def addFiducials(self):
shaderFiducials = slicer.util.getNode('shaderFiducials')
if not shaderFiducials:
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
fiducialNode.SetName('shaderFiducials')
slicer.mrmlScene.AddNode(fiducialNode)
fiducialNode.SetAndObserveDisplayNodeID(displayNode.GetID())
for ras in ((28.338526, 34.064367, 10), (-10, 0, -5)):
fiducialNode.AddFiducial(*ras)
import random
fiducialCount = 10
radius = 75
for index in range(fiducialCount):
uvw = [random.random(), random.random(), random.random()]
ras = map(lambda e: radius * (2. * e - 1.), uvw)
fiducialNode.AddFiducial(*ras)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID(
"vtkMRMLSelectionNodeSingleton")
if (selectionNode is not None):
selectionNode.SetReferenceActivePlaceNodeID(
fiducialNode.GetID())
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()
# 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 = r + 1.0
a = a + 1.0
s = s + 1.0
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()
# 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 = r + 1.0
a = a + 1.0
s = s + 1.0
timeToAddLastFid = timeToAddThisFid
if usefewerModifyCalls == 1:
fidNode.EndModify(mod)
testEndTime = time.clock()
testTime = testEndTime - testStartTime
print "Total time to add ", numToAdd, " = ", testTime
return True
def test_VolumeClipWithModel1(self):
# Download MRHead from sample data
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting MR Head Volume")
inputVolume = sampleDataLogic.downloadMRHead()
# Create empty model node
clippingModel = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(clippingModel)
# Create markup fiducials
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
inputMarkup = slicer.vtkMRMLMarkupsFiducialNode()
inputMarkup.SetName('C')
slicer.mrmlScene.AddNode(inputMarkup)
inputMarkup.SetAndObserveDisplayNodeID(displayNode.GetID())
inputMarkup.AddFiducial(35, -10, -10)
inputMarkup.AddFiducial(-15, 20, -10)
inputMarkup.AddFiducial(-25, -25, -10)
inputMarkup.AddFiducial(-5, -60, -15)
inputMarkup.AddFiducial(-5, 5, 60)
inputMarkup.AddFiducial(-5, -35, -30)
# Create output volume
outputVolume = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputVolume)
# Clip volume
logic = VolumeClipWithModelLogic()
clipOutsideSurface = True
fillOutsideValue = 0
clipInsideSurface = True
fillInsideValue = 255
logic.updateModelFromMarkup(inputMarkup, clippingModel)
logic.clipVolumeWithModel(inputVolume, clippingModel,
clipOutsideSurface, fillOutsideValue,
outputVolume)
logic.showInSliceViewers(outputVolume, ["Red", "Yellow", "Green"])
self.delayDisplay("Test passed!")
def placeFiducials(self):
# Create empty model node
clippingModel = slicer.vtkMRMLModelNode()
clippingModel.SetName('clipModelNode')
slicer.mrmlScene.AddNode(clippingModel)
