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 createMovingLRSToFixedLRS(self, movingLRS = None):
if movingLRS.GetNumberOfFiducials() < 3:
logging.warning('Moving LRS fiducials list needs to contain at least three fiducials!')
return False
fixedLRS = slicer.util.getNode('FixedLRS')
if not fixedLRS:
# Create FixedLRS markups node
fixedLRS = slicer.vtkMRMLMarkupsFiducialNode()
fixedLRS.SetName('FixedLRS')
fixedLRS.AddFiducial(-100.0, 0.0, 0.0)
fixedLRS.SetNthFiducialLabel(0, 'FixedL')
fixedLRS.AddFiducial(100.0, 0.0, 0.0)
fixedLRS.SetNthFiducialLabel(1, 'FixedR')
fixedLRS.AddFiducial(0.0, 0.0, 100.0)
fixedLRS.SetNthFiducialLabel(2, 'FixedS')
slicer.mrmlScene.AddNode(fixedLRS)
fixedLRS.SetDisplayVisibility(False)
movingLRSToFixedLRS = slicer.util.getNode('MovingLRSToFixedLRS')
if not movingLRSToFixedLRS:
# Create MovingLRSToFixedLRS transform node
movingLRSToFixedLRS = slicer.vtkMRMLLinearTransformNode()
movingLRSToFixedLRS.SetName('MovingLRSToFixedLRS')
slicer.mrmlScene.AddNode(movingLRSToFixedLRS)
self.fiducialRegistration(movingLRSToFixedLRS, fixedLRS, movingLRS, "Rigid")
return True
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '5. Place Screws' )
self.setDescription( 'Load screw models and change orientation using sliders' )
self.screwPath = None
self.screwName = None
self.coords = [0,0,0]
self.matrix1 = vtk.vtkMatrix3x3()
self.matrix2 = vtk.vtkMatrix3x3()
self.matrix3 = vtk.vtkMatrix3x3()
self.matrixScrew = vtk.vtkMatrix4x4()
self.fiduciallist = []
self.screwSummary = []
self.screwList = []
self.currentFidIndex = 0
self.currentFidLabel = None
self.fidNode = slicer.vtkMRMLMarkupsFiducialNode()
self.valueTemp1 = 0
self.valueTemp2 = 0
self.driveTemp = 0
self.__loadScrewButton = None
self.__parent = super( ScrewStep, self )
self.timer = qt.QTimer()
self.timer.setInterval(2)
self.timer.connect('timeout()', self.driveScrew)
self.timer2 = qt.QTimer()
self.timer2.setInterval(2)
self.timer2.connect('timeout()', self.reverseScrew)
self.screwInsert = 0.0
def inputFiducialBtnClick(self, volumeType):
# Create Fiducial Node for the cochlea location
if (volumeType == "input"):
print(" ..... getting cochlea location in the input image")
# Reset global point label
self.inputPoint = [0, 0, 0]
self.inputPointEdt.setText("[0, 0, 0]")
# Check if a volume is selected
if not self.inputSelectorCoBx.currentNode():
print >> sys.stderr, "You need to pick a input volume first."
return -1
try:
self.inputNode = self.inputSelectorCoBx.currentNode()
except:
self.suppDICOM()
#end try
# Display Coronal during locating the cochlea
green_logic = slicer.app.layoutManager().sliceWidget(
"Green").sliceLogic()
green_cn = green_logic.GetSliceCompositeNode()
green_cn.SetBackgroundVolumeID(self.inputNode.GetID())
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpGreenSliceView)
# Fit slice to window
sliceNodes = slicer.util.getNodes('vtkMRMLSliceNode*')
layoutManager = slicer.app.layoutManager()
for sliceNode in sliceNodes.values():
sliceWidget = layoutManager.sliceWidget(sliceNode.GetLayoutName())
if sliceWidget:
sliceWidget.sliceLogic().FitSliceToAll()
# Remove old Fiducial nodes
nodes = slicer.util.getNodesByClass('vtkMRMLMarkupsFiducialNode')
for f in nodes:
if ((f.GetName() == "CochleaLocation")):
slicer.mrmlScene.RemoveNode(f)
self.inputFiducialBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.inputFiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
self.inputFiducialNode.SetName("CochleaLocation")
slicer.mrmlScene.AddNode(self.inputFiducialNode)
# Start Fiducial Placement Mode in Slicer
placeModePersistance = 0
slicer.modules.markups.logic().StartPlaceMode(placeModePersistance)
# Observe scene for updates
self.inputFiducialNode.AddObserver(
self.inputFiducialNode.MarkupAddedEvent, self.convRAS2IJK)
self.inputFiducialNode.AddObserver(
self.inputFiducialNode.MarkupRemovedEvent, self.convRAS2IJK)
self.inputFiducialNode.AddObserver(
self.inputFiducialNode.PointModifiedEvent, self.updateIJK)
self.inputFiducialBtn.setStyleSheet(
"QPushButton{ background-color: White }")
def createTodoMarkup( self ):
todoMarkup = slicer.mrmlScene.AddNode(slicer.vtkMRMLMarkupsFiducialNode())
todoMarkup.SetHideFromEditors(1)
todoMarkup.SetName('Interactive Segment Tubes To Do list')
todoMarkup.SetDisplayVisibility(0)
# Set None as an active list otherwise the user might add fiducial to todoMarkup
self.setActivePlaceNodeID(None)
return todoMarkup
def createTodoMarkup(self):
todoMarkup = slicer.mrmlScene.AddNode(
slicer.vtkMRMLMarkupsFiducialNode())
todoMarkup.SetHideFromEditors(1)
todoMarkup.SetName('Interactive Segment Tubes To Do list')
todoMarkup.SetDisplayVisibility(0)
# Set None as an active list otherwise the user might add fiducial to todoMarkup
self.setActivePlaceNodeID(None)
return todoMarkup
def onClippingModelSelect(self, node):
if node != None and node != '':
if node.GetID() not in self.__modelList:
self.__modelList.append(node.GetID())
new_clippingMarkupNode = slicer.vtkMRMLMarkupsFiducialNode()
new_clippingMarkupNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(new_clippingMarkupNode)
self.__markupList.append([node.GetID(), new_clippingMarkupNode.GetID(), 'Convex'])
self.__clippingModelNode = node
self.setAndObserveClippingMarkupNode(Helper.getNodeByID(self.__markupList[self.__modelList.index(node.GetID())][1]))
def addFiducial(self,ras):
if self.isNewContour == True:
self.fiducials = slicer.vtkMRMLMarkupsFiducialNode()
self.fiducials.SetScene( slicer.mrmlScene )
slicer.mrmlScene.AddNode( self.fiducials )
tag = self.fiducials.AddObserver(self.fiducials.PointModifiedEvent, lambda caller,event: self.onFiducialMoved(caller))
print tag
self.observerTags.append( (self.fiducials,tag) )
self.isNewContour = False
self.numberFiducials += 1
self.fiducials.AddFiducial(ras[0],ras[1],ras[2],str(self.numberFiducials))
def SetDefaultValuesClicked(self):
if (not self.toFids):
self.toFids = slicer.vtkMRMLMarkupsFiducialNode()
self.toFids.SetName('toFids')
if (not self.fromFids):
self.fromFids = slicer.vtkMRMLMarkupsFiducialNode()
self.fromFids.SetName('fromFids')
if self.inputSelector1.currentNode():
segmentationNode = self.inputSelector1.currentNode()
TransformNode = self.inputSelector4.currentNode()
segmentation = segmentationNode.GetSegmentation()
segment = segmentation.GetSegment(segmentation.GetNthSegmentID(0))
segment.SetColor(0, 0, 1)
segmentationNode.GetDisplayNode().Visibility2DFillOff()
if TransformNode:
segmentationNode.SetAndObserveTransformNodeID(
TransformNode.GetID())
print("transform successful")
print("color change successful")
else:
slicer.util.errorDisplay("No Segementation selected !")
