[gnuastro-commits] master 9258f68 096/113: Imported recent work in master, minor conflict fixed

[Mohammad Akhlaghi]

branch: master
commit 9258f686a82d69326fb1212d44df8b283b7fb149
Merge: 175354f 13a7e18
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Imported recent work in master, minor conflict fixed
    
    In a previous merge with the master branch a check on the number of input
    dimensions to Convolve wasn't corrected for this branch. This has been
    fixed with this merge.
---
 NEWS                        |  2 ++
 bin/arithmetic/arithmetic.c | 13 ++++++++++---
 bin/arithmetic/main.h       |  1 +
 bin/convolve/ui.c           |  4 ++--
 doc/gnuastro.texi           | 12 ++++++------
 lib/convolve.c              | 11 +++++++++++
 lib/tile-internal.c         |  5 ++---
 lib/type.c                  | 15 +++++++++++----
 lib/wcs.c                   | 11 ++++++-----
 9 files changed, 51 insertions(+), 23 deletions(-)

diff --git a/NEWS b/NEWS
index bf2af0a..8ddb577 100644
--- a/NEWS
+++ b/NEWS
@@ -153,6 +153,8 @@ GNU Astronomy Utilities NEWS                          -*- 
outline -*-
   bug #55025: MakeCatalog's `--prepforconv' option being ignored.
   bug #55079: Blank EPS or PDF page when width options not given.
   bug #55157: No sanity check on values given to Crop's --section.
+  bug #55295: Crash when more than one collapse operator called.
+  bug #55298: Arithmetic reading 255 on command-line as blank.
 
 
 
diff --git a/bin/arithmetic/arithmetic.c b/bin/arithmetic/arithmetic.c
index d747e85..143ebd4 100644
--- a/bin/arithmetic/arithmetic.c
+++ b/bin/arithmetic/arithmetic.c
@@ -733,7 +733,11 @@ arithmetic_collapse(struct arithmeticparams *p, char 
*token, int operator)
 
   /* If a WCS structure has been read, we'll need to pass it to
      `gal_dimension_collapse', so it modifies it respectively. */
-  input->wcs=p->refdata.wcs;
+  if(p->wcs_collapsed==0)
+    {
+      p->wcs_collapsed=1;
+      input->wcs=p->refdata.wcs;
+    }
 
 
   /* Run the relevant library function. */
@@ -770,8 +774,11 @@ arithmetic_collapse(struct arithmeticparams *p, char 
*token, int operator)
      `collapsed->wcs'. So we'll let the freeing of `input' free the old
      `p->refdata.wcs' structure and we'll put the new one there, then we'll
      set `collapsed->wcs' to `NULL', so the new one isn't freed. */
-  p->refdata.wcs = collapsed->wcs;
-  collapsed->wcs = NULL;
+  if(collapsed->wcs)
+    {
+      p->refdata.wcs = collapsed->wcs;
+      collapsed->wcs = NULL;
+    }
 
 
   /* We'll also need to correct the size of the reference dataset. We'll
diff --git a/bin/arithmetic/main.h b/bin/arithmetic/main.h
index ce36ebb..48512d1 100644
--- a/bin/arithmetic/main.h
+++ b/bin/arithmetic/main.h
@@ -79,6 +79,7 @@ struct arithmeticparams
   size_t      tokencounter;  /* Counter for finding place in tokens.    */
 
   /* Operating mode: */
+  int        wcs_collapsed;  /* If the internal WCS is already collapsed.*/
 
   /* Internal: */
   struct operand *operands;  /* The operands linked list.               */
diff --git a/bin/convolve/ui.c b/bin/convolve/ui.c
index 47f7f95..0f43c11 100644
--- a/bin/convolve/ui.c
+++ b/bin/convolve/ui.c
@@ -492,8 +492,8 @@ ui_preparations(struct convolveparams *p)
   ui_read_input(p);
 
 
-  /* Currently Convolve only works on 1D and 2D datasets. */
-  if(p->input->ndim>2)
+  /* Currently Convolve only works on 1D, 2D and 3D datasets. */
+  if(p->input->ndim>3)
     error(EXIT_FAILURE, 0, "%s (hdu %s) has %zu dimensions. Currently "
           "Convolve only operates on 1D (table column, spectrum), 2D "
           "(image), and 3D (data cube) datasets", p->filename, cp->hdu,
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index fc91c2a..99e2840 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -26270,15 +26270,15 @@ linked list. It is recommended to use 
@code{gal_table_read} for generic
 reading of tables, see @ref{Table input output}.
 @end deftypefun
 
-@deftypefun void gal_fits_tab_write (gal_data_t @code{*cols}, gal_list_str_t 
@code{*comments}, int @code{tableformat}, char @code{*filename})
+@deftypefun void gal_fits_tab_write (gal_data_t @code{*cols}, gal_list_str_t 
@code{*comments}, int @code{tableformat}, char @code{*filename}, char 
@code{*extname})
 Write the list of datasets in @code{cols} (see @ref{List of gal_data_t}) as
 separate columns in a FITS table in @code{filename}. If @code{filename}
 already exists then this function will write the table as a new extension
-after all existing ones. The format of the table (ASCII or binary) may be
-specified with the @code{tableformat} (see @ref{Table input output}). If
-@code{comments!=NULL}, each node of the list of strings will be written as
-a @code{COMMENT} keywords in the output FITS file (see @ref{List of
-strings}.
+called @code{extname}, after all existing ones. The format of the table
+(ASCII or binary) may be specified with the @code{tableformat} (see
+@ref{Table input output}). If @code{comments!=NULL}, each node of the list
+of strings will be written as a @code{COMMENT} keywords in the output FITS
+file (see @ref{List of strings}.
 
