mrcfile

mrcfile.py

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mrcfile 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/

This library aims 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
• Asynchronous opening option for background loading of multiple files
• Runs in Python 2 & 3, on Linux, Mac OS X and Windows

Installation

The mrcfile library is available from the Python package index_::

pip install mrcfile

Or from conda-forge_::

conda install --channel conda-forge mrcfile

It is also included in the ccpem-python environment in the CCP-EM_ software suite.

.. _CCP-EM: http://www.ccpem.ac.uk

The source code (including the full test suite) can be found on GitHub_.

.. _Python package index: https://pypi.org/project/mrcfile .. _conda-forge: https://anaconda.org/conda-forge/mrcfile .. _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::

>>> array = np.zeros((5, 5), dtype=np.int8)
>>> with mrcfile.new('tmp.mrc') as mrc:
...     mrc.set_data(array)
...     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)

The data will be saved to disk when the file is closed, either automatically at the end of the with block (like a normal Python file object) or manually by calling close(). You can also call flush() to write any changes to disk and keep the file open.

To validate an MRC file::

>>> mrcfile.validate('tests/test_data/EMD-3197.map')
File does not declare MRC format version 20140 or 20141: nversion = 0
False

>>> mrcfile.validate('tmp.mrc')
True

Documentation

Full documentation is available on Read the Docs_.

.. _Read the Docs: http://mrcfile.readthedocs.org

Citing mrcfile

If you find mrcfile useful in your work, please cite:

Burnley T, Palmer C & Winn M (2017) Recent developments in the CCP-EM software suite. Acta Cryst. D\ 73:469--477. doi: 10.1107/S2059798317007859_

.. _doi: 10.1107/S2059798317007859: https://doi.org/10.1107/S2059798317007859

Contributing

Please use the GitHub issue tracker_ for bug reports and feature requests, or email CCP-EM_.

.. _GitHub issue tracker: https://github.com/ccpem/mrcfile/issues .. _email CCP-EM: [e-mail]

Code contributions are also welcome, please submit pull requests to the GitHub repository_.

.. _GitHub repository: https://github.com/ccpem/mrcfile

To run the test suite, go to the top-level project directory (which contains the mrcfile and tests packages) and run python -m unittest tests. (Or, if you have tox_ installed, run tox.)

.. _tox: http://tox.readthedocs.org

Licence

The project is released under the BSD licence.