def addFid(data, Dim=.5, nodName="N", lableName="1", color="red", GlyphType=1):
"""add a larger point"""
xyz = tuple(data)
tipFiducial = slicer.mrmlScene.AddNode(slicer.vtkMRMLMarkupsFiducialNode())
tipFiducial.SetName(nodName)
tipFiducial.AddFiducial(xyz[0], xyz[1], xyz[2])
tipFiducial.SetNthFiducialLabel(0, lableName)
slicer.mrmlScene.AddNode(tipFiducial)
tipFiducial.SetDisplayVisibility(True)
tipFiducial.GetDisplayNode().SetGlyphType(GlyphType) # Vertex2D
tipFiducial.GetDisplayNode().SetGlyphScale(Dim * 10)
tipFiducial.GetDisplayNode().SetTextScale(3)
tipFiducial.GetDisplayNode().SetSelectedColor(Helper.myColor(color))
''' GlyphShapes {
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 calculateFiducialDistance(self, modelNode, fiducial):
closestFiducial = slicer.util.getNode('CP')
if not closestFiducial:
closestFiducial = slicer.vtkMRMLMarkupsFiducialNode()
closestFiducial.SetName('CP')
closestFiducial.AddFiducial(0, 0, 0)
closestFiducial.SetNthFiducialLabel(0, 'CP')
slicer.mrmlScene.AddNode(closestFiducial)
closestFiducial.SetDisplayVisibility(False)
line = slicer.util.getNode('Line')
if not line:
line = slicer.vtkMRMLModelNode()
line.SetName('Line')
linePolyData = vtk.vtkPolyData()
line.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
line.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(line)
cellLocator = vtk.vtkCellLocator()
cellLocator.SetDataSet(modelNode.GetPolyData())
cellLocator.BuildLocator()
if fiducial.GetNumberOfFiducials() > 0:
ras = [0.0, 0.0, 0.0]
closestPoint = [0.0, 0.0, 0.0]
fiducial.GetNthFiducialPosition(0, ras)
distanceSquared = vtk.mutable(0.0)
subId = vtk.mutable(0)
cellId = vtk.mutable(0)
cell = vtk.vtkGenericCell()
cellLocator.FindClosestPoint(ras, closestPoint, cell, cellId, subId, distanceSquared);
distance = math.sqrt(distanceSquared)
closestFiducial.SetNthFiducialPosition(0, closestPoint[0], closestPoint[1], closestPoint[2])
closestFiducial.SetDisplayVisibility(True)
self.drawLineBetweenPoints(line, ras, closestPoint)
self.set3dViewConernerAnnotation('Distance = ' + "%.2f" % distance + 'mm')
else:
logging.warning('No fiducials in list!')
def getFiducialList(self):
P = self.getFiducialListName()
nodes = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLMarkupsFiducialNode', P)
if nodes.GetNumberOfItems() == 0:
# The list does not exist so we create it
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName(P)
slicer.mrmlScene.AddNode(fidNode)
else:
#The list exists but the observers must be updated
fidNode = nodes.GetItemAsObject(0)
return fidNode
def getFiducialList(self):
P = self.getFiducialListName()
nodes = slicer.mrmlScene.GetNodesByClassByName(
'vtkMRMLMarkupsFiducialNode', P)
if nodes.GetNumberOfItems() == 0:
# The list does not exist so we create it
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName(P)
slicer.mrmlScene.AddNode(fidNode)
else:
#The list exists but the observers must be updated
fidNode = nodes.GetItemAsObject(0)
return fidNode
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 section_MarkupRole(self):
self.delayDisplay("Markup role",self.delayMs)
# Create sample markups node
markupsNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(markupsNode)
markupsNode.SetName(self.sampleMarkupName)
fiducialPosition = [100.0, 0.0, 0.0]
markupsNode.AddFiducialFromArray(fiducialPosition)
# Add markups to subject hierarchy
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
patientNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, None, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelPatient(), 'Patient')
studyNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, patientNode, self.studyName, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelStudy())
markupsShNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, studyNode, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(), self.sampleMarkupName, markupsNode)
self.assertTrue( markupsShNode != None )
self.assertTrue( markupsShNode.GetParentNode() == studyNode )
self.assertTrue( markupsShNode.GetOwnerPluginName() == 'Markups' )
def section_MarkupRole(self):
self.delayDisplay("Markup role",self.delayMs)
# Create sample markups node
markupsNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(markupsNode)
markupsNode.SetName(self.sampleMarkupName)
fiducialPosition = [100.0, 0.0, 0.0]
markupsNode.AddFiducialFromArray(fiducialPosition)
# Add markups to subject hierarchy
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
patientNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, None, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelPatient(), 'Patient')
studyNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, patientNode, self.studyName, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelStudy())
markupsShNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, studyNode, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(), self.sampleMarkupName, markupsNode)
self.assertTrue( markupsShNode != None )
self.assertTrue( markupsShNode.GetParentNode() == studyNode )
self.assertTrue( markupsShNode.GetOwnerPluginName() == 'Markups' )
def test_AnglePlanes(self):
self.delayDisplay('Starting the test')
logic = AnglePlanesLogic()
matrix = numpy.matrix([[0.572236,0.192876,0.797085,0],
[-0.819942,0.152968,0.551631,0],
[0.0155322,0.969226,-0.245681,0],
[0,0,0,1]])
normalVector1 = logic.defineNormal(matrix)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(fidNode)
r1=32
a1=10
s1=4
r2=-9
a2=7
s2=19
r3=9
a3=-4
s3=46
fidNode.AddFiducial(r1,a1,s1)
fidNode.AddFiducial(r2,a2,s2)
fidNode.AddFiducial(r3,a3,s3)
logic.planeLandmarks(1,2,3,1,1)
GA = numpy.matrix([[5],[-2],[3]])
GB = numpy.matrix([[6],[1],[9]])
Normal = logic.normalLandmarks(GA, GB)
logic.getAngle(normalVector1, Normal)
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 runCaliper(self):
inputVolume = self.inputSelector.currentNode()
if not (inputVolume):
qt.QMessageBox.critical(
slicer.util.mainWindow(),
'Deploy Caliper', 'Input volume is required for calculation.')
