Index: /branches/eam_branches/ohana.20160226/src/relastro/Makefile
===================================================================
--- /branches/eam_branches/ohana.20160226/src/relastro/Makefile	(revision 39444)
+++ /branches/eam_branches/ohana.20160226/src/relastro/Makefile	(revision 39445)
@@ -48,4 +48,5 @@
 $(SRC)/UpdateMeasures.$(ARCH).o      \
 $(SRC)/GetAstromError.$(ARCH).o      \
+$(SRC)/MeasFilterTest.$(ARCH).o            \
 $(SRC)/args.$(ARCH).o		     \
 $(SRC)/bcatalog.$(ARCH).o	     \
@@ -121,4 +122,5 @@
 $(SRC)/UpdateMeasures.$(ARCH).o      \
 $(SRC)/GetAstromError.$(ARCH).o      \
+$(SRC)/MeasFilterTest.$(ARCH).o            \
 $(SRC)/args.$(ARCH).o		     \
 $(SRC)/bcatalog.$(ARCH).o	     \
@@ -196,6 +198,5 @@
 $(SRC)/mkpolyterm.$(ARCH).o            \
 $(SRC)/GetAstromError.$(ARCH).o            \
-$(SRC)/ImageOps.$(ARCH).o            \
-$(SRC)/MosaicOps.$(ARCH).o            \
+$(SRC)/MeasFilterTest.$(ARCH).o            \
 $(SRC)/extra.$(ARCH).o            \
 $(SRC)/plotstuff.$(ARCH).o            \
@@ -219,6 +220,5 @@
 $(SRC)/mkpolyterm.$(ARCH).o            \
 $(SRC)/GetAstromError.$(ARCH).o            \
-$(SRC)/ImageOps.$(ARCH).o            \
-$(SRC)/MosaicOps.$(ARCH).o            \
+$(SRC)/MeasFilterTest.$(ARCH).o            \
 $(SRC)/extra.$(ARCH).o            \
 $(SRC)/plotstuff.$(ARCH).o            \
@@ -242,9 +242,15 @@
 $(SRC)/mkpolyterm.$(ARCH).o            \
 $(SRC)/GetAstromError.$(ARCH).o            \
-$(SRC)/ImageOps.$(ARCH).o            \
-$(SRC)/MosaicOps.$(ARCH).o            \
+$(SRC)/MeasFilterTest.$(ARCH).o            \
 $(SRC)/extra.$(ARCH).o            \
 $(SRC)/plotstuff.$(ARCH).o            \
 $(SRC)/fitpoly.$(ARCH).o
+
+# stupid dependencies: 
+# UpdateObjects.c:UpdateObjects_Chips needs
+# ImageOps.c:MeasFilterTiny forces
+# load_images.c:free_astrom_table needs
+# select_images.c
+# MosaicOps.c
 
 $(FITSTK): $(INC)/relastro.h
Index: /branches/eam_branches/ohana.20160226/src/relastro/src/ImageOps.c
===================================================================
--- /branches/eam_branches/ohana.20160226/src/relastro/src/ImageOps.c	(revision 39444)
+++ /branches/eam_branches/ohana.20160226/src/relastro/src/ImageOps.c	(revision 39445)
@@ -931,4 +931,5 @@
 }
 
+# if (0) 
 /** lifted from relphot/StarOps.clean_measures */
 void FlagOutliers2D(Catalog *catalog);
@@ -1298,2 +1299,3 @@
   return TRUE;
 }
+# endif
Index: /branches/eam_branches/ohana.20160226/src/relastro/src/MeasFilterTest.c
===================================================================
--- /branches/eam_branches/ohana.20160226/src/relastro/src/MeasFilterTest.c	(revision 39445)
+++ /branches/eam_branches/ohana.20160226/src/relastro/src/MeasFilterTest.c	(revision 39445)
@@ -0,0 +1,369 @@
+# include "relastro.h"
+
+/** lifted from relphot/StarOps.clean_measures */
+void FlagOutliers2D(Catalog *catalog);
+
+// operates on Full values (not tiny)
+void FlagOutliers (Catalog *catalog) {
