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

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This commit is contained in:
Douglas Gillespie 2022-11-15 17:34:57 +00:00
commit 484109703e
8 changed files with 206 additions and 139 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

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];

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.");

243
src/rocca/RoccaClassifier.java
View File

@ -408,92 +408,102 @@ public class RoccaClassifier {
// load the whistle classifier
if (roccaControl.roccaParameters.isClassifyWhistles()) {
String fname = roccaControl.roccaParameters.roccaClassifierModelFilename.getAbsolutePath();
File f = new File(fname);
if (f.exists() == false) {
WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca whistle classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
roccaControl.roccaParameters.setClassifyWhistles(false);
}
else {
try {
BufferedInputStream input = new BufferedInputStream(
(new ProgressMonitorInputStream(null, "Loading Whistle Classifier - Please wait",
new FileInputStream(fname))));
Object[] modelParams = SerializationHelper.readAll(input);
// separate the classifier model from the training dataset info
// roccaClassifierModel = (AbstractClassifier) modelParams[0];
// trainedDataset = (Instances) modelParams[1];
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) {
WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca whistle classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
roccaControl.roccaParameters.setClassifyWhistles(false);
}
else {
try {
BufferedInputStream input = new BufferedInputStream(
(new ProgressMonitorInputStream(null, "Loading Whistle Classifier - Please wait",
new FileInputStream(fname))));
Object[] modelParams = SerializationHelper.readAll(input);
// separate the classifier model from the training dataset info
// roccaClassifierModel = (AbstractClassifier) modelParams[0];
// trainedDataset = (Instances) modelParams[1];
// there are 2 different styles of model file, the original version and the version
// developed for the 2-stage classifier. Both files contain 2 objects.
// The original version contained the classifier and the training dataset. The newer
// version contains a String description and the classifier. Test the first object;
// if it's a String, then this is the newer version and the String is the description.
// If it's not a String, assume this is the old version and create a RoccaRFModel
// object from the file contents.
if (modelParams[0] instanceof String) {
modelList = (RoccaRFModel) modelParams[1];
} else {
AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
Instances dataset = (Instances) modelParams[1];
RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
for (int i=0; i<dataset.numClasses(); i++) {
models[i]=null;
}
modelList = new RoccaRFModel(classifier, dataset, models);
}
// there are 2 different styles of model file, the original version and the version
// developed for the 2-stage classifier. Both files contain 2 objects.
// The original version contained the classifier and the training dataset. The newer
// version contains a String description and the classifier. Test the first object;
// if it's a String, then this is the newer version and the String is the description.
// If it's not a String, assume this is the old version and create a RoccaRFModel
// object from the file contents.
if (modelParams[0] instanceof String) {
modelList = (RoccaRFModel) modelParams[1];
} else {
AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
Instances dataset = (Instances) modelParams[1];
RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
for (int i=0; i<dataset.numClasses(); i++) {
models[i]=null;
}
modelList = new RoccaRFModel(classifier, dataset, models);
}
} catch (Exception ex) {
System.err.println("Deserialization of Whistle Classifier failed: " + ex.getMessage());
ex.printStackTrace();
roccaControl.roccaParameters.setClassifyWhistles(false);
}
}
} catch (Exception ex) {
System.err.println("Deserialization of Whistle Classifier failed: " + ex.getMessage());
ex.printStackTrace();
roccaControl.roccaParameters.setClassifyWhistles(false);
}
}
}
}
// serialVersionUID=24 2016/08/10 added to load click classifier
if (roccaControl.roccaParameters.isClassifyClicks()) {
String fname = roccaControl.roccaParameters.roccaClickClassifierModelFilename.getAbsolutePath();
File f = new File(fname);
if (f.exists() == false) {
WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca click classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
roccaControl.roccaParameters.setClassifyClicks(false);
}
else {
try {
BufferedInputStream input = new BufferedInputStream(
(new ProgressMonitorInputStream(null, "Loading Click Classifier - Please wait",
new FileInputStream(fname))));
Object[] modelParams = SerializationHelper.readAll(input);
// separate the classifier model from the training dataset info
// roccaClassifierModel = (AbstractClassifier) modelParams[0];
// trainedDataset = (Instances) modelParams[1];
// there are 2 different styles of model file, the original version and the version
// developed for the 2-stage classifier. Both files contain 2 objects.
// The original version contained the classifier and the training dataset. The newer
// version contains a String description and the classifier. Test the first object;
// if it's a String, then this is the newer version and the String is the description.
// If it's not a String, assume this is the old version and create a RoccaRFModel
// object from the file contents.
if (modelParams[0] instanceof String) {
clickModelList = (RoccaRFModel) modelParams[1];
} else {
AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
Instances dataset = (Instances) modelParams[1];
RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
