package jalview.math;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotSame;
+import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;
public class MatrixTest
{
- final static double DELTA = 0.0001d;
+ final static double DELTA = 0.000001d;
@Test(groups = "Timing")
public void testPreMultiply_timing()
{
- int rows = 500;
- int cols = 1000;
+ int rows = 50; // increase to stress test timing
+ int cols = 100;
double[][] d1 = new double[rows][cols];
double[][] d2 = new double[cols][rows];
Matrix m1 = new Matrix(d1);
}
}
Matrix m1 = new Matrix(in);
+
Matrix m2 = (Matrix) m1.copy();
+ assertNotSame(m1, m2);
assertTrue(matrixEquals(m1, m2));
+ assertNull(m2.d);
+ assertNull(m2.e);
+
+ /*
+ * now add d and e vectors and recopy
+ */
+ m1.d = Arrays.copyOf(in[2], in[2].length);
+ m1.e = Arrays.copyOf(in[4], in[4].length);
+ m2 = (Matrix) m1.copy();
+ assertNotSame(m2.d, m1.d);
+ assertNotSame(m2.e, m1.e);
+ assertEquals(m2.d, m1.d);
+ assertEquals(m2.e, m1.e);
}
/**
assertMatricesMatch(m1, m2);
}
- private void assertMatricesMatch(MatrixI m1, MatrixI m2)
+ public static void assertMatricesMatch(MatrixI m1, MatrixI m2)
{
if (m1.height() != m2.height())
{
}
}
}
- ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
- ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
+ ArrayAsserts.assertArrayEquals("D vector", m1.getD(), m2.getD(),
+ 0.00001d);
+ ArrayAsserts.assertArrayEquals("E vector", m1.getE(), m2.getE(),
+ 0.00001d);
+ }
+
+ @Test(groups = "Functional")
+ public void testFindMinMax()
+ {
+ /*
+ * empty matrix case
+ */
+ Matrix m = new Matrix(new double[][] { {} });
+ assertNull(m.findMinMax());
+
+ /*
+ * normal case
+ */
+ double[][] vals = new double[2][];
+ vals[0] = new double[] {7d, 1d, -2.3d};
+ vals[1] = new double[] {-12d, 94.3d, -102.34d};
+ m = new Matrix(vals);
+ double[] minMax = m.findMinMax();
+ assertEquals(minMax[0], -102.34d);
+ assertEquals(minMax[1], 94.3d);
+ }
+
+ @Test(groups = { "Functional", "Timing" })
+ public void testFindMinMax_timing()
+ {
+ Random r = new Random();
+ int size = 1000; // increase to stress test timing
+ double[][] vals = new double[size][size];
+ double max = -Double.MAX_VALUE;
+ double min = Double.MAX_VALUE;
+ for (int i = 0; i < size; i++)
+ {
+ vals[i] = new double[size];
+ for (int j = 0; j < size; j++)
+ {
+ // use nextLong rather than nextDouble to include negative values
+ double d = r.nextLong();
+ if (d > max)
+ {
+ max = d;
+ }
+ if (d < min)
+ {
+ min = d;
+ }
+ vals[i][j] = d;
+ }
+ }
+ Matrix m = new Matrix(vals);
+ long now = System.currentTimeMillis();
+ double[] minMax = m.findMinMax();
+ System.out.println(String.format("findMinMax for %d x %d took %dms",
+ size, size, (System.currentTimeMillis() - now)));
+ assertEquals(minMax[0], min);
+ assertEquals(minMax[1], max);
+ }
+
+ /**
+ * Test range reversal with maximum value becoming zero
+ */
+ @Test(groups = "Functional")
+ public void testReverseRange_maxToZero()
+ {
+ Matrix m1 = new Matrix(
+ new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+
+ /*
+ * subtract all from max: range -3.4 to 15 becomes 18.4 to 0
+ */
+ m1.reverseRange(true);
+ assertEquals(m1.getValue(0, 0), 13d, DELTA);
+ assertEquals(m1.getValue(0, 1), 11.5d, DELTA);
