Make the test - test passes

poseidon-fisheries · Oct 6, 2023 · 8396718 · 8396718
1 parent 7d109a3
commit 8396718
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Showing 3 changed files with 81 additions and 5 deletions.
diff --git a/POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/complicated/RecruitmentBySpawningBiomass.java b/POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/complicated/RecruitmentBySpawningBiomass.java
@@ -36,7 +36,7 @@ public class RecruitmentBySpawningBiomass extends YearlyRecruitmentProcess {
     /**
      * the number of recruits you'd get in a "virgin" state.
      */
-    private final int virginRecruits;
+    private final long virginRecruits;
 
     /**
      * logistic growth parameter
@@ -67,7 +67,7 @@ public class RecruitmentBySpawningBiomass extends YearlyRecruitmentProcess {
 
 
     public RecruitmentBySpawningBiomass(
-        final int virginRecruits,
+        final long virginRecruits,
         final double steepness,
         final double cumulativePhi, final boolean addRelativeFecundityToSpawningBiomass, final double[] maturity,
         final double[] relativeFecundity, final int femaleSubdivision, final boolean recruitEveryDay
@@ -95,7 +95,7 @@ public RecruitmentBySpawningBiomass(
 
 
     public RecruitmentBySpawningBiomass(
-        final int virginRecruits,
+        final long virginRecruits,
         final double steepness,
         final double cumulativePhi, final boolean addRelativeFecundityToSpawningBiomass,
         final Function<Species, double[]> maturity,
@@ -131,6 +131,7 @@ public double computeYearlyRecruitment(
         final Species species, final Meristics meristics, final StructuredAbundance abundance
     ) {
 
+
         //you need to sum up the spawning biomass of the fish:
         final int cohorts = meristics.getNumberOfBins();
 
@@ -193,7 +194,7 @@ public void addNoise(final NoiseMaker noiseMaker) {
      *
      * @return Value for property 'virginRecruits'.
      */
-    public int getVirginRecruits() {
+    public long getVirginRecruits() {
         return virginRecruits;
     }
 

diff --git a/POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/tuna/RecruitmentProcessesFactory.java b/POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/tuna/RecruitmentProcessesFactory.java
@@ -55,7 +55,9 @@ public class RecruitmentProcessesFactory
                         );
                         final float r0 = record.getFloat("R0");
                         return entry(species, new RecruitmentBySpawningBiomass(
-                            Math.round(r0),
+                            (long)(r0),
+
+
                             record.getDouble("h_steepness"),
                             record.getDouble("virgin_ssb") / r0,
                             false,

diff --git a/POSEIDON/src/test/java/uk/ac/ox/oxfish/biology/tuna/EpoRecruitment2022Test.java b/POSEIDON/src/test/java/uk/ac/ox/oxfish/biology/tuna/EpoRecruitment2022Test.java
@@ -0,0 +1,73 @@
+package uk.ac.ox.oxfish.biology.tuna;
+
+import org.apache.commons.lang3.ArrayUtils;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import uk.ac.ox.oxfish.biology.Species;
+import uk.ac.ox.oxfish.geography.currents.CurrentPatternMapSupplier;
+import uk.ac.ox.oxfish.model.FishState;
+import uk.ac.ox.oxfish.model.scenario.EpoAbundanceScenario;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class EpoRecruitment2022Test {
+
+    @Test
+    public void testRunBiologyOnlyScenario() {
+        final EpoAbundanceScenario scenario = new EpoAbundanceScenario();
+/*        ((AbundanceMortalityProcessFromFileFactory)
+            ((ScheduledAbundanceProcessesFactory) scenario.getBiologicalProcesses()
+                .getScheduledProcesses())
+                .getAbundanceMortalityProcess())
+            .setMortalityFile(scenario.testFolder().path("mortality_BP.csv"));*/
+        final FishState fishState = new FishState();
+        fishState.setScenario(scenario);
+        scenario.getFadMap().setCurrentPatternMapSupplier(CurrentPatternMapSupplier.EMPTY);
+
+        fishState.start();
+
+        System.out.println("SeaTiles: " + fishState.getMap().getAllSeaTiles().size());
+        final List<Species> specieses = fishState.getSpecies();
+
+        final Species BET = fishState.getSpecies("Bigeye tuna");
+        final Species SKJ = fishState.getSpecies("Skipjack tuna");
+        final Species YFT = fishState.getSpecies("Yellowfin tuna");
+        final double[][] initialAbundanceBET = fishState.getTotalAbundance(BET);
+        final double[][] initialAbundanceSKJ = fishState.getTotalAbundance(SKJ);
+        final double[][] initialAbundanceYFT = fishState.getTotalAbundance(YFT);
+
+
+//        System.out.println("breakpoint");
+
+
+        final int[] checkDays = {90, 181, 273};
+
+        do {
+
+            if (ArrayUtils.contains(checkDays, fishState.getStep())) {
+//                System.out.println(fishState.getStep() + " " + fishState.getTotalBiomass(fishState.getSpecies(
+ //                   "Bigeye tuna")) / 1000);
+                final double[][] totalAbundanceBET = fishState.getTotalAbundance(BET);
+                final double[][] totalAbundanceSKJ = fishState.getTotalAbundance(SKJ);
+                final double[][] totalAbundanceYFT = fishState.getTotalAbundance(YFT);
+//                System.out.println(fishState.getStep() + "BET[0]= " + (totalAbundanceBET[0][0]+totalAbundanceBET[1][0]));
+ //               System.out.println(fishState.getStep() + "SKJ[0]= " + (totalAbundanceSKJ[0][0]+totalAbundanceSKJ[1][0]));
+//                System.out.println(fishState.getStep() + "YFT[0]= " + (totalAbundanceYFT[0][0]+totalAbundanceYFT[1][0]));
+
+
+                assertEquals(totalAbundanceBET[0][0]+totalAbundanceBET[1][0], 7653070,10);
+                assertEquals((totalAbundanceSKJ[0][0]+totalAbundanceSKJ[1][0])/100000, 154464,10);
+                assertEquals(totalAbundanceYFT[0][0]+totalAbundanceYFT[1][0], 299183000,10);
+
+
+
+//                System.out.println("breakpoint");
+
+            }
+            fishState.schedule.step(fishState);
+        } while (fishState.getYear() < 1);
+    }
+}