Index: branches/2dbias/ppImage/src/ppImage.h =================================================================== --- branches/2dbias/ppImage/src/ppImage.h (revision 42665) +++ branches/2dbias/ppImage/src/ppImage.h (revision 42679) @@ -188,4 +188,5 @@ bool ppImageDetrendFree(pmConfig *config, pmFPAview *view); +bool ppImageDoPatternForView(bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipeName, const char *recipeValue); bool ppImageFringeFree(pmConfig *config, pmFPAview *view); Index: branches/2dbias/ppImage/src/ppImageDetrendPattern.c =================================================================== --- branches/2dbias/ppImage/src/ppImageDetrendPattern.c (revision 42665) +++ branches/2dbias/ppImage/src/ppImageDetrendPattern.c (revision 42679) @@ -5,11 +5,12 @@ #include "ppImage.h" -#define ESCAPE(STATUS,...) { \ - psError(PS_ERR_UNKNOWN, STATUS, __VA_ARGS__); \ - psFree(view); \ - return false; \ - } - -static bool doPatternForView (bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipename, const char *recipevalue); +#define ESCAPE(STATUS, ...) \ + { \ + psError(PS_ERR_UNKNOWN, STATUS, __VA_ARGS__); \ + psFree(view); \ + return false; \ + } + +bool ppImageDoPatternForView(bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipename, const char *recipevalue); bool ppImageDetrendPatternRowApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options); @@ -26,17 +27,21 @@ assert(inputView->readout == -1); - if (!ppImageDetrendPatternRowApply (config, chip, inputView, options)) { - return false; - } - if (!ppImageDetrendPatternContinuityApply (config, chip, inputView, options)) { - return false; - } - if (!ppImageDetrendPatternCellApply (config, chip, inputView, options)) { - return false; - } - if (!ppImageDetrendPatternDeadCellsApply (config, chip, inputView, options)) { - return false; - } - return(true); + if (!ppImageDetrendPatternRowApply(config, chip, inputView, options)) + { + return false; + } + if (!ppImageDetrendPatternContinuityApply(config, chip, inputView, options)) + { + return false; + } + if (!ppImageDetrendPatternCellApply(config, chip, inputView, options)) + { + return false; + } + if (!ppImageDetrendPatternDeadCellsApply(config, chip, inputView, options)) + { + return false; + } + return (true); } @@ -45,6 +50,7 @@ bool status; - if (!options->doPatternRow) return true; - + if (!options->doPatternRow) + return true; + assert(inputView->chip != -1); assert(inputView->cell == -1); @@ -73,7 +79,8 @@ pmHDU *hdu = pmHDUFromChip(chip); - if (psMetadataLookupBool(&status, hdu->header, "PTRN_ROW")) { - psLogMsg("ppImage", PS_LOG_INFO, "Not performing row pattern correction as it has already been done."); - return true; + if (psMetadataLookupBool(&status, hdu->header, "PTRN_ROW")) + { + psLogMsg("ppImage", PS_LOG_INFO, "Not performing row pattern correction as it has already been done."); + return true; } @@ -85,92 +92,108 @@ // grab the PATTERN.ROW.AMP file - pmFPAfile *PRAfile = psMetadataLookupPtr (&status, config->files, "PPIMAGE.PATTERN.ROW.AMP"); - if (!PRAfile) { - psLogMsg("ppImage", PS_LOG_INFO, "Pattern Row Amplitude file not found, applying to all (with limits from ROW.SUBSET) "); - } - + pmFPAfile *PRAfile = psMetadataLookupPtr(&status, config->files, "PPIMAGE.PATTERN.ROW.AMP"); + if (!PRAfile) + { + psLogMsg("ppImage", PS_LOG_INFO, "Pattern Row Amplitude file not found, applying to all (with limits from ROW.SUBSET) "); + } + pmFPAview *view = pmFPAviewAlloc(0); // View for local processing *view = *inputView; pmCell *cell = NULL; - while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { - // const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); - // const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); - // psWarning ("Looping through %s, %s\n", chipName, cellName); - - if (!cell->process || !cell->file_exists) { - continue; - } - - // this forces pmFPAfileRead of the PATTERN.ROW.AMP file (XXX but is this needed?) - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - ESCAPE(false, "load failure for Cell"); - } - - if (!cell->data_exists) { - continue; - } - - if (cell->readouts->n > 1) { - psWarning ("Skipping Video Cell for ppImageDetrendPatternApply"); - continue; - } - - // grab the corresponding cell - if (PRAfile) { - pmCell *PRAcell = pmFPAviewThisCell (view, PRAfile->fpa); - psAssert (PRAcell, "found Pattern Row Amplitude file, but not cell?"); - - // find the nominal signal amplitude (check the ghost and/or crosstalk recipe file) - float amplitude = psMetadataLookupF32 (&status, PRAcell->analysis, "PTN.ROW.AMP"); - if (!status) amplitude = NAN; - - // put the value on the science cell - psMetadataAddF32 (cell->analysis, PS_LIST_TAIL, "PTN.ROW.AMP", PS_META_REPLACE, "", amplitude); - } - - bool doPattern = false; - if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.ROW.SUBSET")) { - ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); - } - if (!doPattern) continue; - - // switch to test threaded version - if (true) { - // I need to allocate a view here to be freed by the - // called function below. - pmFPAview *myView = pmFPAviewAlloc(0); // View for local processing - *myView = *view; - - // allocate a job, construct the arguments for this job - psThreadJob *job = psThreadJobAlloc("PPIMAGE_PATTERN_ROW_CELL"); - psArrayAdd(job->args, 1, config); - psArrayAdd(job->args, 1, input->fpa); - psArrayAdd(job->args, 1, chip); - psArrayAdd(job->args, 1, cell); - psArrayAdd(job->args, 1, myView); - psArrayAdd(job->args, 1, options); - if (!psThreadJobAddPending(job)) { - return false; - } - } else { - // bump the counter since it must be freed by the function below. - psMemIncrRefCounter (view); // View for local processing - if (!ppImageDetrendPatternApplyCell (config, input->fpa, chip, cell, view, options)) { - return false; - } - } + while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) + { + // const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); + // const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); + // psWarning ("Looping through %s, %s\n", chipName, cellName); + + if (!cell->process || !cell->file_exists) + { + continue; + } + + // this forces pmFPAfileRead of the PATTERN.ROW.AMP file (XXX but is this needed?) + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) + { + ESCAPE(false, "load failure for Cell"); + } + + if (!cell->data_exists) + { + continue; + } + + if (cell->readouts->n > 1) + { + psWarning("Skipping Video Cell for ppImageDetrendPatternApply"); + continue; + } + + // grab the corresponding cell + if (PRAfile) + { + pmCell *PRAcell = pmFPAviewThisCell(view, PRAfile->fpa); + psAssert(PRAcell, "found Pattern Row Amplitude file, but not cell?"); + + // find the nominal signal amplitude (check the ghost and/or crosstalk recipe file) + float amplitude = psMetadataLookupF32(&status, PRAcell->analysis, "PTN.ROW.AMP"); + if (!status) + amplitude = NAN; + + // put the value on the science cell + psMetadataAddF32(cell->analysis, PS_LIST_TAIL, "PTN.ROW.AMP", PS_META_REPLACE, "", amplitude); + } + + bool doPattern = false; + if (!ppImageDoPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.ROW.SUBSET")) + { + ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); + } + if (!doPattern) + continue; + + // switch to test threaded version + if (true) + { + // I need to allocate a view here to be freed by the + // called function below. + pmFPAview *myView = pmFPAviewAlloc(0); // View for local processing + *myView = *view; + + // allocate a job, construct the arguments for this job + psThreadJob *job = psThreadJobAlloc("PPIMAGE_PATTERN_ROW_CELL"); + psArrayAdd(job->args, 1, config); + psArrayAdd(job->args, 1, input->fpa); + psArrayAdd(job->args, 1, chip); + psArrayAdd(job->args, 1, cell); + psArrayAdd(job->args, 1, myView); + psArrayAdd(job->args, 1, options); + if (!psThreadJobAddPending(job)) + { + return false; + } + } + else + { + // bump the counter since it must be freed by the function below. + psMemIncrRefCounter(view); // View for local processing + if (!ppImageDetrendPatternApplyCell(config, input->fpa, chip, cell, view, options)) + { + return false; + } + } } // wait here for the threaded jobs to finish - // if no threads are allocated, this - if (!psThreadPoolWait(true, true)) { - psError(PS_ERR_UNKNOWN, false, "Unable to apply bias correction."); - return false; - } - - psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_ROW",PS_META_REPLACE,"PATTERN.ROW correction applied",true); + // if no threads are allocated, this + if (!psThreadPoolWait(true, true)) + { + psError(PS_ERR_UNKNOWN, false, "Unable to apply bias correction."); + return false; + } + + psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_ROW", PS_META_REPLACE, "PATTERN.ROW correction applied", true); psFree(view); - + return true; } @@ -180,5 +203,6 @@ bool status; - if (!options->doPatternContinuity) return true; + if (!options->doPatternContinuity) + return true; assert(inputView->chip != -1); @@ -188,13 +212,14 @@ // see the comment for PATTERN.ROW; the same rules apply for PATTERN.CELL - int numCells = chip->cells->n; // Number of cells + int numCells = chip->cells->n; // Number of cells psVector *tweak = psVectorAlloc(numCells, PS_TYPE_U8); // Tweak cell? - pmFPAview *view = pmFPAviewAlloc(0); // View for local processing + pmFPAview *view = pmFPAviewAlloc(0); // View for local processing *view = *inputView; pmHDU *hdu = pmHDUFromChip(chip); - if (psMetadataLookupBool(&status, hdu->header, "PTRN_CON")) { - psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction as it has already been done."); - return true; + if (psMetadataLookupBool(&status, hdu->header, "PTRN_CON")) + { + psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction as it has already been done."); + return true; } @@ -202,35 +227,40 @@ psLogMsg("ppImage", PS_LOG_INFO, "Performing pattern continuity correction for %s\n", chipName); - for (int i = 0; i < chip->cells->n; i++) { - view->cell = i; - - pmCell *cell = chip->cells->data[i]; // Cell of interest - - if (cell->readouts->n > 1) { - psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction on video cell."); - continue; - } - - bool doPattern = false; - if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CONTINUITY.SUBSET")) { - ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); - } - - if (doPattern) { - tweak->data.U8[i] = 0xFF; - } + for (int i = 0; i < chip->cells->n; i++) + { + view->cell = i; + + pmCell *cell = chip->cells->data[i]; // Cell of interest + + if (cell->readouts->n > 1) + { + psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction on video cell."); + continue; + } + + bool doPattern = false; + if (!ppImageDoPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CONTINUITY.SUBSET")) + { + ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); + } + + if (doPattern) + { + tweak->data.U8[i] = 0xFF; + } } // Tweak the cells if (!pmPatternContinuity(chip, tweak, options->patternCellBG, options->patternCellMean, - options->maskValue, options->darkMask,options->patternContinuityEdgeWidth)) { - psFree(tweak); - psFree(view); - return false; + options->maskValue, options->darkMask, options->patternContinuityEdgeWidth)) + { + psFree(tweak); + psFree(view); + return false; } psFree(tweak); psFree(view); - psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CON",PS_META_REPLACE,"PATTERN.CONTINUITY correction applied",true); + psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CON", PS_META_REPLACE, "PATTERN.CONTINUITY correction applied", true); return true; } @@ -240,5 +270,6 @@ bool status; - if (!options->doPatternCell) return true; + if (!options->doPatternCell) + return true; assert(inputView->chip != -1); @@ -246,13 +277,14 @@ assert(inputView->readout == -1); - int numCells = chip->cells->n; // Number of cells + int numCells = chip->cells->n; // Number of cells psVector *tweak = psVectorAlloc(numCells, PS_TYPE_U8); // Tweak cell? - pmFPAview *view = pmFPAviewAlloc(0); // View for local processing + pmFPAview *view = pmFPAviewAlloc(0); // View for local processing *view = *inputView; pmHDU *hdu = pmHDUFromChip(chip); - if (psMetadataLookupBool(&status, hdu->header, "PTRN_CEL")) { - psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction