Index: /trunk/ppImage/src/ppImage.h =================================================================== --- /trunk/ppImage/src/ppImage.h (revision 26894) +++ /trunk/ppImage/src/ppImage.h (revision 26895) @@ -38,5 +38,6 @@ bool doShutter; // Shutter correction bool doFlat; // Flat-field normalisation - bool doPattern; // Pattern noise subtraction + bool doPatternRow; // Row pattern correction + bool doPatternCell; // Cell pattern correction bool doFringe; // Fringe subtraction bool doPhotom; // Source identification and photometry @@ -95,11 +96,13 @@ float fringeKeep; // Fringe keep fraction - // Pattern noise subtraction - int patternOrder; // Polynomial order - int patternIter; // Clipping iterations - float patternRej; // Clipping threshold - float patternThresh; // Ignore threshold - psStatsOptions patternMean; // Statistic for mean - psStatsOptions patternStdev; // Statistic for stdev + // Pattern correction + int patternRowOrder; // Polynomial order + int patternRowIter; // Clipping iterations + float patternRowRej; // Clipping threshold + float patternRowThresh; // Ignore threshold + psStatsOptions patternRowMean; // Statistic for mean + psStatsOptions patternRowStdev; // Statistic for stdev + psStatsOptions patternCellBG; // statistic for background + psStatsOptions patternCellMean; // Statistic for mean int remnanceSize; // Size for remnance detection Index: /trunk/ppImage/src/ppImageBurntoolMask.c =================================================================== --- /trunk/ppImage/src/ppImageBurntoolMask.c (revision 26894) +++ /trunk/ppImage/src/ppImageBurntoolMask.c (revision 26895) @@ -3,5 +3,5 @@ #endif -/* #define PPIMAGE_BURNTOOL_DEBUG 1 */ +#define PPIMAGE_BURNTOOL_DEBUG 0 #include "ppImage.h" @@ -23,5 +23,5 @@ return(false); } - long Nrows = psFitsTableSize(fits); + long Nrows = psFitsTableSize(fits); long row = 0; @@ -33,8 +33,8 @@ psImage *image = mask->mask; - + /* Set the maskValue from the recipes. */ psImageMaskType maskValue = options->burntoolMask; -#ifdef PPIMAGE_BURNTOOL_DEBUG +#if PPIMAGE_BURNTOOL_DEBUG psLogMsg("ppImageBurntoolMask", 4, "Status: %ld %d\n",Nrows,maskValue); #endif @@ -47,44 +47,44 @@ if (psMetadataLookupS32(&status,rowMD,"cell") == burntool_cell) { - if (((options->burntoolTrails & 0x01)&&(psMetadataLookupS32(&status,rowMD,"nfit") == 0))|| - ((options->burntoolTrails & 0x02)&&(psMetadataLookupS32(&status,rowMD,"up") == 1))|| - ((options->burntoolTrails & 0x04)&&(psMetadataLookupS32(&status,rowMD,"up") == 0))) { - /* If the fit fails, burntool reports zero here. This - signifies that it expected to see a trail (else why - fit) but did not find it when it attempted to - correct. */ -#ifdef PPIMAGE_BURNTOOL_DEBUG - psLogMsg ("ppImageBurntoolMask", 4, "Masking! %d (%d %d %d) %d %d", - psMetadataLookupS32(&status,rowMD,"cell"), - ((options->burntoolTrails & 0x0001)&&(psMetadataLookupS32(&status,rowMD,"nfit") == 0)), - ((options->burntoolTrails & 0x02)&&(psMetadataLookupS32(&status,rowMD,"up") == 1)), - ((options->burntoolTrails & 0x04)&&(psMetadataLookupS32(&status,rowMD,"up") == 0)), - options->burntoolTrails, - maskValue - ); + if (((options->burntoolTrails & 0x01)&&(psMetadataLookupS32(&status,rowMD,"func") == 4))|| + (((options->burntoolTrails & 0x02)&&(psMetadataLookupS32(&status,rowMD,"up") == 1))|| + ((options->burntoolTrails & 0x04)&&(psMetadataLookupS32(&status,rowMD,"up") == 0)))) { + /* If the fit fails, burntool reports zero here. This + signifies that it expected to see a trail (else why + fit) but did not find it when it attempted to + correct. */ +#if PPIMAGE_BURNTOOL_DEBUG + psLogMsg ("ppImageBurntoolMask", 4, "Masking! %d (%d %d %d) %d %d", + psMetadataLookupS32(&status,rowMD,"cell"), + ((options->burntoolTrails & 0x0001)&&(psMetadataLookupS32(&status,rowMD,"nfit") == 0)), + ((options->burntoolTrails & 0x02)&&(psMetadataLookupS32(&status,rowMD,"up") == 