[gnuastro-commits] master 22d0fba 089/113: Imported recent work in master, no conflicts

[Mohammad Akhlaghi]

branch: master
commit 22d0fbaa2faa01b654ff2b76abdc80e4a9319830
Merge: a8428fe 668599c
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Imported recent work in master, no conflicts
    
    There weren't any conflicts in this merge.
---
 NEWS                             |   6 ++-
 bin/arithmetic/operands.c        |   2 +
 bin/fits/args.h                  |  13 +++++
 bin/fits/fits.c                  |  69 +++++++++++++++++++------
 bin/fits/main.h                  |  33 ++++++------
 bin/fits/ui.c                    |  10 +++-
 bin/fits/ui.h                    |   3 +-
 bin/mkcatalog/main.h             |   4 +-
 bin/mkcatalog/ui.c               |   6 +--
 bin/mkcatalog/upperlimit.c       |   8 +--
 bin/mknoise/main.h               |   2 +-
 bin/mknoise/mknoise.c            |   2 +-
 bin/mknoise/ui.c                 |   2 +-
 bin/mkprof/main.h                |   2 +-
 bin/mkprof/mkprof.c              |   2 +-
 bin/mkprof/mkprof.h              |   2 +-
 bin/mkprof/ui.c                  |  15 ++----
 bin/segment/clumps.c             | 109 +++++++++++++++++++++------------------
 doc/gnuastro.texi                |  27 ++++++++--
 lib/checkset.c                   |   3 +-
 lib/fits.c                       |   4 +-
 lib/gnuastro-internal/checkset.h |   2 +-
 lib/gnuastro-internal/timing.h   |   2 +-
 lib/gnuastro/type.h              |   6 ++-
 lib/timing.c                     |  10 +++-
 25 files changed, 218 insertions(+), 126 deletions(-)

diff --git a/NEWS b/NEWS
index d6191b1..e84f45c 100644
--- a/NEWS
+++ b/NEWS
@@ -12,6 +12,9 @@ GNU Astronomy Utilities NEWS                          -*- 
outline -*-
   Arithmetic:
     --onedasimage: write output as an image if it has one dimension, not table.
 
+  Fits:
+    --numhdus: prints the number of HDUs in the given FITS file.
+
   NoiseChisel:
     - New outlier identification algorithm for quantile thresholds. This is
       very useful when there are extended and bright sources in the
@@ -101,7 +104,8 @@ GNU Astronomy Utilities NEWS                          -*- 
outline -*-
   bug #54493: Warp crashes when type isn't set.
   bug #54526: Invalid r, q and truncation of point profiles in MakeProfiles.
   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.
 
 
 
diff --git a/bin/arithmetic/operands.c b/bin/arithmetic/operands.c
index 92ebcc4..400a25d 100644
--- a/bin/arithmetic/operands.c
+++ b/bin/arithmetic/operands.c
@@ -127,6 +127,7 @@ operands_remove_name(struct arithmeticparams *p, char *name)
   /* Nothing in the list points to it now. So we can safely modify and
      return it. */
   free(removed->name);
+  removed->next=NULL;
   removed->name=NULL;
   return removed;
 }
@@ -218,6 +219,7 @@ operands_copy_named(struct arithmeticparams *p, char *name)
             out=gal_data_copy(tmp);
             free(out->name);
             out->name=NULL;
+            out->next=NULL;
           }
         /* The named operand is not used any more. Remove it from the list
            of named datasets and continue. */
diff --git a/bin/fits/args.h b/bin/fits/args.h
index 76baf3c..372c7c1 100644
--- a/bin/fits/args.h
+++ b/bin/fits/args.h
@@ -76,6 +76,19 @@ struct argp_option program_options[] =
       GAL_OPTIONS_NOT_MANDATORY,
       GAL_OPTIONS_NOT_SET
     },
+    {
+      "numhdus",
+      UI_KEY_NUMHDUS,
+      0,
+      0,
+      "Print number of HDUs in the given FITS file.",
+      UI_GROUP_EXTENSION,
+      &p->numhdus,
+      GAL_OPTIONS_NO_ARG_TYPE,
+      GAL_OPTIONS_RANGE_0_OR_1,
+      GAL_OPTIONS_NOT_MANDATORY,
+      GAL_OPTIONS_NOT_SET
+    },
 
