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        "author": "Paul K. Korir, PhD",
        "author_email": "pkorir@ebi.ac.uk, paul.korir@gmail.com",
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        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Topic :: Software Development :: Libraries :: Python Modules",
            "Topic :: Terminals",
            "Topic :: Text Processing",
            "Topic :: Text Processing :: Markup",
            "Topic :: Utilities"
        ],
        "description": "============================\nEMDB-SFF Toolkit (``sfftk``)\n============================\n\n.. contents::\n\nIntroduction\n============\n\n``sfftk`` is a set of utilities that facilitate creation, conversion and\nmodification of `Electron Microscopy Data Bank - Segmentation File Format\n(EMDB-SFF) files <https://github.com/emdb-empiar/sfftk/tree/master/sfftk/test_data/sff>`_.\nEMDB-SFF is an open, community-driven file format to handle annotated\nsegmentations and subtomogram averages that facilitates segmentation file\ninterchange. It is written in Python and provides both a command-line\nsuite of commands and a Python API.\n\nAudience\n--------\n\n``sfftk`` is primarily targeted but not restricted to biological electron\nmicroscopists and developers of image segmentation software.\n\n\nLicense\n-------\n\n``sfftk`` is free and open source software released under the terms of the Apache License, Version 2.0. Source code is\ncopyright EMBL-European Bioinformatics Institute (EMBL-EBI) 2017.\n\nData Model\n----------\n\n``sfftk`` is built to handle EMDB-SFF files. The corresponding schema\n(``v0.8.0.dev1``) may be found at `https://emdb-empiar.github.io/EMDB-SFF <https://emdb-empiar.github.io/EMDB-SFF>`_.\nChanges to the schema are welcome for discussion at the *Segmentation Working Group*\nat `https://listserver.ebi.ac.uk/mailman/listinfo/segtrans-wg\n<https://listserver.ebi.ac.uk/mailman/listinfo/segtrans-wg>`_.\n\n.. _supported_formats:\n\nSupported Formats\n-----------------\n\nThe following file formats are currently supported (in alphabetical order of\nextensions):\n\n-  Amira Mesh (.am)\n\n-  SuRVoS (.h5; experimental support)\n\n-  CCP4 Masks (.map)\n\n-  IMOD (.mod)\n\n-  Segger (.seg)\n\n-  Stereolithography (.stl)\n\n-  Amira HyperSurface (.surf)\n\nContact\n-------\n\nAny questions or comments should be addressed to ``pkorir at ebi dot ac dot uk``.\n\nPublications\n------------\n\n.. Please cite the  whenever ``sfftk`` is used in a publication:\n\n.. .. note::\n\n..    Article to be added\n\nThe EMDB-SFF data model is the result of various community consultations which\nare published in the following articles:\n\n-  `Patwardhan, Ardan, Robert Brandt, Sarah J. Butcher, Lucy Collinson, David Gault, Kay Gr\u00fcnewald, Corey Hecksel et al. Building bridges between cellular and molecular structural biology. eLife 6 (2017). <http://europepmc.org/abstract/MED/28682240>`_\n\n-  `Patwardhan, Ardan, Alun Ashton, Robert Brandt, Sarah Butcher, Raffaella Carzaniga, Wah Chiu, Lucy Collinson et al. A 3D cellular context for the macromolecular world. Nature structural & molecular biology 21, no. 10 (2014): 841-845. <http://europepmc.org/abstract/MED/25289590>`_\n\n-  `Patwardhan, Ardan, Jos\u00e9-Maria Carazo, Bridget Carragher, Richard Henderson, J. Bernard Heymann, Emma Hill, Grant J. Jensen et al. Data management challenges in three-dimensional EM. Nature structural & molecular biology 19, no. 12 (2012): 1203-1207. <http://europepmc.org/abstract/MED/23211764>`_\n\nGetting Started\n===============\n\nObtaining and Installing ``sfftk``\n----------------------------------\n\nDependencies\n~~~~~~~~~~~~\n\nAs with any Python software, we recommend installing it in a virtual environment (of your choice). The only dependency\nthat may be needed is ``numpy`` which can be installed with\n\n.. code:: bash\n\n\t pip install numpy\n\nPyPI\n~~~~\n\n``sfftk`` is available on PyPI meaning that all that one needs to do is run:\n\n.. code:: bash\n\n\t pip install sfftk\n\nSource\n~~~~~~\n\nThe ``sfftk`` source is available from Github `https://github.com/emdb-empiar/sfftk <https://github.com/emdb-empiar/sfftk>`_.\n\nFeatures\n========\n\n``sfftk`` has two principal functions:\n\n- `convert` application-specific segmentation file format (AS-SFF) files to EMDB-SFF;\n\n- `annotate` EMDB-SFF files against known ontologies.\n\nConversion\n----------\n\nSegmentation files may be converted to EMDB-SFF files using the ``convert``\ncommand.\n\n.. code:: bash\n\n\t sff convert file.am -o file.sff\n\nFor a full description of how to perform conversion, please see the\n`guide to format conversion <https://sfftk.readthedocs.io/en/latest/converting.html>`_.\n\nAnnotation\n----------\n\nAnnotation is performed using the ``notes`` utility on EMDB-SFF files.\n\n.. code:: bash\n\n\t sff notes show -H file.sff\n\n``sfftk`` provides a simple set of tools to allow `viewing, searching and\nmodifying annotations` associated with the segmentation and individual\nsegments. The added annotations should be either from a public ontology or be\nan accession from a public database.\n\nSee the `guide to annotating segmentations <https://sfftk.readthedocs.io/en/latest/annotating.html>`_ for a full\ntreatment.\n\nMiscellaneous\n-------------\n\n``sfftk`` may also be used for several miscellaneous operations such as:\n\n-  `Viewing segmentation metadata <https://sfftk.readthedocs.io/en/latest/misc.html#viewing-file-metadata>`_\n\n-  `Prepping segmentations <https://sfftk.readthedocs.io/en/latest/misc.html#prepping-segmentation-files>`_ before conversion to EMDB-SFF\n\n-  `Setting configurations <https://sfftk.readthedocs.io/en/latest/misc.html#setting-configurations>`_ that affect how ``sfftk`` works\n\n-  `Running unit tests <https://sfftk.readthedocs.io/en/latest/misc.html#running-unit-tests>`_  with the ``tests`` command\n\nMore information on this can be found in the `guide to miscellaneous operations <https://sfftk.readthedocs.io/en/latest/misc.html>`_.\n\nDeveloping with ``sfftk``\n-------------------------\n\n``sfftk`` is developed as a set of decoupled packages providing the various\nfunctionality. The main classes involved are found in the `sfftkrw <https://sfftk-rw.readthedocs.io/en/latest/>`_ package.\nThere is also a `guide to developing with sfftk <https://sfftk.readthedocs.io/en/latest/developing.html>`_ which\nprovides useful instructions.\n\nExtending ``sfftk``\n-------------------\n\n``sfftk`` has built with extensibility in mind. It is anticipated that most\nextension will take the form of supporting additional file formats. Please\nread the `guide to extending sfftk <https://sfftk.readthedocs.io/en/latest/extending.html>`_ to learn how to do\nthis.\n\n\n",
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