# Running a Python script for smoothing segmentation from the terminal

**URL:** <https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843>\
**Category:** Development\
**Tags:** python\
**Created:** [August 12, 2024, 1:10pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843 "2024-08-12T13:10:20Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![ruili](https://avatars.discourse-cdn.com/v4/letter/r/dec6dc/32.png) [@ruili](https://discourse.slicer.org/u/ruili)\
**Post date:** [August 12, 2024, 1:10pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/1 "2024-08-12T13:10:20Z")

</div>

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!

```auto
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)

```

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 12, 2024, 3:06pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/2 "2024-08-12T15:06:46Z")

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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()`

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<div class="post-metadata">

**Author:** ![ruili](https://avatars.discourse-cdn.com/v4/letter/r/dec6dc/32.png) [@ruili](https://discourse.slicer.org/u/ruili)\
**Post date:** [August 20, 2024, 12:36pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/3 "2024-08-20T12:36:24Z")

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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?

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 20, 2024, 1:32pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/4 "2024-08-20T13:32:08Z")

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

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<div class="post-metadata">

**Author:** ![ruili](https://avatars.discourse-cdn.com/v4/letter/r/dec6dc/32.png) [@ruili](https://discourse.slicer.org/u/ruili)\
**Post date:** [August 20, 2024, 2:28pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/5 "2024-08-20T14:28:03Z")

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

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 20, 2024, 3:06pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/6 "2024-08-20T15:06:15Z")

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Try calling it after calling the `showMinimized()` method.

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<div class="post-metadata">

**Author:** ![ruili](https://avatars.discourse-cdn.com/v4/letter/r/dec6dc/32.png) [@ruili](https://discourse.slicer.org/u/ruili)\
**Post date:** [August 20, 2024, 8:08pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/7 "2024-08-20T20:08:16Z")

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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](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/9/e9b0d1309db4a5e097255f20b5c39b34200da0aa.png)

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 20, 2024, 8:52pm UTC](https://discourse.slicer.org/t/running-a-python-script-for-smoothing-segmentation-from-the-terminal/37843/8 "2024-08-20T20:52:39Z")

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No, I think that one is hard coded.