def copy_ccube(ccube, outsrcmap, hpx_order):
"""Copy a counts cube into outsrcmap file
reducing the HEALPix order to hpx_order if needed.
"""
sys.stdout.write(" Copying counts cube from %s to %s\n" %
(ccube, outsrcmap))
try:
hdulist_in = fits.open(ccube)
except IOError:
hdulist_in = fits.open("%s.gz" % ccube)
hpx_order_in = hdulist_in[1].header['ORDER']
if hpx_order_in > hpx_order:
hpxmap = HpxMap.create_from_hdulist(hdulist_in)
hpxmap_out = hpxmap.ud_grade(hpx_order, preserve_counts=True)
hpxlist_out = hdulist_in
#hpxlist_out['SKYMAP'] = hpxmap_out.create_image_hdu()
hpxlist_out[1] = hpxmap_out.create_image_hdu()
hpxlist_out[1].name = 'SKYMAP'
hpxlist_out.writeto(outsrcmap)
return hpx_order
else:
os.system('cp %s.gz %s.gz' % (ccube, outsrcmap))
os.system('gunzip -f %s.gz' % (outsrcmap))
return None
def copy_ccube(ccube, outsrcmap, hpx_order):
"""Copy a counts cube into outsrcmap file
reducing the HEALPix order to hpx_order if needed.
"""
sys.stdout.write(" Copying counts cube from %s to %s\n" % (ccube, outsrcmap))
try:
hdulist_in = fits.open(ccube)
except IOError:
hdulist_in = fits.open("%s.gz" % ccube)
hpx_order_in = hdulist_in[1].header['ORDER']
if hpx_order_in > hpx_order:
hpxmap = HpxMap.create_from_hdulist(hdulist_in)
hpxmap_out = hpxmap.ud_grade(hpx_order, preserve_counts=True)
hpxlist_out = hdulist_in
#hpxlist_out['SKYMAP'] = hpxmap_out.create_image_hdu()
hpxlist_out[1] = hpxmap_out.create_image_hdu()
hpxlist_out[1].name = 'SKYMAP'
hpxlist_out.writeto(outsrcmap)
return hpx_order
else:
os.system('cp %s %s' % (ccube, outsrcmap))
#os.system('cp %s.gz %s.gz' % (ccube, outsrcmap))
#os.system('gunzip -f %s.gz' % (outsrcmap))
return None
def append_hdus(hdulist, srcmap_file, source_names, hpx_order):
"""Append HEALPix maps to a list
Parameters
----------
hdulist : list
The list being appended to
srcmap_file : str
Path to the file containing the HDUs
source_names : list of str
Names of the sources to extract from srcmap_file
hpx_order : int
Maximum order for maps
"""
sys.stdout.write(" Extracting %i sources from %s" %
(len(source_names), srcmap_file))
try:
hdulist_in = fits.open(srcmap_file)
except IOError:
try:
hdulist_in = fits.open('%s.gz' % srcmap_file)
except IOError:
sys.stdout.write(" Missing file %s\n" % srcmap_file)
return
for source_name in source_names:
sys.stdout.write('.')
sys.stdout.flush()
if hpx_order is None:
hdulist.append(hdulist_in[source_name])
else:
try:
hpxmap = HpxMap.create_from_hdulist(hdulist_in,
hdu=source_name)
except IndexError:
print(" Index error on source %s in file %s" %
(source_name, srcmap_file))
continue
except KeyError:
print(" Key error on source %s in file %s" %
(source_name, srcmap_file))
continue
hpxmap_out = hpxmap.ud_grade(hpx_order, preserve_counts=True)
hdulist.append(hpxmap_out.create_image_hdu(name=source_name))
sys.stdout.write("\n")
hdulist.flush()
hdulist_in.close()
def append_hdus(hdulist, srcmap_file, source_names, hpx_order):
"""Append HEALPix maps to a list
Parameters
----------
hdulist : list
The list being appended to
srcmap_file : str
Path to the file containing the HDUs
source_names : list of str
Names of the sources to extract from srcmap_file
hpx_order : int
Maximum order for maps
"""
sys.stdout.write(" Extracting %i sources from %s" % (len(source_names), srcmap_file))
try:
hdulist_in = fits.open(srcmap_file)
except IOError:
try:
hdulist_in = fits.open('%s.gz' % srcmap_file)
except IOError:
sys.stdout.write(" Missing file %s\n" % srcmap_file)
return
for source_name in source_names:
sys.stdout.write('.')
