def main():
for i, arg in enumerate(sys.argv):
if (arg[0] == '-') and arg[1].isdigit(): sys.argv[i] = ' ' + arg
parser = ArgumentParser(description="Reliability estimator and"
" direction-dependent sources selection tool."
" M. L. L Sebokolodi <*****@*****.**>")
add = parser.add_argument
add("-v","--version", action="version",version=
"{:s} version {:s}".format(parser.prog, __version__))
add("-i", "--image", dest="image",
help="FITS image name")
add("-p", "--psfimage", dest="psf", default=None,
help="Point Spread Function (PSF) Fits image name. Default = None")
add("-s", "--source-finder", dest="source_finder", default="pybdsm",
help="Source finder name. Default='pybdsm'")
add("--to-pybdsm", dest="to_pybdsm", action="append",
help="PyBDSM process_image options"
" [may be specified multiple times]. E.g thresh_pix=1 etc.")
add("-log", "--log-level",dest="log_level", type=int, default=0,
help="Python logging module, where info=0, debug=1, critial=2 and abort=3")
add("-od", "--output-dir", dest="outdir", default=None,
help="Output products will be dumped here. System Default will be generated")
add("-pref", "-dir-prefix", dest="prefix", default=None,
help="Prefix for output products. System default will be generated")
add("-apsf", "--add-psfcorr", dest="add_psfcorr", action="store_true",
default=False, help="Adds PSF correlation for density estimations. The PSF "
" image must be provided. Default is False. To set True add -apsf")
add("-alv", "--add-localvar", dest="add_locvar", action="store_true",
default=False, help=" Include local variance for density estimations. See -apsf.")
add("-dn", "--do-nearsources", dest="do_nearsources", action="store_true",
default=False, help=" Adds number of neighbours for density estimations. See -apsf")
add("-dmp", "--do-relplots", dest="do_relplots", action="store_false",
default=True, help="Make reliability density plot. Default is True."
" To disable add -dmp on the command line.")
add("-drel", "--reset-rel", dest="reset_rel", action="store_true",
default=False, help=" Assigns R=0 for sources with cf < 0.002 and"
"R > 0.60.")
add("-beam", "--beam-cluster", dest="do_beam", default=False,
action="store_true", help= "Increases the Gaussian groupings by 20 percent the"
" beam size. Default is False.")
add("-pcr", "--psfcorr-region", dest="psfcorr_region", type=int,
default=5, help="The size of the region to correlate, in beam sizes."
" Default value is 5 beam sizes.")
add("-lr", "--local-region", dest="local_region", default=10,
help="The area to compute the local variance, in beam sizes."
" Default value is 10 beam sizes.")
add("-rel_rm", "--rel-rmsrc", dest="rel_rmsrc",
action="append", default=None, help="Delete sources within a radius;"
" e.g ra, dec, radius (in degrees). For more than"
" one region: ra1,dec1,radius1:ra2,dec2,radius2. Default is None.")
add("-ps", "--positive-smooth", dest="pos_smooth", type=float, default=2.0,
help=" Masking threshold in the positive image, e.g pixels 2x noise"
"will be masked. Default is 2.0.")
add("-ns", "--negative-smooth", dest="neg_smooth", type=float, default=2.0,
help="Similar to -ps. Applied to negative image")
add('-pisl', "--thresh-isl", dest="thresh_isl", type=float, default=3,
help=" Source finding threshold for forming islands. For positive image."
" Default is 3.")
add("-ppix", "--thresh-pix", dest="thresh_pix", type=float, default=5,
help="Source finding threshold for model fitting. For positive image."
"Default is 5.")
add("-nisl", "--negthreshold-isl", dest="neg_thresh_isl",
type=float, default=3, help="Similar to -pisl but applied"
" to the negative image. Default is 3.")
add("-npix", "--negthreshold-pix", dest="neg_thresh_pix",
type=float, default=5, help="Similar to -ppix but applied"
" for negative image. Default is 5.")
add("-snr_thr", "--snr-threshold", dest="snr_thresh", type=float,
default=40, help="SNR threshold. High SNR Sources have SNR > 40x min(SNR)"
" Default is 40.")
add("-loc_thr", "--localvar-threshold", dest="locvar_thresh",
type=float, default=0.8, help="Local variance (LV) threshold."
