Example of assigning segment names from table

segment-names.py

import glob
import numpy
import os
import random

includeEdema = True

exec(open("/opt/data/nac/neurosurgicalatlas/MONAI/labels.py").read())

tureSynthSegGlob = "/opt/data/nac/neurosurgicalatlas/MONAI/Ture-subset-2022-12-03-nii-seg/Ture-*-*.nrrd_synthseg.nii.gz"
tureVolumePattern = "/opt/data/nac/neurosurgicalatlas/MONAI/Ture-subset-2022-12-03-nii/Ture-%03d-%s.nrrd.nii.gz"
tureMONIAPattern = "/opt/data/nac/neurosurgicalatlas/MONAI/Ture-subset-2022-12-03/24-NEW-Ture-cases/Ture-%03d.nii.gz"

saveDir = "/opt/data/nac/neurosurgicalatlas/MONAI/Ture-subset-2022-12-03+ss+ml-with-edema"
savePattern = f"{saveDir}/Ture-%03d-%s+ss+ml.seg.nrrd"

os.system(f"mkdir -p {saveDir}")

synthSegLabelsByValue = {}
for label,value in synthSegLabels.items():
    synthSegLabelsByValue[value] = label
synthSegLabelsByValue[10000] = "Brain tumor + necrotic"
synthSegLabelsByValue[10001] = "Edema"

segLogic = slicer.modules.segmentations.logic()

for synthSegPath in glob.glob(tureSynthSegGlob):

    slicer.mrmlScene.Clear()

    caseSplit = os.path.basename(synthSegPath).split("-")
    caseString = caseSplit[1]
    caseNumber = int( caseString[1:] if caseString[0] == "0" else caseString )
    caseContrast = caseSplit[2].split(".")[0]

    print(f"processing {caseString} -> {caseNumber}, {caseContrast}")

    tureVolumePath = tureVolumePattern % (caseNumber, caseContrast)
    tureMONIAPath = tureMONIAPattern % caseNumber

    print(tureVolumePath)
    if not os.path.exists(tureVolumePath):
        print("failed!")
        break
    print(synthSegPath)
    if not os.path.exists(synthSegPath):
        print("failed!")
        break
    print(tureMONIAPath)
    if not os.path.exists(tureMONIAPath):
        print("failed!")
        break

    tureVolume = slicer.util.loadVolume(tureVolumePath)


    ssColors = slicer.mrmlScene.CreateNodeByClass("vtkMRMLColorTableNode")
    ssColors.SetType(slicer.vtkMRMLColorNode.User)
    slicer.mrmlScene.AddNode(ssColors)
    ssColors.SetName(f"ssColors")
    ssColors.SetNumberOfColors(10002)
    random.seed(42)
    for value,label in synthSegLabelsByValue.items():
        ssColors.SetColor(value, label, random.random(), random.random(), random.random(), 1.0)
    ssColors.SetNamesFromColors()
    for value,label in synthSegLabelsByValue.items():
        ssColors.SetColorName(value, label)
    ssColors.SetColor(10000, "Brain tumor + necrotic", random.random(), random.random(), random.random(), 1.0)
    ssColors.SetColor(10001, "Edema", random.random(), random.random(), random.random(), 1.0)

    ssSegmentation = slicer.util.loadSegmentation(synthSegPath, {"colorNodeID": ssColors.GetID()})
    ssSegmentation.SetReferenceImageGeometryParameterFromVolumeNode(tureVolume)

    monaiLabel = slicer.util.loadLabelVolume(tureMONIAPath, {"colorNodeID": ssColors.GetID()})
    monaiLabel.SetName(f"{'Ture-%03d' % caseNumber}-monaiLabel")

    monaiSeg = slicer.mrmlScene.CreateNodeByClass("vtkMRMLSegmentationNode")
    slicer.mrmlScene.AddNode(monaiSeg)
    monaiSeg.SetName(f"{'Ture-%03d' % caseNumber}-monaiSeg")
    monaiSeg.SetReferenceImageGeometryParameterFromVolumeNode(tureVolume)
    segLogic.ImportLabelmapToSegmentationNode(monaiLabel, monaiSeg)

    segLogic.ExportSegmentsToLabelmapNode(
            monaiSeg,
            monaiSeg.GetSegmentation().GetSegmentIDs(),
            monaiLabel,
            tureVolume,
            slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY,
            monaiLabel.GetDisplayNode().GetColorNode())

    mergedLabel = slicer.mrmlScene.CreateNodeByClass("vtkMRMLLabelMapVolumeNode")
    slicer.mrmlScene.AddNode(mergedLabel)
    mergedLabel.SetName(f"mergedLabel")
    segLogic.ExportSegmentsToLabelmapNode(
            ssSegmentation,
            ssSegmentation.GetSegmentation().GetSegmentIDs(),
            mergedLabel,
            tureVolume,
            slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY,
            ssColors)
    mergedLabel.GetDisplayNode().SetAndObserveColorNodeID(ssColors.GetID())

    ssLabelArray = slicer.util.arrayFromVolume(mergedLabel)
    ns16LabelArray = slicer.util.arrayFromVolume(monaiLabel)

    ns16TumorLabel = ns16Labels["Brain tumor + necrotic"]
    ns16EdemaLabel = ns16Labels["Edema"]
    ssLabelArray[ns16LabelArray == ns16TumorLabel] = 10000
    if includeEdema:
        ssLabelArray[ns16LabelArray == ns16EdemaLabel] = 10001
    slicer.util.arrayFromVolumeModified(mergedLabel)

    mergedSeg = slicer.mrmlScene.CreateNodeByClass("vtkMRMLSegmentationNode")
    mergedSeg = slicer.mrmlScene.AddNode(mergedSeg)
    mergedSeg.SetName(f"{'Ture-%03d' % caseNumber}-merged")
    mergedSeg.SetReferenceImageGeometryParameterFromVolumeNode(tureVolume)

    segLogic.ImportLabelmapToSegmentationNode(mergedLabel, mergedSeg)

    slicer.util.saveNode(mergedSeg, savePattern % (caseNumber,caseContrast))