ENH: S-Rep pipelines

Add pipelines for s-rep related tasks.

CMakeLists.txt

@@ -45,6 +45,7 @@ endif()
 add_subdirectory(SRep)
 add_subdirectory(SRepCreator)
 add_subdirectory(SRepRefinement)
+add_subdirectory(SRepPipelines)
 ## NEXT_MODULE
 
 #-----------------------------------------------------------------------------

SRepCreator/Logic/vtkSlicerSRepCreatorLogic.cxx

@@ -15,6 +15,8 @@
 
 ==============================================================================*/
 
+#include "qSlicerCoreApplication.h"
+
 // Logic includes
 #include "vtkSlicerSRepCreatorLogic.h"
 #include "vtkSlicerSRepLogic.h"
@@ -175,7 +177,7 @@ void vtkSlicerSRepCreatorLogic::SetMRMLSceneInternal(vtkMRMLScene * newScene)
 std::string vtkSlicerSRepCreatorLogic::TempFolder() {
   std::stringstream ssTempFolder;
   // putting this pointer in the folder name so multiple logics can exist without interfering with each other
-  ssTempFolder << this->GetApplicationLogic()->GetTemporaryPath() << "/SRepCreator-" << this;
+  ssTempFolder << qSlicerCoreApplication::application()->applicationLogic()->GetTemporaryPath() << "/SRepCreator-" << this;
   const auto tempFolder = ssTempFolder.str();
   if (!vtksys::SystemTools::FileExists(tempFolder, false)) {
     if (!vtksys::SystemTools::MakeDirectory(tempFolder)) {

SRepPipelines/CMakeLists.txt

@@ -0,0 +1,18 @@
+#-----------------------------------------------------------------------------
+set(MODULE_NAME SRepPipelines)
+
+#-----------------------------------------------------------------------------
+set(MODULE_PYTHON_SCRIPTS
+  ${MODULE_NAME}.py
+  )
+
+set(MODULE_PYTHON_RESOURCES
+  )
+
+#-----------------------------------------------------------------------------
+slicerMacroBuildScriptedModule(
+  NAME ${MODULE_NAME}
+  SCRIPTS ${MODULE_PYTHON_SCRIPTS}
+  RESOURCES ${MODULE_PYTHON_RESOURCES}
+  WITH_GENERIC_TESTS
+  )

SRepPipelines/SRepPipelines.py

@@ -0,0 +1,117 @@
+from typing import Annotated
+
+import vtk
+import slicer
+from slicer.parameterNodeWrapper import (
+    Decimals,
+    Default,
+    Maximum,
+    Minimum,
+    SingleStep,
+    WithinRange,
+)
+from slicer.ScriptedLoadableModule import *
+
+from vtkSlicerSRepCreatorModuleLogicPython import vtkSlicerSRepCreatorLogic
+from vtkSlicerSRepRefinementModuleLogicPython import vtkSlicerSRepRefinementLogic
+
+try:
+    from PipelineCreator import slicerPipeline, PipelineProgressCallback
+
+    # Note: the values in Default() are GUI defaults only
+    @slicerPipeline(name="SRep.CreateElliptical", dependencies=["SRepCreator"], categories=["SRep"])
+    def srepCreator(
+        model: slicer.vtkMRMLModelNode,
+        numFoldPoints: Annotated[int, Minimum(0), Default(24)],
+        numStepsToCrest: Annotated[int, Minimum(0), Default(2)],
+        dt: Annotated[float, Decimals(5), SingleStep(1e-5), Default(0.001)],
+        smoothAmount: Annotated[float, SingleStep(1e-2), Default(0.01)],
+        maxIterations: Annotated[int, Default(500)],
+        *,
+        progressCallback: PipelineProgressCallback = PipelineProgressCallback(), 
+    ) -> slicer.vtkMRMLEllipticalSRepNode:
+        logic = vtkSlicerSRepCreatorLogic()
+        logic.SetMRMLScene(slicer.mrmlScene)
+
+        @vtk.calldata_type(vtk.VTK_DOUBLE)
+        def progressCb(caller, event, progress):
+            progressCallback.reportProgress("SRep.CreateElliptical", progress, 0, 1)
+        tag = logic.AddObserver(vtk.vtkCommand.ProgressEvent, progressCb)
+
+        val = logic.Run(model, numFoldPoints, numStepsToCrest, dt, smoothAmount, maxIterations)
+
+        logic.RemoveObserver(tag)
+
+        return val
+
+    @slicerPipeline(name="SRep.Refinement", dependencies=["SRepRefinement"], categories=["SRep"])
+    def srepRefinement(
+        model: slicer.vtkMRMLModelNode,
+        srep: slicer.vtkMRMLEllipticalSRepNode,
+        interpolationLevel: Annotated[int, Minimum(0), Maximum(15), Default(3)],
+        initialRegionSize: Annotated[float, SingleStep(0.1), Decimals(3), WithinRange(0.001, 15), Default(0.01)],
+        finalRegionSize: Annotated[float, SingleStep(0.1), Decimals(3), WithinRange(0.0001, 15), Default(0.001)],
+        maxIterations: Annotated[int, WithinRange(200, 10000), Default(2000)],
+        imageMatchWeight: Annotated[float, Decimals(4), WithinRange(0, 1000), Default(0.004)],
+        normalMatchWeight: Annotated[float, Decimals(4), WithinRange(0, 1000), Default(20)],
+        geometricIllegalityWeight: Annotated[float, Decimals(4), WithinRange(0, 1000), Default(50)],
+        *,
+        progressCallback: PipelineProgressCallback = PipelineProgressCallback(),
+    ) -> slicer.vtkMRMLEllipticalSRepNode:
+        logic = vtkSlicerSRepRefinementLogic()
+        logic.SetMRMLScene(slicer.mrmlScene)
+
+        @vtk.calldata_type(vtk.VTK_DOUBLE)
+        def progressCb(caller, event, progress):
+            progressCallback.reportProgress("SRep.Refinement", progress, 0, 1)
+        tag = logic.AddObserver(vtk.vtkCommand.ProgressEvent, progressCb)
+
+        val = logic.Run(model, srep, initialRegionSize, finalRegionSize, maxIterations, interpolationLevel,
+                  imageMatchWeight, normalMatchWeight, geometricIllegalityWeight)
+
+        logic.RemoveObserver(tag)
+
+        return val
+
+except ImportError:
+    pass
+
+#
+# SRepPipelines
+#
+
+class SRepPipelines(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 = "SRep Pipelines"
+        self.parent.categories = ["SRep.Advanced"]
+        self.parent.dependencies = ["SRep", "SRepCreator", "SRepRefinement"]
+        self.parent.contributors = ["Connor Bowley (Kitware, Inc)"]
+        self.parent.helpText = "This module exists to create pipelines for SRep related actions"
+        self.parent.acknowledgementText = "This file was originally developed by Connor Bowley for SlicerSALT."
+        self.parent.hidden = True
+
+
+#
+# SRepPipelinesLogic
+#
+
+class SRepPipelinesLogic(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)