Index: /trunk/ppMerge/src/ppMergeCombine.c =================================================================== --- /trunk/ppMerge/src/ppMergeCombine.c (revision 16841) +++ /trunk/ppMerge/src/ppMergeCombine.c (revision 16842) @@ -16,7 +16,8 @@ #include "ppMergeVersion.h" +#define TESTING + + #if 0 -static psMemId memId = 0; - static FILE *dumpFile = NULL; @@ -36,6 +37,8 @@ exit(EXIT_FAILURE); } - - +#endif + +#if 0 +static psMemId memId = 0; static void memDump(void) { @@ -52,5 +55,7 @@ psFree(leaks); } - +#endif + +#if 0 static void memCheck(void) { @@ -73,5 +78,5 @@ psTrace("ppMerge", 0, "Memory in use: %zd\n", totalSize); psTrace("ppMerge", 0, "Largest block: %ld\n", largest); - psTrace("ppMerge", 0, "sbrk(): %zd\n", sbrk(0)); + psTrace("ppMerge", 0, "sbrk(): %p\n", sbrk(0)); } return; @@ -119,18 +124,20 @@ } while ((chip = pmFPAviewNextChip(view, fpa, 1))) { - if (chip->hdu) { - // Data will exist soon - pmFPAUpdateNames(data->out, chip, NULL); - chip->data_exists = true; - } + if (!chip->hdu) { + continue; + } + // Data will exist soon + pmFPAUpdateNames(data->out, chip, NULL); + chip->data_exists = true; pmChipWrite(chip, data->outFile, config->database, true, false); // Write header only pmCell *cell; // Cell of interest while ((cell = pmFPAviewNextCell(view, fpa, 1))) { cellNum++; - if (cell->hdu) { - // Data will exist soon - pmFPAUpdateNames(data->out, chip, cell); - chip->data_exists = cell->data_exists = true; - } + if (!cell->hdu) { + continue; + } + // Data will exist soon + pmFPAUpdateNames(data->out, chip, cell); + chip->data_exists = cell->data_exists = true; pmCellWrite(cell, data->outFile, config->database, true); // Write header only pmReadout *readout = pmReadoutAlloc(cell); // Output readout of interest @@ -197,8 +204,8 @@ // If we're combining with weights, we want to generate weights. - if (options->combine->weights) { + if (options->combine->weights && !options->dark) { // If it's a bias or dark, set the gain to zero: noise only contributed by read - if ((!options->zero && !options->scale) || options->darktime) { + if (!options->zero && !options->scale) { pmReadoutSetWeight(stack->data[i], false); } else { @@ -209,5 +216,6 @@ numRead++; } else { - psTrace("ppMerge", 3, "Finished reading file %d, chip %d, cell %d, scan %d\n", i, view->chip, view->cell, numScan); + psTrace("ppMerge", 3, "Finished reading file %d, chip %d, cell %d, scan %d\n", + i, view->chip, view->cell, numScan); } @@ -220,4 +228,7 @@ options->shutterIter, options->shutterRej, options->combine->maskVal); + } else if (options->dark) { + pmDarkCombine(cell, stack, options->darkOrdinates, options->combine->iter, + options->combine->rej, options->combine->maskVal); } else { pmReadoutCombine(readout, stack, cellZeros, cellScales, options->combine); @@ -246,4 +257,5 @@ psFree(stack); +#if 0 // Set the dark time for the output image, since we normalised if (options->darktime) { @@ -253,4 +265,5 @@ expItem->data.F32 = 1.0; } +#endif // Measure the fringes for this cell @@ -334,9 +347,12 @@ if (cell->hdu && !cell->hdu->blankPHU) { psTrace("ppMerge", 5, "Writing out cell HDU.\n"); - pmCellWrite(cell, data->outFile, config->database, false); - if (options->fringe) { - pmCellWriteTable(data->outFile, cell, "FRINGE"); - } - + if (options->dark) { + pmCellWriteDark(cell, data->outFile, config->database, false); + } else { + pmCellWrite(cell, data->outFile, config->database, false); + if (options->fringe) { + pmCellWriteTable(data->outFile, cell, "FRINGE"); + } + } pmCellFreeData(cell); } @@ -354,7 +370,11 @@ if (chip->hdu && !chip->hdu->blankPHU) { psTrace("ppMerge", 5, "Writing out chip HDU.\n"); - pmChipWrite(chip, data->outFile, config->database, false, false); - if (options->fringe) { - pmChipWriteTable(data->outFile, chip, "FRINGE"); + if (options->dark) { + pmChipWriteDark(chip, data->outFile, config->database, false, false); + } else { + pmChipWrite(chip, data->outFile, config->database, false, false); + if (options->fringe) { + pmChipWriteTable(data->outFile, chip, "FRINGE"); + } } @@ -373,7 +393,11 @@ // Write the pixels psTrace("ppMerge", 5, "Writing out FPA HDU.