codebase / stimlib

Commit bda1bd09c5453b550b854962041b66e87068d10e

Authored by Pavel Govyadinov 2017-09-16 19:42:28 -0500

Added a network class implemented in python. Reads, writes NWT files, returns Ne…

…tworkX graph objects, and makes layouts.

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python/network.py 0 → 100644

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	1	+# -- coding: utf-8 --
	2	+"""
	3	+Created on Sat Sep 16 16:34:49 2017
	4	+
	5	+@author: pavel
	6	+"""
	7	+
	8	+import struct
	9	+import numpy as np
	10	+import networkx as nx
	11	+import matplotlib.pyplot as plt
	12	+import math
	13	+
	14	+'''
	15	+ Definition of the Node class
	16	+ Duplicate of the node class in network
	17	+ Stores the physical position, outgoing edges list and incoming edges list.
	18	+'''
	19	+class Node:
	20	+ def __init__(self, point, outgoing, incoming):
	21	+ self.p = point
	22	+ self.o = outgoing
	23	+ self.i = incoming
	24	+
	25	+'''
	26	+ Definition of the Fiber class.
	27	+ Duplicate of the Node class in network
	28	+ Stores the starting vertex, the ending vertex, the points array and the radius array
	29	+'''
	30	+class Fiber:
	31	+
	32	+ def __init__ (self):
	33	+ self.v0 = 0
	34	+ self.v1 = 0
	35	+ self.points = []
	36	+ self.radii = []
	37	+
	38	+ def __init__ (self, p1, p2, pois, rads):
	39	+ self.v0 = p1
	40	+ self.v1 = p2
	41	+ self.points = pois
	42	+ self.radii = rads
	43	+
	44	+ '''
	45	+ return the length of the fiber.
	46	+ '''
	47	+ def length(self):
	48	+ length = 0
	49	+ for i in range(len(self.points)-1):
	50	+ length = length + math.sqrt(pow(self.points[i][0]- self.points[i+1][0],2) + pow(self.points[i][1]- self.points[i+1][1],2) + pow(self.points[i][2]- self.points[i+1][2],2))
	51	+
	52	+ return length
	53	+
	54	+ '''
	55	+ returns the turtuosity of the fiber.
	56	+ '''
	57	+ def turtuosity(self):
	58	+ turtuosity = 0
	59	+ distance = math.sqrt(math.pow(self.points[0][0]- self.points[len(self.points)-1][0],2) + math.pow(self.points[0][1]- self.points[len(self.points)-1][1],2) + math.pow(self.points[0][2]- self.points[len(self.points)-1][2],2))
	60	+ turtuosity = self.length()/distance
	61	+ #print(turtuosity)
	62	+
	63	+ return turtuosity
	64	+
	65	+ '''
	66	+ returns the volume of the fiber.
	67	+ '''
	68	+ def volume(self):
	69	+ volume = 0
	70	+ for i in range(len(self.points)-1):
	71	+ volume = volume + 1.0/3.0 * math.pi * (math.pow(self.radii[i],2) + math.pow(self.radii[i+1],2) + self.radii[i]self.radii[i+1]) math.sqrt(math.pow(self.points[i][0]- self.points[i+1][0],2) + math.pow(self.points[i][1]- self.points[i+1][1],2) + math.pow(self.points[i][2]- self.points[i+1][2],2))
	72	+
	73	+ #print(volume)
	74	+ return volume
	75	+'''
	76	+ Writes the header given and open file descripion, number of verticies and number of edges.
	77	+'''
	78	+def writeHeader(open_file, numVerts, numEdges):
	79	+ txt = "nwtFileFormat fileid(14B), desc(58B), #vertices(4B), #edges(4B): bindata"
	80	+ b = bytearray()
	81	+ b.extend(txt.encode())
	82	+ open_file.write(b)
	83	+ open_file.write(struct.pack('i', numVerts))
	84	+ open_file.write(struct.pack('i', numEdges))
	85	+
	86	+
