X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FRotatableMatrix.java;h=ea67f48056e2d6195726381dc6ba7ff82b013cb0;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=99f0c872d4efe967bd77d2a3ba5ac0fa2e73b5d7;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java index 99f0c87..ea67f48 100755 --- a/src/jalview/math/RotatableMatrix.java +++ b/src/jalview/math/RotatableMatrix.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,327 +20,239 @@ */ package jalview.math; +import jalview.datamodel.Point; + +import java.io.PrintStream; +import java.util.HashMap; +import java.util.Map; + /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * Model for a 3x3 matrix which provides methods for rotation in 3-D space */ public class RotatableMatrix { - float[][] matrix; + private static final int DIMS = 3; - float[] temp; + /* + * cache the most used rotations: +/- 1, 2, 3, 4 degrees around x or y axis + */ + private static Map> cachedRotations; - float[][] rot; + 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); + } + } + } - /** - * Creates a new RotatableMatrix object. - * - * @param rows - * DOCUMENT ME! - * @param cols - * DOCUMENT ME! - */ - public RotatableMatrix(int rows, int cols) + public enum Axis { - matrix = new float[rows][cols]; + X, Y, Z + } - temp = new float[3]; + float[][] matrix; - rot = new float[3][3]; + /** + * 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; + } } /** - * DOCUMENT ME! + * Sets the value at position (i, j) of the matrix * * @param i - * DOCUMENT ME! * @param j - * DOCUMENT ME! * @param value - * DOCUMENT ME! */ - public void addElement(int i, int j, float value) + public void setValue(int i, int j, float value) { matrix[i][j] = value; } /** - * DOCUMENT ME! + * Answers the value at position (i, j) of the matrix + * + * @param i + * @param j + * @return */ - public void print() + public float getValue(int i, int j) { - System.out.println(matrix[0][0] + " " + matrix[0][1] + " " - + matrix[0][2]); - - System.out.println(matrix[1][0] + " " + matrix[1][1] + " " - + matrix[1][2]); + return matrix[i][j]; + } - System.out.println(matrix[2][0] + " " + matrix[2][1] + " " - + matrix[2][2]); + /** + * 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]); } /** - * DOCUMENT ME! + * Rotates the matrix through the specified number of degrees around the + * specified axis * * @param degrees - * DOCUMENT ME! * @param axis - * DOCUMENT ME! */ - public void rotate(float degrees, char axis) + public void rotate(float degrees, Axis axis) { - float costheta = (float) Math.cos((degrees * Math.PI) / (float) 180.0); + float[][] rot = getRotation(degrees, axis); - float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0); + preMultiply(rot); + } - if (axis == 'z') + /** + * 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)) { - 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); + // jalview.bin.Console.outPrintln("getRotation from cache: " + (int) degrees); + return cachedRotations.get(axis).get(floatValue); } - 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; + float costheta = (float) Math.cos(degrees * Math.PI / 180f); - rot[2][0] = (float) 0.0; + float sintheta = (float) Math.sin(degrees * Math.PI / 180f); - rot[2][1] = (float) -sintheta; + float[][] rot = new float[DIMS][DIMS]; - rot[2][2] = (float) costheta; - - preMultiply(rot); - } - - if (axis == 'y') + switch (axis) { - 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); + 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; } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return */ public float[] vectorMultiply(float[] vect) { - temp[0] = vect[0]; - - temp[1] = vect[1]; + float[] result = new float[DIMS]; - temp[2] = vect[2]; - - for (int i = 0; i < 3; i++) + for (int i = 0; i < DIMS; i++) { - temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) + result[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; + return result; } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! */ public void preMultiply(float[][] mat) { - float[][] tmp = new float[3][3]; + float[][] tmp = new float[DIMS][DIMS]; - for (int i = 0; i < 3; i++) + for (int i = 0; i < DIMS; i++) { - for (int j = 0; j < 3; j++) + 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]); } } - for (int i = 0; i < 3; i++) - { - for (int j = 0; j < 3; j++) - { - matrix[i][j] = tmp[i][j]; - } - } + matrix = tmp; } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! */ public void postMultiply(float[][] mat) { - float[][] tmp = new float[3][3]; + float[][] tmp = new float[DIMS][DIMS]; - for (int i = 0; i < 3; i++) + for (int i = 0; i < DIMS; i++) { - for (int j = 0; j < 3; j++) + 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]); } } - for (int i = 0; i < 3; i++) - { - for (int j = 0; j < 3; j++) - { - matrix[i][j] = tmp[i][j]; - } - } + matrix = tmp; } /** - * DOCUMENT ME! + * Performs a vector multiplication whose result is the Point representing the + * input point's value vector post-multiplied by this matrix. * - * @param args - * DOCUMENT ME! - */ - 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]); - } - - /** - * DOCUMENT ME! + * @param coord + * @return */ - public void setIdentity() + public Point vectorMultiply(Point coord) { - 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; + float[] v = vectorMultiply(new float[] { coord.x, coord.y, coord.z }); + return new Point(v[0], v[1], v[2]); } }