 
 
diff --git a/bin/fits/fits.c b/bin/fits/fits.c
index 55c278b..2c47eed 100644
--- a/bin/fits/fits.c
+++ b/bin/fits/fits.c
@@ -221,8 +221,11 @@ fits_print_extension_info(struct fitsparams *p)
         }
     }
 
+  /* Close the file. */
+  fits_close_file(fptr, &status);
 
-  /* Print the resutls. */
+
+  /* Print the results. */
   if(!p->cp.quiet)
     {
       printf("%s\nRun on %s-----\n", PROGRAM_STRING, ctime(&p->rawtime));
@@ -244,6 +247,30 @@ fits_print_extension_info(struct fitsparams *p)
 
 
 static void
+fits_hdu_number(struct fitsparams *p)
+{
+  fitsfile *fptr;
+  int numhdu, status=0;
+
+  /* Read the first extension (necessary for reading the rest). */
+  fptr=gal_fits_hdu_open(p->filename, "0", READONLY);
+
+  /* Get the number of HDUs. */
+  if( fits_get_num_hdus(fptr, &numhdu, &status) )
+    gal_fits_io_error(status, "finding number of HDUs");
+
+  /* Close the file. */
+  fits_close_file(fptr, &status);
+
+  /* Print the result. */
+  printf("%d\n", numhdu);
+}
+
+
+
+
+
+static void
 fits_hdu_remove(struct fitsparams *p, int *r)
 {
   char *hdu;
@@ -332,24 +359,32 @@ fits(struct fitsparams *p)
 
     /* HDU, functions defined here. */
     case FITS_MODE_HDU:
-      if(p->copy)
-        {
-          fits_hdu_copy(p, 0, &r);
-          printhduinfo=0;
-        }
-      if(p->cut)
-        {
-          fits_hdu_copy(p, 1, &r);
-          printhduinfo=0;
-        }
-      if(p->remove)
+      /* Options that must be called alone. */
+      if(p->numhdus)
+        fits_hdu_number(p);
+
+      /* Options that can be called together. */
+      else
         {
-          fits_hdu_remove(p, &r);
-          printhduinfo=0;
-        }
+          if(p->copy)
+            {
+              fits_hdu_copy(p, 0, &r);
+              printhduinfo=0;
+            }
+          if(p->cut)
+            {
+              fits_hdu_copy(p, 1, &r);
+              printhduinfo=0;
+            }
+          if(p->remove)
+            {
+              fits_hdu_remove(p, &r);
+              printhduinfo=0;
+            }
 
-      if(printhduinfo)
-        fits_print_extension_info(p);
+          if(printhduinfo)
+            fits_print_extension_info(p);
+        }
       break;
 
     /* Not recognized. */
diff --git a/bin/fits/main.h b/bin/fits/main.h
index 78681f0..43edc06 100644
--- a/bin/fits/main.h
+++ b/bin/fits/main.h
@@ -53,22 +53,23 @@ enum fits_mode
 struct fitsparams
 {
   /* From the environment. */
-  struct gal_options_common_params cp;  /* Common parameters.       */
-  int  hdu_in_commandline;     /* HDU wasn't given in config. file. */
-  char          *filename;     /* Name of input file.               */
-  gal_list_str_t  *remove;     /* Remove extensions from a file.    */
-  gal_list_str_t    *copy;     /* Copy extensions to output.        */
-  gal_list_str_t     *cut;     /* Copy ext. to output and remove.   */
-  uint8_t    printallkeys;     /* Print all the header keywords.    */
-  uint8_t            date;     /* Set DATE to current time.         */
-  gal_list_str_t    *asis;     /* Strings to write asis.            */
-  gal_list_str_t  *delete;     /* Keywords to remove.               */
-  gal_list_str_t  *rename;     /* Rename a keyword.                 */
-  gal_list_str_t  *update;     /* For keywords to update.           */
-  gal_list_str_t   *write;     /* Full arg. for keywords to add.    */
-  gal_list_str_t *history;     /* HISTORY value.                    */
-  gal_list_str_t *comment;     /* COMMENT value.                    */
-  uint8_t     quitonerror;     /* Quit if an error occurs.          */
+  struct gal_options_common_params cp;  /* Common parameters.           */
+  int  hdu_in_commandline;     /* HDU wasn't given in config. file.     */
+  char          *filename;     /* Name of input file.                   */
+  gal_list_str_t  *remove;     /* Remove extensions from a file.        */
+  gal_list_str_t    *copy;     /* Copy extensions to output.            */
+  gal_list_str_t     *cut;     /* Copy ext. to output and remove.       */
+  uint8_t         numhdus;     /* Print number of HDUs in FITS file.    */
+  uint8_t    printallkeys;     /* Print all the header keywords.        */
+  uint8_t            date;     /* Set DATE to current time.             */
+  gal_list_str_t    *asis;     /* Strings to write asis.                */
+  gal_list_str_t  *delete;     /* Keywords to remove.                   */
+  gal_list_str_t  *rename;     /* Rename a keyword.                     */
+  gal_list_str_t  *update;     /* For keywords to update.               */
+  gal_list_str_t   *write;     /* Full arg. for keywords to add.        */
+  gal_list_str_t *history;     /* HISTORY value.                        */
+  gal_list_str_t *comment;     /* COMMENT value.                        */
+  uint8_t     quitonerror;     /* Quit if an error occurs.              */
 
