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psphotSourceSize.c

Timestamp:

Jan 25, 2010, 7:52:41 PM (16 years ago)

Author:

eugene

Message:

various API updates to work with multiple INPUT files (not yet finished)

File:

: 1 edited

branches/eam_branches/psphot.stack.20100120/src/psphotSourceSize.c (modified) (12 diffs)

Legend:

: Unmodified
: Added
: Removed

branches/eam_branches/psphot.stack.20100120/src/psphotSourceSize.c

-              r26643
+              r26681
 } psphotSourceSizeOptions;
+// local functions:
+bool psphotSourceSizeReadout(pmConfig *config, const pmFPAview *view, const char *filename, int index);
 bool psphotSourceSizePSF (psphotSourceSizeOptions *options, psArray *sources, pmPSF *psf);
 bool psphotSourceClass (pmReadout *readout, psArray *sources, psMetadata *recipe, pmPSF *psf, psphotSourceSizeOptions *options);
 bool psphotSourceClassRegion (psRegion *region, pmPSFClump *psfClump, psArray *sources, psMetadata *recipe, pmPSF *psf, psphotSourceSizeOptions *options);
 bool psphotSourceSizeCR (pmReadout *readout, psArray *sources, psphotSourceSizeOptions *options);
 bool psphotMaskCosmicRay (psImage *mask, pmSource *source, psImageMaskType maskVal, psImageMaskType crMask);
 bool psphotMaskCosmicRayIsophot (pmSource *source, psImageMaskType maskVal, psImageMaskType crMask);
+bool psphotMaskCosmicRay (pmReadout *readout, pmSource *source, psImageMaskType maskVal);
+bool psphotMaskCosmicRayFootprintCheck (psArray *sources);
 // we need to call this function after sources have been fitted to the PSF model and
 …
     bool status = true;
+    // select the appropriate recipe information
+    psMetadata *recipe  = psMetadataLookupPtr (&status, config->recipes, PSPHOT_RECIPE);
+    psAssert (recipe, "missing recipe?");
     int num = psMetadataAddS32 (&status, config->arguments, "PSPHOT.INPUT.NUM");
     psAssert (status, "programming error: must define PSPHOT.INPUT.NUM");
 …
     // loop over the available readouts
     for (int i = 0; i < num; i++) {
         if (!psphotSourceSizeReadout (config, view, "PSPHOT.INPUT", i)) {
+        if (!psphotSourceSizeReadout (config, view, "PSPHOT.INPUT", i, recipe)) {
             psError (PSPHOT_ERR_CONFIG, false, "failed on saturated star deblend analysis for PSPHOT.INPUT entry %d", i);
             return false;
 …
 // XXX use an internal flag to mark sources which have already been measured
+// how to track the sources already measured?
+bool psphotSourceSize(pmConfig *config, const pmFPAview *view, const char *filename, int index)
+bool psphotSourceSizeReadout(pmConfig *config, const pmFPAview *view, const char *filename, int index, psMetadata *recipe)
+{
     bool status;
 …
     psAssert (sources, "missing sources?");
+    if (!sources->n) {
+        psLogMsg ("psphot", PS_LOG_INFO, "no sources, skipping source size");
+        return true;
+    }
     pmPSF *psf = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.PSF");
     psAssert (psf, "missing psf?");
-    // select the appropriate recipe information
-    psMetadata *recipe  = psMetadataLookupPtr (&status, config->recipes, PSPHOT_RECIPE);
-    psAssert (recipe, "missing recipe?");
     // user-defined masks to test for good/bad pixels (build from recipe list if not yet set)
 …
     // We are using the value psfMag - 2.5*log10(moment.Sum) as a measure of the extendedness
     // of and object.  We need to model this distribution for the PSF stars before we can test
+    // of an object.  We need to model this distribution for the PSF stars before we can test
     // the significance for a specific object
     // XXX move this to the code that generates the PSF?
 …
     psphotVisualShowSourceSize (readout, sources);
     psphotVisualPlotApResid (sources, options.ApResid, options.ApSysErr);
+    return true;
+}
+bool psphotMaskCosmicRay (psImage *mask, pmSource *source, psImageMaskType maskVal, psImageMaskType crMask) {
+    psphotVisualShowSatStars (recipe, psf, sources);
+    return true;
+}
+// model the apmifit distribution for the psf stars:
+bool psphotSourceSizePSF (psphotSourceSizeOptions *options, psArray *sources, pmPSF *psf) {
+    // select stats from the psf stars
+    psVector *Ap = psVectorAllocEmpty (100, PS_TYPE_F32);
+    psVector *ApErr = psVectorAllocEmpty (100, PS_TYPE_F32);
+    psImageMaskType maskVal = options->maskVal | options->markVal;
+    // XXX  why PHOT_WEIGHT??
