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#!/usr/bin/env python3
#
# Copyright (c) Weitian LI <weitian@aaronly.me>
# MIT license
#
"""
Create FITS image cube from a series of image slices.
"""
import os
import sys
import argparse
from datetime import datetime, timezone
import numpy as np
from astropy.io import fits
from astropy.wcs import WCS
class FITSCube:
"""
FITS image cube.
"""
def __init__(self, infile=None):
if infile is not None:
self.load(infile)
def load(self, infile):
with fits.open(infile) as f:
self.data = f[0].data
self.header = f[0].header
print("Loaded FITS cube from file: %s" % infile)
print("Cube dimensions: %dx%dx%d" %
(self.width, self.height, self.nslice))
# The Z-axis position of the first slice.
self.zbegin = self.header["CRVAL3"]
# The Z-axis step/spacing between slices.
self.zstep = self.header["CDELT3"]
def add_slices(self, slices, zbegin=0.0, zstep=1.0):
"""
Create a FITS cube from input image slices.
"""
self.slices = slices
self.zbegin = zbegin
self.zstep = zstep
nslice = len(slices)
header, image = self.open_image(slices[0])
shape = (nslice, ) + image.shape
data = np.zeros(shape, dtype=image.dtype)
for i, s in enumerate(slices):
print("[%d/%d] Adding image slice: %s ..." % (i+1, nslice, s))
hdr, img = self.open_image(s)
data[i, :, :] = img
self.data = data
self.header = header.copy(strip=True)
print("Created FITS cube of dimensions: %dx%dx%d" %
(self.width, self.height, self.nslice))
@staticmethod
def open_image(infile):
"""
Open the slice image and return its header and 2D image data.
NOTE
----
The input slice image may have following dimensions:
* NAXIS=2: [Y, X]
* NAXIS=3: [FREQ=1, Y, X]
* NAXIS=4: [STOKES=1, FREQ=1, Y, X]
NOTE
----
Only open slice image that has only ONE frequency and ONE Stokes
parameter.
Returns
-------
header : `~astropy.io.fits.Header`
image : 2D `~numpy.ndarray`
The 2D [Y, X] image part of the slice image.
"""
with fits.open(infile) as f:
header = f[0].header
data = f[0].data
if data.ndim == 2:
# NAXIS=2: [Y, X]
image = data
elif data.ndim == 3 and data.shape[0] == 1:
# NAXIS=3: [FREQ=1, Y, X]
image = data[0, :, :]
elif data.ndim == 4 and data.shape[0] == 1 and data.shape[1] == 1:
# NAXIS=4: [STOKES=1, FREQ=1, Y, X]
image = data[0, 0, :, :]
else:
raise ValueError("Slice '{0}' has invalid dimensions: {1}".format(
infile, data.shape))
return (header, image)
@property
def header(self):
try:
return self.header_
except AttributeError:
return fits.Header()
@header.setter
def header(self, value):
self.header_ = value
for key in ["CTYPE4", "CRPIX4", "CRVAL4", "CDELT4", "CUNIT4"]:
try:
del self.header_[key]
except KeyError:
pass
@property
def wcs(self):
w = WCS(naxis=3)
w.wcs.ctype = ["pixel", "pixel", "pixel"]
w.wcs.crpix = np.array([self.header.get("CRPIX1", 1.0),
self.header.get("CRPIX2", 1.0),
1.0])
w.wcs.crval = np.array([self.header.get("CRVAL1", 0.0),
self.header.get("CRVAL2", 0.0),
self.zbegin])
w.wcs.cdelt = np.array([self.header.get("CDELT1", 1.0),
self.header.get("CDELT2", 1.0),
self.zstep])
return w
def write(self, outfile, clobber=False):
header = self.header
header.extend(self.wcs.to_header(), update=True)
header["DATE"] = (datetime.now(timezone.utc).astimezone().isoformat(),
"File creation date")
header.add_history(" ".join(sys.argv))
hdu = fits.PrimaryHDU(data=self.data, header=header)
try:
hdu.writeto(outfile, overwrite=clobber)
except TypeError:
hdu.writeto(outfile, clobber=clobber)
@property
def width(self):
__, __, w = self.data.shape
return w
@property
def height(self):
__, h, __ = self.data.shape
return h
@property
def nslice(self):
ns, __, __ = self.data.shape
return ns
@property
def zvalues(self):
"""
Calculate the Z-axis positions for all slices
"""
nslice = self.nslice
wcs = self.wcs
pix = np.zeros(shape=(nslice, 3), dtype=np.int)
pix[:, 2] = np.arange(nslice)
world = wcs.wcs_pix2world(pix, 0)
return world[:, 2]
def cmd_info(args):
"""
Sub-command: "info", show FITS cube information
"""
cube = FITSCube(args.infile)
print("Image/slice size: %dx%d" % (cube.width, cube.height))
print("Number of slices: %d" % cube.nslice)
print("Slice step/spacing: %.3f" % cube.zstep)
print("Slice positions:\n{0}".format(cube.zvalues))
def cmd_create(args):
"""
Sub-command: "create", create a FITS cube
"""
if not args.clobber and os.path.exists(args.outfile):
raise FileExistsError("output file already exists: %s" % args.outfile)
cube = FITSCube()
cube.add_slices(args.infiles, zbegin=args.zbegin, zstep=args.zstep)
cube.write(args.outfile, clobber=args.clobber)
print("Created FITS cube: %s" % args.outfile)
def main():
parser = argparse.ArgumentParser(
description="Create FITS cube from a series of image slices.")
subparsers = parser.add_subparsers(dest="subparser_name",
title="sub-commands",
help="additional help")
# sub-command: "info"
parser_info = subparsers.add_parser("info", help="show FITS cube info")
parser_info.add_argument("infile", help="FITS cube filename")
parser_info.set_defaults(func=cmd_info)
# sub-command: "create"
parser_create = subparsers.add_parser("create", help="create a FITS cube")
parser_create.add_argument("-C", "--clobber", dest="clobber",
action="store_true",
help="overwrite existing output file")
parser_create.add_argument("-z", "--z-begin", dest="zbegin",
type=float, default=0.0,
help="Z-axis position of the first slice")
parser_create.add_argument("-s", "--z-step", dest="zstep",
type=float, default=1.0,
help="Z-axis step/spacing between slices")
parser_create.add_argument("-o", "--outfile", dest="outfile",
required=True,
help="output FITS cube filename")
parser_create.add_argument("-i", "--infiles", dest="infiles",
nargs="+", required=True,
help="input image slices (in order)")
parser_create.set_defaults(func=cmd_create)
#
args = parser.parse_args()
args.func(args)
if __name__ == "__main__":
main()
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