Merge pull request #14020 from saimn/cfitsio-4.2.0

Update cfitsio to 4.2.0

astropy/io/fits/setup_package.py

@@ -43,7 +43,7 @@ def _get_compression_extension():
                     "/D",
                     "_CRT_SECURE_NO_DEPRECATE",
                     "/D",
-                    "FF_NO_UNISTD_H",
+                    "YY_NO_UNISTD_H",
                 ]
             )
         else:

cextern/cfitsio/docs/changes.txt

@@ -1,5 +1,60 @@
                    Log of Changes Made to CFITSIO
 
+Version 4.2.0 - Nov 2022
+
+  - This release includes patches to security vulnerabilities.  We
+    strongly encourage this upgrade, particularly for those running 
+    CFITSIO in web accessible applications.
+
+  - Fix to fits_read_key function, which was failing to properly read
+    keywords declared type TUINT on compilers where sizeof(int) =
+    sizeof(long).
+
+  - Added new functions fits_read_cols and fits_write_cols to efficiently 
+    read or write multiple columns in a single function call
+
+  - Added new function fits_copy_selrows to copy only selected rows, such
+    as the selected rows returned by fits_find_rows
+
+  - Added new calculator functions ERF(X), ERFC(X) and GAMMA(X), which are
+    mathematical special functions of the same name
+
+  - Added new calculator function GTIFIND() which reports which GTI row
+    brackets a given time sample
+
+  - Added new calculator functions which operate upon vector table
+    values NAXIS(V), NAXES(V,n), ELEMENTNUM(V) and AXISELEM(V,n),
+    and ARRAY(X,d) which promotes scalar X to a vector or array
+    with given dimensions.
+
+  - The CFITSIO histogramming code now handles binning by any
+    arbitrary calculator expression rather than just a column name.
+    Both the binned columns as well as the optional weights may be
+    calculator expressions, enclosed in parentheses.  
+
+  - Binning of vector columns or expressions is now supported, as long
+    as all binned inputs (as well as the optional weighting) have the
+    same vector dimensions.  Binning of variable-length columns remains
+    unsupported.
+
+  - A bug that caused histogram weights from columns that are null values
+    to be tallied along with non-null values has been fixed.
+
+  - The CFITSIO calculator and histogramming functionality is now
+    fully reentrant and does not require multithreading interlocks.
+
+  - A long-standing segmentation fault bug in the histogramming code
+    related to binning any value using the "reciprocal" /XXXX notation
+    has been fixed.
+
+  - Added mutex locks for thread safety in ftgiou and ftfiou.
+
+  - Added several Fortran wrappers to support image read/write when
+    'fpixel' and 'nelements' are 8-byte integers.
+
+  - Fixed bug which was adding spaces to some cases of long string key
+    value output.
+
 Version 4.1.0 - Feb 2022
 
   - Calls to the zlib inflate() function in zcompress.c now handle

cextern/cfitsio/lib/cfileio.c

@@ -1306,23 +1306,28 @@ int ffopen(fitsfile **fptr,      /* O - FITS file pointer                   */
 
     if (*binspec)
     {
+       char **exprs = 0;
        if (*histfilename  && !(*pixfilter) )
            strcpy(outfile, histfilename); /* the original outfile name */
        else
            strcpy(outfile, "mem://_3");  /* create histogram in memory */
                                          /* if not already copied the file */ 
 
        /* parse the binning specifier into individual parameters */
-       ffbins(binspec, &imagetype, &haxis, colname, 
-                          minin, maxin, binsizein, 
-                          minname, maxname, binname,
-                          &weight, wtcol, &recip, status);
-
+       ffbinse(binspec, &imagetype, &haxis, colname, 
+	       minin, maxin, binsizein, 
+	       minname, maxname, binname,
+	       &weight, wtcol, &recip, &(exprs), status);
+       
        /* Create the histogram primary array and open it as the current fptr */
        /* This will close the table that was used to create the histogram. */
-       ffhist2(fptr, outfile, imagetype, haxis, colname, minin, maxin,
-              binsizein, minname, maxname, binname,
-              weight, wtcol, recip, rowselect, status);
+       ffhist2e(fptr, outfile, imagetype, haxis, 
+		colname, exprs, minin, maxin, binsizein, 
+		minname, maxname, binname,
+		weight, wtcol, (exprs?exprs[4]:0),
+		recip, rowselect, status);
+
+       if (exprs) free(exprs);
 
