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Updates to deep learning module for downloading files and to FX GUI

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This commit is contained in:
Jamie Mac 2024-01-19 16:57:17 +00:00
parent 37fe953474
commit a95db3679d
28 changed files with 2142 additions and 329 deletions
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1
.classpath
View File

@ -6,6 +6,7 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" path="test"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
<attributes>
<attribute name="maven.pomderived" value="true"/>

2
src/Array/HydrophoneElementDialog.java
View File

@ -397,6 +397,8 @@ public class HydrophoneElementDialog extends PamDialog {
dz.setText(null);
}
}
boolean getParams() {
double zCoeff = PamController.getInstance().getGlobalMediumManager().getZCoeff();

76
src/Array/layoutFX/Array3DPane.java
View File

@ -18,6 +18,7 @@ import javafx.scene.PerspectiveCamera;
import javafx.scene.SceneAntialiasing;
import javafx.scene.SubScene;
import javafx.scene.input.MouseEvent;
import javafx.scene.input.PickResult;
import javafx.scene.input.ScrollEvent;
import javafx.scene.paint.Color;
import javafx.scene.paint.PhongMaterial;
@ -56,8 +57,7 @@ public class Array3DPane extends PamBorderPane {
public static final Color DEFAULT_HYDRO_COL = Color.RED;
private static final Color DEFAULT_SENSOR_COL = Color.LIMEGREEN;
// private static final Color DEFAULT_SENSOR_COL = Color.LIMEGREEN;
private double scaleFactor=20;
@ -97,6 +97,11 @@ public class Array3DPane extends PamBorderPane {
* The size of the hydrophone for the 3D display.
*/
private double hydrophoneSize = 0.5;
/**
* Holds a list of hydrophone spheres
*/
private ArrayList<HydrophoneSphere> hydrophonesSpheres = new ArrayList<HydrophoneSphere>();
public Array3DPane(){
@ -131,6 +136,33 @@ public class Array3DPane extends PamBorderPane {
subScene.widthProperty().bind(this.widthProperty());
subScene.heightProperty().bind(this.heightProperty());
subScene.setDepthTest(DepthTest.ENABLE);
subScene.setOnMouseClicked((MouseEvent me) -> {
mousePosX = me.getSceneX();
mousePosY = me.getSceneY();
PickResult pr = me.getPickResult();
// System.out.println("Picked something sphere: " + pr);
//clear selected radius
for (HydrophoneSphere sphere : hydrophonesSpheres) {
sphere.setRadius(hydrophoneSize*scaleFactor);
}
if(pr!=null && pr.getIntersectedNode() != null && pr.getIntersectedNode() instanceof Sphere){
//make the selected sphere slightly larger
HydrophoneSphere s = (HydrophoneSphere) pr.getIntersectedNode();
s.setRadius(hydrophoneSize*scaleFactor*1.2);
hydrophoneSelected(s.getHydrophone());
// System.out.println("Picked a sphere: " + pr);
// distance=pr.getIntersectedDistance();
// s = (Sphere) pr.getIntersectedNode();
// isPicking=true;
// vecIni = unProjectDirection(mousePosX, mousePosY, scene.getWidth(),scene.getHeight());
}
});
//note the fill is actually quite important because if you don't have it mouse rotations etc
//onyl work if you select a 3D shape
@ -152,6 +184,14 @@ public class Array3DPane extends PamBorderPane {
}
/**
* Called whenever a hydrophone is selected.
* @param hydrophone - the selected hydrophone.
*/
public void hydrophoneSelected(Hydrophone hydrophone) {
// TODO Auto-generated method stub
}
/**
* Create a 3D axis with default colours set.
* @param- size of the axis
@ -300,7 +340,7 @@ public class Array3DPane extends PamBorderPane {
*/
public void drawArray(PamArray array) {
System.out.println("DRAW ARRAY: " + array);
// System.out.println("DRAW ARRAY: " + array);
//clear the array
arrayGroup.getChildren().removeAll(arrayGroup.getChildren());
@ -308,8 +348,9 @@ public class Array3DPane extends PamBorderPane {
ArrayList<Hydrophone> hydrophones = array.getHydrophoneArray();
//draw hydrophones
Sphere sphere;
HydrophoneSphere sphere;
Streamer streamer;
hydrophonesSpheres.clear();
for (int i=0; i<hydrophones.size(); i++){
//get the streamer for the hydrophone
@ -319,7 +360,7 @@ public class Array3DPane extends PamBorderPane {
double y = hydrophones.get(i).getY() + hydrophones.get(i).getStreamerId();
double z = hydrophones.get(i).getZ() + hydrophones.get(i).getStreamerId();
sphere=new Sphere(hydrophoneSize*scaleFactor);
sphere=new HydrophoneSphere(hydrophoneSize*scaleFactor);
sphere.setTranslateX(x*scaleFactor);
sphere.setTranslateY(z*scaleFactor);
sphere.setTranslateZ(y*scaleFactor);
@ -330,9 +371,11 @@ public class Array3DPane extends PamBorderPane {
aMaterial.setDiffuseColor(col);
aMaterial.setSpecularColor(col.brighter());
sphere.setMaterial(aMaterial);
sphere.setHydrophone(hydrophones.get(i));
// System.out.println("Add hydrophone: " + x + " " + y + " " +z);
hydrophonesSpheres.add(sphere);
arrayGroup.getChildren().add(sphere);
ArrayList<Point3D> streamerPoints=new ArrayList<Point3D>();
@ -353,7 +396,30 @@ public class Array3DPane extends PamBorderPane {
}
private class HydrophoneSphere extends Sphere {
Hydrophone hydrophone;
public Hydrophone getHydrophone() {
return hydrophone;
}
public void setHydrophone(Hydrophone hydrophone) {
this.hydrophone = hydrophone;
}
public HydrophoneSphere() {
super();
}
public HydrophoneSphere(double radius) {
super(radius);
}
}
// /**
// * Draw the entire array
// * @param pos - hydrophone and streamer positions in the same co-ordinate frame as the reference frame.

