[44] | 1 | package framsticks;
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| 2 |
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| 3 | import java.io.BufferedReader;
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| 4 | import java.io.BufferedWriter;
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| 5 | import java.io.File;
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[50] | 6 | import java.io.FileNotFoundException;
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[44] | 7 | import java.io.FileReader;
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| 8 | import java.io.FileWriter;
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[50] | 9 | import java.io.IOException;
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[44] | 10 | import java.io.InputStreamReader;
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| 11 |
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| 12 | import cecj.interaction.InteractionResult;
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| 13 | import cecj.interaction.RealValuedResult;
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| 14 | import cecj.utils.Pair;
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| 15 | import ec.EvolutionState;
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| 16 | import ec.util.Parameter;
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| 17 |
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| 18 | public class FramsticksUtils {
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| 19 |
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[57] | 20 | private static final String NEW_CMD = "%s \"getsimplest 1 %s\" -q";
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[44] | 21 | private static final String EVAL_CMD = "%s \"ex %s\" \"eval %s %s\" -q";
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[51] | 22 | private static final String MUTATE_CMD = "%s rnd mut -q < %s";
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[44] | 23 | private static final String XOVER_CMD = "%s rnd \"crossover %s %s\" -q";
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| 24 |
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| 25 | private static final String GENOTYPE_DESC = "org:\ngenotype:~\n%s~\n";
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| 26 | private static final String TEMPORARY_FILE_NAME = "temp.gen";
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| 27 |
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| 28 | private static final String P_DIRECTORY_PATH = "directory-path";
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| 29 | private static final String P_SCRIPTS_OUTPUT = "scripts-output";
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| 30 | private static final String P_SETTINGS = "settings-file";
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| 31 | private static final String P_WORKING_DIRECTORY = "working-directory";
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| 32 | private static final String P_EXPERIMENT_DEFINITION = "expdef";
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| 33 | private static final String P_EXECUTABLE_COMMAND = "executable-cmd";
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[48] | 34 | private static final String P_DEBUG = "debug";
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[44] | 35 |
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| 36 | private String directoryPath;
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| 37 | private String scriptsOutputPath;
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| 38 | private String settingsFile;
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| 39 | private String workingDirectory;
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| 40 | private String experimentDefinition;
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| 41 | private String executableCommand;
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[48] | 42 | private boolean debug;
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[44] | 43 |
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| 44 | private static FramsticksUtils instance;
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| 45 |
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| 46 | public synchronized static FramsticksUtils getInstance(final EvolutionState state) {
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| 47 | if (instance == null) {
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| 48 | instance = new FramsticksUtils();
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| 49 | instance.setup(state);
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| 50 | }
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| 51 | return instance;
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| 52 | }
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| 53 |
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| 54 | private void setup(final EvolutionState state) {
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| 55 | Parameter def = FramsticksDefaults.base();
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| 56 | directoryPath = state.parameters.getString(null, def.push(P_DIRECTORY_PATH));
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| 57 | if (directoryPath == null) {
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| 58 | state.output.fatal("No Framsticks directory specified", def.push(P_DIRECTORY_PATH));
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| 59 | }
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| 60 | scriptsOutputPath = state.parameters.getString(null, def.push(P_SCRIPTS_OUTPUT));
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| 61 | if (scriptsOutputPath == null) {
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| 62 | state.output.fatal("No scripts output file specified", def.push(P_SCRIPTS_OUTPUT));
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| 63 | }
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| 64 | settingsFile = state.parameters.getString(null, def.push(P_SETTINGS));
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| 65 | if (settingsFile == null) {
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| 66 | state.output.fatal("No settings file specified", def.push(P_SETTINGS));
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| 67 | }
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| 68 | workingDirectory = state.parameters.getString(null, def.push(P_WORKING_DIRECTORY));
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| 69 | if (workingDirectory == null) {
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| 70 | state.output.fatal("No working directory specified", def.push(P_WORKING_DIRECTORY));
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| 71 | }
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| 72 | experimentDefinition = state.parameters.getString(null, def.push(P_EXPERIMENT_DEFINITION));
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| 73 | if (experimentDefinition == null) {
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| 74 | state.output.fatal("No experiment definition specified", def
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| 75 | .push(P_EXPERIMENT_DEFINITION));
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| 76 | }
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| 77 | executableCommand = state.parameters.getString(null, def.push(P_EXECUTABLE_COMMAND));
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| 78 | if (executableCommand == null) {
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| 79 | state.output.fatal("No executable command specified", def.push(P_EXECUTABLE_COMMAND));
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| 80 | }
