Index: /branches/neb/archive/scripts/src/phase2/pmFPARead.c =================================================================== --- /branches/neb/archive/scripts/src/phase2/pmFPARead.c (revision 5647) +++ /branches/neb/archive/scripts/src/phase2/pmFPARead.c (revision 5648) @@ -7,5 +7,5 @@ #include "pmFPARead.h" -#include "papStuff.h" // For "split" +#include "papStuff.h" // For "split" // NOTE: Need to deal with header inheritance @@ -17,25 +17,30 @@ // Read a FITS extension into a chip -static bool readExtension(p_pmHDU *hdu, // Pixel data into which to read - psFits *fits // The FITS file from which to read - ) +static bool readExtension(p_pmHDU *hdu, // Pixel data into which to read + psFits *fits // The FITS file from which to read + ) { const char *extName = hdu->extname; // Extension name psTrace(__func__, 7, "Moving to extension %s...\n", extName); - if (strncmp(extName, "PHU", 3) == 0) { - if (!psFitsMoveExtNum(fits, 0, false)) { - psError(PS_ERR_IO, false, "Unable to find PHU in FITS file!\n"); - return false; - } - } else if (! psFitsMoveExtName(fits, extName)) { - psError(PS_ERR_IO, false, "Unable to find extension %s in FITS file!\n", extName); - return false; + if (strncmp(extName, "PHU", 3) == 0) + { + if (!psFitsMoveExtNum(fits, 0, false)) + { + psError(PS_ERR_IO, false, "Unable to find PHU in FITS file!\n"); + return false; + } + } + else if (! psFitsMoveExtName(fits, extName)) + { + psError(PS_ERR_IO, false, "Unable to find extension %s in FITS file!\n", extName); + return false; } psTrace(__func__, 7, "Reading header....\n"); psMetadata *header = psFitsReadHeader(NULL, fits); // Header - if (! header) { - psError(PS_ERR_IO, false, "Unable to read FITS header!\n"); - return false; + if (! header) + { + psError(PS_ERR_IO, false, "Unable to read FITS header!\n"); + return false; } @@ -43,53 +48,62 @@ bool mdStatus = false; int nAxis = psMetadataLookupS32(&mdStatus, header, "NAXIS"); - if (!mdStatus) { - psLogMsg(__func__, PS_LOG_WARN, "There is no NAXIS keyword in the FITS header of extension %s!\n", - extName); - } - if (nAxis != 2 && nAxis != 3) { - psLogMsg(__func__, PS_LOG_WARN, "Image is not 2- or 3-dimensional --- reading into a single image " - "anyway.\n"); + if (!mdStatus) + { + psLogMsg(__func__, PS_LOG_WARN, "There is no NAXIS keyword in the FITS header of extension %s!\n", + extName); + } + if (nAxis != 2 && nAxis != 3) + { + psLogMsg(__func__, PS_LOG_WARN, "Image is not 2- or 3-dimensional --- reading into a single image " + "anyway.\n"); } psTrace(__func__, 9, "NAXIS = %d\n", nAxis); - int numPlanes = 1; // Number of planes - if (nAxis == 3) { - numPlanes = psMetadataLookupS32(&mdStatus, header, "NAXIS3"); - if (!mdStatus) { - psError(PS_ERR_IO, false, "Unable to read NAXIS3 for 3-dimensional image!\n"); - return false; - } - } - psRegion region = {0, 0, 0, 0}; // Region to read is everything + int numPlanes = 1; // Number of planes + if (nAxis == 3) + { + numPlanes = psMetadataLookupS32(&mdStatus, header, "NAXIS3"); + if (!mdStatus) + { + psError(PS_ERR_IO, false, "Unable to read NAXIS3 for 3-dimensional image!\n"); + return false; + } + } + psRegion region = {0, 0, 0, 0}; // Region to read is everything // Read each plane into the array psTrace(__func__, 7, "Reading %d planes into array....\n", numPlanes); psArray *pixels = psArrayAlloc(numPlanes); // Array of images - for (int i = 0; i < numPlanes; i++) { - psTrace(__func__, 9, "Reading plane %d\n", i); - psMemCheckCorruption(true); - psImage *image = psFitsReadImage(NULL, fits, region, i); - - // XXX: Type conversion here to support the modules, which don't have multiple type support yet - if (image->type.type != PS_TYPE_F32) { - pixels->data[i] = psImageCopy(NULL, image, PS_TYPE_F32); + for (int i = 0; i < numPlanes; i++) + { + psTrace(__func__, 9, "Reading plane %d\n", i); + psMemCheckCorruption(true); + psImage *image = psFitsReadImage(NULL, fits, region, i); + + // XXX: Type conversion here to support the modules, which don't have multiple type support yet + if (image->type.type != PS_TYPE_F32) + { + pixels->data[i] = psImageCopy(NULL, image, PS_TYPE_F32); #ifndef PRODUCTION - // XXX: Temporary fix for writing images, until psFits gets cleaned up - psMetadataItem *bitpixItem = psMetadataLookup(header, "BITPIX"); - bitpixItem->data.S32 = -32; - psMetadataRemove(header, 0, "BZERO"); - psMetadataRemove(header, 0, "BSCALE"); + // XXX: Temporary fix for writing images, until psFits gets cleaned up + psMetadataItem *bitpixItem = psMetadataLookup(header, "BITPIX"); + bitpixItem->data.S32 = -32; + psMetadataRemove(header, 0, "BZERO"); + psMetadataRemove(header, 0, "BSCALE"); #endif - psFree(image); - } else { - pixels->data[i] = image; - } - psTrace(__func__, 10, "Done\n"); - if (! pixels->data[i]) { - psError(PS_ERR_IO, false, "Unable to read image for extension %s, plane %d\n", extName, i); - return false; - } + psFree(image); + } + else + { + pixels->data[i] = image; + } + psTrace(__func__, 10, "Done\n"); + if (! pixels->data[i]) + { + psError(PS_ERR_IO, false, "Unable to read image for extension %s, plane %d\n", extName, i); + return false; + } } @@ -104,22 +118,24 @@ // Portion out an image into the cell -static bool generateReadouts(pmCell *cell, // The cell that gets its bits - p_pmHDU *hdu // Pixel data, containing image, mask, weights - ) +static bool generateReadouts(pmCell *cell, // The cell that gets its bits + p_pmHDU *hdu // Pixel data, containing image, mask, weights + ) { - psArray *images = hdu->images; // Array of images (each of which is a readout) - psArray *masks = hdu->masks; // Array of masks (one for each readout) + psArray *images = hdu->images; // Array of images (each of which is a readout) + psArray *masks = hdu->masks; // Array of masks (one for each readout) // 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, image, mask, 0,0,1,1); - psFree(readout); // This seems silly, but the alloc registers it with the cell, so we - // don't have to do anything with it. Perhaps we should change - // pmReadoutAlloc to pmReadoutAdd? + 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, image, mask, 0, 0, 1, 1); + psFree(readout); // This seems silly, but the alloc registers it with the cell, so we + // don't have to do anything with it. Perhaps we should change + // pmReadoutAlloc to pmReadoutAdd? } @@ -131,20 +147,22 @@ ////////////////////////////////////////////////////////////////////////////////////////////////////////////// -bool pmFPARead(pmFPA *fpa, // FPA to read into - psFits *fits, // FITS file from which to read - psMetadata *phu, // Primary header - psDB *db // Database handle, for concept ingest - ) +bool pmFPARead(pmFPA *fpa, // FPA to read into + psFits *fits, // FITS file from which to read + psMetadata *phu, // Primary header + psDB *db // Database handle, for concept ingest + ) { - p_pmHDU *hdu = NULL; // Pixel data from FITS file + p_pmHDU *hdu = NULL; // Pixel data from FITS file // Read the PHU, if required - if (! phu) { - if (! psFitsMoveExtNum(fits, 0, false)) { - psError(PS_ERR_IO, false, "Unable to find PHU in FITS file!