\n"); - pmFPAWrite(data->out, data->outFile, config->database, false, false); - if (options->fringe) { - pmFPAWriteTable(data->outFile, fpa, "FRINGE"); + if (options->dark) { + pmFPAWriteDark(data->out, data->outFile, config->database, false, false); + } else { + pmFPAWrite(data->out, data->outFile, config->database, false, false); + if (options->fringe) { + pmFPAWriteTable(data->outFile, fpa, "FRINGE"); + } } } Index: /trunk/ppMerge/src/ppMergeOptions.c =================================================================== --- /trunk/ppMerge/src/ppMergeOptions.c (revision 16841) +++ /trunk/ppMerge/src/ppMergeOptions.c (revision 16842) @@ -10,4 +10,6 @@ #include "ppMerge.h" #include "ppMergeOptions.h" + +#define ARRAY_BUFFER 4 // Number of values to add at once ////////////////////////////////////////////////////////////////////////////////////////////////////////////// @@ -34,5 +36,5 @@ options->zero = false; options->scale = false; - options->darktime = false; + options->dark = false; options->fringe = false; options->shutter = false; @@ -65,4 +67,5 @@ options->badMask = 0x00; options->growPixels = 0; + options->darkOrdinates = NULL; return options; } @@ -174,5 +177,5 @@ options->zero = false; options->scale = false; - options->darktime = false; + options->dark = false; options->fringe = false; options->shutter = false; @@ -181,5 +184,5 @@ options->zero = false; options->scale = false; - options->darktime = true; + options->dark = true; options->fringe = false; options->shutter = false; @@ -188,5 +191,5 @@ options->zero = false; options->scale = true; - options->darktime = false; + options->dark = false; options->fringe = false; options->shutter = false; @@ -195,5 +198,5 @@ options->zero = false; options->scale = true; - options->darktime = false; + options->dark = false; options->fringe = false; options->shutter = false; @@ -202,5 +205,5 @@ options->zero = false; options->scale = true; - options->darktime = false; + options->dark = false; options->fringe = false; options->shutter = false; @@ -209,5 +212,5 @@ options->zero = true; options->scale = true; - options->darktime = false; + options->dark = false; options->fringe = true; options->shutter = false; @@ -216,5 +219,5 @@ options->zero = false; options->scale = false; - options->darktime = false; + options->dark = false; options->fringe = false; options->shutter = true; @@ -225,5 +228,5 @@ options->zero = false; options->scale = false; - options->darktime = false; + options->dark = false; options->fringe = false; options->shutter = false; @@ -255,12 +258,7 @@ #if 0 - // Or you can set them individually - OPTION_PARSE(options->zero, config->arguments, "-zero", Bool); - OPTION_PARSE(options->scale, config->arguments, "-scale", Bool); - OPTION_PARSE(options->darktime, config->arguments, "-exptime", Bool); -#endif - // Number of on/off images OPTION_PARSE(options->onOff, config->arguments, "-onoff", S32); +#endif // Masking options @@ -268,4 +266,49 @@ options->badMask = pmConfigMask("BAD", config); + if (options->dark) { + psMetadata *ordinates = psMetadataLookupMetadata(NULL, recipe, "DARK.ORDINATES"); // Ordinates info + options->darkOrdinates = psArrayAllocEmpty(psListLength(ordinates->list)); + + psMetadataIterator *iter = psMetadataIteratorAlloc(ordinates, PS_LIST_HEAD, NULL); // Iterator + psMetadataItem *item; // Item from iteration + while ((item = psMetadataGetAndIncrement(iter))) { + int order = 0; // Polynomial order + bool scale = false; // Scale values? + float min = NAN, max = NAN; // Minimum and maximum values for scaling + switch (item->type) { + case PS_TYPE_S32: + order = item->data.S32; + break; + case PS_DATA_METADATA: + order = psMetadataLookupS32(NULL, item->data.md, "ORDER"); + bool mdok; // Status of MD lookup + scale = psMetadataLookupBool(&mdok, item->data.md, "SCALE"); + min = psMetadataLookupF32(&mdok, item->data.md, "MIN"); + max = psMetadataLookupF32(&mdok, item->data.md, "MAX"); + break; + default: + psError(PS_ERR_BAD_PARAMETER_TYPE, true, + "Type of DARK.ORDINATES entry %s (%x) is not METADATA or S32", + item->name, item->type); + psFree(options); + return false; + } + if (order <= 0) { + psError(PS_ERR_BAD_PARAMETER_VALUE, true, "ORDER not positive (%d) for DARK.ORDINATES %s", + order, item->name); + psFree(options); + return