diff --git a/.classpath b/.classpath
index 924124d8..576b210a 100644
--- a/.classpath
+++ b/.classpath
@@ -6,8 +6,9 @@
-
+
+
diff --git a/src/PamModel/PamModel.java b/src/PamModel/PamModel.java
index c10958e0..bc475091 100644
--- a/src/PamModel/PamModel.java
+++ b/src/PamModel/PamModel.java
@@ -502,7 +502,8 @@ final public class PamModel implements PamSettings {
mi.setModulesMenuGroup(sensorsGroup);
mi.setToolTipText("Imports CPOD data");
mi.setHidden(SMRUEnable.isEnable() == false);
-
+ mi.addGUICompatabilityFlag(PamGUIManager.FX); //has FX enabled GUI.
+
/*
* ************* Start Displays Group *******************
*/
diff --git a/src/Resources/css/primer-pamguard.css b/src/Resources/css/primer-pamguard.css
index 026332a5..ece247b6 100644
--- a/src/Resources/css/primer-pamguard.css
+++ b/src/Resources/css/primer-pamguard.css
@@ -234,7 +234,8 @@
.popover > .content {
-fx-background-color: -fx-darkbackground;
-fx-background-radius: 5;
- -fx-border-radius: 5;
+ -fx-border-radius: 5;
+ -fx-padding: 0 0 0 0;
}
.popover > .arrow {
diff --git a/src/cpod/dataPlotFX/CPODDDDataInfo.java b/src/cpod/dataPlotFX/CPODDDDataInfo.java
index 5000f5ab..e287db6f 100644
--- a/src/cpod/dataPlotFX/CPODDDDataInfo.java
+++ b/src/cpod/dataPlotFX/CPODDDDataInfo.java
@@ -60,7 +60,12 @@ public class CPODDDDataInfo extends DDDataInfo {
public void setupAxis(PamDataUnit data, double sR, DetectionPlotProjector plotProjector) {
super.setupAxis(data, sR, plotProjector);
+
CPODClick click = (CPODClick) data;
+ if (click.getWaveData()==null) {
+ return;
+ }
+
double lenMS = (1000.*click.getWaveData()[0].length)/FPODReader.FPOD_WAV_SAMPLERATE;
//set the scroller minimum and maximum
plotProjector.setMinScrollLimit(0);
@@ -68,7 +73,6 @@ public class CPODDDDataInfo extends DDDataInfo {
plotProjector.setMaxScrollLimit(lenMS);
plotProjector.setEnableScrollBar(true);
-
plotProjector.setAxisMinMax(0, 250, Side.BOTTOM);
}
@@ -89,7 +93,6 @@ public class CPODDDDataInfo extends DDDataInfo {
public CPODWaveformPlot(DetectionPlotDisplay detectionPlotDisplay) {
super(detectionPlotDisplay);
- // TODO Auto-generated constructor stub
}
@Override
diff --git a/src/cpod/dataPlotFX/CPODPlotInfoFX.java b/src/cpod/dataPlotFX/CPODPlotInfoFX.java
index 5a0a534a..5e7a5b50 100644
--- a/src/cpod/dataPlotFX/CPODPlotInfoFX.java
+++ b/src/cpod/dataPlotFX/CPODPlotInfoFX.java
@@ -325,7 +325,6 @@ public class CPODPlotInfoFX extends GenericDataPlotInfo {
y2= tdProjector.getYPix(nycl);
break;
-
}
if (tdProjector.getOrientation()==Orientation.VERTICAL){
@@ -381,12 +380,14 @@ public class CPODPlotInfoFX extends GenericDataPlotInfo {
@Override
public PamSymbolFX getPamSymbol(PamDataUnit dataUnit, int type) {
PamSymbolFX symbol = super.getPamSymbol(dataUnit, type);
+
if (((CPODClick) dataUnit).getWaveData()!=null && type!=TDSymbolChooserFX.HIGHLIGHT_SYMBOL) {
symbol.setLineColor(symbol.getFillColor().darker());
symbol.setHeight(symbol.getHeight()*1.5);
symbol.setWidth(symbol.getWidth()*1.5);
+ return symbol;
}
-
+
return symbol;
}
diff --git a/src/cpod/dataPlotFX/CPODTDSettingsPane.java b/src/cpod/dataPlotFX/CPODTDSettingsPane.java
index 3727f8c7..12fe0f6d 100644
--- a/src/cpod/dataPlotFX/CPODTDSettingsPane.java
+++ b/src/cpod/dataPlotFX/CPODTDSettingsPane.java
@@ -46,7 +46,7 @@ public class CPODTDSettingsPane implements TDSettingsPane {
public CPODTDSettingsPane(CPODPlotInfoFX cpodPlotInfoFX) {
this.cpodPlotInfoFX=cpodPlotInfoFX;
mainPane = createMainPane();
- mainPane.setPrefWidth(330);
+ mainPane.setPrefWidth(400);
}
/**
diff --git a/src/cpod/fx/CPODGUIFX.java b/src/cpod/fx/CPODGUIFX.java
index 25a39cd1..e33f6e27 100644
--- a/src/cpod/fx/CPODGUIFX.java
+++ b/src/cpod/fx/CPODGUIFX.java
@@ -10,12 +10,12 @@ import pamViewFX.PamControlledGUIFX;
public class CPODGUIFX extends PamControlledGUIFX {
/**
- * The dl control.
