# Licensed under a 3-clause BSD style license - see LICENSE.rst
import logging
import numpy as np
from astropy import units as u
from astropy.table import Table
from astropy.visualization import quantity_support
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
from gammapy.modeling.models import DatasetModels
from gammapy.utils.scripts import make_name, make_path
from .core import Dataset
log = logging.getLogger(__name__)
__all__ = ["FluxPointsDataset"]
[docs]class FluxPointsDataset(Dataset):
"""
Bundle a set of flux points with a parametric model, to compute fit statistic function using chi2 statistics.
Parameters
----------
models : `~gammapy.modeling.models.Models`
Models (only spectral part needs to be set)
data : `~gammapy.estimators.FluxPoints`
Flux points. Must be sorted along the energy axis
mask_fit : `numpy.ndarray`
Mask to apply for fitting
mask_safe : `numpy.ndarray`
Mask defining the safe data range. By default upper limit values are excluded.
meta_table : `~astropy.table.Table`
Table listing information on observations used to create the dataset.
One line per observation for stacked datasets.
Examples
--------
Load flux points from file and fit with a power-law model::
>>> from gammapy.modeling import Fit
>>> from gammapy.modeling.models import PowerLawSpectralModel, SkyModel
>>> from gammapy.estimators import FluxPoints
>>> from gammapy.datasets import FluxPointsDataset
>>> filename = "$GAMMAPY_DATA/tests/spectrum/flux_points/diff_flux_points.fits"
>>> dataset = FluxPointsDataset.read(filename)
>>> model = SkyModel(spectral_model=PowerLawSpectralModel())
>>> dataset.models = model
Make the fit
>>> fit = Fit()
>>> result = fit.run([dataset])
>>> print(result)
OptimizeResult
<BLANKLINE>
backend : minuit
method : migrad
success : True
message : Optimization terminated successfully.
nfev : 135
total stat : 25.21
<BLANKLINE>
CovarianceResult
<BLANKLINE>
backend : minuit
method : hesse
success : True
message : Hesse terminated successfully.
>>> print(result.parameters.to_table())
type name value unit ... max frozen is_norm link
-------- --------- ---------- -------------- ... --- ------ ------- ----
spectral index 2.2159e+00 ... nan False False
spectral amplitude 2.1619e-13 cm-2 s-1 TeV-1 ... nan False True
spectral reference 1.0000e+00 TeV ... nan True False
Note: In order to reproduce the example you need the tests datasets folder.
You may download it with the command
``gammapy download datasets --tests --out $GAMMAPY_DATA``
"""
stat_type = "chi2"
tag = "FluxPointsDataset"
def __init__(
self,
models=None,
data=None,
mask_fit=None,
mask_safe=None,
name=None,
meta_table=None,
):
if data.geom.ndim != 3 or not data.geom.has_energy_axis:
raise ValueError("FluxPointsDataset only supports an energy axis")
self.data = data
self.mask_fit = mask_fit
self._name = make_name(name)
self.models = models
self.meta_table = meta_table
if mask_safe is None:
mask_safe = (~data.is_ul).data[:, 0, 0]
self.mask_safe = mask_safe
@property
def name(self):
return self._name
@property
def gti(self):
"""Good time interval info (`GTI`)"""
return self.data.gti
@property
def models(self):
return self._models
@models.setter
def models(self, models):
if models is None:
self._models = None
else:
models = DatasetModels(models)
self._models = models.select(datasets_names=self.name)
[docs] def write(self, filename, overwrite=False, **kwargs):
"""Write flux point dataset to file.
Parameters
----------
filename : str
Filename to write to.
overwrite : bool
Overwrite existing file.
**kwargs : dict
Keyword arguments passed to `~astropy.table.Table.write`.
