Index: /trunk/ppMerge/src/ppMergeArguments.c =================================================================== --- /trunk/ppMerge/src/ppMergeArguments.c (revision 21364) +++ /trunk/ppMerge/src/ppMergeArguments.c (revision 21365) @@ -6,6 +6,6 @@ * * @author IfA - * @version $Revision: 1.16 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-01 21:43:05 $ + * @version $Revision: 1.17 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-06 02:44:31 $ * Copyright 2009 Institute for Astronomy, University of Hawaii */ @@ -25,6 +25,6 @@ "\tIMAGE(STR): Image filename\n" "\tMASK(STR): Mask filename\n" - "\tWEIGHT(STR) Weight map filename\n" - "where MASK and WEIGHT are optional.", + "\tVARIANCE(STR) Variance map filename\n" + "where MASK and VARIANCE are optional.", program); fprintf(stderr, "\n"); @@ -155,5 +155,5 @@ psMetadataAddF32(arguments, PS_LIST_TAIL, "-frachigh", 0, "Fraction of low pixels to discard", NAN); psMetadataAddS32(arguments, PS_LIST_TAIL, "-nkeep", 0, "Minimum number of pixels in stack to keep", 0); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-weights", 0, "Use image weights in combination?", false); + psMetadataAddBool(arguments, PS_LIST_TAIL, "-variances", 0, "Use image variances in combination?", false); // XXX EAM : not clear this should be allowed on the command line. @@ -300,5 +300,5 @@ VALUE_ARG_RECIPE_FLOAT("-frachigh", "FRACHIGH", F32); VALUE_ARG_RECIPE_INT("-nkeep", "NKEEP", S32, 0); - VALUE_ARG_RECIPE_BOOL("-weights", "WEIGHTS"); + VALUE_ARG_RECIPE_BOOL("-variances", "VARIANCES"); // XXX we do not supply this on the command line Index: /trunk/ppMerge/src/ppMergeCamera.c =================================================================== --- /trunk/ppMerge/src/ppMergeCamera.c (revision 21364) +++ /trunk/ppMerge/src/ppMergeCamera.c (revision 21365) @@ -6,6 +6,6 @@ * * @author IfA - * @version $Revision: 1.8 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-01 21:43:05 $ + * @version $Revision: 1.9 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-06 02:44:31 $ * Copyright 2009 Institute for Astronomy, University of Hawaii */ @@ -96,5 +96,5 @@ { bool haveMasks = false; // Do we have masks? - bool haveWeights = false; // Do we have weight maps? + bool haveVariances = false; // Do we have variance maps? ppMergeType type = psMetadataLookupS32(NULL, config->arguments, "TYPE"); ///< Type of frame @@ -121,6 +121,6 @@ bool mdok; - psString mask = psMetadataLookupStr(&mdok, input, "MASK"); ///< Name of mask - psString weight = psMetadataLookupStr(&mdok, input, "WEIGHT"); ///< Name of weight map + psString mask = psMetadataLookupStr(&mdok, input, "MASK"); // Name of mask + psString variance = psMetadataLookupStr(&mdok, input, "VARIANCE"); // Name of variance map // Add the image file @@ -164,25 +164,26 @@ } - // Optionally add the weight file - if (weight && strlen(weight) > 0) { - haveWeights = true; - psArray *weightFiles = psArrayAlloc(1); ///< Array of filenames for this FPA - weightFiles->data[0] = psMemIncrRefCounter(weight); - psMetadataAddArray(config->arguments, PS_LIST_TAIL, "WEIGHT.FILENAMES", PS_META_REPLACE, - "Filenames of weight files", weightFiles); - psFree(weightFiles); + // Optionally add the variance file + if (variance && strlen(variance) > 0) { + haveVariances = true; + psArray *varianceFiles = psArrayAlloc(1); // Array of filenames for this FPA + varianceFiles->data[0] = psMemIncrRefCounter(variance); + psMetadataAddArray(config->arguments, PS_LIST_TAIL, "VARIANCE.FILENAMES", PS_META_REPLACE, + "Filenames of variance files", varianceFiles); + psFree(varianceFiles); bool status; - pmFPAfile *weightFile = pmFPAfileBindFromArgs(&status, imageFile, config, "PPMERGE.INPUT.WEIGHT", - "WEIGHT.FILENAMES"); + pmFPAfile *varianceFile = pmFPAfileBindFromArgs(&status, imageFile, config, + "PPMERGE.INPUT.VARIANCE", "VARIANCE.FILENAMES"); if (!status) { - psError(PS_ERR_UNKNOWN, false, "Unable to define file from weight %d (%s)", numFiles, weight); - return false; - } - if (weightFile->type != PM_FPA_FILE_WEIGHT) { - psError(PS_ERR_IO, true, "PPMERGE.INPUT.WEIGHT is not of type WEIGHT"); - return false; - } - haveWeights = true; + psError(PS_ERR_UNKNOWN, false, "Unable to define file from variance %d (%s)", + numFiles, variance); + return false; + } + if (varianceFile->type != PM_FPA_FILE_VARIANCE) { + psError(PS_ERR_IO, true, "PPMERGE.INPUT.VARIANCE is not of type VARIANCE"); + return false; + } + haveVariances = true; } @@ -194,6 +195,6 @@ psMetadataRemoveKey(config->arguments, "MASK.FILENAMES"); } - if (psMetadataLookup(config->arguments, "WEIGHT.FILENAMES")) { - psMetadataRemoveKey(config->arguments, "WEIGHT.FILENAMES"); + if (psMetadataLookup(config->arguments, "VARIANCE.FILENAMES")) { + psMetadataRemoveKey(config->arguments, "VARIANCE.FILENAMES"); } if (psMetadataLookup(config->arguments, "PSF.FILENAMES")) { @@ -203,6 +204,6 @@ psMetadataAddS32(config->arguments, PS_LIST_TAIL, "INPUTS.NUM", 0, "Number of input files", numFiles); psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUTS.MASKS", 0, "Got input masks?", haveMasks); - psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUTS.WEIGHTS", 0, - "Got input weights?", haveWeights); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUTS.VARIANCES", 0, + "Got input variances?", haveVariances); Index: /trunk/ppMerge/src/ppMergeFiles.c =================================================================== --- /trunk/ppMerge/src/ppMergeFiles.c (revision 21364) +++ /trunk/ppMerge/src/ppMergeFiles.c (revision 21365) @@ -6,6 +6,6 @@ * * @author IfA - * @version $Revision: 1.7 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-01 21:43:05 $ + * @version $Revision: 1.8 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-06 02:44:31 $ * Copyright 2009 Institute for Astronomy, University of Hawaii */ @@ -13,9 +13,9 @@ #include "ppMerge.h" -const char *allFiles[] = { "PPMERGE.INPUT", "PPMERGE.INPUT.MASK", "PPMERGE.INPUT.WEIGHT", +const char *allFiles[] = { "PPMERGE.INPUT", "PPMERGE.INPUT.MASK", "PPMERGE.INPUT.VARIANCE", "PPMERGE.OUTPUT", "PPMERGE.OUTPUT.COUNT", "PPMERGE.OUTPUT.SIGMA", - NULL }; ///< All files -const char *inputFiles[] = { "PPMERGE.INPUT", "PPMERGE.INPUT.MASK", "PPMERGE.INPUT.WEIGHT", - NULL }; ///< Input