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:
- 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:
- 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.
- close_gaps()
Close any head-to-tail gaps between parent and child branches.
- collapse(on=None)
Collapse all of 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.
- 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:
- 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:
- flatten()
Return the flattened points of the morphology or subtree.
- Return type:
- flatten_labels()
Return the flattened labels of the morphology or subtree.
- Return type:
- flatten_properties()
Return the flattened properties of the morphology or subtree.
- Return type:
- flatten_radii()
Return the flattened radii of the morphology or subtree.
- Return type:
- 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.
- 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.
- 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 specifiedindex
.- Parameters:
branch (
Branch
) – Branch to be attachedindex – 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.
- introduce_point(index, *args, labels=None)[source]
Insert a new point at
index
, before the existing point atindex
.
- 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:
- 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:
- label(labels, points=None)[source]
Add labels to the branch.
- Parameters:
labels (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:
- 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:
- property start
Return the spatial coordinates of the starting point of this branch.
- subtree(labels=None)
- translate(point)
- 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:
- 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]
- classmethod from_arbor(arb_m, centering=True, branch_class=None, meta=None)[source]
- classmethod from_buffer(buffer, branch_class=None, tags=None, meta=None)[source]
- classmethod from_file(path, branch_class=None, tags=None, meta=None)[source]
Create a Morphology from a file on the file system through MorphIO.
- Parameters:
path – path or file-like object to parse.
branch_class (bsb.morphologies.Branch) – Custom branch class
tags (dict) – dictionary mapping morphology label id to its name
meta (dict) – dictionary header containing metadata on morphology
- classmethod from_swc(file, branch_class=None, tags=None, meta=None)[source]
Create a Morphology from an SWC file or file-like object.
- Parameters:
file – path or file-like object to parse.
branch_class (bsb.morphologies.Branch) – Custom branch class
tags (dict) – dictionary mapping morphology label id to its name
meta (dict) – dictionary header containing metadata on morphology
- Returns:
The parsed morphology.
- Return type:
- classmethod from_swc_data(data, branch_class=None, tags=None, meta=None)[source]
Create a Morphology from a SWC-like formatted array.
- Parameters:
data (numpy.ndarray) – (N,7) array.
branch_class (type) – Custom branch class
- Returns:
The parsed morphology, with the SWC tags as a property.
- Return type:
- 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:
- to_swc(file, meta=None)[source]
Create a SWC file from a Morphology. :param file: path or file-like object to parse. :param branch_class: Custom branch class
- 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:
- 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 of 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:
- flatten_labels()[source]
Return the flattened labels of the morphology or subtree.
- Return type:
- flatten_properties()[source]
Return the flattened properties of the morphology or subtree.
- Return type:
- flatten_radii()[source]
Return the flattened radii of the morphology or subtree.
- Return type:
- get_branches(labels=None)[source]
Return a depth-first flattened array of all or the selected branches.
- label(labels, points=None)[source]
Add labels to the morphology or subtree.
- Parameters:
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:
- 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]
- voxelize(N)[source]
Turn the morphology or subtree into an approximating set of axis-aligned cuboids.
- Return type:
- bsb.morphologies.branch_iter(branch)[source]
Iterate over a branch and all of its children depth first.
- class bsb.morphologies.selector.MorphologySelector(*args, _parent=None, _key=None, **kwargs)[source]#
Bases:
ABC
- get_node_name()#
- class bsb.morphologies.selector.NameSelector(*args, _parent=None, _key=None, **kwargs)[source]#
Bases:
MorphologySelector
- get_node_name()#
- names#
- class bsb.morphologies.selector.NeuroMorphoSelector(*args, _parent=None, _key=None, **kwargs)[source]#
Bases:
NameSelector
- get_node_name()#