1)), + ((options->burntoolTrails & 0x04)&&(psMetadataLookupS32(&status,rowMD,"up") == 0)), + options->burntoolTrails, + maskValue + ); #endif - for (int i = psMetadataLookupS32(&status,rowMD,"sxfit"); - i <= psMetadataLookupS32(&status,rowMD,"exfit"); - i++) { + for (int i = psMetadataLookupS32(&status,rowMD,"sxfit"); + i <= psMetadataLookupS32(&status,rowMD,"exfit"); + i++) { - if (psMetadataLookupS32(&status,rowMD,"up") == 0) { - for (int j = 0; j <= psMetadataLookupS32(&status,rowMD,"y1p"); j++) { -/* #ifdef PPIMAGE_BURNTOOL_DEBUG */ -/* psLogMsg("ppImageBurntoolMask", 4, "Noisy!: %d %d %d %d\n", */ -/* i,j,image->data.PS_TYPE_IMAGE_MASK_DATA[j][i],maskValue); */ -/* #endif */ - image->data.PS_TYPE_IMAGE_MASK_DATA[j][i] |= maskValue; - } - } - else { - for (int j = psMetadataLookupS32(&status,rowMD,"y1m"); j < image->numRows ; j++) { -/* #ifdef PPIMAGE_BURNTOOL_DEBUG */ -/* psLogMsg("ppImageBurntoolMask", 4, "Noisy!: %d %d %d %d\n", */ -/* i,j,image->data.PS_TYPE_IMAGE_MASK_DATA[j][i],maskValue); */ -/* #endif */ - image->data.PS_TYPE_IMAGE_MASK_DATA[j][i] |= maskValue; - } - } - } + if (psMetadataLookupS32(&status,rowMD,"up") == 0) { + for (int j = 0; j <= psMetadataLookupS32(&status,rowMD,"y1p"); j++) { +#if PPIMAGE_BURNTOOL_DEBUG + psLogMsg("ppImageBurntoolMask", 4, "Noisy!: %d %d %d %d\n", + i,j,image->data.PS_TYPE_IMAGE_MASK_DATA[j][i],maskValue); +#endif + image->data.PS_TYPE_IMAGE_MASK_DATA[j][i] |= maskValue; + } + } + else { + for (int j = psMetadataLookupS32(&status,rowMD,"y1m"); j < image->numRows ; j++) { +#if PPIMAGE_BURNTOOL_DEBUG + psLogMsg("ppImageBurntoolMask", 4, "Noisy!: %d %d %d %d\n", + i,j,image->data.PS_TYPE_IMAGE_MASK_DATA[j][i],maskValue); +#endif + image->data.PS_TYPE_IMAGE_MASK_DATA[j][i] |= maskValue; + } + } + } } @@ -95,6 +95,2 @@ return(status); } - - - - Index: /trunk/ppImage/src/ppImageDetrendFringe.c =================================================================== --- /trunk/ppImage/src/ppImageDetrendFringe.c (revision 26894) +++ /trunk/ppImage/src/ppImageDetrendFringe.c (revision 26895) @@ -14,6 +14,6 @@ psArray *references = psMemIncrRefCounter(psMetadataLookupPtr(NULL, fringe->analysis, "FRINGE.MEASUREMENTS")); if (!references) { - psError(PS_ERR_IO, false, "Unable to find fringe references.\n"); - return false; + psError(PS_ERR_IO, false, "Unable to find fringe references.\n"); + return false; } @@ -40,7 +40,7 @@ char *scienceFringes = NULL; if (isResidual) { - scienceFringes = psStringCopy ("FRINGE.RESIDUALS"); + scienceFringes = psStringCopy ("FRINGE.RESIDUALS"); } else { - scienceFringes = psStringCopy ("FRINGE.MEASUREMENTS"); + scienceFringes = psStringCopy ("FRINGE.MEASUREMENTS"); } @@ -85,5 +85,5 @@ psArray *fringes = psArrayAlloc(cells->n); // Fringes, to return int video_cell_zero = 0; - + for (int i = 0; i < cells->n; i++) { fringes->data[i] = NULL; @@ -91,29 +91,29 @@ pmCell *cell = cells->data[i]; // Cell of interest - psTrace("psModules.detrend",7,"Readouts: Cell %d chip: %ld\n",i,cell->readouts->n); - // XXX for now, skip the video cells (cell->readouts->n > 1) - // CZW: This mess creates a fake set of fringe stats by stealing the previous one. - // We let the fitting code know that this is all lies by scaling the weights by a crazy amount. - - if ( (cell->readouts->n > 1) ) { - psTrace("psModules.detrend",7,"Should be skipping scichip: %d\n",i); - psWarning ("Skipping Video Cell (%d) for ppImageDetrendFringe.c:getFringes", i); - - if (i == 0) { - video_cell_zero = 1; - } - else { - pmFringeStats *prevFringe = fringes->data[i-1]; - pmFringeStats *fringe = pmFringeStatsAlloc(prevFringe->regions); - for (int j = 0; j < fringe->regions->nRequested; j++) { - fringe->f->data.F32[j] = prevFringe->f->data.F32[j]; - fringe->df->data.F32[j] = prevFringe->df->data.F32[j] / 1e6; - } - fringes->data[i] = fringe; - } - - continue; - } - + psTrace("psModules.detrend",7,"Readouts: Cell %d chip: %ld\n",i,cell->readouts->n); + // XXX for now, skip the video cells (cell->readouts->n > 1) + // CZW: This mess creates a fake set of fringe stats by stealing the previous one. + // We let the fitting code know that this is all lies by scaling the weights by a crazy amount. + + if ( (cell->readouts->n > 1) ) { + psTrace("psModules.detrend",7,"Should be skipping scichip: %d\n",i); + psWarning ("Skipping Video Cell (%d) for ppImageDetrendFringe.c:getFringes", i); + + if (i == 0) { + video_cell_zero = 1; + } + else { + pmFringeStats *prevFringe = fringes->data[i-1]; + pmFringeStats *fringe = pmFringeStatsAlloc(prevFringe->regions); + for (int j = 0; j < fringe->regions->nRequested; j++) { + fringe->f->data.F32[j] = prevFringe->f->data.F32[j]; + fringe->df->data.F32[j] = prevFringe->df->data.F32[j] / 1e6; + } + fringes->data[i] = fringe; + } + + continue; + } + fringes->data[i] = psMemIncrRefCounter(psMetadataLookupPtr(NULL, cell->analysis, source)); } @@ -123,10 +123,10 @@ pmFringeStats *fringe = pmFringeStatsAlloc(prevFringe->regions); for (int j = 0; j < fringe->regions->nRequested; j++) { - fringe->f->data.F32[j] = NAN; - fringe->df->data.F32[j] = 1.0; + fringe->f->data.F32[j] = NAN; + fringe->df->data.F32[j] = 1.0; } fringes->data[0] = fringe; } - + return fringes; } @@ -143,7 +143,7 @@ psArray *science = NULL; if (isResidual) { - science = getFringes(scienceChip, "FRINGE.RESIDUALS"); // Fringe residuals on science chip + science = getFringes(scienceChip, "FRINGE.RESIDUALS"); // Fringe residuals on science chip } else { - science = getFringes(scienceChip, "FRINGE.MEASUREMENTS"); // Fringe measurements on science chip + science = getFringes(scienceChip, "FRINGE.MEASUREMENTS"); // Fringe measurements on science chip } @@ -160,8 +160,8 @@ for (int j = 0; j < references->n; j++) { // Iterate over cells psArray *ref = references->data[j]; // Array of references for this cell - + refs->data[j] = psMemIncrRefCounter(ref->data[i]); } - referencesCat->data[i] = pmFringeStatsConcatenate(refs, NULL, NULL); + referencesCat->data[i] = pmFringeStatsConcatenate(refs, NULL, NULL); psFree(refs); } @@ -174,7 +174,7 @@ if (isResidual) { - psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.RESIDUAL.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); + psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.RESIDUAL.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); } else { - psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); + psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); } @@ -184,22 +184,22 @@ pmHDU *hdu = pmHDUFromCell(science);// HDU of interest for (int i = 0; i < solution->nFringeFrames; i++) { - // write metadata header value - psString keyword = NULL; - if (isResidual) { - psStringAppend (&keyword, "FRES_%02dV", i); - } else { - psStringAppend (&keyword, "FRNG_%02dV", i); - } - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); - psFree (keyword); - - keyword = NULL; - if (isResidual) { - psStringAppend (&keyword, "FRES_%02dE", i); - } else { - psStringAppend (&keyword, "FRNG_%02dE", i); - } - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); - psFree (keyword); + // write metadata header value + psString keyword = NULL; + if (isResidual) { + psStringAppend (&keyword, "FRES_%02dV", i); + } else { + psStringAppend (&keyword, "FRNG_%02dV", i); + } + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); + psFree (keyword); + + keyword = NULL; + if (isResidual) { + psStringAppend (&keyword, "FRES_%02dE", i); + } else { + psStringAppend (&keyword, "FRNG_%02dE", i); + } + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); + psFree (keyword); } # endif @@ -265,15 +265,15 @@ # if (0) - // write metadata header value - // XXX this is measured per cell, but we only have headers per chip - psString keyword = NULL; - psStringAppend (&keyword, "FRNG_%02dV", i); - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); - psFree (keyword); - - keyword = NULL; - psStringAppend (&keyword, "FRNG_%02dE", i); - psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); - psFree (keyword); + // write metadata header value + // XXX this is measured per cell, but we only have headers per chip + psString keyword = NULL; + psStringAppend (&keyword, "FRNG_%02dV", i); + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); + psFree (keyword); + + keyword = NULL; + psStringAppend (&keyword, "FRNG_%02dE", i); + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); + psFree (keyword); # endif @@ -291,13 +291,13 @@ } - // subtract fringe and update mask if fringe value is NAN - for (int iy = 0; iy < readout->image->numRows; iy++) { - for (int ix = 0; ix < readout->image->numCols; ix++) { - readout->image->data.F32[iy][ix] -= sumFringe->data.F32[iy][ix]; - if (!isfinite(sumFringe->data.F32[iy][ix]) && readout->mask) { - readout->mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= maskVal; - } - } - } + // subtract fringe and update mask if fringe value is NAN + for (int iy = 0; iy < readout->image->numRows; iy++) { + for (int ix = 0; ix < readout->image->numCols; ix++) { + readout->image->data.F32[iy][ix] -= sumFringe->data.F32[iy][ix]; + if (!isfinite(sumFringe->data.F32[iy][ix]) && readout->mask) { + readout->mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= maskVal; + } + } + } // XXX: Make generic, so subregions may be subtracted as well @@ -307,6 +307,6 @@ // } - // measure residual fringe amplitude. results go to FRINGE.RESIDUALS - ppImageDetrendFringeMeasure (readout, fringes, true, options); + // measure residual fringe amplitude. results go to FRINGE.RESIDUALS + ppImageDetrendFringeMeasure (readout, fringes, true, options); } psFree(sumFringe); @@ -320,5 +320,5 @@ psFree(timeString); - return sumFringe; + return true; } @@ -338,14 +338,14 @@ pmChip *fringe = pmFPAfileThisChip(config->files, view, "PPIMAGE.FRINGE"); if (!fringe) { - psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); - psFree (view); - return false; + psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); + psFree (view); + return false; } // Solve the fringe system if (!ppImageDetrendFringeSolve(chip, fringe, false, options)) { - psError(PS_ERR_UNKNOWN, false, "failed to solve the fringe system.\n"); - psFree (view); - return false; + psError(PS_ERR_UNKNOWN, false, "failed to solve the fringe system.\n"); + psFree (view); + return false; } @@ -353,35 +353,35 @@ view->cell = view->readout = -1; while ((cell = pmFPAviewNextCell(view, chip->parent, 1)) != NULL) { - if (!cell->process || !cell->file_exists) { - continue; - } - - // Apply the fringe correction - psTrace("ppImage", 3, "Applying fringe correction...\n"); - pmCell *fringeCell = pmFPAfileThisCell(config->files, view, "PPIMAGE.FRINGE"); - if (!fringeCell) { - psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); - psFree (view); - return false; - } - - // XXX for now, skip the video cells (cell->readouts->n > 1) - if (cell->readouts->n > 1) { - psWarning ("Skipping Video Cell for ppImageDetrendFringeApply"); - continue; - } - - if (!ppImageDetrendFringeGenerate(cell, fringeCell, options)) { - psError(PS_ERR_UNKNOWN, false, "failed to apply fringe image.\n"); - psFree (view); - return false; - } + if (!cell->process || !cell->file_exists) { + continue; + } + + // Apply the fringe correction + psTrace("ppImage", 3, "Applying fringe correction...\n"); + pmCell *fringeCell = pmFPAfileThisCell(config->files, view, "PPIMAGE.FRINGE"); + if (!fringeCell) { + psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); + psFree (view); + return false; + } + + // XXX for now, skip the video cells (cell->readouts->n > 1) + if (cell->readouts->n > 1) { + psWarning ("Skipping Video Cell for ppImageDetrendFringeApply"); + continue; + } + + if (!ppImageDetrendFringeGenerate(cell, fringeCell, options)) { + psError(PS_ERR_UNKNOWN, false, "failed to apply fringe image.