CCT 1.0.5: Bugfixes and performance improvements from feedback on use…

…rs of REST clients.

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-1.0.4-runnable.jar
+java -jar coda-calibration/calibration-standalone/target/calibration-standalone-1.0.5-runnable.jar
 ```
 
 #### **GUI alone**
 
 ```shell
-java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.4-runnable.jar
+java -jar coda-calibration/calibration-gui/target/calibration-gui-1.0.5-runnable.jar
 ```
 #### **Calibration REST service alone**
 
 ```shell
-java -jar coda-calibration/calibration-service/application/target/application-1.0.4-runnable.jar
+java -jar coda-calibration/calibration-service/application/target/application-1.0.5-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>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<artifactId>calibration-gui</artifactId>

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

@@ -2,11 +2,11 @@
 * Copyright (c) 2018, Lawrence Livermore National Security, LLC. Produced at the Lawrence Livermore National Laboratory
 * CODE-743439.
 * All rights reserved.
-* This file is part of CCT. For details, see https://github.com/LLNL/coda-calibration-tool. 
-* 
+* This file is part of CCT. For details, see https://github.com/LLNL/coda-calibration-tool.
+*
 * Licensed under the Apache License, Version 2.0 (the “Licensee”); you may not use this file except in compliance with the License.  You may obtain a copy of the License at:
 * http://www.apache.org/licenses/LICENSE-2.0
-* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
+* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and limitations under the license.
 *
 * This work was performed under the auspices of the U.S. Department of Energy
@@ -150,7 +150,7 @@ public void setWaveform(Waveform waveform, SyntheticCoda synth) {
                 // waveform so we need to check that
                 for (WaveformPick pick : picks) {
                     double pickTime;
-                    //"'Bad' pick, plot it at begin time 
+                    //"'Bad' pick, plot it at begin time
                     if (pick.getPickTimeSecFromOrigin() < 0) {
                         pickTime = new TimeT(waveform.getBeginTime()).getEpochTime();
                     } else {
@@ -271,17 +271,20 @@ private void plotSynthetic(Waveform waveform, SyntheticCoda synth, final TimeT b
             if (startTime.lt(endTime)) {
                 interpolatedSeries.cut(startTime, endTime);
                 synthSeriesBeforeEndMarker.cut(startTime, endTime);
-                synthSeriesRemaining.cutBefore(endTime);
 
                 TimeSeries diffSeis = interpolatedSeries.subtract(synthSeriesBeforeEndMarker);
                 int synthStartTimeShift = (int) (startTime.subtractD(beginTime) + 0.5);
-                int remainingStartTimeShift = (int) (endTime.subtractD(beginTime) + 0.5);
                 double median = diffSeis.getMedian();
 
                 subplot.DeletePlotObject(legendRef);
                 subplot.AddPlotObject(createLegend(labelText + "Shift: " + dfmt4.format(median)));
                 subplot.AddPlotObject(createLine(synthStartTimeShift, median, synthSeriesBeforeEndMarker, Color.GREEN), PLOT_ORDERING.MODEL_FIT.getZOrder());
-                subplot.AddPlotObject(createLine(remainingStartTimeShift, median, synthSeriesRemaining, Color.GREEN, 3, PenStyle.DASH), PLOT_ORDERING.MODEL_FIT.getZOrder());
+
+                if (endTime.lt(synthSeriesRemaining.getEndtime())) {
+                    synthSeriesRemaining.cutBefore(endTime);
+                    int remainingStartTimeShift = (int) (endTime.subtractD(beginTime) + 0.5);
+                    subplot.AddPlotObject(createLine(remainingStartTimeShift, median, synthSeriesRemaining, Color.GREEN, 3, PenStyle.DASH), PLOT_ORDERING.MODEL_FIT.getZOrder());
+                }
                 repaint();
             }
         }
@@ -336,7 +339,7 @@ private PlotObject createRectangle(int timeStart, int timeEnd, int heightMin, in
 
     /*
      * (non-Javadoc)
-     * 
+     *
      * @see
      * llnl.gnem.core.gui.waveform.WaveformPlot#handlePickMovedState(java.lang.
      * Object)T

calibration-service/calibration-application/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

calibration-service/calibration-integration/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

calibration-service/calibration-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

calibration-service/calibration-repository/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>calibration-service</artifactId>
-		<version>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

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>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

