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Merge remote-tracking branch 'upstream/main'

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This commit is contained in:
Jamie Mac 2022-06-30 14:08:20 +01:00
commit 8bad89ecfa
62 changed files with 1004 additions and 246 deletions
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5
.settings/org.eclipse.jdt.core.prefs
View File

@ -1,7 +1,12 @@
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=11
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=11
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error

21
buildconfigurations/Build PAMGuard DG.launch Normal file
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@ -0,0 +1,21 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<launchConfiguration type="org.eclipse.m2e.Maven2LaunchConfigurationType">
<booleanAttribute key="M2_DEBUG_OUTPUT" value="false"/>
<stringAttribute key="M2_GOALS" value="package shade:shade"/>
<booleanAttribute key="M2_NON_RECURSIVE" value="false"/>
<booleanAttribute key="M2_OFFLINE" value="false"/>
<stringAttribute key="M2_PROFILES" value=""/>
<listAttribute key="M2_PROPERTIES"/>
<stringAttribute key="M2_RUNTIME" value="EMBEDDED"/>
<booleanAttribute key="M2_SKIP_TESTS" value="true"/>
<intAttribute key="M2_THREADS" value="1"/>
<booleanAttribute key="M2_UPDATE_SNAPSHOTS" value="false"/>
<stringAttribute key="M2_USER_SETTINGS" value=""/>
<booleanAttribute key="M2_WORKSPACE_RESOLUTION" value="false"/>
<booleanAttribute key="org.eclipse.jdt.launching.ATTR_ATTR_USE_ARGFILE" value="false"/>
<booleanAttribute key="org.eclipse.jdt.launching.ATTR_SHOW_CODEDETAILS_IN_EXCEPTION_MESSAGES" value="true"/>
<booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-13/"/>
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-mx6000m&#13;&#10;-Djava.library.path=lib64"/>
<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:/PamGuard Main DG}"/>
</launchConfiguration>

2
dependency-reduced-pom.xml
View File

@ -4,7 +4,7 @@
<groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId>
<name>Pamguard Java12+</name>
<version>2.02.03</version>
<version>2.02.04a</version>
<description>Pamguard for Java 12+, using Maven to control dependcies</description>
<url>www.pamguard.org</url>
<organization>

2
pom.xml
View File

@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId>
<version>2.02.03</version>
<version>2.02.04a</version>
<name>Pamguard Java12+</name>
<description>Pamguard for Java 12+, using Maven to control dependcies</description>
<url>www.pamguard.org</url>

21
src/Acquisition/FolderInputSystem.java
View File

@ -27,6 +27,7 @@ import Acquisition.layoutFX.AcquisitionPaneFX;
import Acquisition.layoutFX.DAQSettingsPane;
import Acquisition.layoutFX.FolderInputPane;
import javafx.application.Platform;
import pamguard.GlobalArguments;
import Acquisition.pamAudio.PamAudioSystem;
import PamController.PamControlledUnitSettings;
import PamController.PamController;
@ -77,6 +78,8 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
protected long eta = -1;
private FolderInputParameters folderInputParameters;
public static final String GlobalWavFolderArg = "wavfilefolder";
/**
@ -110,12 +113,30 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
if (folderInputParameters == null)
setFolderInputParameters(new FolderInputParameters(getSystemType()));
// PamSettingManager.getInstance().registerSettings(this); //calling super already registers this in the FileInputSystem constructor
checkComandLine();
makeSelFileList();
newFileTimer = new Timer(1000, new RestartTimer());
newFileTimer.setRepeats(false);
// timer = new Timer(1000, new TimerAction());
}
/**
* Check to see if acquisition source folder was set in the command line.
*/
private void checkComandLine() {
String globalFolder = GlobalArguments.getParam(GlobalWavFolderArg);
if (globalFolder == null) {
return;
}
// see if it at least exists, though will we want to do this for Network folders ?
File aFile = new File(globalFolder);
if (aFile.exists() == false) {
System.err.println("Command line folder does not exist: " + globalFolder);
}
String[] selList = {globalFolder};
folderInputParameters.setSelectedFiles(selList);
}
/**
* Restarts after a file has ended when processing multiple files.
* 27 Jan 2011 - this now reschedules in the AWT thread

21
src/Acquisition/filedate/StandardFileDate.java
View File

@ -249,6 +249,18 @@ public class StandardFileDate implements FileDate, PamSettings {
String name = file.getName();
name = removeWildChars(name, forcedDateFormat);
String redFormat = forcedDateFormat.replace("#", "");
// see if it's only all milliseconds, i.e. format is only 'S's and > 12 of them
if (allSSSS(redFormat)) {
// try pulling a number from the name.
try {
long millis = Long.valueOf(name);
return millis;
}
catch (NumberFormatException e) {
}
}
SimpleDateFormat sdf = null;
try {
sdf = new SimpleDateFormat(redFormat);
@ -271,6 +283,15 @@ public class StandardFileDate implements FileDate, PamSettings {
return d.getTime();
}
private boolean allSSSS(String redFormat) {
for(int i = 0; i < redFormat.length(); i++) {
if (redFormat.charAt(i) != 'S') {
return false;
}
}
return true;
}
private String removeWildChars(String name, String forcedDateFormat) {
// # is the wild field i s#
if (name == null || forcedDateFormat == null) {

4
src/IshmaelLocator/IshLocProcess.java
View File

@ -380,6 +380,10 @@ abstract public class IshLocProcess extends PamProcess implements SpectrogramMar
} else {
newTime = oldTime*2;
}
/*
* Above causes same error as in Rocca and needs fixing
*/
newTime = Math.min(newTime, 600000); // don't let this exceed 10 minutes.
// System.out.println("Adjusting raw data natural lifetime from " + oldTime + " ms to " + newTime + " ms");
daqBlock.setNaturalLifetimeMillis(newTime); // increase the lifetime to try and prevent this from happening again
return;

4
src/PamController/PamguardVersionInfo.java
View File

@ -31,12 +31,12 @@ public class PamguardVersionInfo {
* Version number, major version.minorversion.sub-release.
* Note: can't go higher than sub-release 'f'
*/
static public final String version = "2.02.03";
static public final String version = "2.02.04a";
/**
* Release date
*/
static public final String date = "8 February 2022";
static public final String date = "23 June 2022";
// /**
// * Release type - Beta or Core

14
src/PamModel/PamDependency.java
View File

@ -20,12 +20,22 @@ public class PamDependency {
private String dataBlockName;
/**
*
* @param requiredDataType Class of Data unit
* @param defaultProvider Class name of default provider.
* @param dataBlockName Specific data block name
*/
public PamDependency(Class requiredDataType, String defaultProvider, String dataBlockName) {
this.requiredDataType = requiredDataType;
this.defaultProvider = defaultProvider;
this.dataBlockName = dataBlockName;
}
/**
* @param requiredDataType Class of Data unit
* @param defaultProvider Class name of default provider.
*/
public PamDependency(Class requiredDataType, String defaultProvider) {
this.requiredDataType = requiredDataType;
this.defaultProvider = defaultProvider;
@ -41,12 +51,10 @@ public class PamDependency {
/**
* @return Returns the requiredDataType.
*/
// public DataType getRequiredDataType() {
// return requiredDataType;
// }
public Class getRequiredDataType() {
return requiredDataType;
}
/**
* @return Returns the dataBlockName.
*/

2
src/PamModel/PamModel.java
View File

@ -451,7 +451,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
mi = PamModuleInfo.registerControlledUnit(EffortControl.class.getName(), EffortControl.unitType);
mi.setToolTipText("Record observer monitoring effort");
mi.setModulesMenuGroup(utilitiesGroup);
mi.setHidden(SMRUEnable.isEnable() == false);
// mi.setHidden(SMRUEnable.isEnable() == false);
mi.setToolTipText("Enables an observer to enter their name and infomation about which displays are being monitored");
mi.setMaxNumber(1);

2
src/PamModel/PamPluginInterface.java
View File

@ -67,6 +67,8 @@ public interface PamPluginInterface extends CommonPluginInterface {
* A short description of the plug in module. This text is used in various informational
* windows displayed to the user. The value returned here is typically the same as the text returned
* from the {@link #getDefaultName() getDefaultName()} method (e.g. <em>Click Detector</em> or <em>FFT (Spectrogram) Engine</em>).
* <br>This is the text used in the main 'Add Modules' menus and is used as the
* second argument to PamModuleInfo.registerControlledUnit
* <p>
* This field cannot be null.
* @return String describing the plugin. Cannot be null.

2
src/PamView/ColourArray.java
View File

@ -344,7 +344,7 @@ public class ColourArray implements Cloneable, Serializable, ManagedParameters {
* @return a contrasting colour.
*/
private Color createContrastingColour() {
Color[] tryCols = {Color.white, Color.red, Color.blue, Color.green, Color.black};
Color[] tryCols = {Color.white, Color.red, Color.CYAN, Color.blue, Color.green, Color.black};
if (colours == null) {
return tryCols[0];
}

