diff options
| -rwxr-xr-x | astro/fits/fitsimage.py | 236 | ||||
| -rwxr-xr-x | astro/fits/fitsimgadd.py | 57 | ||||
| -rwxr-xr-x | astro/fits/fitsimgsub.py | 55 |
3 files changed, 236 insertions, 112 deletions
diff --git a/astro/fits/fitsimage.py b/astro/fits/fitsimage.py new file mode 100755 index 0000000..74b03cf --- /dev/null +++ b/astro/fits/fitsimage.py @@ -0,0 +1,236 @@ +#!/usr/bin/env python3 +# +# Copyright (c) Weitian LI <weitian@aaronly.me> +# MIT license +# + +""" +FITS image manipulate tool. +""" + +import sys +import argparse + +import numpy as np +from astropy.io import fits + + +class FITSImage: + """ + FITS image class that deals with plain 2D image (NAXIS=2), but also + handles single-frequency single-polarized image cube (NAXIS=3, 4), + e.g., created by WSClean. + """ + def __init__(self, infile): + with fits.open(infile) as f: + self.header = f[0].header + self.data = f[0].data + self.ndim = self.data.ndim + self.shape = self.data.shape + + @property + def bunit(self): + return self.header.get("BUNIT") + + @property + def image(self): + """ + Deal with single-frequency and single-polarized image cube. + """ + if self.ndim == 2: + # NAXIS=2: [Y, X] + image = self.data[:, :] + elif self.ndim == 3 and self.shape[0] == 1: + # NAXIS=3: [FREQ=1, Y, X] + image = self.data[0, :, :] + elif self.ndim == 4 and self.shape[0] == 1 and self.shape[1] == 1: + # NAXIS=4: [STOKES=1, FREQ=1, Y, X] + image = self.data[0, 0, :, :] + else: + raise ValueError("invalid data shape: {1}".format(self.shape)) + return image + + @image.setter + def image(self, value): + if self.ndim == 2: + # NAXIS=2: [Y, X] + self.data[:, :] = value + elif self.ndim == 3: + # NAXIS=3: [FREQ=1, Y, X] + self.data[0, :, :] = value + else: + # NAXIS=4: [STOKES=1, FREQ=1, Y, X] + self.data[0, 0, :, :] = value + + def write(self, outfile, clobber=False): + self.header.add_history(" ".join(sys.argv)) + hdu = fits.PrimaryHDU(data=self.data, header=self.header) + try: + hdu.writeto(outfile, overwrite=clobber) + except TypeError: + hdu.writeto(outfile, clobber=clobber) + + +def cmd_info(args): + """ + Sub-command: "info", show FITS image information + """ + fimage = FITSImage(args.infile) + print("Image data shape: {0}".format(fimage.shape)) + print("Data unit: %s" % fimage.bunit) + image = fimage.image + if args.abs: + image = np.abs(image) + if args.center: + print("Central box size: %d" % args.center) + rows, cols = image.shape + rc, cc = rows//2, cols//2 + cs1, cs2 = args.center//2, (args.center+1)//2 + image = image[(rc-cs1):(rc+cs2), (cc-cs1):(cc+cs2)] + mean = np.mean(image) + median = np.median(image) + iqr = np.diff(np.percentile(image, q=(25, 75))) + std = np.std(image) + rms = np.sqrt(np.mean(image**2)) + print("mean: %-12.6e" % mean) + print("median: %-12.6e" % median) + print("std: %-12.6e (standard deviation)" % std) + print("iqr: %-12.6e (interquartile range)" % iqr) + print("rms: %-12.6e (root-mean-squared)" % rms) + + +def cmd_add(args): + """ + Sub-command: "add", add the image by a number or other image(s) + """ + fimage = FITSImage(args.infile) + image = fimage.image + if args.number: + print("Add by number: %g" % args.number) + image += args.number + else: + for fn in args.files: + print("Add by another image from: %s" % fn) + fimage2 = FITSImage(fn) + image += fimage2.image + fimage.image = image + fimage.write(args.outfile, clobber=args.clobber) + print("Saved FITS image to: %s" % args.outfile) + + +def cmd_sub(args): + """ + Sub-command: "sub", subtract the image by a number or other image(s) + """ + fimage = FITSImage(args.infile) + image = fimage.image + if args.number: + print("Subtract by number: %g" % args.number) + image -= args.number + else: + for fn in args.files: + print("Subtract by another image from: %s" % fn) + fimage2 = FITSImage(fn) + image -= fimage2.image + fimage.image = image + fimage.write(args.outfile, clobber=args.clobber) + print("Saved FITS image to: %s" % args.outfile) + + +def cmd_mul(args): + """ + Sub-command: "mul", multiply the image by a number or other image(s) + """ + fimage = FITSImage(args.infile) + image = fimage.image + if args.number: + print("Multiply by number: %g" % args.number) + image *= args.number + else: + for fn in args.files: + print("Multiply by another image from: %s" % fn) + fimage2 = FITSImage(fn) + image *= fimage2.image + fimage.image = image + fimage.write(args.outfile, clobber=args.clobber) + print("Saved FITS image to: %s" % args.outfile) + + +def main(): + parser = argparse.ArgumentParser( + description="FITS image manipulation tool") + subparsers = parser.add_subparsers(dest="subparser_name", + title="sub-commands", + help="additional help") + + # sub-command: "info" + parser_info = subparsers.add_parser( + "info", aliases=["show"], + help="show FITS image info") + parser_info.add_argument("-c", "--center", dest="center", type=int, + help="choose central region of specified size") + parser_info.add_argument("-a", "--abs", dest="abs", action="store_true", + help="take absolute values of image pixels") + parser_info.add_argument("infile", help="FITS image filename") + parser_info.set_defaults(func=cmd_info) + + # sub-command: "add" + parser_add = subparsers.add_parser( + "add", + help="add the image by a number or other image(s)") + parser_add.add_argument("-C", "--clobber", dest="clobber", + action="store_true", + help="overwrite existing output file") + parser_add.add_argument("-i", "--infile", dest="infile", required=True, + help="input FITS image") + parser_add.add_argument("-o", "--outfile", dest="outfile", required=True, + help="output FITS image") + exgrp_add = parser_add.add_mutually_exclusive_group(required=True) + exgrp_add.add_argument("-n", "--number", dest="number", type=float, + help="number to be added by") + exgrp_add.add_argument("-f", "--files", dest="files", nargs="+", + help="FITS image(s) to be added by") + parser_add.set_defaults(func=cmd_add) + + # sub-command: "sub" + parser_sub = subparsers.add_parser( + "sub", aliases=["subtract"], + help="subtract the image by a number or other image(s)") + parser_sub.add_argument("-C", "--clobber", dest="clobber", + action="store_true", + help="overwrite existing output file") + parser_sub.add_argument("-i", "--infile", dest="infile", required=True, + help="input FITS image") + parser_sub.add_argument("-o", "--outfile", dest="outfile", required=True, + help="output FITS image") + exgrp_sub = parser_sub.add_mutually_exclusive_group(required=True) + exgrp_sub.add_argument("-n", "--number", dest="number", type=float, + help="number to be subtracted by") + exgrp_sub.add_argument("-f", "--files", dest="files", nargs="+", + help="FITS image(s) to be subtracted by") + parser_sub.set_defaults(func=cmd_sub) + + # sub-command: "mul" + parser_mul = subparsers.add_parser( + "mul", aliases=["multiply"], + help="multiply the image by a number or other image(s)") + parser_mul.add_argument("-C", "--clobber", dest="clobber", + action="store_true", + help="overwrite existing output file") + parser_mul.add_argument("-i", "--infile", dest="infile", required=True, + help="input FITS image") + parser_mul.add_argument("-o", "--outfile", dest="outfile", required=True, + help="output FITS image") + exgrp_mul = parser_mul.add_mutually_exclusive_group(required=True) + exgrp_mul.add_argument("-n", "--number", dest="number", type=float, + help="number to be multiplied by") + exgrp_mul.add_argument("-f", "--files", dest="files", nargs="+", + help="FITS image(s) to be multiplied by") + parser_mul.set_defaults(func=cmd_mul) + + args = parser.parse_args() + args.func(args) + + +if __name__ == "__main__": + main() diff --git a/astro/fits/fitsimgadd.py b/astro/fits/fitsimgadd.py deleted file mode 100755 index 52afb95..0000000 --- a/astro/fits/fitsimgadd.py +++ /dev/null @@ -1,57 +0,0 @@ -#!