def setupDisplayNode(self, displayNode=None, starBurst=False):
if not displayNode:
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
displayNode.SetTextScale(0)
displayNode.SetGlyphScale(2.5)
if starBurst:
displayNode.SetGlyphType(slicer.vtkMRMLAnnotationPointDisplayNode.StarBurst2D)
return displayNode
def setupDisplayNode(self, displayNode=None, starBurst=False):
if not displayNode:
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
displayNode.SetTextScale(0)
displayNode.SetGlyphScale(2.5)
if starBurst:
displayNode.SetGlyphType(slicer.vtkMRMLAnnotationPointDisplayNode.StarBurst2D)
return displayNode
def cloneFiducials(original, cloneName, keepDisplayNode=False):
clone = slicer.vtkMRMLMarkupsFiducialNode()
clone.Copy(original)
clone.SetName(cloneName)
slicer.mrmlScene.AddNode(clone)
if not keepDisplayNode:
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
clone.SetAndObserveDisplayNodeID(displayNode.GetID())
return clone
def cloneFiducials(original, cloneName, keepDisplayNode=False):
clone = slicer.vtkMRMLMarkupsFiducialNode()
clone.Copy(original)
clone.SetName(cloneName)
slicer.mrmlScene.AddNode(clone)
if not keepDisplayNode:
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
clone.SetAndObserveDisplayNodeID(displayNode.GetID())
return clone
def run(self, numToAdd=100, rOffset=0, usefewerModifyCalls=0):
"""
Run the actual algorithm
"""
print('Running test to add %s fidicuals' % (numToAdd, ))
print('Index\tTime to add fid\tDelta between adds')
print("%(index)04s\t" % {'index': "i"}, "t\tdt'")
r = rOffset
a = 0
s = 0
t1 = 0
t2 = 0
t3 = 0
t4 = 0
timeToAddThisFid = 0
timeToAddLastFid = 0
testStartTime = time.clock()
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
if usefewerModifyCalls == 1:
print("Start modify")
mod = fidNode.StartModify()
import random
# iterate over the number of fiducials to add
for i in range(numToAdd):
# print "i = ", i, "/", numToAdd, ", r = ", r, ", a = ", a, ", s = ", s
t1 = time.clock()
fidNode.AddFiducial(r, a, s)
t2 = time.clock()
timeToAddThisFid = t2 - t1
dt = timeToAddThisFid - timeToAddLastFid
#print '%(index)04d\t' % {'index': i}, timeToAddThisFid, "\t", dt
r = float(i) / numToAdd * 100.0 - 50.0 + random.uniform(
-20.0, 20.0)
a = float(i) / numToAdd * 100.0 - 50.0 + random.uniform(
-20.0, 20.0)
s = random.uniform(-20.0, 20.0)
timeToAddLastFid = timeToAddThisFid
if usefewerModifyCalls == 1:
fidNode.EndModify(mod)
testEndTime = time.clock()
testTime = testEndTime - testStartTime
print("Total time to add ", numToAdd, " = ", testTime)
return True
def run(self,numToAdd=100,rOffset=0,usefewerModifyCalls=0):
"""
Run the actual algorithm
"""
print('Running test to add %s fidicuals' % (numToAdd,))
print('Index\tTime to add fid\tDelta between adds')
print("%(index)04s\t" % {'index': "i"}, "t\tdt'")
r = rOffset
a = 0
s = 0
t1 = 0
t2 = 0
t3 = 0
t4 = 0
timeToAddThisFid = 0
timeToAddLastFid = 0
testStartTime = time.clock()
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
if usefewerModifyCalls == 1:
print("Start modify")
mod = fidNode.StartModify()
import random
# iterate over the number of fiducials to add
for i in range(numToAdd):
# print "i = ", i, "/", numToAdd, ", r = ", r, ", a = ", a, ", s = ", s
t1 = time.clock()
fidNode.AddFiducial(r,a,s)
t2 = time.clock()
timeToAddThisFid = t2 - t1
dt = timeToAddThisFid - timeToAddLastFid
#print '%(index)04d\t' % {'index': i}, timeToAddThisFid, "\t", dt
r = float(i)/numToAdd * 100.0 - 50.0 + random.uniform(-20.0, 20.0)
a = float(i)/numToAdd * 100.0 - 50.0 + random.uniform(-20.0, 20.0)
s = random.uniform(-20.0, 20.0)
timeToAddLastFid = timeToAddThisFid
if usefewerModifyCalls == 1:
fidNode.EndModify(mod)
testEndTime = time.clock()
testTime = testEndTime - testStartTime
print("Total time to add ",numToAdd," = ", testTime)
return True
def createNewMarkupNode(self):
# Create empty markup fiducial node
if self.segmentMarkupNode is None:
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
displayNode.SetTextScale(0)
slicer.mrmlScene.AddNode(displayNode)
self.segmentMarkupNode = slicer.vtkMRMLMarkupsFiducialNode()
self.segmentMarkupNode.SetName('C')
slicer.mrmlScene.AddNode(self.segmentMarkupNode)
self.segmentMarkupNode.SetAndObserveDisplayNodeID(
displayNode.GetID())
self.setAndObserveSegmentMarkupNode(self.segmentMarkupNode)
self.updateGUIFromMRML()
def onImageChanged2(self):
self.InputRegistrationTransformNodeX = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(self.InputRegistrationTransformNodeX)
if self.imageNode2 is not None:
self.imageNode2.SetAndObserveTransformNodeID(None)
self.imageNode2 = None
self.imageNode2 = self.imageSelector2.currentNode()
if self.imageNode2 is None:
print('Please select the right volume')
if self.imageNode2 is not None:
self.cropping = 1
self.imageNode2 = self.imageSelector2.currentNode()
self.clippingModel2 = slicer.vtkMRMLModelNode()
self.clippingModel.SetName('Clipping Model 2')
slicer.mrmlScene.AddNode(self.clippingModel2)
self.displayNode2 = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(self.displayNode2)
self.inputMarkup2 = slicer.vtkMRMLMarkupsFiducialNode()
self.inputMarkup2.SetName('C')
slicer.mrmlScene.AddNode(self.inputMarkup2)
self.inputMarkup2.SetAndObserveDisplayNodeID(self.displayNode2.GetID())
self.inputMarkup2.AddFiducial(234,509,-0.5)
self.inputMarkup2.AddFiducial(234,509,0.0)
self.inputMarkup2.AddFiducial(500,130,0)
self.inputMarkup2.AddFiducial(242,36,0)
self.inputMarkup2.AddFiducial(-26,162,0)
self.inputMarkup2.SetDisplayVisibility(0)
self.outputVolume2 = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(self.outputVolume2)
self.logic.updateModelFromMarkup(self.inputMarkup2,self.clippingModel2)
self.logic.clipVolumeWithModel(self.imageNode2, self.clippingModel2, True, 255, self.outputVolume2)
self.logic.showInSliceViewers(self.outputVolume2, ["Yellow"])
self.cropping == 0
self.rightMat.SetElement(0,0,0)
self.rightMat.SetElement(2,0,-1)
self.rightMat.SetElement(1,1,-1)
self.rightMat.SetElement(0,2,-1)
self.rightMat.SetElement(2,2,0)
self.rightMat.SetElement(1,3,520)
self.rightMat.SetElement(2,3,230)
self.rightTransform.PostMultiply()
self.rightTransform.Identity()
self.rightTransform.Concatenate(self.rightMat)
self.outputVolume2.GetDisplayNode().SetAutoWindowLevel(0)
self.outputVolume2.GetDisplayNode().SetWindowLevelMinMax(25,100)
self.yellowWidget.sliceLogic().GetSliceCompositeNode().SetBackgroundVolumeID(self.outputVolume2.GetID())
self.resliceLogic.SetDriverForSlice(self.outputVolume2.GetID(), slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeYellow'))
self.resliceLogic.SetModeForSlice(self.resliceLogic.MODE_TRANSVERSE, slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeYellow'))
self.clippingModel2.SetDisplayVisibility(False)
slicer.app.layoutManager().sliceWidget('Yellow').sliceLogic().GetSliceNode().SetSliceVisible(True)
slicer.app.layoutManager().sliceWidget("Yellow").sliceController().fitSliceToBackground()
self.outputVolume2.SetAndObserveTransformNodeID(self.InputRegistrationTransformNodeX.GetID())
self.InputRegistrationTransformNodeX.SetMatrixTransformToParent(self.rightTransform.GetMatrix())
if self.imageNode2 is None:
self.cropping = 1
self.imageNode2 = self.imageSelector2.currentNode()
self.clippingModel2 = slicer.vtkMRMLModelNode()
self.clippingModel.SetName('Clipping Model 2')
slicer.mrmlScene.AddNode(self.clippingModel2)
self.displayNode2 = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(self.displayNode2)
self.inputMarkup2 = slicer.vtkMRMLMarkupsFiducialNode()
self.inputMarkup2.SetName('C')
slicer.mrmlScene.AddNode(self.inputMarkup2)
self.inputMarkup2.SetAndObserveDisplayNodeID(self.displayNode2.GetID())
self.inputMarkup2.AddFiducial(234,509,-0.5)
self.inputMarkup2.AddFiducial(234,509,0.0)
self.inputMarkup2.AddFiducial(500,130,0)
self.inputMarkup2.AddFiducial(242,36,0)
self.inputMarkup2.AddFiducial(-26,162,0)
self.inputMarkup2.SetDisplayVisibility(0)
self.outputVolume2 = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(self.outputVolume2)
self.logic.updateModelFromMarkup(self.inputMarkup2,self.clippingModel2)
self.logic.clipVolumeWithModel(self.imageNode2, self.clippingModel2, True, 255, self.outputVolume2)
self.logic.showInSliceViewers(self.outputVolume2, ["Yellow"])
self.cropping = 0
self.rightMat.SetElement(0,0,0)
self.rightMat.SetElement(2,0,-1)
self.rightMat.SetElement(1,1,-1)
self.rightMat.SetElement(0,2,-1)
self.rightMat.SetElement(2,2,0)
self.rightMat.SetElement(1,3,520)
self.rightMat.SetElement(2,3,230)
self.rightTransform.PostMultiply()
self.rightTransform.Identity()
self.rightTransform.Concatenate(self.rightMat)
self.outputVolume2.GetDisplayNode().SetAutoWindowLevel(0)
self.outputVolume2.GetDisplayNode().SetWindowLevelMinMax(25,100)
self.yellowWidget.sliceLogic().GetSliceCompositeNode().SetBackgroundVolumeID(self.outputVolume2.GetID())
self.resliceLogic.SetDriverForSlice(self.outputVolume2.GetID(), slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeYellow'))
self.resliceLogic.SetModeForSlice(self.resliceLogic.MODE_TRANSVERSE, slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeYellow'))
self.clippingModel2.SetDisplayVisibility(False)
slicer.app.layoutManager().sliceWidget('Yellow').sliceLogic().GetSliceNode().SetSliceVisible(True)