46
src/PamView/dialog/GenericSwingDialog.java
View File

@ -1,5 +1,8 @@
package PamView.dialog;
import java.awt.Dimension;
import java.awt.Point;
import java.awt.Toolkit;
import java.awt.Window;
import javax.swing.BoxLayout;
@ -8,9 +11,9 @@ import javax.swing.JPanel;
import javax.swing.border.EmptyBorder;
public class GenericSwingDialog extends PamDialog {
private boolean allOk;
private PamDialogPanel[] dialogPanels;
private GenericSwingDialog(Window parentFrame, String title, PamDialogPanel ...dialogPanels) {
@ -25,15 +28,48 @@ public class GenericSwingDialog extends PamDialog {
}
mainPanel.add(comp);
}
setDialogComponent(mainPanel);
}
public static boolean showDialog(Window parentFrame, String title, PamDialogPanel ...dialogPanels) {
public static boolean showDialog(Window parentFrame, String title, PamDialogPanel ...dialogPanels) {
return showDialog(parentFrame, title, null, dialogPanels);
}
/**
* Show dialog at a specific location on the screen.
* @param parentFrame
* @param title
* @param screenPoint
* @param dialogPanels
* @return
*/
public static boolean showDialog(Window parentFrame, String title, Point screenPoint, PamDialogPanel ...dialogPanels) {
GenericSwingDialog swingDialog = new GenericSwingDialog(parentFrame, title, dialogPanels);
swingDialog.setParams();
swingDialog.pack();
if (screenPoint != null) {
try {
// check we're not going too far off the screen.
Dimension sz = swingDialog.getPreferredSize();
Dimension screen = null;
if (parentFrame != null) {
screen = parentFrame.getSize();
}
else {
screen = Toolkit.getDefaultToolkit().getScreenSize();
}
screenPoint.y = Math.min(screenPoint.y, screen.height-sz.height-10);
screenPoint.y = Math.max(screenPoint.y, 0);
screenPoint.x = Math.min(screenPoint.x, screen.width-sz.width-10);
screenPoint.x = Math.max(screenPoint.x, 0);
swingDialog.setLocation(screenPoint);
}
catch (Exception e) {
// shouldn't happen, but if it does, it doesn't matter much
}
}
swingDialog.setVisible(true);
return swingDialog.allOk;
}

43
src/PamView/dialog/PamDialog.java
View File

@ -3,10 +3,14 @@ package PamView.dialog;
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dialog;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.MouseInfo;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@ -225,6 +229,9 @@ abstract public class PamDialog extends JDialog {
synchronized (this) {
PamColors.getInstance().notifyContianer(this.getContentPane());
}
if (getOwner() == null) {
moveToMouseLocation();
}
}
try{
super.setVisible(visible);
@ -235,6 +242,42 @@ abstract public class PamDialog extends JDialog {
}
}
/**
* put the dialog near the mouse location.
*/
public void moveToMouseLocation() {
Point mouse = MouseInfo.getPointerInfo().getLocation();
moveToLocation(mouse);
}
public void moveToLocation(Point point) {
if (point == null) {
return;
}
// check we're not going too far off the screen.
Dimension sz = getPreferredSize();
Dimension screen = null;
int w, h;
if (getOwner() != null) {
Window owner = getOwner();
Rectangle bounds = owner.getBounds();
w = bounds.x+bounds.width;
h = bounds.y+bounds.height;
screen = getOwner().getSize();
}
else {
screen = Toolkit.getDefaultToolkit().getScreenSize();
w = screen.width;
h = screen.height;
}
point.y = Math.min(point.y, h-sz.height-10);
point.y = Math.max(point.y, 0);
point.x = Math.min(point.x, w-sz.width-10);
point.x = Math.max(point.x, 0);
setLocation(point);
}
/**
* Reschedule closing of the window to happen
* on the AWT thread using SwingUtilities.invokeLater(...)

3
src/PamView/paneloverlay/OverlayCheckboxMenuSelect.java
View File

@ -48,6 +48,9 @@ public class OverlayCheckboxMenuSelect implements ActionListener {
return;
}
DataSelectDialog dataSelectDialog = new DataSelectDialog(javaFrame, dataBlock, dataSelector, symbolChooser);
if (javaFrame == null) {
dataSelectDialog.moveToMouseLocation();
}
boolean ok = dataSelectDialog.showDialog();
if (ok) {
menuItem.setSelected(true);

1
src/PamView/paneloverlay/OverlayDataManager.java
View File

@ -42,7 +42,6 @@ public abstract class OverlayDataManager<TOverlayInfoType extends OverlayDataInf
private ParameterType[] parameterTypes;
private ParameterUnits[] parameterUnits;
/**
* @param generalProjector

3
src/PamView/paneloverlay/overlaymark/ExtMouseAdapter.java
View File

@ -87,7 +87,8 @@ public class ExtMouseAdapter {
}
final public boolean mouseWheelMoved(MouseWheelEvent e) {
return mouseWheelMoved(fxScroll(e));
// return mouseWheelMoved(fxScroll(e));
return false;
}
// private MouseEvent swingMouse(javafx.scene.input.MouseEvent e) {

103
src/PamView/paneloverlay/overlaymark/MarkOverlayDraw.java
View File

@ -76,6 +76,9 @@ public class MarkOverlayDraw extends PanelOverlayDraw {
hoverData.setTransformShape(t);
generalProjector.addHoverData(t, pamDataUnit);
}
if (drawnShape == null) {
return null;
}
return drawnShape.getBounds();
}
@ -143,52 +146,60 @@ public class MarkOverlayDraw extends PanelOverlayDraw {
* To allow for things like the rotated map which no longer show rectangles as
* rectangles, we now need to draw rectangles are irregular polygons too !
*/
int[] x = new int[4];
int[] y = new int[4];
PamCoordinate m0 = mark.getCoordinate(0);
PamCoordinate m1 = mark.getCoordinate(1);
Point p;
p = generalProjector.getCoord3d(m0.getCoordinate(0), m0.getCoordinate(1), 0).getXYPoint();
x[0] = p.x;
y[0] = p.y;
p = generalProjector.getCoord3d(m0.getCoordinate(0), m1.getCoordinate(1), 0).getXYPoint();
x[1] = p.x;
y[1] = p.y;
p = generalProjector.getCoord3d(m1.getCoordinate(0), m1.getCoordinate(1), 0).getXYPoint();
x[2] = p.x;
y[2] = p.y;
p = generalProjector.getCoord3d(m1.getCoordinate(0), m0.getCoordinate(1), 0).getXYPoint();
x[3] = p.x;
y[3] = p.y;
Polygon pgon = new Polygon(x, y, 4);
Color fillCol = getFillCol();
if (fillCol != null) {
g2d.setColor(getFillCol());
g2d.fillPolygon(pgon);
try {
int[] x = new int[4];
int[] y = new int[4];
PamCoordinate m0 = mark.getCoordinate(0);
PamCoordinate m1 = mark.getCoordinate(1);
if (m0 == null || m1 == null) {
return null;
}
Point p;
p = generalProjector.getCoord3d(m0.getCoordinate(0), m0.getCoordinate(1), 0).getXYPoint();
x[0] = p.x;
y[0] = p.y;
p = generalProjector.getCoord3d(m0.getCoordinate(0), m1.getCoordinate(1), 0).getXYPoint();
x[1] = p.x;
y[1] = p.y;
p = generalProjector.getCoord3d(m1.getCoordinate(0), m1.getCoordinate(1), 0).getXYPoint();
x[2] = p.x;
y[2] = p.y;
p = generalProjector.getCoord3d(m1.getCoordinate(0), m0.getCoordinate(1), 0).getXYPoint();
x[3] = p.x;
y[3] = p.y;
Polygon pgon = new Polygon(x, y, 4);
Color fillCol = getFillCol();
if (fillCol != null) {
g2d.setColor(getFillCol());
g2d.fillPolygon(pgon);
}
return pgon;
}
return pgon;
//
// Point p0 = generalProjector.getCoord3d(m0).getXYPoint();
// Point p1 = generalProjector.getCoord3d(m1).getXYPoint();
// g2d.setColor(getLineCol());
// g2d.setStroke(getLineStroke());
// g2d.drawLine(p0.x, p0.y, p1.x, p0.y);
// g2d.drawLine(p1.x, p0.y, p1.x, p1.y);
// g2d.drawLine(p1.x, p1.y, p0.x, p1.y);
// g2d.drawLine(p0.x, p1.y, p0.x, p0.y);
// int x = Math.min(p0.x, p1.x);
// int y = Math.min(p0.y, p1.y);
// int w = Math.abs(p0.x - p1.x);
// int h = Math.abs(p0.y - p1.y);
//
// Color fillCol = getFillCol();
// if (fillCol != null) {
// g2d.setColor(getFillCol());
// g2d.fillRect(x, y, w, h);
// }
// Rectangle r = new Rectangle(x, y, w, h);
// return r;
catch (NullPointerException e) {
return null;
}
//
// Point p0 = generalProjector.getCoord3d(m0).getXYPoint();
// Point p1 = generalProjector.getCoord3d(m1).getXYPoint();
// g2d.setColor(getLineCol());
// g2d.setStroke(getLineStroke());
// g2d.drawLine(p0.x, p0.y, p1.x, p0.y);
// g2d.drawLine(p1.x, p0.y, p1.x, p1.y);
// g2d.drawLine(p1.x, p1.y, p0.x, p1.y);
// g2d.drawLine(p0.x, p1.y, p0.x, p0.y);
// int x = Math.min(p0.x, p1.x);
// int y = Math.min(p0.y, p1.y);
// int w = Math.abs(p0.x - p1.x);
// int h = Math.abs(p0.y - p1.y);
//
// Color fillCol = getFillCol();
// if (fillCol != null) {
// g2d.setColor(getFillCol());
// g2d.fillRect(x, y, w, h);
// }
// Rectangle r = new Rectangle(x, y, w, h);
// return r;
}
@Override
@ -223,7 +234,7 @@ public class MarkOverlayDraw extends PanelOverlayDraw {
public Stroke getLineStroke() {
return plainStroke ;
}
public Stroke getFinalLineStroke() {
return dashed;
}

3
src/PamView/paneloverlay/overlaymark/OverlayMark.java
View File

@ -232,6 +232,9 @@ public class OverlayMark {
}
PamCoordinate c0 = projector.getCoord3d(coordinates.get(0));
PamCoordinate c1 = projector.getCoord3d(coordinates.get(1));
if (c0 == null || c1 == null) {
return null;
}
double x = Math.min(c0.getCoordinate(0), c1.getCoordinate(0));
double y = Math.min(c0.getCoordinate(1), c1.getCoordinate(1));
double w = Math.abs(c0.getCoordinate(0) - c1.getCoordinate(0));

2
src/PamView/paneloverlay/overlaymark/OverlayMarker.java
View File

@ -610,8 +610,6 @@ abstract public class OverlayMarker extends ExtMouseAdapter implements MarkManag
}
}
// Debug.out.printf("OverlayMarker: _ 2 In getSelectedMarkedDataUnits with %d available units\n", selectedData.size());
return selectedData;
}

