BUG: Fully remove VRG-related .tra file export (#161)

This commit follows up on 5cd70dd ("BUG: Remove obsolete VRG Generation
functionality", 2024-11-10) by removing the unused function `extractSubVolumeForVRG`
and all remaining code associated with `.tra` file calculation and export
during partial volume generation in the pre-processing module.

Specifically, `.tra` file export was previously handled by:
1. `Hierarchical3DRegistrationWidget.onExportButton/onImportButton`, already
   removed in 5cd70dd (referenced above).
2. `AutoscoperMLogic.saveSubVolumesFromSegmentation`, updated in this commit to
   remove `.tra` export support (initially introduced in 7a2dd0f, "ENH: Output
   TRA files on PV gen", 2024-05-14).

This ensures that no VRG feature relics remain in the codebase.

AutoscoperM/AutoscoperM.py

@@ -444,7 +444,6 @@ def onGeneratePartialVolumes(self):
             mainOutputDir = self.ui.mainOutputSelector.currentPath
             tiffSubDir = self.ui.tiffSubDir.text
             tfmSubDir = self.ui.tfmSubDir.text
-            trackingSubDir = self.ui.trackingSubDir.text
             modelSubDir = self.ui.modelSubDir.text
             segmentationNode = self.ui.pv_SegNodeComboBox.currentNode()
 
@@ -454,15 +453,13 @@ def onGeneratePartialVolumes(self):
                 mainOutputDir=mainOutputDir,
                 volumeSubDir=tiffSubDir,
                 transformSubDir=tfmSubDir,
-                trackingSubDir=trackingSubDir,
                 modelSubDir=modelSubDir,
             )
 
             self.logic.createPathsIfNotExists(
                 mainOutputDir,
                 os.path.join(mainOutputDir, tiffSubDir),
                 os.path.join(mainOutputDir, tfmSubDir),
-                os.path.join(mainOutputDir, trackingSubDir),
                 os.path.join(mainOutputDir, modelSubDir),
             )
             self.ui.progressBar.setValue(0)
@@ -473,7 +470,6 @@ def onGeneratePartialVolumes(self):
                 mainOutputDir,
                 volumeSubDir=tiffSubDir,
                 transformSubDir=tfmSubDir,
-                trackingSubDir=trackingSubDir,
                 modelSubDir=modelSubDir,
                 progressCallback=self.updateProgressBar,
             )
@@ -1011,7 +1007,6 @@ def saveSubVolumesFromSegmentation(
         outputDir: str,
         volumeSubDir: str = "Volumes",
         transformSubDir: str = "Transforms",
-        trackingSubDir: str = "Tracking",
         modelSubDir: str = "Models",
         progressCallback: Optional[callable] = None,
     ) -> bool:
@@ -1040,13 +1035,6 @@ def progressCallback(x):
         segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
         numSegments = segmentIDs.GetNumberOfValues()
 
-        tfmFiles = glob.glob(os.path.join(outputDir, transformSubDir, "*.tfm"))
-        tfms = [tfm if os.path.basename(tfm).split(".")[0] == "Origin2Dicom" else None for tfm in tfmFiles]
-        try:
-            origin2DicomTransformFile = next(item for item in tfms if item is not None)
-        except StopIteration:
-            origin2DicomTransformFile = None
-
         for idx in range(numSegments):
             segmentID = segmentIDs.GetValue(idx)
             segmentName = segmentationNode.GetSegmentation().GetSegment(segmentID).GetName()
@@ -1086,36 +1074,6 @@ def progressCallback(x):
 
             slicer.mrmlScene.RemoveNode(dicom2autNode)
 
-            # Create TRA file
-            tfm = vtk.vtkMatrix4x4()
-            tfm.SetElement(0, 3, origin[0])
-            tfm.SetElement(1, 3, origin[1])
-            tfm.SetElement(2, 3, origin[2])
-
-            if origin2DicomTransformFile is not None:
-                origin2DicomNode = self.loadTransformFromFile(origin2DicomTransformFile)
-                origin2DicomNode.Inverse()
-                tfm = self.applyOrigin2DicomTransform(tfm, origin2DicomNode)
-                slicer.mrmlScene.RemoveNode(origin2DicomNode)
-
-            tfm = self.applyPVol2AutTransform(tfm, pvol2autNode)
-            slicer.mrmlScene.RemoveNode(pvol2autNode)
-
-            tfmR = vtk.vtkMatrix3x3()
-            vtkAddon.vtkAddonMathUtilities.GetOrientationMatrix(tfm, tfmR)
-
-            # Apply RAS to LPS transform
-            RAS2LPS = vtk.vtkMatrix3x3()
-            RAS2LPS.SetElement(0, 0, -1)
-            RAS2LPS.SetElement(1, 1, -1)
-
-            vtk.vtkMatrix3x3.Multiply3x3(tfmR, RAS2LPS, tfmR)
-            vtkAddon.vtkAddonMathUtilities.SetOrientationMatrix(tfmR, tfm)
-
-            # Save TRA file
-            filename = os.path.join(outputDir, trackingSubDir, f"{segmentName}.tra")
-            IO.writeTRA(filename, [tfm])
-
             # update progress bar
             progressCallback((idx + 1) / numSegments * 100)
 
