created new output analysis which find the home location for each inf…

…ection. This is used to create infection location maps on covid-sim.

src/main/java/org/matsim/episim/EpisimReporting.java

@@ -612,7 +612,7 @@ void reporting(Map<String, InfectionReport> reports, int iteration, String date)
 
 		// Write all reports for each district
 		for (InfectionReport r : reports.values()) {
-			if (r.name.equals("total")) continue;
+//			if (r.name.equals("total")) continue;
 
 			String[] array = new String[InfectionsWriterFields.values().length];
 			array[InfectionsWriterFields.time.ordinal()] = Double.toString(r.time);

src/main/java/org/matsim/episim/analysis/InfectionHomeLocation.java

@@ -0,0 +1,218 @@
+ /* project: org.matsim.*
+  *                                                                         *
+  * *********************************************************************** *
+  *                                                                         *
+  * copyright       : (C) 2020 by the members listed in the COPYING,        *
+  *                   LICENSE and WARRANTY file.                            *
+  * email           : info at matsim dot org                                *
+  *                                                                         *
+  * *********************************************************************** *
+  *                                                                         *
+  *   This program is free software; you can redistribute it and/or modify  *
+  *   it under the terms of the GNU General Public License as published by  *
+  *   the Free Software Foundation; either version 2 of the License, or     *
+  *   (at your option) any later version.                                   *
+  *   See also COPYING, LICENSE and WARRANTY file                           *
+  *                                                                         *
+  * *********************************************************************** */
+
+ package org.matsim.episim.analysis;
+
+
+ import com.google.common.base.Joiner;
+ import com.google.inject.Inject;
+ import it.unimi.dsi.fastutil.doubles.DoubleArrayList;
+ import it.unimi.dsi.fastutil.doubles.DoubleList;
+ import it.unimi.dsi.fastutil.ints.*;
+ import it.unimi.dsi.fastutil.objects.Object2DoubleMap;
+ import it.unimi.dsi.fastutil.objects.Object2DoubleOpenHashMap;
+ import org.apache.logging.log4j.Level;
+ import org.apache.logging.log4j.LogManager;
+ import org.apache.logging.log4j.Logger;
+ import org.apache.logging.log4j.core.config.Configurator;
+ import org.matsim.api.core.v01.Coord;
+ import org.matsim.api.core.v01.Id;
+ import org.matsim.api.core.v01.IdMap;
+ import org.matsim.api.core.v01.Scenario;
+ import org.matsim.api.core.v01.population.Person;
+ import org.matsim.api.core.v01.population.Population;
+ import org.matsim.core.config.Config;
+ import org.matsim.core.config.ConfigUtils;
+ import org.matsim.core.population.PopulationUtils;
+ import org.matsim.core.utils.geometry.CoordUtils;
+ import org.matsim.core.utils.geometry.CoordinateTransformation;
+ import org.matsim.core.utils.geometry.transformations.TransformationFactory;
+ import org.matsim.episim.*;
+ import org.matsim.episim.events.*;
+ import org.matsim.episim.model.VirusStrain;
+ import org.matsim.episim.model.progression.AgeDependentDiseaseStatusTransitionModel;
+ import org.matsim.run.AnalysisCommand;
+ import picocli.CommandLine;
+
+ import java.io.BufferedWriter;
+ import java.io.IOException;
+ import java.nio.file.Files;
+ import java.nio.file.Path;
+ import java.time.LocalDate;
+ import java.util.*;
+ import java.util.stream.Collectors;
+
+
+ /**
+  * @author smueller
+  * Calcualte vaccination effectiveness from events
+  */
+ @CommandLine.Command(
+		 name = "infHomeLoc",
+		 description = "Finds the home location of infected persons."
+ )
+ public class InfectionHomeLocation implements OutputAnalysis {
+
+	 @CommandLine.Option(names = "--output", defaultValue = "./output/")
+	 private Path output;
+
+	 @CommandLine.Option(names = "--input", defaultValue = "/scratch/projects/bzz0020/episim-input")
+	 private String input;
+
+	 @CommandLine.Option(names = "--population-file", defaultValue = "/cologne_snz_entirePopulation_emptyPlans_withDistricts_25pt_split.xml.gz")
+	 private String populationFile;
+
+	 @CommandLine.Option(names = "--input-crs", defaultValue = "EPSG:25832")
+
+	 private String inputCRS;
+
