Index: trunk/psphot/src/Makefile.am =================================================================== --- trunk/psphot/src/Makefile.am (revision 18471) +++ trunk/psphot/src/Makefile.am (revision 18555) @@ -15,4 +15,5 @@ psphotImageLoop.c \ psphotMosaicChip.c \ + psphotSetMaskBits.c \ psphotParseCamera.c @@ -85,4 +86,6 @@ psphotAddNoise.c +# dropped? psphotGrowthCurve.c + include_HEADERS = \ psphot.h \ Index: trunk/psphot/src/psphot.h =================================================================== --- trunk/psphot/src/psphot.h (revision 18471) +++ trunk/psphot/src/psphot.h (revision 18555) @@ -25,4 +25,5 @@ bool psphotReadoutCleanup (pmConfig *config, pmReadout *readout, psMetadata *recipe, pmDetections *detections, pmPSF *psf, psArray *sources); bool psphotDefineFiles (pmConfig *config, pmFPAfile *input); +bool psphotSetMaskBits (pmConfig *config); // XXX test functions @@ -70,8 +71,8 @@ // functions to set the correct source pixels bool psphotInitRadiusPSF (const psMetadata *recipe, const pmModelType type); -bool psphotCheckRadiusPSF (pmReadout *readout, pmSource *source, pmModel *model); -bool psphotCheckRadiusPSFBlend (pmReadout *readout, pmSource *source, pmModel *model, float dR); +bool psphotCheckRadiusPSF (pmReadout *readout, pmSource *source, pmModel *model, psMaskType markVal); +bool psphotCheckRadiusPSFBlend (pmReadout *readout, pmSource *source, pmModel *model, psMaskType markVal, float dR); bool psphotInitRadiusEXT (psMetadata *recipe, pmModelType type); -bool psphotCheckRadiusEXT (pmReadout *readout, pmSource *source, pmModel *model); +bool psphotCheckRadiusEXT (pmReadout *readout, pmSource *source, pmModel *model, psMaskType markVal); // output functions @@ -91,9 +92,9 @@ bool psphotInitLimitsPSF (psMetadata *recipe, pmReadout *readout); bool psphotInitLimitsEXT (psMetadata *recipe); -bool psphotFitBlend (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal); -bool psphotFitBlob (pmReadout *readout, pmSource *source, psArray *sources, pmPSF *psf, psMaskType maskVal); -bool psphotFitPSF (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal); -pmModel *psphotFitEXT (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal); -psArray *psphotFitDBL (pmReadout *readout, pmSource *source, psMaskType maskVal); +bool psphotFitBlend (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal, psMaskType markVal); +bool psphotFitBlob (pmReadout *readout, pmSource *source, psArray *sources, pmPSF *psf, psMaskType maskVal, psMaskType markVal); +bool psphotFitPSF (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal, psMaskType markVal); +pmModel *psphotFitEXT (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal, psMaskType markVal); +psArray *psphotFitDBL (pmReadout *readout, pmSource *source, psMaskType maskVal, psMaskType markVal); // functions to support simultaneous multi-source fitting @@ -124,5 +125,5 @@ bool psphotMakeResiduals (psArray *sources, psMetadata *recipe, pmPSF *psf, psMaskType maskVal); -pmModel *psphotPSFConvModel (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal, int psfSize); +pmModel *psphotPSFConvModel (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal, psMaskType markVal, int psfSize); psKernel *psphotKernelFromPSF (pmSource *source, int nPix); Index: trunk/psphot/src/psphotApResid.c =================================================================== --- trunk/psphot/src/psphotApResid.c (revision 18471) +++ trunk/psphot/src/psphotApResid.c (revision 18555) @@ -25,11 +25,14 @@ } - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType mark = psMetadataLookupU8(&status, recipe, "MASK.MARK"); // Mask value for bad pixels - assert (mark); + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // S/N limit to perform full non-linear fits @@ -65,5 +68,5 @@ psf->growth = pmGrowthCurveAlloc (PSF_FIT_PAD, 