Installing with pip¶

These instructions cover installation with the pip package management tool. This method will install fermipy and its dependencies into the python distribution that comes with the Fermi Science Tools. First verify that you’re running the python from the Science Tools

$ which python

If this doesn’t point to the python in your Science Tools install (i.e. it returns /usr/bin/python or /usr/local/bin/python) then the Science Tools are not properly setup.

Before starting the installation process, you will need to determine whether you have setuptools and pip installed in your local python environment. You may need to install these packages if you are running with the binary version of the Fermi Science Tools distributed by the FSSC. The following command will install both packages in your local environment:

$ curl https://bootstrap.pypa.io/get-pip.py | python -

Check if pip is correctly installed:

$ which pip

Once again, if this isn’t the pip in the Science Tools, something went wrong. Now install fermipy by running

$ pip install fermipy

To run the ipython notebook examples you will also need to install jupyter notebook:

$ pip install jupyter

Finally, check that fermipy imports:

$ python
Python 2.7.8 (default, Aug 20 2015, 11:36:15)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from fermipy.gtanalysis import GTAnalysis
>>> help(GTAnalysis)

Installing with Anaconda Python¶

These instructions cover how to use fermipy with a new or existing conda python installation. These instructions assume that you have already downloaded and installed the Fermi STs from the FSSC and you have set the FERMI_DIR environment variable to point to the location of this installation.

The condainstall.sh script can be used to install fermipy into an existing conda python installation or to create a minimal conda installation from scratch. In either case download and run the condainstall.sh installation script from the fermipy repository:

$ curl -OL https://raw.githubusercontent.com/fermiPy/fermipy/master/condainstall.sh
$ bash condainstall.sh

If you do not already have anaconda python installed on your system this script will create a new installation under $HOME/miniconda. If you already have conda installed and the conda command is in your path the script will use your existing installation. The script will create a separate environment for your fermipy installation called fermi-env.

Once fermipy is installed you can initialize the fermi environment by running condasetup.sh:

$ curl -OL https://raw.githubusercontent.com/fermiPy/fermipy/master/condasetup.sh
$ source condasetup.sh

This will both activate the fermi-env environment and set up your shell environment to run the Fermi Science Tools. The fermi-env python environment can be exited by running:

$ source deactivate

Running at SLAC¶

This section provides specific installation instructions for running in the SLAC computing environment. First download and source the slacsetup.sh script:

$ wget https://raw.githubusercontent.com/fermiPy/fermipy/master/slacsetup.sh -O slacsetup.sh
$ source slacsetup.sh

To initialize the ST environment run the slacsetup function:

$ slacsetup

This will setup your GLAST_EXT path and source the setup script for one of the pre-built ST installations (the current default is 10-01-01). To manually override the ST version you can optionally provide the release tag as an argument to slacsetup:

$ slacsetup 10-XX-XX

Because users don’t have write access to the ST python installation all pip commands that install or uninstall packages must be executed with the --user flag. After initializing the STs environment, install fermipy with pip:

$ pip install fermipy --user

This will install fermipy in $HOME/.local. You can verify that the installation has succeeded by importing GTAnalysis:

$ python
Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://binstar.org
>>> from fermipy.gtanalysis import GTAnalysis

Upgrading¶

By default installing fermipy with pip will get the latest tagged released available on the PyPi package respository. You can check your currently installed version of fermipy with pip show:

$ pip show fermipy
---
Metadata-Version: 2.0
Name: fermipy
Version: 0.6.7
Summary: A Python package for analysis of Fermi-LAT data
Home-page: https://github.com/fermiPy/fermipy
Author: The Fermipy developers
Author-email: fermipy.developers@gmail.com
License: BSD
Location: /home/vagrant/miniconda/envs/fermi-env/lib/python2.7/site-packages
Requires: wcsaxes, astropy, matplotlib, healpy, scipy, numpy, pyyaml

To upgrade your fermipy installation to the latest version run the pip installation command with --upgrade --no-deps:

$ pip install fermipy --upgrade --no-deps
Collecting fermipy
Installing collected packages: fermipy
  Found existing installation: fermipy 0.6.6
    Uninstalling fermipy-0.6.6:
      Successfully uninstalled fermipy-0.6.6
Successfully installed fermipy-0.6.7

Building from Source¶

These instructions describe how to install fermipy from its git source code repository. This is necessary if you want to locally develop fermipy or you want to use features in a development version of the fermipy code. Note that for non-expert users it is recommended to install fermipy with pip following the instructions above. First clone the fermipy repository:

$ git clone https://github.com/fermiPy/fermipy.git
$ cd fermipy

To install the head of the master branch run setup.py install from the root of the source tree:

# Install the latest version
$ git checkout master
$ python setup.py install --user

A useful option if you are doing active code development is to install your working copy as the local installation. This can be done by running setup.py develop:

# Install a link to your source code installation
$ python setup.py develop --user

You can later remove the link to your working copy by running the same command with the --uninstall flag:

# Install a link to your source code installation
$ python setup.py develop --user --uninstall

You also have the option of installing a previous release tag. To see the list of release tags use git tag:

$ git tag
0.4.0
0.5.0
0.5.1
0.5.2
0.5.3
0.5.4
0.6.0
0.6.1

To install a specific release tag, run git checkout with the tag name followed by setup.py install:

# Checkout a specific release tag
$ git checkout X.X.X
$ python setup.py install --user

Issues¶

If you get an error about importing matplotlib (specifically something about the macosx backend) you might change your default backend to get it working. The customizing matplotlib page details the instructions to modify your default matplotlibrc file (you can pick GTK or WX as an alternative). Specifically the TkAgg and macosx backends currently do not work on OSX if you upgrade matplotlib to the version required by fermipy. To get around this issue you can enable the Agg backend at runtime:

>>> import matplotlib
>>> matplotlib.use('Agg')

However this backend does not support interactive plotting.

In some cases the setup.py script will fail to properly install the fermipy package dependecies. If installation fails you can try running a forced upgrade of these packages with pip install --upgrade:

$ pip install --upgrade --user numpy matplotlib scipy astropy pyyaml healpy wcsaxes ipython jupyter

Creating a Configuration File¶

The first step is to compose a configuration file that defines the data selection and analysis parameters. Complete documentation on the configuration file and available options is given in the Configuration page. fermiPy uses the YAML format for its configuration files. The configuration file has a hierarchical structure in which sets of related options are grouped into sections. The following example is a configuration file for a SOURCE-class analysis of Markarian 421 with FRONT+BACK event types (evtype=3).

data:
  evfile : ft1.lst
  scfile : ft2.fits

binning:
  roiwidth   : 10.0
  binsz      : 0.1
  binsperdec : 8

selection :
  emin : 100
  emax : 100000
  zmax    : 90
  evclass : 128
  evtype  : 3
  target : 'mkn421'
  tmin    : 239557414
  tmax    : 428903014
  filter  : null

gtlike:
  edisp : True
  irfs : 'P8R2_SOURCE_V6'
  edisp_disable : ['isodiff','galdiff']

model:
  src_roiwidth : 15.0
  galdiff  : '$FERMI_DIFFUSE_DIR/gll_iem_v06.fits'
  isodiff  : 'iso_P8R2_SOURCE_V6_v06.txt'
  catalogs : ['3FGL']

The data section defines the input data set and spacecraft file for the analysis. Here evfile points to a list of FT1 files that encompass the chosen ROI, energy range, and time selection. The parameters in the binning section define the dimensions of the ROI and the spatial and energy bin size. The selection section defines parameters related to the data selection (energy range, zmax cut, and event class/type). The target parameter in this section defines the ROI center to have the same coordinates as the given source. The model section defines parameters related to the ROI model definition (diffuse templates, point sources).

fermiPy allows the user to combine multiple data selections into a joint likelihood with the components section. The components section contains a list of dictionaries with the same hierarchy as the root analysis configuration. Each element of the list defines the analysis parameters for an independent sub-selection of the data. Any parameters not defined within the component dictionary default to the value defined in the root configuration. The following example shows the components section that could be appended to the previous configuration to define a joint analysis with four PSF event types:

components:
  - { selection : { evtype : 4  } } # PSF0
  - { selection : { evtype : 8  } } # PSF1
  - { selection : { evtype : 16 } } # PSF2
  - { selection : { evtype : 32 } } # PSF3

Any configuration parameter can be changed with this mechanism. The following example shows how to define a different zmax selection and isotropic template for each of the four PSF event types:

components:
  - model: {isodiff: isotropic_source_psf0_4years_P8V3.txt}
    selection: {evtype: 4, zmax: 70}
  - model: {isodiff: isotropic_source_psf1_4years_P8V3.txt}
    selection: {evtype: 8, zmax: 75}
  - model: {isodiff: isotropic_source_psf2_4years_P8V3.txt}
    selection: {evtype: 16, zmax: 85}
  - model: {isodiff: isotropic_source_psf3_4years_P8V3.txt}
    selection: {evtype: 32, zmax: 90}

Creating an Analysis Script¶

Once the configuration file has been composed, the analysis is executed by creating an instance of GTAnalysis with the configuration file as its argument and calling its analysis methods. GTAnalysis serves as a wrapper over the underlying pyLikelihood classes and provides methods to fix/free parameters, add/remove sources from the model, and perform a fit to the ROI. For a complete documentation of the available methods you can refer to the fermipy package page.

