added analysis scripts from matsim-episim-libs

pom.xml

@@ -20,6 +20,7 @@
     </licenses>
 
     <properties>
+<!--        <matsim.episim.version>2025.1</matsim.episim.version>-->
         <matsim.episim.version>2025.1</matsim.episim.version>
         <!--<matsim.version>12.0-2020w09-SNAPSHOT</matsim.version>-->
         <mainClass>org.matsim.run.RunEpisim</mainClass>
@@ -87,7 +88,6 @@
     </repositories>
 
     <dependencies>
-
         <dependency>
             <groupId>com.github.matsim-org</groupId>
             <artifactId>matsim-episim-libs</artifactId>

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

@@ -0,0 +1,52 @@
+package org.matsim.episim.analysis;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.jgrapht.graph.DefaultEdge;
+import org.jgrapht.graph.DefaultUndirectedWeightedGraph;
+import org.jgrapht.nio.graphml.GraphMLImporter;
+import org.matsim.api.core.v01.Id;
+import org.matsim.api.core.v01.population.Person;
+import org.matsim.core.utils.io.IOUtils;
+import picocli.CommandLine;
+
+import java.nio.file.Path;
+import java.util.concurrent.Callable;
+
+/**
+ * Executable class to analyze contacts events.
+ */
+@CommandLine.Command(
+		name = "analyzeGraph",
+		description = "Build contact graph from event file."
+)
+class AnalyzeContactGraph implements Callable<Integer> {
+
+	private static final Logger log = LogManager.getLogger(AnalyzeSnzData.class);
+
+	@CommandLine.Parameters(arity = "1")
+	private Path input;
+
+	public static void main(String[] args) {
+		System.exit(new CommandLine(new AnalyzeContactGraph()).execute(args));
+	}
+
+	@Override
+	public Integer call() throws Exception {
+
+		DefaultUndirectedWeightedGraph<Id<Person>, DefaultEdge> graph = new DefaultUndirectedWeightedGraph<>(DefaultEdge.class);
+
+		GraphMLImporter<Id<Person>, DefaultEdge> importer = new GraphMLImporter<>();
+		importer.setVertexFactory(Id::createPersonId);
+
+		importer.importGraph(graph, IOUtils.getBufferedReader(input.toString()));
+
+		log.info("Imported graph with {} edges and {} nodes", graph.edgeSet().size(), graph.vertexSet().size());
+
+
+		return 0;
+	}
+
+
+
+}

