-
Notifications
You must be signed in to change notification settings - Fork 0
/
DepthNetworkTracking.py
469 lines (389 loc) · 19 KB
/
DepthNetworkTracking.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
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
# -*- coding: utf-8 -*-
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import os
import sys
import json
import math
import imageio
import numpy as np
from subprocess import check_output
import bpy #Requires moving the /2.7.9 directory to where the slicer python exe is in order to properly install
prot_no = 0
class DepthNetworkTracking:
def __init__(self, parent):
parent.title = "Depth Network Tracking"
parent.categories = ["Utilities"]
parent.contributors = ["Franklin King"]
parent.helpText = """
Depth Network Tracking
"""
parent.acknowledgementText = """
"""
#icon
self.parent = parent
class DepthNetworkTrackingWidget:
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.RGB_Paths = []
self.Depth_Paths = []
self.counter = 0
self.surfaceRegistration = slicer.modules.surfaceregistration.widgetRepresentation().self()
def setup(self):
self.imagesDirectory = "D:/w/data/DepthNetworkData/5/"
self.initializeButton = qt.QPushButton("Initialize")
self.initializeButton.clicked.connect(self.Initialize)
self.layout.addWidget(self.initializeButton)
imagesCollapseButton = ctk.ctkCollapsibleButton()
imagesCollapseButton.text = "Images"
self.layout.addWidget(imagesCollapseButton)
imagesLayout = qt.QHBoxLayout(imagesCollapseButton)
self.depthMapImageView = qt.QLabel()
self.RGBImageView = qt.QLabel()
self.depthMapImageView.resize(200, 200)
self.RGBImageView.resize(200, 200)
imagesLayout.addWidget(self.depthMapImageView)
imagesLayout.addWidget(self.RGBImageView)
self.RGBImageView.setSizePolicy(qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.MinimumExpanding)
self.depthMapImageView.setSizePolicy(qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.MinimumExpanding)
self.imageNumber = qt.QLabel("-")
self.layout.addWidget(self.imageNumber)
controlsWidget = qt.QWidget()
self.layout.addWidget(controlsWidget)
forwardsBackwardsLayout = qt.QHBoxLayout(controlsWidget)
self.backwardsButton = qt.QPushButton("<")
self.backwardsButton.clicked.connect(self.Backwards)
forwardsBackwardsLayout.addWidget(self.backwardsButton)
self.forwardsButton = qt.QPushButton(">")
self.forwardsButton.clicked.connect(self.Forwards)
forwardsBackwardsLayout.addWidget(self.forwardsButton)
self.focalLengthBox = ctk.ctkDoubleSpinBox()
self.focalLengthBox.maximum = 100000.0
self.focalLengthBox.minimum = 0.0
self.focalLengthBox.setValue(200.0)
self.layout.addWidget(self.focalLengthBox)
self.depthDividerBox = ctk.ctkDoubleSpinBox()
self.depthDividerBox.setValue(2.5)
self.depthDividerBox.maximum = 100000.0
self.depthDividerBox.minimum = 0.0
self.layout.addWidget(self.depthDividerBox)
self.pointCloudButton = qt.QPushButton("Create and render point cloud")
self.pointCloudButton.clicked.connect(self.OnConvertToPointCloud)
self.layout.addWidget(self.pointCloudButton)
inputsWidget = qt.QWidget()
self.layout.addWidget(inputsWidget)
inputsLayout = qt.QFormLayout(inputsWidget)
self.baseModelSelector = slicer.qMRMLNodeComboBox()
self.baseModelSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.baseModelSelector.selectNodeUponCreation = False
self.baseModelSelector.addEnabled = False
self.baseModelSelector.removeEnabled = True
self.baseModelSelector.renameEnabled = True
self.baseModelSelector.noneEnabled = False
self.baseModelSelector.showHidden = False
self.baseModelSelector.showChildNodeTypes = False
self.baseModelSelector.setMRMLScene(slicer.mrmlScene)
inputsLayout.addRow("Base Model: ", self.baseModelSelector)
self.pointCloudSelector = slicer.qMRMLNodeComboBox()
self.pointCloudSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.pointCloudSelector.selectNodeUponCreation = True
self.pointCloudSelector.addEnabled = True
self.pointCloudSelector.removeEnabled = True
self.pointCloudSelector.renameEnabled = True
self.pointCloudSelector.noneEnabled = False
self.pointCloudSelector.showHidden = False
self.pointCloudSelector.showChildNodeTypes = False
