From 2e796f38dbdc1044c13a768c76fa733ad07b9829 Mon Sep 17 00:00:00 2001
From: Aaron LI <aly@aaronly.me>
Date: Sun, 11 Jun 2017 16:11:31 +0800
Subject: Add astro/21cm/extract_slice.py

---
 astro/21cm/extract_slice.py | 84 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100755 astro/21cm/extract_slice.py

diff --git a/astro/21cm/extract_slice.py b/astro/21cm/extract_slice.py
new file mode 100755
index 0000000..576b7ee
--- /dev/null
+++ b/astro/21cm/extract_slice.py
@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+#
+# Copyright (c) 2017 Weitian LI <weitian@aaronly.me>
+# MIT License
+#
+
+"""
+Extract a slice from the 21cm cube and save as FITS image.
+"""
+
+import os
+import sys
+import argparse
+
+import numpy as np
+import astropy.io.fits as fits
+
+
+def main():
+    outfile_default = "{prefix}_z{z:05.2f}_N{Nside}_L{Lside}_s{sidx}.fits"
+
+    parser = argparse.ArgumentParser(
+        description="Extract a slice from cube and save as FITS image")
+    parser.add_argument("-C", "--clobber", dest="clobber",
+                        action="store_true",
+                        help="overwrite existing files")
+    parser.add_argument("-d", "--dtype", dest="dtype", default="float32",
+                        help="NumPy dtype of data cubes (default: float32)")
+    parser.add_argument("-z", "--redshift", dest="redshift",
+                        type=float, required=True,
+                        help="redshift of the input data cube")
+    parser.add_argument("-L", "--len-side", dest="Lside",
+                        type=float, required=True,
+                        help="Side length of the cube [comoving Mpc]")
+    parser.add_argument("-s", "--slice-idx", dest="sidx",
+                        type=int, default=None,
+                        help="slice index to be extracted (default: "
+                        "the central slice)")
+    parser.add_argument("-u", "--unit", dest="unit",
+                        help="data unit (e.g., K, mK)")
+    parser.add_argument("-i", "--infile", dest="infile", required=True,
+                        help="input data cube")
+    parser.add_argument("-o", "--outfile", dest="outfile",
+                        default=outfile_default,
+                        help="output FITS image slice (default: %s)" %
+                        outfile_default)
+    parser.add_argument("-p", "--prefix", dest="prefix", required=True,
+                        help="prefix for the output FITS image")
+    args = parser.parse_args()
+
+    cube = np.fromfile(open(args.infile, "rb"), dtype=args.dtype)
+    Nside = round(cube.shape[0] ** (1.0/3))
+    print("Read cube: %s (Nside=%d)" % (args.infile, Nside))
+    if args.sidx is None:
+        sidx = int(Nside / 2.0)
+    elif args.idx >= 0 and args.idx < Nside:
+        sidx = args.idx
+    else:
+        raise ValueError("invalid slice index: %s" % args.sidx)
+    outfile = args.outfile.format(prefix=args.prefix, z=args.redshift,
+                                  Nside=Nside, Lside=args.Lside, sidx=sidx)
+    if os.path.exists(outfile) and not args.clobber:
+        raise OSError("output file already exists: %s" % outfile)
+
+    cube = cube.reshape((Nside, Nside, Nside))
+    simg = cube[:, :, sidx]
+    header = fits.Header()
+    header["REDSHIFT"] = args.redshift
+    header["Lside"] = (args.Lside, "Cube side length [comoving Mpc]")
+    header["Nside"] = (Nside, "Number of pixels on each cube side")
+    header["SliceIdx"] = (sidx, "Index of this extracted slice")
+    if args.unit:
+        header["BUNIT"] = (args.unit, "Data unit")
+    header.add_history(" ".join(sys.argv))
+    hdu = fits.PrimaryHDU(data=simg, header=header)
+    try:
+        hdu.writeto(outfile, overwrite=args.clobber)
+    except TypeError:
+        hdu.writeto(outfile, clobber=args.clobber)
+    print("Extracted #%d slice: %s" % (sidx, outfile))
+
+
+if __name__ == "__main__":
+    main()
-- 
cgit v1.2.2