diff --git a/SVolModelROI/subVol_roi_model/CMakeLists.txt b/SVolModelROI/subVol_roi_model/CMakeLists.txt new file mode 100644 index 0000000..f38e068 --- /dev/null +++ b/SVolModelROI/subVol_roi_model/CMakeLists.txt @@ -0,0 +1,26 @@ +cmake_minimum_required(VERSION 3.16.3...3.19.7 FATAL_ERROR) + +project(subVol_roi_model) + +#----------------------------------------------------------------------------- +# Extension meta-information +set(EXTENSION_HOMEPAGE "https://www.slicer.org/wiki/Documentation/Nightly/Extensions/subVol_roi_model") +set(EXTENSION_CONTRIBUTORS "John Doe (AnyWare Corp.)") +set(EXTENSION_DESCRIPTION "This is an example of a simple extension") +set(EXTENSION_ICONURL "https://www.example.com/Slicer/Extensions/subVol_roi_model.png") +set(EXTENSION_SCREENSHOTURLS "https://www.example.com/Slicer/Extensions/subVol_roi_model/Screenshots/1.png") +set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies + +#----------------------------------------------------------------------------- +# Extension dependencies +find_package(Slicer REQUIRED) +include(${Slicer_USE_FILE}) + +#----------------------------------------------------------------------------- +# Extension modules +add_subdirectory(roiFromModelBounds) +## NEXT_MODULE + +#----------------------------------------------------------------------------- +include(${Slicer_EXTENSION_GENERATE_CONFIG}) +include(${Slicer_EXTENSION_CPACK}) diff --git a/SVolModelROI/subVol_roi_model/roiFromModelBounds/CMakeLists.txt b/SVolModelROI/subVol_roi_model/roiFromModelBounds/CMakeLists.txt new file mode 100644 index 0000000..df1da53 --- /dev/null +++ b/SVolModelROI/subVol_roi_model/roiFromModelBounds/CMakeLists.txt @@ -0,0 +1,31 @@ +#----------------------------------------------------------------------------- +set(MODULE_NAME roiFromModelBounds) + +#----------------------------------------------------------------------------- +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/SVolModelROI/subVol_roi_model/roiFromModelBounds/Resources/Icons/roiFromModelBounds.png b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Resources/Icons/roiFromModelBounds.png new file mode 100644 index 0000000..5d83ab4 Binary files /dev/null and b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Resources/Icons/roiFromModelBounds.png differ diff --git a/SVolModelROI/subVol_roi_model/roiFromModelBounds/Resources/UI/roiFromModelBounds.ui b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Resources/UI/roiFromModelBounds.ui new file mode 100644 index 0000000..6769430 --- /dev/null +++ b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Resources/UI/roiFromModelBounds.ui @@ -0,0 +1,254 @@ + + + roiFromModelBounds + + + + 0 + 0 + 451 + 459 + + + + + + + ROI From Model + + + + + + Input: Model Directory + + + + + + + ctkPathLineEdit::Dirs|ctkPathLineEdit::Drives|ctkPathLineEdit::Executable|ctkPathLineEdit::NoDot|ctkPathLineEdit::NoDotDot|ctkPathLineEdit::Readable + + + modelFile_path + + + + + + + Show Model Bounds + + + + + + + Input: Volume Node + + + + + + + true + + + + vtkMRMLScalarVolumeNode + + + + true + + + + + + true + + + Singleton + + + inputVolume + + + + + + + + + + SubVol From ROI + + + + + + Model ROI + + + + + + + false + + + Computed model ROI list + + + + vtkMRMLMarkupsROINode + + + + false + + + true + + + true + + + true + + + modelROI + + + + + + + Cropped volume: + + + + + + + false + + + Crop ROI bounds of InputVolume will be written into this volume + + + + vtkMRMLScalarVolumeNode + + + + false + + + true + + + true + + + true + + + croppedVolume + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + ctkCollapsibleButton + QWidget +
ctkCollapsibleButton.h
+ 1 + + + ctkPathLineEdit + QWidget +
ctkPathLineEdit.h
+ + + qMRMLNodeComboBox + QWidget +
qMRMLNodeComboBox.h
+ + + qMRMLWidget + QWidget +
qMRMLWidget.h
