Merge branch 'dev' into 'master'

1.0.5

Closes #189, #190, and #188

See merge request scicomp/scidev_team/spimacquisition!2

Author: moon

pom.xml

@@ -7,7 +7,7 @@
 
 	<groupId>org.openspim</groupId>
 	<artifactId>uOpenSPIM</artifactId>
-	<version>1.0.4-SNAPSHOT</version>
+	<version>1.0.5-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <name>µOpenSPIM</name>

src/main/java/spim/algorithm/DefaultAntiDrift.java

@@ -1,6 +1,9 @@
 package spim.algorithm;
 
 import ij.ImageStack;
+import ij.plugin.filter.Convolver;
+import ij.plugin.filter.GaussianBlur;
+import ij.plugin.filter.RankFilters;
 import ij.process.*;
 import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
 
@@ -18,6 +21,14 @@ public class DefaultAntiDrift extends AbstractAntiDrift
 	 */
 	private final double sigma;
 	private final AntiDrift.Type type;
+	private final GaussianBlur gaussianBlur = new GaussianBlur();
+	private final Convolver convolver = new Convolver();
+	private final RankFilters filters = new RankFilters();
+	private final float[] kernel = new float[]{-1, -1, -1, -1, -1,
+			-1, -1, -1, -1, -1,
+			-1, -1, 24, -1, -1,
+			-1, -1, -1, -1, -1,
+			-1, -1, -1, -1, -1,};
 
 	public DefaultAntiDrift(double sigmaValue)
 	{
@@ -49,14 +60,16 @@ public void reset()
 	@Override public void addXYSlice( ImageProcessor ip )
 	{
 		ImageProcessor copy = ip.duplicate();
+		gaussianBlur.blurGaussian( copy, sigma );
+		convolver.convolve( copy, kernel, 5, 5 );
+		filters.rank( copy, 2, 2 );
 
 		switch (type) {
 			case CenterOfMass:
 				if(stack == null) stack = new ImageStack( ip.getWidth(), ip.getHeight() );
 				stack.addSlice( copy );
 				break;
 			case PhaseCorrelation:
-				copy.blurGaussian( sigma );
 				latest.addXYSlice( copy );
 				break;
 		}

src/main/java/spim/mm/MicroManager.java

@@ -1331,14 +1331,14 @@ public static void shutdown()
 
 	@Subscribe
 	public void onAcquisitionStart( AcquisitionStartedEvent ae) {
-		System.out.println("Acquisition started");
+//		System.out.println("Acquisition started");
 //		store_ = ae.getDatastore();
 	}
 
 
 	@Subscribe
 	public void onAcquisitionEnd( AcquisitionEndedEvent ae) {
-		System.out.println("Acquisition stopped");
+//		System.out.println("Acquisition stopped");
 //		store_ = null;
 	}
 
@@ -1349,7 +1349,7 @@ public void onSystemConfigurationLoaded(SystemConfigurationLoadedEvent event) {
 
 	@Subscribe
 	public void onStagePositionChanged(StagePositionChangedEvent event) {
-		System.out.println("Stage changed");
+//		System.out.println("Stage changed");
 	}
 
 	@Subscribe

src/main/java/spim/model/data/PositionItem.java

@@ -1,5 +1,11 @@
 package spim.model.data;
 
+import javafx.beans.InvalidationListener;
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+
 /**
  * Description: PositionItem is used for position table.
  *
@@ -15,19 +21,23 @@ public class PositionItem
 	private double zStart;
 	private double zEnd;
 	private double zStep;
+	private final BooleanProperty selected = new SimpleBooleanProperty();
+	private final StringProperty name = new SimpleStringProperty();
 
 	public PositionItem()
 	{
 	}
 
-	public PositionItem( double x, double y, double r, double zStart, double zEnd, double zStep )
+	public PositionItem( double x, double y, double r, double zStart, double zEnd, double zStep, InvalidationListener invalidationListener )
 	{
 		this.x = x;
 		this.y = y;
 		this.r = r;
 		this.zStart = zStart;
 		this.zEnd = zEnd;
 		this.zStep = zStep;
+		this.name.set("");
+		selectedProperty().addListener( observable -> invalidationListener.invalidated( observable ) );
 	}
 
 	public double getX()
@@ -74,6 +84,12 @@ public String getPosZString() {
 			return String.format( "%.0f", zStart );
 	}
 
+	public String getName() {
+		return name.getValue();
+	}
+
+	public StringProperty getNameProperty() { return name; }
+
 	public void setX( double x )
 	{
 		this.x = x;
@@ -105,7 +121,21 @@ public void setZStep( double zStep )
 	}
 
 	public int getNumberOfSlices() {
-		return (int) ((int) (getZEnd() - getZStart() + getZStep()) / getZStep());
+		return (int) ((int) (getZEnd() - getZStart() + getZStep()) / getZStep() + 1);
+	}
+
+	public BooleanProperty selectedProperty() { return selected; }
+
+	public boolean getSelected() {
+		return selected.get();
+	}
+
+	public void setSelected(boolean selected) {
+		this.selected.set( selected );
+	}
+
+	public void setName(String name) {
+		this.name.set(name);
 	}
 
