[gnuastro-commits] master 01dfb1b 05/16: Some code management in Table

[Mohammad Akhlaghi]

branch: master
commit 01dfb1b8dd140febe0a18c2df7b83da096b4255a
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>

    Some code management in Table
    
    To make Table more clear (easy to read) and easy to use, some modifications
    were made (the function to print the column information is now in `ui.c'
    and it is broken up into several functions for more general usage. One of
    those new functions is now put in `lib/fits.c'.
---
 lib/fits.c          |   22 ++++++
 lib/gnuastro/fits.h |    3 +
 src/table/args.h    |    2 +-
 src/table/main.h    |    6 +-
 src/table/table.c   |   67 +---------------
 src/table/ui.c      |  213 +++++++++++++++++++++++++++++++++++++++------------
 6 files changed, 194 insertions(+), 119 deletions(-)

diff --git a/lib/fits.c b/lib/fits.c
index 922ba9a..c4091a5 100644
--- a/lib/fits.c
+++ b/lib/fits.c
@@ -1583,6 +1583,28 @@ gal_fits_tform_to_dtype(char tform)
 
 
 
+/* Get the size of a table HDU. CFITSIO doesn't use size_t, also we want to
+   check status here.*/
+void
+gal_fits_table_size(fitsfile *fitsptr, size_t *nrows, size_t *ncols)
+{
+  long lnrows;
+  int incols, status=0;
+
+  /* Read the sizes and put them in. */
+  fits_get_num_rows(fitsptr, &lnrows, &status);
+  fits_get_num_cols(fitsptr, &incols, &status);
+  *ncols=incols;
+  *nrows=lnrows;
+
+  /* Report an error if any was issued. */
+  gal_fits_io_error(status, NULL);
+}
+
+
+
+
+
 
 
 
diff --git a/lib/gnuastro/fits.h b/lib/gnuastro/fits.h
index 216fdb4..b061bf5 100644
--- a/lib/gnuastro/fits.h
+++ b/lib/gnuastro/fits.h
@@ -218,6 +218,9 @@ gal_fits_atof_correct_wcs(char *filename, char *hdu, int 
bitpix,
 int
 gal_fits_tform_to_dtype(char tform);
 
+void
+gal_fits_table_size(fitsfile *fitsptr, size_t *nrows, size_t *ncols);
+
 
 
 
diff --git a/src/table/args.h b/src/table/args.h
index 0583dcd..711ec8e 100644
--- a/src/table/args.h
+++ b/src/table/args.h
@@ -154,7 +154,7 @@ parse_opt(int key, char *arg, struct argp_state *state)
 
     /* Operating modes: */
     case 'i':
-      p->information=1;
+      p->up.information=1;
       p->up.informationset=1;
       break;
 
diff --git a/src/table/main.h b/src/table/main.h
index 7a15c05..ddfa234 100644
--- a/src/table/main.h
+++ b/src/table/main.h
@@ -42,8 +42,9 @@ along with Gnuastro. If not, see 
<http://www.gnu.org/licenses/>.
 /* User interface structure. */
 struct uiparams
 {
-  char              *fitsname;  /* Name of input FITS file.        */
-  char               *txtname;  /* Name of input text file.        */
+  int             information;  /* ==1, only print FITS information. */
+  char              *fitsname;  /* Name of input FITS file.          */
+  char               *txtname;  /* Name of input text file.          */
 
   int                inputset;
   int          informationset;
@@ -61,7 +62,6 @@ struct tableparams
   struct gal_commonparams  cp;  /* Common parameters.                 */
 
   /* Input: */
-  int             information;  /* ==1: only print information.       */
   fitsfile           *fitsptr;  /* FITS pointer (input or output).    */
 
   /* FITS table */
diff --git a/src/table/table.c b/src/table/table.c
index eb742f5..079800a 100644
--- a/src/table/table.c
+++ b/src/table/table.c
@@ -36,72 +36,7 @@ along with Gnuastro. If not, see 
<http://www.gnu.org/licenses/>.
 
