Index: /trunk/ppMerge/src/ppMerge.c =================================================================== --- /trunk/ppMerge/src/ppMerge.c (revision 13872) +++ /trunk/ppMerge/src/ppMerge.c (revision 13873) @@ -46,16 +46,22 @@ } - psImage *scale = NULL; // The scalings - psImage *zero = NULL; // The zeros - if (options->mask) { // Generate a mask ppMergeMask(data, options, config); } else { + + psImage *scale = NULL; // The scalings + psImage *zero = NULL; // The zeros + psArray *shutters = NULL; // The shutter correction data + // Measure the background in each image - ppMergeScaleZero(&scale, &zero, data, options, config); + ppMergeScaleZero(&scale, &zero, &shutters, data, options, config); // Do the combination and write - ppMergeCombine(scale, zero, data, options, config); + ppMergeCombine(scale, zero, shutters, data, options, config); + + psFree(scale); + psFree(zero); + psFree(shutters); } @@ -73,6 +79,4 @@ // Cleaning up psFree(data); - psFree(scale); - psFree(zero); psFree(options); psFree(config); Index: /trunk/ppMerge/src/ppMergeCombine.c =================================================================== --- /trunk/ppMerge/src/ppMergeCombine.c (revision 13872) +++ /trunk/ppMerge/src/ppMergeCombine.c (revision 13873) @@ -83,4 +83,5 @@ bool ppMergeCombine(psImage *scales, // Scales for each cell of each integration, or NULL psImage *zeros, // Zeros for each cell of each integration, or NULL + psArray *shutters, // Shutter correction data for each cell, or NULL ppMergeData *data, // Data ppMergeOptions *options, // Options @@ -100,4 +101,6 @@ zeros->numCols == data->numCells && zeros->numRows == filenames->n)); + assert(!options->shutter || shutters); + assert(!shutters || (shutters->n == data->numCells)); // Iterate over the FPA @@ -143,4 +146,9 @@ } + float shutterRef; // Reference shutter correction + if (options->shutter) { + shutterRef = pmShutterCorrectionReference(shutters->data[cellNum]); + } + do { numRead = 0; @@ -162,11 +170,11 @@ // Only reading and writing the first readout in each cell (plane 0) - bool readOK; + bool readOK; if (pmReadoutReadNext(&readOK, stack->data[i], fits, 0, options->rows)) { - if (!readOK) { - psError(PS_ERR_IO, false, "Failed to read concepts for cell.\n"); - psErrorStackPrint(stderr, "trouble reading data!\n"); - exit (1); - } + if (!readOK) { + psError(PS_ERR_IO, false, "Failed to read concepts for cell.\n"); + psErrorStackPrint(stderr, "trouble reading data!\n"); + exit (1); + } // If we're creating a bias or a dark, we don't want to generate a mask if ((options->zero || options->scale || options->shutter || options->mask) && @@ -198,9 +206,7 @@ if (options->shutter) { - pmShutterCorrectionMeasure(readout, stack, options->shutterSize, - options->mean, options->stdev, - options->shutterIter, - options->shutterRej, - options->combine->maskVal); + pmShutterCorrectionGenerate(readout, NULL, stack, shutterRef, shutters->data[cellNum], + options->shutterIter, options->shutterRej, + options->combine->maskVal); } else { pmReadoutCombine(readout, stack, cellZeros, cellScales, options->combine); @@ -271,16 +277,12 @@ // Statistics on the merged cell if (data->statsFile) { - if (!data->stats) { - data->stats = psMetadataAlloc(); - } - if (!ppStats(data->stats, - data->out, - view, - options->combine->maskVal, - config)) { + if (!data->stats) { + data->stats = psMetadataAlloc(); + } + if (!ppStats(data->stats, data->out, view, options->combine->maskVal, config)) { psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to generate stats for image.