netica 0.0.5-java

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+log/*
+.rbenv-version

data/.rspec

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+--format specdoc
+--color

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in netica.gemspec
+gemspec
+
+gem 'rake'
+gem 'rspec'

data/LICENSE.txt

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+Copyright (c) 2013 Disruptive Ventures, Inc.
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Netica
+
+The Netica gem provides tools for interacting with Bayesian networks using JRuby and the Netica-J API, published by [Norsys Software Corp.](http://www.norsys.com).
+
+## Installation
+
+Download the Netica-J API from Norsys and place the NeticaJ.jar file in your JRuby load path. Possible locations include...
+
+    /Library/Java/Extensions
+    /Network/Library/Java/Extensions
+    /System/Library/Java/Extensions
+    /usr/lib/java
+
+Add this line to your application's Gemfile:
+
+    gem 'netica'
+
+And then execute:
+
+    $ bundle install
+
+Or install it yourself as:
+
+    $ gem install netica
+
+## Usage
+
+Here's an example, based the Probabilistic Inference example in the Netica-J Manual.
+
+Use Netica::Environment.engage to create a Netica Environ singleton object:
+
+    processor = Netica::Environment.engage
+    => true
+
+Create an ActiveNetwork, using a `.dne` file created in the Netica Application.
+
+    my_network = Netica::ActiveNetwork.new("some_identifiying_token", "./examples/ChestClinic.dne")
+    => #<Netica::ActiveNetwork:0x58767e95 @network=#<Netica::BayesNetwork:0x4b709592 @current_network=#<Java::NorsysNetica::Net:0x75e82fc2>, @dne_file_path="./examples/ChestClinic.dne">, @token="some_identifiying_token">
+
+View the nodes in the network.
+
+    my_network.network.nodes
+    => #<Java::NorsysNetica::NodeList:1738447710 size:8 nodes:["NatureNode:VisitAsia", "NatureNode:Tuberculosis", "NatureNode:Smoking", "NatureNode:Cancer", "NatureNode:TbOrCa", "NatureNode:XRay", "NatureNode:Bronchitis", "NatureNode:Dyspnea"]>
+
+
+Read the value of a Belief node.
+
+    tb_node = my_network.network.node("Tuberculosis")
+    => #<Java::NorsysNetica::NatureNode:Tuberculosis value:{"present"=>0.010399998165667057, "absent"=>0.9896000027656555}>
+
+    tb_node.value("present")
+    => 0.010399998165667057
+
+Set the state of the XRay node to Abnormal.
+
+    xray_node = my_network.network.node("XRay")
+    => #<Java::NorsysNetica::NatureNode:XRay value:{"abnormal"=>0.1102900430560112, "normal"=>0.8897099494934082}>
+
+    xray_node.value = "abnormal"
+    => "abnormal"
+
+Then, re-read the value of the Belief node.
+
+    p tb_node.value("present")
+    0.09241089224815369
+    => 0.09241089224815369
+
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request
+
+## Legal
+
+Netica and Norsys are registered trademarks of Norsys Software Corp.

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rspec'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new do |t|
+  t.rspec_opts = %w(--format progress --colour)
+end

