Difference between revisions of "AHM2012-Slicer-Python"
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In practice, it is very convenient for developers to use the this feature to make shortcuts for interacting with their code. | In practice, it is very convenient for developers to use the this feature to make shortcuts for interacting with their code. | ||
− | See [https://github.com/pieper/SlicerRC] for examples that you can build from. | + | See [https://github.com/pieper/SlicerRC https://github.com/pieper/SlicerRC] for examples that you can build from. |
Here's an excerpt from that example: | Here's an excerpt from that example: |
Revision as of 23:13, 7 January 2012
Home < AHM2012-Slicer-PythonContents
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
Refining the code and UI with slicerrc
Slicer supports a user-specific startup script called slicerrc
- Can be either in ~/.slicerrc.py or in location pointed to by SLICERRC environment variable
- Can do arbitrary startup actions:
- load data
- change the GUI
- initiate computation
In practice, it is very convenient for developers to use the this feature to make shortcuts for interacting with their code.
See https://github.com/pieper/SlicerRC for examples that you can build from.
Here's an excerpt from that example:
def endoscopy(): print "SlicerRC - endoscopy setup..." import imp, sys, os endoPath = '%s/../../Slicer4/Modules/Scripted/Scripts' % slicer.app.slicerHome if not sys.path.__contains__(endoPath): sys.path.insert(0,endoPath) mod = "Endoscopy" sourceFile = endoPath + "/Endoscopy.py" fp = open(sourceFile, "r") globals()[mod] = imp.load_module(mod, fp, sourceFile, ('.py', 'r', imp.PY_SOURCE)) fp.close() globals()['e'] = e = globals()[mod].EndoscopyWidget() def setupMacros(): """Set up hot keys for various development scenarios""" import qt global endoscopy macros = ( ("Shift+Ctrl+2", endoscopy), ) for keys,f in macros: k = qt.QKeySequence(keys) s = qt.QShortcut(k,mainWindow()) s.connect('activated()', f) s.connect('activatedAmbiguously()', f) print "SlicerRC - '%s' -> '%s'" % (keys, f.__name__) # Install macros if mainWindow(verbose=False): setupMacros()
What this does is:
- Registers a hot-key for the application so that when Control-Shift-2 is entered the endoscopy() python function is invoked
- This hot-key reloads the source code for the module and creates a new instance of the module GUI
- The module GUI is accessible via the python console in a global variable 'e'
- The the 'e' variable lets you access internal state, call methods, and otherwise debug your module.
- You can typically edit the module python code and reload the module with Control-Shift-2 without exiting slicer, making the development process very efficient