The set of connection between two different sites of the brain is contained in a edge file file, that makes it convenient to read in the visualization filter in Paraview.
Generating the edge file is done through the command generate_brain_connectivity_edge_file
and requires:
nifti
file that can be read with nibabel
,csv
file encoding the connections between sites in the brain,Warning
This functionality requires the installation of the nibabel
python package. Please make sure you followed
the Installation procedures.
The 3D volume containing all the end-points of the connexels can be generated from the command line in the same manner as for the connectivity file. The generated file is in the VTK format.
Warning
Requires nibabel
(see above) and VTK
(see installation instructions).
The 3D volumetric image may be generated from the command line with the command generate_brain_connectivity_volume_file
.
This call is a wrapper
around the function generate_volume_file()
.
A script for performing the clustering of all the edges is provided. This scripts generates a file that can be given to the visualization filter, which makes the exploration of the different edge clusters much faster.
The command to generate the cluster file is generate_brain_connectivity_cluster_file
. The command
requires:
The output file can be given to the visualization filter in Paraview to avoid expensive computations during the visualization.
Warning
Requires nibabel
(see above) and VTK
(see installation instructions).
Tip
scipy
may be used to speed-up the computation of the k-means if installed.
Provides tools for constructing intermediate files needed for the visualization.
Note
This file is meant to be installed during the installation of the package as a callable script with several commands.
The functions provided here are:
The edge file requires:
generate_cluster_file
(mesh_file, edge_file, number_of_clusters, output_file, max_iterations=100)¶Convenience function for running the clustering on a set of edges
Parameters: |
|
---|
Note
The plugin will not know if the files and parameters are consistent. If you provide a file name that contains the computation of the centroids for a specific edge file, and the edge file is incorrectly given to the plugin, the plugin will be unable to check.
generate_edge_file
(csv_file_path, nifti_edge_file_path, output_file)¶Convenience script for creating an edge file
Parameters: |
|
---|
See also
file_ops.assemble_edges()
generate_edge_volume_file
(nifti_edge_file_path, output_file)¶Convenience script for creating a volume locating all edges end-points
Parameters: |
|
---|
See also
file_ops.assemble_edges()
See also
file_ops.save_points_to_vtk_array()
generate_volume_file
(nifti_volumetric_file_path, output_file)¶Convenience script for creating a VTK compatible volume image file.
Provides tools for generating the XML Paraview plugins.
generatePythonFilterFromFiles
(script_file, output_file, function_name=None)¶Generates an XML plugin file for Paraview from Python source file
Parameters: | function_name – the name of the function containing the plugin entry point. Defaults to RequestData |
---|
generate_plugin_after_install
(output_file)¶Utility for generating the plugin XML file after the package has been successfully installed
This utility uses the plugin.py file as an entry point. This is suitable for running in Paraview in an environment that is not a virtual environment. It requires a Paraview installation of the plugin using pvpython. See the documentation for more details.
generate_plugin_in_virtualenv_after_install
(output_file)¶Utility for generating the plugin XML file after the package has been successfully installed
This utility uses the plugin.py file as an entry point. This is suitable for running in Paraview in an environment that is not a virtual environment. It requires a Paraview installation of the plugin using pvpython. See the documentation for more details.