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2.02.07b

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Fix ICI display bug in click detector
This commit is contained in:
Douglas Gillespie 2023-01-19 17:53:59 +00:00
parent a89279ef81
commit 269398890e
7 changed files with 358 additions and 230 deletions
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2
pom.xml
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@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>org.pamguard</groupId> <groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId> <artifactId>Pamguard</artifactId>
<version>2.02.07a</version> <version>2.02.07b</version>
<name>Pamguard Java12+</name> <name>Pamguard Java12+</name>
<description>Pamguard for Java 12+, using Maven to control dependcies</description> <description>Pamguard for Java 12+, using Maven to control dependcies</description>
<url>www.pamguard.org</url> <url>www.pamguard.org</url>

4
src/PamController/PamguardVersionInfo.java
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@ -31,12 +31,12 @@ public class PamguardVersionInfo {
* Version number, major version.minorversion.sub-release. * Version number, major version.minorversion.sub-release.
* Note: can't go higher than sub-release 'f' * Note: can't go higher than sub-release 'f'
*/ */
static public final String version = "2.02.07a"; static public final String version = "2.02.07b";
/** /**
* Release date * Release date
*/ */
static public final String date = "10 January 2023"; static public final String date = "19 January 2023";
// /** // /**
// * Release type - Beta or Core // * Release type - Beta or Core

5
src/PamguardMVC/PamDataUnit.java
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@ -1697,14 +1697,13 @@ abstract public class PamDataUnit<T extends PamDataUnit, U extends PamDataUnit>
*/ */
public int getColourIndex() { public int getColourIndex() {
/* /*
* This can go wrong when UID > 2^31 since the colour choser takes * This can go wrong when UID > 2^31 since the colour chooser takes
* a mod WRT number of whale colours and it doesn't like negative numbers. * a mod WRT number of whale colours and it doesn't like negative numbers.
* So need to keep the value going in positive. * So need to keep the value going in positive.
*/ */
long uid = getUID(); long uid = getUID();
uid -= uid/2^31; uid &= 0x7FFFFFFF; // avoid anything in top bit of an int32 or higher
return (int) uid; return (int) uid;
// return (int) getUID();
} }
/** /**

391
src/clickDetector/ClickBTDisplay.java
View File

@ -47,6 +47,8 @@ import java.awt.image.BufferedImage;
import java.io.Serializable; import java.io.Serializable;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.ConcurrentModificationException; import java.util.ConcurrentModificationException;
import java.util.HashMap;
import java.util.List;
import java.util.ListIterator; import java.util.ListIterator;
import javax.swing.JCheckBox; import javax.swing.JCheckBox;
@ -134,7 +136,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
private PamScroller hScrollBar; private PamScroller hScrollBar;
// private PamDataBlock<ClickDetection> trackedClicks; // private PamDataBlock<ClickDetection> trackedClicks;
protected BTPlot btPlot; protected BTPlot btPlot;
@ -219,7 +221,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
/** /**
* The symbol chooser for the BT display * The symbol chooser for the BT display
*/ */
// private ClickDetSymbolChooser symbolChooser; // private ClickDetSymbolChooser symbolChooser;
public ClickBTDisplay(ClickControl clickControl, ClickDisplayManager clickDisplayManager, ClickDisplayManager.ClickDisplayInfo clickDisplayInfo) { public ClickBTDisplay(ClickControl clickControl, ClickDisplayManager clickDisplayManager, ClickDisplayManager.ClickDisplayInfo clickDisplayInfo) {
@ -265,7 +267,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
topControls = new TopControls(); topControls = new TopControls();
setNorthPanel(topControls); setNorthPanel(topControls);
// trackedClicks = clickControl.getClickDetector().getTrackedClicks(); // trackedClicks = clickControl.getClickDetector().getTrackedClicks();
highlightSymbol.setLineThickness(3); highlightSymbol.setLineThickness(3);
@ -369,13 +371,49 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
@Override @Override
public void updateData(PamObservable observable, PamDataUnit pamDataUnit) { public void updateData(PamObservable observable, PamDataUnit pamDataUnit) {
if (pamDataUnit instanceof ClickDetection) {
updateClick((ClickDetection) pamDataUnit);
}
}
private void updateClick(ClickDetection clickDetection) {
// ICI may have been set when the click was added to an event
// so work it out there rather than rebuilding the entire list.
SuperDetection superDet = clickDetection.getSuperDetection(0);
if (superDet == null) {
// sortTempICIs();
return;
}
/**
* Work only within the superdetection to find the previous
* click within that for this clicks channel combination and update
* the ICI accordingly. For the first click an event, it won't find
* a preceeding click, but that's OK.
