Add remaining design of experiments

.gitignore

@@ -18,10 +18,13 @@
 *.zip
 *.tar.gz
 *.rar
+*.lst
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
 replay_pid*
 
 # intellij
 .idea
+
+target/

README.md

@@ -1,2 +1,2 @@
-# JDOE
+# doe
 Java Design of Experiments

dependency-reduced-pom.xml

@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.doe</groupId>
+  <artifactId>doe-genereter</artifactId>
+  <name>doe</name>
+  <version>1.0-SNAPSHOT</version>
+  <url>http://maven.apache.org</url>
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-jar-plugin</artifactId>
+        <version>3.4.1</version>
+        <configuration>
+          <archive>
+            <manifest>
+              <mainClass>com.doe.Testing</mainClass>
+            </manifest>
+          </archive>
+        </configuration>
+      </plugin>
+      <plugin>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.6.1</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+            <configuration>
+              <transformers>
+                <transformer />
+              </transformers>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>4.13.2</version>
+      <scope>test</scope>
+      <exclusions>
+        <exclusion>
+          <artifactId>hamcrest-core</artifactId>
+          <groupId>org.hamcrest</groupId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-core</artifactId>
+      <version>5.20.0</version>
+      <scope>test</scope>
+      <exclusions>
+        <exclusion>
+          <artifactId>byte-buddy</artifactId>
+          <groupId>net.bytebuddy</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>byte-buddy-agent</artifactId>
+          <groupId>net.bytebuddy</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>objenesis</artifactId>
+          <groupId>org.objenesis</groupId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-inline</artifactId>
+      <version>5.2.0</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+  <properties>
+    <maven.compiler.target>17</maven.compiler.target>
+    <maven.compiler.source>17</maven.compiler.source>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+</project>

pom.xml

@@ -2,12 +2,12 @@
   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.jdoe</groupId>
+  <groupId>com.doe</groupId>
   <artifactId>doe-genereter</artifactId>
   <version>1.0-SNAPSHOT</version>
   <packaging>jar</packaging>
 
-  <name>JDOE</name>
+  <name>doe</name>
   <url>http://maven.apache.org</url>
 
   <properties>
@@ -54,6 +54,19 @@
       <version>5.2.0</version>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>org.jetbrains</groupId>
+      <artifactId>annotations</artifactId>
+      <version>26.0.2</version>
+      <scope>compile</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>org.projectlombok</groupId>
+      <artifactId>lombok</artifactId>
+      <version>1.18.42</version>
+      <scope>compile</scope>
+    </dependency>
 
   </dependencies>
 
@@ -66,7 +79,7 @@
                 <configuration>
                     <archive>
                         <manifest>
-                            <mainClass>com.jdoe.Testing</mainClass>
+                            <mainClass>com.doe.Testing</mainClass>
                         </manifest>
                     </archive>
                 </configuration>

src/main/java/com/jdoe/Testing.java

@@ -1,7 +1,7 @@
-package com.jdoe;
+package com.doe;
 
-import com.jdoe.algorithms.BoxBehnkenDOE;
-import com.jdoe.algorithms.FactorialDOE;
+import com.doe.algorithms.BoxBehnkenDOE;
+import com.doe.algorithms.FactorialDOE;
 
 /**
  * Hello world!

src/main/java/com/jdoe/algorithms/BoxBehnkenDOE.java

@@ -1,4 +1,4 @@
-package com.jdoe.algorithms;
+package com.doe.algorithms;
 
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
 import org.apache.commons.math3.linear.RealMatrix;

src/main/java/com/jdoe/algorithms/BuildRegressionMatrix.java → src/main/java/com/jdoe/algorithms/BuildRegressionMatrixDOE.java

@@ -1,12 +1,12 @@
-package com.jdoe.algorithms;
+package com.doe.algorithms;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
-import com.jdoe.util.BuildRegressionMatrixUtility;
+import com.doe.util.BuildRegressionMatrixUtility;
 
-public class BuildRegressionMatrix {
+public class BuildRegressionMatrixDOE {
 
     /**
      * Builds a regression matrix from an experimental design matrix and a mathematical model string.

