bsb.morphologies package#

Module contents#

Morphology module

class bsb.morphologies.Branch(points, radii, labels=None, properties=None, children=None)[source]

Bases: object

A vector based representation of a series of point in space. Can be a root or connected to a parent branch. Can be a terminal branch or have multiple children.

as_arc()[source]

Return the branch as a vector of arclengths in the closed interval [0, 1]. An arclength is the distance each point to the start of the branch along the branch axis, normalized by total branch length. A point at the start will have an arclength close to 0, and a point near the end an arclength close to 1

Returns:: Vector of branch points as arclengths.
Return type:: numpy.ndarray

attach_child(branch)[source]

Attach a branch as a child to this branch.

Parameters:: branch (Branch) – Child branch

cached_voxelize(N)[source]

Turn the morphology or subtree into an approximating set of axis-aligned cuboids and cache the result.

Return type:: bsb.voxels.VoxelSet

ceil_arc_point(arc)[source]: Get the index of the nearest distal arc point.

center(): Center the morphology on the origin

property children

Collection of the child branches of this branch.

Returns:: list of Branches
Return type:: list

close_gaps(): Close any head-to-tail gaps between parent and child branches.

collapse(on=None)

Collapse all the roots of the morphology or subtree onto a single point.

Parameters:: on (int) – Index of the root to collapse on. Collapses onto the origin by default.

contains_labels(labels)[source]

Check if this branch contains any points labelled with any of the given labels.

Parameters:: labels (List[str]) – The labels to check for.
Return type:: bool

copy(branch_class=None)[source]

Return a parentless and childless copy of the branch.

Parameters:: branch_class (type) – Custom branch creation class
Returns:: A branch, or branch_class if given, without parents or children.
Return type:: bsb.morphologies.Branch

delete_point(index)[source]

Remove a point from the branch

Parameters:: index (int) – index position of the point to remove
Returns:: the branch where the point has been removed
Return type:: bsb.morphologies.Branch

detach()[source]: Detach the branch from its parent, if one exists.

detach_child(branch)[source]

Remove a branch as a child from this branch.

Parameters:: branch (Branch) – Child branch

property end: Return the spatial coordinates of the terminal point of this branch.

property euclidean_dist: Return the Euclidean distance from the start to the terminal point of this branch.

find_closest_point(coord)[source]

Return the index of the closest on this branch to a desired coordinate.

Parameters:: coord – The coordinate to find the nearest point to
Type:: numpy.ndarray

flatten()

Return the flattened points of the morphology or subtree.

Return type:: numpy.ndarray

flatten_labels()

Return the flattened labels of the morphology or subtree.

Return type:: numpy.ndarray

flatten_properties()

Return the flattened properties of the morphology or subtree.

Return type:: numpy.ndarray

flatten_radii()

Return the flattened radii of the morphology or subtree.

Return type:: numpy.ndarray

floor_arc_point(arc)[source]: Get the index of the nearest proximal arc point.

property fractal_dim: Return the fractal dimension of this branch, computed as the coefficient of the line fitting the log-log plot of path vs euclidean distances of its points.

get_arc_point(arc, eps=1e-10)[source]

Strict search for an arc point within an epsilon.

Parameters:

arc (float) – Arclength position to look for.
eps (float) – Maximum distance/tolerance to accept an arc point as a match.

Returns:

The matched arc point index, or None if no match is found

Return type:

Union[int, None]

get_axial_distances(idx_start=0, idx_end=-1, return_max=False)[source]: Return the displacements or its max value of a subset of branch points from its axis vector. :param idx_start = 0: index of the first point of the subset. :param idx_end = -1: index of the last point of the subset. :param return_max = False: if True the function only returns the max value of displacements, otherwise the entire array.

get_branches(labels=None)

Return a depth-first flattened array of all or the selected branches.

Parameters:: labels (list) – Names of the labels to select.
Returns:: List of all branches, or the ones fully labelled with any of the given labels.
Return type:: list

get_label_mask(labels)[source]

Return a mask for the specified labels

Parameters:: labels (List[str] | numpy.ndarray[str]) – The labels to check for.
Returns:: A boolean mask that selects out the points that match the label.
Return type:: List[numpy.ndarray]

get_points_labelled(labels)[source]

Filter out all points with certain labels

Parameters:: labels (List[str] | numpy.ndarray[str]) – The labels to check for.
Returns:: All points with the labels.
Return type:: List[numpy.ndarray]

insert_branch(branch, index)[source]

Split this branch and insert the given branch at the specified index.

Parameters:

branch (Branch) – Branch to be attached
index – Index or coordinates of the cutpoint; if coordinates are given, the closest point to the coordinates is used.

Type:

Union[numpy.ndarray, int]

introduce_arc_point(arc_val)[source]

Introduce a new point at the given arc length.

