tmd.Tree.Tree¶
TMD class : Tree.
Classes
|
Tree class. |
- class tmd.Tree.Tree.Tree(x, y, z, d, t, p)¶
Bases:
object
Tree class.
- Parameters:
- copy_tree()¶
Returns a deep copy of the Tree.
- extract_simplified()¶
Returns a simplified tree that corresponds to the start - end of the sections points.
- get_bif_term()¶
Return number of children per point.
- get_bifurcations()¶
Return bifurcations.
- get_bounding_box()¶
Get the bounding box of the neurites.
- Parameters:
self – A TMD tree.
- Returns:
- np.array
([xmin,ymin,zmin], [xmax,ymax,zmax])
- Return type:
bounding_box
- get_direction_between(start_id=0, end_id=1)¶
Return direction of a branch.
The direction is defined as end point - start point normalized as a unit vector.
- get_multifurcations()¶
Return bifurcations.
- get_pca(plane='xy', component=0)¶
Return the i-th principal component of PCA of the tree points in the selected plane.
- get_point_path_distances()¶
Tree method to get path distances from the root.
- get_point_projection(vect=(0, 1, 0), point=None)¶
Projects each point in the tree (x,y,z) - input_point to a selected vector.
This gives the orientation of each section according to a vector in space, if normalized, otherwise it return the relative length of the section.
- get_point_radial_distances(point=None, dim='xyz')¶
Tree method to get radial distances from a point.
If point is None, the soma surface -defined by the initial point of the tree- will be used as a reference point.
- get_point_radial_distances_time(point=None, dim='xyz', zero_time=0, time=1)¶
Tree method to get radial distances from a point.
If point is None, the soma surface -defined by the initial point of the tree- will be used as a reference point.
- get_point_section_branch_orders()¶
Tree method to get section lengths.
- get_point_section_lengths()¶
Tree method to get section lengths.
- get_point_weighted_radial_distances(point=None, dim='xyz', w=(1, 1, 1), normed=False)¶
Tree method to get radial distances from a point.
If point is None, the soma surface -defined by the initial point of the tree- will be used as a reference point.
- get_sections_2()¶
Get indices of the parents of the first sections’ points and of their last points.
- get_sections_only_points()¶
Tree method to get the sections’ beginning and ending indices.
- get_segments(seg_ids=None)¶
Return segment coordinates.
- Parameters:
self – A TMD tree.
seg_ids – segment numbers to consider
- Returns:
- np.array
(child[x,y,z], parent[x,y,z])
- Return type:
seg_list
- get_terminations()¶
Return terminations.
- get_trunk_length()¶
Tree method to get the trunk (first section length).
- get_type()¶
Return type of tree.
- is_equal(tree)¶
Tests if all tree lists are the same.
- move_to_point(point=(0, 0, 0))¶
Moves the tree in the x-y-z plane so that it starts from the selected point.
- parents_children¶
Returns the parents and children nodes of each section.
- Returns:
- Each key corresponds to a section id
and the respective values to the parent section ids
- children (dict): Each key corresponds to a section id
and the respective values to the children section ids
- Return type:
parents (dict)
Notes
If 0 exists in starting nodes, the parent from tree is assigned
- rotate_xy(angle)¶
Rotates the tree in the x-y plane by the defined angle.