Sync tm dev

.classpath

@@ -6,9 +6,6 @@
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="lib" path="libs/chutils-1.4.jar" sourcepath="/Users/cogmission/Resources/chutils/chutils-1.4-sources.jar"/>
 	<classpathentry kind="lib" path="libs/hamcrest-core-1.3.jar"/>
-	<classpathentry kind="lib" path="libs/jackson-annotations-2.4.0.jar"/>
-	<classpathentry kind="lib" path="libs/jackson-core-2.4.4.jar"/>
-	<classpathentry kind="lib" path="libs/jackson-databind-2.4.4.jar"/>
 	<classpathentry kind="lib" path="libs/jmh-core-1.5.1.jar"/>
 	<classpathentry kind="lib" path="libs/joda-time-2.5.jar"/>
 	<classpathentry kind="lib" path="libs/junit-4.11.jar"/>
@@ -20,6 +17,9 @@
 	<classpathentry kind="lib" path="libs/java-util-1.19.3.jar" sourcepath="/Users/cogmission/.m2/repository/com/cedarsoftware/java-util/1.19.3/java-util-1.19.3-sources.jar"/>
 	<classpathentry kind="lib" path="libs/objenesis-2.1.jar"/>
 	<classpathentry kind="lib" path="libs/algorithmfoundry-shade-culled-1.3.jar"/>
-	<classpathentry kind="lib" path="libs/fst-2.45.jar"/>
+	<classpathentry kind="lib" path="libs/fst-2.45.jar" sourcepath="/Users/cogmission/git/fast-serialization/src/main/java"/>
+	<classpathentry kind="lib" path="libs/jackson-annotations-2.4.0.jar"/>
+	<classpathentry kind="lib" path="libs/jackson-core-2.4.4.jar"/>
+	<classpathentry kind="lib" path="libs/jackson-databind-2.4.4.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

build.gradle

@@ -4,15 +4,15 @@ apply plugin: 'eclipse'
 apply plugin: 'signing'
 
 group = 'org.numenta'
-version = '0.6.10-SNAPSHOT'
+version = '0.6.9-SNAPSHOT'
 archivesBaseName = 'htm.java'
 
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 
 jar {
     manifest {
-        attributes 'Implementation-Title': 'htm.java', 'Implementation-Version': '0.6.10-SNAPSHOT'
+        attributes 'Implementation-Title': 'htm.java', 'Implementation-Version': '0.6.9-SNAPSHOT'
     }
 }
 
@@ -53,11 +53,11 @@ dependencies {
     compile group: 'com.fasterxml.jackson.core', name: 'jackson-core', version:'2.4.4'
     compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version:'2.4.4'
     compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.10'
-	compile group: 'io.reactivex', name: 'rxjava', version: '1.0.10'
-	compile group: 'de.ruedigermoeller', name: 'fst', version: '2.45'
-	compile group: 'com.cedarsoftware', name: 'java-util', version: '1.19.3'
-	compile group: 'algorithmfoundry', name: 'algorithmfoundry-shade-culled', version:'1.3'
-	testCompile group: 'junit', name: 'junit', version:'4.11'
+    compile group: 'io.reactivex', name: 'rxjava', version: '1.0.10'
+    compile group: 'de.ruedigermoeller', name: 'fst', version: '2.45'
+    compile group: 'com.cedarsoftware', name: 'java-util', version: '1.19.3'
+    compile group: 'algorithmfoundry', name: 'algorithmfoundry-shade-culled', version:'1.3'
+    testCompile group: 'junit', name: 'junit', version:'4.11'
     testCompile group: 'ch.qos.logback', name: 'logback-classic', version:'1.1.2'
 }
 

pom.xml

@@ -4,7 +4,7 @@
 
 	<groupId>org.numenta</groupId>
 	<artifactId>htm.java</artifactId>
-	<version>0.6.10-SNAPSHOT</version>
+	<version>0.6.9-SNAPSHOT</version>
 	<name>htm.java</name>
 	<description>The Java version of Numenta's HTM technology</description>
 

src/jmh/java/org/numenta/nupic/benchmarks/AbstractAlgorithmBenchmark.java

@@ -22,12 +22,12 @@
 
 package org.numenta.nupic.benchmarks;
 