+ * Reference to the CPOD control.
*/
- private CPODControl2 dlControl;
+ private CPODControl2 cpodControl;
public CPODGUIFX(CPODControl2 cpodControl2) {
- // TODO Auto-generated constructor stub
+ cpodControl = cpodControl2;
}
@@ -27,19 +27,19 @@ public class CPODGUIFX extends PamControlledGUIFX {
* @return a Pane containing controls to change settings for module.
*/
public SettingsPane getSettingsPane(){
- dlControl.getSettingsPane().setParams(dlControl.getCPODParam());
- return dlControl.getSettingsPane();
+ cpodControl.getSettingsPane().setParams(cpodControl.getCPODParam());
+ return cpodControl.getSettingsPane();
}
@Override
public void updateParams() {
- CPODParams newParams=dlControl.getSettingsPane().getParams(dlControl.getCPODParam());
+ CPODParams newParams=cpodControl.getSettingsPane().getParams(cpodControl.getCPODParam());
if (newParams!=null) {
- dlControl.setCPODParams(newParams);
+ cpodControl.setCPODParams(newParams);
}
//setup the controlled unit.
- dlControl.setupControlledUnit();
+ cpodControl.setupControlledUnit();
}
@Override
diff --git a/src/dataGram/DatagramManager.java b/src/dataGram/DatagramManager.java
index 1e8db795..206e5fe9 100644
--- a/src/dataGram/DatagramManager.java
+++ b/src/dataGram/DatagramManager.java
@@ -539,6 +539,8 @@ public class DatagramManager {
else {
PamController.getInstance().notifyTaskProgress(
new SimplePamTaskUpdate("Finished Datagram Mapping", PamTaskUpdate.STATUS_DONE));
+ publish(new DatagramProgress(PamTaskUpdate.STATUS_DONE, 1, 1));
+
}
}
diff --git a/src/dataGram/DatagramProgress.java b/src/dataGram/DatagramProgress.java
index 54449946..3fedf3b8 100644
--- a/src/dataGram/DatagramProgress.java
+++ b/src/dataGram/DatagramProgress.java
@@ -77,8 +77,7 @@ public class DatagramProgress extends PamTaskUpdate {
}
@Override
- public double getProgress() {
- System.out.println("DatagramProgress: " + processedUnits + " tot: " + totalUnits);
+ public double getProgress2() {
double progress= ProgressIndicator.INDETERMINATE_PROGRESS;
switch(getStatus()) {
case DatagramProgress.STATUS_BLOCKCOUNT:
@@ -95,13 +94,17 @@ public class DatagramProgress extends PamTaskUpdate {
else progress=0;
break;
}
+
+ //System.out.println("DatagramProgress: " + processedUnits + " tot: " + totalUnits + " progress: " + progress);
+
return progress;
}
@Override
- public double getProgress2(){
+ public double getProgress(){
+ //seems like the current point is simply the percentage done...