*/
synchronized (superDet.getSubDetectionSyncronisation()) {
int subDetInd = superDet.findSubdetectionInfo(clickDetection);
for (int i = subDetInd-1; i >= 0; i--) {
PamDataUnit subDet = superDet.getSubDetection(i);
if (subDet.getChannelBitmap() == clickDetection.getChannelBitmap()) {
double ici = (double) (clickDetection.getTimeMilliseconds() - subDet.getTimeMilliseconds())/1000.;
clickDetection.setTempICI(ici);
break;
}
}
}
} }
private void changedEvent(OfflineEventDataUnit event) { private void changedEvent(OfflineEventDataUnit event) {
sortTempICIs();
btPlot.repaint(10); btPlot.repaint(10);
} }
public void newClick(ClickDetection clickDataUnit) { public void newClick(ClickDetection clickDataUnit) {
sortTempICI(clickDataUnit);
if (shouldPlot(clickDataUnit)){ if (shouldPlot(clickDataUnit)){
// btPlot.drawClick(btPlot.getImageGraphics(), clickDataUnit, null); // btPlot.drawClick(btPlot.getImageGraphics(), clickDataUnit, null);
// btPlot.repaint(minPaintTime); // btPlot.repaint(minPaintTime);
@ -386,6 +424,71 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
} }
private HashMap<Long, ClickDetection> lastClicks = new HashMap<>();
/**
* Sort out all ICI's for all clicks.
*/
private void sortTempICIs() {
// long t1 = System.nanoTime();
PamDataBlock<ClickDetection> clickData = clickControl.getClickDataBlock();
ArrayList<ClickDetection> allClicks = clickData.getDataCopy();
sortTempICIs(allClicks);
// long t2 = System.nanoTime();
// System.out.printf("time to sort %d ICI measures is %3.1fms\n", allClicks.size(), (double) (t2-t1)/1.e6);
}
/**
* Clear ICI history, e.g. when new data are loaded or processing starts.
*/
private void clearICIHistory() {
synchronized(lastClicks) {
lastClicks.clear();
}
}
/**
* Sorts ICI's for a list of clicks.
* @param clicks
*/
private void sortTempICIs(List<ClickDetection> clicks) {
clearICIHistory();
for (ClickDetection aClick : clicks) {
sortTempICI(aClick);
}
}
/**
* Sorts ICI information for a new click.
* @param aClick
*/
private void sortTempICI(ClickDetection aClick) {
long chans = aClick.getChannelBitmap(); // int32 channel group.
long superId = 0;
SuperDetection superDet = aClick.getSuperDetection(0);
if (superDet != null) {
superId = superDet.getUID();
}
/*
* make an overall id for the click in a long. This could in theory wrap
* a superdet, but that is very unlikely and we probably don't care anyway
* since it's unlikely a uid that different would be in memory at the same time.
*/
long totalId = superId<<32 | chans;
synchronized(lastClicks) {
ClickDetection prevClick = lastClicks.get(totalId);
if (prevClick == null) {
aClick.setTempICI(0);
}
else {
double ici = (double) (aClick.getTimeMilliseconds() - prevClick.getTimeMilliseconds()) / 1000.;
aClick.setTempICI(ici);
}
lastClicks.put(totalId, aClick);
}
}
/** /**
@ -467,6 +570,8 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
hScrollManager.reset(); hScrollManager.reset();
} }
clearICIHistory();
// hScrollManager.setupScrollBar(0); // hScrollManager.setupScrollBar(0);
// setupTimeBar(); // setupTimeBar();
repaintBoth(); repaintBoth();
@ -1193,6 +1298,8 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
hScrollBar.setUnitIncrement(getUnitIncrement(getTimeRangeMillis())); hScrollBar.setUnitIncrement(getUnitIncrement(getTimeRangeMillis()));
hScrollBar.setBlockIncrement(getTimeRangeMillis() * 7 / 8); hScrollBar.setBlockIncrement(getTimeRangeMillis() * 7 / 8);
sortTempICIs();
return true; return true;
} }
@ -1265,7 +1372,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
// System.out.println("New max time = " + PamCalendar.formatTime(displayMaxMillis)); // System.out.println("New max time = " + PamCalendar.formatTime(displayMaxMillis));
// System.out.println(String.format("Set up scroll bar at %s", PamCalendar.formatDateTime(displayMaxMillis))); // System.out.println(String.format("Set up scroll bar at %s", PamCalendar.formatDateTime(displayMaxMillis)));
long displayLength = getTimeRangeMillis(); long displayLength = getTimeRangeMillis();
// long currentStart = hScrollBar.getMinimumMillis(); // long currentStart = hScrollBar.getMinimumMillis();
long scrollRange = hScrollBar.getRangeMillis(); // total scrollable range long scrollRange = hScrollBar.getRangeMillis(); // total scrollable range
long currentValue = hScrollBar.getValueMillis(); long currentValue = hScrollBar.getValueMillis();
long displayMinMillis = displayMaxMillis-scrollRange; // start of scrollable region. long displayMinMillis = displayMaxMillis-scrollRange; // start of scrollable region.
