def handle_args(args=None):
"""
Parses command line options & arguments using OptionParser.
Options & default values for the script are defined herein.
"""
parser = get_argparser()
options= parser.parse_args()
# Overwrite 'fixed_coords' with a parsed list of coords
# collated from both command line and file.
options.fixed_coords = parse_monitoringlist_positions(
options, str_name="fixed_posns", list_name="fixed_posns_file"
)
# Quick & dirty check that the position list looks plausible
if options.fixed_coords:
mlist = numpy.array(options.fixed_coords)
if not (len(mlist.shape) == 2 and mlist.shape[1] == 2):
parser.error("Positions for forced-fitting must be [RA,dec] pairs")
# We have four potential modes, of which we choose only one to run:
#
# 1. Blind sourcefinding
# 1.1 Thresholding, no detection image (no extra cmd line options)
# 1.2 Thresholding, detection image (--detection-image)
# 1.3 FDR (--fdr)
#
# 2. Fit to fixed points (--fixed-coords and/or --fixed-list)
if options.fixed_coords:
if options.fdr:
parser.error("--fdr not supported with fixed positions")
elif options.detection_image:
parser.error("--detection-image not supported with fixed positions")
options.mode = "fixed" # mode 2 above
elif options.fdr:
if options.detection_image:
parser.error("--detection-image not supported with --fdr")
options.mode = "fdr" # mode 1.3 above
elif options.detection_image:
options.mode = "detimage" # mode 1.2 above
else:
options.mode = "threshold" # mode 1.1 above
return options, options.files
def handle_args(args=None):
"""
Parses command line options & arguments using OptionParser.
Options & default values for the script are defined herein.
"""
usage = "usage: %prog [options] file1 ... fileN"
parser = OptionParser(usage)
parser.add_option("--fdr",
action="store_true",
dest="fdr",
help="Use False Detection Rate algorithm")
parser.add_option("--alpha", default=1e-2, type="float", help="FDR Alpha")
parser.add_option("--detection",
default=10,
type="float",
help="Detection threshold")
parser.add_option("--analysis",
default=3,
type="float",
help="Analysis threshold")
parser.add_option("--regions",
action="store_true",
help="Generate DS9 region file(s)")
parser.add_option("--residuals",
action="store_true",
help="Generate residual maps")
parser.add_option("--islands",
action="store_true",
help="Generate island maps")
parser.add_option("--deblend-thresholds",
default=0,
type="int",
help="Number of deblending subthresholds; 0 to disable")
parser.add_option("--bmaj", type="float", help="Major axis of beam (deg)")
parser.add_option("--bmin", type="float", help="Minor axis of beam (deg)")
parser.add_option("--bpa", type="float", help="Beam position angle (deg)")
parser.add_option("--grid",
default=64,
type="int",
help="Background grid segment size")
parser.add_option("--margin",
default=0,
type="int",
help="Margin applied to each edge of image (in pixels)")
parser.add_option("--radius",
default=0,
type="float",
help="Radius of usable portion of image (in pixels)")
parser.add_option("--skymodel",
action="store_true",
help="Generate sky model")
parser.add_option(
"--csv",
action="store_true",
help="Generate csv text file for use in programs such as TopCat")
parser.add_option("--rmsmap", action="store_true", help="Generate RMS map")
parser.add_option("--sigmap",
action="store_true",
help="Generate significance map")
parser.add_option("--force-beam",
action="store_true",
help="Force fit axis lengths to beam size")
parser.add_option("--detection-image",
type="string",
help="Find islands on different image")
parser.add_option(
'--fixed-posns',
help="List of position coordinates to "
"force-fit (decimal degrees, JSON, e.g [[123.4,56.7],[359.9,89.9]]) "
"(Will not perform blind extraction in this mode)",
default=None)
parser.add_option(
'--fixed-posns-file',
help="Path to file containing a list of positions to force-fit "
"(Will not perform blind extraction in this mode)",
default=None)
parser.add_option(
'--ffbox',
type='float',
default=3.,
help="Forced fitting positional box size as a multiple of beam width.")
