#@File(style="directory", label="Output directory") destinationDirectory
#@String(label="CCF Compartment (acronym, id, or label)", value="Isocortex") compartmentName
#@String(label="What to save?", choices={"dendrites", "axons", "all"}) subTreeName

import sc.fiji.snt.io.MouseLightLoader
import sc.fiji.snt.annotation.AllenCompartment
import sc.fiji.snt.annotation.AllenUtils
import sc.fiji.snt.Tree
import java.text.DecimalFormat

compartmentOfInterest = AllenUtils.getCompartment(compartmentName)
if (!MouseLightLoader.isDatabaseAvailable() || !compartmentOfInterest) {
    println("""Aborting: Can only proceed with valid compartment and
               successful connection to database""")
    return
}

println("ML Database is online")
for (neuron in 1..MouseLightLoader.getNeuronCount()) {

    // Define a valid cell ID
    id = "AA" + new DecimalFormat("0000").format(neuron)
    loader = loader = new MouseLightLoader(id)
    print("Parsing " + id + "...")
    if (!loader.idExists()) {
        println(" id not found. Skipping...")
        continue
    }

    // Retrieve the 1st node of the soma and its annotated compartment
    soma = loader.getNodes("soma")[0]
    somaCompartment = (AllenCompartment) soma.getAnnotation()

    if (compartmentOfInterest.contains(somaCompartment)) {
        print(" Downloading dendrites...")
        dendroTree = loader.getTree(subTreeName)
        println("\tSWC saved: " + dendroTree.saveAsSWC(""+destinationDirectory+"/"+id+".swc"))
    } else {
        println(" Soma not associated with " + compartmentOfInterest + ". Skipping...")
    }

}
println("Finished parsing of all " + MouseLightLoader.getNeuronCount() + " available neurons")