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| | <noinclude>{{documentation/versioncheck}}</noinclude> | | <noinclude>{{documentation/versioncheck}}</noinclude> |
| − | __TOC__
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| | | | |
| − | | + | {{documentation/banner |
| − | =Community-contributed modules=
| + | | text = [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html This page has been moved to read-the-docs.] |
| − | | + | | background-color = 8FBC8F }} |
| − | 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).
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| − | | |
| − | ==Filters==
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| − | * [https://raw.github.com/pieper/VolumeMasker/master/VolumeMasker.py 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).
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| − | | |
| − | ==DICOM==
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| − | * [https://gist.github.com/pieper/6186477 dicom header browser] to easily scroll through dicom files using dcmdump.
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| − | * [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/BatchProcessing SlicerRT batch processing] to batch convert RT structure sets to labelmap NRRD files.
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| − | | |
| − | ==Informatics==
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| − | * [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/MarkupsInfoModule/MarkupsInfo.py MarkupsInfo.py]: Compute the total length between all the points of a markup list.
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| − | * [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/LineProfile/LineProfile.py LineProfile.py]: Compute intensity profile in a volume along a line.
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| − | | |
| − | =Community-contributed examples=
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| − | | |
| − | Usage: Copy-paste the shown code lines or linked .py file contents into Python console in Slicer.
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| − | | |
| − | ==Capture==
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| − | * Get a MRML node in the scene based on the node name and call methods of that object. For the MRHead sample data:
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| − | vol=slicer.util.getNode('MR*')
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| − | vol.GetImageData().GetDimensions()
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| − | * Capture the full Slicer screen and save it into a file
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| − | img = qt.QPixmap.grabWidget(slicer.util.mainWindow()).toImage()
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| − | img.save('c:/tmp/test.png')
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| − | * [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/CaptureRotationVideo/CaptureRotationVideo.py CaptureRotationVideo.py]: Capture a video of the scene rotating in the 3D view
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| − | | |
| − | ==Launching Slicer==
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| − | * How to open an .mrb file with Slicer at the command line?
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| − | Slicer.exe --python-code "slicer.util.loadScene( 'f:/2013-08-23-Scene.mrb' )"
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| − | * How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
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| − | Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window
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| − | | |
| − | ==DICOM==
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| − | * 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:
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| − | db=slicer.dicomDatabase
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| − | patientList=db.patients()
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| − | studyList=db.studiesForPatient(patientList[0])
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| − | seriesList=db.seriesForStudy(studyList[0])
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| − | fileList=db.filesForSeries(seriesList[0])
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| − | print db.fileValue(fileList[0],'0020,0032')
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| − | | |
| − | * How to access tag of a volume loaded from DICOM? For example, get the patient position stored in a volume:
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| − | volumeName='2: ENT IMRT'
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| − | n=slicer.util.getNode(volumeName)
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| − | instUids=n.GetAttribute('DICOM.instanceUIDs').split()
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| − | filename=slicer.dicomDatabase.fileForInstance(instUids[0])
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| − | print slicer.dicomDatabase.fileValue(filename,'0018,5100')
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| − | | |
| − | * How to access tag of an item in the Subject Hierachy tree? For example, get the content time tag of a structure set:
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| − | rtStructName = '3: RTSTRUCT: PROS'
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| − | rtStructNode = slicer.util.getNode(rtStructName)
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| − | rtStructSubjectHierarchyNode = slicer.vtkMRMLSubjectHierarchyNode.GetAssociatedSubjectHierarchyNode(rtStructNode)
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| − | ctSliceInstanceUids = rtStructSubjectHierarchyNode.GetAttribute('DICOM.ReferencedInstanceUIDs').split()
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| − | filename = slicer.dicomDatabase.fileForInstance(ctSliceInstanceUids[0])
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| − | print slicer.dicomDatabase.fileValue(filename,'0008,0033')
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| − | | |
| − | ==Toolbar functions==
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| − | * How to turn on slice intersections in the crosshair menu on the toolbar:
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| − | viewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceCompositeNode')
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| − | viewNodes.UnRegister(slicer.mrmlScene)
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| − | viewNodes.InitTraversal()
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| − | viewNode = viewNodes.GetNextItemAsObject()
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| − | while viewNode:
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| − | viewNode.SetSliceIntersectionVisibility(1)
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| − | viewNode = viewNodes.GetNextItemAsObject()
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| − | | |
| − | 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.