slicer.app.layoutManager().sliceWidget("Yellow").sliceController().fitSliceToBackground()
self.outputVolume2.SetAndObserveTransformNodeID(self.InputRegistrationTransformNodeX.GetID())
self.InputRegistrationTransformNodeX.SetMatrixTransformToParent(self.rightTransform.GetMatrix())
def run(self):
"""
Run the actual algorithm
"""
print('Running test of the markups in different views')
#
# first load the data
#
print("Getting MR Head Volume")
import SampleData
mrHeadVolume = SampleData.downloadSample("MRHead")
#
# link the viewers
#
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# MR Head in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(mrHeadVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
#
# switch to conventional layout
#
lm = slicer.app.layoutManager()
lm.setLayout(2)
# create a fiducial list
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID(
"vtkMRMLSelectionNodeSingleton")
if (selectionNode is not None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
# add some known points to it
eye1 = [33.4975, 79.4042, -10.2143]
eye2 = [-31.283, 80.9652, -16.2143]
nose = [4.61944, 114.526, -33.2143]
index = fidNode.AddFiducialFromArray(eye1)
fidNode.SetNthFiducialLabel(index, "eye-1")
index = fidNode.AddFiducialFromArray(eye2)
fidNode.SetNthFiducialLabel(index, "eye-2")
# hide the second eye as a test of visibility flags
fidNode.SetNthFiducialVisibility(index, 0)
index = fidNode.AddFiducialFromArray(nose)
fidNode.SetNthFiducialLabel(index, "nose")
self.delayDisplay("Placed 3 fiducials")
# self.printViewAndSliceNodes()
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 0:
self.delayDisplay("Test failed: widget is not visible in view 1")
# self.printViewNodeIDs(displayNode)
return False
#
# switch to 2 3D views layout
#
lm.setLayout(15)
self.delayDisplay("Switched to 2 3D views")
# self.printViewAndSliceNodes()
if self.widgetVisible(fidNode,
'vtkMRMLViewNode1') == 0 or self.widgetVisible(
fidNode, 'vtkMRMLViewNode2') == 0:
self.delayDisplay(
"Test failed: widget is not visible in view 1 and 2")
# self.printViewNodeIDs(displayNode)
return False
#
# show only in view 2
#
displayNode.AddViewNodeID("vtkMRMLViewNode2")
self.delayDisplay("Showing only in view 2")
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 1:
self.delayDisplay(
"Test failed: widget is not supposed to be visible in view 1")
# self.printViewNodeIDs(displayNode)
return False
if self.widgetVisible(fidNode, 'vtkMRMLViewNode2') == 0:
self.delayDisplay("Test failed: widget is not visible in view 2")
# self.printViewNodeIDs(displayNode)
return False
#
# remove it so show in all
#
displayNode.RemoveAllViewNodeIDs()
self.delayDisplay("Showing in both views")
if self.widgetVisible(fidNode,
'vtkMRMLViewNode1') == 0 or self.widgetVisible(
fidNode, 'vtkMRMLViewNode2') == 0:
self.delayDisplay(
"Test failed: widget is not visible in view 1 and 2")
self.printViewNodeIDs(displayNode)
return False
#
# show only in view 1
#
displayNode.AddViewNodeID("vtkMRMLViewNode1")
self.delayDisplay("Showing only in view 1")
if self.widgetVisible(fidNode, 'vtkMRMLViewNode2') == 1:
self.delayDisplay(
"Test failed: widget is not supposed to be visible in view 2")
# self.printViewNodeIDs(displayNode)
return False
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 0:
self.delayDisplay("Test failed: widget is not visible in view 1")
# self.printViewNodeIDs(displayNode)
return False
# switch back to conventional
lm.setLayout(2)
self.delayDisplay("Switched back to conventional layout")
# self.printViewAndSliceNodes()
# test of the visibility in slice views
displayNode.RemoveAllViewNodeIDs()
# jump to the last fiducial
slicer.modules.markups.logic().JumpSlicesToNthPointInMarkup(
fidNode.GetID(), index, 1)
# refocus the 3D cameras as well
slicer.modules.markups.logic().FocusCamerasOnNthPointInMarkup(
fidNode.GetID(), index)
# show only in red
displayNode.AddViewNodeID('vtkMRMLSliceNodeRed')
self.delayDisplay("Show only in red slice")
if self.widgetVisibleOnSlice(fidNode, 'vtkMRMLSliceNodeRed') != 1:
self.delayDisplay("Test failed: widget not displayed on red slice")
# self.printViewNodeIDs(displayNode)
return False
# remove all, add green
# print 'before remove all, after added red'
# self.printViewNodeIDs(displayNode)
displayNode.RemoveAllViewNodeIDs()
# print 'after removed all'
# self.printViewNodeIDs(displayNode)
displayNode.AddViewNodeID('vtkMRMLSliceNodeGreen')
self.delayDisplay('Show only in green slice')
if self.widgetVisibleOnSlice(
fidNode,
'vtkMRMLSliceNodeRed') != 0 or self.widgetVisibleOnSlice(
fidNode, 'vtkMRMLSliceNodeGreen') != 1:
self.delayDisplay(
"Test failed: widget not displayed only on green slice")
print '\tred = ', self.widgetVisibleOnSlice(
fidNode, 'vtkMRMLSliceNodeRed')
print '\tgreen =', self.widgetVisibleOnSlice(
fidNode, 'vtkMRMLSliceNodeGreen')
self.printViewNodeIDs(displayNode)
return False
return True
def run(self,enableScreenshots=0,screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay('Running test of the Neurosurgical Planning tutorial')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule('Welcome')
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Welcome','Welcome module',-1)
else:
# otherwise show the sample data module
moduleSelector.selectModule('SampleData')
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume()
self.delayDisplay("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
self.takeScreenshot('NeurosurgicalPlanning-Loaded','Data loaded',-1)
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget("Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget != None:
popupWidget.pinPopup(1)
self.takeScreenshot('NeurosurgicalPlanning-Link','Link slice viewers',-1)
popupWidget.pinPopup(0)
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# baseline in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(baselineVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-Baseline','Baseline in background',-1)
#
# adjust window level on baseline
#
moduleSelector.selectModule('Volumes')
baselineDisplay = baselineVolume.GetDisplayNode()
baselineDisplay.SetAutoWindowLevel(0)
baselineDisplay.SetWindow(2600)
baselineDisplay.SetLevel(1206)
self.takeScreenshot('NeurosurgicalPlanning-WindowLevel','Set W/L on baseline',-1)
#
# switch to red slice only
#
lm.setLayout(6)
self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly','Set layout to Red Slice only',-1)
#
# segmentation of tumour
#
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, baselineVolume, baselineVolume.GetName() + '-label' )
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# editor module
#
moduleSelector.selectModule('Editor')
self.takeScreenshot('NeurosurgicalPlanning-Editor','Showing Editor Module',-1)
# set the slice offset so drawing is right
sliceNode = sliceLogic.GetSliceNode()
sliceOffset = 58.7
sliceNode.SetSliceOffset(sliceOffset)
#
# paint
#
parameterNode = EditUtil.getParameterNode()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.takeScreenshot('NeurosurgicalPlanning-Paint','Paint tool in Editor Module',-1)
#
# paint in cystic part of tumor, using converstion from RAS coords to
# avoid slice widget size differences
#
EditUtil.setLabel(293)
displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-11, 73, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-12, 85, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-13, 91, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-15, 78, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintCystic','Paint cystic part of tumor',-1)
#
# paint in solid part of tumor
#
EditUtil.setLabel(7)
displayCoords = self.rasToDisplay(-0.5 , 118.5, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-7.4 , 116, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintSolid','Paint solid part of tumor',-1)
#
# paint around the tumor
#
EditUtil.setLabel(295)
rMax = 25
rMin = -50
aMax = 145
aMin = 50
rasStep = 5
# draw the top and bottom
for r in range(rMin, rMax, rasStep):
displayCoords = self.rasToDisplay(r, aMin, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(r, aMax, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
# draw the left and right
for a in range(aMin, aMax, rasStep):
displayCoords = self.rasToDisplay(rMin, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(rMax, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintAround','Paint around tumor',-1)
#
# clean up after painting
#
paintTool.cleanup()
paintTool = None
#
# Grow cut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
self.takeScreenshot('NeurosurgicalPlanning-Growcut','Growcut',-1)
#
# Merge split volume
#
slicer.util.selectModule('Editor')
slicer.util.findChildren(text='Split Merge Volume')[0].clicked()
self.takeScreenshot('NeurosurgicalPlanning-SplitMerge','SplitMerge',-1)
#
# go to the data module
#
moduleSelector.selectModule('Data')
self.takeScreenshot('NeurosurgicalPlanning-SplitMergeData','SplitMerge results in Data',-1)
#
# Ventricles Segmentation
#
moduleSelector.selectModule('Editor')
#
# select the label volume with the area around the tumor
slicer.util.findChildren(name='PerStructureVolumesFrame')[0].collapsed = False
treeView = slicer.util.findChildren(name='StructuresView')[0]
selection = qt.QItemSelection()
