Merge pull request #2348 from cdeil/gammapy.modeling

Add models to gammapy.modeling.models
gammapy · Sep 9, 2019 · 35d5237 · 35d5237
2 parents ed50a58 + d558acd
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -547,9 +547,9 @@ learn about the new maps classes, see the ``intro_maps`` tutorial at
 
 The new ``gammapy.utils.fitting`` contains a simple modeling and fitting
 framework, that allows the use of ``iminuit`` and ``sherpa`` optimisers as
-"backends" for any fit in Gammapy. The classes in `gammapy.spectrum.models` (1D
-spectrum models) are updated, and `gammapy.image.models` (2D spatial models) and
-`gammapy.cube.models` (3D cube models) was added. The ``SpectrumFit`` class was
+"backends" for any fit in Gammapy. The classes in ``gammapy.spectrum.models`` (1D
+spectrum models) are updated, and ``gammapy.image.models`` (2D spatial models) and
+``gammapy.cube.models`` (3D cube models) was added. The ``SpectrumFit`` class was
 updated and a ``MapFit`` to fit models to maps was added. This part of Gammapy
 remains work in progress, some changes and major improvements are planned for
 the coming months.

diff --git a/docs/catalog/index.rst b/docs/catalog/index.rst
@@ -61,8 +61,8 @@ The ``SourceCatalog`` class mostly handles data file loading, as well as source
 access by integer row index or source name. The ``SourceCatalogObject`` class
 implements in ``__str__`` a pretty-printed version of ``source.data``, so that
 you can ``print(source)``, as well as factory methods to create Gammapy objects
-such as `gammapy.spectrum.models.SpectralModel` or
-``gammapy.image.models.SkySpatialModel`` or `gammapy.spectrum.FluxPoints`
+such as `gammapy.modeling.models.SpectralModel` or
+`gammapy.modeling.models.SkySpatialModel` or `gammapy.spectrum.FluxPoints`
 representing spatial and spectral models, or spectral points, which you can then
 print or plot or use for simulation and analysis.
 

diff --git a/docs/cube/index.rst b/docs/cube/index.rst
@@ -38,7 +38,3 @@ Reference/API
 .. automodapi:: gammapy.cube
     :no-inheritance-diagram:
     :include-all-objects:
-
-.. automodapi:: gammapy.cube.models
-    :no-inheritance-diagram:
-    :include-all-objects:
diff --git a/docs/development/pigs/pig-016.rst b/docs/development/pigs/pig-016.rst
@@ -63,7 +63,7 @@ Introduce gammapy.modeling
 Currently our fitting and modeling framework is in gammapy.utils.fitting,
 and the built-in models in Gammapy are distributed like this:
 
-* gammapy.spectrum.models -- 1D spectral models
+* gammapy.modeling.models -- 1D spectral models
 * gammapy.image.models -- 2D spatial models
 * gammapy.cube.models -- 3D cube models
 * gammapy.time.models -- 1D time models

diff --git a/docs/image/index.rst b/docs/image/index.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -37,7 +37,7 @@ To get started with Gammapy, follow the installation and setup instructions in
     data/index
     irf/index
     maps/index
-    image/index
+    modeling/index
     cube/index
     detect/index
     spectrum/index

diff --git a/docs/modeling/index.rst b/docs/modeling/index.rst
@@ -0,0 +1,35 @@
+.. include:: ../references.txt
+
+.. _modeling:
+
+*****************************
+modeling - Models and fitting
+*****************************
+
+.. currentmodule:: gammapy.modeling
+
+Introduction
+============
+
+tbd
+
+Getting Started
+===============
+
+tbd
+
+Using `gammapy.modeling`
+========================
+
+tbd
+
+Reference/API
+=============
+
+.. automodapi:: gammapy.modeling
+    :no-inheritance-diagram:
+    :include-all-objects:
+
+.. automodapi:: gammapy.modeling.models
+    :no-inheritance-diagram:
+    :include-all-objects:
diff --git a/docs/spectrum/fitting.rst b/docs/spectrum/fitting.rst
@@ -23,7 +23,7 @@ simulated crab runs using the `~gammapy.utils.fitting.Fit` class.
 
     from gammapy.spectrum import SpectrumDatasetOnOff
     from gammapy.utils.fitting import Fit
-    from gammapy.spectrum.models import PowerLaw
+    from gammapy.modeling.models import PowerLaw
     import matplotlib.pyplot as plt
 
     path = "$GAMMAPY_DATA/joint-crab/spectra/hess/"

diff --git a/docs/spectrum/index.rst b/docs/spectrum/index.rst
@@ -31,7 +31,7 @@ OGIP format and fit a spectral model.
 