files + NULL }; // All files +const char *inputFiles[] = { "PPMERGE.INPUT", "PPMERGE.INPUT.MASK", "PPMERGE.INPUT.VARIANCE", + NULL }; // Input files const char *outputFiles[] = { "PPMERGE.OUTPUT", "PPMERGE.OUTPUT.COUNT", "PPMERGE.OUTPUT.SIGMA", NULL }; ///< Output files @@ -51,8 +51,8 @@ } } - if (psMetadataLookupBool(&mdok, config->arguments, "INPUTS.WEIGHTS")) { - pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.WEIGHT", num); - if (!pmReadoutReadChunkWeight(readout, file->fits, 0, rows, 0, config)) { - psError(PS_ERR_UNKNOWN, false, "Unable to read readout weight."); + if (psMetadataLookupBool(&mdok, config->arguments, "INPUTS.VARIANCES")) { + pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.VARIANCE", num); + if (!pmReadoutReadChunkVariance(readout, file->fits, 0, rows, 0, config)) { + psError(PS_ERR_UNKNOWN, false, "Unable to read readout variance."); return false; } @@ -91,9 +91,10 @@ psFree(fileView); } - if (psMetadataLookupBool(&mdok, config->arguments, "INPUTS.WEIGHTS")) { - pmFPAfile *weight = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.WEIGHT", num); // Weight file - pmFPAview *fileView = pmFPAviewForLevel(weight->fileLevel, view); - if (!pmFPAfileOpen(weight, fileView, config)) { - psError(PS_ERR_UNKNOWN, false, "Unable to open weight file %d", num); + if (psMetadataLookupBool(&mdok, config->arguments, "INPUTS.VARIANCES")) { + pmFPAfile *variance = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.VARIANCE", + num); // Variance file + pmFPAview *fileView = pmFPAviewForLevel(variance->fileLevel, view); + if (!pmFPAfileOpen(variance, fileView, config)) { + psError(PS_ERR_UNKNOWN, false, "Unable to open variance file %d", num); psFree(fileView); return false; @@ -127,5 +128,5 @@ bool mdok; // Status of MD lookup bool haveMasks = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS"); // Do we have masks? - bool haveWeights = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.WEIGHTS"); // Got weights? + bool haveVariances = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.VARIANCES"); // Got variances? const char **fileList = selectFiles(files); // Files to activate @@ -134,5 +135,5 @@ continue; } - if (!haveWeights && strcmp(fileList[i], "PPMERGE.INPUT.WEIGHT") == 0) { + if (!haveVariances && strcmp(fileList[i], "PPMERGE.INPUT.VARIANCE") == 0) { continue; } @@ -163,5 +164,5 @@ bool mdok; // Status of MD lookup bool haveMasks = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS"); // Do we have masks? - bool haveWeights = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.WEIGHTS"); // Got weights? + bool haveVariances = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.VARIANCES"); // Got variances? psList *list = psListAlloc(NULL); // List of files @@ -171,5 +172,5 @@ continue; } - if (!haveWeights && strcmp(fileList[i], "PPMERGE.INPUT.WEIGHT") == 0) { + if (!haveVariances && strcmp(fileList[i], "PPMERGE.INPUT.VARIANCE") == 0) { continue; } Index: /trunk/ppMerge/src/ppMergeLoop_Threaded.c =================================================================== --- /trunk/ppMerge/src/ppMergeLoop_Threaded.c (revision 21364) +++ /trunk/ppMerge/src/ppMergeLoop_Threaded.c (revision 21365) @@ -6,6 +6,6 @@ * * @author IfA - * @version $Revision: 1.8 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-01 21:43:05 $ + * @version $Revision: 1.9 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-06 02:44:31 $ * Copyright 2009 Institute for Astronomy, University of Hawaii */ @@ -36,13 +36,13 @@ bool mdok; ///< Status of MD lookup bool haveMasks = psMetadataLookupBool(&mdok, arguments, "INPUTS.MASKS"); // Do we have masks? - bool haveWeights = psMetadataLookupBool(&mdok, arguments, "INPUTS.WEIGHTS"); ///< Do we have weights? - - psArray *inputs = ppMergeFileDataLevel(config, "PPMERGE.INPUT", PM_FPA_LEVEL_READOUT); ///< Input images - psArray *masks = NULL, *weights = NULL; ///< Input masks and weights + bool haveVariances = psMetadataLookupBool(&mdok, arguments, "INPUTS.VARIANCES"); // Do we have variances? + + psArray *inputs = ppMergeFileDataLevel(config, "PPMERGE.INPUT", PM_FPA_LEVEL_READOUT); // Input images + psArray *masks = NULL, *variances = NULL; // Input masks and variances if (haveMasks) { masks = ppMergeFileDataLevel(config, "PPMERGE.INPUT.MASK", PM_FPA_LEVEL_READOUT); } - if (haveWeights) { - weights = ppMergeFileDataLevel(config, "PPMERGE.INPUT.WEIGHT", PM_FPA_LEVEL_READOUT); + if (haveVariances) { + variances = ppMergeFileDataLevel(config, "PPMERGE.INPUT.VARIANCE", PM_FPA_LEVEL_READOUT); } @@ -50,23 +50,22 @@ if (!mdok) nThreads = 0; - /** General combination parameters */ - int iter = psMetadataLookupS32(NULL, arguments, "ITER"); ///< Number of rejection iterations - float rej = psMetadataLookupF32(NULL, arguments, "REJ"); ///< Rejection level - float fraclow = psMetadataLookupF32(NULL, arguments, "FRACLOW"); ///< Reject fraction of low pixels - float frachigh = psMetadataLookupF32(NULL, arguments, "FRACHIGH"); ///< Reject fraction of hi pixels - int nKeep = psMetadataLookupS32(NULL, arguments, "NKEEP"); ///< Minimum number of values to keep - psStatsOptions combineStat = psMetadataLookupS32(NULL, arguments, "COMBINE"); ///< Combination statistic - bool useWeights = psMetadataLookupBool(NULL, arguments, "WEIGHTS"); ///< Use weights? - - /** Fringe parameters */ - int fringeNum = psMetadataLookupS32(NULL, arguments, "FRINGE.NUM"); ///< Number of fringe points - int fringeSize = psMetadataLookupS32(NULL, arguments, "FRINGE.SIZE"); ///< Size of fringe regions - int fringeSmoothX = psMetadataLookupS32(NULL, arguments, "FRINGE.XSMOOTH"); ///< Smoothing regions in x - int fringeSmoothY = psMetadataLookupS32(NULL, arguments, "FRINGE.YSMOOTH"); ///< Smoothing regions in y + // General combination parameters + int iter = psMetadataLookupS32(NULL, arguments, "ITER"); // Number of rejection iterations + float rej = psMetadataLookupF32(NULL, arguments, "REJ"); // Rejection level + float fraclow = psMetadataLookupF32(NULL, arguments, "FRACLOW"); // Reject fraction of low pixels + float frachigh = psMetadataLookupF32(NULL, arguments, "FRACHIGH"); // Reject fraction of hi pixels + int nKeep = psMetadataLookupS32(NULL, arguments, "NKEEP"); // Minimum number of values to keep + psStatsOptions combineStat = psMetadataLookupS32(NULL, arguments, "COMBINE"); // Combination statistic + bool useVariances = psMetadataLookupBool(NULL, arguments, "VARIANCES"); // Use variances? + + // Fringe parameters + int fringeNum = psMetadataLookupS32(NULL, arguments, "FRINGE.NUM"); // Number of fringe points + int fringeSize = psMetadataLookupS32(NULL, arguments, "FRINGE.SIZE"); // Size of fringe regions + int fringeSmoothX = psMetadataLookupS32(NULL, arguments, "FRINGE.XSMOOTH"); // Smoothing regions in x + int fringeSmoothY = psMetadataLookupS32(NULL, arguments, "FRINGE.YSMOOTH"); // Smoothing regions in y // set the mask and mark bit values based on the named masks - psImageMaskType maskVal; - psImageMaskType markVal; - if (!pmConfigMaskSetBits (&maskVal, &markVal, config)) { + psImageMaskType maskVal, markVal; + if (!pmConfigMaskSetBits(&maskVal, &markVal, config)) { psError (PS_ERR_UNKNOWN, true, "Unable to define the mask bit values"); return false; @@ -81,5 +80,5 @@ combination->iter = iter; combination->rej = rej; - combination->weights = useWeights; + combination->variances = useVariances; psMetadata *stats = NULL; ///< Statistics for output @@ -344,11 +343,11 @@ psFree(countsRO); - // XXX EAM 2009.01.18 : sigmaCell and countsCell need to have their concepts copied from outCell. - // This was causing segfaults for VYSOS5; Why did this ever work for SIMTEST? - if (!pmConceptsCopyCell(countsCell, outCell)) { - psError(PS_ERR_UNKNOWN, false, "Unable to copy cell concepts."); - psFree(outRO); - goto ERROR; - } + // XXX EAM 2009.01.18 : sigmaCell and countsCell need to have their concepts copied from outCell. + // This was causing segfaults for VYSOS5; Why did this ever work for SIMTEST? + if (!pmConceptsCopyCell(countsCell, outCell)) { + psError(PS_ERR_UNKNOWN, false, "Unable to copy cell concepts."); + psFree(outRO); + goto ERROR; + } pmCell *sigmaCell = pmFPAfileThisCell(config->files, view, "PPMERGE.OUTPUT.SIGMA"); @@ -360,9 +359,9 @@ psFree(sigmaRO); - if (!pmConceptsCopyCell(sigmaCell, outCell)) { - psError(PS_ERR_UNKNOWN, false, "Unable to copy cell concepts."); - psFree(outRO); - goto ERROR; - } + if (!pmConceptsCopyCell(sigmaCell, outCell)) { + psError(PS_ERR_UNKNOWN, false, "Unable to copy cell concepts."); + psFree(outRO); + goto ERROR; + } } @@ -447,5 +446,5 @@ psFree(inputs); psFree(masks); - psFree(weights); + psFree(variances); psFree(stats); return true; @@ -456,5 +455,5 @@ psFree(inputs); psFree(masks); - psFree(weights); + psFree(variances); psFree(stats); return false; Index: /trunk/ppMerge/src/ppMergeMask.c =================================================================== --- /trunk/ppMerge/src/ppMergeMask.c (revision 21364) +++ /trunk/ppMerge/src/ppMergeMask.c (revision 21365) @@ -6,6 +6,6 @@ * * @author IfA - * @version $Revision: 1.17 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-01 21:43:05 $ + * @version $Revision: 1.18 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-06 02:44:31 $ * Copyright 2009 Institute for Astronomy, University of Hawaii */ @@ -38,9 +38,8 @@ float smoothScale = psMetadataLookupF32(&mdok, config->arguments, "MASK.SMOOTH.SCALE"); ///< Radius to grow mask - psImageMaskType markVal; - psImageMaskType maskValRaw; - if (!pmConfigMaskSetBits (&maskValRaw, &markVal, config)) { - psError (PS_ERR_UNKNOWN, true, "Unable to define the mask bit values"); - return false; + psImageMaskType markVal, maskValRaw; + if (!pmConfigMaskSetBits(&maskValRaw, &markVal, config)) { + psError(PS_ERR_UNKNOWN, true, "Unable to define the mask bit values"); + return false; } @@ -48,23 +47,23 @@ psImageMaskType maskValOut = pmConfigMaskGet (maskOutName, config); if (!maskValOut) { - psError (PS_ERR_UNKNOWN, true, "Undefined output mask bit value"); - return false; - } - - psStats *statistics = psStatsAlloc(meanStat | stdevStat); ///< Statistics for background + psError (PS_ERR_UNKNOWN, true, "Undefined output mask bit value"); + return false; + } + + psStats *statistics = psStatsAlloc(meanStat | stdevStat); // Statistics for background psString outName = ppMergeOutputFile(config); ///< Name of output file pmChip *outChip = pmFPAfileThisChip(config->files, view, outName); ///< Output chip psFree(outName); - + int numCells = 1; if (chipStats) { - // count the number of active cells for this chip: - numCells = 0; - for (int i = 0; i < outChip->cells->n; i++) { - pmCell *cell = outChip->cells->data[i]; - if (!cell->process) continue; - numCells ++; - } + // count the number of active cells for this chip: + numCells = 0; + for (int i = 0; i < outChip->cells->n; i++) { + pmCell *cell = outChip->cells->data[i]; + if (!cell->process) continue; + numCells ++; + } } @@ -85,7 +84,7 @@ while ((inCell = pmFPAviewNextCell(inView, inFPA, 1))) { - // the output FPA structure carries the information about which cells to process - pmCell *outCell = pmFPAfileThisCell(config->files, inView, "PPMERGE.OUTPUT.MASK"); ///< Output cell - if (!outCell->process) continue; + // the output FPA structure carries the information about which cells to process + pmCell *outCell = pmFPAfileThisCell(config->files, inView, "PPMERGE.OUTPUT.MASK"); // Output cell + if (!outCell->process) continue; pmHDU *hdu = pmHDUFromCell(inCell); ///< HDU for cell @@ -150,6 +149,6 @@ int y = pixel / numCols; if (mask && (mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & maskValRaw)) continue; - if (outMask && (outMask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & maskValOut)) continue; - if (!isfinite(image->data.F32[y][x])) continue; + if (outMask && (outMask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & maskValOut)) continue; + if (!isfinite(image->data.F32[y][x])) continue; values->data.F32[valueIndex++] = image->data.F32[y][x]; @@ -165,9 +164,9 @@ } - float mean = psStatsGetValue(statistics, meanStat); - float stdev = psStatsGetValue(statistics, stdevStat); - - // this function increments the count for each suspect pixel in each input plane - // maskValRaw is used to test for valid input pixels + float mean = psStatsGetValue(statistics, meanStat); + float stdev = psStatsGetValue(statistics, stdevStat); + + // this function increments the count for each suspect pixel in each input plane + // maskValRaw