Reorganized, no weight

core/src/main/java/com/github/drinkjava2/frog/Env.java

@@ -21,7 +21,7 @@ import com.github.drinkjava2.frog.egg.EggTool;
 @SuppressWarnings("serial")
 public class Env extends JPanel {
 	/** Speed of test */
-	public static final int SHOW_SPEED = 80; // 测试速度，1~1000,可调, 数值越小，速度越慢
+	public static final int SHOW_SPEED = 1; // 测试速度，1~1000,可调, 数值越小，速度越慢
 
 	public static final int ENV_WIDTH = 400; // 虚拟环境的宽度, 可调
 
@@ -40,6 +40,8 @@ public class Env extends JPanel {
 	/** Delete eggs at beginning of each run */
 	public static final boolean DELETE_EGGS = false;// 每次运行是否先删除保存的蛋
 
+	public static final boolean DEBUG_MODE = false; // Debug 模式下会打印出更多的调试信息
+
 	static {
 		if (DELETE_EGGS)
 			EggTool.deleteEggs();
@@ -53,7 +55,7 @@ public class Env extends JPanel {
 
 	public static boolean pause = false; // 暂停按钮按下将暂停测试
 
-	public static final boolean[][] foods = new boolean[ENV_WIDTH][ENV_HEIGHT];// 食物数组定义
+	private static final boolean[][] foods = new boolean[ENV_WIDTH][ENV_HEIGHT];// 食物数组定义
 
 	public List<Frog> frogs = new ArrayList<>();
 
@@ -65,6 +67,26 @@ public class Env extends JPanel {
 		this.setBounds(1, 1, ENV_WIDTH, ENV_HEIGHT);
 	}
 
+	public static boolean insideEnv(int x, int y) {
+		return !(x < 0 || y < 0 || x >= ENV_WIDTH || y >= ENV_HEIGHT);
+	}
+
+	public static boolean outsideEnv(int x, int y) {
+		return x < 0 || y < 0 || x >= ENV_WIDTH || y >= ENV_HEIGHT;
+	}
+
+	public static boolean foundFood(int x, int y) {
+		return !(x < 0 || y < 0 || x >= ENV_WIDTH || y >= ENV_HEIGHT) && Env.foods[x][y];
+	}
+
+	public static boolean foundAndDeleteFood(int x, int y) {// 如果x,y有食物，将其清0，返回true
+		if (foundFood(x, y)) {
+			foods[x][y] = false;
+			return true;
+		}
+		return false;
+	}
+
 	private void rebuildFrogAndFood() {
 		frogs.clear();
 		for (int i = 0; i < ENV_WIDTH; i++) {// 清除食物
@@ -124,7 +146,7 @@ public class Env extends JPanel {
 			for (int i = 0; i < STEPS_PER_ROUND; i++) {
 				if (allDead) {
 					System.out.println("All dead at round:" + i);
-					break; // 全死光了就直接跳到下一轮,以节省时间
+					break; // 青蛙全死光了就直接跳到下一轮,以节省时间
 				}
 				allDead = true;
 				for (Frog frog : frogs)

core/src/main/java/com/github/drinkjava2/frog/Frog.java

@@ -15,43 +15,35 @@ import java.awt.Image;
 import java.io.FileInputStream;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Random;
 
 import javax.imageio.ImageIO;
 
 import com.github.drinkjava2.frog.brain.Cell;
 import com.github.drinkjava2.frog.brain.Input;
 import com.github.drinkjava2.frog.brain.Organ;
-import com.github.drinkjava2.frog.brain.Output;
-import com.github.drinkjava2.frog.brain.Zone;
-import com.github.drinkjava2.frog.brain.group.RandomConnectGroup;
 import com.github.drinkjava2.frog.egg.Egg;
 
 /**
- * Frog = brain + organ, but now let's only focus on brain, organs are hard
- * coded in egg
+ * Frog = organs + brain cells
  * 
- * 青蛙由脑细胞和器官组成，目前脑细胞可以变异、进化、遗传，以由电脑自动生成神经网络，但是器官在蛋里硬编码，不许进化，将来可以考虑器官的进化
+ * 青蛙由器官组成，器官中的Group类会生成各种脑细胞
  * 
  * @author Yong Zhu
  * @since 1.0
  */
 public class Frog {
 
-	public RandomConnectGroup[] cellGroups;
-
 	/** brain cells */
 	public List<Cell> cells = new ArrayList<>();
 
 	/** organs */
 	public List<Organ> organs = new ArrayList<>();
 
-	public int x; // frog在env中的x坐标
-	public int y; // frog在env中的y坐标
-	public long energy = 10000; // 能量为0则死掉
-	public boolean alive = true; // 设为false表示青蛙死掉了，将不参与任何计算和显示，以节省时间
+	public int x; // frog在Env中的x坐标
+	public int y; // frog在Env中的y坐标
+	public long frogEngery = 100000; // 能量为0则死掉
+	public boolean alive = true; // 设为false表示青蛙死掉了，将不参与计算和显示，以节省时间
 
-	static final Random r = new Random();
 	static Image frogImg;
 	static {
 		try {
@@ -64,62 +56,36 @@ public class Frog {
 	public Frog(int x, int y, Egg egg) {
 		this.x = x;
 		this.y = y;
-
-		// Brain cells
-		if (egg.cellGroups != null) {
-			cellGroups = new RandomConnectGroup[egg.cellGroups.length];
-			for (int k = 0; k < egg.cellGroups.length; k++) {
-				RandomConnectGroup g = egg.cellGroups[k];
-				cellGroups[k] = new RandomConnectGroup(g);
-				for (int i = 0; i < g.cellQty; i++) {// 开始根据蛋来创建脑细胞
-					Cell c = new Cell();
-					c.group = k;
-					int cellQTY = Math.round(g.inputQtyPerCell);
-					c.inputs = new Input[cellQTY];
-					for (int j = 0; j < cellQTY; j++) {
-						c.inputs[j] = new Input();
-						c.inputs[j].cell = c;
-						Zone.copyXY(randomPosInZone(g.groupInputZone), c.inputs[j]);
-						c.inputs[j].radius = g.cellInputRadius;
-					}
-					cellQTY = Math.round(g.outputQtyPerCell);
-					c.outputs = new Output[cellQTY];
-					for (int j = 0; j < cellQTY; j++) {
-						c.outputs[j] = new Output();
-						c.outputs[j].cell = c;
-						Zone.copyXY(randomPosInZone(g.groupOutputZone), c.outputs[j]);
-						c.outputs[j].radius = g.cellOutputRadius;
-					}
-					cells.add(c);
-				}
-			}
+		for (Organ org : egg.organs) {
+			organs.add(org);
+			org.init(this);// 每个新器官初始化，如果是Group类，它们会生成许多脑细胞
 		}
-
-		for (Organ org : egg.organs)
-			organs.add(org.newCopy());
-
 	}
 
