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commit d5f504dcd1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Nov 10 18:08:31 2023 +0000

    Bearing localiser offline save

    Bug stopping it correctly saving data from the offline task to the
    database fixed.

commit 7a44d49e27
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Oct 27 09:59:28 2023 +0100

    X3 Version 2.2.3

    Add maven jar files for X3/SUD version 2.2.3

commit fa5fe9943d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Oct 26 14:44:41 2023 +0100

    update sud file management to more efficiently skip to the correct part
    of a sud file when reading data offline.

commit 60435e567a
Author: Brian S Miller <93690136+BrianSMiller@users.noreply.github.com>
Date:   Fri Sep 8 21:54:40 2023 +1000

    Fixes issues #111 and fixes #112 (DIFAR module crashes and ability to use Deep Learning Detections in DIFAR module) (#110)

    * Bugfix for OverlayMarks

    Check for a null pointer exception in OverlayMarks that was causing a crash on startup.

    * Bugfix for null pointer in symbol manager

    Fix a bug that I found where the DIFAR module was crashing the symbol manager. Seems that this was due to this subclass of clip generator having a null value for it's uniqueName. I've fixed by checking for null values and assigning a generic symbol when null.

    * DeepLearning detections canGenerateClips=true

    Set flag in DeepLearning detector so that detections are considered 'clips' by Pamguard. This allows them to be processed automatically in the DIFAR Localisation module (and maybe others).

    * DIFAR: bugfix frequency limits for auto-detections

    Fix a bug in DIFAR module where the frequency limits of automated detections were not being set properly by the DIFAR module.

    * DeepLearning - Bugfix to detection duration

    Fix bug in deep learning detector where duration (in samples) was being set to number of samples in a hop instead of the number of samples in a segment.
This commit is contained in:
Jamie Mac 2023-11-15 06:34:55 +00:00
parent 81907fedb8
commit 47662b5045
14 changed files with 165 additions and 81 deletions
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4
repo/pamguard/org/x3/2.2.3/_remote.repositories Normal file
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@ -0,0 +1,4 @@
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
#Thu Oct 26 14:35:14 BST 2023
x3-2.2.3.jar>=
x3-2.2.3.pom>=

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repo/pamguard/org/x3/2.2.3/m2e-lastUpdated.properties Normal file
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#Thu Oct 26 15:50:39 BST 2023
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repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo|sources=1698327461721
repo|file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardPAMGuard/repo|javadoc=1698327546071
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central|https\://repo1.maven.org/maven2|javadoc=1698327546071
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repo/pamguard/org/x3/2.2.3/x3-2.2.3-javadoc.jar.lastUpdated Normal file
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#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
#Thu Oct 26 14:39:06 BST 2023
@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1698327545863
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@ -0,0 +1,14 @@
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
#Thu Oct 26 15:50:39 BST 2023
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file\://C\:\\Users\\dg50\\source\\repos\\PAMGuardDG/repo/.error=
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repo/pamguard/org/x3/2.2.3/x3-2.2.3.jar Normal file
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repo/pamguard/org/x3/2.2.3/x3-2.2.3.pom Normal file
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@ -0,0 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<modelVersion>4.0.0</modelVersion>
<groupId>pamguard.org</groupId>
<artifactId>x3</artifactId>
<version>2.2.3</version>
<description>POM was created from install:install-file</description>
</project>