double progress;
- if (pointsToUpdate>0) progress=((double)currentPoint)/pointsToUpdate;
+ if (pointsToUpdate>0) progress=((double)currentPoint)/100.;
else progress=0;
switch(getStatus()) {
case DatagramProgress.STATUS_BLOCKCOUNT:
@@ -110,14 +113,16 @@ public class DatagramProgress extends PamTaskUpdate {
progress=0;
break;
case DatagramProgress.STATUS_STARTINGFILE:
- progress=((double)currentPoint)/pointsToUpdate;
+ progress=((double)currentPoint)/100.;
break;
case DatagramProgress.STATUS_ENDINGFILE:
- progress=((double)currentPoint)/pointsToUpdate;
+ progress=((double)currentPoint)/100.;
break;
case DatagramProgress.STATUS_UNITCOUNT:
break;
}
+ //System.out.println("DatagramProgress2: " + currentPoint + " tot: " + pointsToUpdate + " progress: " + progress);
+
return progress;
}
diff --git a/src/dataModelFX/connectionNodes/ModuleIconFactory.java b/src/dataModelFX/connectionNodes/ModuleIconFactory.java
index 13ec59ab..e91144d0 100644
--- a/src/dataModelFX/connectionNodes/ModuleIconFactory.java
+++ b/src/dataModelFX/connectionNodes/ModuleIconFactory.java
@@ -2,6 +2,7 @@ package dataModelFX.connectionNodes;
import dataModelFX.DataModelStyle;
import javafx.scene.Node;
+import javafx.scene.control.Label;
import javafx.scene.image.Image;
import javafx.scene.image.ImageView;
import javafx.scene.layout.StackPane;
@@ -35,7 +36,7 @@ public class ModuleIconFactory {
public enum ModuleIcon {
DATAMAP, NMEA, GPS, MAP, SOUND_AQ, SOUND_OUTPUT, FFT, FILTER, CLICK, CLICK_TRAIN, RECORDER, WHISTLE_MOAN,
NOISE_BAND, NOISE_FILT, DATABASE, BINARY, TIME_DISPLAY, DETECTION_DISPLAY, ARRAY, DEEP_LEARNING, MATCHED_CLICK_CLASSIFIER,
- DECIMATOR
+ DECIMATOR, CPOD
}
/**
@@ -126,6 +127,9 @@ public class ModuleIconFactory {
case DECIMATOR:
iconNode = getSVGIcon("/Resources/modules/decimator.svg");
break;
+ case CPOD:
+ iconNode = new Label("CPOD"); //TEMP
+ break;
default:
break;
}
@@ -261,6 +265,9 @@ public class ModuleIconFactory {
case "decimator.DecimatorControl":
icon=ModuleIcon.DECIMATOR;
break;
+ case "cpod.CPODControl2":
+ icon=ModuleIcon.CPOD;
+ break;
}
return icon;
}
diff --git a/src/dataPlotsFX/data/TDDataInfoFX.java b/src/dataPlotsFX/data/TDDataInfoFX.java
index 45185e3f..c070ed31 100644
--- a/src/dataPlotsFX/data/TDDataInfoFX.java
+++ b/src/dataPlotsFX/data/TDDataInfoFX.java
@@ -12,6 +12,7 @@ import javafx.scene.canvas.GraphicsContext;
import javafx.scene.shape.Polygon;
import PamController.PamController;
import PamUtils.Coordinate3d;
+import PamUtils.PamCalendar;
import PamUtils.PamUtils;
import PamView.HoverData;
import PamView.GeneralProjector.ParameterType;
@@ -373,8 +374,8 @@ public abstract class TDDataInfoFX {
*/
public void drawAllDataUnits(int plotNumber, GraphicsContext g, double scrollStart, TDProjectorFX tdProjector) {
-// System.out.println("Max double value: " + PamCalendar.formatDateTime((long) Double.MAX_EXPONENT));
-// System.out.println("Max long value: " + PamCalendar.formatDateTime((long) Long.MAX_VALUE));
+// System.out.println("Max double value: " + this.getDataName() + PamCalendar.formatDateTime((long) Double.MAX_EXPONENT));
+// System.out.println("Max long value: " + this.getDataName() + PamCalendar.formatDateTime((long) Long.MAX_VALUE));
PamDataUnit dataUnit = null;
@@ -391,7 +392,10 @@ public abstract class TDDataInfoFX {
// scrollStart = PamCalendar.getTimeInMillis();
//work out start and stop times
long loopEnd = (long) (scrollStart + (tdProjector.getVisibleTime() * 1.5));
- long loopStart = (long) (scrollStart - (tdProjector.getVisibleTime() * .5));
+ long loopStart = (long) (scrollStart - (tdProjector.getVisibleTime() * 1.5));
+
+// System.out.println("Loop start: " + this.getDataName() + PamCalendar.formatDateTime((long) loopStart));
+// System.out.println("Loop end: " + this.getDataName() + PamCalendar.formatDateTime((long) loopEnd));
