wehub-resource-sync
7254f7b4d1
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1833 lines
64 KiB
JavaScript
Executable File
1833 lines
64 KiB
JavaScript
Executable File
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// Experimental HDF5 reader
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import * as zip from './zip.js';
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const hdf5 = {};
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hdf5.File = class {
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static open(data) {
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if (data && data.length >= 8) {
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const buffer = data instanceof Uint8Array ? data : data.peek(8);
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const signature = [0x89, 0x48, 0x44, 0x46, 0x0D, 0x0A, 0x1A, 0x0A]; // \x89HDF\r\n\x1A\n
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if (signature.every((value, index) => value === buffer[index])) {
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return new hdf5.File(data);
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}
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}
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return null;
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}
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constructor(data) {
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this.data = data;
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}
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read() {
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if (this.data) {
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// https://support.hdfgroup.org/HDF5/doc/H5.format.html
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const data = this.data;
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delete this.data;
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const reader = hdf5.Reader.open(data);
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reader.skip(8);
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this._globalHeap = new hdf5.GlobalHeap(reader);
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const version = reader.byte();
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switch (version) {
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case 0:
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case 1: {
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this._freeSpaceStorageVersion = reader.byte();
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this._rootGroupEntryVersion = reader.byte();
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reader.skip(1);
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this._sharedHeaderMessageVersionFormat = reader.byte();
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reader.initialize();
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reader.skip(1);
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this._groupLeafNodeK = reader.uint16(); // 0x04?
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this._groupInternalNodeK = reader.uint16(); // 0x10?
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reader.skip(4);
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if (version > 0) {
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this._indexedStorageInternalNodeK = reader.uint16();
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reader.skip(2); // Reserved
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}
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this._baseAddress = reader.offset();
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reader.offset(); // Address of File Free space Info
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this._endOfFileAddress = reader.offset();
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reader.offset(); // Driver Information Block Address
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if (this._baseAddress !== 0) {
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throw new hdf5.Error('Base address is not zero.');
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}
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const rootGroupEntry = new hdf5.SymbolTableEntry(reader);
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this._rootGroup = new hdf5.Group(reader, rootGroupEntry, null, this._globalHeap, '', '');
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break;
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}
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case 2:
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case 3: {
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reader.initialize();
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reader.byte();
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this._baseAddress = reader.offset();
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this._superBlockExtensionAddress = reader.offset();
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this._endOfFileAddress = reader.offset();
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const rootGroupObjectHeader = new hdf5.DataObjectHeader(reader, reader.offset());
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this._rootGroup = new hdf5.Group(reader, null, rootGroupObjectHeader, this._globalHeap, '', '');
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break;
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}
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default:
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throw new hdf5.Error(`Unsupported Superblock version ${version}.`);
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}
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delete this.data;
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}
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return this._rootGroup;
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}
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};
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hdf5.Group = class {
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constructor(reader, entry, objectHeader, globalHeap, parentPath, name) {
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this._reader = reader;
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this._entry = entry;
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this._dataObjectHeader = objectHeader;
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this._globalHeap = globalHeap;
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this._name = name;
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this._path = parentPath === '/' ? (parentPath + name) : (`${parentPath}/${name}`);
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}
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get name() {
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return this._name;
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}
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get path() {
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return this._path;
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}
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group(path) {
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this._decodeGroups();
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if (this._groups.has(path)) {
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return this._groups.get(path);
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}
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const index = path.indexOf('/');
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if (index !== -1) {
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const group = this.group(path.substring(0, index));
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if (group) {
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return group.group(path.substring(index + 1));
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}
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}
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return null;
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}
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get groups() {
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this._decodeGroups();
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return this._groups;
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}
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get attributes() {
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this._decodeDataObject();
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return this._attributes;
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}
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get value() {
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this._decodeDataObject();
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return this._value;
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}
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_decodeDataObject() {
