Metadata-Version: 1.1
Name: mrcfile
Version: 0.2.8
Summary: MRC file I/O library
Home-page: https://github.com/ccpem/mrcfile
Author: Colin Palmer
Author-email: colin.palmer@stfc.ac.uk
License: BSD
Description: mrcfile.py
        ==========
        
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            :alt: Documentation
        
        .. start_of_main_text
        
        mrcfile.py is a Python implementation of the `MRC2014 file format`_, which is
        used in structural biology to store image and volume data.
        
        It allows MRC files to be created and opened easily using a very simple API,
        which exposes the file's header and data as `numpy`_ arrays. The code runs in
        Python 2 and 3 and is fully unit-tested.
        
        .. _MRC2014 file format: http://www.ccpem.ac.uk/mrc_format/mrc2014.php
        .. _numpy: http://www.numpy.org/
        
        The intent of this library is to allow users and developers to read and write
        standard-compliant MRC files in Python as easily as possible, and with no
        dependencies on any compiled libraries except `numpy`_. You can use it
        interactively to inspect files, correct headers and so on, or in scripts and
        larger software packages to provide basic MRC file I/O functions.
        
        Key Features
        ------------
        
        * Clean, simple API for access to MRC files
        * Easy to install and use
        * Validation of files according to the MRC2014 format
        * Seamless support for gzip and bzip2 files
        * Memory-mapped file option for fast random access to very large files
        * Runs in Python 2 & 3
        
        Installation
        ------------
        
        The ``mrcfile`` library is available from the Python package index::
        
            pip install mrcfile
        
        The source code (including the full test suite) can be found on GitHub:
        https://github.com/ccpem/mrcfile
        
        Basic usage
        -----------
        
        The easiest way to open a file is with the `mrcfile.open`_ and `mrcfile.new`_
        functions. These return an `MrcFile`_ object which represents an MRC file on
        disk.
        
        .. _mrcfile.open: http://mrcfile.readthedocs.io/en/latest/source/mrcfile.html#mrcfile.open
        .. _mrcfile.new: http://mrcfile.readthedocs.io/en/latest/source/mrcfile.html#mrcfile.new
        .. _MrcFile: http://mrcfile.readthedocs.io/en/latest/usage_guide.html#using-mrcfile-objects
        
        To open an MRC file and read a slice of data::
        
            >>> import mrcfile
            >>> with mrcfile.open('tests/test_data/EMD-3197.map') as mrc:
            ...     mrc.data[10,10]
            ... 
            array([ 2.58179283,  3.1406002 ,  3.64495397,  3.63812137,  3.61837363,
                    4.0115056 ,  3.66981959,  2.07317996,  0.1251585 , -0.87975615,
                    0.12517013,  2.07319379,  3.66982722,  4.0115037 ,  3.61837196,
                    3.6381247 ,  3.64495087,  3.14059472,  2.58178973,  1.92690361], dtype=float32)
        
        To create a new file with a 2D data array, and change some values::
        
            >>> with mrcfile.new('tmp.mrc') as mrc:
            ...     mrc.set_data(np.zeros((5, 5), dtype=np.int8))
            ...     mrc.data[1:4,1:4] = 10
            ...     mrc.data
            ... 
            array([[ 0,  0,  0,  0,  0],
                   [ 0, 10, 10, 10,  0],
                   [ 0, 10, 10, 10,  0],
                   [ 0, 10, 10, 10,  0],
                   [ 0,  0,  0,  0,  0]], dtype=int8)
        
        Close the file after use by calling ``close()`` which will save the data to disk
        when the file is closed. You can also call ``flush()`` manually to flush the
        data to disk and keep the file open. If you open a file using Python's ``with``
        keyword (as in the examples above), it will be closed automatically at the end
        of the ``with`` block, like a normal Python file object.
        
        To validate an MRC file::
        
            >>> mrcfile.validate('tests/test_data/EMD-3197.map')
            File does not declare MRC format version 20140: nversion = 0
            False
        
            >>> mrcfile.validate('tmp.mrc')
            True
        
        Documentation
        -------------
        
        Full documentation is available at http://mrcfile.readthedocs.org
        
        Contributing
        ------------
        
        Please use the GitHub issue tracker for bug reports and feature requests:
        https://github.com/ccpem/mrcfile/issues
        
        Code contributions are also welcome, please submit pull requests to the GitHub
        repository.
        
        To run the test suite, from the directory which contains the ``mrcfile`` and
        ``tests`` packages, run ``python -m unittest tests``. (Or, if you have `tox`_,
        Python 2.7 and Python 3.5 installed, run ``tox``.)
        
        .. _tox: http://tox.readthedocs.org
        
        Licence
        -------
        
        The project is released under the BSD licence.
        
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