+    pmSourcePhotometryMode photMode = PM_SOURCE_PHOT_WEIGHT;
+    for (int i = 0; i < sources->n; i++) {
+        pmSource *source = sources->data[i];
+        if (!(source->mode & PM_SOURCE_MODE_PSFSTAR)) continue;
+        // replace object in image
+        if (source->tmpFlags & PM_SOURCE_TMPF_SUBTRACTED) {
+            pmSourceAdd (source, PM_MODEL_OP_FULL, options->maskVal);
+        }
+        // clear the mask bit and set the circular mask pixels
+        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
+        psImageKeepCircle (source->maskObj, source->peak->x, source->peak->y, source->apRadius, "OR", options->markVal);
+        // XXX can we test if psfMag is set and calculate only if needed?
+        pmSourceMagnitudes (source, psf, photMode, maskVal); // maskVal includes markVal
+        // clear the mask bit
+        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
+        // re-subtract the object, leave local sky
+        pmSourceSub (source, PM_MODEL_OP_FULL, options->maskVal);
+        float apMag = -2.5*log10(source->moments->Sum);
+        float dMag = source->psfMag - apMag;
+        psVectorAppend (Ap, 100, dMag);
+        psVectorAppend (ApErr, 100, source->errMag);
+    }
+    // model the distribution as a mean or median value and a systematic error from that value:
+    psStats *stats = psStatsAlloc(PS_STAT_ROBUST_MEDIAN);
+    psVectorStats (stats, Ap, NULL, NULL, 0);
+    psVector *dAp = psVectorAlloc (Ap->n, PS_TYPE_F32);
+    for (int i = 0; i < Ap->n; i++) {
+        dAp->data.F32[i] = Ap->data.F32[i] - stats->robustMedian;
+    }
+    options->ApResid = stats->robustMedian;
+    options->ApSysErr = psVectorSystematicError(dAp, ApErr, 0.05);
+    psLogMsg ("psphot", PS_LOG_DETAIL, "psf - Sum: %f +/- %f\n", options->ApResid, options->ApSysErr);
+    psFree (Ap);
+    psFree (ApErr);
+    psFree (stats);
+    psFree (dAp);
+    return true;
+}
+// classify sources based on the combination of psf-mag, Mxx, Myy
+bool psphotSourceClass (pmReadout *readout, psArray *sources, psMetadata *recipe, pmPSF *psf, psphotSourceSizeOptions *options) {
+    bool status;
+    pmPSFClump psfClump;
+    char regionName[64];
+    psLogMsg("psModules.objects", PS_LOG_INFO, "Source Size classifications: %4s %4s %4s %4s %4s %4s", "Npsf", "Next", "Nsat", "Ncr", "Nmiss", "Nskip");
+    int nRegions = psMetadataLookupS32 (&status, readout->analysis, "PSF.CLUMP.NREGIONS");
+    for (int i = 0; i < nRegions; i ++) {
+        snprintf (regionName, 64, "PSF.CLUMP.REGION.%03d", i);
+        psMetadata *regionMD = psMetadataLookupPtr (&status, readout->analysis, regionName);
+        psAssert (regionMD, "regions must be defined by earlier call to psphotRoughClassRegion");
+        psRegion *region = psMetadataLookupPtr (&status, regionMD, "REGION");
+        psAssert (region, "regions must be defined by earlier call to psphotRoughClassRegion");
+        // pull FWHM_X,Y from the recipe, use to define psfClump.X,Y
+        psfClump.X  = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.X");   psAssert (status, "missing PSF.CLUMP.X");
+        psfClump.Y  = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.Y");   psAssert (status, "missing PSF.CLUMP.Y");
+        psfClump.dX = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.DX");  psAssert (status, "missing PSF.CLUMP.DX");
+        psfClump.dY = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.DY");  psAssert (status, "missing PSF.CLUMP.DY");
+        if ((psfClump.X < 0) || (psfClump.Y < 0) || !psfClump.X || !psfClump.Y || isnan(psfClump.X) || isnan(psfClump.Y)) {
+            psLogMsg ("psphot", 4, "Failed to find a valid PSF clump for region %f,%f - %f,%f\n", region->x0, region->y0, region->x1, region->y1);
+            continue;
+        }
+        if (!psphotSourceClassRegion (region, &psfClump, sources, recipe, psf, options)) {
+            psLogMsg ("psphot", 4, "Failed to determine source classification for region %f,%f - %f,%f\n", region->x0, region->y0, region->x1, region->y1);
+            continue;
+        }
+    }
+    return true;
+}
+bool psphotSourceClassRegion (psRegion *region, pmPSFClump *psfClump, psArray *sources, psMetadata *recipe, pmPSF *psf, psphotSourceSizeOptions *options) {
+    PS_ASSERT_PTR_NON_NULL(sources, false);
+    PS_ASSERT_PTR_NON_NULL(recipe, false);
+    int Nsat  = 0;
+    int Next  = 0;
+    int Npsf  = 0;
+    int Ncr   = 0;
+    int Nmiss = 0;
+    int Nskip = 0;
+    pmSourceMode noMoments = PM_SOURCE_MODE_MOMENTS_FAILURE | PM_SOURCE_MODE_SKYVAR_FAILURE | PM_SOURCE_MODE_SKY_FAILURE | PM_SOURCE_MODE_BELOW_MOMENTS_SN;
