Fix/serialisation

build.gradle

@@ -22,7 +22,7 @@ publishing {
         maven(MavenPublication) {
             groupId = 'de.dmi3y.behaiv'
             artifactId = 'behaiv'
-            version = '0.3.0-alpha'
+            version = '0.3.7-alpha'
 
 
             from components.java
@@ -40,13 +40,13 @@ repositories {
 
 dependencies {
     // This dependency is exported to consumers, that is to say found on their compile classpath.
-    implementation 'org.apache.commons:commons-math3:3.6.1'
-    implementation 'org.apache.commons:commons-lang3:3.9'
 
     // This dependency is used internally, and not exposed to consumers on their own compile classpath.
+    implementation 'org.apache.commons:commons-lang3:3.9'
     implementation 'com.google.guava:guava:28.0-jre'
     implementation 'io.reactivex.rxjava3:rxjava:3.0.0-RC2'
-    implementation 'com.google.code.gson:gson:2.8.5'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.9.9'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-core', version: '2.9.9'
 
 
     //ejml (replacement of dl4j)

src/main/java/de/dmi3y/behaiv/Behaiv.java

@@ -9,9 +9,9 @@
 import de.dmi3y.behaiv.provider.ProviderCallback;
 import de.dmi3y.behaiv.session.CaptureSession;
 import de.dmi3y.behaiv.storage.BehaivStorage;
+import de.dmi3y.behaiv.tools.Pair;
 import io.reactivex.rxjava3.core.Observable;
 import io.reactivex.rxjava3.subjects.ReplaySubject;
-import org.apache.commons.math3.util.Pair;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
@@ -100,7 +100,7 @@ protected CaptureSession getCurrentSession() {
     @Override
     public void onFeaturesCaptured(List<Pair<Double, String>> features) {
         if (kernel.readyToPredict() && predict) {
-            subject.onNext(kernel.predictOne(features.stream().map(Pair::getFirst).collect(Collectors.toCollection(ArrayList::new))));
+            subject.onNext(kernel.predictOne(features.stream().map(Pair::getKey).collect(Collectors.toCollection(ArrayList::new))));
         }
     }
 
@@ -111,7 +111,7 @@ public void stopCapturing(boolean discard) {
         }
         String label = currentSession.getLabel();
         List<Pair<Double, String>> features = currentSession.getFeatures();
-        kernel.updateSingle(features.stream().map(Pair::getFirst).collect(Collectors.toCollection(ArrayList::new)), label);
+        kernel.updateSingle(features.stream().map(Pair::getKey).collect(Collectors.toCollection(ArrayList::new)), label);
         if (kernel.readyToPredict()) {
             kernel.fit();
         }

src/main/java/de/dmi3y/behaiv/kernel/Kernel.java

@@ -1,8 +1,9 @@
 package de.dmi3y.behaiv.kernel;
 
-import com.google.gson.Gson;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import de.dmi3y.behaiv.storage.BehaivStorage;
-import org.apache.commons.math3.util.Pair;
+import de.dmi3y.behaiv.tools.Pair;
 
 import java.io.BufferedReader;
 import java.io.BufferedWriter;
@@ -15,9 +16,11 @@ public abstract class Kernel {
 
     protected String id;
     protected Long treshold = 10L;
+    protected ObjectMapper objectMapper;
 
     public Kernel(String id) {
         this.id = id;
+        objectMapper = new ObjectMapper();
     }
 
 
@@ -50,24 +53,28 @@ public void update(ArrayList<Pair<ArrayList<Double>, String>> data) {
     }
 
     public void updateSingle(ArrayList<Double> features, String label) {
-        data.add(Pair.create(features, label));
+        data.add(new Pair<>(features, label));
     }
 
     public abstract String predictOne(ArrayList<Double> features);
 
     public void save(BehaivStorage storage) throws IOException {
-        final Gson gson = new Gson();
 
         try (final BufferedWriter writer = new BufferedWriter(new FileWriter(storage.getNetworkFile(id)))) {
-            writer.write(gson.toJson(data));
+            writer.write(objectMapper.writeValueAsString(data));
         }
     }
 
     public void restore(BehaivStorage storage) throws IOException {
-        final Gson gson = new Gson();
-
+        final TypeReference<ArrayList<Pair<ArrayList<Double>, String>>> typeReference = new TypeReference<ArrayList<Pair<ArrayList<Double>, String>>>() {
+        };
         try (final BufferedReader reader = new BufferedReader(new FileReader(storage.getNetworkFile(id)))) {
-            data = ((ArrayList<Pair<ArrayList<Double>, String>>) gson.fromJson(reader.readLine(), data.getClass()));
+            final String content = reader.readLine();
+            if (content == null || content.isEmpty()) {
+                data = new ArrayList<>();
+            } else {
+                data = objectMapper.readValue(content, typeReference);
+            }
         }
     }
 }

src/main/java/de/dmi3y/behaiv/kernel/LogisticRegressionKernel.java

@@ -1,10 +1,10 @@
 package de.dmi3y.behaiv.kernel;
 