3
src/PamView/symbol/modifier/SuperDetSymbolWrapper.java
View File

@ -32,12 +32,13 @@ public class SuperDetSymbolWrapper extends SymbolModifier {
@Override
public SymbolData getSymbolData(GeneralProjector projector, PamDataUnit dataUnit) {
PamDataUnit superDet = dataUnit.getSuperDetection(superDetDataBlock);
PamDataUnit superDet = dataUnit.getSuperDetection(superDetDataBlock, true);
if (superDet == null) {
return null;
}
return superDetModifier.getSymbolData(getSymbolChooser().getProjector(), superDet);
}
@Override
public String getToolTipText() {

22
src/PamguardMVC/PamDataBlock.java
View File

@ -3705,6 +3705,28 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
return blockDataSelector;
}
/**
* Convenience method to save programmer from having to call into the creator
* all the time.
*
* @param selectorName
* @param allowScores
* @param selectorType Type of selector, generally a ModuleType name, e.g. Map,
* so that options can be tailored to specific needs
* @param includeAnnotations include options from any annotators of this data stream
* @param includeSuperDetections include any possible super detection data selectors.
* @return null or a DataSelector
*/
public DataSelector getDataSelector(String selectorName, boolean allowScores, String selectorType,
boolean includeAnnotations, boolean includeSuperDetections) {
DataSelector blockDataSelector = null;
DataSelectorCreator dsc = getDataSelectCreator();
if (dsc != null) {
blockDataSelector = dsc.getDataSelector(selectorName, allowScores, selectorType, includeAnnotations, includeSuperDetections);
}
return blockDataSelector;
}
/**
* Get any information from the data block about cross referencing in database
* tables.

92
src/PamguardMVC/PamDataUnit.java
View File

@ -943,23 +943,27 @@ abstract public class PamDataUnit<T extends PamDataUnit, U extends PamDataUnit>
}
}
int nAttotations = getNumDataAnnotations();
for (int i = 0; i < nAttotations; i++) {
DataAnnotation an = getDataAnnotation(i);
DataAnnotationType ant = an.getDataAnnotationType();
String anName = ant.getAnnotationName();
String anString = an.toString();
if (anString == null) {
continue;
}
if (anString.contains("<html>")) {
anString = anString.replace("<html>", "");
}
if (anString.contains("</html>")) {
anString = anString.replace("</html>", "");
}
str += anName + ": " + anString + "<br>";
String annotString = getAnnotationsSummaryString();
if (annotString != null) {
str += annotString;
}
// int nAttotations = getNumDataAnnotations();
// for (int i = 0; i < nAttotations; i++) {
// DataAnnotation an = getDataAnnotation(i);
// DataAnnotationType ant = an.getDataAnnotationType();
// String anName = ant.getAnnotationName();
// String anString = an.toString();
// if (anString == null) {
// continue;
// }
// if (anString.contains("<html>")) {
// anString = anString.replace("<html>", "");
// }
// if (anString.contains("</html>")) {
// anString = anString.replace("</html>", "");
// }
// str += anName + ": " + anString + "<br>";
// }
// add frequency and amplitude information
@ -999,6 +1003,36 @@ abstract public class PamDataUnit<T extends PamDataUnit, U extends PamDataUnit>
return str;
}
/**
* Get string information for the annotations. Kept separate so
* it can be called in overridden version of getSummaryString()
* @return
*/
public String getAnnotationsSummaryString() {
int nAnnotations = getNumDataAnnotations();
if (nAnnotations == 0) {
return null;
}
String str = "";
for (int i = 0; i < nAnnotations; i++) {
DataAnnotation an = getDataAnnotation(i);
DataAnnotationType ant = an.getDataAnnotationType();
String anName = ant.getAnnotationName();
String anString = an.toString();
if (anString == null) {
continue;
}
if (anString.contains("<html>")) {
anString = anString.replace("<html>", "");
}
if (anString.contains("</html>")) {
anString = anString.replace("</html>", "");
}
str += anName + ": " + anString + "<br>";
}
return str.length() > 0 ? str : null;
}
/**
* Some functions to do with data annotations
*/
@ -1258,6 +1292,32 @@ abstract public class PamDataUnit<T extends PamDataUnit, U extends PamDataUnit>
return null;
}
/**
* find a super detection form the parent data block of the super detection.
* @param superDataBlock data block of super detection
* @param allowSuperSuper Allow iteration through mutilple super detection layers
* @return data unit from that block, or null.
*/
public SuperDetection getSuperDetection(PamDataBlock superDataBlock, boolean allowSuperSuper) {
synchronized (superDetectionSyncronisation) {
if (superDetections == null) return null;
SuperDetection superDet;
for (int i = 0; i < superDetections.size(); i++) {
superDet = superDetections.get(i);
if (superDet.getParentDataBlock() == superDataBlock) {
return superDet;
}
if (allowSuperSuper) {
SuperDetection supersuper = superDet.getSuperDetection(superDataBlock, allowSuperSuper);
if (supersuper != null) {
return supersuper;
}
}
}
}
return null;
}
public SuperDetection getSuperDetection(int ind) {
synchronized (superDetectionSyncronisation) {
if (superDetections == null || superDetections.size()<=ind) return null;

91
src/PamguardMVC/RawDataTransforms.java
View File

@ -100,10 +100,26 @@ public class RawDataTransforms {
private int shortestFFTLength;
private Object synchObject;
public RawDataTransforms(@SuppressWarnings("rawtypes") PamDataUnit rawDataHolder) {
/**
* Create a RawDataTransforms with a specified synchronisation object. This is mostly the data unit,
* but in some circumstances may need to be a different object to avoid thread lock.
* @param rawDataHolder
* @param synchObject
*/
public RawDataTransforms(@SuppressWarnings("rawtypes") PamDataUnit rawDataHolder, Object synchObject) {
this.rawData=(RawDataHolder) rawDataHolder;
this.dataUnit = rawDataHolder;
this.synchObject = synchObject;
}
/**
* Create raw data transforms using the rawDatAholder for synchronisation.
* @param rawDataHolder
*/
public RawDataTransforms(@SuppressWarnings("rawtypes") PamDataUnit rawDataHolder) {
this(rawDataHolder, rawDataHolder);
}
@ -118,7 +134,7 @@ public class RawDataTransforms {
return powerSpectra;
}
/**
* Get the shortest FFT length for the number of samples.
* The is the
@ -143,12 +159,24 @@ public class RawDataTransforms {
* @param fftLength
* @return Power spectrum
*/
public synchronized double[] getPowerSpectrum(int channel, int minBin, int maxBin, int fftLength) {
if (minBin==0 && maxBin>=this.getWaveData(0).length-1) {
return getPowerSpectrum(channel, fftLength);
}
if (fftLength == 0) {
fftLength = getCurrentSpectrumLength();
public double[] getPowerSpectrum(int channel, int minBin, int maxBin, int fftLength) {
synchronized (synchObject) {
if (minBin==0 && maxBin>=this.getWaveData(0).length-1) {
return getPowerSpectrum(channel, fftLength);
}
if (fftLength == 0) {
fftLength = getCurrentSpectrumLength();
}
double[] waveformTrim = new double[maxBin-minBin];
//System.out.println("minBin: " + minBin + " maxBin: " + maxBin + " raw waveform: " + this.getWaveData(channel).length);
System.arraycopy(this.getWaveData(channel), minBin, waveformTrim, 0, Math.min(this.getWaveData(channel).length-minBin-1, waveformTrim.length));
ComplexArray cData = getComplexSpectrumHann(waveformTrim, fftLength);
return cData.magsq();
}
double[] waveformTrim = new double[maxBin-minBin];
@ -300,8 +328,8 @@ public class RawDataTransforms {
public ClipSpectrogram getSpectrogram(int fftSize, int fftHop) {
return getSpectrogram( fftSize, fftHop, 1);
}
/**
* Get a spectrogram image of the wave clip. The clip is null until called. It is recalculated if the
* FFT length and/or hop size are different.
@ -437,15 +465,18 @@ public class RawDataTransforms {
* @param iChan channel number
* @return envelope of the filtered data.
*/
public synchronized double[] getFilteredAnalyticWaveform(FFTFilterParams fftFilterParams, int iChan) {
if (analyticWaveform == null) {
analyticWaveform = new double[getNChan()][];
public double[] getFilteredAnalyticWaveform(FFTFilterParams fftFilterParams, int iChan) {
synchronized (synchObject) {
if (analyticWaveform == null) {
analyticWaveform = new double[getNChan()][];
}
// if (analyticWaveform[iChan] == null) {
analyticWaveform[iChan] = hilbert.
getHilbert(getFilteredWaveData(fftFilterParams, iChan));
// }
return analyticWaveform[iChan];
}
// if (analyticWaveform[iChan] == null) {
analyticWaveform[iChan] = hilbert.
getHilbert(getFilteredWaveData(fftFilterParams, iChan));
// }
return analyticWaveform[iChan];
}
/**
@ -478,9 +509,12 @@ public class RawDataTransforms {
* @param channelIndex channel index
* @return filtered waveform data
*/
public synchronized double[] getFilteredWaveData(FFTFilterParams filterParams, int channelIndex) {
filteredWaveData = getFilteredWaveData(filterParams);
return filteredWaveData[channelIndex];
public double[] getFilteredWaveData(FFTFilterParams filterParams, int channelIndex) {
synchronized (synchObject) {
filteredWaveData = getFilteredWaveData(filterParams);
return filteredWaveData[channelIndex];
}
}
/**
@ -489,12 +523,15 @@ public class RawDataTransforms {
* @param filterParams filter parameters
* @return array of filtered data
*/
public synchronized double[][] getFilteredWaveData(FFTFilterParams filterParams) {
//System.out.println("Make filterred wave data!: " + (filterParams != oldFFTFilterParams));
if (filteredWaveData == null || filterParams != oldFFTFilterParams) {
filteredWaveData = makeFilteredWaveData(filterParams);
public double[][] getFilteredWaveData(FFTFilterParams filterParams) {
synchronized (synchObject) {
//System.out.println("Make filterred wave data!: " + (filterParams != oldFFTFilterParams));
if (filteredWaveData == null || filterParams != oldFFTFilterParams) {
filteredWaveData = makeFilteredWaveData(filterParams);
}
return filteredWaveData;
}
return filteredWaveData;
}
private double[][] makeFilteredWaveData(FFTFilterParams filterParams) {
@ -574,7 +611,7 @@ public class RawDataTransforms {
public double[] getWaveData(int channel) {
return this.rawData.getWaveData()[channel];
}
/**
* Get the wave data for the given channel in int16 format.
* @param channel channel index