+    pmSourcePhotometryMode photMode = PM_SOURCE_PHOT_WEIGHT;
+    psImageMaskType maskVal = options->maskVal | options->markVal;
+    for (psS32 i = 0 ; i < sources->n ; i++) {
+        pmSource *source = (pmSource *) sources->data[i];
+        // psfClumps are found for image subregions:
+        // skip sources not in this region
+        if (source->peak->x <  region->x0) continue;
+        if (source->peak->x >= region->x1) continue;
+        if (source->peak->y <  region->y0) continue;
+        if (source->peak->y >= region->y1) continue;
+        // skip source if it was already measured
+        if (source->tmpFlags & PM_SOURCE_TMPF_SIZE_MEASURED) {
+            psTrace("psphot", 7, "Not calculating source size since it has already been measured\n");
+            continue;
+        }
+        // source must have been subtracted
+        if (!(source->tmpFlags & PM_SOURCE_TMPF_SUBTRACTED)) {
+            source->mode |= PM_SOURCE_MODE_SIZE_SKIPPED;
+            psTrace("psphot", 7, "Not calculating source size since source is not subtracted\n");
+            continue;
+        }
+        // we are basically classifying by moments; use the default if not found
+        psAssert (source->moments, "why is this source missing moments?");
+        if (source->mode & noMoments) {
+            Nskip ++;
+            continue;
+        }
+        psF32 Mxx = source->moments->Mxx;
+        psF32 Myy = source->moments->Myy;
+        // replace object in image
+        if (source->tmpFlags & PM_SOURCE_TMPF_SUBTRACTED) {
+            pmSourceAdd (source, PM_MODEL_OP_FULL, options->maskVal);
+        }
+        // clear the mask bit and set the circular mask pixels
+        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
+        psImageKeepCircle (source->maskObj, source->peak->x, source->peak->y, source->apRadius, "OR", options->markVal);
+        // XXX can we test if psfMag is set and calculate only if needed?
+        pmSourceMagnitudes (source, psf, photMode, maskVal); // maskVal includes markVal
+        // clear the mask bit
+        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
+        // re-subtract the object, leave local sky
+        pmSourceSub (source, PM_MODEL_OP_FULL, options->maskVal);
+        float apMag = -2.5*log10(source->moments->Sum);
+        float dMag = source->psfMag - apMag;
+        float nSigma = (dMag - options->ApResid) / hypot(source->errMag, options->ApSysErr);
+        source->extNsigma = nSigma;
+        source->tmpFlags |= PM_SOURCE_TMPF_SIZE_MEASURED;
+        // Anything within this region is a probably PSF-like object. Saturated stars may land
+        // in this region, but are detected elsewhere on the basis of their peak value.
+        bool isPSF = ((fabs(nSigma) < options->nSigmaApResid) &&
+                      (fabs(Mxx - psfClump->X) < options->nSigmaMoments*psfClump->dX) &&
+                      (fabs(Myy - psfClump->Y) < options->nSigmaMoments*psfClump->dY));
+        if (isPSF) {
+          psTrace("psphot.czw",4,"CLASS: %g %g\t%g %g  %g %g  %g %g\t%g %g\t%g PSF\t%g %g\n",
+                  source->peak->xf,source->peak->yf,Mxx,Myy,psfClump->X,psfClump->Y,psfClump->dX,psfClump->dY,apMag,dMag,nSigma,
+                  options->nSigmaApResid,options->nSigmaMoments);
+          Npsf ++;
+          continue;
+        }
+        // Defects may not always match CRs from peak curvature analysis
+        // Defects may also be marked as SATSTAR -- XXX deactivate this flag?
+        // XXX this rule is not great
+        if ((Mxx < psfClump->X) || (Myy < psfClump->Y)) {
+          psTrace("psphot.czw",4,"CLASS: %g %g\t%g %g  %g %g  %g %g\t%g %g\t%g CR\t%g %g\n",
+                  source->peak->xf,source->peak->yf,Mxx,Myy,psfClump->X,psfClump->Y,psfClump->dX,psfClump->dY,apMag,dMag,nSigma,
+                  options->nSigmaApResid,options->nSigmaMoments);
+            source->mode |= PM_SOURCE_MODE_DEFECT;
+            Ncr ++;
+            continue;
+        }
+        // saturated star (determined in PSF fit).  These may also be saturated galaxies, or
+        // just large saturated regions.
+        if (source->mode & PM_SOURCE_MODE_SATSTAR) {
+          psTrace("psphot.czw",4,"CLASS: %g %g\t%g %g  %g %g  %g %g\t%g %g\t%g SAT\t%g %g\n",
+                  source->peak->xf,source->peak->yf,Mxx,Myy,psfClump->X,psfClump->Y,psfClump->dX,psfClump->dY,apMag,dMag,nSigma,
+                  options->nSigmaApResid,options->nSigmaMoments);
+            Nsat ++;
+            continue;
+        }
+        // XXX allow the Mxx, Myy to be less than psfClump->X,Y (by some nSigma)?
