Index: /trunk/ppStack/src/ppStackArguments.c =================================================================== --- /trunk/ppStack/src/ppStackArguments.c (revision 19171) +++ /trunk/ppStack/src/ppStackArguments.c (revision 19172) @@ -145,6 +145,7 @@ psMetadataAddF32(arguments, PS_LIST_TAIL, "-combine-rej", 0, "Combination rejection thresold (sigma)", NAN); - psMetadataAddU8(arguments, PS_LIST_TAIL, "-mask-bad", 0, "Mask value for bad pixels", 0); - psMetadataAddU8(arguments, PS_LIST_TAIL, "-mask-blank", 0, "Mask value for blank region", 0); + psMetadataAddStr(arguments, PS_LIST_TAIL, "-mask-val", 0, "Mask value of input bad pixels", NULL); + psMetadataAddStr(arguments, PS_LIST_TAIL, "-mask-bad", 0, "Mask value to give bad pixels", NULL); + psMetadataAddStr(arguments, PS_LIST_TAIL, "-mask-poor", 0, "Mask value to give poor pixels", NULL); psMetadataAddF32(arguments, PS_LIST_TAIL, "-threshold-mask", 0, "Threshold for mask deconvolution", NAN); psMetadataAddF32(arguments, PS_LIST_TAIL, "-image-rej", 0, @@ -219,9 +220,11 @@ VALUE_ARG_RECIPE_INT("-iter", "ITER", S32, 0); VALUE_ARG_RECIPE_FLOAT("-combine-rej", "COMBINE.REJ", F32); - VALUE_ARG_RECIPE_MASK("-mask-bad", "MASK.BAD"); - VALUE_ARG_RECIPE_MASK("-mask-blank", "MASK.BLANK"); VALUE_ARG_RECIPE_FLOAT("-threshold-mask", "THRESHOLD.MASK", F32); VALUE_ARG_RECIPE_FLOAT("-image-rej", "IMAGE.REJ", F32); VALUE_ARG_RECIPE_INT("-rows", "ROWS", S32, 0); + + valueArgRecipeStr(arguments, recipe, "-mask-val", "MASK.VAL", recipe); + valueArgRecipeStr(arguments, recipe, "-mask-bad", "MASK.BAD", recipe); + valueArgRecipeStr(arguments, recipe, "-mask-poor", "MASK.POOR", recipe); VALUE_ARG_RECIPE_FLOAT("-source-radius", "SOURCE.RADIUS", F32); Index: /trunk/ppStack/src/ppStackLoop.c =================================================================== --- /trunk/ppStack/src/ppStackLoop.c (revision 19171) +++ /trunk/ppStack/src/ppStackLoop.c (revision 19172) @@ -803,5 +803,8 @@ if (stats) { psTrace("ppStack", 1, "Gathering statistics on stacked image....\n"); - ppStatsFPA(stats, outCell->parent->parent, view, pmConfigMaskGet("BLANK", config), config); + psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.BAD"); // Name of bits for bad + psMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels + + ppStatsFPA(stats, outCell->parent->parent, view, maskBad, config); } Index: /trunk/ppStack/src/ppStackMatch.c =================================================================== --- /trunk/ppStack/src/ppStackMatch.c (revision 19171) +++ /trunk/ppStack/src/ppStackMatch.c (revision 19172) @@ -34,6 +34,10 @@ int size = psMetadataLookupS32(NULL, ppsub, "KERNEL.SIZE"); // Kernel half-size - psMaskType maskIn = pmConfigMaskGet("MASK.VALUE", config); // Bits to mask going in to pmSubtractionMatch - psMaskType maskOut = pmConfigMaskGet("BLANK", config); // Bits to mask after pmSubtractionMatch + psString maskValStr = psMetadataLookupStr(NULL, recipe, "MASK.VAL"); // Name of bits to mask going in + psMaskType maskVal = pmConfigMaskGet(maskValStr, config); // Bits to mask going in to pmSubtractionMatch + psString maskPoorStr = psMetadataLookupStr(NULL, recipe, "MASK.POOR"); // Name of bits to mask for poor + psMaskType maskPoor = pmConfigMaskGet(maskPoorStr, config); // Bits to mask for poor pixels + psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.BAD"); // Name of bits to mask for bad + psMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels bool mdok; // Status of MD lookup @@ -45,5 +49,5 @@ int threads = psMetadataLookupS32(NULL, config->arguments, "-threads"); // Number of threads - if (!pmReadoutMaskNonfinite(readout, maskIn)) { + if (!pmReadoutMaskNonfinite(readout, maskVal)) { psError(PS_ERR_UNKNOWN, false, "Unable to mask non-finite pixels in readout."); return false; @@ -75,4 +79,5 @@ float optThresh = psMetadataLookupF32(&mdok, ppsub, "OPTIMUM.TOL"); // Tolerance for search int optOrder = psMetadataLookupS32(&mdok, ppsub, "OPTIMUM.ORDER"); // Order for search + float poorFrac = psMetadataLookupF32(&mdok, ppsub, "POOR.FRACTION"); // Fraction for "poor" // These values are specified specifically for stacking @@ -87,5 +92,5 @@ { psStats *bg = psStatsAlloc(PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_STDEV); // Statistics for bg - if (!psImageBackground(bg, NULL, readout->image, readout->mask, maskIn, rng)) { + if (!psImageBackground(bg, NULL, readout->image, readout->mask, maskVal, rng)) { psWarning("Can't measure background for image."); psErrorClear(); @@ -136,5 +141,5 @@ sources, stampsName, type, size, order, widths, orders, inner, ringsOrder, binning, penalty, optimum, optWidths, optOrder, optThresh, iter, rej, - maskIn, maskOut, badFrac, PM_SUBTRACTION_MODE_1)) { + maskVal, maskBad, maskPoor, poorFrac, badFrac, PM_SUBTRACTION_MODE_1)) { psError(PS_ERR_UNKNOWN, false, "Unable to match images."); psFree(fake); @@ -226,5 +231,5 @@ if (renorm) { psLogMsg("ppStack", PS_LOG_INFO, "Renormalising variance map."); - if (!pmReadoutWeightRenorm(readout, maskOut, renormMean, renormStdev, renormWidth, rng)) { + if (!pmReadoutWeightRenorm(readout, maskBad, renormMean, renormStdev, renormWidth, rng)) { psError(PS_ERR_UNKNOWN, false, "Unable to renormalise variances."); psFree(output); @@ -235,5 +240,5 @@ // Ensure the background value is zero psStats *bg = psStatsAlloc(PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_STDEV); // Statistics for background - if (!psImageBackground(bg, NULL, readout->image, readout->mask, maskOut, rng)) { + if (!psImageBackground(bg, NULL, readout->image, readout->mask, maskVal | maskBad, rng)) { psWarning("Can't measure background for image."); psErrorClear(); Index: /trunk/ppStack/src/ppStackReadout.c =================================================================== --- /trunk/ppStack/src/ppStackReadout.c (revision 19171) +++ /trunk/ppStack/src/ppStackReadout.c (revision 19172) @@ -10,7 +10,7 @@ #include "ppStack.h" -//#define REJECTION_FILES // Write rejection mask? -//#define INSPECTION_FILES // Write inspection mask? -//#define COMBINED_FILES // Write combined images? +#define REJECTION_FILES // Write rejection mask? +#define INSPECTION_FILES // Write inspection mask? +#define COMBINED_FILES // Write combined images? @@ -34,5 +34,4 @@ int iter = psMetadataLookupS32(NULL, recipe, "ITER"); // Rejection iterations float combineRej = psMetadataLookupF32(NULL, recipe, "COMBINE.REJ"); // Combination threshold - psMaskType maskVal = pmConfigMaskGet("BLANK", config); // Value to mask bool useVariance = psMetadataLookupBool(&mdok, recipe, "VARIANCE"); // Use variance for rejection? bool safe = psMetadataLookupBool(&mdok, recipe, "SAFE"); // Be safe when combining small numbers of pixels @@ -40,4 +39,9 @@ psMetadata *ppsub = psMetadataLookupMetadata(NULL, config->recipes, "PPSUB"); // PPSUB recipe int kernelSize = psMetadataLookupS32(NULL, ppsub, "KERNEL.SIZE"); // Kernel half-size + + psString maskValStr = psMetadataLookupStr(NULL, recipe, "MASK.VAL"); // Name of bits to mask going in + psMaskType maskVal = pmConfigMaskGet(maskValStr, config); // Bits to mask going in to pmSubtractionMatch + psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.BAD"); // Name of bits to mask for bad + psMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels int num = readouts->n; // Number of inputs @@ -67,5 +71,5 @@ } - if (!pmStackCombine(outRO, stack, maskVal, maskVal, kernelSize, iter, combineRej, true, + if (!pmStackCombine(outRO, stack, maskVal | maskBad, maskBad, kernelSize, iter, combineRej, true, useVariance, safe)) { psError(PS_ERR_UNKNOWN, false, "Unable to combine input readouts with rejection."); @@ -93,5 +97,5 @@ psRegionSet(0, outRO->image->numCols - 1, 0, outRO->image->numRows - 1), - maskVal); + maskBad); psString name = NULL; // Name of image psStringAppend(&name, "inspect_%03d_%03d.fits", sectionNum, i); @@ -143,6 +147,10 @@ bool mdok; // Status of MD lookup - psMaskType maskVal = pmConfigMaskGet("BLANK", config); // Value to mask bool useVariance = psMetadataLookupBool(&mdok, recipe, "VARIANCE"); // Use variance for rejection? + + psString maskValStr = psMetadataLookupStr(NULL, recipe, "MASK.VAL"); // Name of bits to mask going in + psMaskType maskVal = pmConfigMaskGet(maskValStr, config); // Bits to mask going in to pmSubtractionMatch + psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.BAD"); // Name of bits to mask for bad + psMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels int num = readouts->n; // Number of inputs @@ -210,5 +218,5 @@ psRegionSet(0, outRO->image->numCols - 1, 0, outRO->image->numRows - 1), - maskVal); + maskBad); psString name = NULL; // Name of image psStringAppend(&name, "reject_%03d.fits", i); @@ -222,5 +230,6 @@ #endif - if (!pmStackCombine(outRO, stack, maskVal, maskVal, 0, 0, NAN, numGood != num, useVariance, false)) { + if (!pmStackCombine(outRO, stack, maskVal | maskBad, maskBad, 0, 0, NAN, + numGood != num, useVariance, false)) { psError(PS_ERR_UNKNOWN, false, "Unable to combine input readouts."); psFree(fpaList);