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if (!this._dataObjectHeader) {
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this._dataObjectHeader = new hdf5.DataObjectHeader(this._reader, this._entry.objectHeaderAddress);
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}
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if (!this._attributes) {
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this._attributes = new Map();
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for (const attribute of this._dataObjectHeader.attributes) {
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const name = attribute.name;
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const value = attribute.decodeValue(this._globalHeap);
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this._attributes.set(name, value);
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}
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this._value = null;
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const datatype = this._dataObjectHeader.datatype;
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const dataspace = this._dataObjectHeader.dataspace;
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const dataLayout = this._dataObjectHeader.dataLayout;
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const filterPipeline = this._dataObjectHeader.filterPipeline;
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if (datatype && dataspace && dataLayout) {
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this._value = new hdf5.Variable(this._reader, this._globalHeap, datatype, dataspace, dataLayout, filterPipeline);
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}
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}
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if (this._reader.position !== 0) {
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this._reader.seek(0);
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}
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}
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_decodeGroups() {
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if (!this._groups) {
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this._groups = new Map();
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if (this._entry) {
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if (this._entry.treeAddress || this._entry.heapAddress) {
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const heap = new hdf5.Heap(this._reader, this._entry.heapAddress);
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const tree = new hdf5.Tree(this._reader, this._entry.treeAddress);
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for (const node of tree.nodes) {
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for (const entry of node.entries) {
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const name = heap.getString(entry.linkNameOffset);
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const group = new hdf5.Group(this._reader, entry, null, this._globalHeap, this._path, name);
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this._groups.set(name, group);
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}
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}
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}
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} else {
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this._decodeDataObject();
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for (const link of this._dataObjectHeader.links) {
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if (Object.prototype.hasOwnProperty.call(link, 'objectHeaderAddress')) {
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const name = link.name;
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const objectHeader = new hdf5.DataObjectHeader(this._reader, link.objectHeaderAddress);
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const linkGroup = new hdf5.Group(this._reader, null, objectHeader, this._globalHeap, this._path, name);
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this._groups.set(name, linkGroup);
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}
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}
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}
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}
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}
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};
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hdf5.Variable = class {
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constructor(reader, globalHeap, datatype, dataspace, dataLayout, filterPipeline) {
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this._reader = reader;
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this._globalHeap = globalHeap;
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this._datatype = datatype;
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this._dataspace = dataspace;
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this._dataLayout = dataLayout;
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this._filterPipeline = filterPipeline;
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}
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get type () {
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return this._datatype.type;
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}
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get littleEndian() {
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return this._datatype.littleEndian;
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}
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get shape() {
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return this._dataspace.shape;
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}
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get value() {
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const data = this.data;
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if (data) {
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const reader = hdf5.Reader.open(data);
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const array = this._dataspace.read(this._datatype, reader);
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return this._dataspace.decode(this._datatype, array, this._globalHeap);
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}
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return null;
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}
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get data() {
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switch (this._dataLayout.layoutClass) {
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case 1: // Contiguous
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if (this._dataLayout.address && this._dataLayout.address !== -1) {
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const position = this._reader.position;
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this._reader.seek(this._dataLayout.address);
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const stream = this._reader.stream(this._dataLayout.size);
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this._reader.seek(position);
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return stream;
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}
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break;
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case 2: { // Chunked
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const dimensionality = this._dataLayout.dimensionality;
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const tree = new hdf5.Tree(this._reader, this._dataLayout.address, dimensionality);
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const item_size = this._dataLayout.datasetElementSize;
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const chunk_shape = this._dataLayout.dimensionSizes;
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const data_shape = this._dataspace.shape;
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const chunk_size = chunk_shape.reduce((a, b) => a * b, 1);
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const data_size = data_shape.reduce((a, b) => a * b, 1);
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const max_dim = data_shape.length - 1;
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let data_stride = 1;
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const data_strides = new Array(data_shape.length);
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for (let i = data_shape.length - 1; i >= 0; i--) {
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data_strides[i] = data_stride;
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data_stride *= data_shape[i];
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}
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const data = new Uint8Array(data_size * item_size);
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for (const node of tree.nodes) {