+        bool isEXT = (nSigma > options->nSigmaApResid) || ((Mxx > psfClump->X) && (Myy > psfClump->Y));
+        if (isEXT) {
+          psTrace("psphot.czw",4,"CLASS: %g %g\t%g %g  %g %g  %g %g\t%g %g\t%g Ext\t%g %g\n",
+                  source->peak->xf,source->peak->yf,Mxx,Myy,psfClump->X,psfClump->Y,psfClump->dX,psfClump->dY,apMag,dMag,nSigma,
+                  options->nSigmaApResid,options->nSigmaMoments);
+            source->mode |= PM_SOURCE_MODE_EXT_LIMIT;
+            Next ++;
+            continue;
+        }
+        psTrace("psphot.czw",4,"CLASS: %g %g\t%g %g  %g %g  %g %g\t%g %g\t%g Unk\t%g %g\n",
+                source->peak->xf,source->peak->yf,Mxx,Myy,psfClump->X,psfClump->Y,psfClump->dX,psfClump->dY,apMag,dMag,nSigma,
+                options->nSigmaApResid,options->nSigmaMoments);
+        psWarning ("sourse size was missed for %f,%f : %f %f -- %f\n", source->peak->xf, source->peak->yf, Mxx, Myy, nSigma);
+        Nmiss ++;
+    }
+    psLogMsg("psModules.objects", PS_LOG_INFO, "Source Size classifications: %4d %4d %4d %4d %4d %4d", Npsf, Next, Nsat, Ncr, Nmiss, Nskip);
+    return true;
+}
+// given an object suspected to be a defect, generate a pixel mask using the Lapacian transform
+// if enough of the object is detected as 'sharp', consider the object a cosmic ray
+bool psphotSourceSizeCR (pmReadout *readout, psArray *sources, psphotSourceSizeOptions *options) {
+    for (int i = 0; i < sources->n; i++) {
+        pmSource *source = sources->data[i];
+        // Integer position of peak
+        int xPeak = source->peak->xf - source->pixels->col0 + 0.5;
+        int yPeak = source->peak->yf - source->pixels->row0 + 0.5;
+        // Skip sources which are too close to a boundary.  These are mostly caught as DEFECT
+        if (xPeak < 1 || xPeak > source->pixels->numCols - 2 ||
+            yPeak < 1 || yPeak > source->pixels->numRows - 2) {
+            psTrace("psphot", 7, "Not calculating crNsigma due to edge\n");
+            //      psTrace("psphot.czw", 2, "Not calculating crNsigma due to edge\n");
+            continue;
+        }
+        // this source is thought to be a cosmic ray.  flag the detection and mask the pixels
+        if (source->mode & PM_SOURCE_MODE_DEFECT) {
+            // XXX this is running slowly and is too agressive, but it more-or-less works
+            // psphotMaskCosmicRayCZW(readout, source, options->crMask);
+            // XXX these are the old versions which we are not using
+            // psphotMaskCosmicRay (readout->mask, source, maskVal, crMask);
+            // psphotMaskCosmicRay_Old (source, maskVal, crMask);
+        }
+    }
+    // now that we have masked pixels associated with CRs, we can grow the mask
+    if (options->grow > 0) {
+        bool oldThreads = psImageConvolveSetThreads(true); // Old value of threading for psImageConvolveMask
+        psImage *newMask = psImageConvolveMask(NULL, readout->mask, options->crMask, options->crMask, -options->grow, options->grow, -options->grow, options->grow);
+        psImageConvolveSetThreads(oldThreads);
+        if (!newMask) {
+            psError(PS_ERR_UNKNOWN, false, "Unable to grow CR mask");
+            return false;
+        }
+        psFree(readout->mask);
+        readout->mask = newMask;
+    }
+    // XXX test : save the mask image
+    if (0) {
+        psphotSaveImage (NULL, readout->mask,   "mask.fits");
+    }
+    return true;
+}
+// Comments by CZW 20091209 : Mechanics of how to identify CR pixels taken from "Cosmic-Ray
+// Rejection by Laplacian Edge Detection" by Pieter van Dokkum, arXiv:astro-ph/0108003.  This
+// does no repair or recovery of the CR pixels, it only masks them out.  My test code can be
+// found at /data/ipp031.0/watersc1/psphot.20091209/algo_check.c
+bool psphotMaskCosmicRay (pmReadout *readout, pmSource *source, psImageMaskType maskVal) {
+    // Get the actual images and information about the peak.
+    psImage *mask = readout->mask;
+    pmPeak *peak = source->peak;
+    pmFootprint *footprint = peak->footprint;
+    int xm = footprint->bbox.x0;
+    int xM = footprint->bbox.x1;
+    int ym = footprint->bbox.y0;
+    int yM = footprint->bbox.y1;
+    if (xm < 0) { xm = 0; }
+    if (ym < 0) { ym = 0; }
+    if (xM > mask->numCols) { xM = mask->numCols; }
+    if (yM > mask->numRows) { yM = mask->numRows; }
+    int dx = xM - xm;
+    int dy = yM - ym;
+    // Bounding boxes are inclusive of final pixel
+    // XXX ensure dx,dy do not become too large here
+    dx++;
+    dy++;
+    psImage *image= readout->image;
+    psImage *variance = readout->variance;
+    int binning = 1;
+    float sigma_thresh = 2.0;
+    int iteration = 0;
+    int max_iter = 5;
+    float noise_factor = 5.0 / 4.0;  // Intrinsic to the Laplacian making noise spikes spikier.
