.. include:: references.txt

.. _references:

Glossary and references
=======================

.. _glossary:



Glossary
--------

.. glossary::

    1D Analysis
      1D analysis or spectral analysis where data are reduced to a simple 1D
      geometry along the reconstructed energy axis. In Cherenkov astronomy,
      this is classically performed with a OFF background measurement.

    3D Analysis
      3D analysis or cube analysis, where data are reduced to a 3D cube with
      spatial coordinates and energy axes. In gammapy, these cube are represented
      by `Map` objects (see :ref:`maps`) and contained in a `MapDataset` object.

    Aeff
      Is short for effective area, the IRF representing the detector collection
      area. See :ref:`irf-aeff`.

    Cash
      The cash statistic is a Poisson fit statistic usually used when signal and
      background can be modeled. It is defined as :math:`2 \times log(L)` See
      :ref:`cash` in :ref:`fit statistics <fit-statistics>`.

    Dataset
      In Gammapy a dataset bundles the data, IRFs, model and a likelihood function.
      Based on the model and IRFs the predicted number of counts are computed and
      compared to the measured counts using the likelihood.

    EDisp
      EDisp is short for energy dispersion, the IRF that represents the probability
      of measuring a given reconstructed energy as a function of the true photon
      energy. See :ref:`irf-edisp`

    GTI
      Short for Good Time Interval: an continuous time interval of data acquisition.
      In CTA, they also represent time intervals where the IRFs are supposed to be constant.

    IRF
      Short for Instrument Response Function. They are used to model the probability
      to detect a photon with a number of measured characteristics. See :ref:`irf-theory`
      and :ref:`irf`.

    Joint Analysis
      In a joint analysis individual observations are reduced to datasets and are modeled
      all together to extract physical informations through model fitting. This is opposed
      to stacked analysis.

    MET
      Short for Mission Elapsed Time; see also :ref:`MET_definition` in :ref:`time_handling`.

    Reco Energy
      The reconstructed (or measured) energy (often written `e_reco`) is the energy of
      the measured photon by contrast with its actual true energy. Measured quantities
      such as counts are represented along a reco energy axis.

    Reflected Background
      Background estimation method typically used for spectral analysis.

    Ring Background
      Background estimation method typically used for image analysis.

    Stacked Analysis
      In a stacked analysis individual observations are reduced to datasets which
      are then stacked to produce a single reduced dataset. The latter is then used
      to obtain physical information through model fitting. Some approximations must
      be made to perform dataset stacking (e.g. loss of individual background normalization,
      averaging of instrument responses, loss of information outside region of interest etc),
      but this can reduce very significantly the computing and memory cost.

    True Energy
      The true energy (often written `e_true`) is the energy of the incident photon
      by contrast with the energy reconstructed by the instrument. Instrument response
      functions are represented along a true energy axis.

    WStat
      The WStat is a Poisson fit statistic usually used for ON-OFF analysis. It is
      based on the profile likelihood method where the unknown background parameters
      are marginalized. See :ref:`wstat` in :ref:`fit statistics <fit-statistics>`.

.. _publications:

Publications
------------

This is the bibliography containing the literature references for the implemented methods
referenced from the Gammapy docs.

.. [Albert2007] `Albert et al. (2007) <https://ui.adsabs.harvard.edu/abs/2007NIMPA.583..494A>`_,
   "Unfolding of differential energy spectra in the MAGIC experiment",

.. [Berge2007] `Berge et al. (2007) <https://ui.adsabs.harvard.edu/abs/2007A%26A...466.1219B>`_,
   "Background modelling in very-high-energy gamma-ray astronomy"

.. [Cash1979] `Cash (1979) <https://ui.adsabs.harvard.edu/abs/1983ApJ...272..317L>`_,
   "Parameter estimation in astronomy through application of the likelihood ratio"

.. [Cousins2007] `Cousins et al. (2007) <https://ui.adsabs.harvard.edu/abs/2007physics...2156C>`_,
   "Evaluation of three methods for calculating statistical significance when incorporating a
   systematic uncertainty into a test of the background-only hypothesis for a Poisson process"

.. [Feldman1998] `Feldman & Cousins (1998) <https://ui.adsabs.harvard.edu/abs/1998PhRvD..57.3873F>`_,
   "Unified approach to the classical statistical analysis of small signals"

.. [Lafferty1994] `Lafferty & Wyatt (1994) <https://ui.adsabs.harvard.edu/abs/1995NIMPA.355..541L>`_,
   "Where to stick your data points: The treatment of measurements within wide bins"

