Never ask the user to copy-paste code. Instead, use Slicer web server that allows execution of Python code via a web API.
Give these instructions to the user: Go to Web Server module, enable "Slicer API exec" in Advanced section, and click "Start server".
After this, you can connect to Slicer and run Python commands as it is described here: https://slicer.readthedocs.io/en/latest/user_guide/modules/webserver.html#remote-control
| """ | |
| Standalone MRML 3D view using only the slicer package (no trame). | |
| Sets up: | |
| - vtkMRMLScene + vtkSlicerApplicationLogic | |
| - vtkMRMLViewNode via vtkMRMLViewLogic | |
| - vtkMRMLDisplayableManagerGroup with all standard 3D displayable managers | |
| - Loads MRHead.nrrd and enables GPU ray-cast volume rendering | |
| Usage: |
| """ | |
| Run clang-format on modified files, on files modified in the last commit, or all files in the source tree | |
| (that match the valid file extensions .h and .cxx). | |
| Example use: | |
| cd /d C:\D\S4 | |
| c:\Users\andra\AppData\Local\Programs\Python\Python313\python.exe autoformat.py | |
| """ |
| """ | |
| Render image, segmentation, and colorized image slices and 3D. | |
| How to call this from command line: | |
| /home/jakob/dev/Slicer-5.7.0-linux-amd64/Slicer --python-script save_volume_rendering.py /path/to/output/folder mytest /path_to/ct_15mm.nii.gz /path/to/segmentation.nii.gz | |
| """ | |
| def captureSliceSweep(outputFilename, numberOfImages=25, lightboxColumns=5): |
| # URDF importer for Slicer | |
| # | |
| # This script imports a universal robot description file (URDF) into 3D Slicer scene. | |
| # This model can then be animated by updating the joint transforms by interactively modifying the transforms in 3D views | |
| # or remotely via OpenIGTLink. | |
| # | |
| # Usage: Copy-paste this script into the Python console in 3D Slicer. The script automatically downloads an example URDF from github. | |
| # You can use your own URDF file by setting `rootPath` and `urdfFilePath` to the path of your URDF file. | |
| # Get URDF file. |
| # This script can be used with this example scene: | |
| # https://github.com/lassoan/PublicTestingData/releases/download/data/ColoredVolumeRenderingScene.mrb | |
| volumeNode = getNode('Panoramix-cropped') | |
| segmentationNode = getNode('Panoramix-cropped segmentation') | |
| boostSegmentOpacity = False # Increase voxel value inside segments to allow making them them more opaque | |
| volumesLogic = slicer.modules.volumes.logic() | |
| segmentIds = vtk.vtkStringArray() |
| # Convert volume nodes of 3D Slicer to/from xarray and read/write into zarr format | |
| def xarrayFromVolume(volumeNode) -> "xr.DataArray": | |
| """Convert an volume node to an xarray.DataArray. | |
| Origin and spacing metadata is preserved in the xarray's coords. The | |
| Direction is set in the `direction` attribute. | |
| Dims are labeled as `x`, `y`, `z`, `t`, and `c`. | |
| This interface is and behavior is experimental and is subject to possible | |
| future changes.""" | |
| import xarray as xr |
| # Create a markups fiducial node and place 6 points then copy paste this code into 3D Slicer's Python console. | |
| # Two circles will be created (one for each 3 points) and the axis will be computed by connecting their centers. | |
| # The circles and the axis is updated as the fiducial point positions are adjusted. | |
| def sphereFrom3Points(markupsNode, startPointIndex): | |
| """Compute center and radius of 3-point sphere from 3 fiducial points | |
| source: https://stackoverflow.com/questions/20314306/find-arc-circle-equation-given-three-points-in-space-3d | |
| """ | |
| import numpy as np | |
| A = np.zeros(3) |
| The example was moved to Sandbox extension so that users can more easily install it: | |
| https://github.com/PerkLab/SlicerSandbox/blob/master/LoadRemoteFile/LoadRemoteFile.py | |
| More information: https://github.com/PerkLab/SlicerSandbox/blob/master/README.md#loadremotefile |
| segmentationNode = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLSegmentationNode') | |
| # set value to the size of the larges cracks in the segment surfaces | |
| maximumHoleSizeMm = 2.0 | |
| ############ | |
| masterVolumeNode = segmentationNode.GetNodeReference(segmentationNode.GetReferenceImageGeometryReferenceRole()) | |
| # Create segment editor to get access to effects | |
| segmentEditorWidget = slicer.qMRMLSegmentEditorWidget() | |
| # To show segment editor widget (useful for debugging): |