11
src/Acquisition/pamAudio/WavAudioFile.java
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@ -14,6 +14,7 @@ import javax.sound.sampled.UnsupportedAudioFileException;
import org.codehaus.plexus.util.FileUtils; import org.codehaus.plexus.util.FileUtils;
import Acquisition.offlineFuncs.AquisitionLoadPoint; import Acquisition.offlineFuncs.AquisitionLoadPoint;
import PamDetection.RawDataUnit; import PamDetection.RawDataUnit;
//import PamUtils.CPUMonitor;
import PamguardMVC.PamDataBlock; import PamguardMVC.PamDataBlock;
import PamguardMVC.dataOffline.OfflineDataLoadInfo; import PamguardMVC.dataOffline.OfflineDataLoadInfo;
import dataMap.OfflineDataMap; import dataMap.OfflineDataMap;
@ -70,9 +71,13 @@ public class WavAudioFile implements PamAudioFileLoader {
FileDataMapPoint mapPoint = offlineFileServer.findFirstMapPoint(mapIt, offlineDataLoadInfo.getStartMillis(), offlineDataLoadInfo.getEndMillis()); FileDataMapPoint mapPoint = offlineFileServer.findFirstMapPoint(mapIt, offlineDataLoadInfo.getStartMillis(), offlineDataLoadInfo.getEndMillis());
if (openSoundFile(mapPoint.getSoundFile()) == false) { if (openSoundFile(mapPoint.getSoundFile()) == false) {
System.out.println("Could not open .wav sound file " + mapPoint.getSoundFile().getAbsolutePath()); System.out.println("Could not open sound file " + mapPoint.getSoundFile().getAbsolutePath());
return false; return false;
} }
if (offlineDataLoadInfo.cancel) {
return false;
}
File soundFile; File soundFile;
ByteConverter byteConverter = ByteConverter.createByteConverter(audioFormat); ByteConverter byteConverter = ByteConverter.createByteConverter(audioFormat);
@ -106,7 +111,11 @@ public class WavAudioFile implements PamAudioFileLoader {
try { try {
//System.out.println("Skipped " + skipped+ " " + skipBytes + " " + audioInputStream.available()); //System.out.println("Skipped " + skipped+ " " + skipBytes + " " + audioInputStream.available());
// CPUMonitor cpuMonitor = new CPUMonitor();
// cpuMonitor.start();
skipped = audioInputStream.skip(skipBytes); skipped = audioInputStream.skip(skipBytes);
// cpuMonitor.stop();
// System.out.println(cpuMonitor.getSummary("Sound skip: " + skipBytes + " bytes "));
//System.out.println("Offline " + (offlineDataLoadInfo.getStartMillis()-currentTime) + " ms : frame size: " + audioFormat.getFrameSize()); //System.out.println("Offline " + (offlineDataLoadInfo.getStartMillis()-currentTime) + " ms : frame size: " + audioFormat.getFrameSize());
} catch (IOException e) { } catch (IOException e) {

2
src/PamView/paneloverlay/overlaymark/OverlayMarkProviders.java
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@ -49,7 +49,7 @@ public class OverlayMarkProviders {
continue; continue;
} }
String existingName = marker.getMarkerName(); String existingName = marker.getMarkerName();
if (existingName.equals(nameToAdd)) { if (existingName!=null && existingName.equals(nameToAdd)) {
markProviders.remove(i); markProviders.remove(i);
break; break;
} }

2
src/PamView/symbol/PamSymbolManager.java
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@ -125,7 +125,7 @@ abstract public class PamSymbolManager<T extends PamSymbolChooser> implements Pa
* This doesn't work since different displays will still need different options based on * This doesn't work since different displays will still need different options based on
* their projector - so it can work, but need to set the projector. * their projector - so it can work, but need to set the projector.
*/ */
if (managedSymbolData.useGeneric) { if (managedSymbolData.useGeneric || displayName==null) {
displayName = GENERICNAME; displayName = GENERICNAME;
} }

