def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = PowerLawSpectralModel(index=2,
amplitude=1e5 / u.TeV,
reference=0.1 * u.TeV)
self.bkg_model = PowerLawSpectralModel(index=3,
amplitude=1e4 / u.TeV,
reference=0.1 * u.TeV)
self.alpha = 0.1
random_state = get_random_state(23)
npred = self.source_model.integral(binning[:-1], binning[1:])
source_counts = random_state.poisson(npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
# Currently it's necessary to specify a lifetime
self.src.livetime = 1 * u.s
npred_bkg = self.bkg_model.integral(binning[:-1], binning[1:])
bkg_counts = random_state.poisson(npred_bkg)
off_counts = random_state.poisson(npred_bkg * 1.0 / self.alpha)
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_counts)
self.off = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=off_counts)
def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = PowerLawSpectralModel(index=2,
amplitude=1e5 *
u.Unit("cm-2 s-1 TeV-1"),
reference=0.1 * u.TeV)
bkg_model = PowerLawSpectralModel(index=3,
amplitude=1e4 *
u.Unit("cm-2 s-1 TeV-1"),
reference=0.1 * u.TeV)
self.alpha = 0.1
random_state = get_random_state(23)
npred = self.source_model.integral(binning[:-1], binning[1:]).value
source_counts = random_state.poisson(npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
self.src.livetime = 1 * u.s
self.aeff = EffectiveAreaTable.from_constant(binning, "1 cm2")
npred_bkg = bkg_model.integral(binning[:-1], binning[1:]).value
bkg_counts = random_state.poisson(npred_bkg)
off_counts = random_state.poisson(npred_bkg * 1.0 / self.alpha)
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_counts)
self.off = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=off_counts)
def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = PowerLawSpectralModel(index=2.1,
amplitude=1e5 / u.TeV / u.s,
reference=0.1 * u.TeV)
self.livetime = 100 * u.s
bkg_rate = np.ones(self.nbins) / u.s
bkg_expected = bkg_rate * self.livetime
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_expected)
random_state = get_random_state(23)
self.npred = (self.source_model.integral(binning[:-1], binning[1:]) *
self.livetime)
self.npred += bkg_expected
source_counts = random_state.poisson(self.npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
self.dataset = SpectrumDataset(
model=self.source_model,
counts=self.src,
livetime=self.livetime,
background=self.bkg,
)
def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = PowerLawSpectralModel(index=2.1,
amplitude=1e5 *
u.Unit("cm-2 s-1 TeV-1"),
reference=0.1 * u.TeV)
self.livetime = 100 * u.s
aeff = EffectiveAreaTable.from_constant(binning, "1 cm2")
bkg_rate = np.ones(self.nbins) / u.s
bkg_expected = (bkg_rate * self.livetime).to_value("")
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_expected)
random_state = get_random_state(23)
flux = self.source_model.integral(binning[:-1], binning[1:])
self.npred = (flux * aeff.data.data[0] * self.livetime).to_value("")
self.npred += bkg_expected
source_counts = random_state.poisson(self.npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
self.dataset = SpectrumDataset(
model=self.source_model,
counts=self.src,
aeff=aeff,
livetime=self.livetime,
background=self.bkg,
)
def setup(self):
etrue = np.logspace(-1, 1, 10) * u.TeV
self.e_true = etrue
ereco = np.logspace(-1, 1, 5) * u.TeV
elo = ereco[:-1]
ehi = ereco[1:]
self.e_reco = ereco
self.aeff = EffectiveAreaTable(etrue[:-1], etrue[1:],
np.ones(9) * u.cm**2)
self.edisp = EDispKernel.from_diagonal_response(etrue, ereco)
data = np.ones(elo.shape)
data[-1] = 0 # to test stats calculation with empty bins
self.on_counts = CountsSpectrum(elo, ehi, data)
self.off_counts = CountsSpectrum(elo, ehi, np.ones(elo.shape) * 10)
start = u.Quantity([0], "s")
stop = u.Quantity([1000], "s")
time_ref = Time("2010-01-01 00:00:00.0")
self.gti = GTI.create(start, stop, time_ref)
self.livetime = self.gti.time_sum
self.dataset = SpectrumDatasetOnOff(
counts=self.on_counts,
counts_off=self.off_counts,
aeff=self.aeff,
edisp=self.edisp,
livetime=self.livetime,
acceptance=np.ones(elo.shape),
acceptance_off=np.ones(elo.shape) * 10,
name="test",
gti=self.gti,
)
def make_observation_list():
"""obs with dummy IRF"""
nbin = 3
energy = np.logspace(-1, 1, nbin + 1) * u.TeV
livetime = 2 * u.h
data_on = np.arange(nbin)
dataoff_1 = np.ones(3)
dataoff_2 = np.ones(3) * 3
dataoff_1[1] = 0
dataoff_2[1] = 0
on_vector = CountsSpectrum(energy_lo=energy[:-1],
energy_hi=energy[1:],
data=data_on)
off_vector1 = CountsSpectrum(energy_lo=energy[:-1],
energy_hi=energy[1:],
data=dataoff_1)