 	public boolean active(Env v) {
-		energy -= 20;
-		if (!alive)
+		frogEngery -= 1;
+		if (!alive) {
+			frogEngery -= 50;// 死了需要消耗更多的能量，退出生存竞争
 			return false;
-		if (energy < 0) {
+		}
+		if (frogEngery < 0) { // 如果能量小于0则死
 			alive = false;
 			return false;
 		}
-
-		for (Organ o : organs)
+		// for (Cell cell1 : cells) {// 大脑主循环
+		// if (cell1.energy > 0)
+		// cell1.energy--;
+		// for (Input input : cell1.inputs) {
+		// // TODO
+		// }
+		// }
+		for (Organ o : organs) { // 调用每个Organ的active方法
 			o.active(this);
+		}
 		return alive;
 	}
 
-	private static Zone randomPosInZone(Zone z) {
-		return new Zone(z.x - z.radius + z.radius * 2 * r.nextFloat(), z.y - z.radius + z.radius * 2 * r.nextFloat(),
-				0);
-	}
-
-	public void show(Graphics g) {
+	public void show(Graphics g) {// 显示青蛙的图象
 		if (!alive)
 			return;
 		g.drawImage(frogImg, x - 8, y - 8, 16, 16, null);

core/src/main/java/com/github/drinkjava2/frog/brain/BrainPicture.java

@@ -15,7 +15,6 @@ import javax.swing.JPanel;
 
 import com.github.drinkjava2.frog.Application;
 import com.github.drinkjava2.frog.Frog;
-import com.github.drinkjava2.frog.brain.group.RandomConnectGroup;
 
 /**
  * BrainPicture show first frog's brain structure, for debug purpose only
@@ -36,30 +35,30 @@ public class BrainPicture extends JPanel {
 		this.setBounds(x, y, brainDispWidth + 1, brainDispWidth + 1);
 	}
 
-	void drawZone(Graphics g, Zone z) {
+	public void drawZone(Graphics g, Zone z) {
 		float rate = brainDispWidth / brainWidth;
 		int x = Math.round(z.x * rate);
 		int y = Math.round(z.y * rate);
-		int radius = Math.round(z.radius * rate);
+		int radius = Math.round(z.r * rate);
 		g.drawRect(x - radius, y - radius, radius * 2, radius * 2);
 	}
 
-	void drawCircle(Graphics g, Zone z) {
+	public void drawCircle(Graphics g, Zone z) {
 		float rate = brainDispWidth / brainWidth;
 		int x = Math.round(z.x * rate);
 		int y = Math.round(z.y * rate);
 		g.drawArc(x - 5, y - 5, 10, 10, 0, 360);
 	}
 
-	void fillZone(Graphics g, Zone z) {
+	public void fillZone(Graphics g, Zone z) {
 		float rate = brainDispWidth / brainWidth;
 		int x = Math.round(z.x * rate);
 		int y = Math.round(z.y * rate);
-		int radius = Math.round(z.radius * rate);
+		int radius = Math.round(z.r * rate);
 		g.fillRect(x - radius, y - radius, radius * 2, radius * 2);
 	}
 
-	void drawLine(Graphics g, Zone z1, Zone z2) {
+	public void drawLine(Graphics g, Zone z1, Zone z2) {
 		float rate = brainDispWidth / brainWidth;
 		int x1 = Math.round(z1.x * rate);
 		int y1 = Math.round(z1.y * rate);
@@ -68,11 +67,11 @@ public class BrainPicture extends JPanel {
 		g.drawLine(x1, y1, x2, y2);
 	}
 
-	void drawText(Graphics g, Zone z, String text) {
+	public void drawText(Graphics g, Zone z, String text) {
 		float rate = brainDispWidth / brainWidth;
 		int x = Math.round(z.x * rate);
 		int y = Math.round(z.y * rate);
-		g.drawString(text, x - text.length() * 3, y);
+		g.drawString(text, x - text.length() * 3 - 2, y);
 	}
 
 	private static final Color[] rainbow = new Color[] { RED, ORANGE, YELLOW, GREEN, CYAN, BLUE, MAGENTA };
@@ -84,8 +83,10 @@ public class BrainPicture extends JPanel {
 		return rainbow[nextColor++];
 	}
 
-	private static Color color(float i) {
-		if (i <= 1)
+	public static Color color(float i) {
+		if (i == 0)
+			return Color.black;
+		if (i == 1)
 			return Color.RED;
 		if (i <= 3)
 			return Color.ORANGE;
@@ -109,26 +110,7 @@ public class BrainPicture extends JPanel {
 		g.setColor(Color.black);
 		g.drawRect(0, 0, brainDispWidth, brainDispWidth);
 
-		for (Organ organ : frog.organs) {
-			g.setColor(Color.BLACK);
-			drawZone(g, organ);
-			if (organ.name != null)
-				drawText(g, organ, String.valueOf(organ.name));
-		}
-
-		for (RandomConnectGroup group : frog.cellGroups) {
-			if (!group.inherit)
-				g.setColor(Color.lightGray); // 如果是本轮随机生成的，灰色表示
-			else
-				g.setColor(color(group.cellQty)); // 如果是继承的，彩虹色表示，颜色数越往后表示数量越多
-			drawLine(g, group.groupInputZone, group.groupOutputZone);
-			drawZone(g, group.groupInputZone);
-			fillZone(g, group.groupOutputZone);
-			if (group.fat > 0) {
-				g.setColor(Color.BLACK);
-				drawCircle(g, group.groupOutputZone); // 如果胖了，表示激活过了，下次下蛋少不了这一组
-			}
-		}
-
+		for (Organ organ : frog.organs)
+			organ.drawOnBrainPicture(this); // each organ draw itself
 	}
 }

core/src/main/java/com/github/drinkjava2/frog/brain/Cell.java

@@ -10,16 +10,25 @@
  */
 package com.github.drinkjava2.frog.brain;
 