# selecting the last split volume in the third row
row = 2
rowStart = treeView.model().index(row,0)
rowEnd = treeView.model().index(row,treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 3-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel295.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelOutside','Select outside region',-1)
#
# Threshold tool
#
slicer.modules.EditorWidget.toolsBox.selectEffect('ThresholdEffect')
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter('ThresholdEffect,min', str(1700))
slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
self.takeScreenshot('NeurosurgicalPlanning-Ventricles','Ventricles segmentation',-1)
#
# Save Islands
#
slicer.modules.EditorWidget.toolsBox.selectEffect('SaveIslandEffect')
saveIslandLogic = EditorLib.SaveIslandEffectLogic(sliceWidget.sliceLogic())
displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset)
xy = (displayCoords[0], displayCoords[1])
saveIslandLogic.saveIsland(xy)
self.takeScreenshot('NeurosurgicalPlanning-SaveIsland','Ventricles save island',-1)
#
# Merge and build
#
slicer.util.findChildren(text='Merge And Build')[0].clicked()
#
# switch to conventional layout
#
lm.setLayout(2)
self.takeScreenshot('NeurosurgicalPlanning-MergeAndBuild','Merged and built models',-1)
#
# Tractography label map seeding
#
#
# select label volume with label 293, in the second row
#
row = 1
rowStart = treeView.model().index(row,0)
rowEnd = treeView.model().index(row,treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 1-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel293.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelCystic','Select cystic region',-1)
#
# Dilate
#
slicer.modules.EditorWidget.toolsBox.selectEffect('DilateEffect')
EditUtil.setLabel(293)
self.takeScreenshot('NeurosurgicalPlanning-Dilate','Dilate tool',-1)
# tutorial says to click apply three times
for d in range (1,3):
print d
# slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked()
# slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
slicer.modules.EditorWidget.toolsBox.currentOption.onApply()
self.takeScreenshot('NeurosurgicalPlanning-Dilated','Dilated tumor',-1)
#
# Tractography Label Map Seeding module
#
moduleSelector.selectModule('TractographyLabelMapSeeding')
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeedingModule','Showing Tractography Label Seeding Module',-1)
tractographyLabelSeeding = slicer.modules.tractographylabelmapseeding
parameters = {}
parameters['InputVolume'] = dtiVolume.GetID()
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 1-label")
# VTK6 TODO - set 'InputROIPipelineInfo'
parameters['InputROI'] = baselinelabel293.GetID()
fibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fibers)
parameters['OutputFibers'] = fibers.GetID()
parameters['UseIndexSpace'] = 1
parameters['StoppingValue'] = 0.15
parameters['ROIlabel'] = 293
parameters['StoppingMode'] = 'FractionalAnisotropy'
# defaults
# parameters['ClTh'] = 0.3
# parameters['MinimumLength'] = 20
# parameters['MaximumLength'] = 800
# parameters['StoppingCurvature'] = 0.7
# parameters['IntegrationStepLength'] = 0.5
# parameters['SeedSpacing'] = 2
# and run it
slicer.cli.run(tractographyLabelSeeding, None, parameters)
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeeding','Showing Tractography Label Seeding Results',-1)
#
# tractography fiducial seeding
#
moduleSelector.selectModule('TractographyInteractiveSeeding')
self.takeScreenshot('NeurosurgicalPlanning-TIS','Showing Tractography Interactive Seeding Module',-1)
# DTI in background
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# DTI visible in 3D
sliceNode = sliceLogic.GetSliceNode()
sliceLogic.StartSliceNodeInteraction(128)
sliceNode.SetSliceVisible(1)
sliceLogic.EndSliceNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-TIS-DTI','DTI volume with Tractography Interactive Seeding Module',-1)
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName('F')
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
s = sliceOffset
fidNode.AddFiducial(r,a,s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if (selectionNode != None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
self.takeScreenshot('NeurosurgicalPlanning-TIS-Fid1','Fiducial in Tractography Interactive Seeding Module',-1)
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation()
wr.setDiffusionTensorVolumeNode(dtiVolume)
# create a fiber bundle
fiducialFibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fiducialFibers)
wr.setFiberBundleNode(fiducialFibers)
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
self.takeScreenshot('NeurosurgicalPlanning-TIS-Args','Tractography Interactive Seeding arguments',-1)
self.delayDisplay("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
self.delayDisplay(msg,250)
fidNode.SetNthFiducialPosition(0, r, y, s)
self.takeScreenshot('NeurosurgicalPlanning-TIS-Moved','Moved fiducial and did Tractography Interactive Seeding',-1)
return True
def run(self):
"""
Run the actual algorithm
"""
print('Running test of the markups in compare viewers')
#
# first load the data
#
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
#
# link the viewers
#
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# MR Head in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(mrHeadVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
#
# switch to conventional layout
#
lm = slicer.app.layoutManager()
lm.setLayout(2)
# create a fiducial list
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID(
"vtkMRMLSelectionNodeSingleton")
if (selectionNode is not None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
# add some known points to it
eye1 = [33.4975, 79.4042, -10.2143]
eye2 = [-31.283, 80.9652, -16.2143]
nose = [4.61944, 114.526, -33.2143]
index = fidNode.AddFiducialFromArray(eye1)
fidNode.SetNthFiducialLabel(index, "eye-1")
index = fidNode.AddFiducialFromArray(eye2)
fidNode.SetNthFiducialLabel(index, "eye-2")
index = fidNode.AddFiducialFromArray(nose)
fidNode.SetNthFiducialLabel(index, "nose")
self.logicDelayDisplay("Placed 3 fiducials")
#
# switch to 2 viewers compare layout
#
lm.setLayout(12)
self.logicDelayDisplay("Switched to Compare 2 viewers")
#
# get compare slice composite node
#
compareLogic1 = slicer.app.layoutManager().sliceWidget(
'Compare1').sliceLogic()
compareCompositeNode1 = compareLogic1.GetSliceCompositeNode()
# set MRHead in the background
compareLogic1.StartSliceCompositeNodeInteraction(1)
compareCompositeNode1.SetBackgroundVolumeID(mrHeadVolume.GetID())
compareLogic1.EndSliceCompositeNodeInteraction()
compareLogic1.FitSliceToAll()
# make it visible in 3D
compareLogic1.GetSliceNode().SetSliceVisible(1)
# scroll to a fiducial location
compareLogic1.StartSliceOffsetInteraction()
compareLogic1.SetSliceOffset(eye1[2])
compareLogic1.EndSliceOffsetInteraction()
self.logicDelayDisplay("MH Head in background, scrolled to a fiducial")
# scroll around through the range of points
offset = nose[2]
while offset < eye1[2]:
compareLogic1.StartSliceOffsetInteraction()
compareLogic1.SetSliceOffset(offset)
compareLogic1.EndSliceOffsetInteraction()
msg = "Scrolled to " + str(offset)
self.logicDelayDisplay(msg, 250)
offset += 1.0
# switch back to conventional
lm.setLayout(2)
self.logicDelayDisplay("Switched back to conventional layout")
# switch to compare grid
lm.setLayout(23)
compareLogic1.FitSliceToAll()
self.logicDelayDisplay("Switched to Compare grid")
# switch back to conventional
lm.setLayout(2)
self.logicDelayDisplay("Switched back to conventional layout")
return True
def visualizeNewSrep(self, filename):
""" Parse header.xml file, create models from the data, and visualize it. """
# 1. parse header file
tree = ET.parse(filename)
upFileName = ''
crestFileName = ''
downFileName = ''
nCols = 0
nRows = 0
headerFolder = os.path.dirname(filename)
for child in tree.getroot():
if child.tag == 'upSpoke':
if os.path.isabs(child.text):
upFileName = os.path.join(headerFolder, child.text)
upFileName = os.path.join(headerFolder, child.text)
elif child.tag == 'downSpoke':
downFileName = os.path.join(headerFolder, child.text)
elif child.tag == 'crestSpoke':
crestFileName = os.path.join(headerFolder, child.text)
elif child.tag == 'nRows':
nRows = (int)(child.text)
elif child.tag == 'nCols':
nCols = (int)(child.text)
logging.info("upSpoke file: " + upFileName)
logging.info("downSpoke file: " + downFileName)
logging.info("crestSpoke file: " + crestFileName)
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(upFileName)
reader.Update()
upSpokes = reader.GetOutput()
upPointData = upSpokes.GetPointData()
numberOfArrays = upPointData.GetNumberOfArrays()
if numberOfArrays is 0:
logging.warning("File: " + upFileName + " does not contain data")
# medial_polyData = upSpokes # this is poly data for skeleton
scene = slicer.mrmlScene
# base line of medial sheet
fidDisplayNode = slicer.vtkMRMLMarkupsDisplayNode()
scene.AddNode(fidDisplayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
# If we would have more than 100 fiducial points (meant for editing points) better to use a regular MRMLModelNode
# In the future, we would like the user to be able to move the nodes, and the connected structures to update accordingly.