 
 /* Print all the column information: */
-void
-printinfo(struct tableparams *p)
-{
-  size_t i;
-  char *typestring=NULL;
-
-  printf("%s (hdu: %s)\n", p->up.fitsname, p->cp.hdu);
-  printf("Number of rows: %lu\n", p->nrows);
-  printf("Column information\n");
-  printf("------------------\n");
-  for(i=1;i<=p->ncols;++i)
-    {
-      switch(p->typecode[i])
-        {
-        case TBIT:
-          typestring="bit";
-          break;
-        case TBYTE:
-          typestring="byte";
-          break;
-        case TLOGICAL:
-          typestring="logicals";
-          break;
-        case TSTRING:
-          typestring="string";
-          break;
-        case TSHORT:
-          typestring="short";
-          break;
-        case TLONG:
-          typestring="long";
-          break;
-        case TLONGLONG:
-          typestring="longlong";
-          break;
-        case TFLOAT:
-          typestring="float";
-          break;
-        case TDOUBLE:
-          typestring="double";
-          break;
-        case TCOMPLEX:
-          typestring="complex";
-          break;
-        case TDBLCOMPLEX:
-          typestring="dblcomplex";
-          break;
-        case TSBYTE:
-          typestring="signed byte";
-          break;
-        case TUINT:
-          typestring="unsigned int";
-          break;
-        case TUSHORT:
-          typestring="unsigned short";
-          break;
-        default:
-          error(EXIT_FAILURE, 0, "%d (from TFORM%lu='%c') is not a "
-                "recognized CFITSIO datatype.",
-                p->typecode[i], i, p->tform[i][0]);
-        }
-      printf("%-3lu %-25s %-20s %s\n", i, p->ttype[i], typestring,
-             p->tunit[i]);
-    }
 
-}
 
 
 
@@ -110,5 +45,5 @@ printinfo(struct tableparams *p)
 void
 table(struct tableparams *p)
 {
-  if(p->information) printinfo(p);
+
 }
diff --git a/src/table/ui.c b/src/table/ui.c
index bdd75f4..5a5a924 100644
--- a/src/table/ui.c
+++ b/src/table/ui.c
@@ -116,7 +116,7 @@ readconfig(char *filename, struct tableparams *p)
       else if (strcmp(name, "information")==0)
         {
           if(p->up.informationset) continue;
-          gal_checkset_int_zero_or_one(value, &p->information, name,
+          gal_checkset_int_zero_or_one(value, &p->up.information, name,
                                        key, SPACK, filename, lineno);
           p->up.informationset=1;
         }
@@ -142,7 +142,7 @@ readconfig(char *filename, struct tableparams *p)
 void
 printvalues(FILE *fp, struct tableparams *p)
 {
-  /*struct uiparams *up=&p->up;*/
+  struct uiparams *up=&p->up;
   struct gal_commonparams *cp=&p->cp;
 
 
@@ -157,6 +157,9 @@ printvalues(FILE *fp, struct tableparams *p)
      options, then the (possible options particular to this
      program). */
   fprintf(fp, "\n# Operating mode:\n");
+  if(up->informationset)
+    fprintf(fp, CONF_SHOWFMT"%d\n", "information", up->information);
+
   GAL_CONFIGFILES_PRINT_COMMONOPTIONS;
 }
 
@@ -199,9 +202,8 @@ checkifset(struct tableparams *p)
 
 
 
-
 /**************************************************************/
-/***************       Sanity Check         *******************/
+/************     Read and Write column info    ***************/
 /**************************************************************/
 /* This function will read all the table information from a FITS table HDU
    and store them in arrays for use later. It is mainly good for getting
@@ -210,49 +212,39 @@ checkifset(struct tableparams *p)
    the keywords, so it is much more efficient than having to ask for each
    column's information separately.*/
 void
-readallcolinfo(char *filename, char *hdu, size_t *nrows,
-               size_t *ncols, int **otypecode, char ***otform,
-               char ***ottype, char ***otunit, fitsfile **outfptr)
+readallcolinfo(fitsfile *fitsptr, size_t ncols, int **otypecode,
+               char ***otform, char ***ottype, char ***otunit)
 {
-  long lnrows;
   size_t index;
   char *tailptr, **c, **fc;
+  int i, status=0, *typecode;
   char **tform, **ttype, **tunit;
-  int i, status=0, incols, *typecode;
   char keyname[FLEN_KEYWORD]="XXXXXXXXXXXXX", value[FLEN_VALUE];
 
-  /* Set the FITS pointer and check the HDU type. */
-  gal_fits_read_hdu(filename, hdu, 1, outfptr);
-
-  /* Get the size of the table. incols is incremented because the indexs of
-     the FITS keywords start from 1, not zero. */
-  fits_get_num_rows(*outfptr, &lnrows, &status);
-  fits_get_num_cols(*outfptr, &incols, &status);
-  *ncols=incols++;
-  *nrows=lnrows;
 