@ -1444,6 +1551,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
@Override @Override
public void offlineDataChanged() { public void offlineDataChanged() {
sortTempICIs();
repaintBoth(); repaintBoth();
} }
@ -1572,9 +1680,9 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
} }
private double clickAngleToY(ClickDetection click) { private double clickAngleToY(ClickDetection click) {
AbstractLocalisation loc = click.getLocalisation(); AbstractLocalisation loc = click.getLocalisation();
// if (click.getUID() == 110006089) { // if (click.getUID() == 110006089) {
// System.out.println("Click 110006089 angle " + click.getAngle()); // System.out.println("Click 110006089 angle " + click.getAngle());
// } // }
if (loc == null) return 0; if (loc == null) return 0;
double angle = 0; double angle = 0;
GpsData oll; GpsData oll;
@ -1590,20 +1698,20 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
case ArrayManager.ARRAY_TYPE_VOLUME: case ArrayManager.ARRAY_TYPE_VOLUME:
PamVector v = getDisplayVector(click); PamVector v = getDisplayVector(click);
angle = Math.toDegrees(PamVector.vectorToSurfaceBearing(v)); angle = Math.toDegrees(PamVector.vectorToSurfaceBearing(v));
// PamVector[] vecs = null; // PamVector[] vecs = null;
// angle = click.getAngle(); // angle = click.getAngle();
// if (btDisplayParameters.bearingType == BTDisplayParameters.BEARING_FROMVESSEL) { // if (btDisplayParameters.bearingType == BTDisplayParameters.BEARING_FROMVESSEL) {
// have to use real world vectors to get the array rotation vector // have to use real world vectors to get the array rotation vector
// then subtract back off the heading // then subtract back off the heading
// vecs = loc.getPlanarAngles()(); // vecs = loc.getPlanarAngles()();
// if (vecs == null || vecs.length < 1) { // if (vecs == null || vecs.length < 1) {
// return 0; // return 0;
// } // }
// angle = Math.toDegrees(PamVector.vectorToSurfaceBearing(vecs[0])); // angle = Math.toDegrees(PamVector.vectorToSurfaceBearing(vecs[0]));
// oll = click.getOriginLatLong(false); // oll = click.getOriginLatLong(false);
// if (oll != null) { // if (oll != null) {
// angle -= oll.getHeading(); // angle -= oll.getHeading();
// } // }
break; break;
default: default:
return 0; return 0;
@ -1648,7 +1756,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
if (vr != null && vr.length > 0) { if (vr != null && vr.length > 0) {
return vr[0]; return vr[0];
} }
// rotAngles[0] = Math.toRadians(oll.getHeading()); // rotAngles[0] = Math.toRadians(oll.getHeading());
} }
else if (rType == BTDisplayParameters.ROTATE_TONORTH) { else if (rType == BTDisplayParameters.ROTATE_TONORTH) {
PamVector[] vr = loc.getRealWorldVectors(); PamVector[] vr = loc.getRealWorldVectors();
@ -1656,11 +1764,11 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
return vr[0]; return vr[0];
} }
} }
// if (rotAngles[0] == 0 && rotAngles[1] == 0 && rotAngles[2] == 0) { // if (rotAngles[0] == 0 && rotAngles[1] == 0 && rotAngles[2] == 0) {
// return v; // return v;
// } // }
// PamQuaternion pq = new PamQuaternion(rotAngles[0], rotAngles[1], rotAngles[2]); // PamQuaternion pq = new PamQuaternion(rotAngles[0], rotAngles[1], rotAngles[2]);
// PamVector v2 = PamVector.rotateVector(v, pq); // PamVector v2 = PamVector.rotateVector(v, pq);
return v; return v;
} }
@ -1677,16 +1785,16 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
return yStart + (yMax-yPos)/yScale; return yStart + (yMax-yPos)/yScale;
} }
private ClickDetection lastICIClick; // private ClickDetection lastICIClick;
private double clickICIToY(ClickDetection click) { private double clickICIToY(ClickDetection click) {
if (click.getICI() > 0) { // if (click.getTempICI() > 0) {
return btPlot.getHeight() - yAxis.getPosition(click.getICI());
// return click.getICI() * yScale;
}
else {
return btPlot.getHeight() - yAxis.getPosition(click.getTempICI()); return btPlot.getHeight() - yAxis.getPosition(click.getTempICI());
// return click.getTempICI() * yScale; // return click.getICI() * yScale;
} // }
// else {
// return btPlot.getHeight() - yAxis.getPosition(click.getTempICI());
// // return click.getTempICI() * yScale;
// }
} }
@ -1783,7 +1891,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
} }
// private JPopupMenu clickPopupMenu = null; // private JPopupMenu clickPopupMenu = null;
public RangeSpinner rangeSpinner; public RangeSpinner rangeSpinner;
@ -1792,20 +1900,20 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