-import com.google.gson.Gson;
+import com.fasterxml.jackson.core.type.TypeReference;
 import de.dmi3y.behaiv.kernel.logistic.LogisticUtils;
 import de.dmi3y.behaiv.storage.BehaivStorage;
+import de.dmi3y.behaiv.tools.Pair;
 import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.math3.util.Pair;
 import org.ejml.simple.SimpleMatrix;
 
 import java.io.BufferedReader;
@@ -41,19 +41,19 @@ public boolean isEmpty() {
     @Override
     public void fit(ArrayList<Pair<ArrayList<Double>, String>> data) {
         this.data = data;
-        labels = this.data.stream().map(Pair::getSecond).distinct().collect(Collectors.toList());
+        labels = this.data.stream().map(Pair::getValue).distinct().collect(Collectors.toList());
         if (readyToPredict()) {
 
 
             //features
-            double[][] inputs = this.data.stream().map(Pair::getFirst).map(l -> l.toArray(new Double[0]))
+            double[][] inputs = this.data.stream().map(Pair::getKey).map(l -> l.toArray(new Double[0]))
                     .map(ArrayUtils::toPrimitive)
                     .toArray(double[][]::new);
 
             //labels
             double[][] labelArray = new double[data.size()][labels.size()];
             for (int i = 0; i < data.size(); i++) {
-                int dummyPos = labels.indexOf(data.get(i).getSecond());
+                int dummyPos = labels.indexOf(data.get(i).getValue());
                 labelArray[i][dummyPos] = 1.0;
             }
 
@@ -107,22 +107,21 @@ public String predictOne(ArrayList<Double> features) {
 
     @Override
     public void save(BehaivStorage storage) throws IOException {
-        if (theta == null && data == null) {
+        if (theta == null && (data == null || data.isEmpty())) {
             throw new IOException("Not enough data to save, network data is empty");
         }
-        if (labels == null) {
+        if (labels == null || labels.isEmpty()) {
             String message;
             message = "Kernel collected labels but failed to get data, couldn't save network.";
             throw new IOException(message);
         }
         if (theta == null) {
             super.save(storage);
-
         } else {
             theta.saveToFileBinary(storage.getNetworkFile(id).toString());
             try (final BufferedWriter writer = new BufferedWriter(new FileWriter(storage.getNetworkMetadataFile(id)))) {
-                final Gson gson = new Gson();
-                writer.write(gson.toJson(labels));
+
+                writer.write(objectMapper.writeValueAsString(labels));
             } catch (Exception e) {
                 e.printStackTrace();
             }
@@ -139,8 +138,14 @@ public void restore(BehaivStorage storage) throws IOException {
         }
 
         try (final BufferedReader reader = new BufferedReader(new FileReader(storage.getNetworkMetadataFile(id)))) {
-            final Gson gson = new Gson();
-            labels = ((List<String>) gson.fromJson(reader.readLine(), labels.getClass()));
+            final TypeReference<ArrayList<String>> typeReference = new TypeReference<ArrayList<String>>() {
+            };
+            final String labelsData = reader.readLine();
+            if (labelsData == null) {
+                labels = new ArrayList<>();
+            } else {
+                labels = objectMapper.readValue(labelsData, typeReference);
+            }
         } catch (IOException e) {
             e.printStackTrace();
         }

src/main/java/de/dmi3y/behaiv/provider/DayTimeProvider.java

@@ -4,6 +4,7 @@
 import io.reactivex.rxjava3.core.Single;
 
 import javax.annotation.Nullable;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Calendar;
 import java.util.Collections;
@@ -45,7 +46,7 @@ public List<String> availableFeatures() {
         if (compound) {
             return Collections.singletonList("day_time");
         }
-        final List<String> strings = Arrays.asList("day_time_hours", "day_time_minutes");
+        final List<String> strings = new ArrayList<>(Arrays.asList("day_time_hours", "day_time_minutes"));
         if (secondsEnabled) {
             strings.add("day_time_seconds");
         }
@@ -64,10 +65,10 @@ public Single<List<Double>> getFeature() {
         if (compound) {
             return Single.just(Collections.singletonList(hours * 60.0 + minutes));
         }
-        final List<Double> listToSend = Arrays.asList(
+        final List<Double> listToSend = new ArrayList<>(Arrays.asList(
                 (double) hours,
                 (double) minutes
-        );
+        ));
         if (secondsEnabled) {
             final int seconds = calendar.get(Calendar.SECOND);
             listToSend.add((double) seconds);

src/main/java/de/dmi3y/behaiv/provider/ProviderCallback.java

@@ -1,6 +1,6 @@
 package de.dmi3y.behaiv.provider;
 