\n"); - return false; - } - psTrace(__func__, 7, "Reading PHU....\n"); - psMetadata *phu = psFitsReadHeader(NULL, fits); // Primary header + if (! phu) + { + if (! psFitsMoveExtNum(fits, 0, false)) + { + psError(PS_ERR_IO, false, "Unable to find PHU in FITS file!\n"); + return false; + } + psTrace(__func__, 7, "Reading PHU....\n"); + psMetadata *phu = psFitsReadHeader(NULL, fits); // Primary header } fpa->phu = phu; @@ -152,64 +170,74 @@ // Read in.... psTrace(__func__, 1, "Working on FPA...\n"); - if (fpa->hdu) { - hdu = fpa->hdu; - psTrace(__func__, 3, "Reading pixels from extension %s into FPA.\n", hdu->extname); - if (! readExtension(hdu, fits)) { - psError(PS_ERR_IO, false, "Unable to read pixels from extension %s\n", hdu->extname); - return false; - } + if (fpa->hdu) + { + hdu = fpa->hdu; + psTrace(__func__, 3, "Reading pixels from extension %s into FPA.\n", hdu->extname); + if (! readExtension(hdu, fits)) + { + psError(PS_ERR_IO, false, "Unable to read pixels from extension %s\n", hdu->extname); + return false; + } } pmFPAIngestConcepts(fpa, db); - psArray *chips = fpa->chips; // Array of chips + psArray *chips = fpa->chips; // Array of chips // Iterate over the FPA - for (int i = 0; i < chips->n; i++) { - pmChip *chip = chips->data[i]; // The chip - - // Only read chips marked "valid" - if (! chip->valid) { - psTrace(__func__, 2, "Ignoring chip %d...\n", i); - continue; - } - psTrace(__func__, 2, "Reading in chip %d...\n", i); - - if (chip->hdu) { - hdu = chip->hdu; - psTrace(__func__, 3, "Reading pixels from extension %s into chip %d.\n", hdu->extname, i); - if (! readExtension(hdu, fits)) { - psError(PS_ERR_IO, false, "Unable to read pixels from extension %s\n", hdu->extname); - return false; - } - } - pmChipIngestConcepts(chip, db); - - // Iterate over the chip - psArray *cells = chip->cells; // Array of cells - for (int j = 0; j < cells->n; j++) { - pmCell *cell = cells->data[j]; // The cell - - // Only read cells marked "valid" - if (! cell->valid) { - psTrace(__func__, 3, "Ignoring chip %d...\n", i); - continue; - } - psTrace(__func__, 3, "Reading in cell %d...\n", j); - - if (cell->hdu) { - hdu = cell->hdu; - psTrace(__func__, 5, "Reading pixels from extension %s into cell %d.\n", hdu->extname, - j); - if (! readExtension(hdu, fits)) { - psError(PS_ERR_IO, false, "Unable to read pixels from extension %s\n", - hdu->extname); - return false; - } - } - pmCellIngestConcepts(cell, db); - - psTrace(__func__, 5, "Allocating readouts for chip %d cell %d...\n", - i, j); - generateReadouts(cell, hdu); - } + for (int i = 0; i < chips->n; i++) + { + pmChip *chip = chips->data[i]; // The chip + + // Only read chips marked "valid" + if (! chip->valid) + { + psTrace(__func__, 2, "Ignoring chip %d...\n", i); + continue; + } + psTrace(__func__, 2, "Reading in chip %d...\n", i); + + if (chip->hdu) + { + hdu = chip->hdu; + psTrace(__func__, 3, "Reading pixels from extension %s into chip %d.\n", hdu->extname, i); + if (! readExtension(hdu, fits)) + { + psError(PS_ERR_IO, false, "Unable to read pixels from extension %s\n", hdu->extname); + return false; + } + } + pmChipIngestConcepts(chip, db); + + // Iterate over the chip + psArray *cells = chip->cells; // Array of cells + for (int j = 0; j < cells->n; j++) + { + pmCell *cell = cells->data[j]; // The cell + + // Only read cells marked "valid" + if (! cell->valid) + { + psTrace(__func__, 3, "Ignoring chip %d...\n", i); + continue; + } + psTrace(__func__, 3, "Reading in cell %d...\n", j); + + if (cell->hdu) + { + hdu = cell->hdu; + psTrace(__func__, 5, "Reading pixels from extension %s into cell %d.\n", hdu->extname, + j); + if (! readExtension(hdu, fits)) + { + psError(PS_ERR_IO, false, "Unable to read pixels from extension %s\n", + hdu->extname); + return false; + } + } + pmCellIngestConcepts(cell, db); + + psTrace(__func__, 5, "Allocating readouts for chip %d cell %d...\n", + i, j); + generateReadouts(cell, hdu); + } } @@ -218,7 +246,7 @@ // Translate a name from the configuration file, containing something like "%a_%d" to a real value -psString p_pmFPATranslateName(psString name, // The name to translate - pmCell *cell // The cell for which to translate - ) +psString p_pmFPATranslateName(psString name, // The name to translate + pmCell *cell // The cell for which to translate + ) { // %a is the FPA.NAME @@ -230,106 +258,127 @@ psString translation = psMemIncrRefCounter(name); // The translated string - char *temp = NULL; // Temporary string - - pmChip *chip = cell->parent; // Chip of interest - pmFPA *fpa = chip->parent; // FPA of interest + char *temp = NULL; // Temporary string + + pmChip *chip = cell->parent; // Chip of interest + pmFPA *fpa = chip->parent; // FPA of interest // FPA.NAME - if (temp = strstr(translation, "%a")) { - // This is not particularly friendly to the memory allocation, but the cache should make it OK, - // and there's not much of it anyway... - psFree(translation); - translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string - psString fpaName = psMetadataLookupString(NULL, fpa->concepts, "FPA.NAME"); // The value of FPA.NAME - psStringAppend(&translation, "%s%s", fpaName, temp + 2); - // So "translation" now contains the first part, the replaced string, and the last part. + if (temp = strstr(translation, "%a")) + { + // This is not particularly friendly to the memory allocation, but the cache should make it OK, + // and there's not much of it anyway... + psFree(translation); + translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string + psString fpaName = psMetadataLookupString(NULL, fpa->concepts, "FPA.NAME"); // The value of FPA.NAME + psStringAppend(&translation, "%s%s", fpaName, temp + 2); + // So "translation" now contains the first part, the replaced string, and the last part. } // CHIP.NAME - if (temp = strstr(translation, "%b")) { - // This is not particularly friendly to the memory allocation, but the cache should make it OK, - // and there's not much of it anyway... - psFree(translation); - translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string - psString chipName = psMetadataLookupString(NULL, chip->concepts, "CHIP.NAME"); // CHIP.NAME's value - psStringAppend(&translation, "%s%s", chipName, temp + 2); - // So "translation" now contains the first part, the replaced string, and the last part. + if (temp = strstr(translation, "%b")) + { + // This is not particularly friendly to the memory allocation, but the cache should make it OK, + // and there's not much of it anyway... + psFree(translation); + translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string + psString chipName = psMetadataLookupString(NULL, chip->concepts, "CHIP.NAME"); // CHIP.NAME's value + psStringAppend(&translation, "%s%s", chipName, temp + 2); + // So "translation" now contains the first part, the replaced string, and the last part. } // CELL.NAME - if (temp = strstr(translation, "%c")) { - // This