146
src/PamguardMVC/dataOffline/OfflineDataLoading.java
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@ -175,62 +175,62 @@ public class OfflineDataLoading<T extends PamDataUnit> {
long t4 = t2; long t4 = t2;
// String orderDates = String.format(" %s to %s", // String orderDates = String.format(" %s to %s",
// PamCalendar.formatDateTime(startMillis), PamCalendar.formatDateTime(endMillis)); // PamCalendar.formatDateTime(startMillis), PamCalendar.formatDateTime(endMillis));
// System.out.printf("Offline data order in %s %s from %s to %s\n", pamDataBlock.getDataName(), offlineDataInfo.toString(), // System.out.printf("Offline data order in %s %s from %s to %s\n", pamDataBlock.getDataName(), offlineDataInfo.toString(),
// PamCalendar.formatDBDateTime(offlineDataInfo.getStartMillis()), // PamCalendar.formatDBDateTime(offlineDataInfo.getStartMillis()),
// PamCalendar.formatDBDateTime(offlineDataInfo.getEndMillis())); // PamCalendar.formatDBDateTime(offlineDataInfo.getEndMillis()));
// if (offlineDataInfo.getEndMillis()-offlineDataInfo.getStartMillis() > 3600000L) { // if (offlineDataInfo.getEndMillis()-offlineDataInfo.getStartMillis() > 3600000L) {
// System.out.printf("Stupid long load time !"); // System.out.printf("Stupid long load time !");
// return; // return;
// } // }
try { try {
if (orderData != null) { if (orderData != null) {
// System.out.println("order Data is not null"); // System.out.println("order Data is not null");
if (orderData.isDone() == false) { if (orderData.isDone() == false) {
switch (offlineDataInfo.getInterrupt()) { switch (offlineDataInfo.getInterrupt()) {
case OFFLINE_DATA_INTERRUPT: case OFFLINE_DATA_INTERRUPT:
// System.out.println("Request order cancelling"); // System.out.println("Request order cancelling");
if (orderData.cancelOrder()) { if (orderData.cancelOrder()) {
while (orderData!=null || !orderData.isDone()) { while (orderData!=null || !orderData.isDone()) {
try { try {
Thread.sleep(10); Thread.sleep(10);
} catch (InterruptedException e) { } catch (InterruptedException e) {
e.printStackTrace(); e.printStackTrace();
return; return;
}
} }
} }
else {
// System.out.println("Old order could not be cancelled");
}
break;
case OFFLINE_DATA_CANCEL:
// System.out.println("Don't order new data " + orderDates);
return;
case OFFLINE_DATA_WAIT:
int waitCount = 0;
t3 = System.currentTimeMillis();
waitingDataLoads.add(offlineDataInfo);
return;
// // System.out.println("Wait for old lot to complete " + orderDates);
// while (true) {
// if (orderData==null || orderData.isDone() || orderData.isCancelled()) {
// break;
// }
// waitCount++;
// try {
// Thread.sleep(10, 0);
// } catch (InterruptedException e) {
// e.printStackTrace();
// }
// }
} }
else { t4 = System.currentTimeMillis() - t3;
// System.out.println("Old order could not be cancelled");
}
break;
case OFFLINE_DATA_CANCEL:
// System.out.println("Don't order new data " + orderDates);
return;
case OFFLINE_DATA_WAIT:
int waitCount = 0;
t3 = System.currentTimeMillis();
waitingDataLoads.add(offlineDataInfo);
return;
// // System.out.println("Wait for old lot to complete " + orderDates);
// while (true) {
// if (orderData==null || orderData.isDone() || orderData.isCancelled()) {
// break;
// }
// waitCount++;
// try {
// Thread.sleep(10, 0);
// } catch (InterruptedException e) {
// e.printStackTrace();
// }
// }
} }
t4 = System.currentTimeMillis() - t3;
} }
} }
}
catch (NullPointerException e) { catch (NullPointerException e) {
// happens when orderData is set null in a different thread. // happens when orderData is set null in a different thread.
} }
@ -259,16 +259,19 @@ public class OfflineDataLoading<T extends PamDataUnit> {
* @param que * @param que
*/ */
public void cancelDataOrder(boolean que) { public void cancelDataOrder(boolean que) {
synchronized (orderLock) { // threadMessage("Calling cancelDataOrder");
if (orderData != null) { synchronized (orderLock) {
try { // threadMessage("cancelDataOrder is in synchronized oderLock");
orderData.cancelOrder(); if (orderData != null) {
} try {
catch (NullPointerException e) { boolean isCancelled = orderData.cancelOrder();
System.err.println("Null pointer in Cancel data order " + e.getMessage()); // threadMessage("candelDataOrder returned: isCancelled = " + isCancelled);
}
catch (NullPointerException e) {
System.err.println("Null pointer in Cancel data order " + e.getMessage());
}
} }
} }
}
if (que) this.waitingDataLoads.clear(); if (que) this.waitingDataLoads.clear();
} }
/** /**
@ -319,16 +322,19 @@ public class OfflineDataLoading<T extends PamDataUnit> {
@Override @Override
protected Integer doInBackground() { protected Integer doInBackground() {
// threadMessage("Start background");
try { try {
// System.out.println("Enter get offline data " + pamDataBlock.getDataName() + " Thread " + Thread.currentThread().getName()); // System.out.println("Enter get offline data " + pamDataBlock.getDataName() + " Thread " + Thread.currentThread().getName());
