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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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| − | * 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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| − | * Capture all the views save it into a file:
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| − | <pre>
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| − | import ScreenCapture
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| − | cap = ScreenCapture.ScreenCaptureLogic()
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| − | cap.showViewControllers(False)
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| − | cap.captureImageFromView(None,'c:/tmp/test.png')
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| − | cap.showViewControllers(True)
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| − | </pre>
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| − | * Capture a single view:
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| − | <pre>
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| − | viewNodeID = 'vtkMRMLViewNode1'
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| − | import ScreenCapture
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| − | cap = ScreenCapture.ScreenCaptureLogic()
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| − | view = logic.viewFromNode(slicer.mrmlScene.GetNodeByID(viewNodeID))
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| − | cap.captureImageFromView(view,'c:/tmp/test.png')
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| − | </pre>
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| − | Common values for viewNodeID: vtkMRMLSliceNodeRed, vtkMRMLSliceNodeYellow, vtkMRMLSliceNodeGreen, vtkMRMLViewNode1, vtkMRMLViewNode2.
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| − | The ScreenCapture module can also create video animations of rotating views, slice sweeps, etc.
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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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| − | | |
| − | ==Load volume from file==
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| − | When loading a volume from file, it is recommended to set returnNode=True to retrieve the loaded volume node.
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| − | <pre>
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| − | [success, loadedVolumeNode] = slicer.util.loadVolume('c:/Users/abc/Documents/MRHead.nrrd', returnNode=True)
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| − | </pre>
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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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| − | | |
| − | ==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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| − | shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
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| − | rtStructShItemID = shNode.GetItemByDataNode(rtStructNode)
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| − | ctSliceInstanceUids = shNode.GetItemAttribute(rtStructShItemID, '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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| − | | |
| − | === How can I convert DICOM to NRRD on the command line?===
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| − | | |
| − | /Applications/Slicer-4.6.2.app/Contents/MacOS/Slicer --no-main-window --python-code "node=slicer.util.loadVolume('/tmp/series/im0.dcm', returnNode=True)[1]; slicer.util.saveNode(node, '/tmp/output.nrrd'); exit()"
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| − | | |
| − | The same can be done on windows by using the top level Slicer.exe. Be sure to use forward slashes in the pathnames within quotes on the command line.
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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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| − | | |
| − | <pre>
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| − | # Update the sphere from the fiducial points
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| − | def UpdateSphere(param1, param2):
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| − | import math
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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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| − | | |
| − | # Get markup node from scene
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| − | markups=slicer.util.getNode('F')
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| − | sphere = vtk.vtkSphereSource()
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| − | UpdateSphere(0,0)
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| − |
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| − | # Create model node and add to scene
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| − | modelsLogic = slicer.modules.models.logic()
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| − | model = modelsLogic.AddModel(sphere.GetOutput())
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| − | model.GetDisplayNode().SetSliceIntersectionVisibility(True)
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| − | model.GetDisplayNode().SetSliceIntersectionThickness(3)
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| − | model.GetDisplayNode().SetColor(1,1,0)
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| − |
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| − | # Call UpdateSphere whenever the fiducials are changed
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| − | markups.AddObserver("ModifiedEvent", UpdateSphere, 2)
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| − | </pre>
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| − | | |
| − | == Switching to markup fiducial placement mode ==
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| − | | |
| − | To activate a fiducial placement mode, both interaction mode has to be set and a fiducial node has to be selected:
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| − | | |
| − | <pre>
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| − | interactionNode = slicer.app.applicationLogic().GetInteractionNode()
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| − | selectionNode = slicer.app.applicationLogic().GetSelectionNode()
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| − | selectionNode.SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode")
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| − | fiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
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| − | slicer.mrmlScene.AddNode(fiducialNode)
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| − | fiducialNode.CreateDefaultDisplayNodes()
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| − | selectionNode.SetActivePlaceNodeID(fiducialNode.GetID())
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| − | interactionNode.SetCurrentInteractionMode(interactionNode.Place)
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| − | </pre>
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| − | | |
| − | == Show a context menu when a markup point is clicked in a slice or 3D view ==
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| − | | |
| − | <pre>
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| − | | |
| − | # Example actions to perform
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| − | | |
| − | def action1():
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| − | print('Action1 on markup '+str(slicer.clickedMarkupIndex))
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| − | | |
| − | def action2():
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| − | print('Action2 on markup '+str(slicer.clickedMarkupIndex))
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| − | | |
| − | def action3():
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| − | print('Action3 on markup '+str(slicer.clickedMarkupIndex))
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| − | | |
| − | # Clicked markup index is saved here to let the action
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| − | # know which markup needs to be manipulated.
