From a9c75a8f8776af022d4a5bf9d686fd39c07fd096 Mon Sep 17 00:00:00 2001 From: Ye Han Date: Tue, 8 Apr 2025 22:11:56 -0400 Subject: [PATCH] ENH:Add AverageMesh module --- AverageMesh/AverageMesh.py | 328 ++++++++++++++++++++ AverageMesh/CMakeLists.txt | 31 ++ AverageMesh/Resources/Icons/AverageMesh.png | Bin 0 -> 21024 bytes AverageMesh/Resources/UI/AverageMesh.ui | 190 ++++++++++++ AverageMesh/Testing/CMakeLists.txt | 1 + AverageMesh/Testing/Python/CMakeLists.txt | 2 + CMakeLists.txt | 1 + 7 files changed, 553 insertions(+) create mode 100644 AverageMesh/AverageMesh.py create mode 100644 AverageMesh/CMakeLists.txt create mode 100644 AverageMesh/Resources/Icons/AverageMesh.png create mode 100644 AverageMesh/Resources/UI/AverageMesh.ui create mode 100644 AverageMesh/Testing/CMakeLists.txt create mode 100644 AverageMesh/Testing/Python/CMakeLists.txt diff --git a/AverageMesh/AverageMesh.py b/AverageMesh/AverageMesh.py new file mode 100644 index 0000000..3fbdff6 --- /dev/null +++ b/AverageMesh/AverageMesh.py @@ -0,0 +1,328 @@ +import os +import unittest +import logging +import vtk, qt, ctk, slicer +from slicer.ScriptedLoadableModule import * +from slicer.util import VTKObservationMixin + +# +# AverageMesh +# + +class AverageMesh(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 = "Average Mesh" + self.parent.categories = ["Surface Models"] + self.parent.dependencies = [] + self.parent.contributors = ["Ye Han, Jean-Christophe Fillion-Robin, Beatriz Paniagua (Kitware)"] + self.parent.helpText = """ +This module supports computing the arithmetic mean from a set of correspondence established input +models or weighted average between two models. For statistical shape analysis purpose the average model should be +computed after performing procrustes alignment using the Mesh Alignment module. +""" + self.parent.helpText += self.getDefaultModuleDocumentationLink() + self.parent.acknowledgementText = """ +The development of this module was supported by the NIH National Institute of Biomedical Imaging Bioengineering +R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), +with help from Andras Lasso (PerkLab, Queen's University) and Steve Pieper (Isomics, Inc.). +""" + +# +# AverageMeshWidget +# + +class AverageMeshWidget(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/AverageMesh.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 = AverageMeshLogic() + self.logic.updateProcessCallback = self.updateProcess + + # 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) + + # 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.parameterEditWidgets = [ + # (self.ui.CheckableNodeComboBox_inputNodes, "inputNodes"), + (self.ui.MRMLNodeComboBox_outputNode, "outputNode"), + (self.ui.comboBox_method, "method"), + (self.ui.SliderWidget_weight, "weight") + ] + + slicer.util.addParameterEditWidgetConnections(self.parameterEditWidgets, self.updateParameterNodeFromGUI) + self.ui.CheckableNodeComboBox_inputNodes.connect("checkedNodesChanged()", self.updateGUIFromParameterNode) + + # Buttons + self.ui.applyButton.connect('clicked(bool)', self.onApplyButton) + + # Make sure parameter node is initialized (needed for module reload) + self.initializeParameterNode() + self.updateGUIFromParameterNode() + + def cleanup(self): + """ + Called when the application closes and the module widget is destroyed. + """ + self.removeObservers() + + def enter(self): + """ + Called each time the user opens this module. + """ + # Make sure parameter node exists and observed + self.initializeParameterNode() + + 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) + + 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()) + + # Select