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test_analysis.py
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test_analysis.py
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# Licensed under a 3-clause BSD style license - see LICENSE.rst
import logging
from pathlib import Path
import pytest
from numpy.testing import assert_allclose
import astropy.units as u
from astropy.coordinates import SkyCoord
from regions import CircleSkyRegion
from pydantic.error_wrappers import ValidationError
from gammapy.analysis import Analysis, AnalysisConfig
from gammapy.datasets import MapDataset, SpectrumDatasetOnOff
from gammapy.maps import WcsGeom, WcsNDMap
from gammapy.modeling.models import DatasetModels
from gammapy.utils.testing import requires_data
CONFIG_PATH = Path(__file__).resolve().parent / ".." / "config"
MODEL_FILE = CONFIG_PATH / "model.yaml"
MODEL_FILE_1D = CONFIG_PATH / "model-1d.yaml"
def get_example_config(which):
"""Example config: which can be 1d or 3d."""
return AnalysisConfig.read(CONFIG_PATH / f"example-{which}.yaml")
def test_init():
cfg = {"general": {"outdir": "test"}}
analysis = Analysis(cfg)
assert analysis.config.general.outdir == "test"
with pytest.raises(TypeError):
Analysis("spam")
def test_update_config():
analysis = Analysis(AnalysisConfig())
data = {"general": {"outdir": "test"}}
config = AnalysisConfig(**data)
analysis.update_config(config)
assert analysis.config.general.outdir == "test"
analysis = Analysis(AnalysisConfig())
data = """
general:
outdir: test
"""
analysis.update_config(data)
assert analysis.config.general.outdir == "test"
analysis = Analysis(AnalysisConfig())
with pytest.raises(TypeError):
analysis.update_config(0)
def test_get_observations_no_datastore():
config = AnalysisConfig()
analysis = Analysis(config)
analysis.config.observations.datastore = "other"
with pytest.raises(FileNotFoundError):
analysis.get_observations()
@requires_data()
def test_get_observations_all():
config = AnalysisConfig()
analysis = Analysis(config)
analysis.config.observations.datastore = "$GAMMAPY_DATA/cta-1dc/index/gps/"
analysis.get_observations()
assert len(analysis.observations) == 4
@requires_data()
def test_get_observations_obs_ids():
config = AnalysisConfig()
analysis = Analysis(config)
analysis.config.observations.datastore = "$GAMMAPY_DATA/cta-1dc/index/gps/"
analysis.config.observations.obs_ids = ["110380"]
analysis.get_observations()
assert len(analysis.observations) == 1
@requires_data()
def test_get_observations_obs_cone():
config = AnalysisConfig()
analysis = Analysis(config)
analysis.config.observations.datastore = "$GAMMAPY_DATA/hess-dl3-dr1"
analysis.config.observations.obs_cone = {
"frame": "icrs",
"lon": "83d",
"lat": "22d",
"radius": "5d",
}
analysis.get_observations()
assert len(analysis.observations) == 4
@requires_data()
def test_get_observations_obs_file(tmp_path):
config = AnalysisConfig()
analysis = Analysis(config)
analysis.get_observations()
filename = tmp_path / "obs_ids.txt"
filename.write_text("20136\n47829\n")
analysis.config.observations.obs_file = filename
analysis.get_observations()
assert len(analysis.observations) == 2
@requires_data()
def test_get_observations_obs_time(tmp_path):
config = AnalysisConfig()
analysis = Analysis(config)
analysis.config.observations.obs_time = {
"start": "2004-03-26",
"stop": "2004-05-26",
}
analysis.get_observations()
assert len(analysis.observations) == 40
analysis.config.observations.obs_ids = [0]
with pytest.raises(KeyError):
analysis.get_observations()
@requires_data()
def test_get_observations_missing_irf():
config = AnalysisConfig()
analysis = Analysis(config)
analysis.config.observations.datastore = "$GAMMAPY_DATA/joint-crab/dl3/magic/"
analysis.config.observations.obs_ids = ["05029748"]
analysis.config.observations.required_irf = ["aeff", "edisp"]
analysis.get_observations()
assert len(analysis.observations) == 1
@requires_data()
def test_set_models():
config = get_example_config("3d")
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
models_str = Path(MODEL_FILE).read_text()
analysis.set_models(models=models_str)
assert isinstance(analysis.models, DatasetModels)
assert len(analysis.models) == 2
assert analysis.models.names == ["source", "stacked-bkg"]
with pytest.raises(TypeError):
analysis.set_models(0)
new_source = analysis.models["source"].copy(name="source2")
analysis.set_models(models=[new_source], extend=False)
assert len(analysis.models) == 2
