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{{documentation/banner
=Community-contributed modules=
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| text  = [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html This page has been moved to read-the-docs.]
 
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Usage: save the .py file to a directory, add the directory to the additional module paths in the Slicer application settings (choose in the menu: Edit / Application settings, click Modules, click >> next to Additional module paths, click Add, and choose the .py file's location).
 
 
 
==Filters==
 
* [https://raw.github.com/pieper/VolumeMasker/master/VolumeMasker.py VolumeMasker.py]: Update a target volume with the results of setting all input volume voxels to 0 except for those that correspond to a selected label value in an input label map (Used for example in the volume rendering in [https://www.youtube.com/watch?v=dfu2gugHLHs this video).
 
 
 
==DICOM==
 
* [https://gist.github.com/pieper/6186477 dicom header browser] to easily scroll through dicom files using dcmdump.
 
* [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/BatchProcessing SlicerRT batch processing] to batch convert RT structure sets to labelmap NRRD files.
 
 
 
==Informatics==
 
* [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/MarkupsInfoModule/MarkupsInfo.py MarkupsInfo.py]: Compute the total length between all the points of a markup list.
 
* [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/LineProfile/LineProfile.py LineProfile.py]: Compute intensity profile in a volume along a line.
 
 
 
=Community-contributed examples=
 
 
 
Usage: Copy-paste the shown code lines or linked .py file contents into Python console in Slicer.
 
 
 
==Capture==
 
* Get a MRML node in the scene based on the node name and call methods of that object. For the MRHead sample data:
 
  vol=slicer.util.getNode('MR*')
 
  vol.GetImageData().GetDimensions()
 
* Capture the full Slicer screen and save it into a file
 
  img = qt.QPixmap.grabWidget(slicer.util.mainWindow()).toImage()
 
  img.save('c:/tmp/test.png')
 
* [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/CaptureRotationVideo/CaptureRotationVideo.py CaptureRotationVideo.py]: Capture a video of the scene rotating in the 3D view
 
 
 
==Launching Slicer==
 
* How to open an .mrb file with Slicer at the command line?
 
  Slicer.exe --python-code "slicer.util.loadScene( 'f:/2013-08-23-Scene.mrb' )"
 
* How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
 
  Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window
 
 
 
==DICOM==
 
* How to access tags of DICOM images imported into Slicer? For example, to print the first patient's first study's first series' "0020,0032" field:
 
  db=slicer.dicomDatabase
 
  patientList=db.patients()
 
  studyList=db.studiesForPatient(patientList[0])
 
  seriesList=db.seriesForStudy(studyList[0])
 
  fileList=db.filesForSeries(seriesList[0])
 
  print db.fileValue(fileList[0],'0020,0032')
 
 
 
* How to access tag of a volume loaded from DICOM? For example, get the patient position stored in a volume:
 
  volumeName='2: ENT IMRT'
 
  n=slicer.util.getNode(volumeName)
 
  instUids=n.GetAttribute('DICOM.instanceUIDs').split()
 
  filename=slicer.dicomDatabase.fileForInstance(instUids[0])
 
  print slicer.dicomDatabase.fileValue(filename,'0018,5100')
 
 
 
==Toolbar functions==
 
* How to turn on slice intersections in the crosshair menu on the toolbar:
 
  viewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceCompositeNode')
 
  viewNodes.UnRegister(slicer.mrmlScene)
 
  viewNodes.InitTraversal()
 
  viewNode = viewNodes.GetNextItemAsObject()
 
  while viewNode:
 
    viewNode.SetSliceIntersectionVisibility(1)
 
    viewNode = viewNodes.GetNextItemAsObject()
 
 
 
How to find similar functions? For this one I searched for "slice intersections" text in the whole slicer source code, found that the function is implemented in Base\QTGUI\qSlicerViewersToolBar.cxx, then translated the qSlicerViewersToolBarPrivate::setSliceIntersectionVisible(bool visible) method to Python.
 
 
 
==Manipulating objects in the slice viewer==
 
* How to define/edit a circular region of interest in a slice viewer?
 
 
 
Drop two markup points on a slice view and copy-paste the code below into the Python console. After this, as you move the markups you’ll see a circle following the markups.
 
