def Roughfit_PL(obsname,
Sourcename,
obs_suffix='xwtw2po_cl_seporb.pha',
NH=1.0,
PL=2.,
outfile='Roughfit'):
'''Given the observation number file of an
observation, the Sourcename, and the name
of an output file, this will preform a
rough spectral fit to get a handle on the
sources flux.'''
spec = obsname + '/sw' + obsname + obs_suffix
fits = pyfits.open(spec)
xspec.AllData(spec)
xspec.AllData.ignore("bad")
xspec.AllData.ignore("**-0.5 10.0-**")
model = xspec.Model("tbabs(po)")
errorstr = '1.6 2 3'
model.TBabs.nH = NH
model.TBabs.nH.frozen = True
model.powerlaw.PhoIndex.values = [PL, 0.01, -3.0, -2.0, 9.0, 10.0]
xspec.Fit.query = 'yes'
xspec.Fit.perform()
xspec.Fit.perform()
xspec.Plot.xAxis = "keV"
xspec.Plot.device = "/xw"
xspec.Plot("data", "resid")
xspec.Plot()
xspec.Fit.error(errorstr)
try:
xspec.AllModels.calcFlux("0.5 10. err 1000 90")
except (RuntimeError, TypeError, NameError, 'Flux Command Error'):
pass
outf = open(outfile + '.spec', 'w')
nH = xspec.AllModels(1)(1)
outf.write('# nH: %f (%f - %f)\tChisq: %f\tDOF: %f\n' %
(nH.values[0], nH.error[0], nH.error[1], xspec.Fit.statistic,
xspec.Fit.dof))
outf.write(
'# obsid\tflux\tflux_low\tflux_high\tgamma\tgamma_low\tgamma_high\tkT\tkT_low\tkT_high\tPLnorm/kTnorm\n'
)
flux = xspec.AllData(1).flux
output = '%s\t%E\t%E\t%E\t%f\t%f\t%f\t%f\t%f\t%f\t%f\n' %\
( spec, flux[0], flux[1], flux[2],xspec.AllModels(1)(2).values[0],
xspec.AllModels(1)(2).error[0], xspec.AllModels(1)(2).error[1], 0,
0, 0, xspec.AllModels(1)(3).values[0] )
outf.write(output)
outf.close()
xspec.AllData.clear()
xspec.AllModels.clear()
def grid_fe_k_flux(base_nH=1, base_fe=1, out=None):
"""Make a grid """
# Make it shut up
xs.Xset.chatter = 9
# Ensure "standard" normalization
snr = xs.AllModels(1, 'snr_src')
snr.tbnew_gas.nH = base_nH
snr.vnei.Fe = base_fe
snr.vnei.norm = 1
# Temporarily unshutup to affirm baseline parameters
xs.Xset.chatter = 10
snr.show()
xs.Xset.chatter = 9
# First compute flux w/ "standard" norm (effectively, fix mass & distance)
range_Tau = np.logspace(9, 13, 100) # Spans 1e9 to 1e13
range_kT = np.logspace(-1, 1, 100) # Spans 0.1 to 10 keV
# Outputs
erg_fluxes = np.zeros((len(range_Tau), len(range_kT)))
phot_fluxes = np.zeros((len(range_Tau), len(range_kT)))
# Time: ~50 minutes for 100x100 pts (1e9 to 1e13 s cm^{-3}, 0.1 to 10 keV)
# for only one spectrum (0087940201 MOS merged)
for i in range(len(range_Tau)):
print "Tau = {:g}".format(range_Tau[i]), datetime.now()
snr.vnei.Tau = range_Tau[i]
for j in range(len(range_kT)):
if j % 5 == 0:
print " kT = {:g} ...".format(range_kT[j])
snr.vnei.kT = range_kT[j]
snr.vnei.Fe = 0
xs.AllModels.calcFlux("6 7")
continuum_erg = xs.AllData(1).flux[0]
continuum_phot = xs.AllData(1).flux[3]
snr.vnei.Fe = base_fe
xs.AllModels.calcFlux("6 7")
erg_fluxes[i,j] = (xs.AllData(1).flux[0] - continuum_erg) / snr.constant.factor.values[0]
phot_fluxes[i,j] = (xs.AllData(1).flux[3] - continuum_phot) / snr.constant.factor.values[0]
# Reset
xs.Xset.chatter = 10
if out is None:
out = "fe-k_flux_data/grid_nH{:g}_fe{:g}.npz".format(base_nH * 1e22, base_fe)
np.savez(out, Tau=range_Tau, kT=range_kT, erg_fluxes=erg_fluxes,
phot_fluxes=phot_fluxes)
def bkg_only_fit(output, steppar=False, error=False):
"""
Fit bkg region alone to XRB model
"""
out = g309.load_data_and_models(["bkg"], snr_model=None)
set_energy_range(out['bkg'])
xs.AllData.ignore("bad")
# Reset XRB to "typical" values
# As usual, fit is pretty sensitive to initial values
# (initial kT values that are too small drive fit to a bad local minimum)
xrb = xs.AllModels(1, 'xrb')
xrb.setPars({xrb.apec.kT.index : "0.2, , 0, 0, 0.5, 1"}, # Unabsorped apec (local bubble)
{xrb.tbnew_gas.nH.index : "1.5, , 0.01, 0.1, 5, 10"}, # Galactic absorption
{xrb.apec_6.kT.index : "0.7, , 0, 0, 2, 4"}, # Absorbed apec (galactic halo)
{xrb.apec.norm.index : 1e-3},
{xrb.apec_6.norm.index : 1e-3} )
xrb.apec.kT.frozen = False
xrb.tbnew_gas.nH.frozen = False
xrb.apec_6.kT.frozen = False
xrb.apec.norm.frozen = False
xrb.apec_6.norm.frozen = False
xs.Fit.perform()
if xs.Plot.device == "/xs":
xs.Plot("ldata delchi")
if steppar:
xs.Fit.steppar("xrb:{:d} 0.1 0.5 20".format(xs_utils.par_num(xrb, xrb.apec.kT)))
xs.Fit.steppar("xrb:{:d} 0.4 0.8 20".format(xs_utils.par_num(xrb, xrb.apec_6.kT)))
if xs.Plot.device == "/xs":
xs.Plot("ldata delchi")
if error:
xs.Xset.openLog(output + "_error.log")
print "Error run started:", datetime.now()
xs.Fit.error("xrb:{:d}".format(xs_utils.par_num(xrb, xrb.apec.kT))
+ " xrb:{:d}".format(xs_utils.par_num(xrb, xrb.apec.norm))
+ " xrb:{:d}".format(xs_utils.par_num(xrb, xrb.tbnew_gas.nH))
+ " xrb:{:d}".format(xs_utils.par_num(xrb, xrb.apec_6.kT))
+ " xrb:{:d}".format(xs_utils.par_num(xrb, xrb.apec_6.norm)))
print "Error run complete:", datetime.now()
xs.Xset.closeLog()
