DataChunk(int ndim, boolean last) throws IOException { this.size = h5.raf.readInt(); this.filterMask = h5.raf.readInt(); offset = new int[ndim]; for (int i = 0; i < ndim; i++) { long loffset = h5.raf.readLong(); assert loffset < Integer.MAX_VALUE; offset[i] = (int) loffset; } this.filePos = last ? -1 : h5.readAddress(); // if (memTracker != null) memTracker.addByLen("Chunked Data (" + owner + ")", filePos, size); }
DataChunk(int ndim, boolean last) throws IOException { this.size = raf.readInt(); this.filterMask = raf.readInt(); offset = new int[ndim]; for (int i = 0; i < ndim; i++) { long loffset = raf.readLong(); assert loffset < Integer.MAX_VALUE; offset[i] = (int) loffset; } this.filePos = last ? -1 : h5.readAddress(); // if (memTracker != null) memTracker.addByLen("Chunked Data (" + owner + ")", filePos, size); }
DataChunk(int ndim, boolean last) throws IOException { this.size = raf.readInt(); this.filterMask = raf.readInt(); offset = new int[ndim]; for (int i = 0; i < ndim; i++) { long loffset = raf.readLong(); assert loffset < Integer.MAX_VALUE; offset[i] = (int) loffset; } this.filePos = last ? -1 : h5.readAddress(); // if (memTracker != null) memTracker.addByLen("Chunked Data (" + owner + ")", filePos, size); }
GroupNode(long address) throws IOException { this.address = address; raf.seek(getFileOffset(address)); if (debugDetail) debugOut.println("--Group Node position=" + raf.getFilePointer()); // header String magic = raf.readString(4); if (!magic.equals("SNOD")) throw new IllegalStateException(magic + " should equal SNOD"); version = raf.readByte(); raf.readByte(); // skip byte nentries = raf.readShort(); if (debugDetail) debugOut.println(" version=" + version + " nentries=" + nentries); long posEntry = raf.getFilePointer(); for (int i = 0; i < nentries; i++) { SymbolTableEntry entry = new SymbolTableEntry(posEntry); posEntry += entry.getSize(); if (entry.objectHeaderAddress != 0) { // LOOK: Probably a bug in HDF5 file format ?? jc July 16 2010 if (debug1) debugOut.printf(" add %s%n", entry); symbols.add(entry); } else { if (debug1) debugOut.printf(" BAD objectHeaderAddress==0 !! %s%n", entry); } } if (debugDetail) debugOut.println("-- Group Node end position=" + raf.getFilePointer()); long size = 8 + nentries * 40; if (debugTracker) memTracker.addByLen("Group BtreeNode (" + owner + ")", address, size); }
if (debugTracker) memTracker.addByLen("Group BTree (" + owner + ")", address, size);
if (debugTracker) memTracker.addByLen("Group BTree (" + owner + ")", address, size);
if (memTracker != null) memTracker.addByLen("Data BTree (" + owner + ")", address, size); if (debugDataBtree) debugOut.println(" type=" + type + " level=" + level + " nentries=" + nentries + " size = " + size);
if (debugTracker) memTracker.addByLen("Group BtreeNode (" + owner + ")", address, size);
LocalHeap(H5Group group, long address) throws IOException { this.group = group; // header information is in le byte order raf.order(RandomAccessFile.LITTLE_ENDIAN); raf.seek(getFileOffset(address)); if (debugDetail) debugOut.println("-- readLocalHeap position=" + raf.getFilePointer()); // header String magic = raf.readString(4); if (!magic.equals("HEAP")) throw new IllegalStateException(magic + " should equal HEAP"); version = raf.readByte(); raf.skipBytes(3); size = (int) readLength(); freelistOffset = readLength(); dataAddress = readOffset(); if (debugDetail) debugOut.println(" version=" + version + " size=" + size + " freelistOffset=" + freelistOffset + " heap starts at dataAddress=" + dataAddress); if (debugPos) debugOut.println(" *now at position=" + raf.getFilePointer()); // data raf.seek(getFileOffset(dataAddress)); heap = new byte[size]; raf.readFully(heap); //if (debugHeap) printBytes( out, "heap", heap, size, true); if (debugDetail) debugOut.println("-- endLocalHeap position=" + raf.getFilePointer()); int hsize = 8 + 2 * sizeLengths + sizeOffsets; if (debugTracker) memTracker.addByLen("Group LocalHeap (" + group.displayName + ")", address, hsize); if (debugTracker) memTracker.addByLen("Group LocalHeapData (" + group.displayName + ")", dataAddress, size); }
if (debugContinueMessage) debugOut.println(" nmessages read = " + count); if (debugPos) debugOut.println("<--done reading messages for <" + who + ">; position=" + raf.getFilePointer()); if (debugTracker) memTracker.addByLen("Object " + who, getFileOffset(address), headerSize + 16); if (debugTracker) memTracker.addByLen("Message (" + who + ") " + mess.mtype, mess.start, mess.size + 8);
log.debug("-- endGlobalHeap position=" + raf.getFilePointer()); if (debugTracker) memTracker.addByLen("GlobalHeap", address, sizeBytes);
if (debugTracker) memTracker.addByLen("GlobalHeap", address, sizeBytes);
if (memTracker != null) memTracker.addByLen("Data BTree (" + owner + ")", address, size); if (debugDataBtree) debugOut.println(" type=" + type + " level=" + level + " nentries=" + nentries + " size = " + size);
if (memTracker != null) memTracker.addByLen("Data BTree (" + owner + ")", address, size); if (debugDataBtree) debugOut.println(" type=" + type + " level=" + level + " nentries=" + nentries + " size = " + size);