run evaluator at end of two-punch calibration

epo/src/main/java/uk/ac/ox/poseidon/epo/calibration/Calibrator.java

@@ -191,6 +191,7 @@ public Result calibrate(final GenericOptimization optimizationProblem) {
         saveCalibratedScenario(optimizationProblem, solution, calibratedScenarioFile);
         writeBounds(optimizationProblem, solution, boundsFile);
         return new Result(
+            runFolder,
             calibrationFile,
             calibratedScenarioFile,
             logFile,
@@ -390,26 +391,33 @@ public AbstractOptimizer apply(final int populationSize) {
     }
 
     public static class Result {
+        private final Path runFolder;
         private final Path calibrationFile;
         private final Path calibratedScenarioFile;
         private final Path logFile;
         private final Path boundsFile;
         private final double[] solution;
 
         public Result(
+            final Path runFolder,
             final Path calibrationFile,
             final Path calibratedScenarioFile,
             final Path logFile,
             final Path boundsFile,
             final double[] solution
         ) {
+            this.runFolder = runFolder;
             this.calibrationFile = calibrationFile;
             this.calibratedScenarioFile = calibratedScenarioFile;
             this.logFile = logFile;
             this.boundsFile = boundsFile;
             this.solution = solution;
         }
 
+        public Path getRunFolder() {
+            return runFolder;
+        }
+
         @SuppressWarnings("unused")
         public Path getCalibrationFile() {
             return calibrationFile;

epo/src/main/java/uk/ac/ox/poseidon/epo/calibration/Evaluator.java

@@ -27,6 +27,9 @@
 import uk.ac.ox.oxfish.maximization.YearlyResultsRowProvider;
 import uk.ac.ox.oxfish.model.FishState;
 import uk.ac.ox.oxfish.model.data.monitors.loggers.AbundanceFadAttractionEventObserver;
+import uk.ac.ox.oxfish.model.data.monitors.loggers.GlobalBiomassLogger;
+import uk.ac.ox.oxfish.model.data.monitors.loggers.PurseSeineActionsLogger;
+import uk.ac.ox.oxfish.model.data.monitors.loggers.PurseSeineTripLogger;
 import uk.ac.ox.oxfish.model.scenario.Scenario;
 import uk.ac.ox.oxfish.utility.yaml.FishYAML;
 
@@ -57,7 +60,7 @@ public class Evaluator implements JCommanderRunnable {
     @Parameter(names = "--track_fads_of_vessels")
     private Set<String> vesselsWhoseFadsToTrack = ImmutableSet.of(); //"1779", "453", "1552");
     @Parameter(names = {"-r", "--num-runs"})
-    private int numRuns = Math.min(16, getRuntime().availableProcessors());
+    private int numRuns = Math.min(8, getRuntime().availableProcessors());
     @Parameter(names = {"-y", "--years"})
     private int numYearsToRuns = 3;
     @Parameter(names = "--parallel")
@@ -115,7 +118,7 @@ public void run() {
                 scenario = loadScenario();
                 break;
             case "md":
-                scenario = new ScenarioExtractor(calibrationFolder)
+                scenario = new ScenarioExtractor(calibrationFolder, calibrationFolder.resolve(scenarioSource))
                     .getAndWriteToFile(CALIBRATED_SCENARIO_FILENAME);
                 break;
             default:
@@ -144,9 +147,9 @@ public void run() {
         }
 
         runner
-            /*.registerRowProvider("sim_action_events.csv", PurseSeineActionsLogger::new)
+            .registerRowProvider("sim_action_events.csv", PurseSeineActionsLogger::new)
             .registerRowProvider("sim_trip_events.csv", PurseSeineTripLogger::new)
-            .registerRowProvider("sim_global_biomass.csv", GlobalBiomassLogger::new)*/
+            .registerRowProvider("sim_global_biomass.csv", GlobalBiomassLogger::new)
             // turn the following line on or off as needed:
             // .registerRowProvider("death_events.csv", DeathEventsRowProvider::new)
             .run(numYearsToRuns, 1, runCounter);

epo/src/main/java/uk/ac/ox/poseidon/epo/calibration/ScenarioExtractor.java

@@ -37,45 +37,12 @@ public class ScenarioExtractor implements Supplier<Scenario> {
     private final Path calibrationLogFile;
     private final Path calibrationFolder;
 
