From 1c86d7d7151a1bed45b27b8b86a6c2697db32b2d Mon Sep 17 00:00:00 2001 From: Saleem Edah-Tally Date: Fri, 6 Dec 2024 18:24:20 +0100 Subject: [PATCH] Add PreFitTube module. This module pre-fits a Shape::Tube markups node along an input markups curve that represents the axis of a non-aneurysmal artery. --- CMakeLists.txt | 1 + Docs/PreFitTube.md | 18 + Docs/PreFitTube_0.png | Bin 0 -> 37381 bytes PreFitTube/CMakeLists.txt | 31 ++ PreFitTube/PreFitTube.py | 430 ++++++++++++++++++++++ PreFitTube/Resources/Icons/PreFitTube.png | Bin 0 -> 8423 bytes PreFitTube/Resources/UI/PreFitTube.ui | 347 +++++++++++++++++ PreFitTube/Testing/CMakeLists.txt | 1 + PreFitTube/Testing/Python/CMakeLists.txt | 2 + README.md | 1 + 10 files changed, 831 insertions(+) create mode 100644 Docs/PreFitTube.md create mode 100644 Docs/PreFitTube_0.png create mode 100644 PreFitTube/CMakeLists.txt create mode 100644 PreFitTube/PreFitTube.py create mode 100644 PreFitTube/Resources/Icons/PreFitTube.png create mode 100644 PreFitTube/Resources/UI/PreFitTube.ui create mode 100644 PreFitTube/Testing/CMakeLists.txt create mode 100644 PreFitTube/Testing/Python/CMakeLists.txt diff --git a/CMakeLists.txt b/CMakeLists.txt index b184cca..77e6d17 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -68,6 +68,7 @@ add_subdirectory(ClipVessel) if(SlicerVMTK_USE_ExtraMarkups) add_subdirectory(CrossSectionAnalysis) add_subdirectory(StenosisMeasurement3D) + add_subdirectory(PreFitTube) endif() #----------------------------------------------------------------------------- diff --git a/Docs/PreFitTube.md b/Docs/PreFitTube.md new file mode 100644 index 0000000..3b875dc --- /dev/null +++ b/Docs/PreFitTube.md @@ -0,0 +1,18 @@ +# Pre-fit tube + +This module pre-fits a Shape::Tube markups node along an input markups curve that represents the axis of a non-aneurysmal artery. The control points of the tube must be further repositioned to represent the best *estimate* of the arterial wall. + +![Example](PreFitTube_0.png) + +### Usage + +Select a markups curve node, a scalar volume of a CT angiogram and a target dimension profile. Select an output Shape::Tube node, and optionally a segmentation node to keep the segment mask. After applying, the resulting Shape::Tube node may be post-processed to position the control points on the arterial wall. + +### Notes + - This extension is a requirement: [ExtraMarkups](https://github.com/chir-set/SlicerExtraMarkups). + - Use cropped volumes to save time. + - For tiny targets, resampling the volume to increase the resolution may help. + - The input curve should represent the axis of the artery. + - For diseased arteries, the more the curve passes through calcifications and soft lesions, the better for the segment mask. + - An output segmentation node can be specified to view the segment mask. + diff --git a/Docs/PreFitTube_0.png b/Docs/PreFitTube_0.png new file mode 100644 index 0000000000000000000000000000000000000000..9df066a51818530d96f82f780d63fe93820c24c9 GIT binary patch literal 37381 zcmcG$bx<8o*Y67UI-C^VIZfEm*-siqjr%v6v z@&~o4nKd)rJuPc}*0(1_MoI)81{($p3=CdO^p_kM*e6;rFo@q@pg>0iQYx@OKVNM` zRqesR5PCoUz~dr;&!072%Eb_IE{>O1uFh(X;ehQ_6e;>Ek 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zX(&|FzkJpL+8t5d3XOTR0-o>UwU$~usgN$2Q%D;(9Mpz8k50l-+ioFbTUI!Dc&q6GsRo`uh40f>2O{V;dU=HcR!TX=A2)UsW6WA#oN8sHmuO_h1kt zfKK=L0Sbzk3xWdXtU1deJjCn7ZJR{;N;Y&xL&ydnHmEMC-c|8`0+xv{uumodule documentation. +""") + self.parent.acknowledgementText = _(""" +This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc., Andras Lasso, PerkLab, +and Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1. +""") + +# +# PreFitTubeParameterNode +# + +@parameterNodeWrapper +class PreFitTubeParameterNode: + inputVolumeNode: slicer.vtkMRMLScalarVolumeNode + inputCurveNode: slicer.vtkMRMLMarkupsCurveNode + dimensionPreset: int = 3 + outputShapeNode: slicer.vtkMRMLMarkupsShapeNode + outputSegmentationNode: slicer.vtkMRMLSegmentationNode + +class dimensionPresets: + tiny = { + "extrusionKernelSize": 0.5, + "gaussianStandardDeviation": 0.5, + "seedRadius": 0.5, + "shellMargin": 5.0, + "shellThickness": 0.8 + } + small = { + "extrusionKernelSize": 1.5, + "gaussianStandardDeviation": 0.8, + "seedRadius": 0.8, + "shellMargin": 9.0, + "shellThickness": 1.1 + } + medium = { + "extrusionKernelSize": 3.2, + "gaussianStandardDeviation": 1.2, + "seedRadius": 1.0, + "shellMargin": 13.0, + "shellThickness": 1.5 + } + big = { + "extrusionKernelSize": 4.1, + "gaussianStandardDeviation": 1.6, + "seedRadius": 1.0, + "shellMargin": 22.0, + "shellThickness": 2.0 + } + huge = { + "extrusionKernelSize": 5.1, + "gaussianStandardDeviation": 2.1, + "seedRadius": 1.0, + "shellMargin": 32.0, + "shellThickness": 2.2 + } + + presets = (tiny, small, medium, big, huge) + def getPreset(self, index): + if index < 1 or index > len(self.presets): + raise ValueError("Preset index out of range.") + return self.presets[index - 1] +# +# PreFitTubeWidget +# + +class PreFitTubeWidget(ScriptedLoadableModuleWidget, VTKObservationMixin): + """Uses ScriptedLoadableModuleWidget base class, available at: + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def __init__(self, parent=None) -> 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._parameterNodeGuiTag = None + self._updatingGuiFromParameterNode = False + + def setup(self) -> None: + """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/PreFitTube.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) + + # Create logic class. Logic implements all computations that should be possible to run + # in batch mode, without a graphical user interface. + self.logic = PreFitTubeLogic() + + self.ui.dimensionComboBox.addItem(_("Tiny"), DIMENSION_TINY) + self.ui.dimensionComboBox.addItem(_("Small"), DIMENSION_SMALL) + self.ui.dimensionComboBox.addItem(_("Medium"), DIMENSION_MEDIUM) + self.ui.dimensionComboBox.addItem(_("Big"), DIMENSION_BIG) + self.ui.dimensionComboBox.addItem(_("Huge"), DIMENSION_HUGE) + + # Connections + self.ui.dimensionComboBox.connect('currentIndexChanged(int)', self.onDimensionPresetChanged) + + # 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) + + # Buttons + self.ui.applyButton.connect("clicked(bool)", self.onApplyButton) + + # Make sure parameter node is initialized (needed for module reload) + self.initializeParameterNode() + + def cleanup(self) -> None: + """Called when the application closes and the module widget is destroyed.""" + self.removeObservers() + + def enter(self) -> None: + """Called each time the user opens this module.""" + # Make sure parameter node exists and observed + self.initializeParameterNode() + + def exit(self) -> None: + """Called each time the user opens a different module.""" + # Do not react to parameter node changes (GUI will be updated when the user enters into the module) + if self._parameterNode: + self._parameterNode.disconnectGui(self._parameterNodeGuiTag) + self._parameterNodeGuiTag = None + + def onSceneStartClose(self, caller, event) -> None: + """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) -> None: + """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) -> None: + """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: Optional[PreFitTubeParameterNode]) -> None: + """ + Set and observe parameter node. + Observation is needed because when the parameter node is changed then the GUI must be updated immediately. + """ + + if self._parameterNode: + self._parameterNode.disconnectGui(self._parameterNodeGuiTag) + self._parameterNode = inputParameterNode + if self._parameterNode: + # Note: in the .ui file, a Qt dynamic property called "SlicerParameterName" is