27
src/PamguardMVC/dataSelector/DataSelectorCreator.java
View File

@ -62,19 +62,38 @@ public abstract class DataSelectorCreator implements PamSettings {
}
/**
* Get a data selector of a given name.
* Get a data selector of a given name including all possible options for super detections and annotations.
* @param selectorName
* @param allowScores
* @return
* @return data selector for given name.
*/
public synchronized DataSelector getDataSelector(String selectorName, boolean allowScores, String selectorType) {
return getDataSelector(selectorName, allowScores, selectorType, true, true);
}
/**
*
* Get a data selector of a given name with optional inclusion of options for annotations and super detections
* @param selectorName data selector name
* @param allowScores allow scores
* @param selectorType
* @param includeAnnotations include options from any annotators of this data stream
* @param includeSuperDetections include any possible super detection data selectors.
* @return data selector for given name with appropriate options.
*/
public synchronized DataSelector getDataSelector(String selectorName, boolean allowScores, String selectorType,
boolean includeAnnotations, boolean includeSuperDetections) {
DataSelector ds = findDataSelector(selectorName);
if (ds == null) {
ds = createDataSelector(selectorName, allowScores, selectorType);
ds = addAnnotationOptions(ds, selectorName, allowScores, selectorType);
if (includeAnnotations) {
ds = addAnnotationOptions(ds, selectorName, allowScores, selectorType);
}
ds = addSuperDetectionOptions(ds, selectorName, allowScores, selectorType);
if (includeSuperDetections) {
ds = addSuperDetectionOptions(ds, selectorName, allowScores, selectorType);
}
// and get it's params from the centralised list.
DataSelectParams params = dataSelectorSettings.getParams(selectorName);

1
src/PamguardMVC/superdet/SuperDetDataBlock.java
View File

@ -471,6 +471,7 @@ public class SuperDetDataBlock<Tunit extends SuperDetection, TSubDet extends Pam
PamDataUnit subDet = subDetectionFinder.findDataUnit(sdInfo);
sdInfo.setSubDetection(subDet);
if (subDet != null) {
aData.addSubDetection(subDet);
subDet.addSuperDetection(aData);
}
}

11
src/annotation/handler/AnnotationChoiceHandler.java
View File

@ -146,6 +146,17 @@ public abstract class AnnotationChoiceHandler extends AnnotationHandler {
* @param annotationType
*/
public boolean updateAnnotation(PamDataUnit pamDataUnit, DataAnnotationType annotationType) {
/*
* need to check this is actually the right data unit, which matches the datablock of
* this annotatoin handler. Gets very confused when dealing with superdetections
*/
if (pamDataUnit.getParentDataBlock() != this.getPamDataBlock()) {
pamDataUnit = pamDataUnit.getSuperDetection(getPamDataBlock(), true);
if (pamDataUnit == null) {
return false;
}
}
DataAnnotation existingAnnotation = pamDataUnit.findDataAnnotation(annotationType.getAnnotationClass(), annotationType.getAnnotationName());
boolean changed = false;
if (annotationType.canAutoAnnotate()) {

17
src/annotation/string/StringDialogPanel.java
View File

@ -10,6 +10,7 @@ import java.awt.event.WindowEvent;
import javax.swing.JComponent;
import javax.swing.SwingUtilities;
import PamUtils.PamCalendar;
import annotation.AnnotationDialogPanel;
import PamView.DBTextArea;
import PamView.dialog.PamDialogPanel;
@ -51,13 +52,21 @@ public class StringDialogPanel implements AnnotationDialogPanel {
note = note.trim();
}
if (note != null && note.length() > 0) {
StringAnnotation an = (StringAnnotation) pamDataUnit.findDataAnnotation(StringAnnotation.class,
stringAnnotationType.getAnnotationName());
if (an == null) {
StringAnnotation an;
/*
* always add a new annotation rather than editing the old one since
* the old one will get removed to handle annotation types which really
* do need to make a new one each time.
*/
// = (StringAnnotation) pamDataUnit.findDataAnnotation(StringAnnotation.class,
// stringAnnotationType.getAnnotationName());
// if (an == null) {
an = new StringAnnotation(stringAnnotationType);
pamDataUnit.addDataAnnotation(an);
}
// }
an.setString(textArea.getText());
pamDataUnit.setLastUpdateTime(PamCalendar.getTimeInMillis());
}
return true;
}

9
src/clickDetector/ClickBTDisplay.java
View File

@ -1572,6 +1572,9 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
}
private double clickAngleToY(ClickDetection click) {
AbstractLocalisation loc = click.getLocalisation();
// if (click.getUID() == 110006089) {
// System.out.println("Click 110006089 angle " + click.getAngle());
// }
if (loc == null) return 0;
double angle = 0;
GpsData oll;
@ -3657,15 +3660,15 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
/**
* Scroll the display to a specific event.
* @param event event to scroll to
* @param beforeTime seconds before the event to scroll to.
*/
public void gotoEvent(OfflineEventDataUnit event) {
long evStart = event.getTimeMilliseconds();
public void gotoEvent(OfflineEventDataUnit event, int beforeTime) {
long evStart = event.getTimeMilliseconds() - beforeTime*1000;
if (evStart < hScrollBar.getMinimumMillis() || evStart > hScrollBar.getMaximumMillis()) {
long range = hScrollBar.getMaximumMillis() - hScrollBar.getMinimumMillis();
hScrollBar.setRangeMillis(evStart, evStart + range, true);
}
hScrollBar.setValueMillis(evStart);
}
int playbackStatus = PlaybackProgressMonitor.PLAY_END;

4
src/clickDetector/ClickBinaryDataSource.java
View File

@ -210,8 +210,8 @@ public class ClickBinaryDataSource extends BinaryDataSource {
// long uid = binaryObjectData.getDataUnitBaseData().getUID();
// System.out.printf("Loading click with UID %d at %s\n", uid,
// PamCalendar.formatDateTime(binaryObjectData.getTimeMilliseconds()));
// if (uid == lastUID) {
// System.out.println("Click repeat UID: " + lastUID);
// if (uid == 110006089) {
// System.out.println("Click UID: " + 110006089);
// }
// else {
// lastUID = binaryObjectData.getDataUnitBaseData().getUID();

5
src/clickDetector/ClickControl.java
View File

@ -1015,9 +1015,10 @@ public class ClickControl extends PamControlledUnit implements PamSettings {
/**
* Scrolls the display to a specific event.
* @param event event to scroll to
* @param beforeTime
*/
public void gotoEvent(OfflineEventDataUnit event) {
tabPanelControl.clickDisplayManager.gotoEvent(event);
public void gotoEvent(OfflineEventDataUnit event, int beforeTime) {
tabPanelControl.clickDisplayManager.gotoEvent(event, beforeTime);
}
/**

2
src/clickDetector/ClickDetection.java
View File

@ -1328,6 +1328,8 @@ public class ClickDetection extends PamDataUnit<PamDataUnit, PamDataUnit> implem
/**
* Returns the angle in degrees for compatibilty with older version of click detector
* This is really bad to use for anything apart from two element arrays and it would be
* sensible to remove the function entirely.
* @return angle of the click detection in degrees
*/
public double getAngle() {

5
src/clickDetector/ClickDisplayManager.java
View File

@ -463,11 +463,12 @@ public class ClickDisplayManager implements PamSettings {
/**
* Scroll the time displays to a specific event.
* @param event
* @param beforeTime
*/
public void gotoEvent(OfflineEventDataUnit event) {
public void gotoEvent(OfflineEventDataUnit event, int beforeTime) {
for (int i = 0; i < windowList.size(); i++) {
if (windowList.get(i).getClass() == ClickBTDisplay.class) {
((ClickBTDisplay)windowList.get(i)).gotoEvent(event);
((ClickBTDisplay)windowList.get(i)).gotoEvent(event, beforeTime);
}
}
}

22
src/clickDetector/offlineFuncs/EventListDialog.java
View File

@ -175,9 +175,19 @@ public class EventListDialog extends PamDialog {
JPopupMenu menu = new JPopupMenu();
JMenuItem menuItem;
int evNo = event.getDatabaseIndex();
menuItem = new JMenuItem(String.format("Goto event %d ...", evNo));
menuItem.addActionListener(new GotoEvent(event));
menu.add(menuItem);
int[] beforeTimes = {0, 10, 60};
for (int i = 0; i < beforeTimes.length; i++) {
String title;
if (beforeTimes[i] == 0) {
title = String.format("Goto event %d ...", evNo);
}
else {
title = String.format("Goto %ds before event %d ...", beforeTimes[i], evNo);
}
menuItem = new JMenuItem(title);
menuItem.addActionListener(new GotoEvent(event, beforeTimes[i]));
menu.add(menuItem);
}
menuItem = new JMenuItem(String.format("Edit event %d ...", evNo));
menuItem.addActionListener(new EditEvent(event));
menu.add(menuItem);
@ -219,14 +229,16 @@ public class EventListDialog extends PamDialog {
private class GotoEvent implements ActionListener {
private OfflineEventDataUnit event;
private int beforeTime;
public GotoEvent(OfflineEventDataUnit event) {
public GotoEvent(OfflineEventDataUnit event, int beforeTime) {
this.event = event;
this.beforeTime = beforeTime;
}
@Override
public void actionPerformed(ActionEvent arg0) {
clickControl.gotoEvent(event);
clickControl.gotoEvent(event, beforeTime);
}
}