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| − | slicer.clickedMarkupIndex = -1
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| − |
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| − | # Create a simple menu
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| − | | |
| − | menu = qt.QMenu()
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| − | a1 = qt.QAction("Test", slicer.util.mainWindow())
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| − | a1.connect('triggered()', action1)
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| − | menu.addAction(a1)
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| − | a2 = qt.QAction("Action", slicer.util.mainWindow())
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| − | a2.connect('triggered()', action1)
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| − | menu.addAction(a2)
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| − | a3 = qt.QAction("Here", slicer.util.mainWindow())
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| − | a3.connect('triggered()', action1)
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| − | menu.addAction(a3)
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| − | | |
| − | # Add observer to a markup fiducial list
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| − | | |
| − | @vtk.calldata_type(vtk.VTK_INT)
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| − | def markupClickedCallback(caller, eventId, callData):
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| − | slicer.clickedMarkupIndex = callData
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| − | print('Open menu on markup '+str(slicer.clickedMarkupIndex))
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| − | menu.move(qt.QCursor.pos())
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| − | menu.show()
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| − | | |
| − | markupsNode = getNode('F')
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| − | observerTag = markupsNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointClickedEvent, markupClickedCallback)
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| − | | |
| − | </pre>
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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 entire scene as VRML ==
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| − | | |
| − | Save all surface meshes displayed in the scene (models, markups, etc). Solid colors and coloring by scalar is preserved. Textures are not supported.
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| − | | |
| − | <pre>
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| − | exporter = vtk.vtkVRMLExporter()
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| − | exporter.SetRenderWindow(slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow())
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| − | exporter.SetFileName('C:/tmp/something.wrl')
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| − | exporter.Write()
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| − | </pre>
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| − | | |
| − | == Export model to Blender, including color by scalar ==
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| − | | |
| − | <pre>
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| − | modelNode = getNode("Model")
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| − | plyFilePath = "c:/tmp/model.ply"
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| − | | |
| − | modelDisplayNode = modelNode.GetDisplayNode()
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| − | triangles = vtk.vtkTriangleFilter()
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| − | triangles.SetInputConnection(modelDisplayNode.GetOutputPolyDataConnection())
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| − | | |
| − | plyWriter = vtk.vtkPLYWriter()
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| − | plyWriter.SetInputConnection(triangles.GetOutputPort())
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| − | lut = vtk.vtkLookupTable()
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| − | lut.DeepCopy(modelDisplayNode.GetColorNode().GetLookupTable())
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| − | lut.SetRange(modelDisplayNode.GetScalarRange())
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| − | plyWriter.SetLookupTable(lut)
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| − | plyWriter.SetArrayName(modelDisplayNode.GetActiveScalarName())
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| − | | |
| − | plyWriter.SetFileName(plyFilePath)
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| − | plyWriter.Write()
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| − | </pre>
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| − | | |
| − | == Export a fiber tracts to Blender, including color ==
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| − | | |
| − | <pre>
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| − | lineDisplayNode = getNode("*LineDisplay*")
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| − | plyFilePath = "/tmp/fibers.ply"
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| − | | |
| − | tuber = vtk.vtkTubeFilter()
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| − | tuber.SetInputData(lineDisplayNode.GetOutputPolyData())
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| − | tuber.Update()
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| − | tubes = tuber.GetOutput()
