Documentation/Nightly/ScriptRepository
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Contents
- 1 Community-contributed modules
- 2 Community-contributed examples
- 2.1 Capture
- 2.2 Launching Slicer
- 2.3 Load volume from file
- 2.4 Show volume rendering automatically when a volume is loaded
- 2.5 DICOM
- 2.5.1 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:
- 2.5.2 How to access tag of a volume loaded from DICOM? For example, get the patient position stored in a volume:
- 2.5.3 How to access tag of an item in the Subject Hierachy tree? For example, get the content time tag of a structure set:
- 2.5.4 How to get path and filename of a loaded DICOM volume?
- 2.5.5 How can I convert DICOM to NRRD on the command line?
- 2.5.6 Export a volume to DICOM file format
- 2.6 Toolbar functions
- 2.7 Manipulating objects in the slice viewer
- 2.8 Set slice position and orientation from 3 markup fiducials
- 2.9 Switching to markup fiducial placement mode
- 2.10 Get a notification if a markup point position is modified
- 2.11 Get a notification if a transform is modified
- 2.12 Show a context menu when a markup point is clicked in a slice or 3D view
- 2.13 Add a texture mapped plane to the scene as a model
- 2.14 Export entire scene as VRML
- 2.15 Export model to Blender, including color by scalar
- 2.16 Export a tract (FiberBundle) to Blender, including color
- 2.17 Iterate over tract (FiberBundle) streamline points
- 2.18 Clone a node
- 2.19 Clone a volume
- 2.20 Create a new volume
- 2.21 Modify voxels in a volume
- 2.22 Get volume voxel coordinates from markup fiducial RAS coordinates
- 2.23 Get markup fiducial RAS coordinates from volume voxel coordinates
- 2.24 Get the values of all voxels for a label value
- 2.25 Access values in a DTI tensor volume
- 2.26 Change window/level (brightness/contrast) or colormap of a volume
- 2.27 Create custom color table
- 2.28 Manipulate a Slice View
- 2.29 Synchronize zoom factor between slice views
- 2.30 Show a volume in slice views
- 2.31 Change opacity of foreground volume in slice views
- 2.32 Fit slice plane to markup fiducials
- 2.33 Save a series of images from a Slice View
- 2.34 Save the scene into a new directory
- 2.35 Save the scene into a single MRB file
- 2.36 Save a node to file
- 2.37 Center the 3D View on the Scene
- 2.38 Rotate the 3D View
- 2.39 Display text in a 3D view or slice view
- 2.40 Hide slice view annotations (DataProbe)
- 2.41 Turning off interpolation
- 2.42 Customize viewer layout
- 2.43 Customize keyboard shortcuts
- 2.44 Disable certain user interactions in slice views
- 2.45 Change default slice view orientation
- 2.46 Set all slice views linked by default
- 2.47 Set up custom units in slice view ruler
- 2.48 Show a slice view outside the view layout
- 2.49 Running an ITK filter in Python using SimpleITK
- 2.50 Get current mouse coordinates in a slice view
- 2.51 Get DataProbe text
- 2.52 Thick slab reconstruction and maximum/minimum intensity volume projections
- 2.53 Change default file type for nodes (that have never been saved yet)
- 2.54 Change file type for saving for all volumes (with already existing storage nodes)
- 2.55 Segmentations
- 2.55.1 Create a segmentation from a labelmap volume and display in 3D
- 2.55.2 Export labelmap node from segmentation node
- 2.55.3 Export model nodes from segmentation node
- 2.55.4 Show a segmentation in 3D
- 2.55.5 Get a representation of a segment
- 2.55.6 Convert all segments using default path and conversion parameters
- 2.55.7 Convert all segments using custom path or conversion parameters
- 2.55.8 Re-convert using a modified conversion parameter
- 2.55.9 Get centroid of a segment in world (RAS) coordinates
- 2.55.10 How to run segment editor effects from a script
- 2.56 Accessing views, renderers, and cameras
- 2.57 Change 3D view background color
- 2.58 Subject hierarchy
- 2.58.1 Get the pseudo-singleton subject hierarchy node
- 2.58.2 Create subject hierarchy item
- 2.58.3 Get subject hierarchy item
- 2.58.4 Traverse children of a subject hierarchy item
- 2.58.5 Manipulate subject hierarchy item
- 2.58.6 Filter items in TreeView or ComboBox
- 2.58.7 Listen to subject hierarchy item events
- 2.59 Plotting
- 2.60 Execute external applications
Community-contributed modules
The examples in this section are Scripted Modules that provide a user interface in the module panel along with specialized implementation logic.
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
- VolumeMasker.py: Update a target volume with the results of setting all input volume voxels to 0 except for those that correspond to a selected label value in an input label map (Used for example in the volume rendering in [https://www.youtube.com/watch?v=dfu2gugHLHs this video).
DICOM
- dicom header browser to easily scroll through dicom files using dcmdump.
- SlicerRT batch processing to batch convert RT structure sets to labelmap NRRD files.
Informatics
- MarkupsInfo.py: Compute the total length between all the points of a markup list.
- LineProfile.py: Compute intensity profile in a volume along a line.
Community-contributed examples
Usage: Copy-paste the shown code lines or linked .py file contents into Python console in Slicer. Or save them to a file and run them using execfile.
Capture
- 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')
- Capture all the views save it into a file:
import ScreenCapture cap = ScreenCapture.ScreenCaptureLogic() cap.showViewControllers(False) cap.captureImageFromView(None,'c:/tmp/test.png') cap.showViewControllers(True)
- Capture a single view:
viewNodeID = 'vtkMRMLViewNode1' import ScreenCapture cap = ScreenCapture.ScreenCaptureLogic() view = cap.viewFromNode(slicer.mrmlScene.GetNodeByID(viewNodeID)) cap.captureImageFromView(view,'c:/tmp/test.png')
Common values for viewNodeID: vtkMRMLSliceNodeRed, vtkMRMLSliceNodeYellow, vtkMRMLSliceNodeGreen, vtkMRMLViewNode1, vtkMRMLViewNode2. The ScreenCapture module can also create video animations of rotating views, slice sweeps, etc.
- Capture a slice view sweep into a series of PNG files - for example, Red slice view, 30 images, from position -125.0 to 75.0, into c:/tmp folder, with name image_00001.png, image_00002.png, ...
import ScreenCapture ScreenCapture.ScreenCaptureLogic().captureSliceSweep(getNode('vtkMRMLSliceNodeRed'), -125.0, 75.0, 30, "c:/tmp", "image_%05d.png")
- Capture 3D view into PNG file with transparent background
renderWindow = slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow() renderWindow.SetAlphaBitPlanes(1) wti = vtk.vtkWindowToImageFilter() wti.SetInputBufferTypeToRGBA() wti.SetInput(renderWindow) writer = vtk.vtkPNGWriter() writer.SetFileName("c:/tmp/screenshot.png") writer.SetInputConnection(wti.GetOutputPort()) writer.Write()
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
Load volume from file
When loading a volume from file, it is recommended to set returnNode=True to retrieve the loaded volume node.
