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BoneReconstructionPlanner.py
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import os
import unittest
import logging
import vtk, qt, ctk, slicer, math
import numpy as np
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
from BRPLib.helperFunctions import *
#
# BoneReconstructionPlanner
#
class BoneReconstructionPlanner(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "BoneReconstructionPlanner" # TODO: make this more human readable by adding spaces
self.parent.categories = ["Planning"] # TODO: set categories (folders where the module shows up in the module selector)
self.parent.dependencies = [] # TODO: add here list of module names that this module requires
self.parent.contributors = ["Mauro I. Dominguez, Andras Lasso, Manjula Herath"] # TODO: replace with "Firstname Lastname (Organization)"
# TODO: update with short description of the module and a link to online module documentation
self.parent.helpText = """
A 3D Slicer module for virtual surgical planning of mandibular reconstruction with vascularized fibula free flap and generation of patient-specific surgical guides.
See the whole project in <a href="https://github.com/SlicerIGT/SlicerBoneReconstructionPlanner">this link</a>.
"""
# TODO: replace with organization, grant and thanks
self.parent.acknowledgementText = """
Mauro I. Dominguez developed this module for his final project of engineering studies at FCEIA-UNR under the supervision and advice of PhD. Andras Lasso at PerkLab, and the clinical inputs of Dr. Manjula Herath.
"""
# Additional initialization step after application startup is complete
slicer.app.connect("startupCompleted()", registerSampleData)
#
# Register sample data sets in Sample Data module
#
def registerSampleData():
"""
Add data sets to Sample Data module.
"""
# It is always recommended to provide sample data for users to make it easy to try the module,
# but if no sample data is available then this method (and associated startupCompeted signal connection) can be removed.
import SampleData
iconsPath = os.path.join(os.path.dirname(__file__), 'Resources/Icons')
# To ensure that the source code repository remains small (can be downloaded and installed quickly)
# it is recommended to store data sets that are larger than a few MB in a Github release.
# BoneReconstructionPlanner1
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='BoneReconstructionPlanner',
sampleName='FibulaCropped',
# Thumbnail should have size of approximately 260x280 pixels and stored in Resources/Icons folder.
# It can be created by Screen Capture module, "Capture all views" option enabled, "Number of images" set to "Single".
thumbnailFileName=os.path.join(iconsPath, 'iconFibulaCropped.png'),
# Download URL and target file name
uris="https://github.com/SlicerIGT/SlicerBoneReconstructionPlanner/releases/download/TestingData/FibulaCropped.nrrd",
fileNames='FibulaCropped.nrrd',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums = 'SHA256:5febc47a8fba6b43440be2b475f9defadffe9b47b1316d04217208b4497a4f72',
# This node name will be used when the data set is loaded
nodeNames='FibulaCropped'
)
# BoneReconstructionPlanner2
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='BoneReconstructionPlanner',
sampleName='ResectedMandible',
thumbnailFileName=os.path.join(iconsPath, 'iconResectedMandible.png'),
# Download URL and target file name
uris="https://github.com/SlicerIGT/SlicerBoneReconstructionPlanner/releases/download/TestingData/ResectedMandible.nrrd",
fileNames='ResectedMandible.nrrd',
checksums = 'SHA256:352aefed1905bd2ad7373972a6bb115bd494e26e4fc438d2c8679384dcfd2654',
# This node name will be used when the data set is loaded
nodeNames='ResectedMandible'
)
#
# BoneReconstructionPlannerWidget
#
class BoneReconstructionPlannerWidget(ScriptedLoadableModuleWidget, VTKObservationMixin):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent=None):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.__init__(self, parent)
VTKObservationMixin.__init__(self) # needed for parameter node observation
self.logic = None
self._parameterNode = None
self._updatingGUIFromParameterNode = False
def setup(self):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.setup(self)
# Load widget from .ui file (created by Qt Designer).
# Additional widgets can be instantiated manually and added to self.layout.
uiWidget = slicer.util.loadUI(self.resourcePath('UI/BoneReconstructionPlanner.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
# Set scene in MRML widgets. Make sure that in Qt designer the top-level qMRMLWidget's
# "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's.
# "setMRMLScene(vtkMRMLScene*)" slot.
uiWidget.setMRMLScene(slicer.mrmlScene)
self.ui.dentalImplantCylinderSelector.addAttribute('vtkMRMLModelNode','isDentalImplantCylinder','True')
# Create logic class. Logic implements all computations that should be possible to run
# in batch mode, without a graphical user interface.
self.logic = BoneReconstructionPlannerLogic()
# Connections
# These connections ensure that we update parameter node when scene is closed
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent, self.onSceneStartClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent, self.onSceneEndClose)
slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeAboutToBeRemovedEvent, self.onNodeAboutToBeRemovedEvent)
# These connections ensure that whenever user changes some settings on the GUI, that is saved in the MRML scene
# (in the selected parameter node).
self.ui.fibulaLineSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onFibulaPlanesCreationParametersChanged)
self.ui.mandibleCurveSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.mandibularSegmentationSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.fibulaSegmentationSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.fibulaFiducialListSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.fibulaSurgicalGuideBaseSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.miterBoxDirectionLineSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.scalarVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onScalarVolumeChanged)
self.ui.mandibleBridgeModelSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.mandibleSurgicalGuideBaseSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.mandibleFiducialListSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.dentalImplantFiducialListSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.dentalImplantCylinderSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.initialSpinBox.valueChanged.connect(self.onFibulaPlanesCreationParametersChanged)
self.ui.betweenSpinBox.valueChanged.connect(self.onFibulaPlanesCreationParametersChanged)
self.ui.securityMarginOfFibulaPiecesSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.miterBoxSlotWidthSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.miterBoxSlotLengthSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.miterBoxSlotHeightSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.miterBoxSlotWallSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.fibulaScrewHoleCylinderRadiusSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.clearanceFitPrintingToleranceSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.biggerMiterBoxDistanceToFibulaSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.intersectionDistanceMultiplierSpinBox.valueChanged.connect(self.onFibulaPlanesCreationParametersChanged)
self.ui.sawBoxSlotWidthSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.sawBoxSlotLengthSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.sawBoxSlotHeightSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.sawBoxSlotWallSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.biggerSawBoxDistanceToMandibleSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.mandibleScrewHoleCylinderRadiusSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.dentalImplantCylinderRadiusSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.dentalImplantCylinderHeightSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.dentalImplantDrillGuideWallSpinBox.valueChanged.connect(self.updateParameterNodeFromGUI)
self.ui.generateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton.checkBoxToggled.connect(self.updateParameterNodeFromGUI)
# Buttons
self.ui.notLeftFibulaCheckBox.connect('stateChanged(int)', self.updateParameterNodeFromGUI)
self.ui.addCutPlaneButton.connect('clicked(bool)',self.onAddCutPlaneButton)
self.ui.addMandibularCurveButton.connect('clicked(bool)',self.onAddMandibularCurveButton)
self.ui.addFibulaLineButton.connect('clicked(bool)',self.onAddFibulaLineButton)
self.ui.makeModelsButton.connect('clicked(bool)',self.onMakeModelsButton)
self.ui.createMiterBoxesFromFibulaPlanesButton.connect('clicked(bool)',self.onCreateMiterBoxesFromFibulaPlanesButton)
self.ui.createFibulaCylindersFiducialListButton.connect('clicked(bool)',self.onCreateFibulaCylindersFiducialListButton)
self.ui.createCylindersFromFiducialListAndFibulaSurgicalGuideBaseButton.connect('clicked(bool)',self.onCreateCylindersFromFiducialListAndSurgicalGuideBaseButton)
self.ui.makeBooleanOperationsToFibulaSurgicalGuideBaseButton.connect('clicked(bool)', self.onMakeBooleanOperationsToFibulaSurgicalGuideBaseButton)
self.ui.createMandibleCylindersFiducialListButton.connect('clicked(bool)', self.onCreateMandibleCylindersFiducialListButton)
self.ui.createSawBoxesFromFirstAndLastMandiblePlanesButton.connect('clicked(bool)', self.onCreateSawBoxesFromFirstAndLastMandiblePlanesButton)
self.ui.makeBooleanOperationsToMandibleSurgicalGuideBaseButton.connect('clicked(bool)', self.onMakeBooleanOperationsToMandibleSurgicalGuideBaseButton)
self.ui.createCylindersFromFiducialListAndMandibleSurgicalGuideBaseButton.connect('clicked(bool)', self.onCreateCylindersFromFiducialListAndMandibleSurgicalGuideBaseButton)
self.ui.generateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton.connect('clicked(bool)', self.onGenerateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton)
self.ui.centerFibulaLineButton.connect('clicked(bool)', self.onCenterFibulaLineButton)
self.ui.showHideBiggerSawBoxesInteractionHandlesButton.connect('clicked(bool)', self.onShowHideBiggerSawBoxesInteractionHandlesButton)
self.ui.showHideMandiblePlanesInteractionHandlesButton.connect('clicked(bool)', self.onShowHideMandiblePlanesInteractionHandlesButton)
self.ui.create3DModelOfTheReconstructionButton.connect('clicked(bool)', self.onCreate3DModelOfTheReconstructionButton)
self.ui.showHideFibulaSegmentsLengthsButton.connect('clicked(bool)', self.onShowHideFibulaSegmentsLengthsButton)
self.ui.showHideOriginalMandibleButton.connect('clicked(bool)', self.onShowHideOriginalMandibleButton)
self.ui.createDentalImplantCylindersFiducialListButton.connect('clicked(bool)', self.onCreateDentalImplantCylindersFiducialListButton)
self.ui.createCylindersFromFiducialListAndMandibleReconstructionButton.connect('clicked(bool)', self.onCreateCylindersFromFiducialListAndMandibleReconstructionButton)
self.ui.updateFibulaDentalImplantCylindersButton.connect('clicked(bool)', self.onUpdateFibulaDentalImplantCylindersButton)
self.ui.makeAllMandiblePlanesRotateTogetherCheckBox.connect('stateChanged(int)', self.updateParameterNodeFromGUI)
self.ui.useMoreExactVersionOfPositioningAlgorithmCheckBox.connect('stateChanged(int)', self.onUseMoreExactVersionOfPositioningAlgorithmCheckBox)
self.ui.useNonDecimatedBoneModelsForPreviewCheckBox.connect('stateChanged(int)', self.updateParameterNodeFromGUI)
self.ui.mandiblePlanesPositioningForMaximumBoneContactCheckBox.connect('stateChanged(int)', self.updateParameterNodeFromGUI)
self.ui.fixCutGoesThroughTheMandibleTwiceCheckBox.connect('stateChanged(int)', self.onFixCutGoesThroughTheMandibleTwiceCheckBox)
self.ui.checkSecurityMarginOnMiterBoxCreationCheckBox.connect('stateChanged(int)', self.updateParameterNodeFromGUI)
# Make sure parameter node is initialized (needed for module reload)
self.initializeParameterNode()
def getParentFolderItemID(self):
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
sceneItemID = shNode.GetSceneItemID()
folderSubjectHierarchyID = shNode.GetItemByName("BoneReconstructionPlanner")
if folderSubjectHierarchyID:
return folderSubjectHierarchyID
else:
return shNode.CreateFolderItem(sceneItemID,"BoneReconstructionPlanner")
def cleanup(self):
"""
Called when the application closes and the module widget is destroyed.
"""
self.removeObservers()
@vtk.calldata_type(vtk.VTK_OBJECT)
def onNodeAboutToBeRemovedEvent(self, caller, event, callData):
if callData.GetClassName() == 'vtkMRMLMarkupsPlaneNode':
if callData.GetAttribute("isMandibularPlane") == 'True':
if len(self.logic.mandiblePlaneObserversAndNodeIDList) > 0:
for i in range(len(self.logic.mandiblePlaneObserversAndNodeIDList)):
if self.logic.mandiblePlaneObserversAndNodeIDList[i][1] == callData.GetID():
observerIndex = i
callData.RemoveObserver(self.logic.mandiblePlaneObserversAndNodeIDList.pop(observerIndex)[0])
self.logic.onPlaneModifiedTimer(None,None)
if callData.GetAttribute("isSawBoxPlane") == 'True':
if len(self.logic.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList) > 0:
for i in range(len(self.logic.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList)):
if self.logic.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList[i][1] == callData.GetID():
observerIndex = i
callData.RemoveObserver(self.logic.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList.pop(observerIndex)[0])
if callData.GetAttribute("isDentalImplantPlane") == 'True':
if len(self.logic.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList) > 0:
for i in range(len(self.logic.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList)):
if self.logic.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList[i][1] == callData.GetID():
observerIndex = i
callData.RemoveObserver(self.logic.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList.pop(observerIndex)[0])
def enter(self):
"""
Called each time the user opens this module.
