def test_arithmetic():
spec1 = Spectrum.from_powerlaw(1.0, 0.05, 1.0e-4, 0.1, 10.0, 10000)
spec2 = Spectrum.from_powerlaw(2.0, 0.01, 1.0e-3, 0.1, 10.0, 10000)
spec3 = spec1+spec2
flux3 = spec1.flux+spec2.flux
assert_allclose(spec3.flux, flux3)
spec4 = spec3*3.0
spec5 = 3.0*spec3
flux4 = spec3.flux*3.0
assert_allclose(spec4.flux, spec5.flux)
assert_allclose(spec4.flux, flux4)
spec6 = spec3/2.5
flux6 = spec3.flux/2.5
assert_allclose(spec6.flux, flux6)
spec7 = Spectrum.from_constant(1.0e-4, 0.1, 10.0, 10000)
spec8 = spec1+spec7
assert_allclose(spec8.flux.value, spec1.flux.value+1.0e-4)
def test_arithmetic():
spec1 = Spectrum.from_powerlaw(1.0, 0.05, 1.0e-4)
spec2 = Spectrum.from_powerlaw(2.0, 0.01, 1.0e-3)
spec3 = spec1+spec2
flux3 = spec1.flux+spec2.flux
assert_allclose(spec3.flux, flux3)
spec4 = spec3*3.0
spec5 = 3.0*spec3
flux4 = spec3.flux*3.0
assert_allclose(spec4.flux, spec5.flux)
assert_allclose(spec4.flux, flux4)
spec6 = spec3/2.5
flux6 = spec3.flux/2.5
assert_allclose(spec6.flux, flux6)
spec7 = Spectrum.from_constant(1.0e-4)
spec8 = spec1+spec7
assert_allclose(spec8.flux.value, spec1.flux.value+1.0e-4)
def test_absorption_line(answer_store, answer_dir):
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
const_flux = 1.0e-3
line_pos = 1.0
line_width = 0.02
line_amp = 1.0e-5
exp_time = (100.0, "ks")
inst_name = "lynx_xgs"
spec = Spectrum.from_constant(const_flux, 0.1, 3.0, 100000)
spec.add_absorption_line(line_pos, line_width, line_amp)
spectrum_answer_testing(spec, "absorption_line_test.h5", answer_store,
answer_dir)
simulate_spectrum(spec,
inst_name,
exp_time,
"absorption_line_evt.pha",
overwrite=True,
prng=prng)
file_answer_testing("SPECTRUM", "absorption_line_evt.pha", answer_store,
answer_dir)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_read_write():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
spec1 = Spectrum.from_powerlaw(1.0, 0.05, 1.0e-4, 0.1, 10.0, 10000)
spec1.write_file("test_spec.dat", overwrite=True)
spec2 = Spectrum.from_file("test_spec.dat")
assert_allclose(spec1.flux, spec2.flux)
assert_allclose(spec1.emid, spec2.emid)
assert_allclose(spec1.ebins, spec2.ebins)
assert_allclose(spec1.cumspec, spec2.cumspec)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_read_write():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
spec1 = Spectrum.from_powerlaw(1.0, 0.05, 1.0e-4)
spec1.write_file("test_spec.dat", overwrite=True)
spec2 = Spectrum.from_file("test_spec.dat")
assert_allclose(spec1.flux, spec2.flux)
assert_allclose(spec1.emid, spec2.emid)
assert_allclose(spec1.ebins, spec2.ebins)
assert_allclose(spec1.cumspec, spec2.cumspec)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_point_source():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
nH_sim = 0.02
norm_sim = 1.0e-4
alpha_sim = 0.95
redshift = 0.02
exp_time = (100., "ks")
area = (3000., "cm**2")
spec = Spectrum.from_powerlaw(alpha_sim, redshift, norm_sim,
emin=0.1, emax=11.5, nbins=2000)
spec.apply_foreground_absorption(nH_sim, model="tbabs")
positions = [(30.01, 45.0)]
events = make_point_sources(area, exp_time, positions, (30.0, 45.0),
spec, prng=prng)
events.write_simput_file("ptsrc", overwrite=True)
instrument_simulator("ptsrc_simput.fits", "ptsrc_evt.fits",
