Second wave of file commits.

Author: PatMartin

data/gcHeatmap.R

@@ -0,0 +1,13 @@
+library("psych")
+library("akima")
+# Read the data into a dataframe called gc.
+gc <- read.table("gc.csv", header = T, sep=",")
+
+# Output columns
+names(gc)
+
+im <- with(gc, interp(Timestamp,EU,OU))
+with(im,image(x,y,z))
+
+# Descriptive statistics for the variables in the dataframe called ratings
+describe(gc)

data/iris.csv

@@ -0,0 +1,151 @@
+Sepal Length,Sepal Width,Petal Length,Petal Width,Species
+5.1,3.5,1.4,0.2,setosa
+4.9,3.0,1.4,0.2,setosa
+4.7,3.2,1.3,0.2,setosa
+4.6,3.1,1.5,0.2,setosa
+5.0,3.6,1.4,0.2,setosa
+5.4,3.9,1.7,0.4,setosa
+4.6,3.4,1.4,0.3,setosa
+5.0,3.4,1.5,0.2,setosa
+4.4,2.9,1.4,0.2,setosa
+4.9,3.1,1.5,0.1,setosa
+5.4,3.7,1.5,0.2,setosa
+4.8,3.4,1.6,0.2,setosa
+4.8,3.0,1.4,0.1,setosa
+4.3,3.0,1.1,0.1,setosa
+5.8,4.0,1.2,0.2,setosa
+5.7,4.4,1.5,0.4,setosa
+5.4,3.9,1.3,0.4,setosa
+5.1,3.5,1.4,0.3,setosa
+5.7,3.8,1.7,0.3,setosa
+5.1,3.8,1.5,0.3,setosa
+5.4,3.4,1.7,0.2,setosa
+5.1,3.7,1.5,0.4,setosa
+4.6,3.6,1.0,0.2,setosa
+5.1,3.3,1.7,0.5,setosa
+4.8,3.4,1.9,0.2,setosa
+5.0,3.0,1.6,0.2,setosa
+5.0,3.4,1.6,0.4,setosa
+5.2,3.5,1.5,0.2,setosa
+5.2,3.4,1.4,0.2,setosa
+4.7,3.2,1.6,0.2,setosa
+4.8,3.1,1.6,0.2,setosa
+5.4,3.4,1.5,0.4,setosa
+5.2,4.1,1.5,0.1,setosa
+5.5,4.2,1.4,0.2,setosa
+4.9,3.1,1.5,0.1,setosa
+5.0,3.2,1.2,0.2,setosa
+5.5,3.5,1.3,0.2,setosa
+4.9,3.1,1.5,0.1,setosa
+4.4,3.0,1.3,0.2,setosa
+5.1,3.4,1.5,0.2,setosa
+5.0,3.5,1.3,0.3,setosa
+4.5,2.3,1.3,0.3,setosa
+4.4,3.2,1.3,0.2,setosa
+5.0,3.5,1.6,0.6,setosa
+5.1,3.8,1.9,0.4,setosa
+4.8,3.0,1.4,0.3,setosa
+5.1,3.8,1.6,0.2,setosa
+4.6,3.2,1.4,0.2,setosa
+5.3,3.7,1.5,0.2,setosa
+5.0,3.3,1.4,0.2,setosa
+7.0,3.2,4.7,1.4,versicolor
+6.4,3.2,4.5,1.5,versicolor
+6.9,3.1,4.9,1.5,versicolor
+5.5,2.3,4.0,1.3,versicolor
+6.5,2.8,4.6,1.5,versicolor
+5.7,2.8,4.5,1.3,versicolor
+6.3,3.3,4.7,1.6,versicolor
+4.9,2.4,3.3,1.0,versicolor
+6.6,2.9,4.6,1.3,versicolor
+5.2,2.7,3.9,1.4,versicolor
+5.0,2.0,3.5,1.0,versicolor
+5.9,3.0,4.2,1.5,versicolor
+6.0,2.2,4.0,1.0,versicolor
+6.1,2.9,4.7,1.4,versicolor
+5.6,2.9,3.6,1.3,versicolor
+6.7,3.1,4.4,1.4,versicolor
+5.6,3.0,4.5,1.5,versicolor
+5.8,2.7,4.1,1.0,versicolor
+6.2,2.2,4.5,1.5,versicolor
+5.6,2.5,3.9,1.1,versicolor
+5.9,3.2,4.8,1.8,versicolor
+6.1,2.8,4.0,1.3,versicolor
+6.3,2.5,4.9,1.5,versicolor
+6.1,2.8,4.7,1.2,versicolor
+6.4,2.9,4.3,1.3,versicolor
+6.6,3.0,4.4,1.4,versicolor
+6.8,2.8,4.8,1.4,versicolor
+6.7,3.0,5.0,1.7,versicolor
+6.0,2.9,4.5,1.5,versicolor
+5.7,2.6,3.5,1.0,versicolor
+5.5,2.4,3.8,1.1,versicolor
+5.5,2.4,3.7,1.0,versicolor
+5.8,2.7,3.9,1.2,versicolor
+6.0,2.7,5.1,1.6,versicolor
+5.4,3.0,4.5,1.5,versicolor
+6.0,3.4,4.5,1.6,versicolor
+6.7,3.1,4.7,1.5,versicolor
+6.3,2.3,4.4,1.3,versicolor
+5.6,3.0,4.1,1.3,versicolor
+5.5,2.5,4.0,1.3,versicolor
+5.5,2.6,4.4,1.2,versicolor
+6.1,3.0,4.6,1.4,versicolor
+5.8,2.6,4.0,1.2,versicolor
+5.0,2.3,3.3,1.0,versicolor
+5.6,2.7,4.2,1.3,versicolor
+5.7,3.0,4.2,1.2,versicolor
+5.7,2.9,4.2,1.3,versicolor
+6.2,2.9,4.3,1.3,versicolor
+5.1,2.5,3.0,1.1,versicolor
+5.7,2.8,4.1,1.3,versicolor
+6.3,3.3,6.0,2.5,virginica
+5.8,2.7,5.1,1.9,virginica
+7.1,3.0,5.9,2.1,virginica
+6.3,2.9,5.6,1.8,virginica
+6.5,3.0,5.8,2.2,virginica
+7.6,3.0,6.6,2.1,virginica
+4.9,2.5,4.5,1.7,virginica
+7.3,2.9,6.3,1.8,virginica
+6.7,2.5,5.8,1.8,virginica
+7.2,3.6,6.1,2.5,virginica
+6.5,3.2,5.1,2.0,virginica
+6.4,2.7,5.3,1.9,virginica
+6.8,3.0,5.5,2.1,virginica
+5.7,2.5,5.0,2.0,virginica
+5.8,2.8,5.1,2.4,virginica
+6.4,3.2,5.3,2.3,virginica
+6.5,3.0,5.5,1.8,virginica
+7.7,3.8,6.7,2.2,virginica
+7.7,2.6,6.9,2.3,virginica
+6.0,2.2,5.0,1.5,virginica
+6.9,3.2,5.7,2.3,virginica
+5.6,2.8,4.9,2.0,virginica
+7.7,2.8,6.7,2.0,virginica
+6.3,2.7,4.9,1.8,virginica
+6.7,3.3,5.7,2.1,virginica
+7.2,3.2,6.0,1.8,virginica
+6.2,2.8,4.8,1.8,virginica
+6.1,3.0,4.9,1.8,virginica
+6.4,2.8,5.6,2.1,virginica
+7.2,3.0,5.8,1.6,virginica
+7.4,2.8,6.1,1.9,virginica
+7.9,3.8,6.4,2.0,virginica
+6.4,2.8,5.6,2.2,virginica
+6.3,2.8,5.1,1.5,virginica
+6.1,2.6,5.6,1.4,virginica
+7.7,3.0,6.1,2.3,virginica
+6.3,3.4,5.6,2.4,virginica
+6.4,3.1,5.5,1.8,virginica
+6.0,3.0,4.8,1.8,virginica
+6.9,3.1,5.4,2.1,virginica
+6.7,3.1,5.6,2.4,virginica
+6.9,3.1,5.1,2.3,virginica
+5.8,2.7,5.1,1.9,virginica
+6.8,3.2,5.9,2.3,virginica
+6.7,3.3,5.7,2.5,virginica
+6.7,3.0,5.2,2.3,virginica
+6.3,2.5,5.0,1.9,virginica
+6.5,3.0,5.2,2.0,virginica
+6.2,3.4,5.4,2.3,virginica
+5.9,3.0,5.1,1.8,virginica

