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Optimise logging #94

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bc8defa
Tied the calculation of the current population size to the simulation…
RobertManningSmith Nov 21, 2025
ea8929e
Removed all streams from loggingHelperFunctions and replaced them wit…
RobertManningSmith Nov 21, 2025
b4cc249
removed streams from covid logging
RobertManningSmith Nov 21, 2025
fcee828
Removed Streams from demography logging
RobertManningSmith Nov 21, 2025
e195b30
Cleaned up imports on loggers
RobertManningSmith Nov 21, 2025
72a612d
Merge branch 'main' into optimise_logging
RobertManningSmith Nov 24, 2025
9f8f251
Found an error in methodology where new cases which hadn't had their …
RobertManningSmith Jan 27, 2026
f447160
Updated logging with more checks to not count unactivated cases
RobertManningSmith Jan 27, 2026
6eb5f49
remove unused imports
RobertManningSmith Feb 9, 2026
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1 change: 0 additions & 1 deletion Protecs/src/main/java/uk/ac/ucl/protecs/behaviours/Demography.java
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Expand Up @@ -17,7 +17,6 @@
import uk.ac.ucl.protecs.objects.hosts.Person.OCCUPATION;
import uk.ac.ucl.protecs.objects.hosts.Person.SEX;
import uk.ac.ucl.protecs.objects.locations.Household;
import uk.ac.ucl.protecs.objects.locations.Location;
import uk.ac.ucl.protecs.objects.locations.Workplace;
import uk.ac.ucl.protecs.sim.WorldBankCovid19Sim;

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1 change: 0 additions & 1 deletion Protecs/src/main/java/uk/ac/ucl/protecs/behaviours/MovementBehaviourFramework.java
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@@ -1,7 +1,6 @@
package uk.ac.ucl.protecs.behaviours;

import uk.ac.ucl.protecs.objects.hosts.Person;
import uk.ac.ucl.protecs.objects.hosts.Person.SEX;
import uk.ac.ucl.protecs.objects.locations.Location;
import uk.ac.ucl.protecs.sim.*;
import sim.engine.Steppable;
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4 changes: 3 additions & 1 deletion .../ac/ucl/protecs/behaviours/diseaseProgression/CoronavirusDiseaseProgressionFramework.java
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Expand Up @@ -262,7 +262,7 @@ public double next(Steppable s, double time) {
}
((Person) i.getHost()).infectNeighbours();
i.setAsympt();

i.setInfectionActive(true);
// determine when the agent will recover - this is
// only a matter of time in this case
if(time >= i.time_recovered){
Expand Down Expand Up @@ -306,6 +306,8 @@ public double next(Steppable s, double time) {
i.setSymptomatic();
i.setMild();
i.setEligibleForTesting();
i.setInfectionActive(true);

if (i.getHost().getDiseaseSet().containsKey(DISEASE.COVIDSPURIOUSSYMPTOM.key)) {
i.getHost().getDiseaseSet().get(DISEASE.COVIDSPURIOUSSYMPTOM.key).setAsympt();
}
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2 changes: 0 additions & 2 deletions Protecs/src/main/java/uk/ac/ucl/protecs/objects/diseases/CoronavirusInfection.java
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@@ -1,11 +1,9 @@
package uk.ac.ucl.protecs.objects.diseases;

import uk.ac.ucl.protecs.behaviours.diseaseProgression.CoronavirusDiseaseProgressionFramework.CoronavirusBehaviourNodeTitle;
import uk.ac.ucl.protecs.objects.hosts.Person;

import uk.ac.ucl.protecs.objects.locations.Household;
import uk.ac.ucl.protecs.objects.locations.Location;
import uk.ac.ucl.protecs.objects.locations.Workplace;
import uk.ac.ucl.protecs.sim.WorldBankCovid19Sim;
import uk.ac.ucl.protecs.sim.WorldBankCovid19Sim.DISEASE;

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14 changes: 12 additions & 2 deletions Protecs/src/main/java/uk/ac/ucl/protecs/objects/diseases/Disease.java
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Expand Up @@ -59,8 +59,9 @@ public abstract class Disease implements Steppable {
boolean hasRecoveredLogged = false;
boolean hasSusceptibleLogged = false;
boolean hasLogged = false;


boolean isInfectionActive = false;


// =============================================== relevant information on the host ==============================================================
public Host getHost() {return this.host;}

