Running Slicer from PyCharm/external

Development
1

Hello! I want to run a python script for Slicer from PyCharm. I’m using the SegmentEditor module and PyRadiomics, and would like to automate the process for batch processing.

I’m able to write a script that runs on Slicer’s python console but I can’t figure out how to run it from PyCharm. I’m aware slicer has a debugger on pycharm and I tried setting slicer’s python.exe as the interpreter in pycharm. It hasn’t worked for me. Would anyone be able to advise?

2

Is there a reason you want to do this from PyCharm? This sounds more suitable for Jupyter notebooks?

See GitHub - Slicer/SlicerJupyter: Extension for 3D Slicer that allows the application to be used from Jupyter notebook

3

The python interpreter of slicer can’t run on its own, you need the slicer environment if you use the modules and/or the slicer API.

You can run a python script in the slicer environment using this command :
Slicer.exe --python-script "/full/path/to/myscript.py" --no-splash --no-main-window

I haven’t tried but you can probably configure pycharm to execute this command for you if you want to stay in pycharm.

1 Like
4

Thank you for the suggestions! I was able to do what I needed with Jupyter. I wanted to do it on PyCharm since it was what I was familiar with.

5

I ran into a problem with my code. Below is a snippet. When I want to export the features table, the csv is empty; it just has the headers. I think this is because the feature extractor is not done working and the table is already exported as csv, because when I wait for the extracted to be done then save as table, it works fine. However, this won’t be good if I have to do this for every time I extract the features. Can you by any chance advise how to go about this?

inputSeg = slicer.util.getNode("Segmentation")
radiomicsModule = slicer.modules.SlicerRadiomicsWidget
radiomicsModule.inputVolumeSelector.setCurrentNode(volNode)
radiomicsModule.inputMaskSelector.setCurrentNode(inputSeg)
radiomicsModule.manualCustomizationRadioButton.setChecked(True)

#firstorder feature selected by default

radiomicsModule.onApplyButton()

outputTableNode = radiomicsModule.outputTableSelector.currentNode()
outputFilePath = r"path to file"
slicer.util.saveNode(outputTableNode, outputFilePath)