off_vector2 = CountsSpectrum(energy_lo=energy[:-1],
energy_hi=energy[1:],
data=dataoff_2)
aeff = EffectiveAreaTable.from_constant(energy, "1 cm2")
edisp = EDispKernel.from_gauss(e_true=energy,
e_reco=energy,
sigma=0.2,
bias=0)
time_ref = Time("2010-01-01")
gti1 = make_gti({
"START": [5, 6, 1, 2],
"STOP": [8, 7, 3, 4]
},
time_ref=time_ref)
gti2 = make_gti({"START": [14], "STOP": [15]}, time_ref=time_ref)
obs1 = SpectrumDatasetOnOff(
counts=on_vector,
counts_off=off_vector1,
aeff=aeff,
edisp=edisp,
livetime=livetime,
mask_safe=np.ones(on_vector.energy.nbin, dtype=bool),
acceptance=1,
acceptance_off=2,
name="1",
gti=gti1,
)
obs2 = SpectrumDatasetOnOff(
counts=on_vector,
counts_off=off_vector2,
aeff=aeff,
edisp=edisp,
livetime=livetime,
mask_safe=np.ones(on_vector.energy.nbin, dtype=bool),
acceptance=1,
acceptance_off=4,
name="2",
gti=gti2,
)
obs_list = [obs1, obs2]
return obs_list
def setup(self):
etrue = np.logspace(-1, 1, 10) * u.TeV
self.e_true = etrue
ereco = np.logspace(-1, 1, 5) * u.TeV
elo = ereco[:-1]
ehi = ereco[1:]
self.aeff = EffectiveAreaTable(etrue[:-1], etrue[1:],
np.ones(9) * u.cm**2)
self.edisp = EnergyDispersion.from_diagonal_response(etrue, ereco)
data = np.ones(elo.shape)
data[-1] = 0 # to test stats calculation with empty bins
self.on_counts = CountsSpectrum(elo, ehi, data)
self.off_counts = CountsSpectrum(elo, ehi, np.ones(elo.shape) * 10)
self.livetime = 1000 * u.s
self.dataset = SpectrumDatasetOnOff(
counts=self.on_counts,
counts_off=self.off_counts,
aeff=self.aeff,
edisp=self.edisp,
livetime=self.livetime,
acceptance=np.ones(elo.shape),
acceptance_off=np.ones(elo.shape) * 10,
obs_id="test",
)
def _counts_spectrum(self, ebounds):
from gammapy.spectrum import CountsSpectrum
if not ebounds:
ebounds = self._default_plot_ebounds()
spec = CountsSpectrum(energy_lo=ebounds[:-1], energy_hi=ebounds[1:])
spec.fill_energy(self.energy)
return spec
def get_spectrum(self, region=None, func=np.nansum):
"""Extract spectrum in a given region.
The spectrum can be computed by summing (or, more generally, applying ``func``)
along the spatial axes in each energy bin. This occurs only inside the ``region``,
which by default is assumed to be the whole spatial extension of the map.
Parameters
----------
region: `~regions.Region`
Region (pixel or sky regions accepted).
func : numpy.ufunc
Function to reduce the data.
Returns
-------
spectrum : `~gammapy.spectrum.CountsSpectrum`
Spectrum in the given region.
"""
from gammapy.spectrum import CountsSpectrum
energy_axis = self.geom.get_axis_by_name("energy")
if region:
mask = self.geom.region_mask([region])
data = self.data[mask].reshape(energy_axis.nbin, -1)
data = func(data, axis=1)
else:
data = func(self.data, axis=(1, 2))
edges = energy_axis.edges
return CountsSpectrum(data=data,
energy_lo=edges[:-1],
energy_hi=edges[1:],
unit=self.unit)
def test_fake(self):
"""Test the fake dataset"""
source_model = SkyModel(spectral_model=PowerLawSpectralModel())
dataset = SpectrumDatasetOnOff(
counts=self.on_counts,
counts_off=self.off_counts,
models=source_model,
aeff=self.aeff,
livetime=self.livetime,
edisp=self.edisp,
acceptance=1,
acceptance_off=10,
)
real_dataset = dataset.copy()
# Define background model counts
elo = self.on_counts.energy.edges[:-1]
ehi = self.on_counts.energy.edges[1:]
data = np.ones(self.on_counts.data.shape)
background_model = CountsSpectrum(elo, ehi, data)
dataset.fake(background_model=background_model,
random_state=314,
name="fake")
assert real_dataset.counts.data.shape == dataset.counts.data.shape
assert real_dataset.counts_off.data.shape == dataset.counts_off.data.shape
assert (real_dataset.counts.energy.center.mean() ==
dataset.counts.energy.center.mean())
assert real_dataset.acceptance.mean() == dataset.acceptance.mean()
assert real_dataset.acceptance_off.mean(
) == dataset.acceptance_off.mean()
assert dataset.counts_off.data.sum() == 39
assert dataset.counts.data.sum() == 5
assert dataset.name == "fake"
def sens():
etrue = np.logspace(0, 1, 21) * u.TeV
elo = etrue[:-1]
ehi = etrue[1:]
area = np.zeros(20) + 1e6 * u.m**2
arf = EffectiveAreaTable(energy_lo=elo, energy_hi=ehi, data=area)
ereco = np.logspace(0, 1, 5) * u.TeV
rmf = EnergyDispersion.from_diagonal_response(etrue, ereco)
bkg_array = np.ones(4)
bkg_array[-1] = 1e-3
bkg = CountsSpectrum(energy_lo=ereco[:-1],
energy_hi=ereco[1:],
data=bkg_array,
unit="s-1")
sens = SensitivityEstimator(arf=arf,
rmf=rmf,
bkg=bkg,
livetime=1 * u.h,
index=2,
gamma_min=20,
alpha=0.2)
sens.run()
return sens
class TestSimpleFit:
"""Test fit on counts spectra without any IRFs"""
def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = PowerLawSpectralModel(index=2,
amplitude=1e5 / u.TeV,
reference=0.1 * u.TeV)
self.bkg_model = PowerLawSpectralModel(index=3,
amplitude=1e4 / u.TeV,
reference=0.1 * u.TeV)
self.alpha = 0.1
random_state = get_random_state(23)
npred = self.source_model.integral(binning[:-1], binning[1:])
source_counts = random_state.poisson(npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
# Currently it's necessary to specify a lifetime
self.src.livetime = 1 * u.s
npred_bkg = self.bkg_model.integral(binning[:-1], binning[1:])
bkg_counts = random_state.poisson(npred_bkg)
off_counts = random_state.poisson(npred_bkg * 1.0 / self.alpha)
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_counts)
self.off = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=off_counts)
def test_wstat(self):
"""WStat with on source and background spectrum"""
on_vector = self.src.copy()
on_vector.data += self.bkg.data
obs = SpectrumDatasetOnOff(
counts=on_vector,
counts_off=self.off,
acceptance=1,
acceptance_off=1 / self.alpha,
)
obs.model = self.source_model
self.source_model.parameters.index = 1.12
fit = Fit(obs)
result = fit.run()
pars = self.source_model.parameters
assert_allclose(pars["index"].value, 1.997342, rtol=1e-3)
assert_allclose(pars["amplitude"].value, 100245.187067, rtol=1e-3)
assert_allclose(result.total_stat, 30.022316, rtol=1e-3)
class TestCountsSpectrum:
def setup(self):
self.counts = [0, 0, 2, 5, 17, 3]
self.bins = energy_logspace(1, 10, 7, "TeV")
self.spec = CountsSpectrum(data=self.counts,
energy_lo=self.bins[:-1],
energy_hi=self.bins[1:])
def test_wrong_init(self):
bins = energy_logspace(1, 10, 8, "TeV")
with pytest.raises(ValueError):
CountsSpectrum(data=self.counts,
energy_lo=bins[:-1],
energy_hi=bins[1:])
@requires_dependency("matplotlib")
def test_plot(self):
with mpl_plot_check():
self.spec.plot(show_energy=1 * u.TeV)
with mpl_plot_check():
self.spec.plot_hist()
with mpl_plot_check():
self.spec.peek()
def test_io(self, tmpdir):
filename = tmpdir / "test.fits"
self.spec.write(filename)
spec2 = CountsSpectrum.read(filename)
assert_quantity_allclose(spec2.energy.edges, self.bins)
def test_downsample(self):
rebinned_spec = self.spec.downsample(2)
assert rebinned_spec.energy.nbin == self.spec.energy.nbin / 2
assert rebinned_spec.data.shape[0] == self.spec.data.shape[0] / 2
assert rebinned_spec.total_counts == self.spec.total_counts
idx = rebinned_spec.energy.coord_to_idx([2, 3, 5] * u.TeV)
actual = rebinned_spec.data[idx]
desired = [0, 7, 20]
assert (actual == desired).all()
def spectrum_dataset():
e_true = np.logspace(0, 1, 21) * u.TeV
e_reco = np.logspace(0, 1, 5) * u.TeV
aeff = EffectiveAreaTable.from_constant(value=1e6 * u.m**2, energy=e_true)
edisp = EDispKernel.from_diagonal_response(e_true, e_reco)
data = 3600 * np.ones(4)
data[-1] *= 1e-3
background = CountsSpectrum(energy_lo=e_reco[:-1],
energy_hi=e_reco[1:],
data=data)
return SpectrumDataset(aeff=aeff,
livetime="1h",
edisp=edisp,
background=background)
def test_spectrum_dataset_stack_diagonal_safe_mask(self):
aeff = EffectiveAreaTable.from_parametrization(self.src.energy.edges,
"HESS")
edisp = EDispKernel.from_diagonal_response(self.src.energy.edges,
self.src.energy.edges)
livetime = self.livetime
dataset1 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime,
aeff=aeff,
edisp=edisp,
background=self.bkg.copy(),
)
livetime2 = 0.5 * livetime
aeff2 = EffectiveAreaTable(self.src.energy.edges[:-1],
self.src.energy.edges[1:],
2 * aeff.data.data)
bkg2 = CountsSpectrum(
self.src.energy.edges[:-1],
self.src.energy.edges[1:],
data=2 * self.bkg.data,
)
safe_mask2 = np.ones_like(self.src.data, bool)
safe_mask2[0] = False
dataset2 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime2,
aeff=aeff2,
edisp=edisp,
background=bkg2,
mask_safe=safe_mask2,
)
dataset1.stack(dataset2)
assert_allclose(dataset1.counts.data[1:], self.src.data[1:] * 2)
assert_allclose(dataset1.counts.data[0], self.src.data[0])
assert dataset1.livetime == 1.5 * self.livetime
assert_allclose(dataset1.background.data[1:], 3 * self.bkg.data[1:])
assert_allclose(dataset1.background.data[0], self.bkg.data[0])
assert_allclose(
dataset1.aeff.data.data.to_value("m2"),
4.0 / 3 * aeff.data.data.to_value("m2"),
)
assert_allclose(dataset1.edisp.pdf_matrix[1:], edisp.pdf_matrix[1:])
assert_allclose(dataset1.edisp.pdf_matrix[0],
0.5 * edisp.pdf_matrix[0])
def plot_energy_hist(self, ax=None, ebounds=None, **kwargs):
"""
A plot showing counts as a function of energy.
