def trim(args):
# Define region to be trimmed
y0, y1, x0, x1 = args.region
# args.output should be a list of output names. If they do not exist, the outputs should be the same as the
# inputs with whatever suffix, if any, the user gave
if not args.output:
args.output = [utilities.add_suffix_prefix(im_name, suffix=args.suffix) for im_name in args.input]
# Do the actual trimming. We will do it first into a temporary file, then copy it into args.output. This is just
# in case the output and input filenames are the same, or if the output exists. IRAF will not overwrite!
for im_name, new_name in zip(args.input, args.output):
basename = os.path.splitext(os.path.basename(im_name))[0]
_, temp_output = tempfile.mkstemp(prefix=basename, suffix=".fits")
os.unlink(temp_output )
with utilities.tmp_mute():
imcopy(im_name + "[{0}:{1}, {2}:{3}]".format(x0, x1, y0, y1), temp_output)
shutil.move(temp_output, new_name)
# If a mask exists, trim exactly equally
if args.mask_key:
maskname = fits.getheader(im_name)[args.mask_key]
with fits.open(maskname, 'readonly') as mask_im:
mask_im[0].data = mask_im[0].data[y0:y1+1, x0:x1+1]
mask_output = utilities.replace_extension(new_name, ".fits.msk")
fits.writeto(mask_output, mask_im[0].data, mask_im[0].header, clobber=True)
utilities.header_update_keyword(new_name, "MASK", os.path.abspath(mask_output),
comment="Name of mask image. ")
return args.output
def include_wcs(args):
# Copy input names into output names
output_names = args.input[:]
for ii, im_name in enumerate(args.input):
# If it is a domeflat, skyflat or bias image, calculating the astrometry makes little sense
im = astroim.Astroim(im_name)
if im.target.objtype in ["bias", "domeflat", "skyflat", "flat"]:
continue
# Prepare my output file for the resulting image
if args.suffix:
new_file = utilities.add_suffix_prefix(im_name, suffix=args.suffix)
elif args.overwrite:
new_file = im_name
# Copy input image into a temporary file, so that we can modify it freely, for example, remove cosmics
# or filter it (to be done).
basename = get_basename(im_name)
_, input_image = tempfile.mkstemp(prefix=basename, suffix=".fits")
shutil.copy2(im_name, input_image)
# Remove cosmics
if args.cosmics:
perform_cosmic_removal(input_image)
# The output of the WCS process of astrometry.net will go to a .new file, the coordinates to a .coor
output_wcs = utilities.replace_extension(input_image, ".new")
solved_file = utilities.replace_extension(input_image, ".solved")
corrfile = utilities.replace_extension(input_image, ".cor")
# Try first with the defaults of astrometry
arguments_def = ["solve-field", "--no-plots", "--no-fits2fits", "--dir", "/tmp", "--overwrite",
"--new-fits", output_wcs, "--corr", corrfile, "--cpulimit", "1", input_image]
try: # Try to add the RA, DEC, Radius options to constrain the search
ra, dec = im.primary_header.get(im.primary_header.RAk, im.primary_header.DECk)
ra, dec = utilities.sex2deg(ra, dec)
arguments = arguments_def + ["--ra", str(ra), "--dec", str(dec), "--radius", str(args.radius),
"--cpulimit", "20"]
except:
arguments = arguments_def
print "Trying to find WCS with astrometry standard keywords. "
with utilities.tmp_mute():
subprocess.call(arguments)
# Now we will try using sextractor
build_default_sex(args)
# To avoid having too much residual crap in the folder, the output of astrometry will go to tmp (--dir /tmp).
arguments0 = ["solve-field", "--no-plots", "--no-fits2fits", "--use-sextractor", "--dir", "/tmp",
"--x-column", "X_IMAGE", "--y-column", "Y_IMAGE", "--sort-column", "MAG_AUTO",
"--sort-ascending", "--sextractor-config", os.path.join(repipy_path, "default.sex"),
"--overwrite", "--new-fits", output_wcs, "--corr", corrfile, input_image]
arguments0 += args.extras
try: # Try to add the RA, DEC, Radius options to constrain the search
ra, dec = im.primary_header.get(im.primary_header.RAk, im.primary_header.DECk)
ra, dec = utilities.sex2deg(ra, dec)
arguments = arguments0 + ["--ra", str(ra), "--dec", str(dec), "--radius", str(args.radius),
"--cpulimit", "20"]
except:
arguments = arguments0
# Run astrometry, in case of not solving it on the first attempt, try fitting freely (no RA, DEC used)
if not os.path.exists(solved_file):
subprocess.call(arguments)
if not os.path.exists(solved_file):
subprocess.call(arguments0)
# Only if we have a solution
if os.path.exists(solved_file):
# copy the input file into the new file if they are not the same
if os.path.abspath(im_name) != os.path.abspath(new_file):
shutil.copy2(im_name, new_file)
# get WCS from the resulting file, only the part added by astrometry.net
with fits.open(output_wcs) as file_wcs:
hdr_wcs = file_wcs[0].header
ind = hdr_wcs.values().index('Original key: "END"') # new part added by astrometry
hdr_wcs = hdr_wcs[ind:]
# Add that header to the original one of the image
with fits.open(new_file, 'update') as new_im:
new_im[0].header += hdr_wcs
new_im.flush()
# Build a catalogue of RA, DEC for the stars found
with fits.open(corrfile) as table:
cat_radec = utilities.replace_extension(new_file, "radec")
with open(cat_radec, "w") as f:
for ra, dec in zip(table[1].data["field_ra"], table[1].data["field_dec"]):
f.write(str(ra) + " " + str(dec) + "\n")
output_names[ii] = new_file
# If --remove_original is True
if args.remove_orig and not args.overwrite:
os.unlink(im_name)
return output_names
