[gnuastro-commits] master 32e14e6: MakeCatalog: object ID mapping now applied to corrected clump labels

[Mohammad Akhlaghi]

branch: master
commit 32e14e6fbc76028b86ec19743b0e4ee07caf9ea9
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    MakeCatalog: object ID mapping now applied to corrected clump labels
    
    Until now, When MakeCatalog is run on an objects labeled image that has
    non-contiguous labels (for example 23, 25, 800: usually happens when making
    crops of labeled images), it applies an internal mapping of the actual
    labels/IDs with a contiguous set of IDs. But this scenario (of
    non-contiguous IDs) was only tested on generating object catalogs. While
    working on a cropped clumps image (that was accompanied with a cropped
    label and values image), I noticed that MakeCatalog crashes with a
    segmentation fault.
    
    With this commit this issue has been fixed: I noticed that the mapping the
    object IDs wasn't being used in the part where we are identifying the
    clumps, so they were trying to associate themselves with regions far
    outside the allocated number of objects in memory.
    
    This fixes bug #59371.
---
 NEWS                      |  1 +
 bin/mkcatalog/main.h      |  1 +
 bin/mkcatalog/mkcatalog.c |  6 ++++--
 bin/mkcatalog/ui.c        | 28 +++++++++++++++++++++++++---
 4 files changed, 31 insertions(+), 5 deletions(-)

diff --git a/NEWS b/NEWS
index 60a7367..146f103 100644
--- a/NEWS
+++ b/NEWS
@@ -134,6 +134,7 @@ See the end of the file for license conditions.
   bug #59105: Column arithmetic operator degree-to-ra, returning to dec.
   bug #59136: Makeprofiles with --replace is not thread-safe.
   bug #59155: Match cannot find the proper row when coordinates have NaN.
+  bug #59371: MakeCatalog crash with clumps on non-contiguous object labels.
 
 
 
diff --git a/bin/mkcatalog/main.h b/bin/mkcatalog/main.h
index d4c9547..7074161 100644
--- a/bin/mkcatalog/main.h
+++ b/bin/mkcatalog/main.h
@@ -253,6 +253,7 @@ struct mkcatalogparams
   float                medstd;  /* Median standard deviation value.     */
   float               cpscorr;  /* Counts-per-second correction.        */
   int32_t            *outlabs;  /* Labels in output catalog (when necessary) */
+  int32_t         *outlabsinv;  /* Inverse of the 'outlabs' array.      */
   size_t           numobjects;  /* Number of object labels in image.    */
   float               clumpsn;  /* Clump S/N threshold.                 */
   size_t            numclumps;  /* Number of clumps in image.           */
diff --git a/bin/mkcatalog/mkcatalog.c b/bin/mkcatalog/mkcatalog.c
index c8186ec..34d7dac 100644
--- a/bin/mkcatalog/mkcatalog.c
+++ b/bin/mkcatalog/mkcatalog.c
@@ -150,7 +150,7 @@ mkcatalog_single_object(void *in_prm)
          the array positions start from 0. */
       pp.ci       = NULL;
       pp.object   = ( p->outlabs
-                      ? p->outlabs[tprm->indexs[i]]
+                      ? p->outlabs[ tprm->indexs[i] ]
                       : tprm->indexs[i] + 1 );
       pp.tile     = &p->tiles[   tprm->indexs[i] ];
       pp.spectrum = &p->spectra[ tprm->indexs[i] ];
@@ -621,7 +621,9 @@ sort_clumps_by_objid(struct mkcatalogparams *p)
   i=0;
   while(i<p->numclumps)
     {
-      o=p->hostobjid_c[i]-1;
+      o = ( p->outlabsinv
+            ? (p->outlabsinv[ p->hostobjid_c[i] ] + 1)
+            : p->hostobjid_c[i] ) - 1;
       for(j=0; j<p->numclumps_c[o]; ++j)
         permute[i++] = rowstart[o] + j;
     }
diff --git a/bin/mkcatalog/ui.c b/bin/mkcatalog/ui.c
index 4dbe04a..51aad7b 100644
--- a/bin/mkcatalog/ui.c
+++ b/bin/mkcatalog/ui.c
@@ -572,6 +572,7 @@ ui_wcs_info(struct mkcatalogparams *p)
 static size_t
 ui_num_clumps(struct mkcatalogparams *p)
 {
+  int32_t olab;
   char *basename;
   int keepinputdir;
   size_t i, counter, numclumps=0;
@@ -593,13 +594,14 @@ ui_num_clumps(struct mkcatalogparams *p)
       if(*o>0 && *c>0)
         {
           /* See if the label has already been found. */
-          for(tmp=labsinobj[*o];tmp!=NULL;tmp=tmp->next) if(tmp->v==*c) break;
+          olab = p->outlabsinv ? p->outlabsinv[*o] : *o;
+          for(tmp=labsinobj[olab];tmp!=NULL;tmp=tmp->next) if(tmp->v==*c) 
break;
 