Parameters:: arc_val (float) – Arc length between 0 and 1 to introduce new point at.
Returns:: The index of the new point.
Return type:: int

introduce_point(index, *args, labels=None)[source]

Insert a new point at index, before the existing point at index.

Parameters:

index (int) – Index of the new point.
args (float) – Vector coordinates of the new point
labels (list) – The labels to assign to the point.

property is_root

Returns whether this branch is root or if it has a parent.

Returns:: True if this branch has no parent, False otherwise.
Return type:: bool

property is_terminal

Returns whether this branch is terminal or if it has children.

Returns:: True if this branch has no children, False otherwise.
Return type:: bool

label(labels, points=None)[source]

Add labels to the branch.

Parameters:

labels (List[str]) – Label(s) for the branch
points – An integer or boolean mask to select the points to label.

property labels: Return the labels of the points on this branch. Labels are represented as a number that is associated to a set of labels. See Labels for more info.

property labelsets: Return the sets of labels associated to each numerical label.

list_labels()[source]: Return a list of labels present on the branch.

property max_displacement: Return the max displacement of the branch points from its axis vector.

property parent

property path_length: Return the sum of the euclidean distances between the points on the branch.

property point_vectors: Return the individual vectors between consecutive points on this branch.

property points: Return the spatial coordinates of the points on this branch.

property radii: Return the radii of the points on this branch.

root_rotate(rot, downstream_of=0)

Rotate the subtree emanating from each root around the start of that root If downstream_of is provided, will rotate points starting from the index provided (only for subtrees with a single root).

Parameters:

rot (scipy.spatial.transform.Rotation) – Scipy rotation to apply to the subtree.
downstream_of – index of the point in the subtree from which the rotation should be applied. This feature works only when the subtree has only one root branch.

Returns:

rotated Morphology

Return type:

bsb.morphologies.SubTree

rotate(rotation, center=None)

Point rotation

Parameters:

rot – Scipy rotation
center (numpy.ndarray) – rotation offset point.

Type:

Union[scipy.spatial.transform.Rotation, List[float,float,float]]

property segments: Return the start and end points of vectors between consecutive points on this branch.

set_properties(**kwargs)[source]

simplify(epsilon, idx_start=0, idx_end=-1)[source]: Apply Ramer–Douglas–Peucker algorithm to all points or a subset of points of the branch. :param epsilon: Epsilon to be used in the algorithm. :param idx_start = 0: Index of the first element of the subset of points to be reduced. :param epsilon = -1: Index of the last element of the subset of points to be reduced.

simplify_branches(epsilon): Apply Ramer–Douglas–Peucker algorithm to all points of all branches of the SubTree. :param epsilon: Epsilon to be used in the algorithm.

property size

Returns the amount of points on this branch

Returns:: Number of points on the branch.
Return type:: int

property start: Return the spatial coordinates of the starting point of this branch.

subtree(labels=None)

translate(point)

Translate the subtree by a 3D vector.

Parameters:: point (numpy.ndarray) – 3D vector to translate the subtree.
Returns:: the translated subtree
Return type:: bsb.morphologies.SubTree

property vector: Return the vector of the axis connecting the start and terminal points.

property versor: Return the normalized vector of the axis connecting the start and terminal points.

voxelize(N)

Turn the morphology or subtree into an approximating set of axis-aligned cuboids.

Return type:: bsb.voxels.VoxelSet

walk()[source]: Iterate over the points in the branch.

class bsb.morphologies.Morphology(roots, meta=None, shared_buffers=None, sanitize=False)[source]

Bases: SubTree

A multicompartmental spatial representation of a cell based on a directed acyclic graph of branches whom consist of data vectors, each element of a vector being a coordinate or other associated data of a point on the branch.

property adjacency_dictionary: Return a dictonary associating to each key (branch index) a list of adjacent branch indices

as_filtered(labels=None)[source]: Return a filtered copy of the morphology that includes only points that match the current label filter, or the specified labels.

copy()[source]: Copy the morphology.

classmethod empty()[source]

get_label_mask(labels)[source]: Get a mask corresponding to all the points labelled with 1 or more of the given labels

property is_optimized

property labelsets: Return the sets of labels associated to each numerical label.

list_labels()[source]: Return a list of labels present on the morphology.

property meta

optimize(force=False)[source]

set_label_filter(labels)[source]: Set a label filter, so that as_filtered returns copies filtered by these labels.

simplify(*args, optimize=True, **kwargs)[source]

to_graph_array()[source]

Create a SWC-like numpy array from a Morphology.

Warning

Custom SWC tags (above 3) won’t work and throw an error

Returns:: a numpy array with columns storing the standard SWC attributes
Return type:: numpy.ndarray

to_swc(file)[source]: Create a SWC file from a Morphology. :param file: path to write to

class bsb.morphologies.MorphologySet(loaders, m_indices=None, /, labels=None)[source]

Bases: object

Associates a set of StoredMorphologies to cells

clear_soft_cache()[source]

count_morphologies()[source]

count_unique()[source]

classmethod empty()[source]

get(index, cache=True, hard_cache=False)[source]

get_indices(copy=True)[source]

iter_meta(unique=False)[source]

iter_morphologies(cache=True, unique=False, hard_cache=False)[source]

Iterate over the morphologies in a MorphologySet with full control over caching.