\n"); - return false; - } - } + return false; + } + } // We threw away the bias sections --- record this Index: /trunk/ppMerge/src/ppMergeCombine.h =================================================================== --- /trunk/ppMerge/src/ppMergeCombine.h (revision 13872) +++ /trunk/ppMerge/src/ppMergeCombine.h (revision 13873) @@ -11,4 +11,5 @@ bool ppMergeCombine(psImage *scales, // Scales for each cell of each integration, or NULL psImage *zeros, // Zeros for each cell of each integration, or NULL + psArray *shutters, // Shutter correction data for each cell, or NULL ppMergeData *data, // Data ppMergeOptions *options, // Options Index: /trunk/ppMerge/src/ppMergeOptions.c =================================================================== --- /trunk/ppMerge/src/ppMergeOptions.c (revision 13872) +++ /trunk/ppMerge/src/ppMergeOptions.c (revision 13873) @@ -61,5 +61,4 @@ options->satMask = 0x00; options->badMask = 0x00; - return options; } @@ -135,5 +134,5 @@ // First, deal with the recipe. These are parameters that will typically be constant for a camera. - OPTION_PARSE(options->rows, recipe, "ROWS", U16); + OPTION_PARSE(options->rows, recipe, "ROWS", S32); OPTION_PARSE(options->minElectrons, recipe, "ELECTRONS", F32); OPTION_PARSE(options->sample, recipe, "SAMPLE", S32); @@ -215,5 +214,4 @@ options->shutter = true; options->mask = false; - options->rows = 0; // Read the whole image at once } else if (strcasecmp(type, "MASK") == 0) { options->zero = false; Index: /trunk/ppMerge/src/ppMergeScaleZero.c =================================================================== --- /trunk/ppMerge/src/ppMergeScaleZero.c (revision 13872) +++ /trunk/ppMerge/src/ppMergeScaleZero.c (revision 13873) @@ -15,4 +15,5 @@ bool ppMergeScaleZero(psImage **scales, // The scales for each integration/cell psImage **zeros, // The zeroes for each integration/cell + psArray **shutters, // The shutter correction data for each cell ppMergeData *data,// The data const ppMergeOptions *options, // The options @@ -24,5 +25,5 @@ assert(config); - if (!options->scale && !options->zero && !options->darktime) { + if (!options->scale && !options->zero && !options->darktime && !options->shutter) { return true; // We did everything we were asked for } @@ -43,4 +44,6 @@ (*zeros)->numCols == data->numCells && (*zeros)->numRows == filenames->n)); + assert(!options->shutter || shutters); + assert(!shutters || !*shutters || (*shutters)->n == data->numCells); // Allocate the outputs @@ -57,6 +60,14 @@ *zeros = psImageAlloc(data->numCells, filenames->n, PS_TYPE_F32); } - - bool fromConcepts = false; // Do we get the scale and zero points from the concepts + psRandom *rng = NULL; // Random number generator + if (options->shutter) { + if (*shutters) { + psFree(*shutters); + } + *shutters = psArrayAlloc(data->numCells); + rng = psRandomAlloc(PS_RANDOM_TAUS, 0); + } + + bool fromConcepts = false; // Do we get the scale and zero points from the concepts? bool first = true; // Are we on the first cell (that sets the standard for the rest)? bool done = false; // Are we done going through the list? @@ -86,5 +97,5 @@ if (mdok && !isnan(scale)) { if (!first && !fromConcepts) { - psLogMsg(__func__, PS_LOG_WARN, "PPMERGE.SCALE and PPMERGE.ZERO have been set " + psWarning("PPMERGE.SCALE and PPMERGE.ZERO have been set " "for some, but not all cells --- we will re-measure it for all cells."); done = true; @@ -93,7 +104,8 @@ fromConcepts = true; (*scales)->data.F32[i][cellNum] = scale; - psTrace("ppMerge", 9, "Scale for input %ld, chip %ld, cell %ld: %f\n", i, j, k, scale); + psTrace("ppMerge", 9, "Scale for input %ld, chip %ld, cell %ld: %f\n", + i, j, k, scale); } else