"""
table = self.data.to_table()
if self.mask_fit is None:
mask_fit = self.mask_safe
else:
mask_fit = self.mask_fit
table["mask_fit"] = mask_fit
table["mask_safe"] = self.mask_safe
table.write(make_path(filename), overwrite=overwrite, **kwargs)
[docs] @classmethod
def read(cls, filename, name=None, format="gadf-sed"):
"""Read pre-computed flux points and create a dataset
Parameters
----------
filename : str
Filename to read from.
name : str
Name of the new dataset.
format : {"gadf-sed"}
Format of the dataset file.
Returns
-------
dataset : `FluxPointsDataset`
FluxPointsDataset
"""
from gammapy.estimators import FluxPoints
filename = make_path(filename)
table = Table.read(filename)
mask_fit = None
mask_safe = None
if "mask_safe" in table.colnames:
mask_safe = table["mask_safe"].data.astype("bool")
if "mask_fit" in table.colnames:
mask_fit = table["mask_fit"].data.astype("bool")
return cls(
name=make_name(name),
data=FluxPoints.from_table(table, format=format),
mask_fit=mask_fit,
mask_safe=mask_safe,
)
[docs] @classmethod
def from_dict(cls, data, **kwargs):
"""Create flux point dataset from dict.
Parameters
----------
data : dict
Dict containing data to create dataset from.
Returns
-------
dataset : `FluxPointsDataset`
Flux point datasets.
"""
from gammapy.estimators import FluxPoints
filename = make_path(data["filename"])
table = Table.read(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(
name=data["name"],
data=FluxPoints.from_table(table, format="gadf-sed"),
mask_fit=mask_fit,
mask_safe=mask_safe,
)
def __str__(self):
str_ = f"{self.__class__.__name__}\n"
str_ += "-" * len(self.__class__.__name__) + "\n"
str_ += "\n"
str_ += "\t{:32}: {} \n\n".format("Name", self.name)
# data section
n_bins = 0
if self.data is not None:
n_bins = self.data.energy_axis.nbin
str_ += "\t{:32}: {} \n".format("Number of total flux points", n_bins)
n_fit_bins = 0
if self.mask is not None:
n_fit_bins = np.sum(self.mask.data)
str_ += "\t{:32}: {} \n\n".format("Number of fit bins", n_fit_bins)
# likelihood section
str_ += "\t{:32}: {}\n".format("Fit statistic type", self.stat_type)
stat = np.nan
if self.data is not None and self.models is not None:
stat = self.stat_sum()
str_ += "\t{:32}: {:.2f}\n\n".format("Fit statistic value (-2 log(L))", stat)
# model section
n_models = 0
if self.models is not None:
n_models = len(self.models)
str_ += "\t{:32}: {} \n".format("Number of models", n_models)
if self.models is not None:
str_ += "\t{:32}: {}\n".format(
"Number of parameters", len(self.models.parameters)
)
str_ += "\t{:32}: {}\n\n".format(
"Number of free parameters", len(self.models.parameters.free_parameters)
)
str_ += "\t" + "\n\t".join(str(self.models).split("\n")[2:])
return str_.expandtabs(tabsize=2)
[docs] def data_shape(self):
"""Shape of the flux points data (tuple)."""
return self.data.energy_ref.shape
[docs] def flux_pred(self):
"""Compute predicted flux."""
flux = 0.0
for model in self.models:
flux_model = model.spectral_model(self.data.energy_ref)
if model.temporal_model is not None:
integral = model.temporal_model.integral(
self.gti.time_start, self.gti.time_stop
)
flux_model *= np.sum(integral)
flux += flux_model
return flux
[docs] def stat_array(self):
"""Fit statistic array."""
model = self.flux_pred()
data = self.data.dnde.quantity[:, 0, 0]
try:
sigma = self.data.dnde_err
except AttributeError:
sigma = (self.data.dnde_errn + self.data.dnde_errp) / 2
return ((data - model) / sigma.quantity[:, 0, 0]).to_value("") ** 2
[docs] def residuals(self, method="diff"):
"""Compute flux point residuals
Parameters
----------
method: {"diff", "diff/model"}
Method used to compute the residuals. Available options are:
- `diff` (default): data - model
- `diff/model`: (data - model) / model
Returns
-------
residuals : `~numpy.ndarray`
Residuals array.