50
src/Array/layoutFX/ArraySettingsPane.java
View File

@ -1,5 +1,9 @@
package Array.layoutFX;
import java.io.File;
import Array.ArrayManager;
import Array.Hydrophone;
import Array.PamArray;
import PamController.PamController;
import PamController.SettingsPane;
@ -12,9 +16,12 @@ import javafx.scene.layout.Region;
import javafx.geometry.Insets;
import javafx.geometry.Pos;
import javafx.scene.layout.VBox;
import javafx.stage.FileChooser;
import javafx.stage.FileChooser.ExtensionFilter;
import pamViewFX.PamGuiManagerFX;
import pamViewFX.fxGlyphs.PamGlyphDude;
import pamViewFX.fxNodes.PamVBox;
import pamViewFX.fxNodes.pamDialogFX.PamDialogFX;
import pamViewFX.fxNodes.PamBorderPane;
import pamViewFX.fxNodes.PamButton;
import pamViewFX.fxNodes.PamHBox;
@ -67,10 +74,16 @@ public class ArraySettingsPane extends SettingsPane<PamArray >{
/**
* Pane with controls to change speed of sound.
*/
private SettingsPane<PamArray> environmentalPane;
private SettingsPane<PamArray> environmentalPane;
private FileChooser fileChooser;
//a copy of the current array
private PamArray currentArray;
public ArraySettingsPane() {
super(null);
mainPane=new PamBorderPane();
mainPane.setCenter(createArrayPane());
@ -150,7 +163,7 @@ public class ArraySettingsPane extends SettingsPane<PamArray >{
}
private Pane create3DPane() {
this.array3DPane = new Array3DPane();
this.array3DPane = new HydrophoneArray3DPane();
//important because the 3D pane has not default size
array3DPane.setMinWidth(MIN_3D_WIDTH);
@ -184,6 +197,11 @@ public class ArraySettingsPane extends SettingsPane<PamArray >{
arrayImportExportBox.setAlignment(Pos.CENTER_LEFT);
arrayImportExportBox.setPadding(new Insets(5,0,0,0));
fileChooser = new FileChooser();
fileChooser.setTitle("Open Resource File");
fileChooser.getExtensionFilters().addAll(
new ExtensionFilter("PAMNGuard Array Files", "*.paf"));
PamButton importButton = new PamButton("Import...");
importButton.setOnAction((action)->{
importArray();
@ -242,16 +260,23 @@ public class ArraySettingsPane extends SettingsPane<PamArray >{
* Select a file to export array settings to.
*/
private void exportArray() {
// TODO Auto-generated method stub
File file = fileChooser.showSaveDialog(getFXWindow());
if (file==null) return;
PamArray pamArray = getParams(new PamArray("saved_array: ", null));
boolean isSaved = ArrayManager.saveArrayToFile(pamArray);
if (isSaved==false) {
PamDialogFX.showError("Unable to save the array file to \n" + file.toString());
}
}
/**
* Select a file to import array settings
*/
private void importArray() {
// TODO Auto-generated method stub
File file = fileChooser.showOpenDialog(getFXWindow());
if (file==null) return;
PamArray pamArray = ArrayManager.loadArrayFromFile(file.getPath());
this.setParams(pamArray);
}
/**
@ -271,8 +296,9 @@ public class ArraySettingsPane extends SettingsPane<PamArray >{
@Override
public PamArray getParams(PamArray currParams) {
currParams = hydrophonePane.getParams(currParams);
currParams = streamerPane.getParams(currParams);
currParams = hydrophonePane.getParams(currParams);
currParams.setHydrophoneInterpolation(hydrophonePane.getHydrophoneInterp());
currParams = environmentalPane.getParams(currParams);
// System.out.println("Array settings pane: No. streamers: " + currParams.getStreamerCount());
return currParams;
@ -280,6 +306,7 @@ public class ArraySettingsPane extends SettingsPane<PamArray >{
@Override
public void setParams(PamArray input) {
this.currentArray = input.clone();
// System.out.println("Hydrophone array is: "+ input);
setReceieverLabels();
hydrophonePane.setParams(input);
@ -306,5 +333,14 @@ public class ArraySettingsPane extends SettingsPane<PamArray >{
// TODO Auto-generated method stub
}
private class HydrophoneArray3DPane extends Array3DPane {
@Override
public void hydrophoneSelected(Hydrophone hydrophone) {
hydrophonePane.selectHydrophone(hydrophone);
}
}
}

