Index: /trunk/ippconfig/gpc1/ppImage.config =================================================================== --- /trunk/ippconfig/gpc1/ppImage.config (revision 36168) +++ /trunk/ippconfig/gpc1/ppImage.config (revision 36169) @@ -34,5 +34,5 @@ # aditional auxiliary mask applied to corners of all chips in video cells. # Is only applied if MASK.AUXMASK and USE.VIDEO.MASK are both true -AUX.VIDEO.MASK STR neb://any/gpc1/auxmask/mpg.20130506/mask_video_cell_corners.fits +AUX.VIDEO.MASK STR neb://any/gpc1/auxmask/mpg.20130930/mask_video_cell_corners.fits @@ -1292,4 +1292,96 @@ CROSSTALK.MEASURE BOOL FALSE # Subtract model background? NO.COMPRESS BOOL TRUE # turn off image compression + DETREND.CONSTRAINTS METADATA + BIAS METADATA + END + DARK METADATA + EXPTIME STR FPA.EXPOSURE + END + FLAT METADATA + FILTER STR FPA.FILTERID + END + FLATCORR METADATA + FILTER STR FPA.FILTERID + END + FRINGE METADATA + FILTER STR FPA.FILTERID + END + SHUTTER METADATA + END + MASK METADATA + END + AUXMASK METADATA + DETTYPE STR AUXMASK_STS + END + ASTROM METADATA + END + NOISEMAP METADATA + END + LINEARITY METADATA + END + END +END + +# Standard chip processing + auxiliary mask with heavy masking +CHIP_AUXMASK_HEAVY METADATA + BASE.FITS BOOL FALSE # Save base detrended image? + BASE.MASK.FITS BOOL FALSE # Save base detrended image? + BASE.VARIANCE.FITS BOOL FALSE # Save base detrended image? + CHIP.FITS BOOL TRUE # Save chip-mosaic-ed image? + CHIP.MASK.FITS BOOL TRUE # Save chip-mosaic-ed image? + CHIP.VARIANCE.FITS BOOL TRUE # Save chip-mosaic-ed image? + OVERSCAN BOOL TRUE # Overscan subtraction + NONLIN BOOL TRUE # apply non-linearity correction + BIAS BOOL FALSE # Bias subtraction + DARK BOOL TRUE # Dark subtraction + NOISEMAP BOOL TRUE + REMNANCE BOOL FALSE # Remnance masking + SHUTTER BOOL FALSE # Shutter correction + FLAT BOOL TRUE # Flat-field normalisation + MASK BOOL TRUE # Mask bad pixels + MASK.BUILD BOOL TRUE # Build internal mask? + MASK.BURNTOOL BOOL TRUE # Mask potential burntool trails + MASK.AUXMASK BOOL TRUE # augment mask with more restrictive auxiliary mask + PATTERN.ROW BOOL TRUE # Row pattern correction + PATTERN.CELL BOOL FALSE # Cell pattern correction + PATTERN.CONTINUITY BOOL TRUE # Cell pattern correction using edge continuity + FRINGE BOOL TRUE # Fringe subtraction + BIN1.FITS BOOL TRUE # Save 1st binned chip image? + BIN2.FITS BOOL TRUE # Save 2nd binned chip image? + PHOTOM BOOL TRUE # Source identification and photometry + ASTROM.CHIP BOOL FALSE # Astrometry per chip? + ASTROM.MOSAIC BOOL FALSE # Astrometry for mosaic? + BACKGROUND BOOL TRUE # Subtract background? + CROSSTALK.MEASURE BOOL FALSE # Subtract model background? + NO.COMPRESS BOOL TRUE # turn off image compression + DETREND.CONSTRAINTS METADATA + BIAS METADATA + END + DARK METADATA + EXPTIME STR FPA.EXPOSURE + END + FLAT METADATA + FILTER STR FPA.FILTERID + END + FLATCORR METADATA + FILTER STR FPA.FILTERID + END + FRINGE METADATA + FILTER STR FPA.FILTERID + END + SHUTTER METADATA + END + MASK METADATA + END + AUXMASK METADATA + DETTYPE STR AUXMASK_HEAVY + END + ASTROM METADATA + END + NOISEMAP METADATA + END + LINEARITY METADATA + END + END END @@ -1392,4 +1484,33 @@ CROSSTALK.MEASURE BOOL FALSE # Subtract model background? NO.COMPRESS BOOL TRUE # turn off image compression + DETREND.CONSTRAINTS METADATA + BIAS METADATA + END + DARK METADATA + EXPTIME STR FPA.EXPOSURE + END + FLAT METADATA + FILTER STR FPA.FILTERID + END + FLATCORR METADATA + FILTER STR FPA.FILTERID + END + FRINGE METADATA + FILTER STR FPA.FILTERID + END + SHUTTER METADATA + END + MASK METADATA + END + AUXMASK METADATA + DETTYPE STR AUXMASK_HEAVY + END + ASTROM METADATA + END + NOISEMAP METADATA + END + LINEARITY METADATA + END + END END Index: /trunk/ippconfig/recipes/filerules-split.mdc =================================================================== --- /trunk/ippconfig/recipes/filerules-split.mdc (revision 36168) +++ /trunk/ippconfig/recipes/filerules-split.mdc (revision 36169) @@ -38,4 +38,5 @@ PPIMAGE.INPUT.MASK INPUT @FILES CHIP MASK PPIMAGE.VIDEOMASK INPUT @DETDB CHIP MASK +PPIMAGE.AUXMASK INPUT @DETDB CHIP MASK PPIMAGE.INPUT.VARIANCE INPUT @FILES CHIP VARIANCE PPIMAGE.INPUT.PSF INPUT @FILES CHIP PSF Index: /trunk/ippconfig/recipes/ppImage.config =================================================================== --- /trunk/ippconfig/recipes/ppImage.config (revision 36168) +++ /trunk/ippconfig/recipes/ppImage.config (revision 36169) @@ -220,6 +220,31 @@ END -# Standard chip processing +# Standard chip processing with auxillary masking CHIP_AUXMASK METADATA + BASE.FITS BOOL FALSE # Save base detrended image? + BASE.MASK.FITS BOOL FALSE # Save base detrended image? + BASE.VARIANCE.FITS BOOL FALSE # Save base detrended image? + CHIP.FITS BOOL TRUE # Save chip-mosaic-ed image? + CHIP.MASK.FITS BOOL TRUE # Save chip-mosaic-ed image? + CHIP.VARIANCE.FITS BOOL TRUE # Save chip-mosaic-ed image? + OVERSCAN BOOL TRUE # Overscan subtraction + NONLIN BOOL FALSE # Non-linearity correction; not implemented + BIAS BOOL TRUE # Bias subtraction + DARK BOOL TRUE # Dark subtraction + SHUTTER BOOL FALSE # Shutter correction + FLAT BOOL TRUE # Flat-field normalisation + MASK BOOL TRUE # Mask bad pixels + FRINGE BOOL TRUE # Fringe subtraction + BIN1.FITS BOOL TRUE # Save 1st binned chip image? + BIN2.FITS BOOL TRUE # Save 2nd binned chip image? + PHOTOM BOOL TRUE # Source identification and photometry + ASTROM.CHIP BOOL FALSE # Astrometry per chip? + ASTROM.MOSAIC BOOL FALSE # Astrometry for mosaic? + BACKGROUND BOOL TRUE # Subtract background? + MASK.STATS BOOL TRUE # Calculate Mask statistics. +END + +# Standard chip processing with heavy auxillary masking (same as CHIP_AUXMASK here, but different in gpc1) +CHIP_AUXMASK_HEAVY METADATA BASE.FITS BOOL FALSE # Save base detrended image? BASE.MASK.FITS BOOL FALSE # Save base detrended image? Index: /trunk/ippconfig/recipes/reductionClasses.mdc =================================================================== --- /trunk/ippconfig/recipes/reductionClasses.mdc (revision 36168) +++ /trunk/ippconfig/recipes/reductionClasses.mdc (revision 36169) @@ -1126,12 +1126,10 @@ STS_DATASET METADATA - # CHIP_PPIMAGE STR CHIP_AUXMASK - # MPG wants auxiliary masking off for now - CHIP_PPIMAGE STR CHIP + CHIP_PPIMAGE STR CHIP_AUXMASK CHIP_PSPHOT STR CHIP WARP_PSWARP STR WARP - STACK_PPSTACK STR STACK + STACK_PPSTACK STR STACK STACK_PPSUB STR STACK - STACK_PSPHOT STR STACK + STACK_PSPHOT STR STACK DIFF_PPSUB STR DIFF DIFF_PSPHOT STR DIFF @@ -1140,6 +1138,6 @@ FAKEPHOT STR FAKEPHOT ADDSTAR STR ADDSTAR - PSASTRO STR STS_DATASET - STACKPHOT STR STACKPHOT + PSASTRO STR STS_DATASET + STACKPHOT STR