Expand Down Expand Up @@ -274,6 +275,15 @@ public void confirmLogged() {
}

public abstract String writeOut();


public boolean isInfectionActive() {
return isInfectionActive;
}

public void setInfectionActive(boolean isActive) {
this.isInfectionActive = isActive;
}

// =============================================== Disease testing ====================================================================================
public boolean isEligibleForTesting() {
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1 change: 0 additions & 1 deletion Protecs/src/main/java/uk/ac/ucl/protecs/objects/hosts/Water.java
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@@ -1,7 +1,6 @@
package uk.ac.ucl.protecs.objects.hosts;

import java.util.HashMap;
import java.util.HashSet;

import sim.engine.SimState;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.CholeraDiseaseProgressionFramework.CholeraBehaviourNodeInHumans;
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27 changes: 15 additions & 12 deletions Protecs/src/main/java/uk/ac/ucl/protecs/sim/WorldBankCovid19Sim.java
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@@ -1,22 +1,15 @@
package uk.ac.ucl.protecs.sim;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Random;
import java.util.stream.Collectors;

import uk.ac.ucl.protecs.behaviours.*;
import uk.ac.ucl.protecs.objects.diseases.CoronavirusInfection;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.DummyWaterborneDiseaseProgressionFramework;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.DummyNonCommunicableDiseaseProgressionFramework;
import uk.ac.ucl.protecs.objects.diseases.DummyNonCommunicableDisease;
import uk.ac.ucl.protecs.objects.diseases.DummyWaterborneDisease;
import uk.ac.ucl.protecs.objects.diseases.Disease;
import uk.ac.ucl.protecs.objects.diseases.DummyInfectiousDisease;
import uk.ac.ucl.protecs.objects.hosts.Person;
import uk.ac.ucl.protecs.objects.hosts.Person.OCCUPATION;
import uk.ac.ucl.protecs.objects.hosts.Person.SEX;
Expand All @@ -26,11 +19,10 @@
import uk.ac.ucl.protecs.objects.locations.Location;
import uk.ac.ucl.protecs.objects.locations.Workplace;
import uk.ac.ucl.protecs.sim.loggers.LoggingSetup;
import uk.ac.ucl.protecs.sim.loggers.DemographyLogging;
import uk.ac.ucl.protecs.sim.loggers.SocialContactsLogging;
import uk.ac.ucl.protecs.sim.loggers.SharedLoggingBins;
import uk.ac.ucl.protecs.sim.loggers.GeneratePopulationStats;
import uk.ac.ucl.protecs.sim.loggers.CovidLogging;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.SpuriousSymptomDiseaseProgressionFramework;
import uk.ac.ucl.protecs.behaviours.diseaseSpread.DummyNCDOnset;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.CholeraDiseaseProgressionFramework;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.CoronavirusDiseaseProgressionFramework;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.DummyInfectiousDiseaseProgressionFramework;
Expand Down Expand Up @@ -106,11 +98,20 @@ public class WorldBankCovid19Sim extends SimState {
public static int param_schedule_movement = 1;
public static int param_schedule_updating_locations = 5;
public static int param_schedule_infecting = 10;
public static int param_schedule_reporting = 100;
public static int param_schedule_calculate_statistics = 100;
public static int param_schedule_reporting = param_schedule_calculate_statistics + 1;
public static int param_schedule_COVID_SpuriousSymptoms = 98;
public static int param_schedule_COVID_Testing = 99;
public static int param_schedule_reporting_reset = param_schedule_reporting + 1;

public static HashMap<String, Integer> malePopulationSizes = new HashMap<String, Integer>();
public static HashMap<String, Integer> femalePopulationSizes = new HashMap<String, Integer>();
public static HashMap<String, Integer> allPopulationSizes = new HashMap<String, Integer>();

public static GeneratePopulationStats populationStats;
public static Map<SEX, SharedLoggingBins> popStatMap;


// Create a enum list of diseases modelled currently, these will be used to categorise any infections a person may get over the course of the simulation.
public enum DISEASE{
DUMMY_NCD("DUMMY_NCD"), DUMMY_INFECTIOUS("DUMMY_INFECTIOUS"), DUMMY_WATERBORNE("DUMMY_WATERBORNE"), COVID("COVID-19"), COVIDSPURIOUSSYMPTOM("COVID-19_SPURIOUS_SYMPTOM"),
Expand Down Expand Up @@ -442,7 +443,9 @@ public void step(SimState arg0) {
LoggingSetup.setupOutputFileNames(this);
// schedule the logging for the simulation
LoggingSetup.scheduleLoggers(this);