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let chunk = node.data;
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if (this._filterPipeline) {
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for (let i = 0; i < this._filterPipeline.filters.length; i++) {
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if ((node.filterMask & (1 << i)) === 0) {
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const filter = this._filterPipeline.filters[i];
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chunk = filter.decode(chunk);
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}
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}
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}
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const chunk_offset = node.fields.map((x) => x.toNumber());
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const data_pos = chunk_offset.slice();
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const chunk_pos = new Array(data_pos.length).fill(0);
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const length = data_pos.length - 1;
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for (let chunk_index = 0; chunk_index < chunk_size; chunk_index++) {
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for (let i = max_dim; i >= 0; i--) {
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if (chunk_pos[i] >= chunk_shape[i]) {
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chunk_pos[i] = 0;
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data_pos[i] = chunk_offset[i];
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if (i > 0) {
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chunk_pos[i - 1]++;
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data_pos[i - 1]++;
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}
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} else {
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break;
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}
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}
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let index = 0;
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let inbounds = true;
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for (let i = 0; i < length; i++) {
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const position = data_pos[i];
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if (position >= data_shape[i]) {
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inbounds = false;
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break;
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}
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index += position * data_strides[i];
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}
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if (inbounds) {
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let chunk_offset = chunk_index * item_size;
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let target_offset = index * item_size;
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const target_end = target_offset + item_size;
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while (target_offset < target_end) {
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data[target_offset++] = chunk[chunk_offset++];
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}
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}
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chunk_pos[max_dim]++;
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data_pos[max_dim]++;
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}
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}
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return data;
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}
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default: {
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throw new hdf5.Error(`Unsupported data layout class '${this.layoutClass}'.`);
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}
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}
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return null;
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}
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};
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hdf5.Reader = class {
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static open(data) {
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if (data instanceof hdf5.BinaryReader || data instanceof hdf5.StreamReader) {
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return data;
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} else if (data instanceof Uint8Array) {
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return new hdf5.BinaryReader(data);
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} else if (data.length < 0x10000000) {
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const buffer = data.peek();
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return new hdf5.BinaryReader(buffer);
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}
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return new hdf5.StreamReader(data);
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}
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initialize() {
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this._offsetSize = this.byte();
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this._lengthSize = this.byte();
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}
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int8() {
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const position = this.take(1);
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return this._view.getInt8(position);
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}
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byte() {
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const position = this.take(1);
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return this._view.getUint8(position);
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}
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int16() {
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const position = this.take(2);
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return this._view.getInt16(position, true);
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}
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uint16() {
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const position = this.take(2);
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return this._view.getUint16(position, true);
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}
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int32() {
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const position = this.take(4);
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return this._view.getInt32(position, true);
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}
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uint32() {
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const position = this.take(4);
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return this._view.getUint32(position, true);
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}
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int64() {
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const position = this.take(8);
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return this._view.getBigInt64(position, true);
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}
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uint64() {
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const position = this.take(8);
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return this._view.getBigUint64(position, true);
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}
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uint(size) {
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switch (size) {
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case 0: return this.byte();
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case 1: return this.uint16();
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case 2: return this.uint32();
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case 3: return this.uint64().toNumber();
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default: throw new hdf5.Error(`Unsupported uint size '${size}'.`);
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}
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}
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float16() {
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const position = this.take(2);
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const value = this._view.getUint16(position, true);
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// decode float16 value
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const s = (value & 0x8000) >> 15;
