chore!: use ejml DMatrixRMaj instead of Jama Matrix

pom.xml

@@ -168,6 +168,9 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
 		<imglib2.version>7.0.1</imglib2.version>
+		<jitk-tps.version>3.0.4</jitk-tps.version>
+		<ejml-core.version>0.41</ejml-core.version>
+		<ejml-ddense.version>0.41</ejml-ddense.version>
 	</properties>
 
 	<dependencies>
@@ -179,8 +182,14 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 
 		<!-- Third-party dependencies -->
 		<dependency>
-			<groupId>gov.nist.math</groupId>
-			<artifactId>jama</artifactId>
+			<groupId>org.ejml</groupId>
+			<artifactId>ejml-core</artifactId>
+			<version>${ejml-core.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.ejml</groupId>
+			<artifactId>ejml-ddense</artifactId>
+			<version>${ejml-ddense.version}</version>
 		</dependency>
 
 		<!-- Test dependencies -->

src/main/java/net/imglib2/realtransform/AbstractAffineTransform.java

@@ -11,13 +11,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -34,33 +34,33 @@
 
 package net.imglib2.realtransform;
 
+import org.ejml.data.DMatrixRMaj;
+
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealPoint;
 import net.imglib2.RealPositionable;
-import Jama.Matrix;
 
 /**
  * An abstract implementation of an affine transformation that returns default
  * values referring to the identity transformation for all fields.  This
  * implementation is not thread safe.  Create a {@link #copy()} for each
  * consumer.
- * 
+ *
  * @author Stephan Saalfeld
  */
 public abstract class AbstractAffineTransform implements AffineGet, AffineSet
 {
 	final protected int n;
 
-	final protected Matrix a;
+	final protected DMatrixRMaj a;
 
 	final protected double[] t, tmp;
 
 	final protected RealPoint[] ds;
 
-	protected AbstractAffineTransform( final Matrix a, final double[] t )
+	protected AbstractAffineTransform( final DMatrixRMaj a, final double[] t )
 	{
-		assert a.getRowDimension() == t.length &&
-				a.getColumnDimension() == t.length: "The passed arrays must be n*n and the t-vector n.";
+		assert a.getNumRows() == t.length && a.getNumCols() == t.length: "The passed arrays must be n*n and the t-vector n.";
 
 		this.n = t.length;
 		this.a = a;
@@ -73,17 +73,17 @@ protected AbstractAffineTransform( final Matrix a, final double[] t )
 		updateDs();
 	}
 
-	public AbstractAffineTransform( final Matrix matrix )
+	public AbstractAffineTransform( final DMatrixRMaj matrix )
 	{
-		assert matrix.getRowDimension() == matrix.getColumnDimension() - 1: "The passed affine matrix must be of the format (n-1)*n.";
+		assert matrix.getNumRows() == matrix.getNumCols() - 1: "The passed affine matrix must be of the format (n-1)*n.";
 
-		n = matrix.getRowDimension();
-		a = new Matrix( n, n );
+		n = matrix.getNumRows();
+		a = new DMatrixRMaj( n, n );
 		t = new double[ n ];
 		tmp = new double[ n ];
 		ds = new RealPoint[ n ];
 
-		a.setMatrix( 0, n - 1, 0, n - 1, matrix );
+		a.setTo( matrix );
 		for ( int r = 0; r < n; ++r )
 		{
 			t[ r ] = matrix.get( r, n );
@@ -95,7 +95,7 @@ public AbstractAffineTransform( final Matrix matrix )
 	public AbstractAffineTransform( final int n )
 	{
 		this.n = n;
-		a = new Matrix( n, n );
+		a = new DMatrixRMaj( n, n );
 		t = new double[ n ];
 		tmp = new double[ n ];
 		ds = new RealPoint[ n ];
@@ -136,7 +136,7 @@ public int numTargetDimensions()
 	{
 		return n;
 	}
-	
+
 	@Override
 	public void apply( final double[] source, final double[] target )
 	{
@@ -148,11 +148,11 @@ public void apply( final double[] source, final double[] target )
 			for ( int c = 0; c < n; ++c )
 				tmp[ r ] += source[ c ] * a.get( r, c );
 		}
-		
+
 		for ( int r = 0; r < n; ++r )
 			target[ r ] = tmp[ r ] + t[ r ];
 	}
-	
+
 	@Override
 	public void apply( final float[] source, final float[] target )
 	{
@@ -164,7 +164,7 @@ public void apply( final float[] source, final float[] target )
 			for ( int c = 0; c < n; ++c )
 				tmp[ r ] += source[ c ] * a.get( r, c );
 		}
-		
+
 		for ( int r = 0; r < n; ++r )
 			target[ r ] = ( float )( tmp[ r ] + t[ r ] );
 	}
@@ -180,7 +180,7 @@ public void apply( final RealLocalizable source, final RealPositionable target )
 			for ( int c = 0; c < n; ++c )
 				tmp[ r ] += source.getDoublePosition( c ) * a.get( r, c );
 		}
-		
+
 		for ( int r = 0; r < n; ++r )
 			target.setPosition( tmp[ r ] + t[ r ], r );
 	}

