def validate_pha(idval):
"""Check that the PHA dataset in id=idval is
as expected.
"""
assert ui.list_data_ids() == [idval]
pha = ui.get_data(idval)
assert isinstance(pha, DataPHA)
arf = ui.get_arf(idval)
assert isinstance(arf, ARF1D)
rmf = ui.get_rmf(idval)
assert isinstance(rmf, RMF1D)
bpha = ui.get_bkg(idval, bkg_id=1)
assert isinstance(bpha, DataPHA)
barf = ui.get_arf(idval, bkg_id=1)
assert isinstance(barf, ARF1D)
brmf = ui.get_rmf(idval, bkg_id=1)
assert isinstance(brmf, RMF1D)
# normally the background data set would have a different name,
# but this is a PHA Type 3 file.
# assert pha.name == bpha.name
assert arf.name == barf.name
assert rmf.name == brmf.name
def validate_pha(self, idval):
"""Check that the PHA dataset in id=idval is
as expected.
"""
self.assertEqual(ui.list_data_ids(), [idval])
pha = ui.get_data(idval)
self.assertIsInstance(pha, DataPHA)
arf = ui.get_arf(idval)
self.assertIsInstance(arf, ARF1D)
rmf = ui.get_rmf(idval)
self.assertIsInstance(rmf, RMF1D)
bpha = ui.get_bkg(idval, bkg_id=1)
self.assertIsInstance(bpha, DataPHA)
barf = ui.get_arf(idval, bkg_id=1)
self.assertIsInstance(barf, ARF1D)
brmf = ui.get_rmf(idval, bkg_id=1)
self.assertIsInstance(brmf, RMF1D)
# normally the background data set would have a different name,
# but this is a PHA Type 3 file.
# self.assertEqual(pha.name, bpha.name)
self.assertEqual(arf.name, barf.name)
self.assertEqual(rmf.name, brmf.name)
def test_xmm2(self):
self.run_thread('xmm2')
self.assertEqualWithinTol(ui.get_data().channel[0], 1.0, 1e-4)
self.assertEqual(ui.get_rmf().detchans, 800)
self.assertEqual(len(ui.get_rmf().energ_lo), 2400)
self.assertEqual(len(ui.get_rmf().energ_hi), 2400)
self.assertEqual(len(ui.get_rmf().n_grp), 2400)
self.assertEqual(len(ui.get_rmf().f_chan), 2394)
self.assertEqual(len(ui.get_rmf().n_chan), 2394)
self.assertEqual(len(ui.get_rmf().matrix), 1281216)
self.assertEqual(ui.get_rmf().offset, 0)
self.assertEqual(len(ui.get_rmf().e_min), 800)
self.assertEqual(len(ui.get_rmf().e_max), 800)
self.assertEqual(len(ui.get_arf().energ_lo), 2400)
self.assertEqual(len(ui.get_arf().energ_hi), 2400)
self.assertEqual(len(ui.get_arf().specresp), 2400)
def test_xmm2(self):
self.run_thread('xmm2')
self.assertEqualWithinTol(ui.get_data().channel[0], 1.0, 1e-4)
self.assertEqual(ui.get_rmf().detchans, 800)
self.assertEqual(len(ui.get_rmf().energ_lo), 2400)
self.assertEqual(len(ui.get_rmf().energ_hi), 2400)
self.assertEqual(len(ui.get_rmf().n_grp), 2400)
self.assertEqual(len(ui.get_rmf().f_chan), 2394)
self.assertEqual(len(ui.get_rmf().n_chan), 2394)
self.assertEqual(len(ui.get_rmf().matrix), 1281216)
self.assertEqual(ui.get_rmf().offset, 0)
self.assertEqual(len(ui.get_rmf().e_min), 800)
self.assertEqual(len(ui.get_rmf().e_max), 800)
self.assertEqual(len(ui.get_arf().energ_lo), 2400)
self.assertEqual(len(ui.get_arf().energ_hi), 2400)
self.assertEqual(len(ui.get_arf().specresp), 2400)
def set_minimalArea(self, areamin):
"""Define threshold using minimal area.
Extract true energy value from arf file
To be implemented
"""
my_arf = sau.get_arf(self.name)
def get_identity_response(i):
n = ui.get_bkg(i).counts.size
rmf = ui.get_rmf(i)
try:
arf = ui.get_arf(i)
return lambda model: IdentityResponse(n, model, arf=arf, rmf=rmf)
except:
return lambda model: IdentityRMF(n, model, rmf=rmf)
def test_xmm2(run_thread, fix_xspec):
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
run_thread('xmm2')
# NOTE: if this test is run on its own it can generate three warnings,
# with the first being a RuntimeWarnnig about numpy.ndarray size
# changed. We filter this out as it's not at all clear what is going
# on and we have filters in conftest to remove similar warnings
#
ws = [
w for w in ws
if not (w.category == RuntimeWarning and str(w.message).startswith(
'numpy.ndarray size changed, may indicate binary incompatibility.')