is used to test for valid input pixels if (!pmMaskFlagSuspectPixels(outRO, readout, mean, stdev, maskSuspect, maskValRaw)) { psError(PS_ERR_UNKNOWN, false, "Unable to find suspect values in file %d", i); @@ -197,8 +196,7 @@ inView->cell = -1; while ((inCell = pmFPAviewNextCell(inView, inFPA, 1))) { - - // the output FPA structure carries the information about which cells to process - pmCell *outCell = pmFPAfileThisCell(config->files, inView, "PPMERGE.OUTPUT.MASK"); ///< Output cell - if (!outCell->process) continue; + // the output FPA structure carries the information about which cells to process + pmCell *outCell = pmFPAfileThisCell(config->files, inView, "PPMERGE.OUTPUT.MASK"); // Output cell + if (!outCell->process) continue; pmHDU *hdu = pmHDUFromCell(inCell); ///< HDU for cell @@ -210,8 +208,8 @@ pmReadout *outRO = pmFPAfileThisReadout(config->files, inView, "PPMERGE.OUTPUT.MASK"); - float mean = psStatsGetValue(statistics, meanStat); - float stdev = psStatsGetValue(statistics, stdevStat); - - if (!pmMaskFlagSuspectPixels(outRO, readout, mean, stdev, maskSuspect, maskValRaw)) { + float mean = psStatsGetValue(statistics, meanStat); + float stdev = psStatsGetValue(statistics, stdevStat); + + if (!pmMaskFlagSuspectPixels(outRO, readout, mean, stdev, maskSuspect, maskValRaw)) { psError(PS_ERR_UNKNOWN, false, "Unable to find suspect values in file %d", i); goto MERGE_MASK_ERROR; @@ -243,6 +241,6 @@ while ((outCell = pmFPAviewNextCell(outView, outFPA, 1))) { - // skip inactive cells - if (!outCell->process) continue; + // skip inactive cells + if (!outCell->process) continue; pmHDU *hdu = pmHDUFromCell(outCell); ///< HDU for cell @@ -254,12 +252,12 @@ pmReadout *outRO = outCell->readouts->data[0]; ///< Output readout - if (smoothSuspect) { - // XXX test output of suspect pixel image - psImage *suspects = psMetadataLookupPtr(NULL, outRO->analysis, PM_MASK_ANALYSIS_SUSPECT); ///< Suspect img - assert (suspects); - psImageSmooth (suspects, smoothScale, 3); ///< extend smoothing region to 3-sigma - } - - // set the bad pixels to the value 'maskVal' + if (smoothSuspect) { + // XXX test output of suspect pixel image + psImage *suspects = psMetadataLookupPtr(NULL, outRO->analysis, PM_MASK_ANALYSIS_SUSPECT); // Suspect img + assert (suspects); + psImageSmooth (suspects, smoothScale, 3); // extend smoothing region to 3-sigma + } + + // set the bad pixels to the value 'maskVal' if (!pmMaskIdentifyBadPixels(outRO, maskValOut, maskBad, maskMode)) { psError(PS_ERR_UNKNOWN, false, "Unable to mask bad pixels"); @@ -352,9 +350,9 @@ assert(config); - bool mdok; ///< Status of MD lookup - int numFiles = psMetadataLookupS32(NULL, config->arguments, "INPUTS.NUM"); ///< Number of inputs - bool haveMasks = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS"); ///< Do we have masks? - bool haveWeights = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.WEIGHTS"); ///< Do we have weights? - int iter = psMetadataLookupS32(NULL, config->arguments, "ITER"); ///< Number of rejection iterations + bool mdok; // Status of MD lookup + int numFiles = psMetadataLookupS32(NULL, config->arguments, "INPUTS.NUM"); // Number of inputs + bool haveMasks = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS"); // Do we have masks? + bool haveVariances = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.VARIANCES"); // Got variances? + int iter = psMetadataLookupS32(NULL, config->arguments, "ITER"); // Number of rejection iterations PS_ASSERT_INT_POSITIVE(iter, false); @@ -375,7 +373,7 @@ psFree(masks); } - if (haveWeights) { - psArray *weights = ppMergeFileDataLevel(config, "PPMERGE.INPUT.WEIGHT", PM_FPA_LEVEL_READOUT); - psFree(weights); + if (haveVariances) { + psArray *variances = ppMergeFileDataLevel(config, "PPMERGE.INPUT.VARIANCE", PM_FPA_LEVEL_READOUT); + psFree(variances); } @@ -417,21 +415,21 @@ } - if (outChip->data_exists) { - psList *inChips = psListAlloc(NULL); - for (int i=0; i < numFiles; i++) { - pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT", i); ///< Input file - pmChip *chip = pmFPAviewThisChip(view, file->fpa); - psListAdd(inChips, PS_LIST_TAIL, chip); - } - - // XXX I need to call pmConfigMaskWriteHeader for the PHU somewhere, after it is created! - - if (!pmConceptsAverageChips(outChip, inChips, true)) { - psError(PS_ERR_UNKNOWN, false, "Unable to average Chip concepts."); - psFree(inChips); - goto PPMERGE_MASK_ERROR; - } - psFree(inChips); - } + if (outChip->data_exists) { + psList *inChips = psListAlloc(NULL); + for (int i=0; i < numFiles; i++) { + pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT", i); // Input file + pmChip *chip = pmFPAviewThisChip(view, file->fpa); + psListAdd(inChips, PS_LIST_TAIL, chip); + } + + // XXX I need to call pmConfigMaskWriteHeader for the PHU somewhere, after it is created! + + if (!pmConceptsAverageChips(outChip, inChips, true)) { + psError(PS_ERR_UNKNOWN, false, "Unable to average Chip concepts."); + psFree(inChips); + goto PPMERGE_MASK_ERROR; + } + psFree(inChips); + } if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { goto PPMERGE_MASK_ERROR; Index: /trunk/ppMerge/src/ppMergeReadChunk.c =================================================================== --- /trunk/ppMerge/src/ppMergeReadChunk.c (revision 21364) +++ /trunk/ppMerge/src/ppMergeReadChunk.c (revision 21365) @@ -6,6 +6,6 @@ * * @author IfA - * @version $Revision: 1.5 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-01 21:43:05 $ + * @version $Revision: 1.6 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-06 02:44:31 $ * Copyright 2009 Institute for Astronomy, University of Hawaii */ @@ -20,7 +20,8 @@ bool mdok; - bool haveMasks = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS"); ///< Do we have masks? - bool haveWeights = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.WEIGHTS");///< Do we have weights? - int rows = psMetadataLookupS32(NULL, config->arguments, "ROWS"); ///< Number of rows to read per chunk + bool haveMasks = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS"); // Do we have masks? + bool haveVariances = psMetadataLookupBool(&mdok, config->arguments, + "INPUTS.VARIANCES");// Do we have variances? + int rows = psMetadataLookupS32(NULL, config->arguments, "ROWS"); // Number