def data_reduction(instrument):
log.info(f"data_reduction: {instrument}")
config = AnalysisConfig.read(f"config.yaml")
config.observations.datastore = f"$JOINT_CRAB/data/{instrument}"
config.datasets.stack = instrument_opts[instrument]['stack']
config.datasets.containment_correction = instrument_opts[instrument][
'containment']
config.datasets.on_region.radius = instrument_opts[instrument]['on_radius']
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
# TODO remove when safe mask can be set on config
if instrument is 'fact':
from gammapy.datasets import SpectrumDatasetOnOff
stacked = SpectrumDatasetOnOff.create(
e_reco=analysis.datasets[0]._energy_axis.edges,
e_true=analysis.datasets[0]._energy_axis.edges,
region=None)
for ds in analysis.datasets:
ds.mask_safe[:] = True
stacked.stack(ds)
analysis.datasets = Datasets([stacked])
analysis.datasets.write(f"reduced_{instrument}", overwrite=True)
def cli_run_analysis(filename, out, overwrite):
"""Performs automated data reduction process."""
config = AnalysisConfig.read(filename)
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
analysis.datasets.write(out, overwrite=overwrite)
log.info(f"Datasets stored in {out} folder.")
def main(config_path, models_path, output, reference):
config = AnalysisConfig.read(config_path)
analysis = Analysis(config)
log.info(config)
analysis.get_observations()
log.info(analysis)
log.info(dir(analysis))
log.info(analysis.datasets)
log.info(analysis.datasets[0].counts)
analysis.get_datasets()
analysis.read_models(models_path)
# stacked fit and flux estimation
analysis.run_fit()
analysis.get_flux_points()
# Plot flux points
ax_sed, ax_residuals = analysis.flux_points.plot_fit()
if reference:
plot_kwargs = {
"energy_range": [
analysis.config.flux_points.energy.min,
analysis.config.flux_points.energy.max,
],
"energy_power": 2,
"flux_unit": "erg-1 cm-2 s-1",
}
create_crab_spectral_model(reference).plot(
**plot_kwargs, ax=ax_sed, label="Crab reference"
)
ax_sed.legend()
ax_sed.set_ylim(1e-12, 1e-9)
base_out = Path(output)
ax_sed.get_figure().savefig(base_out.with_suffix(".pdf").as_posix())
plt.clf()
analysis.models.write(base_out.with_suffix(".yaml").as_posix(), overwrite=True)
analysis.flux_points.write(
base_out.with_suffix(".fits").as_posix(), overwrite=True
)
ax_excess = analysis.datasets["stacked"].plot_excess()
ax_excess.get_figure().savefig(base_out.with_suffix(".excess.pdf").as_posix())
plt.clf()
config.datasets.stack = False
analysis.get_observations()
analysis.get_datasets()
analysis.read_models(models_path)
lc_maker_low = LightCurveEstimator(
energy_edges=[.2, 5] * u.TeV, source=config.flux_points.source, reoptimize=False
)
lc_low = lc_maker_low.run(analysis.datasets)
ax_lc = lc_low.plot(marker="o", label="1D")
ax_lc.get_figure().savefig(base_out.with_suffix(".lc.pdf").as_posix())
plt.clf()
def run_analysis(estimate):
"""Run analysis from observation selection to model fitting."""
config = AnalysisConfig.read(f"{estimate}/config.yaml")
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
models = Models.read(f"{estimate}/models.yaml")
analysis.set_models(models)
analysis.run_fit()
return analysis
def data_reduction(instrument):
log.info(f"data_reduction: {instrument}")
config = AnalysisConfig.read(f"config.yaml")
config.observations.datastore = str(Path().resolve().parent / "data" /
"joint-crab" / instrument)
config.datasets.stack = instrument_opts[instrument]["stack"]
config.datasets.containment_correction = instrument_opts[instrument][
"containment"]
config.datasets.on_region.radius = instrument_opts[instrument]["on_radius"]
if instrument == "fact":
config.datasets.safe_mask.methods = ["aeff-default"]
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
if instrument == "fact":
counts = analysis.datasets[0].counts
data = counts.geom.energy_mask(emin=0.4 * u.TeV)
analysis.datasets[0].mask_safe = counts.copy(data=data)
analysis.datasets.write(f"reduced_{instrument}", overwrite=True)
