ICR PolySeg-WASM: a WASM module that implements PolySeg for the Web

Introduction

The ICR PolySeg-WASM is an extended WASM wrapper for the PerkLab/PolySeg library, including C++ code repurposed from Slicer and SlicerRT.

Supported conversions

• Planar contour to closed surface → convertContourRoiToSurface.
• Planar contour to labelmap → convertContourRoiToLabelmap.
• Surface to labelmap → convertSurfaceToLabelmap.
• Labelmap to closed surface (using flying edges) → convertLabelmapToSurface.
• Contour to Ribbon → convertContourRoiToRibbon.
• Ribbon to Labelmap → convertRibbonToLabelmap.

Issues and feature requests

This project is under active development. Please report issues here.

Installation

$ npm install @icr/polyseg-wasm
or
$ yarn add @icr/polyseg-wasm

Usage

• Use the provided index.js script to load the wasm module

    import ICRPolySeg from '@icr/polyseg-wasm';
    const icrPolySeg = await ICRPolySeg();
    // Initialize the module and optionally pass a callback for progress updates
    await icrPolySeg.initialize(/*{ updateProgress: updateProgressThrottled }*/);
    // Use the initialized 'instance' to invoke a conversion method
    const instance = icrPolySeg.instance;

• Or, manually import the launcher and wasm to load the module

    import launcher from '@icr/polyseg-wasm/js';
    import wasm from '@icr/polyseg-wasm/wasm';
    // Initialize the module according to your project configuration
    ...

Usage example for planar contour to closed surface conversion

import ICRPolySeg from '@icr/polyseg-wasm';

// Initialize the module and optionally pass a callback for progress updates
const icrPolySeg = await ICRPolySeg();
await icrPolySeg.initialize(/*{ updateProgress: updateProgressThrottled }*/);

// Assuming that an ROI consists of C contours with each contour having an array of points (xyz coordinate tuples)
// Extract and join the ponints from all contours
let flatPointsArray = [];
let numPointsArray = [];
for (let c = 0; c < roi.contours.length; c++) {
    const points = roi.contours[c].points;
    numPointsArray.push(points.length);
    for (let p = 0; p < points.length; p++) {
        const point = points[p];
        flatPointsArray.push(point.x, point.y, point.z);
    }
}
// Use Float32 typed array
flatPointsArray = new Float32Array(flatPointsArray)
numPointsArray = new Float32Array(numPointsArray)

// Run the conversion using the initialized 'instance'
const result = icrPolySeg.instance.convertContourRoiToSurface(flatPointsArray, numPointsArray);

// Create a VTK mesh from the result
const polydata = vtkPolyData.newInstance();
polydata.getPoints().setData(result.points, 3);
polydata.getPolys().setData(result.polys);

Examples

To run and view the examples:

$ $ git clone https://bitbucket.org/icrimaginginformatics/polyseg-wasm.git
$ cd polyseg-wasm/examples
$ yarn install
$ yarn run start

Development

• Clone polyseg-wasm

    $ git clone https://bitbucket.org/icrimaginginformatics/polyseg-wasm.git

• Pull kitware/vtk-wasm Docker image

    $ docker pull kitware/vtk-wasm:v9.2.6-2743-gdcc0ce36db-20230312

• Run build.sh:

    $ cd polyseg-wasm
    $ ./build.sh

• If you have trouble running build.sh, please execute this command chmod +x build.sh and chmod +x build_wasm.sh to allow the shell scripts to excute in your machine.

v0.4.0

• Added three additional converters: surface to labelmap, contour to ribbon, and ribbon to labelmap.
• Refactored examples with code reusability.

v0.3.0

• Improved development by using the VTK-WebAssembly Docker image which provides the pre-built VTK static libraries and the emscripten tool chain, replacing dockcross/web-wasm.
• Added bash scripts to automate the build process.
• Prepared the package for publishing.

v0.2.0

• Added two more converters: planar contour to labelmap and labelmap to closed surface.

v0.1.1

• Fixed the progress update callback.

v0.1.0

• Implemented WASM wrapper for the planar contour to closed surface converter.