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# purposes without further permission.
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# Copyright 2015-2016. Allen Institute. All rights reserved.
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#
import csv
import copy
import math
import six
# Morphology nodes have the following fields. SWC fields are numeric.
NODE_ID = 'id'
NODE_TYPE = 'type'
NODE_X = 'x'
NODE_Y = 'y'
NODE_Z = 'z'
NODE_R = 'radius'
NODE_PN = 'parent'
SWC_COLUMNS = [NODE_ID, NODE_TYPE, NODE_X, NODE_Y, NODE_Z, NODE_R, NODE_PN]
NODE_TREE_ID = 'tree_id'
NODE_CHILDREN = 'children'
# shorthand for dictionary entries, to shorten sometimes long code lines
_N = NODE_ID
_TYP = NODE_TYPE
_X = NODE_X
_Y = NODE_Y
_Z = NODE_Z
_R = NODE_R
_P = NODE_PN
_C = NODE_CHILDREN
_TID = NODE_TREE_ID
########################################################################
[docs]def 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.
"""
compartments = []
line_num = 1
try:
with open(file_name, "r") as f:
for line in f:
# remove comments
if line.lstrip().startswith('#'):
continue
# read values. expected SWC format is:
# ID, type, x, y, z, rad, parent
# x, y, z and rad are floats. the others are ints
toks = line.split(' ')
vals = Compartment({
NODE_ID: int(toks[0]),
NODE_TYPE: int(toks[1]),
NODE_X: float(toks[2]),
NODE_Y: float(toks[3]),
NODE_Z: float(toks[4]),
NODE_R: float(toks[5]),
NODE_PN: int(toks[6].rstrip())
})
# store this compartment
compartments.append(vals)
# increment line number (used for error reporting only)
line_num += 1
except ValueError:
err = "File not recognized as valid SWC file.\n"
err += "Problem parsing line %d\n" % line_num
if line is not None:
err += "Content: '%s'\n" % line
raise IOError(err)
return Morphology(compartment_list=compartments)
########################################################################
########################################################################
[docs]class Compartment(dict):
"""
A dictionary class storing information about a single morphology node
"""
def __init__(self, *args, **kwargs):
super(Compartment, self).__init__(*args, **kwargs)
if (NODE_ID not in self or
NODE_TYPE not in self or
NODE_X not in self or
NODE_Y not in self or
NODE_Z not in self or
NODE_R not in self or
NODE_PN not in self):
raise ValueError(
"Compartment was not initialized with requisite fields")
# Each unconnected graph has its own ID. This is the ID
# of graph that the node resides in
self[NODE_TREE_ID] = -1
# IDs of child nodes
self[NODE_CHILDREN] = []
[docs] def print_node(self):
""" print out compartment information with field names """
print("%d %d %.4f %.4f %.4f %.4f %d %s %d" % (self[_N], self[_TYP], self[
_X], self[_Y], self[_Z], self[_R], self[_P], str(self[_C]), self[_TID]))
[docs]class Morphology(object):
"""
Keep track of the list of compartments in a morphology and provide
a few helper methods (soma, tree information, pruning, etc).
"""
SOMA = 1
AXON = 2
DENDRITE = 3
BASAL_DENDRITE = 3
APICAL_DENDRITE = 4
NODE_TYPES = [SOMA, AXON, DENDRITE, BASAL_DENDRITE, APICAL_DENDRITE]
def __init__(self, compartment_list=None, compartment_index=None):
"""
Try to initialize from a list of compartments first, then from
a dictionary indexed by compartment id if that fails, and finally just
leave everything empty.
