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karlnicholaskarlnicholas
committed
refactor v2 code
1 parent 65aac63 commit 7fc80c4

3 files changed

Lines changed: 110 additions & 114 deletions

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,7 @@ private void run() {
5555
// List all .h5 files in HDF5Examples resources directory
5656
// ATL03_20250302235544_11742607_006_01
5757
// Path dirPath = Paths.get(Objects.requireNonNull(HDF5Debug.class.getClassLoader().getResource("HDF5Examples/h5ex_g_compact2.h5")).toURI());
58-
Path dirPath = Paths.get("c:/users/karln/Downloads/ATL03_20250302235544_11742607_006_01.h5");
58+
Path dirPath = Paths.get("c:/users/karnicho/Downloads/ATL03_20250302235544_11742607_006_01.h5");
5959
processFile(dirPath);
6060
} catch (Exception e) {
6161
throw new IllegalStateException(e);

‎src/main/java/org/hdf5javalib/hdffile/dataobjects/messages/DataLayoutMessage.java‎

Lines changed: 1 addition & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,7 @@
33
import org.hdf5javalib.dataclass.HdfFixedPoint;
44
import org.hdf5javalib.dataclass.reference.HdfDataspaceSelectionInstance;
55
import org.hdf5javalib.datatype.FixedPointDatatype;
6-
import org.hdf5javalib.hdffile.infrastructure.HdfBTreeEntryBase;
76
import org.hdf5javalib.hdffile.infrastructure.HdfBTreeV1;
8-
import org.hdf5javalib.hdffile.infrastructure.HdfChunkBTreeEntry;
97
import org.hdf5javalib.hdfjava.HdfDataFile;
108
import org.hdf5javalib.hdfjava.HdfFileReader;
119
import org.hdf5javalib.utils.HdfDisplayUtils;
@@ -15,12 +13,8 @@
1513
import java.lang.reflect.InvocationTargetException;
1614
import java.nio.ByteBuffer;
1715
import java.nio.ByteOrder;
18-
import java.nio.channels.SeekableByteChannel;
1916
import java.util.*;
2017

21-
import static org.hdf5javalib.hdfjava.HdfFileReader.BTREE_HEADER_INITIAL_SIZE;
22-
import static org.hdf5javalib.hdfjava.HdfFileReader.BTREE_SIGNATURE;
23-
2418
/**
2519
* Represents a Data Layout Message in the HDF5 file format.
2620
* <p>
@@ -161,8 +155,7 @@ public static HdfMessage parseHeaderMessage(int flags, byte[] data, HdfDataFile
161155
8, 0, (8 * 8),
162156
hdfDataFile);
163157

164-
// bTree = HdfFileReader.readBTreeFromSeekableByteChannel(hdfDataFile.getSeekableByteChannel(), chunkedDataAddress.getInstance(Long.class), numDimensions, eightByteFixedPointType, hdfDataFile);
165-
bTree = HdfFileReader.readBTreeFromSeekableByteChannel(hdfDataFile.getSeekableByteChannel(), chunkedDataAddress.getInstance(Long.class), hdfDataFile);
158+
bTree = HdfFileReader.readBTreeFromSeekableByteChannelForChunked(hdfDataFile.getSeekableByteChannel(), chunkedDataAddress.getInstance(Long.class), numDimensions, eightByteFixedPointType, hdfDataFile);
166159
} else {
167160
bTree = null;
168161
}

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

Lines changed: 108 additions & 105 deletions
Original file line numberDiff line numberDiff line change
@@ -156,7 +156,7 @@ private void readV1Structure(long rootObjectHeaderAddr, HdfSymbolTableEntry root
156156
long bTreeAddress = ((HdfSymbolTableEntryCacheWithScratch) rootGroupSTE.getCache()).getbTreeAddress().getInstance(Long.class);
157157