+
+  // XXX FlagOutliers is now just using FlagOutliers2D
+  FlagOutliers2D(catalog);
+  return;
+
+  int Ndel, Nave;
+  off_t i, j, k, m, N, Nmax, TOOFEW, Nsecfilt;
+  double Ns, theta, x, y;
+  double *R, *D, *dR, *dD;
+  StatType statsR, statsD;
+
+  Nsecfilt = GetPhotcodeNsecfilt();
+  assert(catalog[0].Nsecfilt == Nsecfilt);
+
+  if (VERBOSE2) fprintf (stderr, "marking poor measures\n");
+  Nmax = 0;
+  for (i = 0; i < catalog[0].Naverage; i++) {
+    Nmax = MAX (Nmax, catalog[0].average[i].Nmeasure);
+  }
+
+  ALLOCATE (R, double, Nmax);
+  ALLOCATE (D, double, Nmax);
+  ALLOCATE (dR, double, Nmax);
+  ALLOCATE (dD, double, Nmax);
+
+  /* it makes no sense to mark 3-sigma outliers with <5 measurements */
+  TOOFEW = MAX (5, SRC_MEAS_TOOFEW);
+
+  Ns = CLIP_THRESH;
+  Ndel = Nave = 0;
+      
+  /* loop over each object in the catalog */
+  for (j = 0; j < catalog[0].Naverage; j++) {
+    
+    // pointer to this set of measurements
+    m = catalog[0].average[j].measureOffset;
+    Measure *measure = &catalog[0].measure[m];
+
+    /* accumulate list of valid measurements */
+    N = 0;
+    for (k = 0; k < catalog[0].average[j].Nmeasure; k++) {
+      // skip measurements based on user selected criteria
+      if (!MeasFilterTest(&measure[k], FALSE)) continue;
+      R[N] = measure[k].R;
+      D[N] = measure[k].D;
+      dR[N] = GetAstromError (&measure[k], ERROR_MODE_RA);
+      dD[N] = GetAstromError (&measure[k], ERROR_MODE_DEC);
+      if (isnan(R[N]) || isnan(D[N])) continue;
+      N++;
+    }
+    if (N <= TOOFEW) continue;
+    
+    /* 3-sigma clip based on stats of inner 50% */
+    initstats ("MEAN");
+    liststats (R, dR, N, &statsR);
+    liststats (D, dD, N, &statsD);
+    
+    statsR.sigma = MAX (MIN_ERROR, statsR.sigma);
+    statsD.sigma = MAX (MIN_ERROR, statsD.sigma);
+    
+    /* compare per-object distance to this standard deviation, and flag outliers*/
+    N = 0;
+    for (k = 0; k < catalog[0].average[j].Nmeasure; k++) {
+      // reset flag on each invocation
+      measure[k].dbFlags &= ~ID_MEAS_POOR_ASTROM;
+
+      // skip measurements based on user selected criteria
+      if (!MeasFilterTest(&measure[k], FALSE)) continue;
+      
+      x = measure[k].R - statsR.median;
+      y = measure[k].D - statsD.median;
+      theta = atan2(y,x);
+      if ((x*x + y*y) > (SQR(statsR.sigma * Ns * cos(theta)) + 
+			 SQR(statsD.sigma * Ns * sin(theta)))) {   
+	measure[k].dbFlags |= ID_MEAS_POOR_ASTROM;
+	Ndel++;
+      }
+      N++;
+      Nave ++;
+    }
+
+    // examine results
+    // relastroVisualPlotOutliers(catalog, catalog[0].average[j].measureOffset, catalog[0].average[j].Nmeasure, statsR, statsD, Ns);
+  }
+  
+  if (VERBOSE) fprintf (stderr, "%d measures marked poor, %d total\n", Ndel, Nave);
+  free (R);
+  free (dR);
+  free (D);
+  free (dD); 
+}
+
+
+/** an alternative outlier rejection scheme */
+void FlagOutliers2D (Catalog *catalog) {
+