return
# If coordinates modified, use for calculation
if self.coordinatesWidgetModified:
widgetPointsList = slicer.vtkMRMLMarkupsFiducialNode()
widgetPointsList.SetName('WPL')
# widgetNode = slicer.util.getNode('WPL')
slicer.mrmlScene.AddNode(widgetPointsList)
# Grab first widget coordinate and display
print "PointNum1 is: "
pointNum1Str = (str(self.c1Select.coordinates)).split(",")
pointNum1 = [float(i) for i in pointNum1Str]
print pointNum1
widgetPointsList.AddFiducial(pointNum1[0], pointNum1[1], pointNum1[2], 'WP-1')
# Grab second widget coordinate and display
print "PointNum2 is: "
pointNum2Str = (str(self.c2Select.coordinates)).split(",")
pointNum2 = [float(i) for i in pointNum2Str]
print pointNum2
widgetPointsList.AddFiducial(pointNum2[0], pointNum2[1], pointNum2[2], 'WP-2')
# Center the slices on Point 1
slicer.modules.markups.logic().JumpSlicesToLocation(pointNum1[0], pointNum1[1], pointNum1[2], True)
# Calculate distance in mm and print to console
distanceValue = math.sqrt( math.pow((pointNum1[0] - pointNum2[0]), 2) + math.pow((pointNum1[1] - pointNum2[1]), 2) + math.pow((pointNum1[2] - pointNum2[2]), 2))
self.distUpdate.setText("Distance: %.2f mm" % distanceValue)
# Add a ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetDistanceAnnotationVisibility(1)
rulerNode.SetPosition1(pointNum1[0], pointNum1[1], pointNum1[2])
rulerNode.SetPosition2(pointNum2[0], pointNum2[1], pointNum2[2])
rulerNode.SetName('Distance 1')
rulerNode.SetDistanceAnnotationVisibility(False)
rulerNode.Initialize(slicer.mrmlScene)
self.coordinatesWidgetModified = False
else:
# Get interactive coordinates, if any
intNode1 = slicer.util.getNode('IP1')
intNode2 = slicer.util.getNode('IP2')
if ((intNode1.GetNumberOfFiducials() == 1) and (intNode2.GetNumberOfFiducials() == 1)):
z3point1 = [0.0, 0.0, 0.0]
z3point2 = [0.0, 0.0, 0.0]
intNode1.GetNthFiducialPosition(0, z3point1)
intNode2.GetNthFiducialPosition(0, z3point2)
print "Interactive Point 1:"
print z3point1
print "Interactive Point 2:"
print z3point2
interactiveDistance = math.sqrt( math.pow((z3point1[0] - z3point2[0]), 2) + math.pow((z3point1[1] - z3point2[1]), 2) + math.pow((z3point1[2] - z3point2[2]), 2))
self.intDistUpdate.setText("Distance: %.2f mm" % interactiveDistance)
intRulerNode = slicer.vtkMRMLAnnotationRulerNode()
intRulerNode.SetDistanceAnnotationVisibility(1)
intRulerNode.SetPosition1(z3point1[0], z3point1[1], z3point1[2])
intRulerNode.SetPosition2(z3point2[0], z3point2[1], z3point2[2])
intRulerNode.SetName('Distance 2')
intRulerNode.SetDistanceAnnotationVisibility(False)
intRulerNode.Initialize(slicer.mrmlScene)
# Blur if checkbox is checked
if self.blur.isChecked():
gauss = vtk.vtkImageGaussianSmooth()
gauss.SetInputData(inputVolume.GetImageData())
gauss.SetDimensionality(3)
fwhmValue = .01 * distanceValue
gauss.SetStandardDeviation(fwhmValue)
gauss.Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
inputVolume.SetAndObserveImageData(gauss.GetOutput())
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 setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
logic = MyPythonModuleLogic()
self.coordinatesWidgetModified = False
interactivePoint1Node = slicer.vtkMRMLMarkupsFiducialNode()
interactivePoint1Node.SetName('IP1')
interactivePoint2Node = slicer.vtkMRMLMarkupsFiducialNode()
interactivePoint2Node.SetName('IP2')
# slicer.mrmlScene.AddNode(widgetPointsList)
slicer.mrmlScene.AddNode(interactivePoint1Node)
slicer.mrmlScene.AddNode(interactivePoint2Node)
self.CrosshairNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLCrosshairNode')
if self.CrosshairNode:
self.CrosshairNodeObserverTag = self.CrosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, self.interactiveCaliper)
else:
print "Couldn't access crosshair."
# Volumes collapsible button
self.volumeCButton = ctk.ctkCollapsibleButton()
self.volumeCButton.text = "Volume"
self.layout.addWidget(self.volumeCButton)
# Layout within the volumes collapsible button
self.volumeCLayout = qt.QFormLayout(self.volumeCButton)
#
# the volume selectors
#
self.inputFrame = qt.QFrame(self.volumeCButton)
self.inputFrame.setLayout(qt.QHBoxLayout())
self.volumeCLayout.addWidget(self.inputFrame)
self.inputSelector = qt.QLabel("Input Volume: ", self.inputFrame)
self.inputFrame.layout().addWidget(self.inputSelector)
self.inputSelector = slicer.qMRMLNodeComboBox(self.inputFrame)
self.inputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.setMRMLScene( slicer.mrmlScene )
self.inputFrame.layout().addWidget(self.inputSelector)
# Coordinates collapsible button set-up
self.coord = ctk.ctkCollapsibleButton()
self.coord.text = "Manually input coordinates"
self.layout.addWidget(self.coord)
self.coordLayout = qt.QFormLayout(self.coord)
# Coordinate 1 Label and widget
self.c1 = qt.QFrame(self.coord)
self.c1.setLayout(qt.QHBoxLayout())
self.coordLayout.addWidget(self.c1)
self.c1Select = qt.QLabel("Coordinate 1: ", self.c1)
self.c1.layout().addWidget(self.c1Select)
self.c1Select = ctk.ctkCoordinatesWidget(self.c1)
self.c1Select.connect('coordinatesChanged(double*)', self.changedCoordinates)
self.c1.layout().addWidget(self.c1Select)
# Coordinate 2 Label and widget
self.c2 = qt.QFrame(self.coord)
self.c2.setLayout(qt.QHBoxLayout())
self.coordLayout.addWidget(self.c2)
self.c2Select = qt.QLabel("Coordinate 2: ", self.c2)
self.c2.layout().addWidget(self.c2Select)
self.c2Select = ctk.ctkCoordinatesWidget(self.c2)
self.c2Select.connect('coordinatesChanged(double*)', self.changedCoordinates)
self.c2.layout().addWidget(self.c2Select)
# Deploy caliper button
runCaliperButton = qt.QPushButton("Deploy Caliper")
runCaliperButton.toolTip = "Deploy the virtual caliper on the data set."
self.coordLayout.addWidget(runCaliperButton)
runCaliperButton.connect('clicked(bool)', self.runCaliper)
# Label with updating distance value results
self.distanceLabel = qt.QFrame(self.coord)
self.distanceLabel.setLayout(qt.QHBoxLayout())
self.coordLayout.addWidget(self.distanceLabel)
self.distUpdate = qt.QLabel("Distance: ", self.distanceLabel)
self.distanceLabel.layout().addWidget(self.distUpdate)
# Interactive coordinates collapsible button set-up
self.interactiveCoord = ctk.ctkCollapsibleButton()
self.interactiveCoord.text = "Interactive coordinates"
self.layout.addWidget(self.interactiveCoord)
self.interactiveCoordLayout = qt.QFormLayout(self.interactiveCoord)
# Interactive caliper 1 button
buttonIC1 = qt.QPushButton("Interactive Caliper - Point 1")
buttonIC1.toolTip = "Run the interactive caliper for Point 1."
self.interactiveCoordLayout.addWidget(buttonIC1)
buttonIC1.connect('clicked(bool)', logic.saveInteractivePoint1)
# Interactive caliper 2 button
buttonIC2 = qt.QPushButton("Interactive Caliper - Point 2")
buttonIC2.toolTip = "Run the interactive caliper for Point 2."
