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improve outputs during calibration
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@nicolaspayette
nicolaspayette committed Dec 22, 2023
1 parent 565ef81 commit 82ad93f
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Showing 2 changed files with 79 additions and 88 deletions.
157 changes: 71 additions & 86 deletions POSEIDON/src/main/java/uk/ac/ox/oxfish/maximization/GenericOptimization.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,12 +31,18 @@
import java.io.*;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.time.Duration;
import java.time.Instant;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.List;
import java.util.logging.Logger;

import static org.apache.commons.lang3.time.DurationFormatUtils.formatDuration;

public class GenericOptimization extends SimpleProblemDouble implements Serializable {

private static final Logger logger = Logger.getLogger(GenericOptimization.class.getName());
private static final long serialVersionUID = 3621186016008983379L;
private String scenarioFile;

Expand Down Expand Up @@ -76,8 +82,10 @@ public GenericOptimization(
* create smaller optimization problem trying to climb within a small range of previously found optimal parameters
* this assumes however all parameters are simple
*/
public static void buildLocalCalibrationProblem(
final Path optimizationFile, final double[] originalParameters,
@SuppressWarnings("SameParameterValue")
static void buildLocalCalibrationProblem(
final Path optimizationFile,
final double[] originalParameters,
final String newCalibrationName,
final double range
) throws IOException {
Expand All @@ -99,8 +107,6 @@ public static void buildLocalCalibrationProblem(

}
yaml.dump(optimization, new FileWriter(optimizationFile.getParent().resolve(newCalibrationName).toFile()));


}

public List<OptimizationParameter> getParameters() {
Expand All @@ -111,18 +117,27 @@ public void setParameters(final List<OptimizationParameter> parameters) {
this.parameters = parameters;
}

public static Scenario buildScenario(final double[] x, final Path calibrationFile) throws FileNotFoundException {
final FishYAML yaml = new FishYAML();
final GenericOptimization optimization = yaml.loadAs(
new FileReader(calibrationFile.toFile()),
GenericOptimization.class
);
return buildScenario(x, Paths.get(optimization.getScenarioFile()).toFile(), optimization.getParameters());
static GenericOptimization fromFile(final Path calibrationFile) {
final FishYAML yamlReader = new FishYAML();
try (final FileReader fileReader = new FileReader(calibrationFile.toFile())) {
return yamlReader.loadAs(fileReader, GenericOptimization.class);
} catch (final IOException e) {
throw new IllegalStateException(e);
}
}

Scenario buildScenario(final double[] solution) {
try {
return buildScenario(solution, Paths.get(getScenarioFile()).toFile(), getParameters());
} catch (final FileNotFoundException e) {
throw new RuntimeException(e);
}
}

public static Scenario buildScenario(
final double[] x, final File scenarioFile,
final List<OptimizationParameter> parameterList
final double[] x,
final File scenarioFile,
final Iterable<? extends OptimizationParameter> parameterList
)
throws FileNotFoundException {
final FishYAML yaml = new FishYAML();
Expand All @@ -138,7 +153,6 @@ public static Scenario buildScenario(
);
parameter += optimizationParameter.size();
}

return scenario;
}

Expand All @@ -150,42 +164,6 @@ public void setScenarioFile(final String scenarioFile) {
this.scenarioFile = scenarioFile;
}

public static void saveCalibratedScenario(
final double[] optimalParameters, final Path optimizationYamlFile,
final Path pathWhereToSaveScenario
) {


try (final FileWriter fileWriter = new FileWriter(pathWhereToSaveScenario.toFile())) {
final GenericOptimization optimization = GenericOptimization.fromFile(optimizationYamlFile);
final Scenario scenario = GenericOptimization.buildScenario(
optimalParameters,
Paths.get(optimization.getScenarioFile()).toFile(),
optimization.getParameters()
);
new FishYAML().dump(scenario, fileWriter);
} catch (final IOException e) {
throw new IllegalStateException(e);
}
}

public static GenericOptimization fromFile(final Path calibrationFile) {
final FishYAML yamlReader = new FishYAML();
try (final FileReader fileReader = new FileReader(calibrationFile.toFile())) {
return yamlReader.loadAs(fileReader, GenericOptimization.class);
} catch (final IOException e) {
throw new IllegalStateException(e);
}
}

public Scenario buildScenario(final double[] solution) {
try {
return buildScenario(solution, Paths.get(getScenarioFile()).toFile(), getParameters());
} catch (final FileNotFoundException e) {
throw new RuntimeException(e);
}
}

/**
* Return the problem dimension.
*
Expand All @@ -200,82 +178,85 @@ public int getProblemDimension() {
}

/**
* Evaluate a double vector representing a possible problem solution as
* part of an individual in the EvA framework. This makes up the
* target function to be evaluated.
* Evaluate a double vector representing a possible problem solution as part of an individual in the EvA framework.
* This makes up the target function to be evaluated.
*
* @param x a double vector to be evaluated
* @return the fitness vector assigned to x as to the target function
*/
@SuppressWarnings("CallToPrintStackTrace")
@Override
public double[] evaluate(final double[] x) {

// read in and modify parameters
final Instant start = Instant.now();
final Scenario scenario;
try {
double error = 0;

for (int i = 0; i < runsPerSetting; i++) {
//read in and modify parameters
final Scenario scenario = buildScenario(x, Paths.get(scenarioFile).toFile(), parameters);
scenario = buildScenario(x, Paths.get(scenarioFile).toFile(), parameters);
} catch (final FileNotFoundException e) {
throw new RuntimeException(e);
}