"""
# Make sure parameter node exists and observed
self.initializeParameterNode()
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
segmentationModelsFolder = shNode.GetItemByName("Segmentation Models")
fibulaPlanesFolder = shNode.GetItemByName("Fibula planes")
cutBonesFolder = shNode.GetItemByName("Cut Bones")
fibulaCylindersFiducialsListsFolder = shNode.GetItemByName("Fibula Cylinders Fiducials Lists")
mandibleCylindersFiducialsListsFolder = shNode.GetItemByName("Mandible Cylinders Fiducials Lists")
if segmentationModelsFolder:
self.ui.generateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton.enabled = True
if fibulaCylindersFiducialsListsFolder:
self.ui.createCylindersFromFiducialListAndFibulaSurgicalGuideBaseButton.enabled = True
if mandibleCylindersFiducialsListsFolder:
self.ui.createCylindersFromFiducialListAndMandibleSurgicalGuideBaseButton.enabled = True
mandibularPlanesFolder = shNode.GetItemByName("Mandibular planes")
mandibularPlanesList = createListFromFolderID(mandibularPlanesFolder)
for i in range(len(mandibularPlanesList)):
mandibularPlanesList[i].SetLocked(0)
displayNode = mandibularPlanesList[i].GetDisplayNode()
displayNode.HandlesInteractiveOn()
observer = mandibularPlanesList[i].AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent,self.logic.onPlaneModifiedTimer)
self.logic.mandiblePlaneObserversAndNodeIDList.append([observer,mandibularPlanesList[i].GetID()])
sawBoxesPlanesFolder = shNode.GetItemByName("sawBoxes Planes")
sawBoxesTransformsFolder = shNode.GetItemByName("sawBoxes Transforms")
sawBoxesPlanesList = createListFromFolderID(sawBoxesPlanesFolder)
sawBoxesTransformsList = createListFromFolderID(sawBoxesTransformsFolder)
for i in range(len(sawBoxesPlanesList)):
sawBoxesPlanesList[i].SetLocked(0)
displayNode = sawBoxesPlanesList[i].GetDisplayNode()
displayNode.HandlesInteractiveOn()
observer = sawBoxesPlanesList[i].AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent,self.logic.onPlaneModifiedTimer)
self.logic.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList.append([observer,sawBoxesPlanesList[i].GetID(),sawBoxesTransformsList[i].GetID()])
dentalImplantsPlanesFolder = shNode.GetItemByName("dentalImplants Planes")
dentalImplantsCylindersTransformsFolder = shNode.GetItemByName("Dental Implants Cylinders Transforms")
dentalImplantsPlanesList = createListFromFolderID(dentalImplantsPlanesFolder)
dentalImplantsCylindersTransformsList = createListFromFolderID(dentalImplantsCylindersTransformsFolder)
for i in range(len(dentalImplantsPlanesList)):
dentalImplantsPlanesList[i].SetLocked(0)
displayNode = dentalImplantsPlanesList[i].GetDisplayNode()
displayNode.HandlesInteractiveOn()
observer = dentalImplantsPlanesList[i].AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent,self.logic.onPlaneModifiedTimer)
self.logic.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList.append([observer,dentalImplantsPlanesList[i].GetID(),dentalImplantsCylindersTransformsList[i].GetID()])
if self.ui.scalarVolumeSelector.nodeCount() != 0 and self.ui.scalarVolumeSelector.currentNode() == None:
self.ui.scalarVolumeSelector.setCurrentNodeIndex(0)#0 == first scalarVolume
def exit(self):
"""
Called each time the user opens a different module.
"""
# Do not react to parameter node changes (GUI wlil be updated when the user enters into the module)
self.removeObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self.updateGUIFromParameterNode)
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
mandibularPlanesFolder = shNode.GetItemByName("Mandibular planes")
mandibularPlanesList = createListFromFolderID(mandibularPlanesFolder)
for i in range(len(mandibularPlanesList)):
mandibularPlanesList[i].SetLocked(1)
displayNode = mandibularPlanesList[i].GetDisplayNode()
displayNode.HandlesInteractiveOff()
mandibularPlanesList[i].RemoveObserver(self.logic.mandiblePlaneObserversAndNodeIDList[i][0])
self.logic.mandiblePlaneObserversAndNodeIDList = []
sawBoxesPlanesFolder = shNode.GetItemByName("sawBoxes Planes")
sawBoxesPlanesList = createListFromFolderID(sawBoxesPlanesFolder)
for i in range(len(sawBoxesPlanesList)):
sawBoxesPlanesList[i].SetLocked(1)
displayNode = sawBoxesPlanesList[i].GetDisplayNode()
displayNode.HandlesInteractiveOff()
sawBoxesPlanesList[i].RemoveObserver(self.logic.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList[i][0])
self.logic.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList = []
dentalImplantsPlanesFolder = shNode.GetItemByName("dentalImplants Planes")
dentalImplantsPlanesList = createListFromFolderID(dentalImplantsPlanesFolder)
for i in range(len(dentalImplantsPlanesList)):
dentalImplantsPlanesList[i].SetLocked(1)
displayNode = dentalImplantsPlanesList[i].GetDisplayNode()
displayNode.HandlesInteractiveOff()
dentalImplantsPlanesList[i].RemoveObserver(self.logic.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList[i][0])
self.logic.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList = []
def onSceneStartClose(self, caller, event):
"""
Called just before the scene is closed.
"""
# Parameter node will be reset, do not use it anymore
self.setParameterNode(None)
def onSceneEndClose(self, caller, event):
"""
Called just after the scene is closed.
"""
# If this module is shown while the scene is closed then recreate a new parameter node immediately
if self.parent.isEntered:
self.initializeParameterNode()
def initializeParameterNode(self):
"""
Ensure parameter node exists and observed.
"""
# Parameter node stores all user choices in parameter values, node selections, etc.
# so that when the scene is saved and reloaded, these settings are restored.
self.setParameterNode(self.logic.getParameterNode())
def setParameterNode(self, inputParameterNode):
"""
Set and observe parameter node.
Observation is needed because when the parameter node is changed then the GUI must be updated immediately.
"""
if inputParameterNode:
self.logic.setDefaultParameters(inputParameterNode)
# Unobserve previously selected parameter node and add an observer to the newly selected.
# Changes of parameter node are observed so that whenever parameters are changed by a script or any other module
# those are reflected immediately in the GUI.
if self._parameterNode is not None:
self.removeObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self.updateGUIFromParameterNode)
self._parameterNode = inputParameterNode
if self._parameterNode is not None:
self.addObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self.updateGUIFromParameterNode)
# Initial GUI update
self.updateGUIFromParameterNode()
def updateGUIFromParameterNode(self, caller=None, event=None):
"""
This method is called whenever parameter node is changed.
The module GUI is updated to show the current state of the parameter node.