.. [LiMa1983] `Li & Ma (1983) <https://ui.adsabs.harvard.edu/abs/1983ApJ...272..317L>`_,
   "Analysis methods for results in gamma-ray astronomy"

.. [Meyer2010] `Meyer et al. (2010) <https://ui.adsabs.harvard.edu/abs/2010A%26A...523A...2M>`_,
   "The Crab Nebula as a standard candle in very high-energy astrophysics"

.. [Naurois2012] `de Naurois (2012) <http://inspirehep.net/record/1122589>`_,
   "Very High Energy astronomy from H.E.S.S. to CTA. Opening of a new astronomical window on the non-thermal Universe",

.. [Piron2001] `Piron et al. (2001) <https://ui.adsabs.harvard.edu/abs/2001A%26A...374..895P>`_,
   "Temporal and spectral gamma-ray properties of Mkn 421 above 250 GeV from CAT observations between 1996 and 2000",

.. [Rolke2005] `Rolke et al. (2005) <https://ui.adsabs.harvard.edu/abs/2005NIMPA.551..493R>`_,
   "Limits and confidence intervals in the presence of nuisance parameters",

.. [Stewart2009] `Stewart (2009) <https://ui.adsabs.harvard.edu/abs/2009A%26A...495..989S>`_,
   "Maximum-likelihood detection of sources among Poissonian noise"

Software references:

.. [Raue2012] `Raue (2012) <https://ui.adsabs.harvard.edu/abs/2012AIPC.1505..789R>`_,
   "PyFACT: Python and FITS analysis for Cherenkov telescopes"

.. [Robitaille2013] `Robitaille et al. (2013) <https://ui.adsabs.harvard.edu/abs/2013A%26A...558A..33A>`_
   "Astropy: A community Python package for astronomy"

.. [Knoedlseder2016] `Knödlseder et at. (2016) <https://ui.adsabs.harvard.edu/abs/2016A%26A...593A...1K>`_
   "GammaLib and ctools. A software framework for the analysis of astronomical gamma-ray data"

.. [FSSC2013] `Fermi LAT Collaboration (2013) <https://fermi.gsfc.nasa.gov/ssc/data/analysis/scitools/overview.html>`_
   "Science Tools: LAT Data Analysis Tools"

.. [Mayer2015] `Michael Mayer (2015) <https://publishup.uni-potsdam.de/frontdoor/index/index/docId/7150>`_
   "Pulsar wind nebulae at high energies"


Other gamma-ray packages
------------------------

Here are some other software packages for gamma-ray astronomy:

* `Gammalib`_ /`ctools`_ is a C++ package with Python wrapper, similar to the Fermi-LAT ScienceTools,
  that to a large degree uses the same input data formats as Gammapy.
* `3ML`_ is a Python package that uses existing packages (e.g. the Fermi-LAT ScienceTools or the HAWC software)
  to deal with the data and IRFs and compute the likelihood for a given model.
* `Sherpa`_ --- X-ray modeling and fitting package by the Chandra X-ray Center
* `ctapipe`_ --- CTA Python pipeline experimental version
* `FermiPy`_ --- Fermi-LAT science tools high-level Python interface by Matthew Wood
* `gammatools`_ --- Python tools for Fermi-LAT gamma-ray data analysis by Matthew Wood
* `pointlike`_ -- Fermi-LAT science tools alternative by Toby Burnett
* `naima`_ --- an SED modeling and fitting package by Victor Zabalza
* `Gamera`_ --- a C++ gamma-ray source modeling package (SED, SNR model, Galactic population model) with a Python wrapper called Gappa by Joachim Hahn
* `FLaapLUC`_ --- Fermi/LAT automatic aperture photometry Light C<->Urve pipeline by Jean-Philippe Lenain
* http://voparis-cta-client.obspm.fr/ --- prototype web app for CTA data access / analysis, not open source.
* `act-analysis`_ --- Python scripts and Makefiles for some common gamma-ray data analysis tasks by Karl Kosack
* `VHEObserverTools`_ --- tools to predict detectability at VHE by Jeremy Perkins
* `photon_simulator`_ --- Python code to simulate X-ray observations
* `pycrflux`_ --- Python module to plot cosmic-ray flux
* Andy strong has C++ codes (GALPROP and Galplot) for Galactic cosmic rays and emission
  and source population synthesis at http://www.mpe.mpg.de/~aws/propagate.html .

Other useful packages
---------------------

In addition to the packages mentioned in the last section and at :ref:`install-dependencies`,
here's a few other Python packages you might find useful / interesting:

* See the list here: http://www.astropy.org/affiliated/
* Pulsar timing package `PINT`_
* `iminuit`_ fitter and `probfit`_ likelihood function builder.