     from gammapy.spectrum import SpectrumDatasetOnOff
     from gammapy.utils.fitting import Fit
-    from gammapy.spectrum.models import PowerLaw
+    from gammapy.modeling.models import PowerLaw
 
     filename = '$GAMMAPY_DATA/joint-crab/spectra/hess/pha_obs23523.fits'
     dataset = SpectrumDatasetOnOff.from_ogip_files(filename)
@@ -95,7 +95,3 @@ Reference/API
 .. automodapi:: gammapy.spectrum
     :no-inheritance-diagram:
     :include-all-objects:
-
-.. automodapi:: gammapy.spectrum.models
-    :no-inheritance-diagram:
-    :include-all-objects:
diff --git a/docs/time/index.rst b/docs/time/index.rst
@@ -111,7 +111,3 @@ Reference/API
 .. automodapi:: gammapy.time
     :no-inheritance-diagram:
     :include-all-objects:
-
-.. automodapi:: gammapy.time.models
-    :no-inheritance-diagram:
-    :include-all-objects:
diff --git a/examples/example_2_gauss.py b/examples/example_2_gauss.py
@@ -1,14 +1,12 @@
-import matplotlib.pyplot as plt
 import numpy as np
 import astropy.units as u
 from astropy.coordinates import SkyCoord
+import matplotlib.pyplot as plt
+from gammapy.cube import MapEvaluator, make_map_exposure_true_energy
 from gammapy.irf import EffectiveAreaTable2D
-from gammapy.maps import WcsGeom, MapAxis, WcsNDMap
-from gammapy.spectrum.models import PowerLaw
-from gammapy.image.models import SkyGaussian
+from gammapy.maps import MapAxis, WcsGeom, WcsNDMap
+from gammapy.modeling.models import PowerLaw, SkyGaussian, SkyModel
 from gammapy.utils.random import get_random_state
-from gammapy.cube import make_map_exposure_true_energy, MapEvaluator
-from gammapy.cube.models import SkyModel
 
 filename = "$GAMMAPY_DATA/cta-1dc/caldb/data/cta/1dc/bcf/South_z20_50h/irf_file.fits"
 aeff = EffectiveAreaTable2D.read(filename, hdu="EFFECTIVE AREA")

diff --git a/gammapy/__init__.py b/gammapy/__init__.py
@@ -18,18 +18,18 @@
 
 ::
 
- `astro`          --- Astrophysical source and population models
- `catalog`        --- Source catalog tools
- `cube`           --- Cube analysis
- `data`           --- Data and observation handling
- `detect`         --- Source detection tools
- `image`          --- Image processing and analysis tools
- `irf`            --- Instrument response functions (IRFs)
- `maps`           --- Sky map data structures
- `spectrum`       --- Spectrum estimation and modeling
- `stats`          --- Statistics tools
- `time`           --- Time handling and analysis
- `utils`          --- Utility functions and classes
+ astro        --- Astrophysical source and population models
+ catalog      --- Source catalog tools
+ cube         --- Cube analysis
+ data         --- Data and observation handling
+ detect       --- Source detection tools
+ irf          --- Instrument response functions (IRFs)
+ maps         --- Sky map data structures
+ modeling     --- Models and fitting
+ spectrum     --- Spectrum estimation and modeling
+ stats        --- Statistics tools
+ time         --- Time handling and analysis
+ utils        --- Utility functions and classes
 """
 
 __all__ = ["__version__", "test", "song"]

diff --git a/gammapy/astro/darkmatter/profiles.py b/gammapy/astro/darkmatter/profiles.py
@@ -3,7 +3,7 @@
 import abc
 import numpy as np
 import astropy.units as u
-from gammapy.spectrum import integrate_spectrum
+from gammapy.modeling.models.spectrum.utils import integrate_spectrum
 from gammapy.utils.fitting import Parameter, Parameters
 
 __all__ = [
@@ -52,7 +52,7 @@ def integral(self, rmin, rmax, **kwargs):
         rmin, rmax : `~astropy.units.Quantity`
             Lower and upper bound of integration range.
         **kwargs : dict
-            Keyword arguments passed to :func:`~gammapy.spectrum.integrate_spectrum`
+            Keyword arguments passed to :func:`~gammapy.modeling.models.integrate_spectrum`
         """
         integral = integrate_spectrum(self._eval_squared, rmin, rmax, **kwargs)
         return integral.to("GeV2 / cm5")

diff --git a/gammapy/astro/darkmatter/spectra.py b/gammapy/astro/darkmatter/spectra.py
@@ -3,7 +3,7 @@
 import numpy as np
 import astropy.units as u
 from astropy.table import Table
-from gammapy.spectrum.models import SpectralModel, TableModel
+from gammapy.modeling.models import SpectralModel, TableModel
 from gammapy.utils.fitting import Parameter
 from gammapy.utils.scripts import make_path
 
@@ -16,7 +16,7 @@ class PrimaryFlux:
     Based on the precomputed models by Cirelli et al. (2016). All available
     annihilation channels can be found there. The dark matter mass will be set
     to the nearest available value. The spectra will be available as
-    `~gammapy.spectrum.models.TableModel` for a chosen dark matter mass and
+    `~gammapy.modeling.models.TableModel` for a chosen dark matter mass and
     annihilation channel.
 