default input nodes if nothing is selected yet to save a few clicks for the user + if not self._parameterNode.GetNodeReference("targetNode"): + firstModelNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLModelNode") + if firstModelNode: + self._parameterNode.SetNodeReferenceID("targetNode", firstModelNode.GetID()) + + 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 + slicer.util.updateParameterEditWidgetsFromNode(self.parameterEditWidgets, self._parameterNode) + + # Update buttons states and tooltips + self.ui.SliderWidget_weight.setEnabled(self._parameterNode.GetParameter('method') == "Weighted") + self.ui.applyButton.setEnabled(self._parameterNode.GetNodeReference("outputNode") and + not self.ui.CheckableNodeComboBox_inputNodes.noneChecked()) + + # 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 + slicer.util.updateNodeFromParameterEditWidgets(self.parameterEditWidgets, self._parameterNode) + self._parameterNode.EndModify(wasModified) + + def updateProcess(self, value): + """Display changing process value""" + self.ui.applyButton.text = value + self.ui.applyButton.repaint() + + def onApplyButton(self): + """ + Run processing when user clicks "Apply" button. + """ + slicer.app.pauseRender() + qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor) + try: + inputNodes = self.ui.CheckableNodeComboBox_inputNodes.checkedNodes() + outputNode = self._parameterNode.GetNodeReference("outputNode") + self.logic.computeAverage(inputNodes, outputNode, self._parameterNode) + slicer.app.processEvents() + self.ui.applyButton.text = "Apply" + except Exception as e: + slicer.util.errorDisplay("Failed to compute output model: " + str(e)) + import traceback + traceback.print_exc() + finally: + slicer.app.resumeRender() + qt.QApplication.restoreOverrideCursor() + + +class AverageMeshLogic(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.updateProcessCallback = None + + def setDefaultParameters(self, parameterNode): + """ + Initialize parameter node with default settings. + """ + defaultValues = [ + ("method", "Arithmetic"), + ("weight", "0.5") + ] + for parameterName, defaultValue in defaultValues: + if not parameterNode.GetParameter(parameterName): + parameterNode.SetParameter(parameterName, defaultValue) + + def updateProcess(self, message): + if not self.updateProcessCallback: + return + self.updateProcessCallback(message) + + def computeAverage(self, inputNodes, outputNode, parameterNode): + from vtk.util.numpy_support import numpy_to_vtk, vtk_to_numpy + import numpy as np + + if outputNode not in inputNodes: + if outputNode.GetPolyData() is None: + outputNode.SetAndObserveMesh(vtk.vtkPolyData()) + outputNode.GetPolyData().DeepCopy(inputNodes[0].GetPolyData()) + outputNode.CreateDefaultDisplayNodes() + outputNode.AddDefaultStorageNode() + + numberOfPoints = outputNode.GetPolyData().GetNumberOfPoints() + meanPoints = np.zeros([numberOfPoints, 3]) + if parameterNode.GetParameter("method") == "Arithmetic": + for inputNode in inputNodes: + meanPoints = meanPoints + vtk_to_numpy(inputNode.GetPolyData().GetPoints().GetData()) + meanPoints = meanPoints / len(inputNodes) + elif parameterNode.GetParameter("method") == "Weighted": + if len(inputNodes) != 2: + logging.error("Weighted average only supports 2 input models!") + return + points0 = vtk_to_numpy(inputNodes[0].GetPolyData().GetPoints().GetData()) + points1 = vtk_to_numpy(inputNodes[1].GetPolyData().GetPoints().GetData()) + weight = float(parameterNode.GetParameter("weight")) + meanPoints = (1 - weight) * points0 + weight * points1 + else: + logging.error("Wrong method