"""
fp = self.data
model = self.flux_pred()
residuals = self._compute_residuals(fp.dnde.quantity[:, 0, 0], model, method)
# Remove residuals for upper_limits
residuals[fp.is_ul.data[:, 0, 0]] = np.nan
return residuals
[docs] def plot_fit(
self,
ax_spectrum=None,
ax_residuals=None,
kwargs_spectrum=None,
kwargs_residuals=None,
):
"""Plot flux points, best fit model and residuals in two panels.
Calls `~FluxPointsDataset.plot_spectrum` and `~FluxPointsDataset.plot_residuals`.
Parameters
----------
ax_spectrum : `~matplotlib.axes.Axes`
Axes to plot flux points and best fit model on.
ax_residuals : `~matplotlib.axes.Axes`
Axes to plot residuals on.
kwargs_spectrum : dict
Keyword arguments passed to `~FluxPointsDataset.plot_spectrum`.
kwargs_residuals : dict
Keyword arguments passed to `~FluxPointsDataset.plot_residuals`.
Returns
-------
ax_spectrum, ax_residuals : `~matplotlib.axes.Axes`
Flux points, best fit model and residuals plots.
Examples
--------
>>> from gammapy.modeling.models import PowerLawSpectralModel, SkyModel
>>> from gammapy.estimators import FluxPoints
>>> from gammapy.datasets import FluxPointsDataset
>>> #load precomputed flux points
>>> filename = "$GAMMAPY_DATA/tests/spectrum/flux_points/diff_flux_points.fits"
>>> flux_points = FluxPoints.read(filename)
>>> model = SkyModel(spectral_model=PowerLawSpectralModel())
>>> dataset = FluxPointsDataset(model, flux_points)
>>> #configuring optional parameters
>>> kwargs_spectrum = {"kwargs_model": {"color":"red", "ls":"--"}, "kwargs_fp":{"color":"green", "marker":"o"}}
>>> kwargs_residuals = {"color": "blue", "markersize":4, "marker":'s', }
>>> dataset.plot_fit(kwargs_residuals=kwargs_residuals, kwargs_spectrum=kwargs_spectrum) # doctest: +SKIP
"""
fig = plt.figure(figsize=(9, 7))
gs = GridSpec(7, 1)
if ax_spectrum is None:
ax_spectrum = fig.add_subplot(gs[:5, :])
if ax_residuals is None:
ax_residuals = fig.add_subplot(gs[5:, :], sharex=ax_spectrum)
kwargs_spectrum = kwargs_spectrum or {}
kwargs_residuals = kwargs_residuals or {}
kwargs_residuals.setdefault("method", "diff/model")
self.plot_spectrum(ax=ax_spectrum, **kwargs_spectrum)
self.plot_residuals(ax=ax_residuals, **kwargs_residuals)
return ax_spectrum, ax_residuals
@property
def _energy_bounds(self):
try:
return u.Quantity([self.data.energy_min.min(), self.data.energy_max.max()])
except KeyError:
return u.Quantity([self.data.energy_ref.min(), self.data.energy_ref.max()])
@property
def _energy_unit(self):
return self.data.energy_ref.unit
[docs] def plot_residuals(self, ax=None, method="diff", **kwargs):
"""Plot flux point residuals.
Parameters
----------
ax : `~matplotlib.axes.Axes`
Axes to plot on.
method : {"diff", "diff/model"}
Normalization used to compute the residuals, see `FluxPointsDataset.residuals`.
**kwargs : dict
Keyword arguments passed to `~matplotlib.axes.Axes.errorbar`.
Returns
-------
ax : `~matplotlib.axes.Axes`
Axes object.
