Extract soma positions from ML database

ExtractSomaPositions.groovy

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

// The name of the compartment to extract somas from
compartmentOfInterest = AllenUtils.getCompartment("Cerebral cortex")

/*
If MouseLightQuerier is available one could simply do:
	cellIds = MouseLightQuerier.getIDs(compartmentOfInterest)
	for (neuron in cellIds) {
		(...)
	}
*/

println("ID,Soma X,Soma Y,Soma Z,Label ID")
for (neuron in 1..MouseLightLoader.getNeuronCount()) {

    // Define a valid cell ID
    id = "AA" + new DecimalFormat("0000").format(neuron)
    loader = loader = new MouseLightLoader(id)
    if (!loader.idExists()) continue

    // Currently all somas are represented by a single point
    soma = loader.getNodes("soma")[0]
    somaCompartment = (AllenCompartment) soma.getAnnotation()

    if (compartmentOfInterest.contains(somaCompartment)) {
    	somaDetails = [id, soma.getX(), soma.getY(), soma.getZ()]
    	if (somaCompartment) somaDetails << somaCompartment.id()
        println(somaDetails.join(","))
    }

}