self.pointCloudSelector.setMRMLScene(slicer.mrmlScene)
inputsLayout.addRow("Point Cloud Model: ", self.pointCloudSelector)
self.booleanModelSelector = slicer.qMRMLNodeComboBox()
self.booleanModelSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.booleanModelSelector.selectNodeUponCreation = True
self.booleanModelSelector.addEnabled = True
self.booleanModelSelector.removeEnabled = True
self.booleanModelSelector.renameEnabled = True
self.booleanModelSelector.noneEnabled = False
self.booleanModelSelector.showHidden = False
self.booleanModelSelector.showChildNodeTypes = False
self.booleanModelSelector.setMRMLScene(slicer.mrmlScene)
inputsLayout.addRow("Boolean Model: ", self.booleanModelSelector)
self.transientModelSelector = slicer.qMRMLNodeComboBox()
self.transientModelSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.transientModelSelector.selectNodeUponCreation = True
self.transientModelSelector.addEnabled = True
self.transientModelSelector.removeEnabled = True
self.transientModelSelector.renameEnabled = True
self.transientModelSelector.noneEnabled = False
self.transientModelSelector.showHidden = False
self.transientModelSelector.showChildNodeTypes = False
self.transientModelSelector.setMRMLScene(slicer.mrmlScene)
inputsLayout.addRow("Transient Model: ", self.transientModelSelector)
self.transientTransformSelector = slicer.qMRMLNodeComboBox()
self.transientTransformSelector.nodeTypes = ( ("vtkMRMLLinearTransformNode"), "" )
self.transientTransformSelector.selectNodeUponCreation = True
self.transientTransformSelector.addEnabled = True
self.transientTransformSelector.removeEnabled = True
self.transientTransformSelector.renameEnabled = True
self.transientTransformSelector.noneEnabled = False
self.transientTransformSelector.showHidden = False
self.transientTransformSelector.showChildNodeTypes = False
self.transientTransformSelector.setMRMLScene(slicer.mrmlScene)
inputsLayout.addRow("Transient Transform Node: ", self.transientTransformSelector)
self.transformSelector = slicer.qMRMLNodeComboBox()
self.transformSelector.nodeTypes = ( ("vtkMRMLLinearTransformNode"), "" )
self.transformSelector.selectNodeUponCreation = True
self.transformSelector.addEnabled = True
self.transformSelector.removeEnabled = True
self.transformSelector.renameEnabled = True
self.transformSelector.noneEnabled = False
self.transformSelector.showHidden = False
self.transformSelector.showChildNodeTypes = False
self.transformSelector.setMRMLScene(slicer.mrmlScene)
inputsLayout.addRow("Transform Node: ", self.transformSelector)
self.iterationsSpinBox = qt.QSpinBox()
self.iterationsSpinBox.setMaximum(50000)
self.iterationsSpinBox.setMinimum(100)
self.iterationsSpinBox.value = 1000
inputsLayout.addRow("Iterations: ", self.iterationsSpinBox)
self.landmarksSpinBox = qt.QSpinBox()
self.landmarksSpinBox.setMaximum(50000)
self.landmarksSpinBox.setMinimum(100)
self.landmarksSpinBox.value = 1000
inputsLayout.addRow("Landmarks: ", self.landmarksSpinBox)
self.booleanCheckBox = qt.QCheckBox()
self.booleanCheckBox.setChecked(False)
inputsLayout.addRow("Use boolean: ", self.booleanCheckBox)
self.registerButton = qt.QPushButton("Create, render, and register point cloud")
self.registerButton.clicked.connect(self.OnRegister)
self.layout.addWidget(self.registerButton)
spacer = qt.QSpacerItem(1, 14, qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
#self.layout.addItem(spacer)
def Initialize(self):
self.RGB_Paths = []
self.Depth_Paths = []
self.counter = 0
for r,d,f in os.walk(self.imagesDirectory):
for file in f:
if file.startswith('brdf'):
self.RGB_Paths.append(os.path.join(r,file))
if file.startswith('depth'):
self.Depth_Paths.append(os.path.join(r,file))
self.UpdateImages()
def Backwards(self):
if (self.counter > 0):
self.counter = self.counter-1
self.UpdateImages()
def Forwards(self):
self.counter = self.counter+1
self.UpdateImages()
self.OnRegister()
def OnConvertToPointCloud(self):
pointCloudNode = self.DepthMapToPointCloud(self.Depth_Paths[self.counter], self.RGB_Paths[self.counter])
# Permanently apply the transform to the point cloud first so that the ICP registration doesn't fall into a local minimum/maximum
pointCloudNode.SetAndObserveTransformNodeID(self.transformSelector.currentNodeID)
