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#!/usr/bin/env python3
#
# Copyright (c) 2017 Weitian LI <weitian@aaronly.me>
# MIT license
#
"""
Convert the image (e.g., by WSClean) from units [Jy/beam] to [K]
by taking into account the telescope's beam size.
"""
import os
import sys
import argparse
import numpy as np
from astropy.io import fits
import astropy.units as au
def open_image(infile):
"""
Open the FITS image and return its header and data, but requiring
the input image has only ONE frequency.
The input FITS image may have following dimensions:
* NAXIS=2: [Y, X]
* NAXIS=3: [FREQ=1, Y, X]
* NAXIS=4: [STOKES, FREQ=1, Y, X]
"""
with fits.open(infile) as f:
header = f[0].header
data = f[0].data
if ((data.ndim == 3 and data.shape[0] != 1) or
(data.ndim == 4 and data.shape[1] != 1)):
# NAXIS=3: [FREQ!=1, Y, X]
# NAXIS=4: [STOKES, FREQ!=1, Y, X]
raise ValueError("input file '{0}' has invalid dimensions: {1}".format(
infile, data.shape))
print("Read in FITS image from: %s" % infile)
return (header, data)
def calc_beam_size(header):
"""
Calculate the beam/PSF size using the 'WSCNORMF' keyword recorded by
the WSClean imager, which applies to the natural-weighted image, and
is more accurate than the fitted beam (stored as 'BMAJ' and 'BMIN'.)
"""
try:
weight = header["WSCWEIGH"]
normf = header["WSCNORMF"]
print("WSCWEIGH: %s" % weight)
print("WSCNORMF: %.1f" % normf)
except KeyError:
raise RuntimeError("NO necessary WSC* keyword; switch to " +
"--use-fitted-beam instead")
if weight.upper() != "NATURAL":
print("WARNING: weighting scheme is '%s' != natural!" % weight)
width = header["NAXIS1"]
height = header["NAXIS2"]
pixelsize = np.abs(header["CDELT1"]) * 3600 # [arcsec]
print("Image: %dx%d, %.1f [arcsec/pixel]" % (width, height, pixelsize))
beam_size = (width*height * pixelsize**2) / normf
return beam_size
def main():
parser = argparse.ArgumentParser(
description="Convert WSClean created image from [Jy/beam] to [K]",
epilog=("By default the 'WSCNORMF' keyword is taken to derive " +
"the beam/PSF size for natural-weighted image created " +
"by WSClean, which is more accurate than the fitted " +
"beam stored as 'BMAJ' and 'BMIN'."))
parser.add_argument("-C", "--clobber", dest="clobber",
action="store_true",
help="overwrite existing output file")
parser.add_argument("-B", "--use-fitted-beam", dest="use_fitted_beam",
action="store_true",
help="use the fitted beam (i.e., BMAJ and BMIN) " +
"or the beam size specified by --beam-size.")
parser.add_argument("-b", "--beam-size", dest="beam_size", type=float,
help="instrumental beam size [arcsec^2] " +
"(=pi*bmajor*bminor/4/ln(2)) (default: obtain " +
"from the header BMAJ and BMIN keywords); this " +
"argument also implies --use-fitted-beam")
parser.add_argument("-f", "--frequency", dest="frequency",
help="frequency [MHz] of the input image (NOTE: " +
"required if failed to obtain from the header)")
parser.add_argument("infile",
help="input FITS image file (NOTE: only single " +
"frequency supported)")
parser.add_argument("outfile",
help="output filename of the converted image")
args = parser.parse_args()
header, data = open_image(args.infile)
bunit = header["BUNIT"]
if bunit.upper() == "JY/BEAM":
unit = "Jy"
elif bunit.upper() == "MJY/BEAM":
unit = "mJy"
else:
raise ValueError("input image has wrong unit: %s" % bunit)
print("Data unit: %s/beam" % unit)
if args.frequency:
freq = args.frequency # [MHz]
else:
try:
freq = header["FREQ"] # [MHz]
except KeyError:
if header.get("CTYPE3", "").upper() == "FREQ":
freq = header["CRVAL3"] / 1e6 # [MHz]
else:
raise ValueError("--frequency required")
print("Frequency: %.2f [MHz]" % freq)
# Elliptical Gaussian beam (full width at half power; FWHP)
if args.beam_size:
beam_size = args.beam_size
elif args.use_fitted_beam:
bmajor = header["BMAJ"] * 3600 # [arcsec]
bminor = header["BMIN"] * 3600 # [arcsec]
beam_size = np.pi * bmajor*bminor / (4*np.log(2)) # [arcsec^2]
print("Beam: (%.2f, %.2f) [arcsec]" % (bmajor, bminor))
else:
# Derive beam size using 'WSCNORMF' keyword
beam_size = calc_beam_size(header)
print("Beam size: %.2f [arcsec^2]" % beam_size)
equiv = au.brightness_temperature(beam_size*au.arcsec**2, freq*au.MHz)
jybeam2k = au.Unit(unit).to(au.K, equivalencies=equiv)
print("Conversion factor [%s/beam] -> [K]: %g" % (unit, jybeam2k))
header["BUNIT"] = ("K", "Kelvin; converted from [%s/beam]" % unit)
header["JyBeam2K"] = (jybeam2k,
"[%s/beam] -> [K] conversion factor" % unit)
header["FREQ"] = (freq, "[MHz] frequency")
header.add_history(" ".join(sys.argv))
data = data * jybeam2k
if os.path.exists(args.outfile):
if args.clobber:
os.remove(args.outfile)
else:
raise OSError("output file already existed: %s" % args.outfile)
hdu = fits.PrimaryHDU(data=data, header=header)
hdu.writeto(args.outfile)
print("Converted image wrote to: %s" % args.outfile)
if __name__ == "__main__":
main()
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