/usr/bin/env python3 -# -# Copyright (c) Weitian LI <weitian@aaronly.me> -# MIT license -# - -""" -Add multiple FITS images of same shape. -""" - -import os -import sys -import argparse - -from astropy.io import fits - - -def main(): - parser = argparse.ArgumentParser( - description="Add two or more FITS images of same shape") - parser.add_argument("-C", "--clobber", action="store_true", - help="overwrite existing files") - parser.add_argument("-i", "--infile", nargs="+", - help=">=2 FITS images to be added") - parser.add_argument("-o", "--outfile", required=True, - help="filename of added FITS image") - args = parser.parse_args() - - nimg = len(args.infile) - if nimg < 2: - raise RuntimeError("more than 2 input FITS images required") - - if os.path.exists(args.outfile): - if args.clobber: - os.remove(args.outfile) - print("WARNING: removed existing output file: %s" % args.outfile) - else: - raise OSError("output file already exists: %s" % args.outfile) - - with fits.open(args.infile[0]) as f: - image = f[0].data - header = f[0].header - print("Opened 1st image: %s" % args.infile[0]) - print("Image shape: %s" % str(list(reversed(image.shape)))) - - for fn in args.infile[1:]: - print("Adding FITS image: %s ..." % fn) - image += fits.open(fn)[0].data - - header.add_history(" ".join(sys.argv)) - hdu = fits.PrimaryHDU(data=image, header=header) - hdu.writeto(args.outfile) - print("Wrote added FITS image to: %s" % args.outfile) - - -if __name__ == "__main__": - main() diff --git a/astro/fits/fitsimgsub.py b/astro/fits/fitsimgsub.py deleted file mode 100755 index cae0190..0000000 --- a/astro/fits/fitsimgsub.py +++ /dev/null @@ -1,55 +0,0 @@ -#!/usr/bin/env python3 -# -# Copyright (c) Weitian LI <weitian@aaronly.me> -# MIT license -# - -""" -Subtract a FITS image by one or more FITS images of same shape. -""" - -import os -import sys -import argparse - -from astropy.io import fits - - -def main(): - parser = argparse.ArgumentParser( - description="Subtract a FITS image by >=1 images of same shape") - parser.add_argument("-C", "--clobber", action="store_true", - help="overwrite existing files") - parser.add_argument("-1", "--infile1", required=True, - help="the FITS image from which to be subtracted") - parser.add_argument("-2", "--infile2", nargs="+", - help="one or more FITS images to be subtracted by") - parser.add_argument("-o", "--outfile", required=True, - help="filename of subtracted FITS image") - args = parser.parse_args() - - if os.path.exists(args.outfile): - if args.clobber: - os.remove(args.outfile) - print("WARNING: removed existing output file: %s" % args.outfile) - else: - raise OSError("output file already exists: %s" % args.outfile) - - with fits.open(args.infile1) as f: - image = f[0].data - header = f[0].header - print("Opened FITS image: %s" % args.infile1) - print("Image shape: %s" % str(list(reversed(image.shape)))) - - for fn in args.infile2: - print("Subtracting FITS image: %s ..." % fn) - image -= fits.open(fn)[0].data - - header.add_history(" ".join(sys.argv)) - hdu = fits.PrimaryHDU(data=image, header=header) - hdu.writeto(args.outfile) - print("Wrote subtracted FITS image to: %s" % args.outfile) - - -if __name__ == "__main__": - main() |