+  int Ndel, Nave;
+  off_t i, j, k, m, N, Nmax, TOOFEW, Nsecfilt;
+  double *index;
+  double Ns, theta, x, y;
+  double *R, *D, *dR, *dD, *d2;
+  StatType statsR, statsD;
+
+  // XXX we are not going to use this for now
+  return;
+
+  Nsecfilt = GetPhotcodeNsecfilt();
+  assert(catalog[0].Nsecfilt == Nsecfilt);
+
+  if (VERBOSE2) fprintf (stderr, "marking poor measures\n");
+  Nmax = 0;
+  for (i = 0; i < catalog[0].Naverage; i++) {
+    Nmax = MAX (Nmax, catalog[0].average[i].Nmeasure);
+  }
+
+  ALLOCATE (R, double, Nmax);
+  ALLOCATE (D, double, Nmax);
+  ALLOCATE (dR, double, Nmax);
+  ALLOCATE (dD, double, Nmax);
+  ALLOCATE (d2, double, Nmax);
+  ALLOCATE (index, double, Nmax);
+
+  /* it makes no sense to mark 3-sigma outliers with <5 measurements */
+  TOOFEW = MAX (5, SRC_MEAS_TOOFEW);
+
+  Ns = CLIP_THRESH;
+  Ndel = Nave = 0;
+      
+  /* loop over each object in the catalog */
+  for (j = 0; j < catalog[0].Naverage; j++) {
+    
+    // pointer to this set of measurements
+    m = catalog[0].average[j].measureOffset;
+    Measure *measure = &catalog[0].measure[m];
+
+    /* accumulate list of valid measurements */
+    N = 0;
+    for (k = 0; k < catalog[0].average[j].Nmeasure; k++) {
+
+      // reset flag on each invocation
+      measure[k].dbFlags &= ~ID_MEAS_POOR_ASTROM;
+      
+      // skip measurements based on user selected criteria
+      if (!MeasFilterTest(&measure[k], FALSE)) continue;
+      R[N] = measure[k].R;
+      D[N] = measure[k].D;
+      dR[N] = GetAstromError(&measure[k], ERROR_MODE_RA);
+      dD[N] = GetAstromError(&measure[k], ERROR_MODE_DEC);
+      if (isnan(R[N]) || isnan(D[N])) continue;
+      N++;
+    }
+    if (N <= TOOFEW) continue;
+    
+    /* calculate mean of all points*/
+    initstats ("MEAN");
+    liststats (R, dR, N, &statsR);
+    liststats (D, dD, N, &statsD);
+    statsR.sigma = MAX (MIN_ERROR, statsR.sigma);
+    statsD.sigma = MAX (MIN_ERROR, statsD.sigma);
+    
+    /* calculate deviations of all points*/
+    N = 0;
+    for (k = 0; k < catalog[0].average[j].Nmeasure; k++) {
+      // skip bad measurements
+      if (!MeasFilterTest(&measure[k], FALSE)) continue;  
+      x = measure[k].R - statsR.median;
+      y = measure[k].D - statsD.median;
+      theta = atan2(y,x);
+      d2[N] = (x*x + y*y) / (SQR(statsR.sigma * Ns * cos(theta)) + 
+			     SQR(statsD.sigma * Ns * sin(theta)));      
+      index[N] = k;
+      N++;
+    }
+    
+    // sort d2
+    dsortpair(d2, index, N);
+    N = (N/2 > (N-1)) ? N/2 : N-1;
+
+    // recalculate image center, sigma based on closest 50% of points
+    for (k = 0;  k < N; k++) {
+      off_t ind = (off_t) index[k];
+      R[k] = measure[ind].R;
+      D[k] = measure[ind].D;
+      dR[k] = GetAstromError(&measure[ind], ERROR_MODE_RA);
+      dD[k] = GetAstromError(&measure[ind], ERROR_MODE_DEC);
+    }
+    liststats (R, dR, N, &statsR);
+    liststats (D, dD, N, &statsD);