# Dump useful things here...
products(output)
print_model(xrb, output + "_xrb.txt")
def xspec_flux(x):
Temperature, z_, ind_file, El_, Eh_, Z_ = x
L_factor, norm, abundance = 1e44, 1.0, Z_
E_norm = [El_, Eh_]
xspec.Model("apec")
m1 = xspec.AllModels(1)
m1.setPars(Temperature, abundance, z_, norm)
filename = mydirectory+"/parameter_files/xspec/" + str(ind_file) + ".fak"
fs1 = xspec.FakeitSettings(response, ancillary, fileName = filename, \
exposure = 100000.0)
xspec.AllData.fakeit(1,fs1,applyStats=False, noWrite = True)
spec1 = xspec.AllData(1)
xspec.AllModels.setEnergies(".01 100. 1000 log")
xspec.AllModels.calcLumin("%f %f %f" %(E_norm[0],E_norm[1],z_))
L = spec1.lumin[0]
xspec.AllModels.calcFlux("%f %f" %(E_norm[0],E_norm[1]))
F = spec1.flux[0]
new_norm = L_factor / (L * 1e44)
m1.setPars({4:new_norm})
xspec.AllModels.calcLumin("%f %f %f" %(E_norm[0],E_norm[1],z_))
L_new = spec1.lumin[0]
xspec.AllModels.calcFlux("%f %f" %(E_norm[0],E_norm[1]))
F_new = spec1.flux[0]
spec1.ignore("**-%f %f-**" %(E_norm[0],E_norm[1]))
rate = spec1.rate[3]
xspec.AllData.clear()
return [F_new, rate]
def get_models_for_spec(spectrum):
"""Get all active XSPEC models for a given spectrum object's data group
In practice, my spectra usually have data group == index (i.e., ignore data
group entirely because each spectrum has some independent parameter...
different XMM instrumental lines, SP contamination model)
WARNING: not tested on models with no names (i.e. really simple fit cases).
This should be an easy fix (TODO).
Input: XSPEC spectrum object
Output: list of `xspec.Model` objects, ordered by source number
"""
# Suppress "Spectrum X has no response for source Y" console warnings
# that appear at chattiness >= 10
old_chatter = xs.Xset.chatter
old_logChatter = xs.Xset.logChatter
xs.Xset.chatter = 9
xs.Xset.logChatter = 9
models = []
for idx in sorted(xs.AllModels.sources):
# Hack: if spectrum has no response for source number idx,
# XSPEC throws a generic Exception (hence the generic "except")
# This is the only way I know of to get a spectrum's source #s
try:
spectrum.multiresponse[idx - 1] # convert to 0-based index
except:
continue
model_name = xs.AllModels.sources[idx]
models.append(xs.AllModels(spectrum.dataGroup, model_name))
xs.Xset.chatter = old_chatter
xs.Xset.logChatter = old_logChatter
return models
def single_fit(output, region='src', with_bkg=True, free_elements=None,
error=False, error_rerun=False,
tau_scan=False, tau_freeze=None, nH_freeze=None,
snr_model='vnei', **kwargs):
"""Fit any region to an arbitrary remnant model, possibly fitting XRB with
background region as well.
Arguments
output: file stem string
Keyword arguments
region: region spectrum to be fitted
with_bkg: fit to X-ray background region (bkg) simultaneously
snr_model: snr model expression (and parameter setup) to use
free_elements: (default) is [Si,S]
if [], use solar abundances
error: perform single error run
tau_scan: steppar over plausible Tau values to ensure convergence to "correct" best fit
tau_freeze: freeze ionization timescale to provided value
nH_freeze: freeze SNR absorption to provided value
kwargs - passed to g309_models.load_data_and_models
(suffix, mosmerge, marfrmf)
"""
if free_elements is None:
free_elements = ['Si', 'S']
# Set up spectra and models in XSPEC
if with_bkg:
out = g309.load_data_and_models([region, 'bkg'], snr_model=snr_model, **kwargs)
set_energy_range(out['bkg'])
else:
out = g309.load_data_and_models([region], snr_model=snr_model, **kwargs)
set_energy_range(out[region])
xs.AllData.ignore("bad")
if snr_model == 'gauss':
for extr in out[region]:
extr.spec.ignore("**-5.0, 8.0-**")
xrb = xs.AllModels(1, 'xrb')
snr = xs.AllModels(1, 'snr_' + region)
# Reset XRB to "typical" values, do NOT vary yet
if with_bkg:
xrb.setPars({xrb.apec.kT.index : "0.1, , 0, 0, 0.5, 1"}, # Unabsorped apec (local bubble)
{xrb.tbnew_gas.nH.index : "1, , 0.1, 0.5, 5, 10"}, # Extragalactic absorption
{xrb.tbnew_gas_5.nH.index : "1, , 0.1, 0.5, 5, 10"}, # Ridge absorption
{xrb.apec_6.kT.index : "0.5, , 0, 0, 2, 4"}, # Galactic ridge (+ minimal halo maybe)
{xrb.apec.norm.index : 1e-3},
{xrb.apec_6.norm.index : 1e-3} )
xs_utils.freeze_model(xrb)
# Try floating norms to help initial fit
xrb.apec.norm.frozen = False
xrb.apec_6.norm.frozen = False
def thaw_bkg():
for c in [xrb.apec.kT, xrb.tbnew_gas.nH, xrb.tbnew_gas_5.nH,
xrb.apec_6.kT]:
c.frozen = False
xs.Fit.renorm()
