Add scripts/make_blanksky.py (to replace ciao_blanksky.sh)

1 files changed, 228 insertions, 0 deletions

diff --git a/scripts/make_blanksky.py b/scripts/make_blanksky.py
new file mode 100755
index 0000000..8229d39
--- /dev/null
+++ b/scripts/make_blanksky.py
@@ -0,0 +1,228 @@
+#!/usr/bin/env python3
+#
+# Copyright (c) 2017 Weitian LI <liweitianux@live.com>
+# MIT license
+
+"""
+Make the "blank-sky" background for spectral analysis.
+
+This tool first finds the corresponding blank-sky files for this observation,
+then apply further filtering and gain corrections, and finally reproject
+the coordinates to matching the observational data.
+
+
+Reference
+---------
+* Analyzing the ACIS Background with "Blank-sky" Files
+  http://cxc.harvard.edu/ciao/threads/acisbackground/
+"""
+
+import os
+import argparse
+import subprocess
+import shutil
+import stat
+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.header import write_keyword, copy_keyword
+
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def find_blanksky(infile, copy=True, clobber=False):
+    """
+    Find the blanksky files for the input file using ``acis_bkgrnd_lookup``
+    tool, and copy the files to current directory if ``copy=True``.
+    """
+    subprocess.check_call(["punlearn", "acis_bkgrnd_lookup"])
+    subprocess.check_call(["acis_bkgrnd_lookup", "infile=%s" % infile])
+    bkgfiles = subprocess.check_output([
+        "pget", "acis_bkgrnd_lookup", "outfile"
+    ]).decode("utf-8").strip()
+    bkgfiles = bkgfiles.split(",")
+    logger.info("Found blanksky files: {0}".format(bkgfiles))
+    if copy:
+        logger.info("Copy blanksky files into CWD ...")
+        for f in bkgfiles:
+            if os.path.exists(os.path.basename(f)) and (not clobber):
+                raise OSError("File already exists: %s" % os.path.basename(f))
+            shutil.copy(f, ".")
+        bkgfiles = [os.path.basename(f) for f in bkgfiles]
+    return bkgfiles
+
+
+def merge_blanksky(infiles, outfile, clobber=False):
+    """
+    Merge multiple blanksky files (e.g., 4 blanksky files for ACIS-I)
+    into a single file.
+    """
+    if len(infiles) == 1:
+        logger.info("Only one blanksky file, no need to merge.")
+        if os.path.exists(outfile) and (not clobber):
+            raise OSError("File already exists: %s" % outfile)
+        shutil.move(infiles[0], outfile)
+    else:
+        logger.info("Merge multiple blanksky files ...")
+        clobber = "yes" if clobber else "no"
+        subprocess.check_call(["punlearn", "dmmerge"])
+        subprocess.check_call([
+            "dmmerge", "infile=%s" % ",".join(infiles),
+            "outfile=%s" % outfile, "clobber=%s" % clobber
+        ])
+        write_keyword(outfile, keyword="DETNAM", value="ACIS-0123")
+        for f in infiles:
+            os.remove(f)
+    # Add write permission to the background file
+    st = os.stat(outfile)
+    os.chmod(outfile, st.st_mode | stat.S_IWUSR)
+
+
+def clean_vfaint(infile, outfile, clobber=False):
+    """
+    Clean the background file by only keeping events with ``status=0``
+    for ``VFAINT`` mode observations.
+    """
+    subprocess.check_call(["punlearn", "dmkeypar"])
+    datamode = subprocess.check_output([
+        "dmkeypar", "infile=%s" % infile,
+        "keyword=DATAMODE", "echo=yes"
+    ]).decode("utf-8").strip()
+    logger.info("DATAMODE: %s" % datamode)
+    if datamode.upper() == "VFAINT":
+        logger.info("Clean background file using 'status=0' ...")
+        clobber = "yes" if clobber else "no"
+        subprocess.check_call(["punlearn", "dmcopy"])
+        subprocess.check_call([
+            "dmcopy", "infile=%s[status=0]" % infile,
+            "outfile=%s" % outfile, "clobber=%s" % clobber
+        ])
+        os.remove(infile)
+    else:
+        logger.info("No need to clean the background file.")
+        if os.path.exists(outfile) and (not clobber):
+            raise OSError("File already exists: %s" % outfile)
+        shutil.move(infile, outfile)
+
+
+def apply_gainfile(infile, outfile, evt2, clobber=False):
+    """
+    Check whether the ``GAINFILE`` of the background file matches that
+    of the observational evt2 file.
+
+    If they are different, then reprocess the background file with the
+    same ``GAINFILE`` of the evt2 file.
