TubeCanvas.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 5 15:56:47 2019
@author: pavel
"""
"""
Class that extends the vispy SceneCanvas to draw 3D tubes
"""
from vispy import gloo, scene
from vispy.gloo import set_viewport, set_state, clear, set_blend_color, context
from vispy.gloo import gl
from vispy.util.transforms import perspective, translate, rotate, scale
import vispy.gloo.gl as glcore
from vispy.util.quaternion import Quaternion
import numpy as np
import math
import network_dep as nwt
from tube_shaders import FRAG_SHADER, VERT_SHADER
DEBUG = False
if DEBUG:
from mpl_toolkits.mplot3d import Axes3D
import matplotlib
import matplotlib.pyplot as plt
class TubeDraw(scene.SceneCanvas):
#sigUpdate = QtCore.pyqtSignal(float, float, float)
#Initiates the canvas.
def __init__(self, **kwargs):
#Initialte the class by calling the superclass
scene.SceneCanvas.__init__(self, size=(512,512), keys='interactive', **kwargs)
#unfreeze the drawing area to allow for dynamic drawing and interaction
self.unfreeze()
self.edge_dict = {}
self.select = False
#generate dummy buffers for the meshes
self.program = gloo.Program(VERT_SHADER, FRAG_SHADER)
self.cylinder_data = np.zeros(5*5, dtype=[('a_position', np.float32, 3),
('a_normal', np.float32, 3),
('a_fg_color', np.float32, 4),
#('a_linewidth', np.float32, 1),
])
self.triangle_data = np.random.randint(size=(5, 3), low=0,
high=(4-1)).astype(np.uint32)
self.vbo = gloo.VertexBuffer(self.cylinder_data)
self.triangles = gloo.IndexBuffer(self.triangle_data)
#generate an index buffer for the caps.
self.cap_data = np.random.randint(size=(5, 3), low=0, high=(4-1)).astype(np.uint32)
self.caps = gloo.IndexBuffer(self.cap_data)
self.program.bind(self.vbo)
self.scale = [1,1,1]
self.r1 = np.eye(4, dtype=np.float32)
self.r2 = np.eye(4, dtype=np.float32)
set_viewport(0,0,*self.physical_size)
#set_state(clear_color='white', depth_test=True, blend=True,
# blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('less'), cull_face='back')
set_state(clear_color='white', depth_test=True, blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal'))
#set_blend_color(color='black')
#set_state('translucent')
#self.program['u_LightPos'] = [0., 0., -1000.]
#self.camera = self.central_widget.add_view()
#self.camera.camera = 'turntable'
self.down = False
self.camera = np.asarray([0.0, 0.0, 200.0], dtype=np.float32)
self.up = np.asarray([0., 1., 0.], dtype=np.float32)
#self.init_camera = [0.,0.,1000.]
##### prototype #####
#Set the visualization matrices
self.program['u_selection'] = 0.0
self.program['u_eye'] = self.camera
self.program['u_up'] = self.up
self.program['u_target'] = np.asarray([0., 0., 0.], dtype=np.float32)
#Load the data necessary to draw all of the microvessels
def set_data(self, G, bbu, bbl, num_sides):
self.G = G
self.num_sides = num_sides
self.bbu = bbu
self.bbl = bbl
bb = nwt.AABB(G).resample_sides(3)
#create program
self.gen_cylinder_vbo(self.G, self.num_sides)
self.vbo = gloo.VertexBuffer(self.cylinder_data)
#self.triangle_data = np.append(self.triangle_data, self.cap_data, axis=0)
self.triangles = gloo.IndexBuffer(self.triangle_data)
self.caps = gloo.IndexBuffer(self.cap_data)
#self.view = np.eye(4, dtype=np.float32)
self.model = np.eye(4, dtype=np.float32)
self.projection = np.eye(4, dtype=np.float32)
self.projection = perspective(90.0, self.physical_size[0]/self.physical_size[1], 1.0, 1000.0)
#self.projection = perspective(90.0, 1.0, -1.0, 1.0)
self.program['u_model'] = self.model
#self.program['u_LightPos'] = [0., 0., 1000.]
