Added new Generator Implementation for new TemporalMemory, and the test for it.

Author: cogmission

Diff for: [ htm.java Unit Test ] TemporalMemoryTest.launch renamed to [ htm.java Unit Test ] OldTemporalMemoryTest.launch

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <launchConfiguration type="org.eclipse.jdt.junit.launchconfig">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/htm.java/src/test/java/org/numenta/nupic/algorithms/TemporalMemoryTest.java"/>
+<listEntry value="/htm.java/src/test/java/org/numenta/nupic/algorithms/OldTemporalMemoryTest.java"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="1"/>
@@ -25,7 +25,7 @@
 </listAttribute>
 <stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
 <booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.numenta.nupic.algorithms.TemporalMemoryTest"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.numenta.nupic.algorithms.OldTemporalMemoryTest"/>
 <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="htm.java"/>
 <stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
 </launchConfiguration>

Diff for: src/jmh/java/org/numenta/nupic/benchmarks/AbstractAlgorithmBenchmark.java

@@ -26,7 +26,7 @@
 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.algorithms.OldTemporalMemory;
 import org.numenta.nupic.encoders.ScalarEncoder;
 import org.openjdk.jmh.annotations.Scope;
 import org.openjdk.jmh.annotations.Setup;
@@ -38,7 +38,7 @@ public abstract class AbstractAlgorithmBenchmark {
     protected int[] SDR;
     protected ScalarEncoder encoder;
     protected SpatialPooler pooler;
-    protected TemporalMemory temporalMemory;
+    protected OldTemporalMemory temporalMemory;
     protected Connections memory;
 
     @Setup
@@ -65,7 +65,7 @@ public void init() {
         pooler = new SpatialPooler();
         pooler.init(memory);
 
-        temporalMemory = new TemporalMemory();
+        temporalMemory = new OldTemporalMemory();
         temporalMemory.init(memory);
     }
 

Diff for: src/main/java/org/numenta/nupic/ComputeCycle.java

@@ -26,14 +26,14 @@
 import java.util.Map;
 import java.util.Set;
 
-import org.numenta.nupic.algorithms.TemporalMemory;
+import org.numenta.nupic.algorithms.OldTemporalMemory;
 import org.numenta.nupic.model.Cell;
 import org.numenta.nupic.model.Column;
 import org.numenta.nupic.model.DistalDendrite;
 
 /**
  * Contains a snapshot of the state attained during one computational
- * call to the {@link TemporalMemory}. The {@code TemporalMemory} uses
+ * call to the {@link OldTemporalMemory}. The {@code TemporalMemory} uses
  * data from previous compute cycles to derive new data for the current cycle
  * through a comparison between states of those different cycles, therefore
  * this state container is necessary.
@@ -62,7 +62,7 @@ public ComputeCycle() {}
     /**
      * Constructs a new {@code ComputeCycle} initialized with
      * the connections relevant to the current calling {@link Thread} for
-     * the specified {@link TemporalMemory}
+     * the specified {@link OldTemporalMemory}
      * 
      * @param   c       the current connections state of the TemporalMemory
      */
@@ -136,7 +136,7 @@ public Set<Cell> predictedInactiveCells() {
 
     /**
      * Returns the Set of matching {@link DistalDendrite}s from 
-     * {@link TemporalMemory#computePredictiveCells(Connections, ComputeCycle, Map)}
+     * {@link OldTemporalMemory#computePredictiveCells(Connections, ComputeCycle, Map)}
      * @return
      */
     public Set<DistalDendrite> matchingSegments() {
@@ -145,7 +145,7 @@ public Set<DistalDendrite> matchingSegments() {
 
     /**
      * Returns the Set of matching {@link Cell}s from
-     * {@link TemporalMemory#computePredictiveCells(Connections, ComputeCycle, Map)}
+     * {@link OldTemporalMemory#computePredictiveCells(Connections, ComputeCycle, Map)}
      * @return
      */
     public Set<Cell> matchingCells() {

Diff for: src/main/java/org/numenta/nupic/Connections.java

@@ -34,7 +34,7 @@
 
 import org.numenta.nupic.algorithms.PASpatialPooler;
 import org.numenta.nupic.algorithms.SpatialPooler;
-import org.numenta.nupic.algorithms.TemporalMemory;
+import org.numenta.nupic.algorithms.OldTemporalMemory;
 import org.numenta.nupic.model.Cell;
 import org.numenta.nupic.model.Column;
 import org.numenta.nupic.model.DistalDendrite;
@@ -50,7 +50,7 @@
 
 /**
  * Contains the definition of the interconnected structural state of the {@link SpatialPooler} and
- * {@link TemporalMemory} as well as the state of all support structures
+ * {@link OldTemporalMemory} as well as the state of all support structures
  * (i.e. Cells, Columns, Segments, Synapses etc.).
  *
  * In the separation of data from logic, this class represents the data/state.

