def addStopWatch(self): from libs.StopWatch import StopWatch self.stopWatch = StopWatch()
class ConoProbeConnectorLogic(ScriptedLoadableModuleLogic):
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 __del__(self):
self.removeUpdateObserver()
self.viewpointLogic.stopViewpoint()
def initColouring(self, direction, min, max):
if max > min:
newMin = 0
newMax = 255
self.min = min
self.direction = direction
self.normalizingConstant = (newMax - newMin) / (max - min)
return True
else:
logging.warning('Not possible to enable Intuitive Colouring: max <= min')
return False
def addStopWatch(self):
from libs.StopWatch import StopWatch
self.stopWatch = StopWatch()
def startViewpoint(self):
self.viewpointLogic.startViewpoint()
def stopViewpoint(self):
self.viewpointLogic.stopViewpoint()
def initViewpoint(self):
if self.rigidBodyToTrackerTransformNode:
# ConoProbeModelToMeasurement
conoProbeModelToMeasurement = slicer.util.getNode('ConoProbeModelToMeasurement')
if not conoProbeModelToMeasurement:
conoProbeModelToMeasurement=slicer.vtkMRMLLinearTransformNode()
conoProbeModelToMeasurement.SetName("ConoProbeModelToMeasurement")
m = vtk.vtkMatrix4x4()
# Large lens
# m.SetElement( 0, 0, -0.92 ) # Row 1
# m.SetElement( 0, 1, -0.16 )
# m.SetElement( 0, 2, 0.37 )
# m.SetElement( 0, 3, 63.53 )
# m.SetElement( 1, 0, -0.38 ) # Row 2
# m.SetElement( 1, 1, 0.06 )
# m.SetElement( 1, 2, -0.92 )
# m.SetElement( 1, 3, 81.99 )
# m.SetElement( 2, 0, 0.13 ) # Row 3
# m.SetElement( 2, 1, -0.98 )
# m.SetElement( 2, 2, -0.12 )
# m.SetElement( 2, 3, -40.15 )
# Small lens
m.SetElement( 0, 0, -0.92 ) # Row 1
m.SetElement( 0, 1, -0.16 )
m.SetElement( 0, 2, 0.37 )
m.SetElement( 0, 3, 63.53 )
m.SetElement( 1, 0, -0.38 ) # Row 2
m.SetElement( 1, 1, 0.06 )
m.SetElement( 1, 2, -0.92 )
m.SetElement( 1, 3, 81.99 )
m.SetElement( 2, 0, 0.13 ) # Row 3
m.SetElement( 2, 1, -0.98 )
m.SetElement( 2, 2, -0.12 )
m.SetElement( 2, 3, 129.85 )
conoProbeModelToMeasurement.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(conoProbeModelToMeasurement)
conoProbeModelToMeasurement.SetAndObserveTransformNodeID(self.rigidBodyToTrackerTransformNode.GetID())
# ViewPointToMeasurement
viewPointToMeasurement = slicer.util.getNode('ViewPointToMeasurement')
if not viewPointToMeasurement:
viewPointToMeasurement=slicer.vtkMRMLLinearTransformNode()
viewPointToMeasurement.SetName("ViewPointToMeasurement")
m = vtk.vtkMatrix4x4()
# Large lens
# m.SetElement( 0, 0, -1 ) # Row 1
# m.SetElement( 0, 1, 0 )
# m.SetElement( 0, 2, 0 )
# m.SetElement( 0, 3, 53.00 )
# m.SetElement( 1, 0, 0 ) # Row 2
# m.SetElement( 1, 1, -1 )
# m.SetElement( 1, 2, 0 )
# m.SetElement( 1, 3, 88.00 )
# m.SetElement( 2, 0, 0 ) # Row 3
# m.SetElement( 2, 1, 0 )
# m.SetElement( 2, 2, 1 )
# m.SetElement( 2, 3, -106 )
# Small lens
m.SetElement( 0, 0, -1 ) # Row 1
m.SetElement( 0, 1, 0 )
m.SetElement( 0, 2, 0 )
m.SetElement( 0, 3, 53.00 )
m.SetElement( 1, 0, 0 ) # Row 2
m.SetElement( 1, 1, -1 )
m.SetElement( 1, 2, 0 )
m.SetElement( 1, 3, 88.00 )
m.SetElement( 2, 0, 0 ) # Row 3
m.SetElement( 2, 1, 0 )
m.SetElement( 2, 2, 1 )
m.SetElement( 2, 3, 54 )
viewPointToMeasurement.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(viewPointToMeasurement)
viewPointToMeasurement.SetAndObserveTransformNodeID(self.rigidBodyToTrackerTransformNode.GetID())