 
 
  # Update the sphere from the fiducial points
 
  def UpdateSphere(param1, param2): 
 
    centerPointCoord = [0.0, 0.0, 0.0]
 
    markups.GetNthFiducialPosition(0,centerPointCoord)
 
    circumferencePointCoord = [0.0, 0.0, 0.0]
 
    markups.GetNthFiducialPosition(1,circumferencePointCoord)
 
    sphere.SetCenter(centerPointCoord)
 
    radius=math.sqrt((centerPointCoord[0]-circumferencePointCoord[0])**2+(centerPointCoord[1]-circumferencePointCoord[1])**2+(centerPointCoord[2]-circumferencePointCoord[2])**2)
 
    sphere.SetRadius(radius)
 
    sphere.SetPhiResolution(30)
 
    sphere.SetThetaResolution(30)
 
    sphere.Update()
 
 
 
  # Get a reference to the markup
 
  markups=slicer.util.getNode('F')
 
  # Create the sphere that will intersect the slice viewer
 
  sphere = vtk.vtkSphereSource()
 
  # Initial positioning of the sphere
 
  UpdateSphere(0,0)
 
  # Create model node and add to scene
 
  model = slicer.vtkMRMLModelNode()
 
  model.SetAndObservePolyData(sphere.GetOutput())
 
  modelDisplay = slicer.vtkMRMLModelDisplayNode()
 
  modelDisplay.SetSliceIntersectionVisibility(True) # Show in slice view
 
  modelDisplay.SetVisibility(False) # Hide in 3D view
 
  slicer.mrmlScene.AddNode(modelDisplay)
 
  model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
 
  modelDisplay.SetInputPolyData(model.GetPolyData())
 
  slicer.mrmlScene.AddNode(model)
 
  # Call UpdateSphere whenever the fiducials are changed
 
  markups.AddObserver("ModifiedEvent", UpdateSphere, 2)
 
 
 
== Add a texture mapped plane to the scene as a model ==
 
Note that model textures are not exposed in the GUI and are not saved in the scene
 
<pre>
 
# use dummy image data here
 
e = vtk.vtkImageEllipsoidSource()
 
 
 
scene = slicer.mrmlScene
 
 
 
# Create model node
 
model = slicer.vtkMRMLModelNode()
 
model.SetScene(scene)
 
model.SetName(scene.GenerateUniqueName("2DImageModel"))
 
 
 
planeSource = vtk.vtkPlaneSource()
 
model.SetAndObservePolyData(planeSource.GetOutput())
 
 
 
# Create display node
 
modelDisplay = slicer.vtkMRMLModelDisplayNode()
 
modelDisplay.SetColor(1,1,0) # yellow
 
modelDisplay.SetBackfaceCulling(0)
 
modelDisplay.SetScene(scene)
 
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())
 
</pre>
 
 
 
 
 
== Export a model to Blender, including color ==
 
 
 
<pre>
 
plyFilePath = "/tmp/fibers.ply"
 
 
 
lineDisplayNode = getNode("*LineDisplay*")
 
 
 
tuber = vtk.vtkTubeFilter()
 
tuber.SetInput(lineDisplayNode.GetOutputPolyData())
 
 
 
tubes = tuber.GetOutput()
 
tubes.Update()
 
scalars = tubes.GetPointData().GetArray(0)
 
scalars.SetName("scalars")
 
 
 
triangles = vtk.vtkTriangleFilter()
 
triangles.SetInput(tubes)
 
 
 
colorNode = lineDisplayNode.GetColorNode()
 
lookupTable = vtk.vtkLookupTable()
 
lookupTable.DeepCopy(colorNode.GetLookupTable())
 
lookupTable.SetTableRange(0,1)
 
 
 
plyWriter = vtk.vtkPLYWriter()
 
plyWriter.SetInput(triangles.GetOutput())
 
plyWriter.SetLookupTable(lookupTable)
 
plyWriter.SetArrayName("scalars")
 
 
 
plyWriter.SetFileName(plyFilePath)
 
plyWriter.Write()
 
</pre>
 
 
 
== Clone a volume ==
 
This example shows how to clone the MRHead sample volume, including its pixel data and display settings.
 
<pre>
 
sourceVolumeNode = slicer.util.getNode('MRHead')
 
volumesLogic = slicer.modules.volumes.logic()
 
clonedVolumeNode = volumesLogic.CloneVolume(slicer.mrmlScene, sourceVolumeNode, 'Cloned volume')
 
</pre>
 
 
 
== Create a new volume ==
 
This example shows how to create a new empty volume.
 