"High LV Sources have LV > 0.8 x image noise. Default is 0.8")
add("-pc_thr", "--psfcorr-threshold", dest="psfcorr_thresh",
type=float, default=0.5, help="Correlation factor (CF) threshold."
"High CF sources have CF > 0.5. Default is 0.5.")
add("-nneg", "--num-negatives",dest="num_negatives", type=float, default=4,
help="Number of neigbouring (NN) negative detections. Default is 4."
"High NN sources have NN > 4.")
add("-nrgn", "--neg-region", dest="neg_region", type=float, default=10,
help="The size of a region to find -nneg. Default is 10.")
add("-phrm", "--phasecenter-remove", dest="phase_center_rm",
type=float, default=None, help="The radius excluded from"
" direction-dependent source selection. NB: this radius is w.r.t to"
" the phase center. Default is None.")
add('-jc', '--json-config', dest='config', default=None,
help='Json config file : No default')
add("-smp", "--save-posmask", dest="savemask_pos", action="store_true",
default=False, help="If specified, positive mask is saved.")
add("-smn", "--save-negmask", dest="savemask_neg", action="store_true",
default=False, help=" If specified, the negative mask is saved.")
args = parser.parse_args()
pybdsm_opts = dict([ items.split("=") for items in args.to_pybdsm ] ) \
if args.to_pybdsm else {}
if not args.image:
print("ATTENTION: No image provided. Aborting")
# making outdirectory
def get_prefix(prefix, imagename, outdir):
if prefix is None:
prefix = os.path.basename(imagename.split(",")[0]).split(".")[:-1]
prefix = ".".join(prefix)
outdir = outdir or prefix +"_"+ os.path.join(datetime.datetime.now().\
strftime("%Y-%m-%d-%H"))
outdir = os.path.abspath(outdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
prefix = outdir +"/"+ prefix
return prefix
if args.config:
keys = []
images = args.image.split(",") if args.image else None
with open(args.config) as conf:
jdict = json.load(conf)
for key,val in jdict.items():
if isinstance(val, unicode):
jdict[key] = str(val)
prefix = get_prefix(jdict["prefix"],
images[0] if images else jdict["imagename"],
jdict["outdir"])
reldict = jdict["reliability"]
ddict = jdict["dd_tagging"]
sourcefin = jdict["source_finder_opts"]
for key, val in reldict.iteritems():
if isinstance(val, unicode):
reldict[key] = str(val)
for key, val in ddict.iteritems():
if isinstance(val, unicode):
ddict[key] = str(val)
reldict.update(sourcefin)
enable = ddict["enable"]
ddict.pop("enable")
if args.image:
psfs = args.psf.split(",") if args.psf else [None]
if len(images) != len(psfs):
psfs = [psfs[0]]*len(images)
for i, (image, psf) in enumerate(zip(images, psfs)):
prefix = get_prefix(jdict["prefix"],
images[0] if images else jdict["imagename"],
jdict["outdir"])
if len(images) >1:
prefix = prefix + "-%04d"%i
reldict["prefix"] = prefix
mc = rel.load(image, psf, **reldict)
pmodel, nmodel, noise, hdr = mc.get_reliability()
ddict["pmodel"] = pmodel
ddict["nmodel"] = nmodel
ddict["prefix"] = prefix
ddict["noise"] = noise
ddict["header"] = hdr
if enable:
dc = dd.load(image, psfname=psf, **ddict)
pmodel, nmodel = dc.source_selection()
else:
image = jdict["imagename"]
psf = jdict["psfname"]
reldict["prefix"] = prefix
mc = rel.load(image, psf, **reldict)
pmodel, nmodel, noise, hdr = mc.get_reliability()
ddict["pmodel"] = pmodel
ddict["nmodel"] = nmodel
ddict["prefix"] = prefix
ddict["noise"] = noise
ddict["header"] = hdr
if enable:
dc = dd.load(image, psfname=psf, **ddict)
pmodel, nmodel = dc.source_selection()
pmodel.save( prefix+".lsm.html")
nmodel.save( prefix+"_negative.lsm.html")
else:
images = args.image.split(",")
psfs = args.psf.split(",") if args.psf else [None]
psfregion = args.psfcorr_region
locregion = args.local_region
