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cogmissioncogmission
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Merge pull request #496 from cogmission/sync_tm_dev
Sync tm dev
2 parents 473233d + f4eed8d commit 7f4d8f2

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‎.classpath

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@@ -6,9 +6,6 @@
66
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
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<classpathentry kind="lib" path="libs/chutils-1.4.jar" sourcepath="/Users/cogmission/Resources/chutils/chutils-1.4-sources.jar"/>
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<classpathentry kind="lib" path="libs/hamcrest-core-1.3.jar"/>
9-
<classpathentry kind="lib" path="libs/jackson-annotations-2.4.0.jar"/>
10-
<classpathentry kind="lib" path="libs/jackson-core-2.4.4.jar"/>
11-
<classpathentry kind="lib" path="libs/jackson-databind-2.4.4.jar"/>
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<classpathentry kind="lib" path="libs/jmh-core-1.5.1.jar"/>
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<classpathentry kind="lib" path="libs/joda-time-2.5.jar"/>
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<classpathentry kind="lib" path="libs/junit-4.11.jar"/>
@@ -20,6 +17,9 @@
2017
<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"/>
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<classpathentry kind="lib" path="libs/objenesis-2.1.jar"/>
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<classpathentry kind="lib" path="libs/algorithmfoundry-shade-culled-1.3.jar"/>
23-
<classpathentry kind="lib" path="libs/fst-2.45.jar"/>
20+
<classpathentry kind="lib" path="libs/fst-2.45.jar" sourcepath="/Users/cogmission/git/fast-serialization/src/main/java"/>
21+
<classpathentry kind="lib" path="libs/jackson-annotations-2.4.0.jar"/>
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<classpathentry kind="lib" path="libs/jackson-core-2.4.4.jar"/>
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<classpathentry kind="lib" path="libs/jackson-databind-2.4.4.jar"/>
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<classpathentry kind="output" path="bin"/>
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</classpath>

‎build.gradle

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@@ -4,15 +4,15 @@ apply plugin: 'eclipse'
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apply plugin: 'signing'
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group = 'org.numenta'
7-
version = '0.6.10-SNAPSHOT'
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version = '0.6.9-SNAPSHOT'
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archivesBaseName = 'htm.java'
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sourceCompatibility = 1.8
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targetCompatibility = 1.8
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jar {
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manifest {
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attributes 'Implementation-Title': 'htm.java', 'Implementation-Version': '0.6.10-SNAPSHOT'
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attributes 'Implementation-Title': 'htm.java', 'Implementation-Version': '0.6.9-SNAPSHOT'
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}
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}
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@@ -53,11 +53,11 @@ dependencies {
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compile group: 'com.fasterxml.jackson.core', name: 'jackson-core', version:'2.4.4'
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compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version:'2.4.4'
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compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.10'
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compile group: 'io.reactivex', name: 'rxjava', version: '1.0.10'
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compile group: 'de.ruedigermoeller', name: 'fst', version: '2.45'
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compile group: 'com.cedarsoftware', name: 'java-util', version: '1.19.3'
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compile group: 'algorithmfoundry', name: 'algorithmfoundry-shade-culled', version:'1.3'
60-
testCompile group: 'junit', name: 'junit', version:'4.11'
56+
compile group: 'io.reactivex', name: 'rxjava', version: '1.0.10'
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compile group: 'de.ruedigermoeller', name: 'fst', version: '2.45'
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compile group: 'com.cedarsoftware', name: 'java-util', version: '1.19.3'
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compile group: 'algorithmfoundry', name: 'algorithmfoundry-shade-culled', version:'1.3'
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testCompile group: 'junit', name: 'junit', version:'4.11'
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testCompile group: 'ch.qos.logback', name: 'logback-classic', version:'1.1.2'
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}
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‎pom.xml

