X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FRotatableMatrix.java;h=602c5e4bc6cf66c6e3a325d6a95c60017ca1dd13;hb=5321ea8cd291cb631b903a3860476f0430e2fe5a;hp=2385288b46e321d50c88baaf63809e9991a07c1e;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git
diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java
index 2385288..602c5e4 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -1,332 +1,330 @@
-/*
-* 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;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class RotatableMatrix
-{
- float[][] matrix;
- float[] temp;
- float[][] rot;
-
- /**
- * Creates a new RotatableMatrix object.
- *
- * @param rows DOCUMENT ME!
- * @param cols DOCUMENT ME!
- */
- public RotatableMatrix(int rows, int cols)
- {
- matrix = new float[rows][cols];
-
- temp = new float[3];
-
- rot = new float[3][3];
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- * @param value DOCUMENT ME!
- */
- public void addElement(int i, int j, float value)
- {
- matrix[i][j] = value;
- }
-
- /**
- * DOCUMENT ME!
- */
- 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]);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param degrees DOCUMENT ME!
- * @param axis DOCUMENT ME!
- */
- 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);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param vect DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- 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;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param mat DOCUMENT ME!
- */
- 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];
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param mat DOCUMENT ME!
- */
- 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];
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @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!
- */
- 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.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()
+ {
+ 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]);
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args)
+ {
+ RotatableMatrix m = new RotatableMatrix();
+
+ m.setValue(0, 0, 1);
+
+ m.setValue(0, 1, 0);
+
+ m.setValue(0, 2, 0);
+
+ m.setValue(1, 0, 0);
+
+ m.setValue(1, 1, 2);
+
+ m.setValue(1, 2, 0);
+
+ m.setValue(2, 0, 0);
+
+ m.setValue(2, 1, 0);
+
+ m.setValue(2, 2, 1);
+
+ m.print();
+
+ RotatableMatrix n = new RotatableMatrix();
+
+ n.setValue(0, 0, 2);
+
+ n.setValue(0, 1, 1);
+
+ n.setValue(0, 2, 1);
+
+ n.setValue(1, 0, 2);
+
+ n.setValue(1, 1, 1);
+
+ n.setValue(1, 2, 1);
+
+ n.setValue(2, 0, 2);
+
+ n.setValue(2, 1, 1);
+
+ n.setValue(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]);
+ }
+
+ /**
+ * 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]);
+ }
+}