data/examples/ChestClinic.dne

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+// ~->[DNET-1]->~
+
+// File created by an unlicensed user using Netica 5.04 on 10/01/12 at 20:20:06.
+
+bnet ChestClinic {
+autoupdate = FALSE;
+
+node VisitAsia {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (visit, no_visit);
+	statetitles = ("Visited Asia within the last 3 years", );
+	parents = ();
+	probs = 
+		// Visited Asia wit no visit 
+		  (0.01,        0.99);
+	title = "Visit to Asia";
+	};
+
+node Tuberculosis {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (VisitAsia);
+	probs = 
+		// present      absent        // VisitAsia        
+		  (0.05,        0.95,         // Visited Asia wit 
+		   0.01,        0.99);        // no visit         ;
+	};
+
+node Smoking {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (smoker, nonsmoker);
+	parents = ();
+	probs = 
+		// smoker       nonsmoker    
+		  (0.5,         0.5);
+	};
+
+node Cancer {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (Smoking);
+	probs = 
+		// present      absent        // Smoking   
+		  (0.1,         0.9,          // smoker    
+		   0.01,        0.99);        // nonsmoker ;
+	title = "Lung Cancer";
+	};
+
+node TbOrCa {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = DETERMIN;
+	states = (true, false);
+	parents = (Tuberculosis, Cancer);
+	functable = 
+		                    // Tuberculosis Cancer  
+		  (true,            // present      present 
+		   true,            // present      absent  
+		   true,            // absent       present 
+		   false);          // absent       absent  ;
+	equation = "TbOrCa (Tuberculosis, Cancer) = Tuberculosis || Cancer";
+	title = "Tuberculosis or Cancer";
+	};
+
+node XRay {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (abnormal, normal);
+	parents = (TbOrCa);
+	probs = 
+		// abnormal     normal        // TbOrCa 
+		  (0.98,        0.02,         // true   
+		   0.05,        0.95);        // false  ;
+	};
+
+node Bronchitis {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (Smoking);
+	probs = 
+		// present      absent        // Smoking   
+		  (0.6,         0.4,          // smoker    
+		   0.3,         0.7);         // nonsmoker ;
+	};
+
+node Dyspnea {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (TbOrCa, Bronchitis);
+	probs = 
+		// present      absent        // TbOrCa Bronchitis 
+		  (0.9,         0.1,          // true   present    
+		   0.7,         0.3,          // true   absent     
+		   0.8,         0.2,          // false  present    
+		   0.1,         0.9);         // false  absent     ;
+	};
+};

data/examples/chest_clinic.rb

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+#!/usr/bin/env jruby
+require 'netica'
+
+# Use Netica::Environment.engage to create a Netica Environ singleton object:
+processor = Netica::Environment.engage
+
+# Create an ActiveNetwork, using a `.dne` file created in the Netica Application.
+my_network = Netica::ActiveNetwork.new("some_identifiying_token", "#{File.dirname(__FILE__)}/ChestClinic.dne")
+
+# View the nodes in the network.
+p my_network.network.nodes
+
+# Read the value of a Belief node.
+tb_node = my_network.network.node("Tuberculosis")
+belief = tb_node.value("present")
+p "The probability of tuberculosis is #{belief}."
+
+# Set the state of the XRay node to Abnormal.
+xray_node = my_network.network.node("XRay")
+xray_node.value = "abnormal"
+
+# Then, re-read the value of the Belief node.
+belief2 = tb_node.value("present")
+p "Given an abnormal X-ray... The probability of tuberculosis is #{belief2}."

data/lib/netica.rb

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+require 'java'
+require '/lib/NeticaJ.jar'
+
+require "netica/version"
+require "netica/environment"
+require "netica/netica_logger"
+require "netica/node"
+require "netica/node_list"
+require "netica/bayes_network"
+require "netica/active_network"
+
+module Netica
+  include_package "norsys.netica"
+end

data/lib/netica/active_network.rb

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+module Netica
+  require 'json'
+
+  class ActiveNetwork
+    attr_accessor :network, :token
+
+    def initialize(token, filepath = nil)
+      Netica::NeticaLogger.info "initializing active network for #{token}"
+      self.token = token
+      if filepath
+        self.network = BayesNetwork.new(filepath)
+      end
+      processor = Netica::Environment.instance
+      processor.active_networks << self
+    end
+
+    def to_s
+      token
+    end
+
+    def incr_node(nodeName)
+      network.getNode(nodeName).incr() if network
+    end
+
+    def state
+      {
+        :network => network.state,
+        :class   => self.class.to_s
+      }
+    end
+
+    def save
+      if Netica::Environment.instance.redis
+        Netica::Environment.instance.redis.set(token, JSON.dump(state))
+      end
+    end
+
+    def self.find(token)
+      Netica::Environment.instance.active_networks.each do |an|
+        return an if an.token == token
+      end
+      if Netica::Environment.instance.redis
+        stored_state = Netica::Environment.instance.redis.get(token)
+        if stored_state
+          hash = JSON.parse(stored_state)
+          active_network = Object.const_get(hash['class']).new(token)
+          active_network.load_from_saved_state(hash)
+          return active_network
+        end
+      end
+      return nil
+    end
+
+    def load_from_saved_state(hash)
+      self.network = BayesNetwork.new(hash["network"]["dne_file_path"])
+      network.load_from_state(hash["network"])
+    end
+  end
+end