of rows to read per chunk // select an available fileGroup @@ -52,5 +53,5 @@ // override the recorded last scan inRO->thisImageScan = fileGroup->firstScan; - inRO->thisWeightScan = fileGroup->firstScan; + inRO->thisVarianceScan = fileGroup->firstScan; inRO->thisMaskScan = fileGroup->firstScan; inRO->forceScan = true; @@ -81,9 +82,10 @@ } - if (haveWeights && pmReadoutMoreWeight(inRO, file->fits, 0, rows, config)) { + if (haveVariances && pmReadoutMoreVariance(inRO, file->fits, 0, rows, config)) { keepReading = true; - pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.WEIGHT", i); - if (!pmReadoutReadChunkWeight(inRO, file->fits, 0, rows, 0, config)) { - psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPMERGE.INPUT.WEIGHT %d", + pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.VARIANCE", i); + if (!pmReadoutReadChunkVariance(inRO, file->fits, 0, rows, 0, config)) { + psError(PS_ERR_IO, false, + "Unable to read chunk %d for file PPMERGE.INPUT.VARIANCE %d", numChunk, i); *status = false; Index: /trunk/ppMerge/src/ppMergeScaleZero.c =================================================================== --- /trunk/ppMerge/src/ppMergeScaleZero.c (revision 21364) +++ /trunk/ppMerge/src/ppMergeScaleZero.c (revision 21365) @@ -6,6 +6,6 @@ * * @author IfA - * @version $Revision: 1.30 $ $Name: not supported by cvs2svn $ - * @date $Date: 2009-02-02 20:26:26 $ + * @version $Revision: 1.31 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-06 02:44:31 $ * Copyright 2009 Institute for Astronomy, University of Hawaii */ @@ -56,9 +56,9 @@ for (int i = 0; i < numInputs; i++) { pmFPAfileActivate(config->files, false, NULL); - psArray *files = ppMergeFileActivateSingle(config, PPMERGE_FILES_INPUT, true, i); ///< Activated files - pmFPAfile *input = files->data[0]; ///< Representative file; should be the image (not mask or weight) - pmFPA *fpa = input->fpa; ///< FPA of interest - view = pmFPAviewAlloc(0); ///< View to component of interest - int cellNum = 0; ///< Index for cell + psArray *files = ppMergeFileActivateSingle(config, PPMERGE_FILES_INPUT, true, i); // Activated files + pmFPAfile *input = files->data[0]; // Representative file; should be the image (not mask or variance) + pmFPA *fpa = input->fpa; // FPA of interest + view = pmFPAviewAlloc(0); // View to component of interest + int cellNum = 0; // Index for cell if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { goto ERROR; Index: /trunk/ppSim/src/ppSimInsertStars.c =================================================================== --- /trunk/ppSim/src/ppSimInsertStars.c (revision 21364) +++ /trunk/ppSim/src/ppSimInsertStars.c (revision 21365) @@ -39,7 +39,7 @@ float skyRate = psMetadataLookupF32(NULL, recipe, "SKY.RATE"); // Sky rate if (isnan(skyRate)) { - float zp = psMetadataLookupF32(&mdok, recipe, "ZEROPOINT"); assert (mdok); - float scale = psMetadataLookupF32(&mdok, recipe, "PIXEL.SCALE"); assert (mdok); - float skyMags = psMetadataLookupF32(&mdok, recipe, "SKY.MAGS"); assert (mdok); + float zp = psMetadataLookupF32(&mdok, recipe, "ZEROPOINT"); assert (mdok); + float scale = psMetadataLookupF32(&mdok, recipe, "PIXEL.SCALE"); assert (mdok); + float skyMags = psMetadataLookupF32(&mdok, recipe, "SKY.MAGS"); assert (mdok); skyRate = scale * scale * ppSimMagToFlux (skyMags, zp); } @@ -75,5 +75,5 @@ FILE *outfile = fopen (outname, "w"); - // add sources to the readout image & weight + // add sources to the readout image & variance psTrace("ppSim", 1, "Inserting %ld stars...\n", stars->n); for (long i = 0; i < stars->n; i++) { @@ -118,5 +118,5 @@ psF64 Area = 2.0 * M_PI * axes.major * axes.minor; - // this value is the pure (input) flux, and is saved in the output source cmf files + // this value is the pure (input) flux, and is saved in the output source cmf files source->psfMag = -2.5*log10(star->flux); source->errMag = sqrt(Area*PS_SQR(roughNoise) + flux) / flux; @@ -132,5 +132,5 @@ // Blow away the image parts of the source, which makes the memory explode RESET(source->pixels); - RESET(source->weight); + RESET(source->variance); RESET(source->maskObj); RESET(source->maskView); Index: /trunk/ppSim/src/ppSimLoadForceSources.c =================================================================== --- /trunk/ppSim/src/ppSimLoadForceSources.c (revision 21364) +++ /trunk/ppSim/src/ppSimLoadForceSources.c (revision 21365) @@ -56,17 +56,17 @@ // Select the spots within range of this readout. Project the spots to this chip for (int i = 0; i < spots->n; i++) { - pmAstromObj *obj = spots->data[i]; + pmAstromObj *obj = spots->data[i]; - psProject (obj->TP, obj->sky, fpa->toSky); - psPlaneTransformApply (obj->FP, fpa->fromTPA, obj->TP); - psPlaneTransformApply (obj->chip, chip->fromFPA, obj->FP); + psProject (obj->TP, obj->sky, fpa->toSky); + psPlaneTransformApply (obj->FP, fpa->fromTPA, obj->TP); + psPlaneTransformApply (obj->chip, chip->fromFPA, obj->FP); - // limit the X,Y range of the objs to the selected chip - if (obj->chip->x < minX) continue; - if (obj->chip->x > maxX) continue; - if (obj->chip->y < minY) continue; - if (obj->chip->y > maxY) continue; + // limit the X,Y range of the objs to the selected chip + if (obj->chip->x < minX) continue; + if (obj->chip->x > maxX) continue; + if (obj->chip->y < minY) continue; + if (obj->chip->y > maxY) continue; - // convert the pmAstromObj to pmSource + // convert the pmAstromObj to pmSource // instantiate a model for the PSF at this location, Io = 1.0 @@ -74,8 +74,8 @@ // XXX let the flux limit be a user-defined number of sky sigmas (not just 1.0) - // XXX use a fixed radius?? + // XXX use a fixed radius?? // float radius = model->modelRadius (model->params, roughNoise); // radius = PS_MAX (radius, 1.0); - float radius = 5.0; + float radius = 5.0; // construct a source, with model flux pixels set, based on the model @@ -87,10 +87,10 @@ // psF64 Area = 2.0 * M_PI * axes.major * axes.minor; - // these are not really needed since we will be fitting for them + // these are not really needed since we will be fitting for them source->psfMag = NAN; source->errMag = NAN; // insert the source flux in the image - // XXX not sure the offset is really 0,0 + // XXX not sure the offset is really 0,0 