158158
HdfLocalHeap localHeap = readLocalHeapFromSeekableByteChannel(fileChannel, heapOffset, this);
159-
HdfBTreeV1 groupBTree = readBTreeFromSeekableByteChannel(fileChannel, bTreeAddress, this);
159+
HdfBTreeV1 groupBTree = readBTreeFromSeekableByteChannelForGroups(fileChannel, bTreeAddress, this);
160160

161161
String rootGroupName = localHeap.stringAtOffset(rootGroupSTE.getLinkNameOffset());
162162
HdfGroup rootGroup = new HdfGroup(rootGroupName, rootObjectHeader, null, null);
@@ -206,7 +206,7 @@ private void readV1GroupHierarchy(HdfGroup parentGroup, HdfLocalHeap localHeap,
206206
long newHeapOffset = ((HdfSymbolTableEntryCacheWithScratch) symbolTableEntry.getCache()).getLocalHeapAddress().getInstance(Long.class);
207207
long newBTreeAddress = ((HdfSymbolTableEntryCacheWithScratch) symbolTableEntry.getCache()).getbTreeAddress().getInstance(Long.class);
208208
HdfLocalHeap newLocalHeap = readLocalHeapFromSeekableByteChannel(fileChannel, newHeapOffset, this);
209-
HdfBTreeV1 newGroupBTree = readBTreeFromSeekableByteChannel(fileChannel, newBTreeAddress, this);
209+
HdfBTreeV1 newGroupBTree = readBTreeFromSeekableByteChannelForGroups(fileChannel, newBTreeAddress, this);
210210
readV1GroupHierarchy(groupObject, newLocalHeap, newGroupBTree);
211211
}
212212
break;
@@ -576,12 +576,12 @@ public static HdfSuperblock readSuperblockFromSeekableByteChannel(SeekableByteCh
576576
* @return the constructed HdfTree instance
577577
* @throws IOException if an I/O error occurs or the B-Tree data is invalid
578578
*/
579-
public static HdfBTreeV1 readBTreeFromSeekableByteChannel(
579+
public static HdfBTreeV1 readBTreeFromSeekableByteChannelForGroups(
580580
SeekableByteChannel fileChannel,
581581
long btreeAddress,
582582
HdfDataFile hdfDataFile
583583
) throws Exception {
584-
return readFromSeekableByteChannelRecursive(fileChannel, btreeAddress, hdfDataFile, new LinkedHashMap<>());
584+
return readFromSeekableByteChannelRecursiveForGroups(fileChannel, btreeAddress, hdfDataFile, new LinkedHashMap<>());
585585
}
586586

587587
/**
@@ -594,10 +594,10 @@ public static HdfBTreeV1 readBTreeFromSeekableByteChannel(
594594
* @return the constructed HdfTree instance
595595
* @throws IOException if an I/O error occurs or the B-Tree data is invalid
596596
*/
597-
private static HdfBTreeV1 readFromSeekableByteChannelRecursive(SeekableByteChannel fileChannel,
598-
long nodeAddress,
599-
HdfDataFile hdfDataFile,
600-
Map<Long, HdfBTreeV1> visitedNodes
597+
private static HdfBTreeV1 readFromSeekableByteChannelRecursiveForGroups(SeekableByteChannel fileChannel,
598+
long nodeAddress,
599+
HdfDataFile hdfDataFile,
600+
Map<Long, HdfBTreeV1> visitedNodes
601601
) throws Exception {
602602
if (visitedNodes.containsKey(nodeAddress)) {
603603
throw new IllegalStateException("Cycle detected or node re-visited: BTree node address "
@@ -650,7 +650,7 @@ private static HdfBTreeV1 readFromSeekableByteChannelRecursive(SeekableByteChann
650650
HdfGroupBTreeEntry entry;
651651
if (nodeLevel == 1) {
652652
// It's a sub B-Tree
653-
HdfBTreeV1 child = readFromSeekableByteChannelRecursive(fileChannel, childAddress, hdfDataFile, visitedNodes);
653+
HdfBTreeV1 child = readFromSeekableByteChannelRecursiveForGroups(fileChannel, childAddress, hdfDataFile, visitedNodes);
654654
entry = new HdfGroupBTreeEntry(key, childPointer, child, null); // Assuming entry constructor accepts Object for last param
655655
} else {
656656
// It's a SNOD
@@ -663,102 +663,105 @@ private static HdfBTreeV1 readFromSeekableByteChannelRecursive(SeekableByteChann
663663
return currentNode;
664664
}
665665

