diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java
index afa089134115e584668b8e338d7acd32f542720e..04b9ff6fef242bf4b503046b33b5156fc784140b 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDByteArray.java
@@ -69,6 +69,36 @@ public final class MDByteArray extends MDAbstractArray<Byte>
this.flattenedArray = flattenedArray;
}
+ public MDByteArray(byte[][] matrix)
+ {
+ this(matrix, getDimensions(matrix));
+ }
+
+ public MDByteArray(byte[][] matrix, int[] dimensions)
+ {
+ super(dimensions);
+
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ int size = 1;
+ for (int i = 0; i < dimensions.length; ++i)
+ {
+ size *= dimensions[i];
+ }
+ this.flattenedArray = new byte[size];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
+ }
+ }
+
+ private static int[] getDimensions(byte[][] matrix)
+ {
+ assert matrix != null;
+
+ return new int[] { matrix.length, matrix.length == 0 ? 0 : matrix[0].length };
+ }
+
@Override
public int size()
{
@@ -177,6 +207,23 @@ public final class MDByteArray extends MDAbstractArray<Byte>
flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
}
+ /**
+ * Creates and returns a matrix from a two-dimensional array.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public byte[][] toMatrix()
+ {
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ final byte[][] result = new byte[sizeX][sizeY];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(flattenedArray, i * sizeY, result[i], 0, sizeY);
+ }
+ return result;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java
index 38a849547cd255806de22fbeec1dfc362cae73a0..bbdabe9001b65895d3868830e167322ea300dd97 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDDoubleArray.java
@@ -69,6 +69,36 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
this.flattenedArray = flattenedArray;
}
+ public MDDoubleArray(double[][] matrix)
+ {
+ this(matrix, getDimensions(matrix));
+ }
+
+ public MDDoubleArray(double[][] matrix, int[] dimensions)
+ {
+ super(dimensions);
+
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ int size = 1;
+ for (int i = 0; i < dimensions.length; ++i)
+ {
+ size *= dimensions[i];
+ }
+ this.flattenedArray = new double[size];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
+ }
+ }
+
+ private static int[] getDimensions(double[][] matrix)
+ {
+ assert matrix != null;
+
+ return new int[] { matrix.length, matrix.length == 0 ? 0 : matrix[0].length };
+ }
+
@Override
public int size()
{
@@ -177,6 +207,23 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
}
+ /**
+ * Creates and returns a matrix from a two-dimensional array.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public double[][] toMatrix()
+ {
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ final double[][] result = new double[sizeX][sizeY];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(flattenedArray, i * sizeY, result[i], 0, sizeY);
+ }
+ return result;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java
index 86cfccd078bf2a7af086820ccb8e0eaf806c16e3..40bf011740e03cdd5ffe8394b5aa0e6c8671447c 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDFloatArray.java
@@ -69,6 +69,36 @@ public final class MDFloatArray extends MDAbstractArray<Float>
this.flattenedArray = flattenedArray;
}
+ public MDFloatArray(float[][] matrix)
+ {
+ this(matrix, getDimensions(matrix));
+ }
+
+ public MDFloatArray(float[][] matrix, int[] dimensions)
+ {
+ super(dimensions);
+
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ int size = 1;
+ for (int i = 0; i < dimensions.length; ++i)
+ {
+ size *= dimensions[i];
+ }
+ this.flattenedArray = new float[size];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
+ }
+ }
+
+ private static int[] getDimensions(float[][] matrix)
+ {
+ assert matrix != null;
+
+ return new int[] { matrix.length, matrix.length == 0 ? 0 : matrix[0].length };
+ }
+
@Override
public int size()
{
@@ -177,6 +207,23 @@ public final class MDFloatArray extends MDAbstractArray<Float>
flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
}
+ /**
+ * Creates and returns a matrix from a two-dimensional array.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public float[][] toMatrix()
+ {
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ final float[][] result = new float[sizeX][sizeY];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(flattenedArray, i * sizeY, result[i], 0, sizeY);