data/lib/netica/bayes_network.rb

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+module Netica
+  class BayesNetwork
+    attr_accessor :current_network, :dne_file_path
+
+    def initialize(dne_file_path = nil)
+      if dne_file_path
+        self.dne_file_path = dne_file_path
+        load_dne_file
+      end
+    end
+
+    # retrieve a node from the associated network
+    # @param String nodeName
+    # @return Node
+    def node(nodeName)
+      nodes.select{ |n| n if n.name == nodeName }[0]
+    end
+
+    def nodes
+      current_network.nodes
+    end
+
+    def decision_nodes
+      nodes.collect{ |n| n if n.decision_node? }.compact
+    end
+
+    def nature_nodes
+      nodes.collect{ |n| n if n.nature_node? }.compact
+    end
+
+    def load_from_state(network_hash)
+      NeticaLogger.info "network_hash => #{network_hash}"
+      network_hash["decision_nodes"].each do |node_name, node_value|
+        getNode(node_name).value = node_value
+      end
+    end
+
+    def state
+      { :dne_file_path => dne_file_path, :decision_nodes => node_hash(decision_nodes), :nature_nodes => node_hash(nature_nodes) }
+    end
+
+    def node_hash(nodes)
+      node_hash = {}
+      nodes.collect{|dn| node_hash.store(dn.name, dn.value) }
+      node_hash
+    end
+
+    private
+
+    def load_dne_file
+      NeticaLogger.info "Looking for BayesNet .dne file at #{dne_file_path}..."
+      streamer = Java::NorsysNetica::Streamer.new(dne_file_path)
+      self.current_network = Java::NorsysNetica::Net.new(streamer)
+      self.current_network.compile()
+      NeticaLogger.info "Initialized BayesNet -- #{self.current_network.object_id}"
+      self.decision_nodes.each{ |n| n.value = 0 }
+    end
+  end
+end

data/lib/netica/environment.rb

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+require 'singleton'
+require 'redis'
+
+module Netica
+  class Environment
+    include Singleton
+
+    @@active_networks = []
+    @@explorations = []
+    @@processor = nil
+    @@redis = nil
+    @@logfile = nil
+
+    def self.engage(settings = {})
+      if settings[:logfile]
+        @@logfile = settings[:logfile]
+      else
+        @@logfile = "#{File.dirname(__FILE__)}/../../log/netica.log"
+      end
+      if settings[:license_key]
+        @@processor = Java::NorsysNetica::Environ.new(settings[:license_key])
+      else
+        @@processor = Java::NorsysNetica::Environ.new(nil)
+      end
+      if settings[:redis]
+        @@redis = Redis.new(settings[:redis])
+      end
+      NeticaLogger.info "Initializing the Netica Environment #{@@processor.object_id}"
+    end
+
+    def processor
+      @@processor
+    end
+
+    def active_networks
+      @@active_networks
+    end
+
+    def redis
+      @@redis
+    end
+
+    def logfile_path
+      @@logfile
+    end
+  end
+end

data/lib/netica/netica_logger.rb

@@ -0,0 +1,18 @@
+module Netica
+  class NeticaLogger
+    require 'logger'
+    require 'date'
+
+    def self.info(message=nil)
+      self.logfile.info(message) unless message.nil?
+    end
+
+    def self.debug(message=nil)
+      self.logfile.debug(message) unless message.nil?
+    end
+
+    def self.logfile
+      @@my_log ||= Logger.new(File.open(Netica::Environment.instance.logfile_path, File::WRONLY | File::APPEND))
+    end
+  end
+end