clearAllFFTBlocks(); clearAllFFTBlocks();
// threadMessage("Called clearAllFTBlocks");
int ans = getOfflineData(offlineDataInfo); int ans = getOfflineData(offlineDataInfo);
// System.out.println("Leave get offline data " + pamDataBlock.getDataName()); // System.out.println("Leave get offline data " + pamDataBlock.getDataName());
if (this == orderData) { if (this == orderData) {
orderData = null; orderData = null;
} }
// threadMessage("End background exit code " + ans);
return ans; return ans;
} }
catch (Exception e) { catch (Exception e) {
@ -338,9 +344,9 @@ public class OfflineDataLoading<T extends PamDataUnit> {
} }
return 0; return 0;
} }
} }
@Override @Override
protected void done() { protected void done() {
if (this == orderData) { if (this == orderData) {
@ -354,7 +360,7 @@ public class OfflineDataLoading<T extends PamDataUnit> {
if (isCancelled()) { if (isCancelled()) {
status = REQUEST_INTERRUPTED; status = REQUEST_INTERRUPTED;
//check whether the cancelled thread should be saved for later loading. //check whether the cancelled thread should be saved for later loading.
// System.out.println("The load has been cancelled: " + offlineDataInfo.getCurrentObserver().getObserverName()); // System.out.println("The load has been cancelled: " + offlineDataInfo.getCurrentObserver().getObserverName());
checkDataReloadQue(offlineDataInfo); checkDataReloadQue(offlineDataInfo);
} }
else { else {
@ -376,11 +382,11 @@ public class OfflineDataLoading<T extends PamDataUnit> {
} }
// System.out.println("WAITING DATA LOAD"); // System.out.println("WAITING DATA LOAD");
for (int i=0; i<waitingDataLoads.size(); i++){ for (int i=0; i<waitingDataLoads.size(); i++){
// System.out.println("OfflineDataLoading.Done(): " + waitingDataLoads.get(i).getCurrentObserver().getObserverName()); // System.out.println("OfflineDataLoading.Done(): " + waitingDataLoads.get(i).getCurrentObserver().getObserverName());
} }
// System.out.println("WAITING DATA END"); // System.out.println("WAITING DATA END");
if (!isCancelled()) launchQuedReloadThread(); if (!isCancelled()) launchQuedReloadThread();
@ -394,11 +400,17 @@ public class OfflineDataLoading<T extends PamDataUnit> {
} }
// private void threadMessage(String message) {
// String name = Thread.currentThread().getName();
// String now = PamCalendar.formatDBDateTime(System.currentTimeMillis(), true);
// System.out.printf("Thread %s load for %s at %s: %s\n", name, pamDataBlock.getDataName(), now, message);
// }
private void launchQuedReloadThread(){ private void launchQuedReloadThread(){
// System.out.println(" launchQuedReloadThread(): "); // System.out.println(" launchQuedReloadThread(): ");
if (waitingDataLoads.size()>=1){ if (waitingDataLoads.size()>=1){
OfflineDataLoadInfo offlineDataInfo=waitingDataLoads.get(0); OfflineDataLoadInfo offlineDataInfo=waitingDataLoads.get(0);
// System.out.println("Removing: " + offlineDataInfo.getCurrentObserver().getObserverName()); // System.out.println("Removing: " + offlineDataInfo.getCurrentObserver().getObserverName());
waitingDataLoads.remove(0); waitingDataLoads.remove(0);
this.orderOfflineData(offlineDataInfo); this.orderOfflineData(offlineDataInfo);
} }
@ -470,15 +482,15 @@ public class OfflineDataLoading<T extends PamDataUnit> {
pamDataBlock.clearAll(); pamDataBlock.clearAll();
// System.out.println("Start loading some offline data: from " + PamCalendar.formatDateTime(offlineDataInfo.getStartMillis() ) +" to "+ // System.out.println("Start loading some offline data: from " + PamCalendar.formatDateTime(offlineDataInfo.getStartMillis() ) +" to "+
// PamCalendar.formatDateTime(offlineDataInfo.getEndMillis() ) + " "+offlineDataInfo.getCurrentObserver().getObserverName() + // PamCalendar.formatDateTime(offlineDataInfo.getEndMillis() ) + " "+offlineDataInfo.getCurrentObserver().getObserverName() +
// " "+offlineDataInfo.getLoadKeepLayers()); // " "+offlineDataInfo.getLoadKeepLayers());
lastRequestAnswer = pamDataBlock.getParentProcess().getOfflineData(offlineDataInfo); lastRequestAnswer = pamDataBlock.getParentProcess().getOfflineData(offlineDataInfo);
// System.out.println(String.format("getOfflineData %s has %d units ", // System.out.println(String.format("getOfflineData %s has %d units ",
// getDataName(), getUnitsCount())); // getDataName(), getUnitsCount()));
// System.out.println("Orderring done: " + offlineDataInfo.getCurrentObserver().getObserverName() + " " + offlineDataInfo.getLoadKeepLayers()); // System.out.println("Orderring done: " + offlineDataInfo.getCurrentObserver().getObserverName() + " " + offlineDataInfo.getLoadKeepLayers());
//reset some of the changeable variables in offline data info. //reset some of the changeable variables in offline data info.
offlineDataInfo.reset(); offlineDataInfo.reset();