assert analysis.models.names == ["source2", "stacked-bkg"]
@requires_data()
def test_analysis_1d():
cfg = """
observations:
datastore: $GAMMAPY_DATA/hess-dl3-dr1
obs_ids: [23523, 23526]
obs_time: {
start: [J2004.92654346, J2004.92658453, J2004.92663655],
stop: [J2004.92658453, J2004.92663655, J2004.92670773]
}
datasets:
type: 1d
background:
method: reflected
geom:
axes:
energy_true: {min: 0.01 TeV, max: 300 TeV, nbins: 109}
on_region: {frame: icrs, lon: 83.633 deg, lat: 22.014 deg, radius: 0.11 deg}
safe_mask:
methods: [aeff-default, edisp-bias]
parameters: {bias_percent: 10.0}
containment_correction: false
flux_points:
energy: {min: 1 TeV, max: 50 TeV, nbins: 4}
light_curve:
energy_edges: {min: 1 TeV, max: 50 TeV, nbins: 1}
time_intervals: {
start: [J2004.92654346, J2004.92658453, J2004.92663655],
stop: [J2004.92658453, J2004.92663655, J2004.92670773]
}
"""
config = get_example_config("1d")
analysis = Analysis(config)
analysis.update_config(cfg)
analysis.get_observations()
analysis.get_datasets()
analysis.read_models(MODEL_FILE_1D)
analysis.run_fit()
analysis.get_flux_points()
analysis.get_light_curve()
assert len(analysis.datasets) == 3
table = analysis.flux_points.data.to_table(sed_type="dnde")
assert len(table) == 4
dnde = table["dnde"].quantity
assert dnde.unit == "cm-2 s-1 TeV-1"
assert_allclose(dnde[0].value, 8.116854e-12, rtol=1e-2)
assert_allclose(dnde[2].value, 3.444475e-14, rtol=1e-2)
axis = analysis.light_curve.geom.axes["time"]
assert axis.nbin == 3
assert_allclose(axis.time_min.mjd, [53343.92, 53343.935, 53343.954])
flux = analysis.light_curve.flux.data[:, :, 0, 0]
assert_allclose(flux, [[1.688954e-11], [2.347870e-11], [1.604152e-11]], rtol=1e-4)
@requires_data()
def test_geom_analysis_1d():
cfg = """
observations:
datastore: $GAMMAPY_DATA/hess-dl3-dr1
obs_ids: [23523]
datasets:
type: 1d
background:
method: reflected
on_region: {frame: icrs, lon: 83.633 deg, lat: 22.014 deg, radius: 0.11 deg}
geom:
axes:
energy: {min: 0.1 TeV, max: 30 TeV, nbins: 20}
energy_true: {min: 0.03 TeV, max: 100 TeV, nbins: 50}
containment_correction: false
flux_points:
energy: {min: 1 TeV, max: 50 TeV, nbins: 4}
"""
config = get_example_config("1d")
analysis = Analysis(config)
analysis.update_config(cfg)
analysis.get_observations()
analysis.get_datasets()
assert len(analysis.datasets) == 1
axis = analysis.datasets[0].exposure.geom.axes["energy_true"]
assert axis.nbin == 50
assert_allclose(axis.edges[0].to_value("TeV"), 0.03)
assert_allclose(axis.edges[-1].to_value("TeV"), 100)
@requires_data()
def test_exclusion_region(tmp_path):
config = get_example_config("1d")
analysis = Analysis(config)
region = CircleSkyRegion(center=SkyCoord("85d 23d"), radius=1 * u.deg)
geom = WcsGeom.create(npix=(150, 150), binsz=0.05, skydir=SkyCoord("83d 22d"))
exclusion_mask = ~geom.region_mask([region])
filename = tmp_path / "exclusion.fits"
exclusion_mask.write(filename)
config.datasets.background.method = "reflected"
config.datasets.background.exclusion = filename
analysis.get_observations()
analysis.get_datasets()
assert len(analysis.datasets) == 2
config = get_example_config("3d")
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
geom = analysis.datasets[0]._geom
exclusion_mask = ~geom.region_mask([region])
filename = tmp_path / "exclusion3d.fits"
exclusion_mask.write(filename)
config.datasets.background.exclusion = filename
analysis.get_datasets()
assert len(analysis.datasets) == 1
@requires_data()
def test_analysis_1d_stacked_no_fit_range():
cfg = """
observations:
datastore: $GAMMAPY_DATA/hess-dl3-dr1
obs_cone: {frame: icrs, lon: 83.633 deg, lat: 22.014 deg, radius: 5 deg}
obs_ids: [23592, 23559]
datasets:
type: 1d
stack: false
geom:
axes:
energy: {min: 0.01 TeV, max: 100 TeV, nbins: 73}
energy_true: {min: 0.03 TeV, max: 100 TeV, nbins: 50}
on_region: {frame: icrs, lon: 83.633 deg, lat: 22.014 deg, radius: 0.1 deg}
containment_correction: true
background:
method: reflected
"""
config = AnalysisConfig.from_yaml(cfg)
analysis = Analysis(config)
analysis.update_config(cfg)
analysis.config.datasets.stack = True
analysis.get_observations()
analysis.get_datasets()
analysis.read_models(MODEL_FILE_1D)
analysis.run_fit()
with pytest.raises(ValueError):
analysis.get_excess_map()
assert len(analysis.datasets) == 1
assert_allclose(analysis.datasets["stacked"].counts.data.sum(), 184)
pars = analysis.models.parameters
assert_allclose(analysis.datasets[0].mask_fit.data, True)
assert_allclose(pars["index"].value, 2.76913, rtol=1e-2)