if len(images) != len(psfs):
psfs = [psfs[0]]*len(images)
for i, (image, psf) in enumerate(zip(images, psfs)):
prefix = get_prefix(args.prefix, images[0], args.outdir)
if len(images) >1:
prefix = prefix + "-%04d"%i
mc = rel.load(imagename=image, psfname=psf, sourcefinder_name=
args.source_finder, makeplots=args.do_relplots,
do_psf_corr=args.add_psfcorr, do_local_var=args.add_locvar,
psf_corr_region=psfregion, local_var_region=locregion,
rel_excl_src=args.rel_rmsrc, pos_smooth=args.pos_smooth,
neg_smooth=args.neg_smooth, loglevel=args.log_level,
thresh_isl=args.thresh_isl, thresh_pix=args.thresh_pix,
neg_thresh_isl=args.neg_thresh_isl, neg_thresh_pix=
args.neg_thresh_pix, prefix=prefix, reset_rel=args.reset_rel,
do_nearsources=args.do_nearsources, increase_beam_cluster=
args.do_beam, savemask_neg=args.savemask_neg,
savemask_pos=args.savemask_pos, **pybdsm_opts)
# assignign reliability values
pmodel, nmodel, noise, hdr = mc.get_reliability()
# direction dependent detection tagging
dc = dd.load(imagename=image, psfname=psf, pmodel=pmodel, nmodel=nmodel,
header=hdr, snr_thresh=args.snr_thresh, local_thresh=args.locvar_thresh,
high_corr_thresh=args.psfcorr_thresh, negdetec_region=
args.neg_region, negatives_thresh=args.num_negatives, noise=noise,
phasecenter_excl_radius=args.phase_center_rm, prefix=prefix,
loglevel=args.log_level)
# tagging
pmodel, nmodel = dc.source_selection()
pmodel.save( prefix+".lsm.html")
nmodel.save( prefix+"_negative.lsm.html")
os.system("rm -r tmp*.log")
def main():
for i, arg in enumerate(sys.argv):
if (arg[0] == '-') and arg[1].isdigit(): sys.argv[i] = ' ' + arg
parser = ArgumentParser(description="Reliability estimator and"
" direction-dependent sources selection tool."
" M. L. L Sebokolodi <*****@*****.**>")
add = parser.add_argument
add("-v","--version", action="version",version=
"{:s} version {:s}".format(parser.prog, __version__))
add("-i", "--image", dest="image",
help="FITS image name")
add("-p", "--psfimage", dest="psf", default=None,
help="Point Spread Function (PSF) Fits image name. Default=None")
add("-s", "--source-finder", dest="source_finder", default="pybdsm",
help="Source finder name. Current available"
" sourcefinders: pybdsm. Default='pybdsm'")
add("--to-pybdsm", dest="to_pybdsm", action="append",
help="PyBDSM process_image options"
" [may be specified multiple times]. E.g thresh_pix=1 etc.")
add("-log", "--log-level",dest="log_level", type=int, default=0,
help="Python logging module. This ranges between"
" 0-3, where 0, 1, 3, 4 are for info, debug, error and "
" critical respectively. Default is 0")
add("-od", "--output-dir", dest="outdir", default=None,
help="Output products will be dumped here. System Default will be generated")
add("-pref", "-dir-prefix", dest="prefix", default=None,
help="Prefix for output products. System default will be generated")
add("-apsf", "--add-psfcorr", dest="add_psfcorr", action="store_true",
default=False, help="Do and add correlation of the sources with the"
"PSF as an extra source parameter for reliability estimations. The psf"
" name must be provided. Default is False. To set true add -apsf")
add("-alv", "--add-localvar", dest="add_locvar", action="store_true",
default=False, help=" Include local variance as an extra source"
"parameter. See -apsf.")
add("-dn", "--do-nearsources", dest="do_nearsources", action="store_true",
default=False, help=" Include number of nearest sources as an extra source"
"parameter. See -apsf. It looks for sources within 5 beam sizes.")
add("-dmp", "--do-relplots", dest="do_relplots", action="store_false",
default=True, help="Make reliability density plot. Default is True."
