Changeset 42820

Timestamp:

May 8, 2025, 4:10:23 PM (12 months ago)

Author:

eugene

Message:

merge changes from trunk

Location:

branches/eam_branches/ipp-20230313

Files:

• . (modified) (1 prop)
• Nebulous/bin/whichnode (modified) (1 diff)
• PS-IPP-Config (modified) (1 prop)
• PS-IPP-Config/lib/PS/IPP/Config.pm (modified) (1 diff)
• extsrc/gpcsw/gpcsrc/fits/burntool/persistio.c (modified) (2 diffs)
• extsrc/gpcsw/gpcsrc/fits/burntool/stardetect.c (modified) (3 diffs)
• extsrc/gpcsw/gpcsrc/fits/burntool/trailfit.c (modified) (2 diffs)
• ippTasks/mergedvodb.pro (modified) (2 diffs)
• ippTasks/summit.copy.pro (modified) (1 diff)
• ippTools (modified) (1 prop)
• ippTools/src (modified) (1 prop)
• ippTools/src/pxtools.c (modified) (1 diff)
• ippconfig (modified) (1 prop)
• ippconfig/Makefile.am (modified) (3 diffs)
• ippconfig/gpc1/ppImage.config (modified) (1 diff)
• ippconfig/recipes/psphot.config (modified) (2 diffs)
• ippconfig/simple/camera.config (modified) (1 diff)
• ippconfig/simple/format.config (modified) (1 diff)
• ippconfig/simple/ppMerge.config (copied) (copied from trunk/ippconfig/simple/ppMerge.config )
• ippconfig/simquad (copied) (copied from trunk/ippconfig/simquad )
• ippconfig/system.config (modified) (1 diff)
• ppImage (modified) (1 prop)
• ppImage/src/ppImageBurntoolApply.c (modified) (2 diffs)
• ppMerge/src/ppMerge.c (modified) (1 diff)
• ppMerge/src/ppMerge.h (modified) (1 diff)
• ppMerge/src/ppMergeFiles.c (modified) (2 diffs)
• ppMerge/src/ppMergeLoop.c (modified) (13 diffs)
• ppMerge/src/ppMergeMask.c (modified) (1 diff)
• ppMerge/src/ppMergeScaleZero.c (modified) (1 diff)
• psLib (modified) (1 prop)
• psLib/src/db/psDB.c (modified) (1 diff)
• psLib/src/sys/psConfigure.c (modified) (2 diffs)
• psModules (modified) (1 prop)
• psModules/src/camera/pmFPA.c (modified) (3 diffs)
• psModules/src/camera/pmFPAConstruct.c (modified) (3 diffs)
• psModules/src/detrend/pmDark.c (modified) (5 diffs)
• psconfig (modified) (1 prop)
• psconfig/tagsets/ipp-ubuntu.dist (modified) (2 diffs)
• tools (modified) (1 prop)
• tools/eam/neb-apache-check.20241219 (copied) (copied from trunk/tools/eam/neb-apache-check.20241219 )

branches/eam_branches/ipp-20230313/Nebulous/bin/whichnode

@@ -1 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 
 # This script is a temporary "solution" to allow a client to determine whether

branches/eam_branches/ipp-20230313/PS-IPP-Config/lib/PS/IPP/Config.pm

@@ -1371 +1371 @@
 
 
+# Return array of the instances for this nebulous file
+sub find_instances
+{
+    my $self = shift;
+    my $file = shift;
+
+    my $scheme = file_scheme($file);
+    if (!$scheme or ($scheme ne 'neb')) {
+        # if not nebulous, the instance is the file
+        my @result;
+        push @result, $file;
+        return (\@result);
+    }
+
+    my $neb = $self->nebulous;
+    my $uris;
+    eval { $uris = $neb->find_instances($file); };
+    if ($@) { 
+        carp "failed to set user.copies for $file";
+        return 0;
+    }
+    return $uris;
+}
+
 # Return catdir for tessellation, from TESSELLATIONS within the site configuration
 sub tessellation_catdir

branches/eam_branches/ipp-20230313/extsrc/gpcsw/gpcsrc/fits/burntool/persistio.c

@@ -312 +312 @@
                     cell[j].burn[k].fiterr != FIT_TOP_ERROR) continue;
                if(cell[j].burn[k].nfit <= 0) continue;
+               /*kick out burns which are single pixels*/
              }
             } else {
@@ -317 +318 @@
                cell[j].burn[k].fiterr != FIT_TOP_ERROR) continue;
              if(cell[j].burn[k].nfit <= 0) continue;
+             /*kick out burns which are single pixels*/
+
             }
 

branches/eam_branches/ipp-20230313/extsrc/gpcsw/gpcsrc/fits/burntool/stardetect.c

