def skyradec_to_det(ra, dec, teldeffile, alignfile, attfile, time):
"""
Runs and captures the output from pointxform to work out the
detector and sky pixel coord for the given RA, Dec
Returns a tuple of (detx, dety, skyx, skyy)
"""
cmd = 'pointxform fromworld=yes from=\'SKY\' to=\'DET\''
cmd += ' x=' + str(ra)
cmd += ' y=' + str(dec)
cmd += ' teldeffile=' + teldeffile
cmd += ' alignfile=' + alignfile
cmd += ' attfile= ' + attfile
cmd += ' time=' + str(time)
output = execute_cmd(cmd, stdout=subprocess.PIPE)[0]
det_result = re.compile("DET.*\[", re.M).search(output)
sky_result = re.compile("SKY.*\[", re.M).search(output)
if det_result and sky_result:
det_str = (det_result.group())[3:-1].split(',')
sky_str = (sky_result.group())[3:-1].split(',')
detx, dety = float(det_str[0]), float(det_str[1])
skyx, skyy = float(sky_str[0]), float(sky_str[1])
return (detx, dety, skyx, skyy)
else:
return (None, None, None, None)
def barycentre(infile,
outfile,
orbitfile,
RA=None,
Dec=None,
clockfile='CALDB'):
"""
Barycentre the observation. If not provided a RA and Dec, the RA and Dec from
the fits header will be used.
"""
print "Barycentreing observation...\n"
if RA and Dec:
cmd = 'barycorr infile=%s outfile=%s orbitfiles=%s ra=%s dec=%s clobber=yes clockfile=%s' %\
(infile, outfile, orbitfile, RA, Dec, clockfile)
else:
print "No RA and Dec given. Using RA and Dec of target in fits header..."
cmd = 'barycorr infile=%s outfile=%s orbitfiles=%s clobber=yes clockfile=%s' %\
(infile, outfile, orbitfile, clockfile)
execute_cmd(cmd)
def add_spectra(spec_list, outroot, grouping=None):
"""
Add pha files together. Reimplements addspec ftool.
"""
back_tmp_spec = []
src_tmp_spec = []
tmp_arfs = []
weights = []
tstarts = []
tstops = []
i = 0
for spec in spec_list:
fits = pyfits.open(spec)
back_fn = fits[1].header['BACKFILE']
ancr_fn = fits[1].header['ANCRFILE']
resp_fn = fits[1].header['RESPFILE']
exposure = fits[1].header['EXPOSURE']
tstarts.append(fits[1].header['TSTART'])
tstops.append(fits[1].header['TSTOP'])
fits.close()
i += 1
temp_root = 'temp_spec' + str(i)
# copy source spectra to cwd
tmp_spec = temp_root + '.pha'
shutil.copy(spec, tmp_spec)
src_tmp_spec.append(tmp_spec)
# copy back spectra to cwd
tmp_spec = temp_root + '.bak'
shutil.copy(back_fn, tmp_spec)
back_tmp_spec.append(tmp_spec)
# copy arf file to cwd
tmp_arf = temp_root + '.arf'
shutil.copy(ancr_fn, tmp_arf)
tmp_arfs.append(tmp_arf)
weights.append(exposure)
src_math_expr = '+'.join(src_tmp_spec)
back_math_expr = '+'.join(back_tmp_spec)
weights = weights / np.sum(
weights) # response files weighted by exposure time
f = open('tmp_arfs.list', 'w')
for tmp_arf, weight in zip(tmp_arfs, weights):
print(tmp_arf, weight)
f.write(tmp_arf + ' ' + str(weight) + '\n')
f.close()
cmd = "addarf @tmp_arfs.list out_ARF=%s clobber=yes" % (outroot + '.arf')
execute_cmd(cmd)
cmd = "mathpha expr=%s units=C outfil=temp_final_spec.bak exposure=CALC areascal='%%' backscal='%%' ncomment=0 clobber=yes" % (
back_math_expr)
execute_cmd(cmd)
cmd = "mathpha expr=%s units=C outfil=temp_final_spec.pha exposure=CALC areascal='%%' backscal='%%' ncomment=0 clobber=yes" % (
src_math_expr)
execute_cmd(cmd)
#Run grppha to change the auxfile keys and to do grouping if needed
grppha_comm = "chkey backfile %s.bak & chkey ancrfile %s.arf & chkey respfile %s"%\
(outroot, outroot, resp_fn)
if grouping:
grppha_comm += " & group min %d" % grouping
