bacterial cloud prototype

testing the representation of bacteria as clouds of 'process', to work
with compounds as clouds of 'stuff'

.gitignore

@@ -58,6 +58,10 @@ $tf*/
 # Compiled Python
 *.pyc
 
+# Compiled Processing
+application.*/
+web-export/
+
 # CMake/build directory
 [Bb]uild/
 build-win/

bacterial_cloud/Agent.pde

@@ -0,0 +1,26 @@
+//
+//class Agent {
+//
+//  PVector location;
+//  
+//
+//
+//  void display() {
+//    //fill(0,150);
+//    //stroke(0);
+//    //ellipse(location.x,location.y,r,r);
+//    float theta = velocity.heading() + PI/2;
+//    fill(200, 100);
+//    stroke(0);
+//    pushMatrix();
+//    translate(location.x, location.y);
+//    rotate(theta);
+//    beginShape(TRIANGLES);
+//    vertex(0, -r*2);
+//    vertex(-r, r*2);
+//    vertex(r, r*2);
+//    endShape();
+//    popMatrix();
+//  }
+//}
+

bacterial_cloud/Arr2d.pde

@@ -0,0 +1,137 @@
+// Class for 2d arrays, including element wise math
+
+class Arr2d
+{
+  float[][] data;
+  int _xs, _ys;
+
+  Arr2d(int xs, int ys)
+  {
+    this(xs,ys,0);
+  }
+
+  Arr2d(int xs, int ys, float val)
+  {
+    _xs = xs; _ys = ys;
+    data = new float[_xs][_ys];
+    Set(val);
+  }
+
+  Arr2d(float[][] val)
+  {
+    _xs = val.length;
+    _ys = val[0].length;
+    data = new float[_xs][_ys];
+    Set(val);
+  }
+
+  Arr2d(Arr2d clone)
+  {
+    this(clone.data);
+//    data = new float[clone._xs][clone._ys];
+//    Set(clone);
+  }
+
+  void Set(float val)
+  {
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] = val;
+  }
+
+  void Set(float[][] val)
+  {
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] = val[x][y];
+
+  }
+
+  void Set(Arr2d val)
+  {  Set(val.data); }
+
+  void Mult(float val)
+  {  
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] *= val;
+  }
+
+  void Mult(Arr2d val)
+  {    
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] *= val.data[x][y];
+  }
+
+  void Add(float val)
+  {  
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] += val;
+  }
+
+  void Add(Arr2d val)
+  {        
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] += val.data[x][y];
+  }
+
+  void Sub(float val)
+  { Add(-val); }
+
+  void Sub(Arr2d val)
+  {
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] -= val.data[x][y];
+
+  }
+
+  void Conv(Arr2d mask)
+  {    
+    int mx = mask._xs; 
+    int my = mask._ys;
+    int mcx = mx/2;
+    int mcy = my/2;
+
+    float[][] out = new float[_xs][_ys];
+    for (int x = 0; x < _xs; x++)
+      for (int y = 0; y < _ys; y++)
+        out[x][y] = 0;
+
+    for (int x = 0; x < _xs; x++)
+      for (int y = 0; y < _ys; y++)
+        for (int i = 0 - mcx; i < (mx - mcx); i++)
+          for (int j = 0 - mcy; j < (my - mcy); j++)
+          {
+            if ((x+i) < 0 || (x+i) >= _xs || (y+j) < 0 || (y+j) >= _ys)
+              continue;
+            else
+            {
+              out[x][y] += data[x + i][y + j] * mask.data[i+mcx][j+mcy];
+            }
+          }
+    data = out;
+  }
+
+  float Sum()
+  {
+    float total = 0;
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      total += data[x][y];
+
+    return total;
+  }
+
+  void Clamp(float min, float max)
+  {
+    for(int x = 0; x < _xs; x++)
+    for(int y = 0; y < _ys; y++)
+      data[x][y] = constrain(data[x][y], min, max);
+  }
+}
+
+

bacterial_cloud/Bacteria.pde

@@ -0,0 +1,107 @@
+// Includes
+
+int time = 0;
+
+// Grid setup
+int xs = 50;
+int ys = 50;
+int w = 8;
+
+Vehicle[] agents;
+boolean debug = true;
+
+Arr2d mask;
+GridLayers compounds;
+GridLayers bacteria;
+
+void setup(){
+  colorMode(RGB, 1);
+
+  size(xs*w,ys*w);
+
+  agents = new Vehicle[3];
+  for(int i = 0; i < 3; i++)
+    agents[i] = new Vehicle(w * xs/2, (w * ys) * (i + 1) / 4);
+
+  mask = new Arr2d(new float[][]{{0.707,1,0.707},{1,0,1},{0.707,1,0.707}});
+  mask.Mult(0.01);
+  mask.data[1][1] = -mask.Sum();
+
+  compounds = new GridLayers();
+  compounds.Add(new Grid(xs,ys,w), color(1,0,0));
+  compounds.Add(new Grid(xs,ys,w), color(0,1,0));
+  compounds.Add(new Grid(xs,ys,w), color(0,0,1));
+
+  bacteria = new GridLayers();
+  bacteria.Add(new Grid(xs,ys,w), color(0,1,1));
+
+//  PrintArr2d(mask.data);
+//  Arr2d co = new Arr2d(mask.data);
+//  PrintArr2d(co.data);
+//  co.data[1][1] = 5;
+//  PrintArr2d(co.data);
+//  PrintArr2d(mask.data);
+
+//  mask.Mult(mask);
+//  print("\n");
+//  PrintArr2d(mask.data);
+}
+
+int i = 0;
+
+void draw(){
+  if(millis() > time)
+  { // update at most 20 times per second
+//    time = millis() + 50;
+    background(0);
+
+    // Diffuse and display compounds
+    compounds.Diffuse(mask);
+    compounds.Display();
+
+    // React, diffuse, and display bacteria
+    bacteria.get(0).data.data[xs/4][ys/2] = 1; // Seed population
+    bacteria.get(0).React(compounds.get(0), compounds.get(1), compounds.get(2));
+    bacteria.Diffuse(mask);
+    bacteria.DisplayEdges();
+
+//    Arr2d temp = new Arr2d(compounds.get(0).data);
+////    temp.Add(compounds.get(1).data);
+//    Grid g = new Grid(temp, w);
+//    g.DisplayEdges(color(1,1,1));
+
+    // Move and display agents
+    for(int i = 0; i < 3; i++)
+      {
+        agents[i].wander();
+        agents[i].run();
+
+        // Agents leak compounds
+        compounds.get(i).AddAt(agents[i].location, 1);
+        if( i < 2)
+        compounds.get(2).AddAt(agents[i].location, -1);
+      }
+
+    // Test gradient at current mouse position
+    PVector m = new PVector(mouseX, mouseY);
+    PVector g = compounds.get(2).GradAt(m);
+
+    noFill();
+    stroke(1);
+    line(m.x,m.y,m.x + (5* g.x), m.y + (5 * g.y));
+  }
+}
+
+void PrintArr2d(float[][] data)
+{
+  for(int i = 0; i < data.length; i++)
+  {
+      print("\n");
+  for(int j = 0; j < data[i].length; j++)
+     if(j == 0)
+       print(data[i][j]);
+     else
+       print(", ", data[i][j]);
+  }
+}
+

bacterial_cloud/Color.pde

@@ -0,0 +1,9 @@
+class Color
+{
+  public color data;
+
+  Color(int c)
+  {
+    data = c;
+  }
+}