#self.program['u_view'] = self.view
self.program['u_projection'] = self.projection
self.program.bind(self.vbo)
gloo.set_clear_color('white')
self.center = (bbu-bbl)/2.0
self.translate = [-self.center[0], -self.center[1], -self.center[2]]
self.bb = np.ones((26, 3), dtype=np.float32)
for i in range(26):
for j in range(3):
self.bb[i,j] = bb[i][j]
self.program['u_bb'] = self.bb
if DEBUG:
print('bb is ', self.bb)
# for i in range(len(self.translate)):
# self.camera[i] += self.translate[i]
##### prototype #####
self.camera = self.camera - self.translate
self.program['u_eye'] = self.camera
self.up = np.cross((np.asarray(self.center, dtype=np.float32)-np.asarray(self.camera, dtype=np.float32)), np.asarray(self.up))
self.program['u_up'] = self.up
self.program['u_target'] = self.translate
#self.show()
#Called during resize of the window in order to redraw the same image in the
#larger/smaller area.
def on_resize(self, event):
width, height = event.physical_size
gloo.set_viewport(0, 0, width, height)
if DEBUG:
print(self.physical_size)
#overloaded function called during the self.update() call to update the current
#frame using the GLSL frag/vert shaders
def on_draw(self, event):
clear(color='white', depth=True)
gloo.set_clear_color('white')
if self.select:
set_state(clear_color='white', depth_test=True, blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('always'), cull_face='back')
else:
set_state(clear_color='white', depth_test=True, blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal'), cull_face='back')
self.program.draw('triangles', self.triangles)
if self.select:
set_state(clear_color='white', depth_test=True, blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('always'), cull_face=False)
else:
set_state(clear_color='white', depth_test=True, blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal'), cull_face=False)
self.program.draw('triangles', self.caps)
self.projection = perspective(90.0, self.physical_size[0]/self.physical_size[1], 1.0, 1000.0)
self.program['u_projection'] = self.projection
#Creates a cylinder around ever segment in the microvascular network.
def gen_cylinder_vbo(self, G, num_sides = 32):
i = 0
num_pts = 0
num_tri = 0
num_tri_caps = 0
for e in G.edges():
num_pts += len(self.G.edge_properties["x"][e])
num_tri += (len(self.G.edge_properties["x"][e])-1)*num_sides*2
num_tri_caps += (2*(num_sides-2))
self.cylinder_data = np.zeros(num_pts*num_sides, dtype=[('a_position', np.float32, 3),
('a_normal', np.float32, 3),
('a_fg_color', np.float32, 4),
('a_selection', np.float32, 1),
])
self.triangle_data = np.random.randint(size=(num_tri, 3), low=0,
high=(G.num_edges()-1)).astype(np.uint32)
self.cap_data = np.random.randint(size = (num_tri_caps, 3),
low = 0, high=(G.num_edges()-2)).astype(np.uint32)
index = 0
t_index = 0
c_index = 0
#for each edge generate a cylinder.
for e in G.edges():
#print("done")
#for each fiber get all the points and the radii
X = self.G.edge_properties["x"][e]
Y = self.G.edge_properties["y"][e]
Z = self.G.edge_properties["z"][e]
R = self.G.edge_properties["r"][e]
color = G.edge_properties["RGBA"][e]
pts = np.array([X,Y,Z]).T
circle_pts = np.zeros((pts.shape[0], num_sides, 3), dtype = np.float32)
step = 2*np.pi/num_sides
# U = np.zeros(pts.shape, dtype=np.float32)
# V = np.zeros(pts.shape, dtype=np.float32)
# direction = np.zeros(pts.shape, dtype=np.float32)
#for every point in the edge
for p in range(pts.shape[0]):
#if first point, generate the circles.
#In this case we want to generate a cap if we see the first circle or the last.
if(p == 0):
#get the direction
direction = (pts[p+1] - pts[p])
#normalize direction
direction = direction/np.sqrt(direction[0]*direction[0] + direction[1]*direction[1] + direction[2]*direction[2])
#generate a vector to use as an element of the cross product
Y = np.zeros((3,), dtype = np.float32)
Y[0] = 1.
