Index: /trunk/ppImage/src/Makefile.am =================================================================== --- /trunk/ppImage/src/Makefile.am (revision 9951) +++ /trunk/ppImage/src/Makefile.am (revision 9952) @@ -5,4 +5,5 @@ ppImageOptions.h \ ppImageDetrendFringe.h \ + ppImagePreserve.h \ ppMem.h @@ -20,4 +21,5 @@ ppImageDetrendNonLinear.c \ ppImageDetrendFringe.c \ + ppImagePreserve.c \ ppImageRebinReadout.c \ ppImageMosaic.c \ @@ -41,4 +43,5 @@ ppImageDetrendNonLinear.c \ ppImageDetrendFringe.c \ + ppImagePreserve.c \ ppImageRebinReadout.c \ ppImageMosaic.c \ Index: /trunk/ppImage/src/ppImageArguments.c =================================================================== --- /trunk/ppImage/src/ppImageArguments.c (revision 9951) +++ /trunk/ppImage/src/ppImageArguments.c (revision 9952) @@ -33,4 +33,10 @@ "Filename for summary statistics", argv[N]); psArgumentRemove(N, &argc, argv); + } + + if ((N = psArgumentGet(argc, argv, "-fringeimage"))) { + psArgumentRemove(N, &argc, argv); + psMetadataAddBool(options, PS_LIST_TAIL, "INPUT_IS_FRINGE", PS_META_REPLACE, + "Input is fringe image", true); } @@ -73,6 +79,7 @@ if ((N = psArgumentGet(argc, argv, "-norm"))) { psArgumentRemove(N, &argc, argv); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "NORMALISATION", PS_TYPE_F32, - "Normalisation to apply", argv[N]); + float norm = atof(argv[N]); + psMetadataAddF32(config->arguments, PS_LIST_TAIL, "NORMALISATION", 0, + "Normalisation to apply", norm); psArgumentRemove(N, &argc, argv); } Index: /trunk/ppImage/src/ppImageDetrendFringe.c =================================================================== --- /trunk/ppImage/src/ppImageDetrendFringe.c (revision 9951) +++ /trunk/ppImage/src/ppImageDetrendFringe.c (revision 9952) @@ -5,16 +5,29 @@ #include "ppImageDetrendFringe.h" -bool ppImageDetrendFringeMeasure(pmFringeStats **science, // (Ptr to) science fringe measurements - psArray *references, // Array of reference fringe measurements - const pmReadout *readout, // Readout to measure +bool ppImageDetrendFringeMeasure(pmReadout *readout, // Readout to measure + pmCell *fringe, // Fringe cell (each readout is a different component) const ppImageOptions *options // Options ) { - assert(science); - PS_ASSERT_ARRAY_NON_NULL(references, false); + PS_ASSERT_PTR_NON_NULL(readout, false); + PS_ASSERT_PTR_NON_NULL(fringe, false); + PS_ASSERT_PTR_NON_NULL(options, false); + + // Reference fringe measurements + psArray *references = psMemIncrRefCounter(psMetadataLookupPtr(NULL, fringe->analysis, + "FRINGE.MEASUREMENTS")); + if (!references) { + references = pmFringesParse(fringe); // Reference fringes + if (!references) { + psError(PS_ERR_IO, false, "Unable to find fringe references.\n"); + return false; + } + psMetadataAdd(fringe->analysis, PS_LIST_TAIL, "FRINGE.MEASUREMENTS", PS_DATA_UNKNOWN, + "Fringe measurements", references); + } pmFringeStats *reference = references->data[0]; // Take the first as representative pmFringeRegions *regions = reference->regions; // Regions to measure - pmFringeStats *fringe = pmFringeStatsMeasure(regions, readout, options->maskValue); // Fringe stats + pmFringeStats *measurements = pmFringeStatsMeasure(regions, readout, options->maskValue); // Fringe stats // Normalise measurements by the exposure time @@ -23,5 +36,5 @@ if (!mdok || !isfinite(expTime)) { psError(PS_ERR_UNKNOWN, false, "CELL.EXPOSURE is not set for --- can't normalise fringes\n"); - psFree(fringe); + psFree(measurements); return false; } @@ -30,22 +43,21 @@ expTime = 1.0; } - psBinaryOp(fringe->f, fringe->f, "*", psScalarAlloc(1.0 / expTime, PS_TYPE_F32)); - psBinaryOp(fringe->df, fringe->df, "*", psScalarAlloc(1.0 / expTime, PS_TYPE_F32)); + psBinaryOp(measurements->f, measurements->f, "*", psScalarAlloc(1.0 / expTime, PS_TYPE_F32)); + psBinaryOp(measurements->df, measurements->df, "*", psScalarAlloc(1.0 / expTime, PS_TYPE_F32)); - if (!