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/* File getfits.c
* July 26, 2018
* By Jessica Mink, Harvard-Smithsonian Center for Astrophysics
* Send bug reports to jmink@cfa.harvard.edu
Copyright (C) 2002-2018
Smithsonian Astrophysical Observatory, Cambridge, MA USA
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software Foundation,
Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <fcntl.h>
#include <errno.h>
#include <unistd.h>
#include <math.h>
#include "libwcs/fitswcs.h"
#include "libwcs/wcscat.h"
#define MAXRANGE 20
#define MAXFILES 2000
static int maxnfile = MAXFILES;
#define MAXKWD 500
static int maxnkwd = MAXKWD;
static void usage();
static void nextname(); /* Find next available name (namea, nameb, ...) */
static int ExtractFITS();
static int verbose = 0; /* verbose/debugging flag */
static char *RevMsg = "GETFITS WCSTools 3.9.6, 28 July 2018, Jessica Mink (jmink@cfa.harvard.edu)";
static int version = 0; /* If 1, print only program name and version */
static char outname[128]; /* Name for output image */
static char outdir[256]; /* Output directory pathname */
static int first = 1;
static int nlog = 100;
static int xcpix = 0;
static int ycpix = 0;
static int xdpix = 0;
static int ydpix = 0;
static char *rrange; /* Row range string */
static char *crange; /* Column range string */
static double ra0 = -99.0; /* Initial center RA in degrees */
static double dec0 = -99.0; /* Initial center Dec in degrees */
static int syscoor = 0; /* Input search coordinate system */
static double eqcoor = 0.0; /* Input search coordinate system */
int
main (ac, av)
int ac;
char **av;
{
char *str;
char *listfile = NULL;
char **fn;
char filename[256];
char temp[80];
int ifile, nfile, nbytes;
FILE *flist;
char *nextarg;
char rastr[32], decstr[32];
int lstr;
int nkwd = 0; /* Number of keywords to delete */
int nkwd1 = 0; /* Number of keywords in delete file */
int ikwd;
char **kwd = NULL; /* List of keywords to be deleted */
char **kwdnew;
FILE *fdk;
char *klistfile;
crange = NULL;
rrange = NULL;
outname[0] = 0;
outdir[0] = 0;
nfile = 0;
fn = (char **)calloc (maxnfile, sizeof(char *));
klistfile = NULL;
/* Check for help or version command first */
str = *(av+1);
if (!str || !strcmp (str, "help") || !strcmp (str, "-help"))
usage("");
if (!strcmp (str, "version") || !strcmp (str, "-version")) {
version = 1;
usage("");
}
/* crack arguments */
for (av++; --ac > 0; av++) {
/* Set range of pixels to extract */
if (isrange (*av)) {
if (crange == NULL) {
lstr = strlen (*av);
crange = (char *) calloc (lstr+1, sizeof (char) );
strcpy (crange, *av);
}
else {
lstr = strlen (*av);
rrange = (char *) calloc (lstr+1, sizeof (char));
strcpy (rrange, *av);
if (verbose) {
printf ("GETFITS: rows %s, columns %s\n",rrange,crange);
}
}
}
/* Set center RA, Dec, and equinox if colon in argument */
else if (isnum (*av) == 3) {
if (ac < 2)
usage ("Right ascension given but no declination");
else {
strcpy (rastr, *av);
ac--;
av++;
if (isnum (*av) == 3) {
strcpy (decstr, *av);
ra0 = str2ra (rastr);
dec0 = str2dec (decstr);
}
else {
