[gnuastro-commits] master 89be245 7/9: Crop and Table: --polygon now accepts filenames

[Mohammad Akhlaghi]

branch: master
commit 89be245e212d9aeede9ca9fc02fe698890b95f86
Author: Natáli D. Anzanello <natali.anzanello@ufrgs.br>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Crop and Table: --polygon now accepts filenames
    
    Until now, we used the '--polygonfile' option to specify the DS9 region
    filename containing the polygon.
    
    With this commit, the '--polygon' option also accepts a filename of a DS9
    region file. Therefore, the '--polygonfile' option was removed. To do this,
    a check in 'gal_options_parse_colon_sep_csv' (in 'lib/options.c') was added.
---
 bin/crop/args.h    | 13 -----------
 bin/crop/main.h    |  1 -
 bin/crop/ui.c      | 66 ++++++++++++++----------------------------------------
 bin/crop/ui.h      |  1 -
 bin/table/args.h   | 15 +------------
 bin/table/main.h   |  1 -
 bin/table/ui.c     | 35 -----------------------------
 bin/table/ui.h     |  1 -
 lib/ds9.c          | 19 ++++++++--------
 lib/gnuastro/ds9.h |  2 +-
 lib/options.c      | 10 +++++++--
 11 files changed, 37 insertions(+), 127 deletions(-)

diff --git a/bin/crop/args.h b/bin/crop/args.h
index dd1b7d3..7eddd38 100644
--- a/bin/crop/args.h
+++ b/bin/crop/args.h
@@ -307,19 +307,6 @@ struct argp_option program_options[] =
       GAL_OPTIONS_NOT_MANDATORY,
       GAL_OPTIONS_NOT_SET
     },
-    {
-      "polygonfile",
-      UI_KEY_POLYGONFILE,
-      "REG",
-      0,
-      "Input polygon filename made in DS9.",
-      UI_GROUP_REGION,
-      &p->polygonfile,
-      GAL_TYPE_STRING,
-      GAL_OPTIONS_RANGE_ANY,
-      GAL_OPTIONS_NOT_MANDATORY,
-      GAL_OPTIONS_NOT_SET
-    },
 
 
 
diff --git a/bin/crop/main.h b/bin/crop/main.h
index 919d186..f18a88c 100644
--- a/bin/crop/main.h
+++ b/bin/crop/main.h
@@ -99,7 +99,6 @@ struct cropparams
   gal_data_t          *polygon;  /* Input string of polygon vertices.     */
   uint8_t           polygonout;  /* ==1: Keep the inner polygon region.   */
   uint8_t          polygonsort;  /* Don't sort polygon vertices.          */
-  char            *polygonfile;  /* Name of input polygon file.           */
 
   /* Internal */
   size_t                 numin;  /* Number of input images.               */
diff --git a/bin/crop/ui.c b/bin/crop/ui.c
index 4c2e18b..b22e4c9 100644
--- a/bin/crop/ui.c
+++ b/bin/crop/ui.c
@@ -270,51 +270,6 @@ ui_parse_coordinate_mode(struct argp_option *option, char 
*arg,
 /**************************************************************/
 /***************       Sanity Check         *******************/
 /**************************************************************/
-
-/* Do polygon-related sanity checks that can be very low-level. */
-static void
-ui_check_polygon_from_ds9(struct cropparams *p)
-{
-  int ds9regmode;
-
-  /* This is only relevant when a region file is actually given. */
-  if(p->polygonfile)
-    {
-      /* These two options cannot be called together. */
-      if(p->polygon)
-        error(EXIT_FAILURE, errno, "'--polygon' and '--polygonfile' "
-              "cannot be given together. With the first you specify the "
-              "polygon vertices directly on the command-line. With the "
-              "second, you give a DS9 region file and the polygon "
-              "vertices are read from that.");
-      else
-        {
-          /* Extract the polygon and the coordinate mode. */
-          p->polygon=gal_ds9_reg_read_polygon(p->polygonfile,
-                                              &ds9regmode);
-          switch(ds9regmode)
-            {
-            case GAL_DS9_COORD_MODE_IMG: p->mode=IMGCROP_MODE_IMG; break;
-            case GAL_DS9_COORD_MODE_WCS: p->mode=IMGCROP_MODE_WCS; break;
-            default:
-              error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at "
-                    "'%s' to fix the problem. The output coordinate mode "
-                    "of 'gal_ds9_reg_read_polygon' (%d) isn't recognized "
-                    "by this function", __func__, PACKAGE_BUGREPORT,
-                    ds9regmode);
-            }
-        }
-
-      /* Clean up. */
-      free(p->polygonfile);
-      p->polygonfile=NULL;
-    }
-}
-
-
-
-
-
 /* Read and check ONLY the options. When arguments are involved, do the
    check in 'ui_check_options_and_arguments'. */
 static void
@@ -323,10 +278,23 @@ ui_read_check_only_options(struct cropparams *p)
   double *darray;
   int i, checksum;
 