   /* Allocate the arrays to keep the column information. Initialize the
      arrays with a NULL pointer to make sure that they are all found in the
      end if they are necessary.*/
-  errno=0; typecode=*otypecode=malloc(incols * sizeof *typecode);
+  errno=0; typecode=*otypecode=malloc(ncols * sizeof *typecode);
   if(typecode==NULL)
     error(EXIT_FAILURE, errno, "%lu bytes for typecode",
-          incols * sizeof *typecode);
-  errno=0; tform=*otform=malloc(incols * sizeof *tform);
+          ncols * sizeof *typecode);
+  errno=0; tform=*otform=malloc(ncols * sizeof *tform);
   if(tform==NULL)
     error(EXIT_FAILURE, errno, "%lu bytes for tform",
-          incols * sizeof *tform);
-  fc=(c=tform)+incols; do *c++=NULL; while(c<fc);
-  errno=0; ttype=*ottype=malloc(incols * sizeof *ttype);
+          ncols * sizeof *tform);
+  fc=(c=tform)+ncols; do *c++=NULL; while(c<fc);
+  errno=0; ttype=*ottype=malloc(ncols * sizeof *ttype);
   if(ttype==NULL)
     error(EXIT_FAILURE, errno, "%lu bytes for ttype",
-          incols * sizeof *ttype);
-  fc=(c=ttype)+incols; do *c++=NULL; while(c<fc);
-  errno=0; tunit=*otunit=malloc(incols * sizeof *tunit);
+          ncols * sizeof *ttype);
+  fc=(c=ttype)+ncols; do *c++=NULL; while(c<fc);
+  errno=0; tunit=*otunit=malloc(ncols * sizeof *tunit);
   if(tunit==NULL)
     error(EXIT_FAILURE, errno, "%lu bytes for tunit",
-          incols * sizeof *tunit);
-  fc=(c=tunit)+incols; do *c++=NULL; while(c<fc);
+          ncols * sizeof *tunit);
+  fc=(c=tunit)+ncols; do *c++=NULL; while(c<fc);
+
 
   /* Read all the keywords one by one and if they match, then put them in
      the correct value. Note that we are starting from keyword 9 because
@@ -261,16 +253,27 @@ readallcolinfo(char *filename, char *hdu, size_t *nrows,
   for(i=9; strcmp(keyname, "END"); ++i)
     {
       /* Read the next keyword. */
-      fits_read_keyn(*outfptr, i, keyname, value, NULL, &status);
+      fits_read_keyn(fitsptr, i, keyname, value, NULL, &status);
 
       /* Check the type of the keyword. */
       if(strncmp(keyname, "TFORM", 5)==0)
         {
+          /* Currently we can only read repeat==1 cases. When no number
+             exists before the defined capital letter, it defaults to 1,
+             but if a number exists (for example `5D'), then the repeat is
+             5 (there are actually five values here. Note that value[0] is
+             a single quote.*/
+          if(isdigit(value[1] && value[1]!='1'))
+             error(EXIT_FAILURE, 0, "The repeat value of column %d is "
+                   "%c, currently Table can only use columns with a repeat "
+                   "of 1.", i+1, value[1]);
+
+
           /* The values to TFORM are only a single character, so start the
              pointer to copy at 1 and put the string terminator at 3. */
           value[2]='\0';
-          index=strtoul(&keyname[5], &tailptr, 10);
-          if(index<incols)
+          index=strtoul(&keyname[5], &tailptr, 10)-1;
+          if(index<ncols)
             {
               gal_checkset_allocate_copy(&value[1], &tform[index] );
               typecode[index]=gal_fits_tform_to_dtype(value[1]);
@@ -284,57 +287,165 @@ readallcolinfo(char *filename, char *hdu, size_t *nrows,
              remove them to have a simple string that might be used else
              where too (without the single quotes). */
           value[strlen(value)-1]='\0';
-          index=strtoul(&keyname[5], &tailptr, 10);
-          if(index<incols)
+          index=strtoul(&keyname[5], &tailptr, 10)-1;
+          if(index<ncols)
             gal_checkset_allocate_copy(&value[1], &ttype[index] );
         }
       else if(strncmp(keyname, "TUNIT", 5)==0)
         {
           /* similar to ttype, see above.*/
           value[strlen(value)-1]='\0';
-          index=strtoul(&keyname[5], &tailptr, 10);
-          if(index<incols)
+          index=strtoul(&keyname[5], &tailptr, 10)-1;
+          if(index<ncols)
             gal_checkset_allocate_copy(&value[1], &tunit[index] );
         }
     }
 
