add code to rewrite Luxendo XML's for BigStitcher

src/main/java/net/preibisch/mvrecon/headless/definedataset/RewriteLuxendoXML.java

@@ -0,0 +1,124 @@
+package net.preibisch.mvrecon.headless.definedataset;
+
+import java.util.HashMap;
+import java.util.concurrent.Callable;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import mpicbg.spim.data.SpimData;
+import mpicbg.spim.data.XmlIoSpimData;
+import mpicbg.spim.data.sequence.Angle;
+import mpicbg.spim.data.sequence.Channel;
+import mpicbg.spim.data.sequence.Illumination;
+import mpicbg.spim.data.sequence.SequenceDescription;
+import mpicbg.spim.data.sequence.Tile;
+import mpicbg.spim.data.sequence.ViewDescription;
+import net.imglib2.util.Pair;
+import net.imglib2.util.ValuePair;
+import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
+import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
+import picocli.CommandLine;
+import picocli.CommandLine.Option;
+
+public class RewriteLuxendoXML implements Callable<Void> 
+{
+	@Option(names = {"-i", "--input"}, required = true, description = "input XML written by Luxendo MuviSPIM, e.g. -i /home/dataset.xml")
+	private String input = null;
+
+	@Option(names = {"-o", "--output"}, required = false, description = "output XML for the same Luxendo MuviSPIM containing BigStitcher attributes, e.g. -i /home/dataset_bigstitcher.xml")
+	private String output = null;
+
+	// e.g. stack_0-x00-y00_channel_1_obj_right_cam_long
+	// patterns: stack_0-x{xx}-y{yy}_channel_{c}_obj_right_cam_long
+	final static String searchX = "stack_0-x";
+	final static String searchY = "-y";
+	final static String searchCh = "_channel_";
+	final static String searchObj = "_obj_";
+
+	@Override
+	public Void call() throws Exception
+	{
+		// angle and illumination are constant (for now)
+		final Angle angle = new Angle( 0 );
+		final Illumination illum = new Illumination( 0 );
+
+		try
+		{
+			System.out.println( "Loading '" + input + "' ... ");
+
+			final XmlIoSpimData io = new XmlIoSpimData();
+			final SpimData spimData = io.load( input );
+
+			final SpimData2 spimDataOut = SpimData2.convert( spimData );
+			final SequenceDescription s = spimDataOut.getSequenceDescription();
+
+			final HashMap< Pair<Integer, Integer>, Integer > tileIds = new HashMap<>();
+			final AtomicInteger countTileId = new AtomicInteger(0);
+
+			for ( final ViewDescription vd : s.getViewDescriptions().values() )
+			{
+				final String name = vd.getViewSetup().getName();
+
+				System.out.print( "Parsing ViewSetup: " + name + " ... " );
+
+				final int[] p = parseName(name); //x,y,ch
+				tileIds.computeIfAbsent( new ValuePair<>(p[0], p[1]), k -> countTileId.getAndIncrement() );
+
+				System.out.println( "x=" + p[0] + ", y=" + p[1] + ", ch=" + p[2] );
+			}
+
+			for ( final ViewDescription vd : s.getViewDescriptions().values() )
+			{
+				final String name = vd.getViewSetup().getName();
+
+				final int[] p = parseName(name); //x,y,ch
+				final int tileId = tileIds.get( new ValuePair<>(p[0], p[1]) );
+				final int channelId = p[2];
+
+				System.out.println( "Adding Attributes to ViewSetup: " + name +": x=" + p[0] + ", y=" + p[1] + ", tileId=" + tileId + ", ch=" + p[2] + ", channelId=" + channelId );
+
+				// set missing attributes
+				vd.getViewSetup().setAttribute( angle );
+				vd.getViewSetup().setAttribute( illum );
+				vd.getViewSetup().setAttribute( new Channel( channelId ) );
+				vd.getViewSetup().setAttribute( new Tile(tileId, "x=" + p[0] + ", y=" + p[1] ) );
+			}
+
+			System.out.println( "Saving '" + output + "' ... ");
+
+			XmlIoSpimData2.initN5Writing = false;
+			final XmlIoSpimData2 io2 = new XmlIoSpimData2( "" );
+			io2.save(spimDataOut, output);
+
+			System.out.println( "done.");
+		}
+		catch ( Exception e )
+		{
+			System.err.println( "Error rewriting '" + input + "': " + e );
+			e.printStackTrace();
+		}
+
+		return null;
+	}
+
+	public static int[] parseName( final String name )
+	{
+		final int x_i = name.indexOf( searchX );
+		final int y_i = name.indexOf( searchY, x_i);
+		final int ch_i = name.indexOf( searchCh, y_i);
+		final int obj_i = name.indexOf( searchObj, ch_i );
+
+		final String x_string = name.substring(x_i+searchX.length(), y_i);
+		final String y_string = name.substring(y_i+searchY.length(), ch_i);
+		final String ch_string = name.substring(ch_i+searchCh.length(), obj_i);
+
+		final int x = Integer.parseInt( x_string );
+		final int y = Integer.parseInt( y_string );
+		final int ch = Integer.parseInt( ch_string );
+
+		return new int[] {x,y,ch};
+	}
+
+	public static final void main(final String... args) {
+		new CommandLine( new RewriteLuxendoXML() ).execute( args );
+	}
+}