8
src/clickTrainDetector/layout/dataselector/CTDataSelectPanel.java
View File

@ -3,6 +3,7 @@ package clickTrainDetector.layout.dataselector;
import java.awt.BorderLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.util.ArrayList;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
@ -15,6 +16,7 @@ import PamView.dialog.PamDialog;
import PamView.dialog.PamDialogPanel;
import PamView.dialog.PamGridBagContraints;
import PamguardMVC.dataSelector.DataSelectParams;
import clickTrainDetector.classification.CTClassifier;
import clickTrainDetector.classification.CTClassifierManager;
import clickTrainDetector.dataselector.CTDataSelector;
import clickTrainDetector.dataselector.CTSelectParams;
@ -286,10 +288,12 @@ public class CTDataSelectPanel implements PamDialogPanel {
}
// System.out.println("No. count: " + count);
currentParams.classifier = new int[count];
currentParams.classifier = new int[count];
ArrayList<CTClassifier> classifiers = ctDataSelector.getClickControl().getClassifierManager().getCurrentClassifiers();
int used = 0;
for (int i=0; i<classifierCheckBoxes.length; i++) {
if (classifierCheckBoxes[i].isSelected()) {
currentParams.classifier[i] = ctDataSelector.getClickControl().getClassifierManager().getCurrentClassifiers().get(i).getSpeciesID();
currentParams.classifier[used++] = classifiers.get(i).getSpeciesID();
}
}

27
src/dataMap/DataMapControl.java
View File

@ -8,7 +8,6 @@ import java.util.ArrayList;
import javax.swing.SwingUtilities;
import pamScrollSystem.AbstractScrollManager;
import generalDatabase.DBControlUnit;
import binaryFileStorage.BinaryStore;
import dataMap.layoutFX.DataMapGUIFX;
@ -240,6 +239,32 @@ public class DataMapControl extends PamControlledUnit implements PamSettings {
public ArrayList<PamDataBlock> getMappedDataBlocks() {
return mappedDataBlocks;
}
/**
* Update a single data map. Useful when bringing in data
* from 'non standard' sources. Check overall time limits and
* redraw, but no total map creation.
* @param singleDataMap
*/
public void updateSingleDataMap(OfflineDataMap<?> singleDataMap) {
long newLastTime = singleDataMap.getLastDataTime();
long newFirstTime = singleDataMap.getFirstDataTime();
if (mappedDataBlocks == null) {
return;
}
for (PamDataBlock aBlock : mappedDataBlocks) {
int nMaps = aBlock.getNumOfflineDataMaps();
for (int iMap = 0; iMap < nMaps; iMap++) {
OfflineDataMap aMap = aBlock.getOfflineDataMap(iMap);
newFirstTime = Math.min(newFirstTime, aMap.getFirstDataTime());
newLastTime = Math.max(newLastTime, aMap.getLastDataTime());
}
}
firstTime = newFirstTime;
lastTime = newLastTime;
dataMapPanel.repaintAll();
dataMapPanel.getSummaryPanel().newDataSources();
}
/**
* @return the firstTime for any data in any data block

7
src/dataMap/DataMapPanel.java
View File

@ -167,5 +167,12 @@ public class DataMapPanel extends PamBorderPanel implements PamTabPanel {
}
summaryPanel.newDataSources();
}
/**
* @return the summaryPanel
*/
public SummaryPanel getSummaryPanel() {
return summaryPanel;
}
}

3
src/detectiongrouplocaliser/DetectionGroupControl.java
View File

@ -24,7 +24,8 @@ import detectiongrouplocaliser.dialogs.DisplayOptionsHandler;
import userDisplay.UserDisplayControl;
/**
* Class for grouping any type of data together.
* Class for grouping any type of data together. Not really a localiser, but
* does include some localisation options.<br>
* Will attempt to offer a variety of localisation options and will store data for each group
* in a pair of database tables.
* @author dg50

91
src/detectiongrouplocaliser/dialogs/DetectionGroupTable.java
View File

@ -56,23 +56,23 @@ import warnings.PamWarning;
public class DetectionGroupTable extends UserDisplayComponentAdapter implements DetectionGroupObserver {
private JPanel mainPanel;
private DetectionGroupProcess detectionGroupProcess;
private DetectionGroupDataBlock detectionGroupDataBlock;
private DetectionGroupControl detectionGroupControl;
private JTable table;
private TableModel tableModel;
private JScrollPane scrollPane;
private JPanel controlPanel;
private JRadioButton showAll, showCurrent;
private JButton checkIntegrity;
private boolean isViewer;
@ -80,7 +80,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
private DisplayOptionsHandler displayOptionsHandler;
private SwingTableColumnWidths widthManager;
public DetectionGroupTable(DetectionGroupProcess detectionGroupProcess) {
super();
this.detectionGroupProcess = detectionGroupProcess;
@ -95,7 +95,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
mainPanel.add(BorderLayout.CENTER, scrollPane);
detectionGroupControl.addGroupObserver(this);
table.addMouseListener(new TableMouseHandler());
if (isViewer) {
displayOptionsHandler = detectionGroupControl.getDisplayOptionsHandler();
controlPanel = new JPanel(new BorderLayout());
@ -134,9 +134,9 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
}
});
}
// sortColumnWidths();
// sortColumnWidths();
}
@ -144,7 +144,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
public Component getComponent() {
return mainPanel;
}
/* (non-Javadoc)
* @see userDisplay.UserDisplayComponentAdapter#openComponent()
*/
@ -195,7 +195,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
showPopupMenu(e);
}
}
}
@Override
@ -205,7 +205,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
public void editSelectedEvent(MouseEvent e) {
// TODO Auto-generated method stub
}
@ -234,26 +234,39 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
menuItem = annotationHandler.createAnnotationEditMenu(dgdu);
menuItem.setIcon(menuIcon);
pMenu.add(menuItem);
menuItem = new JMenuItem("Scroll to Group UID " + dgdu.getUID() + " at " + PamCalendar.formatDBDateTime(dgdu.getTimeMilliseconds()));
menuItem.setIcon(menuIcon);
menuItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
scrollToEvent(dgdu.getTimeMilliseconds());
int[] beforeTimesSecs = {0, 10, 60};
pMenu.addSeparator();
for (int i = 0; i < beforeTimesSecs.length; i++) {
int before = beforeTimesSecs[i];
String title;
if (before == 0) {
title = "Scroll to Group UID " + dgdu.getUID() + " at " + PamCalendar.formatDBDateTime(dgdu.getTimeMilliseconds());
}
});
pMenu.add(menuItem);
else {
title = String.format("Scroll to %ds before Group UID %d", before, dgdu.getUID());
}
menuItem = new JMenuItem(title);
// menuItem.setIcon(menuIcon);
menuItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
scrollToEvent(dgdu.getTimeMilliseconds()-before*1000);
}
});
pMenu.add(menuItem);
}
pMenu.show(e.getComponent(), e.getX(), e.getY());
}
protected void scrollToEvent(long timeMilliseconds) {
// start a it earlier.
timeMilliseconds -= 5000;
// now WTF - how do I tell every scroller to go to this point in time ?
// now WTF - how do I tell every scroller to go to this point in time ?
AbstractScrollManager scrollManager = AbstractScrollManager.getScrollManager();
scrollManager.startDataAt(detectionGroupDataBlock, timeMilliseconds);
}
@ -300,9 +313,9 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
TableColumn tableCol = table.getColumnModel().getColumn(i);
tableCol.setPreferredWidth(tableModel.getRelativeWidth(i)*50);
}
}
private int getViewOption() {
if (!isViewer) {
return DisplayOptionsHandler.SHOW_ALL;
@ -348,7 +361,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
@Override
public int getRowCount() {
// System.out.println("getRowCount()");
// System.out.println("getRowCount()");
if (getViewOption() == DisplayOptionsHandler.SHOW_ALL) {
firstRowToShow = 0;
return numRowsToShow = detectionGroupDataBlock.getUnitsCount();
@ -396,9 +409,9 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
return null;
}
case 2:
// if (iRow == 0) {
// System.out.println("getValueAt(0,0)");
// }
// if (iRow == 0) {
// System.out.println("getValueAt(0,0)");
// }
return dgdu.getUID();
case 3:
return PamCalendar.formatDateTime(dgdu.getTimeMilliseconds());
@ -416,16 +429,16 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
if (annotation != null) {
return annotation.toString();
}
}
}
catch (Exception e) {
return null;
}
return null;
}
@Override
public Class<?> getColumnClass(int col) {
if (col == 0) {
@ -433,7 +446,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
}
return super.getColumnClass(col);
}
/* (non-Javadoc)
* @see javax.swing.table.AbstractTableModel#fireTableStructureChanged()
*/
@ -486,7 +499,7 @@ public class DetectionGroupTable extends UserDisplayComponentAdapter implements
widthManager = new SwingTableColumnWidths(uniqueName, table);
super.setUniqueName(uniqueName);
}
}

