Changeset 36375 for trunk/psphot

Timestamp:

Dec 10, 2013, 2:55:11 PM (13 years ago)

Author:

eugene

Message:

merge changes from eam_branches/ipp-20130904

Location:

trunk

Files:

• . (modified) (1 prop)
• psphot (modified) (1 prop)
• psphot/src (modified) (2 props)
• psphot/src/Makefile.am (modified) (8 diffs)
• psphot/src/psmakecff.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psmakecff.c )
• psphot/src/psphot.h (modified) (6 diffs)
• psphot/src/psphotArguments.c (modified) (1 diff)
• psphot/src/psphotBlendFit.c (modified) (1 diff)
• psphot/src/psphotChooseAnalysisOptions.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotChooseAnalysisOptions.c )
• psphot/src/psphotDefineFiles.c (modified) (1 diff)
• psphot/src/psphotEllipticalContour.c (modified) (1 diff)
• psphot/src/psphotExtendedSourceAnalysis.c (modified) (8 diffs)
• psphot/src/psphotExtendedSourceFits.c (modified) (21 diffs)
• psphot/src/psphotFullForce.SourceStats.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotFullForce.SourceStats.c )
• psphot/src/psphotFullForce.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotFullForce.c )
• psphot/src/psphotFullForceArguments.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotFullForceArguments.c )
• psphot/src/psphotFullForceImageLoop.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotFullForceImageLoop.c )
• psphot/src/psphotFullForceReadout.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotFullForceReadout.c )
• psphot/src/psphotGalaxyShape.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotGalaxyShape.c )
• psphot/src/psphotImageLoop.c (modified) (1 diff)
• psphot/src/psphotKronFlux.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotKronFlux.c )
• psphot/src/psphotKronIterate.c (modified) (1 diff)
• psphot/src/psphotLoadPSF.c (modified) (2 diffs)
• psphot/src/psphotMergeSources.c (modified) (7 diffs)
• psphot/src/psphotModelTestReadout.c (modified) (1 diff)
• psphot/src/psphotOldCode.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotOldCode.c )
• psphot/src/psphotPetroFlux.c (copied) (copied from branches/eam_branches/ipp-20130904/psphot/src/psphotPetroFlux.c )
• psphot/src/psphotPetrosianRadialBins.c (modified) (1 diff)
• psphot/src/psphotPetrosianStats.c (modified) (7 diffs)
• psphot/src/psphotRadialBins.c (modified) (2 diffs)
• psphot/src/psphotRadialProfile.c (modified) (7 diffs)
• psphot/src/psphotReadout.c (modified) (1 diff)
• psphot/src/psphotRoughClass.c (modified) (1 diff)
• psphot/src/psphotSetThreads.c (modified) (1 diff)
• psphot/src/psphotSourceFits.c (modified) (16 diffs)
• psphot/src/psphotSourceSize.c (modified) (15 diffs)
• psphot/src/psphotSourceStats.c (modified) (3 diffs)
• psphot/src/psphotStackImageLoop.c (modified) (1 prop)
• psphot/src/psphotStackReadout.c (modified) (3 diffs)
• psphot/test/tap_psphot_galaxygrid.pro (modified) (14 diffs)

trunk/psphot/src

@@ -24 +24 @@
 psphotModelTest
 psphotMinimal
+psphotFullForce
+psmakecff

@@ -24 +24 @@
 psphotModelTest
 psphotMinimal
+psphotFullForce
+psmakecff

trunk/psphot/src/Makefile.am

@@ -25 +25 @@
 libpsphot_la_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
 
-bin_PROGRAMS = psphot psphotForced psphotMinimal psphotMakePSF psphotStack psphotModelTest
+bin_PROGRAMS = psphot psphotForced psphotFullForce psphotMinimal psphotMakePSF psphotStack psphotModelTest psmakecff
 # bin_PROGRAMS = psphotPetrosianStudy psphotTest psphotMomentsStudy 
 
@@ -36 +36 @@
 psphotForced_LDADD = libpsphot.la
 
+psphotFullForce_CFLAGS = $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
+psphotFullForce_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
+psphotFullForce_LDADD = libpsphot.la
+
 psphotMinimal_CFLAGS = $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
 psphotMinimal_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
@@ -51 +55 @@
 psphotModelTest_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
 psphotModelTest_LDADD = libpsphot.la
+
+psmakecff_CFLAGS = $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
+psmakecff_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
+psmakecff_LDADD = libpsphot.la
+
 
 # psphotMomentsStudy_CFLAGS = $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
@@ -77 +86 @@
         psphotForced.c             \
         psphotForcedArguments.c    \
+        psphotParseCamera.c        \
+        psphotImageLoop.c          \
+        psphotMosaicChip.c         \
+        psphotCleanup.c
+
+# generalized forced photometry (including Kron, Petro, and Models) of specified positions given a specified psf
+psphotFullForce_SOURCES = \
+        psphotFullForce.c             \
+        psphotFullForceArguments.c    \
         psphotParseCamera.c        \
         psphotImageLoop.c          \
@@ -129 +147 @@
         psphotCleanup.c
 
+# a program that takes a cmf file and makes a cff file (input file for psphotFullForce
+psmakecff_SOURCES = \
+        psmakecff.c
+
 # psphotTest_SOURCES = \
 #         psphotTest.c
@@ -155 +177 @@
         psphotReadoutMinimal.c         \
         psphotForcedReadout.c          \
+        psphotFullForceReadout.c       \
+        psphotFullForce.SourceStats.c \
         psphotMakePSFReadout.c         \
         psphotModelBackground.c        \
@@ -181 +205 @@
         psphotSourceFits.c             \
         psphotRadiusChecks.c           \
+        psphotChooseAnalysisOptions.c  \
         psphotOutput.c                 \
         psphotFakeSources.c            \
@@ -198 +223 @@
         psphotRadialPlot.c             \
         psphotKronIterate.c            \
+        psphotKronFlux.c            \
+        psphotPetroFlux.c            \
+        psphotGalaxyShape.c            \
         psphotRadialProfileWings.c     \
         psphotDeblendSatstars.c        \

trunk/psphot/src/psphot.h

@@ -18 +18 @@
     PSPHOT_SINGLE,
     PSPHOT_FORCED,
+    PSPHOT_FULL_FORCE,
     PSPHOT_MAKE_PSF,
     PSPHOT_MODEL_TEST,
@@ -81 +82 @@
 bool            psphotSourceStatsReadout (pmConfig *config, const pmFPAview *view, const char *filerule, int index, psMetadata *recipe, bool setWindow);
 
+bool            psphotFullForceSourceStats (pmConfig *config, const pmFPAview *view, const char *filerule, bool setWindow);
+bool            psphotFullForceSourceStatsReadout (pmConfig *config, const pmFPAview *view, const char *filerule, int index, psMetadata *recipe, bool setWindow);
+
 bool            psphotDeblendSatstars (pmConfig *config, const pmFPAview *view, const char *filerule);
 bool            psphotDeblendSatstarsReadout (pmConfig *config, const pmFPAview *view, const char *filerule, int index, psMetadata *recipe);
@@ -121 +125 @@
 bool            psphotAddOrSubNoiseReadout (pmConfig *config, const pmFPAview *view, const char *filerule, int index, psMetadata *recipe, bool add);
 bool            psphotAddOrSubNoise_Threaded (psThreadJob *job);
+
+bool            psphotChooseAnalysisOptions (pmConfig *config, const pmFPAview *view, const char *filerule);
+bool            psphotChooseAnalysisOptionsReadout(pmConfig *config, const pmFPAview *view, const char *filerule, int index, psMetadata *recipe);
+bool            psphotChooseAnalysisOptionsByObject(pmConfig *config, const pmFPAview *view, const char *filerule, psArray *objects);
 
 bool            psphotExtendedSourceAnalysis (pmConfig *config, const pmFPAview *view, const char *filerule);
@@ -341 +349 @@
 bool psphotForcedReadout(pmConfig *config, const pmFPAview *view, const char *filerule);
 
+pmConfig *psphotFullForceArguments(int argc, char **argv);
+bool psphotFullForceReadout(pmConfig *config, const pmFPAview *view, const char *filerule);
+
 pmConfig *psphotMinimalArguments(int argc, char **argv);
 bool psphotReadoutMinimal(pmConfig *config, const pmFPAview *view, const char *filerule);
@@ -414 +425 @@
 } psphotStackOptions;
 
+typedef struct {
+    float fRmajorMin;
+    float fRmajorMax;
+    float fRmajorDel;
+    float fRminorMin;
+    float fRminorMax;
+    float fRminorDel;
+} psphotGalaxyShapeOptions;
+
 /*** psphotStackMatchPSF prototypes ***/
 bool psphotStackMatchPSFs (pmConfig *config, const pmFPAview *view);
@@ -497 +517 @@
 bool psphotKronIterate_Threaded (psThreadJob *job);
 
+bool psphotKronFlux (pmConfig *config, const pmFPAview *view, const char *filerule);
+bool psphotKronFluxReadout(pmConfig *config, psMetadata *recipe, const pmFPAview *view, const char *filerule, pmReadout *readout, psArray *sources);
+bool psphotKronFlux_Threaded (psThreadJob *job);
+bool psphotKronFluxSource (pmSource *source, psImageMaskType maskVal);
+
+bool psphotPetroFlux (pmConfig *config, const pmFPAview *view, const char *filerule);
+bool psphotPetroFluxReadout(pmConfig *config, psMetadata *recipe, const pmFPAview *view, const char * filerule, pmReadout *readout, psArray *sources);
+bool psphotPetroFlux_Threaded (psThreadJob *job);
+bool psphotPetroFluxSource (pmSource *source, psImageMaskType maskVal);
+
+bool psphotGalaxyShape (pmConfig *config, const pmFPAview *view, const char *filerule);
+bool psphotGalaxyShapeReadout(pmConfig *config, psMetadata *recipe, const pmFPAview *view, const char * filerule, pmReadout *readout, psArray *sources, pmPSF *psf);
+bool psphotGalaxyShape_Threaded (psThreadJob *job);
+bool psphotGalaxyShapeGrid (pmSource *source, pmSourceFitOptions *fitOptions, psphotGalaxyShapeOptions *opt, psImageMaskType maskVal, int psfSize);
+bool psphotGalaxyShapeSource (pmPCMdata *pcm, pmSource *source, psImageMaskType maskVal, int psfSize, bool saveResults);
+psphotGalaxyShapeOptions *psphotGalaxyShapeOptionsAlloc();
+
 bool psphotRadialProfileWings (pmConfig *config, const pmFPAview *view, const char *filerule);
 bool psphotRadialProfileWingsReadout(pmConfig *config, psMetadata *recipe, const pmFPAview *view, pmReadout *readout, psArray *sources);

trunk/psphot/src/psphotArguments.c

@@ -217 +217 @@
     pmConfigFileSetsMD (config->arguments, &argc, argv, "PSPHOT.PSF", "-psf",      "-psflist");
     pmConfigFileSetsMD (config->arguments, &argc, argv, "SRC",        "-src",      "-srclist");
+    // XXX allow this format? pmConfigFileSetsMD (config->arguments, &argc, argv, "FORCE",      "-force",    "-forcelist");
     pmConfigFileSetsMD (config->arguments, &argc, argv, "EXPNUM",     "-expnum",   "-expnumlist");
 

trunk/psphot/src/psphotBlendFit.c

@@ -274 +274 @@
 
 # if (PS_TRACE_ON)
-        int TEST_ON = false;
 # define TEST_X 653
 # define TEST_Y 466
-        if ((fabs(source->peak->xf - TEST_X) < 5) && (fabs(source->peak->yf - TEST_Y) < 5)) {
+# define TESTING 1
+        int TEST_ON = false;
+        if (TESTING && (fabs(source->peak->xf - TEST_X) < 5) && (fabs(source->peak->yf - TEST_Y) < 5)) {
             fprintf (stderr, "test object\n");
             psTraceSetLevel("psLib.math.psMinimizeLMChi2", 5);

trunk/psphot/src/psphotDefineFiles.c

@@ -150 +150 @@
     }
 
+    if (psMetadataLookupPtr(NULL, config->arguments, "FORCE")) {
+        if (!pmFPAfileDefineFromArgs (&status, config, "PSPHOT.INPUT.CFF", "FORCE")) {
+            psError(PSPHOT_ERR_CONFIG, false, "Failed to find/build PSPHOT.INPUT.CFF");
+            return status;
+        }
+    }
+
     if (psMetadataLookupPtr(NULL, config->arguments, "SRCTEXT")) {
         // XXX cannot use pmFPAfileDefineFromArgs: this is explicitly a FITS-based I/O function

trunk/psphot/src/psphotEllipticalContour.c

@@ -64 +64 @@
         psFree (y);
         psFree (yErr);
+        source->mode2 |= PM_SOURCE_MODE2_ECONTOUR_FEW_PTS;
         return false;
     }

trunk/psphot/src/psphotExtendedSourceAnalysis.c

@@ -1 +1 @@
 # include "psphotInternal.h"
-
-// measure the elliptical radial profile and use this to measure the petrosian parameters for the sources
+void psphotRadialProfileShowSkips ();
+
+// measure the petrosian parameters for the sources
 
 // for now, let's store the detections on the readout->analysis for each readout
@@ -15 +16 @@
     psAssert (recipe, "missing recipe?");
 
-    // perform full non-linear fits / extended source analysis?
-    if (!psMetadataLookupBool (&status, recipe, "EXTENDED_SOURCE_ANALYSIS")) {
+    bool doPetrosian = psMetadataLookupBool (&status, recipe, "EXTENDED_SOURCE_PETROSIAN");
+    bool doAnnuli    = psMetadataLookupBool (&status, recipe, "EXTENDED_SOURCE_ANNULI");
+
+    // measure petrosians?
+    if (!doPetrosian && !doAnnuli) {
         psLogMsg ("psphot", PS_LOG_INFO, "skipping extended source measurements\n");
         return true;
@@ -33 +37 @@
 }
 
+/*** for the moment, this test code : it is not thread safe ***/
+int    Nall = 0;
+int  Nskip1 = 0;
+int  Nskip2 = 0;
+int  Nskip3 = 0;
+int  Nskip4 = 0;
+int  Nskip5 = 0;
+int  Nskip6 = 0;
+
+# define SKIP(VALUE) { VALUE++; continue; }
+
 // aperture-like measurements for extended sources
 bool psphotExtendedSourceAnalysisReadout (pmConfig *config, const pmFPAview *view, const char *filerule, int index, psMetadata *recipe) {
@@ -110 +125 @@
 
