morphoclass.orientation module

Tools for orienting neurons in their 3D embedding vector space.

morphoclass.orientation.fit_3d_ray(points)

Fit a ray through given points in 3D.

This is done by minimizing the norm of the difference between v=(x, y, z) and the projection of v onto the ray

Parameters

points (np.ndarray) – Array of shape (N, 3) containing N points in 3D.

Returns

Spherical coordinates of the point on the unit sphere determining the ray direction. If the fitting fails then None is returned.

Return type

(theta, phi) or None

morphoclass.orientation.fit_tree_pca(tree)

Get the normalized tree principal component in spherical coordinates.

Parameters

tree (tmd.Tree.Tree.Tree) – A TMD tree.

Returns

The normalized principal component vector in spherical coordinates.

Return type

(theta, phi)

morphoclass.orientation.fit_tree_ray(tree)

Fit a ray through the root of the tree.

Parameters

tree (tmd.Tree.Tree.Tree)) – A TMD tree.

Returns

Spherical coordinates of the point on the unit sphere determining the ray direction. If the fitting fails then None is returned

Return type

(theta, phi) or None

morphoclass.orientation.get_angle_deg(v1, v2)

Compute the angle in degrees between two given vectors.

Parameters

  • v1 (np.ndarray) – First vector

  • v2 (np.ndarray) – Second vector.

Returns

The angle in degrees between v1 and v2.

Return type

float

morphoclass.orientation.get_angle_rad(v1, v2)

Compute the angle in radians between two given vectors.

Parameters

  • v1 (np.ndarray) – First vector

  • v2 (np.ndarray) – Second vector.

Returns

The angle in radians between v1 and v2.

Return type

float

morphoclass.orientation.get_tree_origin(tree)

Find the index of the origin node of a tree.

Parameters

tree (tmd.Tree.Tree.Tree) – A TMD tree.

Returns

  • origin (np.ndarray) – The coordinates of the tree origin.

  • origin_idx (int) – The index of the origin node.

morphoclass.orientation.get_tree_pca(tree, kind='3d', shift_to_origin=False)

Compute the PCA components of the given TMD tree.

Parameters

  • tree (tmd.Tree.Tree.Tree) – A TMD tree.

  • kind ({"2d", "3d"}) – The kind of PCA to compute. The 2D PCA only considers the x and y coordinates, while the 3D uses x, y and z.

  • shift_to_origin (bool) – If true shift the tree root to coordinate origin.

Returns

  • mean (np.array) – The mean of tree coordinates.

  • components (np.array) – The three PCA components of the tree.

  • explained_variance_ratio (np.array) – The explained variance ratio.

Raises

ValueError – If the parameter kind has an invalid value. If the tree does not have exactly one root node.

morphoclass.orientation.orient_dataset(orient_fn, dataset_dir, output_dir=None, overwrite=False)

Orient all samples in a given dataset (not implemented yet).

Parameters

  • orient_fn (callable) – The orientation function.

  • dataset_dir (str or pathlib.Path) – The dataset directory.

  • output_dir (str or pathlib.Path (optional)) – The output directory. If None an output directory name will be constructed by appending “_oriented” to the dataset directory name.

  • overwrite (bool (optional)) – If true then the the output directory will be purged in case it already exists.

Returns

Whether or not the orientation was successful.

Return type

bool

morphoclass.orientation.orient_neuron(orient_fn, neuron, in_place=False)

Orient the neuron apicals to point in the y-direction.

Parameters

  • orient_fn (callable) – Function that finds the direction of a tree.

  • neuron – The neuron to orient.

  • in_place (bool (optional)) – If true modify the given neuron instead of returning a copy.

Returns

Oriented copy of the original neuron.

Return type

new_neuron