mvpa2.misc.surfing.volsurf.VolumeBasedSurface

class mvpa2.misc.surfing.volsurf.VolumeBasedSurface(vg)

A surface based on a volume, where every voxel is a node. It has the empty topology, meaning there are no edges between nodes (voxels)

Use case: provide volume-based searchlight behaviour. In that case finding neighbouring nodes is supposed to be faster using the circlearound_n2d method.

XXX make a separate module?

Attributes

average_node_edge_length	Average length of edges associated with each face
center_of_mass	Computes the center of mass
edge2face	A mapping from edges to the face that contains that edge
face_areas
face_edge_length	Length of edges associated with each face
face_normals
faces	Returns:
nanmean_face_normal
neighbors	Finds the neighbours for each node and their (Euclidean) distance.
nfaces	Returns:
node2faces	A mapping from node indices to the faces that contain those nodes.
node_areas
node_normals
nvertices	Returns:
vertices	Returns:

Methods

circlearound_n2d(src, radius[, metric])
connected_components()
connected_components_slow()
coordinates_to_box_indices(box_size[, ...])	‘Boxes’ coordinates into triples
dijkstra_distance(src[, maxdistance])	Computes Dijkstra distance from one node to surrounding nodes
dijkstra_shortest_path(src[, maxdistance])	Computes Dijkstra shortest path from one node to surrounding nodes.
dijkstra_shortest_path_visiting(to_visit)	Computes a list of paths that visit specific nodes
euclidean_distance(src[, trg])	Computes Euclidean distance from one node to other nodes
map_to_high_resolution_surf(highres[, ...])	Finds a mapping to a higher resolution (denser) surface.
map_to_high_resolution_surf_slow(highres[, ...])	Finds a mapping to a higher resolution (denser) surface.
merge(\*others)	Merges the present surface with other surfaces
nearest_node_index(src_coords[, ...])	Computes index of nearest node to src
nodes_on_border([node_indices])	Determines which nodes are on the border of the surface
nodes_on_border_paths()	Find paths of nodes on the border
pairwise_near_nodes([max_distance, src, trg])	Finds the distances between pairs of nodes
project_vertices(n[, v])	Projects vertex coordinates onto a vector
rotate(theta[, center, unit])	Rotates the surface
same_topology(other)	Returns whether another surface has the same topology
split_by_connected_components()	Splits a surface by its connected components
sub_surface(src, radius)	Makes a smaller surface consisting of nodes around a center node
vonoroi_map_to_high_resolution_surf(highres_surf)	Computes a Vonoroi mapping for the current (low-res) surface
write(fn)

Parameters:

vg: Volgeom.volgeom or str or NiftiImage

volume to be used as a surface

Attributes

average_node_edge_length	Average length of edges associated with each face
center_of_mass	Computes the center of mass
edge2face	A mapping from edges to the face that contains that edge
face_areas
face_edge_length	Length of edges associated with each face
face_normals
faces	Returns:
nanmean_face_normal
neighbors	Finds the neighbours for each node and their (Euclidean) distance.
nfaces	Returns:
node2faces	A mapping from node indices to the faces that contain those nodes.
node_areas
node_normals
nvertices	Returns:
vertices	Returns:

Methods

circlearound_n2d(src, radius[, metric])
connected_components()
connected_components_slow()
coordinates_to_box_indices(box_size[, ...])	‘Boxes’ coordinates into triples
dijkstra_distance(src[, maxdistance])	Computes Dijkstra distance from one node to surrounding nodes
dijkstra_shortest_path(src[, maxdistance])	Computes Dijkstra shortest path from one node to surrounding nodes.
dijkstra_shortest_path_visiting(to_visit)	Computes a list of paths that visit specific nodes
euclidean_distance(src[, trg])	Computes Euclidean distance from one node to other nodes
map_to_high_resolution_surf(highres[, ...])	Finds a mapping to a higher resolution (denser) surface.
map_to_high_resolution_surf_slow(highres[, ...])	Finds a mapping to a higher resolution (denser) surface.
merge(\*others)	Merges the present surface with other surfaces
nearest_node_index(src_coords[, ...])	Computes index of nearest node to src
nodes_on_border([node_indices])	Determines which nodes are on the border of the surface
nodes_on_border_paths()	Find paths of nodes on the border
pairwise_near_nodes([max_distance, src, trg])	Finds the distances between pairs of nodes
project_vertices(n[, v])	Projects vertex coordinates onto a vector
rotate(theta[, center, unit])	Rotates the surface
same_topology(other)	Returns whether another surface has the same topology
split_by_connected_components()	Splits a surface by its connected components
sub_surface(src, radius)	Makes a smaller surface consisting of nodes around a center node
vonoroi_map_to_high_resolution_surf(highres_surf)	Computes a Vonoroi mapping for the current (low-res) surface
write(fn)

circlearound_n2d(src, radius, metric='euclidean')