moia-oss
diff --git a/‎contribs/application/src/main/java/org/matsim/application/MATSimApplication.java
+43-12 b/‎contribs/application/src/main/java/org/matsim/application/MATSimApplication.java
+43-12
diff --git a/‎contribs/application/src/main/java/org/matsim/application/ShowGUI.java
+7 b/‎contribs/application/src/main/java/org/matsim/application/ShowGUI.java
+7
diff --git a/‎contribs/application/src/main/java/org/matsim/application/analysis/noise/MergeNoiseOutput.java
+52-45 b/‎contribs/application/src/main/java/org/matsim/application/analysis/noise/MergeNoiseOutput.java
+52-45
@@ -153,7 +153,14 @@ public Integer call() throws Exception {
 
 		// load config if not present yet.
 		if (config == null) {
-			config = loadConfig(Objects.requireNonNull( configPath, "No default scenario location given" ).getAbsoluteFile().toString() );
+			String path = Objects.requireNonNull( configPath, "No default scenario location given" ).getAbsoluteFile().toString();
+			List<ConfigGroup> customModules = getCustomModules();
+
+			final Config config1 = ConfigUtils.loadConfig(path, customModules.toArray(new ConfigGroup[0] ) );
+			Config prepared = prepareConfig( config1 );
+
+			config = prepared != null ? prepared : config1;
+			// (The above lines of code come from inlining so maybe it happened there: I cannot see how prepared could be null but config1 not except if user code returns null which I would consider a bug.  kai, aug'24)
 		} else {
 			Config tmp = prepareConfig(config);
 			config = tmp != null ? tmp : config;
@@ -306,15 +313,6 @@ protected final void addRunOption(Config config, String option) {
 		addRunOption(config, option, "");
 	}
 
-	private Config loadConfig(String path) {
-		List<ConfigGroup> customModules = getCustomModules();
-
-		final Config config = ConfigUtils.loadConfig(path, customModules.toArray(new ConfigGroup[0]));
-		Config prepared = prepareConfig(config);
-
-		return prepared != null ? prepared : config;
-	}
-
 	@Override
 	public String defaultValue(CommandLine.Model.ArgSpec argSpec) throws Exception {
 		Object obj = argSpec.userObject();
@@ -374,8 +372,39 @@ public static void run(Class<? extends MATSimApplication> clazz, String... args)
 	}
 
 	/**
-	 * Convenience method to run a scenario from code or automatically with gui when desktop application is detected.
-	 * This method may also be used to predefine some default arguments.
+	 * <p>Convenience method to run a scenario from code or automatically with gui when desktop application is detected.
+	 * This method may also be used to predefine some default arguments.</p>
+	 *
+	 * <p>With respect to args it looks like arguments are treated in the following sequence (programmed in the run method):
+	 * <ul>
+	 *         <li>ConfigUtils.loadConfig without args</li>
+	 *         <li>prepareConfig which is usually overwritten</li>
+	 *         <li>config options from some yaml file which can be provided as a command line option</li>
+	 *         <li>config options on command line </li>
+	 * </ul></p>
+	 *
+	 * <p>defaultArgs could be used to provide defaults when calling this method here; they would go in addition to what is coming in from "upstream" which is typically the command line.</p>
+	 *
+	 * <p>There are many execution paths that can be reached from this class, but a typical one for matsim-scenarios seems to be:<ul>
+	 * <li> This method runs MATSimApplication.run( TheScenarioClass.class , args ).</li>
+	 * <li> That run class will instantiate an instance of TheScenarioClass (*), then do some args consistenty checking, then call the piccoli execute method. </li>
+	 * <li> The piccoli execute method will essentially call the "call" method of MATSimApplication. </li>
+	 * <li> I think that in the described execution path, this.config in that call method will initially be null.  (The ctor of MATSimApplication was called via reflection at (*); I think that it was called there without a config argument.) </li>
+	 * <li> This call method then will do: <ul>
+	 * 		<li> getCustomModules() (which is empty by default but can be overriden) </li>
+	 * 		<li>ConfigUtils.loadConfig(...) _without_ passing on the args</li>
+	 * 		<li>prepareConfig(...) (which is empty by default but is typically overridden, in this case in OpenBerlinScenario).  In our case, this sets the typical scoring params and the typical replanning strategies.
+	 * 		<li>next one can override the config from some yaml file provided as a commandline option
+	 * 		<li> next args is parsed and set
+	 * 		<li>then some standard CL options are detected and set
+	 * 		<li>then createScenario(config) is called (which can be overwritten but is not)
+	 * 		<li>then prepareScenario(scenario) is called (which can be overwritten but is not)
+	 * 		<li>then a standard controler is created from scenario
+	 * 		<li>then prepareControler is called which can be overwritten
+	 * 	</ul>
+	 * 	</ul>
+	 * 	</p>
+	 *
 	 * @param clazz class of the scenario to run
 	 * @param args pass arguments from the main method
 	 * @param defaultArgs predefined default arguments that will always be present
@@ -384,6 +413,8 @@ public static void runWithDefaults(Class<? extends MATSimApplication> clazz, Str
 
