Update examples to use Paths (#391)

* Update examples to use Paths
* Add examples of reading filters

README.md

@@ -8,8 +8,7 @@ The intention is to make a clean Java API to access HDF5 data. Currently, the pr
 Here is an example of reading a dataset with `jHDF` (see [ReadDataset.java](jhdf/src/main/java/io/jhdf/examples/ReadDataset.java))
 
 ```java
-File file = new File("/path/to/file.hdf5");
-try (HdfFile hdfFile = new HdfFile(file)) {
+try (HdfFile hdfFile = new HdfFile(Paths.get("/path/to/file.hdf5")) {
 	Dataset dataset = hdfFile.getDatasetByPath("/path/to/dataset");
 	// data will be a Java array with the dimensions of the HDF5 dataset
 	Object data = dataset.getData();

jhdf/src/main/java/io/jhdf/examples/PrintTree.java

@@ -14,7 +14,7 @@
 import io.jhdf.api.Node;
 import org.apache.commons.lang3.StringUtils;
 
-import java.io.File;
+import java.nio.file.Paths;
 
 /**
  * An example of recursively parsing a HDF5 file tree and printing it to the
@@ -30,10 +30,8 @@ public class PrintTree {
 	 * @param args ["path/to/file.hdf5""]
 	 */
 	public static void main(String[] args) {
-		File file = new File(args[0]);
-		System.out.println(file.getName());
-
-		try (HdfFile hdfFile = new HdfFile(file)) {
+		try (HdfFile hdfFile = new HdfFile(Paths.get(args[0]))) {
+			System.out.println(hdfFile.getFile().getName()); //NOSONAR - sout in example
 			recursivePrintGroup(hdfFile, 0);
 		}
 	}
@@ -42,7 +40,7 @@ private static void recursivePrintGroup(Group group, int level) {
 		level++;
 		String indent = StringUtils.repeat("    ", level);
 		for (Node node : group) {
-			System.out.println(indent + node.getName());
+			System.out.println(indent + node.getName()); //NOSONAR - sout in example
 			if (node instanceof Group) {
 				recursivePrintGroup((Group) node, level);
 			}

jhdf/src/main/java/io/jhdf/examples/RawChunkAccess.java

@@ -14,8 +14,8 @@
 import io.jhdf.api.dataset.ChunkedDataset;
 import org.apache.commons.lang3.ArrayUtils;
 
-import java.io.File;
 import java.nio.ByteBuffer;
+import java.nio.file.Paths;
 
 /**
  * Example application for raw chunk access from HDF5
@@ -24,21 +24,19 @@
  */
 public class RawChunkAccess {
 	public static void main(String[] args) {
-		File file = new File(args[0]);
-
-		try (HdfFile hdfFile = new HdfFile(file)) {
+		try (HdfFile hdfFile = new HdfFile(Paths.get(args[0]))) {
 			Dataset dataset = hdfFile.getDatasetByPath(args[1]);
 			if (dataset instanceof ChunkedDataset) {
 				ChunkedDataset chunkedDataset = (ChunkedDataset) dataset;
 				int[] chunkOffset = new int[chunkedDataset.getChunkDimensions().length];
-				System.out.println("Chunk offset: " + ArrayUtils.toString(chunkOffset));
+				System.out.println("Chunk offset: " + ArrayUtils.toString(chunkOffset)); //NOSONAR - sout in example
 				// For the example just get the zero chunk but you can get any
 				ByteBuffer rawChunkBuffer = chunkedDataset.getRawChunkBuffer(chunkOffset);
 				// If you need the buffer just use it directly here, if you want the byte[]
 				byte[] byteArray = new byte[rawChunkBuffer.capacity()];
 				rawChunkBuffer.get(byteArray);
 				// Now you have the byte[] to use as you like
-				System.out.println("Raw bytes: " + ArrayUtils.toString(byteArray));
+				System.out.println("Raw bytes: " + ArrayUtils.toString(byteArray)); //NOSONAR - sout in example
 			} else {
 				throw new IllegalArgumentException("Dataset is not chunked");
 			}

jhdf/src/main/java/io/jhdf/examples/ReadAttribute.java

@@ -14,7 +14,7 @@
 import io.jhdf.api.Node;
 import org.apache.commons.lang3.ArrayUtils;
 
-import java.io.File;
+import java.nio.file.Paths;
 
 /**
  * Example application for reading an attribute from HDF5
@@ -27,13 +27,11 @@ public class ReadAttribute {
