a zero-dependency WebAssembly-powered library for reading and writing HDF5 files from javascript
(built on the HDF5 C API)
The built binaries (esm and node) will be attached to the latest release as h5wasm-{version}.tgz
The wasm-compiled libraries libhdf5.a, libhdf5_cpp.a ... and the related include/ folder are retrieved from libhdf5-wasm during the build.
Instead of importing a namespace "*", it is now possible to import the important h5wasm components in an object, from the default export:
// in hdf5_hl.ts:
export const h5wasm = {
File,
Group,
Dataset,
ready,
ACCESS_MODES
}The Emscripten filesystem is important for operations, and it can be accessed after the WASM is loaded as below.
import h5wasm from "https://cdn.jsdelivr.net/npm/[email protected]/dist/esm/hdf5_hl.js";
// the WASM loads asychronously, and you can get the module like this:
const Module = await h5wasm.ready;
// then you can get the FileSystem object from the Module:
const { FS } = Module;
// Or, you can directly get the FS if you don't care about the rest
// of the module:
// const { FS } = await h5wasm.ready;
let response = await fetch("https://ncnr.nist.gov/pub/ncnrdata/vsans/202003/24845/data/sans59510.nxs.ngv");
let ab = await response.arrayBuffer();
FS.writeFile("sans59510.nxs.ngv", new Uint8Array(ab));
// use mode "r" for reading. All modes can be found in h5wasm.ACCESS_MODES
let f = new h5wasm.File("sans59510.nxs.ngv", "r");
// File {path: "/", file_id: 72057594037927936n, filename: "data.h5", mode: "r"}Since ESM is not supported in all web worker contexts (e.g. Firefox), an additional ./dist/iife/h5wasm.js is provided in the package for h5wasm>=0.4.8; it can be loaded in a worker and used as in the example below (which uses the WORKERFS file system for random access on local files):
// worker.js
onmessage = async function(e) {
const { FS } = await h5wasm.ready;
// send in a file opened from an <input type="file" />
const f_in = e.data[0];
FS.mkdir('/work');
FS.mount(FS.filesystems.WORKERFS, { files: [f_in] }, '/work');
const f = new h5wasm.File(`/work/${f_in.name}`, 'r');
console.log(f);
}
self.importScripts('../dist/iife/h5wasm.js');npm i h5wasm or yarn add h5wasm
then in your file
// index.js
import h5wasm from "h5wasm";
const { FS } = await h5wasm.ready;
let f = new h5wasm.File("test.h5", "w");
f.create_dataset({name: "text_data", data: ["this", "that"]});
// ...note: you must configure your build system to target >= ES2020 (for bigint support)
The host filesystem is made available through Emscripten "NODERAWFS=1".
Enabling BigInt support may be required for nodejs < 16
npm i h5wasm
node --experimental-wasm-bigint
const h5wasm = await import("h5wasm/node");
await h5wasm.ready;
let f = new h5wasm.File("/home/brian/Downloads/sans59510.nxs.ngv", "r");
/*
File {
path: '/',
file_id: 72057594037927936n,
filename: '/home/brian/Downloads/sans59510.nxs.ngv',
mode: 'r'
}
*/(all examples are written in ESM - for Typescript some type casting is probably required, as get returns either Group or Dataset)
let f = new h5wasm.File("sans59510.nxs.ngv", "r");
// list keys:
f.keys()
// ["entry"]
f.get("entry/instrument").keys()
// ["attenuator","beam","beam_monitor_low","beam_monitor_norm","beam_stop_C2","beam_stop_C3","collimator","converging_pinholes","detector_B","detector_FB","detector_FL","detector_FR","detector_FT","detector_MB","detector_ML","detector_MR","detector_MT","lenses","local_contact","name","sample_aperture","sample_aperture_2","sample_table","source","source_aperture","type"]
let data = f.get("entry/instrument/detector_MR/data")
// Dataset {path: "/entry/instrument/detector_MR/data", file_id: 72057594037927936n}
data.metadata
/*
{
"signed": true,
"vlen": false,
"littleEndian": true,
"type": 0,