src/main/java/com/jdoe/algorithms/CompositeDOE.java

@@ -0,0 +1,142 @@
+package com.doe.algorithms;
+
+import org.apache.commons.math3.linear.Array2DRowFieldMatrix;
+import org.apache.commons.math3.linear.Array2DRowRealMatrix;
+import org.apache.commons.math3.linear.RealMatrix;
+import org.jetbrains.annotations.NotNull;
+
+import com.doe.util.GenericDOEUtil;
+
+public class CompositeDOE {
+
+    private static final String[] alphaParamLegalExpressions = {"orthogonal", "o", "rotatable", "r"};
+
+    private static final String[] faceParamLegalExpressions = {"circumscribed", "ccc", "inscribed", "cci", "faced", "ccf"};
+
+    public static RealMatrix centralCompositeDesign(@NotNull int numberOfFactors, @NotNull int[] centerPoints, @NotNull String alpha, @NotNull String face) {
+        validateCompositeDegisnParameters(numberOfFactors, centerPoints, alpha, face);
+
+        RealMatrix factorialDesignMatrix;
+        RealMatrix starDesignMatrix;
+        double alphaValue;
+
+        // Orthogonal Design
+        if (alpha.toLowerCase().equals("orthogonal") || alpha.toLowerCase().equals("o")) {
+            Object[] starResult = StarDOE.star(numberOfFactors, "orthogonal", centerPoints);
+            starDesignMatrix = new Array2DRowRealMatrix((double[][]) starResult[0]); // Convert array to RealMatrix
+            alphaValue = (double) starResult[1];
+        }
+        // Rotatable Design
+        else if (alpha.toLowerCase().equals("rotatable") || alpha.toLowerCase().equals("r")) {
+            Object[] starResult = StarDOE.star(numberOfFactors, "rotatable", new int[]{0, 0});
+            starDesignMatrix = new Array2DRowRealMatrix((double[][]) starResult[0]); // Convert array to RealMatrix
+            alphaValue = (double) starResult[1];
+        } else {
+            throw new IllegalArgumentException("Invalid alpha parameter: " + alpha);
+        }
+
+        // Inscribed CCD
+        if (face.toLowerCase().equals("inscribed") || face.toLowerCase().equals("cci")) {
+            factorialDesignMatrix = FactorialDOE.fullFactorial2Level(numberOfFactors);
+            factorialDesignMatrix = factorialDesignMatrix.scalarMultiply(1.0 / alphaValue);  // Scale down the factorial points
+            Object[] starResult = StarDOE.star(numberOfFactors, alpha, centerPoints);
+            starDesignMatrix = new Array2DRowRealMatrix((double[][]) starResult[0]); // Convert array to RealMatrix
+            alphaValue = (double) starResult[1];
+        }
+        // Faced CCD
+        else if (face.toLowerCase().equals("faced") || face.toLowerCase().equals("ccf")) {
+            Object[] starResult = StarDOE.star(numberOfFactors, alpha, centerPoints);
+            starDesignMatrix = new Array2DRowRealMatrix((double[][]) starResult[0]); // Convert array to RealMatrix
+            alphaValue = 1.0;
+            // Value of alpha is always 1 in Faced CCD
+            factorialDesignMatrix = FactorialDOE.fullFactorial2Level(numberOfFactors);
+        }
+        // Circumscribed CCD
+        else if (face.toLowerCase().equals("circumscribed") || face.toLowerCase().equals("ccc")) {
+            factorialDesignMatrix = FactorialDOE.fullFactorial2Level(numberOfFactors);
+        } else {
+            throw new IllegalArgumentException("Invalid face parameter: " + face);
+        }
+
+        RealMatrix centerPointsMatrix1 = RepeatCenterDOE.repeatCenter(numberOfFactors, centerPoints[0]);
+        RealMatrix centerPointsMatrix2 = RepeatCenterDOE.repeatCenter(numberOfFactors, centerPoints[1]);
+
+        factorialDesignMatrix = UnionDOE.matrixUnion(factorialDesignMatrix, centerPointsMatrix1);
+        starDesignMatrix = UnionDOE.matrixUnion(starDesignMatrix, centerPointsMatrix2);
+        RealMatrix finalDesignMatrix = UnionDOE.matrixUnion(factorialDesignMatrix, starDesignMatrix);
+
+        return finalDesignMatrix;
+    }
+
+    //<-----------------------------Utility Methods---------------------------------->
+
+    public static void validateCompositeDegisnParameters(int numberOfFactors, int[] centerPoints, String alpha, String face) {
+        if (numberOfFactors < 1) {
+            throw new IllegalArgumentException("number of factors must be greater than 1");
+        }
+        if (centerPoints.length != 2) {  // Fixed: was == now !=
+            throw new IllegalArgumentException(String.format("Invalid number of values for \"center\" (expected 2, but got %d)", centerPoints.length));
