Source code for brainlit.algorithms.trace_analysis.fit_spline

from typing import Tuple
import numpy as np
from scipy.interpolate import splprep, splev, BSpline, CubicHermiteSpline, PPoly
from scipy.interpolate._cubic import prepare_input
import pandas as pd
import math
import warnings
import networkx as nx
import itertools
from brainlit.utils.util import (
from typing import Union, List

[docs]def compute_parameterization(positions: np.array) -> np.array: """Computes list of parameter values to be used for a list of positions using piecewise linear arclength. Parameters ---------- positions : np.array nxd array containing coordinates of the n points in d dimentional space. Returns ------- TotalDist : np.array n array containing parameter values, first element is 0. """ NodeDist = np.linalg.norm(np.diff(positions, axis=0), axis=1) TotalDist = np.concatenate(([0], np.cumsum(NodeDist))) return TotalDist
[docs]class CubicHermiteChain(PPoly): """A third order spline class (continuous piecewise cubic representation), that is fit to a set of positions and one-sided derivatives. This is not a standard spline class (e.g. b-splines), because the derivatives are not necessarily continuous at the knots. A subclass of PPoly, a piecewise polynomial class from scipy. Arguments: x (np.array): Independent variable, shape n. y (np.array): Independent variable, shape n x d. left_dydx (np.array): Derivatives on left sides of cubic segments (i.e. right hand derivatives of knots), shape n-1 x d. right_dy_dx (np.array): Derivatives on right sides of cubic segments (i.e. left hand derivatives of knots), shape n-1 x d. extrapolate (np.array, optional): If bool, determines whether to extrapolate to out-of-bounds points based on first and last intervals, or to return NaNs. If ‘periodic’, periodic extrapolation is used. Attributes: axis: Raises: ValueError: Left derivatives (left_dydx) and right derivatives (right_dydx) must have same shape. """ def __init__( self, x: np.array, y: np.array, left_dydx: np.array, right_dydx: np.array, extrapolate=None, ): if extrapolate is None: extrapolate = True x, dx, y, axis, _ = prepare_input(x, y, axis=0) if not np.array_equal(left_dydx.shape, right_dydx.shape): raise ValueError( f"Left derivatives shape {left_dydx.shape} must be equal to right derivatives shape {right_dydx.shape}" ) dxr = dx.reshape([dx.shape[0]] + [1] * (y.ndim - 1)) slope = np.diff(y, axis=0) / dxr t = (left_dydx + right_dydx - 2 * slope) / dxr c = np.empty((4, len(x) - 1) + y.shape[1:], dtype=t.dtype) c[0] = t / dxr c[1] = (slope - left_dydx) / dxr - t c[2] = left_dydx c[3] = y[:-1] super().__init__(c, x, extrapolate=extrapolate) self.axis = axis
""" Geometric Graph class """
[docs]class GeometricGraph(nx.Graph): """The shape of the neurons are expressed and fitted with splines in this undirected graph class. The geometry of the neurons are projected on undirected graphs, based on which the trees of neurons consisted for splines is constructed. It is required that each node has a loc attribute identifying that points location in space, and the location should be defined in 3-dimensional cartesian coordinates. It extends `nx.Graph` and rejects duplicate node input. Arguments: df (pd.DataFrame, optional): Indices, coordinates, and parents of each node in the swc. Defaults to None. root (int, optional): Sample index (in the dataframe) that is the root node. Defaults to 1. remove_duplicates (bool, optional): Whether to automatically remove consecutive nodes with the same location. Defaults to False. Defaults to False. Attributes: root: Sample index corresponding to the root node. spline_type: Whether splines are b-splines or cubic hermite splines. spline_tree: Tree of splines that model the trace branches. removed_duplicates: Whether connected nodes with the same loc attribute were merged. Raises: ValueError: If two nodes in a row in the SWC file have the same location and the user has not opted to remove duplicates. """ def __init__( self, df: pd.DataFrame = None, root=1, remove_duplicates=False ) -> None: super(GeometricGraph, self).