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<groupId>org.numenta</groupId>
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<artifactId>htm.java</artifactId>
7-
<version>0.6.10-SNAPSHOT</version>
7+
<version>0.6.9-SNAPSHOT</version>
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<name>htm.java</name>
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<description>The Java version of Numenta's HTM technology</description>
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‎src/jmh/java/org/numenta/nupic/benchmarks/AbstractAlgorithmBenchmark.java

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package org.numenta.nupic.benchmarks;
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import org.numenta.nupic.Connections;
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import org.numenta.nupic.Parameters;
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import org.numenta.nupic.Parameters.KEY;
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import org.numenta.nupic.algorithms.SpatialPooler;
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import org.numenta.nupic.algorithms.TemporalMemory;
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import org.numenta.nupic.encoders.ScalarEncoder;
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import org.numenta.nupic.model.Connections;
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import org.openjdk.jmh.annotations.Scope;
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import org.openjdk.jmh.annotations.Setup;
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import org.openjdk.jmh.annotations.State;

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

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import java.util.concurrent.TimeUnit;
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import org.numenta.nupic.ComputeCycle;
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import org.numenta.nupic.model.ComputeCycle;
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import org.numenta.nupic.util.ArrayUtils;
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import org.openjdk.jmh.annotations.Benchmark;
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import org.openjdk.jmh.annotations.BenchmarkMode;

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

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import org.numenta.nupic.algorithms.TemporalMemory;
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import org.numenta.nupic.model.Cell;
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import org.numenta.nupic.model.Column;
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import org.numenta.nupic.model.ComputeCycle;
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import org.numenta.nupic.model.DistalDendrite;
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import org.numenta.nupic.model.Connections;
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import org.numenta.nupic.model.Persistable;
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import org.numenta.nupic.util.ArrayUtils;
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import org.numenta.nupic.util.BeanUtil;
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import org.numenta.nupic.util.MersenneTwister;

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

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import java.util.List;
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import java.util.Map;
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import org.numenta.nupic.Persistable;
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import org.numenta.nupic.model.Persistable;
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import org.numenta.nupic.util.ArrayUtils;
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import gnu.trove.list.TDoubleList;

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

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package org.numenta.nupic.algorithms;
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import gnu.trove.iterator.TDoubleIterator;
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import gnu.trove.list.TDoubleList;
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import gnu.trove.list.array.TDoubleArrayList;
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import gnu.trove.map.TObjectDoubleMap;
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30-
import java.io.IOException;
31-
import java.io.StringWriter;
3225
import java.util.ArrayList;
3326
import java.util.Arrays;
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import java.util.List;
@@ -40,14 +33,9 @@
4033
import org.slf4j.Logger;
4134
import org.slf4j.LoggerFactory;
4235

43-
import com.fasterxml.jackson.core.JsonFactory;
44-
import com.fasterxml.jackson.core.JsonGenerator;
45-
import com.fasterxml.jackson.core.JsonProcessingException;
46-
import com.fasterxml.jackson.databind.ObjectMapper;
47-
import com.fasterxml.jackson.databind.SerializationFeature;
48-
import com.fasterxml.jackson.databind.node.ArrayNode;
49-
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
50-
import com.fasterxml.jackson.databind.node.ObjectNode;
36+
import gnu.trove.list.TDoubleList;
37+
import gnu.trove.list.array.TDoubleArrayList;
38+
import gnu.trove.map.TObjectDoubleMap;
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5240
/**
5341
* <p>The anomaly likelihood computer.</p>
@@ -607,9 +595,6 @@ public boolean isValidEstimatorParams(NamedTuple params) {
607595
public static class AnomalyParams extends NamedTuple {
608596
private static final long serialVersionUID = 1L;
609597

610-
/** Cached Json formatting. Possible because Objects of this class are immutable */
611-
private ObjectNode cachedNode;
612-
613598
private final Statistic distribution;
614599
private final MovingAverage movingAverage;
615600
private final double[] historicalLikelihoods;
@@ -666,90 +651,6 @@ public int windowSize() {
666651
return windowSize;
667652
}
668653

