Version 5.3.8

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.3.7</version>
+    <version>5.3.8</version>
     <!-- mvn clean install -Dmaven.test.skip=true -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-MoBIE.app -->
 
     <!--  ../scijava-scripts/release-version.sh - -skip-version-check - -skip-license-update -->

src/main/java/org/embl/mobie/lib/table/TableView.java

@@ -50,6 +50,7 @@
 import org.embl.mobie.lib.select.SelectionModel;
 import org.embl.mobie.ui.ColumnColoringModelDialog;
 import net.imglib2.type.numeric.ARGBType;
+import org.embl.mobie.ui.StringArraySelectorDialog;
 import org.embl.mobie.ui.UserInterfaceHelper;
 
 import javax.swing.*;
@@ -371,12 +372,13 @@ private JMenuItem createColumnSearchMenuItem()
 		menuItem.addActionListener( e ->
 				SwingUtilities.invokeLater( () ->
 				{
-					final String[] columnNames = Tables.getColumnNamesAsArray( jTable );
-					final GenericDialog gd = new GenericDialog( "Focus Column" );
-					gd.addChoice( "Column", columnNames, columnNames[ 0 ] );
-					gd.showDialog();
-					if ( gd.wasCanceled() ) return;
-					final String columnName = gd.getNextChoice();
+					StringArraySelectorDialog dialog =
+							new StringArraySelectorDialog(
+									"Column Selector",
+									Tables.getColumnNamesAsArray( jTable )
+							);
+					if ( ! dialog.show() ) return;
+					final String columnName = dialog.getSelectedItem();
 					int columnIndex = jTable.getColumnModel().getColumnIndex( columnName );
 					JViewport viewport = (JViewport) jTable.getParent();
 					Rectangle rect = jTable.getCellRect(0, columnIndex, true);

src/main/java/org/embl/mobie/ui/StringArraySelectorDialog.java

@@ -0,0 +1,89 @@
+package org.embl.mobie.ui;
+
+import org.embl.mobie.MoBIE;
+import org.embl.mobie.lib.io.FileLocation;
+import org.embl.mobie.lib.serialize.View;
+import org.jetbrains.annotations.NotNull;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.File;
+import java.util.Arrays;
+
+import static org.embl.mobie.lib.view.save.ViewSaver.CREATE_SELECTION_GROUP;
+
+public class StringArraySelectorDialog
+{
+    private final String title;
+    private final String[] array;
+
+    private JComboBox< String > arrayComboBox;
+
+    private boolean isOkPressed;
+
+    private JDialog dialog;
+
+    public StringArraySelectorDialog( String title, String[] array )
+    {
+        this.title = title;
+        this.array = array;
+    }
+
+    public boolean show()
+    {
+        dialog = new JDialog( ( Frame ) null, title, true );
+        dialog.setLayout( new BoxLayout( dialog.getContentPane(), BoxLayout.Y_AXIS ) );
+
+        // Array item selection
+        //
+        JPanel selectionPanel = SwingHelper.horizontalLayoutPanel();
+        arrayComboBox = new JComboBox<>( array );
+        Dimension maximumSize = new Dimension( 300, 20 );
+        arrayComboBox.setMaximumSize( maximumSize );
+        selectionPanel.add( new JLabel("Select item:  ") );
+        selectionPanel.add( arrayComboBox );
+
+        dialog.add( selectionPanel );
+
+        // OK and Cancel button
+        //
+        JPanel buttonPanel = new JPanel();
+        JButton okButton = new JButton( "OK" );
+        JButton cancelButton = new JButton( "Cancel" );
+        buttonPanel.add( okButton );
+        buttonPanel.add( cancelButton );
+        dialog.add( buttonPanel );
+
+        okButton.addActionListener( e ->
+        {
+            isOkPressed = true;
+            dialog.setVisible( false );
+        } );
+
+        cancelButton.addActionListener( e ->
+        {
+            isOkPressed = false;
+            dialog.setVisible( false );
+        } );
+
+        dialog.setPreferredSize( new Dimension( 250, 120 ) );
+        dialog.setLocation(
+                Toolkit.getDefaultToolkit().getScreenSize().width / 2 - 200,
+                Toolkit.getDefaultToolkit().getScreenSize().height / 2 - 200
+        );
+        dialog.pack();
+        dialog.setVisible( true );
+
+        return isOkPressed;
+    }
+
+    public String getSelectedItem()
+    {
+        return (String) arrayComboBox.getSelectedItem();
+    }
+}
+