+ 1 + + + + + + roiFromModelBounds + mrmlSceneChanged(vtkMRMLScene*) + modelROISelector + setMRMLScene(vtkMRMLScene*) + + + 82 + 135 + + + 326 + 237 + + + + + roiFromModelBounds + mrmlSceneChanged(vtkMRMLScene*) + cropVolSelector + setMRMLScene(vtkMRMLScene*) + + + 161 + 8 + + + 279 + 263 + + + + + roiFromModelBounds + mrmlSceneChanged(vtkMRMLScene*) + volumeSelector + setMRMLScene(vtkMRMLScene*) + + + 225 + 229 + + + 282 + 76 + + + + + diff --git a/SVolModelROI/subVol_roi_model/roiFromModelBounds/Testing/CMakeLists.txt b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Testing/CMakeLists.txt new file mode 100644 index 0000000..655007a --- /dev/null +++ b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Testing/CMakeLists.txt @@ -0,0 +1 @@ +add_subdirectory(Python) diff --git a/SVolModelROI/subVol_roi_model/roiFromModelBounds/Testing/Python/CMakeLists.txt b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Testing/Python/CMakeLists.txt new file mode 100644 index 0000000..5658d8b --- /dev/null +++ b/SVolModelROI/subVol_roi_model/roiFromModelBounds/Testing/Python/CMakeLists.txt @@ -0,0 +1,2 @@ + +#slicer_add_python_unittest(SCRIPT ${MODULE_NAME}ModuleTest.py) diff --git a/SVolModelROI/subVol_roi_model/roiFromModelBounds/roiFromModelBounds.py b/SVolModelROI/subVol_roi_model/roiFromModelBounds/roiFromModelBounds.py new file mode 100644 index 0000000..0d0da3b --- /dev/null +++ b/SVolModelROI/subVol_roi_model/roiFromModelBounds/roiFromModelBounds.py @@ -0,0 +1,421 @@ +""" +For debugging in Slicer, use the folling to manipulate the module objects: + +mWidget = slicer.modules.roifrommodelbounds.widgetRepresentation().self() +mLogic = mWidget.logic +mNode = mLogic.getParameterNode() +""" + + +import glob +import os +import pathlib +from typing import Optional + +import numpy as np +import slicer +import vtk +from slicer import vtkMRMLMarkupsROINode, vtkMRMLModelNode, vtkMRMLScalarVolumeNode +from slicer.i18n import tr as _ +from slicer.parameterNodeWrapper import ( + parameterNodeWrapper, +) +from slicer.ScriptedLoadableModule import ( + ScriptedLoadableModule, + ScriptedLoadableModuleLogic, + ScriptedLoadableModuleTest, + ScriptedLoadableModuleWidget, +) +from slicer.util import VTKObservationMixin + +# +# roiFromModelBounds +# + + +class roiFromModelBounds(ScriptedLoadableModule): + """Uses ScriptedLoadableModule base class, available at: + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def __init__(self, parent): + ScriptedLoadableModule.__init__(self, parent) + self.parent.title = _("roiFromModelBounds") # TODO: make this more human readable by adding spaces + # TODO: set categories (folders where the module shows up in the module selector) + self.parent.categories = ["Tracking"] + self.parent.dependencies = [] # TODO: add here list of module names that this module requires + self.parent.contributors = ["Amy Morton (Brown University)"] + + # _() function marks text as translatable to other languages + self.parent.helpText = _( + """ +WIP module part of SlicerAutoscoperM +Intended to act as foundation for subvolume 3d-3d volume registration +""" + ) + # TODO: replace with organization, grant and thanks + self.parent.acknowledgementText = _( + """ +Template for 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. +""" + ) + + # 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. + + # roiFromModelBounds1 + SampleData.SampleDataLogic.registerCustomSampleDataSource( + # Category and sample name displayed in Sample Data module + category="roiFromModelBounds", + sampleName="roiFromModelBounds1", + # 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, "roiFromModelBounds1.png"), + # Download URL and target file name + uris="https://github.com/Slicer/SlicerTestingData/releases/download/SHA256/998cb522173839c78657f4bc0ea907cea09fd04e44601f17c82ea27927937b95", + fileNames="roiFromModelBounds1.nrrd", + # Checksum