Fixed missing javadocs and code cleanup

pom.xml

@@ -119,10 +119,10 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.11.0</version>
+                <version>3.12.0</version>
                 <configuration>
-                    <source>8</source>
-                    <target>8</target>
+                    <source>9</source>
+                    <target>9</target>
                     <encoding>${project.build.sourceEncoding}</encoding>
                 </configuration>
             </plugin>

src/main/java/com/github/psambit9791/jdsp/filter/FIRWin2.java

@@ -144,6 +144,10 @@ public FIRWin2(int numTaps) {
         }
     }
 
+    /**
+     * Returns the filter type determined from numTaps
+     * @return int the filter type
+     */
     public int getFilterType() {
         return this.ftype;
     }

src/main/java/com/github/psambit9791/jdsp/filter/_IIRFilter.java

@@ -28,7 +28,7 @@ public interface _IIRFilter {
      * @param cutoffFreq The cutoff frequency for the filter
      * @return double[] Filtered signal
      */
-    public double[] lowPassFilter(double[] signal, int order, double cutoffFreq);
+    double[] lowPassFilter(double[] signal, int order, double cutoffFreq);
 
     /**
      * This method implements a high pass filter with given parameters, filters the signal and returns it.
@@ -37,7 +37,7 @@ public interface _IIRFilter {
      * @param cutoffFreq The cutoff frequency for the filter
      * @return double[] Filtered signal
      */
-    public double[] highPassFilter(double[] signal, int order, double cutoffFreq);
+    double[] highPassFilter(double[] signal, int order, double cutoffFreq);
 
     /**
      * This method implements a band pass filter with given parameters, filters the signal and returns it.
@@ -47,7 +47,7 @@ public interface _IIRFilter {
      * @param highCutoff The upper cutoff frequency for the filter
      * @return double[] Filtered signal
      */
-    public double[] bandPassFilter(double[] signal, int order, double lowCutoff, double highCutoff);
+    double[] bandPassFilter(double[] signal, int order, double lowCutoff, double highCutoff);
 
     /**
      * This method implements a band stop filter with given parameters, filters the signal and returns it.
@@ -57,6 +57,6 @@ public interface _IIRFilter {
      * @param highCutoff The upper cutoff frequency for the filter
      * @return double[] Filtered signal
      */
-    public double[] bandStopFilter(double[] signal, int order, double lowCutoff, double highCutoff);
+    double[] bandStopFilter(double[] signal, int order, double lowCutoff, double highCutoff);
 
 }

src/main/java/com/github/psambit9791/jdsp/filter/_KernelFilter.java

@@ -26,5 +26,5 @@ public interface _KernelFilter {
      * @param signal Signal to be filtered
      * @return double[] Filtered signal
      */
-    public double[] filter(double[] signal);
+    double[] filter(double[] signal);
 }

src/main/java/com/github/psambit9791/jdsp/filter/adaptive/_Adaptive.java

@@ -25,7 +25,7 @@ public interface _Adaptive {
      *      RANDOM: filter weights get an initial random value ranging from 0 to 1
      *      ZEROS: filter weights get initial value 0
      */
-    public enum WeightsFillMethod {
+    enum WeightsFillMethod {
         RANDOM,
         ZEROS
     }
@@ -36,5 +36,5 @@ public enum WeightsFillMethod {
      * @param desired desired signal that you want after filtering of x
      * @param x input signal that you want to filter with the LMS adaptive filter to achieve the desired signal
      */
-    public void filter(double[] desired, double[] x);
+    void filter(double[] desired, double[] x);
 }

src/main/java/com/github/psambit9791/jdsp/io/WAV.java

@@ -227,6 +227,12 @@ else if (type.equals("double")) {
         }
     }
 
+    /**
+     * Return data in provided datatype
+     * @param type Datatype provided. Must be one of int, long or double
+     * @return double[][] WAV data as a 2D array
+     * @throws java.lang.IllegalArgumentException if type is not one of int, long or double
+     */
     public double[][] getData(String type) throws IllegalArgumentException {
         if (type.equals("int")) {
             return this.dataInt;

src/main/java/com/github/psambit9791/jdsp/misc/Random.java

@@ -79,6 +79,7 @@ public double randomNormalSample() {
 
     /**
      * Generate a 1D array of random samples from the normal distribution
+     * @param shape The dimension of the 1D array to generate. Must have only 1 value.
      * @return double[] 1D array of random samples from the normal distribution
      */
     public double[] randomNormal1D(int[] shape) {
@@ -94,6 +95,7 @@ public double[] randomNormal1D(int[] shape) {
 