sys.stdout.flush()
if hpx_order is None:
hdulist.append(hdulist_in[source_name])
else:
try:
hpxmap = HpxMap.create_from_hdulist(hdulist_in, hdu=source_name)
except IndexError:
print(" Index error on source %s in file %s" % (source_name, srcmap_file))
continue
except KeyError:
print(" Key error on source %s in file %s" % (source_name, srcmap_file))
continue
hpxmap_out = hpxmap.ud_grade(hpx_order, preserve_counts=True)
hdulist.append(hpxmap_out.create_image_hdu(name=source_name))
sys.stdout.write("\n")
hdulist.flush()
hdulist_in.close()
def main():
import sys
import argparse
# Argument defintion
usage = "usage: %(prog)s [options]"
description = "Collect all the new source"
parser = argparse.ArgumentParser(usage, description=__abstract__)
parser.add_argument("-i",
"--input",
type=argparse.FileType('r'),
required=True,
help="Input file")
parser.add_argument("-e",
"--extension",
type=str,
default="SKYMAP",
help="FITS HDU with HEALPix map")
parser.add_argument("--ebin",
type=str,
default=None,
help="Energy bin, integer or 'ALL'")
parser.add_argument("--zscale",
type=str,
default='log',
help="Scaling for color scale")
parser.add_argument("--zmin",
type=float,
default=None,
help="Minimum z-axis value")
parser.add_argument("--zmax",
type=float,
default=None,
help="Maximum z-axis value")
parser.add_argument("-o",
"--output",
type=argparse.FileType('w'),
help="Output file. Leave blank for interactive.")
# Parse the command line
args = parser.parse_args(sys.argv[1:])
# Get the model
f = pf.open(args.input.name)
# We need a better check
maptype = "None"
model_hdu = f[args.extension]
hpxmap = HpxMap.create_from_hdulist(f, hdu=args.extension)
outdata = []
if args.ebin == "ALL":
wcsproj = hpxmap.hpx.make_wcs(naxis=2,
proj='MOL',
energies=None,
oversample=2)
mapping = HpxToWcsMapping(hpxmap.hpx, wcsproj)
for i, data in enumerate(hpxmap.counts):
ip = ImagePlotter(data=data, proj=hpxmap.hpx, mapping=mapping)
fig = plt.figure(i)
im, ax = ip.plot(zscale=args.zscale,
vmin=args.zmin,
vmax=args.zmax)
outdata.append(fig)
elif args.ebin is None:
ip = ImagePlotter(data=hpxmap.counts, proj=hpxmap.hpx)
im, ax = ip.plot(zscale=args.zscale, vmin=args.zmin, vmax=args.zmax)
outdata.append((im, ax))
else:
try:
ibin = int(args.ebin)
ip = ImagePlotter(data=hpxmap.counts[ibin], proj=hpxmap.hpx)
im, ax = ip.plot(zscale=args.zscale,
vmin=args.zmin,
vmax=args.zmax)
outdata.append((im, ax))
except:
raise ValueError("--ebin argument must be an integer or 'ALL'")
if args.output is None:
plt.show()
else:
if len(outdata) == 1:
plt.savefig(args.output.name)
else:
base, ext = os.path.splitext(args.output.name)
for i, fig in enumerate(outdata):
fig.savefig("%s_%02i%s" % (base, i, ext))
def main():
import sys
import argparse
# Argument defintion
usage = "usage: %(prog)s [options]"
description = "Collect all the new source"
parser = argparse.ArgumentParser(usage,description=__abstract__)
parser.add_argument("-i", "--input",type=argparse.FileType('r'),required=True,
help="Input file")
parser.add_argument("-e", "--extension",type=str,default="SKYMAP",
help="FITS HDU with HEALPix map")
parser.add_argument("--ebin",type=str,default=None,
help="Energy bin, integer or 'ALL'")
parser.add_argument("-o", "--output",type=argparse.FileType('w'),
help="Output file. Leave blank for interactive.")