           /* When it wasn't found, 'tmp==NULL'. */
           if(tmp==NULL)
             {
               ++numclumps;
-              gal_list_i32_add(&labsinobj[*o], *c);
+              gal_list_i32_add(&labsinobj[olab], *c);
             }
         }
 
@@ -618,7 +620,8 @@ ui_num_clumps(struct mkcatalogparams *p)
       if(*o>0 && *c>0)
         {
           counter=0;
-          for(tmp=labsinobj[*o];tmp!=NULL;tmp=tmp->next)
+          olab = p->outlabsinv ? p->outlabsinv[*o] : *o;
+          for(tmp=labsinobj[olab];tmp!=NULL;tmp=tmp->next)
             { counter++; if(tmp->v==*c) {*c=counter; break;} }
         }
 
@@ -763,9 +766,25 @@ ui_one_tile_per_object_correct_numobjects(struct 
mkcatalogparams *p)
                                       "p->outlabs");
       for(i=0;i<p->numobjects;++i) if(rarray[i]==0) p->outlabs[j++]=i+1;
 
+      /* Allocate an array for easy finding of the proper label and fill it
+         with the new labels. This array should have an element for each of
+         the original labels (that are not contiguous). */
+      if(p->clumpscat)
+        {
+          p->outlabsinv=gal_pointer_allocate(GAL_TYPE_UINT32,
+                                             p->numobjects+1, 1,
+                                             __func__, "p->outlabsinv");
+          for(i=0;i<no;++i) p->outlabsinv[ p->outlabs[i] ] = i;
+        }
+
       /* Correct numobjects and clean up. */
       p->numobjects=no;
       gal_data_free(rowsremove);
+
+      /* For a check:
+      for(i=0;i<p->numobjects;++i)
+        printf("outlabs[%zu]: %d\n", i, p->outlabs[i]);
+      */
     }
 
   /* For a check.
@@ -821,6 +840,7 @@ ui_read_labels(struct mkcatalogparams *p)
           "is currently only defined on 3D datasets", p->objectsfile,
           p->cp.hdu, p->objects->ndim);
 
+
   /* See if the total number of objects is given in the header keywords. */
   keys[0].name="NUMLABS";
   keys[0].type=GAL_TYPE_SIZE_T;
@@ -833,6 +853,7 @@ ui_read_labels(struct mkcatalogparams *p)
       gal_data_free(tmp);
     }
 
+
   /* If there were no objects in the input, then inform the user with an
      error (it is pointless to build a catalog). */
   if(p->numobjects==0)
@@ -1985,6 +2006,7 @@ ui_free_report(struct mkcatalogparams *p, struct timeval 
*t1)
   gal_list_data_free(p->clumpcols);
   gal_list_data_free(p->objectcols);
   gal_list_data_free(p->specsliceinfo);
+  if(p->outlabsinv) free(p->outlabsinv);
   if(p->upcheckout) free(p->upcheckout);
   gal_data_array_free(p->tiles, p->numobjects, 0);