usage ("Declination not in sexigesimal");
}
ac--;
if (ac < 1) {
syscoor = WCS_J2000;
eqcoor = 2000.0;
}
else if ((syscoor = wcscsys (*(av+1))) >= 0) {
eqcoor = wcsceq (*++av);
ac--;
}
else {
syscoor = WCS_J2000;
eqcoor = 2000.0;
}
xcpix = -1;
ycpix = -1;
}
}
/* Read command */
else if (*(str = *av) == '-') {
char c;
while ((c = *++str)) {
switch (c) {
case 'v': /* more verbosity */
verbose++;
break;
case 'c': /* center coordinates for extraction */
if (ac < 3)
usage ("-c needs two arguments");
xcpix = atoi (*++av);
ac--;
ycpix = atoi (*++av);
ac--;
break;
case 'd': /* output directory */
if (ac < 2)
usage ("-d needs a directory");
strcpy (outdir, *++av);
ac--;
break;
case 'k': /* Read keywords to delete from this file */
if (ac < 2)
usage ("-k needs a file of keywords");
klistfile = *av++;
nkwd1 = getfilelines (klistfile);
if (nkwd1 + nkwd > maxnkwd) {
maxnkwd = maxnkwd + nkwd1;
kwdnew = (char **)calloc (maxnkwd, sizeof(char *));
if (nkwd > 0) {
for (ikwd = 0; ikwd < nkwd; ikwd++)
kwdnew[ikwd] = kwd[ikwd];
free (kwd);
}
kwd = kwdnew;
}
if ((fdk = fopen (klistfile, "r")) == NULL) {
fprintf (stderr,"GETFITS: File %s cannot be read\n",
klistfile);
}
else {
for (ikwd = nkwd; ikwd < nkwd+nkwd1; ikwd++) {
kwd[ikwd] = (char *) calloc (32, sizeof (char));
first_token (fdk, 31, kwd[ikwd]);
}
fclose (fdk);
}
ac--;
break;
case 'i': /* logging interval */
if (ac < 2)
usage ("-i needs an argument");
nlog = atoi (*++av);
ac--;
break;
case 'o': /* output file name */
if (ac < 2)
usage ("-o needs an argument");
strcpy (outname, *++av);
ac--;
break;
case 's': /* output to stdout */
strcpy (outname, "stdout");
break;
case 'x': /* width and height for extraction */
if (ac < 2)
usage ("-x needs at least one argument");
xdpix = atoi (*++av);
ac--;
if (ac > 1) {
nextarg = *(av+1);
if (isnum (nextarg) == 1) {
ydpix = atoi (nextarg);
av++;
ac--;
}
else
ydpix = xdpix;
}
else
ydpix = xdpix;
break;
default:
sprintf (temp, "Illegal argument '%c'", c);
usage(temp);
break;
}
}
}
/* Center or center and size of section to extract */
else if (isnum (*av)) {
if (ac > 2 && isnum (*(av+1)) && (syscoor = wcscsys (*(av+2))) > 0) {
ra0 = str2ra (*av++);
ac--;
dec0 = str2dec (*av++);
ac--;
eqcoor = wcsceq (*av);
xcpix = -1;
ycpix = -1;
}
else {
if (!xcpix)
xcpix = atoi (str);
else if (!ycpix)
ycpix = atoi (str);
else if (!xdpix)
xdpix = atoi (str);
else if (!ydpix)
ydpix = atoi (str);
}
}
/* File with list of image files */
else if (*av[0] == '@') {
listfile = *av + 1;
}
/* Image file */
else if (isfits (*av) || isiraf (*av)) {
if (nfile >= maxnfile) {
maxnfile = maxnfile * 2;
nbytes = maxnfile * sizeof (char *);
fn = (char **) realloc ((void *)fn, nbytes);
}
fn[nfile] = *av;
nfile++;
}
}
/* If center is set, but not size, extract 500x500 image */
if (!crange) {
if (xcpix && ycpix && xdpix == 0)
xdpix = 500;
if (xcpix && ycpix && ydpix == 0)
ydpix = xdpix;
}
/* If column range is set, but not row range, set them to be the same */
else if (!rrange && ydpix == 0) {
rrange = crange;
}
/* If one side is set, set the other */
if (xdpix && !ydpix)
