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| | <noinclude>{{documentation/versioncheck}}</noinclude> | | <noinclude>{{documentation/versioncheck}}</noinclude> |
| − | __TOC__
| |
| | | | |
| − | | + | {{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).
| |
| − | | |
| − | ==Filters== | |
| − | * [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).
| |
| − | | |
| − | ==DICOM==
| |
| − | * [https://gist.github.com/pieper/6186477 dicom header browser] to easily scroll through dicom files using dcmdump.
| |
| − | * [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/BatchProcessing SlicerRT batch processing] to batch convert RT structure sets to labelmap NRRD files.
| |
| − | | |
| − | ==Informatics==
| |
| − | * [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.
| |
| − | * [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/LineProfile/LineProfile.py 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')
| |
| − | * [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
| |
| − | | |
| − | ==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')
| |
| − | | |
| − | * How to access tag of an item in the Subject Hierachy tree? For example, get the content time tag of a structure set:
| |
| − | rtStructName = '3: RTSTRUCT: PROS'
| |
| − | rtStructNode = slicer.util.getNode(rtStructName)
| |
| − | rtStructSubjectHierarchyNode = slicer.vtkMRMLSubjectHierarchyNode.GetAssociatedSubjectHierarchyNode(rtStructNode)
| |
| − | ctSliceInstanceUids = rtStructSubjectHierarchyNode.GetAttribute('DICOM.ReferencedInstanceUIDs').split()
| |
| − | filename = slicer.dicomDatabase.fileForInstance(ctSliceInstanceUids[0])
| |
| − | print slicer.dicomDatabase.fileValue(filename,'0008,0033')
| |
| − | | |
| − | ==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
| |
| − | <pre>
| |
| − | # 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)
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| − | scene.AddNode(modelDisplay)
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| − | model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
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| − | | |
| − | # Add to scene
| |
| − | modelDisplay.SetAndObserveTextureImageData(e.GetOutput())
| |
| − | scene.AddNode(model)
| |
| − | | |
| − | | |
| − | transform = slicer.vtkMRMLLinearTransformNode()
| |
| − | scene.AddNode(transform)
| |
| − | model.SetAndObserveTransformNodeID(transform.GetID())
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| − | | |
| − | vTransform = vtk.vtkTransform()
| |
| − | vTransform.Scale(50,50,50)
| |
| − | vTransform.RotateX(30)
| |
| − | transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
| |
| − | </pre>
| |
| − | | |
| − | | |
| − | == Export a model to Blender, including color ==
| |
| − | | |
| − | <pre>
| |
| − | plyFilePath = "/tmp/fibers.ply"
| |
| − | | |
| − | lineDisplayNode = getNode("*LineDisplay*")
| |
| − | | |
| − | tuber = vtk.vtkTubeFilter()
| |
| − | tuber.SetInput(lineDisplayNode.GetOutputPolyData())
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| − | | |
| − | tubes = tuber.GetOutput()
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| − | tubes.Update()
| |
| − | scalars = tubes.GetPointData().GetArray(0)
| |
| − | scalars.SetName("scalars")
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| − | | |
| − | triangles = vtk.vtkTriangleFilter()
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| − | triangles.SetInput(tubes)
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| − | | |
| − | colorNode = lineDisplayNode.GetColorNode()
| |
| − | lookupTable = vtk.vtkLookupTable()
| |
| − | lookupTable.DeepCopy(colorNode.GetLookupTable())
| |
| − | lookupTable.SetTableRange(0,1)
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| − | | |
| − | plyWriter = vtk.vtkPLYWriter()
| |
| − | 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)
| |
| − | plyWriter.Write()
| |
| − | </pre>
| |
| − | | |
| − | == Clone a volume ==
| |
| − | This example shows how to clone the MRHead sample volume, including its pixel data and display settings.
| |
| − | <pre>
| |
| − | sourceVolumeNode = slicer.util.getNode('MRHead')
| |
| − | volumesLogic = slicer.modules.volumes.logic()
| |
| − | clonedVolumeNode = volumesLogic.CloneVolume(slicer.mrmlScene, sourceVolumeNode, 'Cloned volume')
| |
| − | </pre>
| |
| − | | |
| − | == Create a new volume ==
| |
| − | This example shows how to create a new empty volume.
