F PSPHOT.OUTPUT PSPHOT.OUT.CMF.MEF'\n" + " -D name stringval\n" + " set a string-valued config parameter\n" + " -Di name intval\n" + " set an integer-valued config parameter\n" + " -Df name fval\n" + " set a float-valued config parameter\n" + " -Db name boolval\n" + " set a boolean-valued config parameter\n" + " -v, -vv, -vvv\n" + " set increasing levels of verbosity\n" + " -logfmt FormatString\n" + " set format string used for log messages\n" + " -trace Fac Lvl\n" + " set tracing for facility Fac to integer Lvl, e.g. '-trace err 10'\n" + " -trace-levels\n" + " print current trace levels\n"); + psFree(config); + pmConfigDone(); + psLibFinalize(); + exit(PS_EXIT_SUCCESS); +} + +static void usage(pmConfig *config, // Configuration + int exitCode + ) +{ + fprintf(stderr, + "Usage: psphotStack -input input.mdc outroot\n" + "Try 'psphotStack -help' for more options and explanation\n"); + + if (exitCode != PS_EXIT_SUCCESS) psErrorStackPrint(stderr, "Error reading arguments\n"); + + psFree(config); + pmConfigDone(); + psLibFinalize(); + exit(exitCode); +} + Index: /branches/eam_branches/20091201/psphot/src/psphotStackImageLoop.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotStackImageLoop.c (revision 26523) +++ /branches/eam_branches/20091201/psphot/src/psphotStackImageLoop.c (revision 26523) @@ -0,0 +1,36 @@ +# include "psphotStandAlone.h" + +# define ESCAPE(MESSAGE) { \ + psError(PSPHOT_ERR_DATA, false, MESSAGE); \ + psFree (view); \ + return false; \ +} + +bool psphotImageLoop (pmConfig *config) { + + bool status; + pmChip *chip; + pmCell *cell; + pmReadout *readout; + + pmFPAview *view = pmFPAviewAlloc (0); + + // XXX for now, just load the full set of images up front + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE ("failed input for fpa in psphot."); + + // XXX for now, we assume there is only a single chip in the PHU: + psphotReadoutStack (config, view); + + + // fail if we failed to handle an error + if (psErrorCodeLast() != PS_ERR_NONE) psAbort ("failed to handle an error!"); + + psFree (view); + return true; +} + +/* + the easiest way to implement this is to assume we can pre-load the full set of images up front. + with 5 filters and 6000^2 (image, mask, var = 10 byte per pixel), we need 1.8GB, which is not too bad. + */ + Index: /branches/eam_branches/20091201/psphot/src/psphotStackParseCamera.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotStackParseCamera.c (revision 26523) +++ /branches/eam_branches/20091201/psphot/src/psphotStackParseCamera.c (revision 26523) @@ -0,0 +1,102 @@ +# include "psphotStandAlone.h" + +static pmFPAfile *defineFile(pmConfig *config, pmFPAfile *bind, const char *name, const char *filename, pmFPAfileType type); + +// define the needed / desired I/O files +bool psphotStackParseCamera (pmConfig *config) { + + bool status = false; + + // the input images are defined as a set of metadatas in the INPUTS metadata folder + psMetadata *inputs = psMetadataLookupMetadata(&status, config->arguments, "INPUTS"); // The inputs info + if (!inputs) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find inputs."); + return false; + } + + psMetadata *item == NULL; + int nInputs = 0; + while ((item = psMetadataGetIndex(inputs, nInputs)) != NULL) { + if (item->type != PS_DATA_METADATA) { + psError(PS_ERR_BAD_PARAMETER_TYPE, true, "Component %s of the input metadata is not of type METADATA", item->name); + return false; + } + + psMetadata *input = item->data.md; // The input metadata of interest + + // look for 'IMAGE', 'MASK', 'VARIANCE' in folder (only 'IMAGE' is required) + + psString image = psMetadataLookupStr(NULL, input, "IMAGE"); // Name of image + if (!image || strlen(image) == 0) { + psError(PS_ERR_BAD_PARAMETER_VALUE, true, "Component %s lacks IMAGE of type STR", item->name); + return false; + } + pmFPAfile *imageFile = defineFile(config, NULL, "PSPHOT.INPUT", image, PM_FPA_FILE_IMAGE); // File for image + if (!imageFile) { + psError(PS_ERR_UNKNOWN, false, "Unable to define file from image %d (%s)", i, image); + return false; + } + + psString mask = psMetadataLookupStr(&status, input, "MASK"); // Name of mask + if (mask && strlen(mask) > 0) { + if (!defineFile(config, imageFile, "PSPHOT.INPUT.MASK", mask, PM_FPA_FILE_MASK)) { + psError(PS_ERR_UNKNOWN, false, "Unable to define file from mask %d (%s)", i, mask); + return false; + } + } + + psString variance = psMetadataLookupStr(&mdok, input, "VARIANCE"); // Name of variance map + if (variance && strlen(variance) > 0) { + if (!defineFile(config, imageFile, "PSPHOT.INPUT.VARIANCE", variance, PM_FPA_FILE_VARIANCE)) { + psError(PS_ERR_UNKNOWN, false, "Unable to define file from variance %d (%s)", i, variance); + return false; + } + } + nInputs ++; + } + psMetadataRemoveKey(config->arguments, "FILENAMES"); + psMetadataAddS32 (config->arguments, PS_LIST_TAIL, "INPUTS.NUM", PS_META_REPLACE, "number of inputs", nInputs); + + // define the additional input/output files associated with psphot + // XXX figure out which files are needed by psphotStack + if (false && !psphotDefineFiles (config, input)) { + psError(PSPHOT_ERR_CONFIG, false, "Trouble defining the additional input/output files"); + return false; + } + + psTrace("psphot", 1, "Done with psphotStackParseCamera...\n"); + + psErrorClear(); // some metadata lookup may have failed + return true; +} + +// Define a file +static pmFPAfile *defineFile(pmConfig *config, // Configuration + pmFPAfile *bind, // File to which to bind + const char *name, // Name of file rule + const char *filename, // Name of file + pmFPAfileType type // Type of file + ) +{ + + psArray *dummy = psArrayAlloc(1); // Dummy array of filenames for this FPA + dummy->data[0] = psStringCopy(filename); + psMetadataAddArray(config->arguments, PS_LIST_TAIL, "FILENAMES", PS_META_REPLACE, + "Filenames for file rule definition", dummy); + psFree(dummy); + + bool found = false; // Found the file? + pmFPAfile *file = bind ? pmFPAfileBindFromArgs(&found, bind, config, name, "FILENAMES") : + pmFPAfileDefineFromArgs(&found, config, name, "FILENAMES"); + if (!file || !found) { + psError(PS_ERR_UNKNOWN, false, "Unable to define file %s from %s", name, filename); + return NULL; + } + if (file->type != type) { + psError(PS_ERR_IO, true, "%s is not of type %s", name, pmFPAfileStringFromType(type)); + return NULL; + } + + return file; +} + Index: /branches/eam_branches/20091201/psphot/src/psphotSubtractBackground.c =================================================================== --- /branches/eam_branches/20091201/psphot/src/psphotSubtractBackground.c (revision 26522) +++ /branches/eam_branches/20091201/psphot/src/psphotSubtractBackground.c (revision 26523) @@ -112,2 +112,37 @@ return true; } + +// XXX supply filename or keep PSPHOT.INPUT fixed? +bool psphotStackSubtractBackground (pmConfig *config, const pmFPAview *view) +{ + bool status = true; + + int num = psMetadataAddS32 (&status, config->arguments, "INPUTS.NUM"); + psAbort (!status, "programming error: must define INPUTS.NUM"); + + // loop over the available readouts + for (int i = 0; i < num; i++) { + + pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PSPHOT.INPUT", i); // File of interest + + // find the currently selected readout + pmReadout *readout = pmFPAviewThisReadout (view, file->fpa); + PS_ASSERT_PTR_NON_NULL (readout, false); + + psImageBinning *binning = psphotBackgroundBinning(readout->image, config); // Image binning parameters + pmReadout *model = pmFPAGenerateReadout(config, view, "PSPHOT.BACKMDL", inFPA, binning); // this needs to be a MULTI like PSPHOT.INPUT + pmReadout *modelStdev = pmFPAGenerateReadout(config, view, "PSPHOT.BACKMDL.STDEV", inFPA, binning); // this needs to be a MULTI like PSPHOT.INPUT + + // XXX save results on model->analysis or readout->analysis?? + // XXX need to create a worker function from the function above... + if (!backgroundModel(model->image, modelStdev->image, model->analysis, readout, binning, config)) { + psError(PS_ERR_UNKNOWN, false, "Unable to generate background model"); + return false; + } + // display the backsub and backgnd images + psphotVisualShowBackground (config, view, readout); + + npass ++; + } + return true; +}