-
Notifications
You must be signed in to change notification settings - Fork 0
/
sv.py
executable file
·318 lines (257 loc) · 10.7 KB
/
sv.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
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
#!/usr/bin/env python
"""Simple visualization for vtk, off, or freesurfer surfaces
"""
import argparse
import nibabel as nb
import numpy as np
import sv_io
import sys
import vtk
class SurfaceInteractor(vtk.vtkInteractorStyleTrackballCamera):
def __init__(self, interactor, key_callback, mouse_callback):
self.interactor = interactor
self.picker = vtk.vtkCellPicker()
self.key_callback = key_callback
self.mouse_callback = mouse_callback
self.AddObserver("KeyPressEvent", self.key_pressed)
self.AddObserver("MouseMoveEvent", self.mouse_moved)
def key_pressed(self, obj, event):
key = self.interactor.GetKeyCode()
if key == ",":
self.key_callback(False)
elif key == ".":
self.key_callback(True)
def mouse_moved(self, obj, event):
coords = self.interactor.GetEventPosition()
if self.picker.Pick(
coords[0], coords[1], 0,
self.interactor.GetRenderWindow().GetRenderers(
).GetFirstRenderer()):
if self.mouse_callback is not None:
self.mouse_callback(self.picker.GetCellId(),
self.picker.GetPickPosition())
self.OnMouseMove()
class SurfaceViewer(object):
def __init__(self, options, points=None, face_list=None, overlays=None):
self.options = options
self.surface = None
self.surface_overlays = []
self.surface_overlay_data = []
self.coord_transform = None
self.last_overlay_value = None
self.last_min_point = None
self.points = []
self.point_clouds = []
self._no_show = False
if points is None:
assert face_list is None
surf_file = options.surface[0]
overlay_files = options.overlays
points, face_list = sv_io.read_surf(surf_file)
overlays = []
for overlay_file in overlay_files:
if overlay_file.endswith(".vtk"):
overlays.append(np.array(read_scalars(overlay_file)[0]))
print "read VTK overlay"
else:
labels = sv_io.read_surf_cdata(overlay_file)
try:
labels = sv_io.read_surf_cdata(overlay_file)
print "read LAB overlay"
except:
try:
labels, _, _ = nb.freesurfer.read_annot(
overlay_file)
except:
try:
labels = nb.freesurfer.read_w_data(
overlay_file)
except:
labels = nb.freesurfer.read_morph_data(
overlay_file)
print "read FreeSurfer overlay"
overlays.append(labels)
if options.combine_overlays:
overlays = [np.sum(np.vstack(overlays), 0)]
vertices = vtk.vtkPoints()
for pt in points:
vertices.InsertNextPoint(pt)
faces = vtk.vtkCellArray()
for face in face_list:
faces.InsertNextCell(3)
for pt in face:
faces.InsertCellPoint(pt)
self.set_surface(vertices, faces)
# overlays
self.scalars = []
self.current_overlay = -1
if options.coord_transform is not None:
vol = nb.load(options.coord_transform)
self.coord_transform = np.matrix(vol.get_affine()).I
else:
self.coord_transform = np.eye(4)
if options.colormap:
colormap = np.loadtxt(options.colormap)
else:
colormap = None
for data in overlays:
if data.shape[0] > 0:
self.add_surface_overlay(data, colormap)
def set_surface(self, points, faces):
assert self.surface is None
poly_data = vtk.vtkPolyData()
poly_data.SetPoints(points)
poly_data.SetPolys(faces)
self.points.append(points)
self.surface = poly_data
def add_surface_overlay(self, data, colormap=None):
scalar = vtk.vtkUnsignedCharArray()
scalar.SetNumberOfComponents(3)
if colormap is None:
ran = (np.amin(data), np.amax(data))
mid = (ran[0] + ran[1]) / 2.
