def _make_xselect_commands(infile, outfile, elow, ehigh, usrgti=False):
'''
Helper script to generate the xselect commands to make an image in a given NuSTAR range
'''
xsel = open("xsel.xco", "w")
xsel.write("session1\n")
xsel.write("read events \n")
evdir = os.path.dirname(infile)
xsel.write(f'{evdir} \n ')
evfile = os.path.basename(infile)
xsel.write(f'{evfile} \n ')
xsel.write('yes \n')
pi_low = energy_to_chan(elow)
pi_high = energy_to_chan(ehigh)
if usrgti is not False:
xsel.write(f'filter time \n')
xsel.write('file \n')
xsel.write(f'{usrgti}\n')
xsel.write('extract events\n')
xsel.write('filter pha_cutoff {} {} \n'.format(pi_low, pi_high))
xsel.write('set xybinsize 1\n')
xsel.write("extract image\n")
xsel.write("save image\n")
xsel.write("%s \n" % outfile)
xsel.write('exit\n')
xsel.write('n \n')
xsel.close()
return 'xsel.xco'
def _make_xselect_commands_det1(infile, outfile, elow, ehigh):
'''
Helper script to generate the xselect commands to make an image in a
given NuSTAR energy range
'''
import glob
for oldfile in glob.glob("session1*"):
os.system(f"rm {oldfile}")
xsel = open("xsel.xco", "w")
xsel.write("session1\n")
xsel.write("read events \n")
evdir = os.path.dirname(infile)
xsel.write(f'{evdir} \n ')
evfile = os.path.basename(infile)
xsel.write(f'{evfile} \n ')
xsel.write('yes \n')
xsel.write('set xyname\n')
xsel.write('DET1X\n')
xsel.write('DET1Y\n')
pi_low = energy_to_chan(elow)
pi_high = energy_to_chan(ehigh)
xsel.write('filter pha_cutoff {} {} \n'.format(pi_low, pi_high))
xsel.write('set xybinsize 1\n')
xsel.write("extract image\n")
xsel.write("save image\n")
xsel.write("%s \n" % outfile)
xsel.write('exit\n')
xsel.write('n \n')
xsel.close()
return 'xsel.xco'
def make_det1_lightcurve(infile,
mod,
obs,
time_bin=100 * u.s,
mode='01',
elow=3,
ehigh=20,
stemout=False,
gtifile=False):
'''
Generate a script to run nuproducts to make a lightcurve using the whole
FoV and turning off all vignetting and PSF effects. Assumes that infile
has already been filtered using extract_det1_events().
Parameters
----------
infile: str
Full path to the input event file. This should be pre-filtered by
by extract_det1_events
mod: str
'A' or 'B'
obs: nustar_gen.info.Observation
Observation meta data
Other Parameters
-------------------
elow: float, optional, default = 3 keV
Low-energy bound
ehigh: float, optional, default is 20 keV
High-energy bound
mode: str, optional, default is '01'
Optional. Used to specify stemout if you're doing mode06 analysis and want
to specify output names that are more complicated.
gtifile: str
Path to a GTI file. If this is set, then this is passed to nuproducts.
stemout: str, optional
Use the specified stemout string when calling nuproducts. Otherwise
uses the default value.
'''
from astropy.io.fits import getheader
# Make sure environment is set up properly
_check_environment()
# Check to see that all files exist:
assert os.path.isfile(
infile), 'make_det1_lightcurve: infile does not exist!'
# evdir = os.path.dirname(infile)
evdir = obs.evdir
seqid = obs.seqid
# seqid = os.path.basename(os.path.dirname(evdir))
outdir = obs.out_path
# if outpath is None:
# outdir = evdir
# else:
# outdir = outpath
hdr = getheader(infile)
ra = hdr['RA_OBJ']
dec = hdr['DEC_OBJ']
time_bin = int((time_bin.to(u.s)).value)
if stemout is False:
stemout = f'nu{seqid}{mod}{mode}_full_FoV_{elow}to{ehigh}_{time_bin}s'
lc_script = f'{outdir}/rundet1lc_{stemout}.sh'
pi_low = energy_to_chan(elow)
pi_high = energy_to_chan(ehigh)
with open(lc_script, 'w') as f:
f.write('nuproducts phafile=NONE bkgphafile=NONE imagefile=NONE ')
f.write(f'infile={infile} ')
f.write('runmkarf=no runmkrmf=no ')
f.write(f'indir={evdir} outdir={outdir} instrument=FPM{mod} ')
f.write(f'steminputs=nu{seqid} stemout={stemout} ')
f.write(f'pilow={pi_low} pihigh={pi_high} ')
f.write(f'bkgextract=no ')
f.write(f'binsize={time_bin} ')
f.write(
f'srcra={ra} srcdec={dec} srcregionfile=DEFAULT srcradius=299 ')
# Turn off all of the time-dependent corrections for the pointing here
f.write(f'lcpsfflag=no lcexpoflag=no lcvignflag=no ')
if (gtifile != False):
f.write(f'usrgtifile={gtifile} ')
f.write('clobber=yes')
os.chmod(lc_script, stat.S_IRWXG + stat.S_IRWXU)
return lc_script
def make_lightcurve(infile,
mod,
src_reg,
barycorr=False,
time_bin=100 * u.s,
mode='01',
bgd_reg='None',
outpath='None',
elow=3,
ehigh=20):
'''
Generate a script to run nuproducts
Parameters
----------
infile: str
Full path to the input event file.
mod: str
'A' or 'B'
src_reg: str
Full path to source region.
