CCT 1.0.6 Bugfixes and stability release.

Site calibration incorrectly handled weighting when three conditions are met on loaded data, see SiteCalibrationServiceImplTest.java for details. Envelope tool was not blocking correctly while file IO was finishing which could lead to dropped channels during stacking under certain circumstances. Envelope tool was interpolating too early in the processing chain and producing oversmoothing if using the default configuration. Fixed a series of unnecessary overhead objects being created during signal processing which was using more RAM than needed (especially noticable while making envelopes). Fixed a very rare synchronization bug with map icon painting. Fixed a path optimization dimension mismatch introduced by parallelizing code that was incorrectly caching a shared variable.
LLNL · Aug 22, 2019 · 2e33bbf · 2e33bbf
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diff --git a/README.md b/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-1.0.5-runnable.jar
+java -jar coda-calibration/calibration-standalone/target/calibration-standalone-1.0.6-runnable.jar
 ```
 
 #### **GUI alone**
 
 ```shell
-java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.5-runnable.jar
+java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.6-runnable.jar
 ```
 #### **Calibration REST service alone**
 
 ```shell
-java -jar coda-calibration/calibration-service/application/target/application-1.0.5-runnable.jar
+java -jar coda-calibration/calibration-service/application/target/application-1.0.6-runnable.jar
 ```
 
 #### A note about HTTPS

diff --git a/calibration-gui/pom.xml b/calibration-gui/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>coda-calibration</artifactId>
-		<version>1.0.5</version>
+		<version>1.0.6</version>
 	</parent>
 
 	<artifactId>calibration-gui</artifactId>

diff --git a/...-gui/src/main/java/gov/llnl/gnem/apps/coda/calibration/gui/plotting/CodaWaveformPlot.java b/...-gui/src/main/java/gov/llnl/gnem/apps/coda/calibration/gui/plotting/CodaWaveformPlot.java
@@ -114,7 +114,7 @@ public void setWaveform(Waveform waveform, SyntheticCoda synth) {
         this.clear();
         pickLineMap.clear();
 
-        if (waveform != null && waveform.getSegment() != null && waveform.getBeginTime() != null) {
+        if (waveform != null && waveform.hasData() && waveform.getBeginTime() != null) {
             final TimeT beginTime = new TimeT(waveform.getBeginTime());
             final float[] waveformSegment = doublesToFloats(waveform.getSegment());
             final TimeSeries rawSeries = new TimeSeries(waveformSegment, waveform.getSampleRate(), beginTime);
@@ -200,7 +200,7 @@ public void setWaveform(Waveform waveform, SyntheticCoda synth) {
                     try {
                         velocityClient.getNoiseForWaveform(waveform.getId()).subscribe(measurement -> {
                             if (measurement != null && measurement.getNoiseEndSecondsFromOrigin() != 0.0) {
-                                int lineLength = (int) (waveform.getSegment().length / waveform.getSampleRate()) + 10;
+                                int lineLength = (int) (waveform.getSegmentLength() / waveform.getSampleRate()) + 10;
                                 subplot.AddPlotObject(createFixedLine(measurement.getNoiseLevel(), lineLength, Color.BLACK, PenStyle.DASH), PLOT_ORDERING.NOISE_LINE.getZOrder());
                                 subplot.AddPlotObject(createFixedLine(measurement.getNoiseLevel() + params.getMinSnr(), lineLength, Color.BLACK, PenStyle.SOLID), PLOT_ORDERING.NOISE_LINE.getZOrder());
                                 repaint();

diff --git a/calibration-service/calibration-application/pom.xml b/calibration-service/calibration-application/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.5</version>
+		<version>1.0.6</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/calibration-service/calibration-integration/pom.xml b/calibration-service/calibration-integration/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.5</version>
+		<version>1.0.6</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/calibration-service/calibration-model/pom.xml b/calibration-service/calibration-model/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.5</version>
+		<version>1.0.6</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/calibration-service/calibration-repository/pom.xml b/calibration-service/calibration-repository/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.5</version>
+		<version>1.0.6</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/calibration-service/calibration-service-api/pom.xml b/calibration-service/calibration-service-api/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.5</version>
+		<version>1.0.6</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/calibration-service/calibration-service-impl/pom.xml b/calibration-service/calibration-service-impl/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.5</version>
+		<version>1.0.6</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/...src/main/java/gov/llnl/gnem/apps/coda/calibration/service/impl/Joint1DPathCorrection.java b/...src/main/java/gov/llnl/gnem/apps/coda/calibration/service/impl/Joint1DPathCorrection.java
@@ -99,7 +99,7 @@ public class Joint1DPathCorrection implements PathCalibrationService {
 