STACKPHOT END Index: /trunk/ppImage/src/ppImageAuxiliaryMask.c =================================================================== --- /trunk/ppImage/src/ppImageAuxiliaryMask.c (revision 36168) +++ /trunk/ppImage/src/ppImageAuxiliaryMask.c (revision 36169) @@ -35,4 +35,8 @@ return NULL; } + if (image->type.type != PS_TYPE_IMAGE_MASK) { + psWarning("auxiliary mask image %s has unexpected type %d\n", realName, image->type.type); + return false; + } psFree(realName); @@ -72,27 +76,10 @@ } - // Find a suitable detRun with type AUXMASK - - psTime *time = psMetadataLookupPtr(NULL, input->fpa->concepts, "FPA.TIME"); - if (time->sec == 0 && time->nsec == 0) { - psLogMsg ("psModules.camera", PS_LOG_WARN, "FPA.TIME has not been set.\n"); - } - - char *cameraName = psMetadataLookupStr(NULL, input->fpa->concepts, "FPA.CAMERA"); - pmDetrendSelectOptions *detrendOptions = pmDetrendSelectOptionsAlloc(cameraName, *time, PM_DETREND_TYPE_AUXMASK); - - pmDetrendSelectResults *results = pmDetrendSelect(detrendOptions, config); - psFree(detrendOptions); - if (!results) { - psError (psErrorCodeLast(), false, "no matching auxiliary mask found"); - return false; - } - - pmFPALevel fileLevel = pmFPALevelFromName(results->level); - if (fileLevel != PM_FPA_LEVEL_CHIP) { - psError (PM_ERR_CONFIG, false, "invalid file level %d for selected auxiliary mask", fileLevel); - return false; - } - + pmFPAfile *auxmask = psMetadataLookupPtr(&status, config->files, "PPIMAGE.AUXMASK"); + if (!status) { + psError(PS_ERR_UNEXPECTED_NULL, true, "PPIMAGE.CHIP file is not defined"); + return false; + } + // Go find the readout // code to find the readouts was adapted from ppImageSubtractBackground @@ -129,31 +116,38 @@ return true; } - // not needed psImage *image = ro->image; + psImage *mask = ro->mask; - // now read the auxiliary mask file - psString class_id = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); - - char *auxMaskFileName = pmDetrendFile(results->detID, class_id, config); - if (!auxMaskFileName) { - psError (PM_ERR_CONFIG, false, "unable to find auxiliary mask file name for %s %s", results->detID, class_id); - return false; - } - psLogMsg ("ppImage", PS_LOG_INFO, "Auxiliary mask file: %s", auxMaskFileName); - - psFree(results); - // record that we read this file in the config dump file. - // Note: this value isn't used during updates though. - pmConfigRunFilenameAddRead(config, "PPIMAGE.AUXMASK", auxMaskFileName); - recordFileInHeader(chip, "DETREND.AUXMASK", "auxiliary mask", auxMaskFileName); - - psImage *auxMask = readAuxiliaryMask(config, auxMaskFileName); - psFree(auxMaskFileName); - if (!auxMask) { - psError(PS_ERR_UNKNOWN, false, "failed to read auxiliary mask file"); - return false; - } - - // if the cell has video and the recipe value + if (mask->type.type != PS_TYPE_IMAGE_MASK) { + psWarning("mask image has unexpected type %d\n", mask->type.type); + return false; + } + + pmChip *auxMaskChip = pmFPAviewThisChip(view, auxmask->fpa); + if (!auxMaskChip) { + psWarning("failed to find pmChip for auxiliary mask"); + return false; + } + pmCell *auxMaskCell = auxMaskChip->cells->data[0]; + if (!auxMaskCell) { + psWarning("failed to find pmCell for auxiliary mask"); + return false; + } + pmReadout *auxMaskReadout = auxMaskCell->readouts->data[0]; + if (!auxMaskReadout) { + psWarning("failed to find