Moved UnitTests to tests/ and Skills to src/

src/FactorGraphs/Factor.php

@@ -0,0 +1,113 @@
+<?php
+namespace Moserware\Skills\FactorGraphs;
+
+require_once(dirname(__FILE__) . "/../Guard.php");
+require_once(dirname(__FILE__) . "/../HashMap.php");
+require_once(dirname(__FILE__) . "/Message.php");
+require_once(dirname(__FILE__) . "/Variable.php");
+
+use Moserware\Skills\Guard;
+use Moserware\Skills\HashMap;
+
+abstract class Factor
+{
+    private $_messages = array();
+    private $_messageToVariableBinding;
+
+    private $_name;
+    private $_variables = array();
+
+    protected function __construct($name)
+    {
+        $this->_name = "Factor[" . $name . "]";
+        $this->_messageToVariableBinding = new HashMap();
+    }
+
+    /**
+     * @return The log-normalization constant of that factor
+     */
+    public function getLogNormalization()
+    {
+        return 0;
+    }
+
+    /**
+     * @return The number of messages that the factor has
+     */
+    public function getNumberOfMessages()
+    {
+        return count($this->_messages);
+    }
+    
+    protected function &getVariables()
+    {
+        return $this->_variables;
+    }
+    
+    protected function &getMessages()
+    {
+        return $this->_messages;
+    }
+
+    /**
+     * Update the message and marginal of the i-th variable that the factor is connected to
+     */
+    public function updateMessageIndex($messageIndex)
+    {
+        Guard::argumentIsValidIndex($messageIndex, count($this->_messages), "messageIndex");
+        $message = &$this->_messages[$messageIndex];
+        $variable = &$this->_messageToVariableBinding->getValue($message);        
+        return $this->updateMessageVariable($message, $variable);
+    }
+
+    protected function updateMessageVariable(Message $message, Variable $variable)
+    {
+        throw new Exception();
+    }
+
+    /**
+     * Resets the marginal of the variables a factor is connected to
+     */
+    public function resetMarginals()
+    {
+        $allValues = &$this->_messageToVariableBinding->getAllValues();
+        foreach ($allValues as &$currentVariable)
+        {
+            $currentVariable->resetToPrior();
+        }
+    }
+
+    /**
+     * Sends the ith message to the marginal and returns the log-normalization constant
+     */
+    public function sendMessageIndex($messageIndex)
+    {
+        Guard::argumentIsValidIndex($messageIndex, count($this->_messages), "messageIndex");
+
+        $message = &$this->_messages[$messageIndex];
+        $variable = &$this->_messageToVariableBinding->getValue($message);
+        return $this->sendMessageVariable($message, $variable);
+    }
+
+    protected abstract function sendMessageVariable(Message &$message, Variable &$variable);
+
+    public abstract function &createVariableToMessageBinding(Variable &$variable);
+
+    protected function &createVariableToMessageBindingWithMessage(Variable &$variable, Message &$message)
+    {
+        $index = count($this->_messages);
+        $localMessages = &$this->_messages;
+        $localMessages[] = &$message;
+        $this->_messageToVariableBinding->setValue($message, $variable);
+        $localVariables = &$this->_variables;
+        $localVariables[] = &$variable;
+        return $message;
+    }
+
+    public function __toString()
+    {
+        return ($this->_name != null) ? $this->_name : base::__toString();
+    }
+}
+
+?>

src/FactorGraphs/FactorGraph.php

@@ -0,0 +1,21 @@
+<?php
+namespace Moserware\Skills\FactorGraphs;
+
+require_once(dirname(__FILE__) . "/VariableFactory.php");
+
+class FactorGraph
+{
+    private $_variableFactory;
+
+    public function &getVariableFactory()
+    {
+        $factory = &$this->_variableFactory;
+        return $factory;
+    }
+
+    public function setVariableFactory(VariableFactory &$factory)
+    {
+        $this->_variableFactory = &$factory;
+    }
+}
+?>