[success, loadedVolumeNode] = slicer.util.loadVolume('c:/Users/abc/Documents/MRHead.nrrd', returnNode=True)
- 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()
Show volume rendering automatically when a volume is loaded
To show volume rendering of a volume automatically when it is loaded, add the lines below to your .slicerrc file.
@vtk.calldata_type(vtk.VTK_OBJECT) def onNodeAdded(caller, event, calldata): node = calldata if isinstance(node, slicer.vtkMRMLVolumeNode): # Call showVolumeRendering using a timer instead of calling it directly # to allow the volume loading to fully complete. qt.QTimer.singleShot(0, lambda: showVolumeRendering(node)) def showVolumeRendering(volumeNode): print("Show volume rendering of node "+volumeNode.GetName()) volRenLogic = slicer.modules.volumerendering.logic() displayNode = volRenLogic.CreateDefaultVolumeRenderingNodes(volumeNode) displayNode.SetVisibility(True) scalarRange = volumeNode.GetImageData().GetScalarRange() if scalarRange[1]-scalarRange[0] < 1500: # small dynamic range, probably MRI displayNode.GetVolumePropertyNode().Copy(volRenLogic.GetPresetByName('MR-Default')) else: # larger dynamic range, probably CT displayNode.GetVolumePropertyNode().Copy(volRenLogic.GetPresetByName('CT-Chest-Contrast-Enhanced')) slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent, onNodeAdded)
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) shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene) rtStructShItemID = shNode.GetItemByDataNode(rtStructNode) ctSliceInstanceUids = shNode.GetItemAttribute(rtStructShItemID, 'DICOM.ReferencedInstanceUIDs').split() filename = slicer.dicomDatabase.fileForInstance(ctSliceInstanceUids[0]) print slicer.dicomDatabase.fileValue(filename,'0008,0033')
How to get path and filename of a loaded DICOM volume?
def pathFromNode(node): storageNode=node.GetStorageNode() if storageNode is not None: # loaded via drag-drop filepath=storageNode.GetFullNameFromFileName() else: # loaded via DICOM browser instanceUIDs=node.GetAttribute('DICOM.instanceUIDs').split() filepath=slicer.dicomDatabase.fileForInstance(instUids[0]) return filepath # example: node=slicer.util.getNode('volume1') path=self.pathFromNode(node) print("DICOM path=%s" % path)
How can I convert DICOM to NRRD on the command line?
/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()"
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.
Export a volume to DICOM file format
volumeNode = getNode('CTChest') outputFolder = "c:/tmp/dicom-output" # Create patient and study and put the volume under the study shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene) patientItemID = shNode.CreateSubjectItem(shNode.GetSceneItemID(), "test patient") studyItemID = shNode.CreateStudyItem(patientItemID, "test study") volumeShItemID = shNode.GetItemByDataNode(volumeNode) shNode.SetItemParent(volumeShItemID, studyItemID) import DICOMScalarVolumePlugin exporter = DICOMScalarVolumePlugin.DICOMScalarVolumePluginClass() exportables = exporter.examineForExport(volumeShItemID) for exp in exportables: exp.directory = outputFolder exporter.export(exportables)
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): import math 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 markup node from scene markups=slicer.util.getNode('F') sphere = vtk.vtkSphereSource() UpdateSphere(0,0) # Create model node and add to scene modelsLogic = slicer.modules.models.logic() model = modelsLogic.AddModel(sphere.GetOutput()) model.GetDisplayNode().SetSliceIntersectionVisibility(True) model.GetDisplayNode().SetSliceIntersectionThickness(3) model.GetDisplayNode().SetColor(1,1,0) # Call UpdateSphere whenever the fiducials are changed markups.AddObserver("ModifiedEvent", UpdateSphere, 2)
Set slice position and orientation from 3 markup fiducials
Drop 3 markup points in the scene and copy-paste the code below into the Python console. After this, as you move the markups you’ll see the red slice view position and orientation will be set to make it fit to the 3 points.
# Update plane from fiducial points def UpdateSlicePlane(param1=None, param2=None): # Get point positions as numpy array import numpy as np nOfFiduciallPoints = markups.GetNumberOfFiducials() if nOfFiduciallPoints < 3: return # not enough points points = np.zeros([3,nOfFiduciallPoints]) for i in range(0, nOfFiduciallPoints): markups.GetNthFiducialPosition(i, points[:,i]) # Compute plane position and normal planePosition = points.mean(axis=1) planeNormal = np.cross(points[:,1] - points[:,0], points[:,2] - points[:,0]) planeX = points[:,1] - points[:,0] sliceNode.SetSliceToRASByNTP(planeNormal[0], planeNormal[1], planeNormal[2], planeX[0], planeX[1], planeX[2], planePosition[0], planePosition[1], planePosition[2], 0) # Get markup node from scene sliceNode = slicer.app.layoutManager().sliceWidget('Red').mrmlSliceNode() markups = slicer.util.getNode('F') # Update slice plane manually UpdateSlicePlane() # Update slice plane automatically whenever points are changed markupObservation = [markups, markups.AddObserver("ModifiedEvent", UpdateSlicePlane, 2)]
To stop automatic updates, run this:
markupObservation[0].RemoveObserver(markupObservation[1])
Switching to markup fiducial placement mode
To activate a fiducial placement mode, both interaction mode has to be set and a fiducial node has to be selected:
interactionNode = slicer.app.applicationLogic().GetInteractionNode() selectionNode = slicer.app.applicationLogic().GetSelectionNode() selectionNode.SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode") fiducialNode = slicer.vtkMRMLMarkupsFiducialNode() slicer.mrmlScene.AddNode(fiducialNode) fiducialNode.CreateDefaultDisplayNodes() selectionNode.SetActivePlaceNodeID(fiducialNode.GetID()) interactionNode.SetCurrentInteractionMode(interactionNode.Place)
Get a notification if a markup point position is modified
def onMarkupsNodeModified(markupsNode, unusedArg2=None, unusedArg3=None): sliceView = markupsNode.GetAttribute('Markups.MovingInSliceView') if not sliceView: print("Markup list was modified") return movingMarkupIndex = markupsNode.GetAttribute('Markups.MovingMarkupIndex') pos = [0,0,0] markupsNode.GetNthFiducialPosition(int(movingMarkupIndex), pos) print("Markup {0} was moved in slice view {1} to {2}".format(movingMarkupIndex, sliceView, pos)) markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode") markupsNode.CreateDefaultDisplayNodes() markupsNode.AddFiducial(0,0,0) markupsNode.AddObserver(vtk.vtkCommand.ModifiedEvent, onMarkupsNodeModified)
