def run(self, dataset):
"""Make the profiles
Parameters
----------
dataset : `~gammapy.datasets.MapDataset` or `~gammapy.datasets.MapDatasetOnOff`
the dataset to use for profile extraction
Returns
--------
imageprofile : `~gammapy.estimators.ImageProfile`
Return an image profile class containing the result
"""
if self.energy_edges is not None:
axis = MapAxis.from_energy_edges(self.energy_edges)
dataset = dataset.resample_energy_axis(energy_axis=axis)
else:
dataset = dataset.to_image()
spectrum_datasets = self.get_spectrum_datasets(dataset)
results = self.make_prof(spectrum_datasets)
table = table_from_row_data(results)
if isinstance(self.regions[0], RectangleSkyRegion):
table.meta["PROFILE_TYPE"] = "orthogonal_rectangle"
table.meta["SPECTRAL_MODEL"] = self.spectrum.to_dict()
# return ImageProfile(table)
return table
def fit_gather(model_name, livetime, binned=False):
rows = []
path = (
BASE_PATH /
f"results/models/{model_name}/fit_{livetime.value:.0f}{livetime.unit}")
if binned:
path = Path(str(path).replace("/fit", "/fit_fake"))
for filename in path.glob("*.yaml"):
# model_best_fit = read_best_fit_model(filename)
model_best_fit = Models.read(filename)
model_best_fit = model_best_fit[model_name]
row = {}
for par in model_best_fit.parameters:
row[par.name] = par.value
row[par.name + "_err"] = par.error
rows.append(row)
table = table_from_row_data(rows)
name = f"fit-results-all_{livetime.value:.0f}{livetime.unit}"
if binned:
name = "fit_binned-results-all"
filename = f"results/models/{model_name}/{name}.fits.gz"
log.info(f"Writing {filename}")
table.write(str(filename), overwrite=True)
def run(self, datasets):
"""Run the flux point estimator for all energy groups.
Parameters
----------
datasets : list of `~gammapy.datasets.Dataset`
Datasets
Returns
-------
flux_points : `FluxPoints`
Estimated flux points.
"""
datasets = Datasets(datasets).copy()
rows = []
for energy_min, energy_max in zip(
self.energy_edges[:-1], self.energy_edges[1:]
):
row = self.estimate_flux_point(
datasets, energy_min=energy_min, energy_max=energy_max,
)
rows.append(row)
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
model = datasets.models[self.source]
return FluxPoints(table, reference_spectral_model=model.spectral_model.copy())
def run(self, steps="all"):
"""Run the flux point estimator for all energy groups.
Returns
-------
flux_points : `FluxPoints`
Estimated flux points.
steps : list of str
Which steps to execute. See `estimate_flux_point` for details
and available options.
"""
rows = []
for e_group in self.e_groups:
if e_group["bin_type"].strip() != "normal":
log.debug(
"Skipping under-/ overflow bin in flux point estimation.")
continue
row = self.estimate_flux_point(e_group, steps=steps)
rows.append(row)
meta = OrderedDict([("SED_TYPE", "likelihood")])
table = table_from_row_data(rows=rows, meta=meta)
return FluxPoints(table).to_sed_type("dnde")
def info_table(self, cumulative=False, region=None):
"""Get info table for datasets.
Parameters
----------
cumulative : bool
Cumulate info across all observations
Returns
-------
info_table : `~astropy.table.Table`
Info table.
"""
if not self.is_all_same_type:
raise ValueError("Info table not supported for mixed dataset type.")
stacked = self[0].copy(name=self[0].name)
rows = [stacked.info_dict()]
for dataset in self[1:]:
if cumulative:
stacked.stack(dataset)
row = stacked.info_dict()
else:
row = dataset.info_dict()
rows.append(row)
return table_from_row_data(rows=rows)
def run(self, datasets):
"""Run the flux point estimator for all energy groups.