#if direction and Y are parallel, change Y
if(np.cos(np.dot(Y, direction)) < 0.087):
Y[0] = 0.0
Y[2] = 1.0
#generate first plane vector
U = np.cross(direction, Y)
U = U/np.sqrt(U[0]*U[0] + U[1]*U[1] + U[2]*U[2])
#generate second plane vector
V = np.cross(direction, U)
V = V/np.sqrt(V[0]*V[0] + V[1]*V[1] + V[2]*V[2])
#print(R[p],pts[p])
#generate circle.
for s in range(num_sides):
circle_pts[p][s][0] = R[p]*np.cos(s*step)*V[0]*0.5 + R[p]*np.sin(s*step)*U[0]*0.5
circle_pts[p][s][1] = R[p]*np.cos(s*step)*V[1]*0.5 + R[p]*np.sin(s*step)*U[1]*0.5
circle_pts[p][s][2] = R[p]*np.cos(s*step)*V[2]*0.5 + R[p]*np.sin(s*step)*U[2]*0.5
#if last point, copy the previous circle.
elif(p == pts.shape[0]-1):
for s in range(num_sides):
circle_pts[p][s] = circle_pts[p-1][s]
for v in range(pts.shape[0]):
circle_pts[v,:,0] += pts[v][0]
circle_pts[v,:,1] += pts[v][1]
circle_pts[v,:,2] += pts[v][2]
#otherwise, rotate the circle
else:
#print(R[p], pts[p])
#generate a new direction vector.
dir_new = (pts[p+1]-pts[p])
dir_new = dir_new/np.sqrt(dir_new[0]*dir_new[0] + dir_new[1]*dir_new[1] + dir_new[2]*dir_new[2])
dir_new2 = (pts[p]-pts[p-1])
dir_new2 = dir_new2/np.sqrt(dir_new2[0]*dir_new2[0] + dir_new2[1]*dir_new2[1] + dir_new2[2]*dir_new2[2])
dir_new = dir_new+dir_new2
dir_new = dir_new/np.sqrt(dir_new[0]*dir_new[0] + dir_new[1]*dir_new[1] + dir_new[2]*dir_new[2])
#print(dir_new, direction)
#generate the quaternion rotation vector for the shortest arc
k = 1.0 + np.dot(direction, dir_new)
s = 1/np.sqrt(k+k)
r = s*np.cross(direction, dir_new)
theta = k*s
#r = np.cross(direction, dir_new)
#r = r/np.sqrt(r[0]*r[0] + r[1]*r[1] + r[2]*r[2])
#calculate the degree of quaternion rotation.
#cos_theta = np.sqrt(np.sqrt(np.dot(dir_new, dir_new)) * np.sqrt(np.dot(direction, direction))) + np.dot(dir_new, direction)
#cos_theta = np.dot(direction, dir_new)
#theta = np.arccos(cos_theta)/2.0
#print(r, cos_theta, theta)
#quat = np.append(theta, r)
q = Quaternion(w=theta, x = r[0], y = r[1], z = r[2]).normalize()
#print(quat)
#q = np.quaternion(quat[0], quat[1], quat[2], quat[3])
#rot = Rotation.from_quat(quat, normalized=False)
#rot.as_quat()
for s in range(num_sides):
circle_pts[p][s] = q.rotate_point(circle_pts[p-1][s])
#circle_pts[p][s] = rot.apply(circle_pts[p-1][s])
#circle_pts[p][s] = q.rotate(circle_pts[p-1][s])
#circle_pts[p][s] = np.quaternion.rotate_vectors(q, circle_pts[p][s])
#circle_pts[p][s] = q.rotate_vectors(q, circle_pts[p][s])
#circle_pts[p][s] = circle_pts[p][s]
direction = dir_new
#generate the triangles
triangles = np.random.randint(size=((pts.shape[0]-1)*2*(num_sides), 3), low=0,
high=(G.num_edges()-1)).astype(np.uint32)
cap_triangles = np.random.randint(size=((num_sides-2)*2 , 3), low=0, high=(num_sides-2)).astype(np.uint32)
t_index_temp = 0
c_index_temp = 0
#for every ring in the fiber
for ring in range(0, pts.shape[0], pts.shape[0]-1):
#if we have the first ring or the last ring add a cap.