set on each + # ui element that needs connection. + self._parameterNodeGuiTag = self._parameterNode.connectGui(self.ui) + self.updateGuiFromParameterNode() + + def onApplyButton(self) -> None: + """Run processing when user clicks "Apply" button.""" + with slicer.util.tryWithErrorDisplay(_("Failed to compute results."), waitCursor=True): + self.logic.process() + + def onDimensionPresetChanged(self, index): + if self._parameterNode: + self._parameterNode.dimensionPreset = self.ui.dimensionComboBox.currentData + + def updateGuiFromParameterNode(self): + if not self._parameterNode or self._updatingGuiFromParameterNode: + return + self._updatingGuiFromParameterNode = True + + index = self.ui.dimensionComboBox.findData(self._parameterNode.dimensionPreset) + self.ui.dimensionComboBox.setCurrentIndex(index) + self.ui.ouitputOptionsCollapsibleButton.collapsed = (self._parameterNode.outputSegmentationNode is None) + + self._updatingGuiFromParameterNode = False +# +# PreFitTubeLogic +# + +class PreFitTubeLogic(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/main/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def __init__(self) -> None: + """Called when the logic class is instantiated. Can be used for initializing member variables.""" + ScriptedLoadableModuleLogic.__init__(self) + self._parameterNode = None + + def getParameterNode(self): + self._parameterNode = PreFitTubeParameterNode(super().getParameterNode()) + return self._parameterNode + + # 56.56s for 10⁴ points. + def getFarthestPoints(self, points : vtk.vtkPoints): + numberOfPoints = points.GetNumberOfPoints() + distances = vtk.vtkFloatArray() + distances.SetNumberOfComponents(7) + for i in range(numberOfPoints): + referencePoint = [0] * 3 + points.GetPoint(i, referencePoint) + for j in range(numberOfPoints): + nextPoint = [0] * 3 + points.GetPoint(j, nextPoint) + distance2 = vtk.vtkMath.Distance2BetweenPoints(referencePoint, nextPoint) + distances.InsertNextTuple((referencePoint[0], referencePoint[1], referencePoint[2], + nextPoint[0], nextPoint[1], nextPoint[2], + distance2)) + + sorter = vtk.vtkSortDataArray() + sorter.SortArrayByComponent(distances, 6, 1) + farthest = distances.GetTuple(0) + + result = vtk.vtkPoints() + result.InsertNextPoint((farthest[0], farthest[1], farthest[2])) + result.InsertNextPoint((farthest[3], farthest[4], farthest[5])) + + return result + + def process(self) -> None: + + import time + + startTime = time.time() + logging.info(_("Processing started.")) + + curveNode = self._parameterNode.inputCurveNode + if not curveNode: + raise ValueError("No input curve node specified.") + + volumeNode = self._parameterNode.inputVolumeNode + if not volumeNode: + raise ValueError("No input volume node specified.") + + shapeNode = self._parameterNode.outputShapeNode + if not shapeNode: + raise ValueError("No output shape node specified.") + + segmentationNode = self._parameterNode.outputSegmentationNode + if not segmentationNode: + segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") + + profiles = dimensionPresets() + profile = profiles.getPreset(self._parameterNode.dimensionPreset) + + """ + Create a segment than can overlap on contrast calcifications and soft + lesions. The more the curve can pass through each type of structure, + the better. But the curve should represent the axis of the vessel. + """ + import GuidedVeinSegmentation + gvsLogic = GuidedVeinSegmentation.GuidedVeinSegmentationLogic() + segmentID = gvsLogic.process( + inputCurve = curveNode, + inputVolume = volumeNode, + inputSegmentation = segmentationNode, + extrusionKernelSize = profile["extrusionKernelSize"], + gaussianStandardDeviation = profile["gaussianStandardDeviation"], + seedRadius = profile["seedRadius"], + shellMargin = profile["shellMargin"], + shellThickness = profile["shellThickness"], + subtractOtherSegments = False # Do not account for prior work in the same segmentation. + ) + segmentationNode.CreateClosedSurfaceRepresentation() + # At this step, the segment editor is already setup. + + # Get segment as polydata. + segmentPolyData = vtk.vtkPolyData() + if not segmentationNode.GetClosedSurfaceRepresentation(segmentID, segmentPolyData): + if not self._parameterNode.outputSegmentationNode: + slicer.mrmlScene.RemoveNode(segmentationNode) + raise RuntimeError(_("Failed to get segment polydata.")) + + # Reset shape node and ensure it is a Tube. + shapeNode.RemoveAllControlPoints() + shapeNode.SetShapeName(slicer.vtkMRMLMarkupsShapeNode.Tube) + shapeNode.CreateDefaultDisplayNodes() + + numberOfControlPoints = curveNode.GetNumberOfControlPoints() + curvePolyData = curveNode.GetCurveWorld() + for controlPointindex in range(numberOfControlPoints): + curvePointIndex = curveNode.GetCurvePointIndexFromControlPointIndex(controlPointindex) + # GetCurveDirectionAtPointIndexWorld() can be troublesome. + p1 = [0.0] * 3 + p2 = [0.0] * 3 + planeOrigin = [0.0] * 3 + if controlPointindex < (numberOfControlPoints - 1): + curvePolyData.GetPoint(curvePointIndex, p1) + curvePolyData.GetPoint(curvePointIndex + 1, p2) + vtk.vtkMath.Assign(p1, planeOrigin) + else: + curvePolyData.GetPoint(curvePointIndex - 1, p1) + curvePolyData.GetPoint(curvePointIndex, p2) + vtk.vtkMath.Assign(p2, planeOrigin) + direction = [0.0] * 3 + vtk.vtkMath.Subtract(p2, p1, direction) + + # Place a plane perpendicular to the curve. + plane = vtk.vtkPlane() + plane.SetOrigin(planeOrigin) + plane.SetNormal(direction) + + # Cut through the segment closed surface and get the points of the contour. + planeCut = vtk.vtkCutter() + planeCut.SetInputData(segmentPolyData) + planeCut.SetCutFunction(plane) + planeCut.Update() + planePoints = planeCut.GetOutput().GetPoints() + if (not planePoints) or (planePoints.GetNumberOfPoints == 0): + logging.info(_("Skipping empty section.")) + continue + + # Keep the closest connected region around the control point. + connectivityFilter = vtk.vtkConnectivityFilter() + connectivityFilter.SetInputData(planeCut.GetOutput()) + connectivityFilter.SetClosestPoint(planeOrigin) + connectivityFilter.SetExtractionModeToClosestPointRegion() + connectivityFilter.Update() + closestPoints = connectivityFilter.GetOutput().GetPoints() + if (not closestPoints) or (closestPoints.GetNumberOfPoints == 0): + logging.info(_("Skipping empty closest section.")) # ! + continue + + # Get farthest points of the contour. + farthestPoints = self.getFarthestPoints(closestPoints) + + # Add control points to the tube. + shapeNode.AddControlPoint(farthestPoints.GetPoint(0)) + shapeNode.AddControlPoint(farthestPoints.GetPoint(1)) + + # If we created the segmentation, remove it. + if not self._parameterNode.outputSegmentationNode: + slicer.mrmlScene.RemoveNode(segmentationNode) + + stopTime = time.time() + durationValue = '%.2f' % (stopTime-startTime) + logging.info(_("Processing completed in {duration} seconds").format(duration=durationValue)) + +# +# PreFitTubeTest +# + + +class PreFitTubeTest(ScriptedLoadableModuleTest): + """ + This is the test case for your scripted module. + Uses ScriptedLoadableModuleTest base class, available at: + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def setUp(self): + """Do whatever is needed to reset the state - typically a scene clear will be enough.""" + slicer.mrmlScene.Clear() + + def runTest(self): + """Run as few or as many tests as needed here.""" + self.setUp() + self.test_PreFitTube1() + + def test_PreFitTube1(self): + """Ideally you should have several levels of tests. At the lowest level + tests should exercise the functionality of the logic with different inputs + (both valid and invalid). At higher levels your tests should