+	 private static final Logger log = LogManager.getLogger(HospitalNumbersFromEvents.class);
+
+	 private final String DAY = "daysSinceStart";
+
+	 private final String HOME_LON = "home_lon";
+
+	 private final String HOME_LAT = "home_lat";
+
+	 @Inject
+	 private Scenario scenario;
+
+	 private Population population;
+	 public static void main(String[] args) {
+		 System.exit(new CommandLine(new InfectionHomeLocation()).execute(args));
+	 }
+
+	 @Override
+	 public Integer call() throws Exception {
+		 // logger configuration
+		 Configurator.setLevel("org.matsim.core.config", Level.WARN);
+		 Configurator.setLevel("org.matsim.core.controler", Level.WARN);
+		 Configurator.setLevel("org.matsim.core.events", Level.WARN);
+		 Configurator.setLevel("org.matsim.core.utils", Level.WARN);
+
+		 // check if events file exists
+		 if (!Files.exists(output)) {
+			 log.error("Output path {} does not exist.", output);
+			 return 2;
+		 }
+
+		 // read population
+		 population = PopulationUtils.readPopulation(input + populationFile);
+
+
+		 // Part 1: calculate home locs for each seed and save as csv
+		 AnalysisCommand.forEachScenario(output, pathToScenario -> {
+			 try {
+				 // analyzeOutput is where the post processing
+				 analyzeOutput(pathToScenario);
+
+			 } catch (IOException e) {
+				 log.error("Failed processing {}", pathToScenario, e);
+			 }
+		 });
+
+		 log.info("done");
+
+
+		 return 0;
+	 }
+
+	 @Override
+	 public void analyzeOutput(Path pathToScenario) throws IOException {
+
+		 if (scenario != null)
+			 population = scenario.getPopulation();
+
+		 String id = AnalysisCommand.getScenarioPrefix(pathToScenario);
+
+		 // builds the path to the output file that is produced by this analysis
+		 final Path csvPath = pathToScenario.resolve(id + "infectionLoc.csv");
+		 CoordinateTransformation coordinateTransformation = TransformationFactory.getCoordinateTransformation(inputCRS, TransformationFactory.WGS84);;
+
+
+		 // calculates home locations
+		 try (BufferedWriter bw = Files.newBufferedWriter(csvPath)) {
+			 Joiner joiner = Joiner.on(",");
+			 bw.write(joiner.join(DAY, HOME_LON, HOME_LAT));
+			 Handler handler = new Handler(population, coordinateTransformation);
+
+			 List<String> eventFiles = AnalysisCommand.forEachEvent(pathToScenario, s -> {
+			 }, true, handler);
+
+
+			 if (handler.days.size() != handler.lons.size() || handler.days.size() != handler.lats.size()) {
+				 throw new RuntimeException("all three datasets should have same size");
+			 }
+
+			 for (int i = 0; i < handler.days.size(); i++) {
+				 bw.newLine();
+				 bw.write(joiner.join(handler.days.getInt(i), handler.lons.get(i), handler.lats.get(i)));
+			 }
+		 }
+
+		 log.info("Calculated results for output {}", pathToScenario);
+
+	 }
+
+
+	 public static final class Handler implements EpisimInfectionEventHandler, EpisimInitialInfectionEventHandler{
+		 private final Population population;
+
+		 private final IntList days;
+		 private final List<Double> lats;
+		 private final List<Double> lons;
+
+		 private final CoordinateTransformation coordinateTransformation;
+
+
+		 Handler(Population population, CoordinateTransformation coordinateTransformation) {
+
+			 this.population = population;
+			 this.coordinateTransformation = coordinateTransformation;
+			 this.days = new IntArrayList();
+			 this.lats = new ArrayList<>();
+			 this.lons = new ArrayList<>();
+
+		 }
+
+
+		 @Override
+		 public void handleEvent(EpisimInfectionEvent event) {
+
+			 int day = (int) (event.getTime() / 86_400);
+			 days.add(day);
+
+			 double home_x =  (double) population.getPersons().get(event.getPersonId()).getAttributes().getAttribute("homeX");
+			 double home_y = (double) population.getPersons().get(event.getPersonId()).getAttributes().getAttribute("homeY");
+
+			 Coord coord = new Coord(home_x, home_y);
+			 Coord coordWgs84 = coordinateTransformation.transform(coord);
+
+			 lats.add(Math.round(coordWgs84.getY() * 10000.0) / 10000.0);
+			 lons.add(Math.round(coordWgs84.getX() * 10000.0) / 10000.0);
+
+		 }
+
+		 @Override
+		 public void handleEvent(EpisimInitialInfectionEvent event) {
+			 handleEvent(event.asInfectionEvent());
+		 }
+
+
+	 }
+ }

src/main/java/org/matsim/run/CreateBatteryForCluster.java

@@ -84,10 +84,10 @@ public class CreateBatteryForCluster<T> implements Callable<Integer> {
 	@CommandLine.Option(names = "--jvm-opts", description = "Additional options for JVM", defaultValue = "-Xms82G -Xmx82G -XX:+UseParallelGC")
 	private String jvmOpts;
 