self.interactiveCoordLayout.addWidget(buttonIC2)
buttonIC2.connect('clicked(bool)', logic.saveInteractivePoint2)
# Interactive caliper 1 label with axes
self.labelIC1 = qt.QFrame(self.interactiveCoord)
self.labelIC1.setLayout(qt.QHBoxLayout())
self.interactiveCoordLayout.addWidget(self.labelIC1)
self.labelIC1update = qt.QLabel("X: NaN Y: NaN Z: NaN ", self.labelIC1)
self.labelIC1.layout().addWidget(self.labelIC1update)
# Label with updating distance value results
self.intDistanceLabel = qt.QFrame(self.interactiveCoord)
self.intDistanceLabel.setLayout(qt.QHBoxLayout())
self.interactiveCoordLayout.addWidget(self.intDistanceLabel)
self.intDistUpdate = qt.QLabel("Distance: ", self.intDistanceLabel)
self.intDistanceLabel.layout().addWidget(self.intDistUpdate)
# Blur gaussian collapsible button set-up
self.blurButton = ctk.ctkCollapsibleButton()
self.blurButton.text = "Add gaussian blur"
self.layout.addWidget(self.blurButton)
self.blurButtonLayout = qt.QFormLayout(self.blurButton)
# Blur checkmark
self.blur = qt.QCheckBox("Blur image", self.blurButton)
self.blur.toolTip = "When checked, blur image based on distance"
self.blur.checked = False
self.blurButtonLayout.addWidget(self.blur)
self.blur.connect('stateChanged(int)', self.blurCheckBox)
# Display original checkmark
self.orig = qt.QCheckBox("Display original", self.blurButton)
self.orig.toolTip = "When checked, blur image based on distance"
self.orig.checked = True
self.blurButtonLayout.addWidget(self.orig)
self.orig.connect('stateChanged(int)', self.origCheckBox)
# Add vertical spacer
self.layout.addStretch(1)
# Set local var as instance attribute
self.runCaliperButton = runCaliperButton
def locateCochlea(self, inputVolumeNode, inputPointEdt, volumeType):
# Create Fiducial Node for the cochlea location
print(" ..... getting cochlea location in "+volumeType+ " image")
# Display Coronal during locating the cochlea
green_logic = slicer.app.layoutManager().sliceWidget("Green").sliceLogic()
green_cn = green_logic.GetSliceCompositeNode()
green_cn.SetBackgroundVolumeID(inputVolumeNode.GetID())
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpGreenSliceView)
# Fit slice to window
sliceNodes = slicer.util.getNodes('vtkMRMLSliceNode*')
layoutManager = slicer.app.layoutManager()
for sliceNode in sliceNodes.values():
sliceWidget = layoutManager.sliceWidget(sliceNode.GetLayoutName())
if sliceWidget:
sliceWidget.sliceLogic().FitSliceToAll()
#endif
#endfor
# Remove old Fiducial nodes
nodes = slicer.util.getNodesByClass('vtkMRMLMarkupsFiducialNode')
for f in nodes:
if ((f.GetName() == volumeType+"Point") ):
slicer.mrmlScene.RemoveNode(f)
#endif
#endfor
# Reset global point label
inputPoint = [0,0,0]
inputPointEdt.setText("[0, 0, 0]")
# Check if a volume is selected
#
if not inputVolumeNode:
print >> sys.stderr, "You need to select a "+ volumeType +" image first."
return -1
#endif
#TODO: reduce this code
if volumeType=="fixed":
self.fixedVolumeNode = inputVolumeNode
self.fixedPointEdt = inputPointEdt
self.fixedMarkupNode = slicer.vtkMRMLMarkupsFiducialNode()
self.fixedMarkupNode.SetName(volumeType+"Point")
slicer.mrmlScene.AddNode(self.fixedMarkupNode)
# Start Fiducial Placement Mode in Slicer
placeModePersistance = 0
slicer.modules.markups.logic().StartPlaceMode(placeModePersistance)
# Observe scene for updates
self.fixedMarkupNode.AddObserver(self.fixedMarkupNode.MarkupAddedEvent, self.convRAS2IJK)
self.fixedMarkupNode.AddObserver(self.fixedMarkupNode.MarkupRemovedEvent, self.convRAS2IJK)
self.fixedMarkupNode.AddObserver(self.fixedMarkupNode.PointModifiedEvent, self.convRAS2IJK)
elif volumeType=="moving":
self.movingVolumeNode = inputVolumeNode
self.movingPointEdt = inputPointEdt
self.movingMarkupNode = slicer.vtkMRMLMarkupsFiducialNode()
self.movingMarkupNode.SetName(volumeType+"Point")
slicer.mrmlScene.AddNode(self.movingMarkupNode)
# Start Fiducial Placement Mode in Slicer
placeModePersistance = 0
slicer.modules.markups.logic().StartPlaceMode(placeModePersistance)
# Observe scene for updates
self.movingMarkupNode.AddObserver(self.movingMarkupNode.MarkupAddedEvent, self.convRAS2IJK)
self.movingMarkupNode.AddObserver(self.movingMarkupNode.MarkupRemovedEvent, self.convRAS2IJK)
self.movingMarkupNode.AddObserver(self.movingMarkupNode.PointModifiedEvent, self.convRAS2IJK)
def setupScene(self): # applet specific
logging.debug("setupScene")
Guidelet.setupScene(self)
logging.debug("Create transforms")
self.cauteryTipToCautery = slicer.util.getNode("CauteryTipToCautery")
if not self.cauteryTipToCautery:
self.cauteryTipToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryTipToCautery.SetName("CauteryTipToCautery")
m = self.readTransformFromSettings("CauteryTipToCautery")
if m:
self.cauteryTipToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryTipToCautery)
self.cauteryModelToCauteryTip = slicer.util.getNode("CauteryModelToCauteryTip")
if not self.cauteryModelToCauteryTip:
self.cauteryModelToCauteryTip = slicer.vtkMRMLLinearTransformNode()
self.cauteryModelToCauteryTip.SetName("CauteryModelToCauteryTip")
m = self.readTransformFromSettings("CauteryModelToCauteryTip")
if m:
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryModelToCauteryTip)
self.needleTipToNeedle = slicer.util.getNode("NeedleTipToNeedle")
if not self.needleTipToNeedle:
self.needleTipToNeedle = slicer.vtkMRMLLinearTransformNode()
self.needleTipToNeedle.SetName("NeedleTipToNeedle")
m = self.readTransformFromSettings("NeedleTipToNeedle")
if m:
self.needleTipToNeedle.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedle)
self.needleModelToNeedleTip = slicer.util.getNode("NeedleModelToNeedleTip")
if not self.needleModelToNeedleTip:
self.needleModelToNeedleTip = slicer.vtkMRMLLinearTransformNode()
self.needleModelToNeedleTip.SetName("NeedleModelToNeedleTip")
m = self.readTransformFromSettings("NeedleModelToNeedleTip")
if m:
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleModelToNeedleTip)
self.cauteryCameraToCautery = slicer.util.getNode("CauteryCameraToCautery")
if not self.cauteryCameraToCautery:
self.cauteryCameraToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryCameraToCautery.SetName("CauteryCameraToCautery")
m = vtk.vtkMatrix4x4()
m.SetElement(0, 0, 0)
m.SetElement(0, 2, -1)
m.SetElement(1, 1, 0)
m.SetElement(1, 0, 1)
m.SetElement(2, 2, 0)
m.SetElement(2, 1, -1)
self.cauteryCameraToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryCameraToCautery)
self.CauteryToNeedle = slicer.util.getNode("CauteryToNeedle")
if not self.CauteryToNeedle:
self.CauteryToNeedle = slicer.vtkMRMLLinearTransformNode()
self.CauteryToNeedle.SetName("CauteryToNeedle")
slicer.mrmlScene.AddNode(self.CauteryToNeedle)
# Create transforms that will be updated through OpenIGTLink
self.cauteryToReference = slicer.util.getNode("CauteryToReference")
if not self.cauteryToReference:
self.cauteryToReference = slicer.vtkMRMLLinearTransformNode()
self.cauteryToReference.SetName("CauteryToReference")
slicer.mrmlScene.AddNode(self.cauteryToReference)
self.needleToReference = slicer.util.getNode("NeedleToReference")
if not self.needleToReference:
self.needleToReference = slicer.vtkMRMLLinearTransformNode()
