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Commit b42580a9 authored by patrick.lambert's avatar patrick.lambert
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with a exportToR of exchanges between catchments

parent 862b12ed
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src/main/java/analysis/EasyRun.java
View file @ b42580a9
......@@ -118,7 +118,7 @@ public class EasyRun {
public static void main(String[] args) throws Exception {
// blank are important
String[] batchArguments = ("-simDuration 40 -simBegin 1 -timeStepDuration 1 -RNGStatusIndex 1 "
String[] batchArguments = ("-simDuration 100 -simBegin 1 -timeStepDuration 1 -RNGStatusIndex 1 "
+ "-groups data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml" + " "
+ "-env data/input/northeastamerica/RIOBNneaBasins_Rjava.xml" + " "
+ "-observers data/input/northeastamerica/RIO_obs_empty.xml").split("\\ ");
......@@ -156,12 +156,13 @@ public class EasyRun {
System.out.println("\n== AnalyseLikelihoodOfPresence ==");
System.out.println(getSingleValueFromAquanismGroupProcess("processes.processesAtEnd.0.getLogLikelihood"));
// List truc = getAListFromAquanismGroupProcess("processes.processesAtEnd.0.getRecords");
// System.out.println(truc.get(0).toString());
// System.out.println(getAListFromAquanismGroupProcess("processes.processesAtEnd.1.getRecords"));
// System.out.println("\ngetMeanLastPercOfAut");
// System.out.println(Arrays.toString(getValuesFromEnvironment("getMeanLastPercOfAut")));
System.out.println("\n== ExportExchangeSBetweenCatchments ==");
String[][] exchangeSBetweenCatchments = getValuesFromAquanismGroupProcess("processes.processesEachStep.16.exportToR");
for (String[] record : exchangeSBetweenCatchments) {
for (String value : record)
System.out.print(value + "\t");
System.out.println();
}
}
}
src/main/java/analysis/ExportExchangesBetweenCatchments.java
View file @ b42580a9
......@@ -24,14 +24,18 @@ import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Serializable;
import java.util.Hashtable;
import java.util.Map;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.RIOBasinNetwork;
import environment.RiverBasin;
import environment.Time;
import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot;
import observer.ObservableRecord;
import species.DiadromousFish;
import species.DiadromousFishGroup;
......@@ -39,7 +43,7 @@ import species.DiadromousFishGroup;
/**
*
*/
public class ExportExchangeSBetweenCatchments extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
public class ExportExchangesBetweenCatchments extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
/**
*
......@@ -111,38 +115,60 @@ public class ExportExchangeSBetweenCatchments extends AquaNismsGroupProcess<Diad
private Season fluxesSeason = Season.SPRING;
private String fileNameOutput = "effectiveFluxes";
private transient RiverBasin[] riverBasins;
private transient BufferedWriter bW;
private transient String sep;
/**
* 1st key: migration basin 2nd key: natal basin 3nd key: year value : effective
*
* @unit
*/
private transient Map<RiverBasin, Map<RiverBasin, Map<Long, Double>>> exchanges;
public static void main(String[] args) {
System.out.println((new XStream(new DomDriver())).toXML(new ExportExchangeSBetweenCatchments()));
System.out.println((new XStream(new DomDriver())).toXML(new ExportExchangesBetweenCatchments()));
}
//
// @Override
// public void initTransientParameters(Pilot pilot) {
// super.initTransientParameters(pilot);
// // create output file if necessary
// if (fileNameOutput != null) {
// sep = ",";
//
// String outputPath = ((DiadromousFishGroup)
// pilot.getAquaticWorld().getAquaNismsGroupsList().get(0)).getOutputPath();
// String simulationId = ((DiadromousFishGroup) pilot.getAquaticWorld().getAquaNismsGroupsList().get(0))
// .getSimulationId();
// try {
// new File(outputPath + fileNameOutput).getParentFile().mkdirs();
// bW = new BufferedWriter(new FileWriter(new File(outputPath + fileNameOutput + simulationId + ".csv")));
//
// bW.write("year" + sep + "destinationBasin" + sep + "originBasin" + sep + "effective");
// bW.write("\n");
// } catch (IOException e) {
// e.printStackTrace();
// }
// }
//
// }
@Override
public void initTransientParameters(Pilot pilot) {
super.initTransientParameters(pilot);
riverBasins = ((RIOBasinNetwork) pilot.getAquaticWorld().getEnvironment()).getRiverBasins();
exchanges = new Hashtable<RiverBasin, Map<RiverBasin, Map<Long, Double>>>();