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const e = (value & 0x7C00) >> 10;
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const f = value & 0x03FF;
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if (e === 0) {
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return (s ? -1 : 1) * Math.pow(2, -14) * (f / Math.pow(2, 10));
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} else if (e === 0x1F) {
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return f ? NaN : ((s ? -1 : 1) * Infinity);
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}
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return (s ? -1 : 1) * Math.pow(2, e - 15) * (1 + (f / Math.pow(2, 10)));
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}
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float32() {
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const position = this.take(4);
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return this._view.getFloat32(position, true);
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}
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float64() {
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const position = this.take(8);
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return this._view.getFloat64(position, true);
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}
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offset() {
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switch (this._offsetSize) {
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case 8: {
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const position = this.take(8);
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const value = this._view.getBigUint64(position, true);
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if (value === 0xffffffffffffffffn) {
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return -1;
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}
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if (value >= Number.MAX_SAFE_INTEGER) {
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throw new Error(`64-bit value '${value.toString(16)}' exceeds safe integer.`);
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}
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return value.toNumber();
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}
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case 4: {
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const value = this.uint32();
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if (value === 0xffffffff) {
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return undefined;
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}
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return value;
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}
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default: {
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throw new hdf5.Error(`Unsupported offset size '${this._offsetSize}'.`);
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}
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}
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}
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length() {
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switch (this._lengthSize) {
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case 8: {
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const position = this.take(8);
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const value = this._view.getBigUint64(position, true);
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if (value === 0xffffffffffffffffn) {
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return -1;
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}
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if (value >= Number.MAX_SAFE_INTEGER) {
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throw new Error(`64-bit value '${value.toString(16)}' exceeds safe integer.`);
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}
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return value.toNumber();
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}
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case 4: {
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const value = this.uint32();
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if (value === 0xffffffff) {
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return undefined;
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}
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return value;
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}
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default: {
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throw new hdf5.Error(`Unsupported length size '${this._lengthSize}'.`);
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}
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}
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}
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string(size, encoding) {
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if (!size || size === -1) {
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size = this.size(0x00);
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}
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let data = null;
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if (size < 16) {
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data = new Uint8Array(size);
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for (let i = 0; i < size; i++) {
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data[i] = this.byte();
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}
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} else {
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data = this.read(size);
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}
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if (encoding === 'utf-8') {
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hdf5.Reader._utf8Decoder = hdf5.Reader._utf8Decoder || new TextDecoder('utf-8');
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return hdf5.Reader._utf8Decoder.decode(data).replace(/\0/g, '');
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}
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hdf5.Reader._asciiDecoder = hdf5.Reader._asciiDecoder || new TextDecoder('ascii');
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return hdf5.Reader._asciiDecoder.decode(data).replace(/\0/g, '');
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}
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match(signature) {
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const position = this.position;
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for (let i = 0; i < signature.length; i++) {
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if (signature.charCodeAt(i) !== this.byte()) {
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this.seek(position);
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return false;
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}
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}
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return true;
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}
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expect(signature) {
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if (!this.match(signature)) {
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throw new hdf5.Error(`Invalid '${signature}' block signature.`);
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}
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}
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};
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hdf5.BinaryReader = class extends hdf5.Reader {
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constructor(buffer, view, offset, position, offsetSize, lengthSize) {
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super();
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this._buffer = buffer;
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this._length = buffer.length;
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this._view = view || new DataView(buffer.buffer, buffer.byteOffset, buffer.byteLength);
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this._offset = offset || 0;
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this._position = position || 0;
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this._offsetSize = offsetSize;
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this._lengthSize = lengthSize;
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}
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get position() {
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return this._position + this._offset;
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}
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take(offset) {
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const position = this._offset + this._position;