   /* Internal: */
   int                         mode;  /* Operating on HDUs or keywords.  */
diff --git a/bin/fits/ui.c b/bin/fits/ui.c
index 787b9e4..6482d17 100644
--- a/bin/fits/ui.c
+++ b/bin/fits/ui.c
@@ -237,14 +237,20 @@ ui_read_check_only_options(struct fitsparams *p)
     }
 
   /* Same for the extension-related options */
-  if( p->remove || p->copy || p->cut )
+  if( p->remove || p->copy || p->cut || p->numhdus)
     {
       /* A small sanity check. */
       if(p->mode!=FITS_MODE_INVALID)
         error(EXIT_FAILURE, 0, "extension and keyword manipulation options "
               "cannot be called together");
 
-      /* Set the mode and turn on the `needshdu' flag. */
+      /* Unlike the rest of the HDU-related options, `--numhdus' must be
+         called alone. */
+      if(p->numhdus==1 && (p->remove || p->copy || p->cut) )
+        error(EXIT_FAILURE, 0, "`--numhdus' option must be called alone (it "
+              "cannot be called with other extension or keyword options)");
+
+      /* Set the operating mode. */
       p->mode=FITS_MODE_HDU;
 
       /* Make sure the output name is set. */
diff --git a/bin/fits/ui.h b/bin/fits/ui.h
index e2668c8..be7fccf 100644
--- a/bin/fits/ui.h
+++ b/bin/fits/ui.h
@@ -43,7 +43,7 @@ enum program_args_groups
 
 /* Available letters for short options:
 
-   b e f g i j l m n s v x y z
+   b e f g i j l m s v x y z
    A B E G J L O W X Y
  */
 enum option_keys_enum
@@ -52,6 +52,7 @@ enum option_keys_enum
   UI_KEY_REMOVE       = 'R',
   UI_KEY_COPY         = 'C',
   UI_KEY_CUT          = 'k',
+  UI_KEY_NUMHDUS      = 'n',
   UI_KEY_PRINTALLKEYS = 'p',
   UI_KEY_ASIS         = 'a',
   UI_KEY_DELETE       = 'd',
diff --git a/bin/mkcatalog/main.h b/bin/mkcatalog/main.h
index b2f8e28..349b3c2 100644
--- a/bin/mkcatalog/main.h
+++ b/bin/mkcatalog/main.h
@@ -218,8 +218,8 @@ struct mkcatalogparams
   pthread_mutex_t       mutex;  /* Mutex to change the total numbers.   */
   size_t      clumprowsfilled;  /* No. filled clump rows at this moment.*/
   gsl_rng                *rng;  /* Main random number generator.        */
-  uint64_t               seed;  /* Random number generator seed.        */
-  const char         *rngname;  /* Name of random number generator.     */
+  unsigned long int  rng_seed;  /* Random number generator seed.        */
+  const char        *rng_name;  /* Name of random number generator.     */
   size_t               rngmin;  /* Minimum possible value of RNG.       */
   size_t              rngdiff;  /* Difference of RNG max and min.       */
   uint8_t      uprangewarning;  /* A warning must be printed.           */
diff --git a/bin/mkcatalog/ui.c b/bin/mkcatalog/ui.c
index 090cfe2..e038270 100644
--- a/bin/mkcatalog/ui.c
+++ b/bin/mkcatalog/ui.c
@@ -1448,7 +1448,7 @@ ui_preparations_upperlimit(struct mkcatalogparams *p)
           "that is reported as the upper-limit");
 
