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Commit 562f7472 authored by Lambert Patrick's avatar Lambert Patrick
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typing correction

parent 12575da1
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src/main/java/species/WriteEffectiveAndBiomassFluxes.java
View file @ 562f7472
......@@ -46,35 +46,42 @@ public class WriteEffectiveAndBiomassFluxes extends AquaNismsGroupProcess<Diadro
private String fileNameOutput = "effectiveBiomassFluxes";
private transient BufferedWriter bW;
private transient String sep=";";
private transient String sep = ";";
public static void main(String[] args) {
System.out.println((new XStream(new DomDriver()))
.toXML(new WriteEffectiveAndBiomassFluxes()));
System.out.println((new XStream(new DomDriver())).toXML(new WriteEffectiveAndBiomassFluxes()));
}
/* (non-Javadoc)
* @see fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.pilot.Pilot)
/*
* (non-Javadoc)
*
* @see
* fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.
* pilot.Pilot)
*/
@Override
public void initTransientParameters(Pilot pilot) {
super.initTransientParameters(pilot);
sep=";";
sep = ";";
}
@Override
public void doProcess(DiadromousFishGroup group) {
if (bW==null){
if (fileNameOutput != null){
new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
// prepare the output file
if (bW == null) {
if (fileNameOutput != null) {
new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
try {
bW = new BufferedWriter(new FileWriter(new File(group.getOutputPath()+
fileNameOutput +group.getSimulationId()+ ".csv")));
bW = new BufferedWriter(new FileWriter(
new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
bW.write("year"+sep+"type"+ sep+"originBasin" ); //create the field of the column
bW.write("year" + sep + "type" + sep + "originBasin"); // create the field of the column
for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
bW.write(sep + birthBasinName); // write each basin name in the file
bW.write(sep + birthBasinName); // write each basin name in the file
}
bW.write("\n");
......@@ -85,40 +92,46 @@ public class WriteEffectiveAndBiomassFluxes extends AquaNismsGroupProcess<Diadro
}
Time time = group.getEnvironment().getTime();
if (time.getSeason(pilot) == exportSeason & time.getYear(pilot) >= group.getMinYearToWrite()) {
//Create the map to get the biomass in each migration basin and birth basin
Map<String, Map<String, Long>> spawnerEffectivePerDestination = new HashMap<String, Map<String, Long>>(group.getEnvironment().getRiverBasinNames().length);
//Create the map to get the abundance in each migration and birth birth basin
Map<String, Map<String, Double>> spawnerBiomassPerDestination = new HashMap<String, Map<String, Double>>(group.getEnvironment().getRiverBasinNames().length);
// Create the map to get the biomass in each migration basin and birth basin
Map<String, Map<String, Long>> spawnerEffectivePerDestination = new HashMap<String, Map<String, Long>>(
group.getEnvironment().getRiverBasinNames().length);
// Create the map to get the abundance in each migration and birth birth basin
Map<String, Map<String, Double>> spawnerBiomassPerDestination = new HashMap<String, Map<String, Double>>(
group.getEnvironment().getRiverBasinNames().length);
// initialise maps with 0
for (String destinationName: group.getEnvironment().getRiverBasinNames()) {
Map<String, Long> spawnerEffectivePerOrigin = new HashMap<String, Long>(group.getEnvironment().getRiverBasinNames().length);
Map<String, Double> spawnerBiomassPerOrigin = new HashMap<String, Double>(group.getEnvironment().getRiverBasinNames().length);
for (String originName : group.getEnvironment().getRiverBasinNames()){
spawnerEffectivePerOrigin.put(originName, 0L);
for (String destinationName : group.getEnvironment().getRiverBasinNames()) {
