CCT 1.0.8

New Features:
 MW spectra truncation
   When a calibration is performed with events with and without apparent stress both loaded
     Those events with apparent stress values are treated as GT spectra and will not use the loaded MDAC model. These events will impact the site term fitting across the entire frequency spectra.
     Those events with only Mw values will be treated as a constraint on the magnitude by setting a very low apparent stress value and truncating the spectra at the computed corner frequency. In effect these events can still influence your overall site correction terms at the low frequency, and thereby help constrain the Mw value, but don't contribute to the roll-off shape of the spectra overall.
   **Enabled by default** you can toggle the old behavior back on via the --spectraTruncationEnabled=false flag at runtime.
 **BETA** UQ measurements for the final spectra results in calibration and measurement
   The confidence regions presently generated are relative to the optimizer's inversion walk on the theoretical spectra model vs. the measured values. This should be interpreted as the inversions confidence in finding a global minimum in the model misfit and **should not be treated as a confidence on the data itself**.
   A variety of metrics that can be diagnostic for QC, including misfit and data counts per event, are now reported in the Mw tables and exported JSON.
    * e.g. A model may have a very low misfit, and tight confidence bounds, but still be suspect due to having good spectra coverage on only the long period level at a few stations.
   These metrics are very much a work in progress but can be useful and **community input** on additional reporting that may prove useful is welcome.
 Persistent measurement intermediary artifacts
   Measurements will now save auto-picks, synthetics, and various other intermediary measurements that a calibration would typically be recording to support iterative QC from the GUI when looking at the spectra and inspecting related waveforms.
   The GUI has this feature enabled by default for the interactive workflow.
   The REST API now includes options to enable/disable this function (disabled by default)
 Capability to export diagnostic plots as images
   Export individual plots to SVG where possible
   Export specific overall views as high resolution PNGs
   Export polygon based map layers as SVG (icons, events, paths, etc)
   Export raster based map layers as high resolution PNGs (aerial imagery, topography, lithography, etc)

Improvements and Bugfixes:
 Significant performance improvements to the envelope tool across the board when generating envelopes.
 Minor performance improvements on Path calibration.
 Corrected a envelope stacking bug related to performance (no behavior changes).
 Updates to support very long, very low sample rate envelopes w.r.t. shape fitting and envelope creation.
 Updated the example notebook to have the latest API changes for the REST endpoints.

README.md

@@ -42,18 +42,18 @@ We don't presently deploy versioned artifacts into a public repository like the
 #### **As a single runnable JAR**
 
 ```shell
-java -jar coda-calibration/calibration-standalone/target/calibration-standalone-1.0.7-runnable.jar
+java -jar coda-calibration/calibration-standalone/target/calibration-standalone-1.0.8-runnable.jar
 ```
 
 #### **GUI alone**
 
 ```shell
-java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.7-runnable.jar
+java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.8-runnable.jar
 ```
 #### **Calibration REST service alone**
 
 ```shell
-java -jar coda-calibration/calibration-service/application/target/application-1.0.7-runnable.jar
+java -jar coda-calibration/calibration-service/application/target/application-1.0.8-runnable.jar
 ```
 
 #### A note about HTTPS

calibration-gui/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>coda-calibration</artifactId>
-		<version>1.0.7.1</version>
+		<version>1.0.8</version>
 	</parent>
 
 	<artifactId>calibration-gui</artifactId>

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

@@ -18,9 +18,11 @@
 import java.util.List;
 
 import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.stereotype.Component;
 
 import gov.llnl.gnem.apps.coda.common.mapping.WMSLayerDescriptor;
 
+@Component
 @ConfigurationProperties("app")
 public class AppProperties {
 

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

@@ -25,6 +25,7 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.ScheduledExecutorService;
 import java.util.concurrent.TimeUnit;
+import java.util.function.Consumer;
 
 import javax.annotation.PreDestroy;
 
@@ -43,6 +44,8 @@
 import gov.llnl.gnem.apps.coda.calibration.gui.controllers.MeasuredMwsController;
 import gov.llnl.gnem.apps.coda.calibration.gui.controllers.PathController;
 import gov.llnl.gnem.apps.coda.calibration.gui.controllers.ReferenceEventLoadingController;
+import gov.llnl.gnem.apps.coda.calibration.gui.controllers.RefreshableController;
+import gov.llnl.gnem.apps.coda.calibration.gui.controllers.ScreenshotEnabledController;
 import gov.llnl.gnem.apps.coda.calibration.gui.controllers.ShapeController;
 import gov.llnl.gnem.apps.coda.calibration.gui.controllers.SiteController;
 import gov.llnl.gnem.apps.coda.calibration.gui.controllers.parameters.ParametersController;
@@ -59,15 +62,19 @@
 import gov.llnl.gnem.apps.coda.common.gui.data.client.api.WaveformClient;
 import gov.llnl.gnem.apps.coda.common.gui.events.ShowFailureReportEvent;
 import gov.llnl.gnem.apps.coda.common.gui.util.ProgressMonitor;
+import gov.llnl.gnem.apps.coda.common.gui.util.SnapshotUtils;
 import gov.llnl.gnem.apps.coda.common.mapping.api.GeoMap;
+import gov.llnl.gnem.apps.coda.common.model.domain.Pair;
 import javafx.application.Platform;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.CheckMenuItem;
+import javafx.scene.control.ContentDisplay;
 import javafx.scene.control.Label;
 import javafx.scene.control.Tab;
+import javafx.scene.control.TabPane;
 import javafx.scene.input.TransferMode;
 import javafx.stage.DirectoryChooser;
 import javafx.stage.FileChooser;
@@ -83,11 +90,15 @@ public class CodaGuiController {
 
