* Updated to Spring 6

* Spectral inversion results in CERT are now plotted as misfit in mean absolute deviation
* CERT spectra now includes calculated HFL/LFL values for inversions and, if available, CCT magnitudes HFL/LFL reference lines
* Added function to set user-specified high and low frequency asymptotes to the spectral ratio plot and include them in the exported report if they are available. These buttons can be found in the modebar on the top-right of the spectra ratio plot.
* Updated the spectra download functions so that event report information, including the inversion results and user set frequency values will be exported in the .json file.
* Changes to validation events to remove them also from the site correction re-averaging during calibrations.
* Add path corrected plot back in to site tab, co-located with the raw amplitude plot.
* Plots for the CERT module have been updated and reworked in many cases to clean up and/or add additional information or interactivity.

.github/workflows/maven-publish.yml

@@ -16,10 +16,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v3
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'adopt'
         server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
         settings-path: ${{ github.workspace }} # location for the settings.xml file

README.md

@@ -51,19 +51,19 @@ mvn clean install
 #### **As a single runnable JAR**
 
 ```shell
-java -jar coda-calibration/calibration-standalone/target/calibration-standalone-1.0.20-runnable.jar
+java -jar coda-calibration/calibration-standalone/target/calibration-standalone-1.0.22-runnable.jar
 ```
 
 #### **GUI alone**
 
 ```shell
-java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.20-runnable.jar
+java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.22-runnable.jar
 ```
 
 #### **Calibration REST service alone**
 
 ```shell
-java -jar coda-calibration/calibration-service/application/target/application-1.0.20-runnable.jar
+java -jar coda-calibration/calibration-service/application/target/application-1.0.22-runnable.jar
 ```
 
 #### A note about HTTPS

calibration-gui/pom.xml

@@ -1,11 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="https://maven.apache.org/POM/4.0.0" xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="https://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="https://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>coda-calibration</artifactId>
-		<version>1.0.21.1</version>
+		<version>1.0.22</version>
 	</parent>
 
 	<artifactId>calibration-gui</artifactId>
@@ -52,10 +54,6 @@
 			<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 			<artifactId>calibration-model</artifactId>
 			<exclusions>
-				<exclusion>
-					<groupId>org.eclipse.persistence</groupId>
-					<artifactId>javax.persistence</artifactId>
-				</exclusion>
 				<exclusion>
 					<groupId>org.aspectj</groupId>
 					<artifactId>aspectjweaver</artifactId>
@@ -69,8 +67,8 @@
 					<artifactId>spring-aspects</artifactId>
 				</exclusion>
 				<exclusion>
-					<groupId>javax.validation</groupId>
-					<artifactId>validation-api</artifactId>
+					<groupId>jakarta.validation</groupId>
+					<artifactId>jakarta.validation-api</artifactId>
 				</exclusion>
 				<exclusion>
 					<groupId>org.springframework.data</groupId>
@@ -95,7 +93,6 @@
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-webflux</artifactId>
 		</dependency>
-
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-test</artifactId>
@@ -177,6 +174,8 @@
 				<artifactId>maven-dependency-plugin</artifactId>
 				<executions>
 					<execution>
+						<!-- Tells Eclipses m2e adapter to only execute this when using the maven->update project button -->
+						<?m2eexecute onConfiguration?>
 						<goals>
 							<goal>unpack</goal>
 						</goals>
@@ -207,6 +206,10 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
+				<configuration>
+					<source>${java.version}</source>
+					<target>${java.version}</target>
+				</configuration>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
@@ -221,7 +224,8 @@
 							<Implementation-Build>${buildNumber}</Implementation-Build>
 							<Build-Branch>${scmBranch}</Build-Branch>
 							<Build-Timestamp>${maven.build.timestamp}</Build-Timestamp>
-							<JavaFX-Preloader-Class>gov.llnl.gnem.apps.coda.calibration.gui.CodaGuiPreloader</JavaFX-Preloader-Class>
+							<JavaFX-Preloader-Class>
+								gov.llnl.gnem.apps.coda.calibration.gui.CodaGuiPreloader</JavaFX-Preloader-Class>
 						</manifestEntries>
 					</archive>
 				</configuration>

calibration-gui/src/main/java/gov/llnl/gnem/apps/coda/calibration/gui/CodaGuiController.java