)
]
assert len(ws) == 2
cats = set([w.category for w in ws])
assert cats == set([UserWarning])
# The order of reading the ARF and RMF is not guaranteed,
# so do not force it here when testing the two warning
# messages.
#
arffile = 'MNLup_2138_0670580101_EMOS1_S001_spec.arf'
rmffile = 'MNLup_2138_0670580101_EMOS1_S001_spec.rmf'
emsg_arf = "The minimum ENERG_LO in the ARF " + \
"'{}' ".format(arffile) + \
"was 0 and has been replaced by {}".format(EMIN)
emsg_rmf = "The minimum ENERG_LO in the RMF " + \
"'{}' ".format(rmffile) + \
"was 0 and has been replaced by {}".format(EMIN)
emsgs = set([emsg_arf, emsg_rmf])
wmsgs = set([str(w.message) for w in ws])
assert wmsgs == emsgs
assert ui.get_data().channel[0] == approx(1.0, rel=1e-4)
rmf = ui.get_rmf()
arf = ui.get_arf()
assert rmf.detchans == 800
assert len(rmf.energ_lo) == 2400
assert len(rmf.energ_hi) == 2400
assert len(rmf.n_grp) == 2400
assert len(rmf.f_chan) == 2394
assert len(rmf.n_chan) == 2394
assert len(rmf.matrix) == 1281216
assert rmf.offset == 0
assert len(rmf.e_min) == 800
assert len(rmf.e_max) == 800
assert len(arf.energ_lo) == 2400
assert len(arf.energ_hi) == 2400
assert len(arf.specresp) == 2400
etol = EMIN / 100.0
assert rmf.energ_lo[0] == approx(EMIN, rel=etol)
assert arf.energ_lo[0] == approx(EMIN, rel=etol)
def test_sherpa(self, tmpdir, extraction):
"""Same as above for files to be used with sherpa"""
extraction.run(outdir=tmpdir, use_sherpa=True)
import sherpa.astro.ui as sau
sau.load_pha(str(tmpdir / 'ogip_data' / 'pha_obs23523.fits'))
arf = sau.get_arf()
actual = arf._arf._specresp
desired = extraction.observations[0].aeff.data.data.value
assert_allclose(actual, desired)
def test_sherpa(self, tmpdir, extraction):
"""Same as above for files to be used with sherpa"""
extraction.run(outdir=tmpdir, use_sherpa=True)
import sherpa.astro.ui as sau
sau.load_pha(str(tmpdir / 'ogip_data' / 'pha_obs23523.fits'))
arf = sau.get_arf()
actual = arf._arf._specresp
desired = extraction.observations[0].aeff.data.data.value
assert_allclose(actual, desired)
def setup_order_plot(make_data_path):
"""Set up a faked dataset with multiple orders."""
pha = make_data_path('3c273.pi')
ui.load_pha(pha)
# It has already loaded in one response
arf = ui.get_arf(resp_id=1)
arf.specresp *= 0.5
for order, scale in enumerate([0.4, 0.25], 2):
ui.load_arf(make_data_path('3c273.arf'), resp_id=order)
ui.load_rmf(make_data_path('3c273.rmf'), resp_id=order)
arf = ui.get_arf(resp_id=order)
arf.specresp *= scale
ui.set_source(ui.powlaw1d.pl)
ui.notice(0.5, 7)
ui.ignore(3, 4)
def test_sherpa(self, tmpdir, extraction):
"""Same as above for files to be used with sherpa"""
import sherpa.astro.ui as sau
extraction.run()
extraction.write(outdir=tmpdir, use_sherpa=True, overwrite=True)
sau.load_pha(str(tmpdir / "ogip_data" / "pha_obs23523.fits"))
arf = sau.get_arf()
actual = arf._arf._specresp
desired = extraction.spectrum_observations[0].aeff.data.data.to_value("cm2")
assert_allclose(actual, desired)
def test_sherpa(self, tmpdir, extraction):
"""Same as above for files to be used with sherpa"""
import sherpa.astro.ui as sau
extraction.run()
extraction.write(outdir=tmpdir, use_sherpa=True, overwrite=True)
sau.load_pha(str(tmpdir / "ogip_data" / "pha_obs23523.fits"))
arf = sau.get_arf()
actual = arf._arf._specresp
desired = extraction.spectrum_observations[0].aeff.data.data.value
assert_allclose(actual, desired)
def test_xmm2(self):
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
self.run_thread('xmm2')
assert len(ws) == 2
cats = set([w.category for w in ws])
assert cats == set([UserWarning])