Parameters
----------
datasets : list of `~gammapy.datasets.Dataset`
Datasets
Returns
-------
flux_points : `FluxPoints`
Estimated flux points.
"""
datasets = Datasets(datasets).copy()
rows = []
for e_min, e_max in zip(self.e_edges[:-1], self.e_edges[1:]):
row = self.estimate_flux_point(datasets, e_min=e_min, e_max=e_max)
rows.append(row)
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
#TODO: this should be changed once likelihood is fully supported
return FluxPoints(table).to_sed_type("dnde")
def optimize(self, datasets):
"""Run the optimization.
Parameters
----------
datasets : `Datasets` or list of `Dataset`
Datasets to optimize.
Returns
-------
optimize_result : `OptimizeResult`
Optimization result
"""
datasets, parameters = self._parse_datasets(datasets=datasets)
datasets.parameters.check_limits()
parameters.autoscale()
kwargs = self.optimize_opts.copy()
backend = kwargs.pop("backend", self.backend)
compute = registry.get("optimize", backend)
# TODO: change this calling interface!
# probably should pass a fit statistic, which has a model, which has parameters
# and return something simpler, not a tuple of three things
factors, info, optimizer = compute(
parameters=parameters,
function=datasets.stat_sum,
store_trace=self.store_trace,
**kwargs,
)
if backend == "minuit":
self._minuit = optimizer
kwargs["method"] = "migrad"
trace = table_from_row_data(info.pop("trace"))
if self.store_trace:
idx = [
parameters.index(par)
for par in parameters.unique_parameters.free_parameters
]
unique_names = np.array(
datasets.models.parameters_unique_names)[idx]
trace.rename_columns(trace.colnames[1:], list(unique_names))
# Copy final results into the parameters object
parameters.set_parameter_factors(factors)
parameters.check_limits()
return OptimizeResult(
parameters=parameters,
total_stat=datasets.stat_sum(),
backend=backend,
method=kwargs.get("method", backend),
trace=trace,
**info,
)
def to_table(self):
"""Convert parameter attributes to `~astropy.table.Table`."""
rows = [p.to_dict() for p in self._parameters]
table = table_from_row_data(rows)
for name in ["value", "error", "min", "max"]:
table[name].format = ".3e"
return table
def get_flux_points(self, coord=None):
"""Extract flux point at a given position.
The flux points are returned in the the form of a `~gammapy.estimators.FluxPoints` object
(which stores the flux points in an `~astropy.table.Table`)
Parameters
---------
coord : `~astropy.coordinates.SkyCoord`
the coordinate where the flux points are extracted.
Returns
-------
fluxpoints : `~gammapy.estimators.FluxPoints`
the flux points object
"""
if coord is None:
coord = self.geom.center_skydir
energies = self.energy_ref
coords = MapCoord.create(dict(skycoord=coord, energy=energies))
ref = self.dnde_ref.squeeze()
fp = dict()
fp["norm"] = self.norm.get_by_coord(coords) * self.norm.unit
for quantity in self._available_quantities:
norm_quantity = f"norm_{quantity}"
res = getattr(self, norm_quantity).get_by_coord(coords)
res *= getattr(self, norm_quantity).unit
fp[norm_quantity] = res
for additional_quantity in self._additional_maps:
res = self.data[additional_quantity].get_by_coord(coords)
res *= self.data[additional_quantity].unit
fp[additional_quantity] = res
# TODO: add support of norm and stat scan
rows = []
for idx, energy in enumerate(self.energy_ref):
result = dict()
result["e_ref"] = energy
result["e_min"] = self.energy_min[idx]
result["e_max"] = self.energy_max[idx]
result["ref_dnde"] = ref[idx]
result["norm"] = fp["norm"][idx]
for quantity in self._available_quantities:
norm_quantity = f"norm_{quantity}"
result[norm_quantity] = fp[norm_quantity][idx]
for key in self._additional_maps:
result[key] = fp[key][idx]
rows.append(result)
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
return FluxPoints(table).to_sed_type('dnde')
def run(self, datasets):
"""Run light curve extraction.