9
src/Array/layoutFX/HydrophoneSettingsPane.java
View File

@ -126,7 +126,7 @@ public class HydrophoneSettingsPane extends DynamicSettingsPane<Hydrophone> {
PamHBox interpHolder = new PamHBox();
interpHolder.setSpacing(5);
interpHolder.setAlignment(Pos.CENTER);
interpHolder.setAlignment(Pos.CENTER_LEFT);
interpHolder.getChildren().addAll(new Label("Method"), interpPane);
holderPane.getChildren().addAll(recieverIDLabel, createGeneralPane(), coOrdLabel, createPositionPane(), interpLabel, interpHolder);
@ -520,6 +520,8 @@ public class HydrophoneSettingsPane extends DynamicSettingsPane<Hydrophone> {
double zCoeff = PamController.getInstance().getGlobalMediumManager().getZCoeff();
setCoordsText();
interpPane.setSelection(currentArray.getHydrophoneInterpolation());
xPos.setText(Double.toString(hydrophone.getX()));
yPos.setText(Double.toString(hydrophone.getY()));
@ -552,8 +554,11 @@ public class HydrophoneSettingsPane extends DynamicSettingsPane<Hydrophone> {
hydrophone.setdX(Double.valueOf(xPosErr.getText()));
hydrophone.setdY(Double.valueOf(yPosErr.getText()));
hydrophone.setdZ(Double.valueOf(zPosErr.getText()));
int hi = interpPane.getSelection();
if (hi >= 0) {
this.currentArray.setHydrophoneInterpolation(interpPane.getSelectedInterpType());
}
}
catch (Exception Ex) {
System.err.println("There is a problem with one of the parameters in the hydrophone panel");

40
src/Array/layoutFX/HydrophonesPane.java
View File

@ -19,6 +19,7 @@ import javafx.scene.control.TableColumn;
import javafx.scene.control.cell.TextFieldTableCell;
import javafx.util.converter.IntegerStringConverter;
import pamViewFX.fxNodes.PamBorderPane;
import pamViewFX.fxNodes.PamColorsFX;
import pamViewFX.fxNodes.flipPane.PamFlipPane;
import pamViewFX.fxNodes.table.TableSettingsPane;
@ -153,7 +154,7 @@ public class HydrophonesPane extends PamBorderPane {
super(hydrophoneData);
z = new TableColumn<HydrophoneProperty,Number>("depth");
z.setCellValueFactory(cellData -> cellData.getValue().getZ());
z.setCellValueFactory(cellData -> cellData.getValue().getZ().multiply(PamController.getInstance().getGlobalMediumManager().getZCoeff()));
z.setEditable(true);
//need to set up all the rows.
@ -170,8 +171,7 @@ public class HydrophonesPane extends PamBorderPane {
Callback<TableColumn<HydrophoneProperty, Integer>, TableCell<HydrophoneProperty, Integer>> cellFactory = col -> {
TableCell<HydrophoneProperty, Integer> cell = defaultCellFactory.call(col);
cell.itemProperty().addListener((obs, oldValue, newValue) -> {
System.out.println("Hello set colour: " + newValue);
// System.out.println("Hello set colour: " + newValue);
if (newValue == null) {
cell.setStyle("cell-selection-color: -fx-selection-bar ;");
} else {
@ -180,9 +180,7 @@ public class HydrophonesPane extends PamBorderPane {
// cell.setStyle("cell-selection-color: "+ formattedColor + " ;");
cell.setStyle("-fx-background: "+ formattedColor + " ;");
cell.setStyle("-fx-background-color: "+ formattedColor + " ;");
System.out.println("Hello set style: " + formattedColor);
// System.out.println("Hello set style: " + formattedColor);
}
});
return cell;
@ -224,8 +222,11 @@ public class HydrophonesPane extends PamBorderPane {
// Create color based on int value. Just use value as hue, full saturation and brightness:
private Color createColor(int x) {
return Color.hsb(x, 1.0, 1.0);
private Color createColor(int i) {
//get channel colour and add a bit of transparancy to make less abnoxious
return PamColorsFX.getInstance().getChannelColor(i).deriveColor(1, 1, 1, 0.5);
// return Color.hsb(x, 1.0, 1.0);
}
// Format color as string for CSS (#rrggbb format, values in hex).
@ -384,4 +385,27 @@ public class HydrophonesPane extends PamBorderPane {
}
/**
* Select the current hydrophone in table.
*/
public void selectHydrophone(Hydrophone hydrophone) {
//select the current hydrophone in the table
tableArrayPane.getTableView().getSelectionModel().select(hydrophone.getID());
}
public void setCurrentArray(PamArray currentArray) {
this.currentArray=currentArray;
}
/**
* Get the hydrophone interpolation. Note that this is stored in the
* currentArray because the interpolator must be the same for all hydrophones.
*
* @return the inteprolation selection.
*/
public int getHydrophoneInterp() {
return currentArray.getHydrophoneInterpolation();
}
}

5
src/Array/layoutFX/StreamerSettingsPane.java
View File

@ -721,7 +721,10 @@ public class StreamerSettingsPane extends SettingsPane<Streamer> {
}
public void setRecieverLabels() {
// TODO Auto-generated method stub
String recieverDepthString = PamController.getInstance().getGlobalMediumManager().getZString();
depthLabel.setText(recieverDepthString );
depthSensorLabel.setText(recieverDepthString + " Sensor");
}

