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

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This commit is contained in:
Douglas Gillespie 2025-04-02 09:29:43 +01:00
commit 7665c1257f
20 changed files with 602 additions and 191 deletions
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2
pom.xml
View File

@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId>
<version>2.02.16</version>
<version>2.02.16a</version>
<name>Pamguard</name>
<description>Pamguard using Maven to control dependencies</description>
<url>www.pamguard.org</url>

361
src/PamController/PamController.java
View File

@ -246,11 +246,11 @@ public class PamController implements PamControllerInterface, PamSettings {
private int nStarts;
private RestartRunnable restartRunnable;
private boolean batchFirst = true; // flag for starting batch offline tasks.
/**
* Subclass of URLClassLoader, to handle loading of plugins
*/
// private static PluginClassloader classLoader;
// private static PluginClassloader classLoader;
private PamController(int runMode, Object object) {
@ -285,7 +285,27 @@ public class PamController implements PamControllerInterface, PamSettings {
guiFrameManager = PamGUIManager.createGUI(this, object);
guiFrameManager.init(); // perform any start up processes for the GUI.
installFolder = getInstallLocation();
setupPamguard();
setupGarbageCollector();
// if (PamGUIManager.getGUIType() == PamGUIManager.NOGUI) {
// }
// diagnosticTimer = new Timer(1000, new DiagnosticTimer());
// diagnosticTimer.start();
}
/**
* Get the location of the install folder. Note that this will be system dependent.
* @return the location of the install folder.
*/
private String getInstallLocation() {
// figure out the installation folder
String installFolder = null;
try {
File theURL = new File(
this.getClass().getProtectionDomain().getCodeSource().getLocation().toURI().getPath());
@ -296,15 +316,18 @@ public class PamController implements PamControllerInterface, PamSettings {
installFolder = null;
}
setupPamguard();
//if a Mac AND we are inside the applications folder then
if (System.getProperty("os.name").startsWith("Mac")) {
String macAppFolder = new String("/Applications/PAMGuard.app/Contents");
if (installFolder.startsWith(macAppFolder)) {
//PAMGuard is running form a .app bundle in the Applications directory on macOS
installFolder = macAppFolder + File.separator;
}
//otherwise the install folder stays the same as we are using an IDE
}
setupGarbageCollector();
// if (PamGUIManager.getGUIType() == PamGUIManager.NOGUI) {
// }
// diagnosticTimer = new Timer(1000, new DiagnosticTimer());
// diagnosticTimer.start();
return installFolder;
}
class DiagnosticTimer implements ActionListener {
@ -549,9 +572,9 @@ public class PamController implements PamControllerInterface, PamSettings {
* to update existing settings That should probably be done here before the
* final calls to setup processes, etc.
*/
// if (getRunMode() == RUN_PAMVIEW && PamSettingManager.remote_psf != null) {
// loadOtherSettings(PamSettingManager.remote_psf);
// }
// if (getRunMode() == RUN_PAMVIEW && PamSettingManager.remote_psf != null) {
// loadOtherSettings(PamSettingManager.remote_psf);
// }
/*
* Get any other required modules for this run mode.
@ -731,9 +754,9 @@ public class PamController implements PamControllerInterface, PamSettings {
// }
void setupProcesses() {
// for (int i = 0; i < pamControlledUnits.size(); i++) {
// pamControlledUnits.get(i).setupControlledUnit();
// }
// for (int i = 0; i < pamControlledUnits.size(); i++) {
// pamControlledUnits.get(i).setupControlledUnit();
// }
pamConfiguration.setupProcesses();
}
@ -872,7 +895,7 @@ public class PamController implements PamControllerInterface, PamSettings {
System.err.println("Exception while loading " + moduleName);
//this.removeControlledUnt(unitBeingLoaded);
this.clearLoadedUnit();
}
if (unitBeingLoaded == null) {
return null;
@ -962,22 +985,22 @@ public class PamController implements PamControllerInterface, PamSettings {
return false;
}
// private boolean reOrderModules(int[] newOrder) {
//
// if (pamControlledUnits.size() != newOrder.length) return false;
//
// ArrayList<PamControlledUnit> newList = new ArrayList<PamControlledUnit>();
//
// for (int i = 0; i < newOrder.length; i++) {
//
// newList.add(pamControlledUnits.get(newOrder[i]));
//
// }
//
// pamControlledUnits = newList;
//
// return true;
// }
// private boolean reOrderModules(int[] newOrder) {
//
// if (pamControlledUnits.size() != newOrder.length) return false;
//
// ArrayList<PamControlledUnit> newList = new ArrayList<PamControlledUnit>();
//
// for (int i = 0; i < newOrder.length; i++) {
//
// newList.add(pamControlledUnits.get(newOrder[i]));
//
// }
//
// pamControlledUnits = newList;
//
// return true;
// }
/**
* Swaps the positions of two modules in the main list of modules and also swaps
@ -1155,7 +1178,7 @@ public class PamController implements PamControllerInterface, PamSettings {
* later in the AWT event queue.
*/
public void startLater() {
// SwingUtilities.invokeLater(new StartLater(true));