\n"); + psFree (view); + return false; + } } // Solve the residual fringe system if (!ppImageDetrendFringeSolve(chip, fringe, true, options)) { - psError(PS_ERR_UNKNOWN, false, "failed to solve the residual fringe system.\n"); - psFree (view); - return false; + psError(PS_ERR_UNKNOWN, false, "failed to solve the residual fringe system.\n"); + psFree (view); + return false; } Index: /trunk/ppImage/src/ppImageDetrendPattern.c =================================================================== --- /trunk/ppImage/src/ppImageDetrendPattern.c (revision 26894) +++ /trunk/ppImage/src/ppImageDetrendPattern.c (revision 26895) @@ -5,9 +5,11 @@ #include "ppImage.h" -#define ESCAPE(MESSAGE) { \ - psError(PS_ERR_UNKNOWN, false, MESSAGE); \ +#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); bool ppImageDetrendPatternApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, @@ -16,65 +18,137 @@ pmCell *cell = NULL; - assert (options->doPattern); // do not call if not needed - assert (inputView->chip != -1); - assert (inputView->cell == -1); - assert (inputView->readout == -1); - bool status; - pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT"); + assert(options->doPatternRow || options->doPatternCell); // do not call if not needed + assert(inputView->chip != -1); + assert(inputView->cell == -1); + assert(inputView->readout == -1); - pmFPAview *view = pmFPAviewAlloc(0); // View for local processing - *view = *inputView; + if (options->doPatternRow) { + bool status; + pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT"); + pmFPAview *view = pmFPAviewAlloc(0); // View for local processing + *view = *inputView; + while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { + if (!cell->process || !cell->file_exists) { + continue; + } + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE(false, "load failure for Cell"); + } - while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { - if (!cell->process || !cell->file_exists) { - continue; - } - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - ESCAPE("load failure for Cell"); - } - - if (!cell->data_exists) { - continue; - } - - if (cell->readouts->n > 1) { - psWarning ("Skipping Video Cell for ppImageDetrendPatternApply"); - continue; - } - - psMetadataItem *doPattern = pmConfigRecipeValueByView(config, RECIPE_NAME, "PATTERN.SUBSET", - chip->parent, view); // Do we do pattern sub? - if (!doPattern || doPattern->type != PS_DATA_BOOL) { - ESCAPE("Unable to determine whether pattern matching should be applied."); - } - if (!doPattern->data.B) { - continue; - } - - psLogMsg("ppImage", PS_LOG_INFO, "Performing pattern subtraction for %d,%d\n", view->chip, view->cell); - - // process each of the readouts - pmReadout *readout; // Readout from cell - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - ESCAPE("load failure for Readout"); - } - if (!readout->data_exists) { + if (!cell->data_exists) { continue; } - // perfore pattern correction - if (!pmPatternRow(readout, options->patternOrder, options->patternIter, options->patternRej, - options->patternThresh, options->patternMean, options->patternStdev, - options->maskValue, options->darkMask)) { - psFree(view); - return(false); + if (cell->readouts->n > 1) { + psWarning ("Skipping Video Cell for ppImageDetrendPatternApply"); + continue; + } + + 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; + + const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); + const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); + psLogMsg("ppImage", PS_LOG_INFO, "Performing row pattern correction for %s, %s\n", + chipName, cellName); + + // process each of the readouts + pmReadout *readout; // Readout from cell + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE(false, "load