options, files = parser.parse_args(args=args)
# Overwrite 'fixed_coords' with a parsed list of coords
# collated from both command line and file.
options.fixed_coords = parse_monitoringlist_positions(
options, str_name="fixed_posns", list_name="fixed_posns_file")
# Quick & dirty check that the position list looks plausible
if options.fixed_coords:
mlist = numpy.array(options.fixed_coords)
if not (len(mlist.shape) == 2 and mlist.shape[1] == 2):
parser.error("Positions for forced-fitting must be [RA,dec] pairs")
# We have four potential modes, of which we choose only one to run:
#
# 1. Blind sourcefinding
# 1.1 Thresholding, no detection image (no extra cmd line options)
# 1.2 Thresholding, detection image (--detection-image)
# 1.3 FDR (--fdr)
#
# 2. Fit to fixed points (--fixed-coords and/or --fixed-list)
if options.fixed_coords:
if options.fdr:
parser.error("--fdr not supported with fixed positions")
elif options.detection_image:
parser.error(
"--detection-image not supported with fixed positions")
options.mode = "fixed" # mode 2 above
elif options.fdr:
if options.detection_image:
parser.error("--detection-image not supported with --fdr")
options.mode = "fdr" # mode 1.3 above
elif options.detection_image:
options.mode = "detimage" # mode 1.2 above
else:
options.mode = "threshold" # mode 1.1 above
return options, files
def handle_args(args=None):
"""
Parses command line options & arguments using OptionParser.
Options & default values for the script are defined herein.
"""
usage = "usage: %prog [options] file1 ... fileN"
parser = OptionParser(usage)
parser.add_option("--fdr", action="store_true", dest="fdr", help="Use False Detection Rate algorithm")
parser.add_option("--alpha", default=1e-2, type="float", help="FDR Alpha")
parser.add_option("--detection", default=10, type="float", help="Detection threshold")
parser.add_option("--analysis", default=3, type="float", help="Analysis threshold")
parser.add_option("--regions", action="store_true", help="Generate DS9 region file(s)")
parser.add_option("--residuals", action="store_true", help="Generate residual maps")
parser.add_option("--islands", action="store_true", help="Generate island maps")
parser.add_option(
"--deblend-thresholds", default=0, type="int", help="Number of deblending subthresholds; 0 to disable"
)
parser.add_option("--bmaj", type="float", help="Major axis of beam (deg)")
parser.add_option("--bmin", type="float", help="Minor axis of beam (deg)")
parser.add_option("--bpa", type="float", help="Beam position angle (deg)")
parser.add_option("--grid", default=64, type="int", help="Background grid segment size")
parser.add_option("--margin", default=0, type="int", help="Margin applied to each edge of image (in pixels)")
parser.add_option("--radius", default=0, type="float", help="Radius of usable portion of image (in pixels)")
parser.add_option("--skymodel", action="store_true", help="Generate sky model")
parser.add_option("--csv", action="store_true", help="Generate csv text file for use in programs such as TopCat")
parser.add_option("--rmsmap", action="store_true", help="Generate RMS map")
parser.add_option("--sigmap", action="store_true", help="Generate significance map")
parser.add_option("--force-beam", action="store_true", help="Force fit axis lengths to beam size")
parser.add_option("--detection-image", type="string", help="Find islands on different image")
parser.add_option(
"--fixed-posns",
help="List of coordinate pairs to " "force-fit (decimal degrees, JSON, e.g [[123.4,56.7],[359.9,89.9]])",
default=None,
)
parser.add_option("--fixed-posn-file", help="Filename containing a list of positions to force-fit", default=None)
parser.add_option(
"--ffbox", type="float", default=3.0, help="Forced fitting positional box size as a multiple of beam width."
)
options, files = parser.parse_args(args=args)
# Overwrite 'fixed_coords' with a parsed list of coords
# collated from both command line and file.
options.fixed_coords = parse_monitoringlist_positions(options, str_name="fixed", list_name="fixed_list")
# Quick & dirty check that the position list looks plausible
if options.fixed_coords:
mlist = numpy.array(options.fixed_coords)
if not (len(mlist.shape) == 2 and mlist.shape[1] == 2):
parser.error("Positions for forced-fitting must be [RA,dec] pairs")
# We have four potential modes, of which we choose only one to run:
#
# 1. Blind sourcefinding
# 1.1 Thresholding, no detection image (no extra cmd line options)
# 1.2 Thresholding, detection image (--detection-image)
# 1.3 FDR (--fdr)
#
# 2. Fit to fixed points (--fixed-coords and/or --fixed-list)
if options.fixed_coords:
if options.fdr:
parser.error("--fdr not supported with fixed positions")
elif options.detection_image:
parser.error("--detection-image not supported with fixed positions")
options.mode = "fixed" # mode 2 above
elif options.fdr:
if options.detection_image:
parser.error("--detection-image not supported with --fdr")
options.mode = "fdr" # mode 1.3 above
elif options.detection_image:
options.mode = "detimage" # mode 1.2 above
else:
options.mode = "threshold" # mode 1.1 above
return options, files