# Let SNR model vary (NOTE: this assumes default to be vnei...)
if snr_model.startswith('vnei'):
xs_utils.freeze_model(snr)
# Configure initial SNR parameters
if nH_freeze:
snr.tbnew_gas.nH = nH_freeze
else:
snr.tbnew_gas.nH.frozen=False
snr.vnei.kT.frozen=False
snr.vnei.norm.frozen=False
if tau_freeze:
snr.vnei.Tau = tau_freeze
else:
snr.vnei.Tau.frozen = False
for elem in free_elements:
comp = snr.vnei.__getattribute__(elem)
comp.frozen = False
if snr_model == 'vnei+nei':
snr.nei.norm = 0
elif snr_model == 'vnei+powerlaw':
snr.powerlaw.PhoIndex = 2
snr.powerlaw.norm = 0 # zero
elif snr_model == 'vnei+srcutlog':
# srcutlog, w/ one free parameter, behaves better than powerlaw
snr.srcutlog.__getattribute__('break').frozen = False
# Run initial fit
if with_bkg:
# Fit has enormous trouble converging
if tau_freeze:
thaw_bkg()
xs.Fit.perform()
else:
snr.vnei.Tau = 2e10
snr.vnei.Tau.frozen = True
xs.Fit.perform()
thaw_bkg()
xs.Fit.perform()
snr.vnei.Tau.frozen = False
xs.Fit.perform()
else:
xs.Fit.perform()
# Post-processing on initial fit
if tau_scan:
xs.Fit.steppar("log {:s}:{:d} 1e9 5e13 15".format(snr.name,
xs_utils.par_num(snr, snr.vnei.Tau)))
if snr_model == 'vnei+nei':
snr.nei.kT.frozen = False
snr.nei.Tau.frozen = False
snr.nei.norm.frozen = False
xs.Fit.perform()
elif snr_model == 'vnei+powerlaw':
snr.powerlaw.PhoIndex = 2
snr.powerlaw.norm = 0 # zero
snr.powerlaw.norm.frozen = False
xs.Fit.perform()
snr.powerlaw.PhoIndex.frozen = False
xs.Fit.perform()
# Because powerlaw norm generally runs to zero, traverse moderately
# strong power law cases
xs.Fit.steppar("log {:s}:{:d} 1e-5 1e-2 30".format(snr.name,
xs_utils.par_num(snr, snr.powerlaw.norm)))
elif snr_model == 'vnei+srcutlog':
# Check reasonably high break values: 15 -- 17
xs.Fit.steppar("{:s}:{:d} 15 17 20".format(snr.name,
xs_utils.par_num(snr, snr.srcutlog.__getattribute__('break'))
))
elif snr_model == 'vpshock':
xs_utils.freeze_model(snr)
snr.tbnew_gas.nH.frozen=False
snr.vpshock.kT.frozen=False
snr.vpshock.norm.frozen=False
if tau_freeze:
raise Exception("ERROR: vpshock not configured for fixed Tau")
for elem in free_elements:
comp = snr.vpshock.__getattribute__(elem)
comp.frozen = False
# vpshock fits are very ill behaved, must coerce into best fit
snr.vpshock.Tau_l = 1e8
snr.vpshock.Tau_u = 5e10
xs.Fit.perform()
if with_bkg:
thaw_bkg()
xs.Fit.perform()
snr.vpshock.Tau_l.frozen = False
snr.vpshock.Tau_u.frozen = False
xs.Fit.perform()
if tau_scan:
# Since Tau_u is constrained to be greater than Tau_l (?) this
# should ensure that both Tau_u and Tau_l traverse a range of
# values. But I haven't checked it yet...
xs.Fit.steppar("log {:s}:{:d} 1e9 5e13 15".format(snr.name,
xs_utils.par_num(snr, snr.vpshock.Tau_u)))
elif snr_model == 'gauss':
# Not supported! Not at all constrained . . .
assert not with_bkg
xs_utils.freeze_model(snr)
# Coupling between code is too tight, abstractions keep leaking.
# Because models must be addressed by NUMBER in XSPEC
# commands to tweak model parameters necessarily break
# abstraction interface between "load models" and "fit models"
# Possible solutions: (1) give up and let interfaces merge
# (monolithic "g309_models_fits"), or . . . (2) stop whining
if 'mosmerge' not in kwargs or kwargs['mosmerge']:
instr_1 = xs.AllModels(1, 'instr_1')
#instr_2 = xs.AllModels(2, 'instr_2') # Let PN instr lines fit
instr_3 = xs.AllModels(3, 'instr_3')
for instr in [instr_1, instr_3]:
# Must update parameter lower limits
instr.constant.factor.values = "0, , 0, 0, , "
instr.constant.factor.frozen = True
else: # No MOS merging
instr_1 = xs.AllModels(1, 'instr_1')
instr_2 = xs.AllModels(2, 'instr_2')
#instr_3 = xs.AllModels(3, 'instr_3') # Let PN instr lines fit
instr_4 = xs.AllModels(4, 'instr_4')
instr_5 = xs.AllModels(5, 'instr_5')
for instr in [instr_1, instr_2, instr_4, instr_5]:
# Must update parameter lower limits
instr.constant.factor.values = "0, , 0, 0, , "
instr.constant.factor.frozen = True
snr.tbnew_gas.nH = 0
snr.tbnew_gas.nH.frozen = True
# LineE: lower/upper bounds set from Yamaguchi+ 2014
# Sigma: prevent line from over-widening to fit as "constant" addition
# norm: no bounds
snr.setPars({snr.gaussian.LineE.index : "6.55, , 6.2, 6.3, 6.8, 6.9",
snr.gaussian.Sigma.index : "0.1, , 0, 0, 0.2, 0.5"} )
snr.gaussian.LineE.frozen=False
snr.gaussian.Sigma.frozen=False
snr.gaussian.norm.frozen=False
xs.Fit.perform()
else:
raise Exception("Invalid SNR model - please add branch")
# Compute standard 90% errors
if error:
xs.Xset.openLog(output + "_error.log")
if with_bkg:
xs.Fit.error(error_str_all_free(xrb))
xs.Fit.error(error_str_all_free(snr))
if error_rerun:
if with_bkg:
xs.Fit.error(error_str_all_free(xrb))
xs.Fit.error(error_str_all_free(snr))
xs.Xset.closeLog()
# Dump standard outputs
products(output)
print_model(snr, output + "_{:s}.txt".format(snr.name))
if with_bkg:
print_model(xrb, output + "_xrb.txt")
def load_cxrb(model_n, model_name, extracted_spectra):
"""Load cosmic X-ray background for each spectrum in
extracted_spectra.
Set appropriate RMF & ARF files, initialize XRB model and parameter
values, apply BACKSCAL ratio scaling.
ExtractedSpectrum objects additionally _must_ have an attached
xs.Spectrum object, referenced via .spec attribute.
Arguments
model_n: XSPEC model number, 1-based
model_name: XSPEC model name, string (no spaces)
extracted_spectra: list of ExtractedSpectrum objects
Output:
None. Global XSPEC objects configured for XRB model.
"""
# Set responses of <xs.Spectrum> objects
for extr in extracted_spectra:
extr.spec.multiresponse[model_n - 1] = extr.rmf_flat()
extr.spec.multiresponse[model_n - 1].arf = extr.arf_flat()
# Initialize XRB model with reasonable "global" parameters
xrb = xs.Model("constant * (apec + tbnew_gas*powerlaw + tbnew_gas*apec)",
model_name, model_n)