failure for Readout"); + } + 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); } - psFree(view); + if (options->doPatternCell) { + 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 + *view = *inputView; + for (int i = 0; i < chip->cells->n; i++) { + view->cell = i; + + 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; + } + } + + // Tweak the cells + if (!pmPatternCell(chip, tweak, options->patternCellBG, options->patternCellMean, + options->maskValue, options->darkMask)) { + psFree(tweak); + psFree(view); + return false; + } + psFree(tweak); + psFree(view); + } + return(true); } +static bool doPatternForView (bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipeName, const char *recipeValue) { + *doit = false; + + psMetadataItem *doPattern = pmConfigRecipeValueByView(config, recipeName, recipeValue, chip->parent, view); + 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) { + *doit = doPattern->data.B; + return true; + } + 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)); + return false; + } + 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': + *doit = true; + return true; + default: + psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET chip string %s (unknown value %c))", string, string[view->cell]); + return false; + } + psAbort("imposible to reach here"); + } + psError(PS_ERR_UNKNOWN, true, "error in PATTERN.ROW.SUBSET : invalid data type"); + return false; +} Index: /trunk/ppImage/src/ppImageLoop.c =================================================================== --- /trunk/ppImage/src/ppImageLoop.c (revision 26894) +++ /trunk/ppImage/src/ppImageLoop.c (revision 26895) @@ -163,6 +163,6 @@ } - // Apply the pattern noise correction - if (options->doPattern) { + // Apply the pattern correction + if (options->doPatternRow || options->doPatternCell) { if (!ppImageDetrendPatternApply(config,chip,view,options)) { ESCAPE("Unable to apply pattern corrections"); Index: /trunk/ppImage/src/ppImageOptions.c =================================================================== --- /trunk/ppImage/src/ppImageOptions.c (revision 26894) +++ /trunk/ppImage/src/ppImageOptions.c (revision 26895) @@ -32,5 +32,6 @@ options->doShutter = false; // Shutter correction options->doFlat = false; // Flat-field normalisation - options->doPattern = false; // Pattern noise subtraction + options->doPatternRow = false; // Row pattern correction + options->doPatternCell = false; // Cell pattern correction options->doFringe = false; // Fringe subtraction options->doPhotom = false; // Source identification and photometry @@ -90,12 +91,14 @@ options->fringeKeep = 1.0; // Fringe keep fraction - // Pattern noise values - - options->patternOrder = 0; // Polynomial order - options->patternIter = 0; // Clipping iterations - options->patternRej = NAN; // Clipping rejection threshold - options->patternThresh = NAN; // Threshold for ignoring pixels - options->patternMean = PS_STAT_NONE; // Statistic for mean - options->patternStdev = PS_STAT_NONE; // Statistic for standard deviation + // Pattern correction values + + options->patternRowOrder = 0; // Polynomial order + options->patternRowIter = 0; // Clipping iterations + options->patternRowRej = NAN; // Clipping rejection threshold + options->patternRowThresh = NAN; // Threshold for ignoring pixels + options->patternRowMean = PS_STAT_NONE; // Statistic for mean + options->patternRowStdev = PS_STAT_NONE; // Statistic for standard deviation + options->patternCellBG = PS_STAT_NONE; // Statistic for background + options->patternCellMean = PS_STAT_NONE; // Statistic for mean // Remnance values @@ -238,5 +241,6 @@ options->doFringe = psMetadataLookupBool(NULL, recipe, "FRINGE"); options->doShutter = psMetadataLookupBool(NULL, recipe, "SHUTTER"); - options->doPattern = psMetadataLookupBool(NULL, recipe, "PATTERN"); + options->doPatternRow = psMetadataLookupBool(NULL, recipe, "PATTERN.ROW"); + options->doPatternCell = psMetadataLookupBool(NULL, recipe, "PATTERN.CELL"); options->doStats = false; @@ -250,14 +254,14 @@ options->burntoolTrails = psMetadataLookupS32(&status, recipe, "BURNTOOL.TRAILS"); psTrace("psModules.detrend", 7, "burntoolTrails: %d BURNTOOL.TRAILS: %d Status: %d\n", - options->burntoolTrails,psMetadataLookupS32(&status,recipe,"BURNTOOL.TRAILS"),status); + options->burntoolTrails,psMetadataLookupS32(&status,recipe,"BURNTOOL.TRAILS"),status); if (!status) { psWarning("BURNTOOL.TRAILS not found in recipe: setting to default value.\n"); } - + // binned image options options->xBin1 = psMetadataLookupS32(&status, recipe, "BIN1.XBIN"); if (!status) { psWarning("BIN1.XBIN not found in recipe: setting to default value.\n"); - options->xBin1 = 4; + options->xBin1 = 4; } options->yBin1 = psMetadataLookupS32(&status, recipe, "BIN1.YBIN"); @@ -320,11 +324,13 @@ options->fringeKeep = psMetadataLookupF32(NULL, recipe, "FRINGE.KEEP"); - // Pattern noise - options->patternOrder = psMetadataLookupS32(NULL, recipe, "PATTERN.ORDER"); - options->patternIter = psMetadataLookupS32(NULL, recipe, "PATTERN.ITER"); - options->patternRej = psMetadataLookupF32(NULL, recipe, "PATTERN.REJ"); - options->patternThresh = psMetadataLookupF32(NULL, recipe, "PATTERN.THRESH"); - options->patternMean = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.MEAN")); - options->patternStdev = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.STDEV")); + // Pattern correction + options->patternRowOrder = psMetadataLookupS32(NULL, recipe, "PATTERN.ROW.ORDER"); + options->patternRowIter = psMetadataLookupS32(NULL, recipe, "PATTERN.ROW.ITER"); + options->patternRowRej = psMetadataLookupF32(NULL, recipe, "PATTERN.ROW.REJ"); + options->patternRowThresh = psMetadataLookupF32(NULL, recipe, "PATTERN.ROW.THRESH"); + options->patternRowMean = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.ROW.MEAN")); + options->patternRowStdev = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.ROW.STDEV")); + options->patternCellBG = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.CELL.BG")); + options->patternCellMean = psStatsOptionFromString(psMetadataLookupStr(NULL, recipe, "PATTERN.CELL.MEAN")); // Remnance options Index: /trunk/ppImage/src/ppImageParseCamera.c =================================================================== --- /trunk/ppImage/src/ppImageParseCamera.c (revision 26894) +++ /trunk/ppImage/src/ppImageParseCamera.c (revision 26895) @@ -79,4 +79,14 @@ int nScanRows = psMetadataLookupS32(&status, recipe, "SCAN.ROWS"); pmDetrendSetThreadTasks(nScanRows); + } + + if (options->doPatternRow || options->doPatternCell) { + pmFPAfile *outPattern = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.PATTERN"); + if (!outPattern) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.PATTERN")); + psFree(options); + return NULL; + } + outPattern->save = true; } @@ -255,4 +265,7 @@ pmFPAfile *psphotInput = pmFPAfileDefineFromFile (config, chipImage, 1, 1, "PSPHOT.INPUT"); PS_ASSERT (psphotInput, false); + + // specify the number of psphot input images + psMetadataAddS32 (config->arguments, PS_LIST_TAIL, "PSPHOT.INPUT.NUM", PS_META_REPLACE, "number of inputs", 1); // define associated psphot input/output files Index: /trunk/ppImage/src/ppImageReplaceBackground.c =================================================================== --- /trunk/ppImage/src/ppImageReplaceBackground.c (revision 26894) +++ /trunk/ppImage/src/ppImageReplaceBackground.c (revision 26895) @@ -80,5 +80,5 @@ // the background model has not been defined, or at least not generated if (!modelFile || !modelRO) { - if (!psphotModelBackground(config, &roView, "PPIMAGE.CHIP")) { + if (!psphotModelBackgroundReadoutFileIndex(config, &roView, "PPIMAGE.CHIP", 0)) { psError(PS_ERR_UNKNOWN, false, "Unable to model background"); return false;