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Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main

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This commit is contained in:
Douglas Gillespie 2022-11-15 17:37:14 +00:00
commit 76e8467201
12 changed files with 241 additions and 140 deletions
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2
.classpath
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@ -6,7 +6,7 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Java 17">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
<attributes>
<attribute name="module" value="true"/>
<attribute name="maven.pomderived" value="true"/>

1
.gitignore vendored
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@ -39,3 +39,4 @@ settings.xml
.classpath
.classpath
.classpath
.classpath

2
repo/pamguard/org/x3/2.2.0/_remote.repositories
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@ -1,4 +1,4 @@
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
#Fri Nov 11 13:13:18 GMT 2022
#Mon Nov 14 09:57:39 GMT 2022
x3-2.2.0.jar>=
x3-2.2.0.pom>=

7
repo/pamguard/org/x3/2.2.0/m2e-lastUpdated.properties Normal file
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@ -0,0 +1,7 @@
#Fri Nov 11 13:38:50 GMT 2022
central|https\://repo1.maven.org/maven2|sources=1668173930657
repo|file\:///Users/au671271/git/PAMGuard/repo|sources=1668173930657
talan|https\://nexus.talanlabs.com/content/repositories/releases/|sources=1668173930657
bintray-macster110-jtorch4pam|macster110|https\://dl.bintray.com/macster110/jtorch4pam|sources=1668173930657
bedatadriven|https\://nexus.bedatadriven.com/content/groups/public/|sources=1668173930657
unidata-all|https\://artifacts.unidata.ucar.edu/repository/unidata-all/|sources=1668173930657

14
repo/pamguard/org/x3/2.2.0/x3-2.2.0-sources.jar.lastUpdated Normal file
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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.
#Fri Nov 11 13:38:50 GMT 2022
@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1668173930381
https\://dl.bintray.com/macster110/jtorch4pam/.error=Could not transfer artifact pamguard.org\:x3\:jar\:sources\:2.2.0 from/to bintray-macster110-jtorch4pam (https\://dl.bintray.com/macster110/jtorch4pam)\: Remote host terminated the handshake
https\://repo1.maven.org/maven2/.error=
file\:///Users/au671271/git/PAMGuard/repo/.error=
https\://nexus.bedatadriven.com/content/groups/public/.error=
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1668173930064
https\://repo1.maven.org/maven2/.lastUpdated=1668173930657
https\://nexus.talanlabs.com/content/repositories/releases/.error=Could not transfer artifact pamguard.org\:x3\:jar\:sources\:2.2.0 from/to talan (https\://nexus.talanlabs.com/content/repositories/releases/)\: Access denied to https\://nexus.talanlabs.com/content/repositories/releases/pamguard/org/x3/2.2.0/x3-2.2.0-sources.jar. Error code 401, Unauthorized
file\:///Users/au671271/git/PAMGuard/repo/.lastUpdated=1668173929099
4d1f727a0c17e3b21ef2f6654eed0b3113a4db97@default-bintray-macster110-jtorch4pam-https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1668173929096
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1668173930217

12
src/PamguardMVC/PamObservable.java
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@ -400,7 +400,7 @@ public class PamObservable {//extends PanelOverlayDraw {
}
}
private Timer t = new Timer(1000, new ActionListener() {
private Timer t = new Timer(4321, new ActionListener() {
public void actionPerformed(ActionEvent evt) {
long now = System.currentTimeMillis();
if (cpuUsage == null) return;
@ -413,6 +413,16 @@ public class PamObservable {//extends PanelOverlayDraw {
}
});
/**
* Had some issues with the Timer holding a reference to the underlying PamDataBlock
* (RoccaContourDataBlock, in this case) and not releasing it for garbage collection.
* Added in this method to force the timer to stop and release it's hold.
*/
public void stopTimer() {
t.stop();
}
public double getCPUPercent(int objectIndex) {
if (objectIndex < 0 || objectIndex >= cpuPercent.length) return -1;
return cpuPercent[objectIndex];