Convert to a `~gammapy.spectrum.CountsSpectrum` internally
"""
if ebounds is None:
emin = np.min(self['ENERGY'].quantity)
emax = np.max(self['ENERGY'].quantity)
ebounds = EnergyBounds.equal_log_spacing(emin, emax, 100)
from gammapy.spectrum import CountsSpectrum
spec = CountsSpectrum.from_eventlist(self, ebounds)
spec.plot(ax=ax, **kwargs)
return ax
def plot_energy_hist(self, ax=None, ebounds=None, **kwargs):
"""
A plot showing counts as a function of energy.
Convert to a `~gammapy.spectrum.CountsSpectrum` internally
"""
if ebounds is None:
emin = np.min(self['ENERGY'].quantity)
emax = np.max(self['ENERGY'].quantity)
ebounds = EnergyBounds.equal_log_spacing(emin, emax, 100)
from gammapy.spectrum import CountsSpectrum
spec = CountsSpectrum.from_eventlist(self, ebounds)
spec.plot(ax=ax, **kwargs)
return ax
def setup(self):
self.counts = [0, 0, 2, 5, 17, 3]
self.bins = energy_logspace(1, 10, 7, "TeV")
self.spec = CountsSpectrum(
data=self.counts, energy_lo=self.bins[:-1], energy_hi=self.bins[1:]
)
def test_io(self, tmpdir):
filename = tmpdir / "test.fits"
self.spec.write(filename)
spec2 = CountsSpectrum.read(filename)
assert_quantity_allclose(spec2.energy.edges, self.bins)
class TestSpectrumDataset:
"""Test fit on counts spectra without any IRFs"""
def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = SkyModel(spectral_model=PowerLawSpectralModel(
index=2.1,
amplitude=1e5 * u.Unit("cm-2 s-1 TeV-1"),
reference=0.1 * u.TeV,
))
self.livetime = 100 * u.s
aeff = EffectiveAreaTable.from_constant(binning, "1 cm2")
bkg_rate = np.ones(self.nbins) / u.s
bkg_expected = (bkg_rate * self.livetime).to_value("")
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_expected)
random_state = get_random_state(23)
flux = self.source_model.spectral_model.integral(
binning[:-1], binning[1:])
self.npred = (flux * aeff.data.data[0] * self.livetime).to_value("")
self.npred += bkg_expected
source_counts = random_state.poisson(self.npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
self.dataset = SpectrumDataset(
models=self.source_model,
counts=self.src,
aeff=aeff,
livetime=self.livetime,
background=self.bkg,
name="test",
)
def test_data_shape(self):
assert self.dataset.data_shape[0] == self.nbins
def test_energy_range(self):
energy_range = self.dataset.energy_range
assert energy_range.unit == u.TeV
assert_allclose(energy_range.to_value("TeV"), [0.1, 10.0])
def test_cash(self):
"""Simple CASH fit to the on vector"""
fit = Fit([self.dataset])
result = fit.run()
# assert result.success
assert "minuit" in repr(result)
npred = self.dataset.npred().data.sum()
assert_allclose(npred, self.npred.sum(), rtol=1e-3)
assert_allclose(result.total_stat, -18087404.624, rtol=1e-3)
pars = result.parameters
assert_allclose(pars["index"].value, 2.1, rtol=1e-2)
assert_allclose(pars.error("index"), 0.00127, rtol=1e-2)
assert_allclose(pars["amplitude"].value, 1e5, rtol=1e-3)
assert_allclose(pars.error("amplitude"), 153.450, rtol=1e-2)
def test_fake(self):
"""Test the fake dataset"""
real_dataset = self.dataset.copy()
self.dataset.fake(314)
assert real_dataset.counts.data.shape == self.dataset.counts.data.shape
assert real_dataset.background.data.sum(
) == self.dataset.background.data.sum()
assert int(real_dataset.counts.data.sum()) == 907010
assert self.dataset.counts.data.sum() == 907331
def test_incorrect_mask(self):
mask_fit = np.ones(self.nbins, dtype=np.dtype("float"))
with pytest.raises(ValueError):
SpectrumDataset(
models=self.source_model,
counts=self.src,
livetime=self.livetime,
mask_fit=mask_fit,
background=self.bkg,
)
def test_set_model(self):
aeff = EffectiveAreaTable.from_parametrization(self.src.energy.edges,
"HESS")
edisp = EDispKernel.from_diagonal_response(self.src.energy.edges,
self.src.energy.edges)
dataset = SpectrumDataset(None, self.src, self.livetime, None, aeff,
edisp, self.bkg)
spectral_model = PowerLawSpectralModel()
model = SkyModel(spectral_model=spectral_model, name="test")
dataset.models = model
