N5SourceFromMetadataTest.java

package org.janelia.saalfeldlab.n5.bdv;

import static org.junit.Assert.*;

import java.io.IOException;
import java.nio.file.Files;
import java.util.Optional;

import org.janelia.saalfeldlab.n5.N5FSWriter;
import org.janelia.saalfeldlab.n5.RawCompression;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.n5.metadata.MetadataSource;
import org.janelia.saalfeldlab.n5.metadata.N5CosemMetadata;
import org.janelia.saalfeldlab.n5.metadata.N5CosemMetadata.CosemTransform;
import org.janelia.saalfeldlab.n5.metadata.canonical.CanonicalMetadata;
import org.janelia.saalfeldlab.n5.metadata.canonical.CanonicalMetadataParser;
import org.janelia.saalfeldlab.n5.translation.TranslatedN5Reader;
import org.janelia.saalfeldlab.n5.metadata.N5CosemMetadataParser;
import org.janelia.saalfeldlab.n5.metadata.N5DatasetMetadata;
import org.janelia.saalfeldlab.n5.metadata.N5SingleScaleMetadata;
import org.janelia.saalfeldlab.n5.metadata.N5SingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.metadata.N5ViewerDatasetMetadataWriter;
import org.junit.Before;
import org.junit.Test;

import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.array.ArrayImg;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.img.basictypeaccess.array.ByteArray;
import net.imglib2.type.numeric.integer.ByteType;
import net.imglib2.util.Intervals;

public class N5SourceFromMetadataTest {
	
	private static String testDirPath = createTestDirPath("n5-test");
	private static String createTestDirPath(String dirName) {
		try {
			return Files.createTempDirectory(dirName).toString();
		} catch (IOException exc) {
			return System.getProperty("user.home") + "/tmp/" + dirName;
		}
	}
	static private String testBaseDatasetName = "/test/bdvSourceMetadata";
	
	private N5FSWriter n5;

	@Before
	public void before() {
		try {
			n5 = new N5FSWriter(testDirPath);

			final ArrayImg<ByteType, ByteArray> img = ArrayImgs.bytes( 7, 5, 3 );
			final ArrayImg<ByteType, ByteArray> img6d = ArrayImgs.bytes( 3, 5, 7, 11, 13, 17 );

			// write 6d
			final String dataset6d = testBaseDatasetName + "/img6d";
			N5Utils.save(img6d, n5, dataset6d, new int[]{17,17,17,17,17,17}, new RawCompression());

			// cosem
			final String datasetCosem = testBaseDatasetName + "/cosem";
			final N5CosemMetadata meta = new N5CosemMetadata("",
					new CosemTransform(
							new String[]{"z","y","x"}, 
							new double[]{2,3,4}, 
							new double[]{-1,-2,-3}, 
							new String[]{"um","um","um"}),
					null);
			final N5CosemMetadataParser pcosem = new N5CosemMetadataParser();

			N5Utils.save(img, n5, datasetCosem, new int[]{7,7,7}, new RawCompression());
			pcosem.writeMetadata(meta, n5, datasetCosem);


			// n5v
			final String n5vDataset = testBaseDatasetName + "/n5v";
			final N5ViewerDatasetMetadataWriter n5vWriter = new N5ViewerDatasetMetadataWriter();

			N5Utils.save(img, n5, n5vDataset, new int[]{7,7,7}, new RawCompression());
			n5vWriter.writeMetadata(meta, n5, n5vDataset);

		} catch (IOException e) {
			fail(e.getMessage());
		} catch (Exception e) {
			fail(e.getMessage());
		}
	}
	
	@Test
	public void sixDimTests() {
		
		final String dataset = "/test/bdvSourceMetadata/img6d";

		// raw size: [ 3, 5, 7, 11, 13, 17 ]
		final String axisOrder1 = "[\"x\",\"y\",\"z\",\"t\",\"c\",\"q\"]";
		final long[] sz1 = new long[] { 3, 5, 7 };
		final int nt1 = 11;

		final String axisOrder2 = "[\"t\",\"c\",\"q\",\"x\",\"y\",\"z\"]";
		final long[] sz2 = new long[] { 11, 13, 17 };
		final int nt2 = 3;

		final String axisOrder3 = "[\"x\",\"q\",\"w\",\"y\",\"z\",\"o\"]";
		final long[] sz3 = new long[] { 3, 11, 13 };
		final int nt3 = 1;

		final String xlationBase = "include \"n5\";\n"
		+ "def setMeta: identityAsFlatAffine(6) as $id | \n"
		+ " . + arrayUnitAxisToTransform( $id;\n"
		+ "	     \"mm\"; \n"
		+ "	     axesFromLabels( %s ;\"mm\"));\n"
		+ "addPaths | getSubTree(\"%s\") |= (.attributes |= setMeta)";

		checkTranslatedSizes( String.format(xlationBase, axisOrder1, dataset), dataset, nt1, sz1, "1");
		checkTranslatedSizes( String.format(xlationBase, axisOrder2, dataset), dataset, nt2, sz2, "2");
		checkTranslatedSizes( String.format(xlationBase, axisOrder3, dataset), dataset, nt3, sz3, "3");
	}
	
	private void checkTranslatedSizes( String translation, String dataset, int ntTrue, long[] szTrue, String suffix ) {
		
		final CanonicalMetadataParser parser = new CanonicalMetadataParser();
		TranslatedN5Reader xlated = new TranslatedN5Reader( n5, translation , "."); 
		Optional<CanonicalMetadata> meta1 = parser.parseMetadata(xlated, dataset);
		MetadataSource<?> src = new MetadataSource<>(xlated, (N5DatasetMetadata)meta1.get());

		assertEquals("nt " + suffix, ntTrue, src.numTimePoints() );
		assertArrayEquals("sz " + suffix, szTrue, Intervals.dimensionsAsLongArray( src.getSource(0, 0)));
	}
	
	@Test
	public void cosemTest() {

		final N5CosemMetadataParser p = new N5CosemMetadataParser();
		final String dataset = testBaseDatasetName + "/cosem";

		final Optional<N5CosemMetadata> parsedMeta = p.parseMetadata(n5, dataset);
		final Optional<MetadataSource<?>> srcOpt = parsedMeta.map( m -> new MetadataSource<>( n5, m ));

		assertTrue( "cosem src exists", srcOpt.isPresent());
		MetadataSource<?> src = srcOpt.get();

		assertEquals( "cosem nt=1", 1, src.numTimePoints());

		RandomAccessibleInterval<?> srcImg = src.getSource(0, 0);
		assertEquals( "cosem is 3d", 3, srcImg.numDimensions() );
	}
	
	@Test
	public void n5vTest()
	{
		final N5SingleScaleMetadataParser p = new N5SingleScaleMetadataParser();
		final String dataset = testBaseDatasetName + "/n5v";

		final Optional<N5SingleScaleMetadata> parsedMeta = p.parseMetadata(n5, dataset);
		final Optional<MetadataSource<?>> srcOpt = parsedMeta.map( m -> new MetadataSource<>( n5, m ));

		assertTrue( "n5v src exists", srcOpt.isPresent());
		MetadataSource<?> src = srcOpt.get();

		assertEquals( "n5v nt=1", 1, src.numTimePoints());

		RandomAccessibleInterval<?> srcImg = src.getSource(0, 0);
		assertEquals( "n5v is 3d", 3, srcImg.numDimensions() );
	}

}