13
src/help/sound_processing/AcquisitionHelp/docs/sudfiles.html
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@ -18,6 +18,19 @@ SoundTrap recorders from
<p>Inflating SUD files to WAV files generally required between 3 and 5 times as much disk space and could also take
a fair amount of time, so not inflating will save both!</p>
<h3>SUD Index Files</h3>
<p>To efficiently navigate SUD files, PAMGuard makes a map of each file and stores it in a new file in the same
folder as the original SUD file. The index files have the same name as the original file, but end with .sudx.
The index files are about 2.5% of the size of the original SUD files. When processing SUD files it is therefore
important that a) the drive containing the SUD files is less than 95% full and b) that the system running PAMGuard has
write access to the folder containing the SUD files. </p>
<h3>SUD File Times</h3>
<p>The name of each SUD file contains the device serial number and a timestamp (data and time) in the form YYMMDDhhmmss.
Note that these time stamps are in local time. When processing the file, PAMGuard will extract a UTC timestamp from within
each SUD file and apply the UTC time to the data. you may therefore notice that the times of binary files and database
entries differ from the times in the file names. </p>
<h3>Mixing SUD and WAV files</h3>
<p>If a SUD file and a WAV file with the same name are in the same folder, then PAMGuard will ignore the SUD file
and process the WAV file. Note that in this case, PAMGuard will be unable to extract any metadata from the SUD file

8
src/pamguard/Pamguard.java
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@ -23,17 +23,14 @@ package pamguard;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import Acquisition.AcquisitionControl;
import Acquisition.FolderInputSystem;
import PamController.PamController;
import PamController.PamGUIManager;
import PamController.PamSettingManager;
import PamController.PamguardVersionInfo;
import PamController.pamBuoyGlobals;
import PamController.command.TerminalController;
import PamModel.SMRUEnable;
import PamUtils.FileFunctions;
import PamUtils.PamCalendar;
import PamUtils.PamExceptionHandler;
import PamUtils.PlatformInfo;
import PamUtils.Splash;
@ -45,6 +42,7 @@ import PamguardMVC.debug.Debug;
import binaryFileStorage.BinaryStore;
import dataPlotsFX.JamieDev;
import generalDatabase.DBControl;
import rocca.RoccaDev;
import java.io.BufferedReader;
import java.io.File;
@ -190,6 +188,10 @@ public class Pamguard {
JamieDev.setEnabled(true);
System.out.println("Enabling Jamie Macaulay modifications.");
}
else if (anArg.equalsIgnoreCase("-rocca")) {
RoccaDev.setEnabled(true);
System.out.println("Enabling Rocca development mode");
}
else if (anArg.equalsIgnoreCase(Debug.flag)) {
Debug.setPrintDebug(true);
Debug.out.println("Enabling debug terminal output.");

15
src/rocca/RoccaClassifier.java
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@ -408,6 +408,10 @@ public class RoccaClassifier {
// load the whistle classifier
if (roccaControl.roccaParameters.isClassifyWhistles()) {
if (roccaControl.roccaParameters.roccaClassifierModelFilename==null) {
roccaControl.roccaParameters.setClassifyWhistles(false);
}
else {
String fname = roccaControl.roccaParameters.roccaClassifierModelFilename.getAbsolutePath();
File f = new File(fname);
if (f.exists() == false) {
@ -450,9 +454,14 @@ public class RoccaClassifier {
}
}
}
}
// serialVersionUID=24 2016/08/10 added to load click classifier
if (roccaControl.roccaParameters.isClassifyClicks()) {
if (roccaControl.roccaParameters.roccaClickClassifierModelFilename==null) {
roccaControl.roccaParameters.setClassifyClicks(false);
}
else {
String fname = roccaControl.roccaParameters.roccaClickClassifierModelFilename.getAbsolutePath();
File f = new File(fname);
if (f.exists() == false) {
@ -495,6 +504,7 @@ public class RoccaClassifier {
}
}
}
}
// if we didn't load either classifier, don't bother loading trying to load an encounter
// classifier because it relies on the species. Just reset the side panel and return
@ -505,6 +515,10 @@ public class RoccaClassifier {
// serialVersionUID=24 2016/08/10 added to load event classifier
if (roccaControl.roccaParameters.isClassifyEvents()) {
if (roccaControl.roccaParameters.roccaEventClassifierModelFilename==null) {
roccaControl.roccaParameters.setClassifyEvents(false);
}
else {
String fname = roccaControl.roccaParameters.roccaEventClassifierModelFilename.getAbsolutePath();
File f = new File(fname);
if (f.exists() == false) {
@ -543,6 +557,7 @@ public class RoccaClassifier {
}
}
}
}
resetSidePanel();
return true;

27
src/rocca/RoccaDev.java Normal file
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@ -0,0 +1,27 @@
package rocca;
/**
* Global flag set at runtime for Rocca development flags.
* @author mo55
*
*/
public class RoccaDev {
private static boolean enabled = false;
/**
* @return the enabled
*/
public static boolean isEnabled() {
return enabled;
}
/**
* @param enabled the enabled to set
*/
public static void setEnabled(boolean enabled) {
RoccaDev.enabled = enabled;
}
}

