##DESCRIPTION Shark Viewer is a web-based viewer for swc neuron files. It is written entirely in javascript using three.js. To view swc format guidelines visit: http://research.mssm.edu/cnic/swc.html

##QUICK START

1. Load javascript files onto page

<script src="js/threejs/three.js"></script>
<script src="js/threejs/TrackballControls.js"></script>
<script src="js/shark_viewer.js"></script>

2. Load a swc file into json. There is a helper function swc_parser(swc_text) available, or you can write your own to process it server side and load via AJAX.

var  swc = swc_parser(document.getElementById("swc").text);

3. Create a new shark viewer object. At a minimum you need to give it the swc json and a DOM element to attach a canvas to.

var s = new SharkViewer({ swc: swc, dom_element: 'container' });

4. Initialize the shark viewer

s.init();

5. Animate the shark viewer

s.animate();

Shark_Viewer.html shows an example of this setup.

swc json object:
               { id : {
                       type: <type number of node (string)>,
                       x: <x position of node (float)>,
                       y: <y position of node (float)>,
                       z: <z position of node (float)>,
                       parent: <id number of node's parent (-1 if no parent)>,
                       radius: <radius of node (float)>,
                       }
               }

##OPTIONS swc - swc neuron json object Default: {}

dom_element - html element that will receive webgl canvas Default: 'container'

mode - sphere (full 3-D rendering for nodes and connections, slow), particle (uses particle system to speed rendering and make it look better), or skeleton (no nodes, just connections, very fast) Default: 'particle'

HEIGHT - height of canvas Default: window.innerHeight

WIDTH - width of canvas Default: window.innerWidth

center_node - which node to center neuron on (starts at 1), -1 to center at center of bounding box Default: 1

show_stats - shows fps rendering stats if true Default: false

effect - Renders using effects to allow viewing with specialized equipment: noeffect (none), parallax (parallax barrier), rift (oculus rift) Default: 'noeffect'

show_cones - show cones between cylinders for particle and sphere mode Default: true;

colors - color array for display, nodes of type 0 show as first color, etc. Default: [ 0x00be9e, 0x3919cb, 0x7d0bc4, 0xff6700, 0x3eef00, 0xffce00, 0xf50027, 0x606060, ]