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fix: jacobian determinant source for 2D transformations
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* minor cleanup and optimization
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@bogovicj
bogovicj committed Oct 30, 2024
1 parent bac6855 commit bcf6b1a
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Showing 2 changed files with 36 additions and 41 deletions.
42 changes: 24 additions & 18 deletions src/main/java/bigwarp/source/JacobianDeterminantRandomAccess.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,9 @@ public class JacobianDeterminantRandomAccess< T extends RealType<T>> extends Abs
{
protected DifferentiableRealTransform transform;

final private T value;
final double[] warpRes;
private final T value;
private final double[] x;
private final double[] x3;

protected JacobianDeterminantRandomAccess( double[] dimensions )
{
Expand All @@ -50,10 +51,11 @@ protected JacobianDeterminantRandomAccess( double[] dimensions )

protected JacobianDeterminantRandomAccess( final double[] dimensions, final T value, final DifferentiableRealTransform transform )
{
super( dimensions.length );
super( 3 );
setTransform( transform );
this.value = value;
warpRes = new double[ numDimensions() ];
this.value = value.copy();
x = new double[ dimensions.length ];
x3 = new double[3];
}

public void setTransform( final DifferentiableRealTransform transform )
Expand All @@ -67,29 +69,29 @@ public void setTransform( final DifferentiableRealTransform transform )
@Override
public T get()
{
// TODO check the below
// copy value here so this is thread safe
T out = value.copy();
if( transform == null )
{
out.setZero();
return out;
value.setOne();
return value;
}

// compute the jacobian determinant at this point
double[] x = new double[ numDimensions() ];
localize( x );
AffineTransform jacobian = transform.jacobian( x );
DMatrixRMaj jacMtx = new DMatrixRMaj();
localize( x3 );
System.arraycopy(x3, 0, x, 0, x.length);

final AffineTransform jacobian = transform.jacobian( x );
final DMatrixRMaj jacMtx = new DMatrixRMaj();
jacMtx.data = jacobian.getRowPackedCopy();
out.setReal( CommonOps_DDRM.det( jacMtx ) );
value.setReal( CommonOps_DDRM.det( jacMtx ) );

return out;
return value;
}

public RealRandomAccess<T> copy()
{
return new JacobianDeterminantRandomAccess< T >( new double[ position.length ], value.copy(),
transform );
return new JacobianDeterminantRandomAccess<T>(new double[x.length], value.copy(), transform);
}

public RealRandomAccess<T> copyRandomAccess()
Expand Down Expand Up @@ -266,10 +268,14 @@ public static class JacobianDeterminantRandomAccessibleInterval<T extends RealTy
{
protected final JacobianDeterminantRandomAccess< T > ra;

public JacobianDeterminantRandomAccessibleInterval( Interval interval, T t, DifferentiableRealTransform warp )
public JacobianDeterminantRandomAccessibleInterval( Interval interval, T t, DifferentiableRealTransform transform )
{
super( interval );
ra = new JacobianDeterminantRandomAccess< T >( new double[ interval.numDimensions() ], t, warp );
int nd = interval.dimension(2) < 2 ? 2 : 3;
if( nd == 2)
ra = new JacobianDeterminantRandomAccess< T >( new double[ nd ], t, transform );
else
ra = new JacobianDeterminantRandomAccess< T >( new double[ nd ], t, transform );
}

@Override
Expand Down
35 changes: 12 additions & 23 deletions src/main/java/bigwarp/source/JacobianDeterminantSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,6 @@
*/
package bigwarp.source;

import java.util.Arrays;

import bdv.viewer.Interpolation;
import bdv.viewer.Source;
import bigwarp.BigWarpData;
Expand All @@ -32,7 +30,6 @@
import net.imglib2.Cursor;
import net.imglib2.Interval;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.RealRandomAccess;
import net.imglib2.RealRandomAccessible;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.realtransform.BoundingBoxEstimation;
Expand All @@ -58,20 +55,13 @@ public JacobianDeterminantSource( String name, BigWarpData<?> data, T t )
{
this.name = name;
this.type = t;

sourceData = data;

//RandomAccessibleInterval<?> fixedsrc = sourceData.sources.get( 1 ).getSpimSource().getSource( 0, 0 );
// interval = sourceData.sources.get( sourceData.targetSourceIndices[ 0 ] ).getSpimSource().getSource( 0, 0 );
// interval = sourceData.getTargetSource( 0 ).getSpimSource().getSource( 0, 0 );

final BoundingBoxEstimation bbe = new BoundingBoxEstimation();
final AffineTransform3D affine = new AffineTransform3D();
data.getTargetSource( 0 ).getSpimSource().getSourceTransform( 0, 0, affine );
interval = bbe.estimatePixelInterval( affine, data.getTargetSource( 0 ).getSpimSource().getSource( 0, 0 ) );
interval = bbe.estimatePixelInterval( affine, data.getTargetSource( 0 ).getSpimSource().getSource( 0, 0 ) );


// VoxelDimensions srcVoxDims = sourceData.sources.get( sourceData.targetSourceIndices[ 0 ] ).getSpimSource().getVoxelDimensions();
VoxelDimensions srcVoxDims = sourceData.getTargetSource( 0 ).getSpimSource().getVoxelDimensions();
String unit = "pix";
if( srcVoxDims != null )
Expand All @@ -81,7 +71,7 @@ public JacobianDeterminantSource( String name, BigWarpData<?> data, T t )

jacDetImg = new JacobianDeterminantRandomAccess.JacobianDeterminantRandomAccessibleInterval< T >( interval, t, null );
}

public double getMax( LandmarkTableModel lm )
{
double maxVal = 0.0;
Expand All @@ -108,31 +98,30 @@ public void setTransform( final DifferentiableRealTransform transform )
jacDetImg.setTransform( transform );
}

@Deprecated
public void debug( double[] pt )
{
RealRandomAccess<T> rra = jacDetImg.realRandomAccess();

rra.setPosition( pt );

System.out.println("at : " + Arrays.toString( pt ) );
System.out.println( "get val: " + rra.get());

// RealRandomAccess<T> rra = jacDetImg.realRandomAccess();
//
// rra.setPosition( pt );
//
// System.out.println("at : " + Arrays.toString( pt ) );
// System.out.println( "get val: " + rra.get());
//
// double[] warpRes = new double[ jacDetImg.ra.warp.numTargetDimensions() ];
// jacDetImg.ra.warp.apply( pt, warpRes );
//
// System.out.println( "base res: " + baseRes[0] + " " + baseRes[1]);
// System.out.println( "warp res: " + warpRes[0] + " " + warpRes[1]);

}

public double[] minMax()
{
double[] minmax = new double[ 2 ];
final double[] minmax = new double[ 2 ];
minmax[ 0 ] = Double.MAX_VALUE;
minmax[ 1 ] = Double.MIN_VALUE;

Cursor<T> curs = Views.iterable( this.getSource( 0,0 ) ).cursor();

final Cursor<T> curs = this.getSource( 0,0 ).cursor();
while( curs.hasNext() )
{
double val = curs.next().getRealDouble();
Expand Down

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