Get a notification if a transform is modified
def onTransformNodeModified(transformNode, unusedArg2=None, unusedArg3=None): transformMatrix = vtk.vtkMatrix4x4() transformNode.GetMatrixTransformToWorld(transformMatrix) print("Position: [{0}, {1}, {2}]".format(transformMatrix.GetElement(0,3), transformMatrix.GetElement(1,3), transformMatrix.GetElement(2,3))) transformNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTransformNode") transformNode.AddObserver(slicer.vtkMRMLTransformNode.TransformModifiedEvent, onTransformNodeModified)
# Example actions to perform def action1(): print('Action1 on markup '+str(slicer.clickedMarkupIndex)) def action2(): print('Action2 on markup '+str(slicer.clickedMarkupIndex)) def action3(): print('Action3 on markup '+str(slicer.clickedMarkupIndex)) # Clicked markup index is saved here to let the action # know which markup needs to be manipulated. slicer.clickedMarkupIndex = -1 # Create a simple menu menu = qt.QMenu() a1 = qt.QAction("Test", slicer.util.mainWindow()) a1.connect('triggered()', action1) menu.addAction(a1) a2 = qt.QAction("Action", slicer.util.mainWindow()) a2.connect('triggered()', action1) menu.addAction(a2) a3 = qt.QAction("Here", slicer.util.mainWindow()) a3.connect('triggered()', action1) menu.addAction(a3) # Add observer to a markup fiducial list @vtk.calldata_type(vtk.VTK_INT) def markupClickedCallback(caller, eventId, callData): slicer.clickedMarkupIndex = callData print('Open menu on markup '+str(slicer.clickedMarkupIndex)) menu.move(qt.QCursor.pos()) menu.show() markupsNode = getNode('F') observerTag = markupsNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointClickedEvent, markupClickedCallback)
Add a texture mapped plane to the scene as a model
Note that model textures are not exposed in the GUI and are not saved in the scene
# use dummy image data here e = vtk.vtkImageEllipsoidSource() scene = slicer.mrmlScene # Create model node model = slicer.vtkMRMLModelNode() model.SetScene(scene) model.SetName(scene.GenerateUniqueName("2DImageModel")) planeSource = vtk.vtkPlaneSource() model.SetAndObservePolyData(planeSource.GetOutput()) # Create display node modelDisplay = slicer.vtkMRMLModelDisplayNode() modelDisplay.SetColor(1,1,0) # yellow modelDisplay.SetBackfaceCulling(0) modelDisplay.SetScene(scene) scene.AddNode(modelDisplay) model.SetAndObserveDisplayNodeID(modelDisplay.GetID()) # Add to scene modelDisplay.SetAndObserveTextureImageData(e.GetOutput()) scene.AddNode(model) transform = slicer.vtkMRMLLinearTransformNode() scene.AddNode(transform) model.SetAndObserveTransformNodeID(transform.GetID()) vTransform = vtk.vtkTransform() vTransform.Scale(50,50,50) vTransform.RotateX(30) transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
Export entire scene as VRML
Save all surface meshes displayed in the scene (models, markups, etc). Solid colors and coloring by scalar is preserved. Textures are not supported.
exporter = vtk.vtkVRMLExporter() exporter.SetRenderWindow(slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow()) exporter.SetFileName('C:/tmp/something.wrl') exporter.Write()
Export model to Blender, including color by scalar
modelNode = getNode("Model") plyFilePath = "c:/tmp/model.ply" modelDisplayNode = modelNode.GetDisplayNode() triangles = vtk.vtkTriangleFilter() triangles.SetInputConnection(modelDisplayNode.GetOutputPolyDataConnection()) plyWriter = vtk.vtkPLYWriter() plyWriter.SetInputConnection(triangles.GetOutputPort()) lut = vtk.vtkLookupTable() lut.DeepCopy(modelDisplayNode.GetColorNode().GetLookupTable()) lut.SetRange(modelDisplayNode.GetScalarRange()) plyWriter.SetLookupTable(lut) plyWriter.SetArrayName(modelDisplayNode.GetActiveScalarName()) plyWriter.SetFileName(plyFilePath) plyWriter.Write()
Export a tract (FiberBundle) to Blender, including color
Note: an interactive version of this script is now included in the SlicerDMRI extension (module code). After installing SlicerDMRI, go to Modules -> Diffusion -> Import and Export -> Export tractography to PLY (mesh).
The example below shows how to export a tractography "FiberBundleNode" to a PLY file:
lineDisplayNode = getNode("*LineDisplay*") plyFilePath = "/tmp/fibers.ply" tuber = vtk.vtkTubeFilter() tuber.SetInputData(lineDisplayNode.GetOutputPolyData()) tuber.Update() tubes = tuber.GetOutputDataObject(0) scalars = tubes.GetPointData().GetArray(0) scalars.SetName("scalars") triangles = vtk.vtkTriangleFilter() triangles.SetInputData(tubes) triangles.Update() colorNode = lineDisplayNode.GetColorNode() lookupTable = vtk.vtkLookupTable() lookupTable.DeepCopy(colorNode.GetLookupTable()) lookupTable.SetTableRange(0,1) plyWriter = vtk.vtkPLYWriter() plyWriter.SetInputData(triangles.GetOutput()) plyWriter.SetLookupTable(lookupTable) plyWriter.SetArrayName("scalars") plyWriter.SetFileName(plyFilePath) plyWriter.Write()
Iterate over tract (FiberBundle) streamline points
This example shows how to access the points in each line of a FiberBundle as a numpy array (view).
from vtk.util.numpy_support import vtk_to_numpy fb = getNode("FiberBundle_F") # <- fill in node ID here # get point data as 1d array points = slicer.util.arrayFromModelPoints(fb) # get line cell ids as 1d array line_ids = vtk_to_numpy(fb.GetPolyData().GetLines().GetData()) # VTK cell ids are stored as # [ N0 c0_id0 ... c0_id0 # N1 c1_id0 ... c1_idN1 ] # so we need to # - read point count for each line (cell) # - grab the ids in that range from `line_ids` array defined above # - index the `points` array by those ids cur_idx = 1 for _ in range(pd.GetLines().GetNumberOfCells()): # - read point count for this line (cell) count = lines[cur_idx - 1] # - grab the ids in that range from `lines` index_array = line_ids[ cur_idx : cur_idx + count] # update to the next range cur_idx += count + 1 # - index the point array by those ids line_points = points[index_array] # do work here
Clone a node
This example shows how to make a copy of any node that appears in Subject Hierarchy (in Data module).