 	 * @param args ["path/to/file.hdf5", "path/to/node", "attributeName"]
 	 */
 	public static void main(String[] args) {
-		File file = new File(args[0]);
-
-		try (HdfFile hdfFile = new HdfFile(file)) {
+		try (HdfFile hdfFile = new HdfFile(Paths.get(args[0]))) {
 			Node node = hdfFile.getByPath(args[1]);
 			Attribute attribute = node.getAttribute(args[2]);
 			Object attributeData = attribute.getData();
-			System.out.println(ArrayUtils.toString(attributeData));
+			System.out.println(ArrayUtils.toString(attributeData)); //NOSONAR - sout in example
 		}
 	}
 }

jhdf/src/main/java/io/jhdf/examples/ReadDataset.java

@@ -13,7 +13,7 @@
 import io.jhdf.api.Dataset;
 import org.apache.commons.lang3.ArrayUtils;
 
-import java.io.File;
+import java.nio.file.Paths;
 
 /**
  * Example application for reading a dataset from HDF5
@@ -22,13 +22,11 @@
  */
 public class ReadDataset {
 	public static void main(String[] args) {
-		File file = new File(args[0]);
-
-		try (HdfFile hdfFile = new HdfFile(file)) {
+		try (HdfFile hdfFile = new HdfFile(Paths.get(args[0]))) {
 			Dataset dataset = hdfFile.getDatasetByPath(args[1]);
 			// data will be a java array of the dimensions of the HDF5 dataset
 			Object data = dataset.getData();
-			System.out.println(ArrayUtils.toString(data));
+			System.out.println(ArrayUtils.toString(data)); //NOSONAR - sout in example
 		}
 	}
 }

jhdf/src/main/java/io/jhdf/examples/ReadFilters.java

@@ -0,0 +1,33 @@
+/*
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ *
+ * http://jhdf.io
+ *
+ * Copyright (c) 2022 James Mudd
+ *
+ * MIT License see 'LICENSE' file
+ */
+package io.jhdf.examples;
+
+import io.jhdf.HdfFile;
+import io.jhdf.api.Dataset;
+import io.jhdf.filter.PipelineFilterWithData;
+
+import java.nio.file.Paths;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+/**
+ * Example of reading the filters applied to a dataset
+ */
+public class ReadFilters {
+
+	public static void main(String[] args) {
+		try (HdfFile hdfFile = new HdfFile(Paths.get(args[0]))) {
+			Dataset dataset = hdfFile.getDatasetByPath(args[1]);
+			List<PipelineFilterWithData> filters = dataset.getFilters();
+			System.out.println(filters.stream().map(Objects::toString).collect(Collectors.joining(" -> "))); //NOSONAR - sout in example
+		}
+	}
+}

jhdf/src/test/java/io/jhdf/examples/ReadFiltersTest.java

@@ -0,0 +1,56 @@
+/*
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ *
+ * http://jhdf.io
+ *
+ * Copyright (c) 2022 James Mudd
+ *
+ * MIT License see 'LICENSE' file
+ */
+package io.jhdf.examples;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+import java.net.URL;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.stream.Stream;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsString;
+
+class ReadFiltersTest {
+
+	private ByteArrayOutputStream outputStream;
+
+	@BeforeEach
+	void setUp() {
+		outputStream = new ByteArrayOutputStream();
+		System.setOut(new PrintStream(outputStream));
+	}
+
+
+	static Stream<Arguments> getTests() {
+		return Stream.of(
+			Arguments.of("/hdf5/test_byteshuffle_compressed_datasets_latest.hdf5", "/float/float32", "shuffle (id=2) data=[4] -> deflate (id=1) data=[4]"),
+			Arguments.of("/hdf5/bitshuffle_datasets.hdf5", "float32_bs8_comp2", "bitshuffle (id=32008) data=[0, 4, 4, 8, 2]")
+		);
+	}
+
+	@ParameterizedTest
+	@MethodSource("getTests")
+	void testReadFilters(String resourcePath, String datasetPath, String expectedOutput) throws Exception {
+
+		URL resource = ReadFiltersTest.class.getResource(resourcePath);
+		Path absolutePath = Paths.get(resource.toURI()).toAbsolutePath();
+
+		ReadFilters.main(new String[]{absolutePath.toString(), datasetPath});
+
+		assertThat(outputStream.toString(), containsString(expectedOutput));
+	}
+}