idx_ori = index+ring*num_sides
for side in range(0, num_sides-2):
idx_current_point = index+ring*num_sides + side
if(side < num_sides-2):
cap_tri = [idx_ori, idx_current_point+1, idx_current_point+2]
else:
cap_tri = [idx_ori, idx_current_point+1, idx_ori]
cap_triangles[c_index_temp] = cap_tri
self.cap_data[c_index] = cap_tri
c_index_temp += 1
c_index += 1
for ring in range(pts.shape[0]-1):
#otherwise generate the sides.
for side in range(num_sides):
if(side < num_sides-1):
idx_current_point = index+ring*num_sides + side
idx_next_ring = index + (ring+1) * num_sides + side
triangle1 = [idx_current_point, idx_next_ring, idx_next_ring+1]
triangle2 = [idx_next_ring+1, idx_current_point+1, idx_current_point]
triangles[t_index_temp] = [idx_current_point, idx_next_ring, idx_next_ring+1]
triangles[t_index_temp+1] = [idx_next_ring+1, idx_current_point+1, idx_current_point]
self.triangle_data[t_index] = triangle1
self.triangle_data[t_index+1] = triangle2
t_index += 2
t_index_temp += 2
else:
idx_current_point = index + ring*num_sides + side
idx_next_ring = index + (ring+1)*num_sides + side
triangle1 = [idx_current_point, idx_next_ring, idx_next_ring-num_sides+1]
triangle2 = [idx_next_ring-num_sides+1, idx_current_point-num_sides+1, idx_current_point]
triangles[t_index_temp] = [idx_current_point, idx_next_ring-num_sides, idx_next_ring-num_sides+1]
triangles[t_index_temp+1] = [idx_next_ring-num_sides+1, idx_current_point-num_sides+1, idx_current_point]
self.triangle_data[t_index] = triangle1
self.triangle_data[t_index+1] = triangle2
t_index += 2
t_index_temp += 2
#generate the points data structure
circle_pts_data = circle_pts.reshape((pts.shape[0]*num_sides, 3))
self.cylinder_data['a_position'][index:(pts.shape[0]*num_sides+index)] = circle_pts_data
self.cylinder_data['a_fg_color'][index:(pts.shape[0]*num_sides+index)] = color
self.cylinder_data['a_selection'][index:(pts.shape[0]*num_sides+index)] = 0.0
#generate the normals data structure
pts_normals = circle_pts.copy()
for p in range(pts.shape[0]):
pts_normals[p][:] = pts_normals[p][:] - pts[p]
for s in range(num_sides):
pts_normals[p][s] = pts_normals[p][s]/np.sqrt(pts_normals[p][s][0]*pts_normals[p][s][0] \
+ pts_normals[p][s][1]*pts_normals[p][s][1] + pts_normals[p][s][2]*pts_normals[p][s][2])
self.cylinder_data['a_normal'][index:(pts.shape[0]*num_sides+index)] = \
pts_normals.reshape((pts.shape[0]*num_sides, 3))
index += pts.shape[0]*num_sides
self.edge_dict[(int(e.source()), int(e.target()))] = (index-pts.shape[0]*num_sides, index)
#Add the caps for each of the endpoints.