pmSourceAddWithOffset (source, PM_MODEL_OP_FULL, 0xff, 0.0, 0.0); pmSourceAddWithOffset (source, PM_MODEL_OP_FULL | PM_MODEL_OP_NOISE, 0xff, 0.0, 0.0); @@ -98,5 +98,5 @@ // Blow away the image parts of the source, which makes the memory explode RESET(source->pixels); - RESET(source->weight); + RESET(source->variance); RESET(source->maskObj); RESET(source->maskView); @@ -105,5 +105,5 @@ RESET(source->blends); - psArrayAdd (sources, 100, source); + psArrayAdd (sources, 100, source); psFree(source); // Drop local reference } Index: /trunk/ppSim/src/ppSimLoop.c =================================================================== --- /trunk/ppSim/src/ppSimLoop.c (revision 21364) +++ /trunk/ppSim/src/ppSimLoop.c (revision 21365) @@ -34,14 +34,14 @@ psArray *galaxies = psArrayAllocEmpty (1); if (type == PPSIM_TYPE_OBJECT) { - // Load forced-photometry positions (these are placed on fpa->analysis for use in ppSimPhotomReadout) - if (!ppSimLoadSpots (fpa, config)) ESCAPE (PS_ERR_UNKNOWN, "failed to load forced-photometry spots"); - - // Load catalogue stars + // Load forced-photometry positions (these are placed on fpa->analysis for use in ppSimPhotomReadout) + if (!ppSimLoadSpots (fpa, config)) ESCAPE (PS_ERR_UNKNOWN, "failed to load forced-photometry spots"); + + // Load catalogue stars if (!ppSimLoadStars (stars, fpa, config)) ESCAPE (PS_ERR_UNKNOWN, "failed to load catalog stars"); - // Add random stars + // Add random stars if (!ppSimMakeStars (stars, fpa, config, rng)) ESCAPE (PS_ERR_UNKNOWN, "failed to make random stars"); - // Add random galaxies + // Add random galaxies if (!ppSimMakeGalaxies (galaxies, fpa, config, rng)) ESCAPE (PS_ERR_UNKNOWN, "failed to make random galaxies"); } @@ -105,8 +105,8 @@ // TO DO: Decide if cell is to be windowed, reduce numCols, numRows appropriately readout->image = psImageAlloc(numCols, numRows, PS_TYPE_F32); // Signal in pixels - readout->weight = psImageAlloc(numCols, numRows, PS_TYPE_F32); // Noise in pixels + readout->variance = psImageAlloc(numCols, numRows, PS_TYPE_F32); // Noise in pixels psImageInit (readout->image, 0.0); - psImageInit (readout->weight, 0.0); + psImageInit (readout->variance, 0.0); psFree(readout); // Drop reference @@ -115,12 +115,12 @@ psVector *biasCols = ppSimMakeBiassec (cell, config); - pmReadout *readout; - while ((readout = pmFPAviewNextReadout (view, fpa, 1))) { - - // if we have not read in a weight or generated a fake image above, we need to + pmReadout *readout; + while ((readout = pmFPAviewNextReadout (view, fpa, 1))) { + + // if we have not read in a variance or generated a fake image above, we need to // build one here - if (!readout->weight) { - if (!pmReadoutGenerateWeight(readout, true)) { - psError (PS_ERR_UNKNOWN, false, "trouble creating weight"); + if (!readout->variance) { + if (!pmReadoutGenerateVariance(readout, true)) { + psError (PS_ERR_UNKNOWN, false, "trouble creating variance"); return false; } @@ -133,8 +133,8 @@ psVector *biasRows = ppSimMakeBias (&status, readout, config, rng); - if (!status) ESCAPE (PS_ERR_UNKNOWN, "problem generating dark structure"); + if (!status) ESCAPE (PS_ERR_UNKNOWN, "problem generating dark structure"); if (type == PPSIM_TYPE_BIAS) goto done; - if (!ppSimMakeDark (readout, config)) ESCAPE (PS_ERR_UNKNOWN, "problem generating dark structure"); + if (!ppSimMakeDark (readout, config)) ESCAPE (PS_ERR_UNKNOWN, "problem generating dark structure"); if (type == PPSIM_TYPE_DARK) goto done; @@ -153,5 +153,5 @@ done: - if (!ppSimAddNoise(readout->image, readout->weight, cell, config, rng)) ESCAPE (PS_ERR_UNKNOWN, "problem adding noise"); + if (!ppSimAddNoise(readout->image, readout->variance, cell, config, rng)) ESCAPE (PS_ERR_UNKNOWN, "problem adding noise"); if (!ppSimSaturate(readout, config)) ESCAPE (PS_ERR_UNKNOWN, "problem setting saturation levels"); @@ -165,6 +165,6 @@ readout->parent->parent->data_exists = true; - // if there is an input image, merge it with the simulated image - if (!ppSimMergeReadouts (config, view)) ESCAPE (PS_ERR_UNKNOWN, "problem merging input image with simulated image"); + // if there is an input image, merge it with the simulated image + if (!ppSimMergeReadouts (config, view)) ESCAPE (PS_ERR_UNKNOWN, "problem merging input image with simulated image"); } psFree(biasCols); @@ -173,5 +173,5 @@ if (cell->hdu) { - // XXX only do this if there is no INPUT image? + // XXX only do this if there is no INPUT image? if (!ppSimInitHeader(config, NULL, NULL, cell)) ESCAPE (PS_ERR_UNKNOWN, "problem setting output header"); } @@ -186,13 +186,13 @@ } - // XXX why no UpdateConceptsChip?? + // XXX why no UpdateConceptsChip?? if (chip->hdu) { - // XXX only do this if there is no INPUT image + // XXX only do this if there is no INPUT image if (!ppSimInitHeader(config, NULL, chip, NULL)) ESCAPE (PS_ERR_UNKNOWN, "problem setting output header"); } // we perform photometry on the readouts of this chip in the output - if (!ppSimPhotom (config, view)) ESCAPE (PS_ERR_UNKNOWN, "problem performing photometry"); + if (!ppSimPhotom (config, view)) ESCAPE (PS_ERR_UNKNOWN, "problem performing photometry"); if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { Index: /trunk/ppSim/src/ppSimMakeBias.c =================================================================== --- /trunk/ppSim/src/ppSimMakeBias.c (revision 21364) +++ /trunk/ppSim/src/ppSimMakeBias.c (revision 21365) @@ -20,15 +20,15 @@ float readnoise = psMetadataLookupF32(NULL, cell->concepts, "CELL.READNOISE");// CCD read noise, e if (isnan(readnoise)) { - psWarning("CELL.READNOISE is not set; reverting to recipe value READNOISE."); - readnoise = psMetadataLookupF32(&mdok, recipe, "READNOISE"); - if (!mdok) { - psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to find READNOISE in recipe."); - *status = false; - return NULL; - } + psWarning("CELL.READNOISE is not set; reverting to recipe value READNOISE."); + readnoise = psMetadataLookupF32(&mdok, recipe, "READNOISE"); + if (!mdok) { + psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to find READNOISE in recipe."); + *status = false; + return NULL; + } } psImage *signal = readout->image; - psImage *variance = readout->weight; + psImage *variance = readout->variance; int numRows = signal->numRows; @@ -38,5 +38,5 @@ psPolynomial1D *biasPoly = psPolynomial1DAlloc(PS_POLYNOMIAL_CHEB, biasOrder); for (int j = 0; j < biasOrder + 1; j++) { - biasPoly->coeff[j] = biasRange * psRandomGaussian(rng); + biasPoly->coeff[j] = biasRange * psRandomGaussian(rng); } @@ -45,15 +45,15 @@ for (int y = 0; y < numRows; y++) { - // Adjust bias level for this row - biasRows->data.F32[y] = psPolynomial1DEval(biasPoly, (float)(y + biasOffset) / - (float)numRows - 0.5) + biasLevel; + // Adjust bias level for this row + biasRows->data.F32[y] = psPolynomial1DEval(biasPoly, (float)(y + biasOffset) / + (float)numRows - 0.5) + biasLevel; - for (int x = 0; x < numCols; x++) { + for (int x = 0; x < numCols; x++) { - // Bias level - signal->data.F32[y][x] += biasRows->data.F32[y]; - variance->data.F32[y][x] += PS_SQR(readnoise); + // Bias level + signal->data.F32[y][x] += biasRows->data.F32[y]; + variance->data.F32[y][x] += PS_SQR(readnoise); - } + } } psFree(biasPoly); Index: /trunk/ppSim/src/ppSimMakeDark.c =================================================================== --- /trunk/ppSim/src/ppSimMakeDark.c (revision 21364) +++ /trunk/ppSim/src/ppSimMakeDark.c (revision 21365) @@ -7,5 +7,5 @@ psImage *signal = readout->image; - psImage *variance = readout->weight; + psImage *variance = readout->variance; psMetadata *recipe = psMetadataLookupMetadata(&mdok, config->recipes, PPSIM_RECIPE); // Recipe @@ -29,11 +29,11 @@ for (int y = 0; y < signal->numRows; y++) { - for (int x = 0; x < signal->numCols; x++) { - - // Dark current - float darkCurrent = darkRate * expTime; // Dark current accumulated - signal->data.F32[y][x] += darkCurrent; - variance->data.F32[y][x] += darkCurrent; - } + for (int x = 0; x < signal->numCols; x++) { + + // Dark current + float darkCurrent = darkRate * expTime; // Dark current accumulated + signal->data.F32[y][x] += darkCurrent; + variance->data.F32[y][x] += darkCurrent; + } } return true; Index: /trunk/ppSim/src/ppSimMakeSky.c =================================================================== --- /trunk/ppSim/src/ppSimMakeSky.c (revision 21364) +++ /trunk/ppSim/src/ppSimMakeSky.c (revision 21365) @@ -9,5 +9,5 @@ psImage *signal = readout->image; - psImage *variance = readout->weight; + psImage *variance = readout->variance; pmCell *cell = readout->parent; @@ -19,5 +19,5 @@ bool sky = psMetadataLookupBool(&status, recipe, "SKY"); // Generate a SKY flux? bool flat = psMetadataLookupBool(&status, recipe, "FLAT"); // Apply flat-field term? - + float expTime = psMetadataLookupF32(&status, recipe, "EXPTIME"); // Exposure time @@ -29,7 +29,7 @@ float skyMags = psMetadataLookupF32(&status, recipe, "SKY.MAGS"); assert (status); if (!isnan(skyMags)) { - float zp = psMetadataLookupF32(&status, recipe, "ZEROPOINT"); assert (status); - float scale = psMetadataLookupF32(&status, recipe, "PIXEL.SCALE"); assert (status); - skyRate = scale * scale * ppSimMagToFlux (skyMags, zp); + float zp = psMetadataLookupF32(&status, recipe, "ZEROPOINT"); assert (status); + float scale = psMetadataLookupF32(&status, recipe, "PIXEL.SCALE"); assert (status); + skyRate = scale * scale * ppSimMagToFlux (skyMags, zp); } if (type == PPSIM_TYPE_FLAT) { @@ -37,11 +37,11 @@ } - int x0Chip = psMetadataLookupS32(&status, chip->concepts, "CHIP.X0"); - int y0Chip = psMetadataLookupS32(&status, chip->concepts, "CHIP.Y0"); + int x0Chip = psMetadataLookupS32(&status, chip->concepts, "CHIP.X0"); + int y0Chip = psMetadataLookupS32(&status, chip->concepts, "CHIP.Y0"); int xParityChip = psMetadataLookupS32(&status, chip->concepts, "CHIP.XPARITY"); int yParityChip = psMetadataLookupS32(&status, chip->concepts, "CHIP.YPARITY"); - int x0Cell = psMetadataLookupS32(&status, cell->concepts, "CELL.X0"); - int y0Cell = psMetadataLookupS32(&status, cell->concepts, "CELL.Y0"); + int x0Cell = psMetadataLookupS32(&status, cell->concepts, "CELL.X0"); + int y0Cell = psMetadataLookupS32(&status, cell->concepts, "CELL.Y0"); int xParityCell = psMetadataLookupS32(&status, cell->concepts, "CELL.XPARITY"); int yParityCell = psMetadataLookupS32(&status, cell->concepts, "CELL.YPARITY"); @@ -72,28 +72,28 @@ // Gaussian flat-field over the FPA with flatValue = 1.0 at the field center float flatValue = 1.0; - if (flat) { - // we make the flat-field have a response of 1.0 at the field center (like a vignetting) - flatValue = expf(-0.5 / PS_SQR(flatSigma) * (PS_SQR(yFPA) + PS_SQR(xFPA))); - } + if (flat) { + // we make the flat-field have a response of 1.0 at the field center (like a vignetting) + flatValue = expf(-0.5 / PS_SQR(flatSigma) * (PS_SQR(yFPA) + PS_SQR(xFPA))); + } - float scatterRate = 0.0; + float scatterRate = 0.0; - if (sky) { - // add a scattered light term to the flat-field images - if (type == PPSIM_TYPE_FLAT) { - scatterRate = scatterFrac * PS_SQR(xFPA); - } + if (sky) { + // add a scattered light term to the flat-field images + if (type == PPSIM_TYPE_FLAT) { + scatterRate = scatterFrac * PS_SQR(xFPA); + } - // Sky background - float skyFlux = (skyRate * (flatValue + scatterRate)) * realExpTime; // Flux from sky - signal->data.F32[y][x] += skyFlux; - variance->data.F32[y][x] += skyFlux; - } + // Sky background + float skyFlux = (skyRate * (flatValue + scatterRate)) * realExpTime; // Flux from sky + signal->data.F32[y][x] += skyFlux; + variance->data.F32[y][x] += skyFlux; + } - // used later to modify the star and galaxy photometry - if (expCorr) { - // exposure correction is (effective exposure time) * (flatValue) - expCorr->data.F32[y][x] = flatValue * realExpTime / expTime; - } + // used later to modify the star and galaxy photometry + if (expCorr) { + // exposure correction is (effective exposure time) * (flatValue) + expCorr->data.F32[y][x] = flatValue * realExpTime / expTime; + } // TO DO: Add fringes Index: /trunk/ppSim/src/ppSimMergeReadouts.c =================================================================== --- /trunk/ppSim/src/ppSimMergeReadouts.c (revision 21364) +++ /trunk/ppSim/src/ppSimMergeReadouts.c (revision 21365) @@ -14,8 +14,8 @@ if (!inReadout) return true; - if (!inReadout->weight) { - if (!pmReadoutGenerateWeight(inReadout, true)) { - psError (PS_ERR_UNKNOWN, false, "trouble creating weight"); - return false; + if (!inReadout->variance) { + if (!pmReadoutGenerateVariance(inReadout, true)) { + psError (PS_ERR_UNKNOWN, false, "trouble creating variance"); + return false; } } @@ -30,8 +30,8 @@ psImage *inSignal = inReadout->image; - psImage *inVariance = inReadout->weight; + psImage *inVariance = inReadout->variance; psImage *outSignal = outReadout->image; - psImage *outVariance = outReadout->weight; + psImage *outVariance = outReadout->variance; assert (inSignal->numRows == outSignal->numRows); @@ -39,8 +39,8 @@ for (int y = 0; y < inSignal->numRows; y++) { - for (int x = 0; x < inSignal->numCols; x++) { - outSignal->data.F32[y][x] += inSignal->data.F32[y][x]; - outVariance->data.F32[y][x] += inVariance->data.F32[y][x]; - } + for (int x = 0; x < inSignal->numCols; x++) { + outSignal->data.F32[y][x] += inSignal->data.F32[y][x]; + outVariance->data.F32[y][x] += inVariance->data.F32[y][x]; + } } return true; Index: /trunk/ppSim/src/ppSimPhotomReadoutFake.c =================================================================== --- /trunk/ppSim/src/ppSimPhotomReadoutFake.c (revision 21364) +++ /trunk/ppSim/src/ppSimPhotomReadoutFake.c (revision 21365) @@ -12,5 +12,5 @@ } -# if 0 +# if 0 // set the photcode for this image if (!psphotAddPhotcode (recipe, config, view, "PPSIM.FAKE.CHIP")) { @@ -22,5 +22,5 @@ // *** in this section, perform the photometry for real + fake sources on PPSIM.FAKE.CHIP *** - // find the currently selected readout. + // find the currently selected readout. // we always perform photometry on the mosaiced chip pmReadout *readout = pmFPAfileThisReadout (config->files, view, "PPSIM.FAKE.CHIP"); @@ -35,6 +35,6 @@ PS_ASSERT_PTR_NON_NULL (injectedSources, false); - // Generate the mask and weight images, including the user-defined analysis region of interest - psphotSetMaskAndWeight (config, readout, recipe); + // Generate the mask and variance images, including the user-defined analysis region of interest + psphotSetMaskAndVariance (config, readout, recipe); // XXX need to define the source pixels @@ -53,13 +53,13 @@ psArray *realSources = psArrayAlloc (realMeasuredSources->n); for (int i = 0; i < realMeasuredSources->n; i++) { - realSources->data[i] = pmSourceCopy (realMeasuredSources->data[i]); + realSources->data[i] = pmSourceCopy (realMeasuredSources->data[i]); } // load the psf model, if suppled. FWHM_X,FWHM_Y,etc are saved in the recipe - // this function uses PSPHOT.PSF.LOAD as the pmFPAfile + // this function uses PSPHOT.PSF.LOAD as the pmFPAfile pmPSF *psf = psphotLoadPSF (config, view, recipe); assert (psf); - // remove all sources + // remove all sources psphotRemoveAllSources (realSources, recipe); @@ -76,5 +76,5 @@ // XXX fake sources should measure peak->x,y, force sources should not - psImageMaskType maskVal = 0xff; + psImageMaskType maskVal = 0xff; psImage *significance = psphotSignificanceImage (readout, recipe, 1, maskVal); ppSimDetections (significance, recipe, fakeSources); @@ -90,5 +90,5 @@ psphotGuessModels (config, readout, realSources, psf); psphotGuessModels (config, readout, fakeSources, psf); - + // linear fit to real + fake sources psArray *sources = ppSimMergeSources (realSources, fakeSources); @@ -113,6 +113,6 @@ pmReadout *fakeReadout = pmFPAfileThisReadout (config->files, view, "PPSIM.FAKE.SOURCES"); if (!fakeReadout) { - fakeReadout = pmReadoutAlloc (fakeCell); - psFree (fakeReadout); // there is a copy on 'cell' as well + fakeReadout = pmReadoutAlloc (fakeCell); + psFree (fakeReadout); // there is a copy on 'cell' as well } psAssert (fakeReadout, "no fakeReadout?"); Index: /trunk/ppSim/src/ppSimPhotomReadoutForce.c =================================================================== --- /trunk/ppSim/src/ppSimPhotomReadoutForce.c (revision 21364) +++ /trunk/ppSim/src/ppSimPhotomReadoutForce.c (revision 21365) @@ -12,5 +12,5 @@ } -# if 0 +# if 0 // set the photcode for this image if (!psphotAddPhotcode (recipe, config, view, "PPSIM.FAKE.CHIP")) { @@ -22,5 +22,5 @@ // *** in this section, perform the photometry for real + force sources on PPSIM.FORCE.CHIP *** - // find the currently selected readout. + // find the currently selected readout. // we always perform photometry on the mosaiced chip pmReadout *readout = pmFPAfileThisReadout (config->files, view, "PPSIM.FORCE.CHIP"); @@ -35,6 +35,6 @@ psAssert (forceSources, "failed to load force photometry sources"); - // Generate the mask and weight images, including the user-defined analysis region of interest - psphotSetMaskAndWeight (config, readout, recipe); + // Generate the mask and variance images, including the user-defined analysis region of interest + psphotSetMaskAndVariance (config, readout, recipe); // XXX need to define the source pixels @@ -46,13 +46,13 @@ psArray *realSources = psArrayAlloc (realMeasuredSources->n); for (int i = 0; i < realMeasuredSources->n; i++) { - realSources->data[i] = pmSourceCopy (realMeasuredSources->data[i]); + realSources->data[i] = pmSourceCopy (realMeasuredSources->data[i]); } // load the psf model, if suppled. FWHM_X,FWHM_Y,etc are saved in the recipe - // this function uses PSPHOT.PSF.LOAD as the pmFPAfile + // this function uses PSPHOT.PSF.LOAD as the pmFPAfile pmPSF *psf = psphotLoadPSF (config, view, recipe); assert (psf); - // remove all sources + // remove all sources psphotRemoveAllSources (realSources, recipe); @@ -69,5 +69,5 @@ // XXX fake sources should measure peak->x,y, force sources should not - psImageMaskType maskVal = 0xff; + psImageMaskType maskVal = 0xff; psImage *significance = psphotSignificanceImage (readout, recipe, 1, maskVal); ppSimDetections (significance, recipe, forceSources); @@ -83,5 +83,5 @@ psphotGuessModels (config, readout, realSources, psf); psphotGuessModels (config, readout, forceSources, psf); - + // linear fit to real + force sources psArray *sources = ppSimMergeSources (realSources, forceSources); @@ -106,6 +106,6 @@ pmReadout *forceReadout = pmFPAfileThisReadout (config->files, view, "PPSIM.FORCE.SOURCES"); if (!forceReadout) { - forceReadout = pmReadoutAlloc (forceCell); - psFree (forceReadout); // there is a copy on 'cell' as well + forceReadout = pmReadoutAlloc (forceCell); + psFree (forceReadout); // there is a copy on 'cell' as well } psAssert (forceReadout, "no forceReadout?");