"""
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
# Make sure GUI changes do not call updateParameterNodeFromGUI (it could cause infinite loop)
self._updatingGUIFromParameterNode = True
# Update node selectors and sliders
self.ui.fibulaLineSelector.setCurrentNode(self._parameterNode.GetNodeReference("fibulaLine"))
self.ui.mandibleCurveSelector.setCurrentNode(self._parameterNode.GetNodeReference("mandibleCurve"))
self.ui.mandibularSegmentationSelector.setCurrentNode(self._parameterNode.GetNodeReference("mandibularSegmentation"))
self.ui.fibulaSegmentationSelector.setCurrentNode(self._parameterNode.GetNodeReference("fibulaSegmentation"))
self.ui.fibulaFiducialListSelector.setCurrentNode(self._parameterNode.GetNodeReference("fibulaFiducialList"))
self.ui.fibulaSurgicalGuideBaseSelector.setCurrentNode(self._parameterNode.GetNodeReference("fibulaSurgicalGuideBaseModel"))
self.ui.miterBoxDirectionLineSelector.setCurrentNode(self._parameterNode.GetNodeReference("miterBoxDirectionLine"))
self.ui.mandibleBridgeModelSelector.setCurrentNode(self._parameterNode.GetNodeReference("mandibleBridgeModel"))
self.ui.mandibleSurgicalGuideBaseSelector.setCurrentNode(self._parameterNode.GetNodeReference("mandibleSurgicalGuideBaseModel"))
self.ui.mandibleFiducialListSelector.setCurrentNode(self._parameterNode.GetNodeReference("mandibleFiducialList"))
self.ui.scalarVolumeSelector.setCurrentNode(self._parameterNode.GetNodeReference("currentScalarVolume"))
self.ui.dentalImplantFiducialListSelector.setCurrentNode(self._parameterNode.GetNodeReference("dentalImplantsFiducialList"))
self.ui.dentalImplantCylinderSelector.setCurrentNode(self._parameterNode.GetNodeReference("selectedDentalImplantCylinderModel"))
if self._parameterNode.GetParameter("initialSpace") != '':
self.ui.initialSpinBox.setValue(float(self._parameterNode.GetParameter("initialSpace")))
if self._parameterNode.GetParameter("additionalBetweenSpaceOfFibulaPlanes") != '':
self.ui.betweenSpinBox.setValue(float(self._parameterNode.GetParameter("additionalBetweenSpaceOfFibulaPlanes")))
if self._parameterNode.GetParameter("securityMarginOfFibulaPieces") != '':
self.ui.securityMarginOfFibulaPiecesSpinBox.setValue(float(self._parameterNode.GetParameter("securityMarginOfFibulaPieces")))
if self._parameterNode.GetParameter("miterBoxSlotWidth") != '':
self.ui.miterBoxSlotWidthSpinBox.setValue(float(self._parameterNode.GetParameter("miterBoxSlotWidth")))
if self._parameterNode.GetParameter("miterBoxSlotLength") != '':
self.ui.miterBoxSlotLengthSpinBox.setValue(float(self._parameterNode.GetParameter("miterBoxSlotLength")))
if self._parameterNode.GetParameter("miterBoxSlotHeight") != '':
self.ui.miterBoxSlotHeightSpinBox.setValue(float(self._parameterNode.GetParameter("miterBoxSlotHeight")))
if self._parameterNode.GetParameter("miterBoxSlotWall") != '':
self.ui.miterBoxSlotWallSpinBox.setValue(float(self._parameterNode.GetParameter("miterBoxSlotWall")))
if self._parameterNode.GetParameter("fibulaScrewHoleCylinderRadius") != '':
self.ui.fibulaScrewHoleCylinderRadiusSpinBox.setValue(float(self._parameterNode.GetParameter("fibulaScrewHoleCylinderRadius")))
if self._parameterNode.GetParameter("clearanceFitPrintingTolerance") != '':
self.ui.clearanceFitPrintingToleranceSpinBox.setValue(float(self._parameterNode.GetParameter("clearanceFitPrintingTolerance")))
if self._parameterNode.GetParameter("biggerMiterBoxDistanceToFibula") != '':
self.ui.biggerMiterBoxDistanceToFibulaSpinBox.setValue(float(self._parameterNode.GetParameter("biggerMiterBoxDistanceToFibula")))
if self._parameterNode.GetParameter("intersectionDistanceMultiplier") != '':
self.ui.intersectionDistanceMultiplierSpinBox.setValue(float(self._parameterNode.GetParameter("intersectionDistanceMultiplier")))
if self._parameterNode.GetParameter("sawBoxSlotWidth") != '':
self.ui.sawBoxSlotWidthSpinBox.setValue(float(self._parameterNode.GetParameter("sawBoxSlotWidth")))
if self._parameterNode.GetParameter("sawBoxSlotLength") != '':
self.ui.sawBoxSlotLengthSpinBox.setValue(float(self._parameterNode.GetParameter("sawBoxSlotLength")))
if self._parameterNode.GetParameter("sawBoxSlotHeight") != '':
self.ui.sawBoxSlotHeightSpinBox.setValue(float(self._parameterNode.GetParameter("sawBoxSlotHeight")))
if self._parameterNode.GetParameter("sawBoxSlotWall") != '':
self.ui.sawBoxSlotWallSpinBox.setValue(float(self._parameterNode.GetParameter("sawBoxSlotWall")))
if self._parameterNode.GetParameter("biggerSawBoxDistanceToMandible") != '':
self.ui.biggerSawBoxDistanceToMandibleSpinBox.setValue(float(self._parameterNode.GetParameter("biggerSawBoxDistanceToMandible")))
if self._parameterNode.GetParameter("mandibleScrewHoleCylinderRadius") != '':
self.ui.mandibleScrewHoleCylinderRadiusSpinBox.setValue(float(self._parameterNode.GetParameter("mandibleScrewHoleCylinderRadius")))
if self._parameterNode.GetParameter("dentalImplantCylinderRadius") != '':
self.ui.dentalImplantCylinderRadiusSpinBox.setValue(float(self._parameterNode.GetParameter("dentalImplantCylinderRadius")))
if self._parameterNode.GetParameter("dentalImplantCylinderHeight") != '':
self.ui.dentalImplantCylinderHeightSpinBox.setValue(float(self._parameterNode.GetParameter("dentalImplantCylinderHeight")))
if self._parameterNode.GetParameter("dentalImplantDrillGuideWall") != '':
self.ui.dentalImplantDrillGuideWallSpinBox.setValue(float(self._parameterNode.GetParameter("dentalImplantDrillGuideWall")))
self.ui.notLeftFibulaCheckBox.checked = self._parameterNode.GetParameter("notLeftFibula") == "True"
self.ui.makeAllMandiblePlanesRotateTogetherCheckBox.checked = self._parameterNode.GetParameter("makeAllMandiblePlanesRotateTogether") == "True"
self.ui.useMoreExactVersionOfPositioningAlgorithmCheckBox.checked = self._parameterNode.GetParameter("useMoreExactVersionOfPositioningAlgorithm") == "True"
self.ui.useNonDecimatedBoneModelsForPreviewCheckBox.checked = self._parameterNode.GetParameter("useNonDecimatedBoneModelsForPreview") == "True"
self.ui.mandiblePlanesPositioningForMaximumBoneContactCheckBox.checked = self._parameterNode.GetParameter("mandiblePlanesPositioningForMaximumBoneContact") == "True"
self.ui.checkSecurityMarginOnMiterBoxCreationCheckBox.checked = self._parameterNode.GetParameter("checkSecurityMarginOnMiterBoxCreation") != "False"
if self._parameterNode.GetParameter("updateOnMandiblePlanesMovement") == "True":
self.ui.generateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton.checkState = 2
else:
self.ui.generateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton.checkState = 0
# All the GUI updates are done
self._updatingGUIFromParameterNode = False
def updateParameterNodeFromGUI(self, caller=None, event=None):
"""
This method is called when the user makes any change in the GUI.
The changes are saved into the parameter node (so that they are restored when the scene is saved and loaded).