# Meanwhile, we lock the moving.
fidNode.SetLocked(True)
fidDisplayNode.SetGlyphScale(0.01)
fidDisplayNode.SetSelectedColor(1.0, 1.0, 0.0)
fidDisplayNode.SetTextScale(0.0)
scene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(fidDisplayNode.GetID())
# \TODO come up with better name later
# prepare for arrows for upspokes
upSpoke_points = vtk.vtkPoints()
upSpoke_lines = vtk.vtkCellArray()
arr_length = upPointData.GetArray('spokeLength')
arr_dirs = upPointData.GetArray('spokeDirection')
for i in range(upSpokes.GetNumberOfPoints()):
pt = [0] * 3
upSpokes.GetPoint(i, pt)
# base point of up arrows
id0 = upSpoke_points.InsertNextPoint(pt)
# head of up arrows
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt1 = [0] * 3
pt1[0] = pt[0] + spoke_length * dirX
pt1[1] = pt[1] + spoke_length * dirY
pt1[2] = pt[2] + spoke_length * dirZ
id1 = upSpoke_points.InsertNextPoint(pt1)
up_arrow = vtk.vtkLine()
up_arrow.GetPointIds().SetId(0, id0)
up_arrow.GetPointIds().SetId(1, id1)
upSpoke_lines.InsertNextCell(up_arrow)
fidNode.AddFiducial(pt[0], pt[1], pt[2])
# boundary_point_ids = []
# model node for medial mesh
medial_model = slicer.vtkMRMLModelNode()
medial_model.SetScene(scene)
medial_model.SetName("Medial Mesh")
medial_model.SetAndObservePolyData(reader.GetOutput())
# model display node for the medial mesh
medial_model_display = slicer.vtkMRMLModelDisplayNode()
medial_model_display.SetColor(0, 0.5, 0)
medial_model_display.SetScene(scene)
medial_model_display.SetLineWidth(3.0)
medial_model_display.SetRepresentation(1)
medial_model_display.SetBackfaceCulling(0)
scene.AddNode(medial_model_display)
medial_model.SetAndObserveDisplayNodeID(medial_model_display.GetID())
scene.AddNode(medial_model)
# model node for up spoke (poly data for arrows)
upSpoke_polyData = vtk.vtkPolyData()
upSpoke_polyData.SetPoints(upSpoke_points)
upSpoke_polyData.SetLines(upSpoke_lines)
upSpoke_model = slicer.vtkMRMLModelNode()
upSpoke_model.SetScene(scene)
upSpoke_model.SetName("Top Spoke")
upSpoke_model.SetAndObservePolyData(upSpoke_polyData)
# model display node for the top spoke
# cyan for the top spoke
upSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
upSpoke_model_display.SetColor(0, 1, 1)
upSpoke_model_display.SetScene(scene)
upSpoke_model_display.SetLineWidth(3.0)
upSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(upSpoke_model_display)
upSpoke_model.SetAndObserveDisplayNodeID(upSpoke_model_display.GetID())
scene.AddNode(upSpoke_model)
# prepare for down spokes
reader.SetFileName(downFileName)
reader.Update()
downSpokes = reader.GetOutput()
downSpoke_polyData = vtk.vtkPolyData()
downSpoke_lines = vtk.vtkCellArray()
downSpoke_points = vtk.vtkPoints()
downPointData = downSpokes.GetPointData()
arr_length = downPointData.GetArray('spokeLength')
arr_dirs = downPointData.GetArray('spokeDirection')
for i in range(downSpokes.GetNumberOfPoints()):
# tail of arrows
pt_tail = [0] * 3
downSpokes.GetPoint(i, pt_tail)
id0 = downSpoke_points.InsertNextPoint(pt_tail)
# head of arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = downSpoke_points.InsertNextPoint(pt_head)
# connection between head and tail
con = vtk.vtkLine()
con.GetPointIds().SetId(0, id0)
con.GetPointIds().SetId(1, id1)
downSpoke_lines.InsertNextCell(con)
downSpoke_polyData.SetPoints(downSpoke_points)
downSpoke_polyData.SetLines(downSpoke_lines)
downSpoke_model = slicer.vtkMRMLModelNode()
downSpoke_model.SetScene(scene)
downSpoke_model.SetName("Bottom Spoke")
downSpoke_model.SetAndObservePolyData(downSpoke_polyData)
# model display node for the down spoke
downSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
downSpoke_model_display.SetColor(1, 0, 1)
downSpoke_model_display.SetScene(scene)
downSpoke_model_display.SetLineWidth(3.0)
downSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(downSpoke_model_display)
downSpoke_model.SetAndObserveDisplayNodeID(
downSpoke_model_display.GetID())
scene.AddNode(downSpoke_model)
# crest spoke
new_reader = vtk.vtkXMLPolyDataReader()
new_reader.SetFileName(crestFileName)
new_reader.Update()
foldCurve_polyData = new_reader.GetOutput()
foldPointData = foldCurve_polyData.GetPointData()
arr_length = foldPointData.GetArray('spokeLength')
arr_dirs = foldPointData.GetArray('spokeDirection')
crest_arrows_polydata = vtk.vtkPolyData()
crest_arrows_points = vtk.vtkPoints()
crest_arrows_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
# tail of crest arrows
pt_tail = [0] * 3
foldCurve_polyData.GetPoint(i, pt_tail)
id0 = crest_arrows_points.InsertNextPoint(pt_tail)
# head of crest arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = crest_arrows_points.InsertNextPoint(pt_head)
crest_line = vtk.vtkLine()
crest_line.GetPointIds().SetId(0, id0)
crest_line.GetPointIds().SetId(1, id1)
crest_arrows_lines.InsertNextCell(crest_line)
crest_arrows_polydata.SetPoints(crest_arrows_points)
crest_arrows_polydata.SetLines(crest_arrows_lines)
# show crest arrows
crestSpoke_model = slicer.vtkMRMLModelNode()
crestSpoke_model.SetScene(scene)
crestSpoke_model.SetName("Crest Spoke")
crestSpoke_model.SetAndObservePolyData(crest_arrows_polydata)
# model display node
crestSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
crestSpoke_model_display.SetColor(1, 1, 0)
crestSpoke_model_display.SetScene(scene)
crestSpoke_model_display.SetLineWidth(3.0)
crestSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(crestSpoke_model_display)
crestSpoke_model.SetAndObserveDisplayNodeID(
crestSpoke_model_display.GetID())
scene.AddNode(crestSpoke_model)
# show fold curve
foldCurve_model = slicer.vtkMRMLModelNode()
foldCurve_model.SetScene(scene)
foldCurve_model.SetName("Fold Curve")
foldCurve_model.SetAndObservePolyData(foldCurve_polyData)
# model display node
foldCurve_model_display = slicer.vtkMRMLModelDisplayNode()
foldCurve_model_display.SetColor(1, 1, 0)
foldCurve_model_display.SetScene(scene)
foldCurve_model_display.SetLineWidth(3.0)
foldCurve_model_display.SetBackfaceCulling(0)
scene.AddNode(foldCurve_model_display)
foldCurve_model.SetAndObserveDisplayNodeID(
foldCurve_model_display.GetID())
scene.AddNode(foldCurve_model)
# show connections to fold curve point from nearby interior points
# compute the nearest interior point
connection_polydata = vtk.vtkPolyData()
connection_points = vtk.vtkPoints()
connection_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
min_dist = 100000.0
nearest_index = 0
pt_fold = [0] * 3
foldCurve_polyData.GetPoint(i, pt_fold)
id0 = connection_points.InsertNextPoint(pt_fold)
for j in range(upSpokes.GetNumberOfPoints()):
pt_interior = [0] * 3
upSpokes.GetPoint(j, pt_interior)
dist = self.distance(pt_fold, pt_interior)
if dist < min_dist:
min_dist = dist
nearest_index = j
pt_nearest_interior = upSpokes.GetPoint(nearest_index)
id1 = connection_points.InsertNextPoint(pt_nearest_interior)
line = vtk.vtkLine()
line.GetPointIds().SetId(0, id0)
line.GetPointIds().SetId(1, id1)
connection_lines.InsertNextCell(line)
connection_polydata.SetPoints(connection_points)
connection_polydata.SetLines(connection_lines)
connection_model = slicer.vtkMRMLModelNode()
connection_model.SetScene(scene)
connection_model.SetName("Connection to Fold Curve")
connection_model.SetAndObservePolyData(connection_polydata)
# model display node
connection_model_display = slicer.vtkMRMLModelDisplayNode()
connection_model_display.SetColor(0, 0, 0)
connection_model_display.SetScene(scene)
connection_model_display.SetLineWidth(3.0)
connection_model_display.SetBackfaceCulling(0)
scene.AddNode(connection_model_display)
connection_model.SetAndObserveDisplayNodeID(
connection_model_display.GetID())
scene.AddNode(connection_model)
def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay(
'Running test of the Neurosurgical Planning tutorial')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule('Welcome')
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Welcome',
'Welcome module', -1)
else:
# otherwise show the sample data module
moduleSelector.selectModule('SampleData')
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume(
)
self.delayDisplay("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
self.takeScreenshot('NeurosurgicalPlanning-Loaded', 'Data loaded', -1)
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget(
"Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget != None:
popupWidget.pinPopup(1)
self.takeScreenshot('NeurosurgicalPlanning-Link',
'Link slice viewers', -1)
popupWidget.pinPopup(0)