 	@Override public String toString()

src/main/java/spim/ui/view/component/AcquisitionPanel.java

@@ -389,6 +389,7 @@ public AcquisitionPanel(SPIMSetup setup, Studio studio, StagePanel stagePanel, T
 		{
 			@Override public void changed( ObservableValue< ? extends Number > observable, Number oldValue, Number newValue )
 			{
+//				System.out.println(String.format("%f / %d", newValue.doubleValue(), totalImages.getValue()));
 				pi.setProgress( newValue.doubleValue() / totalImages.getValue() );
 			}
 		} );
@@ -1207,6 +1208,13 @@ private void updateUI ( AcquisitionSetting setting ) {
 		positionItems = setting.getPositionItems();
 		positionItemTableView.getItems().setAll( positionItems );
 
+		InvalidationListener invalidationListener = observable -> computeTotalPositionImages();
+		for(int i = 0; i < positionItems.size(); i++) {
+//			positionItems.get( i ).setValue( positionItems.get(i).getValue() );
+//			positionItems.get( i ).setSelected( positionItems.get(i).getSelected() );
+			positionItems.get( i ).selectedProperty().addListener( observable -> invalidationListener.invalidated( observable ) );
+		}
+
 		// 3. Z-Stack panel
 		enabledZStacks.set( setting.getEnabledZStacks() );
 
@@ -1353,7 +1361,7 @@ public boolean startAcquisition( Button acquireButton )
 		if ( enabledSaveImages.get() )
 		{
 			if(null != folder.listFiles()) {
-				boolean found = folder.exists();
+				boolean found = folder.exists() && folder.listFiles().length > 1;
 
 				if(found) {
 					Optional< ButtonType > results = new Alert( Alert.AlertType.WARNING, "The filename already exists. All files with the same name will be replaced. Do you want to proceed?\nPress No to create another folder and keep all files.",
@@ -1462,7 +1470,7 @@ public boolean startAcquisition( Button acquireButton )
 				engine.performAcquisition( getStudio(), getSpimSetup(), stagePanel, ( java.awt.Rectangle) roiRectangle.get(), tp,
 						timePointItemTableView.getItems(), currentTP, waitSeconds,
 						arduinoSelected, finalFolder, filename.getValue(),
-						positionItemTableView.getItems(), channelItemList, processedImages,
+						positionItemTableView.getItems().filtered(p -> p.getSelected()), channelItemList, processedImages,
 						enabledSaveImages.get(), savingFormat.getValue(), saveMIP.getValue(), antiDrift.getValue(), experimentNote.getValue(),
 						antiDriftLog, antiDriftRefCh.get(), antiDriftTypeToggle, onTheFly.getValue() );
 
@@ -1515,17 +1523,19 @@ static double getUnit(String unitString) {
 	private Node createPositionListPane( TableView< PositionItem > positionItemTableView ) {
 		positionItemTableView.setEditable( true );
 
+		InvalidationListener invalidationListener = observable -> computeTotalPositionImages();
+
 		EventHandler newEventHandler = ( EventHandler< ActionEvent > ) event -> {
 			SPIMSetup spimSetup = getSpimSetup();
 			if(spimSetup != null ) {
 				double r = spimSetup.getThetaStage().getPosition();
 				double x = spimSetup.getXStage().getPosition();
 				double y = spimSetup.getYStage().getPosition();
 				double z = spimSetup.getZStage().getPosition();
-				positionItemTableView.getItems().add( new PositionItem( x, y, r, z, z, zStackStepSize ) );
+				positionItemTableView.getItems().add( new PositionItem( x, y, r, z, z, zStackStepSize, invalidationListener ) );
 			}
 			else {
-				positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, 20, 50, 10 ) );
+				positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, 20, 50, 10, invalidationListener ) );
 			}
 		};
 
@@ -1610,12 +1620,12 @@ public void computeTotalPositionImages() {
 		long totalImages = 0;
 		for(PositionItem item : positionItemTableView.getItems())
 		{
-			if(item.getZEnd() > item.getZStart()) {
+			if(item.getSelected() && item.getZEnd() > item.getZStart()) {
 				totalImages += item.getNumberOfSlices();
 			}
 		}
 
-		propertyMap.get("positions").setValue( positionItemTableView.getItems().size() + "" );
+		propertyMap.get("positions").setValue( positionItemTableView.getItems().filtered(p -> p.getSelected()).size() + "" );
 		propertyMap.get("slices").setValue( totalImages + "" );
 	}
 
@@ -1853,6 +1863,8 @@ private LabeledPane createSummaryPane() {
 		label.textProperty().bind( propertyMap.get("positions") );
 		label.textProperty().addListener( observable -> computeTotal() );
 