# ConoProbeModel
conoProbeModel = slicer.util.getNode('ConoProbeModel')
if not conoProbeModel:
moduleDirectoryPath = slicer.modules.conoprobeconnector.path.replace('ConoProbeConnector.py', '')
slicer.util.loadModel(qt.QDir.toNativeSeparators(moduleDirectoryPath + '../../Data/Models/ConoProbeModel.stl'))
conoProbeModel=slicer.util.getNode(pattern="ConoProbeModel")
conoProbeModel.SetName("ConoProbeModel")
conoProbeModel.GetDisplayNode().SetOpacity(0.7)
conoProbeModel.SetAndObserveTransformNodeID(conoProbeModelToMeasurement.GetID())
# Camera
camera = slicer.util.getNode('Camera')
if not camera:
camera=slicer.vtkMRMLCameraNode()
camera.SetName("Camera")
slicer.mrmlScene.AddNode(camera)
threeDView = slicer.util.getNode("view1")
camera.SetActiveTag(threeDView.GetID())
# Viewpoint
self.viewpointLogic.setCameraNode(camera)
self.viewpointLogic.setTransformNode(viewPointToMeasurement)
self.viewpointLogic.setModelPOVOnNode(conoProbeModel)
self.viewpointLogic.SetCameraXPosMm(53)
self.viewpointLogic.SetCameraYPosMm(72)
self.viewpointLogic.SetCameraZPosMm(119)
self.viewpointLogic.startViewpoint()
def getLensMinMax(self):
minMax = [0, 0]
self.parametersToMeasurerTransformNode.GetMatrixTransformToParent(self.m)
minMax[0] = self.m.GetElement(2, 0)
minMax[1] = self.m.GetElement(2, 1)
return minMax
def saveRecordedDataToDefault(self):
self.recordedDataBufferDefault = self.recordedDataBuffer
def performPostProcessing(self, snrThreshold, distanceMinimumValue, distanceMaximumValue):
# Create new vtkPolyData
newPoints = vtk.vtkPoints()
newVertices = vtk.vtkCellArray()
newPolyData = vtk.vtkPolyData()
newPolyData.SetPoints(newPoints)
newPolyData.SetVerts(newVertices)
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
newPolyData.GetPointData().SetScalars(colorArray)
# Filter accordingly to the input parameters
recordedDataBufferFiltered = []
for idx in range(len(self.recordedDataBuffer)):
d = self.recordedDataBuffer[idx][3]
snr = self.recordedDataBuffer[idx][4]
if (snr > snrThreshold and
d < distanceMaximumValue and
d > distanceMinimumValue):
recordedDataBufferFiltered.append(self.recordedDataBuffer[idx])
self.addPointToPolyData(newPolyData, self.recordedDataBuffer[idx][0:3])
# Update recorded model and buffer
self.recordedModelNode.GetPolyData().DeepCopy(newPolyData)
self.recordedModelNode.GetPolyData().Modified()
self.recordedDataBuffer = recordedDataBufferFiltered
def showColouring(self):
self.recordedModelNode.GetModelDisplayNode().SetActiveScalarName('Colors')
self.recordedModelNode.GetModelDisplayNode().SetScalarVisibility(True)
def undoPostProcessing(self):
# Create new vtkPolyData
newPoints = vtk.vtkPoints()
newVertices = vtk.vtkCellArray()
newPolyData = vtk.vtkPolyData()
newPolyData.SetPoints(newPoints)
newPolyData.SetVerts(newVertices)
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
newPolyData.GetPointData().SetScalars(colorArray)
# Filter accordingly to the input parameters
recordedDataBufferFiltered = []
for idx in range(len(self.recordedDataBufferDefault)):
self.addPointToPolyData(newPolyData, self.recordedDataBufferDefault[idx][0:3])
# Update recorded model and buffer
self.recordedModelNode.GetPolyData().DeepCopy(newPolyData)
self.recordedModelNode.GetPolyData().Modified()