"size": 4,
"shape": [
48,
128
],
"total_size": 6144
}
*/
// for convenience, these are extracted from metadata:
data.dtype
// "<i"
data.shape
// (2) [48, 128]
// data are loaded into a matching TypedArray in javascript if one exists, otherwise raw bytes are returned (there is no Float16Array, for instance). In this case the matching type is Int32Array
data.value
/*
Int32Array(6144) [0, 0, 0, 2, 2, 2, 3, 1, 1, 7, 3, 5, 7, 8, 9, 21, 43, 38, 47, 8, 8, 7, 3, 6, 1, 7, 3, 7, 47, 94, 91, 99, 76, 81, 86, 112, 98, 103, 85, 100, 83, 122, 111, 123, 136, 129, 134, 164, 130, 164, 176, 191, 200, 211, 237, 260, 304, 198, 32, 9, 5, 2, 6, 5, 8, 6, 25, 219, 341, 275, 69, 11, 4, 5, 5, 45, 151, 154, 141, 146, 108, 107, 105, 113, 99, 101, 96, 84, 86, 77, 78, 107, 73, 80, 105, 65, 75, 79, 62, 31, …]
*/
// take a slice from 0:10 on axis 0, keeping all of axis 1:
// (slicing is done through libhdf5 instead of in the javascript library - should be very efficient)
data.slice([[0,10],[]])
/*
Int32Array(1280) [0, 0, 0, 2, 2, 2, 3, 1, 1, 7, 3, 5, 7, 8, 9, 21, 43, 38, 47, 8, 8, 7, 3, 6, 1, 7, 3, 7, 47, 94, 91, 99, 76, 81, 86, 112, 98, 103, 85, 100, 83, 122, 111, 123, 136, 129, 134, 164, 130, 164, 176, 191, 200, 211, 237, 260, 304, 198, 32, 9, 5, 2, 6, 5, 8, 6, 25, 219, 341, 275, 69, 11, 4, 5, 5, 45, 151, 154, 141, 146, 108, 107, 105, 113, 99, 101, 96, 84, 86, 77, 78, 107, 73, 80, 105, 65, 75, 79, 62, 31, …]
*/
// Convert to nested Array, with JSON-compatible elements:
data.to_array()
/*
[
[
0, 0, 0, 2, 2, 2, 3, 1, 1, 7, 3, 5,
7, 8, 9, 21, 43, 38, 47, 8, 8, 7, 3, 6,
1, 7, 3, 7, 47, 94, 91, 99, 76, 81, 86, 112,
98, 103, 85, 100, 83, 122, 111, 123, 136, 129, 134, 164,
130, 164, 176, 191, 200, 211, 237, 260, 304, 198, 32, 9,
5, 2, 6, 5, 8, 6, 25, 219, 341, 275, 69, 11,
4, 5, 5, 45, 151, 154, 141, 146, 108, 107, 105, 113,
99, 101, 96, 84, 86, 77, 78, 107, 73, 80, 105, 65,
75, 79, 62, 31,
... 28 more items
],
[
0, 0, 2, 2, 4, 1, 2, 7, 2, 3, 2, 5,
6, 3, 6, 24, 37, 42, 25, 8, 3, 5, 4, 8,
2, 6, 7, 9, 61, 81, 81, 89, 104, 110, 82, 82,
104, 92, 97, 99, 104, 115, 106, 128, 134, 111, 125, 123,
159, 155, 182, 228, 227, 242, 283, 290, 295, 114, 11, 6,
5, 6, 8, 4, 4, 10, 59, 401, 401, 168, 10, 6,
6, 4, 10, 37, 150, 152, 146, 121, 125, 117, 122, 88,
100, 97, 86, 79, 90, 87, 78, 87, 87, 87, 84, 76,
76, 66, 51, 11,
... 28 more items
],
... 46 more items
*/(single writer multiple readers)
const swmr_file = new h5wasm.File("swmr.h5", "Sr");
let dset = swmr_file.get("data");
dset.shape;
// 12
// ...later
dset.refresh();
dset.shape;
// 16let new_file = new h5wasm.File("myfile.h5", "w");
new_file.create_group("entry");
// shape and dtype will match input if omitted
new_file.get("entry").create_dataset({name: "auto", data: [3.1, 4.1, 0.0, -1.0]});
new_file.get("entry/auto").shape
// [4]
new_file.get("entry/auto").dtype
// "<d"
new_file.get("entry/auto").value
// Float64Array(4) [3.1, 4.1, 0, -1]
// make float array instead of double (shape will still match input if it is set to null)
new_file.get("entry").create_dataset({name: "data", data: [3.1, 4.1, 0.0, -1.0], shape: null, dtype: '<f'});
new_file.get("entry/data").shape
// [4]
new_file.get("entry/data").value
//Float32Array(4) [3.0999999046325684, 4.099999904632568, 0, -1]
// create a dataset with shape=[2,2]
// The dataset stored in the HDF5 file with the correct shape,
// but no attempt is made to make a 2x2 array out of it in javascript
new_file.get("entry").create_dataset({name: "square_data", data: [3.1, 4.1, 0.0, -1.0], shape: [2,2], dtype: '<d'});
new_file.get("entry/square_data").shape
// (2) [2, 2]
new_file.get("entry/square_data").value
//Float64Array(4) [3.1, 4.1, 0, -1]
// create a dataset with compression
const long_data = [...new Array(1000000)].map((_, i) => i);
new_file.get("entry").create_dataset({name: "compressed", data: long_data, shape: [1000, 1000], dtype: '<f', chunks: [100,100], compression: 9});
// equivalent to:
// new_file.get("entry").create_dataset({name: "compressed", data: long_data, shape: [1000, 1000], dtype: '<f', chunks=[100,100], compression='gzip', compression_opts=[9]});
new_file.get("entry/compressed").filters
// [{id: 1, name: 'deflate'}]);
new_file.get("entry/compressed").slice([[2,3]]);
// Float32Array(1000) [ 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, … ]
// create an attribute (creates a VLEN string by default for a string)
new_file.get("entry").create_attribute("myattr", "a string");
Object.keys(new_file.get("entry").attrs)
// ["myattr"]
new_file.get("entry").attrs["myattr"]
// {value: "a string", shape: Array(0), dtype: "S"}
new_file.get("entry").create_attribute("fixed", ["hello", "you"], null, "S5")
new_file.get("entry").attrs["fixed"]
/*
{
"value": [
"hello",
"you"
],
"shape": [
2
],
"dtype": "S5"
}
*/
// close the file - reading and writing will no longer work.
// calls H5Fclose on the file_id.
new_file.close()let new_file = new h5wasm.File("myfile.h5", "w");
new_file.create_group("entry");
new_file.get("entry").create_dataset({name: "auto", data: [3.1, 4.1, 0.0, -1.0]});
// create a soft link in root:
new_file.create_soft_link("/entry/auto", "my_soft_link");
new_file.get("my_soft_link").value;
// Float64Array(4) [3.1, 4.1, 0, -1]
// create a hard link:
new_file.create_hard_link("/entry/auto", "my_hard_link");
new_file.get("my_hard_link").value;
// Float64Array(4) [3.1, 4.1, 0, -1]
// create an external link:
new_file.create_external_link("other_file.h5", "other_dataset", "my_external_link");
new_file.get_external_link("my_external_link");
// {filename: "other_file.h5", obj_path: "other_dataset"}
// create a soft link in a group:
new_file.create_group("links");
const links_group = new_file.get("links");
links_group.create_soft_link("/entry/auto", "soft_link");
new_file.get("/links/soft_link").value;
// Float64Array(4) [3.1, 4.1, 0, -1]
new_file.get_link("/links/soft_link");
// "/entry/auto"
new_file.get_link("/entry/auto");
// null // (null is returned if the path is not a symbolic link);
new_file.close()One can also open an existing file and write to it:
let f = new h5wasm.File("myfile.h5", "a");
f.create_attribute("new_attr", "something wicked this way comes");
f.close()Optional, to support uploads and downloads
import {uploader, download, UPLOADED_FILES} from "https://cdn.jsdelivr.net/npm/h5wasm@latest/dist/esm/file_handlers.js";
//
// Attach to a file input element:
// will save to Module.FS (memfs) with the name of the uploaded file
document.getElementById("upload_selector").onchange = uploader;
// file can be found with
let f = new h5wasm.File(UPLOADED_FILES[UPLOADED_FILES.length -1], "r");
let new_file = new h5wasm.File("myfile.h5", "w");
new_file.create_group("entry");
// shape and dtype will match input if omitted
new_file.get("entry").create_dataset({name: "auto", data: [3.1, 4.1, 0.0, -1.0]});
// this will download a snapshot of the HDF5 in its current state, with the same name
// (in this case, a file named "myfile.h5" would be downloaded)
download(new_file);To persist the emscripten virtual filesystem between sessions, use IDBFS (syncs with browser IndexedDB), e.g.
// create a local mount of the IndexedDB filesystem:
FS.mount(FS.filesystems.IDBFS, {}, "/home/web_user")
// to read from the browser IndexedDB into the active filesystem:
FS.syncfs(true, (e) => {console.log(e)});
// to push all current files in /home/web_user to IndexedDB, e.g. when closing your application:
FS.syncfs(false, (e) => {console.log(e)})
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