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import { decompressSync } from 'fflate';
import DataAccessHelper from 'vtk.js/Sources/IO/Core/DataAccessHelper';
import Base64 from 'vtk.js/Sources/Common/Core/Base64';
import macro from 'vtk.js/Sources/macros';
import vtkDataArray from 'vtk.js/Sources/Common/Core/DataArray';
import vtkStringArray from 'vtk.js/Sources/Common/Core/StringArray';
import BinaryHelper from 'vtk.js/Sources/IO/Core/BinaryHelper';
// Enable data soure for DataAccessHelper
import 'vtk.js/Sources/IO/Core/DataAccessHelper/LiteHttpDataAccessHelper'; // Just need HTTP
// import 'vtk.js/Sources/IO/Core/DataAccessHelper/HttpDataAccessHelper'; // HTTP + zip
// import 'vtk.js/Sources/IO/Core/DataAccessHelper/HtmlDataAccessHelper'; // html + base64 + zip
// import 'vtk.js/Sources/IO/Core/DataAccessHelper/JSZipDataAccessHelper'; // zip
// ----------------------------------------------------------------------------
// Global methods
// ----------------------------------------------------------------------------
export function findAllTags(node, tagName) {
return [...node.getElementsByTagName(tagName)];
}
export function findFirstTag(node, tagName) {
return findAllTags(node, tagName)[0];
}
function parseXML(xmlStr) {
// see xmlbuilder2 docs on the object format
return create(xmlStr);
}
function extractAppendedData(buffer) {
// search for appended data tag
const prefixRegex = /^\s*<AppendedData\s+encoding="raw">\s*_/m;
const suffixRegex = /\n\s*<\/AppendedData>/m;
return BinaryHelper.extractBinary(buffer, prefixRegex, suffixRegex);
}
// ----------------------------------------------------------------------------
const TYPED_ARRAY = {
Int8: Int8Array,
UInt8: Uint8Array,
Int16: Int16Array,
UInt16: Uint16Array,
Int32: Int32Array,
UInt32: Uint32Array,
Int64: Int32Array, // Not supported with JavaScript will cause error in binary
UInt64: Uint32Array, // Not supported with JavaScript will cause error in binary
Float32: Float32Array,
Float64: Float64Array,
};
// ----------------------------------------------------------------------------
const TYPED_ARRAY_BYTES = {
Int8: 1,
UInt8: 1,
Int16: 2,
UInt16: 2,
Int32: 4,
UInt32: 4,
Int64: 8, // Not supported with JavaScript will cause error in binary
UInt64: 8, // Not supported with JavaScript will cause error in binary
Float32: 4,
Float64: 8,
};
// ----------------------------------------------------------------------------
function integer64to32(array) {
const maxIdx = array.length - 1; // Skip last
return array.filter((v, i) => i < maxIdx && i % 2 === 0);
}
// ----------------------------------------------------------------------------
/**
* Reads the data of a length-prefixed blob.
*
* Int64 headers and values are not supported.
*
* @param {Uint8Array} uint8 a uint8 view of the length-prefixed blob.
* @param {string} dataType
* @param {string} headerType either UInt64 or UInt32
*/
function readLengthPrefixedData(uint8, dataType, headerType) {
if (!['UInt64', 'UInt32'].includes(headerType)) {
throw new Error(`Cannot handle a header type of ${headerType}`);
}
let HeaderTypedArray = TYPED_ARRAY[headerType];
let DataTypedArray = TYPED_ARRAY[dataType];
let dataFallbackTo32 = false;
if (headerType === 'UInt64') {
HeaderTypedArray = TYPED_ARRAY.UInt32;
}
if (/^U?Int64$/.test(dataType)) {
dataFallbackTo32 = true;
DataTypedArray = TYPED_ARRAY[dataType.replace('64', '32')];
}
const { byteOffset } = uint8;
const dataWordSize = TYPED_ARRAY_BYTES[dataType];
const headerWordSize = TYPED_ARRAY_BYTES[headerType];
// slice if offset is not word aligned
let header;
if (byteOffset % headerWordSize === 0) {
header = new HeaderTypedArray(uint8.buffer, byteOffset, 1);
} else {
header = new HeaderTypedArray(
uint8.buffer.slice(byteOffset, byteOffset + headerWordSize)
);
}
const dataByteLength = Number(header[0]);
// read values
let values;
let arraySize = dataByteLength / dataWordSize;
if (dataFallbackTo32) {
// We are reading int64 data with an int32 typed array.
