Merge pull request #3 from openspim/dev

1.0.11

pom.xml

@@ -7,7 +7,7 @@
 
 	<groupId>org.openspim</groupId>
 	<artifactId>uOpenSPIM</artifactId>
-	<version>1.0.10-SNAPSHOT</version>
+	<version>1.0.11-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <name>µOpenSPIM</name>
@@ -18,6 +18,7 @@
         <ij.version>1.52p</ij.version>
         <mmj.jar.path>${project.basedir}/lib/MMJ_.jar</mmj.jar.path>
         <mmcore.jar.path>${project.basedir}/lib/MMCoreJ.jar</mmcore.jar.path>
+        <mmacq.jar.path>${project.basedir}/lib/MMAcqEngine.jar</mmacq.jar.path>
 	</properties>
 
 	<repositories>
@@ -161,6 +162,12 @@
             <version>2.0.0</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.micromanager</groupId>
+            <artifactId>MMAcqEngine</artifactId>
+            <version>2.0.0</version>
+        </dependency>
+
         <dependency>
             <groupId>net.haesleinhuepf</groupId>
             <artifactId>clijx_</artifactId>
@@ -261,6 +268,24 @@
         </resources>
         <pluginManagement>
             <plugins>
+                <plugin>
+                    <groupId>org.codehaus.mojo</groupId>
+                    <artifactId>exec-maven-plugin</artifactId>
+                    <version>1.2.1</version>
+                    <executions>
+                        <execution>
+                            <goals>
+                                <goal>java</goal>
+                            </goals>
+                        </execution>
+                    </executions>
+                    <configuration>
+                        <mainClass>spim.microOpenSPIM</mainClass>
+                        <arguments>
+                            <argument>test</argument>
+                        </arguments>
+                    </configuration>
+                </plugin>
                 <plugin>
                     <groupId>com.zenjava</groupId>
                     <artifactId>javafx-maven-plugin</artifactId>

scripts/installMMDeps.sh

@@ -12,4 +12,9 @@ mvn org.apache.maven.plugins:maven-install-plugin:2.3.1:install-file \
                          -DartifactId=MMJ_ -Dversion=2.0.0 \
                          -Dpackaging=jar -DlocalRepositoryPath=local-repo/
 
-mvn install:install-file -DgroupId=jdk.tools -DartifactId=jdk.tools -Dpackaging=jar -Dversion=1.8 -Dfile=lib/tools.jar -DgeneratePom=true
+mvn org.apache.maven.plugins:maven-install-plugin:2.3.1:install-file \
+                         -Dfile=lib/MMAcqEngine.jar -DgroupId=org.micromanager \
+                         -DartifactId=MMAcqEngine -Dversion=2.0.0 \
+                         -Dpackaging=jar -DlocalRepositoryPath=local-repo/
+
+mvn install:install-file -DgroupId=jdk.tools -DartifactId=jdk.tools -Dpackaging=jar -Dversion=1.8 -Dfile=lib/tools.jar -DgeneratePom=true

src/main/java/spim/io/BDVMicroManagerStorage.java

@@ -361,7 +361,8 @@ public static void main( String[] args ) throws SpimDataException, IOException {
 
 				// create SourceTransform from the images calibration
 				final AffineTransform3D sourceTransform = new AffineTransform3D();
-				sourceTransform.set( 1.0, 0, 0, 0, 0, 1.0, 0, 0, 0, 0, 9.378, 0 );
+				double zUnit = 1.524d;
+				sourceTransform.set( 1.0, 0, 0, 0, 0, 1.0, 0, 0, 0, 0, zUnit, 0 );
 
 				for ( int t = 0; t < numTimepoints; ++t )
 					registrations.add( new ViewRegistration( t, angles * j + i, sourceTransform ) );
@@ -555,7 +556,7 @@ public void putImage(Image image) throws IOException {
 					}
 				}
 
-				System.out.println(coords.getC() + "/" + channels);
+				// System.out.println(coords.getC() + "/" + channels);
 
 				if(fusionChannel_ && coords.getC() % 2 == 1)
 				{

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

@@ -68,6 +68,7 @@ public double getZEnd()
 
 	public double getZStep()
 	{
+		if( zStep == 0 ) zStep = 1.524;
 		return zStep;
 	}
 
