refactored the interface for Classifier to deprecate the Map based me…

README.md

@@ -2,6 +2,8 @@
 
 This project aims to used text exported ML models generated by sci-kit learn and make them usable in Java.
 
+[![javadoc](https://javadoc.io/badge2/rocks.vilaverde/scikit-learn-2-java/javadoc.svg)](https://javadoc.io/doc/rocks.vilaverde/scikit-learn-2-java)
+
 ## Support
 * The tree.DecisionTreeClassifier is supported
   * Supports `predict()`,
@@ -48,24 +50,25 @@ As an example, a DecisionTreeClassifier model trained on the Iris dataset and ex
 ```
 
 The exported text can then be executed in Java. Note that when calling `export_text` it is 
-recommended that `max_depth` be set to sys.maxsize so that the tree isn't truncated.
+recommended that `max_depth` be set to `sys.maxsize` so that the tree isn't truncated.
 
 ### Java Example
-In this example the iris model exported using `export_tree` is parsed, features are created as a Java Map
+In this example the iris model exported using `export_text` is parsed, features are created as a Java Map
 and the decision tree is asked to predict the class.
 
 ```
     Reader tree = getTrainedModel("iris.model");
     final Classifier<Integer> decisionTree = DecisionTreeClassifier.parse(tree,
                 PredictionFactory.INTEGER);
 
-    Map<String, Double> features = new HashMap<>();
-    features.put("sepal length (cm)", 3.0);
-    features.put("sepal width (cm)", 5.0);
-    features.put("petal length (cm)", 4.0);
-    features.put("petal width (cm)", 2.0);
+    Features features = Features.of("sepal length (cm)",
+                "sepal width (cm)",
+                "petal length (cm)",
+                "petal width (cm)");
+    FeatureVector fv = features.newSample();
+    fv.add(0, 3.0).add(1, 5.0).add(2, 4.0).add(3, 2.0);
 
-    Integer prediction = decisionTree.predict(features);
+    Integer prediction = decisionTree.predict(fv);
     System.out.println(prediction.toString());
 ```
 
@@ -107,7 +110,7 @@ Then you can use the RandomForestClassifier class to parse the TAR archive.
     ...
 
     TarArchiveInputStream tree = getArchive("iris.tgz");
-    final Classifier<Integer> decisionTree = RandomForestClassifier.parse(tree,
+    final Classifier<Double> decisionTree = RandomForestClassifier.parse(tree,
                 PredictionFactory.DOUBLE);
 ```
 

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>rocks.vilaverde</groupId>
     <artifactId>scikit-learn-2-java</artifactId>
-    <version>1.0.3-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
 
     <name>${project.groupId}:${project.artifactId}</name>
     <description>A sklearn exported_text models parser for executing in the Java runtime.</description>

src/main/java/rocks/vilaverde/classifier/AbstractTreeClassifier.java

@@ -0,0 +1,50 @@
+package rocks.vilaverde.classifier;
+
+import rocks.vilaverde.classifier.dt.TreeClassifier;
+
+import java.util.Map;
+
+/**
+ * Abstract base class for Tree classifiers.
+ */
+public abstract class AbstractTreeClassifier<T> implements TreeClassifier<T> {
+
+    /**
+     * Predict class or regression value for features.
+     *
+     * @param samples input samples
+     * @return class probabilities of the input sample
+     */
+    @Override
+    public T predict(Map<String, Double> samples) {
+        FeatureVector fv = toFeatureVector(samples);
+        return predict(fv).get(0);
+    }
+
+    /**
+     * Predict class probabilities of the input samples features.
+     * The predicted class probability is the fraction of samples of the same class in a leaf.
+     *
+     * @param samples the input samples
+     * @return the class probabilities of the input sample
+     */
+    @Override
+    public double[] predict_proba(Map<String, Double> samples) {
+        FeatureVector fv = toFeatureVector(samples);
+        return predict_proba(fv)[0];
+    }
+
+    /**
+     * Convert a Map of features to a {@link FeatureVector}.
+     * @param samples a KV map of feature name to value
+     * @return FeatureVector
+     */
+    private FeatureVector toFeatureVector(Map<String, Double> samples) {
+        Features features = Features.fromSet(samples.keySet());
+        FeatureVector fv = features.newSample();
+        for (Map.Entry<String, Double> entry : samples.entrySet()) {
+            fv.add(entry.getKey(), entry.getValue());
+        }
+        return fv;
+    }
+}

src/main/java/rocks/vilaverde/classifier/Classifier.java

@@ -1,24 +1,44 @@
 package rocks.vilaverde.classifier;
 
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
 public interface Classifier<T> {
 
+  /**
+   * Predict class or regression value for samples. Predictions will be
+   * returned at the same index of the sample provided.
+   * @param samples input samples
+   * @return class probabilities of the input sample
+   */
+  List<T> predict(FeatureVector ... samples);
+
+  /**
+   * Predict class probabilities of the input samples. Probabilities will be
+   * returned at the same index of the sample provided.
+   * The predicted class probability is the fraction of samples of the same class in a leaf.
+   * @param samples the input samples
+   * @return the class probabilities of the input sample
+   */
+  double[][] predict_proba(FeatureVector ... samples);
+
   /**
    * Predict class or regression value for features.
-   * @param features input samples
+   * @param samples input samples
    * @return class probabilities of the input sample
    */
-  T predict(Map<String, Double> features);
+  @Deprecated
+  T predict(Map<String, Double> samples);
 