+    """
+    subprocess.check_call(["punlearn", "dmkeypar"])
+    gainfile_bkg = subprocess.check_output([
+        "dmkeypar", "infile=%s" % infile,
+        "keyword=GAINFILE", "echo=yes"
+    ]).decode("utf-8").strip()
+    gainfile_evt2 = subprocess.check_output([
+        "dmkeypar", "infile=%s" % evt2,
+        "keyword=GAINFILE", "echo=yes"
+    ]).decode("utf-8").strip()
+    if gainfile_bkg == gainfile_evt2:
+        logger.info("GAINFILE's are the same for background and evt2.")
+        if os.path.exists(outfile) and (not clobber):
+            raise OSError("File already exists: %s" % outfile)
+        shutil.move(infile, outfile)
+    else:
+        # Reprocess the background
+        gainfile = os.path.join(os.environ["CALDB"],
+                                "data/chandra/acis/det_gain",
+                                gainfile_evt2)
+        logger.info("Reprocess background using gainfile: %s ..." % gainfile)
+        clobber = "yes" if clobber else "no"
+        eventdef = [
+            "s:ccd_id", "s:node_id", "i:expno", "s:chip",
+            "s:tdet", "f:det", "f:sky", "s:phas",
+            "l:pha", "l:pha_ro", "f:energy", "l:pi",
+            "s:fltgrade", "s:grade", "x:status"
+        ]
+        subprocess.check_call(["punlearn", "acis_process_events"])
+        subprocess.check_call([
+            "acis_process_events", "infile=%s" % infile,
+            "outfile=%s" % outfile, "acaofffile=NONE", "stop=none",
+            "doevtgrade=no", "apply_cti=yes", "apply_tgain=no",
+            "calculate_pi=yes", "pix_adj=NONE", "gainfile=%s" % gainfile,
+            "eventdef={%s}" % ",".join(eventdef),
+            "clobber=%s" % clobber
+        ])
+        os.remove(infile)
+
+
+def reproject_blanksky(infile, outfile, evt2, asol, clobber=False):
+    """
+    Reproject the background to match the coordinates of the observational
+    evt2 data.
+    """
+    clobber = "yes" if clobber else "no"
+    logger.info("Reprojecting the background to match the evt2 file ...")
+    subprocess.check_call(["punlearn", "reproject_events"])
+    subprocess.check_call([
+        "reproject_events", "infile=%s" % infile, "outfile=%s" % outfile,
+        "aspect=%s" % asol, "match=%s" % evt2, "random=0",
+        "clobber=%s" % clobber
+    ])
+    os.remove(infile)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Make blanksky background")
+    parser.add_argument("-i", "--infile", dest="infile",
+                        help="input evt2 file " +
+                        "(default: 'evt2_clean' from manifest)")
+    parser.add_argument("-o", "--outfile", dest="outfile",
+                        help="output blanksky background file " +
+                        "(default: 'blanksky_c{chips}.fits')")
+    parser.add_argument("-C", "--clobber", dest="clobber", action="store_true",
+                        help="overwrite existing file")
+    args = parser.parse_args()
+
+    setup_pfiles(["acis_bkgrnd_lookup", "dmcopy", "dmmerge", "dmkeypar",
+                  "dmhedit", "reproject_events", "acis_process_events"])
+
+    manifest = get_manifest()
+    if args.infile:
+        infile = args.infile
+    else:
+        infile = manifest.getpath("evt2_clean", relative=True)
+    chips = ACIS.get_chips_str(infile, sep="-")
+    if args.outfile:
+        outfile = args.outfile
+    else:
+        outfile = "blanksky_c{chips}.fits".format(chips=chips)
+    asol = manifest.getpath("asol", relative=True, sep=",")
+    logger.info("infile: %s" % infile)
+    logger.info("outfile: %s" % outfile)
+    logger.info("chips: %s" % chips)
+    logger.info("asol: %s" % asol)
+
+    bkgfiles = find_blanksky(infile, copy=True, clobber=args.clobber)
+    bkg_orig = os.path.splitext(outfile)[0] + "_orig.fits"
+    merge_blanksky(bkgfiles, bkg_orig, clobber=args.clobber)
+    bkg_clean = os.path.splitext(outfile)[0] + "_clean.fits"
+    clean_vfaint(bkg_orig, bkg_clean, clobber=args.clobber)
+    bkg_gained = os.path.splitext(outfile)[0] + "_gained.fits"
+    apply_gainfile(bkg_clean, bkg_gained, evt2=infile, clobber=args.clobber)
+    # Add the PNT header keywords
+    copy_keyword(infile, bkg_gained,
+                 keyword=["RA_PNT", "DEC_PNT", "ROLL_PNT"])
+    reproject_blanksky(bkg_gained, outfile, evt2=infile,
+                       asol=asol, clobber=args.clobber)
+
+    # Add blanksky background to manifest
+    key = "bkg_blank"
+    manifest.setpath(key, outfile)
+    logger.info("Added '%s' to manifest: %s" % (key, manifest.get(key)))
+
+
+if __name__ == "__main__":
+    main()