Index: trunk/psastro/src/Makefile.am
===================================================================
--- trunk/psastro/src/Makefile.am	(revision 38012)
+++ trunk/psastro/src/Makefile.am	(revision 38040)
@@ -1,23 +1,8 @@
 lib_LTLIBRARIES = libpsastro.la
-
-if HAVE_SVNVERSION
-PSASTRO_VERSION=`$(SVNVERSION) ..`
-else
-PSASTRO_VERSION="UNKNOWN"
-endif
-
-if HAVE_SVN
-PSASTRO_BRANCH=`$(SVN) info .. | $(SED) -n -e '/URL:/ h' -e '/Repository Root:/ { x; H; x; s|Repository Root: \(.*\)\nURL: \1\(.*\)|\2| ; s|^/|| ; s|/[a-zA-Z]*/src.*|| ; p }'`
-PSASTRO_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'`
-else
-PSASTRO_BRANCH="UNKNOWN"
-PSASTRO_SOURCE="UNKNOWN"
-endif
 
 # Force recompilation of psastroVersion.c, since it gets the version information
 psastroVersion.c: psastroVersionDefinitions.h
 psastroVersionDefinitions.h: psastroVersionDefinitions.h.in FORCE
-	-$(RM) psastroVersionDefinitions.h
-	$(SED) -e "s|@PSASTRO_VERSION@|\"$(PSASTRO_VERSION)\"|" -e "s|@PSASTRO_BRANCH@|\"$(PSASTRO_BRANCH)\"|" -e "s|@PSASTRO_SOURCE@|\"$(PSASTRO_SOURCE)\"|" psastroVersionDefinitions.h.in > psastroVersionDefinitions.h
+	pslib-setsvnversion.pl PSASTRO psastroVersionDefinitions.h.in psastroVersionDefinitions.h
 FORCE: ;
 
@@ -87,4 +72,5 @@
 
 libpsastro_la_SOURCES = \
+	psastroGalaxyShapeErrors.c  \
 	psastroMaskUpdates.c        \
 	psastroMaskUtils.c          \
Index: trunk/psastro/src/psastro.h
===================================================================
--- trunk/psastro/src/psastro.h	(revision 38012)
+++ trunk/psastro/src/psastro.h	(revision 38040)
@@ -197,4 +197,6 @@
 bool              psastroExtractFreeChipBounds(void);
 
+bool              psastroGalaxyShapeErrors (psMetadata *recipe, pmReadout *readout);
+
 ///@}
 # endif /* PSASTRO_H */
Index: trunk/psastro/src/psastroConvert.c
===================================================================
--- trunk/psastro/src/psastroConvert.c	(revision 38012)
+++ trunk/psastro/src/psastroConvert.c	(revision 38040)
@@ -335,4 +335,16 @@
   pmChip *chip = readout->parent->parent;
   char *chipName = psMetadataLookupStr (NULL, chip->concepts, "CHIP.NAME");
+
+  // skip stacks
+  if (!strcmp(chipName, "SkyChip")) {
+    psLogMsg ("psastro.correctKH", PS_LOG_DETAIL, "skipping KH correction: not a gpc1 chip\n");
+    return true;
+  }
+
+  // only try to address gpc1 chips (should probably check the camera)
+  if (strncmp(chipName, "XY", 2)) {
+    psLogMsg ("psastro.correctKH", PS_LOG_DETAIL, "skipping KH correction: not a gpc1 chip\n");
+    return true;
+  }
 
   psAssert (strlen(chipName) == 4, "error in chip name");
Index: trunk/psastro/src/psastroDataSave.c
===================================================================
--- trunk/psastro/src/psastroDataSave.c	(revision 38012)
+++ trunk/psastro/src/psastroDataSave.c	(revision 38040)
@@ -69,4 +69,6 @@
                 if (!readout->data_exists) { continue; }
 
+		psastroGalaxyShapeErrors (recipe, readout);
+
                 // Put version information into the header
                 pmHDU *hdu = pmHDUGetHighest(output->fpa, chip, cell);
Index: trunk/psastro/src/psastroGalaxyShapeErrors.c
===================================================================