@@ -34 +34 @@
    starcut = STAR_THRESH/2 + cell->sky + cell->bias;
 
-   /*try a new value for thresh_lo which is 1 sigmas above the background, but with a safety limit of 1000 counts*/
+   /*try a new value for thresh_lo which is 10 sigmas above the background, but with a safety limit of 1000 counts*/
         trailthresh = cell->sky + (10*cell->rms);
         if(trailthresh <= 1000) trailthresh = 1000;
         trailthresh = trailthresh + cell->bias;
+        thresh_lo = trailthresh;
+
+   /*try a new value for burnthresh which is twice the bias above the sky background, but with a safety limit of 30000 counts*/
+        burnthresh = cell->sky + (2*cell->bias);
+        if(burnthresh <= BURN_THRESH) burnthresh = BURN_THRESH;
+        thresh_hi = burnthresh;
 
 /* Look at all the pixels which pass the burn threshold */
@@ -81 +87 @@
                 boxbuf[nbox].ey = k-1;
                 grow_box(nx, ny, NX, data, thresh_lo, boxbuf+nbox);
+                
            /* Fill in max and center info */
                 boxbuf[nbox].max = 0;
@@ -100 +107 @@
                              boxbuf[nbox].ex, boxbuf[nbox].ey,
                              boxbuf[nbox].max);
+                        fflush(stdout);
+                  }
+/* Mark the veto mask so as not to trigger on this one again */
+                  for(l=boxbuf[nbox].sy; l<=boxbuf[nbox].ey; l++) {
+                         for(k=boxbuf[nbox].sx; k<=boxbuf[nbox].ex; k++) {
+                          veto[k+l*NX] = boxbuf[nbox].max;
+                         }
+                  }
+                  xon = -1;
+                  continue;
+                }
+
+/* A box that is composed of a single pixel should not be considered a burn */
+                if((boxbuf[nbox].ex - boxbuf[nbox].sx) <= 2 && (boxbuf[nbox].ey - boxbuf[nbox].sy) <= 2) {
+                  if(VERBOSE & VERB_DETECT) {
+                        printf("Ditching box %d %d %d %d  for being too small\n",
+                             boxbuf[nbox].sx, boxbuf[nbox].sy,
+                             boxbuf[nbox].ex, boxbuf[nbox].ey);
                         fflush(stdout);
                   }

branches/eam_branches/ipp-20230313/extsrc/gpcsw/gpcsrc/fits/burntool/trailfit.c

@@ -290 +290 @@
 
    if(!strcmp(camera,"gpc2")) {
-
      /*Conpute the mean and standard deviation of the trail along x*/
      for(i=xs; i<=xe; i++) {
@@ -384 +383 @@
      }
      /* Update fit ranges */
-     if(box->nfit > 0) {
+     if(box->nfit > 1) {
         box->sxfit = box->xfit[0];
         box->exfit = box->xfit[box->nfit-1];

branches/eam_branches/ipp-20230313/ippTasks/mergedvodb.pro

@@ -7 +7 @@
 
 
-#There is a book for each task, because I don't use labels. 
+#There is a book for each task, because I dont use labels. 
 
