Fix bug that rendered transformations singular

N5 writers were not closed properly, which led to their caches not being
flushed, which in turn led to transformations being written as all-zeros

Author: minnerbe

src/main/java/io/SpatialDataIO.java

@@ -229,22 +229,21 @@ public void writeData(STDataAssembly data) throws IOException {
 		if (readOnly)
 			throw new IllegalStateException("Trying to write to read-only file.");
 
-		N5Writer writer = (N5Writer) ioSupplier.get();
-		STData stData = data.data();
+		try (N5Writer writer = (N5Writer) ioSupplier.get()) {
+			STData stData = data.data();
 
-		logger.debug( "Saving spatial data ... " );
-		long time = System.currentTimeMillis();
-
-		initializeDataset(writer, stData);
+			logger.debug("Saving spatial data ... ");
+			long time = System.currentTimeMillis();
 
-		writeExpressionValues(writer, stData.getAllExprValues());
-		writeLocations(writer, stData.getLocations());
-		updateTransformation(writer, data.transform(), transformFieldName);
-		//writeTransformation(writer, data.intensityTransform(), "intensity_transform");
+			initializeDataset(writer, stData);
 
-		updateStoredAnnotations(stData.getAnnotations());
+			writeExpressionValues(writer, stData.getAllExprValues());
+			writeLocations(writer, stData.getLocations());
+			updateTransformation(writer, data.transform(), transformFieldName);
 
-		logger.debug("Saving took {} ms.", System.currentTimeMillis() - time);
+			updateStoredAnnotations(stData.getAnnotations());
+			logger.debug("Saving took {} ms.", System.currentTimeMillis() - time);
+		}
 	}
 
 	/**
@@ -256,14 +255,15 @@ public void updateStoredAnnotations(Map<String, RandomAccessibleInterval<? exten
 		if (readOnly)
 			throw new IllegalStateException("Trying to write to read-only file.");
 
-		N5Writer writer = (N5Writer) ioSupplier.get();
-		List<String> existingAnnotations = detectAnnotations(writer);
+		try (N5Writer writer = (N5Writer) ioSupplier.get()) {
+			List<String> existingAnnotations = detectAnnotations(writer);
 
-		for (Entry<String, RandomAccessibleInterval<? extends NativeType<?>>> newEntry : metadata.entrySet()) {
-			if (existingAnnotations.contains(newEntry.getKey()))
-				logger.warn("Metadata '{}' already exists. Skip writing.", newEntry.getKey());
-			else
-				writeAnnotations(writer, newEntry.getKey(), newEntry.getValue());
+			for (Entry<String, RandomAccessibleInterval<? extends NativeType<?>>> newEntry : metadata.entrySet()) {
+				if (existingAnnotations.contains(newEntry.getKey()))
+					logger.warn("Metadata '{}' already exists. Skip writing.", newEntry.getKey());
+				else
+					writeAnnotations(writer, newEntry.getKey(), newEntry.getValue());
+			}
 		}
 	}
 
@@ -276,14 +276,15 @@ public void updateStoredGeneAnnotations(Map<String, RandomAccessibleInterval<? e
 		if (readOnly)
 			throw new IllegalStateException("Trying to write to read-only file.");
 
-		N5Writer writer = (N5Writer) ioSupplier.get();
-		List<String> existingGeneAnnotations = detectGeneAnnotations(writer);
+		try (N5Writer writer = (N5Writer) ioSupplier.get()) {
+			List<String> existingGeneAnnotations = detectGeneAnnotations(writer);
 
-		for (Entry<String, RandomAccessibleInterval<? extends NativeType<?>>> newEntry : metadata.entrySet()) {
-			if (existingGeneAnnotations.contains(newEntry.getKey()))
-				logger.warn("Metadata '{}' already exists. Skip writing.", newEntry.getKey());
-			else
-				writeGeneAnnotations(writer, newEntry.getKey(), newEntry.getValue());
+			for (Entry<String, RandomAccessibleInterval<? extends NativeType<?>>> newEntry : metadata.entrySet()) {
+				if (existingGeneAnnotations.contains(newEntry.getKey()))
+					logger.warn("Metadata '{}' already exists. Skip writing.", newEntry.getKey());
+				else
+					writeGeneAnnotations(writer, newEntry.getKey(), newEntry.getValue());
+			}
 		}
 	}
 
@@ -327,8 +328,9 @@ public void updateTransformation(AffineGet transform, String name) throws IOExce
 		if (readOnly)
 			throw new IllegalStateException("Trying to modify a read-only file.");
 
-		N5Writer writer = (N5Writer) ioSupplier.get();
-		updateTransformation(writer, transform, name);
+		try (N5Writer writer = (N5Writer) ioSupplier.get()) {
+			updateTransformation(writer, transform, name);
+		}
 	}
 
 	/**

src/test/java/IOTest.java

@@ -17,6 +17,7 @@
 import java.util.Arrays;
 import java.util.List;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.junit.jupiter.api.Assertions.fail;
 import static org.junit.jupiter.api.Named.named;
@@ -60,15 +61,18 @@ public void io_works_for_transformations(String path) {
 		STData data = TestUtils.createTestDataSet();
 		STDataStatistics stats = new STDataStatistics(data);
 		final AffineTransform2D transform = new AffineTransform2D();
-		transform.rotate(3.14159 / 4);
+		transform.rotate(3.14159 / 6);
 		STDataAssembly expected = new STDataAssembly(data, stats, transform);
 
 		try {
 			SpatialDataIO sdio = SpatialDataIO.open(getPlaygroundPath(path), executorService);
 			sdio.writeData(expected);
 			STDataAssembly actual = sdio.readData();
-
-			TestUtils.compareSTDataAssemblies(actual, expected);
+			for (int i = 0; i < 2; i++) {
+				for (int j = 0; j < 2; j++) {
+					assertEquals(transform.get(i, j), actual.transform().get(i, j));
+				}
+			}
 		}
 		catch (IOException e) {
 			fail("Could not write / read file: ", e);