https://github.com/garrettmflynn/hdf5-io

Simple utility for reading / writing HDF5 files
https://github.com/garrettmflynn/hdf5-io

browser hdf5 javascript

Last synced: about 2 months ago
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Simple utility for reading / writing HDF5 files

• Host: GitHub
• URL: https://github.com/garrettmflynn/hdf5-io
• Owner: garrettmflynn
• License: agpl-3.0
• Created: 2022-02-17T23:10:11.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2023-08-22T21:46:54.000Z (over 1 year ago)
• Last Synced: 2024-11-09T03:19:12.894Z (2 months ago)
• Topics: browser, hdf5, javascript
• Language: TypeScript
• Homepage: https://brainsatplay.com/hdf5-io/
• Size: 8.27 MB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# hdf5-io

Simple utility for reading / writing HDF5 files on the browser

![status](https://img.shields.io/npm/v/hdf5-io) 

![downloads](https://img.shields.io/npm/dt/hdf5-io)

![lic](https://img.shields.io/npm/l/hdf5-io)

## Description

**hdf5-io** is a simple utility for handling reading / writing HDF5IO files. As an extension to the **h5wasm** library, it immediately emits and consumes JavaScript objects containing all the relevent data.

## Getting Started

``` javascript 

// Import hdf5-io Library

import HDF5IO from "https://cdn.jsdelivr.net/npm/hdf5-io/dist/index.esm.js";

// Initialize HDF5IO instance (all optional parameters)

const io = new HDF5IO(

    {

        postprocess: (hdf5Object) => hdf5Object,

        debug: true

    },

    

)

await io.initFS('/hdf5-test') // initialize local filesystem

// load a remote file

const file = await io.fetch(

     'https://raw.githubusercontent.com/OpenSourceBrain/NWBShowcase/master/FergusonEtAl2015/FergusonEtAl2015.nwb', // URL to get file from

    'FergusonEtAl2015.nwb',  // Save the file with this name

    (ratio) => console.log('Load Status', `${(ratio * 100).toFixed(2)}%`),

    (remote) => console.log('Origin', (remote) ? path : 'Local')

)

// save the file to local storage

const filename = io.save(file)

// list files in local storage

const files = await io.list()

// get specific file from local storage

const lsFile = await io.load(filename)

```

## Conventions

### Datasets

When reading an HDF5 file, both datasets and attributes are transformed into JavaScript objects that hold their respective metadata:

```javascript

const datasetValue = 1 // From HDF5 file

const output = new Number(datasetValue)

```

If you are adding a new dataset, this **must** be an Object when written to the file:

```javascript

const object = {

    dataset: new Number(1),

    attribute: 1

}

```

## Known Issues

- Files that previous could be streamed (e.g. https://dandiarchive.s3.amazonaws.com/blobs/aff/5f6/aff5f64d-9a69-4ff3-a6fe-13a3f30dca50) no longer work

- Node.js doesn't work when bundled—unless you manually provide a `h5wasm` instance

- Streaming doesn't work in Node.js

## Acknowledgments

**hdf5-io** was originally prototyped by [Garrett Flynn](https;//github.com/garrettmflynn) as the [**WebNWB**](https;//github.com/brainsatplay/WebNWB) project at the [2022 NWB-DANDI Remote Developer Hackathon](https://neurodatawithoutborders.github.io/nwb_hackathons/HCK12_2022_Remote/).