Documentation/Nightly/ScriptRepository
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Community-contributed modules
Usage: save the .py file to a directory, add the directory to the additional module paths in the Slicer application settings (choose in the menu: Edit / Application settings, click Modules, click >> next to Additional module paths, click Add, and choose the .py file's location).
Segmentation
- FillRoi.py: Fill a region of interest in a labelmap volume with a constant value. This can be used after an automatic segmentation for removing certain regions of a volume (such as remove the table from a CT image).
Filters
- VolumeMasker.py: Update a target volume with the results of setting all input volume voxels to 0 except for those that correspond to a selected label value in an input label map (Used for example in the volume rendering in [https://www.youtube.com/watch?v=dfu2gugHLHs this video).
DICOM
- dicom header browser to easily scroll through dicom files using dcmdump.
Informatics
- MarkupsInfo.py: Compute the total length between all the points of a markup list.
- LineProfile.py: Compute intensity profile in a volume along a line.
Community-contributed examples
Usage: Copy-paste the shown code lines or linked .py file contents into Python console in Slicer.
Capture
- Get a MRML node in the scene based on the node name and call methods of that object. For the MRHead sample data:
vol=slicer.util.getNode('MR*') vol.GetImageData().GetDimensions()
- Capture the full Slicer screen and save it into a file
img = qt.QPixmap.grabWidget(slicer.util.mainWindow()).toImage() img.save('c:/tmp/test.png')
- CaptureRotationVideo.py: Capture a video of the scene rotating in the 3D view
Launching Slicer
- How to open an .mrb file with Slicer at the command line?
Slicer.exe --python-code "slicer.util.loadScene( 'f:/2013-08-23-Scene.mrb' )"
- How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window
DICOM
- How to access tags of DICOM images imported into Slicer? For example, to print the first patient's first study's first series' "0020,0032" field:
db=slicer.dicomDatabase patientList=db.patients() studyList=db.studiesForPatient(patientList[0]) seriesList=db.seriesForStudy(studyList[0]) fileList=db.filesForSeries(seriesList[0]) print db.fileValue(fileList[0],'0020,0032')
- How to access tag of a volume loaded from DICOM? For example, get the patient position stored in a volume:
volumeName='2: ENT IMRT' n=slicer.util.getNode(volumeName) instUids=n.GetAttribute('DICOM.instanceUIDs').split() filename=slicer.dicomDatabase.fileForInstance(instUids[0]) print slicer.dicomDatabase.fileValue(filename,'0018,5100')
Toolbar functions
- How to turn on slice intersections in the crosshair menu on the toolbar:
viewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceCompositeNode') viewNodes.UnRegister(slicer.mrmlScene) viewNodes.InitTraversal() viewNode = viewNodes.GetNextItemAsObject() while viewNode: viewNode.SetSliceIntersectionVisibility(1) viewNode = viewNodes.GetNextItemAsObject()
How to find similar functions? For this one I searched for "slice intersections" text in the whole slicer source code, found that the function is implemented in Base\QTGUI\qSlicerViewersToolBar.cxx, then translated the qSlicerViewersToolBarPrivate::setSliceIntersectionVisible(bool visible) method to Python.
Manipulating objects in the slice viewer
- How to define/edit a circular region of interest in a slice viewer?
Drop two markup points on a slice view and copy-paste the code below into the Python console. After this, as you move the markups you’ll see a circle following the markups.