+ }
+ return result;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java
index e785d679e64d34025f7692f2d4ea2b21b80b1c03..67c72c99662fe73cab905f69020bdaf14de897a5 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDIntArray.java
@@ -69,6 +69,36 @@ public final class MDIntArray extends MDAbstractArray<Integer>
this.flattenedArray = flattenedArray;
}
+ public MDIntArray(int[][] matrix)
+ {
+ this(matrix, getDimensions(matrix));
+ }
+
+ public MDIntArray(int[][] matrix, int[] dimensions)
+ {
+ super(dimensions);
+
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ int size = 1;
+ for (int i = 0; i < dimensions.length; ++i)
+ {
+ size *= dimensions[i];
+ }
+ this.flattenedArray = new int[size];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
+ }
+ }
+
+ private static int[] getDimensions(int[][] matrix)
+ {
+ assert matrix != null;
+
+ return new int[] { matrix.length, matrix.length == 0 ? 0 : matrix[0].length };
+ }
+
@Override
public int size()
{
@@ -177,6 +207,23 @@ public final class MDIntArray extends MDAbstractArray<Integer>
flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
}
+ /**
+ * Creates and returns a matrix from a two-dimensional array.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public int[][] toMatrix()
+ {
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ final int[][] result = new int[sizeX][sizeY];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(flattenedArray, i * sizeY, result[i], 0, sizeY);
+ }
+ return result;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java
index 21178606291c5ac957b9f790e709f3f317b47ebc..09ef27135ba4d79e221af1b83b75545bc6a9a076 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDLongArray.java
@@ -69,6 +69,36 @@ public final class MDLongArray extends MDAbstractArray<Long>
this.flattenedArray = flattenedArray;
}
+ public MDLongArray(long[][] matrix)
+ {
+ this(matrix, getDimensions(matrix));
+ }
+
+ public MDLongArray(long[][] matrix, int[] dimensions)
+ {
+ super(dimensions);
+
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ int size = 1;
+ for (int i = 0; i < dimensions.length; ++i)
+ {
+ size *= dimensions[i];
+ }
+ this.flattenedArray = new long[size];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
+ }
+ }
+
+ private static int[] getDimensions(long[][] matrix)
+ {
+ assert matrix != null;
+
+ return new int[] { matrix.length, matrix.length == 0 ? 0 : matrix[0].length };
+ }
+
@Override
public int size()
{
@@ -177,6 +207,23 @@ public final class MDLongArray extends MDAbstractArray<Long>
flattenedArray[computeIndex(indexX, indexY, indexZ)] = value;
}
+ /**
+ * Creates and returns a matrix from a two-dimensional array.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public long[][] toMatrix()
+ {
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ final long[][] result = new long[sizeX][sizeY];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(flattenedArray, i * sizeY, result[i], 0, sizeY);
+ }
+ return result;
+ }
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java b/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java
index 9fcb027803c7462c9f6536acf8124d2f9a723985..22b8f94f801a73f08e8c65419b60468abb6077f0 100644
--- a/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java
+++ b/common/source/java/ch/systemsx/cisd/common/array/MDShortArray.java
@@ -69,6 +69,36 @@ public final class MDShortArray extends MDAbstractArray<Short>
this.flattenedArray = flattenedArray;
}
+ public MDShortArray(short[][] matrix)
+ {
+ this(matrix, getDimensions(matrix));
+ }
+
+ public MDShortArray(short[][] matrix, int[] dimensions)
+ {
+ super(dimensions);
+
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ int size = 1;
+ for (int i = 0; i < dimensions.length; ++i)
+ {
+ size *= dimensions[i];
+ }
+ this.flattenedArray = new short[size];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(matrix[i], 0, flattenedArray, i * sizeY, sizeY);
+ }
+ }
+
+ private static int[] getDimensions(short[][] matrix)
+ {
+ assert matrix != null;
+
+ return new int[] { matrix.length, matrix.length == 0 ? 0 : matrix[0].length };
+ }
+
@Override
public int size()
{
@@ -181,6 +211,23 @@ public final class MDShortArray extends MDAbstractArray<Short>
// Object
//
+ /**
+ * Creates and returns a matrix from a two-dimensional array.