Normalize integral and energy flux between emin and emax.
Parameters
----------
datasets : list of `~gammapy.datasets.SpectrumDataset` or `~gammapy.datasets.MapDataset`
Spectrum or Map datasets.
Returns
-------
lightcurve : `~gammapy.estimators.LightCurve`
the Light Curve object
"""
datasets = Datasets(datasets)
if self.time_intervals is None:
gti = datasets.gti
else:
gti = GTI.from_time_intervals(self.time_intervals)
gti = gti.union(overlap_ok=False, merge_equal=False)
rows = []
for t_min, t_max in gti.time_intervals:
datasets_to_fit = datasets.select_time(t_min=t_min,
t_max=t_max,
atol=self.atol)
if len(datasets_to_fit) == 0:
log.debug(
f"No Dataset for the time interval {t_min} to {t_max}")
continue
row = {"time_min": t_min.mjd, "time_max": t_max.mjd}
row.update(self.estimate_time_bin_flux(datasets_to_fit))
rows.append(row)
if len(rows) == 0:
raise ValueError(
"LightCurveEstimator: No datasets in time intervals")
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
model = datasets.models[self.source]
# TODO: cleanup here...
fp = FluxPoints(table,
reference_spectral_model=model.spectral_model.copy())
table_flux = fp.to_table(sed_type="flux")
table_flux.remove_columns(["stat", "ts", "sqrt_ts", "e_min", "e_max"])
return LightCurve(hstack([table, table_flux]))
def to_table(self):
"""Convert parameter attributes to `~astropy.table.Table`."""
rows = []
for p in self._parameters:
d = p.to_dict()
rows.append({**dict(type=p.type), **d})
table = table_from_row_data(rows)
table["value"].format = ".4e"
for name in ["error", "min", "max"]:
table[name].format = ".3e"
return table
def _loops(self, run, nuisance, stat_profile_opts, optimize_opts,
covariance_opts):
"""Loop in channels and masses."""
for ch in self.channels:
table_rows = []
for mass in self.masses:
# modify and set flux model
dataset_loop = self._set_model_dataset(ch, mass)
# build profile from fitting
j_best, sv_best, likemin, statprofile = self._fit_dataset(
dataset_loop,
nuisance,
run,
ch,
mass,
stat_profile_opts=stat_profile_opts,
optimize_opts=optimize_opts,
covariance_opts=covariance_opts,
)
# calculate results from a profile
fit_result = self._produce_results(j_best, sv_best, likemin,
statprofile)
# not valid run
if fit_result["sigma_v"] is None:
self._make_bad_run_row(run, fit_result)
return False
# build table of results incrementally
row = {
"mass": mass,
"sigma_v": fit_result["sigma_v"],
"sv_ul": fit_result["sv_ul"],
"sv_best": fit_result["sv_best"],
"j_best": fit_result["j_best"],
"statprofile": fit_result["statprofile"],
}
table_rows.append(row)
self.sigmas[ch][mass.value][run] = row["sigma_v"]
self.js[ch][mass.value][run] = row["j_best"]
table = table_from_row_data(rows=table_rows)
table["sigma_v"].unit = self.XSECTION.unit
table["j_best"].unit = self.dataset.models.parameters[
"jfactor"].unit
self.result["runs"][ch][run] = table
return True
def run(self, datasets):
"""Run light curve extraction.
Normalize integral and energy flux between emin and emax.
Parameters
----------
datasets : list of `~gammapy.spectrum.SpectrumDataset` or `~gammapy.cube.MapDataset`
Spectrum or Map datasets.