   /* Set the random number generator. */
-  p->rng=gal_checkset_gsl_rng(p->envseed, &p->rngname, &p->seed);
+  p->rng=gal_checkset_gsl_rng(p->envseed, &p->rng_name, &p->rng_seed);
 
   /* Keep the minimum and maximum values of the random number generator. */
   p->rngmin=gsl_rng_min(p->rng);
@@ -1657,8 +1657,8 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct 
mkcatalogparams *p)
                p->upmaskfile, p->cp.hdu);
       if(p->upperlimit)
         {
-          printf("  - Random number generator name: %s\n", p->rngname);
-          printf("  - Random number generator seed: %"PRIu64"\n", p->seed);
+          printf("  - Random number generator name: %s\n", p->rng_name);
+          printf("  - Random number generator seed: %lu\n", p->rng_seed);
         }
     }
 }
diff --git a/bin/mkcatalog/upperlimit.c b/bin/mkcatalog/upperlimit.c
index c28be22..96e9600 100644
--- a/bin/mkcatalog/upperlimit.c
+++ b/bin/mkcatalog/upperlimit.c
@@ -317,11 +317,11 @@ upperlimit_write_comments(struct mkcatalogparams *p,
       gal_list_str_add(comments, str, 0);
     }
 
-  if( asprintf(&str, "Random number generator name: %s", p->rngname)<0 )
+  if( asprintf(&str, "Random number generator name: %s", p->rng_name)<0 )
     error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
   gal_list_str_add(comments, str, 0);
 
-  if( asprintf(&str, "Random number generator seed: %"PRIu64, p->seed)<0 )
+  if( asprintf(&str, "Random number generator seed: %lu", p->rng_seed)<0 )
     error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
   gal_list_str_add(comments, str, 0);
 
@@ -770,7 +770,7 @@ upperlimit_calculate(struct mkcatalog_passparams *pp)
   struct mkcatalogparams *p=pp->p;
 
   /* First find the upper limit magnitude for this object. */
-  upperlimit_one_tile(pp, pp->tile, p->seed+pp->object, 0);
+  upperlimit_one_tile(pp, pp->tile, p->rng_seed+pp->object, 0);
 
   /* If a clumps image is present (a clump catalog is requested) and this
      object has clumps, then find the upper limit magnitude for the clumps
@@ -798,7 +798,7 @@ upperlimit_calculate(struct mkcatalog_passparams *pp)
          IDs. */
       for(i=0;i<pp->clumpsinobj;++i)
         {
-          seed = p->seed + p->numobjects + p->numclumps * pp->object + i;
+          seed = p->rng_seed + p->numobjects + p->numclumps * pp->object + i;
           upperlimit_one_tile(pp, &clumptiles[i], seed, i+1);
         }
 
diff --git a/bin/mknoise/main.h b/bin/mknoise/main.h
index c443f2c..634a08b 100644
--- a/bin/mknoise/main.h
+++ b/bin/mknoise/main.h
@@ -55,7 +55,7 @@ struct mknoiseparams
   double      background;    /* Background in units of brightness.       */
   gsl_rng           *rng;    /* Main instance of random number generator.*/
   const char   *rng_name;    /* The type/name of the Random number gen.  */
-  uint64_t      rng_seed;    /* Seed of Random number generator.         */
+  unsigned long rng_seed;    /* Seed of Random number generator.         */
   time_t         rawtime;    /* Starting time of the program.            */
 };
 