+import com.github.drinkjava2.frog.brain.group.Group;
+
 /**
- * Cell is a brain nerve cell, this is the basic unit of frog's brain
+ * Cell is the basic unit of frog's brain
  * 
  * @author Yong Zhu
  * @since 1.0
  */
 public class Cell {
-	public int group; // this cell belong to which group
-	public Input[] inputs; // inputs of cell
-	public Output[] outputs; // outputs of cell
-	public long energy;
+	// this cell belong to frog's which organ
+	public Group group;
+
+	// inputs of cell
+	public Input[] inputs; // 每个细胞有一组输入触突
+
+	// outputs of cell
+	public Output[] outputs; // 每个细胞有一组输出触突
+
+	// energy of cell, energy got from food
+	public long energy; // 每个细胞当前的能量值
 
 }

core/src/main/java/com/github/drinkjava2/frog/brain/Input.java

@@ -18,5 +18,9 @@ package com.github.drinkjava2.frog.brain;
  */
 @SuppressWarnings("serial")
 public class Input extends Zone {
-	public Cell cell;
+	public Cell cell; // 这个输入触突属于哪个脑细胞
+
+	public Input(Zone z) {
+		super(z);
+	}
 }

core/src/main/java/com/github/drinkjava2/frog/brain/Organ.java

@@ -10,6 +10,9 @@
  */
 package com.github.drinkjava2.frog.brain;
 
+import java.awt.Color;
+import java.awt.Graphics;
+
 import com.github.drinkjava2.frog.Frog;
 
 /**
@@ -20,20 +23,23 @@ import com.github.drinkjava2.frog.Frog;
  * @author Yong Zhu
  * @since 1.0.4
  */
-public class Organ extends Zone {
+public abstract class Organ extends Zone {
 	private static final long serialVersionUID = 1L;
-	public String name; // 显示在脑图上的器官名称
-	public long fat = 0; // 如果细胞活跃多，fat值高，则保留（以及变异）的可能性大，反之则舍弃掉
-	public int qtyLimit = 5; // 最多允许数量
-	public boolean inherit = false; // 器官是继承来的，还是变异来的，后者淘汰率会高
+	public String name; // 显示在脑图上的器官名称，可选
+
+	 public long fat = 0; // 如果活跃多，fat值高，则保留（及变异）的可能性大，反之则很可能丢弃掉
+
+	public boolean allowBorrow() { // 是否允许在精子中将这个器官借出
+		return false;
+	}
 
 	/** If active in this organ's zone? */
 	public boolean outputActive(Frog f) {
 		for (Cell cell : f.cells) {
 			for (Output output : cell.outputs) { //
 				if (cell.energy > 10 && this.nearby(output)) {
-					f.cellGroups[cell.group].fat++;
-					cell.energy -= 30;
+					cell.group.fat++;
+					cell.energy -= 1;
 					return true;
 				}
 			}
@@ -41,43 +47,49 @@ public class Organ extends Zone {
 		return false;
 	}
 
+	/** Set X, Y, Radius, name of current Organ */
+	public Organ setXYRN(float x, float y, float r, String name) {
+		this.x = x;
+		this.y = y;
+		this.r = r;
+		this.name = name;
+		return this;
+	}
+
+	/** Child class can override this method to drawing picture */
+	public void drawOnBrainPicture(BrainPicture pic) {// 把自已这个器官在脑图上显示出来，子类可以重写这个方法
+		Graphics g = pic.getGraphics();// border
+		g.setColor(Color.BLACK); // 缺省是黑色
+		pic.drawZone(g, this);
+		if (this.name != null)
+			pic.drawText(g, this, String.valueOf(this.name));
+	}
+
 	/** make a new copy of current organ */
-	public Organ newCopy() { // 新建一份，用于从蛋复制到Frog
+	public Organ newCopy() { // 创建一个当前器官的副本
 		Organ newOrgan = null;
 		try {
 			newOrgan = this.getClass().newInstance();
 			copyXYR(this, newOrgan);
 			newOrgan.name = this.name;
-			newOrgan.fat = this.fat;
+			newOrgan.fat = this.fat; 
 			return newOrgan;
 		} catch (Exception e) {
 			throw new UnknownError("Can not make new Organ copy for " + this);
 		}
 	}
 
-	/** Set X, Y, Radius of current Organ */
-	public Organ setXYR(float x, float y, float radius) {
-		this.x = x;
-		this.y = y;
-		this.radius = radius;
-		return this;
-	}
-
-	/** Set X, Y, Radius, name of current Organ */
-	public Organ setXYRN(float x, float y, float radius, String name) {
-		this.x = x;
-		this.y = y;
-		this.radius = radius;
-		this.name = name;
-		return this;
+	/** Only call once when frog created , Child class can override this method */
+	public void init(Frog f) { // 仅在Frog生成时这个方法会调用一次，缺省啥也不干，通常用于Group子类的初始化
 	}
 
 	/** Only call once when frog created , Child class can override this method */
-	public void init(Frog f) {
+	public Organ[] vary() { // 在下蛋时每个器官会调用这个方法，缺省返回自已的副本，Group类通常要覆盖这个方法
+		return new Organ[] { newCopy() };
 	}
 
 	/** Each loop step call active method, Child class can override this method */
-	public void active(Frog f) {
+	public void active(Frog f) { // 每一步都会调用器官的active方法 ，缺省啥也不干
 	}
 
