test: BdvMetadataIoTests improvements

* use temp folder * use try-with n5writer
saalfeldlab · Oct 4, 2024 · 677aa02 · 677aa02
1 parent 71b7a89
commit 677aa02
Showing 1 changed file with 60 additions and 58 deletions.
diff --git a/src/test/java/org/janelia/saalfeldlab/n5/bdv/BdvMetadataIoTests.java b/src/test/java/org/janelia/saalfeldlab/n5/bdv/BdvMetadataIoTests.java
@@ -7,6 +7,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
+import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -15,7 +16,6 @@
 import java.util.concurrent.Executors;
 import java.util.stream.Collectors;
 
-import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.ij.N5Importer;
 import org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter;
@@ -54,8 +54,12 @@ public class BdvMetadataIoTests {
 	@Before
 	public void before() {
 
-		final URL configUrl = BdvMetadataIoTests.class.getResource("/plugins.config");
-		baseDir = new File(configUrl.getFile()).getParentFile();
+		try {
+			baseDir = Files.createTempDirectory("n5-ij-tests-").toFile();
+			baseDir.deleteOnExit();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
 	}
 
 	public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & NumericType<V>> void readWriteParseTest(
@@ -77,64 +81,62 @@ public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & Numeri
 
 		final String readerDataset = dataset;
 
-		final N5Reader n5 = new N5Factory().openReader(outputPath);
-		final N5DatasetDiscoverer datasetDiscoverer = new N5DatasetDiscoverer(n5, Executors.newSingleThreadExecutor(), (x) -> true,
-				Arrays.asList(N5ViewerCreator.n5vParsers),
-				Arrays.asList(N5ViewerCreator.n5vGroupParsers));
-
-		final N5TreeNode root = datasetDiscoverer.discoverAndParseRecursive("");
-		final Optional<N5TreeNode> metaOpt = root.getDescendant(readerDataset);
-		if (!metaOpt.isPresent())
-			fail("could not find metadata at: " + readerDataset);
-
-		final List<ConverterSetup> converterSetups = new ArrayList<>();
-		final List<SourceAndConverter<T>> sourcesAndConverters = new ArrayList<>();
-
-		final SharedQueue sharedQueue = new SharedQueue(1);
-		final BdvOptions options = BdvOptions.options().frameTitle("N5 Viewer");
-
-		final int numTimepoints = N5Viewer.buildN5Sources(
-				n5,
-				new DataSelection(n5, Collections.singletonList(metaOpt.get().getMetadata())),
-				sharedQueue,
-				converterSetups,
-				sourcesAndConverters,
-				options);
-
-		assertEquals(String.format("channels for %s", dataset), imp.getNChannels(), sourcesAndConverters.size());
-		assertEquals(String.format("time points for %s", dataset), imp.getNFrames(), numTimepoints);
-
-		final Source<T> src0 = sourcesAndConverters.get(0).getSpimSource();
-		assertEquals(String.format("slices for %s", dataset), imp.getNSlices(),
-				src0.getSource(0, 0).dimension(2));
-
-		final AffineTransform3D tform = new AffineTransform3D();
-		src0.getSourceTransform(0, 0, tform);
-		final double rx = tform.get(0, 0);
-		final double ry = tform.get(1, 1);
-		final double rz = tform.get(2, 2);
-		final String unit = src0.getVoxelDimensions().unit();
-
-		if (testMeta) {
-			final boolean resEqual = rx == imp.getCalibration().pixelWidth &&
-					ry == imp.getCalibration().pixelHeight &&
-					rz == imp.getCalibration().pixelDepth;
-
-			assertTrue(String.format("%s resolutions ", dataset), resEqual);
-			assertTrue(String.format("%s units ", dataset),
-					unit.equals(imp.getCalibration().getUnit()));
+		try( final N5Writer n5 = new N5Factory().openWriter(outputPath) ) {
 
-		}
+			final N5DatasetDiscoverer datasetDiscoverer = new N5DatasetDiscoverer(n5, Executors.newSingleThreadExecutor(), (x) -> true,
+					Arrays.asList(N5ViewerCreator.n5vParsers),
+					Arrays.asList(N5ViewerCreator.n5vGroupParsers));
 
-		if (testData) {
-			final List<Source<T>> srcList = sourcesAndConverters.stream().map(sac -> sac.getSpimSource()).collect(Collectors.toList());
-			assertTrue(String.format("%s data ", dataset), sourceDataIdentical(imp, srcList));
-		}
-		n5.close();
+			final N5TreeNode root = datasetDiscoverer.discoverAndParseRecursive("");
+			final Optional<N5TreeNode> metaOpt = root.getDescendant(readerDataset);
+			if (!metaOpt.isPresent())
+				fail("could not find metadata at: " + readerDataset);
+
+			final List<ConverterSetup> converterSetups = new ArrayList<>();
+			final List<SourceAndConverter<T>> sourcesAndConverters = new ArrayList<>();
+
+			final SharedQueue sharedQueue = new SharedQueue(1);
+			final BdvOptions options = BdvOptions.options().frameTitle("N5 Viewer");
+
+			final int numTimepoints = N5Viewer.buildN5Sources(
+					n5,
+					new DataSelection(n5, Collections.singletonList(metaOpt.get().getMetadata())),
+					sharedQueue,
+					converterSetups,
+					sourcesAndConverters,
+					options);
+
+			assertEquals(String.format("channels for %s", dataset), imp.getNChannels(), sourcesAndConverters.size());
+			assertEquals(String.format("time points for %s", dataset), imp.getNFrames(), numTimepoints);
 
-		// remove
-		final N5Writer n5w = new N5Factory().openWriter(outputPath);
-		n5w.remove();
+			final Source<T> src0 = sourcesAndConverters.get(0).getSpimSource();
+			assertEquals(String.format("slices for %s", dataset), imp.getNSlices(),
+					src0.getSource(0, 0).dimension(2));
+
+			final AffineTransform3D tform = new AffineTransform3D();
+			src0.getSourceTransform(0, 0, tform);
+			final double rx = tform.get(0, 0);
+			final double ry = tform.get(1, 1);
+			final double rz = tform.get(2, 2);
+			final String unit = src0.getVoxelDimensions().unit();
+
+			if (testMeta) {
+				final boolean resEqual = rx == imp.getCalibration().pixelWidth &&
+						ry == imp.getCalibration().pixelHeight &&
+						rz == imp.getCalibration().pixelDepth;
+
+				assertTrue(String.format("%s resolutions ", dataset), resEqual);
+				assertTrue(String.format("%s units ", dataset),
+						unit.equals(imp.getCalibration().getUnit()));
+
+			}
+
+			if (testData) {
+				final List<Source<T>> srcList = sourcesAndConverters.stream().map(sac -> sac.getSpimSource()).collect(Collectors.toList());
+				assertTrue(String.format("%s data ", dataset), sourceDataIdentical(imp, srcList));
+			}
+			n5.remove();
+		}
 	}
 
 	/*