ydpix = xdpix;
/* Process files from listfile one at a time */
if (listfile && isimlist (listfile)) {
nfile = getfilelines (listfile);
if ((flist = fopen (listfile, "r")) == NULL) {
fprintf (stderr,"GETFITS: Image list file %s cannot be read\n",
listfile);
usage ();
}
for (ifile = 0; ifile < nfile; ifile++) {
first_token (flist, 254, filename);
(void) ExtractFITS (filename,kwd,nkwd);
}
fclose (flist);
}
/* Process files from command line */
else if (fn) {
for (ifile = 0; ifile < nfile; ifile++) {
(void) ExtractFITS (fn[ifile],kwd,nkwd);
}
}
return (0);
}
static void
usage (errmsg)
char *errmsg; /* Error message */
{
fprintf (stderr,"%s\n",RevMsg);
if (version)
exit (-1);
if (*errmsg)
fprintf (stderr, "*** %s ***\n", errmsg);
fprintf (stderr,"Extract FITS files from FITS image files\n");
fprintf(stderr,"Usage: getfits -sv [-i num] [-o name] [-d dir] file.fits xrange yrange...\n");
fprintf(stderr," or : getfits -sv [-i num] [-o name] [-d dir] file.fits [x y dx [dy] ...\n");
fprintf(stderr," or : getfits [-sv1][-i num][-o name] [-d path] @fitslist xrange yrange\n");
fprintf(stderr," or : getfits [-sv1][-i num][-o name] [-d path] @fitslist x y dx [dy]\n");
fprintf(stderr," xrange: Columns to extract in format x1-x2\n");
fprintf(stderr," yrange: Rows to extract in format y1-y2\n");
fprintf(stderr," x y: Center pixel of region to extract\n");
fprintf(stderr," column row or\n");
fprintf(stderr," hh:mm:ss dd:mm:ss system (sky coordinates)\n");
fprintf(stderr," dx dy: Width and height in pixels of region to extract\n");
fprintf(stderr," (Height is same as width if omitted)\n");
fprintf(stderr," -d dir: write FITS file(s) to this directory\n");
fprintf(stderr," -i num: log rows as they are copied at this interval\n");
fprintf(stderr," -k file: file of keyword names to delete from output header\n");
fprintf(stderr," -o name: output name for one file\n");
fprintf(stderr," -s: write output to standard output\n");
fprintf(stderr," -x dx dy: dimensions of image section to be extracted\n");
fprintf(stderr," -v: verbose\n");
exit (1);
}
static int
ExtractFITS (name, kwd, nkwd)
char *name;
char **kwd;
int nkwd;
{
char *header; /* FITS header */
int lhead; /* Maximum number of bytes in FITS header */
int nbhead; /* Actual number of bytes in FITS header */
char history[128]; /* for HISTORY line */
char fitsname[256]; /* Name of FITS file */
char fitspath[256]; /* Pathname of FITS file */
char *fitsfile;
double crpix1, crpix2;
double cxpix, cypix;
double ra, dec;
double bzero, bscale, dmin, dmax, drange;
int offscl;
int wp; /* Image width in pixels (returned) */
int hp; /* Image height in pixels (returned) */
double eqout=0.0; /* Equinox to return (0=image, returned) */
int ifrow1, ifrow2; /* First and last rows to extract */
int ifcol1, ifcol2; /* First and last columns to extracT */
int npimage; /* Number of pixels in image */
int nbimage; /* Number of bytes in image */
int ikwd;
char *endchar;
char *ltime;
char *newimage;
char *kw, *kwl;
int bitpix;
int bytepix;
int nblock, nbleft;
int nrows, ncols;
char rastr[32], decstr[32], cstr[32];
