Merge branch 'tpsRmMpicbg'

pom.xml

@@ -131,6 +131,7 @@
 		<dependency>
 			<groupId>jitk</groupId>
 			<artifactId>jitk-tps</artifactId>
+			<version>2.1.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>com.opencsv</groupId>

src/main/java/bdv/viewer/BigWarpOverlay.java

@@ -9,9 +9,8 @@
 
 import javax.swing.JTable;
 
-import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
-import mpicbg.models.CoordinateTransform;
 import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.realtransform.RealTransform;
 import bdv.gui.BigWarpLandmarkPanel;
 import bdv.viewer.state.ViewerState;
 import bigwarp.landmarks.LandmarkTableModel;
@@ -27,7 +26,7 @@ public class BigWarpOverlay {
 
 	protected LandmarkTableModel landmarkModel;
 
-	protected CoordinateTransform estimatedXfm;
+	protected RealTransform estimatedXfm;
 
 	protected boolean isTransformed = false;
 
@@ -214,13 +213,14 @@ else if( hoveredIndex == index )
 
 	/**
 	 * Update data to show in the overlay.
+	 * @param state the viewer state
 	 */
 	public void setViewerState( final ViewerState state )
 	{
 		this.state = state;
 	}
 
-	public void setEstimatedTransform( final ThinPlateR2LogRSplineKernelTransform estimatedXfm )
+	public void setEstimatedTransform( final RealTransform estimatedXfm )
 	{
 		this.estimatedXfm = estimatedXfm;
 	}

src/main/java/bigwarp/BigWarp.java

@@ -551,10 +551,10 @@ else if ( ARGBType.class.isInstance( baseType ) )
 
 	/**
 	 * TODO Make a PR that updates this method in InitializeViewerState in bdv-core
-	 * @param cumulativeMinCutoff
-	 * @param cumulativeMaxCutoff
-	 * @param state
-	 * @param setupAssignments
+	 * @param cumulativeMinCutoff the min image intensity
+	 * @param cumulativeMaxCutoff the max image intensity
+	 * @param state the viewer state 
+	 * @param setupAssignments the setup assignments 
 	 */
 	public static void initBrightness( final double cumulativeMinCutoff, final double cumulativeMaxCutoff, final ViewerState state, final SetupAssignments setupAssignments )
 	{
@@ -1026,6 +1026,7 @@ public int getSelectedUnpairedRow( boolean isMoving )
 	 *
 	 * @param ptarray the point location
 	 * @param isMoving is the point location in moving image space
+	 * @param viewer the viewer panel
 	 * @return an error string if an error occurred, empty string otherwise
 	 */
 	public String addPoint( final double[] ptarray, final boolean isMoving, final BigWarpViewerPanel viewer )
@@ -1074,6 +1075,7 @@ protected int selectedLandmark( final double[] pt, final boolean isMoving )
 	 *
 	 * @param pt the point location
 	 * @param isMoving is the point location in moving image space
+	 * @param selectInTable also select the landmark in the table 
 	 * @return the index of the selected landmark
 	 */
 	protected int selectedLandmark( final double[] pt, final boolean isMoving, final boolean selectInTable )
@@ -1774,8 +1776,9 @@ private void setTransformationAll( final ThinPlateR2LogRSplineKernelTransform tr
 		final WarpMagnitudeSource< ? > wmSrc = ( ( WarpMagnitudeSource< ? > ) sources.get( warpMagSourceIndex ).getSpimSource() );
 		final GridSource< ? > gSrc = ( ( GridSource< ? > ) sources.get( gridSourceIndex ).getSpimSource() );
 
-		wmSrc.setWarp( transform );
-		gSrc.setWarp( transform );
+		TpsTransformWrapper tpsRealXfm = new TpsTransformWrapper( 3, transform );
+		wmSrc.setWarp( tpsRealXfm );
+		gSrc.setWarp( tpsRealXfm );
 	}
 
 	public boolean restimateTransformation()
@@ -1840,6 +1843,7 @@ protected int detectNumDims()
 