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# baseline in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(baselineVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-Baseline',
'Baseline in background', -1)
#
# adjust window level on baseline
#
moduleSelector.selectModule('Volumes')
baselineDisplay = baselineVolume.GetDisplayNode()
baselineDisplay.SetAutoWindowLevel(0)
baselineDisplay.SetWindow(2600)
baselineDisplay.SetLevel(1206)
self.takeScreenshot('NeurosurgicalPlanning-WindowLevel',
'Set W/L on baseline', -1)
#
# switch to red slice only
#
lm.setLayout(6)
self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly',
'Set layout to Red Slice only', -1)
#
# segmentation of tumour
#
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, baselineVolume,
baselineVolume.GetName() + '-label')
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# editor module
#
moduleSelector.selectModule('Editor')
self.takeScreenshot('NeurosurgicalPlanning-Editor',
'Showing Editor Module', -1)
# set the slice offset so drawing is right
sliceNode = sliceLogic.GetSliceNode()
sliceOffset = 58.7
sliceNode.SetSliceOffset(sliceOffset)
#
# paint
#
parameterNode = EditUtil.getParameterNode()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.takeScreenshot('NeurosurgicalPlanning-Paint',
'Paint tool in Editor Module', -1)
#
# paint in cystic part of tumor, using converstion from RAS coords to
# avoid slice widget size differences
#
EditUtil.setLabel(293)
displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-11, 73, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-12, 85, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-13, 91, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-15, 78, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintCystic',
'Paint cystic part of tumor', -1)
#
# paint in solid part of tumor
#
EditUtil.setLabel(7)
displayCoords = self.rasToDisplay(-0.5, 118.5, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-7.4, 116, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintSolid',
'Paint solid part of tumor', -1)
#
# paint around the tumor
#
EditUtil.setLabel(295)
rMax = 25
rMin = -50
aMax = 145
aMin = 50
rasStep = 5
# draw the top and bottom
for r in range(rMin, rMax, rasStep):
displayCoords = self.rasToDisplay(r, aMin, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(r, aMax, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
# draw the left and right
for a in range(aMin, aMax, rasStep):
displayCoords = self.rasToDisplay(rMin, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(rMax, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintAround',
'Paint around tumor', -1)
#
# clean up after painting
#
paintTool.cleanup()
paintTool = None
#
# Grow cut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
self.takeScreenshot('NeurosurgicalPlanning-Growcut', 'Growcut', -1)
#
# Merge split volume
#
slicer.util.selectModule('Editor')
slicer.util.findChildren(text='Split Merge Volume')[0].clicked()
self.takeScreenshot('NeurosurgicalPlanning-SplitMerge', 'SplitMerge',
-1)
#
# go to the data module
#
moduleSelector.selectModule('Data')
self.takeScreenshot('NeurosurgicalPlanning-SplitMergeData',
'SplitMerge results in Data', -1)
#
# Ventricles Segmentation
#
moduleSelector.selectModule('Editor')
#
# select the label volume with the area around the tumor
slicer.util.findChildren(
name='PerStructureVolumesFrame')[0].collapsed = False
treeView = slicer.util.findChildren(name='StructuresView')[0]
selection = qt.QItemSelection()
# selecting the last split volume in the third row
row = 2
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row,
treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 3-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel295.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelOutside',
'Select outside region', -1)
#
# Threshold tool
#
slicer.modules.EditorWidget.toolsBox.selectEffect('ThresholdEffect')
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter('ThresholdEffect,min', str(1700))
slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
self.takeScreenshot('NeurosurgicalPlanning-Ventricles',
'Ventricles segmentation', -1)
#
# Save Islands
#
slicer.modules.EditorWidget.toolsBox.selectEffect('SaveIslandEffect')
saveIslandLogic = EditorLib.SaveIslandEffectLogic(
sliceWidget.sliceLogic())
displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset)
xy = (displayCoords[0], displayCoords[1])
saveIslandLogic.saveIsland(xy)
self.takeScreenshot('NeurosurgicalPlanning-SaveIsland',
'Ventricles save island', -1)
#
# Merge and build
#
slicer.util.findChildren(text='Merge And Build')[0].clicked()
#
# switch to conventional layout
#
lm.setLayout(2)
self.takeScreenshot('NeurosurgicalPlanning-MergeAndBuild',
'Merged and built models', -1)
#
# Tractography label map seeding
#
#
# select label volume with label 293, in the second row
#
row = 1
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row,
treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 1-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel293.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelCystic',
'Select cystic region', -1)
#
# Dilate
#
slicer.modules.EditorWidget.toolsBox.selectEffect('DilateEffect')
EditUtil.setLabel(293)
self.takeScreenshot('NeurosurgicalPlanning-Dilate', 'Dilate tool', -1)
# tutorial says to click apply three times
for d in range(1, 3):
print d
# slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked()
# slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
slicer.modules.EditorWidget.toolsBox.currentOption.onApply()
self.takeScreenshot('NeurosurgicalPlanning-Dilated', 'Dilated tumor',
-1)
#
# Tractography Label Map Seeding module
#
moduleSelector.selectModule('TractographyLabelMapSeeding')
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeedingModule',
'Showing Tractography Label Seeding Module', -1)
tractographyLabelSeeding = slicer.modules.tractographylabelmapseeding
parameters = {}
parameters['InputVolume'] = dtiVolume.GetID()
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 1-label")
# VTK6 TODO - set 'InputROIPipelineInfo'
parameters['InputROI'] = baselinelabel293.GetID()
fibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fibers)
parameters['OutputFibers'] = fibers.GetID()
parameters['UseIndexSpace'] = 1
parameters['StoppingValue'] = 0.15
parameters['ROIlabel'] = 293
parameters['StoppingMode'] = 'FractionalAnisotropy'
# defaults
# parameters['ClTh'] = 0.3
# parameters['MinimumLength'] = 20
# parameters['MaximumLength'] = 800
# parameters['StoppingCurvature'] = 0.7
# parameters['IntegrationStepLength'] = 0.5
# parameters['SeedSpacing'] = 2
# and run it
slicer.cli.run(tractographyLabelSeeding, None, parameters)
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeeding',
'Showing Tractography Label Seeding Results', -1)
#
# tractography fiducial seeding
#
moduleSelector.selectModule('TractographyInteractiveSeeding')
self.takeScreenshot('NeurosurgicalPlanning-TIS',
'Showing Tractography Interactive Seeding Module',
-1)
# DTI in background
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# DTI visible in 3D
sliceNode = sliceLogic.GetSliceNode()
sliceLogic.StartSliceNodeInteraction(128)
sliceNode.SetSliceVisible(1)
sliceLogic.EndSliceNodeInteraction()
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-DTI',
'DTI volume with Tractography Interactive Seeding Module', -1)
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName('F')
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
s = sliceOffset
fidNode.AddFiducial(r, a, s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID(
"vtkMRMLSelectionNodeSingleton")
if (selectionNode != None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-Fid1',
'Fiducial in Tractography Interactive Seeding Module', -1)
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation(
)
wr.setDiffusionTensorVolumeNode(dtiVolume)
# create a fiber bundle
fiducialFibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fiducialFibers)
wr.setFiberBundleNode(fiducialFibers)
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
self.takeScreenshot('NeurosurgicalPlanning-TIS-Args',
'Tractography Interactive Seeding arguments', -1)
self.delayDisplay("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
self.delayDisplay(msg, 250)
fidNode.SetNthFiducialPosition(0, r, y, s)
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-Moved',
'Moved fiducial and did Tractography Interactive Seeding', -1)
return True
def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay("Running test of the Neurosurgical Planning tutorial")