13
src/Array/layoutFX/StreamersPane.java
View File

@ -153,7 +153,7 @@ public class StreamersPane extends PamBorderPane {
y.setEditable(false);
z = new TableColumn<StreamerProperty,Number>("depth");
z.setCellValueFactory(cellData -> cellData.getValue().getZ());
z.setCellValueFactory(cellData -> cellData.getValue().getZ().multiply(PamController.getInstance().getGlobalMediumManager().getZCoeff()));
z.setEditable(false);
TableColumn posColumn=new TableColumn("Position (m)");
@ -229,7 +229,7 @@ public class StreamersPane extends PamBorderPane {
@Override
public void deleteData(StreamerProperty data){
super.deleteData(data);
notifyStreamerListeners(data);
notifyStreamerListeners(null);
}
private StreamerProperty createDefaultStreamerProperty() {
@ -269,6 +269,7 @@ public class StreamersPane extends PamBorderPane {
public PamArray getParams(PamArray currParams) {
//add all new streamers - bit weird because the PamArray requires that at least one streamer exists.
for (int i=0; i<tableArrayPane.getStreamers().size(); i++) {
if (i<currentArray.getStreamerCount()) {
@ -279,12 +280,11 @@ public class StreamersPane extends PamBorderPane {
}
}
while (currentArray.getStreamerCount()>tableArrayPane.getStreamers().size()) {
while (currParams.getStreamerCount()>tableArrayPane.getStreamers().size()) {
currParams.removeStreamer(currParams.getStreamerCount()-1);
}
// currentArray.updateStreamer(tableArrayPane.getStreamers().indexOf(currentStreamerData), streamer);
System.out.println("Get params streamer: " + currentArray.getNumStreamers());
return currParams;
}
@ -306,5 +306,10 @@ public class StreamersPane extends PamBorderPane {
this.streamerChangeListeners.add(e);
}
public void setCurrentArray(PamArray currentArray) {
this.currentArray=currentArray;
}
}

325
src/Resources/modules/Click Detector Icon.svg
View File

@ -1,35 +1,296 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with Vectornator (http://vectornator.io/) -->
<svg height="100.0px" stroke-miterlimit="10" style="fill-rule:nonzero;clip-rule:evenodd;stroke-linecap:round;stroke-linejoin:round;" version="1.1" viewBox="0 0 100 100" width="100.0px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<defs/>
<g id="layer">
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Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 7.1 KiB

After

Width:  |  Height:  |  Size: 8.4 KiB

433
src/Resources/modules/clicktrain.svg
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Side by Side Swipe Overlay

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10
src/dataModelFX/DataModelPaneFX.java
View File

@ -529,7 +529,7 @@ public class DataModelPaneFX extends PamBorderPane {
continue;
}
System.out.println("Checking: child: " + childNode + " parent: " + potentialParent);
// System.out.println("Checking: child: " + childNode + " parent: " + potentialParent);
if (ConnectionPane.isNodeConnected(childNode, potentialParent, true, true)) {
// everything is fine. Connected;
// System.out.println("The module "+
@ -545,10 +545,10 @@ public class DataModelPaneFX extends PamBorderPane {
// " should be connected to " +
// potentialParent.getPamControlledUnit().getUnitName());
if (useNodeConnection) {
System.out.println("DataModelPaneFX: CONNECTING TWO NODES: childNode: "
+childNode.getPamControlledUnit().getUnitName() +" to parentNode "
+potentialParent.getPamControlledUnit().getUnitName()+ " "
+potentialParent.isEnableConnectListeners());
// System.out.println("DataModelPaneFX: CONNECTING TWO NODES: childNode: "
// +childNode.getPamControlledUnit().getUnitName() +" to parentNode "
// +potentialParent.getPamControlledUnit().getUnitName()+ " "
// +potentialParent.isEnableConnectListeners());
childNode.connectNode(potentialParent);
} else {
// System.out.println("DataModelPaneFX: DISCONNECTING TWO NODES: childNode: "

