Index: /trunk/dvoTools/src/dvoApplyCorr.h =================================================================== --- /trunk/dvoTools/src/dvoApplyCorr.h (revision 20179) +++ /trunk/dvoTools/src/dvoApplyCorr.h (revision 20180) @@ -32,5 +32,6 @@ // apply the correction factor pixel-by-pixel -bool dvoApplyCorrReadout (pmConfig *config, pmFPAview *view, char *inName, char *corrName); +// XXX : old value bool dvoApplyCorrReadout (pmConfig *config, pmFPAview *view, char *inName, char *corrName); +bool dvoApplyCorrReadout (pmCell *inCell, pmChip *corrChip); // free memory, check for leaks Index: /trunk/dvoTools/src/dvoApplyCorrArguments.c =================================================================== --- /trunk/dvoTools/src/dvoApplyCorrArguments.c (revision 20179) +++ /trunk/dvoTools/src/dvoApplyCorrArguments.c (revision 20180) @@ -35,10 +35,10 @@ // save the following additional recipe values based on command-line options // these options override the DVOCORR recipe values loaded from recipe files - psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); + // psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); // XXX add options from command-line here // drop the local view on the options (saved on config->arguments) - psFree (options); + // psFree (options); // chip selection is used to limit chips to be processed Index: /trunk/dvoTools/src/dvoApplyCorrLoop.c =================================================================== --- /trunk/dvoTools/src/dvoApplyCorrLoop.c (revision 20179) +++ /trunk/dvoTools/src/dvoApplyCorrLoop.c (revision 20180) @@ -10,5 +10,4 @@ pmChip *chip; pmCell *cell; - pmReadout *readout; // psMetadata *recipe = psMetadataLookupMetadata(&status, config->recipes, RECIPE_NAME); @@ -17,5 +16,12 @@ pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "DVOFLAT.INPUT"); if (!status) { - psErrorStackPrint(stderr, "Can't find input data!\n"); + psErrorStackPrint(stderr, "Can't find input flat-field image\n"); + exit(EXIT_FAILURE); + } + + // select the input image + pmFPAfile *corr = psMetadataLookupPtr(&status, config->files, "DVOFLAT.CORR"); + if (!status) { + psErrorStackPrint(stderr, "Can't find correction image\n"); exit(EXIT_FAILURE); } @@ -40,4 +46,6 @@ } + pmChip *corrChip = pmFPAviewThisChip(view, corr->fpa); + // process each cell in the Chip while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { @@ -50,21 +58,9 @@ } - // process each of the readouts - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - psError(PS_ERR_UNKNOWN, false, "failed IO for chip %d, cell %d, readout %d in dvoApplyCorr\n", view->chip, view->cell, view->readout); - psFree (view); - return false; - } - if (!readout->data_exists) continue; - - // XXX put the function here which multiplies the input image and the correction image - dvoApplyCorrReadout (config, view, "DVOFLAT.INPUT", "DVOFLAT.CORR"); - - if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) { - psError(PS_ERR_UNKNOWN, false, "failed IO for chip %d, cell %d, readout %d in dvoApplyCorr\n", view->chip, view->cell, view->readout); - psFree (view); - return false; - } + // multiply the input image and the correction image + if (!dvoApplyCorrReadout (cell, corrChip)) { + psError(PS_ERR_UNKNOWN, false, "failed to apply correction to chip %d, cell %d dvoApplyCorr\n", view->chip, view->cell); + psFree (view); + return false; } if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) { Index: /trunk/dvoTools/src/dvoApplyCorrParseCamera.c =================================================================== --- /trunk/dvoTools/src/dvoApplyCorrParseCamera.c (revision 20179) +++ /trunk/dvoTools/src/dvoApplyCorrParseCamera.c (revision 20180) @@ -4,4 +4,5 @@ # include "dvoApplyCorr.h" +bool dvoApplyCorrSelectCorrFile (pmConfig *config, pmFPA *input); dvoApplyCorrOptions *dvoApplyCorrParseCamera (pmConfig *config) { @@ -29,12 +30,8 @@ return NULL; } + output->save = TRUE; // find the flat-field correction image (from command-line, config file, or detrend db) - status = false; - pmFPAfileDefineFromArgs (&status, config, "DVOFLAT.CORR", "CORR"); - psErrorClear(); - pmFPAfileDefineFromConf (&status, config, "DVOFLAT.CORR"); - psErrorClear(); - pmFPAfileDefineFromDetDB (&status, config, "DVOFLAT.CORR", input->fpa, PM_DETREND_TYPE_FLAT_CORRECTION); + status = dvoApplyCorrSelectCorrFile (config, input->fpa); if (!status) { psError (PS_ERR_IO, false, "can't find a flat-field correction image source"); @@ -52,5 +49,5 @@ if (! pmFPASelectChip(output->fpa, chipNum, false)) { psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum); - return false; + return NULL; } } @@ -59,2 +56,48 @@ return (options); } + +bool dvoApplyCorrSelectCorrFile (pmConfig *config, pmFPA *input) { + + bool status; + pmFPAfile *file = NULL; + + file = pmFPAfileDefineFromArgs (&status, config, "DVOFLAT.CORR", "CORR"); + if (!status) { + psError (PS_ERR_UNKNOWN, false, "failed to load file definition"); + return false; + } + if (file) { + if (file->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "DVOFLAT.CORR is not of type IMAGE"); + return false; + } + return true; + } + + file = pmFPAfileDefineFromConf (&status, config, "DVOFLAT.CORR"); + if (!status) { + psError (PS_ERR_UNKNOWN, false, "failed to load file definition"); + return false; + } + if (file) { + if (file->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "DVOFLAT.CORR is not of type IMAGE"); + return false; + } + return true; + } + + file = pmFPAfileDefineFromDetDB (&status, config, "DVOFLAT.CORR", input, PM_DETREND_TYPE_FLAT_CORRECTION); + if (!status) { + psError (PS_ERR_UNKNOWN, false, "failed to load file definition"); + return false; + } + if (file) { + if (file->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "DVOFLAT.CORR is not of type IMAGE"); + return false; + } + return true; + } + return false; +} Index: /trunk/dvoTools/src/dvoApplyCorrReadout.c =================================================================== --- /trunk/dvoTools/src/dvoApplyCorrReadout.c (revision 20179) +++ /trunk/dvoTools/src/dvoApplyCorrReadout.c (revision 20180) @@ -5,40 +5,52 @@ #include "dvoApplyCorr.h" -// this function is operating on each readout, assuming there is a correspondence between -// readouts in the input (raw) flat-field image and the correction frame. this is not really -// true +// this function is operating on each cell (well, readout) of the flat to be corrected. The +// input chip is supplied, but may be in a different format (eg, chip-mosaic vs single cell) -bool dvoApplyCorrReadout (pmConfig *config, pmFPAview *view, char *inName, char *corrName) { +bool dvoApplyCorrReadout (pmCell *inCell, pmChip *corrChip) { + // XXX for now, let's just assume the input is per-cell, and the correction is per-chip + // Also, let's assume they are both binned 1x1 + bool status; - pmFPAfile *inFile = psMetadataLookupPtr (&status, config->files, inName); - pmFPAfile *corrFile = psMetadataLookupPtr (&status, config->files, corrName); - assert (inFile); - assert (corrFile); + pmCell *corrCell = corrChip->cells->data[0]; + pmReadout *corrRO = corrCell->readouts->data[0]; + psImage *corrImage = corrRO->image; - pmReadout *inData = pmFPAviewThisReadout (view, inFile->fpa); - pmReadout *corrData = pmFPAviewThisReadout (view, corrFile->fpa); - assert (inData); - assert (corrData); + pmReadout *inRO = inCell->readouts->data[0]; + psImage *inImage = inRO->image; - // dimensions of input image: - assert (inData->image->numCols == corrData->image->numCols); - assert (inData->image->numRows == corrData->image->numRows); + int x0 = psMetadataLookupS32(&status, inCell->concepts, "CELL.X0"); // Position of (0,0) on chip + if (!status) { + psError(PS_ERR_UNKNOWN, true, "CELL.X0 hasn't been set for cell.