669-
/**
670-
* Lazily creates and returns a JSON ObjectNode containing this {@code AnomalyParams}' data.
671-
*
672-
* @param factory
673-
* @return
674-
*/
675-
public ObjectNode toJsonNode(JsonNodeFactory factory) {
676-
if(cachedNode == null) {
677-
ObjectNode distribution = factory.objectNode();
678-
distribution.put(KEY_MEAN, this.distribution.mean);
679-
distribution.put(KEY_VARIANCE, this.distribution.variance);
680-
distribution.put(KEY_STDEV, this.distribution.stdev);
681-
682-
double[] historicalLikelihoods = (double[])get(KEY_HIST_LIKE);
683-
ArrayNode historics = factory.arrayNode();
684-
for(double d : historicalLikelihoods) {
685-
historics.add(d);
686-
}
687-
688-
ObjectNode mvgAvg = factory.objectNode();
689-
mvgAvg.put(KEY_WINDOW_SIZE, windowSize);
690-
691-
ArrayNode histVals = factory.arrayNode();
692-
TDoubleList hVals = this.movingAverage.getSlidingWindow();
693-
for(TDoubleIterator it = hVals.iterator();it.hasNext();) {
694-
histVals.add(it.next());
695-
}
696-
mvgAvg.set(KEY_HIST_VALUES, histVals);
697-
mvgAvg.put(KEY_TOTAL, this.movingAverage.getTotal());
698-
699-
cachedNode = factory.objectNode();
700-
cachedNode.set(KEY_DIST, distribution);
701-
cachedNode.set(KEY_HIST_LIKE, historics);
702-
cachedNode.set(KEY_MVG_AVG, mvgAvg);
703-
}
704-
705-
return cachedNode;
706-
}
707-
708-
/**
709-
* Returns the processed Json Node with possible pretty print indentation
710-
* formatting if the flag specified is true.
711-
*
712-
* @param doPrettyPrint
713-
* @return
714-
*/
715-
public String toJson(boolean doPrettyPrint) {
716-
// Create the node factory that gives us nodes.
717-
JsonNodeFactory factory = new JsonNodeFactory(false);
718-
719-
// create a json factory to write the tree node as json. for the example
720-
// we just write to console
721-
JsonFactory jsonFactory = new JsonFactory();
722-
JsonGenerator generator = null;
723-
StringWriter out = new StringWriter();
724-
try {
725-
generator = jsonFactory.createGenerator(out);
726-
}catch(IOException e) {
727-
LOG.error("Error while creating JsonGenerator", e);
728-
}
729-
730-
ObjectMapper mapper = new ObjectMapper();
731-
if(doPrettyPrint) {
732-
mapper.enable(SerializationFeature.INDENT_OUTPUT);
733-
}
734-
try {
735-
mapper.writeTree(generator, toJsonNode(factory));
736-
} catch(JsonProcessingException e) {
737-
LOG.error("Error while writing json", e);
738-
} catch(IOException e) {
739-
LOG.error("Error while writing json", e);
740-
}
741-
742-
return out.getBuffer().toString();
743-
}
744-
745-
/**
746-
* Returns the processed Json Node as a String
747-
* @return
748-
*/
749-
public String toJson() {
750-
return toJson(false);
751-
}
752-
753654
/* (non-Javadoc)
754655
* @see java.lang.Object#hashCode()
755656
*/

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

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import java.util.Arrays;
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import java.util.List;
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import org.numenta.nupic.Persistable;
3029
import org.numenta.nupic.algorithms.Anomaly.AveragedAnomalyRecordList;
3130
import org.numenta.nupic.algorithms.AnomalyLikelihood.AnomalyParams;
31+
import org.numenta.nupic.model.Persistable;
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3333
/**
3434
* Container class to hold the results of {@link AnomalyLikelihood} estimations

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

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package org.numenta.nupic.algorithms;
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import org.numenta.nupic.Persistable;
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import org.numenta.nupic.model.Persistable;
2626
import org.numenta.nupic.util.ArrayUtils;
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import gnu.trove.list.TDoubleList;

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