 // set this to 0 to run without threading
-# if (1)            
+# if (0)            
             if (!psThreadJobAddPending(job)) {
                 psError(PS_ERR_UNKNOWN, false, "Unable to guess model.");
@@ -164 +179 @@
     psLogMsg ("psphot", PS_LOG_INFO, "  %d annuli\n", Nannuli);
 
+# if (PS_TRACE_ON)
+    fprintf (stderr, "ext analysis skipped @ 1  : %d\n", Nskip1);
+    fprintf (stderr, "ext analysis skipped @ 2  : %d\n", Nskip2);
+    fprintf (stderr, "ext analysis skipped @ 3  : %d\n", Nskip3);
+    fprintf (stderr, "ext analysis skipped @ 4  : %d\n", Nskip4);
+    fprintf (stderr, "ext analysis skipped @ 5  : %d\n", Nskip5);
+    fprintf (stderr, "ext analysis skipped @ 6  : %d\n", Nskip6);
+#endif
+
+    psphotRadialProfileShowSkips ();
+
     psphotVisualShowResidualImage (readout, false);
 
-    bool doPetrosian    = psMetadataLookupBool (&status, recipe, "EXTENDED_SOURCE_PETROSIAN");
-    if (doPetrosian) {
-        psphotVisualShowPetrosians (sources);
-    }
+    psphotVisualShowPetrosians (sources);
 
     return true;
@@ -190 +213 @@
     float skynoise          = PS_SCALAR_VALUE(job->args->data[4],F32);
 
-    // S/N limit to perform full non-linear fits
-    float SN_LIM = psMetadataLookupF32 (&status, recipe, "EXTENDED_SOURCE_SN_LIM");
-
-    // which extended source analyses should we perform?
     bool doPetrosian    = psMetadataLookupBool (&status, recipe, "EXTENDED_SOURCE_PETROSIAN");
-    bool doAnnuli       = psMetadataLookupBool (&status, recipe, "EXTENDED_SOURCE_ANNULI");
-    bool doPetroStars   = psMetadataLookupBool (&status, recipe, "PETROSIAN_FOR_STARS");
 
     // user-defined masks to test for good/bad pixels (build from recipe list if not yet set)
@@ -207 +224 @@
         pmSource *source = sources->data[i];
 
-        // if we have checked the source validity on the basis of the object set, then 
-        // we either skip these tests below or we skip the source completely
-        if (source->tmpFlags & PM_SOURCE_TMPF_PETRO_SKIP) continue;
-        if (source->tmpFlags & PM_SOURCE_TMPF_PETRO_KEEP) goto keepSource;
-
-        // skip PSF-like and non-astronomical objects
-        if (source->type == PM_SOURCE_TYPE_DEFECT) continue;
-        if (source->type == PM_SOURCE_TYPE_SATURATED) continue;
-        if (source->mode & PM_SOURCE_MODE_DEFECT) continue;
-        if (source->mode & PM_SOURCE_MODE_SATSTAR) continue;
-
-        // skip saturated stars modeled with a radial profile 
-        if (source->mode2 & PM_SOURCE_MODE2_SATSTAR_PROFILE) continue;
-
-        // optionally allow non-extended objects to get petrosians as well
-        if (!doPetroStars) {
-            if (!(source->mode & PM_SOURCE_MODE_EXT_LIMIT)) continue;
-            if (source->type == PM_SOURCE_TYPE_STAR) continue;
-        }
-
-        // limit selection to some SN limit
-        // assert (source->peak); // how can a source not have a peak?
-        // limit selection to some SN limit
-        bool skipSource = false;
-        if (source->mode & PM_SOURCE_MODE_EXT_LIMIT) {
-            skipSource = (source->moments->KronFlux < SN_LIM * source->moments->KronFluxErr);
-        } else {
-            skipSource = (sqrt(source->peak->detValue) < SN_LIM);
-        }
-        if (skipSource) continue;
-
-        // limit selection by analysis region (this automatically apply
-        if (source->peak->x < region->x0) continue;
-        if (source->peak->y < region->y0) continue;
-        if (source->peak->x > region->x1) continue;
-        if (source->peak->y > region->y1) continue;
-
-    keepSource:
+        Nall ++;
+
+        // rules for measuring petrosian parameters for specific objects are set in
+        // psphotChooseAnalysisOptions.c
+        if (!(source->tmpFlags & PM_SOURCE_TMPF_PETRO)) SKIP (Nskip1);
+
+        // limit selection by analysis region (XXX move this into psphotChooseAnalysisOption?)
+        if (source->peak->x < region->x0) SKIP (Nskip2);
+        if (source->peak->y < region->y0) SKIP (Nskip3);
+        if (source->peak->x > region->x1) SKIP (Nskip4);
+        if (source->peak->y > region->y1) SKIP (Nskip5);
 
         // replace object in image
@@ -259 +249 @@
         pmSourceRedefinePixels (source, readout, source->peak->xf, source->peak->yf, 1.5*radius);
 
-        // if we request any of these measurements, we require the radial profile
-        if (doPetrosian || doAnnuli) {
-            if (!psphotRadialProfile (source, recipe, skynoise, maskVal)) {
-                // all measurements below require the radial profile; skip them all
-                // re-subtract the object, leave local sky
-                psTrace ("psphot", 5, "failed to extract radial profile for source at %7.1f, %7.1f", source->moments->Mx, source->moments->My);
-                pmSourceSub (source, PM_MODEL_OP_FULL, maskVal);
-                continue;
-            }
-            Nannuli ++;
-            source->mode |= PM_SOURCE_MODE_RADIAL_FLUX;
-        }
+        // measure the radial profile
+        if (!psphotRadialProfile (source, recipe, skynoise, maskVal)) {
+          // re-subtract the object, leave local sky
+          psTrace ("psphot", 5, "failed to extract radial profile for source at %7.1f, %7.1f", source->moments->Mx, source->moments->My);
+          pmSourceSub (source, PM_MODEL_OP_FULL, maskVal);
+          SKIP (Nskip6);
+        }
+
+        Nannuli ++;
+        source->mode |= PM_SOURCE_MODE_RADIAL_FLUX;
 
         // Petrosian Mags
         if (doPetrosian) {
-            if (!psphotPetrosian (source, recipe, skynoise, maskVal)) {
-                psTrace ("psphot", 5, "FAILED petrosian flux & radius for source at %7.1f, %7.1f", source->moments->Mx, source->moments->My);
-            } else {
-                psTrace ("psphot", 5, "measured petrosian flux & radius for source at %7.1f, %7.1f", source->moments->Mx, source->moments->My);
-                Npetro ++;
-                source->mode |= PM_SOURCE_MODE_EXTENDED_STATS;
-            }
+          if (!psphotPetrosian (source, recipe, skynoise, maskVal)) {
+            psTrace ("psphot", 5, "FAILED petrosian flux & radius for source at %7.1f, %7.1f", source->moments->Mx, source->moments->My);
+          } else {
+            psTrace ("psphot", 5, "measured petrosian flux & radius for source at %7.1f, %7.1f", source->moments->Mx, source->moments->My);
+            Npetro ++;
+            source->mode |= PM_SOURCE_MODE_EXTENDED_STATS;
+          }
         }
 

trunk/psphot/src/psphotExtendedSourceFits.c

@@ -65 +65 @@
     psphotVisualShowImage(readout);
 
-    // psphotSaveImage (NULL, readout->image, "test.01.fits");
-
     pmDetections *detections = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.DETECTIONS");
     psAssert (detections, "missing detections?");
@@ -111 +109 @@
     if (!status || !isfinite(fitMaxTol) || fitMaxTol <= 0) {
         fitMaxTol = 1.0;
+    }
+
+    float fitNsigmaConv = psMetadataLookupF32 (&status, recipe, "EXT_FIT_NSIGMA_CONV"); // number of sigma for the convolution
+    if (!status || !isfinite(fitNsigmaConv) || fitNsigmaConv <= 0) {
+        fitNsigmaConv = 5.0;
     }
 
@@ -137 +140 @@
     fitOptions->minTol         = fitMinTol;
     fitOptions->maxTol         = fitMaxTol;
+    fitOptions->nsigma         = fitNsigmaConv;
 
     fitOptions->gainFactorMode   = gainFactorMode;
     fitOptions->chisqConvergence = chisqConvergence;
     fitOptions->isInteractive    = isInteractive;
+
+    // use poissonian errors or local-sky errors
+    fitOptions->poissonErrors = psMetadataLookupBool (&status, recipe, "EXTENDED_SOURCE_FITS_POISSON");
+    if (!status) fitOptions->poissonErrors = true;
 
     // maskVal is used to test for rejected pixels, and must include markVal
@@ -285 +293 @@
             psArrayAdd(job->args, 1, cells->data[j]); // sources
             psArrayAdd(job->args, 1, models);
+
             // Allocate a metadata iterator here because psMetadataIteratorAlloc/Free are not thread safe
             psMetadataIterator *iter = psMetadataIteratorAlloc (models, PS_LIST_HEAD, NULL);
@@ -386 +395 @@
     psphotSersicModelClassCleanup();
 
-    // psphotSaveImage (NULL, readout->image, "test.02.fits");
-
     psphotVisualShowResidualImage (readout, false);
 
@@ -428 +435 @@
     // psTraceSetLevel ("psLib.math.psMinimizeLMChi2_Alt", 5);
 
+    pmModelStatus badModel = PM_MODEL_STATUS_NONE;
+    badModel |= PM_MODEL_STATUS_BADARGS;
+    badModel |= PM_MODEL_STATUS_OFFIMAGE;
+    badModel |= PM_MODEL_STATUS_NAN_CHISQ;
+    badModel |= PM_MODEL_SERSIC_PCM_FAIL_GUESS;
+    badModel |= PM_MODEL_SERSIC_PCM_FAIL_GRID;
+    badModel |= PM_MODEL_PCM_FAIL_GUESS;
+
     // choose the sources of interest
     for (int i = 0; i < sources->n; i++) {
@@ -433 +448 @@
         pmSource *source = sources->data[i];
 
-        // skip PSF-like and non-astronomical objects
-        if (!(source->mode & PM_SOURCE_MODE_EXT_LIMIT)) continue;
-        if (source->type == PM_SOURCE_TYPE_DEFECT) continue;
-        if (source->type == PM_SOURCE_TYPE_SATURATED) continue;
-
-        // skip saturated stars modeled with a radial profile 
-        if (source->mode2 & PM_SOURCE_MODE2_SATSTAR_PROFILE) continue;
-
-        // XXX this should use peak?
+        // rules for measuring petrosian parameters for specific objects are set in
+        // psphotChooseAnalysisOptions.c
+        if (!(source->tmpFlags & PM_SOURCE_TMPF_EXT_FIT)) continue;
+
+        // limit selection by analysis region (XXX move this into psphotChooseAnalysisOption?)
         if (source->peak->x < region->x0) continue;
         if (source->peak->y < region->y0) continue;
         if (source->peak->x > region->x1) continue;
         if (source->peak->y > region->y1) continue;
-
-
-        // XXX for a test, just do the obvious trail
-        // XXX if (source->peak->xf < 1100) continue;
-        // XXX if (source->peak->xf > 1400) continue;
-        // XXX if (source->peak->yf >  245) continue;
 
         // replace object in image
@@ -462 +467 @@
         psphotSetRadiusMomentsExact(&fitRadius, &windowRadius, readout, source, markVal); // NOTE : 6 allocs
 
-        // XXX WATCH OUT HERE!!
-        // fitRadius = 30;
-
         // UPDATE : we have changed the moments calculation.  There is now an iteration within 
         // psphotKronMasked to determine moments appropriate for a larger object.  The values
@@ -475 +477 @@
         }
 
+# ifdef TEST_OBJECT
         bool testObject = false;
-        // testObject |= ((fabs(source->peak->xf -  179) < 5) && (fabs(source->peak->yf - 1138) < 5));
-        // testObject |= ((fabs(source->peak->xf - 5047) < 5) && (fabs(source->peak->yf -  151) < 5));
-        // testObject |= ((fabs(source->peak->xf - 3929) < 5) && (fabs(source->peak->yf - 4109) < 5));
-        // testObject |= ((fabs(source->peak->xf -  915) < 5) && (fabs(source->peak->yf - 5998) < 5));
-        // testObject |= ((fabs(source->peak->xf - 5406) < 5) && (fabs(source->peak->yf -  326) < 5));
+        testObject |= ((fabs(source->peak->xf -  179) < 5) && (fabs(source->peak->yf - 1138) < 5));
         if (testObject) {
             fprintf (stderr, "test object @ %f, %f\n", source->peak->xf, source->peak->yf);
@@ -486 +485 @@
             psTraceSetLevel ("psphot.psphotExtendedSourceFits_Threaded", 5);
         }
+# endif 
 
         // loop here over the models chosen for each source (exclude by S/N)
@@ -501 +501 @@
           assert (status);
 
-          // limit selection to some SN limit
-          bool skipSource = false;
-          if (source->mode & PM_SOURCE_MODE_EXT_LIMIT) {
-              skipSource = (source->moments->KronFlux < FIT_SN_LIM * source->moments->KronFluxErr);
-          } else {
-              skipSource = (sqrt(source->peak->detValue) < FIT_SN_LIM);
-          }
-          if (skipSource) {
+          // limit selection to some SN limit for specific models (this value only applies if > EXTENDED_SOURCE_SN_LIM)
+          if (isfinite(FIT_SN_LIM)) {
+            if (source->moments->KronFlux < FIT_SN_LIM * source->moments->KronFluxErr) {
               Nfaint ++;
               continue;
+            }
           }
+
+          source->mode2 |= PM_SOURCE_MODE2_EXT_FITS_RUN;
 