78
src/dataModelFX/connectionNodes/ModuleIconFactory.java
View File

@ -43,69 +43,94 @@ public class ModuleIconFactory {
* @return the icon for the controlled unit
*/
public Node getModuleNode(ModuleIcon icon){
long time1 = System.currentTimeMillis();
Node iconNode =null;
switch (icon){
case ARRAY:
// return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/array_manager.png")));
return getSVGIcon("/Resources/modules/Array Icon2.svg",Color.BLACK, 3);
iconNode = getSVGIcon("/Resources/modules/Array Icon2.svg",Color.BLACK, 3);
break;
case BINARY:
// return PamGlyphDude.createModuleGlyph(OctIcon.FILE_BINARY);
return PamGlyphDude.createModuleIcon("mdi2f-file-star-outline");
iconNode = PamGlyphDude.createModuleIcon("mdi2f-file-star-outline");
break;
case CLICK:
// return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/click.png")));
return getSVGIcon("/Resources/modules/Click Detector Icon.svg", Color.BLACK, 2);
iconNode = getSVGIcon("/Resources/modules/Click Detector Icon.svg", Color.BLACK, 2);
break;
case CLICK_TRAIN:
// return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/clicktrain.png")));
return getSVGIcon("/Resources/modules/clicktrain.svg",Color.BLACK, 2);
iconNode = getSVGIcon("/Resources/modules/clicktrain.svg",Color.BLACK, 2);
break;
case DATABASE:
// return PamGlyphDude.createModuleGlyph(FontAwesomeIcon.DATABASE);
return PamGlyphDude.createModuleIcon("mdi2d-database");
iconNode = PamGlyphDude.createModuleIcon("mdi2d-database");
break;
case DATAMAP:
return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/dataMap.png")));
iconNode = new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/dataMap.png")));
break;
case FFT:
// return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/fft.png")));
return getSVGIcon("/Resources/modules/fft.svg",Color.BLACK, 2);
iconNode = getSVGIcon("/Resources/modules/fft.svg",Color.BLACK, 2);
break;
case FILTER:
// return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/filters.png")));
return getSVGIcon("/Resources/modules/filters.svg",Color.BLACK, 2);
iconNode = getSVGIcon("/Resources/modules/filters.svg",Color.BLACK, 2);
break;
case GPS:
// return PamGlyphDude.createModuleGlyph(MaterialIcon.GPS_FIXED);
return PamGlyphDude.createModuleIcon("mdi2c-crosshairs-gps");
iconNode = PamGlyphDude.createModuleIcon("mdi2c-crosshairs-gps");
break;
case MAP:
// return PamGlyphDude.createModuleGlyph(MaterialIcon.MAP);
return PamGlyphDude.createModuleIcon("mdi2m-map");
iconNode = PamGlyphDude.createModuleIcon("mdi2m-map");
break;
case NMEA:
return createNMEASymbol();
iconNode = createNMEASymbol();
case NOISE_BAND:
return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/filterdNoiseMeasurementBank.png")));
iconNode = new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/filterdNoiseMeasurementBank.png")));
break;
case NOISE_FILT:
return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/filterdNoiseMeasurement.png")));
iconNode = new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/filterdNoiseMeasurement.png")));
break;
case RECORDER:
return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/recorder.png")));
iconNode = new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/recorder.png")));
break;
case SOUND_AQ:
return getSVGIcon("/Resources/modules/noun_Soundwave_1786340.svg");
iconNode = getSVGIcon("/Resources/modules/noun_Soundwave_1786340.svg");
break;
case MATCHED_CLICK_CLASSIFIER:
return getSVGIcon("/Resources/modules/matched_click_classifier.svg",Color.BLACK, 2);
iconNode = getSVGIcon("/Resources/modules/matched_click_classifier.svg",Color.BLACK, 2);
break;
//return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/aquisition.png")));
case SOUND_OUTPUT:
// return PamGlyphDude.createModuleGlyph(MaterialDesignIcon.HEADPHONES);
return PamGlyphDude.createModuleIcon("mdi2h-headphones");
//return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/playback.png")));
iconNode = PamGlyphDude.createModuleIcon("mdi2h-headphones");
break;
//return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/playback.png")));
case WHISTLE_MOAN:
return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/whistles.png")));
iconNode = new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/whistles.png")));
break;
case TIME_DISPLAY:
return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/timeDisplay.png")));
iconNode = new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/timeDisplay.png")));
break;
case DETECTION_DISPLAY:
return new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/detectionDisplay.png")));
iconNode = new ImageView(new Image(getClass().getResourceAsStream("/Resources/modules/detectionDisplay.png")));
break;
case DEEP_LEARNING:
//System.out.println("------GET THE SVG ICON FOR DEEP LEARNING--------");
return getSVGIcon("/Resources/modules/noun_Deep Learning_2486374.svg");
iconNode = getSVGIcon("/Resources/modules/noun_Deep Learning_2486374.svg");
break;
default:
break;
}
return null;
long time2 = System.currentTimeMillis();
System.out.println("GET MODULE ICON: " + icon + " load time: " + (time2-time1));
return iconNode;
};
/**
@ -182,7 +207,6 @@ public class ModuleIconFactory {
* @return the module icon enum
*/
public ModuleIcon getModuleIcon(String className) {
System.out.println("CLASS NAME: " + className);
ModuleIcon icon = null;
switch (className) {
case "Acquisition.AcquisitionControl":