is not particularly friendly to the memory allocation, but the cache should make it OK, - // and there's not much of it anyway... - psFree(translation); - translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string - psString cellName = psMetadataLookupString(NULL, cell->concepts, "CELL.NAME"); // CELL.NAME's value - psStringAppend(&translation, "%s%s", cellName, temp + 2); - // So "translation" now contains the first part, the replaced string, and the last part. + if (temp = strstr(translation, "%c")) + { + // This is not particularly friendly to the memory allocation, but the cache should make it OK, + // and there's not much of it anyway... + psFree(translation); + translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string + psString cellName = psMetadataLookupString(NULL, cell->concepts, "CELL.NAME"); // CELL.NAME's value + psStringAppend(&translation, "%s%s", cellName, temp + 2); + // So "translation" now contains the first part, the replaced string, and the last part. } // Chip number - if (temp = strstr(translation, "%d")) { - // This is not particularly friendly to the memory allocation, but the cache should make it OK, - // and there's not much of it anyway... - psFree(translation); - translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string - // Search for the pointer to get the chip number - int chipNum = -1; - psArray *chips = fpa->chips; // The array of chips - for (int i = 0; i < chips->n && chipNum < 0; i++) { - if (chips->data[i] == chip) { - chipNum = i; - } - } - if (chipNum < 0) { - psError(PS_ERR_IO, true, "Unable to find chip to get name: %s\n", name); - // Try to muddle on by leaving the number out - psStringAppend(&translation, "%s", temp + 2); - } else { - psStringAppend(&translation, "%d%s", chipNum, temp + 2); - } - // So "translation" now contains the first part, the replaced string, and the last part. + if (temp = strstr(translation, "%d")) + { + // This is not particularly friendly to the memory allocation, but the cache should make it OK, + // and there's not much of it anyway... + psFree(translation); + translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string + // Search for the pointer to get the chip number + int chipNum = -1; + psArray *chips = fpa->chips; // The array of chips + for (int i = 0; i < chips->n && chipNum < 0; i++) + { + if (chips->data[i] == chip) + { + chipNum = i; + } + } + if (chipNum < 0) + { + psError(PS_ERR_IO, true, "Unable to find chip to get name: %s\n", name); + // Try to muddle on by leaving the number out + psStringAppend(&translation, "%s", temp + 2); + } + else + { + psStringAppend(&translation, "%d%s", chipNum, temp + 2); + } + // So "translation" now contains the first part, the replaced string, and the last part. } // Cell number - if (temp = strstr(translation, "%e")) { - // This is not particularly friendly to the memory allocation, but the cache should make it OK, - // and there's not much of it anyway... - psFree(translation); - translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string - // Search for the pointer to get the cell number - int cellNum = -1; - psArray *cells = chip->cells; // The array of cells - for (int i = 0; i < cells->n && cellNum < 0; i++) { - if (cells->data[i] == cell) { - cellNum = i; - } - } - if (cellNum < 0) { - psError(PS_ERR_IO, true, "Unable to find cell to get name: %s\n", name); - // Try to muddle on by leaving the number out - psStringAppend(&translation, "%s", temp + 2); - } else { - psStringAppend(&translation, "%d%s", cellNum, temp + 2); - } - // So "translation" now contains the first part, the replaced string, and the last part. + if (temp = strstr(translation, "%e")) + { + // This is not particularly friendly to the memory allocation, but the cache should make it OK, + // and there's not much of it anyway... + psFree(translation); + translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string + // Search for the pointer to get the cell number + int cellNum = -1; + psArray *cells = chip->cells; // The array of cells + for (int i = 0; i < cells->n && cellNum < 0; i++) + { + if (cells->data[i] == cell) + { + cellNum = i; + } + } + if (cellNum < 0) + { + psError(PS_ERR_IO, true, "Unable to find cell to get name: %s\n", name); + // Try to muddle on by leaving the number out + psStringAppend(&translation, "%s", temp + 2); + } + else + { + psStringAppend(&translation, "%d%s", cellNum, temp + 2); + } + // So "translation" now contains the first part, the replaced string, and the last part. } // Extension name - if (temp = strstr(translation, "%f")) { - // This is not particularly friendly to the memory allocation, but the cache should make it OK, - // and there's not much of it anyway... - psFree(translation); - translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string - const char *extname = NULL; - if (cell->hdu) { - extname = cell->hdu->extname; - } else if (chip->hdu) { - extname = chip->hdu->extname; - } else if (fpa->hdu) { - extname = fpa->hdu->extname; - } - psStringAppend(&translation, "%s%s", extname, temp + 2); - // So "translation" now contains the first part, the replaced string, and the last part. + if (temp = strstr(translation, "%f")) + { + // This is not particularly friendly to the memory allocation, but the cache should make it OK, + // and there's not much of it anyway... + psFree(translation); + translation = psStringNCopy(name, strlen(name) - strlen(temp)); // Copy first part of string + const char *extname = NULL; + if (cell->hdu) + { + extname = cell->hdu->extname; + } + else if (chip->hdu) + { + extname = chip->hdu->extname; + } + else if (fpa->hdu) + { + extname = fpa->hdu->extname; + } + psStringAppend(&translation, "%s%s", extname, temp + 2); + // So "translation" now contains the first part, the replaced string, and the last part. } @@ -338,144 +387,171 @@ // Read a mask into the FPA -bool pmFPAReadMask(pmFPA *fpa, // FPA to read into - psFits *source // Source FITS file (for the original data) - ) +bool pmFPAReadMask(pmFPA *fpa, // FPA to read into + psFits *source // Source FITS file (for the original data) + ) { const psMetadata *camera = fpa->camera; // Camera configuration for FPA - bool mdok = false; // Status of MD lookup + bool mdok = false; // Status of MD lookup // Get the required information from the camera configuration psMetadata *supps = psMetadataLookupMD(&mdok, camera, "SUPPLEMENTARY"); // Rules for supplementary data - if (! mdok || ! supps) { - psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); - return false; + if (! mdok || ! supps) + { + psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); + return false; } psString sourceType = psMetadataLookupString(&mdok, supps, "MASK.SOURCE"); // Type of source: EXT | FILE - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find MASK.SOURCE in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find MASK.SOURCE in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } psString name = psMetadataLookupString(&mdok, supps, "MASK.NAME"); // Name of mask - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find MASK.NAME in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find MASK.NAME in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } // Go through the FPA to each cell/readout to get the mask - p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the mask - psArray *chips = fpa->chips; // Array of chips - for (int chipNum = 0; chipNum < chips->n; chipNum++) { - pmChip *chip = chips->data[chipNum]; // The current chip of interest - if (chip->valid) { - if (chip->hdu) { - hdu = chip->hdu; - } - psArray *cells = chip->cells; // Array of cells - for (int cellNum = 0; cellNum < cells->n; cellNum++) { - pmCell *cell = cells->data[cellNum]; // The current cell of interest - if (cell->valid) { - if (cell->hdu) { - hdu = cell->hdu; - } - - // Now, need to find out where to get the pixels - psFits *maskSource = source; // Source of mask image - if (strcasecmp(sourceType, "FILE") == 0) { - // Source is a file (with optional extension, e.g., "myMaskFile.fits:thisExt" - psString filenameExt = p_pmFPATranslateName(name, cell); - char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn - psString filename = NULL; // The filename - psString extname = NULL;// The extenstion name - if (colon) { - filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); - if (strlen(colon) > 1) { - extname = psStringCopy(colon + 1); - } - } else { - filename = psMemIncrRefCounter(filenameExt); - } - - maskSource = psFitsAlloc(filename); - if (extname) { - if (! psFitsMoveExtName(maskSource, extname)) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to find extension %s to read mask.\n", - extname); - return false; - } - } - psFree(filename); - psFree(extname); - psFree(filenameExt); - } else if (strncasecmp(sourceType, "EXT", 3) == 0) { - // Source is an extension in the original file - psString extname = p_pmFPATranslateName(name, cell); - psFitsMoveExtName(maskSource, extname); - } - - // We've arrived where the pixels are. Now we need to read them in. - psMetadata *header = psFitsReadHeader(NULL, maskSource); // The header - bool mdStatus = false; - int nAxis = psMetadataLookupS32(&mdStatus, header, "NAXIS"); - if (!mdStatus) { - psLogMsg(__func__, PS_LOG_WARN, "There is no NAXIS keyword in the FITS header for " - "mask (%s)!\n", name); - } - if (nAxis != 2 && nAxis != 3) { - psLogMsg(__func__, PS_LOG_WARN, "Image is not 2- or 3-dimensional --- reading into " - "a single image anyway.\n"); - } - - int numPlanes = 1; // Number of planes - if (nAxis == 3) { - numPlanes = psMetadataLookupS32(&mdStatus, header, "NAXIS3"); - if (!mdStatus) { - psError(PS_ERR_IO, false, "Unable to read NAXIS3 for 3-dimensional image!\n"); - // Try to proceed by taking only the first plane - numPlanes = 1; - } - if (numPlanes != 1 && numPlanes != cell->readouts->n) { - psError(PS_ERR_IO, false, "Number of masks (%d) does not match number of " - "readouts (%d)\n", numPlanes, cell->readouts->n); - // Try to proceed by taking only the first plane - numPlanes = 1; - } - } - - hdu->masks = psArrayAlloc(hdu->images->n); - - // Read each plane into the array - psArray *readouts = cell->readouts; // The array of readouts - for (int i = 0; i < hdu->masks->n; i++) { - psImage *mask = NULL; // The mask to be added - if (i < numPlanes) { - // Read the mask from the file - psTrace(__func__, 9, "Reading plane %d\n", i); - psRegion region = {0, 0, 0, 0}; - mask = psFitsReadImage(NULL, maskSource, region, i); - } else { - // One mask in the file is provided for all planes in the original image - psTrace(__func__, 9, "Copying plane 0 into plane %d\n", i); - psImage *original = hdu->masks->data[0]; - mask = psImageCopy(NULL, original, original->type.type); - } - hdu->masks->data[0] = mask; - pmReadout *readout = readouts->data[i]; - readout->mask = mask; - // Check the dimensions - // XXX: Perhaps this check should be against the CELL.TRIMSEC, not the image size? - if (mask->numCols < readout->image->numCols || - mask->numRows < readout->image->numRows) - { - psError(PS_ERR_IO, false, "Mask size (%dx%d) not compatible with image (%dx%d)\n", - mask->numCols, mask->numRows, readout->image->numCols, - readout->image->numRows); - return false; - } - } // Iterating over readouts - } // Valid cells - } // Iterating over cells - } // Valid chips + p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the mask + psArray *chips = fpa->chips; // Array of chips + for (int chipNum = 0; chipNum < chips->n; chipNum++) + { + pmChip *chip = chips->data[chipNum]; // The current chip of interest + if (chip->valid) + { + if (chip->hdu) + { + hdu = chip->hdu; + } + psArray *cells = chip->cells; // Array of cells + for (int cellNum = 0; cellNum < cells->n; cellNum++) + { + pmCell *cell = cells->data[cellNum]; // The current cell of interest + if (cell->valid) + { + if (cell->hdu) + { + hdu = cell->hdu; + } + + // Now, need to find out where to get the pixels + psFits *maskSource = source; // Source of mask image + if (strcasecmp(sourceType, "FILE") == 0) + { + // Source is a file (with optional extension, e.g., "myMaskFile.fits:thisExt" + psString filenameExt = p_pmFPATranslateName(name, cell); + char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn + psString filename = NULL; // The filename + psString extname = NULL; // The extenstion name + if (colon) + { + filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); + if (strlen(colon) > 1) + { + extname = psStringCopy(colon + 1); + } + } + else + { + filename = psMemIncrRefCounter(filenameExt); + } + + maskSource = psFitsAlloc(filename); + if (extname) + { + if (! psFitsMoveExtName(maskSource, extname)) + { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find extension %s to read mask.\n", + extname); + return false; + } + } + psFree(filename); + psFree(extname); + psFree(filenameExt); + } + else if (strncasecmp(sourceType, "EXT", 3) == 0) + { + // Source is an extension in the original file + psString extname = p_pmFPATranslateName(name, cell); + psFitsMoveExtName(maskSource, extname); + } + + // We've arrived where the pixels are. Now we need to read them in. + psMetadata *header = psFitsReadHeader(NULL, maskSource); // The header + bool mdStatus = false; + int nAxis = psMetadataLookupS32(&mdStatus, header, "NAXIS"); + if (!mdStatus) + { + psLogMsg(__func__, PS_LOG_WARN, "There is no NAXIS keyword in the FITS header for " + "mask (%s)!\n", name); + } + if (nAxis != 2 && nAxis != 3) + { + psLogMsg(__func__, PS_LOG_WARN, "Image is not 2- or 3-dimensional --- reading into " + "a single image anyway.\n"); + } + + int numPlanes = 1; // Number of planes + if (nAxis == 3) + { + numPlanes = psMetadataLookupS32(&mdStatus, header, "NAXIS3"); + if (!mdStatus) + { + psError(PS_ERR_IO, false, "Unable to read NAXIS3 for 3-dimensional image!