-    public ScenarioExtractor(
-        final Path calibrationFolder
-    ) {
-        this(calibrationFolder, Paths.get("calibration_log.md"));
-    }
-
     public ScenarioExtractor(
         final Path calibrationFolder,
         final Path calibrationLogFile
     ) {
-        this.calibrationLogFile = calibrationLogFile;
         this.calibrationFolder = calibrationFolder;
-    }
-
-    public Scenario getAndWriteToFile(final String outputFileName) {
-        final Scenario scenario = get();
-        writeScenarioToFile(scenario, outputFileName);
-        return scenario;
-    }
-
-    @Override
-    public Scenario get() {
-        final Path calibrationFilePath = findCalibrationFile(calibrationFolder);
-        final Path logFilePath = calibrationFolder.resolve(calibrationLogFile);
-        final double[] solution = new SolutionExtractor(logFilePath).bestSolution().getKey();
-        final GenericOptimization optimization = GenericOptimization.fromFile(calibrationFilePath);
-        return makeScenario(optimization, solution);
-    }
-
-    private void writeScenarioToFile(
-        final Scenario scenario,
-        final String outputFileName
-    ) {
-        final File outputFile = calibrationFolder.resolve(outputFileName).toFile();
-        try (final Writer writer = new FileWriter(outputFile)) {
-            new FishYAML().dump(scenario, writer);
-        } catch (final IOException e) {
-            throw new IllegalStateException("Error while writing file: " + outputFile, e);
-        }
+        this.calibrationLogFile = calibrationLogFile;
     }
 
     private static Path findCalibrationFile(final Path folder) {
@@ -117,4 +84,31 @@ private static boolean isCalibrationFile(final Path path) {
             throw new IllegalStateException(e);
         }
     }
+
+    public Scenario getAndWriteToFile(final String outputFileName) {
+        final Scenario scenario = get();
+        writeScenarioToFile(scenario, outputFileName);
+        return scenario;
+    }
+
+    @Override
+    public Scenario get() {
+        final Path calibrationFilePath = findCalibrationFile(calibrationFolder);
+        final Path logFilePath = calibrationFolder.resolve(calibrationLogFile);
+        final double[] solution = new SolutionExtractor(logFilePath).bestSolution().getKey();
+        final GenericOptimization optimization = GenericOptimization.fromFile(calibrationFilePath);
+        return makeScenario(optimization, solution);
+    }
+
+    private void writeScenarioToFile(
+        final Scenario scenario,
+        final String outputFileName
+    ) {
+        final File outputFile = calibrationFolder.resolve(outputFileName).toFile();
+        try (final Writer writer = new FileWriter(outputFile)) {
+            new FishYAML().dump(scenario, writer);
+        } catch (final IOException e) {
+            throw new IllegalStateException("Error while writing file: " + outputFile, e);
+        }
+    }
 }

epo/src/main/java/uk/ac/ox/poseidon/epo/calibration/TwoPunchCalibration.java

@@ -153,7 +153,7 @@ public void run() {
             buildLocalCalibrationProblem(globalCalibratorResult.getSolution(), 0.2);
         localCalibrationProblem.setRunsPerSetting(2);
 
-        new Calibrator(
+        final Calibrator.Result localCalibratorResult = new Calibrator(
             "local",
             50,
             maxLocalCalls,
@@ -166,9 +166,10 @@ public void run() {
             new Calibrator.ParticleSwarmOptimizationGCPSOInitializer()
         ).calibrate(localCalibrationProblem);
 
-        // TODO run Evaluator and maybe sensitivity
-        // new Evaluator()
-
+        final Evaluator evaluator = new Evaluator();
+        evaluator.setCalibrationFolder(localCalibratorResult.getRunFolder());
+        evaluator.setScenarioSource(localCalibratorResult.getCalibratedScenarioFile());
+        evaluator.run();
     }
 
 }