# The order of reading the ARF and RMF is not guaranteed,
# so do not force it here when testing the two warning
# messages.
#
arffile = 'MNLup_2138_0670580101_EMOS1_S001_spec.arf'
rmffile = 'MNLup_2138_0670580101_EMOS1_S001_spec.rmf'
emsg_arf = "The minimum ENERG_LO in the ARF " + \
"'{}' ".format(arffile) + \
"was 0 and has been replaced by {}".format(EMIN)
emsg_rmf = "The minimum ENERG_LO in the RMF " + \
"'{}' ".format(rmffile) + \
"was 0 and has been replaced by {}".format(EMIN)
emsgs = set([emsg_arf, emsg_rmf])
wmsgs = set([str(w.message) for w in ws])
assert wmsgs == emsgs
assert ui.get_data().channel[0] == approx(1.0, rel=1e-4)
rmf = ui.get_rmf()
arf = ui.get_arf()
self.assertEqual(rmf.detchans, 800)
self.assertEqual(len(rmf.energ_lo), 2400)
self.assertEqual(len(rmf.energ_hi), 2400)
self.assertEqual(len(rmf.n_grp), 2400)
self.assertEqual(len(rmf.f_chan), 2394)
self.assertEqual(len(rmf.n_chan), 2394)
self.assertEqual(len(rmf.matrix), 1281216)
self.assertEqual(rmf.offset, 0)
self.assertEqual(len(rmf.e_min), 800)
self.assertEqual(len(rmf.e_max), 800)
self.assertEqual(len(arf.energ_lo), 2400)
self.assertEqual(len(arf.energ_hi), 2400)
self.assertEqual(len(arf.specresp), 2400)
etol = EMIN / 100.0
assert rmf.energ_lo[0] == approx(EMIN, rel=etol)
assert arf.energ_lo[0] == approx(EMIN, rel=etol)
def estimate_expmap(self, *args):
"""Estimate the exposure map given an ARF.
If no argumenhts are supplied then the ARF of the Sherpa
dataset associated with this obhect is used (``self.id``).
Although the arguments are listed with parameter names
below, the function **does not** accept named arguments.
It uses positional arguments and type checks to determine
the parameters.
Parameters
----------
crate
A TABLECrate, containing ``energ_lo``, ``energ_hi``,
and ``specresp`` columns.
filename : string
The name of an ARF file
xlo, xhi, y : arrays of numbers
The arrays taken to be the ``energ_lo``, ``energ_hi``, and
``specresp`` columns
Return
------
expmap : number
An estimate of the exposure map at the position
of the source, and has units of cm^2 count / self.fluxtype
Notes
-----
The ARF is linearly interpolated onto the energy grid
of the dataset and the weighted sum calculated. The
ARF is assumed to have units of cm^2 count / photon, and
be defined on a grid given in keV.
"""
nargs = len(args)
if nargs == 0:
darf = ui.get_arf(self.id)
return self._estimate_expmap(darf.energ_lo, darf.energ_hi,
darf.specresp)
else:
return self._estimate_expmap(*args)
def test_can_use_swift_data(make_data_path, clean_astro_ui):
"""A basic check that we can read in and use the Swift data.
Unlike the previous tests, that directly access the io module,
this uses the ui interface.
"""
# The Swift PHA file does not have the ANCRFILE/RESPFILE keywords
# set up, so the responses have to be manually added.
#
ui.load_pha(make_data_path(PHAFILE))
rmffile = make_data_path(RMFFILE)
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
ui.load_rmf(rmffile)
validate_replacement_warning(ws, 'RMF', rmffile)
arffile = make_data_path(ARFFILE)
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
ui.load_arf(arffile)
validate_replacement_warning(ws, 'ARF', arffile)
assert ui.get_analysis() == 'energy'
arf = ui.get_arf()
rmf = ui.get_rmf()
assert arf.energ_lo[0] == EMIN
assert rmf.energ_lo[0] == EMIN
assert rmf.e_min[0] == 0.0
ui.set_source(ui.powlaw1d.pl)
ui.set_par('pl.ampl', 0.0003)
stat = ui.calc_stat()
# This check is purely a regression test, so the value has
# not been externally validated.
#
assert_allclose(stat, 58.2813692358182)