82
src/effortmonitor/EffortControl.java
View File

@ -5,6 +5,7 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
@ -18,14 +19,18 @@ import PamController.PamController;
import PamController.PamSettingManager;
import PamController.PamSettings;
import PamUtils.PamCalendar;
import PamView.PamSidePanel;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamProcess;
import PamguardMVC.debug.Debug;
import effortmonitor.swing.EffortDataMapGraph;
import effortmonitor.swing.EffortDialog;
import effortmonitor.swing.EffortDisplayProvider;
import effortmonitor.swing.EffortSidePanel;
import pamScrollSystem.AbstractPamScroller;
import pamScrollSystem.AbstractScrollManager;
import pamScrollSystem.PamScroller;
import pamScrollSystem.PamScrollerData;
import userDisplay.UserDisplayControl;
public class EffortControl extends PamControlledUnit implements PamSettings{
@ -42,6 +47,10 @@ public class EffortControl extends PamControlledUnit implements PamSettings{
private EffortDataMapGraph dataMapGraph;
private HashMap<AbstractPamScroller, PamScrollerData> lastOuterStarts = new HashMap<>();
private EffortSidePanel effortSidePanel;
public EffortControl(String unitName) {
super("unitType", unitName);
EffortProcess effortProc = new EffortProcess();
@ -50,12 +59,22 @@ public class EffortControl extends PamControlledUnit implements PamSettings{
effortProc.addOutputDataBlock(effortDataBlock);
effortDataBlock.SetLogging(new EffortLogging(this, effortDataBlock));
dataMapGraph = new EffortDataMapGraph(this);
// PamScroller
UserDisplayControl.addUserDisplayProvider(new EffortDisplayProvider(this));
PamSettingManager.getInstance().registerSettings(this);
}
@Override
public PamSidePanel getSidePanel() {
if (effortSidePanel == null) {
effortSidePanel = new EffortSidePanel(this);
}
return effortSidePanel;
}
@Override
public void notifyModelChanged(int changeType) {
super.notifyModelChanged(changeType);
@ -65,6 +84,10 @@ public class EffortControl extends PamControlledUnit implements PamSettings{
break;
case PamController.NEW_SCROLL_TIME:
updateScrollerInfo();
break;
case PamController.DATA_LOAD_COMPLETE:
updateScrollerInfo();
break;
}
}
@ -102,7 +125,25 @@ public class EffortControl extends PamControlledUnit implements PamSettings{
*/
return;
}
boolean newOuter = isNewOuter(scroller);
if (effortParams.outserScrollOnly) {
if (newOuter) {
logOuterScroll(scroller);
}
}
else {
logInnerScroll(scroller);
}
}
private void logOuterScroll(AbstractPamScroller scroller) {
EffortDataUnit effortData = new EffortDataUnit(scroller, effortParams.getObserver(), effortParams.getObjective());
effortData.setOuterLimits();
effortDataBlock.addPamData(effortData);
}
private void logInnerScroll(AbstractPamScroller scroller) {
// checkObserverName();
EffortDataUnit effortData = effortDataBlock.findActiveUnit(scroller);
@ -129,6 +170,38 @@ public class EffortControl extends PamControlledUnit implements PamSettings{
}
}
/**
* Has the outer scroll moved.
* @param scroller
* @return true if the outer has moved.
*/
private boolean isNewOuter(AbstractPamScroller scroller) {
PamScrollerData lastData = lastOuterStarts.get(scroller);
PamScrollerData nowVal = scroller.getScrollerData();
if (nowVal == null) {
return false; // shouldn't happen !
}
boolean changed = isChanged(lastData, nowVal);
if (changed) {
lastOuterStarts.put(scroller, nowVal.clone());
}
return changed;
}
private boolean isChanged(PamScrollerData lastData, PamScrollerData nowVal) {
if (lastData == null || nowVal == null) {
return true;
}
if (lastData.getMinimumMillis() != nowVal.getMinimumMillis()) {
return true;
}
if (lastData.getMaximumMillis() != nowVal.getMaximumMillis()) {
return true;
}
return false;
}
/**
* Quick and dirty to get observer name.
*/
@ -203,9 +276,11 @@ public class EffortControl extends PamControlledUnit implements PamSettings{
existingUnit.setObserver(newParams.getObserver());
existingUnit.setObjective(newParams.getObjective());
}
return true;
}
return false;
if (effortSidePanel != null) {
effortSidePanel.updateSettings();
}
return newParams!=null;
}
public void goToTime(AbstractPamScroller scroller, long timeInMilliseconds) {
@ -235,6 +310,9 @@ public class EffortControl extends PamControlledUnit implements PamSettings{
@Override
public boolean restoreSettings(PamControlledUnitSettings pamControlledUnitSettings) {
effortParams = ((EffortParams) pamControlledUnitSettings.getSettings());
if (effortSidePanel != null) {
effortSidePanel.updateSettings();
}
return true;
}

10
src/effortmonitor/EffortDataUnit.java
View File

@ -42,6 +42,7 @@ public class EffortDataUnit extends PamDataUnit {
getBasicData().setEndTime(scroller.getValueMillis()+scroller.getVisibleAmount());
}
/**
* Constructor to use when reloading from database.
* @param databaseIndex
@ -210,4 +211,13 @@ public class EffortDataUnit extends PamDataUnit {
return runMode;
}
/**
* Set the limits as the outer limits of the scroller.
*/
public void setOuterLimits() {
setTimeMilliseconds(scroller.getMinimumMillis());
getBasicData().setEndTime(scroller.getMaximumMillis());
}
}

5
src/effortmonitor/EffortParams.java
View File

@ -16,6 +16,11 @@ public class EffortParams implements Cloneable, Serializable, ManagedParameters
public transient boolean isSet;
/**
* Only log outer scroll events when paging forwards, not every little movement.
*/
public boolean outserScrollOnly = false;
private static final int MAX_OBSERVERS = 10;
private static final int MAX_OBJECTIVES = 10;

18
src/effortmonitor/swing/EffortDialog.java
View File

@ -8,9 +8,11 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.LinkedList;
import javax.swing.ButtonGroup;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.border.TitledBorder;
import PamView.DBTextArea;
@ -29,6 +31,7 @@ public class EffortDialog extends PamDialog {
private JComboBox<String> observer;
private JComboBox<String> oldObjectives;
private DBTextArea objective;
private JRadioButton outerOnly, allActions;
private EffortDialog(Window parentFrame, EffortControl effortControl) {
super(parentFrame, effortControl.getUnitName(), false);
@ -40,6 +43,18 @@ public class EffortDialog extends PamDialog {
mainPanel.add(new JLabel("Observer name or initials"), c);
c.gridx++;
mainPanel.add(observer = new JComboBox<String>(), c);
outerOnly = new JRadioButton("Log uter scroll only");
allActions = new JRadioButton("Log all scroll actions");
ButtonGroup bg = new ButtonGroup();
bg.add(allActions);
bg.add(outerOnly);
c.gridx = 0;
c.gridy++;
c.gridwidth = 1;
mainPanel.add(allActions, c);
c.gridx+=c.gridwidth;
mainPanel.add(outerOnly, c);
c.gridx = 0;
c.gridy++;
c.gridwidth = 2;
@ -80,6 +95,8 @@ public class EffortDialog extends PamDialog {
for (String obs : oldObs) {
observer.addItem(obs);
}
allActions.setSelected(effortParams.outserScrollOnly == false);
outerOnly.setSelected(effortParams.outserScrollOnly);
oldObjectives.removeAllItems();
oldObjectives.addItem("");
for (String obj : effortParams.getRecentObjectives()) {
@ -100,6 +117,7 @@ public class EffortDialog extends PamDialog {
if (obs == null || obs.length() == 0) {
return showWarning("You must give your name or initials to contine");
}
effortParams.outserScrollOnly = outerOnly.isSelected();
effortParams.setObserver(obs);
effortParams.setObjective(objective.getText());
return true;

99
src/effortmonitor/swing/EffortSidePanel.java Normal file
View File

@ -0,0 +1,99 @@
package effortmonitor.swing;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JTextField;
import javax.swing.border.TitledBorder;
import PamView.PamSidePanel;
import PamView.component.PamSettingsIconButton;
import PamView.dialog.PamCheckBox;
import PamView.dialog.PamGridBagContraints;
import PamView.dialog.PamLabel;
import PamView.dialog.PamTextField;
import PamView.panel.PamPanel;
import effortmonitor.EffortControl;
import effortmonitor.EffortObserver;
import effortmonitor.EffortParams;
public class EffortSidePanel implements PamSidePanel, EffortObserver {
private PamPanel mainPanel;
private PamTextField person;
private PamCheckBox logging;
private PamSettingsIconButton settingsButton;
private EffortControl effortControl;
public EffortSidePanel(EffortControl effortControl) {
this.effortControl = effortControl;
mainPanel = new PamPanel(new GridBagLayout());
mainPanel.setBorder(new TitledBorder(effortControl.getUnitName()));
GridBagConstraints c = new PamGridBagContraints();
mainPanel.add(new PamLabel("Person ", JLabel.RIGHT), c);
c.gridx++;
mainPanel.add(person = new PamTextField(6), c);
person.setEditable(false);
c.gridx = 0;
c.gridy++;
c.gridwidth = 1;
mainPanel.add(logging = new PamCheckBox("Log effort"), c);
c.gridx += c.gridwidth;
mainPanel.add(settingsButton = new PamSettingsIconButton(), c);
settingsButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
settings();
}
});
effortControl.addObserver(this);
logging.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
loggingButton();
}
});
updateSettings();
}
protected void loggingButton() {
effortControl.setOnEffort(logging.isSelected());
}
protected void settings() {
effortControl.showSettingsDialog(effortControl.getGuiFrame(), null);
}
public void updateSettings() {
EffortParams params = effortControl.getEffortParams();
person.setText(params.getObserver());
logging.setSelected(params.isSet);
}
@Override
public JComponent getPanel() {
return mainPanel;
}
@Override
public void rename(String newName) {
mainPanel.setBorder(new TitledBorder(newName));
}
@Override
public void statusChange() {
updateSettings();
}
}

2
src/generalDatabase/DBControl.java
View File

@ -91,6 +91,8 @@ PamSettingsSource {
private boolean fullTablesCheck = false;
static private String dbUnitType = "Pamguard Database";
static public final String GlobalDatabaseNameArg = "-databasefile";
private DBControl THIS;

6
src/generalDatabase/PamTableItem.java
View File

@ -426,7 +426,11 @@ public class PamTableItem implements Cloneable {
return (Double) value;
}
/**
* Get a float value, being aware that some DBMS may have
* decided to store as a Double anyway. Return Float.NaN for null data
* @return float value or NaN
*/
public float getFloatValue() {
if (value == null) {
return Float.NaN;

3
src/generalDatabase/backup/DatabaseBackupStream.java
View File

@ -120,6 +120,9 @@ public class DatabaseBackupStream extends FileBackupStream {
public FileLocation getSourceLocation() {
File dbFile = getDatabaesFile();
if (dbFile == null) {
return null;
}
FileLocation sl = new FileLocation();
sl.path = dbFile.getAbsolutePath();
sl.canEditMask = false;