assert dataset.models["test"] is model
models = Models([model])
dataset.models = models
assert dataset.models["test"] is model
def test_npred_models(self):
e_reco = MapAxis.from_energy_bounds("1 TeV", "10 TeV", nbin=3).edges
dataset = SpectrumDataset.create(e_reco=e_reco)
dataset.livetime = 1 * u.h
dataset.aeff.data.data += 1e10 * u.Unit("cm2")
pwl_1 = PowerLawSpectralModel(index=2)
pwl_2 = PowerLawSpectralModel(index=2)
model_1 = SkyModel(spectral_model=pwl_1)
model_2 = SkyModel(spectral_model=pwl_2)
dataset.models = Models([model_1, model_2])
npred = dataset.npred()
assert_allclose(npred.data.sum(), 64.8)
def test_str(self):
assert "SpectrumDataset" in str(self.dataset)
def test_spectrumdataset_create(self):
e_reco = u.Quantity([0.1, 1, 10.0], "TeV")
e_true = u.Quantity([0.05, 0.5, 5, 20.0], "TeV")
empty_dataset = SpectrumDataset.create(e_reco, e_true, name="test")
assert empty_dataset.name == "test"
assert empty_dataset.counts.total_counts == 0
assert empty_dataset.data_shape[0] == 2
assert empty_dataset.background.total_counts == 0
assert empty_dataset.background.energy.nbin == 2
assert empty_dataset.aeff.data.axis("energy").nbin == 3
assert empty_dataset.edisp.data.axis("e_reco").nbin == 2
assert empty_dataset.livetime.value == 0
assert len(empty_dataset.gti.table) == 0
assert empty_dataset.energy_range[0] is None
assert_allclose(empty_dataset.mask_safe, 0)
def test_spectrum_dataset_stack_diagonal_safe_mask(self):
aeff = EffectiveAreaTable.from_parametrization(self.src.energy.edges,
"HESS")
edisp = EDispKernel.from_diagonal_response(self.src.energy.edges,
self.src.energy.edges)
livetime = self.livetime
dataset1 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime,
aeff=aeff,
edisp=edisp,
background=self.bkg.copy(),
)
livetime2 = 0.5 * livetime
aeff2 = EffectiveAreaTable(self.src.energy.edges[:-1],
self.src.energy.edges[1:],
2 * aeff.data.data)
bkg2 = CountsSpectrum(
self.src.energy.edges[:-1],
self.src.energy.edges[1:],
data=2 * self.bkg.data,
)
safe_mask2 = np.ones_like(self.src.data, bool)
safe_mask2[0] = False
dataset2 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime2,
aeff=aeff2,
edisp=edisp,
background=bkg2,
mask_safe=safe_mask2,
)
dataset1.stack(dataset2)
assert_allclose(dataset1.counts.data[1:], self.src.data[1:] * 2)
assert_allclose(dataset1.counts.data[0], self.src.data[0])
assert dataset1.livetime == 1.5 * self.livetime
assert_allclose(dataset1.background.data[1:], 3 * self.bkg.data[1:])
assert_allclose(dataset1.background.data[0], self.bkg.data[0])
assert_allclose(
dataset1.aeff.data.data.to_value("m2"),
4.0 / 3 * aeff.data.data.to_value("m2"),
)
assert_allclose(dataset1.edisp.pdf_matrix[1:], edisp.pdf_matrix[1:])
assert_allclose(dataset1.edisp.pdf_matrix[0],
0.5 * edisp.pdf_matrix[0])
def test_spectrum_dataset_stack_nondiagonal_no_bkg(self):
aeff = EffectiveAreaTable.from_parametrization(self.src.energy.edges,
"HESS")
edisp1 = EDispKernel.from_gauss(self.src.energy.edges,
self.src.energy.edges, 0.1, 0.0)
livetime = self.livetime
dataset1 = SpectrumDataset(counts=None,
livetime=livetime,
aeff=aeff,
edisp=edisp1,
background=None)
livetime2 = livetime
aeff2 = EffectiveAreaTable(self.src.energy.edges[:-1],
self.src.energy.edges[1:], aeff.data.data)
edisp2 = EDispKernel.from_gauss(self.src.energy.edges,
self.src.energy.edges, 0.2, 0.0)
dataset2 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime2,
aeff=aeff2,
edisp=edisp2,
background=None,
)
dataset1.stack(dataset2)
assert dataset1.counts is None
assert dataset1.background is None
assert dataset1.livetime == 2 * self.livetime
assert_allclose(dataset1.aeff.data.data.to_value("m2"),
aeff.data.data.to_value("m2"))
assert_allclose(dataset1.edisp.get_bias(1 * u.TeV), 0.0, atol=1.2e-3)
assert_allclose(dataset1.edisp.get_resolution(1 * u.TeV),
0.1581,
atol=1e-2)
def test_info_dict(self):
info_dict = self.dataset.info_dict()
assert_allclose(info_dict["n_on"], 907010)
assert_allclose(info_dict["background"], 3000.0)