@@ -27,7 +27,6 @@
 import java.util.concurrent.TimeUnit;
 import java.util.function.Consumer;
 
-import javax.annotation.PreDestroy;
 import javax.net.ssl.HostnameVerifier;
 import javax.net.ssl.SSLContext;
 
@@ -80,6 +79,7 @@
 import gov.llnl.gnem.apps.coda.envelope.gui.LoadRatioEventsGuiController;
 import gov.llnl.gnem.apps.coda.spectra.gui.RatioStatusProgressListener;
 import gov.llnl.gnem.apps.coda.spectra.gui.SpectraRatioGuiController;
+import jakarta.annotation.PreDestroy;
 import javafx.application.Platform;
 import javafx.concurrent.Worker;
 import javafx.event.ActionEvent;
@@ -112,7 +112,7 @@ public class CodaGuiController {
 
     private static final String SCREENSHOT_TITLE = "CERT_Screenshot";
 
-    private static final String ABOUT_TEXT = "Version 1.0.21";
+    private static final String ABOUT_TEXT = "Version 1.0.22";
 
     @FXML
     private Node rootElement;
@@ -313,17 +313,21 @@ private void changeAppMode() {
                 refreshButton.setGraphic(refreshLabel);
             });
         } else {
+            activeTabRefresh = data.getRefreshFunction();
+
             spectraGui.loadEnvelopes();
             siteTab.setOnSelectionChanged(e -> {
                 if (siteTab.isSelected()) {
                     activeTabRefresh = eventTableRefreshFunction;
+                    activeTabRefresh.run();
                     activeTabScreenshot = basicPngScreenshot(siteTab);
                 } else {
                     siteTab.setGraphic(null);
                 }
             });
 
             Platform.runLater(() -> {
+                dataTab.setGraphic(activeMapIcon);
                 mainTabPane.getTabs().remove(shapeTab);
                 mainTabPane.getTabs().remove(pathTab);
                 mainTabPane.getTabs().remove(measuredMwsTab);
@@ -509,7 +513,7 @@ private void runCalibration() {
 
     @FXML
     private void measureMws() {
-        measuredMws.getRefreshFunction().run();
+        Platform.runLater(measuredMws::reload);
     }
 
     @FXML
@@ -550,12 +554,8 @@ public void initialize() {
         snapshotButton.setGraphic(makeSnapshotLabel());
         snapshotButton.setContentDisplay(ContentDisplay.CENTER);
 
-        addEnabledTabListeners(dataTab, data);
-
         activeTabScreenshot = folder -> SnapshotUtils.writePng(folder, new Pair<>(dataTab.getText(), dataTab.getContent()));
 
-        data.setVisible(true);
-
         paramTab.setOnSelectionChanged(e -> {
             if (paramTab.isSelected()) {
                 cctMapController.clearIcons();
@@ -565,6 +565,9 @@ public void initialize() {
             }
         });
 
+        data.setVisible(true);
+        addEnabledTabListeners(dataTab, data);
+
         if (GuiApplication.getStartupMode() == ApplicationMode.CCT) {
             dataTab.setGraphic(activeMapIcon);
             addEnabledTabListeners(shapeTab, shape);
@@ -575,12 +578,14 @@ public void initialize() {
             siteTab.setOnSelectionChanged(e -> {
                 if (siteTab.isSelected()) {
                     activeTabRefresh = eventTableRefreshFunction;
+                    activeTabRefresh.run();
                     activeTabScreenshot = basicPngScreenshot(siteTab);
                 } else {
                     siteTab.setGraphic(null);
                 }
             });
             Platform.runLater(() -> {
+                dataTab.setGraphic(activeMapIcon);
                 mainTabPane.getTabs().remove(shapeTab);
                 mainTabPane.getTabs().remove(pathTab);
                 mainTabPane.getTabs().remove(measuredMwsTab);
@@ -657,6 +662,9 @@ private Consumer<File> basicPngScreenshot(Tab tab) {
     @FXML
     private void refreshTab(ActionEvent e) {
         activeTabRefresh.run();
+        if (rootElement.getParent() != null) {
+            rootElement.getParent().requestLayout();
+        }
     }
 
     @FXML

calibration-gui/src/main/java/gov/llnl/gnem/apps/coda/calibration/gui/GuiApplication.java