pointCloudNode.HardenTransform()
def UpdateImages(self):
pixmap = qt.QPixmap(self.RGB_Paths[self.counter])
self.RGBImageView.setPixmap(pixmap.scaled(self.RGBImageView.size))
pixmap = qt.QPixmap(self.Depth_Paths[self.counter])
self.depthMapImageView.setPixmap(pixmap.scaled(self.depthMapImageView.size))
self.imageNumber.setText(str(self.counter))
def OnRegister(self):
self.OnConvertToPointCloud()
if self.booleanCheckBox.isChecked():
self.IntersectBaseModel()
self.RegisterToBaseModel()
def IntersectBaseModel(self):
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
self.transformSelector.currentNode().GetMatrixTransformToParent(matrix)
transform.SetMatrix(matrix)
#transform.RotateX(-90.0)
# cylinder = vtk.vtkCylinderSource()
# cylinder.SetCenter(np.array([0.0, 0.0, 0.0]))
# cylinder.SetRadius(25)
# cylinder.SetHeight(60)
# cylinder.SetResolution(100)
# cylinder.Update()
originalCylinder_path = os.path.dirname(os.path.realpath(__file__)) + "\\Models\\OriginalCylinder.stl"
originalCylinderModelNode = slicer.util.loadModel(originalCylinder_path)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputData(originalCylinderModelNode.GetPolyData())
transformFilter.SetTransform(transform)
transformFilter.ReleaseDataFlagOn()
transformFilter.Update()
modelNode = self.booleanModelSelector.currentNode()
modelNode.SetAndObservePolyData(transformFilter.GetOutput())
modelDisplayNode = modelNode.GetModelDisplayNode()
if modelDisplayNode is None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode)
modelNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
modelDisplayNode.SetOpacity(0.2)
modelDisplayNode.SetColor(0,1,0)
modelNode2 = self.transientModelSelector.currentNode()
modelDisplayNode2 = self.transientModelSelector.currentNode().GetModelDisplayNode()
if modelDisplayNode2 is None:
modelDisplayNode2 = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode2.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode2)
modelNode2.SetAndObserveDisplayNodeID(modelDisplayNode2.GetID())
modelDisplayNode2.SetOpacity(1.0)
modelDisplayNode2.SetColor(0,1,0)
cylinder_path = os.path.dirname(os.path.realpath(__file__)) + "\\Models\\cylinder.stl"
slicer.util.saveNode(modelNode, cylinder_path)
slicer.mrmlScene.RemoveNode(originalCylinderModelNode)
self.blenderBoolean()
def blenderBoolean(self):
bpy.ops.wm.read_factory_settings()
for scene in bpy.data.scenes:
for obj in scene.objects:
scene.objects.unlink(obj)
# only worry about data in the startup scene
for bpy_data_iter in (bpy.data.objects, bpy.data.meshes, bpy.data.lamps, bpy.data.cameras):
for id_data in bpy_data_iter:
bpy_data_iter.remove(id_data)
dir_path = os.path.dirname(os.path.realpath(__file__)) + "\\Models\\"
#dir_path = "D:\\w\\s\\DepthNetworkTracking\\Model\\"
airwayPath = dir_path + "airwayNoWall.stl"
cylinderPath = dir_path + "cylinder.stl"
bpy.ops.import_mesh.stl(filepath=airwayPath)
bpy.ops.import_mesh.stl(filepath=cylinderPath)
objects = bpy.data.objects
airwayNoWall = objects['airwayNoWall']
cylinder = objects['Cylinder']
airwayBoolean = airwayNoWall.modifiers.new(type="BOOLEAN", name="bool_7")
airwayBoolean.object = cylinder
airwayBoolean.operation = 'INTERSECT'
cylinder.hide = True
bpy.context.scene.objects.active = bpy.data.objects['airwayNoWall']
bpy.ops.object.modifier_apply(apply_as='DATA', modifier=airwayBoolean.name)
airwayNoWall.select = False
cylinder.select = True
bpy.ops.object.delete()
airwayNoWall.select = True
airwayIsolatedPath = dir_path + "airwayIsolated.stl"
bpy.ops.export_mesh.stl(filepath=airwayIsolatedPath)
outputModelPath = dir_path + "airwayIsolated.STL"
outputModelNode = slicer.util.loadModel(outputModelPath)
modelNode2 = self.transientModelSelector.currentNode()
modelDisplayNode2 = self.transientModelSelector.currentNode().GetModelDisplayNode()
if modelDisplayNode2 is None:
modelDisplayNode2 = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode2.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode2)
modelNode2.SetAndObserveDisplayNodeID(modelDisplayNode2.GetID())
modelDisplayNode2.SetOpacity(0.7)
modelDisplayNode2.SetColor(0,1,0)