           // check on the model type
@@ -529 +527 @@
                   psTrace ("psphot", 5, "failed to fit psf-conv model for object at %f, %f", source->moments->Mx, source->moments->My);
                   Nfail ++;
+                  source->mode2 |= PM_SOURCE_MODE2_EXT_FITS_FAIL;
                   continue;
               }
@@ -534 +533 @@
                        source->moments->Mx, source->moments->My, pmModelClassGetName (modelFit->type), modelFit->chisq, modelFit->nPix, modelFit->nIter);
               Nconvolve ++;
-              if (!(modelFit->flags & (PM_MODEL_STATUS_BADARGS | PM_MODEL_STATUS_NONCONVERGE | PM_MODEL_STATUS_OFFIMAGE))) {
+              if (!(modelFit->flags & badModel)) {
                   NconvolvePass ++;
                   source->mode |= PM_SOURCE_MODE_EXTENDED_FIT;
@@ -548 +547 @@
                       Nfail ++;
                       doneFits = true;
+                      source->mode2 |= PM_SOURCE_MODE2_EXT_FITS_FAIL;
                       continue;
                   }
                   psTrace ("psphot", 4, "fit plain model for %f, %f : %s chisq = %f (npix: %d, niter: %d)\n", source->moments->Mx, source->moments->My, pmModelClassGetName (modelFit->type), modelFit->chisq, modelFit->nPix, modelFit->nIter);
                   Nplain ++;
-                  if (!(modelFit->flags & (PM_MODEL_STATUS_BADARGS | PM_MODEL_STATUS_NONCONVERGE | PM_MODEL_STATUS_OFFIMAGE))) {
+                  if (!(modelFit->flags & badModel)) {
                       NplainPass ++;
                       source->mode |= PM_SOURCE_MODE_EXTENDED_FIT;
@@ -576 +576 @@
                           fprintf (stderr, "update window : %f %f : %f -> %f\n", source->peak->xf, source->peak->yf, fitRadius, 2*fitRadius);
                           psphotSetWindowTrail (&fitRadius, &windowRadius, readout, source, markVal, fitRadius*2.0);
+                          source->mode2 |= PM_SOURCE_MODE2_EXT_FITS_RETRY;
                       }
                   }
               }
           }
-          // XXX really need to do this in a cleaner way:
-          if (!modelFit) continue;
+          psAssert (modelFit, "modelFit not set?");
 
           // test for fit quality / result
@@ -590 +590 @@
         }
 
+        // we are allowed to fit both stars and non-stars here -- if we have fitted
+        // something which we think is a star, we should use that model to subtract the
+        // object from the image.
+        if (source->type == PM_SOURCE_TYPE_STAR) {
+          // ensure the modelPSF is cached
+          pmSourceCacheModel (source, maskVal);
+          pmSourceSub (source, PM_MODEL_OP_FULL, maskVal);
+          continue;
+        }
+
         // evaluate the relative quality of the models, choose one
+        // the PSF model might be the best fit : allow it to succeed
         float minChisq = NAN;
         int minModel = -1;
@@ -596 +607 @@
             pmModel *model = source->modelFits->data[i];
 
+            // skip the really bad fits
             if (!(model->flags & PM_MODEL_STATUS_FITTED)) continue;
-
-            if (model->flags & (PM_MODEL_STATUS_BADARGS)) continue;
+            if (model->flags & badModel) continue;
+
             // if (model->flags & (PM_MODEL_STATUS_NONCONVERGE)) continue;
-            if (model->flags & (PM_MODEL_STATUS_OFFIMAGE)) continue;
 
             if ((minModel < 0) || (model->chisq < minChisq)) {
@@ -618 +629 @@
           pmSourceCacheModel (source, maskVal);
 
+# if (PS_TRACE_ON)
           pmModel *model = source->modelFits->data[0];
           int flags = 0xffffffff;
@@ -623 +635 @@
             flags = model->flags;
           }
-
           fprintf (stderr, "failed to fit extended source model to object %d @ %f, %f (%x)\n", source->id, source->moments->Mx, source->moments->My, flags);
+#endif
           pmSourceSub (source, PM_MODEL_OP_FULL, maskVal);
 
+          source->mode2 |= PM_SOURCE_MODE2_EXT_FITS_NONE;
           continue;
         }
@@ -643 +656 @@
         if (source->modelEXT->isPCM) {
             // fprintf (stderr, "subtract PCM extended source model for object %d @ %f, %f\n", source->id, source->moments->Mx, source->moments->My);
-            pmPCMCacheModel (source, maskVal, psfSize);
+            pmPCMCacheModel (source, maskVal, psfSize, fitOptions->nsigma);
         } else {
             // fprintf (stderr, "subtract non-PCM extended source model for object %d @ %f, %f\n", source->id, source->moments->Mx, source->moments->My);
             pmSourceCacheModel (source, maskVal);
         }
+        source->modelEXT->flags |= PM_MODEL_BEST_FIT;
 
         // subtract the best fit from the object, leave local sky
@@ -655 +669 @@
         psTrace ("psphot", 5, "extended source model for source at %7.1f, %7.1f", source->moments->Mx, source->moments->My);
 
+# ifdef TEST_OBJECT
         if (testObject) {
             psTraceSetLevel ("psModules.objects.pmPCM_MinimizeChisq", 0);
             psTraceSetLevel ("psphot.psphotExtendedSourceFits_Threaded", 0);
         }
+# endif
     }
 

trunk/psphot/src/psphotImageLoop.c

@@ -132 +132 @@
                     }
                     break;
+                  case PSPHOT_FULL_FORCE:
+                    if (!psphotFullForceReadout (config, view, "PSPHOT.INPUT")) {
+                        psError(psErrorCodeLast(), false, "failure in psphotReadout for chip %d, cell %d, readout %d\n", view->chip, view->cell, view->readout);
+                        psFree (view);
+                        return false;
+                    }
+                    break;
                   case PSPHOT_MAKE_PSF:
                     if (!psphotMakePSFReadout (config, view, "PSPHOT.INPUT")) {

trunk/psphot/src/psphotKronIterate.c

@@ -166 +166 @@
     }
 
+# if (PS_TRACE_ON)
     fprintf (stderr, "--- starting KRON ---\n");
+#endif
 
     // We measure the Kron Radius on a smoothed copy of the readout image

trunk/psphot/src/psphotLoadPSF.c

@@ -1 +1 @@
 # include "psphotInternal.h"
+
+// PSPHOT.PSF.LOAD vs input file -- see note at top
+bool psphotLoadPSF (pmConfig *config, const pmFPAview *view, const char *filerule) {
+
+    int num = psphotFileruleCount(config, filerule);
+
+    // loop over the available readouts
+    for (int i = 0; i < num; i++) {
+
+        // Generate the mask and weight images, including the user-defined analysis region of interest
+        if (!psphotLoadPSFReadout (config, view, filerule, "PSPHOT.PSF.LOAD", i)) {
+            psError (PSPHOT_ERR_CONFIG, false, "failed to load PSF model for PSPHOT.PSF.LOAD entry %d", i);
+            return false;
+        }
+    }
+    return true;
+}
 
 // NOTE : pmPSF_IO.c functions must load the psf model onto the chip->analysis metadata because
@@ -58 +75 @@
     return true;
 }
-
-// PSPHOT.PSF.LOAD vs input file -- see note at top
-bool psphotLoadPSF (pmConfig *config, const pmFPAview *view, const char *filerule) {
-
-    int num = psphotFileruleCount(config, filerule);
-
-    // loop over the available readouts
-    for (int i = 0; i < num; i++) {
-
-        // Generate the mask and weight images, including the user-defined analysis region of interest
-        if (!psphotLoadPSFReadout (config, view, filerule, "PSPHOT.PSF.LOAD", i)) {
-            psError (PSPHOT_ERR_CONFIG, false, "failed to load PSF model for PSPHOT.PSF.LOAD entry %d", i);
-            return false;
-        }
-    }
-    return true;
-}

trunk/psphot/src/psphotMergeSources.c

@@ -39 +39 @@
     psAssert (newSources, "missing sources?");
 
-    // XXX TEST:
-    if (detections->allSources) {
-        psphotMaskCosmicRayFootprintCheck(detections->allSources);
-    }
-    if (detections->newSources) {
-        psphotMaskCosmicRayFootprintCheck(detections->newSources);
-    }
-
     if (!detections->allSources) {
         detections->allSources = psArrayAllocEmpty(newSources->n);
@@ -65 +57 @@
 // Merge the externally supplied sources with the existing sources.  Mark them as having mode
 // PM_SOURCE_MODE_EXTERNAL.
+
+// XXX this function needs to be updated slightly for psphotFullForce:
+// * load the additional parameters to guide the new concepts
 
 // XXX This function needs to be updated to loop over set of input files.  At the moment, we
@@ -73 +68 @@
     bool status;
     pmDetections *extCMF = NULL;
+    pmDetections *extCFF = NULL;
     psArray *extSourcesTXT = NULL;
     int index = 0;
@@ -102 +98 @@
     {
         pmReadout *readoutCMF = pmFPAfileThisReadout (config->files, view, "PSPHOT.INPUT.CMF");
-        if (!readoutCMF) goto loadTXT;
+        if (!readoutCMF) goto loadCFF;
 
         extCMF = psMetadataLookupPtr (NULL, readoutCMF->analysis, "PSPHOT.DETECTIONS");
@@ -125 +121 @@
     }
 
+loadCFF:
+    // load data from input CFF file:
+    {
+        pmReadout *readoutCFF = pmFPAfileThisReadout (config->files, view, "PSPHOT.INPUT.CFF");
+        if (!readoutCFF) goto loadTXT;
+
+        extCFF = psMetadataLookupPtr (NULL, readoutCFF->analysis, "PSPHOT.DETECTIONS");
+        if (extCFF) {
+            psF32 exptime = psMetadataLookupF32(NULL, readout->parent->concepts, "CELL.EXPOSURE");
+            for (int i = 0; i < extCFF->allSources->n; i++) {
+                pmSource *source = extCFF->allSources->data[i];
+
+                // setting this bit not only tracks the inputs, it makes pmSourceMoments
+                // keep the Mx,My values for the centroid.  
+                source->mode |= PM_SOURCE_MODE_EXTERNAL;
+
+                // source->peak->detValue,rawFlux,smoothFlux all set to input flux value which is scaled
+                // to 1 second exposure time. Scale to this image's exposure.
+                source->peak->rawFlux    *= exptime;
+                source->peak->smoothFlux *= exptime;
+                source->peak->detValue   *= exptime;
+                // source->peak->xf,yf, moments->Mx,My all set to input position
+
+                // drop the loaded source modelPSF
+                psFree (source->modelPSF);
+                source->modelPSF = NULL;
+                source->imageID = index;
+
+                psArrayAdd (detections->newSources, 100, source);
+            }
+        }
+    }
+
 loadTXT:
 
@@ -157 +186 @@
     psFree (detections);
 
-    if (!extCMF && !extSourcesTXT) {
+    if (!(extCMF || extCFF || extSourcesTXT)) {
         psLogMsg ("psphot", 3, "no external sources for this readout");
         return true;
@@ -163 +192 @@
 
     int nCMF = extCMF        ? extCMF->allSources->n        : 0;
-    int nTXT = extSourcesTXT ? extSourcesTXT->n : 0;
-
-    psLogMsg ("psphot", 3, "%d external sources (%d cmf, %d text) merged to yield %ld total sources",
-              nCMF + nTXT, nCMF, nTXT, sources->n);
+    int nCFF = extCFF        ? extCFF->allSources->n        : 0;
+    int nTXT = extSourcesTXT ? extSourcesTXT->n             : 0;
+
+    psLogMsg ("psphot", 3, "%d external sources (%d cmf, %d cff, %d text) merged to yield %ld total sources",
+              nCMF + nCFF + nTXT, nCMF, nCFF, nTXT, sources->n);
     return true;
 }

trunk/psphot/src/psphotModelTestReadout.c

@@ -125 +125 @@
 
             // get the source moments
-            status = pmSourceMoments (source, radius, 0.25*radius, 0.0, MIN_KRON_RADIUS, maskVal);
+          status = pmSourceMoments (source, radius, 0.25*radius, 0.0, MIN_KRON_RADIUS, maskVal);
             if (!status) psAbort("psSourceMoments error");
 

trunk/psphot/src/psphotPetrosianRadialBins.c

@@ -186 +186 @@
         psFree(values);
         psFree(stats);
+        source->mode2 |= PM_SOURCE_MODE2_RADBIN_NAN_CENTER;
         return true;
     }

trunk/psphot/src/psphotPetrosianStats.c

@@ -6 +6 @@
 // generate the Petrosian radius and flux from the mean surface brightness (r_i)
 
+float InterpolateValuesQuadratic (float *Xin, float *Yin, float X);
 float InterpolateValues     (float X0, float Y0, float X1, float Y1, float X);
 float InterpolateValuesErrX (float X0, float Y0, float X1, float Y1, float X, float dX0, float dX1);
@@ -20 +21 @@
     if (!profile->binSB) {
         psLogMsg ("psphot", PS_LOG_DETAIL, "no petrosian profile, skipping source %f, %f", source->peak->xf, source->peak->yf);
+        source->mode2 |= PM_SOURCE_MODE2_PETRO_NO_PROFILE;
         return true;
     }
@@ -53 +55 @@
     float dFsum2 = 0.0;
 
