X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fmath%2FRotatableMatrix.java;h=f3bf436e13bb5b03877a796fa04a2ac4a1c54316;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=d9f4bd588af1b88d35d0a3e3f053eba53bbb47cd;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java
index d9f4bd5..f3bf436 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -1,389 +1,258 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.math;
-
-
-
-public class RotatableMatrix {
-
- float matrix[][];
-
- float[] temp;
-
- float[][] rot;
-
-
-
- public RotatableMatrix(int rows, int cols) {
-
- matrix = new float[rows][cols];
-
- temp = new float[3];
-
- rot = new float[3][3];
-
- }
-
-
-
- public void addElement(int i, int j, float value) {
-
- matrix[i][j] = value;
-
- }
-
-
-
- public void print() {
-
- System.out.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);
-
- System.out.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);
-
- System.out.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);
-
- }
-
-
-
- public void rotate (float degrees, char axis) {
-
-
-
- float costheta = (float)Math.cos(degrees*Math.PI/(float)180.0);
-
- float sintheta = (float)Math.sin(degrees*Math.PI/(float)180.0);
-
-
-
- if (axis == 'z') {
-
-
-
- rot[0][0] = (float)costheta;
-
- rot[0][1] = (float)-sintheta;
-
- rot[0][2] = (float)0.0;
-
-
-
- rot[1][0] = (float)sintheta;
-
- rot[1][1] = (float)costheta;
-
- rot[1][2] = (float)0.0;
-
-
-
- rot[2][0] = (float)0.0;
-
- rot[2][1] = (float)0.0;
-
- rot[2][2] = (float)1.0;
-
-
-
- preMultiply(rot);
-
- }
-
- if (axis == 'x') {
-
- rot[0][0] = (float)1.0;
-
- rot[0][1] = (float)0.0;
-
- rot[0][2] = (float)0.0;
-
-
-
- rot[1][0] = (float)0.0;
-
- rot[1][1] = (float)costheta;
-
- rot[1][2] = (float)sintheta;
-
-
-
- rot[2][0] = (float)0.0;
-
- rot[2][1] = (float)-sintheta;
-
- rot[2][2] = (float)costheta;
-
-
-
- preMultiply(rot);
-
-
-
- }
-
- if (axis == 'y') {
-
- rot[0][0] = (float)costheta;
-
- rot[0][1] = (float)0.0;
-
- rot[0][2] = (float)-sintheta;
-
-
-
- rot[1][0] = (float)0.0;
-
- rot[1][1] = (float)1.0;
-
- rot[1][2] = (float)0.0;
-
-
-
- rot[2][0] = (float)sintheta;
-
- rot[2][1] = (float)0.0;
-
- rot[2][2] = (float)costheta;
-
-
-
- preMultiply(rot);
-
-
-
- }
-
-
-
- }
-
-
-
- public float[] vectorMultiply(float[] vect) {
-
- temp[0] = vect[0];
-
- temp[1] = vect[1];
-
- temp[2] = vect[2];
-
-
-
- for (int i = 0; i < 3; i++) {
-
- temp[i] = matrix[i][0]*vect[0] + matrix[i][1]*vect[1] + matrix[i][2]*vect[2];
-
- }
-
-
-
- vect[0] = temp[0];
-
- vect[1] = temp[1];
-
- vect[2] = temp[2];
-
-
-
- return vect;
-
- }
-
-
-
- public void preMultiply(float mat[][]) {
-
- float tmp[][] = new float[3][3];
-
-
-
- for (int i = 0; i < 3 ; i++) {
-
- for (int j = 0; j < 3; j++ ) {
-
- tmp[i][j] = mat[i][0]*matrix[0][j] +
-
- mat[i][1]*matrix[1][j] +
-
- mat[i][2]*matrix[2][j];
-
- }
-
- }
-
-
-
- for (int i = 0; i < 3 ; i++) {
-
- for (int j = 0; j < 3; j++ ) {
-
- matrix[i][j] = tmp[i][j];
-
- }
-
- }
-
- }
-
-
-
- public void postMultiply(float mat[][]) {
-
- float tmp[][] = new float[3][3];
-
-
-
- for (int i = 0; i < 3 ; i++) {
-
- for (int j = 0; j < 3; j++ ) {
-
- tmp[i][j] = matrix[i][0]*mat[0][j] +
-
- matrix[i][1]*mat[1][j] +
-
- matrix[i][2]*mat[2][j];
-
- }
-
- }
-