self.needleToReference.SetName("NeedleToReference")
slicer.mrmlScene.AddNode(self.needleToReference)
# Cameras
logging.debug("Create cameras")
self.LeftCamera = slicer.util.getNode("Left Camera")
if not self.LeftCamera:
self.LeftCamera = slicer.vtkMRMLCameraNode()
self.LeftCamera.SetName("Left Camera")
slicer.mrmlScene.AddNode(self.LeftCamera)
self.RightCamera = slicer.util.getNode("Right Camera")
if not self.RightCamera:
self.RightCamera = slicer.vtkMRMLCameraNode()
self.RightCamera.SetName("Right Camera")
slicer.mrmlScene.AddNode(self.RightCamera)
# Models
logging.debug("Create models")
self.cauteryModel_CauteryTip = slicer.util.getNode("CauteryModel")
if not self.cauteryModel_CauteryTip:
if self.parameterNode.GetParameter("TestMode") == "True":
moduleDirectoryPath = slicer.modules.lumpnav.path.replace("LumpNav.py", "")
slicer.util.loadModel(
qt.QDir.toNativeSeparators(moduleDirectoryPath + "../../../models/temporary/cautery.stl")
)
self.cauteryModel_CauteryTip = slicer.util.getNode(pattern="cautery")
else:
slicer.modules.createmodels.logic().CreateNeedle(100, 1.0, 2.5, 0)
self.cauteryModel_CauteryTip = slicer.util.getNode(pattern="NeedleModel")
self.cauteryModel_CauteryTip.GetDisplayNode().SetColor(1.0, 1.0, 0)
self.cauteryModel_CauteryTip.SetName("CauteryModel")
self.needleModel_NeedleTip = slicer.util.getNode("NeedleModel")
if not self.needleModel_NeedleTip:
slicer.modules.createmodels.logic().CreateNeedle(80, 1.0, 2.5, 0)
self.needleModel_NeedleTip = slicer.util.getNode(pattern="NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode().SetColor(0.333333, 1.0, 1.0)
self.needleModel_NeedleTip.SetName("NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode().SliceIntersectionVisibilityOn()
# Create surface from point set
logging.debug("Create surface from point set")
self.tumorModel_Needle = slicer.util.getNode("TumorModel")
if not self.tumorModel_Needle:
self.tumorModel_Needle = slicer.vtkMRMLModelNode()
self.tumorModel_Needle.SetName("TumorModel")
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(0.001)
self.tumorModel_Needle.SetPolyDataConnection(sphereSource.GetOutputPort())
slicer.mrmlScene.AddNode(self.tumorModel_Needle)
# Add display node
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(0, 1, 0) # Green
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(4)
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
self.tumorModel_Needle.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
tumorMarkups_Needle = slicer.util.getNode("T")
if not tumorMarkups_Needle:
tumorMarkups_Needle = slicer.vtkMRMLMarkupsFiducialNode()
tumorMarkups_Needle.SetName("T")
slicer.mrmlScene.AddNode(tumorMarkups_Needle)
tumorMarkups_Needle.CreateDefaultDisplayNodes()
tumorMarkups_Needle.GetDisplayNode().SetTextScale(0)
self.setAndObserveTumorMarkupsNode(tumorMarkups_Needle)
# Set up breach warning node
logging.debug("Set up breach warning")
self.breachWarningNode = slicer.util.getNode("LumpNavBreachWarning")
if not self.breachWarningNode:
self.breachWarningNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLBreachWarningNode")
self.breachWarningNode.SetName("LumpNavBreachWarning")
slicer.mrmlScene.AddNode(self.breachWarningNode)
self.breachWarningNode.SetPlayWarningSound(True)
self.breachWarningNode.SetWarningColor(1, 0, 0)
self.breachWarningNode.SetOriginalColor(self.tumorModel_Needle.GetDisplayNode().GetColor())
self.breachWarningNode.SetAndObserveToolTransformNodeId(self.cauteryTipToCautery.GetID())
self.breachWarningNode.SetAndObserveWatchedModelNodeID(self.tumorModel_Needle.GetID())
# Set up breach warning light
import BreachWarningLight
logging.debug("Set up breach warning light")
self.breachWarningLightLogic = BreachWarningLight.BreachWarningLightLogic()
self.breachWarningLightLogic.setMarginSizeMm(
float(self.parameterNode.GetParameter("BreachWarningLightMarginSizeMm"))
)
if self.parameterNode.GetParameter("EnableBreachWarningLight") == "True":
logging.debug("BreachWarningLight: active")
self.breachWarningLightLogic.startLightFeedback(self.breachWarningNode, self.connectorNode)
else:
logging.debug("BreachWarningLight: shutdown")
self.breachWarningLightLogic.shutdownLight(self.connectorNode)
# Build transform tree
logging.debug("Set up transform tree")
self.cauteryToReference.SetAndObserveTransformNodeID(self.ReferenceToRas.GetID())
self.cauteryCameraToCautery.SetAndObserveTransformNodeID(self.cauteryToReference.GetID())
self.cauteryTipToCautery.SetAndObserveTransformNodeID(self.cauteryToReference.GetID())
self.cauteryModelToCauteryTip.SetAndObserveTransformNodeID(self.cauteryTipToCautery.GetID())
self.needleToReference.SetAndObserveTransformNodeID(self.ReferenceToRas.GetID())
self.needleTipToNeedle.SetAndObserveTransformNodeID(self.needleToReference.GetID())
self.needleModelToNeedleTip.SetAndObserveTransformNodeID(self.needleTipToNeedle.GetID())
self.cauteryModel_CauteryTip.SetAndObserveTransformNodeID(self.cauteryModelToCauteryTip.GetID())
self.needleModel_NeedleTip.SetAndObserveTransformNodeID(self.needleModelToNeedleTip.GetID())
self.tumorModel_Needle.SetAndObserveTransformNodeID(self.needleToReference.GetID())
self.tumorMarkups_Needle.SetAndObserveTransformNodeID(self.needleToReference.GetID())
# self.liveUltrasoundNode_Reference.SetAndObserveTransformNodeID(self.ReferenceToRas.GetID())
# Hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
logging.debug("Hide slice view annotations")
import DataProbe
dataProbeUtil = DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode = dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter("showSliceViewAnnotations", "0")
def setup(self):
self.__clippingModelNode = None
self.__clippingMarkupNode = None
self.__clippingMarkupNodeObserver = None
self.toFids = slicer.vtkMRMLMarkupsFiducialNode()
self.fromFids = slicer.vtkMRMLMarkupsFiducialNode()
self.toFids.SetName('toFids')
self.fromFids.SetName('fromFids')
slicer.mrmlScene.AddNode(self.toFids)
slicer.mrmlScene.AddNode(self.fromFids)
self.__markupList = []
# create a callapsible button
collapsibleButton = ctk.ctkCollapsibleButton()
collapsibleButton.text = "Cubic Spline Image Segmentation Correction"
# bind collapsibleButton to root Layout
self.layout.addWidget(collapsibleButton)
# new layout for collapsible button
self.formLayout = qt.QFormLayout(collapsibleButton)
# volume selector
self.formFrame = qt.QFrame(collapsibleButton)
self.formFrame1 = qt.QFrame(collapsibleButton)
self.formFrame4 = qt.QFrame(collapsibleButton)
self.formFrame2 = qt.QFrame(collapsibleButton)
self.formFrame5 = qt.QFrame(collapsibleButton)
self.formFrame3 = qt.QFrame(collapsibleButton)
# set a layout to horizontal
self.formFrame.setLayout(qt.QHBoxLayout())
self.formFrame1.setLayout(qt.QHBoxLayout())
self.formFrame4.setLayout(qt.QHBoxLayout())
self.formFrame2.setLayout(qt.QHBoxLayout())
self.formFrame5.setLayout(qt.QHBoxLayout())
self.formFrame3.setLayout(qt.QHBoxLayout())
# bind a new frame to existing layout in collapsible menu
self.formLayout.addWidget(self.formFrame)
self.formLayout.addWidget(self.formFrame1)
self.formLayout.addWidget(self.formFrame4)
self.formLayout.addWidget(self.formFrame2)
self.formLayout.addWidget(self.formFrame5)