for val in data:
if val < mid:
gr = 255.0 * (val - ran[0]) / (mid - ran[0])
else:
gr = 255.0 * (ran[1] - val) / (ran[1] - mid)
scalar.InsertNextTuple3(
255 * (val - ran[0]) / (ran[1] - ran[0]),
gr,
255 * (ran[1] - val) / (ran[1] - ran[0]))
else:
for val in data:
if val < colormap[0][0]:
ind = 0
elif val > colormap[-1][0]:
ind = colormap.shape[0] - 1
else:
for ind in xrange(colormap.shape[0] - 1):
if val < colormap[ind + 1][0]:
break
scalar.InsertNextTuple3(255 * colormap[ind][1],
255 * colormap[ind][2],
255 * colormap[ind][3])
self.surface_overlays.append(scalar)
self.surface_overlay_data.append(data)
def add_point_cloud(self, points, indices=None, rgb=(255, 255, 0)):
point_data = vtk.vtkPoints()
cell_data = vtk.vtkCellArray()
scalar_data = vtk.vtkUnsignedCharArray()
scalar_data.SetNumberOfComponents(3)
for idx in indices if indices is not None else xrange(len(points)):
cell_data.InsertNextCell(1)
cell_data.InsertCellPoint(point_data.InsertNextPoint(points[idx]))
scalar_data.InsertNextTuple3(*rgb)
point_poly = vtk.vtkPolyData()
point_poly.SetPoints(point_data)
point_poly.SetVerts(cell_data)
point_poly.GetPointData().SetScalars(scalar_data)
self.point_clouds.append(point_poly)
def add_point_cloud_from_surf_indices(self, indices, rgb=(255, 255, 0)):
cell_data = vtk.vtkCellArray()
scalar_data = vtk.vtkUnsignedCharArray()
scalar_data.SetNumberOfComponents(3)
for idx in indices:
cell_data.InsertNextCell(1)
cell_data.InsertCellPoint(idx)
scalar_data.InsertNextTuple3(*rgb)
point_poly = vtk.vtkPolyData()
point_poly.SetPoints(self.points[0])
point_poly.SetVerts(cell_data)
point_poly.GetCellData().SetScalars(scalar_data)
self.point_clouds.append(point_poly)
def change_overlay(self, move_up):
if len(self.surface_overlays) < 1:
return
if move_up:
self.current_overlay += 1
if self.current_overlay >= len(self.surface_overlays):
self.current_overlay = 0
else:
self.current_overlay -= 1
if self.current_overlay < 0:
self.current_overlay = len(self.surface_overlays) - 1
print "showing overlay %d" % self.current_overlay
self.surface.GetPointData().SetScalars(
self.surface_overlays[self.current_overlay])
self.surface.Modified()
self.ren_win.Render()
def over_cell(self, cell_id, position):
face_vertices = self.surface.GetCell(cell_id).GetPointIds()
min_dist = float('inf')
min_point = None
for i in range(0, 3):
dist = sum((np.array(self.surface.GetPoint(
face_vertices.GetId(i))) -
np.array(position))**2)
if dist < min_dist:
min_dist = dist
min_point = face_vertices.GetId(i)
point_id = min_point
if len(self.surface_overlays) < 1:
if min_point == self.last_min_point:
return
ras = list(self.surface.GetPoint(min_point))
ras.append(1)
vox = self.coord_transform * np.array([ras]).T
print np.diag(vox)
return
if (self.last_overlay_value ==
self.surface_overlay_data[self.current_overlay][point_id]):
return
print "%d: %f" % (
point_id, self.surface_overlay_data[self.current_overlay][point_id])
self.last_overlay_value = \
self.surface_overlay_data[self.current_overlay][point_id]
def show(self):
if self._no_show:
return 0
ren = vtk.vtkRenderer()
self.ren_win = vtk.vtkRenderWindow()
self.ren_win.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(self.ren_win)
iren.SetInteractorStyle(
SurfaceInteractor(iren, self.change_overlay,
self.over_cell if self.options.show_values
else None))
surf_mapper = vtk.vtkDataSetMapper()
surf_mapper.SetInput(self.surface)
surf_actor = vtk.vtkActor()
# TODO: allow interactive toggling of edges.
# surf_actor.GetProperty().SetEdgeColor(0.5, 0.5, 0.5)
# surf_actor.GetProperty().EdgeVisibilityOn()
surf_actor.SetMapper(surf_mapper)
ren.AddActor(surf_actor)
for cloud in self.point_clouds:
pt_mapper = vtk.vtkDataSetMapper()
pt_mapper.SetInput(cloud)
pt_mapper.SetScalarVisibility(1)
pt_actor = vtk.vtkActor()
pt_actor.GetProperty().SetPointSize(5)
pt_actor.SetMapper(pt_mapper)
ren.AddActor(pt_actor)
ren.ResetCamera()
iren.Initialize()
self.change_overlay(True)
iren.Start()
def parse_args(args):
parser = argparse.ArgumentParser()
parser.add_argument('--show-values', '-s', action="store_true",
help="Mouse over vertices to show their values")
parser.add_argument('--coord_transform', '-v',
help="Shown vertices are modified by the transform "
"in this volume")
parser.add_argument('--combine-overlays', '-c', action="store_true",
help="Combine the values of all overlays into one")
parser.add_argument('--colormap', '-m',
help="File containing a colormap definition")
parser.add_argument('surface', nargs=1,
help="VTK, OFF, or FreeSurfer surface file to display")
parser.add_argument('overlays', nargs='*',
help="VTK, LAB, or FreeSurfer files to overlay")
return parser.parse_args(args)
if __name__ == "__main__":
SurfaceViewer(parse_args(sys.argv[1:])).show()
sys.exit(0)