package cmd;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.List;

import java.util.concurrent.Callable;

import java.util.concurrent.ExecutorService;

import java.util.concurrent.Executors;

import gui.STDataAssembly;

import gui.STDataExplorer;

import io.SpatialDataContainer;

import io.SpatialDataIO;

import picocli.CommandLine;

import picocli.CommandLine.Command;

import picocli.CommandLine.Option;

import org.apache.logging.log4j.Logger;

import util.LoggerUtil;

import util.Threads;

@Command(name = "st-explorer", mixinStandardHelpOptions = true, version = "0.3.2-SNAPSHOT", description = "Spatial Transcriptomics as IMages project - interactive viewer for ST data")

public class View implements Callable<Void> {

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

@Option(names = {"-i", "--input"}, required = true, description = "input file or N5 container path, e.g. -i /home/ssq.n5.")

private String inputPath = null;

@Option(names = {"-d", "--datasets"}, required = false, description = "if input is a container: comma separated list of datasets, e.g. -d 'Puck_180528_20,Puck_180528_22' (default: open all datasets)")

private String datasets = null;

@Override

public Void call() throws IOException {

if (! SpatialDataContainer.exists(inputPath)) {

logger.error("Container / dataset '{}' does not exist. Stopping.", inputPath);

return null;

}

final ExecutorService service = Executors.newFixedThreadPool(Threads.numThreads());

final List<STDataAssembly> dataToVisualize = new ArrayList<>();

final List<String> datasetNames = new ArrayList<>();

if (SpatialDataContainer.isCompatibleContainer(inputPath)) {

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

if (datasets != null && !datasets.trim().isEmpty()) {

Arrays.stream(datasets.split(","))

.map(String::trim)

.forEach(datasetNames::add);

} else {

datasetNames.addAll(container.getDatasets());

}

for (final String dataset : datasetNames) {

logger.info("Opening dataset '{}' in '{}' ...", dataset, inputPath);

dataToVisualize.add(container.openDataset(dataset).readData());

}

}

else {

logger.info("Opening dataset '{}' ...", inputPath);

dataToVisualize.add(SpatialDataIO.openReadOnly(inputPath, service).readData());

datasetNames.add(inputPath);

}

new STDataExplorer(dataToVisualize, inputPath, datasetNames);

service.shutdown();

return null;

}

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

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

cmd.execute(args);

}

}