Returns
-------
lightcurve : `~gammapy.time.LightCurve`
the Light Curve object
"""
datasets = Datasets(datasets)
if self.time_intervals is None:
gti = datasets.gti
else:
gti = GTI.from_time_intervals(self.time_intervals)
gti = gti.union(overlap_ok=False, merge_equal=False)
rows = []
for t_min, t_max in gti.time_intervals:
datasets_to_fit = datasets.select_time(t_min=t_min,
t_max=t_max,
atol=self.atol)
if len(datasets_to_fit) == 0:
log.debug(
f"No Dataset for the time interval {t_min} to {t_max}")
continue
row = {"time_min": t_min.mjd, "time_max": t_max.mjd}
data = self.estimate_time_bin_flux(datasets_to_fit)
row.update(data)
row.update(self.estimate_counts(datasets_to_fit))
rows.append(row)
if len(rows) == 0:
raise ValueError(
"LightCurveEstimator: No datasets in time intervals")
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
table = FluxPoints(table).to_sed_type("flux").table
return LightCurve(table)
def run(self, e_ref, e_min, e_max, steps="all"):
"""Run light curve extraction.
Normalize integral and energy flux between emin and emax.
Parameters
----------
e_ref : `~astropy.unit.Quantity`
reference energy of dnde flux normalization
e_min : `~astropy.unit.Quantity`
minimum energy of integral and energy flux normalization interval
e_max : `~astropy.unit.Quantity`
minimum energy of integral and energy flux normalization interval
steps : list of str
Which steps to execute. Available options are:
* "err": estimate symmetric error.
* "errn-errp": estimate asymmetric errors.
* "ul": estimate upper limits.
* "ts": estimate ts and sqrt(ts) values.
* "norm-scan": estimate likelihood profiles.
By default all steps are executed.
Returns
-------
lightcurve : `~gammapy.time.LightCurve`
the Light Curve object
"""
self.e_ref = e_ref
self.e_min = e_min
self.e_max = e_max
rows = []
for dataset in self.datasets.datasets:
row = {
"time_min": dataset.counts.meta["t_start"].mjd,
"time_max": dataset.counts.meta["t_stop"].mjd,
}
row.update(self.estimate_time_bin_flux(dataset, steps))
rows.append(row)
meta = OrderedDict([("SED_TYPE", "likelihood")])
table = table_from_row_data(rows=rows, meta=meta)
table = FluxPoints(table).to_sed_type("flux").table
return LightCurve(table)
def _make_bad_run_row(self, run, fit_result):
"""Add only likelihood profile for a bad run."""
for ch in self.channels:
table_rows = []
for mass in self.masses:
row = {
"mass": mass,
"sigma_v": None,
"sv_ul": None,
"sv_best": None,
"j_best": None,
"statprofile": fit_result["statprofile"],
}
table_rows.append(row)
self.sigmas[ch][mass.value][run] = None
table = table_from_row_data(rows=table_rows)
self.result["runs"][ch][run] = table
def to_table(self):
"""Convert parameter attributes to `~astropy.table.Table`."""
rows = []
for p in self._parameters:
d = p.to_dict()
if "link" not in d:
d["link"] = ""
for key in ["scale_method", "interp"]:
if key in d:
del d[key]
rows.append({**dict(type=p.type), **d})
table = table_from_row_data(rows)
table["value"].format = ".4e"
for name in ["error", "min", "max"]:
table[name].format = ".3e"
return table
def run(self, datasets):
"""Run the flux point estimator for all energy groups.
Parameters
----------
datasets : list of `~gammapy.datasets.Dataset`
Datasets
Returns
-------
flux_points : `FluxPoints`
Estimated flux points.