as it has already been done."); - return true; + if (psMetadataLookupBool(&status, hdu->header, "PTRN_CEL")) + { + psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction as it has already been done."); + return true; } @@ -260,115 +292,135 @@ psLogMsg("ppImage", PS_LOG_INFO, "Performing cell pattern correction for %s\n", chipName); - for (int i = 0; i < chip->cells->n; i++) { - view->cell = i; - - pmCell *cell = chip->cells->data[i]; // Cell of interest - - if (cell->readouts->n > 1) { - psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction on video cell."); - continue; - } - - bool doPattern = false; - if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CELL.SUBSET")) { - ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); - } - if (doPattern) { - tweak->data.U8[i] = 0xFF; - } + for (int i = 0; i < chip->cells->n; i++) + { + view->cell = i; + + pmCell *cell = chip->cells->data[i]; // Cell of interest + + if (cell->readouts->n > 1) + { + psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction on video cell."); + continue; + } + + bool doPattern = false; + if (!ppImageDoPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CELL.SUBSET")) + { + ESCAPE(false, "Unable to determine whether row pattern matching should be applied."); + } + if (doPattern) + { + tweak->data.U8[i] = 0xFF; + } } // Tweak the cells if (!pmPatternCell(chip, tweak, options->patternCellBG, options->patternCellMean, - options->maskValue, options->darkMask)) { - psFree(tweak); - psFree(view); - return false; + options->maskValue, options->darkMask)) + { + psFree(tweak); + psFree(view); + return false; } psFree(tweak); psFree(view); - psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CEL",PS_META_REPLACE,"PATTERN.CELL correction applied",true); + psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CEL", PS_META_REPLACE, "PATTERN.CELL correction applied", true); return true; } -bool ppImageDetrendPatternDeadCellsMask (pmChip *chip, psImageMaskType maskVal) { - - int numCells = chip->cells->n; // Number of cells +bool ppImageDetrendPatternDeadCellsMask(pmChip *chip, psImageMaskType maskVal) +{ + + int numCells = chip->cells->n; // Number of cells // now mask bad cells - for (int i = 0; i < numCells; i++) { - pmCell *cell = chip->cells->data[i]; // Cell of interest + for (int i = 0; i < numCells; i++) + { + pmCell *cell = chip->cells->data[i]; // Cell of interest pmReadout *ro = cell->readouts->data[0]; // Readout of interest - psImage *mask = ro->mask; // mask of interest - int numCols = mask->numCols, numRows = mask->numRows; // Size of image - - for (int y = 0; y < numRows; y++) { - for (int x = 0; x < numCols; x++) { - mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= maskVal; - } - } + psImage *mask = ro->mask; // mask of interest + int numCols = mask->numCols, numRows = mask->numRows; // Size of image + + for (int y = 0; y < numRows; y++) + { + for (int x = 0; x < numCols; x++) + { + mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= maskVal; + } + } } return true; } -bool ppImageDetrendPatternDeadCellsXY42 (pmChip *chip, psImageMaskType maskVal) { +bool ppImageDetrendPatternDeadCellsXY42(pmChip *chip, psImageMaskType maskVal) +{ bool status; // extract the MEDIAN_CELL_BACKGROUND values to check for problems - int numCells = chip->cells->n; // Number of cells - psVector *cellBackground = psVectorAllocEmpty (numCells, PS_DATA_F32); - - for (int i = 0; i < numCells; i++) { - pmCell *cell = chip->cells->data[i];; - - if (!cell->process || !cell->file_exists || !cell->data_exists) continue; - - // select the HDU for this cell - pmHDU *cellHDU = pmHDUFromCell(cell); // HDU of interest - - psF32 BackValue = psMetadataLookupF32(&status, cellHDU->header, "BACK_VAL"); - if (!status) continue; - - psF32 BackError = psMetadataLookupF32(&status, cellHDU->header, "BACK_ERR"); - if (!status) continue; - - if (BackValue == 0.0) continue; - if (BackError == 0.0) continue; - - psVectorAppend (cellBackground, BackValue / BackError); - } - - if (cellBackground->n < 0.375*numCells) { - // Chip is bad, mask the whole thing - ppImageDetrendPatternDeadCellsMask (chip, maskVal); - psFree (cellBackground); - return true; + int numCells = chip->cells->n; // Number of cells + psVector *cellBackground = psVectorAllocEmpty(numCells, PS_DATA_F32); + + for (int i = 0; i < numCells; i++) + { + pmCell *cell = chip->cells->data[i]; + ; + + if (!cell->process || !cell->file_exists || !cell->data_exists) + continue; + + // select the HDU for this cell + pmHDU *cellHDU = pmHDUFromCell(cell); // HDU of interest + + psF32 BackValue = psMetadataLookupF32(&status, cellHDU->header, "BACK_VAL"); + if (!status) + continue; + + psF32 BackError = psMetadataLookupF32(&status, cellHDU->header, "BACK_ERR"); + if (!status) + continue; + + if (BackValue == 0.0) + continue; + if (BackError == 0.0) + continue; + + psVectorAppend(cellBackground, BackValue / BackError); + } + + if (cellBackground->n < 0.375 * numCells) + { + // Chip is bad, mask the whole thing + ppImageDetrendPatternDeadCellsMask(chip, maskVal); + psFree(cellBackground); + return true; } // Second, calculate the median - psVectorSortInPlace (cellBackground); + psVectorSortInPlace(cellBackground); int midPt = cellBackground->n / 2.0; - float median = cellBackground->n % 2 ? cellBackground->data.F32[midPt] : 0.5*(cellBackground->data.F32[midPt] + cellBackground->data.F32[midPt-1]); - psFree (cellBackground); + float median = cellBackground->n % 2 ? cellBackground->data.F32[midPt] : 0.5 * (cellBackground->data.F32[midPt] + cellBackground->data.F32[midPt - 1]); + psFree(cellBackground); // XXX hardwired number - if (median < 3.0) { - // Chip is bad, mask the whole thing - ppImageDetrendPatternDeadCellsMask (chip, maskVal); - } - psFree (cellBackground); + if (median < 3.0) + { + // Chip is bad, mask the whole thing + ppImageDetrendPatternDeadCellsMask(chip, maskVal); + } + psFree(cellBackground); return true; } // to apply the dead cell pattern, we need to transfer the pattern for this chip from the -// pmFPAfile for the pattern to the one for the