# Get a node from SampleData that we will clone import SampleData nodeToClone = SampleData.SampleDataLogic().downloadMRHead() # Clone the node shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene) itemIDToClone = shNode.GetItemByDataNode(nodeToClone) clonedItemID = slicer.modules.subjecthierarchy.logic().CloneSubjectHierarchyItem(shNode, itemIDToClone) clonedNode = shNode.GetItemDataNode(clonedItemID)
Clone a volume
This example shows how to clone the MRHead sample volume, including its pixel data and display settings.
sourceVolumeNode = slicer.util.getNode('MRHead') volumesLogic = slicer.modules.volumes.logic() clonedVolumeNode = volumesLogic.CloneVolume(slicer.mrmlScene, sourceVolumeNode, 'Cloned volume')
Create a new volume
This example shows how to create a new empty volume.
nodeName = "MyNewVolume" imageSize = [512, 512, 512] voxelType=vtk.VTK_UNSIGNED_CHAR imageOrigin = [0.0, 0.0, 0.0] imageSpacing = [1.0, 1.0, 1.0] imageDirections = [[1,0,0], [0,1,0], [0,0,1]] fillVoxelValue = 0 # Create an empty image volume, filled with fillVoxelValue imageData = vtk.vtkImageData() imageData.SetDimensions(imageSize) imageData.AllocateScalars(voxelType, 1) thresholder = vtk.vtkImageThreshold() thresholder.SetInputData(imageData) thresholder.SetInValue(fillVoxelValue) thresholder.SetOutValue(fillVoxelValue) thresholder.Update() # Create volume node volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", nodeName) volumeNode.SetOrigin(imageOrigin) volumeNode.SetSpacing(imageSpacing) volumeNode.SetIJKToRASDirections(imageDirections) volumeNode.SetAndObserveImageData(thresholder.GetOutput()) volumeNode.CreateDefaultDisplayNodes() volumeNode.CreateDefaultStorageNode()
Modify voxels in a volume
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:
nodeName = 'MRHead' thresholdValue = 100 voxelArray = array(nodeName) # get voxels as numpy array voxelArray[voxelArray < thresholdValue] = 0 # modify voxel values getNode(nodeName).Modified() # at the end of all processing, notify Slicer that the image modification is completed
This example shows how to change voxels values of the MRHead sample volume. The values will be computed by function f(r,a,s,) = (r-10)*(r-10)+(a+15)*(a+15)+s*s.
volumeNode=slicer.util.getNode('MRHead') ijkToRas = vtk.vtkMatrix4x4() volumeNode.GetIJKToRASMatrix(ijkToRas) imageData=volumeNode.GetImageData() extent = imageData.GetExtent() for k in xrange(extent[4], extent[5]+1): for j in xrange(extent[2], extent[3]+1): for i in xrange(extent[0], extent[1]+1): position_Ijk=[i, j, k, 1] position_Ras=ijkToRas.MultiplyPoint(position_Ijk) r=position_Ras[0] a=position_Ras[1] s=position_Ras[2] functionValue=(r-10)*(r-10)+(a+15)*(a+15)+s*s imageData.SetScalarComponentFromDouble(i,j,k,0,functionValue) imageData.SetScalarComponentFromFloat(distortionVectorPosition_Ijk[0], distortionVectorPosition_Ijk[1], distortionVectorPosition_Ijk[2], 0, fillValue) imageData.Modified()
Get volume voxel coordinates from markup fiducial RAS coordinates
This example shows how to get voxel coordinate of a volume corresponding to a markup fiducial point position.
# Inputs volumeNode = getNode('MRHead') markupsNode = getNode('F') markupsIndex = 0 # Get point coordinate in RAS point_Ras = [0, 0, 0, 1] markupsNode.GetNthFiducialWorldCoordinates(markupsIndex, point_Ras) # If volume node is transformed, apply that transform to get volume's RAS coordinates transformRasToVolumeRas = vtk.vtkGeneralTransform() slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(None, volumeNode.GetParentTransformNode(), transformRasToVolumeRas) point_VolumeRas = transformRasToVolumeRas.TransformPoint(point_Ras[0:3]) # Get voxel coordinates from physical coordinates volumeRasToIjk = vtk.vtkMatrix4x4() volumeNode.GetRASToIJKMatrix(volumeRasToIjk) point_Ijk = [0, 0, 0, 1] volumeRasToIjk.MultiplyPoint(np.append(point_VolumeRas,1.0), point_Ijk) point_Ijk = [ int(round(c)) for c in point_Ijk[0:3] ] # Print output print(point_Ijk)
Get markup fiducial RAS coordinates from volume voxel coordinates
This example shows how to get position of maximum intensity voxel of a volume (determined by numpy, in IJK coordinates) in RAS coordinates so that it can be marked with a markup fiducial.
# Inputs volumeNode = getNode('MRHead') markupsNode = getNode('F') # Get voxel position in IJK coordinate system import numpy as np volumeArray = slicer.util.arrayFromVolume(volumeNode) # Get position of highest voxel value point_Kji = np.where(volumeArray == volumeArray.max()) point_Ijk = [point_Kji[2][0], point_Kji[1][0], point_Kji[0][0]] # Get physical coordinates from voxel coordinates volumeIjkToRas = vtk.vtkMatrix4x4() volumeNode.GetIJKToRASMatrix(volumeIjkToRas) point_VolumeRas = [0, 0, 0, 1] volumeIjkToRas.MultiplyPoint(np.append(point_Ijk,1.0), point_VolumeRas) # If volume node is transformed, apply that transform to get volume's RAS coordinates transformVolumeRasToRas = vtk.vtkGeneralTransform() slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(volumeNode.GetParentTransformNode(), None, transformVolumeRasToRas) point_Ras = transformVolumeRasToRas.TransformPoint(point_VolumeRas[0:3]) # Add a markup at the computed position and print its coordinates markupsNode.AddFiducial(point_Ras[0], point_Ras[1], point_Ras[2], "max") print(point_Ras)
Get the values of all voxels for a label value
If you have a background image called ‘Volume’ and a mask called ‘Volume-label’ created with the Editor you could do something like this:
import numpy volume = array(‘Volume’) label = array(‘Volume-label’) points = numpy.where( label == 1 ) # or use another label number depending on what you segmented values = volume[points] # this will be a list of the label values values.mean() # should match the mean value of LabelStatistics calculation as a double-check numpy.savetxt(‘values.txt’, values)
Access values in a DTI tensor volume
This example shows how to access individual tensors at the voxel level.
First load your DWI volume and estimate tensors to produce a DTI volume called ‘Output DTI Volume’
Then open the python window: View->Python interactor
Use this command to access tensors through numpy:
tensors = array('Output DTI Volume')
Type the following code into the Python window to access all tensor components using vtk commands:
volumeNode=slicer.util.getNode('Output DTI Volume') imageData=volumeNode.GetImageData() tensors = imageData.GetPointData().GetTensors() extent = imageData.GetExtent() idx = 0 for k in xrange(extent[4], extent[5]+1): for j in xrange(extent[2], extent[3]+1): for i in xrange(extent[0], extent[1]+1): tensors.GetTuple9(idx) idx += 1
Change window/level (brightness/contrast) or colormap of a volume
This example shows how to change window/level of the MRHead sample volume.
volumeNode = getNode('MRHead') displayNode = volumeNode.GetDisplayNode() displayNode.AutoWindowLevelOff() displayNode.SetWindow(50) displayNode.SetLevel(100)
Change color mapping from grayscale to rainbow:
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeRainbow')
Create custom color table
This example shows how to create a new color table, for example with inverted color range from the default Ocean color table.
invertedocean = slicer.vtkMRMLColorTableNode() invertedocean.SetTypeToUser() invertedocean.SetNumberOfColors(256) invertedocean.SetName("InvertedOcean") for i in range(0,255): invertedocean.SetColor(i, 0.0, 1 - (i+1e-16)/255.0, 1.0, 1.0) slicer.mrmlScene.AddNode(invertedocean)
Manipulate a Slice View
Change the slice offset
Equivalent to moving the slider in slice view controller.
layoutManager = slicer.app.layoutManager() red = layoutManager.sliceWidget('Red') redLogic = red.sliceLogic() # Print current slice offset position print redLogic.GetSliceOffset() # Change slice position redLogic.SetSliceOffset(20)
Show slice views in 3D window
Equivalent to clicking 'eye' icon in the slice view controller.
layoutManager = slicer.app.layoutManager() for sliceViewName in layoutManager.sliceViewNames(): controller = layoutManager.sliceWidget(sliceViewName).sliceController() controller.setSliceVisible(True)
Reset field of view to show background volume maximized
Equivalent to click small rectangle button ("Adjust the slice viewer's field of view...") in the slice view controller.
slicer.util.resetSliceViews()
Rotate slice views to volume plane
Aligns slice views to volume axes, shows original image acquisition planes in slice views.
volumeNode = slicer.util.getNode('MRHead') layoutManager = slicer.app.layoutManager() for sliceViewName in layoutManager.sliceViewNames(): layoutManager.sliceWidget(sliceViewName).mrmlSliceNode().RotateToVolumePlane(volumeNode)
Iterate over current visible slice views, and set foreground and background images
slicer.util.setSliceViewerLayers(background=mrVolume, foreground=ctVolume)
Internally, this method performs something like this:
for sliceViewName in layoutManager.sliceViewNames(): sliceWidget = layoutManager.sliceWidget(sliceViewName) # setup background volume compositeNode.SetBackgroundVolumeID(mrVolume.GetID()) # setup foreground volume compositeNode.SetForegroundVolumeID(ctVolume.GetID()) # change opacity compositeNode.SetForegroundOpacity(0.3)
Synchronize zoom factor between slice views
slicer.sliceNodes = [slicer.app.layoutManager().sliceWidget(viewName).mrmlSliceNode() for viewName in slicer.app.layoutManager().sliceViewNames()] slicer.updatingSliceNodes = False def sliceModified(caller, event): if slicer.updatingSliceNodes: # prevent infinite loop of slice node updates triggering slice node updates return slicer.updatingSliceNodes = True fov = caller.GetFieldOfView() for sliceNode in slicer.sliceNodes: if sliceNode != caller: sliceNode.SetFieldOfView(*fov) slicer.updatingSliceNodes = False for sliceNode in slicer.sliceNodes: sliceNode.AddObserver(vtk.vtkCommand.ModifiedEvent, sliceModified)
Show a volume in slice views
Recommended:
volumeNode = slicer.util.getNode('YourVolumeNode') slicer.util.setSliceViewerLayers(background=volumeNode)
or
Show volume in all visible views where volume selection propagation is enabled:
volumeNode = slicer.util.getNode('YourVolumeNode') applicationLogic = slicer.app.applicationLogic() selectionNode = applicationLogic.GetSelectionNode() selectionNode.SetSecondaryVolumeID(volumeNode.GetID()) applicationLogic.PropagateForegroundVolumeSelection(0)
or
Show volume in selected views:
n = slicer.util.getNode('YourVolumeNode') for color in ['Red', 'Yellow', 'Green']: slicer.app.layoutManager().sliceWidget(color).sliceLogic().GetSliceCompositeNode().SetForegroundVolumeID(n.GetID())
Change opacity of foreground volume in slice views
slicer.util.setSliceViewerLayers(foregroundOpacity=0.4)
or
Change opacity in a selected view
lm = slicer.app.layoutManager() sliceLogic = lm.sliceWidget('Red').sliceLogic() compositeNode = sliceLogic.GetSliceCompositeNode() compositeNode.SetForegroundOpacity(0.4)
Fit slice plane to markup fiducials
sliceNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSliceNodeRed") markupsNode = slicer.mrmlScene.GetFirstNodeByName("F") # Get markup point positions as numpy arrays import numpy as np p1 = np.array([0,0,0]) p2 = np.array([0,0,0]) p3 = np.array([0,0,0]) markupsNode.GetNthFiducialPosition(0, p1) markupsNode.GetNthFiducialPosition(1, p2) markupsNode.GetNthFiducialPosition(2, p3) # Get plane axis directions n = np.cross(p2-p1, p2-p3) # plane normal direction n = n/np.linalg.norm(n) t = np.cross([0, 0, 1], n) # plane transverse direction t = t/np.linalg.norm(t) # Set slice plane orientation and position sliceNode.SetSliceToRASByNTP(n[0], n[1], n[2], t[0], t[1], t[2], p1[0], p1[1], p1[2], 0)
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')"
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)
Save the scene into a new directory
# 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")
Save the scene into a single MRB file
# 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")
Save a node to file
Save a transform node to file (should work with any other node type, if file extension is set to a supported one):
myNode = getNode("LinearTransform_3") myStorageNode = myNode.CreateDefaultStorageNode() myStorageNode.SetFileName("c:/tmp/something.tfm") myStorageNode.WriteData(myNode)
Center the 3D View on the Scene
layoutManager = slicer.app.layoutManager() threeDWidget = layoutManager.threeDWidget(0) threeDView = threeDWidget.threeDView() threeDView.resetFocalPoint()
Rotate the 3D View
layoutManager = slicer.app.layoutManager() threeDWidget = layoutManager.threeDWidget(0) threeDView = threeDWidget.threeDView() threeDView.yaw()
Display text in a 3D view or slice view
The easiest way to show information overlaid on a viewer is to use corner annotations.
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()
Hide slice view annotations (DataProbe)
# Disable slice annotations immediately slicer.modules.DataProbeInstance.infoWidget.sliceAnnotations.sliceViewAnnotationsEnabled=False slicer.modules.DataProbeInstance.infoWidget.sliceAnnotations.updateSliceViewFromGUI() # Disable slice annotations persistently (after Slicer restarts) settings = qt.QSettings() settings.setValue('DataProbe/sliceViewAnnotations.enabled', 0)
Turning off interpolation
You can turn off interpolation for newly loaded volumes with this script from Steve Pieper.
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)
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:
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)
See description of standard layouts (that can be used as examples) here: https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx
Customize keyboard shortcuts
Keyboard shortcuts can be specified for activating any Slicer feature by adding a couple of lines to your .slicerrc file.
For example, this script registers Ctrl+b, Ctrl+n, Ctrl+m, Ctrl+, keyboard shortcuts to switch between red, yellow, green, and 4-up view layouts.
shortcuts = [ ('Ctrl+b', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)), ('Ctrl+n', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpYellowSliceView)), ('Ctrl+m', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpGreenSliceView)), ('Ctrl+,', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)) ] for (shortcutKey, callback) in shortcuts: shortcut = qt.QShortcut(slicer.util.mainWindow()) shortcut.setKey(qt.QKeySequence(shortcutKey)) shortcut.connect( 'activated()', callback)
Disable certain user interactions in slice views
For example, disable slice browsing using mouse wheel and keyboard shortcuts in the red slice viewer:
interactorStyle = slicer.app.layoutManager().sliceWidget('Red').sliceView().sliceViewInteractorStyle() interactorStyle.SetActionEnabled(interactorStyle.BrowseSlice, False)
Hide all slice view controllers:
lm = slicer.app.layoutManager() for sliceViewName in lm.sliceViewNames(): lm.sliceWidget(sliceViewName).sliceController().setVisible(False)
Hide all 3D view controllers:
lm = slicer.app.layoutManager() for viewIndex in range(slicer.app.layoutManager().threeDViewCount): lm.threeDWidget(0).threeDController().setVisible(False)
Change default slice view orientation
You can left-right "flip" slice view orientation presets (show patient left side on left/right side of the screen) by copy-pasting the script below to your .slicerrc.py file.
# Axial slice axes: # 1 0 0 # 0 1 0 # 0 0 1 axialSliceToRas=vtk.vtkMatrix3x3() # Coronal slice axes: # 1 0 0 # 0 0 -1 # 0 1 0 coronalSliceToRas=vtk.vtkMatrix3x3() coronalSliceToRas.SetElement(1,1, 0) coronalSliceToRas.SetElement(1,2, -1) coronalSliceToRas.SetElement(2,1, 1) coronalSliceToRas.SetElement(2,2, 0) # Replace orientation presets in all existing slice nodes and in the default slice node sliceNodes = slicer.util.getNodesByClass('vtkMRMLSliceNode') sliceNodes.append(slicer.mrmlScene.GetDefaultNodeByClass('vtkMRMLSliceNode')) for sliceNode in sliceNodes: orientationPresetName = sliceNode.GetOrientation() sliceNode.RemoveSliceOrientationPreset("Axial") sliceNode.AddSliceOrientationPreset("Axial", axialSliceToRas) sliceNode.RemoveSliceOrientationPreset("Coronal") sliceNode.AddSliceOrientationPreset("Coronal", coronalSliceToRas) sliceNode.SetOrientation(orientationPresetName)
Set all slice views linked by default
You can make slice views linked by default (when application starts or the scene is cleared) by copy-pasting the script below to your .slicerrc.py file.
# Set linked slice views in all existing slice composite nodes and in the default node sliceCompositeNodes = slicer.util.getNodesByClass('vtkMRMLSliceCompositeNode') defaultSliceCompositeNode = slicer.mrmlScene.GetDefaultNodeByClass('vtkMRMLSliceCompositeNode') if not defaultSliceCompositeNode: defaultSliceCompositeNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLSliceCompositeNode') slicer.mrmlScene.AddDefaultNode(defaultSliceCompositeNode) sliceCompositeNodes.append(defaultSliceCompositeNode) for sliceCompositeNode in sliceCompositeNodes: sliceCompositeNode.SetLinkedControl(True)
Set up custom units in slice view ruler
For microscopy or micro-CT images you may want to switch unit to micrometer instead of the default mm. To do that, 1. change the unit in Application settings / Units and 2. update ruler display settings using the script below (it can be copied to your Application startup script):
lm = slicer.app.layoutManager() for sliceViewName in lm.sliceViewNames(): sliceView = lm.sliceWidget(sliceViewName).sliceView() displayableManagerCollection = vtk.vtkCollection() sliceView.getDisplayableManagers(displayableManagerCollection) for dmIndex in xrange(displayableManagerCollection.GetNumberOfItems()): displayableManager = displayableManagerCollection.GetItemAsObject(dmIndex) if not displayableManager.IsA("vtkMRMLRulerDisplayableManager"): continue displayableManager.RemoveAllRulerScalePresets() displayableManager.AddRulerScalePreset( 0.001, 5, 2, "nm", 1000.0) displayableManager.AddRulerScalePreset( 0.010, 5, 2, "nm", 1000.0) displayableManager.AddRulerScalePreset( 0.100, 5, 2, "nm", 1000.0) displayableManager.AddRulerScalePreset( 0.500, 5, 1, "nm", 1000.0) displayableManager.AddRulerScalePreset( 1.0, 5, 2, "um", 1.0) displayableManager.AddRulerScalePreset( 5.0, 5, 1, "um", 1.0) displayableManager.AddRulerScalePreset( 10.0, 5, 2, "um", 1.0) displayableManager.AddRulerScalePreset( 50.0, 5, 1, "um", 1.0) displayableManager.AddRulerScalePreset( 100.0, 5, 2, "um", 1.0) displayableManager.AddRulerScalePreset( 500.0, 5, 1, "um", 1.0) displayableManager.AddRulerScalePreset(1000.0, 5, 2, "mm", 0.001)
Show a slice view outside the view layout
sliceLayoutName = "TestSlice" sliceLayoutLabel = "T" # ownerNode manages this view instead of the layout manager (it can be any node in the scene) viewOwnerNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScriptedModuleNode") # Create MRML nodes sliceNode = slicer.vtkMRMLSliceNode() sliceNode.SetName(sliceLayoutName) sliceNode.SetLayoutName(sliceLayoutName) sliceNode.SetLayoutLabel(sliceLayoutLabel) sliceNode.SetLayoutColor(1, 1, 0) sliceNode.SetAndObserveParentLayoutNodeID(viewOwnerNode.GetID()) sliceNode = slicer.mrmlScene.AddNode(sliceNode) sliceCompositeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSliceCompositeNode") sliceCompositeNode.SetLayoutName(sliceLayoutName) # Create widget sliceWidget = slicer.qMRMLSliceWidget() sliceWidget.sliceViewName = sliceLayoutName sliceWidget.sliceViewLabel = sliceLayoutLabel c = sliceNode.GetLayoutColor() sliceWidget.sliceViewColor = qt.QColor.fromRgbF(c[0],c[1],c[2]) sliceWidget.setMRMLScene(slicer.mrmlScene) sliceWidget.setMRMLSliceNode(sliceNode) sliceWidget.show()
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:
import SimpleITK as sitk import sitkUtils inputImage = sitkUtils.PullFromSlicer('MRHead') filter = sitk.SignedMaurerDistanceMapImageFilter() outputImage = filter.Execute(inputImage) sitkUtils.PushToSlicer(outputImage,'outputImage')
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:
def onMouseMoved(observer,eventid): ras=[0,0,0] crosshairNode.GetCursorPositionRAS(ras) print(ras) crosshairNode=slicer.util.getNode('Crosshair') crosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, onMouseMoved)
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.
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)
Thick slab reconstruction and maximum/minimum intensity volume projections
Set up 'red' slice viewer to show thick slab reconstructed from 3 slices:
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()
Set up 'red' slice viewer to show maximum intensity projection (MIP):
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()
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:
defaultModelStorageNode = slicer.vtkMRMLModelStorageNode() defaultModelStorageNode.SetDefaultWriteFileExtension('stl') slicer.mrmlScene.AddDefaultNode(defaultModelStorageNode)
To permanently change default file extension on your computer, copy-paste the code above into your application startup script (you can find its location in menu: Edit / Application settings / General / Application startup script).
Change file type for saving for all volumes (with already existing storage nodes)
If it is not necessary to preserve file paths then the simplest is to configure default storage node (as shown in the example above), then delete all existing storage nodes. When save dialog is opened, default storage nodes will be recreated.
# Delete existing model storage nodes so that they will be recreated with default settings existingModelStorageNodes = slicer.util.getNodesByClass('vtkMRMLModelStorageNode') for modelStorageNode in existingModelStorageNodes: slicer.mrmlScene.RemoveNode(modelStorageNode)
To update existing storage nodes to use new file extension (but keep all other parameters unchanged) you can use this approach (example is for volume storage):
requiredFileExtension = '.nia' originalFileExtension = '.nrrd' volumeNodes = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode') for volumeNode in volumeNodes: volumeStorageNode = volumeNode.GetStorageNode() if not volumeStorageNode: volumeNode.AddDefaultStorageNode() volumeStorageNode = volumeNode.GetStorageNode() volumeStorageNode.SetFileName(volumeNode.GetName()+requiredFileExtension) else: volumeStorageNode.SetFileName(volumeStorageNode.GetFileName().replace(originalFileExtension, requiredFileExtension))
To set all volume nodes to save uncompressed by default (add this to .slicerrc.py so it takes effect for the whole session):
#set the default volume storage to not compress by default defaultVolumeStorageNode = slicer.vtkMRMLVolumeArchetypeStorageNode() defaultVolumeStorageNode.SetUseCompression(0) slicer.mrmlScene.AddDefaultNode(defaultVolumeStorageNode) logging.info("Volume nodes will be stored uncompressed by default")
Same thing as above, but applied to all segmentations instead of volumes:
#set the default volume storage to not compress by default defaultVolumeStorageNode = slicer.vtkMRMLSegmentationStorageNode() defaultVolumeStorageNode.SetUseCompression(0) slicer.mrmlScene.AddDefaultNode(defaultVolumeStorageNode) logging.info("Segmentation nodes will be stored uncompressed
Segmentations
Create a segmentation from a labelmap volume and display in 3D
labelmapVolumeNode = getNode('label') seg = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode') slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, seg) seg.CreateClosedSurfaceRepresentation() slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
The last line is optional. It removes the original labelmap volume so that the same information is not shown twice.
Export labelmap node from segmentation node
seg = getNode('Segmentation') labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode') slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(seg, labelmapVolumeNode)
Export model nodes from segmentation node
seg = getNode('Segmentation') exportedModelsNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelHierarchyNode') slicer.modules.segmentations.logic().ExportAllSegmentsToModelHierarchy(seg, exportedModelsNode)
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:
segmentation.CreateClosedSurfaceRepresentation()
Get a representation of a segment
Access binary labelmap stored in a segmentation node (without exporting it to a volume node) - if it does not exist, it will return None:
image = segmentationNode.GetBinaryLabelmapRepresentation(segmentID)
Get closed surface, if it does not exist, it will return None:
polydata = segmentationNode.GetClosedSurfaceRepresentation(segmentID)
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):
import vtkSegmentationCorePython as vtkSegmentationCore outputOrientedImageData = vtkSegmentationCore.vtkOrientedImageData() slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, outputOrientedImageData)
Same as above, for closed surface representation:
outputPolyData = vtk.vtkPolyData() slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentClosedSurfaceRepresentation(segmentationNode, segmentID, outputPolyData)
Convert all segments using default path and conversion parameters
segmentationNode.CreateBinaryLabelmapRepresentation()
Convert all segments using custom path or conversion parameters
Change reference image geometry parameter based on an existing referenceImageData image:
import vtkSegmentationCorePython as vtkSegmentationCore referenceGeometry = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(referenceImageData) segmentation.SetConversionParameter(vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), referenceGeometry)
Re-convert using a modified conversion parameter
Changing smoothing factor for closed surface generation:
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())
Get centroid of a segment in world (RAS) coordinates
This example shows how to get centroid of a segment in world coordinates and show that position in all slice views.
