UpdateBot: Nightly -> 4.4

2014-12-25T06:44:12Z

Nightly -> 4.4

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='''Developer FAQ: {{{1}}}'''=
</includeonly>

== How to systematically execute custom python code at startup ? ==

Each time Slicer starts, it will look up for a file named <code>.slicerrc.py</code> into your HOME folder.

See [[Documentation/{{documentation/version}}/FAQ/General#What_is_my_HOME_folder_.3F|What is my HOME folder ?]]

== How to save an image/volume using python ? ==

The module <code>slicer.util</code> provides methods allowing to save either a node or an entire scene:
* saveNode
* saveScene

For more details see:
* https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/util.py#L229-267
* https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/tests/test_slicer_util_save.py

== How to assign a volume to a Slice view ? ==

Assuming the <code>MRHead</code> sample data has been loaded, you could do the following:

<pre>
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
red_logic.GetSliceCompositeNode().SetBackgroundVolumeID(slicer.util.getNode('MRHead').GetID())
</pre>

Discussion: http://slicer-devel.65872.n3.nabble.com/Assign-volumes-to-views-tt4028694.html

== How to access vtkRenderer in Slicer 3D view ? ==

<pre>
renderer = slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow().GetRenderers().GetFirstRenderer()
</pre>

== Should I used 'old style' or 'new style' python classes in my scripted module ==

When python classes have no superclass specified they are 'old style' as described here [http://docs.python.org/2/reference/datamodel.html#new-style-and-classic-classes].

In general it doesn't matter for the classes in a scripted module, since they won't be subclassed either old or new style should be the same.

For other python code in slicer where you might be subclassing, it's better to use new style classes. See the class hierarchies in the [https://github.com/Slicer/Slicer/tree/master/Modules/Scripted/EditorLib EditorLib] and the [https://github.com/Slicer/Slicer/tree/master/Modules/Scripted/DICOM/DICOMLib DICOMLib] for examples.

== How to harden a transform ? ==

<pre>
>>> n = getNode('Bone')
>>> logic = slicer.vtkSlicerTransformLogic()
>>> logic.hardenTransform(n)
</pre>

Discussion: http://slicer-devel.65872.n3.nabble.com/Scripting-hardened-transforms-tt4029456.html

== Where can I find example scripts? ==

Have a look at [[Documentation/{{documentation/version}}/ScriptRepository]].

== How can I use a visual debugger for step-by-step debugging ==
Visual debugging (setting breakpoints, execute code step-by-step, view variables, stack, etc.) of Python scripted module is possible by using [http://pydev.org/ PyDev] by using the [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] extension.

'''See detailed instructions at the [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger's extension page]].'''
[[File:PyDevRemoteDebugSlicer.png|800px|thumb|center|Visual debugging of Python modules in Slicer]]

== Why can't I access my C++ Qt class from python ==
* Python wrapping of a Qt class requires a Qt style constructor with QObject as argument (it can be defaulted to null though), which is public. If one of these are missing, python wrapping will fail for that class
* [Other reasons go here]

== How can I access callData argument in a VTK object observer callback function ==

To get notification about an event emitted by a VTK object you can simply use the AddObserver method, for example:
<pre>
def sceneModifiedCallback(caller, eventId):
print "Scene modified"
print "There are {0} nodes in the scene". format(slicer.mrmlScene.GetNumberOfNodes())

sceneModifiedObserverTag = slicer.mrmlScene.AddObserver(vtk.vtkCommand.ModifiedEvent, sceneModifiedCallback)
</pre>

If an event also contains additional information as CallData then the type of this argument has to be specified as well, for example:
<pre>
@vtk.calldata_type(vtk.VTK_OBJECT)
def nodeAddedCallback(caller, eventId, callData):
print "Node added"
print "New node: {0}".format(callData.GetName())

nodeAddedModifiedObserverTag = slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent, nodeAddedCallback)
</pre>

Note: @vtk.calldata_type is a Python decorator, which modifies properties of a function that is declared right after the decorator. The decorator is defined in VTK (in Wrapping\Python\vtk\util\misc.py).

Usage from a class:

<pre>
from slicer.util import VTKObservationMixin

class MyClass(VTKObservationMixin):
def __init__(self):
VTKObservationMixin.__init__(self)
self.addObserver(slicer.mrmlScene, slicer.vtkMRMLScene.NodeAddedEvent, self.nodeAddedCallback)

@vtk.calldata_type(vtk.VTK_OBJECT)
def nodeAddedCallback(self, caller, eventId, callData):
print "Node added"
print "New node: {0}".format(callData.GetName())

myObject = MyClass()
</pre>

Allowed CallDataType values: VTK_STRING, VTK_OBJECT, VTK_INT, VTK_LONG, VTK_DOUBLE, VTK_FLOAT, "string0". See more information here:
https://github.com/Kitware/VTK/blob/master/Wrapping/PythonCore/vtkPythonCommand.cxx

Note: VTKObservationMixin is a Python mix-in that allows adding a set of methods to a class by inheritance. VTKObservationMixin includes addObserver, hasObserver, observer, removeObserver, removeObservers methods, defined in Slicer (in Base\Python\slicer\util.py).

Documentation/4.4/Developers/FAQ/Python Scripting - Revision history

UpdateBot: Nightly -> 4.4