+    // Temporary images.
+    psImage *mypix  = psImageAlloc(dx,dy,image->type.type);
+    psImage *myvar  = psImageAlloc(dx,dy,image->type.type);
+    psImage *binned = psImageAlloc(dx * binning,dy * binning,image->type.type);
+    psImage *conved = psImageAlloc(dx * binning,dy * binning,image->type.type);
+    psImage *edges  = psImageAlloc(dx,dy,image->type.type);
+    psImage *mymask = psImageAlloc(dx,dy,PS_TYPE_IMAGE_MASK);
+    int x,y;
+    // Load my copy of things.
+    for (x = 0; x < dx; x++) {
+        for (y = 0; y < dy; y++) {
+            psImageSet(mypix,x,y,psImageGet(image,x+xm,y+ym));
+            psImageSet(myvar,x,y,psImageGet(variance,x+xm,y+ym));
+            mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] = 0x00;
+        }
+    }
+    // Mask so I can see on the output image where the footprint is.
+    for (int i = 0; i < footprint->spans->n; i++) {
+        pmSpan *sp = footprint->spans->data[i];
+        for (int j = sp->x0; j <= sp->x1; j++) {
+            y = sp->y - ym;
+            x = j - xm;
+            mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= 0x01;
+        }
+    }
+    int CRpix_count = 0;
+    do {
+        CRpix_count = 0;
+        // Zero out my temp images.
+        for (x = 0; x < binning * dx; x++) {
+            for (y = 0; y < binning * dy; y++) {
+                psImageSet(binned,x,y,0.0);
+                psImageSet(conved,x,y,0.0);
+                psImageSet(edges,x/binning,y/ binning,0.0);
+            }
+        }
+        // Make subsampled image. Maybe this should be called "unbinned" or something
+        for (x = 0; x < binning * dx; x++) {
+            for (y = 0; y < binning * dy; y++) {
+                psImageSet(binned,x,y,psImageGet(mypix,x / binning,y / binning));
+            }
+        }
+        // Apply Laplace transform (kernel = [[0 -0.25 0][-0.25 1 -0.25][0 -0.25 0]]), clipping at zero
+        for (x = 1; x < dx - 1; x++) {
+            for (y = 1; y < dy - 1; y++) {
+                psImageSet(conved,x,y,psImageGet(binned,x,y) - 0.25 *
+                           (psImageGet(binned,x-1,y) + psImageGet(binned,x+1,y) +
+                            psImageGet(binned,x,y-1) + psImageGet(binned,x,y+1)));
+                if (psImageGet(conved,x,y) < 0.0) {
+                    psImageSet(conved,x,y,0.0);
+                }
+            }
+        }
+        // Create an edge map by rebinning
+        for (x = 0; x < binning * dx; x++) {
+            for (y = 0; y < binning * dy; y++) {
+                psImageSet(edges,x / binning, y / binning,
+                           psImageGet(edges, x / binning, y / binning) +
+                           psImageGet(conved,x,y));
+            }
+        }
+        // Modify my mask if we're above the significance threshold
+        for (x = 0; x < dx; x++) {
+            for (y = 0; y < dy; y++) {
+                if ( psImageGet(edges,x,y) / (binning * sqrt(noise_factor * psImageGet(myvar,x,y))) > sigma_thresh ) {
+                    if (mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & 0x01) {
+                        mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= 0x40;
+                        CRpix_count++;
+                    }
+                }
+            }
+        }
+        // "Repair" Masked pixels for the next round.
+        for (x = 1; x < dx - 1; x++) {
+            for (y = 1; y < dy - 1; y++) {
+                if (mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & 0x40) {
+                    psImageSet(mypix,x,y,0.25 *
+                               (psImageGet(mypix,x-1,y) + psImageGet(mypix,x+1,y) +
+                                psImageGet(mypix,x,y-1) + psImageGet(mypix,x,y+1)));
+                }
+            }
+        }
+# if 0
+        if ((psTraceGetLevel("psphot.czw") >= 2)&&(abs(xm - 2770) < 5)&&(abs(ym - 2581) < 5)&&(iteration == 0)) {
+          psTrace("psphot.czw",2,"TRACEMOTRON %d %d %d %d %d\n",xm,ym,dx,dy,iteration);
+          psphotSaveImage (NULL, mypix,   "czw.pix.fits");
+          psphotSaveImage (NULL, myvar,   "czw.var.fits");
+          psphotSaveImage (NULL, binned,  "czw.binn.fits");
+          psphotSaveImage (NULL, conved,  "czw.conv.fits");
+          psphotSaveImage (NULL, edges,   "czw.edge.fits");
+          psphotSaveImage (NULL, mymask,  "czw.mask.fits");
+        }
+# endif
+        psTrace("psphot.czw",2,"Iter: %d Count: %d",iteration,CRpix_count);
+        iteration++;
+    } while ((iteration < max_iter)&&(CRpix_count > 0));
+    // A solitary masked pixel is likely a lie. Remove those.