In the following python examples we show how to initialize and run a basic analysis of a source. First we instantiate a GTAnalysis object with the path to the configuration file and run setup().

from fermipy.gtanalysis import GTAnalysis

gta = GTAnalysis('config.yaml',logging={'verbosity' : 3})
gta.setup()

The setup() method performs the data preparation and response calculations needed for the analysis (selecting the data, creating counts and exposure maps, etc.). Depending on the data selection and binning of the analysis this will often be the slowest step in the analysis sequence. The output of setup() is cached in the analysis working directory so subsequent calls to setup() will run much faster.

Before running any other analysis methods it is recommended to first run optimize():

gta.optimize()

This will loop over all model components in the ROI and fit their normalization and spectral shape parameters. This method also computes the TS of all sources which can be useful for identifying weak sources that could be fixed or removed from the model. We can check the results of the optimization step by calling print_roi():

gta.print_roi()

By default all models parameters are initially fixed. The free_source() and free_sources() methods can be use to free or fix parameters of the model. In the following example we free the normalization of catalog sources within 3 deg of the ROI center and free the galactic and isotropic components by name.

# Free Normalization of all Sources within 3 deg of ROI center
gta.free_sources(distance=3.0,pars='norm')

# Free all parameters of isotropic and galactic diffuse components
gta.free_source('galdiff')
gta.free_source('isodiff')

The minmax_ts and minmax_npred arguments to free_sources() can be used to free or fixed sources on the basis of their current TS or Npred values:

# Free sources with TS > 10
gta.free_sources(minmax_ts=[10,None],pars='norm')

# Fix sources with TS < 10
gta.free_sources(minmax_ts=[None,10],free=False,pars='norm')

# Fix sources with 10 < Npred < 100
gta.free_sources(minmax_npred=[10,100],free=False,pars='norm')

When passing a source name argument both case and whitespace are ignored. When using a FITS catalog file a source can also be referred to by any of its associations. When using the 3FGL catalog, the following calls are equivalent ways of freeing the parameters of Mkn 421:

# These calls are equivalent
gta.free_source('mkn421')
gta.free_source('Mkn 421')
gta.free_source('3FGL J1104.4+3812')
gta.free_source('3fglj1104.4+3812')

After freeing parameters of the model we can execute a fit by calling fit(). The will maximize the likelihood with respect to the model parameters that are currently free.

gta.fit()

After the fitting is complete we can write the current state of the model with write_roi:

gta.write_roi('fit_model')

This will write several output files including an XML model file and an ROI dictionary file. The names of all output files will be prepended with the prefix argument to write_roi().

Once we have optimized our model for the ROI we can use the residmap() and tsmap() methods to assess the fit quality and look for new sources.

# Dictionary defining the spatial/spectral template
model = {'SpatialModel' : 'PointSource', 'Index' : 2.0,
         'SpectrumType' ; 'PowerLaw'}

# Both methods return a dictionary with the maps
m0 = gta.residmap('fit_model',model=model)
m1 = gta.tsmap('fit_model',model=model)

More documentation about these methods is available in the Source Detection page.

By default, calls to fit() will execute a global spectral fit over the entire energy range of the analysis. To extract a bin-by-bin flux spectrum (i.e. a SED) you can call sed() method with the name of the source:

gta.sed('mkn421')

More information about sed() method can be found in the SED Analysis page.

Extracting Analysis Results¶

Results of the analysis can be extracted from the dictionary file written by write_roi(). This method writes the current ROI model to both an XML model file and a results dictionary. The results dictionary is written in both npy and yaml formats and can be loaded from a python session after your analysis is complete. The following example demonstrates how to load the dictionary from either format:

>>> # Load from yaml
>>> import yaml
>>> c = yaml.load(open('fit_model.yaml'))
>>>
>>> # Load from npy
>>> import np
>>> c = np.load('fit_model.npy').flat[0]
>>>
>>> print c.keys()
['roi', 'config', 'sources']

The output dictionary contains the following top-level elements:

roi

A dictionary containing information about the ROI as a whole.

config

The configuration dictionary of the GTAnalysis instance.

sources

A dictionary containing information for individual sources in the model (diffuse and point-like). Each element of this dictionary maps to a single source in the ROI model.

version

The version of the fermiPy package that was used to run this analysis. This will automatically be generated from the git release tag.

Each source dictionary collects the properties of the given source (TS, NPred, best-fit parameters, etc.) computed up to that point in the analysis.

>>> print c['sources'].keys()
['3FGL J0954.2+4913',
 '3FGL J0957.4+4728',
 '3FGL J1006.7+3453',

 ...

 '3FGL J1153.4+4932',
 '3FGL J1159.5+2914',
 '3FGL J1203.2+3847',
 '3FGL J1209.4+4119',
 'galdiff',
 'isodiff']

Reloading from a Previous State¶

One can reload an analysis instance that was saved with write_roi() by calling either the create() or load_roi() methods. The create() method can be used to construct an entirely new instance of GTAnalysis from a previously saved results file:

from fermipy.gtanalysis import GTAnalysis
gta = GTAnalysis.create('fit_model.npy')

# Continue running analysis starting from the previously saved
# state
gta.fit()

where the argument is the path to an output file produced with write_roi(). This function will instantiate a new analysis object, run the setup() method, and load the state of the model parameters at the time that write_roi() was called.

The load_roi() method can be used to reload a previous state of the analysis to an existing instance of GTAnalysis.

from fermipy.gtanalysis import GTAnalysis

gta = GTAnalysis('config.yaml')
gta.setup()

gta.write_roi('prefit_model')

# Fit a source
gta.free_source('mkn421')
gta.fit()

# Restore the analysis to its prior state before the fit of mkn421
# was executed
gta.load_roi('prefit_model')

Using load_roi() is generally faster than create() when an analysis instance already exists.

IPython Notebook Tutorials¶

Additional tutorials with more detailed fermipy examples are available as IPython notebooks in the notebooks directory of the fermipy respository. To run any of the notebooks, download the fermipy repository and run jupyter notebook followed by the notebook name:

git clone https://github.com/fermiPy/fermipy.git
cd fermipy/notebooks
jupyter notebook PG\ 1553+113.ipynb

Note that this will require you to have both ipython and jupyter installed in your python environment. These can be installed in a conda- or pip-based installation as follows:

# Install with conda
$ conda install ipython jupyter

# Install with pip
$ pip install ipython jupyter

Class Configuration¶

Classes in the fermiPy package follow a common convention by which the the runtime behavior of a class instance can be controlled. Internally every class instance has a dictionary that defines its configuration state. Elements of this dictionary can be scalars (str, int ,float) or dictionaries defining nested blocks of the configuration.

The class configuration dictionary is set at the time of object creation by passing a dictionary or a path to YAML configuration file to the class constructor. Optional kwargs arguments can be used to override options in the input dictionary. For instance in the following example the config dictionary defines values for the parameters emin and emax. By passing an additional dictionary for the selection block, the value of emax in the kwargs argument (10000) overrides the value of this parameter in the config dictionary.

config = {
'selection' : { 'emin' : 100,
                'emax' : 1000 }
}

gta = GTAnalysis(config,selection={'emax' : 10000})

Alternatively the config argument can be the path to a YAML configuration file:

gta = GTAnalysis('config.yaml',selection={'emax' : 10000})

Configuration File¶

fermiPy uses YAML configuration files which define a hierarchy of parameters organized in sections that group sets of related options. The configuration file mirrors the layout of the configuration dictionary. The options that can be set in each section are described below.

binning:

  # Binning
  roiwidth   : 10.0
  npix       : null
  binsz      : 0.1 # spatial bin size in deg
  binsperdec : 8   # nb energy bins per decade
  projtype   : WCS

# Component section for Front/Back analysis with list style
components:
  - { selection : { evtype : 1 } } # Front
  - { selection : { evtype : 2 } } # Back

# Component section for Front/Back analysis with dictionary style
components:
  front : { selection : { evtype : 1 } } # Front
  back  : { selection : { evtype : 2 } } # Back

data :
  evfile : ft1.lst
  scfile : ft2.fits
  ltcube : null

fileio:
   outdir : null
   logfile : null
   usescratch : False
   scratchdir  : '/scratch'

model :

  # Diffuse components
  galdiff  : '$FERMI_DIR/refdata/fermi/galdiffuse/gll_iem_v06.fits'
  isodiff  : '$FERMI_DIR/refdata/fermi/galdiffuse/iso_P8R2_SOURCE_V6_v06.txt'

