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3D Slicer scripted module for measuring angle between rulers
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| # | |
| # Installation: | |
| # - Save this file as AngleMeasurement.py to a directory on your computer | |
| # - Add the directory to the additional module paths in the Slicer application settings: | |
| # - Choose in the menu: Edit / Application settings | |
| # - Click Modules, click >> next to Additional module paths | |
| # - Click Add, and choose the .py file's location | |
| # - After you restart Slicer, "Angle Measurment" module should show up in Quantification category | |
| # | |
| import os | |
| import unittest | |
| import vtk, qt, ctk, slicer | |
| from slicer.ScriptedLoadableModule import * | |
| from slicer.util import VTKObservationMixin | |
| import logging | |
| # | |
| # AngleMeasurement | |
| # | |
| class AngleMeasurement(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 = "Angle Measurement" | |
| self.parent.categories = ["Quantification"] | |
| self.parent.dependencies = [] | |
| self.parent.contributors = ["Andras Lasso (PerkLab)"] | |
| self.parent.helpText = """ | |
| Measure angles between rulers | |
| """ | |
| self.parent.acknowledgementText = """ | |
| """ # replace with organization, grant and thanks. | |
| # | |
| # AngleMeasurementWidget | |
| # | |
| class AngleMeasurementWidget(ScriptedLoadableModuleWidget, VTKObservationMixin): | |
| """Uses ScriptedLoadableModuleWidget base class, available at: | |
| https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py | |
| """ | |
| def __init__(self, parent): | |
| ScriptedLoadableModuleWidget.__init__(self, parent) | |
| VTKObservationMixin.__init__(self) | |
| # Members | |
| self.numberOfRulersInScene = 0 | |
| self.ruler1 = None | |
| self.ruler2 = None | |
| self.angleDeg = None | |
| self.rulerNodeClass = 'vtkMRMLAnnotationRulerNode' | |
| def setup(self): | |
| ScriptedLoadableModuleWidget.setup(self) | |
| # Instantiate and connect widgets ... | |
| # | |
| # Parameters Area | |
| # | |
| parametersCollapsibleButton = ctk.ctkCollapsibleButton() | |
| parametersCollapsibleButton.text = "Parameters" | |
| self.layout.addWidget(parametersCollapsibleButton) | |
| # Layout within the dummy collapsible button | |
| parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton) | |
| # | |
| # input volume selector | |
| # | |
| self.resultPreview = qt.QLabel() | |
| parametersFormLayout.addRow("Angle: ", self.resultPreview) | |
| # | |
| # Add Button | |
| # | |
| self.applyButton = qt.QPushButton("Add to table") | |
| self.applyButton.setAutoFillBackground(True) | |
| self.applyButton.setStyleSheet("background-color: rgb(150, 255, 150); color: rgb(0, 0, 0); height: 40px") | |
| self.applyButton.enabled = False | |
| parametersFormLayout.addRow(self.applyButton) | |
| if not hasattr(slicer, 'angleMeasurementData'): | |
| # Store table in an internal scene so that results table is preserved | |
| # even when we close the scene | |
| slicer.angleMeasurementData = {} | |
| self.internalScene = slicer.vtkMRMLScene() | |
| self.resultsTableNode = slicer.vtkMRMLTableNode() | |
| self.resultsTableNode.SetName('Angle measurements') | |
| self.resultsTableNode.SetUseColumnNameAsColumnHeader(True) | |
| self.resultsTableNode.AddColumn().SetName('Image') | |
| self.resultsTableNode.AddColumn().SetName('Angle') | |
| self.resultsTableNode.AddColumn().SetName('Comment') | |
| self.internalScene.AddNode(self.resultsTableNode) | |
| slicer.angleMeasurementData["internalScene"] = self.internalScene | |
| slicer.angleMeasurementData["resultsTableNode"] = self.resultsTableNode | |
| else: | |
| self.internalScene = slicer.angleMeasurementData["internalScene"] | |
| self.resultsTableNode = slicer.angleMeasurementData["resultsTableNode"] | |
| self.resultsTableView = slicer.qMRMLTableView() | |
| self.resultsTableView.setMRMLScene(self.internalScene) | |
| self.resultsTableView.setMRMLTableNode(self.resultsTableNode) | |
| policy = qt.QSizePolicy() | |
| policy.setVerticalStretch(1) | |
| policy.setHorizontalPolicy(qt.QSizePolicy.Expanding) | |
| policy.setVerticalPolicy(qt.QSizePolicy.Expanding) | |
| self.resultsTableView.setSizePolicy(policy) | |
| parametersFormLayout.addRow(self.resultsTableView) | |
| # | |
| # Clear button | |
| # | |
| self.clearRulersButton = qt.QPushButton("Clear rulers") | |
| self.clearRulersButton.setAutoFillBackground(True) | |
| self.clearRulersButton.setStyleSheet("background-color: rgb(255, 100, 100); color: rgb(0, 0, 0)") | |
| parametersFormLayout.addRow(self.clearRulersButton) | |