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this.skip(offset);
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return position;
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}
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seek(position) {
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this._offset = position;
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this._position = 0;
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if (this._offset > this._length) {
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throw new Error(`Unexpected end of file. Expected ${this._offset - this._length} more bytes. The file might be corrupted.`);
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}
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}
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skip(offset) {
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this._position += offset;
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if (this._offset + this._position > this._buffer.length) {
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throw new hdf5.Error(`Unexpected end of file. Expected ${this._offset + this._position - this._buffer.length} more bytes. The file might be corrupted.`);
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}
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}
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align(mod) {
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if (this._position % mod !== 0) {
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this._position = (Math.floor(this._position / mod) + 1) * mod;
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}
|
|
}
|
|
|
|
peek(length) {
|
|
const position = this._offset + this._position;
|
|
length = length === undefined ? this._buffer.length - position : length;
|
|
this.take(length);
|
|
const buffer = this._buffer.subarray(position, position + length);
|
|
this._position = position - this._offset;
|
|
return buffer;
|
|
}
|
|
|
|
read(length) {
|
|
const position = this.take(length);
|
|
return this._buffer.subarray(position, position + length);
|
|
}
|
|
|
|
stream(length) {
|
|
const position = this.take(length);
|
|
const buffer = this._buffer.subarray(position, position + length);
|
|
return new hdf5.BinaryReader(buffer, undefined, undefined, undefined, this._offsetSize, this._lengthSize);
|
|
}
|
|
|
|
size(terminator) {
|
|
let position = this._offset + this._position;
|
|
while (this._buffer[position] !== terminator) {
|
|
position++;
|
|
}
|
|
return position - this._offset - this._position + 1;
|
|
}
|
|
};
|
|
|
|
hdf5.StreamReader = class extends hdf5.Reader {
|
|
|
|
constructor(stream, view, window, offset, position, offsetSize, lengthSize) {
|
|
super();
|
|
this._stream = stream;
|
|
this._length = stream.length;
|
|
this._view = view;
|
|
this._window = window || 0;
|
|
this._offset = offset || 0;
|
|
this._position = position || 0;
|
|
this._offsetSize = offsetSize;
|
|
this._lengthSize = lengthSize;
|
|
}
|
|
|
|
get position() {
|
|
return this._offset + this._position;
|
|
}
|
|
|
|
seek(position) {
|
|
this._offset = position;
|
|
this._position = 0;
|
|
if (this._offset > this._length) {
|
|
throw new Error(`Unexpected end of file. Expected ${this._offset - this._length} more bytes. The file might be corrupted.`);
|
|
}
|
|
}
|
|
|
|
skip(offset) {
|
|
this._position += offset;
|
|
if (this._position + this._offset > this._length) {
|
|
throw new hdf5.Error(`Unexpected end of file. Expected ${this._position + this._offset - this._length} more bytes. The file might be corrupted.`);
|
|
}
|
|
}
|
|
|
|
align(mod) {
|
|
if (this._position % mod !== 0) {
|
|
this._position = (Math.floor(this._position / mod) + 1) * mod;
|
|
}
|
|
}
|
|
|
|
read(length) {
|
|
const position = this._stream.position;
|
|
this._stream.seek(this._offset + this._position);
|
|
const buffer = this._stream.read(length);
|
|
this._stream.seek(position);
|
|
this.skip(length);
|
|
return buffer;
|
|
}
|
|
|
|
stream(length) {
|
|
const position = this._stream.position;
|
|
this._stream.seek(this._offset + this._position);
|
|
this.skip(length);
|
|
const stream = this._stream.stream(length);
|
|
this._stream.seek(position);
|
|
return stream;
|
|
}
|
|
|
|
byte() {
|
|
const position = this.take(1);
|
|
return this._view.getUint8(position);
|
|
}
|
|
|
|
uint16() {
|
|
const position = this.take(2);
|
|
return this._view.getUint16(position, true);
|
|
}
|
|
|
|
int32() {
|
|
const position = this.take(4);
|
|
return this._view.getInt32(position, true);
|
|
}
|
|
|
|
uint32() {
|
|
const position = this.take(4);
|
|
return this._view.getUint32(position, true);
|
|
}
|
|
|
|
int64() {
|
|
const position = this.take(8);
|
|
return this._view.getBigInt64(position, true);
|
|
}
|
|
|
|
float32() {
|
|
const position = this.take(4);
|
|
return this._view.getFloat32(position, true);
|
|
}
|
|
|
|
float64() {
|
|
const position = this.take(8);
|
|
return this._view.getFloat64(position, true);
|
|
}
|
|
|
|
size(terminator) {
|
|
const position = this._position;
|
|
let size = 0;
|
|
while (this.byte() !== terminator) {
|
|
size++;
|
|
}
|
|
this._position = position;
|
|
return size;
|
|
}
|
|
|
|
take(length) {
|
|
const position = this.position;
|
|
if (position + length > this._length) {
|
|
throw new Error(`Expected ${position + length - this._length} more bytes. The file might be corrupted. Unexpected end of file.`);
|
|
}
|
|
if (!this._view || position < this._window || position + length > this._window + this._view.byteLength) {
|
|
this._window = position;
|
|
const current = this._stream.position;
|
|
this._stream.seek(this._window);
|
|
const buffer = this._stream.read(Math.min(0x100, this._length - this._window)).slice();
|
|
this._view = new DataView(buffer.buffer, buffer.byteOffset, buffer.byteLength);
|
|
this._stream.seek(current);
|
|
}
|
|
this._position += length;
|
|
return position - this._window;
|
|
}
|
|
};
|
|
|
|
hdf5.SymbolTableNode = class {
|
|
|
|
constructor(reader, offset) {
|
|
const position = reader.position;
|
|
reader.seek(offset);
|
|
reader.expect('SNOD');
|
|
const version = reader.byte();
|
|
if (version === 1) {
|
|
reader.skip(1);
|
|
const entriesUsed = reader.uint16();
|
|
this.entries = [];
|
|
for (let i = 0; i < entriesUsed; i++) {
|
|
const entry = new hdf5.SymbolTableEntry(reader);
|
|
this.entries.push(entry);
|
|
}
|
|
} else {
|
|
throw new hdf5.Error(`Unsupported symbol table node version '${version}'.`);
|
|
}
|
|
reader.seek(position);
|
|
}
|
|
};
|
|
|
|
hdf5.SymbolTableEntry = class {
|
|
|
|
constructor(reader) {
|
|
this.linkNameOffset = reader.offset();
|
|
this.objectHeaderAddress = reader.offset();
|
|
const cacheType = reader.uint32();
|
|
reader.skip(4); // Reserved
|
|
switch (cacheType) {
|
|
case 0:
|
|
break;
|
|
case 1: {
|
|
const position = reader.position;
|
|
this.treeAddress = reader.offset();
|
|
this.heapAddress = reader.offset();
|
|
reader.seek(position);
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported cache type '${cacheType}'.`);
|
|
}
|
|
reader.skip(16); // Scratch-pad space
|
|
}
|
|
};
|
|
|
|
hdf5.DataObjectHeader = class {
|
|
|
|
constructor(reader, offset) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#ObjectHeader
|
|
const position = reader.position;
|
|
reader.seek(offset);
|
|
this.attributes = [];
|
|
this.links = [];
|
|
this.continuations = [];
|
|
reader.match('OHDR');
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1: {
|
|
reader.skip(1);
|
|
const count = reader.uint16();
|
|
reader.uint32();
|
|
const objectHeaderSize = reader.uint32();
|
|
reader.align(8);
|
|
let end = reader.position + objectHeaderSize;
|
|
for (let i = 0; i < count; i++) {
|
|
const type = reader.uint16();
|
|
const size = reader.uint16();
|
|
const flags = reader.byte();
|
|
reader.skip(3);
|
|
reader.align(8);
|
|
const next = this._readMessage(reader, type, size, flags);
|
|
if ((!next || reader.position >= end) && this.continuations.length > 0) {
|
|
const continuation = this.continuations.shift();
|
|
reader.seek(continuation.offset);
|
|
end = continuation.offset + continuation.length;
|
|
} else {
|
|
reader.align(8);
|
|
}
|
|
}
|
|
break;
|
|
}
|
|
case 2: {
|
|
const flags = reader.byte();
|
|
if ((flags & 0x20) !== 0) {
|
|
reader.uint32(); // access time
|
|
reader.uint32(); // modification time
|
|
reader.uint32(); // change time
|
|
reader.uint32(); // birth time
|
|
}
|
|
if ((flags & 0x10) !== 0) {
|
|
reader.uint16(); // max compact attributes
|
|
reader.uint16(); // min compact attributes
|
|
}
|
|
const order = (flags & 0x04) !== 0;
|
|
const size = reader.uint(flags & 0x03);
|
|
let next = true;
|
|
let end = reader.position + size;
|
|
while (next && reader.position < end) {
|
|
const type = reader.byte();
|
|
const size = reader.uint16();
|
|
const flags = reader.byte();
|
|
if (reader.position < end) {
|
|
if (order) {
|
|
reader.uint16(); // creation order
|
|
}
|
|
next = this._readMessage(reader, type, size, flags);
|
|
}
|
|
if ((!next || reader.position >= end) && this.continuations.length > 0) {
|
|