"""
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
wasModified = self._parameterNode.StartModify() # Modify all properties in a single batch
self._parameterNode.SetNodeReferenceID("mandibleCurve", self.ui.mandibleCurveSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("mandibularSegmentation", self.ui.mandibularSegmentationSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("fibulaSegmentation", self.ui.fibulaSegmentationSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("fibulaFiducialList", self.ui.fibulaFiducialListSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("fibulaSurgicalGuideBaseModel", self.ui.fibulaSurgicalGuideBaseSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("miterBoxDirectionLine", self.ui.miterBoxDirectionLineSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("mandibleBridgeModel", self.ui.mandibleBridgeModelSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("mandibleSurgicalGuideBaseModel", self.ui.mandibleSurgicalGuideBaseSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("mandibleFiducialList", self.ui.mandibleFiducialListSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("dentalImplantsFiducialList", self.ui.dentalImplantFiducialListSelector.currentNodeID)
self._parameterNode.SetNodeReferenceID("selectedDentalImplantCylinderModel", self.ui.dentalImplantCylinderSelector.currentNodeID)
self._parameterNode.SetParameter("securityMarginOfFibulaPieces", str(self.ui.securityMarginOfFibulaPiecesSpinBox.value))
self._parameterNode.SetParameter("miterBoxSlotWidth", str(self.ui.miterBoxSlotWidthSpinBox.value))
self._parameterNode.SetParameter("miterBoxSlotLength", str(self.ui.miterBoxSlotLengthSpinBox.value))
self._parameterNode.SetParameter("miterBoxSlotHeight", str(self.ui.miterBoxSlotHeightSpinBox.value))
self._parameterNode.SetParameter("miterBoxSlotWall", str(self.ui.miterBoxSlotWallSpinBox.value))
self._parameterNode.SetParameter("fibulaScrewHoleCylinderRadius", str(self.ui.fibulaScrewHoleCylinderRadiusSpinBox.value))
self._parameterNode.SetParameter("clearanceFitPrintingTolerance", str(self.ui.clearanceFitPrintingToleranceSpinBox.value))
self._parameterNode.SetParameter("biggerMiterBoxDistanceToFibula", str(self.ui.biggerMiterBoxDistanceToFibulaSpinBox.value))
self._parameterNode.SetParameter("sawBoxSlotWidth", str(self.ui.sawBoxSlotWidthSpinBox.value))
self._parameterNode.SetParameter("sawBoxSlotLength", str(self.ui.sawBoxSlotLengthSpinBox.value))
self._parameterNode.SetParameter("sawBoxSlotHeight", str(self.ui.sawBoxSlotHeightSpinBox.value))
self._parameterNode.SetParameter("sawBoxSlotWall", str(self.ui.sawBoxSlotWallSpinBox.value))
self._parameterNode.SetParameter("biggerSawBoxDistanceToMandible", str(self.ui.biggerSawBoxDistanceToMandibleSpinBox.value))
self._parameterNode.SetParameter("mandibleScrewHoleCylinderRadius", str(self.ui.mandibleScrewHoleCylinderRadiusSpinBox.value))
self._parameterNode.SetParameter("dentalImplantCylinderRadius", str(self.ui.dentalImplantCylinderRadiusSpinBox.value))
self._parameterNode.SetParameter("dentalImplantCylinderHeight", str(self.ui.dentalImplantCylinderHeightSpinBox.value))
self._parameterNode.SetParameter("dentalImplantDrillGuideWall", str(self.ui.dentalImplantDrillGuideWallSpinBox.value))
if self.ui.notLeftFibulaCheckBox.checked:
self._parameterNode.SetParameter("notLeftFibula","True")
else:
self._parameterNode.SetParameter("notLeftFibula","False")
if self.ui.makeAllMandiblePlanesRotateTogetherCheckBox.checked:
self._parameterNode.SetParameter("makeAllMandiblePlanesRotateTogether","True")
else:
self._parameterNode.SetParameter("makeAllMandiblePlanesRotateTogether","False")
if self.ui.mandiblePlanesPositioningForMaximumBoneContactCheckBox.checked:
self._parameterNode.SetParameter("mandiblePlanesPositioningForMaximumBoneContact","True")
else:
self._parameterNode.SetParameter("mandiblePlanesPositioningForMaximumBoneContact","False")
if self.ui.useMoreExactVersionOfPositioningAlgorithmCheckBox.checked:
self._parameterNode.SetParameter("useMoreExactVersionOfPositioningAlgorithm","True")
else:
self._parameterNode.SetParameter("useMoreExactVersionOfPositioningAlgorithm","False")
if self.ui.useNonDecimatedBoneModelsForPreviewCheckBox.checked:
self._parameterNode.SetParameter("useNonDecimatedBoneModelsForPreview","True")
else:
self._parameterNode.SetParameter("useNonDecimatedBoneModelsForPreview","False")
if self.ui.checkSecurityMarginOnMiterBoxCreationCheckBox.checked:
self._parameterNode.SetParameter("checkSecurityMarginOnMiterBoxCreation","True")
else:
self._parameterNode.SetParameter("checkSecurityMarginOnMiterBoxCreation","False")
if self.ui.generateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton.checkState == qt.Qt.Checked:
self._parameterNode.SetParameter("updateOnMandiblePlanesMovement","True")
else:
self._parameterNode.SetParameter("updateOnMandiblePlanesMovement","False")
self._parameterNode.EndModify(wasModified)
def onFibulaPlanesCreationParametersChanged(self, caller=None, event=None):
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
wasModified = self._parameterNode.StartModify()
self._parameterNode.SetParameter("fibulaPlanesCreationParametersChanged", "True")
self._parameterNode.SetParameter("initialSpace", str(self.ui.initialSpinBox.value))
self._parameterNode.SetParameter("additionalBetweenSpaceOfFibulaPlanes", str(self.ui.betweenSpinBox.value))
self._parameterNode.SetParameter("intersectionDistanceMultiplier", str(self.ui.intersectionDistanceMultiplierSpinBox.value))
self._parameterNode.SetNodeReferenceID("fibulaLine", self.ui.fibulaLineSelector.currentNodeID)
self._parameterNode.EndModify(wasModified)
def onFixCutGoesThroughTheMandibleTwiceCheckBox(self):
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
wasModified = self._parameterNode.StartModify()
if self.ui.fixCutGoesThroughTheMandibleTwiceCheckBox.checked:
self._parameterNode.SetParameter("fixCutGoesThroughTheMandibleTwice","True")