@@ -118,7 +119,8 @@ public void setZEnd( double zEnd )
 
 	public void setZStep( double zStep )
 	{
-		this.zStep = zStep;
+		if (zStep != 0)
+			this.zStep = zStep;
 	}
 
 	public int getNumberOfSlices() {
@@ -139,6 +141,12 @@ public void setName(String name) {
 		this.name.set(name);
 	}
 
+	public PositionItem clone(InvalidationListener invalidationListener) {
+		PositionItem clone = new PositionItem(x, y, r, zStart, zEnd, zStep, invalidationListener );
+		clone.setName( getName() + " Copy" );
+		return clone;
+	}
+
 	@Override public String toString()
 	{
 		StringBuilder sb = new StringBuilder(  );

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

@@ -13,6 +13,7 @@
 import javafx.collections.FXCollections;
 import javafx.collections.ListChangeListener;
 import javafx.collections.ObservableList;
+import javafx.concurrent.Task;
 import javafx.event.ActionEvent;
 import javafx.event.EventHandler;
 import javafx.geometry.Insets;
@@ -47,9 +48,11 @@
 import org.micromanager.display.DisplayWindow;
 import org.micromanager.events.internal.DefaultGUIRefreshEvent;
 import org.micromanager.internal.MMStudio;
+import org.micromanager.internal.utils.ReportingUtils;
 import spim.hardware.Camera;
 import spim.hardware.SPIMSetup;
 import spim.hardware.VersaLase;
+import spim.mm.MicroManager;
 import spim.model.data.AcquisitionSetting;
 import spim.model.data.ChannelItem;
 import spim.model.data.PinItem;
@@ -75,6 +78,10 @@
 import java.text.SimpleDateFormat;
 import java.util.*;
 import java.util.List;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
 import java.util.stream.Collectors;
 
 import static spim.ui.view.component.util.TableViewUtil.createTimePointItemDataView;
@@ -749,7 +756,7 @@ public void handle(ActionEvent actionEvent) {
 		Tab onTheFlyTab = new Tab("On-the-fly", new VBox(2, onTheFlyHBox, onFusionchannelHBox));
 		onTheFlyTab.setClosable(false);
 
-		CheckBox ablationCheckbox = new CheckBox( "Generate ablation.tiff (works with OMETIFF as saving format)" );
+		CheckBox ablationCheckbox = new CheckBox( "Generate ablation.tiff (works with Single Plane TIFF as saving format)" );
 
 		ablationSupport = ablationCheckbox.selectedProperty();
 		ablationDisabled = ablationCheckbox.disableProperty();
@@ -1495,6 +1502,14 @@ public boolean startAcquisition( Button acquireButton )
 			return false;
 		}
 
+		if ((savingFormat.getValue().equals("BDV format") || savingFormat.getValue().equals("N5 format")) &&
+				!positionItemTableView.getItems().filtered(p -> p.getSelected() && p.getZStart() == p.getZEnd()).isEmpty()) {
+			new Alert( Alert.AlertType.WARNING, "BDV and N5 format support only multi-stack images.").showAndWait();
+
+			System.err.println("Acquisition stopped due to a single stack setup.");
+			return false;
+		}
+
 		// Write the experiment note
 		try {
 			writeNote(folderFile);
@@ -1541,39 +1556,66 @@ public boolean startAcquisition( Button acquireButton )
 		fileName = fileName.replace("<timepoints>", timepoints);
 
 		String finalFileName = fileName;
-		acquisitionThread = new Thread(() ->
-		{
-			Thread.currentThread().setContextClassLoader( HalcyonMain.class.getClassLoader() );
 
