Metadata-Version: 1.2
Name: cmapfile
Version: 2021.2.26
Summary: Write Chimera Map (CMAP) files
Home-page: https://www.lfd.uci.edu/~gohlke/
Author: Christoph Gohlke
Author-email: cgohlke@uci.edu
License: BSD
Project-URL: Bug Tracker, https://github.com/cgohlke/cmapfile/issues
Project-URL: Source Code, https://github.com/cgohlke/cmapfile
Description: 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, 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 <https://www.lfd.uci.edu/~gohlke/>`_
        
        :Organization:
          Laboratory for Fluorescence Dynamics. University of California, Irvine
        
        :License: BSD 3-Clause
        
        :Version: 2021.2.26
        
        Requirements
        ------------
        * `CPython >= 3.7 <https://www.python.org>`_
        * `Numpy 1.15 <https://www.numpy.org>`_
        * `Scipy 1.4 <https://www.scipy.org>`_
        * `H5py 2.10 <https://www.h5py.org/>`_
        * `Tifffile 2019.8.25 <https://pypi.org/project/tifffile/>`_
        * `Oiffile 2020.9.18 <https://pypi.org/project/oiffile/>`_
        
        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
        ---------
        2021.2.26
            Fix LSM conversion with tifffile >= 2021.2.26.
            Remove support for Python 3.6 (NEP 29).
        2020.1.1
            Do not write name attribute.
            Remove support for Python 2.7 and 3.5.
            Update copyright.
        2018.8.30
            Move cmapfile.py into cmapfile package.
        2014.10.10
            Initial release.
        
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.7
