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Tidy up refactoring
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@jamesmudd
jamesmudd committed Nov 20, 2024
1 parent ebb6711 commit 0ffd2d5
Showing 1 changed file with 47 additions and 43 deletions.
90 changes: 47 additions & 43 deletions jhdf/src/main/java/io/jhdf/dataset/chunked/indexing/FixedArrayIndex.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ public FixedArrayDataBlockInitializer(HdfBackingStorage hdfBackingStorage) {
@Override
protected FixedArrayDataBlock initialize() {
logger.info("Initializing data block");
return new FixedArrayDataBlock(FixedArrayIndex.this, hdfBackingStorage, FixedArrayIndex.this.dataBlockAddress);
return new FixedArrayDataBlock(hdfBackingStorage, FixedArrayIndex.this.dataBlockAddress);
}

}
Expand All @@ -112,10 +112,10 @@ private class FixedArrayDataBlock {

private final List<Chunk> chunks = new ArrayList<>(maxNumberOfEntries);

private FixedArrayDataBlock(FixedArrayIndex fixedArrayIndex, HdfBackingStorage hdfBackingStorage, long address) {
private FixedArrayDataBlock(HdfBackingStorage hdfBackingStorage, long address) {

int pageBitmapBytes = (pages + 7) / 8;
int headerSize = 6 + hdfBackingStorage.getSizeOfOffsets() + fixedArrayIndex.entrySize * fixedArrayIndex.maxNumberOfEntries + 4;
int headerSize = 6 + hdfBackingStorage.getSizeOfOffsets() + FixedArrayIndex.this.entrySize * FixedArrayIndex.this.maxNumberOfEntries + 4;
if(pages > 1) {
headerSize += pageBitmapBytes + (4 * pages);
}
Expand All @@ -137,77 +137,81 @@ private FixedArrayDataBlock(FixedArrayIndex fixedArrayIndex, HdfBackingStorage h
}

final int dataBlockclientId = bb.get();
if (dataBlockclientId != fixedArrayIndex.clientId) {
if (dataBlockclientId != FixedArrayIndex.this.clientId) {
throw new HdfException("Fixed array client ID mismatch. Possible file corruption detected");
}

final long headerAddress = Utils.readBytesAsUnsignedLong(bb, hdfBackingStorage.getSizeOfOffsets());
if (headerAddress != fixedArrayIndex.address) {
if (headerAddress != FixedArrayIndex.this.address) {
throw new HdfException("Fixed array data block header address missmatch");
}

if(pages > 1) {
logger.info("Reading paged");
byte[] pageBitmap = new byte[pageBitmapBytes];
bb.get(pageBitmap);
readPaged(hdfBackingStorage, pageBitmapBytes, bb, dataBlockclientId);
} else {
// Unpaged
logger.info("Reading unpaged");
if (dataBlockclientId == 0) { // Not filtered
for (int i = 0; i < FixedArrayIndex.this.maxNumberOfEntries; i++) {
readUnfiltered(hdfBackingStorage.getSizeOfOffsets(), bb, i);
}
} else if (dataBlockclientId == 1) { // Filtered
for (int i = 0; i < FixedArrayIndex.this.maxNumberOfEntries; i++) {
readFiltered(hdfBackingStorage, bb, i);
}
} else {
throw new HdfException("Unrecognized client ID = " + dataBlockclientId);
}

ChecksumUtils.validateChecksumFromMark(bb);
}
}

int chunkIndex = 0;
for(int page = 0; page < pages; page++) {
final int currentPageSize;
if(page == pages -1) {
// last page so not a full page
currentPageSize = fixedArrayIndex.maxNumberOfEntries % fixedArrayIndex.pageSize;
} else {
currentPageSize = fixedArrayIndex.pageSize;
}
private void readPaged(HdfBackingStorage hdfBackingStorage, int pageBitmapBytes, ByteBuffer bb, int dataBlockclientId) {
logger.info("Reading paged");
byte[] pageBitmap = new byte[pageBitmapBytes];
bb.get(pageBitmap);