"""
# TODO: remove copy here...
datasets = Datasets(datasets).copy()
rows = []
for energy_min, energy_max in progress_bar(zip(self.energy_edges[:-1],
self.energy_edges[1:]),
desc="Energy bins"):
row = self.estimate_flux_point(
datasets,
energy_min=energy_min,
energy_max=energy_max,
)
rows.append(row)
meta = {
"n_sigma": self.n_sigma,
"n_sigma_ul": self.n_sigma_ul,
"sed_type_init": "likelihood"
}
table = table_from_row_data(rows=rows, meta=meta)
model = datasets.models[self.source]
return FluxPoints.from_table(table=table,
reference_model=model.copy(),
gti=datasets.gti,
format="gadf-sed")
def run(self, dataset, steps="all"):
"""Make the profiles
Parameters
----------
dataset : `~gammapy.datasets.MapDataset` or `~gammapy.datasets.MapDatasetOnOff`
the dataset to use for profile extraction
steps : list of str
the steps to be used.
Returns
--------
imageprofile : `~gammapy.estimators.ImageProfile`
Return an image profile class containing the result
"""
spectrum_datasets = self.get_spectrum_datasets(dataset)
results = self.make_prof(spectrum_datasets, steps)
table = table_from_row_data(results)
if isinstance(self.regions[0], RectangleSkyRegion):
table.meta["PROFILE_TYPE"] = "orthogonal_rectangle"
table.meta["SPECTRAL_MODEL"] = self.spectrum.to_dict()
# return ImageProfile(table)
return table
def run(self, datasets, steps="all"):
"""Run the flux point estimator for all energy groups.
Parameters
----------
datasets : list of `~gammapy.spectrum.SpectrumDataset`
Spectrum datasets.
steps : list of str
Which steps to execute. See `estimate_flux_point` for details
and available options.
Returns
-------
flux_points : `FluxPoints`
Estimated flux points.
"""
datasets = self._check_datasets(datasets)
if not datasets.is_all_same_type or not datasets.is_all_same_energy_shape:
raise ValueError(
"Flux point estimation requires a list of datasets"
" of the same type and data shape."
)
self.datasets = datasets.copy()
rows = []
for e_group in self.e_groups:
if e_group["bin_type"].strip() != "normal":
log.debug("Skipping under-/ overflow bin in flux point estimation.")
continue
row = self._estimate_flux_point(e_group, steps=steps)
rows.append(row)
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
return FluxPoints(table).to_sed_type("dnde")
def test_table_from_row_data():
rows = [dict(a=1, b=1 * u.m, c="x"), dict(a=2, b=2 * u.km, c="yy")]
table = table_from_row_data(rows)
assert isinstance(table, Table)
assert table["b"].unit == "m"
assert_allclose(table["b"].data, [1, 2000])
def optimize(self, datasets):
"""Run the optimization.
Parameters
----------
datasets : `Datasets` or list of `Dataset`
Datasets to optimize.
Returns
-------
fit_result : `FitResult`
Results
"""
datasets, parameters = self._parse_datasets(datasets=datasets)
datasets.parameters.check_limits()
# TODO: expose options if / when to scale? On the Fit class?
if np.all(datasets.models.covariance.data == 0):
parameters.autoscale()
kwargs = self.optimize_opts.copy()
backend = kwargs.pop("backend", self.backend)
compute = registry.get("optimize", backend)
# TODO: change this calling interface!
# probably should pass a fit statistic, which has a model, which has parameters
# and return something simpler, not a tuple of three things
factors, info, optimizer = compute(
parameters=parameters,
function=datasets.stat_sum,
store_trace=self.store_trace,
**kwargs,
)
# TODO: Change to a stateless interface for minuit also, or if we must support
# stateful backends, put a proper, backend-agnostic solution for this.
# As preliminary solution would like to provide a possibility that the user
# can access the Minuit object, because it features a lot useful functionality
if backend == "minuit":
self.minuit = optimizer
trace = table_from_row_data(info.pop("trace"))
if self.store_trace:
idx = [
parameters.index(par)
for par in parameters.unique_parameters.free_parameters
]
unique_names = np.array(
datasets.models.parameters_unique_names)[idx]
trace.rename_columns(trace.colnames[1:], list(unique_names))
# Copy final results into the parameters object
parameters.set_parameter_factors(factors)
parameters.check_limits()
return OptimizeResult(
parameters=parameters,
total_stat=datasets.stat_sum(),
backend=backend,
method=kwargs.get("method", backend),
trace=trace,
**info,
)
def optimize(self, backend="minuit", **kwargs):
"""Run the optimization.