image being processed. +// pmFPAfile for the pattern to the one for the image being processed. bool ppImageDetrendPatternDeadCellsApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options) { bool status; - if (!options->doPatternDeadCells) return true; + if (!options->doPatternDeadCells) + return true; assert(inputView->chip != -1); @@ -380,20 +432,23 @@ pmHDU *hdu = pmHDUFromChip(chip); - if (psMetadataLookupBool(&status, hdu->header, "PTRN_DED")) { - psLogMsg("ppImage", PS_LOG_INFO, "Not performing dead cell pattern correction as it has already been done."); - return true; - } - - if (!strcmp (chipName, "XY40") || !strcmp (chipName, "XY42")) { - // special case : check for BACK_VAL / BACK_ERR > 3 or < 3 - psLogMsg("ppImage", PS_LOG_INFO, "Using special case for XY40 and XY42"); - ppImageDetrendPatternDeadCellsXY42 (chip, options->blankMask); - return true; + if (psMetadataLookupBool(&status, hdu->header, "PTRN_DED")) + { + psLogMsg("ppImage", PS_LOG_INFO, "Not performing dead cell pattern correction as it has already been done."); + return true; + } + + if (!strcmp(chipName, "XY40") || !strcmp(chipName, "XY42")) + { + // special case : check for BACK_VAL / BACK_ERR > 3 or < 3 + psLogMsg("ppImage", PS_LOG_INFO, "Using special case for XY40 and XY42"); + ppImageDetrendPatternDeadCellsXY42(chip, options->blankMask); + return true; } pmFPAfile *pattern = psMetadataLookupPtr(&status, config->files, "PPIMAGE.PATTERN.DEAD.CELLS"); - if (!pattern) { - psLogMsg("ppImage", PS_LOG_INFO, "Pattern Dead Cells file not found, skipping"); - return true; + if (!pattern) + { + psLogMsg("ppImage", PS_LOG_INFO, "Pattern Dead Cells file not found, skipping"); + return true; } @@ -401,44 +456,49 @@ *view = *inputView; - pmChip *patternChip = pmFPAviewThisChip (view, pattern->fpa); + pmChip *patternChip = pmFPAviewThisChip(view, pattern->fpa); // grab the pattern from the input pattern file chip - psImage *deadCellPattern = (psImage *) psMetadataLookupPtr (&status, patternChip->analysis, "PTN.DEAD.CELL"); - if (!deadCellPattern) { + psImage *deadCellPattern = (psImage *)psMetadataLookupPtr(&status, patternChip->analysis, "PTN.DEAD.CELL"); + if (!deadCellPattern) + { psLogMsg("psModules.detrend", PS_LOG_DETAIL, "No DEAD CELL pattern for chip, skipping\n"); - psFree (view); - return true; + psFree(view); + return true; } // copy the pattern pointer to the chip of the image being processed - psMetadataAddImage (chip->analysis, PS_LIST_TAIL, "PTN.DEAD.CELL", PS_META_REPLACE, "", deadCellPattern); + psMetadataAddImage(chip->analysis, PS_LIST_TAIL, "PTN.DEAD.CELL", PS_META_REPLACE, "", deadCellPattern); // extract the MEDIAN_CELL_BACKGROUND values to check for problems - int numCells = chip->cells->n; // Number of cells - psVector *cellBackground = psVectorAllocEmpty (numCells, PS_DATA_F32); + int numCells = chip->cells->n; // Number of cells + psVector *cellBackground = psVectorAllocEmpty(numCells, PS_DATA_F32); pmCell *cell = NULL; - while ((cell = pmFPAviewNextCell(view, chip->parent, 1)) != NULL) { - if (!cell->process || !cell->file_exists || !cell->data_exists) { - psVectorAppend (cellBackground, NAN); - continue; - } - - // select the HDU for this cell - pmHDU *cellHDU = pmHDUFromCell(cell); // HDU of interest - - psF32 value = psMetadataLookupF32(&status, cellHDU->header, "BACK_VAL"); - if (!status) { - psVectorAppend (cellBackground, NAN); - continue; - } - psVectorAppend (cellBackground, value); + while ((cell = pmFPAviewNextCell(view, chip->parent, 1)) != NULL) + { + if (!cell->process || !cell->file_exists || !cell->data_exists) + { + psVectorAppend(cellBackground, NAN); + continue; + } + + // select the HDU for this cell + pmHDU *cellHDU = pmHDUFromCell(cell); // HDU of interest + + psF32 value = psMetadataLookupF32(&status, cellHDU->header, "BACK_VAL"); + if (!status) + { + psVectorAppend(cellBackground, NAN); + continue; + } + psVectorAppend(cellBackground, value); } // match cellBackground pattern to registered patterns and mask as needed - if (!pmPatternDeadCells(chip, cellBackground, options->blankMask)) { - psFree(cellBackground); - psFree(view); - return false; + if (!pmPatternDeadCells(chip, cellBackground, options->blankMask)) + { + psFree(cellBackground); + psFree(view); + return false; } psFree(cellBackground); @@ -449,5 +509,6 @@ } -static bool doPatternForView (bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipeName, const char *recipeValue) { +bool ppImageDoPatternForView(bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipeName, const char *recipeValue) +{ *doit = false; @@ -456,36 +517,41 @@ doPattern = pmConfigRecipeValueByView(config, recipeName, recipeValue, chip->parent, view); - - if (!doPattern) { + + if (!doPattern) + { psError(PS_ERR_UNKNOWN, false, "Unable to determine whether row pattern matching should be applied."); return false; } - if (doPattern->type == PS_DATA_BOOL) { + if (doPattern->type == PS_DATA_BOOL) + { *doit = doPattern->data.B; return true; } - if (doPattern->type == PS_DATA_STRING) { + if (doPattern->type == PS_DATA_STRING) + { // expect a string of the form "000110001001" with at least view->cell entries char *string = doPattern->data.str; - if (strlen(string) < view->cell) { - psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET chip string (too few elements %d)", (int) strlen(string)); + if (strlen(string) < view->cell) + { + psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET chip string (too few elements %d)", (int)strlen(string)); return false; } - switch (string[view->cell]) { - case '0': - case 'f': - case 'F': - case 'n': - case 'N': + switch (string[view->cell]) + { + case '0': + case 'f': + case 'F': + case 'n': + case 'N': *doit = false; return true; - case '1': - case 't': - case 'T': - case 'y': - case 'Y': + case '1': + case 't': + case 'T': + case 'y': + case 'Y': *doit = true; return true; - default: + default: psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET chip string %s (unknown value %c))", string, string[view->cell]); return false; @@ -497,47 +563,54 @@ } -// thread safety : -bool ppImageDetrendPatternApplyCell (pmConfig *config, pmFPA *fpa, pmChip *chip, pmCell *cell, pmFPAview *view, ppImageOptions *options) { - +// thread safety : +bool ppImageDetrendPatternApplyCell(pmConfig *config, pmFPA *fpa, pmChip *chip, pmCell *cell, pmFPAview *view, ppImageOptions *options) +{ + // process each of the readouts - pmReadout *readout; // Readout from cell - while ((readout = pmFPAviewNextReadout (view, fpa, 1)) != NULL) { - if (!readout->data_exists) { - continue; - } - - // Perform pattern correction - if (!pmPatternRow(readout, options->patternRowOrder, options->patternRowIter, - options->patternRowRej, options->patternRowThresh, options->patternRowMean, - options->patternRowStdev, options->maskValue, options->darkMask)) { - psFree (view); - return false; - } - } - psFree (view); // supplied view must be freeable + pmReadout *readout; // Readout from cell + while ((readout = pmFPAviewNextReadout(view, fpa, 1)) != NULL) + { + if (!readout->data_exists) + { + continue; + } + + // Perform pattern correction + if (!pmPatternRow(readout, options->patternRowOrder, options->patternRowIter, + options->patternRowRej, options->patternRowThresh, options->patternRowMean, + options->patternRowStdev, options->maskValue, options->darkMask)) + { + psFree(view); + return false; + } + } + psFree(view); // supplied view must be freeable return true; } -psVector *ppImageDetrendPatternCellFailures(pmFPAfile *input, const pmFPAview *inputView) { - +psVector *ppImageDetrendPatternCellFailures(pmFPAfile *input, const pmFPAview *inputView) +{ + bool status = false; pmCell *cell = NULL; - + pmFPAview *view = pmFPAviewAlloc(0); // View for local processing *view = *inputView; // extract the MEDIAN_CELL_BACKGROUND values to check for problems - psVector *cellBackground = psVectorAllocEmpty (64, PS_DATA_F32); - while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { - if (!cell->process || !cell->file_exists || !cell->data_exists) { - psVectorAppend (cellBackground, NAN); - continue; - } - - // select the HDU for this cell - pmHDU *hdu = pmHDUFromCell(cell); // HDU of interest - - psF32 value = psMetadataLookupF32(&status, hdu->header, "BACK_VAL"); - psVectorAppend (cellBackground, value); + psVector *cellBackground = psVectorAllocEmpty(64, PS_DATA_F32); + while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) + { + if (!cell->process || !cell->file_exists || !cell->data_exists) + { + psVectorAppend(cellBackground, NAN); + continue; + } + + // select the HDU for this cell + pmHDU *hdu = pmHDUFromCell(cell); // HDU of interest + + psF32 value = psMetadataLookupF32(&status, hdu->header, "BACK_VAL"); + psVectorAppend(cellBackground, value); } return cellBackground; Index: branches/2dbias/ppImage/src/ppImageDetrendReadout.c =================================================================== --- branches/2dbias/ppImage/src/ppImageDetrendReadout.c (revision 42665) +++ branches/2dbias/ppImage/src/ppImageDetrendReadout.c (revision 42679) @@ -5,7 +5,14 @@ #include "ppImage.h" +#define ESCAPE(STATUS, ...) \ + { \ + psError(PS_ERR_UNKNOWN, STATUS, __VA_ARGS__); \ + psFree(view); \ + return false; \ + } + bool ppImageDetrendReadout(pmConfig *config, ppImageOptions *options, pmFPAview *view) { - // psTimerStart("detrend.readout"); + // psTimerStart("detrend.readout"); // construct a view for the detrend images (which have only one readout) @@ -18,22 +25,26 @@ // Check that the gain is set (this is used by both pmReadoutGenerateMask and pmReadoutGenerateVariance) - { - float gain = psMetadataLookupF32(NULL, input->parent->concepts, "CELL.GAIN"); // Gain for cell - if (!isfinite(gain)) { - psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, RECIPE_NAME); // Recipe - psAssert(recipe, "Should be there!"); - bool override = psMetadataLookupBool(NULL, recipe, "GAIN.OVERRIDE"); // Override the bad gain? - if (override) { - psWarning("CELL.GAIN is not set for readout (%d,%d,%d) --- setting to unity.", view->chip, view->cell, view->readout); - psMetadataItem *item = psMetadataLookup(input->parent->concepts, "CELL.GAIN"); // Gain item - psAssert(item, "Should be there!"); - item->data.F32 = 1.0; - - // for unity gain, there is no modification for the readnoise, note that it has (effectively) been updated - psMetadataRemoveKey(input->parent->concepts, "CELL.READNOISE.UPDATE"); - } else { - psWarning("CELL.GAIN is NAN for readout (%d,%d,%d), image will be masked.", view->chip, view->cell, view->readout); - } - } + { + float gain = psMetadataLookupF32(NULL, input->parent->concepts, "CELL.GAIN"); // Gain for cell + if (!isfinite(gain)) + { + psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, RECIPE_NAME); // Recipe + psAssert(recipe, "Should be there!"); + bool override = psMetadataLookupBool(NULL, recipe, "GAIN.OVERRIDE"); // Override the bad gain? + if (override) + { + psWarning("CELL.GAIN is not set for readout (%d,%d,%d) --- setting to unity.", view->chip, view->cell, view->readout); + psMetadataItem *item = psMetadataLookup(input->parent->concepts, "CELL.GAIN"); // Gain item + psAssert(item, "Should be there!"); + item->data.F32 = 1.0; + + // for unity gain, there is no modification for the readnoise, note that it has (effectively) been updated + psMetadataRemoveKey(input->parent->concepts, "CELL.READNOISE.UPDATE"); + } + else + { + psWarning("CELL.GAIN is NAN for readout (%d,%d,%d), image will be masked.", view->chip, view->cell, view->readout); + } + } } // psLogMsg ("ppImage", 6, "check gain: %f sec\n", psTimerMark ("detrend.readout")); @@ -43,22 +54,29 @@ bool hasVideo = false; { - // XXX test for GPC1? or CAN_HAVE_VIDEO in camera config? - bool status = false; - if (!input) goto done_video_check; - if (!input->parent) goto done_video_check; - if (!input->parent->parent) goto done_video_check; - if (!input->parent->parent->hdu) goto done_video_check; - if (!input->parent->parent->hdu->header) goto done_video_check; - char *ptr = psMetadataLookupStr(&status,input->parent->parent->hdu->header,"CELLMODE"); - if (status) { - psLogMsg ("ppImage.detrend", PS_LOG_DETAIL, "VIDEO: %d %d %d\n",(int) options->hasVideo,(int) options->useVideoDark, (int) options->useVideoMask); - char *Vptr = strchr(ptr,'V'); - if (Vptr) { - hasVideo = options->hasVideo = true; - psLogMsg ("ppImage.detrend", PS_LOG_INFO, "VIDEO: %d %d %d\n",(int) options->hasVideo,(int) options->useVideoDark, (int) options->useVideoMask); - } - } - } - done_video_check: + // XXX test for GPC1? or CAN_HAVE_VIDEO in camera config? + bool status = false; + if (!input) + goto done_video_check; + if (!input->parent) + goto done_video_check; + if (!input->parent->parent) + goto done_video_check; + if (!input->parent->parent->hdu) + goto done_video_check; + if (!input->parent->parent->hdu->header) + goto done_video_check; + char *ptr = psMetadataLookupStr(&status, input->parent->parent->hdu->header, "CELLMODE"); + if (status) + { + psLogMsg("ppImage.detrend", PS_LOG_DETAIL, "VIDEO: %d %d %d\n", (int)options->hasVideo, (int)options->useVideoDark, (int)options->useVideoMask); + char *Vptr = strchr(ptr, 'V'); + if (Vptr) + { + hasVideo = options->hasVideo = true; + psLogMsg("ppImage.detrend", PS_LOG_INFO, "VIDEO: %d %d %d\n", (int)options->hasVideo, (int)options->useVideoDark, (int)options->useVideoMask); + } + } + } +done_video_check: // psLogMsg ("ppImage", 6, "check video: %f sec\n", psTimerMark ("detrend.readout")); @@ -74,25 +92,30 @@ // Masking on the basis of pixel value needs to be done before anything else, so the values are pristine. - if (options->doMaskBuild) { + if (options->doMaskBuild) + { psImageMaskType satMask = options->doMaskSat ? options->satMask : 0; psImageMaskType lowMask = options->doMaskLow ? options->lowMask : 0; - if (!pmReadoutGenerateMask(input, satMask, lowMask)) { - psError(PS_ERR_UNKNOWN, false, "Unable to generate a mask."); - psFree(detview); - return false; - } - // psLogMsg ("ppImage", 6, "generate mask: %f sec\n", psTimerMark ("detrend.readout")); + if (!pmReadoutGenerateMask(input, satMask, lowMask)) + { + psError(PS_ERR_UNKNOWN, false, "Unable to generate a mask."); + psFree(detview); + return false; + } + // psLogMsg ("ppImage", 6, "generate mask: %f sec\n", psTimerMark ("detrend.readout")); } // apply the externally supplied mask to the input->mask pixels - if (options->doMask) { - pmReadout *mask; - if ((options->useVideoMask)&&(hasVideo)) { - mask = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.VIDEOMASK"); - } - else { - mask = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.MASK"); - } - pmMaskBadPixels(input, mask, options->maskValue); - // psLogMsg ("ppImage", 6, "apply mask: %f sec\n", psTimerMark ("detrend.readout")); + if (options->doMask) + { + pmReadout *mask; + if ((options->useVideoMask) && (hasVideo)) + { + mask = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.VIDEOMASK"); + } + else + { + mask = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.MASK"); + } + pmMaskBadPixels(input, mask, options->maskValue); + // psLogMsg ("ppImage", 6, "apply mask: %f sec\n", psTimerMark ("detrend.readout")); } @@ -101,116 +124,150 @@ // extern bool ppImageBurntoolApply(pmConfig *, ppImageOptions *, pmFPAview *, pmReadout *); ppImageBurntoolApply(config, options, view, input); - // psLogMsg ("ppImage", 6, "apply burntool: %f sec\n", psTimerMark ("detrend.readout")); - } - - if (options->doMaskBurntool) { - if (options->doApplyBurntool) { + // psLogMsg ("ppImage", 6, "apply burntool: %f sec\n", psTimerMark ("detrend.readout")); + } + + if (options->doMaskBurntool) + { + if (options->doApplyBurntool) + { // build burntool mask from data input burntool table - ppImageBurntoolMaskFromTable(config,options,view,input); - } else { + ppImageBurntoolMaskFromTable(config, options, view, input); + } + else + { // build burntool mask from data in the input image's fits extension - ppImageBurntoolMask(config,options,view,input); - } - // psLogMsg ("ppImage", 6, "apply burntool mask: %f sec\n", psTimerMark ("detrend.readout")); + ppImageBurntoolMask(config, options, view, input); + } + // psLogMsg ("ppImage", 6, "apply burntool mask: %f sec\n", psTimerMark ("detrend.readout")); } // Subtract the overscan - if (options->doOverscan) { - if (!pmOverscanSubtract (input, options->overscan)) { - psError(PS_ERR_UNKNOWN, false, "Unable to subtract overscan."); - psFree(detview); - return false; - } - // psLogMsg ("ppImage", 6, "subtract overscan: %f sec\n", psTimerMark ("detrend.readout")); + if (options->doOverscan) + { + bool doTwoDOverscan = false; + if (options->overscan->TwoD) + { + pmChip *chip = pmFPAfileThisChip(config->files, view, "PPIMAGE.INPUT"); + if (!ppImageDoPatternForView(&doTwoDOverscan, config, chip, view, RECIPE_NAME, "OVERSCAN.2D.SUBSET")) + { + ESCAPE(false, "Unable to determine whether 2D Overscan subtraction should be applied."); + } + } + if (!pmOverscanSubtract(input, options->overscan, doTwoDOverscan)) + { + psError(PS_ERR_UNKNOWN, false, "Unable to subtract overscan."); + psFree(detview); + return false; + } + // psLogMsg ("ppImage", 6, "subtract overscan: %f sec\n", psTimerMark ("detrend.readout")); } // measure the overscan-subtracted readoutBackground here (or subtract the overscan value?) // XXX this is the measurements and should be independent of the pattern masking - if (options->doPatternDeadCells) { - psStats *stats = psStatsAlloc (PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_STDEV); - psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS); - psImageBackground (stats, NULL, input->image, NULL, 0xffff, rng); - - // save this value somewhere - pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest - psMetadataAddF32(hdu->header, PS_LIST_TAIL, "BACK_VAL", PS_META_REPLACE, "Median cell background", stats->robustMedian); - psMetadataAddF32(hdu->header, PS_LIST_TAIL, "BACK_ERR", PS_META_REPLACE, "Stdev of cell background", stats->robustStdev); - psFree (stats); - psFree (rng); + if (options->doPatternDeadCells) + { + psStats *stats = psStatsAlloc(PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_STDEV); + psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS); + psImageBackground(stats, NULL, input->image, NULL, 0xffff, rng); + + // save this value somewhere + pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest + psMetadataAddF32(hdu->header, PS_LIST_TAIL, "BACK_VAL", PS_META_REPLACE, "Median cell background", stats->robustMedian); + psMetadataAddF32(hdu->header, PS_LIST_TAIL, "BACK_ERR", PS_META_REPLACE, "Stdev of cell background", stats->robustStdev); + psFree(stats); + psFree(rng); } // Non-linearity correction - if (options->doNonLin) { - if (!ppImageDetrendNonLinear(input,detview,config)) { - psError(PS_ERR_UNKNOWN, false, "Unable to correct NonLinearity"); - psFree(detview); - return(false); - } - // psLogMsg ("ppImage", 6, "nonlinear correction: %f sec\n", psTimerMark ("detrend.readout")); + if (options->doNonLin) + { + if (!ppImageDetrendNonLinear(input, detview, config)) + { + psError(PS_ERR_UNKNOWN, false, "Unable to correct NonLinearity"); + psFree(detview); + return (false); + } + // psLogMsg ("ppImage", 6, "nonlinear correction: %f sec\n", psTimerMark ("detrend.readout")); } // New Non-linearity correction (exclusive of the above) - if (options->doNewNonLin) { - if (!ppImageDetrendNewNonLinear(input, detview, config)) { - psError(PS_ERR_UNKNOWN, false, "Unable to correct Non-Linearity with new version (2023)"); - psFree(detview); - return(false); - } - // psLogMsg ("ppImage", 6, "nonlinear correction: %f sec\n", psTimerMark ("detrend.readout")); + if (options->doNewNonLin) + { + if (!ppImageDetrendNewNonLinear(input, detview, config)) + { + psError(PS_ERR_UNKNOWN, false, "Unable to correct Non-Linearity with new version (2023)"); + psFree(detview); + return (false); + } + // psLogMsg ("ppImage", 6, "nonlinear correction: %f sec\n", psTimerMark ("detrend.readout")); } // set up the dark and bias - pmCell *dark = NULL; // Multi-dark - pmReadout *oldDark = NULL; // Old-fashioned dark - pmReadout *bias = NULL; - if (options->doBias) { + pmCell *dark = NULL; // Multi-dark + pmReadout *oldDark = NULL; // Old-fashioned dark + pmReadout *bias = NULL; + if (options->doBias) + { bias = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.BIAS"); } - if (options->doDark) { - bool mdok; // Status of MD lookup - psMetadata *recipe = psMetadataLookupPtr (&mdok, config->recipes, RECIPE_NAME); + if (options->doDark) + { + bool mdok; // Status of MD lookup + psMetadata *recipe = psMetadataLookupPtr(&mdok, config->recipes, RECIPE_NAME); assert(mdok && recipe); - if ((options->useVideoDark)&&(hasVideo)) { - if (psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { - oldDark = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.VIDEODARK"); - } else { - dark = pmFPAfileThisCell(config->files, detview, "PPIMAGE.VIDEODARK"); - } - } - else { - if (psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { - oldDark = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.DARK"); - } else { - dark = pmFPAfileThisCell(config->files, detview, "PPIMAGE.DARK"); - } - } + if ((options->useVideoDark) && (hasVideo)) + { + if (psMetadataLookupBool(&mdok, recipe, "OLDDARK")) + { + oldDark = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.VIDEODARK"); + } + else + { + dark = pmFPAfileThisCell(config->files, detview, "PPIMAGE.VIDEODARK"); + } + } + else + { + if (psMetadataLookupBool(&mdok, recipe, "OLDDARK")) + { + oldDark = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.DARK"); + } + else + { + dark = pmFPAfileThisCell(config->files, detview, "PPIMAGE.DARK"); + } + } } // Bias and temperature-independent-dark subtraction are merged. - if (options->doBias) { - if (!pmBiasSubtract(input, bias, oldDark, view)) { + if (options->doBias) + { + if (!pmBiasSubtract(input, bias, oldDark, view)) + { psError(PS_ERR_UNKNOWN, false, "Unable to subtract bias."); psFree(detview); return false; } - // psLogMsg ("ppImage", 6, "apply bias: %f sec\n", psTimerMark ("detrend.readout")); - } - + // psLogMsg ("ppImage", 6, "apply bias: %f sec\n", psTimerMark ("detrend.readout")); + } + // Weight on the basis of pixel value needs to be done after the overscan has been subtracted - if (options->doVarianceBuild) { + if (options->doVarianceBuild) + { // create the target mask and variance images psImage *noiseImage = NULL; - if (options->doNoiseMap) { + if (options->doNoiseMap) + { // XXX convert the noiseMap image to a binned image pmReadout *noiseMap = NULL; noiseMap = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.NOISEMAP"); - noiseImage = psImageCopy (NULL, input->image, PS_TYPE_F32); - psImageInit (noiseImage, 0.0); + noiseImage = psImageCopy(NULL, input->image, PS_TYPE_F32); + psImageInit(noiseImage, 0.0); // XXX this works, but is not really quite right: the model shoud include the // offset information, we are not really getting exactly the right mapping from the // original file. - // CZW 2012-03-21: I do not believe this is true anymore. In any case, this seems to be what - // ppImageReplaceBackground does to do sky subtraction. + // CZW 2012-03-21: I do not believe this is true anymore. In any case, this seems to be what + // ppImageReplaceBackground does to do sky subtraction. psImageBinning *binning = psImageBinningAlloc(); binning->nXruff = noiseMap->image->numCols; @@ -220,72 +277,82 @@ psImageBinningSetScale(binning, PS_IMAGE_BINNING_LEFT); - psImageUnbin (noiseImage, noiseMap->image, binning); - psFree (binning); - } - - if (!pmReadoutGenerateVariance(input, noiseImage, true)) { - psError(PS_ERR_UNKNOWN, false, "Unable to generate a variance image."); - psFree(detview); - return false; - } - psFree (noiseImage); - // psLogMsg ("ppImage", 6, "generate variance: %f sec\n", psTimerMark ("detrend.readout")); - } - - if (options->doDark && dark) { - if (!pmDarkApply(input, dark, options->darkMask)) { + psImageUnbin(noiseImage, noiseMap->image, binning); + psFree(binning); + } + + if (!pmReadoutGenerateVariance(input, noiseImage, true)) + { + psError(PS_ERR_UNKNOWN, false, "Unable to generate a variance image."); + psFree(detview); + return false; + } + psFree(noiseImage); + // psLogMsg ("ppImage", 6, "generate variance: %f sec\n", psTimerMark ("detrend.readout")); + } + + if (options->doDark && dark) + { + if (!pmDarkApply(input, dark, options->darkMask)) + { psError(PS_ERR_UNKNOWN, false, "Unable