forked from csn92/Visualization
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathorth_anim.py
182 lines (144 loc) · 6.1 KB
/
orth_anim.py
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
import sys
import argparse
import os.path
import numpy as np
from vispy import app, gloo, visuals
from sima import Sequence
from sima import ImagingDataset
vertex = """
attribute vec2 a_position;
attribute vec2 a_texcoord;
varying vec2 v_texcoord;
void main()
{
gl_Position = vec4(a_position, 0.0, 1.0);
v_texcoord = a_texcoord;
}
"""
fragment = """
uniform sampler2D u_texture;
varying vec2 v_texcoord;
uniform float u_time;
void main() {
vec4 clr1 = texture2D(u_texture, v_texcoord);
gl_FragColor = vec4(clr1.rgb,1.0);
}
"""
# This value was derived as the 95th percentile of testing experiment volume.
# TODO: determine a better metric (or dynamic update) for this
NORMING_VAL = 2194
class Canvas(app.Canvas):
def __init__(self, path, channel=0, start=0):
app.Canvas.__init__(self, position=(300, 100),
size=(800, 800), keys='interactive')
self.program = gloo.Program(vertex, fragment)
self.program['a_position'] = [(-1., -.5, 0.), (-1., +1.,0.),
(+0.5, -.5, 0.), (+0.5, +1,0.)]
self.program['a_texcoord'] = [(0., 0.), (0., +1),
(+1., 0.), (+1, +1)]
self.program2 = gloo.Program(vertex, fragment)
self.program2['a_position'] = [(-1., -1., 0.), (-1., -0.55,0.),
(+0.5, -1., 0.), (+0.5, -0.55,0.)]
self.program2['a_texcoord'] = [(0., 0.), (0., +1.),
(+1., 0.), (+1., +1.)]
self.program3 = gloo.Program(vertex, fragment)
self.program3['a_position'] = [(0.55, -0.5, 0.), (0.55, +1.,0.),
(+1., -0.5, 0.), (+1., +1.,0.)]
self.program3['a_texcoord'] = [(0., 0.), (0., +1.),
(+1., 0.), (+1., +1.)]
if os.path.splitext(path)[-1] == '.sima':
ds = ImagingDataset.load(path)
self.sequence = ds.__iter__().next()
else:
self.sequence = Sequence.create('HDF5',path,'tzyxc')
self.frame_counter = start
self.step_size = 1
self.channel = channel
self.length = len(self.sequence)
vol = self.sequence._get_frame(self.frame_counter).astype('float32')
vol /= NORMING_VAL
vol = np.clip(vol, 0, 1)
#surf = np.sum(vol,axis=0)[:,:,channel]/vol.shape[0]
surf = np.nanmean(vol,axis=0)[:,:,channel]
self.program['u_texture'] = surf
#surf2 = np.sum(vol,axis=1)[:,:,channel]/vol.shape[1]
surf2 = np.nanmean(vol,axis=1)[:,:,channel]
self.program2['u_texture'] = surf2
#surf3 = np.fliplr((np.sum(vol,axis=2)[:,:,channel]).T)/vol.shape[2]
surf3 = np.fliplr((np.nanmean(vol,axis=2)[:,:,channel]).T)
self.program3['u_texture'] = surf3
self.text = visuals.TextVisual('',font_size=14,color='r',pos=(700, 700))
self.text.text = "{} / {}".format(self.frame_counter, self.length)
self.steptext = visuals.TextVisual('step_size: 1',font_size=10,color='r',pos=(700, 725))
self.tr_sys = visuals.transforms.TransformSystem(self)
self.timer = app.Timer(0.25, connect=self.on_timer, start=True)
def on_key_press(self,event):
if event.text == ' ' or event.text == 'p':
if self.timer.running:
self.timer.stop()
self.steptext.text = "paused"
else:
self.timer.start()
self.steptext.text = "step size: {}".format(self.step_size)
self.update()
if event.text == '.':
if self.step_size == -1:
self.step_size *= -1
elif self.step_size > 0:
self.step_size *= 2
else:
self.step_size /= 2
self.steptext.text = "step size: {}".format(self.step_size)
self.update()
if event.text == ',':
if self.step_size == 1:
self.step_size /= -1
elif self.step_size > 0:
self.step_size /= 2
else:
self.step_size *= 2
self.steptext.text = "step size: {}".format(self.step_size)
self.update()
def on_timer(self, event):
self.frame_counter += self.step_size
if self.frame_counter < 0 or self.frame_counter >= self.length:
self.frame_counter -= self.step_size
self.step_text.text = "end"
return
vol = self.sequence._get_frame(self.frame_counter).astype('float32')
vol /= NORMING_VAL
vol = np.clip(vol, 0, 1)
#surf = np.sum(vol,axis=0)[:,:,self.channel]/vol.shape[0]
surf = np.nanmean(vol,axis=0)[:,:,self.channel]
self.program['u_texture'] = surf
#surf = np.sum(vol,axis=1)[:,:,self.channel]/vol.shape[1]
surf = np.nanmean(vol,axis=1)[:,:,self.channel]
self.program2['u_texture'] = surf
#surf = np.fliplr((np.sum(vol,axis=2)[:,:,self.channel]).T)/vol.shape[2]
surf = np.fliplr((np.nanmean(vol,axis=2)[:,:,self.channel]).T)
self.program3['u_texture'] = surf
self.text.text = "{} / {}".format(self.frame_counter, self.length)
self.update()
def on_resize(self, event):
width, height = event.size
gloo.set_viewport(0, 0, width, height)
def on_draw(self, event):
gloo.clear('black')
gloo.set_viewport(0, 0, *self.size)
self.program.draw('triangle_strip')
self.program2.draw('triangle_strip')
self.program3.draw('triangle_strip')
self.text.draw(self.tr_sys)
self.steptext.draw(self.tr_sys)
def main(argv):
argParser = argparse.ArgumentParser()
argParser.add_argument('-s', '--start_frame', action='store', type=int, default=0,
help='starting frame for viewing the sequence')
argParser.add_argument("path", action="store", type=str,
help="path to either .sima folder or imaging sequence")
args = argParser.parse_args(argv)
canvas = Canvas(args.path, start=args.start_frame)
canvas.show()
app.run()
if __name__ == '__main__':
main(sys.argv[1:])