else:
self._parameterNode.SetParameter("fixCutGoesThroughTheMandibleTwice","False")
self._parameterNode.SetParameter("fixCutGoesThroughTheMandibleTwiceCheckBoxChanged","True")
self._parameterNode.EndModify(wasModified)
def onUseMoreExactVersionOfPositioningAlgorithmCheckBox(self):
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
wasModified = self._parameterNode.StartModify()
if self.ui.useMoreExactVersionOfPositioningAlgorithmCheckBox.checked:
self._parameterNode.SetParameter("useMoreExactVersionOfPositioningAlgorithm","True")
else:
self._parameterNode.SetParameter("useMoreExactVersionOfPositioningAlgorithm","False")
self._parameterNode.SetParameter("useMoreExactVersionOfPositioningAlgorithmCheckBoxChanged","True")
self._parameterNode.EndModify(wasModified)
def onAddMandibularCurveButton(self):
self.logic.addMandibularCurve()
def onAddFibulaLineButton(self):
self.logic.addFibulaLine()
def onScalarVolumeChanged(self):
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
self._parameterNode.SetNodeReferenceID("currentScalarVolume", self.ui.scalarVolumeSelector.currentNodeID)
scalarVolume = self.ui.scalarVolumeSelector.currentNode()
if scalarVolume != None:
scalarVolumeID = scalarVolume.GetID()
redSliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
redSliceLogic.GetSliceCompositeNode().SetBackgroundVolumeID(scalarVolumeID)
greenSliceLogic = slicer.app.layoutManager().sliceWidget('Green').sliceLogic()
greenSliceLogic.GetSliceCompositeNode().SetBackgroundVolumeID(scalarVolumeID)
yellowSliceLogic = slicer.app.layoutManager().sliceWidget('Yellow').sliceLogic()
yellowSliceLogic.GetSliceCompositeNode().SetBackgroundVolumeID(scalarVolumeID)
slicer.util.resetSliceViews()
fibulaCentroidX = self._parameterNode.GetParameter("fibulaCentroidX")
fibulaCentroidY = self._parameterNode.GetParameter("fibulaCentroidY")
fibulaCentroidZ = self._parameterNode.GetParameter("fibulaCentroidZ")
mandibleCentroidX = self._parameterNode.GetParameter("mandibleCentroidX")
mandibleCentroidY = self._parameterNode.GetParameter("mandibleCentroidY")
mandibleCentroidZ = self._parameterNode.GetParameter("mandibleCentroidZ")
if fibulaCentroidX != "":
fibulaCentroid = np.array([float(fibulaCentroidX),float(fibulaCentroidY),float(fibulaCentroidZ)])
mandibleCentroid = np.array([float(mandibleCentroidX),float(mandibleCentroidY),float(mandibleCentroidZ)])
bounds = [0,0,0,0,0,0]
scalarVolume.GetBounds(bounds)
bounds = np.array(bounds)
centerOfScalarVolume = np.array([(bounds[0]+bounds[1])/2,(bounds[2]+bounds[3])/2,(bounds[4]+bounds[5])/2])
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
mandibularPlanesFolder = shNode.GetItemByName("Mandibular planes")
fibulaPlanesFolder = shNode.GetItemByName("Fibula planes")
biggerMiterBoxesFolder = shNode.GetItemByName("biggerMiterBoxes Models")
cutBonesFolder = shNode.GetItemByName("Cut Bones")
transformedFibulaPiecesFolder = shNode.GetItemByName("Transformed Fibula Pieces")
mandibularPlanesList = createListFromFolderID(mandibularPlanesFolder)
fibulaPlanesList = createListFromFolderID(fibulaPlanesFolder)
biggerMiterBoxesList = createListFromFolderID(biggerMiterBoxesFolder)
cutBonesList = createListFromFolderID(cutBonesFolder)
transformedFibulaPiecesList = createListFromFolderID(transformedFibulaPiecesFolder)
redSliceNode = slicer.mrmlScene.GetSingletonNode("Red", "vtkMRMLSliceNode")
fibulaDisplayNodesWereUpdatedFlag = self._parameterNode.GetParameter("fibulaDisplayNodesWereUpdatedFlag")
if np.linalg.norm(fibulaCentroid-centerOfScalarVolume) < np.linalg.norm(mandibleCentroid-centerOfScalarVolume):
#When fibulaScalarVolume:
if fibulaDisplayNodesWereUpdatedFlag == "" or fibulaDisplayNodesWereUpdatedFlag == "False":
addIterationList = biggerMiterBoxesList + cutBonesList[0:(len(cutBonesList)-1)]
removeIterationList = [cutBonesList[len(cutBonesList)-1]] + transformedFibulaPiecesList
for i in range(len(addIterationList)):
displayNode = addIterationList[i].GetDisplayNode()
displayNode.AddViewNodeID(redSliceNode.GetID())
for i in range(len(removeIterationList)):
displayNode = removeIterationList[i].GetDisplayNode()
displayNode.RemoveViewNodeID(redSliceNode.GetID())
self._parameterNode.SetParameter("fibulaDisplayNodesWereUpdatedFlag","True")
else:
#When mandibleScalarVolume:
if fibulaDisplayNodesWereUpdatedFlag == "" or fibulaDisplayNodesWereUpdatedFlag == "True":
addIterationList = [cutBonesList[len(cutBonesList)-1]] + transformedFibulaPiecesList
removeIterationList = biggerMiterBoxesList + cutBonesList[0:(len(cutBonesList)-1)]
for i in range(len(addIterationList)):
displayNode = addIterationList[i].GetDisplayNode()
displayNode.AddViewNodeID(redSliceNode.GetID())
for i in range(len(removeIterationList)):
displayNode = removeIterationList[i].GetDisplayNode()
displayNode.RemoveViewNodeID(redSliceNode.GetID())
self._parameterNode.SetParameter("fibulaDisplayNodesWereUpdatedFlag","False")
def onAddCutPlaneButton(self):
self.logic.addCutPlane()
def onMakeModelsButton(self):
self.logic.makeModels()
self.ui.generateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton.enabled = True
def onCreateMiterBoxesFromFibulaPlanesButton(self):
self.logic.createMiterBoxesFromFibulaPlanes()
def onCreateFibulaCylindersFiducialListButton(self):
self.logic.createFibulaCylindersFiducialList()
self.ui.createCylindersFromFiducialListAndFibulaSurgicalGuideBaseButton.enabled = True
def onCreateCylindersFromFiducialListAndSurgicalGuideBaseButton(self):
self.logic.createCylindersFromFiducialListAndFibulaSurgicalGuideBase()
def onMakeBooleanOperationsToFibulaSurgicalGuideBaseButton(self):
self.logic.makeBooleanOperationsToFibulaSurgicalGuideBase()
def onCreateMandibleCylindersFiducialListButton(self):
self.ui.createCylindersFromFiducialListAndMandibleSurgicalGuideBaseButton.enabled = True
self.logic.createMandibleCylindersFiducialList()
def onCreateDentalImplantCylindersFiducialListButton(self):