to subtract dark."); psFree(detview); return false; } - // psLogMsg ("ppImage", 6, "apply dark: %f sec\n", psTimerMark ("detrend.readout")); - } - - if (options->doRemnance) { + // psLogMsg ("ppImage", 6, "apply dark: %f sec\n", psTimerMark ("detrend.readout")); + } + + if (options->doRemnance) + { if (!pmRemnance(input, options->maskValue, options->lowMask, - options->remnanceSize, options->remnanceThresh)) { + options->remnanceSize, options->remnanceThresh)) + { psError(PS_ERR_UNKNOWN, false, "Unable to mask remnance."); psFree(detview); return false; } - // psLogMsg ("ppImage", 6, "mask remnance: %f sec\n", psTimerMark ("detrend.readout")); + // psLogMsg ("ppImage", 6, "mask remnance: %f sec\n", psTimerMark ("detrend.readout")); } // Shutter correction - if (options->doShutter) { + if (options->doShutter) + { pmReadout *shutter = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.SHUTTER"); - if (!pmShutterCorrectionApply(input, shutter, pmConfigMaskGet("FLAT", config))) { - psFree(detview); - return false; - } - // psLogMsg ("ppImage", 6, "shutter correction: %f sec\n", psTimerMark ("detrend.readout")); + if (!pmShutterCorrectionApply(input, shutter, pmConfigMaskGet("FLAT", config))) + { + psFree(detview); + return false; + } + // psLogMsg ("ppImage", 6, "shutter correction: %f sec\n", psTimerMark ("detrend.readout")); } // Flat-field correction (no options used?) - if (options->doFlat) { + if (options->doFlat) + { pmReadout *flat = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.FLAT"); - if (!pmFlatField(input, flat, options->flatMask)) { - psFree(detview); - return false; - } - // psLogMsg ("ppImage", 6, "apply flat: %f sec\n", psTimerMark ("detrend.readout")); - } - -/* // Pattern noise correction */ -/* if (options->doPattern) { */ -/* if (!pmPatternRow(input, options->patternOrder, options->patternIter, options->patternRej, */ -/* options->patternThresh, options->patternMean, options->patternStdev, */ -/* options->maskValue, options->darkMask)) { */ -/* psFree(detview); */ -/* return false; */ -/* } */ -/* } */ + if (!pmFlatField(input, flat, options->flatMask)) + { + psFree(detview); + return false; + } + // psLogMsg ("ppImage", 6, "apply flat: %f sec\n", psTimerMark ("detrend.readout")); + } + + /* // Pattern noise correction */ + /* if (options->doPattern) { */ + /* if (!pmPatternRow(input, options->patternOrder, options->patternIter, options->patternRej, */ + /* options->patternThresh, options->patternMean, options->patternStdev, */ + /* options->maskValue, options->darkMask)) { */ + /* psFree(detview); */ + /* return false; */ + /* } */ + /* } */ // Normalization by a single (known) constant - bool mdok; // Status of MD lookup + bool mdok; // Status of MD lookup float norm = psMetadataLookupF32(&mdok, config->arguments, "NORMALIZATION"); - if (mdok && isfinite(norm) && norm != 1.0) { + if (mdok && isfinite(norm) && norm != 1.0) + { pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest - psString comment = NULL; // Comment to add + psString comment = NULL; // Comment to add psStringAppend(&comment, "Normalization: %f", norm); psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, comment, ""); @@ -293,16 +360,18 @@ psBinaryOp(input->image, input->image, "*", psScalarAlloc(norm, PS_TYPE_F32)); - // psLogMsg ("ppImage", 6, "renormalize: %f sec\n", psTimerMark ("detrend.readout")); - } - -# if (1) + // psLogMsg ("ppImage", 6, "renormalize: %f sec\n", psTimerMark ("detrend.readout")); + } + +#if (1) // Normalization by per-class values psMetadata *normlist = psMetadataLookupMetadata(&mdok, config->arguments, "NORMALIZATION.TABLE"); - if (normlist) { + if (normlist) + { pmFPAfile *inputFile = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.INPUT"); // get the menu of class IDs psMetadata *menu = psMetadataLookupMetadata(&mdok, inputFile->camera, "CLASSID"); - if (!menu) { + if (!menu) + { psError(PS_ERR_IO, false, "Unable to find CLASSID metadata in camera configuration"); psFree(detview); @@ -311,5 +380,6 @@ // get the rule for class_id for the desired class const char *rule = psMetadataLookupStr(&mdok, menu, options->normClass); - if (!rule) { + if (!rule) + { psError(PS_ERR_IO, false, "Unable to find NORM.CLASS value %s in CLASSID in camera configuration", options->normClass); psFree(detview); @@ -318,5 +388,6 @@ // get the class_id from the rule char *classID = pmFPAfileNameFromRule(rule, inputFile, view); - if (!classID) { + if (!classID) + { psError(PS_ERR_IO, false, "error converting CLASSID rule %s to name\n", rule); psFree(detview); @@ -325,6 +396,7 @@ // get normalization from the class_id - float norm = psMetadataLookupF32 (&mdok, normlist, classID); - if (!mdok) { + float norm = psMetadataLookupF32(&mdok, normlist, classID); + if (!mdok) + { psError(PS_ERR_IO, false, "failed to find class ID %s in normalization table\n", classID); psFree(detview); @@ -333,5 +405,5 @@ pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest - psString comment = NULL; // Comment to add + psString comment = NULL; // Comment to add psStringAppend(&comment, "Normalization: %f", norm); psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, comment, ""); @@ -341,17 +413,19 @@ psBinaryOp(input->image, input->image, "*", psScalarAlloc(norm, PS_TYPE_F32)); - psFree (classID); - - // psLogMsg ("ppImage", 6, "renormalize by class: %f sec\n", psTimerMark ("detrend.readout")); - } -# endif - - if (options->doFringe) { + psFree(classID); + + // psLogMsg ("ppImage", 6, "renormalize by class: %f sec\n", psTimerMark ("detrend.readout")); + } +#endif + + if (options->doFringe) + { pmCell *fringe = pmFPAfileThisCell(config->files, detview, "PPIMAGE.FRINGE"); - if (!ppImageDetrendFringeMeasure(input, fringe, false, options)) { - psFree(detview); - return false; - } - // psLogMsg ("ppImage", 6, "measure fringe: %f sec\n", psTimerMark ("detrend.readout")); + if (!ppImageDetrendFringeMeasure(input, fringe, false, options)) + { + psFree(detview); + return false; + } + // psLogMsg ("ppImage", 6, "measure fringe: %f sec\n", psTimerMark ("detrend.readout")); }