//run the model
double error = 0;
for (int i = 0; i < runsPerSetting; i++) {
try {
// run the model
error += computeErrorGivenScenario(scenario, simulatedYears);

}

double finalError = error / (double) runsPerSetting;
if (maximization)
finalError = finalError * (-1);
if (!Double.isFinite(finalError)) {
System.out.println("was NAN!");
finalError = translateNANto;
} catch (final Exception e) {
e.printStackTrace();
error += translateNANto;
}
}
final Instant finish = Instant.now();

System.out.println(Arrays.toString(x) + " ---> " + finalError);
return new double[]{finalError};

} catch (final Exception e) {
e.printStackTrace();
System.out.println("was NAN!");
System.out.println(Arrays.toString(x) + " ---> " + translateNANto);
double finalError = error / (double) runsPerSetting;
if (maximization)
finalError = finalError * (-1);

return new double[]{translateNANto};
if (!Double.isFinite(finalError)) {
finalError = translateNANto;
}

logger.info(String.format(
"%n error: %.2f, runs: %d, duration: %s%n solution: %s",
finalError,
runsPerSetting,
formatDuration(Duration.between(start, finish).toMillis(), "HH:mm:ss"),
Arrays.toString(Arrays.stream(x).mapToObj(v -> String.format("%.2f", v)).toArray())
));
return new double[]{finalError};
}

public double computeErrorGivenScenario(
private double computeErrorGivenScenario(
final Scenario scenario,
final int simulatedYears
) {
final FishState model = new FishState(System.currentTimeMillis());

double error = 0;
model.setScenario(scenario);
model.start();
System.out.println("starting run");
while (model.getYear() < simulatedYears) {
model.schedule.step(model);
}
model.schedule.step(model);

//collect error
for (final DataTarget target : targets) {
error += target.computeError(model);
}
return error;
return targets.stream().mapToDouble(t -> t.computeError(model)).sum();
}

@SuppressWarnings("WeakerAccess")
public List<DataTarget> getTargets() {
return targets;
}

@SuppressWarnings("unused")
public void setTargets(final List<DataTarget> targets) {
this.targets = targets;
}

@SuppressWarnings("unused")
public int getRunsPerSetting() {
return runsPerSetting;
}

@SuppressWarnings("WeakerAccess")
public void setRunsPerSetting(final int runsPerSetting) {
this.runsPerSetting = runsPerSetting;
}
Expand All @@ -285,6 +266,7 @@ public void setRunsPerSetting(final int runsPerSetting) {
*
* @return Value for property 'simulatedYears'.
*/
@SuppressWarnings("unused")
public int getSimulatedYears() {
return simulatedYears;
}
Expand All @@ -294,6 +276,7 @@ public int getSimulatedYears() {
*
* @param simulatedYears Value to set for property 'simulatedYears'.
*/
@SuppressWarnings("unused")
public void setSimulatedYears(final int simulatedYears) {
this.simulatedYears = simulatedYears;
}
Expand Down Expand Up @@ -321,6 +304,7 @@ public void setMaximization(final boolean maximization) {
*
* @return Value for property 'translateNANto'.
*/
@SuppressWarnings("unused")
public double getTranslateNANto() {
return translateNANto;
}
Expand All @@ -330,6 +314,7 @@ public double getTranslateNANto() {
*
* @param translateNANto Value to set for property 'translateNANto'.
*/
@SuppressWarnings("unused")
public void setTranslateNANto(final double translateNANto) {
this.translateNANto = translateNANto;
}
Expand Down
10 changes: 8 additions & 2 deletions POSEIDON/src/main/java/uk/ac/ox/oxfish/model/scenario/EpoScenario.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
import java.time.Month;
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Logger;

import static uk.ac.ox.oxfish.geography.currents.CurrentPattern.*;
import static uk.ac.ox.oxfish.utility.Dummyable.maybeUseDummyData;
Expand All @@ -72,6 +73,7 @@ public abstract class EpoScenario<B extends LocalBiology>
"East", entry(new Coordinate(-89.5, 49.5), new Coordinate(-70.5, -49.5))
)
);
private static final Logger logger = Logger.getLogger(EpoScenario.class.getName());
private IntegerParameter targetYear = new IntegerParameter(2022);
private InputPath inputFolder = InputPath.of("inputs", "epo_inputs");
private final InputPath testInputFolder = inputFolder.path("tests");
Expand Down Expand Up @@ -105,7 +107,11 @@ public abstract class EpoScenario<B extends LocalBiology>
);
private AlgorithmFactory<ScenarioPopulation> fleet = new EmptyFleet();

public static int dayOfYear(final int year, final Month month, final int dayOfMonth) {
public static int dayOfYear(
final int year,
final Month month,
final int dayOfMonth
) {
return LocalDate.of(year, month, dayOfMonth).getDayOfYear();
}

Expand Down Expand Up @@ -200,7 +206,7 @@ public LocalDate getStartDate() {

@Override
public ScenarioEssentials start(final FishState fishState) {
System.out.println("Starting model...");
logger.info("Starting model...");

final NauticalMap nauticalMap =
getMapInitializer()
Expand Down

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