//find a number close to the index start,
ListIterator it = getUnitIterator( loopStart, plotNumber);
@@ -402,6 +406,7 @@ public abstract class TDDataInfoFX {
dataUnit = it.next();
count++;
if (dataUnit!=null && shouldDraw(plotNumber, dataUnit)) {
+
if (dataUnit.getEndTimeInMilliseconds() < loopStart) {
continue;
}
@@ -409,11 +414,13 @@ public abstract class TDDataInfoFX {
break;
}
+ drawCalls++;
drawDataUnit(plotNumber, dataUnit, g, scrollStart,
tdProjector ,TDSymbolChooserFX.NORMAL_SYMBOL);
}
}
+// System.out.println("Found: " + drawCalls + " " + this.getDataName() + " to draw");
lastUnitDrawn(g, scrollStart, tdProjector, plotNumber);
}
//System.out.println("Total data units: " + count+ " draw calls: " +drawCalls );
diff --git a/src/dataPlotsFX/data/generic/GenericLinePlotInfo.java b/src/dataPlotsFX/data/generic/GenericLinePlotInfo.java
index 97a06ed9..92e19034 100644
--- a/src/dataPlotsFX/data/generic/GenericLinePlotInfo.java
+++ b/src/dataPlotsFX/data/generic/GenericLinePlotInfo.java
@@ -2,6 +2,7 @@ package dataPlotsFX.data.generic;
import PamController.PamController;
import PamUtils.Coordinate3d;
+import PamUtils.PamCalendar;
import PamView.GeneralProjector;
import PamView.HoverData;
import PamView.symbol.PamSymbolChooser;
@@ -47,21 +48,18 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
}
-
-
/* (non-Javadoc)
* @see dataPlotsFX.data.TDDataInfoFX#drawDataUnit(int, PamguardMVC.PamDataUnit, javafx.scene.canvas.GraphicsContext, long, dataPlotsFX.projector.TDProjectorFX, int)
*/
@Override
public Polygon drawDataUnit(int plotNumber, PamDataUnit pamDataUnit, GraphicsContext g, double scrollStart,
TDProjectorFX tdProjector, int type) {
-
return drawPredicition(plotNumber, pamDataUnit, g, scrollStart, tdProjector, type);
-
}
+
/**
- * Get the line data. Each double[] is a seperate line with N evenly spaced data points.
+ * Get the line data. Each double[] is a separate line with N evenly spaced data points.
* @param pamDataUnit - the pam data unit containing the data.
* @return the line data.
*/
@@ -98,15 +96,12 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
double timeMillis = pamDataUnit.getTimeMilliseconds()+pamDataUnit.getDurationInMilliseconds()/2;
double tC=tdProjector.getTimePix(timeMillis-scrollStart);
-
//draws lines so tc should be some slop in pixels.
if (tC < -1000 || tC>tdProjector.getWidth()+1000) {
+ //System.out.println("Line is outside display " + tC);
return null;
}
- //TODO -must sort out wrap
- //dlControl.getDLParams().sampleHop;
-
double dataPixel;
Coordinate3d c;
Color color;
@@ -128,16 +123,13 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
//brighten the colour up.
//color = Color.color(color.getRed()*0.8, color.getGreen()*0.8, color.getBlue()*0.8);
-
- //System.out.println("TDDataInfoFX: tc: "+tC+ " dataUnitTime: "+PamCalendar.formatTime(timeMillis)+" scrollStart: "
- //+PamCalendar.formatTime((long) scrollStart)+" (timeMillis-scrollStart)/1000. "+((timeMillis-scrollStart)/1000.));
-
-
+// System.out.println("TDDataInfoFX: tc: "+tC+ " dataUnitTime: "+PamCalendar.formatTime((long) timeMillis)+" scrollStart: "
+// +PamCalendar.formatTime((long) scrollStart)+" (timeMillis-scrollStart)/1000. "+((timeMillis-scrollStart)/1000.));
+
c = tdProjector.getCoord3d(timeMillis, detData[i][j], 0);
dataPixel = tdProjector.getYPix(detData[i][j]);
-
if (lastUnits[chan][i]==null) {
lastUnits[chan][i] = new Point2D(tC, dataPixel);
g.fillOval(tC, dataPixel, 5,5);
@@ -147,7 +139,6 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
if (tC>lastUnits[chan][i].getX() && (!this.getTDGraph().isWrap() ||
(tC=0 && lastUnits[chan][i].getX()0)) {
//in wrap mode we can get some weird effects with tC co-ordintates. Still have not quite cracked this...
