/**
* This is a test for viewing the result of mate or other operation can be executed from two
* genome the first genome is xFileNameA and second genome is xFileNameB
*/
public static void Experiment4(String xFileNameA, String xFileNameB) {
StringTokenizer st;
String curword;
String xline;
String fnamebuf;
IOseq xFile;
int id;
Genome gA = null;
Genome gB = null;
System.out.println("------ Start experiment 4 -------");
// read genome A
//
xFile = new IOseq(xFileNameA);
boolean ret = xFile.IOseqOpenR();
if (ret) {
try {
System.out.println(" Read genome-A");
xline = xFile.IOseqRead();
st = new StringTokenizer(xline);
// skip
curword = st.nextToken();
// id of genome can be readed
curword = st.nextToken();
id = Integer.parseInt(curword);
gA = new Genome(id, xFile);
// view genotype A
} catch (Throwable e) {
System.err.println(e + " : error during read " + xFileNameA);
}
xFile.IOseqCloseR();
} else System.err.print("\n : error during openA " + xFileNameA);
//
// read genome B
//
xFile = new IOseq(xFileNameB);
ret = xFile.IOseqOpenR();
if (ret) {
try {
System.out.println("\n Read genome-B");
xline = xFile.IOseqRead();
st = new StringTokenizer(xline);
// skip
curword = st.nextToken();
// id of genome can be readed
curword = st.nextToken();
id = Integer.parseInt(curword);
gB = new Genome(id, xFile);
// view genotype A
} catch (Throwable e) {
System.err.println(e + " : error during open " + xFileNameB);
}
xFile.IOseqCloseR();
} else System.err.print("\n : error during openB " + xFileNameB);
// Genome gC = gA.mate_multipoint(gB,3,0.6,0.3);
// Genome gC = gA.mate_multipoint_avg(gB,3,0.6,0.3);
System.out.println("\n ----genome-A----------");
gA.op_view();
System.out.println("\n ----genome-B----------");
gB.op_view();
// gA.DEBUGmate_singlepoint(gB,3);
System.out.println("\n ----genome-RESULT----------");
Genome gC = gA.mate_singlepoint(gB, 999);
// this step is for verify if correct genome
gC.verify();
// this step is for verify the phenotype created
gC.genesis(999);
// the step print the result genome
gC.op_view();
// for viewing the imagine of two genome input and the genome output
System.out.println("\n ******* D I S P L A Y G R A P H *********");
gA.View_mate_singlepoint(gB, 999);
System.out.println("\n *************************************************");
System.out.println("\n\n End of experiment");
}
/**
* This is a test for compute depth of genome and compute if has a path from two nodes (is a test
* for new version of method is_recur()) --> has_a_path(..) is not necessary for network
* simulation
*/
public static void Experiment5(String xFileName, int potin, int potout) {
StringTokenizer st;
String curword;
String xline;
String fnamebuf;
IOseq xFile;
int id;
Genome g1 = null;
Network net = null;
xFile = new IOseq(xFileName);
boolean ret = xFile.IOseqOpenR();
if (ret) {
try {
System.out.println("------ Start experiment 5 -------");
// read genome A
System.out.println(" Read start genome..");
xline = xFile.IOseqRead();
st = new StringTokenizer(xline);
// skip
curword = st.nextToken();
// id of genome can be readed
curword = st.nextToken();
id = Integer.parseInt(curword);
g1 = new Genome(id, xFile);
// generate a link mutation
g1.mutate_link_weight(Neat.p_weight_mut_power, 1.0, NeatConstant.GAUSSIAN);
// generate from genome the phenotype
g1.genesis(id);
// view genotype
g1.op_view();
// assign reference to genotype
net = g1.phenotype;
// compute first the 'teorical' depth
int lx = net.max_depth();
// compute . after, the 'pratical' depth passing
// the virtual depth;
int dx = net.is_stabilized(lx);
System.out.print("\n Max depth virtuale=" + lx);
System.out.print(", max depth reale=" + dx);
// search the inode
NNode inode = null;
NNode onode = null;
NNode curnode = null;
boolean rc = false;
int cnt = 0;
for (int ix = 0; (ix < net.allnodes.size()) && (cnt < 2); ix++) {
curnode = (NNode) net.allnodes.elementAt(ix);
if (curnode.node_id == potin) {
inode = curnode;
cnt++;
}
if (curnode.node_id == potout) {
onode = curnode;
cnt++;
}
}
// if exist , point to exitsting version
if (cnt < 2) {
System.out.print("\n ERROR :nodes in e/o out wrong's : retype!");
} else {
net.status = 0;
rc = net.has_a_path(inode, onode, 0, 30);
System.out.print("\n Result for example " + xFileName + " for ipotetic path ");
System.out.print(
"\n inode[" + potin + "] ---> onode[" + potout + "] is return code=" + rc);
System.out.print(", status = " + net.status);
}
// after reset all value of net
net.flush();
// ok : the propagation is completed
} catch (Throwable e) {
System.err.println(e + " : error during read " + xFileName);
}
xFile.IOseqCloseR();
} else System.err.print("\n : error during open " + xFileName);
System.out.println("\n\n End of experiment");
}
/**
* This is a test for compute depth of genome and trace all debug information for viewing all
* signal flowing is not necessary for network simulation
*/
public static void Experiment2(String xFileName) {
StringTokenizer st;
String curword;
String xline;
String fnamebuf;
IOseq xFile;
int id;
Genome g1 = null;
Network net = null;
System.out.println("------ Start experiment 2 -------");
xFile = new IOseq(xFileName);
boolean ret = xFile.IOseqOpenR();
if (ret) {
try {
System.out.println(" Start experiment 2");
System.out.println(" Read start genome..");
xline = xFile.IOseqRead();
st = new StringTokenizer(xline);
// skip
curword = st.nextToken();
// id of genome can be readed
curword = st.nextToken();
id = Integer.parseInt(curword);
g1 = new Genome(id, xFile);
// generate a link mutation
g1.mutate_link_weight(Neat.p_weight_mut_power, 1.0, NeatConstant.GAUSSIAN);
// generate from genome the phenotype
g1.genesis(id);
// view genotype
g1.op_view();
// assign reference to genotype
net = g1.phenotype;
// compute first the 'teorical' depth
int lx = net.max_depth();
// compute . after, the 'pratical' depth passing
// the virtual depth;
int dx = net.is_stabilized(lx);
// after reset all value of net
net.flush();
System.out.print("\n For genome : " + xFileName + " : max depth virtuale=" + lx);
System.out.print(", max depth reale=" + dx);
if (dx != lx) System.out.print("\n *ALERT* This net is NOT S T A B L E ");
net.flush();
double errorsum = 0.0;
double[] out = new double[4]; // The four outputs
int numnodes = 0;
int net_depth = 0; // The max depth of the network to be activated
int count = 0;
boolean success = false;
double in[] = {1.0, 1.0, 1.0};
count = 0;
// first activation from sensor to first next level of neurons
net.load_sensors(in);
// first activation....
success = net.activate();
// next activation while last level is reached !
// use depth to ensure relaxation
for (int relax = 1; relax <= dx; relax++) {
success = net.activate();
// System.out.print("\n -----TIME <"+relax+"> -----");
}
// ok : the propagation is completed
} catch (Throwable e) {
System.err.println(e + " : error during open " + xFileName);
}
xFile.IOseqCloseR();
} else System.err.print("\n : error during open " + xFileName);
System.out.println("\n\n End of experiment");
}