Index: trunk/ppMerge/src/ppMergeMask.c =================================================================== --- trunk/ppMerge/src/ppMergeMask.c (revision 21244) +++ 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;