# Create markup display fiducials - why do i need that?
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
# create markup fiducial node
inputMarkup = slicer.vtkMRMLMarkupsFiducialNode()
inputMarkup.SetName('inputMarkupNode')
slicer.mrmlScene.AddNode(inputMarkup)
inputMarkup.SetAndObserveDisplayNodeID(displayNode.GetID())
# add Observer
inputMarkup.AddObserver(vtk.vtkCommand.ModifiedEvent,self.updateModel)
return True
def addFiducials(self):
shaderFiducials = slicer.util.getNode('shaderFiducials')
if not shaderFiducials:
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
fiducialNode.SetName('shaderFiducials')
slicer.mrmlScene.AddNode(fiducialNode)
fiducialNode.SetAndObserveDisplayNodeID(displayNode.GetID())
for ras in ((28.338526, 34.064367, 10), (-10, 0, -5)):
fiducialNode.AddFiducial(*ras)
import random
fiducialCount = 10
radius = 75
for index in range(fiducialCount):
uvw = [random.random(), random.random(), random.random()]
ras = map(lambda e: radius * (2. * e - 1.), uvw)
fiducialNode.AddFiducial(*ras)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if (selectionNode is not None):
selectionNode.SetReferenceActivePlaceNodeID(fiducialNode.GetID())
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
#
editUtil = EditorLib.EditUtil.EditUtil()
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 = slicer.modules.EditorWidget.toolsBox.currentOption.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 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 != 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)
# 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
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 != 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 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 != 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 testSegmentationWizard(self):
""" Test the ChangeTracker module
"""
self.delayDisplay("Starting the test")
try:
self.delayDisplay("Loading sample data")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
head = sampleDataLogic.downloadMRHead()
braintumor1 = sampleDataLogic.downloadMRBrainTumor1()
braintumor2 = sampleDataLogic.downloadMRBrainTumor2()
self.delayDisplay("Getting scene variables")
mainWindow = slicer.util.mainWindow()
layoutManager = slicer.app.layoutManager()
threeDView = layoutManager.threeDWidget(0).threeDView()
redWidget = layoutManager.sliceWidget('Red')
redController = redWidget.sliceController()
viewNode = threeDView.mrmlViewNode()
cameras = slicer.util.getNodes('vtkMRMLCameraNode*')
mainWindow.moduleSelector().selectModule('SegmentationWizard')
modelsegmentation_module = slicer.modules.modelsegmentation.widgetRepresentation(
).self()
self.delayDisplay('Select Volumes')
baselineNode = braintumor1
followupNode = braintumor2
modelsegmentation_module.Step1._VolumeSelectStep__enableSubtractionMapping.setChecked(
True)
modelsegmentation_module.Step1._VolumeSelectStep__baselineVolumeSelector.setCurrentNode(
baselineNode)
modelsegmentation_module.Step1._VolumeSelectStep__followupVolumeSelector.setCurrentNode(
followupNode)
self.delayDisplay('Go Forward')
modelsegmentation_module.workflow.goForward()
self.delayDisplay('Register Images')
modelsegmentation_module.Step2.onRegistrationRequest(
wait_for_completion=True)
self.delayDisplay('Go Forward')
modelsegmentation_module.workflow.goForward()
self.delayDisplay('Normalize Images')
modelsegmentation_module.Step3.onGaussianNormalizationRequest()
self.delayDisplay('Subtract Images')
modelsegmentation_module.Step3.onSubtractionRequest(
wait_for_completion=True)
self.delayDisplay('Go Forward')
modelsegmentation_module.workflow.goForward()
self.delayDisplay('Load model')
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
inputMarkup = slicer.vtkMRMLMarkupsFiducialNode()
inputMarkup.SetName('Test')
slicer.mrmlScene.AddNode(inputMarkup)
inputMarkup.SetAndObserveDisplayNodeID(displayNode.GetID())
modelsegmentation_module.Step4._ROIStep__clippingMarkupSelector.setCurrentNode(
inputMarkup)
inputMarkup.AddFiducial(35, -10, -10)
inputMarkup.AddFiducial(-15, 20, -10)
inputMarkup.AddFiducial(-25, -25, -10)
inputMarkup.AddFiducial(-5, -60, -15)
inputMarkup.AddFiducial(-5, 5, 60)
inputMarkup.AddFiducial(-5, -35, -30)
self.delayDisplay('Go Forward')
modelsegmentation_module.workflow.goForward()
self.delayDisplay('Set Thresholds')
modelsegmentation_module.Step5._ThresholdStep__threshRange.minimumValue = 50
modelsegmentation_module.Step5._ThresholdStep__threshRange.maximumValue = 150
self.delayDisplay('Go Forward')
modelsegmentation_module.workflow.goForward()