false; + } + + pmDarkOrdinate *ord = pmDarkOrdinateAlloc(item->name, order); + ord->scale = scale; + ord->min = min; + ord->max = max; + psArrayAdd(options->darkOrdinates, options->darkOrdinates->n, ord); + psFree(ord); + } + psFree(iter); + } + return options; } Index: /trunk/ppMerge/src/ppMergeOptions.h =================================================================== --- /trunk/ppMerge/src/ppMergeOptions.h (revision 16841) +++ /trunk/ppMerge/src/ppMergeOptions.h (revision 16842) @@ -21,5 +21,5 @@ bool zero; // Subtract background before combining? bool scale; // Scale by the background before combining? - bool darktime; // Normalise by the dark time (time since flush)? + bool dark; // Generate dark? bool fringe; // Make fringe measurements? bool shutter; // Generate shutter correction? @@ -37,6 +37,6 @@ float maskSuspect; // Threshold for identifying suspect pixels float maskBad; // Threshold for identifying bad pixels - bool statsByChip; // measure statistics for masking by chip or readout? - pmMaskIdentifyMode maskMode; // how to set the limit based on the threshold value above? + bool statsByChip; // measure statistics for masking by chip or readout? + pmMaskIdentifyMode maskMode; // how to set the limit based on the threshold value above? ppOnOff onOff; // On/off pairs? pmCombineParams *combine; // Combination parameters @@ -44,4 +44,5 @@ psMaskType badMask; // Mask value for bad (low) pixels int growPixels; + psArray *darkOrdinates; // Ordinates for dark combination } ppMergeOptions; Index: /trunk/ppMerge/src/ppMergeScaleZero.c =================================================================== --- /trunk/ppMerge/src/ppMergeScaleZero.c (revision 16841) +++ /trunk/ppMerge/src/ppMergeScaleZero.c (revision 16842) @@ -25,5 +25,5 @@ assert(config); - if (!options->scale && !options->zero && !options->darktime && !options->shutter) { + if (!options->scale && !options->zero && !options->shutter) { return true; // We did everything we were asked for } @@ -151,10 +151,6 @@ psStats *bgStats = psStatsAlloc(options->mean); // Statistic to measure the background psVector *gains = NULL; // The gains for each cell - psImage *darktime = NULL; // The dark time for each integration of each cell if (options->scale) { gains = psVectorAlloc(data->numCells, PS_TYPE_F32); - } - if (options->darktime) { - darktime = psImageAlloc(data->numCells, filenames->n, PS_TYPE_F32); } @@ -187,42 +183,4 @@ if (!pmCellReadHeader(cell, inFile)) { continue; - } - - // Normalising by the exposure time - if (options->darktime) { - darktime->data.F32[i][cellNum] = psMetadataLookupF32(NULL, cell->concepts, - "CELL.DARKTIME"); - if (isnan(darktime->data.F32[i][cellNum])) { - psWarning("CELL.DARKTIME for file %s chip %d cell %d is not set.\n", name, j, k); - status = false; - } else { - view->chip = j; - view->cell = k; - - // This step applies the dark exptime / background relationship: F = - // polymomial(exptime). Below, the input images are scaled by the - // output of this relationship. - - // For devices with linear dark and no residual bias, this relationship - // is not defined in the configuration system, and the transformation - // is defined (when loaded by the concepts) to be F = exptime. Thus, - // in this case, the resulting dark image consists of counts/sec. - - // For devices with a different relationship, the transformation yields - // the expected number of counts in the given exposure, based on the - // recorded exptime. Thus, in this case, the resulting dark image - // should have a median value of 1.0. - - // note that these corrections must be applied differently when used to - // correct a science image. - - darktime->data.F32[i][cellNum] = pmFPADarkNorm(fpa, view, - darktime->data.F32[i][cellNum]); - if (isnan(darktime->data.F32[i][cellNum])) { - psWarning("Cannot get dark normalisation for file %s chip %d cell %d.\n", - name, j, k); - status = false; - } - } } @@ -355,13 +313,4 @@ } - if (options->darktime) { - if (!options->scale) { - // Copy over the exposure times - *scales = psImageCopy(*scales, darktime, PS_TYPE_F32); - } else { - *scales = (psImage*)psBinaryOp(*scales, *scales, "*", darktime); - } - } - if (options->zero) { if (!*zeros) {