def check_integrals():
"""Check that Sherpa normed models integrate to 1."""
from sherpa.astro import ui
from sherpa.astro.ui import normgauss2d
from models import normdisk2d, normshell2d
ui.clean()
g = normgauss2d('g')
g.xpos, g.ypos, g.ampl, g.fwhm = 100, 100, 42, 5
d = normdisk2d('d')
d.xpos, d.ypos, d.ampl, d.r0 = 100, 100, 42, 50
s = normshell2d('s')
s.xpos, s.ypos, s.ampl, s.r0, s.width = 100, 100, 42, 30, 20
models = [g, d, s]
ui.dataspace2d((200, 200))
for model in models:
ui.set_model(model)
# In sherpa normed model values are flux per pixel area.
# So to get the total flux (represented by the `ampl` parameter)
# one can simply sum over all pixels, because a pixel has area 1 pix^2.
# :-)
integral = ui.get_model_image().y.sum()
print model.name, integral
def test_eqwith_err1(make_data_path, restore_xspec_settings):
def check1(e0, e1, e2):
assert e0 == pytest.approx(0.028335201547206704, rel=1.0e-3)
assert e1 == pytest.approx(-0.00744118799274448756, rel=1.0e-3)
assert e2 == pytest.approx(0.0706249544851336, rel=1.0e-3)
ui.set_xsabund('angr')
ui.set_xsxsect('bcmc')
ui.load_pha(make_data_path('3c273.pi'))
ui.notice(0.5, 7.0)
ui.set_stat("chi2datavar")
ui.set_method("simplex")
ui.set_model('powlaw1d.p1+gauss1d.g1')
g1.fwhm = 0.1
g1.pos = 2.0
ui.freeze(g1.pos, g1.fwhm)
ui.fit()
np.random.seed(2345)
e = ui.eqwidth(p1, p1 + g1, error=True, niter=100)
check1(e[0], e[1], e[2])
params = e[3]
np.random.seed(2345)
e = ui.eqwidth(p1, p1 + g1, error=True, params=params, niter=100)
check1(e[0], e[1], e[2])
parvals = ui.get_fit_results().parvals
assert parvals[0] == pytest.approx(1.9055272902160334, rel=1.0e-3)
assert parvals[1] == pytest.approx(0.00017387966749772638, rel=1.0e-3)
assert parvals[2] == pytest.approx(1.279415076070516e-05, rel=1.0e-3)
def test_ARFModelPHA(self):
from sherpa.astro import ui
ui.load_pha(self.make_path("3c120_meg_1.pha"))
# remove the RMF to ensure this is an ARF-only analysis
# (which is what is needed to trigger the bug that lead to #699)
ui.get_data().set_rmf(None)
ui.group_counts(20)
ui.notice(0.5, 6)
ui.subtract()
ui.set_model(ui.xsphabs.abs1 * (ui.xsapec.bubble + ui.powlaw1d.p1))
ui.set_xsabund('angr')
ui.set_xsxsect('vern')
abs1.nh = 0.163
abs1.nh.freeze()
p1.ampl = 0.017
p1.gamma = 1.9
bubble.kt = 0.5
bubble.norm = 4.2e-5
tol = 1.0e-2
ui.set_method_opt('ftol', tol)
ui.fit()
result = ui.get_fit_results()
assert result.numpoints == self._fit_using_ARFModelPHA['numpoints']
assert result.dof == self._fit_using_ARFModelPHA['dof']
def test_eqwith_err1(make_data_path, restore_xspec_settings):
def check1(e0, e1, e2):
assert e0 == approx(0.028335201547206704, rel=1.0e-3)
assert e1 == approx(-0.00744118799274448756, rel=1.0e-3)
assert e2 == approx(0.0706249544851336, rel=1.0e-3)
ui.set_xsabund('angr')
ui.set_xsxsect('bcmc')
ui.load_pha(make_data_path('3c273.pi'))
ui.notice(0.5, 7.0)
ui.set_stat("chi2datavar")
ui.set_method("simplex")
ui.set_model('powlaw1d.p1+gauss1d.g1')
g1.fwhm = 0.1
g1.pos = 2.0
ui.freeze(g1.pos, g1.fwhm)
ui.fit()
numpy.random.seed(2345)
e = ui.eqwidth(p1, p1 + g1, error=True, niter=100)
check1(e[0], e[1], e[2])
params = e[3]
numpy.random.seed(2345)
e = ui.eqwidth(p1, p1 + g1, error=True, params=params, niter=100)
check1(e[0], e[1], e[2])
parvals = ui.get_fit_results().parvals
assert parvals[0] == approx(1.9055272902160334, rel=1.0e-3)
assert parvals[1] == approx(0.00017387966749772638, rel=1.0e-3)
assert parvals[2] == approx(1.279415076070516e-05, rel=1.0e-3)
def test_sherpa_fit(self, tmpdir):
# this is to make sure that the written PHA files work with sherpa
import sherpa.astro.ui as sau
from sherpa.models import PowLaw1D
# TODO: this works a little bit, but some info and warnings
# from Sherpa remain. Not sure what to do, OK as-is for now.
import logging
logging.getLogger("sherpa").setLevel("ERROR")
for obs in self.obs_list:
obs.to_ogip_files(str(tmpdir), use_sherpa=True)
filename = tmpdir / "pha_obs23523.fits"
sau.load_pha(str(filename))
sau.set_stat("wstat")
model = PowLaw1D("powlaw1d.default")
model.ref = 1e9
model.ampl = 1
model.gamma = 2
sau.set_model(model * 1e-20)
sau.fit()
assert_allclose(model.pars[0].val, 2.732, rtol=1e-3)
assert_allclose(model.pars[2].val, 4.647, rtol=1e-3)
def test_bug_276(make_data_path):
ui.load_pha(make_data_path('3c273.pi'))
ui.set_model('polynom1d.p1')
ui.fit()
ui.covar()
scal = ui.get_covar_results().parmaxes
ui.sample_flux(ui.get_model_component('p1'), 0.5, 1, num=5, correlated=False, scales=scal)
def fit_coeffs(method='simplex'):
method = method
dummy_data = np.zeros(100)
dummy_times = np.arange(100)
ui.load_arrays(1, dummy_times, dummy_data)
ui.set_method(method)
ui.get_method().config.update(SHERPA_CONFIGS.get(method, {}))
calc_model = CalcModel()
ui.load_user_model(calc_model, 'axo_mod') # sets global axo_mod
parnames = []
for row in range(N_ROWS):
for col in range(N_COLS):
parnames.append('adj_{}_{}'.format(row, col))
ui.add_user_pars('axo_mod', parnames)
ui.set_model(1, 'axo_mod')
calc_stat = CalcStat(axo_mod, M_2d, displ_x)
ui.load_user_stat('axo_stat', calc_stat, lambda x: np.ones_like(x))
ui.set_stat(axo_stat)
calc_model.set_calc_stat(calc_stat)
# Set frozen, min, and max attributes for each axo_mod parameter
for par in axo_mod.pars:
par.val = 0.0
par.min = -5
par.max = 5
ui.fit(1)
coeffs = np.array([(par.val) for pars in axo_mod.pars])
return coeffs
def check_integrals():
"""Check that Sherpa normed models integrate to 1."""