// SwingUtilities.invokeLater(new StartLater(true));
startLater(true);
}
@ -1316,17 +1339,17 @@ public class PamController implements PamControllerInterface, PamSettings {
* off, etc.
* This get's handled even if there is a worker thread.
*/
// String reprocessString = GlobalArguments.getParam(ReprocessStoreChoice.paramName);
// ReprocessStoreChoice reprocesschoice = null;
// if (reprocessString != null) {
// try {
// reprocesschoice = ReprocessStoreChoice.valueOf(reprocessString);
// }
// catch (Exception e) {
// System.out.println("Invalid reprocess choice command: " + reprocessString);
// }
// }
// String reprocessString = GlobalArguments.getParam(ReprocessStoreChoice.paramName);
// ReprocessStoreChoice reprocesschoice = null;
// if (reprocessString != null) {
// try {
// reprocesschoice = ReprocessStoreChoice.valueOf(reprocessString);
// }
// catch (Exception e) {
// System.out.println("Invalid reprocess choice command: " + reprocessString);
// }
// }
if (saveSettings && getRunMode() == RUN_NORMAL) { // only true on a button press or network start.
checkReprocessManager(saveSettings, startTime);
}
@ -1335,7 +1358,7 @@ public class PamController implements PamControllerInterface, PamSettings {
}
return true;
}
/**
* Check the reprocess manager in a swing worker thread.
* @param saveSettings
@ -1344,17 +1367,17 @@ public class PamController implements PamControllerInterface, PamSettings {
private void checkReprocessManager(boolean saveSettings, long startTime) {
ReprocessMon mon = new ReprocessMon(saveSettings, startTime);
ReprocessManager reprocessManager = new ReprocessManager();
// boolean goonthen = reprocessManager.checkOutputDataStatus();
// if (!goonthen) {
// System.out.println(
// "Data processing will not start since you've chosen not to overwrite existing output data");
// pamStop();
// setPamStatus(PAM_IDLE);
// return false;
// }
// boolean goonthen = reprocessManager.checkOutputDataStatus();
// if (!goonthen) {
// System.out.println(
// "Data processing will not start since you've chosen not to overwrite existing output data");
// pamStop();
// setPamStatus(PAM_IDLE);
// return false;
// }
reprocessManager.startCheckingThread(getMainFrame(), mon);
}
private class ReprocessMon implements ReprocessManagerMonitor {
private boolean saveSettings;
private long startTime;
@ -1368,7 +1391,7 @@ public class PamController implements PamControllerInterface, PamSettings {
reprocessManagerDone(continueStart, continueStart, startTime);
}
}
private void reprocessManagerDone(boolean goonthen, boolean saveSettings, long startTime) {
if (!goonthen) {
System.out.println(
@ -1392,7 +1415,7 @@ public class PamController implements PamControllerInterface, PamSettings {
public boolean continueStart(boolean saveSettings, long startTime) {
if (saveSettings) {
startTime = PamCalendar.getSessionStartTime();
// System.out.printf("Saving settings for start time %s\n", PamCalendar.formatDBDateTime(startTime));
// System.out.printf("Saving settings for start time %s\n", PamCalendar.formatDBDateTime(startTime));
saveSettings(PamCalendar.getSessionStartTime());
}
@ -1464,10 +1487,10 @@ public class PamController implements PamControllerInterface, PamSettings {
// start the status check timer, so that we know when all the threads have
// actually stopped
// statusCheckThread = new Thread(new StatusTimer());
// statusCheckThread.start();
// statusCheckThread = new Thread(new StatusTimer());
// statusCheckThread.start();
ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
long stopTime = PamCalendar.getTimeInMillis();
// tell all controlled units to stop
@ -1561,13 +1584,13 @@ public class PamController implements PamControllerInterface, PamSettings {
private void finishStopping() {
detectorEndThread = null;
// this was never getting invoked for some reason.
// SwingUtilities.invokeLater(new Runnable() {
//
// @Override
// public void run() {
// SwingUtilities.invokeLater(new Runnable() {
//
// @Override
// public void run() {
pamStopped();
// }
// });
// }
// });
}
/**
@ -1579,7 +1602,7 @@ public class PamController implements PamControllerInterface, PamSettings {
* If it's running in multithreading mode, then at this point it is necessary to
* make sure that all internal datablock buffers have had time to empty.
*/
// System.out.println("Arrived in PamStopped() in thread " + Thread.currentThread().toString());
// System.out.println("Arrived in PamStopped() in thread " + Thread.currentThread().toString());
ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
@ -1592,18 +1615,18 @@ public class PamController implements PamControllerInterface, PamSettings {
// wait here until the status has changed to Pam_Idle, so that we know
// that we've really finished processing all data
// Debug.out.println("PamController waiting for all threaded observers to stop...");
//
// while (getPamStatus()!=PAM_IDLE) {
// try {
// Thread.sleep(10);
// } catch (InterruptedException e) {
// e.printStackTrace();
// }
// }
// Debug.out.println("PamController waiting for all threaded observers to stop...");