# Hickox and Markevitch (2006) norm
# convert 10.9 photons cm^-2 s^-1 sr^-1 keV^-1 to photons cm^-2 s^-1 keV^-1
# sr^-1 --> XMM detector pixels (backscal unit, 0.05 arcsec^2)
#
# The prefactor 0.61 comes from removing point sources brighter than
# 1e-14 erg cm^-2 s^-1 in 0.4-7.2 keV band. After accounting for
# absorption + rescaling to 2-10 keV band, the point source threshold is
# ~1.46e-14 erg cm^-2 sec^-1 in 2-10 keV band.
# I integrate the distribution of Moretti+ (2003) to get the excluded
# surface brightness, which is 39% of the total EXRB surf. brightness
# in 2-10 keV, based on Hickox/Markevitch (2006) model.
# Therefore, scale down EXRB normalization from 10.9 --> (1-0.39)*10.9
exrb_norm = 0.61 * 10.9 * (180 / pi)**-2 * 60**-4 * (
1 / 0.05)**-2 * ExtractedSpectrum.FIDUCIAL_BACKSCAL
# NOTE HARDCODED -- best fit values from src/bkg combined fit
# after error runs on some parameters of interest
# Corresponds to: 20161015_src_bkg_mg.log outputs
xrb.setPars({
xrb.powerlaw.PhoIndex.index: 1.4,
xrb.powerlaw.norm.index: exrb_norm,
xrb.apec.kT.index: 0.265, # Unabsorped apec (local bubble)
xrb.apec.norm.index: 2.36e-4,
xrb.tbnew_gas.nH.index:
1.12, # Galactic absorption (for extragal background)
xrb.tbnew_gas_5.nH.index: 1.39, # Halo absorption
xrb.apec_6.kT.index: 0.744, # Absorbed apec (galactic halo)
xrb.apec_6.norm.index: 1.94e-3
})
xs_utils.freeze_model(xrb)
# Set individal spectrum parameters
for extr in extracted_spectra:
xrb_curr = xs.AllModels(extr.spec.index, model_name)
# Apply backscal ratio scalings
# Re-freeze because changing value from link thaws by default
xrb_curr.constant.factor = extr.backscal(
) / ExtractedSpectrum.FIDUCIAL_BACKSCAL
xrb_curr.constant.factor.frozen = True
def load_soft_proton(model_n, model_name, extracted_spectra, broken=True):
"""Set soft proton contamination power laws for each spectrum in
extracted_spectra.
Set appropriate RMF & ARF files, initialize parameters and parameter
bounds, apply BACKSCAL ratio scaling.
Ties power-law indices between MOS1 and MOS2 exposures in same obsid.
Requires that each obsid has only one MOS1 and one MOS2 exposure.
ExtractedSpectrum objects additionally _must_ have an attached
xs.Spectrum object, referenced via .spec attribute.
Arguments
model_n: XSPEC model number, 1-based
model_name: XSPEC model name, string (no spaces)
extracted_spectra: list of ExtractedSpectrum objects
broken: use broken power law?
Output:
None. Global XSPEC objects configured for soft proton model.
"""
# Set responses of <xs.Spectrum> objects
for extr in extracted_spectra:
extr.spec.multiresponse[model_n - 1] = extr.rmf_diag()
extr.spec.multiresponse[model_n - 1].arf = "none"
# Initialize sp model
if broken:
sp = xs.Model("constant * bknpower", model_name, model_n)
else:
sp = xs.Model("constant * powerlaw", model_name, model_n)
# Set individal spectrum parameters
for extr in extracted_spectra:
sp_curr = xs.AllModels(extr.spec.index, model_name)
# Let power law indices, norms vary independently
# Must set index limits for each model; parameter limits do not
# propagate through links
if broken:
if extr.obsid == '0551000201':
sp_curr.bknpower.PhoIndx1.link = ""
sp_curr.bknpower.PhoIndx1.values = "0.3, , 0, 0.1, 1, 2"
sp_curr.bknpower.PhoIndx1.frozen = False
sp_curr.bknpower.PhoIndx2.link = ""
sp_curr.bknpower.PhoIndx2.values = "0.6, , 0, 0.1, 2, 3"
sp_curr.bknpower.PhoIndx2.frozen = False
sp_curr.bknpower.BreakE.link = ""
sp_curr.bknpower.BreakE.values = "2.0, , 0, 0.5, 10, 20"
sp_curr.bknpower.BreakE.frozen = False
sp_curr.bknpower.norm.link = ""
sp_curr.bknpower.norm.frozen = False
elif extr.obsid == '0087940201':
sp_curr.bknpower.PhoIndx1.link = ""
sp_curr.bknpower.PhoIndx1.values = "0.4, , 0, 0.1, 1, 2"
sp_curr.bknpower.PhoIndx1.frozen = False
sp_curr.bknpower.PhoIndx2.link = xs_utils.link_name(
sp_curr, sp_curr.bknpower.PhoIndx1)
sp_curr.bknpower.PhoIndx2.frozen = False
sp_curr.bknpower.BreakE.link = ""
sp_curr.bknpower.BreakE.values = 20
sp_curr.bknpower.BreakE.frozen = True
sp_curr.bknpower.norm.link = ""
sp_curr.bknpower.norm.frozen = False
else:
raise Exception("sp model not set for {:s}".format(extr.obsid))
else:
sp_curr.powerlaw.PhoIndex.link = ""
sp_curr.powerlaw.PhoIndex.values = "0.4, , 0, 0.1, 1, 2" # Hard/soft limits
sp_curr.powerlaw.PhoIndex.frozen = False
sp_curr.powerlaw.norm.link = ""
sp_curr.powerlaw.norm.frozen = False
# Apply backscal ratio scalings to make comparing norms easier
sp_curr.constant.factor = extr.backscal(
) / ExtractedSpectrum.FIDUCIAL_BACKSCAL
sp_curr.constant.factor.frozen = True
# Tie MOS1/MOS2 photon indices together
for x in extracted_spectra:
if x.instr != 'mos1':
continue
sp_mos1 = xs.AllModels(x.spec.index, model_name)
sp_mos2 = None
# Find matching MOS2 observation
for y in extracted_spectra:
if y.instr == 'mos2' and y.reg == x.reg and y.obsid == x.obsid:
if sp_mos2: # May occur in complex XMM pointings
raise Exception("Extra mos2 spectrum!")
sp_mos2 = xs.AllModels(y.spec.index, model_name)
# Tie photon indices
if broken:
sp_mos2.bknpower.PhoIndx1.link = xs_utils.link_name(
sp_mos1, sp_mos1.bknpower.PhoIndx1)
sp_mos2.bknpower.PhoIndx2.link = xs_utils.link_name(
sp_mos1, sp_mos1.bknpower.PhoIndx2)
else:
sp_mos2.powerlaw.PhoIndex.link = xs_utils.link_name(
sp_mos1, sp_mos1.powerlaw.PhoIndex)
def load_data_and_models(regs,
snr_model='vnei',
suffix='grp01',
mosmerge=True,
marfrmf=True,
sp_bknpower=False):
"""
Load G309.2-0.6 data and initialize responses and models.