60
src/generalDatabase/sqlite/SqliteDialogPanel.java
View File

@ -91,69 +91,15 @@ public class SqliteDialogPanel implements SystemDialogPanel {
String newDB = sqliteSystem.browseDatabases(parent);
if (newDB != null) {
// see if this file exists in the list and if it does, remove it
for (int i = 0; i < sqliteSystem.getRecentDatabases().size(); i++) {
if (sqliteSystem.getRecentDatabases().get(i).toString().equalsIgnoreCase(newDB)) {
sqliteSystem.getRecentDatabases().remove(i);
}
}
// then insert the file at the top of the list.
File newFile = new File(newDB);
// if the file doesn't exit, consider creating it.
if (newFile.exists() == false) {
newFile = createNewDatabase(newDB);
if (newFile == null) {
System.out.println("Unable to create "+newFile);
return;
}
}
sqliteSystem.getRecentDatabases().add(0, newFile);
sqliteSystem.setDatabaseName(newDB);
setParams();
}
}
}
public File createNewDatabase(String newDB) {
File newFile = new File(newDB);
newFile = PamFileFilter.checkFileEnd(newFile, ".sqlite3", true);
int ans = JOptionPane.showConfirmDialog(parent, "Create blank database " + newFile.getAbsolutePath() + " ?", "Sqlite", JOptionPane.OK_CANCEL_OPTION);
if (ans == JOptionPane.CANCEL_OPTION) {
return null;
}
Connection connection = null;
try {
// create a database connection;
// Sqlite will automatically create file if it does not exist;
connection = DriverManager.getConnection("jdbc:sqlite:" + newFile);
}
catch(SQLException e)
{
System.err.println(e.getMessage());
}
finally
{
try
{
if(connection != null)
connection.close();
}
catch(SQLException e)
{
// connection close failed.
System.err.println(e);
}
}
return newFile;
}
}

107
src/generalDatabase/sqlite/SqliteSystem.java
View File

@ -3,6 +3,7 @@ package generalDatabase.sqlite;
import generalDatabase.pamCursor.NonScrollablePamCursor;
import generalDatabase.pamCursor.PamCursor;
import javafx.stage.FileChooser;
import pamguard.GlobalArguments;
import java.awt.Component;
import java.awt.Desktop;
@ -10,10 +11,12 @@ import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.util.ArrayList;
import javax.swing.JFileChooser;
import javax.swing.JOptionPane;
import org.sqlite.SQLiteConfig;
@ -82,6 +85,53 @@ public class SqliteSystem extends DBSystem implements PamSettings {
if (sqliteParameters.getRecentDatabases() == null) {
sqliteParameters.setRecentDatabases(new ArrayList<File>());
}
checkCommandLineOption();
}
/**
* Check to see if the database name was included as a command line option,
* in which case, put it at the top of the list. this is better than just using
* it,since it then gets stored within it's own settings.
*/
private void checkCommandLineOption() {
// TODO Auto-generated method stub
/*
* If a database name was passed as a global argument, then use the passed name instead of
* the name in the list of recent databases.
*/
String commandName = GlobalArguments.getParam(DBControl.GlobalDatabaseNameArg);
if (commandName == null) {
return;
}
setDatabaseName(commandName);
}
/**
* Set the database name, check it exists, check it's end
* and add to top of list of databases.
* @param databaseName
*/
public void setDatabaseName(String databaseName) {
// see if this file exists in the list and if it does, remove it
for (int i = 0; i < getRecentDatabases().size(); i++) {
if (getRecentDatabases().get(i).toString().equalsIgnoreCase(databaseName)) {
getRecentDatabases().remove(i);
}
}
// then insert the file at the top of the list.
File newFile = new File(databaseName);
// if the file doesn't exit, consider creating it.
if (newFile.exists() == false) {
newFile = createNewDatabase(databaseName, null, true);
if (newFile == null) {
System.out.println("Unable to create "+newFile);
return;
}
}
getRecentDatabases().add(0, newFile);
}
@Override
@ -111,6 +161,52 @@ public class SqliteSystem extends DBSystem implements PamSettings {
}
return null;
}
/**
* Create a new empty database file.
* @param newDB full path for database file (can be missing .sqlit3 if you like - this will get checked and added).
* @param parent window (for confirm dialog, can be null)
* @param askFirst show a confirm dialog before creating the database file.
* @return a path to the file, whether created or no.
*/
public File createNewDatabase(String newDB, Component parent, boolean askFirst) {
File newFile = new File(newDB);
newFile = PamFileFilter.checkFileEnd(newFile, ".sqlite3", true);
if (askFirst) {
int ans = JOptionPane.showConfirmDialog(parent, "Create blank database " + newFile.getAbsolutePath() + " ?", "Sqlite", JOptionPane.OK_CANCEL_OPTION);
if (ans == JOptionPane.CANCEL_OPTION) {
return null;
}
}
Connection connection = null;
try {
// create a database connection;
// Sqlite will automatically create file if it does not exist;
connection = DriverManager.getConnection("jdbc:sqlite:" + newFile);
}
catch(SQLException e)
{
System.err.println(e.getMessage());
}
finally
{
try
{
if(connection != null)
connection.close();
}
catch(SQLException e)
{
// connection close failed.
System.err.println(e);
}
}
return newFile;
}
@Override
public boolean canCreate() {
@ -208,6 +304,15 @@ public class SqliteSystem extends DBSystem implements PamSettings {
@Override
public String getDatabaseName() {
/*
* If a database name was passed as a global argument, then use the passed name instead of
* the name in the list of recent databases.
*/
String commandName = GlobalArguments.getParam(DBControl.GlobalDatabaseNameArg);
if (commandName != null) {
return commandName;
}
if (getRecentDatabases() == null) return null;
if (getRecentDatabases().size() < 1) return null;
return getRecentDatabases().get(0).getAbsolutePath();
@ -271,7 +376,7 @@ public class SqliteSystem extends DBSystem implements PamSettings {
public boolean restoreSettings(PamControlledUnitSettings pamControlledUnitSettings) {
Object settings = pamControlledUnitSettings.getSettings();
if (settings instanceof ArrayList) {
if (settings instanceof ArrayList) { // deal with old format which just stored a list.
sqliteParameters.getRecentDatabases().clear();
sqliteParameters.getRecentDatabases().addAll((ArrayList) settings);
}

2
src/group3dlocaliser/Group3DProcess.java
View File

@ -193,6 +193,7 @@ public class Group3DProcess extends PamProcess implements DetectionGroupMonitor
// will have to make a data unit for each group now...
Group3DDataUnit[] group3dDataUnits = new Group3DDataUnit[nGroups];
// System.out.println("Enter newGRoupedDataSet with groups: " + detectionGroupedSet.getNumGroups());
// if (detectionGroupedSet.hasUID(14045004731L)) {
// Debug.out.println(" found it");
// }
@ -209,6 +210,7 @@ public class Group3DProcess extends PamProcess implements DetectionGroupMonitor
// localiserAlgorithm3D.process(detectionGroupedSet.getGroup(i));
abstractLocalisation = localiserAlgorithm3D.runModel(group3dDataUnits[i], null, false);
if (abstractLocalisation == null) {
System.out.println("Group 3D process null localisation from " + localiserAlgorithm3D.getName());
continue;
}
// log all outputs ..

10
src/group3dlocaliser/grouper/DetectionGrouper.java
View File

@ -160,9 +160,15 @@ public class DetectionGrouper {
if (motherGroup.getTotalChannelMap() == 0) {
return;
}
// if (maybeCloseMotherGroup(0, sampleNumber - (long) (sampleRate / 2))) {
// motherGroup.
// int lastGroup = motherGroup.getLastChannelGroup();
long buffer = (long) this.maxInterGroupSample;
// if (shouldCloseMotherGroup(lastGroup, sampleNumber, buffer)) {
if (sampleNumber > motherGroup.getVeryLastSample() + buffer + sampleRate) {
closeMotherGroup();
// if (maybeCloseMotherGroup(motherGroup.getLastChannelGroup(), sampleNumber - (long) (sampleRate / 2))) {
// System.out.println("Mother group closed on timer");
// }
}
}
private synchronized boolean maybeCloseMotherGroup(int iChanGroup, long currentSample) {

10
src/group3dlocaliser/grouper/FirstGrouping.java
View File

@ -24,6 +24,8 @@ public class FirstGrouping {
private long veryLastSample;
private int[] groupCount;
private int lastChannelGroup;
public FirstGrouping(int nChannelGroups, int channelGroup, PamDataUnit pamDataUnit) {
this.nChannelGroups = nChannelGroups;
@ -44,6 +46,7 @@ public class FirstGrouping {
lastSamples[channelGroup] += pamDataUnit.getSampleDuration();
}
veryLastSample = Math.max(veryLastSample, lastSamples[channelGroup]);
lastChannelGroup = channelGroup;
}
// /**
@ -92,4 +95,11 @@ public class FirstGrouping {
return dataUnits;
}
/**
* @return the lastChannelGroup
*/
public int getLastChannelGroup() {
return lastChannelGroup;
}
}

12
src/offlineProcessing/OfflineTask.java
View File

@ -4,6 +4,7 @@ import generalDatabase.DBControlUnit;
import generalDatabase.PamConnection;
import generalDatabase.SQLLogging;
import generalDatabase.SQLTypes;
import generalDatabase.SuperDetLogging;
import generalDatabase.clauses.FixedClause;
import generalDatabase.clauses.FromClause;
import generalDatabase.clauses.PAMSelectClause;
@ -354,6 +355,7 @@ public abstract class OfflineTask<T extends PamDataUnit> {
}
aBlock.clearAll();
SQLLogging logging = aBlock.getLogging();
if (logging == null) {
@ -382,7 +384,15 @@ public abstract class OfflineTask<T extends PamDataUnit> {
System.out.println("Unknown data selection option in OfflineTask.deleteOldData: " + taskGroupParams.dataChoice);
return;
}
logging.deleteData(clause);
while (logging != null) {
logging.deleteData(clause);
if (logging instanceof SuperDetLogging) {
logging = ((SuperDetLogging) logging).getSubLogging();
}
else {
break;
}
}
}

