allensdk.internal.morphology.morphology module

class allensdk.internal.morphology.morphology.Morphology(node_list=None)

Bases: object

Keep track of the list of nodes in a morphology and provide a few helper methods (soma, tree information, pruning, etc).

APICAL_DENDRITE = 4

AXON = 2

BASAL_DENDRITE = 3

NODE_TYPES = [1, 2, 3, 4]

SOMA = 1

append(self, nodes)

Add additional nodes to this Morphology. Those nodes must originate from another morphology object.

Parameters:

nodes: list of Morphology nodes

apply_affine(self, aff, scale=None)

Apply an affine transform to all nodes in this morphology. Compartment radius is adjusted as well.

Format of the affine matrix is:

[x0 y0 z0] [tx] [x1 y1 z1] [ty] [x2 y2 z2] [tz]

where the left 3x3 the matrix defines the affine rotation and scaling, and the right column is the translation vector.

The matrix must be collapsed and stored in a list as follows:

[x0 y0, z0, x1, y1, z1, x2, y2, z2, tx, ty, tz]

Parameters:

aff: 3x4 array of floats (python 2D list, or numpy 2D array)

the transformation matrix

apply_affine_only_rotation(self, aff)

Apply an affine transform to all nodes in this morphology. Only the rotation element of the transform is performed (i.e., although the entire transformation and translation matrix is supplied, only the rotation element is used). The morphology is translated to the point where the soma root is at 0,0,0.

Format of the affine matrix is:

[x0 y0 z0] [tx] [x1 y1 z1] [ty] [x2 y2 z2] [tz]

where the left 3x3 the matrix defines the affine rotation and scaling, and the right column is the translation vector.

The matrix must be collapsed and stored in a list as follows:

[x0 y0, z0, x1, y1, z1, x2, y2, z2, tx, ty, tz]

Parameters:

aff: 3x4 array of floats (python 2D list, or numpy 2D array)

the transformation matrix

change_parent(self, child, parent)

Change the parent of a node. The child node is adjusted to point to the new parent, the child is taken off of the previous parent’s child list, and it is added to the new parent’s child list.

Parameters:

child: integer or Morphology Object

The ID of the child node, or the child node itself

parent: integer or Morphology Object

The ID of the parent node, or the parent node itself

Returns:

Nothing

children_of(self, seg)

Returns a list of the children of the specified node

Parameters:

seg: integer or Morphology Object

The ID of the parent node, or the parent node itself

Returns:

A list of the child morphology objects. If the ID of the parent

node is invalid, None is returned.

clone(self)

Create a clone (deep copy) of this morphology

compartment(self, n)

Returns the morphology Compartment having the specified ID.

Parameters:

n: integer

ID of desired compartment

Returns:

A morphology object having the specified ID, or None if such a

node doesn’t exist

compartment_list

convert_type(self, from_type, to_type)

Convert all nodes in morphology from one type to another

Parameters:

from_type: enum

The node type that will be eliminated and replaced. Use one of the following constants: SOMA, AXON, BASAL_DENDRITE, or APICAL_DENDRITE

to_type: enum

The new type that will replace it. Use one of the following constants: SOMA, AXON, BASAL_DENDRITE, or APICAL_DENDRITE

delete_tree(self, n)

Delete tree, and all of its nodes, from the morphology.

Parameters:

n: Integer

The tree number to delete

find(self, x, y, z, dist, node_type=None)

Returns a list of Morphology Objects located within ‘dist’ of coordinate (x,y,z). If node_type is specified, the search will be constrained to return only nodes of that type.

Parameters:

x, y, z: float

The x,y,z coordinates from which to search around

dist: float

The search radius

node_type: enum (optional)

One of the following constants: SOMA, AXON, BASAL_DENDRITE or APICAL_DENDRITE

Returns:

A list of all Morphology Objects matching the search criteria

get_dimensions(self)

Returns tuple of overall width, height and depth of morphology. WARNING: if locations of nodes in morphology are manipulated then this value can become incorrect. It can be reset and recalculated by programmitcally setting self.dims to None.

Returns:

3 real arrays: [width, height, depth], [min_x, min_y, min_z],

[max_x, max_y, max_z]

node(self, n)

Returns the morphology node having the specified ID.

Parameters:

n: integer

ID of desired node

Returns:

A morphology node having the specified ID, or None if such a

node doesn’t exist

node_list

Return the node list. This is a property to ensure that the node list and node index are in sync.

node_list_by_type(self, node_type)

Return an list of all nodes having the specified node type.

Parameters:

node_type: int

Desired node type

Returns:

A list of of Morphology Objects

num_nodes

Return the number of nodes in the morphology.

num_trees

Return the number of trees in the morphology. A tree is defined as everything following from a single root node.

parent_of(self, seg)

Returns parent of the specified node.

Parameters:

seg: integer or Morphology Object

The ID of the child node, or the child node itself

Returns:

A morphology object, or None if no parent exists or if the

specified node ID doesn’t exist

save(self, file_name)

Write this morphology out to an SWC file

Parameters:

file_name: string

desired name of your SWC file

soma_root(self)

Returns root node of soma, if present

sparsify(self, modulo)

Return a new Morphology object that has a given number of non-leaf, non-root nodes removed.

Parameters:

modulo: int

keep 1 out of every modulo nodes.

Returns:

Morphology

A new morphology instance

strip_all_other_types(self, node_type, keep_soma=True)

Strips everything from the morphology except for the specified type. Parent and child relationships are updated accordingly, creating new roots when necessary.

Parameters:

node_type: enum

The node type to keep in the morphology. Use one of the following constants: SOMA, AXON, BASAL_DENDRITE, or APICAL_DENDRITE

keep_soma: Boolean (optional)

True (default) if soma nodes should remain in the morpyhology, and False if the soma should also be stripped

strip_type(self, node_type)

Strips all nodes of the specified type from the morphology. Parent and child relationships are updated accordingly, creating new roots when necessary.

Parameters:

node_type: enum

The node type to strip from the morphology. Use one of the following constants: SOMA, AXON, BASAL_DENDRITE, or APICAL_DENDRITE

stumpify_axon(self, count=10)

Remove all axon nodes except the first ‘count’ nodes, as counted from the connected axon root.

Parameters:

count: Integer

The length of the axon ‘stump’, in number of nodes

to_dict(self)

Returns a dictionary of Node objects. These Nodes are a copy of the Morphology. Modifying them will not modify anything in the Morphology itself.

tree(self, n)

Returns a list of all Morphology nodes within the specified tree. A tree is defined as a fully connected graph of nodes. Each tree has exactly one root.

Parameters:

n: integer

ID of desired tree

Returns:

A list of all morphology objects in the specified tree, or None

if the tree doesn’t exist

write(self, file_name)