Metadata-Version: 2.1
Name: sfftk
Version: 0.5.5.dev1
Summary: Toolkit for working with EMDB-SFF and other segmentation file formats
Home-page: https://emdb-empiar.github.io/EMDB-SFF/
Author: Paul K. Korir, PhD
Author-email: pkorir@ebi.ac.uk, paul.korir@gmail.com
License: Apache License
Project-URL: Report Issues, https://github.com/emdb-empiar/sfftk/issues
Project-URL: Documentation, http://sfftk.readthedocs.io/en/latest/index.html
Project-URL: Souce Code, https://github.com/emdb-empiar/sfftk
Description: ============================
        EMDB-SFF Toolkit (``sfftk``)
        ============================
        
        .. contents::
        
        Introduction
        ============
        
        ``sfftk`` is a set of utilities that facilitate creation, conversion and
        modification of `Electron Microscopy Data Bank - Segmentation File Format
        (EMDB-SFF) files <https://github.com/emdb-empiar/sfftk/tree/master/sfftk/test_data/sff>`_.
        EMDB-SFF is an open, community-driven file format to handle annotated
        segmentations and subtomogram averages that facilitates segmentation file
        interchange. It is written in Python and provides both a command-line
        suite of commands and a Python API.
        
        Audience
        --------
        
        ``sfftk`` is primarily targeted but not restricted to biological electron
        microscopists and developers of image segmentation software.
        
        
        License
        -------
        
        ``sfftk`` is free and open source software released under the terms of the Apache License, Version 2.0. Source code is
        copyright EMBL-European Bioinformatics Institute (EMBL-EBI) 2017.
        
        Data Model
        ----------
        
        ``sfftk`` is built to handle EMDB-SFF files. The corresponding schema
        (``v0.8.0.dev1``) may be found at `https://emdb-empiar.github.io/EMDB-SFF <https://emdb-empiar.github.io/EMDB-SFF>`_.
        Changes to the schema are welcome for discussion at the *Segmentation Working Group*
        at `https://listserver.ebi.ac.uk/mailman/listinfo/segtrans-wg
        <https://listserver.ebi.ac.uk/mailman/listinfo/segtrans-wg>`_.
        
        .. _supported_formats:
        
        Supported Formats
        -----------------
        
        The following file formats are currently supported (in alphabetical order of
        extensions):
        
        -  Amira Mesh (.am)
        
        -  SuRVoS (.h5; experimental support)
        
        -  CCP4 Masks (.map)
        
        -  IMOD (.mod)
        
        -  Segger (.seg)
        
        -  Stereolithography (.stl)
        
        -  Amira HyperSurface (.surf)
        
        Contact
        -------
        
        Any questions or comments should be addressed to ``pkorir at ebi dot ac dot uk``.
        
        Publications
        ------------
        
        .. Please cite the  whenever ``sfftk`` is used in a publication:
        
        .. .. note::
        
        ..    Article to be added
        
        The EMDB-SFF data model is the result of various community consultations which
        are published in the following articles:
        
        -  `Patwardhan, Ardan, Robert Brandt, Sarah J. Butcher, Lucy Collinson, David Gault, Kay Grünewald, Corey Hecksel et al. Building bridges between cellular and molecular structural biology. eLife 6 (2017). <http://europepmc.org/abstract/MED/28682240>`_
        
        -  `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>`_
        
        -  `Patwardhan, Ardan, José-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>`_
        
        Getting Started
        ===============
        
        Obtaining and Installing ``sfftk``
        ----------------------------------
        
        Dependencies
        ~~~~~~~~~~~~
        
        As with any Python software, we recommend installing it in a virtual environment (of your choice). The only dependency
        that may be needed is ``numpy`` which can be installed with
        
        .. code:: bash
        
        	 pip install numpy
        
        PyPI
        ~~~~
        
        ``sfftk`` is available on PyPI meaning that all that one needs to do is run:
        
        .. code:: bash
        
        	 pip install sfftk
        
        Source
        ~~~~~~
        
        The ``sfftk`` source is available from Github `https://github.com/emdb-empiar/sfftk <https://github.com/emdb-empiar/sfftk>`_.
        
        Features
        ========
        
        ``sfftk`` has two principal functions:
        
        - `convert` application-specific segmentation file format (AS-SFF) files to EMDB-SFF;
        
        - `annotate` EMDB-SFF files against known ontologies.
        
        Conversion
        ----------
        
        Segmentation files may be converted to EMDB-SFF files using the ``convert``
        command.
        
        .. code:: bash
        
        	 sff convert file.am -o file.sff
        
        For a full description of how to perform conversion, please see the
        `guide to format conversion <https://sfftk.readthedocs.io/en/latest/converting.html>`_.
        
        Annotation
        ----------
        
        Annotation is performed using the ``notes`` utility on EMDB-SFF files.
        
        .. code:: bash
        
        	 sff notes show -H file.sff
        
        ``sfftk`` provides a simple set of tools to allow `viewing, searching and
        modifying annotations` associated with the segmentation and individual
        segments. The added annotations should be either from a public ontology or be
        an accession from a public database.
        
        See the `guide to annotating segmentations <https://sfftk.readthedocs.io/en/latest/annotating.html>`_ for a full
        treatment.
        
        Miscellaneous
        -------------
        
        ``sfftk`` may also be used for several miscellaneous operations such as:
        
        -  `Viewing segmentation metadata <https://sfftk.readthedocs.io/en/latest/misc.html#viewing-file-metadata>`_
        
        -  `Prepping segmentations <https://sfftk.readthedocs.io/en/latest/misc.html#prepping-segmentation-files>`_ before conversion to EMDB-SFF
        
        -  `Setting configurations <https://sfftk.readthedocs.io/en/latest/misc.html#setting-configurations>`_ that affect how ``sfftk`` works
        
        -  `Running unit tests <https://sfftk.readthedocs.io/en/latest/misc.html#running-unit-tests>`_  with the ``tests`` command
        
        More information on this can be found in the `guide to miscellaneous operations <https://sfftk.readthedocs.io/en/latest/misc.html>`_.
        
        Developing with ``sfftk``
        -------------------------
        
        ``sfftk`` is developed as a set of decoupled packages providing the various
        functionality. The main classes involved are found in the `sfftkrw <https://sfftk-rw.readthedocs.io/en/latest/>`_ package.
        There is also a `guide to developing with sfftk <https://sfftk.readthedocs.io/en/latest/developing.html>`_ which
        provides useful instructions.
        
        Extending ``sfftk``
        -------------------
        
        ``sfftk`` has built with extensibility in mind. It is anticipated that most
        extension will take the form of supporting additional file formats. Please
        read the `guide to extending sfftk <https://sfftk.readthedocs.io/en/latest/extending.html>`_ to learn how to do
        this.
        
Keywords: EMDB-SFF,SFF,segmentation
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Terminals
Classifier: Topic :: Text Processing
Classifier: Topic :: Text Processing :: Markup
Classifier: Topic :: Utilities
Description-Content-Type: text/x-rst; charset=UTF-8