Diff for: src/main/java/org/numenta/nupic/Parameters.java

@@ -33,7 +33,7 @@
 import java.util.Set;
 
 import org.numenta.nupic.algorithms.SpatialPooler;
-import org.numenta.nupic.algorithms.TemporalMemory;
+import org.numenta.nupic.algorithms.OldTemporalMemory;
 import org.numenta.nupic.model.Cell;
 import org.numenta.nupic.model.Column;
 import org.numenta.nupic.model.DistalDendrite;
@@ -47,13 +47,13 @@
 import com.cedarsoftware.util.DeepEquals;
 
 /**
- * Specifies parameters to be used as a configuration for a given {@link TemporalMemory}
+ * Specifies parameters to be used as a configuration for a given {@link OldTemporalMemory}
  * or {@link SpatialPooler}
  *
  * @author David Ray
  * @author Kirill Solovyev
  * @see SpatialPooler
- * @see TemporalMemory
+ * @see OldTemporalMemory
  * @see Connections
  * @see ComputeCycle
  */
@@ -140,7 +140,7 @@ public class Parameters implements Persistable {
     }
 
     /**
-     * Constant values representing configuration parameters for the {@link TemporalMemory}
+     * Constant values representing configuration parameters for the {@link OldTemporalMemory}
      */
     public static enum KEY {
         /////////// Universal Parameters ///////////

Diff for: src/main/java/org/numenta/nupic/algorithms/TemporalMemory.java renamed to src/main/java/org/numenta/nupic/algorithms/OldTemporalMemory.java

@@ -27,20 +27,20 @@
  * @author Chetan Surpur
  * @author David Ray
  */
-public class TemporalMemory implements ComputeDecorator, Serializable {
+public class OldTemporalMemory implements ComputeDecorator, Serializable {
     private static final long serialVersionUID = 1L;
 
     /**
      * Constructs a new {@code TemporalMemory}
      */
-    public TemporalMemory() {}
+    public OldTemporalMemory() {}
 
     /**
      * Uses the specified {@link Connections} object to Build the structural 
      * anatomy needed by this {@code TemporalMemory} to implement its algorithms.
      * 
      * The connections object holds the {@link Column} and {@link Cell} infrastructure,
-     * and is used by both the {@link SpatialPooler} and {@link TemporalMemory}. Either of
+     * and is used by both the {@link SpatialPooler} and {@link OldTemporalMemory}. Either of
      * these can be used separately, and therefore this Connections object may have its
      * Columns and Cells initialized by either the init method of the SpatialPooler or the
      * init method of the TemporalMemory. We check for this so that complete initialization

Diff for: src/main/java/org/numenta/nupic/model/Column.java

@@ -31,7 +31,7 @@
 
 import org.numenta.nupic.Connections;
 import org.numenta.nupic.algorithms.SpatialPooler;
-import org.numenta.nupic.algorithms.TemporalMemory;
+import org.numenta.nupic.algorithms.OldTemporalMemory;
 
 /**
  * Abstraction of both an input bit and a columnal collection of
@@ -109,7 +109,7 @@ public int getIndex() {
 
     /**
      * Returns the configured number of cells per column for
-     * all {@code Column} objects within the current {@link TemporalMemory}
+     * all {@code Column} objects within the current {@link OldTemporalMemory}
      * @return
      */
     public int getNumCellsPerColumn() {

Diff for: src/main/java/org/numenta/nupic/monitor/MonitoredTemporalMemory.java

@@ -73,7 +73,7 @@ public MonitoredTemporalMemory(ComputeDecorator decorator, Connections cnx) {
 
     /**
      * Returns the original class which is being tested. In this 
-     * case it is the {@link TemporalMemory}
+     * case it is the {@link OldTemporalMemory}
      */
     @SuppressWarnings("unchecked")
     @Override

Diff for: src/main/java/org/numenta/nupic/monitor/mixin/MonitorMixinBase.java

@@ -47,7 +47,7 @@
  *      <li>Create MonitorMixinBase extension mixin type (interface) (this does most of the mixin work) see {@link TemporalMemoryMonitorMixin}</li>
  *      <li>Create Extension of both {@link MonitorMixinBase} and interface (see {@link MonitoredTemporalMemory})</li>
  *      <li>Create constructor in extension class which takes above interface (A) which is the target class which must implement (A)</li>
- *      <li>Make the Original class (see {@link TemporalMemory}) to be tested, implement the Decorator interface (A)</li>
+ *      <li>Make the Original class (see {@link OldTemporalMemory}) to be tested, implement the Decorator interface (A)</li>
  *      <li>Use the "joining" extension class as you would the original class</li>
  * </OL>
  *      

