Fix labels from Slicer plugin offset by extra background class #716
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Signed-off-by: Adam Aji <[email protected]>
| @@ -1279,8 +1279,9 @@ def onSaveLabel(self): | |||
| qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor) | |||
| segmentationNode = self._segmentNode | |||
| labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode") | |||
| slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode( | |||
| segmentationNode, labelmapVolumeNode, self._volumeNode | |||
| save_segment_ids = [segment_id for segment_id in segmentationNode.GetSegmentation().GetSegmentIDs() if segment_id != "background"] | |||
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yes, we can discard the background label (which is normally used by deepedit multilabel model) along with scribbles background/foreground when you save the label..
but the fix possibly by adding "background" to the list mentioned at: https://github.com/Project-MONAI/MONAILabel/blob/main/plugins/slicer/MONAILabel/MONAILabel.py#L1293
| _, segment = self.currentSegment() | ||
| selected_label_name = segment.GetName() | ||
| save_segment_ids = [selected_label_name, "background_scribbles", "foreground_scribbles"] | ||
| slicer.modules.segmentations.logic().ExportSegmentsToLabelmapNode( |
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there is a known issue for scribbles.. it currently can't support/persist scribbles per label.. specially in case for multi-label.. what you need is save/persist the bg/fg scribbles (similar to fg/bg fudical/click points) per label.. so the behavior/user experience in case of multilabel might not be good.
However, i will let @masadcv to decide what he needs from the label node.. i guess he might want to get all labels and pick fg/bg label masks as part of pre-transforms + current label name (i guess he needs current label name in case of he wants all labels; which might be the reason, it's not working) and send back the results with corrections..
again only corrected label should get updated.. i guess it needs to be fixed/verified as well..
In future these methods might want to use existing label masks as input along with fg/bg label masks..
Or until that future comes, it's ok for me to include only fg/bg scribbles sent to server to run the scribbles action..
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@adamaji @SachidanandAlle understood.
I would like to keep labels and do selection on the server side. This is to make it future-proof where we can use more advanced multi-label post-processing methods such as CRF that take into account other labels as well.
The scribbles labels are currently hard-coded in server app, these need to be passed from the client - in case the order changes or similar shift in label are present (due to any changes to client). Hence, a need for dynamic updates for this.
As Sachi said, background may need to be removed before saving final segmentation output, but this can be done at https://github.com/Project-MONAI/MONAILabel/blob/main/plugins/slicer/MONAILabel/MONAILabel.py#L1293
I will continue this in PR #717 where I will merge the changes from here for updating the current label and provide a generalisable solution to the problem that we can extend in future to multi-label problems. As this needs proper testing with multilabel problem, I will take sometime and get back with an update when ready.
| _, segment = self.currentSegment() | ||
| label = segment.GetName() | ||
| self.updateSegmentationMask(result_file, [label]) | ||
| self.updateSegmentationMask(result_file, [selected_label_name]) |
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yes,, this will make sure we update the selected mask only 👍
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Closing because this PR will be superseded by work from #717 . |
Signed-off-by: Adam Aji [email protected]
This PR addresses #713. When running the Slicer plugin, I saw that having the "background" segment visible would affect scribbles by offsetting the expected labels of "2"/"3" for "background_scribbles"/"foreground_scribbles" to "3"/"4". This can also affect saving labels via "Submit Label" by incrementing all classes after "background" by 1.
I'm assuming this offset isn't intended from other references in the code
MONAILabel/monailabel/scribbles/infer.py
Lines 103 to 104 in f9e37fe
The main change here is to replace
ExportVisibleSegmentsToLabelmapNodewithExportSegmentsToLabelmapNodeand specify exactly which segments should be exported. For scribbles, I opted to export only the selectedcurrentSegmentwith the foreground and background scribble segments.Because of that, this is a potential soft-workaround for #607, as it should allow you to associate the scribbles with different segments in the segmentation. It's still somewhat unclear that that
currentSegmentcombobox is connected to scribbles since it lives under the "SmartEdit / DeepGrow" heading, but since scribbles was already using it, I thought this should be fine for now.