// =============================== Initialise tracking of population stats =======================================================
popStatMap = GeneratePopulationStats.buildStats(this);
GeneratePopulationStats.setUpAgeHashMapKeys(this);

// SCHEDULE LOCKDOWNS
Steppable lockdownTrigger = new Steppable() {
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5 changes: 2 additions & 3 deletions Protecs/src/main/java/uk/ac/ucl/protecs/sim/loadInfectionsInHumans.java
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Expand Up @@ -10,15 +10,12 @@
import uk.ac.ucl.protecs.behaviours.diseaseProgression.DummyNonCommunicableDiseaseProgressionFramework;
import uk.ac.ucl.protecs.behaviours.diseaseProgression.DummyWaterborneDiseaseProgressionFramework;
import uk.ac.ucl.protecs.behaviours.diseaseSpread.DummyNCDOnset;
import uk.ac.ucl.protecs.behaviours.diseaseSpread.DummyNCDOnset.causeDummyNCDs;
import uk.ac.ucl.protecs.objects.diseases.Cholera;
import uk.ac.ucl.protecs.objects.diseases.CoronavirusInfection;
import uk.ac.ucl.protecs.objects.diseases.DummyInfectiousDisease;
import uk.ac.ucl.protecs.objects.diseases.DummyNonCommunicableDisease;
import uk.ac.ucl.protecs.objects.diseases.DummyWaterborneDisease;
import uk.ac.ucl.protecs.objects.hosts.Person;
import uk.ac.ucl.protecs.objects.hosts.Water;
import uk.ac.ucl.protecs.objects.locations.Household;
import uk.ac.ucl.protecs.objects.locations.Location;
import uk.ac.ucl.protecs.sim.WorldBankCovid19Sim.DISEASE;

Expand Down Expand Up @@ -79,9 +76,11 @@ static void seed_infections_in_humans(WorldBankCovid19Sim world) {
CoronavirusInfection inf = new CoronavirusInfection(p, null, world.covidInfectiousFramework.getInfectedEntryPoint(l), world, 0);
if (inf.getBehaviourName().equals("asymptomatic")) {
inf.setAsympt();
inf.setInfectionActive(true);
}
else {
inf.setMild();
inf.setInfectionActive(true);
}
world.schedule.scheduleOnce(1, world.param_schedule_infecting, inf);
break;
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2 changes: 0 additions & 2 deletions Protecs/src/main/java/uk/ac/ucl/protecs/sim/loadInfectionsInOtherHosts.java
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Expand Up @@ -8,9 +8,7 @@
import uk.ac.ucl.protecs.behaviours.diseaseProgression.DummyWaterborneDiseaseProgressionFramework;
import uk.ac.ucl.protecs.objects.diseases.Cholera;
import uk.ac.ucl.protecs.objects.diseases.DummyWaterborneDisease;
import uk.ac.ucl.protecs.objects.hosts.Person;
import uk.ac.ucl.protecs.objects.hosts.Water;
import uk.ac.ucl.protecs.objects.locations.Household;
import uk.ac.ucl.protecs.objects.locations.Location;
import uk.ac.ucl.protecs.sim.WorldBankCovid19Sim.DISEASE;

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10 changes: 0 additions & 10 deletions Protecs/src/main/java/uk/ac/ucl/protecs/sim/loggers/CholeraLogging.java
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@@ -1,18 +1,8 @@
package uk.ac.ucl.protecs.sim.loggers;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

import sim.engine.SimState;
import sim.engine.Steppable;
import uk.ac.ucl.protecs.objects.diseases.Disease;
import uk.ac.ucl.protecs.objects.hosts.Person;
import uk.ac.ucl.protecs.objects.hosts.Person.OCCUPATION;
import uk.ac.ucl.protecs.objects.hosts.Person.SEX;
import uk.ac.ucl.protecs.sim.ImportExport;
import uk.ac.ucl.protecs.sim.WorldBankCovid19Sim;
import uk.ac.ucl.protecs.sim.WorldBankCovid19Sim.DISEASE;

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