src/FactorGraphs/FactorGraphLayer.php

@@ -0,0 +1,74 @@
+<?php
+namespace Moserware\Skills\FactorGraphs;
+
+require_once(dirname(__FILE__) . "/Factor.php");
+require_once(dirname(__FILE__) . "/FactorGraph.php");
+require_once(dirname(__FILE__) . "/Schedule.php");
+
+abstract class FactorGraphLayer
+{
+    private $_localFactors = array();
+    private $_outputVariablesGroups = array();    
+    private $_inputVariablesGroups = array();
+    private $_parentFactorGraph;
+
+    protected function __construct(FactorGraph &$parentGraph)
+    {
+        $this->_parentFactorGraph = &$parentGraph;
+    }
+
+    protected function &getInputVariablesGroups()
+    {
+        $inputVariablesGroups = &$this->_inputVariablesGroups;
+        return $inputVariablesGroups;
+    }
+
+    // HACK
+
+    public function &getParentFactorGraph()
+    {
+        $parentFactorGraph = &$this->_parentFactorGraph;
+        return $parentFactorGraph;
+    }
+
+    public function &getOutputVariablesGroups()
+    {
+        $outputVariablesGroups = &$this->_outputVariablesGroups;
+        return $outputVariablesGroups;
+    }
+
+    public function &getLocalFactors()
+    {
+        $localFactors = &$this->_localFactors;
+        return $localFactors;
+    }
+
+    public function setInputVariablesGroups(&$value)
+    {
+        $this->_inputVariablesGroups = $value;
+    }
+
+    protected function scheduleSequence(array $itemsToSequence, $name)
+    {
+        return new ScheduleSequence($name, $itemsToSequence);
+    }
+
+    protected function addLayerFactor(Factor &$factor)
+    {
+        $this->_localFactors[] = $factor;
+    }
+
+    public abstract function buildLayer();
+
+    public function createPriorSchedule()
+    {
+        return null;
+    }
+
+    public function createPosteriorSchedule()
+    {
+        return null;
+    }
+}
+
+?>

src/FactorGraphs/FactorList.php

@@ -0,0 +1,60 @@
+<?php
+
+namespace Moserware\Skills\FactorGraphs;
+
+require_once(dirname(__FILE__) . "/Factor.php");
+
+/**
+ * Helper class for computing the factor graph's normalization constant.
+ */
+class FactorList
+{
+    private $_list = array();
+
+    public function getLogNormalization()
+    {
+        $list = &$this->_list;
+        foreach($list as &$currentFactor)
+        {
+            $currentFactor->resetMarginals();
+        }
+
+        $sumLogZ = 0.0;
+
+        $listCount = count($this->_list);
+
+        for ($i = 0; $i < $listCount; $i++)
+        {
+            $f = $this->_list[$i];
+
+            $numberOfMessages = $f->getNumberOfMessages();
+
+            for ($j = 0; $j < $numberOfMessages; $j++)
+            {
+                $sumLogZ += $f->sendMessageIndex($j);
+            }
+        }
+
+        $sumLogS = 0;
+
+        foreach($list as &$currentFactor)
+        {
+            $sumLogS = $sumLogS + $currentFactor->getLogNormalization();
+        }
+
+        return $sumLogZ + $sumLogS;
+    }
+
+    public function count()
+    {
+        return count($this->_list);
+    }
+
+    public function &addFactor(Factor &$factor)
+    {
+        $this->_list[] = $factor;
+        return $factor;
+    }
+}
+
+?>

src/FactorGraphs/Message.php

@@ -0,0 +1,32 @@
+<?php
+namespace Moserware\Skills\FactorGraphs;
+
+class Message
+{
+    private $_name;    
+    private $_value;
+
+    public function __construct(&$value = null, $name = null)
+    {
+        $this->_name = $name;        
+        $this->_value = $value;
+    }
+
+    public function& getValue()
+    {
+        $value = &$this->_value;
+        return $value;
+    }
+
+    public function setValue(&$value)
+    {        
+        $this->_value = &$value;
+    }
+
+    public function __toString()
+    {
+        return $this->_name; 
+    }
+}
+
+?>