2
src/PamguardMVC/dataSelector/DataSelectorSettings.java
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@ -23,7 +23,9 @@ public class DataSelectorSettings implements Serializable, ManagedParameters {
if (selectorParams == null) { if (selectorParams == null) {
selectorParams = new Hashtable<>(); selectorParams = new Hashtable<>();
} }
if (name != null) {
selectorParams.put(name, params); selectorParams.put(name, params);
}
} }
/** /**

1
src/bearinglocaliser/offline/BLOfflineTask.java
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@ -22,6 +22,7 @@ public class BLOfflineTask extends OfflineTask {
this.bearingLocaliserControl = bearingLocaliserControl; this.bearingLocaliserControl = bearingLocaliserControl;
bearingProcess = bearingLocaliserControl.getBearingProcess(); bearingProcess = bearingLocaliserControl.getBearingProcess();
this.addRequiredDataBlock(rawOrFFTBlock = bearingProcess.getParentDataBlock()); this.addRequiredDataBlock(rawOrFFTBlock = bearingProcess.getParentDataBlock());
addAffectedDataBlock(detectionBlock);
// PamDataBlock detectionSource = bearingLocaliserControl.getDetectionMonitor().getParentDataBlock(); // PamDataBlock detectionSource = bearingLocaliserControl.getDetectionMonitor().getParentDataBlock();
// this.setParentDataBlock(detectionSource); // this.setParentDataBlock(detectionSource);
// setParentDataBlock(bearingProcess.getParentDataBlock()); // setParentDataBlock(bearingProcess.getParentDataBlock());