101
src/pamViewFX/fxNodes/PamColorsFX.java
View File

@ -75,106 +75,7 @@ public class PamColorsFX implements PamSettings {
//PamSettingManager.getInstance().registerSettings(this, PamSettingManager.LIST_SYSTEMGLOBAL);
}
// public JMenuItem getMenu(JFrame parentFrame) {
//
// JMenu colorMenu = new JMenu("Color Scheme");
//
// JMenuItem menuItem;
//
// int n = colorSettings.getNumSchemes();
// for (int i = 0; i < n; i++) {
// String name = colorSettings.getScheme(i).getName();
// menuItem = new JMenuItem(name);
// menuItem.addActionListener(new SelectScheme(name));
// colorMenu.add(menuItem);
// }
//
//
// menuItem = new JMenu("Edit");
// colorMenu.addSeparator();
// colorMenu.add(menuItem);
//
// JMenuItem editItem = new JMenuItem("Whale Colours");
// editItem.addActionListener(new EditWhaleColours(parentFrame));
// menuItem.add(editItem);
// editItem = new JMenuItem("Channel Colours");
// editItem.addActionListener(new EditChannelColours(parentFrame));
// menuItem.add(editItem);
//
//
//// dayMenuItem = new JCheckBoxMenuItem("Day");
//// dayMenuItem.addActionListener(new menuColorDay());
//// colorMenu.add(dayMenuItem);
//// dayMenuEnabler.addMenuItem(dayMenuItem);
////
//// nightMenuItem = new JCheckBoxMenuItem("Night");
//// nightMenuItem.addActionListener(new menuColorNight());
//// colorMenu.add(nightMenuItem);
//// nightMenuEnabler.addMenuItem(nightMenuItem);
////
//// printMenuItem = new JCheckBoxMenuItem("Print");
//// printMenuItem.addActionListener(new menuColorPrint());
//// if ( SMRUEnable.isEnable() )
//// colorMenu.add(printMenuItem);
////
//// printMenuEnabler.addMenuItem(printMenuItem);
//
// return colorMenu;
// }
// private class SelectScheme implements ActionListener {
//
// private String schemeName;
//
// public SelectScheme(String schemeName) {
// super();
// this.schemeName = schemeName;
// }
//
// @Override
// public void actionPerformed(ActionEvent e) {
// colourScheme = colorSettings.selectScheme(schemeName);
// setColors();
// }
//
// }
// private class EditWhaleColours implements ActionListener {
//
// private JFrame parentFrame;
//
// public EditWhaleColours(JFrame parentFrame) {
// this.parentFrame = parentFrame;
// }
//
// @Override
// public void actionPerformed(ActionEvent e) {
// Color[] wCols = colourScheme.getWhaleColors();
//// Color[] newCols = ColourListDialog.show(parentFrame, "Whale Colours", wCols);
//// if (newCols) {
//// colourScheme.setWhaleColors(newCols);
//// setColors();
//// }
// }
// }
// private class EditChannelColours implements ActionListener {
//
// private JFrame parentFrame;
//
// public EditChannelColours(JFrame parentFrame) {
// this.parentFrame = parentFrame;
// }
//
// @Override
// public void actionPerformed(ActionEvent e) {
// Color[] wCols = colourScheme.getChannelColors();
//// Color[] newCols = ColourListDialog.show(parentFrame, "Whale Colours", wCols);
//// if (newCols) {
//// colourScheme.setChannelColors(newCols);
//// setColors();
//// }
// }
// }
static public PamColorsFX getInstance() {
if (singleInstance == null) {

17
src/rawDeepLearningClassifier/DLControl.java
View File

@ -35,6 +35,7 @@ import rawDeepLearningClassifier.dlClassification.DLClassifyProcess;
import rawDeepLearningClassifier.dlClassification.animalSpot.SoundSpotClassifier;
import rawDeepLearningClassifier.dlClassification.genericModel.GenericDLClassifier;
import rawDeepLearningClassifier.dlClassification.ketos.KetosClassifier;
import rawDeepLearningClassifier.layoutFX.DLModelSelectPane;
import rawDeepLearningClassifier.layoutFX.DLSidePanelSwing;
import rawDeepLearningClassifier.layoutFX.DLSymbolManager;
import rawDeepLearningClassifier.layoutFX.PredictionSymbolManager;
@ -187,6 +188,8 @@ public class DLControl extends PamControlledUnit implements PamSettings {
*/
private DLClassifierChooser dlClassifierChooser;
private DLDownloadManager modelDownloadManager;
/**
@ -215,7 +218,11 @@ public class DLControl extends PamControlledUnit implements PamSettings {
// classify the raw data segments.
addPamProcess(dlClassifyProcess = new DLClassifyProcess(this, segmenterProcess.getSegmenterDataBlock()));
//manages the names assigned to different output classes.
dlClassNameManager = new DLClassNameManager(this);
//manages downloading models
modelDownloadManager = new DLDownloadManager();
// add storage options etc.
dlBinaryDataSource = new DLResultBinarySource(dlClassifyProcess);
@ -267,7 +274,7 @@ public class DLControl extends PamControlledUnit implements PamSettings {
//create the classiifer chooser.
dlClassifierChooser = new DLClassifierChooser(this);
// ensure everything is updated.
updateParams(rawDLParmas);
}
@ -576,6 +583,14 @@ public class DLControl extends PamControlledUnit implements PamSettings {
return dlClassifierChooser;
}
/**
* Get the download manager for downloading models offline.
* @return the download manager.
*/
public DLDownloadManager getDownloadManager() {
return modelDownloadManager;
}
}