diff --git a/bin/mknoise/mknoise.c b/bin/mknoise/mknoise.c
index 5c9d085..954fe85 100644
--- a/bin/mknoise/mknoise.c
+++ b/bin/mknoise/mknoise.c
@@ -91,7 +91,7 @@ convertsaveoutput(struct mknoiseparams *p)
                             "Random number generator (by GSL) type.",
                             0, NULL);
   strcpy(keyname5, "RNGSEED");
-  gal_fits_key_list_add_end(&headers, GAL_TYPE_UINT64, keyname5, 0,
+  gal_fits_key_list_add_end(&headers, GAL_TYPE_ULONG, keyname5, 0,
                             &p->rng_seed, 0,
                             "Random number generator (by GSL) seed.",
                             0, NULL);
diff --git a/bin/mknoise/ui.c b/bin/mknoise/ui.c
index 54a807d..471328d 100644
--- a/bin/mknoise/ui.c
+++ b/bin/mknoise/ui.c
@@ -400,7 +400,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct 
mknoiseparams *p)
              ctime(&p->rawtime));
       sprintf(message, "Random number generator type: %s", p->rng_name);
       gal_timing_report(NULL, message, 1);
-      sprintf(message, "Random number generator seed: %"PRIu64, p->rng_seed);
+      sprintf(message, "Random number generator seed: %lu", p->rng_seed);
       gal_timing_report(NULL, message, 1);
     }
 }
diff --git a/bin/mkprof/main.h b/bin/mkprof/main.h
index aa908bc..53f6699 100644
--- a/bin/mkprof/main.h
+++ b/bin/mkprof/main.h
@@ -177,7 +177,7 @@ struct mkprofparams
   float                  *t;  /* Truncation distance.                     */
   gsl_rng              *rng;  /* Main instance of random number generator.*/
   const char      *rng_name;  /* Name of random number generator.         */
-  uint64_t         rng_seed;  /* Fixed seed of random number generator.   */
+  unsigned long    rng_seed;  /* Fixed seed of random number generator.   */
   time_t            rawtime;  /* Starting time of the program.            */
   double               *cat;  /* Input catalog.                           */
   gal_data_t           *log;  /* Log data to be printed.                  */
diff --git a/bin/mkprof/mkprof.c b/bin/mkprof/mkprof.c
index 2f575b4..997e4c8 100644
--- a/bin/mkprof/mkprof.c
+++ b/bin/mkprof/mkprof.c
@@ -225,7 +225,7 @@ saveindividual(struct mkonthread *mkp)
   gal_fits_key_list_add(&keys, GAL_TYPE_STRING, "RNGNAME", 0,
                         (void *)(p->rng_name), 0,
                         "Name of random number generator", 0, NULL);
-  gal_fits_key_list_add(&keys, GAL_TYPE_LONG, "RNGSEED", 0,
+  gal_fits_key_list_add(&keys, GAL_TYPE_ULONG, "RNGSEED", 0,
                         &mkp->rng_seed, 0, "Seed of random number generator",
                         0, NULL);
   gal_fits_key_list_add(&keys, GAL_TYPE_SIZE_T, "NUMRANDOM", 0,
diff --git a/bin/mkprof/mkprof.h b/bin/mkprof/mkprof.h
index c97fcdc..9794d03 100644
--- a/bin/mkprof/mkprof.h
+++ b/bin/mkprof/mkprof.h
@@ -48,7 +48,7 @@ struct mkonthread
   long            *onaxes;   /* Sides of the unover-sampled image.    */
   long        fpixel_i[3];   /* fpixel_i before running overlap.      */
   int          correction;   /* ==1: correct the pixels afterwards.   */
-  long           rng_seed;   /* Seed used to generate this profile.   */
+  unsigned long  rng_seed;   /* Seed used to generate this profile.   */
 
   /* Random number generator: */
   gsl_rng            *rng;   /* Copy of main random number generator. */
diff --git a/bin/mkprof/ui.c b/bin/mkprof/ui.c
index 7cc505c..5475d63 100644
--- a/bin/mkprof/ui.c
+++ b/bin/mkprof/ui.c
@@ -1759,16 +1759,11 @@ ui_print_intro(struct mkprofparams *p)
     error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
   gal_timing_report(NULL, jobname, 1);
   free(jobname);
-  if(p->envseed)
-    {
-      if( asprintf(&jobname, "RNG seed for all profiles: %lu",
-                   gsl_rng_default_seed)<0 )
-        error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
-      gal_timing_report(NULL, jobname, 1);
-      free(jobname);
-    }
-  else
-    gal_timing_report(NULL, "RNG seed differs for each profile.", 1);
+
+  if( asprintf(&jobname, "Basic RNG seed: %lu", p->rng_seed)<0 )
+    error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
+  gal_timing_report(NULL, jobname, 1);
+  free(jobname);
 
   if(p->kernel==NULL)
     {
diff --git a/bin/segment/clumps.c b/bin/segment/clumps.c
index cead77b..5f15794 100644
--- a/bin/segment/clumps.c
+++ b/bin/segment/clumps.c
@@ -229,56 +229,62 @@ clumps_correct_sky_labels_for_check(struct 
clumps_thread_params *cltprm,
   size_t len=cltprm->numinitclumps+1;
   struct segmentparams *p=cltprm->clprm->p;
 
