Merge pull request #20 from ska-sa/fiela

Fiela

Owlcat/bin/fitstool.py

@@ -26,185 +26,6 @@
 # 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 #
 
-import sys
-import re
-import os.path
-import numpy
-## ugly hack to get around UGLY FSCKING ARROGNAT (misspelling fully intentional) pyfits-2.3 bug
-import Kittens.utils
-pyfits = Kittens.utils.import_pyfits();
-import scipy.ndimage.measurements
-import math
+from Owlcat.FitsTool import main
 
-SANITIZE_DEFAULT = 12345e-7689
-
-if __name__ == "__main__":
-
-  # setup some standard command-line option parsing
-  #
-  from optparse import OptionParser
-  parser = OptionParser(usage="""%prog: [options] <image names...>""");
-  parser.add_option("-o","--output",dest="output",type="string",
-                    help="name of output FITS file");
-  parser.add_option("-r","--replace",action="store_true",
-                    help="replace (first) input file by output. Implies '--force'.");
-  parser.add_option("-f","--force",dest="force",action="store_true",
-                    help="overwrite output file even if it exists");
-  parser.add_option("-S","--sanitize",type="float",metavar="VALUE",
-                    help="sanitize FITS files by replacing NANs and INFs with VALUE");
-  parser.add_option("-N","--nonneg",action="store_true",
-                    help="replace negative values by 0");
-  parser.add_option("-m","--mean",dest="mean",action="store_true",
-                    help="take mean of input images");
-  parser.add_option("-d","--diff",dest="diff",action="store_true",
-                    help="take difference of 2 input images");
-  parser.add_option("-t","--transfer",action="store_true",
-                    help="transfer data from image 2 into image 1, preserving the FITS header of image 1");
-  parser.add_option("-z","--zoom",dest="zoom",type="int",metavar="NPIX",                    
-                    help="zoom into central region of NPIX x NPIX size");
-  parser.add_option("-R","--rescale",dest="rescale",type="float",
-                    help="rescale image values");
-  parser.add_option("-E","--edit-header",metavar="KEY=VALUE",type="string",action="append",
-                    help="replace header KEY with VALUE. Use KEY=VALUE for floats and KEY='VALUE' for strings.");
-  parser.add_option("-H","--header",action="store_true",help="print header(s) of input image(s)");
-  parser.add_option("-s","--stats",action="store_true",help="print stats on images and exit. No output images will be written.");
-
-  parser.set_defaults(output="",mean=False,zoom=0,rescale=1,edit_header=[]);
-
-  (options,imagenames) = parser.parse_args();
-
-  if not imagenames:
-    parser.error("No images specified. Use '-h' for help.");
-
-  # print "%d input image(s): %s"%(len(imagenames),", ".join(imagenames));
-  images = [ pyfits.open(img) for img in imagenames ];
-  updated = False;
-
-  if options.header:
-    for filename,img in zip(imagenames,images):
-      if len(imagenames)>1:
-        print "======== FITS header for",filename;
-      for hdrline in img[0].header.ascard:
-        print hdrline; 
-
-  if options.replace or len(imagenames)<2:
-    if options.output:
-      parser.error("Cannot combine -r/--replace with -o/--output");
-    outname = imagenames[0];
-    options.force = True;
-    autoname = False;
-  else:
-    outname = options.output;
-    autoname = not outname;
-    if autoname:
-      outname = re.split('[_]',imagenames[0],1)[-1];
-
-  for keyval in options.edit_header:
-    key,val = keyval.split("=");
-    q = ''
-    if val[0] == "'" and val[-1] == "'":
-      images[0][0].header[key] = val[1:-1:];
-      q = '"'
-    elif val[-1] == 'd' or key.startswith('NAXIS'):
-      images[0][0].header[key] = int(val[:-1] if val[-1]=='d' else val);
-    else:
-      try:
-        images[0][0].header[key] = float(val);
-      except:
-        images[0][0].header[key] = val;
-        q = '"';
-    print "Setting header %s=%s%s%s"%(key,q,val,q);
-    updated = True;
-
-  if options.sanitize is not None:
-    print "Sanitizing: replacing INF/NAN with",options.sanitize;
-    for img in images:
-      d = img[0].data;
-      d[numpy.isnan(d)+numpy.isinf(d)] = options.sanitize;
-    # if using stats, do not generate output
-    if not options.stats:
-      updated = True;
-
-  if options.nonneg:
-    print "Replacing negative value by 0";
-    for img,name in zip(images,imagenames)[:1]:
-      d = img[0].data;
-      wh = d<0;
-      d[wh] = 0;
-      print "Image %s: replaced %d points"%(name,wh.sum());
-    updated = True;
-
-  if options.transfer:
-    if len(images) != 2:
-      parser.error("The --transfer option requires exactly two input images.");
-    if autoname:
-      outname = "xfer_" + outname;
-    print "Transferring %s into coordinate system of %s"%(imagenames[1],imagenames[0]);
-    images[0][0].data[...] = images[1][0].data;
-    updated = True;
-  elif options.diff:
-    if len(images) != 2:
-      parser.error("The --diff option requires exactly two input images.");
-    if autoname:
-      outname = "diff_" + outname;
-    print "Computing difference";
-    data = images[0][0].data;
-    data -= images[1][0].data;
-    updated = True;
-  elif options.mean:
-    if autoname:
-      outname = "mean%d_"%len(images) + outname;
-    print "Computing mean";
-    data = images[0][0].data;
-    for img in images[1:]:
-      data += img[0].data;
-    data /= len(images);
-    images = [ images[0] ];
-    updated = True;
-
-  if options.zoom:
-    z = options.zoom;
-    if autoname:
-      outname = "zoom%d_"%z + outname;
-    if len(images) > 1:
-      "Too many input images specified for this operation, at most 1 expected";
-      sys.exit(2);
-    data = images[0][0].data;
-    nx = data.shape[2];
-    ny = data.shape[3];
-    zdata = data[:,:,(nx-z)/2:(nx+z)/2,(ny-z)/2:(ny+z)/2];
-    print "Making zoomed image of shape","x".join(map(str,zdata.shape));
-    images = [ pyfits.PrimaryHDU(zdata) ];
-    updated = True;
-
-  if options.rescale != 1:
-    if autoname and not updated:
-      outname = "rescale_" + outname;
-    if len(images) > 1:
-      "Too many input images specified for this operation, at most 1 expected";
-      sys.exit(2);
-    print "Applying scaling factor of %f to image values"%options.rescale;
-    images[0][0].data *= options.rescale;
-    updated = True;
-
-  if updated:
-    imagenames[0] = outname;
-
-  if options.stats:
-    for ff,filename in zip(images,imagenames):
-      data = ff[0].data;
-      min,max,dum1,dum2 = scipy.ndimage.measurements.extrema(data);
-      sum = data.sum();
-      mean = sum/data.size;
-      std = math.sqrt(((data-mean)**2).mean());
-      print "%s: min %g, max %g, sum %g, np %d, mean %g, std %g"%(filename,min,max,sum,data.size,mean,std); 
-    sys.exit(0);
-
-  if updated:
-    print "Writing output image",outname;
-    if os.path.exists(outname) and not options.force:
-      print "Output image exists, rerun with the -f switch to overwrite.";
-      sys.exit(1);
-    images[0].writeto(outname,clobber=True);
-  elif not options.header:
-    print "No operations specified. Use --help for help."
+main()