Bigwarp 9.0.0

.gitignore

@@ -30,3 +30,10 @@ hs_err_pid*
 /bin/
 /target/
 
+# ignore files generated during test
+/src/test/resources/bigwarp/url/imgDir3d/img3d0000.tif
+/src/test/resources/bigwarp/url/imgDir3d/img3d0001.tif
+/src/test/resources/bigwarp/url/imgDir3d/img3d0002.tif
+/src/test/resources/bigwarp/url/imgDir3d/img3d0003.tif
+/src/test/resources/bigwarp/url/img.tif
+/src/test/resources/bigwarp/url/img2d.png

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>bigwarp_fiji</artifactId>
-	<version>8.0.1-SNAPSHOT</version>
+	<version>9.0.0-SNAPSHOT</version>
 
 	<name>BigWarp plugin for Fiji</name>
 	<description>A tool for manual pointwise deformable registration using bigdataviewer.</description>
@@ -118,16 +118,25 @@
 		<license.projectName>BigWarp plugin for Fiji.</license.projectName>
 		<license.excludes>**/resources/*.xml</license.excludes>
 
+		<imglib2.version>6.2.0</imglib2.version>
+		<imglib2-realtransform.version>4.0.1</imglib2-realtransform.version>
+
 		<jcommander.version>1.48</jcommander.version>
 		<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
+		<jitk-tps.version>3.0.3</jitk-tps.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<n5.version>3.0.0</n5.version>
-		<n5-ij.version>3.2.4</n5-ij.version>
+		<n5.version>3.0.2</n5.version>
+		<n5-ij.version>3.2.6</n5-ij.version>
+		<n5-hdf5.version>2.0.1</n5-hdf5.version>
+		<n5-aws-s3.version>4.0.1</n5-aws-s3.version>
+		<n5-google-cloud.version>4.0.0</n5-google-cloud.version>
 		<n5-imglib2.version>7.0.0</n5-imglib2.version>
-		<n5-universe.version>1.0.1</n5-universe.version>
+		<n5-universe.version>1.2.0</n5-universe.version>
+		<n5-viewer_fiji.version>5.3.1</n5-viewer_fiji.version>
+		<n5-zarr.version>1.0.1</n5-zarr.version>
 		<bigdataviewer-core.version>10.4.8</bigdataviewer-core.version>
 
 	</properties>
@@ -145,6 +154,10 @@
 			<groupId>net.imagej</groupId>
 			<artifactId>ij</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>imagej</artifactId>
+		</dependency>
 
 		<!-- ImgLib2 dependencies -->
 		<dependency>
@@ -236,13 +249,27 @@
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-imglib2</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-aws-s3</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-google-cloud</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-viewer_fiji</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-zarr</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-universe</artifactId>
 			<version>${n5-universe.version}</version>
 		</dependency>
-
-
 		<!-- OME dependencies -->
 		<dependency>
 			<groupId>ome</groupId>
@@ -306,12 +333,56 @@
 			<artifactId>alphanumeric-comparator</artifactId>
 			<version>${alphanumeric-comparator.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>com.formdev</groupId>
+			<artifactId>flatlaf</artifactId>
+		</dependency>
 
 		<!-- Test scope dependencies -->
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>xmlunit</groupId>
+			<artifactId>xmlunit</artifactId>
+			<version>1.5</version>
+		</dependency>
+
 	</dependencies>
+
+	<profiles>
+		<profile>
+			<id>default</id>
+			<activation>
+				<activeByDefault>true</activeByDefault>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-surefire-plugin</artifactId>
+						<configuration>
+							<excludes>
+								<exclude>**/SerializationTest.java</exclude>
+							</excludes>
+						</configuration>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+		<profile>
+			<id>uiTests</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-surefire-plugin</artifactId>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+
 </project>

