package cmd;

import java.util.concurrent.Callable;

import java.util.concurrent.ExecutorService;

import java.util.concurrent.Executors;

import analyze.Entropy;

import analyze.ExtractGeneLists;

import data.STData;

import io.SpatialDataContainer;

import net.imglib2.RandomAccessibleInterval;

import net.imglib2.type.numeric.real.DoubleType;

import picocli.CommandLine;

import picocli.CommandLine.Command;

import picocli.CommandLine.Option;

import org.apache.logging.log4j.Logger;

import util.LoggerUtil;

// In the future, this will support more methods for computing the std

@Command(name = "st-add-entropy", mixinStandardHelpOptions = true, version = "0.3.2-SNAPSHOT", description = "Spatial Transcriptomics as IMages project - add annotations to slice-dataset")

public class AddEntropy implements Callable<Void> {

private static final Logger logger = LoggerUtil.getLogger();

@Option(names = {"-i", "--input"}, required = true, description = "input container for which to pre-compute entropy, e.g. -i /home/ssq.n5")

private String inputPath = null;

@Option(names = {"-m", "--method"}, required = false, description = "method to compute gene entropy")

private Entropy entropy = Entropy.STDEV;

@Option(names = {"--overwrite"}, required = false, description = "overwrite existing entropy values")

private boolean overwrite = false;

@Option(names = {"--numThreads"}, required = false, description = "number of threads for parallel processing")

private int numThreads = 8;

@Override

public Void call() throws Exception {

if (inputPath == null) {

logger.error("No input path defined. Stopping.");

return null;

}

final ExecutorService service = Executors.newFixedThreadPool(numThreads);

final SpatialDataContainer container = SpatialDataContainer.openExisting(inputPath, service);

logger.info("Computing gene variability with method '{}' (might take a while)", entropy.label());

int i = 0;

for (final String dataset : container.getDatasets()) {

logger.info("Computing gene variability for {} ({}/{})", dataset, ++i, container.getDatasets().size());

if (container.hasEntropyValues(dataset, entropy) && !overwrite) {

logger.info("Entropy values already exist for dataset '{}', skipping.", dataset);

continue;

}

final STData stData = container.openDataset(dataset).readData().data();

final RandomAccessibleInterval<DoubleType> entropyValues = ExtractGeneLists.computeOrderedEntropy(stData, entropy, numThreads);

container.saveEntropyValues(entropyValues, dataset, entropy);

}

logger.debug("Done.");

service.shutdown();

return null;

}

public static void main(final String... args) {

final CommandLine cmd = new CommandLine(new AddEntropy());

cmd.execute(args);

}

}