-  /* If there are no clumps in this tile, then this function can be
-     ignored. */
-  if(cltprm->snind->size==0) return;
-
-
-  /* A small sanity check. */
-  if(gal_tile_block(tile)!=p->clabel)
-    error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to address "
-          "the problem. `tile->block' must point to the `clabel' dataset",
-          __func__, PACKAGE_BUGREPORT);
-
-
-  /* Allocate a dataset with the new indexs, note that it will need to have
-     one element for each initial label (the excluded clumps need to be set
-     to zero). So we also need to clear the allocated space. */
-  newinds=gal_data_alloc(NULL, p->clabel->type, 1, &len, NULL, 0,
-                         p->cp.minmapsize, NULL, NULL, NULL);
-
-
-  /* Get the next available label for these clumps. If more than one thread
-     was used, we are first going to lock the mutex (so no other thread
-     changes these values), we will then read the shared number for this
-     thread to use, then update the shared number and finally, unlock the
-     mutex so other threads can do the same when they get to this point. */
-  if(p->cp.numthreads>1) pthread_mutex_lock(&cltprm->clprm->labmutex);
-  curlab        = p->numclumps+1;   /* Note that counting begins from 1. */
-  p->numclumps += cltprm->snind->size;
-  if(p->cp.numthreads>1) pthread_mutex_unlock(&cltprm->clprm->labmutex);
-
-
-  /* Initialize the newinds array to GAL_LABEL_INIT (which be used as a new
-     label for all the clumps that must be removed. */
-  lf = (l=newinds->array) + newinds->size;
-  do *l++=GAL_LABEL_INIT; while(l<lf);
+  /* If any of the clumps must be kept (`cltprm->snind->size!=0'), then
+     re-label them for the check image. Otherwise, remove all clumps. */
+  if(cltprm->snind->size)
+    {
+      /* A small sanity check. */
+      if(gal_tile_block(tile)!=p->clabel)
+        error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to "
+              "address the problem. `tile->block' must point to the "
+              "`clabel' dataset", __func__, PACKAGE_BUGREPORT);
+
+
+      /* Allocate a dataset with the new indexs, note that it will need to
+         have one element for each initial label (the excluded clumps need
+         to be set to zero). So we also need to clear the allocated
+         space. */
+      newinds=gal_data_alloc(NULL, p->clabel->type, 1, &len, NULL, 0,
+                             p->cp.minmapsize, NULL, NULL, NULL);
+
+
+      /* Get the next available label for these clumps. If more than one
+         thread was used, we are first going to lock the mutex (so no other
+         thread changes these values), we will then read the shared number
+         for this thread to use, then update the shared number and finally,
+         unlock the mutex so other threads can do the same when they get to
+         this point. */
+      if(p->cp.numthreads>1) pthread_mutex_lock(&cltprm->clprm->labmutex);
+      curlab        = p->numclumps+1; /* Note that counting begins from 1. */
+      p->numclumps += cltprm->snind->size;
+      if(p->cp.numthreads>1) pthread_mutex_unlock(&cltprm->clprm->labmutex);
+
+
+      /* Initialize the newinds array to GAL_LABEL_INIT (which be used as a
+         new label for all the clumps that must be removed. */
+      lf = (l=newinds->array) + newinds->size;
+      do *l++=GAL_LABEL_INIT; while(l<lf);
 
 
-  /* The new indexs array has been initialized to zero. So we just need to
-     go over the labels in `cltprm->sninds' and give them a value of
-     `curlab++'. */
-  ninds=newinds->array;
-  lf = (l=cltprm->snind->array) + cltprm->snind->size;
-  do { ninds[*l]=curlab++; *l=ninds[*l]; } while(++l<lf);
+      /* The new indexs array has been initialized to zero. So we just need
+         to go over the labels in `cltprm->sninds' and give them a value of
+         `curlab++'. */
+      ninds=newinds->array;
+      lf = (l=cltprm->snind->array) + cltprm->snind->size;
+      do { ninds[*l]=curlab++; *l=ninds[*l]; } while(++l<lf);
 
 
-  /* Go over this tile and correct the values. */
-  GAL_TILE_PARSE_OPERATE( tile, NULL, 0, 1,
-                          {if(*i>0) *i=ninds[ *(int32_t *)i ];} );
+      /* Go over this tile and correct the values. */
+      GAL_TILE_PARSE_OPERATE( tile, NULL, 0, 1,
+                              {if(*i>0) *i=ninds[ *(int32_t *)i ];} );
 
