Brain atlas Module

class coperniFUS.modules.atlas.AsynchronousOnlineAtlasListRetrieval(skip_online_atlas_retreival)

Bases: QThread

Handles network issues when retrieving online atlas lists.

finished

Signal emitted whenever the atlas retreival is done (or has failed).

run(self)

class coperniFUS.modules.atlas.BrainAtlasMultiLayerNDImageLUT(parent_viewer, parent_brainatlas_module, ndimage_name='Multi-layer ndimage', **kwargs)

Bases: MultiLayerNDImageLUT

property ndimage_tmat

class coperniFUS.modules.atlas.BrainAtlas(parent_viewer, skip_online_atlas_retreival=False, **kwargs)

Bases: Module

BrainAtlas module.

property atlas_resolution

Resultion of the reference altas in meters (x, y, z) Suplampling is accounted for in the returned value.

property brain_atlas_tmat

Holds the atlas volume affine transformation matrix

property bg_atlas

Holds the Brain Globe instance currently loaded in the module

property available_atlases

Get a list of all (online and offline) available atlases in the dictionary form

add_reference_atlas(offline_atlas_name)

Add a reference atlas to the module

remove_reference_atlas()

Delete the reference atlas currently loaded in the module

add_structure_layer(structure, hemisphere)

Add a brain structure layer to the atlas

remove_altas_layer(layer_name=None, tree_viewer_layer_index=None)

Delete one of the currently loaded brain structure layer from the rendered atlas

update_tooltip_to_layer_centroid()

Updates the Tooltip location according to the checkbox selection in the module dock

release_tooltip()

Releases the tooltip location from the selected location in the module. Please call CoperniFUS viewer release_from_modules method to release the tooltip from all loaded modules.

init_dock()

Called on GUI setup to add a module dock

add_rendered_object()

Called when populating the viewer with the module rendered objects

update_rendered_object()

Called on render view updates

delete_rendered_object()

Called on deletion of the module rendered objects

get_user_param(param_name, default_value=None)

Get module configuration parameter stored in cache (or default values if non existant)

set_user_param(param_name, param_value)

Set module configuration parameter to cache