self.recordedDataBuffer = self.recordedDataBufferDefault
def setOutPutLabels(self, labels):
self.outputLabels = labels
def saveData(self):
dateAndTime = time.strftime("_%Y-%m-%d_%H-%M-%S")
path = self.pathToCreatedSaveDir + '/Points' + dateAndTime
# Save model to .vtk
slicer.modules.models.logic().SaveModel(path + '.vtk', self.recordedModelNode)
# Save data to .csv
self.writeRecordedDataBufferToFile(path + '.csv')
saveDir = self.pathToCreatedSaveDir.split('SlicerModules')[1] # Just to remove unnecessary information
self.outputLabels[3].setText('Data saved to: ' + saveDir)
def writeRecordedDataBufferToFile(self, path):
with open(path, 'wb') as csvfile:
writer = csv.writer(csvfile, delimiter=",")
writer.writerow(['x_ConoProbe', 'y_ConoProbe', 'z_ConoProbe', 'd', 'snr', 'total', 'x_RigidBody', 'y_RigidBody', 'z_RigidBody', 'Rxx', 'Rxy', 'Rxz', 'Ryx', 'Ryy', 'Ryz', 'Rzx', 'Rzy', 'Rzz'])
for idx in range(len(self.recordedDataBuffer)):
writer.writerow(self.recordedDataBuffer[idx])
def getModelXYZ(self):
xyz = []
for idx in range(self.recordedModelNode.GetPolyData().GetPoints().GetNumberOfPoints()):
point = [0, 0, 0]
self.recordedModelNode.GetPolyData().GetPoint(idx, point)
xyz.append(point)
return xyz
def createShareDirectory(self):
date = time.strftime("%Y-%m-%d")
shareDirPath = slicer.modules.conoprobeconnector.path.replace("ConoProbeConnector.py","") + 'Output/' + date
if not os.path.exists(shareDirPath):
os.makedirs(shareDirPath)
return shareDirPath
def addModelToScene(self, polyData, name):
scene = slicer.mrmlScene
node = slicer.vtkMRMLModelNode()
node.SetScene(scene)
node.SetName(name)
node.SetAndObservePolyData(polyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(0, 1, 0)
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
node.SetAndObserveDisplayNodeID(modelDisplay.GetID())
scene.AddNode(node)
return node
def clearPointsInRecordedModel(self):
self.recordedDataBuffer = []
newPoints = vtk.vtkPoints()
newVertices = vtk.vtkCellArray()
newPolyData = vtk.vtkPolyData()
newPolyData.SetPoints(newPoints)
newPolyData.SetVerts(newVertices)
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
newPolyData.GetPointData().SetScalars(colorArray)
self.recordedModelNode.GetPolyData().DeepCopy(newPolyData)
self.recordedModelNode.GetPolyData().Modified()
def setupPlus(self):
connectorNode = self.createPlusConnector()
connectorNode.Start()
self.plus = Plus(connectorNode.GetID(), self.pathToCreatedSaveDir)
def plusStartRecording(self):
dateAndTime = time.strftime("_%Y-%m-%d_%H-%M-%S")
self.plus.startStopRecording(True, 'PlusRecording' + dateAndTime + '.mha')
def plusStopRecording(self):
self.plus.startStopRecording(False)
def createTransformTree(self):
# Get transform nodes from scene
if not self.rigidBodyToTrackerTransformNode:
self.rigidBodyToTrackerTransformNode = slicer.util.getNode('RigidBodyToTracker')
if not self.measurementToMeasurerTransformNode:
self.measurementToMeasurerTransformNode = slicer.util.getNode('MeasurementToMeasure')
if not self.parametersToMeasurerTransformNode:
self.parametersToMeasurerTransformNode = slicer.util.getNode('ParametersToMeasurer')
if not self.measurementToMeasurerTransformNode or not self.parametersToMeasurerTransformNode:
logging.error('Missing transform! Is Plus properly configured?')