+ * <p>
+ * <b>Do not call for arrays other than two-dimensional!</b>
+ */
+ public short[][] toMatrix()
+ {
+ final int sizeX = dimensions[0];
+ final int sizeY = dimensions[1];
+ final short[][] result = new short[sizeX][sizeY];
+ for (int i = 0; i < sizeX; ++i)
+ {
+ System.arraycopy(flattenedArray, i * sizeY, result[i], 0, sizeY);
+ }
+ return result;
+ }
+
@Override
public int hashCode()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java b/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java
index eaf663a1d4fa9fd71f64ed19625a2b2975514b04..424c82c41bad1d43fc4c3e4a160d521a66644303 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/array/MDArraytest.java
@@ -24,12 +24,12 @@ import static org.testng.AssertJUnit.*;
/**
* Test cases for {@link MDAbstractArray}.
- *
+ *
* @author Bernd Rinn
*/
public class MDArraytest
{
-
+
static class TestMDArray extends MDAbstractArray<Void>
{
protected TestMDArray(int[] shape)
@@ -58,58 +58,110 @@ public class MDArraytest
@Test
public void testGetLength()
{
- assertEquals(0, MDAbstractArray.getLength(new int[] { 0 }));
- assertEquals(1, MDAbstractArray.getLength(new int[] { 1 }));
- assertEquals(15, MDAbstractArray.getLength(new int[] { 5, 3 }));
- assertEquals(1, MDAbstractArray.getLength(new int[] { 1, 1, 1 }));
- assertEquals(8, MDAbstractArray.getLength(new int[] { 2, 2, 2 }));
- assertEquals(2, MDAbstractArray.getLength(new int[] { 1, 1, 2 }));
- assertEquals(2, MDAbstractArray.getLength(new int[] { 1, 2, 1 }));
- assertEquals(2, MDAbstractArray.getLength(new int[] { 2, 1, 1 }));
- assertEquals(50, MDAbstractArray.getLength(new int[] { 10, 1, 5 }));
- assertEquals(50, MDAbstractArray.getLength(new long[] { 10, 1, 5 }));
+ assertEquals(0, MDAbstractArray.getLength(new int[]
+ { 0 }));
+ assertEquals(1, MDAbstractArray.getLength(new int[]
+ { 1 }));
+ assertEquals(15, MDAbstractArray.getLength(new int[]
+ { 5, 3 }));
+ assertEquals(1, MDAbstractArray.getLength(new int[]
+ { 1, 1, 1 }));
+ assertEquals(8, MDAbstractArray.getLength(new int[]
+ { 2, 2, 2 }));
+ assertEquals(2, MDAbstractArray.getLength(new int[]
+ { 1, 1, 2 }));
+ assertEquals(2, MDAbstractArray.getLength(new int[]
+ { 1, 2, 1 }));
+ assertEquals(2, MDAbstractArray.getLength(new int[]
+ { 2, 1, 1 }));
+ assertEquals(50, MDAbstractArray.getLength(new int[]
+ { 10, 1, 5 }));
+ assertEquals(50, MDAbstractArray.getLength(new long[]
+ { 10, 1, 5 }));
}
-
+
@Test
public void testToInt()
{
- assertTrue(Arrays.equals(new int[] { 1, 2, 3 }, MDAbstractArray.toInt(new long[] { 1, 2, 3 })));
- assertTrue(Arrays.equals(new int[] { }, MDAbstractArray.toInt(new long[] { })));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 2, 3 }, MDAbstractArray.toInt(new long[]
+ { 1, 2, 3 })));
+ assertTrue(Arrays.equals(new int[] {}, MDAbstractArray.toInt(new long[] {})));
}
-
+
@Test
public void testComputeIndex()
{
TestMDArray array;
- array = new TestMDArray(new int[] { 33 });
- assertEquals(17, array.computeIndex(new int[] { 17 }));
- array = new TestMDArray(new int[] { 100, 10 });
- assertEquals(10 * 42 + 17, array.computeIndex(new int[] { 42, 17 }));
