Move various Python tools from 'scripts/' to 'bin/'

1 files changed, 0 insertions, 207 deletions

diff --git a/scripts/clean_evt2.py b/scripts/clean_evt2.py
deleted file mode 100755
index 5b53922..0000000
--- a/scripts/clean_evt2.py
+++ /dev/null
@@ -1,207 +0,0 @@
-#!/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()