Skip to main content
Warning: You are using the test version of PyPI. This is a pre-production deployment of Warehouse. Changes made here affect the production instance of TestPyPI (testpypi.python.org).
Help us improve Python packaging - Donate today!

MRC file I/O library

Project Description

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
  • 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, on Linux, Mac OS X and Windows

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.

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)

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: nversion = 0
False

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

Documentation

Full documentation is available on Read the Docs.

Contributing

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

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

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, Python 2.7 and Python 3.5 installed, run tox.)

Licence

The project is released under the BSD licence.

Release History

Release History

This version
History Node

1.0.0

History Node

0.2.12

History Node

0.2.11

History Node

0.2.10

History Node

0.2.9

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
mrcfile-1.0.0-py2.py3-none-any.whl (32.6 kB) Copy SHA256 Checksum SHA256 py2.py3 Wheel May 22, 2017
mrcfile-1.0.0.tar.gz (22.6 kB) Copy SHA256 Checksum SHA256 Source May 22, 2017

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting