@niivue/niimath

@niivue/niimath is a JavaScript + WASM library for performing mathemetical operations on NIFTI files. This library is intended to be used in the browser, not in a Node.js environment.

All image processing operations are performed using the WASM build of niimath, making it much faster than a pure JavaScript implementation. The image processing takes place in a separate worker thread, so it won't block the main thread in your application.

Usage

The @niivue/niimath JavaScript library offers an object oriented API for working with the niimath CLI. Since niimath is a CLI tool, the API implemented in @niivue/niimath is just a wrapper around the CLI options and arguments.

Example: volumes

For example, the difference of gaussian command niimath input.nii -dog 2 3.2 output.nii can be executed using the following @niivue/niimath JavaScript code:

import { Niimath } from '@niivue/niimath';

const niimath = new Niimath();
// call the init() method to load the wasm before processing images
await niimath.init();

// 1. selectedFile is a browser File object
// 2. note the use of the final run() method to execute the command. 
// 3. note the use of await. The run method returns a promise that resolves to the output file if the command is successful.
const outFile = await niimath.image(selectedFile).dog(2, 3.2).run();

Example: meshes

The @niivue/niimath library also supports the -mesh options available in the niimath CLI. However, the JavaScript API is slightly different from the volume processing due to the use of the -mesh suboptions.

import { Niimath } from '@niivue/niimath';
const niimath = new Niimath();
await niimath.init();
const outName = 'out.mz3'; // outname must be a mesh format!
const outMesh = await niimath.image(selectedFile)
  .mesh({
    i: 'm', // 'd'ark, 'm'edium, 'b'right or numeric (e.g. 128) isosurface
    b: 1, // fill bubbles
  })
  .run(outName);
/*
Here's the help from the niimath CLI program
The mesh option has multiple sub-options:
 -mesh                    : meshify requires 'd'ark, 'm'edium, 'b'right or numeric isosurface ('niimath bet -mesh -i d mesh.gii')
        -i <isovalue>            : 'd'ark, 'm'edium, 'b'right or numeric isosurface
        -a <atlasFile>           : roi based atlas to mesh
        -b <fillBubbles>         : fill bubbles
        -l <onlyLargest>         : only largest
        -o <originalMC>          : original marching cubes
        -q <quality>             : quality
        -s <postSmooth>          : post smooth
        -r <reduceFraction>      : reduce fraction
        -v <verbose>             : verbose
*/

Installation

To install @niivue/niimath in your project, run the following command:

# TODO: publish to npm
# npm install @niivue/niimath

To install a local build of the library

Fist, cd into the js directory of the niimath repository.

# from niimath root directory
cd js

To install a local build of the library, run the following command:

npm run build

Then, install the library using the following command:

npm pack # will create a .tgz file in the root directory

Then, install the @niivue/niimath library in your application locally using the following command:

npm install /path/to/niivue-niimath.tgz

Development

First cd into the js directory of the niimath repository.

# from niimath root directory
cd js

To install the dependencies, run the following command:

npm install

To build the library, run the following command

npm run build

To run the tests, run the following command:

npm run test

Test using a simple demo

To test that the @niivue/niimath library is working correctly, you can run the following command:

npm run demo