-  /* Check if all values were set: */
-  for(i=1;i<=*ncols;++i)
-    {
-      if(!tform[i])
-         error(EXIT_FAILURE, 0, "TFORM%d could not be found in header", i);
-      if(!ttype[i])
-         error(EXIT_FAILURE, 0, "TTYPE%d could not be found in header", i);
-      if(!tunit[i])
-         error(EXIT_FAILURE, 0, "TUNIT%d could not be found in header", i);
-    }
+
+  /* Check if the mandatory TFORMn values are set: */
+  for(i=0;i<ncols;++i)
+    if(!tform[i])
+      error(EXIT_FAILURE, 0, "TFORM%d could not be found in header", i+1);
 
 
   /* For a checkup:
   for(i=1;i<=*ncols;++i)
     printf("%d: %s, %s, %s\n", i, tform[i], ttype[i], tunit[i]);
   */
+}
+
+
+
 
+/* Print the column information. */
+void
+printinfo(struct tableparams *p)
+{
+  size_t i;
+  char *typestring=NULL;
+
+  printf("%s (hdu: %s)\n", p->up.fitsname, p->cp.hdu);
+  printf("Column information\n");
+  printf("---------------------------------------------------------\n");
+  printf("%-5s%-25s%-20s%s\n", "No.", "Column name", "Data type",
+         "Units");
+  printf("---------------------------------------------------------\n");
+  for(i=0;i<p->ncols;++i)
+    {
+      switch(p->typecode[i])
+        {
+        case TBIT:
+          typestring="bit";
+          break;
+        case TBYTE:
+          typestring="byte";
+          break;
+        case TLOGICAL:
+          typestring="logicals";
+          break;
+        case TSTRING:
+          typestring="string";
+          break;
+        case TSHORT:
+          typestring="short";
+          break;
+        case TLONG:
+          typestring="long";
+          break;
+        case TLONGLONG:
+          typestring="longlong";
+          break;
+        case TFLOAT:
+          typestring="float";
+          break;
+        case TDOUBLE:
+          typestring="double";
+          break;
+        case TCOMPLEX:
+          typestring="complex";
+          break;
+        case TDBLCOMPLEX:
+          typestring="dblcomplex";
+          break;
+        case TSBYTE:
+          typestring="signed byte";
+          break;
+        case TUINT:
+          typestring="unsigned int";
+          break;
+        case TUSHORT:
+          typestring="unsigned short";
+          break;
+        default:
+          error(EXIT_FAILURE, 0, "%d (from TFORM%lu='%c') is not a "
+                "recognized CFITSIO datatype.",
+                p->typecode[i], i, p->tform[i][0]);
+        }
+      printf("%-5lu%-25s%-20s%s\n", i+1, p->ttype[i] ? p->ttype[i] : "---",
+             typestring, p->tunit[i] ? p->tunit[i] : "---");
+    }
+
+
+  /* Print the number of rows: */
+  printf("---------------------------------------------------------\n");
+  printf("Number of rows: %lu\n", p->nrows);
 }
 
 
 
 
 
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/**************************************************************/
+/***************       Sanity Check         *******************/
+/**************************************************************/
 void
 sanitycheck(struct tableparams *p)
 {
 
   /* Set the FITS pointer and check the type of the fits file. */
   if(p->up.fitsname)
-    readallcolinfo(p->up.fitsname, p->cp.hdu, &p->nrows,
-                   &p->ncols, &p->typecode, &p->tform,
-                   &p->ttype, &p->tunit, &p->fitsptr);
+    {
+      gal_fits_read_hdu(p->up.fitsname, p->cp.hdu, 1, &p->fitsptr);
+      gal_fits_table_size(p->fitsptr, &p->nrows, &p->ncols);
+    }
   else
     error(EXIT_FAILURE, 0, "Table is a new addition to Gnuastro and "
           "and under heavy development, it currently doesn't support "
           "anything other than a FITS binary table.");
 
+
+
+  /* Print the column information and exit successfully if the
+     `--information' option is given. */
+  if(p->up.information)
+    {
+      if(p->up.fitsname)
+        {
+          readallcolinfo(p->fitsptr, p->ncols, &p->typecode,
+                         &p->tform, &p->ttype, &p->tunit);
+          printinfo(p);
+          freeandreport(p);
+          exit(EXIT_SUCCESS);
+        }
+      else
+        error(EXIT_FAILURE, 0, "the `--information' (`-i') option is only "
+              "defined for FITS tables");
+    }
 }
 
 
@@ -451,7 +562,11 @@ freeandreport(struct tableparams *p)
   int status=0;
 
   /* Free the allocated arrays: */
+  free(p->tform);
+  free(p->ttype);
+  free(p->tunit);
   free(p->cp.hdu);
+  free(p->typecode);
   free(p->cp.output);
 
   /* Close the FITS file: */