     /**
      * Generate a 2D array of random samples from the normal distribution
+     * @param shape The dimension of the 2D array to generate. Must have only 2 values.
      * @return double[][] 2D array of random samples from the normal distribution
      */
     public double[][] randomNormal2D(int[] shape) {
@@ -111,6 +113,7 @@ public double[][] randomNormal2D(int[] shape) {
 
     /**
      * Generate a 3D array of random samples from the normal distribution
+     * @param shape The dimension of the 3D array to generate. Must have only 3 values.
      * @return double[][][] 3D array of random samples from the normal distribution
      */
     public double[][][] randomNormal3D(int[] shape) {
@@ -138,6 +141,7 @@ public double randomDoubleSample() {
 
     /**
      * Generate a 1D array of random samples between 0.0 and 1.0
+     * @param shape The dimension of the 1D array to generate. Must have only 1 value.
      * @return double[] 1D array of random decimals
      */
     public double[] randomDouble1D(int[] shape) {
@@ -153,6 +157,7 @@ public double[] randomDouble1D(int[] shape) {
 
     /**
      * Generate a 2D array of random samples between 0.0 and 1.0
+     * @param shape The dimension of the 2D array to generate. Must have only 2 values.
      * @return double[][] 2D array of random decimals
      */
     public double[][] randomDouble2D(int[] shape) {
@@ -170,6 +175,7 @@ public double[][] randomDouble2D(int[] shape) {
 
     /**
      * Generate a 3D array of random samples between 0.0 and 1.0
+     * @param shape The dimension of the 3D array to generate. Must have only 3 values.
      * @return double[][][] 3D array of random decimals
      */
     public double[][][] randomDouble3D(int[] shape) {
@@ -213,6 +219,7 @@ public int randomIntSample(int lower_bound, int upper_bound) {
 
     /**
      * Generate a 1D array of random integer between 0 and the upper bound
+     * @param shape The dimension of the 1D array to generate. Must have only 1 value.
      * @param upper_bound The maximum number up to which the integers can be generated
      * @return int[] 1D array of random integers
      */
@@ -230,6 +237,7 @@ public int[] randomInt1D(int[] shape, int upper_bound) {
 
     /**
      * Generate a 1D array of random integer between the lower bound and the upper bound
+     * @param shape The dimension of the 1D array to generate. Must have only 1 value.
      * @param lower_bound The minimum number from which the integers can be generated
      * @param upper_bound The maximum number up to which the integers can be generated
      * @return int[] 1D array of random integers
@@ -251,6 +259,7 @@ public int[] randomInt1D(int[] shape, int lower_bound, int upper_bound) {
 
     /**
      * Generate a 2D array of random integer between 0 and the upper bound
+     * @param shape The dimension of the 2D array to generate. Must have only 2 values.
      * @param upper_bound The maximum number up to which the integers can be generated
      * @return int[][] 2D array of random integers
      */
@@ -270,6 +279,7 @@ public int[][] randomInt2D(int[] shape, int upper_bound) {
 
     /**
      * Generate a 2D array of random integer between the lower bound and the upper bound
+     * @param shape The dimension of the 2D array to generate. Must have only 2 values.
      * @param lower_bound The minimum number from which the integers can be generated
      * @param upper_bound The maximum number up to which the integers can be generated
      * @return int[][] 2D array of random integers
@@ -293,6 +303,7 @@ public int[][] randomInt2D(int[] shape, int lower_bound, int upper_bound) {
 
     /**
      * Generate a 3D array of random integer between 0 and the upper bound
+     * @param shape The dimension of the 3D array to generate. Must have only 3 values.
      * @param upper_bound The maximum number up to which the integers can be generated
      * @return int[][][] 3D array of random integers
      */
@@ -314,6 +325,7 @@ public int[][][] randomInt3D(int[] shape, int upper_bound) {
 
