Source code for allensdk.internal.morphology.morphology

# Copyright 2015-2016 Allen Institute for Brain Science
# This file is part of Allen SDK.
#
# Allen SDK is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, version 3 of the License.
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
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import copy
import math
import numpy as np
from allensdk.internal.morphology.node import Node
from allensdk.internal.morphology.compartment import Compartment


[docs]class Morphology( object ): """ Keep track of the list of nodes in a morphology and provide a few helper methods (soma, tree information, pruning, etc). """ SOMA = 1 AXON = 2 BASAL_DENDRITE = 3 APICAL_DENDRITE = 4 NODE_TYPES = [ SOMA, AXON, BASAL_DENDRITE, APICAL_DENDRITE ] def __init__(self, node_list=None): """ Try to initialize from a list of nodes first, then from a dictionary indexed by node id if that fails, and finally just leave everything empty. Parameters ---------- node_list: list list of Node objects """ self._node_list = [] # list of morphology node IDs self._compartment_list = [] # list of morphology compartment IDs ############################################## # define tree list here for clarity, even though it's reset below # when nodes are assigned self._tree_list = [] ############################################## # dimensions of morphology, including min and max values on xyz # this is cached value # NOTE: if morphology is manually manipulated, this value can # become incorrect self.dims = None ############################################## # construct the node list # first try to do so using the node list, then try using # the node index and if that fails then complain if node_list: self.node_list = node_list ############################################## # verify morphology is consistent with morphology rules (e.g., # no dendrite branching from an axon) num_errors = self._check_consistency() if num_errors > 0: raise ValueError("Morphology appears to be inconsistent") ############################################## # restructure morphology as necessary (eg, renumber nodes) # and construct internal associations self._reconstruct() #################################################################### #################################################################### # class properties, and helper functions for them @property def node_list(self): """ Return the node list. This is a property to ensure that the node list and node index are in sync. """ return self._node_list @node_list.setter def node_list(self, node_list): """ Update the node list. """ self._set_nodes(node_list) @property def compartment_list(self): return self._compartment_list @property def num_trees(self): """ Return the number of trees in the morphology. A tree is defined as everything following from a single root node. """ return len(self._tree_list) @property def num_nodes(self): """ Return the number of nodes in the morphology. """ return len(self.node_list) # internal function def _set_nodes(self, node_list): """ take a list of SWC node objects and turn those into morphology nodes need to be able to initialize from a list supplied by an SWC file while also being able to initialize from the node list of an existing Morphology object. As nodes in a morphology object contain reference to nodes in that object, make a shallow copy of input nodes and overwrite known references (ie, the 'children' array) """ self._node_list = [] for obj in node_list: seg = copy.copy(obj) seg.tree_id = -1 seg.children = [] self._node_list.append(seg) # list data now set. remove holes in sequence and re-index self._reconstruct() # removed old 'soma' and 'root' calls as these were ambiguous # a soma can consist of multiple compartments, and there can # be multiple roots # replaced those calls with new soma_root(), which returns the # same thing as the old soma() when only a single soma node is # present
[docs] def soma_root(self): """ Returns root node of soma, if present""" if len(self._tree_list) > 0 and self._tree_list[0][0].t == 1: return self._tree_list[0][0] return None
#################################################################### #################################################################### # tree and node access
