def test_compute_lima_on_off_image():
"""
Test Li & Ma image with snippet from the H.E.S.S. survey data.
"""
filename = "$GAMMAPY_DATA/tests/unbundled/hess/survey/hess_survey_snippet.fits.gz"
n_on = Map.read(filename, hdu="ON")
counts = image_to_cube(n_on, "1 TeV", "100 TeV")
n_off = Map.read(filename, hdu="OFF")
counts_off = image_to_cube(n_off, "1 TeV", "100 TeV")
a_on = Map.read(filename, hdu="ONEXPOSURE")
acceptance = image_to_cube(a_on, "1 TeV", "100 TeV")
a_off = Map.read(filename, hdu="OFFEXPOSURE")
acceptance_off = image_to_cube(a_off, "1 TeV", "100 TeV")
dataset = MapDatasetOnOff(
counts=counts,
counts_off=counts_off,
acceptance=acceptance,
acceptance_off=acceptance_off,
)
significance = Map.read(filename, hdu="SIGNIFICANCE")
significance = image_to_cube(significance, "1 TeV", "10 TeV")
estimator = ExcessMapEstimator("0.1 deg")
results = estimator.run(dataset)
# Reproduce safe significance threshold from HESS software
results["sqrt_ts"].data[results["counts"].data < 5] = 0
# crop the image at the boundaries, because the reference image
# is cut out from a large map, there is no way to reproduce the
# result with regular boundary handling
actual = results["sqrt_ts"].crop((11, 11)).data
desired = significance.crop((11, 11)).data
# Set boundary to NaN in reference image
# The absolute tolerance is low because the method used here is slightly different from the one used in HGPS
# n_off is convolved as well to ensure the method applies to true ON-OFF datasets
assert_allclose(actual, desired, atol=0.2)
def test_compute_lima_image():
"""
Test Li & Ma image against TS image for Tophat kernel
"""
filename = "$GAMMAPY_DATA/tests/unbundled/poisson_stats_image/input_all.fits.gz"
counts = Map.read(filename, hdu="counts")
counts = image_to_cube(counts, "1 GeV", "100 GeV")
background = Map.read(filename, hdu="background")
background = image_to_cube(background, "1 GeV", "100 GeV")
dataset = MapDataset(counts=counts, background=background)
estimator = ExcessMapEstimator("0.1 deg")
result_lima = estimator.run(dataset)
assert_allclose(result_lima["sqrt_ts"].data[:, 100, 100],
30.814916,
atol=1e-3)
assert_allclose(result_lima["sqrt_ts"].data[:, 1, 1], 0.164, atol=1e-3)
assert_allclose(result_lima["npred_background"].data[:, 1, 1],
37,
atol=1e-3)
assert_allclose(result_lima["npred"].data[:, 1, 1], 38, atol=1e-3)
assert_allclose(result_lima["npred_excess"].data[:, 1, 1], 1, atol=1e-3)
def get_excess_map(self):
"""Calculate excess map with respect to the current model."""
excess_settings = self.config.excess_map
log.info("Computing excess maps.")