# Pick an energy range which isn't affected by the first
# bin.
#
# Unfortunately, using a range of 0.3-8.0 gives 771 bins
# in XSPEC - channels 30 to 800 - but 770 bins in Sherpa,
# channels 31 to 800.
#
# Note that the channel numbering starts at 0:
# % dmlist target_sr.pha header,clean,raw | grep TLMIN
# TLMIN1 = 0 / Lowest legal channel number
#
# and so it's not clear when XSPEC says 30-800 what it
# means. From https://github.com/sherpa/sherpa/issues/1211#issuecomment-881647128
# we have that the first bin it is using is
# 0.29-0.30
# and the last bin is
# 7.99-8.00
# and I've checked with iplot that it has renumbered the
# channels to 1-1024 from 0-1023
#
# % dmlist swxpc0to12s6_20130101v014.rmf.gz"[ebounds][channel=28:31]" data,clean
# CHANNEL E_MIN E_MAX
# 28 0.28000000119209 0.28999999165535
# 29 0.28999999165535 0.30000001192093
# 30 0.30000001192093 0.31000000238419
# 31 0.31000000238419 0.31999999284744
# % dmlist swxpc0to12s6_20130101v014.rmf.gz"[ebounds][channel=798:801]" data,clean
# CHANNEL E_MIN E_MAX
# 798 7.9800000191 7.9899997711
# 799 7.9899997711 8.0
# 800 8.0 8.0100002289
# 801 8.0100002289 8.0200004578
#
# If I use ignore(None, 0.3); ignore(8.0, None) instead then the
# result is 771 bins (channels 31 to 800). This is because the
# e_min/max of the RMF has channel widths of 0.01 keV, starting at
# 0, so both 0.3 and 8.0 fall on a bin boundary. So, it's either a
# difference in < or <= (or > vs >=), or a rounding issue due to
# floating-point conversion leading to one bin boundary being
# slightly different in Sherpa vs XSPEC).
#
# When using ui.notice(0.3, 8.0); ui.get_indep(filter=True)
# returns 770 channels, 31 to 800.
#
# Using ui.notice(0.3, 7.995) selects channels 31 to 800.
# Using ui.notice(0.299, 8.0) selects channels 30 to 800.
# Using ui.notice(0.299, 7.995) selects channels 30 to 800.
#
ui.notice(0.299, 8.0)
# Check the selected range
pha = ui.get_data()
expected = np.zeros(1024, dtype=bool)
expected[29:800] = True
assert pha.mask == pytest.approx(expected)
assert pha.get_mask() == pytest.approx(expected)
# XSPEC 12.9.1b calculation of the statistic:
# chi sq = 203.88 from 771 bins with 769 dof
# cstat = 568.52
#
# There are known differences between XSPEC and Sherpa
# with chi2xspecvar. This only affects data sets where
# there is background subtraction, which is not the case
# here. See https://github.com/sherpa/sherpa/issues/356
#
ui.set_stat('chi2xspecvar')
stat_xvar = ui.get_stat_info()
assert len(stat_xvar) == 1
stat_xvar = stat_xvar[0]
assert stat_xvar.numpoints == 771
assert stat_xvar.dof == 769
assert_allclose(stat_xvar.statval, 203.88, rtol=0, atol=0.005)
ui.set_stat('cstat')
stat_cstat = ui.get_stat_info()
assert len(stat_cstat) == 1
stat_cstat = stat_cstat[0]
assert stat_cstat.numpoints == 771
assert stat_cstat.dof == 769
assert_allclose(stat_cstat.statval, 568.52, rtol=0, atol=0.005)
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])
# Check multiple responses have been loaded
#
d1 = ui.get_data(1)
d2 = ui.get_data(2)
assert d1.response_ids == [1, 2]
assert d2.response_ids == [1, 2]
# Unfortunately we load the same response so it's hard
# to tell the difference here!
#
assert ui.get_arf(resp_id=1).name == arf
assert ui.get_arf(resp_id=2).name == arf
assert ui.get_rmf(2, resp_id=1).name == rmf
assert ui.get_rmf(2, resp_id=2).name == rmf
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_can_use_swift_data(make_data_path):
"""A basic check that we can read in and use the Swift data.
Unlike the previous tests, that directly access the io module,
this uses the ui interface.
"""
# QUS are there pytest fixtures that ensure the state is
# clean on entry and exit?
ui.clean()
# The Swift PHA file does not have the ANCRFILE/RESPFILE keywords
# set up, so the responses have to be manually added.
#
ui.load_pha(make_data_path(PHAFILE))
ui.load_rmf(make_data_path(RMFFILE))
ui.load_arf(make_data_path(ARFFILE))
assert ui.get_analysis() == 'energy'
ui.set_source(ui.powlaw1d.pl)
ui.set_par('pl.ampl', 0.0003)
# The responses have the first bin start at an energy of 0,
# which causes issues for Sherpa. There should be a
# RuntimeWarning due to a divide by zero.
#
with pytest.warns(RuntimeWarning) as record:
stat = ui.calc_stat()
# The exact form of the message depends on the Python version;
# this could be checked, but it feels excessive for this
# particular test, which is just a regression check, so use a
# more lax approach.
#
assert len(record) == 1
assert record[0].message.args[0] in \
['divide by zero encountered in divide',
'divide by zero encountered in true_divide']
