whr = np.where(list_images["type"] == "blanks")
create_masks.main(arguments=["--max_val", "30000", "--min_val", "1000", "--stars",
"--circular"] + list(list_images["filename"][whr]))
# Combine bias images
print "Combining bias images"
whr = np.where(list_images["type"] == "bias")
bias_images = list(list_images["filename"][whr])
superbias = combine_images.main(arguments=["--average", "median",
"--all_together", "--output", "superbias.fits",
"--mask_key", "mask", "--filterk", filterk] + bias_images[:])
# Subtract bias from all images.
print "Subtracting bias"
newname = arith.main(arguments=["--suffix", " -b", "--message",
"BIAS SUBTRACTED", "--mask_key",
"mask"] + list(list_images["filename"]) +
[ "-", superbias["AllFilters"]])
list_images["filename"][:] = newname
# Combine skyflats using blocks to distinguish between sunset and sunrise flats.
print "Combining sky flats"
skyflat_indices = np.where(list_images["type"] == "skyflats")
times = list_images["time"][skyflat_indices] # times of the skyflat images
block_limits = utilities.group_images_in_blocks(times, limit=20)
master_skyflats = {}
for ii in range(len(block_limits)-1):
block = list_images["filename"][skyflat_indices][block_limits[ii]:block_limits[ii+1]]
time_block = utilities.mean_datetime(list_images["time"][skyflat_indices]
[block_limits[ii]:block_limits[ii+1]] )
skyflat = combine_images.main(arguments=["--average", "median", "--norm",
"--scale", "median",
print "Bias images", bias_images
output_bias = os.path.join(directory, "superbias.fits")
superbias = combine_images.main(arguments=["--average", "median",
"--all_together",
"--output", output_bias,
"--mask_key", "mask",
"--filterk", filterk] +\
bias_images[:])
print "Subtract bias"
for ii, im in enumerate(list_images["filename"]):
if list_images["type"][ii] not in ["bias", "unknown"]:
args = ["--suffix", " -b", "--message", "BIAS SUBTRACTED", "--mask_key", "mask", im, "-", superbias["AllFilters"]]
if type_of_bias_subtraction:
args = [type_of_bias_subtraction] + args
newname = arith.main(arguments=args)
list_images["filename"][ii] = newname
print "Combine flats"
output_flats = os.path.join(directory, "masterskyflat.fits")
flat_indices = np.where(list_images["type"] == "skyflats")
flats = combine_images.main(arguments=["--average", "median", "--norm",
"--scale", "median", "--output",
output_flats, "--mask_key", "mask",
"--filterk", filterk] +
list(list_images["filename"][flat_indices]))
print "Correct flat-field"
for ii,im in enumerate(list_images["filename"]):
if list_images["type"][ii] not in ["bias", "unknown"]:
# Guess the filter of the image from the name, find correct flat
def combine(args):
# Create the folders that do not already exist for the output file
outdir, outfile = os.path.split(os.path.abspath(args.output))
if outdir == "":
outdir = "."
utils.if_dir_not_exists_create(outdir)
# Build a list of the filter of each image
#filter_list, images_filters = build_filter_list(args)
images_filters = utils.collect_from_images(args.input, args.filterk)
# If user wants all images to be combined together, regardless of filter:
if args.all_together:
images_filters = ["AllFilters"] * len(images_filters)
# Create a default dictionary for the resulting images
result = collections.defaultdict(str)
# For each of the filters present combine the images (and write)
for filt in set(images_filters):
# list of objects with current filter (exception: allfilters is true)
list1 = [args.input[p] for p,f in enumerate(images_filters) if f == filt ]
# Check that all images have same dimension. If not, exit program
if not utils.check_dimensions(list1):
sys.exit("Dimensions of images to combine are different!")