" To disable add -dmp on the command line.")
add("-rel", "--rel-thresh", dest="rel_thresh", default=None, type=float,
help= "Set a reliability threshold. Default is None.")
add("-pcr", "--psfcorr-region", dest="psfcorr_region", type=int,
default=5, help="Data size to correlate, given in beam sizes."
" Default is 5 beam sizes.")
add("-lr", "--local-region", dest="local_region", default=10,
help="Data size to load the local variance, in beam sizes."
" Default is 10 beam sizes.")
add("-rel_rm", "--rel-sources-excl", dest="rel_src_excl",
action="append", default=None, help="Remove sources in a given"
"region to exclude in reliability estimations."
"E.g ra, dec, radius (in degrees). For more than"
" one region: ra1,dec1,radius1:ra2,dec2,radius2. Default is None.")
add("-ps", "--positive-smooth", dest="pos_smooth", type=float, default=1.6,
help="Data smoothing to eliminate noise/data peaks given by -ps * noise."
" This is for positive side of an Fits image. Default is 1.6.")
add("-ns", "--negative-smooth", dest="neg_smooth", type=float, default=0.8,
help="This is similar to -ps above but for negative side"
"of an image. Default is 0.8.")
add('-pisl', "--thresh-isl", dest="thresh_isl", type=float, default=3,
help="Threshold for the island boundary in number of sigma above"
" the mean. Determines extent of island used for fitting [pybdsm]."
" For positive pixels. Default is 3.")
add("-ppix", "--thresh-pix", dest="thresh_pix", type=float, default=5,
help="Source detection threshold: threshold for the island peak"
" in number of sigma above the mean. For positive pixels."
" Default is 5.")
add("-nisl", "--negthreshold-isl", dest="neg_thresh_isl",
type=float, default=3, help="Similar to -pisl but applied"
"to the negative pixels. Default is 3.")
add("-npix", "--negthreshold-pix", dest="neg_thresh_pix",
type=float, default=5, help="Similar to -ppix but applied"
"for negative pixels. Default is 5.")
add("-snr_thr", "--snr-threshold", dest="snr_thresh", type=float,
default=80, help="Signal-to-noise threshold with reference"
"to the minimum source flux in an image, e.g 80* min(snr), sources with"
" snr > than this are referred to high SNR sources."
" Default is 80.")
add("-loc_thr", "--localvar-threshold", dest="locvar_thresh",
type=float, default=0.9, help="Local variance threshold."
"For -loc-thr of 0.9 means that"
" sources with local variance > 0.9 * negative noise"
" are considered sources of high local variance."
" Default is 0.9")
add("-pc_thr", "--psfcorr-threshold", dest="psfcorr_thresh",
type=float, default=0.5, help="Correlation factor threshold."
"Sources with threshold larger than the specified are"
"considered sources of high correlation. Default is 0.5.")
add("-nneg", "--num-negatives",dest="num_negatives", type=float, default=8,
help="Number of negative detections around a given source."
" If N > threshold then sources will be considered as requiring"
" direction-dependent calibratio solutions. Default is 8.")
add("-nrgn", "--neg-region", dest="neg_region", type=float, default=10,
help="The size of a region around a sources to lookup for"
" negatives. In Beams in sizes. Default is 10.")
add("-nphrm", "--phasecenter-remove", dest="phase_center_rm",
type=float, default=None, help="The radius from the phase center"
"not to consider for final direction-dependent source selection."
