-
Notifications
You must be signed in to change notification settings - Fork 0
/
vis_utils.py
302 lines (249 loc) · 12.9 KB
/
vis_utils.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
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
import numpy as np
import vtk
from vtk.util import numpy_support
from scipy.ndimage import zoom
def load_volume(file, scale=None):
raw_arr = np.fromfile(file, dtype=np.uint8)
volume_dims_str = file.split('_')[-1].split('.')[0].split('x')
dims_order = (2, 1, 0)
volume_dims = [int(volume_dims_str[i]) for i in dims_order]
arr = raw_arr.reshape(volume_dims)
if scale is not None:
arr = zoom(arr, scale, order=0)
return arr
def get_transform_function(mid_point, delta, central_value, margin_value):
transform_function = vtk.vtkPiecewiseFunction()
transform_function.AddPoint(mid_point - delta, margin_value)
transform_function.AddPoint(mid_point, central_value)
transform_function.AddPoint(mid_point + delta, margin_value)
transform_function.AddPoint(0, 0)
return transform_function
def get_color_function(mid_point, primary_color):
volumeColor = vtk.vtkColorTransferFunction()
volumeColor.AddRGBPoint(mid_point - 50, *(0, 0, 0))
volumeColor.AddRGBPoint(mid_point, *primary_color)
volumeColor.AddRGBPoint(mid_point + 50, *(0, 0, 0))
return volumeColor
class SliderWrapper:
def __init__(self, title_text, value_range, initial_value, position):
slider_rep = vtk.vtkSliderRepresentation2D()
slider_rep.GetPoint1Coordinate().SetCoordinateSystemToNormalizedDisplay()
slider_rep.GetPoint1Coordinate().SetValue(*position[0])
slider_rep.GetPoint2Coordinate().SetCoordinateSystemToNormalizedDisplay()
slider_rep.GetPoint2Coordinate().SetValue(*position[1])
slider_rep.SetMinimumValue(value_range[0])
slider_rep.SetMaximumValue(value_range[1])
slider_rep.SetValue(initial_value)
slider_rep.SetTitleText(title_text)
self._slider_rep = slider_rep
def get_widget(self, interactor):
widget = vtk.vtkSliderWidget()
widget.SetInteractor(interactor)
widget.SetRepresentation(self._slider_rep)
widget.SetAnimationModeToAnimate()
widget.EnabledOn()
return widget
class VolumeVisualizer:
def __init__(self, volume, binary=True, data_scalar_range='auto'):
self._volume = volume
self._binary = binary
if data_scalar_range == 'auto':
data_scalar_range = (int(volume.min()), int(volume.max()))
self._data_scalar_range = data_scalar_range
self._dynamic_properties = {
'opacity_function_midpoint': (data_scalar_range[0] + data_scalar_range[1]) / 2.,
'opacity_function_max': 1.,
'opacity_function_width': (data_scalar_range[1] - data_scalar_range[0]) / 2.