modelNode2.SetAndObservePolyData(outputModelNode.GetPolyData())
slicer.mrmlScene.RemoveNode(outputModelNode)
def RegisterToBaseModel(self):
# ICP Registration
if self.booleanCheckBox.isChecked():
self.surfaceRegistration.inputFixedModelSelector.currentNodeID = self.transientModelSelector.currentNodeID
else:
self.surfaceRegistration.inputFixedModelSelector.currentNodeID = self.baseModelSelector.currentNodeID
self.surfaceRegistration.inputMovingModelSelector.currentNodeID = self.pointCloudSelector.currentNodeID
self.surfaceRegistration.outputTransformSelector.currentNodeID = self.transientTransformSelector.currentNodeID
#self.surfaceRegistration.landmarkTransformTypeButtonsSimilarity.checked = True
self.surfaceRegistration.numberOfIterations.setValue(self.iterationsSpinBox.value)
self.surfaceRegistration.numberOfLandmarks.setValue(self.landmarksSpinBox.value)
self.surfaceRegistration.onComputeButton()
# Add transient transform to total transform
transientMatrix = vtk.vtkMatrix4x4()
matrix = vtk.vtkMatrix4x4()
resultMatrix = vtk.vtkMatrix4x4()
self.transformSelector.currentNode().GetMatrixTransformToParent(matrix)
self.transientTransformSelector.currentNode().GetMatrixTransformToParent(transientMatrix)
vtk.vtkMatrix4x4.Multiply4x4(transientMatrix, matrix, resultMatrix)
self.transformSelector.currentNode().SetMatrixTransformToParent(resultMatrix)
def DepthMapToPointCloud(self, depthmapFilename, rgbFilename):
# Create point cloud
depthImage = imageio.imread(depthmapFilename)
rgbImage = imageio.imread(rgbFilename)
height = len(depthImage)
width = len(depthImage[0])
minimumDepth = np.amin(depthImage)
maximumDepth = np.amax(depthImage)
print(maximumDepth)
points = vtk.vtkPoints()
fx_d = self.focalLengthBox.value
fy_d = self.focalLengthBox.value
for u in range(height):
for v in range(width):
vflipped = width - (v + 1)
z = depthImage[u][vflipped]
z = z[0] / self.depthDividerBox.value
if z < 60:
#if True:
points.InsertNextPoint(np.array([z * (u - (height/2)) / fx_d, z * (v - (width/2)) / fy_d, z]))
# Create junk polygons so that Slicer can actually display the point cloud
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
poly = vtk.vtkPolygon()
poly.GetPointIds().SetNumberOfIds(points.GetNumberOfPoints())
for n in range(points.GetNumberOfPoints()):
poly.GetPointIds().SetId(n, n)
polys = vtk.vtkCellArray()
polys.InsertNextCell(poly)
polydata.SetPolys(polys)
# Display the point cloud
modelNode = self.pointCloudSelector.currentNode()
modelNode.SetAndObservePolyData(polydata)
modelDisplayNode = modelNode.GetModelDisplayNode()
if modelDisplayNode is None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode)
modelNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
modelDisplayNode.SetRepresentation(modelDisplayNode.PointsRepresentation)
modelDisplayNode.SetPointSize(4)
modelDisplayNode.SetOpacity(0.2)
modelDisplayNode.SetColor(1,0,0)
return modelNode
def polydataBoolean(self, polyData1, polyData2, operation, triangleFilter=False, loop=False, clean=True):
# Subtract/add polyData2 from polyData1
if (not polyData1) or (not polyData2):
return polyData1
booleanFilter = vtk.vtkBooleanOperationPolyDataFilter()
if loop:
booleanFilter = vtk.vtkLoopBooleanPolyDataFilter()
if operation=="difference" or operation=="subtract":
booleanFilter.SetOperationToDifference()
elif operation=="union" or operation=="addition":
booleanFilter.SetOperationToUnion()
elif operation=="intersection":
booleanFilter.SetOperationToIntersection()
else:
return None
if triangleFilter:
triangleFilter1 = vtk.vtkTriangleFilter()
triangleFilter1.SetInputData(polyData1)
triangleFilter1.Update()
triangleFilter2 = vtk.vtkTriangleFilter()
triangleFilter2.SetInputData(polyData2)
triangleFilter2.Update()
booleanFilter.SetInputData(0, triangleFilter1.GetOutput())
booleanFilter.SetInputData(1, triangleFilter2.GetOutput())
else:
booleanFilter.SetInputData(0, polyData1)
booleanFilter.SetInputData(1, polyData2)
booleanFilter.Update()
if clean:
cleanFilter = vtk.vtkCleanPolyData()
cleanFilter.SetInputData(booleanFilter.GetOutput())
cleanFilter.PointMergingOn()
cleanFilter.Update()
print("blah")
return cleanFilter.GetOutput()
else:
return booleanFilter.GetOutput()