--- trunk/psastro/src/psastroGalaxyShapeErrors.c	(revision 38040)
+++ trunk/psastro/src/psastroGalaxyShapeErrors.c	(revision 38040)
@@ -0,0 +1,176 @@
+/** @file psastroGalaxyShapeError.c
+ *
+ *  @brief: monte carlo transformation of Sxx,Sxy,Syy -> Major,Minor,Theta
+ *
+ *  @ingroup psastro
+ *
+ *  @author IfA
+ *  @version $Revision: 1.15 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-07 02:03:34 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+# include "psastroInternal.h"
+
+double psastroNormalizeAngleToMidpoint (double angle, double midpoint);
+
+bool psastroGalaxyShapeErrors (psMetadata *recipe, pmReadout *readout) {
+
+    bool status = false;
+
+    bool TransformGalaxyShapeErrors = psMetadataLookupBool (&status, recipe, "TRANSFORM.GALAXY.SHAPE.ERRORS");
+    if (!TransformGalaxyShapeErrors) return true;
+
+    psTimerStart ("psastro.galaxy.shape.errors");
+
+    pmDetections *detections = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.DETECTIONS");
+    if (!detections) return false;
+
+    psArray *sources = detections->allSources;
+    if (!detections) return false;
+
+    psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS);
+
+    int nSample = 1000;
+    psVector *majorValues = psVectorAllocEmpty (nSample, PS_TYPE_F32);
+    psVector *minorValues = psVectorAllocEmpty (nSample, PS_TYPE_F32);
+    psVector *thetaValues = psVectorAllocEmpty (nSample, PS_TYPE_F32);
+
+    psStats *stats = psStatsAlloc(PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_STDEV);
+
+    int nObjects = 0;
+
+    // don't try and use bad models
+    pmModelStatus badModel = PM_MODEL_STATUS_NONE;
+    // badModel |= PM_MODEL_STATUS_NONCONVERGE;  this causes most objects to get unmeasured
+    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;
+    badModel |= PM_MODEL_STATUS_LIMITS;
+
+    // transform all sources, regardless of quality.  the source flags tell us the state
+    for (int i = 0; i < sources->n; i++) {
+
+        pmSource *source = sources->data[i];
+        if (source->modelFits == NULL) continue;
+
+        // We have multiple model fits to each source
+        for (int j = 0; j < source->modelFits->n; j++) {
+
+            // choose each model
+            pmModel *model = source->modelFits->data[j];
+            assert (model);
+
+	    // skip models which were not actually fitted
+	    if (model->flags & badModel) continue;
+
+            float *PAR = model->params->data.F32;
+            float *dPAR = model->dparams->data.F32;
+
+	    if (!(isfinite(PAR[PM_PAR_SXX]) && isfinite(PAR[PM_PAR_SXY]) && isfinite(PAR[PM_PAR_SYY]))) {
+	      // set a mask bit
+	      model->flags |= PM_MODEL_STATUS_NAN_SHAPE;
+	      continue;
+	    }
+	    if (!(isfinite(dPAR[PM_PAR_SXX]) && isfinite(dPAR[PM_PAR_SXY]) && isfinite(dPAR[PM_PAR_SYY]))) {
+	      // set a (different) mask bit
+	      model->flags |= PM_MODEL_STATUS_NAN_SHAPE_ERR;
+	      continue;
+	    }
+
+	    // psphot writes out dPAR, but PAR is writen as MAJOR,MINOR,THETA but transformed
+	    // to PAR[SXX,SXY,SYY] when the cmf is read.  here we use a monte carlo to generate
+	    // a set of PAR[] values which are converted to MAJOR,MINOR,THETA so sigma can be
+	    // measured.
