SNT script that checks for the presence of an unknown ARA ID detected on manually downloaded MouseLight reconstructions.

DiekProblematicCells.groovy

/*
 * SNT script that checks for the presence of a misterious ARA ID that
 * somehow was detected on manually downloaded MouseLight reconstructions.
 */

import tracing.io.MouseLightLoader;
import org.json.*

ids = ["AA0189", "AA0360", "AA0362"]
unknowCompartmentID = 484682464


for (id in ids) {
	println("Parsing id "+ id)
	jsonData = new MouseLightLoader(id).getJSON()
	neurons = jsonData.getJSONObject("contents").getJSONArray("neurons")
	for (neuron in neurons) {
		somaCompartment = neuron.getJSONObject("soma").getInt("allenId");
		println("\tSoma in unknown compartment? "+ somaCompartment)
		for (dendriteNode in neuron.getJSONArray("dendrite")) {
			allenId = dendriteNode.getInt("allenId")
			found = allenId == unknowCompartmentID
			println("\tDendrite node in ARA compartment "+ allenId + "\tUnknown? " + found)
			if (found) return;
		}
		for (axonNode in neuron.getJSONArray("axon")) {
			allenId = axonNode.getInt("allenId")
			found = allenId == unknowCompartmentID
			println("\tAxon node in ARA compartment "+ allenId + "\tUnknown? " + found)
			if (found) return;
		}
	}
	println("Parsing of id "+ id + " completed")
}
println("All ids parsed")