| |
| − | <pre>
| |
| − | imageSize=[512, 512, 512]
| |
| − | imageSpacing=[1.0, 1.0, 1.0]
| |
| − | voxelType=vtk.VTK_UNSIGNED_CHAR
| |
| − | # Create an empty image volume
| |
| − | imageData=vtk.vtkImageData()
| |
| − | imageData.SetDimensions(imageSize)
| |
| − | imageData.AllocateScalars(voxelType, 1)
| |
| − | thresholder=vtk.vtkImageThreshold()
| |
| − | thresholder.SetInputData(imageData)
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| − | thresholder.SetInValue(0)
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| − | thresholder.SetOutValue(0)
| |
| − | # Create volume node
| |
| − | volumeNode=slicer.vtkMRMLScalarVolumeNode()
| |
| − | volumeNode.SetSpacing(imageSpacing)
| |
| − | volumeNode.SetImageDataConnection(thresholder.GetOutputPort())
| |
| − | # Add volume to scene
| |
| − | slicer.mrmlScene.AddNode(volumeNode)
| |
| − | displayNode=slicer.vtkMRMLScalarVolumeDisplayNode()
| |
| − | slicer.mrmlScene.AddNode(displayNode)
| |
| − | colorNode = slicer.util.getNode('Grey')
| |
| − | displayNode.SetAndObserveColorNodeID(colorNode.GetID())
| |
| − | volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
| |
| − | volumeNode.CreateDefaultStorageNode()
| |
| − | </pre>
| |
| − | | |
| − | == 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.
| |
| − | <pre>
| |
| − | volumeNode=slicer.util.getNode('MRHead')
| |
| − | 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):
| |
| − | 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()
| |
| − | </pre>
| |
| − | | |
| − | == Access values in a DTI tensor volume ==
| |
| − | This example shows how to access individual tensors at the voxel level.
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| − | | |
| − | First load your DWI volume and estimate tensors to produce a DTI volume called ‘Output DTI Volume’
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| − | | |
| − | Then open the python window: View->Python interactor
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| − | | |
| − | Use this command to access tensors through numpy:
| |
| − | | |
| − | <pre>
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| − | tensors = array('Output DTI Volume')
| |
| − | </pre>
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| − | | |
| − | Type the following code into the Python window to access all tensor components using vtk commands:
| |
| − | | |
| − | <pre>
| |
| − | volumeNode=slicer.util.getNode('Output DTI Volume')
| |
| − | imageData=volumeNode.GetImageData()
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| − | tensors = imageData.GetPointData().GetTensors()
| |
| − | extent = imageData.GetExtent()
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| − | idx = 0
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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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| − | tensors.GetTuple9(idx)
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| − | idx += 1
| |
| − | </pre>
| |
| − | | |
| − | == Change window/level (brightness/contrast) or colormap of a volume ==
| |
| − | This example shows how to change window/level of the MRHead sample volume.