//
// while (getPamStatus()!=PAM_IDLE) {
// try {
// Thread.sleep(10);
// } catch (InterruptedException e) {
// e.printStackTrace();
// }
// }
// send out the pamHasStopped message
// Debug.out.println("PamController letting everyone know PAMGuard has stopped.");
// Debug.out.println("PamController letting everyone know PAMGuard has stopped.");
for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
pamControlledUnits.get(iU).pamHasStopped();
}
@ -1615,13 +1638,13 @@ public class PamController implements PamControllerInterface, PamSettings {
guiFrameManager.pamEnded();
// no good having this here since it get's called at the end of every file.
// if (GlobalArguments.getParam(PamController.AUTOEXIT) != null) {
//// can exit here, since we've auto started, can auto exit.
// if (canClose()) {
// pamClose();
// shutDownPamguard();
// }
// }
// if (GlobalArguments.getParam(PamController.AUTOEXIT) != null) {
//// can exit here, since we've auto started, can auto exit.
// if (canClose()) {
// pamClose();
// shutDownPamguard();
// }
// }
}
public void batchProcessingComplete() {
@ -1642,25 +1665,25 @@ public class PamController implements PamControllerInterface, PamSettings {
* @author mo55
*
*/
// private class StatusTimer implements Runnable {
// @Override
// public void run() {
// boolean stillRunning = true;
// while (stillRunning) {
// try {
// Thread.sleep(200);
// } catch (InterruptedException e) {
// e.printStackTrace();
// }
//
// if (checkRunStatus() == true) {
// setPamStatus(PAM_IDLE);
// break;
// }
// }
// System.out.println("Status timer completed, all processes have received last data");
// }
// }
// private class StatusTimer implements Runnable {
// @Override
// public void run() {
// boolean stillRunning = true;
// while (stillRunning) {
// try {
// Thread.sleep(200);
// } catch (InterruptedException e) {
// e.printStackTrace();
// }
//
// if (checkRunStatus() == true) {
// setPamStatus(PAM_IDLE);
// break;
// }
// }
// System.out.println("Status timer completed, all processes have received last data");
// }
// }
/**
* Check the status of every threaded observer to see if it has emptied out it's
@ -1670,39 +1693,39 @@ public class PamController implements PamControllerInterface, PamSettings {
* @return true if ANY process is still running
*/
private boolean checkRunStatus() {
// boolean areWeFinished = true;
// Debug.out.println("Checking run status...");
// for (PamControlledUnit aUnit : pamControlledUnits) {
// int numProcesses = aUnit.getNumPamProcesses();
// for (int i=0; i<numProcesses; i++) {
// PamProcess aProcess = aUnit.getPamProcess(i);
// ArrayList<PamDataBlock> outputBlocks = aProcess.getOutputDataBlocks();
// for (PamDataBlock aBlock : outputBlocks) {
// int numObs = aBlock.countObservers();
// for (int j=0; j<numObs; j++) {
// PamObserver anObs = aBlock.getPamObserver(j);
// if (ThreadedObserver.class.isAssignableFrom(anObs.getClass())) {
// if (((ThreadedObserver) anObs).isEmptyRead() == false) {
// Debug.out.println(" Thread " + anObs.getObserverName() + "-" + System.identityHashCode(anObs) +
// " (" + Thread.currentThread().getName() +
// "-" + Thread.currentThread().getId() +
// ") is STILL processing");
// areWeFinished = false;
// break; // if we've found one still going, no need to check any further
// }
// else {
// Debug.out.println(" Thread " + anObs.getObserverName() + "-" + System.identityHashCode(anObs) +
// " (" + Thread.currentThread().getName() +
// "-" + Thread.currentThread().getId() +
// ") is finished processing");
// }
// }
// }
// }
// }
// }
// Debug.out.println(" Are we finished? " + areWeFinished);
// return areWeFinished;
// boolean areWeFinished = true;
// Debug.out.println("Checking run status...");
// for (PamControlledUnit aUnit : pamControlledUnits) {
// int numProcesses = aUnit.getNumPamProcesses();
// for (int i=0; i<numProcesses; i++) {
// PamProcess aProcess = aUnit.getPamProcess(i);
// ArrayList<PamDataBlock> outputBlocks = aProcess.getOutputDataBlocks();
// for (PamDataBlock aBlock : outputBlocks) {
// int numObs = aBlock.countObservers();
// for (int j=0; j<numObs; j++) {
// PamObserver anObs = aBlock.getPamObserver(j);
// if (ThreadedObserver.class.isAssignableFrom(anObs.getClass())) {
// if (((ThreadedObserver) anObs).isEmptyRead() == false) {
// Debug.out.println(" Thread " + anObs.getObserverName() + "-" + System.identityHashCode(anObs) +
// " (" + Thread.currentThread().getName() +
// "-" + Thread.currentThread().getId() +
// ") is STILL processing");
// areWeFinished = false;
// break; // if we've found one still going, no need to check any further
// }
// else {
// Debug.out.println(" Thread " + anObs.getObserverName() + "-" + System.identityHashCode(anObs) +
// " (" + Thread.currentThread().getName() +
// "-" + Thread.currentThread().getId() +
// ") is finished processing");
// }
// }
// }
// }
// }
// }
// Debug.out.println(" Are we finished? " + areWeFinished);
// return areWeFinished;
ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