-	@CommandLine.Option(names = "--setup", defaultValue = "org.matsim.run.batch.StarterBatchCologne")
+	@CommandLine.Option(names = "--setup", defaultValue = "org.matsim.run.batch.StarterBatchBrandenburg")
 	private Class<? extends BatchRun<T>> setup;
 
-	@CommandLine.Option(names = "--params", defaultValue = "org.matsim.run.batch.StarterBatchCologne$Params")
+	@CommandLine.Option(names = "--params", defaultValue = "org.matsim.run.batch.StarterBatchBrandenburg$Params")
 	private Class<T> params;
 
 	@SuppressWarnings("rawtypes")

src/main/java/org/matsim/run/batch/StarterBatchBrandenburg.java

@@ -6,6 +6,7 @@
 import org.matsim.episim.BatchRun;
 import org.matsim.episim.EpisimConfigGroup;
 import org.matsim.episim.VirusStrainConfigGroup;
+import org.matsim.episim.analysis.InfectionHomeLocation;
 import org.matsim.episim.analysis.OutputAnalysis;
 import org.matsim.episim.model.InfectionModelWithAntibodies;
 import org.matsim.run.RunParallel;
@@ -41,7 +42,7 @@ private SnzBrandenburgProductionScenario getBindings(Params params) {
 			.setInfectionModel(InfectionModelWithAntibodies.class)
 //			.setEasterModel(SnzBerlinProductionScenario.EasterModel.no)
 //			.setChristmasModel(SnzBerlinProductionScenario.ChristmasModel.no)
-			.setSample(1)
+			.setSample(25)
 			.build();
 	}
 
@@ -59,7 +60,8 @@ public Metadata getMetadata() {
 	 */
 	@Override
 	public Collection<OutputAnalysis> postProcessing() {
-		return List.of();
+		return List.of(new InfectionHomeLocation().withArgs("--output","./output/","--input","/scratch/projects/bzz0020/episim-input",
+			"--population-file", "br_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt_split.xml.gz"));
 	}
 
 	/*
@@ -91,10 +93,10 @@ public Config prepareConfig(int id, Params params) {
 	 */
 	public static final class Params {
 		// general
-		@GenerateSeeds(1)
+		@GenerateSeeds(5)
 		public long seed;
 
-		@Parameter({1.0, 2.0})
+		@Parameter({0.8, 0.9, 1.0, 1.1, 1.2})
 		public double thetaFactor;
 	}
 
@@ -108,7 +110,7 @@ public static void main(String[] args) {
 				RunParallel.OPTION_SETUP, StarterBatchBrandenburg.class.getName(),
 				RunParallel.OPTION_PARAMS, Params.class.getName(),
 				RunParallel.OPTION_TASKS, Integer.toString(8),
-				RunParallel.OPTION_ITERATIONS, Integer.toString(50),
+				RunParallel.OPTION_ITERATIONS, Integer.toString(20),
 				RunParallel.OPTION_METADATA
 		};
 

src/main/java/org/matsim/run/batch/UtilsJR.java

@@ -149,7 +149,7 @@ private static void producePlot(DateColumn records, DoubleColumn values, StringC
 	}
 
 
-    protected static void printInitialAntibodiesToConsole(Map<ImmunityEvent, Map<VirusStrain, Double>> initialAntibodies, boolean ignoreSuperfluous) {
+    public static void printInitialAntibodiesToConsole(Map<ImmunityEvent, Map<VirusStrain, Double>> initialAntibodies, boolean ignoreSuperfluous) {
 
 		List<ImmunityEvent> ignoredEvents = new ArrayList<>();
 		if (ignoreSuperfluous) {

src/main/resources/collect.sh

@@ -59,6 +59,9 @@ aggregate_run() {
 
     rm -r "${tmp:?}/$run"
 
+    gzip --best *.infectionLoc.csv
+    copy_output *.infectionLoc.csv.gz $tmp
+
     cd "$cwd" || exit
 }