Other Parameters
-------------------
bgd_reg: str
If not 'None', then must be the full path to the background region file
barycorr: bool
Default is 'False'. If 'True', then queries the infile for the OBJ J2000
coordinates and uses these for the barycenter correction.
elow: float
Low-eneryg bound. Default is 3 keV.
ehigh: float
High-energy bound. Default is 20 keV.
outpath: str
Optional. Default is to put the lightcurves in the same location as infile
mode: str
Optional. Used primarily if you're doing mode06 analysis and need to specify
output names that are more complicated.
'''
from astropy.io.fits import getheader
# Make sure environment is set up properly
_check_environment()
# Check to see that all files exist:
assert os.path.isfile(infile), 'make_lightcurve: infile does not exist!'
assert os.path.isfile(src_reg), 'make_lightcurve: src_reg does not exist!'
if bgd_reg != 'None':
assert os.path.isfile(
bgd_reg), 'make_lightcurve: bgd_reg does not exist!'
bkgextract = 'yes'
else:
bkgextract = 'no'
reg_base = os.path.basename(src_reg)
reg_base = os.path.splitext(reg_base)[0]
evdir = os.path.dirname(infile)
seqid = os.path.basename(os.path.dirname(evdir))
if outpath == 'None':
outdir = evdir
else:
outdir = outpath
try:
os.makedirs(outdir)
except FileExistsError:
# directory already exists
pass
time_bin = (time_bin.to(u.s)).value
stemout = f'nu{seqid}{mod}{mode}_{reg_base}_{elow}to{ehigh}_{time_bin:3.4}s'
lc_script = outdir + f'/runlc_{stemout}.sh'
pi_low = energy_to_chan(elow)
pi_high = energy_to_chan(ehigh)
with open(lc_script, 'w') as f:
f.write('nuproducts phafile=NONE bkgphafile=NONE imagefile=NONE ')
f.write(f'runmkarf=no runmkrmf=no pilow={pi_low} pihigh={pi_high} ')
f.write(f'indir={evdir} outdir={outdir} instrument=FPM{mod} ')
f.write(f'steminputs=nu{seqid} stemout={stemout} ')
f.write(f'srcregionfile={src_reg} ')
if bkgextract == 'no':
f.write(f'bkgextract=no ')
else:
f.write(f'bkgextract=yes bkgregionfile={bgd_reg} ')
f.write(f'binsize={time_bin} ')
if barycorr:
attorb = evdir + f'/nu{seqid}{mod}.attorb'
hdr = getheader(infile)
ra = hdr['RA_OBJ']
dec = hdr['DEC_OBJ']
f.write(f'barycorr=yes srcra_barycorr={ra} srcdec_barycorr={dec} ')
f.write(f'orbitfile={attorb} ')
f.write('clobber=yes')
os.chmod(lc_script, stat.S_IRWXG + stat.S_IRWXU)
return lc_script
def make_det1_lightcurve(infile,
mod,
barycorr=False,
time_bin=100 * u.s,
mode='01',
outpath=None,
elow=3,
ehigh=20):
'''
Generate a script to run nuproducts to make a lightcurve using the whole
FoV and turning off all vignetting and PSF effects. Assumes that infile
has already been filtered using extract_det1_events().
Parameters
----------
infile: str
Full path to the input event file.
mod: str
'A' or 'B'
Optional Parameters
-------------------
bgd_reg: str
If not 'None', then must be the full path to the background region file
barycorr: bool
Default is 'False'. If 'True', then queries the infile for the OBJ J2000
coordinates and uses these for the barycenter correction.
elow: float
Low-eneryg bound. Default is 3 keV.
ehigh: float
High-energy bound. Default is 20 keV.
outpath: str
Optional. Default is to put the lightcurves in the same location as infile
mode: str
Optional. Used primarily if you're doing mode06 analysis and need to specify
output names that are more complicated.