- array = new TestMDArray(new int[] { 2, 7, 3 });
- assertEquals(3 * 7 * 1 + 3 * 2 + 3, array.computeIndex(new int[] { 1, 2, 3 }));
+ array = new TestMDArray(new int[]
+ { 33 });
+ assertEquals(17, array.computeIndex(new int[]
+ { 17 }));
+ array = new TestMDArray(new int[]
+ { 100, 10 });
+ assertEquals(10 * 42 + 17, array.computeIndex(new int[]
+ { 42, 17 }));
+ array = new TestMDArray(new int[]
+ { 2, 7, 3 });
+ assertEquals(3 * 7 * 1 + 3 * 2 + 3, array.computeIndex(new int[]
+ { 1, 2, 3 }));
}
@Test
public void testComputeIndex2D()
{
TestMDArray array;
- array = new TestMDArray(new int[] { 100, 10 });
- assertEquals(array.computeIndex(new int[] { 5, 8, }), array.computeIndex(5, 8));
- assertEquals(array.computeIndex(new int[] { 9, 1, }), array.computeIndex(9, 1));
- array = new TestMDArray(new int[] { 101, 11 });
- assertEquals(array.computeIndex(new int[] { 5, 8, }), array.computeIndex(5, 8));
- assertEquals(array.computeIndex(new int[] { 9, 1, }), array.computeIndex(9, 1));
+ array = new TestMDArray(new int[]
+ { 100, 10 });
+ assertEquals(array.computeIndex(new int[]
+ { 5, 8, }), array.computeIndex(5, 8));
+ assertEquals(array.computeIndex(new int[]
+ { 9, 1, }), array.computeIndex(9, 1));
+ array = new TestMDArray(new int[]
+ { 101, 11 });
+ assertEquals(array.computeIndex(new int[]
+ { 5, 8, }), array.computeIndex(5, 8));
+ assertEquals(array.computeIndex(new int[]
+ { 9, 1, }), array.computeIndex(9, 1));
}
@Test
public void testComputeIndex3()
{
TestMDArray array;
- array = new TestMDArray(new int[] { 100, 10, 17 });
- assertEquals(array.computeIndex(new int[] { 5, 8, 16 }), array.computeIndex(5, 8, 16));
- assertEquals(array.computeIndex(new int[] { 9, 1, 5 }), array.computeIndex(9, 1, 5));
- array = new TestMDArray(new int[] { 101, 11, 3 });
- assertEquals(array.computeIndex(new int[] { 5, 8, 0 }), array.computeIndex(5, 8, 0));
- assertEquals(array.computeIndex(new int[] { 9, 1, 2 }), array.computeIndex(9, 1, 2));
+ array = new TestMDArray(new int[]
+ { 100, 10, 17 });
+ assertEquals(array.computeIndex(new int[]
+ { 5, 8, 16 }), array.computeIndex(5, 8, 16));
+ assertEquals(array.computeIndex(new int[]
+ { 9, 1, 5 }), array.computeIndex(9, 1, 5));
+ array = new TestMDArray(new int[]
+ { 101, 11, 3 });
+ assertEquals(array.computeIndex(new int[]
+ { 5, 8, 0 }), array.computeIndex(5, 8, 0));
+ assertEquals(array.computeIndex(new int[]
+ { 9, 1, 2 }), array.computeIndex(9, 1, 2));
+ }
+
+ @Test
+ public void testMDFloatArrayMatrix()
+ {
+ final float[][] matrix1 = new float[][]
+ {
+ { 1f, 2f, 3f, 4f },
+ { 5f, 6f, 7f, 8f },
+ { 9f, 10f, 11f, 12f } };
+ final MDFloatArray array = new MDFloatArray(matrix1);
+ assertEquals(2, array.rank());
+ assertEquals(12, array.size());
+ assertEquals(3, array.size(0));
+ assertEquals(4, array.size(1));
+ assertEquals(7f, array.get(1, 2));
+ final float[][] matrix2 = array.toMatrix();
+ assertEquals(matrix1.length, matrix2.length);
+ for (int i = 0; i < matrix1.length; ++i)
+ {
+ assertTrue(Arrays.equals(matrix1[i], matrix2[i]));
+ }
}
}