+ assertEquals(m1.getValue(0, 2), 11d, DELTA);
+ assertEquals(m1.getValue(1, 0), 18.4d, DELTA);
+ assertEquals(m1.getValue(1, 1), 11d, DELTA);
+ assertEquals(m1.getValue(1, 2), 0d, DELTA);
+
+ /*
+ * repeat operation - range is now 0 to 18.4
+ */
+ m1.reverseRange(true);
+ assertEquals(m1.getValue(0, 0), 5.4d, DELTA);
+ assertEquals(m1.getValue(0, 1), 6.9d, DELTA);
+ assertEquals(m1.getValue(0, 2), 7.4d, DELTA);
+ assertEquals(m1.getValue(1, 0), 0d, DELTA);
+ assertEquals(m1.getValue(1, 1), 7.4d, DELTA);
+ assertEquals(m1.getValue(1, 2), 18.4d, DELTA);
+ }
+
+ /**
+ * Test range reversal with minimum and maximum values swapped
+ */
+ @Test(groups = "Functional")
+ public void testReverseRange_swapMinMax()
+ {
+ Matrix m1 = new Matrix(
+ new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+
+ /*
+ * swap all values in min-max range
+ * = subtract from (min + max = 11.6)
+ * range -3.4 to 15 becomes 18.4 to -3.4
+ */
+ m1.reverseRange(false);
+ assertEquals(m1.getValue(0, 0), 9.6d, DELTA);
+ assertEquals(m1.getValue(0, 1), 8.1d, DELTA);
+ assertEquals(m1.getValue(0, 2), 7.6d, DELTA);
+ assertEquals(m1.getValue(1, 0), 15d, DELTA);
+ assertEquals(m1.getValue(1, 1), 7.6d, DELTA);
+ assertEquals(m1.getValue(1, 2), -3.4d, DELTA);
+
+ /*
+ * repeat operation - original values restored
+ */
+ m1.reverseRange(false);
+ assertEquals(m1.getValue(0, 0), 2d, DELTA);
+ assertEquals(m1.getValue(0, 1), 3.5d, DELTA);
+ assertEquals(m1.getValue(0, 2), 4d, DELTA);
+ assertEquals(m1.getValue(1, 0), -3.4d, DELTA);
+ assertEquals(m1.getValue(1, 1), 4d, DELTA);
+ assertEquals(m1.getValue(1, 2), 15d, DELTA);
+ }
+
+ @Test(groups = "Functional")
+ public void testMultiply()
+ {
+ Matrix m = new Matrix(new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+ m.multiply(2d);
+ assertEquals(m.getValue(0, 0), 4d, DELTA);
+ assertEquals(m.getValue(0, 1), 7d, DELTA);
+ assertEquals(m.getValue(0, 2), 8d, DELTA);
+ assertEquals(m.getValue(1, 0), -6.8d, DELTA);
+ assertEquals(m.getValue(1, 1), 8d, DELTA);
+ assertEquals(m.getValue(1, 2), 30d, DELTA);
+ }
+
+ @Test(groups = "Functional")
+ public void testConstructor()
+ {
+ double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+ Matrix m = new Matrix(values);
+ assertEquals(m.getValue(0, 0), 1d, DELTA);
+
+ /*
+ * verify the matrix has a copy of the original array
+ */
+ assertNotSame(values[0], m.getRow(0));
+ values[0][0] = -1d;
+ assertEquals(m.getValue(0, 0), 1d, DELTA); // unchanged
+ }
+
+ @Test(groups = "Functional")
+ public void testEquals()
+ {
+ double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+ Matrix m1 = new Matrix(values);
+ double[][] values2 = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+ Matrix m2 = new Matrix(values2);
+
+ double delta = 0.0001d;
+ assertTrue(m1.equals(m1, delta));
+ assertTrue(m1.equals(m2, delta));
+ assertTrue(m2.equals(m1, delta));
+
+ double[][] values3 = new double[][] { { 1, 2, 3 }, { 4, 5, 7 } };
+ m2 = new Matrix(values3);
+ assertFalse(m1.equals(m2, delta));
+ assertFalse(m2.equals(m1, delta));
+
+ // must be same shape
+ values2 = new double[][] { { 1, 2, 3 } };
+ m2 = new Matrix(values2);
+ assertFalse(m2.equals(m1, delta));
+
+ assertFalse(m1.equals(null, delta));
}
}
git://source.jalview.org / jalview.git / blobdiff