from sherpa.astro import ui
from sherpa.astro.ui import normgauss2d
from models import normdisk2d, normshell2d
ui.clean()
g = normgauss2d('g')
g.xpos, g.ypos, g.ampl, g.fwhm = 100, 100, 42, 5
d = normdisk2d('d')
d.xpos, d.ypos, d.ampl, d.r0 = 100, 100, 42, 50
s = normshell2d('s')
s.xpos, s.ypos, s.ampl, s.r0, s.width = 100, 100, 42, 30, 20
models = [g, d, s]
ui.dataspace2d((200, 200))
for model in models:
ui.set_model(model)
# In sherpa normed model values are flux per pixel area.
# So to get the total flux (represented by the `ampl` parameter)
# one can simply sum over all pixels, because a pixel has area 1 pix^2.
# :-)
integral = ui.get_model_image().y.sum()
print model.name, integral
def test_user_stat_unit():
given_stat_error = [1.1, 2.2, 3.3]
given_sys_error = [10.1, 10.2, 10.3]
def calc_stat(data, _model, staterror, syserror=None, weight=None):
# Make sure values are being injected correctly
np.testing.assert_array_equal(given_stat_error, staterror)
np.testing.assert_array_equal(given_sys_error, syserror)
return 3.235, np.ones_like(data)
xdata = [1, 2, 3]
ydata = xdata
ui.load_arrays(1, xdata, ydata, None, given_sys_error, Data1D)
ui.set_model(1, 'polynom1d.p')
ui.load_user_stat('customstat', calc_stat, lambda x: given_stat_error)
ui.set_stat(eval('customstat'))
try:
ui.fit(1)
except StatErr:
pytest.fail("Call should not be throwing any exception (bug #341)")
# Test the result is what we made the user stat return
assert 3.235 == ui.get_fit_results().statval
def match_wcs(wcs_img, sky_img, sky_ref, opt_alg='scipy'):
"""Adjust ``wcs_img`` (CRVAL{1,2} and CD{1,2}_{1,2}) using a rotation and linear
offset so that ``coords_img`` matches ``coords_ref``.
:param sky_img: list of (world_x, world_y) [aka RA, Dec] coords in input image
:param sky_ref: list of reference (world_x, world_y) coords to match
:param wcs_img: pywcs WCS object for input image
:returns: d_ra, d_dec, d_theta
"""
pix_img = wcs_img.wcs_sky2pix(sky_img, 1)
wcsmodel = WcsModel(wcs_img, sky_ref, pix_img)
y = np.array(pix_img).flatten()
if opt_alg == 'sherpa':
x = np.arange(len(y))
import sherpa.astro.ui as ui
ui.load_user_model(wcsmodel.calc_pix, 'wcsmod')
ui.add_user_pars('wcsmod', ['d_ra', 'd_dec', 'd_theta'])
wcsmod.d_ra = 0.0
wcsmod.d_dec = 0.0
wcsmod.d_theta = 0.0
ui.load_arrays(1, x, y, np.ones(len(y)))
ui.set_model(1, wcsmod)
ui.set_method('simplex')
ui.fit()
else:
import scipy.optimize
x0 = np.array([0.0, 0.0, 0.0])
d_ra, d_dec, d_theta = scipy.optimize.fmin(wcsmodel.calc_resid2, x0)
print 'Scipy fit values:', d_ra, d_dec, d_theta
return wcsmodel.wcs
def test_plot_pvalue(make_data_path, clean_astro_ui, hide_log_output):
fname = make_data_path("qso.pi")
ui.load_pha(fname)
ui.set_stat('cstat')
ui.set_method("neldermead")
ui.group_counts(10)
ui.notice(0.3, 8)
ui.set_model("xsphabs.abs1*xspowerlaw.p1")
ui.set_model("abs1*(p1+gauss1d.g1)")
# move the fit close to the best fit to save a small amount
# of time.
abs1.nh = 0.05
p1.phoindex = 1.28
p1.norm = 2e-4
g1.ampl = 1.8e-5
g1.pos = 3.
ui.freeze(g1.pos)
g1.fwhm = 0.1
ui.freeze(g1.fwhm)
ui.fit()
ui.plot_pvalue(p1, p1 + g1, num=100)
tmp = ui.get_pvalue_results()
assert tmp.null == pytest.approx(210.34566845619273)
assert tmp.alt == pytest.approx(207.66618095925094)
assert tmp.lr == pytest.approx(2.679487496941789)
def fit_coeffs(method='simplex'):
method = method
dummy_data = np.zeros(100)
dummy_times = np.arange(100)
ui.load_arrays(1, dummy_times, dummy_data)
ui.set_method(method)
ui.get_method().config.update(SHERPA_CONFIGS.get(method, {}))
calc_model = CalcModel()
ui.load_user_model(calc_model, 'axo_mod') # sets global axo_mod
parnames = []
for row in range(N_ROWS):
for col in range(N_COLS):
parnames.append('adj_{}_{}'.format(row, col))
ui.add_user_pars('axo_mod', parnames)
ui.set_model(1, 'axo_mod')
calc_stat = CalcStat(axo_mod, M_2d, displ_x)
ui.load_user_stat('axo_stat', calc_stat, lambda x: np.ones_like(x))
ui.set_stat(axo_stat)
calc_model.set_calc_stat(calc_stat)
# Set frozen, min, and max attributes for each axo_mod parameter
for par in axo_mod.pars:
par.val = 0.0
par.min = -5
par.max = 5
ui.fit(1)
coeffs = np.array([(par.val) for pars in axo_mod.pars])
return coeffs
def test_background():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
kT_sim = 1.0
Z_sim = 0.0
norm_sim = 4.0e-2
nH_sim = 0.04
redshift = 0.01
exp_time = (200., "ks")
area = (1000., "cm**2")
wcs = create_dummy_wcs()
abs_model = WabsModel(nH_sim)
events = EventList.create_empty_list(exp_time, area, wcs)
spec_model = TableApecModel(0.05, 12.0, 5000, thermal_broad=False)
spec = spec_model.return_spectrum(kT_sim, Z_sim, redshift, norm_sim)
new_events = events.add_background(spec_model.ebins, spec, prng=prng,
absorb_model=abs_model)
new_events = ACIS_I(new_events, rebin=False, convolve_psf=False, prng=prng)
new_events.write_spectrum("background_evt.pi", clobber=True)
os.system("cp %s ." % new_events.parameters["ARF"])
os.system("cp %s ." % new_events.parameters["RMF"])
load_user_model(mymodel, "wapec")
add_user_pars("wapec", ["nH", "kT", "metallicity", "redshift", "norm"],
[0.01, 4.0, 0.2, redshift, norm_sim*0.8],
parmins=[0.0, 0.1, 0.0, -20.0, 0.0],
parmaxs=[10.0, 20.0, 10.0, 20.0, 1.0e9],