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule("Welcome")
self.delayDisplay("Screenshot")
self.takeScreenshot("NeurosurgicalPlanning-Welcome", "Welcome module", -1)
else:
# otherwise show the sample data module
moduleSelector.selectModule("SampleData")
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume()
self.delayDisplay("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
self.takeScreenshot("NeurosurgicalPlanning-Loaded", "Data loaded", -1)
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, baselineVolume, baselineVolume.GetName() + "-label"
)
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
data = slicer.util.array(baselineVolume.GetName() + "-label")
data[6:15, 110:140, 130:160] = 293
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget("Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget is not None:
popupWidget.pinPopup(1)
self.takeScreenshot("NeurosurgicalPlanning-Link", "Link slice viewers", -1)
popupWidget.pinPopup(0)
#
# Tractography Label Map Seeding module
#
moduleSelector.selectModule("TractographyLabelMapSeeding")
self.takeScreenshot(
"NeurosurgicalPlanning-LabelMapSeedingModule", "Showing Tractography Label Seeding Module", -1
)
tractographyLabelSeeding = slicer.modules.tractographylabelmapseeding
parameters = {}
parameters["InputVolume"] = dtiVolume.GetID()
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-label")
# VTK6 TODO - set 'InputROIPipelineInfo'
parameters["InputROI"] = baselinelabel293.GetID()
fibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fibers)
parameters["OutputFibers"] = fibers.GetID()
parameters["UseIndexSpace"] = 1
parameters["StoppingValue"] = 0.15
parameters["ROIlabel"] = 293
parameters["ThresholdMode"] = "FractionalAnisotropy"
# defaults
# parameters['ClTh'] = 0.3
# parameters['MinimumLength'] = 20
# parameters['MaximumLength'] = 800
# parameters['StoppingCurvature'] = 0.7
# parameters['IntegrationStepLength'] = 0.5
# parameters['SeedSpacing'] = 2
# and run it
slicer.cli.run(tractographyLabelSeeding, None, parameters)
self.takeScreenshot("NeurosurgicalPlanning-LabelMapSeeding", "Showing Tractography Label Seeding Results", -1)
#
# tractography fiducial seeding
#
moduleSelector.selectModule("TractographyInteractiveSeeding")
self.takeScreenshot("NeurosurgicalPlanning-TIS", "Showing Tractography Interactive Seeding Module", -1)
# DTI in background
sliceLogic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# DTI visible in 3D
sliceNode = sliceLogic.GetSliceNode()
sliceLogic.StartSliceNodeInteraction(128)
sliceNode.SetSliceVisible(1)
sliceLogic.EndSliceNodeInteraction()
self.takeScreenshot(
"NeurosurgicalPlanning-TIS-DTI", "DTI volume with Tractography Interactive Seeding Module", -1
)
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName("F")
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
sliceOffset = 58.7
s = sliceOffset
fidNode.AddFiducial(r, a, s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if selectionNode is not None:
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
self.takeScreenshot("NeurosurgicalPlanning-TIS-Fid1", "Fiducial in Tractography Interactive Seeding Module", -1)
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation()
wr.setDiffusionTensorVolumeNode(dtiVolume)
# create a fiber bundle
fiducialFibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fiducialFibers)
wr.setFiberBundleNode(fiducialFibers)
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
self.takeScreenshot("NeurosurgicalPlanning-TIS-Args", "Tractography Interactive Seeding arguments", -1)
self.delayDisplay("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
self.delayDisplay(msg, 250)
fidNode.SetNthFiducialPosition(0, r, y, s)
self.takeScreenshot(
"NeurosurgicalPlanning-TIS-Moved", "Moved fiducial and did Tractography Interactive Seeding", -1
)
return True
def run(self):
"""
Run the actual algorithm
"""
print('Running test of the markups in compare viewers')
#
# first load the data
#
print("Getting MR Head Volume")
import SampleData
mrHeadVolume = SampleData.downloadSample("MRHead")
#
# link the viewers
#
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# MR Head in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(mrHeadVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
#
# switch to conventional layout
#
lm = slicer.app.layoutManager()
lm.setLayout(2)
# create a fiducial list
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if (selectionNode is not None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
# add some known points to it
eye1 = [33.4975, 79.4042, -10.2143]
eye2 = [-31.283, 80.9652, -16.2143]
nose = [4.61944, 114.526, -33.2143]
index = fidNode.AddFiducialFromArray(eye1)
fidNode.SetNthFiducialLabel(index, "eye-1")
index = fidNode.AddFiducialFromArray(eye2)
fidNode.SetNthFiducialLabel(index, "eye-2")
index = fidNode.AddFiducialFromArray(nose)
fidNode.SetNthFiducialLabel(index, "nose")
self.delayDisplay("Placed 3 fiducials")
#
# switch to 2 viewers compare layout
#
lm.setLayout(12)
self.delayDisplay("Switched to Compare 2 viewers")
#
# get compare slice composite node
#
compareLogic1 = slicer.app.layoutManager().sliceWidget('Compare1').sliceLogic()
compareCompositeNode1 = compareLogic1.GetSliceCompositeNode()
# set MRHead in the background
compareLogic1.StartSliceCompositeNodeInteraction(1)
compareCompositeNode1.SetBackgroundVolumeID(mrHeadVolume.GetID())
compareLogic1.EndSliceCompositeNodeInteraction()
compareLogic1.FitSliceToAll()
# make it visible in 3D
compareLogic1.GetSliceNode().SetSliceVisible(1)
# scroll to a fiducial location
compareLogic1.StartSliceOffsetInteraction()
compareLogic1.SetSliceOffset(eye1[2])
compareLogic1.EndSliceOffsetInteraction()
self.delayDisplay("MH Head in background, scrolled to a fiducial")
# scroll around through the range of points
offset = nose[2]
while offset < eye1[2]:
compareLogic1.StartSliceOffsetInteraction()
compareLogic1.SetSliceOffset(offset)
compareLogic1.EndSliceOffsetInteraction()
msg = "Scrolled to " + str(offset)
self.delayDisplay(msg,250)
offset += 1.0
# switch back to conventional
lm.setLayout(2)
self.delayDisplay("Switched back to conventional layout")
# switch to compare grid
lm.setLayout(23)
compareLogic1.FitSliceToAll()
self.delayDisplay("Switched to Compare grid")
# switch back to conventional
lm.setLayout(2)
self.delayDisplay("Switched back to conventional layout")
return True
def visualizeNewSrep(self, filename):
# 1. parse header file
tree = ET.parse(filename)
upFileName = ''
crestFileName = ''
downFileName = ''
nCols = 0
nRows = 0
for child in tree.getroot():
if child.tag == 'upSpoke':
upFileName = child.text
elif child.tag == 'downSpoke':
downFileName = child.text
elif child.tag == 'crestSpoke':
crestFileName = child.text
elif child.tag == 'nRows':
nRows = (int)(child.text)
elif child.tag == 'nCols':
nCols = (int)(child.text)
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(upFileName)
reader.Update()
upSpokes = reader.GetOutput()
upPointData = upSpokes.GetPointData()
medial_polyData = upSpokes # this is poly data for skeleton
scene = slicer.mrmlScene
# base line of medial sheet
fidDisplayNode = slicer.vtkMRMLMarkupsDisplayNode()
scene.AddNode(fidDisplayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidDisplayNode.SetGlyphScale(0.01)
fidDisplayNode.SetSelectedColor(1.0, 1.0, 0.0)
fidDisplayNode.SetTextScale(0.0)
scene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(fidDisplayNode.GetID())
# \TODO come up with better name later
# prepare for arrows for upspokes
upSpoke_points = vtk.vtkPoints()
upSpoke_lines = vtk.vtkCellArray()
arr_length = upPointData.GetArray('spokeLength')
arr_dirs = upPointData.GetArray('spokeDirection')
for i in range(upSpokes.GetNumberOfPoints()):
pt = [0] * 3
upSpokes.GetPoint(i, pt)
# base point of up arrows
id0 = upSpoke_points.InsertNextPoint(pt)
# head of up arrows
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt1 = [0] * 3
pt1[0] = pt[0] + spoke_length * dirX
pt1[1] = pt[1] + spoke_length * dirY
pt1[2] = pt[2] + spoke_length * dirZ
id1 = upSpoke_points.InsertNextPoint(pt1)
up_arrow = vtk.vtkLine()
up_arrow.GetPointIds().SetId(0, id0)
up_arrow.GetPointIds().SetId(1, id1)
upSpoke_lines.InsertNextCell(up_arrow)
fidNode.AddFiducial(pt[0], pt[1], pt[2])
boundary_point_ids = []
# model node for medial mesh
medial_model = slicer.vtkMRMLModelNode()
medial_model.SetScene(scene)
medial_model.SetName("Medial Mesh")
medial_model.SetAndObservePolyData(reader.GetOutput())
