Index: trunk/ppMerge/src/ppMergeArguments.c =================================================================== --- trunk/ppMerge/src/ppMergeArguments.c (revision 21265) +++ 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 21265) +++ 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 21265) +++ 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 21265) +++ 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 21265) +++ 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 21265) +++ 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 21265) +++ 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;