Merge pull request #187 from saalfeldlab/fix/export

fix: behavior of inverse estimation

Author: bogovicj

pom.xml

@@ -120,6 +120,7 @@
 
 		<jcommander.version>1.48</jcommander.version>
 		<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
+		<imglib2-realtransform.version>4.0.4</imglib2-realtransform.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
@@ -324,7 +325,6 @@
 			<artifactId>xmlunit</artifactId>
 			<version>1.5</version>
 		</dependency>
-
 	</dependencies>
 
 	<profiles>

src/main/java/bigwarp/BigWarp.java

@@ -618,9 +618,17 @@ public boolean accept( final File f )
 			viewerFrameQ.getTransformBehaviours().updateKeyConfig( keymap.getConfig() );
 		} );
 
+		// default inverse tolerance is 0.5 a pixell in the target space
+		if ( data.numTargetSources() > 0 )
+		{
+			final double res = data.getTargetSource( 0 ).getSpimSource().getVoxelDimensions().dimension( 0 );
+			bwTransform.setInverseTolerance( 0.5 * res );
+		}
+
 		// this call has to come after the actions are set
 		warpVisDialog.setActions();
 		warpVisDialog.toleranceSpinner.setValue( bwTransform.getInverseTolerance() );
+		warpVisDialog.maxIterSpinner.setValue( bwTransform.getInverseMaxIterations() );
 
 		setUpViewerMenu( viewerFrameP );
 		setUpViewerMenu( viewerFrameQ );
@@ -669,8 +677,6 @@ public boolean accept( final File f )
 		if( data.sources.size() > 0 )
 			initialize();
 
-
-
 //		viewerQ.state().changeListeners().add(warpVisDialog.transformGraphPanel);
 
 		SwingUtilities.invokeLater( () -> {

src/main/java/bigwarp/WarpVisFrame.java

@@ -125,7 +125,6 @@ public class WarpVisFrame extends JDialog
 	// autosave
 	private final AutosaveOptionsPanel autoSaveOptionsPanel;
 
-
 	public static final int minGridSpacing = 5;
 	public static final int maxGridSpacing = 400;
 	public static final int defaultGridSpacing = 100;
@@ -280,7 +279,7 @@ public void stateChanged( ChangeEvent e )
 
 		final JPanel maxIterPanel = new JPanel();
 		maxIterSpinner = new JSpinner();
-		final SpinnerNumberModel itermodel = new SpinnerNumberModel( 200, 1, 5000, 1 );
+		final SpinnerNumberModel itermodel = new SpinnerNumberModel( 1000, 1, 5000, 1 );
 		maxIterSpinner.setModel( itermodel );
 		maxIterSpinner.addChangeListener( new ChangeListener()
 		{
@@ -590,10 +589,6 @@ else if( setWarpMagButton.isSelected() )
 			setGridOptionsVisibility( false );
 			setMagOptionsVisibility( true );
 		}
-		else
-		{
-//			System.out.println(" UHOH ");
-		}
 		pack();
 	}
 

src/main/java/bigwarp/transforms/BigWarpTransform.java

@@ -86,7 +86,7 @@ public class BigWarpTransform
 
 	private double inverseTolerance = 0.5;
 
-	private int maxIterations = 200;
+	private int maxIterations = 1000;
 
 	private RealRandomAccessible<? extends RealType<?>> lambdaRaw;
 
@@ -273,7 +273,8 @@ public InvertibleRealTransform getTransformation( final int index, final boolean
 			final WrappedIterativeInvertibleRealTransform<?> tpsXfm = (WrappedIterativeInvertibleRealTransform< ? >) solver.solve( tableModel, index );
 			tpsXfm.getOptimzer().setMaxIters(maxIterations);
 			tpsXfm.getOptimzer().setTolerance(inverseTolerance);
-			tpsXfm.getOptimzer().setMaxStep(500);
+			tpsXfm.getOptimzer().setBeta(0.5);
+			tpsXfm.getOptimzer().setMaxStep(1000);
 			invXfm = tpsXfm;
 		}
 		else