\n"); + return false; + } + int y0 = psMetadataLookupS32(&status, inCell->concepts, "CELL.Y0"); // Position of (0,0) on chip + if (!status) { + psError(PS_ERR_UNKNOWN, true, "CELL.Y0 hasn't been set for cell.\n"); + return false; + } - // NOTE : the output pmFPA points at the same pixels as the input pmFPA + int xParity = psMetadataLookupS32(&status, inCell->concepts, "CELL.XPARITY"); // Parity in x + if (!status) { + psError(PS_ERR_UNKNOWN, true, "CELL.XPARITY hasn't been set for cell.\n"); + return false; + } + int yParity = psMetadataLookupS32(&status, inCell->concepts, "CELL.YPARITY"); // Parity in y + if (!status) { + psError(PS_ERR_UNKNOWN, true, "CELL.YPARITY hasn't been set for cell.\n"); + return false; + } - // the corr image is a multiplicative factor - for (int j = 0; j < inData->image->numRows; j++) { - for (int i = 0; i < inData->image->numCols; i++) { - inData->image->data.F32[j][i] *= corrData->image->data.F32[j][i]; + // The corr image is a multiplicative factor. Need to convert the input flat pixel + // coordinates to the correction cell/pixel coords. + for (int j = 0; j < inImage->numRows; j++) { + int jC = (yParity < 0) ? y0 + j*yParity : y0 + j*yParity + 1; + for (int i = 0; i < inImage->numCols; i++) { + int iC = (xParity < 0) ? x0 + i*xParity : x0 + i*xParity + 1; + inImage->data.F32[j][i] *= corrImage->data.F32[jC][iC]; } } - - // psFits *fits = psFitsOpen ("tmp.fits", "w"); - // psFitsWriteImage (fits, NULL, inData->image, 0, NULL); - // psFitsClose (fits); - // exit (0); - return true; } Index: /trunk/dvoTools/src/dvoMakeCorr.h =================================================================== --- /trunk/dvoTools/src/dvoMakeCorr.h (revision 20179) +++ /trunk/dvoTools/src/dvoMakeCorr.h (revision 20180) @@ -32,5 +32,5 @@ // convert low-res image to hi-res image -bool dvoMakeCorrUnbin (pmConfig *config, pmFPAview *view, char *outName, char *inName, char *refName); +bool dvoMakeCorrUnbin (pmConfig *config, pmFPAview *view, char *outName, psImage *inImage, pmChip *inChip, char *refName); // free memory, check for leaks Index: /trunk/dvoTools/src/dvoMakeCorrArguments.c =================================================================== --- /trunk/dvoTools/src/dvoMakeCorrArguments.c (revision 20179) +++ /trunk/dvoTools/src/dvoMakeCorrArguments.c (revision 20180) @@ -35,10 +35,7 @@ // save the following additional recipe values based on command-line options // these options override the DVOCORR recipe values loaded from recipe files - psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); + // psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); // XXX add options from command-line here - - // drop the local view on the options (saved on config->arguments) - psFree (options); // the input file is a required argument; if not found, we will exit Index: /trunk/dvoTools/src/dvoMakeCorrLoop.c =================================================================== --- /trunk/dvoTools/src/dvoMakeCorrLoop.c (revision 20179) +++ /trunk/dvoTools/src/dvoMakeCorrLoop.c (revision 20180) @@ -5,4 +5,7 @@ #include "dvoMakeCorr.h" +// XXX currently, the input image (the grid map generated by relphot) does not supply enough +// header information so the camera and format can be identified. + bool dvoMakeCorrLoop (pmConfig *config, dvoMakeCorrOptions *options) { @@ -10,7 +13,14 @@ pmChip *chip; pmCell *cell; - pmReadout *readout; + psRegion fullImage = {0, 0, 0, 0}; // psMetadata *recipe = psMetadataLookupMetadata(&status, config->recipes, RECIPE_NAME); + + // use the reference image to identify the desired extension from DVOCORR.INPUT + pmFPAfile *refhead = psMetadataLookupPtr(&status, config->files, "DVOCORR.REFHEAD"); + if (!status) { + psErrorStackPrint(stderr, "Can't find reference image\n"); + exit(EXIT_FAILURE); + } pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "DVOCORR.INPUT"); @@ -29,6 +39,14 @@ } + // XXX for now, do not use the I/O system to read this file; do it manually + if (!pmFPAfileOpen (input, view, config)) { + psError(PS_ERR_UNKNOWN, false, "failed to open grid file\n"); + psFree (view); + return false; + } + input->state = PM_FPA_STATE_INACTIVE; + // process each chip in the FPA - while ((chip = pmFPAviewNextChip(view, input->fpa, 1)) != NULL) { + while ((chip = pmFPAviewNextChip(view, refhead->fpa, 1)) != NULL) { psLogMsg ("dvoMakeCorrLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); if (!chip->process || !chip->file_exists) continue; @@ -39,6 +57,13 @@ } + // load the input data for this extension + pmChip *inChip = pmFPAviewThisChip (view, input->fpa); + char *inName = psMetadataLookupStr (&status, inChip->concepts, "CHIP.NAME"); + psFitsMoveExtName (input->fits, inName); + psImage *inImage = psFitsReadImage (input->fits, fullImage, 0); + assert (inImage); + // process each cell in the Chip - while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { + while ((cell = pmFPAviewNextCell(view, refhead->fpa, 1)) != NULL) { psLogMsg ("dvoMakeCorrLoop", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); if (!cell->process || !cell->file_exists) continue; @@ -49,22 +74,7 @@ } - // process each of the readouts - while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { - if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { - psError(PS_ERR_UNKNOWN, false, "failed IO for chip %d, cell %d, readout %d in dvoMakeCorr\n", view->chip, view->cell, view->readout); - psFree (view); - return false; - } - if (!readout->data_exists) continue; + // XXX put the function here which unbins the input image + dvoMakeCorrUnbin (config, view, "DVOCORR.OUTPUT", inImage, inChip, "DVOCORR.REFHEAD"); - // XXX put the function here which unbins the input image - dvoMakeCorrUnbin (config, view, "DVOCORR.OUTPUT", "DVOCORR.INPUT", "DVOCORR.REFHEAD"); - - if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) { - psError(PS_ERR_UNKNOWN, false, "failed IO for chip %d, cell %d, readout %d in dvoMakeCorr\n", view->chip, view->cell, view->readout); - psFree (view); - return false; - } - } if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) { psError(PS_ERR_UNKNOWN, false, "failed IO for chip %d, cell %d in dvoMakeCorr\n", view->chip, view->cell); @@ -73,4 +83,6 @@ } } + psFree (inImage); + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) { psError(PS_ERR_UNKNOWN, false, "failed IO for chip %d in dvoMakeCorr\n", view->chip); @@ -85,4 +97,5 @@ } + pmFPAfileClose (input, view); psFree (view); Index: /trunk/dvoTools/src/dvoMakeCorrParseCamera.c =================================================================== --- /trunk/dvoTools/src/dvoMakeCorrParseCamera.c (revision 20179) +++ /trunk/dvoTools/src/dvoMakeCorrParseCamera.c (revision 20180) @@ -7,15 +7,15 @@ dvoMakeCorrOptions *dvoMakeCorrParseCamera (pmConfig *config) { + // the REFERENCE image defines the camera, and all recipes and options the follow + pmFPAfile *refhead = pmFPAfileDefineFromArgs (NULL, config, "DVOCORR.REFHEAD", "REFHEAD"); + if (!refhead) { + psError(PS_ERR_IO, false, "Failed to build FPA from DVOCORR.REFHEAD"); + return NULL; + } + // the input image defines the camera, and all recipes and options the follow pmFPAfile *input = pmFPAfileDefineFromArgs (NULL, config, "DVOCORR.INPUT", "INPUT"); if (!input) { psError(PS_ERR_IO, false, "Failed to build FPA from DVOCORR.INPUT"); - return NULL; - } - - // the input image defines the camera, and all