mrcfile 0.2.4

MRC file I/O library

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.

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

• Seamless support for gzip 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.

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.

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.)

Licence

The project is released under the BSD licence.