Tmp n5 parser for caleb

N5GenericSingleScaleMetadataParser.java

package org.janelia.saalfeldlab.n5.metadata;

import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5TreeNode;

import java.io.IOException;
import java.util.Map;
import java.util.Optional;

import static org.janelia.saalfeldlab.n5.metadata.MultiscaleMetadata.IS_LABEL_MULTISET_KEY;

public class N5GenericSingleScaleMetadataParser implements N5MetadataParser<N5GenericSingleScaleMetadata> {
	// extends AbstractN5DatasetMetadataParser<N5GenericSingleScaleMetadata> {

	public static final String MIN = "min";
	public static final String MAX = "max";
	public static final String RESOLUTION = "resolution";
	public static final String OFFSET = "offset";
	public static final String IS_LABEL_MULTISET = "isLabelMultiset";
	public static final String DOWNSAMPLING_FACTORS = "downsamplingFactors";

	// {
	// keysToTypes.put(MIN, double.class);
	// keysToTypes.put(MAX, double.class);
	// keysToTypes.put(RESOLUTION, double[].class);
	// keysToTypes.put(OFFSET, double[].class);
	// keysToTypes.put(DOWNSAMPLING_FACTORS, double[].class);
	// keysToTypes.put(IS_LABEL_MULTISET, boolean.class);
	// }

	// @Override
	// public boolean check(final Map<String, Object> metaMap) {
	//
	// final Map<String, Class<?>> requiredKeys =
	// AbstractN5DatasetMetadataParser.datasetAtttributeKeys();
	// for (final String k : requiredKeys.keySet()) {
	// if (!metaMap.containsKey(k))
	// return false;
	// else if (metaMap.get(k) == null)
	// return false;
	// }
	//
	// return true;
	// }

	@Override
	public Optional<N5GenericSingleScaleMetadata> parseMetadata(final N5Reader n5, final N5TreeNode node) {

		try {
			final DatasetAttributes attributes = n5.getDatasetAttributes(node.getPath());

			if (attributes == null)
				return Optional.empty();

			final double min = Optional.ofNullable(n5.getAttribute(node.getPath(), MIN, double.class))
					.orElse(0.0);

			final double max = Optional.ofNullable(n5.getAttribute(node.getPath(), MAX, double.class))
					.orElseGet(() -> PainteraBaseMetadata.maxForDataType(attributes.getDataType()));

			final double[] resolution = Optional.ofNullable(n5.getAttribute(node.getPath(), RESOLUTION, double[].class))
					.orElse(new double[]{1.0, 1.0, 1.0});

			if (resolution.length != 3) {
				return Optional.empty();
			}

			final double[] offset = Optional.ofNullable(n5.getAttribute(node.getPath(), OFFSET, double[].class))
					.orElse(new double[]{1.0, 1.0, 1.0});

			final double[] downsamplingFactors = Optional.ofNullable(n5.getAttribute(node.getPath(), DOWNSAMPLING_FACTORS, double[].class))
					.orElse(new double[]{1.0, 1.0, 1.0});

			final Boolean isLabelMultiset = Optional.ofNullable(n5.getAttribute(node.getPath(), IS_LABEL_MULTISET, Boolean.class))
					.orElse(false);

			N5GenericSingleScaleMetadata metadata = new N5GenericSingleScaleMetadata(node.getPath(), attributes, min, max, resolution, offset,
					downsamplingFactors, isLabelMultiset);

			if (metadata.offset.length != 3)
				return Optional.empty();

			return Optional.of(metadata);

		} catch (IOException e) {
			return Optional.empty();
		}
	}
}