	87	+'''
	88	+ Writes a single vertex to a file.
	89	+'''
	90	+def writeVertex(open_file, vertex):
	91	+ open_file.write(struct.pack('<f',vertex.p[0]))
	92	+ open_file.write(struct.pack('<f',vertex.p[1]))
	93	+ open_file.write(struct.pack('<f',vertex.p[2]))
	94	+ open_file.write(struct.pack('i', len(vertex.o)))
	95	+ open_file.write(struct.pack('i', len(vertex.i)))
	96	+ for j in range(len(vertex.o)):
	97	+ open_file.write(struct.pack('i',vertex.o[j]))
	98	+
	99	+ for j in range(len(vertex.i)):
	100	+ open_file.write(struct.pack('i', vertex.i[j]))
	101	+
	102	+ return
	103	+
	104	+'''
	105	+ Writes a single fiber to a file.
	106	+'''
	107	+def writeFiber(open_file, edge):
	108	+ open_file.write(struct.pack('i',edge.v0))
	109	+ open_file.write(struct.pack('i',edge.v1))
	110	+ open_file.write(struct.pack('i',len(edge.points)))
	111	+ for j in range(len(edge.points)):
	112	+ open_file.write(struct.pack('<f', edge.points[j][0]))
	113	+ open_file.write(struct.pack('<f', edge.points[j][1]))
	114	+ open_file.write(struct.pack('<f', edge.points[j][2]))
	115	+ open_file.write(struct.pack('<f', edge.radii[j]))
	116	+
	117	+ return
	118	+
	119	+'''
	120	+ Writes the entire network to a file in str given the vertices array and the edges array.
	121	+'''
	122	+def exportNWT(str, vertices, edges):
	123	+ with open(str, "wb") as file:
	124	+ writeHeader(file, len(vertices), len(edges))
	125	+ for i in range(len(vertices)):
	126	+ writeVertex(file, vertices[i])
	127	+
	128	+ for i in range(len(edges)):
	129	+ writeFiber(file, edges[i])
	130	+
	131	+ return
	132	+
	133	+
	134	+'''
	135	+ Reads a single vertex from an open file and returns a node Object.
	136	+'''
	137	+def readVertex(open_file):
	138	+ points = np.tile(0., 3)
	139	+ bytes = open_file.read(4)
	140	+ points[0] = struct.unpack('f', bytes)[0]
	141	+ bytes = open_file.read(4)
	142	+ points[1] = struct.unpack('f', bytes)[0]
	143	+ bytes = open_file.read(4)
	144	+ points[2] = struct.unpack('f', bytes)[0]
	145	+ bytes = open_file.read(4)
	146	+
	147	+ numO = int.from_bytes(bytes, byteorder='little')
	148	+ outgoing = np.tile(0, numO)
	149	+ bts = open_file.read(4)
	150	+ numI = int.from_bytes(bts, byteorder='little')
	151	+ incoming = np.tile(0, numI)
	152	+ for j in range(numO):
	153	+ bytes = open_file.read(4)
	154	+ outgoing[j] = int.from_bytes(bytes, byteorder='little')
	155	+
	156	+ for j in range(numI):
	157	+ bytes = open_file.read(4)
	158	+ incoming[j] = int.from_bytes(bytes, byteorder='little')
	159	+
	160	+ node = Node(points, outgoing, incoming)
	161	+ return node
	162	+
	163	+
	164	+'''
	165	+ Reads a single fiber from an open file and returns a Fiber object .
	166	+'''
	167	+def readFiber(open_file):
	168	+ bytes = open_file.read(4)
	169	+ vtx0 = int.from_bytes(bytes, byteorder = 'little')
	170	+ bytes = open_file.read(4)
	171	+ vtx1 = int.from_bytes(bytes, byteorder = 'little')
	172	+ bytes = open_file.read(4)
	173	+ numVerts = int.from_bytes(bytes, byteorder = 'little')
	174	+ pts = []
	175	+ rads = []
	176	+
	177	+ for j in range(numVerts):
	178	+ point = np.tile(0., 3)
	179	+ bytes = open_file.read(4)
	180	+ point[0] = struct.unpack('f', bytes)[0]