 if (not($?havemergedvodbBooks))
@@ -44 +44 @@
 end
 
-## you get no choice - you add all of them in at the same time. you can always turn off the tasks you don't want to run.
+## you get no choice - you add all of them in at the same time. you can always turn off the tasks you dont want to run.
 macro add.mergedvodb
   if ($0 != 2)

branches/eam_branches/ipp-20230313/ippTasks/summit.copy.pro

@@ -49 +49 @@
 macro summitcopy.reset
     summitcopy.reset
+end
+
+# pzgetexp is loading exposure files to summitExp 
+macro pzgetexp.on
+  task pzgetexp
+    active true
+  end
+end
+
+macro pzgetexp.off
+  task pzgetexp
+    active false
+  end
 end
 

branches/eam_branches/ipp-20230313/ippTools/src/pxtools.c

@@ -36 +36 @@
     if (!strcmp(state, "wait")) return true;
     if (!strcmp(state, "keep")) return true;
+    if (!strcmp(state, "ignore")) return true;
     if (!strcmp(state, "goto_cleaned")) return true;
     if (!strcmp(state, "error_cleaned")) return true;

branches/eam_branches/ipp-20230313/ippconfig/Makefile.am

@@ +1 @@
+TGT  = $(PSCONFDIR)/$(PSCONFIG)/etc/compress.mgc
+
 SUBDIRS = \
         recipes \
@@ -36 +38 @@
 built_files = \
         ipprc.config \
-        dvo.site
+        dvo.site \
+        $(TGT)
 
 installdir = $(datadir)/ippconfig
@@ -64 +67 @@
 
 
-TGTDIR  = $(PSCONFDIR)/$(PSCONFIG)/etc
-SRC     =       compress
-TGT     =       $(TGTDIR)/compress.mgc
-
-install: $(TGT)
-build:   $(MGC)
 
 if HAVE_LINUX

branches/eam_branches/ipp-20230313/ippconfig/gpc1/ppImage.config

@@ -1139 +1139 @@
 END
 
+# CZW 2018-02-14
+# The default PPIMAGE_N includes BACKGROUND=T, and that breaks detrend construction
+PPIMAGE_N          METADATA
+  BASE.FITS        BOOL    TRUE            # Save base detrended image?
+  BASE.MASK.FITS   BOOL    FALSE           # Save base detrended image?
+  BASE.VARIANCE.FITS BOOL    FALSE           # Save base detrended image?
+  CHIP.FITS        BOOL    FALSE           # Save chip-mosaic-ed image? 
+  CHIP.MASK.FITS   BOOL    FALSE           # Save chip-mosaic-ed image? 
+  CHIP.VARIANCE.FITS BOOL    FALSE           # Save chip-mosaic-ed image? 
+  OVERSCAN         BOOL    FALSE           # Overscan subtraction
+  NONLIN           BOOL    FALSE           # Non-linearity correction; not implemented
+  BIAS             BOOL    FALSE           # Bias subtraction
+  DARK             BOOL    FALSE           # Dark subtraction
+  SHUTTER          BOOL    FALSE           # Shutter correction
+  FLAT             BOOL    FALSE           # Flat-field normalisation
+  MASK             BOOL    FALSE           # Mask bad pixels
+  MASK.BUILD       BOOL    FALSE           # Build internal mask?
+  FRINGE           BOOL    FALSE           # Fringe subtraction
+  PHOTOM           BOOL    FALSE           # Source identification and photometry
+  ASTROM.CHIP      BOOL    FALSE           # Astrometry per chip?
+  ASTROM.MOSAIC    BOOL    FALSE           # Astrometry for mosaic?
+  BIN1.FITS        BOOL    TRUE            # Save 1st binned chip image?
+  BIN2.FITS        BOOL    TRUE            # Save 2nd binned chip image?
+  BACKGROUND       BOOL    FALSE           # Subtract background?
+END
+
 # JPEG images for different types of residual images
 # Save JPEG from BIN1 for bias

branches/eam_branches/ipp-20230313/ippconfig/recipes/psphot.config

@@ -107 +107 @@
 PSF_CLUMP_NY                        S32   1               # selecting PSF stars
 
+PSF_CLUMP_USE_CLIPPED_STATS         BOOL  TRUE            # define clump usig CLIPPED stats or ROBUST stats
+
 PSF_MIN_DS                          F32   0.01
 PSF_PARAM_WEIGHTS                   BOOL  FALSE
@@ -113 +115 @@
 LMM_FIT_GAIN_FACTOR_MODE            S32   0               # there are 3 options to determine the gain factor (0,1,2)
 LMM_FIT_USE_REWEIGHTING             BOOL  FALSE           # use IRLS-style reweighting (TRUE) or ordinary LMM
+
+PSF_FIT_STAR_COORDS                 BOOL  FALSE           # if TRUE, fit position as well as shape for PSF stars
 