src/main/java/net/imglib2/realtransform/AffineGet.java

@@ -11,13 +11,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -41,15 +41,15 @@
  * An <em>n</em>-dimensional affine transformation whose <em>n</em>&times;(
  * <em>n</em>+1) affine transformation matrix can be accessed via row and column
  * index.
- * 
+ *
  * @author Stephan Saalfeld
  */
 public interface AffineGet extends InvertibleRealTransform, EuclideanSpace
 {
 	/**
 	 * Get a field of the <em>n</em>&times;(<em>n</em>+1) affine transformation
 	 * matrix.
-	 * 
+	 *
 	 * @param row
 	 *            the row index
 	 * @param column
@@ -60,15 +60,15 @@ public interface AffineGet extends InvertibleRealTransform, EuclideanSpace
 
 	/**
 	 * Get a copy of the <em>n</em>&times;(<em>n</em>+1) affine transformation
-	 * matrix as a row packed array similar to Jama.
-	 * 
+	 * matrix as a row packed array.
+	 *
 	 * @return the array of values
 	 */
 	public double[] getRowPackedCopy();
 
 	/**
 	 * Get the constant partial differential vector for dimension d.
-	 * 
+	 *
 	 * @param d
 	 *            the dimension
 	 * @return the partial differential vector

src/main/java/net/imglib2/realtransform/AffineTransform.java

@@ -11,13 +11,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -34,7 +34,9 @@
 
 package net.imglib2.realtransform;
 
-import Jama.Matrix;
+import org.ejml.data.DMatrixRMaj;
+import org.ejml.dense.row.CommonOps_DDRM;
+
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealPositionable;
 import net.imglib2.concatenate.Concatenable;
@@ -57,7 +59,7 @@ public AffineTransform( final int n )
 		inverse.updateDs();
 	}
 
-	protected AffineTransform( final Matrix a, final double[] t )
+	protected AffineTransform( final DMatrixRMaj a, final double[] t )
 	{
 		super( a, t );
 
@@ -66,7 +68,7 @@ protected AffineTransform( final Matrix a, final double[] t )
 		inverse.updateDs();
 	}
 
-	public AffineTransform( final Matrix matrix )
+	public AffineTransform( final DMatrixRMaj matrix )
 	{
 		super( matrix );
 
@@ -101,8 +103,7 @@ protected void invertT()
 
 	protected void invert()
 	{
-		final Matrix ii = a.inverse();
-		inverse.a.setMatrix( 0, n - 1, 0, n - 1, ii );
+		CommonOps_DDRM.invert( a, inverse.a );
 		invertT();
 	}
 
@@ -175,7 +176,7 @@ public AffineTransform concatenate( final AffineGet affine )
 	{
 		assert affine.numSourceDimensions() == n: "Dimensions do not match.";
 
-		final Matrix matrix = new Matrix( n, n );
+		final DMatrixRMaj matrix = new DMatrixRMaj(n, n);
 		final double[] translation = new double[ n ];
 		for ( int r = 0; r < n; ++r )
 		{
@@ -191,7 +192,7 @@ public AffineTransform concatenate( final AffineGet affine )
 				tr += get( r, k ) * affine.get( k, n );
 			translation[ r ] = tr;
 		}
-		a.setMatrix( 0, n - 1, 0, n - 1, matrix );
+		a.setTo( matrix );
 		System.arraycopy( translation, 0, t, 0, t.length );
 
 		updateDs();
@@ -212,7 +213,7 @@ public AffineTransform preConcatenate( final AffineGet affine )
 	{
 		assert affine.numSourceDimensions() == n: "Dimensions do not match.";
 
-		final Matrix matrix = new Matrix( n, n );
+		final DMatrixRMaj matrix = new DMatrixRMaj(n, n);
 		final double[] translation = new double[ n ];
 		for ( int r = 0; r < n; ++r )
 		{
@@ -228,7 +229,7 @@ public AffineTransform preConcatenate( final AffineGet affine )
 				tr += affine.get( r, k ) * get( k, n );
 			translation[ r ] = tr;
 		}
-		a.setMatrix( 0, n - 1, 0, n - 1, matrix );
+		a.setTo( matrix );
 		System.arraycopy( translation, 0, t, 0, t.length );
 
 		updateDs();

src/main/java/net/imglib2/realtransform/AffineTransform2D.java

@@ -11,13 +11,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -120,7 +120,7 @@ protected void invert()
 	{
 		final double det = a.det();
 
-		/* similar to Jama, throw a RunTimeException for singular matrices. */
+		/* throw a RunTimeException for singular matrices. */
 		if ( det == 0 )
 			throw new RuntimeException( "Matrix is singular." );
 

src/main/java/net/imglib2/realtransform/AffineTransform3D.java

@@ -11,13 +11,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -356,7 +356,7 @@ protected void invert()
 	{
 		final double det = a.det();
 
-		/* similar to Jama, throw a RunTimeException for singular matrices. */
+		/* throw a RunTimeException for singular matrices. */
 		if ( det == 0 )
 			throw new RuntimeException( "Matrix is singular." );