Parameters
----------
compartment_list: list
list of compartment dictionaries
compartment_index: dict
dictionary of compartments indexed by id
"""
self._compartment_list = []
self._compartment_index = {}
##############################################
# define tree list here for clarity, even though it's reset below
# when nodes are assigned
self._tree_list = []
##############################################
# construct the compartment list and index
# first try to do so using the compartment list, then try using
# the compartment index and if that fails then complain
if compartment_list:
self.compartment_list = compartment_list
elif compartment_index:
self.compartment_index = compartment_index
##############################################
# 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")
##############################################
# root node (this must be part of the soma)
self._soma = None
for i in range(len(self.compartment_list)):
seg = self.compartment_list[i]
if seg[NODE_TYPE] == Morphology.SOMA and seg[NODE_PN] < 0:
if self._soma is not None:
raise ValueError("Multiple somas detected in SWC file")
self._soma = seg
####################################################################
####################################################################
# class properties, and helper functions for them
@property
def compartment_list(self):
""" Return the compartment list. This is a property to ensure that the
compartment list and compartment index are in sync. """
return self._compartment_list
@compartment_list.setter
def compartment_list(self, compartment_list):
""" Update the compartment list. Update the compartment index. """
self._set_compartments(compartment_list)
@property
def compartment_index(self):
""" Return the compartment index. This is a property to ensure that the
compartment list and compartment index are in sync. """
return self._compartment_index
@compartment_index.setter
def compartment_index(self, compartment_index):
""" Update the compartment index. Update the compartment list. """
self._set_compartments(compartment_index.values())
@property
def num_trees(self):
""" Return the number of trees in the morphology. A tree is
defined as everything following from a single root compartment. """
return len(self._tree_list)
# TODO add filter for number of nodes of a particular type
@property
def num_nodes(self):
""" Return the number of compartments in the morphology. """
return len(self.compartment_list)
# internal function
def _set_compartments(self, compartment_list):
"""
take a list of SWC-like 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 compartment 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._compartment_list = []
for obj in compartment_list:
seg = copy.copy(obj)
seg[NODE_TREE_ID] = -1
seg[NODE_CHILDREN] = []
self._compartment_list.append(seg)
# list data now set. remove holes in sequence and re-index
self._reconstruct()
@property
def soma(self):
""" Returns root node of soma, if present"""
return self._soma
@property
def root(self):
""" [deprecated] Returns root node of soma, if present. Use 'soma' instead of 'root'"""
return self._soma
####################################################################
####################################################################
# 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 object 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 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 compartment
# 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[NODE_PN] >= 0:
return self._compartment_list[seg[NODE_PN]]
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._compartment_list[c] for c in seg[NODE_CHILDREN]]
###################################################################
###################################################################
# 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 compartment passed then we don't need to convert anything
# if compartment not passed, try converting value to int
# and using that as an index
if not isinstance(seg, Compartment):
try:
seg = int(seg)
if seg < 0 or seg >= len(self._compartment_list):
return None
seg = self._compartment_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[NODE_PN] >= 0:
old_par = self.node(child_seg[NODE_PN])
old_par[NODE_CHILDREN].remove(child_seg[NODE_ID])
parent_seg[NODE_CHILDREN].append(child_seg[NODE_ID])
child_seg[NODE_PN] = parent_seg[NODE_ID]
# returns a list of nodes 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, DENDRITE,
BASAL_DENDRITE or APICAL_DENDRITE
Returns
-------
A list of all Morphology Objects matching the search criteria
"""
found = []
for seg in self.compartment_list:
dx = seg[NODE_X] - x
dy = seg[NODE_Y] - y
dz = seg[NODE_Z] - z
if math.sqrt(dx * dx + dy * dy + dz * dz) <= dist:
if node_type is None or seg[NODE_TYPE] == node_type:
found.append(seg)
return found
[docs] def compartment_list_by_type(self, 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
"""
return [x for x in self._compartment_list if x[NODE_TYPE] == compartment_type]
[docs] def compartment_index_by_type(self, 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
"""
return {c[NODE_ID]: c for c in self._compartment_list if c[NODE_TYPE] == compartment_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.compartment_list:
f.write("%d %d " % (seg[NODE_ID], seg[NODE_TYPE]))
f.write("%0.4f " % seg[NODE_X])
f.write("%0.4f " % seg[NODE_Y])
f.write("%0.4f " % seg[NODE_Z])
f.write("%0.4f " % seg[NODE_R])
f.write("%d\n" % seg[NODE_PN])
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, 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
"""
compartments = self.compartment_index
root = self.root
keep = {}
# figure out which compartments to toss
ct = 0
for i, c in six.iteritems(compartments):
pid = c[NODE_PN]
cid = c[NODE_ID]
ctype = c[NODE_TYPE]
# keep the root, soma, junctions, and the first child of the root
# (for visualization)
if pid < 0 or len(c[NODE_CHILDREN]) != 1 or pid == root[NODE_ID] or ctype == Morphology.SOMA:
keep[cid] = True
else:
keep[cid] = (ct % modulo) == 0
ct += 1
# hook children up to their new parents
for i, c in six.iteritems(compartments):
comp_id = c[NODE_ID]
if keep[comp_id] is False:
parent_id = c[NODE_PN]
while keep[parent_id] is False:
parent_id = compartments[parent_id][NODE_PN]
for child_id in c[NODE_CHILDREN]:
compartments[child_id][NODE_PN] = parent_id
# filter out the orphans
sparsified_compartments = {k: v for k,
v in six.iteritems(compartments) if keep[k]}
if compress_ids:
ids = sorted(sparsified_compartments.keys(), key=lambda x: int(x))
id_hash = {fid: str(i + 1) for i, fid in enumerate(ids)}
id_hash[-1] = -1
# build the final compartment index
out_compartments = {}
for cid, compartment in six.iteritems(sparsified_compartments):
compartment[NODE_ID] = id_hash[cid]
compartment[NODE_PN] = id_hash[compartment[NODE_PN]]
out_compartments[compartment[NODE_ID]] = compartment
return Morphology(compartment_index=out_compartments)
else:
return Morphology(compartment_index=sparsified_compartments)
####################################################################
####################################################################
def _reconstruct(self):
"""
internal function that restructures data and establishes
appropriate internal linking. data is re-order, removing 'holes'
in sequence so that each object ID corresponds to its position
in compartment list. trees are (re)calculated
parent-child indices are recalculated as is compartment table
construct a map between new and old IDs
"""
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.compartment_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 seg in self.compartment_list:
if seg is not None:
remap[seg[NODE_ID]] = new_id
seg[NODE_ID] = new_id
tmp_list.append(seg)
new_id += 1
# use map to reset parent values. copy objs to new list
for seg in tmp_list:
if seg[NODE_PN] >= 0:
seg[NODE_PN] = remap[seg[NODE_PN]]
# replace compartment list with newly created node list
self._compartment_list = tmp_list
# reconstruct parent/child relationship links
# forget old relations
for seg in self.compartment_list:
seg[NODE_CHILDREN] = []
# add each object to its parents child list
for seg in self.compartment_list:
par_num = seg[NODE_PN]
if par_num >= 0:
self.compartment_list[par_num][
NODE_CHILDREN].append(seg[NODE_ID])
# update tree lists
self._separate_trees()
############################
# Rebuild internal index and links between parents and children
self._compartment_index = {
c[NODE_ID]: c for c in self.compartment_list}
# compartment 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 seg in self._compartment_list:
seg[NODE_CHILDREN] = []
for seg in self._compartment_list:
if seg[NODE_PN] >= 0:
self._compartment_list[seg[NODE_PN]][
NODE_CHILDREN].append(seg[NODE_ID])
# verify that each node ID is the same as its position in the
# compartment list
for i in range(len(self.compartment_list)):
if i != self.node(i)[NODE_ID]:
raise RuntimeError(
"Internal error detected -- compartment list not properly formed")
[docs] def append(self, node_list):
""" Add additional nodes to this Morphology. Those nodes must
originate from another morphology object.
Parameters
----------
node_list: list of Morphology nodes
"""
# construct a map between new and old IDs of added nodes
remap = {}
for i in range(len(node_list)):
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.compartment_list)
new_id = old_count
for seg in node_list:
if seg is not None:
remap[seg[NODE_ID]] = new_id
seg[NODE_ID] = new_id
self._compartment_list.append(seg)
new_id += 1
# use map to reset parent values. copy objs to new list
for i in range(old_count, len(self.compartment_list)):
seg = self.compartment_list[i]
if seg[NODE_PN] >= 0:
seg[NODE_PN] = remap[seg[NODE_PN]]
self._reconstruct()
[docs] def stumpify_axon(self, 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
"""
# find connected axon root
axon_root = None
for seg in self.compartment_list:
if seg[NODE_TYPE] == Morphology.AXON:
par_id = seg[NODE_PN]
if par_id >= 0:
par = self.compartment_list[par_id]
if par[NODE_TYPE] != 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 i in range(count):
# ignore bifurcations -- go 'count' deep on one line only
ax["flag"] = i
children = ax[NODE_CHILDREN]
if len(children) > 0:
ax = children[0]
# strip out all axons that aren't flagged
for i in range(len(self.compartment_list)):
seg = self.compartment_list[i]
if seg[NODE_TYPE] == Morphology.AXON:
if "flag" not in seg:
self.compartment_list[i] = None
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 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