100.0, REF_RADIUS); - if (!pmGrowthCurveGenerate (readout, psf, IGNORE_GROWTH, maskVal, mark)) { + if (!pmGrowthCurveGenerate (readout, psf, IGNORE_GROWTH, maskVal, markVal)) { psError(PSPHOT_ERR_APERTURE, false, "Fitting aperture corrections"); psFree(psf->growth); psf->growth = NULL; @@ -92,5 +95,5 @@ // get growth-corrected, apTrend-uncorrected magnitudes in scaled apertures // will fail if below S/N threshold or model is missing - if (!pmSourceMagnitudes (source, psf, photMode, maskVal, mark)) { + if (!pmSourceMagnitudes (source, psf, photMode, maskVal)) { Nskip ++; psTrace ("psphot", 3, "skip : bad source mag"); Index: trunk/psphot/src/psphotBlendFit.c =================================================================== --- trunk/psphot/src/psphotBlendFit.c (revision 18471) +++ trunk/psphot/src/psphotBlendFit.c (revision 18555) @@ -12,7 +12,14 @@ psTimerStart ("psphot"); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); + + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // source analysis is done in S/N order (brightest first) @@ -81,5 +88,5 @@ // I should try EXT if the source size measurement says it is large if (source->mode & PM_SOURCE_MODE_EXT_LIMIT) { - if (psphotFitBlob (readout, source, sources, psf, maskVal)) { + if (psphotFitBlob (readout, source, sources, psf, maskVal, markVal)) { source->type = PM_SOURCE_TYPE_EXTENDED; psTrace ("psphot", 5, "source at %7.1f, %7.1f is ext", source->moments->x, source->moments->y); @@ -88,5 +95,5 @@ } } else { - if (psphotFitBlend (readout, source, psf, maskVal)) { + if (psphotFitBlend (readout, source, psf, maskVal, markVal)) { source->type = PM_SOURCE_TYPE_STAR; psTrace ("psphot", 5, "source at %7.1f, %7.1f is psf", source->moments->x, source->moments->y); Index: trunk/psphot/src/psphotChoosePSF.c =================================================================== --- trunk/psphot/src/psphotChoosePSF.c (revision 18471) +++ trunk/psphot/src/psphotChoosePSF.c (revision 18555) @@ -8,11 +8,14 @@ psTimerStart ("psphot"); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType mark = psMetadataLookupU8(&status, recipe, "MASK.MARK"); // Mask value for bad pixels - assert (mark); + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // examine PSF sources in S/N order (brightest first) @@ -147,5 +150,5 @@ for (int i = 0; i < modelNames->n; i++) { char *modelName = modelNames->data[i]; - pmPSFtry *try = pmPSFtryModel (stars, modelName, options, maskVal, mark); // Attempt at fit + pmPSFtry *try = pmPSFtryModel (stars, modelName, options, maskVal, markVal); // Attempt at fit if (!try) { // No big deal --- we'll try another model @@ -321,7 +324,7 @@ // use pmModelSub because modelFlux has not been generated assert (source->maskObj); - psImageKeepCircle (source->maskObj, x, y, options->radius, "OR", PM_MASK_MARK); + psImageKeepCircle (source->maskObj, x, y, options->radius, "OR", markVal); pmModelSub (source->pixels, source->maskObj, source->modelPSF, PM_MODEL_OP_FULL, maskVal); - psImageKeepCircle (source->maskObj, x, y, options->radius, "AND", PS_NOT_U8(PM_MASK_MARK)); + psImageKeepCircle (source->maskObj, x, y, options->radius, "AND", PS_NOT_U8(markVal)); } Index: trunk/psphot/src/psphotExtendedSourceFits.c =================================================================== --- trunk/psphot/src/psphotExtendedSourceFits.c (revision 18471) +++ trunk/psphot/src/psphotExtendedSourceFits.c (revision 18555) @@ -15,4 +15,10 @@ psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels assert (maskVal); + + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); // Mask value for bad pixels + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // perform full extended source non-linear fits? @@ -155,5 +161,5 @@ pmModel *modelFit = NULL; if (convolved) { - modelFit = psphotPSFConvModel (readout, source, modelType, maskVal, psfSize); + modelFit = psphotPSFConvModel (readout, source, modelType, maskVal, markVal, psfSize); if (!modelFit) { psTrace ("psphot", 5, "failed to fit psf-conv model for object at %f, %f", source->moments->x, source->moments->y); @@ -168,5 +174,5 @@ psFree (source->modelFlux); source->modelFlux = NULL; - modelFit = psphotFitEXT (readout, source, modelType, maskVal); + modelFit = psphotFitEXT (readout, source, modelType, maskVal, markVal); if (!modelFit) { psTrace ("psphot", 5, "failed to fit plain model for object at %f, %f", source->moments->x, source->moments->y); Index: trunk/psphot/src/psphotFitSourcesLinear.c =================================================================== --- trunk/psphot/src/psphotFitSourcesLinear.c (revision 18471) +++ trunk/psphot/src/psphotFitSourcesLinear.c (revision 18555) @@ -10,5 +10,5 @@ // the analysis is performed wrt the simulated pixel values -static bool SetBorderMatrixElements (psSparseBorder *border, pmReadout *readout, psArray *sources, bool constant_weights, int SKY_FIT_ORDER); +static bool SetBorderMatrixElements (psSparseBorder *border, pmReadout *readout, psArray *sources, bool constant_weights, int SKY_FIT_ORDER, psMaskType markVal); bool psphotFitSourcesLinear (pmReadout *readout, psArray *sources, psMetadata *recipe, pmPSF *psf, bool final) { @@ -22,7 +22,14 @@ psTimerStart ("psphot"); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); + + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // source analysis is done in spatial order @@ -157,5 +164,5 @@ // set the sky, sky_x, sky_y components of border matrix - SetBorderMatrixElements (border, readout, fitSources, CONSTANT_PHOTOMETRIC_WEIGHTS, SKY_FIT_ORDER); + SetBorderMatrixElements (border, readout, fitSources, CONSTANT_PHOTOMETRIC_WEIGHTS, SKY_FIT_ORDER, markVal); psLogMsg ("psphot.ensemble", PS_LOG_MINUTIA, "set border: %f (%d elements)\n", psTimerMark ("psphot"), sparse->Nelem); @@ -221,5 +228,5 @@ // on the pixels which correspond to all of the sources of interest. These elements fill in // the border matrix components in the sparse matrix equation. -static bool SetBorderMatrixElements (psSparseBorder *border, pmReadout *readout, psArray *sources, bool constant_weights, int SKY_FIT_ORDER) { +static bool SetBorderMatrixElements (psSparseBorder *border, pmReadout *readout, psArray *sources, bool constant_weights, int SKY_FIT_ORDER, psMaskType markVal) { // generate the image-wide weight terms @@ -227,5 +234,5 @@ psRegion fullArray = psRegionSet (0, 0, 0, 0); fullArray = psRegionForImage (readout->mask, fullArray); - psImageMaskRegion (readout->mask, fullArray, "OR", PM_MASK_MARK); + psImageMaskRegion (readout->mask, fullArray, "OR", markVal); psLogMsg ("psphot.ensemble", PS_LOG_INFO, "step 1: %f sec\n", psTimerMark ("psphot")); @@ -237,5 +244,5 @@ float x = model->params->data.F32[PM_PAR_XPOS]; float y = model->params->data.F32[PM_PAR_YPOS]; - psImageMaskCircle (source->maskView, x, y, model->radiusFit, "AND", PS_NOT_U8(PM_MASK_MARK)); + psImageMaskCircle (source->maskView, x, y, model->radiusFit, "AND", PS_NOT_U8(markVal)); } psLogMsg ("psphot.ensemble", PS_LOG_INFO, "step 2: %f sec\n", psTimerMark ("psphot")); @@ -279,5 +286,5 @@ // turn off MARK for all image pixels - psImageMaskRegion (readout->mask, fullArray, "AND", PS_NOT_U8(PM_MASK_MARK)); + psImageMaskRegion (readout->mask, fullArray, "AND", PS_NOT_U8(markVal)); psLogMsg ("psphot.ensemble", PS_LOG_INFO, "step 4: %f sec\n", psTimerMark ("psphot")); Index: trunk/psphot/src/psphotGuessModels.c =================================================================== --- trunk/psphot/src/psphotGuessModels.c (revision 18471) +++ trunk/psphot/src/psphotGuessModels.c (revision 18555) @@ -23,7 +23,14 @@ psTimerStart ("psphot"); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); + + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // setup