     private WaveformGui waveformGui;
     private DataController data;
+    private ParametersController param;
     private ShapeController shape;
     private PathController path;
     private SiteController site;
     private MeasuredMwsController measuredMws;
 
+    @FXML
+    private TabPane mainTabPane;
+
     @FXML
     private Tab dataTab;
 
@@ -106,20 +117,18 @@ public class CodaGuiController {
     @FXML
     private Tab measuredMwsTab;
 
-    private Runnable dataRefresh;
-    private Runnable paramRefresh;
-    private Runnable shapeRefresh;
-    private Runnable pathRefresh;
-    private Runnable siteRefresh;
-    private Runnable measuredMwsRefresh;
     private Runnable activeTabRefresh;
+    private Consumer<File> activeTabScreenshot;
 
     @FXML
     private Button showMapButton;
 
     @FXML
     private Button refreshButton;
 
+    @FXML
+    private Button snapshotButton;
+
     @FXML
     private CheckMenuItem waveformFocus;
 
@@ -140,6 +149,8 @@ public class CodaGuiController {
     private CalibrationClient calibrationClient;
 
     private DirectoryChooser sacDirFileChooser = new DirectoryChooser();
+    private DirectoryChooser screenshotFolderChooser = new DirectoryChooser();
+
     private FileChooser sacFileChooser = new FileChooser();
     private FileChooser codaParamsFileChooser = new FileChooser();
     private FileChooser codaJsonParamsFileChooser = new FileChooser();
@@ -179,22 +190,19 @@ public CodaGuiController(GeoMap mapController, WaveformClient waveformClient, En
         this.paramExporter = paramExporter;
         this.waveformGui = waveformGui;
         this.data = data;
+        this.param = param;
         this.shape = shape;
         this.path = path;
         this.site = site;
         this.measuredMws = measuredMws;
         this.bus = bus;
         bus.register(this);
 
-        dataRefresh = data.getRefreshFunction();
-        paramRefresh = param.getRefreshFunction();
-        shapeRefresh = shape.getRefreshFunction();
-        pathRefresh = path.getRefreshFunction();
-        siteRefresh = site.getRefreshFunction();
-        measuredMwsRefresh = measuredMws.getRefreshFunction();
-        activeTabRefresh = dataRefresh;
+        activeTabRefresh = data.getRefreshFunction();
 
         sacDirFileChooser.setTitle("Coda STACK File Directory");
+        screenshotFolderChooser.setTitle("Screenshot Export Folder");
+
         sacFileChooser.getExtensionFilters().add(new ExtensionFilter("Coda STACK Files (.sac,.env)", "*.sac", "*.env"));
         sacFileChooser.getExtensionFilters().add(allFilesFilter);
 
@@ -301,7 +309,7 @@ private void openMdacFiWindow() {
 
     @FXML
     private void runCalibration() {
-        calibrationClient.runCalibration(Boolean.FALSE).subscribe(value -> log.trace(value), err -> log.trace(err.getMessage(), err));
+        calibrationClient.runCalibration(Boolean.FALSE).doOnError(err -> log.trace(err.getMessage(), err)).subscribe();
     }
 
     @FXML
@@ -311,12 +319,14 @@ private void measureMws() {
 
     @FXML
     private void clearData() {
-        calibrationClient.clearData().subscribe(value -> log.trace(value), err -> log.trace(err.getMessage(), err), () -> dataRefresh.run());
+        calibrationClient.clearData().subscribe(val -> {
+        }, err -> log.trace(err.getMessage(), err), () -> data.getRefreshFunction().run());
     }
 
     @FXML
     private void runAutoPickingCalibration() {
-        calibrationClient.runCalibration(Boolean.TRUE).subscribe(value -> log.trace(value), err -> log.trace(err.getMessage(), err));
+        calibrationClient.runCalibration(Boolean.TRUE).subscribe(value -> {
+        }, err -> log.trace(err.getMessage(), err));
     }
 
     @FXML
@@ -329,20 +339,25 @@ public void initialize() {
         activeMapIcon = makeMapLabel();
         showMapIcon = makeMapLabel();
 