assert_allclose(info_dict["significance"], 2924.522174)
assert_allclose(info_dict["excess"], 904010)
assert_allclose(info_dict["livetime"].value, 1e2)
assert info_dict["name"] == "test"
@requires_dependency("matplotlib")
def test_peek(self):
with mpl_plot_check():
self.dataset.peek()
self.dataset.edisp = None
with mpl_plot_check():
self.dataset.peek()
@requires_dependency("matplotlib")
def test_plot_fit(self):
with mpl_plot_check():
self.dataset.plot_fit()
class TestSpectrumDataset:
"""Test fit on counts spectra without any IRFs"""
def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = PowerLawSpectralModel(index=2.1,
amplitude=1e5 / u.TeV / u.s,
reference=0.1 * u.TeV)
self.livetime = 100 * u.s
bkg_rate = np.ones(self.nbins) / u.s
bkg_expected = bkg_rate * self.livetime
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_expected)
random_state = get_random_state(23)
self.npred = (self.source_model.integral(binning[:-1], binning[1:]) *
self.livetime)
self.npred += bkg_expected
source_counts = random_state.poisson(self.npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
self.dataset = SpectrumDataset(
model=self.source_model,
counts=self.src,
livetime=self.livetime,
background=self.bkg,
)
def test_data_shape(self):
assert self.dataset.data_shape[0] == self.nbins
def test_energy_range(self):
energy_range = self.dataset.energy_range
assert energy_range.unit == u.TeV
assert_allclose(energy_range.to_value("TeV"), [0.1, 10.0])
def test_cash(self):
"""Simple CASH fit to the on vector"""
fit = Fit(self.dataset)
result = fit.run()
assert result.success
assert "minuit" in repr(result)
npred = self.dataset.npred().data.sum()
assert_allclose(npred, self.npred.sum(), rtol=1e-3)
assert_allclose(result.total_stat, -18087404.624, rtol=1e-3)
pars = result.parameters
assert_allclose(pars["index"].value, 2.1, rtol=1e-2)
assert_allclose(pars.error("index"), 0.00127, rtol=1e-2)
assert_allclose(pars["amplitude"].value, 1e5, rtol=1e-3)
assert_allclose(pars.error("amplitude"), 153.450, rtol=1e-2)
def test_fake(self):
"""Test the fake dataset"""
real_dataset = self.dataset.copy()
self.dataset.fake(314)
assert real_dataset.counts.data.shape == self.dataset.counts.data.shape
assert real_dataset.background.data.sum(
) == self.dataset.background.data.sum()
assert int(real_dataset.counts.data.sum()) == 907010
assert self.dataset.counts.data.sum() == 907331
def test_incorrect_mask(self):
mask_fit = np.ones(self.nbins, dtype=np.dtype("float"))
with pytest.raises(ValueError):
SpectrumDataset(
model=self.source_model,
counts=self.src,
livetime=self.livetime,
mask_fit=mask_fit,
background=self.bkg,
)
def test_set_model(self):
aeff = EffectiveAreaTable.from_parametrization(self.src.energy.edges,
"HESS")
edisp = EnergyDispersion.from_diagonal_response(
self.src.energy.edges, self.src.energy.edges)
dataset = SpectrumDataset(None, self.src, self.livetime, None, aeff,
edisp, self.bkg)
with pytest.raises(AttributeError):
dataset.parameters
dataset.model = self.source_model
assert dataset.parameters[0] == self.source_model.parameters[0]
def test_str(self):
assert "SpectrumDataset" in str(self.dataset)
def test_spectrumdataset_create(self):
e_reco = u.Quantity([0.1, 1, 10.0], "TeV")
e_true = u.Quantity([0.05, 0.5, 5, 20.0], "TeV")
empty_dataset = SpectrumDataset.create(e_reco, e_true)
assert empty_dataset.counts.total_counts == 0
assert empty_dataset.data_shape[0] == 2
assert empty_dataset.background.total_counts == 0
assert empty_dataset.background.energy.nbin == 2
assert empty_dataset.aeff.data.axis("energy").nbin == 3
assert empty_dataset.edisp.data.axis("e_reco").nbin == 2
assert empty_dataset.livetime.value == 0
assert len(empty_dataset.gti.table) == 0
assert empty_dataset.energy_range[0] is None
assert_allclose(empty_dataset.mask_safe, 0)
def test_spectrum_dataset_stack_diagonal_safe_mask(self):
aeff = EffectiveAreaTable.from_parametrization(self.src.energy.edges,
"HESS")
edisp = EnergyDispersion.from_diagonal_response(