 		if (ApplicationUtils.isRunFromDesktop() && args.length == 0) {
 
+			System.setProperty("MATSIM_GUI_DESKTOP", "true");
+
 			if (defaultArgs.length > 0) {
 				String value = String.join(ARGS_DELIMITER, defaultArgs);
 				System.setProperty("MATSIM_GUI_ARGS", value);
 
@@ -40,6 +40,13 @@ public Integer call() throws Exception {
 
         Gui gui = f.get();
 
+		// Set the current working directory to be used in the gui, when run from the command line
+		// If the gui is run from desktop, the working directory is not overwritten
+
+		// Assumption is that starting something from command line, the user expects that the working directory remains the same
+		if (!System.getProperty("MATSIM_GUI_DESKTOP", "false").equals("true"))
+			gui.setWorkingDirectory(new File(""));
+
         while (gui.isShowing())
             Thread.sleep(250);
 
 
@@ -13,11 +13,14 @@
 import org.apache.avro.file.DataFileWriter;
 import org.apache.avro.io.DatumWriter;
 import org.apache.avro.specific.SpecificDatumWriter;
+import org.apache.commons.lang.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.matsim.api.core.v01.Coord;
 import org.matsim.application.avro.XYTData;
+import org.matsim.core.config.Config;
 import org.matsim.core.utils.io.IOUtils;
+import org.matsim.core.utils.misc.Time;
 import tech.tablesaw.api.*;
 import tech.tablesaw.io.csv.CsvReadOptions;
 
@@ -29,7 +32,8 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.*;
-import java.util.stream.Collectors;
+
+import static org.geotools.gml3.v3_2.GML.coordinateSystem;
 
 /**
  * Merges noise data from multiple files into one file.
@@ -44,17 +48,16 @@ final class MergeNoiseOutput {
 	 */
 	private static final boolean CREATE_CSV_FILES = false;
 
-	private final String[] inputPath;
 	private final Path outputDirectory;
 	private final String crs;
-	private final String[] labels = {"immission", "emission"};
 	private final int minTime = 3600;
 	private int maxTime = 24 * 3600;
 
-	MergeNoiseOutput(String[] inputPath, Path outputDirectory, String crs) {
-		this.inputPath = inputPath;
-		this.outputDirectory = outputDirectory;
-		this.crs = crs;
+	private final Map<String,Float> totalReceiverPointValues = new HashMap<>();
+
+	MergeNoiseOutput(Path path, String coordinateSystem ) {
+		this.outputDirectory = path;
+		this.crs = coordinateSystem;
 	}
 