-  /* Clean up. */
-  gal_data_free(newinds);
+      /* Clean up. */
+      gal_data_free(newinds);
+    }
+  else
+    /* There were no usable clumps in this tile, so just set all the pixels
+       larger than zero (a clump) to `GAL_LABEL_INIT'. */
+    GAL_TILE_PARSE_OPERATE( tile, NULL, 0, 1, {*i=*i>0?GAL_LABEL_INIT:*i;} );
 }
 
 
@@ -472,11 +478,6 @@ clumps_find_make_sn_table(void *in_prm)
                                        cltprm.sn, cltprm.snind);
 
 
-          /* If there were no clumps, then just set the S/N table to NULL. */
-          if( cltprm.clprm->sn[ cltprm.id ].size==0 )
-            cltprm.snind=cltprm.sn=NULL;
-
-
           /* If the user wanted to check the steps, remove the clumps that
              weren't used from the `clabel' image (they have been already
              excluded from the table). */
@@ -484,6 +485,14 @@ clumps_find_make_sn_table(void *in_prm)
             clumps_correct_sky_labels_for_check(&cltprm, tile);
 
 
+          /* If there were no clumps, then just set the S/N table to
+             NULL. This must be done after the check image creation (if
+             necessary), because we use `cltprm.snind' as a proxy for the
+             check image.*/
+          if( cltprm.clprm->sn[ cltprm.id ].size==0 )
+            cltprm.snind=cltprm.sn=NULL;
+
+
           /* Clean up. */
           gal_data_free(cltprm.indexs);
         }
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index ec32028..704b9c0 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -2911,7 +2911,7 @@ omatter  0.3
 You can now tell CosmicCalculator to read this file for option values
 immediately using the @option{--config} option as shown below. Do you see
 how the output of the following command corresponds to the option values in
-@file{my-cosmology.txt} (previous command)?
+@file{my-cosmology.conf} (previous command)?
 
 @example
 $ astcosmiccal --config=my-cosmology.conf -z2
@@ -2976,9 +2976,9 @@ $ astwarp flat-ir/xdf-f160w.fits --rotate=20
 @end example
 
 @noindent
-Open the output and see the output. If your final image is already aligned
-with RA and Dec, you can simply use the @option{--align} option and let
-Warp calculate the necessary rotation.
+Open the output and see it. If your final image is already aligned with RA
+and Dec, you can simply use the @option{--align} option and let Warp
+calculate the necessary rotation and apply it.
 
 Warp can generally be used for any kind of pixel grid manipulation
 (warping). For example the outputs of the commands below will respectively
@@ -9862,6 +9862,17 @@ HDUs given to this option (see @ref{Automatic output}).
 
 @table @option
 
+@item -n
+@itemx --numhdus
+Print the number of extensions/HDUs in the given file. Note that this
+option must be called alone and will only print a single number. It is thus
+useful in scripts, for example when you need to do check the number of
+extensions in a FITS file.
+
+For a complete list of basic meta-data on the extensions in a FITS file,
+don't use any of the options in this section or in @ref{Keyword
+manipulation}. For more, see @ref{Invoking astfits}.
+
 @item -C STR
 @itemx --copy=STR
 Copy the specified extension into the output file, see explanations above.
@@ -23148,6 +23159,12 @@ Identifier for a @code{size_t} type. This is just an 
alias to
 respectively.
 @end deffn
 
+@deffn {Global integer}  GAL_TYPE_ULONG
+Identifier for a @code{unsigned long} type. This is just an alias to
+@code{uint32}, or @code{uint64} types for 32-bit, or 64-bit systems
+respectively.
+@end deffn
+
 @deffn {Global integer}  GAL_TYPE_LONG
 Identifier for a @code{long} type. This is just an alias to @code{int32},
 or @code{int64} types for 32-bit, or 64-bit systems respectively.
@@ -30657,7 +30674,7 @@ completely rely.
 @end quotation
 
