Skip to main content

Write Chimera Map (CMAP) files

Project description

Cmapfile is a Python library and console script to write Chimera Map (CMAP) files, HDF5 files containing series of 3D XYZ datasets.

CMAP files can be created from numpy arrays and various file formats containing volume data, e.g. BIN, TIFF, LSM, OIF, and OIB.

CMAP files can be visualized using UCSF Chimera [2], a highly extensible program for interactive visualization and analysis of molecular structures and related data.

For command line usage run python -m cmapfile --help

Author:Christoph Gohlke
Organization:Laboratory for Fluorescence Dynamics. University of California, Irvine
Version:2019.1.1

References

  1. Thomas Goddard. [Chimera-users] reading in hdf5 files in chimera. https://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003052.html
  2. UCSF Chimera, an extensible molecular modeling system. https://www.cgl.ucsf.edu/chimera/
  3. Globals for Images - SimFCS. https://www.lfd.uci.edu/globals/

Examples

Convert a 5D LSM file to CMAP file:

python -m cmapfile "/my data directory/large.lsm"

Convert all BIN files in the current directory to test.cmap. The BIN files are known to contain 128x128x64 samples of 16 bit integers. The CMAP file will store float32 maps using subsampling up to 16:

python -m cmapfile --shape 128,128,64 --step 1,1,2 --dtype i2
                   --cmap test.cmap --subsample 16 --astype float32 *.bin

Change the step size in the CMAP file:

python -m cmapfile --step 1,1,1.5 test.cmap

Notes

The CMAP file format according to [1]:

Example of HDF format written by Chimera (Chimera map format) follows.
The Chimera map file reader will allow all fields to be missing (except
the 3D data).

/image (group, any name allowed)
 name "centriole" (attribute)
 step (1.2, 1.2, 1.2) (attribute)
 origin (-123.4, -522, 34.5) (attribute)
 cell_angles (90.0, 90.0, 90.0) (attribute)
 rotation_axis (0.0, 0.0, 1.0) (attribute)
 rotation_angle 45.0 (attribute, degrees)
 /data (3d array of uint8 (123,542,82)) (dataset, any name allowed)
 /data_x (3d array of uint8 (123,542,82), alternate chunk shape) (dataset)
 /data_2 (3d array of uint8 (61,271,41)) (dataset, any name allowed)
    subsample_spacing (2, 2, 2) (attribute)
 (more subsampled or alternate chunkshape versions of same data)

Revisions

2019.1.1
Update copyright.
2018.8.30
Move cmapfile.py into cmapfile package.
2014.10.10
Initial release.

Project details


Download files

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

Filename, size & hash SHA256 hash help File type Python version Upload date
cmapfile-2019.1.1-py2.py3-none-any.whl (11.8 kB) Copy SHA256 hash SHA256 Wheel py2.py3
cmapfile-2019.1.1.tar.gz (10.4 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page