parfrozen=[False, False, False, True, False])
load_pha("background_evt.pi")
set_stat("cstat")
set_method("simplex")
ignore(":0.5, 8.0:")
set_model("wapec")
fit()
set_covar_opt("sigma", 1.6)
covar()
res = get_covar_results()
assert np.abs(res.parvals[0]-nH_sim) < res.parmaxes[0]
assert np.abs(res.parvals[1]-kT_sim) < res.parmaxes[1]
assert np.abs(res.parvals[2]-Z_sim) < res.parmaxes[2]
assert np.abs(res.parvals[3]-norm_sim) < res.parmaxes[3]
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_background():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
kT_sim = 1.0
Z_sim = 0.0
norm_sim = 4.0e-2
nH_sim = 0.04
redshift = 0.01
exp_time = (200., "ks")
area = (1000., "cm**2")
fov = (10.0, "arcmin")
prng = 24
agen = ApecGenerator(0.05, 12.0, 5000, broadening=False)
spec = agen.get_spectrum(kT_sim, Z_sim, redshift, norm_sim)
spec.apply_foreground_absorption(norm_sim)
events = make_background(area, exp_time, fov, (30.0, 45.0), spec, prng=prng)
events.write_simput_file("bkgnd", overwrite=True)
instrument_simulator("bkgnd_simput.fits", "bkgnd_evt.fits",
exp_time, "sq_acisi_cy19", [30.0, 45.0],
overwrite=True, foreground=False, ptsrc_bkgnd=False,
instr_bkgnd=False,
prng=prng)
write_spectrum("bkgnd_evt.fits", "background_evt.pi", overwrite=True)
os.system("cp %s %s ." % (arf.filename, rmf.filename))
load_user_model(mymodel, "wapec")
add_user_pars("wapec", ["nH", "kT", "metallicity", "redshift", "norm"],
[0.01, 4.0, 0.2, redshift, norm_sim*0.8],
parmins=[0.0, 0.1, 0.0, -20.0, 0.0],
parmaxs=[10.0, 20.0, 10.0, 20.0, 1.0e9],
parfrozen=[False, False, False, True, False])
load_pha("background_evt.pi")
set_stat("cstat")
set_method("simplex")
ignore(":0.5, 8.0:")
set_model("wapec")
fit()
res = get_fit_results()
assert np.abs(res.parvals[0]-nH_sim)/nH_sim < 0.1
assert np.abs(res.parvals[1]-kT_sim)/kT_sim < 0.05
assert np.abs(res.parvals[2]-Z_sim) < 0.05
assert np.abs(res.parvals[3]-norm_sim)/norm_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_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_load_multi_arfsrmfs(make_data_path, clean_astro_ui):
"""Added in #728 to ensure cache parameter is sent along by
MultiResponseSumModel (fix #717).
This has since been simplified to switch from xsapec to
powlaw1d as it drops the need for XSPEC and is a simpler
model, so is less affected by changes in the model code.
A fit of the Sherpa powerlaw-model to 3c273.pi with a
single response in CIAO 4.11 (background subtracted,
0.5-7 keV) returns gamma = 1.9298, ampl = 1.73862e-4
so doubling the response should halve the amplitude but
leave the gamma value the same when using two responses,
as below. This is with chi2datavar.
"""
pha_pi = make_data_path("3c273.pi")
ui.load_pha(1, pha_pi)
ui.load_pha(2, pha_pi)
arf = make_data_path("3c273.arf")
rmf = make_data_path("3c273.rmf")
ui.load_multi_arfs(1, [arf, arf], [1, 2])
ui.load_multi_arfs(2, [arf, arf], [1, 2])
ui.load_multi_rmfs(1, [rmf, rmf], [1, 2])
ui.load_multi_rmfs(2, [rmf, rmf], [1, 2])
ui.notice(0.5, 7)
ui.subtract(1)
ui.subtract(2)
src = ui.create_model_component('powlaw1d', 'src')
ui.set_model(1, src)
ui.set_model(2, src)
# ensure the test is repeatable by running with a known
# statistic and method
#
ui.set_method('levmar')
ui.set_stat('chi2datavar')
# Really what we care about for fixing #717 is that
# fit does not error out, but it's useful to know that
# the fit has changed the parameter values (which were
# both 1 before the fit).
#
ui.fit()
fr = ui.get_fit_results()
assert fr.succeeded
assert fr.datasets == (1, 2)
assert src.gamma.val == pytest.approx(1.9298, rel=1.0e-4)
assert src.ampl.val == pytest.approx(1.73862e-4 / 2, rel=1.0e-4)
def test_ui(self, tol=1.0e-3):
# from shepa.astro.ui import *
ui.load_ascii_with_errors(1, self.gro_delta_fname, delta=True)
ui.set_stat('leastsq')
ui.set_model('powlaw1d.p1')
ui.fit()
sample = ui.resample_data(1, 10, seed=123)
self.assertEqualWithinTol(self._resample_bench_10['p1.gamma'],
sample['p1.gamma'])
self.assertEqualWithinTol(self._resample_bench_10['p1.ampl'],
sample['p1.ampl'])
def test_warning(self):
ui.load_ascii_with_errors(1, self.gro_fname)
data = ui.get_data(1)
powlaw1d = PowLaw1D('p1')
ui.set_model(powlaw1d)
fit = Fit(data, powlaw1d)
results = fit.fit()
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
ui.resample_data(1, 3)
assert len(w) == 0
def test_ui(make_data_path):
infile = make_data_path('gro_delta.txt')
ui.load_ascii_with_errors(1, infile, delta=True)
ui.set_stat('leastsq')
ui.set_model('powlaw1d.p1')
ui.fit()
sample = ui.resample_data(1, 10, seed=123)
for p in ['p1.gamma', 'p1.ampl']:
assert sample[p] == pytest.approx(RESAMPLE_BENCH_10[p], rel=1e-4)
def test_warning(make_data_path):
infile = make_data_path('gro.txt')
ui.load_ascii_with_errors(1, infile)
powlaw1d = PowLaw1D('p1')
ui.set_model(powlaw1d)
ui.fit()
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
ui.resample_data(1, 3)
assert len(w) == 0
def fit_adjuster_set(coeffs, adj_idxs, method='simplex'):
"""
Find best fit parameters for an arbitrary subset of adjustors
specified by the array ``adj_idxs``. The input ``coeffs`` are
the best-fit adjustor coefficients for the last iteration.
"""
import sherpa.astro.ui as ui
dummy_data = np.zeros(100)
dummy_times = np.arange(100)
ui.load_arrays(1, dummy_times, dummy_data)
ui.set_method(method)
ui.get_method().config.update(SHERPA_CONFIGS.get(method, {}))
calc_model = CalcModel()
ui.load_user_model(calc_model, 'axo_mod') # sets global axo_mod
parnames = []
for adj_idx in adj_idxs:
parnames.append('adj_{}'.format(adj_idx))
ui.add_user_pars('axo_mod', parnames)
ui.set_model(1, 'axo_mod')
coeffs = coeffs.copy() # Don't modify input coeffs
coeffs[coeffs < 0] = 0 # Don't allow negative coeffs
# Set frozen, min, and max attributes for each axo_mod parameter
for adj_idx, par in zip(adj_idxs, axo_mod.pars):
par.min = -1000
par.max = 1000
par.val = coeffs[adj_idx]
print 'Setting {} to {}'.format(adj_idx, par.val)
# Compute base adjusted displacements assuming all the fitted actuators
# have zero drive level.
coeffs[adj_idxs] = 0
base_adj_displ = M_2d.dot(coeffs)
m_2d = M_2d[:, adj_idxs].copy()
print m_2d.shape
calc_stat = CalcStat(base_adj_displ, m_2d, DISPL_X)
ui.load_user_stat('axo_stat', calc_stat, lambda x: np.ones_like(x))
ui.set_stat(axo_stat)
calc_model.set_calc_stat(calc_stat)
ui.fit(1)
# Update coeffs with the values determined in fitting
for adj_idx, par in zip(adj_idxs, axo_mod.pars):
coeffs[adj_idx] = abs(par.val)
return coeffs, ui.get_fit_results()
def test_bug_276(make_data_path):
ui.load_pha(make_data_path('3c273.pi'))
ui.set_model('polynom1d.p1')
ui.fit()
ui.covar()
scal = ui.get_covar_results().parmaxes
ui.sample_flux(ui.get_model_component('p1'),
0.5,
1,
num=5,
correlated=False,
scales=scal)
def test_missmatch_arf(make_data_path):
ui.load_pha(1, make_data_path("source1.pi"))
ui.load_bkg(1, make_data_path("back1.pi"))
ui.load_arf(1, make_data_path("arf_1024.fits"))
ui.load_rmf(1, make_data_path("rmf_1024.fits"))
ui.set_method('levmar')
ui.set_model(ui.powlaw1d.p1 * ui.xswabs.abs1)
ui.set_par('p1.ampl', 0.0001)
ui.set_stat('cash')
ui.fit()
parvals = ui.get_fit_results().parvals
assert parvals[0] == approx(1.47969, rel=1.0e-3)
assert parvals[1] == approx(0.0019491, rel=1.0e-3)
assert parvals[2] == approx(2.35452, rel=1.0e-3)
def test_ui_regrid1d_non_overlapping_not_allowed():
"""Integrated data space must not overlap"""
ui.dataspace1d(1, 100, 2, dstype=Data1DInt)
b1 = Box1D()
ui.set_model(b1)
b1.xlow = 10
b1.xhi = 80
b1.ampl.max = 100
grid_hi = np.linspace(2, 101, 600)
grid_lo = np.linspace(1, 100, 600)
with pytest.raises(ModelErr) as excinfo:
rb1 = b1.regrid(grid_lo, grid_hi)
assert ModelErr.dict['needsint'] in str(excinfo.value)
def test_sherpa_fit(tmpdir):
# this is to make sure that the written PHA files work with sherpa
pha1 = gammapy_extra.filename("datasets/hess-crab4_pha/pha_obs23592.fits")
import sherpa.astro.ui as sau
from sherpa.models import PowLaw1D
sau.load_pha(pha1)
sau.set_stat('wstat')
model = PowLaw1D('powlaw1d.default')
model.ref = 1e9
model.ampl = 1
model.gamma = 2
sau.set_model(model * 1e-20)
sau.fit()
assert_allclose(model.pars[0].val, 2.0281484215403616, atol=1e-4)
assert_allclose(model.pars[2].val, 2.3528406790143097, atol=1e-4)
def test_sherpa_fit(tmpdir):
# this is to make sure that the written PHA files work with sherpa
pha1 = gammapy_extra.filename("datasets/hess-crab4_pha/pha_obs23592.fits")
import sherpa.astro.ui as sau
from sherpa.models import PowLaw1D
sau.load_pha(pha1)
sau.set_stat('wstat')
model = PowLaw1D('powlaw1d.default')
model.ref = 1e9
model.ampl = 1
model.gamma = 2
sau.set_model(model * 1e-20)
sau.fit()
assert_allclose(model.pars[0].val, 2.0281484215403616, atol=1e-4)
assert_allclose(model.pars[2].val, 2.3528406790143097, atol=1e-4)
def test_sherpa_fit(self, tmpdir):
# this is to make sure that the written PHA files work with sherpa
import sherpa.astro.ui as sau
from sherpa.models import PowLaw1D
self.obs_list.write(tmpdir, use_sherpa=True)
filename = tmpdir / 'pha_obs23523.fits'
sau.load_pha(str(filename))
sau.set_stat('wstat')
model = PowLaw1D('powlaw1d.default')
model.ref = 1e9
model.ampl = 1
model.gamma = 2
sau.set_model(model * 1e-20)
sau.fit()
assert_allclose(model.pars[0].val, 2.0881699260935838)
assert_allclose(model.pars[2].val, 1.6234222129479836)
def test_sherpa_fit(tmpdir):
# this is to make sure that the written PHA files work with sherpa
import sherpa.astro.ui as sau
from sherpa.models import PowLaw1D
filename = gammapy_extra.filename(
"datasets/hess-crab4_pha/pha_obs23592.fits")
sau.load_pha(filename)
sau.set_stat('wstat')
model = PowLaw1D('powlaw1d.default')
model.ref = 1e9
model.ampl = 1
model.gamma = 2
sau.set_model(model * 1e-20)
sau.fit()
assert_allclose(model.pars[0].val, 2.0033101181778026)
assert_allclose(model.pars[2].val, 2.2991681244938498)
def test_sherpa_fit(self, tmpdir):
# this is to make sure that the written PHA files work with sherpa
import sherpa.astro.ui as sau
from sherpa.models import PowLaw1D
self.obs_list.write(tmpdir, use_sherpa=True)
filename = tmpdir / 'pha_obs23523.fits'
sau.load_pha(str(filename))
sau.set_stat('wstat')
model = PowLaw1D('powlaw1d.default')
model.ref = 1e9
model.ampl = 1
model.gamma = 2
sau.set_model(model * 1e-20)
sau.fit()
assert_allclose(model.pars[0].val, 2.0881699, rtol=1e-3)
assert_allclose(model.pars[2].val, 1.6234222, rtol=1e-3)
def test_user_model_stat_docs():
"""
This test reproduces the documentation shown at:
http://cxc.harvard.edu/sherpa4.4/statistics/#userstat
and:
http://cxc.harvard.edu/sherpa/threads/user_model/
I tried to be as faithful as possible to the original, although the examples in thedocs
are not completely self-contained, so some changes were necessary. I changed the numpy
reference, as it is imported as `np` here, and added a clean up of the environment
before doing anything.
