allensdk.core.swc module

class allensdk.core.swc.Compartment(*args, **kwargs)

Bases: dict

A dictionary class storing information about a single morphology node

print_node()

print out compartment information with field names

class allensdk.core.swc.Marker(*args, **kwargs)

Bases: dict

Simple dictionary class for handling reconstruction marker objects.

CUT_DENDRITE = 10

NO_RECONSTRUCTION = 20

SPACING = [0.1144, 0.1144, 0.28]

class allensdk.core.swc.Morphology(compartment_list=None, compartment_index=None)

Bases: object

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

APICAL_DENDRITE = 4

AXON = 2

BASAL_DENDRITE = 3

DENDRITE = 3

NODE_TYPES = [1, 2, 3, 3, 4]

SOMA = 1

append(node_list)

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

Parameters:

node_list: list of Morphology nodes

apply_affine(aff, scale=None)

Apply an affine transform to all compartments in this morphology. Node 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

change_parent(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(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.

compartment_index

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

compartment_index_by_type(compartment_type)

Return an dictionary of compartments indexed by id that all have a particular compartment type.

Parameters:

compartment_type: int

Desired compartment type

Returns:

A dictionary of Morphology Objects, indexed by ID

compartment_list

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

compartment_list_by_type(compartment_type)

Return an list of all compartments having the specified compartment type.

Parameters:

compartment_type: int

Desired compartment type

Returns:

A list of of Morphology Objects

convert_type(old_type, new_type)

Converts all compartments from one type to another. Nodes of the original type are not affected so this procedure can also be used as a merge procedure.

Parameters:

old_type: enum

The compartment type to be changed. Use one of the following constants: SOMA, AXON, DENDRITE, BASAL_DENDRITE, or APICAL_DENDRITE

new_type: enum

The target compartment type. Use one of the following constants: SOMA, AXON, DENDRITE, BASAL_DENDRITE, or APICAL_DENDRITE

delete_tree(n)

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

Parameters:

n: Integer

The tree number to delete

find(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, DENDRITE, BASAL_DENDRITE or APICAL_DENDRITE

Returns:

A list of all Morphology Objects matching the search criteria

node(n)

Returns the morphology node having the specified ID.

Parameters:

n: integer

ID of desired node

Returns:

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

node doesn’t exist

num_nodes

Return the number of compartments in the morphology.

num_trees

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

parent_of(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

root

[deprecated] Returns root node of soma, if present. Use ‘soma’ instead of ‘root’

save(file_name)

Write this morphology out to an SWC file

Parameters:

file_name: string

desired name of your SWC file

soma

Returns root node of soma, if present

sparsify(modulo, compress_ids=False)

Return a new Morphology object that has a given number of non-leaf, non-root nodes removed. IDs can be reassigned so as to be continuous.

Parameters:

modulo: int

keep 1 out of every modulo nodes.

compress_ids: boolean

Reassign ids so that ids are continuous (no missing id numbers).

Returns:

Morphology

A new morphology instance

strip_all_other_types(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 compartment type to keep in the morphology. Use one of the following constants: SOMA, AXON, DENDRITE, 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(node_type)

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

Parameters:

node_type: enum

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

stumpify_axon(count=10)

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

Parameters:

count: Integer

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

tree(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(file_name)

allensdk.core.swc.read_marker_file(file_name)

read in a marker file and return a list of dictionaries

allensdk.core.swc.read_swc(file_name, columns='NOT_USED', numeric_columns='NOT_USED')

Read in an SWC file and return a Morphology object.

Parameters:

file_name: string

SWC file name.

Returns:

Morphology

A Morphology instance.