Index: /trunk/ppStack/src/ppStack.c =================================================================== --- /trunk/ppStack/src/ppStack.c (revision 29551) +++ /trunk/ppStack/src/ppStack.c (revision 29552) @@ -124,4 +124,5 @@ psLibFinalize(); pmVisualClose(); + pmVisualCleanup (); exitValue = ppStackExitCode(exitValue); Index: /trunk/ppStack/src/ppStackCombineFinal.c =================================================================== --- /trunk/ppStack/src/ppStackCombineFinal.c (revision 29551) +++ /trunk/ppStack/src/ppStackCombineFinal.c (revision 29552) @@ -93,5 +93,13 @@ // Sum covariance matrices + // the array may be defined, but no covariances actually supplied. + bool haveCovariances = false; if (covariances) { + for (int i = 0; i < covariances->n; i++) { + haveCovariances |= (covariances->data[i] != NULL); + } + } + + if (haveCovariances) { outRO->covariance = psImageCovarianceAverageWeighted(covariances, options->weightings); } else { Index: /trunk/ppStack/src/ppStackLoop.c =================================================================== --- /trunk/ppStack/src/ppStackLoop.c (revision 29551) +++ /trunk/ppStack/src/ppStackLoop.c (revision 29552) @@ -204,4 +204,5 @@ #if 1 // Unconvolved stack --- it's cheap to calculate, compared to everything else! + // XXX unconvolved stack is currently using the convolved mask! oops! if (options->convolve) { // Start threading Index: /trunk/ppStack/src/ppStackMatch.c =================================================================== --- /trunk/ppStack/src/ppStackMatch.c (revision 29551) +++ /trunk/ppStack/src/ppStackMatch.c (revision 29552) @@ -68,5 +68,5 @@ // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMetadataAddU8(psphotRecipe, PS_LIST_TAIL, "MASK.PSPHOT", PS_META_REPLACE, "user-defined mask", maskBad); + psMetadataAddImageMask(psphotRecipe, PS_LIST_TAIL, "MASK.PSPHOT", PS_META_REPLACE, "user-defined mask", maskBad); psImage *binned = psphotModelBackgroundReadoutNoFile(ro, config); // Binned background model @@ -153,5 +153,6 @@ int threads = psMetadataLookupS32(NULL, config->arguments, "-threads"); // Number of threads - if (!pmReadoutMaskNonfinite(readout, maskVal)) { + // Replaced pmReadoutMaskNonfinite with pmReadoutMaskInvalid (tests for already masked pixels) + if (!pmReadoutMaskInvalid(readout, maskVal, maskBad)) { psError(psErrorCodeLast(), false, "Unable to mask non-finite pixels in readout."); return false; @@ -319,9 +320,10 @@ } } else { + // we need to register the FWHM values for use downstream + pmSubtractionSetFWHMs(options->inputSeeing->data.F32[index], options->targetSeeing); + // Scale the input parameters psVector *widthsCopy = psVectorCopy(NULL, widths, PS_TYPE_F32); // Copy of kernel widths - if (scale && !pmSubtractionParamsScale(&size, &footprint, widthsCopy, - options->inputSeeing->data.F32[index], - options->targetSeeing, scaleRef, scaleMin, scaleMax)) { + if (scale && !pmSubtractionParamsScale(&size, &footprint, widthsCopy, scaleRef, scaleMin, scaleMax)) { psError(psErrorCodeLast(), false, "Unable to scale kernel parameters"); psFree(fake); Index: /trunk/ppStack/src/ppStackPSF.c =================================================================== --- /trunk/ppStack/src/ppStackPSF.c (revision 29551) +++ /trunk/ppStack/src/ppStackPSF.c (revision 29552) @@ -15,43 +15,60 @@ { bool mdok = false; + pmPSF *psf = NULL; -#ifndef TESTING // Get the recipe values psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // ppStack recipe