Parameters
----------
backend : str
Which backend to use (see ``gammapy.modeling.registry``)
**kwargs : dict
Keyword arguments passed to the optimizer. For the `"minuit"` backend
see https://iminuit.readthedocs.io/en/latest/api.html#iminuit.Minuit
for a detailed description of the available options. If there is an entry
'migrad_opts', those options will be passed to `iminuit.Minuit.migrad()`.
For the `"sherpa"` backend you can from the options `method = {"simplex", "levmar", "moncar", "gridsearch"}`
Those methods are described and compared in detail on
http://cxc.cfa.harvard.edu/sherpa/methods/index.html. The available
options of the optimization methods are described on the following
pages in detail:
* http://cxc.cfa.harvard.edu/sherpa/ahelp/neldermead.html
* http://cxc.cfa.harvard.edu/sherpa/ahelp/montecarlo.html
* http://cxc.cfa.harvard.edu/sherpa/ahelp/gridsearch.html
* http://cxc.cfa.harvard.edu/sherpa/ahelp/levmar.html
For the `"scipy"` backend the available options are desribed in detail here:
https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.minimize.html
Returns
-------
fit_result : `FitResult`
Results
"""
parameters = self._parameters
parameters.check_limits()
# TODO: expose options if / when to scale? On the Fit class?
if np.all(self._models.covariance.data == 0):
parameters.autoscale()
compute = registry.get("optimize", backend)
# TODO: change this calling interface!
# probably should pass a fit statistic, which has a model, which has parameters
# and return something simpler, not a tuple of three things
factors, info, optimizer = compute(
parameters=parameters,
function=self.datasets.stat_sum,
store_trace=self.store_trace,
**kwargs,
)
# TODO: Change to a stateless interface for minuit also, or if we must support
# stateful backends, put a proper, backend-agnostic solution for this.
# As preliminary solution would like to provide a possibility that the user
# can access the Minuit object, because it features a lot useful functionality
if backend == "minuit":
self.minuit = optimizer
trace = table_from_row_data(info.pop("trace"))
if self.store_trace:
pars = self._models.parameters
idx = [
pars.index(par)
for par in pars.unique_parameters.free_parameters
]
unique_names = np.array(self._models.parameters_unique_names)[idx]
trace.rename_columns(trace.colnames[1:], list(unique_names))
# Copy final results into the parameters object
parameters.set_parameter_factors(factors)
parameters.check_limits()
return OptimizeResult(
parameters=parameters,
total_stat=self.datasets.stat_sum(),
backend=backend,
method=kwargs.get("method", backend),
trace=trace,
**info,
)
def run(
self,
runs,
nuisance=False,
stat_profile_opts=None,
optimize_opts=None,
covariance_opts=None,
):
"""Run the SigmaVEstimator for all channels and masses.
Parameters
----------
runs: int
Number of runs where to perform the fitting.
nuisance: bool
Flag to perform fitting with nuisance parameters. Default False.
stat_profile_opts : dict
Options passed to `~gammapy.utils.fitting.Fit.stat_profile`.
optimize_opts : dict
Options passed to `~gammapy.utils.fitting.Fit.optimize`.
covariance_opts : dict
Options passed to `~gammapy.utils.fitting.Fit.covariance`.
Returns
-------
result : dict
result['mean'] provides mean and std values for sigma v vs. mass for each channel.
result['runs'] provides a table of sigma v vs. mass and likelihood profiles for each run and channel.