-    float nSigma = 3.0;
+    float nSigma = 2.0;
     int lowestSignificantRadius = 0;
     float lowestSignificantRatio = 1.0;
@@ -117 +119 @@
                 petRadius    = InterpolateValues     (1.0, 0.0, petRatio->data.F32[nOut], refRadius->data.F32[nOut], PETROSIAN_RATIO);
                 petRadiusErr = InterpolateValuesErrX (1.0, 0.0, petRatio->data.F32[nOut], refRadius->data.F32[nOut], PETROSIAN_RATIO, 0.0, petRatioErr->data.F32[nOut]);
-            } else {
-                petRadius    = InterpolateValues     (petRatio->data.F32[nOut-1], refRadius->data.F32[nOut-1], petRatio->data.F32[nOut], refRadius->data.F32[nOut], PETROSIAN_RATIO);
-                petRadiusErr = InterpolateValuesErrX (petRatio->data.F32[nOut-1], refRadius->data.F32[nOut-1], petRatio->data.F32[nOut], refRadius->data.F32[nOut], PETROSIAN_RATIO, petRatioErr->data.F32[nOut-1], petRatioErr->data.F32[nOut]);
+                source->mode2 |= PM_SOURCE_MODE2_PETRO_RATIO_ZEROBIN;
+            } else {
+              // petRadius    = InterpolateValues     (petRatio->data.F32[nOut-1], refRadius->data.F32[nOut-1], petRatio->data.F32[nOut], refRadius->data.F32[nOut], PETROSIAN_RATIO);
+              if (nOut > 1) {
+                petRadius    = InterpolateValuesQuadratic (&petRatio->data.F32[nOut-2], &refRadius->data.F32[nOut-2],   PETROSIAN_RATIO);
+              } else {
+                petRadius    = InterpolateValuesQuadratic (&petRatio->data.F32[nOut-3], &refRadius->data.F32[nOut-3], PETROSIAN_RATIO);
+              }
+# if (PS_TRACE_ON)
+              float petRadiusLinear = InterpolateValues     (petRatio->data.F32[nOut-1], refRadius->data.F32[nOut-1], petRatio->data.F32[nOut], refRadius->data.F32[nOut], PETROSIAN_RATIO);
+              if (fabs(petRadius - petRadiusLinear) > fabs(refRadius->data.F32[nOut] - refRadius->data.F32[nOut-1])) { 
+                fprintf (stderr, "big difference : %f vs %f\n", petRadius, petRadiusLinear); 
+              }
+#endif
+              petRadiusErr = InterpolateValuesErrX (petRatio->data.F32[nOut-1], refRadius->data.F32[nOut-1], petRatio->data.F32[nOut], refRadius->data.F32[nOut], PETROSIAN_RATIO, petRatioErr->data.F32[nOut-1], petRatioErr->data.F32[nOut]);
             }
             above = false;
@@ -148 +162 @@
             fprintf (stderr, "nan pet radius\n");
         }
+        source->mode2 |= PM_SOURCE_MODE2_PETRO_INSIG_RATIO;
     }
 
@@ -180 +195 @@
     bool found50 = false;
     bool found90 = false;
+
     // XXX use bisection to do this faster:
     for (int i = 0; !(found50 && found90) && i < refRadius->n; i++) {
@@ -235 +251 @@
 }
 
+// Lagrange's form of the interpolating polynomial...
+float InterpolateValuesQuadratic (float *Xin, float *Yin, float X) {
+
+  float dx01 = Xin[0] - Xin[1];
+  float dx02 = Xin[0] - Xin[2];
+  float dx12 = Xin[1] - Xin[2];
+
+  float dx0  = X - Xin[0];
+  float dx1  = X - Xin[1];
+  float dx2  = X - Xin[2];
+
+  float y0 = Yin[0]*dx1*dx2/(dx01*dx02);
+  float y1 = Yin[1]*dx0*dx2/(dx01*dx12); // need - sign
+  float y2 = Yin[2]*dx0*dx1/(dx02*dx12); 
+
+  float Y = y0 - y1 + y2;
+  return Y;
+}
+
 float InterpolateValues (float X0, float Y0, float X1, float Y1, float X) {
     float dydx = (Y1 - Y0) / (X1 - X0);

trunk/psphot/src/psphotRadialBins.c

@@ -44 +44 @@
     psVector *radMin = psMetadataLookupPtr (&status, recipe, "RADIAL.ANNULAR.BINS.LOWER");
     psVector *radMax = psMetadataLookupPtr (&status, recipe, "RADIAL.ANNULAR.BINS.UPPER");
-    if (!radMin || !radMin->n) {
-        psError (PSPHOT_ERR_CONFIG, true, "error in definition of annular bins (radMin missing or empty)");
-        return false;
-    }
-    if (!radMax || !radMax->n) {
-        psError (PSPHOT_ERR_CONFIG, true, "error in definition of annular bins (radMax missing or empty)");
-        return false;
-    }
+    psAssert (radMin, "RADIAL.ANNULAR.BINS.LOWER is missing from recipe");
+    psAssert (radMin->n, "RADIAL.ANNULAR.BINS.LOWER is empty in recipe");
+    psAssert (radMax, "RADIAL.ANNULAR.BINS.UPPER is missing from recipe");
+    psAssert (radMax->n, "RADIAL.ANNULAR.BINS.UPPER is empty in recipe");
 
     psVector *binSB      = psVectorAllocEmpty(radMin->n, PS_TYPE_F32); // surface brightness of radial bin
@@ -161 +157 @@
         psFree(values);
         psFree(stats);
+        source->mode2 |= PM_SOURCE_MODE2_RADBIN_NAN_CENTER;
         return true;
     }

trunk/psphot/src/psphotRadialProfile.c

@@ -1 +1 @@
 # include "psphotInternal.h"
+
+static int Nskip1 = 0;
+static int Nskip2 = 0;
+static int Nskip3 = 0;
+static int Nskip4 = 0;
+static int Nskip5 = 0;
+
+# define SKIP(VALUE) { VALUE++; return false; }
 
 bool psphotRadialProfile (pmSource *source, psMetadata *recipe, float skynoise, psImageMaskType maskVal) {
@@ -23 +31 @@
     if (!psphotRadialProfilesByAngles (source, Nsec, Rmax)) {
         psError (PS_ERR_UNKNOWN, false, "failed to measure radial profile for petrosian");
-        return false;
+        SKIP (Nskip1);
     }
     // allocate: extpars->radFlux->radii,fluxes,theta
@@ -32 +40 @@
     if (!psphotRadiiFromProfiles (source, fluxMin, fluxMax)) {
         psError (PS_ERR_UNKNOWN, false, "failed to measure isophotal radii from profiles");
-        return false;
+        SKIP (Nskip2);
     }
     // allocate : extpars->radFlux->isophotalRadii (use profile->radii,fluxes)
@@ -40 +48 @@
     if (!psphotEllipticalContour (source)) {
         // psLogMsg ("psphot", 3, "failed to measure elliptical contour");
-        return false;
+        SKIP (Nskip3);
     }
     // use extpars->radFlux->isophotalRadii,theta (result in extpars->axes)
@@ -48 +56 @@
     if (!psphotEllipticalProfile (source, RAW_RADIUS)) {
         psError (PS_ERR_UNKNOWN, false, "failed to generate elliptical profile");
-        return false;
+        SKIP (Nskip4);
     }
     // allocate extpars->ellipticalFlux->radiusElliptical,fluxElliptical (use axes to scale raw pixels)
@@ -55 +63 @@
     if (!psphotRadialBins (recipe, source, Rmax, skynoise)) {
         psError (PS_ERR_UNKNOWN, false, "failed to generate radial bins");
-        return false;
+        SKIP (Nskip5);
     }
     // allocate extpars->radProfile->binSB, binSBstdv, binSum, binFill, radialBins, area (small lengths)
@@ -62 +70 @@
     return true;
 }
+
+void psphotRadialProfileShowSkips () {
+# if (PS_TRACE_ON)
+  fprintf (stderr, "radial profile skipped @ 1  : %d\n", Nskip1);
+  fprintf (stderr, "radial profile skipped @ 2  : %d\n", Nskip2);
+  fprintf (stderr, "radial profile skipped @ 3  : %d\n", Nskip3);
+  fprintf (stderr, "radial profile skipped @ 4  : %d\n", Nskip4);
+  fprintf (stderr, "radial profile skipped @ 5  : %d\n", Nskip5);
+#endif
+}

trunk/psphot/src/psphotReadout.c

@@ -316 +316 @@
     psphotSourceSize (config, view, filerule, false); // pass 2 (detections->allSources)
 
+    // XXX currently we are doing both the analysis of the size and the assessment of "fit ext"
+    // in source size.  this overloads the bit MODE_EXT_LIMIT to mean "fit ext" not just
+    // "bigger than a PSF"
+
+    // decide which source(s) are to be fitted with the extended source analysis code.
+    psphotChooseAnalysisOptions (config, view, filerule);
+
     psphotExtendedSourceAnalysis (config, view, filerule); // pass 1 (detections->allSources)
     psphotExtendedSourceFits (config, view, filerule); // pass 1 (detections->allSources)

trunk/psphot/src/psphotRoughClass.c

@@ -87 +87 @@
     if (NX > NY) {
         NXuse = ScaleForClump;
-        NYuse = (int) (ScaleForClump * (NY / NX) + 0.5);
+        NYuse = (int) (ScaleForClump * (NX / NY) + 0.5);
     } else {
         NYuse = ScaleForClump;

trunk/psphot/src/psphotSetThreads.c

@@ -47 +47 @@
     psFree(task);
 
+    task = psThreadTaskAlloc("PSPHOT_KRON_FLUX", 4);
+    task->function = &psphotKronFlux_Threaded;
+    psThreadTaskAdd(task);
+    psFree(task);
+
+    task = psThreadTaskAlloc("PSPHOT_PETRO_FLUX", 4);
+    task->function = &psphotPetroFlux_Threaded;
+    psThreadTaskAdd(task);
+    psFree(task);
+
+    task = psThreadTaskAlloc("PSPHOT_GALAXY_SHAPES", 7);
+    task->function = &psphotGalaxyShape_Threaded;
+    psThreadTaskAdd(task);
+    psFree(task);
+
     task = psThreadTaskAlloc("PSPHOT_BLEND_FIT", 10);
     task->function = &psphotBlendFit_Threaded;

trunk/psphot/src/psphotSourceFits.c

@@ -19 +19 @@
 static int NfitIterPCM = 0;
 static int NfitPixPCM = 0;
+
+bool psphotPCMfitCheckSize (pmPCMdata *pcm, pmSource *source, psImageMaskType maskVal, float psfSize);
+bool psphotPCMfitRetry (pmPCMdata *pcm, pmSource *source, pmSourceFitOptions *fitOptions, psImageMaskType maskVal, psImageMaskType markVal, float psfSize);
 
 bool psphotFitInit (int nThreads) {
@@ -579 +582 @@
     maskVal |= markVal;
 
-    // allocate the model
+    // allocate the model (this can only fail on a config error)
     pmModel *model = pmModelAlloc(modelType);
-    if (!model) {
-        return NULL;
-    }
-
-    float t1, t2, t4, t5;
-    t1 = t2 = t4 = t5 = 0.0;
+    psAssert (model, "invalid extended model name");
+
+    float t1, t2, t3, t4, t5;
+    t1 = t2 = t3 = t4 = t5 = 0.0;
     if (TIMING) { psTimerStart ("psphotFitPCM"); }
 
@@ -619 +620 @@
         if (!psphotSersicModelGuessPCM (pcm, source, maskVal, psfSize)) {
             psFree (pcm);
-            model->flags |= PM_MODEL_STATUS_BADARGS;
+            model->flags |= PM_MODEL_SERSIC_PCM_FAIL_GUESS;
             return model;
         }
@@ -628 +629 @@
         if (!psphotFitSersicShapeAndIndexGridAuto (pcm, readout, source, &options, maskVal, markVal, psfSize)) {
             psFree (pcm);
-            model->flags |= PM_MODEL_STATUS_BADARGS;
+            model->flags |= PM_MODEL_SERSIC_PCM_FAIL_GRID;
             psError(PS_ERR_UNKNOWN, true, "Failed to find a index & shape");
             psErrorClear (); // clear the polynomial error
@@ -637 +638 @@
         if (!pmSourceModelGuessPCM (pcm, source, maskVal, markVal)) {
             psFree (pcm);
-            model->flags |= PM_MODEL_STATUS_BADARGS;
+            model->flags |= PM_MODEL_PCM_FAIL_GUESS;
             return model;
         }
     }
 
-    if (TIMING) { t4 = psTimerMark ("psphotFitPCM"); }
+    if (TIMING) { t3 = psTimerMark ("psphotFitPCM"); }
 
     // psTraceSetLevel("psLib.math.psMinimizeLMChi2", 5);
@@ -648 +649 @@
     NfitIterPCM += pcm->modelConv->nIter;
     NfitPixPCM += pcm->modelConv->nDOF;
+    if (TIMING) { t4 = psTimerMark ("psphotFitPCM"); }
+
+    // XXX we might make this more efficient by setting NITER to be fairly small.  if we hit the iteration
+    // limit, then we could do a small grid search on the size and try again from the best fit 
+
+    if (options.isInteractive) psphotPCMfitCheckSize (pcm, source, maskVal, psfSize);
+    // if (pcm->modelConv->nIter == fitOptions->nIter) {
+    //  psphotPCMfitRetry (pcm, source, &options, maskVal, markVal, psfSize);
+    // }
     if (TIMING) { t5 = psTimerMark ("psphotFitPCM"); }
 
     if (TIMING) {
         int nPixBig = source->pixels->numCols * source->pixels->numRows;
-        fprintf (stderr, "psphotFitPCM : nIter: %2d, radius: %6.1f, npix: %5d of %5d, t1: %6.4f, t2: %6.4f, t4: %6.4f, t5: %6.4f\n", model->nIter, model->fitRadius, model->nPix, nPixBig, t1, t2, t4, t5);
+        fprintf (stderr, "psphotFitPCM : nIter: %2d, radius: %6.1f, npix: %5d of %5d, t1: %6.4f, t2: %6.4f, t3: %6.4f, t4: %6.4f, t5: %6.4f\n", model->nIter, model->fitRadius, model->nPix, nPixBig, t1, t2, t3, t4, t5);
     }
     if (EXTRA_VERBOSE && !TIMING) {
@@ -778 +788 @@
 }
 
-// float indexGuessInv[] = {0.5, 0.33, 0.25, 0.167, 0.125, 0.083};
-float indexGuessInv[] = {0.5, 0.4, 0.3, 0.25, 0.20, 0.15, 0.125};
-# define N_INDEX_GUESS_INV 7
-
-// float reffGuess[] = {3.0, 10.0, 20.0, 30.0, 40.0};
-float reffGuess[] = {0.5, 0.75, 1.0, 1.4, 2.0};
+// 0.5 / n for (1.0, 1.25, 1.66, 2.0, 3.33, 4.0)
+// float indexGuessInv[] = {0.5, 0.4, 0.3, 0.25, 0.20, 0.15, 0.125};
+
+// 0.5 / n for (0.5, 1.0, 1.5, 2.0, 3.0, 4.0, 5.0, 6.0)
+float indexGuessInv[] = {1.00, 0.50, 0.333, 0.25, 0.166, 0.125, 0.10, 0.0833};
+float indexGuessR1q[] = {1.06, 1.19, 1.335, 1.48, 1.840, 2.290, 2.84, 3.5300};
+# define N_INDEX_GUESS_INV 8
+
+// we are going to guess in fractions about the R1-based guess
+float reffGuess[] = {0.8, 0.9, 1.0, 1.12, 1.25};
 # define N_REFF_GUESS 5
 