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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.SetInputData(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.SetInputData(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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| − | | |
| − | Typically the fastest and simplest way of modifying voxels is by using numpy operators. Voxels can be retrieved in a numpy array using the `array` method and modified using standard numpy methods. For example, threshold a volume:
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| − | | |
| − | <pre>
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| − | nodeName = 'MRHead'
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| − | thresholdValue = 100
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| − | voxelArray = array(nodeName) # get voxels as numpy array
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| − | voxelArray[voxelArray < thresholdValue] = 0 # modify voxel values
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| − | getNode(nodeName).Modified() # at the end of all processing, notify Slicer that the image modification is completed
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| − | </pre>
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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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| − | | |
| − | == Access values in a DTI tensor volume ==
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| − | 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:
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| − | | |
| − | <pre>
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| − | tensors = array('Output DTI Volume')
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| − | </pre>
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| − | | |
| − | Type the following code into the Python window to access all tensor components using vtk commands:
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| − | | |
| − | <pre>
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| − | volumeNode=slicer.util.getNode('Output DTI Volume')
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| − | imageData=volumeNode.GetImageData()
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| − | tensors = imageData.GetPointData().GetTensors()
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| − | 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()
| |
| − | displayNode.AutoWindowLevelOff()
| |
| − | displayNode.SetWindow(50)
| |
| − | displayNode.SetLevel(100)
| |
| − | </pre>
| |
| − | | |
| − | Change color mapping from grayscale to rainbow:
| |
| − | <pre>
| |
| − | 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
| |
| − | 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
| |
| − | logic.GetSliceBounds(bounds)
| |
| − | | |
| − | 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>
| |
| − | | |
| − | == Save the scene into a single MRB file ==
| |
| − | <pre>
| |
| − | # Generate file name
| |
| − | import time
| |
| − | sceneSaveFilename = slicer.app.temporaryPath + "/saved-scene-" + time.strftime("%Y%m%d-%H%M%S") + ".mrb"
| |
| − | | |
| − | # Save scene
| |
| − | if slicer.util.saveScene(sceneSaveFilename):
| |
| − | logging.info("Scene saved to: {0}".format(sceneSaveFilename))
| |
| − | 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 | |
| − | | |
| − | == Disable certain user interactions in slice views ==
| |
| − | | |
| − | For example, disable slice browsing using mouse wheel and keyboard shortcuts in the red slice viewer:
| |
| − | | |
| − | <pre>
| |
| − | interactorStyle = slicer.app.layoutManager().sliceWidget('Red').sliceView().sliceViewInteractorStyle()
| |
| − | interactorStyle.SetActionEnabled(interactorStyle.BrowseSlice, False)
| |
| − | </pre>
| |
| − | | |
| − | Hide all slice view controllers:
| |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | for sliceViewName in lm.sliceViewNames():
| |
| − | lm.sliceWidget(sliceViewName).sliceController().setVisible(False)
| |
| − | </pre>
| |
| − | | |
| − | Hide all 3D view controllers:
| |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | for viewIndex in range(slicer.app.layoutManager().threeDViewCount):
| |
| − | lm.threeDWidget(0).threeDController().setVisible(False)
| |
| − | </pre>
| |
| − | | |
| − | == 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>
| |
| − | import SimpleITK as sitk
| |
| − | import sitkUtils
| |
| − | 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>
| |
| − | | |
| − | == Get DataProbe text ==
| |
| − | | |
| − | You can get the mouse location in pixel coordinates along with the pixel value at the mouse by hitting the '.' (period) key in a slice view after pasting in the following code.
| |
| − | | |
| − | <pre>
| |
| − | def printDataProbe():
| |
| − | infoWidget = slicer.modules.DataProbeInstance.infoWidget
| |
| − | for layer in ('B', 'F', 'L'):
| |
| − | print(infoWidget.layerNames[layer].text, infoWidget.layerIJKs[layer].text, infoWidget.layerValues[layer].text)
| |
| − | | |
| − | s = qt.QShortcut(qt.QKeySequence('.'), mainWindow())
| |
| − | s.connect('activated()', printDataProbe)
| |
| − | </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 ==
| |
| − | | |
| − | === Create a segmentation from a labelmap volume and display in 3D ===
| |
| − | | |
| − | <pre>
| |
| − | labelmapVolumeNode = getNode('label')
| |
| − | seg = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
| |
| − | slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, seg)
| |
| − | seg.CreateClosedSurfaceRepresentation()
| |
| − | slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | The last line is optional. It removes the original labelmap volume so that the same information is not shown twice.
