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.gitignore

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*.ipynb_checkpoints
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tevpy/tevpy.cfg
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gammapy/gammapy.cfg
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docs/_generated

MANIFEST.in

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include README.rst
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include distribute_setup.py
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recursive-include tevpy *.pyx *.c
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recursive-include gammapy *.pyx *.c
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recursive-include docs *
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recursive-include licenses *

README.rst

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tevpy
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gammapy
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=====
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TeV gamma-ray astronomy high-level data analysis Python package
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* Code: https://github.com/gammapy/tevpy
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* Docs: https://tevpy.readthedocs.org/
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* Code: https://github.com/gammapy/gammapy
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* Docs: https://gammapy.readthedocs.org/
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.. image:: https://travis-ci.org/gammapy/tevpy.png
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:target: https://travis-ci.org/gammapy/tevpy
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.. image:: https://travis-ci.org/gammapy/gammapy.png
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:target: https://travis-ci.org/gammapy/gammapy

docs/conf.py

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# -- Project information ------------------------------------------------------
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# This does not *have* to match the package name, but typically does
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project = u'tevpy'
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author = u'The tevpy Developers'
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project = u'gammapy'
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author = u'The gammapy Developers'
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copyright = u'2012, ' + author
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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# built documents.
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import tevpy
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import gammapy
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# The short X.Y version.
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version = tevpy.__version__.split('-', 1)[0]
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version = gammapy.__version__.split('-', 1)[0]
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# The full version, including alpha/beta/rc tags.
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release = tevpy.__version__
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release = gammapy.__version__
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# -- Options for HTML output ---------------------------------------------------
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# First TeV gamma-ray image: the supernova remnant RX J1713 with HESS
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# http://apod.nasa.gov/apod/ap041105.html
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html_favicon = '_static/tevpy_logo.ico'
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html_favicon = '_static/gammapy_logo.ico'
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# TODO: set this image also in the title bar
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# (html_logo is not the right option)
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# Don't import the module as "version" or it will override the
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# "version" configuration parameter
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from tevpy import version as versionmod
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edit_on_github_project = "gammapy/tevpy"
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from gammapy import version as versionmod
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edit_on_github_project = "gammapy/gammapy"
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if versionmod.release:
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edit_on_github_branch = "v" + versionmod.version
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else:

docs/index.rst

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.. toctree::
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:maxdepth: 2
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tevpy/index.rst
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gammapy/index.rst
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.. note:: Do not edit this page - instead, place all documentation for the
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affiliated package inside ``packagename/``

docs/tevpy/astro/index.rst

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**********************************************************
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Astrophysical source and population models (`tevpy.astro`)
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Astrophysical source and population models (`gammapy.astro`)
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**********************************************************
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.. currentmodule:: tevpy.astro
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.. currentmodule:: gammapy.astro
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Introduction
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============
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`tevpy.astro` implements some common astrophysical source and population models.
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`gammapy.astro` implements some common astrophysical source and population models.
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TODO: describe
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Reference/API
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=============
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.. automodapi:: tevpy.astro
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.. automodapi:: gammapy.astro
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:no-inheritance-diagram:

docs/tevpy/background/index.rst

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********************************************************
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Background estimation and modeling (`tevpy.background`)
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Background estimation and modeling (`gammapy.background`)
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********************************************************
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.. currentmodule:: tevpy.background
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.. currentmodule:: gammapy.background
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Introduction
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============
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`tevpy.background` contains methods to estimate and model background.
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`gammapy.background` contains methods to estimate and model background.
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At the moment it also contains a lot of image-processing related functionality
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that maybe should be split into a separate `image` package.
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The main data structure is the `~tevpy.background.maps.Maps` container ... TODO
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The main data structure is the `~gammapy.background.maps.Maps` container ... TODO
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Most of the methods implemented are described in [Berge2007]_.
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Section 7.3 "Background subtraction"
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TODO
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.. automodapi:: tevpy.background
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.. automodapi:: gammapy.background
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:no-inheritance-diagram:
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docs/tevpy/data/formats/run_lists.rst