scripts/processing/NetworkFlow.pde

@@ -0,0 +1,224 @@
+// An animated drawing of a Neural Network
+// Daniel Shiffman <http://www.shiffman.net>
+// Nature of Code
+
+Network network;
+
+void setup() {
+  size(800, 200); 
+  smooth();
+  
+  // Create the Network object
+  network = new Network(width/2, height/2);
+
+  // Create a bunch of Neurons
+  Neuron a = new Neuron(-350, 0);
+  Neuron b = new Neuron(-200, 0);
+  Neuron c = new Neuron(0, 75);
+  Neuron d = new Neuron(0, -75);
+  Neuron e = new Neuron(200, 0);
+  Neuron f = new Neuron(350, 0);
+
+  // Connect them
+  network.connect(a, b,1);
+  network.connect(b, c,random(1));
+  network.connect(b, d,random(1));
+  network.connect(c, e,random(1));
+  network.connect(d, e,random(1));
+  network.connect(e, f,1);
+
+  // Add them to the Network
+  network.addNeuron(a);
+  network.addNeuron(b);
+  network.addNeuron(c);
+  network.addNeuron(d);
+  network.addNeuron(e);
+  network.addNeuron(f);
+}
+
+void draw() {
+  background(255);
+  // Update and display the Network
+  network.update();
+  network.display();
+  
+  // Every 30 frames feed in an input
+  if (frameCount % 30 == 0) {
+    network.feedforward(random(1));
+  }
+}
+
+class Network {
+  
+  // The Network has a list of neurons
+  ArrayList<Neuron> neurons;
+  
+  // The Network now keeps a duplicate list of all Connection objects.
+  // This makes it easier to draw everything in this class
+  ArrayList<Connection> connections;
+  PVector location;
+
+  Network(float x, float y) {
+    location = new PVector(x, y);
+    neurons = new ArrayList<Neuron>();
+    connections = new ArrayList<Connection>();
+  }
+
+  // We can add a Neuron
+  void addNeuron(Neuron n) {
+    neurons.add(n);
+  }
+
+  // We can connection two Neurons
+  void connect(Neuron a, Neuron b, float weight) {
+    Connection c = new Connection(a, b, weight);
+    a.addConnection(c);
+    // Also add the Connection here
+    connections.add(c);
+  } 
+  
+  // Sending an input to the first Neuron
+  // We should do something better to track multiple inputs
+  void feedforward(float input) {
+    Neuron start = neurons.get(0);
+    start.feedforward(input);
+  }
+  
+  // Update the animation
+  void update() {
+    for (Connection c : connections) {
+      c.update();
+    }
+  }
+  
+  // Draw everything
+  void display() {
+    pushMatrix();
+    translate(location.x, location.y);
+    for (Neuron n : neurons) {
+      n.display();
+    }
+
+    for (Connection c : connections) {
+      c.display();
+    }
+    popMatrix();
+  }
+}
+
+class Connection {
+  // Connection is from Neuron A to B
+  Neuron a;
+  Neuron b;
+  
+  // Connection has a weight
+  float weight;
+
+  // Variables to track the animation
+  boolean sending = false;
+  PVector sender;
+  
+  // Need to store the output for when its time to pass along
+  float output = 0;
+
+  Connection(Neuron from, Neuron to, float w) {
+    weight = w;
+    a = from;
+    b = to;
+  }
+  
+  
+  // The Connection is active
+  void feedforward(float val) {
+    output = val*weight;        // Compute output
+    sender = a.location.get();  // Start animation at Neuron A
+    sending = true;             // Turn on sending
+  }
+  
+  // Update traveling sender
+  void update() {
+    if (sending) {
+      // Use a simple interpolation
+      sender.x = lerp(sender.x, b.location.x, 0.1);
+      sender.y = lerp(sender.y, b.location.y, 0.1);
+      float d = PVector.dist(sender, b.location);
+      // If we've reached the end
+      if (d < 1) {
+        // Pass along the output!
+        b.feedforward(output);
+        sending = false;
+      }
+    }
+  }
+  
+  // Draw line and traveling circle
+  void display() {
+    stroke(0);
+    strokeWeight(1+weight*4);
+    line(a.location.x, a.location.y, b.location.x, b.location.y);
+
+    if (sending) {
+      fill(0);
+      strokeWeight(1);
+      ellipse(sender.x, sender.y, 16, 16);
+    }
+  }
+}
+
+class Neuron {
+  // Neuron has a location
+  PVector location;
+
+  // Neuron has a list of connections
+  ArrayList<Connection> connections;
+  
+  // We now track the inputs and sum them
+  float sum = 0;
+  
+  // The Neuron's size can be animated
+  float r = 32;
+  
+  Neuron(float x, float y) {
+    location = new PVector(x, y);
+    connections = new ArrayList<Connection>();
+  }
+
+  // Add a Connection
+  void addConnection(Connection c) {
+    connections.add(c);
+  } 
+  
+  // Receive an input
+  void feedforward(float input) {
+    // Accumulate it
+    sum += input;
+    // Activate it?
+    if (sum > 1) {
+      fire();
+      sum = 0;  // Reset the sum to 0 if it fires
+    } 
+  }
+  
+  // The Neuron fires
+  void fire() {
+    r = 64;   // It suddenly is bigger
+    
+    // We send the output through all connections
+    for (Connection c : connections) {
+       c.feedforward(sum);
+    } 
+  }
+  
+  // Draw it as a circle
+  void display() {
+    stroke(0);
+    strokeWeight(1);
+    // Brightness is mapped to sum
+    float b = map(sum,0,1,255,0);
+    fill(b);
+    ellipse(location.x, location.y, r, r);
+    
+    // Size shrinks down back to original dimensions
+    r = lerp(r,32,0.1);
+  }
+}