-  /* If a DS9 region file should be used for the polygon, read it. This is
-     done first for two reasons. 1) It can change the value of '--mode'. 2)
-     It will set the '--polygon' option's value (if not set). */
-  ui_check_polygon_from_ds9(p);
+  /* If it's on the polygon mode and a filename was passed to polygon, then
+     we have to set the mode. It can change the value of '--mode', so this
+     is checked first. */
+  if(p->polygon && p->polygon->status)
+    {
+      switch(p->polygon->status)
+        {
+          case GAL_DS9_COORD_MODE_IMG: p->mode=IMGCROP_MODE_IMG; break;
+          case GAL_DS9_COORD_MODE_WCS: p->mode=IMGCROP_MODE_WCS; break;
+          default:
+            error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at "
+                  "'%s' to fix the problem. The output coordinate mode "
+                  "of 'gal_ds9_reg_read_polygon' (%d) isn't recognized "
+                  "by this function", __func__, PACKAGE_BUGREPORT,
+                  p->polygon->status);
+        }
+    }
 
   /* Make sure that only one of the crop definitions is given. */
   checksum = ( (p->center!=NULL)
diff --git a/bin/crop/ui.h b/bin/crop/ui.h
index d6f4326..9a34fa2 100644
--- a/bin/crop/ui.h
+++ b/bin/crop/ui.h
@@ -70,7 +70,6 @@ enum option_keys_enum
   UI_KEY_HENDWCS,
   UI_KEY_POLYGONOUT,
   UI_KEY_POLYGONSORT,
-  UI_KEY_POLYGONFILE,
   UI_KEY_CHECKCENTER,
   UI_KEY_PRIMARYIMGHDU,
 };
diff --git a/bin/table/args.h b/bin/table/args.h
index 91991d3..7e07bff 100644
--- a/bin/table/args.h
+++ b/bin/table/args.h
@@ -224,7 +224,7 @@ struct argp_option program_options[] =
     {
       "polygon",
       UI_KEY_POLYGON,
-      "FLT:FLT[,...]",
+      "STR,FLT:FLT[,...]",
       0,
       "Polygon for '--inpolygon' or '--outpolygon'.",
       UI_GROUP_OUTROWS,
@@ -236,19 +236,6 @@ struct argp_option program_options[] =
       gal_options_parse_colon_sep_csv
     },
     {
-      "polygonfile",
-      UI_KEY_POLYGONFILE,
-      "REG",
-      0,
-      "Polygon filename for '--inpolygon' or '--outpolygon'.",
-      UI_GROUP_OUTROWS,
-      &p->polygonfile,
-      GAL_TYPE_STRING,
-      GAL_OPTIONS_RANGE_ANY,
-      GAL_OPTIONS_NOT_MANDATORY,
-      GAL_OPTIONS_NOT_SET
-    },
-    {
       "equal",
       UI_KEY_EQUAL,
       "STR,FLT[,...]",
diff --git a/bin/table/main.h b/bin/table/main.h
index 11235bd..065302a 100644
--- a/bin/table/main.h
+++ b/bin/table/main.h
@@ -98,7 +98,6 @@ struct tableparams
   gal_data_t       *inpolygon;  /* Columns to check if inside polygon.  */
   gal_data_t      *outpolygon;  /* Columns to check if outside polygon. */
   gal_data_t         *polygon;  /* Values of vertices of the polygon.   */
-  char           *polygonfile;  /* Name of input polygon file           */
   gal_data_t           *equal;  /* Values to keep in output.            */
   gal_data_t        *notequal;  /* Values to not include in output.     */
   char                  *sort;  /* Column name or number for sorting.   */
diff --git a/bin/table/ui.c b/bin/table/ui.c
index 50845b9..2751230 100644
--- a/bin/table/ui.c
+++ b/bin/table/ui.c
@@ -222,37 +222,6 @@ parse_opt(int key, char *arg, struct argp_state *state)
 /**************************************************************/
 /***************       Sanity Check         *******************/
 /**************************************************************/
-/* Do polygon-related sanity checks */
-static void
-ui_check_polygon_from_ds9(struct tableparams *p)
-{
-  int ds9regmode;
-
-  /* This is only relevant when a region file is actually given. */
-  if(p->polygonfile)
-    {
-      /* These two options cannot be called together. */
-      if(p->polygon)
-       error(EXIT_FAILURE, errno, "'--polygon' and '--polygonfile' "
-              "cannot be given together. With the first you specify the "
-              "polygon vertices directly on the command-line. With the "
-              "second, you give a DS9 region file and the polygon "
-              "vertices are read from that.");
-
-      /* Extract the polygon and the coordinate mode. */
-      else
-        p->polygon=gal_ds9_reg_read_polygon(p->polygonfile, &ds9regmode);
-
-      /* Clean up. */
-      free(p->polygonfile);
-      p->polygonfile=NULL;
-    }
-}
-
-
-
-
-
 /* Read and check ONLY the options. When arguments are involved, do the
    check in 'ui_check_options_and_arguments'. */
 static void
@@ -261,10 +230,6 @@ ui_read_check_only_options(struct tableparams *p)
   double *darr;
   gal_data_t *tmp;
 