+		propertyMap.get("slices").addListener( observable -> computeTotal() );
+
 		Label label2 = new Label();
 		label2.textProperty().bind( propertyMap.get("totalImages") );
 		gridpane.addRow( 0, new Label("No. of positions: "), label, new Label("Total images: "), label2 );
@@ -2097,7 +2109,8 @@ public void changed(ObservableValue<? extends String> observable, String oldValu
 //			}
 //		} );
 
-		Button clearButton = new Button( "New Z-stack" );
+		Button clearButton = new Button( "Define new Z-stack" );
+		clearButton.setStyle("-fx-base: #ffbec4;");
 		clearButton.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
 			public void handle(ActionEvent event) {
@@ -2134,7 +2147,7 @@ public void handle(ActionEvent event) {
 			}
 		} );
 
-		zStackGridPane.addRow( 3, new HBox( newButton, clearButton ) );
+		zStackGridPane.addRow( 3, new VBox( newButton, clearButton ) );
 
 		// create a group
 		HBox b = new HBox(new Label("Stage"));
@@ -2148,13 +2161,15 @@ public void handle(ActionEvent event) {
 		Button helpButton = createHelpButton();
 		helpButton.setOnAction( event -> new HelpWindow().show(HelpType.ZSTACK));
 
-		CheckboxPane pane = new CheckboxPane( "Define Z-stacks", zStackGroup, helpButton );
+		CheckboxPane pane = new CheckboxPane( "Z-stacks", zStackGroup, helpButton );
 		enabledZStacks = pane.selectedProperty();
 		return pane;
 	}
 
 	private void addNewPosition( int zStart, int zEnd, double zStep ) {
 		SPIMSetup spimSetup = getSpimSetup();
+		InvalidationListener invalidationListener = observable -> computeTotalPositionImages();
+
 		if(spimSetup != null ) {
 			double r = spimSetup.getThetaStage().getPosition();
 			double x = spimSetup.getXStage().getPosition();
@@ -2164,13 +2179,13 @@ private void addNewPosition( int zStart, int zEnd, double zStep ) {
 
 			if( zStart < 0 && zEnd < 0 ) {
 				double z = spimSetup.getZStage().getPosition();
-				positionItemTableView.getItems().add(new PositionItem(x, y, r, z, z, zStep));
+				positionItemTableView.getItems().add(new PositionItem(x, y, r, z, z, zStep, invalidationListener));
 			} else {
-				positionItemTableView.getItems().add(new PositionItem(x, y, r, zStart, zEnd, zStep));
+				positionItemTableView.getItems().add(new PositionItem(x, y, r, zStart, zEnd, zStep, invalidationListener));
 			}
 		}
 		else {
-			positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, zStart, zEnd, zStep ) );
+			positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, zStart, zEnd, zStep, invalidationListener ) );
 		}
 	}
 

src/main/java/spim/ui/view/component/MMAcquisitionEngine.java

@@ -380,13 +380,15 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
 				if(toogleGroupValue.equals("Centre of mass")) {
 					driftCompMap.put(positionItem, new DefaultAntiDrift());
 				} else if(toogleGroupValue.equals("Phase correlation")) {
-					driftCompMap.put(positionItem, new DefaultAntiDrift(10));
+					driftCompMap.put(positionItem, new DefaultAntiDrift(2));
 				}
 			}
 		}
 
 		AcqWrapperEngine engine = new AcqWrapperEngine( setup, frame, store, currentCamera, cameras, outFolder, acqFilenamePrefix, channelItems, arduinoSelected, processedImages, driftCompMap, adReferenceChannel, onTheFly);
 
+		SystemInfo.dumpMemoryStatusToLog(core);
+
 		mainLoop:
 		for(TimePointItem tpItem : timePointItems ) {
 			if(tpItem.getType().equals( TimePointItem.Type.Acq ))
@@ -398,8 +400,6 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
 
 					int step = 0;
 
-					SystemInfo.dumpMemoryStatusToLog(core);
-
 					for ( PositionItem positionItem : positionItems )
 					{
 						final int tp = timePoints;
@@ -482,7 +482,7 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
 						}
 
 						core.logMessage("MMAcquisition started");
-						System.out.println("MMAcquisition started");
+//						System.out.println("MMAcquisition started");
 						engine.startAcquire( timePoints, step, positionItem );
 
 						while(engine.isAcquisitionRunning()) {
@@ -498,7 +498,7 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
 						}
 
 						core.logMessage("MMAcquisition finished");
-						System.out.println("MMAcquisition finished");
+//						System.out.println("MMAcquisition finished");
 
 						if(setup.getArduino1() != null)
 							setup.getArduino1().setSwitchState( "0" );
@@ -594,6 +594,8 @@ else if(tpItem.getType().equals( TimePointItem.Type.Wait ))
 			}
 		}
 
+		SystemInfo.dumpMemoryStatusToLog(core);
+
 		engine.exit();
 		store.freeze();
 		System.err.println("AcquisitionEngine exited.");