psAssert(recipe, "We've thrown an error on this before."); - int psfInstances = psMetadataLookupS32(NULL, recipe, "PSF.INSTANCES"); // Number of instances for PSF - float psfRadius = psMetadataLookupF32(NULL, recipe, "PSF.RADIUS"); // Radius for PSF - const char *psfModel = psMetadataLookupStr(NULL, recipe, "PSF.MODEL"); // Model for PSF - int psfOrder = psMetadataLookupS32(NULL, recipe, "PSF.ORDER"); // Spatial order for PSF - - psString maskValStr = psMetadataLookupStr(&mdok, recipe, "MASK.VAL"); // Name of bits to mask going in - if (!mdok || !maskValStr) { - psError(PPSTACK_ERR_CONFIG, false, "Unable to find MASK.VAL in recipe"); - return false; - } - psImageMaskType maskVal = pmConfigMaskGet(maskValStr, config); // Bits to mask - - for (int i = 0; i < psfs->n; i++) { - if (inputMask->data.U8[i]) { - psFree(psfs->data[i]); - psfs->data[i] = NULL; - } + bool autosize = psMetadataLookupBool(&mdok, recipe, "PSF.AUTOSIZE"); // Spatial order for PSF + if (!mdok) { + // older config files which lack PSF.AUTOSIZE used TRUE as the default + autosize = true; } - // Solve for the target PSF - pmPSF *psf = pmPSFEnvelope(numCols, numRows, psfs, psfInstances, psfRadius, psfModel, psfOrder, psfOrder, maskVal); - if (!psf) { - psError(PPSTACK_ERR_PSF, false, "Unable to determine output PSF."); - return NULL; + char *psfModel = psMetadataLookupStr(NULL, recipe, "PSF.MODEL"); // Model for PSF + + if (autosize) { + + int psfInstances = psMetadataLookupS32(NULL, recipe, "PSF.INSTANCES"); // Number of instances for PSF + float psfRadius = psMetadataLookupF32(NULL, recipe, "PSF.RADIUS"); // Radius for PSF + int psfOrder = psMetadataLookupS32(NULL, recipe, "PSF.ORDER"); // Spatial order for PSF + + psString maskValStr = psMetadataLookupStr(&mdok, recipe, "MASK.VAL"); // Name of bits to mask going in + if (!mdok || !maskValStr) { + psError(PPSTACK_ERR_CONFIG, false, "Unable to find MASK.VAL in recipe"); + return NULL; + } + psImageMaskType maskVal = pmConfigMaskGet(maskValStr, config); // Bits to mask + + for (int i = 0; i < psfs->n; i++) { + if (inputMask->data.U8[i]) { + psFree(psfs->data[i]); + psfs->data[i] = NULL; + } + } + + // Solve for the target PSF + psf = pmPSFEnvelope(numCols, numRows, psfs, psfInstances, psfRadius, psfModel, psfOrder, psfOrder, maskVal); + if (!psf) { + psError(PPSTACK_ERR_PSF, false, "Unable to determine output PSF."); + return NULL; + } + } else { + + // Manually defined target PSF + float psfFWHM = psMetadataLookupF32(&mdok, recipe, "PSF.OUTPUT.FWHM"); // Radius for PSF + if (!mdok) { + psfFWHM = 4.0; + } + + float Mxx = M_SQRT2 * psfFWHM / 2.35; + + psf = pmPSFBuildSimple(psfModel, Mxx, Mxx, 0.0, 0.0); + if (!psf) { + psError(PPSTACK_ERR_PSF, false, "Unable to build dummy PSF."); + return NULL; + } } -#else - // Dummy PSF - pmPSF *psf = pmPSFBuildSimple("PS_MODEL_PS1_V1", 4.0, 4.0, 0.0, 1.0); - if (!psf) { - psError(PPSTACK_ERR_PSF, false, "Unable to build dummy PSF."); - return NULL; - } -#endif return psf; Index: /trunk/ppStack/src/ppStackReadout.c =================================================================== --- /trunk/ppStack/src/ppStackReadout.c (revision 29551) +++ /trunk/ppStack/src/ppStackReadout.c (revision 29552) @@ -130,10 +130,23 @@ int kernelSize = psMetadataLookupS32(NULL, ppsub, "KERNEL.SIZE"); // Kernel half-size - psString maskValStr = psMetadataLookupStr(NULL, recipe, "MASK.VAL"); // Name of bits to mask going in - psImageMaskType maskVal = pmConfigMaskGet(maskValStr, config); // Bits