diff --git a/pom.xml b/pom.xml
index 86d1ae16..1e597d64 100644
--- a/pom.xml
+++ b/pom.xml
@@ -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>
diff --git a/src/PamController/PamguardVersionInfo.java b/src/PamController/PamguardVersionInfo.java
index 1f17d80c..62896aaf 100644
--- a/src/PamController/PamguardVersionInfo.java
+++ b/src/PamController/PamguardVersionInfo.java
@@ -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
diff --git a/src/PamModel/PamModel.java b/src/PamModel/PamModel.java
index 928a552c..4f4dd769 100644
--- a/src/PamModel/PamModel.java
+++ b/src/PamModel/PamModel.java
@@ -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");
diff --git a/src/PamUtils/LittleEndianDataInputStream.java b/src/PamUtils/LittleEndianDataInputStream.java
new file mode 100644
index 00000000..297ac7fa
--- /dev/null
+++ b/src/PamUtils/LittleEndianDataInputStream.java
@@ -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
+
+}
diff --git a/src/PamView/PamGui.java b/src/PamView/PamGui.java
index bf746071..48b0aabb 100644
--- a/src/PamView/PamGui.java
+++ b/src/PamView/PamGui.java
@@ -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) {
diff --git a/src/PamView/dialog/PamDialog.java b/src/PamView/dialog/PamDialog.java
index 95fcba0f..44e4122f 100644
--- a/src/PamView/dialog/PamDialog.java
+++ b/src/PamView/dialog/PamDialog.java
@@ -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;
diff --git a/src/PamView/dialog/SourcePanel.java b/src/PamView/dialog/SourcePanel.java
index 7b6087db..90d1770b 100644
--- a/src/PamView/dialog/SourcePanel.java
+++ b/src/PamView/dialog/SourcePanel.java
@@ -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
diff --git a/src/clickDetector/ClickDetector.java b/src/clickDetector/ClickDetector.java
index 3ce20376..bb14fef2 100644
--- a/src/clickDetector/ClickDetector.java
+++ b/src/clickDetector/ClickDetector.java
@@ -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][];
diff --git a/src/ravendata/RavenControl.java b/src/ravendata/RavenControl.java
index 79a2be15..4b817169 100644
--- a/src/ravendata/RavenControl.java
+++ b/src/ravendata/RavenControl.java
@@ -131,4 +131,11 @@ public class RavenControl extends PamControlledUnit implements PamSettings {
return true;
}
+ /**
+ * @return the ravenParameters
+ */
+ public RavenParameters getRavenParameters() {
+ return ravenParameters;
+ }
+
}
diff --git a/src/ravendata/RavenParameters.java b/src/ravendata/RavenParameters.java
index 93792833..9e0d09e0 100644
--- a/src/ravendata/RavenParameters.java
+++ b/src/ravendata/RavenParameters.java
@@ -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() {
diff --git a/src/ravendata/RavenProcess.java b/src/ravendata/RavenProcess.java
index 196116a4..a611fb81 100644
--- a/src/ravendata/RavenProcess.java
+++ b/src/ravendata/RavenProcess.java
@@ -92,7 +92,7 @@ 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) {
diff --git a/src/ravendata/swing/RavenImportDialog.java b/src/ravendata/swing/RavenImportDialog.java
index af82e452..6f001899 100644
--- a/src/ravendata/swing/RavenImportDialog.java
+++ b/src/ravendata/swing/RavenImportDialog.java
@@ -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;
}
diff --git a/src/wavFiles/WavHeader.java b/src/wavFiles/WavHeader.java
index 2d0a69c8..d0bfbb85 100644
--- a/src/wavFiles/WavHeader.java
+++ b/src/wavFiles/WavHeader.java
@@ -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
diff --git a/src/wavFiles/xwav/HarpHeader.java b/src/wavFiles/xwav/HarpHeader.java
new file mode 100644
index 00000000..433561ed
--- /dev/null
+++ b/src/wavFiles/xwav/HarpHeader.java
@@ -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());
+ }
+ }
+
+}
diff --git a/src/wavFiles/xwav/XWavException.java b/src/wavFiles/xwav/XWavException.java
new file mode 100644
index 00000000..7eb6b470
--- /dev/null
+++ b/src/wavFiles/xwav/XWavException.java
@@ -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
+ }
+
+}