+
+	    majorValues->n = 0;
+	    minorValues->n = 0;
+	    thetaValues->n = 0;
+
+	    bool useReff = model->class->useReff;
+	    psEllipseAxes axes;
+
+	    float SxxRef = PAR[PM_PAR_SXX];
+	    float SxyRef = PAR[PM_PAR_SXY];
+	    float SyyRef = PAR[PM_PAR_SYY];
+	    if (!(isfinite(SxxRef) && isfinite(SxyRef) && isfinite(SyyRef))) {
+	      // skip objects which are already poor ellipses
+	      model->flags |= PM_MODEL_STATUS_NAN_SHAPE;
+	      continue;
+	    }
+	    pmModelParamsToAxes (&axes, SxxRef, SxyRef, SyyRef, useReff);
+	    if (!(isfinite(axes.major) && isfinite(axes.minor) && isfinite(axes.theta))) {
+	      // skip objects which are already poor ellipses
+	      model->flags |= PM_MODEL_STATUS_NAN_SHAPE;
+	      continue;
+	    }
+	    double ThetaRef = axes.theta;
+
+	    for (int k = 0; k < nSample; k++) {
+
+		float Sxx = PAR[PM_PAR_SXX] + dPAR[PM_PAR_SXX]*psRandomGaussian(rng);
+		float Sxy = PAR[PM_PAR_SXY] + dPAR[PM_PAR_SXY]*psRandomGaussian(rng);
+		float Syy = PAR[PM_PAR_SYY] + dPAR[PM_PAR_SYY]*psRandomGaussian(rng);
+		if (!(isfinite(Sxx) && isfinite(Sxy) && isfinite(Syy))) {
+		  continue;
+		}
+
+		pmModelParamsToAxes (&axes, Sxx, Sxy, Syy, useReff);
+		if (!(isfinite(axes.major) && isfinite(axes.minor) && isfinite(axes.theta))) continue;
+
+		// theta should be in range ThetaRef - PI : ThetaRef + PI
+		double ThetaNorm = psastroNormalizeAngleToMidpoint (axes.theta, ThetaRef);
+
+		psVectorAppend (majorValues, axes.major);
+		psVectorAppend (minorValues, axes.minor);
+		psVectorAppend (thetaValues, ThetaNorm);
+	    }
+	    if (majorValues->n == 0) {
+		psWarning ("failed mc error search");
+		model->flags |= PM_MODEL_STATUS_FAIL_SHAPE_ERR;
+		continue;
+	    }
+
+	    psStatsInit (stats);
+	    psVectorStats (stats, majorValues, NULL, NULL, 0);
+	    float dMajor = stats->robustStdev;
+
+	    psStatsInit (stats);
+	    psVectorStats (stats, minorValues, NULL, NULL, 0);
+	    float dMinor = stats->robustStdev;
+
+	    // overload the results back on the PAR[] vectors
+	    dPAR[PM_PAR_SXX] = dMajor;
+	    dPAR[PM_PAR_SYY] = dMinor;
+	    nObjects ++;
+	}
+    }
+    psFree (rng);
+    psFree (stats);
+    psFree (majorValues);
+    psFree (minorValues);
+    psFree (thetaValues);
+
+    psMetadata *header = psMetadataLookupMetadata (&status, readout->analysis, "PSASTRO.HEADER");
+    psMetadataAddStr (header, PS_LIST_TAIL, "GALAXY.SHAPE.ERRORS", PS_META_REPLACE, "error analysis mode", "MONTE CARLO");
+
+    psLogMsg ("psastro.galaxy", PS_LOG_INFO, "monte carlo shape errors for %d of %d objects: %f sec\n", nObjects, (int) sources->n, psTimerMark ("psastro.galaxy.shape.errors"));
+    return true;
+}
+
+// these angles are in radians
+double psastroNormalizeAngleToMidpoint (double angle, double midpoint) {
+
+    double x = cos(angle);
+    double y = sin(angle);
+
+    double result = atan2 (y, x);