assert_allclose(pars["amplitude"].value, 5.479729e-11, rtol=1e-2)
@requires_data()
def test_analysis_ring_background():
config = get_example_config("3d")
config.datasets.background.method = "ring"
config.datasets.background.parameters = {"r_in": "0.7 deg", "width": "0.7 deg"}
config.datasets.geom.axes.energy.nbins = 1
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
analysis.get_excess_map()
assert isinstance(analysis.datasets[0], MapDataset)
assert_allclose(
analysis.datasets[0].npred_background().data[0, 10, 10], 0.091799, rtol=1e-2
)
assert isinstance(analysis.excess_map["sqrt_ts"], WcsNDMap)
assert_allclose(analysis.excess_map.npred_excess.data[0, 62, 62], 134.12389)
@requires_data()
def test_analysis_ring_3d():
config = get_example_config("3d")
config.datasets.background.method = "ring"
config.datasets.background.parameters = {"r_in": "0.7 deg", "width": "0.7 deg"}
analysis = Analysis(config)
analysis.get_observations()
with pytest.raises(ValueError):
analysis.get_datasets()
@requires_data()
def test_analysis_no_bkg_1d(caplog):
config = get_example_config("1d")
analysis = Analysis(config)
with caplog.at_level(logging.WARNING):
analysis.get_observations()
analysis.get_datasets()
assert not isinstance(analysis.datasets[0], SpectrumDatasetOnOff)
assert "No background maker set. Check configuration." in [
_.message for _ in caplog.records
]
@requires_data()
def test_analysis_no_bkg_3d(caplog):
config = get_example_config("3d")
config.datasets.background.method = None
analysis = Analysis(config)
with caplog.at_level(logging.WARNING):
analysis.get_observations()
analysis.get_datasets()
assert isinstance(analysis.datasets[0], MapDataset)
assert "No background maker set. Check configuration." in [
_.message for _ in caplog.records
]
@requires_data()
def test_analysis_3d():
config = get_example_config("3d")
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
analysis.read_models(MODEL_FILE)
analysis.datasets["stacked"].background_model.spectral_model.tilt.frozen = False
analysis.run_fit()
analysis.get_flux_points()
assert len(analysis.datasets) == 1
assert len(analysis.models.parameters) == 8
res = analysis.models.parameters
assert res["amplitude"].unit == "cm-2 s-1 TeV-1"
table = analysis.flux_points.data.to_table(sed_type="dnde")
assert len(table) == 2
dnde = table["dnde"].quantity
assert_allclose(dnde[0].value, 1.339052e-11, rtol=1e-2)
assert_allclose(dnde[-1].value, 2.772374e-13, rtol=1e-2)
assert_allclose(res["index"].value, 3.097613, rtol=1e-2)
assert_allclose(res["tilt"].value, -0.207792, rtol=1e-2)
@requires_data()
def test_analysis_3d_joint_datasets():
config = get_example_config("3d")
config.datasets.stack = False
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
assert len(analysis.datasets) == 2
assert_allclose(
analysis.datasets[0].background_model.spectral_model.norm.value,
1.031743694988066,
rtol=1e-6,
)
assert_allclose(
analysis.datasets[0].background_model.spectral_model.tilt.value,
0.0,
rtol=1e-6,
)
assert_allclose(
analysis.datasets[1].background_model.spectral_model.norm.value,
0.9776349021876344,
rtol=1e-6,
)
@requires_data()
def test_usage_errors():
config = get_example_config("1d")
analysis = Analysis(config)
with pytest.raises(RuntimeError):
analysis.get_datasets()
with pytest.raises(RuntimeError):
analysis.read_datasets()
with pytest.raises(RuntimeError):
analysis.write_datasets()
with pytest.raises(TypeError):
analysis.read_models()
with pytest.raises(RuntimeError):
analysis.write_models()
with pytest.raises(RuntimeError):
analysis.run_fit()
with pytest.raises(RuntimeError):
analysis.get_flux_points()
with pytest.raises(ValidationError):
analysis.config.datasets.type = "None"
@requires_data()
def test_datasets_io(tmpdir):
config = get_example_config("3d")
analysis = Analysis(config)
analysis.get_observations()
analysis.get_datasets()
models_str = Path(MODEL_FILE).read_text()
analysis.models = models_str
config.general.datasets_file = tmpdir / "datasets.yaml"
config.general.models_file = tmpdir / "models.yaml"
analysis.write_datasets()
analysis = Analysis(config)
analysis.read_datasets()
assert len(analysis.datasets.models) == 2
assert analysis.models.names == ["source", "stacked-bkg"]
analysis.models[0].parameters["index"].value = 3
analysis.write_models()
analysis = Analysis(config)
analysis.read_datasets()
assert len(analysis.datasets.models) == 2
assert analysis.models.names == ["source", "stacked-bkg"]
assert analysis.models[0].parameters["index"].value == 3