Index: /branches/eam_rel9_p0/psModules/src/astrom/pmChipMosaic.c =================================================================== --- /branches/eam_rel9_p0/psModules/src/astrom/pmChipMosaic.c (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/astrom/pmChipMosaic.c (revision 6080) @@ -37,4 +37,5 @@ int yMin = INT_MAX; int yMax = - INT_MAX; + psElemType type = 0; for (int i = 0; i < source->n; i++) { psImage *image = source->data[i]; // The image of interest @@ -43,5 +44,11 @@ } - assert(image->type.type == PS_TYPE_F32); // Only implemented for F32 images so far. + // Only implemented for F32 and U8 images so far. + assert(image->type.type == PS_TYPE_F32 || image->type.type == PS_TYPE_U8); + // All input types must be the same + if (type == 0) { + type = image->type.type; + } + assert(type == image->type.type); // Size of cell in x and y @@ -71,5 +78,5 @@ psTrace(__func__, 3, "Spliced image will be %dx%d\n", (int)xSize, (int)ySize); - psImage *mosaic = psImageAlloc((int)xSize, (int)ySize, PS_TYPE_F32); // The mosaic image + psImage *mosaic = psImageAlloc((int)xSize, (int)ySize, type); // The mosaic image psImageInit(mosaic, 0.0); @@ -96,12 +103,24 @@ // In case the original image is binned but the mosaic is not, we need to fill in the // values in the mosaic. - for (int j = 0; j < yBinSource->data.S32[i]; j++) { - int yTarget = (int)(yTargetBase + yParity * (float)j / (float)yBinTarget); - for (int i = 0; i < xBinSource->data.S32[i]; i++) { - int xTarget = (int)(xTargetBase + xParity * (float)i / (float)xBinTarget); - - mosaic->data.F32[yTarget][xTarget] += image->data.F32[y][x]; - } - } // Iterating over mosaic image for binned input image + #define FILL_IN(TYPE) \ + for (int j = 0; j < yBinSource->data.S32[i]; j++) { \ + int yTarget = (int)(yTargetBase + yParity * (float)j / (float)yBinTarget); \ + for (int i = 0; i < xBinSource->data.S32[i]; i++) { \ + int xTarget = (int)(xTargetBase + xParity * (float)i / (float)xBinTarget); \ + mosaic->data.TYPE[yTarget][xTarget] += image->data.TYPE[y][x]; \ + } \ + } + + switch (type) { + case PS_TYPE_F32: + FILL_IN(F32); + break; + case PS_TYPE_U8: + FILL_IN(U8); + break; + default: + psAbort(__func__, "Should never get here.\n"); + } + } } // Iterating over input image @@ -158,8 +177,4 @@ } - // Trim the image to get rid of the overscan - psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); - psTrace(__func__, 7, "Cell %d trimsec: [%.0f:%.0f,%.0f:%.0f]\n", i, trimsec->x0, trimsec->x1, - trimsec->y0, trimsec->y1); psArray *readouts = cell->readouts; // The array of readouts if (readouts->n > 1) { @@ -167,10 +182,10 @@ "be mosaicked.\n", i); } - psImage *image = ((pmReadout*)readouts->data[0])->image; // The image to put into the mosaic - psImage *weight = ((pmReadout*)readouts->data[0])->weight; - psImage *mask = ((pmReadout*)readouts->data[0])->weight; - images->data[i] = psImageSubset(image, *trimsec); // Trimmed image - weights->data[i] = weight ? psImageSubset(weight, *trimsec) : NULL; - masks->data[i] = mask ? psImageSubset(mask, *trimsec) : NULL; + pmReadout *readout = readouts->data[0]; // The only readout we'll bother with + + // The images to put into the mosaic + images->data[i] = readout->image; + weights->data[i] = readout->weight; + masks->data[i] = readout->mask; } // Mosaic the images together and we're done Index: /branches/eam_rel9_p0/psModules/src/astrom/pmConcepts.c =================================================================== --- /branches/eam_rel9_p0/psModules/src/astrom/pmConcepts.c (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/astrom/pmConcepts.c (revision 6080) @@ -160,4 +160,8 @@ while ((item = psMetadataGetAndIncrement(iter))) { const char *name = item->name; // Name of the concept + if (!strcmp(name, "CELL.NAME") || !strcmp(name, "CHIP.NAME")) { + // These concepts are not written out; they are set from things like the FITS extname + continue; + } psMetadataItem *specItem = psMetadataLookup(*specs, name); // Specification for the concept if (specItem) { Index: /branches/eam_rel9_p0/psModules/src/astrom/pmFPA.c =================================================================== --- /branches/eam_rel9_p0/psModules/src/astrom/pmFPA.c (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/astrom/pmFPA.c (revision 6080) @@ -12,6 +12,6 @@ * XXX: Should we implement non-linear cell->chip transforms? * -* @version $Revision: 1.1.2.1 $ $Name: not supported by cvs2svn $ -* @date $Date: 2006-01-20 02:36:41 $ +* @version $Revision: 1.1.2.2 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-01-20 09:47:06 $ * * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii @@ -23,8 +23,10 @@ #include #include +#include #include "pslib.h" #include "pmFPA.h" #include "pmConcepts.h" +#include "pmMaskBadPixels.h" /****************************************************************************** @@ -163,4 +165,5 @@ tmpReadout->mask = NULL; tmpReadout->weight = NULL; + tmpReadout->bias = psListAlloc(NULL); tmpReadout->analysis = psMetadataAlloc(); tmpReadout->parent = cell; @@ -390,4 +393,25 @@ } +bool pmChipSelectCell(pmChip *chip, + int cellNum + ) +{ + assert(chip); + + psArray *cells = chip->cells; // Component cells + if (!cells || cellNum > cells->n) { + return false; + } + + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; + if (!cell) { + continue; + } + cell->process = (i == cellNum); + } + + return true; +} /***************************************************************************** @@ -437,4 +461,31 @@ } +int pmChipExcludeCell(pmChip *chip, + int cellNum + ) +{ + assert(chip); + + psArray *cells = chip->cells; // The component cells + if (!cells || cellNum > cells->n) { + return 0; + } + + int numCells = 0; // Number of cells to be processed + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; + if (!cell) { + continue; + } + if (i == cellNum) { + cell->process = false; + } else { + numCells++; + } + } + + return numCells; +} + bool pmCellSetWeights(pmCell *cell // Cell for which to set weights @@ -444,4 +495,6 @@ float readnoise = psMetadataLookupF32(NULL, cell->concepts, "CELL.READNOISE"); // Cell read noise psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); // Trim section + float saturation = psMetadataLookupF32(NULL, cell->concepts, "CELL.SATURATION"); // Saturation level + float bad = psMetadataLookupF32(NULL, cell->concepts, "CELL.BAD"); // Bad level p_pmHDU *hdu = cell->hdu; // The data unit, containing the weight and mask originals @@ -478,5 +531,4 @@ psImage *image = pixels->data[i]; masks->data[i] = psImageAlloc(image->numCols, image->numRows, PS_TYPE_U8); - psImageInit(masks->data[i], 0); } hdu->masks = masks; @@ -489,17 +541,27 @@ if (! readout->weight) { - readout->weight = weights->data[i]; + readout->weight = psImageSubset(weights->data[i], *trimsec); } if (! readout->mask) { - readout->mask = masks->data[i]; - } - - // Mask is already set to 0 + readout->mask = psImageSubset(masks->data[i], *trimsec); + } + + // Set up the mask + psImage *image = readout->image;// Pixels + psImage *mask = readout->mask; // Mask image + for (int i = 0; i < image->numRows; i++) { + for (int j = 0; j < image->numCols; j++) { + if (image->data.F32[i][j] > saturation) { + mask->data.F32[i][j] = PM_MASK_SAT; + } + if (image->data.F32[i][j] < bad) { + mask->data.F32[i][j] = PM_MASK_BAD; + } + } + } // Set weight image to the variance = g*f + rn^2 - psImage *image = psImageSubset(readout->image, *trimsec); // The pixels - psImage *weight = psImageSubset(readout->weight, *trimsec); // The weight map - psBinaryOp(weight, image, "*", psScalarAlloc(gain, PS_TYPE_F32)); - psBinaryOp(weight, weight, "+", psScalarAlloc(readnoise*readnoise, PS_TYPE_F32)); + psBinaryOp(readout->weight, image, "*", psScalarAlloc(gain, PS_TYPE_F32)); + psBinaryOp(readout->weight, readout->weight, "+", psScalarAlloc(readnoise*readnoise, PS_TYPE_F32)); } Index: /branches/eam_rel9_p0/psModules/src/astrom/pmFPA.h =================================================================== --- /branches/eam_rel9_p0/psModules/src/astrom/pmFPA.h (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/astrom/pmFPA.h (revision 6080) @@ -7,6 +7,6 @@ * @author GLG, MHPCC * -* @version $Revision: 1.1.2.1 $ $Name: not supported by cvs2svn $ -* @date $Date: 2006-01-20 02:36:41 $ +* @version $Revision: 1.1.2.2 $ $Name: not supported by cvs2svn $ +* @date $Date: 2006-01-20 09:47:06 $ * * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii @@ -153,4 +153,5 @@ psImage *mask; ///< Mask of input image psImage *weight; ///< Weight of input image + psList *bias; ///< Overscan images psMetadata *analysis; ///< Readout-level analysis metadata pmCell *parent; ///< Parent cell @@ -261,4 +262,8 @@ ); +bool pmChipSelectCell(pmChip *chip, + int cellNum + ); + /** * @@ -275,4 +280,7 @@ ); +int pmChipExcludeCell(pmChip *chip, + int cellNum + ); // Set the weights and masks within a cell, based on the gain and RN Index: /branches/eam_rel9_p0/psModules/src/astrom/pmFPARead.c =================================================================== --- /branches/eam_rel9_p0/psModules/src/astrom/pmFPARead.c (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/astrom/pmFPARead.c (revision 6080) @@ -1,4 +1,5 @@ #include #include +#include #include "pslib.h" @@ -105,17 +106,29 @@ { psArray *images = hdu->images; // Array of images (each of which is a readout) - psArray *masks = hdu->masks; // Array of masks (one for each readout) + + psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); + psList *biassecs = psMetadataLookupPtr(NULL, cell->concepts, "CELL.BIASSEC"); + // Iterate over each of the image planes for (int i = 0; i < images->n; i++) { psImage *image = images->data[i]; // The i-th plane - psImage *mask = NULL; // The mask - if (masks) { - mask = masks->data[i]; - } - pmReadout *readout = pmReadoutAlloc(cell); - readout->image = image; - readout->mask = mask; - psFree(readout); + + readout->image = psImageSubset(image, *trimsec); // The image corresponding to the trim region + + // Get the list of overscans + psListIterator *iter = psListIteratorAlloc(biassecs, PS_LIST_HEAD, false); // Iterator + psRegion *biassec = NULL; // A BIASSEC region from the list + while ((biassec = psListGetAndIncrement(iter))) { + psImage *overscan = psImageSubset(image, *biassec); + psListAdd(readout->bias, PS_LIST_TAIL, overscan); + psFree(overscan); + } + psFree(iter); + + readout->mask = NULL; + readout->weight = NULL; + + psFree(readout); // Drop reference } @@ -164,6 +177,6 @@ pmChip *chip = chips->data[i]; // The chip - // Only read chips marked to "process" - if (! chip->process) { + // Only read chips marked to "read" + if (! chip->process || chip->exists) { psTrace(__func__, 2, "Ignoring chip %d...