config.flux_points.energy = {"min": "1 TeV", "max": "10 TeV", "nbins": 3}
# We're all set.
# But before we go on let's see how to save or import `AnalysisConfig` objects though YAML files.
# ### Using YAML configuration files
#
# One can export/import the `AnalysisConfig` to/from a YAML file.
# In[ ]:
config.write("config.yaml", overwrite=True)
# In[ ]:
config = AnalysisConfig.read("config.yaml")
print(config)
# ## Running the analysis
#
# We first create an `~gammapy.analysis.Analysis` object from our configuration.
# In[ ]:
analysis = Analysis(config)
# ### Observation selection
#
# We can directly select and load the observations from disk using `~gammapy.analysis.Analysis.get_observations()`:
# In[ ]:
def get_example_config(which):
"""Example config: which can be 1d or 3d."""
return AnalysisConfig.read(CONFIG_PATH / f"example-{which}.yaml")
path = Path("analysis_3d")
path.mkdir(exist_ok=True)
config_joint.write(path=path / "config_joint.yaml", overwrite=True)
config_stack.write(path=path / "config_stack.yaml", overwrite=True)
# ## Stacked analysis
#
# ### Data reduction
#
# We first show the steps for the stacked analysis and then repeat the same for the joint analysis later
#
# In[ ]:
# Reading yaml file:
config_stacked = AnalysisConfig.read(path=path / "config_stack.yaml")
# In[ ]:
analysis_stacked = Analysis(config_stacked)
# In[ ]:
get_ipython().run_cell_magic(
'time', '',
'# select observations:\nanalysis_stacked.get_observations()\n\n# run data reduction\nanalysis_stacked.get_datasets()'
)
# We have one final dataset, which you can print and explore
# In[ ]:
def run_analyses(targets):
log.info("Run small source extension check.")
info = {}
targets = list(AVAILABLE_TARGETS) if targets == "all-targets" else [
targets
]
for target in targets:
t = time.time()
config = AnalysisConfig.read(f"configs/config_{target}.yaml")
analysis = Analysis(config)
analysis.get_observations()
info["data_preparation"] = time.time() - t
t = time.time()
analysis.get_datasets()
info["data_reduction"] = time.time() - t
models = Models.read(f"models/model_{target}.yaml")
point_models = Models(define_model_pointlike(models[0]))
analysis.set_models(point_models)
t = time.time()
analysis.run_fit()
info["point_model_fitting"] = time.time() - t
log.info(f"\n{point_models.to_parameters_table()}")
log.info("Fitting extended gaussian source.")
analysis.datasets.models = []
analysis.set_models(models)
t = time.time()
analysis.run_fit()
info["gauss_model_fitting"] = time.time() - t
log.info(analysis.fit_result)
log.info(f"\n{models.to_parameters_table()}")
log.info("Extract size error, UL and stat profile.")
t = time.time()
analysis.models[0].spatial_model.lon_0.frozen = True
analysis.models[0].spatial_model.lat_0.frozen = True
analysis.models[0].spectral_model.index.frozen = True
size_est = ExtensionEstimator(
source=models[0].name,
energy_edges=[0.2, 10.0] * u.TeV,
selection_optional=["errn-errp", "ul", "scan"],
size_min="0.08 deg",
size_max="0.12 deg",
size_n_values=20,
reoptimize=True)
res = size_est.run(analysis.datasets)
info["estimator"] = time.time() - t
t = time.time()
log.info(res)
plot_profile(res[0], target)
Path(f"bench_{target}.yaml").write_text(
yaml.dump(info, sort_keys=False, indent=4))
analysis.models.to_parameters_table().write(
f"results/{target}_results.ecsv", overwrite=True)