-
// if (Math.abs(tC - lastUnits[chan][i].getX())>100) {
// System.out.println("tC: " + tC + " lastUnits[i].getX(): " + lastUnits[chan][i].getX()
// + " " + tdProjector. getTimeAxis().getPosition((timeMillis-scrollStart)/1000.) + " " + tdProjector.getWidth());
@@ -155,12 +146,9 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
g.strokeLine(tC, dataPixel, lastUnits[chan][i].getX(), lastUnits[chan][i].getY());
}
lastUnits[chan][i] = new Point2D(tC, dataPixel);
-
}
tdProjector.addHoverData(new HoverData(c , pamDataUnit, 0, plotNumber));
-
}
-
//getSymbolChooser().getPamSymbol(pamDataUnit,type).draw(g, new Point2D(tC, dataPixel));
}
}
@@ -192,7 +180,8 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
* @return the color for that prediciton
*/
public abstract LineInfo getColor(int i);
-
+
+
@Override
public Double getDataValue(PamDataUnit pamDataUnit) {
//this is not used because we have overridden the super drawing class.
@@ -206,15 +195,13 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
* @param changeType - notification flag.
*/
public void notifyChange(int changeType) {
- //System.out.println("Prediction NOTIFYMODELCHANGED: ");
+// System.out.println("Prediction NOTIFYMODELCHANGED: " + changeType);
switch (changeType) {
case PamController.CHANGED_PROCESS_SETTINGS:
lastUnits = new Point2D[PamConstants.MAX_CHANNELS][];
-;
break;
case PamController.RUN_NORMAL:
lastUnits = new Point2D[PamConstants.MAX_CHANNELS][];
-
break;
case PamController.PAM_STOPPING:
lastUnits = new Point2D[PamConstants.MAX_CHANNELS][];
diff --git a/src/dataPlotsFX/layout/TDDisplayFX.java b/src/dataPlotsFX/layout/TDDisplayFX.java
index 94592e3f..afbcdb52 100644
--- a/src/dataPlotsFX/layout/TDDisplayFX.java
+++ b/src/dataPlotsFX/layout/TDDisplayFX.java
@@ -615,9 +615,10 @@ public class TDDisplayFX extends PamBorderPane {
* @param milliSeconds - the master clock position.
*/
public void scrollDisplayEnd(long milliSeconds) {
+
- if (!isViewer() && milliSeconds <= lastUpdate && milliSeconds > lastUpdate - tdParametersFX.visibleTimeRange) {
- //System.out.println("milliSeconds <= lastUpdate && milliSeconds > lastUpdate - visibleRange");
+ if (!isViewer() && lastUpdate>0 && milliSeconds <= lastUpdate && milliSeconds > lastUpdate - tdParametersFX.visibleTimeRange) {
+// System.out.println("milliSeconds <= lastUpdate && milliSeconds > lastUpdate - visibleRange");
return;
}
@@ -849,7 +850,6 @@ public class TDDisplayFX extends PamBorderPane {
@Override
public void scrollValueChanged(AbstractPamScroller pamScroller) {
- // System.out.println("TDDisplayFX: Scroll Value changed: " + System.currentTimeMillis());
// System.out.println(String.format("Scroller value changed get start %s, End %s, pos %s", PamCalendar.formatTime(timeScrollerFX.getMinimumMillis()),
// PamCalendar.formatTime(timeScrollerFX.getMaximumMillis()),PamCalendar.formatTime(timeScrollerFX.getValueMillis())));
//have to set the repaint wait millis param to zero or else when scroll bar is moved quickly painting does not occur correctly.
@@ -1183,11 +1183,15 @@ public class TDDisplayFX extends PamBorderPane {
break;
}
+ //forces a repaint after any changes.