<pre>
 
imageSize=[512, 512, 512]
 
imageSpacing=[1.0, 1.0, 1.0]
 
voxelType=vtk.VTK_UNSIGNED_CHAR
 
# Create an empty image volume
 
imageData=vtk.vtkImageData()
 
imageData.SetDimensions(imageSize)
 
imageData.AllocateScalars(voxelType, 1)
 
thresholder=vtk.vtkImageThreshold()
 
thresholder.SetInputData(imageData)
 
thresholder.SetInValue(0)
 
thresholder.SetOutValue(0)
 
# Create volume node
 
volumeNode=slicer.vtkMRMLScalarVolumeNode()
 
volumeNode.SetSpacing(imageSpacing)
 
volumeNode.SetImageDataConnection(thresholder.GetOutputPort())
 
# Add volume to scene
 
slicer.mrmlScene.AddNode(volumeNode)
 
displayNode=slicer.vtkMRMLScalarVolumeDisplayNode()
 
slicer.mrmlScene.AddNode(displayNode)
 
colorNode = slicer.util.getNode('Grey')
 
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
 
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
 
volumeNode.CreateDefaultStorageNode()
 
</pre>
 
 
 
== Modify voxels in a volume ==
 
This example shows how to change voxels values of the MRHead sample volume.
 
The values will be computed by function f(r,a,s,) = (r-10)*(r-10)+(a+15)*(a+15)+s*s.
 
<pre>
 
volumeNode=slicer.util.getNode('MRHead')
 
ijkToRas = vtk.vtkMatrix4x4()
 
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()
 
</pre>
 
 
 
== Manipulate a Slice View ==
 
 
 
<pre>
 
lm = slicer.app.layoutManager()
 
red = lm.sliceWidget('Red')
 
redLogic = red.sliceLogic()
 
# Print current slice offset position
 
print redLogic.GetSliceOffset()
 
# Change slice position
 
redLogic.SetSliceOffset(20)
 
</pre>
 
 
 
== Display text in a 3D view or slice view ==
 
 
 
The easiest way to show information overlaid on a viewer is to use corner annotations.
 
 
 
<pre>
 
view=slicer.app.layoutManager().threeDWidget(0).threeDView()
 
# Set text to "Something"
 
view.cornerAnnotation().SetText(vtk.vtkCornerAnnotation.UpperRight,"Something")
 
# Set color to red
 
view.cornerAnnotation().GetTextProperty().SetColor(1,0,0)
 
# Update the view
 
view.forceRender()
 
</pre>
 
 
 
== Customize viewer layout ==
 
 
 
Show a custom layout of a 3D view on top of the red slice view:
 
 
 
<pre>
 
customLayout = ("<layout type=\"vertical\" split=\"true\" >"
 
  " <item>"
 
  "  <view class=\"vtkMRMLViewNode\" singletontag=\"1\">"
 
  "    <property name=\"viewlabel\" action=\"default\">1</property>"
 
  "  </view>"
 
  " </item>"
 
  " <item>"
 
  "  <view class=\"vtkMRMLSliceNode\" singletontag=\"Red\">"
 
  "  <property name=\"orientation\" action=\"default\">Axial</property>"
 
  "  <property name=\"viewlabel\" action=\"default\">R</property>"
 
  "  <property name=\"viewcolor\" action=\"default\">#F34A33</property>"
 
  "  </view>"
 
  " </item>"
 
  "</layout>")
 
 
 
customLayoutId=501
 
 
 
layoutManager = slicer.app.layoutManager()
 
layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)                                       
 
layoutManager.setLayout(customLayoutId)
 
</pre>
 
 
 
See description of standard layouts (that can be used as examples) here:
 
https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx
 
 
 
== Running an ITK filter in Python using SimpleITK ==
 
Open the "Sample Data" module and download "MR Head", then paste the following snippet in Python interactor:
 
<pre>
 
inputImage = sitkUtils.PullFromSlicer('MRHead')
 
filter = sitk.SignedMaurerDistanceMapImageFilter()
 
outputImage = filter.Execute(inputImage)
 
sitkUtils.PushToSlicer(outputImage,'outputImage')
 
</pre>
 
 
 
More information:
 
* See the SimpleITK documentation for SimpleITK examples: http://www.itk.org/SimpleITKDoxygen/html/examples.html
 
* sitkUtils in Slicer is used for pushing and pulling images from Slicer to SimpleITK: https://github.com/Slicer/Slicer/blob/master/Base/Python/sitkUtils.py
 

Latest revision as of 04:06, 24 April 2021

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