18
src/rocca/RoccaParametersDialog.java
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@ -26,7 +26,6 @@ import java.awt.Frame;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.Point;
import java.util.ArrayList;
import java.util.Objects;
import java.util.Vector;
@ -48,8 +47,6 @@ import PamUtils.PamFileChooser;
import PamView.dialog.PamDialog;
import PamView.dialog.SourcePanel;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import java.awt.Dimension;
import java.awt.Insets;
import java.awt.event.ActionEvent;
@ -60,20 +57,14 @@ import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultComboBoxModel;
import javax.swing.GroupLayout;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JRadioButton;
import javax.swing.JFileChooser;
import javax.swing.JScrollPane;
@ -87,7 +78,6 @@ import javax.swing.border.EtchedBorder;
import clickDetector.ClickControl;
import clickDetector.ClickDetection;
import clickDetector.NoiseDataBlock;
import weka.classifiers.AbstractClassifier;
import weka.core.Attribute;
import weka.core.Instances;
import weka.core.SerializationHelper;
@ -523,7 +513,13 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
reclassifyButton.addActionListener(this);
reclassifyButton.setToolTipText("Load the whistle data from the contour stats output file, and run it through the current Classifier");
reclassifyButton.setVisible(true);
extraButtonsSubPanel.setVisible(true); // ******** THIS LINES CONTROLS THE VISIBILITY ********
// ******** THIS LINES CONTROLS THE VISIBILITY ********
if (RoccaDev.isEnabled()) {
extraButtonsSubPanel.setVisible(true);
} else {
extraButtonsSubPanel.setVisible(false);
}
GroupLayout extraPanelLayout = new GroupLayout(extraButtonsSubPanel);
extraButtonsSubPanel.setLayout(extraPanelLayout);
extraPanelLayout.setAutoCreateGaps(true);

26
src/rocca/RoccaProcess.java
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@ -388,7 +388,9 @@ public class RoccaProcess extends PamProcess {
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 1.5 ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) < 2000. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 28000. )) {
rcdb.setNaturalLifetimeMillis(0);
// rcdb.setNaturalLifetimeMillis(0);
rcdb.stopTimer();
rcdb = null;
return;
}
if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("HIWhist.model") &&
@ -402,7 +404,9 @@ public class RoccaProcess extends PamProcess {
rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 60000. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQRANGE) < 800. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQRANGE) > 14000. )) {
rcdb.setNaturalLifetimeMillis(0);
// rcdb.setNaturalLifetimeMillis(0);
rcdb.stopTimer();
rcdb = null;
return;
}
if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("NWAtlWhist.model") &&
@ -412,7 +416,9 @@ public class RoccaProcess extends PamProcess {
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 2.5 ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) < 9100. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 82000. )) {
rcdb.setNaturalLifetimeMillis(0);
// rcdb.setNaturalLifetimeMillis(0);
rcdb.stopTimer();
rcdb = null;
return;
}
}
@ -431,7 +437,9 @@ public class RoccaProcess extends PamProcess {
saveContourPoints(rcdb, rcdb.getChannelMap(), ++numDetections, sNum);
saveContourStats(rcdb, rcdb.getChannelMap(), numDetections, sNum);
saveContour(rcdb, rcdb.getChannelMap(), numDetections, sNum);
rcdb.setNaturalLifetimeMillis(0);
// rcdb.setNaturalLifetimeMillis(0);
rcdb.stopTimer();
rcdb = null;
/* if this is a click detection (signal, not noise) */
} else if (o==manClickSourceData || o==autoClickSourceData) {
@ -499,18 +507,24 @@ public class RoccaProcess extends PamProcess {
(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 35. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.005 ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
rcdb.stopTimer();
rcdb = null;
return;
}
if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("HIClick.model") &&
(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 40. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.01 ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
rcdb.stopTimer();
rcdb = null;
return;
}
if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("NWAtlClick.model") &&
(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 35. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.005 ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
rcdb.stopTimer();
rcdb = null;
return;
}
}
@ -529,7 +543,9 @@ public class RoccaProcess extends PamProcess {
// add call to update side panel. Set the isClick flag to True
updateSidePanel(rcdb, true);
saveContourStats(rcdb, rcdb.getChannelMap(), numDetections, sNum);
rcdb.setNaturalLifetimeMillis(0);
// rcdb.setNaturalLifetimeMillis(0);
rcdb.stopTimer();
rcdb = null;
}