     /**
      * Generate a 3D array of random integer between the lower bound and the upper bound
+     * @param shape The dimension of the 3D array to generate. Must have only 3 values.
      * @param lower_bound The minimum number from which the integers can be generated
      * @param upper_bound The maximum number up to which the integers can be generated
      * @return int[][][] 3D array of random integers

src/main/java/com/github/psambit9791/jdsp/misc/UtilMethods.java

@@ -31,6 +31,12 @@
  * @author  Sambit Paul
  */
 
+/**
+ * A collection of utilities
+ *
+ * @author Sambit Paul
+ * @version 1.0
+ */
 public class UtilMethods {
 
     /**

src/main/java/com/github/psambit9791/jdsp/signal/peaks/Peak.java

@@ -39,9 +39,21 @@ public class Peak {
 
     private double relative_height;
 
-    public Peak(double[] s, int[] m, int[] l, int[] r, String mode) {
+    /**
+     * This constructor initialises the prerequisites required to use Peak class. relative_height is set to 0.5 by default.
+     * @param signal The signal to be processed
+     * @param m List of midpoints
+     * @param l List of left edges
+     * @param r List of right edges
+     * @param mode mode can be one of 'peak' or 'trough'
+     * @throws java.lang.IllegalArgumentException if mode is not peak or trough
+     */
+    public Peak(double[] signal, int[] m, int[] l, int[] r, String mode) throws IllegalArgumentException {
+        if (!mode.equals("peak") && !mode.equals("trough")) {
+            throw new IllegalArgumentException("mode must be peak or trough");
+        }
 
-        this.signal = s;
+        this.signal = signal;
 
         // Peak Information
         this.midpoints = m;
@@ -54,10 +66,10 @@ public Peak(double[] s, int[] m, int[] l, int[] r, String mode) {
 
         for (int i=0; i<m.length; i++) {
             if (mode.equals("peak")) {
-                this.height[i] = s[this.midpoints[i]];
+                this.height[i] = signal[this.midpoints[i]];
             }
-            else if (mode.equals("trough")) {
-                this.height[i] = 0 - s[this.midpoints[i]];
+            else {
+                this.height[i] = 0 - signal[this.midpoints[i]];
             }
             this.plateau_size[i] = Math.abs(r[i] - l[i] + 1);
         }
@@ -81,9 +93,26 @@ else if (mode.equals("trough")) {
         this.width = widthData[0];
     }
 
-    public Peak(double[] s, int[] m, int[] l, int[] r, double rel_height, String mode) {
+    /**
+     * This constructor initialises the prerequisites required to use Peak class.
+     * @param signal The signal to be processed
+     * @param m List of midpoints
+     * @param l List of left edges
+     * @param r List of right edges
+     * @param rel_height relative height at which the peak width is measured as a percentage of its prominence.
+     * @param mode mode can be one of 'peak' or 'trough'
+     * @throws java.lang.IllegalArgumentException if mode is not peak or trough
+     * @throws java.lang.IllegalArgumentException if rel_height is not between 0.0 and 1.0
+     */
+    public Peak(double[] signal, int[] m, int[] l, int[] r, double rel_height, String mode) throws IllegalArgumentException {
+        if (!mode.equals("peak") && !mode.equals("trough")) {
+            throw new IllegalArgumentException("mode must be peak or trough");
+        }
+        if ((rel_height < 0) || (rel_height>1)) {
+            throw new IllegalArgumentException("rel_height should be between 0.0 and 1.0");
+        }
 
-        this.signal = s;
+        this.signal = signal;
 
         // Peak Information
         this.midpoints = m;
@@ -96,10 +125,10 @@ public Peak(double[] s, int[] m, int[] l, int[] r, double rel_height, String mod
 
         for (int i=0; i<m.length; i++) {
             if (mode.equals("peak")) {
-                this.height[i] = s[this.midpoints[i]];
+                this.height[i] = signal[this.midpoints[i]];
             }
             else if (mode.equals("trough")) {
-                this.height[i] = 0 - s[this.midpoints[i]];
+                this.height[i] = 0 - signal[this.midpoints[i]];
             }
             this.plateau_size[i] = Math.abs(r[i] - l[i] + 1);
         }
@@ -118,7 +147,7 @@ else if (mode.equals("trough")) {
 
         // Peak Width Information (Equivalent to scipy.signal.find_peaks() width parameter)
         // Refer to https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.peak_widths.html
-        this.relative_height = 0.5;
+        this.relative_height = rel_height;
         this.widthData = this.findPeakWidth(this.midpoints, this.relative_height);
         this.width = widthData[0];
     }

src/main/java/com/github/psambit9791/jdsp/signal/peaks/Spike.java

@@ -34,6 +34,13 @@ public class Spike {
     private double[] max_spike;
     private double[] min_spike;
 
