segmentation / graph_gui

Commit 68f91f03488fe3943dc0c1941a570f9f494136ca

Authored by Pavel Govyadinov
1 parent 3cc9b7dd

added fibernet for sanity

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fibernet.py 0 → 100644
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  1 +# -*- coding: utf-8 -*-
  2 +"""
  3 +Created on Sat Jan 19 2018
  4 +
  5 +@author: Jiabing
  6 +"""
  7 +
  8 +import struct
  9 +import numpy as np
  10 +import scipy as sp
  11 +import networkx as nx
  12 +import matplotlib.pyplot as plt
  13 +import math
  14 +from mpl_toolkits.mplot3d import Axes3D
  15 +from itertools import chain
  16 +
  17 +class Node:
  18 + def __init__(self, point, outgoing, incoming):
  19 + self.p = point
  20 + self.o = outgoing
  21 + self.i = incoming
  22 +
  23 +
  24 +class Fiber:
  25 + def __init__ (self, indices):
  26 + self.indices = indices
  27 +
  28 +class Point:
  29 + def __init__(self, x, y, z, r):
  30 + self.x = x
  31 + self.y = y
  32 + self.z = z
  33 + self.r = r
  34 +
  35 +class Edge:
  36 + def __init__(self, indices_num, pois, radius):
  37 + self.indices_num = indices_num
  38 + self.points = pois
  39 + self.radius = radius
  40 +
  41 +
  42 +class NWT:
  43 +
  44 + def readVertex(open_file):
  45 + points = np.tile(0., 3)
  46 + bytes = open_file.read(4)
  47 + points[0] = struct.unpack('f', bytes)[0]
  48 + bytes = open_file.read(4)
  49 + points[1] = struct.unpack('f', bytes)[0]
  50 + bytes = open_file.read(4)
  51 + points[2] = struct.unpack('f', bytes)[0]
  52 + bytes = open_file.read(4)
  53 +
  54 + numO = int.from_bytes(bytes, byteorder='little')
  55 + outgoing = np.tile(0, numO)
  56 + bts = open_file.read(4)
  57 + numI = int.from_bytes(bts, byteorder='little')
  58 + incoming = np.tile(0, numI)
  59 + for j in range(numO):
  60 + bytes = open_file.read(4)
  61 + outgoing[j] = int.from_bytes(bytes, byteorder='little')
  62 +
  63 + for j in range(numI):
  64 + bytes = open_file.read(4)
  65 + incoming[j] = int.from_bytes(bytes, byteorder='little')
  66 +
  67 + node = Node(points, outgoing, incoming)
  68 + return node
  69 +
  70 +
  71 + '''
  72 + Reads a single fiber from an open file and returns a Fiber object .
  73 + '''
  74 + def readFiber(open_file):
  75 + bytes = open_file.read(4)
  76 + vtx0 = int.from_bytes(bytes, byteorder = 'little')
  77 + bytes = open_file.read(4)
  78 + vtx1 = int.from_bytes(bytes, byteorder = 'little')
  79 + bytes = open_file.read(4)
  80 + numVerts = int.from_bytes(bytes, byteorder = 'little')
  81 + pts = []
  82 + rads = []
  83 +
  84 + for j in range(numVerts):
  85 + point = np.tile(0., 3)
  86 + bytes = open_file.read(4)
  87 + point[0] = struct.unpack('f', bytes)[0]
  88 + bytes = open_file.read(4)
  89 + point[1] = struct.unpack('f', bytes)[0]
  90 + bytes = open_file.read(4)
  91 + point[2] = struct.unpack('f', bytes)[0]
  92 + bytes = open_file.read(4)
  93 + radius = struct.unpack('f', bytes)[0]
  94 + pts.append(point)
  95 + rads.append(radius)
  96 +
  97 + # F = Fiber(pts)
  98 + E = Edge(numVerts, pts, radius)
  99 + #E = Edge(pts)
  100 + return E
  101 +
  102 +
  103 +class fibernet:
  104 + def __init__(self, filename):
  105 +
  106 + with open(filename, "rb") as file:
  107 + header = file.read(72)
  108 + bytes = file.read(4)
  109 + numVertex = int.from_bytes(bytes, byteorder='little')