2
src/pamScrollSystem/PamScrollerData.java
View File

@ -58,7 +58,7 @@ public class PamScrollerData implements Serializable, Cloneable {
@Override
protected PamScrollerData clone() {
public PamScrollerData clone() {
try {
return (PamScrollerData) super.clone();
} catch (CloneNotSupportedException e) {

13
src/pamguard/Pamguard.java
View File

@ -23,6 +23,7 @@ package pamguard;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import Acquisition.FolderInputSystem;
import PamController.PamController;
import PamController.PamGUIManager;
import PamController.PamSettingManager;
@ -41,6 +42,8 @@ import PamView.dialog.warn.WarnOnce;
import PamguardMVC.debug.Debug;
import binaryFileStorage.BinaryStore;
import dataPlotsFX.JamieDev;
import generalDatabase.DBControl;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
@ -216,11 +219,15 @@ public class Pamguard {
}
else if (anArg.equalsIgnoreCase(BinaryStore.GlobalFolderArg)) {
// output folder for binary files.
GlobalArguments.setParam(anArg, args[iArg++]);
GlobalArguments.setParam(BinaryStore.GlobalFolderArg, args[iArg++]);
}
else if (anArg.equalsIgnoreCase("-databasefile")) {
else if (anArg.equalsIgnoreCase(DBControl.GlobalDatabaseNameArg)) {
// database file name
GlobalArguments.setParam(anArg, args[iArg++]);
GlobalArguments.setParam(DBControl.GlobalDatabaseNameArg, args[iArg++]);
}
else if (anArg.equalsIgnoreCase(FolderInputSystem.GlobalWavFolderArg)) {
// source folder for wav files (or other supported sound files)
GlobalArguments.setParam(FolderInputSystem.GlobalWavFolderArg, args[iArg++]);
}
else if (anArg.equalsIgnoreCase("-help")) {
System.out.println("--PamGuard Help");

19
src/rocca/RoccaControl.java
View File

@ -69,6 +69,11 @@ public class RoccaControl extends PamControlledUnit implements PamSettings {
*/
public static final String unitType = "Rocca";
/*
* Max max data keep time to avoid memory overflows. Currently at 15 minutes.
*/
private static final int MAXMAXDATAKEEPTIME = 900000;
/**
* reference to the ClickControl module when it is loaded in Viewer mode
*/
@ -193,6 +198,17 @@ public class RoccaControl extends PamControlledUnit implements PamSettings {
return 1;
}
/**
* A bit of a fudge to deal with some old code which kept doubling the
* keep time of the raw data, which eventually led to raw data using too
* much memory and bringing down PG. I don't fully understand that code so
* have left as much of it as possible, but put this in as an absolute
* maximum which cannot be exceeded.
* @return max in milliseconds as int, which is what's used in PAMDataBlock.
*/
public int getMaxDataKeepTime() {
return MAXMAXDATAKEEPTIME;
}
/**
*
* @param eventList
@ -242,18 +258,21 @@ public class RoccaControl extends PamControlledUnit implements PamSettings {
(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 35. ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.005 ||
rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
rcdb.setNaturalLifetimeMillis(0);
return;
}
if (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.setNaturalLifetimeMillis(0);
return;
}
if (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.setNaturalLifetimeMillis(0);
return;
}

13
src/rocca/RoccaProcess.java
View File

@ -363,6 +363,9 @@ public class RoccaProcess extends PamProcess {
// 2017/12/4 set the natural lifetime to Integer.Max, so that we definitely keep all of the data
// units during this code block. Set the lifetime back to 0 at the end of the block
/*
* DG June '22 made sure this is the case when the function returns early !
*/
rcdb.setNaturalLifetimeMillis(Integer.MAX_VALUE);
rcdb.calculateStatistics();
@ -385,6 +388,7 @@ 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);
return;
}
if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("HIWhist.model") &&
@ -398,6 +402,7 @@ 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);
return;
}
if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("NWAtlWhist.model") &&
@ -407,6 +412,7 @@ 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);
return;
}
}
@ -736,13 +742,15 @@ public class RoccaProcess extends PamProcess {
PamUtils.makeChannelMap(lowestChanList));
int firstIndx = prdb.getUnitIndex(firstRDU);
if (firstIndx==-1) {
System.out.println("RoccaProcess: Cannot determine firstIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
int newTime;
if (prdb.getNaturalLifetimeMillis() > Integer.MAX_VALUE/2) {
newTime = Integer.MAX_VALUE;
} else {
newTime = prdb.getNaturalLifetimeMillis()*2;
}
// stop it getting silly.
newTime = Math.min(newTime, roccaControl.getMaxDataKeepTime());
System.out.println("RoccaProcess: Cannot determine firstIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
prdb.setNaturalLifetimeMillis(newTime); // increase the lifetime to try and prevent this from happening again
return null;
}
@ -769,13 +777,14 @@ public class RoccaProcess extends PamProcess {
PamUtils.makeChannelMap(highestChanList));
int lastIndx = prdb.getUnitIndex(lastRDU);
if (lastIndx==-1) {
System.out.println("RoccaProcess: Cannot determine lastIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
int newTime;
if (prdb.getNaturalLifetimeMillis() > Integer.MAX_VALUE/2) {
newTime = Integer.MAX_VALUE;
} else {
newTime = prdb.getNaturalLifetimeMillis()*2;
}
newTime = Math.min(newTime, roccaControl.getMaxDataKeepTime());
System.out.println("RoccaProcess: Cannot determine lastIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
prdb.setNaturalLifetimeMillis(newTime); // increase the lifetime to try and prevent this from happening again
return null;
}

8
src/rocca/RoccaSidePanel.java
View File

@ -114,7 +114,13 @@ public class RoccaSidePanel extends PamObserverAdapter implements PamSidePanel
this.rsdb = new RoccaSightingDataBlock
(roccaControl.roccaProcess,
roccaControl.roccaParameters.getChannelMap());
rsdb.setNaturalLifetimeMillis(Integer.MAX_VALUE);
/*
* this one probably OK to never delete ? Nope lots of stuff goes in
* here, so it seems it will eventually bring the system down.
*/
rsdb.setNaturalLifetimeMillis(roccaControl.getMaxDataKeepTime());
rdl = new RoccaDetectionLogger(this, rsdb);
rsdb.SetLogging(rdl);
rsdb.setMixedDirection(PamDataBlock.MIX_INTODATABASE);

10
src/rocca/RoccaWhistleSelect.java
View File

@ -171,6 +171,8 @@ public class RoccaWhistleSelect extends PamProcess implements SpectrogramMarkObs
roccaControl.roccaSidePanel.sidePanel.addASighting(false);
// if the user hit cancel, just exit
if (dummy == RoccaSightingDataUnit.NONE) {
selectedWhistle.setNaturalLifetimeMillis(0);
selectedWhistleRaw.setNaturalLifetimeMillis(0);
return;
}
}
@ -198,6 +200,14 @@ public class RoccaWhistleSelect extends PamProcess implements SpectrogramMarkObs
selectedWhistleRaw,
display,
channel);
/**
* DG June '22.
* I hope IT's K to set these back here. It's possible it's also
* done elsewhere.
*/
selectedWhistle.setNaturalLifetimeMillis(0);
selectedWhistleRaw.setNaturalLifetimeMillis(0);
}
}

2
src/simulatedAcquisition/SimProcess.java
View File

@ -304,7 +304,7 @@ public class SimProcess extends DaqSystem implements PamSettings {
/* simulate the noise, need to divide fs by 2 to only generate for 0 to Nyquist to get correct values out.
* that match the results of the noise band monitor modules.
*/
double dbNse = simParameters.backgroundNoise + 10*Math.log10(getSampleRate()/2);
double dbNse = simParameters.backgroundNoise + 10*Math.log10(getSampleRate()/2.);
nse = daqControl.getDaqProcess().dbMicropascalToSignal(i, dbNse);
generateNoise(channelData, nse);
// generateNoiseQuickly(channelData, nse, i);

3
src/simulatedAcquisition/sounds/SimSignals.java
View File

@ -27,6 +27,9 @@ public class SimSignals {
simSignalList.add(new ClickSound("Click", 3000, 3000, 2e-3, WINDOWTYPE.DECAY));
simSignalList.add(new ClickSound("Chirp", 3000, 6000, 0.1, WINDOWTYPE.TAPER10));
simSignalList.add(new ClickSound("Chirp", 3000, 8000, 0.5, WINDOWTYPE.TAPER10));
simSignalList.add(new ClickSound("Dolphin Click", 60000, 60000, 20.e-6, WINDOWTYPE.DECAY));
simSignalList.add(new ClickSound("Fin 20Hz", 20, 20, 0.5, WINDOWTYPE.HANN));
simSignalList.add(new ClickSound("Fin 40Hz", 40, 40, 0.5, WINDOWTYPE.HANN));
// simSignalList.add(new LinearChirp(simProcess.getSampleRate(), 3000, 6000, 0.1));
// simSignalList.add(new LinearChirp(simProcess.getSampleRate(), 3000, 8000, .5));
simSignalList.add(new RandomWhistles());

3
src/warnings/SingleLineWarningDisplay.java
View File

@ -67,7 +67,8 @@ public class SingleLineWarningDisplay implements WarningDisplay {
lastWarning.setToolTipText(null);
}
else {
String str = String.format("Warning: %s-%s ", w.getWarningSource(), w.getWarningMessage());
String str = w.getWarnignLevel() > 0 ? "Warning: " : "";
str += String.format("%s-%s ", w.getWarningSource(), w.getWarningMessage());
lastWarning.setText(str);
lastWarning.setWarningLevel(w.getWarnignLevel());
lastWarning.setToolTipText(w.getWarningTip());