boolean running = false;
@ -1715,7 +1738,7 @@ public class PamController implements PamControllerInterface, PamSettings {
sayStatusWarning("Waiting for " + aProcess.getProcessName());
running = true;
}
// System.out.printf("Process %s is in state %d\n", aProcess.getProcessName(), lastNotification);
// System.out.printf("Process %s is in state %d\n", aProcess.getProcessName(), lastNotification);
}
}
return running;
@ -1734,7 +1757,7 @@ public class PamController implements PamControllerInterface, PamSettings {
* via the database and binary storage modules.
*/
private void saveEndSettings(long timeNow) {
// System.out.printf("Updating settings with end time %s\n", PamCalendar.formatDBDateTime(timeNow));
// System.out.printf("Updating settings with end time %s\n", PamCalendar.formatDBDateTime(timeNow));
ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
PamControlledUnit pcu;
PamSettingsSource settingsSource;
@ -1763,19 +1786,19 @@ public class PamController implements PamControllerInterface, PamSettings {
* @return path to the binary store.
*/
public String findBinaryStorePath() {
// TODO get rid of the singleton binary store control and do from the Config.class
// BinaryStore binaryControl = BinaryStore.findBinaryStoreControl();
// if (binaryControl == null) {
// return null;
// }
// String storeLoc = binaryControl.getBinaryStoreSettings().getStoreLocation();
// if (storeLoc == null) {
// return "";
// }
// if (storeLoc.endsWith(File.separator) == false) {
// storeLoc += File.separator;
// }
// return storeLoc;
// TODO get rid of the singleton binary store control and do from the Config.class
// BinaryStore binaryControl = BinaryStore.findBinaryStoreControl();
// if (binaryControl == null) {
// return null;
// }
// String storeLoc = binaryControl.getBinaryStoreSettings().getStoreLocation();
// if (storeLoc == null) {
// return "";
// }
// if (storeLoc.endsWith(File.separator) == false) {
// storeLoc += File.separator;
// }
// return storeLoc;
return pamConfiguration.findBinaryStorePath();
}
@ -1919,9 +1942,9 @@ public class PamController implements PamControllerInterface, PamSettings {
// }
// }
// }
// private ArrayList<PamDataBlock> makeDataBlockList(Class classType, boolean includSubClasses) {
// return pamConfiguration.makeDataBlockList(classType, includSubClasses);
// }
// private ArrayList<PamDataBlock> makeDataBlockList(Class classType, boolean includSubClasses) {
// return pamConfiguration.makeDataBlockList(classType, includSubClasses);
// }
/**
* Find a block of a given type with the id number, or null if the number is out
@ -2037,7 +2060,7 @@ public class PamController implements PamControllerInterface, PamSettings {
// System.out.printf("***** notify %d on thread %s is EventDispatch = %s\n", changeType, currentThread.getName(), isEvDT.toString());
// }
// System.out.println("PamController: notify model changed: " +changeType );
if (changeType == CHANGED_MULTI_THREADING) {
changedThreading();
}
@ -2239,7 +2262,7 @@ public class PamController implements PamControllerInterface, PamSettings {
public void setPamStatus(int pamStatus) {
this.pamStatus = pamStatus;
// System.out.println("Set PAM Status: " + pamStatus);
// System.out.println("Set PAM Status: " + pamStatus);
/*
* This only get's called once when set idle at viewer mode startup.
*/
@ -2342,7 +2365,7 @@ public class PamController implements PamControllerInterface, PamSettings {
statusWarning.setWarningMessage(warningMessage);
statusWarning.setWarnignLevel(1);
warningSystem.addWarning(statusWarning);
// System.out.println(warningMessage);
// System.out.println(warningMessage);
}
}
@ -2877,14 +2900,14 @@ public class PamController implements PamControllerInterface, PamSettings {
public void storageOptions(JFrame parentFrame) {
StorageOptions.getInstance().showDialog(parentFrame);
}
/**
* Show export options tp export data to other formats
* @param parentFrame
*/
public void exportData(JFrame parentFrame) {
ExportOptions.getInstance().showDialog(parentFrame);
}
@ -2970,16 +2993,16 @@ public class PamController implements PamControllerInterface, PamSettings {
}
}
// int pos = version.indexOf('.'); // get the index of the first decimal
// if (pos==-1) { // if there is no decimal place (e.g. Java 13) then just use the full string
// pos=version.length();
// }
// else {
// pos = version.indexOf('.', pos+1); // get the position of the second decimal
// if (pos==-1) { // if there is no second decimal place (e.g. Java 12.0) then just use the full string
// pos=version.length();
// }
// }
// int pos = version.indexOf('.'); // get the index of the first decimal
// if (pos==-1) { // if there is no decimal place (e.g. Java 13) then just use the full string
// pos=version.length();
// }
// else {
// pos = version.indexOf('.', pos+1); // get the position of the second decimal
// if (pos==-1) { // if there is no second decimal place (e.g. Java 12.0) then just use the full string
// pos=version.length();
// }
// }
double mainVersion = 0;
try {
mainVersion = Double.parseDouble(version.substring(0, iLen));

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 = "2.02.16";
static public final String version = "2.02.16a";
/**
* Release date
*/
static public final String date = "20 February 2025";
static public final String date = "April 2025";
// /**
// * Release type - Beta or Core

4
src/PamModel/PamModel.java
View File

@ -467,7 +467,7 @@ final public class PamModel implements PamSettings {
mi.setToolTipText("Record observer monitoring effort");
mi.setModulesMenuGroup(utilitiesGroup);
// mi.setHidden(SMRUEnable.isEnable() == false);
mi.setToolTipText("Enables an observer to enter their name and infomation about which displays are being monitored");
mi.setToolTipText("Enables an observer to enter their name and information about which displays are being monitored");
mi.setMaxNumber(1);
mi = PamModuleInfo.registerControlledUnit(BackupManager.class.getName(), BackupManager.defaultName);
@ -708,7 +708,7 @@ final public class PamModel implements PamSettings {
mi = PamModuleInfo.registerControlledUnit("envelopeTracer.EnvelopeControl", "Envelope Tracing");
mi.addDependency(new PamDependency(RawDataUnit.class, "Acquisition.AcquisitionControl"));
mi.setToolTipText("");
mi.setToolTipText("Traces the envelope of audio data and outputs it as a new waveform");
mi.setModulesMenuGroup(processingGroup);
mi.setModulesMenuGroup(processingGroup);
mi.setHelpPoint("sound_processing/EnvelopeTrace/Docs/EnvelopeOverview.html");

167
src/PamUtils/LittleEndianDataInputStream.java Normal file
View File

@ -0,0 +1,167 @@
package PamUtils;
import java.io.DataInput;
import java.io.DataInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.Charset;
/**
* Copied from https://www.peterfranza.com/2008/09/26/little-endian-input-stream/
* @author dg50
*
*/
public class LittleEndianDataInputStream extends InputStream implements DataInput {
public LittleEndianDataInputStream(InputStream in) {
this.in = in;
this.d = new DataInputStream(in);
w = new byte[8];
}
public int available() throws IOException {
return d.available();
}
public final short readShort() throws IOException
{
d.readFully(w, 0, 2);
return (short)(
(w[1]&0xff) << 8 |
(w[0]&0xff));
}
/**
* Note, returns int even though it reads a short.
*/
public final int readUnsignedShort() throws IOException
{
d.readFully(w, 0, 2);
return (
(w[1]&0xff) << 8 |
(w[0]&0xff));
}
/**
* like DataInputStream.readChar except little endian.
*/
public final char readChar() throws IOException
{
d.readFully(w, 0, 2);
return (char) (
(w[1]&0xff) << 8 |
(w[0]&0xff));
}
/**
* like DataInputStream.readInt except little endian.
*/
public final int readInt() throws IOException
{
d.readFully(w, 0, 4);
return
(w[3]) << 24 |
(w[2]&0xff) << 16 |
(w[1]&0xff) << 8 |
(w[0]&0xff);
}
/**
* like DataInputStream.readUnsignedInt except little endian.
*/
public final long readUnsignedInt() throws IOException
{
int v = readInt();
return Integer.toUnsignedLong(v);
// ByteArray.to
// return
// (w[3]) << 24 |
// (w[2]&0xff) << 16 |
// (w[1]&0xff) << 8 |
// (w[0]&0xff);
}
/**
* like DataInputStream.readLong except little endian.
*/
public final long readLong() throws IOException
{
d.readFully(w, 0, 8);
return
(long)(w[7]) << 56 |
(long)(w[6]&0xff) << 48 |
(long)(w[5]&0xff) << 40 |
(long)(w[4]&0xff) << 32 |
(long)(w[3]&0xff) << 24 |
(long)(w[2]&0xff) << 16 |
(long)(w[1]&0xff) << 8 |
(long)(w[0]&0xff);
}
public final float readFloat() throws IOException {
// still need to byteswap
return Float.intBitsToFloat(readInt());
}
public final double readDouble() throws IOException {
// still need to byteswap
return Double.longBitsToDouble(readLong());
}
public final int read(byte b[], int off, int len) throws IOException {
return in.read(b, off, len);
}
public final void readFully(byte b[]) throws IOException {
d.readFully(b, 0, b.length);
}
public final void readFully(byte b[], int off, int len) throws IOException {
d.readFully(b, off, len);
}
public final int skipBytes(int n) throws IOException {
return d.skipBytes(n);
}
public final long skip(long n) throws IOException {
return d.skipBytes((int) n);
}
public final boolean readBoolean() throws IOException {
return d.readBoolean();
}
public final byte readByte() throws IOException {
return d.readByte();
}
public int read() throws IOException {
return in.read();
}
public final int readUnsignedByte() throws IOException {
return d.readUnsignedByte();
}
@Deprecated
public final String readLine() throws IOException {
return d.readLine();
}
public final String readUTF() throws IOException {
return d.readUTF();
}
public final void close() throws IOException {
d.close();
}
private DataInputStream d; // to get at high level readFully methods of
// DataInputStream
private InputStream in; // to get at the low-level read methods of
// InputStream
private byte w[]; // work array for buffering input
}

9
src/PamUtils/Splash.java
View File

@ -49,6 +49,7 @@ import javax.swing.border.EmptyBorder;
import PamController.PamController;
import PamController.PamguardVersionInfo;
import PamController.PamguardVersionInfo.ReleaseType;
import PamUtils.PlatformInfo.OSType;
import pamguard.Pamguard;
@ -163,11 +164,15 @@ public class Splash extends JWindow implements Runnable {
else if (runMode == PamController.RUN_PAMVIEW) {
modeText = "Viewer";
}
String typeText = " " + PamguardVersionInfo.getReleaseType().toString();
if (PamguardVersionInfo.getReleaseType() == ReleaseType.CORE) {
typeText = "";
}
if (modeText != null) {
version = modeText + " " + PamguardVersionInfo.version + " " + PamguardVersionInfo.getReleaseType().toString();
version = modeText + " " + PamguardVersionInfo.version + typeText;
}
else {
version = "Version " + PamguardVersionInfo.version + " " + PamguardVersionInfo.getReleaseType().toString();
version = "Version " + PamguardVersionInfo.version + typeText;
}
// get image graphics handle.

3
src/PamView/PamGui.java
View File

@ -641,15 +641,18 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
menuItem = new JMenuItem("Module Ordering ...");
menuItem.addActionListener(new menuModuleOrder());
menuItem.setToolTipText("Change the order of modules in the PAMGuard configuration");
orderModulesEnabler.addMenuItem(menuItem);
fileMenu.add(menuItem);
menuItem = new JMenuItem("Show Object List ...");
menuItem.addActionListener(new menuShowObjectList());
menuItem.setToolTipText("Show a list of data and detections currnetly held in memory for each module");
fileMenu.add(menuItem);
menuItem = new JMenuItem("Show Data Model ...");
menuItem.addActionListener(new menuShowObjectDiagram());
menuItem.setToolTipText("Show a graphical representation of modules and their interconnections");
fileMenu.add(menuItem);
if (!isViewer) {

7
src/PamView/dialog/PamDialog.java
View File

@ -620,6 +620,13 @@ abstract public class PamDialog extends JDialog {
return showWarning(warningTitle, warningText);
}
/**
* Display a warning text.
* @param owner
* @param warningTitle
* @param warningText
* @return
*/
public static boolean showWarning(Window owner, String warningTitle, String warningText) {
JOptionPane.showMessageDialog(owner, warningText, warningTitle, JOptionPane.ERROR_MESSAGE);
return false;

7
src/PamView/dialog/SourcePanel.java
View File

@ -1,7 +1,6 @@
package PamView.dialog;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Window;
@ -16,20 +15,14 @@ import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.border.TitledBorder;
import PamController.PamController;
import PamDetection.LocalisationInfo;
import PamUtils.PamUtils;
import PamguardMVC.PamConstants;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import PamguardMVC.PamProcess;
/**
* Standard panel for dialogs that shows a list of

12
src/clickDetector/ClickDetector.java
View File

@ -143,7 +143,7 @@ public class ClickDetector extends PamProcess {
private PamDataBlock<TriggerLevelDataUnit> triggerDataBlock;
private PamRawDataBlock doubleFilteredData;
// private PamRawDataBlock doubleFilteredData;
// protected PamDataBlock<ClickDetection> trackedClicks;
private PamDataBlock trackedClicks;
@ -730,12 +730,12 @@ public class ClickDetector extends PamProcess {
// }
if ((newRawData.getChannelBitmap() & clickControl.clickParameters.getChannelBitmap()) == 0)
return;
return; // not a channel we're interested in
//
// if (obs == filteredDataBlock || obs == doubleFilteredData)
// return;
clickControl.newRawData(obs, newData);
clickControl.newRawData(obs, newData); // does nothing
// see if it's time to start a new file
// only do this here if it's not multithread
@ -1496,7 +1496,9 @@ public class ClickDetector extends PamProcess {
int keepMillis = (int) (relSamplesToMilliseconds(requiredKeepSamples) * 2);
// int keepSeconds = Math.max(1, (int)
// relSamplesToMilliseconds(requiredKeepSamples)/1000);
keepMillis = Math.max(1000, keepMillis);
// add an extra second on 2025-04-01 to try to avoid null clicks.
keepMillis = Math.max(1000, keepMillis) + 1000;
// filteredDataBlock.setNaturalLifetime(keepSeconds);
finalDataSource = filteredDataBlock;
finalDataSource.setNaturalLifetimeMillis(keepMillis);
@ -1642,7 +1644,7 @@ public class ClickDetector extends PamProcess {
/*
* Waveform data ends up pointing either to the raw data, or the output of the
* fist filter if there is one. new wavefformData is created every time (or
* recycled from the data block) since we may beed to go back a while to find
* recycled from the data block) since we may need to go back a while to find
* data from a previous block
*/
double[][] waveformData = new double[nChannels][];

9
src/dataPlotsFX/data/generic/GenericLinePlotInfo.java
View File

@ -36,6 +36,11 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
* TRhe managed symbol chooser.
*/
private TDSymbolChooserFX managedSymbolChooser;
/**
* The radius if drawing a point instead of a line i.e. if there is only one data point.
*/
public static final double OVAL_RADIUS = 10;
/**
* The last units
@ -157,7 +162,9 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
if (lastUnits[chan][i]==null) {
lastUnits[chan][i] = new TimePoint2D(tC, dataPixel, pamDataUnit.getTimeMilliseconds() );
g.fillOval(tC, dataPixel, 10,10);
g.fillOval(tC-OVAL_RADIUS/2, dataPixel-OVAL_RADIUS/2, OVAL_RADIUS,OVAL_RADIUS);
// System.out.println("Fill oval:");
return null;
}

7
src/ravendata/RavenControl.java
View File

@ -131,4 +131,11 @@ public class RavenControl extends PamControlledUnit implements PamSettings {
return true;
}
/**
* @return the ravenParameters
*/
public RavenParameters getRavenParameters() {
return ravenParameters;
}
}

2
src/ravendata/RavenParameters.java
View File

@ -9,6 +9,8 @@ public class RavenParameters implements Serializable, Cloneable {
public String importFile;
public double timeOffsetSeconds = 0;
private ArrayList<RavenColumnInfo> extraColumns;
public ArrayList<RavenColumnInfo> getExtraColumns() {

2
src/ravendata/RavenProcess.java
View File

@ -95,7 +95,7 @@ public class RavenProcess extends PamProcess {
* this as an option in future releases.
* Offset of 2843100 needed for mn23_055a tag data.
*/
long offsetMillis = 0;//2843100;
long offsetMillis = (long) (ravenControl.getRavenParameters().timeOffsetSeconds * 1000.);
RavenDataRow prevRow = null;
for (RavenDataRow ravenRow : ravenData) {

31
src/ravendata/swing/RavenImportDialog.java
View File

@ -10,6 +10,7 @@ import java.io.File;
import javax.swing.JButton;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.border.TitledBorder;
@ -30,6 +31,7 @@ public class RavenImportDialog extends PamDialog {
private JButton chooseButton;
private JTextField timeOffset;
private RavenImportDialog(Window parentFrame) {
@ -40,10 +42,30 @@ public class RavenImportDialog extends PamDialog {
ravenFile = new JTextField(80);
ravenFile.setEditable(false);
chooseButton = new JButton("Select ...");
c.gridwidth = 2;
c.gridx = c.gridy = 0;
mainPanel.add(ravenFile, c);
JPanel p2 = new JPanel(new GridBagLayout());
GridBagConstraints c2 = new PamGridBagContraints();
c2.gridx = 1;
c2.gridwidth = 1;
p2.add(chooseButton, c2);
c2.gridx = 0;
c2.gridy++;
c2.gridwidth = 1;
p2.add(new JLabel("Time offset (s) ", JLabel.RIGHT), c2);
c2.gridx++;
p2.add(timeOffset = new JTextField(7), c2);
String tip = "Added to data as it's read from file";
timeOffset.setToolTipText(tip);
c.gridwidth = 2;
c.gridy++;
mainPanel.add(new PamAlignmentPanel(chooseButton, BorderLayout.EAST), c);
mainPanel.add(new PamAlignmentPanel(p2, BorderLayout.EAST), c);
chooseButton.addActionListener(new ActionListener() {
@Override
@ -80,6 +102,7 @@ public class RavenImportDialog extends PamDialog {
private void setParams(RavenParameters ravenParameters) {
this.ravenParameters = ravenParameters;
ravenFile.setText(ravenParameters.importFile);
timeOffset.setText(String.format("%5.3f", ravenParameters.timeOffsetSeconds));
}
@Override
@ -94,6 +117,12 @@ public class RavenImportDialog extends PamDialog {
return showWarning(str);
}
ravenParameters.importFile = fn;
try {
ravenParameters.timeOffsetSeconds = Double.valueOf(timeOffset.getText());
}
catch (NumberFormatException e) {
return showWarning("Invalid time offset value. Must be a number");
}
return true;
}

2
src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPane.java
View File

@ -69,6 +69,8 @@ public class DLPredictionPane extends PamBorderPane implements TDSettingsPane {
predColHolder.setPadding(new Insets(5,0,0,0));
this.setParams();
mainPane.setPrefWidth(300);
// if (dlPredictionPlotInfoFX.getDlControl().getDLModel()!=null) {
// layoutColourPanes( dlPredictionPlotInfoFX.getDlControl().getDLModel().getClassNames());

4
src/test/rawDeepLearningClassifier/ClickDLTest.java
View File

@ -21,6 +21,10 @@ import us.hebi.matlab.mat.format.Mat5File;
import us.hebi.matlab.mat.types.Matrix;
import us.hebi.matlab.mat.types.Struct;
/**
* Model from Thomas webber which is a good way to test the click based stuff is working in PAMGUard.
*/
public class ClickDLTest {