Map<String, Long> spawnerEffectivePerOrigin = new HashMap<String, Long>(
group.getEnvironment().getRiverBasinNames().length);
Map<String, Double> spawnerBiomassPerOrigin = new HashMap<String, Double>(
group.getEnvironment().getRiverBasinNames().length);
for (String originName : group.getEnvironment().getRiverBasinNames()) {
spawnerEffectivePerOrigin.put(originName, 0L);
spawnerBiomassPerOrigin.put(originName, 0.);
}
spawnerEffectivePerDestination.put(destinationName,spawnerEffectivePerOrigin );
spawnerBiomassPerDestination.put(destinationName,spawnerBiomassPerOrigin );
spawnerEffectivePerDestination.put(destinationName, spawnerEffectivePerOrigin);
spawnerBiomassPerDestination.put(destinationName, spawnerBiomassPerOrigin);
}
for (RiverBasin destinationBasin: group.getEnvironment().getRiverBasins()) {
//compute the cumulative effective and biomass per birth basin
for (RiverBasin destinationBasin : group.getEnvironment().getRiverBasins()) {
// compute the cumulative effective and biomass per birth basin
if (destinationBasin.getFishs(group) != null) {
for (DiadromousFish fish : destinationBasin.getFishs(group)) {
if (fish.getStage() == Stage.MATURE) {
String originBasinName = fish.getBirthBasin().getName();
spawnerEffectivePerDestination.get(destinationBasin.getName()).
put(originBasinName, spawnerEffectivePerDestination.get(destinationBasin.getName()).get(originBasinName) + fish.getAmount() );
spawnerEffectivePerDestination.get(destinationBasin.getName()).put(originBasinName,
spawnerEffectivePerDestination.get(destinationBasin.getName()).get(originBasinName)
+ fish.getAmount());
double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount();
spawnerBiomassPerDestination.get(destinationBasin.getName()).
put(originBasinName, spawnerBiomassPerDestination.get(destinationBasin.getName()).get(originBasinName) + biomass );
spawnerBiomassPerDestination.get(destinationBasin.getName()).put(originBasinName,
spawnerBiomassPerDestination.get(destinationBasin.getName()).get(originBasinName)
+ biomass);
}
}
}
......@@ -126,29 +139,29 @@ public class WriteEffectiveAndBiomassFluxes extends AquaNismsGroupProcess<Diadro
try {
// write effective
for (String originBasinName: group.getEnvironment().getRiverBasinNames()) {
bW.write(time.getYear(pilot)+ sep + "effective" + sep + originBasinName );
for (String originBasinName : group.getEnvironment().getRiverBasinNames()) {
bW.write(time.getYear(pilot) + sep + "effective" + sep + originBasinName);
for (String destinationBasinName : group.getEnvironment().getRiverBasinNames()) {
bW.write(sep+spawnerEffectivePerDestination.get(destinationBasinName).get(originBasinName));
bW.write(sep + spawnerEffectivePerDestination.get(destinationBasinName).get(originBasinName));
}
// write an end-of-line
bW.write("\n");
}
// write biomass
for (String originBasinName: group.getEnvironment().getRiverBasinNames()) {
bW.write(time.getYear(pilot)+ sep + "biomass"+ sep + originBasinName );
for (String originBasinName : group.getEnvironment().getRiverBasinNames()) {
bW.write(time.getYear(pilot) + sep + "biomass" + sep + originBasinName);
for (String destinationBasinName : group.getEnvironment().getRiverBasinNames()) {
bW.write(sep+spawnerBiomassPerDestination.get(destinationBasinName).get(originBasinName));
bW.write(sep + spawnerBiomassPerDestination.get(destinationBasinName).get(originBasinName));
}
// write an end-of-line
bW.write("\n");
}
if (group.getPilot().getCurrentTime()== group.getPilot().getSimBegin()+group.getPilot().getSimDuration()-1) {
if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin()
+ group.getPilot().getSimDuration() - 1) {
bW.flush();
bW.close();
}
......@@ -158,4 +171,3 @@ public class WriteEffectiveAndBiomassFluxes extends AquaNismsGroupProcess<Diadro
}
}
}
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