to mask going in to pmSubtractionMatch + psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.VAL"); // Name of bits to mask for bad + psImageMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels + psString maskSuspectStr = psMetadataLookupStr(NULL, recipe, "MASK.SUSPECT"); // Name of suspect mask bits psImageMaskType maskSuspect = pmConfigMaskGet(maskSuspectStr, config); // Suspect bits - psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.BAD"); // Name of bits to mask for bad - psImageMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels + + bool status = false; + psImageMaskType maskBlank; + psString maskBlankStr = psMetadataLookupStr(&status, recipe, "MASK.BLANK"); // Name of bits to set for empty pixels + if (maskBlankStr) { + maskBlank = pmConfigMaskGet(maskBlankStr, config); // Bits to mask for bad pixels + } else { + maskBlankStr = psMetadataLookupStr(&status, recipe, "MASK.BAD"); // Old name for MASK.BLANK + if (maskBlankStr) { + maskBlank = pmConfigMaskGet(maskBlankStr, config); // Bits to mask for bad pixels + } else { + maskBlank = pmConfigMaskGet("BLANK", config); // Bits to mask for bad pixels + } + } int num = readouts->n; // Number of inputs @@ -157,5 +170,5 @@ } - if (!pmStackCombine(outRO, NULL, stack, maskVal | maskBad, maskSuspect, maskBad, kernelSize, iter, + if (!pmStackCombine(outRO, NULL, stack, maskBad, maskSuspect, maskBlank, kernelSize, iter, combineRej, combineSys, combineDiscard, useVariance, safe, false)) { psError(PS_ERR_UNKNOWN, false, "Unable to combine input readouts with rejection."); @@ -215,10 +228,23 @@ bool safe = psMetadataLookupBool(&mdok, recipe, "SAFE"); // Be safe when combining small numbers of pixels - psString maskValStr = psMetadataLookupStr(NULL, recipe, "MASK.VAL"); // Name of bits to mask going in - psImageMaskType maskVal = pmConfigMaskGet(maskValStr, config); // Bits to mask going in to pmSubtractionMatch + psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.VAL"); // Name of bits to mask for bad + psImageMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels + psString maskSuspectStr = psMetadataLookupStr(NULL, recipe, "MASK.SUSPECT"); // Name of suspect mask bits psImageMaskType maskSuspect = pmConfigMaskGet(maskSuspectStr, config); // Suspect bits - psString maskBadStr = psMetadataLookupStr(NULL, recipe, "MASK.BAD"); // Name of bits to mask for bad - psImageMaskType maskBad = pmConfigMaskGet(maskBadStr, config); // Bits to mask for bad pixels + + bool status = false; + psImageMaskType maskBlank; + psString maskBlankStr = psMetadataLookupStr(&status, recipe, "MASK.BLANK"); // Name of bits to set for empty pixels + if (maskBlankStr) { + maskBlank = pmConfigMaskGet(maskBlankStr, config); // Bits to mask for bad pixels + } else { + maskBlankStr = psMetadataLookupStr(&status, recipe, "MASK.BAD"); // Old name for MASK.BLANK + if (maskBlankStr) { + maskBlank = pmConfigMaskGet(maskBlankStr, config); // Bits to mask for bad pixels + } else { + maskBlank = pmConfigMaskGet("BLANK", config); // Bits to mask for bad pixels + } + } int num = readouts->n; // Number of inputs @@ -257,5 +283,5 @@ } - if (!pmStackCombine(outRO, expRO, stack, maskVal | maskBad, maskSuspect, maskBad, 0, iter, combineRej, + if (!pmStackCombine(outRO, expRO, stack, maskBad, maskSuspect, maskBlank, 0, iter, combineRej, combineSys, combineDiscard, useVariance, safe, rejected)) { psError(PS_ERR_UNKNOWN, false, "Unable to combine input readouts.");