def __init__(
self,
model=None,
counts=None,
exposure=None,
mask_fit=None,
psf=None,
edisp=None,
background_model=None,
name="",
evaluation_mode="local",
mask_safe=None,
gti=None,
):
if model is None:
model = SkyModels([])
if mask_fit is not None and mask_fit.data.dtype != np.dtype("bool"):
raise ValueError("mask data must have dtype bool")
if mask_safe is not None and mask_safe.data.dtype != np.dtype("bool"):
raise ValueError("mask data must have dtype bool")
self.evaluation_mode = evaluation_mode
self.counts = counts
self.exposure = exposure
self.mask_fit = mask_fit
self.psf = psf
self.edisp = edisp
self.background_model = background_model
self.model = model
self.name = name
self.mask_safe = mask_safe
self.gti = gti
def from_dict(cls, data, components, models):
"""Create flux point dataset from dict.
Parameters
----------
data : dict
Dict containing data to create dataset from.
components : list of dict
Not used.
models : list of `SkyModel`
List of model components.
Returns
-------
dataset : `SpectrumDatasetOnOff`
Spectrum dataset on off.
"""
model = SkyModels(
[model for model in models if model.name in data["models"]])
# TODO: assumes that the model is a skymodel
# so this will work only when this change will be effective
filename = data["filename"]
dataset = cls.from_ogip_files(filename=filename)
dataset.mask_fit = None
dataset.model = model
return dataset
def from_dict(cls, data, components, models):
"""Create flux point dataset from dict.
Parameters
----------
data : dict
Dict containing data to create dataset from.
components : list of dict
Not used.
models : list of `SkyModel`
List of model components.
Returns
-------
dataset : `FluxPointDataset`
Flux point datasets.
"""
models_list = [
model for model in models if model.name in data["models"]
]
# TODO: assumes that the model is a skymodel
# so this will work only when this change will be effective
table = Table.read(data["filename"])
mask_fit = table["mask_fit"].data.astype("bool")
mask_safe = table["mask_safe"].data.astype("bool")
table.remove_columns(["mask_fit", "mask_safe"])
return cls(
model=SkyModels(models_list),
name=data["name"],
data=FluxPoints(table),
mask_fit=mask_fit,
mask_safe=mask_safe,
likelihood=data["likelihood"],
)
def sky_model(self, which="best"):
"""Source sky model.
Parameters
----------
which : {'best', 'pl', 'ecpl'}
Which spectral model
Returns
-------
sky_model : `~gammapy.modeling.models.SkyModel`
Sky model of the catalog object.
"""
if self.spatial_model_type in {"2-gaussian", "3-gaussian"}:
models = []
spectral_model = self.spectral_model(which=which)
for component in self.components:
weight = component.data["Flux_Map"] / self.data["Flux_Map"]
spectral_model_comp = spectral_model.copy()
# weight amplitude of the component
spectral_model_comp.parameters["amplitude"].value *= weight
models.append(
SkyModel(
component.spatial_model(),
spectral_model_comp,
name=component.name,
))
return SkyModels(models)
else:
return SkyModel(self.spatial_model(),
self.spectral_model(which=which),
name=self.name)
def model(self, model):
if isinstance(model, SkyModel):
model = SkyModels([model])
self._model = model
if model is not None:
evaluators = []
for component in model:
evaluator = MapEvaluator(component,
evaluation_mode=self.evaluation_mode)
evaluator.update(self.exposure, self.psf, self.edisp)
evaluators.append(evaluator)
self._evaluators = evaluators
def to_sky_models(self):
"""Convert to a `~gammapy.modeling.models.SkyModels`.
TODO: add an option whether to skip or raise on missing models or data.
"""
source_list = []
for source_idx in range(len(self.table)):
source = self[source_idx]
try:
source_list.append(source.sky_model)
except NoDataAvailableError:
log.warning(
f"Skipping source {source.name} (missing data in gamma-cat)"
)
continue
return SkyModels(source_list)
def from_dict(cls, data, components, models):
"""Create from dicts and models list generated from YAML serialization."""