 PSF_FIT_ITER                        S32   50              # Maximum number of fitting iterations for PSF

branches/eam_branches/ipp-20230313/ippconfig/simple/camera.config

@@ -42 +42 @@
 RECIPES         METADATA
         PPIMAGE         STR     simple/ppImage.config   # Default: all (normal) options on
+        PPMERGE         STR     simple/ppMerge.config   # Default: all (normal) options on
         PSPHOT          STR     simple/psphot.config    # psphot details
 END

branches/eam_branches/ipp-20230313/ippconfig/simple/format.config

@@ -20 +20 @@
 CELLS   METADATA
         amplifier       METADATA
-                CELL.TRIMSEC.SOURCE     STR     VALUE
-                CELL.TRIMSEC            STR     [0:0,0:0]
+                # CELL.TRIMSEC.SOURCE   STR     VALUE
+                # CELL.TRIMSEC          STR     [0:0,0:0]
                 # alternatives for getting these from the headers
-                # CELL.TRIMSEC.SOURCE   STR     HEADER
-                # CELL.BIASSEC.SOURCE   STR     VALUE
-                # CELL.TRIMSEC          STR     DATASEC
-                # CELL.BIASSEC          STR     BIASSEC
+                CELL.TRIMSEC.SOURCE     STR     HEADER
+                CELL.BIASSEC.SOURCE     STR     HEADER
+                CELL.TRIMSEC            STR     DATASEC
+                CELL.BIASSEC            STR     BIASSEC
         END
 END

branches/eam_branches/ipp-20230313/ippconfig/system.config

@@ -23 +23 @@
         SUPRIMECAM              STR     suprime/camera.config           # Subaru Suprimecam
         SIMMOSAIC               STR     simmosaic/camera.config         # Simulated mosaic, for testing
-        SIMTEST                 STR     simtest/camera.config           # Simulation test camera
+        SIMTEST                 STR     simtest/camera.config           # Simulation test camera
+#       SIMQUAD                 STR     simquad/camera.config           # Simulation test camera
         SIMPLE                  STR     simple/camera.config            # If all else fails....
 END

branches/eam_branches/ipp-20230313/ppImage/src/ppImageBurntoolApply.c

@@ -226 +226 @@
         /* do separate masking strategy for old (14 and lower) and new burntool tables*/
         if (BURNTOOL_STATE_GOOD >= 15) {
-         printf("DET: New burntool style %d\n",BURNTOOL_STATE_GOOD);
+         /*printf("DET: New burntool style %d\n",BURNTOOL_STATE_GOOD);*/
           for (int i = box->sxfit; i<= box->exfit; i++) {
               if (box->up == 0) {
@@ -248 +248 @@
 
         } else {
-         printf("DET: Old burntool style %d\n",BURNTOOL_STATE_GOOD);
+        /* printf("DET: Old burntool style %d\n",BURNTOOL_STATE_GOOD);*/
           for (int i = box->sxfit; i<= box->exfit; i++) {
               if (box->up == 0) {

branches/eam_branches/ipp-20230313/ppMerge/src/ppMerge.c

@@ -159 +159 @@
     psLibFinalize();
 
+    psLogMsg("ppMerge", PS_LOG_INFO, "Memory leaks: %d\\n", psMemCheckLeaks(0, NULL, stdout, false));
+
     exit(exitValue);
 }

branches/eam_branches/ipp-20230313/ppMerge/src/ppMerge.h

@@ -117 +117 @@
     );
 