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[51] | 81 |
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[48] | 82 | debug = state.parameters.getBoolean(null, def.push(P_DEBUG), false);
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[44] | 83 | }
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| 84 |
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| 85 | private String executeCommand(String command) {
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[49] | 86 | if (debug) {
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| 87 | System.err.println("Executing command : " + command);
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| 88 | }
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[51] | 89 |
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[50] | 90 | String result = new String();
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[44] | 91 | try {
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| 92 | File f = new File(directoryPath);
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[62] | 93 |
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| 94 | String[] cmd;
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| 95 | String os = System.getProperty("os.name");
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| 96 | if(os.contains("Linux"))
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| 97 | {
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| 98 | cmd = new String[] { "/bin/bash", "-c", directoryPath + command };
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| 99 | }
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| 100 | else if(os.contains("Windows"))
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| 101 | {
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| 102 | cmd = new String[] { "cmd.exe", "/C", directoryPath + command };
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| 103 | }
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| 104 | else
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| 105 | {
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| 106 | throw new Exception("Not supported OS");
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| 107 | }
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| 108 |
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| 109 | Process p = Runtime.getRuntime().exec(cmd, null, f);
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| 110 |
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[44] | 111 | BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
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[50] | 112 | result = readInput(input);
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[44] | 113 | } catch (Exception ex) {
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| 114 | ex.printStackTrace();
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| 115 | }
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| 116 |
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[48] | 117 | if (debug) {
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[49] | 118 | System.err.println("Result : " + result);
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[48] | 119 | }
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[50] | 120 |
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[44] | 121 | return result;
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| 122 | }
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[62] | 123 |
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[44] | 124 | private void saveToFile(String filePath, String contents) {
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| 125 | try {
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| 126 | BufferedWriter output = new BufferedWriter(new FileWriter(filePath));
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| 127 | output.write(contents);
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| 128 | output.close();
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| 129 | } catch (Exception ex) {
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| 130 | ex.printStackTrace();
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| 131 | }
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| 132 | }
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| 133 |
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| 134 | private String readFromFile(String filePath) {
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[50] | 135 | String result = new String();
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[44] | 136 | try {
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| 137 | BufferedReader input = new BufferedReader(new FileReader(filePath));
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[50] | 138 | result = readInput(input);
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| 139 | } catch (FileNotFoundException e) {
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| 140 | e.printStackTrace();
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| 141 | }
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| 142 | return result;
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| 143 | }
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[51] | 144 |
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[50] | 145 | private String readInput(BufferedReader input) {
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| 146 | StringBuilder result = new StringBuilder();
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[51] | 147 |
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[50] | 148 | try {
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| 149 | String line;
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[44] | 150 | while ((line = input.readLine()) != null) {
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[50] | 151 | result.append(line + '\n');
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[44] | 152 | }
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| 153 | input.close();
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[50] | 154 | } catch (IOException ex) {
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[44] | 155 | ex.printStackTrace();
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| 156 | }
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| 157 |
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[51] | 158 | // Delete last newline character
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[50] | 159 | if (result.length() > 0) {
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| 160 | return result.substring(0, result.length() - 1);
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| 161 | } else {
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| 162 | return result.toString();
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| 163 | }
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[44] | 164 | }
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| 165 |
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| 166 | public float evaluateGenotype(String genotype, String fileName) {
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| 167 | String fileContents = String.format(GENOTYPE_DESC, genotype);
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| 168 | String filePath = workingDirectory + fileName;
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| 169 |
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| 170 | saveToFile(filePath, fileContents);
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| 171 | executeCommand(String.format(EVAL_CMD, executableCommand, experimentDefinition,
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| 172 | settingsFile, filePath));