grppha_comm += " & exit"
cmd = "grppha infile=temp_final_spec.pha outfile=%s.pha clobber=yes comm=\"%s\""%\
(outroot, grppha_comm)
execute_cmd(cmd)
shutil.copy('temp_final_spec.bak', outroot + '.bak')
# put TSTART and TSTOP keywords into final spectrum
out_spec_fits = pyfits.open(outroot + '.pha', mode='update')
out_spec_fits[0].header['TSTART'] = (np.min(tstarts), 'time start')
out_spec_fits[0].header['TSTOP'] = (np.max(tstops), 'time stop')
out_spec_fits.close()
for temp_fn in src_tmp_spec + back_tmp_spec + tmp_arfs:
os.remove(temp_fn)
os.remove('temp_final_spec.bak')
os.remove('temp_final_spec.pha')
os.remove('tmp_arfs.list')
def extract_spectrum(outroot,infile,chan_low=None,chan_high=None,energy_low=None,energy_high=None,\
grouping=20,grade=None,expmap=None,source_region=None,back_region=None, \
offaxis_angle=None):
"""
Extract a spectrum.
If both the PHA channel limits and energy limits are None will extract entire band.
Arguments:
- outroot: root of the output files. Will attach extension depending on
type of output (.img, .evt, etc.)
- infile: Input file to extract from.
Optional Arguments:
- chan_low, chan_high: limits of PHA channels to extract.
Default = None.
- energy_low, energy_high: energy limits in keV to extract.
Will be superceded by chan_low and chan_high.
Default=None.
- grouping: the minimum counts per bin for the spectrum.
Default=20
- expmap: exposure map file to use in xrtmkarf.
Default=None
- source_region: region file to use to extract source spectrum.
Default=None
- back_region: region file to use to extract background spectrum.
Default=None
- offaxis_angle: offaxis angle (in arcmin) of source to feed to xrtmkarf for
the vignetting correction.
Default is to let xrtmkarf do its own calculation.
"""
print("Extracting spectrum...\n")
if chan_high == None or chan_low == None:
if energy_low == None or energy_high == None:
chan_low = 0
chan_high = 1023
else:
chan_low = int(energy_low * 100.0)
chan_high = int(energy_high * 100.0)
if offaxis_angle:
x, y = '-1', '-1'
else:
x, y = find_centroid(infile)
if grade != None:
outroot += '_g%s' % grade
extract("temp_source",infile=infile, events=False, pha=True,\
region=source_region, chanlow=chan_low, chanhigh=chan_high,grade=grade)
extract(outroot + "_back",infile=infile, events=False, pha=True,\
region=back_region, chanlow=chan_low, chanhigh=chan_high,grade=grade)
cmd = "xrtmkarf outfile=%s_source.arf phafile=temp_source.pha psfflag=yes srcx=%s srcy=%s clobber=yes"%\
(outroot, x, y)
if expmap:
cmd += " expofile=%s" % (expmap)
if offaxis_angle:
cmd += " offaxis=%f" % (offaxis_angle)
xrtmkarf_out = execute_cmd(cmd, stdout=subprocess.PIPE)[0]
print(xrtmkarf_out)
rmf_re = re.compile("Processing \'(?P<rmf>.*)\.rmf\' CALDB file\.")
rmf_search = rmf_re.search(xrtmkarf_out)
if rmf_search:
rmf = rmf_search.groupdict()['rmf'] + '.rmf'
else:
print("ERROR: No rmf filename found from xrtmkarf output.")
if grade and grade != '0':
print(
"Grade selection not 0 or default, rmf in 'respfile' keyword may be wrong."
)
grppha_comm = "chkey backfile %s_back.pha & chkey ancrfile %s_source.arf & chkey respfile %s"%\
(outroot, outroot, rmf)
if grouping:
grppha_comm += " & group min %d" % grouping
grppha_comm += " & exit"
cmd = "grppha infile=temp_source.pha outfile=%s_source.pha clobber=yes comm=\"%s\""%\
(outroot, grppha_comm)
execute_cmd(cmd)
os.remove('temp_source.pha')