exp_time, "sq_aciss_cy20", [30.0, 45.0],
overwrite=True, foreground=False, ptsrc_bkgnd=False,
instr_bkgnd=False,
prng=prng)
write_spectrum("ptsrc_evt.fits", "point_source_evt.pi", overwrite=True)
os.system("cp %s %s ." % (arf.filename, rmf.filename))
load_user_model(mymodel, "tplaw")
add_user_pars("tplaw", ["nH", "norm", "redshift", "alpha"],
[0.02, norm_sim*0.8, redshift, 0.9],
parmins=[0.0, 0.0, 0.0, 0.1],
parmaxs=[10.0, 1.0e9, 10.0, 10.0],
parfrozen=[True, False, True, False])
load_pha("point_source_evt.pi")
set_stat("cstat")
set_method("simplex")
ignore(":0.4, 9.0:")
set_model("tplaw")
fit()
res = get_fit_results()
assert np.abs(res.parvals[0]-norm_sim)/norm_sim < 0.05
assert np.abs(res.parvals[1]-alpha_sim)/alpha_sim < 0.05
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_point_source():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
nH_sim = 0.02
norm_sim = 1.0e-4
alpha_sim = 0.95
redshift = 0.02
exp_time = (100., "ks")
area = (3000., "cm**2")
spec = Spectrum.from_powerlaw(alpha_sim, redshift, norm_sim,
emin=0.1, emax=11.5, nbins=2000)
spec.apply_foreground_absorption(nH_sim, model="tbabs")
positions = [(30.01, 45.0)]
events = make_point_sources(area, exp_time, positions, (30.0, 45.0),
spec, prng=prng)
events.write_simput_file("ptsrc", overwrite=True)
instrument_simulator("ptsrc_simput.fits", "ptsrc_evt.fits",
exp_time, "sq_aciss_cy19", [30.0, 45.0],
overwrite=True, foreground=False, ptsrc_bkgnd=False,
instr_bkgnd=False,
prng=prng)
write_spectrum("ptsrc_evt.fits", "point_source_evt.pi", overwrite=True)
os.system("cp %s %s ." % (arf.filename, rmf.filename))
load_user_model(mymodel, "tplaw")
add_user_pars("tplaw", ["nH", "norm", "redshift", "alpha"],
[0.02, norm_sim*0.8, redshift, 0.9],
parmins=[0.0, 0.0, 0.0, 0.1],
parmaxs=[10.0, 1.0e9, 10.0, 10.0],
parfrozen=[True, False, True, False])
load_pha("point_source_evt.pi")
set_stat("cstat")
set_method("simplex")
ignore(":0.4, 9.0:")
set_model("tplaw")
fit()
res = get_fit_results()
assert np.abs(res.parvals[0]-norm_sim)/norm_sim < 0.05
assert np.abs(res.parvals[1]-alpha_sim)/alpha_sim < 0.05
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_convolved_spectra():
arf = AuxiliaryResponseFile("xrs_hdxi_3x10.arf")
spec1 = Spectrum.from_powerlaw(2.0, 0.01, 1.0, 0.1, 10.0, 1000)
cspec1 = ConvolvedSpectrum(spec1, arf)
cspec2 = spec1*arf
spec2 = cspec1.deconvolve()
assert_array_equal(cspec1.ebins.value, cspec2.ebins.value)
assert_array_equal(spec1.ebins.value, spec2.ebins.value)
assert_array_equal(cspec1.flux.value, cspec2.flux.value)
assert_allclose(spec1.flux.value, spec2.flux.value)
def test_rescale_flux():
spec = Spectrum.from_powerlaw(2.0, 0.01, 1.0, 0.1, 10.0, 10000)
spec.rescale_flux(1.0e-4, emin=0.5, emax=7.0, flux_type="photons")
f = spec.get_flux_in_band(0.5, 7.0)[0]
assert_allclose(1.0e-4, f.value)
spec.rescale_flux(1.0e-12, emin=0.4, emax=1.0, flux_type="energy")
f = spec.get_flux_in_band(0.4, 1.0)[1]
assert_allclose(1.0e-12, f.value)
def test_rescale_flux():
spec = Spectrum.from_powerlaw(2.0, 0.01, 1.0)
spec.rescale_flux(1.0e-4, emin=0.5, emax=7.0, flux_type="photons")
f = spec.get_flux_in_band(0.5, 7.0)[0]
assert_allclose(1.0e-4, f.value)
spec.rescale_flux(1.0e-12, emin=0.4, emax=1.0, flux_type="energy")
f = spec.get_flux_in_band(0.4, 1.0)[1]