  # List of catalogs to be used in the model.
  catalogs :
    - '3FGL'
    - 'extra_sources.xml'

  sources :
    - { 'name' : 'SourceA', 'ra' : 60.0, 'dec' : 30.0, 'SpectrumType' : PowerLaw }
    - { 'name' : 'SourceB', 'ra' : 58.0, 'dec' : 35.0, 'SpectrumType' : PowerLaw }

  # Include catalog sources within this distance from the ROI center
  src_radius  : null

  # Include catalog sources within a box of width roisrc.
  src_roiwidth : 15.0

selection:

  # gtselect parameters
  emin    : 100
  emax    : 100000
  zmax    : 90
  evclass : 128
  evtype  : 3
  tmin    : 239557414
  tmax    : 428903014

  # gtmktime parameters
  filter : 'DATA_QUAL>0 && LAT_CONFIG==1'
  roicut : 'no'

  # Set the ROI center to the coordinates of this source
  target : 'mkn421'

Configuring Diffuse Components¶

The simplest configuration uses a single file for the galactic and isotropic diffuse components. By default the galactic diffuse and isotropic components will be named galdiff and isodiff respectively. An alias for each component will also be created with the name of the mapcube or file spectrum. For instance the galactic diffuse can be referred to as galdiff or gll_iem_v06 in the following example.

model:
  src_roiwidth : 10.0
  galdiff  : '$FERMI_DIFFUSE_DIR/gll_iem_v06.fits'
  isodiff  : '$FERMI_DIFFUSE_DIR/isotropic_source_4years_P8V3.txt'
  catalogs : ['gll_psc_v14.fit']

To define two or more galactic diffuse components you can optionally define the galdiff and isodiff parameters as lists. A separate component will be generated for each element in the list with the name galdiffXX or isodiffXX where XX is an integer position in the list.

model:
  galdiff  :
    - '$FERMI_DIFFUSE_DIR/diffuse_component0.fits'
    - '$FERMI_DIFFUSE_DIR/diffuse_component1.fits'

To explicitly set the name of a component you can define any element as a dictionary containing name and file fields:

model:
  galdiff  :
    - { 'name' : 'component0' : 'file' : '$FERMI_DIFFUSE_DIR/diffuse_component0.fits' }
    - { 'name' : 'component1' : 'file' : '$FERMI_DIFFUSE_DIR/diffuse_component1.fits' }

Configuring Source Components¶

The list of sources for inclusion in the ROI model is set by defining a list of catalogs with the catalogs parameter. Catalog files can be in either XML or FITS format. Sources from the catalogs in this list that satisfy either the src_roiwidth or src_radius selections are added to the ROI model. If a source is defined in multiple catalogs the source definition from the last file in the catalogs list takes precedence.

model:

  src_radius: 5.0
  src_roiwidth: 10.0
  catalogs :
    - 'gll_psc_v14.fit'
    - 'extra_sources.xml'

Sources in addition to those in the catalog file can be defined with the sources parameter. This parameter contains a list of dictionaries that define the parameters of individual sources. The keys of the source dictionary map to the spectral and spatial source properties as they would be defined in the XML model file.

model:
  sources  :
    - { name: 'SourceA', glon : 120.0, glat : -3.0,
     SpectrumType : 'PowerLaw', Index : 2.0, Scale : 1000, Prefactor : !!float 1e-11,
     SpatialModel: 'PointSource' }
    - { name: 'SourceB', glon : 122.0, glat : -3.0,
     SpectrumType : 'LogParabola', norm : !!float 1E-11, Scale : 1000, beta : 0.0,
     SpatialModel: 'PointSource' }

For parameters defined as scalars, the scale and value properties will be assigned automatically from the input value. To set these manually a parameter can alternatively initialized with a dictionary that explicitly sets the value and scale properties:

model:
  sources  :
    - { name: 'SourceA', glon : 120.0, glat : -3.0,
        SpectrumType : 'PowerLaw', Index : 2.0, Scale : 1000,
        Prefactor : { value : 1.0, scale : !!float 1e-11, free : '0' },
        SpatialModel: 'PointSource' }

fermiPy supports three types of pre-defined spatial templates which can be defined by setting the SpatialModel property: PointSource (the default), DiskSource, and GaussianSource. The spatial extension of DiskSource and GaussianSource can be controlled with the SpatialWidth parameter which defines respectively the radius or 68% containment radius in degrees. Note that sources with the DiskSource and GaussianSource spatial property can only be defined with the sources parameter.

model:
  sources  :
    - { name: 'MyDiskSource', glon : 120.0, glat : 0.0,
     SpectrumType : 'PowerLaw', Index : 2.0, Scale : 1000, Prefactor : !!float 1e-11,
     SpatialModel: 'DiskSource', SpatialWidth: 1.0 }
    - { name: 'MyGaussSource', glon : 120.0, glat : 0.0,
     SpectrumType : 'PowerLaw', Index : 2.0, Scale : 1000, Prefactor : !!float 1e-11,
     SpatialModel: 'GaussianSource', SpatialWidth: 1.0 }

Editing the Model at Runtime¶

The model can be manually editing at runtime with the add_source() and delete_source() methods. Sources can be added either before or after calling setup() as shown in the following example.

from fermipy.gtanalysis import GTAnalysis

gta = GTAnalysis('config.yaml',logging={'verbosity' : 3})

# Remove isodiff from the model
gta.delete_source('isodiff')

# Add SourceA to the model
gta.add_source('SourceA',{ 'glon' : 120.0, 'glat' : -3.0,
                'SpectrumType' : 'PowerLaw', 'Index' : 2.0,
                'Scale' : 1000, 'Prefactor' : 1e-11,
                'SpatialModel' : 'PointSource' })

gta.setup()

# Add SourceB to the model
gta.add_source('SourceB',{ 'glon' : 121.0, 'glat' : -2.0,
                 'SpectrumType' : 'PowerLaw', 'Index' : 2.0,
                 'Scale' : 1000, 'Prefactor' : 1e-11,
                 'SpatialModel' : 'PointSource' })

Sources added before calling setup() will be appended to the XML model definition. Sources added after calling setup() will be created dynamically through the pyLikelihood object creation mechanism.

Submodules¶

fermipy.config module¶

class fermipy.config.ConfigManager[source]¶

Bases: object

static create(configfile)[source]¶

Create a configuration dictionary from a yaml config file. This function will first populate the dictionary with defaults taken from pre-defined configuration files. The configuration dictionary is then updated with the user-defined configuration file. Any settings defined by the user will take precedence over the default settings.

static load(path)[source]¶

class fermipy.config.Configurable(config, **kwargs)[source]¶

Bases: object

The base class provides common facilities like loading and saving configuration state.

config¶

Return the configuration dictionary of this class.

configure(config, **kwargs)[source]¶

classmethod get_config()[source]¶

Return a default configuration dictionary for this class.

print_config(logger, loglevel=None)[source]¶

write_config(outfile)[source]¶

Write the configuration dictionary to an output file.

fermipy.config.cast_config(config, defaults)[source]¶

fermipy.config.create_default_config(defaults)[source]¶

Create a configuration dictionary from a defaults dictionary. The defaults dictionary defines valid configuration keys with default values and docstrings. Each dictionary element should be a tuple or list containing (default value,docstring,type).

fermipy.config.validate_config(config, defaults, block='root')[source]¶

fermipy.defaults module¶

fermipy.defaults.make_default_dict(d)[source]¶

fermipy.gtanalysis module¶

class fermipy.gtanalysis.GTAnalysis(config, **kwargs)[source]¶

Bases: fermipy.config.Configurable

High-level analysis interface that internally manages a set of analysis component objects. Most of the functionality of the fermiPy package is provided through the methods of this class. The class constructor accepts a dictionary that defines the configuration for the analysis. Keyword arguments provided in **kwargs can be used to override parameter values in the configuration dictionary.

add_source(name, src_dict, free=False, init_source=True, save_source_maps=True, **kwargs)[source]¶

Add a source to the ROI model. This function may be called either before or after setup().

Parameters:	name (str) – Source name. src_dict (dict or Source object) – Dictionary or source object defining the source properties (coordinates, spectral parameters, etc.). free (bool) – Initialize the source with a free normalization parameter.

cleanup()[source]¶

components¶

Return the list of analysis components.

counts_map()[source]¶

Return a Map representation of the counts map.

Returns:	map
Return type:	Map

static create(infile, config=None)[source]¶

Create a new instance of GTAnalysis from an analysis output file generated with write_roi. By default the new instance will inherit the configuration of the saved analysis instance. The configuration may be overriden by passing a config file path with the config argument.

