HappyDoc Generated Documentation Class: Chimera_HDF_Data

/ . / VolumeData / cmap / cmap_format.py / Chimera_HDF_Data 

Read 3d array data from a Chimera HDF5 file using PyTables (table).

Example HDF5 format written by Chimera.

/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, any name allowed) /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)

Methods   
  find_arrays  
find_arrays (
        self,
        parent,
        anodes=None,
        )

Return list of grouped arrays. Each element is a tuple containing a group and a list of 2-d and 3-d arrays that are children of the group.

  read_matrix  
read_matrix (
        self,
        ijk_origin,
        ijk_size,
        ijk_step,
        array_paths,
        array,
        progress,
        )

Reads a submatrix returning 3D NumPy matrix with zyx index order. array_path can be a HDF5 path to a 3d array or a list of paths to a stack of 2d arrays.

  __init__  
__init__ ( self,  path )
Exceptions   

ValueError, 'Chimera HDF5 file %s contains no 3d arrays' % path
This document was automatically generated Fri May 30 21:13:41 2008 by HappyDoc version 3.1