"""
# default options in sv curve
if stat_profile_opts is None:
stat_profile_opts = dict(bounds=(-25, 150), nvalues=50)
# initialize data containers
for ch in self.channels:
self.result["mean"][ch] = None
self.result["runs"][ch] = {}
self.sigmas[ch] = {}
self.js[ch] = {}
for mass in self.masses:
self.sigmas[ch][mass.value] = {}
self.js[ch][mass.value] = {}
okruns = 0
# loop in runs
for run in range(runs):
self.dataset.fake(background_model=self.dataset.counts)
valid = self._loops(run, nuisance, stat_profile_opts,
optimize_opts, covariance_opts)
# skip the run and continue with the next on if fails for a mass of a specific channel
if not valid:
log.warning(f"Skipping run {run}")
continue
else:
okruns += 1
# calculate means / std
if okruns:
for ch in self.channels:
table_rows = []
for mass in self.masses:
row = {"mass": mass}
listsigmas = [
val
for key, val in self.sigmas[ch][mass.value].items()
]
npsigmas = np.array(listsigmas, dtype=np.float)
sigma_mean = np.nanmean(npsigmas)
sigma_std = np.nanstd(npsigmas)
row["sigma_v"] = sigma_mean * self.XSECTION.unit
row["sigma_v_std"] = sigma_std * self.XSECTION.unit
listjs = [
val for key, val in self.js[ch][mass.value].items()
]
if listjs.count(None) != len(listjs):
npjs = np.array(listjs, dtype=np.float)
js_mean = np.nanmean(npjs)
js_std = np.nanstd(npjs)
row["jfactor"] = js_mean * self.dataset.models.parameters[
"jfactor"].unit
row["jfactor_std"] = js_std * self.dataset.models.parameters[
"jfactor"].unit
else:
row["jfactor"] = None
row["jfactor_std"] = None
table_rows.append(row)
table = table_from_row_data(rows=table_rows)
self.result["mean"][ch] = table
log.info(f"Number of good runs: {okruns}")
return self.result
def run(self, datasets, steps="all"):
"""Run light curve extraction.
Normalize integral and energy flux between emin and emax.
Parameters
----------
datasets : list of `~gammapy.spectrum.SpectrumDataset` or `~gammapy.cube.MapDataset`
Spectrum or Map datasets.
steps : list of str
Which steps to execute. Available options are:
* "err": estimate symmetric error.
* "errn-errp": estimate asymmetric errors.
* "ul": estimate upper limits.
* "ts": estimate ts and sqrt(ts) values.
* "norm-scan": estimate fit statistic profiles.
By default all steps are executed.
Returns
-------
lightcurve : `~gammapy.time.LightCurve`
the Light Curve object
"""
if self.input_time_intervals is None:
time_intervals = [
Time([d.gti.time_start[0], d.gti.time_stop[-1]])
for d in datasets
]
else:
time_intervals = self.input_time_intervals
time_intervals = self._check_and_sort_time_intervals(time_intervals)
rows = []
self.group_table_info = group_datasets_in_time_interval(
datasets=datasets, time_intervals=time_intervals, atol=self.atol)
if np.all(self.group_table_info["Group_ID"] == -1):
raise ValueError(
"LightCurveEstimator: No datasets in time intervals")
for igroup, time_interval in enumerate(time_intervals):
index_dataset = np.where(
self.group_table_info["Group_ID"] == igroup)[0]
if len(index_dataset) == 0:
log.debug("No Dataset for the time interval " + str(igroup))
continue
row = {
"time_min": time_interval[0].mjd,
"time_max": time_interval[1].mjd
}
interval_list_dataset = Datasets(
[datasets[int(_)] for _ in index_dataset])
row.update(
self.estimate_time_bin_flux(interval_list_dataset,
time_interval, steps))
rows.append(row)
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
table = FluxPoints(table).to_sed_type("flux").table
return LightCurve(table)
def run(self, e_ref, e_min, e_max, steps="all", atol="1e-6 s"):
"""Run light curve extraction.