+        }
+        if (validateExpression(alpha, alphaParamLegalExpressions) == Boolean.FALSE) {
+            throw new IllegalArgumentException(String.format("Invalid value for \"alpha\" (expected one of %s)", java.util.Arrays.toString(alphaParamLegalExpressions)));
+        }
+        if (validateExpression(face, faceParamLegalExpressions) == Boolean.FALSE) {
+            throw new IllegalArgumentException(String.format("Invalid value for \"face\" (expected one of %s)", java.util.Arrays.toString(faceParamLegalExpressions)));
+        }
+    }
+
+    public static Boolean validateExpression(String expression, String[] legalExpressions) {
+        Boolean validInput = Boolean.FALSE;
+        for (String legalExpression : legalExpressions) {
+            if (legalExpression.equals(expression)) {
+                validInput = Boolean.TRUE;
+                break;
+            }
+        }
+        return validInput;
+    }
+
+}
+
+//<-----------------------------STEPS---------------------------------->
+
+/**
+ * Detailed Steps to Port Central Composite Design Script to Java
+ * <p>
+ * $ 1. Create CompositeDOE Class Structure Create CompositeDOE.java in com.doe.algorithms package Add imports:
+ * org.apache.commons.math3.linear.* for matrix operations Define method signature: public static RealMatrix centralCompositeDesign(int n,
+ * int[] center, String alpha, String face) Set default parameters handling for center, alpha, and face
+ * <p>
+ * $ 2. Implement Input Validation Logic Add assertion: assert n > 1 : "\"n\" must be an integer greater than 1" Validate alpha parameter
+ * with: alpha.toLowerCase() and check against allowed values Validate face parameter with: face.toLowerCase() and check against allowed
+ * values Validate center array length: if (center.length != 2) throw IllegalArgumentException Format error messages to match Python
+ * implementation
+ * <p>
+ * $ 3. Implement Star Point Generation Create StarDOE.java class with star method Calculate alpha based on alpha type: For orthogonal:
+ * alpha = Math.pow(2 * factorial(n), 0.25) where factorial(n) = n! For rotatable: alpha = Math.pow(2, 0.5) for 2D, Math.pow(3, 0.5) for 3D,
+ * etc. Generate 2n star points with values [±alpha, 0, ..., 0], [0, ±alpha, ..., 0], etc. Return both star matrix and alpha value as an
+ * Object array
+ * <p>
+ * 4. Enhance FactorialDOE Class Add ff2n method that generates 2-level factorial design Create 2^n × n matrix with values -1 and +1 Use bit
+ * manipulation: for each row i and column j, set value to ((i >> j) & 1) == 0 ? -1 : 1 Return RealMatrix object
+ * <p>
+ * 5. Create UnionDOE Class Implement union method that combines two matrices vertically Use Array2DRowRealMatrix constructor to create new
+ * matrix with combined rows Copy data from both input matrices to the result matrix Return the concatenated matrix
+ * <p>
+ * 6. Create RepeatCenterDOE Class Implement repeatCenter method that generates center points Create repeats × n matrix filled with zeros
+ * Use new Array2DRowRealMatrix(repeats, n) to initialize matrix Return the center point matrix
+ * <p>
+ * 7. Implement Core Algorithm Logic Initialize H1 andH2 matrices based on face type For inscribed (cci): scale factorial points H1 =
+ * H1.scalarMultiply(1.0/a) For faced (ccf): set alpha to 1.0 For circumscribed (ccc): keep original factorial points Generate center points
+ * C1 and C2 using repeatCenter Combine matrices: H1 = union(H1, C1), H2 = union(H2, C2), H = union(H1, H2)
+ * <p>
+ * 8. Handle Matrix Operations Implement matrix scaling using scalarMultiply() method from Commons Math Ensure all matrix dimensions are
+ * compatible for union operations Use getSubMatrix() and setSubMatrix() for matrix manipulations Return final RealMatrix object
+ * <p>
+ * 9. Create Unit Tests Create CompositeDOETest.java with comprehensive test cases Test all three face types: ccc, cci, ccf Test both alpha
+ * types: orthogonal, rotatable Validate matrix dimensions: (2^n + 2n + sum(center)) × n Verify center point counts and star point
+ * distances
+ * <p>
+ * 10. Add Documentation and Error Handling Add JavaDoc explaining parameters, return value, and exceptions Implement proper exception
+ * handling for invalid inputs Include example usage in documentation Follow the same error message format as Python implementation
+ */