For the model, the difference is that I am not importing the function from an
external module, plus the dataset is different.
Also, the stats docs do not perform a fit.
"""
def my_stat_func(data, model, staterror, syserror=None, weight=None):
# A simple function to replicate χ2
fvec = ((data - model) / staterror)**2
stat = fvec.sum()
return (stat, fvec)
def my_staterr_func(data):
# A simple staterror function
return np.sqrt(data)
def myline(pars, x):
return pars[0]*x + pars[1]
x = [1, 2, 3]
y = [4, 5, 6.01]
ui.clean()
ui.load_arrays(1, x, y)
ui.load_user_stat("mystat", my_stat_func, my_staterr_func)
ui.set_stat(eval('mystat'))
ui.load_user_model(myline, "myl")
ui.add_user_pars("myl", ["m", "b"])
ui.set_model(eval('myl'))
ui.fit()
assert ui.get_par("myl.m").val == approx(1, abs=0.01)
assert ui.get_par("myl.b").val == approx(3, abs=0.01)
def test_rsp(self):
fname = self.make_path("qso.pi")
ui.load_pha(fname)
ui.set_stat("chi2xspecvar")
ui.set_method("neldermead")
ui.group_counts(10)
ui.notice(0.3, 8)
ui.set_model("xsphabs.abs1*xspowerlaw.p1")
ui.set_model("abs1*(p1+gauss1d.g1)")
g1.pos = 3.
ui.freeze(g1.pos)
g1.fwhm = 0.1
ui.freeze(g1.fwhm)
ui.set_stat('cstat')
ui.fit()
ui.plot_pvalue(p1, p1 + g1, num=100)
tmp = ui.get_pvalue_results()
expected = [210.34566845619273, 207.66618095925094, 2.679487496941789]
self.compare_results(expected, [tmp.null, tmp.alt, tmp.lr])
def test_eqwith_err(make_data_path, restore_xspec_settings):
def check(a0, a1, a2):
assert a0 == pytest.approx(0.16443033244310976, rel=1e-3)
assert a1 == pytest.approx(0.09205564216156815, rel=1e-3)
assert a2 == pytest.approx(0.23933118287470895, rel=1e-3)
ui.set_method('neldermead')
ui.set_stat('cstat')
ui.set_xsabund('angr')
ui.set_xsxsect('bcmc')
ui.load_data(make_data_path('12845.pi'))
ui.notice(0.5, 7)
ui.set_model("xsphabs.gal*xszphabs.zabs*(powlaw1d.p1+xszgauss.g1)")
ui.set_par(gal.nh, 0.08)
ui.freeze(gal)
ui.set_par(zabs.redshift, 0.518)
ui.set_par(g1.redshift, 0.518)
ui.set_par(g1.Sigma, 0.01)
ui.freeze(g1.Sigma)
ui.set_par(g1.LineE, min=6.0, max=7.0)
ui.fit()
np.random.seed(12345)
result = ui.eqwidth(p1, p1 + g1, error=True, niter=100)
check(result[0], result[1], result[2])
params = result[3]
np.random.seed(12345)
result = ui.eqwidth(p1, p1 + g1, error=True, params=params, niter=100)
check(result[0], result[1], result[2])
parvals = ui.get_fit_results().parvals
assert parvals[0] == pytest.approx(0.6111340686157877, rel=1.0e-3)
assert parvals[1] == pytest.approx(1.6409785803466297, rel=1.0e-3)
assert parvals[2] == pytest.approx(8.960926761312153e-05, rel=1.0e-3)
assert parvals[3] == pytest.approx(6.620017726014523, rel=1.0e-3)
assert parvals[4] == pytest.approx(1.9279114810359657e-06, rel=1.0e-3)
def test_eqwith_err(make_data_path, restore_xspec_settings):
def check(a0, a1, a2):
assert a0 == approx(0.16443033244310976, rel=1e-3)
assert a1 == approx(0.09205564216156815, rel=1e-3)
assert a2 == approx(0.23933118287470895, rel=1e-3)
ui.set_method('neldermead')
ui.set_stat('cstat')
ui.set_xsabund('angr')
ui.set_xsxsect('bcmc')
ui.load_data(make_data_path('12845.pi'))
ui.notice(0.5, 7)
ui.set_model("xsphabs.gal*xszphabs.zabs*(powlaw1d.p1+xszgauss.g1)")
ui.set_par(gal.nh, 0.08)
ui.freeze(gal)
ui.set_par(zabs.redshift, 0.518)
ui.set_par(g1.redshift, 0.518)
ui.set_par(g1.Sigma, 0.01)
ui.freeze(g1.Sigma)
ui.set_par(g1.LineE, min=6.0, max=7.0)
ui.fit()
numpy.random.seed(12345)
result = ui.eqwidth(p1, p1 + g1, error=True, niter=100)
check(result[0], result[1], result[2])
params = result[3]
numpy.random.seed(12345)
result = ui.eqwidth(p1, p1 + g1, error=True, params=params, niter=100)
check(result[0], result[1], result[2])
parvals = ui.get_fit_results().parvals
assert parvals[0] == approx(0.6111340686157877, rel=1.0e-3)
assert parvals[1] == approx(1.6409785803466297, rel=1.0e-3)
assert parvals[2] == approx(8.960926761312153e-05, rel=1.0e-3)
assert parvals[3] == approx(6.620017726014523, rel=1.0e-3)
assert parvals[4] == approx(1.9279114810359657e-06, rel=1.0e-3)
def test_set_analysis_wave_fabrizio(self):
rmf = self.datadir + '/ciao4.3/fabrizio/Data/3c273.rmf'
arf = self.datadir + '/ciao4.3/fabrizio/Data/3c273.arf'
ui.set_model("fabrizio", "xspowerlaw.p1")
ui.fake_pha("fabrizio", arf, rmf, 10000)
model = ui.get_model("fabrizio")
bare_model, _ = ui._session._get_model_status("fabrizio")