+    for (x = 0; x < dx; x++) {
+        for (y = 0; y < dy; y++) {
+            if (mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & 0x40) {
+                if ((x-1 >= 0)&&(mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x-1] & 0x40)) {
+                    continue;
+                }
+                if ((y-1 >= 0)&&(mymask->data.PS_TYPE_IMAGE_MASK_DATA[y-1][x] & 0x40)) {
+                    continue;
+                }
+                if ((x+1 < dx)&&(mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x+1] & 0x40)) {
+                    continue;
+                }
+                if ((y+1 < dy)&&(mymask->data.PS_TYPE_IMAGE_MASK_DATA[y+1][x] & 0x40)) {
+                    continue;
+                }
+                mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] ^= 0x40;
+            }
+        }
+    }
+    // transfer temporary mask to real mask
+    for (x = 0; x < dx; x++) {
+        for (y = 0; y < dy; y++) {
+            if (mymask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & 0x40) {
+                mask->data.PS_TYPE_IMAGE_MASK_DATA[y+ym+mask->row0][x+xm+mask->col0] |= maskVal;
+            }
+        }
+    }
+    // XXX if we decide this REALLY is a cosmic ray, set the CR_LIMIT bit
+    source->mode |= PM_SOURCE_MODE_CR_LIMIT;
+    psFree(mypix);
+    psFree(myvar);
+    psFree(binned);
+    psFree(conved);
+    psFree(edges);
+    psFree(mymask);
+    return true;
+}
+bool psphotMaskCosmicRayFootprintCheck (psArray *sources) {
+    for (int i = 0; i < sources->n; i++) {
+        pmSource *source = sources->data[i];
+        pmPeak *peak = source->peak;
+        pmFootprint *footprint = peak->footprint;
+        if (!footprint) continue;
+        for (int j = 0; j < footprint->spans->n; j++) {
+            pmSpan *sp = footprint->spans->data[j];
+            psAssert (sp, "missing span");
+        }
+    }
+    return true;
+}
+/**** ------ old versions of cosmic ray masking ----- ****/
+// This attempt to mask the cosmic rays used the isophotal boundary
+bool psphotMaskCosmicRay_V1 (psImage *mask, pmSource *source, psImageMaskType maskVal, psImageMaskType crMask) {
     // replace the source flux
 …
     pmFootprint *footprint = peak->footprint;
     if (!footprint) {
+      psTrace("psphot.czw",2,"Using isophot CR mask code.");
         // if we have not footprint, use the old code to mask by isophot
         psphotMaskCosmicRayIsophot (source, maskVal, crMask);
 …
     if (!footprint->spans) {
+      psTrace("psphot.czw",2,"Using isophot CR mask code.");
         // if we have no footprint, use the old code to mask by isophot
         psphotMaskCosmicRayIsophot (source, maskVal, crMask);
         return true;
+    }
+    psphotMaskCosmicRayIsophot (source, maskVal, crMask);
     // mask all of the pixels covered by the spans of the footprint
     for (int j = 1; j < footprint->spans->n; j++) {
+        pmSpan *span1 = footprint->spans->data[j];
+        int iy = span1->y;
+        int xs = span1->x0;
+        int xe = span1->x1;
+        for (int ix = xs; ix < xe; ix++) {
+            mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= crMask;
+        }
+    }
+    for (int j = 1; j < footprint->spans->n; j++) {
+        pmSpan *span1 = footprint->spans->data[j];
+        int iy = span1->y;
+        int xs = span1->x0;
+        int xe = span1->x1;
+        for (int ix = xs; ix < xe; ix++) {
+            mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= crMask;
+        }
+    }
     return true;
+}
 …
+        }
+    }
-    return true;
+}
-// model the apmifit distribution for the psf stars:
-bool psphotSourceSizePSF (psphotSourceSizeOptions *options, psArray *sources, pmPSF *psf) {
-    // select stats from the psf stars
-    psVector *Ap = psVectorAllocEmpty (100, PS_TYPE_F32);
-    psVector *ApErr = psVectorAllocEmpty (100, PS_TYPE_F32);
-    psImageMaskType maskVal = options->maskVal | options->markVal;
-    // XXX  why PHOT_WEIGHT??
-    pmSourcePhotometryMode photMode = PM_SOURCE_PHOT_WEIGHT;
-    for (int i = 0; i < sources->n; i++) {
-        pmSource *source = sources->data[i];
-        if (!(source->mode & PM_SOURCE_MODE_PSFSTAR)) continue;
-        // replace object in image
-        if (source->tmpFlags & PM_SOURCE_TMPF_SUBTRACTED) {
-            pmSourceAdd (source, PM_MODEL_OP_FULL, options->maskVal);
+        }
-        // clear the mask bit and set the circular mask pixels
-        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
-        psImageKeepCircle (source->maskObj, source->peak->x, source->peak->y, source->apRadius, "OR", options->markVal);
-        // XXX can we test if psfMag is set and calculate only if needed?