assert_allclose(1.0e-12, f.value)
def to_scaled_spectrum(self, fov, focal_length=None):
from soxs.instrument import FlatResponse
fov = parse_value(fov, "arcmin")
if focal_length is None:
focal_length = self.default_focal_length
else:
focal_length = parse_value(focal_length, "m")
flux = self.flux.value * fov * fov
flux *= (focal_length / self.default_focal_length)**2
arf = FlatResponse(self.ebins.value[0], self.ebins.value[-1], 1.0,
self.ebins.size - 1)
return ConvolvedSpectrum(Spectrum(self.ebins.value, flux), arf)
def plaw_fit(alpha_sim, answer_store, answer_dir):
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
nH_sim = 0.02
norm_sim = 1.0e-4
redshift = 0.01
exp_time = (50.0, "ks")
area = 40000.0
inst_name = "new_hdxi"
spec = Spectrum.from_powerlaw(alpha_sim, redshift, norm_sim, 0.1, 10.0,
20000)
spec.apply_foreground_absorption(nH_sim, model="tbabs")
spectrum_answer_testing(spec, f"power_law_{alpha_sim}.h5", answer_store,
answer_dir)
pt_src_pos = PointSourceModel(30.0, 45.0)
pt_src = SimputPhotonList.from_models("plaw_model",
spec,
pt_src_pos,
exp_time,
area,
prng=prng)
cat = SimputCatalog.from_source("plaw_model_simput.fits",
pt_src,
overwrite=True)
instrument_simulator("plaw_model_simput.fits",
f"plaw_model_{alpha_sim}_evt.fits",
exp_time,
inst_name, [30.0, 45.0],
instr_bkgnd=False,
ptsrc_bkgnd=False,
foreground=False,
prng=prng)
write_spectrum(f"plaw_model_{alpha_sim}_evt.fits",
f"plaw_model_{alpha_sim}_evt.pha",
overwrite=True)
file_answer_testing("EVENTS", f"plaw_model_{alpha_sim}_evt.fits",
answer_store, answer_dir)
file_answer_testing("SPECTRUM", f"plaw_model_{alpha_sim}_evt.pha",
answer_store, answer_dir)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_emission_line(answer_store, answer_dir):
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
const_flux = 1.0e-4
line_pos = 5.0
line_width = 0.02
line_amp = 1.0e-5
exp_time = (100.0, "ks")
area = 30000.0
inst_name = "lynx_lxm"
spec = Spectrum.from_constant(const_flux, 1.0, 10.0, 20000)
spec.add_emission_line(line_pos, line_width, line_amp)
spectrum_answer_testing(spec, "emission_line_test.h5", answer_store,
answer_dir)
pt_src_pos = PointSourceModel(30.0, 45.0)
sim_cat = SimputCatalog.from_models("emission_line",
"emission_line",
spec,
pt_src_pos,
exp_time,
area,
prng=prng)
sim_cat.write_catalog(overwrite=True)
instrument_simulator("emission_line_simput.fits",
"emission_line_evt.fits",
exp_time,
inst_name, [30.0, 45.0],
instr_bkgnd=False,
ptsrc_bkgnd=False,
foreground=False,
prng=prng)
write_spectrum("emission_line_evt.fits",
"emission_line_evt.pha",
overwrite=True)
file_answer_testing("EVENTS", "emission_line_evt.fits", answer_store,
answer_dir)
file_answer_testing("SPECTRUM", "emission_line_evt.pha", answer_store,
answer_dir)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_append():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
exp_time = (50.0, "ks")
area = (4.0, "m**2")
ra0 = 30.0
dec0 = 45.0
spec = Spectrum.from_powerlaw(1.1, 0.05, 1.0e-4)
e1 = spec.generate_energies(exp_time, area, prng=prng)
pt_src1 = PointSourceModel(ra0 + 0.05, dec0 + 0.05, e1.size)
e2 = spec.generate_energies(exp_time, area, prng=prng)
pt_src2 = PointSourceModel(ra0 - 0.05, dec0 - 0.05, e1.size)
write_photon_list("pt_src",