+    /**
+     * This constructor initialises the prerequisites required to use Peak class.
+     * @param signal The signal to be processed
+     * @param peaks The detected peaks
+     * @param left The troughs on the left (corresponding to the peak indices)
+     * @param right The troughs on the right (corresponding to the peak indices)
+     */
     public Spike(double[] signal, int[] peaks, int[] left, int[] right) {
         this.signal = signal;
         this.peaks = peaks;

src/main/java/com/github/psambit9791/jdsp/transform/DiscreteCosine.java

@@ -183,7 +183,7 @@ public void transform() {
     }
 
     /**
-     * Gets the length of the input signal.
+     * Returns the length of the input signal.
      *
      * @return int The updated length of the input signal.
      */

src/main/java/com/github/psambit9791/jdsp/transform/DiscreteFourier.java

@@ -41,7 +41,8 @@ public DiscreteFourier(double[] s) {
     }
 
     /**
-     * Return the length of the modified signal (padded length)
+     * Returns the length of the modified signal (padded length)
+     * @return int The modified length of the input signal
      */
     public int getSignalLength() {
         return this.signal.length;

src/main/java/com/github/psambit9791/jdsp/transform/DiscreteSine.java

@@ -167,7 +167,7 @@ public void transform() {
     }
 
     /**
-     * Gets the length of the input signal.
+     * Returns the length of the input signal.
      *
      * @return int The updated length of the input signal.
      */

src/main/java/com/github/psambit9791/jdsp/transform/FastCosine.java

@@ -106,7 +106,7 @@ public double[] getOutput() throws ExceptionInInitializerError {
     }
 
     /**
-     * Gets the length of the input signal after preprocessing for FastSine (padded to nearest power of 2).
+     * Returns the length of the input signal after preprocessing for FastSine (padded to nearest power of 2).
      *
      * @return int The updated length of the input signal.
      */

src/main/java/com/github/psambit9791/jdsp/transform/FastFourier.java

@@ -49,7 +49,8 @@ private void extendSignal() {
     }
 
     /**
-     * Return the length of the modified signal (padded length)
+     * Returns the length of the modified signal (padded length)
+     * @return int The modified length of the input signal
      */
     public int getSignalLength() {
         return this.signal.length;

src/main/java/com/github/psambit9791/jdsp/transform/FastSine.java

@@ -106,7 +106,7 @@ public double[] getOutput() throws ExceptionInInitializerError {
     }
 
     /**
-     * Gets the length of the input signal after preprocessing for FastSine (padded to nearest power of 2).
+     * Returns the length of the input signal after preprocessing for FastSine (padded to nearest power of 2).
      *
      * @return int The updated length of the input signal.
      */

src/main/java/com/github/psambit9791/jdsp/transform/ICA.java

@@ -131,6 +131,7 @@ public ICA(double[][] signal, String func, String whiten, double[][] w_init, int
      * @param func The functional form of the G function used in the approximation to neg-entropy. Can be "logcosh", "exp" or "cube".
      * @param whiten Specifies the whitening strategy. Can be one of "unit-variance", "arbitrary-variance" or empty string.
      * @param max_iter Maximum number of iterations during fit.
+     * @param tol A positive scalar giving the tolerance at which the un-mixing matrix is considered to have converged. Defaults to 1E-4.
      * @param alpha G Function argument - only used in case of logcosh.
      * @param random_state Random seed to initialise w_init.
      */
@@ -278,11 +279,12 @@ public ICA(double[][] signal, String func) {
     /**
      * This constructor initialises the prerequisites required to use ICA.
      * @param signal Multi-dimensional signal to be transformed. Dimension 1: Samples, Dimension 2: Channels
+     * @param random_state Random seed to initialise w_init.
      */
-    public ICA(double[][] signal, long seed) {
+    public ICA(double[][] signal, long random_state) {
         this.signal = signal;
         this.components = this.signal[0].length;
-        this.seed = seed;
+        this.seed = random_state;
         Random r1 = new Random(this.seed);
         this.w_init = r1.randomNormal2D(new int[] {this.components, this.components});
     }