@@ -791 +805 @@
 
     // we get a reasonable guess from:
-    // * Reff = Kron R1
+    // * Reff = Kron R1 / Q(index) -- Q comes from Graham & Driver 
     // * Rmajor / Rminor & Theta from moments
     // * Io from total Kron flux
@@ -813 +827 @@
     psEllipseAxes momentAxes = psEllipseMomentsToAxes (moments, 20.0);
 
-    if (0) {
-        psEllipseAxes guessAxes;
-        guessAxes.major = source->moments->Mrf;
-        guessAxes.minor = (momentAxes.minor / momentAxes.minor) * guessAxes.major;
-        guessAxes.theta = momentAxes.theta;
-
-        if (!isfinite(guessAxes.major)) return false;
-        if (!isfinite(guessAxes.minor)) return false;
-        if (!isfinite(guessAxes.theta)) return false;
-
-        // convert the major,minor,theta to shape parameters for an Reff-like model
-        pmModelAxesToParams (&PAR[PM_PAR_SXX], &PAR[PM_PAR_SXY], &PAR[PM_PAR_SYY], guessAxes, true);
-    }
-
     // set the model position
     if (!pmModelSetPosition(&PAR[PM_PAR_XPOS], &PAR[PM_PAR_YPOS], source)) {
@@ -846 +846 @@
     // loop over index guesses and find the best fit
     for (int j = 0; j < N_REFF_GUESS; j++) {
-
-        psEllipseAxes guessAxes;
-        guessAxes.major = reffGuess[j] * source->moments->Mrf;
-        guessAxes.minor = guessAxes.major * (momentAxes.minor / momentAxes.major);
-        guessAxes.theta = momentAxes.theta;
-
-        if (!isfinite(guessAxes.major)) return false;
-        if (!isfinite(guessAxes.minor)) return false;
-        if (!isfinite(guessAxes.theta)) return false;
-
-        // convert the major,minor,theta to shape parameters for an Reff-like model
-        pmModelAxesToParams (&PAR[PM_PAR_SXX], &PAR[PM_PAR_SXY], &PAR[PM_PAR_SYY], guessAxes, true);
-
         for (int i = 0; i < N_INDEX_GUESS_INV; i++) {
             PAR[PM_PAR_7] = indexGuessInv[i];
 
+            psEllipseAxes guessAxes;
+            guessAxes.major = reffGuess[j] * source->moments->Mrf / indexGuessR1q[i];
+            guessAxes.minor = guessAxes.major * (momentAxes.minor / momentAxes.major);
+            guessAxes.theta = momentAxes.theta;
+
+            if (!isfinite(guessAxes.major)) return false;
+            if (!isfinite(guessAxes.minor)) return false;
+            if (!isfinite(guessAxes.theta)) return false;
+
+            // convert the major,minor,theta to shape parameters for an Reff-like model
+            pmModelAxesToParams (&PAR[PM_PAR_SXX], &PAR[PM_PAR_SXY], &PAR[PM_PAR_SYY], guessAxes, true);
+
             // generated the modelFlux
-            pmPCMMakeModel (source, pcm->modelConv, maskVal, psfSize);
+            // XXX note that this does not add sky to model
+            pmPCMMakeModel (source, pcm->modelConv, pcm->nsigma, maskVal, psfSize);
         
             float YY = 0.0;
@@ -901 +901 @@
                 iMin = Io;
                 sMin = indexGuessInv[i];
-                rMin = reffGuess[j];
+                rMin = reffGuess[j] / indexGuessR1q[i];
             }
-            // fprintf (stderr, "%d | %f %f %f %f | %f %f %f %f", i, indexGuessInv[i], reffGuess[j], Io, Chisq, sMin, rMin, iMin, xMin);
-            // fprintf (stderr, "\n");
+            if (EXTRA_VERBOSE) {
+                fprintf (stderr, "%d | %f %f %f %f | %f %f %f %f", i, indexGuessInv[i], reffGuess[j], Io, Chisq, sMin, rMin, iMin, xMin);
+                fprintf (stderr, "\n");
+            }
         }
     }
@@ -1007 +1009 @@
     psVector *Sidx = psVectorAllocEmpty (16, PS_TYPE_F32);
 
-    PAR[PM_PAR_7] = indexGuessInv[nStart];
+    float Sm = NAN, Sp = NAN, So = NAN;
+    if (nStart == 0) {
+        Sm = indexGuessInv[nStart];
+        So = 0.5*(indexGuessInv[nStart + 1] + indexGuessInv[nStart]);
+        Sp = indexGuessInv[nStart + 1];
+    } else if (nStart == N_INDEX_GUESS_INV - 1) {
+        Sp = indexGuessInv[nStart];
+        So = 0.5*(indexGuessInv[nStart - 1] + indexGuessInv[nStart]);
+        Sm = indexGuessInv[nStart - 1];
+    } else {
+        Sm = 0.5*(indexGuessInv[nStart - 1] + indexGuessInv[nStart]);
+        So = indexGuessInv[nStart];
+        Sp = 0.5*(indexGuessInv[nStart + 1] + indexGuessInv[nStart]);
+    }
+    
+    PAR[PM_PAR_7] = Sm;
     pmSourceFitPCM (pcm, source, &options, maskVal, markVal, psfSize);
     if (EXTRA_VERBOSE) fprintf (stderr, "%d >>> %d %f : %f - %f %f - %f %f %f - %f\n", source->id, model->nIter, model->chisqNorm, PAR[7], PAR[2], PAR[3], PAR[4], PAR[5], PAR[6], PAR[1]);
@@ -1013 +1030 @@
     psVectorAppend (chi2, model->chisqNorm);
 
-    PAR[PM_PAR_7] = (nStart < N_INDEX_GUESS_INV - 1) ? 0.5*(indexGuessInv[nStart + 1] + indexGuessInv[nStart]) : 0.1;
+    PAR[PM_PAR_7] = So;
     pmSourceFitPCM (pcm, source, &options, maskVal, markVal, psfSize);
     if (EXTRA_VERBOSE) fprintf (stderr, "%d >>> %d %f : %f - %f %f - %f %f %f - %f\n", source->id, model->nIter, model->chisqNorm, PAR[7], PAR[2], PAR[3], PAR[4], PAR[5], PAR[6], PAR[1]);
@@ -1019 +1036 @@
     psVectorAppend (chi2, model->chisqNorm);
 
-    PAR[PM_PAR_7] = (nStart > 0) ? 0.5*(indexGuessInv[nStart - 1] + indexGuessInv[nStart]) : 0.55;
+    PAR[PM_PAR_7] = Sp;
     pmSourceFitPCM (pcm, source, &options, maskVal, markVal, psfSize);
     if (EXTRA_VERBOSE) fprintf (stderr, "%d >>> %d %f : %f - %f %f - %f %f %f - %f\n", source->id, model->nIter, model->chisqNorm, PAR[7], PAR[2], PAR[3], PAR[4], PAR[5], PAR[6], PAR[1]);
     psVectorAppend (Sidx, 100*PAR[PM_PAR_7]);
     psVectorAppend (chi2, model->chisqNorm);
-
-    if (chi2->data.F32[1] < chi2->data.F32[2]) {
-      if (nStart == N_INDEX_GUESS_INV - 1) {
-        PAR[PM_PAR_7] = 0.11;
-      } else {
-        PAR[PM_PAR_7] = indexGuessInv[nStart + 1];
-      }
-    } else {
-      if (nStart == 0) {
-        PAR[PM_PAR_7] = 0.52;
-      } else {
-        PAR[PM_PAR_7] = indexGuessInv[nStart - 1];
-      }
-    }
 
     psPolynomial1D *poly = psPolynomial1DAlloc (PS_POLYNOMIAL_ORD, 2);
@@ -1051 +1054 @@
     float Smin = -0.5 * poly->coeff[1] / poly->coeff[2] / 100.0;
 
-    // constrain Smin to be in a valid range (1.0 - 0.1, corresponding to 0.5 (Gauss) to 5.0 (slightly peakier than Dev)
-    Smin = PS_MAX(PS_MIN(Smin, 1.0), 0.1);
+    // constrain Smin to be in a valid range: allow the fitted range to go a bit beyond the 3 trial points, but no further
+    float Smx = Sm - 0.25*(So - Sm);
+    float Spx = Sp + 0.25*(Sp - So);
+    Smin = PS_MAX(PS_MIN(Smin, Smx), Spx);
     PAR[PM_PAR_7] = Smin;
+
+    // XXX I could set the error on PAR_7 here if I knew how to roughly convert these chisq values to true chisq values
 
     // return to the original fitting mode (fitOptions)
@@ -1246 +1253 @@
 }
 
- 
+// # define N_REFF_CHECK 11
+// float drefCheck[] = {-0.02, -0.04, -0.06, 0.0, 0.85, 0.90, 0.95, 1.00, 1.05, 1.10, 1.15, 1.20, 1.25};
+
+// we have an initial fit, check to see if the current size is besst
+bool psphotPCMfitCheckSize (pmPCMdata *pcm, pmSource *source, psImageMaskType maskVal, float psfSize) {
+
+    // PAR is already at my current best guess
+    psF32 *PAR = pcm->modelConv->params->data.F32;
+
+    // store best guess as a shape
+    psEllipseAxes centerAxes;
+    pmModelParamsToAxes (&centerAxes, PAR[PM_PAR_SXX], PAR[PM_PAR_SXY], PAR[PM_PAR_SYY], true);
+
+    float xMin = NAN;
+    float iMin = NAN;
+    float rMin = NAN;
+
+    // loop over Reff, keeping the ARatio and Theta constant
+    for (int j = -4; j <= 4; j++) {
+
+        float dref = j * 0.01;
+
+        psEllipseAxes guessAxes;
+        guessAxes.major = centerAxes.major + dref;
+        guessAxes.minor = guessAxes.major * centerAxes.minor / centerAxes.major;
+        guessAxes.theta = centerAxes.theta;
+
+        if (!isfinite(guessAxes.major)) return false;
+        if (!isfinite(guessAxes.minor)) return false;
+        if (!isfinite(guessAxes.theta)) return false;
+
+        // convert the major,minor,theta to shape parameters for an Reff-like model
+        pmModelAxesToParams (&PAR[PM_PAR_SXX], &PAR[PM_PAR_SXY], &PAR[PM_PAR_SYY], guessAxes, true);
+
+        // generated the modelFlux
+            // XXX note that this does not add sky to model
+        pmPCMMakeModel (source, pcm->modelConv, pcm->nsigma, maskVal, psfSize);
+        
+        float YY = 0.0;
+        float YM = 0.0;
+        float MM = 0.0;
+        bool usePoisson = false;
+
+        for (int iy = 0; iy < source->pixels->numRows; iy++) {
+            for (int ix = 0; ix < source->pixels->numCols; ix++) {
+                // skip masked points
+                if (source->maskObj->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix]) {
+                    continue;
+                }
+                // skip zero-variance points
+                if (source->variance->data.F32[iy][ix] == 0) {
+                    continue;
+                }
+                // skip nan value points
+                if (!isfinite(source->pixels->data.F32[iy][ix])) {
+                    continue;
+                }
+
+                float fy = source->pixels->data.F32[iy][ix];
+                float fm = source->modelFlux->data.F32[iy][ix];
+                float wt = (usePoisson) ? 1.0 / source->variance->data.F32[iy][ix] : 1.0;
+
+                YY += PS_SQR(fy) * wt;
+                YM += fm * fy * wt;
+                MM += PS_SQR(fm) * wt;
+            }
+        }
+
+        float Io = YM / MM;
+        float Chisq = YY - 2 * Io * YM + Io * Io * MM;
+        if (isnan(xMin) || (Chisq < xMin)) {
+            xMin = Chisq;
+            iMin = Io;
+            rMin = dref;
+        }
+        // fprintf (stderr, "%d | %f %f %f | %f %f %f\n", j, dref, Io, Chisq, rMin, iMin, xMin);
+    }
+
+    psEllipseAxes guessAxes;
+    guessAxes.major = centerAxes.major + rMin;
+    guessAxes.minor = guessAxes.major * centerAxes.minor / centerAxes.major;
+    guessAxes.theta = centerAxes.theta;
+
+    if (!isfinite(guessAxes.major)) return false;
+    if (!isfinite(guessAxes.minor)) return false;
+    if (!isfinite(guessAxes.theta)) return false;
+
+    // convert the major,minor,theta to shape parameters for an Reff-like model
+    pmModelAxesToParams (&PAR[PM_PAR_SXX], &PAR[PM_PAR_SXY], &PAR[PM_PAR_SYY], guessAxes, true);
+    PAR[PM_PAR_I0] = iMin;
+
+    return true;
+}
+
+// we have an initial fit, check to see if the current size is besst
+bool psphotPCMfitRetry (pmPCMdata *pcm, pmSource *source, pmSourceFitOptions *fitOptions, psImageMaskType maskVal, psImageMaskType markVal, float psfSize) {
+
+    // PAR is already at my current best guess
+    psF32 *PAR = pcm->modelConv->params->data.F32;
+
+    // store best guess as a shape
+    psEllipseAxes centerAxes;
+    pmModelParamsToAxes (&centerAxes, PAR[PM_PAR_SXX], PAR[PM_PAR_SXY], PAR[PM_PAR_SYY], true);
+
+    // retry with axes smaller by 1 pixel
+    psEllipseAxes guessAxes;
+    guessAxes.major = centerAxes.major - 0.08;
+    guessAxes.minor = guessAxes.major * centerAxes.minor / centerAxes.major;
+    guessAxes.theta = centerAxes.theta;
+
+    if (!isfinite(guessAxes.major)) return false;
+    if (!isfinite(guessAxes.minor)) return false;
+    if (!isfinite(guessAxes.theta)) return false;
+
+    // convert the major,minor,theta to shape parameters for an Reff-like model
+    pmModelAxesToParams (&PAR[PM_PAR_SXX], &PAR[PM_PAR_SXY], &PAR[PM_PAR_SYY], guessAxes, true);
+
+    // generated the modelFlux
+            // XXX note that this does not add sky to model
+    pmPCMMakeModel (source, pcm->modelConv, pcm->nsigma, maskVal, psfSize);
+        
+    float YY = 0.0;
+    float YM = 0.0;
+    float MM = 0.0;
+    bool usePoisson = false;
+
+    for (int iy = 0; iy < source->pixels->numRows; iy++) {
+        for (int ix = 0; ix < source->pixels->numCols; ix++) {
+            // skip masked points
+            if (source->maskObj->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix]) {
+                continue;
+            }
+            // skip zero-variance points
+            if (source->variance->data.F32[iy][ix] == 0) {
+                continue;
+            }
+            // skip nan value points
+            if (!isfinite(source->pixels->data.F32[iy][ix])) {
+                continue;
+            }
+
+            float fy = source->pixels->data.F32[iy][ix];
+            float fm = source->modelFlux->data.F32[iy][ix];
+            float wt = (usePoisson) ? 1.0 / source->variance->data.F32[iy][ix] : 1.0;
+
+            YY += PS_SQR(fy) * wt;
+            YM += fm * fy * wt;
+            MM += PS_SQR(fm) * wt;
+        }
+    }
+
+    float Io = YM / MM;
+    PAR[PM_PAR_I0] = Io;
+
+    pmSourceFitPCM (pcm, source, fitOptions, maskVal, markVal, psfSize);  // NOTE : 1687 allocs in here
+
+    return true;
+}
+
+