   /**
    * Predict class probabilities of the input samples features.
    * The predicted class probability is the fraction of samples of the same class in a leaf.
-   * @param features the input samples
+   * @param samples the input samples
    * @return the class probabilities of the input sample
    */
-  double[] predict_proba(Map<String, Double> features);
+  @Deprecated
+  double[] predict_proba(Map<String, Double> samples);
 
   /**
    * Get the names of all the features in the model.

src/main/java/rocks/vilaverde/classifier/FeatureVector.java

@@ -0,0 +1,53 @@
+package rocks.vilaverde.classifier;
+
+/**
+ * A container for the values for each feature of a sample that will be predicted.
+ */
+public class FeatureVector {
+
+    private final Features features;
+    private final double[] vector;
+
+    public FeatureVector(Features features) {
+        this.features = features;
+        this.vector = new double[features.getLength()];
+    }
+
+    public FeatureVector add(String feature, boolean value) {
+        add(feature, value ? 1.0 : 0.0);
+        return this;
+    }
+
+    public FeatureVector add(int index, boolean value) {
+        add(index, value ? 1.0 : 0.0);
+        return this;
+    }
+
+    public FeatureVector add(int index, double value) {
+        this.vector[index] = value;
+        return this;
+    }
+
+    public FeatureVector add(String feature, double value) {
+        int index = this.features.getFeatureIndex(feature);
+        add(index, value);
+        return this;
+    }
+
+    public double get(int index) {
+        if (index >= vector.length) {
+            throw new IllegalArgumentException(String.format("index must be less than %d", index));
+        }
+
+        return vector[index];
+    }
+
+    public double get(String feature) {
+        int index = features.getFeatureIndex(feature);
+        return get(index);
+    }
+
+    public boolean hasFeature(String feature) {
+        return this.features.getFeatureNames().contains(feature);
+    }
+}

src/main/java/rocks/vilaverde/classifier/Features.java

@@ -0,0 +1,91 @@
+package rocks.vilaverde.classifier;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.OptionalInt;
+import java.util.Set;
+
+/**
+ * Container class for the set of named features that will be provided for each sample.
+ * Call {@link Features#newSample()} to create a {@link FeatureVector} to provide the
+ * values for the sample.
+ */
+public class Features {
+
+    /* Map of feature name to index */
+    private final Map<String, Integer> features = new HashMap<>();
+    /* Feature can be added as long as no samples have yet to be created,
+       at that point this is immutable */
+    private boolean allowFeatureAdd = true;
+
+    /**
+     * Convienence creation method.
+     * @param features the set of features.
+     * @return Features
+     */
+    public static Features of(String ... features) {
+
+        // make sure all the features are unique
+        Set<String> featureSet = new HashSet<>(Arrays.asList(features));
+        if (featureSet.size() != features.length) {
+            throw new IllegalArgumentException("features names are not unique");
+        }
+
+        return new Features(features);
+    }
+
+    public static Features fromSet(Set<String> features) {
+        return new Features(features.toArray(new String[0]));
+    }
+
+    /**
+     * Constructor
+     * @param features order list of features.
+     */
+    private Features(String ... features) {
+        for (int i = 0; i < features.length; i++) {
+            this.features.put(features[i], i);
+        }
+    }
+
+    FeatureVector newSample() {
+        allowFeatureAdd = false;
+        return new FeatureVector(this);
+    }
+
+    public void addFeature(String feature) {
+        if (!allowFeatureAdd) {
+            throw new IllegalStateException("features are immutable");
+        }
+
+        if (!this.features.containsKey(feature)) {
+            int next = 0;
+            OptionalInt optionalInt = features.values().stream().mapToInt(integer -> integer).max();
+            if (optionalInt.isPresent()) {
+                next = optionalInt.getAsInt() + 1;
+            }
+
+            this.features.put(feature, next);
+        }
+    }
+
+    public int getLength() {
+        return this.features.size();
+    }
+
+    public int getFeatureIndex(String feature) {
+        Integer index = this.features.get(feature);
+        if (index == null) {
+            throw new IllegalArgumentException(String.format("feature %s does not exist", feature));
+        }
+
+        return index;
+    }
+
+    public Set<String> getFeatureNames() {
+        return Collections.unmodifiableSet(this.features.keySet());
+    }
+}

src/main/java/rocks/vilaverde/classifier/dt/ChoiceNode.java

@@ -6,7 +6,7 @@
  * Represents a Choice in the decision tree, where when the expression is evaluated,
  * if true will result in the child node of the choice being selected.
  */
-class ChoiceNode extends TreeNode {
+public class ChoiceNode extends TreeNode {
   private final Operator op;
   private final Double value;
 
@@ -38,7 +38,7 @@ public String toString() {
     return String.format("%s %s", op.toString(), value.toString());
   }
 
-  public boolean eval(Double featureValue) {
+  public boolean eval(double featureValue) {
     return op.apply(featureValue, value);
   }
 }

src/main/java/rocks/vilaverde/classifier/dt/DecisionNode.java

@@ -1,14 +1,11 @@
 package rocks.vilaverde.classifier.dt;
 
-import java.util.ArrayList;
-import java.util.List;
-
 /**
  * Represents a decision in the DecisionTreeClassifier. The decision will have
  * a left and right hand {@link ChoiceNode} to be evaluated.
  * A {@link ChoiceNode} may have nested {@link DecisionNode} or {@link EndNode}.
  */
-class DecisionNode extends TreeNode {
+public class DecisionNode extends TreeNode {
 
   private final String featureName;
 
@@ -26,7 +23,7 @@ public static DecisionNode create(String feature) {
 
   /**
    * Private Constructor.
-   * @param featureName
+   * @param featureName the name of the feature used in this decision
    */
   private DecisionNode(String featureName) {
     this.featureName = featureName.intern();