}
def visualize(self, scale=1, interpolation_order=0, primary_color=None):
volume = zoom(self._volume, scale, order=interpolation_order)
flat_volume = volume.transpose((2, 1, 0)).flatten()
# --- data_importer
data_importer = vtk.vtkImageImport()
data_string = flat_volume.tostring()
data_importer.CopyImportVoidPointer(data_string, len(data_string))
data_importer.SetDataScalarTypeToUnsignedChar()
data_importer.SetNumberOfScalarComponents(1)
data_importer.SetDataExtent(0, volume.shape[0] - 1, 0, volume.shape[1] - 1, 0, volume.shape[2] - 1)
data_importer.SetWholeExtent(0, volume.shape[0] - 1, 0, volume.shape[1] - 1, 0, volume.shape[2] - 1)
# --- mapper
mapper = vtk.vtkSmartVolumeMapper()
mapper.SetInputConnection(data_importer.GetOutputPort())
# --- actor
actor = vtk.vtkVolume()
actor.SetMapper(mapper)
# --- renderer
renderer = vtk.vtkRenderer()
renderer.AddActor(actor)
# --- window
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window.SetSize(800, 600)
# --- interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(render_window)
if self._binary:
actor.GetProperty().SetScalarOpacity(0, get_transform_function(1, 0.5, 1, 0))
color_function = get_color_function(1, primary_color if primary_color is not None else (1, 1, 1))
actor.GetProperty().SetColor(0, color_function)
else:
def slider_callback_wrapper(property_name):
def callback(caller, _):
value = caller.GetSliderRepresentation().GetValue()
self._dynamic_properties[property_name] = value
transform_function = get_transform_function(
mid_point=self._dynamic_properties['opacity_function_midpoint'],
delta=self._dynamic_properties['opacity_function_width'] / 2.,
margin_value=0.,
central_value=self._dynamic_properties['opacity_function_max']
)
actor.GetProperty().SetScalarOpacity(0, transform_function)
if primary_color is not None:
color_function = get_color_function(self._dynamic_properties['opacity_function_midpoint'],
primary_color)
actor.GetProperty().SetColor(0, color_function)
render_window.Render()
return callback
midpoint_slider_widget = SliderWrapper(
title_text='opacity function midpoint',
value_range=self._data_scalar_range,
initial_value=self._dynamic_properties['opacity_function_midpoint'],
position=((.7, .1), (.9, .1))
).get_widget(interactor)
midpoint_slider_widget.AddObserver('InteractionEvent', slider_callback_wrapper('opacity_function_midpoint'))
width_slider_widget = SliderWrapper(
title_text='opacity function width',
value_range=(0, self._data_scalar_range[1] - self._data_scalar_range[0]),
initial_value=self._dynamic_properties['opacity_function_width'],
position=((.7, .25), (.9, .25))
).get_widget(interactor)
width_slider_widget.AddObserver('InteractionEvent', slider_callback_wrapper('opacity_function_width'))
opacity_slider_widget = SliderWrapper(
title_text='max opacity',
value_range=(0., 1.),
initial_value=1.,
position=((.7, .4), (.9, .4))
).get_widget(interactor)
opacity_slider_widget.AddObserver('InteractionEvent', slider_callback_wrapper('opacity_function_max'))
transform_function = get_transform_function(
mid_point=self._dynamic_properties['opacity_function_midpoint'],
delta=self._dynamic_properties['opacity_function_width'] / 2.,
margin_value=0.,
central_value=self._dynamic_properties['opacity_function_max']
)
actor.GetProperty().SetScalarOpacity(0, transform_function)
if primary_color is not None:
color_function = get_color_function(self._dynamic_properties['opacity_function_midpoint'],
primary_color)
actor.GetProperty().SetColor(0, color_function)
# --- start
render_window.Render()
style = vtk.vtkInteractorStyleTrackballCamera()
interactor.SetInteractorStyle(style)
interactor.Initialize()
interactor.Start()
class ColorMapVisualizer:
def __init__(self, color_map):
self._color_map = color_map
self._data_scalar_range = (int(color_map.min()), int(color_map.max()))
self._dynamic_properties = {
'opacity_function_midpoint': (self._data_scalar_range[0] + self._data_scalar_range[1]) / 2.,
'opacity_function_max': 1.,
'opacity_function_width': (self._data_scalar_range[1] - self._data_scalar_range[0]) / 2.