trunk/psphot/src/psphotSourceSize.c

@@ -1 +1 @@
 # include "psphotInternal.h"
-# include <gsl/gsl_sf_gamma.h>
-
+
+// this structure is only used internally to simplify the function parameters
 typedef struct {
     psImageMaskType maskVal;
@@ -13 +13 @@
     bool altDiffExt;
     float altDiffExtThresh;
-    bool extFitAll;
-    bool extFitAllReadout;
-    float extFitAllThresh;
     float soft;
     int grow;
@@ -33 +30 @@
 bool psphotSourceSelectCR (pmReadout *readout, psArray *sources, psphotSourceSizeOptions *options);
 bool psphotMaskCosmicRay (pmReadout *readout, pmSource *source, psImageMaskType maskVal, int maxWindowCR);
-bool psphotMaskCosmicRayFootprintCheck (psArray *sources);
 int  psphotMaskCosmicRayConnected (int xPeak, int yPeak, psImage *mymask, psImage *myvar, psImage *edges, int binning, float sigma_thresh);
 float psphotSourceSizeFindThreshold (psVector *value, psVector *mask, int maskValue, float minValue, float maxValue, float delta, float guess, float fraction);
@@ -41 +37 @@
 
 // we need to call this function after sources have been fitted to the PSF model and
-// subtracted.  To determine the CR-nature, this function examines the 9 pixels in the 3x3
-// square containing the peak and compares the observed flux to the model.  To determine
-// the EXT-nature, this function measures the amount of positive or negative total
-// deviation from the psf model at the r = FWHM/2 position
+// subtracted.  
 
 // for now, let's store the detections on the readout->analysis for each readout
@@ -121 +114 @@
     assert (status);
 
-    // XXX recipe name is not great
+    // XXX recipe name is not great (NOTE : not used!)
     options.nSigmaMoments = psMetadataLookupF32 (&status, recipe, "PSPHOT.EXT.NSIGMA.MOMENTS");
     assert (status);
 
-    // Optional extended source measurement algorithm to improve diff image trails
+    // Optional algorithm to define if a source is extended (used by DIFF analysis)
     options.altDiffExt = psMetadataLookupBool(&status, recipe, "PSPHOT.EXT.DIFF.ALTERNATE");
     assert (status);
+
     // Threshold for this alternate method
     options.altDiffExtThresh = psMetadataLookupF32(&status, recipe, "PSPHOT.EXT.DIFF.ALTERNATE.THRESH");
     assert (status);
-    // Option to enable fitting of all objects with extended model.
-    options.extFitAll = psMetadataLookupBool(&status, recipe, "PSPHOT.EXT.FIT.ALL.SOURCES");
-    assert (status);
-    // Fitting everything is fine, but if the source density is high, we probably shouldn't.
-    options.extFitAllThresh = psMetadataLookupF32(&status, recipe, "PSPHOT.EXT.FIT.ALL.THRESH");
-    assert (status);
-    
+
     // location of a single test source
     options.xtest = psMetadataLookupS32 (&status, recipe, "PSPHOT.CRMASK.XTEST");
@@ -422 +410 @@
 
     psLogMsg("psModules.objects", PS_LOG_INFO, "Source Size classifications: %4s %4s %4s %4s %4s", "Npsf", "Next", "Nsat", "Ncr", "Nskip");
-    // Determine if this readout is above the threshold to ext fit all sources
-    options->extFitAllReadout = false;
-    if (options->extFitAll) {
-      float maskFrac = psMetadataLookupF32(&status,readout->analysis,"READOUT.MASK.FRAC");
-      if (status) {
-        maskFrac = 0.0;
-      }
-      if (sources->n * (1.0 - maskFrac) > options->extFitAllThresh) {
-        options->extFitAllReadout = false;
-      }
-      else {
-        options->extFitAllReadout = true;
-      }
-    }
-    
+
     if (!psphotSourceClassRegion (NULL, &psfClump, sources, recipe, psf, options)) {
         psLogMsg ("psphot", 4, "Failed to determine source classification for full image\n");
@@ -444 +418 @@
     return true;
     
+    // NOTE : this section is deactivated (EAM : I think we were getting poor boundary effects?)
     int nRegions = psMetadataLookupS32 (&status, readout->analysis, "PSF.CLUMP.NREGIONS");
     for (int i = 0; i < nRegions; i ++) {
@@ -582 +557 @@
         // * SAT stars should not be faint, but defects may?
 
-        // If the recipe requests we do extended source fits to everything, set
-        // the EXT_LIMIT flag
-        if (options->extFitAllReadout) {
-          psTrace("psphotSourceClassRegion.EXTALT",10,"In extFitAll: %d %d\n",options->extFitAll,options->extFitAllReadout);
-          source->mode |= PM_SOURCE_MODE_EXT_LIMIT;
-        }
         // Defects may not always match CRs from peak curvature analysis
         // Defects may also be marked as SATSTAR -- XXX deactivate this flag?
@@ -595 +564 @@
 
         // saturated star (too many saturated pixels or peak above saturation limit).  These
-        // may also be saturated galaxies, or just large saturated regions.
+        // may also be saturated galaxies, or just large saturated regions.  They are never
+        // marked as 'extended'
         if (source->mode & PM_SOURCE_MODE_SATSTAR) {
             psTrace("psphotSourceClassRegion.SAT",4,"CLASS: %g %g\t%g %g\t%g %g\t%g %g\t%g SAT\n",
@@ -604 +574 @@
         }
 
-        // any sources missing a large fraction should just be treated as PSFs
+        // any sources missing a large fraction should just be treated as PSFs. They are never
+        // marked as 'extended'
         if ((source->pixWeightNotBad < 0.9) || (source->pixWeightNotPoor < 0.9)) {
             psTrace("psphotSourceClassRegion.PSF",4,"CLASS: %g %g\t%g %g  %g %g  %g %g\t%g %g\t%g PSF\t%g %g\n",
@@ -634 +605 @@
             psTrace("psphotSourceClassRegion.EXT",4,"CLASS: %g %g\t%g %g\t%g %g\t%g %g\t%g EXT\n",
                     source->peak->xf, source->peak->yf, Mminor, kMag, dMag, nSigmaMAG, options->sizeLimitCR, options->magLimitCR, options->nSigmaApResid);
+            source->type = PM_SOURCE_TYPE_EXTENDED;
             source->mode |= PM_SOURCE_MODE_EXT_LIMIT;
             source->tmpFlags |= PM_SOURCE_TMPF_SIZE_MEASURED;
@@ -639 +611 @@
             continue;
         }
+
         // Alternate extended source limit calculation
         if (options->altDiffExt) {
@@ -652 +625 @@
                     source->peak->xf, source->peak->yf, Mminor, kMag, dMag, nSigmaMAG, options->sizeLimitCR, options->magLimitCR, options->nSigmaApResid,
                     momentRatioVeres,options->altDiffExtThresh);
+            source->type = PM_SOURCE_TYPE_EXTENDED;
             source->mode |= PM_SOURCE_MODE_EXT_LIMIT;
             source->tmpFlags |= PM_SOURCE_TMPF_SIZE_MEASURED;
@@ -968 +942 @@
 }
 
-bool psphotMaskCosmicRayFootprintCheck (psArray *sources) {
-#ifdef CHECK_FOOTPRINTS
-    // This gets really expensive for complex images
-    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");
-        }
-    }
-#endif
-    return true;
-}
-
-/**** ------ old versions of cosmic ray masking ----- ****/
-
-bool psphotMaskCosmicRayIsophot (pmSource *source, psImageMaskType maskVal, psImageMaskType crMask);
-
-// 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
-    pmSourceAdd (source, PM_MODEL_OP_FULL, maskVal);
-
-    // flag this as a CR
-    source->mode |= PM_SOURCE_MODE_CR_LIMIT;
-    pmPeak *peak = source->peak;
-    psAssert (peak, "NULL peak");
-
-    // grab the matching footprint
-    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);
-        return true;
-    }
-
-    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;
-        }
-    }
-    return true;
-}
-
 # define VERBOSE 0
 int psphotMaskCosmicRayConnected (int xPeak, int yPeak, psImage *mymask, psImage *myvar, psImage *edges, int binning, float sigma_thresh) {
@@ -1176 +1085 @@
 }
 