	181	+ bytes = open_file.read(4)
	182	+ point[1] = struct.unpack('f', bytes)[0]
	183	+ bytes = open_file.read(4)
	184	+ point[2] = struct.unpack('f', bytes)[0]
	185	+ bytes = open_file.read(4)
	186	+ radius = struct.unpack('f', bytes)[0]
	187	+ pts.append(point)
	188	+ rads.append(radius)
	189	+
	190	+ F = Fiber(vtx0, vtx1, pts, rads)
	191	+
	192	+ return F
	193	+
	194	+'''
	195	+ Imports a NWT file at location str.
	196	+ Returns a list of Nodes objects and a list of Fiber objects.
	197	+'''
	198	+def importNWT(str):
	199	+ with open(str, "rb") as file:
	200	+ header = file.read(72)
	201	+ bytes = file.read(4)
	202	+ numVertex = int.from_bytes(bytes, byteorder='little')
	203	+ bytes = file.read(4)
	204	+ numEdges = int.from_bytes(bytes, byteorder='little')
	205	+
	206	+ nodeList = []
	207	+ fiberList = []
	208	+ for i in range(numVertex):
	209	+ node = readVertex(file)
	210	+ nodeList.append(node)
	211	+
	212	+ for i in range(numEdges):
	213	+ edge = readFiber(file)
	214	+ fiberList.append(edge)
	215	+
	216	+ exportNWT("/home/pavel/Documents/Python/NetLayout/from_python_seg.nwt", nodeList, fiberList)
	217	+ print(str)
	218	+ return nodeList, fiberList;
	219	+
	220	+'''
	221	+Creates a graph from a list of nodes and a list of edges.
	222	+Uses edge length as weight.
	223	+Returns a NetworkX Object.
	224	+'''
	225	+
	226	+def createLengthGraph(nodeList, edgeList):
	227	+ G = nx.Graph()
	228	+ for i in range(len(nodeList)):
	229	+ G.add_node(i, p=V[i].p)
	230	+ for i in range(len(edgeList)):
	231	+ G.add_edge(edgeList[i].v0, edgeList[i].v1, weight = E[i].length())
	232	+
	233	+ return G
	234	+
	235	+'''
	236	+Creates a graph from a list of nodes and a list of edges.
	237	+Uses edge turtuosity as weight.
	238	+Returns a NetworkX Object.
	239	+'''
	240	+def createTortuosityGraph(nodeList, edgeList):
	241	+ G = nx.Graph()
	242	+ for i in range(len(nodeList)):
	243	+ G.add_node(i, p=V[i].p)
	244	+ for i in range(len(edgeList)):
	245	+ G.add_edge(edgeList[i].v0, edgeList[i].v1, weight = E[i].turtuosity())
	246	+
	247	+ return G
	248	+
	249	+
	250	+'''
	251	+Creates a graph from a list of nodes and a list of edges.
	252	+Uses edge volume as weight.
	253	+Returns a NetworkX Object.
	254	+'''
	255	+def createVolumeGraph(nodeList, edgeList):
	256	+ G = nx.Graph()
	257	+ for i in range(len(nodeList)):
	258	+ G.add_node(i, p=V[i].p)
	259	+ for i in range(len(edgeList)):
	260	+ G.add_edge(edgeList[i].v0, edgeList[i].v1, weight = E[i].volume())
	261	+
	262	+ return G
	263	+'''
	264	+Returns the positions dictionary for the Circular layout.
	265	+'''
	266	+def getCircularLayout(graph, dim, radius):
	267	+ return nx.circular_layout(graph, dim, radius)
	268	+
	269	+'''
	270	+Return the positions dictionary for the Spring layout.
	271	+'''
	272	+def getSpringLayout(graph, pos, iterations, scale):
	273	+ return nx.spring_layout(graph, 2, None, pos, iterations, weight='weight', scale, None)
	274	+
	275	+'''
	276	+Draws the graph.
	277	+'''
	278	+def drawGraph(graph, pos):
	279	+ nx.draw(graph, pos)
	280	+ return
0	281	\ No newline at end of file
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