+ lastUpdate=-1;
+
if (tdGraphs != null) {
for (TDGraphFX tdg:tdGraphs) {
tdg.notifyModelChanged(changeType);
}
}
+
}
/**
diff --git a/src/dataPlotsFX/layout/TDGraphFX.java b/src/dataPlotsFX/layout/TDGraphFX.java
index c5b39858..4090f9dd 100644
--- a/src/dataPlotsFX/layout/TDGraphFX.java
+++ b/src/dataPlotsFX/layout/TDGraphFX.java
@@ -1124,7 +1124,7 @@ public class TDGraphFX extends PamBorderPane {
*
*/
public synchronized void repaint(long tm, int flag) {
-
+
// clear the current canvas's
if (hasCanvas(flag, BASE_CANVAS)) {
baseCanvas.getGraphicsContext2D().clearRect(0, 0, baseCanvas.getWidth(), baseCanvas.getHeight());
@@ -1151,16 +1151,18 @@ public class TDGraphFX extends PamBorderPane {
boolean hasBase = false;
synchronized (dataList) {
for (TDDataInfoFX dataInfo : dataList) {
+
base = false;
+
if (!dataInfo.isShowing()) {
- // System.out.println("dataInfo.isShowing(): " + dataInfo.getDataName());
+ System.out.println("!dataInfo.isShowing(): " + dataInfo.getDataName());
continue;
}
scaleInfo = dataInfo.getScaleInfo();
if (scaleInfo == null) {
- // System.out.println("scale info null " + dataInfo.getDataName() + "index:
- // "+dataInfo.getScaleInfoIndex());
+// System.out.println("scale info null " + dataInfo.getDataName() + "index:
+// "+dataInfo.getScaleInfoIndex());
continue;
}
@@ -1183,7 +1185,7 @@ public class TDGraphFX extends PamBorderPane {
}
;
- // ok so only repaint if we have the right CANVAS
+ // OK so only repaint if we have the right CANVAS
if (base && hasCanvas(flag, BASE_CANVAS)) {
paintDataUnits(gc, dataInfo, false);
} else if (!base && hasCanvas(flag, FRONT_CANVAS)) {
@@ -1287,6 +1289,7 @@ public class TDGraphFX extends PamBorderPane {
// PamDataBlock dataBlock = dataInfo.getDataBlock();
// scroll start is the end of the display i.e. the last visible time in the past
+
// in real time mode.
scrollStart = tdDisplay.getTimeScroller().getValueMillisD();
@@ -1524,7 +1527,7 @@ public class TDGraphFX extends PamBorderPane {
* @param tm- if within millis of last repaint don't repaint
*/
public synchronized void repaint(long tm, int flag) {
-
+
// Start of block moved over from the panel repaint(tm) function.
long currentTime = System.currentTimeMillis();
if (currentTime - lastTime < tm) {
diff --git a/src/dataPlotsFX/overlaymark/popUpMenu/TDPopUpMenuAdv.java b/src/dataPlotsFX/overlaymark/popUpMenu/TDPopUpMenuAdv.java
index f2e452dc..8e1647e4 100644
--- a/src/dataPlotsFX/overlaymark/popUpMenu/TDPopUpMenuAdv.java
+++ b/src/dataPlotsFX/overlaymark/popUpMenu/TDPopUpMenuAdv.java
@@ -66,7 +66,8 @@ public class TDPopUpMenuAdv implements ExtPopMenu {
}
if (PamGUIManager.isFX()) {
- popOver.show(tdGraphFX.getScene().getWindow(), e.getScreenX(), e.getScreenY()); //FX
+ //TODO - need to shift by the distance to arrow- not arbitrary 40 pixels
+ popOver.show(tdGraphFX.getScene().getWindow(), e.getScreenX(), e.getScreenY()-40); //FX
}
else {
popOver.show(tdGraphFX, e.getScreenX(), e.getScreenY()); //Swing
diff --git a/src/detectionPlotFX/rawDDPlot/RawSpectrumPlot.java b/src/detectionPlotFX/rawDDPlot/RawSpectrumPlot.java
index f9242258..ef98e221 100644
--- a/src/detectionPlotFX/rawDDPlot/RawSpectrumPlot.java
+++ b/src/detectionPlotFX/rawDDPlot/RawSpectrumPlot.java
@@ -54,30 +54,7 @@ public class RawSpectrumPlot extends SpectrumPlot {
plotProjector.setEnableScrollBar(true);
}
-
-// @Override
-// public double[][] getPowerSpectrum(PamDataUnit data) {
-// return ((RawDataHolder) data).getDataTransforms().getPowerSpectrum(((RawDataHolder) data).getWaveData()[0].length);
-// }
-// @Override
-// public double[][] getCepstrum(PamDataUnit data) {
-// return ((RawDataHolder) data).getDataTransforms().getCepstrum(((RawDataHolder) data).getWaveData()[0].length);
-// //return data.getRawDataTransforms().getCepstrum(channel, cepLength)
-// }
-
-
-
-//
-// public ClickSpectrumPlot(DetectionPlotDisplay displayPlot) {
-// super(displayPlot);
-// }
-//
-//
-// @Override
-// public String getName() {
-// return "Spectrum";
-// }
-//
+
/**
* New click added to the display.
