def TestSection_2_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
# Use MRHead and Tinypatient for testing
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
mrVolumeNode = sampleDataLogic.downloadMRHead()
[tinyVolumeNode, tinySegmentationNode] = sampleDataLogic.downloadSample('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.GetSegmentation().SetMasterRepresentationName(binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), geometryStr)
slicer.mrmlScene.AddNode(segmentationNode)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0,0.0,1.0)
segment.AddRepresentation(binaryLabelmapReprName, segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData() # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0,3,24.5)
translationTransformMatrix.SetElement(1,3,24.5)
translationTransformMatrix.SetElement(2,3,11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (224.3439, 223.7890, -135.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(23,23,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(24.5, 24.5, 11.5), (261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter('Smoothing factor', '0.0')
self.assertTrue(tinySegmentationNode.GetSegmentation().CreateRepresentation(closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(closedSurfaceReprName)
tinySegmentationNode.Modified() # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy )
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -58.6623, -249.228),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0], [0.7071, -0.7071, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5221241)
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0]*3
center = [0]*3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = map(lambda x: x/2.0, xyz)
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-216.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def TestSection_03_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
binaryLabelmapReprName = slicer.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName(
)
closedSurfaceReprName = slicer.vtkSegmentationConverter.GetClosedSurfaceRepresentationName(
)
# Use MRHead and Tinypatient for testing
import SampleData
mrVolumeNode = SampleData.downloadSample("MRHead")
[tinyVolumeNode,
tinySegmentationNode] = SampleData.downloadSamples('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(
mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentationNode.GetSegmentation().SetMasterRepresentationName(
binaryLabelmapReprName)
geometryStr = slicer.vtkSegmentationConverter.SerializeImageGeometry(
mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
slicer.vtkSegmentationConverter.
GetReferenceImageGeometryParameterName(), geometryStr)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = slicer.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = slicer.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0, 0.0, 1.0)
segment.AddRepresentation(binaryLabelmapReprName,
segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = slicer.vtkOrientedImageData(
) # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0, 3, 24.5)
translationTransformMatrix.SetElement(1, 3, 24.5)
translationTransformMatrix.SetElement(2, 3, 11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(
translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(
translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (273.3439, 272.7890, -112.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (23, 23, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (24.5, 24.5, 11.5),
(261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter(
'Smoothing factor', '0.0')
self.assertTrue(
tinySegmentationNode.GetSegmentation().CreateRepresentation(
closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(
closedSurfaceReprName)
tinySegmentationNode.Modified(
) # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData,
(1, 1, 1),
(-86.645, 133.929,
116.786), # current origin of the segmentation is kept
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223040)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
outputFolderId = shNode.CreateFolderItem(shNode.GetSceneItemID(),
'ModelsFolder')
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModels(
tinySegmentationNode, outputFolderId)
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData,
(1, 1, 1),
(-86.645, 133.929,
116.786), # current origin of the segmentation is kept
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223040)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(
rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-86.645, 177.282, -12.122),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0],
[0.7071, -0.7071, 0.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5229164)
# ROI source
roiNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLAnnotationROINode", 'SourceROI')
xyz = [0.0, 0.0, 0.0]
center = [0.0, 0.0, 0.0]
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = [x / 2.0 for x in xyz]
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (0.0, 0.0, 0.0),
[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]))
slicer.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5224232)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def TestSection_2_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
# Use MRHead and Tinypatient for testing
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
mrVolumeNode = sampleDataLogic.downloadMRHead()
[tinyVolumeNode, tinySegmentationNode] = sampleDataLogic.downloadSample('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.GetSegmentation().SetMasterRepresentationName(binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), geometryStr)
slicer.mrmlScene.AddNode(segmentationNode)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0,0.0,1.0)
segment.AddRepresentation(binaryLabelmapReprName, segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData() # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with no transforms - OK')
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0,3,24.5)
translationTransformMatrix.SetElement(1,3,24.5)
translationTransformMatrix.SetElement(2,3,11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (224.3439, 223.7890, -135.25),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Transformed volume source - OK')
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(23,23,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with isotropic spacing - OK')
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(24.5, 24.5, 11.5), (261.0939, 260.5390, -129.5),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with oversampling - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Segmentation source with binary labelmap master - OK')
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter('Smoothing factor', '0.0')
self.assertTrue(tinySegmentationNode.GetSegmentation().CreateRepresentation(closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(closedSurfaceReprName)
tinySegmentationNode.Modified() # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
# Manually resample and check if the output is non-empty
# Note: This is done for all poly data based geometry calculations below
#TODO: Come up with proper geometry baselines for these too
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Segmentation source with closed surface master - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy )
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Model source with no transform - OK')
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Transformed model source - OK')
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0]*3
center = [0]*3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = map(lambda x: x/2.0, xyz)
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('ROI source - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')