edits to README.md and delete a couple of files

README.md

@@ -2,7 +2,7 @@ General Information
 ===================
 
 fitscut is designed to extract cutouts from FITS image format files.
-FITS, PNG, and JPEG output types are supported.  
+FITS, PNG, and JPEG output types are supported.
 
 When multiple input files are specified and the output type is PNG or
 JPEG the resulting image is an RGB color image.
@@ -12,37 +12,32 @@ Information on the FITS file format is available from
 http://fits.gsfc.nasa.gov/.
 
 
-A cgi interface to fiscut is avilable here: https://hla.stsci.edu/fitscutcgi_interface.html
+A cgi interface to fitscut is available here: https://hla.stsci.edu/fitscutcgi_interface.html
 
 Dependencies
 ============
 
 In order to build fitscut you will need:
 
-  CFITSIO library  
-    <http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html>
+- CFITSIO library: <http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html>
 
-  LIBPNG
-    <http://www.libpng.org/pub/png/libpng.html>
+- LIBPNG: <http://www.libpng.org/pub/png/libpng.html>
 
-  JPEG library
-    <http://www.ijg.org/>
+- JPEG library: <http://www.ijg.org/>
 
-And optionally:
-
-  WCS Subroutine library
-    <ftp://cfa-ftp.harvard.edu/pub/gsc/WCSTools/>
-
+- WCS Subroutine library: <http://tdc-www.harvard.edu/software/wcstools/>\
+(The WCS library was originally optional but is required in this version of fitscut.)
 
 Supported Platforms
 ===================
 
 fitscut has been tested and is known to work on:
 
-  RedHat Linux 8, 9
-  RedHat Enterprise Linux 3
-  Fedora Core 1
-  Solaris 8, 9
+RedHat Linux 8, 9\
+RedHat Enterprise Linux 3\
+Fedora Core 1\
+Solaris 8, 9
+MacOS 10.12 (and other OSX versions)
 
 Installation
 ============
@@ -51,13 +46,18 @@ Please see the INSTALL file.
 
 This usually consists of:
 
-  % gzip -cd fitscut-1.4.0.tar.gz | tar xvf -     # unpack the sources
+```
+  % tar xzvf fitscut-1.4.0.tar.gz                 # unpack the sources
   % cd fitscut-1.4.0                              # change to the directory
   % ./configure                                   # run the 'configure' script
   % make                                          # build fitscut
   [ Become root if necessary ]
   % make install                                  # install fitscut
+```
 
+The usual configure options are available (e.g., `--prefix=/your/install/location` to specify where the binary executable should be installed).
+You can define the `CFLAGS` and `LDFLAGS` environment variables to specify the locations of include files and libraries before running
+`./configure`.
 
 -----
 Copyright (C) 2001 William Jon McCann

extract.c

@@ -646,7 +646,15 @@ extract_fits (FitsCutImage *Image)
 
         /* determine zoomed image size */
 
-        if (Image->output_zoom[k] > 0) {
+        if (Image->output_alignment == ALIGN_REF) {
+            /* estimate zoom factor based on image region and output sizes */
+            zoom_factor = ((float) Image->nrowsref)/((float) nrows);
+            if (zoom_factor > 1) {
+                zoom_factor = 1.0;
+            } else {
+                zoom_factor = 1.0/lround(1.0/zoom_factor);
+            }
+        } else if (Image->output_zoom[k] > 0) {
             zoom_factor = Image->output_zoom[k];
         }
         else {
@@ -658,6 +666,7 @@ extract_fits (FitsCutImage *Image)
         get_zoom_size_channel (ncols, nrows, zoom_factor, Image->output_size,
             &pixfac, &zoomcols, &zoomrows, &doshrink);
         fitscut_message (1, "\tZoomed output size is %d x %d\n", zoomcols, zoomrows);
+        fitscut_message(2, "\tpixfac = %d\n", pixfac);
 
         /* CFITSIO starts indexing at 1 */
         x0 += 1;
@@ -731,6 +740,7 @@ extract_fits (FitsCutImage *Image)
                  zoomcols, zoomrows);
         arrayptr = cutout_alloc (zoomcols, zoomrows, NAN);
 
+        nbad = 0;
         if (cols_read > 0 && rows_read > 0) {
             if (pixfac > 1) {
                 fitscut_message (2, "\tAllocating space for %d x %d buffer\n",
@@ -845,7 +855,7 @@ extract_fits (FitsCutImage *Image)
             Image->output_zoom[k] = 1.0;
         }
 
