📝 Update documentation

src/main/java/weka/core/progress/CommandLineProgressBar.java

@@ -8,8 +8,8 @@
 import java.util.TimerTask;
 
 @Log4j2
-/**
- * Command line implementation of a progress bar
+/*
+  Command line implementation of a progress bar
  */
 public class CommandLineProgressBar extends AbstractProgressBar {
 

src/main/java/weka/dl4j/interpretability/AbstractCNNSaliencyMapGenerator.java

@@ -14,7 +14,11 @@
 import java.util.ArrayList;
 import java.util.List;
 
-// TODO document
+/**
+ * Generic class for a saliency map generator.
+ * Only implemented by ScoreCAM currently so some fields may need to be refactored when implementing a new
+ * generator method.
+ */
 public abstract class AbstractCNNSaliencyMapGenerator {
 
     protected ComputationGraph computationGraph = null;

src/main/java/weka/dl4j/interpretability/AbstractCNNSaliencyMapWrapper.java

@@ -20,8 +20,12 @@
 import java.util.Arrays;
 import java.util.Enumeration;
 
-// TODO Document
-
+/**
+ * WEKA Wrapper for a Saliency Map Generator (e.g., ScoreCAM).
+ * Provides the WEKA handles and getters/setters to control the
+ * generator from the command line/GUI.
+ *
+ */
 @Log4j2
 public abstract class AbstractCNNSaliencyMapWrapper implements Serializable, OptionHandler {
 
@@ -64,6 +68,7 @@ public void saveResult(BufferedImage completeCompositeImage) {
         }
     }
 
+    @ProgrammaticProperty
     public String[] getClassMap() {
         return classMap;
     }
@@ -72,6 +77,7 @@ public void setClassMap(String[] classMap) {
         this.classMap = classMap;
     }
 
+    @ProgrammaticProperty
     public Dl4jMlpClassifier getDl4jMlpClassifier() {
         return dl4jMlpClassifier;
     }
@@ -80,6 +86,7 @@ public void setDl4jMlpClassifier(Dl4jMlpClassifier dl4jMlpClassifier) {
         this.dl4jMlpClassifier = dl4jMlpClassifier;
     }
 
+    @ProgrammaticProperty
     public CustomModelSetup getCustomModelSetup() {
         return customModelSetup;
     }

src/main/java/weka/dl4j/interpretability/ScoreCAM.java

@@ -29,7 +29,10 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 
-// TODO document
+
+/**
+ *
+ */
 @Log4j2
 public class ScoreCAM extends AbstractCNNSaliencyMapGenerator {
 

src/main/java/weka/dl4j/interpretability/WekaScoreCAM.java

@@ -8,7 +8,28 @@
 import java.awt.image.BufferedImage;
 import java.io.File;
 
-// TODO Document
+/**
+ * WEKA Wrapper for the Deeplearning4j ScoreCAM implementation.
+ * <!-- options-start -->
+ * Valid options are: <p>
+ *
+ * <pre> -bs &lt;int&gt;
+ *  The mini batch size to use for map generation</pre>
+ *
+ * <pre> -target-classes &lt;int,int,...&gt;
+ *  Output class to generate saliency maps for; default is -1 (use the highest probability class). This only needs to be set if wanting to use a non-default class from the *command line*; if using the *GUI*, the 'View Saliency Map' window contains the interface for setting this.</pre>
+ *
+ * <pre> -output &lt;file location&gt;
+ *  File for the saliency map to be saved in</pre>
+ *
+ * <pre> -normalize
+ *  When generating the heatmap, should the values be normalized to be in [0, 1]</pre>
+ *
+ * <!-- options-end -->
+ *
+ * <!-- globalinfo-start -->
+ * <!-- globalinfo-end -->
+ */
 @Log4j2
 public class WekaScoreCAM extends AbstractCNNSaliencyMapWrapper {
 

src/main/java/weka/filters/unsupervised/attribute/Dl4jStringToWordEmbeddings.java

@@ -421,6 +421,7 @@ public void setTokenizerFactory(TokenizerFactory m_tokenizerFactory) {
       commandLineParamSynopsis = "-preprocessor <String>",
       displayOrder = 5
   )
+
   /**
    * Gets the action for the selected preprocessor.
    *