self.src.energy.edges, self.src.energy.edges)
livetime = self.livetime
dataset1 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime,
aeff=aeff,
edisp=edisp,
background=self.bkg.copy(),
)
livetime2 = 0.5 * livetime
aeff2 = EffectiveAreaTable(self.src.energy.edges[:-1],
self.src.energy.edges[1:],
2 * aeff.data.data)
bkg2 = CountsSpectrum(
self.src.energy.edges[:-1],
self.src.energy.edges[1:],
data=2 * self.bkg.data,
)
safe_mask2 = np.ones_like(self.src.data, bool)
safe_mask2[0] = False
dataset2 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime2,
aeff=aeff2,
edisp=edisp,
background=bkg2,
mask_safe=safe_mask2,
)
dataset1.stack(dataset2)
assert_allclose(dataset1.counts.data[1:], self.src.data[1:] * 2)
assert_allclose(dataset1.counts.data[0], self.src.data[0])
assert dataset1.livetime == 1.5 * self.livetime
assert_allclose(dataset1.background.data[1:], 3 * self.bkg.data[1:])
assert_allclose(dataset1.background.data[0], self.bkg.data[0])
assert_allclose(
dataset1.aeff.data.data.to_value("m2"),
4.0 / 3 * aeff.data.data.to_value("m2"),
)
assert_allclose(dataset1.edisp.pdf_matrix[1:], edisp.pdf_matrix[1:])
assert_allclose(dataset1.edisp.pdf_matrix[0],
0.5 * edisp.pdf_matrix[0])
def test_spectrum_dataset_stack_nondiagonal_no_bkg(self):
aeff = EffectiveAreaTable.from_parametrization(self.src.energy.edges,
"HESS")
edisp1 = EnergyDispersion.from_gauss(self.src.energy.edges,
self.src.energy.edges, 0.1, 0.0)
livetime = self.livetime
dataset1 = SpectrumDataset(counts=None,
livetime=livetime,
aeff=aeff,
edisp=edisp1,
background=None)
livetime2 = livetime
aeff2 = EffectiveAreaTable(self.src.energy.edges[:-1],
self.src.energy.edges[1:], aeff.data.data)
edisp2 = EnergyDispersion.from_gauss(self.src.energy.edges,
self.src.energy.edges, 0.2, 0.0)
dataset2 = SpectrumDataset(
counts=self.src.copy(),
livetime=livetime2,
aeff=aeff2,
edisp=edisp2,
background=None,
)
dataset1.stack(dataset2)
assert dataset1.counts is None
assert dataset1.background is None
assert dataset1.livetime == 2 * self.livetime
assert_allclose(dataset1.aeff.data.data.to_value("m2"),
aeff.data.data.to_value("m2"))
assert_allclose(dataset1.edisp.get_bias(1 * u.TeV), 0.0, atol=1e-3)
assert_allclose(dataset1.edisp.get_resolution(1 * u.TeV),
0.1581,
atol=1e-2)
def test_wrong_init(self):
bins = MapAxis.from_energy_bounds(1, 10, 8, "TeV").edges
with pytest.raises(ValueError):
CountsSpectrum(data=self.counts,
energy_lo=bins[:-1],
energy_hi=bins[1:])
def setup(self):
self.counts = [0, 0, 2, 5, 17, 3]
self.bins = MapAxis.from_energy_bounds(1, 10, 6, "TeV").edges
self.spec = CountsSpectrum(data=self.counts,
energy_lo=self.bins[:-1],
energy_hi=self.bins[1:])
# In[ ]:
arf.data.data *= containment
# ## Estimate background
#
# We now provide a workaround to estimate the background from the tabulated IRF in the energy bins we consider.
# In[ ]:
bkg_data = irfs["bkg"].evaluate_integrate(fov_lon=0 * u.deg,
fov_lat=offset,
energy_reco=energy_reco)
bkg = CountsSpectrum(energy_reco[:-1],
energy_reco[1:],
data=(bkg_data * solid_angles))
# ## Compute sensitivity
#
# We impose a minimal number of expected signal counts of 5 per bin and a minimal significance of 3 per bin. We assume an alpha of 0.2 (ratio between ON and OFF area).
# We then run the sensitivity estimator.
# In[ ]:
sensitivity_estimator = SensitivityEstimator(arf=arf,
rmf=rmf,
bkg=bkg,
livetime="5h",
gamma_min=5,
sigma=3,
# In[ ]:
arf.data.data *= containment
# ## Estimate background
#
# We now provide a workaround to estimate the background from the tabulated IRF in the energy bins we consider.
# In[ ]:
bkg_data = irfs["bkg"].evaluate_integrate(fov_lon=0 * u.deg,
fov_lat=offset,
energy_reco=energy_reco)
bkg = CountsSpectrum(
energy_reco[:-1],
energy_reco[1:],
data=(bkg_data * solid_angles).to_value("s-1"),
unit="s-1",
)
# ## Compute sensitivity
#
# We impose a minimal number of expected signal counts of 5 per bin and a minimal significance of 3 per bin. We assume an alpha of 0.2 (ratio between ON and OFF area).