 This is a low-level function for tables. It is recommended to use
 @code{gal_table_write} for generic writing of tables in a variety of
diff --git a/lib/convolve.c b/lib/convolve.c
index 5fd9b62..0423b55 100644
--- a/lib/convolve.c
+++ b/lib/convolve.c
@@ -501,6 +501,17 @@ gal_convolve_spatial_general(gal_data_t *tiles, gal_data_t 
*kernel,
     error(EXIT_FAILURE, 0, "%s: only accepts `float32' type input and "
           "kernel currently", __func__);
 
+  /* It may happen that an input dataset is part of a linked list, but it
+     is not actually a tile structure (the user wants to convolve the whole
+     dataset without using tiles)! In that case, this function should break
+     beacuse a linked list is interpretted as a tile structure here.*/
+  if( tiles->block==NULL && tiles->next && tiles->next->block==NULL )
+    error(EXIT_FAILURE, 0, "%s: the input is a linked list but not a "
+          "tessellation (a list of tiles). This function is optimized to "
+          "work on a list of tiles. Please (temporarily) set the `next' "
+          "element of the input to `NULL' and call this funciton again",
+          __func__);
+
 
   /* Set the output datastructure.  */
   if(tocorrect) out=tocorrect;
diff --git a/lib/tile-internal.c b/lib/tile-internal.c
index 7e51fe2..7a83e6d 100644
--- a/lib/tile-internal.c
+++ b/lib/tile-internal.c
@@ -106,7 +106,7 @@ tileinternal_no_outlier_work(gal_data_t *first, gal_data_t 
*second,
   nbs=gal_statistics_no_blank_sorted(second, 0);
   outlier=gal_statistics_outlier_positive(nbs, nbs->size, outliersigma,
                                           outliersclip[0], outliersclip[1],
-                                          0, 0);
+                                          0, 1);
   gal_data_free(nbs);
   if(outlier)
     {
@@ -124,7 +124,7 @@ tileinternal_no_outlier_work(gal_data_t *first, gal_data_t 
*second,
       outlier=gal_statistics_outlier_positive(nbs, nbs->size/2,
                                               outliersigma,
                                               outliersclip[0],
-                                              outliersclip[1], 0, 0);
+                                              outliersclip[1], 0, 1);
       gal_data_free(nbs);
       if(outlier)
         {
@@ -143,7 +143,6 @@ tileinternal_no_outlier_work(gal_data_t *first, gal_data_t 
*second,
         if(third) arr3[i] = NAN;
       }
 
-
   /* Correct the values, if they were changed. */
   if(start || tottilesinch!=osize)
     {
diff --git a/lib/type.c b/lib/type.c
index 5d89a72..5a42e84 100644
--- a/lib/type.c
+++ b/lib/type.c
@@ -568,10 +568,17 @@ gal_type_string_to_number(char *string, uint8_t *type)
         }
       else
         {
-          if     (d<=UINT8_MAX)  { u8=d;  ptr=&u8;  *type=GAL_TYPE_UINT8;  }
-          else if(d<=UINT16_MAX) { u16=d; ptr=&u16; *type=GAL_TYPE_UINT16; }
-          else if(d<=UINT32_MAX) { u32=d; ptr=&u32; *type=GAL_TYPE_UINT32; }
-          else                   { u64=d; ptr=&u64; *type=GAL_TYPE_UINT64; }
+          /* Note that the blank values are set to the maximum values in
+             unsigned types. A blank value should be given as a blank
+             string to this function (`GAL_BLANK_STRING'). So, to avoid
+             confusing situations (for example when the user gives 255), if
+             the value is equal to the given maximum of the given type,
+             we'll assign it to a larger type. In other words, we won't be
+             using the `<=MAX', but `<MAX'. */
+          if     (d<UINT8_MAX)  { u8=d;  ptr=&u8;  *type=GAL_TYPE_UINT8;  }
+          else if(d<UINT16_MAX) { u16=d; ptr=&u16; *type=GAL_TYPE_UINT16; }
+          else if(d<UINT32_MAX) { u32=d; ptr=&u32; *type=GAL_TYPE_UINT32; }
+          else                  { u64=d; ptr=&u64; *type=GAL_TYPE_UINT64; }
         }
     }
   else
diff --git a/lib/wcs.c b/lib/wcs.c
index dfb3d83..8d3cb5a 100644
--- a/lib/wcs.c
+++ b/lib/wcs.c
@@ -288,17 +288,18 @@ wcs_ctype_has_tan(char *str)
 void
 gal_wcs_remove_dimension(struct wcsprm *wcs, size_t fitsdim)
 {
-  size_t c, i, j, naxis=wcs->naxis;
+  size_t c, i, j, naxis;
+
+  /* If the WCS structure is NULL, just return. */
+  if(wcs==NULL) return;
 
   /* Sanity check. */
-  if(fitsdim==0 || fitsdim>wcs->naxis)
+  naxis=wcs->naxis;
+  if(fitsdim==0 || fitsdim>naxis)
     error(EXIT_FAILURE, 0, "%s: requested dimension (fitsdim=%zu) must be "
           "larger than zero and smaller than the number of dimensions in "
           "the given WCS structure (%zu)", __func__, fitsdim, naxis);
 
-  /* If the WCS structure is NULL, just return. */
-  if(wcs==NULL) return;
-
   /**************************************************/
 #if WCS_REMOVE_DIM_CHECK
   printf("\n\nfitsdim: %zu\n", fitsdim);