src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java

@@ -1237,7 +1237,7 @@ public static JButton createFocusButton( AbstractDisplay< ? > sourceDisplay,
 											 BdvHandle bdvHandle,
 											 List< Source< ? > > sources )
 	{
-		JButton button =  getIconButton( "focus.png" );
+		JButton button = getIconButton( "focus.png" );
 		button.setToolTipText( "Fit image to viewer" );
 
 		button.addActionListener( e ->

src/test/java/org/embl/mobie/command/open/OpenIlastik2DImageAndSegmentationCommandTest.java → src/test/java/org/embl/mobie/command/open/Open2DTIFFImageAndIlastikSegmentationCommandTest.java

@@ -32,7 +32,7 @@
 
 import java.io.File;
 
-public class OpenIlastik2DImageAndSegmentationCommandTest
+public class Open2DTIFFImageAndIlastikSegmentationCommandTest
 {
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 

src/test/java/org/embl/mobie/command/open/OpenIlastik2ChannelImageCommandTest.java

@@ -0,0 +1,49 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2024 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.embl.mobie.command.open;
+
+import net.imagej.ImageJ;
+import org.junit.jupiter.api.Test;
+
+import java.io.File;
+
+public class OpenIlastik2ChannelImageCommandTest
+{
+	static { net.imagej.patcher.LegacyInjector.preinit(); }
+
+	@Test
+	public void test( )
+	{
+		new ImageJ().ui().showUI(); // initialise SciJava Services
+
+		final OpenImageAndLabelsCommand command = new OpenImageAndLabelsCommand();
+		command.image = new File( "src/test/resources/ilastik-2d/probabilities-2channels.h5" );
+		command.run();
+	}
+}

src/test/java/org/embl/mobie/command/open/OpenIlastik2ChannelImagesCommandTest.java

@@ -0,0 +1,51 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2024 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.embl.mobie.command.open;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.lib.transform.GridType;
+import org.junit.jupiter.api.Test;
+
+import java.io.File;
+
+public class OpenIlastik2ChannelImagesCommandTest
+{
+	static { net.imagej.patcher.LegacyInjector.preinit(); }
+
+	@Test
+	public void test( )
+	{
+		new ImageJ().ui().showUI(); // initialise SciJava Services
+
+		final OpenMultipleImagesAndLabelsCommand command = new OpenMultipleImagesAndLabelsCommand();
+		command.image0 = new File( "src/test/resources/ilastik-2d/probabilities-2channels.h5;0" );
+		command.image1 = new File( "src/test/resources/ilastik-2d/probabilities-2channels.h5;1" );
+		command.run();
+	}
+}

src/test/java/org/embl/mobie/command/open/OpenIlastikImageAndSegmentationCommandTest.java

@@ -0,0 +1,51 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2024 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.embl.mobie.command.open;
+
+import net.imagej.ImageJ;
+import org.junit.jupiter.api.Test;
+
+import java.io.File;
+
+public class OpenIlastikImageAndSegmentationCommandTest
+{
+	static { net.imagej.patcher.LegacyInjector.preinit(); }
+
+	@Test
+	public void test( )
+	{
+		new ImageJ().ui().showUI(); // initialise SciJava Services
+
+		final OpenImageAndLabelsCommand command = new OpenImageAndLabelsCommand();
+		command.image = new File( "src/test/resources/ilastik-2d/probabilities.h5" );
+		command.labels = new File( "src/test/resources/ilastik-2d/labels.h5" );
+		command.table = new File( "src/test/resources/ilastik-2d/table.csv" );
+		command.run();
+	}
+}