export_results.groovy

import qupath.lib.gui.tools.MeasurementExporter
import qupath.lib.objects.PathDetectionObject
import qupath.lib.objects.PathAnnotationObject

// Get the list of all images in the current project
def project = getProject()
//def imagesToExport = project.getImageList()

def viewer = getCurrentViewer()
def imagesToExport = viewer.getImageData()

// Separate each measurement value in the output file with a tab ("\t")
def separator = "\t"

// Choose the columns that will be included in the export
// Note: if 'columnsToInclude' is empty, all columns will be included
def columnsToInclude = new String[]{}

// Choose the type of objects that the export will process
// Other possibilities include:
//    1. PathAnnotationObject
//    2. PathDetectionObject
//    3. PathRootObject
//PathCellObject.class
// Note: import statements should then be modified accordingly
def exportType = PathAnnotationObject.class

// Choose your *full* output path
def outputPath = "/home/ninatubau/detections_1.csv"
def outputFile = new File(outputPath)

// Create the measurementExporter and start the export
def exporter  = new MeasurementExporter()
                  .imageList(imagesToExport)            // Images from which measurements will be exported
                  .separator(separator)                 // Character that separates values
                  .includeOnlyColumns(columnsToInclude) // Columns are case-sensitive
                  .exportType(exportType)               // Type of objects to export
                  .exportMeasurements(outputFile)        // Start the export process

print "Done!"