const continuation = this.continuations.shift();
|
|
reader.seek(continuation.offset);
|
|
end = continuation.offset + continuation.length;
|
|
reader.expect('OCHK');
|
|
next = true;
|
|
}
|
|
}
|
|
break;
|
|
}
|
|
default: {
|
|
throw new hdf5.Error(`Unsupported data object header version '${version}'.`);
|
|
}
|
|
}
|
|
reader.seek(position);
|
|
}
|
|
|
|
_readMessage(reader, type, size, flags) {
|
|
const position = reader.position;
|
|
switch (type) {
|
|
case 0x0000: // NIL
|
|
return false;
|
|
case 0x0001: // Dataspace
|
|
this.dataspace = (size !== 4 || flags !== 1) ? new hdf5.Dataspace(reader) : null;
|
|
break;
|
|
case 0x0002: // Link Info
|
|
this.linkInfo = new hdf5.LinkInfo(reader);
|
|
break;
|
|
case 0x0003: // Datatype
|
|
this.datatype = new hdf5.Datatype(reader);
|
|
break;
|
|
case 0x0004:
|
|
case 0x0005: // Fill Value
|
|
this.fillValue = new hdf5.FillValue(reader, type);
|
|
break;
|
|
case 0x0006: // Link
|
|
this.links.push(new hdf5.Link(reader));
|
|
break;
|
|
case 0x0008: // Data Layout
|
|
this.dataLayout = new hdf5.DataLayout(reader);
|
|
break;
|
|
case 0x000A: // Group Info
|
|
this.groupInfo = new hdf5.GroupInfo(reader);
|
|
break;
|
|
case 0x000B: // Filter Pipeline
|
|
this.filterPipeline = new hdf5.FilterPipeline(reader);
|
|
break;
|
|
case 0x000C: // Attribute
|
|
this.attributes.push(new hdf5.Attribute(reader));
|
|
break;
|
|
case 0x000D: // Object Comment Message
|
|
this.comment = reader.string(-1, 'ascii');
|
|
break;
|
|
case 0x0010: // Object Header Continuation
|
|
this.continuations.push(new hdf5.ObjectHeaderContinuation(reader));
|
|
break;
|
|
case 0x0011: // Symbol Table
|
|
this.symbolTable = new hdf5.SymbolTable(reader);
|
|
break;
|
|
case 0x000E: // Object Modification Time (Old)
|
|
case 0x0012: // Object Modification Time
|
|
this.objectModificationTime = new hdf5.ObjectModificationTime(reader, type);
|
|
break;
|
|
case 0x0015: // Attribute Info
|
|
this.attributeInfo = new hdf5.AttributeInfo(reader);
|
|
break;
|
|
default:
|
|
throw new hdf5.Error(`Unsupported message type '${type}'.`);
|
|
}
|
|
reader.seek(position);
|
|
reader.skip(size);
|
|
return true;
|
|
}
|
|
};
|
|
|
|
hdf5.Message = class {
|
|
|
|
constructor(type, data, flags) {
|
|
this._type = type;
|
|
this._data = data;
|
|
this._flags = flags;
|
|
}
|
|
};
|
|
|
|
hdf5.Dataspace = class {
|
|
|
|
constructor(reader) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#DataspaceMessage
|
|
this._sizes = [];
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1:
|
|
this._dimensions = reader.byte();
|
|
this._flags = reader.byte();
|
|
reader.skip(1);
|
|
reader.skip(4);
|
|
for (let i = 0; i < this._dimensions; i++) {
|
|
this._sizes.push(reader.length());
|
|
}
|
|
if ((this._flags & 0x01) !== 0) {
|
|
this._maxSizes = [];
|
|
for (let j = 0; j < this._dimensions; j++) {
|
|
this._maxSizes.push(reader.length());
|
|
if (this._maxSizes[j] >= 0 && this._sizes[j] > this._maxSizes[j]) {
|
|
throw new hdf5.Error('Dimension size exceeds max size.');
|
|
}
|
|
}
|
|
}
|
|
if ((this._flags & 0x02) !== 0) {
|
|
throw new hdf5.Error('Permutation indices not supported.');
|
|
}
|
|
break;
|
|
case 2:
|
|
this._dimensions = reader.byte();
|
|
this._flags = reader.byte();
|
|
this._type = reader.byte(); // 0 scalar, 1 simple, 2 null
|
|
for (let k = 0; k < this._dimensions; k++) {
|
|
this._sizes.push(reader.length());
|
|
}
|
|
if ((this._flags & 0x01) !== 0) {
|
|
this._maxSizes = [];
|
|
for (let l = 0; l < this._dimensions; l++) {
|
|
this._maxSizes.push(reader.length());
|
|
}
|
|
}
|
|
break;
|
|
default:
|
|
throw new hdf5.Error(`Unsupported dataspace message version '${version}'.`);
|
|
}
|
|
}
|
|
|
|
get shape() {
|
|
return this._sizes;
|
|
}
|
|
|
|
read(datatype, reader) {
|
|
if (this._dimensions === 0) {
|
|
return datatype.read(reader);
|
|
}
|
|
return this._readArray(datatype, reader, this._sizes, 0);
|
|
}
|
|
|
|
_readArray(datatype, reader, shape, dimension) {
|
|
const array = [];
|
|
const size = shape[dimension];
|
|
if (dimension === shape.length - 1) {
|
|
for (let i = 0; i < size; i++) {
|
|
array.push(datatype.read(reader));
|
|
}
|
|
} else {
|
|
for (let j = 0; j < size; j++) {
|
|
array.push(this._readArray(datatype, reader, shape, dimension + 1));
|
|
}
|
|
}
|
|
return array;
|
|
}
|
|
|
|
decode(datatype, data, globalHeap) {
|
|
if (this._dimensions === 0) {
|
|
return datatype.decode(data, globalHeap);
|
|
}
|
|
return this._decodeArray(datatype, data, globalHeap, this._sizes, 0);
|
|
}
|
|
|
|
_decodeArray(datatype, data, globalHeap, shape, dimension) {
|
|
const size = shape[dimension];
|
|
if (dimension === shape.length - 1) {
|
|
for (let i = 0; i < size; i++) {
|
|
data[i] = datatype.decode(data[i], globalHeap);
|
|
}
|
|
} else {
|
|
for (let j = 0; j < size; j++) {
|
|
data[j] = this._decodeArray(datatype, data[j], shape, dimension + 1);
|
|
}
|
|
}
|
|
return data;
|
|
}
|
|
};
|
|
|
|
hdf5.LinkInfo = class {
|
|
|
|
constructor(reader) {
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 0: {
|
|
const flags = reader.byte();
|
|
if ((flags & 1) !== 0) {
|
|
this.maxCreationIndex = reader.uint64();
|
|
}
|
|
this.fractalHeapAddress = reader.offset();
|
|
this.nameIndexTreeAddress = reader.offset();
|
|
if ((flags & 2) !== 0) {
|
|
this.creationOrderIndexTreeAddress = reader.offset();
|
|
}
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported link info message version '${version}'.`);
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.Datatype = class {
|
|
|
|
constructor(reader) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#DatatypeMessage
|
|
const format = reader.byte();
|
|
const version = format >> 4;
|
|
this._class = format & 0xf;
|
|
switch (version) {
|
|
case 1:
|
|
case 2:
|
|
case 3: {
|
|
this._flags = reader.byte() | reader.byte() << 8 | reader.byte() << 16;
|
|
this._size = reader.uint32();
|
|
switch (this._class) {
|
|
case 0: { // fixed-point
|
|
this._bitOffset = reader.uint16();
|
|
this._bitPrecision = reader.uint16();
|
|
break;
|
|
}
|
|
case 1: { // floating-point
|
|
this._bitOffset = reader.uint16();
|
|
this._bitPrecision = reader.uint16();
|
|
this._exponentLocation = reader.byte();
|
|
this._exponentSize = reader.byte();
|
|
this._mantissaLocation = reader.byte();
|
|
this._mantissaSize = reader.byte();
|
|
this._exponentBias = reader.uint32();
|
|
break;
|
|
}
|
|
case 2: { // time
|
|
this._bitPrecision = reader.uint16();
|
|
break;
|
|
}
|
|
case 4: { // bit field
|
|
this._bitOffset = reader.uint16();
|
|
this._bitPrecision = reader.uint16();
|
|
break;
|
|
}
|
|
case 6: { // compound
|
|
const count = this._flags & 0xffff;
|
|
// version 1 and 2 use a 4 byte member offset, version 3 uses the number of bytes needed to store the datatype size
|
|
let offsetSize = 4;
|
|
if (version >= 3) {
|
|
offsetSize = 0;
|
|
for (let size = this._size; size > 0; size >>= 8) {
|
|
offsetSize++;
|
|
}
|
|
}
|
|
this._members = new Array(count);
|
|
for (let i = 0; i < count; i++) {
|
|
let name = null;
|
|
let offset = 0;
|
|
if (version < 3) {
|
|
reader.seek(reader.position);
|
|
name = reader.string(-1, 'ascii');
|
|
reader.align(8); // names are padded to a multiple of 8 bytes
|
|
offset = reader.uint32();
|
|
if (version === 1) {
|
|
reader.skip(28); // dimensionality, reserved, permutation, reserved and dimension sizes
|
|
}
|
|
} else {
|
|
name = reader.string(-1, 'ascii');
|
|
for (let j = 0; j < offsetSize; j++) {
|
|
offset |= reader.byte() << (8 * j);
|
|
}
|
|
}
|
|
const datatype = new hdf5.Datatype(reader);
|
|
this._members[i] = { name, offset, datatype };
|
|
}
|
|
break;
|
|
}
|
|
case 8: { // enumerated
|
|
this._base = new hdf5.Datatype(reader);
|
|
reader.seek(reader.position);
|
|
const size = this._flags & 0xffff;
|
|
this._names = new Array(size);
|
|
for (let i = 0; i < size; i++) {
|
|
this._names[i] = reader.string(-1, 'ascii');
|
|
if (version < 3) {
|
|
reader.align(8);
|
|
}
|
|
}
|
|
this._values = new Array(size);
|
|
for (let i = 0; i < size; i++) {
|
|
this._values[i] = this._base.read(reader);
|
|
}
|
|
break;
|
|
}
|
|
case 9: { // variable-length
|
|
this._base = new hdf5.Datatype(reader);
|
|
break;
|
|
}
|
|
default: {
|
|
break;
|
|
}
|
|
}
|
|
break;
|
|
}
|
|
default: {
|
|
throw new hdf5.Error(`Unsupported datatype version '${version}'.`);
|
|
}
|
|
}
|
|
}
|
|
|
|
get type() {
|
|
switch (this._class) {
|
|
case 0: // fixed-point
|
|
if ((this._flags & 0xfff6) === 0) {
|
|
if ((this._flags && 0x08) === 0) {
|
|
switch (this._size) {
|
|
case 1: return 'uint8';
|
|
case 2: return 'uint16';
|
|
case 4: return 'uint32';
|
|
case 8: return 'uint64';
|
|
default: throw new hdf5.Error(`Unsupported uint size '${this._size}'.`);
|
|
}
|
|
} else {
|
|
switch (this._size) {
|
|
case 1: return 'int8';
|
|
case 2: return 'int16';
|
|
case 4: return 'int32';
|
|
case 8: return 'int64';
|
|
default: throw new hdf5.Error(`Unsupported int size '${this._size}'.`);
|
|
}
|
|
}
|
|
}
|
|
break;
|
|
case 1: // floating-point
|
|
if (this._size === 2 && this._flags === 0x0f20) {
|
|
return 'float16';
|
|
} else if (this._size === 4 && this._flags === 0x1f20) {
|
|
return 'float32';
|
|