+bool ppMergeFileFreeInput(pmConfig *config, const pmFPAview *view, int num);
+
 /**
  * Set the data level for files specified by name; return an array of the files
  */
 psArray *ppMergeFileDataLevel(const pmConfig *config, ///< Configuration
-                              const char *name, ///< Name of files
-                              pmFPALevel level ///< Level for file data level
+                              const char *name ///< Name of files
     );
 

branches/eam_branches/ipp-20230313/ppMerge/src/ppMergeFiles.c

@@ -105 +105 @@
 }
 
-psArray *ppMergeFileDataLevel(const pmConfig *config, const char *name, pmFPALevel level)
+bool ppMergeFileFreeInput(pmConfig *config, const pmFPAview *view, int num)
+{
+    {
+        pmFPAfile *input = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT", num);
+        if (!pmFPAfileFreeData(input, view)) {
+            psError(PS_ERR_UNKNOWN, false, "Unable to free data for image file %d", num);
+            return false;
+        }
+    }
+    bool mdok;          // Status of MD lookup
+    if (psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS")) {
+        pmFPAfile *mask = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.MASK", num); // Mask file
+        if (!pmFPAfileFreeData(mask, view)) {
+            psError(PS_ERR_UNKNOWN, false, "Unable to free data for mask file %d", num);
+            return false;
+        }
+    }
+    if (psMetadataLookupBool(&mdok, config->arguments, "INPUTS.VARIANCES")) {
+        pmFPAfile *variance = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.VARIANCE", num); // Variance file
+        if (!pmFPAfileFreeData(variance, view)) {
+            psError(PS_ERR_UNKNOWN, false, "Unable to free data for variance file %d", num);
+            return false;
+        }
+    }
+    return true;
+}
+
+// Select the specified input files and assign the dataLevel and freeLevel,
+// saving a pointer on output array.
+// This function takes the argument pmFPALevel and sets the dataLevel based on that value.
+// However, this is only used with the value PM_FPA_LEVEL_READOUT, and it must be set
+// to that level for the rest of ppMerge to work correctly.  Furthermore, the freeLevel
+// must be set to Cell.  Remove the (false) option.
+psArray *ppMergeFileDataLevel(const pmConfig *config, const char *name)
 {
     assert(config);
@@ -115 +148 @@
     for (int i = 0; i < numFiles; i++) {
         pmFPAfile *file = pmFPAfileSelectSingle(config->files, name, i); // Image file
-        file->dataLevel = level;
-        file->freeLevel = level;
+        file->dataLevel = PM_FPA_LEVEL_READOUT;
+        file->freeLevel = PM_FPA_LEVEL_CELL;
         files->data[i] = psMemIncrRefCounter(file);
     }

branches/eam_branches/ipp-20230313/ppMerge/src/ppMergeLoop.c

@@ -39 +39 @@
     bool haveVariances = psMetadataLookupBool(&mdok, arguments, "INPUTS.VARIANCES"); // Do we have variances?
 
-    psArray *inputs = ppMergeFileDataLevel(config, "PPMERGE.INPUT", PM_FPA_LEVEL_READOUT); // Input images
-    psArray *masks = NULL, *variances = NULL; // Input masks and variances
-    if (haveMasks) {
-        masks = ppMergeFileDataLevel(config, "PPMERGE.INPUT.MASK", PM_FPA_LEVEL_READOUT);
-    }
-    if (haveVariances) {
-        variances = ppMergeFileDataLevel(config, "PPMERGE.INPUT.VARIANCE", PM_FPA_LEVEL_READOUT);
-    }
+    psArray *inputs    = ppMergeFileDataLevel(config, "PPMERGE.INPUT"); // Input images
+    psArray *masks     = haveMasks ? ppMergeFileDataLevel(config, "PPMERGE.INPUT.MASK") : NULL; // Input masks 
+    psArray *variances = haveVariances ? ppMergeFileDataLevel(config, "PPMERGE.INPUT.VARIANCE") : NULL; // Input variances
 
     int nThreads = psMetadataLookupS32 (&mdok, arguments, "NTHREADS");
@@ -135 +130 @@
     psString darkNorm = psMetadataLookupStr(&mdok, arguments, "DARK.NORM"); ///< Dark normalisation
 
-
     if (!ppMergeFileActivate(config, PPMERGE_FILES_ALL, true)) {
         psError(PS_ERR_UNKNOWN, false, "Unable to activate files.");
@@ -152 +146 @@
     }
 