\n"); + // Try to proceed by taking only the first plane + numPlanes = 1; + } + if (numPlanes != 1 && numPlanes != cell->readouts->n) + { + psError(PS_ERR_IO, false, "Number of masks (%d) does not match number of " + "readouts (%d)\n", numPlanes, cell->readouts->n); + // Try to proceed by taking only the first plane + numPlanes = 1; + } + } + + hdu->masks = psArrayAlloc(hdu->images->n); + + // Read each plane into the array + psArray *readouts = cell->readouts; // The array of readouts + for (int i = 0; i < hdu->masks->n; i++) + { + psImage *mask = NULL; // The mask to be added + if (i < numPlanes) + { + // Read the mask from the file + psTrace(__func__, 9, "Reading plane %d\n", i); + psRegion region = {0, 0, 0, 0}; + mask = psFitsReadImage(NULL, maskSource, region, i); + } + else + { + // One mask in the file is provided for all planes in the original image + psTrace(__func__, 9, "Copying plane 0 into plane %d\n", i); + psImage *original = hdu->masks->data[0]; + mask = psImageCopy(NULL, original, original->type.type); + } + hdu->masks->data[0] = mask; + pmReadout *readout = readouts->data[i]; + readout->mask = mask; + // Check the dimensions + // XXX: Perhaps this check should be against the CELL.TRIMSEC, not the image size? + if (mask->numCols < readout->image->numCols || + mask->numRows < readout->image->numRows) + { + psError(PS_ERR_IO, false, "Mask size (%dx%d) not compatible with image (%dx%d)\n", + mask->numCols, mask->numRows, readout->image->numCols, + readout->image->numRows); + return false; + } + } // Iterating over readouts + } // Valid cells + } // Iterating over cells + } // Valid chips } // Iterating over chips @@ -486,144 +562,171 @@ // Read a mask into the FPA // This is just a copy of the above pmFPAReadMask, replacing "mask" with "weight" throughout. -bool pmFPAReadWeight(pmFPA *fpa, // FPA to read into - psFits *source // Source FITS file (for the original data) - ) +bool pmFPAReadWeight(pmFPA *fpa, // FPA to read into + psFits *source // Source FITS file (for the original data) + ) { const psMetadata *camera = fpa->camera; // Camera configuration for FPA - bool mdok = false; // Status of MD lookup + bool mdok = false; // Status of MD lookup // Get the required information from the camera configuration psMetadata *supps = psMetadataLookupMD(&mdok, camera, "SUPPLEMENTARY"); // Rules for supplementary data - if (! mdok || ! supps) { - psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); - return false; + if (! mdok || ! supps) + { + psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); + return false; } psString sourceType = psMetadataLookupString(&mdok, supps, "WEIGHT.SOURCE"); // Type of source: EXT | FILE - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find WEIGHT.SOURCE in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find WEIGHT.SOURCE in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } psString name = psMetadataLookupString(&mdok, supps, "WEIGHT.NAME"); // Name of weight - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find WEIGHT.NAME in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find WEIGHT.NAME in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } // Go through the FPA to each cell/readout to get the weight - p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the weight - psArray *chips = fpa->chips; // Array of chips - for (int chipNum = 0; chipNum < chips->n; chipNum++) { - pmChip *chip = chips->data[chipNum]; // The current chip of interest - if (chip->valid) { - if (chip->hdu) { - hdu = chip->hdu; - } - psArray *cells = chip->cells; // Array of cells - for (int cellNum = 0; cellNum < cells->n; cellNum++) { - pmCell *cell = cells->data[cellNum]; // The current cell of interest - if (cell->valid) { - if (cell->hdu) { - hdu = cell->hdu; - } - - // Now, need to find out where to get the pixels - psFits *weightSource = source; // Source of weight image - if (strcasecmp(sourceType, "FILE") == 0) { - // Source is a file (with optional extension, e.g., "myWeightFile.fits:thisExt" - psString filenameExt = p_pmFPATranslateName(name, cell); - char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn - psString filename = NULL; // The filename - psString extname = NULL;// The extenstion name - if (colon) { - filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); - if (strlen(colon) > 1) { - extname = psStringCopy(colon + 1); - } - } else { - filename = psMemIncrRefCounter(filenameExt); - } - - weightSource = psFitsAlloc(filename); - if (extname) { - if (! psFitsMoveExtName(weightSource, extname)) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to find extension %s to read " - "weight.\n", extname); - return false; - } - } - psFree(filename); - psFree(extname); - psFree(filenameExt); - } else if (strncasecmp(sourceType, "EXT", 3) == 0) { - // Source is an extension in the original file - psString extname = p_pmFPATranslateName(name, cell); - psFitsMoveExtName(weightSource, extname); - } - - // We've arrived where the pixels are. Now we need to read them in. - psMetadata *header = psFitsReadHeader(NULL, weightSource); // The header - bool mdStatus = false; - int nAxis = psMetadataLookupS32(&mdStatus, header, "NAXIS"); - if (!mdStatus) { - psLogMsg(__func__, PS_LOG_WARN, "There is no NAXIS keyword in the FITS header for " - "weight (%s)!\n", name); - } - if (nAxis != 2 && nAxis != 3) { - psLogMsg(__func__, PS_LOG_WARN, "Image is not 2- or 3-dimensional --- reading into " - "a single image anyway.\n"); - } - - int numPlanes = 1; // Number of planes - if (nAxis == 3) { - numPlanes = psMetadataLookupS32(&mdStatus, header, "NAXIS3"); - if (!mdStatus) { - psError(PS_ERR_IO, false, "Unable to read NAXIS3 for 3-dimensional image!\n"); - // Try to proceed by taking only the first plane - numPlanes = 1; - } - if (numPlanes != 1 && numPlanes != cell->readouts->n) { - psError(PS_ERR_IO, false, "Number of weights (%d) does not match number of " - "readouts (%d)\n", numPlanes, cell->readouts->n); - // Try to proceed by taking only the first plane - numPlanes = 1; - } - } - - hdu->weights = psArrayAlloc(hdu->images->n); - - // Read each plane into the array - psArray *readouts = cell->readouts; // The array of readouts - for (int i = 0; i < hdu->weights->n; i++) { - psImage *weight = NULL; // The weight to be added - if (i < numPlanes) { - // Read the weight from the file - psTrace(__func__, 9, "Reading plane %d\n", i); - psRegion region = {0, 0, 0, 0}; - weight = psFitsReadImage(NULL, weightSource, region, i); - } else { - // One weight in the file is provided for all planes in the original image - psTrace(__func__, 9, "Copying plane 0 into plane %d\n", i); - psImage *original = hdu->weights->data[0]; - weight = psImageCopy(NULL, original, original->type.type); - } - hdu->weights->data[0] = weight; - pmReadout *readout = readouts->data[i]; - readout->weight = weight; - // Check the dimensions - // XXX: Perhaps this check should be against the CELL.TRIMSEC, not the image size? - if (weight->numCols < readout->image->numCols || - weight->numRows < readout->image->numRows) - { - psError(PS_ERR_IO, false, "Weight size (%dx%d) not compatible with image " - "(%dx%d)\n", weight->numCols, weight->numRows, readout->image->numCols, - readout->image->numRows); - return false; - } - } // Iterating over readouts - } // Valid cells - } // Iterating over cells - } // Valid chips + p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the weight + psArray *chips = fpa->chips; // Array of chips + for (int chipNum = 0; chipNum < chips->n; chipNum++) + { + pmChip *chip = chips->data[chipNum]; // The current chip of interest + if (chip->valid) + { + if (chip->hdu) + { + hdu = chip->hdu; + } + psArray *cells = chip->cells; // Array of cells + for (int cellNum = 0; cellNum < cells->n; cellNum++) + { + pmCell *cell = cells->data[cellNum]; // The current cell of interest + if (cell->valid) + { + if (cell->hdu) + { + hdu = cell->hdu; + } + + // Now, need to find out where to get the pixels + psFits *weightSource = source; // Source of weight image + if (strcasecmp(sourceType, "FILE") == 0) + { + // Source is a file (with optional extension, e.g., "myWeightFile.fits:thisExt" + psString filenameExt = p_pmFPATranslateName(name, cell); + char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn + psString filename = NULL; // The filename + psString extname = NULL; // The extenstion name + if (colon) + { + filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); + if (strlen(colon) > 1) + { + extname = psStringCopy(colon + 1); + } + } + else + { + filename = psMemIncrRefCounter(filenameExt); + } + + weightSource = psFitsAlloc(filename); + if (extname) + { + if (! psFitsMoveExtName(weightSource, extname)) + { + psLogMsg(__func__, PS_LOG_WARN, "Unable to find extension %s to read " + "weight.\n", extname); + return false; + } + } + psFree(filename); + psFree(extname); + psFree(filenameExt); + } + else if (strncasecmp(sourceType, "EXT", 3) == 0) + { + // Source is an extension in the original file + psString extname = p_pmFPATranslateName(name, cell); + psFitsMoveExtName(weightSource, extname); + } + + // We've arrived where the pixels are. Now we need to read them in. + psMetadata *header = psFitsReadHeader(NULL, weightSource); // The header + bool mdStatus = false; + int nAxis = psMetadataLookupS32(&mdStatus, header, "NAXIS"); + if (!mdStatus) + { + psLogMsg(__func__, PS_LOG_WARN, "There is no NAXIS keyword in the FITS header for " + "weight (%s)!\n", name); + } + if (nAxis != 2 && nAxis != 3) + { + psLogMsg(__func__, PS_LOG_WARN, "Image is not 2- or 3-dimensional --- reading into " + "a single image anyway.\n"); + } + + int numPlanes = 1; // Number of planes + if (nAxis == 3) + { + numPlanes = psMetadataLookupS32(&mdStatus, header, "NAXIS3"); + if (!mdStatus) + { + psError(PS_ERR_IO, false, "Unable to read NAXIS3 for 3-dimensional image!\n"); + // Try to proceed by taking only the first plane + numPlanes = 1; + } + if (numPlanes != 1 && numPlanes != cell->readouts->n) + { + psError(PS_ERR_IO, false, "Number of weights (%d) does not match number of " + "readouts (%d)\n", numPlanes, cell->readouts->n); + // Try to proceed by taking only the first plane + numPlanes = 1; + } + } + + hdu->weights = psArrayAlloc(hdu->images->n); + + // Read each plane into the array + psArray *readouts = cell->readouts; // The array of readouts + for (int i = 0; i < hdu->weights->n; i++) + { + psImage *weight = NULL; // The weight to be added + if (i < numPlanes) + { + // Read the weight from the file + psTrace(__func__, 9, "Reading plane %d\n", i); + psRegion region = {0, 0, 0, 0}; + weight = psFitsReadImage(NULL, weightSource, region, i); + } + else + { + // One weight in the file is provided for all planes in the original image + psTrace(__func__, 9, "Copying plane 0 into plane %d\n", i); + psImage *original = hdu->weights->data[0]; + weight = psImageCopy(NULL, original, original->type.type); + } + hdu->weights->data[0] = weight; + pmReadout *readout = readouts->data[i]; + readout->weight = weight; + // Check the dimensions + // XXX: Perhaps this check should be against the CELL.TRIMSEC, not the image size? + if (weight->numCols < readout->image->numCols || + weight->numRows < readout->image->numRows) + { + psError(PS_ERR_IO, false, "Weight size (%dx%d) not compatible with image " + "(%dx%d)\n", weight->numCols, weight->numRows, readout->image->numCols, + readout->image->numRows); + return false; + } + } // Iterating over readouts + } // Valid cells + } // Iterating over cells + } // Valid chips } // Iterating over chips Index: /branches/neb/archive/scripts/src/phase2/pmFPAWrite.c =================================================================== --- /branches/neb/archive/scripts/src/phase2/pmFPAWrite.c (revision 5647) +++ /branches/neb/archive/scripts/src/phase2/pmFPAWrite.c (revision 5648) @@ -7,12 +7,13 @@ #include "pmFPARead.h" -static bool writeHDU(psFits *fits, // FITS file to which to write - p_pmHDU *hdu // Pixel data to write - ) +static bool writeHDU(psFits *fits, // FITS file to which to write + p_pmHDU *hdu // Pixel data to write + ) { - bool status = true; // Status of write, to return - for (int i = 0; i < hdu->images->n; i++) { - status &= psFitsWriteImage(fits, hdu->header, hdu->images->data[i], i); - // XXX: Insert here the writing on mask and weight images + bool status = true; // Status of write, to return + for (int i = 0; i < hdu->images->n; i++) + { + status &= psFitsWriteImage(fits, hdu->header, hdu->images->data[i], i); + // XXX: Insert here the writing on mask and weight images } @@ -21,49 +22,55 @@ -bool pmFPAWrite(psFits *fits, // FITS file to which to write - pmFPA *fpa, // FPA to write - psDB *db // Database to update - ) +bool pmFPAWrite(psFits *fits, // FITS file to which to write + pmFPA *fpa, // FPA to write + psDB *db // Database to update + ) { - bool status = true; // Status of writing, to return + bool status = true; // Status of writing, to return pmFPAOutgestConcepts(fpa, db); // Write the primary header - if (fpa->phu) { - status &= psFitsMoveExtNum(fits, 0, false); - status &= psFitsWriteHeader(fpa->phu, fits); - } - - psArray *chips = fpa->chips; // Array of component chips - for (int i = 0; i < chips->n; i++) { - pmChip *chip = chips->data[i]; // The component chip - if (chip->valid) { - pmChipOutgestConcepts(chip, db); - - psArray *cells = chip->cells; // Array of component cells - for (int j = 0; j < cells->n; j++) { - pmCell *cell = cells->data[j]; // The component cell - if (cell->valid) { - pmCellOutgestConcepts(cell, db); - - if (cell->hdu && strlen(cell->hdu->extname) > 0) { - status &= writeHDU(fits, cell->hdu); - } - } - } - - if (chip->hdu && strlen(chip->hdu->extname) > 0) { - status &= writeHDU(fits, chip->hdu); - } - } - - } - - if (fpa->hdu && strlen(fpa->hdu->extname) > 0) { - status &= writeHDU(fits, fpa->hdu); - } - - + if (fpa->phu) + { + status &= psFitsMoveExtNum(fits, 0, false); + status &= psFitsWriteHeader(fpa->phu, fits); + } + + psArray *chips = fpa->chips; // Array of component chips + for (int i = 0; i < chips->n; i++) + { + pmChip *chip = chips->data[i]; // The component chip + if (chip->valid) + { + pmChipOutgestConcepts(chip, db); + + psArray *cells = chip->cells; // Array of component cells + for (int j = 0; j < cells->n; j++) + { + pmCell *cell = cells->data[j]; // The component cell + if (cell->valid) + { + pmCellOutgestConcepts(cell, db); + + if (cell->hdu && strlen(cell->hdu->extname) > 0) + { + status &= writeHDU(fits, cell->hdu); + } + } + } + + if (chip->hdu && strlen(chip->hdu->extname) > 0) + { + status &= writeHDU(fits, chip->hdu); + } + } + + } + + if (fpa->hdu && strlen(fpa->hdu->extname) > 0) + { + status &= writeHDU(fits, fpa->hdu); + } return status; @@ -71,101 +78,123 @@ -bool pmFPAWriteMask(pmFPA *fpa, // FPA containing mask to write - psFits *fits // FITS file for image - ) +bool pmFPAWriteMask(pmFPA *fpa, // FPA containing mask to write + psFits *fits // FITS file for image + ) { const psMetadata *camera = fpa->camera; // Camera configuration for FPA - bool mdok = false; // Status of MD lookup + bool mdok = false; // Status of MD lookup // Get the required information from the camera configuration psMetadata *supps = psMetadataLookupMD(&mdok, camera, "SUPPLEMENTARY"); // Rules for supplementary data - if (! mdok || ! supps) { - psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); - return false; + if (! mdok || ! supps) + { + psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); + return false; } psString sourceType = psMetadataLookupString(&mdok, supps, "MASK.SOURCE"); // Type of source: EXT | FILE - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find MASK.SOURCE in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find MASK.SOURCE in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } psString name = psMetadataLookupString(&mdok, supps, "MASK.NAME"); // Name of mask - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find MASK.NAME in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find MASK.NAME in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } // Go through the FPA to each cell/readout to get the mask - p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the mask - psArray *chips = fpa->chips; // Array of chips - for (int chipNum = 0; chipNum < chips->n; chipNum++) { - pmChip *chip = chips->data[chipNum]; // The current chip of interest - if (chip->valid) { - if (chip->hdu) { - hdu = chip->hdu; - } - psArray *cells = chip->cells; // Array of cells - for (int cellNum = 0; cellNum < cells->n; cellNum++) { - pmCell *cell = cells->data[cellNum]; // The current cell of interest - if (cell->valid) { - if (cell->hdu) { - hdu = cell->hdu; - } - - // Now, need to find out where to write the pixels - psFits *maskDest = psMemIncrRefCounter(fits); // Destination of mask image - psMetadata *header = psMetadataAlloc(); // A dummy header, containing the extension name - if (strcasecmp(sourceType, "FILE") == 0) { - // Source is a file (with optional extension, e.g., "myMaskFile.fits:thisExt" - psString filenameExt = p_pmFPATranslateName(name, cell); - char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn - psString filename = NULL; // The filename - psString extname = NULL;// The extenstion name - if (colon) { - filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); - if (strlen(colon) > 1) { - extname = psStringCopy(colon + 1); - } - } else { - filename = psMemIncrRefCounter(filenameExt); - } - - psFree(maskDest); - maskDest = psFitsAlloc(filename); - if (extname) { - psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); - } - psFree(filename); - psFree(extname); - psFree(filenameExt); - } else if (strncasecmp(sourceType, "EXT", 3) == 0) { - // Source is an extension in the original file - psString extname = p_pmFPATranslateName(name, cell); - psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); - psFree(extname); - } - - // We've arrived where the pixels are. Now we need to write them out. - psArray *readouts = cell->readouts; // The array of readouts - for (int readNum = 0; readNum < readouts->n; readNum++) { - pmReadout *readout = readouts->data[readNum]; // The readout of interest - if (! readout->mask) { - psLogMsg(__func__, PS_LOG_WARN, "No mask to write out in %d,%d,%d\n", - chipNum, cellNum, readNum); - } else { - // XXX: Need to add the extname to the existing header - if (! psFitsWriteImage(maskDest, header, readout->mask, readNum)) { - psError(PS_ERR_IO, false, "Unable to write mask plane %d in extension %s\n", - readNum, hdu->extname); - return false; - } - } - } // Iterating over readouts - psFree(header); - psFree(maskDest); - } // Valid cells - } // Iterating over cells - } // Valid chips + p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the mask + psArray *chips = fpa->chips; // Array of chips + for (int chipNum = 0; chipNum < chips->n; chipNum++) + { + pmChip *chip = chips->data[chipNum]; // The current chip of interest + if (chip->valid) + { + if (chip->hdu) + { + hdu = chip->hdu; + } + psArray *cells = chip->cells; // Array of cells + for (int cellNum = 0; cellNum < cells->n; cellNum++) + { + pmCell *cell = cells->data[cellNum]; // The current cell of interest + if (cell->valid) + { + if (cell->hdu) + { + hdu = cell->hdu; + } + + // Now, need to find out where to write the pixels + psFits *maskDest = psMemIncrRefCounter(fits); // Destination of mask image + psMetadata *header = psMetadataAlloc(); // A dummy header, containing the extension name + if (strcasecmp(sourceType, "FILE") == 0) + { + // Source is a file (with optional extension, e.g., "myMaskFile.fits:thisExt" + psString filenameExt = p_pmFPATranslateName(name, cell); + char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn + psString filename = NULL; // The filename + psString extname = NULL; // The extenstion name + if (colon) + { + filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); + if (strlen(colon) > 1) + { + extname = psStringCopy(colon + 1); + } + } + else + { + filename = psMemIncrRefCounter(filenameExt); + } + + psFree(maskDest); + maskDest = psFitsAlloc(filename); + if (extname) + { + psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); + } + psFree(filename); + psFree(extname); + psFree(filenameExt); + } + else if (strncasecmp(sourceType, "EXT", 3) == 0) + { + // Source is an extension in the original file + psString extname = p_pmFPATranslateName(name, cell); + psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); + psFree(extname); + } + + // We've arrived where the pixels are. Now we need to write them out. + psArray *readouts = cell->readouts; // The array of readouts + for (int readNum = 0; readNum < readouts->n; readNum++) + { + pmReadout *readout = readouts->data[readNum]; // The readout of interest + if (! readout->mask) + { + psLogMsg(__func__, PS_LOG_WARN, "No mask to write out in %d,%d,%d\n", + chipNum, cellNum, readNum); + } + else + { + // XXX: Need to add the extname to the existing header + if (! psFitsWriteImage(maskDest, header, readout->mask, readNum)) + { + psError(PS_ERR_IO, false, "Unable to write mask plane %d in extension %s\n", + readNum, hdu->extname); + return false; + } + } + } // Iterating over readouts + psFree(header); + psFree(maskDest); + } // Valid cells + } // Iterating over cells + } // Valid chips } // Iterating over chips @@ -174,100 +203,122 @@ -bool pmFPAWriteWeight(pmFPA *fpa, // FPA containing mask to write - psFits *fits // FITS file for image - ) +bool pmFPAWriteWeight(pmFPA *fpa, // FPA containing mask to write + psFits *fits // FITS file for image + ) { const psMetadata *camera = fpa->camera; // Camera configuration for FPA - bool mdok = false; // Status of MD lookup + bool mdok = false; // Status of MD lookup // Get the required information from the camera configuration psMetadata *supps = psMetadataLookupMD(&mdok, camera, "SUPPLEMENTARY"); // Rules for supplementary data - if (! mdok || ! supps) { - psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); - return false; + if (! mdok || ! supps) + { + psError(PS_ERR_IO, false, "Unable to find SUPPLEMENTARY in camera configuration!