# Parse the command line
args = parser.parse_args(sys.argv[1:])
# Get the model
f = pf.open(args.input.name)
# We need a better check
maptype = "None"
model_hdu = f[args.extension]
hpxmap = HpxMap.create_from_hdulist(f,extname=args.extension,ebounds="EBOUNDS")
outdata = []
if args.ebin == "ALL":
wcsproj = hpxmap.hpx.make_wcs(naxis=2,proj='AIT',energies=None,oversample=2)
mapping = HpxToWcsMapping(hpxmap.hpx,wcsproj)
for i,data in enumerate(hpxmap.counts):
ip = ImagePlotter(data=data,proj=hpxmap.hpx,mapping=mapping)
fig = plt.figure(i)
im,ax = ip.plot(zscale='log')
outdata.append(fig)
elif args.ebin is None:
ip = ImagePlotter(data=hpxmap.counts,proj=hpxmap.hpx)
im,ax = ip.plot(zscale='log')
outdata.append((im,ax))
else:
try:
ibin = int(args.ebin)
ip = ImagePlotter(data=hpxmap.counts[ibin],proj=hpxmap.hpx)
im,ax = ip.plot(zscale='log')
outdata.append((im,ax))
except:
print("--ebin argument must be an integer or 'ALL'")
if args.output is None:
plt.show()
else:
plt.savefig(args.output.name)
def merge_hpx_counts_cubes(filelist):
""" Merge all the files in filelist, assuming that they HEALPix counts cubes
"""
out_prim = None
out_skymap = None
out_ebounds = None
datalist_gti = []
exposure_sum = 0.
nfiles = len(filelist)
ngti = np.zeros(nfiles, int)
out_name = None
for i, filename in enumerate(filelist):
fin = fits.open(filename)
sys.stdout.write('.')
sys.stdout.flush()
if i == 0:
out_prim = update_null_primary(fin[0], out_prim)
out_name = fin[1].name
map_in = HpxMap.create_from_hdulist(fin)
out_skymap = update_hpx_skymap_allsky(map_in, out_skymap)
if i == 0:
try:
out_ebounds = update_ebounds(fin["EBOUNDS"], out_ebounds)
except KeyError:
out_ebounds = update_energies(fin["ENERGIES"], out_ebounds)
try:
(gti_data, exposure, tstop) = extract_gti_data(fin["GTI"])
datalist_gti.append(gti_data)
exposure_sum += exposure
ngti[i] = len(gti_data)
except KeyError:
pass
if i == 0:
first = fin
elif i == nfiles - 1:
try:
date_end = fin[0].header['DATE-END']
except KeyError:
date_end = None
else:
fin.close()
out_skymap_hdu = out_skymap.create_image_hdu("SKYMAP")
hdulist = [out_prim, out_skymap_hdu, out_ebounds]
if len(datalist_gti) > 0:
out_gti = merge_all_gti_data(datalist_gti, ngti, first['GTI'])
out_gti.header['EXPOSURE'] = exposure_sum
out_gti.header['TSTOP'] = tstop
hdulist.append(out_gti)
for hdu in hdulist:
if date_end:
hdu.header['DATE-END'] = date_end
out_prim.update_header()
sys.stdout.write("!\n")
return fits.HDUList(hdulist)
def merge_hpx_counts_cubes(filelist):
""" Merge all the files in filelist, assuming that they HEALPix counts cubes
"""
out_prim = None
out_skymap = None
out_ebounds = None
datalist_gti = []
exposure_sum = 0.
nfiles = len(filelist)
ngti = np.zeros(nfiles, int)
out_name = None
for i, filename in enumerate(filelist):
fin = fits.open(filename)
sys.stdout.write('.')
sys.stdout.flush()
if i == 0:
out_prim = update_null_primary(fin[0], out_prim)
out_name = fin[1].name
map_in = HpxMap.create_from_hdulist(fin)
out_skymap = update_hpx_skymap_allsky(map_in, out_skymap)
if i == 0:
try:
out_ebounds = update_ebounds(fin["EBOUNDS"], out_ebounds)
except KeyError:
out_ebounds = update_energies(fin["ENERGIES"], out_ebounds)
try:
(gti_data, exposure, tstop) = extract_gti_data(fin["GTI"])
datalist_gti.append(gti_data)
exposure_sum += exposure
ngti[i] = len(gti_data)
except KeyError:
pass
if i == 0:
first = fin
elif i == nfiles - 1:
try:
date_end = fin[0].header['DATE-END']
except KeyError:
date_end = None
else:
fin.close()
out_skymap_hdu = out_skymap.create_image_hdu("SKYMAP")
hdulist = [out_prim, out_skymap_hdu, out_ebounds]
if len(datalist_gti) > 0:
out_gti = merge_all_gti_data(datalist_gti, ngti, first['GTI'])
out_gti.header['EXPOSURE'] = exposure_sum
out_gti.header['TSTOP'] = tstop
hdulist.append(out_gti)
for hdu in hdulist:
if date_end:
hdu.header['DATE-END'] = date_end
out_prim.update_header()
sys.stdout.write("!\n")
return fits.HDUList(hdulist)