the PSF fit radius details @@ -85,5 +92,5 @@ // XXX need to define the guess flux? // set the fit radius based on the object flux limit and the model - psphotCheckRadiusPSF (readout, source, modelPSF); + psphotCheckRadiusPSF (readout, source, modelPSF, markVal); // set the source PSF model Index: trunk/psphot/src/psphotMagnitudes.c =================================================================== --- trunk/psphot/src/psphotMagnitudes.c (revision 18471) +++ trunk/psphot/src/psphotMagnitudes.c (revision 18555) @@ -8,11 +8,14 @@ psTimerStart ("psphot"); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType mark = psMetadataLookupU8(&status, recipe, "MASK.MARK"); // Mask value for bad pixels - assert (mark); + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; pmSourceMagnitudesInit (recipe); @@ -35,5 +38,5 @@ for (int i = 0; i < sources->n; i++) { pmSource *source = (pmSource *) sources->data[i]; - status = pmSourceMagnitudes (source, psf, photMode, maskVal, mark); + status = pmSourceMagnitudes (source, psf, photMode, maskVal); if (status) Nap ++; Index: trunk/psphot/src/psphotMaskReadout.c =================================================================== --- trunk/psphot/src/psphotMaskReadout.c (revision 18471) +++ trunk/psphot/src/psphotMaskReadout.c (revision 18555) @@ -7,27 +7,10 @@ // ** Interpret the mask values: - - // single-bit named masks - psMaskType maskMark = pmConfigMask("MARK", config); // Mask value for marking - psMetadataAddU8 (recipe, PS_LIST_TAIL, "MASK.MARK", PS_META_REPLACE, "user-defined mask", maskMark); - - psMaskType maskSat = pmConfigMask("SAT", config); // Mask value for saturated pixels + // XXX drop the write to recipe and move config into psphotRoughClass? + psMaskType maskSat = pmConfigMaskGet("SAT", config); // Mask value for saturated pixels psMetadataAddU8 (recipe, PS_LIST_TAIL, "MASK.SAT", PS_META_REPLACE, "user-defined mask", maskSat); - psMaskType maskBad = pmConfigMask("BAD", config); // Mask value for bad pixels + psMaskType maskBad = pmConfigMaskGet("BAD", config); // Mask value for bad pixels psMetadataAddU8 (recipe, PS_LIST_TAIL, "MASK.BAD", PS_META_REPLACE, "user-defined mask", maskBad); - - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "PSPHOT"); // Mask value for bad pixels - if (!maskVal) { - const char *maskValStr = psMetadataLookupStr(NULL, recipe, "MASKVAL"); // String with mask names - if (!maskValStr) { - psError(PSPHOT_ERR_CONFIG, false, "Missing recipe item: MASKVAL(STR)"); - return false; - } - maskVal = pmConfigMask(maskValStr, config); // Mask values to mask against - psMetadataAddU8 (recipe, PS_LIST_TAIL, "MASK.PSPHOT", PS_META_REPLACE, "user-defined mask", maskVal); - assert (maskVal); - } // generate mask & weight images if they don't already exit Index: trunk/psphot/src/psphotModelTest.c =================================================================== --- trunk/psphot/src/psphotModelTest.c (revision 18471) +++ trunk/psphot/src/psphotModelTest.c (revision 18555) @@ -12,9 +12,14 @@ pmSourceFitMode fitMode; - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels - psMaskType mark = psMetadataLookupU8(&status, recipe, "MASK.MARK"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); - assert (mark); + + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // run model fitting tests on a single source? @@ -130,5 +135,5 @@ // find the local sky - status = pmSourceLocalSky (source, PS_STAT_SAMPLE_MEDIAN, INNER, maskVal, mark); + status = pmSourceLocalSky (source, PS_STAT_SAMPLE_MEDIAN, INNER, maskVal, markVal); if (!status) psAbort("pmSourceLocalSky error"); @@ -195,5 +200,5 @@ // define the pixels used for the fit - psImageKeepCircle (source->maskObj, xObj, yObj, RADIUS, "OR", mark); + psImageKeepCircle (source->maskObj, xObj, yObj, RADIUS, "OR", markVal); psphotSaveImage (NULL, source->maskObj, "mask1.fits"); @@ -213,5 +218,5 @@ assert (status); - model = psphotPSFConvModel (readout, source, modelType, maskVal, psfSize); + model = psphotPSFConvModel (readout, source, modelType, maskVal, markVal, psfSize); params = model->params->data.F32; } else { Index: trunk/psphot/src/psphotMosaicChip.c =================================================================== --- trunk/psphot/src/psphotMosaicChip.c (revision 18471) +++ trunk/psphot/src/psphotMosaicChip.c (revision 18555) @@ -25,8 +25,10 @@ } + psMaskType blankMask = pmConfigMaskGet("BLANK", config); + // mosaic the chip, forcing a deep copy (resulting images are not subimages) psTrace("pmChipMosaic", 5, "mosaic chip %s to %s (xbin,ybin: %d,%d to %d,%d)\n", in->name, out->name, in->xBin, in->yBin, out->xBin, out->yBin); - status = pmChipMosaic(outChip, inChip, true, pmConfigMask("BLANK", config)); + status = pmChipMosaic(outChip, inChip, true, blankMask); return status; } Index: trunk/psphot/src/psphotPSFConvModel.c =================================================================== --- trunk/psphot/src/psphotPSFConvModel.c (revision 18471) +++ trunk/psphot/src/psphotPSFConvModel.c (revision 18555) @@ -9,6 +9,9 @@ // modelConv to contain the fitted parameters, and the modelFlux to contain the // convolved model image. -pmModel *psphotPSFConvModel (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal, int psfSize) { +pmModel *psphotPSFConvModel (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal, psMaskType markVal, int psfSize) { + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; + // make sure we save a cached copy of the psf flux pmSourceCachePSF (source, maskVal); @@ -65,5 +68,5 @@ psVector *dparams = modelConv->dparams; - psphotCheckRadiusEXT (readout, source, modelConv); + psphotCheckRadiusEXT (readout, source, modelConv, markVal); // create the minimization constraints Index: trunk/psphot/src/psphotParseCamera.c =================================================================== --- trunk/psphot/src/psphotParseCamera.c (revision 18471) +++ trunk/psphot/src/psphotParseCamera.c (revision 18555) @@ -17,10 +17,28 @@ // if MASK or WEIGHT was supplied on command line, bind files to 'load' // the mask and weight will be mosaicked with the image - pmFPAfileBindFromArgs (&status, load, config, "PSPHOT.MASK", "MASK"); + pmFPAfile *mask = pmFPAfileBindFromArgs (&status, load, config, "PSPHOT.MASK", "MASK"); if (!status) { psError (PS_ERR_UNKNOWN, false, "failed to load find definition"); return NULL; } - + if (mask) { + // 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 PSPHOT.MASK"); + return NULL; + } + // XXX should this be done in pmFPAfileIO.c read functions? + if (!pmConfigMaskReadHeader (config, hdu->header)) { + psError(PS_ERR_IO, false, "error in mask bits"); + return NULL; + } + } + if (!psphotSetMaskBits (config)) { + psError (PS_ERR_UNKNOWN, false, "failed to set mask bit values"); + return NULL; + } + pmFPAfileBindFromArgs (&status, load, config, "PSPHOT.WEIGHT", "WEIGHT"); if (!status) { Index: trunk/psphot/src/psphotRadiusChecks.c =================================================================== --- trunk/psphot/src/psphotRadiusChecks.c (revision 18471) +++ trunk/psphot/src/psphotRadiusChecks.c (revision 18555) @@ -7,7 +7,6 @@ // and a per-object radius is calculated) -bool psphotInitRadiusPSF(const psMetadata *recipe, - const pmModelType type) -{ +bool psphotInitRadiusPSF(const psMetadata *recipe, const pmModelType type) { + bool status = true; @@ -20,5 +19,5 @@ // call this function whenever you (re)-define the PSF model -bool psphotCheckRadiusPSF (pmReadout *readout, pmSource *source, pmModel *model) +bool psphotCheckRadiusPSF (pmReadout *readout, pmSource *source, pmModel *model, psMaskType markVal) { psF32 *PAR = model->params->data.F32; @@ -47,9 +46,9 @@ // set the mask to flag the excluded pixels - psImageKeepCircle (source->maskObj, PAR[PM_PAR_XPOS], PAR[PM_PAR_YPOS], model->radiusFit, "OR", PM_MASK_MARK); + psImageKeepCircle (source->maskObj, PAR[PM_PAR_XPOS], PAR[PM_PAR_YPOS], model->radiusFit, "OR", markVal); return status; } -bool psphotCheckRadiusPSFBlend (pmReadout *readout, pmSource *source, pmModel *model, float dR) { +bool psphotCheckRadiusPSFBlend (pmReadout *readout, pmSource *source, pmModel *model, psMaskType markVal, float dR) { psF32 *PAR = model->params->data.F32; @@ -69,5 +68,5 @@ // set the mask to flag the excluded pixels - psImageKeepCircle (source->maskObj, PAR[PM_PAR_XPOS], PAR[PM_PAR_YPOS], model->radiusFit, "OR", PM_MASK_MARK); + psImageKeepCircle (source->maskObj, PAR[PM_PAR_XPOS], PAR[PM_PAR_YPOS], model->radiusFit, "OR", markVal); return status; } @@ -87,5 +86,5 @@ // call this function whenever you (re)-define the EXT model -bool psphotCheckRadiusEXT (pmReadout *readout, pmSource *source, pmModel *model) { +bool psphotCheckRadiusEXT (pmReadout *readout, pmSource *source, pmModel *model, psMaskType markVal) { psF32 *PAR = model->params->data.F32; @@ -102,5 +101,5 @@ // set the mask to flag the excluded pixels - psImageKeepCircle (source->maskObj, PAR[PM_PAR_XPOS], PAR[PM_PAR_YPOS], model->radiusFit, "OR", PM_MASK_MARK); + psImageKeepCircle (source->maskObj, PAR[PM_PAR_XPOS], PAR[PM_PAR_YPOS], model->radiusFit, "OR", markVal); return status; } Index: trunk/psphot/src/psphotSourceFits.c =================================================================== --- trunk/psphot/src/psphotSourceFits.c (revision 18471) +++ trunk/psphot/src/psphotSourceFits.c (revision 18555) @@ -21,11 +21,14 @@ } -bool psphotFitBlend (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal) { +bool psphotFitBlend (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal, psMaskType markVal) { float x, y, dR; + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // if this source is not a possible blend, just fit as PSF if ((source->blends == NULL) || (source->mode & PM_SOURCE_MODE_SATSTAR)) { - bool status = psphotFitPSF (readout, source, psf, maskVal); + bool status = psphotFitPSF (readout, source, psf, maskVal, markVal); return status; } @@ -80,5 +83,5 @@ // extend source radius as needed - psphotCheckRadiusPSFBlend (readout, source, PSF, dR); + psphotCheckRadiusPSFBlend (readout, source, PSF, markVal, dR); // fit PSF model (set/unset the pixel mask) @@ -139,7 +142,10 @@ } -bool psphotFitPSF (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal) { +bool psphotFitPSF (pmReadout *readout, pmSource *source, pmPSF *psf, psMaskType maskVal, psMaskType markVal) { double chiTrend; + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; NfitPSF ++; @@ -150,5 +156,5 @@ // extend source radius as needed - psphotCheckRadiusPSF (readout, source, PSF); + psphotCheckRadiusPSF (readout, source, PSF, markVal); // fit PSF model (set/unset the pixel mask) @@ -197,5 +203,5 @@ } -bool psphotFitBlob (pmReadout *readout, pmSource *source, psArray *sources, pmPSF *psf, psMaskType maskVal) { +bool psphotFitBlob (pmReadout *readout, pmSource *source, psArray *sources, pmPSF *psf, psMaskType maskVal, psMaskType markVal) { bool okEXT, okDBL; @@ -215,14 +221,15 @@ psTrace ("psphot", 5, "trying blob...