if (!first && fromConcepts) { - psLogMsg(__func__, PS_LOG_WARN, "PPMERGE.SCALE and PPMERGE.ZERO have been set " + psWarning("PPMERGE.SCALE and PPMERGE.ZERO have been set " "for some, but not all cells --- we will re-measure it for all cells."); fromConcepts = false; @@ -107,5 +119,5 @@ if (mdok && !isnan(zero)) { if (!first && !fromConcepts) { - psLogMsg(__func__, PS_LOG_WARN, "PPMERGE.SCALE and PPMERGE.ZERO have been set " + psWarning("PPMERGE.SCALE and PPMERGE.ZERO have been set " "for some, but not all cells --- we will re-measure it for all cells."); done = true; @@ -116,5 +128,5 @@ psTrace("ppMerge", 9, "Zero for input %ld, chip %ld, cell %ld: %f\n", i, j, k, zero); } else if (!first && fromConcepts) { - psLogMsg(__func__, PS_LOG_WARN, "PPMERGE.SCALE and PPMERGE.ZERO have been set " + psWarning("PPMERGE.SCALE and PPMERGE.ZERO have been set " "for some, but not all cells --- we will re-measure it for all cells."); fromConcepts = false; @@ -131,4 +143,5 @@ if (fromConcepts) { // We've already done everything we need to + psFree(rng); return true; } @@ -205,5 +218,5 @@ if (cell->readouts->n > 1) { - psLogMsg(__func__, PS_LOG_WARN, "File %s chip %d cell %d contains more than one " + psWarning("File %s chip %d cell %d contains more than one " "readout --- ignoring all but the first.\n", name, j, k); status = false; @@ -222,5 +235,5 @@ gains->data.F32[cellNum] = psMetadataLookupF32(&mdok, cell->concepts, "CELL.GAIN"); if (!mdok || isnan(gains->data.F32[cellNum])) { - psLogMsg(__func__, PS_LOG_WARN, "CELL.GAIN for file %s chip %d cell %d is not " + psWarning("CELL.GAIN for file %s chip %d cell %d is not " "set.\n", name, j, k); gains->data.F32[cellNum] = NAN; @@ -259,4 +272,35 @@ } + // Shutter correction + if (options->shutter) { + if (!pmCellRead(cell, inFile, config->database)) { + // Nothing here + pmCellFreeData(cell); + continue; + } + + if (cell->readouts->n > 1) { + psWarning("File %s chip %d cell %d contains more than one " + "readout --- ignoring all but the first.\n", name, j, k); + status = false; + } + pmReadout *readout = cell->readouts->data[0]; // The readout of interest + + pmShutterCorrectionData *shutter = (*shutters)->data[cellNum]; // Shutter correction data + if (!shutter) { + shutter = pmShutterCorrectionDataAlloc(readout->image->numCols, + readout->image->numRows, + options->shutterSize); + (*shutters)->data[cellNum] = shutter; + } + if (!pmShutterCorrectionAddReadout(shutter, readout, options->mean, options->stdev, + options->combine->maskVal, rng)) { + psWarning("Can't add file %s chip %d cell %d to shutter correction --- ignored.", + name, j, k); + status = false; + } + } + + pmCellFreeData(cell); } @@ -265,4 +309,5 @@ pmFPAFreeData(fpa); } + psFree(rng); psFree(bgStats); psFree(view); @@ -277,5 +322,5 @@ psVector *fluxes = NULL; // Solution to fluxes if (!pmFlatNormalize(&fluxes, &gains, background)) { - psLogMsg(__func__, PS_LOG_WARN, "Normalisation failed to converge --- continuing anyway.\n"); + psWarning("Normalisation failed to converge --- continuing anyway.\n"); status = false; } Index: /trunk/ppMerge/src/ppMergeScaleZero.h =================================================================== --- /trunk/ppMerge/src/ppMergeScaleZero.h (revision 13872) +++ /trunk/ppMerge/src/ppMergeScaleZero.h (revision 13873) @@ -11,4 +11,5 @@ bool ppMergeScaleZero(psImage **scales, // The scales for each integration/cell psImage **zeros, // The zeroes for each integration/cell + psArray **shutter,// The shutter correction data for each cell ppMergeData *data,// The data const ppMergeOptions *options, // The options