Arbitrary slicing (aka. obliques) of large multiresolution voxel dataset, using shaders on GPU, webGL and octree data structure. Also able to load meshes. Work in progress.
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readme.md

Shader Navigator

[DEMO] using the BigBrain data.

A work in progress to perform arbitrary slicing (aka. obliques) of large voxel dataset, using shaders on GPU, webGL, an octree data structure and few other things.

capture

Dependencies

We use Rollup to generate a singe file project compatible with ES6 spec. Install it globally with:

npm install -g rollup

At some point, we were using using Gulp to auto generate the project at every update, but it does not play well with the Rollup plugin that transform shader files into JS string.

We use DocumentationJS (as a devDependencies) to generate the documentation.

Building

Build project:

$ npm run build

The single file output is build/shadernavigator/shadernavigator.js

Build a minified project:

$ npm run build-min

The single file output is build/shadernavigator/shadernavigator.min.js


NOTE: ShaderNavigator was developed using ES6 standards meaning the regular/not-minified version uses ES6 classes, among other ES6 features. The minified version is automatically generate in ES5 and uses object prototypes.
While it's easier to maintain the codebase in ES6, the minified version is certainly compatible with more older browsers.


Build the documentation:

npm rund doc

The documentation is a web project (with an index.html) located in the folder doc.

Configure

ShaderNavigator needs to be fed with a multiresolution octree architecture of 3D tile data. This config occurs in the file ShaderNavigator/index.html:

// create a QuadScene instance
var quadScene = new SHAD.QuadScene("container", 0);

// loads the octree of 3D texture using the tileset config file
quadScene.loadData({
    datatype: "precomputed_octree_tiles",
    url: "../data_raster/info2.json"
});

Using the very same pattern, you can load other kind of data, like...

A collection of meshes

// Loads the mesh collection using a mesh config file
quadScene.loadData({
    datatype: "mesh_collection",
    url: "../data_mesh/meshes/bigbrain_gray.json"
});

A collection of colormaps

// loads the colormaps using a colormap config file
quadScene.loadData({
    datatype: "colormap_collection",
    url: "colormaps/colormaps.json"
});

Note: the config file URL used above are local but could absolutely be remote, as long as the server allows CORS.

Auto positioning with URL args

[Optional] As you can see in ShaderNavigator/index.html, an instance of SHAD.HashIO() is used to parse the URL and position and rotate automatically the orthogonal planes.

Let's see how it works:

http://localhost:5000/ShaderNavigator/index.html#4/1.0177538710434886,1.0044899689452085,0.9562499976158154/-0.23786303165127878,0.2604096266561844,-1.0412456579550184e-16

The part to consider is after the hash (#):

4/1.0177538710434886,1.0044899689452085,0.9562499976158154/-0.23786303165127878,0.2604096266561844,-1.0412456579550184e-16

The pattern is the following:
zoomLevel / xPosition / yPosition / zPosition / xEuler / yEuler / zEuler

  • zoomLevel, integer values in [0, 6] with:
    • 0 --> 1280um
    • 1 --> 640um
    • 2 --> 320um
    • 3 --> 160um
    • 4 --> 80um
    • 5 --> 40um
    • 6 --> 20um
  • xPosition, yPosition and zPosition, in [0, 2]. this is the equivalent of [0, 8192] pixel at 20um.
  • xEuler, yEuler and zEuler, the Euler angle in radians, in [-π, +π].

Why using it? Setting URL arguments is not mandatory (and can actually be quite cumbersome), meaning you can use a URL with no args, like http://localhost:5000/ShaderNavigator/index.html and the otho planes will be automatically positioned in the middle of the dataset.

Still, the URL args will be updated as long as you move and rotate within the dataset, making it easy to refresh the browser page and go back to the same position, or to share a URL so that a collaborator can go to the same position.

Run

Run a web server in the root directory and open ShaderNavigator/index.html.

Config file

axisInfo

This group is mandatory and give some important information about the three axis. By default, we consider the original dataset has been enlarged or padded to fit a power of 2 size (required for zooming). The information about the original size, the enlarged size and the offset are essential to build a bridge between multiple visualization platforms, for example from ShaderNavigator to Atelier3D (where data are not enlarged).
The three axis x, y and z from the internal 3D space do not necessary respect the x, y and z for the original data and they may even not be called so in the original dataset. Still, having named axes usually matters to the user.

"axisInfo": {
  "x": { // "x" from the webGL environment
    "name": "sagittal", // name of this axis in the original dataset
    "originalSize": 6572, // size of the original dataset along this axis, before being extended to a power of 2 size
    "offset": 810, // offset applied at the beginning of the axis, if extended (can be 0)
    "finalSize": 8192, // power of 2 size (can be the same as originalSize if already pow of 2)
    "minName": "left", // name of the min bound of the axis
    "maxName": "right", // name of the max bound of the axis
    "reversed": true  // should we count from 0->8191 (false) or from 8191->0 (true)
  },
  "y": {
    "name": "coronal",
    "originalSize": 7404,
    "offset": 0,
    "finalSize": 8192,
    "minName": "posterior",
    "maxName": "anterior",
    "reversed": false
  },
  "z": {
    "name": "axial",
    "originalSize": 5711,
    "offset": 1240,
    "finalSize": 8192,
    "minName": "inferior",
    "maxName": "superior",
    "reversed": true
  }
},