# TODO: Here we could possibly stack the datasets if needed
# or allow to compute the excess map for each dataset
if len(self.datasets) > 1:
raise ValueError("Datasets must be stacked to compute the excess map")
if self.datasets[0].tag not in ["MapDataset", "MapDatasetOnOff"]:
raise ValueError("Cannot compute excess map for 1D dataset")
energy_edges = self._make_energy_axis(excess_settings.energy_edges)
if energy_edges is not None:
energy_edges = energy_edges.edges
excess_map_estimator = ExcessMapEstimator(
correlation_radius=excess_settings.correlation_radius,
energy_edges=energy_edges,
**excess_settings.parameters,
)
self.excess_map = excess_map_estimator.run(self.datasets[0])
def test_excess_map_estimator_map_dataset_on_off_with_correlation_mask_fit(
simple_dataset_on_off, ):
geom = simple_dataset_on_off.counts.geom
mask_fit = Map.from_geom(geom, data=1, dtype=bool)
mask_fit.data[:, :, 10] = False
mask_fit.data[:, 10, :] = False
simple_dataset_on_off.mask_fit = mask_fit
estimator_image = ExcessMapEstimator(0.11 * u.deg, correlate_off=True)
result_image = estimator_image.run(simple_dataset_on_off)
assert result_image["npred"].data.shape == (1, 20, 20)
assert_allclose(result_image["sqrt_ts"].data[0, 10, 10], np.nan, atol=1e-3)
assert_allclose(result_image["npred"].data[0, 10, 10], np.nan)
assert_allclose(result_image["npred_excess"].data[0, 10, 10], np.nan)
assert_allclose(result_image["sqrt_ts"].data[0, 9, 9], 7.186745, atol=1e-3)
assert_allclose(result_image["npred"].data[0, 9, 9], 304)
assert_allclose(result_image["npred_excess"].data[0, 9, 9], 152)
assert result_image["flux"].unit == u.Unit("cm-2s-1")
assert_allclose(result_image["flux"].data[0, 9, 9],
1.190928e-08,
rtol=1e-3)
def test_significance_map_estimator_incorrect_dataset():
with pytest.raises(ValueError):
ExcessMapEstimator("bad")
def test_significance_map_estimator_map_dataset_on_off_with_correlation(
simple_dataset_on_off, ):
exposure = simple_dataset_on_off.exposure
exposure.data += 1e6
# First without exposure
simple_dataset_on_off.exposure = None
estimator = ExcessMapEstimator(0.11 * u.deg,
energy_edges=[0.1, 1, 10] * u.TeV,
correlate_off=True)
result = estimator.run(simple_dataset_on_off)
assert result["counts"].data.shape == (2, 20, 20)
assert_allclose(result["counts"].data[:, 10, 10], 194)
assert_allclose(result["excess"].data[:, 10, 10], 97)
assert_allclose(result["background"].data[:, 10, 10], 97)
assert_allclose(result["sqrt_ts"].data[:, 10, 10], 5.741116, atol=1e-5)
assert_allclose(result["flux"].data[:, 10, 10], np.nan)
# Test with exposure
simple_dataset_on_off.exposure = exposure
estimator_image = ExcessMapEstimator(0.11 * u.deg,
energy_edges=[0.1, 1] * u.TeV,
correlate_off=True)
result_image = estimator_image.run(simple_dataset_on_off)
assert result_image["counts"].data.shape == (1, 20, 20)
assert_allclose(result_image["counts"].data[0, 10, 10], 194)
assert_allclose(result_image["excess"].data[0, 10, 10], 97)
assert_allclose(result_image["background"].data[0, 10, 10], 97)
assert_allclose(result_image["sqrt_ts"].data[0, 10, 10],
5.741116,
atol=1e-3)
assert_allclose(result_image["flux"].data[:, 10, 10], 9.7e-9, atol=1e-5)
# Test with mask fit
mask_fit = Map.from_geom(
simple_dataset_on_off._geom,
data=np.ones(simple_dataset_on_off.counts.data.shape, dtype=bool),
)
mask_fit.data[:, :, 10] = False
mask_fit.data[:, 10, :] = False
simple_dataset_on_off.mask_fit = mask_fit
estimator_image = ExcessMapEstimator(0.11 * u.deg,
apply_mask_fit=True,
correlate_off=True)
result_image = estimator_image.run(simple_dataset_on_off)
assert result_image["counts"].data.shape == (1, 20, 20)
assert_allclose(result_image["sqrt_ts"].data[0, 10, 10], np.nan, atol=1e-3)
assert_allclose(result_image["counts"].data[0, 10, 10], np.nan)
assert_allclose(result_image["excess"].data[0, 10, 10], np.nan)
assert_allclose(result_image["background"].data[0, 10, 10], np.nan)
assert_allclose(result_image["sqrt_ts"].data[0, 9, 9], 7.186745, atol=1e-3)
assert_allclose(result_image["counts"].data[0, 9, 9], 304)
assert_allclose(result_image["excess"].data[0, 9, 9], 152)
assert_allclose(result_image["background"].data[0, 9, 9], 152)
assert result_image["flux"].unit == u.Unit("cm-2s-1")
assert_allclose(result_image["flux"].data[0, 9, 9], 1.52e-8, rtol=1e-3)