-			try
-			{
-				engine.performAcquisition( getStudio(), getSpimSetup(), stagePanel, ( java.awt.Rectangle) roiRectangle.get(), tp,
+		Task<Void> task = new Task<Void>() {
+			@Override
+            protected Void call() throws Exception
+            {
+				engine.performAcquisition( getStudio(), getSpimSetup(), stagePanel, (java.awt.Rectangle) roiRectangle.get(), tp,
 						timePointItemTableView.getItems(), currentTP, waitSeconds,
 						arduinoSelected, finalFolder, finalFileName,
 						positionItemTableView.getItems().filtered(p -> p.getSelected()), channelItemList, processedImages, totalImages.getValue(),
 						enabledSaveImages.get(), savingFormat.getValue(), saveMIP.getValue(), ablationSupport.getValue(), antiDrift.getValue(), experimentNote.getValue(),
 						antiDriftLog, antiDriftRefCh.get(), antiDriftTypeToggle, onTheFly.getValue(), onChannelFusion.getValue() );
 
-//				new MMAcquisitionRunner().runAcquisition();
-
-//				engine.performAcquisitionMM( spimSetup, stagePanel, (java.awt.Rectangle) roiRectangle.get(), tp, deltaT * unit, arduinoSelected, new File(directory.getValue()), filename.getValue(), positionItemTableView.getItems(), channelItemList, processedImages, enabledSaveImages.get());
-
-
 				acquisitionThread = null;
 				engine = null;
 				Platform.runLater( () -> {
 					acquireButton.setText( "Acquire" );
 					acquireButton.setStyle("-fx-font: 18 arial; -fx-base: #69e760;");
 				} );
+                return null;
+            }
+		};
 
-//				Thread.currentThread().setContextClassLoader( getClass().getClassLoader() );
-			}
-			catch ( Exception e )
-			{
-				e.printStackTrace();
-			}
+        task.setOnSucceeded( (e) -> {
+			System.out.println("task.onSucceeded");
+
+//			CompletableFuture<Void> future = CompletableFuture.runAsync(() -> {
+//				//read data through usb device and add it into array;
+//				try {
+//					Thread.sleep(10000);
+//				} catch (InterruptedException ex) {
+//					throw new RuntimeException(ex);
+//				}
+//			});
+//
+//			try {
+//				future.get(5, TimeUnit.SECONDS);
+//				ReportingUtils.showErrorOn( true );
+//				// get here if read was successful
+//			} catch (InterruptedException ie) {
+//				Thread.currentThread().interrupt();
+//			} catch (ExecutionException ee) {
+//				// exception was thrown by code reading usb device
+//			} catch (TimeoutException te) {
+//				// timeout occurred
+//			}
+
+			Timer timer = new java.util.Timer();
+
+			timer.schedule(new TimerTask() {
+				public void run() {
+					ReportingUtils.showErrorOn( true );
+
+				}
+			}, 5000);
 		} );
+		task.setOnFailed(e -> {
+        } );
 
+		ReportingUtils.showErrorOn( false );
+		acquisitionThread = new Thread(task);
 		acquisitionThread.start();
 
 		return true;
@@ -1618,14 +1660,23 @@ private Node createPositionListPane( TableView< PositionItem > positionItemTable
 				double r = spimSetup.getAngle();
 				double x = spimSetup.getXStage().getPosition();
 				double y = spimSetup.getYStage().getPosition();
-				double z = spimSetup.getZStage().getPosition();
+				double z = stagePanel.getZTargetValue();
+//				double z = spimSetup.getZStage().getPosition();
 				positionItemTableView.getItems().add( new PositionItem( x, y, r, z, z, zStackStepSize, invalidationListener ) );
 			}
 			else {
 				positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, 20, 50, 10, invalidationListener ) );
 			}
 		};
 
+		EventHandler dupEventHandler = ( EventHandler< ActionEvent > ) event -> {
+			if(positionItemTableView.getSelectionModel().getSelectedIndex() > -1) {
+				PositionItem clone = positionItemTableView.getItems().get(positionItemTableView.getSelectionModel().getSelectedIndex()).clone(invalidationListener);
+				positionItemTableView.getItems().add( clone );
+			}
+		};
+
+
 		EventHandler deleteEventHandler = new EventHandler< ActionEvent >()
 		{
 			@Override public void handle( ActionEvent event )
@@ -1639,6 +1690,10 @@ private Node createPositionListPane( TableView< PositionItem > positionItemTable
 		newButton.setMinHeight(30);
 		newButton.setOnAction( newEventHandler );
 