to ensure file integrity. Can be computed by this command: + # import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest()) + checksums="SHA256:998cb522173839c78657f4bc0ea907cea09fd04e44601f17c82ea27927937b95", + # This node name will be used when the data set is loaded + nodeNames="roiFromModelBounds1", + ) + + # roiFromModelBounds2 + SampleData.SampleDataLogic.registerCustomSampleDataSource( + # Category and sample name displayed in Sample Data module + category="roiFromModelBounds", + sampleName="roiFromModelBounds2", + thumbnailFileName=os.path.join(iconsPath, "roiFromModelBounds2.png"), + # Download URL and target file name + uris="https://github.com/Slicer/SlicerTestingData/releases/download/SHA256/1a64f3f422eb3d1c9b093d1a18da354b13bcf307907c66317e2463ee530b7a97", + fileNames="roiFromModelBounds2.nrrd", + checksums="SHA256:1a64f3f422eb3d1c9b093d1a18da354b13bcf307907c66317e2463ee530b7a97", + # This node name will be used when the data set is loaded + nodeNames="roiFromModelBounds2", + ) + + +# +# roiFromModelBoundsParameterNode +# + + +@parameterNodeWrapper +class roiFromModelBoundsParameterNode: + """ + The parameters needed by module. + + modelFile_path- load several stl inputModels from file + inputVolume- Voume for ROI crop + modelROI - The output volume that will contain the thresholded volume. + croppedVolume - The output volume that will be . + """ + + modelFile_path: pathlib.Path + inputVolume: vtkMRMLScalarVolumeNode + #modelBounds: float + modelROI: vtkMRMLMarkupsROINode + croppedVolume: vtkMRMLScalarVolumeNode + altVol: vtkMRMLScalarVolumeNode + + +# +# roiFromModelBoundsWidget +# + + +class roiFromModelBoundsWidget(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 + + 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/roiFromModelBounds.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 = roiFromModelBoundsLogic() + + # 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) + + # Buttons + self.ui.showBounds_pb.connect("clicked(bool)", self.onShowModelBoundsButton) + + # 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 + self.removeObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self._checkCanGenModelROI) + + 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()) + + # Select default input nodes if nothing is selected yet to save a few clicks for the user + if not self._parameterNode.modelROI: + firstModelNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLMarkupsROINode") + if firstModelNode: + self._parameterNode.modelROI = firstModelNode + + if not self._parameterNode.inputVolume: + firstVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode") + if firstVolumeNode: + self._parameterNode.inputVolume = firstVolumeNode + + def setParameterNode(self, inputParameterNode: Optional[roiFromModelBoundsParameterNode]) -> 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.removeObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self._checkCanGenModelROI) + 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.addObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self._checkCanGenModelROI) + self._checkCanGenModelROI() + + def _checkCanGenModelROI(self, _caller=None, _event=None) -> None: + if self._parameterNode and self._parameterNode.inputVolume and self._parameterNode.modelFile_path: + self.ui.showBounds_pb.toolTip = _("Compute output volume") + self.ui.showBounds_pb.enabled = True + else: + self.ui.showBounds_pb.toolTip = _("Select input ModelPath and volume node") + self.ui.showBounds_pb.enabled = True + + def onShowModelBoundsButton(self) -> None: + """Load Models from folder, compute bounds, assign to new roi""" + self.logic.loadModelsComputeBounds() + + +# +# roiFromModelBoundsLogic +# + + +class roiFromModelBoundsLogic(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) + + def getParameterNode(self): + return roiFromModelBoundsParameterNode(super().getParameterNode()) + + def loadModelsComputeBounds(self): + parameterNode = self.getParameterNode() + #TO DO error checking on model path and volume node + + modelFileDir = parameterNode.modelFile_path + + modelFiles = glob.glob(os.path.join(modelFileDir, "*.