+    statsR.sigma = MAX (MIN_ERROR, statsR.sigma);
+    statsD.sigma = MAX (MIN_ERROR, statsD.sigma);
+    
+    // use these new statistics to flag outliers 
+    N = 0;
+    for (k = 0; k < catalog[0].average[j].Nmeasure; k++) {
+      //skip bad measurements
+      if (!MeasFilterTest(&measure[k], FALSE)) continue;  
+      x = measure[k].R - statsR.median;
+      y = measure[k].D - statsD.median;
+      theta = atan2(y,x);
+      d2[N] = (x*x + y*y) / (SQR(statsR.sigma * Ns * cos(theta)) + 
+			     SQR(statsD.sigma * Ns * sin(theta)));      
+      if ((d2[N]) > 1) {
+	measure[k].dbFlags |= ID_MEAS_POOR_ASTROM;
+	Ndel ++;
+      }
+      N++;
+      Nave++;
+    }  // done rejecting outliers
+
+    // examine results
+    // relastroVisualPlotOutliers(catalog, catalog[0].average[j].measureOffset, catalog[0].average[j].Nmeasure, statsR, statsD, Ns);
+    
+  } // done looping over objects
+  
+  if (VERBOSE) fprintf (stderr, "%d measures marked poor, %d total\n", Ndel, Nave);
+  free (R);
+  free (dR);
+  free (D);
+  free (dD); 
+  free (d2);
+  free (index);
+}
+
+/** Determine whether a measurement should be included in the analysis, based on supplied filter criteria */ 
+// we only optionally apply the sigma limit: for object averages, this should not be used
+int MeasFilterTestTiny(MeasureTiny *measure, int applySigmaLim) {
+  int found, k;
+  long mask;
+  PhotCode *code;
+  float mag;
+
+  if (!finite(measure[0].R) || !finite(measure[0].D)) return FALSE;
+  if (!finite(measure[0].M)) return FALSE; //XXX is this necessary for all relastro tasks?
+  if (!finite(measure[0].dM)) return FALSE; //XXX is this necessary for all relastro tasks?
+  
+  if ((MinBadQF > 0.0) && (isGPC1chip(measure[0].photcode) || isGPC1stack(measure[0].photcode))) {
+    if (!isfinite(measure[0].psfQF)) { return FALSE; };
+    if (measure[0].psfQF < MinBadQF) { return FALSE; };
+  }
+
+  /* select measurements by photcode, or equiv photcode, if specified */
+  if (NphotcodesKeep > 0) {
+    found = FALSE;
+    for (k = 0; (k < NphotcodesKeep) && !found; k++) {
+      if (photcodesKeep[k][0].code == measure[0].photcode) found = TRUE;
+      if (photcodesKeep[k][0].code == GetPhotcodeEquivCodebyCode(measure[0].photcode)) found = TRUE;
+    }
+    if (!found) return FALSE;
+  }
+  
+  if (NphotcodesSkip > 0) {
+    found = FALSE;
+    for (k = 0; (k < NphotcodesSkip) && !found; k++) {
+      if (photcodesSkip[k][0].code == measure[0].photcode) found = TRUE;
+      if (photcodesSkip[k][0].code == GetPhotcodeEquivCodebyCode(measure[0].photcode)) found = TRUE;
+    }
+    if (found) return FALSE;
+  }  
+  
+  /* select measurements by time */
+  if (TimeSelect) {
+    if (measure[0].t < TSTART) return FALSE;
+    if (measure[0].t > TSTOP) return FALSE;
+  }
+  
+  /* select measurements by quality */
+  if (PhotFlagSelect) {
+    if (PhotFlagBad) {
+      mask = PhotFlagBad;
+    } else {