emulate the + way the user would interact with your code and confirm that it still works + the way you intended. + One of the most important features of the tests is that it should alert other + developers when their changes will have an impact on the behavior of your + module. For example, if a developer removes a feature that you depend on, + your test should break so they know that the feature is needed. + """ + + self.delayDisplay("Starting the test") + + self.delayDisplay("Test passed") + +DIMENSION_TINY = 1 +DIMENSION_SMALL = 2 +DIMENSION_MEDIUM = 3 +DIMENSION_BIG = 4 +DIMENSION_HUGE = 5 diff --git a/PreFitTube/Resources/Icons/PreFitTube.png b/PreFitTube/Resources/Icons/PreFitTube.png new file mode 100644 index 0000000000000000000000000000000000000000..0674fa78095823961af50ee4e4daef9963e21288 GIT binary patch literal 8423 zcmVEX>4Tx04R}tkv&MmKpe$iQ?()$g?11T%ut=|q9Ts93Pq?8YK2xEOfLO`CJjl7 zi=*ILaPVWX>fqw6tAnc`2!4P#J2)x2NQwVT3N2ziIPS;0dyl(!fKV?p&FYE)nr@q^ zL|n{dSH-|9g6KgAqZpK#Wz0!Z5*^3aJ$!t(`8@D`M&FbLLbpKQn%7%%AEysMnz~Bf00)P_ zc!9FlJG{HMy|;hQH2eDjZ@qG*s)DeSad^gZEa<4bO1wgWnpw> zWFU8GbZ8()Nlj2!fese{03N?dL_t(|+U;FwkR@4F{_f4~)zaI*jDyTDVkjZabXQmR z$fBZXKnOE33!4!b0{$Qr`C$N}NDwSW3`>L(qJl&ifTAe-FbFOTYXpiQhy;kpbXQgP z3@9qYOn1FCGw=0BX1;gxAPj*(0zm-Cp!l4A6cUgEkP;B)M^U^cMEOAR5ysarK8`;K0J`{Em;W(8 zYHd6epp37f0ad-Xd`&4J&w(_<11iUzN{J8N`4N4;@oO)0;7^HTL8xyI13Wp3@Q^Sp z0IxkH5SYdw>kkTe4SX0z;9~&HrC}IF1vm5hEyrMKg-02E^7n0 z;k39?Nd3Gh#1o?k2?ah3O3+Os2ngtM0ygz{S%NJI=ruzq|1DztNz)KC`J{>h(Di6g z0k6tOt_(xalSpA2!ewaytEcdzafD}vA)XLLh)v+bumqlY)V#h5^^);?#{+17UJL!g z9hNms4a`GT9-kLRP<;f7fAjKkVHo|vWtIX?t>95ngy+T)9zD+QrKgACf-;8GoS-)04J}< zL*p3Fk7E3E96?4A0X~|9`!Jla`YPW`X?VQ@{I;;qhJ1zu3Ie!r7y#u4nyC=3x)L~Y zr2cJ!7|($;fa{NoBXOdi6UTUJ93hUP384!^ATm7O^n7WMyg)MEPs+Sj12DY4@wEed zK~NFg7rI#;2!W#y{~=s+b`4*D@PnY1mfU|Q4In&FM6g5yE*NM+4&w+{J>+UUs6W7B z7-F-*DVV?6fr$VsCvYN)@!}-G!{ai%R~~-k2p;?kPr;+QU8JA+EdDu=P_)LEfuGk? 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ctkCollapsibleButton.h
+ 1 + + + qMRMLNodeComboBox + QWidget +
qMRMLNodeComboBox.h
+ 1 + + + qMRMLWidget + QWidget +
qMRMLWidget.h
+ 1 + + + + + + PreFitTube + mrmlSceneChanged(vtkMRMLScene*) + inputCurveSelector + setMRMLScene(vtkMRMLScene*) + + + 162 + 155 + + + 216 + 55 + + + + + PreFitTube + mrmlSceneChanged(vtkMRMLScene*) + inputVolumeSelector + setMRMLScene(vtkMRMLScene*) + + + 162 + 155 + + + 216 + 86 + + + + + PreFitTube + mrmlSceneChanged(vtkMRMLScene*) + outputShapeSelector + setMRMLScene(vtkMRMLScene*) + + + 162 + 155 + + + 199 + 203 + + + + + PreFitTube + mrmlSceneChanged(vtkMRMLScene*) + outputSegmentationSelector + setMRMLScene(vtkMRMLScene*) + + + 162 + 155 + + + 206 + 191 + + + + + diff --git a/PreFitTube/Testing/CMakeLists.txt b/PreFitTube/Testing/CMakeLists.txt new file mode 100644 index 0000000..655007a --- /dev/null +++ b/PreFitTube/Testing/CMakeLists.txt @@ -0,0 +1 @@ +add_subdirectory(Python) diff --git a/PreFitTube/Testing/Python/CMakeLists.txt b/PreFitTube/Testing/Python/CMakeLists.txt new file mode 100644 index 0000000..5658d8b --- /dev/null +++ b/PreFitTube/Testing/Python/CMakeLists.txt @@ -0,0 +1,2 @@ + +#slicer_add_python_unittest(SCRIPT ${MODULE_NAME}ModuleTest.py) diff --git a/README.md b/README.md index 64c4e2d..f766f52 100644 --- a/README.md +++ b/README.md @@ -35,6 +35,7 @@ Workflows: - [Arterial calcification pre-processor](Docs/ArterialCalcificationPreProcessor.md): Segment arterial calcifications within a specified distance around a lumen. - [Centerline disassembly](Docs/CenterlineDisassembly.md): Break down a bifurcated centerline model into parts. - [Clip vessel](Docs/ClipVessel.md): Clip a segmentation or model normal to the centerline. + - [Pre-fit tube](Docs/PreFitTube.md): Pre-fit a Shape::Tube markups node around an artery. Legacy modules (replaced by other modules, not developed anymore):