Metadata-Version: 1.1
Name: sfftk
Version: 0.3.1.dev3
Summary: Toolkit for working with EMDB-SFF and other segmentation file formats
Home-page: http://sfftk.readthedocs.io/en/latest/index.html
Author: Paul K. Korir, PhD
Author-email: pkorir@ebi.ac.uk, paul.korir@gmail.com
License: Apache License
Description: ============================
        EMDB-SFF Toolkit (``sfftk``)
        ============================
        
        .. image:: https://badge.fury.io/py/sfftk.svg
            :target: https://badge.fury.io/py/sfftk
            
        .. image:: https://travis-ci.org/emdb-empiar/sfftk.svg?branch=master
            :target: https://travis-ci.org/emdb-empiar/sfftk
        
        .. image:: https://coveralls.io/repos/github/emdb-empiar/sfftk/badge.svg?branch=master
        	:target: https://coveralls.io/github/emdb-empiar/sfftk?branch=master
        	
        .. image:: https://readthedocs.org/projects/sfftk/badge/?version=latest
        	:target: http://sfftk.readthedocs.io/en/latest/?badge=latest
        	:alt: Documentation Status
        
        .. 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 predominantly written in Python with some functionality 
        implemented as C-extensions for performance. It 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 released under an Apache License, Version 2.0 and is copyright of 
        EMBL-European Bioinformatics Institute (EMBL-EBI) 2017.
        
        Data Model
        ----------
        
        ``sfftk`` is built to handle EMDB-SFF files. The corresponding schema 
        (``v0.7.0.dev0``) may be obtained at `http://wwwdev.ebi.ac.uk/pdbe/emdb/emdb_static/doc/segmentation_da_docs/segmentation_da.html
        <http://wwwdev.ebi.ac.uk/pdbe/emdb/emdb_static/doc/segmentation_da_docs/segmentation_da.html>`_. 
        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)
        
        -  CCP4 Masks (.map)
        
        -  IMOD (.mod)
        
        -  Segger (.seg)
        
        -  Stereolithography (.stl)
        
        -  Amira HyperSurface (.surf)
        
        Contact
        -------
        
        Any questions or comments should be addressed to 
        `ardan@ebi.ac.uk <mailto:ardan@ebi.ac.uk>`_ or 
        `pkorir@ebi.ac.uk <mailto:pkorir@ebi.ac.uk>`_.
        
        Publications
        ------------
        
        The following articles should be cited whenever ``sfftk`` is used in a 
        publication:
        
        .. todo::
        
        	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
        ~~~~~~~~~~~~
        
        We highly recommend installing ``sfftk`` in an anaconda environment because 
        this makes it easy to obtain some of the dependencies. You can find out more 
        about installing anaconda at `https://www.anaconda.com/download/ 
        <https://www.anaconda.com/download/>`_.
        
        The following dependencies are required and will be automatically installed 
        when using PyPI:
        
        -  `ahds <http://ahds.readthedocs.io/en/latest/>`_ (v.0.1.6 or greater)
        
        -  lxml
        
        -  h5py
        
        -  requests
        
        -  scikit-image
        
        -  bitarray
        
        -  numpy
        
        -  scipy
        
        These packages should automatically be installed during installation of ``sfftk``.
        
        
        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>`_ 
        or from CCP-EM Gitlab repository 
        `https://gitlab.com/ccpem/ccpem/tree/master/src/ccpem_progs/emdb_sfftk 
        <https://gitlab.com/ccpem/ccpem/tree/master/src/ccpem_progs/emdb_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 
        :doc:`guide to format conversion <converting>`.
        
        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 :doc:`guide to annotating segmentations <annotating>` for a full 
        treatment.
        
        Miscellaneous
        -------------
        
        ``sfftk`` may also be used for several miscellaneous operations such as:
        
        -  Viewing segmentation metadata
        
        -  Setting configurations that affect how ``sfftk`` works
        
        -  Running unit tests with the ``tests`` command
        
        More information on this can be found in the :doc:`guide to miscellaneous 
        operations <misc>`.
        
        Developing with ``sfftk``
        -------------------------
        
        ``sfftk`` is developed as a set of decoupled packages providing the various 
        functionality. The main classes involved are found in the ``sfftk.schema 
        package``. Please see `full API <http://sfftk.readthedocs.io/en/latest/sfftk.html>`_. 
        There is also a :doc:`guide to developing with sfftk <developing>` 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 :doc:`guide to extending sfftk <extending>` 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: Programming Language :: Python :: 2.7