y = bare_model.calc([1, 1], model.xlo, model.xhi)
y_m = numpy.mean(y)
ui.set_analysis("fabrizio", "wave")
model2 = ui.get_model("fabrizio")
bare_model2, _ = ui._session._get_model_status("fabrizio")
y2 = bare_model2.calc([1, 1], model2.xlo, model2.xhi)
y2_m = numpy.mean(y2)
self.assertAlmostEqual(y_m, y2_m)
def test_set_analysis_wave_fabrizio(self):
rmf = self.datadir + '/ciao4.3/fabrizio/Data/3c273.rmf'
arf = self.datadir + '/ciao4.3/fabrizio/Data/3c273.arf'
ui.set_model("fabrizio", "xspowerlaw.p1")
ui.fake_pha("fabrizio", arf, rmf, 10000)
model = ui.get_model("fabrizio")
bare_model, _ = ui._session._get_model_status("fabrizio")
y = bare_model.calc([1,1], model.xlo, model.xhi)
y_m = numpy.mean(y)
ui.set_analysis("fabrizio","wave")
model2 = ui.get_model("fabrizio")
bare_model2, _ = ui._session._get_model_status("fabrizio")
y2 = bare_model2.calc([1,1], model2.xlo, model2.xhi)
y2_m = numpy.mean(y2)
self.assertAlmostEqual(y_m, y2_m)
def test_load_multi_arfsrmfs(make_data_path):
pha_pi = make_data_path("3c273.pi")
ui.load_pha(1, pha_pi)
ui.load_pha(2, pha_pi)
bkg_pi = make_data_path("3c273_bg.pi")
ui.load_bkg(1, bkg_pi)
ui.load_bkg(2, bkg_pi)
arf = make_data_path("3c273.arf")
ui.load_multi_arfs(1, [arf, arf], [1, 2])
ui.load_multi_arfs(2, [arf, arf], [1, 2])
rmf = make_data_path("3c273.rmf")
ui.load_multi_rmfs(1, [rmf, rmf], [1, 2])
ui.load_multi_rmfs(2, [rmf, rmf], [1, 2])
ui.set_model(1, ui.xsapec.src)
ui.set_model(2, ui.xsapec.src)
ui.fit()
parvals = ui.get_fit_results().parvals
assert (parvals[0] == pytest.approx(1.03364, rel=1.0e-3))
assert (parvals[1] == pytest.approx(4.56712e-05, rel=1.03e-3))
def test_set_analysis_wave_fabrizio(self):
rmf = self.make_path('3c273.rmf')
arf = self.make_path('3c273.arf')
ui.set_model("fabrizio", "xspowerlaw.p1")
ui.fake_pha("fabrizio", arf, rmf, 10000)
parvals = [1, 1]
model = ui.get_model("fabrizio")
bare_model, _ = ui._session._get_model_status("fabrizio")
y = bare_model.calc(parvals, model.xlo, model.xhi)
y_m = numpy.mean(y)
ui.set_analysis("fabrizio", "wave")
model2 = ui.get_model("fabrizio")
bare_model2, _ = ui._session._get_model_status("fabrizio")
y2 = bare_model2.calc(parvals, model2.xlo, model2.xhi)
y2_m = numpy.mean(y2)
self.assertAlmostEqual(y_m, y2_m)
def test_set_analysis_wave_fabrizio(clean_astro_ui, make_data_path):
rmf = make_data_path('3c273.rmf')
arf = make_data_path('3c273.arf')
ui.set_model("fabrizio", "xspowerlaw.p1")
ui.fake_pha("fabrizio", arf, rmf, 10000)
parvals = [1, 1]
model = ui.get_model("fabrizio")
bare_model, _ = ui._session._get_model_status("fabrizio")
y = bare_model.calc(parvals, model.xlo, model.xhi)
y_m = numpy.mean(y)
ui.set_analysis("fabrizio", "wave")
model2 = ui.get_model("fabrizio")
bare_model2, _ = ui._session._get_model_status("fabrizio")
y2 = bare_model2.calc(parvals, model2.xlo, model2.xhi)
y2_m = numpy.mean(y2)
assert y2_m == pytest.approx(y_m)
def test_set_analysis_wave_fabrizio(self):
rmf = self.make_path('3c273.rmf')
arf = self.make_path('3c273.arf')
ui.set_model("fabrizio", "xspowerlaw.p1")
ui.fake_pha("fabrizio", arf, rmf, 10000)
parvals = [1, 1]
model = ui.get_model("fabrizio")
bare_model, _ = ui._session._get_model_status("fabrizio")
y = bare_model.calc(parvals, model.xlo, model.xhi)
y_m = numpy.mean(y)
ui.set_analysis("fabrizio", "wave")
model2 = ui.get_model("fabrizio")
bare_model2, _ = ui._session._get_model_status("fabrizio")
y2 = bare_model2.calc(parvals, model2.xlo, model2.xhi)
y2_m = numpy.mean(y2)
self.assertAlmostEqual(y_m, y2_m)
def test_sherpa_fit(self, tmpdir):
# this is to make sure that the written PHA files work with sherpa
import sherpa.astro.ui as sau
from sherpa.models import PowLaw1D
# TODO: this works a little bit, but some info and warnings
# from Sherpa remain. Not sure what to do, OK as-is for now.
import logging
logging.getLogger("sherpa").setLevel("ERROR")
self.obs_list.write(tmpdir, use_sherpa=True)
filename = tmpdir / "pha_obs23523.fits"
sau.load_pha(str(filename))
sau.set_stat("wstat")
model = PowLaw1D("powlaw1d.default")
model.ref = 1e9
model.ampl = 1
model.gamma = 2
sau.set_model(model * 1e-20)
sau.fit()
assert_allclose(model.pars[0].val, 2.732, rtol=1e-3)
assert_allclose(model.pars[2].val, 4.647, rtol=1e-3)
def do_beta_model(source, v_field, em_field):
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = source.ds
A = 3000.