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| − | | |
| − | ==Manipulating objects in the slice viewer==
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| − | * How to define/edit a circular region of interest in a slice viewer?
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| − | | |
| − | 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.
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| − | | |
| − | # Update the sphere from the fiducial points
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| − | def UpdateSphere(param1, param2):
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| − | centerPointCoord = [0.0, 0.0, 0.0]
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| − | markups.GetNthFiducialPosition(0,centerPointCoord)
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| − | circumferencePointCoord = [0.0, 0.0, 0.0]
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| − | markups.GetNthFiducialPosition(1,circumferencePointCoord)
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| − | sphere.SetCenter(centerPointCoord)
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| − | radius=math.sqrt((centerPointCoord[0]-circumferencePointCoord[0])**2+(centerPointCoord[1]-circumferencePointCoord[1])**2+(centerPointCoord[2]-circumferencePointCoord[2])**2)
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| − | sphere.SetRadius(radius)
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| − | sphere.SetPhiResolution(30)
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| − | sphere.SetThetaResolution(30)
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| − | sphere.Update()
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| − |
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| − | # Get a reference to the markup
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| − | markups=slicer.util.getNode('F')
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| − | # Create the sphere that will intersect the slice viewer
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| − | sphere = vtk.vtkSphereSource()
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| − | # Initial positioning of the sphere
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| − | UpdateSphere(0,0)
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| − | # Create model node and add to scene
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| − | model = slicer.vtkMRMLModelNode()
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| − | model.SetAndObservePolyData(sphere.GetOutput())
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| − | modelDisplay = slicer.vtkMRMLModelDisplayNode()
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| − | modelDisplay.SetSliceIntersectionVisibility(True) # Show in slice view
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| − | modelDisplay.SetVisibility(False) # Hide in 3D view
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| − | slicer.mrmlScene.AddNode(modelDisplay)
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| − | model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
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| − | modelDisplay.SetInputPolyData(model.GetPolyData())
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| − | slicer.mrmlScene.AddNode(model)
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| − | # Call UpdateSphere whenever the fiducials are changed
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| − | markups.AddObserver("ModifiedEvent", UpdateSphere, 2)
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| − | | |
| − | == Add a texture mapped plane to the scene as a model ==
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| − | Note that model textures are not exposed in the GUI and are not saved in the scene
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| − | <pre>
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| − | # use dummy image data here
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| − | e = vtk.vtkImageEllipsoidSource()
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| − | | |
| − | scene = slicer.mrmlScene
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| − | | |
| − | # Create model node
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| − | model = slicer.vtkMRMLModelNode()
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| − | model.SetScene(scene)
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| − | model.SetName(scene.GenerateUniqueName("2DImageModel"))
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| − | | |
| − | planeSource = vtk.vtkPlaneSource()
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| − | model.SetAndObservePolyData(planeSource.GetOutput())
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| − | | |
| − | # Create display node
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| − | modelDisplay = slicer.vtkMRMLModelDisplayNode()
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| − | modelDisplay.SetColor(1,1,0) # yellow
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| − | modelDisplay.SetBackfaceCulling(0)
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| − | modelDisplay.SetScene(scene)
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| − | scene.AddNode(modelDisplay)
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| − | model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
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| − | | |
| − | # Add to scene
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| − | modelDisplay.SetAndObserveTextureImageData(e.GetOutput())
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| − | scene.AddNode(model)
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| − | | |
| − | | |
| − | transform = slicer.vtkMRMLLinearTransformNode()
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| − | scene.AddNode(transform)
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| − | model.SetAndObserveTransformNodeID(transform.GetID())
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| − | | |
| − | vTransform = vtk.vtkTransform()
