Convert Exported Aperio Image Scope Annotations to QuPath Annotations

AperioToQuPath.groovy

import qupath.lib.scripting.QP
import qupath.lib.geom.Point2
import qupath.lib.roi.PolygonROI
import qupath.lib.objects.PathAnnotationObject
import qupath.lib.images.servers.ImageServer


//Aperio Image Scope displays images in a different orientation
def rotated = true

def server = QP.getCurrentImageData().getServer()
def h = server.getHeight()
def w = server.getWidth()

// need to add annotations to hierarchy so qupath sees them
def hierarchy = QP.getCurrentHierarchy()


//Prompt user for exported aperio image scope annotation file
def file = getQuPath().getDialogHelper().promptForFile('xml', null, 'aperio xml file', null)
def text = file.getText()

def list = new XmlSlurper().parseText(text)


list.Annotation.each {

    it.Regions.Region.each { region ->

        def tmp_points_list = []

        region.Vertices.Vertex.each{ vertex ->

            if (rotated) {
                X = vertex.@Y.toDouble()
                Y = h - vertex.@X.toDouble()
            }
            else {
                X = vertex.@X.toDouble()
                Y = vertex.@Y.toDouble()
            }
            tmp_points_list.add(new Point2(X, Y))
        }

        def roi = new PolygonROI(tmp_points_list)

        def annotation = new PathAnnotationObject(roi)

        hierarchy.addPathObject(annotation, false)
    }
}

The latter error and the solution can be found on the image.sc forum.

I am not sure about the XmlSlurper though. It is likely due to reorganization of the functions used: https://stackoverflow.com/questions/55169114/unable-to-add-xmlslurper-to-eclipse-groovy-project
https://stackoverflow.com/questions/11245073/groovy-2-cant-find-jsonslurper-and-xmlslurper-anymore
Etc. I am not sure what the exact solution for QuPath will be.

Thanks for the answer. I have managed to make it work :

Here is the script that worked for me :

"import qupath.lib.scripting.QP
import qupath.lib.geom.Point2
import qupath.lib.roi.PolygonROI
import qupath.lib.objects.PathAnnotationObject
import qupath.lib.images.servers.ImageServer

//Aperio Image Scope displays images in a different orientation
def rotated = false

def server = QP.getCurrentImageData().getServer()
def h = server.getHeight()
def w = server.getWidth()

// need to add annotations to hierarchy so qupath sees them
def hierarchy = QP.getCurrentHierarchy()

//Prompt user for exported aperio image scope annotation file
def file = Dialogs.promptForFile('xml', null, 'aperio xml file', null)
def text = file.getText()

def list = new XmlSlurper().parseText(text)

list.Annotation.each {

it.Regions.Region.each { region ->

    def tmp_points_list = []

    region.Vertices.Vertex.each{ vertex ->

        if (rotated) {
            X = vertex.@Y.toDouble()
            Y = h - vertex.@X.toDouble()
        }
        else {
            X = vertex.@X.toDouble()
            Y = vertex.@Y.toDouble()
        }
        tmp_points_list.add(new Point2(X, Y))
    }

    def roi = new PolygonROI(tmp_points_list)

    def annotation = new PathAnnotationObject(roi)

    hierarchy.addObject(annotation, false)
}

}"

I changed the following ::

replace getQuPath().getDialogHelper().promptForFile( with Dialogs.promptForFile(
replace hierarchy.addPathObject(annotation, false) with hierarchy.addObject(annotation, false)
Used version groovy-xml-3.0.17

Hope it helps