write_grid_data (
        h5file,
        grid_data,
        g,
        settings,
        progress,
        )

Write volume data in Chimera hdf5 format.

chunk_shape (
        shape,
        name,
        chunk_elements,
        )

Name corresponds to slow-medium-fast axes.

data_name ( grid_data )

Determine name used to distinguish multiple maps in file.

make_arrays (
        h5file,
        g,
        size,
        atom,
        settings,
        )

write_grid_as_chimera_map (
        grid_data,
        path,
        options=None,
        progress=None,
        )

Write volume data in hdf5 format.

Example HDF5 format written by Chimera.

/Chimera /image1 chimera_map_version 1 chimera_version "1.2422" name "centriole" step (1.2, 1.2, 1.2) origin (-123.4, -522, 34.5) cell_angles (90.0, 90.0, 90.0) rotation_axis (0.0, 0.0, 1.0) rotation_angle 45.0 symmetries (((0,-1,0,0),(1,0,0,0),(0,0,1,0)),...) data_zyx (3d array of uint8 (123,542,82)) data_yzx (3d array of uint8 (123,542,82), alternate chunk shape) data_zyx_2 (3d array of uint8 (61,271,41)) subsample_spacing (2, 2, 2) (more subsampled or alternate chunkshape versions of same data)

Names "Chimera", "chimera_version", "name", "step", "origin", "cell_angles", "rotation_axis", "rotation_angle", "symmetries", "subsample_spacing" are fixed while "image1", "data_zyx", "data_yzx" and "data_zyx_2" can be any name.

In the example "Chimera" and "image1" are HDF groups, "chimera_version", "name", "step", "origin", "cell_angles", "rotation_axis", "rotation_angle", "symmetries" are group attributes, "data_zyx", "data_yzx" and "data_zyx_2" are hdf datasets (arrays), and "subsample_step" is a dataset attribute.

All data sets within the group represent the same data, such as optional subsampled arrays or alternate chunk shape for efficient disk access.

Cell angles need not be included if they are 90,90,90. They are included for handling crystallographic density maps. An identity rotation need not be included. The rotation angle is in degrees. Symmetries need not be included.

The file is saved with the Python PyTables modules which includes additional attributes "VERSION", "CLASS", "TITLE", "PYTABLES_FORMAT_VERSION".

next_suffix_number ( group,  prefix )

Used to produce new group name when adding maps to an existing hdf file.