Slicer API

Tutorials

Check out these developer tutorials to get started with customizing and extending 3D Slicer using Python scripting or C++.

C++

Majority of Slicer core modules and all basic infrastructure are implemented in C++. Documentation of these classes are available at: https://apidocs.slicer.org/main

Python

Native Python documentation

Python-style documentation is available for the following packages:

• mrml
• slicer
  • app
  • mrmlScene
  • modules
  • moduleNames
  • slicer.cli
  • slicer.logic
  • slicer.ScriptedLoadableModule
  • slicer.testing
  • slicer.util
• vtkTeem
• vtkAddon
• vtkITK

Doxygen-style documentation

Slicer core infrastructure is mostly implemented in C++ and it is made available in Python in the slicer namespace. Documentation of these classes is available at: https://apidocs.slicer.org/main/

C++ classes are made available in Python using two mechanisms: PythonQt and VTK Python wrapper. They have a few slight differences:

• Qt classes (class name starts with q or Q): for example, qSlicerMarkupsPlaceWidget. These classes are all derived from QObject and follow Qt conventions. They support properties, signals, and slots.

• VTK classes (class name starts with vtk): for example, vtkMRMLModelDisplayNode. These classes are all derived from vtkObject and follow VTK conventions.

This documentation is generated using the Doxygen tool, which uses C++ syntax. The following rules can help in interpreting this documentation for Python:

• Public member functions: They can be accessed as objectName.memberFunctionName(arguments) for example a method of the slicer.mrmlScene object can be called as: slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLTransformNode'). In Qt classes, only methods that have Q_INVOKABLE keyword next to them are available from Python. virtual and override specifiers can be ignored (they just indicate that the method can be or is overridden in a child class).

  • className (for Qt classes): constructor, shows the arguments that can be passed when an object is created. Qt objects can be instantiated using qt.QSomeObject(). For example myObj = qt.QComboBox().

  • New (for VTK classes): constructor, never needs an argument. VTK objects can be instantiated using vtk.vtkSomeObject(). For example myObj = vtk.vtkPolyData().

  • ~className: destructor, can be ignored, Python calls it automatically when needed (when there are no more references to an object). If a variable holds the last reference to an object then it can be deleted by calling del or setting the variable to a new value. For example: del(myObj) or myObj = None.

  • SafeDownCast (for VTK classes): not needed for Python, as type conversions are automatic.

• Static Public Member Functions: can be accessed as slicer.className.memberFunctionName(arguments) for example: slicer.vtkMRMLModelDisplayNode.GetSliceDisplayModeAsString(0).

• Properties (for Qt classes): these are values that are accessible as object attributes in Python and can be read and written as objectName.propertyName. For example:

  >>> w = slicer.qSlicerMarkupsPlaceWidget()
  >>> w.deleteAllControlPointsOptionVisible
  True
  >>> w.deleteAllControlPointsOptionVisible=False
  >>> w.deleteAllControlPointsOptionVisible
  False
  

• Public slots (for Qt classes): publicly available methods. Note that setSomeProperty methods show up in the documentation but in Python these methods are not available and instead property values can be set using someProperty = ....

• Signals (for Qt classes): signals that can be connected to Python methods

  def someFunction():
    print("clicked!")
  
  b = qt.QPushButton("MyButton")
  b.connect("clicked()", someFunction)  # someFunction will be called when the button is clicked
  b.show()
  

• Public Types: most commonly used for specifying enumerated values (indicated by enum type). These values can be accessed as slicer.className.typeName, for example slicer.qSlicerMarkupsPlaceWidget.HidePlaceMultipleMarkupsOption

• Protected Slots, Member Functions, Attributes: for internal use only, not accessible in Python.

Mapping commonly used data types from C++ documentation to Python:

• void -> Python: if the return value of a method is this type then it means that no value is returned

• someClass* (object pointer) -> Python: since Python takes care of reference counting, it can be simply interpreted in Python as someClass. The called method can modify the object.

• int, char, short (with optional signed or unsigned prefix) -> Python: int

• float, double -> Python: float

• double[3] -> Python: initialize a variable before the method call as point = np.zeros(3) (or point = [0.0, 0.0, 0.0]) and use it as argument in the function

• const char *, std::string, QString, const QString& -> Python: str

• bool -> Python: bool