"In beam sizes. Default is None.")
add('-jc', '--json-config', dest='config', default=None,
help='Json config file : No default')
args = parser.parse_args()
pybdsm_opts = dict([ items.split("=") for items in args.to_pybdsm ] ) \
if args.to_pybdsm else {}
if args.rel_src_excl:
rel_rmsrc = args.rel_src_excl[0].split(':')
else:
rel_rmsrc = None
# making outdirectory
def get_prefix(prefix, imagename, outdir):
if prefix is None:
prefix = os.path.basename(imagename.split(",")[0]).split(".")[:-1]
prefix = ".".join(prefix)
outdir = outdir or prefix +"_"+ os.path.join(datetime.datetime.now().\
strftime("%Y-%m-%d-%H"))
outdir = os.path.abspath(outdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
prefix = outdir +"/"+ prefix
return prefix
if args.config:
keys = []
images = args.image.split(",") if args.image else None
with open(args.config) as conf:
jdict = json.load(conf)
for key,val in jdict.items():
if isinstance(val, unicode):
jdict[key] = str(val)
prefix = get_prefix(jdict["prefix"],
images[0] if images else jdict["imagename"],
jdict["outdir"])
reldict = jdict["reliability"]
ddict = jdict["dd_tagging"]
sourcefin = jdict["source_finder_opts"]
for key, val in reldict.iteritems():
if isinstance(val, unicode):
reldict[key] = str(val)
for key, val in ddict.iteritems():
if isinstance(val, unicode):
ddict[key] = str(val)
reldict.update(sourcefin)
enable = ddict["enable"]
ddict.pop("enable")
if args.image:
psfs = args.psf.split(",") if args.psf else [None]
if len(images) != len(psfs):
psfs = [psfs[0]]*len(images)
for i, (image, psf) in enumerate(zip(images, psfs)):
prefix = get_prefix(jdict["prefix"],
images[0] if images else jdict["imagename"],
jdict["outdir"])
if len(images) >1:
prefix = prefix + "-%04d"%i
reldict["prefix"] = prefix
mc = rel.load(image, psf, **reldict)
pos, neg = mc.get_reliability()
ddict["poscatalog"] = pos
ddict["negcatalog"] = neg
ddict["prefix"] = prefix
if args.rel_thresh:
os.system("tigger-convert --select='rel>%.3f' %s %s -f"
%(args.rel_thresh, pos, pos))
if enable and args.psf:
dc = dd.load(image, psf, **ddict)
ppos, nneg = dc.source_selection()
else:
image = jdict["imagename"]
psf = jdict["psfname"]
reldict["prefix"] = prefix
mc = rel.load(image, psf, **reldict)
pos, neg = mc.get_reliability()
ddict["poscatalog"] = pos
ddict["negcatalog"] = neg
ddict["prefix"] = prefix
if args.rel_thresh:
os.system("tigger-convert --select='rel>%.3f' %s %s -f"
%(args.rel_thresh, pos, pos))
if enable and psf:
dc = dd.load(image, psf, **ddict)
ppos, nneg = dc.source_selection()
else:
# reliability
images = args.image.split(",")
psfs = args.psf.split(",") if args.psf else [None]
psfregion = args.psfcorr_region
locregion = args.local_region
if len(images) != len(psfs):
psfs = [psfs[0]]*len(images)
for i, (image, psf) in enumerate(zip(images, psfs)):
prefix = get_prefix(args.prefix, images[0], args.outdir)
if len(images) >1:
prefix = prefix + "-%04d"%i
mc = rel.load(imagename=image, psfname=psf, sourcefinder_name=
args.source_finder, makeplots=args.do_relplots,
do_psf_corr=args.add_psfcorr, do_local_var=args.add_locvar,
psf_corr_region=psfregion, local_var_region=locregion,
rel_excl_src=rel_rmsrc, pos_smooth=args.pos_smooth,
neg_smooth=args.neg_smooth, loglevel=args.log_level,
thresh_isl=args.thresh_isl, thresh_pix=args.thresh_pix,
neg_thresh_isl=args.neg_thresh_isl, neg_thresh_pix=
args.neg_thresh_pix, prefix=prefix,
do_nearsources=args.do_nearsources, **pybdsm_opts)
# assignign reliability values
pos, neg = mc.get_reliability()
if args.rel_thresh:
os.system("tigger-convert --select='rel>%.3f' %s %s -f"
%(args.rel_thresh, pos, pos))
# direction dependent detection tagging
if args.psf:
dc = dd.load(imagename=image, psfname=psf, poscatalog=pos, negcatalog=neg,
snr_thresh=args.snr_thresh, local_thresh=args.locvar_thresh,
local_region=locregion, psfcorr_region=psfregion,
high_corr_thresh=args.psfcorr_thresh, negdetec_region=
args.neg_region, negatives_thresh=args.num_negatives,
phasecenter_excl_radius=args.phase_center_rm, prefix=prefix,
loglevel=args.log_level)
# tagging
ppose, nneg = dc.source_selection()
os.system("rm -r *.pybdsm.log")
def main():
for i, arg in enumerate(sys.argv):
if (arg[0] == '-') and arg[1].isdigit(): sys.argv[i] = ' ' + arg
parser = ArgumentParser(description="Reliability estimator and"
" direction-dependent sources selection tool."