| |
| − | <pre>
| |
| − | volumeNode = getNode('MRHead')
| |
| − | displayNode = volumeNode.GetDisplayNode()
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| − | displayNode.AutoWindowLevelOff()
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| − | displayNode.SetWindow(50)
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| − | displayNode.SetLevel(100)
| |
| − | </pre>
| |
| − | | |
| − | Change color mapping from grayscale to rainbow:
| |
| − | <pre>
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| − | displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeRainbow')
| |
| − | </pre>
| |
| − | | |
| − | == Manipulate a Slice View ==
| |
| − | | |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | red = lm.sliceWidget('Red')
| |
| − | redLogic = red.sliceLogic()
| |
| − | # Print current slice offset position
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| − | print redLogic.GetSliceOffset()
| |
| − | # Change slice position
| |
| − | redLogic.SetSliceOffset(20)
| |
| − | </pre>
| |
| − | | |
| − | == Save a series of images from a Slice View ==
| |
| − | | |
| − | You can use ScreenCapture module to capture series of images. To do it programmatically, save the following into a file such as '/tmp/record.py' and then in the slicer python console type "execfile('/tmp/record.py')"
| |
| − | | |
| − | <pre>
| |
| − | layoutName = 'Green'
| |
| − | imagePathPattern = '/tmp/image-%03d.png'
| |
| − | steps = 10
| |
| − | | |
| − | widget = slicer.app.layoutManager().sliceWidget(layoutName)
| |
| − | view = widget.sliceView()
| |
| − | logic = widget.sliceLogic()
| |
| − | bounds = [0,]*6
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| − | logic.GetSliceBounds(bounds)
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| − | | |
| − | for step in range(steps):
| |
| − | offset = bounds[4] + step/(1.*steps) * (bounds[5]-bounds[4])
| |
| − | logic.SetSliceOffset(offset)
| |
| − | view.forceRender()
| |
| − | image = qt.QPixmap.grabWidget(view).toImage()
| |
| − | image.save(imagePathPattern % step)
| |
| − | </pre>
| |
| − | | |
| − | == Save the scene into a new directory ==
| |
| − | | |
| − | <pre>
| |
| − | # Create a new directory where the scene will be saved into
| |
| − | import time
| |
| − | sceneSaveDirectory = slicer.app.temporaryPath + "/saved-scene-" + time.strftime("%Y%m%d-%H%M%S")
| |
| − | if not os.access(sceneSaveDirectory, os.F_OK):
| |
| − | os.makedirs(sceneSaveDirectory)
| |
| − | | |
| − | # Save the scene
| |
| − | if slicer.app.applicationLogic().SaveSceneToSlicerDataBundleDirectory(sceneSaveDirectory, None):
| |
| − | logging.info("Scene saved to: {0}".format(sceneSaveDirectory))
| |
| − | else:
| |
| − | logging.error("Scene saving failed")
| |
| − | </pre>
| |
| − | | |
| − | == Show a volume in the Slice Views ==
| |
| − | | |
| − | <pre>
| |
| − | volumeNode = slicer.util.getNode('YourVolumeNode')
| |
| − | applicationLogic = slicer.app.applicationLogic()
| |
| − | selectionNode = applicationLogic.GetSelectionNode()
| |
| − | selectionNode.SetSecondaryVolumeID(volumeNode.GetID())
| |
| − | applicationLogic.PropagateForegroundVolumeSelection(0)
| |
| − | </pre>
| |
| − | | |
| − | or
| |
| − | | |
| − | <pre>
| |
| − | n = slicer.util.getNode('YourVolumeNode')
| |
| − | for color in ['Red', 'Yellow', 'Green']:
| |
| − | slicer.app.layoutManager().sliceWidget(color).sliceLogic().GetSliceCompositeNode().SetForegroundVolumeID(n.GetID())
| |
| − | </pre>
| |
| − | | |
| − | == Change opacity of foreground volume in the Slice Views ==
| |
| − | | |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | sliceLogic = lm.sliceWidget('Red').sliceLogic()
| |
| − | compositeNode = sliceLogic.GetSliceCompositeNode()
| |
| − | compositeNode.SetForegroundOpacity(0.4)
| |
| − | </pre>
| |
| − | | |
| − | == Center the 3D View on the Scene ==
| |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | threeDWidget = layoutManager.threeDWidget(0)
| |
| − | threeDView = threeDWidget.threeDView()
| |
| − | threeDView.resetFocalPoint()
| |
| − | </pre>
| |
| − | | |
| − | == Display text in a 3D view or slice view ==
| |
| − | | |
| − | The easiest way to show information overlaid on a viewer is to use corner annotations.
| |
| − | | |
| − | <pre>
| |
| − | view=slicer.app.layoutManager().threeDWidget(0).threeDView()
| |
| − | # Set text to "Something"
| |
| − | view.cornerAnnotation().SetText(vtk.vtkCornerAnnotation.UpperRight,"Something")
| |
| − | # Set color to red
| |
| − | view.cornerAnnotation().GetTextProperty().SetColor(1,0,0)
| |
| − | # Update the view
| |
| − | view.forceRender()
| |
| − | </pre>
| |
| − | | |
| − | == Turning off interpolation ==
| |
| − | | |
| − | You can turn off interpolation for newly loaded volumes with this script from Steve Pieper.
