package org.biojava.nbio.structure.geometry;
import javax.vecmath.Matrix3d;
import javax.vecmath.Matrix4d;
import javax.vecmath.Vector3d;
import org.biojava.nbio.structure.jama.Matrix;
/**
* Matrices contains static methods to operate and transform matrices used in 3D
* geometry (transformation matrices and rotation matrices).
* <p>
* This class complements and extends the functionallity of vecmath and JAMA.
*
* @author Aleix Lafita
* @since 5.0.0
*
*/
public class Matrices {
/** Prevent instantiation */
private Matrices(){}
/**
* Convert a transformation matrix into a JAMA rotation matrix. Because the
* JAMA matrix is a pre-multiplication matrix and the Vecmath matrix is a
* post-multiplication one, the rotation matrix is transposed to ensure that
* the transformation they produce is the same.
*
* @param transform
* Matrix4d with transposed rotation matrix
* @return rotation matrix as JAMA object
*/
public static Matrix getRotationJAMA(Matrix4d transform) {
Matrix rot = new Matrix(3, 3);
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
rot.set(j, i, transform.getElement(i, j)); // transposed
}
}
return rot;
}
/**
* Convert a transformation matrix into a rotation matrix.
*
* @param transform
* Matrix4d
* @return rotation matrix
*/
public static Matrix3d getRotationMatrix(Matrix4d transform) {
Matrix3d rot = new Matrix3d();
transform.setRotationScale(rot);
return rot;
}
/**
* Extract the translational vector of a transformation matrix.
*
* @param transform
* Matrix4d
* @return Vector3d translation vector
*/
public static Vector3d getTranslationVector(Matrix4d transform) {
Vector3d transl = new Vector3d();
transform.get(transl);
return transl;
}
/**
* Convert JAMA rotation and translation to a Vecmath transformation matrix.
* Because the JAMA matrix is a pre-multiplication matrix and the Vecmath
* matrix is a post-multiplication one, the rotation matrix is transposed to
* ensure that the transformation they produce is the same.
*
* @param rot
* 3x3 Rotation matrix
* @param trans
* 3x1 Translation matrix
* @return 4x4 transformation matrix
*/
public static Matrix4d getTransformation(Matrix rot, Matrix trans) {
return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
new Vector3d(trans.getColumnPackedCopy()), 1.0);
}
}