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

@@ -0,0 +1,191 @@
+/* *********************************************************************** *
+ * project: org.matsim.*
+ * Controler.java
+ *                                                                         *
+ * *********************************************************************** *
+ *                                                                         *
+ * copyright       : (C) 2007 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 java.io.BufferedWriter;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Objects;
+import java.util.concurrent.Callable;
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.matsim.core.utils.io.IOUtils;
+
+import com.google.common.base.Joiner;
+import it.unimi.dsi.fastutil.objects.Object2DoubleLinkedOpenHashMap;
+import it.unimi.dsi.fastutil.objects.Object2DoubleMap;
+import it.unimi.dsi.fastutil.objects.Object2IntLinkedOpenHashMap;
+import it.unimi.dsi.fastutil.objects.Object2IntMap;
+import picocli.CommandLine;
+
+/**
+ * @author: rewert
+ * This class reads the DIVI data for every day. The data is filtered for every Bundesland. 
+ */
+@CommandLine.Command(name = "analyzeDIVIData", description = "Analyze DIVI data.")
+public class AnalyzeDiviData implements Callable<Integer> {
+
+	private static final Logger log = LogManager.getLogger(AnalyzeDiviData.class);
+	private static final Joiner JOIN = Joiner.on("\t");
+
+	@CommandLine.Parameters(defaultValue = "../public-svn/matsim/scenarios/countries/de/episim/original-data/Fallzahlen/DIVI/Daily_reports/")
+	private Path inputFolder;
+
+	@CommandLine.Option(names = "--output", defaultValue = "../public-svn/matsim/scenarios/countries/de/episim/original-data/Fallzahlen/DIVI/")
+	private Path outputFolder;
+
+	public static void main(String[] args) {
+		System.exit(new CommandLine(new AnalyzeDiviData()).execute(args));
+	}
+
+	/**
+	 * This method searches all files with an certain name in a given folder.
+	 */
+	private static List<File> findInputFiles(File inputFolder) {
+		List<File> fileData = new ArrayList<File>();
+
+		for (File file : Objects.requireNonNull(inputFolder.listFiles())) {
+			if (file.getName().contains("DIVI"))
+				fileData.add(file);
+		}
+		return fileData;
+	}
+
+	@Override
+	public Integer call() throws Exception {
+
+		HashMap<Integer, String> bundeslandCodes = new HashMap<Integer, String>();
+		bundeslandCodes.put(1, "Schleswig-Holstein");
+		bundeslandCodes.put(2, "Hamburg");
+		bundeslandCodes.put(3, "Niedersachsen");
+		bundeslandCodes.put(4, "Bremen");
+		bundeslandCodes.put(5, "Nordrhein-Westfalen");
+		bundeslandCodes.put(6, "Hessen");
+		bundeslandCodes.put(7, "Rheinland-Pfalz");
+		bundeslandCodes.put(8, "Baden-Wuertenberg");
+		bundeslandCodes.put(9, "Bayern");
+		bundeslandCodes.put(10, "Saarland");
+		bundeslandCodes.put(11, "Berlin");
+		bundeslandCodes.put(12, "Brandenburg");
+		bundeslandCodes.put(13, "Mecklenburg-Vorpommern");
+		bundeslandCodes.put(14, "Sachsen");
+		bundeslandCodes.put(15, "Sachsen-Anhalt");
+		bundeslandCodes.put(16, "Thueringen");
+
+		log.info("Searching for files in the folder: " + inputFolder);
+		List<File> filesWithData = findInputFiles(inputFolder.toFile());
+		log.info("Amount of found files: " + filesWithData.size());
+
+		analyzeDataForCertainArea("Bundesland", filesWithData, bundeslandCodes);
+
+		log.info("Done!");
+
+		return 0;
+	}
+
+	private void analyzeDataForCertainArea(String area, List<File> filesWithData, HashMap<Integer, String> bundeslandCodes) throws IOException {
+
+		log.info("Analyze data for " + area);
+
+		Path outputFile = outputFolder.resolve(area + "-divi-processed_until.csv");
+
+		BufferedWriter writer = IOUtils.getBufferedWriter(outputFile.toString());
+		try {
+
+			JOIN.appendTo(writer, HeaderTable.values());
+			writer.write("\n");
+
+			int countingDays = 1;
+
+			// will contain the last parsed date
+			String dateString = "";
+
+			for (File file : filesWithData) {
+
+				Object2IntMap<Integer> sums_casesCovidICU = new Object2IntLinkedOpenHashMap<>();
+				Object2IntMap<Integer> sums_beatmet = new Object2IntLinkedOpenHashMap<>();
+				Object2DoubleMap<Integer> sums_freeBeds = new Object2DoubleLinkedOpenHashMap<>();
+				Object2DoubleMap<Integer> sums_occupiedBeds = new Object2DoubleLinkedOpenHashMap<>();
+
+				dateString = file.getName().split("_")[1];
+
+				CSVParser parse = CSVFormat.DEFAULT.withDelimiter(',').withFirstRecordAsHeader()
+						.parse(IOUtils.getBufferedReader(file.toString()));
+
+				for (CSVRecord record : parse) {
+
+					int bundeslandCode = Integer.parseInt(record.get("bundesland"));
+					int aktuellICU = Integer.parseInt(record.get("faelle_covid_aktuell"));
+					int aktuellBeatmet = Integer.parseInt(record.get("faelle_covid_aktuell_beatmet"));
+					double freeBeds = Double.parseDouble(record.get("betten_frei"));
+					double occupiedBeds = Double.parseDouble(record.get("betten_belegt"));
+
+					sums_casesCovidICU.mergeInt(bundeslandCode, aktuellICU, Integer::sum);
+					sums_beatmet.mergeInt(bundeslandCode, aktuellBeatmet, Integer::sum);
+					sums_freeBeds.mergeDouble(bundeslandCode, freeBeds, Double::sum);
+					sums_occupiedBeds.mergeDouble(bundeslandCode, occupiedBeds, Double::sum);
+
+				}
+
+				for (int bundeslandCode : sums_beatmet.keySet()) {
+
+					List<String> row = new ArrayList<>();
+					row.add(dateString);
+
+					row.add(String.valueOf(bundeslandCodes.get(bundeslandCode)));
+					row.add(String.valueOf(sums_casesCovidICU.getInt(bundeslandCode)));
+					row.add(String.valueOf(sums_beatmet.getInt(bundeslandCode)));
+					row.add(String.valueOf(sums_freeBeds.getDouble(bundeslandCode)));
+					row.add(String.valueOf(sums_occupiedBeds.getDouble(bundeslandCode)));
+
+					JOIN.appendTo(writer, row);
+					writer.write("\n");
+				}		
+
+				if (countingDays == 1 || countingDays % 5 == 0)
+					log.info("Finished day " + countingDays);
+
+				countingDays++;
+			}
+			writer.close();
+
+			Path finalPath = Path.of(outputFile.toString().replace("until", "until" + dateString));
+			Files.move(outputFile, finalPath, StandardCopyOption.REPLACE_EXISTING);
+
+			log.info("Write analyze of " + countingDays + " is writen to " + finalPath);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+
+	private enum HeaderTable {
+		date, Bundesland, covid_faelle_aktuell, covid_aktuell_beatmet, bettenFrei, bettenBelegt
+	}
+}

