Importig Annotation path objects after classifying outside of QuPath

QuPathImportAnnotations.groovy

// Title:   Importig Annotation path objects after classifying outside of QuPath
// Author:  Leslie Solorzano
// Date:    9 dec 2020

import qupath.lib.objects.PathObjects
import qupath.lib.roi.ROIs
import qupath.lib.regions.ImagePlane
import qupath.lib.io.GsonTools
import qupath.lib.geom.Point2
import qupath.lib.objects.classes.PathClass
import qupath.lib.objects.classes.PathClassFactory

def plane = ImagePlane.getPlane(0, 0)

//Dialogs didn't work so I just add the filename manually
def loc="/home/leslie/"

def gson=GsonTools.getInstance(true)
BufferedReader bufferedReader = new BufferedReader(new FileReader(loc+"file.json"));
HashMap<String, String> myjson = gson.fromJson(bufferedReader, HashMap.class); 

def classmap=["Class0":[41, 83, 185] ,"Class1":[255, 127, 14] ,"Class2":[234, 134, 213] ,
"Class3":[234, 35, 37] ,"Class4":[148, 103, 189] ,"Class5":[38, 153, 177]]

pathClasses=[]

for(c in classmap){
    v=c.value;k=c.key;
    pathClasses.add(PathClassFactory.getPathClass(k, getColorRGB(v[0],v[1],v[2])));
}

xCoords = myjson["allx"]; yCoords = myjson["ally"]
classes_index = myjson["allc"]

//this should be empty , I just call it to get the right data type for the list
annotations = getAnnotationObjects()

for (c=0; c < xCoords.size(); c++) {
    //copy points because (double[], double[], plane) didn't work
    List<Point2> points = []    
    def xarr= xCoords[c] as double[]
    def yarr= yCoords[c] as double[]
    
    for( i=0; i< xarr.size();i++){
        points.add(new Point2(xarr[i], yarr[i]));        
    }

    def cell_roi = ROIs.createPolygonROI(points, plane)
    def cell = PathObjects.createAnnotationObject(cell_roi)
    annotations.add(cell)
    cell.setPathClass(pathClasses[ classes_index[c] ])
}

def viewer = getCurrentViewer()
def imageData = viewer.getImageData()
def hierarchy = imageData.getHierarchy()
hierarchy.getRootObject().addPathObjects(annotations);
hierarchy.fireHierarchyChangedEvent(this)

print "Done"