"""
flagged_for_removal = {}
# scan nodes and see which ones should be removed. keep a record
# of them
for seg in self.compartment_list:
if seg[NODE_TYPE] == node_type:
remove = False
elif seg[NODE_TYPE] == 1 and keep_soma:
remove = False
else:
remove = True
if remove:
flagged_for_removal[seg[NODE_ID]] = True
# remove selected nodes andreset parent links
for i in range(len(self.compartment_list)):
seg = self.compartment_list[i]
if seg[NODE_ID] in flagged_for_removal:
# eliminate node
self.compartment_list[i] = None
elif seg[NODE_PN] in flagged_for_removal:
# parent was eliminated. make this a new root
seg[NODE_PN] = -1
self._reconstruct()
# strip out the specified SWC type
[docs] def strip_type(self, 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
"""
flagged_for_removal = {}
for seg in self.compartment_list:
if seg[NODE_TYPE] == node_type:
remove = True
else:
remove = False
if remove:
flagged_for_removal[seg[NODE_ID]] = True
for i in range(len(self.compartment_list)):
seg = self.compartment_list[i]
if seg[NODE_ID] in flagged_for_removal:
# eliminate node
self.compartment_list[i] = None
elif seg[NODE_PN] in flagged_for_removal:
# parent was eliminated. make this a new root
seg[NODE_PN] = -1
self._reconstruct()
# strip out the specified SWC type
[docs] def convert_type(self, 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
"""
for seg in self.compartment_list:
if seg[NODE_TYPE] == old_type:
seg[NODE_TYPE] = new_type
[docs] def apply_affine(self, 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
"""
# 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
det0 = aff[0] * (aff[4] * aff[8] - aff[5] * aff[7])
det1 = aff[1] * (aff[3] * aff[8] - aff[5] * aff[6])
det2 = aff[2] * (aff[3] * aff[7] - aff[4] * aff[6])
det = det0 + det1 + det2
# determinant is change of volume that occurred during transform
# assume equal scaling along all axes. take 3rd root to get
# scale factor
det_scale = math.pow(abs(det), 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.compartment_list:
x = seg[NODE_X] * aff[0] + seg[NODE_Y] * \
aff[1] + seg[NODE_Z] * aff[2] + aff[9]
y = seg[NODE_X] * aff[3] + seg[NODE_Y] * \
aff[4] + seg[NODE_Z] * aff[5] + aff[10]
z = seg[NODE_X] * aff[6] + seg[NODE_Y] * \
aff[7] + seg[NODE_Z] * aff[8] + aff[11]
seg[NODE_X] = x
seg[NODE_Y] = y
seg[NODE_Z] = z
seg[NODE_R] *= scale
def _separate_trees(self):
"""
construct list of independent trees (each tree has a root of -1)
"""
trees = []
# reset each node's tree ID to indicate that it's not assigned
for seg in self.compartment_list:
seg[NODE_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.compartment_list:
# see what trees this node is adjacent to
local_trees = []
if seg[NODE_PN] >= 0 and self.compartment_list[seg[NODE_PN]][NODE_TREE_ID] >= 0:
local_trees.append(self.compartment_list[
seg[NODE_PN]][NODE_TREE_ID])
for child_id in seg[NODE_CHILDREN]:
child = self.compartment_list[child_id]
if child[NODE_TREE_ID] >= 0:
local_trees.append(child[NODE_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.compartment_list:
if node[NODE_TREE_ID] == dead_tree:
node[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[NODE_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.compartment_list:
if seg[NODE_TYPE] == 1:
soma_tree = seg[NODE_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][NODE_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.compartment_list:
if seg[NODE_PN] >= 0:
if seg[NODE_PN] >= n:
print("Parent for node %d is invalid (%d)" %
(seg[NODE_ID], seg[NODE_PN]))
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][NODE_PN] == -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[NODE_TYPE] == Morphology.AXON:
par_id = child[NODE_PN]
while par_id >= 0:
par = self.compartment_list[par_id]
if par[NODE_TYPE] == Morphology.AXON:
print("Branch has multiple axon roots")
print(child)
print(par)
errs += 1
break
par_id = par[NODE_PN]
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.compartment_list:
par = self.parent_of(node)
if par is None:
continue
if node[NODE_TYPE] != par[NODE_TYPE]:
adoptees.append(node)
return adoptees
# remove tree from swc's "forest"
[docs] def delete_tree(self, n):
""" Delete tree, and all of its compartments, 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.compartment_list[tree[i][NODE_ID]] = 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.compartment_list:
print(node)
########################################################################
[docs]class Marker(dict):
""" Simple dictionary class for handling reconstruction marker objects. """
SPACING = [.1144, .1144, .28]
CUT_DENDRITE = 10
NO_RECONSTRUCTION = 20
def __init__(self, *args, **kwargs):
super(Marker, self).__init__(*args, **kwargs)
# marker file x,y,z coordinates are offset by a single image-space
# pixel
self['x'] -= self.SPACING[0]
self['y'] -= self.SPACING[1]
self['z'] -= self.SPACING[2]
[docs]def read_marker_file(file_name):
""" read in a marker file and return a list of dictionaries """
with open(file_name, 'r') as f:
rows = csv.DictReader((r for r in f if not r.startswith('#')),
fieldnames=['x', 'y', 'z', 'radius', 'shape', 'name', 'comment',
'color_r', 'color_g', 'color_b'])
return [Marker({'x': float(r['x']),
'y': float(r['y']),
'z': float(r['z']),
'name': int(r['name'])}) for r in rows]