v2 arch support

Author: karlnicholas

src/main/java/org/hdf5javalib/examples/hdf5examples/HDF5Debug.java

@@ -54,8 +54,8 @@ private void run() {
         try {
             // List all .h5 files in HDF5Examples resources directory
             // ATL03_20250302235544_11742607_006_01
-            Path dirPath = Paths.get(Objects.requireNonNull(HDF5Debug.class.getClassLoader().getResource("HDF5Examples/h5ex_g_compact2.h5")).toURI());
-//            Path dirPath = Paths.get("c:/users/karln/Downloads/ATL03_20250302235544_11742607_006_01.h5");
+//            Path dirPath = Paths.get(Objects.requireNonNull(HDF5Debug.class.getClassLoader().getResource("HDF5Examples/h5ex_g_compact2.h5")).toURI());
+            Path dirPath = Paths.get("c:/users/karnicho/Downloads/ATL03_20250302235544_11742607_006_01.h5");
             processFile(dirPath);
         } catch (Exception e) {
             throw new IllegalStateException(e);
@@ -65,18 +65,18 @@ private void run() {
     private static void processFile(Path filePath) {
         try (SeekableByteChannel channel = Files.newByteChannel(filePath, StandardOpenOption.READ)) {
             HdfFileReader reader = new HdfFileReader(channel).readFile();
-            for (HdfDataset dataSet : reader.getDatasets()) {
-                System.out.println("{} " + dataSet);
-//                log.info("{} ", dataSet);
-                HdfDisplayCountUtils.displayData(channel, dataSet, reader);
-//                displayScalarData(channel, dataSet, HdfFloatPoint.class, reader);
-            }
-//            HdfDataset dataSet = reader.getDataset("/ancillary_data/calibrations/low_link_impulse_response/hist_x").get();
-//            System.out.println("{} " + dataSet);
-////                System.out.println("{} " + dataSet.getObjectPath());
+//            for (HdfDataset dataSet : reader.getDatasets()) {
+//                System.out.println("{} " + dataSet);
 ////                log.info("{} ", dataSet);
-//                HdfDisplayUtils.displayData(channel, dataSet, reader);
+//                HdfDisplayCountUtils.displayData(channel, dataSet, reader);
 ////                displayScalarData(channel, dataSet, HdfFloatPoint.class, reader);
+//            }
+            HdfDataset dataSet = reader.getDataset("/gt1l/heights/delta_time").get();
+            System.out.println("{} " + dataSet);
+//                System.out.println("{} " + dataSet.getObjectPath());
+//                log.info("{} ", dataSet);
+                HdfDisplayUtils.displayData(channel, dataSet, reader);
+//                displayScalarData(channel, dataSet, HdfFloatPoint.class, reader);
         } catch (Exception e) {
             log.error("Exception in processFile: {}", filePath, e);
         }

src/main/java/org/hdf5javalib/hdfjava/HdfFileReader.java

@@ -13,6 +13,8 @@
 import org.hdf5javalib.hdffile.metadata.HdfSuperblock;
 import org.hdf5javalib.utils.HdfReadUtils;
 import org.hdf5javalib.utils.HdfWriteUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
@@ -42,6 +44,7 @@
  * </p>
  */
 public class HdfFileReader implements HdfDataFile {
+    private static final Logger log = LoggerFactory.getLogger(HdfFileReader.class);
 //    /** The superblock containing metadata about the HDF5 file. */
     public static final byte[] BTREE_SIGNATURE = {'T', 'R', 'E', 'E'};
     public static final int BTREE_HEADER_INITIAL_SIZE = 8;
@@ -88,6 +91,7 @@ public HdfFileReader(SeekableByteChannel fileChannel) {
     public HdfFileReader readFile() throws Exception {
         long superblockOffset = findSuperblockOffset(fileChannel);
         superblock = readSuperblockFromSeekableByteChannel(fileChannel, superblockOffset, this);
+        log.debug("HdfFileReader::readFile superblock: {}", superblock);
 
         // Step 1: Get the root object header address. This logic IS dependent on the superblock version.
         long rootObjectHeaderAddr;
@@ -297,15 +301,16 @@ private void processLink(HdfGroup parentGroup, String linkName, long objectHeade
         if (isGroup) {
             HdfGroup groupObject = new HdfGroup(linkName, objectHeader, parentGroup, hardLink);
             parentGroup.addChild(groupObject);
-            System.out.println("ADDED GROUP: " + groupObject.getObjectPath() + " at " + objectHeaderOffset);
+            log.debug("HdfFileReader::processLink - added group {} at {}", groupObject.getObjectPath(), objectHeaderOffset);
 
             if (hardLink == null) {
                 processV2GroupLinks(groupObject);
             }
         } else {
             HdfDataset datasetObject = new HdfDataset(linkName, objectHeader, parentGroup, hardLink);
             parentGroup.addChild(datasetObject);
-            System.out.println("ADDED DATASET: " + datasetObject.getObjectPath() + " at " + objectHeaderOffset);
+            log.debug("HdfFileReader::processLink - added dataset {} at {}", datasetObject.getObjectPath(), objectHeaderOffset);
+            log.trace("HdfFileReader::processLink - added dataset {}:{}", datasetObject.getObjectPath(), datasetObject.getObjectHeader());
         }
     }
 
@@ -475,10 +480,10 @@ public static HdfSuperblock readSuperblockFromSeekableByteChannel(SeekableByteCh
         FixedPointDatatype fixedPointDatatypeForLength;
 
         // Parse addresses using HdfFixedPoint
-        HdfFixedPoint baseAddress = null;
+        HdfFixedPoint baseAddress;
         HdfFixedPoint freeSpaceAddress = null;
         HdfFixedPoint extensionAddress = null;
-        HdfFixedPoint endOfFileAddress = null;
+        HdfFixedPoint endOfFileAddress;
         HdfFixedPoint driverInformationAddress = null;
         HdfFixedPoint rootObjectHeaderAddress = null;
         buffer.position(SIGNATURE_SIZE + VERSION_SIZE); // Skip the file signature
@@ -540,7 +545,7 @@ public static HdfSuperblock readSuperblockFromSeekableByteChannel(SeekableByteCh
 
         }
 
-        HdfSuperblock superblock = new HdfSuperblock(
+        return new HdfSuperblock(
                 version,
                 freeSpaceVersion,
                 rootGroupVersion,
@@ -559,7 +564,6 @@ public static HdfSuperblock readSuperblockFromSeekableByteChannel(SeekableByteCh
                 fixedPointDatatypeForOffset,
                 fixedPointDatatypeForLength
         );
-        return superblock;
     }
 
     /**