After successful load (~1-10 minutes), global XSPEC session has
5*len(regs) spectra loaded (for the five XMM exposures we're using)
and ready to be simultaneously fit to a model with sources:
cosmic x-ray background
source model (set by snr_model kwarg)
soft proton power laws
instrumental lines fixed from FWC data fits
The returned hash is used to manipulate individual spectra or models
Input: region stems for extracted XMM ESAS spectra; duplicates disallowed
Keyword arguments:
snr_model = vnei, vpshock None
suffix = grp01, grp50
Output: hash keying each region to 5 ExtractedSpectrum objects,
one per XMM exposure in use
"""
if len(set(regs)) != len(regs):
raise Exception("Duplicate regions not allowed")
# ExtractedSpectrum objects allow script to easily resolve pipeline outputs
# order of regs sets the order of XSPEC datagroup assignment
extrs_from = {}
all_extrs = [] # Keep regs ordering for XSPEC datagroup assignment
for reg in regs:
if mosmerge:
extrs = [
ExtractedSpectrum("0087940201",
"mosmerge",
reg,
suffix=suffix,
marfrmf=marfrmf),
ExtractedSpectrum("0087940201",
"pnS003",
reg,
suffix=suffix,
marfrmf=marfrmf),
ExtractedSpectrum("0551000201",
"mosmerge",
reg,
suffix=suffix,
marfrmf=marfrmf)
]
else:
extrs = [
ExtractedSpectrum("0087940201", "mos1S001", reg,
suffix=suffix),
ExtractedSpectrum("0087940201", "mos2S002", reg,
suffix=suffix),
ExtractedSpectrum("0087940201", "pnS003", reg, suffix=suffix),
ExtractedSpectrum("0551000201", "mos1S001", reg,
suffix=suffix),
ExtractedSpectrum("0551000201", "mos2S002", reg, suffix=suffix)
]
extrs_from[reg] = extrs
all_extrs.extend(extrs)
# Spectrum and response assignment
# --------------------------------
for i, extr in enumerate(all_extrs, start=1):
spec = xs_utils.load_spec(i,
extr.pha(),
background=extr.qpb(),
default_dir=extr.repro_dir())
extr.spec = spec
# Load models
# -----------
# 1: x-ray background
# 2: instrumental lines
# 3, ... (3+n_reg-1): SNR plasma model
# (3+n_reg), ..., (3+n_reg+n_spec): soft proton background
# NOTE: loader methods below require that ExtractedSpectrum objects have
# xs.Spectrum objects attached in .spec attribute
# Attach xs.Model objects to ExtractedSpectrum for convenience
# no need to address by: xs.AllModels(extr.spec.index, model_name)
for extr in all_extrs:
extr.models = {}
load_cxrb(1, 'xrb', all_extrs)
load_soft_proton(2, 'sp', all_extrs, broken=sp_bknpower)
for extr in all_extrs:
extr.models['sp'] = xs.AllModels(extr.spec.index, 'sp')
extr.models['xrb'] = xs.AllModels(extr.spec.index, 'xrb')
# SNR model -- distinct source model for each region
# if "bkg" in regs, source numbering will be discontinuous
for n_reg, reg in enumerate(regs):
if reg == "bkg" or snr_model is None:
continue
model_n = 3 + n_reg
load_remnant_model(model_n,
"snr_" + reg,
extrs_from[reg],
case=snr_model)
for extr in extrs_from[reg]:
extr.models['snr'] = xs.AllModels(extr.spec.index, "snr_" + reg)
# One instrumental line model per spectrum
for n_extr, extr in enumerate(all_extrs):
model_n = 3 + len(regs) + n_extr
load_instr(model_n, "instr_{:d}".format(n_extr + 1), extr)
extr.models['instr'] = xs.AllModels(extr.spec.index,
"instr_{:d}".format(n_extr + 1))
return extrs_from
src.setPars({src.gaussian.Sigma.index: "0"})
src.gaussian.LineE.frozen = False
src.gaussian.Sigma.frozen = True
src.gaussian.norm.frozen = False
elif case == 'vsedov':
raise Exception("Need to test vsedov further, doesn't work")
#src = xs.Model("constant * tbnew_gas * vsedov", model_name, model_n)
#snr.vsedov.kT = 2
#snr.vsedov.kT_i = 1
else:
print "Warning: case {} not pre-configured, please freeze and set parameters manually"
# Set individal spectrum parameters
for extr in extracted_spectra:
src_curr = xs.AllModels(extr.spec.index, model_name)
# Apply backscal ratio scalings
src_curr.constant.factor = extr.backscal(
) / ExtractedSpectrum.FIDUCIAL_BACKSCAL
src_curr.constant.factor.frozen = True
# Save model for this spectrum
def load_soft_proton(model_n, model_name, extracted_spectra, broken=True):
"""Set soft proton contamination power laws for each spectrum in
extracted_spectra.
Set appropriate RMF & ARF files, initialize parameters and parameter
bounds, apply BACKSCAL ratio scaling.
Ties power-law indices between MOS1 and MOS2 exposures in same obsid.
Requires that each obsid has only one MOS1 and one MOS2 exposure.
'7.11 -0.0711 7 7 10 10',
'1.9 -0.019 0 0 3 3',
'95 -0.95 0.01 1 100 200',
'300 -3 1 1 1e+06 1e+06',
'1 -0.01 0 0 1 1', '0',
'0.5 -0.005 -0.999 -0.999 10 10',
'1 -0.01 0 0 1e+20 1e+24',
'6.4 -0.064 0 0 1e+06 1e+06',
'0.05 -0.0005 0 0 10 20', '= p11',
'0.01 2.6316e-11 0 0 1e+20 1e+24',
'0.02 -0.0002 0 0 0.1 0.1', '= p6',
'= p12/(1. + p11)/(1./(1. + p11))^( - p6)', '= p6',
'300 -3 1 1 1e+06 1e+06',
'-1 -0.01 -3 -3 -1e-09 -1e-09', '= p11',
'1 -0.01 0 0 1e+06 1e+06',
'1 -0.01 0 0 1e+06 1e+06',
'0.45 -0.0045 0.05 0.05 0.95 0.95', '= p19',
'1 -0.01 0.01 0.01 100 100'
]
XS.AllModels(1).setPars(pars)
for nH in n.arange(20, 26.2, 0.2):
XS.AllModels(1).plcabs.nH = 10**(nH - 22)
for z in n.arange(6.0, 6.2, 0.1):
XS.AllModels(1).plcabs.Redshift = z
for nb in 2**n.arange(2, 11):
filename = 'NH' + str(n.round(nH, 1)) + '_Z' + \
str(n.round(z, 1)) + '_N' + str(int(nb)) + '.fits'
print(filename)
saveintofile(filename, nb)
xcm.append('arf ' + src.response.arf)
xcm.append('ignore ' + src.ignoredString())
xcm.append('model ' + m.expression)
for i in np.arange(m.nParameters) + 1:
p = m(i).values
parvals = str(p[0])
for k in np.arange(len(p) - 1) + 1:
parvals = parvals + ', ' + str(p[k])
xcm.append(parvals)
xcm.append('statistic ' + xspec.Fit.statMethod)
nh = m.wabs.nH.values[0]
kt = m.apec.kT.values[0]
norm = m.apec.norm.values[0]
nh3 = m.wabs_3.nH.values[0]
xspec.Fit.error("2.706 6") # param 6 is nh3
p6 = xspec.AllModels(1)(6)
nhmin = p6.error[0]
nhmax = p6.error[1]
kt4 = m.apec_4.kT.values[0]
norm4 = m.apec_4.norm.values[0]
gnorm = m.gaussian.norm.values[0]
"""
now add cflux component, set the values to the previous best fit,
freeze apec norms, and refit to get the cflux and its errors
"""
mostring2 = "wabs*apec + cflux*wabs*(apec + gaussian)"
m2 = xspec.Model(mostring2)
m2.wabs.nH = [nh, -0.1]
m2.apec.kT = [kt, -0.1]
m2.apec.norm = [norm, -0.1]
m2.wabs_4.nH = [nh3, -0.1]
def calculate_hi(low_e=3.0, high_e=16.0, soft=(6.4, 9.7), hard=(9.7, 16.)):
'''
Function to calculate hardness & intensity values.
