Index: trunk/ppStack/src/Makefile.am =================================================================== --- trunk/ppStack/src/Makefile.am (revision 23575) +++ trunk/ppStack/src/Makefile.am (revision 23576) @@ -29,4 +29,5 @@ ppStackPrepare.c \ ppStackConvolve.c \ + ppStackCombinePrepare.c \ ppStackCombineInitial.c \ ppStackReject.c \ Index: trunk/ppStack/src/ppStackCamera.c =================================================================== --- trunk/ppStack/src/ppStackCamera.c (revision 23575) +++ trunk/ppStack/src/ppStackCamera.c (revision 23576) @@ -51,4 +51,11 @@ bool status = false; // Status of file definition + psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // Recipe for ppSim + if (!recipe) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find recipe %s", PPSTACK_RECIPE); + return false; + } + bool convolve = psMetadataLookupBool(NULL, recipe, "CONVOLVE"); // Convolve images before stack? + psArray *runImages = pmFPAfileDefineMultipleFromRun(&status, NULL, config, "PPSTACK.INPUT"); // Input images from previous run @@ -98,5 +105,5 @@ } if (!runSrc) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to define input sources from RUN metadta."); + psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to define input sources from RUN metadata."); psFree(runImages); return false; @@ -104,17 +111,20 @@ psFree(runSrc); - psArray *runKernel = pmFPAfileDefineMultipleFromRun(&status, runImages, config, - "PPSTACK.CONV.KERNEL"); // Convolution kernels - if (!status) { - psError(PS_ERR_UNKNOWN, false, "Unable to define convolution kernels from RUN metadata."); - psFree(runImages); - return false; - } - if (!runSrc) { - psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to define convolution kernels from RUN metadta."); - psFree(runImages); - return false; - } - psFree(runKernel); + if (convolve) { + psArray *runKernel = pmFPAfileDefineMultipleFromRun(&status, runImages, config, + "PPSTACK.CONV.KERNEL"); // Convolution kernels + if (!status) { + psError(PS_ERR_UNKNOWN, false, "Unable to define convolution kernels from RUN metadata."); + psFree(runImages); + return false; + } + if (!runKernel) { + psError(PS_ERR_UNEXPECTED_NULL, true, + "Unable to define convolution kernels from RUN metadata."); + psFree(runImages); + return false; + } + psFree(runKernel); + } psFree(runImages); @@ -200,10 +210,12 @@ } - pmFPAfile *kernel = pmFPAfileDefineOutput(config, imageFile->fpa, "PPSTACK.CONV.KERNEL"); - if (!kernel) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PPSTACK.CONV.KERNEL")); - return false; - } - kernel->save = true; + if (convolve) { + pmFPAfile *kernel = pmFPAfileDefineOutput(config, imageFile->fpa, "PPSTACK.CONV.KERNEL"); + if (!kernel) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPSTACK.CONV.KERNEL")); + return false; + } + kernel->save = true; + } i++; @@ -300,11 +312,4 @@ } jpeg2->save = true; - - - psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // Recipe for ppSim - if (!recipe) { - psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find recipe %s", PPSTACK_RECIPE); - return false; - } // For photometry, we operate on the chip-mosaicked image Index: trunk/ppStack/src/ppStackCombineInitial.c =================================================================== --- trunk/ppStack/src/ppStackCombineInitial.c (revision 23575) +++ trunk/ppStack/src/ppStackCombineInitial.c (revision 23576) @@ -23,40 +23,8 @@ psTimerStart("PPSTACK_INITIAL"); - psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // ppStack recipe - psAssert(recipe, "We've thrown an error on this before."); - psMetadata *ppsub = psMetadataLookupMetadata(NULL, config->recipes, "PPSUB"); // PPSUB recipe int overlap = 2 * psMetadataLookupS32(NULL, ppsub, "KERNEL.SIZE"); // Overlap by kernel size between consecutive scans - pmFPAview *view = NULL; // View to readout - - int row0, col0; // Offset for readout - int numCols, numRows; // Size