simple_dataset_on_off.psf = None
# TODO: this has never worked...
model = SkyModel(
PowerLawSpectralModel(amplitude="1e-9 cm-2 s-1TeV-1"),
GaussianSpatialModel(lat_0=0.0 * u.deg,
lon_0=0.0 * u.deg,
sigma=0.1 * u.deg,
frame="icrs"),
name="sky_model",
)
simple_dataset_on_off.models = [model]
estimator_mod = ExcessMapEstimator(0.11 * u.deg,
apply_mask_fit=False,
correlate_off=True)
result_mod = estimator_mod.run(simple_dataset_on_off)
assert result_mod["counts"].data.shape == (1, 20, 20)
assert_allclose(result_mod["sqrt_ts"].data[0, 10, 10], 8.899278, atol=1e-3)
assert_allclose(result_mod["counts"].data[0, 10, 10], 388)
assert_allclose(result_mod["excess"].data[0, 10, 10], 190.68057)
assert_allclose(result_mod["background"].data[0, 10, 10], 197.31943)
assert result_mod["flux"].unit == "cm-2s-1"
assert_allclose(result_mod["flux"].data[0, 10, 10],
1.906806e-08,
rtol=1e-3)
assert_allclose(result_mod["flux"].data.sum(), 5.920642e-06, rtol=1e-3)
spectral_model = PowerLawSpectralModel(index=15)
estimator_mod = ExcessMapEstimator(
0.11 * u.deg,
apply_mask_fit=False,
correlate_off=True,
spectral_model=spectral_model,
)
result_mod = estimator_mod.run(simple_dataset_on_off)
assert result_mod["flux"].unit == "cm-2s-1"
assert_allclose(result_mod["flux"].data.sum(), 5.920642e-06, rtol=1e-3)
reco_exposure = estimate_exposure_reco_energy(
simple_dataset_on_off, spectral_model=spectral_model)
assert_allclose(reco_exposure.data.sum(), 7.977796e+12, rtol=0.001)
def test_significance_map_estimator_map_dataset_on_off(simple_dataset_on_off):
exposure = simple_dataset_on_off.exposure
exposure.data += 1e6
# First without exposure
simple_dataset_on_off.exposure = None
estimator = ExcessMapEstimator(
0.11 * u.deg,
selection_optional=None,
energy_edges=[0.1, 1, 10] * u.TeV,
)
result = estimator.run(simple_dataset_on_off)
assert result["counts"].data.shape == (2, 20, 20)
assert_allclose(result["counts"].data[:, 10, 10], 194)
assert_allclose(result["excess"].data[:, 10, 10], 97)
assert_allclose(result["background"].data[:, 10, 10], 97)
assert_allclose(result["sqrt_ts"].data[:, 10, 10], 5.741116, atol=1e-5)
assert_allclose(result["flux"].data[:, 10, 10], np.nan)
# Test with exposure
simple_dataset_on_off.exposure = exposure
estimator_image = ExcessMapEstimator(0.11 * u.deg,
energy_edges=[0.1, 1] * u.TeV)
result_image = estimator_image.run(simple_dataset_on_off)
assert result_image["counts"].data.shape == (1, 20, 20)
assert_allclose(result_image["counts"].data[0, 10, 10], 194)
assert_allclose(result_image["excess"].data[0, 10, 10], 97)
assert_allclose(result_image["background"].data[0, 10, 10], 97)
assert_allclose(result_image["sqrt_ts"].data[0, 10, 10],
5.741116,
atol=1e-3)
assert_allclose(result_image["flux"].data[:, 10, 10], 9.7e-9, atol=1e-5)
# Test with mask fit
mask_fit = Map.from_geom(
simple_dataset_on_off._geom,
data=np.ones(simple_dataset_on_off.counts.data.shape, dtype=bool),
)
mask_fit.data[:, :, 10] = False
mask_fit.data[:, 10, :] = False
simple_dataset_on_off.mask_fit = mask_fit
estimator_image = ExcessMapEstimator(0.11 * u.deg, apply_mask_fit=True)
result_image = estimator_image.run(simple_dataset_on_off)
assert result_image["counts"].data.shape == (1, 20, 20)
assert_allclose(result_image["sqrt_ts"].data[0, 10, 10], np.nan, atol=1e-3)
assert_allclose(result_image["counts"].data[0, 10, 10], np.nan)
assert_allclose(result_image["excess"].data[0, 10, 10], np.nan)
assert_allclose(result_image["background"].data[0, 10, 10], np.nan)
assert_allclose(result_image["sqrt_ts"].data[0, 9, 9], 7.186745, atol=1e-3)
assert_allclose(result_image["counts"].data[0, 9, 9], 304)
assert_allclose(result_image["excess"].data[0, 9, 9], 152)
assert_allclose(result_image["background"].data[0, 9, 9], 152)
assert result_image["flux"].unit == u.Unit("cm-2s-1")
assert_allclose(result_image["flux"].data[0, 9, 9], 1.52e-8, rtol=1e-3)