data/lib/netica/node.rb

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+class Java::NorsysNetica::Node
+  attr_accessor :value
+
+  # from https://github.com/SixArm/sixarm_ruby_netica
+  NODE_KINDS = {
+   Java::NorsysNetica::Node::NATURE_NODE => :nature,
+   Java::NorsysNetica::Node::DECISION_NODE => :decision,
+   Java::NorsysNetica::Node::UTILITY_NODE => :utility,
+   Java::NorsysNetica::Node::CONSTANT_NODE => :constant,
+   Java::NorsysNetica::Node::DISCONNECTED_NODE => :disconnected,
+  }
+
+  NODE_TYPES = {
+   Java::NorsysNetica::Node::DISCRETE_TYPE => :nature,
+   Java::NorsysNetica::Node::CONTINUOUS_TYPE => :decision,
+  }
+
+  def name
+    getName
+  end
+
+  def kind
+    NODE_KINDS[getKind]
+  end
+
+  def type
+    NODE_TYPES[getType]
+  end
+
+  def decision_node?
+    type == :decision
+  end
+
+  def nature_node?
+    type == :nature
+  end
+
+  def beliefs
+    states.collect{ |st| getBelief(st.to_s) }
+  end
+
+  def hint
+    user().getString("Hint")
+  end
+
+  def top_parent_node
+    getParents().sort_by_belief()[0]
+  end
+
+  def value(state_name = nil)
+    if decision_node?
+      finding().getReal()
+    elsif state_name
+      states.collect{ |st| return getBelief(st.to_s) if state_name == st.to_s }
+    else
+      state_values = {}
+      states.collect{ |st| state_values.store(st.to_s, getBelief(st.to_s)) }
+      state_values
+    end
+  end
+
+  def value=(new_value)
+    Netica::NeticaLogger.info "Setting #{self.name} to #{new_value}"
+    if decision_node?
+      finding().setReal(new_value)
+    elsif nature_node?
+      finding.enterState(new_value)
+    end
+  end
+
+  def incr
+    if decision_node?
+      self.value = value + 1
+    end
+  end
+
+  def to_s
+    if type == kind
+      prefix = type.capitalize
+    else
+      prefix = "#{type.capitalize}#{kind.capitalize}"
+    end
+
+    "#{prefix}Node:#{name}"
+  end
+
+  def inspect
+    "#<Java::NorsysNetica::#{self.to_s} value:#{value}>"
+  end
+
+  def states
+    (0...getNumStates()).map{|i| state(i) }
+  end
+
+  def free
+    begin
+      NeticaLogger.info "Deleting #{self.to_s}"
+      finalize()
+      delete()
+      states.each{|s| s==nil or s.free() }
+    rescue Java::NorsysNetica::NeticaException
+    end
+  end
+end

data/lib/netica/node_list.rb

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+class Java::NorsysNetica::NodeList
+  def sort_by_belief
+    nodes.sort{|a,b| b.beliefs <=> a.beliefs }
+  end
+
+  def nodes
+    (0...size).map{|i| getNode(i) }
+  end
+
+  def to_s
+    "NodeList:#{object_id}"
+  end
+
+  def inspect
+    "#<Java::NorsysNetica::NodeList:#{object_id} size:#{size} nodes:#{nodes.collect{|n| n.to_s }}>"
+  end
+
+  def free
+    begin
+      NeticaLogger.info "Deleting #{self.to_s}"
+      finalize()
+      nodes.each{|n| n==nil or n.free() }
+    rescue Java::NorsysNetica::NeticaException
+    end
+  end
+end

data/lib/netica/state.rb

@@ -0,0 +1,9 @@
+class Java::NorsysNetica::State
+  def to_s
+    "#{getName}"
+  end
+
+  def inspect
+    "#{getName}"
+  end
+end

data/lib/netica/version.rb

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+module Netica
+  VERSION = "0.0.5"
+end

data/netica.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'netica/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "netica"
+  gem.version       = Netica::VERSION
+  gem.authors       = ["Jerry Richardson"]
+  gem.email         = ["jerry@jerryr.com"]
+  gem.description   = "Netica Bayes Network Management"
+  gem.summary       = "Tools to manage Bayes Networks with the NeticaJ API"
+  gem.homepage      = "http://disruptive.github.io/netica/"
+  gem.license       = "MIT"
+  gem.platform      = "java"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+end

