cmapfile 2025.1.1

Write Chimera Map (CMAP) files

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, for example, BIN, TIFF, LSM, OIF, and OIB.

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

Author:

Christoph Gohlke

License:

BSD 3-Clause

Version:

2025.1.1

Quickstart

Install the cmapfile package and all dependencies from the Python Package Index:

python -m pip install -U cmapfile[all]

Print the command line usage:

python -m cmapfile --help

See Examples for usage cases.

Source code and support are available on GitHub.

Requirements

This revision was tested with the following requirements and dependencies (other versions may work):

• CPython 3.10.11, 3.11.9, 3.12.8, 3.13.1 64-bit

• NumPy 2.1.3

• Scipy 1.14.1

• H5py 3.12.1

• Tifffile 2024.12.12

• Oiffile 2025.1.1

Revisions

2025.1.1

• Improve type hints.

• Support Python 3.13.

2024.8.28

• Fix lsm2cmap with tifffile > 2024.8.24.

• Drop support for Python 3.9 and numpy < 1.24 (NEP29).

2023.8.30

• Drop support for Python 3.8 and numpy < 1.22 (NEP29).

2022.9.29

• Make subsampling compatible with ChimeraX (breaking).

• Fix deprecated import of scipy.ndimage.interpolation.zoom.

• Switch to Google style docstrings.

2022.2.2

• Add type hints.

• Drop support for Python 3.7 and numpy < 1.19 (NEP29).

2021.2.26

• Fix LSM conversion with tifffile >= 2021.2.26.

• Drop support for Python 3.6 (NEP 29).

2020.1.1

• Do not write name attribute.

• Drop support for Python 2.7 and 3.5.

• Update copyright.

2018.8.30

• Move cmapfile.py into cmapfile package.

2014.10.10

• Initial release.

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)
 color (1.0, 1.0, 0, 1.0) (attribute, rgba 0-1 float)
 time 5 (attribute, time series frame number)
 channel 0 (attribute, integer for multichannel data)
 /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)

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

Print the cmapfile script usage:

$ python -m cmapfile --help

Usage: cmapfile [options] files

Convert volume data files to Chimera MAP files.

Options:
--version             show program's version number and exit
-h, --help            show this help message and exit
-q, --quiet
--filetype=FILETYPE   type of input file(s).
                      For example, BIN, LSM, OIF, TIF
--dtype=DTYPE         type of data in BIN files. For example, uint16
--shape=SHAPE         shape of data in BIN files in F order.
                      For example, 256,256,32
--offset=OFFSET       number of bytes to skip at beginning of BIN files
--step=STEP           stepsize of data in files in F order.
                      For example, 1.0,1.0,8.0
--cmap=CMAP           name of output CMAP file
--astype=ASTYPE       type of data in CMAP file. For example, float32
--subsample=SUBSAMPLE
                      write subsampled datasets to CMAP file