[docs] def 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 """ if n < 0 or n >= len(self._tree_list): return None return self._tree_list[n]
[docs] def 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 """ # undocumented feature -- if a node is supplied instead of a # node ID, the node is returned and no error is # triggered return self._resolve_node_type(n)
[docs] def 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 """ if n < 0 or n >= len(self.compartment_list): return None return self._compartment_list[n]
[docs] def 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 """ # if ID passed in, make sure it's converted to a node # don't trap for exception here -- if supplied segment is # incorrect, make sure the user knows about it seg = self._resolve_node_type(seg) # return parent of specified node if seg is not None and seg.parent >= 0: return self._node_list[seg.parent] return None
[docs] def 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. """ seg = self._resolve_node_type(seg) return [ self._node_list[c] for c in seg.children ]
[docs] def 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. """ return { c.n: c.to_dict() for c in self._node_list }
################################################################### ################################################################### # Information querying and data manipulation # internal function. takes an integer and returns the node having # that ID. IF a node is passed in instead, it is returned def _resolve_node_type(self, seg): # if node passed then we don't need to convert anything # if node not passed, try converting value to int # and using that as an index if not isinstance(seg, Node): try: seg = int(seg) if seg < 0 or seg >= len(self._node_list): return None seg = self._node_list[seg] except ValueError: raise TypeError("Object not recognized as morphology Node or index") return seg
[docs] def 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 """ child_seg = self._resolve_node_type(child) parent_seg = self._resolve_node_type(parent) # if child has former parent, remove it from parent's child list if child_seg.parent >= 0: old_par = self.node(child_seg.parent) old_par.children.remove(child_seg.n) parent_seg.children.append(child_seg.n) child_seg.parent = parent_seg.n
[docs] def 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] """ if self.dims is None: min_x = self.node_list[0].x max_x = self.node_list[0].x min_y = self.node_list[0].y max_y = self.node_list[0].y min_z = self.node_list[0].z max_z = self.node_list[0].z for node in self.node_list: max_x = max(node.x, max_x) max_y = max(node.y, max_y) max_z = max(node.z, max_z) # min_x = min(node.x, min_x) min_y = min(node.y, min_y) min_z = min(node.z, min_z) self.dims = [(max_x-min_x), (max_y-min_y), (max_z-min_z)], [min_x, min_y, min_z], [max_x, max_y, max_z] return self.dims
# returns a list of node located within dist of x,y,z
[docs] def 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 """ found = [] for seg in self.node_list: dx = seg.x - x dy = seg.y - y dz = seg.z - z if math.sqrt(dx*dx + dy*dy + dz*dz) <= dist: if node_type is None or seg.t == node_type: found.append(seg) return found
[docs] def 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 """ return [x for x in self._node_list if x.t == node_type]
[docs] def save(self, file_name): """ Write this morphology out to an SWC file Parameters ---------- file_name: string desired name of your SWC file """ f = open(file_name, "w") f.write("#n,type,x,y,z,radius,parent\n") for seg in self.node_list: f.write("%d %d " % (seg.n, seg.t)) f.write("%0.4f " % seg.x) f.write("%0.4f " % seg.y) f.write("%0.4f " % seg.z) f.write("%0.4f " % seg.radius) f.write("%d\n" % seg.parent) f.close()
# keep for backward compatibility, but don't publish in docs
[docs] def write(self, file_name): self.save(file_name)
[docs] def 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 """ # create and return a new morphology instance. make a copy of # this morphology's node list and manipulate that nodes = copy.deepcopy(self.node_list) # figure out which nodes to toss keep = {} ctr = 0 # mod counter -- keep every modulo element (starting w/ 1st) for seg in nodes: nid = seg.n if (seg.parent < 0 or len(seg.children) != 1 or nodes[seg.parent].t == Morphology.SOMA or seg.t == Morphology.SOMA): keep[nid] = True else: if ctr % modulo == 0: keep[nid] = True else: keep[nid] = False ctr += 1 # hook children up to their new parents for seg in nodes: if keep[seg.n] is False: parent_id = seg.parent while keep[parent_id] is False: parent_id = nodes[parent_id].parent for child_id in seg.children: nodes[child_id].parent = parent_id # filter out orphans sparse = [] for seg in nodes: if keep[seg.n] is True: sparse.append(seg) return Morphology(sparse)
