[gnuastro-commits] master 13b05cf 2/2: Catalog read before finalizing output size in MakeProfiles

[Mohammad Akhlaghi]

branch: master
commit 13b05cfebe68b6b7547fd6fa1d683a7d18ae24da
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>

    Catalog read before finalizing output size in MakeProfiles
    
    Due to some previous changes in the way MakeProfiles reads columns and
    prepares the output array, we were mistakenly finalizing the output size
    before actually reading the column contents. Therefore the `--prepforconv'
    option (which needs to see if a PSF profile was requested and also needs
    its size) had effectively become useless.
    
    Since reading of the columns needs knowledge of the output's
    dimensionality, the steps to find the dimensionality are now separated into
    a separate function that is done before reading columns. After the columns
    are read, we'll go onto finalizing the output's array size.
    
    Fernando Buitrago reported this bug.
    
    This fixes bug #55025.
---
 NEWS                         |   2 +-
 bin/mkprof/ui.c              | 147 ++++++++++++++++++++++++-------------------
 doc/announce-acknowledge.txt |   1 +
 3 files changed, 86 insertions(+), 64 deletions(-)

diff --git a/NEWS b/NEWS
index 82d39da..cb24499 100644
--- a/NEWS
+++ b/NEWS
@@ -128,7 +128,7 @@ GNU Astronomy Utilities NEWS                          -*- 
outline -*-
   bug #54579: NoiseChisel pseudo-detection failure when dataset is negative.
   bug #54782: Segment's check image not removing sky clumps some tiles.
   bug #54810: Arithmetic crash when previously named operand renamed.
-
+  bug #55025: MakeCatalog's `--prepforconv' option being ignored.
 
 
 
diff --git a/bin/mkprof/ui.c b/bin/mkprof/ui.c
index 4239de6..590eda2 100644
--- a/bin/mkprof/ui.c
+++ b/bin/mkprof/ui.c
@@ -1004,7 +1004,6 @@ ui_prepare_canvas(struct mkprofparams *p)
 {
   float *f, *ff;
   double truncr;
-  gal_data_t *keysll;
   long width[2]={1,1};
   int status=0, setshift=0;
   size_t i, nshift=0, *dsize=NULL, ndim_counter;
@@ -1013,52 +1012,13 @@ ui_prepare_canvas(struct mkprofparams *p)
      image to build the profiles over. */
   if(p->backname)
     {
-      /* Make sure the kernel option is not called. */
-      if(p->kernel)
-        error(EXIT_FAILURE, 0, "the `--kernel' and `--background' options "
-              "cannot be called together");
-
-      /* Small sanity check. */
-      if(p->backhdu==NULL)
-        error(EXIT_FAILURE, 0, "no hdu specified for the background image "
-              "%s. Please run again `--backhdu' option", p->backname);
-
       /* Read in the background image and its coordinates, note that when
          no merged image is desired, we just need the WCS information of
          the background image and the number of its dimensions. So
          `ndim==0' and what `dsize' points to is irrelevant. */
-      if(p->nomerged)
-        {
-          /* Get the number of the background image's dimensions. */
-          keysll=gal_data_array_calloc(1);
-          keysll->name="NAXIS";   keysll->type=GAL_TYPE_SIZE_T;
-          gal_fits_key_read(p->backname, p->backhdu, keysll, 0, 0);
-          p->ndim = *(size_t *)(keysll->array);
-          keysll->name=NULL;
-          gal_data_array_free(keysll, 1, 1);
-
-          /* Read the WCS structure of the background image. */
-          p->wcs=gal_wcs_read(p->backname, p->backhdu, 0, 0, &p->nwcs);
-        }
-      else
+      p->wcs=gal_wcs_read(p->backname, p->backhdu, 0, 0, &p->nwcs);
+      if(p->nomerged==0)
         {
-          /* Read the image. */
-          p->out=gal_array_read_one_ch_to_type(p->backname, p->backhdu,
-                                               NULL, GAL_TYPE_FLOAT32,
-                                               p->cp.minmapsize);
-          p->out->wcs=gal_wcs_read(p->backname, p->backhdu, 0, 0,
-                                   &p->out->nwcs);
-
-          /* Put the WCS structure and number of dimensions in the
-             MakeProfiles's main structure for generality. The WCS
-             structure will be put back in the end when writing. */
-          p->wcs=p->out->wcs;
-          p->nwcs=p->out->nwcs;
-          p->ndim=p->out->ndim;
-          p->out->wcs=NULL;
-          p->out->nwcs=0;
-
-
           /* If p->dsize was given as an option, free it. */
           if( p->dsize ) free(p->dsize);
 
@@ -1072,14 +1032,6 @@ ui_prepare_canvas(struct mkprofparams *p)
             {ff=(f=p->out->array)+p->out->size; do *f++=0.0f; while(f<ff);}
         }
 