-import org.numenta.nupic.Connections;
 import org.numenta.nupic.Parameters;
 import org.numenta.nupic.Parameters.KEY;
 import org.numenta.nupic.algorithms.SpatialPooler;
 import org.numenta.nupic.algorithms.TemporalMemory;
 import org.numenta.nupic.encoders.ScalarEncoder;
+import org.numenta.nupic.model.Connections;
 import org.openjdk.jmh.annotations.Scope;
 import org.openjdk.jmh.annotations.Setup;
 import org.openjdk.jmh.annotations.State;

src/jmh/java/org/numenta/nupic/benchmarks/TemporalMemoryBenchmark.java

@@ -24,7 +24,7 @@
 
 import java.util.concurrent.TimeUnit;
 
-import org.numenta.nupic.ComputeCycle;
+import org.numenta.nupic.model.ComputeCycle;
 import org.numenta.nupic.util.ArrayUtils;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.BenchmarkMode;

src/main/java/org/numenta/nupic/Parameters.java

@@ -36,7 +36,10 @@
 import org.numenta.nupic.algorithms.TemporalMemory;
 import org.numenta.nupic.model.Cell;
 import org.numenta.nupic.model.Column;
+import org.numenta.nupic.model.ComputeCycle;
 import org.numenta.nupic.model.DistalDendrite;
+import org.numenta.nupic.model.Connections;
+import org.numenta.nupic.model.Persistable;
 import org.numenta.nupic.util.ArrayUtils;
 import org.numenta.nupic.util.BeanUtil;
 import org.numenta.nupic.util.MersenneTwister;

src/main/java/org/numenta/nupic/algorithms/Anomaly.java

@@ -26,7 +26,7 @@
 import java.util.List;
 import java.util.Map;
 
-import org.numenta.nupic.Persistable;
+import org.numenta.nupic.model.Persistable;
 import org.numenta.nupic.util.ArrayUtils;
 
 import gnu.trove.list.TDoubleList;

src/main/java/org/numenta/nupic/algorithms/AnomalyLikelihood.java

@@ -22,13 +22,6 @@
 
 package org.numenta.nupic.algorithms;
 
-import gnu.trove.iterator.TDoubleIterator;
-import gnu.trove.list.TDoubleList;
-import gnu.trove.list.array.TDoubleArrayList;
-import gnu.trove.map.TObjectDoubleMap;
-
-import java.io.IOException;
-import java.io.StringWriter;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -40,14 +33,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.core.JsonFactory;
-import com.fasterxml.jackson.core.JsonGenerator;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.databind.node.ArrayNode;
-import com.fasterxml.jackson.databind.node.JsonNodeFactory;
-import com.fasterxml.jackson.databind.node.ObjectNode;
+import gnu.trove.list.TDoubleList;
+import gnu.trove.list.array.TDoubleArrayList;
+import gnu.trove.map.TObjectDoubleMap;
 
 /**
  * <p>The anomaly likelihood computer.</p>
@@ -607,9 +595,6 @@ public boolean isValidEstimatorParams(NamedTuple params) {
     public static class AnomalyParams extends NamedTuple {
         private static final long serialVersionUID = 1L;
 
-        /** Cached Json formatting. Possible because Objects of this class are immutable */
-        private ObjectNode cachedNode;
-
         private final Statistic distribution;
         private final MovingAverage movingAverage;
         private final double[] historicalLikelihoods;
@@ -666,90 +651,6 @@ public int windowSize() {
             return windowSize;
         }
 