# The stat value depends on what power-law model is used. With
# xspowerlaw it is NaN, but with powlaw1d it is finite.
#
# This check is purely a regression test, so the value has
# not been externally validated.
#
# assert np.isnan(stat)
assert_allclose(stat, 58.2813692358182)
# Manually adjust the first bin to avoid this problem.
# Add in asserts just in case this gets "fixed" in the
# I/O layer (as XSPEC does).
#
arf = ui.get_arf()
rmf = ui.get_rmf()
assert arf.energ_lo[0] == 0.0
assert rmf.energ_lo[0] == 0.0
assert rmf.e_min[0] == 0.0
# The bin widths are ~ 0.005 or ~ 0.01 keV, so pick a value
# smaller than this.
#
ethresh = 1e-6
arf.energ_lo[0] = ethresh
rmf.energ_lo[0] = ethresh
rmf.e_min[0] = ethresh
# Pick an energy range which isn't affected by the first
# bin.
#
# Unfortunately, using a range of 0.3-8.0 gives 771 bins
# in XSPEC - channels 30 to 800 - but 772 bins in Sherpa.
# If I use ignore(None, 0.3); ignore(8.0, None) instead
# then the result is 771 bins. This is because the e_min/max
# of the RMF has channel widths of 0.01 keV, starting at 0,
# so both 0.3 and 8.0 fall on a bin boundary. So, it's either
# a difference in < or <= (or > vs >=), or a rounding issue
# due to floating-point conversion leading to one bin boundary
# being slightly different in Sherpa vs XSPEC).
#
# When using ui.notice(0.3, 8.0); ui.get_indep(filter=True)
# returns 772 channels, 30 to 801.
#
# Using ui.notice(0.3, 7.995) selects channels 30 to 800. So
# this range is used. Alternatively, channel 801 could have been
# excluded explicitly.
#
# ui.notice(0.3, 8.0)
ui.notice(0.3, 7.995)
# XSPEC 12.9.1b calculation of the statistic:
# chi sq = 203.88 from 771 bins with 769 dof
# cstat = 568.52
#
# There are known differences between XSPEC and Sherpa
# with chi2xspecvar. This only affects data sets where
# there is background subtraction, which is not the case
# here. See https://github.com/sherpa/sherpa/issues/356
#
ui.set_stat('chi2xspecvar')
stat_xvar = ui.get_stat_info()
assert len(stat_xvar) == 1
stat_xvar = stat_xvar[0]
assert stat_xvar.numpoints == 771
assert stat_xvar.dof == 769
assert_allclose(stat_xvar.statval, 203.88,
rtol=0, atol=0.005)
ui.set_stat('cstat')
stat_cstat = ui.get_stat_info()
assert len(stat_cstat) == 1
stat_cstat = stat_cstat[0]
assert stat_cstat.numpoints == 771
assert stat_cstat.dof == 769
assert_allclose(stat_cstat.statval, 568.52,
rtol=0, atol=0.005)
ui.clean()
def test_plot_order_multi(make_data_path, clean_astro_ui):
"""Rather than fake data, use a known dataset.
Here we pretend we have three orders but with the same
response (except that the ARF is 0.5, 0.4, 0.25 of the
normal ARF).
"""
pha = make_data_path('3c273.pi')
ui.load_pha(pha)
# It has already loaded in one response
arf = ui.get_arf(resp_id=1)
arf.specresp *= 0.5
for order, scale in enumerate([0.4, 0.25], 2):
ui.load_arf(make_data_path('3c273.arf'), resp_id=order)
ui.load_rmf(make_data_path('3c273.rmf'), resp_id=order)
arf = ui.get_arf(resp_id=order)
arf.specresp *= scale
ui.set_source(ui.powlaw1d.pl)
ui.notice(0.5, 7)
ui.ignore(3, 4)
fplot = ui.get_fit_plot()
oplot = ui.get_order_plot()
# The idea is to compare the X range of plot_fit to plot_order
# (but accessed just using the plot objects rather than creating
# an actual plot).
#
# First some safety checks
assert fplot.dataplot.xlo == pytest.approx(fplot.modelplot.xlo)
assert fplot.dataplot.xhi == pytest.approx(fplot.modelplot.xhi)
assert len(oplot.xlo) == 3
assert len(oplot.xhi) == 3
assert len(oplot.y) == 3
assert oplot.xlo[1] == pytest.approx(oplot.xlo[0])
assert oplot.xlo[2] == pytest.approx(oplot.xlo[0])
assert oplot.xhi[1] == pytest.approx(oplot.xhi[0])
assert oplot.xhi[2] == pytest.approx(oplot.xhi[0])