\n", i); continue; @@ -187,6 +200,6 @@ pmCell *cell = cells->data[j]; // The cell - // Only read cells marked to "process" - if (! cell->process) { + // Only read cells marked to "read" + if (! cell->process || cell->exists) { psTrace(__func__, 3, "Ignoring chip %d...\n", i); continue; @@ -400,5 +413,5 @@ for (int chipNum = 0; chipNum < chips->n; chipNum++) { pmChip *chip = chips->data[chipNum]; // The current chip of interest - if (chip->process) { + if (chip->process && !chip->exists) { if (chip->hdu) { hdu = chip->hdu; @@ -407,5 +420,5 @@ for (int cellNum = 0; cellNum < cells->n; cellNum++) { pmCell *cell = cells->data[cellNum]; // The current cell of interest - if (cell->process) { + if (cell->process && !cell->exists) { if (cell->hdu) { hdu = cell->hdu; @@ -538,5 +551,5 @@ for (int chipNum = 0; chipNum < chips->n; chipNum++) { pmChip *chip = chips->data[chipNum]; // The current chip of interest - if (chip->process) { + if (chip->process && !chip->exists) { if (chip->hdu) { hdu = chip->hdu; @@ -545,5 +558,5 @@ for (int cellNum = 0; cellNum < cells->n; cellNum++) { pmCell *cell = cells->data[cellNum]; // The current cell of interest - if (cell->process) { + if (cell->process && !cell->exists) { if (cell->hdu) { hdu = cell->hdu; Index: /branches/eam_rel9_p0/psModules/src/detrend/pmFlatField.c =================================================================== --- /branches/eam_rel9_p0/psModules/src/detrend/pmFlatField.c (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/detrend/pmFlatField.c (revision 6080) @@ -24,6 +24,6 @@ * @author Ross Harman, MHPCC * - * @version $Revision: 1.4.8.1.2.2 $ $Name: not supported by cvs2svn $ - * @date $Date: 2006-01-20 06:01:02 $ + * @version $Revision: 1.4.8.1.2.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-01-20 09:47:06 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -53,8 +53,4 @@ psElemType flatType; psElemType maskType; - psImage *inImage = NULL; - psImage *inMask = NULL; - psImage *flatImage = NULL; - // Check for nulls @@ -67,11 +63,13 @@ } - // Get the TRIMSEC of each image - { - psRegion *trimsec = psMetadataLookupPtr(NULL, in->parent->concepts, "CELL.TRIMSEC"); - inImage = psImageSubset(in->image, *trimsec); - trimsec = psMetadataLookupPtr(NULL, flat->parent->concepts, "CELL.TRIMSEC"); - flatImage = psImageSubset(flat->image, *trimsec); - } + psImage *inImage = in->image; // Input image + psImage *inMask = in->mask; // Mask for input image + psImage *flatImage = flat->image; // Flat-field image + + // Offsets on the chip + int x0in = psMetadataLookupS32(NULL, in->parent->concepts, "CELL.X0"); + int y0in = psMetadataLookupS32(NULL, in->parent->concepts, "CELL.Y0"); + int x0flat = psMetadataLookupS32(NULL, flat->parent->concepts, "CELL.X0"); + int y0flat = psMetadataLookupS32(NULL, flat->parent->concepts, "CELL.Y0"); if (inImage == NULL) { @@ -84,5 +82,4 @@ return false; } - inMask = in->mask; // Check input image and its mask are not larger than flat image @@ -102,6 +99,6 @@ // Determine total offset based on image offset with chip offset - totOffCol = inImage->col0 + in->col0; - totOffRow = inImage->row0 + in->row0; + totOffCol = inImage->col0 + y0in - flatImage->col0 - y0flat; + totOffRow = inImage->row0 + x0in - flatImage->row0 - x0flat; // Check that offsets are within image limits Index: /branches/eam_rel9_p0/psModules/src/detrend/pmMaskBadPixels.h =================================================================== --- /branches/eam_rel9_p0/psModules/src/detrend/pmMaskBadPixels.h (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/detrend/pmMaskBadPixels.h (revision 6080) @@ -24,6 +24,6 @@ * @author Ross Harman, MHPCC * - * @version $Revision: 1.2.8.1.2.1 $ $Name: not supported by cvs2svn $ - * @date $Date: 2006-01-20 02:38:28 $ + * @version $Revision: 1.2.8.1.2.2 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-01-20 09:47:06 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -38,5 +38,6 @@ PM_MASK_BADCOL = 0x0002, ///< The pixel is a bad column. PM_MASK_SAT = 0x0004, ///< The pixel is saturated. - PM_MASK_FLAT = 0x0008 ///< The pixel is non-positive in the flat-field. + PM_MASK_BAD = 0x0008, ///< The pixel is low + PM_MASK_FLAT = 0x0010 ///< The pixel is non-positive in the flat-field. } pmMaskValue; Index: /branches/eam_rel9_p0/psModules/src/imsubtract/pmSubtractBias.c =================================================================== --- /branches/eam_rel9_p0/psModules/src/imsubtract/pmSubtractBias.c (revision 6079) +++ /branches/eam_rel9_p0/psModules/src/imsubtract/pmSubtractBias.c (revision 6080) @@ -11,6 +11,6 @@ * @author GLG, MHPCC * - * @version $Revision: 1.6.8.1.2.3 $ $Name: not supported by cvs2svn $ - * @date $Date: 2006-01-20 06:03:29 $ + * @version $Revision: 1.6.8.1.2.4 $ $Name: not supported by cvs2svn $ + * @date $Date: 2006-01-20 09:47:06 $ * * Copyright 2004 Maui High Performance Computing Center, University of Hawaii @@ -102,11 +102,8 @@ assert(sub); - // Get the trim sections - psRegion *inTrimsec = psMetadataLookupPtr(NULL, in->parent->concepts, "CELL.TRIMSEC"); - psRegion *subTrimsec = psMetadataLookupPtr(NULL, sub->parent->concepts, "CELL.TRIMSEC"); - psImage *inImage = psImageSubset(in->image, *inTrimsec); // The input image - psImage *subImage = psImageSubset(sub->image, *subTrimsec); // The image to be subtracted - psImage *inMask = in->mask ? psImageSubset(in->mask, *inTrimsec) : NULL; // The input mask - psImage *subMask = sub->mask ? psImageSubset(sub->mask, *subTrimsec) : NULL; // The input mask + psImage *inImage = in->image; // The input image + psImage *inMask = in->mask; // The input mask + psImage *subImage = sub->image; // The image to be subtracted + psImage *subMask = sub->mask; // The mask for the subtraction image // Offsets of the cells @@ -425,7 +422,5 @@ PS_ASSERT_READOUT_TYPE(in, PS_TYPE_F32, NULL); - pmCell *cell = in->parent; // The parent cell - psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC"); // The trim region - psImage *image = psImageSubset(in->image, *trimsec); // The image corresponding to the trim region + psImage *image = in->image; // The input image // Overscan processing @@ -438,15 +433,5 @@ } - // Get the list of overscans - psList *overscanRegions = psMetadataLookupPtr(NULL, cell->concepts, "CELL.BIASSEC"); - psList *overscans = psListAlloc(NULL); // List of the overscan images - psListIterator *iter = psListIteratorAlloc(overscanRegions, PS_LIST_HEAD, false); // Iterator - psRegion *biassec = NULL; // A BIASSEC region from the list - while ((biassec = psListGetAndIncrement(iter))) { - psImage *overscan = psImageSubset(in->image, *biassec); - psListAdd(overscans, PS_LIST_TAIL, overscan); - psFree(overscan); - } - psFree(iter); + psList *overscans = in->bias; // List of the overscan images psStats *myStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN); // A new psStats, to avoid clobbering original @@ -482,5 +467,6 @@ // We do the regular overscan subtraction - bool readRows = psMetadataLookupBool(NULL, cell->concepts, "CELL.READDIR"); // Read direction + + bool readRows = psMetadataLookupBool(NULL, in->parent->concepts, "CELL.READDIR");// Read direction if (readRows) {