+      code = GetPhotcodebyCode (measure[0].photcode);
+      if (!code) return FALSE;
+      mask = code[0].astromBadMask;
+    }
+    if (mask & measure[0].photFlags) return FALSE;
+  }
+
+  /* select measurements by measurement error */
+  // this is a bit convoluted: applySigmaLim is only TRUE when this function is
+  // called by bcatalog.  for UpdateObjects, it is FALSE
+  if (applySigmaLim && (SIGMA_LIM > 0) && (measure[0].dM > SIGMA_LIM)) {
+    return FALSE;
+  }
+  
+  /* select measurements by mag limit */
+  if (ImagSelect) {
+    mag = PhotInstTiny (measure, MAG_CLASS_PSF);
+    if (mag < ImagMin || mag > ImagMax) return FALSE;
+  }
+  
+  return TRUE;
+}
+
+# define SUPER_VERBOSE 0
+
+/** Determine whether a measurement should be included in the analysis, based on supplied filter criteria */ 
+// we only optionally apply the sigma limit: for object averages, this should not be used (should it?)
+int MeasFilterTest(Measure *measure, int applySigmaLim) {
+  int found, k;
+  long mask;
+  PhotCode *code;
+  float mag;
+
+  if (!finite(measure[0].R) || !finite(measure[0].D)) { if (SUPER_VERBOSE) fprintf (stderr, "filter 1\n"); return FALSE; };
+  if (!finite(measure[0].M)) { if (SUPER_VERBOSE) fprintf (stderr, "filter 2\n"); return FALSE; }; //XXX is this necessary for all relastro tasks?
+  if (!finite(measure[0].dM)) { if (SUPER_VERBOSE) fprintf (stderr, "filter 3\n"); return FALSE; }; //XXX is this necessary for all relastro tasks?
+  
+  /* select measurements by photcode, or equiv photcode, if specified */
+  if (NphotcodesKeep > 0) {
+    found = FALSE;
+    for (k = 0; (k < NphotcodesKeep) && !found; k++) {
+      if (photcodesKeep[k][0].code == measure[0].photcode) found = TRUE;
+      if (photcodesKeep[k][0].code == GetPhotcodeEquivCodebyCode(measure[0].photcode)) found = TRUE;
+    }
+    if (!found) { if (SUPER_VERBOSE) fprintf (stderr, "filter 4\n"); return FALSE; };
+  }
+  
+  if (NphotcodesSkip > 0) {
+    found = FALSE;
+    for (k = 0; (k < NphotcodesSkip) && !found; k++) {
+      if (photcodesSkip[k][0].code == measure[0].photcode) found = TRUE;
+      if (photcodesSkip[k][0].code == GetPhotcodeEquivCodebyCode(measure[0].photcode)) found = TRUE;
+    }
+    if (found) { if (SUPER_VERBOSE) fprintf (stderr, "filter 5\n"); return FALSE; };
+  }  
+  
+  if ((MinBadQF > 0.0) && isGPC1chip(measure[0].photcode)) {
+    if (!isfinite(measure[0].psfQF)) { if (SUPER_VERBOSE) fprintf (stderr, "filter 6\n"); return FALSE; };
+    if (measure[0].psfQF < MinBadQF) { if (SUPER_VERBOSE) fprintf (stderr, "filter 7\n"); return FALSE; };
+  }
+
+  /* select measurements by time */
+  if (TimeSelect) {
+    if (measure[0].t < TSTART) { if (SUPER_VERBOSE) fprintf (stderr, "filter 8\n"); return FALSE; };
+    if (measure[0].t > TSTOP) { if (SUPER_VERBOSE) fprintf (stderr, "filter 9\n"); return FALSE; };
+  }
+  
+  /* select measurements by quality */
+  if (PhotFlagSelect) {
+    if (PhotFlagBad) {