-        pmSourceMagnitudes (source, psf, photMode, maskVal); // maskVal includes markVal
-        // clear the mask bit
-        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
-        // re-subtract the object, leave local sky
-        pmSourceSub (source, PM_MODEL_OP_FULL, options->maskVal);
-        float apMag = -2.5*log10(source->moments->Sum);
-        float dMag = source->psfMag - apMag;
-        psVectorAppend (Ap, dMag);
-        psVectorAppend (ApErr, source->errMag);
+    }
-    // model the distribution as a mean or median value and a systematic error from that value:
-    psStats *stats = psStatsAlloc(PS_STAT_ROBUST_MEDIAN);
-    psVectorStats (stats, Ap, NULL, NULL, 0);
-    psVector *dAp = psVectorAlloc (Ap->n, PS_TYPE_F32);
-    for (int i = 0; i < Ap->n; i++) {
-        dAp->data.F32[i] = Ap->data.F32[i] - stats->robustMedian;
+    }
-    options->ApResid = stats->robustMedian;
-    options->ApSysErr = psVectorSystematicError(dAp, ApErr, 0.05);
-    // XXX this is quite arbitrary...
-    if (!isfinite(options->ApSysErr)) options->ApSysErr = 0.01;
-    psLogMsg ("psphot", PS_LOG_DETAIL, "psf - Sum: %f +/- %f\n", options->ApResid, options->ApSysErr);
-    psFree (Ap);
-    psFree (ApErr);
-    psFree (stats);
-    psFree (dAp);
-    return true;
+}
-// classify sources based on the combination of psf-mag, Mxx, Myy
-bool psphotSourceClass (pmReadout *readout, psArray *sources, psMetadata *recipe, pmPSF *psf, psphotSourceSizeOptions *options) {
-    bool status;
-    pmPSFClump psfClump;
-    char regionName[64];
-    psLogMsg("psModules.objects", PS_LOG_INFO, "Source Size classifications: %4s %4s %4s %4s %4s %4s", "Npsf", "Next", "Nsat", "Ncr", "Nmiss", "Nskip");
-    int nRegions = psMetadataLookupS32 (&status, readout->analysis, "PSF.CLUMP.NREGIONS");
-    for (int i = 0; i < nRegions; i ++) {
-        snprintf (regionName, 64, "PSF.CLUMP.REGION.%03d", i);
-        psMetadata *regionMD = psMetadataLookupPtr (&status, readout->analysis, regionName);
-        psAssert (regionMD, "regions must be defined by earlier call to psphotRoughClassRegion");
-        psRegion *region = psMetadataLookupPtr (&status, regionMD, "REGION");
-        psAssert (region, "regions must be defined by earlier call to psphotRoughClassRegion");
-        // pull FWHM_X,Y from the recipe, use to define psfClump.X,Y
-        psfClump.X  = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.X");   psAssert (status, "missing PSF.CLUMP.X");
-        psfClump.Y  = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.Y");   psAssert (status, "missing PSF.CLUMP.Y");
-        psfClump.dX = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.DX");  psAssert (status, "missing PSF.CLUMP.DX");
-        psfClump.dY = psMetadataLookupF32 (&status, regionMD, "PSF.CLUMP.DY");  psAssert (status, "missing PSF.CLUMP.DY");
-        if ((psfClump.X < 0) || (psfClump.Y < 0) || !psfClump.X || !psfClump.Y || isnan(psfClump.X) || isnan(psfClump.Y)) {
-            psLogMsg ("psphot", 4, "Failed to find a valid PSF clump for region %f,%f - %f,%f\n", region->x0, region->y0, region->x1, region->y1);
-            continue;
+        }
-        if (!psphotSourceClassRegion (region, &psfClump, sources, recipe, psf, options)) {
-            psLogMsg ("psphot", 4, "Failed to determine source classification for region %f,%f - %f,%f\n", region->x0, region->y0, region->x1, region->y1);
-            continue;
+        }
+    }
-    return true;
+}
-bool psphotSourceClassRegion (psRegion *region, pmPSFClump *psfClump, psArray *sources, psMetadata *recipe, pmPSF *psf, psphotSourceSizeOptions *options) {
-    PS_ASSERT_PTR_NON_NULL(sources, false);
-    PS_ASSERT_PTR_NON_NULL(recipe, false);
-    int Nsat  = 0;
-    int Next  = 0;
-    int Npsf  = 0;
-    int Ncr   = 0;
-    int Nmiss = 0;
-    int Nskip = 0;
-    pmSourceMode noMoments = PM_SOURCE_MODE_MOMENTS_FAILURE | PM_SOURCE_MODE_SKYVAR_FAILURE | PM_SOURCE_MODE_SKY_FAILURE | PM_SOURCE_MODE_BELOW_MOMENTS_SN;
-    pmSourcePhotometryMode photMode = PM_SOURCE_PHOT_WEIGHT;
-    psImageMaskType maskVal = options->maskVal | options->markVal;
-    for (psS32 i = 0 ; i < sources->n ; i++) {
-        pmSource *source = (pmSource *) sources->data[i];
-        // psfClumps are found for image subregions:
-        // skip sources not in this region
-        if (source->peak->x <  region->x0) continue;