public ClickDetSymbolChooser symbolChooser; public ClickDetSymbolChooser symbolChooser;
private JPopupMenu getClickPUMenu(ClickDetection click) { private JPopupMenu getClickPUMenu(ClickDetection click) {
// if (clickPopupMenu == null){ // if (clickPopupMenu == null){
// clickPopupMenu = new JPopupMenu(); // clickPopupMenu = new JPopupMenu();
// JMenuItem menuItem; // JMenuItem menuItem;
// PamSymbol pamSymbol; // PamSymbol pamSymbol;
// Color symbolColour; // Color symbolColour;
// for (int i = 0; i < PamColors.getInstance().getNWhaleColours(); i++) { // for (int i = 0; i < PamColors.getInstance().getNWhaleColours(); i++) {
// menuItem = new JMenuItem(" Whale Train " + i); // menuItem = new JMenuItem(" Whale Train " + i);
// symbolColour = PamColors.getInstance().getWhaleColor(i); // symbolColour = PamColors.getInstance().getWhaleColor(i);
// pamSymbol = new PamSymbol(PamSymbol.SYMBOL_CIRCLE, 12, 12, true, symbolColour, symbolColour); // pamSymbol = new PamSymbol(PamSymbol.SYMBOL_CIRCLE, 12, 12, true, symbolColour, symbolColour);
// menuItem.setIcon(pamSymbol); // menuItem.setIcon(pamSymbol);
// menuItem.addActionListener(new clickPUListener(i)); // menuItem.addActionListener(new clickPUListener(i));
// clickPopupMenu.add(menuItem); // clickPopupMenu.add(menuItem);
// } // }
// } // }
/* /*
* Make a menu based on which whales are currently alive and active and also * Make a menu based on which whales are currently alive and active and also
* a "new" category at the end ... * a "new" category at the end ...
@ -1830,7 +1938,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
OfflineEventDataUnit clickGroup = it.next(); OfflineEventDataUnit clickGroup = it.next();
whaleId = clickGroup.getEventId(); whaleId = clickGroup.getEventId();
if (click.getSuperDetection(0) == clickGroup) continue; if (click.getSuperDetection(0) == clickGroup) continue;
// if (whaleId == click.getEventId()) continue; // if (whaleId == click.getEventId()) continue;
biggestId = Math.max(biggestId, whaleId); biggestId = Math.max(biggestId, whaleId);
menuItem = new JMenuItem("Click Train " + whaleId); menuItem = new JMenuItem("Click Train " + whaleId);
symbolColour = PamColors.getInstance().getWhaleColor(clickGroup.getColourIndex()); symbolColour = PamColors.getInstance().getWhaleColor(clickGroup.getColourIndex());
@ -1841,9 +1949,9 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
} }
whaleId = biggestId + 1; whaleId = biggestId + 1;
menuItem = new JMenuItem("New Click Train"); menuItem = new JMenuItem("New Click Train");
// symbolColour = PamColors.getInstance().getWhaleColor(whaleId); // symbolColour = PamColors.getInstance().getWhaleColor(whaleId);
// pamSymbol = new PamSymbol(PamSymbol.SYMBOL_CIRCLE, 12, 12, true, symbolColour, symbolColour); // pamSymbol = new PamSymbol(PamSymbol.SYMBOL_CIRCLE, 12, 12, true, symbolColour, symbolColour);
// menuItem.setIcon(pamSymbol); // menuItem.setIcon(pamSymbol);
menuItem.addActionListener(new clickPUListener(whaleId)); menuItem.addActionListener(new clickPUListener(whaleId));
clickPopupMenu.add(menuItem, 0); clickPopupMenu.add(menuItem, 0);
@ -1921,7 +2029,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
if (popupClick == null) return; if (popupClick == null) return;
// popupClick.setEventId(whaleId); // popupClick.setEventId(whaleId);
trackClick(popupClick, whaleId); trackClick(popupClick, whaleId);
@ -1962,7 +2070,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
private void trackClick(ClickDetection click, int whaleId) { private void trackClick(ClickDetection click, int whaleId) {
click.setTracked(true); click.setTracked(true);
// clickControl.clickDetector.reWriteClick(click, false); // clickControl.clickDetector.reWriteClick(click, false);
// ClickDetection newDataUnit = new ClickDetection(click.getChannelBitmap(), click.getStartSample(), // ClickDetection newDataUnit = new ClickDetection(click.getChannelBitmap(), click.getStartSample(),
// click.getDuration(), click.clickDetector, click.triggerList); // click.getDuration(), click.clickDetector, click.triggerList);
@ -2000,35 +2108,35 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
if (scaleManager == null) { if (scaleManager == null) {
return; return;
} }
// scaleManager // scaleManager
// System.out.println(String.format("set y range from %s %3.4f to %3.4fs", scaleManager.getTitle(), // System.out.println(String.format("set y range from %s %3.4f to %3.4fs", scaleManager.getTitle(),
