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#!/usr/bin/env python3
#
# Copyright (c) 2017 Weitian LI <liweitianux@live.com>
# MIT license
"""
Further process the reprocessed evt2 file to make a cleaned one
for later scientific analysis.
The following steps are carried out:
1. Filter out the chips of interest;
2. Detect (point) sources, visually check and manually update;
3. Remove the updated sources;
4. Extract light curve of the background regions (away from the object);
5. Check and clip the light curve to create a GTI;
6. Remove flares by filtering the GTI to create the finally cleaned evt2.
"""
import os
import argparse
import subprocess
import shutil
import logging
from _context import acispy
from acispy.manifest import get_manifest
from acispy.pfiles import setup_pfiles
from acispy.acis import ACIS
from acispy.ds9 import ds9_view
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
def filter_chips(infile, outfile, chips, clobber=False):
"""
Filter out the chips of interest, e.g., ``ccd_id=7`` for ACIS-S
observation, and ``ccd_id=0:3`` for ACIS-I observation.
"""
chips = chips.replace("-", ":")
clobber = "yes" if clobber else "no"
logger.info("Filter out chips of interest: %s" % chips)
logger.info("Outfile: %s" % outfile)
subprocess.check_call(["punlearn", "dmcopy"])
subprocess.check_call([
"dmcopy", "infile=%s[ccd_id=%s]" % (infile, chips),
"outfile=%s" % outfile, "clobber=%s" % clobber
])
logger.info("Done!\n")
def detect_sources(infile, outfile, clobber=False):
"""
Detect (point) sources using ``celldetect``; examine the detected
sources in DS9, and update the source regions and save.
"""
src_fits = os.path.splitext(outfile)[0] + ".fits"
clobber = "yes" if clobber else "no"
logger.info("Detect sources using 'celldetect' ...")
logger.info("Outfile: %s" % outfile)
subprocess.check_call(["punlearn", "celldetect"])
subprocess.check_call([
"celldetect", "infile=%s" % infile,
"outfile=%s" % src_fits, "regfile=%s" % outfile,
"clobber=%s" % clobber
])
os.remove(src_fits)
shutil.copy(outfile, outfile+".orig")
logger.warning("Check and update detected source regions; " +
"and save/overwrite file: %s" % outfile)
ds9_view(infile, regfile=outfile)
logger.info("Done!\n")
def remove_sources(infile, outfile, srcfile, clobber=False):
"""
Remove detected sources
"""
clobber = "yes" if clobber else "no"
logger.info("Remove detected sources ...")
logger.info("Outfile: %s" % outfile)
subprocess.check_call(["punlearn", "dmcopy"])
subprocess.check_call([
"dmcopy", "infile=%s[exclude sky=region(%s)]" % (infile, srcfile),
"outfile=%s" % outfile, "clobber=%s" % clobber
])
logger.info("Done!\n")
def extract_lightcurve(infile, outfile, bintime=200, clobber=False):
"""
Extract the light curve from regions away from the object.
"""
clobber = "yes" if clobber else "no"
logger.info("Extract light curve for GTI generation ...")
logger.info("Outfile: %s" % outfile)
regfile = os.path.splitext(outfile)[0] + ".reg"
# Credit: https://stackoverflow.com/a/12654798/4856091
open(regfile, "a").close()
logger.warning("Select a large region containing most of the object, " +
"but also leaving enough area outside as background; " +
"and save as file: %s" % regfile)
ds9_view(infile)
fsky = "exclude sky=region(%s)" % regfile
fbintime = "bin time=::%s" % bintime
subprocess.check_call(["punlearn", "dmextract"])
subprocess.check_call([
"dmextract", "infile=%s[%s][%s]" % (infile, fsky, fbintime),
"outfile=%s" % outfile, "opt=ltc1", "clobber=%s" % clobber
])
logger.info("Done!\n")
def make_gti(infile, outfile, scale=1.2, clobber=False):
"""
Examine the light curve for flares, and clip it to make the GTI.
"""
logger.info("Examine the light curve and create GTI ...")
logger.info("Outfile: %s" % outfile)
chipsfile = os.path.splitext(outfile)[0] + ".chips"
if (not clobber) and (os.path.exists(outfile) or
os.path.exists(chipsfile)):
raise OSError("'%s' or '%s' already exists" % (outfile, chipsfile))
outimg = os.path.splitext(outfile)[0] + "_lc.jpg"
lines = [
"from lightcurves import lc_clean",
"lc_clean('%s')" % infile,
"lc_clean('%s', scale=%s, outfile='%s')" % (infile, scale, outfile),
"print_window('%s', ['format', 'jpg', 'clobber', 'True'])" % outimg
]
open(chipsfile, "w").write("\n".join(lines) + "\n")
subprocess.check_call(["chips", "-x", chipsfile])
if not os.path.exists(outfile):
# workaround the problem that ``chips`` sometimes just failed
logger.warning("*** Failed to create GTI: %s ***" % outfile)
logger.warning("You need to create the GTI manually.")
input("When finished GTI creation, press Enter to continue ...")
logger.info("Done!\n")
def filter_gti(infile, outfile, gti, clobber=False):
"""
Removing flares by filtering on GTI to create the finally cleaned
evt2 file.
"""
clobber = "yes" if clobber else "no"
logger.info("Filter on GTI to create cleaned evt2 file ...")
logger.info("Outfile: %s" % outfile)
subprocess.check_call(["punlearn", "dmcopy"])
subprocess.check_call([
"dmcopy", "infile=%s[@%s]" % (infile, gti),
"outfile=%s" % outfile, "clobber=%s" % clobber
])
logger.info("Done!\n")
def main():
parser = argparse.ArgumentParser(
description="Make a cleaned evt2 for scientific analysis")
parser.add_argument("-i", "--infile", dest="infile",
help="input evt2 produced by 'chandra_repro' " +
"(default: request from manifest)")
parser.add_argument("-C", "--clobber", dest="clobber", action="store_true",
help="overwrite existing file")
args = parser.parse_args()
setup_pfiles(["dmkeypar", "dmcopy", "celldetect", "dmextract"])
manifest = get_manifest()
if args.infile:
infile = args.infile
else:
infile = manifest.getpath("evt2", relative=True)
chips = ACIS.get_chips_str(infile, sep="-")
logger.info("infile: %s" % infile)
logger.info("chips: %s" % chips)
evt2_chips = "evt2_c{chips}_orig.fits".format(chips=chips)
evt2_rmsrc = "evt2_c{chips}_rmsrc.fits".format(chips=chips)
evt2_clean = "evt2_c{chips}_clean.fits".format(chips=chips)
srcfile = "sources_celld.reg"
lcfile = "ex_bkg.lc"
gtifile = os.path.splitext(lcfile)[0] + ".gti"
filter_chips(infile, evt2_chips, chips, clobber=args.clobber)
detect_sources(evt2_chips, srcfile, clobber=args.clobber)
remove_sources(evt2_chips, evt2_rmsrc, srcfile, clobber=args.clobber)
extract_lightcurve(evt2_rmsrc, lcfile, clobber=args.clobber)
make_gti(lcfile, gtifile, clobber=args.clobber)
filter_gti(evt2_rmsrc, evt2_clean, gtifile, clobber=args.clobber)
# Add cleaned evt2 to manifest
key = "evt2_clean"
manifest.setpath(key, evt2_clean)
logger.info("Added '%s' to manifest: %s" % (key, manifest.get(key)))
# Remove useless intermediate files
os.remove(evt2_chips)
os.remove(evt2_rmsrc)
if __name__ == "__main__":
main()
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