        if (rowselect)
           free(rowselect);
@@ -1736,6 +1741,38 @@ static int find_quote(char **string)
     }
     return(1);  /* opps, didn't find the closing character */
 }
+
+/*--------------------------------------------------------------------------*/
+char *fits_find_match_delim(char *string, char delim)
+/*
+  Find matching delimiter, respecting quoting and (potentially nested) parentheses
+  
+  char *string - null-terminated string to be searched for delimiter
+  char delim - single delimiter to search for (one of '")]} )
+
+  returns: pointer to character after delimiter, or 0 if not found
+*/
+{
+  char *tstr = string;
+  int retval = 0;
+
+  if (!string) return 0;
+  switch (delim) {
+  case '\'': retval = find_quote(&tstr); break;
+  case '"':  retval = find_doublequote(&tstr); break;
+  case '}':  retval = find_curlybracket(&tstr); break;
+  case ']':  retval = find_bracket(&tstr); break;
+  case ')':  retval = find_paren(&tstr); break;
+  default: return 0; /* Invalid delimeter, return failure */
+  }
+
+  /* Delimeter not found, return failure */
+  if (retval) return 0;
+
+  /* Delimeter was found, return next position */
+  return (tstr);
+}
+
 /*--------------------------------------------------------------------------*/
 static int find_doublequote(char **string)
 
@@ -6121,11 +6158,12 @@ int ffifile2(char *url,       /* input filename */
                     return(*status = URL_PARSE_ERROR);
             }
 
-            strcpy(binspec, ptr1 + 1);       
-            ptr2 = strchr(binspec, ']');
+            strcpy(binspec, ptr1 + 1);
+	    ptr2 = fits_find_match_delim(binspec, ']');
 
             if (ptr2)      /* terminate the binning filter */
             {
+	        --ptr2;    /* points beyond delimeter, so rewind by 1 */
                 *ptr2 = '\0';
 
                 if ( *(--ptr2) == ' ')  /* delete trailing spaces */
@@ -6141,9 +6179,16 @@ int ffifile2(char *url,       /* input filename */
         }
 
         /* delete the binning spec from the row filter string */
-        ptr2 = strchr(ptr1, ']');
-        strcpy(tmpstr, ptr2+1);  /* copy any chars after the binspec */
-        strcpy(ptr1, tmpstr);    /* overwrite binspec */
+	ptr2 = fits_find_match_delim(ptr1+1, ']');
+	if (ptr2) {
+	  strcpy(tmpstr, ptr2);    /* copy any chars after the binspec */
+	  strcpy(ptr1, tmpstr);    /* overwrite binspec */
+	} else {
+	  ffpmsg("input file URL is missing closing bracket ']'");
+	  ffpmsg(rowfilter);
+	  free(infile);
+	  return(*status = URL_PARSE_ERROR);  /* error, no closing ] */
+	}
     }
 
     /* --------------------------------------------------------- */

cextern/cfitsio/lib/drvrmem.c

@@ -1237,6 +1237,37 @@ int mem_write(int hdl, void *buffer, long nbytes)
     return(0);
 }
 
+/*--------------------------------------------------------------------------*/
+int mem_zuncompress_and_write(int hdl, void *buffer, long nbytes)
+/*
+  uncompress input buffer, length nbytes and write bytes to current
+  position in file.  output buffer needs to be at position 0 to start.
+*/
+{
+  size_t newsize;
+  int status = 0;
+
+  if (memTable[hdl].currentpos != 0) {
+      ffpmsg("cannot append uncompressed data (mem_uncompress_and_write)");
+      return(WRITE_ERROR);
+  }
+
+  uncompress2mem_from_mem(buffer, nbytes,
+			  memTable[hdl].memaddrptr,
+			  memTable[hdl].memsizeptr,
+			  memTable[hdl].mem_realloc, 
+			  &newsize, &status);
+
+  if (status) {
+    ffpmsg("unabled to uncompress memory file (mem_uncompress_and_write)");
+    return(WRITE_ERROR);
+  }
+
+  memTable[hdl].currentpos += newsize;
+  memTable[hdl].fitsfilesize = newsize;
+  return(0);
+}
+
 
 #if HAVE_BZIP2
 void bzip2uncompress2mem(char *filename, FILE *diskfile, int hdl,