 	/**
@@ -90,25 +93,9 @@ public void setMaxTime(int maxTime) {
 	 * Merges noise data from multiple files into one file.
 	 */
 	public void run() {
-
-		// Loop over all paths
-		for (int i = 0; i < labels.length; i++) {
-
-			// Select the correct method based on the label
-			switch (labels[i]) {
-				case "immission" -> {
-					if (CREATE_CSV_FILES) {
-						mergeImmissionsCSV(inputPath[i], labels[i]);
-					} else {
-						mergeImissions(inputPath[i], labels[i]);
-					}
-
-				}
-				case "emission" -> mergeEmissions(inputPath[i], labels[i]);
-				default -> log.warn("Unknown path: " + inputPath[i]);
-			}
-
-		}
+		mergeReceiverPointData(outputDirectory + "/immissions/", "immission");
+		mergeReceiverPointData(outputDirectory + "/damages_receiverPoint/", "damages_receiverPoint");
+		mergeLinkData(outputDirectory.toString() + "/emissions/", "emission");
 	}
 
 	/**
@@ -118,6 +105,7 @@ public void run() {
 	 * @param output
 	 */
 	private void writeAvro(XYTData xytData, File output) {
+		log.info(String.format("Start writing avro file to %s", output.toString() ));
 		DatumWriter<XYTData> datumWriter = new SpecificDatumWriter<>(XYTData.class);
 		try (DataFileWriter<XYTData> dataFileWriter = new DataFileWriter<>(datumWriter)) {
 			dataFileWriter.setCodec(CodecFactory.deflateCodec(9));
@@ -128,7 +116,7 @@ private void writeAvro(XYTData xytData, File output) {
 		}
 	}
 
-	private void mergeEmissions(String pathParameter, String label) {
+	private void mergeLinkData(String pathParameter, String label) {
 		log.info("Merging emissions data for label {}", label);
 		Object2DoubleMap<String> mergedData = new Object2DoubleOpenHashMap<>();
 		Table csvOutputMerged = Table.create(TextColumn.create("Link Id"), DoubleColumn.create("value"));
@@ -143,9 +131,8 @@ private void mergeEmissions(String pathParameter, String label) {
 				.separator(';').build());
 
 			for (Row row : table) {
-				// index for Noise Emission xx:xx:xx -> 7
 				String linkId = row.getString("Link Id");
-				double value = row.getDouble(7);
+				double value = row.getDouble(row.columnCount() - 1);
 				mergedData.mergeDouble(linkId, value, Double::max);
 
 			}
@@ -165,38 +152,49 @@ private void mergeEmissions(String pathParameter, String label) {
 	}
 
 	/**
-	 * Merges the immissions data
+	 * Merges receiverPoint data (written by {@link org.matsim.contrib.noise.NoiseWriter}
 	 *
-	 * @param pathParameter path to the immissions data
-	 * @param label         label for the immissions data
+	 * @param outputDir path to the receiverPoint data
+	 * @param label         label for the receiverPoint data (which kind of data)
 	 */
-	private void mergeImissions(String pathParameter, String label) {
+	private void mergeReceiverPointData(String outputDir, String label) {
 
 		// data per time step, maps coord to value
 		Int2ObjectMap<Object2FloatMap<FloatFloatPair>> data = new Int2ObjectOpenHashMap<>();
 
 		// Loop over all files
+		//TODO could be adjusted to time bin size from noise config group
+		String substrToCapitalize = null;
 		for (int time = minTime; time <= maxTime; time += 3600) {
 
-			String path = pathParameter + label + "_" + round(time, 1) + ".csv";
+			String timeDataFile = outputDir + label + "_" + round(time, 1) + ".csv";
+
 			Object2FloatOpenHashMap<FloatFloatPair> values = new Object2FloatOpenHashMap<>();
 
-			if (!Files.exists(Path.of(path))) {
-				log.warn("File {} does not exist", path);
+			if (!Files.exists(Path.of(timeDataFile))) {
+				log.warn("File {} does not exist", timeDataFile);
 				continue;
 			}
 