-
     // Average concepts across inputs
     {
@@ -180 +173 @@
         {
             psList *inChips = psListAlloc(NULL);
-            for (int i=0; i < numFiles; i++) {
+            for (int i = 0; i < numFiles; i++) {
                 pmChip *chip = pmFPAviewThisChip(view, ((pmFPAfile *)inputs->data[i])->fpa);
                 psListAdd(inChips, PS_LIST_TAIL, chip);
@@ -193 +186 @@
 
         pmCell *outCell;                ///< Cell of interest
-
-        // XXX TEST : force a single loop
-        // outCell = pmFPAviewNextCell(view, outFPA, 1); {
 
         while ((outCell = pmFPAviewNextCell(view, outFPA, 1))) {
@@ -291 +281 @@
                 psAssert (fileGroups->n > 0, "no valid file groups defined");
                 fileGroup = fileGroups->data[0];
+
                 if (!pmDarkCombinePrepare(outCell, fileGroup->readouts, darkOrdinates, darkNorm)) {
                     goto ERROR;
@@ -305 +296 @@
                 psAbort("Should never get here.");
             }
+            fprintf (stderr, "after pmDarkCombinePrepare / pmReadoutCombinePrepare:\n");
+            psMemStats(true, NULL, NULL);
 
             // Read input data by chunks
@@ -349 +342 @@
                       psArrayAdd(job->args, 1, outCell);
                       psArrayAdd(job->args, 1, fileGroup);
-                      psArrayAdd(job->args, 1, psScalarAlloc(iter, PS_TYPE_S32));
-                      psArrayAdd(job->args, 1, psScalarAlloc(rej, PS_TYPE_F32));
-                      psArrayAdd(job->args, 1, psScalarAlloc(maskVal, PS_TYPE_IMAGE_MASK));
+                      
+                      // need to free the allocated scalars:
+                      { psScalar *tmpVal = psScalarAlloc(iter,    PS_TYPE_S32);        psArrayAdd(job->args, 1, tmpVal); psFree (tmpVal); }
+                      { psScalar *tmpVal = psScalarAlloc(rej,     PS_TYPE_F32);        psArrayAdd(job->args, 1, tmpVal); psFree (tmpVal); }
+                      { psScalar *tmpVal = psScalarAlloc(maskVal, PS_TYPE_IMAGE_MASK); psArrayAdd(job->args, 1, tmpVal); psFree (tmpVal); }
 
                       // call: pmDarkCombine(outCell, fileGroup->readouts, iter, rej, maskVal);
                       if (!psThreadJobAddPending(job)) {
-                        //                          goto ERROR;
-                        // continue; // I don't care.
+                        // CZW commented this out with a note that this was needed to allow ppMerge to work even if some inputs are invalid.
+                        // EAM thinks pmDarkCombine will only return FALSE if there is a programming or setup error (see pmDark.c:pmDarkCombine)
+                        // if so, we should raise an error here.
+                        // goto ERROR;
                       }
                       break;
@@ -398 +395 @@
 
             psFree(fileGroups);
-            //            psFree(zeros);
 
             // XXX eventually need to keep both the shutter and the pattern, as we do with dark
@@ -539 +535 @@
             }
 
+            // free the data used by the input files (we need to do the work ourselves)
+            for (int i = 0; i < numFiles; i++) {
+                if (!ppMergeFileFreeInput(config, view, i)) {
+                    psError(PS_ERR_UNKNOWN, false, "Unable to open file %d", i);
+                    goto ERROR;
+                }
+            }
+
             psFree(outRO);
             cellNum++;
@@ -545 +549 @@
                 goto ERROR;
             }
+
+            // pmFPAfileIOList (config);
         }
 
@@ -562 +568 @@
     psFree(variances);
     psFree(stats);
+    psFree(zeros);
     return true;
 
@@ -571 +578 @@
     psFree(variances);
     psFree(stats);
+    psFree(zeros);
     return false;
 }

branches/eam_branches/ipp-20230313/ppMerge/src/ppMergeMask.c

@@ -427 +427 @@
     }
 
-    psArray *inputs = ppMergeFileDataLevel(config, "PPMERGE.INPUT", PM_FPA_LEVEL_READOUT); ///< Input images
+    psArray *inputs = ppMergeFileDataLevel(config, "PPMERGE.INPUT"); ///< Input images
     psFree(inputs);
     if (haveMasks) {
-        psArray *masks = ppMergeFileDataLevel(config, "PPMERGE.INPUT.MASK", PM_FPA_LEVEL_READOUT);
+        psArray *masks = ppMergeFileDataLevel(config, "PPMERGE.INPUT.MASK");
         psFree(masks);
     }
     if (haveVariances) {
-        psArray *variances = ppMergeFileDataLevel(config, "PPMERGE.INPUT.VARIANCE", PM_FPA_LEVEL_READOUT);
+        psArray *variances = ppMergeFileDataLevel(config, "PPMERGE.INPUT.VARIANCE");
         psFree(variances);
     }