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Run,Telescope_Pattern,Date,Duration,GLON,GLAT,Target,Zenith
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1234,24,2013-03-22 14:32,1832,83.7,-5.2,Crab Nebula,32
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Special column names that the `tevpy` analysis tools understand:
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Special column names that the `gammapy` analysis tools understand:
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* `Run` --- Run number (int)
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* `Telescope_Pattern` --- Binary pattern describing which telescopes participated in the run

docs/tevpy/data/index.rst

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***********************
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Datasets (`tevpy.data`)
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Datasets (`gammapy.data`)
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***********************
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.. currentmodule:: tevpy.data
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.. currentmodule:: gammapy.data
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Introduction
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============
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`tevpy.data` holds a few datasets used in the examples and tests.
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Some are included with `tevpy`, some are downloaded from the web via
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`gammapy.data` holds a few datasets used in the examples and tests.
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Some are included with `gammapy`, some are downloaded from the web via
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>>> import tevpy.data
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>>> tevpy.data.download_datasets()
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>>> import gammapy.data
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>>> gammapy.data.download_datasets()
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TODO: Give summary table of available datasets here.
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Reference/API
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=============
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.. automodapi:: tevpy.data
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.. automodapi:: gammapy.data
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:no-inheritance-diagram:

docs/tevpy/detect/index.rst

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***************************************
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Source detection tools (`tevpy.detect`)
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Source detection tools (`gammapy.detect`)
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***************************************
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.. currentmodule:: tevpy.detect
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.. currentmodule:: gammapy.detect
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Introduction
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============
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`tevpy.detect` holds source detection methods that turn event lists or images or cubes
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`gammapy.detect` holds source detection methods that turn event lists or images or cubes
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into source catalogs.
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* TODO: Describe references: [Stewart2009]_
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Reference/API
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=============
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.. automodapi:: tevpy.detect.blob
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.. automodapi:: gammapy.detect.blob
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.. automodapi:: tevpy.detect.cwt
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.. automodapi:: gammapy.detect.cwt
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.. automodapi:: tevpy.detect.matched_filter
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.. automodapi:: gammapy.detect.matched_filter
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.. automodapi:: tevpy.detect.sex
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.. automodapi:: gammapy.detect.sex
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:no-inheritance-diagram:
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.. automodapi:: tevpy.detect.test_statistic
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.. automodapi:: gammapy.detect.test_statistic
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.. automodapi:: tevpy.detect.utils
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.. automodapi:: gammapy.detect.utils
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docs/tevpy/image/index.rst

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***************************************************
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Image processing and analysis tools (`tevpy.image`)
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Image processing and analysis tools (`gammapy.image`)
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***************************************************
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.. currentmodule:: tevpy.image
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.. currentmodule:: gammapy.image
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Introduction
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============
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`tevpy.image` contains image processing and analysis methods that are
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`gammapy.image` contains image processing and analysis methods that are
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not readily found (yet) in `scipy.ndimage`, `scikit-image`, `astropy` or `photutils`:
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* `tevpy.image.profile`: Compute 1D profiles from 2D images
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* `tevpy.image.measure`: Measure source properties in labeled regions
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* `gammapy.image.profile`: Compute 1D profiles from 2D images
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* `gammapy.image.measure`: Measure source properties in labeled regions
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Getting Started
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.. automodapi:: tevpy.image
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.. automodapi:: gammapy.image
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:no-inheritance-diagram:

docs/tevpy/index.rst

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`tevpy`
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`gammapy`
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=======
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What is it?
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-----------
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`tevpy` is an open source (BSD licensed) TeV gamma-ray astronomy high-level data analysis Python package.
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`gammapy` is an open source (BSD licensed) TeV gamma-ray astronomy high-level data analysis Python package.
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It contains some analysis methods,
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but it's main purpose is to be the glue between the many
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existing data formats and other tools.
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* Code / Bug reports / Feature requests / Development: https://github.com/gammapy/tevpy
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* Docs: https://tevpy.readthedocs.org/
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* Code / Bug reports / Feature requests / Development: https://github.com/gammapy/gammapy
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* Docs: https://gammapy.readthedocs.org/
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* Mailing list: http://groups.google.com/group/gammapy
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* License: BSD-3-Clause
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Using `tevpy`
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Using `gammapy`
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-------------
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Start by reading the :ref:`introduction`.
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Found a bug or missing feature?
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Make an issue or pull request on `GitHub <https://github.com/gammapy/tevpy>`_.
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Make an issue or pull request on `GitHub <https://github.com/gammapy/gammapy>`_.
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docs/tevpy/install.rst

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Installation
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============
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To install the latest `tevpy` stable version the easiest way is using the `pip <http://www.pip-installer.org/>`_ installer::
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To install the latest `gammapy` stable version the easiest way is using the `pip <http://www.pip-installer.org/>`_ installer::
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pip install tevpy
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pip install gammapy
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To install the latest developer version of `tevpy`, use::
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To install the latest developer version of `gammapy`, use::
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git clone https://github.com/gammapy/tevpy.git
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git clone https://github.com/gammapy/gammapy.git
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cd astropy
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To check if `gammapy` is correctly installed, start up python or ipython, import `gammapy` and run the unit tests::
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>>> import tevpy
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>>> import gammapy
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>>> gammapy.test()
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To check if the `tevpy` command line tools are on your `$PATH` try this::
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* `imfun`_ for a trous wavelet decomposition
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.. note:: I didn't put any effort into minimizing the number of dependencies,
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since `gammapy` is a prototype. Should it develop into a package that is actually used
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.. _scikit-image: http://scikit-image.org

docs/tevpy/introduction.rst

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Show me some code!
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------------------
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`tevpy` gives you easy access to some frequently used methods in TeV gamma-ray astronomy from Python.
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`gammapy` gives you easy access to some frequently used methods in TeV gamma-ray astronomy from Python.
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What's the statistical significance when 10 events have been observed with a known background level of 4.2
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`tevpy.stats` knows::
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`gammapy.stats` knows::
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>>> from tevpy.stats import significance
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>>> from gammapy.stats import significance
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>>> significance(n_observed=10, mu_background=4.2, method='lima')
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`gammapy.spec` knows::
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>>> from tevpy.spec import crab
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>>> from gammapy.spec import crab
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>>> energy = 3
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>>> crab.diff_flux(energy, ref='meyer')
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2.6763224503600429
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All functionality is in subpackages (e.g. `tevpy.stats` or `tevpy.spec`) ...
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All functionality is in subpackages (e.g. `gammapy.stats` or `gammapy.spec`) ...
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browse their docs (see list below) to see if it contains the methods you want.
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But I don't know how to code in Python!
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---------------------------------------
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Hmm ... OK.
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Some of the `tevpy` functionality can be called from command line tools.
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Some of the `gammapy` functionality can be called from command line tools.
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But, to be honest, if you're an astronomer, you should learn to code in Python.
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There are several other great open source packages for
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TeV data analysis (alphabetical order):
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* `act-analysis`_ --- a similar package as ``tevpy`` by Karl Kosack
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* `act-analysis`_ --- a similar package as ``gammapy`` by Karl Kosack
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* `gammafits`_ --- an SED modeling and fitting package by Victor Zabalza
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* `gammalib`_ and `ctools`_ --- Gamma-ray data analysis library and tools by Jürgen Knödlseder
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* `gamma-speed`_ --- benchmarking of TeV data analysis tools by Andrei Ignat
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* `PyFACT`_ --- a similar package as ``tevpy`` by Martin Raue
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* `PyFACT`_ --- a similar package as ``gammapy`` by Martin Raue
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.. _act-analysis: https://bitbucket.org/kosack/act-analysis
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.. _PyFACT: http://pyfact.readthedocs.org

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