"pt_src1",
e1.flux,
pt_src1.ra,
pt_src1.dec,
e1,
overwrite=True)
write_photon_list("pt_src",
"pt_src2",
e2.flux,
pt_src2.ra,
pt_src2.dec,
e2,
append=True)
assert os.path.exists("pt_src_simput.fits")
assert os.path.exists("pt_src1_phlist.fits")
assert os.path.exists("pt_src2_phlist.fits")
f = pyfits.open("pt_src_simput.fits")
cat = f["SRC_CAT"].data["SPECTRUM"]
assert cat[0] == "pt_src1_phlist.fits[PHLIST,1]"
assert cat[1] == "pt_src2_phlist.fits[PHLIST,1]"
f.close()
os.chdir(curdir)
shutil.rmtree(tmpdir)
def plaw_fit(alpha_sim, answer_store, answer_dir):
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
nH_sim = 0.02
norm_sim = 1.0e-4
redshift = 0.01
exp_time = (50.0, "ks")
area = 40000.0
inst_name = "new_hdxi"
spec = Spectrum.from_powerlaw(alpha_sim, redshift, norm_sim, 0.1, 10.0, 20000)
spec.apply_foreground_absorption(nH_sim, model="tbabs")
spectrum_answer_testing(spec, "power_law_%s.h5" % alpha_sim, answer_store,
answer_dir)
pt_src_pos = PointSourceModel(30.0, 45.0)
sim_cat = SimputCatalog.from_models("plaw_model", "plaw_model", spec, pt_src_pos,
exp_time, area, prng=prng)
sim_cat.write_catalog(overwrite=True)
instrument_simulator("plaw_model_simput.fits", "plaw_model_%s_evt.fits" % alpha_sim,
exp_time, inst_name, [30.0, 45.0], instr_bkgnd=False,
ptsrc_bkgnd=False, foreground=False, prng=prng)
write_spectrum("plaw_model_%s_evt.fits" % alpha_sim,
"plaw_model_%s_evt.pha" % alpha_sim,
overwrite=True)
file_answer_testing("EVENTS", "plaw_model_%s_evt.fits" % alpha_sim,
answer_store, answer_dir)
file_answer_testing("SPECTRUM", "plaw_model_%s_evt.pha" % alpha_sim,
answer_store, answer_dir)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_append():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
exp_time = (50.0, "ks")
area = (4.0, "m**2")
ra0 = 30.0
dec0 = 45.0
spec = Spectrum.from_powerlaw(1.1, 0.05, 1.0e-4, 0.1, 10.0, 10000)
pos1 = PointSourceModel(ra0+0.05, dec0+0.05)
pos2 = PointSourceModel(ra0-0.05, dec0-0.05)
pl1 = SimputPhotonList.from_models("pt_src1", spec, pos1, exp_time, area)
pl2 = SimputPhotonList.from_models("pt_src2", spec, pos2, exp_time, area)
sc = SimputCatalog.from_source("pt_src_simput.fits", pl1,
src_filename="pt_src1_phlist.fits",
overwrite=True)
sc.append(pl2, src_filename="pt_src2_phlist.fits",
overwrite=True)
assert os.path.exists("pt_src1_phlist.fits")
assert os.path.exists("pt_src2_phlist.fits")
assert os.path.exists("pt_src_simput.fits")
f = pyfits.open("pt_src_simput.fits")
cat = f["SRC_CAT"].data["SPECTRUM"]
assert cat[0] == "pt_src1_phlist.fits[PHLIST,1]"
assert cat[1] == "pt_src2_phlist.fits[PHLIST,1]"
f.close()
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_append():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
exp_time = (50.0, "ks")
area = (4.0, "m**2")
ra0 = 30.0
dec0 = 45.0
spec = Spectrum.from_powerlaw(1.1, 0.05, 1.0e-4, 0.1, 10.0, 10000)
e1 = spec.generate_energies(exp_time, area, prng=prng)
ra1, dec1 = PointSourceModel(ra0+0.05, dec0+0.05).generate_coords(e1.size, prng=prng)
e2 = spec.generate_energies(exp_time, area, prng=prng)
ra2, dec2 = PointSourceModel(ra0-0.05, dec0-0.05).generate_coords(e1.size, prng=prng)
write_photon_list("pt_src", "pt_src1", e1.flux, ra1, dec1, e1, overwrite=True)