self.logic.createDentalImplantCylindersFiducialList()
def onCreateCylindersFromFiducialListAndMandibleReconstructionButton(self):
self.logic.createCylindersFromFiducialListAndMandibleReconstruction()
def onCreateSawBoxesFromFirstAndLastMandiblePlanesButton(self):
self.logic.createSawBoxesFromFirstAndLastMandiblePlanes()
def onMakeBooleanOperationsToMandibleSurgicalGuideBaseButton(self):
self.logic.makeBooleanOperationsToMandibleSurgicalGuideBase()
def onCreateCylindersFromFiducialListAndMandibleSurgicalGuideBaseButton(self):
self.logic.createCylindersFromFiducialListAndMandibleSurgicalGuideBase()
def onGenerateFibulaPlanesFibulaBonePiecesAndTransformThemToMandibleButton(self):
self.logic.onGenerateFibulaPlanesTimerTimeout()
def onCenterFibulaLineButton(self):
self.logic.centerFibulaLine()
def onShowHideBiggerSawBoxesInteractionHandlesButton(self):
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
sawBoxesPlanesFolder = shNode.GetItemByName("sawBoxes Planes")
sawBoxesPlanesList = createListFromFolderID(sawBoxesPlanesFolder)
for i in range(len(sawBoxesPlanesList)):
displayNode = sawBoxesPlanesList[i].GetDisplayNode()
handlesVisibility = displayNode.GetHandlesInteractive()
displayNode.SetHandlesInteractive(not handlesVisibility)
def onShowHideMandiblePlanesInteractionHandlesButton(self):
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
mandibularPlanesFolder = shNode.GetItemByName("Mandibular planes")
mandibularPlanesList = createListFromFolderID(mandibularPlanesFolder)
for i in range(len(mandibularPlanesList)):
displayNode = mandibularPlanesList[i].GetDisplayNode()
handlesVisibility = displayNode.GetHandlesInteractive()
displayNode.SetHandlesInteractive(not handlesVisibility)
def onShowHideFibulaSegmentsLengthsButton(self):
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
fibulaSegmentsLengthsFolder = shNode.GetItemByName("Fibula Segments Lengths")
fibulaSegmentsLengthsList = createListFromFolderID(fibulaSegmentsLengthsFolder)
for i in range(len(fibulaSegmentsLengthsList)):
lineDisplayNode = fibulaSegmentsLengthsList[i].GetDisplayNode()
visibility = lineDisplayNode.GetVisibility()
lineDisplayNode.SetVisibility(not visibility)
def onCreate3DModelOfTheReconstructionButton(self):
self.logic.create3DModelOfTheReconstruction()
def onShowHideOriginalMandibleButton(self):
mandibleModelNode = self._parameterNode.GetNodeReference("mandibleModelNode")
decimatedMandibleModelNode = self._parameterNode.GetNodeReference("decimatedMandibleModelNode")
useNonDecimatedBoneModelsForPreviewChecked = self._parameterNode.GetParameter("useNonDecimatedBoneModelsForPreview") == "True"
mandibleModelDisplayNode = mandibleModelNode.GetDisplayNode()
decimatedMandibleModelDisplayNode = decimatedMandibleModelNode.GetDisplayNode()
if mandibleModelDisplayNode.GetVisibility() or decimatedMandibleModelDisplayNode.GetVisibility():
mandibleModelDisplayNode.SetVisibility(False)
decimatedMandibleModelDisplayNode.SetVisibility(False)
else:
if useNonDecimatedBoneModelsForPreviewChecked:
mandibleModelDisplayNode.SetVisibility(True)
else:
decimatedMandibleModelDisplayNode.SetVisibility(True)
def onUpdateFibulaDentalImplantCylindersButton(self):
self.logic.updateFibulaDentalImplantCylinders()
#
# BoneReconstructionPlannerLogic
#
class BoneReconstructionPlannerLogic(ScriptedLoadableModuleLogic):
"""This class should implement all the actual
computation done by your module. The interface
should be such that other python code can import
this class and make use of the functionality without
requiring an instance of the Widget.
Uses ScriptedLoadableModuleLogic base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self):
"""
Called when the logic class is instantiated. Can be used for initializing member variables.
"""
ScriptedLoadableModuleLogic.__init__(self)
self.mandiblePlaneObserversAndNodeIDList = []
self.sawBoxPlaneObserversPlaneNodeIDAndTransformIDList = []
self.dentalImplantPlaneObserversPlaneNodeIDAndTransformIDList = []
self.mandibleToFibulaRegistrationTransformMatricesList = []
self.generateFibulaPlanesTimer = qt.QTimer()
self.generateFibulaPlanesTimer.setInterval(300)
self.generateFibulaPlanesTimer.setSingleShot(True)
self.generateFibulaPlanesTimer.connect('timeout()', self.onGenerateFibulaPlanesTimerTimeout)
customLayout = """
<layout type="vertical">
<item>
<layout type="horizontal">
<item>
<view class="vtkMRMLViewNode" singletontag="1">
<property name="viewlabel" action="default">1</property>
</view>
</item>
<item>
<view class="vtkMRMLSliceNode" singletontag="Red">
<property name="orientation" action="default">Axial</property>
<property name="viewlabel" action="default">R</property>
<property name="viewcolor" action="default">#F34A33</property>
</view>
</item>
</layout>
</item>
<item>
<view class="vtkMRMLViewNode" singletontag="2">
<property name="viewlabel" action="default">2</property>
</view>
</item>
</layout>
"""
# Built-in layout IDs are all below 100, so you can choose any large random number
# for your custom layout ID.
self.customLayoutId=101
layoutManager = slicer.app.layoutManager()
layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(self.customLayoutId, customLayout)
# Add button to layout selector toolbar for this custom layout
viewToolBar = slicer.util.mainWindow().findChild('QToolBar', 'ViewToolBar')
layoutMenu = viewToolBar.widgetForAction(viewToolBar.actions()[0]).menu()
layoutSwitchActionParent = layoutMenu # use `layoutMenu` to add inside layout list, use `viewToolBar` to add next the standard layout list
layoutSwitchAction = layoutSwitchActionParent.addAction("BoneReconstructionPlanner") # add inside layout list
layoutSwitchAction.setData(self.customLayoutId)
layoutSwitchAction.setIcon(qt.QIcon(':Icons/Go.png'))
layoutSwitchAction.setToolTip('3D Mandible View, Red Slice and 3D Fibula View')
def setDefaultParameters(self, parameterNode):
"""
Initialize parameter node with default settings.