Parameters:	infile (str) – Path to the ROI results file. config (str) – Path to a configuration file. This will override the configuration in the ROI results file.

defaults = {'sourcefind': {'max_iter': (3, 'Set the number of search iterations.', <type 'int'>), 'min_separation': (1.0, 'Set the minimum separation in deg for sources added in each iteration.', <type 'float'>), 'tsmap_fitter': ('tsmap', 'Set the method for generating the TS map.', <type 'str'>), 'sqrt_ts_threshold': (5.0, 'Set the threshold on sqrt(TS).', <type 'float'>), 'model': (None, 'Set the source model dictionary. By default the test source will be a PointSource with an Index 2 power-law specturm.', <type 'dict'>), 'sources_per_iter': (3, '', <type 'int'>)}, 'roiopt': {'npred_frac': (0.95, '', <type 'float'>), 'shape_ts_threshold': (100.0, '', <type 'float'>), 'npred_threshold': (1.0, '', <type 'float'>)}, 'selection': {'radius': (None, 'Radius of data selection. If none this will be automatically set from the ROI size.', <type 'float'>), 'tmin': (None, 'Minimum time (MET).', <type 'int'>), 'target': (None, 'Choose an object on which to center the ROI. This option takes precendence over ra/dec or glon/glat.', <type 'str'>), 'glon': (None, '', <type 'float'>), 'emin': (None, 'Minimum Energy (MeV)', <type 'float'>), 'emax': (None, 'Maximum Energy (MeV)', <type 'float'>), 'tmax': (None, 'Maximum time (MET).', <type 'int'>), 'glat': (None, '', <type 'float'>), 'filter': (None, 'Filter string for ``gtmktime`` selection.', <type 'str'>), 'logemax': (None, 'Maximum Energy (log10(MeV))', <type 'float'>), 'ra': (None, '', <type 'float'>), 'evtype': (None, 'Event type selection.', <type 'int'>), 'evclass': (None, 'Event class selection.', <type 'int'>), 'zmax': (None, 'Maximum zenith angle.', <type 'float'>), 'logemin': (None, 'Minimum Energy (log10(MeV))', <type 'float'>), 'dec': (None, '', <type 'float'>), 'roicut': ('no', '', <type 'str'>), 'convtype': (None, 'Conversion type selection.', <type 'int'>)}, 'logging': {'verbosity': (3, '', <type 'int'>), 'chatter': (3, 'Set the chatter parameter of the STs.', <type 'int'>)}, 'tsmap': {'multithread': (False, '', <type 'bool'>), 'model': (None, 'Dictionary defining the properties of the test source.', <type 'dict'>), 'erange': (None, 'Lower and upper energy bounds in log10(E/MeV). By default the calculation will be performed over the full analysis energy range.', <type 'list'>), 'max_kernel_radius': (3.0, '', <type 'float'>)}, 'mc': {'seed': (None, '', <type 'int'>)}, 'components': (None, '', <type 'list'>), 'localize': {'dtheta_max': (0.3, 'Half-width of the search region in degrees used for the first pass of the localization search.', <type 'float'>), 'nstep': (5, 'Number of steps along each spatial dimension in the refined likelihood scan.', <type 'int'>), 'fix_background': (True, 'Fix background parameters when fitting the source flux in each energy bin.', <type 'bool'>), 'update': (False, 'Update the source model with the best-fit position.', <type 'bool'>)}, 'binning': {'projtype': ('WCS', 'Projection mode (WCS or HPX).', <type 'str'>), 'binsperdec': (8, 'Number of energy bins per decade.', <type 'float'>), 'enumbins': (None, 'Number of energy bins. If none this will be inferred from energy range and ``binsperdec`` parameter.', <type 'int'>), 'roiwidth': (10.0, 'Width of the ROI in degrees. The number of pixels in each spatial dimension will be set from ``roiwidth`` / ``binsz`` (rounded up).', <type 'float'>), 'hpx_ebin': (True, 'Include energy binning', <type 'bool'>), 'binsz': (0.1, 'Spatial bin size in degrees.', <type 'float'>), 'npix': (None, 'Number of pixels. If none then this will be set from ``roiwidth`` and ``binsz``.', <type 'int'>), 'hpx_order': (10, 'Order of the map (int between 0 and 12, included)', <type 'int'>), 'proj': ('AIT', 'Spatial projection for WCS mode.', <type 'str'>), 'coordsys': ('CEL', 'Coordinate system of the spatial projection (CEL or GAL).', <type 'str'>), 'hpx_ordering_scheme': ('RING', 'HEALPix Ordering Scheme', <type 'str'>)}, 'extension': {'save_model_map': (False, '', <type 'bool'>), 'width': (None, 'Parameter vector for scan over spatial extent. If none then the parameter vector will be set from ``width_min``, ``width_max``, and ``width_nstep``.', <type 'str'>), 'fix_background': (False, 'Fix any background parameters that are currently free in the model when performing the likelihood scan over extension.', <type 'bool'>), 'save_templates': (False, '', <type 'bool'>), 'width_max': (1.0, 'Maximum value in degrees for the likelihood scan over spatial extent.', <type 'float'>), 'width_min': (0.01, 'Minimum value in degrees for the likelihood scan over spatial extent.', <type 'float'>), 'spatial_model': ('GaussianSource', 'Spatial model use for extension test.', <type 'str'>), 'update': (False, 'Update the source model with the best-fit spatial extension.', <type 'bool'>), 'width_nstep': (21, 'Number of steps for the spatial likelihood scan.', <type 'int'>)}, 'sed': {'use_local_index': (False, 'Use a power-law approximation to the shape of the global spectrum in each bin. If this is false then a constant index set to `bin_index` will be used.', <type 'bool'>), 'bin_index': (2.0, 'Spectral index that will be use when fitting the energy distribution within an energy bin.', <type 'float'>), 'fix_background': (True, 'Fix background parameters when fitting the source flux in each energy bin.', <type 'bool'>), 'ul_confidence': (0.95, 'Confidence level for upper limit calculation.', <type 'float'>)}, 'fileio': {'workdir': (None, 'Override the working directory.', <type 'str'>), 'savefits': (True, 'Save intermediate FITS files.', <type 'bool'>), 'scratchdir': ('/scratch', 'Path to the scratch directory.', <type 'str'>), 'outdir': (None, 'Path of the output directory. If none this will default to the directory containing the configuration file.', <type 'str'>), 'logfile': (None, 'Path to log file. If None then log will be written to fermipy.log.', <type 'str'>), 'usescratch': (False, 'Run analysis in a temporary directory under ``scratchdir``.', <type 'bool'>)}, 'gtlike': {'irfs': (None, 'Set the IRF string.', <type 'str'>), 'minbinsz': (0.05, 'Set the minimum bin size used for resampling diffuse maps.', <type 'float'>), 'bexpmap': (None, '', <type 'str'>), 'edisp': (True, 'Enable the correction for energy dispersion.', <type 'bool'>), 'srcmap': (None, '', <type 'str'>), 'resample': (True, '', <type 'bool'>), 'convolve': (True, '', <type 'bool'>), 'rfactor': (2, '', <type 'int'>), 'edisp_disable': (None, 'Provide a list of sources for which the edisp correction should be disabled.', <type 'list'>)}, 'residmap': {'model': (None, 'Dictionary defining the properties of the test source. By default the test source will be a PointSource with an Index 2 power-law specturm.', <type 'dict'>), 'erange': (None, 'Lower and upper energy bounds in log10(E/MeV). By default the calculation will be performed over the full analysis energy range.', <type 'list'>)}, 'optimizer': {'retries': (3, 'Set the number of times to retry the fit when the fit quality is less than ``min_fit_quality``.', <type 'int'>), 'verbosity': (0, '', <type 'int'>), 'optimizer': ('MINUIT', 'Set the optimization algorithm to use when maximizing the likelihood function.', <type 'str'>), 'min_fit_quality': (3, 'Set the minimum fit quality.', <type 'int'>), 'tol': (0.0001, 'Set the optimizer tolerance.', <type 'float'>)}, 'model': {'catalogs': (None, '', <type 'list'>), 'limbdiff': (None, '', <type 'list'>), 'src_radius_roi': (None, 'Half-width of the ROI selection. This parameter can be used in lieu of src_roiwidth.', <type 'float'>), 'extdir': ('Extended_archive_v15', '', <type 'str'>), 'sources': (None, '', <type 'list'>), 'assoc_xmatch_columns': (['3FGL_Name'], 'Choose a set of association columns on which to cross-match catalogs.', <type 'list'>), 'diffuse': (None, '', <type 'list'>), 'src_roiwidth': (None, 'Select sources within a box of RxR centered on the ROI. If none then no cut is applied.', <type 'float'>), 'isodiff': (None, 'Set the isotropic template.', <type 'list'>), 'merge_sources': (True, 'Merge properties of sources that appear in multiple source catalogs. If merge_sources=false then subsequent sources with the same name will be ignored.', <type 'bool'>), 'extract_diffuse': (False, 'Extract a copy of all mapcube components centered on the ROI.', <type 'bool'>), 'src_radius': (None, 'Set the maximum distance for inclusion of sources in the ROI model. Selects all sources within a circle of this radius centered on the ROI. If none then no selection is applied. This selection will be ORed with sources passing the cut on src_roiwidth.', <type 'float'>), 'galdiff': (None, 'Set the galactic IEM mapcube.', <type 'list'>)}, 'data': {'evfile': (None, 'Path to FT1 file or list of FT1 files.', <type 'str'>), 'scfile': (None, 'Path to FT2 (spacecraft) file.', <type 'str'>), 'ltcube': (None, 'Path to livetime cube. If none a livetime cube will be generated with ``gtmktime``.', <type 'str'>)}, 'plotting': {'graticule_radii': (None, 'Define a list of radii at which circular graticules will be drawn.', <type 'list'>), 'erange': (None, '', <type 'list'>), 'cmap': ('ds9_b', 'Set the colormap for 2D plots.', <type 'str'>), 'catalogs': (None, '', <type 'list'>), 'format': ('png', '', <type 'str'>)}, 'tscube': {'do_sed': (True, 'Compute the energy bin-by-bin fits', <type 'bool'>), 'remake_test_source': (False, 'If true, recomputes the test source image (otherwise just shifts it)', <type 'bool'>), 'st_scan_level': (0, 'Level to which to do ST-based fitting (for testing)', <type 'int'>), 'cov_scale': (-1.0, 'Scale factor to apply to broadband fitting cov. matrix in bin-by-bin fits ( < 0 -> fixed ) ', <type 'float'>), 'max_iter': (30, 'Maximum number of iterations for the Newtons method fitter.', <type 'int'>), 'nnorm': (10, 'Number of points in the likelihood v. normalization scan', <type 'int'>), 'norm_sigma': (5.0, 'Number of sigma to use for the scan range ', <type 'float'>), 'tol_type': (0, 'Absoulte (0) or relative (1) criteria for convergence.', <type 'int'>), 'cov_scale_bb': (-1.0, 'Scale factor to apply to global fitting cov. matrix in broadband fits. ( < 0 -> no prior ) ', <type 'float'>), 'tol': (0.001, 'Critetia for fit convergence (estimated vertical distance to min < tol )', <type 'float'>), 'model': (None, 'Dictionary defining the properties of the test source. By default the test source will be a PointSource with an Index 2 power-law specturm.', <type 'dict'>)}}¶