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

@@ -0,0 +1,109 @@
+/* *********************************************************************** *
+ * project: org.matsim.*
+ * Controler.java
+ *                                                                         *
+ * *********************************************************************** *
+ *                                                                         *
+ * copyright       : (C) 2007 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 org.matsim.api.core.v01.Id;
+import org.matsim.api.core.v01.population.Person;
+import org.matsim.api.core.v01.population.Population;
+import org.matsim.core.population.PopulationUtils;
+import org.matsim.core.utils.geometry.CoordUtils;
+import org.matsim.core.utils.io.IOUtils;
+import org.matsim.facilities.*;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * This class aims to analyze the age distribution within home facilities of the input population. It classifies the inhabitants of each home facility into age groups and dumps
+ * out a csv containing the number of people belonging to every age group, for every home facility.
+ */
+final class AnalyzeHomeFacilities {
+
+	private static final String INPUT_POPULATION = "D:/svn/shared-svn/projects/episim/matsim-files/snz/Berlin/episim-input/be_entirePopulation_noPlans.xml.gz";
+	private static final String OUTPUT_CSV = "D:/svn/shared-svn/projects/episim/matsim-files/snz/Berlin/processed-data/be_entirePopulation_noPlans_homeIdCounts.csv";
+	private static final String OUTPUT_FACILITIES = "D:/svn/shared-svn/projects/episim/matsim-files/snz/Berlin/processed-data/be_entirePopulation_noPlans_homeFacilities.xml";
+
+	private AnalyzeHomeFacilities() {
+	}
+
+	public static void main(String[] args) {
+
+		Population population = PopulationUtils.readPopulation(INPUT_POPULATION);
+		Map<String, List<Person>> map = mapPersonsToHomeId(population);
+
+		BufferedWriter writer = IOUtils.getBufferedWriter(OUTPUT_CSV);
+
+		ActivityFacilities facilities = FacilitiesUtils.createActivityFacilities();
+		ActivityFacilitiesFactory factory = facilities.getFactory();
+
+		try {
+			writer.write("homeId;0-2;2-14;15-18;19-63;63-80;over80");
+			for (String home : map.keySet()) {
+				List<Person> inhabitants = map.get(home);
+
+				double x = (double) inhabitants.get(0).getAttributes().getAttribute("homeX");
+				double y = (double) inhabitants.get(0).getAttributes().getAttribute("homeY");
+
+				facilities.addActivityFacility(factory.createActivityFacility(Id.create(home, ActivityFacility.class), CoordUtils.createCoord(x,y)));
+
+				writer.newLine();
+				long nrClass1 = inhabitants.stream().map(person -> (int) person.getAttributes().getAttribute("age")).filter(age -> age <= 2).count();
+				long nrClass2 = inhabitants.stream().map(person -> (int) person.getAttributes().getAttribute("age")).filter(age -> age > 2 && age <= 14).count();
+				long nrClass3 = inhabitants.stream().map(person -> (int) person.getAttributes().getAttribute("age")).filter(age -> age > 14 && age <= 18).count();
+				long nrClass4 = inhabitants.stream().map(person -> (int) person.getAttributes().getAttribute("age")).filter(age -> age > 18 && age <= 63).count();
+				long nrClass5 = inhabitants.stream().map(person -> (int) person.getAttributes().getAttribute("age")).filter(age -> age > 63 && age <= 80).count();
+				long nrClass6 = inhabitants.stream().map(person -> (int) person.getAttributes().getAttribute("age")).filter(age -> age > 80).count();
+
+				writer.write(home + ";" + nrClass1 + ";" + nrClass2 + ";" + nrClass3 + ";" + nrClass4 + ";" + nrClass5 + ";" + nrClass6);
+			}
+			writer.close();
+
+			new FacilitiesWriter(facilities).write(OUTPUT_FACILITIES);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+	}
+
+
+
+	private static Map<String, List<Person>> mapPersonsToHomeId(Population childrenPopulation) {
+		Map<String, List<Person>> homeIdToPersons = new HashMap<>();
+
+		for (Person person : childrenPopulation.getPersons().values()) {
+			String homeIdStr = person.getAttributes().getAttribute("homeId").toString();
+			if (homeIdToPersons.containsKey(homeIdStr)) {
+				homeIdToPersons.get(homeIdStr).add(person);
+			} else {
+				List<Person> list = new ArrayList<>();
+				list.add(person);
+				homeIdToPersons.put(homeIdStr, list);
+			}
+		}
+		return homeIdToPersons;
+	}
+
+
+}