# We know the y values are 0.5, 0.4, 0.25 times the original arf
# so we can compare them.
#
assert oplot.y[1] == pytest.approx(oplot.y[0] * 0.4 / 0.5)
assert oplot.y[2] == pytest.approx(oplot.y[0] * 0.25 / 0.5)
xlo = oplot.xlo[0]
xhi = oplot.xhi[0]
assert len(xlo) == 564
assert xlo[0] == pytest.approx(0.46720001101493835)
assert xhi[-1] == pytest.approx(9.869600296020508)
# The model plot is technically drawn the same way as the order plot
# (ungrouped) but it uses different code (sherpa.astro.plot.ModelHistogram)
# so let's compare.
#
mplot = ui.get_model_plot()
assert mplot.xlo[0] == pytest.approx(0.46720001101493835)
assert mplot.xhi[-1] == pytest.approx(9.869600296020508)
# Also compare to the fit plot (which is grouped)
#
assert fplot.modelplot.xlo[0] == pytest.approx(0.46720001101493835)
assert fplot.modelplot.xhi[-1] == pytest.approx(9.869600296020508)
def test_fake_pha_issue_1209(make_data_path, clean_astro_ui, tmp_path):
"""Check issue #1209.
See also sherpa/astro/tests/test_fake_pha.py for
test_fake_pha_has_valid_ogip_keywords_all_fake
test_fake_pha_has_valid_ogip_keywords_from_real
The session fake_pha includes quite a lot of logic which
makes that the test case for #1209 should be done at this
level, to complement the tests mentioned above.
"""
infile = make_data_path("acisf01575_001N001_r0085_pha3.fits.gz")
ui.load_pha(infile)
ui.set_source(ui.powlaw1d.pl)
pl.gamma = 1.8
pl.ampl = 1e-4
arf = ui.get_arf()
rmf = ui.get_rmf()
# check the TOTCTS setting in the input file
d1 = ui.get_data()
assert d1.header["TOTCTS"] == 855
assert d1.counts.sum() == 855
ui.set_source("newid", pl)
ui.fake_pha("newid",
exposure=ui.get_exposure(),
bkg=ui.get_bkg(),
rmf=rmf,
arf=arf,
backscal=ui.get_backscal())
stat = ui.calc_stat("newid")
outfile = tmp_path / "sim.pha"
ui.save_pha("newid", str(outfile))
ui.load_pha(3, str(outfile))
d3 = ui.get_data(3)
assert isinstance(d3, ui.DataPHA)
assert d3.exposure == pytest.approx(37664.157219191)
assert d3.areascal == pytest.approx(1.0)
assert d3.backscal == pytest.approx(2.2426552620567e-06)
assert d3.background_ids == []
assert d3.response_ids == []
# check the header
hdr = d3.header
assert hdr["TELESCOP"] == "CHANDRA"
assert hdr["INSTRUME"] == "ACIS"
assert hdr["FILTER"] == "none"
# check some other values related to #1209 and #488 (OGIP)
#
assert "TOTCTS" not in hdr
assert hdr["GROUPING"] == 0
assert hdr["QUALITY"] == 0
assert hdr["SYS_ERR"] == 0
# We should get the same value - the responses are not written
# to the temporary directory and so we need to load them
# directly.
#
ui.set_rmf(3, rmf)
ui.set_arf(3, arf)
ui.set_source(3, pl)
assert ui.calc_stat(3) == pytest.approx(stat)
def _get_chart_spectrum(id=None,
elow=None,
ehigh=None,
ewidth=None,
norm=None):
"""Helper routine for *_chart_spectrum."""
# What source expression are we using?
# get_model/source will throw an IdentifierErr if the expression
# is not defined; we do not, at present catch/re-throw this
#
if id is None:
id = s.get_default_id()
mdl = s.get_source(id)
# What energy grid to use? Since we do not want to restrict users
# to only using PHA datasets (i.e. if I just want to create
# something simple) then we have to look for a range of errors
# from get_arf
#
if elow is None or ehigh is None or ewidth is None:
try:
arf = s.get_arf(id)
except (IdentifierErr, ArgumentErr):
# a) PHA dataset, no ARF
# b) Assume this means the dataset is not derived from the
# PHA class
arf = None
if arf is None:
emsg = "No ARF found for dataset {} ".format(repr(id)) + \
"so unable to create energy grid"
raise TypeError(emsg)
if elow is None:
elow = arf.energ_lo[0]
if ehigh is None:
ehigh = arf.energ_hi[-1]
if ewidth is None:
# Assume constant grid spacing in the ARF
de = arf.energ_hi[-1] - arf.energ_lo[0]
nelem = np.size(arf.energ_lo)
ewidth = de * 1.0 / nelem
if elow >= ehigh:
emsg = "elow is >= ehigh: " + \
"elow={} ehigh={}".format(elow, ehigh)
raise TypeError(emsg)
if ewidth <= 0.0:
raise TypeError("ewidth is <= 0.0: ewidth={0}".format(ewidth))
# The following is wasteful if we have an ARF and the user
# supplies no elow, ehigh, or ewidth arguments.
#
# Should I check that nbins is a sensible number (e.g. >= 2)?
#
nbins = 1 + np.rint((ehigh - elow) / ewidth)
erange = elow + ewidth * np.arange(nbins)
elo = erange[:-1]
ehi = erange[1:]
flux = mdl(elo, ehi)
emid = 0.5 * (ehi + elo)
# do we want to renormalize?
if norm is not None:
flux *= norm
return {
"x": emid,
"xlo": elo,
"xhi": ehi,
"y": flux,
"id": id,
"model": mdl.name
}
def test_can_use_swift_data(make_data_path):
"""A basic check that we can read in and use the Swift data.