* @param newClick
@@ -169,18 +146,16 @@ public class RawSpectrumPlot extends SpectrumPlot {
@Override
public void paintPlot(PamDataUnit data, GraphicsContext gc, Rectangle rectangle, DetectionPlotProjector projector, int flag) {
-// this.lastDataUnit=data;
- //System.out.println("Paint plot projector: "+ projector);
+
+ if (((RawDataHolder) data).getWaveData()==null) {
+ gc.clearRect(0, 0, rectangle.getWidth(), rectangle.getHeight());
+ return;
+ }
+
if (flag== DetectionPlot.SCROLLPANE_DRAW) {
-
double[][] waveformTemp = ((RawDataHolder) data).getWaveData();
- if (waveformTemp==null) return;
-
-// System.out.println("Spectrum plot: " + " " + projector.getMinScrollLimit() + " "
-// + projector.getMaxScrollLimit() + " " + projector.getAxis(Side.TOP).getMaxVal() + " wvfrm: " + WaveformPlot.getYScale(waveformTemp));
-
WaveformPlot.paintWaveform(waveformTemp, data.getSequenceBitmap(), gc, rectangle, 0, waveformTemp[0].length,
WaveformPlot.getYScale(waveformTemp), null, true, false);
}
diff --git a/src/pamScrollSystem/LoadQueueProgressData.java b/src/pamScrollSystem/LoadQueueProgressData.java
index bebb4a9a..949c4cec 100644
--- a/src/pamScrollSystem/LoadQueueProgressData.java
+++ b/src/pamScrollSystem/LoadQueueProgressData.java
@@ -34,11 +34,13 @@ public class LoadQueueProgressData extends PamTaskUpdate {
this.loadEnd = loadEnd;
this.loadCurrent = loadCurrent;
this.nLoaded = nLoaded;
+ setDualProgressUpdate(true);
}
public LoadQueueProgressData(int status) {
super();
this.setStatus(PamTaskUpdate.STATUS_DONE);
+ setDualProgressUpdate(true);
}
@@ -119,6 +121,7 @@ public class LoadQueueProgressData extends PamTaskUpdate {
@Override
public double getProgress() {
+// System.out.println( getStreamName() + " progress: " + iStream + " of " + totalStreams);
if (getStreamName() != null) {
return (double )iStream/ (double) totalStreams;
}
@@ -127,6 +130,7 @@ public class LoadQueueProgressData extends PamTaskUpdate {
@Override
public String getProgressString() {
+
if (getState() == LoadQueueProgressData.STATE_LINKINGSUBTABLE) {
return String.format("Linking subtable data %d of %d",
getIStream(), getTotalStreams());
@@ -141,13 +145,15 @@ public class LoadQueueProgressData extends PamTaskUpdate {
}
@Override
- public double getProgress2() {
+ public double getProgress2() {
+// System.out.println( getStreamName() + " progress2: " + getLoadStart() );
long interval =getLoadEnd() - getLoadStart();
- if (interval == 0) {
+ if (interval <= 0) {
return ProgressIndicator.INDETERMINATE_PROGRESS;
}
else {
long done =getLoadCurrent() - getLoadStart();
+// System.out.println( getStreamName() + " progress2: " + done + " " + interval + " start " + getLoadStart() + " end " + getLoadEnd())
return ((double) done )/ interval;
}
}
diff --git a/src/pamViewFX/PamGuiFX.java b/src/pamViewFX/PamGuiFX.java
index aca3d2cc..2acb7f03 100644
--- a/src/pamViewFX/PamGuiFX.java
+++ b/src/pamViewFX/PamGuiFX.java
@@ -252,7 +252,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
/**create left hiding pane**/
loadPane=new PamLoadingPane(this.pamGuiManagerFX);
hidingLoadPane=new HidingPane(Side.TOP, loadPane, this, false);
- hidingLoadPane.setPrefHeight(90);
+ hidingLoadPane.setPrefHeight(110);
hidingLoadPane.removeHideButton();
hidingLoadPane.showHidePane(false);
diff --git a/src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPlotInfoFX.java b/src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPlotInfoFX.java
index e4e31b42..44fdca6f 100644
--- a/src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPlotInfoFX.java
+++ b/src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPlotInfoFX.java
@@ -210,7 +210,7 @@ public class DLPredictionPlotInfoFX extends GenericLinePlotInfo {
public Polygon drawDataUnit(int plotNumber, PamDataUnit pamDataUnit, GraphicsContext g, double scrollStart,
TDProjectorFX tdProjector, int type) {
- //System.out.println("Get data type: " + getScaleInfo().getDataType());
+// System.out.println("Get prediciton data type: " + getScaleInfo().getDataType());
if (getScaleInfo().getDataType().equals(ParameterType.FREQUENCY)) { // frequency data !
