PIG 7 - Models

  • Author: Axel Donath, Christoph Deil & Regis Terrier
  • Created: Dec 17, 2018
  • Withdrawn: Oct 7, 2019
  • Status: withdrawn
  • Discussion: GH 1971

Introduction

One of the most important features of Gammapy is the modeling of gamma-ray data by parametric models. This includes the modeling of source spectra by spectral models, the modeling of source morphologies by spatial models, the modeling of light curves or phase curves with temporal models and combinations thereof. Instrument specific characteristics, such as PSF, energy resolution, effective area and background are also considered as part of the model framework. Models are used both in interactive analysis, as well as scripted or command line based analyses. For this reason they must implement an easy to use API as well as serialization to disk. Gammapy should provide a variety of built-in models, allow to combine existing models using limited arithmetics and offer the possibility for users to easily implement custom models. A lot of development work has already put into the modeling framework of Gammapy. This PIG outlines the missing development work on the model framework for Gammapy v1.0.

Proposal

Introduce naming scheme for models

Currently Gammapy implements mainly four categories of models: spectral models, morphology or spatial models, combined spectral and spatial models (SkyModel) and lightcurve or phase models. We propose a uniform naming scheme for these model classes, based on the prefixes Spectral..., Spatial..., Temporal:

Base class Template class IRF folded class Background class Model classes
SpectralModel (SpectralModel) SpectralTemplate (TableModel) SpectralIRFModel SpectralBackground Powerlaw, LogParabola, …
SpatialModel (SkySpatialModel) SpatialTemplate (SkyDiffuseMap) SpatialIRFModel? SpatialBackground? Shell, SpatialGaussian, …
TemporalModel PhaseCurveTemplate, LightCurveTemplate (PhaseCurveTableModel), (LightCurveTableModel)   TemporalBackground? Sine, Exponential, …
SourceModel (SkyModel) SourceTemplate (SkyDiffuseCube) SourceIRFModel SourceBackground Arithmetic spectral/spatial models?

The current class names are given in parentheses. Optional model classes, where the need is unclear are marked with a question mark.

Parametric models are named after their parametrization, such as Powerlaw or Gaussian. In case the name is not unique (e.g. for a gaussian spectral and spatial model, the corresponding prefix should be used, such as SpectralGaussian or SpatialGaussian or SpatialConstant and SpectralConstant).

In addition there is the SourceModels class to represent a sum of SourceModel objects.

Unify calling interface for models

For model evaluation we would like to have a nice user interface, that supports Quantity and SkyCoord objects on the one hand and a performance oriented and flexible interface for efficient evaluation for model fitting. The latter We propose a unified implementation scheme for __call__ and .evaluate() for all parametric models.

The actual arthmetics of the model is defined in .evaluate() and should be implemented using numpy expressions only. This ensure compatibility with all the possible higher level callers that use Quantity, SkyCoords or autograd tools.

# for "normal" models it can be a static method
@staticmethod
def evaluate(energy, amplitude, index, reference):
    value = np.power(energy / reference, -index)
    return amplitude * value

# "template" models, that need to access ``self.interpolate()``
def evaluate(self, energy, amplitude):
    value = self.interpolate(energy)
    return amplitude * value

# "IRF" models, that need to access ``self.geom``, ``self.psf`` etc.
def evaluate(self, **kwargs):
    value = self.model(self.energy, **kwargs)
    npred = self.apply_psf(value)
    return npred

A nice user interface as well as parameter dispatching is implemented in the model base classe’s __call__ method:

# spectral model
def __call__(self, energy):
    pars = self.parameters.quantities
    value = self.evaluate(energy, **pars)
    return value

def __call__(self, skycoord):
    pars = self.parameters.quantities
    lon = lon.wrap_at("")
    value = self.evaluate(lon, lat, **pars)
    return value

Model evaluation for fitting will be first implement using the __call__ interface. In case we find performance issue related to Quantity and SkyCoord handling or need auto differentiation tools such as autograd, we can later implement a more efficient interface relying directly on Model.evaluate().

Introduction of background models

For any kind of IACTs analysis hadronic background models are required, which model the residual hadronic (gamma-like) background emission from templates provided by DL3 or by generic parametric models. The background template differ from source templates, because they are defined in reconstructed spatial and energy coordinates. We propose the introduction of the following two model classes:

BackgroundModel

Base class for all background models.