+		Button dupButton = new Button("Duplicate");
+		dupButton.setMinHeight(30);
+		dupButton.setOnAction( dupEventHandler );
+
 		Button deleteButton = new Button("Delete position");
 		deleteButton.setMinHeight(30);
 		deleteButton.setOnAction( deleteEventHandler );
@@ -1690,7 +1745,7 @@ private Node createPositionListPane( TableView< PositionItem > positionItemTable
 		Button helpButton = createHelpButton();
 		helpButton.setOnAction( event -> new HelpWindow().show(HelpType.POSITION));
 
-		HBox hbox = new HBox( 5, newButton, deleteButton, showAllPositionsButton );
+		HBox hbox = new HBox( 5, newButton, dupButton, deleteButton, showAllPositionsButton );
 
 		// If it gives the confusion changing position values without intention,
 		// Remove the currentPosition change event handler,
@@ -1837,14 +1892,14 @@ public void handle(ActionEvent event) {
 		c.valueProperty().addListener(new ChangeListener() {
 			@Override
 			public void changed(ObservableValue observableValue, Object o, Object t1) {
-				if(ablationSupport != null && !t1.equals("OMETIFF Image stack")) {
+				if(ablationSupport != null && !t1.equals("Single Plane TIFF")) {
 					ablationSupport.set(false);
 				}
 			}
 		});
 
 		savingFormat = c.valueProperty();
-		ablationDisabled.bind(savingFormat.isNotEqualTo("OMETIFF Image stack"));
+		ablationDisabled.bind(savingFormat.isNotEqualTo("Single Plane TIFF"));
 
 		gridpane.addRow( 3, new Label( "Saving format:" ), c );
 
@@ -2380,7 +2435,7 @@ private void addNewPosition( int zStart, int zEnd, double zStep ) {
 			y = Math.ceil(y * 100) / 100;
 
 			if( zStart < 0 && zEnd < 0 ) {
-				double z = spimSetup.getZStage().getPosition();
+				double z = stagePanel.getZTargetValue();
 				positionItemTableView.getItems().add(new PositionItem(x, y, r, z, z, zStep, invalidationListener));
 			} else {
 				positionItemTableView.getItems().add(new PositionItem(x, y, r, zStart, zEnd, zStep, invalidationListener));
@@ -2403,7 +2458,8 @@ private void setupMouseClickedHandler( Button startButton, TextField zStartField
 			{
 				SPIMSetup spimSetup = getSpimSetup();
 				if(spimSetup != null && spimSetup.getZStage() != null) {
-					int currPos = (int) spimSetup.getZStage().getPosition();
+//					int currPos = (int) spimSetup.getZStage().getPosition();
+					int currPos = (int) stagePanel.getZTargetValue();
 					if(zEndField.getText().isEmpty()) {
 						zStartField.setText(currPos + "");
 						zStartField.setDisable(true);
@@ -2436,7 +2492,8 @@ private void setupMouseClickedHandler( Button startButton, TextField zStartField
 						zStepComboBox.getSelectionModel().select(1);
 					}
 
-					int currPos = (int) spimSetup.getZStage().getPosition();
+//					int currPos = (int) spimSetup.getZStage().getPosition();
+					int currPos = (int) stagePanel.getZTargetValue();
 					if(zStartField.getText().isEmpty()) {
 						zEndField.setText(currPos + "");
 						zEndField.setDisable(true);

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

@@ -17,6 +17,7 @@
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import spim.hardware.SPIMSetup;
+import spim.mm.MicroManager;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -203,6 +204,7 @@ final void createBeanshellREPL() {
 		}
 
 		beanshellThread = new Thread(beanshellREPLint_, "BeanShell interpreter");
+		beanshellThread.setContextClassLoader( MicroManager.getMMStudio().getClass().getClassLoader() );
 		beanshellThread.start();
 
 		running_ = false;

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

@@ -58,7 +58,7 @@ public void start( Stage primaryStage )
 		{
 			@Override public void run()
 			{
-				Thread.currentThread().setContextClassLoader( getClass().getClassLoader() );
+//				Thread.currentThread().setContextClassLoader( getClass().getClassLoader() );
 				try
 				{
 					Thread.sleep(1000);