 }

core/src/main/java/com/github/drinkjava2/frog/brain/Output.java

@@ -18,5 +18,9 @@ package com.github.drinkjava2.frog.brain;
  */
 @SuppressWarnings("serial")
 public class Output extends Zone {
-	public Cell cell;
+	public Cell cell; // 这个输出触突属于哪个脑细胞
+
+	public Output(Zone z) {
+		super(z);
+	}
 }

core/src/main/java/com/github/drinkjava2/frog/brain/Zone.java

@@ -22,18 +22,19 @@ import com.github.drinkjava2.frog.Env;
  */
 public class Zone implements Serializable {
 	private static final long serialVersionUID = 1L;
+
 	public float x;
 	public float y;
-	public float radius;// so width of the zone= radius*2
+	public float r;// r为这个矩形区边长的一半
 
 	public Zone() {
-		// 空构造器不能省，FastJSON实例化时要用到
+		// 空构造器不能省
 	}
 
-	public Zone(float x, float y, float radius) {
+	public Zone(float x, float y, float r) {
 		this.x = x;
 		this.y = y;
-		this.radius = radius;
+		this.r = r;
 		if (this.x < 0)
 			this.x = 0;
 		if (this.y < 0)
@@ -47,11 +48,11 @@ public class Zone implements Serializable {
 	public Zone(Zone z) {
 		this.x = z.x;
 		this.y = z.y;
-		this.radius = z.radius;
+		this.r = z.r;
 	}
 
 	public boolean nearby(Zone z) {
-		float dist = radius + z.radius;
+		float dist = r + z.r;
 		return (Math.abs(x - z.x) < dist && Math.abs(y - z.y) < dist);
 	}
 
@@ -71,6 +72,13 @@ public class Zone implements Serializable {
 	public static void copyXYR(Zone from, Zone to) {
 		to.x = from.x;
 		to.y = from.y;
-		to.radius = from.radius;
+		to.r = from.r;
+	}
+
+	public void setXYR(float x, float y, float r) {
+		this.x = x;
+		this.y = y;
+		this.r = r;
 	}
+
 }

core/src/main/java/com/github/drinkjava2/frog/brain/group/Group.java

@@ -10,6 +10,7 @@
  */
 package com.github.drinkjava2.frog.brain.group;
 
+import com.github.drinkjava2.frog.Frog;
 import com.github.drinkjava2.frog.brain.Organ;
 
 /**
@@ -19,15 +20,32 @@ import com.github.drinkjava2.frog.brain.Organ;
  * 
  * 为了与旧版CellGroup区分，新版的这个类命名为Group，它代表了一组分布于一个正方形内的细胞群，细胞数量、每个细胞的触突连接方式等参数由当前Group决定,
  * 可以说每一种Group代表了一种神经网络算法， 通过无数个Group随机的分布、进化、变异，达到最终脑结构适应环境的变化
- * CellGroup会参与遗传和进化，但是它生成的细胞不会参与遗传。 各个Group生成的细胞相加总和就是脑细胞总数。
+ * Group会参与遗传和进化，但是它生成的细胞不会参与遗传。 各个Group生成的细胞相加总和就是脑细胞总数。
  * 
- * Group在脑活动中不起作用，可以把Group比作播种机，把种子排列好后，就撒手不管了,在遗传过程中有一个fat参数，如果细胞活跃多，则保留及变异的可能性大，反之则舍弃掉。
- * Group是器官的一种，所以蛋里存放着所有Group的位置、大小、内部参数等信息，但是蛋里面不保存具体的细胞。这样通过控制有多少个"播种机"，就可以控制大脑的结构了。
- * Group可以进行位置、大小变动、复制、分裂等多种形式的变异,原则上Group遗传的一下代与父代是同一个播种类型，但不排除也有可能突变成另一个类型的Group。
+ * Group在脑活动中不起作用，可以把Group比作播种机，把种子排列好后，就撒手不管了,在遗传过程中有一个fat参数，如果细胞活跃多，则Group保留及变异的可能性大，反之则舍弃掉。
+ * Group是器官的一种，所以蛋里存放着所有Group的位置、大小、内部参数等信息，但是蛋里面不保存具体的细胞。这样通过控制有多少个"播种机"，就可以控制大脑的结构了，这样可以缩小蛋的尺寸。
+ * 原则上Group遗传的一下代与父代是同一个播种(算法)类型，但不排除也有可能突变成另一个类型的Group。
  * 
  * @author Yong Zhu
  * @since 1.0
  */
-public class Group extends Organ {
+public abstract class Group extends Organ { 
 	private static final long serialVersionUID = 1L;
+
+	@Override
+	public boolean allowBorrow() { // 是否允许在精子中将这个器官借出
+		return true;
+	}
+
+	/** Each loop step call active method, Child class can override this method */
+	@Override
+	public void active(Frog f) { // 每一步都会调用器官的active方法
+		f.frogEngery -= 3; // 每个器官运动都要消耗能量, 死了也要消耗能量
+		if (!f.alive)
+			return;
+		if (f.frogEngery < 0) { // 如果能量小于0则死
+			f.alive = false;
+			return;
+		}
+	}
 }

core/src/main/java/com/github/drinkjava2/frog/brain/group/RandomConnectGroup.java

@@ -10,17 +10,25 @@
  */
 package com.github.drinkjava2.frog.brain.group;
 
-import java.util.Random;
+import java.awt.Color;
+import java.awt.Graphics;
 
+import com.github.drinkjava2.frog.Frog;
+import com.github.drinkjava2.frog.brain.BrainPicture;
+import com.github.drinkjava2.frog.brain.Cell;
+import com.github.drinkjava2.frog.brain.Input;
+import com.github.drinkjava2.frog.brain.Organ;
+import com.github.drinkjava2.frog.brain.Output;
 import com.github.drinkjava2.frog.brain.Zone;
+import com.github.drinkjava2.frog.util.RandomUtils;
 
 /**
  * RandomConnectGroup
  * 
- * 这是一个随机方式连接两端的Group，它是从旧版的CellGroup改造过来，这是一种最简单的神经元排列方式，只有
- * 它代表一组细胞，触突输入区和输出区分别位于Zone内的任意随机两点。至于是否合理则由frog的遗传进化来决定，不合理的RandomConnectGroup会被淘汰掉。
+ * 这是一个随机方式连接两端的Group，它是从旧版的CellGroup改造过来，这是一种最简单的神经元排列方式，只有一组细胞，触突输入区和输出区分别位于Zone内的任意随机两点。
+ * 至于是否合理则由frog的遗传进化来决定，不合理的RandomConnectGroup会被淘汰掉。
  * 
- *  (还没改造完成，在不破坏原有外在表现的基础上，要平滑将它改造成一个标准Group的子类，也是第一个子类 )
+ * (还没改造完成，在不破坏原有外在表现的基础上，要平滑将它改造成一个标准Group的子类，也是第一个子类 )
  * 
  * @author Yong Zhu
  * @since 1.0
@@ -28,50 +36,58 @@ import com.github.drinkjava2.frog.brain.Zone;
 public class RandomConnectGroup extends Group {
 	private static final long serialVersionUID = 1L;
 