@@ -1178,57 +1136,6 @@ def createPathsIfNotExists(*args: tuple) -> None:
             if not os.path.exists(arg):
                 os.makedirs(arg)
 
-    @staticmethod
-    def extractSubVolumeForVRG(
-        volumeNode: slicer.vtkMRMLVolumeNode,
-        segmentationNode: slicer.vtkMRMLSegmentationNode,
-        cameraDebugMode: bool = False,
-    ) -> tuple[vtk.vtkImageData, list[float]]:
-        """
-        Extracts a subvolume from the volumeNode that contains all of the segments in the segmentationNode
-
-        :param volumeNode: volume node
-        :param segmentationNode: segmentation node
-        :param cameraDebugMode: Whether or not to keep the extracted volume in the scene, defaults to False
-
-        :return: tuple containing the extracted volume and the bounds of the volume
-        """
-        mergedSegmentationNode = SubVolumeExtraction.mergeSegments(volumeNode, segmentationNode)
-        newVolumeNode = SubVolumeExtraction.extractSubVolume(
-            volumeNode, mergedSegmentationNode, mergedSegmentationNode.GetSegmentation().GetNthSegmentID(0)
-        )
-        newVolumeNode.SetName(volumeNode.GetName() + " - Bone Subvolume")
-
-        bounds = [0, 0, 0, 0, 0, 0]
-        newVolumeNode.GetBounds(bounds)
-
-        # Copy the metadata from the original volume into the ImageData
-        newVolumeImageData = vtk.vtkImageData()
-        newVolumeImageData.DeepCopy(newVolumeNode.GetImageData())  # So we don't modify the original volume
-        newVolumeImageData.SetSpacing(newVolumeNode.GetSpacing())
-        origin = list(newVolumeNode.GetOrigin())
-        origin[0:2] = [x * -1 for x in origin[0:2]]
-        newVolumeImageData.SetOrigin(origin)
-
-        # Ensure we are in the correct orientation (RAS vs LPS)
-        imageReslice = vtk.vtkImageReslice()
-        imageReslice.SetInputData(newVolumeImageData)
-
-        axes = vtk.vtkMatrix4x4()
-        axes.Identity()
-        axes.SetElement(0, 0, -1)
-        axes.SetElement(1, 1, -1)
-
-        imageReslice.SetResliceAxes(axes)
-        imageReslice.Update()
-        newVolumeImageData = imageReslice.GetOutput()
-
-        if not cameraDebugMode:
-            slicer.mrmlScene.RemoveNode(newVolumeNode)
-            slicer.mrmlScene.RemoveNode(mergedSegmentationNode)
-
-        return newVolumeImageData, bounds
-
     @staticmethod
     def getItemInSequence(sequenceNode: slicer.vtkMRMLSequenceNode, idx: int) -> slicer.vtkMRMLNode:
         """
@@ -1291,24 +1198,6 @@ def GetVolumeSpacing(node: Union[slicer.vtkMRMLVolumeNode, slicer.vtkMRMLSequenc
             return AutoscoperMLogic.getItemInSequence(node, 0)[0].GetSpacing()
         return node.GetSpacing()
 
-    @staticmethod
-    def loadTransformFromFile(transformFileName: str) -> slicer.vtkMRMLLinearTransformNode:
-        return slicer.util.loadNodeFromFile(transformFileName)
-
-    @staticmethod
-    def applyOrigin2DicomTransform(
-        transform: vtk.vtkMatrix4x4,
-        origin2DicomTransformNode: slicer.vtkMRMLLinearTransformNode,
-    ) -> vtk.vtkMatrix4x4:
-        """Utility function for converting a transform between the dicom centered and
-        world centered coordinate systems."""
-        origin2DicomTransformMatrix = vtk.vtkMatrix4x4()
-        origin2DicomTransformNode.GetMatrixTransformToParent(origin2DicomTransformMatrix)
-
-        vtk.vtkMatrix4x4.Multiply4x4(origin2DicomTransformMatrix, transform, transform)
-
-        return transform
-
     @staticmethod
     def applyPVol2AutTransform(
         transform: vtk.vtkMatrix4x4,

AutoscoperM/AutoscoperMLib/IO.py

@@ -1,6 +1,5 @@
 import logging
 import os
-from itertools import product
 
 import numpy as np
 import slicer
@@ -202,12 +201,3 @@ def writeTFMFile(filename: str, spacing: list[float], origin: list[float]):
     slicer.util.exportNode(transformNode, filename)
 
     slicer.mrmlScene.RemoveNode(transformNode)
-
-
-def writeTRA(fileName: str, transforms: list[vtk.vtkMatrix4x4]) -> None:
-    rowWiseStrings = []
-    for transform in transforms:
-        rowWiseStrings.append([str(transform.GetElement(i, j)) for i, j in product(range(4), range(4))])
-    with open(fileName, "w+") as traFile:
-        for row in rowWiseStrings:
-            traFile.write(",".join(row) + "\n")

AutoscoperM/Resources/UI/AutoscoperM.ui

@@ -462,6 +462,9 @@
             <property name="text">
              <string>Tracking</string>
             </property>
+            <property name="enabled">
+             <bool>False</bool>
+            </property>
            </widget>
           </item>
           <item row="5" column="0">