for (int i=0; i<dataset.numClasses(); i++) {
models[i]=null;
}
clickModelList = new RoccaRFModel(classifier, dataset, models);
}
} catch (Exception ex) {
System.err.println("Deserialization of Click Classifier failed: " + ex.getMessage());
ex.printStackTrace();
roccaControl.roccaParameters.setClassifyClicks(false);
}
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) {
WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca click classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
roccaControl.roccaParameters.setClassifyClicks(false);
}
else {
try {
BufferedInputStream input = new BufferedInputStream(
(new ProgressMonitorInputStream(null, "Loading Click Classifier - Please wait",
new FileInputStream(fname))));
Object[] modelParams = SerializationHelper.readAll(input);
// separate the classifier model from the training dataset info
// roccaClassifierModel = (AbstractClassifier) modelParams[0];
// trainedDataset = (Instances) modelParams[1];
// there are 2 different styles of model file, the original version and the version
// developed for the 2-stage classifier. Both files contain 2 objects.
// The original version contained the classifier and the training dataset. The newer
// version contains a String description and the classifier. Test the first object;
// if it's a String, then this is the newer version and the String is the description.
// If it's not a String, assume this is the old version and create a RoccaRFModel
// object from the file contents.
if (modelParams[0] instanceof String) {
clickModelList = (RoccaRFModel) modelParams[1];
} else {
AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
Instances dataset = (Instances) modelParams[1];
RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
for (int i=0; i<dataset.numClasses(); i++) {
models[i]=null;
}
clickModelList = new RoccaRFModel(classifier, dataset, models);
}
} catch (Exception ex) {
System.err.println("Deserialization of Click Classifier failed: " + ex.getMessage());
ex.printStackTrace();
roccaControl.roccaParameters.setClassifyClicks(false);
}
}
}
}
// if we didn't load either classifier, don't bother loading trying to load an encounter
@ -505,43 +515,48 @@ public class RoccaClassifier {
// serialVersionUID=24 2016/08/10 added to load event classifier
if (roccaControl.roccaParameters.isClassifyEvents()) {
String fname = roccaControl.roccaParameters.roccaEventClassifierModelFilename.getAbsolutePath();
File f = new File(fname);
if (f.exists() == false) {
WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca events classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
roccaControl.roccaParameters.setClassifyEvents(false);
}
else {
try {
BufferedInputStream input = new BufferedInputStream(
(new ProgressMonitorInputStream(null, "Loading Event Classifier - Please wait",
new FileInputStream(fname))));
Object[] modelParams = SerializationHelper.readAll(input);
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) {
WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca events classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
roccaControl.roccaParameters.setClassifyEvents(false);
}
else {
try {
BufferedInputStream input = new BufferedInputStream(
(new ProgressMonitorInputStream(null, "Loading Event Classifier - Please wait",
new FileInputStream(fname))));
Object[] modelParams = SerializationHelper.readAll(input);
// there are 2 different styles of model file, the original version and the version
// developed for the 2-stage classifier. Both files contain 2 objects.
// The original version contained the classifier and the training dataset. The newer
// version contains a String description and the classifier. Test the first object;
// if it's a String, then this is the newer version and the String is the description.
// If it's not a String, assume this is the old version and create a RoccaRFModel
// object from the file contents.
if (modelParams[0] instanceof String) {
eventModelList = (RoccaRFModel) modelParams[1];
} else {
AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
Instances dataset = (Instances) modelParams[1];
RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
for (int i=0; i<dataset.numClasses(); i++) {
models[i]=null;
}
eventModelList = new RoccaRFModel(classifier, dataset, models);
}
// there are 2 different styles of model file, the original version and the version
// developed for the 2-stage classifier. Both files contain 2 objects.
// The original version contained the classifier and the training dataset. The newer
// version contains a String description and the classifier. Test the first object;
// if it's a String, then this is the newer version and the String is the description.
// If it's not a String, assume this is the old version and create a RoccaRFModel
// object from the file contents.
if (modelParams[0] instanceof String) {
eventModelList = (RoccaRFModel) modelParams[1];
} else {
AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
Instances dataset = (Instances) modelParams[1];
RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
for (int i=0; i<dataset.numClasses(); i++) {
models[i]=null;
}
eventModelList = new RoccaRFModel(classifier, dataset, models);
}
} catch (Exception ex) {
System.err.println("Deserialization of Event Classifier failed: " + ex.getMessage());
roccaControl.roccaParameters.setClassifyEvents(false);
}
}
} catch (Exception ex) {
System.err.println("Deserialization of Event Classifier failed: " + ex.getMessage());
roccaControl.roccaParameters.setClassifyEvents(false);
}
}
}
}
resetSidePanel();

27
src/rocca/RoccaDev.java Normal file
View File

@ -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
View File

@ -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
View File

@ -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;
}