self.outputLabels[3].setText('Missing transform! Is PlusServer running and properly configured?')
self.outputLabels[3].setStyleSheet(self.errorStyleSheet)
return False
if not self.rigidBodyToTrackerTransformNode:
logging.warning('No tracking transform present, only raw measurement.')
self.outputLabels[3].setText(' ')
self.outputLabels[3].setStyleSheet(self.defaultStyleSheet)
if self.measurementToMeasurerTransformNode:
self.measurementPointMarkupsFiducialNode.SetAndObserveTransformNodeID(self.measurementToMeasurerTransformNode.GetID())
if self.rigidBodyToTrackerTransformNode:
self.measurementToMeasurerTransformNode.SetAndObserveTransformNodeID(self.rigidBodyToTrackerTransformNode.GetID())
else:
self.outputLabels[3].setText('No tracking transform present, only raw measurement.')
return True
# From: SlicerIGT/GuideletLib
# Takes for granted IP:port is localhost:18944
def createPlusConnector(self):
connectorNode = slicer.util.getNode('PlusConnector')
if not connectorNode:
connectorNode = slicer.vtkMRMLIGTLConnectorNode()
slicer.mrmlScene.AddNode(connectorNode)
connectorNode.SetName('PlusConnector')
hostNamePort = "localhost:18944"
[hostName, port] = hostNamePort.split(':')
connectorNode.SetTypeClient(hostName, int(port))
logging.debug("PlusConnector created")
return connectorNode
def addUpdateObserver(self):
if self.outputObserverTag == -1:
self.outputObserverTag = self.rigidBodyToTrackerTransformNode.AddObserver('ModifiedEvent', self.updateSceneCallback)
logging.info('addOutputObserver')
def removeUpdateObserver(self):
if self.outputObserverTag != -1:
self.parametersToMeasurerTransformNode.RemoveObserver(self.outputObserverTag)
self.outputObserverTag = -1
logging.info('removeOutputObserver')
def updateSceneCallback(self, modifiedNode, event=None):
# This lowers the update rate of the labels to only every self.LABEL_UPDATE_RATE measurement
self.labelUpdateCount = self.labelUpdateCount + 1
updateLabels = not self.labelUpdateCount % self.LABEL_UPDATE_RATE
if self.reset:
self.clearPointsInRecordedModel()
self.reset = False
if updateLabels or self.record:
# Get ConoProbe parameters
self.parametersToMeasurerTransformNode.GetMatrixTransformToParent(self.m)
self.d = self.m.GetElement(0, 0)
self.snr = self.m.GetElement(0, 1)
self.total = self.m.GetElement(0, 2)
self.power = self.m.GetElement(1, 1)
self.frequency = self.m.GetElement(1, 0)
self.lensMaxDistance = self.m.GetElement(2, 0)
self.lensMinDistance = self.m.GetElement(2, 1)
# Get measurement coordinate
self.measurementPointMarkupsFiducialNode.GetNthFiducialWorldCoordinates(0, self.ras)
if updateLabels:
# Update output labels
self.updateOutputLabels()
self.labelUpdateCount = 0
if (self.record and self.snr > self.snrThreshold and self.d < self.distanceMaximumValue and self.d > self.distanceMinimumValue):
self.acquireSingleMeasurement()
def acquireSingleMeasurement(self):
# Only for printing tracker position to file
xRigidBodyToTracker = 0
yRigidBodyToTracker = 0
zRigidBodyToTracker = 0
Rxx = 0
Rxy = 0
Rxz = 0
Ryx = 0
Ryy = 0
Ryz = 0
Rzx = 0
Rzy = 0
Rzz = 0
if self.rigidBodyToTrackerTransformNode:
self.rigidBodyToTrackerTransformNode.GetMatrixTransformToParent(self.m)
xRigidBodyToTracker = self.m.GetElement(0, 3)