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>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

calibration-service/calibration-service-impl/src/main/java/gov/llnl/gnem/apps/coda/calibration/service/impl/Joint1DPathCorrection.java

@@ -24,7 +24,6 @@
 import java.util.Set;
 import java.util.stream.IntStream;
 
-import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.math3.analysis.MultivariateFunction;
 import org.apache.commons.math3.exception.TooManyEvaluationsException;
 import org.apache.commons.math3.optim.ConvergenceChecker;
@@ -37,7 +36,7 @@
 import org.apache.commons.math3.optim.nonlinear.scalar.ObjectiveFunction;
 import org.apache.commons.math3.optim.nonlinear.scalar.noderiv.CMAESOptimizer;
 import org.apache.commons.math3.random.MersenneTwister;
-import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.eclipse.collections.impl.list.mutable.primitive.DoubleArrayList;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -348,7 +347,7 @@ public double costFunction(Map<Event, Map<Station, SpectraMeasurement>> evidStaD
             Event evid = evidEntry.getKey();
             Map<Station, SpectraMeasurement> stationMapData = evidEntry.getValue();
 
-            List<Double> dataVec = new ArrayList<>(optimizationParams.length);
+            DoubleArrayList dataVec = new DoubleArrayList(stationMapData.size());
             for (Entry<Station, SpectraMeasurement> entry : stationMapData.entrySet()) {
                 double del = distanceMap.get(evid).get(entry.getKey());
                 double site = optimizationParams[stationIdxMap.get(entry.getKey())];
@@ -367,7 +366,7 @@ public double costFunction(Map<Event, Map<Station, SpectraMeasurement>> evidStaD
 
             if (dataVec.size() > 1) {
                 double huberDel = .5d;
-                double median = new DescriptiveStatistics(ArrayUtils.toPrimitive(dataVec.toArray(new Double[0]))).getPercentile(50d);
+                double median = dataVec.median();
                 for (Entry<Station, SpectraMeasurement> entry1 : stationMapData.entrySet()) {
                     double diff = Math.abs(localDataMap.get(evid).get(entry1.getKey()) - median);
                     cost = cost + (Math.pow(huberDel, 2.0) + (Math.sqrt(1d + Math.pow(diff / huberDel, 2.0)) - 1d));

calibration-service/calibration-service-impl/src/main/java/gov/llnl/gnem/apps/coda/calibration/service/impl/processing/CalibrationCurveFitter.java

@@ -19,6 +19,7 @@
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.concurrent.ThreadLocalRandom;
+import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
 
@@ -159,6 +160,14 @@ public EnvelopeFit fitCodaCMAES(final float[] segment) {
         return fit;
     }
 
+    private PointValuePair bestByFunction(MultivariateFunction prediction, Function<Integer, PointValuePair> mapper) {
+        return IntStream.range(0, 1 + ITER_COUNT)
+                        .parallel()
+                        .mapToObj(mapper::apply)
+                        .reduce((left, right) -> left.getValue() < right.getValue() ? left : right)
+                        .orElseGet(() -> new PointValuePair(new double[4], Double.MAX_VALUE));
+    }
+
     public double[] gridSearchCodaVApacheCMAES(List<Entry<Double, Double>> velocityDistancePairs) {
         return gridSearchCodaVApacheCMAES(velocityDistancePairs, YVV_MIN, YVV_MAX, 0, V_DIST_MAX);
     }
@@ -192,23 +201,14 @@ public double[] gridSearchCodaVApacheCMAES(final List<Entry<Double, Double>> vel
             return sum;
         };
 
-        PointValuePair bestResult = optimizeCMAES(
+        Function<Integer, PointValuePair> mapper = (i) -> optimizeCMAES(
                 prediction,
                     new InitialGuess(new double[] { ThreadLocalRandom.current().nextDouble(minP1, maxP1), ThreadLocalRandom.current().nextDouble(minP2, maxP2),
                             ThreadLocalRandom.current().nextDouble(minP3, maxP3) }),
                     new CMAESOptimizer.Sigma(new double[] { 1, 75, 100 }),
                     new SimpleBounds(new double[] { minP1, minP2, minP3 }, new double[] { maxP1, maxP2, maxP3 }));
-        for (int i = 1; i < ITER_COUNT; i++) {
-            PointValuePair result = optimizeCMAES(
-                    prediction,
-                        new InitialGuess(new double[] { ThreadLocalRandom.current().nextDouble(minP1, maxP1), ThreadLocalRandom.current().nextDouble(minP2, maxP2),
-                                ThreadLocalRandom.current().nextDouble(minP3, maxP3) }),
-                        new CMAESOptimizer.Sigma(new double[] { 1, 75, 100 }),
-                        new SimpleBounds(new double[] { minP1, minP2, minP3 }, new double[] { maxP1, maxP2, maxP3 }));
-            if (result.getValue() < bestResult.getValue()) {
-                bestResult = result;
-            }
-        }
+
+        PointValuePair bestResult = bestByFunction(prediction, mapper);
 