Diff for: src/main/java/org/numenta/nupic/monitor/mixin/TemporalMemoryMonitorMixin.java

@@ -33,7 +33,7 @@
 
 import org.numenta.nupic.ComputeCycle;
 import org.numenta.nupic.Connections;
-import org.numenta.nupic.algorithms.TemporalMemory;
+import org.numenta.nupic.algorithms.OldTemporalMemory;
 import org.numenta.nupic.model.Cell;
 import org.numenta.nupic.model.Column;
 import org.numenta.nupic.model.DistalDendrite;
@@ -51,7 +51,7 @@
  * and create {@link Metric}s from them for analysis and pretty-printing
  * 
  * This interface contains "defender" methods or Traits that are used to collect
- * result data for the {@link TemporalMemory}.
+ * result data for the {@link OldTemporalMemory}.
  * 
  * @author cogmission
  *
@@ -487,7 +487,7 @@ default ComputeCycle compute(Connections cnx, int[] activeColumns, String sequen
     }
 
     /**
-     * Called to delegate a {@link TemporalMemory#reset(Connections)} call and
+     * Called to delegate a {@link OldTemporalMemory#reset(Connections)} call and
      * then set a flag locally which controls remaking of test {@link Trace}s.
      * 
      * @param c
@@ -500,7 +500,7 @@ default void resetSequences(Connections c) {
 
     /**
      * Returns a list of {@link Trace} objects containing data sets used
-     * to analyze the behavior and state of the {@link TemporalMemory} This
+     * to analyze the behavior and state of the {@link OldTemporalMemory} This
      * method is called from all of the "mmXXX" methods to make sure that
      * the data represents the most current execution cycle of the TM.
      * 
@@ -535,7 +535,7 @@ default <T extends Trace<?>> List<T> mmGetDefaultTraces(int verbosity) {
 
     /**
      * Returns a list of {@link Metric} objects containing statistics used
-     * to analyze the behavior and state of the {@link TemporalMemory} This
+     * to analyze the behavior and state of the {@link OldTemporalMemory} This
      * method is called from all of the "mmXXX" methods to make sure that
      * the data represents the most current execution cycle of the TM.
      * 

Diff for: src/main/java/org/numenta/nupic/network/Inference.java

@@ -29,7 +29,7 @@
 import org.numenta.nupic.algorithms.CLAClassifier;
 import org.numenta.nupic.algorithms.Classification;
 import org.numenta.nupic.algorithms.SpatialPooler;
-import org.numenta.nupic.algorithms.TemporalMemory;
+import org.numenta.nupic.algorithms.OldTemporalMemory;
 import org.numenta.nupic.encoders.Encoder;
 import org.numenta.nupic.model.Cell;
 import org.numenta.nupic.util.NamedTuple;
@@ -125,7 +125,7 @@ public interface Inference extends Persistable {
      */
     public int[] getFeedForwardSparseActives();
     /**
-     * Returns the column activation from a {@link TemporalMemory}
+     * Returns the column activation from a {@link OldTemporalMemory}
      * @return
      */
     public Set<Cell> getActiveCells();

Diff for: src/main/java/org/numenta/nupic/network/Layer.java

@@ -44,7 +44,7 @@
 import org.numenta.nupic.algorithms.CLAClassifier;
 import org.numenta.nupic.algorithms.Classification;
 import org.numenta.nupic.algorithms.SpatialPooler;
-import org.numenta.nupic.algorithms.TemporalMemory;
+import org.numenta.nupic.algorithms.OldTemporalMemory;
 import org.numenta.nupic.encoders.DateEncoder;
 import org.numenta.nupic.encoders.Encoder;
 import org.numenta.nupic.encoders.EncoderTuple;
@@ -186,7 +186,7 @@ public class Layer<T> implements Persistable {
     protected HTMSensor<?> sensor;
     protected MultiEncoder encoder;
     protected SpatialPooler spatialPooler;
-    protected TemporalMemory temporalMemory;
+    protected OldTemporalMemory temporalMemory;
     private Boolean autoCreateClassifiers;
     private Anomaly anomalyComputer;
 
@@ -203,11 +203,11 @@ public class Layer<T> implements Persistable {
     protected int[] feedForwardActiveColumns;
     /** Active column indexes from the {@link SpatialPooler} at time "t" */
     private int[] feedForwardSparseActives;
-    /** Predictive {@link Cell}s in the {@link TemporalMemory} at time "t - 1" */
+    /** Predictive {@link Cell}s in the {@link OldTemporalMemory} at time "t - 1" */
     private Set<Cell> previousPredictiveCells;
-    /** Predictive {@link Cell}s in the {@link TemporalMemory} at time "t" */
+    /** Predictive {@link Cell}s in the {@link OldTemporalMemory} at time "t" */
     private Set<Cell> predictiveCells;
-    /** Active {@link Cell}s in the {@link TemporalMemory} at time "t" */
+    /** Active {@link Cell}s in the {@link OldTemporalMemory} at time "t" */
     private Set<Cell> activeCells;
 
