Generate updates for 0.1.4 version.

Author: karlnicholas

.gitignore

@@ -38,3 +38,17 @@ build/
 /*.h5
 hdf5/*/*.h5
 /bouml/
+/src/main/resources/h5ex_t/h5ex_t_array.h5
+/src/main/resources/h5ex_t/h5ex_t_bit.h5
+/src/main/resources/h5ex_t/h5ex_t_cmpd.h5
+/src/main/resources/h5ex_t/h5ex_t_commit.h5
+/src/main/resources/h5ex_t/h5ex_t_cpxcmpd.h5
+/src/main/resources/h5ex_t/h5ex_t_enum.h5
+/src/main/resources/h5ex_t/h5ex_t_float.h5
+/src/main/resources/h5ex_t/h5ex_t_int.h5
+/src/main/resources/h5ex_t/h5ex_t_objref.h5
+/src/main/resources/h5ex_t/h5ex_t_opaque.h5
+/src/main/resources/h5ex_t/h5ex_t_regref.h5
+/src/main/resources/h5ex_t/h5ex_t_string.h5
+/src/main/resources/h5ex_t/h5ex_t_vlen.h5
+/src/main/resources/h5ex_t/h5ex_t_vlstring.h5

src/main/java/org/hdf5javalib/dataclass/reference/HdfAttributeReference.java

@@ -16,7 +16,7 @@ public HdfAttributeReference(byte[] bytes, ReferenceDatatype dt, boolean externa
     }
 
     @Override
-    public HdfDataHolder getData(HdfDataFile dataFile) {
+    public HdfDataHolder getData() {
         throw new UnsupportedOperationException("Attribute Reference not supported yet.");
     }
 }

src/main/java/org/hdf5javalib/dataclass/reference/HdfDatasetRegionReference.java

@@ -61,7 +61,7 @@ public String toString() {
     }
 
     @Override
-    public HdfDataHolder getData(HdfDataFile dataFile) {
+    public HdfDataHolder getData() {
         return hdfDataHolder;
     }
 }

src/main/java/org/hdf5javalib/dataclass/reference/HdfObjectReference.java

@@ -153,7 +153,7 @@ public String toString() {
     }
 
     @Override
-    public HdfDataHolder getData(HdfDataFile dataFile) {
+    public HdfDataHolder getData() {
         return hdfDataHolder;
     }
 }

src/main/java/org/hdf5javalib/dataclass/reference/HdfReferenceInstance.java

@@ -4,5 +4,5 @@
 import org.hdf5javalib.utils.HdfDataHolder;
 
 public interface HdfReferenceInstance {
-    HdfDataHolder getData(HdfDataFile dataFile);
+    HdfDataHolder getData();
 }

src/main/java/org/hdf5javalib/datatype/ReferenceDatatype.java

@@ -160,7 +160,7 @@ public String toString(byte[] bytes) {
 //        for (byte b : bytes) sb.append(String.format("%02X", b));
 //        return "Reference[" + getReferenceType(classBitField).description + "]=" + sb;
         HdfReferenceInstance referenceInstance = getInstance(HdfReferenceInstance.class, bytes);
-        HdfDataHolder data = referenceInstance.getData(dataFile);
+        HdfDataHolder data = referenceInstance.getData();
         if ( data.isScalar()) {
             return data.getScalar().toString();
         } else {

src/main/java/org/hdf5javalib/examples/HDF5Examples/ReferenceRead.java

@@ -58,7 +58,7 @@ private void run() {
 //        }
         try {
 //            Path filePath = getResourcePath("HDF5Examples/h5ex_t_cpxcmpd.h5");
-            Path filePath = getResourcePath("HDF5Examples/soft_link.h5");
+            Path filePath = getResourcePath("HDF5Examples/h5ex_t_cpxcmpd.h5");
             System.out.println(filePath.toFile().getAbsolutePath());
             try (SeekableByteChannel channel = Files.newByteChannel(filePath, StandardOpenOption.READ)) {
                 HdfFileReader reader = new HdfFileReader(channel).readFile();

src/main/java/org/hdf5javalib/examples/h5ex_t/h5ex_t_read.java

@@ -0,0 +1,70 @@
+package org.hdf5javalib.examples.h5ex_t;
+
+import org.hdf5javalib.datasource.TypedDataSource;
+import org.hdf5javalib.hdfjava.HdfDataset;
+import org.hdf5javalib.hdfjava.HdfFileReader;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.channels.SeekableByteChannel;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+
+import static org.hdf5javalib.utils.HdfDisplayUtils.displayData;
+
+/**
+ * Demonstrates reading and processing compound data from an HDF5 file.
+ * <p>
+ * The {@code CompoundRead} class serves as an example application that reads
+ * a compound dataset from an HDF5 file, processes it using a {@link TypedDataSource},
+ * and displays the results. It showcases filtering and mapping operations on the
+ * dataset, as well as conversion to a custom Java class.
+ * </p>
+ */
+public class h5ex_t_read {
+    private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(h5ex_t_read.class);
+
+    /**
+     * Entry point for the application.
+     *
+     * @param args command-line arguments (not used)
+     */
+    public static void main(String[] args) {
+        new h5ex_t_read().run();
+    }
+
+    /**
+     * Executes the main logic of reading and displaying compound data from an HDF5 file.
+     */
+    private void run() {
+        try {
+
+            // List all .h5 files in HDF5Examples resources directory
+            Path dirPath = Paths.get(h5ex_t_read.class.getClassLoader().getResource("h5ex_t").toURI());
+            Files.list(dirPath)
+                    .filter(p -> p.toString().endsWith(".h5"))
+                    .forEach(p -> {
+                        System.out.println("Running " + p.getFileName());
+                        displayFile(p);
+                    });
+        } catch (URISyntaxException e) {
+            throw new RuntimeException(e);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    public void displayFile(Path filePath) {
+        try (SeekableByteChannel channel = Files.newByteChannel(filePath, StandardOpenOption.READ)) {
+            HdfFileReader reader = new HdfFileReader(channel).readFile();
+            for (HdfDataset dataSet : reader.getDatasets()) {
+                log.info("{} ", dataSet);
+                displayData(channel, dataSet, reader);
+            }
+        } catch (Exception e) {
+            log.error("Exception in displayFile: {}", filePath, e);
+        }
+    }
+}