-        /**
-         * Lazily creates and returns a JSON ObjectNode containing this {@code AnomalyParams}' data.
-         * 
-         * @param factory
-         * @return
-         */
-        public ObjectNode toJsonNode(JsonNodeFactory factory) {
-            if(cachedNode == null) {
-                ObjectNode distribution = factory.objectNode();
-                distribution.put(KEY_MEAN, this.distribution.mean);
-                distribution.put(KEY_VARIANCE, this.distribution.variance);
-                distribution.put(KEY_STDEV, this.distribution.stdev);
-
-                double[] historicalLikelihoods = (double[])get(KEY_HIST_LIKE);
-                ArrayNode historics = factory.arrayNode();
-                for(double d : historicalLikelihoods) {
-                    historics.add(d);
-                }
-
-                ObjectNode mvgAvg = factory.objectNode();
-                mvgAvg.put(KEY_WINDOW_SIZE, windowSize);
-
-                ArrayNode histVals = factory.arrayNode();
-                TDoubleList hVals = this.movingAverage.getSlidingWindow();
-                for(TDoubleIterator it = hVals.iterator();it.hasNext();) {
-                    histVals.add(it.next());
-                }
-                mvgAvg.set(KEY_HIST_VALUES, histVals);
-                mvgAvg.put(KEY_TOTAL, this.movingAverage.getTotal());
-
-                cachedNode = factory.objectNode();
-                cachedNode.set(KEY_DIST, distribution);
-                cachedNode.set(KEY_HIST_LIKE, historics);
-                cachedNode.set(KEY_MVG_AVG, mvgAvg);
-            }
-
-            return cachedNode;
-        }
-
-        /**
-         * Returns the processed Json Node with possible pretty print indentation
-         * formatting if the flag specified is true.
-         * 
-         * @param doPrettyPrint
-         * @return
-         */
-        public String toJson(boolean doPrettyPrint) {
-            // Create the node factory that gives us nodes.
-            JsonNodeFactory factory = new JsonNodeFactory(false);
-
-            // create a json factory to write the tree node as json. for the example
-            // we just write to console
-            JsonFactory jsonFactory = new JsonFactory();
-            JsonGenerator generator = null;
-            StringWriter out = new StringWriter();
-            try {
-                 generator = jsonFactory.createGenerator(out);
-            }catch(IOException e) {
-                LOG.error("Error while creating JsonGenerator", e);
-            }
-
-            ObjectMapper mapper = new ObjectMapper();
-            if(doPrettyPrint) {
-                mapper.enable(SerializationFeature.INDENT_OUTPUT);
-            }
-            try {
-                mapper.writeTree(generator, toJsonNode(factory));
-            } catch(JsonProcessingException e) {
-                LOG.error("Error while writing json", e);
-            } catch(IOException e) {
-                LOG.error("Error while writing json", e);
-            }
-
-            return out.getBuffer().toString();
-        }
-
-        /**
-         * Returns the processed Json Node as a String
-         * @return
-         */
-        public String toJson() {
-            return toJson(false);
-        }
-
         /* (non-Javadoc)
          * @see java.lang.Object#hashCode()
          */

src/main/java/org/numenta/nupic/algorithms/AnomalyLikelihoodMetrics.java

@@ -26,9 +26,9 @@
 import java.util.Arrays;
 import java.util.List;
 
-import org.numenta.nupic.Persistable;
 import org.numenta.nupic.algorithms.Anomaly.AveragedAnomalyRecordList;
 import org.numenta.nupic.algorithms.AnomalyLikelihood.AnomalyParams;
+import org.numenta.nupic.model.Persistable;
 
 /**
  * Container class to hold the results of {@link AnomalyLikelihood} estimations

src/main/java/org/numenta/nupic/algorithms/BitHistory.java

@@ -22,7 +22,7 @@
 
 package org.numenta.nupic.algorithms;
 