*science) { - // Only a single readout - *science = fringe; - } else { + // Science fringe measurements + pmFringeStats *previous = psMetadataLookupPtr(NULL, readout->parent->analysis, "FRINGE.MEASUREMENTS"); + if (previous) { // Multiple readouts: concatenate psArray *concatenate = psArrayAlloc(2); // Array to hold fringes // Concatenate science measurements - concatenate->data[0] = *science; - concatenate->data[1] = fringe; - pmFringeStats *sciNew = pmFringeStatsConcatenate(concatenate, NULL, NULL); // New measurements - psFree(*science); - *science = sciNew; + concatenate->data[0] = previous; + concatenate->data[1] = measurements; + pmFringeStats *new = pmFringeStatsConcatenate(concatenate, NULL, NULL); // New measurements + psFree(measurements); + measurements = new; - // Concatenate reference measurements + // Concatenate reference measurements (duplication, so the science and reference line up) for (int i = 0; i < references->n; i++) { concatenate->data[0] = concatenate->data[1] = references->data[i]; @@ -54,8 +66,13 @@ references->data[i] = refNew; } - concatenate->data[0] = concatenate->data[1] = NULL; psFree(concatenate); } + + psMetadataAdd(readout->parent->analysis, PS_LIST_TAIL, "FRINGE.MEASUREMENTS", + PS_DATA_UNKNOWN | PS_META_REPLACE, "Fringe measurements", measurements); + psFree(measurements); + + psFree(references); return true; @@ -63,16 +80,38 @@ +// Pull the fringes out of the cell analysis FRINGE.MEASUREMENTS for a chip +static psArray *getFringes(const pmChip *chip // Chip of interest + ) +{ + psArray *cells = chip->cells; // Component cells + psArray *fringes = psArrayAlloc(cells->n); // Fringes, to return + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // Cell of interest + fringes->data[i] = psMemIncrRefCounter(psMetadataLookupPtr(NULL, cell->analysis, + "FRINGE.MEASUREMENTS")); + } + + return fringes; +} + // Solve the fringe system: we have science fringe measurements for each cell, and an array of reference // fringe measurements for each cell. Need to concatenate these together first, and then solve. -pmFringeScale *ppImageDetrendFringeSolve(psArray *science, // Science fringe measurements (per cell) - psArray *references, // Array of array of fringe measurements - const ppImageOptions *options // Options +bool ppImageDetrendFringeSolve(pmChip *scienceChip, // Chip with science + const pmChip *refChip, // Chip with reference fringes + const ppImageOptions *options // Options ) { + PS_ASSERT_PTR_NON_NULL(scienceChip, NULL); + PS_ASSERT_PTR_NON_NULL(refChip, NULL); + PS_ASSERT_PTR_NON_NULL(options, NULL); + + psArray *science = getFringes(scienceChip); // Fringe measurements on science chip pmFringeStats *scienceCat = pmFringeStatsConcatenate(science, NULL, NULL); // Science fringes + psFree(science); // Need to transform the array of cells each with an array of fringes --> array of fringes for the chip as // a whole + psArray *references = getFringes(refChip); // Fringe measurements on reference chip int numRefs = ((psArray*)references->data[0])->n; // Number of reference fringes psArray *referencesCat = psArrayAlloc(numRefs); // Reference fringes @@ -86,4 +125,5 @@ psFree(refs); } + psFree(references); // Now we can solve @@ -92,18 +132,22 @@ options->fringeIter, options->fringeKeep); + psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.SOLUTION", PS_DATA_UNKNOWN, + "Fringe solution", solution); + psFree(solution); psFree(scienceCat); psFree(referencesCat); - return solution; + return true; } psImage *ppImageDetrendFringeGenerate(pmCell *science, // Science cell - pmCell *fringes, // Fringe cell, one readout per fringe component - const pmFringeScale *solution // Fringe solution to apply + pmCell *fringes // Fringe cell, one readout per fringe component ) { PS_ASSERT_PTR_NON_NULL(science, false); - PS_ASSERT_PTR_NON_NULL(solution, false); + PS_ASSERT_PTR_NON_NULL(fringes, false); + + pmFringeScale *solution = psMetadataLookupPtr(NULL, science->parent->analysis, "FRINGE.SOLUTION"); assert(fringes->readouts->n == solution->nFringeFrames); Index: /trunk/ppImage/src/ppImageDetrendFringe.h =================================================================== --- /trunk/ppImage/src/ppImageDetrendFringe.h (revision 9951) +++ /trunk/ppImage/src/ppImageDetrendFringe.h (revision 9952) @@ -6,19 +6,19 @@ #include "ppImageOptions.h" -bool ppImageDetrendFringeMeasure(pmFringeStats **science, // (Ptr to) science fringe measurements - psArray *references, // Array of reference fringe measurements - const pmReadout *readout, // Readout to measure +bool ppImageDetrendFringeMeasure(pmReadout *readout, // Readout to measure + pmCell *fringe, // Fringe cell (each readout is a different component) const ppImageOptions *options // Options ); -pmFringeScale *ppImageDetrendFringeSolve(psArray *science, // Science fringe measurements (per cell) - psArray *references, // Array of array of fringe measurements - const ppImageOptions *options // Options +bool ppImageDetrendFringeSolve(pmChip *scienceChip, // Chip with science + const pmChip *refChip, // Chip with reference fringes + const ppImageOptions *options // Options ); + psImage *ppImageDetrendFringeGenerate(pmCell *science, // Science cell - pmCell *fringes, // Fringe cell, one readout per fringe component - const pmFringeScale *solution // Fringe solution to apply + pmCell *fringes // Fringe cell, one readout per fringe component ); + #endif Index: /trunk/ppImage/src/ppImageDetrendReadout.c =================================================================== --- /trunk/ppImage/src/ppImageDetrendReadout.c (revision 9951) +++ /trunk/ppImage/src/ppImageDetrendReadout.c (revision 9952) @@ -4,4 +4,5 @@ #include "ppImage.h" +#include "ppImageDetrendFringe.h" bool ppImageDetrendReadout (pmConfig *config, ppImageOptions *options, pmFPAview *view) @@ -72,4 +73,11 @@ } + if (options->doFringe) { + pmCell *fringe = pmFPAfileThisCell(config->files, detview, "PPIMAGE.FRINGE"); + if (!ppImageDetrendFringeMeasure(input, fringe, options)) { + return false; + } + } + psFree (detview); return true; Index: /trunk/ppImage/src/ppImageLoop.c =================================================================== --- /trunk/ppImage/src/ppImageLoop.c (revision 9951) +++ /trunk/ppImage/src/ppImageLoop.c (revision 9952) @@ -6,4 +6,5 @@ #include "ppImage.h" #include "ppImageDetrendFringe.h" + bool ppImageLoop (pmConfig *config, ppImageOptions *options) { @@ -45,30 +46,8 @@ if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) return false; - const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); // Name of chip - psArray *fringeRef = NULL; // Array of array of fringe statistics for reference --- for each cell - psArray *fringeSci = NULL; // Array of fringe statistics for science --- for each cell - if (options->doFringe) { - fringeRef = psArrayAlloc(chip->cells->n); - fringeSci = psArrayAlloc(chip->cells->n); - } - while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { psLogMsg ("ppImageLoop", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); if (!cell->process || !cell->file_exists) { continue; } if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) return false; - const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of cell - - if (options->doFringe) { - pmFPAfile *fringeFile = psMetadataLookupPtr(&status, config->files, "PPIMAGE.FRINGE"); - if (!status || !fringeFile) { - psErrorStackPrint(stderr, "Can't find fringe data!\n"); - exit(EXIT_FAILURE); - } - - psString fringeExt = NULL; // Fringe extension name - psStringAppend(&fringeExt, "FRINGE_%s_%s", chipName, cellName); - fringeRef->data[view->cell] = pmFringesReadFits(NULL, fringeFile->fits, fringeExt); - psFree(fringeExt); - } // process each of the readouts @@ -80,17 +59,13 @@ if (!ppImageDetrendReadout (config, options, view)) return false; - if (options->doFringe) { - ppImageDetrendFringeMeasure((pmFringeStats**)(&fringeSci->data[view->cell]), - fringeRef->data[view->cell], readout, options); - } } } // Solve the fringe system - pmFringeScale *fringeSoln = NULL; // Solution for the fringes if (options->doFringe) { - fringeSoln = ppImageDetrendFringeSolve(fringeSci, fringeRef, options); - psFree(fringeSci); - psFree(fringeRef); + pmChip *fringe = pmFPAfileThisChip(config->files, view, "PPIMAGE.FRINGE"); + if (!ppImageDetrendFringeSolve(chip, fringe, options)) { + return false; + } } @@ -103,8 +78,6 @@ if (options->doFringe) { psTrace("ppImage", 3, "Applying fringe correction...\n"); - bool mdok; // Status of MD lookup - pmFPAfile *fringeFile = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.FRINGE"); - pmCell *fringeCell = pmFPAviewThisCell(view, fringeFile->fpa); - psImage *fringe = ppImageDetrendFringeGenerate(cell, fringeCell, fringeSoln); + pmCell *fringeCell = pmFPAfileThisCell(config->files, view, "PPIMAGE.FRINGE"); + psImage *fringe = ppImageDetrendFringeGenerate(cell, fringeCell); while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { if (!readout->data_exists) { continue; } @@ -125,5 +98,4 @@ if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) return false; } - psFree(fringeSoln); ppImageMosaicChip (config, view, "PPIMAGE.OUTPUT.CHIP", "PPIMAGE.OUTPUT"); @@ -163,5 +135,6 @@ if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) return false; - psFree (view); + psFree(view); + return true; } Index: /trunk/ppImage/src/ppImageParseCamera.c =================================================================== --- /trunk/ppImage/src/ppImageParseCamera.c (revision 9951) +++ /trunk/ppImage/src/ppImageParseCamera.c (revision 9952) @@ -12,5 +12,5 @@ // the input image defines the camera, and all recipes and options the follow pmFPAfile *input = pmFPAfileDefineFromArgs (&status, config, "PPIMAGE.INPUT", "INPUT"); - if (!status) { + if (!status || !input) { psError(PS_ERR_IO, false, "Failed to build FPA from PPIMAGE.INPUT"); return NULL; @@ -177,4 +177,10 @@ psFree (chips); + if (psMetadataLookupBool(NULL, recipe, "INPUT_IS_FRINGE")) { + // It's a fringe file, so change the file type + input->type = PM_FPA_FILE_FRINGE; + output->type = PM_FPA_FILE_FRINGE; + } + return (options); }