delete_source(name, save_template=True, delete_source_map=False, **kwargs)[source]¶

Delete a source from the model.

Parameters:	name (str) – Source name.
Returns:	src – The deleted source object.
Return type:	Model

delete_sources(cuts=None, distance=None, minmax_ts=None, minmax_npred=None, square=False)[source]¶

Delete sources in the ROI model satisfying the given selection criteria.

Returns:	srcs – A list of Model objects.
Return type:	list

energies¶

Return the energy bin edges.

enumbins¶

Return the number of energy bins.

erange¶

extension(name, **kwargs)[source]¶

Test this source for spatial extension with the likelihood ratio method (TS_ext). This method will substitute an extended spatial model for the given source and perform a one-dimensional scan of the spatial extension parameter over the range specified with the width parameters. The 1-D profile likelihood is then used to compute the best-fit value, upper limit, and TS for extension. Any background parameters that are free will also be simultaneously profiled in the likelihood scan.

Parameters:	name (str) – Source name. spatial_model (str) – Spatial model that will be used when testing extension (e.g. DiskSource, GaussianSource). width_min (float) – Minimum value in degrees for the spatial extension scan. width_max (float) – Maximum value in degrees for the spatial extension scan. width_nstep (int) – Number of scan points between width_min and width_max. Scan points will be spaced evenly on a logarithmic scale between log(width_min) and log(width_max). width (array-like) – Sequence of values in degrees for the spatial extension scan. If this argument is None then the scan points will be determined from width_min/width_max/width_nstep. fix_background (bool) – Fix all background sources when performing the extension fit. update (bool) – Update this source with the best-fit model for spatial extension. save_model_map (bool) – Save model maps for all steps in the likelihood scan.
Returns:	extension – Dictionary containing results of the extension analysis. The same dictionary is also saved to the dictionary of this source under ‘extension’.
Return type:	dict

find_sources(prefix='', **kwargs)[source]¶

An iterative source-finding algorithm.

Parameters:

model (dict) – Dictionary defining the properties of the test source. This is the model that will be used for generating TS maps. sqrt_ts_threshold (float) – Source threshold in sqrt(TS). Only peaks with sqrt(TS) exceeding this threshold will be used as seeds for new sources. min_separation (float) – Minimum separation in degrees of sources detected in each iteration. The source finder will look for the maximum peak in the TS map within a circular region of this radius. max_iter (int) – Maximum number of source finding iterations. The source finder will continue adding sources until no additional peaks are found or the number of iterations exceeds this number. sources_per_iter (int) – Maximum number of sources that will be added in each iteration. If the number of detected peaks in a given iteration is larger than this number, only the N peaks with the largest TS will be used as seeds for the current iteration. tsmap_fitter (str) – Set the method used internally for generating TS maps. Valid options: tsmap tscube tsmap (dict) – Keyword arguments dictionary for tsmap method. tscube (dict) – Keyword arguments dictionary for tscube method.

fit(update=True, **kwargs)[source]¶

Run the likelihood optimization. This will execute a fit of all parameters that are currently free in the ROI model and update the charateristics (TS, Npred, etc.) of the corresponding model components. The fit will be repeated N times (set with the retries parameter) until a fit quality of 3 is obtained.

Parameters:	update (bool) – Do not update the ROI model. tol (float) – Set the optimizer tolerance. verbosity (int) – Set the optimizer output level. retries (int) – Set the number of times to rerun the fit when the fit quality is < 3. min_fit_quality (int) – Set the minimum fit quality. If the fit quality is smaller than this value then all model parameters will be restored to their values prior to the fit. reoptimize (bool) – Refit background sources when updating source properties (TS and likelihood profiles).
Returns:	fit – Dictionary containing diagnostic information for the fit (fit quality, parameter covariances, etc.).
Return type:	dict

free_index(name, free=True)[source]¶

Free/Fix index of a source.

Parameters:	name (str) – Source name. free (bool) – Choose whether to free (free=True) or fix (free=False).

free_norm(name, free=True)[source]¶

Free/Fix normalization of a source.

Parameters:	name (str) – Source name. free (bool) – Choose whether to free (free=True) or fix (free=False).

free_parameter(name, par, free=True)[source]¶

free_shape(name, free=True)[source]¶

Free/Fix shape parameters of a source.

Parameters:	name (str) – Source name. free (bool) – Choose whether to free (free=True) or fix (free=False).

free_source(name, free=True, pars=None)[source]¶

Free/Fix parameters of a source.

Parameters:	name (str) – Source name. free (bool) – Choose whether to free (free=True) or fix (free=False) source parameters. pars (list) – Set a list of parameters to be freed/fixed for this source. If none then all source parameters will be freed/fixed with the exception of those defined in the skip_pars list.

free_sources(free=True, pars=None, cuts=None, distance=None, minmax_ts=None, minmax_npred=None, square=False, exclude_diffuse=False)[source]¶

Free or fix sources in the ROI model satisfying the given selection. When multiple selections are defined, the selected sources will be those satisfying the logical AND of all selections (e.g. distance < X && minmax_ts[0] < ts < minmax_ts[1] && ...).

Parameters:	free (bool) – Choose whether to free (free=True) or fix (free=False) source parameters. pars (list) – Set a list of parameters to be freed/fixed for this source. If none then all source parameters will be freed/fixed. If pars=’norm’ then only normalization parameters will be freed. cuts (dict) – Dictionary of [min,max] selections on source properties. distance (float) – Distance out to which sources should be freed or fixed. If this parameter is none no selection will be applied. minmax_ts (list) – Free sources that have TS in the range [min,max]. If either min or max are None then only a lower (upper) bound will be applied. If this parameter is none no selection will be applied. minmax_npred (list) – Free sources that have Npred in the range [min,max]. If either min or max are None then only a lower (upper) bound will be applied. If this parameter is none no selection will be applied. square (bool) – Switch between applying a circular or square (ROI-like) selection on the maximum projected distance from the ROI center. exclude_diffuse (bool) – Exclude diffuse sources.
Returns:	srcs – A list of Model objects.
Return type:	list

free_sources_by_position(free=True, pars=None, distance=None, square=False)[source]¶

Free/Fix all sources within a certain distance of the given sky coordinate. By default it will use the ROI center.

