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#!/usr/bin/env python3
#
# Copyright (c) 2016 Aaron LI
# MIT license
#
# Extract surface brightness profile, with optional background
# subtraction and region exclusion.
#
# The input file can be the following 2 cases:
# (1) (RECOMMENDED) binned image file:
# e.g., the binned 0.7-7.0 keV image with its dimensions determined
# by the `skyfov.fits` file.
# Use this type of input file is recommended, as the required exposure
# map is also an image and thus has identical dimensions with the input
# image, therefore, the extraction region area can be accurately
# calculated with both the excluded point sources and the regions
# beyond the CCD edges accounted. And the final extracted surface
# brightness results (`SUR_FLUX`) will not be biased due to the regions
# lying beyond the CCD edges.
# In addition, using image as the input is also much faster.
# (2) events file (evt2):
# e.g., the cleaned evt2 file
# If the extraction region is beyond the CCD edges, the source extraction
# region will be *bigger* than the region for `MEAN_SRC_EXP` calculation,
# because the exposure image has specific boundaries while the events file
# dose not. In consequence, the final `SUR_FLUX` will be under-estimated.
# As a workaround, the original extraction regions need additional
# process that intersect with the CCD boundaries (extracted from the
# `skyfov.fits`).
#
# Created: 2016-05-17
#
# Change log:
# 2016-06-07:
# * Remove unused argument `--json`
# 2016-06-06:
# * Add explanations on image/evt2 input file
#
import os
import re
import argparse
import subprocess
import tempfile
import numpy as np
from astropy.io import fits
def check_acis_type(infile):
"""
Check the ACIS type of the infile: ACIS-I or ACIS-S
"""
subprocess.run(["punlearn", "dmkeypar"])
ret = subprocess.run(["dmkeypar", infile, "DETNAM", "echo=yes"],
check=True, stdout=subprocess.PIPE)
detnam = ret.stdout.decode("utf-8")
if re.match(r"^ACIS-0123[4-9]*", detnam):
results = {"type": "ACIS-I", "ccd": "0:3"}
elif re.match(r"^ACIS-[0-6]*7", detnam):
results = {"type": "ACIS-S", "ccd": "7"}
else:
raise ValueError("unknown DETNAM: %s" % detnam)
return results
def make_sbp_region(regfile, exclude_regfile=None, fov=None, ccd=None):
"""
Make the regions for SBP extraction, considering the regions to be
excluded and FoV constraint.
Return a list containing all the SBP regions.
"""
regions = map(str.strip, open(regfile).readlines())
regions = list(filter(lambda x: re.match(r"^(circle|annulus|pie).*",
x, re.I),
regions))
if exclude_regfile is not None:
ex_regions = map(str.strip, open(exclude_regfile).readlines())
ex_regions = list(filter(lambda x: not re.match(r"^\s*(|#.*)\s*$", x),
ex_regions))
ex_regions = "*!".join([""] + ex_regions)
regions = [reg+ex_regions for reg in regions]
if fov is not None:
with tempfile.NamedTemporaryFile() as fp:
subprocess.run(["punlearn", "dmmakereg"])
subprocess.run(args=[
"dmmakereg",
"region=region(%s[ccd_id=%s])" % (fov, ccd),
"outfile=%s" % fp.name,
"kernel=ascii",
"clobber=yes"
])
fov_regions = map(str.strip, open(fp.name).readlines())
fov_regions = list(filter(lambda x: re.match(r"^physical;polygon.*$",
x, re.I),
fov_regions))
fov_regions = [re.sub(r"^physical;\s*", "",
re.sub(r"\s*#\s*$", "", reg))
for reg in fov_regions]
regions = [
"+".join([
reg + "*" + fov for fov in fov_regions
])
for reg in regions
]
return regions
def extract_sbp(infile, expmap, regfile, outprefix, bkg=None, erange=None):
"""
Extract the surface brightness profile
If `bkg` is provided, then background subtraction is considered.
