initial push

.gitignore

@@ -1,6 +1,9 @@
+.*
+*~
+target/*
 *.class
-
-# Package Files #
-*.jar
-*.war
-*.ear
+bin/
+build/
+.project
+.idea/
+*.iml

License_Numenta.txt

@@ -0,0 +1,57 @@
+This software is based upon or includes certain works and algorithms related
+to hierarchical temporal memory ("HTM") technology published by Numenta Inc.
+
+
+Numenta holds patent rights related to HTM and the algorithms used in this 
+software.
+
+Numenta has agreed not to assert its patent rights against 
+development or use of independent HTM systems, as long as such development 
+or use is for research purposes only, and not for any commercial or production 
+use.
+
+Any commercial or production use of HTM technology that infringes on 
+Numenta's patents will require a commercial license from Numenta.
+
+
+
+Based on the foregoing, this software is licensed under the terms below, for 
+research purposes only and not for any commercial or production use.
+
+Numenta License for Non-Commercial Use:
+
+For 
+purposes of this license, "commercial or production use" includes training an 
+HTM network with the intent of later deploying the trained network or 
+application for commercial or production purposes, and using or permitting 
+others to use the output from HTM technology for commercial or production 
+purposes.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted (subject to the limitations in the disclaimer 
+below) provided that the following conditions are met:
+
+* Redistributions of source code, including any modifications or derivative 
+works, must retain the full text of this license and the following disclaimer, 
+and be subject to the terms and conditions of this license.
+
+* Redistributions in binary form, including any modifications or derivative 
+works, must reproduce the full text of this license and the following 
+disclaimer in the documentation and/or other materials provided with the 
+distribution, and be subject to the terms and conditions of this license.
+
+* Neither the name of Numenta, Inc., Barry Maturkanich, nor the names of other 
+contributors may be used to endorse or promote products derived from this 
+software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PATENT RIGHTS ARE GRANTED BY THIS 
+LICENSE.  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,4 +1,7 @@
 htm-visualizer
 ==============
 
-HTM Cortical Learning Algorithm visualizer in JAVA
+Visualization of Hiearchical temporal memory (HTM) cortical learning algorithms (CLA) in JAVA
+Implementation is based on Numenta's CLA white paper:
+https://www.groksolutions.com/htm-overview/education/HTM_CorticalLearningAlgorithms.pdf
+

pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>htm</groupId>
+  <artifactId>htm-visualizer</artifactId>
+  <packaging>jar</packaging>
+  <version>1.0</version>
+  <name>HTM-CLA Visualizer</name>
+  <dependencies>
+
+    <dependency>
+      <groupId>log4j</groupId>
+      <artifactId>log4j</artifactId>
+      <version>1.2.9</version>
+      <scope>runtime</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>commons-logging</groupId>
+      <artifactId>commons-logging</artifactId>
+      <version>1.1.3</version>
+    </dependency>
+
+
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>3.8.1</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <configuration>
+          <source>1.6</source>
+          <target>1.6</target>
+        </configuration>
+      </plugin>
+      <plugin>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>jar-assembly</id>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+            <configuration>
+              <archive>
+                <manifestEntries>
+                  <Main-Class>peacetech.gao.locator.adconversion.ConversionRunner</Main-Class>
+                  <Implementation-Title>${project.description}</Implementation-Title>
+                  <Implementation-Version>${project.version}</Implementation-Version>
+                </manifestEntries>
+              </archive>
+              <descriptorRefs>
+                <descriptorRef>jar-with-dependencies</descriptorRef>
+              </descriptorRefs>
+            </configuration>
+          </execution>
+          <execution>
+            <id>distribution-assembly</id>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+            <configuration>
+              <descriptors>
+                <descriptor>src/main/assembly/distribution.xml</descriptor>
+              </descriptors>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <artifactId>maven-source-plugin</artifactId>
+      </plugin>
+    </plugins>
+  </build>
+</project>

run.bat

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+java  -classpath "lib\commons-logging-1.1.3.jar;lib\log4j-1.2.9.jar;htm-visualizer.jar" htm.visualizer.Viewer
+
+

src/main/assembly/distribution.xml

@@ -0,0 +1,28 @@
+<assembly>
+  <id>dist</id>
+  <includeBaseDirectory>false</includeBaseDirectory>
+  <formats>
+    <format>zip</format>
+  </formats>
+  <files>
+    <file>
+      <source>target/${project.build.finalName}.jar</source>
+      <destName>htm-visualizer.jar</destName>
+      <fileMode>0644</fileMode>
+    </file>
+    <file>
+      <source>run.bat</source>
+      <destName>run.bat</destName>
+      <filtered>true</filtered>
+      <fileMode>0644</fileMode>
+    </file>
+  </files>
+  <dependencySets>
+    <dependencySet>
+      <outputDirectory>/lib</outputDirectory>
+      <excludes>
+        <exclude>htm:htm-visualizer</exclude>
+      </excludes>
+    </dependencySet>
+  </dependencySets>
+</assembly>