| |
| − | | |
| − | <pre>
| |
| − | def NoInterpolate(caller,event):
| |
| − | for node in slicer.util.getNodes('*').values():
| |
| − | if node.IsA('vtkMRMLScalarVolumeDisplayNode'):
| |
| − | node.SetInterpolate(0)
| |
| − |
| |
| − | slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeAddedEvent, NoInterpolate)
| |
| − | </pre>
| |
| − | | |
| − | The below link explains how to put this in your startup script.
| |
| − | | |
| − | http://www.na-mic.org/Wiki/index.php/AHM2012-Slicer-Python#Refining_the_code_and_UI_with_slicerrc
| |
| − | | |
| − | | |
| − | == Customize viewer layout ==
| |
| − | | |
| − | Show a custom layout of a 3D view on top of the red slice view:
| |
| − | | |
| − | <pre>
| |
| − | customLayout = ("<layout type=\"vertical\" split=\"true\" >"
| |
| − | " <item>"
| |
| − | " <view class=\"vtkMRMLViewNode\" singletontag=\"1\">"
| |
| − | " <property name=\"viewlabel\" action=\"default\">1</property>"
| |
| − | " </view>"
| |
| − | " </item>"
| |
| − | " <item>"
| |
| − | " <view class=\"vtkMRMLSliceNode\" singletontag=\"Red\">"
| |
| − | " <property name=\"orientation\" action=\"default\">Axial</property>"
| |
| − | " <property name=\"viewlabel\" action=\"default\">R</property>"
| |
| − | " <property name=\"viewcolor\" action=\"default\">#F34A33</property>"
| |
| − | " </view>"
| |
| − | " </item>"
| |
| − | "</layout>")
| |
| − |
| |
| − | customLayoutId=501
| |
| − | | |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)
| |
| − | layoutManager.setLayout(customLayoutId)
| |
| − | </pre>
| |
| − | | |
| − | See description of standard layouts (that can be used as examples) here:
| |
| − | https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx
| |
| − | | |
| − | == Running an ITK filter in Python using SimpleITK ==
| |
| − | Open the "Sample Data" module and download "MR Head", then paste the following snippet in Python interactor:
| |
| − | <pre>
| |
| − | inputImage = sitkUtils.PullFromSlicer('MRHead')
| |
| − | filter = sitk.SignedMaurerDistanceMapImageFilter()
| |
| − | outputImage = filter.Execute(inputImage)
| |
| − | sitkUtils.PushToSlicer(outputImage,'outputImage')
| |
| − | </pre>
| |
| − | | |
| − | More information:
| |
| − | * See the SimpleITK documentation for SimpleITK examples: http://www.itk.org/SimpleITKDoxygen/html/examples.html
| |
| − | * 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
| |
| − | | |
| − | == Get current mouse coordinates in a slice view ==
| |
| − | | |
| − | You can get 3D (RAS) coordinates of the current mouse cursor from the crosshair singleton node as shown in the example below:
| |
| − | | |
| − | <pre>
| |
| − | def onMouseMoved(observer,eventid):
| |
| − | ras=[0,0,0]
| |
| − | crosshairNode.GetCursorPositionRAS(ras)
| |
| − | print(ras)
| |
| − | | |
| − | crosshairNode=slicer.util.getNode('Crosshair')
| |
| − | 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')
| |
| − | appLogic = slicer.app.applicationLogic()
| |
| − | sliceLogic = appLogic.GetSliceLogic(sliceNode)
| |
| − | sliceLayerLogic = sliceLogic.GetBackgroundLayer()
| |
| − | reslice = sliceLayerLogic.GetReslice()
| |
| − | reslice.SetSlabModeToMean()
| |
| − | reslice.SetSlabNumberOfSlices(10) # mean of 10 slices will computed
| |
| − | 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')
| |
| − | appLogic = slicer.app.applicationLogic()
| |
| − | sliceLogic = appLogic.GetSliceLogic(sliceNode)
| |
| − | sliceLayerLogic = sliceLogic.GetBackgroundLayer()
| |
| − | reslice = sliceLayerLogic.GetReslice()
| |
| − | reslice.SetSlabModeToMax()
| |
| − | reslice.SetSlabNumberOfSlices(600) # use a large number of slices (600) to cover the entire volume
| |
| − | 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()''.