 Please get in touch with the Gnuastro maintainer (currently Mohammad
-Akhlaghi, akhlaghi -at- gnu -dot- org) to follow the procedures. It is
+Akhlaghi, mohammad -at- akhlaghi -dot- org) to follow the procedures. It is
 possible to do this for each change (good for for a single contribution),
 and also more generally for all the changes/additions you do in the future
 within Gnuastro. So if you have already assigned the copyright of your work
diff --git a/lib/checkset.c b/lib/checkset.c
index b58e96f..063de37 100644
--- a/lib/checkset.c
+++ b/lib/checkset.c
@@ -50,7 +50,8 @@ along with Gnuastro. If not, see 
<http://www.gnu.org/licenses/>.
    environment. This function is designed to make the job easier for any
    program using GSL's RNG. If the user doesn't want to set the */
 gsl_rng *
-gal_checkset_gsl_rng(uint8_t envseed_bool, const char **name, uint64_t *seed)
+gal_checkset_gsl_rng(uint8_t envseed_bool, const char **name,
+                     unsigned long int *seed)
 {
   gsl_rng *rng;
 
diff --git a/lib/fits.c b/lib/fits.c
index ad6a854..9e6f77e 100644
--- a/lib/fits.c
+++ b/lib/fits.c
@@ -300,8 +300,8 @@ gal_fits_type_to_datatype(uint8_t type)
     case GAL_TYPE_STRING:           return TSTRING;
 
     /* Types that depend on the host system. The C standard says that the
-       `short', `int' and `long' types are ATLEAST 2, 2, 4 bytes, so be
-       safe, we will checking all of them for the 32-bit types.*/
+       `short', `int' and `long' types are ATLEAST 2, 2, 4 bytes, so to be
+       safe, we will check all of them for the 32-bit types.*/
     case GAL_TYPE_UINT16:
       w=2;
       if     ( sizeof(short)    == w )   return TUSHORT;
diff --git a/lib/gnuastro-internal/checkset.h b/lib/gnuastro-internal/checkset.h
index 204c325..e528b6e 100644
--- a/lib/gnuastro-internal/checkset.h
+++ b/lib/gnuastro-internal/checkset.h
@@ -55,7 +55,7 @@ __BEGIN_C_DECLS  /* From C++ preparations */
 /**************************************************************/
 gsl_rng *
 gal_checkset_gsl_rng(uint8_t envseed_bool, const char **name,
-                     uint64_t *seed);
+                     unsigned long int *seed);
 
 
 
diff --git a/lib/gnuastro-internal/timing.h b/lib/gnuastro-internal/timing.h
index d43d76a..245b1a0 100644
--- a/lib/gnuastro-internal/timing.h
+++ b/lib/gnuastro-internal/timing.h
@@ -52,7 +52,7 @@ __BEGIN_C_DECLS  /* From C++ preparations */
 #define GAL_TIMING_VERB_MSG_LENGTH_V     50
 #define GAL_TIMING_VERB_MSG_LENGTHS_2_V  65
 
-long
+unsigned long
 gal_timing_time_based_rng_seed();
 
 void
diff --git a/lib/gnuastro/type.h b/lib/gnuastro/type.h
index 975ce17..e3ae316 100644
--- a/lib/gnuastro/type.h
+++ b/lib/gnuastro/type.h
@@ -106,9 +106,11 @@ enum gal_types
 #endif
 
 #if GAL_CONFIG_SIZEOF_LONG == 4
-#define GAL_TYPE_LONG GAL_TYPE_INT32
+#define GAL_TYPE_LONG  GAL_TYPE_INT32
+#define GAL_TYPE_ULONG GAL_TYPE_UINT32
 #elif GAL_CONFIG_SIZEOF_LONG == 8
-#define GAL_TYPE_LONG GAL_TYPE_INT64
+#define GAL_TYPE_LONG  GAL_TYPE_INT64
+#define GAL_TYPE_ULONG GAL_TYPE_UINT64
 #endif
 
 
diff --git a/lib/timing.c b/lib/timing.c
index cdb88fb..86b66e4 100644
--- a/lib/timing.c
+++ b/lib/timing.c
@@ -31,8 +31,14 @@ along with Gnuastro. If not, see 
<http://www.gnu.org/licenses/>.
 
 /* Micro-second based timer, which can be used to generate random numbers.
    The type of `tv_sec' and `tv_usec' is `long int' (from the GNU C Library
-   manual), so this function will also return long. */
-long
+   manual). But the expected type used by GSL's random number generator is
+   `unsigned long int'. Since the only random number generator that is
+   currently in Gnuastro is GSL's (and it asks for seeds of type `unsigned
+   long int'), this function will return in `unsigned long int'. Note that
+   `unsigned long' will be able to hold any positive `long' integer, which
+   is the case for `tv_sec' and `tv_usec': they are both positive, while
+   the opposite isn't true. */
+unsigned long int
 gal_timing_time_based_rng_seed()
 {
   struct timeval tv;