Index: branches/eam_branches/20090522/ppImage/notes.txt =================================================================== --- branches/eam_branches/20090522/ppImage/notes.txt (revision 24238) +++ branches/eam_branches/20090522/ppImage/notes.txt (revision 24557) @@ -1,23 +1,15 @@ -ppImage pmFPAfiles: +20090611 : adjusting things to allow the readnoise to be an image map for each cell - pmFPAfile *input = pmFPAfileDefineFromArgs (&status, config, "PPIMAGE.INPUT", "INPUT"); - pmFPAfile *inputMask = pmFPAfileBindFromArgs(&status, input, config, "PPIMAGE.INPUT.MASK", "INPUT.MASK"); - pmFPAfile *inputWeight = pmFPAfileBindFromArgs(&status, input, config, "PPIMAGE.INPUT.WEIGHT", "INPUT.WEIGHT"); - pmFPAfile *output = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT"); - pmFPAfile *outMask = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.MASK"); - pmFPAfile *outWeight = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.WEIGHT"); - pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, input->fpa, "PPIMAGE.CHIP"); - pmFPAfile *chipMask = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.MASK"); - pmFPAfile *chipWeight = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.WEIGHT"); - pmFPAfile *byFPA1 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA1"); - pmFPAfile *byFPA2 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA2"); + * pmReadoutSetVaraince : when variance is created, we are suppling a single CELL.READNOISE value -- change this to an optional image (carried through concepts?) - pmFPAfile *psphotInput = pmFPAfileDefineFromFPA (config, chipImage->fpa, 1, 1, "PSPHOT.INPUT"); - pmFPAfile *psphotOutput = psMetadataLookupPtr (&status, config->files, "PSPHOT.OUTPUT"); - pmFPAfile *psastroInput = pmFPAfileDefineInput (config, psphotOutput->fpa, "PSASTRO.INPUT"); + I need to: - pmFPAfile *bin1 = pmFPAfileDefineFromFPA (config, chipImage->fpa, options->xBin1, options->yBin1, "PPIMAGE.BIN1"); - pmFPAfile *bin2 = pmFPAfileDefineFromFPA (config, chipImage->fpa, options->xBin2, options->yBin2, "PPIMAGE.BIN2"); - pmFPAfile *jpg1 = pmFPAfileDefineOutput (config, byFPA1->fpa, "PPIMAGE.JPEG1"); - pmFPAfile *jpg2 = pmFPAfileDefineOutput (config, byFPA2->fpa, "PPIMAGE.JPEG2"); + * define a format for the readnoise map (image map in SPLIT/MEF format?) + * load the readnoise map + + * supply the map for each cell to the pmReadoutSetVariance (pointer to ppImageMap?) + pmReadoutSetVariance -> add psImageMap to API (also pmReadoutGenerateVariance) + + * add recipe information to define the source of the READNOISE info. + Index: branches/eam_branches/20090522/ppImage/src/ppImage.h =================================================================== --- branches/eam_branches/20090522/ppImage/src/ppImage.h (revision 24238) +++ branches/eam_branches/20090522/ppImage/src/ppImage.h (revision 24557) @@ -31,4 +31,5 @@ bool doNonLin; // Non-linearity correction bool doOverscan; // Overscan subtraction + bool doNoiseMap; // Bias subtraction bool doBias; // Bias subtraction bool doDark; // Dark subtraction Index: branches/eam_branches/20090522/ppImage/src/ppImageArguments.c =================================================================== --- branches/eam_branches/20090522/ppImage/src/ppImageArguments.c (revision 24238) +++ branches/eam_branches/20090522/ppImage/src/ppImageArguments.c (revision 24557) @@ -17,4 +17,5 @@ fprintf(stderr, "\n"); fprintf(stderr, "Input options (single file / file list):\n"); + fprintf(stderr, "\t-noisemap/-noisemaplist: Noise Map image.\n"); fprintf(stderr, "\t-bias/-biaslist: Bias image.\n"); fprintf(stderr, "\t-dark/-darklist: Dark image.