yRigidBodyToTracker = self.m.GetElement(1, 3)
zRigidBodyToTracker = self.m.GetElement(2, 3)
Rxx = self.m.GetElement(0, 0)
Rxy = self.m.GetElement(0, 1)
Rxz = self.m.GetElement(0, 2)
Ryx = self.m.GetElement(1, 0)
Ryy = self.m.GetElement(1, 1)
Ryz = self.m.GetElement(1, 2)
Rzx = self.m.GetElement(2, 0)
Rzy = self.m.GetElement(2, 1)
Rzz = self.m.GetElement(2, 2)
self.recordedDataBuffer.append([self.ras[0], self.ras[1], self.ras[2],
self.d, self.snr, self.total,
xRigidBodyToTracker, yRigidBodyToTracker, zRigidBodyToTracker,
Rxx, Rxy, Rxz, Ryx, Ryy, Ryz, Rzx, Rzy, Rzz])
self.addPointToPolyData(self.recordedModelNode.GetPolyData(), self.ras)
def updateOutputLabels(self):
self.outputLabels[0].setText('%.1f' % self.d)
self.outputLabels[1].setText('%.0f' % self.snr)
self.outputLabels[2].setText('%.0f' % self.total)
self.outputLabels[4].setText('[' + '%.1f' % self.ras[0] + ', ' + '%.1f' % self.ras[1] + ', '+ '%.1f' % self.ras[2] + ']')
self.outputLabels[5].setText(str(self.recordedModelNode.GetPolyData().GetPoints().GetNumberOfPoints()))
self.outputLabels[6].setText('%.2f' % self.stopWatch.getElapsedTime())
self.outputLabels[7].setText('%.0f' % self.power)
self.outputLabels[8].setText('%.0f' % self.frequency)
self.outputLabels[10].setText('%.1f' % self.lensMaxDistance)
self.outputLabels[9].setText('%.1f' % self.lensMinDistance)
def addPointToPolyData(self, polyData, ras):
pid = vtk.vtkIdList()
pid.SetNumberOfIds(1);
temp = polyData.GetPoints().InsertNextPoint(ras[0], ras[1], ras[2])
pid.SetId(0, temp)
polyData.GetVerts().InsertNextCell(pid)
if self.direction > -1:
color = [0, 0, 0, 0]
tableValue = 1 + (ras[self.direction] - self.min) * self.normalizingConstant
if tableValue > 255:
tableValue = 255
elif tableValue < 0:
tableValue = 0
self.colorTable.GetColor(int(tableValue), color) # 0 -> 255
self.recordedModelNode.GetPolyData().GetPointData().GetScalars('Colors').InsertTuple(self.recordedModelNode.GetPolyData().GetPoints().GetNumberOfPoints() - 1, color)
if self.addColours:
self.showColouring()
self.addColours = False
polyData.Modified()
def openProbeDialog(self):
self.plus.showProbeDialog()
def setLayout(self):
lm=slicer.app.layoutManager()
lm.setLayout(4) # One 3D-view
self.resetLayoutFocalPoint(0)
self.zoomInThreeDView(0, 8)
self.setAxisAndBoxVisibility('View1', False)
def setAxisAndBoxVisibility(self, viewName, visible):
view = slicer.mrmlScene.GetFirstNodeByName(viewName)
view.SetAxisLabelsVisible(visible)
view.SetBoxVisible(visible)
def resetLayoutFocalPoint(self, viewIdx):
threeDWidget = slicer.app.layoutManager().threeDWidget(viewIdx)
threeDView = threeDWidget.threeDView()
threeDView.resetFocalPoint()
def zoomInThreeDView(self, viewIdx, zoomFactor):
threeDWidget = slicer.app.layoutManager().threeDWidget(viewIdx)
threeDView = threeDWidget.threeDView()
for zoom in range(zoomFactor):
threeDView.zoomIn()
# Available ctkAxes:
# - ctk.ctkAxesWidget.Right
# - ctk.ctkAxesWidget.Left
# - ctk.ctkAxesWidget.Inferior
# - ctk.ctkAxesWidget.Superior
# - ctk.ctkAxesWidget.Posterior
# - ctk.ctkAxesWidget.Anterior
def setFocalPointByAxis(self, viewIdx, ctkAxis):
view=slicer.app.layoutManager().threeDWidget(viewIdx).threeDView()
view.lookFromViewAxis(ctkAxis)