| |
| − | | |
| − | === Show a segmentation in 3D ===
| |
| − | Segmentation can only be shown in 3D if closed surface representation (or other 3D-displayable representation) is available. To create closed surface representation:
| |
| − | <pre>
| |
| − | segmentation.CreateClosedSurfaceRepresentation()
| |
| − | </pre>
| |
| − | | |
| − | === Get a representation of a segment ===
| |
| − | Get binary labelmap, if it does not exist, it will return None:
| |
| − | <pre>
| |
| − | image = segmentationNode.GetBinaryLabelmapRepresentation(segmentID)
| |
| − | </pre>
| |
| − | Get closed surface, if it does not exist, it will return None:
| |
| − | <pre>
| |
| − | polydata = segmentationNode.GetClosedSurfaceRepresentation(segmentID)
| |
| − | </pre>
| |
| − | Get binary labelmap representation. If it does not exist then it will be created for that single segment. Applies parent transforms by default (if not desired, another argument needs to be added to the end: false):
| |
| − | <pre>
| |
| − | import vtkSegmentationCorePython as vtkSegmentationCore
| |
| − | outputOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
| |
| − | slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, outputOrientedImageData)
| |
| − | </pre>
| |
| − | Same as above, for closed surface representation:
| |
| − | <pre>
| |
| − | outputPolyData = vtk.vtkPolyData()
| |
| − | slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentClosedSurfaceRepresentation(segmentationNode, segmentID, outputPolyData)
| |
| − | </pre>
| |
| − | | |
| − | === Convert all segments using default path and conversion parameters ===
| |
| − | <pre>
| |
| − | segmentationNode.CreateBinaryLabelmapRepresentation()
| |
| − | </pre>
| |
| − | | |
| − | === Convert all segments using custom path or conversion parameters ===
| |
| − | Change reference image geometry parameter based on an existing referenceImageData image:
| |
| − | <pre>
| |
| − | import vtkSegmentationCorePython as vtkSegmentationCore
| |
| − | referenceGeometry = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(referenceImageData)
| |
| − | segmentation.SetConversionParameter(vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), referenceGeometry)
| |
| − | </pre>
| |
| − | | |
| − | === Re-convert using a modified conversion parameter ===
| |
| − | Changing smoothing factor for closed surface generation:
| |
| − | <pre>
| |
| − | import vtkSegmentationCorePython as vtkSegmentationCore
| |
| − | segmentation = getNode('Segmentation').GetSegmentation()
| |
| − | | |
| − | # Turn of surface smoothing
| |
| − | segmentation.SetConversionParameter('Smoothing factor','0.0')
| |
| − | | |
| − | # Recreate representation using modified parameters (and default conversion path)
| |
| − | segmentation.RemoveRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName())
| |
| − | segmentation.CreateRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName())
| |
| − | </pre>
| |
| − | | |
| − | === How to run segment editor effects from a script ===
| |
| − | | |
| − | Editor effects are complex because they need to handle changing master volumes, undo/redo, masking operations, etc. Therefore, instead of using a segment editor effect, it is simpler to run the underlying filters directly from script.
| |
| − | | |
| − | This example demonstrates how to run grow from seeds effect in batch mode (without GUI, using qMRMLSegmentEditorWidget):
| |
| − | https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/samples/PythonScripts/SegmentGrowCut/SegmentGrowCutSimple.py
| |
| − | | |
| − | This example demonstrates how to perform grow from seeds using VTK filters:
| |
| − | https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/samples/PythonScripts/SegmentGrowCut/SegmentGrowCut.py
| |
| − | | |
| − | == Accessing views, renderers, and cameras ==
| |
| − | | |
| − | Iterate through all 3D views in current layout:
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | for threeDViewIndex in range(layoutManager.threeDViewCount) :
| |
| − | view = layoutManager.threeDWidget(threeDViewIndex).threeDView()
| |
| − | threeDViewNode = view.mrmlViewNode()
| |
| − | cameraNode = slicer.modules.cameras.logic().GetViewActiveCameraNode(threeDViewNode)
| |
| − | print('View node for 3D widget ' + str(threeDViewIndex))
| |
| − | print(' Name: ' + threeDViewNode .GetName())
| |
| − | print(' ID: ' + threeDViewNode .GetID())
| |
| − | print(' Camera ID: ' + cameraNode.GetID())
| |
| − | </pre>
| |
| − | | |
| − | Iterate through all slice views in current layout:
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | for sliceViewName in layoutManager.sliceViewNames():
| |
| − | view = layoutManager.sliceWidget(sliceViewName).sliceView()
| |
| − | sliceNode = view.mrmlSliceNode()
| |
| − | sliceLogic = slicer.app.applicationLogic().GetSliceLogic(sliceNode)
| |
| − | compositeNode = sliceLogic.GetSliceCompositeNode()
| |
| − | print('Slice view ' + str(sliceViewName))
| |
| − | print(' Name: ' + sliceNode.GetName())
| |
| − | print(' ID: ' + sliceNode.GetID())
| |
| − | print(' Background volume: {0}'.format(compositeNode.GetBackgroundVolumeID()))
| |
| − | print(' Foreground volume: {0} (opacity: {1})'.format(compositeNode.GetForegroundVolumeID(), compositeNode.GetForegroundOpacity()))
| |
| − | print(' Label volume: {0} (opacity: {1})'.format(compositeNode.GetLabelVolumeID(), compositeNode.GetLabelOpacity()))
| |
| − | </pre>
| |
| − | | |
| − | For low-level manipulation of views, it is possible to access VTK render windows, renderers and cameras of views in the current layout.
