[gnuastro-commits] master 032a0e5: Library (fits.h): can read tables with TNULL before TFORM

[Mohammad Akhlaghi]

branch: master
commit 032a0e5357ebe60fc207100d16740a45ee488b6a
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Library (fits.h): can read tables with TNULL before TFORM
    
    Until now, when a FITS table had the 'TNULL' (value for blank rows) keyword
    before the 'TFORM' keyword (value containing the numerical data type), that
    table couldn't be read by any of the programs. The problem was that we
    needed to know the type of the column to allocate space for the value of
    'TNULL'.
    
    With this commit, when this happens, the keyname and value are stored in a
    list and inserted into the internal data structure after all other keywords
    have been read.
    
    This bug was reported by Samane Raji.
    
    This fixes bug #59019.
---
 NEWS       |  2 +-
 lib/fits.c | 58 +++++++++++++++++++++++++++++++++++++++++++++++++++++-----
 2 files changed, 54 insertions(+), 6 deletions(-)

diff --git a/NEWS b/NEWS
index 17893cc..8e0ebc5 100644
--- a/NEWS
+++ b/NEWS
@@ -133,7 +133,7 @@ See the end of the file for license conditions.
   bug #58898: Plain text string columns touching next, clear first character.
   bug #58901: Blank values for non-standard integer types in FITS tables.
   bug #58974: WCS conversion not reasonable on processed TPV data.
-
+  bug #59019: FITS Table crash when TFORM comes before TNULL.
 
 
 
diff --git a/lib/fits.c b/lib/fits.c
index c9498f1..ef4cb76 100644
--- a/lib/fits.c
+++ b/lib/fits.c
@@ -2599,6 +2599,11 @@ gal_fits_tab_info(char *filename, char *hdu, size_t 
*numcols,
   int status=0, datatype, *tscal;
   char keyname[FLEN_KEYWORD]="XXXXXXXXXXXXX", value[FLEN_VALUE];
 
+  /* Necessary when a keyword can't be written immediately as it is read in
+     the FITS header and it actually depends on other data before. */
+  gal_list_str_t *tmp_n, *later_name=NULL;
+  gal_list_str_t *tmp_v, *later_value=NULL;
+  gal_list_sizet_t *tmp_i, *later_index=NULL;
 
   /* Open the FITS file and get the basic information. */
   fptr=gal_fits_hdu_open_format(filename, hdu, 1);
@@ -2754,11 +2759,12 @@ gal_fits_tab_info(char *filename, char *hdu, size_t 
*numcols,
           index = strtoul(&keyname[5], &tailptr, 10) - 1;
           if(index<tfields )
             {
-              if(allcols[index].type<0)
-                fprintf(stderr, "%s (hdu: %s): %s is located before "
-                        "TFORM%zu, so the proper type to read/store the "
-                        "blank value cannot be deduced", filename, hdu,
-                        keyname, index+1);
+              if(allcols[index].type==0)
+                {
+                  gal_list_str_add(&later_name, keyname, 1);
+                  gal_list_str_add(&later_value, value, 1);
+                  gal_list_sizet_add(&later_index, index);
+                }
               else
                 {
                   /* Put in the blank value. */
@@ -2787,11 +2793,53 @@ gal_fits_tab_info(char *filename, char *hdu, size_t 
*numcols,
       /* Column zero. */
     }
 
+
+  /* If any columns should be added later because of missing information,
+     add them here. */
+  if(later_name)
+    {
+      /* Interpret the necessary 'later_' keys. */
+      tmp_i=later_index;
+      tmp_v=later_value;
+      for(tmp_n=later_name; tmp_n!=NULL; tmp_n=tmp_n->next)
+        {
+          /* Go over the known types and do the job. */
+          if(strncmp(tmp_n->v, "TNULL", 5)==0)
+            {
+              /* Put in the blank value. */
+              gal_tableintern_read_blank(&allcols[tmp_i->v], tmp_v->v);
+
+              /* This flag is not relevant for FITS tables. */
+              if(allcols[tmp_i->v].flag
+                 ==GAL_TABLEINTERN_FLAG_ARRAY_IS_BLANK_STRING)
+                {
+                  allcols[tmp_i->v].flag=0;
+                  free(allcols[tmp_i->v].array);
+                }
+            }
+          else
+            error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to "
+                  "fix the problem. Post-processing of keyword '%s' failed",
+                  __func__, PACKAGE_BUGREPORT, tmp_n->v);
+
+          /* Increment the other two lists too. */
+          tmp_v=tmp_v->next;
+          tmp_i=tmp_i->next;
+        }
+
+      /* Clean up. */
+      gal_list_sizet_free(later_index);
+      gal_list_str_free(later_name, 1);
+      gal_list_str_free(later_value, 1);
+    }
+
+
   /* Correct integer types, then free the allocated arrays. */
   fits_correct_bin_table_int_types(allcols, tfields, tscal, tzero);
   free(tscal);
   free(tzero);
 
+
   /* Close the FITS file and report an error if we had any. */
   fits_close_file(fptr, &status);
   gal_fits_io_error(status, NULL);