*")) + #return modelFiles + + for _indx, file in enumerate(modelFiles): + modelNode = slicer.util.loadNodeFromFile(file) + modelNode.CreateDefaultDisplayNodes() + roi_this = self.modelBounds(modelNode) + parameterNode.modelROI =roi_this + #parameterNode.croppedVolume = self.doCropVolume() + self.doCropVolume() + + + def modelBounds(self, inputModel): + + inputModel: vtkMRMLModelNode + + tB = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] + inputModel.GetBounds(tB) + # print(tB) + # modelC = [0.0]*3 + # modelSize = [0.0]*3 + # strange that the model nodes have a getBounds- but no center and size.. + # and the roi has bno.. set Bounds- just center and size + + # numpy for array operatots: + tnp_min = np.array([tB[0], tB[2], tB[4]]) + tnp_max = np.array([tB[1], tB[3], tB[5]]) + + tnp_C = (tnp_min + tnp_max) / 2 + tnpS = tnp_min - tnp_max + + # inputModel.GetCenter(modelC) + # inputModel.GetSize(modelSize) + mname = inputModel.GetName() + + # use tB lims to size roi + # Create ROI node + modelROI = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsROINode") + modelROI.SetCenter(tnp_C.tolist()) + modelROI.SetSize(tnpS.tolist()) + modelROI.CreateDefaultDisplayNodes() # only needed for display + + roi_name = mname + "_roi" + modelROI.SetName(roi_name) + + return modelROI + + + def doCropVolume(self)->None: + + parameterNode = self.getParameterNode() + #TO DO error checking on model path and volume node + + inVolume = parameterNode.inputVolume + roi = parameterNode.modelROI + + fillValue = 0.0 + interpolate = False + spacingScalingConst = 1.0 + isotropicResampling = False + interpolationMode = slicer.vtkMRMLCropVolumeParametersNode().InterpolationLinear + cropLogic = slicer.modules.cropvolume.logic() + cvpn = slicer.vtkMRMLCropVolumeParametersNode() + + cvpn.SetROINodeID(roi.GetID()) + cvpn.SetInputVolumeNodeID(inVolume.GetID()) + cvpn.SetFillValue(fillValue) + cvpn.SetVoxelBased(not interpolate) + cvpn.SetSpacingScalingConst(spacingScalingConst) + cvpn.SetIsotropicResampling(isotropicResampling) + cvpn.SetInterpolationMode(interpolationMode) + cropLogic.Apply(cvpn) + roi.SetDisplayVisibility(False) + + outputVolumeNodeID = cvpn.GetOutputVolumeNodeID() + #https://www.slicer.org/wiki/Documentation/4.3/Developers/Python_scripting + views = slicer.app.layoutManager().sliceViewNames() + for view in views: + view_logic = slicer.app.layoutManager().sliceWidget(view).sliceLogic() + view_cn = view_logic.GetSliceCompositeNode() + view_cn.SetBackgroundVolumeID(outputVolumeNodeID) + view_logic.FitSliceToAll() + + #TO DO rename with model file name + outVolNode = cvpn.GetOutputVolumeNode + #TO DO wrong format- this is 'cropvole' needs to be 'scalarVolume' + #return outVolNode + + + + +# +# roiFromModelBoundsTest +# + + +class roiFromModelBoundsTest(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_roiFromModelBounds1() + + def test_roiFromModelBounds1(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("TO DO configure test for this module ") diff --git a/SVolModelROI/subVol_roi_model/subVol_roi_model.png b/SVolModelROI/subVol_roi_model/subVol_roi_model.png new file mode 100644 index 0000000..6aae6ab Binary files /dev/null and b/SVolModelROI/subVol_roi_model/subVol_roi_model.png differ diff --git a/pyproject.toml b/pyproject.toml index f18c84a..1ad881a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,6 @@ select = [ "PGH", # pygrep-hooks "PIE", # flake8-pie "PL", # pylint - "PT", # flake8-pytest-style "RET", # flake8-return "RUF", # Ruff-specific "S", # flake8-bandit