Add 'htm.java' detector

.gitignore

@@ -5,6 +5,7 @@
 data_test/
 deprecated/
 nab.egg-info/
+.idea/
 
 # Generated files
 

README.md

@@ -85,13 +85,15 @@ run without likelihood, set the variable `self.useLikelihood` in
 [numenta_detector.py](https://github.com/numenta/NAB/blob/master/nab/detectors/numenta/numenta_detector.py)
 to `False`.
 * [nab-comportex](https://github.com/floybix/nab-comportex) is a twist on HTM  anomaly detection using [Comportex](https://github.com/htm-community/comportex), a community-driven HTM implementation in Clojure. Please see [Felix Andrew's blog post](http://floybix.github.io/2016/07/01/attempting-nab) on experiments with this algorithm.
+* [HTM Java](https://github.com/numenta/htm.java) is a Community-Driven Java port of HTM.
 
 
 | Detector      |Standard Profile | Reward Low FP | Reward Low FN |
 |---------------|---------|------------------|---------------|---------------|
 | Numenta HTM*   | 65.3             | 58.6       | 69.4          |
 | [nab-comportex](https://github.com/floybix/nab-comportex)† | 64.6             | 58.8       | 69.6          |
 | [NumentaTM HTM](https://github.com/numenta/NAB/blob/master/nab/detectors/numenta/numentaTM_detector.py)* | 61.2             | 52.4       | 66.1          |
+| [HTM Java](https://github.com/numenta/NAB/blob/master/nab/detectors/htmjava) | 57.54 | 49.71 | 62.33 |
 | Numenta HTM*, no likelihood | 52.52 | 41.09    | 58.25         |
 
 \* The results correspond to NuPIC and nupic.core SHAs 42f701d and c030b84
@@ -198,7 +200,6 @@ the specific version of NuPIC (and associated nupic.core) that is noted in the
     cd /path/to/nupic.core/
     git checkout -b nab {TAG NAME}
 
-
 ##### Run full NAB
 
     cd /path/to/nab
@@ -219,7 +220,7 @@ subset of the NAB data files or on your own set of data files. You can do that
 by creating a custom `combined_windows.json` file that only contains labels for
 the files you want to run. This new file should be in exactly the same format as
 `combined_windows.json` except it would only contain windows for the files you
-are interested in. 
+are interested in.
 
 **Example**: an example file containing two files is in
 `labels/combined_windows_tiny.json`.  The following command shows you how to run

config/thresholds.json

@@ -41,18 +41,18 @@
             "threshold": 0.9947875976562506
         }
     },
-    "relativeEntropy": {
+    "htmjava": {
         "reward_low_FN_rate": {
-            "score": -27.2288224715,
-            "threshold": 0.5
+            "score": -15.092683287919897,
+            "threshold": 0.501556396484375
         },
         "reward_low_FP_rate": {
-            "score": -5.57182391716,
-            "threshold": 0.5
+            "score": -0.668792875255821,
+            "threshold": 0.5416503906250002
         },
         "standard": {
-            "score": 10.7711775285,
-            "threshold": 0.5
+            "score": 17.499891977504333,
+            "threshold": 0.514062309265137
         }
     },
     "null": {
@@ -111,6 +111,20 @@
             "threshold": 0.9984497070312507
         }
     },
+    "relativeEntropy": {
+        "reward_low_FN_rate": {
+            "score": -27.2288224715,
+            "threshold": 0.5
+        },
+        "reward_low_FP_rate": {
+            "score": -5.57182391716,
+            "threshold": 0.5
+        },
+        "standard": {
+            "score": 10.7711775285,
+            "threshold": 0.5
+        }
+    },
     "skyline": {
         "reward_low_FN_rate": {
             "score": -77.20605964639174,
@@ -153,4 +167,4 @@
             "threshold": 1.0
         }
     }
-}
+}

nab/detectors/htmjava/.gitignore

@@ -0,0 +1,7 @@
+.gradle
+build
+/bin/
+.classpath
+.project
+.settings
+.idea

nab/detectors/htmjava/README.md

@@ -0,0 +1,17 @@
+## [HTM Java](https://github.com/numenta/htm.java) NAB detector
+
+##### Run [htm.java](https://github.com/numenta/htm.java) with NAB
+
+First make sure you have __java 8__ installed
+
+    java -version
+
+Build __htm.java__ NAB detector:
+
+    cd nab/detectors/htmjava
+    ./gradlew clean build
+
+Run __htm.java__ NAB detector:
+
+    cd /path/to/nab
+    python run.py -d htmjava --detect --score --normalize

nab/detectors/htmjava/build.gradle

@@ -0,0 +1,43 @@
+apply plugin: 'java'
+
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+archivesBaseName = 'htm.java-nab'
+
+
+repositories {
+  mavenCentral()
+  maven {
+    url 'https://oss.sonatype.org/content/repositories/snapshots'
+  }
+  maven {
+    url 'http://metaware.us/maven3'
+  }
+}
+
+dependencies {
+    compile group: 'org.numenta', name: 'htm.java', version: '0.6.9-SNAPSHOT'
+    compile group: 'com.google.guava', name: 'guava', version: '19.0'
+    compile group: 'org.slf4j', name: 'slf4j-api', version: '1.7.10'
+    compile group: 'org.slf4j', name: 'slf4j-log4j12', version: '1.7.10'
+    compile group: 'net.sf.jopt-simple', name: 'jopt-simple', version: '4.6'
+}
+
+jar {
+    manifest {
+        attributes 'Implementation-Title': 'NAB detector for htm.java',
+                   'Implementation-Version': '0.0.1',
+                   'Main-Class': 'nab.detectors.htmjava.HTMModel',
+                   'Class-Path': configurations.runtime.files.collect {"$it.name"}.join(' ')
+    }
+}
+
+clean {
+  delete fileTree(dir: '../../../' , include: 'htmjava.log')
+}
+
+task copyToLib(type: Copy) {
+    into "$buildDir/libs"
+    from configurations.runtime
+}
+assemble.dependsOn(copyToLib)

nab/detectors/htmjava/gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,6 @@
+#Sun Mar 27 18:56:14 PDT 2016
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.5-all.zip

nab/detectors/htmjava/gradlew

@@ -0,0 +1,164 @@
+#!/usr/bin/env bash
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+esac
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched.
+if $cygwin ; then
+    [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+fi
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >&-
+APP_HOME="`pwd -P`"
+cd "$SAVED" >&-
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
+function splitJvmOpts() {
+    JVM_OPTS=("$@")
+}
+eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
+JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+
+exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"