dataset = cls.read(data["filename"], name=data["name"])
bkg_name = data["background"]
model_names = data["models"]
for component in components["components"]:
if component["type"] == "BackgroundModel":
if component["name"] == bkg_name:
if "filename" not in component:
component["map"] = dataset.background_model.map
background_model = BackgroundModel.from_dict(component)
dataset.background_model = background_model
models_list = [model for model in models if model.name in model_names]
dataset.model = SkyModels(models_list)
if"likelihood" in data:
dataset.likelihood_type = data["likelihood"]
return dataset
def test_flux_point_dataset_serialization(tmp_path):
path = "$GAMMAPY_DATA/tests/spectrum/flux_points/diff_flux_points.fits"
data = FluxPoints.read(path)
data.table["e_ref"] = data.e_ref.to("TeV")
# TODO: remove duplicate definition this once model is redefine as skymodel
spatial_model = ConstantSpatialModel()
spectral_model = PowerLawSpectralModel(index=2.3,
amplitude="2e-13 cm-2 s-1 TeV-1",
reference="1 TeV")
model = SkyModel(spatial_model, spectral_model, name="test_model")
dataset = FluxPointsDataset(SkyModels([model]), data, name="test_dataset")
Datasets([dataset]).to_yaml(tmp_path, prefix="tmp")
datasets = Datasets.from_yaml(tmp_path / "tmp_datasets.yaml",
tmp_path / "tmp_models.yaml")
new_dataset = datasets[0]
assert_allclose(new_dataset.data.table["dnde"], dataset.data.table["dnde"],
1e-4)
if dataset.mask_fit is None:
assert np.all(new_dataset.mask_fit == dataset.mask_safe)
assert np.all(new_dataset.mask_safe == dataset.mask_safe)
assert new_dataset.name == "test_dataset"
def sky_models_2(sky_model):
sky_model_4 = sky_model.copy(name="source-4")
sky_model_5 = sky_model.copy(name="source-5")
return SkyModels([sky_model_4, sky_model_5])
def sky_models(sky_model):
sky_model_2 = sky_model.copy(name="source-2")
sky_model_3 = sky_model.copy(name="source-3")
return SkyModels([sky_model_2, sky_model_3])
def make_example_2():
spatial = GaussianSpatialModel("0 deg", "0 deg", "1 deg")
model = SkyModel(spatial, PowerLawSpectralModel())
models = SkyModels([model])
models.to_yaml(DATA_PATH / "example2.yaml")
def run_region(self, kr, lon, lat, radius):
# TODO: for now we have to read/create the allsky maps each in each job
# because we can't pickle <functools._lru_cache_wrapper object
# send this back to init when fixed
# exposure
exposure_hpx = Map.read(
self.datadir + "/fermi_3fhl/fermi_3fhl_exposure_cube_hpx.fits.gz")
exposure_hpx.unit = "cm2 s"
# background iem
infile = self.datadir + "/catalogs/fermi/gll_iem_v06.fits.gz"
outfile = self.resdir + "/gll_iem_v06_extra.fits"
model_iem = extrapolate_iem(infile, outfile, self.logEc_extra)
# ROI
roi_time = time()
ROI_pos = SkyCoord(lon, lat, frame="galactic", unit="deg")
width = 2 * (radius + self.psf_margin)
# Counts
counts = Map.create(
skydir=ROI_pos,
width=width,
proj="CAR",
coordsys="GAL",
binsz=self.dlb,
axes=[self.energy_axis],
dtype=float,
)
counts.fill_by_coord({
"skycoord": self.events.radec,
"energy": self.events.energy
})
axis = MapAxis.from_nodes(counts.geom.axes[0].center,
name="energy",
unit="GeV",
interp="log")
wcs = counts.geom.wcs
geom = WcsGeom(wcs=wcs, npix=counts.geom.npix, axes=[axis])
coords = counts.geom.get_coord()
# expo
data = exposure_hpx.interp_by_coord(coords)
exposure = WcsNDMap(geom, data, unit=exposure_hpx.unit, dtype=float)
# read PSF
psf_kernel = PSFKernel.from_table_psf(self.psf,
counts.geom,
max_radius=self.psf_margin *
u.deg)
# Energy Dispersion
e_true = exposure.geom.axes[0].edges
e_reco = counts.geom.axes[0].edges
edisp = EnergyDispersion.from_diagonal_response(e_true=e_true,
e_reco=e_reco)
# fit mask
if coords["lon"].min() < 90 * u.deg and coords["lon"].max(
) > 270 * u.deg:
coords["lon"][coords["lon"].value > 180] -= 360 * u.deg
mask = (
(coords["lon"] >= coords["lon"].min() + self.psf_margin * u.deg)
& (coords["lon"] <= coords["lon"].max() - self.psf_margin * u.deg)
& (coords["lat"] >= coords["lat"].min() + self.psf_margin * u.deg)
& (coords["lat"] <= coords["lat"].max() - self.psf_margin * u.deg))
mask_fermi = WcsNDMap(counts.geom, mask)
# IEM
eval_iem = MapEvaluator(model=model_iem,
exposure=exposure,
psf=psf_kernel,
edisp=edisp)
bkg_iem = eval_iem.compute_npred()
# ISO
eval_iso = MapEvaluator(model=self.model_iso,
exposure=exposure,
edisp=edisp)
bkg_iso = eval_iso.compute_npred()
# merge iem and iso, only one local normalization is fitted
background_total = bkg_iem + bkg_iso
background_model = BackgroundModel(background_total)
background_model.parameters["norm"].min = 0.0
# Sources model
in_roi = self.FHL3.positions.galactic.contained_by(wcs)
FHL3_roi = []
for ks in range(len(self.FHL3.table)):
if in_roi[ks] == True:
model = self.FHL3[ks].sky_model()
model.spatial_model.parameters.freeze_all() # freeze spatial
model.spectral_model.parameters["amplitude"].min = 0.0
if isinstance(model.spectral_model, PowerLawSpectralModel):
model.spectral_model.parameters["index"].min = 0.1
model.spectral_model.parameters["index"].max = 10.0
else:
model.spectral_model.parameters["alpha"].min = 0.1
model.spectral_model.parameters["alpha"].max = 10.0
FHL3_roi.append(model)
model_total = SkyModels(FHL3_roi)
# Dataset
dataset = MapDataset(
model=model_total,
counts=counts,
exposure=exposure,
psf=psf_kernel,
edisp=edisp,
background_model=background_model,
mask_fit=mask_fermi,
name="3FHL_ROI_num" + str(kr),
)
cat_stat = dataset.stat_sum()
datasets = Datasets([dataset])
fit = Fit(datasets)
results = fit.run(optimize_opts=self.optimize_opts)
print("ROI_num", str(kr), "\n", results)
fit_stat = datasets.stat_sum()
if results.message == "Optimization failed.":
pass
else:
datasets.to_yaml(path=Path(self.resdir),
prefix=dataset.name,
overwrite=True)
np.save(
self.resdir + "/3FHL_ROI_num" + str(kr) + "_covariance.npy",
results.parameters.covariance,
)
np.savez(
self.resdir + "/3FHL_ROI_num" + str(kr) + "_fit_infos.npz",
message=results.message,
stat=[cat_stat, fit_stat],
)
exec_time = time() - roi_time
print("ROI", kr, " time (s): ", exec_time)
for model in FHL3_roi:
if (self.FHL3[model.name].data["ROI_num"] == kr
and self.FHL3[model.name].data["Signif_Avg"] >=
self.sig_cut):
flux_points = FluxPointsEstimator(
datasets=datasets,
e_edges=self.El_flux,
source=model.name,
sigma_ul=2.0,
).run()
filename = self.resdir + "/" + model.name + "_flux_points.fits"
flux_points.write(filename, overwrite=True)
exec_time = time() - roi_time - exec_time
print("ROI", kr, " Flux points time (s): ", exec_time)
reference=1 * u.TeV,
)
sky_model = SkyModel(spatial_model=spatial_model,
spectral_model=spectral_model,
name="crab")
# Now we freeze these parameters that we don't want the light curve estimator to change
sky_model.parameters["index"].frozen = True
sky_model.parameters["lon_0"].frozen = True
sky_model.parameters["lat_0"].frozen = True
# We assign them the model to be fitted to each dataset
# In[ ]:
models = SkyModels([sky_model])
analysis_3d.set_models(models)
# ## Light Curve estimation: by observation
#
# We can now create the light curve estimator.
#
# We pass it the list of datasets and the name of the model component for which we want to build the light curve.
# We can optionally ask for parameters reoptimization during fit, that is most of the time to fit background normalization in each time bin.
#
# If we don't set any time interval, the `~gammapy.time.LightCurveEstimator` is determines the flux of each dataset and places it at the corresponding time in the light curve.