char temp[80];
int xdim = 1;
int ydim = 1;
int istnx = 0;
struct Range *xrange; /* Column range structure */
struct Range *yrange; /* Row range structure */
struct WorldCoor *wcs, *GetWCSFITS();
/* Check to see if this is a FITS file */
if (!isfits (name)) {
fprintf (stderr, "File %s is not a FITS file\n", name);
return (-1);
}
/* Read FITS header */
if ((header = fitsrhead (name, &lhead, &nbhead)) == NULL) {
fprintf (stderr, "Cannot read FITS file %s\n", name);
return (-1);
}
/* If requested, delete keywords one at a time */
for (ikwd = 0; ikwd < nkwd; ikwd++) {
/* Make keyword all upper case */
kwl = kwd[ikwd] + strlen (kwd[ikwd]);
for (kw = kwd[ikwd]; kw < kwl; kw++) {
if (*kw > 96 && *kw < 123)
*kw = *kw - 32;
}
/* Delete keyword */
if (hdel (header, kwd[ikwd]) && verbose)
printf ("%s: %s deleted\n", name, kwd[ikwd]);
}
if (verbose && first) {
fprintf (stderr,"%s\n",RevMsg);
fprintf (stderr, "Extract from FITS image file %s\n", name);
}
if (ra0 > -99.0 && dec0 > -99.0) {
wcs = GetWCSFITS (name, verbose);
if (wcs->lngcor != NULL) {
istnx = 1;
}
if (iswcs (wcs)) {
ra = ra0;
dec = dec0;
wcscon (syscoor, wcs->syswcs, eqcoor, eqout, &ra, &dec, wcs->epoch);
wcs2pix (wcs, ra, dec, &cxpix, &cypix, &offscl);
xcpix = (int) (cxpix + 0.5);
ycpix = (int) (cypix + 0.5);
wcsfree (wcs);
}
else {
fprintf (stderr, "No WCS in FITS image file %s\n", name);
wcsfree (wcs);
return (-1);
}
}
ncols = 0;
(void) hgeti4 (header, "NAXIS1", &ncols);
nrows = 1;
(void) hgeti4 (header, "NAXIS2", &nrows);
bitpix = 16;
(void) hgeti4 (header, "BITPIX", &bitpix);
if (bitpix < 0)
bytepix = -bitpix / 8;
else
bytepix = bitpix / 8;
/* Set up limiting rows to read */
if (rrange) {
yrange = RangeInit (rrange, ydim);
ifrow1 = yrange->ranges[0];
ifrow2 = yrange->ranges[1];
}
else if (xcpix && ycpix) {
int ydpix2 = ydpix / 2;
ifrow1 = ycpix - ydpix2 + 1;
ifrow2 = ifrow1 + ydpix - 1;
}
else{
ifrow1 = 1;
ifrow2 = nrows;
}
/* Return with error if both first and last row off image */
if ((ifrow1 < 1 && ifrow2 < 1) ||
(ifrow1 > nrows && ifrow2 > nrows)) {
fprintf (stderr,"GETFITS: Rows %d-%d off image %s\n",
ifrow1, ifrow2, name);
return (1);
}
/* Keep extracted region within image height (nrows) */
if (ifrow1 < 1)
ifrow1 = 1;
if (ifrow2 < 1)
ifrow2 = 1;
if (ifrow1 > nrows)
ifrow1 = nrows;
if (ifrow2 > nrows)
ifrow2 = nrows;
hp = ifrow2 - ifrow1 + 1;
/* Set up first and number of columns to write */
if (crange) {
xrange = RangeInit (crange, xdim);
ifcol1 = xrange->ranges[0];
ifcol2 = xrange->ranges[1];
}
else if (xdpix) {
int xdpix2 = xdpix / 2;
ifcol1 = xcpix - xdpix2 + 1;
ifcol2 = ifcol1 + xdpix - 1;
}
else {
ifcol1 = 1;
ifcol2 = ncols;
}
/* Return with error if both first and last column off image */
if ((ifcol1 < 1 && ifcol2 < 1) ||
(ifcol1 > ncols && ifcol2 > ncols)) {
fprintf (stderr,"GETFITS: Columns %d-%d off image %s\n",
ifcol1, ifcol2, name);
return (1);
}
/* Keep extracted region within image width (ncols) */
if (ifcol1 < 1)
ifcol1 = 1;
if (ifcol2 < 1)
ifcol2 = 1;
if (ifcol1 > ncols)
ifcol1 = ncols;
if (ifcol2 > ncols)
