annoa-hdf5

HDF5 is a node module for reading and writing the HDF5 file format.

Documentation

API documentation is available at http://hdf-ni.github.io/hdf5.node

npm install hdf5

See http://hdf-ni.github.io/hdf5.node/doc/install-setup.html for the native requirements and details. If your native hdf5 libraries aren't at the default you can set the path with --hdf5_home_linux switch on this project as well as dependent projects.

npm install hdf5 --hdf5_home_linux=<your native hdf path>

For mac and windows the switches are --hdf5_home_mac & --hdf5_home_win

To install with yarn first need to configure so it knows where the libraries are:

yarn config set hdf5_home_linux $HDF5_HOME
yarn install

Note: If node-gyp isn't installed

npm install -g node-gyp

Quick start to open and read from an h5 file

var hdf5 = require('hdf5').hdf5;

var Access = require('hdf5/lib/globals').Access;
var file = new hdf5.File('/tmp/foo.h5', Access.ACC_RDONLY);
var group = file.openGroup('bar');

Notes on Recent Releases

• Note: Release v0.3.5

  • Strictly for upgrading the build on Windows. Tested with VS 2017

• Note: Release v0.3.4

  • Reference attributes on datasets and groups are now available properties.
  • Reserved propeties such as type, rank, rows etc. are now settable in options for dataset functions.
  • Typescript definition files now available.
  • For static native linkng, link_type command line switch is provided in binding.gyp(darwin,win untested).
  • Added custom 64 bit signed (Int64) and unsigned (Uint64) integer attributes read/write since they aren't yet supported by javascript.
  • Added a file method enableSingleWriteMultiRead (if native version older than 1.10.x it is a noop).
  • Synchronous iterate and visit is now available on file and group children.
  • Bug fixes on dimensioning have been made

• Note: asynchronous i/o is coming but not in this release

• Note: Release v0.3.3 Minor fix on fixed length of strings in array. Handles the situation where the strings are contiguous without all having null bytes.

• Note: Release v0.3.2 tested with nodejs v6.11.2, v7.5.0 and v8.4.0. Code was changed to allow v8.4.0 to work while still working with the earlier versions. It may work back as far as v4.2.1 let me know if you have a version in between that needs testing. Variable length array of strings can be be read as regions.

• Note: Release v0.3.1 is based on new V8 API changes coming with nodejs v7.

• Note: Release v0.1.0 was built with nodejs v4.2.1. If you want nodejs v0.12.x then stay with release v0.0.20. npm will continue with nodejs v4.x.x line and any fixes or features needed by prior versions will be from github branches.

• Note: Release v0.0.20 is for prebuilts with hdf5-1.8.15-patch1. If you want hdf5-1.8.14 stay with v0.0.19.

Philosophy

This module, hdf5.node, is intended to be a pure API for reading and writing HDF5 files. Graphical user interfaces or other layers should be implemented in separate modules.

Unlike other languages that wrap hdf5 API's this interface takes advantage of the compatibility of V8 and HDF5. The result is a direct map to javascript behavior with the least amount of data copying and coding tasks for the user. Hopefully you won't need to write yet another layer in your code to accomplish your goals.

Other Feature Notes

The node::Buffer and streams are being investigated so native hdf5 data's only destination is client browser window or client in general.

Dimension Scales

Mostly implemented (missing H5DSiterate_scales[ found a way to make callback functions from te native side and looking to finish this and use the technique for other h5 iterators])

High-level Functions for Region References, Hyperslabs, and Bit-fields

Writing an interface based on the standard hdf5 library. Currently you can write and read a subset from a two rank dataset. Other ranks may work yet are untested. See tutorial http://hdf-ni.github.io/hdf5.node/tut/subset_tutorial.html for example applied to node Buffers.

Filters and Compression

Testing filters and compression. Have the gzip filter working. For some applications getting the uncompressed data from the h5 would reduce the number of compressions and decompressions. For example an image could be sent to client before unzipping and rezipping on the server side.

Third party filters can be used. Those do take separate compiled libraries yet are independent. They get picked up by native hdf5 from the HDF5_PLUGIN_PATH.

Image

The h5im namespace is being designed to meet the Image Spec 1.2 http://www.hdfgroup.org/HDF5/doc/ADGuide/ImageSpec.html. Hyperslabs/regions of images can now be read.

Contributors

• Christian Nienhaus (@NINI1988) added typescript definitions and many pull requests and bug fixes for hdf5 native calls.
• John Shumway (@shumway) refurbished the documentation when the project was split into an organization.

Contact

My twitch stream is https://www.twitch.tv/sylvanmats