Sync latest sp

build.gradle

@@ -33,10 +33,11 @@ test {
 }
 
 // UNCOMMENT TO SEE STANDARD_OUT & STANDARD_ERR DURING BUILD
-
+/*
 test {
     testLogging.showStandardStreams = true
 }
+*/
 
 dependencies {
     compile group: 'joda-time', name: 'joda-time', version: '2.5'

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

@@ -56,6 +56,7 @@
 import org.numenta.nupic.util.FlatMatrix;
 import org.numenta.nupic.util.SparseMatrix;
 import org.numenta.nupic.util.SparseObjectMatrix;
+import org.numenta.nupic.util.Topology;
 import org.numenta.nupic.util.Tuple;
 import org.numenta.nupic.util.UniversalRandom;
 
@@ -92,6 +93,7 @@ public class Connections implements Persistable {
     private double predictedSegmentDecrement = 0.0;
     private int dutyCyclePeriod = 1000;
     private double maxBoost = 10.0;
+    private boolean wrapAround = true;
 
     private int numInputs = 1;  //product of input dimensions
     private int numColumns = 1; //product of column dimensions
@@ -111,7 +113,11 @@ public class Connections implements Persistable {
 
     public double[] boostedOverlaps;
     public int[] overlaps;
-
+
+    /** Manages input neighborhood transformations */
+    private Topology inputTopology;
+    /** Manages column neighborhood transformations */
+    private Topology columnTopology;
     /** A matrix representing the shape of the input. */
     protected SparseMatrix<?> inputMatrix;
     /**
@@ -152,8 +158,8 @@ public class Connections implements Persistable {
 
     private double[] overlapDutyCycles;
     private double[] activeDutyCycles;
-    private double[] minOverlapDutyCycles;
-    private double[] minActiveDutyCycles;
+    private volatile double[] minOverlapDutyCycles;
+    private volatile double[] minActiveDutyCycles;
     private double[] boostFactors;
 
     /////////////////////////////////////// Temporal Memory Vars ///////////////////////////////////////////
@@ -379,6 +385,44 @@ public void setMemory(SparseObjectMatrix<Column> mem) {
     public SparseObjectMatrix<Column> getMemory() {
         return memory;
     }
+
+    /**
+     * Returns the {@link Topology} overseeing input 
+     * neighborhoods.
+     * @return 
+     */
+    public Topology getInputTopology() {
+        return inputTopology;
+    }
+
+    /**
+     * Sets the {@link Topology} overseeing input 
+     * neighborhoods.
+     * 
+     * @param topology  the input Topology
+     */
+    public void setInputTopology(Topology topology) {
+        this.inputTopology = topology;
+    }
+
+    /**
+     * Returns the {@link Topology} overseeing {@link Column} 
+     * neighborhoods.
+     * @return
+     */
+    public Topology getColumnTopology() {
+        return columnTopology;
+    }
+
+    /**
+     * Sets the {@link Topology} overseeing {@link Column} 
+     * neighborhoods.
+     * 
+     * @param topology  the column Topology
+     */
+    public void setColumnTopology(Topology topology) {
+        this.columnTopology = topology;
+    }
 
     /**
      * Returns the input column mapping
@@ -950,6 +994,25 @@ public double getMaxBoost() {
         return maxBoost;
     }
 
+    /**
+     * Specifies whether neighborhoods wider than the 
+     * borders wrap around to the other side.
+     * @param b
+     */
+    public void setWrapAround(boolean b) {
+        this.wrapAround = b;
+    }
+
+    /**
+     * Returns a flag indicating whether neighborhoods
+     * wider than the borders, wrap around to the other
+     * side.
+     * @return
+     */
+    public boolean isWrapAround() {
+        return wrapAround;
+    }
+
     /**
      * Sets and Returns the boosted overlap score for each column
      * @param boostedOverlaps
@@ -1051,6 +1114,10 @@ public double[] getOverlapDutyCycles() {
         return overlapDutyCycles;
     }
 
+    /**
+     * Sets the overlap duty cycles
+     * @param overlapDutyCycles
+     */
     public void setOverlapDutyCycles(double[] overlapDutyCycles) {
         this.overlapDutyCycles = overlapDutyCycles;
     }
@@ -2294,9 +2361,10 @@ public String getPrintString() {
         pw.println("synPermConnected           = " + getSynPermConnected());
         pw.println("synPermBelowStimulusInc    = " + getSynPermBelowStimulusInc());
         pw.println("synPermTrimThreshold       = " + getSynPermTrimThreshold());
-        pw.println("minPctOverlapDutyCycles     = " + getMinPctOverlapDutyCycles());
-        pw.println("minPctActiveDutyCycles      = " + getMinPctActiveDutyCycles());
+        pw.println("minPctOverlapDutyCycles    = " + getMinPctOverlapDutyCycles());
+        pw.println("minPctActiveDutyCycles     = " + getMinPctActiveDutyCycles());
         pw.println("dutyCyclePeriod            = " + getDutyCyclePeriod());
+        pw.println("wrapAround                 = " + isWrapAround());
         pw.println("maxBoost                   = " + getMaxBoost());
         pw.println("version                    = " + getVersion());
 

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

@@ -113,6 +113,7 @@ public class Parameters implements Persistable {
         defaultSpatialParams.put(KEY.MIN_PCT_ACTIVE_DUTY_CYCLES, 0.001);
         defaultSpatialParams.put(KEY.DUTY_CYCLE_PERIOD, 1000);
         defaultSpatialParams.put(KEY.MAX_BOOST, 10.0);
+        defaultSpatialParams.put(KEY.WRAP_AROUND, true);
         defaultSpatialParams.put(KEY.LEARN, true);
         DEFAULTS_SPATIAL = Collections.unmodifiableMap(defaultSpatialParams);
         defaultParams.putAll(DEFAULTS_SPATIAL);
@@ -245,7 +246,7 @@ public static enum KEY {
         MIN_PCT_ACTIVE_DUTY_CYCLES("minPctActiveDutyCycles", Double.class),//TODO add range here?
         DUTY_CYCLE_PERIOD("dutyCyclePeriod", Integer.class),//TODO add range here?
         MAX_BOOST("maxBoost", Double.class), //TODO add range here?
-        //SP_VERBOSITY("spVerbosity", Integer.class, 0, 10),
+        WRAP_AROUND("wrapAround", Boolean.class),
 
         ///////////// SpatialPooler / Network Parameter(s) /////////////
         /** Number of cycles to send through the SP before forwarding data to the rest of the network. */