\n"); @@ -112,4 +113,5 @@ // if these command-line options are supplied, load the file name lists into config->arguments // override any configuration-specified source for these files + pmConfigFileSetsMD (config->arguments, &argc, argv, "NOISEMAP", "-noisemap", "-noisemaplist"); pmConfigFileSetsMD (config->arguments, &argc, argv, "BIAS", "-bias", "-biaslist"); pmConfigFileSetsMD (config->arguments, &argc, argv, "DARK", "-dark", "-darklist"); Index: branches/eam_branches/20090522/ppImage/src/ppImageDetrendFree.c =================================================================== --- branches/eam_branches/20090522/ppImage/src/ppImageDetrendFree.c (revision 24238) +++ branches/eam_branches/20090522/ppImage/src/ppImageDetrendFree.c (revision 24557) @@ -8,4 +8,5 @@ static char *detrendTypes[] = { "PPIMAGE.MASK", + "PPIMAGE.NOISEMAP", "PPIMAGE.BIAS", "PPIMAGE.DARK", Index: branches/eam_branches/20090522/ppImage/src/ppImageDetrendReadout.c =================================================================== --- branches/eam_branches/20090522/ppImage/src/ppImageDetrendReadout.c (revision 24238) +++ branches/eam_branches/20090522/ppImage/src/ppImageDetrendReadout.c (revision 24557) @@ -64,5 +64,27 @@ if (options->doVarianceBuild) { // create the target mask and variance images - pmReadoutGenerateVariance(input, true); + psImage *noiseImage = NULL; + if (options->doNoiseMap) { + // XXX convert the noiseMap image to a binned image + pmReadout *noiseMap = NULL; + noiseMap = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.NOISEMAP"); + noiseImage = psImageCopy (NULL, input->image, PS_TYPE_F32); + psImageInit (noiseImage, 0.0); + + // XXX this works, but is not really quite right: the model shoud include the + // offset information, we are not really getting exactly the right mapping from the + // original file. + psImageBinning *binning = psImageBinningAlloc(); + binning->nXruff = noiseMap->image->numCols; + binning->nYruff = noiseMap->image->numRows; + binning->nXfine = input->image->numCols; + binning->nYfine = input->image->numRows; + psImageBinningSetScale(binning, PS_IMAGE_BINNING_LEFT); + + psImageUnbin (noiseImage, noiseMap->image, binning); + psFree (binning); + } + pmReadoutGenerateVariance(input, noiseImage, true); + psFree (noiseImage); } Index: branches/eam_branches/20090522/ppImage/src/ppImageDetrendRecord.c =================================================================== --- branches/eam_branches/20090522/ppImage/src/ppImageDetrendRecord.c (revision 24238) +++ branches/eam_branches/20090522/ppImage/src/ppImageDetrendRecord.c (revision 24557) @@ -67,12 +67,11 @@ psMetadataAddMetadata(cell->analysis, PS_LIST_TAIL, "DETREND", 0, "Detrend information", detrend); - detrendRecord(options->doMask, detrend, config, view, "PPIMAGE.MASK", "DETREND.MASK", "Mask filename"); - detrendRecord(options->doBias, detrend, config, view, "PPIMAGE.BIAS", "DETREND.BIAS", "Bias filename"); - detrendRecord(options->doDark, detrend, config, view, "PPIMAGE.DARK", "DETREND.DARK", "Dark filename"); - detrendRecord(options->doShutter, detrend, config, view, "PPIMAGE.SHUTTER", "DETREND.SHUTTER", - "Shutter correction filename"); - detrendRecord(options->doFlat, detrend, config, view, "PPIMAGE.FLAT", "DETREND.FLAT", "Flat filename"); - detrendRecord(options->doFringe, detrend, config, view, "PPIMAGE.FRINGE", "DETREND.FRINGE", - "Fringe filename"); + detrendRecord(options->doMask, detrend, config, view, "PPIMAGE.MASK", "DETREND.MASK", "Mask filename"); + detrendRecord(options->doNoiseMap, detrend, config, view, "PPIMAGE.NOISEMAP", "DETREND.NOISEMAP", "Noise Map filename"); + detrendRecord(options->doBias, detrend, config, view, "PPIMAGE.BIAS", "DETREND.BIAS", "Bias