     private static final double efact = Math.log10(Math.E);
     private PathCalibrationMeasurementService pathCalibrationMeasurementService;
-    private List<double[]> paramPoints;
+
     @Value(value = "${path.use-aggressive-opt:true}")
     private boolean agressiveOptimization;
 
@@ -387,9 +387,6 @@ public double costFunction(Map<Event, Map<Station, SpectraMeasurement>> evidStaD
      *             if optimizationBounds.length < 2
      */
     private List<double[]> makeParamPoints(int numberOfTerms, boolean agressiveOptimization, double[]... optimizationBounds) {
-        if (paramPoints != null && !paramPoints.isEmpty() && paramPoints.get(0).length == numberOfTerms) {
-            return paramPoints;
-        }
         if (optimizationBounds.length < 2) {
             throw new IllegalStateException("Optmization bounds needs at least two entries for the low and high boundary conditions. Got: " + optimizationBounds.length);
         }
@@ -421,8 +418,7 @@ private List<double[]> makeParamPoints(int numberOfTerms, boolean agressiveOptim
             params.add(param);
         }
 
-        paramPoints = params;
-        return paramPoints;
+        return params;
     }
 
     private int[] nextIndex(int[] selectionIndex, int base) {

diff --git a/...ain/java/gov/llnl/gnem/apps/coda/calibration/service/impl/SiteCalibrationServiceImpl.java b/...ain/java/gov/llnl/gnem/apps/coda/calibration/service/impl/SiteCalibrationServiceImpl.java
@@ -24,6 +24,8 @@
 import java.util.stream.Collectors;
 
 import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -48,6 +50,8 @@
 @Service
 public class SiteCalibrationServiceImpl implements SiteCalibrationService {
 
+    private static final Logger log = LoggerFactory.getLogger(SiteCalibrationServiceImpl.class);
+
     private static final double UNUSED_DISTANCE = -1d;
     private static final double DYNE_LOG10_ADJUSTMENT = 7d;
     private MdacCalculatorService mdac;
@@ -131,7 +135,7 @@ public Map<FrequencyBand, Map<Station, SiteFrequencyBandParameters>> measureSite
             double centerFreq = (highFreq + lowFreq) / 2;
             for (Entry<Event, Map<Station, SpectraMeasurement>> staMwMap : evidStaMap.getValue().entrySet()) {
                 Event evid = staMwMap.getKey();
-                if (refMws.containsKey(evid.getEventId())) {
+                if (refMws != null && refMws.containsKey(evid.getEventId())) {
                     List<ReferenceMwParameters> refMwsParams = refMws.get(evid.getEventId());
                     ReferenceMwParameters refMw = refMwsParams.stream().findFirst().orElse(null);
                     if (refMw != null) {
@@ -163,6 +167,7 @@ public Map<FrequencyBand, Map<Station, SiteFrequencyBandParameters>> measureSite
                         }
                     }
                 }
+                weightFunctionMapByEvent.putIfAbsent(evid, this::lowerFreqHigherWeights);
             }
         }
 
@@ -195,9 +200,6 @@ public Map<FrequencyBand, Map<Station, SiteFrequencyBandParameters>> measureSite
                 Event evid = evidStaEntry.getKey();
                 if (averageMapByEvent.containsKey(evid) && averageMapByEvent.get(evid).containsKey(freqBand)) {
                     for (Entry<Station, SpectraMeasurement> staMwEntry : evidStaEntry.getValue().entrySet()) {
-                        if (!weightFunctionMapByEvent.containsKey(evid)) {
-                            weightFunctionMapByEvent.put(evid, this::lowerFreqHigherWeights);
-                        }
                         double amp = staMwEntry.getValue().getPathCorrected();
                         if (!staFreqBandSiteCorrectionMapAverage.containsKey(staMwEntry.getKey())) {
                             staFreqBandSiteCorrectionMapAverage.put(staMwEntry.getKey(), new HashMap<FrequencyBand, SummaryStatistics>());
@@ -315,10 +317,48 @@ public static Map<FrequencyBand, Map<Event, Map<Station, SpectraMeasurement>>> m
                         }
                         Map<Station, SpectraMeasurement> stationMap = eventMap.get(event);
                         stationMap.put(station, entry);
+                    } else {
+                        log.debug("No valid waveform for {}", entry);
                     }
                 }
             }
         }
         return data;
     }
+
+    public MdacCalculatorService getMdac() {
+        return mdac;
+    }
+
+    public SiteCalibrationServiceImpl setMdac(MdacCalculatorService mdac) {
+        this.mdac = mdac;
+        return this;
+    }
+
+    public SiteFrequencyBandParametersService getSiteParamsService() {
+        return siteParamsService;
+    }
+
+    public SiteCalibrationServiceImpl setSiteParamsService(SiteFrequencyBandParametersService siteParamsService) {
+        this.siteParamsService = siteParamsService;
+        return this;
+    }
+
+    public MeasuredMwsService getMeasuredMwsService() {
+        return measuredMwsService;
+    }
+
+    public SiteCalibrationServiceImpl setMeasuredMwsService(MeasuredMwsService measuredMwsService) {
+        this.measuredMwsService = measuredMwsService;
+        return this;
+    }
+
+    public SpectraCalculator getSpectraCalc() {
+        return spectraCalc;
+    }
+
+    public SiteCalibrationServiceImpl setSpectraCalc(SpectraCalculator spectraCalc) {
+        this.spectraCalc = spectraCalc;
+        return this;
+    }
 }