     /** Used to track and document the # of records processed */
@@ -363,12 +363,12 @@ public void setNetwork(Network network) {
      * @param e                         (optional) The Network API only uses a {@link MultiEncoder} at
      *                                  the top level because of its ability to delegate to child encoders.
      * @param sp                        (optional) {@link SpatialPooler}
-     * @param tm                        (optional) {@link TemporalMemory}
+     * @param tm                        (optional) {@link OldTemporalMemory}
      * @param autoCreateClassifiers     (optional) Indicates that the {@link Parameters} object
      *                                  contains the configurations necessary to create the required encoders.
      * @param a                         (optional) An {@link Anomaly} computer.
      */
-    public Layer(Parameters params, MultiEncoder e, SpatialPooler sp, TemporalMemory tm, Boolean autoCreateClassifiers, Anomaly a) {
+    public Layer(Parameters params, MultiEncoder e, SpatialPooler sp, OldTemporalMemory tm, Boolean autoCreateClassifiers, Anomaly a) {
 
         // Make sure we have a valid parameters object
         if(params == null) {
@@ -549,7 +549,7 @@ public Layer<T> close() {
 
     /**
      * Called from {@link FunctionFactory#createSpatialFunc(SpatialPooler)} and from {@link #close()}
-     * to calculate the size of the input vector given the output source either being a {@link TemporalMemory}
+     * to calculate the size of the input vector given the output source either being a {@link OldTemporalMemory}
      * or a {@link SpatialPooler} - from this {@link Region} or a previous {@link Region}.
      * 
      * @return  the length of the input vector
@@ -590,7 +590,7 @@ int calculateInputWidth() {
 
     /**
      * For internal use only. Returns a flag indicating whether this {@link Layer}
-     * contains a {@link TemporalMemory}
+     * contains a {@link OldTemporalMemory}
      * @return
      */
     boolean hasTM() {
@@ -804,12 +804,12 @@ public Layer<T> add(SpatialPooler sp) {
     }
 
     /**
-     * Adds a {@link TemporalMemory} to this {@code Layer}
+     * Adds a {@link OldTemporalMemory} to this {@code Layer}
      * 
      * @param tm    the added TemporalMemory
      * @return this Layer instance (in fluent-style)
      */
-    public Layer<T> add(TemporalMemory tm) {
+    public Layer<T> add(OldTemporalMemory tm) {
         if(isClosed) {
             throw new IllegalStateException("Layer already \"closed\"");
         }
@@ -1194,7 +1194,7 @@ public int[] getFeedForwardActiveColumns() {
     }
 
     /**
-     * Returns the {@link Cell}s activated in the {@link TemporalMemory} at time
+     * Returns the {@link Cell}s activated in the {@link OldTemporalMemory} at time
      * "t"
      * 
      * @return
@@ -1263,7 +1263,7 @@ public Layer<T> resetRecordNum() {
     }
 
     /**
-     * Resets the {@link TemporalMemory} if it exists.
+     * Resets the {@link OldTemporalMemory} if it exists.
      */
     public void reset() {
         if(temporalMemory == null) {
@@ -1275,7 +1275,7 @@ public void reset() {
 
     /**
      * Returns a flag indicating whether this {@code Layer} contains a
-     * {@link TemporalMemory}.
+     * {@link OldTemporalMemory}.
      * 
      * @return
      */
@@ -1784,7 +1784,7 @@ private Observable<ManualInput> fillInOrderedSequence(Observable<ManualInput> o)
                 } else {
                     o = o.map(factory.createSpatialFunc(spatialPooler));
                 }
-            } else if(node instanceof TemporalMemory) {
+            } else if(node instanceof OldTemporalMemory) {
                 o = o.map(factory.createTemporalFunc(temporalMemory));
             }
         }
@@ -1947,7 +1947,7 @@ protected int[] spatialInput(int[] input) {
     }
 
     /**
-     * Called internally to invoke the {@link TemporalMemory}
+     * Called internally to invoke the {@link OldTemporalMemory}
      * 
      * @param input     the current input vector
      * @param mi        the current input inference container
@@ -2293,7 +2293,7 @@ public ManualInput call(ManualInput t1) {
             };
         }
 
-        public Func1<ManualInput, ManualInput> createTemporalFunc(final TemporalMemory tm) {
+        public Func1<ManualInput, ManualInput> createTemporalFunc(final OldTemporalMemory tm) {
             return new Func1<ManualInput, ManualInput>() {
 
                 @Override