666-
// /**
667-
// * Reads an HdfTree from a file channel.
668-
// *
669-
// * @param fileChannel the file channel to read from
670-
// * @param hdfDataFile the HDF5 file context
671-
// * @return the constructed HdfTree instance
672-
// * @throws IOException if an I/O error occurs or the B-Tree data is invalid
673-
// */
674-
// public static HdfBTreeV1 readBTreeFromSeekableByteChannel(
675-
// SeekableByteChannel fileChannel,
676-
// long btreeAddress,
677-
// int dimensions,
678-
// FixedPointDatatype eightByteFixedPointType,
679-
// HdfDataFile hdfDataFile
680-
// ) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
681-
// return readFromSeekableByteChannelRecursive(fileChannel, btreeAddress, dimensions, eightByteFixedPointType, hdfDataFile, new LinkedHashMap<>());
682-
// }
683-
//
684-
// /**
685-
// * Recursively reads an HdfTree from a file channel, handling cycles.
686-
// *
687-
// * @param fileChannel the file channel to read from
688-
// * @param nodeAddress the address of the current node
689-
// * @param visitedNodes a map of visited node addresses to detect cycles
690-
// * @param hdfDataFile the HDF5 file context
691-
// * @return the constructed HdfTree instance
692-
// * @throws IOException if an I/O error occurs or the B-Tree data is invalid
693-
// */
694-
// private static HdfBTreeV1 readFromSeekableByteChannelRecursive(SeekableByteChannel fileChannel,
695-
// long nodeAddress,
696-
// int dimensions,
697-
// FixedPointDatatype eightByteFixedPointType,
698-
// HdfDataFile hdfDataFile,
699-
// Map<Long, HdfBTreeV1> visitedNodes
700-
// ) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
701-
// if (visitedNodes.containsKey(nodeAddress)) {
702-
// throw new IllegalStateException("Cycle detected or node re-visited: BTree node address "
703-
// + nodeAddress + " encountered again during recursive read.");
704-
// }
705-
//
706-
// fileChannel.position(nodeAddress);
707-
// FixedPointDatatype hdfOffset = hdfDataFile.getSuperblock().getFixedPointDatatypeForOffset();
708-
// final int offsetSize = hdfOffset.getSize();
709-
//
710-
// int headerSize = BTREE_HEADER_INITIAL_SIZE + offsetSize + offsetSize;
711-
// ByteBuffer headerBuffer = ByteBuffer.allocate(headerSize).order(ByteOrder.LITTLE_ENDIAN);
712-
// fileChannel.read(headerBuffer);
713-
// headerBuffer.flip();
714-
//
715-
// byte[] signatureBytes = new byte[BTREE_SIGNATURE.length];
716-
// headerBuffer.get(signatureBytes);
717-
// if (Arrays.compare(signatureBytes, BTREE_SIGNATURE) != 0) {
718-
// throw new IOException("Invalid B-tree node signature: '" + Arrays.toString(signatureBytes) + "' at position " + nodeAddress);
719-
// }
720-
//
721-
// int nodeType = Byte.toUnsignedInt(headerBuffer.get());
722-
// int nodeLevel = Byte.toUnsignedInt(headerBuffer.get());
723-
// int entriesUsed = Short.toUnsignedInt(headerBuffer.getShort());
724-
//
725-
// HdfFixedPoint leftSiblingAddress = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, headerBuffer);
726-
// HdfFixedPoint rightSiblingAddress = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, headerBuffer);
727-
//
728-
// int entriesDataSize = (4 + 4 + 8*dimensions + offsetSize + offsetSize) * entriesUsed;
729-
// ByteBuffer entriesBuffer = ByteBuffer.allocate(entriesDataSize).order(ByteOrder.LITTLE_ENDIAN);