segmentationNode = getNode('Segmentation') segmentId = 'Segment_1' # Get array voxel coordinates import numpy as np seg=arrayFromSegment(segmentation_node, segmentId) # numpy array has voxel coordinates in reverse order (KJI instead of IJK) # and the array is cropped to minimum size in the segmentation mean_KjiCropped = [coords.mean() for coords in np.nonzero(seg)] # Get segmentation voxel coordinates segImage = segmentationNode.GetBinaryLabelmapRepresentation(segmentId) segImageExtent = segImage.GetExtent() # origin of the array in voxel coordinates is determined by the start extent mean_Ijk = [mean_KjiCropped[2], mean_KjiCropped[1], mean_KjiCropped[0]] + np.array([segImageExtent[0], segImageExtent[2], segImageExtent[4]]) # Get segmentation physical coordinates ijkToWorld = vtk.vtkMatrix4x4() segImage.GetImageToWorldMatrix(ijkToWorld) mean_World = [0, 0, 0, 1] ijkToRas.MultiplyPoint(np.append(mean_Ijk,1.0), mean_World) mean_World = mean_World[0:3] # If segmentation node is transformed, apply that transform to get RAS coordinates transformWorldToRas = vtk.vtkGeneralTransform() slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(segmentationNode.GetParentTransformNode(), None, transformWorldToRas) mean_Ras = transformWorldToRas.TransformPoint(mean_World) # Show mean position value and jump to it in all slice viewers print(mean_Ras) slicer.modules.markups.logic().JumpSlicesToLocation(mean_Ras[0], mean_Ras[1], mean_Ras[2], True)
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 use Segment editor effects (without GUI, using qMRMLSegmentEditorWidget):
- brain tumor segmentation using grow from seeds effect
- skin surface extraction using thresholding and smoothing
- mask a volume with segments and compute histogram for each region
This example shows how to perform operations on segmentations using VTK filters:
Accessing views, renderers, and cameras
Iterate through all 3D views in current layout:
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())
Iterate through all slice views in current layout:
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()))
For low-level manipulation of views, it is possible to access VTK render windows, renderers and cameras of views in the current layout.
renderWindow = view.renderWindow() renderers = renderWindow.GetRenderers() renderer = renderers.GetItemAsObject(0) camera = cameraNode.GetCamera()
Change 3D view background color
renderWindow = slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow() renderer = renderWindow.GetRenderers().GetFirstRenderer() renderer.SetBackground(1,0,0) renderer.SetBackground2(1,0,0) renderWindow.Render()
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: sceneItemID = shNode.GetSceneItemID() # Get direct child by name subjectItemID = shNode.GetItemChildWithName(sceneItemID, 'Subject_1') # Get item for data node itemID = shNode.GetItemByDataNode(dataNode) # Get item by UID (such as DICOM) itemID = shNode.GetItemByUID(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(), seriesInstanceUid) itemID = shNode.GetItemByUIDList(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMInstanceUIDName(), instanceUID) # Invalid item ID for checking validity of a given ID (most functions return the invalid ID when item is not found) invalidItemID = slicer.vtkMRMLSubjectHierarchyNode.GetInvalidItemID()
Traverse children of a subject hierarchy item
children = vtk.vtkIdList() shNode.GetItemChildren(parent, children) for i in xrange(children.GetNumberOfIds()): child = children.GetId(i) ...
Manipulate subject hierarchy item
Instead of node operations on the individual subject hierarchy nodes, item operations are performed on the one subject hierarchy node.
# Set item name shNode.SetItemName(itemID, 'NewName') # Set item parent (reparent) shNode.SetItemParent(itemID, newParentItemID) # Set visibility of data nodes associated to items in a branch (or a leaf item) shNode.SetDisplayVisibilityForBranch(itemID, 1)
Filter items in TreeView or ComboBox
Displayed items can be filtered using setAttributeFilter method. An example of the usage can be found in the unit test. Modified version here:
print shTreeView.displayedItemCount() # 5 shTreeView.setAttributeFilter('DICOM.Modality') # Nodes must have this attribute print shTreeView.displayedItemCount() # 3 shTreeView.setAttributeFilter('DICOM.Modality','CT') # Have attribute and equal 'CT' print shTreeView.displayedItemCount() # 1 shTreeView.removeAttributeFilter() print shTreeView.displayedItemCount() # 5
Listen to subject hierarchy item events
The subject hierarchy node sends the node item id as calldata. Item IDs are vtkIdType, which are NOT vtkObjects. You need to use vtk.calldata_type(vtk.VTK_LONG) (otherwise the application crashes).
class MyListenerClass(VTKObservationMixin): def __init__(self): VTKObservationMixin.__init__(self) shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene) self.addObserver(shNode, shNode.SubjectHierarchyItemModifiedEvent, self.shItemModifiedEvent) @vtk.calldata_type(vtk.VTK_LONG) def shItemModifiedEvent(self, caller, eventId, callData): print("SH Node modified") print("SH item ID: {0}".format(callData))
Plotting
Create histogram plot of a volume
# Get a volume from SampleData import SampleData volumeNode = SampleData.SampleDataLogic().downloadMRHead() # Compute histogram values import numpy as np histogram = np.histogram(arrayFromVolume(volumeNode), bins=50) # Save results to a new table node tableNode=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode") updateTableFromArray(tableNode, histogram) tableNode.GetTable().GetColumn(0).SetName("Count") tableNode.GetTable().GetColumn(1).SetName("Intensity") # Create plot plotSeriesNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", volumeNode.GetName() + ' histogram') plotSeriesNode.SetAndObserveTableNodeID(tableNode.GetID()) plotSeriesNode.SetXColumnName("Intensity") plotSeriesNode.SetYColumnName("Count") plotSeriesNode.SetPlotType(plotSeriesNode.PlotTypeScatterBar) plotSeriesNode.SetColor(0, 0.6, 1.0) # Create chart and add plot plotChartNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotChartNode") plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode.GetID()) plotChartNode.YAxisRangeAutoOff() plotChartNode.SetYAxisRange(0, 500000) # Show plot in layout slicer.modules.plots.logic().ShowChartInLayout(plotChartNode)
Execute external applications
How to run external applications from Slicer.
Run process in default environment
When a process is launched from Slicer then by default Slicer's ITK, VTK, Qt, etc. libraries are used. If an external application has its own version of these libraries, then the application is expected to crash. To prevent crashing, the application must be run in the environment where Slicer started up (without all Slicer-specific library paths). This startup environment can be retrieved using slicer.util.startupEnvironment().
Example: run Python3 script from Slicer:
command_to_execute = ["/usr/bin/python3", "-c", "print('hola')"] from subprocess import check_output check_output( command_to_execute, env=slicer.util.startupEnvironment() )
will output:
'hola\n'
On some systems, shell=True must be specified as well.