Exports all cell measurements within selections to a csv file

ExportMeasurements-2018.06.22-FB.groovy

import qupath.lib.gui.QuPathGUI
import qupath.lib.measurements.MeasurementList
import qupath.lib.scripting.QP

/**
 *  Exports detection results to excel file
 *
 *  @Author Frank Bonini
 *  @Author Caleb Grenko (did admittedly little)
 */


print 'Running script'

        print 'Inside \'Run\''

        /*
        CHANGE THIS FILEPATH BEFORE USING THIS SCRIPT.
         */
        def imageName = QuPathGUI.getInstance().getImageData().getServerPath()
        imageName = imageName.substring(imageName.lastIndexOf('\\') + 1, imageName.lastIndexOf('.'))
        print("Image name: $imageName")
        def path = "" + QuPathGUI.getInstance().getProjectExportDirectory(true) + "\\${imageName}.csv"


//        saveAnnotationMeasurements(path)

        print 'Results exported to ' + path

        print 'SAVE THESE RESULTS! THEY WILL BE OVERWRITTEN DURING THE NEXT TIME THIS SCRIPT IS RUN.'

        def Annotations = QuPathGUI.getInstance().getImageData().getHierarchy().getSelectionModel().getSelectedObjects()

        print "Annotations has this many elements: " + Annotations.size()
        def Measurements = new ArrayList<MeasurementList>()
        /*
        For each annotation in the list
         */
        for(a in Annotations){

            for(c in a.childObjects){

                Measurements.add(c.getMeasurementList())
//                print c.getMeasurementList()
            }
        }




def MeasurementNames = Measurements.get(0).getMeasurementNames()
def rawMeasurements = new ArrayList<String>()

rawMeasurements.add(MeasurementNames.toString())

//Go through each cell
for(m in Measurements){

    def measurementString = ''

    //Go through each value and format it correctly
    for(n in MeasurementNames){
        measurementString += (m.getMeasurementValue(n) + ', ')
    }
    rawMeasurements.add(measurementString)
}

//print rawMeasurements
File file = new File(path)

for(m in rawMeasurements){
    file << (m + System.getProperty("line.separator"))
}

print("Done!")