Parameters:	free (bool) – Choose whether to free (free=True) or fix (free=False) source parameters. pars (list) – Set a list of parameters to be freed/fixed for this source. If none then all source parameters will be freed/fixed. If pars=’norm’ then only normalization parameters will be freed. distance (float) – Distance in degrees out to which sources should be freed or fixed. If none then all sources will be selected. square (bool) – Apply a square (ROI-like) selection on the maximum distance in either X or Y in projected cartesian coordinates.
Returns:	srcs – A list of Source objects.
Return type:	list

generate_model(model_name=None)[source]¶

Generate model maps for all components. model_name should be a unique identifier for the model. If model_name is None then the model maps will be generated using the current parameters of the ROI.

generate_model_map(model_name, name=None)[source]¶

Parameters:	model_name (str) – String that will be append to the name of the output file. name (str) – Name of the component.

get_free_params()[source]¶

get_free_source_params(name)[source]¶

get_model_map(name=None)[source]¶

get_source_name(name)[source]¶

Return the name of a source as it is defined in the pyLikelihood model object.

get_sources(cuts=None, distance=None, minmax_ts=None, minmax_npred=None, square=False)[source]¶

Retrieve list of sources in the ROI model satisfying the given selections.

Returns:	srcs – A list of Model objects.
Return type:	list

get_src_model(name, paramsonly=False, reoptimize=False, npts=20)[source]¶

Compose a dictionary for the given source with the current best-fit parameters.

Parameters:	name (str) – paramsonly (bool) – reoptimize (bool) – Re-fit background parameters in likelihood scan. npts (int) – Number of points for likelihood scan.

like¶

Return the global likelihood object.

load_roi(infile)[source]¶

This function reloads the analysis state from a previously saved instance generated with write_roi.

load_xml(xmlfile)[source]¶

Load model definition from XML.

localize(name, **kwargs)[source]¶

Find the best-fit position of a source. Localization is performed in two steps. First a TS map is computed centered on the source with half-width set by dtheta_max. A fit is then performed to the maximum TS peak in this map. The source position is then further refined by scanning the likelihood in the vicinity of the peak found in the first step. The size of the scan region is set to encompass the 99% positional uncertainty contour as determined from the peak fit.

Parameters:	name (str) – Source name. dtheta_max (float) – Maximum offset in RA/DEC in deg from the nominal source position that will be used to define the boundaries of the TS map search region. nstep (int) – Number of steps in longitude/latitude that will be taken when refining the source position. The bounds of the scan range are set to the 99% positional uncertainty as determined from the TS map peak fit. The total number of sampling points will be nstep**2. fix_background (bool) – Fix background parameters when fitting the source position. update (bool) – Update the model for this source with the best-fit position. If newname=None this will overwrite the existing source map of this source with one corresponding to its new location. newname (str) – Name that will be assigned to the relocalized source when update=True. If newname is None then the existing source name will be used.
Returns:	localize – Dictionary containing results of the localization analysis. This dictionary is also saved to the dictionary of this source in ‘localize’.
Return type:	dict

make_plots(prefix, mcube_maps, **kwargs)[source]¶

model_counts_map(name=None, exclude=None)[source]¶

Return the model counts map for a single source, a list of sources, or for the sum of all sources in the ROI. The exclude parameter can be used to exclude one or more components when generating the model map.

Parameters:	name (str or list of str) – Parameter controlling the set of sources for which the model counts map will be calculated. If name=None the model map will be generated for all sources in the ROI. exclude (str or list of str) – List of sources that will be excluded when calculating the model map.
Returns:	maps – A list of Map objects.
Return type:	list

model_counts_spectrum(name, emin=None, emax=None, summed=False)[source]¶

Return the predicted number of model counts versus energy for a given source and energy range. If summed=True return the counts spectrum summed over all components otherwise return a list of model spectra.

npix¶

Return the number of energy bins.

optimize(**kwargs)[source]¶

Iteratively optimize the ROI model. The optimization is performed in three sequential steps:

• Free the normalization of the N largest components (as determined from NPred) that contain a fraction npred_frac of the total predicted counts in the model and perform a simultaneous fit of the normalization parameters of these components.
• Individually fit the normalizations of all sources that were not included in the first step in order of their Npred values. Skip any sources that have NPred < npred_threshold.
• Individually fit the shape and normalization parameters of all sources with TS > shape_ts_threshold where TS is determined from the first two steps of the ROI optimization.

To ensure that the model is fully optimized this method can be run multiple times.

Parameters:

npred_frac (float) – Threshold on the fractional number of counts in the N largest components in the ROI. This parameter determines the set of sources that are fit in the first optimization step. npred_threshold (float) – Threshold on the minimum number of counts of individual sources. This parameter determines the sources that are fit in the second optimization step. shape_ts_threshold (float) – Threshold on source TS used for determining the sources that will be fit in the third optimization step.

print_model()[source]¶

print_roi()[source]¶

profile(name, parName, emin=None, emax=None, reoptimize=False, xvals=None, npts=None, savestate=True)[source]¶

Profile the likelihood for the given source and parameter.

profile_norm(name, emin=None, emax=None, reoptimize=False, xvals=None, npts=20, savestate=True)[source]¶

Profile the normalization of a source.

Parameters:	name (str) – Source name. reoptimize (bool) – Re-optimize all free parameters in the model at each point in the profile likelihood scan.

projtype¶

Return the type of projection to use

reload_source(name)[source]¶

Delete and reload a source in the model. This will refresh the spatial model of this source to the one defined in the XML model.

residmap(prefix='', **kwargs)[source]¶

Generate 2-D spatial residual maps using the current ROI model and the convolution kernel defined with the model argument.

Parameters:	prefix (str) – String that will be prefixed to the output residual map files. model (dict) – Dictionary defining the properties of the convolution kernel. exclude (str or list of str) – Source or sources that will be removed from the model when computing the residual map. erange (list) – Restrict the analysis to an energy range (emin,emax) in log10(E/MeV) that is a subset of the analysis energy range. By default the full analysis energy range will be used. If either emin/emax are None then only an upper/lower bound on the energy range wil be applied. make_plots (bool) – Write image files. make_fits (bool) – Write FITS files.
Returns:	maps – A dictionary containing the Map objects for the residual significance and amplitude.
Return type:	dict

restore_counts_maps()[source]¶

Revert counts maps to their state prior to injecting any simulated components.

roi¶

Return the ROI object.

scale_parameter(name, par, scale)[source]¶

sed(name, profile=True, energies=None, **kwargs)[source]¶

Generate an SED for a source. This function will fit the normalization of a given source in each energy bin.

Parameters:	name (str) – Source name. profile (bool) – Profile the likelihood in each energy bin. energies (ndarray) – Sequence of energies in log10(E/MeV) defining the edges of the energy bins. If this argument is None then the analysis energy bins will be used. The energies in this sequence must align with the bin edges of the underyling analysis instance. bin_index (float) – Spectral index that will be use when fitting the energy distribution within an energy bin. use_local_index (bool) – Use a power-law approximation to the shape of the global spectrum in each bin. If this is false then a constant index set to bin_index will be used. fix_background (bool) – Fix background components when fitting the flux normalization in each energy bin. If fix_background=False then all background parameters that are currently free in the fit will be profiled. By default fix_background=True. ul_confidence (float) – Set the confidence level that will be used for the calculation of flux upper limits in each energy bin.
Returns:	sed – This dictionary is also saved to the ‘sed’ dictionary of the Source instance.
Return type:	dict Dictionary containing output of the SED analysis.

setEnergyRange(emin, emax)[source]¶

Set the energy range of the analysis.

set_edisp_flag(name, flag=True)[source]¶

Enable or disable the energy dispersion correction for the given source.

set_free_params(free)[source]¶

set_log_level(level)[source]¶

set_norm(name, value)[source]¶

set_norm_scale(name, value)[source]¶

set_parameter(name, par, value, true_value=True, scale=None, bounds=None, update_source=True)[source]¶

set_parameter_bounds(name, par, bounds)[source]¶

Set the bounds of a parameter.

Parameters:	name (str) – Source name. par (str) – Parameter name. bounds (list) – Upper and lower bound.

setup(init_sources=True, overwrite=False)[source]¶

Run pre-processing for each analysis component and construct a joint likelihood object. This function performs the following tasks: data selection (gtselect, gtmktime), data binning (gtbin), and model generation (gtexpcube2,gtsrcmaps).

Parameters:	init_sources (bool) – Choose whether to compute properties (flux, TS, etc.) for individual sources. overwrite (bool) – Run all pre-processing steps even if the output file of that step is present in the working directory. By default this function will skip any steps for which the output file already exists.

simulate_roi()[source]¶

Perform a simulation of the whole ROI. This will replace the current counts cube with a simulated realization of the current model. The counts cube can be restored to its original state by calling restore_counts_maps.

simulate_source(src_dict=None)[source]¶

Inject a simulated source into the ROI.

