QuPath scripting - combining two annotations

Image Analysis
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#1

Hi, I’ve hit the limit of my scripting abilities again and hoping someone can help.

I’m using the following script to create two annotations:

createAnnotationsFromPixelClassifier("Tissue Detection", 1000000.0, 1000.0, "SELECT_NEW")
runPlugin('qupath.lib.plugins.objects.DilateAnnotationPlugin', '{"radiusMicrons": -40.0,  "lineCap": "Round",  "removeInterior": false,  "constrainToParent": true}');
clearSelectedObjects(true);
clearSelectedObjects();
runPlugin('qupath.lib.plugins.objects.RefineAnnotationsPlugin', '{"minFragmentSizeMicrons": 10000.0,  "maxHoleSizeMicrons": 1000.0}');
resetSelection();
createAnnotationsFromPixelClassifier("Vessel Detection", 200.0, 1000.0, "SELECT_NEW")

It’s working nicely, but I then need to subtract the ‘Vessel’ annotation from the ‘Tissue’ annotation - which I can do using Edit Multiple - Subtract but I’d like to add this to the code.

Note: I think I’ve read every post in here about combining annotations but my scripting skills haven’t been able to translate them to this particular circustance.

Can anyone help?
TIA

#2

The closest immediate script is probably this recent one by Pete:

Which looks like this with some quick modifications:

def tissue = getAnnotationObjects().find {it.getPathClass() == getPathClass("Positive")}
def vessel = getAnnotationObjects().find {it.getPathClass() == getPathClass("Negative")}
def plane = tissue.getROI().getImagePlane()
if (plane != vessel.getROI().getImagePlane()) {
    println 'Annotations are on different planes!'
    return    
}
// Convert to geometries & compute distance
// Note: see https://locationtech.github.io/jts/javadoc/org/locationtech/jts/geom/Geometry.html#distance-org.locationtech.jts.geom.Geometry-
def g1 = tissue.getROI().getGeometry()
def g2 = vessel.getROI().getGeometry()

def difference = g1.difference(g2)
if (difference.isEmpty())
    println "No intersection between areas"
else {
    def roi = GeometryTools.geometryToROI(difference, plane)
    def annotation = PathObjects.createAnnotationObject(roi, getPathClass('Difference'))
    addObject(annotation)
    selectObjects(annotation)
    println "Annotated created for subtraction"
}

That does not remove the original annotations, you may want to add

removeObject(tissue, true)
removeObject(vessel, true)

May also want to change the final class “Difference” back to “Tissue”.

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#3

Thank you! You are amazing, that works perfectly!

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