/** * 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"); }
/** * 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 standard experiment for XOR emulation; is passed a name of a started genome and a * number of times can be execute this experiment; */ public static void Experiment1(String xFileName, int gens) { String fname_prefix = "c:\\jneat\\dati\\population.natural"; Population pop = null; StringTokenizer st; String curword; String xline; String fnamebuf; int gen; IOseq xFile; int id; int expcount = 0; String mask6 = "000000"; DecimalFormat fmt6 = new DecimalFormat(mask6); System.out.println("------ Start experiment 1 -------"); xFile = new IOseq(xFileName); boolean ret = xFile.IOseqOpenR(); if (ret) { try { System.out.println(" Start XOR experiment"); 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); System.out.println(" .create genome id " + id); Genome start_genome = new Genome(id, xFile); // backup this 'initial' genome (is only for test // if the read & write are correct start_genome.print_to_filename("c:\\jneat\\dati\\genome.readed"); for (expcount = 0; expcount < Neat.p_num_runs; expcount++) { System.out.println(" Spawned population off genome"); pop = new Population(start_genome, Neat.p_pop_size); System.out.print("\n\n Verifying Spawned Pop"); pop.verify(); System.out.print("\n"); for (gen = 1; gen <= gens; gen++) { System.out.print("\n---------------- E P O C H < " + gen + " >--------------"); fnamebuf = "g_" + fmt6.format(gen); boolean esito = xor_epoch(pop, gen, fnamebuf); } System.out.print("\n Population : innov num = " + pop.getCur_innov_num()); System.out.print("\n : cur_node_id = " + pop.getCur_node_id()); pop.print_to_filename(fname_prefix); } } 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"); }