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#!/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()
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