# Update the sphere from the fiducial points def UpdateSphere(param1, param2): centerPointCoord = [0.0, 0.0, 0.0] markups.GetNthFiducialPosition(0,centerPointCoord) circumferencePointCoord = [0.0, 0.0, 0.0] markups.GetNthFiducialPosition(1,circumferencePointCoord) sphere.SetCenter(centerPointCoord) radius=math.sqrt((centerPointCoord[0]-circumferencePointCoord[0])**2+(centerPointCoord[1]-circumferencePointCoord[1])**2+(centerPointCoord[2]-circumferencePointCoord[2])**2) sphere.SetRadius(radius) sphere.SetPhiResolution(30) sphere.SetThetaResolution(30) sphere.Update() # Get a reference to the markup markups=slicer.util.getNode('F') # Create the sphere that will intersect the slice viewer sphere = vtk.vtkSphereSource() # Initial positioning of the sphere UpdateSphere(0,0) # Create model node and add to scene model = slicer.vtkMRMLModelNode() model.SetAndObservePolyData(sphere.GetOutput()) modelDisplay = slicer.vtkMRMLModelDisplayNode() modelDisplay.SetSliceIntersectionVisibility(True) # Show in slice view modelDisplay.SetVisibility(False) # Hide in 3D view slicer.mrmlScene.AddNode(modelDisplay) model.SetAndObserveDisplayNodeID(modelDisplay.GetID()) modelDisplay.SetInputPolyData(model.GetPolyData()) slicer.mrmlScene.AddNode(model) # Call UpdateSphere whenever the fiducials are changed markups.AddObserver("ModifiedEvent", UpdateSphere, 2)
Add a texture mapped plane to the scene as a model
Note that model textures are not exposed in the GUI and are not saved in the scene
# use dummy image data here e = vtk.vtkImageEllipsoidSource() scene = slicer.mrmlScene # Create model node model = slicer.vtkMRMLModelNode() model.SetScene(scene) model.SetName(scene.GenerateUniqueName("2DImageModel")) planeSource = vtk.vtkPlaneSource() model.SetAndObservePolyData(planeSource.GetOutput()) # Create display node modelDisplay = slicer.vtkMRMLModelDisplayNode() modelDisplay.SetColor(1,1,0) # yellow modelDisplay.SetBackfaceCulling(0) modelDisplay.SetScene(scene) scene.AddNode(modelDisplay) model.SetAndObserveDisplayNodeID(modelDisplay.GetID()) # Add to scene modelDisplay.SetAndObserveTextureImageData(e.GetOutput()) scene.AddNode(model) transform = slicer.vtkMRMLLinearTransformNode() scene.AddNode(transform) model.SetAndObserveTransformNodeID(transform.GetID()) vTransform = vtk.vtkTransform() vTransform.Scale(50,50,50) vTransform.RotateX(30) transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
Clone a volume
This example shows how to clone the MRHead sample volume, including its pixel data and display settings.
sourceVolumeNode = slicer.util.getNode('MRHead') clonedVolumeNode = slicer.mrmlScene.CopyNode(sourceVolumeNode) if sourceVolumeNode.GetDisplayNode() : clonedVolumeDisplayNode = slicer.mrmlScene.CopyNode(sourceVolumeNode.GetDisplayNode()) clonedVolumeDisplayNode.Copy(sourceVolumeNode.GetDisplayNode()) clonedVolumeNode.SetAndObserveDisplayNodeID(clonedVolumeDisplayNode.GetID()) if sourceVolumeNode.GetImageData() : clonedImageData = vtk.vtkImageData() clonedImageData.DeepCopy(sourceVolumeNode.GetImageData()) clonedVolumeNode.SetAndObserveImageData(clonedImageData)
Modify voxels in a volume
This example shows how to change voxels values of the MRHead sample volume. The values will be computed by function f(r,a,s,) = (r-10)*(r-10)+(a+15)*(a+15)+s*s.
volumeNode=slicer.util.getNode('MRHead') ijkToRas = vtk.vtkMatrix4x4() volumeNode.GetIJKToRASMatrix(ijkToRas) imageData=volumeNode.GetImageData() extent = imageData.GetExtent() for k in xrange(extent[4], extent[5]+1): for j in xrange(extent[2], extent[3]+1): for i in xrange(extent[0], extent[1]+1): position_Ijk=[i, j, k, 1] position_Ras=ijkToRas.MultiplyPoint(position_Ijk) r=position_Ras[0] a=position_Ras[1] s=position_Ras[2] functionValue=(r-10)*(r-10)+(a+15)*(a+15)+s*s imageData.SetScalarComponentFromDouble(i,j,k,0,functionValue) imageData.SetScalarComponentFromFloat(distortionVectorPosition_Ijk[0], distortionVectorPosition_Ijk[1], distortionVectorPosition_Ijk[2], 0, fillValue) imageData.Modified()