Added CreateXmlForImarisPlugIn to write .xml file for .ims file

src/main/java/bdv/ij/CreateXmlForImarisPlugIn.java

@@ -0,0 +1,171 @@
+/*-
+ * #%L
+ * Fiji plugins for starting BigDataViewer and exporting data.
+ * %%
+ * Copyright (C) 2014 - 2023 BigDataViewer developers.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+package bdv.ij;
+
+import java.awt.FileDialog;
+import java.awt.Frame;
+import java.io.File;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import javax.swing.JFileChooser;
+import javax.swing.filechooser.FileFilter;
+
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
+import bdv.BigDataViewer;
+import bdv.ij.util.ProgressWriterIJ;
+import bdv.img.imaris.Imaris;
+import bdv.spimdata.SpimDataMinimal;
+import bdv.spimdata.XmlIoSpimDataMinimal;
+import bdv.viewer.ViewerOptions;
+import ij.IJ;
+import ij.ImageJ;
+import ij.Prefs;
+import mpicbg.spim.data.SpimDataException;
+
+@Plugin(type = Command.class,
+	menuPath = "Plugins>BigDataViewer>Create XML for Imaris file")
+public class CreateXmlForImarisPlugIn implements Command
+{
+	static String lastDatasetPath = "";
+
+	public static void main( final String[] args )
+	{
+		ImageJ.main( args );
+		new CreateXmlForImarisPlugIn().run();
+	}
+	@Override
+	public void run()
+	{
+		if ( Prefs.setIJMenuBar )
+			System.setProperty( "apple.laf.useScreenMenuBar", "true" );
+
+		File file = null;
+
+		if ( Prefs.useJFileChooser )
+		{
+			final JFileChooser fileChooser = new JFileChooser();
+			fileChooser.setSelectedFile( new File( lastDatasetPath ) );
+			fileChooser.setFileFilter( new FileFilter()
+			{
+				@Override
+				public String getDescription()
+				{
+					return "ims files";
+				}
+
+				@Override
+				public boolean accept( final File f )
+				{
+					if ( f.isDirectory() )
+						return true;
+					if ( f.isFile() )
+					{
+				        final String s = f.getName();
+				        final int i = s.lastIndexOf('.');
+				        if (i > 0 &&  i < s.length() - 1) {
+				            final String ext = s.substring(i+1).toLowerCase();
+				            return ext.equals( "ims" );
+				        }
+					}
+					return false;
+				}
+			} );
+
+			final int returnVal = fileChooser.showOpenDialog( null );
+			if ( returnVal == JFileChooser.APPROVE_OPTION )
+				file = fileChooser.getSelectedFile();
+		}
+		else // use FileDialog
+		{
+			final FileDialog fd = new FileDialog( ( Frame ) null, "Open", FileDialog.LOAD );
+			fd.setDirectory( new File( lastDatasetPath ).getParent() );
+			fd.setFile( new File( lastDatasetPath ).getName() );
+			final AtomicBoolean workedWithFilenameFilter = new AtomicBoolean( false );
+			fd.setFilenameFilter( new FilenameFilter()
+			{
+				private boolean firstTime = true;
+
+				@Override
+				public boolean accept( final File dir, final String name )
+				{
+					if ( firstTime )
+					{
+						workedWithFilenameFilter.set( true );
+						firstTime = false;
+					}
+
+					final int i = name.lastIndexOf( '.' );
+					if ( i > 0 && i < name.length() - 1 )
+					{
+						final String ext = name.substring( i + 1 ).toLowerCase();
+						return ext.equals( "ims" );
+					}
+					return false;
+				}
+			} );
+			fd.setVisible( true );
+			if ( !workedWithFilenameFilter.get() )
+			{
+				fd.setFilenameFilter( null );
+				fd.setVisible( true );
+			}
+			final String filename = fd.getFile();
+			if ( filename != null )
+			{
+				file = new File( fd.getDirectory() + filename );
+			}
+		}
+
+		if ( file != null )
+		{
+			try
+			{
+				final String imsFilename = file.getAbsolutePath();
+				lastDatasetPath = imsFilename;
+				final SpimDataMinimal spimData = Imaris.openIms( imsFilename );
+				final String xmlFilename = xmlFilename( imsFilename );
+				new XmlIoSpimDataMinimal().save( spimData, xmlFilename );
+				IJ.showMessage( "created " + xmlFilename );
+			}
+			catch ( final IOException | SpimDataException e )
+			{
+				throw new RuntimeException( e );
+			}
+		}
+	}
+
+	private static String xmlFilename( String s )
+	{
+		String f = s.endsWith( ".ims" ) ? s.substring( 0, s.length() - 4 ) : s;
+		if ( !new File( f + ".xml" ).exists() )
+			return f + ".xml";
+
+		int i = 2;
+		while ( new File( f + i + ".xml" ).exists() )
+			++i;
+		return f + i + ".xml";
+	}
+}