src/main/java/com/jdoe/algorithms/CranleyPattersonShiftDOE.java

@@ -0,0 +1,66 @@
+package com.doe.algorithms;
+
+import org.apache.commons.math3.linear.Array2DRowRealMatrix;
+import org.apache.commons.math3.linear.RealMatrix;
+import org.apache.commons.math3.random.RandomDataGenerator;
+import org.apache.commons.math3.random.JDKRandomGenerator;
+
+public class CranleyPattersonShiftDOE {
+
+    public static RealMatrix cranleyPattersonShift(double[][] points, Integer seed) {
+        if (points == null || points.length == 0 || points[0].length == 0) {
+            throw new IllegalArgumentException("Input `points` must be a non-null 2D array with at least one element.");
+        }
+
+        RealMatrix pointsMatrix = new Array2DRowRealMatrix(points);
+
+        int nSamples = pointsMatrix.getRowDimension();
+        int dim = pointsMatrix.getColumnDimension();
+
+        // Initialize random generator with seed if provided
+        RandomDataGenerator rng;
+        if (seed != null) {
+            JDKRandomGenerator jdkRng = new JDKRandomGenerator();
+            jdkRng.setSeed(seed);
+            rng = new RandomDataGenerator(jdkRng);  // Use Apache Commons Math generator
+        } else {
+            rng = new RandomDataGenerator();
+        }
+
+        // Generate random shift vector
+        double[] shiftVector = new double[dim];
+        for (int i = 0; i < dim; i++) {
+            shiftVector[i] = rng.nextUniform(0.0, 1.0);
+        }
+
+        // Create a matrix with the shift vector replicated for each sample
+        double[][] shiftMatrixData = new double[nSamples][dim];
+        for (int i = 0; i < nSamples; i++) {
+            for (int j = 0; j < dim; j++) {
+                shiftMatrixData[i][j] = shiftVector[j];
+            }
+        }
+
+        RealMatrix shiftMatrix = new Array2DRowRealMatrix(shiftMatrixData);
+
+        // Add the shift vector to all points
+        RealMatrix shiftedPoints = pointsMatrix.add(shiftMatrix);
+
+        // Wrap values to [0, 1) using modulo operation
+        double[][] resultData = shiftedPoints.getData();
+        for (int i = 0; i < nSamples; i++) {
+            for (int j = 0; j < dim; j++) {
+                resultData[i][j] = resultData[i][j] - Math.floor(resultData[i][j]);
+            }
+        }
+
+        return new Array2DRowRealMatrix(resultData);
+    }
+
+    /**
+     * Overloaded method without seed parameter
+     */
+    public static RealMatrix cranleyPattersonShift(double[][] points) {
+        return cranleyPattersonShift(points, null);
+    }
+}