-        if (source->peak->x >= region->x1) continue;
-        if (source->peak->y <  region->y0) continue;
-        if (source->peak->y >= region->y1) continue;
-        // skip source if it was already measured
-        if (source->tmpFlags & PM_SOURCE_TMPF_SIZE_MEASURED) {
-            psTrace("psphot", 7, "Not calculating source size since it has already been measured\n");
-            continue;
+        }
-        // source must have been subtracted
-        if (!(source->tmpFlags & PM_SOURCE_TMPF_SUBTRACTED)) {
-            source->mode |= PM_SOURCE_MODE_SIZE_SKIPPED;
-            psTrace("psphot", 7, "Not calculating source size since source is not subtracted\n");
-            continue;
+        }
-        // we are basically classifying by moments; use the default if not found
-        psAssert (source->moments, "why is this source missing moments?");
-        if (source->mode & noMoments) {
-            Nskip ++;
-            continue;
+        }
-        psF32 Mxx = source->moments->Mxx;
-        psF32 Myy = source->moments->Myy;
-        // replace object in image
-        if (source->tmpFlags & PM_SOURCE_TMPF_SUBTRACTED) {
-            pmSourceAdd (source, PM_MODEL_OP_FULL, options->maskVal);
+        }
-        // clear the mask bit and set the circular mask pixels
-        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
-        psImageKeepCircle (source->maskObj, source->peak->x, source->peak->y, source->apRadius, "OR", options->markVal);
-        // XXX can we test if psfMag is set and calculate only if needed?
-        pmSourceMagnitudes (source, psf, photMode, maskVal); // maskVal includes markVal
-        // clear the mask bit
-        psImageMaskPixels (source->maskObj, "AND", PS_NOT_IMAGE_MASK(options->markVal));
-        // re-subtract the object, leave local sky
-        pmSourceSub (source, PM_MODEL_OP_FULL, options->maskVal);
-        float apMag = -2.5*log10(source->moments->Sum);
-        float dMag = source->psfMag - apMag;
-        float nSigma = (dMag - options->ApResid) / hypot(source->errMag, options->ApSysErr);
-        source->extNsigma = nSigma;
-        source->tmpFlags |= PM_SOURCE_TMPF_SIZE_MEASURED;
-        // Anything within this region is a probably PSF-like object. Saturated stars may land
-        // in this region, but are detected elsewhere on the basis of their peak value.
-        bool isPSF = (fabs(nSigma) < options->nSigmaApResid) && (fabs(Mxx - psfClump->X) < options->nSigmaMoments*psfClump->dX) && (fabs(Myy - psfClump->Y) < options->nSigmaMoments*psfClump->dY);
-        if (isPSF) {
-            Npsf ++;
-            continue;
+        }
-        // Defects may not always match CRs from peak curvature analysis
-        // Defects may also be marked as SATSTAR -- XXX deactivate this flag?
-        // XXX this rule is not great
-        if ((Mxx < psfClump->X) || (Myy < psfClump->Y)) {
-            source->mode |= PM_SOURCE_MODE_DEFECT;
-            Ncr ++;
-            continue;
+        }
-        // saturated star (determined in PSF fit).  These may also be saturated galaxies, or
-        // just large saturated regions.
-        if (source->mode & PM_SOURCE_MODE_SATSTAR) {
-            Nsat ++;
-            continue;
+        }
-        // XXX allow the Mxx, Myy to be less than psfClump->X,Y (by some nSigma)?
-        bool isEXT = (nSigma > options->nSigmaApResid) || ((Mxx > psfClump->X) && (Myy > psfClump->Y));
-        if (isEXT) {
-            source->mode |= PM_SOURCE_MODE_EXT_LIMIT;
-            Next ++;
-            continue;
+        }
-        psWarning ("sourse size was missed for %f,%f : %f %f -- %f\n", source->peak->xf, source->peak->yf, Mxx, Myy, nSigma);
-        Nmiss ++;
+    }
-    psLogMsg("psModules.objects", PS_LOG_INFO, "Source Size classifications: %4d %4d %4d %4d %4d %4d", Npsf, Next, Nsat, Ncr, Nmiss, Nskip);
     return true;
+}
 …
+}
+bool psphotSourceSizeCR (pmReadout *readout, psArray *sources, psphotSourceSizeOptions *options) {
+// this was an old attempt to identify cosmic rays based on the peak curvature
+bool psphotSourcePeakCurvature (pmReadout *readout, psArray *sources, psphotSourceSizeOptions *options) {
     // classify the sources based on the CR test (place this in a function?)
 …
     return true;
+}

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