selection.") + outputNode.GetPolyData().GetPoints().SetData(numpy_to_vtk(meanPoints)) + + +class AverageMeshTest(ScriptedLoadableModuleTest): + """ + This is the test case for your scripted module. + Uses ScriptedLoadableModuleTest base class, available at: + https://github.com/Slicer/Slicer/blob/master/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(0) + + def runTest(self): + """Run as few or as many tests as needed here. + """ + self.setUp() + self.test_AllProcessing() + + def test_AllProcessing(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!') diff --git a/AverageMesh/CMakeLists.txt b/AverageMesh/CMakeLists.txt new file mode 100644 index 0000000..8744092 --- /dev/null +++ b/AverageMesh/CMakeLists.txt @@ -0,0 +1,31 @@ +#----------------------------------------------------------------------------- +set(MODULE_NAME AverageMesh) + +#----------------------------------------------------------------------------- +set(MODULE_PYTHON_SCRIPTS + ${MODULE_NAME}.py + ) + +set(MODULE_PYTHON_RESOURCES + Resources/Icons/${MODULE_NAME}.png + Resources/UI/${MODULE_NAME}.ui + ) + +#----------------------------------------------------------------------------- +slicerMacroBuildScriptedModule( + NAME ${MODULE_NAME} + SCRIPTS ${MODULE_PYTHON_SCRIPTS} + RESOURCES ${MODULE_PYTHON_RESOURCES} + WITH_GENERIC_TESTS + ) + +#----------------------------------------------------------------------------- +if(BUILD_TESTING) + + # Register the unittest subclass in the main script as a ctest. + # Note that the test will also be available at runtime. + slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py) + + # Additional build-time testing + add_subdirectory(Testing) +endif() diff --git a/AverageMesh/Resources/Icons/AverageMesh.png b/AverageMesh/Resources/Icons/AverageMesh.png new file mode 100644 index 0000000000000000000000000000000000000000..5d83ab4f05067d6d5e30808fe07df6b4ac035349 GIT binary patch literal 21024 zcmV)tK$pLXP)Px#24YJ`L;(K){{a7>y{D4^000SaNLh0L01FcU01FcV0GgZ_00007bV*G`2iyW1 z2_`QyE^zn&03ZNKL_t(|+U&h~lpV!+2l}h3?t5p|j7IB>M$%{lEg<$q!U6+!z+g6G zRuf{J=jX&*oH*VcFG=h;PUP6Jv7J0`EM~_n7T6A8KuCy9MhIfT$5&Jq;{s+EoRjRQuigo>!uxJ;XTZ{#<@OeNbeSl22%0PKVBOAAl{vV zhcqQ^=g70|>p-q=hRCpOw}L5S<*#+JO}BKp}Kr$4EnTdWl*Z z97p2=vr9#ILbxeA}AsdV<1JK1m8oIR>~i%UQ8%ZbEr4H%!rxB!FD10=vW 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qMRMLCheckableNodeComboBox.h
+ + + qMRMLNodeComboBox + QWidget +
qMRMLNodeComboBox.h
+ + + qMRMLWidget + QWidget +
qMRMLWidget.h
+ 1 + + + ctkSliderWidget + QWidget +
ctkSliderWidget.h
+ + + + + + AverageMesh + mrmlSceneChanged(vtkMRMLScene*) + MRMLNodeComboBox_outputNode + setMRMLScene(vtkMRMLScene*) + + + 122 + 132 + + + 248 + 61 + + + + + AverageMesh + mrmlSceneChanged(vtkMRMLScene*) + CheckableNodeComboBox_inputNodes + setMRMLScene(vtkMRMLScene*) + + + 122 + 132 + + + 248 + 61 + + + + + diff --git a/AverageMesh/Testing/CMakeLists.txt b/AverageMesh/Testing/CMakeLists.txt new file mode 100644 index 0000000..655007a --- /dev/null +++ b/AverageMesh/Testing/CMakeLists.txt @@ -0,0 +1 @@ +add_subdirectory(Python) diff --git a/AverageMesh/Testing/Python/CMakeLists.txt b/AverageMesh/Testing/Python/CMakeLists.txt new file mode 100644 index 0000000..5658d8b --- /dev/null +++ b/AverageMesh/Testing/Python/CMakeLists.txt @@ -0,0 +1,2 @@ + +#slicer_add_python_unittest(SCRIPT ${MODULE_NAME}ModuleTest.py) diff --git a/CMakeLists.txt b/CMakeLists.txt index faad0d2..12a0d58 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -12,6 +12,7 @@ include(${Slicer_USE_FILE}) add_subdirectory(Decimation) add_subdirectory(SurfaceToolbox) add_subdirectory(DynamicModeler) +add_subdirectory(AverageMesh) ## NEXT_MODULE