-bool psphotMaskCosmicRayIsophot (pmSource *source, psImageMaskType maskVal, psImageMaskType crMask) {
-
-    source->mode |= PM_SOURCE_MODE_CR_LIMIT;
-    pmPeak *peak = source->peak;
-    psAssert (peak, "NULL peak");
-
-    psImage *mask   = source->maskView;
-    psImage *pixels = source->pixels;
-    psImage *variance = source->variance;
-
-    // XXX This should be a recipe variable
-# define SN_LIMIT 5.0
-
-    int xo = peak->x - pixels->col0;
-    int yo = peak->y - pixels->row0;
-
-    // mark the pixels in this row to the left, then the right
-    for (int ix = xo; ix >= 0; ix--) {
-        float SN = pixels->data.F32[yo][ix] / sqrt(variance->data.F32[yo][ix]);
-        if (SN > SN_LIMIT) {
-            mask->data.PS_TYPE_IMAGE_MASK_DATA[yo][ix] |= crMask;
-        }
-    }
-    for (int ix = xo + 1; ix < pixels->numCols; ix++) {
-        float SN = pixels->data.F32[yo][ix] / sqrt(variance->data.F32[yo][ix]);
-        if (SN > SN_LIMIT) {
-            mask->data.PS_TYPE_IMAGE_MASK_DATA[yo][ix] |= crMask;
-        }
-    }
-
-    // for each of the neighboring rows, mark the high pixels if they have a marked neighbor
-    // first go up:
-    for (int iy = PS_MIN(yo, mask->numRows-2); iy >= 0; iy--) {
-        // mark the pixels in this row to the left, then the right
-        for (int ix = 0; ix < pixels->numCols; ix++) {
-            float SN = pixels->data.F32[iy][ix] / sqrt(variance->data.F32[iy][ix]);
-            if (SN < SN_LIMIT) continue;
-
-            bool valid = false;
-            valid |= (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy+1][ix] & crMask);
-            valid |= (ix > 0) ? (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy+1][ix-1] & crMask) : 0;
-            valid |= (ix <= mask->numCols) ? (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy+1][ix+1] & crMask) : 0;
-
-            if (!valid) continue;
-            mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= crMask;
-        }
-    }
-    // next go down:
-    for (int iy = PS_MIN(yo+1, mask->numRows-1); iy < pixels->numRows; iy++) {
-        // mark the pixels in this row to the left, then the right
-        for (int ix = 0; ix < pixels->numCols; ix++) {
-            float SN = pixels->data.F32[iy][ix] / sqrt(variance->data.F32[iy][ix]);
-            if (SN < SN_LIMIT) continue;
-
-            bool valid = false;
-            valid |= (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy-1][ix] & crMask);
-            valid |= (ix > 0) ? (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy-1][ix-1] & crMask) : 0;
-            valid |= (ix <= mask->numCols) ? (mask->data.PS_TYPE_IMAGE_MASK_DATA[iy-1][ix+1] & crMask) : 0;
-
-            if (!valid) continue;
-            mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= crMask;
-        }
-    }
-    return true;
-}
-
-// given the PSF ellipse parameters, navigate around the 1sigma contour, return the total
-// deviation in sigmas.  This is measured on the residual image - should we ignore negative
-// deviations?  NOTE: This function was an early attempt to classify extended objects, and is
-// no longer used by psphot.
-float psphotModelContour(const psImage *image, const psImage *variance, const psImage *mask,
-                         psImageMaskType maskVal, const pmModel *model, float Ro)
-{
-    psF32 *PAR = model->params->data.F32; // Model parameters
-    float sxx = PAR[PM_PAR_SXX], sxy = PAR[PM_PAR_SXY], syy = PAR[PM_PAR_SYY]; // Ellipse parameters
-
-    // We treat the contour as an ellipse:
-    // Ro = (x / SXX)^2 + (y / SYY)^2 + x y SXY
-    // y^2 (1/SYY^2) + y (x SXY) + (x / SXX)^2 - Ro = 0;
-    // This is a quadratic, Ay^2 + By + C with A = 1/SYY^2, B = x*SXY, C = (x / SXX)^2 - Ro
-    // The solution is y = [-B +/- sqrt (B^2 - 4 A C)] / [2 A], so:
-    // y = [-(x SXY) +/- sqrt ((x SXY)^2 - 4 (1/SYY^2) ((x/SXX)^2 - Ro))] * [SYY^2 / 2]
-
-    // min/max value of x is where B^2 - 4AC = 0; solve this for x
-    float Q = Ro * PS_SQR(sxx) / (1.0 - PS_SQR(sxx * syy * sxy) / 4.0);
-    if (Q < 0.0) {
-        // ellipse is imaginary
-        return NAN;
-    }
-
-    int radius = sqrtf(Q) + 0.5;        // Radius of ellipse
-    int nPts = 0;                       // Number of points in ellipse
-    float nSigma = 0.0;                 //
-
-    for (int x = -radius; x <= radius; x++) {
-        // Polynomial coefficients
-        // XXX Should we be using the centre of the pixel as x or x+0.5?
-        float A = PS_SQR (1.0 / syy);
-        float B = x * sxy;
-        float C = PS_SQR (x / sxx) - Ro;
-        float T = PS_SQR(B) - 4*A*C;
-        if (T < 0.0) {
-            continue;
-        }
-
-        // y position in source frame
-        float yP = (-B + sqrt (T)) / (2.0 * A);
-        float yM = (-B - sqrt (T)) / (2.0 * A);
-
-        // Get the closest pixel positions (image frame)
-        int xPix  = x  + PAR[PM_PAR_XPOS] - image->col0 + 0.5;
-        int yPixM = yM + PAR[PM_PAR_YPOS] - image->row0 + 0.5;
-        int yPixP = yP + PAR[PM_PAR_YPOS] - image->row0 + 0.5;
-
-        if (xPix < 0 || xPix >= image->numCols) {
-            continue;
-        }
-
-        if (yPixM >= 0 && yPixM < image->numRows &&
-            !(mask && (mask->data.PS_TYPE_IMAGE_MASK_DATA[yPixM][xPix] & maskVal))) {
-            float dSigma = image->data.F32[yPixM][xPix] / sqrtf(variance->data.F32[yPixM][xPix]);
-            nSigma += dSigma;
-            nPts++;
-        }
-
-        if (yPixM == yPixP) {
-            continue;
-        }
-
-        if (yPixP >= 0 && yPixP < image->numRows &&
-            !(mask && (mask->data.PS_TYPE_IMAGE_MASK_DATA[yPixP][xPix] & maskVal))) {
-            float dSigma = image->data.F32[yPixP][xPix] / sqrtf(variance->data.F32[yPixP][xPix]);
-            nSigma += dSigma;
-            nPts++;
-        }
-    }
-    nSigma /= nPts;
-    return nSigma;
-}
-
-// 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?)
-    // XXX use an internal flag to mark sources which have already been measured
-    for (int i = 0; i < sources->n; i++) {
-        pmSource *source = sources->data[i];
-
-        // 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;
-        }
-
-        psF32 **resid  = source->pixels->data.F32;
-        psF32 **variance = source->variance->data.F32;
-        psImageMaskType **mask = source->maskObj->data.PS_TYPE_IMAGE_MASK_DATA;
-
-        // 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");
-            continue;
-        }
-
-        // Skip sources with masked pixels.  These are mostly caught as DEFECT
-        bool keep = true;
-        for (int iy = -1; (iy <= +1) && keep; iy++) {
-            for (int ix = -1; (ix <= +1) && keep; ix++) {
-                if (mask[yPeak+iy][xPeak+ix] & options->maskVal) {
-                    keep = false;
-                }
-            }
-        }
-        if (!keep) {
-            psTrace("psphot", 7, "Not calculating crNsigma due to masked pixels\n");
-            continue;
-        }
-
-        // Compare the central pixel with those on either side, for the four possible lines through it.
-
-        // Soften variances (add systematic error)
-        float softening = options->soft * PS_SQR(source->peak->rawFlux); // Softening for variances
-
-        // Across the middle: y = 0
-        float cX = 2*resid[yPeak][xPeak]   - resid[yPeak+0][xPeak-1]  - resid[yPeak+0][xPeak+1];
-        float dcX = 4*variance[yPeak][xPeak] + variance[yPeak+0][xPeak-1] + variance[yPeak+0][xPeak+1];
-        float nX = cX / sqrtf(dcX + softening);
-
-        // Up the centre: x = 0
-        float cY = 2*resid[yPeak][xPeak]   - resid[yPeak-1][xPeak+0]  - resid[yPeak+1][xPeak+0];
-        float dcY = 4*variance[yPeak][xPeak] + variance[yPeak-1][xPeak+0] + variance[yPeak+1][xPeak+0];
-        float nY = cY / sqrtf(dcY + softening);
-
-        // Diagonal: x = y
-        float cL = 2*resid[yPeak][xPeak]   - resid[yPeak-1][xPeak-1]  - resid[yPeak+1][xPeak+1];
-        float dcL = 4*variance[yPeak][xPeak] + variance[yPeak-1][xPeak-1] + variance[yPeak+1][xPeak+1];
-        float nL = cL / sqrtf(dcL + softening);
-
-        // Diagonal: x = - y
-        float cR = 2*resid[yPeak][xPeak]   - resid[yPeak+1][xPeak-1]  - resid[yPeak-1][xPeak+1];
-        float dcR = 4*variance[yPeak][xPeak] + variance[yPeak+1][xPeak-1] + variance[yPeak-1][xPeak+1];
-        float nR = cR / sqrtf(dcR + softening);
-
-        // P(chisq > chisq_obs; Ndof) = gamma_Q (Ndof/2, chisq/2)
-        // Ndof = 4 ? (four measurements, no free parameters)
-        // XXX this value is going to be biased low because of systematic errors.
-        // we need to calibrate it somehow
-        // source->psfProb = gsl_sf_gamma_inc_Q (2, 0.5*chisq);
-
-        // not strictly accurate: overcounts the chisq contribution from the center pixel (by
-        // factor of 4); also biases a bit low if any pixels are masked
-        // XXX I am not sure I want to keep this value...
-        source->psfChisq = PS_SQR(nX) + PS_SQR(nY) + PS_SQR(nL) + PS_SQR(nR);
-
-        float fCR = 0.0;
-        int nCR = 0;
-        if (nX > 0.0) {
-            fCR += nX;
-            nCR ++;
-        }
-        if (nY > 0.0) {
-            fCR += nY;
-            nCR ++;
-        }
-        if (nL > 0.0) {
-            fCR += nL;
-            nCR ++;
-        }
-        if (nR > 0.0) {
-            fCR += nR;
-            nCR ++;
-        }
-        source->crNsigma  = (nCR > 0)  ? fCR / nCR : 0.0;
-        source->tmpFlags |= PM_SOURCE_TMPF_SIZE_MEASURED;
-
-        if (!isfinite(source->crNsigma)) {
-            continue;
-        }
-
-        // this source is thought to be a cosmic ray.  flag the detection and mask the pixels
-        if (source->crNsigma > options->nSigmaCR) {
-            source->mode |= PM_SOURCE_MODE_CR_LIMIT;
-            // XXX still testing... : psphotMaskCosmicRay (readout->mask, source, maskVal, crMask);
-            // XXX acting strange... 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;
-    }
-    return true;
-}
-
 float psphotSourceSizeFindThreshold (psVector *value, psVector *mask, int maskValue, float minValue, float maxValue, float delta, float guess, float fraction) {
 

trunk/psphot/src/psphotSourceStats.c

@@ -58 +58 @@
     pmDetections *detections = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.DETECTIONS");
     psAssert (detections, "missing detections?");
-
-    // XXX TEST:
-    if (detections->allSources) {
-        psphotMaskCosmicRayFootprintCheck(detections->allSources);
-    }
-    if (detections->newSources) {
-        psphotMaskCosmicRayFootprintCheck(detections->newSources);
-    }
 
     // determine the number of allowed threads
@@ -246 +238 @@
     psphotVisualShowMoments (sources);
 
-    // clear the mark bits
-    // psImageMaskPixels (readout->mask, "AND", PS_NOT_IMAGE_MASK(markVal));
-
-    if (detections->allSources) {
-        psphotMaskCosmicRayFootprintCheck(detections->allSources);
-    }
-    if (detections->newSources) {
-        psphotMaskCosmicRayFootprintCheck(detections->newSources);
-    }
-
     return true;
 }
@@ -572 +554 @@
 
             // measure basic source moments (no S/N clipping on input pixels)
+            // sources with (mode & MODE_EXTERNAL) or (mode2 & MODE2_MATCHED) use the 
+            // supplied Mx,My value for the centroid (not recalculated)
             status = pmSourceMoments (source, 4*sigma[i], sigma[i], 0.0, 0.0, maskVal);
         }

trunk/psphot/src/psphotStackReadout.c

@@ -124 +124 @@
         return psphotReadoutCleanup (config, view, STACK_RAW);
     }
-
-// XXX TEST for background:
-    if (!psphotModelBackground (config, view, STACK_RAW)) {
-        return psphotReadoutCleanup (config, view, STACK_RAW);
-    }
-    if (!psphotSubtractBackground (config, view, STACK_RAW)) {
-        return psphotReadoutCleanup (config, view, STACK_RAW);
-    }
-    if (!psphotModelBackground (config, view, STACK_RAW)) {
-        return psphotReadoutCleanup (config, view, STACK_RAW);
-    }
-    if (!psphotSubtractBackground (config, view, STACK_RAW)) {
-        return psphotReadoutCleanup (config, view, STACK_RAW);
-    }
-// XXX TEST END 
 
 #ifdef MAKE_CHISQ_IMAGE
@@ -319 +304 @@
     psphotStackObjectsUnifyPosition (objects);
 
-    psphotStackObjectsSelectForAnalysis (config, view, STACK_RAW, objects);
+    // psphotStackObjectsSelectForAnalysis (config, view, STACK_RAW, objects);
 
     // final linear fit. NOTE: if splitLinearFit is true above, this pass will only fit
@@ -346 +331 @@
     // measure kron fluxes for the matched sources only
     psphotKronIterate(config, view, STACK_RAW, 3);
+
+    // decide which source(s) are to be fitted with the extended source analysis code.
+    psphotChooseAnalysisOptionsByObject (config, view, STACK_RAW, objects);
 
     // measure elliptical apertures, petrosians (objects sorted by S/N)

trunk/psphot/test/tap_psphot_galaxygrid.pro

@@ -30 +30 @@
 $RefOptions = $RefOptions -nx 3000 -ny 3000
 
+if (not($?PSFMODEL))
+  $PSFMODEL = PS1_V1
+end
+
+macro reset.options
 # options for the simulated images (using the refimage for the stars)
 $FakeOptions = $BaseOptions
 $FakeOptions = $FakeOptions -exptime 30.0
-$FakeOptions = $FakeOptions -D PSF.MODEL PS_MODEL_GAUSS
+# $FakeOptions = $FakeOptions -D PSF.MODEL PS_MODEL_GAUSS
+$FakeOptions = $FakeOptions -D PSF.MODEL PS_MODEL_$PSFMODEL
 $FakeOptions = $FakeOptions -nx 3000 -ny 3000
   
@@ -69 +75 @@
 $FakeConfig = $FakeConfig -Di GALAXY.GRID.DX 300
 $FakeConfig = $FakeConfig -Di GALAXY.GRID.DY 300
+end
+
+if (not($?FakeConfig)) reset.options
 
 list fwhm 
@@ -75 +84 @@
  1.2 
  1.5
+end
+
+if (not($?CONVOLVE_NSIGMA)) set CONVOLVE_NSIGMA = 5.0
+
+# generate fake images and run psphot on them
+macro mkexp.devexp.single
+  if ($0 != 5)
+    echo "USAGE: mkexp.devexp.single (basename) (type) (Rmajor) (fwhm)"  
+    break
+  end
+
+  $basename = $1
+  $type = $2
+  $Rmajor = $3
+  $fwhm = $4
+
+  $Aratio = 1.0
+
+  $FakeConfig = -camera SIMTEST
+  $FakeConfig = $FakeConfig -recipe PPSIM STACKTEST.RUN
+  $FakeConfig = $FakeConfig -D PSASTRO:PSASTRO.CATDIR catdir.ref
+  $FakeConfig = $FakeConfig -Db STARS.FAKE F                         ; # only use stars from catdir.ref
+  $FakeConfig = $FakeConfig -Db MATCH.DENSITY F
+  $FakeConfig = $FakeConfig -Db PSF.CONVOLVE T
+  $FakeConfig = $FakeConfig -Db GALAXY.FAKE T                        ; # generate a "realistic" distribution of galaxies
+  $FakeConfig = $FakeConfig -Df GALAXY.MAG 17.0
+  $FakeConfig = $FakeConfig -Df GALAXY.GRID.MAG 14.5
+  $FakeConfig = $FakeConfig -Db GALAXY.GRID T                        ; # generate a grid of galaxies (constant mag)
+  $FakeConfig = $FakeConfig -Df GALAXY.THETA.MIN 0 
+  $FakeConfig = $FakeConfig -Df GALAXY.THETA.MAX 180
+  $FakeConfig = $FakeConfig -Di GALAXY.GRID.DX 300
+  $FakeConfig = $FakeConfig -Di GALAXY.GRID.DY 300
+  $FakeConfig = $FakeConfig -Df GALAXY.INDEX.MIN 1.0
+  $FakeConfig = $FakeConfig -Df GALAXY.INDEX.MAX 1.0
+  $FakeConfig = $FakeConfig -Df CONVOLVE.NSIGMA $CONVOLVE_NSIGMA 
+  $BaseConfig = $FakeConfig
+
+  $FakeConfig = $BaseConfig
+  $FakeConfig = $FakeConfig -Df GALAXY.RMAJOR.MIN $Rmajor
+  $FakeConfig = $FakeConfig -Df GALAXY.RMAJOR.MAX $Rmajor
+  $FakeConfig = $FakeConfig -Df GALAXY.ARATIO.MIN $Aratio
+  $FakeConfig = $FakeConfig -Df GALAXY.ARATIO.MAX $Aratio
+          
+  mkexp $basename $fwhm $type
 end
 
@@ -272 +325 @@
   label -x sequence -y "M_out| - M_in|"
   resize 700 320
+
+  # check on magnitude
+  set dI = Iot_s - Iin_s
+  lim -n 4$1 n -1.0 1.0; clear; box; plot n dI
+  label -x sequence -y "I_out| - I_in|"
+  resize 700 320
+end
+
+macro grid.plot.stars
+  if ($0 != 2)
+    echo "USAGE: grid.plot.stars (version)"
+    break
+  end
+  # things to examine: theta, Rmajor, AR
+
+  # go.grid.check.devexp
+
+  # check on position
+  set dX = Xot_s - int(Xin_s) - 0.5
+  set dY = Yot_s - int(Yin_s) - 0.5
+  set ARin = rin_s / Rin_s
+  set dR = Rin_s - Rot_s
+
+  create n 0 dR[]
+  set dRf = dR / Rin_s
+  lim -n 1$1 n -0.5 0.5; clear; box; plot n dRf
+  label -x sequence -y "1 - R_out| / R_in|"
+  resize 700 320
+
+  # check on A.Ratio
+  set ARot = rot_s / Rot_s
+  # lim ARin ARot; clear; box; plot ARin ARot
+  set fAR = ARot / ARin
+  lim -n 2$1 n 0.5 1.5; clear; box; plot n fAR
+  label -x sequence -y "AR_out| / AR_in|"
+  resize 700 320
+
+  # check on magnitude
+  set dM = Mot_s - Min_s
+  lim -n 3$1 n -0.5 0.5; clear; box; plot n dM    
+  label -x sequence -y "M_out| - M_in|"
+  resize 700 320
+
+  lim -n 4$1 n -1.5 1.5; clear; box; plot n dX
+  label -x sequence -y "X_out| - X_in|"
+  resize 700 320
+
+  lim -n 5$1 n -1.5 1.5; clear; box; plot n dY
+  label -x sequence -y "Y_out| - Y_in|"
+  resize 700 320
 end
 