Arguments:
Energy ranges in keV
- low_e (float): Lower energy boundary for selection
- high_e (float): Higher energy boundary for selection
- soft (tuple of floats): Energy range between which to integrate
the soft range
- hard (tuple of floats): Energy range between which to integrate
the hard range
'''
purpose = 'Calculating hardness & intensity values'
print len(purpose) * '=' + '\n' + purpose + '\n' + len(purpose) * '='
print 'Soft:', soft, 'Hard:', hard, '\n' + len(purpose) * '-'
import os
import pandas as pd
import glob
import xspec
from collections import defaultdict
from math import isnan
from numpy import genfromtxt
import paths
import logs
import execute_shell_commands as shell
import database
# Set log file
filename = __file__.split('/')[-1].split('.')[0]
logs.output(filename)
# Import data
os.chdir(paths.data)
db = pd.read_csv(paths.database)
# Compile Fortran code for later use
cmpl = [
'gfortran', paths.subscripts + 'integflux.f', '-o',
paths.subscripts + 'integflux.xf'
]
shell.execute(cmpl)
# Only want spectra from std2
d = defaultdict(list)
for sp, group in db[(db.modes == 'std2')].groupby('spectra'):
# Determine variables
obsid = group.obsids.values[0]
path_obsid = group.paths_obsid.values[0]
bkg_sp = group.spectra_bkg.values[0]
rsp = group.rsp.values[0]
fltr = group.filters.values[0]
print obsid
# Check whether response file is there
if not os.path.isfile(rsp):
print 'ERROR: No response file'
continue
# XSPEC Commands to unfold spectrum around flat powerlaw
# Reason as per Heil et al. (see doi:10.1093/mnras/stv240):
# "In order to measure the energy spectral hardness independantly of
# long term changes in the PCA instrument response, fluxes are
# generated in a model-independant way by dividing the PCA standard
# 2 mode spectrum by the effective area of the intstrument response
# in each spectral channel. This is carried out by unfolding the
# spectrum with respect to a zero-slope power law (i.e. a constant)
# in the XSPEC spectral-fitting software, and measuring the unfolded
# flux over the specified energy range (interpolating where the
# specified energy does not fall neatly at the each of a spectral
# channel)."
#xspec.Plot.device = '/xs'
s1 = xspec.Spectrum(sp)
s1.background = bkg_sp
s1.response = os.path.join(paths.data, rsp)
# Not really sure why you need to do ignore, and then notice
s1.ignore('**-' + str(low_e + 1.) + ' ' + str(high_e - 1) + '-**')
s1.notice(str(low_e) + '-' + str(high_e))
xspec.Model('powerlaw')
xspec.AllModels(1).setPars(0.0, 1.0) # Index, Norm
xspec.AllModels(1)(1).frozen = True
xspec.AllModels(1)(2).frozen = True
xspec.Plot('eufspec')
# Output unfolded spectrum to lists
e = xspec.Plot.x()
e_err = xspec.Plot.xErr()
ef = xspec.Plot.y()
ef_err = xspec.Plot.yErr()
model = xspec.Plot.model()
# Pipe output to file
eufspec = path_obsid + 'eufspec.dat'
with open(eufspec, 'w') as f:
#Give header of file - must be three lines
h = [
'#Unfolded spectrum', '#',
'#Energy EnergyError Energy*Flux Energy*FluxError ModelValues'
]
f.write('\n'.join(h) + '\n')
for i in range(len(e)):
data = [e[i], e_err[i], ef[i], ef_err[i], model[i]]
line = [str(j) for j in data]
f.write(' '.join(line) + '\n')
# Create a file to input into integflux
integflux = path_obsid + 'integflux.in'
with open(integflux, 'w') as f:
#intgr_low, intgr_high, soft_low, soft_high, hard_low, hard_high
line = [
'eufspec.dat',
str(low_e),
str(high_e),
str(soft[0]),
str(soft[-1]),
str(hard[0]),
str(hard[-1])
]
line = [str(e) for e in line]
f.write(' '.join(line) + '\n')
# Remove previous versions of the output
if os.path.isfile(path_obsid + 'hardint.out'):
os.remove(path_obsid + 'hardint.out')
# Run fortran script to create calculate hardness-intensity values
# Will output a file with the columns (with flux in Photons*ergs/cm^2/s)
# flux flux_err ratio ratio_error
os.chdir(path_obsid)
shell.execute(paths.subscripts + 'integflux.xf')
os.chdir(paths.data)
# Get ouput of the fortran script
txt = genfromtxt(path_obsid + 'hardint.out')
flux = float(txt[0])
flux_err = float(txt[1])
ratio = float(txt[2])
ratio_err = float(txt[3])
d['spectra'].append(sp)
d['flux_i3t16_s6p4t9p7_h9p7t16'].append(flux)
d['flux_err_i3t16_s6p4t9p7_h9p7t16'].append(flux_err)
d['hardness_i3t16_s6p4t9p7_h9p7t16'].append(ratio)
d['hardness_err_i3t16_s6p4t9p7_h9p7t16'].append(ratio_err)
# Clear xspec spectrum
xspec.AllData.clear()
# Update database and save
df = pd.DataFrame(d)
cols = [
'flux_i3t16_s6p4t9p7_h9p7t16', 'flux_err_i3t16_s6p4t9p7_h9p7t16',
'hardness_i3t16_s6p4t9p7_h9p7t16',
'hardness_err_i3t16_s6p4t9p7_h9p7t16'
]
db = database.merge(db, df, cols)
print 'Number of unique elements in database'
print '======================='
print db.apply(pd.Series.nunique)
print '======================='
print 'Pipeline completed'
