Plot Nodes in Slicer

Development
1

Hi everyone,

I am working on a module to generate a 2D Visualization of the Brain Connectome Network.

I am trying to understand all the 2D plot options in Slicer with Python. So my question is the following:
What are all the node classes that can be added in slicer.mrmlScene.AddNewNodeByClass( ? ) ?

Also, if I would like to plot a vtkSpiderPlot() in an existing window of Slicer, would that be possible? Until now I’ve only managed to plot it in a pop up window that uses the OpenGL Visualization ToolKit.

Thank you all in advance!

2

Currently line, scatter, and bar plots are available via the GUI. To show spider plots, you would need to do some Python scripting. I would recommend to show this plot first in a plain VTK render window. Once you have that working, then I can help with making that window show up in the view layout.

3

Thank you for your reply Andras.

I am pretty new to VTK and Slicer.

I have generated the spider plot in a plain VTK render window, which is the pop up window I was talking about before. To do so I used vtkRenderer(), vtkRenderWindow(), vtkRenderWindowInteractor().

So as I would like to make that window show up in Slicer you suggest me to use the view layout.
Should I look at the slicer.app.layoutManager() ? If so, could you help me understand how that should be implemented and what vtkMRML Node to use?

4

@Sunderlandkyl could you advise how the view class that you recently added to Slicer could be used for this? Thank you.

5

You can add your vtkRenderWindow to a QVTKWidget, and then add that widget to a layout using qSlicerSingletonViewFactory.

Ex.

  • Add view factory to layout manager:

      singletonViewFactory = slicer.qSlicerSingletonViewFactory()
  singletonViewFactory.setTag("yourtagname")
  singletonViewFactory.setWidget(yourWidget)
  slicer.app.layoutManager().registerViewFactory(singletonViewFactory)

  • Add custom layout to layout manager:

      yourLayoutID = 1234
  layoutManager = slicer.app.layoutManager()
  layout = (
    "<layout type=\"horizontal\">"
    " <item>"
    "  <yourtagname></yourtagname>"
    " </item>"
    "</layout>"
  )
  layoutNode = slicer.app.layoutManager().layoutLogic().GetLayoutNode()
  layoutNode.AddLayoutDescription(
    yourLayoutID, layout)

  • Switch to layout with custom widget:

    slicer.app.layoutManager().setLayout(yourLayoutID)
1 Like
6

Hi @Sunderlandkyl,

Thank you for your response.

I think I am close. I just can’t access QVTKWidget or QVTKRenderWindowInteractor.
I am using 3D Slicer version 4.10.1-2019-01-16. with qt5.
Do you know how I can access those ?
I tried calling defining it like this :

qWidget = vtk.QVTKWidget()

But I get:

AttributeError: ‘module’ object has no attribute ‘QVTKWidget’

7

@lassoan Do you know of an alternative to QVTKWidget that is wrapped in python?

Alternatively, is there a better way to embed a vtkRenderWindow() in a QWidget?

8

ctkVTKOpenGLNativeWidget can be used for this.

1 Like
9

hi, lassoan, When I use ctkVTKOpenGLNativeWidget in python, I encounter a problem. Show “AttributeError: ctkVTKOpenGLNativeWidget has no
attribute named ‘setRenderWindow’”. Here is a screenshot below.
(U4$A74Z}7LN~NF45~E1M
But i noticed that it has been used like this in the ctk source code.

{G{VTHYAFHTIELDH3XWWIPW
{G{VTHYAFHTIELDH3XWWIPW879×444 16.8 KB

And, when I was reviewing the source code in ctk,
i found that ctkVTKOpenGLNativeWidget may inherit from three classes, and all of the parent classes has a public function setRenderWindow or SetRenderWindow .
So, I wonder to know if it is not obtainable in python .I am not familiar with python’s wrapper. Thanks a lot.

10

@lassoan In addition, i used slicer version is 5.2.2. I can get ctkVTKOpenGLNativeWidget’s setRenderWindow function in a c++ loadable module.

11

The generic Python-wrapped Qt widget for VTK rendering is ctk.ctkVTKRenderView(). A complete example:

widget = ctk.ctkVTKRenderView()
renderer = widget.renderWindow().GetRenderers().GetFirstRenderer()

cylinder = vtk.vtkCylinderSource()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(cylinder.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
renderer.AddActor(actor)

renderer.ResetCamera()
widget.show()
1 Like
12

Thank you, I’ll try it.