-	// TODO need delete below fields, use grid replace
-	public Zone groupInputZone; // input distribute zone
+	public Zone inputZone; // 输入触突区
+	public Zone outputZone; // 输出触突区
 
-	public Zone groupOutputZone; // output distribute zone
+	@Override
+	public void init(Frog f) {
+		if (inputZone == null)
+			inputZone = RandomUtils.randomPosInZone(this);
+		if (outputZone == null)
+			outputZone = RandomUtils.randomPosInZone(this);
 
-	public float cellInputRadius; // input radius of each cell
-	public float cellOutputRadius; // output radius of each cell
+		Cell c = new Cell();
+		Input in = new Input(inputZone);
+		in.cell = c;
+		c.inputs = new Input[] { in };
 
-	public float inputQtyPerCell; // input qty per cell
-	public float outputQtyPerCell; // output qty per cell
-	// TODO need delete above fields
+		Output out = new Output(outputZone);
+		out.cell = c;
+		c.outputs = new Output[] { out };
 
-	public float cellQty; // how many nerve cells in this CellGroup
-
-	private static final Random r = new Random();
-
-	public RandomConnectGroup() {
+		c.group = this;
+		f.cells.add(c);
+	}
 
+	@Override
+	public Organ[] vary() {
+		if (fat <= 0)
+			if (RandomUtils.percent(30))
+				return new Organ[] {};
+		if (RandomUtils.percent(80))
+			return new Organ[] { this };
+		return new Organ[] { this, newRandomConnGroup(this) };
 	}
 
-	public RandomConnectGroup(RandomConnectGroup g) {// clone old CellGroup
-		groupInputZone = new Zone(g.groupInputZone);
-		groupOutputZone = new Zone(g.groupOutputZone);
-		cellInputRadius = g.cellInputRadius;
-		cellOutputRadius = g.cellOutputRadius;
-		cellQty = g.cellQty;
-		inputQtyPerCell = g.inputQtyPerCell;
-		outputQtyPerCell = g.outputQtyPerCell;
-		fat = g.fat;
-		inherit = g.inherit;
+	public static RandomConnectGroup newRandomConnGroup(Zone z) {
+		RandomConnectGroup newOne = new RandomConnectGroup();
+		newOne.inputZone = RandomUtils.randomPosInZone(z);
+		newOne.outputZone = RandomUtils.randomPosInZone(z);
+		return newOne;
 	}
 
-	public RandomConnectGroup(float brainWidth, int randomCellQtyPerGroup, int randomInputQtyPerCell,
-			int randomOutQtyPerCell) {
-		inherit = false;
-		groupInputZone = new Zone(r.nextFloat() * brainWidth, r.nextFloat() * brainWidth,
-				(float) (r.nextFloat() * brainWidth * .01));
-		groupOutputZone = new Zone(r.nextFloat() * brainWidth, r.nextFloat() * brainWidth,
-				(float) (r.nextFloat() * brainWidth * .01));
-		cellQty = 1 + r.nextInt(randomCellQtyPerGroup);
-		cellInputRadius = (float) (0.001 + r.nextFloat() * 2);
-		cellOutputRadius = (float) (0.001 + r.nextFloat() * 2);
-		inputQtyPerCell = 1 + r.nextInt(randomInputQtyPerCell);
-		outputQtyPerCell = 1 + r.nextInt(randomOutQtyPerCell);
+	/** Child class can override this method to drawing picture */
+	public void drawOnBrainPicture(BrainPicture pic) {// 把自已这个器官在脑图上显示出来，子类可以重写这个方法
+		Graphics g = pic.getGraphics();// border
+		g.setColor(Color.gray); // 缺省是灰色
+		pic.drawZone(g, this);
+		pic.drawLine(g, inputZone, outputZone);
+		pic.drawZone(g, inputZone);
+		pic.fillZone(g, outputZone);
+		if (fat > 0) {
+			g.setColor(Color.red);
+			pic.drawCircle(g, outputZone); // 如果胖了，表示激活过了，下次下蛋少不了这一组
+		}
 	}
 
 }

core/src/main/java/com/github/drinkjava2/frog/brain/organ/Eat.java

@@ -15,24 +15,15 @@ import com.github.drinkjava2.frog.Frog;
 import com.github.drinkjava2.frog.brain.Organ;
 
 /**
- * Move up frog 1 unit if outputs of nerve cells active in this zone
+ * Eat food at current x, y position
  */
-public class Eat extends Organ {
+public class Eat extends Organ {// Eat这个类将食物转化为能量，能量小于0，则青蛙死掉
 	private static final long serialVersionUID = 1L;
 
 	@Override
 	public void active(Frog f) {
-		int x = f.x;
-		int y = f.y;
-		if (x < 0 || x >= Env.ENV_WIDTH || y < 0 || y >= Env.ENV_HEIGHT) {// 越界者死！
-			f.alive = false;
-			return;
-		}
-
-		if (Env.foods[x][y]) {
-			Env.foods[x][y] = false;
-			f.energy = f.energy + 1000;// 吃掉food，能量境加
-		}
+		if (Env.foundAndDeleteFood(f.x, f.y))
+			f.frogEngery = f.frogEngery + 1000;// 如果青蛙的坐标与食物重合，吃掉food，能量境加
 	}
 
 }

core/src/main/java/com/github/drinkjava2/frog/brain/organ/Eye.java

@@ -27,15 +27,11 @@ import com.github.drinkjava2.frog.brain.Zone;
 public class Eye extends Organ {
 	private static final long serialVersionUID = 1L;
 