 	/**
 	 * The display will be in 3d if any of the input sources are 3d.
+	 * @param sources the sources
 	 * @return dimension of the input sources
 	 */
 	protected static int detectNumDims( Collection< SourceAndConverter< ? > > sources )
@@ -2210,6 +2214,8 @@ public void mouseMoved( final MouseEvent e )
 
 		/**
 		 * Adds a point in the moving and fixed images at the same point.
+		 * @param pt the point
+		 * @param isMovingImage is the point in moving image space
 		 */
 		public void addFixedPoint( final RealPoint pt, final boolean isMovingImage )
 		{

src/main/java/bigwarp/landmarks/LandmarkTableModel.java

@@ -716,7 +716,6 @@ public void updateAllWarpedPoints()
 	 * necessary.
 	 * <p>
 	 * An action is taken if, for the input row if:
-	 * <p>
 	 * <ul><li>1) There is a point in moving space, and
 	 * <li>2) There is not a point in target space, and
 	 * <li>3) A transformation has been estimated.

src/main/java/bigwarp/source/GridRandomAccess.java

@@ -1,24 +1,24 @@
 package bigwarp.source;
 
-import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
-import mpicbg.models.CoordinateTransform;
+
 import net.imglib2.AbstractLocalizable;
 import net.imglib2.Localizable;
 import net.imglib2.RandomAccess;
+import net.imglib2.realtransform.RealTransform;
 import net.imglib2.type.numeric.RealType;
 
 public class GridRandomAccess< T extends RealType<T>> extends AbstractLocalizable implements RandomAccess< T >
 {
 
-	CoordinateTransform warp;
+	RealTransform warp;
 	T value;
 
 	protected GridRandomAccess( long[] dimensions )
 	{
 		this( dimensions, null, null );
 	}
 
-	protected GridRandomAccess( long[] dimensions, T value, CoordinateTransform warp )
+	protected GridRandomAccess( long[] dimensions, T value, RealTransform warp )
 	{
 		super( dimensions.length );
 		this.value = value;
@@ -30,8 +30,9 @@ public T get()
 
 		double[] mypt = new double[ this.numDimensions() ];
 		this.localize( mypt );
-
-		double[] warpRes = warp.apply( mypt );
+
+		double[] warpRes = new double[ warp.numTargetDimensions() ];
+		warp.apply( mypt, warpRes );
 
 		T out = value.copy();
 
@@ -62,8 +63,7 @@ private boolean withinRad( double[] pt1, double[] pt2, double rad )
 
 	public RandomAccess<T> copy() 
 	{
-		return new GridRandomAccess< T >( new long[ position.length ], value.copy(), 
-				((ThinPlateR2LogRSplineKernelTransform)warp) );
+		return new GridRandomAccess< T >( new long[ position.length ], value.copy(), warp );
 	}
 
 	public RandomAccess<T> copyRandomAccess() 

src/main/java/bigwarp/source/GridRandomAccessibleInterval.java

@@ -1,18 +1,18 @@
 package bigwarp.source;
 
-import mpicbg.models.CoordinateTransform;
 import net.imglib2.AbstractInterval;
 import net.imglib2.Interval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.realtransform.RealTransform;
 import net.imglib2.type.numeric.RealType;
 
 public class GridRandomAccessibleInterval<T extends RealType<T>> extends AbstractInterval implements RandomAccessibleInterval<T> 
 {
-	CoordinateTransform warp;
+	RealTransform warp;
 	GridRandomAccess< T > ra;
 
-	public GridRandomAccessibleInterval( Interval interval, T t, CoordinateTransform warp )
+	public GridRandomAccessibleInterval( Interval interval, T t, RealTransform warp )
 	{
 		super( interval );
 		this.warp = warp;

src/main/java/bigwarp/source/GridRealRandomAccess.java

@@ -1,20 +1,19 @@
 package bigwarp.source;
 
 import bigwarp.source.GridSource.GRID_TYPE;
-import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
-import mpicbg.models.CoordinateTransform;
 import net.imglib2.AbstractRealLocalizable;
 import net.imglib2.Localizable;
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealRandomAccess;
+import net.imglib2.realtransform.RealTransform;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.DoubleType;
 
 
 public class GridRealRandomAccess< T extends RealType<T>> extends AbstractRealLocalizable implements RealRandomAccess< T >
 {
 
