Change label color using python script

Development
1

Dear all,

how can I combine all the colors in the “label” image to one color using python script.

Thanks

IIbraheem

2

Get the image data from the labelmap volume node, and apply vtkImageThreshold filter.

3

Thanks Andras. I will try this. I thought there maybe an easier way by using the “ChangeLabelEffect” from the editor module.

4

If you want to modify labels from your own script then manipulating the voxels using numpy is probably the simplest. For example, to change all non-zero voxels to 2:

a = slicer.util.array('Output Volume-label')
a[a>0] = 2

Using the vtkImageThreshold filter would be about 5-6 lines.

If you manipulate segmentations using GUI then I would recommend to use Segment Editor module instead of the old, relatively limited Editor module.

5

Thanks for the tips. I think numpy is the fastest way to do this. Could you please share how to write the array back to the volume?
lb= slicer.util.getNode('input-label')
lbd = lb.GetImageData()
lbd[lbd>0] = 2
I can not find sothomig like
lb.SettImageData(lbd)

6

found it :grin:
I forgot to update the dispaly.
these commands are enough:
lb= slicer.util.getNode('input-label')
lb[lb>0] = 2

1 Like
7

Yes, if you just toggle the slice slider the update volume will show up.

But if you want to do it automatically from a script you need to inform VTK/Slicer that numpy has changed the binary data so it will render automatically.

So you need something like this to trigger a redraw

a = slicer.util.array('Output Volume-label')
a[a>0] = 2
node = slicer.util.getNode('Output Volume-label')
node.GetImageData().GetPointData().GetScalars().Modified()
node.Modified()
8

many thanks for the code. It helps a lot.