Parameters:	src_dict (dict) –

stage_input()[source]¶

Copy data products to intermediate working directory.

stage_output()[source]¶

Copy data products to final output directory.

tscube(prefix='', **kwargs)[source]¶

Generate a spatial TS map for a source component with properties defined by the model argument. This method uses the gttscube ST application for source fitting and will simultaneously fit the test source normalization as well as the normalizations of any background components that are currently free. The output of this method is a dictionary containing Map objects with the TS and amplitude of the best-fit test source. By default this method will also save maps to FITS files and render them as image files.

Parameters:	prefix (str) – Optional string that will be prepended to all output files (FITS and rendered images). model (dict) – Dictionary defining the properties of the test source. do_sed (bool) – Compute the energy bin-by-bin fits. nnorm (int) – Number of points in the likelihood v. normalization scan. norm_sigma (float) – Number of sigma to use for the scan range. tol (float) – Critetia for fit convergence (estimated vertical distance to min < tol ). tol_type (int) – Absoulte (0) or relative (1) criteria for convergence. max_iter (int) – Maximum number of iterations for the Newton’s method fitter remake_test_source (bool) – If true, recomputes the test source image (otherwise just shifts it) st_scan_level (int) – make_plots (bool) – Write image files. make_fits (bool) – Write FITS files.
Returns:	maps – A dictionary containing the Map objects for TS and source amplitude.
Return type:	dict

tsmap(prefix='', **kwargs)[source]¶

Generate a spatial TS map for a source component with properties defined by the model argument. The TS map will have the same geometry as the ROI. The output of this method is a dictionary containing Map objects with the TS and amplitude of the best-fit test source. By default this method will also save maps to FITS files and render them as image files.

This method uses a simplified likelihood fitting implementation that only fits for the normalization of the test source. Before running this method it is recommended to first optimize the ROI model (e.g. by running optimize()).

Parameters:	prefix (str) – Optional string that will be prepended to all output files (FITS and rendered images). model (dict) – Dictionary defining the properties of the test source. exclude (str or list of str) – Source or sources that will be removed from the model when computing the TS map. erange (list) – Restrict the analysis to an energy range (emin,emax) in log10(E/MeV) that is a subset of the analysis energy range. By default the full analysis energy range will be used. If either emin/emax are None then only an upper/lower bound on the energy range wil be applied. max_kernel_radius (float) – Set the maximum radius of the test source kernel. Using a smaller value will speed up the TS calculation at the loss of accuracy. The default value is 3 degrees. make_plots (bool) – Write image files. make_fits (bool) – Write FITS files.
Returns:	maps – A dictionary containing the Map objects for TS and source amplitude.
Return type:	dict

unzero_source(name)[source]¶

update_source(name, paramsonly=False, reoptimize=False, npts=20)[source]¶

Update the dictionary for this source.

Parameters:	name (str) – paramsonly (bool) – reoptimize (bool) – Re-fit background parameters in likelihood scan. npts (int) – Number of points for likelihood scan.

workdir¶

Return the analysis working directory.

write_roi(outfile=None, make_residuals=False, make_tsmap=False, save_model_map=True, format=None, **kwargs)[source]¶

Write current model to a file. This function will write an XML model file and an ROI dictionary in both YAML and npy formats.

Parameters:	outfile (str) – Name of the output file. The extension of this string will be stripped when generating the XML, YAML and Numpy filenames. make_residuals (bool) – Run residual analysis. save_model_map (bool) – Save the current counts model as a FITS file. format (str) – Set the output file format (yaml or npy).

write_xml(xmlfile)[source]¶

Save current model definition as XML file.

Parameters:	xmlfile (str) – Name of the output XML file.

zero_source(name)[source]¶

fermipy.logger module¶

class fermipy.logger.Logger[source]¶

Bases: object

This class provides helper functions which facilitate creating instances of the built-in logger class.

static get(name, logfile, loglevel=10)[source]¶

static setup(config=None, logfile=None)[source]¶

This method sets up the default configuration of the logger. Once this method is called all subsequent instances Logger instances will inherit this configuration.

class fermipy.logger.StreamLogger(name='stdout', logfile=None, quiet=True)[source]¶

Bases: object

File-like object to log stdout/stderr using the logging module.

close()[source]¶

flush()[source]¶

write(msg, level=10)[source]¶

fermipy.logger.logLevel(level)[source]¶

This is a function that returns a python like level from a HEASOFT like level.

fermipy.roi_model module¶

class fermipy.roi_model.Catalog(table, extdir='')[source]¶

Bases: object

Source catalog object. This class provides a simple wrapper around FITS catalog tables.

static create(name)[source]¶

glonlat¶

radec¶

skydir¶

table¶

Return the Table representation of this catalog.

class fermipy.roi_model.Catalog2FHL(fitsfile=None, extdir=None)[source]¶

Bases: fermipy.roi_model.Catalog

class fermipy.roi_model.Catalog3FGL(fitsfile=None, extdir=None)[source]¶

Bases: fermipy.roi_model.Catalog

class fermipy.roi_model.IsoSource(name, data)[source]¶

Bases: fermipy.roi_model.Model

diffuse¶

filefunction¶

write_xml(root)[source]¶

class fermipy.roi_model.MapCubeSource(name, data)[source]¶

Bases: fermipy.roi_model.Model

diffuse¶

mapcube¶

write_xml(root)[source]¶

class fermipy.roi_model.Model(name, data=None)[source]¶

Bases: object

Base class for source objects. This class is a container for both spectral and spatial parameters as well as other source properties such as TS, Npred, and location within the ROI.

add_name(name)[source]¶

assoc¶

check_cuts(cuts)[source]¶

static create_from_dict(src_dict)[source]¶

data¶

get_norm()[source]¶

items()[source]¶

name¶

names¶

params¶

set_name(name, names=None)[source]¶

set_spectral_pars(spectral_pars)[source]¶

spatial_pars¶

spectral_pars¶

update_data(d)[source]¶

update_from_source(src)[source]¶

class fermipy.roi_model.PowerLaw(phi0, x0, index)[source]¶

Bases: object

dfde(x)[source]¶

static eval_dfde(x, phi0, x0, index)[source]¶

static eval_flux(phi0, x0, index, xmin, xmax)[source]¶

static eval_norm(x0, index, xmin, xmax, flux)[source]¶

params¶

class fermipy.roi_model.ROIModel(config=None, **kwargs)[source]¶

Bases: fermipy.config.Configurable

This class is responsible for managing the ROI model (both sources and diffuse emission components). Source catalogs can be read from either FITS or XML files. Individual components are represented by instances of Model and can be accessed by name using the bracket operator.

• Create an ROI with all 3FGL sources and print a summary of its contents:

>>> skydir = astropy.coordinates.SkyCoord(0.0,0.0,unit='deg')
>>> roi = ROIModel({'catalogs' : ['3FGL'],'src_roiwidth' : 10.0},skydir=skydir)
>>> print roi
name                SpatialModel   SpectrumType     offset        ts       Npred
--------------------------------------------------------------------------------
3FGL J2357.3-0150   PointSource    PowerLaw          1.956       nan         0.0
3FGL J0006.2+0135   PointSource    PowerLaw          2.232       nan         0.0
3FGL J0016.3-0013   PointSource    PowerLaw          4.084       nan         0.0
3FGL J0014.3-0455   PointSource    PowerLaw          6.085       nan         0.0

• Print a summary of an individual source

>>> print roi['3FGL J0006.2+0135']

• Get the SkyCoord for a source

>>> dir = roi['SourceA'].skydir

• Loop over all sources and print their names

>>> for s in roi.sources: print s.name

clear()[source]¶

Clear the contents of the ROI.

copy_source(name)[source]¶

static create(selection, config, **kwargs)[source]¶

Create an ROIModel instance.

static create_from_position(skydir, config, **kwargs)[source]¶

Create an ROIModel instance centered on a sky direction.

Parameters:	skydir (SkyCoord) – Sky direction on which the ROI will be centered. config (dict) – Model configuration dictionary.

static create_from_roi_data(datafile)[source]¶

Create an ROI model.

static create_from_source(name, config, **kwargs)[source]¶

Create an ROI centered on the given source.

static create_roi_from_ft1(ft1file, config)[source]¶

Create an ROI model by extracting the sources coordinates form an FT1 file.

create_source(name, src_dict, build_index=True, merge_sources=True)[source]¶

Add a new source to the ROI model from a dictionary or an existing source object.