// scaleManager.getCurrentStart(), scaleManager.getCurrentEnd())); // scaleManager.getCurrentStart(), scaleManager.getCurrentEnd()));
yAxis.setRange(scaleManager.getCurrentStart(), scaleManager.getCurrentEnd()); yAxis.setRange(scaleManager.getCurrentStart(), scaleManager.getCurrentEnd());
yAxis.setLogScale(btDisplayParameters.logICIScale && btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI); yAxis.setLogScale(btDisplayParameters.logICIScale && btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI);
yAxis.setInterval(scaleManager.getYAxisInterval()); yAxis.setInterval(scaleManager.getYAxisInterval());
yAxis.setLabel(scaleManager.getTitle()); yAxis.setLabel(scaleManager.getTitle());
yAxis.setAutoFormat(false); yAxis.setAutoFormat(false);
// String format = getYAxisFormat() // String format = getYAxisFormat()
// double range = Math.abs(scaleManager.currentRange); // double range = Math.abs(scaleManager.currentRange);
// if (range > 30) { // if (range > 30) {
// yAxis.setFormat("%d"); // yAxis.setFormat("%d");
// } // }
// else if (range > 8) { // else if (range > 8) {
// yAxis.setFormat("%3.1f"); // yAxis.setFormat("%3.1f");
// } // }
// else if (range > 1) { // else if (range > 1) {
// yAxis.setFormat("%3.1f"); // yAxis.setFormat("%3.1f");
// } // }
// else if (range > .1) { // else if (range > .1) {
// yAxis.setFormat("%3.2f"); // yAxis.setFormat("%3.2f");
// } // }
// else if (range <= 0) { // else if (range <= 0) {
// yAxis.setFormat("%3.2f"); // yAxis.setFormat("%3.2f");
// } // }
// else { // else {
// int nDP = (int)Math.ceil(Math.abs(Math.log10(range))); // int nDP = (int)Math.ceil(Math.abs(Math.log10(range)));
// yAxis.setFormat(String.format("%%%d.%df", nDP+2, nDP)); // yAxis.setFormat(String.format("%%%d.%df", nDP+2, nDP));
// } // }
// switch (btDisplayParameters.VScale) { // switch (btDisplayParameters.VScale) {
// //
@ -2227,7 +2335,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
* @return * @return
*/ */
private JPopupMenu getPopupMenu(ClickDetection clickedClick) { private JPopupMenu getPopupMenu(ClickDetection clickedClick) {
// System.out.println("Create click right click menu....."); // System.out.println("Create click right click menu.....");
boolean isView = PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW; boolean isView = PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW;
JPopupMenu menu = new JPopupMenu(); JPopupMenu menu = new JPopupMenu();
JMenuItem menuItem; JMenuItem menuItem;
@ -2289,23 +2397,23 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
menu.addSeparator(); menu.addSeparator();
} }
// menuItem = new JCheckBoxMenuItem("Colour by species id", // menuItem = new JCheckBoxMenuItem("Colour by species id",
// btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_SPECIES); // btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_SPECIES);
// menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_SPECIES)); // menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_SPECIES));
// menu.add(menuItem); // menu.add(menuItem);
// menuItem = new JCheckBoxMenuItem("Colour by click train", // menuItem = new JCheckBoxMenuItem("Colour by click train",
// btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_TRAIN); // btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_TRAIN);
// menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_TRAIN)); // menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_TRAIN));
// menu.add(menuItem); // menu.add(menuItem);
// menuItem = new JCheckBoxMenuItem("Colour by train, then species", // menuItem = new JCheckBoxMenuItem("Colour by train, then species",
// btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_TRAINANDSPECIES); // btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_TRAINANDSPECIES);
// menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_TRAINANDSPECIES)); // menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_TRAINANDSPECIES));
// menu.add(menuItem); // menu.add(menuItem);
// // if (isNetReceiver) { // // if (isNetReceiver) {
// menuItem = new JCheckBoxMenuItem("Colour by hydrophone", // menuItem = new JCheckBoxMenuItem("Colour by hydrophone",
// btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_HYDROPHONE); // btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_HYDROPHONE);
// menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_HYDROPHONE)); // menuItem.addActionListener(new ColourByAction(BTDisplayParameters.COLOUR_BY_HYDROPHONE));
// menu.add(menuItem); // menu.add(menuItem);
// } // }
menuItem = new JCheckBoxMenuItem("Bearing / Time"); menuItem = new JCheckBoxMenuItem("Bearing / Time");
menuItem.addActionListener(new AxesMenuAction(BTDisplayParameters.DISPLAY_BEARING)); menuItem.addActionListener(new AxesMenuAction(BTDisplayParameters.DISPLAY_BEARING));
@ -2639,23 +2747,23 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
} }
} }
// class ColourByAction implements ActionListener { // class ColourByAction implements ActionListener {
// //
// private int colourChoice; // private int colourChoice;
// //
// public ColourByAction(int colourChoice) { // public ColourByAction(int colourChoice) {
// super(); // super();
// this.colourChoice = colourChoice; // this.colourChoice = colourChoice;
// } // }
// public void actionPerformed(ActionEvent e) { // public void actionPerformed(ActionEvent e) {
// btDisplayParameters.colourScheme = colourChoice; // btDisplayParameters.colourScheme = colourChoice;
// symbolChooser.setSymbolType(colourChoice); // symbolChooser.setSymbolType(colourChoice);
// //
// btPlot.setTotalRepaint(); // btPlot.setTotalRepaint();
// btPlot.repaint(minPaintTime); // btPlot.repaint(minPaintTime);
// btPlot.createKey(); // btPlot.createKey();
// } // }
// } // }
class SettingsMenuAction implements ActionListener { class SettingsMenuAction implements ActionListener {
@ -2670,7 +2778,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
getVScaleManager().setSelected(); getVScaleManager().setSelected();
} }
btAxis.makeAxis(); btAxis.makeAxis();
// System.out.println("360: "+btDisplayParameters.view360); // System.out.println("360: "+btDisplayParameters.view360);
repaintBoth(); repaintBoth();
btPlot.createKey(); btPlot.createKey();
if (clickControl.getOfflineToolbar() != null) { if (clickControl.getOfflineToolbar() != null) {
@ -2694,16 +2802,16 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
Rectangle b = null ; Rectangle b = null ;
if (btAmplitudeSelector != null) { if (btAmplitudeSelector != null) {
b= btAmplitudeSelector.getFrame().getBounds(); b= btAmplitudeSelector.getFrame().getBounds();
// btAmplitudeSelector.getFrame().setVisible(true); // btAmplitudeSelector.getFrame().setVisible(true);
// // btAmplitudeSelector.getFrame(). // // btAmplitudeSelector.getFrame().
} }
// else { // else {
btAmplitudeSelector = BTAmplitudeSelector.showAmplitudeFrame(clickControl, this); btAmplitudeSelector = BTAmplitudeSelector.showAmplitudeFrame(clickControl, this);
if(b!=null){ if(b!=null){
btAmplitudeSelector.getFrame().setBounds(b); btAmplitudeSelector.getFrame().setBounds(b);
} }
// } // }
} }
private void checkBTAmplitudeSelectHisto() { private void checkBTAmplitudeSelectHisto() {
@ -2895,7 +3003,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
public boolean redrawAllClicks(){ public boolean redrawAllClicks(){
// System.out.println("redrawAllClicks " + hScrollBar.getValueMillis()+ " "+vScrollBar.getValue()+" "+ hScrollBar.getMaximumMillis()+" "+hScrollBar.getStepSizeMillis()); // System.out.println("redrawAllClicks " + hScrollBar.getValueMillis()+ " "+vScrollBar.getValue()+" "+ hScrollBar.getMaximumMillis()+" "+hScrollBar.getStepSizeMillis());
if (totalRepaint) { if (totalRepaint) {
return true; return true;
} }
@ -2914,7 +3022,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
} }
} }
// double lastPaintTime; // double lastPaintTime;
public void paintClicks(Graphics g, Rectangle clipRectangle) { public void paintClicks(Graphics g, Rectangle clipRectangle) {
long t0 = System.nanoTime(); long t0 = System.nanoTime();
@ -2928,18 +3036,21 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
zoomer.paintShape(g, this, true); zoomer.paintShape(g, this, true);
} }
// long t1 = System.nanoTime(); // long t1 = System.nanoTime();
synchronized (clickData.getSynchLock()) { synchronized (clickData.getSynchLock()) {
// long t2 = System.nanoTime(); // long t2 = System.nanoTime();
// double ms = ((double) (t2-t1)) / 1000000.; // double ms = ((double) (t2-t1)) / 1000000.;
// if (btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI) {
// sortTempICIs();
// }
ListIterator<ClickDetection> clickIterator = clickData.getListIterator(PamDataBlock.ITERATOR_END); ListIterator<ClickDetection> clickIterator = clickData.getListIterator(PamDataBlock.ITERATOR_END);
while (clickIterator.hasPrevious()) { while (clickIterator.hasPrevious()) {
click = clickIterator.previous(); click = clickIterator.previous();
if (shouldPlot(prevPlottedClick)){ if (shouldPlot(prevPlottedClick)){