-
-
- for (int i = 0; i < 3 ; i++) {
-
- for (int j = 0; j < 3; j++ ) {
-
- matrix[i][j] = tmp[i][j];
-
- }
-
- }
-
- }
-
-
-
- public static void main(String[] args) {
-
-
-
- RotatableMatrix m = new RotatableMatrix(3,3);
-
- m.addElement(0,0,1);
-
- m.addElement(0,1,0);
-
- m.addElement(0,2,0);
-
- m.addElement(1,0,0);
-
- m.addElement(1,1,2);
-
- m.addElement(1,2,0);
-
- m.addElement(2,0,0);
-
- m.addElement(2,1,0);
-
- m.addElement(2,2,1);
-
-
-
- m.print();
-
-
-
- RotatableMatrix n = new RotatableMatrix(3,3);
-
- n.addElement(0,0,2);
-
- n.addElement(0,1,1);
-
- n.addElement(0,2,1);
-
- n.addElement(1,0,2);
-
- n.addElement(1,1,1);
-
- n.addElement(1,2,1);
-
- n.addElement(2,0,2);
-
- n.addElement(2,1,1);
-
- n.addElement(2,2,1);
-
-
-
- n.print();
-
-
-
- //m.postMultiply(n.matrix);
-
- //m.print();
-
- // m.rotate(45,'z',new RotatableMatrix(3,3));
-
-
-
- float vect[] = new float[3];
-
- vect[0] = 2;
-
- vect[1] = 4;
-
- vect[2] = 6;
-
-
-
- vect = m.vectorMultiply(vect);
-
- System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
-
-
-
- }
-
- public void setIdentity() {
-
- matrix[0][0] = (float)1.0;
-
- matrix[1][1] = (float)1.0;
-
- matrix[2][2] = (float)1.0;
-
- matrix[0][1] = (float)0.0;
-
- matrix[0][2] = (float)0.0;
-
- matrix[1][0] = (float)0.0;
-
- matrix[1][2] = (float) 0.0;
-
- matrix[2][0] = (float)0.0;
-
- matrix[2][1] = (float)0.0;
-
- }
-
-}
-
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.math;
+
+import jalview.datamodel.Point;
+
+import java.io.PrintStream;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Model for a 3x3 matrix which provides methods for rotation in 3-D space
+ */
+public class RotatableMatrix
+{
+ private static final int DIMS = 3;
+
+ /*
+ * cache the most used rotations: +/- 1, 2, 3, 4 degrees around x or y axis
+ */
+ private static Map> cachedRotations;
+
+ static
+ {
+ cachedRotations = new HashMap<>();
+ for (Axis axis : Axis.values())
+ {
+ HashMap map = new HashMap<>();
+ cachedRotations.put(axis, map);
+ for (int deg = 1; deg < 5; deg++)
+ {
+ float[][] rotation = getRotation(deg, axis);
+ map.put(Float.valueOf(deg), rotation);
+ rotation = getRotation(-deg, axis);
+ map.put(Float.valueOf(-deg), rotation);
+ }
+ }
+ }
+
+ public enum Axis
+ {
+ X, Y, Z
+ }
+
+ float[][] matrix;
+
+ /**
+ * Constructor creates a new identity matrix (all values zero except for 1 on
+ * the diagonal)
+ */
+ public RotatableMatrix()
+ {
+ matrix = new float[DIMS][DIMS];
+ for (int j = 0; j < DIMS; j++)
+ {
+ matrix[j][j] = 1f;
+ }
+ }
+
+ /**
+ * Sets the value at position (i, j) of the matrix
+ *
+ * @param i
+ * @param j
+ * @param value
+ */
+ public void setValue(int i, int j, float value)
+ {
+ matrix[i][j] = value;
+ }
+
+ /**
+ * Answers the value at position (i, j) of the matrix
+ *
+ * @param i
+ * @param j
+ * @return
+ */
+ public float getValue(int i, int j)
+ {
+ return matrix[i][j];
+ }
+
+ /**
+ * Prints the matrix in rows of space-delimited values
+ */
+ public void print(PrintStream ps)
+ {
+ ps.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);
+ ps.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);
+ ps.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);
+ }
+
+ /**
+ * Rotates the matrix through the specified number of degrees around the