self.formLayout.addWidget(self.formFrame3)
# creating new volume selector
self.inputSelector = qt.QLabel("Input Volume: ", self.formFrame)
self.formFrame.layout().addWidget(self.inputSelector)
self.inputSelector = slicer.qMRMLNodeComboBox(self.formFrame)
self.inputSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector1 = qt.QLabel("Input segmentation: ",
self.formFrame1)
self.formFrame1.layout().addWidget(self.inputSelector1)
self.inputSelector1 = slicer.qMRMLNodeComboBox(self.formFrame1)
self.inputSelector1.nodeTypes = (("vtkMRMLSegmentationNode"), "")
self.inputSelector1.addEnabled = False
self.inputSelector1.removeEnabled = False
self.inputSelector4 = qt.QLabel("Input transformation: ",
self.formFrame4)
self.formFrame4.layout().addWidget(self.inputSelector4)
self.inputSelector4 = slicer.qMRMLNodeComboBox(self.formFrame4)
self.inputSelector4.nodeTypes = (("vtkMRMLTransformNode"), "")
self.inputSelector4.addEnabled = False
self.inputSelector4.removeEnabled = False
self.inputSelector2 = qt.QLabel("Set default Segmentation display : ",
self.formFrame2)
self.formFrame2.layout().addWidget(self.inputSelector2)
self.inputSelector5 = qt.QLabel("Add markups : ", self.formFrame3)
self.formFrame5.layout().addWidget(self.inputSelector5)
self.inputSelector3 = qt.QLabel("Segmentation Correction: ",
self.formFrame3)
self.formFrame3.layout().addWidget(self.inputSelector3)
# bind the current volume selector to the current scene of slicer
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector1.setMRMLScene(slicer.mrmlScene)
self.inputSelector4.setMRMLScene(slicer.mrmlScene)
# bind the input selector to the frame
self.formFrame.layout().addWidget(self.inputSelector)
self.formFrame1.layout().addWidget(self.inputSelector1)
self.formFrame4.layout().addWidget(self.inputSelector4)
# testing
button = qt.QPushButton("Load Volume")
self.formFrame.layout().addWidget(button)
button.connect("clicked()", slicer.util.openAddVolumeDialog)
button.show()
# button for importing mesh files
button1 = qt.QPushButton("Load Segemntation")
self.formFrame1.layout().addWidget(button1)
button1.connect("clicked()", slicer.util.openAddSegmentationDialog)
button1.show()
# button for importing mesh files
button4 = qt.QPushButton("Load Transform")
self.formFrame4.layout().addWidget(button4)
button4.connect("clicked()", slicer.util.openAddTransformDialog)
button4.show()
# button for setting default segmentation display
button2 = qt.QPushButton("Set default")
self.formFrame2.layout().addWidget(button2)
button2.connect("clicked(bool)", self.SetDefaultValuesClicked)
button2.show()
# button for Final work
self.button5 = qt.QToolButton()
self.button5.icon = qt.QIcon(
os.path.join(os.path.dirname(__file__),
'MarkupsMouseModePlace.png'))
self.button5.setCheckable(1)
self.formFrame5.layout().addWidget(self.button5)
self.button5.connect("clicked(bool)", self.enableaddmarkuponclick)
self.button5.show()
# button for Final work
button3 = qt.QPushButton("Do corrections")
self.formFrame3.layout().addWidget(button3)
button3.connect("clicked(bool)", self.do_correctionsClicked)
button3.show()
def __init__(self, modelNode):
self.modelNode = modelNode
self.toolTipToTool = None
self.toolToReference = None
self.modelTransform = None
self.transformedModel = slicer.util.getNode('Transformed Model')
if not self.transformedModel:
self.transformedModel = slicer.vtkMRMLModelNode()
self.transformedModel.SetName('Transformed Model')
self.transformedModel.SetAndObservePolyData(self.modelNode.GetPolyData())
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
self.transformedModel.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.transformedModel)
self.transformedModel.SetDisplayVisibility(False)
self.closestFiducial = slicer.util.getNode('CP')
if not self.closestFiducial:
self.closestFiducial = slicer.vtkMRMLMarkupsFiducialNode()
self.closestFiducial.SetName('CP')
self.closestFiducial.AddFiducial(0, 0, 0)
self.closestFiducial.SetNthFiducialLabel(0, '')
slicer.mrmlScene.AddNode(self.closestFiducial)
self.closestFiducial.SetDisplayVisibility(False)
self.closestFiducial.GetDisplayNode().SetGlyphScale(3.0)
self.closestFiducial.GetDisplayNode().SetGlyphType(4) # ThickCross2D
self.closestFiducial.GetDisplayNode().SetSelectedColor(0,0,1)
self.tipFiducial = slicer.util.getNode('Tip')
if not self.tipFiducial:
self.tipFiducial = slicer.vtkMRMLMarkupsFiducialNode()
self.tipFiducial.SetName('Tip')
self.tipFiducial.AddFiducial(0, 0, 0)
self.tipFiducial.SetNthFiducialLabel(0, '')
slicer.mrmlScene.AddNode(self.tipFiducial)
self.tipFiducial.SetDisplayVisibility(True)
self.tipFiducial.GetDisplayNode().SetGlyphType(1) # Vertex2D
self.tipFiducial.GetDisplayNode().SetTextScale(1.3)
self.tipFiducial.GetDisplayNode().SetSelectedColor(1,1,1)
self.line = slicer.util.getNode('Line')
if not self.line:
self.line = slicer.vtkMRMLModelNode()
self.line.SetName('Line')
linePolyData = vtk.vtkPolyData()
self.line.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
self.line.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.line)
# VTK objects
self.transformPolyDataFilter = vtk.vtkTransformPolyDataFilter()
self.cellLocator = vtk.vtkCellLocator()
# 3D View
threeDWidget = slicer.app.layoutManager().threeDWidget(0)
self.threeDView = threeDWidget.threeDView()
self.callbackObserverTag = -1
def FiducialButtonClick(self, volumeType):
# Remove old Fiducial nodes
nodes = slicer.util.getNodesByClass('vtkMRMLMarkupsFiducialNode')
for f in nodes:
if ((f.GetName() == "FixedImageFiducial")
or (f.GetName() == "MovingImageFiducial")):
slicer.mrmlScene.RemoveNode(f)
# Create Fiducial Node for the cochlea location in both images
if (volumeType == "fixed"):
print(" ..... getting cochlea location in the fixed image")
# Reset global point label
self.fixedPoint = [0, 0, 0]
self.fixedPointLbl.setText("[0, 0, 0]")
# Check if a volume is selected
if not self.fixedSelectorCoBx.currentNode():
print >> sys.stderr, "ERROR: No fixed volume"
return -1
# TODO bug: if the fiducial placement mode is cancelled using the Slicer Fiducial button, the button remains colored
self.fixedFiducialBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.movingFiducialBtn.setStyleSheet(
"QPushButton{ background-color: White }")
self.fixedFiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
self.fixedFiducialNode.SetName("FixedImageFiducial")
slicer.mrmlScene.AddNode(self.fixedFiducialNode)
self.displayCoronalView(self.fixedSelectorCoBx.currentNode())
# Start Fiducial Placement Mode in Slicer
placeModePersistance = 0
slicer.modules.markups.logic().StartPlaceMode(placeModePersistance)
# Observe scene for updates
self.fixedFiducialNode.AddObserver(
self.fixedFiducialNode.MarkupAddedEvent, self.convRAS2IJK)
self.fixedFiducialNode.AddObserver(
self.fixedFiducialNode.MarkupRemovedEvent, self.convRAS2IJK)
elif (volumeType == "moving"):
print(" ..... getting cochlea location in the moving image")
# Reset global point label
self.movingPoint = [0, 0, 0]
self.movingPointLbl.setText("[0, 0, 0]")
# Check if a volume is selected
if not self.movingSelectorCoBx.currentNode():
print >> sys.stderr, "ERROR: No moving volume, Bad Path or DICOM."
