PERF: Remove use of Scripted CLI and threshold directly in VRG module

AutoscoperM/AutoscoperM.py

@@ -1264,16 +1264,6 @@ def generateVRGForCameras(
         :param filename: filename of the VRG
         """
         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)
 
         # write a temporary volume to disk
         volumeFileName = "AutoscoperM_VRG_GEN_TEMP.mhd"

VirtualRadiographGeneration/VirtualRadiographGeneration.py

@@ -26,9 +26,19 @@ def generateVRG(
     :param height: Height of the output image
     """
 
+    # Remove air and low-density materials by applying a threshold to the volume image data
+    # In CT scans, air has a value of -1000 HU and other low-density materials like fat range from -60 to -120 HU
+    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 +56,7 @@ def generateVRG(
 
     # create the volume mapper
     volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
-    volumeMapper.SetInputData(volumeImageData)
+    volumeMapper.SetInputData(thresholdedImageData)
     volumeMapper.SetBlendModeToComposite()
     volumeMapper.SetBlendModeToComposite()
     volumeMapper.SetUseJittering(False)