1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
|
#!/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 Nx(self):
"""
Number of pixels along the X axis (i.e., image width)
"""
return self.shape[-1]
@property
def Ny(self):
"""
Number of pixels along the Y axis (i.e., image height)
"""
return self.shape[-2]
@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 size: %dx%d" % (fimage.Nx, fimage.Ny))
print("Data unit: %s" % fimage.bunit)
data = fimage.image
if args.abs:
data = np.abs(data)
if args.center:
print("Central box size: %d" % args.center)
rows, cols = data.shape
rc, cc = rows//2, cols//2
cs1, cs2 = args.center//2, (args.center+1)//2
data = data[(rc-cs1):(rc+cs2), (cc-cs1):(cc+cs2)]
mean = np.mean(data)
median = np.median(data)
std = np.std(data)
iqr = np.diff(np.percentile(data, q=(25, 75)))
mad = np.median(np.abs(data - median))
rms = np.sqrt(np.mean(data**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("mad: %-12.6e (median absolute deviation)" % mad)
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()
|
