mrcfile 0.1.0

mrcfile.py
==========

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.. start_of_main_text

mrcfile.py is a Python implementation of the `MRC2014 file format`_. 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: MRC2014_
.. _MRC2014: http://www.ccpem.ac.uk/mrc_format/mrc2014.php
.. _numpy: http://www.numpy.org/

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`_.

.. _on Github: https://github.com/ccpem/mrcfile

Basic usage
-----------

The easiest way to open a file is with the :func:`~mrcfile.open` and
:func:`~mrcfile.new` functions. These return an
:class:`~mrcfile.mrcfile.MrcFile` object which represents an MRC file on disk.

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
array([[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]], dtype=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 :meth:`~mrcfile.mrcfile.MrcFile.close`
which will save the data to disk when the file is closed. You can also call
:meth:`~mrcfile.mrcfile.MrcFile.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.