Documentation/Nightly/ScriptRepository

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Contents


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

DICOM

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 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()

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.

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)

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)

Show a context menu when a markup point is clicked in a slice or 3D view


# 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 fiber tracts to Blender, including color

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()

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 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')

Manipulate a Slice View

Change the slice offset

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)

Iterate over current visible slice views, and modify 3D visibility

for sliceViewName in layoutManager.sliceViewNames():
     sliceWidget = layoutManager.sliceWidget(sliceViewName)
     
     controller = sliceWidget.sliceController()
     controller.setSliceVisible(True)

Iterate over current visible slice views, and set foreground and background images

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)

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")

Show a volume in the Slice Views

volumeNode = slicer.util.getNode('YourVolumeNode')
applicationLogic = slicer.app.applicationLogic()
selectionNode = applicationLogic.GetSelectionNode()
selectionNode.SetSecondaryVolumeID(volumeNode.GetID())
applicationLogic.PropagateForegroundVolumeSelection(0)

or 

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 the Slice Views

lm = slicer.app.layoutManager()
sliceLogic = lm.sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetForegroundOpacity(0.4)

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

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)

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:

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))

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)

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())

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):

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

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)
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