         double[] curve = new double[4];
         curve[0] = bestResult.getPoint()[0] / V0_REG;
@@ -256,25 +256,15 @@ public double[] gridSearchCodaBApacheCMAES(final List<Entry<Double, Double>> bet
             return sum;
         };
 
-        PointValuePair bestResult = optimizeCMAES(
+        Function<Integer, PointValuePair> mapper = (i) -> optimizeCMAES(
                 prediction,
                     new InitialGuess(new double[] { ThreadLocalRandom.current().nextDouble(minP1, maxP1), ThreadLocalRandom.current().nextDouble(minP2, maxP2),
                             ThreadLocalRandom.current().nextDouble(minP3, maxP3) }),
                     new CMAESOptimizer.Sigma(new double[] { .05, 0.5, 750 }),
                     50,
                     new SimpleBounds(new double[] { minP1, minP2, minP3 }, new double[] { maxP1, maxP2, maxP3 }));
-        for (int i = 1; i < ITER_COUNT; i++) {
-            PointValuePair result = optimizeCMAES(
-                    prediction,
-                        new InitialGuess(new double[] { ThreadLocalRandom.current().nextDouble(minP1, maxP1), ThreadLocalRandom.current().nextDouble(minP2, maxP2),
-                                ThreadLocalRandom.current().nextDouble(minP3, maxP3) }),
-                        new CMAESOptimizer.Sigma(new double[] { .05, 0.5, 750 }),
-                        50,
-                        new SimpleBounds(new double[] { minP1, minP2, minP3 }, new double[] { maxP1, maxP2, maxP3 }));
-            if (result.getValue() < bestResult.getValue()) {
-                bestResult = result;
-            }
-        }
+
+        PointValuePair bestResult = bestByFunction(prediction, mapper);
 
         double[] curve = new double[4];
         curve[0] = bestResult.getPoint()[0] / B0_REG;
@@ -338,27 +328,15 @@ public double[] gridSearchCodaGApacheCMAES(final List<Entry<Double, Double>> gam
 
         ConvergenceChecker<PointValuePair> convergenceChecker = new SimplePointChecker<>(0.005, 0.005, 100000);
 
-        PointValuePair bestResult = optimizeCMAES(
+        Function<Integer, PointValuePair> mapper = (i) -> optimizeCMAES(
                 prediction,
                     new InitialGuess(new double[] { ThreadLocalRandom.current().nextDouble(minP1, maxP1), minP2, minP3 }),
                     new CMAESOptimizer.Sigma(new double[] { 1, 50, 50 }),
                     convergenceChecker,
                     50,
                     new SimpleBounds(new double[] { minP1, minP2, minP3 }, new double[] { maxP1, maxP2, maxP3 }));
-        for (int i = 1; i < ITER_COUNT; i++) {
-
-            PointValuePair result = optimizeCMAES(
-                    prediction,
-                        new InitialGuess(new double[] { ThreadLocalRandom.current().nextDouble(minP1, maxP1), ThreadLocalRandom.current().nextDouble(minP2, maxP2),
-                                ThreadLocalRandom.current().nextDouble(minP3, maxP3) }),
-                        new CMAESOptimizer.Sigma(new double[] { 1, 50, 50 }),
-                        convergenceChecker,
-                        50,
-                        new SimpleBounds(new double[] { minP1, minP2, minP3 }, new double[] { maxP1, maxP2, maxP3 }));
-            if (result.getValue() < bestResult.getValue()) {
-                bestResult = result;
-            }
-        }
+
+        PointValuePair bestResult = bestByFunction(prediction, mapper);
 
         double[] curve = new double[4];
         curve[0] = bestResult.getPoint()[0] / G0_REG;

calibration-service/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>coda-calibration</artifactId>
-		<version>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

calibration-standalone/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>coda-calibration</artifactId>
-		<version>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

common-gui/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>gov.llnl.gnem.apps.coda.calibration</groupId>
 		<artifactId>coda-calibration</artifactId>
-		<version>1.0.4-SNAPSHOT</version>
+		<version>1.0.5</version>
 	</parent>
 