write_photon_list("pt_src", "pt_src2", e2.flux, ra2, dec2, e2, append=True)
assert os.path.exists("pt_src_simput.fits")
assert os.path.exists("pt_src1_phlist.fits")
assert os.path.exists("pt_src2_phlist.fits")
f = pyfits.open("pt_src_simput.fits")
cat = f["SRC_CAT"].data["SPECTRUM"]
assert cat[0] == "pt_src1_phlist.fits[PHLIST,1]"
assert cat[1] == "pt_src2_phlist.fits[PHLIST,1]"
f.close()
os.chdir(curdir)
shutil.rmtree(tmpdir)
def plaw_fit(alpha_sim):
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
nH_sim = 0.02
norm_sim = 1.0e-4
redshift = 0.01
exp_time = 5.0e4
area = 40000.0
inst_name = "hdxi"
spec = Spectrum.from_powerlaw(alpha_sim, redshift, norm_sim)
spec.apply_foreground_absorption(nH_sim)
e = spec.generate_energies(exp_time, area)
pt_src = PointSourceModel(30.0, 45.0, e.size)
write_photon_list("plaw_model",
"plaw_model",
e.flux,
pt_src.ra,
pt_src.dec,
e,
clobber=True)
instrument_simulator("plaw_model_simput.fits",
"plaw_model_evt.fits",
exp_time,
inst_name, [30.0, 45.0],
astro_bkgnd=None,
instr_bkgnd_scale=0.0)
inst = get_instrument_from_registry(inst_name)
arf = AuxiliaryResponseFile(inst["arf"])
rmf = RedistributionMatrixFile(inst["rmf"])
os.system("cp %s ." % arf.filename)
os.system("cp %s ." % rmf.filename)
write_spectrum("plaw_model_evt.fits", "plaw_model_evt.pha", clobber=True)
load_user_model(mymodel, "wplaw")
add_user_pars("wplaw", ["nH", "norm", "redshift", "alpha"],
[0.01, norm_sim * 0.8, redshift, 0.9],
parmins=[0.0, 0.0, 0.0, 0.1],
parmaxs=[10.0, 1.0e9, 10.0, 10.0],
parfrozen=[False, False, True, False])
load_pha("plaw_model_evt.pha")
set_stat("cstat")
set_method("simplex")
ignore(":0.5, 9.0:")
set_model("wplaw")
fit()
set_covar_opt("sigma", 1.645)
covar()
res = get_covar_results()
assert np.abs(res.parvals[0] - nH_sim) < res.parmaxes[0]
assert np.abs(res.parvals[1] - norm_sim) < res.parmaxes[1]
assert np.abs(res.parvals[2] - alpha_sim) < res.parmaxes[2]
os.chdir(curdir)
shutil.rmtree(tmpdir)
instrument_simulator, make_background_file, simulate_spectrum
from soxs.background.foreground import hm_astro_bkgnd
from soxs.background.spectra import ConvolvedBackgroundSpectrum
from soxs.spectra import Spectrum
from soxs.response import AuxiliaryResponseFile, RedistributionMatrixFile
from soxs.utils import soxs_files_path
from numpy.random import RandomState
from numpy.testing import assert_allclose
import astropy.io.fits as pyfits
import tempfile
import os
import shutil
import numpy as np
import astropy.units as u
acisi_particle_bkgnd = Spectrum.from_file(
os.path.join(soxs_files_path, "acisi_particle_bkgnd.h5"))
def test_uniform_bkgnd_scale():
prng = RandomState(25)
hdxi_arf = AuxiliaryResponseFile("xrs_hdxi_3x10.arf")
events, event_params = make_background((50, "ks"), "lynx_hdxi", [30., 45.],
foreground=True, instr_bkgnd=True,
ptsrc_bkgnd=False, prng=prng)
ncts = np.logical_and(events["energy"] >= 0.7, events["energy"] <= 2.0).sum()
t_exp = event_params["exposure_time"]
fov = (event_params["fov"]*60.0)**2
S = ncts/t_exp/fov
dS = np.sqrt(ncts)/t_exp/fov
foreground = ConvolvedBackgroundSpectrum.convolve(hm_astro_bkgnd, hdxi_arf)
f_sum = foreground.get_flux_in_band(0.7, 2.0)[0]
def to_spectrum(self, fov):
fov = parse_value(fov, "arcmin")
flux = self.flux.value*fov*fov
return Spectrum(self.ebins.value, flux)