if DEBUG:
if(i == 2):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
#ax.scatter(circle_pts[:,:,0], circle_pts[:,:,1], circle_pts[:,:,2])
ax.plot(pts[:,0], pts[:,1], pts[:,2])
for j in range(pts.shape[0]):
ax.plot(circle_pts[j,:,0], circle_pts[j,:,1], circle_pts[j,:,2])
for j in range(cap_triangles.shape[0]):
tri = np.zeros((3,4))
tri[:,0] = self.cylinder_data['a_position'][cap_triangles[j][0]]
tri[:,1] = self.cylinder_data['a_position'][cap_triangles[j][1]]
tri[:,2] = self.cylinder_data['a_position'][cap_triangles[j][2]]
tri[:,3] = self.cylinder_data['a_position'][cap_triangles[j][0]]
ax.plot(tri[0,:], tri[1,:], tri[2,:], c='b')
for j in range(triangles.shape[0]):
tri = np.zeros((3,4))
tri[:,0] = self.cylinder_data['a_position'][triangles[j][0]]
tri[:,1] = self.cylinder_data['a_position'][triangles[j][1]]
tri[:,2] = self.cylinder_data['a_position'][triangles[j][2]]
tri[:,3] = self.cylinder_data['a_position'][triangles[j][0]]
ax.plot(tri[0,:], tri[1,:], tri[2,:], c='b')
for j in range(triangles.shape[0]):
tri = np.zeros((3,3))
tri[:,0] = self.cylinder_data['a_position'][triangles[j][0]]
tri[:,1] = self.cylinder_data['a_position'][triangles[j][1]]
tri[:,2] = self.cylinder_data['a_position'][triangles[j][2]]
norm = np.zeros((3,3))
norm[:,0] = self.cylinder_data['a_normal'][triangles[j][0]]
norm[:,1] = self.cylinder_data['a_normal'][triangles[j][1]]
norm[:,2] = self.cylinder_data['a_normal'][triangles[j][2]]
ax.quiver(tri[0,:], tri[1,:], tri[2,:], norm[0,:], norm[1,:], norm[2,:], colors = 'r')
plt.show()
i+=1
#create the data.
def select_edges(self, edges):
#gloo.context.set_current_canvas(gloo.context.get_current_canvas())
if len(edges) > 0:
self.select = True
#gloo.set_depth_func('always')
#clear(color='white', depth=True)
#gl.GL_DEPTH_FUNC('always')
#print(gloo.wrappers.get_gl_configuration())
self.program['u_selection'] = 1.0
for e in edges:
if e in self.edge_dict:
idx = self.edge_dict[e]
#print(self.canvas.edge_dict[e])
elif (e[1], e[0]) in self.edge_dict:
idx = self.edge_dict[(e[1],e[0])]
else:
print("WHAT THE FUCK HAPPENED")
self.cylinder_data["a_selection"][idx[0]:idx[1]] = 1.0
self.vbo = gloo.VertexBuffer(self.cylinder_data)
self.program.bind(self.vbo)
#self.update()
else:
self.program['u_selection'] = 0.0
self.select = False
#set_state(clear_color='white', depth_test=True, blend=True,
# blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal'))
#gloo.set_depth_func('lequal')
#clear(color='white', depth=True)
#print(gloo.wrappers.get_gl_configuration())
self.update()
#print(self.canvas.edge_dict[(e[1], e[0])])
#Handles the mouse wheel event, i.e., zoom
def on_mouse_wheel(self, event):
# self.scale[0] = self.scale[0] + self.scale[0]*event.delta[1]*0.05
# self.scale[1] = self.scale[1] + self.scale[1]*event.delta[1]*0.05
# self.scale[2] = self.scale[2] + self.scale[2]*event.delta[1]*0.05
## self.view[0][0] = self.scale[0]
## self.view[1][1] = self.scale[1]
## self.view[2][2] = self.scale[2]
# print("in mouse wheel ", self.r1, self.r2)
# self.view = np.matmul(translate((self.translate[0], self.translate[1], self.translate[2])), self.r1)
# self.view = np.matmul(self.view, self.r2)
# self.view = np.matmul(self.view, scale((self.scale[0], self.scale[1], self.scale[2])))
# #self.view = np.matmul(self.view, self.r1)
# #self.view = np.matmul(self.view, self.r2)
# #self.view = np.matmul(translate((self.translate[0], self.translate[1], self.translate[2])), scale((self.scale[0], self.scale[1], self.scale[2])))