#################################################################### #################################################################### def _reconstruct(self): """ Internal function. Restructures data and establishes appropriate internal linking. Data is re-order, removing 'holes' in the ID sequence so that each object ID corresponds to its position in node list. Dictionaries mapping IDs to objects are no longer necessary. Trees are (re)calculated Parent-child indices are recalculated A new compartment list is created """ remap = {} # everything defaults to root. this way if a parent was deleted # the child will become a new root for i in range(len(self.node_list)): remap[i] = -1 # map old old node numbers to new ones. reset n to the new ID # and put node in new list new_id = 0 tmp_list = [] for node in self.node_list: if node is not None: remap[node.n] = new_id node.n = new_id tmp_list.append(node) new_id += 1 # use map to reset parent values. copy objs to new list for node in tmp_list: if node.parent >= 0: node.parent = remap[node.parent] # replace node list with newly created node list self._node_list = tmp_list # reconstruct parent/child relationship links ############################ # node list is complete and sequential so don't need index # to resolve relationships # for each node, reset children array # for each node, add self to parent's child list for node in self._node_list: node.children = [] node.compartment = -1 for node in self._node_list: if node.parent >= 0: self._node_list[node.parent].children.append(node.n) # update tree lists self._separate_trees() # verify that each node ID is the same as its position in the # node list for i in range(len(self.node_list)): if i != self.node(i).n: raise RuntimeError("Internal error detected -- node list not properly formed") # construct compartment list # (a compartment spans the distance between two nodes) self._compartment_list = [] for node in self.node_list: node.compartment_id = -1 for node in self.node_list: for child_id in node.children: endpoint = self.node(child_id) compartment = Compartment(node, endpoint) endpoint.compartment_id = len(self._compartment_list) self._compartment_list.append(compartment)
[docs] def append(self, nodes): """ Add additional nodes to this Morphology. Those nodes must originate from another morphology object. Parameters ---------- nodes: list of Morphology nodes """ # construct a map between new and old IDs of added nodes remap = {} for i in range(len(nodes)): remap[i] = -1 # map old old node numbers to new ones. reset n to the new ID # append new nodes to existing node list old_count = len(self.node_list) new_id = old_count for node in nodes: if node is not None: remap[node.n] = new_id node.n = new_id self._node_list.append(node) new_id += 1 # use map to reset parent values. copy objs to new list for i in range(old_count, len(self.node_list)): node = self.node_list[i] if node.parent >= 0: node.parent = remap[node.parent] self._reconstruct()
[docs] def 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 """ for node in self.node_list: if node.t == from_type: node.t = to_type
[docs] def 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 """ # find connected axon root axon_root = None for seg in self.node_list: if seg.t == Morphology.AXON: par_id = seg.parent if par_id >= 0: par = self.node_list[par_id] if par.t != Morphology.AXON: axon_root = seg break if axon_root is None: return # flag the first 'count' nodes from the axon root ax = axon_root for node in self.node_list: node.flag = None for i in range(count): # ignore bifurcations -- go 'count' deep on one line only ax.flag = i #ax["flag"] = i children = ax.children if len(children) > 0: ax = self.node(children[0]) # strip out all axons that aren't flagged for i in range(len(self.node_list)): seg = self.node_list[i] if seg.t == Morphology.AXON: #if "flag" not in seg: if seg.flag is None: self.node_list[i] = None self._reconstruct()