| self.clearLastMeasurementButton = qt.QPushButton("Remove last measurement") | |
| self.clearLastMeasurementButton.setAutoFillBackground(True) | |
| self.clearLastMeasurementButton.setStyleSheet("background-color: rgb(255, 100, 100); color: rgb(0, 0, 0)") | |
| parametersFormLayout.addRow(self.clearLastMeasurementButton) | |
| # connections | |
| self.applyButton.connect('clicked(bool)', self.onAddToTableButton) | |
| self.clearRulersButton.connect('clicked(bool)', self.onClearRulers) | |
| self.clearLastMeasurementButton.connect('clicked(bool)', self.onClearLastMeasurement) | |
| self.addObserver(slicer.mrmlScene, slicer.vtkMRMLScene.NodeAddedEvent, self.onSceneUpdated) | |
| self.addObserver(slicer.mrmlScene, slicer.vtkMRMLScene.NodeRemovedEvent, self.onSceneUpdated) | |
| self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent, self.onSceneUpdated) | |
| self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndImportEvent, self.onSceneUpdated) | |
| self.onSceneUpdated() | |
| self.onRulerChanged() | |
| selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton") | |
| # call the set reference to make sure the event is invoked | |
| selectionNode.SetReferenceActivePlaceNodeClassName(self.rulerNodeClass) | |
| selectionNode.SetActivePlaceNodeID(None) | |
| interactionNode = slicer.app.applicationLogic().GetInteractionNode() | |
| interactionNode.SetPlaceModePersistence(True) | |
| def cleanup(self): | |
| self.removeObservers() | |
| def onAddToTableButton(self): | |
| rowIndex = self.resultsTableNode.AddEmptyRow() | |
| volumeNode = slicer.util.getNode(self.ruler1.GetAttribute('AssociatedNodeID')) | |
| self.resultsTableNode.SetCellText(rowIndex, 0, volumeNode.GetName() if volumeNode else "") | |
| self.resultsTableNode.SetCellText(rowIndex, 1, "{:.1f}".format(self.angleDeg)) | |
| self.onClearRulers() | |
| def onSceneUpdated(self, caller = None, event = None): | |
| if not self.parent.isEntered: | |
| return | |
| oldNumberOfRulersInScene = self.numberOfRulersInScene | |
| oldRuler1 = self.ruler1 | |
| oldRuler2 = self.ruler2 | |
| newRuler1 = None | |
| newRuler2 = None | |
| self.numberOfRulersInScene = slicer.mrmlScene.GetNumberOfNodesByClass(self.rulerNodeClass) | |
| if self.numberOfRulersInScene == 2: | |
| newRuler1 = slicer.mrmlScene.GetNthNodeByClass(0, self.rulerNodeClass) | |
| newRuler2 = slicer.mrmlScene.GetNthNodeByClass(1, self.rulerNodeClass) | |
| if newRuler1 == oldRuler1 and newRuler2 == oldRuler2 and oldNumberOfRulersInScene == self.numberOfRulersInScene: | |
| # no change | |
| return | |
| if self.numberOfRulersInScene >= 2: | |
| interactionNode = slicer.app.applicationLogic().GetInteractionNode() | |
| interactionNode.SetCurrentInteractionMode(interactionNode.ViewTransform) | |
| self.ruler1 = newRuler1 | |
| self.ruler2 = newRuler2 | |
| self.removeObservers(self.onRulerChanged) | |
| if self.ruler1 and self.ruler2: | |
| self.addObserver(self.ruler1, vtk.vtkCommand.ModifiedEvent, self.onRulerChanged) | |
| self.addObserver(self.ruler2, vtk.vtkCommand.ModifiedEvent, self.onRulerChanged) | |
| self.onRulerChanged() | |
| def onRulerChanged(self, caller = None, event = None): | |
| if self.numberOfRulersInScene != 2: | |
| if self.numberOfRulersInScene < 2: | |
| self.resultPreview.text = "Not enough rulers" | |
| else: | |
| self.resultPreview.text = "There are more than two rulers" | |
| self.angleDeg = None | |
| self.applyButton.enabled = False | |
| return | |
| import numpy as np | |
| import math | |
| directionVectors = [] | |
| for ruler in [self.ruler1, self.ruler2]: | |
| p1=np.array([0,0,0]) | |
| p2=np.array([0,0,0]) | |
| ruler.GetControlPointWorldCoordinates(0,p1) | |
| ruler.GetControlPointWorldCoordinates(1,p2) | |
| directionVectors.append(p2-p1) | |
| # Compute angle (0 <= angle <= 90) | |
| cosang = np.dot(directionVectors[0], directionVectors[1]) | |
| sinang = np.linalg.norm(np.cross(directionVectors[0], directionVectors[1])) | |
| angleDeg = math.fabs(np.arctan2(sinang, cosang)*180.0/math.pi) | |
| self.angleDeg = angleDeg | |
| self.resultPreview.text = "{:.1f}".format(self.angleDeg) | |
| self.applyButton.enabled = True | |
| def onClearRulers(self): | |
| rulers = slicer.util.getNodesByClass(self.rulerNodeClass) | |
| for ruler in rulers: | |
| slicer.mrmlScene.RemoveNode(ruler) | |
| def onClearLastMeasurement(self): | |
| numOfRows = self.resultsTableNode.GetNumberOfRows() | |
| if numOfRows>0: | |
| self.resultsTableNode.RemoveRow(numOfRows-1) |
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Hello Prof,
In which directory should I put this angle measurement file so that I can incorporate this in Slicer?