Unlike the previous tests, that directly access the io module,
this uses the ui interface.
"""
# QUS are there pytest fixtures that ensure the state is
# clean on entry and exit?
ui.clean()
# The Swift PHA file does not have the ANCRFILE/RESPFILE keywords
# set up, so the responses have to be manually added.
#
ui.load_pha(make_data_path(PHAFILE))
rmffile = make_data_path(RMFFILE)
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
ui.load_rmf(rmffile)
validate_replacement_warning(ws, 'RMF', rmffile)
arffile = make_data_path(ARFFILE)
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
ui.load_arf(arffile)
validate_replacement_warning(ws, 'ARF', arffile)
assert ui.get_analysis() == 'energy'
arf = ui.get_arf()
rmf = ui.get_rmf()
assert arf.energ_lo[0] == EMIN
assert rmf.energ_lo[0] == EMIN
assert rmf.e_min[0] == 0.0
ui.set_source(ui.powlaw1d.pl)
ui.set_par('pl.ampl', 0.0003)
stat = ui.calc_stat()
# This check is purely a regression test, so the value has
# not been externally validated.
#
assert_allclose(stat, 58.2813692358182)
# Pick an energy range which isn't affected by the first
# bin.
#
# Unfortunately, using a range of 0.3-8.0 gives 771 bins
# in XSPEC - channels 30 to 800 - but 772 bins in Sherpa.
# If I use ignore(None, 0.3); ignore(8.0, None) instead
# then the result is 771 bins. This is because the e_min/max
# of the RMF has channel widths of 0.01 keV, starting at 0,
# so both 0.3 and 8.0 fall on a bin boundary. So, it's either
# a difference in < or <= (or > vs >=), or a rounding issue
# due to floating-point conversion leading to one bin boundary
# being slightly different in Sherpa vs XSPEC).
#
# When using ui.notice(0.3, 8.0); ui.get_indep(filter=True)
# returns 772 channels, 30 to 801.
#
# Using ui.notice(0.3, 7.995) selects channels 30 to 800. So
# this range is used. Alternatively, channel 801 could have been
# excluded explicitly.
#
# ui.notice(0.3, 8.0)
ui.notice(0.3, 7.995)
# XSPEC 12.9.1b calculation of the statistic:
# chi sq = 203.88 from 771 bins with 769 dof
# cstat = 568.52
#
# There are known differences between XSPEC and Sherpa
# with chi2xspecvar. This only affects data sets where
# there is background subtraction, which is not the case
# here. See https://github.com/sherpa/sherpa/issues/356
#
ui.set_stat('chi2xspecvar')
stat_xvar = ui.get_stat_info()
assert len(stat_xvar) == 1
stat_xvar = stat_xvar[0]
assert stat_xvar.numpoints == 771
assert stat_xvar.dof == 769
assert_allclose(stat_xvar.statval, 203.88,
rtol=0, atol=0.005)
ui.set_stat('cstat')
stat_cstat = ui.get_stat_info()
assert len(stat_cstat) == 1
stat_cstat = stat_cstat[0]
assert stat_cstat.numpoints == 771
assert stat_cstat.dof == 769
assert_allclose(stat_cstat.statval, 568.52,
rtol=0, atol=0.005)
ui.clean()
type=str,
help="Spectra files (*.pi, *.pha)")
args = parser.parse_args()
from sherpa.astro.ui import load_pha, get_rmf, get_arf, get_fit_plot, load_table_model, set_xsabund, set_xsxsect, ignore, notice, set_xlog, set_ylog
from sherpa.astro.ui import xsapec, set_full_model, get_bkg_model, get_bkg_scale, set_stat, get_bkg, group_adapt, set_analysis, calc_stat, get_data, set_model, get_response, get_model, calc_energy_flux
id = 1
filename = args.filenames[0]
elo, ehi = args.energyrange.split(':')
elo, ehi = float(elo), float(ehi)
load_pha(id, filename)
try:
assert get_rmf(id).energ_lo[0] > 0
assert get_arf(id).energ_lo[0] > 0
assert (get_bkg(id).counts > 0).sum() > 0
except:
traceback.print_exc()
sys.exit(0)
set_xlog()
set_ylog()
set_stat('cstat')
set_xsabund('wilm')
set_xsxsect('vern')
set_analysis(id, 'ener', 'counts')
ignore(None, elo)
ignore(ehi, None)
notice(elo, ehi)
def test_can_use_swift_data(make_data_path, is_known_warning):
"""A basic check that we can read in and use the Swift data.