# Calculate scale of images
scales = compute_scales(list1, args.scale, args.mask_key)
# Get the sizes of the images
lx, ly = utils.get_from_header(list1[0], "NAXIS2", "NAXIS1")
# Now, in order to avoid loading many images in memory, we need to slice the images in pieces and combine a slice
# of all the images at a time
n_slices = 32 # divide the slow axis in this many pieces
# Define the whole image and set all elements of mask to False
whole_image = numpy.ma.zeros([lx,ly])
whole_image.mask = numpy.zeros_like(whole_image.data)
for xmin in range(0, lx, lx/n_slices):
xmax = min(xmin + lx/n_slices, lx)
# Now we can build and sort a section of the cube with all the images
cube = cube_images(list1, args.mask_key, scales, limits=[xmin, 0, xmax, ly])
cube.sort(axis=0)
# Finally, average! Remember that the cube is sorted so that
# cube[0,ii,jj] < cube[1,ii,jj] and that the highest values of all
# are the masked elements. We will take advantage of it if the median
# is selected, because nowadays the masked median is absurdly slow:
# https://github.com/numpy/numpy/issues/1811
map_cube = numpy.ma.count(cube, axis=0) # number non-masked values per pixel
if args.average == "mean":
image = numpy.ma.mean(cube, axis=0)
non_masked_equivalent = numpy.mean(cube.data, axis=0)
elif args.average == "median":
image = home_made_median(map_cube, cube)
non_masked_equivalent = numpy.median(cube.data, axis=0)
# Image is a masked array, we need to fill in masked values with the
# args.fill_val if user provided it. Also, values with less than
# args.nmin valid values should be masked out. If user did not provide
# a fill_val argument, we will substitute masked values with the
# unmasked equivalent operation.
image.mask[map_cube < args.nmin] = 1
mask = image.mask
if args.fill_val != '':
image = image.filled(args.fill_val)
else:
image.data[mask == True] = non_masked_equivalent[mask == True]
image = image.data
whole_image.data[xmin:xmax, 0:ly] = image[:,:]
whole_image.mask[xmin:xmax, 0:ly] = mask[:,:]
# And save images. If all_together is activated, use the file name given by user. If not, we need
# to separate by filter, so compose a new name with the one given by the user adding the filter
if args.all_together:
newfile = args.output
else:
newfile = os.path.join(outdir, utils.add_suffix_prefix(outfile, suffix="_" + filt) )
if args.out_mask != "":
name_mask = args.out_mask
else:
name_mask = newfile + ".msk"
if os.path.isfile(newfile):
os.remove(newfile)
if os.path.isfile(name_mask):
os.remove(name_mask)
fits.writeto(newfile, whole_image.data)
fits.writeto(name_mask, whole_image.mask.astype(numpy.int))
result[filt] = newfile
# Add comments to the headers
string1 = " - Image built from the combination of the images: "+\
", ".join(list1)
string2 = " combine = " + args.average + ", scale = " + args.scale
utils.add_history_line(newfile, string1 + string2 )
utils.add_history_line(name_mask, " - Mask of image: " + newfile)
if args.mask_key != "":
utils.header_update_keyword(newfile, args.mask_key, name_mask,
"Mask for this image")
# To normalize calculate median and call arith_images to divide by it.
if args.norm == True:
median = compute_scales([newfile], args.scale, args.mask_key)[0]
msg = "- NORMALIZED USING MEDIAN VALUE:"
arith_images.main(arguments=["--message", msg, "--output", newfile,
"--mask_key", args.mask_key, "--fill_val",
args.fill_val, newfile, "/", str(median)])
return result
"--sigma_key", sky_stdk,
"--gain_key", gaink,
"--ron_key", read_noisek,
"--expt_key", exptimek,
"--airm_key", airmassk,
"--FWHM_k", seeingk] + obj_images)
list_images["filename"][np.where(list_images["objname"] == obj)] = output_images
print "Normalize using exposure time. "
for ii, im_name in enumerate(list_images["filename"]):
if list_images["type"][ii] in ["cig", "clusters"]:
tt = float(utils.get_from_header(im_name, exptimek))
newname = utils.add_suffix_prefix(im_name, suffix="-t")
mssg = "Normalized to exptime (divided by " + str(tt) + ")"
arith_images.main(arguments=["--output", newname, "--message", mssg, "--mask_key", "MASK", im_name, "/", str(tt)])
mssg = "Before normalizing: " + str(tt)
# Update values for the exptime, the sky, the sky std...
utils.header_update_keyword(newname, exptimek, 1, mssg)
ss = float(utils.get_from_header(im_name, skyk))
utils.header_update_keyword(newname, skyk, ss/tt)
ss_std = float(utils.get_from_header(im_name, sky_stdk))
utils.header_update_keyword(newname, sky_stdk, ss_std/tt)
list_images["filename"][ii] = newname
print "Correct for atmospheric extinction."
for ii, im_name in enumerate(list_images["filename"]):
if list_images["type"][ii] in ["cig", "clusters", "standards"]:
airmass = float(utils.get_from_header(im_name, airmassk))
correcting_factor = 10**(ext_coeff * airmass / 2.5)