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Script Editor

Slicer and Python

You can use the internal python console of Slicer to:

  • Automate things (run the same things over a number of specimens)
  • Implement customization (e.g., assign certain keys as shortcuts to your favorite tools)
  • Extend the functionality of Slicer by implementing new
  • Document the workflow for posterity

A good place to start with simple scripting and programming in Slicer is the Slicer Script Repository, where you can find code examples for specific modules, as well as examples of how to put together functions to do complex tasks. From here you can copy the code and paste into the Slicer's python console directly to execute. However, to apply these examples to your data or project, you often need to change the file path, file names or variables, which can be done using any text editor. However, Python is pretty strict with the indentations and how whitespaces (space or tab) is used to nest functions or loops. In such cases it is preferable to use a coding editor, which typically offer additional benefits such as syntax highlighting or auto-completion. There are many editors out there that you can explore. The primary issue with using a separate application, you end up having a file (your python script) independent of your data in Slicer.

Slicer's ScriptEditor extension provides a such simple programming editor inside the Slicer. Your scripts end up objects inside the Slicer scene, much like your volumes, models or markups. You can save them with your Slicer scene or package them along with the data using MRB format of the Slicer. You can even use the ScriptEditor to make short texts or readmes for your future self. ScriptEditor is a separate extension.

Getting Started

Make sure, you are using the latest stable (as of right now v5.10), as ScriptEditor does not work with well with older version of Slicer. Go to the extension manager, search for ScriptEditor and install the extension. Restart Slicer for changes to take effect. Once Slicer is restarted search for ScriptEditor (CTRL/CMD +F).

NOTE: Screenshots belong to an earlier version of the ScriptEditor, but the functionality is the same. In the current version you can also adjust the theme (light vs dark), as well as the Editor's font size.

Once the ScriptEditor is activated it should look like this:

You can switch between dark and light themes, and also adjust the font size.

You can set the default location for the script objects to be saved via the Save Location:

Go ahead and click on the Script: dropdown selector and choose (Create New Python Script) which will create a new Python text node. You can rename it by right-clicking the node name in the selector

Then copy and paste the following code into the editor:

import SampleData
import sitkUtils
import SimpleITK as sitk

# Load sample volume
sampleVolume = SampleData.SampleDataLogic().downloadMRHead()

# Apply Gaussian smoothing
inputImage = sitkUtils.PullVolumeFromSlicer(sampleVolume)
smoothedImage = sitk.SmoothingRecursiveGaussian(inputImage, sigma=2.0)

# Push the result back to Slicer
smoothedVolume = sitkUtils.PushVolumeToSlicer(smoothedImage, name='SmoothedVolume')
slicer.util.setSliceViewerLayers(background=smoothedVolume)

You can expand the width of the editor window, by dragging the module pane to the right.

You can highlight any section of the code by clicking the left mouse button and dragging the text, then use the right mouse click to bring the context menu, which will allow you to execute the highlighted section in the python console using Send Selection to Python Console (CTRL+Enter or CMD+Enter). If your python console is not visible in the application window, you can make it visible by pressing CTRL+3 (on macs CMD+3).

When you paste the full code into the python console, it should download the MRHead sample file, and apply a smoothing filter to the image. Your Slicer window should look like this:

It is important to understand that your scripts are saved into your scene like any other object in Slicer. The scripts are automatically stored as Python text nodes in your scene. To save the script object to disk:

  1. Go to Data module
  2. Right-click on your script object (it should have the Python icon to distinguish it from other text objects)
  3. In the pop-up dialog box, choose the directory where you want to save it
  4. Set the Export format to Python Script (.py) from the default .txt

Alternatively, you can set a default save location in the ScriptEditor module using the Save Location: field and Browse... button. When you set a save location, your scripts will automatically be configured to save to that directory as .py files.