pmReadout for auxiliary mask"); + return false; + } + psImage *auxMaskImage = auxMaskReadout->mask; + if (!auxMaskImage) { + psWarning("failed to find psImage for auxiliary mask"); + return false; + } + if (auxMaskImage->type.type != PS_TYPE_IMAGE_MASK) { + psWarning("auxiliary mask image has unexpected type %d\n", auxMaskImage->type.type); + return false; + } + + // if the cell has video and the recipe value is set or in the video mask if (options->hasVideo && options->auxVideoMask && strcmp(options->auxVideoMask, "NULL")) { psImage *videoMask = readAuxiliaryMask(config, options->auxVideoMask); @@ -166,7 +160,7 @@ recordFileInHeader(chip, "DETREND.AUXVIDEOMASK", "auxiliary video mask", options->auxVideoMask); - // compute auxMask *= videoMask - if (!psBinaryOp(auxMask, auxMask, "*", videoMask)) { - psError(PS_ERR_UNKNOWN, false, "mulitplication of auxiliary mask and auxiliary video mask failed"); + // compute auxMask |= videoMask + if (!psBinaryOp(auxMaskImage, auxMaskImage, "|", videoMask)) { + psError(PS_ERR_UNKNOWN, false, "combination of auxiliary mask and auxiliary video mask failed"); return false; } @@ -174,6 +168,6 @@ } - if ((mask->numRows != auxMask->numRows) || (mask->numCols != auxMask->numCols) || - (mask->row0 != auxMask->row0) || (mask->col0 != auxMask->col0)) { + if ((mask->numRows != auxMaskImage->numRows) || (mask->numCols != auxMaskImage->numCols) || + (mask->row0 != auxMaskImage->row0) || (mask->col0 != auxMaskImage->col0)) { psError(PS_ERR_IO, false, "structure of auxiliary mask does not match this chip"); return false; @@ -187,11 +181,12 @@ psAssert(staticMaskVal, "Need staticMaskVal!"); + // XXX: now that we are using an auxilary mask that matches the format of ps masks, we could just + // do psBinaryOp(mask, mask, "|", auxMaskImage) but run an explicit loop so that we can measure + // and log the number of additional pixels masked int numCols = mask->numCols, numRows = mask->numRows; // Size of image unsigned long numMasked = 0; for (int y = 0; y < numRows; y++) { for (int x = 0; x < numCols; x++) { - // auxMask is floating point type image with pixel value 0 meaning mask it - // XXX: support other types and get the mask value from the header - if (auxMask->data.F32[y][x] == 0) { + if (auxMaskImage->data.U16[y][x] != 0) { if ((mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & staticMaskVal) == 0) { // pixel was not previously included in the static mask so mask it @@ -200,6 +195,6 @@ } // I don't need to do this. + // image->data.F32[y][x] = 0.0; // The background subtraction code runs after us and will do it there - // image->data.F32[y][x] = 0.0; } } @@ -213,6 +208,4 @@ } - psFree(auxMask); - return true; } Index: /trunk/ppImage/src/ppImageParseCamera.c =================================================================== --- /trunk/ppImage/src/ppImageParseCamera.c (revision 36168) +++ /trunk/ppImage/src/ppImageParseCamera.c (revision 36169) @@ -72,4 +72,12 @@ PM_FPA_FILE_MASK, PM_DETREND_TYPE_VIDEOMASK)) { psError(PS_ERR_IO, false, "Can't find a mask image source"); + psFree(options); + return NULL; + } + } + if (options->doAuxMask) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.AUXMASK", "MASK", + PM_FPA_FILE_MASK, PM_DETREND_TYPE_AUXMASK)) { + psError(PS_ERR_IO, false, "Can't find a auxillary mask image source"); psFree(options); return NULL;