arraySize *= 2;
}
// slice if offset is not word aligned
const dataOffset = byteOffset + headerWordSize;
if (dataOffset % dataWordSize === 0) {
values = new DataTypedArray(uint8.buffer, dataOffset, arraySize);
} else {
values = new DataTypedArray(
uint8.buffer.slice(dataOffset, dataOffset + dataByteLength)
);
}
if (dataFallbackTo32) {
// remove higher order 32 bits
values = integer64to32(values);
}
return values;
}
// ----------------------------------------------------------------------------
function readerHeader(uint8, headerType) {
// We do not handle endianness or if more than 32 bits are needed to encode the data
if (headerType === 'UInt64') {
const offset = 8;
let uint32 = new Uint32Array(uint8.buffer, 0, 6);
const nbBlocks = uint32[0];
const s1 = uint32[2];
const s2 = uint32[4];
const resultArray = [offset, nbBlocks, s1, s2];
uint32 = new Uint32Array(uint8.buffer, 3 * 8, nbBlocks * 2);
for (let i = 0; i < nbBlocks; i++) {
resultArray.push(uint32[i * 2]);
}
return resultArray;
}
// UInt32
let uint32 = new Uint32Array(uint8.buffer, 0, 3);
const offset = 4;
const nbBlocks = uint32[0];
const s1 = uint32[1];
const s2 = uint32[2];
const resultArray = [offset, nbBlocks, s1, s2];
uint32 = new Uint32Array(uint8.buffer, 3 * 4, nbBlocks);
for (let i = 0; i < nbBlocks; i++) {
resultArray.push(uint32[i]);
}
return resultArray;
}
// ----------------------------------------------------------------------------
/**
* Given the return value of readerHeader, return header byte length.
*/
function getHeaderByteLength(header, headerType) {
// ignore the first number, which isn't actually part of the header.
const [headerWordSize] = header;
return (header.length - 1) * headerWordSize;
}
// ----------------------------------------------------------------------------
function uncompressBlock(compressedUint8, output) {
const uncompressedBlock = decompressSync(compressedUint8);
output.uint8.set(uncompressedBlock, output.offset);
output.offset += uncompressedBlock.length;
}
// ----------------------------------------------------------------------------
function decompressZLib(bytes, headerType) {
// ----------------------------------------------------------------------
// Layout of the data
// header[N, s1, s2, blockSize1, ..., blockSizeN], [padding???], block[compressedData], ..., block[compressedData]
// [header] N, s1 and s2 are uint 32 or 64 (defined by header_type="UInt64" attribute on the root node)
// [header] s1: uncompress size of each block except the last one
// [header] s2: uncompress size of the last blocks
// [header] blockSize: size of the block in compressed space that represent to bloc to inflate in zlib. (This also give the offset to the next block)
// ----------------------------------------------------------------------
// Header reading: [offset, numBlocks, s1, s2]
const header = readerHeader(bytes, headerType);
const nbBlocks = header[1];
const s1 = header[2];
const s2 = header[3];
let dataByteLength = 0;
if (nbBlocks > 0) {
// If the last block's size is labeled as 0, that means the last block
// really has size header[2].
if (s2 === 0) {
dataByteLength = nbBlocks * s1;
} else {
dataByteLength = (nbBlocks - 1) * s1 + s2;
}
}
const buffer = new ArrayBuffer(dataByteLength);
const output = {
offset: 0,
uint8: new Uint8Array(buffer),
};
let offset = getHeaderByteLength(header, headerType);
// Starting from end of the data header, find the zlib header, which starts with 0x78.
// This accounts for any padding between the header and the compressed data.
while (offset < bytes.length && bytes[offset] !== 0x78) {
offset++;
}
for (let i = 0; i < nbBlocks; i++) {
const blockSize = header[4 + i];
const compressedBlock = new Uint8Array(bytes.buffer, offset, blockSize);
uncompressBlock(compressedBlock, output);
offset += blockSize;
}
return output.uint8;
}
// ----------------------------------------------------------------------------
function processDataArray(
size,
dataArrayElem,
compressor,
byteOrder,
headerType,
binaryBuffer
) {
const dataType = dataArrayElem.getAttribute('type');
const name = dataArrayElem.getAttribute('Name');
const format = dataArrayElem.getAttribute('format'); // binary, ascii, appended
const numberOfComponents = Number(
dataArrayElem.getAttribute('NumberOfComponents') || '1'
);
let values = null;
if (format === 'ascii') {
values = new TYPED_ARRAY[dataType](size * numberOfComponents);
let offset = 0;
dataArrayElem.firstChild.nodeValue.split(/[\\t \\n]+/).forEach((token) => {
if (token.trim().length) {
values[offset++] = Number(token);
}
});
} else if (format === 'binary') {
const uint8 = new Uint8Array(
Base64.toArrayBuffer(dataArrayElem.firstChild.nodeValue.trim())
);
if (compressor === 'vtkZLibDataCompressor') {
const data = decompressZLib(uint8, headerType);
values = new TYPED_ARRAY[dataType](data.buffer);
// Handle (u)int64 hoping for no overflow...
if (/^U?Int64$/.test(dataType)) {
values = integer64to32(values);
}
} else {
values = new TYPED_ARRAY[dataType](
uint8.buffer,
TYPED_ARRAY_BYTES[headerType]
);
// Handle (u)int64 hoping no overflow...
if (dataType.indexOf('Int64') !== -1) {
values = integer64to32(values);
}
}
} else if (format === 'appended') {
const offset = Number(dataArrayElem.getAttribute('offset'));
values = readLengthPrefixedData(
new Uint8Array(binaryBuffer, offset),
dataType,
headerType
);
} else {
console.error('Format not supported', format);
}
return { name, values, numberOfComponents };
}
// ----------------------------------------------------------------------------
function decodeStringArrayFromBytes(bytes) {
const decoder = new TextDecoder();
const decoded = decoder.decode(bytes);
// strings are null-terminated
return decoded.split('\x00').slice(0, -1);
}
// ----------------------------------------------------------------------------
function processStringArray(
stringArrayElem,
compressor,
byteOrder,
headerType,
binaryBuffer
) {
const name = stringArrayElem.getAttribute('Name');
const format = stringArrayElem.getAttribute('format'); // binary, ascii, appended
const numberOfComponents = Number(
stringArrayElem.getAttribute('NumberOfComponents') || '1'
);
const numberOfTuples = Number(
stringArrayElem.getAttribute('NumberOfTuples') || '1'
);
const nbStrings = numberOfTuples * numberOfComponents;
const strings = [];
if (format === 'ascii') {
const tokens = stringArrayElem.firstChild.nodeValue.trim().split(/\s+/);
let tokIdx = 0;
const strChars = [];
while (strings.length < nbStrings) {
const token = Number(tokens[tokIdx++]);
if (token === 0) {
strings.push(strChars.join(''));
strChars.length = 0;
} else {
strChars.push(String.fromCharCode(token));
}
}
} else if (format === 'binary') {
const uint8 = new Uint8Array(
Base64.toArrayBuffer(stringArrayElem.firstChild.nodeValue.trim())
);
if (compressor === 'vtkZLibDataCompressor') {
const decompressed = decompressZLib(uint8, headerType);
strings.push(...decodeStringArrayFromBytes(decompressed));
} else {
const strData = readLengthPrefixedData(uint8, 'UInt8', headerType);
strings.push(...decodeStringArrayFromBytes(strData));
}
} else if (format === 'appended') {
const offset = Number(stringArrayElem.getAttribute('offset'));
const values = readLengthPrefixedData(
new Uint8Array(binaryBuffer, offset),
'UInt8',
headerType
);
strings.push(...decodeStringArrayFromBytes(values));
} else {
macro.vtkErrorMacro(`Format not supported: ${format}`);
}
return { name, values: strings, numberOfComponents };
}
// ----------------------------------------------------------------------------
function processCells(
size,
containerElem,
compressor,
byteOrder,
headerType,
binaryBuffer
) {
const arrayElems = {};
const dataArrayElems = containerElem.getElementsByTagName('DataArray');
for (let elIdx = 0; elIdx < dataArrayElems.length; elIdx++) {
const el = dataArrayElems[elIdx];
arrayElems[el.getAttribute('Name')] = el;
}
const offsets = processDataArray(
size,
arrayElems.offsets,
compressor,
byteOrder,
headerType,
binaryBuffer
).values;
const connectivitySize = offsets[offsets.length - 1];
const connectivity = processDataArray(
connectivitySize,
arrayElems.connectivity,
compressor,
byteOrder,
headerType,
binaryBuffer
).values;
const values = new Uint32Array(size + connectivitySize);
let writeOffset = 0;
let previousOffset = 0;
offsets.forEach((v) => {
const cellSize = v - previousOffset;
values[writeOffset++] = cellSize;
for (let i = 0; i < cellSize; i++) {
values[writeOffset++] = connectivity[previousOffset + i];
}
// save previous offset
previousOffset = v;
});
return values;
}
// ----------------------------------------------------------------------------
function processFieldData(
size,
fieldElem,
fieldContainer,
compressor,
byteOrder,
headerType,
binaryBuffer
) {
if (fieldElem) {
const attributes = ['Scalars', 'Vectors', 'Normals', 'Tensors', 'TCoords'];
const nameBinding = {};
attributes.forEach((attrName) => {
const arrayName = fieldElem.getAttribute(attrName);
Iif (arrayName) {
nameBinding[arrayName] = fieldContainer[`set${attrName}`];
}
});
const dataArrayElems = fieldElem.getElementsByTagName('DataArray');
const nbArrays = dataArrayElems.length;
for (let idx = 0; idx < nbArrays; idx++) {
const array = dataArrayElems[idx];
const dataArray = vtkDataArray.newInstance(
processDataArray(
size,
array,
compressor,
byteOrder,
headerType,
binaryBuffer
)
);
const name = dataArray.getName();
(nameBinding[name] || fieldContainer.addArray)(dataArray);
}
}
}
// ----------------------------------------------------------------------------
function handleFieldDataArrays(
fieldDataElem,
compressor,
byteOrder,
headerType,
binaryBuffer
) {
const dataArrays = [...fieldDataElem.getElementsByTagName('DataArray')].map(
(daElem) =>
vtkDataArray.newInstance(
processDataArray(
Number(daElem.getAttribute('NumberOfTuples')),
daElem,
compressor,
byteOrder,
headerType,
binaryBuffer
)
)
);
const stringArrays = [...fieldDataElem.getElementsByTagName('Array')]
.filter((elem) => elem.getAttribute('type') === 'String')
.map((arrElem) => {
const sa = vtkStringArray.newInstance(
processStringArray(
arrElem,
compressor,
byteOrder,
headerType,
binaryBuffer
)
);
return sa;
});
return [...dataArrays, ...stringArrays];
}
// ----------------------------------------------------------------------------
// vtkXMLReader methods
// ----------------------------------------------------------------------------
function vtkXMLReader(publicAPI, model) {
// Set our className
model.classHierarchy.push('vtkXMLReader');
// Create default dataAccessHelper if not available
if (!model.dataAccessHelper) {
model.dataAccessHelper = DataAccessHelper.get('http');
}
// Internal method to fetch Array
function fetchData(url, option = {}) {
return model.dataAccessHelper.fetchBinary(url, option);
}
// Set DataSet url
publicAPI.setUrl = (url, option = {}) => {
model.url = url;
// Remove the file in the URL
const path = url.split('/');
path.pop();
model.baseURL = path.join('/');
// Fetch metadata
return publicAPI.loadData(option);
};
// Fetch the actual data arrays
publicAPI.loadData = (option = {}) =>
fetchData(model.url, option).then(publicAPI.parseAsArrayBuffer);
publicAPI.parseAsArrayBuffer = (arrayBuffer) => {
Iif (!arrayBuffer) {
return false;
}
if (arrayBuffer !== model.rawDataBuffer) {
publicAPI.modified();
} else E{
return true;
}
const { text: content, binaryBuffer } = extractAppendedData(arrayBuffer);
model.rawDataBuffer = arrayBuffer;
model.binaryBuffer = binaryBuffer;
// Parse data here...
const doc = parseXML(content);
const root = doc.root();
const rootElem = root.node;
const type = rootElem.getAttribute('type');
const compressor = rootElem.getAttribute('compressor');
const byteOrder = rootElem.getAttribute('byte_order');
// default to UInt32. I think version 0.1 vtp/vti files default to UInt32.