ifcol2 = ncols;
wp = ifcol2 - ifcol1 + 1;
if (verbose) {
printf ("GETFITS: Extracting %d rows %d - %d, %d columns %d - %d\n",
hp, ifrow1, ifrow2, wp, ifcol1, ifcol2);
}
/* Extract image */
newimage = fitsrsect (name, header, nbhead, ifcol1, ifrow1, wp, hp, nlog);
hputi4 (header, "NAXIS", 2);
hputi4 (header, "NAXIS1", wp);
hputi4 (header, "NAXIS2", hp);
hdel (header, "NAXIS3");
hdel (header, "NAXIS4");
hdel (header, "NAXIS5");
npimage = wp * hp;
nbimage = npimage * bytepix;
nblock = nbimage / 2880;
nbleft = (nblock + 1) * 2880 - nbimage;
if (nbleft > 2880)
nbleft = 0;
/* Set data limits for scaling when converting image formats */
bscale = 1.0;
hgetr8 (header, "BSCALE", &bscale);
bzero = 0.0;
hgetr8 (header, "BZERO", &bzero);
dmin = minvec (newimage, bitpix, bzero, bscale, 0, npimage);
dmax = maxvec (newimage, bitpix, bzero, bscale, 0, npimage);
drange = dmax - dmin;
dmin = dmin - (0.2 * drange);
dmax = dmax + (0.2 * drange);
hputnr8 (header, "DATAMIN", 0, dmin);
hputnr8 (header, "DATAMAX", 0, dmax);
/* Reset image WCS if present */
if (ifcol1 > 1 || ifrow1 > 1) {
/* If IRAF TNX image, keep all WCS keywords, but add dependency on PLATE WCS */
if (istnx) {
hputs (header, "WCSDEP", "PLATE");
}
/* Otherwise, reset reference pixel coordinate */
else {
if (hgetr8 (header, "CRPIX1", &crpix1)) {
crpix1 = crpix1 - (double) (ifcol1 - 1);
hputr8 (header, "CRPIX1", crpix1);
}
else {
hputs (header, "CTYPE1", "PIXEL");
hputi4 (header, "CRPIX1", 1);
hputi4 (header, "CRVAL1", ifcol1);
hputi4 (header, "CDELT1", 1);
}
if (hgetr8 (header, "CRPIX2", &crpix2)) {
crpix2 = crpix2 - (double) (ifrow1 - 1);
hputr8 (header, "CRPIX2", crpix2);
}
else {
hputs (header, "CTYPE2", "PIXEL");
hputi4 (header, "CRPIX2", 1);
hputi4 (header, "CRVAL2", ifrow1);
hputi4 (header, "CDELT2", 1);
}
}
/* Set up output pixel to original pixel transformation */
if (hgetr8 (header, "CRPIX1P", &crpix1)) {
crpix1 = crpix1 - (double) (ifcol1 - 1);
hputr8 (header, "CRPIX1P", crpix1);
}
else {
hputs (header, "WCSNAMEP", "PLATE");
hputs (header, "CTYPE1P", "PIXEL");
hputi4 (header, "CRPIX1P", 1);
hputi4 (header, "CRVAL1P", ifcol1);
hputi4 (header, "CDELT1P", 1);
}
if (hgetr8 (header, "CRPIX2P", &crpix2)) {
crpix2 = crpix2 - (double) (ifrow1 - 1);
hputr8 (header, "CRPIX2P", crpix2);
}
else {
hputs (header, "CTYPE2P", "PIXEL");
hputi4 (header, "CRPIX2P", 1);
hputi4 (header, "CRVAL2P", ifrow1);
hputi4 (header, "CDELT2P", 1);
}
}
/* Add HISTORY notice of this conversion */
if (ra0 > -99.0 && dec0 > -99.0) {
strcpy (history, RevMsg);
endchar = strchr (history, ',');
*endchar = (char) 0;
strcat (history, " ");
ltime = lt2fd ();
strcat (history, ltime);
endchar = strrchr (history,':');
*endchar = (char) 0;
ra2str (rastr, 31, ra0, 3);
dec2str (decstr, 31, dec0, 2);
wcscstr (cstr, syscoor, eqcoor, 0.0);
sprintf (temp, " %d x %d centered on %s %s %s",
xdpix, ydpix, rastr, decstr, cstr);
strcat (history, temp);
hputc (header, "HISTORY", history);
}
if (xcpix && ycpix) {
strcpy (history, RevMsg);
endchar = strchr (history, ',');
*endchar = (char) 0;
strcat (history, " ");