Unlike the previous tests, that directly access the io module,
this uses the ui interface.
"""
# QUS are there pytest fixtures that ensure the state is
# clean on entry and exit?
ui.clean()
# The Swift PHA file does not have the ANCRFILE/RESPFILE keywords
# set up, so the responses have to be manually added.
#
ui.load_pha(make_data_path(PHAFILE))
rmffile = make_data_path(RMFFILE)
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
ui.load_rmf(rmffile)
validate_replacement_warning(ws, 'RMF', rmffile, is_known_warning)
arffile = make_data_path(ARFFILE)
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter("always")
ui.load_arf(arffile)
validate_replacement_warning(ws, 'ARF', arffile, is_known_warning)
assert ui.get_analysis() == 'energy'
arf = ui.get_arf()
rmf = ui.get_rmf()
assert arf.energ_lo[0] == EMIN
assert rmf.energ_lo[0] == EMIN
assert rmf.e_min[0] == 0.0
ui.set_source(ui.powlaw1d.pl)
ui.set_par('pl.ampl', 0.0003)
stat = ui.calc_stat()
# This check is purely a regression test, so the value has
# not been externally validated.
#
assert_allclose(stat, 58.2813692358182)
# Pick an energy range which isn't affected by the first
# bin.
#
# Unfortunately, using a range of 0.3-8.0 gives 771 bins
# in XSPEC - channels 30 to 800 - but 772 bins in Sherpa.
# If I use ignore(None, 0.3); ignore(8.0, None) instead
# then the result is 771 bins. This is because the e_min/max
# of the RMF has channel widths of 0.01 keV, starting at 0,
# so both 0.3 and 8.0 fall on a bin boundary. So, it's either
# a difference in < or <= (or > vs >=), or a rounding issue
# due to floating-point conversion leading to one bin boundary
# being slightly different in Sherpa vs XSPEC).
#
# When using ui.notice(0.3, 8.0); ui.get_indep(filter=True)
# returns 772 channels, 30 to 801.
#
# Using ui.notice(0.3, 7.995) selects channels 30 to 800. So
# this range is used. Alternatively, channel 801 could have been
# excluded explicitly.
#
# ui.notice(0.3, 8.0)
ui.notice(0.3, 7.995)
# XSPEC 12.9.1b calculation of the statistic:
# chi sq = 203.88 from 771 bins with 769 dof
# cstat = 568.52
#
# There are known differences between XSPEC and Sherpa
# with chi2xspecvar. This only affects data sets where
# there is background subtraction, which is not the case
# here. See https://github.com/sherpa/sherpa/issues/356
#
ui.set_stat('chi2xspecvar')
stat_xvar = ui.get_stat_info()
assert len(stat_xvar) == 1
stat_xvar = stat_xvar[0]
assert stat_xvar.numpoints == 771
assert stat_xvar.dof == 769
assert_allclose(stat_xvar.statval, 203.88,
rtol=0, atol=0.005)
ui.set_stat('cstat')
stat_cstat = ui.get_stat_info()
assert len(stat_cstat) == 1
stat_cstat = stat_cstat[0]
assert stat_cstat.numpoints == 771
assert stat_cstat.dof == 769
assert_allclose(stat_cstat.statval, 568.52,
rtol=0, atol=0.005)
ui.clean()
import datastack
from acis_bkg_model import acis_bkg_model
import sherpa.astro.ui as ui
ds = datastack.DataStack()
ds[1].load_pha("acisf04938_000N002_r0043_pha3.fits")
ds[2].load_pha("acisf07867_000N001_r0002_pha3.fits")
detnam = "acis2i"
for dataset in ds.datasets:
id_ = dataset["id"]
rmf = ui.get_rmf(id_)
arf = ui.get_arf(id_)
ui.load_bkg_arf(id_, arf.name)
bkg_arf = ui.get_bkg_arf(id_)
bkg_rmf = ui.get_bkg_rmf(id_)
bkg_arf.specresp = bkg_arf.specresp * 0 + 100.0
bkg_scale = ui.get_data(id_).sum_background_data(lambda x, y: 1)
bkg_model = bkg_rmf(bkg_arf(ui.const1d.bkg_constID * acis_bkg_model(detnam)))
src_model = rmf(arf(ui.const1d.src_constID * ui.powlaw1d.powlaw))
ds[id_].set_full_model(src_model + bkg_scale * bkg_model)
ds[id_].set_bkg_full_model(bkg_model)
ds[1].set_par("src_const.c0", 1.0)
ds[1].freeze("src_const")
ds.ignore(None, 0.5)
ds.ignore(7, None)
ds.fit()