+    if (result < midpoint - M_PI) result += 2.0*M_PI;
+    if (result > midpoint + M_PI) result -= 2.0*M_PI;
+
+    return result;
+}
+
Index: trunk/psastro/src/setsvnversion.pl
===================================================================
--- trunk/psastro/src/setsvnversion.pl	(revision 38012)
+++ 	(revision )
@@ -1,100 +1,0 @@
-#!/usr/bin/env perl
-$VERBOSE = 0;
-
-if (@ARGV != 3) { die "USAGE: setsvnversion.pl (prgname) (src) (tgt)\n"; }
-
-if (! -e $ARGV[1]) { die "setsvnversion.pl cannot find input version file\n"; }
-
-$prgname = $ARGV[0];
-
-$svnversion = `which svnversion`;
-chomp $svnversion;
-if ($?) {
-    $svnversion = "NONE";
-}
-if ($VERBOSE) { print "svnversion: $svnversion\n";}
-
-$svn = `which svn`;
-chomp $svn;
-if ($?) {
-    $svn = "NONE";
-}
-if ($VERBOSE) {print "svn: $svn\n";}
-
-if ($svnversion eq "NONE") {
-    $VERSION = "UNKNOWN";
-} else {
-    $VERSION = `$svnversion`;
-    chomp $VERSION;
-}
-if ($VERBOSE) {print "VERSION: $VERSION\n";}
-
-if ($svn eq "NONE") {
-    $BRANCH = "UNKNOWN";
-    $SOURCE = "UNKNOWN";
-} else {
-    $fullURL = "";
-    $reproot = "";
-    $UUID = "";
-    @lines = `$svn info ..`;
-    foreach $line (@lines) {
-	chomp $line;
-	($key, $value) = split (":", $line, 2);
-	if ($VERBOSE == 2) { print "key: $key\n";}
-	if ($VERBOSE == 2) { print "value: $value\n"; }
-	if ($key eq "URL")             { $fullURL = $value; }
-	if ($key eq "Repository UUID") { $UUID = $value;    }
-	if ($key eq "Repository Root") { $reproot = $value; }
-    }
-    if ($fullURL eq "") { die "failed to find URL\n"; }
-    if ($reproot eq "") { die "failed to find reproot\n"; }
-    if ($UUID    eq "") { die "failed to find UUID\n"; }
-
-    # remove surrounding whitespace
-    $fullURL =~ s/^\s+//;  $fullURL =~ s/\s+$//;
-    $reproot =~ s/^\s+//;  $reproot =~ s/\s+$//;
-    $UUID    =~ s/^\s+//;  $UUID    =~ s/\s+$//;
-
-    ($BRANCH) = $fullURL =~ m|$reproot/(.+)|;
-    if ($BRANCH eq "")  { die "failed to get branch from fullURL $fullURL\n"; }
-   
-    $SOURCE = $UUID;
-}
-
-if ($VERBOSE) { print "SOURCE: $SOURCE\n";}
-if ($VERBOSE) { print "BRANCH: $BRANCH\n";}
-
-open (FILE, "$ARGV[1]");
-@list = <FILE>;
-close (FILE);
-
-$version_field = sprintf "@%s_VERSION@", $prgname;
-$source_field = sprintf "@%s_SOURCE@", $prgname;
-$branch_field = sprintf "@%s_BRANCH@", $prgname;
-
-foreach $line (@list) {
-    $line =~ s|$version_field|"$VERSION"|;
-    $line =~ s|$source_field|"$SOURCE"|;
-    $line =~ s|$branch_field|"$BRANCH"|;
-}
-
-$output = sprintf "%s.tmp", $ARGV[2];
-
-open (FILE, ">$output");
-foreach $line (@list) {
-    print FILE $line;
-}
-close (FILE);
-
-$difflines = `diff $ARGV[2] $output`;
-if ($difflines eq "") {
-    if ($VERBOSE) { print "no change to $ARGV[2], keeping old version\n"; }
-} else {
-    if ($VERBOSE) { 
-	print "$ARGV[2] changed:\n";
-	print $difflines;
-    }
-    rename $output, $ARGV[2];
-}
-
-exit (0);