| |
| − | <pre>
| |
| − | renderWindow = view.renderWindow()
| |
| − | renderers = renderWindow.GetRenderers()
| |
| − | renderer = renderers.GetItemAsObject(0)
| |
| − | camera = cameraNode.GetCamera()
| |
| − | </pre>
| |
| − | | |
| − | == Subject hierarchy ==
| |
| − | ==== Get the pseudo-singleton subject hierarchy node ====
| |
| − | It manages the whole hierarchy and provides functions to access and manipulate
| |
| − | shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
| |
| − | | |
| − | ==== Create subject hierarchy item ====
| |
| − | # If it is for a data node, it is automatically created, but the create function can be used to set parent:
| |
| − | shNode.CreateItem(parentItemID, dataNode)
| |
| − | # If it is a hierarchy item without a data node, then the create function must be used:
| |
| − | shNode.CreateSubjectItem(parentItemID, name)
| |
| − | shNode.CreateFolderItem(parentItemID, name)
| |
| − | shNode.CreateHierarchyItem(parentItemID, name, level) # Advanced method to set level attribute manually (usually subject, study, or folder, but it can be a virtual branch for example)
| |
| − | | |
| − | ==== Get subject hierarchy item ====
| |
| − | Items in subject hierarchy are uniquely identified by integer IDs
| |
| − | # Get scene item ID first because it is the root item:
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| − | sceneItemID = shNode.GetSceneItemID()
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| − | # Get direct child by name
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| − | subjectItemID = shNode.GetItemChildWithName(sceneItemID, 'Subject_1')
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| − | # Get item for data node
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| − | itemID = shNode.GetItemByDataNode(dataNode)
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| − | # Get item by UID (such as DICOM)
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| − | itemID = shNode.GetItemByUID(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(), seriesInstanceUid)
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| − | itemID = shNode.GetItemByUIDList(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMInstanceUIDName(), instanceUID)
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| − | # Invalid item ID for checking validity of a given ID (most functions return the invalid ID when item is not found)
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| − | invalidItemID = slicer.vtkMRMLSubjectHierarchyNode.GetInvalidItemID()
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| − | | |
| − | ==== Traverse children of a subject hierarchy item ====
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| − | children = vtk.vtkIdList()
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| − | shNode.GetItemChildren(parent, children)
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| − | for i in xrange(children.GetNumberOfIds()):
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| − | child = children.GetId(i)
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| − | ...
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| − | | |
| − | ==== Manipulate subject hierarchy item ====
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| − | Instead of node operations on the individual subject hierarchy nodes, item operations are performed on the one subject hierarchy node.
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| − | # Set item name
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| − | shNode.SetItemName(itemID, 'NewName')
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| − | # Set item parent (reparent)
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| − | shNode.SetItemParent(itemID, newParentItemID)
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| − | # Set visibility of data nodes associated to items in a branch (or a leaf item)
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| − | shNode.SetDisplayVisibilityForBranch(itemID, 1)
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| − | | |
| − | ==== Filter nodes in TreeView or ComboBox ====
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| − | Subject hierarchy module [https://github.com/Slicer/Slicer/tree/master/Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins provides] Qt Designer plugins for qMRMLSubjectHierarchyTreeView or qMRMLSubjectHierarchyComboBox.
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| − | TreeView can be used to display subject hierarchy and ComboBox to select nodes from the hierarchy. Displayed nodes can be filtered using ''setAttributeFilter'' method. An example of the usage can be found in the [https://github.com/Slicer/Slicer/blob/e66e3b08e35384526528e6ae678e9ec9f079f286/Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py#L352-L360 unit test]. Modified version here:
| |
| − | print shTreeView.displayedItemCount() # 5
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| − | shTreeView.setAttributeFilter('DICOM.Modality') # Nodes must have this attribute
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| − | print shTreeView.displayedItemCount() # 3
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| − | shTreeView.setAttributeFilter('DICOM.Modality','CT') # Have attribute and equal 'CT'
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| − | print shTreeView.displayedItemCount() # 1
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| − | shTreeView.removeAttributeFilter()
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| − | print shTreeView.displayedItemCount() # 5
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