database.save(db)
logs.stop_logging()
def fit_ecsrcbin10(
obsid,
WorkDir="/Users/corcoran/Dropbox/Eta_Car/swift/quicklook/work",
emin=2.0,
emax=10.0,
rmfdir='/caldb/data/swift/xrt/cpf/rmf',
chatter=0):
import xspec
import glob
import pyfits
import numpy as np
from astropy.time import Time
xspec.AllData.clear()
xspec.Xset.chatter = chatter
xspec.FitManager.query = "yes"
xspec.Fit.query = "yes"
xspec.Fit.nIterations = 100
xspecdir = WorkDir + "/" + obsid.strip() + "/xspec"
cwd = os.getcwd()
print "\n"
os.chdir(xspecdir)
src = xspec.Spectrum("ec_srcbin10.pha")
try:
hdu = pyfits.open("ec_srcbin10.arf")
except:
print "ARF ec_srcbin10.arf not found; Returning"
return
arfhd = hdu[1].header
try:
respfile = arfhd['RESPFILE']
except:
print "RESPFILE keyword in ec_srcbin10.arf not found; Returning"
return
try:
rmffile = glob.glob(rmfdir + '/' + respfile)[0]
except:
print "Response file %s does not exist; Returning" % (rmfdir + '/' +
respfile)
return
src.response = rmffile
src.response.arf = "ec_srcbin10.arf"
src.background = "ec_bkg.pha"
src.ignore("0.0-1.0 7.9-**")
hdulist = pyfits.open("ec_srcbin10.pha")
prihdr = hdulist[0].header
"""
dateobs=prihdr['DATE-OBS']
dateend=prihdr['DATE-END']
t=Time(dateobs,scale='utc', format='isot')
te=Time(dateend,scale='utc',format='isot')
"""
mjds = prihdr['MJD-OBS']
mjde = prihdr['MJD-OBS'] + (prihdr['TSTOP'] - prihdr['TSTART']) / 86400.0
t = Time(mjds, scale='utc', format='mjd')
dateobs = t.iso.replace(' ', 'T')
te = Time(mjde, scale='utc', format='mjd')
tmid = (te.jd - t.jd) / 2.0 + t.jd
xspec.AllData.ignore("bad")
"""
first fit without the cflux component
"""
mostring = "wabs*apec + wabs*(apec + gaussian)"
m = xspec.Model(mostring)
m.wabs.nH = [1.1, 0.1, 0, 0, 5, 5]
m.apec.kT = [1.0, 0.1, 0.1, 0.1, 2, 2]
m.apec.norm = [0.1, 0.1, 0.0, 0.0, 2, 2]
m.wabs_3.nH = [10, 0.1, 0, 0, 100, 100]
m.apec_4.kT = [4.5, -0.1, 2.0, 2.0, 6.0, 6.0]
m.apec_4.norm = [0.1, 0.1, 0.0, 0.0, 2, 2]
m.apec_4.Abundanc = 0.4
m.gaussian.LineE = [6.4, -0.1]
m.gaussian.Sigma = [0.01, -0.01]
m.gaussian.norm = [1e-4, 1e-5, 0, 0, 0.1, 0.1]
m.show()
xspec.Fit.perform()
m.show()
xspec.Plot.xAxis = "KeV"
xspec.Plot.device = "/xw"
xspec.Plot("ldata")
xspec.AllModels.calcFlux(str(emin) + " " + str(emax))
oflux = src.flux[0]
"""
Create XCM output
"""
xcm = ['data ' + src.fileName]
xcm.append('back ' + src.background.fileName)
xcm.append('resp ' + src.response.rmf)
xcm.append('arf ' + src.response.arf)
xcm.append('ignore ' + src.ignoredString())
xcm.append('model ' + m.expression)
for i in np.arange(m.nParameters) + 1:
p = m(i).values
parvals = str(p[0])
for k in np.arange(len(p) - 1) + 1:
parvals = parvals + ', ' + str(p[k])
xcm.append(parvals)
xcm.append('statistic ' + xspec.Fit.statMethod)
nh = m.wabs.nH.values[0]
kt = m.apec.kT.values[0]
norm = m.apec.norm.values[0]
nh3 = m.wabs_3.nH.values[0]
xspec.Fit.error("2.706 6") # param 6 is nh3
p6 = xspec.AllModels(1)(6)
nhmin = p6.error[0]
nhmax = p6.error[1]
kt4 = m.apec_4.kT.values[0]
norm4 = m.apec_4.norm.values[0]
gnorm = m.gaussian.norm.values[0]
"""
now add cflux component, set the values to the previous best fit,
freeze apec norms, and refit to get the cflux and its errors
"""
mostring2 = "wabs*apec + cflux*wabs*(apec + gaussian)"
m2 = xspec.Model(mostring2)
m2.wabs.nH = [nh, -0.1]
m2.apec.kT = [kt, -0.1]
m2.apec.norm = [norm, -0.1]
m2.wabs_4.nH = [nh3, -0.1]
m2.apec_5.kT = [kt4, -0.1]
m2.apec_5.norm = [norm4, -0.0001]
m2.apec_5.Abundanc = 0.4
m2.gaussian.LineE = [6.4, -0.1]
m2.gaussian.Sigma = [0.01, -0.01]
m2.gaussian.norm = [gnorm, -0.0001]
m2.cflux.Emin = emin
m2.cflux.Emax = emax
xspec.Fit.perform()
m2.show()
cf = m2.cflux.lg10Flux.values[0]
print "%5.1f - %5.1f keV flux from cflux = %10.4e" % (emin, emax, 10**cf)
xspec.Fit.error("2.706 8") # param 8 is cflux
p8 = xspec.AllModels(1)(8)
cfmin = p8.error[0]
cfmax = p8.error[1]
duration = te.jd - t.jd
nhpluserr = nhmax - nh3
nhminerr = nh3 - nhmin
output = {
'obsid': obsid,
't_start': t.jd,
't_end': te.jd,
't_mid': tmid,
'duration': duration,
'exposure': src.exposure,
'flux': oflux,
'fluxplus': 10**cfmax - 10**cf,
'fluxmin': 10**cf - 10**cfmin,
'dateobs': dateobs,
'nh': nh3,
'nhplus': nhpluserr,
'nhmin': nhminerr,
'emin': emin,
'emax': emax
}
"""
Write xcm file; warn user if it exists and give option to overwrite
"""
filename = xspecdir + '/ec_srcbin10.xcm'
if os.path.isfile(filename):
print "File %s exists" % filename
ans = raw_input('Overwrite [y]/n? ')
if ans.strip().lower() == 'n':
print "File %s not overwritten; Returning" % filename
return output, xcm
print "Writing file %s" % filename
f = open(filename, 'w')
for i in xcm:
f.write(i + "\n")
f.close()
#print "Changing directory back to %s" % cwd
print "\n"
os.chdir(cwd)
return output, xcm
def deneme(self):
xspec.AllData.clear()