data/spec/netica/active_network_spec.rb

@@ -0,0 +1,42 @@
+require 'spec_helper'
+
+describe Netica::ActiveNetwork do
+  describe "#new" do
+    before(:all) do
+      Netica::Environment.engage
+    end
+    after(:all) do
+      Netica::Environment.instance.processor.finalize
+    end
+
+    context "with ChestClinic.dne" do
+      before(:all) do
+        @active_network = Netica::ActiveNetwork.new("fake_token_identifier", "#{File.dirname(__FILE__)}/../../examples/ChestClinic.dne")
+      end
+
+      it "should be an active network" do
+        @active_network.should be_an_instance_of(Netica::ActiveNetwork)
+      end
+
+      it "should have 8 nodes" do
+        @active_network.network.nodes.length.should == 8
+      end
+
+      it "should export it state as a hash" do
+        @active_network.network.state.should be_an_instance_of(Hash)
+      end
+
+      context "the tuberculosis node" do
+        it "should be less than 0.02 initially" do
+          @active_network.network.node("Tuberculosis").value("present").should be_less_than 0.011
+        end
+
+        it "should be over 0.90 with an abnormal xray" do
+          @active_network.network.node("XRay").value = "abnormal"
+          @active_network.network.node("Tuberculosis").value("present").should be_greater_than 0.092
+        end
+      end
+    end
+  end
+end
+

data/spec/netica/environment_spec.rb

@@ -0,0 +1,16 @@
+require 'spec_helper'
+
+describe Netica::Environment do
+  describe "#engage" do
+    it 'should create a Netica environment' do
+      Netica::Environment.engage.should be_true
+      Netica::Environment.instance.processor.finalize
+    end
+
+    it 'should create a logfile' do
+      Netica::Environment.engage
+      Netica::NeticaLogger.info "Test logfile entry"
+      Netica::Environment.instance.processor.finalize
+    end
+  end
+end

data/spec/netica_spec.rb

@@ -0,0 +1,7 @@
+require 'spec_helper'
+
+describe Netica do
+  it 'should have a version number' do
+    Netica::VERSION.should_not be_nil
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,19 @@
+$LOAD_PATH.unshift File.expand_path('../../lib', __FILE__)
+require 'netica'
+
+RSpec.configure do |config|
+  config.color_enabled = true
+  config.formatter     = 'progress'
+end
+
+RSpec::Matchers.define :be_less_than do |expected|
+  match do |actual|
+    actual<expected
+  end
+end
+
+RSpec::Matchers.define :be_greater_than do |expected|
+  match do |actual|
+    actual>expected
+  end
+end

metadata

@@ -0,0 +1,75 @@
+--- !ruby/object:Gem::Specification
+name: netica
+version: !ruby/object:Gem::Version
+  version: 0.0.5
+  prerelease:
+platform: java
+authors:
+- Jerry Richardson
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2013-04-14 00:00:00.000000000 Z
+dependencies: []
+description: Netica Bayes Network Management
+email:
+- jerry@jerryr.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- examples/ChestClinic.dne
+- examples/chest_clinic.rb
+- lib/netica.rb
+- lib/netica/active_network.rb
+- lib/netica/bayes_network.rb
+- lib/netica/environment.rb
+- lib/netica/netica_logger.rb
+- lib/netica/node.rb
+- lib/netica/node_list.rb
+- lib/netica/state.rb
+- lib/netica/version.rb
+- netica.gemspec
+- spec/netica/active_network_spec.rb
+- spec/netica/environment_spec.rb
+- spec/netica_spec.rb
+- spec/spec_helper.rb
+homepage: http://disruptive.github.io/netica/
+licenses:
+- MIT
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: !binary |-
+        MA==
+  none: false
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: !binary |-
+        MA==
+  none: false
+requirements: []
+rubyforge_project:
+rubygems_version: 1.8.24
+signing_key:
+specification_version: 3
+summary: Tools to manage Bayes Networks with the NeticaJ API
+test_files:
+- spec/netica/active_network_spec.rb
+- spec/netica/environment_spec.rb
+- spec/netica_spec.rb
+- spec/spec_helper.rb
+has_rdoc: