Merge pull request #10 from rhyolight/cleanup

Cleaning up and doccing

bin/highbrow.bundle.js

@@ -353,7 +353,7 @@ class Layer extends Renderable {
     }
 
     getNeuronByIndex(index) {
-        return this.getNeurons().find(n => n.index == index);
+        return this.getNeurons()[index];
     }
 
     getNeuronByXyz(x, y, z) {
@@ -386,7 +386,6 @@ class Layer extends Renderable {
     _buildLayer() {
         this._neurons = [];
         times(this._config.neuronCount)(i => this._neurons.push(new Neuron({
-            index: i,
             state: NeuronState.inactive,
             origin: getXyzFromIndex(i, this._config.dimensions.x, this._config.dimensions.y, this._config.dimensions.z)
         }, this)));

examples/htm-highbrow-layer.js

@@ -0,0 +1,47 @@
+/**
+ * This interface is used to update cell data within the SpToInputVisualization.
+ * Once created, use it to update cell values.
+ * @param {Layer} layer - from Highbrow.
+ */
+function HtmHighbrowLayer(layer) {
+    this.layer = layer
+    this.dimensions = layer.getDimensions()
+}
+
+HtmHighbrowLayer.prototype.getX = function() {
+    return this.dimensions.x
+};
+
+HtmHighbrowLayer.prototype.getY = function() {
+    return this.dimensions.y
+};
+
+HtmHighbrowLayer.prototype.getZ = function() {
+    return this.dimensions.z
+};
+
+/**
+ * Gets the value of the cell given the coordinates.
+ * @param x (int) x coordinate
+ * @param y (int) y coordinate
+ * @param z (int) z coordinate
+ * @returns {*} whatever value was in the cell
+ */
+HtmHighbrowLayer.prototype.getCellValue = function(x, y, z) {
+    let neuronState = this.layer.getNeuronByXyz(x, y, z).state
+    let out = { state: neuronState }
+    if (neuronState == "inactive") {
+        out.color = new THREE.Color('#FFFEEE')
+    } else {
+        out.color = new THREE.Color('orange')
+    }
+    return out;
+};
+
+/**
+ * Send in one object to update the whole layer state. If the data doesn't match
+ * the structure of the layer, bad things will probably happen.
+ */
+HtmHighbrowLayer.prototype.update = function(data) {
+    this.network.update(data)
+};

examples/webgl.html

@@ -19,7 +19,7 @@
 
             $(function() {
                 const dimensions = {
-                    x: 10, y: 10, z: 1
+                    x: 100, y: 100, z: 1
                 }
                 const simple = {
                     name: "simple network",
@@ -42,7 +42,7 @@
                 animateCells(layer);
 
                 // Renders the canvas with empty cells into the DOM and canvas.
-                cellviz.render({initialDistance: 100});
+                cellviz.render();
 
                 setInterval(function() {
                     animateCells(layer);
@@ -51,7 +51,7 @@
 
                 function animateCells(layer) {
                     for (let neuron of layer.getNeurons()) {
-                        if (Math.random() >= 0.5) {
+                        if (Math.random() >= 0.98) {
                             neuron.activate()
                         } else {
                             neuron.deactivate()

src/layer.js

@@ -65,20 +65,40 @@ class Layer extends Renderable {
     }
 
     /**
+     * Will return a list of {@link Neuron}s in global cell order.
      * @override
+     * @returns {Neuron[]} all the neurons in global cell order
      */
     getChildren() {
         return this.getNeurons()
     }
 
+    /**
+     * Will return a list of {@link Neuron}s in global cell order.
+     * @override
+     * @returns {Neuron[]} all the neurons in global cell order
+     */
     getNeurons() {
         return this._neurons
     }
 
+    /**
+     * Get {@link Neuron} by global cell index.
+     * @param {int} index - index of neuron to get
+     * @returns {Neuron} the neuron at specified index
+     * @throws {KeyError} if invalid index
+     */
     getNeuronByIndex(index) {
-        return this.getNeurons().find(n => n.index == index)
+        return this.getNeurons()[index]
     }
 
+    /**
+     * Get {@link Neuron} by 3D coordinate.
+     * @param {number} x - x
+     * @param {number} y - y
+     * @param {number} z - z
+     * @returns {Neuron} the neuron at specified index
+     */
     getNeuronByXyz(x, y, z) {
         var dims = this.getDimensions()
         let globalIndex = z * dims.x * dims.y
@@ -108,13 +128,12 @@ class Layer extends Renderable {
     }
 
     /*
-     * Builds out the layer from scratch, using an Z,X,Y structure
+     * Builds out the layer from scratch.
      */
     _buildLayer() {
         this._neurons = []
         times(this._config.neuronCount) (i =>
             this._neurons.push(new Neuron({
-                index: i,
                 state: NeuronState.inactive,
                 origin: getXyzFromIndex(
                     i,