+      mask = PhotFlagBad;
+    } else {
+      code = GetPhotcodebyCode (measure[0].photcode);
+      if (!code) { if (SUPER_VERBOSE) fprintf (stderr, "filter 10\n"); return FALSE; };
+      mask = code[0].astromBadMask;
+    }
+    if (mask & measure[0].photFlags) { if (SUPER_VERBOSE) fprintf (stderr, "filter 11\n"); return FALSE; };
+  }
+
+  /* select measurements by measurement error */
+  if (applySigmaLim && (SIGMA_LIM > 0) && (measure[0].dM > SIGMA_LIM)) {
+    { if (SUPER_VERBOSE) fprintf (stderr, "filter 12\n"); return FALSE; };
+  }
+  
+  /* select measurements by mag limit */
+  if (ImagSelect) {
+    mag = PhotInst (measure, MAG_CLASS_PSF);
+    if (mag < ImagMin || mag > ImagMax) { if (SUPER_VERBOSE) fprintf (stderr, "filter 13\n"); return FALSE; };
+  }
+  
+  return TRUE;
+}
Index: /branches/eam_branches/ohana.20160226/src/relastro/src/fitobj.c
===================================================================
--- /branches/eam_branches/ohana.20160226/src/relastro/src/fitobj.c	(revision 39444)
+++ /branches/eam_branches/ohana.20160226/src/relastro/src/fitobj.c	(revision 39445)
@@ -240,2 +240,17 @@
   return catalog;
 }
+
+// these dummy functions are used to avoid including ImageOps, etc
+int areImagesMatched () {
+  return FALSE;
+}
+float getColorBlue (off_t meas, int cat) {
+  OHANA_UNUSED_PARAM(meas);
+  OHANA_UNUSED_PARAM(cat);
+  return (NAN);
+}
+float getColorRed (off_t meas, int cat) {
+  OHANA_UNUSED_PARAM(meas);
+  OHANA_UNUSED_PARAM(cat);
+  return (NAN);
+}
Index: /branches/eam_branches/ohana.20160226/src/relastro/src/fitobj2.c
===================================================================
--- /branches/eam_branches/ohana.20160226/src/relastro/src/fitobj2.c	(revision 39444)
+++ /branches/eam_branches/ohana.20160226/src/relastro/src/fitobj2.c	(revision 39445)
@@ -265,2 +265,17 @@
   return catalog;
 }
+
+// these dummy functions are used to avoid including ImageOps, etc
+int areImagesMatched () {
+  return FALSE;
+}
+float getColorBlue (off_t meas, int cat) {
+  OHANA_UNUSED_PARAM(meas);
+  OHANA_UNUSED_PARAM(cat);
+  return (NAN);
+}
+float getColorRed (off_t meas, int cat) {
+  OHANA_UNUSED_PARAM(meas);
+  OHANA_UNUSED_PARAM(cat);
+  return (NAN);
+}
Index: /branches/eam_branches/ohana.20160226/src/relastro/src/fitstk.c
===================================================================
--- /branches/eam_branches/ohana.20160226/src/relastro/src/fitstk.c	(revision 39444)
+++ /branches/eam_branches/ohana.20160226/src/relastro/src/fitstk.c	(revision 39445)
@@ -279,2 +279,17 @@
   return catalog;
 }
+
+// these dummy functions are used to avoid including ImageOps, etc
+int areImagesMatched () {
+  return FALSE;
+}
+float getColorBlue (off_t meas, int cat) {
+  OHANA_UNUSED_PARAM(meas);
+  OHANA_UNUSED_PARAM(cat);
+  return (NAN);
+}
+float getColorRed (off_t meas, int cat) {
+  OHANA_UNUSED_PARAM(meas);
+  OHANA_UNUSED_PARAM(cat);
+  return (NAN);
+}