ltime = lt2fd ();
strcat (history, ltime);
endchar = strrchr (history,':');
*endchar = (char) 0;
sprintf (temp, " %d x %d centered on [%d,%d]",
xdpix, ydpix, xcpix, ycpix);
strcat (history, temp);
hputc (header, "HISTORY", history);
}
else if (crange && rrange) {
strcpy (history, RevMsg);
endchar = strchr (history, ',');
*endchar = (char) 0;
strcat (history, " ");
ltime = lt2fd ();
strcat (history, ltime);
endchar = strrchr (history,':');
*endchar = (char) 0;
sprintf (temp, " Rows %d - %d, Columns %d - %d",
ifrow1, ifrow2, ifcol1, ifcol2);
strcat (history, temp);
hputc (header, "HISTORY", history);
}
/* If assigned output name, use it */
if (outname[0] != (char) 0)
strcpy (fitsname, outname);
/* Otherwise, create a new name */
else
nextname (name, fitsname);
/* Write FITS file to a specified directory */
if (outdir[0] > 0) {
strcpy (fitspath, outdir);
strcat (fitspath, "/");
fitsfile = strrchr (fitsname,'/');
if (fitsfile == NULL)
strcat (fitspath, fitsname);
else
strcat (fitspath, fitsfile+1);
}
else
strcpy (fitspath, fitsname);
if (fitswimage (fitspath, header, newimage) > 0) {
if (verbose)
fprintf (stderr, "%s: written successfully.\n", fitspath);
else
printf ("%s\n", fitspath);
}
else if (verbose)
fprintf (stderr, "NEWFITS: File %s not written.\n", fitspath);
if (verbose)
fprintf (stderr, "\n");
free (newimage);
free (header);
return (0);
}
static void
nextname (name, newname)
char *name;
char *newname;
{
char *ext, *sufchar;
int lname;
ext = strrchr (name, '.');
if (ext)
lname = ext - name;
else
lname = strlen (name);
strncpy (newname, name, lname);
sufchar = newname + lname;
*sufchar = 'a';
*(sufchar+1) = (char) 0;
strcat (newname, ext);
while (!access (newname, F_OK)) {
if (*sufchar < 'z')
(*sufchar)++;
else {
*sufchar = 'a';
sufchar++;
*sufchar = 'a';
*(sufchar+1) = (char) 0;
strcat (newname, ext);
}
}
return;
}
/* Oct 22 2002 New program based on t2f
* Dec 6 2002 Initialize bytepix, which wasn't
* Dec 16 2002 Add -k option to delete FITS keywords when copying
*
* Jan 30 2003 Fix typo in variable name
* May 2 2003 Fix bug if no keywords are deleted
*
* Apr 16 2004 Delete NAXISn for n > 2 in output image
* Sep 15 2004 Fix bug dealing with center specified as sky coordinates
* Sep 17 2004 Add option to set extraction center as decimal degrees
* Dec 6 2004 Don't print gratuitous newline at end of process
*
* Sep 30 2005 Convert input center coordinates to image system
*
* Jun 21 2006 Clean up code
*
* Jan 10 2007 Use range subroutines in library
* Jun 11 2007 Compute minimum and maximum data values in output image
*
* Apr 4 2008 Make extracted TNX WCS dependent on original PLATE WCS
*
* Apr 10 2010 Fix bug so WCS is not accessed after it is freed
*
* Jan 22 2012 Print error, not blank file, if requested region is off image
* Sep 17 2013 Include fitswcs.h
*
* Jun 9 2016 Fix isnum() tests for added coloned times and dashed dates
* Jun 24 2016 Decrement argument counter after reading center RA
* Jul 26 2018 Add statement of limits in verbose mode
*/
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