return drawFrequencyData(plotNumber, pamDataUnit, g, scrollStart, tdProjector, type);
}
diff --git a/src/rawDeepLearningClassifier/dlClassification/archiveModel/ArchiveModelWorker.java b/src/rawDeepLearningClassifier/dlClassification/archiveModel/ArchiveModelWorker.java
index ac045382..10c4bc51 100644
--- a/src/rawDeepLearningClassifier/dlClassification/archiveModel/ArchiveModelWorker.java
+++ b/src/rawDeepLearningClassifier/dlClassification/archiveModel/ArchiveModelWorker.java
@@ -113,8 +113,8 @@ public class ArchiveModelWorker extends GenericModelWorker {
//HACK there seems to be some sort of bug in ketos where the params input shape is correct but the model input shape is wrong.
if (dlModel.getInputShape()==null || !dlModel.getInputShape().equals(modelParams.defaultInputShape)) {
- System.out.println("Model input shape: " + modelParams.defaultInputShape);
- WarnOnce.showWarning("Model shape", "The model shape does not match the model metadata. \n Metadata shape will be used used.", WarnOnce.OK_OPTION);
+ System.err.println("Model input shape does not match: params: " + modelParams.defaultInputShape + " model: " + dlModel.getInputShape());
+ //WarnOnce.showWarning("Model shape", "The model shape does not match the model metadata. \n Metadata shape will be used used.", WarnOnce.OK_OPTION);
dlModel.setInputShape(modelParams.defaultInputShape);
}
diff --git a/src/rawDeepLearningClassifier/dlClassification/genericModel/GenericPrediction.java b/src/rawDeepLearningClassifier/dlClassification/genericModel/GenericPrediction.java
index 8e50f89e..57e83218 100644
--- a/src/rawDeepLearningClassifier/dlClassification/genericModel/GenericPrediction.java
+++ b/src/rawDeepLearningClassifier/dlClassification/genericModel/GenericPrediction.java
@@ -39,6 +39,12 @@ public class GenericPrediction implements PredictionResult {
public double analysisTime=0;
+ /**
+ * Constructor for a typical generic prediciton.
+ * @param prob - the probability for each class.
+ * @param classNameID - the ID's of the class names.
+ * @param isBinary - true if the model result passed a binary test (usually one species above a threshold)
+ */
public GenericPrediction(float[] prob, short[] classNameID, boolean isBinary) {
this.prob=prob;
this.classNameID = classNameID;
diff --git a/src/rawDeepLearningClassifier/logging/ModelResultBinaryFactory.java b/src/rawDeepLearningClassifier/logging/ModelResultBinaryFactory.java
index 08fb00ee..91b10536 100644
--- a/src/rawDeepLearningClassifier/logging/ModelResultBinaryFactory.java
+++ b/src/rawDeepLearningClassifier/logging/ModelResultBinaryFactory.java
@@ -115,7 +115,6 @@ public class ModelResultBinaryFactory {
try {
//System.out.println("Make model result: ");
-
int type = dis.readByte();
boolean isBinary = dis.readBoolean();
double scale = dis.readFloat();
@@ -150,9 +149,7 @@ public class ModelResultBinaryFactory {
result = new GenericPrediction(data, isBinary);
break;
}
-
//System.out.println("New model result: "+ type);
-
return result;
} catch (IOException e) {