-        if (pixfac > 1) {
+        if (pixfac > 1 && cols_read > 0 && rows_read > 0) {
             free(bufferptr);
         }
 

output_fits.c

@@ -242,6 +242,26 @@ fitscut_clean_header(fitsfile *fptr, FitsCutImage *Image, int *status) {
     if (*status) printerror (*status);
 }
 
+
+/* return true if the keyword exists in the header */
+static int
+header_has_key(fitsfile *fptr, char *keyname, int *status)
+{
+char value[81];
+
+    if (*status == 0) {
+        fits_read_keyword(fptr, keyname, value, NULL, status);
+        if (*status == VALUE_UNDEFINED || *status == KEY_NO_EXIST) {
+            *status = 0;
+            return 0; /* no such keyword */
+        } else if (*status == 0) {
+            return 1; /* keyword found */
+        }
+    }
+    /* error in status */
+    return 0;
+}
+
 void
 write_to_fits(FitsCutImage *Image)
 {
@@ -338,6 +358,28 @@ write_to_fits(FitsCutImage *Image)
             fits_update_key(fptr, TDOUBLE, "CRPIX1", &crpix,
                 "Reference pixel shifted for cutout", &status);
             fitscut_message  (2, "\tUpdated CRPIX1 to %f\n", crpix);
+            /*
+             * add RADESYS keyword if it is missing (for PS1 images)
+             * only do this if both RADESYS and EQUINOX are missing and the
+             * image has the old PC001001 keyword
+             */
+            if (status == 0) {
+                if ((! header_has_key(fptr, "RADESYS", &status))
+                  & (! header_has_key(fptr, "EQUINOX", &status))
+                  & header_has_key(fptr, "PC001001", &status) ) {
+                    /* keyword not found, add it */
+                    if (fits_write_key(fptr, TSTRING, "RADESYS", "FK5", "added by fitscut", &status))
+                        printerror (status);
+                    fitscut_message  (2, "\tAdded RADESYS keyword\n");
+                    /* also add the TIMESYS keyword for PS1 images (which are the source of the RADESYS problem) */
+                    if (! header_has_key(fptr, "TIMESYS", &status)) {
+                        /* keyword not found, add it */
+                        if (fits_write_key(fptr, TSTRING, "TIMESYS", "TAI", "added by fitscut", &status))
+                            printerror (status);
+                        fitscut_message  (2, "\tAdded TIMESYS keyword\n");
+                    }
+                }
+            }
         } else if (status == VALUE_UNDEFINED || status == KEY_NO_EXIST) {
             /* no CRPIX, so skip updating WCS */
             fitscut_message  (2, "\tNo CRPIX1 found, header not updated\n");

output_graphic.c

@@ -367,12 +367,13 @@ static void
 jpg_add_header_info(FitsCutImage *Image, GraphicsInfo *info)
 {
     struct jpeg_compress_struct *cinfo_ptr = &(info->jpeg_info);
-    char output_text[11*80];
+    char output_text[15*80];
 	/* initialize these to eliminate compiler warnings */
-    double crval1=0, crval2=0, crpix1=0, crpix2=0, cd1_1=1, cd1_2=0, cd2_1=0, cd2_2=1, cdelt1=1, cdelt2=1, crota2=0, zoom=1;
+    double crval1=0, crval2=0, crpix1=0, crpix2=0, cd1_1=1, cd1_2=0, cd2_1=0, cd2_2=1,
+		cdelt1=1, cdelt2=1, crota2=0, pc1_1=0, pc1_2=0, pc2_1=0, pc2_2=0, zoom=1;
     char ctype1[FLEN_VALUE], ctype2[FLEN_VALUE];
     /* counts for various classes of keywords */
-    int crcount = 0, cdcount = 0, delcount = 0, rotcount = 0;
+    int crcount = 0, cdcount = 0, delcount = 0, rotcount = 0, pccount=0;
 