BackgroundIRFModel

Class to represent a template background model. It is initialized with a background map template and introduces additional background parameters to adjust the spectral shape and amplitude. This model can only be evaluated on a fixed grid, defined by the input map. The model is interpolated in the preparation step. No IRFs are applied.

from gammapy.cube import BackgroundTemplate

background_map = Map()
background = BackgroundTemplate(template=background_map, norm=1, tilt=0.1)
npred = background.evaluate()

Introduction of “forward folded” models

To combine parametric model components with their correspoding instrument response functions, such as PSF, energy dispersion and exposure, we propose the introduction of “forward folded” models. These take a fixed data grid, typically defined by the exposure map, on which the model is evaluated. After application of instrument reponse functions, the number of prediced counts is returned by the .evaluate() method. We propose to introduce the following classes:

SpectralIRFModel

A “forward folded” spectral model, that applies energy dispersion and effective area to a SpectralModel. It corresponds in functionality to the current CountsPredictor.

from gammapy.spectrum import Powerlaw, SpectralIRFModel

pwl = Powerlaw()
spectral_irf_model = SpectralIRFModel(model=pwl, exposure=exposure, edisp=edisp)
npred = spectral_irf_model.evaluate()

SpatialIRFModel

A convolved model, that applies the PSF and exposure to a SpatialModel. The need for this model is not clear, as we might solve the use case of morphology fitting by a combined spatial and spectral analysis with one energy bin.

SourceIRFModel

A “forward folded” source model, that applies IRFs to a SourceModel instance and returns an integrated quantity corresponding to predicted counts. It can only be evaluated on a fixed grid, which is defined on initialization by the exposure map. In addition it takes reduced PSF and EDISP objects. In functionality it corresponds to the current MapEvaluator, but with the model parameters attached and the background handling removed. Additional “hidden” IRF parameters e.g. to propagate systematics could be optionally introduced later. This class will replace the current MapEvaluator.

from gammapy.cube import SourceIRFModel, SourceModel

model = SourceModel()
source_irf_model = SourceIRFModel(model, exposure=exposure, edisp=edisp, psf=psf)
npred = source_irf_model.evaluate()

Improve SourceModels class

The existing CompoundSkyModel is a nice very generic abstraction to support any kind of arithmetics between SkyModel objects, but the number of use cases for other operators, except for “+” is very limited and can always be achieved by implementing a custom model. Serilization and component handling of this hierarchical model component structure is intrinsically difficult. For this reason we propose to first support and improve the existing SourceModels that implements an easier to handle flat hierarchy for model components. Support for arbitrary model arithmetics can be introduced, if needed, after Gammapy v1.0. We propose to remove the CompoundSourceModel and reimplement the + operator using the SourceModels class.

from gammapy.cube import SourceModel, SourceModels

component_1 = SourceModel()
component_2 = SourceModel()

total_model = component_1 + component_2
assert isinstance(total_model, SourceModels)

# becomes quivalent to

total_model = SourceModels([component_1, component_2])

Possibly remove the SpectralCompoundModel for consistency.

Introduction of model name attributes

The SourceModel class should be improved to support model component names. This way the SourceModels object can be improved to access model components by name, as well as the XML serialization (which supports names) becomes complete. The following example should work:

from gammapy.cube import SourceModel, SourceModels

component_1 = SourceModel(name="source_1")
component_2 = SourceModel(name="source_2")

total_model = SourceModels([component_1, component_2])

total_model["source_1"].parameters["index"].value = 2.3

# or alternatively??

total_model.parameters["source_1.index"].value = 2.3

# delete a model component in place
del model["source_2"]

This is also simplifies the parameter access in the fitting back-end, because parameter names become unique. E.g. no need for cryptic par_00X_ parameter names in the minuit backend, which simplifies debugging and interaction by the user with methods such as Fit.likelihood_profile() or Fit.confidence(), where parameter identifiers must be given.

Improve and implement model serilization

Serialization of models is an important feature for standard analyses. In gammapy.utils.serialization there is a prototype implementation of XML serialization for SourceModels, We propose to fix this existing XML serilization prototype so that the following easily works:

from gammapy.cube import SourceModels

model = SourceModels.read("model.xml")
print(model)

model.write("model.xml")

In addition we propose to implement an additional YAML serialization format, which results in human-readable model configuration files. Once available the YAML format should be the preferred serialization:

model = SourceModels.read("model.yaml")
print(model)

model.write("model.yaml")

The two file formats should be handled automatically in SourceModel.read() and SourceModel.write().