xspec.Fit.statMethod = str(self.statistic)
xspec.Fit.query = "yes"
os.chdir(self.path)
xspec.AllData("1:1 {} 2:2 {} 3:3 {} 4:4 {}".format(
self.spectrum_files["mos1"], self.spectrum_files["mos2"],
self.spectrum_files["pn"], self.spectrum_files["rass"]))
self.spec_mos1 = xspec.AllData(1)
self.spec_mos1.ignore(self.energy_range["mos1"])
self.spec_mos2 = xspec.AllData(2)
self.spec_mos2.ignore(self.energy_range["mos2"])
xspec.AllModels += "apec+gau+gau"
self.m1 = xspec.AllModels(1)
self.m2 = xspec.AllModels(2)
self.m3 = xspec.AllModels(3)
self.m4 = xspec.AllModels(4)
m1_apec1 = Apec(1, 3, 0.3, 0.233)
m1_gau1 = Gaussian(1, 1.48)
m1_gau2 = Gaussian(1, 1.74)
m2_apec1 = Apec(1, 3, 0.3, 0.233)
m2_gau1 = Gaussian(1, 1.48)
m2_gau2 = Gaussian(1, 1.74)
m3_apec1 = Apec(1, 3, 0.3, 0.233)
m3_gau1 = Gaussian(1, 1.48)
m3_gau2 = Gaussian(1, 1.74)
m4_apec1 = Apec(1, 3, 0.3, 0.233)
m4_gau1 = Gaussian(1, 1.48)
m4_gau2 = Gaussian(1, 1.74)
m1_comp1 = self.m1.apec
m1_comp2 = self.m1.gaussian
m1_comp3 = self.m1.gaussian_3
m2_comp1 = self.m2.apec
m2_comp2 = self.m2.gaussian
m2_comp3 = self.m2.gaussian_3
m3_comp1 = self.m3.apec
m3_comp2 = self.m3.gaussian
m3_comp3 = self.m3.gaussian_3
m4_comp1 = self.m4.apec
m4_comp2 = self.m4.gaussian
m4_comp3 = self.m4.gaussian_3
Apec.set_params(m1_comp1, m1_apec1)
Gaussian.set_params(m1_comp2, m1_gau1)
Gaussian.set_params(m1_comp3, m1_gau2)
Apec.set_params(m2_comp1, m2_apec1)
Gaussian.set_params(m2_comp2, m2_gau1)
Gaussian.set_params(m2_comp3, m2_gau2)
Apec.set_params(m3_comp1, m3_apec1)
Gaussian.set_params(m3_comp2, m3_gau1)
Gaussian.set_params(m3_comp3, m3_gau2)
Apec.set_params(m4_comp1, m4_apec1)
Gaussian.set_params(m4_comp2, m4_gau1)
Gaussian.set_params(m4_comp3, m4_gau2)
MyModel.freeze_parameter(m1_comp1.norm)
MyModel.set_norm_zero(m4_comp1)
xspec.AllModels.show()
def fit(data, reference_instrument, model_setter, emin_values, fn_prefix="", systematic_fraction=0):
importlib.reload(xspec)
fit_by_lt = {}
fn_by_lt={}
xspec.AllModels.systematic=systematic_fraction
for c_emin in emin_values:
xspec.AllData.clear()
xspec.AllModels.clear()
isgri, ref_ind = model_setter(data, reference_instrument, c_emin)
max_chi=np.ceil(xspec.Fit.statistic / xspec.Fit.dof)
m1=xspec.AllModels(1)
if ref_ind is not None:
n_spec = 2
if isinstance(ref_ind, list):
n_spec = len(ref_ind) + 1
xspec.Fit.error("1.0 max %.1f 1-%d"%(max_chi, n_spec*m1.nParameters))
ref = ref_ind[0]
else:
xspec.Fit.error("1.0 max %.1f 1-%d" % (max_chi,m1.nParameters))
models={}
lt_key='%.10lg'%c_emin
fit_by_lt[lt_key]=dict(
emin=c_emin,
chi2_red=xspec.Fit.statistic/xspec.Fit.dof,
chi2=xspec.Fit.statistic,
ndof=xspec.Fit.dof,
models=models,
)
for m, ss in (isgri, 'isgri'), (ref, 'ref'):
if m is None: continue
#initialize dictionaries
models[ss]={}
#models[ss]['flux']={}
#fills dictionaries
for i in range(1,m.nParameters+1):
if (not m(i).frozen) and (not bool(m(i).link)):
#use the name plus position because there could be parameters with same name from multiple
#model components (e.g., several gaussians)
print(m(i).name, "%.2f"%(m(i).values[0]), m(i).frozen,bool(m(i).link) )
models[ss][m(i).name+"_%02d"%(i)]=[ m(i).values[0], m(i).error[0], m(i).error[1] ]
# for flux_e1, flux_e2 in [(30,80), (80,200)]:
# xspec.AllModels.calcFlux("{} {} err".format(flux_e1, flux_e2))
# #print ( xspec.AllData(1).flux)
# models['isgri']['flux'][(flux_e1, flux_e2)] = xspec.AllData(1).flux
# models['ref']['flux'][(flux_e1, flux_e2)] = xspec.AllData(2).flux
xcmfile="saved"+fn_prefix+"_"+reference_instrument+".xcm"
if os.path.exists(xcmfile):
os.remove(xcmfile)
xspec.XspecSettings.save(xspec.XspecSettings, xcmfile, info='a')
xspec.Plot.device="/png"
#xspec.Plot.addCommand("setplot en")
xspec.Plot.xAxis="keV"
xspec.Plot("ldata del")
xspec.Plot.device="/png"
fn="fit_lt%.5lg.png"%c_emin
fn_by_lt[lt_key] = fn
shutil.move("pgplot.png_2", fn)
_=display(Image(filename=fn,format="png"))
return fit_by_lt, fn_by_lt
)
spectrum1 = xspec.AllData(1)
spectrum1.background = f"bgspecRGS1_gti{i}.fits"
spectrum1.response = f"../{pairs_respli[0][0]}"
spectrum2 = xspec.AllData(2)
spectrum2.background = f"bgspecRGS2_gti{i}.fits"
spectrum2.response = f"../{pairs_respli[0][1]}"
xspec.AllData.ignore("bad")
xspec.AllData.ignore('**-0.331 2.001-**')
for model in model_list:
m1 = xspec.Model(model)
m2 = xspec.AllModels(
2) #Retrieve the model object assigned to data group 2
#Freeze constant of RGS1 to 1 to account for calibration
m1.constant.factor = 1
m1.constant.factor.frozen = True
#Freeze redshift for both RGS1 and RGS2
if m1.expression == 'constant*TBabs*zpowerlw':
m1.zpowerlw.Redshift = target_redshift
m1.zpowerlw.Redshift.frozen = True
m2.zpowerlw.Redshift = target_redshift
m2.zpowerlw.Redshift.frozen = True
if m1.expression == 'constant*TBabs*zlogpar':
m1.zlogpar.Redshift = target_redshift
