Merge pull request #101 from jacobdwatters/develop

Add sparse CSR matrix implementations.

pom.xml

@@ -3,19 +3,16 @@
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
-
-    <groupId>com.flag4j</groupId>
+    <groupId>org.flag4j</groupId>
     <artifactId>flag4j</artifactId>
-    <version>v0.0.1-beta</version>
-
+    <version>v0.1.0-beta</version>
     <distributionManagement>
         <repository>
             <id>github</id>
             <name>GitHub jacobdwatters Apache Maven Packages</name>
             <url>https://maven.pkg.github.com/jacobdwatters/Flag4j</url>
         </repository>
     </distributionManagement>
-
     <dependencies>
         <dependency>
             <groupId>junit</groupId>
@@ -30,18 +27,15 @@
             <scope>test</scope>
         </dependency>
     </dependencies>
-
     <properties>
         <maven.compiler.source>16</maven.compiler.source>
         <maven.compiler.target>16</maven.compiler.target>
         <sonar.organization>jacobdwatters</sonar.organization>
         <sonar.host.url>https://sonarcloud.io</sonar.host.url>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     </properties>
-
     <build>
         <testSourceDirectory>src/test/java</testSourceDirectory>
-
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -52,7 +46,6 @@
                     <target>11</target>
                 </configuration>
             </plugin>
-
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
@@ -61,7 +54,6 @@
                     <testFailureIgnore>true</testFailureIgnore>
                 </configuration>
             </plugin>
-
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
@@ -88,5 +80,4 @@
             </plugin>
         </plugins>
     </build>
-
 </project>

src/main/java/org/flag4j/arrays/dense/CTensor.java

@@ -184,8 +184,7 @@ protected CTensor makeTensor(Shape shape, CNumber[] entries) {
      */
     @Override
     public CooCTensor toCoo() {
-        // TODO: Implementation.
-        return null;
+        return CooCTensor.fromDense(this);
     }
 
 

src/main/java/org/flag4j/arrays/dense/CVector.java

@@ -1144,7 +1144,7 @@ public CVector flatten() {
      */
     @Override
     public CVector flatten(int axis) {
-        return null;
+        return this.copy();
     }
 
 
@@ -1159,6 +1159,36 @@ public int size() {
     }
 
 
+    /**
+     * Repeats a vector {@code n} times along a certain axis to create a matrix.
+     *
+     * @param n Number of times to repeat vector.
+     * @param axis Axis along which to repeat vector. If {@code axis=0} then each row of the resulting matrix will be equivalent to
+     * this vector. If {@code axis=1} then each column of the resulting matrix will be equivalent to this vector.
+     *
+     * @return A matrix whose rows/columns are this vector repeated.
+     */
+    @Override
+    public CMatrix repeat(int n, int axis) {
+        ParameterChecks.assertInRange(axis, 0, 1, "axis");
+        ParameterChecks.assertGreaterEq(0, n, "n");
+        Shape tiledShape;
+        CNumber[] tiledEntries = new CNumber[size*n];
+
+        if(axis==0) {
+            tiledShape = new Shape(n, size);
+            for(int i=0; i<n; i++) // Set each row of the tiled matrix to be the vector values.
+                ArrayUtils.arraycopy(entries, 0, tiledEntries, i*size, size);
+        } else {
+            tiledShape = new Shape(size, n);
+            for(int i=0; i<size; i++) // Fill each row of the tiled matrix with a single value from the vector.
+                ArrayUtils.fill(tiledEntries, i*n, (i+1)*n, entries[i]);
+        }
+
+        return new CMatrix(tiledShape, tiledEntries);
+    }
+
+
     /**
      * Factory to create a tensor with the specified shape and size.
      *

src/main/java/org/flag4j/arrays/dense/Vector.java

@@ -1105,6 +1105,37 @@ public int size() {
     }
 
 
+    /**
+     * Repeats a vector {@code n} times along a certain axis to create a matrix.
+     *
+     * @param n Number of times to repeat vector.
+     * @param axis Axis along which to repeat vector. If {@code axis=0} then each row of the resulting matrix will be equivalent to
+     * this vector. If {@code axis=1} then each column of the resulting matrix will be equivalent to this vector.
+     *
+     * @return A matrix whose rows/columns are this vector repeated.
+     */
+    @Override
+    public Matrix repeat(int n, int axis) {
+        ParameterChecks.assertInRange(axis, 0, 1, "axis");
+        ParameterChecks.assertGreaterEq(0, n, "n");
+        Matrix tiled;
+
+        if(axis==0) {
+            tiled = new Matrix(new Shape(n, size));
+
+            for(int i=0; i<tiled.numRows; i++) // Set each row of the tiled matrix to be the vector values.
+                System.arraycopy(entries, 0, tiled.entries, i*tiled.numCols, size);
+        } else {
+            tiled = new Matrix(new Shape(size, n));
+
+            for(int i=0; i<tiled.numRows; i++) // Fill each row of the tiled matrix with a single value from the vector.
+                Arrays.fill(tiled.entries, i*tiled.numCols, (i+1)*tiled.numCols, entries[i]);
+        }
+
+        return tiled;
+    }
+
+
     /**
      * Flattens a tensor along the specified axis. For a vector, this simply copies the vector.
      *

