[gnuastro-commits] master 1570d28a: MakeCatalog: added check to avoid objects images with negative values

[Mohammad Akhlaghi]

branch: master
commit 1570d28a44197baff5713356b24bc28177d93f18
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    MakeCatalog: added check to avoid objects images with negative values
    
    Until now, when MakeCatalog was given an input (labeled) image that
    contained negative values, it would crash with a segmentation fault
    (because the negative pixels in an un-signed array index would lead to
    extremely large values).
    
    With this commit, on the first time that we parse the input object labels,
    if we find a non-blank negative pixels in the image, an informative warning
    is printed and MakeCatalog aborts cleanly.
    
    This bug was reported by Sepideh Eskandarlou.
    
    This fixes bug #62309.
---
 NEWS               |  3 +++
 bin/mkcatalog/ui.c | 53 ++++++++++++++++++++++++++++++++++++-----------------
 2 files changed, 39 insertions(+), 17 deletions(-)

diff --git a/NEWS b/NEWS
index 986ef884..a2a3c0b5 100644
--- a/NEWS
+++ b/NEWS
@@ -51,6 +51,9 @@ See the end of the file for license conditions.
   bug #62305: Not reading the 'MemFree' keyword in '/proc/meminfo' to find
               the available RAM (and thus printing an annoying
               warning). Reported by Juan Miro.
+  bug #62309: MakeCatalog segmentation fault when clumps image given as
+              main input (objects should be given). Reported by Sepideh
+              Eskandarlou.
 
 
 
diff --git a/bin/mkcatalog/ui.c b/bin/mkcatalog/ui.c
index 50b0653a..c3c4dadf 100644
--- a/bin/mkcatalog/ui.c
+++ b/bin/mkcatalog/ui.c
@@ -686,23 +686,42 @@ ui_one_tile_per_object_correct_numobjects(struct 
mkcatalogparams *p)
   start=p->objects->array;
   lf=(l=p->objects->array)+p->objects->size;
   do
-    if(*l>0)
-      {
-        /* Get the coordinates of this pixel. */
-        gal_dimension_index_to_coord(l-start, ndim, p->objects->dsize,
-                                     coord);
-
-        /* Check to see this coordinate is the smallest/largest found so
-           far for this label. Note that labels start from 1, while indexs
-           here start from zero. */
-        min = &minmax[ (*l-1) * width        ];
-        max = &minmax[ (*l-1) * width + ndim ];
-        for(d=0;d<ndim;++d)
-          {
-            if( coord[d] < min[d] ) min[d] = coord[d];
-            if( coord[d] > max[d] ) max[d] = coord[d];
-          }
-      }
+    {
+      /* Small sanity check: the objects image shouldn't have negative
+         values (can happen when the user gives a clump image). */
+      if(*l!=GAL_BLANK_INT32 && *l<0)
+        error(EXIT_FAILURE, 0, "the main labeled image ('OBJECTS' HDU "
+              "when using Segment), shouldn't contain negative values. "
+              "This can happen when you mistakenly give Segment's "
+              "clumps as the main input labeled image. If you want to "
+              "treat clumps as objects, please use 'astarithmetic' to "
+              "convert all negative pixels to 0 before calling "
+              "MakeCatalog. For example this command: "
+              "'astarithmetic file.fits -hCLUMPS set-i i i 0 lt "
+              "0 where'. For this scenario, a better solution is to "
+              "only keep the clumps and give them each a separate "
+              "label with a command like this: 'astarithmetic file.fits "
+              "-hCLUMPS set-i i i 0 gt 2 connected-components'");
+
+      /* We are on an object. */
+      if(*l>0)
+        {
+          /* Get the coordinates of this pixel. */
+          gal_dimension_index_to_coord(l-start, ndim, p->objects->dsize,
+                                       coord);
+
+          /* Check to see this coordinate is the smallest/largest found so
+             far for this label. Note that labels start from 1, while indexs
+             here start from zero. */
+          min = &minmax[ (*l-1) * width        ];
+          max = &minmax[ (*l-1) * width + ndim ];
+          for(d=0;d<ndim;++d)
+            {
+              if( coord[d] < min[d] ) min[d] = coord[d];
+              if( coord[d] > max[d] ) max[d] = coord[d];
+            }
+        }
+    }
   while(++l<lf);
 
   /* If a label doesn't exist in the image, then write over it and define