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| − | vTransform.Scale(50,50,50)
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| − | vTransform.RotateX(30)
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| − | transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
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| − | </pre>
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| − | | |
| − | | |
| − | == Export a model to Blender, including color ==
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| − | | |
| − | <pre>
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| − | plyFilePath = "/tmp/fibers.ply"
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| − | | |
| − | lineDisplayNode = getNode("*LineDisplay*")
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| − | | |
| − | tuber = vtk.vtkTubeFilter()
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| − | tuber.SetInput(lineDisplayNode.GetOutputPolyData())
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| − | | |
| − | tubes = tuber.GetOutput()
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| − | tubes.Update()
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| − | scalars = tubes.GetPointData().GetArray(0)
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| − | scalars.SetName("scalars")
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| − | | |
| − | triangles = vtk.vtkTriangleFilter()
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| − | triangles.SetInput(tubes)
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| − | | |
| − | colorNode = lineDisplayNode.GetColorNode()
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| − | lookupTable = vtk.vtkLookupTable()
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| − | lookupTable.DeepCopy(colorNode.GetLookupTable())
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| − | lookupTable.SetTableRange(0,1)
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| − | | |
| − | plyWriter = vtk.vtkPLYWriter()
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| − | plyWriter.SetInput(triangles.GetOutput())
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| − | plyWriter.SetLookupTable(lookupTable)
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| − | plyWriter.SetArrayName("scalars")
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| − | | |
| − | plyWriter.SetFileName(plyFilePath)
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| − | plyWriter.Write()
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| − | </pre>
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| − | | |
| − | == Clone a volume ==
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| − | This example shows how to clone the MRHead sample volume, including its pixel data and display settings.
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| − | <pre>
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| − | sourceVolumeNode = slicer.util.getNode('MRHead')
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| − | volumesLogic = slicer.modules.volumes.logic()
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| − | clonedVolumeNode = volumesLogic.CloneVolume(slicer.mrmlScene, sourceVolumeNode, 'Cloned volume')
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| − | </pre>
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| − | | |
| − | == Create a new volume ==
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| − | This example shows how to create a new empty volume.
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| − | <pre>
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| − | imageSize=[512, 512, 512]
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| − | imageSpacing=[1.0, 1.0, 1.0]
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| − | voxelType=vtk.VTK_UNSIGNED_CHAR
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| − | # Create an empty image volume
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| − | imageData=vtk.vtkImageData()
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| − | imageData.SetDimensions(imageSize)
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| − | imageData.AllocateScalars(voxelType, 1)
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| − | thresholder=vtk.vtkImageThreshold()
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| − | thresholder.SetInputData(imageData)
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| − | thresholder.SetInValue(0)
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| − | thresholder.SetOutValue(0)
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| − | # Create volume node
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| − | volumeNode=slicer.vtkMRMLScalarVolumeNode()
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| − | volumeNode.SetSpacing(imageSpacing)
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| − | volumeNode.SetImageDataConnection(thresholder.GetOutputPort())
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| − | # Add volume to scene
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| − | slicer.mrmlScene.AddNode(volumeNode)
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| − | displayNode=slicer.vtkMRMLScalarVolumeDisplayNode()
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| − | slicer.mrmlScene.AddNode(displayNode)
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| − | colorNode = slicer.util.getNode('Grey')
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| − | displayNode.SetAndObserveColorNodeID(colorNode.GetID())
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| − | volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
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| − | volumeNode.CreateDefaultStorageNode()
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| − | </pre>
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| − | | |
| − | == Modify voxels in a volume ==
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| − | This example shows how to change voxels values of the MRHead sample volume.
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| − | The values will be computed by function f(r,a,s,) = (r-10)*(r-10)+(a+15)*(a+15)+s*s.