simple_dataset_on_off.psf = None
# TODO: this has never worked...
model = SkyModel(
PowerLawSpectralModel(amplitude="1e-9 cm-2 s-1TeV-1"),
GaussianSpatialModel(lat_0=0.0 * u.deg,
lon_0=0.0 * u.deg,
sigma=0.1 * u.deg,
frame="icrs"),
name="sky_model",
)
#
simple_dataset_on_off.models = [model]
estimator_mod = ExcessMapEstimator(0.11 * u.deg, apply_mask_fit=False)
result_mod = estimator_mod.run(simple_dataset_on_off)
assert result_mod["counts"].data.shape == (1, 20, 20)
assert_allclose(result_mod["sqrt_ts"].data[0, 10, 10], 6.240846, atol=1e-3)
assert_allclose(result_mod["counts"].data[0, 10, 10], 388)
assert_allclose(result_mod["excess"].data[0, 10, 10], 148.68057)
assert_allclose(result_mod["background"].data[0, 10, 10], 239.31943)
assert result_mod["flux"].unit == u.Unit("cm-2s-1")
assert_allclose(result_mod["flux"].data[0, 10, 10],
1.486806e-08,
rtol=1e-3)
def test_significance_map_estimator_map_dataset_on_off(simple_dataset_on_off):
estimator = ExcessMapEstimator(
0.11 * u.deg,
selection_optional=None,
e_edges=[0.1 * u.TeV, 1 * u.TeV, 10 * u.TeV],
)
result = estimator.run(simple_dataset_on_off)
assert result["counts"].data.shape == (2, 20, 20)
assert_allclose(result["counts"].data[:, 10, 10], 194)
assert_allclose(result["excess"].data[:, 10, 10], 97)
assert_allclose(result["background"].data[:, 10, 10], 97)
assert_allclose(result["significance"].data[:, 10, 10], 5.741116, atol=1e-5)
estimator_image = ExcessMapEstimator(0.11 * u.deg, e_edges=[0.1 * u.TeV, 1 * u.TeV])
result_image = estimator_image.run(simple_dataset_on_off)
assert result_image["counts"].data.shape == (1, 20, 20)
assert_allclose(result_image["significance"].data[0, 10, 10], 5.741116, atol=1e-3)
mask_fit = Map.from_geom(
simple_dataset_on_off._geom,
data=np.ones(simple_dataset_on_off.counts.data.shape, dtype=bool),
)
mask_fit.data[:, :, 10] = False
mask_fit.data[:, 10, :] = False
simple_dataset_on_off.mask_fit = mask_fit
estimator_image = ExcessMapEstimator(0.11 * u.deg, apply_mask_fit=True)
simple_dataset_on_off.exposure.data = (
np.ones(simple_dataset_on_off.exposure.data.shape) * 1e6
)
result_image = estimator_image.run(simple_dataset_on_off)
assert result_image["counts"].data.shape == (1, 20, 20)
assert_allclose(result_image["significance"].data[0, 10, 10], 7.186745, atol=1e-3)
assert_allclose(result_image["counts"].data[0, 10, 10], 304)
assert_allclose(result_image["excess"].data[0, 10, 10], 152)
assert_allclose(result_image["background"].data[0, 10, 10], 152)
assert result_image["flux"].unit == u.Unit("cm-2s-1")
assert_allclose(result_image["flux"].data[0, 10, 10], 7.6e-9, rtol=1e-3)
# test with an npred()
simple_dataset_on_off.exposure.data = (
np.ones(simple_dataset_on_off.exposure.data.shape) * 1e10
)
simple_dataset_on_off.psf = None
model = SkyModel(
PowerLawSpectralModel(),
GaussianSpatialModel(
lat_0=0.0 * u.deg, lon_0=0.0 * u.deg, sigma=0.1 * u.deg, frame="icrs"
),
datasets_names=[simple_dataset_on_off.name],
name="sky_model",
)
simple_dataset_on_off.models.append(model)
estimator_mod = ExcessMapEstimator(0.11 * u.deg, apply_mask_fit=False)