src/main/java/org/flag4j/arrays/sparse/CooCMatrix.java

@@ -893,17 +893,17 @@ public CMatrix mult(Matrix B) {
     /**
      * Computes the matrix-vector multiplication.
      *
-     * @param B Vector to multiply this matrix to.
+     * @param b Vector to multiply this matrix to.
      * @return The vector result from multiplying this matrix by the vector {@code B}.
      * @throws IllegalArgumentException If the number of columns in this matrix do not equal the number of
      *                                  entries {@code B}.
      */
     @Override
-    public CVector mult(CooCVector B) {
-        ParameterChecks.assertEquals(numCols, B.size);
+    public CVector mult(CooCVector b) {
+        ParameterChecks.assertEquals(numCols, b.size);
         CNumber[] dest = ComplexSparseMatrixMultiplication.standardVector(
                 entries, rowIndices, colIndices, shape,
-                B.entries, B.indices
+                b.entries, b.indices
         );
         return new CVector(dest);
     }

src/main/java/org/flag4j/arrays/sparse/CooCTensor.java

@@ -25,11 +25,15 @@
 package org.flag4j.arrays.sparse;
 
 import org.flag4j.arrays.dense.CTensor;
+import org.flag4j.arrays.dense.Tensor;
 import org.flag4j.complex_numbers.CNumber;
 import org.flag4j.core.Shape;
 import org.flag4j.core.sparse_base.ComplexSparseTensorBase;
 import org.flag4j.operations.sparse.coo.complex.ComplexSparseEquals;
 
+import java.util.ArrayList;
+import java.util.List;
+
 
 /**
  * Complex sparse tensor. Stored in coordinate (COO) format.
@@ -671,7 +675,32 @@ protected CooTensor makeRealTensor(Shape shape, double[] entries, int[][] indice
      */
     @Override
     public void sortIndices() {
+        // TODO: Implementation
+    }
+
+
+    /**
+     * Converts a sparse {@link CooCTensor} from a dense {@link Tensor}. This is likely only worthwhile for very sparse tensors.
+     * @param src Dense tensor to convert to sparse COO tensor.
+     * @return A COO tensor which is equivalent to the {@code src} dense tensor.
+     */
+    public static CooCTensor fromDense(CTensor src) {
+        List<CNumber> entries = new ArrayList<>();
+        List<int[]> indices = new ArrayList<>();
+
+        int size = src.entries.length;
+        CNumber value;
+
+        for(int i=0; i<size; i++) {
+            value = src.entries[i].copy();
+
+            if(value.equals(CNumber.zero())) {
+                entries.add(value);
+                indices.add(src.shape.getIndices(i));
+            }
+        }
 
+        return new CooCTensor(src.shape.copy(), entries.toArray(new CNumber[0]), indices.toArray(new int[0][]));
     }
 
 

src/main/java/org/flag4j/arrays/sparse/CooCVector.java

@@ -1471,6 +1471,49 @@ public int size() {
     }
 
 
+    /**
+     * Repeats a vector {@code n} times along a certain axis to create a matrix.
+     *
+     * @param n Number of times to repeat vector.
+     * @param axis Axis along which to repeat vector. If {@code axis=0} then each row of the resulting matrix will be equivalent to
+     * this vector. If {@code axis=1} then each column of the resulting matrix will be equivalent to this vector.
+     *
+     * @return A matrix whose rows/columns are this vector repeated.
+     */
+    @Override
+    public CooCMatrix repeat(int n, int axis) {
+        ParameterChecks.assertInRange(axis, 0, 1, "axis");
+        ParameterChecks.assertGreaterEq(0, n, "n");
+
+        Shape tiledShape;
+        CNumber[] tiledEntries = new CNumber[n*entries.length];
+        int[] tiledRows = new int[tiledEntries.length];
+        int[] tiledCols = new int[tiledEntries.length];
+        int nnz = entries.length;
+
+        if(axis==0) {
+            tiledShape = new Shape(n, size);
+
+            for(int i=0; i<n; i++) { // Copy values into row and set col indices as vector indices.
+                ArrayUtils.arraycopy(entries, 0, tiledEntries, i*nnz, nnz);
+                System.arraycopy(indices, 0, tiledCols, i*nnz, indices.length);
+                Arrays.fill(tiledRows, i*nnz, (i+1)*nnz, i);
+            }
+        } else {
+            int[] colIndices = ArrayUtils.intRange(0, n);
+            tiledShape = new Shape(size, n);
+
+            for(int i=0; i<entries.length; i++) {
+                ArrayUtils.fill(tiledEntries, i*n, (i+1)*n, entries[i]);
+                Arrays.fill(tiledRows, i*n, (i+1)*n, indices[i]);
+                System.arraycopy(colIndices, 0, tiledCols, i*n, n);
+            }
+        }
+
+        return new CooCMatrix(tiledShape, tiledEntries, tiledRows, tiledCols);
+    }
+
+
     /**
      * Converts this sparse tensor to an equivalent dense tensor.
      *