| |
| − | | |
| − | == Change default file type for nodes (that have never been saved yet) ==
| |
| − | Default node can be specified that will be used as a basis of all new storage nodes. This can be used for setting default file extension. For example, change file format to STL for model nodes:
| |
| − | <pre>
| |
| − | msn=slicer.vtkMRMLModelStorageNode()
| |
| − | msn.SetDefaultWriteFileExtension('stl')
| |
| − | slicer.mrmlScene.AddDefaultNode(msn)
| |
| − | </pre>
| |
| − | | |
| − | == Change file type for saving for all volumes (with already existing storage nodes) ==
| |
| − | <pre>
| |
| − | requiredFileExtension = '.nia'
| |
| − | originalFileExtension = '.nrrd'
| |
| − | volumeNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLScalarVolumeNode')
| |
| − | volumeNodes.UnRegister(slicer.mrmlScene)
| |
| − | volumeNodes.InitTraversal()
| |
| − | volumeNode = volumeNodes.GetNextItemAsObject()
| |
| − | while volumeNode:
| |
| − | volumeStorageNode = volumeNode.GetStorageNode()
| |
| − | if not volumeStorageNode:
| |
| − | volumeStorageNode = volumeNode.CreateDefaultStorageNode()
| |
| − | slicer.mrmlScene.AddNode(volumeStorageNode)
| |
| − | volumeStorageNode.UnRegister(None)
| |
| − | volumeNode.SetAndObserveStorageNodeID(volumeStorageNode.GetID())
| |
| − | volumeStorageNode.SetFileName(volumeNode.GetName()+requiredFileExtension)
| |
| − | else:
| |
| − | volumeStorageNode.SetFileName(volumeStorageNode.GetFileName().replace(originalFileExtension,requiredFileExtension))
| |
| − | volumeNode = volumeNodes.GetNextItemAsObject()
| |
| − | </pre>
| |
| − | | |
| − | == Segmentations ==
| |
| − | | |
| − | For all operations accessing or manupilating the internals of a segmentation will need this import!
| |
| − | <pre>
| |
| − | import vtkSegmentationCorePython as vtkSegmentationCore
| |
| − | </pre>
| |
| − | | |
| − | === Get a segment ===
| |
| − | <pre>
| |
| − | segmentation = segmentationNode.GetSegmentation()
| |
| − | segment = segmentation.GetSegment(segmentID)
| |
| − | </pre>
| |
| − | | |
| − | === Get a representation of a segment ===
| |
| − | <pre>
| |
| − | # Get representation from a single segment. If it does not exist, it will return None
| |
| − | segment.GetRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()) # This gets the binary labelmap, but same idea for all others
| |
| − | | |
| − | # Get representation for a single segment. Convert temporarily for that particular segment if needed. Applies parent transforms by default (if not desired, another argument needs to be added to the end: false)
| |
| − | slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, outputOrientedImageData) # Get labelmap
| |
| − | slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentRepresentation(segmentationNode, segmentID, vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName(), outputPolyData) # Any representation
| |
| − | </pre>
| |
| − | | |
| − | === Convert using default path and conversion parameters ===
| |
| − | <pre>
| |
| − | segmentation.CreateRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()) # This creates binary labelmap, but same idea for all others
| |
| − | </pre>
| |
| − | | |
| − | === Convert using custom path or conversion parameters ===
| |
| − | <pre>
| |
| − | # Custom path
| |
| − | TODO
| |
| − | | |
| − | # Custom conversion parameter
| |
| − | referenceGeometry=vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(referenceImageData)
| |
| − | segmentation.SetConversionParameter(vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), referenceGeometry)
| |
| − | </pre>
| |