@@ -16,18 +16,13 @@
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.net.URL;
 import java.util.Locale;
 import java.util.TimeZone;
 import java.util.concurrent.CancellationException;
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.TimeoutException;
-import java.util.jar.Attributes;
-import java.util.jar.Manifest;
-
-import javax.annotation.PostConstruct;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -43,6 +38,7 @@
 import gov.llnl.gnem.apps.coda.calibration.gui.events.CalibrationStageShownEvent;
 import gov.llnl.gnem.apps.coda.common.gui.SimpleGuiPreloader;
 import gov.llnl.gnem.apps.coda.common.gui.util.CommonGuiUtils;
+import jakarta.annotation.PostConstruct;
 import javafx.application.Application;
 import javafx.application.Platform;
 import javafx.fxml.FXMLLoader;
@@ -137,43 +133,14 @@ public void start(Stage primaryStage) throws Exception {
             Hooks.onOperatorDebug();
         }
 
-        try {
-            Class<GuiApplication> clazz = GuiApplication.class;
-            String className = clazz.getSimpleName() + ".class";
-            String classPath = clazz.getResource(className).toString();
-            String baseTitle = "";
-
-            if (GuiApplication.getStartupMode() == ApplicationMode.CCT) {
-                baseTitle = CCT_TITLE;
-            } else {
-                baseTitle = CERT_TITLE;
-            }
-
-            if (classPath.startsWith("jar")) {
-                String manifestPath = classPath.substring(0, classPath.indexOf('!') + 1) + "/META-INF/MANIFEST.MF";
-                Manifest mf = new Manifest(new URL(manifestPath).openStream());
-                Attributes atts = mf.getMainAttributes();
-                // Put this info in the log to help with analysis
-                log.debug(
-                        "Version:{} Commit:{} Branch:{} By:{} at {}",
-                            atts.getValue("Implementation-Version"),
-                            atts.getValue("Implementation-Build"),
-                            atts.getValue("Build-Branch"),
-                            atts.getValue("Built-By"),
-                            atts.getValue("Build-Timestamp"));
-                // Update the title bar
-                baseTitle += " Built at " + atts.getValue("Build-Timestamp");
-            } else {
-                // Class not from JAR
-                log.debug("{} not running from a jar.", baseTitle);
-            }
-            props.setBaseTitle(baseTitle);
-        } catch (IOException e) {
-            // should never happen...
-            log.error("Failed initializing!", e);
+        String baseTitle = "";
+        if (GuiApplication.getStartupMode() == ApplicationMode.CCT) {
+            baseTitle = CCT_TITLE;
+        } else {
+            baseTitle = CERT_TITLE;
         }
 
-        Platform.setImplicitExit(true);
+        props.setBaseTitle(baseTitle);
         FXMLLoader fxmlLoader = null;
 
         if (startupMode == ApplicationMode.CERT) {
@@ -199,7 +166,6 @@ public void start(Stage primaryStage) throws Exception {
     }
 
     static public void changeApplicationMode() {
-
         if (GuiApplication.getStartupMode() == ApplicationMode.CCT) {
             GuiApplication.startupMode = ApplicationMode.CERT;
         } else {
@@ -224,6 +190,7 @@ static public void changeApplicationMode() {
         try {
             Parent root = fxmlLoader.load();
             Platform.runLater(() -> {
+                Font.loadFont(GuiApplication.class.getResource("/fxml/MaterialIcons-Regular.ttf").toExternalForm(), 18);
                 primaryStage.setTitle(props.getBaseTitle());
                 Scene scene = new Scene(root, props.getHeight(), props.getWidth());
                 primaryStage.setScene(scene);

calibration-gui/src/main/java/gov/llnl/gnem/apps/coda/calibration/gui/WebfluxConfig.java

@@ -25,6 +25,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.module.SimpleAbstractTypeResolver;
 import com.fasterxml.jackson.databind.module.SimpleModule;
+import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
 
 import gov.llnl.gnem.apps.coda.calibration.model.domain.SiteFrequencyBandParameters;
 import gov.llnl.gnem.apps.coda.calibration.model.domain.SpectraMeasurementMetadata;
@@ -43,6 +44,7 @@ public class WebfluxConfig {
     @Autowired
     public WebfluxConfig(ObjectMapper objectMapper) {
         this.objectMapper = objectMapper;
+        this.objectMapper.registerModule(new Jdk8Module());
         this.objectMapper.addMixIn(SharedFrequencyBandParameters.class, SharedFrequencyBandParametersJsonMixin.class);
         this.objectMapper.addMixIn(SiteFrequencyBandParameters.class, SiteFrequencyBandParametersJsonMixin.class);
 

calibration-gui/src/main/java/gov/llnl/gnem/apps/coda/calibration/gui/controllers/AbstractMeasurementController.java