exp_time = 1.0e5
redshift = 0.05
nH_sim = 0.02
apec_model = TableApecModel(0.1, 11.5, 20000, thermal_broad=False)
abs_model = TBabsModel(nH_sim)
sphere = ds.sphere("c", (0.5, "Mpc"))
kT_sim = source.kT
Z_sim = source.Z
thermal_model = ThermalSourceModel(apec_model,
Zmet=Z_sim,
prng=source.prng)
photons = PhotonList.from_data_source(sphere, redshift, A, exp_time,
thermal_model)
D_A = photons.parameters["FiducialAngularDiameterDistance"]
norm_sim = sphere.quantities.total_quantity(em_field)
norm_sim *= 1.0e-14 / (4 * np.pi * D_A * D_A * (1. + redshift) *
(1. + redshift))
norm_sim = float(norm_sim.in_cgs())
v1, v2 = sphere.quantities.weighted_variance(v_field, em_field)
sigma_sim = float(v1.in_units("km/s"))
mu_sim = -float(v2.in_units("km/s"))
events = photons.project_photons("z",
absorb_model=abs_model,
prng=source.prng)
events = ACIS_I(events, rebin=False, convolve_psf=False, prng=source.prng)
events.write_spectrum("beta_model_evt.pi", clobber=True)
os.system("cp %s ." % events.parameters["ARF"])
os.system("cp %s ." % events.parameters["RMF"])
load_user_model(mymodel, "tbapec")
add_user_pars("tbapec", ["nH", "kT", "metallicity", "redshift", "norm"],
[0.01, 4.0, 0.2, redshift, norm_sim * 0.8],
parmins=[0.0, 0.1, 0.0, -20.0, 0.0],
parmaxs=[10.0, 20.0, 10.0, 20.0, 1.0e9],
parfrozen=[False, False, False, True, False])
load_pha("beta_model_evt.pi")
set_stat("cstat")
set_method("simplex")
ignore(":0.5, 8.0:")
set_model("tbapec")
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] - kT_sim) < res.parmaxes[1]
assert np.abs(res.parvals[2] - Z_sim) < res.parmaxes[2]
assert np.abs(res.parvals[3] - norm_sim) < res.parmaxes[3]
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_341():
"""
The original reporter of bug #341 had a special implementation that should be captured
by this test. The implementation has a proxy model that takes care of updating the actual
model when it is evaluated. During a recent refactoring of the Stat and Fit code
(PR #287) a regression was introduced by short-circuiting the evaluation of the model.
"""
class ExampleModel(object):
""" Class to define model
"""
def __init__(self, x, y):
self.x = np.array(x)
self.y = np.array(y)
self.parvals = [1, 2]
self.parnames = ("m", "b")
def calc_stat(self):
return float(np.sum(np.abs(self.y - self.model())))
def model(self):
return self.parvals[0] * self.x + self.parvals[1]
class CalcModel(object):
""" Class to update model parameters
"""
def __init__(self, model):
self.model = model
def __call__(self, pars, x):
self.model.parvals = pars
return np.ones_like(x)
class CalcStat(object):
""" Class to determine fit statistic
"""
def __init__(self, model):
self.model = model
def __call__(self, _data, _model, *args, **kwargs):
fit_stat = self.model.calc_stat()
return fit_stat, np.ones(1)
xdata = [1, 2, 3]
ydata = [4, 5, 6]
newmodel = ExampleModel(xdata, ydata)
dummy_data = np.zeros(1)
dummy_times = np.arange(1)
ui.load_arrays(1, dummy_times, dummy_data)
method = 'simplex'
ui.set_method(method)
ui.load_user_model(CalcModel(newmodel), 'simplemodel')
ui.add_user_pars('simplemodel', newmodel.parnames)
ui.set_model(1, 'simplemodel')
calc_stat = CalcStat(newmodel)
ui.load_user_stat('customstat', calc_stat, lambda x: np.ones_like(x))
ui.set_stat(eval('customstat'))
ui.fit(1)
assert ui.get_par("simplemodel.m").val == approx(1, abs=0.00001)
assert ui.get_par("simplemodel.b").val == approx(3, abs=0.00001)
def test_vapec_beta_model():
bms = BetaModelSource()
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
prng = 45
ds = bms.ds
A = 30000.
exp_time = 1.0e4
redshift = 0.05
nH_sim = 0.02
sphere = ds.sphere("c", (0.5, "Mpc"))
kT_sim = bms.kT
Z_sim = bms.Z
O_sim = bms.O
Ca_sim = bms.Ca
var_elem = {"O": ("stream", "oxygen"),
"Ca": ("stream", "calcium")}
thermal_model = ThermalSourceModel("apec", 0.1, 11.5, 20000,
var_elem=var_elem,
Zmet=("gas","metallicity"),
prng=prng)
photons = PhotonList.from_data_source(sphere, redshift, A, exp_time,
thermal_model)
D_A = photons.parameters["fid_d_a"]
norm_sim = sphere.quantities.total_quantity("emission_measure")
norm_sim *= 1.0e-14/(4*np.pi*D_A*D_A*(1.+redshift)*(1.+redshift))
norm_sim = float(norm_sim.in_cgs())
events = photons.project_photons("z", [30.0, 45.0], absorb_model="tbabs",
nH=nH_sim, prng=prng, no_shifting=True)
new_events = Lynx_Calorimeter(events, prng=prng)
os.system("cp %s %s ." % (arf.filename, rmf.filename))
new_events.write_channel_spectrum("var_abund_beta_model_evt.pha", overwrite=True)
load_user_model(mymodel_var, "tbapec")
add_user_pars("tbapec", ["nH", "kT", "abund", "redshift", "norm", "O", "Ca"],
[nH_sim, 4.0, Z_sim, redshift, norm_sim*0.8, 0.3, 0.5],
parmins=[0.0, 0.1, 0.0, -20.0, 0.0, 0.0, 0.0],
parmaxs=[10.0, 20.0, 10.0, 20.0, 1.0e9, 10.0, 10.0],
parfrozen=[True, False, True, True, False, False, False])
load_pha("var_abund_beta_model_evt.pha")
set_stat("cstat")
set_method("levmar")
ignore(":0.6, 8.0:")
set_model("tbapec")
fit()
res = get_fit_results()
assert np.abs(res.parvals[0]-kT_sim)/kT_sim < 0.05
assert np.abs(res.parvals[1]-norm_sim)/norm_sim < 0.05
assert np.abs(res.parvals[2]-O_sim)/O_sim < 0.05
assert np.abs(res.parvals[3]-Ca_sim)/Ca_sim < 0.15
os.chdir(curdir)
shutil.rmtree(tmpdir)
def do_beta_model(source, v_field, em_field, axis="z",
prng=None):
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
if prng is None:
prng = source.prng
ds = source.ds
A = 30000.
