Please critique my script : sequences, merged sequences, CINE, color, opacity, .mrb

Support
1

Below is a script that I am using to save CINE CTA volumes and segmentations as an mrb. Def works!!! Provides custom color and opacity. Plays as CINE.

Looking for any performance improvements. Memory improvements.

My subject hierarchy looks good. Below with 1 timepoint.
I am concerned that I have two segmentation sequences and two volume sequences in All nodes.

Screenshot from 2024-01-03 10-52-14
Screenshot from 2024-01-03 10-52-14727×185 15.7 KB

Screenshot from 2024-01-03 10-53-14

import slicer  # Import slicer module

# Default Medical Record Number (MRN)
mrn='123456'

def saveMRB(mrn=mrn):
   """
   Save the scene to a file named after the MRN in an anonymized directory.
   """
   anonymized_save_directory = "/path/to/save/directory/"  # Anonymized directory path
   sceneSaveFilename = f"{anonymized_save_directory}{mrn}.mrb"
   slicer.util.saveScene(sceneSaveFilename)

# Anonymized directory paths for image and segmentation data


anonymized_img_directory = "/path/to/image/directory/"
anonymized_seg_directory = "/path/to/segmentation/directory/"



# Process each MRN
try:
   print("Processing MRN: ", mrn)

   dir_img = anonymized_img_directory
   dir_seg = anonymized_seg_directory
   seg_prefix = "_v10 "

   # Variables for segmentation color and opacity settings
   vars_name = [var1,…]  # 18
   vars_color = {var1: [1, 1, 1], … }
   op1 = 0.4
   vars_opacity = {var1: 1, }

   # Create sequence nodes for volume and segmentation
   volumeSequenceNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode", "Volume sequence")
   segmentationSequenceNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode", "Segmentation sequence")
   mergedSequenceBrowserNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceBrowserNode", "Merged")

   for count in range(10):  # Adjust the range as needed
       print("Timepoint: ", count)
        # = getNode(f"{mrn}_{str(count).zfill(3)}_0000")
       volumeNode =slicer.util.loadVolume(f"{dir_img}{mrn}/{mrn}_{str(count*5).zfill(3)}_0000.nii.gz")
       volumeSequenceNode.SetDataNodeAtValue(volumeNode, str(count))

       segmentationNode = slicer.util.loadSegmentation(f"{dir_seg}{mrn}{seg_prefix}/{mrn}_{str(count*5).zfill(3)}.nii.gz")
       displayNode = segmentationNode.GetDisplayNode()
       displayNode.SetOpacity3D(1.0)
       segmentation = segmentationNode.GetSegmentation()

       for count_seg in range(18):
           sourceSegmentName = "Segment_" + str(count_seg + 1)
           sourceSegmentId = segmentation.GetSegmentIdBySegmentName(sourceSegmentName)
           if sourceSegmentId:
               segment = segmentation.GetSegment(sourceSegmentId)
               segment.SetName(vars_name[count_seg])
               segment.SetColor(vars_color[vars_name[count_seg]][0], vars_color[vars_name[count_seg]][1], vars_color[vars_name[count_seg]][2])
               segmentation.SetConversionParameter("Smoothing factor", "0.15")

       segmentationNode.CreateClosedSurfaceRepresentation()
       segmentationSequenceNode.SetDataNodeAtValue(segmentationNode, str(count))
       slicer.mrmlScene.RemoveNode(segmentationNode.GetDisplayNode())
       slicer.mrmlScene.RemoveNode(segmentationNode)

   mergedSequenceBrowserNode.AddSynchronizedSequenceNode(segmentationSequenceNode)
   mergedSequenceBrowserNode.SetSaveChanges(segmentationSequenceNode, True)
   mergedSequenceBrowserNode.AddSynchronizedSequenceNode(volumeSequenceNode)
   mergedSequenceBrowserNode.SetSaveChanges(volumeSequenceNode, True)
   slicer.modules.sequences.toolBar().setActiveBrowserNode(mergedSequenceBrowserNode)
   mergedProxyNode = mergedSequenceBrowserNode.GetProxyNode(segmentationSequenceNode)
   slicer.util.setSliceViewerLayers(foreground=mergedProxyNode)
   mergedProxyNode = mergedSequenceBrowserNode.GetProxyNode(volumeSequenceNode)
   slicer.util.setSliceViewerLayers(background=mergedProxyNode)

   v = slicer.util.getNode('View1')
   v.SetBoxVisible(False)
   v.SetAxisLabelsVisible(False)

   layoutManager = slicer.app.layoutManager()
   threeDWidget = layoutManager.threeDWidget(0)
   threeDView = threeDWidget.threeDView()
   threeDView.resetFocalPoint()

   sequenceProxyNode = mergedSequenceBrowserNode.GetProxyNode(segmentationSequenceNode)
   segmentationSequenceDisplayNode = sequenceProxyNode.GetDisplayNode()

   for count_seg in range(18):
       sourceSegmentName = "Segment_" + str(count_seg + 1)
       segmentationSequenceDisplayNode.SetSegmentOpacity3D(sourceSegmentName, vars_opacity[vars_name[count_seg]])

   saveMRB(mrn)

except Exception as e:
   print("Error processing MRN", mrn, ":", e)
   slicer.mrmlScene.Clear(0)
2

Regarding the apparent duplication of the sequences, check the mrml node type on each of those (there’s a “Show MRML ID’s” checkbox below the list). I suspect one of the duplicates is the actual sequence node, and the other is the proxy node, and they just have the same name.