+ * specified axis
+ *
+ * @param degrees
+ * @param axis
+ */
+ public void rotate(float degrees, Axis axis)
+ {
+ float[][] rot = getRotation(degrees, axis);
+
+ preMultiply(rot);
+ }
+
+ /**
+ * Answers a matrix which, when it pre-multiplies another matrix, applies a
+ * rotation of the specified number of degrees around the specified axis
+ *
+ * @param degrees
+ * @param axis
+ * @return
+ * @see https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations
+ */
+ protected static float[][] getRotation(float degrees, Axis axis)
+ {
+ Float floatValue = Float.valueOf(degrees);
+ if (cachedRotations.get(axis).containsKey(floatValue))
+ {
+ // System.out.println("getRotation from cache: " + (int) degrees);
+ return cachedRotations.get(axis).get(floatValue);
+ }
+
+ float costheta = (float) Math.cos(degrees * Math.PI / 180f);
+
+ float sintheta = (float) Math.sin(degrees * Math.PI / 180f);
+
+ float[][] rot = new float[DIMS][DIMS];
+
+ switch (axis)
+ {
+ case X:
+ rot[0][0] = 1f;
+ rot[1][1] = costheta;
+ rot[1][2] = sintheta;
+ rot[2][1] = -sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Y:
+ rot[0][0] = costheta;
+ rot[0][2] = -sintheta;
+ rot[1][1] = 1f;
+ rot[2][0] = sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Z:
+ rot[0][0] = costheta;
+ rot[0][1] = -sintheta;
+ rot[1][0] = sintheta;
+ rot[1][1] = costheta;
+ rot[2][2] = 1f;
+ break;
+ }
+ return rot;
+ }
+
+ /**
+ * Answers a new array of float values which is the result of pre-multiplying
+ * this matrix by the given vector. Each value of the result is the dot
+ * product of the vector with one column of this matrix. The matrix and input
+ * vector are not modified.
+ *
+ * @param vect
+ *
+ * @return
+ */
+ public float[] vectorMultiply(float[] vect)
+ {
+ float[] result = new float[DIMS];
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ result[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+ + (matrix[i][2] * vect[2]);
+ }
+
+ return result;
+ }
+
+ /**
+ * Performs pre-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of mat
with
+ * the j'th column of this matrix.
+ *
+ * @param mat
+ */
+ public void preMultiply(float[][] mat)
+ {
+ float[][] tmp = new float[DIMS][DIMS];
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ for (int j = 0; j < DIMS; j++)
+ {
+ tmp[i][j] = (mat[i][0] * matrix[0][j]) + (mat[i][1] * matrix[1][j])
+ + (mat[i][2] * matrix[2][j]);
+ }
+ }
+
+ matrix = tmp;
+ }
+
+ /**
+ * Performs post-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of this matrix with the
+ * j'th column of mat
.
+ *
+ * @param mat
+ */
+ public void postMultiply(float[][] mat)
+ {
+ float[][] tmp = new float[DIMS][DIMS];
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ for (int j = 0; j < DIMS; j++)
+ {
+ tmp[i][j] = (matrix[i][0] * mat[0][j]) + (matrix[i][1] * mat[1][j])
+ + (matrix[i][2] * mat[2][j]);
+ }
+ }
+
+ matrix = tmp;
+ }
+
+ /**
+ * Performs a vector multiplication whose result is the Point representing the
+ * input point's value vector post-multiplied by this matrix.
+ *
+ * @param coord
+ * @return
+ */
+ public Point vectorMultiply(Point coord)
+ {
+ float[] v = vectorMultiply(new float[] { coord.x, coord.y, coord.z });
+ return new Point(v[0], v[1], v[2]);
+ }
+}