const headerType = rootElem.getAttribute('header_type') || 'UInt32';
Iif (compressor && compressor !== 'vtkZLibDataCompressor') {
console.error('Invalid compressor', compressor);
return false;
}
Iif (byteOrder && byteOrder !== 'LittleEndian') {
console.error('Only LittleEndian encoding is supported');
return false;
}
Iif (type !== model.dataType) {
console.error('Invalid data type', type, 'expecting', model.dataType);
return false;
}
// appended format
if (findFirstTag(rootElem, 'AppendedData')) {
const appendedDataElem = findFirstTag(rootElem, 'AppendedData');
const encoding = appendedDataElem.getAttribute('encoding');
const arrays = root
.filter(
(xmlNode) => {
const { node } = xmlNode;
return (
node.nodeType === Node.ELEMENT_NODE &&
node.getAttribute('format') === 'appended' &&
node.hasAttribute('offset')
);
},
false,
true
)
.map((xmlNode) => ({
node: xmlNode.node,
offset: Number(xmlNode.node.getAttribute('offset')),
}));
// sort dataElems by increasing offset
arrays.sort((a, b) => a.offset - b.offset);
let appendedBuffer = model.binaryBuffer;
if (encoding === 'base64') {
// substr(1) is to remove the '_' prefix
appendedBuffer = appendedDataElem.textContent.trim().substr(1);
}
// get data array chunks
const dataArrays = [];
for (let i = 0; i < arrays.length; ++i) {
const offset = arrays[i].offset;
let nextOffset = 0;
if (i === arrays.length - 1) {
nextOffset = appendedBuffer.length || appendedBuffer.byteLength;
} else {
nextOffset = arrays[i + 1].offset;
}
if (encoding === 'base64') {
dataArrays.push(
new Uint8Array(
Base64.toArrayBuffer(appendedBuffer.substring(offset, nextOffset))
)
);
} else {
// encoding === 'raw'
// Need to slice the ArrayBuffer so readerHeader() works properly
dataArrays.push(
new Uint8Array(appendedBuffer.slice(offset, nextOffset))
);
}
}
if (compressor === 'vtkZLibDataCompressor') {
for (let arrayidx = 0; arrayidx < dataArrays.length; ++arrayidx) {
const dataArray = dataArrays[arrayidx];
const uncompressed = decompressZLib(dataArray, headerType);
const data = new Uint8Array(
uncompressed.length + TYPED_ARRAY_BYTES[headerType]
);
// set length header
// TODO this does not work for lengths that are greater than the max Uint32 value.
new TYPED_ARRAY[headerType](data.buffer, 0, 1)[0] =
uncompressed.length;
data.set(uncompressed, TYPED_ARRAY_BYTES[headerType]);
dataArrays[arrayidx] = data;
}
}
const bufferLength = dataArrays.reduce((acc, arr) => acc + arr.length, 0);
const buffer = new ArrayBuffer(bufferLength);
const view = new Uint8Array(buffer);
for (let i = 0, offset = 0; i < dataArrays.length; ++i) {
// set correct offsets
arrays[i].node.setAttribute('offset', offset);
// set final buffer data
view.set(dataArrays[i], offset);
offset += dataArrays[i].length;
}
model.binaryBuffer = buffer;
Iif (!model.binaryBuffer) {
console.error(
'Processing appended data format: requires binaryBuffer to parse'
);
return false;
}
}
publicAPI.parseXML(rootElem, type, compressor, byteOrder, headerType);
const datasetElem = rootElem.getElementsByTagName(type)[0];
const fieldDataElem = datasetElem.getElementsByTagName('FieldData')[0];
Iif (fieldDataElem) {
const fieldDataArrays = handleFieldDataArrays(
fieldDataElem,
compressor,
byteOrder,
headerType,
model.binaryBuffer
);
for (let i = 0; i < model.output.length; i++) {
const fieldData = model.output[i].getFieldData();
for (let j = 0; j < fieldDataArrays.length; j++) {
fieldData.addArray(fieldDataArrays[j]);
}
}
}
return true;
};
publicAPI.requestData = (inData, outData) => {
publicAPI.parseAsArrayBuffer(model.rawDataBuffer);
};
}
// ----------------------------------------------------------------------------
// Object factory
// ----------------------------------------------------------------------------
const DEFAULT_VALUES = {
// baseURL: null,
// dataAccessHelper: null,
// url: null,
};
// ----------------------------------------------------------------------------
export function extend(publicAPI, model, initialValues = {}) {
Object.assign(model, DEFAULT_VALUES, initialValues);
// Build VTK API
macro.obj(publicAPI, model);
macro.get(publicAPI, model, ['url', 'baseURL']);
macro.setGet(publicAPI, model, ['dataAccessHelper']);
macro.algo(publicAPI, model, 0, 1);
// vtkXMLReader methods
vtkXMLReader(publicAPI, model);
}
// ----------------------------------------------------------------------------
export default { extend, processDataArray, processFieldData, processCells };
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