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| 173 | String evaluation = readFromFile(scriptsOutputPath);
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| 174 |
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| 175 | return Float.parseFloat(evaluation.split("\t")[1]);
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| 176 | }
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| 177 |
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[59] | 178 | @Deprecated
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| 179 | public Pair<? extends InteractionResult> pseudoCoevolutionaryEvaluate(String candidate,
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| 180 | String test, String fileName) {
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[44] | 181 | float candidateResult = evaluateGenotype(candidate, fileName);
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| 182 | float testResult = evaluateGenotype(test, fileName);
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| 183 |
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| 184 | return new Pair<RealValuedResult>(new RealValuedResult(candidateResult),
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| 185 | new RealValuedResult(testResult));
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| 186 | }
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[61] | 187 |
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| 188 | private static float chasingBest = 2.0f;
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| 189 | private static float chasedBest = 2.0f;
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[44] | 190 |
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[59] | 191 | public Pair<? extends InteractionResult> coevolutionaryEvaluate(String candidate, String test,
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| 192 | String fileName) {
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| 193 | String fileContents = String.format(GENOTYPE_DESC, candidate) + "\n"
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| 194 | + String.format(GENOTYPE_DESC, test);
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| 195 | String filePath = workingDirectory + fileName;
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| 196 | saveToFile(filePath, fileContents);
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| 197 |
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| 198 | executeCommand(String.format(EVAL_CMD, executableCommand, experimentDefinition,
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| 199 | settingsFile, filePath));
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| 200 | String evaluation = readFromFile(scriptsOutputPath);
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[61] | 201 |
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| 202 | float candidateResult = 0;
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| 203 | float testResult = 0;
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[59] | 204 |
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[61] | 205 | try {
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| 206 |
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| 207 | String[] str = evaluation.split("\n");
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| 208 | candidateResult = Float.parseFloat(str[0].split("\t")[1]); //chasing
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| 209 | testResult = Float.parseFloat(str[1].split("\t")[1]); //chased
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| 210 |
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| 211 | chasingBest = ((candidateResult < chasingBest)?(candidateResult):(chasingBest));
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| 212 | chasedBest = ((chasedBest < testResult )?(chasedBest ):(testResult));
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| 213 |
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| 214 | System.out.printf("%7.4f %7.4f --> %7.4f %7.4f\n", candidateResult, chasingBest, testResult, chasedBest);
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| 215 | }
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| 216 | catch(Exception ex) {
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| 217 |
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| 218 | System.out.println(scriptsOutputPath + " in bad format. There must be 2 lines with results.");
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| 219 | }
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[59] | 220 |
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| 221 | return new Pair<RealValuedResult>(new RealValuedResult(candidateResult),
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| 222 | new RealValuedResult(testResult));
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| 223 | }
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| 224 |
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[44] | 225 | public String mutateGenotype(String genotype) {
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| 226 | String filePath = workingDirectory + TEMPORARY_FILE_NAME;
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| 227 | saveToFile(filePath, genotype);
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| 228 | return executeCommand(String.format(MUTATE_CMD, executableCommand, filePath));
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| 229 | }
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| 230 |
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| 231 | public String crossoverGenotypes(String genotype1, String genotype2) {
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| 232 | String filePath1 = workingDirectory + TEMPORARY_FILE_NAME;
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| 233 | String filePath2 = workingDirectory + "_" + TEMPORARY_FILE_NAME;
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| 234 | saveToFile(filePath1, genotype1);
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| 235 | saveToFile(filePath2, genotype2);
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| 236 | return executeCommand(String.format(XOVER_CMD, executableCommand, filePath1, filePath2));
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| 237 | }
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| 238 |
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[57] | 239 | public String getNewGenotype(int initializationType) {
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| 240 | return executeCommand(String.format(NEW_CMD, executableCommand, initializationType));
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[44] | 241 | }
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| 242 |
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| 243 | /*
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| 244 | * Sample usage :
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| 245 | */
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| 246 | /*
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| 247 | * public static void main(String[] args) { FramsticksUtils utils =
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| 248 | * FramsticksUtils.getInstance(); System.out.println(utils.evaluateGenotype("X", "halo1.gen"));
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| 249 | * System.out.println(utils.mutateGenotype("X"));
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| 250 | * System.out.println(utils.crossoverGenotypes("AX", "MX"));
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| 251 | * System.out.println(utils.getNewGenotype()); }
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| 252 | */
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| 253 | }
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