-        addMapEnabledTabListeners(dataTab, data, dataRefresh);
+        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()) {
                 mapController.clearIcons();
-                activeTabRefresh = paramRefresh;
+                activeTabRefresh = param.getRefreshFunction();
+                activeTabScreenshot = (folder) -> SnapshotUtils.writePng(folder, new Pair<>(paramTab.getText(), paramTab.getContent()));
             }
         });
 
-        addMapEnabledTabListeners(shapeTab, shape, shapeRefresh);
-        addMapEnabledTabListeners(pathTab, path, pathRefresh);
-        addMapEnabledTabListeners(siteTab, site, siteRefresh);
-        addMapEnabledTabListeners(measuredMwsTab, measuredMws, measuredMwsRefresh);
+        addEnabledTabListeners(shapeTab, shape);
+        addEnabledTabListeners(pathTab, path);
+        addEnabledTabListeners(siteTab, site);
+        addEnabledTabListeners(measuredMwsTab, measuredMws);
 
         rootElement.setOnDragOver(event -> {
             if (event.getGestureSource() != rootElement && event.getDragboard().hasFiles()) {
@@ -370,13 +385,22 @@ public void initialize() {
 
     }
 
-    private void addMapEnabledTabListeners(Tab tab, MapListeningController controller, Runnable runnable) {
+    private void addEnabledTabListeners(Tab tab, MapListeningController controller) {
         tab.setOnSelectionChanged(e -> {
             if (tab.isSelected()) {
                 controller.setVisible(true);
                 controller.refreshView();
                 tab.setGraphic(activeMapIcon);
-                activeTabRefresh = runnable;
+                if (controller instanceof RefreshableController) {
+                    activeTabRefresh = ((RefreshableController) controller).getRefreshFunction();
+                } else {
+                    activeTabRefresh = () -> controller.refreshView();
+                }
+                if (controller instanceof ScreenshotEnabledController) {
+                    activeTabScreenshot = ((ScreenshotEnabledController) controller).getScreenshotFunction();
+                } else {
+                    activeTabScreenshot = (folder) -> SnapshotUtils.writePng(folder, new Pair<>(tab.getText(), tab.getContent()));
+                }
             } else {
                 tab.setGraphic(null);
                 controller.setVisible(false);
@@ -389,6 +413,19 @@ private void refreshTab(ActionEvent e) {
         activeTabRefresh.run();
     }
 
+    @FXML
+    private void snapshotTab(ActionEvent e) {
+        File folder = screenshotFolderChooser.showDialog(rootElement.getScene().getWindow());
+        try {
+            if (folder != null && folder.exists() && folder.isDirectory() && folder.canWrite()) {
+                screenshotFolderChooser.setInitialDirectory(folder);
+                Platform.runLater(() -> activeTabScreenshot.accept(folder));
+            }
+        } catch (SecurityException ex) {
+            log.warn("Exception trying to write screenshots to folder {} : {}", folder, ex.getLocalizedMessage(), ex);
+        }
+    }
+
     private Label makeMapLabel() {
         Label mapLabel = new Label("\uE55B");
         mapLabel.getStyleClass().add("material-icons-medium");
@@ -405,6 +442,14 @@ private Label makeRefreshLabel() {
         return label;
     }
 
+    private Label makeSnapshotLabel() {
+        Label label = new Label("\uE3B0");
+        label.getStyleClass().add("material-icons-medium");
+        label.setMaxHeight(16);
+        label.setMinWidth(16);
+        return label;
+    }
+
     //TODO: Move this to a controller
     @Subscribe
     private void listener(CalibrationStatusEvent event) {

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

@@ -58,8 +58,12 @@ public WebfluxConfig(ObjectMapper objectMapper) {
     @Bean
     public ExchangeStrategies configureJacksonExchangeStrategies() {
         return ExchangeStrategies.builder().codecs(clientCodecConfigurer -> {
-            clientCodecConfigurer.customCodecs().decoder(new Jackson2JsonDecoder(objectMapper));
+            Jackson2JsonDecoder decoder = new Jackson2JsonDecoder(objectMapper);
+            decoder.setMaxInMemorySize(-1);
+            clientCodecConfigurer.customCodecs().decoder(decoder);
             clientCodecConfigurer.customCodecs().encoder(new Jackson2JsonEncoder(objectMapper));
+            //Unlimited
+            clientCodecConfigurer.defaultCodecs().maxInMemorySize(-1);
         }).build();
     }
 }

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

@@ -62,6 +62,7 @@
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.ContextMenu;
 import javafx.scene.control.MenuItem;
+import javafx.scene.control.ScrollPane;
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.TableColumn.CellDataFeatures;
@@ -77,6 +78,9 @@ public class DataController implements MapListeningController, RefreshableContro
     @FXML
     private MenuItem importWaveforms;
 
+    @FXML
+    private ScrollPane scrollPane;
+
     @FXML
     private TableView<Waveform> tableView;