     References
@@ -114,7 +114,7 @@ def channel(self, channel):
 
     @property
     def table_model(self):
-        """Spectrum as `~gammapy.spectrum.models.TableModel`."""
+        """Spectrum as `~gammapy.modeling.models.TableModel`."""
         subtable = self.table[self.table["mDM"] == self.mDM.value]
         energies = (10 ** subtable["Log[10,x]"]) * self.mDM
         channel_name = self.channel_registry[self.channel]
@@ -142,7 +142,7 @@ class DMAnnihilation(SpectralModel):
     scale : float
         Scale parameter for model fitting
     jfactor : `~astropy.units.Quantity`
-        Integrated J-Factor needed when `~gammapy.image.models.SkyPointSource` spatial model is used
+        Integrated J-Factor needed when `~gammapy.modeling.models.SkyPointSource` spatial model is used
     z: float
         Redshift value
     k: int

diff --git a/gammapy/catalog/fermi.py b/gammapy/catalog/fermi.py
@@ -5,18 +5,21 @@
 import astropy.units as u
 from astropy.table import Column, Table
 from astropy.time import Time
-from gammapy.cube.models import SkyModel
-from gammapy.image.models import SkyDiffuseMap, SkyDisk, SkyGaussian, SkyPointSource
 from gammapy.maps import Map
-from gammapy.spectrum import FluxPoints
-from gammapy.spectrum.models import (
+from gammapy.modeling.models import (
     ExponentialCutoffPowerLaw3FGL,
     LogParabola,
     PLSuperExpCutoff3FGL,
     PLSuperExpCutoff4FGL,
     PowerLaw,
     PowerLaw2,
+    SkyDiffuseMap,
+    SkyDisk,
+    SkyGaussian,
+    SkyModel,
+    SkyPointSource,
 )
+from gammapy.spectrum import FluxPoints
 from gammapy.time import LightCurve
 from gammapy.utils.scripts import make_path
 from gammapy.utils.table import table_standardise_units_inplace
@@ -52,7 +55,7 @@ class SourceCatalogObject4FGL(SourceCatalogObject):
 
     @property
     def spectral_model(self):
-        """Best fit spectral model (`~gammapy.spectrum.models.SpectralModel`)."""
+        """Best fit spectral model (`~gammapy.modeling.models.SpectralModel`)."""
         spec_type = self.data["SpectrumType"].strip()
 
         pars, errs = {}, {}
@@ -332,7 +335,7 @@ def _info_lightcurve(self):
 
     @property
     def spectral_model(self):
-        """Best fit spectral model (`~gammapy.spectrum.models.SpectralModel`)."""
+        """Best fit spectral model (`~gammapy.modeling.models.SpectralModel`)."""
         spec_type = self.data["SpectrumType"].strip()
 
         pars, errs = {}, {}
@@ -375,7 +378,7 @@ def spectral_model(self):
     @property
     def spatial_model(self):
         """
-        Source spatial model (`~gammapy.image.models.SkySpatialModel`).
+        Source spatial model (`~gammapy.modeling.models.SkySpatialModel`).
         """
         d = self.data
 
@@ -409,7 +412,7 @@ def spatial_model(self):
 
     @property
     def sky_model(self):
-        """Source sky model (`~gammapy.cube.models.SkyModel`)."""
+        """Source sky model (`~gammapy.modeling.models.SkyModel`)."""
         spatial_model = self.spatial_model
         spectral_model = self.spectral_model
         return SkyModel(spatial_model, spectral_model, name=self.name)
@@ -564,7 +567,7 @@ def flux_points(self):
 
     @property
     def spectral_model(self):
-        """Best fit spectral model `~gammapy.spectrum.models.SpectralModel`."""
+        """Best fit spectral model `~gammapy.modeling.models.SpectralModel`."""
         pars, errs = {}, {}
         pars["amplitude"] = self.data["Flux"]
         pars["emin"], pars["emax"] = self.energy_range
@@ -636,7 +639,7 @@ def flux_points(self):
 
     @property
     def spectral_model(self):
-        """Best fit spectral model (`~gammapy.spectrum.models.SpectralModel`)."""
+        """Best fit spectral model (`~gammapy.modeling.models.SpectralModel`)."""
         pars, errs = {}, {}
         pars["amplitude"] = self.data["Flux50"]
         pars["emin"], pars["emax"] = self.energy_range
@@ -850,7 +853,7 @@ def _info_other(self):
 
     @property
     def spectral_model(self):
-        """Best fit spectral model (`~gammapy.spectrum.models.SpectralModel`)."""
+        """Best fit spectral model (`~gammapy.modeling.models.SpectralModel`)."""
         d = self.data
         spec_type = self.data["SpectrumType"].strip()
 
@@ -913,7 +916,7 @@ def flux_points(self):
 
     @property
     def spatial_model(self):
-        """Source spatial model (`~gammapy.image.models.SkySpatialModel`)."""
+        """Source spatial model (`~gammapy.modeling.models.SkySpatialModel`)."""
         d = self.data
 
         pars = {}
@@ -946,7 +949,7 @@ def spatial_model(self):
 
     @property
     def sky_model(self):
-        """Source sky model (`~gammapy.cube.models.SkyModel`)."""
+        """Source sky model (`~gammapy.modeling.models.SkyModel`)."""
         spatial_model = self.spatial_model
         spectral_model = self.spectral_model
         return SkyModel(spatial_model, spectral_model, name=self.name)