-	protected CoordinateTransform warp;
+	protected RealTransform warp;
 
 	private T value;
 	private GRID_TYPE method = GRID_TYPE.MOD;
@@ -30,12 +29,12 @@ protected GridRealRandomAccess( double[] dimensions )
 		this( dimensions, null, null );
 	}
 
-	protected GridRealRandomAccess( double[] dimensions, T value, CoordinateTransform warp )
+	protected GridRealRandomAccess( double[] dimensions, T value, RealTransform warp )
 	{
 		this( dimensions, value, warp, GRID_TYPE.MOD );
 	}
 
-	protected GridRealRandomAccess( double[] dimensions, T value, CoordinateTransform warp, GRID_TYPE method )
+	protected GridRealRandomAccess( double[] dimensions, T value, RealTransform warp, GRID_TYPE method )
 	{
 		super( dimensions.length );
 		this.value = value;
@@ -92,10 +91,14 @@ private T getLine( double[] pt )
 	{
 		double[] warpRes;
 		if( warp != null )
-			warpRes = warp.apply( pt );
+		{
+			warpRes = new double[ warp.numTargetDimensions() ];
+			warp.apply( pt, warpRes );
+		}
 		else
+		{
 			warpRes = pt;
-
+		}
 		int nd = warpRes.length;
 		if( is2d )
 			nd = 2;
@@ -127,9 +130,7 @@ else if( tmp >= (gridSpacing - gridHalfWidth ) )
 			}
 
 		}
-
-//		if( i > 0 ) val /= i;
-
+
 		T out = value.copy();
 		if( val < gridWidth )
 		{
@@ -146,10 +147,15 @@ private T getMod( double[] pt )
 	{
 		double[] warpRes;
 		if( warp != null )
-			warpRes = warp.apply( pt );
+		{
+			warpRes = new double[ warp.numTargetDimensions() ];
+			warp.apply( pt, warpRes );
+		}
 		else
+		{
 			warpRes = pt;
-
+		}
+
 		double val = 0.0;
 		for( int d = 0; d < warpRes.length; d++ )
 		{
@@ -193,7 +199,7 @@ public RealRandomAccess<T> copy()
 		else
 		{
 			GridRealRandomAccess< T > ra = new GridRealRandomAccess< T >( new double[ position.length ], value.copy(), 
-					((ThinPlateR2LogRSplineKernelTransform)warp), this.method  );
+					warp, this.method  );
 			ra.gridSpacing = this.gridSpacing;
 			ra.gridWidth = this.gridWidth;
 			ra.gridHalfWidth = this.gridHalfWidth;

src/main/java/bigwarp/source/GridRealRandomAccessibleRealInterval.java

@@ -1,18 +1,18 @@
 package bigwarp.source;
 
-import mpicbg.models.CoordinateTransform;
 import net.imglib2.AbstractRealInterval;
 import net.imglib2.Interval;
 import net.imglib2.RealInterval;
 import net.imglib2.RealRandomAccess;
 import net.imglib2.RealRandomAccessibleRealInterval;
+import net.imglib2.realtransform.RealTransform;
 import net.imglib2.type.numeric.RealType;
 
 public class GridRealRandomAccessibleRealInterval<T extends RealType<T>> extends AbstractRealInterval implements RealRandomAccessibleRealInterval<T> 
 {
 	GridRealRandomAccess<T> ra;
 
-	public GridRealRandomAccessibleRealInterval( Interval interval, T t, CoordinateTransform warp )
+	public GridRealRandomAccessibleRealInterval( Interval interval, T t, RealTransform warp )
 	{
 		super( interval );
 		ra = new GridRealRandomAccess< T >( new double[ interval.numDimensions() ], t, warp );

src/main/java/bigwarp/source/GridSource.java

@@ -3,12 +3,12 @@
 import bdv.viewer.Interpolation;
 import bdv.viewer.Source;
 import bigwarp.BigWarp.BigWarpData;
-import mpicbg.models.CoordinateTransform;
 import mpicbg.spim.data.sequence.VoxelDimensions;
 import net.imglib2.Interval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.RealRandomAccessible;
 import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.realtransform.RealTransform;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.view.Views;
 