self.delayDisplay('Restart Module')
modelsegmentation_module.Step6.Restart()
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
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 Neurosurgical Planning tutorial')
#
# first load the data
#
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume(
)
print("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
#
# link the viewers
#
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()
#
# adjust window level on baseline
#
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Volumes')
baselineVolume.GetDisplayNode().SetWindow(2600)
baselineVolume.GetDisplayNode().SetLevel(1206)
#
# switch to red slice only
#
lm = slicer.app.layoutManager()
lm.setLayout(6)
#
# skip segmentation of tumour
#
#
# switch to conventional layout
#
lm.setLayout(2)
#
# skip tractography label map seeding
#
#
# tractography fiducial seeding
#
mainWindow.moduleSelector().selectModule(
'TractographyInteractiveSeeding')
# DTI in background
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
s = 58.74121
fidNode.AddFiducial(r, a, s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID(
"vtkMRMLSelectionNodeSingleton")
if (selectionNode != None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation(
)
wr.setDiffusionTensorVolumeNode(dtiVolume)
# fiber bundle is created automatically
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
print("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
print msg
moveMsg = qt.QDialog()
moveMsg.setLayout(qt.QVBoxLayout())
moveMsg.layout().addWidget(qt.QLabel(msg))
qt.QTimer.singleShot(250, moveMsg.close)
moveMsg.exec_()
fidNode.SetNthFiducialPosition(0, r, y, s)
return True
def readPlane(self):
filename = qt.QFileDialog.getOpenFileName(parent=self,caption='Open file')
print 'filename:', filename
fichier2 = open(filename, 'r')
fichier2.readline()
NodeRed = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
matRed = NodeRed.GetSliceToRAS()
for i in range(0, 4):
ligne = fichier2.readline()
ligne = ligne.replace('[', '')
ligne = ligne.replace(' ', ' ')
ligne = ligne.replace(']', '')
ligne = ligne.replace('\n', '')
print ligne
items = ligne.split()
print items
for j in range(0, 4):
matRed.SetElement(i, j, float(items[j]))
print matRed
compare_red = 0
for i in range(0,4):
for j in range(0,4):
if matRed.GetElement(i,j) == self.matRed_init[i,j]:
compare_red = compare_red + 1
print compare_red
if compare_red != 16:
self.redslice = slicer.util.getNode('vtkMRMLSliceNodeRed')
if self.red_plane_box.isChecked():
self.red_plane_box.setChecked(False)
self.redslice.SetWidgetVisible(False)
self.red_plane_box.setChecked(True)
self.redPlaneCheckBoxClicked()
fichier2.readline()
fichier2.readline()
NodeGreen = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeGreen')
matGreen = NodeGreen.GetSliceToRAS()
for i in range (0,4):
ligne = fichier2.readline()
ligne = ligne.replace('[', '')
ligne = ligne.replace(' ', ' ')
ligne = ligne.replace(']', '')
ligne = ligne.replace('\n', '')
print ligne
items = ligne.split()
print items
for j in range(0, 4):
matGreen.SetElement(i, j, float(items[j]))
print matGreen
compare_green = 0
for i in range(0,4):
for j in range(0,4):
if matGreen.GetElement(i,j) == self.matGreen_init[i,j]:
compare_green = compare_green + 1
print compare_green
if compare_green != 16:
self.greenslice = slicer.util.getNode('vtkMRMLSliceNodeGreen')
if self.green_plane_box.isChecked():
self.green_plane_box.setChecked(False)
self.greenslice.SetWidgetVisible(False)
self.green_plane_box.setChecked(True)
self.greenPlaneCheckBoxClicked()
fichier2.readline()
fichier2.readline()
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
ligne = fichier2.readline()
ligne = ligne.replace('[', '')
ligne = ligne.replace(' ', ' ')
ligne = ligne.replace(']', '')
ligne = ligne.replace('\n', '')
print ligne
items = ligne.split()
print items
r = float(items[0])
a = float(items[1])
s = float(items[2])
fidNode.AddFiducial(r,a,s)
fichier2.readline()
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
ligne = fichier2.readline()
ligne = ligne.replace('[', '')
ligne = ligne.replace(' ', ' ')
ligne = ligne.replace(']', '')
ligne = ligne.replace('\n', '')
print ligne
items = ligne.split()
print items
r = float(items[0])
a = float(items[1])
s = float(items[2])
fidNode.AddFiducial(r,a,s)
fichier2.readline()
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
ligne = fichier2.readline()
ligne = ligne.replace('[', '')
ligne = ligne.replace(' ', ' ')
ligne = ligne.replace(']', '')
ligne = ligne.replace('\n', '')
print ligne
items = ligne.split()
print items
r = float(items[0])