-import org.numenta.nupic.Persistable;
+import org.numenta.nupic.model.Persistable;
 import org.numenta.nupic.util.ArrayUtils;
 
 import gnu.trove.list.TDoubleList;

src/main/java/org/numenta/nupic/algorithms/CLAClassifier.java

@@ -28,7 +28,7 @@
 import java.util.List;
 import java.util.Map;
 
-import org.numenta.nupic.Persistable;
+import org.numenta.nupic.model.Persistable;
 import org.numenta.nupic.util.ArrayUtils;
 import org.numenta.nupic.util.Deque;
 import org.numenta.nupic.util.Tuple;

src/main/java/org/numenta/nupic/algorithms/Classification.java

@@ -2,7 +2,7 @@
 
 import java.util.Arrays;
 
-import org.numenta.nupic.Persistable;
+import org.numenta.nupic.model.Persistable;
 
 import gnu.trove.map.TIntObjectMap;
 import gnu.trove.map.hash.TIntObjectHashMap;

src/main/java/org/numenta/nupic/algorithms/MovingAverage.java

@@ -22,7 +22,7 @@
 
 package org.numenta.nupic.algorithms;
 
-import org.numenta.nupic.Persistable;
+import org.numenta.nupic.model.Persistable;
 
 import gnu.trove.list.TDoubleList;
 import gnu.trove.list.array.TDoubleArrayList;

src/main/java/org/numenta/nupic/algorithms/SDRClassifier.java

@@ -29,7 +29,8 @@
 import java.util.Map;
 
 import no.uib.cipr.matrix.sparse.FlexCompRowMatrix;
-import org.numenta.nupic.Persistable;
+
+import org.numenta.nupic.model.Persistable;
 import org.numenta.nupic.util.ArrayUtils;
 import org.numenta.nupic.util.Deque;
 import org.numenta.nupic.util.Tuple;

src/main/java/org/numenta/nupic/algorithms/Sample.java

@@ -23,7 +23,7 @@
 package org.numenta.nupic.algorithms;
 
 import org.joda.time.DateTime;
-import org.numenta.nupic.Persistable;
+import org.numenta.nupic.model.Persistable;
 
 /**
  * A sample data point or record consisting of a timestamp, value, and score.

src/main/java/org/numenta/nupic/algorithms/SpatialPooler.java

@@ -25,9 +25,9 @@
 import java.util.Comparator;
 import java.util.stream.IntStream;
 
-import org.numenta.nupic.Connections;
-import org.numenta.nupic.Persistable;
 import org.numenta.nupic.model.Column;
+import org.numenta.nupic.model.Connections;
+import org.numenta.nupic.model.Persistable;
 import org.numenta.nupic.model.Pool;
 import org.numenta.nupic.util.ArrayUtils;
 import org.numenta.nupic.util.Condition;

src/main/java/org/numenta/nupic/algorithms/Statistic.java

@@ -22,12 +22,9 @@
 
 package org.numenta.nupic.algorithms;
 
-import org.numenta.nupic.Persistable;
+import org.numenta.nupic.model.Persistable;
 import org.numenta.nupic.util.NamedTuple;
 
-import com.fasterxml.jackson.databind.node.JsonNodeFactory;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
 /**
  * Container to hold a specific calculation for a statistical data point.
  * 
@@ -61,21 +58,6 @@ public Statistic(double mean, double variance, double stdev) {
         this.entries = new NamedTuple(new String[] { "mean", "variance", "stdev" }, mean, variance, stdev);
     }
 
-    /**
-     * Creates and returns a JSON ObjectNode containing this Statistic's data.
-     * 
-     * @param factory
-     * @return
-     */
-    public ObjectNode toJson(JsonNodeFactory factory) {
-        ObjectNode distribution = factory.objectNode();
-        distribution.put("mean", mean);
-        distribution.put("variance", variance);
-        distribution.put("stdev", stdev);
-
-        return distribution;
-    }
-
     @Override
     public int hashCode() {
         final int prime = 31;