return -1
# TODO bug: if the fiducial placement mode is cancelled using the Slicer Fiducial button, the button remains colored
self.movingFiducialBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.fixedFiducialBtn.setStyleSheet(
"QPushButton{ background-color: White }")
self.movingFiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
self.movingFiducialNode.SetName("MovingImageFiducial")
slicer.mrmlScene.AddNode(self.movingFiducialNode)
self.displayCoronalView(self.movingSelectorCoBx.currentNode())
# Start Fiducial Placement Mode in Slicer
placeModePersistance = 0
slicer.modules.markups.logic().StartPlaceMode(placeModePersistance)
# Observe scene for updates
self.movingFiducialNode.AddObserver(
self.movingFiducialNode.MarkupAddedEvent, self.convRAS2IJK)
self.movingFiducialNode.AddObserver(
self.movingFiducialNode.MarkupRemovedEvent, self.convRAS2IJK)
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
def setupScene(self): #applet specific
logging.debug('setupScene')
Guidelet.setupScene(self)
logging.debug('Create transforms')
self.cauteryTipToCautery = slicer.util.getNode('CauteryTipToCautery')
if not self.cauteryTipToCautery:
self.cauteryTipToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryTipToCautery.SetName("CauteryTipToCautery")
m = self.readTransformFromSettings('CauteryTipToCautery')
if m:
self.cauteryTipToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryTipToCautery)
self.cauteryModelToCauteryTip = slicer.util.getNode(
'CauteryModelToCauteryTip')
if not self.cauteryModelToCauteryTip:
self.cauteryModelToCauteryTip = slicer.vtkMRMLLinearTransformNode()
self.cauteryModelToCauteryTip.SetName("CauteryModelToCauteryTip")
m = self.readTransformFromSettings('CauteryModelToCauteryTip')
if m:
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryModelToCauteryTip)
self.needleTipToNeedle = slicer.util.getNode('NeedleTipToNeedle')
if not self.needleTipToNeedle:
self.needleTipToNeedle = slicer.vtkMRMLLinearTransformNode()
self.needleTipToNeedle.SetName("NeedleTipToNeedle")
m = self.readTransformFromSettings('NeedleTipToNeedle')
if m:
self.needleTipToNeedle.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedle)
self.needleModelToNeedleTip = slicer.util.getNode(
'NeedleModelToNeedleTip')
if not self.needleModelToNeedleTip:
self.needleModelToNeedleTip = slicer.vtkMRMLLinearTransformNode()
self.needleModelToNeedleTip.SetName("NeedleModelToNeedleTip")
m = self.readTransformFromSettings('NeedleModelToNeedleTip')
if m:
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleModelToNeedleTip)
self.cauteryCameraToCautery = slicer.util.getNode(
'CauteryCameraToCautery')
if not self.cauteryCameraToCautery:
self.cauteryCameraToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryCameraToCautery.SetName("CauteryCameraToCautery")
m = vtk.vtkMatrix4x4()
m.SetElement(0, 0, 0)
m.SetElement(0, 2, -1)
m.SetElement(1, 1, 0)
m.SetElement(1, 0, 1)
m.SetElement(2, 2, 0)
m.SetElement(2, 1, -1)
self.cauteryCameraToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryCameraToCautery)
self.CauteryToNeedle = slicer.util.getNode('CauteryToNeedle')
if not self.CauteryToNeedle:
self.CauteryToNeedle = slicer.vtkMRMLLinearTransformNode()
self.CauteryToNeedle.SetName("CauteryToNeedle")
slicer.mrmlScene.AddNode(self.CauteryToNeedle)
# Create transforms that will be updated through OpenIGTLink
self.cauteryToReference = slicer.util.getNode('CauteryToReference')
if not self.cauteryToReference:
self.cauteryToReference = slicer.vtkMRMLLinearTransformNode()
self.cauteryToReference.SetName("CauteryToReference")
slicer.mrmlScene.AddNode(self.cauteryToReference)
self.needleToReference = slicer.util.getNode('NeedleToReference')
if not self.needleToReference:
self.needleToReference = slicer.vtkMRMLLinearTransformNode()
self.needleToReference.SetName("NeedleToReference")
slicer.mrmlScene.AddNode(self.needleToReference)
# Cameras
logging.debug('Create cameras')
self.LeftCamera = slicer.util.getNode('Left Camera')
if not self.LeftCamera:
self.LeftCamera = slicer.vtkMRMLCameraNode()
self.LeftCamera.SetName("Left Camera")
slicer.mrmlScene.AddNode(self.LeftCamera)
self.RightCamera = slicer.util.getNode('Right Camera')
if not self.RightCamera:
self.RightCamera = slicer.vtkMRMLCameraNode()
self.RightCamera.SetName("Right Camera")
slicer.mrmlScene.AddNode(self.RightCamera)
# Models
logging.debug('Create models')
self.cauteryModel_CauteryTip = slicer.util.getNode('CauteryModel')
if not self.cauteryModel_CauteryTip:
if (self.parameterNode.GetParameter('TestMode') == 'True'):
moduleDirectoryPath = slicer.modules.lumpnav.path.replace(
'LumpNav.py', '')
slicer.util.loadModel(
qt.QDir.toNativeSeparators(
moduleDirectoryPath +
'../../../models/temporary/cautery.stl'))
self.cauteryModel_CauteryTip = slicer.util.getNode(
pattern="cautery")
else:
slicer.modules.createmodels.logic().CreateNeedle(
100, 1.0, 2.5, 0)
self.cauteryModel_CauteryTip = slicer.util.getNode(
pattern="NeedleModel")
self.cauteryModel_CauteryTip.GetDisplayNode().SetColor(
1.0, 1.0, 0)
self.cauteryModel_CauteryTip.SetName("CauteryModel")
self.needleModel_NeedleTip = slicer.util.getNode('NeedleModel')
if not self.needleModel_NeedleTip:
slicer.modules.createmodels.logic().CreateNeedle(80, 1.0, 2.5, 0)
self.needleModel_NeedleTip = slicer.util.getNode(
pattern="NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode().SetColor(
0.333333, 1.0, 1.0)
self.needleModel_NeedleTip.SetName("NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode(
).SliceIntersectionVisibilityOn()
# Create surface from point set
logging.debug('Create surface from point set')
self.tumorModel_Needle = slicer.util.getNode('TumorModel')
if not self.tumorModel_Needle:
self.tumorModel_Needle = slicer.vtkMRMLModelNode()
self.tumorModel_Needle.SetName("TumorModel")
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(0.001)
self.tumorModel_Needle.SetPolyDataConnection(
sphereSource.GetOutputPort())
slicer.mrmlScene.AddNode(self.tumorModel_Needle)
# Add display node
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(0, 1, 0) # Green
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(4)
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
self.tumorModel_Needle.SetAndObserveDisplayNodeID(
modelDisplayNode.GetID())
tumorMarkups_Needle = slicer.util.getNode('T')
if not tumorMarkups_Needle:
tumorMarkups_Needle = slicer.vtkMRMLMarkupsFiducialNode()
tumorMarkups_Needle.SetName("T")
slicer.mrmlScene.AddNode(tumorMarkups_Needle)
tumorMarkups_Needle.CreateDefaultDisplayNodes()
tumorMarkups_Needle.GetDisplayNode().SetTextScale(0)
self.setAndObserveTumorMarkupsNode(tumorMarkups_Needle)
# Set up breach warning node
logging.debug('Set up breach warning')
self.breachWarningNode = slicer.util.getNode('LumpNavBreachWarning')
if not self.breachWarningNode:
self.breachWarningNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLBreachWarningNode')
self.breachWarningNode.SetName("LumpNavBreachWarning")
slicer.mrmlScene.AddNode(self.breachWarningNode)
self.breachWarningNode.SetPlayWarningSound(True)
self.breachWarningNode.SetWarningColor(1, 0, 0)
self.breachWarningNode.SetOriginalColor(
self.tumorModel_Needle.GetDisplayNode().GetColor())
self.breachWarningNode.SetAndObserveToolTransformNodeId(
self.cauteryTipToCautery.GetID())
self.breachWarningNode.SetAndObserveWatchedModelNodeID(
self.tumorModel_Needle.GetID())
# Set up breach warning light
import BreachWarningLight
logging.debug('Set up breach warning light')
self.breachWarningLightLogic = BreachWarningLight.BreachWarningLightLogic(
)
self.breachWarningLightLogic.setMarginSizeMm(
float(
self.parameterNode.GetParameter(
'BreachWarningLightMarginSizeMm')))
if (self.parameterNode.GetParameter('EnableBreachWarningLight') ==
'True'):
logging.debug("BreachWarningLight: active")
self.breachWarningLightLogic.startLightFeedback(
self.breachWarningNode, self.connectorNode)
else:
logging.debug("BreachWarningLight: shutdown")
self.breachWarningLightLogic.shutdownLight(self.connectorNode)
# Build transform tree
logging.debug('Set up transform tree')
self.cauteryToReference.SetAndObserveTransformNodeID(
self.ReferenceToRas.GetID())
self.cauteryCameraToCautery.SetAndObserveTransformNodeID(
self.cauteryToReference.GetID())
self.cauteryTipToCautery.SetAndObserveTransformNodeID(
self.cauteryToReference.GetID())
self.cauteryModelToCauteryTip.SetAndObserveTransformNodeID(
self.cauteryTipToCautery.GetID())
self.needleToReference.SetAndObserveTransformNodeID(
self.ReferenceToRas.GetID())
self.needleTipToNeedle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
self.needleModelToNeedleTip.SetAndObserveTransformNodeID(
self.needleTipToNeedle.GetID())
self.cauteryModel_CauteryTip.SetAndObserveTransformNodeID(
self.cauteryModelToCauteryTip.GetID())
self.needleModel_NeedleTip.SetAndObserveTransformNodeID(
self.needleModelToNeedleTip.GetID())
self.tumorModel_Needle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
self.tumorMarkups_Needle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
# self.liveUltrasoundNode_Reference.SetAndObserveTransformNodeID(self.ReferenceToRas.GetID())
# Hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
logging.debug('Hide slice view annotations')
import DataProbe
dataProbeUtil = DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode = dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter('showSliceViewAnnotations', '0')
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 __init__(self):
# Member variables
self.outputLabels = None
self.recordedDataBuffer = []
self.record = False
self.reset = False
self.outputObserverTag = -1
self.rigidBodyToTrackerTransformNode = None
self.measurementToMeasurerTransformNode = None
self.parametersToMeasurerTransformNode = None
self.plus = None
self.m = vtk.vtkMatrix4x4()
self.direction = -1
self.ras = [0, 0, 0, 1]
self.d = 0.0
self.snr = 0
self.total = 0
self.LABEL_UPDATE_RATE = 10
self.labelUpdateCount = 0
self.snrThreshold = 40
self.distanceMaximumValue = 1000.0
self.distanceMinimumValue = 0.0
self.lensMaxDistance = 0.0
self.lensMinDistance = 0.0
self.normalizingConstant = 0.0
self.min = -1000.0
self.addColours = True
import Viewpoint # Viewpoint
self.viewpointLogic = Viewpoint.ViewpointLogic()
self.stopWatch = None # StopWatch
# Create style sheets
self.errorStyleSheet = "QLabel { color : #FF0000; \
font: bold 14px}"
self.defaultStyleSheet = "QLabel { color : #000000; \
font: bold 14px}"
# Create rainbow colour table
self.colorTable=slicer.vtkMRMLColorTableNode()
self.colorTable.SetTypeToRainbow ()
# Add MeasurementPoint
self.measurementPointMarkupsFiducialNode = slicer.util.getNode('MeasurementPoint')
if not self.measurementPointMarkupsFiducialNode:
self.measurementPointMarkupsFiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
self.measurementPointMarkupsFiducialNode.SetName('MeasurementPoint')
self.measurementPointMarkupsFiducialNode.AddFiducial(0, 0, 0)
self.measurementPointMarkupsFiducialNode.SetNthFiducialLabel(0, '')
slicer.mrmlScene.AddNode(self.measurementPointMarkupsFiducialNode)
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetGlyphScale(2.0)
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetGlyphType(13) # Sphere3D
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetSelectedColor(1, 0, 0)
# Add RecordedModel
self.recordedModelNode = slicer.util.getNode('RecordedModel')
if not self.recordedModelNode:
recordedPoints = vtk.vtkPoints()
recordedVertices = vtk.vtkCellArray()
recordedPolyData = vtk.vtkPolyData()
recordedPolyData.SetPoints(recordedPoints)
recordedPolyData.SetVerts(recordedVertices)
self.recordedModelNode = self.addModelToScene(recordedPolyData, "RecordedModel")
self.recordedModelNode.GetModelDisplayNode().SetPointSize(3)
# Set up coloured scalars
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
self.recordedModelNode.GetPolyData().GetPointData().SetScalars(colorArray)
# Create share directory
self.pathToCreatedSaveDir = self.createShareDirectory()
# Post-Processing default (for undo)
self.recordedDataBufferDefault = []
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):
"""
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 createFiducialMap(self, name):
if slicer.util.getNode(name) is None:
fiducial = slicer.mrmlScene.AddNode(slicer.vtkMRMLMarkupsFiducialNode())
fiducial.SetName(name)
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 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')
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 createFiducialMap(self, name):
if slicer.util.getNode(name) is None:
fiducial = slicer.mrmlScene.AddNode(
slicer.vtkMRMLMarkupsFiducialNode())
fiducial.SetName(name)