-	private static boolean hasFood(int x, int y) {
-		return x >= 0 && y >= 0 && x < Env.ENV_WIDTH && y < Env.ENV_HEIGHT && Env.foods[x][y];
-	}
-
 	@Override
 	public void active(Frog f) {
 		// 第一个眼睛只能观察上、下、左、右四个方向有没有食物
-		float qRadius = radius / 4;
-		float q3Radius = (float) (radius * .75);
+		float qRadius = r / 4;
+		float q3Radius = (float) (r * .75);
 		Zone seeUp = new Zone(x, y + q3Radius, qRadius);
 		Zone seeDown = new Zone(x, y - q3Radius, qRadius);
 		Zone seeLeft = new Zone(x - q3Radius, y, qRadius);
@@ -49,28 +45,28 @@ public class Eye extends Organ {
 
 		int seeDist = 10;
 		for (int i = 1; i < seeDist; i++)
-			if (hasFood(f.x, f.y + i)) {
+			if (Env.foundFood(f.x, f.y + i)) {
 				seeFood = true;
 				foodAtUp = true;
 				break;
 			}
 
 		for (int i = 1; i < seeDist; i++)
-			if (hasFood(f.x, f.y - i)) {
+			if (Env.foundFood(f.x, f.y - i)) {
 				seeFood = true;
 				foodAtDown = true;
 				break;
 			}
 
 		for (int i = 1; i < seeDist; i++)
-			if (hasFood(f.x - i, f.y)) {
+			if (Env.foundFood(f.x - i, f.y)) {
 				seeFood = true;
 				foodAtLeft = true;
 				break;
 			}
 
 		for (int i = 1; i < seeDist; i++)
-			if (hasFood(f.x + i, f.y)) {
+			if (Env.foundFood(f.x + i, f.y)) {
 				seeFood = true;
 				foodAtRight = true;
 				break;

core/src/main/java/com/github/drinkjava2/frog/brain/organ/Hungry.java

@@ -23,11 +23,8 @@ public class Hungry extends Organ {
 
 	@Override
 	public void active(Frog f) {
-		for (Cell cell : f.cells) {
-			if (cell.energy > 0)
-				cell.energy--;
-
-			if (f.energy < 10000 && cell.energy < 100)
+		for (Cell cell : f.cells) {  
+			if (f.frogEngery < 10000 && cell.energy < 1000)
 				for (Input input : cell.inputs)
 					if (input.nearby(this)) // input zone near by hungry zone
 						cell.energy += 2;

core/src/main/java/com/github/drinkjava2/frog/egg/CellGroup.java

@@ -0,0 +1,14 @@
+/*
+ * Copyright 2018 the original author or authors. 
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not
+ * use this file except in compliance with the License. You may obtain a copy of
+ * the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by
+ * applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
+ * OF ANY KIND, either express or implied. See the License for the specific
+ * language governing permissions and limitations under the License.
+ */
+package com.github.drinkjava2.frog.egg;
+
+public class CellGroup {
+}

core/src/main/java/com/github/drinkjava2/frog/egg/Egg.java

@@ -13,12 +13,10 @@ package com.github.drinkjava2.frog.egg;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Random;
 
-import com.github.drinkjava2.frog.Env;
 import com.github.drinkjava2.frog.Frog;
 import com.github.drinkjava2.frog.brain.Organ;
-import com.github.drinkjava2.frog.brain.Zone;
+import com.github.drinkjava2.frog.brain.group.Group;
 import com.github.drinkjava2.frog.brain.group.RandomConnectGroup;
 import com.github.drinkjava2.frog.brain.organ.Eat;
 import com.github.drinkjava2.frog.brain.organ.Eye;
@@ -27,6 +25,7 @@ import com.github.drinkjava2.frog.brain.organ.MoveDown;
 import com.github.drinkjava2.frog.brain.organ.MoveLeft;
 import com.github.drinkjava2.frog.brain.organ.MoveRight;
 import com.github.drinkjava2.frog.brain.organ.MoveUp;
+import com.github.drinkjava2.frog.util.RandomUtils;
 
 /**
  * Egg is the static structure description of frog, can save as text file, to
@@ -40,109 +39,12 @@ import com.github.drinkjava2.frog.brain.organ.MoveUp;
  */
 public class Egg implements Serializable {
 	private static final long serialVersionUID = 1L;
-	public int randomCellGroupQty = 30; // 随机生成多少个组
-	public int randomCellQtyPerGroup = 3; // 每个组有多少个脑细胞
-	public int randomInputQtyPerCell = 3;// 每个脑细胞有多少个输入触突
-	public int randomOutQtyPerCell = 2; // 每个脑细胞有多少个输出触突
 
-	public RandomConnectGroup[] cellGroups;
+	public List<Organ> organs = new ArrayList<>();
 
-	public List<Organ> organs = new ArrayList<Organ>();
+	public List<Group> groups = new ArrayList<>();
 