__init__() self.root = root self.spline_type = None self.spline_tree = None self.removed_duplicates = False if df is not None: self.__init_from_df(df, remove_duplicates=remove_duplicates) def __init_from_df( self, df_neuron: pd.DataFrame, remove_duplicates=False ) -> "GeometricGraph": """Converts dataframe of swc in voxel coordinates into a GeometricGraph Args: df_neuron (pd.DataFrame): Indices, coordinates, and parents of each node in the swc. remove_duplicates (bool, optional): Whether to automatically remove consecutive nodes with the same location. Defaults to False. Raises: ValueError: If two nodes in a row in the SWC file have the same location and the user has not opted to remove duplicates. Returns: GeometricGraph: Neuron from swc represented as GeometricGraph. Coordinates `x,y,z` are accessible in the `loc` attribute. """ nodes = [] edges = [] min_parent = min(df_neuron["parent"]) # build graph for _, row in df_neuron.iterrows(): id = int(row["sample"]) nodes.append((id, {"loc": np.array([row["x"], row["y"], row["z"]])})) parent = int(row["parent"]) if parent > min_parent: edges.append((parent, id)) self.add_nodes_from(nodes) self.add_edges_from(edges) if remove_duplicates: self._remove_duplicate_nodes() else: dx = np.expand_dims(np.diff(df_neuron["x"].to_numpy()), axis=0).T dy = np.expand_dims(np.diff(df_neuron["y"].to_numpy()), axis=0).T dz = np.expand_dims(np.diff(df_neuron["z"].to_numpy()), axis=0).T dr = np.concatenate((dx, dy, dz), axis=1) if not all([any(du != 0) for du in dr]) and not remove_duplicates: raise ValueError("cannot build GeometricGraph with duplicate nodes") def _remove_duplicate_nodes(self): """Collapse consecutive nodes at the same location into a single node""" replacements = {} for node in self.nodes: nbrs = self.neighbors(node) for nbr in nbrs: if np.all(self.nodes[node]["loc"] == self.nodes[nbr]["loc"]): sorted = np.sort([node, nbr]) replacements[sorted[1]] = sorted[0] changes = True while changes: changes = False for key in replacements.keys(): replacement = replacements[key] if replacement in replacements: replacements[key] = replacements[replacement] changes = True for key in replacements.keys(): replacement = replacements[key] nbrs = self.neighbors(key) for nbr in nbrs: if nbr != replacement: self.add_edge(replacement, nbr) self.remove_node(key) self.removed_duplicates = True
[docs] def fit_spline_tree_invariant( self, spline_type: Union[BSpline, CubicHermiteSpline] = BSpline, k=3 ): """Construct a spline tree based on the path lengths. Args: spline_type (Union[BSpline, CubicHermiteSpline], optional): spline type that will be fit to the data. BSplines are typically used to fit position data only, and CubicHermiteSplines can only be used if derivative, and independent variable information is also known. Defaults to BSpline. k (int, optional): Order of spline for bsplines. Defaults to 3. Raises: KeyError: Make sure all nodes have loc attribute. ValueError: loc attributes must be flat arrays ValueError: loc attributes must not be empty ValueError: loc attributes must contain 3 coordinates ValueError: loc attributes must be unique for different nodes. ValueError: graph must be connected. ValueError: graph cannot contain cycles. ValueError: graph must be connected. Returns: nx.DiGraph: graph of splines that model the branches. """ # check integrity of 'loc' attributes in the neuron if any([self.nodes[node].get("loc") is None for node in self.nodes]): raise KeyError("some nodes are missing the 'loc' attribute") for node in self.nodes: check_type(self.nodes[node].get("loc"), np.ndarray) if any([self.nodes[node].get("loc").ndim != 1 for node in self.nodes]): raise ValueError("nodes must be flat arrays") if any([len(self.nodes[node].get("loc")) == 0 for node in self.nodes]): raise ValueError("nodes cannot have empty 