How to call the "Islands" function of the Segment Editor from a python script with "Keep selected island"

[rbumm (Rudolf Bumm)]

Hi,

I am developing an semiautomated script for CT lung masking.
After thresholding and cutting out segments of the trachea and left main bronchus (works), I normally use the “Islands” function of the Segment Editor next with the parameter “Keep selected island”.

However, something like this

    ...
    segmentEditorWidget.setActiveEffectByName("Islands")
    effect = segmentEditorWidget.activeEffect()
    effect.setParameter("Operation","KEEP_SELECTED_ISLAND")
    effect.setParameter("MinimumSize","1000")
    effect.self().onApply()
    ...

does not work from my script.
How can I pass coordinates / selected slice view / mouse click ?
Would be glad if someone had an idea or a code snippet.

Thanks, best regards
rudolf

[rbumm (Rudolf Bumm)]

@rbumm

...

def rasToDisplay(self, r, a, s):
    displayCoords = [0, 0, 0, 1]

    # get the slice node
    lm = slicer.app.layoutManager()
    sliceWidget = lm.sliceWidget('Red')
    sliceLogic = sliceWidget.sliceLogic()
    sliceNode = sliceLogic.GetSliceNode()

    xyToRASMatrix = sliceNode.GetXYToRAS()
    rasToXyMatrix = vtk.vtkMatrix4x4()
    rasToXyMatrix.Invert(xyToRASMatrix, rasToXyMatrix)

    worldCoords = [r, a, s, 1.0]
    rasToXyMatrix.MultiplyPoint(worldCoords, displayCoords)

    return (int(displayCoords[0]), int(displayCoords[1]))

... 
def how_to_call_keep_selected_islands():
...
    lm = slicer.app.layoutManager()
    sliceWidget = lm.sliceWidget('Red')
    segmentEditorWidget.setActiveEffectByName("Islands")
    effect = segmentEditorWidget.activeEffect()
    effect.setParameter("Operation","KEEP_SELECTED_ISLAND")
    slicer.util.clickAndDrag(sliceWidget, start=self.rasToDisplay(25.3, 5.8, sliceOffset), end=self.rasToDisplay(25.3, 5.8, sliceOffset), steps=1)
    ...

Found the solution myself.
Enjoy.

[lassoan (Andras Lasso)]

Thanks for sharing. You could make your code simpler and more robust by slightly changing the Islands effect so that it can take a 3D coordinate directly (not just an interaction event that you need to simulate via the GUI). The effect is a simple Python script, which you can freely modify locally (you could inject the 3D coordinate here). If the modification works well for you then you can send us a pull request so that we can integrate that change into Slicer core.

[jumbojing]

@rbumm

...

def rasToDisplay(self, r, a, s):
    displayCoords = [0, 0, 0, 1]

    # get the slice node
    lm = slicer.app.layoutManager()
    sliceWidget = lm.sliceWidget('Red')
    sliceLogic = sliceWidget.sliceLogic()
    sliceNode = sliceLogic.GetSliceNode()

    xyToRASMatrix = sliceNode.GetXYToRAS()
    rasToXyMatrix = vtk.vtkMatrix4x4()
    rasToXyMatrix.Invert(xyToRASMatrix, rasToXyMatrix)

    worldCoords = [r, a, s, 1.0]
    rasToXyMatrix.MultiplyPoint(worldCoords, displayCoords)

    return (int(displayCoords[0]), int(displayCoords[1]))

... 
def how_to_call_keep_selected_islands():
...
    lm = slicer.app.layoutManager()
    sliceWidget = lm.sliceWidget('Red')
    segmentEditorWidget.setActiveEffectByName("Islands")
    effect = segmentEditorWidget.activeEffect()
    effect.setParameter("Operation","KEEP_SELECTED_ISLAND")
    slicer.util.clickAndDrag(sliceWidget, start=self.rasToDisplay(25.3, 5.8, sliceOffset), end=self.rasToDisplay(25.3, 5.8, sliceOffset), steps=1)
    ...

@rbumm 我想知道这个代码只是在一个slice上选点,可是这个slice如何确定呢…我想说的是三维空间的第三个点怎么确定呢?

I want to know that this code just selects a point on a slice, but how to determine this slice…What I want to konw is how to determine the third point in the three-dimensional space?

[jumbojing]

@lassoan 没有更简洁的方法,直接输入the 3D coordinate来获取island?

There is no more concise way that inject the 3D coordinate to get the island…e.g. effiect.setparameter()