recipes and options the follow - pmFPAfile *refhead = pmFPAfileDefineFromArgs (NULL, config, "DVOCORR.REFHEAD", "REFHEAD"); - if (!refhead) { - psError(PS_ERR_IO, false, "Failed to build FPA from DVOCORR.REFHEAD"); return NULL; } @@ -29,5 +29,5 @@ // the following files are output targets // XXX get the binning from where? - pmFPAfile *output = pmFPAfileDefineFromFPA(config, input->fpa, 1, 1, "DVOCORR.OUTPUT"); + pmFPAfile *output = pmFPAfileDefineFromFPA(config, refhead->fpa, 1, 1, "DVOCORR.OUTPUT"); if (!output) { psError(PS_ERR_IO, false, _("Unable to generate output file from DVOCORR.OUTPUT")); @@ -35,4 +35,5 @@ return NULL; } + output->save = TRUE; // Chip selection: turn on only the chips specified (pass status to suppress missing-key log msg) Index: /trunk/dvoTools/src/dvoMakeCorrUnbin.c =================================================================== --- /trunk/dvoTools/src/dvoMakeCorrUnbin.c (revision 20179) +++ /trunk/dvoTools/src/dvoMakeCorrUnbin.c (revision 20180) @@ -5,12 +5,10 @@ #include "dvoMakeCorr.h" -bool dvoMakeCorrUnbin (pmConfig *config, pmFPAview *view, char *outName, char *inName, char *refName) { +bool dvoMakeCorrUnbin (pmConfig *config, pmFPAview *view, char *outName, psImage *inImage, pmChip *inChip, char *refName) { bool status; - pmFPAfile *inFile = psMetadataLookupPtr (&status, config->files, inName); pmFPAfile *refFile = psMetadataLookupPtr (&status, config->files, refName); pmFPAfile *outFile = psMetadataLookupPtr (&status, config->files, outName); - assert (inFile); assert (refFile); assert (outFile); @@ -19,6 +17,6 @@ assert (refCell); - pmReadout *inData = pmFPAviewThisReadout (view, inFile->fpa); - assert (inData); + pmChip *refChip = pmFPAviewThisChip (view, refFile->fpa); + assert (refChip); // determine the output array size based on the reference TRIMSEC values @@ -28,27 +26,36 @@ // I have the fine and ruff image sizes, determine the binning factor psImageBinning *binning = psImageBinningAlloc(); - binning->nXruff = inData->image->numCols; - binning->nYruff = inData->image->numRows; + binning->nXruff = inImage->numCols; + binning->nYruff = inImage->numRows; binning->nXfine = trimsec->x1 - trimsec->x0; binning->nYfine = trimsec->y1 - trimsec->y0; psImageBinningSetScale (binning, PS_IMAGE_BINNING_CENTER); - psImageBinningSetSkip(binning, inData->image); + psImageBinningSetSkip(binning, inImage); + + // generate a local view of the 0th readout + pmFPAview *myView = pmFPAviewAlloc (0); + *myView = *view; + myView->readout = 0; // construct the supporing pmFPA/pmChip/pmCell structures - pmReadout *outData = pmFPAviewThisReadout (view, outFile->fpa); + pmReadout *outData = pmFPAviewThisReadout (myView, outFile->fpa); if (outData == NULL) { - pmChip *inChip = pmFPAviewThisChip (view, inFile->fpa); - pmChip *outChip = pmFPAviewThisChip (view, outFile->fpa); + pmChip *outChip = pmFPAviewThisChip (myView, outFile->fpa); + pmCell *outCell = pmFPAviewThisCell (myView, outFile->fpa); - pmChipCopyStructure (outChip, inChip, binning->nXbin, binning->nYbin); - outData = pmFPAviewThisReadout (view, outFile->fpa); + pmChipCopyStructure (outChip, refChip, 1, 1); + + outData = pmReadoutAlloc (outCell); assert (outData != NULL); + + // outData = pmFPAviewThisReadout (myView, outFile->fpa); + // assert (outData != NULL); } // generate the output (fine-scale) image array - psImageRecycle (outData->image, binning->nXfine, binning->nYfine, PS_TYPE_F32); + outData->image = psImageRecycle (outData->image, binning->nXfine, binning->nYfine, PS_TYPE_F32); // linear interpolation to full fine scale - if (!psImageUnbin (outData->image, inData->image, binning)) { + if (!psImageUnbin (outData->image, inImage, binning)) { psError (PS_ERR_UNKNOWN, true, "failed to unbin image"); psFree (binning);