-  /* If a polygon filename is given, use it. This is done first because it
-     can set the '--polygon' option's value. */
-  ui_check_polygon_from_ds9(p);
-
   /* Check if the format of the output table is valid, given the type of
      the output. */
   gal_tableintern_check_fits_format(p->cp.output, p->cp.tableformat);
diff --git a/bin/table/ui.h b/bin/table/ui.h
index 8f13311..a898b19 100644
--- a/bin/table/ui.h
+++ b/bin/table/ui.h
@@ -73,7 +73,6 @@ enum option_keys_enum
   UI_KEY_ROWRANDOM,
   UI_KEY_INPOLYGON,
   UI_KEY_OUTPOLYGON,
-  UI_KEY_POLYGONFILE,
   UI_KEY_CATCOLUMNRAWNAME,
 };
 
diff --git a/lib/ds9.c b/lib/ds9.c
index 707665f..fbea66b 100644
--- a/lib/ds9.c
+++ b/lib/ds9.c
@@ -40,22 +40,20 @@ along with Gnuastro. If not, see 
<http://www.gnu.org/licenses/>.
 /* Read the polygon specified in the given DS9 region file and parse it in
    the standard format. */
 gal_data_t *
-gal_ds9_reg_read_polygon(char *filename, int *coordmode)
+gal_ds9_reg_read_polygon(char *filename)
 {
   FILE *fp;
   char *polygonstr;
   gal_data_t *out=NULL;
   size_t commacounter=0;
   size_t plinelen, linesize=10, lineno=0;
+  int coordmode=GAL_DS9_COORD_MODE_INVALID;
   char *c, *line, *ds9regstart="# Region file format: DS9";
   char *polygonformaterr="It is expected for the line to have "
     "this format: 'polygon(AAA,BBB,...)'. Where 'AAA' and 'BBB' "
     "are numbers and '...' signifies that any number of points "
     "are possible";
 
-  /* Initialize 'coordmode'. */
-  *coordmode=GAL_DS9_COORD_MODE_INVALID;
-
   /* Allocate size to the lines on the file and check if it was sucessfull.
      The getline function reallocs the necessary memory. */
   errno=0;
@@ -92,13 +90,13 @@ gal_ds9_reg_read_polygon(char *filename, int *coordmode)
       if( !strcmp(line, "fk5\n") || !strcmp(line, "image\n") )
         {
           /* Make sure it hasn't been called more than once. */
-          if(*coordmode!=GAL_DS9_COORD_MODE_INVALID)
+          if(coordmode!=GAL_DS9_COORD_MODE_INVALID)
             error_at_line(EXIT_FAILURE, 0, filename, lineno,
                           "more than one coordinate line defined");
 
           /* Set the proper mode. */
-          if(!strcmp(line, "fk5\n")) *coordmode=GAL_DS9_COORD_MODE_WCS;
-          else                       *coordmode=GAL_DS9_COORD_MODE_IMG;
+          if(!strcmp(line, "fk5\n")) coordmode=GAL_DS9_COORD_MODE_WCS;
+          else                       coordmode=GAL_DS9_COORD_MODE_IMG;
 
           /* Stop parsing the file if the polygon has also been found by
              this point (we don't need any more information, no need to
@@ -135,12 +133,12 @@ gal_ds9_reg_read_polygon(char *filename, int *coordmode)
           /* Stop parsing the file if the coordinate mode has also been
              found by this point (we don't need any more information, no
              need to waste the user's CPU and time). */
-          if(*coordmode!=GAL_DS9_COORD_MODE_INVALID) break;
+          if(coordmode!=GAL_DS9_COORD_MODE_INVALID) break;
         }
     }
 
   /* If no coordinate mode was found in the file, print an error. */
-  if(*coordmode==GAL_DS9_COORD_MODE_INVALID)
+  if(coordmode==GAL_DS9_COORD_MODE_INVALID)
     error(EXIT_FAILURE, 0, "%s: no coordinate mode found! "
           "We expect one line to be either 'fk5' or 'image'",
           filename);
@@ -152,6 +150,9 @@ gal_ds9_reg_read_polygon(char *filename, int *coordmode)
           "file given to '--polygonfile' option. %s", filename,
           polygonformaterr);
 
+  /* Write the coordinate mode into the status component. */
+  out->status = coordmode;
+
   /* Clean up and return. */
   free(line);
   fclose(fp);
diff --git a/lib/gnuastro/ds9.h b/lib/gnuastro/ds9.h
index 41e5719..3aef2fe 100644
--- a/lib/gnuastro/ds9.h
+++ b/lib/gnuastro/ds9.h
@@ -63,7 +63,7 @@ enum gal_ds9_coord_modes
 
 
 gal_data_t *
-gal_ds9_reg_read_polygon(char *filename, int *coordmode);
+gal_ds9_reg_read_polygon(char *filename);
 
 
 
diff --git a/lib/options.c b/lib/options.c
index 2dbbb04..6149840 100644
--- a/lib/options.c
+++ b/lib/options.c
@@ -31,6 +31,7 @@ along with Gnuastro. If not, see 
<http://www.gnu.org/licenses/>.
 #include <gnuastro/wcs.h>
 #include <gnuastro/git.h>
 #include <gnuastro/txt.h>
+#include <gnuastro/ds9.h>
 #include <gnuastro/fits.h>
 #include <gnuastro/list.h>
 #include <gnuastro/data.h>
@@ -1529,8 +1530,13 @@ gal_options_parse_colon_sep_csv(struct argp_option 
*option, char *arg,
         error_at_line(EXIT_FAILURE, 0, filename, lineno, "no value "
                       "given to '--%s'", option->name);
 
-      /* Parse the desired format and put it in this option's pointer. */
-      dataset=gal_options_parse_colon_sep_csv_raw(arg, filename, lineno);
+      /* Check if the argument is a string (it contains a ':' or a ',') or
+         a filename. Then parse the desired format and put it in this
+         option's pointer. */
+      if( strchr(arg, ',')==NULL && strchr(arg, ':')==NULL )
+        dataset=gal_ds9_reg_read_polygon(arg);
+      else
+        dataset=gal_options_parse_colon_sep_csv_raw(arg, filename, lineno);
 
       /* Add the given dataset to the end of an existing dataset. */
       existing = *(gal_data_t **)(option->value);