for (RiverBasin migrationBasin : riverBasins) {
Map<RiverBasin, Map<Long, Double>> natal_yearEffective = new Hashtable<RiverBasin, Map<Long, Double>>();
for (RiverBasin natalBasin : riverBasins) {
Map<Long, Double> year_effective = new Hashtable<Long, Double>();
for (Long year = yearStart; year <= yearEnd; year++) {
year_effective.put(year, 0.);
}
natal_yearEffective.put(natalBasin, year_effective);
}
exchanges.put(migrationBasin, natal_yearEffective);
}
// create output file if necessary
if (fileNameOutput != null) {
sep = ",";
String outputPath = ((DiadromousFishGroup) pilot.getAquaticWorld().getAquaNismsGroupsList().get(0)).getOutputPath();
String simulationId = ((RIOBasinNetwork) pilot.getAquaticWorld().getEnvironment()).getSimulationId();
try {
new File(outputPath + fileNameOutput).getParentFile().mkdirs();
bW = new BufferedWriter(new FileWriter(new File(outputPath + fileNameOutput + simulationId + ".csv")));
bW.write("year" + sep + "destinationBasin" + sep + "originBasin" + sep + "effective");
bW.write("\n");
} catch (IOException e) {
e.printStackTrace();
}
}
}
/*
......@@ -153,46 +179,30 @@ public class ExportExchangeSBetweenCatchments extends AquaNismsGroupProcess<Diad
@Override
public void doProcess(DiadromousFishGroup group) {
// write header in the file
if (bW == null) {
if (fileNameOutput != null) {
sep = ",";
try {
new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
bW = new BufferedWriter(new FileWriter(new File(
group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
bW.write("year" + sep + "migrationBasin" + sep + "natalBasin" + sep + "effective");
bW.write("\n");
} catch (IOException e) {
e.printStackTrace();
}
}
}
if (exchanges == null)
initTransientParameters(group.getPilot());
Time time = group.getEnvironment().getTime();
if (time.getYear(group.getPilot()) >= yearStart && time.getYear(group.getPilot()) <= yearEnd
&& time.getSeason(group.getPilot()) == fluxesSeason) {
String[] basinNames = group.getEnvironment().getRiverBasinNames();
long year = time.getYear(group.getPilot());
if (year >= yearStart && year <= yearEnd && time.getSeason(group.getPilot()) == fluxesSeason) {
// display headers on console
if (consoleDisplay) {
System.out.print("migration\\natal" + "\t");
for (String basinName : basinNames) {
System.out.print(basinName + "\t");
for (RiverBasin riverBasin : riverBasins) {
System.out.print(riverBasin.getName() + "\t");
}
System.out.println();
}
for (RiverBasin migrationBasin : group.getEnvironment().getRiverBasins()) {
for (RiverBasin migrationBasin : riverBasins) {
// /display data on console
if (consoleDisplay) {
System.out.print(migrationBasin.getName() + '\t');
}
for (String natalBasinName : basinNames) {
double effective = Math.round(migrationBasin.getSpawnerOrigins().getMeans().get(natalBasinName));
for (RiverBasin natalBasin : riverBasins) {
double effective = Math.round(migrationBasin.getSpawnerOrigins().getMeans().get(natalBasin.getName()));
if (consoleDisplay)
System.out.print(effective + "\t");
......@@ -200,13 +210,15 @@ public class ExportExchangeSBetweenCatchments extends AquaNismsGroupProcess<Diad
// write in the file
if (fileNameOutput != null) {
try {
bW.write(time.getYear(group.getPilot()) + sep + migrationBasin.getName() + sep + natalBasinName);
bW.write(year + sep + migrationBasin.getName() + sep + natalBasin.getName());
bW.write(sep + effective + "\n");
} catch (IOException e) {
e.printStackTrace();
}
}
// put in exhanges
exchanges.get(migrationBasin).get(natalBasin).put(year, effective);
}
if (consoleDisplay) {
System.out.println();
......@@ -224,4 +236,42 @@ public class ExportExchangeSBetweenCatchments extends AquaNismsGroupProcess<Diad
}
}
}
public String[][] exportToR() {
int i, j;
String[][] export = new String[riverBasins.length + 1][riverBasins.length + 1];
// headers
export[0][0] = "migrationBasin";
j = 1;
for (RiverBasin natalBasin : riverBasins) {
export[0][j] = natalBasin.getName();
j++;
}
i = 1;
for (RiverBasin migrationBasin : riverBasins) {
export[i][0] = migrationBasin.getName();
j = 1;
for (RiverBasin natalBasin : riverBasins) {
Map<Long, Double> year_effective = exchanges.get(migrationBasin).get(natalBasin);
int n = 0;
double sum = 0;
for (Double effective : year_effective.values()) {
if (Double.isFinite(effective)) {
n++;
sum += effective;
}
}
export[i][j] = String.valueOf(Math.round(10. * sum / n) / 10);
j++;
}
i++;
}
return export;
}
}
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