Source code for allensdk.core.swc

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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)
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[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]