branches/eam_branches/ipp-20230313/ppMerge/src/ppMergeScaleZero.c

@@ -232 +232 @@
     }
 
+    psFree(gains);
     psFree(background);
     psFree(shutters);

branches/eam_branches/ipp-20230313/psLib/src/db/psDB.c

@@ -1039 +1039 @@
     fieldCount = mysql_num_fields(result);
 
+<<<<<<< .working
     // annoyingly, in some versions of mysql the value my_ulonglong is actually unsigned long long and in others
     // it is actually unsigned long.  rather than try to set a print type which depends on the build, we just
     // cast here to the unsigned long since it is rare that we would need such a large rowCount
     psTrace("psLib.db", PS_LOG_INFO, "query returned %lu rows with %d fields", (unsigned long) rowCount, fieldCount);
+||||||| .merge-left.r42748
+    psTrace("psLib.db", PS_LOG_INFO, "query returned %lld rows with %d fields",             rowCount, fieldCount);
+=======
+    psTrace("psLib.db", PS_LOG_INFO, "query returned %lu rows with %d fields", (long unsigned int) rowCount, fieldCount);
+>>>>>>> .merge-right.r42814
 
     while ((row = mysql_fetch_row(result))) {

branches/eam_branches/ipp-20230313/psLib/src/sys/psConfigure.c

@@ -29 +29 @@
 #include <fftw3.h>
 #include <gsl/gsl_version.h>
+#include <gsl/gsl_errno.h>
 #ifdef HAVE_PSDB
 #include <mysql.h>
@@ -157 +158 @@
     // XXX: Still needs error codes to be set
 
+  gsl_set_error_handler_off();
+
     if (timeConfig && strlen(timeConfig) > 0) {
         if (!psTimeInit(timeConfig)) {

branches/eam_branches/ipp-20230313/psModules/src/camera/pmFPA.c

@@ -53 +53 @@
     }
     psTrace("psModules.camera", 9, "Freeing cell %zd\n", (size_t)cell);
+
     pmCellFreeReadouts(cell);
     psFree(cell->readouts);
-
     psFree(cell->concepts);
     psFree(cell->analysis);
@@ -166 +166 @@
     psFree(readout->variance);
     psFree(readout->covariance);
+    psFree(readout->analysis);
     psFree(readout->bias);
 
@@ -173 +174 @@
     readout->variance = NULL;
     readout->covariance = NULL;
+    readout->analysis = NULL;
     readout->mask = NULL;
-
-    readout->bias = psListAlloc(NULL);
+    readout->bias = NULL;
 
     readout->col0 = 0;

branches/eam_branches/ipp-20230313/psModules/src/camera/pmFPAConstruct.c

@@ -52 +52 @@
 
 // Parse a list of first:second:third pairs in a string
+// EAM : this function takes an input 'string' and attempts to parse out
+// groups of the form FIRST:SECOND:THIRD into the arrays (first, second, third).
+
+// The input string may have multiple entries of this form separated by spaces, commas, or
+// semi-colons.  The number of arrays which are supplied must match the string format or
+// an error will be raised.
+
+// e.g., the string could be CHIP:CELL:TYPE in which case all three arrays must exist
+// or, the string could be CHIP:CELL only, in which case the array 'third' must be NULL
+ 
 static int parseContent(psArray **first, // Array of the first values
                          psArray **second, // Array of the second values
@@ -83 +93 @@
     while ((value = psListGetAndIncrement(valuesIter))) {
         psArray *fst = psStringSplitArray(value, ":", true); // First, second, third
+        if (fst->n != numArrays) {
+          psError(PS_ERR_BAD_PARAMETER_VALUE, false, "string %s does not match expected format (%ld colon-separated items supplied, %d expected)", value, fst->n, numArrays);
+          return 0;
+        }
         switch (numArrays) {
           case 3:
@@ -1126 +1140 @@
     pmFPAview *view = pmFPAviewAlloc(0); // View, to be returned
     if (phuView) {
-        // Copy the view, for the case where we're given a view.
+        // Copy the view values, for the case where we're given a view.
         *view = *phuView;
     }