  110 + bytes = file.read(4)
  111 + numEdges = int.from_bytes(bytes, byteorder='little')
  112 +
  113 + #self.P = []
  114 + self.F = []
  115 + self.N = []
  116 +
  117 + for i in range(numVertex):
  118 + node = NWT.readVertex(file)
  119 + self.N.append(node)
  120 +
  121 + for i in range( numEdges):
  122 + edge = NWT.readFiber(file)
  123 + #self.F.append(np.arange(num,num+edge.indices_num,1))
  124 + #self.P= chain(self.P, edge.points)
  125 + self.F.append(edge.points)
  126 + #num += edge.indices_num
  127 +
  128 + def aabb(self):
  129 +
  130 + lower = self.N[0].p.copy()
  131 + upper = lower.copy()
  132 + for i in self.N:
  133 + for c in range(len(lower)):
  134 + if lower[c] > i.p[c]:
  135 + lower[c] = i.p[c]
  136 + if upper[c] < i.p[c]:
  137 + upper[c] = i.p[c]
  138 + return lower, upper
  139 +
  140 +
  141 +
  142 + def distancefield(self, R=(100, 100, 100)):
  143 +
  144 + #generate a meshgrid of the appropriate size and resolution to surround the network
  145 + lower, upper = self.aabb() #get the space occupied by the network
  146 + x = np.linspace(lower[0], upper[0], R[0]) #get the grid points for uniform sampling of this space
  147 + y = np.linspace(lower[1], upper[1], R[1])
  148 + z = np.linspace(lower[2], upper[2], R[2])
  149 + X, Y, Z = np.meshgrid(x, y, z)
  150 + #Z = 150 * numpy.ones(X.shape)
  151 +
  152 + Q = np.stack((X, Y, Z), 3)
  153 + d_x = abs(x[1]-x[0]);
  154 + d_y = abs(y[1]-y[0]);
  155 + d_z = abs(z[1]-z[0]);
  156 + dis1 = math.sqrt(pow(d_x,2)+pow(d_y,2)+pow(d_z ,2))
  157 + #dx = abs(x[1]-x[0])
  158 +
  159 + #dy = abs(y[1]-y[0])
  160 + #dz = abs(z[1]-z[0])
  161 + #get a list of all node positions in the network
  162 + P = []
  163 +
  164 + for e in self.F[12:13]: #12-17
  165 + for p in e:
  166 + P.append(p)
  167 +
  168 + for j in range(len(e)-1):
  169 + d_t = e[j+1]-e[j]
  170 + dis2 = math.sqrt(pow(d_t[0],2)+pow(d_t[1],2)+pow(d_t[2],2))
  171 + ins = max(int(d_t[0]/d_x), int(d_t[1]/d_y), int(d_t[2]/d_z))
  172 + if( ins>0 ):
  173 + ins = ins+1;
  174 + for k in range(ins):
  175 + p_ins =e[j]+(k+1)*(e[j+1]-e[j])/ins;
  176 + P.append(p_ins);
  177 + #turn that list into a Numpy array so that we can create a KD tree
  178 + P = np.array(P)
  179 +
  180 + #generate a KD-Tree out of the network point array
  181 + tree = sp.spatial.cKDTree(P)
  182 +
  183 + #specify the resolution of the ouput grid
  184 + # R = (200, 200, 200)
  185 +
  186 + D, I = tree.query(Q)
  187 +
  188 +
  189 +
  190 + return D, Q, dis1
  191 +
  192 +
  193 +'''
  194 +##read NWT file
  195 +f= fibernet("full_seg.nwt")
  196 +#P = tuple(f.P)
  197 +plist = f.F
  198 +
  199 +fig = plt.figure()
  200 +ax = fig.add_subplot(111, projection='3d')
  201 +
  202 +xs = []
  203 +ys = []
  204 +zs = []
  205 +for i in range(10):
  206 + for j in range(len(F[i])):
  207 + xs.append(P[F[i][j]][0])
  208 + ys.append(P[F[i][j]][1])
  209 + zs.append(P[F[i][j]][2])
  210 +
  211 +
  212 +#ax.scatter(xs, ys, zs)
  213 +#ax = fig.gca(projection='3d')
  214 +ax.set_xlabel('X Label')
  215 +ax.set_ylabel('Y Label')
  216 +ax.set_zlabel('Z Label')
  217 +
  218 +ax.plot(xs, ys, zs, label='center lines')
  219 +ax.legend()
  220 +plt.savefig('p.png', dpi=100)
  221 +plt.show()
  222 +'''
0 223 \ No newline at end of file
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