src/main/java/org/flag4j/arrays/sparse/CooMatrix.java

@@ -54,7 +54,17 @@
 import java.util.List;
 
 /**
- * Real sparse matrix. Matrix is stored in coordinate list (COO) format.
+ * <p>Real sparse matrix. Matrix is stored in coordinate list (COO) format.</p>
+ *
+ * <p>COO matrices are best suited for efficient modification and construction of sparse matrices. Coo matrices are <b>not</b> well
+ * suited for matrix-matrix or matrix-vector multiplication (see {@link CsrMatrix}).</p>
+ *
+ * <p>If a sparse matrix needs to be incrementally constructed, then a COO matrix should be used to construct the matrix as it
+ * allows for efficient modification. If the matrix then needs to be used in a matrix-matrix or matrix-vector multiplication
+ * problem, it should first be converted to a {@link CsrMatrix} in most cases.</p>
+ *
+ * @see CsrMatrix
+ * @see CooCMatrix
  */
 public class CooMatrix
         extends RealSparseTensorBase<CooMatrix, Matrix, CooCMatrix, CMatrix>
@@ -1074,10 +1084,10 @@ public Matrix mult(Matrix B) {
 
 
     @Override
-    public Vector mult(CooVector B) {
+    public Vector mult(CooVector b) {
         double[] dest = RealSparseMatrixMultiplication.standardVector(
                 entries, rowIndices, colIndices, shape,
-                B.entries, B.indices
+                b.entries, b.indices
         );
         return new Vector(dest);
     }

src/main/java/org/flag4j/arrays/sparse/CooVector.java

@@ -1267,6 +1267,49 @@ public int size() {
     }
 
 
+    /**
+     * Repeats a vector {@code n} times along a certain axis to create a matrix.
+     *
+     * @param n Number of times to repeat vector.
+     * @param axis Axis along which to repeat vector. If {@code axis=0} then each row of the resulting matrix will be equivalent to
+     * this vector. If {@code axis=1} then each column of the resulting matrix will be equivalent to this vector.
+     *
+     * @return A matrix whose rows/columns are this vector repeated.
+     */
+    @Override
+    public CooMatrix repeat(int n, int axis) {
+        ParameterChecks.assertInRange(axis, 0, 1, "axis");
+        ParameterChecks.assertGreaterEq(0, n, "n");
+
+        Shape tiledShape;
+        double[] tiledEntries = new double[n*entries.length];
+        int[] tiledRows = new int[tiledEntries.length];
+        int[] tiledCols = new int[tiledEntries.length];
+        int nnz = entries.length;
+
+        if(axis==0) {
+            tiledShape = new Shape(n, size);
+
+            for(int i=0; i<n; i++) { // Copy values into row and set col indices as vector indices.
+                System.arraycopy(entries, 0, tiledEntries, i*nnz, nnz);
+                System.arraycopy(indices, 0, tiledCols, i*nnz, indices.length);
+                Arrays.fill(tiledRows, i*nnz, (i+1)*nnz, i);
+            }
+        } else {
+            int[] colIndices = ArrayUtils.intRange(0, n);
+            tiledShape = new Shape(size, n);
+
+            for(int i=0; i<entries.length; i++) {
+                Arrays.fill(tiledEntries, i*n, (i+1)*n, entries[i]);
+                Arrays.fill(tiledRows, i*n, (i+1)*n, indices[i]);
+                System.arraycopy(colIndices, 0, tiledCols, i*n, n);
+            }
+        }
+
+        return new CooMatrix(tiledShape, tiledEntries, tiledRows, tiledCols);
+    }
+
+
     /**
      * Simply returns a reference of this tensor.
      *