def _strip(self, flagged_for_removal): """ Internal function with code common between strip_all_other_types() and strip_type() """ # if parent will be stripped and node will remain, convert # parent to this type so it becomes root (otherwise root # will move) root = self.soma_root() for node_id in self._node_list: node = self.node(node_id) if node.parent >= 0: parent = self.node(node.parent) parent_flag = flagged_for_removal[parent.n] node_flag = flagged_for_removal[node.n] if parent_flag and not node_flag: # don't do this for soma root if parent.n != root.n: parent.t = node.t flagged_for_removal[parent.n] = False # removed flagged items for i in range(len(self.node_list)): seg = self.node_list[i] if flagged_for_removal[seg.n]: # eliminate node self.node_list[i] = None elif seg.parent >= 0 and flagged_for_removal[seg.parent]: # parent was eliminated. make this a new root seg.parent = -1 self._reconstruct() # strip out everything but the soma and the specified SWC type
[docs] def 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 """ flagged_for_removal = {} # scan nodes and see which ones should be removed. keep a record # of them for seg in self.node_list: if seg.t == node_type: remove = False elif seg.t == 1 and keep_soma: remove = False else: remove = True if remove: flagged_for_removal[seg.n] = True else: flagged_for_removal[seg.n] = False self._strip(flagged_for_removal)
# strip out the specified SWC type
[docs] def 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 """ flagged_for_removal = {} for seg in self.node_list: if seg.t == node_type: remove = True else: remove = False if remove: flagged_for_removal[seg.n] = True else: flagged_for_removal[seg.n] = False self._strip(flagged_for_removal)
[docs] def clone(self): """ Create a clone (deep copy) of this morphology """ return copy.deepcopy(self)
[docs] def 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 """ affine = np.copy(aff) # remove scale on each axis scale_x = abs(affine[0] + affine[3] + affine[6]) if scale_x != 0.0: affine[0] /= scale_x affine[3] /= scale_x affine[6] /= scale_x scale_y = abs(affine[1] + affine[4] + affine[7]) if scale_y != 0.0: affine[1] /= scale_y affine[4] /= scale_y affine[7] /= scale_y scale_z = abs(affine[2] + affine[5] + affine[8]) if scale_z != 0.0: affine[2] /= scale_z affine[5] /= scale_z affine[8] /= scale_z # apply rotation for seg in self.node_list: x = seg.x*affine[0] + seg.y*affine[1] + seg.z*affine[2] y = seg.x*affine[3] + seg.y*affine[4] + seg.z*affine[5] z = seg.x*affine[6] + seg.y*affine[7] + seg.z*affine[8] seg.x = x seg.y = y seg.z = z
# # relocate back to zero # soma = self.soma_root() # if soma is not None: # for seg in self.node_list: # seg.x -= soma.x # seg.y -= soma.y # seg.z -= soma.z
[docs] def 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 """ # In addition to transforming the locations of the morphology # nodes, the radius of each node must be adjusted. # There are 2 ways to measure scale from a transform. Assuming # an isotropic transform, the scale is the cube root of the # matrix determinant. The other ways is to measure scale # independently along each axis. # For now, the node radius is only updated based on the average # scale along all 3 axes (eg, isotropic assumption), so calculate # scale using the determinant # if scale is None: # calculate the determinant determinant = np.linalg.det(np.reshape(aff[0:9], (3, 3))) # determinant is change of volume that occurred during transform # assume equal scaling along all axes. take 3rd root to get # scale factor det_scale = np.power(abs(determinant), 1.0 / 3.0) ## measure scale along each axis ## keep this code here in case #scale_x = abs(aff[0] + aff[3] + aff[6]) #scale_y = abs(aff[1] + aff[4] + aff[7]) #scale_z = abs(aff[2] + aff[5] + aff[8]) #avg_scale = (scale_x + scale_y + scale_z) / 3.0; # # use determinant for scaling for now as it's most simple scale = det_scale for seg in self.node_list: x = seg.x*aff[0] + seg.y*aff[1] + seg.z*aff[2] + aff[9] y = seg.x*aff[3] + seg.y*aff[4] + seg.z*aff[5] + aff[10] z = seg.x*aff[6] + seg.y*aff[7] + seg.z*aff[8] + aff[11] seg.x = x seg.y = y seg.z = z seg.radius *= scale