-import org.apache.commons.math3.util.Pair;
+import de.dmi3y.behaiv.tools.Pair;
 
 import java.util.List;
 

src/main/java/de/dmi3y/behaiv/session/CaptureSession.java

@@ -2,7 +2,7 @@
 
 import de.dmi3y.behaiv.Behaiv;
 import de.dmi3y.behaiv.provider.Provider;
-import org.apache.commons.math3.util.Pair;
+import de.dmi3y.behaiv.tools.Pair;
 
 import java.util.ArrayList;
 import java.util.InputMismatchException;

src/main/java/de/dmi3y/behaiv/tools/Pair.java

@@ -0,0 +1,51 @@
+package de.dmi3y.behaiv.tools;
+
+public class Pair<K, V> {
+    private K key;
+    private V value;
+
+    public Pair(K k, V v) {
+        this.key = k;
+        this.value = v;
+    }
+
+
+    public Pair(de.dmi3y.behaiv.tools.Pair<? extends K, ? extends V> entry) {
+        this(entry.getKey(), entry.getValue());
+    }
+
+    public Pair() {
+    }
+
+    public K getKey() {
+        return this.key;
+    }
+
+    public V getValue() {
+        return this.value;
+    }
+
+    public int hashCode() {
+        int result = this.key == null ? 0 : this.key.hashCode();
+        int h = this.value == null ? 0 : this.value.hashCode();
+        result = 37 * result + h ^ h >>> 16;
+        return result;
+    }
+
+    public String toString() {
+        return "[" + this.getKey() + ", " + this.getValue() + "]";
+    }
+
+    public static <K, V> Pair<K, V> create(K k, V v) {
+        return new Pair<K, V>(k, v);
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        Pair<?, ?> pair = (Pair<?, ?>) o;
+        return key.equals(pair.key) &&
+                value.equals(pair.value);
+    }
+}

src/test/java/de/dmi3y/behaiv/LibraryTest.java

@@ -4,10 +4,9 @@
 package de.dmi3y.behaiv;
 
 import de.dmi3y.behaiv.kernel.KernelTest;
-import de.dmi3y.behaiv.kernel.LogisticRegressionKernel;
 import de.dmi3y.behaiv.provider.TestProvider;
 import io.reactivex.rxjava3.core.Observable;
-import org.apache.commons.math3.util.Pair;
+import de.dmi3y.behaiv.tools.Pair;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -37,10 +36,10 @@ public void setUp() throws Exception {
     @Test
     public void behaivTest_basicTestFlow_predictsJob() throws Exception {
         for (Pair<ArrayList<Double>, String> fToL : data) {
-            ArrayList<Double> features = fToL.getFirst();
+            ArrayList<Double> features = fToL.getKey();
             timeProvider.next(new Double[]{features.get(0)});
             positionProvider.next(new Double[]{features.get(1), features.get(2)});
-            capture(fToL.getSecond());
+            capture(fToL.getValue());
         }
 
         Observable<String> register = behaiv.subscribe();

src/test/java/de/dmi3y/behaiv/kernel/KernelTest.java

@@ -1,7 +1,7 @@
 package de.dmi3y.behaiv.kernel;
 
 import de.dmi3y.behaiv.storage.SimpleStorage;
-import org.apache.commons.math3.util.Pair;
+import de.dmi3y.behaiv.tools.Pair;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -39,8 +39,8 @@ public void setUp() throws Exception {
     @Test
     public void setTreshold() {
         dummyKernel.setTreshold(1L);
-        dummyKernel.data.add(Pair.create(null, null));
-        dummyKernel.data.add(Pair.create(null, null));
+        dummyKernel.data.add(new Pair<>(null, null));
+        dummyKernel.data.add(new Pair<>(null, null));
         boolean readyToPredict = dummyKernel.readyToPredict();
         assertTrue(readyToPredict);
         dummyKernel.setTreshold(10L);