a = float(items[1])
s = float(items[2])
fidNode.AddFiducial(r,a,s)
fichier2.close()
def run(self,enableScreenshots=0,screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay('Running test of the Neurosurgical Planning tutorial')
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule('Welcome')
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Welcome','Welcome module',-1,screenshotScaleFactor)
# but use the sample data module logic to load it 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()
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Loaded','Data loaded',-1,screenshotScaleFactor)
#
# link the viewers
#
if enableScreenshots == 1:
# for the tutorial, pop up the linking control
# TODO: pipPopup is not exposed to python
sliceController = slicer.app.layoutManager().sliceWidget("Red").sliceController()
# sliceController.pinPopup(1)
# self.delayDisplay("Screenshot")
# self.takeScreenshot('NeurosurgicalPlanning-Link','Link slice viewers',-1,screenshotScaleFactor)
# sliceController.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()
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Baseline','Baseline in background',-1,screenshotScaleFactor)
#
# adjust window level on baseline
#
moduleSelector.selectModule('Volumes')
baselineVolume.GetDisplayNode().SetWindow(2600)
baselineVolume.GetDisplayNode().SetLevel(1206)
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-WindowLevel','Set W/L on baseline',-1,screenshotScaleFactor)
#
# switch to red slice only
#
lm = slicer.app.layoutManager()
lm.setLayout(6)
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly','Set layout to Red Slice only',-1,screenshotScaleFactor)
#
# skip segmentation of tumour
#
#
# switch to conventional layout
#
lm.setLayout(2)
#
# skip tractography label map seeding
#
#
# tractography fiducial seeding
#
moduleSelector.selectModule('TractographyInteractiveSeeding')
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-TIS','Showing Tractography Interactive Seeding Module',-1,screenshotScaleFactor)
# 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()
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-TIS-DTI','DTI volume with Tractography Interactive Seeding Module',-1,screenshotScaleFactor)
# 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 = 58.74121
fidNode.AddFiducial(r,a,s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if (selectionNode != None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-TIS-Fid1','Fiducial in Tractography Interactive Seeding Module',-1,screenshotScaleFactor)
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation()
wr.setDiffusionTensorVolumeNode(dtiVolume)
# fiber bundle is created automatically
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-TIS-Args','Tractography Interactive Seeding arguments',-1,screenshotScaleFactor)
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)
if enableScreenshots == 1:
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-TIS-Moved','Moved fiducial and did Tractography Interactive Seeding',-1,screenshotScaleFactor)
return True
def run(self):
"""
Run the actual algorithm
"""
print('Running test of the Neurosurgical Planning tutorial')
#
# first load the data
#
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume()
print("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
#
# link the viewers
#
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()
#
# adjust window level on baseline
#
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Volumes')
baselineVolume.GetDisplayNode().SetWindow(2600)
baselineVolume.GetDisplayNode().SetLevel(1206)
#
# switch to red slice only
#
lm = slicer.app.layoutManager()
lm.setLayout(6)
#
# skip segmentation of tumour
#
#
# switch to conventional layout
#
lm.setLayout(2)
#
# skip tractography label map seeding
#
#
# tractography fiducial seeding
#
mainWindow.moduleSelector().selectModule('TractographyInteractiveSeeding')
# DTI in background
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
s = 58.74121
fidNode.AddFiducial(r,a,s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if (selectionNode != None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation()
wr.setDiffusionTensorVolumeNode(dtiVolume)
# fiber bundle is created automatically
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
print("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
print msg
moveMsg = qt.QDialog()
moveMsg.setLayout(qt.QVBoxLayout())
moveMsg.layout().addWidget(qt.QLabel(msg))
qt.QTimer.singleShot(250, moveMsg.close)
moveMsg.exec_()
fidNode.SetNthFiducialPosition(0, r, y, s)
return True