'loc' attributes") for node in self.nodes: check_iterable_type(self.nodes[node].get("loc"), (np.integer, float)) if any([len(self.nodes[node].get("loc")) != 3 for node in self.nodes]): raise ValueError("'loc' attributes must contain 3 coordinates") # check there are no duplicate nodes LOCs = [np.ndarray.tolist(self.nodes[node]["loc"]) for node in self.nodes] LOCs.sort() unique_LOCs = list(LOC for LOC, _ in itertools.groupby(LOCs)) if len(LOCs) != len(unique_LOCs): if self.removed_duplicates: warnings.warn( "There are still duplicate locations after removing connected duplicates." ) else: raise ValueError( "there are duplicate nodes and this object was initialized with remove_duplicates=False" ) # check the graph is edge-covering if not nx.algorithms.is_edge_cover(self, self.edges): raise ValueError("the edges are not a valid cover of the graph") # check there are no undirected cycles in the graph if not nx.algorithms.tree.recognition.is_forest(self): raise ValueError("the graph contains undirected cycles") # check there are no disconnected segments if not nx.algorithms.tree.recognition.is_tree(self): raise ValueError("the graph contains disconnected segments") # Identify paths spline_tree = nx.DiGraph() curr_spline_num = 0 stack = [] root = self.root tree = nx.algorithms.traversal.depth_first_search.dfs_tree(self, source=root) main_branch, collateral_branches = self.__find_main_branch(tree) spline_tree.add_node(curr_spline_num, path=main_branch, starting_length=0) for tree in collateral_branches: stack.append((tree, curr_spline_num)) while len(stack) > 0: curr_spline_num = curr_spline_num + 1 treenum = stack.pop() tree = treenum[0] parent_num = treenum[1] main_branch, collateral_branches = self.__find_main_branch( tree[0], starting_length=tree[2] ) main_branch.insert(0, tree[1]) spline_tree.add_node( curr_spline_num, path=main_branch, starting_length=tree[2] ) spline_tree.add_edge(parent_num, curr_spline_num) for tree in collateral_branches: stack.append((tree, curr_spline_num)) # Fit splines self.spline_type = spline_type for node in spline_tree.nodes: main_branch = spline_tree.nodes[node]["path"] if spline_type == BSpline: # each node must have "loc" attribute spline_tree.nodes[node]["spline"] = self.__fit_bspline_path( main_branch, k=k ) elif ( spline_type == CubicHermiteSpline ): # each node must have "u," "loc," and "deriv" attributes spline_tree.nodes[node]["spline"] = self.__fit_chspline_path( main_branch ) self.spline_tree = spline_tree return spline_tree
def __fit_bspline_path(self, path, k): r"""Fit a B-Spline to a path. Compute the knots, coefficients, and the degree of the B-Spline fitting the path Arguments: path: list, a list of nodes. Raises: ValueError: Nodes should be defined under loc attribute TypeError: loc should be of numpy.ndarray class ValueError: loc should be 3-dimensional Returns: tck: tuple, contains the vector of knots, the coefficients, and the degree of the B-Spline. u: list, contains the values of the parameters where the B-Spline is evaluated. """ x = np.zeros((len(path), 3)) for row, node in enumerate(path): x[row, :] = self.nodes[node]["loc"] path_length = x.shape[0] TotalDist = compute_parameterization(x) # old # if path_length != 5: # k = np.amin([path_length - 1, 5]) # else: # k = 3 k = np.amin([k, path_length - 1]) # change tck, u = splprep([x[:, 0], x[:, 1], x[:, 2]], s=0, u=TotalDist, k=k) return tck, u def __fit_chspline_path(self, path: List): """Fit cubic hermite spline to path of nodes that has independent variable (u), position (loc) and derivative (deriv) attributes. Args: path (List): sequence of nodes to which the spline will be fit. Returns: CubicHermiteSpline: spline that fits the nodes in path. """ x = np.zeros((len(path))) y = np.zeros((len(path), 3)) dy = np.zeros((len(path), 3)) for row, node in enumerate(path): x[row] = self.nodes[node]["u"] y[row, :] = self.nodes[node]["loc"] dy[row, :] = self.nodes[node]["deriv"] chspline = CubicHermiteSpline(x, y, dy) return chspline def __find_main_branch(self, tree: nx.DiGraph, starting_length: float = 0): r"""Find the main branch in a directed graph. It is used in `fit_spline_tree_invariant` to identify the main branch in a neuron and group the collateral branches for later analysis. The main branch is defined as the longest possible path connecting the neuron's nodes, in terms of spatial distance. An example is provided in the following figure: .. figure:: :scale: 25% :alt: find_main_branch example Graphic example of `find_main_branch()` functionality. Arguments: tree: nx.DiGraph, a directed graph. It is the result of nx.algorithms.traversal.depth_first_search.dfs_tree() which returns an oriented tree constructed from a depth-first search of the neuron. starting_length: float, optional. It is the spatial distance between the root of the neuron (i.e `self.root`) and the root of the current main branch. It must be real-valued, non-negative. It is defaulted to `0` for the first main branch, that starts from the root of the neuron. Returns: main_branch: list, a list of nodes. collateral_branches: list, directed graphs of children trees. """ # Initialize the list of collateral branches collateral_branches = [] # If there is only one node in the tree, that is the main branch if len(tree.nodes) == 1: main_branch = tree.nodes else: # Find the root of the tree. # A node is a candidate to be the root if it does not # have any edges pointing to it (i.e. in_degree == 0) roots = [node for node, degree in tree.in_degree() if degree == 0] root = roots[0] # Find the leaves of the tree. # A node is a leaf if it has only one edge pointing # to it (i.e. in_degree == 1), and no edges pointing # out of it (i.e. out_degree == 0) leaves = [ node for node in tree.nodes() if tree.out_degree(node) == 0 and tree.in_degree(node) == 1 ] # For each leaf, compute the shortest path to reach it shortest_paths = [ nx.algorithms.shortest_paths.generic.shortest_path( tree, source=root, target=l ) for l in leaves ] # Compute the lengths of the paths lengths = [self.__path_length(path) for path in shortest_paths] # Find the longest path longest_path_idx = np.argmax(lengths) furthest_leaf = leaves[longest_path_idx] # Find the main branch main_branch = nx.algorithms.shortest_paths.generic.shortest_path( tree, source=root, target=furthest_leaf ) # Here, we walk on the main branch to find # the collateral branches for i, node in enumerate(main_branch): # Increase starting_length by the size of # the step on the main branch if i > 0: loc1 = self.nodes[node]["loc"] loc2 = self.nodes[main_branch[i - 1]]["loc"] starting_length += np.linalg.norm(loc2 - loc1) # Find all successors of the current node on # the main branch. A node m is a successor of the node # n if there is a directed edge that goes from n to m children = tree.successors(node) for child in children: # If the successor is not on the main branch, then # we found a branching point of the neuron if child != main_branch[i + 1]: # Explore the newly-found branch and # append it to the list of collateral branches collateral_branches.append( ( nx.algorithms.traversal.depth_first_search.dfs_tree( tree, source=child ), node, starting_length, ) ) return list(main_branch), collateral_branches def __path_length(self, path: list) -> float: r"""Compute the length of a path. Given a path ::math::`p = (r_1, \dots, r_N)`, where ::math::`r_k = [x_k, y_k, z_k], k = 1, \dots, N`, the length `l` of a path is computed as the sum of the lengths of the edges of the path. We can write: .. math:: l = \sum_{k=2}^N \lVert r_k - r_{k-1} \rVert Arguments: path: a list of nodes. The integrity of the nodes is checked for at the beginning of `fit_spline_tree_invariant`. Returns: length: float. It is the length of the path. """ length = sum( [ np.linalg.norm(self.nodes[node]["loc"] - self.nodes[path[i - 1]]["loc"]) if i >= 1 else 0 for i, node in enumerate(path) ] ) return length