# model display node for the medial mesh
medial_model_display = slicer.vtkMRMLModelDisplayNode()
medial_model_display.SetColor(0, 0.5, 0)
medial_model_display.SetScene(scene)
medial_model_display.SetLineWidth(3.0)
medial_model_display.SetRepresentation(1)
medial_model_display.SetBackfaceCulling(0)
scene.AddNode(medial_model_display)
medial_model.SetAndObserveDisplayNodeID(medial_model_display.GetID())
scene.AddNode(medial_model)
# model node for up spoke (poly data for arrows)
upSpoke_polyData = vtk.vtkPolyData()
upSpoke_polyData.SetPoints(upSpoke_points)
upSpoke_polyData.SetLines(upSpoke_lines)
upSpoke_model = slicer.vtkMRMLModelNode()
upSpoke_model.SetScene(scene)
upSpoke_model.SetName("Top Spoke")
upSpoke_model.SetAndObservePolyData(upSpoke_polyData)
# model display node for the top spoke
# cyan for the top spoke
upSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
upSpoke_model_display.SetColor(0, 1, 1)
upSpoke_model_display.SetScene(scene)
upSpoke_model_display.SetLineWidth(3.0)
upSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(upSpoke_model_display)
upSpoke_model.SetAndObserveDisplayNodeID(upSpoke_model_display.GetID())
scene.AddNode(upSpoke_model)
# prepare for down spokes
reader.SetFileName(downFileName)
reader.Update()
downSpokes = reader.GetOutput()
downSpoke_polyData = vtk.vtkPolyData()
downSpoke_lines = vtk.vtkCellArray()
downSpoke_points = vtk.vtkPoints()
downPointData = downSpokes.GetPointData()
arr_length = downPointData.GetArray('spokeLength')
arr_dirs = downPointData.GetArray('spokeDirection')
for i in range(downSpokes.GetNumberOfPoints()):
# tail of arrows
pt_tail = [0] * 3
downSpokes.GetPoint(i, pt_tail)
id0 = downSpoke_points.InsertNextPoint(pt_tail)
# head of arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = downSpoke_points.InsertNextPoint(pt_head)
# connection between head and tail
con = vtk.vtkLine()
con.GetPointIds().SetId(0, id0)
con.GetPointIds().SetId(1, id1)
downSpoke_lines.InsertNextCell(con)
downSpoke_polyData.SetPoints(downSpoke_points)
downSpoke_polyData.SetLines(downSpoke_lines)
downSpoke_model = slicer.vtkMRMLModelNode()
downSpoke_model.SetScene(scene)
downSpoke_model.SetName("Bottom Spoke")
downSpoke_model.SetAndObservePolyData(downSpoke_polyData)
# model display node for the down spoke
downSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
downSpoke_model_display.SetColor(1, 0, 1)
downSpoke_model_display.SetScene(scene)
downSpoke_model_display.SetLineWidth(3.0)
downSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(downSpoke_model_display)
downSpoke_model.SetAndObserveDisplayNodeID(
downSpoke_model_display.GetID())
scene.AddNode(downSpoke_model)
# crest spoke
new_reader = vtk.vtkXMLPolyDataReader()
new_reader.SetFileName(crestFileName)
new_reader.Update()
foldCurve_polyData = new_reader.GetOutput()
foldPointData = foldCurve_polyData.GetPointData()
arr_length = foldPointData.GetArray('spokeLength')
arr_dirs = foldPointData.GetArray('spokeDirection')
crest_arrows_polydata = vtk.vtkPolyData()
crest_arrows_points = vtk.vtkPoints()
crest_arrows_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
# tail of crest arrows
pt_tail = [0] * 3
foldCurve_polyData.GetPoint(i, pt_tail)
id0 = crest_arrows_points.InsertNextPoint(pt_tail)
# head of crest arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = crest_arrows_points.InsertNextPoint(pt_head)
crest_line = vtk.vtkLine()
crest_line.GetPointIds().SetId(0, id0)
crest_line.GetPointIds().SetId(1, id1)
crest_arrows_lines.InsertNextCell(crest_line)
crest_arrows_polydata.SetPoints(crest_arrows_points)
crest_arrows_polydata.SetLines(crest_arrows_lines)
# show crest arrows
crestSpoke_model = slicer.vtkMRMLModelNode()
crestSpoke_model.SetScene(scene)
crestSpoke_model.SetName("Crest Spoke")
crestSpoke_model.SetAndObservePolyData(crest_arrows_polydata)
# model display node
crestSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
crestSpoke_model_display.SetColor(1, 1, 0)
crestSpoke_model_display.SetScene(scene)
crestSpoke_model_display.SetLineWidth(3.0)
crestSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(crestSpoke_model_display)
crestSpoke_model.SetAndObserveDisplayNodeID(
crestSpoke_model_display.GetID())
scene.AddNode(crestSpoke_model)
# show fold curve
foldCurve_model = slicer.vtkMRMLModelNode()
foldCurve_model.SetScene(scene)
foldCurve_model.SetName("Fold Curve")
foldCurve_model.SetAndObservePolyData(foldCurve_polyData)
# model display node
foldCurve_model_display = slicer.vtkMRMLModelDisplayNode()
foldCurve_model_display.SetColor(1, 1, 0)
foldCurve_model_display.SetScene(scene)
foldCurve_model_display.SetLineWidth(3.0)
foldCurve_model_display.SetBackfaceCulling(0)
scene.AddNode(foldCurve_model_display)
foldCurve_model.SetAndObserveDisplayNodeID(
foldCurve_model_display.GetID())
scene.AddNode(foldCurve_model)
# show connections to fold curve point from nearby interior points
# compute the nearest interior point
connection_polydata = vtk.vtkPolyData()
connection_points = vtk.vtkPoints()
connection_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
min_dist = 100000.0
nearest_index = 0
pt_fold = [0] * 3
foldCurve_polyData.GetPoint(i, pt_fold)
id0 = connection_points.InsertNextPoint(pt_fold)
for j in range(upSpokes.GetNumberOfPoints()):
pt_interior = [0] * 3
upSpokes.GetPoint(j, pt_interior)
dist = math.sqrt((pt_fold[0] - pt_interior[0])**2 +
(pt_fold[1] - pt_interior[1])**2 +
(pt_fold[2] - pt_interior[2])**2)
if dist < min_dist:
min_dist = dist
nearest_index = j
pt_nearest_interior = upSpokes.GetPoint(nearest_index)
id1 = connection_points.InsertNextPoint(pt_nearest_interior)
line = vtk.vtkLine()
line.GetPointIds().SetId(0, id0)
line.GetPointIds().SetId(1, id1)
connection_lines.InsertNextCell(line)
connection_polydata.SetPoints(connection_points)
connection_polydata.SetLines(connection_lines)
connection_model = slicer.vtkMRMLModelNode()
connection_model.SetScene(scene)
connection_model.SetName("Connection to Fold Curve")
connection_model.SetAndObservePolyData(connection_polydata)
# model display node
connection_model_display = slicer.vtkMRMLModelDisplayNode()
connection_model_display.SetColor(0, 0, 0)
connection_model_display.SetScene(scene)
connection_model_display.SetLineWidth(3.0)
connection_model_display.SetBackfaceCulling(0)
scene.AddNode(connection_model_display)
connection_model.SetAndObserveDisplayNodeID(
connection_model_display.GetID())
scene.AddNode(connection_model)
def findAxisOfMotion(self, origins):
#Following guide from: http://sebastianraschka.com/Articles/2014_pca_step_by_step.html
#scale factor for better display:
scale = 100
#Calculate mean position
meanVector = [0, 0 ,0]
for i in range(3):
meanVector[i] = np.mean(origins[i, :])
#Computing covariance matrix
convMatrix = np.cov([origins[0, :], origins[1, :], origins[2, :]])
#Get eigenvectors
eig_val, eig_vec = np.linalg.eig(convMatrix)
# Make a list of (eigenvalue, eigenvector) tuples
eig_pairs = [(np.abs(eig_val[i]), eig_vec[:,i]) for i in range(len(eig_val))]
# Sort the (eigenvalue, eigenvector) tuples from high to low
eig_pairs.sort()
# eig_pairs.reverse()
matrix_w = np.hstack((eig_pairs[0][1].reshape(3, 1),
eig_pairs[1][1].reshape(3, 1),
eig_pairs[2][1].reshape(3, 1)))
print('Matrix W:\n', matrix_w)
#Create linear transform for contour propagation
vtkMatrix = vtk.vtkMatrix4x4()
transform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transform)
for i in range(3):
for j in range(3):
vtkMatrix.SetElement(j, i, matrix_w[i, j])
transform.SetAndObserveMatrixTransformFromParent(vtkMatrix)
#Plot eigenvectors from mean position
fiducials = slicer.vtkMRMLMarkupsFiducialNode()
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
# vtkNew<vtkMRMLMarkupsFiducialStorageNode> wFStorageNode;
slicer.mrmlScene.AddNode(displayNode)
slicer.mrmlScene.AddNode(fiducials)
fiducials.SetAndObserveDisplayNodeID(displayNode.GetID())
fiducials.AddFiducialFromArray(meanVector, "Mean Position")
for i in range(len(eig_vec)):
# fiducials.AddFiducialFromArray(meanVector + scale * eig_vec[i], " P " + str(i+1))
#Plot ruler
ruler = slicer.vtkMRMLAnnotationRulerNode()
displayRuler = slicer.vtkMRMLAnnotationLineDisplayNode()
displayRuler.SetLabelVisibility(0)
displayRuler.SetMaxTicks(0)
displayRuler.SetLineWidth(5)
slicer.mrmlScene.AddNode(displayRuler)
slicer.mrmlScene.AddNode(ruler)
ruler.SetAndObserveDisplayNodeID(displayRuler.GetID())
ruler.SetPosition1(meanVector)
ruler.SetPosition2(meanVector + scale * eig_vec[i])
return matrix_w