\n"); + return false; } psString sourceType = psMetadataLookupString(&mdok, supps, "WEIGHT.SOURCE"); // Type of source: EXT | FILE - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find WEIGHT.SOURCE in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find WEIGHT.SOURCE in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } psString name = psMetadataLookupString(&mdok, supps, "WEIGHT.NAME"); // Name of weight - if (! mdok || strlen(sourceType) <= 0) { - psError(PS_ERR_IO, false, "Unable to find WEIGHT.NAME in SUPPLEMENTARY section of camera " - "configuration!\n"); - return false; + if (! mdok || strlen(sourceType) <= 0) + { + psError(PS_ERR_IO, false, "Unable to find WEIGHT.NAME in SUPPLEMENTARY section of camera " + "configuration!\n"); + return false; } // Go through the FPA to each cell/readout to get the weight - p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the weight - psArray *chips = fpa->chips; // Array of chips - for (int chipNum = 0; chipNum < chips->n; chipNum++) { - pmChip *chip = chips->data[chipNum]; // The current chip of interest - if (chip->valid) { - if (chip->hdu) { - hdu = chip->hdu; - } - psArray *cells = chip->cells; // Array of cells - for (int cellNum = 0; cellNum < cells->n; cellNum++) { - pmCell *cell = cells->data[cellNum]; // The current cell of interest - if (cell->valid) { - if (cell->hdu) { - hdu = cell->hdu; - } - - // Now, need to find out where to write the pixels - psFits *weightDest = psMemIncrRefCounter(fits); // Destination of weight image - psMetadata *header = psMetadataAlloc(); // A dummy header, containing the extension name - if (strcasecmp(sourceType, "FILE") == 0) { - // Source is a file (with optional extension, e.g., "myWeightFile.fits:thisExt" - psString filenameExt = p_pmFPATranslateName(name, cell); - char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn - psString filename = NULL; // The filename - psString extname = NULL;// The extenstion name - if (colon) { - filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); - if (strlen(colon) > 1) { - extname = psStringCopy(colon + 1); - } - } else { - filename = psMemIncrRefCounter(filenameExt); - } - - psFree(weightDest); - weightDest = psFitsAlloc(filename); - if (extname) { - psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); - } - psFree(filename); - psFree(extname); - psFree(filenameExt); - } else if (strncasecmp(sourceType, "EXT", 3) == 0) { - // Source is an extension in the original file - psString extname = p_pmFPATranslateName(name, cell); - psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); - psFree(extname); - } - - // We've arrived where the pixels are. Now we need to write them out. - psArray *readouts = cell->readouts; // The array of readouts - for (int readNum = 0; readNum < readouts->n; readNum++) { - pmReadout *readout = readouts->data[readNum]; // The readout of interest - if (! readout->weight) { - psLogMsg(__func__, PS_LOG_WARN, "No weight image to write out in %d,%d,%d\n", - chipNum, cellNum, readNum); - } else { - if (! psFitsWriteImage(weightDest, header, readout->weight, readNum)) { - psError(PS_ERR_IO, false, "Unable to write weight plane %d in extension %s\n", - readNum, hdu->extname); - return false; - } - } - } // Iterating over readouts - psFree(header); - psFree(weightDest); - } // Valid cells - } // Iterating over cells - } // Valid chips + p_pmHDU *hdu = fpa->hdu; // The HDU into which we will read the weight + psArray *chips = fpa->chips; // Array of chips + for (int chipNum = 0; chipNum < chips->n; chipNum++) + { + pmChip *chip = chips->data[chipNum]; // The current chip of interest + if (chip->valid) + { + if (chip->hdu) + { + hdu = chip->hdu; + } + psArray *cells = chip->cells; // Array of cells + for (int cellNum = 0; cellNum < cells->n; cellNum++) + { + pmCell *cell = cells->data[cellNum]; // The current cell of interest + if (cell->valid) + { + if (cell->hdu) + { + hdu = cell->hdu; + } + + // Now, need to find out where to write the pixels + psFits *weightDest = psMemIncrRefCounter(fits); // Destination of weight image + psMetadata *header = psMetadataAlloc(); // A dummy header, containing the extension name + if (strcasecmp(sourceType, "FILE") == 0) + { + // Source is a file (with optional extension, e.g., "myWeightFile.fits:thisExt" + psString filenameExt = p_pmFPATranslateName(name, cell); + char *colon = strchr(filenameExt, ':'); // Pointer to a colon in the filename-extn + psString filename = NULL; // The filename + psString extname = NULL; // The extenstion name + if (colon) + { + filename = psStringNCopy(filenameExt, strlen(filenameExt) - strlen(colon)); + if (strlen(colon) > 1) + { + extname = psStringCopy(colon + 1); + } + } + else + { + filename = psMemIncrRefCounter(filenameExt); + } + + psFree(weightDest); + weightDest = psFitsAlloc(filename); + if (extname) + { + psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); + } + psFree(filename); + psFree(extname); + psFree(filenameExt); + } + else if (strncasecmp(sourceType, "EXT", 3) == 0) + { + // Source is an extension in the original file + psString extname = p_pmFPATranslateName(name, cell); + psMetadataAddStr(header, PS_LIST_TAIL, "EXTNAME", 0, "Extension name", extname); + psFree(extname); + } + + // We've arrived where the pixels are. Now we need to write them out. + psArray *readouts = cell->readouts; // The array of readouts + for (int readNum = 0; readNum < readouts->n; readNum++) + { + pmReadout *readout = readouts->data[readNum]; // The readout of interest + if (! readout->weight) + { + psLogMsg(__func__, PS_LOG_WARN, "No weight image to write out in %d,%d,%d\n", + chipNum, cellNum, readNum); + } + else + { + if (! psFitsWriteImage(weightDest, header, readout->weight, readNum)) + { + psError(PS_ERR_IO, false, "Unable to write weight plane %d in extension %s\n", + readNum, hdu->extname); + return false; + } + } + } // Iterating over readouts + psFree(header); + psFree(weightDest); + } // Valid cells + } // Iterating over cells + } // Valid chips } // Iterating over chips