" M. L. L Sebokolodi <*****@*****.**>")
add = parser.add_argument
add("-v","--version", action="version",version=
"{:s} version {:s}".format(parser.prog, __version__))
add("-i", "--image", dest="image",
help=" FITS image name")
add("-p", "--psfimage", dest="psf", default=None,
help=" Point Spread Function (PSF) Fits image name. Default = None")
add("-ds", "--disable-smoothing", dest="disable_smoothing", action="store_true",
help=" Smooth data before running source finder.")
add("-s", "--source-finder", dest="source_finder", default="pybdsm",
help=" Source finder name. Default='pybdsm'.")
add("-catype", "--catalog-format", dest="catalogue_format", default="gaul",
help=" Type of a catalogue. Gaussian cataog is 'gaul', source list is 'srl'")
add("--to-pybdsm", dest="to_pybdsm", action="append",
help=" PyBDSM process_image option. E.g 'thresh_pix=1,thresh_pix=2'")
add("-log", "--log-level",dest="log_level", type=int, default=0,
help=" Python logging module, where info=0, debug=1, critial=2 and abort=3.")
add("-od", "--output-dir", dest="outdir", default=None,
help=" Output products will be dumped here. System Default will be generated.")
add("-pref", "-dir-prefix", dest="prefix", default=None,
help=" Prefix for output products. System default will be generated.")
add("-apsf", "--add-psfcorr", dest="add_psfcorr", action="store_true",
default=False, help=" Adds PSF correlation for density estimations. The PSF "
" image must be provided. Default is False. To set True add -apsf")
add("-alv", "--add-localvar", dest="add_locvar", action="store_true",
default=False, help=" Include local variance for density estimations. See -apsf.")
add("-dn", "--do-nearsources", dest="do_nearsources", action="store_true",
default=False, help=" Adds number of neighbours for density estimations. See -apsf")
add("-dmp", "--do-relplots", dest="do_relplots", action="store_false",
default=True, help=" Make reliability density plot. Default is True."
" To disable add -dmp on the command line.")
add("-drel", "--reset-rel", dest="reset_rel", action="store_true",
default=False, help=" Assigns R=0 for sources with cf < 0.002 and"
"R > 0.60.")
add("-beam", "--beam-cluster", dest="do_beam", default=False,
action="store_true", help= " Increases the Gaussian groupings by 20 percent the"
" beam size. Default is False.")
add("-pcr", "--psfcorr-region", dest="psfcorr_region", type=int,
default=5, help=" The size of the region to correlate, in beam sizes."
" Default value is 5 beam sizes.")
add("-lr", "--local-region", dest="local_region", default=10,
help=" The area to compute the local variance, in beam sizes."