14
src/difar/DifarProcess.java
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@ -316,11 +316,19 @@ public class DifarProcess extends PamProcess {
sP = difarControl.getDifarParameters().findSpeciesParams(difarDataUnit); sP = difarControl.getDifarParameters().findSpeciesParams(difarDataUnit);
} }
difarDataUnit.setDisplaySampleRate(sP.sampleRate); difarDataUnit.setDisplaySampleRate(sP.sampleRate);
if (!sP.useMarkedBandsForSpectrogramClips){ if (difarDataUnit.triggerName.equals(difarControl.getUnitName())) { // User detection
double[] frequency = {sP.processFreqMin, sP.processFreqMax}; if (!sP.useMarkedBandsForSpectrogramClips ){
difarDataUnit.setFrequency(frequency); double[] frequency = {sP.processFreqMin, sP.processFreqMax};
difarDataUnit.setFrequency(frequency);
}
} else { //Check whether to override auto detection freq limits with DIFAR limits
if (!sP.useDetectionLimitsForTriggeredDetections ){ // Auto-detection
double[] frequency = {sP.processFreqMin, sP.processFreqMax};
difarDataUnit.setFrequency(frequency);
}
} }
demuxDataUnit(difarDataUnit, demuxWorker, startTime); demuxDataUnit(difarDataUnit, demuxWorker, startTime);
calculateDifarGram(difarDataUnit, demuxWorker, startTime); calculateDifarGram(difarDataUnit, demuxWorker, startTime);

5
src/rawDeepLearningClassifier/dlClassification/DLClassifyProcess.java
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@ -106,7 +106,8 @@ public class DLClassifyProcess extends PamInstantProcess {
addOutputDataBlock(dlDetectionDataBlock); addOutputDataBlock(dlDetectionDataBlock);
dlDetectionDataBlock.setNaturalLifetimeMillis(600*1000); //keep this data for a while. dlDetectionDataBlock.setNaturalLifetimeMillis(600*1000); //keep this data for a while.
dlDetectionDataBlock.addDataAnnotationType(dlAnnotationType); dlDetectionDataBlock.addDataAnnotationType(dlAnnotationType);
//ClipGeneration allows processing of detections by DIFAR module (and possibly others)
dlDetectionDataBlock.setCanClipGenerate(true);
//add custom graphics //add custom graphics
PamDetectionOverlayGraphics overlayGraphics = new DLGraphics(dlModelResultDataBlock); PamDetectionOverlayGraphics overlayGraphics = new DLGraphics(dlModelResultDataBlock);
overlayGraphics.setDetectionData(true); overlayGraphics.setDetectionData(true);
@ -482,7 +483,7 @@ public class DLClassifyProcess extends PamInstantProcess {
DataUnitBaseData basicData = groupDataBuffer.get(0).getBasicData().clone(); DataUnitBaseData basicData = groupDataBuffer.get(0).getBasicData().clone();
basicData.setMillisecondDuration(1000.*rawdata[0].length/this.sampleRate); basicData.setMillisecondDuration(1000.*rawdata[0].length/this.sampleRate);
basicData.setSampleDuration((long) (groupDataBuffer.size()*dlControl.getDLParams().sampleHop)); basicData.setSampleDuration((long) (groupDataBuffer.size()*dlControl.getDLParams().rawSampleSize));
// System.out.println("Model result: " + modelResult.size()); // System.out.println("Model result: " + modelResult.size());
DLDetection dlDetection = new DLDetection(basicData, rawdata); DLDetection dlDetection = new DLDetection(basicData, rawdata);