if (btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI) { // if (btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI) {
prevPlottedClick.setTempICI((double) (prevPlottedClick.getStartSample()-click.getStartSample()) / sampleRate); // prevPlottedClick.setTempICI((double) (prevPlottedClick.getStartSample()-click.getStartSample()) / sampleRate);
} // }
if (drawClick(g, prevPlottedClick, clipRectangle) < -0){ if (drawClick(g, prevPlottedClick, clipRectangle) < -0){
break; break;
} }
@ -2949,16 +3060,16 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
if (shouldPlot(prevPlottedClick)){ // and draw the last one ! if (shouldPlot(prevPlottedClick)){ // and draw the last one !
drawClick(g, prevPlottedClick, clipRectangle); drawClick(g, prevPlottedClick, clipRectangle);
} }
// g.drawString(String.format("Wait synch %3.3fms", ms), 0, 20); // g.drawString(String.format("Wait synch %3.3fms", ms), 0, 20);
} }
// long t3 = System.nanoTime(); // long t3 = System.nanoTime();
// g.drawString(String.format("Last draw %3.3fms", lastPaintTime), 0, 20); // g.drawString(String.format("Last draw %3.3fms", lastPaintTime), 0, 20);
// lastPaintTime = ((double) (t3-t0)) / 1000000.; // lastPaintTime = ((double) (t3-t0)) / 1000000.;
} }
@Override @Override
public void paintPanel(Graphics g, Rectangle clipRectangle) { public void paintPanel(Graphics g, Rectangle clipRectangle) {
// long tNow = System.currentTimeMillis(); // long tNow = System.currentTimeMillis();
redrawClicks=redrawAllClicks(); redrawClicks=redrawAllClicks();
/** /**
* Need to call this every time since the original symbol chooser will get deleted after * Need to call this every time since the original symbol chooser will get deleted after
@ -3090,11 +3201,11 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
if (pt.x - width > clipRegion.x + clipRegion.width) return +1; if (pt.x - width > clipRegion.x + clipRegion.width) return +1;
} }
if (click.tracked) { if (click.tracked) {
// System.out.println("Drawing tracked click"); // System.out.println("Drawing tracked click");
} }
//set the colour scheme. //set the colour scheme.
// symbolChooser.setSymbolType(btDisplayParameters.colourScheme); // symbolChooser.setSymbolType(btDisplayParameters.colourScheme);
PamSymbol symbol = symbolChooser.getPamSymbol(btProjector, click); PamSymbol symbol = symbolChooser.getPamSymbol(btProjector, click);
//.getClickSymbol(clickControl.getClickIdentifier(), click, btDisplayParameters.colourScheme); //.getClickSymbol(clickControl.getClickIdentifier(), click, btDisplayParameters.colourScheme);
@ -3156,8 +3267,8 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
return null; return null;
} }
String tip = click.getSummaryString(); String tip = click.getSummaryString();
// String tip = String.format("<html>UID. %d; Click No. %d; Channels %s", click.getUID(), // String tip = String.format("<html>UID. %d; Click No. %d; Channels %s", click.getUID(),
// click.clickNumber, PamUtils.getChannelList(click.getChannelBitmap())); // click.clickNumber, PamUtils.getChannelList(click.getChannelBitmap()));
byte type = click.getClickType(); byte type = click.getClickType();
if (clickControl.getClickIdentifier() != null) { if (clickControl.getClickIdentifier() != null) {
String typeStr = clickControl.getClickIdentifier().getSpeciesName(type); String typeStr = clickControl.getClickIdentifier().getSpeciesName(type);
@ -3262,7 +3373,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
setKeyPosition(CornerLayoutContraint.LAST_LINE_START); setKeyPosition(CornerLayoutContraint.LAST_LINE_START);
} }
catch (NullPointerException e) { catch (NullPointerException e) {
// e.printStackTrace(); // e.printStackTrace();
} }
} }
@ -3342,7 +3453,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
return false; return false;
} }
if (btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI) { if (btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI) {
// if (btDisplayParameters.showUnassignedICI == false && click.getICI() < 0) return false; // if (btDisplayParameters.showUnassignedICI == false && click.getICI() < 0) return false;
if (btDisplayParameters.showUnassignedICI == false && click.getSuperDetectionsCount() <= 0) return false; if (btDisplayParameters.showUnassignedICI == false && click.getSuperDetectionsCount() <= 0) return false;
// otherwise may be ok, since will estimate all ici's on teh fly. // otherwise may be ok, since will estimate all ici's on teh fly.