src/main/java/bdv/gui/AutosaveOptionsPanel.java

@@ -0,0 +1,184 @@
+package bdv.gui;
+
+import bigwarp.BigWarp;
+import bigwarp.BigWarpAutoSaver;
+import java.awt.Container;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.File;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSpinner;
+import javax.swing.JSpinner.DefaultEditor;
+import javax.swing.JTextField;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+public class AutosaveOptionsPanel extends JPanel
+{
+	private static final long serialVersionUID = 2449704984531905538L;
+
+	private final BigWarp< ? > bw;
+
+	private final SpinnerNumberModel savePeriodModel;
+	private final JSpinner autoSavePeriodSpinner;
+	private final JCheckBox doAutoSaveBox;
+	private final JTextField autoSaveFolderText;
+
+	private int lastAutoSaveFreq = 5;
+	private boolean updating = false;
+
+	public AutosaveOptionsPanel( final BigWarp< ? > bw, final Container content )
+	{
+		super( new GridBagLayout() );
+		this.bw = bw;
+
+		doAutoSaveBox = new JCheckBox( "Auto-save landmarks" );
+
+		final JLabel autoSavePeriodLabel = new JLabel( "Frequency (minutes)" );
+		autoSavePeriodSpinner = new JSpinner();
+		savePeriodModel = new SpinnerNumberModel( 0, 0, 0, 1 );
+		getAutoSavePeriodSpinner().setModel( savePeriodModel );
+		((DefaultEditor)getAutoSavePeriodSpinner().getEditor()).getTextField().setEditable( false );
+		((DefaultEditor)getAutoSavePeriodSpinner().getEditor()).getTextField().setEnabled( false );
+		getAutoSavePeriodSpinner().addChangeListener( new ChangeListener()
+		{
+			@Override
+			public void stateChanged( ChangeEvent e )
+			{
+				if ( getDoAutoSaveBox().isSelected() && !updating )
+				{
+					long periodMillis = ((Integer) savePeriodModel.getValue()).longValue() * 60000;
+					BigWarpAutoSaver autoSaver = bw.getAutoSaver();
+					if ( autoSaver != null )
+						autoSaver.stop();
+
+					bw.setAutoSaver( new BigWarpAutoSaver( bw, periodMillis ));
+				}
+			}
+		} );
+
+		getDoAutoSaveBox().addItemListener( new ItemListener()
+		{
+			@Override
+			public void itemStateChanged( ItemEvent e )
+			{
+				bw.stopAutosave();
+				if ( getDoAutoSaveBox().isSelected() )
+				{
+					updating = true;
+					((DefaultEditor)getAutoSavePeriodSpinner().getEditor()).getTextField().setEditable( true );
+					((DefaultEditor)getAutoSavePeriodSpinner().getEditor()).getTextField().setEnabled( true );
+					savePeriodModel.setMinimum( 1 );
+					savePeriodModel.setMaximum( 5000 );
+					savePeriodModel.setValue( lastAutoSaveFreq );
+
+					long periodMillis = ((Integer) savePeriodModel.getValue()).longValue() * 60000;
+					bw.setAutoSaver( new BigWarpAutoSaver( bw, periodMillis ));
+					updating = false;
+				}
+				else
+				{
+					lastAutoSaveFreq =  ((Integer) savePeriodModel.getValue());
+					savePeriodModel.setMinimum( 0 );
+					savePeriodModel.setMaximum( 0 );
+					savePeriodModel.setValue( 0 );
+					((DefaultEditor)getAutoSavePeriodSpinner().getEditor()).getTextField().setEditable( false );
+					((DefaultEditor)getAutoSavePeriodSpinner().getEditor()).getTextField().setEnabled( false );
+				}
+			}
+		} );
+
+		final JLabel destDirLabel = new JLabel( "Directory" );
+		final File startingFolder = bw.getBigwarpSettingsFolder();
+		autoSaveFolderText = new JTextField();
+		getAutoSaveFolderText().setText( startingFolder.getAbsolutePath() );
+
+		final JButton browseBtn = new JButton( "Browse" );
+		browseBtn.addActionListener( e -> {
+
+			final JFileChooser fileChooser = new JFileChooser();
+			fileChooser.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY );
+			fileChooser.setCurrentDirectory( startingFolder );
+
+			final int ret = fileChooser.showOpenDialog( content );
+			if ( ret == JFileChooser.APPROVE_OPTION )
+			{
+				final File folder = fileChooser.getSelectedFile();
+				getAutoSaveFolderText().setText( folder.getAbsolutePath() );
+				bw.getAutoSaver().setAutosaveFolder( folder );
+			}
+		} );
+
+		final GridBagConstraints gbc = new GridBagConstraints();
+		gbc.gridx = 1;
+		gbc.gridy = 0;
+		gbc.gridwidth = 1;
+		gbc.gridheight = 1;
+		gbc.weightx = 1.0;
+		gbc.anchor = GridBagConstraints.LINE_END;
+		gbc.fill = GridBagConstraints.NONE;
+		gbc.insets = new Insets( 5, 5, 5, 5 );
+
+		add( getDoAutoSaveBox(), gbc );
+
+		gbc.weightx = 1.0;
+		gbc.gridx = 2;
+		gbc.gridwidth = 1;
+		gbc.gridy = 0;
+		gbc.anchor = GridBagConstraints.LINE_END;
+		add( autoSavePeriodLabel, gbc );
+
+		gbc.gridx = 3;
+		gbc.gridwidth = 1;
+		gbc.weightx = 1.0;
+		gbc.anchor = GridBagConstraints.LINE_START;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		add( getAutoSavePeriodSpinner(), gbc );
+
+		gbc.gridy = 2;
+		gbc.gridx = 0;
+		gbc.gridwidth = 1;
+		gbc.weightx = 0.0;
+		gbc.anchor = GridBagConstraints.LINE_START;
+		gbc.fill = GridBagConstraints.NONE;
+		add( destDirLabel, gbc );
+
+		gbc.gridy = 2;
+		gbc.gridx = 1;
+		gbc.gridwidth = 3;
+		gbc.weightx = 1.0;
+		gbc.anchor = GridBagConstraints.LINE_START;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		add( getAutoSaveFolderText(), gbc );
+
+		gbc.gridx = 4;
+		gbc.weightx = 0.0;
+		gbc.anchor = GridBagConstraints.LINE_END;
+		gbc.fill = GridBagConstraints.NONE;
+		add( browseBtn, gbc );
+	}
+
+	public JSpinner getAutoSavePeriodSpinner()
+	{
+		return autoSavePeriodSpinner;
+	}
+
+	public JCheckBox getDoAutoSaveBox()
+	{
+		return doAutoSaveBox;
+	}
+
+	public JTextField getAutoSaveFolderText()
+	{
+		return autoSaveFolderText;
+	}
+
+}