def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay(
'Running test of the Neurosurgical Planning tutorial')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule('Welcome')
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Welcome',
'Welcome module', -1)
else:
# otherwise show the sample data module
moduleSelector.selectModule('SampleData')
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume(
)
self.delayDisplay("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
self.takeScreenshot('NeurosurgicalPlanning-Loaded', 'Data loaded', -1)
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, baselineVolume,
baselineVolume.GetName() + '-label')
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
data = slicer.util.array(baselineVolume.GetName() + "-label")
data[6:15, 110:140, 130:160] = 293
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget(
"Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget is not None:
popupWidget.pinPopup(1)
self.takeScreenshot('NeurosurgicalPlanning-Link',
'Link slice viewers', -1)
popupWidget.pinPopup(0)
#
# Tractography Label Map Seeding module
#
moduleSelector.selectModule('TractographyLabelMapSeeding')
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeedingModule',
'Showing Tractography Label Seeding Module', -1)
tractographyLabelSeeding = slicer.modules.tractographylabelmapseeding
parameters = {}
parameters['InputVolume'] = dtiVolume.GetID()
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-label")
# VTK6 TODO - set 'InputROIPipelineInfo'
parameters['InputROI'] = baselinelabel293.GetID()
fibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fibers)
parameters['OutputFibers'] = fibers.GetID()
parameters['UseIndexSpace'] = 1
parameters['StoppingValue'] = 0.15
parameters['ROIlabel'] = 293
parameters['ThresholdMode'] = 'FractionalAnisotropy'
# defaults
# parameters['ClTh'] = 0.3
# parameters['MinimumLength'] = 20
# parameters['MaximumLength'] = 800
# parameters['StoppingCurvature'] = 0.7
# parameters['IntegrationStepLength'] = 0.5
# parameters['SeedSpacing'] = 2
# and run it
slicer.cli.run(tractographyLabelSeeding, None, parameters)
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeeding',
'Showing Tractography Label Seeding Results', -1)
#
# tractography fiducial seeding
#
moduleSelector.selectModule('TractographyInteractiveSeeding')
self.takeScreenshot('NeurosurgicalPlanning-TIS',
'Showing Tractography Interactive Seeding Module',
-1)
# DTI in background
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# DTI visible in 3D
sliceNode = sliceLogic.GetSliceNode()
sliceLogic.StartSliceNodeInteraction(128)
sliceNode.SetSliceVisible(1)
sliceLogic.EndSliceNodeInteraction()
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-DTI',
'DTI volume with Tractography Interactive Seeding Module', -1)
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName('F')
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
sliceOffset = 58.7
s = sliceOffset
fidNode.AddFiducial(r, a, s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID(
"vtkMRMLSelectionNodeSingleton")
if (selectionNode is not None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-Fid1',
'Fiducial in Tractography Interactive Seeding Module', -1)
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation(
)
wr.setDiffusionTensorVolumeNode(dtiVolume)
# create a fiber bundle
fiducialFibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fiducialFibers)
wr.setFiberBundleNode(fiducialFibers)
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
self.takeScreenshot('NeurosurgicalPlanning-TIS-Args',
'Tractography Interactive Seeding arguments', -1)
self.delayDisplay("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
self.delayDisplay(msg, 250)
fidNode.SetNthFiducialPosition(0, r, y, s)
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-Moved',
'Moved fiducial and did Tractography Interactive Seeding', -1)
return True
def run(self):
"""
Run the actual algorithm
"""
print('Running test of the markups in different views')
#
# first load the data
#
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
#
# link the viewers
#
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# MR Head in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(mrHeadVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
#
# switch to conventional layout
#
lm = slicer.app.layoutManager()
lm.setLayout(2)
# create a fiducial list
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if (selectionNode is not None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
# add some known points to it
eye1 = [33.4975, 79.4042, -10.2143]
eye2 = [-31.283, 80.9652, -16.2143]
nose = [4.61944, 114.526, -33.2143]
index = fidNode.AddFiducialFromArray(eye1)
fidNode.SetNthFiducialLabel(index, "eye-1")
index = fidNode.AddFiducialFromArray(eye2)
fidNode.SetNthFiducialLabel(index, "eye-2")
# hide the second eye as a test of visibility flags
fidNode.SetNthFiducialVisibility(index, 0)
index = fidNode.AddFiducialFromArray(nose)
fidNode.SetNthFiducialLabel(index, "nose")
self.logicDelayDisplay("Placed 3 fiducials")
# self.printViewAndSliceNodes()
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 0:
self.logicDelayDisplay("Test failed: widget is not visible in view 1")
# self.printViewNodeIDs(displayNode)
return False
#
# switch to 2 3D views layout
#
lm.setLayout(15)
self.logicDelayDisplay("Switched to 2 3D views")
# self.printViewAndSliceNodes()
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 0 or self.widgetVisible(fidNode, 'vtkMRMLViewNode2') == 0:
self.logicDelayDisplay("Test failed: widget is not visible in view 1 and 2")
# self.printViewNodeIDs(displayNode)
return False
#
# show only in view 2
#
displayNode.AddViewNodeID("vtkMRMLViewNode2")
self.logicDelayDisplay("Showing only in view 2")
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 1:
self.logicDelayDisplay("Test failed: widget is not supposed to be visible in view 1")
# self.printViewNodeIDs(displayNode)
return False
if self.widgetVisible(fidNode, 'vtkMRMLViewNode2') == 0:
self.logicDelayDisplay("Test failed: widget is not visible in view 2")
# self.printViewNodeIDs(displayNode)
return False
#
# remove it so show in all
#
displayNode.RemoveAllViewNodeIDs()
self.logicDelayDisplay("Showing in both views")
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 0 or self.widgetVisible(fidNode, 'vtkMRMLViewNode2') == 0:
self.logicDelayDisplay("Test failed: widget is not visible in view 1 and 2")
self.printViewNodeIDs(displayNode)
return False
#
# show only in view 1
#
displayNode.AddViewNodeID("vtkMRMLViewNode1")
self.logicDelayDisplay("Showing only in view 1")
if self.widgetVisible(fidNode, 'vtkMRMLViewNode2') == 1:
self.logicDelayDisplay("Test failed: widget is not supposed to be visible in view 2")
# self.printViewNodeIDs(displayNode)
return False
if self.widgetVisible(fidNode, 'vtkMRMLViewNode1') == 0:
self.logicDelayDisplay("Test failed: widget is not visible in view 1")
# self.printViewNodeIDs(displayNode)
return False
# switch back to conventional
lm.setLayout(2)
self.logicDelayDisplay("Switched back to conventional layout")
# self.printViewAndSliceNodes()
# test of the visibility in slice views
displayNode.RemoveAllViewNodeIDs()
# jump to the last fiducial
slicer.modules.markups.logic().JumpSlicesToNthPointInMarkup(fidNode.GetID(), index, 1)
# refocus the 3D cameras as well
slicer.modules.markups.logic().FocusCamerasOnNthPointInMarkup(fidNode.GetID(), index)
# show only in red
displayNode.AddViewNodeID('vtkMRMLSliceNodeRed')
self.logicDelayDisplay("Show only in red slice")
if self.widgetVisibleOnSlice(fidNode,'vtkMRMLSliceNodeRed') != 1:
self.logicDelayDisplay("Test failed: widget not displayed on red slice")
# self.printViewNodeIDs(displayNode)
return False
# remove all, add green
# print 'before remove all, after added red'
# self.printViewNodeIDs(displayNode)
displayNode.RemoveAllViewNodeIDs()
# print 'after removed all'
# self.printViewNodeIDs(displayNode)
displayNode.AddViewNodeID('vtkMRMLSliceNodeGreen')
self.logicDelayDisplay('Show only in green slice')
if self.widgetVisibleOnSlice(fidNode,'vtkMRMLSliceNodeRed') != 0 or self.widgetVisibleOnSlice(fidNode,'vtkMRMLSliceNodeGreen') != 1:
self.logicDelayDisplay("Test failed: widget not displayed only on green slice")
print '\tred = ',self.widgetVisibleOnSlice(fidNode,'vtkMRMLSliceNodeRed')
print '\tgreen =',self.widgetVisibleOnSlice(fidNode,'vtkMRMLSliceNodeGreen')
self.printViewNodeIDs(displayNode)
return False
return True