" Default value is 10 beam sizes.")
add("-rel_rm", "--rel-rmsrc", dest="rel_rmsrc",
action="append", default=None, help=" Delete sources within a radius;"
" e.g ra, dec, radius (in degrees). For more than"
" one region: ra1,dec1,radius1:ra2,dec2,radius2. Default is None.")
add("-ps", "--positive-smooth", dest="pos_smooth", type=float, default=2.0,
help=" Masking threshold in the positive image, e.g pixels 2x noise"
" will be masked. Default is 2.0.")
add("-ns", "--negative-smooth", dest="neg_smooth", type=float, default=2.0,
help=" Similar to -ps. Applied to negative image.")
add('-pisl', "--thresh-isl", dest="thresh_isl", type=float, default=3,
help=" Source finding threshold for forming islands. For positive image."
" Default is 3.")
add("-ppix", "--thresh-pix", dest="thresh_pix", type=float, default=5,
help=" Source finding threshold for model fitting. For positive image."
" Default is 5.")
add("-nisl", "--negthreshold-isl", dest="neg_thresh_isl",
type=float, default=3, help=" Similar to -pisl but applied"
" to the negative image. Default is 3.")
add("-npix", "--negthreshold-pix", dest="neg_thresh_pix",
type=float, default=5, help=" Similar to -ppix but applied"
" for negative image. Default is 5.")
add("-snr_thr", "--snr-threshold", dest="snr_thresh", type=float,
default=40, help=" SNR threshold. High SNR Sources have SNR > 40x min(SNR)"
" Default is 40.")
add("-pc_thr", "--psfcorr-threshold", dest="psfcorr_thresh",
type=float, default=0.5, help="Correlation factor (CF) threshold."
"High CF sources have CF > 0.5. Default is 0.5.")
add("-nneg", "--num-negatives",dest="num_negatives", type=float, default=4,
help="Number of neigbouring (NN) negative detections. Default is 4."
"High NN sources have NN > 4.")
add("-nrgn", "--neg-region", dest="neg_region", type=float, default=10,
help="The size of a region to find -nneg. Default is 10.")
add("-phrm", "--phasecenter-remove", dest="phase_center_rm",
type=float, default=None, help="The radius excluded from"
" direction-dependent source selection. NB: this radius is w.r.t to"
" the phase center. Default is None.")
add('-jc', '--json-config', dest='config', default=None,
help='Json config file : No default')
add("-smp", "--save-posmask", dest="savemask_pos", action="store_true",
default=False, help="If specified, positive mask is saved.")
add("-smn", "--save-negmask", dest="savemask_neg", action="store_true",
default=False, help=" If specified, the negative mask is saved.")
args = parser.parse_args()
to_pybdsm = args.to_pybdsm[0].split(",") if args.to_pybdsm else None
pybdsm_opts = dict([ items.split("=") for items in to_pybdsm ] ) \
if to_pybdsm else {}
for key, val in pybdsm_opts.iteritems():
if not callable(val):
try:
pybdsm_opts[key] = eval(key)
except NameError:
pybdsm_opts[key] = val
if not args.image:
print("ATTENTION: No image provided. Unless specified inside JSON file otherwise"
" the execution is aborted")
# making outdirectory
def get_prefix(prefix, imagename, outdir):
if prefix is None:
prefix = os.path.basename(imagename.split(",")[0]).split(".")[:-1]
prefix = ".".join(prefix)
outdir = outdir or prefix +"_"+ os.path.join(datetime.datetime.now().\
strftime("%Y-%m-%d-%H"))
outdir = os.path.abspath(outdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
prefix = outdir +"/"+ prefix
return prefix
if args.config:
keys = []
images = args.image.split(",") if args.image else None
with open(args.config) as conf:
jdict = json.load(conf)
for key,val in jdict.items():