232
src/rawDeepLearningClassifier/DLDownloadManager.java Normal file
View File

@ -0,0 +1,232 @@
package rawDeepLearningClassifier;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.net.HttpURLConnection;
import java.net.URI;
import java.net.URL;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.FilenameUtils;
import rawDeepLearningClassifier.defaultModels.RightWhaleModel1;
/**
* Manages the downloading and unzipping of models.
*/
public class DLDownloadManager {
public DLDownloadManager() {
}
/**
* Check whether has been downloaded already to a default local folder?
* @param modelURI - the URL of the model
* @return
* @return true if the model has been downloaded.
*/
public boolean isModelDownloaded(URL modelURL) {
return isModelDownloaded(modelURL, getModelName(modelURL));
}
/**
* Check whether has been downloaded already?
* @param modelURI - the URL of the model
* @param modelName - the model name that has been used to name the temporary folder.
* @return true if the model has been downloaded.
*/
public boolean isModelDownloaded(URL modelURL, String modelName) {
return getModelDownloadedFile( modelURL, modelName).exists();
}
/**
* Get the path to the model if it has been downloaded.
* @param modelURL - the URL to the model
* @param modelName - the model name. Use getModelName(modelURL) to use the default model name.
* @return a file object - may not exist.
*/
public File getModelDownloadedFile(URL modelURL, String modelName) {
//get the name of the file
String fileName = FilenameUtils.getName(modelURL.toString());
return new File(getModelFolder(modelName) + File.separator + fileName);
}
/**
* Get the path to a model. If the URI is a URL then the model is download to a local folder and the path to
* the local folder is returned.
* @param model - the model to load.
* @param modelName - the name of the model - this is used to create the local folder name if the model is downloaded.
* @return the path to the model The model might be a zip file, py file, koogu file.
*/
public URI downloadModel(URI modelURI) {
String modelName = getModelName(modelURI);
return downloadModel( modelURI, modelName);
}
/**
* Get a model name based on it's filename
* @param modelURI - URI to the model
* @return the model name.
*/
private String getModelName(URI modelURI) {
return FilenameUtils.getBaseName(modelURI.getPath());
}
/**
* Get a model name based on it's filename
* @param modelURL - URL to the model
* @return the model name.
*/
private String getModelName(URL modelURI) {
return FilenameUtils.getBaseName(modelURI.getPath());
}
/**
* Get the path to a model. If the URI is a URL then the model is download to a local folder and the path to
* the local folder is returned.
* @param model - the model to load.
* @param modelName - the name of the model - this is used to create the local folder name if the model is downloaded.
* @return the path to the model The model might be a zip file, py file, .kgu file.
*/
public URI downloadModel(URI modelURI, String modelName) {
if ("file".equalsIgnoreCase(modelURI.getScheme())) {
// It's a file path
return modelURI; //the model is already a path.
} else {
// It's a URL
try {
System.out.println("Download: " + modelURI.toURL().getPath());
String folder = getModelFolder(modelName);
if (folder==null) {
System.err.println("DLDefaultModelManager.loadModel: Unable to make model folder: ");
}
File file = downLoadModel(modelURI.toURL(), getModelFolder(modelName) );
return file.toURI();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return null;
}
}
}
private static boolean isRedirected( Map<String, List<String>> header ) {
for( String hv : header.get( null )) {
if( hv.contains( " 301 " )
|| hv.contains( " 302 " )) return true;
}
return false;
}
/**
* Get the model folder - create it if it doesn't exist.
* @return file object for new folder
*/
static public String getModelFolder() {
String settingsFolder = System.getProperty("user.home");
settingsFolder += File.separator + "Pamguard_deep_learning";
// now check that folder exists
File folder = makeFolder( settingsFolder);
if (folder==null) return null;
return folder.getPath();
}
/**
* Get the model folder - create it if it doesn't exist.
* @param modelname - the name of the model - this is used to create the local folder name.
* @return file object for new folder
*/
static public String getModelFolder(String modelname) {
String folder = getModelFolder();
if (folder == null) return null;
// now check that folder exists
File dlFolder = makeFolder( folder + File.separator + modelname);
if (dlFolder==null) return null;
return dlFolder.getPath();
}
/**
* Make a settings folder.
* @param settingsFolder
* @return
*/
private static File makeFolder(String settingsFolder) {
File folder = new File(settingsFolder);
if (folder.exists() == false) {
folder.mkdirs();
if (folder.exists() == false) {
return null;
}
}
return folder;
}
/**
* Download a model to the default file location.
* @param link - the link to download from
* @param outFolder - the folder in which to save the file.
* @return the model file output.
* @throws IOException - exception if something goes wrong.
*/
private static File downLoadModel(URL url, String outFolder) throws IOException {
String link = url.toString();
//get the name of the file
String fileName = FilenameUtils.getName(link);
File outFile = new File( outFolder + File.separator + fileName);
HttpURLConnection http = (HttpURLConnection)url.openConnection();
Map< String, List< String >> header = http.getHeaderFields();
//handle any redorects - e.g. from GitHub
while( isRedirected( header )) {
link = header.get( "Location" ).get( 0 );
url = new URL( link );
http = (HttpURLConnection)url.openConnection();
header = http.getHeaderFields();
}
InputStream input = http.getInputStream();
byte[] buffer = new byte[4096]; //download in 4kB chunks
int n = -1;
OutputStream output = new FileOutputStream(outFile);
while ((n = input.read(buffer)) != -1) {
System.out.println("Chunk: " + n);
output.write( buffer, 0, n );
}
output.close();
return outFile;
}
public static void main(String[] args) {
DLDownloadManager dlDefaultModelManager = new DLDownloadManager();
System.out.println("Test downloading a model: ");
URI path = dlDefaultModelManager.downloadModel(new RightWhaleModel1().getModelURI(), new RightWhaleModel1().getModelName());
}
}

63
src/rawDeepLearningClassifier/defaultModels/DLDefaultModelManager.java Normal file
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@ -0,0 +1,63 @@
package rawDeepLearningClassifier.defaultModels;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.HttpURLConnection;
import java.net.URI;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import PamUtils.FileFunctions;
import java.io.OutputStream;
import java.io.InputStream;
import rawDeepLearningClassifier.DLControl;
/**
* Manages default models.
*/
public class DLDefaultModelManager {
/**
* A list of the default models
*/
private ArrayList<DLModel> defaultModels = new ArrayList<DLModel>();
/**
* Reference ot the DL control.
*/
private DLControl dlControl;
/**
* Constructor for the Defulat Model Manager.
* @param dlControl - reference to the controller for this model manager.
*/
public DLDefaultModelManager(DLControl dlControl) {
this.dlControl = dlControl;
}
/**
* Get a default model at index i
* @param i - the index of the default model
*/
public DLModel getDefaultModel(int i) {
return defaultModels.get(i);
}
/**
* Get the number of default models
* @return the number of default models.
*/
public int getNumDefaultModels() {
return defaultModels.size();
}
}