@@ -487 +590 @@
 end
 
+if (not($?NSIGMA_CONV)) set NSIGMA_CONV = 5.0
+
 # create a realistic distribution of fake stars, GAUSS PSF
 macro fitexp
@@ -507 +612 @@
   $psphotConfig = $psphotConfig -Db PSPHOT:SAVE.RESID T
   $psphotConfig = $psphotConfig -D  PSPHOT:EXTENDED_SOURCE_MODELS_SELECTION $fitModel
+  $psphotConfig = $psphotConfig -D  PSPHOT:PSF_MODEL PS_MODEL_$PSFMODEL
+
+  $psphotConfig = $psphotConfig -Db PSPHOT:PSF.RESIDUALS F
+  $psphotConfig = $psphotConfig -Db PSPHOT:POISSON.ERRORS.PHOT.LMM F
+  $psphotConfig = $psphotConfig -Db PSPHOT:EXTENDED_SOURCE_FITS_POISSON F
+  $psphotConfig = $psphotConfig -Di PSPHOT:EXT_FIT_ITER 15
+  $psphotConfig = $psphotConfig -Df PSPHOT:PSF_FIT_RADIUS_SCALE 3.75
+  $psphotConfig = $psphotConfig -Df PSPHOT:EXT_FIT_NSIGMA_CONV $NSIGMA_CONV
 
   # ppImage / psphot on the output
@@ -516 +629 @@
 end
 
+macro cmf.load.reset
+  $fields = X Y M T R r MT I
+  foreach field $fields
+    foreach set in ot
+      delete -q $field\$set\_s
+    end
+  end
+
+  delete -q min_S Min_S
+end
+
 macro cmf.load.concat
   if ($0 != 4)
-    echo "USAGE: cmf.load.concat (dat) (cmf) (type)"
+    echo "USAGE: cmf.load.concat (dat) (cmf) (inType)"
     break
   end
@@ -525 +649 @@
   read Xin_all 1 Yin_all 2 Fin_all 3 Type 4 Min_all 5 RmajIn_all 7 RminIn_all 8 ThetaIn_all 9 IndexIn_all 10
 
+  $TYPE_S = 83
+  $TYPE_D = 68
+  $TYPE_E = 69
+  if ("$3" == "SERSIC")
+    $InType = $TYPE_S
+  end
+  if ("$3" == "DEV")
+    $InType = $TYPE_D
+    set IndexIn_all = 0.125 + zero(Xin_all)
+  end
+  if ("$3" == "EXP")
+    $InType = $TYPE_E
+    set IndexIn_all = 0.5 + zero(Xin_all)
+  end
+
+  # select only the galaxies 
   subset Xin = Xin_all if (Type == 1)
   subset Yin = Yin_all if (Type == 1)
@@ -539 +679 @@
   subset IndexIn = IndexIn_all if (Type == 1)
 
-  $TYPE_S = 83
-  $TYPE_D = 68
-  $TYPE_E = 69
-  if ("$3" == "SERSIC")
-    $InType = $TYPE_S
-  end
-  if ("$3" == "DEV")
-    $InType = $TYPE_D
-  end
-  if ("$3" == "EXP")
-    $InType = $TYPE_E
-  end
-
   data $2
 
   break -auto off
+  output -err /dev/null
   read -fits Chip.xfit X_EXT Y_EXT EXT_INST_MAG EXT_WIDTH_MAJ EXT_WIDTH_MIN EXT_THETA MODEL_TYPE EXT_PAR_07
   $reread = not($STATUS)
+  output -err stderr
   break -auto on
   if ($reread)
     read -fits Chip.xfit X_EXT Y_EXT EXT_INST_MAG EXT_WIDTH_MAJ EXT_WIDTH_MIN EXT_THETA MODEL_TYPE 
-    set EXT_PAR_07 = (MODEL_TYPE:9 == 68)*4 + (MODEL_TYPE:9 == 69)
+    set EXT_PAR_07 = (MODEL_TYPE:9 == 68)*0.125 + (MODEL_TYPE:9 == 69)*0.5
   end
 
@@ -589 +718 @@
   reindex rin_m = RminIn using index2
   
-  if ("$3" == "SERSIC")
-    reindex Iot_m = EXT_PAR_07 using index1
-    reindex Iin_m = IndexIn using index2
-   $fields = X Y M T R r MT I
-  else
-   $fields = X Y M T R r MT
-  end
+  reindex Iot_m = EXT_PAR_07 using index1
+  reindex Iin_m = IndexIn using index2
+  $fields = X Y M T R r MT I
   
   foreach field $fields
@@ -605 +730 @@
   concat min min_S
   concat Min Min_S
+end
+
+macro cmf.load.stars.concat
+  if ($0 != 3)
+    echo "USAGE: cmf.load.concat (dat) (cmf)"
+    break
+  end
+
+  data $1
+  read Xin_all 1 Yin_all 2 Type 4 Min_all 5 RmajIn_all 7 RminIn_all 8 ThetaIn_all 9 IndexIn_all 10
+
+  subset Xin     = Xin_all     if (Type == 0)
+  subset Yin     = Yin_all     if (Type == 0)
+  subset Min     = Min_all     if (Type == 0)
+  subset RmajIn  = RmajIn_all  if (Type == 0)
+  subset RminIn  = RminIn_all  if (Type == 0)
+  subset IndexIn = IndexIn_all if (Type == 0)
+  subset Tin_rad = ThetaIn_all if (Type == 0)
+  set Tin = Tin_rad * 180 / 3.14159265
+
+  data $2
+
+  break -auto off
+  read -fits Chip.psf X_PSF Y_PSF PSF_INST_MAG PSF_MAJOR PSF_MINOR PSF_THETA
+  set PSF_THETA_ALT = PSF_THETA * (PSF_THETA >= 0.0) + (PSF_THETA + 3.14159265) * (PSF_THETA < 0.0)
+  set PSF_THETA = PSF_THETA_ALT * 180 / 3.14159265
+  
+  match2d X_PSF Y_PSF Xin Yin 1.0 -index1 index1 -index2 index2
+
+  reindex Xot_m = X_PSF using index1
+  reindex Yot_m = Y_PSF using index1
+
+  reindex Xin_m = Xin using index2
+  reindex Yin_m = Yin using index2
+
+  reindex Mot_m = PSF_INST_MAG using index1
+  reindex Tot_m = PSF_THETA using index1
+
+  reindex Min_m = Min using index2
+  reindex Tin_m = Tin using index2
+
+  reindex Rot_m = PSF_MAJOR using index1
+  reindex rot_m = PSF_MINOR using index1
+
+  reindex Rin_m = RmajIn using index2
+  reindex rin_m = RminIn using index2
+  
+  $fields = X Y M T R r
+  foreach field $fields
+    foreach set in ot
+      concat $field\$set\_m $field\$set\_s
+    end
+  end
 end
 
@@ -1078 +1256 @@
 
 macro load.normdata
-  if ($0 != 2)
-    echo "USAGE: load.normdata (file)"
+  if ($0 != 3)
+    echo "USAGE: load.normdata (file) [clear/noclear]"
     break
   end
@@ -1090 +1268 @@
   set dm = mg - Mg
   set n = ramp(dm)
-  lim n dm; clear; box; plot n dm
+  if ("$2" == "clear")
+    lim n dm; clear; box; 
+  end
+  plot n dm
 end
 
@@ -1097 +1278 @@
   exit 0
 end
+
+# note that t1 = original confi
+# t2 = no residuals
+# t3 = const weight PSF fit
+# t4 = const weight galaxy fits
+
+macro run.radius.loop
+  local radius Nrun 
+
+  if (1)
+    $Nrun = 0
+    foreach radius 1.0 1.5 2.0 2.5 3.0 4.0 6.0 8.0
+      mkexp.devexp.single tests.20131120/testrad.ps1v1.exp.$Nrun EXP $radius 1.0
+      fitexp tests.20131120/testrad.ps1v1.exp.$Nrun tests.20131120/testrad.ps1v1.exp.$Nrun.t4b EXP_CONV
+      $Nrun ++
+    end
+  end
+
+  $Nrun = 0
+  foreach radius 1.0 1.5 2.0 2.5 3.0 4.0 6.0 8.0
+    cmf.load.concat tests.20131120/testrad.ps1v1.exp.$Nrun.dat tests.20131120/testrad.ps1v1.exp.$Nrun.t4b.cmf EXP
+    echo -no-return $radius ""
+    check.fit tests.20131120/testrad.ps1v1.exp.$Nrun.dat tests.20131120/testrad.ps1v1.exp.$Nrun.t4b.cmf EXP
+    $Nrun ++
+  end
+
+  grid.plots.devexp a
+end
+
+macro check.radius.loop
+  if ($0 != 2)
+    echo "USAGE: check.radius.loop (ext)"
+    break
+  end
+
+  # cmf.load.reset
+
+  local radius Nrun 
+
+  $Nrun = 0
+  foreach radius 1.0 1.5 2.0 2.5 3.0 4.0 6.0 8.0
+    echo -no-return $radius ""
+    check.fit tests.20131120/testrad.ps1v1.exp.$Nrun.dat tests.20131120/testrad.ps1v1.exp.$Nrun.$1.cmf EXP
+    $Nrun ++
+  end
+
+  grid.plots.devexp a
+end
+
+macro check.fit
+  if ($0 != 4)
+    echo "USAGE: check.fit (dat) (cmf) (type)"
+    break
+  end
+
+  cmf.load.concat $1 $2 $3
+  set dM_m = Mot_m - Min_m
+  vstat -q dM_m
+  $mag_off = $MEDIAN
+  set dR_m = Rot_m - Rin_m
+  vstat -q dR_m
+  $rad_off = $MEDIAN
+  echo $mag_off $rad_off
+end
+
+macro make.circles
+
+  delete Xo Yo Ro
+
+  for ix 0 16
+    for iy $ix 16
+      $r2 = $ix^2 + $iy^2
+      if ($r2 > 15^2) continue
+      concat $ix Xo
+      concat $iy Yo
+      concat $r2 Ro
+    end
+  end
+
+  sort Ro Xo Yo
+  $Rold = -1
+  $N = -1
+  for i 0 Ro[]
+    if (Ro[$i] != $Rold)
+      $N ++
+      $Rold = Ro[$i]
+    end
+    if ((Xo[$i] == 0) && (Yo[$i] == 0))
+      fprintf "// center is 0,0"
+      continue
+    end
+    if (Xo[$i] == 0)
+      fprintf "ADD_AXIS (%3d, %2d)     // r^2 = %3d" $N Yo[$i] Ro[$i]
+      continue
+    end
+    if (Xo[$i] == Yo[$i])
+      fprintf "ADD_DIAG (%3d, %2d)     // r^2 = %3d" $N Xo[$i] Ro[$i]
+      continue
+    end
+
+    fprintf "ADD_RAND (%3d, %2d, %2d) // r^2 = %3d" $N Xo[$i] Yo[$i] Ro[$i]
+ end
+end
+
+# EXP : tests.20131120/test.nsig
+# DEV : tests.20131120/test.dev
+
+# run.convolve.loop tests.20131120/test.nsig tests.20131120/test.nsig   EXP EXP_CONV
+# run.convolve.loop tests.20131120/test.dev  tests.20131120/test.dev    DEV DEV_CONV
+# run.convolve.loop tests.20131120/test.nsig tests.20131120/test.serexp EXP SER_CONV
+# run.convolve.loop tests.20131120/test.dev  tests.20131120/test.serdev DEV SER_CONV
+
+macro run.convolve.loop
+  if ($0 != 5)
+    echo "run.convolve.loop (inName) (fitName) (inType) (fitType)"
+    break
+  end
+
+  local radius
+  $radius = 3.0
+  cmf.load.reset
+
+  # foreach Cin 3 5 7 9 11
+  foreach Cin 11
+    $CONVOLVE_NSIGMA = $Cin
+    sprintf nameIn %s.%02d $1 $Cin
+    mkexp.devexp.single $nameIn $3 $radius 1.0
+    foreach Cot 3 5 7 9 11
+      $NSIGMA_CONV = $Cot
+      sprintf nameOt %s.%02d.%02d $2 $Cin $Cot
+      fitexp $nameIn $nameOt $4
+    end
+  end
+
+  # foreach Cin 3 5 7 9 11
+  foreach Cin 11
+    sprintf nameIn %s.%02d $1 $Cin
+    foreach Cot 3 5 7 9 11
+      sprintf nameOt %s.%02d.%02d $2 $Cin $Cot
+      check.fit $nameIn.dat $nameOt.cmf 
+    end
+  end
+  grid.plots.devexp a
+end
+
+macro check.convolve.loop
+  if ($0 != 4)
+    echo "run.convolve.loop (inName) (fitName) (inType)"
+    break
+  end
+
+  local radius
+  $radius = 3.0
+  cmf.load.reset
+
+  # foreach Cin 3 5 7 9 11
+  foreach Cin 11
+    sprintf nameIn %s.%02d $1 $Cin
+    foreach Cot 3 5 7 9 11
+      sprintf nameOt %s.%02d.%02d $2 $Cin $Cot
+      echo -no-return $Cin $Cot " "
+      check.fit $nameIn.dat $nameOt.cmf $3
+    end
+  end
+  grid.plots.devexp a
+end

@@ -24 +24 @@
 psphotModelTest
 psphotMinimal
+psphotFullForce
+psmakecff