# #self.rotate = [0., 0.]
# #self.camera =
#
# #self.view[1][1] = self.view[1][1]+self.view[1][1]*event.delta[1]*0.05
# #print(self.view[0][0], " ",self.view[1][1])
# #print(self.view)
# self.camera = [0.0, 0.0, -100.0, 1.0]
## for i in range(len(self.translate)):
## self.camera[i] += self.translate[i]
# self.program['u_view'] = self.view
# if(np.asarray(self.camera).all() == np.asarray([0., 0., 0.]).all()):
# self.camera = np.asarray([0., 0., 0.])
# else:
direction = np.asarray(self.translate) - np.asarray(self.camera)
direction = direction/np.sqrt(np.dot(direction, direction))
for i in range(3):
self.camera[i] = self.camera[i] + direction[i]*event.delta[1]*2.0
self.program['u_eye'] = self.camera
#print(self.view)
#print(event.delta[1])
self.update()
#Handles the mouse press event to rotate the camera if the left mouse button
#if clicked down.
def on_mouse_press(self, event):
def update_view():
self.location = event.pos
#self.program['u_view'] = self.view
self.down = True
if(event.button == 1):
update_view()
#Handles the rotation of the camera using a quaternion centered around the
#focus point.
def on_mouse_move(self, event):
if(self.down == True):
coord = self.transforms.get_transform('canvas', 'render').map(self.location)[:2]
coord2 = self.transforms.get_transform('canvas', 'render').map(event.pos)[:2]
#coord[1] = 0
#coord2[1] = 0
phi = (coord[0]-coord2[0])*360.0/2.0/np.pi
theta = (coord[1]-coord2[1])*360.0/2.0/np.pi
if DEBUG:
print(theta*360.0/2.0/np.pi, -phi*360.0/2.0/np.pi)
self.camera = self.camera - self.translate
q1 = Quaternion.create_from_axis_angle(angle=phi, ax=0.0, ay=1.0, az=0.0, degrees=True)
q2 = Quaternion.create_from_axis_angle(angle=theta, ax=1.0, ay=0.0, az=0.0, degrees=True)
#q1 = Quaternion(w=theta, x = 0, y = 1, z = 0).inverse().normalize()
#q2 = Quaternion(w=-phi, x = 1, y = 0, z = 0).inverse().normalize()
q = q1*q2
# #print("Angle in Degrees is ", theta, " ", phi, coord[0] - coord2[0])
# self.r1 = rotate(theta, (0, 1, 0))
# self.r2 = rotate(-phi, (1, 0, 0))
#
# print("in on mouse move ", self.r1, self.r2)
#
# self.view = np.matmul(self.view, self.r1)
# #print("r1", self.view)
# self.view = np.matmul(self.view, self.r2)
# #print("r2", self.view)
#
## self.view = np.matmul(self.view, q1.get_matrix().T)
## self.view = np.matmul(self.view, q2.get_matrix().T)
#
# self.program['u_view'] = self.view
#
self.location = event.pos
# #print("Angle in Degrees is ", theta, " ", phi)
# #print(self.camera)
self.camera = np.asarray(q.rotate_point(self.camera), dtype=np.float)
self.camera = self.camera + self.translate
self.up = np.asarray(q.rotate_point(self.up), dtype=np.float)
self.up = self.up/np.sqrt(np.dot(self.up, self.up))
#self.rotate[0] = self.rotate[0] + theta
#self.rotate[1] = self.rotate[1] + phi
#print(self.rotate)f
#radius = np.sqrt(np.dot(self.center, self.center))*2
#test = np.linalg.inv(self.view).T
#print(test)
#self.camera = sph2cart(self.rotate[0]/360.0*2.0*np.pi+np.pi, self.rotate[1]/360.0*2.0*np.pi+np.pi, 1000.0)
#self.camera[0] = self.camera[0] + self.center[0]
#self.camera[1] = self.camera[1] + self.center[1]
#self.camera[2] = self.camera[2] - self.center[2]
if DEBUG:
print("current position ", self.camera, " and up vector ", self.up)
self.program['u_eye'] = self.camera
self.program['u_up'] = self.up
#self.program['u_LightPos'] = [self.camera[0], self.camera[1], self.camera[2]]
self.update()
#reverts the mouse state during release.
def on_mouse_release(self, event):
self.down = False