Parameters:

cache (bool) – Use Soft caching (1 copy stored in mem per cache miss, 1 copy created from that per cache hit).
hard_cache – Use Soft caching (1 copy stored on the loader, always same copy returned from that loader forever).

merge(other)[source]

property names

set_label_filter(labels)[source]

class bsb.morphologies.RotationSet(data)[source]

Bases: object

Set of rotations. Returned rotations are of scipy.spatial.transform.Rotation

iter(cache=False)[source]

class bsb.morphologies.SubTree(branches, sanitize=True)[source]

Bases: object

Collection of branches, not necesarily all connected.

property bounds

property branch_adjacency: Return a dictonary containing mapping the id of the branch to its children.

property branches: Return a depth-first flattened array of all branches.

cached_voxelize(N)[source]

Turn the morphology or subtree into an approximating set of axis-aligned cuboids and cache the result.

Return type:: bsb.voxels.VoxelSet

center()[source]: Center the morphology on the origin

close_gaps()[source]: Close any head-to-tail gaps between parent and child branches.

collapse(on=None)[source]

Collapse all the roots of the morphology or subtree onto a single point.

Parameters:: on (int) – Index of the root to collapse on. Collapses onto the origin by default.

flatten()[source]

Return the flattened points of the morphology or subtree.

Return type:: numpy.ndarray

flatten_labels()[source]

Return the flattened labels of the morphology or subtree.

Return type:: numpy.ndarray

flatten_properties()[source]

Return the flattened properties of the morphology or subtree.

Return type:: numpy.ndarray

flatten_radii()[source]

Return the flattened radii of the morphology or subtree.

Return type:: numpy.ndarray

get_branches(labels=None)[source]

Return a depth-first flattened array of all or the selected branches.

Parameters:: labels (list) – Names of the labels to select.
Returns:: List of all branches, or the ones fully labelled with any of the given labels.
Return type:: list

label(labels, points=None)[source]

Add labels to the morphology or subtree.

Parameters:

labels (list[str]) – Labels to add to the subtree.
points (numpy.ndarray) – Optional boolean or integer mask for the points to be labelled.

property labels

property origin

property path_length: Return the total path length as the sum of the euclidian distances between consecutive points.

property points

property properties

property radii

root_rotate(rot, downstream_of=0)[source]

Rotate the subtree emanating from each root around the start of that root If downstream_of is provided, will rotate points starting from the index provided (only for subtrees with a single root).

Parameters:

rot (scipy.spatial.transform.Rotation) – Scipy rotation to apply to the subtree.
downstream_of – index of the point in the subtree from which the rotation should be applied. This feature works only when the subtree has only one root branch.

Returns:

rotated Morphology

Return type:

bsb.morphologies.SubTree

rotate(rotation, center=None)[source]

Point rotation

Parameters:

rot – Scipy rotation
center (numpy.ndarray) – rotation offset point.

Type:

Union[scipy.spatial.transform.Rotation, List[float,float,float]]

simplify_branches(epsilon)[source]: Apply Ramer–Douglas–Peucker algorithm to all points of all branches of the SubTree. :param epsilon: Epsilon to be used in the algorithm.

property size

subtree(labels=None)[source]

translate(point)[source]

Translate the subtree by a 3D vector.

Parameters:: point (numpy.ndarray) – 3D vector to translate the subtree.
Returns:: the translated subtree
Return type:: bsb.morphologies.SubTree

voxelize(N)[source]

Turn the morphology or subtree into an approximating set of axis-aligned cuboids.

Return type:: bsb.voxels.VoxelSet

bsb.morphologies.branch_iter(branch)[source]: Iterate over a branch and all of its children depth first.

bsb.morphologies.parse_morphology_file(file, **kwargs)[source]

class bsb.morphologies.selector.MorphologySelector(*args, _parent=None, _key=None, **kwargs)[source]#

Bases: ABC

get_node_name()#

abstract pick(morphology)[source]#

scaffold: Scaffold#

select#: Base implementation of all the different configuration attributes. Call the factory function attr() instead.

abstract validate(all_morphos)[source]#

class bsb.morphologies.selector.NameSelector(*args, _parent=None, _key=None, **kwargs)[source]#

Bases: MorphologySelector

get_node_name()#

names: cfglist[str]#

pick(morphology)[source]#

validate(all_morphos)[source]#

class bsb.morphologies.selector.NeuroMorphoSelector(*args, _parent=None, _key=None, **kwargs)[source]#

Bases: NameSelector

get_node_name()#

bsb.morphologies package#

Subpackages#

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