src/main/java/htm/model/Cell.java

@@ -0,0 +1,113 @@
+/**
+ * Copyright (c) 2011, Peace Technology, Inc.
+ * $Author:$
+ * $Revision:$
+ * $Date:$
+ * $NoKeywords$
+ */
+
+package htm.model;
+
+import htm.visualizer.utils.CircularArrayList;
+
+public class Cell {
+
+  public static final int ACTIVE_STATE = 1;
+  public static final int LEARN_STATE = 2;
+
+  public static final int BEFORE = 1;
+  public static final int NOW = 0;
+
+  /**
+   * cell will keep a buffer of its last TIME_STEPS output values
+   */
+  private static int TIME_STEPS = 2;
+
+  private final Column belongsToColumn;
+  private final int cellIndex;
+  /**
+   * Boolean vector of Cell's active state in time t-n, ..., t-1, t
+   */
+  private CellStateBuffer activeState = new CellStateBuffer();
+
+  /**
+   * Boolean vector of Cell's predictive state in time t-n, ..., t-1, t
+   */
+  private CellStateBuffer predictiveState = new CellStateBuffer();
+  /**
+   * learnState(c, i, t) A boolean indicating whether cell i in column c is
+   * chosen as the cell to learn on.
+   */
+  private CellStateBuffer learnState = new CellStateBuffer();
+
+  public Cell(Column belongsToColumn, int cellIndex) {
+    this.belongsToColumn = belongsToColumn;
+    this.cellIndex = cellIndex;
+  }
+
+   /*
+  *Set Learn State in current time Cell.NOW
+   */
+  public void setLearnState(boolean learnState) {
+    this.learnState.setState(learnState);
+  }
+
+  /**
+   * Get Learn state in Time
+   *
+   * @param time
+   */
+  public boolean getLearnState(int time) {
+    return this.learnState.get(time);
+  }
+
+  /**
+   * Set active state
+   */
+  public void setActiveState(boolean activeState) {
+    this.activeState.setState(activeState);
+  }
+
+  /**
+   * Get Active state in Time
+   *
+   * @param time
+   */
+  public boolean getActiveState(int time) {
+    return this.activeState.get(time);
+  }
+
+  /**
+   * Set Predictive state
+   */
+  public void setPredictiveState(boolean predictiveState) {
+    this.predictiveState.setState(predictiveState);
+  }
+
+  /**
+   * Get Predictive state in Time
+   *
+   * @param time
+   */
+  public boolean getPredictiveState(int time) {
+    return this.predictiveState.get(time);
+  }
+
+  private static class CellStateBuffer extends CircularArrayList<Boolean>{
+    public CellStateBuffer() {
+      super(TIME_STEPS);
+      for (int i = 0; i < TIME_STEPS; i++) {
+         this.add(false);
+      }
+    }
+
+    /**
+    * Set the current state(time NOW)
+    *
+    * @param state
+    **/
+    void setState(boolean state){
+      this.set(NOW, state);
+    }
+  }
+}

src/main/java/htm/model/Column.java

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+/**
+ * Copyright (c) 2011, Peace Technology, Inc.
+ * $Author:$
+ * $Revision:$
+ * $Date:$
+ * $NoKeywords$
+ */
+
+package htm.model;
+
+import htm.visualizer.utils.CircularArrayList;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class Column {
+  public static int CELLS_PER_COLUMN = 3;
+  private static final int COLUMN_MAX_ACTIVE = 1000;
+  private final int columnIndex;
+  private final List<Cell> cells = new ArrayList<Cell>();
+  private ArrayList<Boolean> activeList = new CircularArrayList<Boolean>(COLUMN_MAX_ACTIVE);
+
+  /**
+   * activeDutyCycle(c) A sliding average representing how often column c has
+   * been active after inhibition (e.g. over the last 1000 iterations).
+   */
+  private double activeDutyCycle;
+
+  public Column(int columnIndex) {
+    this.columnIndex = columnIndex;
+    for (int i = 0; i < CELLS_PER_COLUMN; i++) {
+      cells.add(new Cell(this, i));
+    }
+  }
+
+  public int getColumnIndex() {
+    return columnIndex;
+  }
+
+  public List<Cell> getCells() {
+    return Collections.unmodifiableList(cells);
+  }
+
+  public Cell getCellByIndex(int index){
+    return cells.get(index);
+  }
+
+  /**
+      * updateActiveDutyCycle(c) Computes a moving average of how often column c
+      * has been active after inhibition.
+      *
+      * @return
+      */
+     private double updateActiveDutyCycle() {
+         int totalActive = 0;
+         for (boolean act : activeList) {
+             if (act) {
+                 totalActive++;
+             }
+         }
+         this.activeDutyCycle = (double) totalActive / activeList.size();
+         return activeDutyCycle;
+     }
+
+     public void setActive(boolean active) {
+         // logger.log(Level.INFO, "activeList" + activeList.size());
+         activeList.add(0, active);
+         updateActiveDutyCycle();
+     }
+
+     public boolean isActive() {
+         return this.activeList.size() > 0 ? activeList.get(0) : false;
+     }
+}