     int status = 0;
     char *header, keyname[FLEN_KEYWORD];
@@ -422,6 +423,22 @@ jpg_add_header_info(FitsCutImage *Image, GraphicsInfo *info)
                 fits_parse_value (card, value_string, comment, &status);
                 cd2_2 = strtod (value_string, (char **)NULL);
                 cdcount += 1;
+            } else if (strequ (keyname, "PC001001") || strequ(keyname, "PC1_1")) {
+                fits_parse_value (card, value_string, comment, &status);
+                pc1_1 = strtod (value_string, (char **)NULL);
+                pccount += 1;
+            } else if (strequ (keyname, "PC001002") || strequ(keyname, "PC1_2")) {
+                fits_parse_value (card, value_string, comment, &status);
+                pc1_2 = strtod (value_string, (char **)NULL);
+                pccount += 1;
+            } else if (strequ (keyname, "PC002001") || strequ(keyname, "PC2_1")) {
+                fits_parse_value (card, value_string, comment, &status);
+                pc2_1 = strtod (value_string, (char **)NULL);
+                pccount += 1;
+            } else if (strequ (keyname, "PC002002") || strequ(keyname, "PC2_2")) {
+                fits_parse_value (card, value_string, comment, &status);
+                pc2_2 = strtod (value_string, (char **)NULL);
+                pccount += 1;
             } else if (strequ (keyname, "CDELT1")) {
                 fits_parse_value (card, value_string, comment, &status);
                 cdelt1 = strtod (value_string, (char **)NULL);
@@ -449,8 +466,8 @@ jpg_add_header_info(FitsCutImage *Image, GraphicsInfo *info)
 
     /* update WCS info */
 
-    fitscut_message (3, "\tWCS counts: crval/pix/type %d cd1_1 %d cdelt %d rota %d\n",
-		   crcount, cdcount, delcount, rotcount);
+    fitscut_message (3, "\tWCS counts: crval/pix/type %d cd1_1 %d pc1_1 %d cdelt %d rota %d\n",
+		   crcount, cdcount, pccount, delcount, rotcount);
     if (crcount == 6 && (cdcount == 4 || delcount == 2)) {
         zoom = Image->output_zoom[0];
 		if (zoom == 0.0) zoom = 1.0;
@@ -483,20 +500,41 @@ jpg_add_header_info(FitsCutImage *Image, GraphicsInfo *info)
             cdelt2 = cdelt2/zoom;
 		   	/* CROTA2 is optional */
 			if (rotcount == 0) crota2 = 0.0;
-            sprintf(output_text,
-                "CTYPE1  = %s\n"
-                "CTYPE2  = %s\n"
-                "CRPIX1  = %.15g\n"
-                "CRPIX2  = %.15g\n"
-                "CRVAL1  = %.15g\n"
-                "CRVAL2  = %.15g\n"
-                "CDELT1  = %.15g\n"
-                "CDELT2  = %.15g\n"
-                "CROTA2  = %.15g\n"
-                "COMMENT Created by fitscut %s (William Jon McCann)\n",
-                ctype1, ctype2, crpix1, crpix2, crval1, crval2,
-                cdelt1, cdelt2, crota2, VERSION);
-			fitscut_message (2, "\tAdded CDELT1 format WCS to JPEG comment\n");
+			if (pccount == 4) {
+				sprintf(output_text,
+					"CTYPE1  = %s\n"
+					"CTYPE2  = %s\n"
+					"CRPIX1  = %.15g\n"
+					"CRPIX2  = %.15g\n"
+					"CRVAL1  = %.15g\n"
+					"CRVAL2  = %.15g\n"
+					"CDELT1  = %.15g\n"
+					"CDELT2  = %.15g\n"
+					"CROTA2  = %.15g\n"
+					"PC1_1   = %.15g\n"
+					"PC1_2   = %.15g\n"
+					"PC2_1   = %.15g\n"
+					"PC2_2   = %.15g\n"
+					"COMMENT Created by fitscut %s (William Jon McCann)\n",
+					ctype1, ctype2, crpix1, crpix2, crval1, crval2,
+					cdelt1, cdelt2, crota2, pc1_1, pc1_2, pc2_1, pc2_2, VERSION);
+				fitscut_message (2, "\tAdded PC/CDELT1 format WCS to JPEG comment\n");
+			} else {
+				sprintf(output_text,
+					"CTYPE1  = %s\n"
+					"CTYPE2  = %s\n"
+					"CRPIX1  = %.15g\n"
+					"CRPIX2  = %.15g\n"
+					"CRVAL1  = %.15g\n"
+					"CRVAL2  = %.15g\n"
+					"CDELT1  = %.15g\n"
+					"CDELT2  = %.15g\n"
+					"CROTA2  = %.15g\n"
+					"COMMENT Created by fitscut %s (William Jon McCann)\n",
+					ctype1, ctype2, crpix1, crpix2, crval1, crval2,
+					cdelt1, cdelt2, crota2, VERSION);
+				fitscut_message (2, "\tAdded CDELT1 format WCS to JPEG comment\n");
+			}
         }
     } else {
         /* no WCS found, so just add the comment */