-
-      /* Currently, things are only implemented for 2D. */
-      if(p->ndim!=2)
-        error(EXIT_FAILURE, 0, "%s (hdu %s) has %zu dimensions. Currently "
-              "only a 2 dimensional background image is acceptable",
-              p->backname, p->backhdu, p->ndim);
-
-
       /* When a background image is specified, oversample must be 1 and
          there is no shifts. */
       p->oversample=1;
@@ -1089,16 +1041,6 @@ ui_prepare_canvas(struct mkprofparams *p)
     }
   else
     {
-      /* Get the number of dimensions. */
-      ndim_counter=0;
-      for(i=0;p->dsize[i]!=GAL_BLANK_SIZE_T;++i) ++ndim_counter;
-      p->ndim=ndim_counter;
-
-      /* Currently, things are only implemented for 2D. */
-      if(p->ndim!=2)
-        error(EXIT_FAILURE, 0, "%zu numbers given to `--mergedsize', only 2 "
-              "values may be given", p->ndim);
-
       /* If any of the shift elements are zero, the others should be too!*/
       if(p->shift && p->shift[0] && p->shift[1])
         {
@@ -1345,8 +1287,90 @@ ui_make_log(struct mkprofparams *p)
 
 
 static void
+ui_read_ndim(struct mkprofparams *p)
+{
+  gal_data_t *keysll;
+  size_t i, ndim_counter;
+
+  if(p->kernel)
+    {
+      /* The kernel's dimensionality is fixed. */
+      p->ndim=2;
+
+      /* Make sure the kernel and background are not given together. */
+      if(p->backname)
+        error(EXIT_FAILURE, 0, "the `--kernel' and `--background' options "
+              "cannot be called together");
+    }
+  else
+    {
+      /* Packground image is given. */
+      if(p->backname)
+        {
+          /* Small sanity check. */
+          if(p->backhdu==NULL)
+            error(EXIT_FAILURE, 0, "no hdu specified for the background "
+                  "image %s. Please run again `--backhdu' option",
+                  p->backname);
+
+          /* If `--nomerged' is given, we don't actually need to load the
+             image, we just need its WCS later. */
+          if(p->nomerged)
+            {
+              /* Get the number of the background image's dimensions. */
+              keysll=gal_data_array_calloc(1);
+              keysll->name="NAXIS";   keysll->type=GAL_TYPE_SIZE_T;
+              gal_fits_key_read(p->backname, p->backhdu, keysll, 0, 0);
+              p->ndim = *(size_t *)(keysll->array);
+              keysll->name=NULL;
+              gal_data_array_free(keysll, 1, 1);
+            }
+          else
+            {
+              /* Read the image. */
+              p->out=gal_array_read_one_ch_to_type(p->backname, p->backhdu,
+                                                   NULL, GAL_TYPE_FLOAT32,
+                                                   p->cp.minmapsize);
+              p->ndim=p->out->ndim;
+            }
+
+          /* Make sure the dimensionality is supported. */
+          if(p->ndim!=2)
+            error(EXIT_FAILURE, 0, "%s (hdu %s) has %zu dimensions. Currently "
+                  "only 2 dimensional outputs can be produced",
+                  p->backname, p->backhdu, p->ndim);
+        }
+      else
+        {
+          /* Get the number of dimensions from the user's options. */
+          ndim_counter=0;
+          for(i=0;p->dsize[i]!=GAL_BLANK_SIZE_T;++i) ++ndim_counter;
+          p->ndim=ndim_counter;
+
+          /* Make sure the dimensionality is supported. */
+          if(p->ndim!=2)
+            error(EXIT_FAILURE, 0, "%zu values given to `--mergedsize'. "
+                  "Currently only 2 dimensional outputs can be produced",
+                  p->ndim);
+        }
+    }
+}
+
+
+
+
+
+static void
 ui_preparations(struct mkprofparams *p)
 {
+  /* Set the output dimensionality (necessary to know which columns to
+     use). */
+  ui_read_ndim(p);
+
+  /* Read in all the columns (necessary for `--prepforconf' when we want to
+     build the profiles). */
+  ui_prepare_columns(p);
+
   /* If the kernel option was given, some parameters need to be
      over-written: */
   if(p->kernel)
@@ -1364,9 +1388,6 @@ ui_preparations(struct mkprofparams *p)
   else
     ui_prepare_canvas(p);
 
-  /* Read in all the columns. */
-  ui_prepare_columns(p);
-
   /* Read the (possible) RA/Dec inputs into X and Y for the builder.*/
   if(p->wcs)
     ui_finalize_coordinates(p);
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index a46f0b1..cffd52c 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -1,5 +1,6 @@
 Alphabetically ordered list to acknowledge in the next release.
 
+Fernando Buitrago
 Pierre-Alain Duc
 Gaspar Galaz
 Johan Knapen