From 3f7a32bae85b8e6e8efb1647ece9046773973ff7 Mon Sep 17 00:00:00 2001
From: John Bogovic <bogovicj@janelia.hhmi.org>
Date: Wed, 15 Jul 2026 13:38:07 -0400
Subject: [PATCH] feat: fix RealTransformFiniteDerivatives copy

* expose step size in constructor
* expose step size in WrappedIterativeInvertibleRealTransform
---
 .../RealTransformFiniteDerivatives.java       | 30 ++++++++++++-------
 ...appedIterativeInvertibleRealTransform.java | 20 +++++++++++--
 2 files changed, 37 insertions(+), 13 deletions(-)

diff --git a/src/main/java/net/imglib2/realtransform/inverse/RealTransformFiniteDerivatives.java b/src/main/java/net/imglib2/realtransform/inverse/RealTransformFiniteDerivatives.java
index bb9b6de..1c84a85 100644
--- a/src/main/java/net/imglib2/realtransform/inverse/RealTransformFiniteDerivatives.java
+++ b/src/main/java/net/imglib2/realtransform/inverse/RealTransformFiniteDerivatives.java
@@ -53,13 +53,30 @@ public class RealTransformFiniteDerivatives extends AbstractDifferentiableRealTr
 
 	protected double step;
 
+	private int ndims;
+	private double[] p;
+	private double[] q;
+	private double[] qc;
+	private double[][] newjac;
+
 	public RealTransformFiniteDerivatives( final RealTransform transform )
+	{
+		this( transform, 0.01);
+	}
+
+	public RealTransformFiniteDerivatives( final RealTransform transform, double step )
 	{
 		this.transform = transform;
 		int srcD = transform.numSourceDimensions();
 		int tgtD = transform.numTargetDimensions();
 		jacobian = new AffineTransform( srcD > tgtD ? srcD : tgtD );
-		step = 0.01;
+		this.step = step;
+
+		ndims = numSourceDimensions();
+		p = new double[ ndims ];
+		q = new double[ ndims ];
+		qc = new double[ ndims ];
+		newjac = new double[ ndims ][ ndims+1 ];
 	}
 
 	public void setStep( double step )
@@ -89,7 +106,7 @@ public void apply( RealLocalizable source, RealPositionable target )
 
 	public RealTransformFiniteDerivatives copy()
 	{
-		return new RealTransformFiniteDerivatives( transform.copy() );
+		return new RealTransformFiniteDerivatives( transform.copy(), step );
 	}
 
 	/**
@@ -102,15 +119,7 @@ public RealTransformFiniteDerivatives copy()
 	 */
 	public AffineTransform jacobian( double[] x )
 	{
-		int ndims = numSourceDimensions();
-		double[] p = new double[ ndims ];
-		double[] q = new double[ ndims ];
-		double[] qc = new double[ ndims ];
-
-		double[][] newjac = new double[ ndims ][ ndims+1 ];
-
 		transform.apply( x, qc );
-
 		for ( int i = 0; i < ndims; i++ )
 		{
 			for ( int j = 0; j < ndims; j++ )
@@ -127,7 +136,6 @@ public AffineTransform jacobian( double[] x )
 			}
 		}
 		jacobian.set( newjac );
-
 		return jacobian;
 	}
 	
diff --git a/src/main/java/net/imglib2/realtransform/inverse/WrappedIterativeInvertibleRealTransform.java b/src/main/java/net/imglib2/realtransform/inverse/WrappedIterativeInvertibleRealTransform.java
index 88da041..7f02547 100644
--- a/src/main/java/net/imglib2/realtransform/inverse/WrappedIterativeInvertibleRealTransform.java
+++ b/src/main/java/net/imglib2/realtransform/inverse/WrappedIterativeInvertibleRealTransform.java
@@ -49,15 +49,31 @@ public class WrappedIterativeInvertibleRealTransform< T extends RealTransform >
 
 	public WrappedIterativeInvertibleRealTransform( final T xfm )
 	{
-		this.forwardTransform = xfm;
+		this(xfm, 0.01);
+	}
 
+	/**
+	 * WrappedIterativeInvertibleRealTransform constructor. Wrapps the given
+	 * transform with a {@link RealTransformFiniteDerivatives} if needed, using
+	 * the provided step.
+	 * 
+	 * @param xfm
+	 *            transformation to wrap
+	 * @param finiteDerivativeStep
+	 *            step size for finite derivatives if needed
+	 */
+	public WrappedIterativeInvertibleRealTransform( final T xfm, double finiteDerivativeStep )
+	{
+		this.forwardTransform = xfm;
 		if( xfm instanceof DifferentiableRealTransform )
 		{
 			differentiableTransform = (DifferentiableRealTransform) xfm;
 		}
 		else
 		{
-			differentiableTransform = new RealTransformFiniteDerivatives( xfm );
+			final RealTransformFiniteDerivatives tformFinite = new RealTransformFiniteDerivatives( xfm );
+			tformFinite.setStep(finiteDerivativeStep);
+			differentiableTransform  = tformFinite;
 		}
 
 		inverseTransform = new InverseRealTransformGradientDescent( xfm.numSourceDimensions(), differentiableTransform );