} else if (this._size === 8 && this._flags === 0x3f20) {
|
|
return 'float64';
|
|
}
|
|
break;
|
|
case 3: // string
|
|
return 'string';
|
|
case 5: // opaque
|
|
return 'uint8';
|
|
case 6: // compound
|
|
return 'object';
|
|
case 8: // enumerated
|
|
if (this._base.type === 'int8' &&
|
|
this._names.length === 2 && this._names[0] === 'FALSE' && this._names[1] === 'TRUE' &&
|
|
this._values.length === 2 && this._values[0] === 0 && this._values[1] === 1) {
|
|
return 'boolean';
|
|
}
|
|
break;
|
|
case 9: // variable-length
|
|
if ((this._flags & 0x0f) === 1) { // type
|
|
return 'string';
|
|
}
|
|
break;
|
|
default:
|
|
break;
|
|
}
|
|
throw new hdf5.Error(`Unsupported datatype class '${this._class}'.`);
|
|
}
|
|
|
|
get littleEndian() {
|
|
switch (this._class) {
|
|
case 0: // fixed-point
|
|
case 1: // floating-point
|
|
return (this.flags & 0x01) === 0;
|
|
default:
|
|
return true;
|
|
}
|
|
}
|
|
|
|
read(reader) {
|
|
switch (this._class) {
|
|
case 0: // fixed-point
|
|
if (this._size === 1) {
|
|
return this._flags & 0x8 ? reader.int8() : reader.byte();
|
|
} else if (this._size === 2) {
|
|
return this._flags & 0x8 ? reader.int16() : reader.uint16();
|
|
} else if (this._size === 4) {
|
|
return this._flags & 0x8 ? reader.int32() : reader.uint32();
|
|
} else if (this._size === 8) {
|
|
return this._flags & 0x8 ? reader.int64() : reader.uint64();
|
|
}
|
|
throw new hdf5.Error('Unsupported fixed-point datatype.');
|
|
case 1: // floating-point
|
|
if (this._size === 2 && this._flags === 0x0f20) {
|
|
return reader.float16();
|
|
} else if (this._size === 4 && this._flags === 0x1f20) {
|
|
return reader.float32();
|
|
} else if (this._size === 8 && this._flags === 0x3f20) {
|
|
return reader.float64();
|
|
}
|
|
throw new hdf5.Error('Unsupported floating-point datatype.');
|
|
case 3: // string
|
|
switch ((this._flags >> 8) & 0x0f) { // character set
|
|
case 0:
|
|
return reader.string(this._size, 'ascii');
|
|
case 1:
|
|
return reader.string(this._size, 'utf-8');
|
|
default:
|
|
throw new hdf5.Error('Unsupported character encoding.');
|
|
}
|
|
case 5: // opaque
|
|
return reader.read(this._size);
|
|
case 6: { // compound
|
|
const position = reader.position;
|
|
const obj = {};
|
|
for (const member of this._members) {
|
|
reader.seek(position + member.offset);
|
|
obj[member.name] = member.datatype.read(reader);
|
|
}
|
|
reader.seek(position + this._size);
|
|
return obj;
|
|
}
|
|
case 8: // enumerated
|
|
return reader.read(this._size);
|
|
case 9: // variable-length
|
|
return {
|
|
length: reader.uint32(),
|
|
globalHeapID: new hdf5.GlobalHeapID(reader)
|
|
};
|
|
default:
|
|
throw new hdf5.Error(`Unsupported datatype class '${this._class}'.`);
|
|
}
|
|
}
|
|
|
|
decode(data, globalHeap) {
|
|
switch (this._class) {
|
|
case 0: // fixed-point
|
|
return data;
|
|
case 1: // floating-point
|
|
return data;
|
|
case 3: // string
|
|
return data;
|
|
case 5: // opaque
|
|
return data;
|
|
case 6: { // compound
|
|
const obj = {};
|
|
for (const member of this._members) {
|
|
obj[member.name] = member.datatype.decode(data[member.name], globalHeap);
|
|
}
|
|
return obj;
|
|
}
|
|
case 8: // enumerated
|
|
return data;
|
|
case 9: { // variable-length
|
|
const globalHeapObject = globalHeap.get(data.globalHeapID);
|
|
if (globalHeapObject !== null) {
|
|
const characterSet = (this._flags >> 8) & 0x0f;
|
|
const reader = globalHeapObject.reader();
|
|
switch (characterSet) {
|
|
case 0:
|
|
return reader.string(reader.length(), 'ascii');
|
|
case 1:
|
|
return reader.string(reader.length(), 'utf-8');
|
|
default:
|
|
throw new hdf5.Error('Unsupported character encoding.');
|
|
}
|
|
}
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported datatype class '${this._class}'.`);
|
|
}
|
|
return null;
|
|
}
|
|
};
|
|
|
|
hdf5.FillValue = class {
|
|
|
|
constructor(reader, type) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#FillValueMessage
|
|
switch (type) {
|
|
case 0x0004: {
|
|
const size = reader.uint32();
|
|
this.data = reader.read(size);
|
|
break;
|
|
}
|
|
case 0x0005:
|
|
default: {
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1:
|
|
case 2: {
|
|
reader.byte();
|
|
reader.byte();
|
|
const valueDefined = reader.byte();
|
|
if (version === 1 || valueDefined === 1) {
|
|
const size = reader.uint32();
|
|
this.data = reader.read(size);
|
|
}
|
|
break;
|
|
}
|
|
case 3: {
|
|
const flags = reader.byte();
|
|
if ((flags & 0x20) !== 0) {
|
|
const size = reader.uint32();
|
|
this.data = reader.read(size);
|
|
}
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported fill value version '${version}'.`);
|
|
}
|
|
break;
|
|
}
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.Link = class {
|
|
|
|
constructor(reader) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#FillValueMessage
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1: {
|
|
const flags = reader.byte();
|
|
this.type = (flags & 0x08) === 0 ? 0 : reader.byte();
|
|
if ((flags & 0x04) !== 0) {
|
|
this.creationOrder = reader.uint32();
|
|
}
|
|
const encoding = ((flags & 0x10) !== 0 && reader.byte() === 1) ? 'utf-8' : 'ascii';
|
|
const size = reader.uint(flags & 0x03);
|
|
this.name = reader.string(size, encoding);
|
|
switch (this.type) {
|
|
case 0: // hard link
|
|
this.objectHeaderAddress = reader.offset();
|
|
break;
|
|
case 1: // soft link
|
|
break;
|
|
default:
|
|
throw new hdf5.Error(`Unsupported link message type '${this.type}'.`);
|
|
}
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported link message version '${version}'.`);
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.DataLayout = class {
|
|
|
|
constructor(reader) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#LayoutMessage
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1:
|
|
case 2: {
|
|
this.dimensionality = reader.byte();
|
|
this.layoutClass = reader.byte();
|
|
reader.skip(5);
|
|
switch (this.layoutClass) {
|
|
case 1:
|
|
this.address = reader.offset();
|
|
this.dimensionSizes = [];
|
|
for (let i = 0; i < this.dimensionality - 1; i++) {
|
|
this.dimensionSizes.push(reader.int32());
|
|
}
|
|
break;
|
|
case 2: // Chunked
|
|
this.address = reader.offset();
|
|
this.dimensionSizes = [];
|
|
for (let i = 0; i < this.dimensionality - 1; i++) {
|
|
this.dimensionSizes.push(reader.int32());
|
|
}
|
|
this.datasetElementSize = reader.int32();
|
|
break;
|
|
default:
|
|
throw new hdf5.Error(`Unsupported data layout class '${this.layoutClass}'.`);
|
|
}
|
|
break;
|
|
}
|
|
case 3: {
|
|
this.layoutClass = reader.byte();
|
|
switch (this.layoutClass) {
|
|
case 0: // Compact
|
|
this.size = reader.uint16();
|
|
reader.skip(2);
|
|
this.address = reader.position;
|
|
break;
|
|
case 1: // Contiguous
|
|
this.address = reader.offset();
|
|
this.size = reader.length();
|
|
break;
|
|
case 2: // Chunked
|
|
this.dimensionality = reader.byte();
|
|
this.address = reader.offset();
|
|
this.dimensionSizes = [];
|
|
for (let i = 0; i < this.dimensionality - 1; i++) {
|
|
this.dimensionSizes.push(reader.int32());
|
|
}
|
|
this.datasetElementSize = reader.int32();
|
|
break;
|
|
default:
|
|
throw new hdf5.Error(`Unsupported data layout class '${this.layoutClass}'.`);
|
|
}
|
|
break;
|
|
}
|
|
default: {
|
|
throw new hdf5.Error(`Unsupported data layout version '${version}'.`);
|
|
}
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.GroupInfo = class {
|
|
|
|
constructor(reader) {
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 0: {
|
|
const flags = reader.byte();
|
|
if ((flags & 0x01) !== 0) {
|
|
this.maxCompactLinks = reader.uint16();
|
|
this.minDenseLinks = reader.uint16();
|
|
}
|
|
if ((flags & 0x02) !== 0) {
|
|
this.estimatedEntriesNumber = reader.uint16();
|
|
this.estimatedLinkNameLengthEntries = reader.uint16();
|
|
}
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported group info version '${version}'.`);
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.FilterPipeline = class {
|
|
|
|
constructor(reader) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#FilterMessage
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1: {
|
|
this.filters = [];
|
|
const numberOfFilters = reader.byte();
|
|
reader.skip(2);
|
|
reader.skip(4);
|
|
for (let i = 0; i < numberOfFilters; i++) {
|
|
this.filters.push(new hdf5.Filter(reader));
|
|
reader.align(8);
|
|
}
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported filter pipeline message version '${version}'.`);
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.Filter = class {
|
|
|
|
constructor(reader) {
|
|
this.id = reader.int16();
|
|
const nameLength = reader.int16();
|
|
this.flags = reader.int16();
|
|
const clientDataSize = reader.int16();
|
|
this.name = reader.string(nameLength, 'ascii');
|
|
this.clientData = reader.read(clientDataSize * 4);
|
|
}
|
|
|
|
decode(data) {
|
|
switch (this.id) {
|
|
case 1: return this._deflate(data);
|
|
case 32000: return this._lzf(data);
|
|
default: throw new hdf5.Error(`Unsupported filter '${this.id}:${this.name}'.`);
|
|
}
|
|
}
|
|
|
|
_deflate(input) {
|
|
const archive = zip.Archive.open(input);
|
|
return archive.entries.get('').peek();
|
|
}
|
|
|
|