50
src/rawDeepLearningClassifier/defaultModels/DLModel.java Normal file
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@ -0,0 +1,50 @@
package rawDeepLearningClassifier.defaultModels;
import java.net.URI;
import rawDeepLearningClassifier.dlClassification.animalSpot.StandardModelParams;
/**
* A default model that can be loaded from a file or a URL.
*/
public interface DLModel {
/**
* Get a brief description of the model.
* @return a brief description of the model.
*/
public String getDescription();
/**
* Get a name for the model
* @return
*/
public String getName();
/**
* Get the citation for the model
* @return - the citation.
*/
public String getCitation();
/**
* Get the URI to the model file
* @return the model URI.
*/
public URI getModelURI();
/**
* Get the model settings - these are used to ensure the model is set up correctly once loaded.
*/
public StandardModelParams getModelSettings();
/**
* The model name. This is used if, for example, a model is downloaded as a zip file and the model
* file is located somewhere within the saved folder. For Tensorflow models this will often be saved_model.pb
* @return the model name;
*/
public String getModelName();
}

59
src/rawDeepLearningClassifier/defaultModels/RightWhaleModel1.java Normal file
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@ -0,0 +1,59 @@
package rawDeepLearningClassifier.defaultModels;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import rawDeepLearningClassifier.dlClassification.animalSpot.StandardModelParams;
/**
* Right whale model from Shiu et al. 2019
* <p>
* * <p>
* Shiu, Y., Palmer, K.J., Roch, M.A., Fleishman, E., Liu, X., Nosal, E.-M., Helble, T., Cholewiak, D., Gillespie, D., Klinck, H., 2020.
* Deep neural networks for automated detection of marine mammal species. Scientific Reports 10, 607. https://doi.org/10.1038/s41598-020-57549-y
*/
public class RightWhaleModel1 implements DLModel {
@Override
public String getDescription() {
return "Detects right whales";
}
@Override
public String getName() {
return "Right Whale";
}
@Override
public String getCitation() {
return " Shiu, Y., Palmer, K.J., Roch, M.A., Fleishman, E., Liu, X., Nosal, E.-M., Helble, T., Cholewiak, D., Gillespie, D., Klinck, H., 2020."
+ " Deep neural networks for automated detection of marine mammal species. Scientific Reports 10, 607. https://doi.org/10.1038/s41598-020-57549-y";
}
@Override
public URI getModelURI() {
try {
return new URL("https://github.com/PAMGuard/deeplearningmodels/raw/master/right_whale_1/model_lenet_dropout_input_conv_all.zip").toURI();
} catch (MalformedURLException | URISyntaxException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}
@Override
public StandardModelParams getModelSettings() {
// TODO Auto-generated method stub
return null;
}
@Override
public String getModelName() {
return "saved_model.pb";
}
}

2
src/rawDeepLearningClassifier/dlClassification/DLClassiferModel.java
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@ -102,8 +102,6 @@ public interface DLClassiferModel {
*/
public boolean checkModelOK();
/**
* Get warnings for the classifier model. This is called when the user confirms settings and
* used to return a warning dialog.

8
src/rawDeepLearningClassifier/layoutFX/DLModelSelectPane.java
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@ -247,8 +247,10 @@ public class DLModelSelectPane extends PamBorderPane {
// runnable for that thread
public void run() {
try {
newModelSelected(uri);
currentSelectedFile = uri;
URI modelPath = dlControl.getDownloadManager().downloadModel(uri);
newModelSelected(modelPath);
currentSelectedFile = modelPath;
Thread.sleep(1000); //just show the user something happened if model loading is rapid.
} catch (InterruptedException e) {
// TODO Auto-generated catch block
@ -282,6 +284,8 @@ public class DLModelSelectPane extends PamBorderPane {
return;
}
this.currentClassifierModel = this.dlControl.getDlClassifierChooser().selectClassiferModel(file);
System.out.println("New classifier model selected!: " + currentClassifierModel);

0
src/test/DummyPamControllerInterface.java → test/test/DummyPamControllerInterface.java
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0
src/test/java/rawDeepLearningClassifier/DLJSONParserTest.java → test/test/java/rawDeepLearningClassifier/DLJSONParserTest.java
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0
src/test/java/rawDeepLearningClassifier/KetosClassifierTest.java → test/test/java/rawDeepLearningClassifier/KetosClassifierTest.java
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0
src/test/java/rawDeepLearningClassifier/StandardClassifierTest.java → test/test/java/rawDeepLearningClassifier/StandardClassifierTest.java
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0
src/test/resources/rawDeepLearningClassifier/Generic/right_whale/legacy_format/right_whale_DL_settings.pdtf → test/test/resources/rawDeepLearningClassifier/Generic/right_whale/legacy_format/right_whale_DL_settings.pdtf
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0
src/test/resources/rawDeepLearningClassifier/Generic/right_whale/right_whale_DL_settings.pdtf → test/test/resources/rawDeepLearningClassifier/Generic/right_whale/right_whale_DL_settings.pdtf
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