730-
// fileChannel.read(entriesBuffer);
731-
// entriesBuffer.flip();
732-
//
733-
// List<HdfBTreeEntryBase> entries = new ArrayList<>(entriesUsed);
734-
//
735-
// HdfBTreeV1 currentNode = new HdfBTreeV1(nodeType, nodeLevel, entriesUsed, leftSiblingAddress, rightSiblingAddress, null, entries, hdfDataFile);
736-
// visitedNodes.put(nodeAddress, currentNode);
737-
//
738-
// // (4 + 4 + 8*dimensions + 1*length + 1*length) * entriesUsed
739-
// // 4 + 4 + 8*dimensions + 8 + 8
740-
// // 8 + 24 + 16
741-
// // 48
742-
//
743-
// for (int i = 0; i < entriesUsed; i++) {
744-
// long sizeOfChunk = Integer.toUnsignedLong(entriesBuffer.getInt());
745-
// long filterMask = Integer.toUnsignedLong(entriesBuffer.getInt());
746-
// List<HdfFixedPoint> dimensionOffsets = new ArrayList<>();
747-
// for (int j = 0; j < dimensions; j++) {
748-
// dimensionOffsets.add(HdfReadUtils.readHdfFixedPointFromBuffer(eightByteFixedPointType, entriesBuffer));
749-
// }
750-
// HdfFixedPoint zeroValue = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, entriesBuffer);
751-
// HdfFixedPoint childPointer = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, entriesBuffer);
752-
//
753-
// if ( nodeLevel == 0 ) {
754-
// entries.add(new HdfChunkBTreeEntry(null, childPointer, null, sizeOfChunk, filterMask, dimensionOffsets));
755-
// } else {
756-
// HdfBTreeV1 bTree = readFromSeekableByteChannelRecursive(fileChannel, childPointer.getInstance(Long.class), dimensions, eightByteFixedPointType, hdfDataFile, visitedNodes);
757-
// }
758-
// }
759-
// return currentNode;
760-
// }
761-
//
666+
/**
667+
* Reads an HdfTree from a file channel.
668+
*
669+
* @param fileChannel the file channel to read from
670+
* @param hdfDataFile the HDF5 file context
671+
* @return the constructed HdfTree instance
672+
* @throws IOException if an I/O error occurs or the B-Tree data is invalid
673+
*/
674+
public static HdfBTreeV1 readBTreeFromSeekableByteChannelForChunked(
675+
SeekableByteChannel fileChannel,
676+
long btreeAddress,
677+
int dimensions,
678+
FixedPointDatatype eightByteFixedPointType,
679+
HdfDataFile hdfDataFile
680+
) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
681+
return readFromSeekableByteChannelRecursiveForChunked(fileChannel, btreeAddress, dimensions, eightByteFixedPointType, hdfDataFile, new LinkedHashMap<>());
682+
}
683+
684+
/**
685+
* Recursively reads an HdfTree from a file channel, handling cycles.
686+
*
687+
* @param fileChannel the file channel to read from
688+
* @param nodeAddress the address of the current node
689+
* @param visitedNodes a map of visited node addresses to detect cycles
690+
* @param hdfDataFile the HDF5 file context
691+
* @return the constructed HdfTree instance
692+
* @throws IOException if an I/O error occurs or the B-Tree data is invalid
693+
*/
694+
private static HdfBTreeV1 readFromSeekableByteChannelRecursiveForChunked(SeekableByteChannel fileChannel,
695+
long nodeAddress,
696+
int dimensions,
697+
FixedPointDatatype eightByteFixedPointType,
698+
HdfDataFile hdfDataFile,
699+
Map<Long, HdfBTreeV1> visitedNodes
700+
) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
701+
if (visitedNodes.containsKey(nodeAddress)) {
702+
throw new IllegalStateException("Cycle detected or node re-visited: BTree node address "