of readout - ppStackThread *thread = stack->threads->data[0]; // Representative thread - if (!pmReadoutStackSetOutputSize(&col0, &row0, &numCols, &numRows, thread->readouts)) { - psError(PS_ERR_UNKNOWN, false, "problem setting output readout size."); - return false; - } - - pmFPAfileActivate(config->files, false, NULL); - ppStackFileActivation(config, PPSTACK_FILES_COMBINE, true); - view = ppStackFilesIterateDown(config); - if (!view) { - return false; - } - - pmCell *outCell = pmFPAfileThisCell(config->files, view, "PPSTACK.OUTPUT"); // Output cell - options->outRO = pmReadoutAlloc(outCell); // Output readout - psFree(view); - - 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 - if (!pmReadoutStackDefineOutput(options->outRO, col0, row0, numCols, numRows, true, true, maskBad)) { - psError(PS_ERR_UNKNOWN, false, "Unable to prepare output."); - return false; - } - - psFree(options->cells); options->cells = NULL; bool status; // Status of read Index: trunk/ppStack/src/ppStackCombinePrepare.c =================================================================== --- trunk/ppStack/src/ppStackCombinePrepare.c (revision 23576) +++ trunk/ppStack/src/ppStackCombinePrepare.c (revision 23576) @@ -0,0 +1,47 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include +#include + +#include "ppStack.h" +#include "ppStackLoop.h" + +bool ppStackCombinePrepare(ppStackThreadData *stack, ppStackOptions *options, pmConfig *config) +{ + psAssert(stack, "Require stack"); + psAssert(options, "Require options"); + psAssert(config, "Require configuration"); + + int row0, col0; // Offset for readout + int numCols, numRows; // Size of readout + ppStackThread *thread = stack->threads->data[0]; // Representative thread + if (!pmReadoutStackSetOutputSize(&col0, &row0, &numCols, &numRows, thread->readouts)) { + psError(PS_ERR_UNKNOWN, false, "problem setting output readout size."); + return false; + } + + pmFPAfileActivate(config->files, false, NULL); + ppStackFileActivation(config, PPSTACK_FILES_COMBINE, true); + pmFPAview *view = ppStackFilesIterateDown(config); // View to readout + if (!view) { + return false; + } + + pmCell *outCell = pmFPAfileThisCell(config->files, view, "PPSTACK.OUTPUT"); // Output cell + options->outRO = pmReadoutAlloc(outCell); // Output readout + psFree(view); + + psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // ppStack recipe + psAssert(recipe, "We've thrown an error on this before."); + 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 + if (!pmReadoutStackDefineOutput(options->outRO, col0, row0, numCols, numRows, true, true, maskBad)) { + psError(PS_ERR_UNKNOWN, false, "Unable to prepare output."); + return false; + } + + return true; +} Index: trunk/ppStack/src/ppStackLoop.c =================================================================== --- trunk/ppStack/src/ppStackLoop.c (revision 23575) +++ trunk/ppStack/src/ppStackLoop.c (revision 23576) @@ -59,4 +59,13 @@ if (!stack) { psError(PS_ERR_IO, false, "Unable to initialise stack threads."); + psFree(options); + return false; + } + psFree(options->cells); options->cells = NULL; + + // Prepare for combination + if (!ppStackCombinePrepare(stack, options, config)) { + psError(PS_ERR_UNKNOWN, false, "Unable to prepare for combination."); + psFree(stack); psFree(options); return false; Index: trunk/ppStack/src/ppStackLoop.h =================================================================== --- trunk/ppStack/src/ppStackLoop.h (revision 23575) +++ trunk/ppStack/src/ppStackLoop.h (revision 23576) @@ -30,4 +30,11 @@ // Convolve inputs to match target PSF bool ppStackConvolve( + ppStackOptions *options, // Options + pmConfig *config // Configuration + ); + +// Prepare for combination +bool ppStackCombinePrepare( + ppStackThreadData *stack, // Stack ppStackOptions *options, // Options pmConfig *config // Configuration Index: trunk/ppStack/src/ppStackReadout.c =================================================================== --- trunk/ppStack/src/ppStackReadout.c (revision 23575) +++ trunk/ppStack/src/ppStackReadout.c (revision 23576) @@ -185,6 +185,5 @@ assert(outRO); assert(readouts); - assert(rejected); - assert(readouts->n == rejected->n); + assert(!rejected || readouts->n == rejected->n); assert(mask && mask->n == readouts->n && mask->type.type == PS_TYPE_VECTOR_MASK); assert(weightings && weightings->n == readouts->n && weightings->type.type == PS_TYPE_F32); @@ -207,10 +206,13 @@ psArray *stack = psArrayAlloc(num); // Array for stacking - int numGood = num; // Number of good inputs: images that haven't been completely rejected + bool entire = (rejected ? false : true); // Combine entire image? for (int i = 0; i < num; i++) { pmReadout *ro = readouts->data[i]; - if (!ro || !rejected->data[i] || mask->data.PS_TYPE_VECTOR_MASK_DATA[i]) { - // Image completely rejected - numGood--; + if (mask->data.U8[i] & (PPSTACK_MASK_REJECT | PPSTACK_MASK_BAD)) { + // Image completely rejected since previous combination + entire = true; + continue; + } else if (mask->data.U8[i]) { + // Image completely rejected before original combination continue; } @@ -234,10 +236,10 @@ pmStackData *data = pmStackDataAlloc(ro, weightings->data.F32[i], addVariance ? addVariance->data.F32[i] : NAN); - data->reject = psMemIncrRefCounter(rejected->data[i]); + data->reject = rejected ? psMemIncrRefCounter(rejected->data[i]) : NULL; stack->data[i] = data; } if (!pmStackCombine(outRO, stack, maskVal | maskBad, maskBad, 0, 0, NAN, NAN, NAN, - numGood != num, useVariance, false)) { + entire, useVariance, false)) { psError(PS_ERR_UNKNOWN, false, "Unable to combine input readouts."); psFree(stack); Index: trunk/ppStack/src/ppStackSetup.c =================================================================== --- trunk/ppStack/src/ppStackSetup.c (revision 23575) +++ trunk/ppStack/src/ppStackSetup.c (revision 23576) @@ -14,5 +14,6 @@ // Generate an array of input filenames -static psArray *stackNameArray(pmConfig *config, // Configuration +static psArray *stackNameArray(const ppStackOptions *options, // Stack options + pmConfig *config, // Configuration const char *name // Name of file ) @@ -21,19 +22,16 @@ psAssert(config, "Require file name"); - psString regex = NULL; // Regular expression for selecting file - psStringAppend(®ex, "^%s$", name); - psMetadataIterator *iter = psMetadataIteratorAlloc(config->files, PS_LIST_HEAD, regex); // Iterator - psFree(regex); - psMetadataItem *item; // Item from iteration - psArray *array = psArrayAlloc(BUFFER); // Array of file names - while ((item = psMetadataGetAndIncrement(iter))) { - psAssert(item->type == PS_DATA_UNKNOWN, "Should be this type"); - pmFPAfile *file = item->data.V; // An input file + psArray *array = psArrayAllocEmpty(options->num); // Array with filenames + pmFPAview *view = pmFPAviewAlloc(0);// View to readout + view->chip = view->cell = view->readout = -1; - psString filename = psStringCopy(file->filename); // Filename of interest + for (int i = 0; i < options->num; i++) { + pmFPAfile *file = pmFPAfileSelectSingle(config->files, name, i); // File of interest + + psString filename = pmFPAfileName(file, view, config); // Filename of interest + psAssert(filename, "Can't determine filename"); psArrayAdd(array, array->n, filename); psFree(filename); // Drop reference } - psFree(iter); return array; @@ -114,7 +112,7 @@ psFree(outputName); } else { - options->imageNames = stackNameArray(config, "PPSTACK.INPUT"); - options->maskNames = stackNameArray(config, "PPSTACK.INPUT.MASK"); - options->varianceNames = stackNameArray(config, "PPSTACK.INPUT.VARIANCE"); + options->imageNames = stackNameArray(options, config, "PPSTACK.INPUT"); + options->maskNames = stackNameArray(options, config, "PPSTACK.INPUT.MASK"); + options->varianceNames = stackNameArray(options, config, "PPSTACK.INPUT.VARIANCE"); }