\n"); - // psTraceSetLevel("psModules.objects.pmSourceFitSet", 5); + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // this temporary source is used as a place-holder by the psphotEval functions below pmSource *tmpSrc = pmSourceAlloc (); - pmModel *EXT = psphotFitEXT (readout, source, modelTypeEXT, maskVal); + pmModel *EXT = psphotFitEXT (readout, source, modelTypeEXT, maskVal, markVal); okEXT = psphotEvalEXT (tmpSrc, EXT); chiEXT = EXT->chisq / EXT->nDOF; - psArray *DBL = psphotFitDBL (readout, source, maskVal); + psArray *DBL = psphotFitDBL (readout, source, maskVal, markVal); okDBL = psphotEvalDBL (tmpSrc, DBL->data[0]); okDBL &= psphotEvalDBL (tmpSrc, DBL->data[1]); @@ -306,5 +313,5 @@ // fit a double PSF source to an extended blob -psArray *psphotFitDBL (pmReadout *readout, pmSource *source, psMaskType maskVal) { +psArray *psphotFitDBL (pmReadout *readout, pmSource *source, psMaskType maskVal, psMaskType markVal) { float dx, dy; @@ -317,4 +324,7 @@ NfitDBL ++; + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; + // make a guess at the position of the two sources moments.x2 = source->moments->Sx; @@ -329,5 +339,5 @@ // save the PSF model from the Ensemble fit PSF = source->modelPSF; - psphotCheckRadiusPSFBlend (readout, source, PSF, 8.0); + psphotCheckRadiusPSFBlend (readout, source, PSF, markVal, 8.0); if (isnan(PSF->params->data.F32[1])) psAbort("nan in dbl fit"); @@ -351,7 +361,10 @@ } -pmModel *psphotFitEXT (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal) { +pmModel *psphotFitEXT (pmReadout *readout, pmSource *source, pmModelType modelType, psMaskType maskVal, psMaskType markVal) { NfitEXT ++; + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // use the source moments, etc to guess basic model parameters @@ -361,5 +374,5 @@ // if (isnan(EXT->params->data.F32[1])) psAbort("nan in ext fit"); - psphotCheckRadiusEXT (readout, source, EXT); + psphotCheckRadiusEXT (readout, source, EXT, markVal); if ((source->moments->Sx < 1e-3) || (source->moments->Sx < 1e-3)) { Index: trunk/psphot/src/psphotSourceStats.c =================================================================== --- trunk/psphot/src/psphotSourceStats.c (revision 18471) +++ trunk/psphot/src/psphotSourceStats.c (revision 18555) @@ -9,11 +9,14 @@ psTimerStart ("psphot"); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels + // bit-masks to test for good/bad pixels + psMaskType maskVal = psMetadataLookupU8(&status, recipe, "MASK.PSPHOT"); assert (maskVal); - // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) - psMaskType mark = psMetadataLookupU8(&status, recipe, "MASK.MARK"); // Mask value for bad pixels - assert (mark); + // bit-mask to mark pixels not used in analysis + psMaskType markVal = psMetadataLookupU8(&status, recipe, "MARK.PSPHOT"); + assert (markVal); + + // maskVal is used to test for rejected pixels, and must include markVal + maskVal |= markVal; // determine properties (sky, moments) of initial sources @@ -67,5 +70,5 @@ // measure a local sky value // the local sky is now ignored; kept here for reference only - status = pmSourceLocalSky (source, PS_STAT_SAMPLE_MEDIAN, INNER, maskVal, mark); + status = pmSourceLocalSky (source, PS_STAT_SAMPLE_MEDIAN, INNER, maskVal, markVal); if (!status) { psFree (source); @@ -77,5 +80,5 @@ // measure the local sky variance (needed if noise is not sqrt(signal)) // XXX EAM : this should use ROBUST not SAMPLE median, but it is broken - status = pmSourceLocalSkyVariance (source, PS_STAT_SAMPLE_MEDIAN, INNER, maskVal, mark); + status = pmSourceLocalSkyVariance (source, PS_STAT_SAMPLE_MEDIAN, INNER, maskVal, markVal); if (!status) { psFree (source); Index: trunk/psphot/src/psphotTestPSF.c =================================================================== --- trunk/psphot/src/psphotTestPSF.c (revision 18471) +++ trunk/psphot/src/psphotTestPSF.c (revision 18555) @@ -109,7 +109,7 @@ // set temporary object mask and fit object // fit model as EXT, not PSF - psImageKeepCircle (source->mask, x, y, RADIUS, "OR", PM_MASK_MARK); + psImageKeepCircle (source->mask, x, y, RADIUS, "OR", markVal); status = pmSourceFitModel (source, model, PM_SOURCE_FIT_EXT); - psImageKeepCircle (source->mask, x, y, RADIUS, "AND", PS_NOT_U8(PM_MASK_MARK)); + psImageKeepCircle (source->mask, x, y, RADIUS, "AND", PS_NOT_U8(markVal)); // write fitted parameters to file