@@ -28,7 +28,7 @@ public enum GRID_TYPE { MOD, LINE };
 
 	protected T type;
 
-	public GridSource( String name, BigWarpData data, T t, CoordinateTransform warp  )
+	public GridSource( String name, BigWarpData data, T t, RealTransform warp  )
 	{
 		this.name = name;
 		this.type = t.copy();
@@ -62,7 +62,7 @@ public void setGridWidth( double width )
 //		
 //	}
 
-	public void setWarp( CoordinateTransform warp )
+	public void setWarp( RealTransform warp )
 	{
 		gridImg.ra.warp = warp;
 	}

src/main/java/bigwarp/source/WarpMagnitudeRandomAccess.java

@@ -1,17 +1,17 @@
 package bigwarp.source;
 
 import mpicbg.models.AbstractModel;
-import mpicbg.models.CoordinateTransform;
 import net.imglib2.AbstractRealLocalizable;
 import net.imglib2.Localizable;
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealRandomAccess;
+import net.imglib2.realtransform.RealTransform;
 import net.imglib2.type.numeric.RealType;
 
 public class WarpMagnitudeRandomAccess< T extends RealType<T>> extends AbstractRealLocalizable implements RealRandomAccess< T >
 {
 
-	CoordinateTransform warp;
+	RealTransform warp;
 	AbstractModel<?> base; 
 
 	T value;
@@ -21,7 +21,7 @@ protected WarpMagnitudeRandomAccess( double[] dimensions )
 		this( dimensions, null, null, null );
 	}
 
-	protected WarpMagnitudeRandomAccess( double[] dimensions, T value, CoordinateTransform warp, AbstractModel<?> base )
+	protected WarpMagnitudeRandomAccess( double[] dimensions, T value, RealTransform warp, AbstractModel<?> base )
 	{
 		super( dimensions.length );
 		if( warp != null)
@@ -40,9 +40,11 @@ public T get()
 		double[] mypt = new double[ this.numDimensions() ];
 		this.localize( mypt );
 
-		double[] warpRes = warp.apply( mypt );
+		double[] warpRes = new double[ warp.numTargetDimensions() ]; 
+		warp.apply( mypt, warpRes );
+
 		double[] baseRes = base.apply( mypt );
-		
+
 		double dist = 0.0;
 		for( int d = 0; d < warpRes.length; d++ )
 			dist += ( warpRes[ d ] - baseRes[ d ] ) * ( warpRes[ d ] - baseRes[ d ] );  

src/main/java/bigwarp/source/WarpMagnitudeRandomAccessibleInterval.java

@@ -2,22 +2,22 @@
 
 import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
 import mpicbg.models.AbstractModel;
-import mpicbg.models.CoordinateTransform;
 import net.imglib2.AbstractRealInterval;
 import net.imglib2.FinalInterval;
 import net.imglib2.FinalRealInterval;
 import net.imglib2.Interval;
 import net.imglib2.RealInterval;
 import net.imglib2.RealRandomAccess;
 import net.imglib2.RealRandomAccessibleRealInterval;
+import net.imglib2.realtransform.RealTransform;
 import net.imglib2.type.numeric.RealType;
 
 public class WarpMagnitudeRandomAccessibleInterval<T extends RealType<T>> extends AbstractRealInterval implements RealRandomAccessibleRealInterval<T> 
 {
 
 	WarpMagnitudeRandomAccess< T > ra;
 
-	public WarpMagnitudeRandomAccessibleInterval( Interval interval, T t, CoordinateTransform warp, AbstractModel<?> base )
+	public WarpMagnitudeRandomAccessibleInterval( Interval interval, T t, RealTransform warp, AbstractModel<?> base )
 	{
 		super( interval );
 		ra = new WarpMagnitudeRandomAccess< T >( new double[ interval.numDimensions() ], t, warp, base );