14
src/wavFiles/WavHeader.java
View File

@ -6,6 +6,8 @@ import java.util.ArrayList;
import javax.sound.sampled.AudioFormat;
import clickDetector.WindowsFile;
import wavFiles.xwav.HarpHeader;
import wavFiles.xwav.XWavException;
public class WavHeader {
@ -110,6 +112,18 @@ public class WavHeader {
windowsWavFile.seek(fmtEnd);
// break;
}
else if (testString.equals("harp")) {
chunkSize = windowsWavFile.readWinInt();
headChunk = new byte[chunkSize];
windowsWavFile.read(headChunk);
try {
HarpHeader.readHarpHeader(headChunk);
} catch (XWavException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// wavHeadChunks.add(new WavHeadChunk(testString, headChunk));
}
else {
/*
* As an example, SCRIPPS HARP .x.wav files have a chunk

112
src/wavFiles/xwav/HarpHeader.java Normal file
View File

@ -0,0 +1,112 @@
package wavFiles.xwav;
import java.io.ByteArrayInputStream;
import java.io.DataInputStream;
import java.io.IOException;
import java.util.Calendar;
import PamUtils.LittleEndianDataInputStream;
import PamUtils.PamCalendar;
public class HarpHeader {
private HarpHeader() {
// TODO Auto-generated constructor stub
}
/**
* Unpack harp data junk from a xwav file.
* @param chunkData
* @return
*/
public static HarpHeader readHarpHeader(byte[] chunkData) throws XWavException {
/*
* Based on matlab code found at https://github.com/MarineBioAcousticsRC/Wav2XWav/blob/main/wrxwavhdX.m
*/
LittleEndianDataInputStream dis = new LittleEndianDataInputStream(new ByteArrayInputStream(chunkData));
// new LittleEnd
try {
int harpSize = chunkData.length;
int xhdVersion = dis.readUnsignedByte();
String firmwareVersion = readString(dis, 10);
String insId = readString(dis, 4);
String site = readString(dis, 4);
String experiment = readString(dis, 8);// could be 8 in example
int diskSequenceNumber = dis.readUnsignedByte();
String diskSerialNumber = readString(dis, 8);
int numRF = dis.readUnsignedShort();
int longitude = dis.readInt(); // defo written as integers. guessing float*1e5.
int latitude = dis.readInt();
// float longitude = dis.readFloat();
// float latitude = dis.readFloat();
int depth = dis.readShort();
// skip 8.
dis.skip(8);
/*
* then read numRF chunks, each of which is 32 bytes. In this example, we
* have harpSize = 29752, so expecting about (29752-50)/32
*/
long lastT = 0;
for (int iRF = 0; iRF < numRF; iRF++) {
// time is from datevec, so it's year, month ... second in the first six
int[] dateVec = new int[7];
for (int i = 0; i < 6; i++) {
dateVec[i] = dis.readUnsignedByte();
}
dateVec[6] = dis.readUnsignedShort(); // number of millis.
long byteLoc = dis.readUnsignedInt();
long byteLength = dis.readUnsignedInt();
long writeLength = dis.readUnsignedInt();
long sampleRate = dis.readUnsignedInt();
int gain = dis.readUnsignedByte();
dis.skip(7);
long tMillis = dateVec2Millis(dateVec);
// if (lastT != 0) {
// System.out.printf("%s length %d = %3.3fs, step = %dms\n", PamCalendar.formatDBDateTime(tMillis, true), byteLength,
// (double) byteLength / (double) sampleRate / 2., tMillis-lastT);
// }
// else {
// System.out.printf("%s length %d = %3.3fs\n", PamCalendar.formatDBDateTime(tMillis, true), byteLength,
// (double) byteLength / (double) sampleRate / 2.);
// }
lastT = tMillis;
}
} catch (IOException e) {
throw new XWavException(e.getMessage());
}
return null;
}
/**
* Convert datevec read from file to Java millis.
* @param dateVec
*/
private static long dateVec2Millis(int[] dateVec) {
// format is yy, mm, dd, hh, mm, ss, ms as int values.
Calendar c = Calendar.getInstance();
c.setTimeZone(PamCalendar.defaultTimeZone);
c.clear();
int yy = dateVec[0];
if (yy < 90) {
yy += 2000;
}
c.set(yy, dateVec[1]-1, dateVec[2], dateVec[3], dateVec[4], dateVec[5]);
long millis = c.getTimeInMillis() + dateVec[6];
return millis;
}
private static String readString(LittleEndianDataInputStream dis, int bytes) throws XWavException {
byte[] data;
try {
data = dis.readNBytes(bytes);
String str = new String(data);
return str;
} catch (IOException e) {
throw new XWavException(e.getMessage());
}
}
}

34
src/wavFiles/xwav/XWavException.java Normal file
View File

@ -0,0 +1,34 @@
package wavFiles.xwav;
public class XWavException extends Exception {
/**
*
*/
private static final long serialVersionUID = 1L;
public XWavException() {
// TODO Auto-generated constructor stub
}
public XWavException(String message) {
super(message);
// TODO Auto-generated constructor stub
}
public XWavException(Throwable cause) {
super(cause);
// TODO Auto-generated constructor stub
}
public XWavException(String message, Throwable cause) {
super(message, cause);
// TODO Auto-generated constructor stub
}
public XWavException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
// TODO Auto-generated constructor stub
}
}