"""
if not parameterNode.GetParameter("Threshold"):
parameterNode.SetParameter("Threshold", "100.0")
if not parameterNode.GetParameter("Invert"):
parameterNode.SetParameter("Invert", "false")
def getParentFolderItemID(self):
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
sceneItemID = shNode.GetSceneItemID()
folderSubjectHierarchyID = shNode.GetItemByName("BoneReconstructionPlanner")
if folderSubjectHierarchyID:
return folderSubjectHierarchyID
else:
return shNode.CreateFolderItem(sceneItemID,"BoneReconstructionPlanner")
def getMandiblePlanesFolderItemID(self):
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
folderSubjectHierarchyID = shNode.GetItemByName("Mandibular planes")
if folderSubjectHierarchyID:
return folderSubjectHierarchyID
else:
return shNode.CreateFolderItem(self.getParentFolderItemID(),"Mandibular planes")
def addMandibularCurve(self):
curveNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLMarkupsCurveNode")
curveNode.SetName("temp")
slicer.mrmlScene.AddNode(curveNode)
slicer.modules.markups.logic().AddNewDisplayNodeForMarkupsNode(curveNode)
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
curveNodeItemID = shNode.GetItemByDataNode(curveNode)
shNode.SetItemParent(curveNodeItemID, self.getParentFolderItemID())
curveNode.SetName(slicer.mrmlScene.GetUniqueNameByString("mandibularCurve"))
displayNode = curveNode.GetDisplayNode()
mandibleViewNode = slicer.mrmlScene.GetSingletonNode("1", "vtkMRMLViewNode")
displayNode.AddViewNodeID(mandibleViewNode.GetID())
#setup placement
slicer.modules.markups.logic().SetActiveListID(curveNode)
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")
interactionNode.SwitchToSinglePlaceMode()
def addFibulaLine(self):
parameterNode = self.getParameterNode()
scalarVolume = parameterNode.GetNodeReference("currentScalarVolume")
fibulaCentroidX = parameterNode.GetParameter("fibulaCentroidX")
fibulaCentroidY = parameterNode.GetParameter("fibulaCentroidY")
fibulaCentroidZ = parameterNode.GetParameter("fibulaCentroidZ")
mandibleCentroidX = parameterNode.GetParameter("mandibleCentroidX")
mandibleCentroidY = parameterNode.GetParameter("mandibleCentroidY")
mandibleCentroidZ = parameterNode.GetParameter("mandibleCentroidZ")
fibulaCentroid = np.array([float(fibulaCentroidX),float(fibulaCentroidY),float(fibulaCentroidZ)])
mandibleCentroid = np.array([float(mandibleCentroidX),float(mandibleCentroidY),float(mandibleCentroidZ)])
bounds = [0,0,0,0,0,0]
scalarVolume.GetBounds(bounds)
bounds = np.array(bounds)
centerOfScalarVolume = np.array([(bounds[0]+bounds[1])/2,(bounds[2]+bounds[3])/2,(bounds[4]+bounds[5])/2])
lineNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLMarkupsLineNode")
lineNode.SetName("temp")
slicer.mrmlScene.AddNode(lineNode)
slicer.modules.markups.logic().AddNewDisplayNodeForMarkupsNode(lineNode)
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
lineNodeItemID = shNode.GetItemByDataNode(lineNode)
shNode.SetItemParent(lineNodeItemID, self.getParentFolderItemID())
lineNode.SetName(slicer.mrmlScene.GetUniqueNameByString("fibulaLine"))
displayNode = lineNode.GetDisplayNode()
fibulaViewNode = slicer.mrmlScene.GetSingletonNode("2", "vtkMRMLViewNode")
displayNode.AddViewNodeID(fibulaViewNode.GetID())
if np.linalg.norm(fibulaCentroid-centerOfScalarVolume) < np.linalg.norm(mandibleCentroid-centerOfScalarVolume):
redSliceNode = slicer.mrmlScene.GetSingletonNode("Red", "vtkMRMLSliceNode")
displayNode.AddViewNodeID(redSliceNode.GetID())
#setup placement
slicer.modules.markups.logic().SetActiveListID(lineNode)
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")
interactionNode.SwitchToSinglePlaceMode()
def addCutPlane(self):
parameterNode = self.getParameterNode()
colorIndexStr = parameterNode.GetParameter("colorIndex")
if colorIndexStr != "":
colorIndex = int(colorIndexStr) + 1
parameterNode.SetParameter("colorIndex", str(colorIndex))
else:
colorIndex = 0
parameterNode.SetParameter("colorIndex", str(colorIndex))
planeNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLMarkupsPlaneNode")
planeNode.SetName("temp")
slicer.mrmlScene.AddNode(planeNode)
slicer.modules.markups.logic().AddNewDisplayNodeForMarkupsNode(planeNode)
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
mandibularFolderID = self.getMandiblePlanesFolderItemID()
planeNodeItemID = shNode.GetItemByDataNode(planeNode)
shNode.SetItemParent(planeNodeItemID, mandibularFolderID)
planeNode.SetName(slicer.mrmlScene.GetUniqueNameByString("mandibularPlane"))
planeNode.SetAttribute("isMandibularPlane","True")
aux = slicer.mrmlScene.GetNodeByID('vtkMRMLColorTableNodeFileMediumChartColors.txt')
colorTable = aux.GetLookupTable()
ind = colorIndex%8
colorwithalpha = colorTable.GetTableValue(ind)
color = [colorwithalpha[0],colorwithalpha[1],colorwithalpha[2]]
#display node of the plane
displayNode = planeNode.GetDisplayNode()
displayNode.SetGlyphScale(2.5)
displayNode.SetSelectedColor(color)
mandibleViewNode = slicer.mrmlScene.GetSingletonNode("1", "vtkMRMLViewNode")
displayNode.AddViewNodeID(mandibleViewNode.GetID())
#conections
self.planeNodeObserver = planeNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointPositionDefinedEvent,self.onPlanePointAdded)
#setup placement
slicer.modules.markups.logic().SetActiveListID(planeNode)
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")
interactionNode.SwitchToSinglePlaceMode()
def onPlanePointAdded(self,sourceNode,event):
parameterNode = self.getParameterNode()
mandibleCurve = parameterNode.GetNodeReference("mandibleCurve")
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
mandibularPlanesFolder = shNode.GetItemByName("Mandibular planes")
mandibularPlanesList = createListFromFolderID(mandibularPlanesFolder)
temporalOrigin = [0,0,0]
sourceNode.GetNthControlPointPosition(0,temporalOrigin)
self.setupMandiblePlaneStraightOverMandibleCurve(sourceNode,temporalOrigin, mandibleCurve, self.planeNodeObserver)
displayNode = sourceNode.GetDisplayNode()
displayNode.HandlesInteractiveOn()
for i in range(3):
sourceNode.SetNthControlPointVisibility(i,False)
observer = sourceNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent,self.onPlaneModifiedTimer)
self.mandiblePlaneObserversAndNodeIDList.append([observer,sourceNode.GetID()])
mandiblePlaneAndCurvePointIndexList = []
for i in range(len(mandibularPlanesList)):
origin = [0,0,0]
mandibularPlanesList[i].GetNthControlPointPosition(0,origin)
closestCurvePoint = [0,0,0]
closestCurvePointIndex = mandibleCurve.GetClosestPointPositionAlongCurveWorld(origin,closestCurvePoint)
mandiblePlaneAndCurvePointIndexList.append([mandibularPlanesList[i],closestCurvePointIndex])
mandiblePlaneAndCurvePointIndexList.sort(key = lambda item : item[1])
mandibularPlanesFolder2 = shNode.CreateFolderItem(self.getParentFolderItemID(),"Mandibular planes 2")
for i in range(len(mandiblePlaneAndCurvePointIndexList)):
mandiblePlane = mandiblePlaneAndCurvePointIndexList[i][0]
mandiblePlaneItemID = shNode.GetItemByDataNode(mandiblePlane)
shNode.SetItemParent(mandiblePlaneItemID, mandibularPlanesFolder2)