# Here one dataset equals to one observing run.
# In[ ]:
lc_maker_3d = LightCurveEstimator(analysis_3d.datasets,
# ## Fit
#
# Finally, the big finale: let's do a 3D map fit for the source at the Galactic center, to measure it's position and spectrum. We keep the background normalization free.
# In[ ]:
spatial_model = PointSpatialModel(lon_0="0 deg",
lat_0="0 deg",
frame="galactic")
spectral_model = PowerLawSpectralModel(index=2.5,
amplitude="1e-11 cm-2 s-1 TeV-1",
reference="100 GeV")
source = SkyModel(spectral_model=spectral_model, spatial_model=spatial_model)
models = SkyModels([source, diffuse_gal, diffuse_iso])
dataset = MapDataset(
models=models,
counts=counts,
exposure=exposure,
psf=psf_kernel,
edisp=edisp,
)
# In[ ]:
get_ipython().run_cell_magic('time', '',
'fit = Fit([dataset])\nresult = fit.run()')
# In[ ]:
def analysis_3d_summary(analysis, target):
log.info(f"analysis_3d_summary: {target}")
# TODO:
# - how to plot a SkyModels ?
# - PowerLawSpectralModel hardcoded need to find auto way
path = f"{target}/{target}_3d_bestfit.rst"
tab = Table.read(path, format="ascii")
tab.add_index("name")
dt = "U30"
comp_tab = Table(names=("Param", "DC1 Ref", "gammapy 3d"),
dtype=[dt, dt, dt])
ref_model = SkyModels.read(f"{target}/reference/dc1_model_3d.yaml")
pars = ref_model.parameters.names
pars.remove("reference") # need to find a better way to handle this
for par in pars:
ref = ref_model.parameters[par].value
value = tab.loc[par]["value"]
name = tab.loc[par]["name"]
error = tab.loc[par]["error"]
comp_tab.add_row([name, ref, f"{value}±{error}"])
analysis.datasets["stacked"].counts.sum_over_axes().plot(add_cbar=True)
plt.savefig(f"{target}/{target}_counts.png", bbox_inches="tight")
plt.close()
analysis.datasets["stacked"].plot_residuals(method="diff/sqrt(model)",
vmin=-0.5,
vmax=0.5)
plt.savefig(f"{target}/{target}_residuals.png", bbox_inches="tight")
plt.close()
ax_sed, ax_residuals = analysis.flux_points.peek(
) # Cannot specify flux_unit outputs in cm-2 s-1 TeV-1. Default to erg
ref_dict = ref_model.parameters.to_dict()
spec_comp_id = {'cas_a': 2, 'hess_j1702': 5} #REally bad hack
ref_dict_spectral = {
'parameters': ref_dict['parameters'][spec_comp_id[target]:]
} #keep only spectral parameters. Is there a better way ?
pwl = PowerLawSpectralModel.from_dict(
ref_dict_spectral) #need to find a way to find spectral model auto
ax_sed = pwl.plot((0.1, 50) * u.TeV,
ax=ax_sed,
energy_power=2,
flux_unit='cm-2 s-1 erg-1',
label='Reference',
ls='--')
ax_sed.legend()
plt.savefig(f"{target}/{target}_fluxpoints.png", bbox_inches="tight")
plt.close()
# Generate README.md file with table and plots
path = f"{target}/spectral_comparison_table.md"
comp_tab.write(path, format="ascii.html", overwrite=True)
txt = Path(f"{target}/spectral_comparison_table.md").read_text()
im1 = f"\n "
im2 = f"\n "
im3 = f"\n "
out = txt + im1 + im2 + im3
Path(f"{target}/README.md").write_text(out)
flux.sum_over_axes().smooth("0.1 deg").plot(stretch="sqrt", add_cbar=True)
# ## Fit
#
# Finally, the big finale: let's do a 3D map fit for the source at the Galactic center, to measure it's position and spectrum. We keep the background normalization free.
# In[ ]:
model = SkyModel(
PointSpatialModel("0 deg", "0 deg", frame="galactic"),
PowerLawSpectralModel(index=2.5,
amplitude="1e-11 cm-2 s-1 TeV-1",
reference="100 GeV"),
)
model_total = SkyModels([model, model_diffuse, model_iso])
dataset = MapDataset(model=model_total,
counts=counts,
exposure=exposure,
psf=psf_kernel)
fit = Fit(dataset)
result = fit.run()
# In[ ]:
print(result)
# In[ ]:
dataset.parameters.to_table()