if (dataBlockclientId == 0) { // Not filtered
for (int i = 0; i < currentPageSize; i++) {
readUnfiltered(fixedArrayIndex, hdfBackingStorage.getSizeOfOffsets(), bb, chunkIndex++);
}
} else if (dataBlockclientId == 1) { // Filtered
for (int i = 0; i < currentPageSize; i++) {
readFiltered(fixedArrayIndex, hdfBackingStorage, bb, chunkIndex++);
}
} else {
throw new HdfException("Unrecognized client ID = " + dataBlockclientId);
}
ChecksumUtils.validateChecksumFromMark(bb);
ChecksumUtils.validateChecksumFromMark(bb);

int chunkIndex = 0;
for(int page = 0; page < pages; page++) {
final int currentPageSize;
if(page == pages -1) {
// last page so not a full page
currentPageSize = FixedArrayIndex.this.maxNumberOfEntries % FixedArrayIndex.this.pageSize;
} else {
currentPageSize = FixedArrayIndex.this.pageSize;
}
} else {
// Unpaged
logger.info("Reading unpaged");

if (dataBlockclientId == 0) { // Not filtered
for (int i = 0; i < fixedArrayIndex.maxNumberOfEntries; i++) {
readUnfiltered(fixedArrayIndex, hdfBackingStorage.getSizeOfOffsets(), bb, i);
for (int i = 0; i < currentPageSize; i++) {
readUnfiltered(hdfBackingStorage.getSizeOfOffsets(), bb, chunkIndex++);
}
} else if (dataBlockclientId == 1) { // Filtered
for (int i = 0; i < fixedArrayIndex.maxNumberOfEntries; i++) {
readFiltered(fixedArrayIndex, hdfBackingStorage, bb, i);
for (int i = 0; i < currentPageSize; i++) {
readFiltered(hdfBackingStorage, bb, chunkIndex++);
}
} else {
throw new HdfException("Unrecognized client ID = " + dataBlockclientId);
}

ChecksumUtils.validateChecksumFromMark(bb);
}
}

private void readFiltered(FixedArrayIndex fixedArrayIndex, HdfBackingStorage hdfBackingStorage, ByteBuffer bb, int i) {
private void readFiltered(HdfBackingStorage hdfBackingStorage, ByteBuffer bb, int i) {
final long chunkAddress = Utils.readBytesAsUnsignedLong(bb, hdfBackingStorage.getSizeOfOffsets());
final int chunkSizeInBytes = Utils.readBytesAsUnsignedInt(bb, fixedArrayIndex.entrySize - hdfBackingStorage.getSizeOfOffsets() - 4);
final int chunkSizeInBytes = Utils.readBytesAsUnsignedInt(bb, FixedArrayIndex.this.entrySize - hdfBackingStorage.getSizeOfOffsets() - 4);
final BitSet filterMask = BitSet.valueOf(new byte[]{bb.get(), bb.get(), bb.get(), bb.get()});
final int[] chunkOffset = Utils.chunkIndexToChunkOffset(i, fixedArrayIndex.chunkDimensions, fixedArrayIndex.datasetDimensions);
final int[] chunkOffset = Utils.chunkIndexToChunkOffset(i, FixedArrayIndex.this.chunkDimensions, FixedArrayIndex.this.datasetDimensions);

chunks.add(new ChunkImpl(chunkAddress, chunkSizeInBytes, chunkOffset, filterMask));
}

private void readUnfiltered(FixedArrayIndex fixedArrayIndex, int sizeOfOffsets, ByteBuffer bb, int chunkIndex) {
private void readUnfiltered(int sizeOfOffsets, ByteBuffer bb, int chunkIndex) {
final long chunkAddress = Utils.readBytesAsUnsignedLong(bb, sizeOfOffsets);
final int[] chunkOffset = Utils.chunkIndexToChunkOffset(chunkIndex, fixedArrayIndex.chunkDimensions, fixedArrayIndex.datasetDimensions);
chunks.add(new ChunkImpl(chunkAddress, fixedArrayIndex.unfilteredChunkSize, chunkOffset));
final int[] chunkOffset = Utils.chunkIndexToChunkOffset(chunkIndex, FixedArrayIndex.this.chunkDimensions, FixedArrayIndex.this.datasetDimensions);
chunks.add(new ChunkImpl(chunkAddress, FixedArrayIndex.this.unfilteredChunkSize, chunkOffset));
}
}

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