BUG: Fix VRGs not generating in center AUT space

AutoscoperM/AutoscoperM.py

@@ -504,7 +504,7 @@ def onGenerateVRG(self):
             self.logic.createPathsIfNotExists(os.path.join(mainOutputDir, tfmPath))
             if not self.logic.IsSequenceVolume(volumeNode):
                 volumeNode.AddCenteringTransform()
-                tfmNode = slicer.util.getNode(f"{volumeNode.GetName()} centering transform")
+                tfmNode = volumeNode.GetParentTransformNode()
                 volumeNode.HardenTransform()
                 volumeNode.SetAndObserveTransformNodeID(None)
                 tfmPath = os.path.join(mainOutputDir, tfmPath, "Origin2Dicom.tfm")
@@ -513,33 +513,42 @@ def onGenerateVRG(self):
                 slicer.mrmlScene.RemoveNode(tfmNode)
             else:
                 # Just export the first frame
-                currentNode, _ = self.logic.getItemInSequence(volumeNode, 0)
+                proxyNode = self.logic.getItemInSequence(volumeNode, 0)[0]
+                proxyNode.AddCenteringTransform()
+                tfmNode = proxyNode.GetParentTransformNode()
+                proxyNode.SetAndObserveTransformNodeID(None)
+
+                tfmPath = os.path.join(mainOutputDir, tfmPath, "Origin2Dicom.tfm")
+                tfmNode.Inverse()
+                slicer.util.saveNode(tfmNode, tfmPath)
+                tfmNode.Inverse()
+
+                currentNode = volumeNode.GetNthDataNode(0)
                 currentNode.AddCenteringTransform()
                 tfmNode = currentNode.GetParentTransformNode()
                 currentNode.HardenTransform()
                 currentNode.SetAndObserveTransformNodeID(None)
-                tfmPath = os.path.join(mainOutputDir, tfmPath, "Origin2Dicom.tfm")
-                tfmNode.Inverse()
-                slicer.util.saveNode(tfmNode, tfmPath)
-                slicer.mrmlScene.RemoveNode(tfmNode)
+                volumeNode.SetDataNodeAtValue(currentNode, "0")
 
-                # Harden and remove the transform from the sequence
+                # Apply to all frames
                 for i in range(1, volumeNode.GetNumberOfDataNodes()):
-                    currentNode, _ = self.logic.getItemInSequence(volumeNode, i)
-                    currentNode.AddCenteringTransform()
-                    tfmNode = currentNode.GetParentTransformNode()
+                    currentNode = volumeNode.GetNthDataNode(i)
+                    currentNode.SetAndObserveTransformNodeID(tfmNode.GetID())
                     currentNode.HardenTransform()
                     currentNode.SetAndObserveTransformNodeID(None)
-                    slicer.mrmlScene.RemoveNode(tfmNode)
+                    volumeNode.SetDataNodeAtValue(currentNode, f"{i}")
+
+                # slicer.mrmlScene.RemoveNode(tfmNode)
 
             numFrames = 1
             currentNode = volumeNode
             curName = volumeNode.GetName()
             if self.logic.IsSequenceVolume(currentNode):
                 numFrames = volumeNode.GetNumberOfDataNodes()
-                currentNode, curName = self.logic.getItemInSequence(volumeNode, 0)
+                currentNode = volumeNode.GetNthDataNode(0)
+                curName = currentNode.GetName()
             bounds = [0] * 6
-            currentNode.GetBounds(bounds)
+            currentNode.GetRASBounds(bounds)
 
             # Generate all possible camera positions
             camOffset = self.ui.camOffSetSpin.value
@@ -572,7 +581,8 @@ def onGenerateVRG(self):
                 self.updateProgressBar(progress)
 
                 if self.logic.IsSequenceVolume(volumeNode):
-                    currentNode, curName = self.logic.getNextItemInSequence(volumeNode)
+                    currentNode = volumeNode.GetNthDataNode(i)
+                    curName = currentNode.GetName()
 
             # Optimize the camera positions
             bestCameras = RadiographGeneration.optimizeCameras(
@@ -1239,15 +1249,15 @@ def generateVRGForCameras(
         """
         self.createPathsIfNotExists(outputDir)
         # Apply a thresh of 0 to the volume to remove air from the volume
-        thresholdScalarVolume = slicer.modules.thresholdscalarvolume
-        parameters = {
-            "InputVolume": volumeNode.GetID(),
-            "OutputVolume": volumeNode.GetID(),
-            "ThresholdValue": 0,
-            "ThresholdType": "Below",
-            "Lower": 0,
-        }
-        slicer.cli.runSync(thresholdScalarVolume, None, parameters)
+        # thresholdScalarVolume = slicer.modules.thresholdscalarvolume
+        # parameters = {
+        #     "InputVolume": volumeNode.GetID(),
+        #     "OutputVolume": volumeNode.GetID(),
+        #     "ThresholdValue": 0,
+        #     "ThresholdType": "Below",
+        #     "Lower": 0,
+        # }
+        # slicer.cli.runSync(thresholdScalarVolume, None, parameters)
 
