1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
|
# -*- coding: utf-8 -*-
# vispy: gallery 30
# -----------------------------------------------------------------------------
# 2014, Aurore Deschildre, Gael Goret, Cyrille Rossant, Nicolas P. Rougier.
# Distributed under the terms of the new BSD License.
# -----------------------------------------------------------------------------
import numpy as np
from vispy import gloo
from vispy import app
from vispy.util.transforms import perspective, translate, rotate
from vispy.io import load_data_file
vertex = """
#version 120
uniform mat4 u_model;
uniform mat4 u_view;
uniform mat4 u_projection;
uniform vec3 u_light_position;
uniform vec3 u_light_spec_position;
attribute vec3 a_position;
attribute vec3 a_color;
attribute float a_radius;
varying vec3 v_color;
varying vec4 v_eye_position;
varying float v_radius;
varying vec3 v_light_direction;
void main (void) {
v_radius = a_radius;
v_color = a_color;
v_eye_position = u_view * u_model * vec4(a_position,1.0);
v_light_direction = normalize(u_light_position);
float dist = length(v_eye_position.xyz);
gl_Position = u_projection * v_eye_position;
// stackoverflow.com/questions/8608844/...
// ... resizing-point-sprites-based-on-distance-from-the-camera
vec4 proj_corner = u_projection * vec4(a_radius, a_radius, v_eye_position.z, v_eye_position.w); // # noqa
gl_PointSize = 512.0 * proj_corner.x / proj_corner.w;
}
"""
fragment = """
#version 120
uniform mat4 u_model;
uniform mat4 u_view;
uniform mat4 u_projection;
uniform vec3 u_light_position;
uniform vec3 u_light_spec_position;
varying vec3 v_color;
varying vec4 v_eye_position;
varying float v_radius;
varying vec3 v_light_direction;
void main()
{
// r^2 = (x - x0)^2 + (y - y0)^2 + (z - z0)^2
vec2 texcoord = gl_PointCoord* 2.0 - vec2(1.0);
float x = texcoord.x;
float y = texcoord.y;
float d = 1.0 - x*x - y*y;
if (d <= 0.0)
discard;
float z = sqrt(d);
vec4 pos = v_eye_position;
pos.z += v_radius*z;
vec3 pos2 = pos.xyz;
pos = u_projection * pos;
// gl_FragDepth = 0.5*(pos.z / pos.w)+0.5;
vec3 normal = vec3(x,y,z);
float diffuse = clamp(dot(normal, v_light_direction), 0.0, 1.0);
// Specular lighting.
vec3 M = pos2.xyz;
vec3 O = v_eye_position.xyz;
vec3 L = u_light_spec_position;
vec3 K = normalize(normalize(L - M) + normalize(O - M));
// WARNING: abs() is necessary, otherwise weird bugs may appear with some
// GPU drivers...
float specular = clamp(pow(abs(dot(normal, K)), 40.), 0.0, 1.0);
vec3 v_light = vec3(1., 1., 1.);
gl_FragColor.rgba = vec4(.15*v_color + .55*diffuse * v_color
+ .35*specular * v_light, 1.0);
}
"""
class Canvas(app.Canvas):
def __init__(self):
app.Canvas.__init__(self, title='Molecular viewer',
keys='interactive', size=(1200, 800))
self.ps = self.pixel_scale
self.translate = 40
self.program = gloo.Program(vertex, fragment)
self.view = translate((0, 0, -self.translate))
self.model = np.eye(4, dtype=np.float32)
self.projection = np.eye(4, dtype=np.float32)
self.apply_zoom()
fname = load_data_file('molecular_viewer/micelle.npz')
self.load_molecule(fname)
self.load_data()
self.theta = 0
self.phi = 0
gloo.set_state(depth_test=True, clear_color='black')
self.timer = app.Timer('auto', connect=self.on_timer, start=True)
self.show()
def load_molecule(self, fname):
molecule = np.load(fname)['molecule']
self._nAtoms = molecule.shape[0]
# The x,y,z values store in one array
self.coords = molecule[:, :3]
# The array that will store the color and alpha scale for all the atoms
self.atomsColours = molecule[:, 3:6]
# The array that will store the scale for all the atoms.
self.atomsScales = molecule[:, 6]
def load_data(self):
n = self._nAtoms
data = np.zeros(n, [('a_position', np.float32, 3),
('a_color', np.float32, 3),
('a_radius', np.float32)])
data['a_position'] = self.coords
data['a_color'] = self.atomsColours
data['a_radius'] = self.atomsScales*self.ps
self.program.bind(gloo.VertexBuffer(data))
self.program['u_model'] = self.model
self.program['u_view'] = self.view
self.program['u_light_position'] = 0., 0., 2.
self.program['u_light_spec_position'] = -5., 5., -5.
def on_key_press(self, event):
if event.text == ' ':
if self.timer.running:
self.timer.stop()
else:
self.timer.start()
def on_timer(self, event):
self.theta += .25
self.phi += .25
self.model = np.dot(rotate(self.theta, (0, 0, 1)),
rotate(self.phi, (0, 1, 0)))
self.program['u_model'] = self.model
self.update()
def on_resize(self, event):
width, height = event.physical_size
gloo.set_viewport(0, 0, width, height)
self.projection = perspective(25.0, width / float(height), 2.0, 100.0)
self.program['u_projection'] = self.projection
def apply_zoom(self):
width, height = self.physical_size
gloo.set_viewport(0, 0, width, height)
self.projection = perspective(25.0, width / float(height), 2.0, 100.0)
self.program['u_projection'] = self.projection
def on_mouse_wheel(self, event):
self.translate -= event.delta[1]
self.translate = max(-1, self.translate)
self.view = translate((0, 0, -self.translate))
self.program['u_view'] = self.view
self.update()
def on_draw(self, event):
gloo.clear()
self.program.draw('points')
if __name__ == '__main__':
mvc = Canvas()
app.run()
|