branches/eam_branches/ipp-20230313/psModules/src/detrend/pmDark.c

@@ -252 +252 @@
     }
 
+# if (PS_TRACE_ON)
     if (psTraceGetLevel("psModules.detrend") > 9) {
         for (int i = 0; i < inputs->n; i++) {
             psVector *val = values->data[i];
-            (void) val; // avoid unused variable message when tracing is compiled out
             for (int j = 0; j < ordinates->n; j++) {
                 psTrace("psModules.detrend", 9, "Image %d, ordinate %d: %f\n", i, j, val->data.F32[j]);
@@ -261 +261 @@
         }
     }
+# endif
 
     int numTerms = 1;                   // Number of terms in polynomial
@@ -292 +293 @@
         pmReadout *readout = output->readouts->data[i]; // Readout to update
         if (!readout) {
-            readout = output->readouts->data[i] = pmReadoutAlloc(output);
-        }
-
+            // pmReadoutAlloc places a reference to the readout on cell->readouts
+            // and returns a second mem reference to the readout
+            readout = pmReadoutAlloc(output);
+            psFree (readout); // free the extra mem reference returned by pmReadoutAlloc
+        }
         pmReadoutStackDefineOutput(readout, col0, row0, numCols, numRows, false, false, 0);
         psTrace("psModules.imcombine", 7, "Output minimum: %d,%d\n", col0, row0);
@@ -469 +472 @@
               for (int m = 0; m < poly->deviations->n; m++) {
                 logL->data.F64[k] += pow(poly->deviations->data.F32[m] / polySig->stdevFit,2);
-/*              if ((xOut == 20) && (yOut == 256)) { */
-/*                psTrace("psModules.detrend",3,"pmDarkCombine DEV: %d %d: input %d models: Norders: %d logL: %g value: %g\n", */
-/*                        xOut,yOut,m,k,logL->data.F64[k],poly->deviations->data.F32[m]); */
-/*              } */
               }
               if (k > 0) {
@@ -487 +486 @@
               k_best = 1;
             }
-/*          k_best = 1; */
+
             // Select the polynomial that seems best.
             psPolynomialMD *poly = poly_set->data[k_best];
               
-            //            for (int k = 0; k < poly->coeff->n; k++) {
             for (int k = 0; k < max_orders->n + 1; k++) { // There is one more coefficient than is stored here.
                 pmReadout *ro = output->readouts->data[k]; // Readout of interest
                 if (k < poly->coeff->n) {
                   ro->image->data.F32[yOut][xOut] = poly->coeff->data.F64[k];
-                }
-                else {
+                } else {
                   ro->image->data.F32[yOut][xOut] = 0.0;
                 }

branches/eam_branches/ipp-20230313/psconfig/tagsets/ipp-ubuntu.dist

@@ -69 +69 @@
   YYYYY  ippScripts             ipp-2-9          -0
   YYYYY  ippTasks               ipp-2-9          -0
-# YNYYY  ippToPsps              ipp-2-9          -0 : moved to $svn/psps
+  YNYYY  ippToPsps              ipp-2-9          -0 : moved to $svn/psps
           
   YNYYN  psconfig               ipp-2-9          -0
@@ -82 +82 @@
 
   YYYYY  extsrc/gpcsw           ipp-2-9          -0
-# YYYYY  magic                  ipp-2-9          -0
-# YYYYY  magic/censorObjects    ipp-2-9          -0
-# YYYYY  magic/remove           ipp-2-9          -0
-  YYYYY  console                ipp-2-9          -0
+  YNYYY  magic                  ipp-2-9          -0
+  YNYYY  magic/censorObjects    ipp-2-9          -0
+  YNYYY  magic/remove           ipp-2-9          -0
+  YNYYY  console                ipp-2-9          -0
 
 # there are externally required C libraries and perl modules (see INSTALL)