         # write a temporary volume to disk
         volumeFileName = "AutoscoperM_VRG_GEN_TEMP.mhd"

AutoscoperM/AutoscoperMLib/RadiographGeneration.py

@@ -82,7 +82,7 @@ def generateNCameras(
     :return: List of cameras
     """
     # find the center of the bounds
-    center = [(bounds[0] + bounds[1]) / 2, (bounds[2] + bounds[3]) / 2, (bounds[4] + bounds[5]) / 2]
+    center = [(bounds[i + 1] + bounds[i]) / 2 for i in range(0, 6, 2)]
 
     # find the largest dimension of the bounds
     largestDimension = max([bounds[1] - bounds[0], bounds[3] - bounds[2], bounds[5] - bounds[4]])

Tracking3D/Tracking3DLib/TreeNode.py

@@ -135,6 +135,12 @@ def exportTransformsAsTRAFile(self):
             currentArray = currentArray @ neutralArray
             transforms[idx] = self.autoscoperLogic.numpyToVtk(currentArray)
 
+        # Move each transform from the DICOM space into AUT space
+        # TODO: Get this file from user
+        o2dFile = r"AutoscoperM-Pre-Processing\Autoscoper Scene\Transforms\Origin2Dicom.tfm"
+        o2dFile = os.path.join(slicer.mrmlScene.GetCacheManager().GetRemoteCacheDirectory(), o2dFile)
+        transforms = [self.autoscoperLogic.applyOrigin2DicomTransform(tfm, o2dFile) for tfm in transforms]
+
         # Write out tra
         # TODO: Make the directory user defined
         exportDir = r"AutoscoperM-Pre-Processing\Tracking"

VirtualRadiographGeneration/VirtualRadiographGeneration.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python-real
 
-import concurrent.futures as cf
 import glob
 import json
 import os
@@ -26,9 +25,18 @@ def generateVRG(
     :param height: Height of the output image
     """
 
+    # Zero threshold the image
+    thresholder = vtk.vtkImageThreshold()
+    thresholder.ThresholdByLower(0)
+    thresholder.ReplaceInOn()
+    thresholder.SetInValue(0)
+    thresholder.SetInputData(volumeImageData)
+    thresholder.Update()
+    thresholdedImageData = thresholder.GetOutput()
+
     # find the min and max scalar values
     hist = vtk.vtkImageHistogramStatistics()
-    hist.SetInputData(volumeImageData)
+    hist.SetInputData(thresholdedImageData)
     hist.Update()
     minVal = hist.GetMinimum()
     maxVal = hist.GetMaximum()
@@ -46,7 +54,7 @@ def generateVRG(
 
     # create the volume mapper
     volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
-    volumeMapper.SetInputData(volumeImageData)
+    volumeMapper.SetInputData(thresholdedImageData)
     volumeMapper.SetBlendModeToComposite()
     volumeMapper.SetBlendModeToComposite()
     volumeMapper.SetUseJittering(False)
@@ -157,12 +165,14 @@ def _createVTKCameras(cameraDir: str, radiographMainDir: str):
     reader.Update()
 
     # generate the virtual radiograph
-    with cf.ThreadPoolExecutor() as executor:
-        futures = [
-            executor.submit(
-                generateVRG, cam, reader.GetOutput(), os.path.join(camDir, outputFileName), outputWidth, outputHeight
-            )
-            for cam, camDir in cameras.items()
-        ]
-        for future in cf.as_completed(futures):
-            future.result()
+    # with cf.ThreadPoolExecutor() as executor:
+    #     futures = [
+    #         executor.submit(
+    #             generateVRG, cam, reader.GetOutput(), os.path.join(camDir, outputFileName), outputWidth, outputHeight
+    #         )
+    #         for cam, camDir in cameras.items()
+    #     ]
+    #     for future in cf.as_completed(futures):
+    #         future.result()
+    for cam, camDir in cameras.items():
+        generateVRG(cam, reader.GetOutput(), os.path.join(camDir, outputFileName), outputWidth, outputHeight)