"""
ax = ax or plt.gca()
fp = self.data
residuals = self.residuals(method)
xerr = self.data.energy_axis.as_plot_xerr
yerr = fp._plot_get_flux_err(sed_type="dnde")
if method == "diff/model":
model = self.flux_pred()
yerr = (yerr[0].quantity[:, 0, 0] / model), (
yerr[1].quantity[:, 0, 0] / model
)
elif method == "diff":
yerr = yerr[0].quantity[:, 0, 0], yerr[1].quantity[:, 0, 0]
else:
raise ValueError('Invalid method, choose between "diff" and "diff/model"')
kwargs.setdefault("color", kwargs.pop("c", "black"))
kwargs.setdefault("marker", "+")
kwargs.setdefault("linestyle", kwargs.pop("ls", "none"))
with quantity_support():
ax.errorbar(fp.energy_ref, residuals, xerr=xerr, yerr=yerr, **kwargs)
ax.axhline(0, color=kwargs["color"], lw=0.5)
# format axes
ax.set_xlabel(f"Energy [{self._energy_unit}]")
ax.set_xscale("log")
label = self._residuals_labels[method]
ax.set_ylabel(f"Residuals\n {label}")
ymin = np.nanmin(residuals - yerr[0])
ymax = np.nanmax(residuals + yerr[1])
ymax = max(abs(ymin), ymax)
ax.set_ylim(-1.05 * ymax, 1.05 * ymax)
return ax
[docs] def plot_spectrum(self, ax=None, kwargs_fp=None, kwargs_model=None):
"""Plot spectrum including flux points and model.
Parameters
----------
ax : `~matplotlib.axes.Axes`
Axes to plot on.
kwargs_fp : dict
Keyword arguments passed to `gammapy.estimators.FluxPoints.plot`.
kwargs_model : dict
Keyword arguments passed to `gammapy.modeling.models.SpectralModel.plot` and
`gammapy.modeling.models.SpectralModel.plot_error`.
Returns
-------
ax : `~matplotlib.axes.Axes`
Axes object.
Examples
--------
>>> from gammapy.modeling.models import PowerLawSpectralModel, SkyModel
>>> from gammapy.estimators import FluxPoints
>>> from gammapy.datasets import FluxPointsDataset
>>> #load precomputed flux points
>>> filename = "$GAMMAPY_DATA/tests/spectrum/flux_points/diff_flux_points.fits"
>>> flux_points = FluxPoints.read(filename)
>>> model = SkyModel(spectral_model=PowerLawSpectralModel())
>>> dataset = FluxPointsDataset(model, flux_points)
>>> #configuring optional parameters
>>> kwargs_model = {"color":"red", "ls":"--"}
>>> kwargs_fp = {"color":"green", "marker":"o"}
>>> dataset.plot_spectrum(kwargs_fp=kwargs_fp, kwargs_model=kwargs_model) # doctest: +SKIP
"""
kwargs_fp = (kwargs_fp or {}).copy()
kwargs_model = (kwargs_model or {}).copy()
# plot flux points
kwargs_fp.setdefault("label", "Flux points")
kwargs_fp.setdefault("sed_type", "e2dnde")
ax = self.data.plot(ax, **kwargs_fp)
kwargs_model.setdefault("energy_bounds", self._energy_bounds)
kwargs_model.setdefault("label", "Best fit model")
kwargs_model.setdefault("sed_type", "e2dnde")
kwargs_model.setdefault("zorder", 10)
for model in self.models:
if model.datasets_names is None or self.name in model.datasets_names:
model.spectral_model.plot(ax=ax, **kwargs_model)
kwargs_model["color"] = ax.lines[-1].get_color()
kwargs_model.pop("label")
for model in self.models:
if model.datasets_names is None or self.name in model.datasets_names:
model.spectral_model.plot_error(ax=ax, **kwargs_model)
return ax