@@ -920,7 +920,7 @@ protected void reloadData() {
                     for (final SpectraMeasurement meas : spectralMeasurements) {
                         final String evid = meas.getWaveform().getEvent().getEventId();
                         final Double freq = centerFreq(meas.getWaveform());
-                        evidStats.computeIfAbsent(evid, key -> new HashMap<>()).computeIfAbsent(freq, key -> new SummaryStatistics()).addValue(meas.getPathAndSiteCorrected());
+                        evidStats.computeIfAbsent(evid, key -> new HashMap<>()).computeIfAbsent(freq, key -> new SummaryStatistics()).addValue(meas.getPathAndSiteCorrected() - 7.0);
                     }
 
                     for (final Map<Double, SummaryStatistics> freqStats : evidStats.values()) {
@@ -1048,7 +1048,7 @@ private List<EventSpectraReport> getFormattedValues(String eventId, List<Spectra
             if (!eventId.equalsIgnoreCase("All")) {
                 filteredMeasurements = filterToEvent(eventId, measurements);
             }
-            Map<String, Map<Double, Double>> averageValues = new HashMap<>();
+            Map<String, Map<Double, SummaryStatistics>> averageValues = new HashMap<>();
             for (SpectraMeasurement meas : filteredMeasurements) {
                 String key = meas.getWaveform().getEvent().getEventId()
                         + "-"
@@ -1063,17 +1063,20 @@ private List<EventSpectraReport> getFormattedValues(String eventId, List<Spectra
                                                         new ArrayList<>()));
 
                 Double freq = centerFreq(meas.getWaveform());
-                valuesMap.get(key).add(new Pair<>(freq, meas.getPathAndSiteCorrected()));
-                averageValues.computeIfAbsent(meas.getWaveform().getEvent().getEventId(), k -> new TreeMap<>()).merge(freq, meas.getPathAndSiteCorrected(), (l, r) -> (l + r) / 2.0);
+                valuesMap.get(key).add(new Pair<>(freq, meas.getPathAndSiteCorrected() - 7.0));
+                averageValues.computeIfAbsent(meas.getWaveform().getEvent().getEventId(), k -> new TreeMap<>()).computeIfAbsent(freq, x -> {
+                    SummaryStatistics sum = new SummaryStatistics();
+                    return sum;
+                }).addValue(meas.getPathAndSiteCorrected() - 7.0);
             }
 
-            for (Entry<String, Map<Double, Double>> average : averageValues.entrySet()) {
+            for (Entry<String, Map<Double, SummaryStatistics>> average : averageValues.entrySet()) {
                 valuesMap.put(
                         "Average-" + average.getKey(),
                             new EventSpectraReport(average.getKey(),
                                                    null,
                                                    "Average",
-                                                   average.getValue().entrySet().stream().map(e -> new Pair<>(e.getKey(), e.getValue())).collect(Collectors.toList())));
+                                                   average.getValue().entrySet().stream().map(e -> new Pair<>(e.getKey(), e.getValue().getMean())).collect(Collectors.toList())));
             }
         }
         return new ArrayList<>(valuesMap.values());

calibration-gui/src/main/java/gov/llnl/gnem/apps/coda/calibration/gui/controllers/CodaParamLoadingController.java

@@ -27,7 +27,6 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
-import org.w3c.dom.events.Event;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.google.common.eventbus.EventBus;
@@ -46,6 +45,7 @@
 import gov.llnl.gnem.apps.coda.calibration.model.domain.ValidationMwParameters;
 import gov.llnl.gnem.apps.coda.calibration.model.domain.VelocityConfiguration;
 import gov.llnl.gnem.apps.coda.common.gui.converters.api.FileToWaveformConverter;
+import gov.llnl.gnem.apps.coda.common.model.domain.Event;
 import gov.llnl.gnem.apps.coda.common.model.domain.SharedFrequencyBandParameters;
 import reactor.core.publisher.Mono;