exp_time = 1.0e4
redshift = 0.05
nH_sim = 0.02
sphere = ds.sphere("c", (0.5, "Mpc"))
kT_sim = source.kT
Z_sim = source.Z
thermal_model = ThermalSourceModel("apec", 0.1, 11.5, 20000,
Zmet=Z_sim, prng=prng)
photons = PhotonList.from_data_source(sphere, redshift, A, exp_time,
thermal_model)
D_A = photons.parameters["fid_d_a"]
norm_sim = sphere.quantities.total_quantity(em_field)
norm_sim *= 1.0e-14/(4*np.pi*D_A*D_A*(1.+redshift)*(1.+redshift))
norm_sim = float(norm_sim.in_cgs())
v1, v2 = sphere.quantities.weighted_variance(v_field, em_field)
if isinstance(axis, string_types):
if axis == "z":
fac = 1.0
else:
fac = 0.0
else:
axis /= np.sqrt(np.dot(axis, axis))
fac = np.dot(axis, [0.0, 0.0, 1.0])
sigma_sim = fac*float(v1.in_units("km/s"))
mu_sim = -fac*float(v2.in_units("km/s"))
events = photons.project_photons(axis, [30.0, 45.0], absorb_model="tbabs",
nH=nH_sim, prng=prng)
events.write_simput_file("beta_model", overwrite=True)
instrument_simulator("beta_model_simput.fits", "beta_model_evt.fits",
exp_time, "mucal", [30.0, 45.0],
overwrite=True, foreground=False, ptsrc_bkgnd=False,
instr_bkgnd=False,
prng=prng)
write_spectrum("beta_model_evt.fits", "beta_model_evt.pi", overwrite=True)
os.system("cp %s %s ." % (arf.filename, rmf.filename))
load_user_model(mymodel, "tbapec")
add_user_pars("tbapec", ["nH", "kT", "metallicity", "redshift", "norm", "velocity"],
[0.02, 4.0, 0.2, 0.04, norm_sim*0.8, 300.0],
parmins=[0.0, 0.1, 0.0, -200.0, 0.0, 0.0],
parmaxs=[10.0, 20.0, 10.0, 200.0, 1.0e9, 20000.0],
parfrozen=[True, False, False, False, False, False])
load_pha("beta_model_evt.pi")
set_stat("cstat")
set_method("levmar")
ignore(":0.6, 8.0:")
set_model("tbapec")
fit()
res = get_fit_results()
redshift_sim = (1.0+mu_sim/ckms)*(1.0+redshift) - 1.0
assert np.abs(res.parvals[0]-kT_sim)/kT_sim < 0.05
assert np.abs(res.parvals[1]-Z_sim)/Z_sim < 0.05
assert np.abs(res.parvals[2]-redshift_sim)/redshift_sim < 0.05
assert np.abs(res.parvals[3]-norm_sim) < 0.05
assert np.abs(res.parvals[4]-sigma_sim) < 30.0
os.chdir(curdir)
shutil.rmtree(tmpdir)
from bb import BoxBOD, report_results
# Load data
ui.load_arrays(1, BoxBOD.x, BoxBOD.y, np.ones_like(BoxBOD.x))
# @todo: It is possible to give no staterror, but I'm not sure
# what Sherpa does then. fr.statval is no longer the correct chi2.
# Set up the model and load it as a Sherpa model
def boxbod_func(pars, x):
b1, b2 = pars
return BoxBOD.model(x, b1, b2)
ui.load_user_model(boxbod_func, "boxbod")
ui.add_user_pars("boxbod", ["b1", "b2"])
bb = boxbod
ui.set_model(bb)
bb.b1, bb.b2 = BoxBOD.p0[0], BoxBOD.p0[1]
# Perform fit
ui.set_stat('chi2datavar')
#ui.set_method('levmar') # ['levmar', 'moncar', 'neldermead', 'simplex']
ui.set_method_opt('xtol', 1e-10)
ui.fit() # Compute best-fit parameters
ui.set_covar_opt('eps', 1e-5) # @todo: Why does this parameter have no effect
ui.covariance() # Compute covariance matrix (i.e. errors)
#ui.conf() # Compute profile errors
#ui.show_all() # Print a very nice summary of your session to less
# Report results
fr = ui.get_fit_results()
cr = ui.get_covar_results()
dummy_data = np.zeros(100)
dummy_times = np.arange(100)
ui.load_arrays(1, dummy_times, dummy_data)
ui.set_method(method)
ui.get_method().config.update(SHERPA_CONFIGS.get(method, {}))
calc_model = CalcModel()
ui.load_user_model(calc_model, "axo_mod") # sets global axo_mod
parnames = []
for row in range(N_ROWS):
for col in range(N_COLS):
parnames.append("adj_{}_{}".format(row, col))
ui.add_user_pars("axo_mod", parnames)
ui.set_model(1, "axo_mod")
calc_stat = CalcStat(axo_mod, M_2d, displ_x)
ui.load_user_stat("axo_stat", calc_stat, lambda x: np.ones_like(x))
ui.set_stat(axo_stat)
calc_model.set_calc_stat(calc_stat)
# Set frozen, min, and max attributes for each axo_mod parameter
for par in axo_mod.pars:
par.val = 0.0
# par.frozen = par.frozen
par.min = -5
par.max = 5
ui.fit(1)
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")
wcs = create_dummy_wcs()
ebins = np.linspace(0.1, 11.5, 2001)
emid = 0.5*(ebins[1:]+ebins[:-1])
spec = norm_sim*(emid*(1.0+redshift))**(-alpha_sim)
de = np.diff(ebins)[0]
abs_model = TBabsModel(nH_sim)
events = EventList.create_empty_list(exp_time, area, wcs)
positions = [(30.01, 45.0)]
new_events = events.add_point_sources(positions, ebins, spec, prng=prng,
absorb_model=abs_model)
new_events = ACIS_S(new_events, prng=prng)
scalex = float(np.std(new_events['xpix'])*sigma_to_fwhm*new_events.parameters["dtheta"])
scaley = float(np.std(new_events['ypix'])*sigma_to_fwhm*new_events.parameters["dtheta"])
psf_scale = ACIS_S.psf_scale
assert (scalex - psf_scale)/psf_scale < 0.01
assert (scaley - psf_scale)/psf_scale < 0.01
new_events.write_spectrum("point_source_evt.pi", clobber=True)
os.system("cp %s ." % new_events.parameters["ARF"])
os.system("cp %s ." % new_events.parameters["RMF"])
load_user_model(mymodel, "tplaw")
add_user_pars("tplaw", ["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("point_source_evt.pi")
set_stat("cstat")
set_method("simplex")
ignore(":0.5, 9.0:")
set_model("tplaw")
fit()
set_covar_opt("sigma", 1.6)
covar()
res = get_covar_results()
assert np.abs(res.parvals[0]-nH_sim) < res.parmaxes[0]
assert np.abs(res.parvals[1]-norm_sim/de) < res.parmaxes[1]
assert np.abs(res.parvals[2]-alpha_sim) < res.parmaxes[2]
os.chdir(curdir)
shutil.rmtree(tmpdir)
import sherpa.astro.ui as ui from spec import load_data, report_results # Load data x, y, y_err = load_data() ui.load_arrays(1, x, y, y_err) # Set up the model ui.set_model(ui.powlaw1d.pl) pl.gamma, pl.ampl = 2, 1e-12 # Perform fit ui.fit() # Compute best-fit parameters ui.covar() # Compute covariance matrix (i.e. errors) # ui.conf() # Compute profile errors # ui.show_all() # Print a very nice summary of your session to less # Report results fr = ui.get_fit_results() cr = ui.get_covar_results() package = "sherpa" gamma, norm = fr.parvals chi2 = fr.statval gamma_err, norm_err = cr.parmaxes cov = cr.extra_output[1, 0] corr = cov / (norm_err * gamma_err) report_results(package, norm, norm_err, gamma, gamma_err, chi2, cov, corr)