-			// Read the file
-			Table table = Table.read().csv(CsvReadOptions.builder(IOUtils.getBufferedReader(path))
-				.columnTypesPartial(Map.of("x", ColumnType.FLOAT, "y", ColumnType.FLOAT, "Receiver Point Id", ColumnType.INTEGER, "t", ColumnType.DOUBLE))
+			//we need "damages_receiverPoint" -> "Damages 01:00:00" and "immission" -> "Immision 01:00:00"
+			substrToCapitalize = label.contains("_") ? label.substring(0, label.lastIndexOf("_")) : label;
+			String valueHeader = StringUtils.capitalize(substrToCapitalize) + " " + Time.writeTime(time, Time.TIMEFORMAT_HHMMSS);
+
+			// Read the data file
+			Table dataTable = Table.read().csv(CsvReadOptions.builder(IOUtils.getBufferedReader(timeDataFile))
+				.columnTypesPartial(Map.of("x", ColumnType.FLOAT,
+					"y", ColumnType.FLOAT,
+					"Receiver Point Id", ColumnType.INTEGER,
+					"t", ColumnType.DOUBLE,
+					valueHeader, ColumnType.DOUBLE))
 				.sample(false)
 				.separator(';').build());
 
-			// Loop over all rows in the file
-			for (Row row : table) {
+			// Loop over all rows in the data file
+			for (Row row : dataTable) {
 				float x = row.getFloat("x");
 				float y = row.getFloat("y");
-				float value = (float) row.getDouble(1); // 1
+				float value = (float) row.getDouble(valueHeader);
 				FloatFloatPair coord = FloatFloatPair.of(x, y);
 				values.put(coord, value);
 			}
@@ -232,7 +230,7 @@ private void mergeImissions(String pathParameter, String label) {
 			}
 		}
 
-		xytHourData.setData(Map.of("imissions", raw));
+		xytHourData.setData(Map.of(label, raw));
 		xytHourData.setCrs(crs);
 
 		File out = outputDirectory.getParent().resolve(label + "_per_hour.avro").toFile();
@@ -254,15 +252,18 @@ private void mergeImissions(String pathParameter, String label) {
 		xytDayData.setTimestamps(List.of(0));
 		xytDayData.setXCoords(xCoords);
 		xytDayData.setYCoords(yCoords);
-		xytDayData.setData(Map.of("imissions", raw));
+		xytDayData.setData(Map.of(label, raw));
 		xytDayData.setCrs(crs);
 
 		File outDay = outputDirectory.getParent().resolve(label + "_per_day.avro").toFile();
 
 		writeAvro(xytDayData, outDay);
+		//cache the overall sum
+		this.totalReceiverPointValues.put(substrToCapitalize, raw.stream().reduce(0f, Float::sum));
 	}
 
 	// Merges the immissions data
+
 	@Deprecated
 	private void mergeImmissionsCSV(String pathParameter, String label) {
 		log.info("Merging immissions data for label {}", label);
@@ -278,7 +279,10 @@ private void mergeImmissionsCSV(String pathParameter, String label) {
 
 			// Read the file
 			Table table = Table.read().csv(CsvReadOptions.builder(IOUtils.getBufferedReader(path))
-				.columnTypesPartial(Map.of("x", ColumnType.DOUBLE, "y", ColumnType.DOUBLE, "Receiver Point Id", ColumnType.INTEGER, "t", ColumnType.DOUBLE))
+				.columnTypesPartial(Map.of("x", ColumnType.DOUBLE,
+					"y", ColumnType.DOUBLE,
+					"Receiver Point Id", ColumnType.INTEGER,
+					"t", ColumnType.DOUBLE))
 				.sample(false)
 				.separator(';').build());
 
@@ -319,4 +323,7 @@ private void mergeImmissionsCSV(String pathParameter, String label) {
 		log.info("Merged noise data written to {} ", outPerDay);
 
 	}
+	public Map<String, Float> getTotalReceiverPointValues() {
+		return totalReceiverPointValues;
+	}
 }