Overall cell ratio for annotations

[Okan Gultekin]

Dear all, 

I have started Qupath for my master thesis. I know a little bit coding but I found coding for qupath little bit rough. Therefore, I have a problem to merge two code, not merging but converting. 

I want to get overall cell number ( in percentage) in annotations, not in TMAs. I found the code for TMA ;

import qupath.lib.objects.PathCellObject

def hierarchy = getCurrentHierarchy()

def cores = hierarchy.getTMAGrid().getTMACoreList()

def list = ["foxp3", "dapi", "CD8", "CD8+Foxp3", "PDCD1", "PDCD1+CD8", "PDCD1+Foxp3", "PC1+fox+cd8"]

cores.each {

    //Find the cell count in this core

   def total = hierarchy.getDescendantObjects(it, null, PathCellObject).size()

   //Prevent divide by zero errors in empty TMA cores

   if (total != 0){

      for (className in list) {

        def cellType = hierarchy.getDescendantObjects(it,null, PathCellObject).findAll{it.getPathClass() == getPathClass(className)}.size()

        it.getMeasurementList().putMeasurement(className+" cell %", cellType/(total)*100)

      }

   }

   else {

     for (className in list) {

        it.getMeasurementList().putMeasurement(className+" cell %", 0)

     }

   }

}

SO, Could you help me to change the TMA parts into annotaions? Thank you for help and all the effort

Regards, Okan

[micros...@gmail.com]

Ah, don't have a chance to really code right now, but is this the sort of thing you are looking for?

https://gist.github.com/Svidro/68dd668af64ad91b2f76022015dd8a45#file-class-cell-counts-percentages-and-density-to-parent-annotation-groovy

[Okan Gultekin]

Yes, Exactly! Thank you so much :) have a great day!