Normalize integral and energy flux between emin and emax.
Parameters
----------
e_ref : `~astropy.units.Quantity`
reference energy of dnde flux normalization
e_min : `~astropy.units.Quantity`
minimum energy of integral and energy flux normalization interval
e_max : `~astropy.units.Quantity`
minimum energy of integral and energy flux normalization interval
steps : list of str
Which steps to execute. Available options are:
* "err": estimate symmetric error.
* "errn-errp": estimate asymmetric errors.
* "ul": estimate upper limits.
* "ts": estimate ts and sqrt(ts) values.
* "norm-scan": estimate fit statistic profiles.
By default all steps are executed.
atol : `~astropy.units.Quantity`
Tolerance value for time comparison with different scale. Default 1e-6 sec.
Returns
-------
lightcurve : `~gammapy.time.LightCurve`
the Light Curve object
"""
atol = u.Quantity(atol)
self.e_ref = e_ref
self.e_min = e_min
self.e_max = e_max
rows = []
self.group_table_info = group_datasets_in_time_interval(
datasets=self.datasets,
time_intervals=self.time_intervals,
atol=atol)
if np.all(self.group_table_info["Group_ID"] == -1):
raise ValueError(
"LightCurveEstimator: No datasets in time intervals")
for igroup, time_interval in enumerate(self.time_intervals):
index_dataset = np.where(
self.group_table_info["Group_ID"] == igroup)[0]
if len(index_dataset) == 0:
log.debug("No Dataset for the time interval " + str(igroup))
continue
row = {
"time_min": time_interval[0].mjd,
"time_max": time_interval[1].mjd
}
interval_list_dataset = Datasets(
[self.datasets[int(_)].copy() for _ in index_dataset])
self._set_scale_model(interval_list_dataset)
row.update(
self.estimate_time_bin_flux(interval_list_dataset,
time_interval, steps))
rows.append(row)
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
table = FluxPoints(table).to_sed_type("flux").table
return LightCurve(table)
def position(self):
"""Source position (`~astropy.coordinates.SkyCoord`)."""
table = table_from_row_data([self.data])
return _skycoord_from_table(table)[0]
def run(self, datasets):
"""Run light curve extraction.
Normalize integral and energy flux between emin and emax.
Parameters
----------
datasets : list of `~gammapy.datasets.SpectrumDataset` or `~gammapy.datasets.MapDataset`
Spectrum or Map datasets.
Returns
-------
lightcurve : `~gammapy.estimators.LightCurve`
the Light Curve object
"""
datasets = Datasets(datasets)
if self.time_intervals is None:
gti = datasets.gti
else:
gti = GTI.from_time_intervals(self.time_intervals)
gti = gti.union(overlap_ok=False, merge_equal=False)
rows = []
for t_min, t_max in progress_bar(gti.time_intervals,
desc="Time intervals"):
datasets_to_fit = datasets.select_time(t_min=t_min,
t_max=t_max,
atol=self.atol)
if len(datasets_to_fit) == 0:
log.debug(
f"No Dataset for the time interval {t_min} to {t_max}")
continue
row = {"time_min": t_min.mjd, "time_max": t_max.mjd}
fp = self.estimate_time_bin_flux(datasets_to_fit)
fp_table = fp.to_table()
for column in fp_table.colnames:
if column == "counts":
data = fp_table[column].quantity.sum(axis=1)
else:
data = fp_table[column].quantity
row[column] = data
fp_table_flux = fp.to_table(sed_type="flux")
for column in fp_table_flux.colnames:
if "flux" in column:
row[column] = fp_table_flux[column].quantity
rows.append(row)
if len(rows) == 0:
raise ValueError(
"LightCurveEstimator: No datasets in time intervals")
table = table_from_row_data(rows=rows, meta={"SED_TYPE": "likelihood"})
# TODO: use FluxPoints here
return LightCurve(table=table)