703+
+ nodeAddress + " encountered again during recursive read.");
704+
}
705+
706+
fileChannel.position(nodeAddress);
707+
FixedPointDatatype hdfOffset = hdfDataFile.getSuperblock().getFixedPointDatatypeForOffset();
708+
final int offsetSize = hdfOffset.getSize();
709+
710+
int headerSize = BTREE_HEADER_INITIAL_SIZE + offsetSize + offsetSize;
711+
ByteBuffer headerBuffer = ByteBuffer.allocate(headerSize).order(ByteOrder.LITTLE_ENDIAN);
712+
fileChannel.read(headerBuffer);
713+
headerBuffer.flip();
714+
715+
byte[] signatureBytes = new byte[BTREE_SIGNATURE.length];
716+
headerBuffer.get(signatureBytes);
717+
if (Arrays.compare(signatureBytes, BTREE_SIGNATURE) != 0) {
718+
throw new IOException("Invalid B-tree node signature: '" + Arrays.toString(signatureBytes) + "' at position " + nodeAddress);
719+
}
720+
721+
int nodeType = Byte.toUnsignedInt(headerBuffer.get());
722+
int nodeLevel = Byte.toUnsignedInt(headerBuffer.get());
723+
int entriesUsed = Short.toUnsignedInt(headerBuffer.getShort());
724+
725+
HdfFixedPoint leftSiblingAddress = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, headerBuffer);
726+
HdfFixedPoint rightSiblingAddress = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, headerBuffer);
727+
728+
int entriesDataSize = (4 + 4 + 8*dimensions + offsetSize + offsetSize) * entriesUsed;
729+
ByteBuffer entriesBuffer = ByteBuffer.allocate(entriesDataSize).order(ByteOrder.LITTLE_ENDIAN);
730+
fileChannel.read(entriesBuffer);
731+
entriesBuffer.flip();
732+
733+
List<HdfBTreeEntryBase> entries = new ArrayList<>(entriesUsed);
734+
735+
HdfBTreeV1 currentNode = new HdfBTreeV1(nodeType, nodeLevel, entriesUsed, leftSiblingAddress, rightSiblingAddress, null, entries, hdfDataFile);
736+
visitedNodes.put(nodeAddress, currentNode);
737+
738+
// (4 + 4 + 8*dimensions + 1*length + 1*length) * entriesUsed
739+
// 4 + 4 + 8*dimensions + 8 + 8
740+
// 8 + 24 + 16
741+
// 48
742+
743+
for (int i = 0; i < entriesUsed; i++) {
744+
long sizeOfChunk = Integer.toUnsignedLong(entriesBuffer.getInt());
745+
long filterMask = Integer.toUnsignedLong(entriesBuffer.getInt());
746+
List<HdfFixedPoint> dimensionOffsets = new ArrayList<>();
747+
for (int j = 0; j < dimensions; j++) {
748+
dimensionOffsets.add(HdfReadUtils.readHdfFixedPointFromBuffer(eightByteFixedPointType, entriesBuffer));
749+
}
750+
HdfFixedPoint zeroValue = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, entriesBuffer);
751+
HdfFixedPoint childPointer = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, entriesBuffer);
752+
753+
HdfBTreeEntryBase hdfBTreeEntryBase;
754+
if ( nodeLevel == 0 ) {
755+
hdfBTreeEntryBase = new HdfChunkBTreeEntry(zeroValue, childPointer, null, sizeOfChunk, filterMask, dimensionOffsets);
756+
} else {
757+
HdfBTreeV1 bTree = readFromSeekableByteChannelRecursiveForChunked(fileChannel, childPointer.getInstance(Long.class), dimensions, eightByteFixedPointType, hdfDataFile, visitedNodes);
758+
hdfBTreeEntryBase = new HdfGroupBTreeEntry(zeroValue, childPointer, bTree, null);
759+
}
760+
entries.add(hdfBTreeEntryBase);
761+
}
762+
return currentNode;
763+
}
764+
762765
/**
763766
* Reads an HdfGroupSymbolTableNode from a file channel.
764767
*

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