}
def visualize(self, scale=1, interpolation_order=0, interactive=True, gradient=False):
volume = zoom(self._color_map, scale, order=interpolation_order)
flat_volume = volume.transpose((2, 1, 0)).flatten()
# --- data_importer
data_importer = vtk.vtkImageImport()
data_string = flat_volume.tostring()
data_importer.CopyImportVoidPointer(data_string, len(data_string))
data_importer.SetDataScalarTypeToUnsignedChar()
data_importer.SetNumberOfScalarComponents(1)
data_importer.SetDataExtent(0, volume.shape[0] - 1, 0, volume.shape[1] - 1, 0, volume.shape[2] - 1)
data_importer.SetWholeExtent(0, volume.shape[0] - 1, 0, volume.shape[1] - 1, 0, volume.shape[2] - 1)
# --- mapper
mapper = vtk.vtkSmartVolumeMapper()
mapper.SetInputConnection(data_importer.GetOutputPort())
# --- actor
actor = vtk.vtkVolume()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(0, self.get_rainbow_color_function(gradient))
# --- renderer
renderer = vtk.vtkRenderer()
renderer.AddActor(actor)
# --- window
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window.SetSize(800, 600)
# --- interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(render_window)
# --- setting actor properties
if interactive:
def slider_callback_wrapper(property_name):
def callback(caller, _):
value = caller.GetSliderRepresentation().GetValue()
self._dynamic_properties[property_name] = value
transform_function = get_transform_function(
mid_point=self._dynamic_properties['opacity_function_midpoint'],
delta=self._dynamic_properties['opacity_function_width'] / 2.,
margin_value=0.,
central_value=self._dynamic_properties['opacity_function_max']
)
actor.GetProperty().SetScalarOpacity(0, transform_function)
render_window.Render()
return callback
midpoint_slider_widget = SliderWrapper(
title_text='opacity function midpoint',
value_range=self._data_scalar_range,
initial_value=self._dynamic_properties['opacity_function_midpoint'],
position=((.7, .1), (.9, .1))
).get_widget(interactor)
midpoint_slider_widget.AddObserver('InteractionEvent', slider_callback_wrapper('opacity_function_midpoint'))
width_slider_widget = SliderWrapper(
title_text='opacity function width',
value_range=(0, 3 * (self._data_scalar_range[1] - self._data_scalar_range[0])),
initial_value=self._dynamic_properties['opacity_function_width'],
position=((.7, .25), (.9, .25))
).get_widget(interactor)
width_slider_widget.AddObserver('InteractionEvent', slider_callback_wrapper('opacity_function_width'))
opacity_slider_widget = SliderWrapper(
title_text='max opacity',
value_range=(0., 1.),
initial_value=1.,
position=((.7, .4), (.9, .4))
).get_widget(interactor)
opacity_slider_widget.AddObserver('InteractionEvent', slider_callback_wrapper('opacity_function_max'))
transform_function = get_transform_function(
mid_point=self._dynamic_properties['opacity_function_midpoint'],
delta=self._dynamic_properties['opacity_function_width'] / 2.,
margin_value=0.,
central_value=self._dynamic_properties['opacity_function_max']
)
actor.GetProperty().SetScalarOpacity(0, transform_function)
else:
actor.GetProperty().SetScalarOpacity(0, self.get_full_transfer_function())
# --- start
render_window.Render()
style = vtk.vtkInteractorStyleTrackballCamera()
interactor.SetInteractorStyle(style)
interactor.Initialize()
interactor.Start()
def get_full_transfer_function(self, central_value=1):
transfer_function = vtk.vtkPiecewiseFunction()
transfer_function.AddPoint(0, 0)
for i in range(1, self._data_scalar_range[1] + 1):
transfer_function.AddPoint(i, central_value)
return transfer_function
def get_rainbow_color_function(self, gradient):
colors = [(1, 0, 0), (0, 1, 0), (0, 0, 1), (1, 1, 0), (1, 0, 1), (0, 1, 1)]
volume_color = vtk.vtkColorTransferFunction()
volume_color.AddRGBPoint(0, *(0, 0, 0))
if gradient:
volume_color.AddRGBPoint(1, *(1, 0, 0))
volume_color.AddRGBPoint(self._data_scalar_range[1], *(0, 0, 1))
else:
for i in range(1, self._data_scalar_range[1] + 1):
volume_color.AddRGBPoint(i, *(colors[i % len(colors)]))
return volume_color