-	public Egg() {
-		// default constructor
-	}
-
-	private static Random r = new Random();
-
-	/** Create a egg by join 2 eggs, x+y=zygote */
-	public Egg(Egg x, Egg y) {
-		// 模拟XY染色体，不能做简单加法，会撑暴内存的，现在每次只随机加一个y的cellgroup进来，这也不太好，因为基因会越加越多，只好用用进废退原则来加大淘汰率。
-
-		// x里原来的CellGroup
-		cellGroups = new RandomConnectGroup[x.cellGroups.length + 1 + randomCellGroupQty];
-		for (int i = 0; i < x.cellGroups.length; i++) {
-			RandomConnectGroup oldCellGroup = x.cellGroups[i];
-			RandomConnectGroup cellGroup = new RandomConnectGroup();
-			cellGroups[i] = cellGroup;
-			cellGroup.inherit = true;
-			cellGroup.groupInputZone = new Zone(oldCellGroup.groupInputZone);
-			cellGroup.groupOutputZone = new Zone(oldCellGroup.groupOutputZone);
-			cellGroup.cellQty = oldCellGroup.cellQty;
-			cellGroup.cellInputRadius = oldCellGroup.cellInputRadius;
-			cellGroup.cellOutputRadius = oldCellGroup.cellOutputRadius;
-			cellGroup.inputQtyPerCell = oldCellGroup.inputQtyPerCell;
-			cellGroup.outputQtyPerCell = oldCellGroup.outputQtyPerCell;
-		}
-
-		// 从y里借一个CellGroup
-		RandomConnectGroup randomY = y.cellGroups[r.nextInt(y.cellGroups.length)];
-		RandomConnectGroup cellGroup = new RandomConnectGroup(randomY);
-		cellGroups[x.cellGroups.length] = cellGroup;
-
-		// 随机生成一批CellGroup
-		for (int i = 0; i < randomCellGroupQty; i++)
-			cellGroups[i + x.cellGroups.length + 1] = new RandomConnectGroup(Env.FROG_BRAIN_WIDTH, x.randomCellQtyPerGroup,
-					x.randomInputQtyPerCell, x.randomOutQtyPerCell);
-
-		addInitialOrgans();
-	}
-
-	/** create a brand new Egg */
-	public static Egg createBrandNewEgg() { // 无中生有，创建一个蛋，先有蛋，后有鸡
-		Egg egg = new Egg();
-		egg.cellGroups = new RandomConnectGroup[egg.randomCellGroupQty];
-		for (int i = 0; i < egg.randomCellGroupQty; i++)
-			egg.cellGroups[i] = new RandomConnectGroup(Env.FROG_BRAIN_WIDTH, egg.randomCellQtyPerGroup,
-					egg.randomInputQtyPerCell, egg.randomOutQtyPerCell);
-		egg.addInitialOrgans();
-		return egg;
-	}
-
-	private static boolean percent(int percent) {
-		return r.nextInt(100) < percent;
-	}
-
-	private static float vary(float f) { // 大部分时候不变，有极小机会变异,有极极小机会大变异，有极极极小机会大大大变异
-		int i = r.nextInt(100);
-		if (i < 95)
-			return f;
-		float rate = .05f;
-		if (i > 97)
-			rate = .1f;
-		return (float) (f * ((1 - rate) + r.nextFloat() * rate * 2));
-	}
-
-	/** Create egg from frog */
-	public Egg(Frog frog) { // 青蛙下蛋，蛋的基因生成遵循用进废退、随机变异两个原则
-		List<RandomConnectGroup> gpList = new ArrayList<>();
-		for (int i = 0; i < frog.cellGroups.length; i++) {
-			if (frog.cellGroups[i].fat <= 0) {
-				if (!frog.cellGroups[i].inherit)
-					continue;// 从未激活过的神经元，并且就是本轮随机生成的，丢弃之
-				if (percent(5))
-					continue;// 继承下来的神经元，但是本轮并没用到， 扔掉又可惜，可以小概率丢掉
-			}
-			RandomConnectGroup cellGroup = new RandomConnectGroup();
-			RandomConnectGroup oldGp = frog.cellGroups[i];
-			cellGroup.groupInputZone = new Zone(vary(oldGp.groupInputZone.x), vary(oldGp.groupInputZone.y),
-					vary(oldGp.groupInputZone.radius));
-			cellGroup.groupOutputZone = new Zone(vary(oldGp.groupOutputZone.x), vary(oldGp.groupOutputZone.y),
-					vary(oldGp.groupOutputZone.radius));
-			cellGroup.cellQty = Math.round(vary(oldGp.cellQty));
-			cellGroup.cellInputRadius = vary(oldGp.cellInputRadius);
-			cellGroup.cellOutputRadius = vary(oldGp.cellOutputRadius);
-			cellGroup.inputQtyPerCell = Math.round(vary(oldGp.inputQtyPerCell));
-			cellGroup.outputQtyPerCell = Math.round(vary(oldGp.outputQtyPerCell));
-			cellGroup.inherit = true;
-			gpList.add(cellGroup);
-		}
-		cellGroups = gpList.toArray(new RandomConnectGroup[gpList.size()]);
-		addInitialOrgans();
-	}
-
-	/** Hard code add initial organs */
-	public void addInitialOrgans() { // 这是硬编码添加初始器官， 器官的数量、位置、内部参数会参加遗传、变异
+	public Egg() {// 无中生有，创建一个蛋，先有蛋，后有鸡
 		organs.add(new Hungry().setXYRN(300, 100, 100, "Hungry"));
 		organs.add(new MoveUp().setXYRN(800, 100, 60, "Up"));
 		organs.add(new MoveDown().setXYRN(800, 400, 60, "Down"));
@@ -150,7 +52,44 @@ public class Egg implements Serializable {
 		organs.add(new MoveRight().setXYRN(900, 250, 60, "Right"));
 		organs.add(new Eat().setXYRN(0, 0, 0, "Eat"));
 		organs.add(new Eye().setXYRN(100, 400, 100, "Eye"));
-		//organs.add(new Eye().setXYRN(100, 700, 100, "Eye"));
+		for (int i = 0; i <10; i++) {
+			organs.add( new RandomConnectGroup().setXYRN(500, 500, 500, null));
+		} 
+
+	}
+
+	/** Create egg from frog */
+	public Egg(Frog frog) { // 青蛙下蛋，每个青蛙的器官会创建自已的副本或变异，可以是0或多个
+		for (Organ organ : frog.organs)
+			for (Organ newOrgan : organ.vary())
+				organs.add(newOrgan); 
+		for (int i = 0; i <10; i++) {
+			organs.add( new RandomConnectGroup().setXYRN(500, 500, 500, null));
+		} 
+	}
+
+	/**
+	 * Create a egg by join 2 eggs, x+y=zygote 模拟X、Y 染色体合并，两个蛋生成一个新的蛋， X从Y里借一个器官,
+	 * 不用担心器官会越来越多，因为通过用进废退原则来筛选,没用到的器官会在几代之后被自然淘汰掉
+	 * 器官不是越多越好，因为器官需要消耗能量，器官数量多了，在生存竞争中也是劣势
+	 * 
+	 */
+	public Egg(Egg x, Egg y) {
+		// x里原来的organ
+		for (Organ organ : x.organs)
+			for (Organ newOrgan : organ.vary())
+				organs.add(newOrgan);
+
+		// 从y里借一个organ
+		int yOrganSize = y.organs.size();
+		if (yOrganSize > 0) {
+			Organ o = y.organs.get(RandomUtils.nextInt(yOrganSize));
+			if (o.allowBorrow())
+				organs.add(o);
+		}
+		for (int i = 0; i <10; i++) {
+			organs.add( new RandomConnectGroup().setXYRN(500, 500, 500, null));
+		}
 	}
 
