AHM2012-Slicer-Python
Contents
What is accessible via python
Qt
Interfaces are build with PythonQt which exposes most of the Qt interface so that sophisticated interfaces can be easily created.
import slicer def widgetTree(root=""): if not root: root = slicer.util.mainWindow() global treeItems tree = qt.QTreeWidget() tree.setHeaderLabels(["Widget", "Class", "Title", "Text", "Name"]) treeItems = {} treeItems[root] = qt.QTreeWidgetItem(tree) parents = [root] while parents != []: widget = parents.pop() if not widget: break widgetItem = qt.QTreeWidgetItem(treeItems[widget]) children = widget.children() for child in children: treeItems[child] = widgetItem parents += children widgetItem.setText(0, str(widget)) try: widgetItem.setText(1, widget.className()) except AttributeError: pass try: widgetItem.setText(2, widget.title) except AttributeError: pass try: widgetItem.setText(3, widget.text) except AttributeError: pass try: widgetItem.setText(4, widget.name) except AttributeError: pass tree.setGeometry(100, 100, 1000, 500) tree.setColumnWidth(0,200) tree.setColumnWidth(0,300) tree.expandAll() tree.show() return tree
VTK and MRML
It is possible to implement the logic of the effect using VTK Python binding. You can get ideas of what is possible from the VTK tutorials.
Because MRML and most of the slicer functionality is written as VTK subclasses, they are available in python via the same mechanism.
class EndoscopyPathModel: """Create a vtkPolyData for a polyline: - Add one point per path point. - Add a single polyline """ def __init__(self, path, fiducialListNode): fids = fiducialListNode scene = slicer.mrmlScene points = vtk.vtkPoints() polyData = vtk.vtkPolyData() polyData.SetPoints(points) lines = vtk.vtkCellArray() polyData.SetLines(lines) linesIDArray = lines.GetData() linesIDArray.Reset() linesIDArray.InsertNextTuple1(0) polygons = vtk.vtkCellArray() polyData.SetPolys( polygons ) idArray = polygons.GetData() idArray.Reset() idArray.InsertNextTuple1(0) for point in path: pointIndex = points.InsertNextPoint(*point) linesIDArray.InsertNextTuple1(pointIndex) linesIDArray.SetTuple1( 0, linesIDArray.GetNumberOfTuples() - 1 ) lines.SetNumberOfCells(1) # Create model node model = slicer.vtkMRMLModelNode() model.SetScene(scene) model.SetName("Path-%s" % fids.GetName()) model.SetAndObservePolyData(polyData) # Create display node modelDisplay = slicer.vtkMRMLModelDisplayNode() modelDisplay.SetColor(1,1,0) # yellow modelDisplay.SetScene(scene) scene.AddNodeNoNotify(modelDisplay) model.SetAndObserveDisplayNodeID(modelDisplay.GetID()) # Add to scene modelDisplay.SetPolyData(model.GetPolyData()) scene.AddNode(model) # Camera cursor sphere = vtk.vtkSphereSource() sphere.Update() # Create model node cursor = slicer.vtkMRMLModelNode() cursor.SetScene(scene) cursor.SetName("Cursor-%s" % fids.GetName()) cursor.SetAndObservePolyData(sphere.GetOutput()) # Create display node cursorModelDisplay = slicer.vtkMRMLModelDisplayNode() cursorModelDisplay.SetColor(1,0,0) # red cursorModelDisplay.SetScene(scene) scene.AddNodeNoNotify(cursorModelDisplay) cursor.SetAndObserveDisplayNodeID(cursorModelDisplay.GetID()) # Add to scene cursorModelDisplay.SetPolyData(sphere.GetOutput()) scene.AddNode(cursor) # Create transform node transform = slicer.vtkMRMLLinearTransformNode() transform.SetName('Transform-%s' % fids.GetName()) scene.AddNode(transform) cursor.SetAndObserveTransformNodeID(transform.GetID()) self.transform = transform
Numpy
Slicer also comes bundled with numpy so many interesting array operations are easy to perform on image data.
Here's an excerpt from a working example:
# # Get the numpy array for the bg and label # import vtk.util.numpy_support backgroundImage = backgroundNode.GetImageData() labelImage = labelNode.GetImageData() shape = list(backgroundImage.GetDimensions()) shape.reverse() backgroundArray = vtk.util.numpy_support.vtk_to_numpy(backgroundImage.GetPointData().GetScalars()).reshape(shape) labelArray = vtk.util.numpy_support.vtk_to_numpy(labelImage.GetPointData().GetScalars()).reshape(shape)
CLI Modules
It is also possible to invoke slicer command line modules from python. These can be written in any language, but often rely on ITK for processing. In the near future SimpleITK should be available directly inside slicer. See the Slicer4 Python page for examples.
Here's an example from the Editor Module that calls the ModelMaker CLI:
def onApply(self): # # create a model using the command line module # based on the current editor parameters # volumeNode = self.editUtil.getLabelVolume() if not volumeNode: return # # set up the model maker node # parameters = {} parameters['Name'] = self.modelName.text parameters["InputVolume"] = volumeNode.GetID() parameters['FilterType'] = "Sinc" # build only the currently selected model. parameters['Labels'] = self.getPaintLabel() parameters["StartLabel"] = -1 parameters["EndLabel"] = -1 parameters['GenerateAll'] = False parameters["JointSmoothing"] = False parameters["SplitNormals"] = True parameters["PointNormals"] = True parameters["SkipUnNamed"] = True if self.smooth.checked: parameters["Decimate"] = 0.25 parameters["Smooth"] = 10 else: parameters["Decimate"] = 0 parameters["Smooth"] = 0 # # output # - make a new hierarchy node if needed # numNodes = slicer.mrmlScene.GetNumberOfNodesByClass( "vtkMRMLModelHierarchyNode" ) outHierarchy = None for n in xrange(numNodes): node = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLModelHierarchyNode" ) if node.GetName() == "Editor Models": outHierarchy = node break if not outHierarchy: outHierarchy = slicer.vtkMRMLModelHierarchyNode() outHierarchy.SetScene( slicer.mrmlScene ) outHierarchy.SetName( "Editor Models" ) slicer.mrmlScene.AddNode( outHierarchy ) parameters["ModelSceneFile"] = outHierarchy modelMaker = slicer.modules.modelmaker # # run the task (in the background) # - use the GUI to provide progress feedback # - use the GUI's Logic to invoke the task # - model will show up when the processing is finished # self.CLINode = slicer.cli.run(modelMaker, self.CLINode, parameters) self.statusText( "Model Making Started..." )
Using the console
(See J2's excellent demo video)
The python console in Slicer4:
- is a Qt widget that is part of CTK's extensions to PythonQt
- has syntax highlighting
- has command completion
- provides handy access for testing and experimenting
Writing a Scripted Module
The Endoscopy module is a good example to look at for writing a scripted module.
You can get started by using the ModuleWizard to create your skeleton module.
Then you implement the functionality using the methods described above:
- Use PythonQt to create the interface
- Implement the Logic with vtk/vtkITK/CLI Modules
- Access MRML Data via numpy