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| − | <pre>
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| − | volumeNode=slicer.util.getNode('MRHead')
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| − | ijkToRas = vtk.vtkMatrix4x4()
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| − | volumeNode.GetIJKToRASMatrix(ijkToRas)
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| − | imageData=volumeNode.GetImageData()
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| − | extent = imageData.GetExtent()
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| − | for k in xrange(extent[4], extent[5]+1):
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| − | for j in xrange(extent[2], extent[3]+1):
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| − | for i in xrange(extent[0], extent[1]+1):
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| − | position_Ijk=[i, j, k, 1]
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| − | position_Ras=ijkToRas.MultiplyPoint(position_Ijk)
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| − | r=position_Ras[0]
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| − | a=position_Ras[1]
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| − | s=position_Ras[2]
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| − | functionValue=(r-10)*(r-10)+(a+15)*(a+15)+s*s
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| − | imageData.SetScalarComponentFromDouble(i,j,k,0,functionValue)
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| − | imageData.SetScalarComponentFromFloat(distortionVectorPosition_Ijk[0], distortionVectorPosition_Ijk[1], distortionVectorPosition_Ijk[2], 0, fillValue)
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| − | imageData.Modified()
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| − | </pre>
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| − | | |
| − | == Manipulate a Slice View ==
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| − | | |
| − | <pre>
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| − | lm = slicer.app.layoutManager()
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| − | red = lm.sliceWidget('Red')
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| − | redLogic = red.sliceLogic()
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| − | # Print current slice offset position
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| − | print redLogic.GetSliceOffset()
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| − | # Change slice position
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| − | redLogic.SetSliceOffset(20)
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| − | </pre>
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| − | | |
| − | == Show a volume in the Slice Views ==
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| − | | |
| − | <pre>
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| − | volumeNode = slicer.util.getNode('YourVolumeNode')
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| − | applicationLogic = slicer.app.applicationLogic()
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| − | selectionNode = applicationLogic.GetSelectionNode()
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| − | selectionNode.SetSecondaryVolumeID(volumeNode.GetID())
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| − | applicationLogic.PropagateForegroundVolumeSelection(0)
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| − | </pre>
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| − | | |
| − | or
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| − | | |
| − | <pre>
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| − | n = slicer.util.getNode('YourVolumeNode')
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| − | for color in ['Red', 'Yellow', 'Green']:
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| − | slicer.app.layoutManager().sliceWidget(color).sliceLogic().GetSliceCompositeNode().SetForegroundVolumeID(n.GetID())
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| − | </pre>
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| − | | |
| − | == Center the 3D View on the Scene ==
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| − | <pre>
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| − | layoutManager = slicer.app.layoutManager()
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| − | threeDWidget = layoutManager.threeDWidget(0)
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| − | threeDView = threeDWidget.threeDView()
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| − | threeDView.resetFocalPoint()
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| − | </pre>
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| − | | |
| − | == Display text in a 3D view or slice view ==
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| − | | |
| − | The easiest way to show information overlaid on a viewer is to use corner annotations.
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| − | | |
| − | <pre>
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| − | view=slicer.app.layoutManager().threeDWidget(0).threeDView()
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| − | # Set text to "Something"
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| − | view.cornerAnnotation().SetText(vtk.vtkCornerAnnotation.UpperRight,"Something")
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| − | # Set color to red
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| − | view.cornerAnnotation().GetTextProperty().SetColor(1,0,0)
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| − | # Update the view
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| − | view.forceRender()
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| − | </pre>
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| − | | |
| − | == Turning off interpolation ==
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| − | | |
| − | You can turn off interpolation for newly loaded volumes with this script from Steve Pieper.
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| − | | |
| − | <pre>
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| − | def NoInterpolate(caller,event):
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| − | for node in slicer.util.getNodes('*').values():
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| − | if node.IsA('vtkMRMLScalarVolumeDisplayNode'):
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| − | node.SetInterpolate(0)
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| − |
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| − | slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeAddedEvent, NoInterpolate)
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| − | </pre>
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| − | | |
| − | The below link explains how to put this in your startup script.