'''
from astropy.io.fits import getheader
# Make sure environment is set up properly
_check_environment()
# Check to see that all files exist:
assert os.path.isfile(
infile), 'make_det1_lightcurve: infile does not exist!'
evdir = os.path.dirname(infile)
seqid = os.path.basename(os.path.dirname(evdir))
if outpath is None:
outdir = evdir
else:
outdir = outpath
hdr = getheader(infile)
ra = hdr['RA_OBJ']
dec = hdr['DEC_OBJ']
time_bin = int((time_bin.to(u.s)).value)
stemout = f'nu{seqid}{mod}{mode}_full_FoV_{elow}to{ehigh}_{time_bin}s'
lc_script = f'{outdir}/rundet1lc_{stemout}.sh'
pi_low = energy_to_chan(elow)
pi_high = energy_to_chan(ehigh)
with open(lc_script, 'w') as f:
f.write('nuproducts phafile=NONE bkgphafile=NONE imagefile=NONE ')
f.write(f'infile={infile} ')
f.write('runmkarf=no runmkrmf=no ')
f.write(f'indir={evdir} outdir={outdir} instrument=FPM{mod} ')
f.write(f'steminputs=nu{seqid} stemout={stemout} ')
f.write(f'pilow={pi_low} pihigh={pi_high} ')
f.write(f'bkgextract=no ')
f.write(f'binsize={time_bin} ')
f.write(
f'srcra={ra} srcdec={dec} srcregionfile=DEFAULT srcradius=299 ')
# Turn off all of the time-dependent corrections for the pointing here
f.write(f'lcpsfflag=no lcexpoflag=no lcvignflag=no ')
if barycorr:
attorb = evdir + f'/nu{seqid}{mod}.attorb'
f.write(f'barycorr=yes srcra_barycorr={ra} srcdec_barycorr={dec} ')
f.write(f'orbitfile={attorb} ')
f.write('clobber=yes')
os.chmod(lc_script, stat.S_IRWXG + stat.S_IRWXU)
return lc_script
def make_straylight_arf(det1im, regfile, filt_file, mod, obs):
'''
Produces an ARF for a given observation. Currently uses counts-weighting to
determine the contribution of the detabs parameters for each detector.
SHOULD PROBABLY BE MOVED TO WRAPPERS OR SOMETHING?
Parameters
----------
det1im : str
Full path to the DET1 exposure image file.
regfil : str
Full path to the region file, assumed to be a ds9 region file in "IMAGE"
coordinates
filt_file : str
Full path to the DET1 screened event file (i.e. output of
nustar_gen.wrappers.extract_det1_events() ). This used to scale the ARF by
the number of 3--10 keV counts on each detector.
mod : str
'A' or 'B'
obs: nustar_gen.info.Observation
Observation meta data
Returns
-------
out_arf: string
Full path to the new arf file
'''
from astropy.io import fits
import glob
from nustar_gen import io
from nustar_gen.utils import energy_to_chan
# Check to see that all files exist:
assert os.path.isfile(det1im), \
f'straylight_area: DET1 exposure map not found: {det1im}'
assert os.path.isfile(regfile), \
f'straylight_area: Region file not found: {regfile}'
assert os.path.isfile(filt_file), \
f'straylight_area: Event file not found: {evf}'
outdir = obs.out_path
out_arf = outdir+'/'+os.path.splitext(os.path.basename(filt_file))[0]+'.arf'
# Get the effective are target:
area = straylight_area(det1im, regfile, filt_file)
# Use counts relative scaling to blend the ARFs:
ev_hdu = fits.open(filt_file)
evts = ev_hdu[1].data
scale_evts = evts[ (evts['PI']>energy_to_chan(3.)) & (evts['PI'] < energy_to_chan(10.) )]
dethist, detedges = np.histogram(scale_evts['DET_ID'], range=[0, 3],bins = 4)
totcts = dethist.sum()
scale = [ float(x) / totcts for x in dethist]
ev_hdu.close()
# Load the base ARF file:
arf_file = io.find_arf_template()
arf_hdu = fits.open(arf_file)
arf = arf_hdu[1].data
arf_header = arf_hdu[1].header
# Trim header
arf_hdu[1].header = arf_header[0:26]
# Mock up an ARF that's flat with just the detector area
arf['SPECRESP'] = [area.value for x in arf['SPECRESP']]
caldb = os.environ['CALDB']
detabs_files = glob.glob(caldb+f'/**/nu{mod}detabs*', recursive=True)
use = len(detabs_files)-1
detabs_hdu = fits.open(detabs_files[use])
for detind, isc in enumerate(scale):
detabs = detabs_hdu[detind+1].data
if detind == 0:
arfabs = detabs['DETABS'] * isc
else:
arfabs += detabs['DETABS'] * isc
arf['SPECRESP'] *= arfabs
detabs_hdu.close()
be_file = io.find_be_arf()
be_arf = fits.getdata(be_file, 1)
arf['SPECRESP'] *= be_arf['SPECRESP']
arf_hdu.writeto(out_arf, overwrite=True)
arf_hdu.close()
return out_arf