Improve spatial models

Implement sky coordinate handling

Implement support for coordinate systems. Add an interface for SkyCoord, by introducing a SpatialModel.skycood attribute.

from astropy.coordinates import SkyCoord
from gammapy.image.models import PointSource

# instanciation using a SkyCoord object
point_source = PointSource(skycood=SkyCoord(0, 0, frame="galactic", unit="deg"))
# or
point_source = PointSource(lon="0 deg", lat="0 deg", frame="galactic")

skycoord = point_source.skycoord
assert isinstance(skycoord, SkyCoord)

# evaluation of models using sky coordinates
coords = SkyCoord([0, 1], [0.5, 0.5], frame="galactic", unit="deg")
values = point_source(coords)

# maybe override evaluation for efficient evaluation for fitting
values = point_source(lon, lat)

Implement default parameters

For spectral models Gammapy has defined default parameters, which simplifes the interactive usage of the models. From this experience we propose to introduce default parameters for SpatialModel as well as SourceModel.

from gammapy.image.models import Shell
from gammapy.cube.models import SourceModels

shell = Shell()
print(shell)

Implement evaluation region specifications

For efficient evaluation of model components, we propose that SpatialModel classes declare a circular region .evaluation_radius, they are evaluated on.

from gammapy.image.models import Shell

shell = Shell()
print(shell.evaluation_radius)

The .evaluation_radius should be a property of the model, that is computed depending of the model parameter, that determines the spatial extension of the model. The handling of PointSource and additional evaluation margins, which depend on the pixel size, is done in the step, where the model component is evaluated.

Expose model parameters as attributes

To simplify the interactive handling of model instances, model parameters should be exposed as attribues on the model, so that the following works:

from gammapy.spectrum.models import Powerlaw

pwl = Powerlaw()

pwl.amplitude.value = "1e-12 cm-2 s-1 TeV-1"

# instead of
pwl.parameters["amplitude"].value = "1e-12 cm-2 s-1 TeV-1"

The attributes should be auto-generated in the Model base class, based on the list of parameters defined by the model.

Add new parametric models

We propose to implement the following parametric models:

  • SkyGaussianElongated: Non radial-symmetric Gaussian. In planar approximation…
  • SkyDiskElongated: Non radial-symmetric disk. In planar approximation…
  • SpectralGaussian: Spectral Gaussian model. LogGaussian?

Task list

This is a proposal for a list of pull requests implementing the proposed changes, ordered by priority:

  1. Implement a BackgroundModel base class and a BackgroundIRFModel class. Use the BackgroundIRFModel object in the current MapEvaluator. Join the background parameters with the source model parameters and expose the joined parameter list at the MapEvaluator object, so that it can be used be used in current MapFit. (v0.10)
  2. Reimplement the “+” operator for SkyModel using the SkyModels class. Remove the CompoundSkyModel class. (v0.XX)
  3. Implement support for model component names in SkyModel. Implement SkyModels.__getitem__ to allow for access of model components by name. (v0.XX)
  4. Fix existing XML serilization of SkyModels and add serialization of the model component name. (v0.XX)
  5. Implement a prototype YAML serialization for SkyModels. Add SkyModels.from_yaml() and SkyModels.to_yaml() methods. Extend SkyModels.read() to recognise the file type. (v0.XX)
  6. Implement support for coordinate systems in the SpatialModel base class. Add a SpatialModel.skycoord attribute to return a SkyCoord object and allow initialization of the spatial model positions with SkyCoord. (v0.XX)
  7. Implement the evaluation_radius property for all spatial models. (v0.XX)
  8. Implement default parameter values for spatial models and SourceModel. (v0.XX)
  9. Expose model parameters as attributes on the models. (v0.XX)
  10. Rename all models according to the proposed naming scheme. (v0.XX)
  11. Rename existing MapEvaluator to SourceIRFModel and remove background handling. Temporarily move the background handling to the MapFit class. (v0.XX)
  12. Rename existing CountsPredictor to SpectralIRFModel and unify API with SourceIRFModel as much as possible. (v0.XX)

Alternatives

The proposed model names are open for discussion. Instead of Spectral..., Spatial... and Source... one could also use the suffixes ...1D, ...2D or ...3D. Instead of ...Template one could use ...TableModel.

The ...IRFModel class are basically evaluating models on given coordinate grids and correspond in functionality to the current MapEvaluator. A naming scheme based on ModelEvaluator seems a good alternative proposal. This would include a SpectralEvaluator and a SourceEvaluator and BackgroundEvaluator class.

Decision

The authors decided to withdraw the PIG. Most of the proposed changes have been discussed and implemented independently.