if isinstance(val, unicode):
jdict[key] = str(val)
prefix = get_prefix(jdict["prefix"],
images[0] if images else jdict["imagename"],
jdict["outdir"])
reldict = jdict["reliability"]
ddict = jdict["dd_tagging"]
sourcefin = jdict["source_finder_opts"]
for key, val in reldict.iteritems():
if isinstance(val, unicode):
reldict[key] = str(val)
for key, val in ddict.iteritems():
if isinstance(val, unicode):
ddict[key] = str(val)
reldict.update(sourcefin)
enable = ddict["enable"]
ddict.pop("enable")
if args.image:
psfs = args.psf.split(",") if args.psf else [None]
if len(images) != len(psfs):
psfs = [psfs[0]]*len(images)
for i, (image, psf) in enumerate(zip(images, psfs)):
prefix = get_prefix(jdict["prefix"],
images[0] if images else jdict["imagename"],
jdict["outdir"])
if len(images) >1:
prefix = prefix + "-%04d"%i
reldict["prefix"] = prefix
mc = rel.load(image, psf, **reldict)
pmodel, nmodel, step = mc.get_reliability()
reldict["prefix"] = prefix
ddict["pmodel"] = pmodel
ddict["nmodel"] = nmodel
ddict["prefix"] = prefix
ddict["imagename"] = image
ddict["local_step"] = step
if enable:
dc = dd.load( psfname=psf, **ddict)
pmodel, nmodel = dc.source_selection()
pmodel.save( prefix+".lsm.html")
nmodel.save( prefix+"_negative.lsm.html")
utils.xrun("tigger-convert", ["--rename -f", prefix + ".lsm.html"])
else:
image = jdict["imagename"]
psf = jdict["psfname"]
reldict["prefix"] = prefix
mc = rel.load(image, psf, **reldict)
pmodel, nmodel, step = mc.get_reliability()
ddict["pmodel"] = pmodel
ddict["nmodel"] = nmodel
ddict["prefix"] = prefix
ddict["imagename"] = image
ddict["local_step"] = step
if enable:
dc = dd.load(psfname=psf, **ddict)
pmodel, nmodel = dc.source_selection()
pmodel.save( prefix+".lsm.html")
nmodel.save( prefix+"_negative.lsm.html")
else:
images = args.image.split(",")
psfs = args.psf.split(",") if args.psf else [None]
psfregion = args.psfcorr_region
locregion = args.local_region
if len(images) != len(psfs):
psfs = [psfs[0]]*len(images)
for i, (image, psf) in enumerate(zip(images, psfs)):
prefix = get_prefix(args.prefix, images[0], args.outdir)
if len(images) >1:
prefix = prefix + "-%04d"%i
mc = rel.load(imagename=image, psfname=psf, sourcefinder_name=
args.source_finder, makeplots=args.do_relplots,
saveformat=args.catalogue_format, do_psf_corr=args.add_psfcorr,
do_local_var=args.add_locvar,
psf_corr_region=psfregion, local_var_region=locregion,
rel_excl_src=args.rel_rmsrc, pos_smooth=args.pos_smooth,
neg_smooth=args.neg_smooth, loglevel=args.log_level,
thresh_isl=args.thresh_isl, thresh_pix=args.thresh_pix,
neg_thresh_isl=args.neg_thresh_isl, neg_thresh_pix=
args.neg_thresh_pix, prefix=prefix, reset_rel=args.reset_rel,
do_nearsources=args.do_nearsources, increase_beam_cluster=
args.do_beam, savemask_neg=args.savemask_neg,
savemask_pos=args.savemask_pos,
no_smooth=args.disable_smoothing, **pybdsm_opts)
# assignign reliability values
pmodel, nmodel, step = mc.get_reliability()
# direction dependent detection tagging
dc = dd.load(imagename=image, psfname=psf, pmodel=pmodel, nmodel=nmodel,
local_step=step, snr_thresh=args.snr_thresh,
high_corr_thresh=args.psfcorr_thresh, negdetec_region=
args.neg_region, negatives_thresh=args.num_negatives,
phasecenter_excl_radius=args.phase_center_rm, prefix=prefix,
loglevel=args.log_level)
# tagging
pmodel, nmodel = dc.source_selection()
pmodel.save( prefix+".lsm.html")
nmodel.save( prefix+"_negative.lsm.html")
utils.xrun("tigger-convert", ["--rename -f", prefix + ".lsm.html"])