} }
@ -3436,7 +3547,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
* to zero. However DO call these functions which were previously in * to zero. However DO call these functions which were previously in
* reset(); * reset();
*/ */
// reset(); // reset();
int channels = clickControl.clickParameters.getChannelBitmap(); int channels = clickControl.clickParameters.getChannelBitmap();
int[] channelGroups = clickControl.clickParameters.getChannelGroups(); int[] channelGroups = clickControl.clickParameters.getChannelGroups();
int nChannelGroups = GroupedSourcePanel.countChannelGroups(channels, channelGroups); int nChannelGroups = GroupedSourcePanel.countChannelGroups(channels, channelGroups);
@ -3502,8 +3613,8 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
this.btDisplayParameters = ((BTDisplayParameters) pamControlledUnitSettings this.btDisplayParameters = ((BTDisplayParameters) pamControlledUnitSettings
.getSettings()).clone(); .getSettings()).clone();
// rangeScrollBar.setValue(btDisplayParameters.vScrollValue); // rangeScrollBar.setValue(btDisplayParameters.vScrollValue);
// rangeSpinner.setSpinnerValue(btDisplayParameters.getTimeRange()); // rangeSpinner.setSpinnerValue(btDisplayParameters.getTimeRange());
// btPlot.createKey(); // btPlot.createKey();
return true; return true;
} }

2
src/clickDetector/ClickDetection.java
View File

@ -1511,7 +1511,7 @@ public class ClickDetection extends PamDataUnit<PamDataUnit, PamDataUnit> implem
* @param iCI the iCI to set * @param iCI the iCI to set
*/ */
public void setICI(double iCI) { public void setICI(double iCI) {
ICI = iCI; this.ICI = iCI;
} }
protected void setChannelGroupDetector(ChannelGroupDetector channelGroupDetector) { protected void setChannelGroupDetector(ChannelGroupDetector channelGroupDetector) {

1
src/pamScrollSystem/PamScrollSlider.java
View File

@ -140,6 +140,7 @@ public class PamScrollSlider extends AbstractPamScrollerAWT {
valueMillis = Math.max(scrollerData.minimumMillis, Math.min(scrollerData.maximumMillis, valueMillis)); valueMillis = Math.max(scrollerData.minimumMillis, Math.min(scrollerData.maximumMillis, valueMillis));
int val = (int) ((valueMillis - scrollerData.minimumMillis) / scrollerData.getStepSizeMillis()); int val = (int) ((valueMillis - scrollerData.minimumMillis) / scrollerData.getStepSizeMillis());
if (val >= slider.getMinimum() && val <= slider.getMaximum()) { if (val >= slider.getMinimum() && val <= slider.getMaximum()) {
// System.out.printf("Set slider val %d in range %d to %d\n", val, slider.getMinimum(), slider.getMaximum());
slider.setValue(val); slider.setValue(val);
} }
} }

17
src/pamScrollSystem/ViewerScrollerManager.java
View File

@ -699,6 +699,23 @@ public class ViewerScrollerManager extends AbstractScrollManager implements PamS
if (aScroller == pamScroller) { if (aScroller == pamScroller) {
continue; continue;
} }
/*
* Can end up with some horrible feedback here if two
* coupled scrollers bring in rounding errors and start
* to oscillate each other.
*/
long currentVal = aScroller.getValueMillis();
long change = Math.abs(value-currentVal);
long range = aScroller.getMaximumMillis() - aScroller.getMinimumMillis();
if (range == 0) {
aScroller.setValueMillis(aScroller.getMinimumMillis());
continue;
}
double fracChange = (double) change / (double) range;
if (fracChange <= .0001) {
continue;
}
aScroller.setValueMillis(value); aScroller.setValueMillis(value);
} }
} }