# We then run the sensitivity estimator.
# In[ ]:
sensitivity_estimator = SensitivityEstimator(arf=arf,
rmf=rmf,
bkg=bkg,
livetime="5h",
gamma_min=5,
class TestFit:
"""Test fit on counts spectra without any IRFs"""
def setup(self):
self.nbins = 30
binning = np.logspace(-1, 1, self.nbins + 1) * u.TeV
self.source_model = PowerLawSpectralModel(index=2,
amplitude=1e5 *
u.Unit("cm-2 s-1 TeV-1"),
reference=0.1 * u.TeV)
bkg_model = PowerLawSpectralModel(index=3,
amplitude=1e4 *
u.Unit("cm-2 s-1 TeV-1"),
reference=0.1 * u.TeV)
self.alpha = 0.1
random_state = get_random_state(23)
npred = self.source_model.integral(binning[:-1], binning[1:]).value
source_counts = random_state.poisson(npred)
self.src = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=source_counts)
self.src.livetime = 1 * u.s
self.aeff = EffectiveAreaTable.from_constant(binning, "1 cm2")
npred_bkg = bkg_model.integral(binning[:-1], binning[1:]).value
bkg_counts = random_state.poisson(npred_bkg)
off_counts = random_state.poisson(npred_bkg * 1.0 / self.alpha)
self.bkg = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=bkg_counts)
self.off = CountsSpectrum(energy_lo=binning[:-1],
energy_hi=binning[1:],
data=off_counts)
def test_cash(self):
"""Simple CASH fit to the on vector"""
dataset = SpectrumDataset(
model=self.source_model,
counts=self.src,
aeff=self.aeff,
livetime=self.src.livetime,
)
npred = dataset.npred().data
assert_allclose(npred[5], 660.5171, rtol=1e-5)
stat_val = dataset.likelihood()
assert_allclose(stat_val, -107346.5291, rtol=1e-5)
self.source_model.parameters["index"].value = 1.12
fit = Fit([dataset])
result = fit.run()
# These values are check with sherpa fits, do not change
pars = result.parameters
assert_allclose(pars["index"].value, 1.995525, rtol=1e-3)
assert_allclose(pars["amplitude"].value, 100245.9, rtol=1e-3)
def test_wstat(self):
"""WStat with on source and background spectrum"""
on_vector = self.src.copy()
on_vector.data += self.bkg.data
dataset = SpectrumDatasetOnOff(
counts=on_vector,
counts_off=self.off,
aeff=self.aeff,
livetime=self.src.livetime,
acceptance=1,
acceptance_off=1 / self.alpha,
)
dataset.model = self.source_model
self.source_model.parameters.index = 1.12
fit = Fit([dataset])
result = fit.run()
pars = self.source_model.parameters
assert_allclose(pars["index"].value, 1.997342, rtol=1e-3)
assert_allclose(pars["amplitude"].value, 100245.187067, rtol=1e-3)
assert_allclose(result.total_stat, 30.022316, rtol=1e-3)
def test_fit_range(self):
"""Test fit range without complication of thresholds"""
dataset = SpectrumDatasetOnOff(counts=self.src,
mask_safe=np.ones(self.src.energy.nbin,
dtype=bool))
dataset.model = self.source_model
assert np.sum(dataset.mask_safe) == self.nbins
e_min, e_max = dataset.energy_range
assert_allclose(e_max.value, 10)
assert_allclose(e_min.value, 0.1)
def test_likelihood_profile(self):
dataset = SpectrumDataset(
model=self.source_model,
aeff=self.aeff,
livetime=self.src.livetime,
counts=self.src,
mask_safe=np.ones(self.src.energy.nbin, dtype=bool),
)
fit = Fit([dataset])
result = fit.run()
true_idx = result.parameters["index"].value
values = np.linspace(0.95 * true_idx, 1.05 * true_idx, 100)
profile = fit.likelihood_profile("index", values=values)
actual = values[np.argmin(profile["likelihood"])]
assert_allclose(actual, true_idx, rtol=0.01)
def test_wrong_init(self):
bins = energy_logspace(1, 10, 8, "TeV")
with pytest.raises(ValueError):
CountsSpectrum(data=self.counts, energy_lo=bins[:-1], energy_hi=bins[1:])
def test_io(self, tmp_path):
self.spec.write(tmp_path / "tmp.fits")
spec2 = CountsSpectrum.read(tmp_path / "tmp.fits")
assert_quantity_allclose(spec2.energy.edges, self.bins)
#
# In this section we will include a background component extracted from the IRF. Furthermore, we will also simulate more than one observation and fit each one individually in order to get average fit results.
# In[ ]:
# We assume a PowerLawSpectralModel shape of the background as well
bkg_data = (
cta_irf["bkg"].evaluate_integrate(
fov_lon=0 * u.deg, fov_lat=offset, energy_reco=energy
)
* solid_angle
* livetime
)
bkg = CountsSpectrum(
energy[:-1], energy[1:], data=bkg_data.to_value(""), unit=""
)
# In[ ]:
dataset = SpectrumDatasetOnOff(
aeff=aeff,
edisp=edisp,
model=model_ref,
livetime=livetime,
acceptance=1,
acceptance_off=5,
)