 }

core/src/main/java/com/github/drinkjava2/frog/egg/EggTool.java

@@ -23,10 +23,11 @@ import java.util.List;
 import com.github.drinkjava2.frog.Application;
 import com.github.drinkjava2.frog.Env;
 import com.github.drinkjava2.frog.Frog;
+import com.github.drinkjava2.frog.brain.Organ;
 import com.github.drinkjava2.frog.util.FrogFileUtils;
 
 /**
- * EggTool store public static methods of egg
+ * EggTool save eggs to disk
  * 
  * @author Yong Zhu
  * @since 1.0
@@ -34,18 +35,30 @@ import com.github.drinkjava2.frog.util.FrogFileUtils;
 public class EggTool {
 
 	/**
+	 * Frogs which have higher energy lay eggs
+	 * 
 	 * 利用Java串行机制存盘。 能量多(也就是吃的更多，更fat)的Frog下蛋并存盘, 以进行下一伦测试，能量少的Frog被淘汰，没有下蛋的资格。
+	 * 用能量的多少来简化生存竟争模拟
 	 */
 	public static void layEggs(Env env) {
 		sortFrogsOrderByEnergyDesc(env);
-		System.out.print("First frog has " + env.frogs.get(0).cellGroups.length + " cellgroups, energy="
-				+ env.frogs.get(0).energy);
-		System.out.print(", Last frog energy=" + env.frogs.get(env.frogs.size() - 1).energy + ", ");
+
+		Frog first = env.frogs.get(0);
+		Frog last = env.frogs.get(env.frogs.size() - 1);
+
+		System.out.print("First frog has " + first.organs.size() + " organs, energy=" + first.frogEngery);
+		System.out.print(", Last frog has " + last.organs.size() + " organs, energy=" + last.frogEngery);
+		if (Env.DEBUG_MODE)
+			for (int i = 0; i < first.organs.size(); i++) {
+				Organ org = first.organs.get(i);
+				System.out.println("Organ(" + i + ")=" + org + ", fat=" + org.fat);
+			}
+
 		try {
 			List<Egg> newEggs = new ArrayList<>();
 			for (int i = 0; i < Env.EGG_QTY; i++)
 				newEggs.add(new Egg(env.frogs.get(i)));
-			System.out.print("EggCellGroups=" + newEggs.get(0).cellGroups.length + ", ");
+			System.out.print("organs =" + newEggs.get(0).organs.size() + ", ");
 
 			FileOutputStream fo = new FileOutputStream(Application.CLASSPATH + "eggs.ser");
 			ObjectOutputStream so = new ObjectOutputStream(fo);
@@ -53,20 +66,19 @@ public class EggTool {
 			so.close();
 
 			env.eggs = newEggs;
-			System.out
-					.println("Saved " + env.eggs.size() + " eggs to file '" + Application.CLASSPATH + "eggs.ser" + "'");
+			System.out.println(
+					", Saved " + env.eggs.size() + " eggs to file '" + Application.CLASSPATH + "eggs.ser" + "'");
 		} catch (IOException e) {
 			System.out.println(e);
 		}
 	}
 
-	private static void sortFrogsOrderByEnergyDesc(Env env) {
+	private static void sortFrogsOrderByEnergyDesc(Env env) {// 按能量多少给青蛙排序
 		Collections.sort(env.frogs, new Comparator<Frog>() {
-
 			public int compare(Frog a, Frog b) {
-				if (a.energy > b.energy)
+				if (a.frogEngery > b.frogEngery)
 					return -1;
-				else if (a.energy == b.energy)
+				else if (a.frogEngery == b.frogEngery)
 					return 0;
 				else
 					return 1;
@@ -75,7 +87,6 @@ public class EggTool {
 	}
 
 	public static void deleteEggs() {
-		FrogFileUtils.deleteFile(Application.CLASSPATH + "eggs.json");
 		FrogFileUtils.deleteFile(Application.CLASSPATH + "eggs.ser");
 	}
 
@@ -100,7 +111,7 @@ public class EggTool {
 					+ " new eggs to do test.");
 			env.eggs = new ArrayList<Egg>();
 			for (int i = 0; i < Env.EGG_QTY; i++)
-				env.eggs.add(Egg.createBrandNewEgg());
+				env.eggs.add(new Egg());
 		}
 	}
 

core/src/main/java/com/github/drinkjava2/frog/util/RandomUtils.java

@@ -0,0 +1,53 @@
+/* Copyright 2018-2020 the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not
+ * use this file except in compliance with the License. You may obtain a copy of
+ * the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by
+ * applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
+ * OF ANY KIND, either express or implied. See the License for the specific
+ * language governing permissions and limitations under the License.
+ */
+package com.github.drinkjava2.frog.util;
+
+import java.util.Random;
+
+import com.github.drinkjava2.frog.brain.Zone;
+
+/**
+ * Random Utilities used in this project
+ * 
+ * @author Yong Zhu
+ * @since 1.0
+ */
+public class RandomUtils {
+	private static final Random rand = new Random();
+
+	public static int nextInt(int i) {
+		return rand.nextInt(i);
+	}
+
+	public static float nextFloat() {
+		return rand.nextFloat();
+	}
+
+	public static Zone randomPosInZone(Zone z) {
+		return new Zone(z.x - z.r + z.r * 2 * rand.nextFloat(), z.y - z.r + z.r * 2 * rand.nextFloat(),
+				z.r * rand.nextFloat() * .02f);
+	}
+
+	public static boolean percent(int percent) {
+		return rand.nextInt(100) < percent;
+	}
+
+	public static float vary(float f) { // 大部分时候不变，有极小机会变异,有极极小机会大变异，有极极极小机会大大大变异
+		int i = rand.nextInt(100);
+		if (i < 95)
+			return f;
+		float rate = .05f;
+		if (i > 97)
+			rate = .1f;
+		return (float) (f * ((1 - rate) + rand.nextFloat() * rate * 2));
+	}
+
+}