 	<groupId>gov.llnl.gnem.apps.coda.common</groupId>

common-gui/src/main/java/gov/llnl/gnem/apps/coda/common/gui/converters/sac/SacExporter.java

@@ -2,11 +2,11 @@
 * Copyright (c) 2018, Lawrence Livermore National Security, LLC. Produced at the Lawrence Livermore National Laboratory
 * CODE-743439.
 * All rights reserved.
-* This file is part of CCT. For details, see https://github.com/LLNL/coda-calibration-tool. 
-* 
+* This file is part of CCT. For details, see https://github.com/LLNL/coda-calibration-tool.
+*
 * Licensed under the Apache License, Version 2.0 (the “Licensee”); you may not use this file except in compliance with the License.  You may obtain a copy of the License at:
 * http://www.apache.org/licenses/LICENSE-2.0
-* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
+* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and limitations under the license.
 *
 * This work was performed under the auspices of the U.S. Department of Energy
@@ -42,8 +42,6 @@
 @Component
 public class SacExporter {
     private static final String SEP = "_";
-    private final NumberFormat dfmt4 = NumberFormatFactory.fourDecimalOneLeadingZero();
-
     private static final Logger log = LoggerFactory.getLogger(SacExporter.class);
 
     public Result<String> writeWaveformToDirectory(File exportDirectory, Waveform w) {
@@ -104,24 +102,23 @@ public Result<String> writeWaveformToDirectory(File exportDirectory, Waveform w)
                     }
                     os.flush();
 
-                    return new Result<String>(true, filename);
+                    return new Result<>(true, filename);
                 }
             } catch (IOException e) {
                 log.error(e.getMessage(), e);
-                return new Result<String>(false, e.toString()).setErrors(Collections.singletonList(e));
+                return new Result<>(false, e.toString()).setErrors(Collections.singletonList(e));
             }
         }
 
         String message = "Waveform is missing required information or is malformed; waveform: " + w;
         log.error(message);
-        return new Result<String>(false, message);
+        return new Result<>(false, message);
     }
 
     private boolean waveformFullySpecified(Waveform w) {
         return w != null
                 && w.getLowFrequency() != null
                 && w.getHighFrequency() != null
-                && present(w.getSegmentType())
                 && w.getSampleRate() != null
                 && w.getBeginTime() != null
                 && w.getEndTime() != null
@@ -136,6 +133,7 @@ && present(w.getStream().getChannelName())
 
     public String getFileName(Waveform w) {
         if (waveformFullySpecified(w)) {
+            NumberFormat dfmt4 = NumberFormatFactory.fourDecimalOneLeadingZero();
             Stream stream = w.getStream();
             Event ev = w.getEvent();
 

common-gui/src/main/java/gov/llnl/gnem/apps/coda/common/gui/converters/sac/SacLoader.java

@@ -2,11 +2,11 @@
 * Copyright (c) 2018, Lawrence Livermore National Security, LLC. Produced at the Lawrence Livermore National Laboratory
 * CODE-743439.
 * All rights reserved.
-* This file is part of CCT. For details, see https://github.com/LLNL/coda-calibration-tool. 
-* 
+* This file is part of CCT. For details, see https://github.com/LLNL/coda-calibration-tool.
+*
 * Licensed under the Apache License, Version 2.0 (the “Licensee”); you may not use this file except in compliance with the License.  You may obtain a copy of the License at:
 * http://www.apache.org/licenses/LICENSE-2.0
-* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
+* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and limitations under the license.
 *
 * This work was performed under the auspices of the U.S. Department of Energy
@@ -209,7 +209,7 @@ public Result<Waveform> convertSacFileToWaveform(File file) {
             double[] segment = new double[rawVals.length];
             try {
                 IntStream.range(0, rawVals.length).forEach(index -> {
-                    segment[index] = Double.valueOf(rawVals[index]);
+                    segment[index] = rawVals[index];
                     if (!Double.isFinite(segment[index])) {
                         throw new LightweightIllegalStateException("Invalid data in segment for file: " + fileName);
                     }