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.

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* 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.

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

Installation

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


Usage

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

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

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js
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:

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


Development

* Clone polyseg-wasm

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


* Pull

kitware/vtk-wasm

 Docker image

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

* Run build.sh:`bash $ cd polyseg-wasm $ ./build.sh`* If you have trouble runningbuild.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.