Running a Python script for smoothing segmentation from the terminal

Development
1

Hello,

I have the following script that smooths a binary segmentation using the Joint Taubin method from slicer. Suppose this script is saved at smoothing.py, I am calling it with this command: path/to/slicer --no-splash --python-script smoothing.py -mask path/to/mask -volume path/to/volume -output path/to/output. This will open the slicer software and does the job properly.

However, ideally I want to run it without opening the slicer window. I tried adding the --no-main-window flag, but then it simply does not do the smoothing and no output is generated. I’m wondering if any of the functions I am using in this script requires the slicer main window to be open to work? Help will be very much appreciated!

import slicer
import argparse

def smooth_mask(mask_path, volume_path, output_path):
    slicer.util.showStatusMessage("Loading files")
    segmentationNode = slicer.util.loadSegmentation(mask_path)
    masterVolumeNode = slicer.util.loadVolume(volume_path)

    # Create segment editor to get access to effects
    segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
    segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
    segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
    segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
    segmentEditorWidget.setSegmentationNode(segmentationNode)
    segmentEditorWidget.setSourceVolumeNode(masterVolumeNode)

    # Smoothing
    slicer.util.showStatusMessage("Smoothing LSA PA mask")
    segmentEditorWidget.setActiveEffectByName("Smoothing")
    effect = segmentEditorWidget.activeEffect()
    effect.setParameter("SmoothingMethod", "JOINT_TAUBIN")
    effect.setParameter("JointTaubinSmoothingFactor", 0.5)
    effect.self().onApply()

    # Clean up
    segmentEditorWidget = None
    slicer.mrmlScene.RemoveNode(segmentEditorNode)

    # Export segmentation to a labelmap
    labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
    slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, masterVolumeNode)
    slicer.util.saveNode(labelmapVolumeNode, output_path)
    slicer.util.showStatusMessage("Saved smoothed LSA PA mask")
    return None



if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('-mask', help='Path to a binary segmentation mask')
    parser.add_argument('-volume', help='Path to the master volume that the segmentation corresponds to')
    parser.add_argument('-output', help='Path to save output mask')

    args = parser.parse_args()
    smooth_mask(args.mask, args.volume, args.output)
2

You could make this work by avoiding using the module widget so you don’t need the main window, but a simple workaround could be to add this to your script:

slicer.util.mainWindow().showMinimized()

3

Sorry for my late reply. I added the suggested line of code to the beginning of the smooth_mask function, but it did not actually prevent the window of slicer from popping up. Nothing seemed to change. I was running the script on a mac machine. Do you know by any chance how I may fix this?

4

You may need to call slicer.app.processEvents() if you are running from a script that never uses the GUI.

5

Yes, I am actually just running the script from terminal. May I ask where in the script should this line of code be called?

6

Try calling it after calling the showMinimized() method.

7

That successfully suppressed the main window of slicer. Thank you! The only problem remaining was that it couldn’t stop the pop-up window when loading the files like this one below. Do you know any quick fix for this as well? If not, it is completely fine as well.

Screenshot 2024-08-20 at 21.00.40
Screenshot 2024-08-20 at 21.00.40691×95 17.5 KB

8

No, I think that one is hard coded.

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