"""
if erange is not None:
erange = "[energy=%s]" % erange
else:
erange = ""
sbpfile = outprefix + ".fits"
cmd_args = [
"dmextract",
"infile=%s%s[bin sky=@%s]" % (infile, erange, regfile),
"outfile=%s" % sbpfile,
"exp=%s" % expmap,
"opt=generic",
"clobber=yes"
]
if bkg is not None:
# consider background subtraction
subprocess.run(["punlearn", "dmkeypar"])
ret = subprocess.run(args=["dmkeypar", infile, "EXPOSURE", "echo=yes"],
check=True, stdout=subprocess.PIPE)
exposure_evt = float(ret.stdout.decode("utf-8"))
ret = subprocess.run(args=["dmkeypar", bkg, "EXPOSURE", "echo=yes"],
check=True, stdout=subprocess.PIPE)
exposure_bkg = float(ret.stdout.decode("utf-8"))
bkg_norm = exposure_evt / exposure_bkg
cmd_args += [
"bkg=%s%s[bin sky=@%s]" % (bkg, erange, regfile),
"bkgnorm=%s" % bkg_norm,
"bkgexp=)exp"
]
subprocess.run(["punlearn", "dmextract"])
subprocess.run(args=cmd_args)
# add `RMID` and `R_ERR` columns
sbpfile_rmid = outprefix + "_rmid.fits"
subprocess.run(["punlearn", "dmtcalc"])
subprocess.run(args=[
"dmtcalc",
"infile=%s" % sbpfile,
"outfile=%s" % sbpfile_rmid,
"expression=RMID=(R[0]+R[1])/2,R_ERR=(R[1]-R[0])/2",
"clobber=yes"
])
# dump SBP data
with fits.open(sbpfile_rmid) as sbpfits:
rmid = sbpfits["HISTOGRAM"].data["RMID"]
r_err = sbpfits["HISTOGRAM"].data["R_ERR"]
sur_flux = sbpfits["HISTOGRAM"].data["SUR_FLUX"]
sur_flux_err = sbpfits["HISTOGRAM"].data["SUR_FLUX_ERR"]
sbpdata = np.column_stack([rmid, r_err, sur_flux, sur_flux_err])
sbp_txt = outprefix + ".txt"
np.savetxt(sbp_txt, sbpdata, header="RMID R_ERR SUR_FLUX SUR_FLUX_ERR")
# create a QDP file
sbp_qdp = map(str.strip, open(sbp_txt).readlines())
sbp_qdp = [re.sub(r"#", "!", line) for line in sbp_qdp]
sbp_qdp = [
"READ SERR 1 2",
'LABEL T "Surface Brightness Profile"',
'LABEL X "Radius (pixel)"',
'LABEL Y "Surface Flux (photons/cm\\u2\\d/pixel\\u2\\d/s)"',
"LOG X Y ON"
] + sbp_qdp
open(outprefix + ".qdp", "w").write("\n".join(sbp_qdp) + "\n")
def main():
parser = argparse.ArgumentParser(
description="Extract surface brightness profile")
parser.add_argument("-r", "--region", dest="region",
required=False, default="sbprofile.reg",
help="surface brightness profile region file " +
"(default: sbprofile.reg)")
parser.add_argument("-R", "--exclude-region", dest="exclude_region",
default=None,
help="file containing regions to be excluded")
parser.add_argument("-i", "--infile", dest="infile", required=True,
help="input binned image (RECOMMENDED) or EVT2 file")
parser.add_argument("-e", "--expmap", dest="expmap", required=True,
help="exposure map of the input file")
parser.add_argument("-b", "--bkg", dest="bkg", default=None,
help="background event/image of the input file")
parser.add_argument("-E", "--erange", dest="erange", default=None,
help="energy range of interest (for input evt2 file)")
parser.add_argument("-F", "--fov", dest="fov", default=None,
help="FoV FITS file (for applying FoV constraint " +
"to the SBP regions; recommended if use " +
"evt2 file as the input file)")
parser.add_argument("-o", "--outprefix", dest="outprefix",
required=False,
help="prefix of output files (default: same " +
"basename as the input region file)")
args = parser.parse_args()
# set output prefix if not specified
if not args.outprefix:
args.outprefix = os.path.splitext(args.region)[0]
acis_type = check_acis_type(args.infile)
regions = make_sbp_region(regfile=args.region,
exclude_regfile=args.exclude_region,
fov=args.fov, ccd=acis_type["ccd"])
regfile_out = args.outprefix + "_fix.reg"
open(regfile_out, "w").write("\n".join(regions) + "\n")
extract_sbp(infile=args.infile, expmap=args.expmap,
regfile=regfile_out, outprefix=args.outprefix,
bkg=args.bkg, erange=args.erange)
if __name__ == "__main__":
main()
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