Parameters:	name (str) – src_dict (dict or Source) –
Returns:	src
Return type:	Source

defaults = {'logfile': (None, '', <type 'str'>), 'catalogs': (None, '', <type 'list'>), 'src_roiwidth': (None, 'Select sources within a box of RxR centered on the ROI. If none then no cut is applied.', <type 'float'>), 'limbdiff': (None, '', <type 'list'>), 'src_radius_roi': (None, 'Half-width of the ROI selection. This parameter can be used in lieu of src_roiwidth.', <type 'float'>), 'extract_diffuse': (False, 'Extract a copy of all mapcube components centered on the ROI.', <type 'bool'>), 'galdiff': (None, 'Set the galactic IEM mapcube.', <type 'list'>), 'extdir': ('Extended_archive_v15', '', <type 'str'>), 'sources': (None, '', <type 'list'>), 'fileio': {'workdir': (None, 'Override the working directory.', <type 'str'>), 'savefits': (True, 'Save intermediate FITS files.', <type 'bool'>), 'scratchdir': ('/scratch', 'Path to the scratch directory.', <type 'str'>), 'outdir': (None, 'Path of the output directory. If none this will default to the directory containing the configuration file.', <type 'str'>), 'logfile': (None, 'Path to log file. If None then log will be written to fermipy.log.', <type 'str'>), 'usescratch': (False, 'Run analysis in a temporary directory under ``scratchdir``.', <type 'bool'>)}, 'logging': {'verbosity': (3, '', <type 'int'>), 'chatter': (3, 'Set the chatter parameter of the STs.', <type 'int'>)}, 'isodiff': (None, 'Set the isotropic template.', <type 'list'>), 'merge_sources': (True, 'Merge properties of sources that appear in multiple source catalogs. If merge_sources=false then subsequent sources with the same name will be ignored.', <type 'bool'>), 'assoc_xmatch_columns': (['3FGL_Name'], 'Choose a set of association columns on which to cross-match catalogs.', <type 'list'>), 'diffuse': (None, '', <type 'list'>), 'src_radius': (None, 'Set the maximum distance for inclusion of sources in the ROI model. Selects all sources within a circle of this radius centered on the ROI. If none then no selection is applied. This selection will be ORed with sources passing the cut on src_roiwidth.', <type 'float'>)}¶

delete_sources(srcs)[source]¶

diffuse_sources¶

get_nearby_sources(name, dist, min_dist=None, square=False)[source]¶

get_source_by_name(name, unique=False)[source]¶

Return a source in the ROI by name. The input name string can match any of the strings in the names property of the source object. Case and whitespace are ignored when matching name strings.

Parameters:	name (str) – unique (bool) – Require a unique match. If more than one source exists with this name an exception is raised.

get_sources(cuts=None, distance=None, minmax_ts=None, minmax_npred=None, square=False, exclude_diffuse=False, coordsys='CEL')[source]¶

Retrieve list of sources satisfying the given selections.

Returns:	srcs – List of source objects.
Return type:	list

get_sources_by_position(skydir, dist, min_dist=None, square=False, coordsys='CEL')[source]¶

Retrieve sources within a certain angular distance of a sky coordinate. This function supports two types of geometric selections: circular (square=False) and square (square=True). The circular selection finds all sources with a given angular distance of the target position. The square selection finds sources within an ROI-like region of size R x R where R = 2 x dist.

Parameters:	skydir (SkyCoord) – Sky direction with respect to which the selection will be applied. dist (float) – Maximum distance in degrees from the sky coordinate. square (bool) – Choose whether to apply a circular or square selection. coordsys (str) – Coordinate system to use when applying a selection with square=True.

get_sources_by_property(pname, pmin, pmax=None)[source]¶

has_source(name)[source]¶

load(**kwargs)[source]¶

Load both point source and diffuse components.

load_diffuse_srcs()[source]¶

load_fits_catalog(name, **kwargs)[source]¶

Load sources from a FITS catalog file.

Parameters:	name (str) – Catalog name or path to a catalog FITS file.

load_source(src, build_index=True, merge_sources=True, **kwargs)[source]¶

Load a single source.

Parameters:	src (Source) – Source object that will be added to the ROI. merge_sources (bool) – When a source matches an existing source in the model update that source with the properties of the new source. build_index (bool) – Re-make the source index after loading this source.

load_sources(sources)[source]¶

Delete all sources in the ROI and load the input source list.

load_xml(xmlfile, **kwargs)[source]¶

Load sources from an XML file.

match_source(src)[source]¶

Look for source or sources in the model that match the given source. Sources are matched by name and any association columns defined in the assoc_xmatch_columns parameter.

point_sources¶

skydir¶

Return the sky direction objection corresponding to the center of the ROI.

sources¶

src_name_cols = ['Source_Name', 'ASSOC', 'ASSOC1', 'ASSOC2', 'ASSOC_GAM', '1FHL_Name', '2FGL_Name', '3FGL_Name', 'ASSOC_GAM1', 'ASSOC_GAM2', 'ASSOC_TEV']¶

write_xml(xmlfile)[source]¶

Save this ROI model as an XML file.

class fermipy.roi_model.Source(name, data=None, radec=None)[source]¶

Bases: fermipy.roi_model.Model

Class representation of a source (non-diffuse) model component. A source object serves as a container for the properties of that source (position, spatial/spectral parameters, TS, etc.) as derived in the current analysis. Most properties of a source object can be accessed with the bracket operator:

# Return the TS of this source >>> print src[‘ts’]

# Get a skycoord representation of the source position >>> print src.skydir

associations¶

static create_from_dict(src_dict)[source]¶

Create a source object from a python dictionary.

static create_from_xml(root, extdir=None)[source]¶

Create a Source object from an XML node.

data¶

diffuse¶

extended¶

load_from_catalog()[source]¶

Load spectral parameters from catalog values.

radec¶

separation(src)[source]¶

set_position(skydir)[source]¶

Set the position of the source.

Parameters:	skydir (SkyCoord) –

set_roi_direction(roidir)[source]¶

set_spatial_model(spatial_model, spatial_width=None)[source]¶

skydir¶

Return a SkyCoord representation of the source position.

Returns:	skydir
Return type:	SkyCoord

update_data(d)[source]¶

write_xml(root)[source]¶

Write this source to an XML node.

fermipy.roi_model.add_columns(t0, t1)[source]¶

Add columns of table t1 to table t0.

fermipy.roi_model.create_model_name(src)[source]¶

fermipy.roi_model.get_dist_to_edge(skydir, lon, lat, width, coordsys='CEL')[source]¶

fermipy.roi_model.get_linear_dist(skydir, lon, lat, coordsys='CEL')[source]¶

fermipy.roi_model.get_skydir_distance_mask(src_skydir, skydir, dist, min_dist=None, square=False, coordsys='CEL')[source]¶

Retrieve sources within a certain angular distance of an (ra,dec) coordinate. This function supports two types of geometric selections: circular (square=False) and square (square=True). The circular selection finds all sources with a given angular distance of the target position. The square selection finds sources within an ROI-like region of size R x R where R = 2 x dist.

Parameters:	src_skydir (SkyCoord) – Array of sky directions. skydir (SkyCoord) – Sky direction with respect to which the selection will be applied. dist (float) – Maximum distance in degrees from the sky coordinate. square (bool) – Choose whether to apply a circular or square selection. coordsys (str) – Coordinate system to use when applying a selection with square=True.

fermipy.roi_model.join_tables(t0, t1, key0, key1)[source]¶

fermipy.roi_model.lonlat_to_xyz(lon, lat)[source]¶

fermipy.roi_model.make_parameter_dict(pdict, fixed_par=False)[source]¶

fermipy.roi_model.project(lon0, lat0, lon1, lat1)[source]¶

This function performs a stereographic projection on the unit vector (lon1,lat1) with the pole defined at the reference unit vector (lon0,lat0).

fermipy.roi_model.resolve_file_path(path, **kwargs)[source]¶

fermipy.roi_model.row_to_dict(row)[source]¶

fermipy.roi_model.scale_parameter(p)[source]¶

fermipy.roi_model.strip_columns(t)[source]¶

fermipy.roi_model.xyz_to_lonlat(*args)[source]¶

fermipy.utils module¶

class fermipy.utils.Map(counts, wcs)[source]¶

Bases: fermipy.utils.Map_Base

Representation of a 2D or 3D counts map using WCS.

static create_from_fits(fitsfile, **kwargs)[source]¶

static create_from_hdu(hdu, wcs)[source]¶

create_image_hdu(name=None)[source]¶

create_primary_hdu()[source]¶

ipix_swap_axes(ipix, colwise=False)[source]¶

Return the transposed pixel index from the pixel xy coordinates

if colwise is True (False) this assumes the original index was in column wise scheme

ipix_to_xypix(ipix, colwise=False)[source]¶

Return the pixel xy coordinates from the pixel index

if colwise is True (False) this uses columnwise (rowwise) indexing

pix_center¶

Return the ROI center in pixel coordinates.

pix_size¶

Return the pixel size along the two image dimensions.

skydir¶

Return the sky coordinate of the Map center.

sum_over_energy()[source]¶

Reduce a 3D counts cube to a 2D counts map

wcs¶

width¶

Return the sky coordinate of the Map center.

xy_pix_to_ipix(xypix, colwise=False)[source]¶

Return the pixel index from the pixel xy coordinates

if colwise is True (False) this uses columnwise (rowwise) indexing