result_mod = estimator_mod.run(simple_dataset_on_off)
assert result_mod["counts"].data.shape == (1, 20, 20)
assert_allclose(result_mod["significance"].data[0, 10, 10], 8.119164, atol=1e-3)
assert_allclose(result_mod["counts"].data[0, 10, 10], 388)
assert_allclose(result_mod["excess"].data[0, 10, 10], 194)
assert_allclose(result_mod["background"].data[0, 10, 10], 194)
assert result_mod["flux"].unit == u.Unit("cm-2s-1")
assert_allclose(result_image["flux"].data[0, 10, 10], 7.6e-9, rtol=1e-3)
def estimate_significance_luca(
dataset,
first_guess_exclusion,
correlation_radii,
energy_edgess,
n_iter,
low,
high,
negative=False
):
for nn in range(n_iter):
print(f"###########")
print(nn)
print(f"###########")
results = []
for correlation_radius, energy_edges in zip(correlation_radii, energy_edgess):
estimator_excess = ExcessMapEstimator(
correlation_radius=correlation_radius,
n_sigma=1,
n_sigma_ul=3,
selection_optional=None,
energy_edges=energy_edges,
)
results.append(estimator_excess.run(dataset))
def _reproject_exclusion_mask(geom, exclusion):
"""Reproject the exclusion on the dataset geometry"""
mask_map = Map.from_geom(geom)
coords = geom.get_coord()
vals = exclusion.get_by_coord(coords)
mask_map.data += vals
return mask_map
first_guess_exclusion = _reproject_exclusion_mask(dataset.counts.geom, first_guess_exclusion).slice_by_idx({"energy" : 0})
plt.figure(figsize=(8, 6))
for correlation_radius, energy_edges, result in zip(correlation_radii, energy_edgess, results):
(result["sqrt_ts"].slice_by_idx({"energy" : 0})*first_guess_exclusion).plot(add_cbar=True, cmap="coolwarm", vmin=-5, vmax=5)
plt.title(f"{correlation_radius} {energy_edges}")
plt.show()
plt.close()
exclusion_enlarged = first_guess_exclusion.copy()
# Enlarge exclusion mask
for result, radius in zip(results, correlation_radii):
mask_map_significance = result["sqrt_ts"].copy().slice_by_idx({"energy" : 0})
mask_map_significance.data = np.nan_to_num(mask_map_significance.data)
mask_map = mask_map_significance.copy()
mask_map.data = ~apply_hysteresis_threshold(mask_map_significance.data, low=low, high=high)
if negative == True:
mask_map.data *= ~apply_hysteresis_threshold(-mask_map_significance.data, low=low, high=high)
exclusion_enlarged *= mask_map
plt.figure(figsize=(8, 6))
first_guess_exclusion.plot()
plt.contour(exclusion_enlarged.data, levels=1, colors="r", inewidths=2)
plt.show()
plt.close()
for correlation_radius, energy_edges, result in zip(correlation_radii, energy_edgess, results):
pretty_plot_1d_significance(result, correlation_radius, energy_edges, exclusion_enlarged)
first_guess_exclusion = exclusion_enlarged
print(f"###########")
print("Final result")
print(f"###########")
for correlation_radius, energy_edges, result in zip(correlation_radii, energy_edgess, results):
plt.figure(figsize=(8, 6))
final = (result["sqrt_ts"].slice_by_idx({"energy" : 0}))
final.plot(add_cbar=True, cmap="coolwarm", vmin=-5, vmax=5)
cs = plt.contour(final.data, levels=(-15, -10, -7, -5, -3, 3, 5, 7, 10, 15), colors="k")
plt.clabel(cs, colors="k")
plt.title(f"{correlation_radius} {energy_edges}")
plt.show()
plt.close()