_lzf(input) {
|
|
let i = 0;
|
|
let o = 0;
|
|
while (i < input.length) {
|
|
let c = input[i++];
|
|
if (c < (1 << 5)) {
|
|
c++;
|
|
i += c;
|
|
o += c;
|
|
if (i > input.length) {
|
|
throw new Error('Invalid LZF compressed data.');
|
|
}
|
|
} else {
|
|
let length = c >> 5;
|
|
if (i >= input.length) {
|
|
throw new Error('Invalid LZF compressed data.');
|
|
}
|
|
if (length === 7) {
|
|
length += input[i++];
|
|
if (i >= input.length) {
|
|
throw new Error('Invalid LZF compressed data.');
|
|
}
|
|
}
|
|
const ref = (o - ((c & 0x1f) << 8) - 1) - input[i++];
|
|
if (ref < 0) {
|
|
throw new Error('Invalid LZF compressed data.');
|
|
}
|
|
o += length + 2;
|
|
}
|
|
}
|
|
const output = new Uint8Array(o);
|
|
i = 0;
|
|
o = 0;
|
|
while (i < input.length) {
|
|
let c = input[i++];
|
|
if (c < (1 << 5)) {
|
|
c++;
|
|
output.set(input.subarray(i, i + c), o);
|
|
i += c;
|
|
o += c;
|
|
} else {
|
|
let length = c >> 5;
|
|
if (length === 7) {
|
|
length += input[i++];
|
|
}
|
|
length += 2;
|
|
let ref = o - ((c & 0x1f) << 8) - 1 - input[i++];
|
|
do {
|
|
output[o++] = output[ref++];
|
|
} while (--length);
|
|
}
|
|
}
|
|
return output;
|
|
}
|
|
};
|
|
|
|
hdf5.Attribute = class {
|
|
|
|
constructor(reader) {
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1: {
|
|
reader.skip(1);
|
|
const nameSize = reader.uint16();
|
|
const datatypeSize = reader.uint16();
|
|
const dataspaceSize = reader.uint16();
|
|
this.name = reader.string(nameSize, 'utf-8');
|
|
reader.align(8);
|
|
const datatypePosition = reader.position;
|
|
this._datatype = new hdf5.Datatype(reader);
|
|
reader.seek(datatypePosition);
|
|
reader.skip(datatypeSize);
|
|
reader.align(8);
|
|
const dataspacePosition = reader.position;
|
|
this._dataspace = new hdf5.Dataspace(reader);
|
|
reader.seek(dataspacePosition);
|
|
reader.skip(dataspaceSize);
|
|
reader.align(8);
|
|
this._data = this._dataspace.read(this._datatype, reader);
|
|
break;
|
|
}
|
|
case 3: {
|
|
reader.byte();
|
|
const nameSize = reader.uint16();
|
|
const datatypeSize = reader.uint16();
|
|
const dataspaceSize = reader.uint16();
|
|
const encoding = reader.byte() === 1 ? 'utf-8' : 'ascii';
|
|
this.name = reader.string(nameSize, encoding);
|
|
const datatypePosition = reader.position;
|
|
this._datatype = new hdf5.Datatype(reader);
|
|
reader.seek(datatypePosition);
|
|
reader.skip(datatypeSize);
|
|
const dataspacePosition = reader.position;
|
|
this._dataspace = new hdf5.Dataspace(reader);
|
|
reader.seek(dataspacePosition);
|
|
reader.skip(dataspaceSize);
|
|
this._data = this._dataspace.read(this._datatype, reader);
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported attribute message version '${version}'.`);
|
|
}
|
|
}
|
|
|
|
decodeValue(globalHeap) {
|
|
if (this._data) {
|
|
return this._dataspace.decode(this._datatype, this._data, globalHeap);
|
|
}
|
|
return null;
|
|
}
|
|
};
|
|
|
|
hdf5.ObjectHeaderContinuation = class {
|
|
|
|
constructor(reader) {
|
|
this.offset = reader.offset();
|
|
this.length = reader.length();
|
|
}
|
|
};
|
|
|
|
hdf5.SymbolTable = class {
|
|
|
|
constructor(reader) {
|
|
this.treeAddress = reader.offset();
|
|
this.heapAddress = reader.offset();
|
|
}
|
|
};
|
|
|
|
hdf5.ObjectModificationTime = class {
|
|
|
|
constructor(reader, type) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#ModificationTimeMessage
|
|
switch (type) {
|
|
case 0x000E: {
|
|
this.year = reader.uint32();
|
|
this.month = reader.uint16();
|
|
this.day = reader.uint16();
|
|
this.hour = reader.uint16();
|
|
this.minute = reader.uint16();
|
|
this.second = reader.uint16();
|
|
reader.skip(2);
|
|
break;
|
|
}
|
|
case 0x0012: {
|
|
const version = reader.byte();
|
|
reader.skip(3);
|
|
switch (version) {
|
|
case 1:
|
|
this.timestamp = reader.uint32();
|
|
break;
|
|
default:
|
|
throw new hdf5.Error(`Unsupported object modification time message version '${version}'.`);
|
|
}
|
|
break;
|
|
}
|
|
default: {
|
|
throw new hdf5.Error(`Unsupported object modification time message type '${type}'.`);
|
|
}
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.AttributeInfo = class {
|
|
|
|
constructor(reader) {
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 0: {
|
|
const flags = reader.byte();
|
|
if ((flags & 1) !== 0) {
|
|
this.maxCreationIndex = reader.uint64();
|
|
}
|
|
this.fractalHeapAddress = reader.offset();
|
|
this.attributeNameTreeAddress = reader.offset();
|
|
if ((flags & 2) !== 0) {
|
|
this.attributeCreationOrderTreeAddress = reader.offset();
|
|
}
|
|
break;
|
|
}
|
|
default:
|
|
throw new hdf5.Error(`Unsupported attribute info message version '${version}'.`);
|
|
}
|
|
}
|
|
};
|
|
|
|
hdf5.Tree = class {
|
|
|
|
constructor(reader, offset, dimensionality) {
|
|
// https://support.hdfgroup.org/HDF5/doc/H5.format.html#V1Btrees
|
|
const position = reader.position;
|
|
reader.seek(offset);
|
|
reader.expect('TREE');
|
|
this.type = reader.byte();
|
|
this.level = reader.byte();
|
|
const entries = reader.uint16();
|
|
reader.offset(); // address of left sibling
|
|
reader.offset(); // address of right sibling
|
|
this.nodes = [];
|
|
switch (this.type) {
|
|
case 0: { // Group nodes
|
|
for (let i = 0; i < entries; i++) {
|
|
reader.length();
|
|
const childPointer = reader.offset();
|
|
if (this.level === 0) {
|
|
const node = new hdf5.SymbolTableNode(reader, childPointer);
|
|
this.nodes.push(node);
|
|
} else {
|
|
const tree = new hdf5.Tree(reader, childPointer);
|
|
this.nodes.push(...tree.nodes);
|
|
}
|
|
}
|
|
break;
|
|
}
|
|
case 1: { // Raw data chunk nodes
|
|
for (let i = 0; i < entries; i++) {
|
|
const size = reader.int32();
|
|
const filterMask = reader.int32();
|
|
const fields = [];
|
|
for (let j = 0; j < dimensionality; j++) {
|
|
fields.push(reader.uint64());
|
|
}
|
|
const childPointer = reader.offset();
|
|
if (this.level === 0) {
|
|
const position = reader.position;
|
|
reader.seek(childPointer);
|
|
const data = reader.read(size);
|
|
this.nodes.push({ data, fields, filterMask });
|
|
reader.seek(position);
|
|
} else {
|
|
const tree = new hdf5.Tree(reader, childPointer, dimensionality);
|
|
this.nodes.push(...tree.nodes);
|
|
}
|
|
}
|
|
break;
|
|
}
|
|
default: {
|
|
throw new hdf5.Error(`Unsupported B-Tree node type '${this.type}'.`);
|
|
}
|
|
}
|
|
reader.seek(position);
|
|
}
|
|
};
|
|
|
|
hdf5.Heap = class {
|
|
|
|
constructor(reader, offset) {
|
|
const position = reader.position;
|
|
reader.seek(offset);
|
|
this._reader = reader;
|
|
reader.expect('HEAP');
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 0: {
|
|
reader.skip(3);
|
|
this._dataSize = reader.length();
|
|
this._offsetToHeadOfFreeList = reader.length();
|
|
this._dataAddress = reader.offset();
|
|
break;
|
|
}
|
|
default: {
|
|
throw new hdf5.Error(`Unsupported Local Heap version '${version}'.`);
|
|
}
|
|
}
|
|
reader.seek(position);
|
|
}
|
|
|
|
getString(offset) {
|
|
const position = this._reader.position;
|
|
this._reader.seek(this._dataAddress + offset);
|
|
const value = this._reader.string(-1, 'utf-8');
|
|
this._reader.seek(position);
|
|
return value;
|
|
}
|
|
};
|
|
|
|
hdf5.GlobalHeap = class {
|
|
|
|
constructor(reader) {
|
|
this._reader = reader;
|
|
this._collections = new Map();
|
|
}
|
|
|
|
get(globalHeapID) {
|
|
const address = globalHeapID.address;
|
|
if (!this._collections.has(address)) {
|
|
this._collections.set(address, new hdf5.GlobalHeapCollection(this._reader, address));
|
|
}
|
|
const collection = this._collections.get(globalHeapID.address);
|
|
return collection.getObject(globalHeapID.objectIndex);
|
|
}
|
|
};
|
|
|
|
hdf5.GlobalHeapCollection = class {
|
|
|
|
constructor(reader, offset) {
|
|
const position = reader.position;
|
|
reader.seek(offset);
|
|
const start = reader.position;
|
|
reader.expect('GCOL');
|
|
const version = reader.byte();
|
|
switch (version) {
|
|
case 1: {
|
|
reader.skip(3);
|
|
this._objects = new Map();
|
|
const size = reader.length();
|
|
const end = start + size;
|
|
while (reader.position < end) {
|
|
const index = reader.uint16();
|
|
if (index === 0) {
|
|
break;
|
|
}
|
|
this._objects.set(index, new hdf5.GlobalHeapObject(reader));
|
|
reader.align(8);
|
|
}
|
|
break;
|
|
}
|
|
default: {
|
|
throw new hdf5.Error(`Unsupported global heap collection version '${version}'.`);
|
|
}
|
|
}
|
|
reader.seek(position);
|
|
}
|
|
|
|
getObject(objectIndex) {
|
|
if (this._objects.has(objectIndex)) {
|
|
return this._objects.get(objectIndex);
|
|
}
|
|
return null;
|
|
}
|
|
};
|
|
|
|
hdf5.GlobalHeapObject = class {
|
|
|
|
constructor(reader) {
|
|
reader.uint16();
|
|
reader.skip(4);
|
|
this._position = reader.position;
|
|
this._reader = reader;
|
|
const length = reader.length();
|
|
reader.skip(length);
|
|
}
|
|
|
|
reader() {
|
|
this._reader.seek(this._position);
|
|
return this._reader;
|
|
}
|
|
};
|
|
|
|
hdf5.GlobalHeapID = class {
|
|
|
|
constructor(reader) {
|
|
this.address = reader.offset();
|
|
this.objectIndex = reader.uint32();
|
|
}
|
|
};
|
|
|
|
hdf5.Error = class extends Error {
|
|
|
|
constructor(message) {
|
|
super(message);
|
|
this.name = 'HDF5 Error';
|
|
}
|
|
};
|
|
|
|
export const File = hdf5.File;
|