def _separate_trees(self): """ Construct list of independent trees (each tree has a root of -1). The soma root, if it exists, is in tree 0. """ trees = [] # reset each node's tree ID to indicate that it's not assigned for seg in self.node_list: seg.tree_id = -1 # construct trees for each node # if a node is adjacent an existing tree, merge to it # if a node is adjacent multiple trees, merge all for seg in self.node_list: # see what trees this node is adjacent to local_trees = [] if seg.parent >= 0 and self.node_list[seg.parent].tree_id >= 0: local_trees.append(self.node_list[seg.parent].tree_id) for child_id in seg.children: child = self.node_list[child_id] if child.tree_id >= 0: local_trees.append(child.tree_id) # figure out which tree to put node into # if there are muliple possibilities, merge all of them if len(local_trees) == 0: tree_num = len(trees) # create new tree elif len(local_trees) == 1: tree_num = local_trees[0] # use existing tree elif len(local_trees) > 1: # this node is an intersection of multiple trees # merge all trees into the first one found tree_num = local_trees[0] for j in range(1,len(local_trees)): dead_tree = local_trees[j] trees[dead_tree] = [] for node in self.node_list: if node.tree_id == dead_tree: node.tree_id = tree_num # merge node into tree # ensure there's space while len(trees) <= tree_num: trees.append([]) trees[tree_num].append(seg) seg.tree_id = tree_num # consolidate tree lists into class's tree list object self._tree_list = [] for tree in trees: if len(tree) > 0: self._tree_list.append(tree) # make soma's tree be the first tree, if soma present # this should be the case if the file is properly ordered, but # don't assume that soma_tree = -1 for seg in self.node_list: if seg.t == 1: soma_tree = seg.tree_id break if soma_tree > 0: # swap soma tree for first tree in list tmp = self._tree_list[soma_tree] self._tree_list[soma_tree] = self._tree_list[0] self._tree_list[0] = tmp # reset node tree_id to correct tree number self._reset_tree_ids() def _reset_tree_ids(self): """ reset each node's tree_id value to the correct tree number """ for i in range(len(self._tree_list)): for j in range(len(self._tree_list[i])): self._tree_list[i][j].tree_id = i def _check_consistency(self): """ internal function -- don't publish in the docs TODO? print warning if unrecognized types are present Return value: number of errors detected in file """ errs = 0 # Make sure that the parents are of proper ID range n = self.num_nodes for seg in self.node_list: if seg.parent >= 0: if seg.parent >= n: print("Parent for node %d is invalid (%d)" % (seg.n, seg.parent)) errs += 1 # make sure that each tree has exactly one root for i in range(self.num_trees): tree = self.tree(i) root = -1 for j in range(len(tree)): if tree[j].parent == -1: if root >= 0: print("Too many roots in tree %d" % i) errs += 1 root = j if root == -1: print("No root present in tree %d" % i) errs += 1 # make sure each axon has at most one root # find type boundaries. at each axon boundary, walk back up # tree to root and make sure another axon segment not # encountered adoptees = self._find_type_boundary() for child in adoptees: if child.t == Morphology.AXON: par_id = child.parent while par_id >= 0: par = self.node_list[par_id] if par.t == Morphology.AXON: print("Branch has multiple axon roots") print(child) print(par) errs += 1 break par_id = par.parent if errs > 0: print("Failed consistency check: %d errors encountered" % errs) return errs def _find_type_boundary(self): """ return a list of segments who have parents that are a different type """ adoptees = [] for node in self.node_list: par = self.parent_of(node) if par is None: continue if node.t != par.t: adoptees.append(node) return adoptees # remove tree from swc's "forest"
[docs] def delete_tree(self, n): """ Delete tree, and all of its nodes, from the morphology. Parameters ---------- n: Integer The tree number to delete """ if n < 0: return if n >= self.num_trees: print("Error -- attempted to delete non-existing tree (%d)" % n) raise ValueError tree = self.tree(n) for i in range(len(tree)): self.node_list[tree[i].n] = None del self._tree_list[n] self._reconstruct() # reset node tree_id to correct tree number self._reset_tree_ids()
def _print_all_nodes(self): """ debugging function. prints all nodes """ for node in self.node_list: print(node.short_string())