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| − | | |
| − | http://www.na-mic.org/Wiki/index.php/AHM2012-Slicer-Python#Refining_the_code_and_UI_with_slicerrc
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| − | | |
| − | | |
| − | == Customize viewer layout ==
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| − | | |
| − | Show a custom layout of a 3D view on top of the red slice view:
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| − | | |
| − | <pre>
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| − | customLayout = ("<layout type=\"vertical\" split=\"true\" >"
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| − | " <item>"
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| − | " <view class=\"vtkMRMLViewNode\" singletontag=\"1\">"
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| − | " <property name=\"viewlabel\" action=\"default\">1</property>"
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| − | " </view>"
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| − | " </item>"
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| − | " <item>"
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| − | " <view class=\"vtkMRMLSliceNode\" singletontag=\"Red\">"
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| − | " <property name=\"orientation\" action=\"default\">Axial</property>"
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| − | " <property name=\"viewlabel\" action=\"default\">R</property>"
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| − | " <property name=\"viewcolor\" action=\"default\">#F34A33</property>"
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| − | " </view>"
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| − | " </item>"
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| − | "</layout>")
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| − |
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| − | customLayoutId=501
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| − | | |
| − | layoutManager = slicer.app.layoutManager()
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| − | layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)
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| − | layoutManager.setLayout(customLayoutId)
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| − | </pre>
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| − | | |
| − | See description of standard layouts (that can be used as examples) here:
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| − | https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx
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| − | | |
| − | == Running an ITK filter in Python using SimpleITK ==
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| − | Open the "Sample Data" module and download "MR Head", then paste the following snippet in Python interactor:
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| − | <pre>
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| − | inputImage = sitkUtils.PullFromSlicer('MRHead')
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| − | filter = sitk.SignedMaurerDistanceMapImageFilter()
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| − | outputImage = filter.Execute(inputImage)
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| − | sitkUtils.PushToSlicer(outputImage,'outputImage')
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| − | </pre>
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| − | | |
| − | More information:
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| − | * See the SimpleITK documentation for SimpleITK examples: http://www.itk.org/SimpleITKDoxygen/html/examples.html
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| − | * sitkUtils in Slicer is used for pushing and pulling images from Slicer to SimpleITK: https://github.com/Slicer/Slicer/blob/master/Base/Python/sitkUtils.py
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| − | | |
| − | == Get current mouse coordinates in a slice view ==
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| − | | |
| − | You can get 3D (RAS) coordinates of the current mouse cursor from the crosshair singleton node as shown in the example below:
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| − | | |
| − | <pre>
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| − | def onMouseMoved(observer,eventid):
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| − | ras=[0,0,0]
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| − | crosshairNode.GetCursorPositionRAS(ras)
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| − | print(ras)
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| − | | |
| − | crosshairNode=slicer.util.getNode('Crosshair')
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| − | crosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, onMouseMoved)
| |
| − | </pre>
| |
| − | | |
| − | == Thick slab reconstruction and maximum/minimum intensity volume projections ==
| |
| − | | |
| − | Set up 'red' slice viewer to show thick slab reconstructed from 3 slices:
| |
| − | <pre>
| |
| − | sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
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| − | appLogic = slicer.app.applicationLogic()
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| − | sliceLogic = appLogic.GetSliceLogic(sliceNode)
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| − | sliceLayerLogic = sliceLogic.GetBackgroundLayer()
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| − | reslice = sliceLayerLogic.GetReslice()
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| − | reslice.SetSlabModeToMean()
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| − | reslice.SetSlabNumberOfSlices(10) # mean of 10 slices will computed
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| − | reslice.SetSlabSliceSpacingFraction(0.3) # spacing between each slice is 0.3 pixel (total 10 * 0.3 = 3 pixel neighborhood)
| |
| − | sliceNode.Modified()
| |
| − | </pre>
| |
| − | | |
| − | Set up 'red' slice viewer to show maximum intensity projection (MIP):
| |
| − | <pre>
| |
| − | sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
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| − | appLogic = slicer.app.applicationLogic()
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| − | sliceLogic = appLogic.GetSliceLogic(sliceNode)
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| − | sliceLayerLogic = sliceLogic.GetBackgroundLayer()
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| − | reslice = sliceLayerLogic.GetReslice()
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| − | reslice.SetSlabModeToMax()
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| − | reslice.SetSlabNumberOfSlices(600) # use a large number of slices (600) to cover the entire volume
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| − | reslice.SetSlabSliceSpacingFraction(0.5) # spacing between slices are 0.5 pixel (supersampling is useful to reduce interpolation artifacts)
| |
| − | sliceNode.Modified()
| |
| − | </pre>
| |
| − | | |
| − | The projected image is available in a ''vtkImageData'' object by calling ''reslice.GetOutput()''.
| |
