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Add support for .seg.nrrd in UpdateSegmentationMask() of the Slicer extension #768

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Merged
SachidanandAlle merged 2 commits into from
May 9, 2022
Merged

Add support for .seg.nrrd in UpdateSegmentationMask() of the Slicer extension #768

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07051c9
add support for .seg.nrrd
jlvahldiek May 5, 2022
6feee14
Merge branch 'main' into main
SachidanandAlle May 9, 2022
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165 changes: 89 additions & 76 deletions plugins/slicer/MONAILabel/MONAILabel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1578,85 +1578,98 @@ def updateSegmentationMask(self, in_file, labels, sliceIndex=None, freeze=None):
segmentation.AddEmptySegment(label, label, self.getLabelColor(label))
return True

labels = [label for label in labels if label != "background"]
print(f"Update Segmentation Mask using Labels: {labels}")

# segmentId, segment = self.currentSegment()
labelImage = sitk.ReadImage(in_file)
labelmapVolumeNode = sitkUtils.PushVolumeToSlicer(labelImage, None, className="vtkMRMLLabelMapVolumeNode")

existing_label_ids = {}
for label in labels:
id = segmentation.GetSegmentIdBySegmentName(label)
if id:
existing_label_ids[label] = id

freeze = [freeze] if freeze and isinstance(freeze, str) else freeze
print(f"Import only Freezed label: {freeze}")

numberOfExistingSegments = segmentation.GetNumberOfSegments()
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, segmentationNode)
slicer.mrmlScene.RemoveNode(labelmapVolumeNode)

numberOfAddedSegments = segmentation.GetNumberOfSegments() - numberOfExistingSegments
logging.debug(f"Adding {numberOfAddedSegments} segments")

addedSegmentIds = [
segmentation.GetNthSegmentID(numberOfExistingSegments + i) for i in range(numberOfAddedSegments)
]
for i, segmentId in enumerate(addedSegmentIds):
segment = segmentation.GetSegment(segmentId)
print(f"Setting new segmentation with id: {segmentId} => {segment.GetName()}")

label = labels[i] if i < len(labels) else f"unknown {i}"
# segment.SetName(label)
# segment.SetColor(self.getLabelColor(label))

if freeze and label not in freeze:
print(f"Discard label update for: {label}")
elif label in existing_label_ids:
segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(self._volumeNode)
segmentEditorWidget.setCurrentSegmentID(existing_label_ids[label])

effect = segmentEditorWidget.effectByName("Logical operators")
labelmap = slicer.vtkOrientedImageData()
segmentationNode.GetBinaryLabelmapRepresentation(segmentId, labelmap)

if sliceIndex:
selectedSegmentLabelmap = effect.selectedSegmentLabelmap()
dims = selectedSegmentLabelmap.GetDimensions()
count = 0
for x in range(dims[0]):
for y in range(dims[1]):
if selectedSegmentLabelmap.GetScalarComponentAsDouble(x, y, sliceIndex, 0):
count = count + 1
selectedSegmentLabelmap.SetScalarComponentFromDouble(x, y, sliceIndex, 0, 0)

logging.debug(f"Total Non Zero: {count}")

# Clear the Slice
if count:
if in_file.endswith(".seg.nrrd") and self.file_ext == ".seg.nrrd":
source_node = slicer.modules.segmentations.logic().LoadSegmentationFromFile(in_file, False)
destination_node = segmentationNode
destination_segmentations = destination_node.GetSegmentation()
source_segmentations = source_node.GetSegmentation()

destination_segmentations.DeepCopy(source_segmentations)

if self._volumeNode:
destination_node.SetReferenceImageGeometryParameterFromVolumeNode(self._volumeNode)

slicer.mrmlScene.RemoveNode(source_node)
else:
labels = [label for label in labels if label != "background"]
print(f"Update Segmentation Mask using Labels: {labels}")

# segmentId, segment = self.currentSegment()
labelImage = sitk.ReadImage(in_file)
labelmapVolumeNode = sitkUtils.PushVolumeToSlicer(labelImage, None, className="vtkMRMLLabelMapVolumeNode")

existing_label_ids = {}
for label in labels:
id = segmentation.GetSegmentIdBySegmentName(label)
if id:
existing_label_ids[label] = id

freeze = [freeze] if freeze and isinstance(freeze, str) else freeze
print(f"Import only Freezed label: {freeze}")

numberOfExistingSegments = segmentation.GetNumberOfSegments()
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, segmentationNode)
slicer.mrmlScene.RemoveNode(labelmapVolumeNode)

numberOfAddedSegments = segmentation.GetNumberOfSegments() - numberOfExistingSegments
logging.debug(f"Adding {numberOfAddedSegments} segments")

addedSegmentIds = [
segmentation.GetNthSegmentID(numberOfExistingSegments + i) for i in range(numberOfAddedSegments)
]
for i, segmentId in enumerate(addedSegmentIds):
segment = segmentation.GetSegment(segmentId)
print(f"Setting new segmentation with id: {segmentId} => {segment.GetName()}")

label = labels[i] if i < len(labels) else f"unknown {i}"
# segment.SetName(label)
# segment.SetColor(self.getLabelColor(label))

if freeze and label not in freeze:
print(f"Discard label update for: {label}")
elif label in existing_label_ids:
segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(self._volumeNode)
segmentEditorWidget.setCurrentSegmentID(existing_label_ids[label])

effect = segmentEditorWidget.effectByName("Logical operators")
labelmap = slicer.vtkOrientedImageData()
segmentationNode.GetBinaryLabelmapRepresentation(segmentId, labelmap)

if sliceIndex:
selectedSegmentLabelmap = effect.selectedSegmentLabelmap()
dims = selectedSegmentLabelmap.GetDimensions()
count = 0
for x in range(dims[0]):
for y in range(dims[1]):
if selectedSegmentLabelmap.GetScalarComponentAsDouble(x, y, sliceIndex, 0):
count = count + 1
selectedSegmentLabelmap.SetScalarComponentFromDouble(x, y, sliceIndex, 0, 0)

logging.debug(f"Total Non Zero: {count}")

# Clear the Slice
if count:
effect.modifySelectedSegmentByLabelmap(
selectedSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet
)

# Union label map
effect.modifySelectedSegmentByLabelmap(
selectedSegmentLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet
labelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd
)
else:
# adding bypass masking to not overwrite other layers,
# needed for preserving scribbles during updates
# help from: https://github.com/Slicer/Slicer/blob/master
# /Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorLogicalEffect.py
bypassMask = True
effect.modifySelectedSegmentByLabelmap(
labelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet, bypassMask
)

# Union label map
effect.modifySelectedSegmentByLabelmap(
labelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd
)
else:
# adding bypass masking to not overwrite other layers,
# needed for preserving scribbles during updates
# help from: https://github.com/Slicer/Slicer/blob/master
# /Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorLogicalEffect.py
bypassMask = True
effect.modifySelectedSegmentByLabelmap(
labelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet, bypassMask
)

segmentationNode.RemoveSegment(segmentId)
segmentationNode.RemoveSegment(segmentId)

self.showSegmentationsIn3D()
logging.info(f"Time consumed by updateSegmentationMask: {time.time() - start:3.1f}")
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