filename"); + detrendRecord(options->doDark, detrend, config, view, "PPIMAGE.DARK", "DETREND.DARK", "Dark filename"); + detrendRecord(options->doShutter, detrend, config, view, "PPIMAGE.SHUTTER", "DETREND.SHUTTER", "Shutter correction filename"); + detrendRecord(options->doFlat, detrend, config, view, "PPIMAGE.FLAT", "DETREND.FLAT", "Flat filename"); + detrendRecord(options->doFringe, detrend, config, view, "PPIMAGE.FRINGE", "DETREND.FRINGE", "Fringe filename"); psFree (detrend); Index: branches/eam_branches/20090522/ppImage/src/ppImageOptions.c =================================================================== --- branches/eam_branches/20090522/ppImage/src/ppImageOptions.c (revision 24238) +++ branches/eam_branches/20090522/ppImage/src/ppImageOptions.c (revision 24557) @@ -25,4 +25,5 @@ options->doNonLin = false; // Non-linearity correction options->doOverscan = false; // Overscan subtraction + options->doNoiseMap = false; // Apply Read Noise Map options->doBias = false; // Bias subtraction options->doDark = false; // Dark subtraction @@ -217,4 +218,5 @@ options->doCrosstalkCorrect = psMetadataLookupBool(NULL, recipe, "CROSSTALK.CORRECT"); + options->doNoiseMap = psMetadataLookupBool(NULL, recipe, "NOISEMAP"); options->doBias = psMetadataLookupBool(NULL, recipe, "BIAS"); options->doDark = psMetadataLookupBool(NULL, recipe, "DARK"); @@ -278,5 +280,5 @@ // even if not requested explicitly, if any of these are set, build an internal mask and variance: - if (options->doBias || options->doOverscan || options->doDark || options->doShutter || options->doFlat || + if (options->doNoiseMap || options->doBias || options->doOverscan || options->doDark || options->doShutter || options->doFlat || options->doPhotom) { options->doMaskBuild = true; Index: branches/eam_branches/20090522/ppImage/src/ppImageParseCamera.c =================================================================== --- branches/eam_branches/20090522/ppImage/src/ppImageParseCamera.c (revision 24238) +++ branches/eam_branches/20090522/ppImage/src/ppImageParseCamera.c (revision 24557) @@ -25,4 +25,12 @@ // otherwise they revert to the config information // not all input or output images are used in a given recipe + if (options->doNoiseMap) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.NOISEMAP", "NOISEMAP", + PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_NOISEMAP)) { + psError(PS_ERR_IO, false, "Can't find a noise map image source"); + psFree(options); + return NULL; + } + } if (options->doBias) { if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.BIAS", "BIAS", @@ -48,30 +56,4 @@ return NULL; } - -#if 0 - // I think this is now done automatically in the pmFPAfileDefine and pmFPAfileIOChecks -- PAP. - - // XXX have ppImageDefineFile return the pmFPAfile? - pmFPAfile *mask = psMetadataLookupPtr(&status, config->files, "PPIMAGE.MASK"); - psAssert(mask, "Just defined the mask!"); - - // Need to read the names of bit masks from the mask header and set them in the - // recipe. If we are loading this from the detrend db, this action will happen - // when the file is resolved. - if (!mask->detrend) { - // XXX need to load the mask bit names from one of the headers - // this grabs the first available hdu : no guarantee that it will be valid, though - pmHDU *hdu = pmHDUGetFirst(mask->fpa); - if (!hdu) { - psError(PS_ERR_IO, true, "no valid HDU for PPIMAGE.INPUT.MASK"); - return NULL; - } - // XXX is this consistent with the pmConfigMaskReadHeader call above? - if (!pmConfigMaskReadHeader(config, hdu->header)) { - psError(PS_ERR_IO, false, "error in mask bits"); - return NULL; - } - } -#endif } if (options->doShutter) {