src/FactorGraphs/Schedule.php

@@ -0,0 +1,94 @@
+<?php
+namespace Moserware\Skills\FactorGraphs;
+
+require_once(dirname(__FILE__) . "/Factor.php");
+
+abstract class Schedule
+{
+    private $_name;
+
+    protected function __construct($name)
+    {
+        $this->_name = $name;
+    }
+
+    public abstract function visit($depth = -1, $maxDepth = 0);
+
+    public function __toString()
+    {
+        return $this->_name;
+    }
+}
+
+class ScheduleStep extends Schedule
+{
+    private $_factor;
+    private $_index;
+
+    public function __construct($name, Factor &$factor, $index)
+    {
+        parent::__construct($name);
+        $this->_factor = $factor;
+        $this->_index = $index;
+    }
+
+    public function visit($depth = -1, $maxDepth = 0)
+    {
+        $currentFactor = &$this->_factor;        
+        $delta = $currentFactor->updateMessageIndex($this->_index);
+        return $delta;
+    }
+}
+
+class ScheduleSequence extends Schedule
+{
+    private $_schedules;
+
+    public function __construct($name, array $schedules)
+    {
+        parent::__construct($name);
+        $this->_schedules = $schedules;
+    }
+
+    public function visit($depth = -1, $maxDepth = 0)
+    {
+        $maxDelta = 0;
+
+        $schedules = &$this->_schedules;
+        foreach ($schedules as &$currentSchedule)
+        {
+            $currentVisit = $currentSchedule->visit($depth + 1, $maxDepth);
+            $maxDelta = max($currentVisit, $maxDelta);
+        }
+
+        return $maxDelta;
+    }
+}
+
+class ScheduleLoop extends Schedule
+{
+    private $_maxDelta;
+    private $_scheduleToLoop;
+
+    public function __construct($name, Schedule &$scheduleToLoop, $maxDelta)
+    {
+        parent::__construct($name);
+        $this->_scheduleToLoop = $scheduleToLoop;
+        $this->_maxDelta = $maxDelta;
+    }
+
+    public function visit($depth = -1, $maxDepth = 0)
+    {
+        $totalIterations = 1;
+        $delta = $this->_scheduleToLoop->visit($depth + 1, $maxDepth);
+        while ($delta > $this->_maxDelta)
+        {
+            $delta = $this->_scheduleToLoop->visit($depth + 1, $maxDepth);
+            $totalIterations++;
+        }
+
+        return $delta;
+    }
+}
+
+?>

src/FactorGraphs/Variable.php

@@ -0,0 +1,73 @@
+<?php
+namespace Moserware\Skills\FactorGraphs;
+
+class Variable
+{
+    private $_name;
+    private $_prior;
+    private $_value;
+
+    public function __construct($name, &$prior)
+    {
+        $this->_name = "Variable[" . $name . "]";
+        $this->_prior = $prior;
+        $this->resetToPrior();
+    }
+
+    public function &getValue()
+    {
+        $value = &$this->_value;        
+        return $value;
+    }
+
+    public function setValue(&$value)
+    {        
+        $this->_value = &$value;
+    }
+
+    public function resetToPrior()
+    {
+        $this->_value = $this->_prior;
+    }
+
+    public function __toString()
+    {
+        return $this->_name;
+    }
+}
+
+class DefaultVariable extends Variable
+{
+    public function __construct()
+    {
+        parent::__construct("Default", null);
+    }
+
+    public function &getValue()
+    {
+        return null;
+    }
+
+    public function setValue(&$value)
+    {
+        throw new Exception();
+    }
+}
+
+class KeyedVariable extends Variable
+{
+    private $_key;
+    public function __construct(&$key, $name, &$prior)
+    {
+        parent::__construct($name, $prior);
+        $this->_key = &$key;
+    }
+
+    public function &getKey()
+    {
+        $key = &$this->_key;
+        return $key;
+    }
+}
+
+?>

src/FactorGraphs/VariableFactory.php

@@ -0,0 +1,32 @@
+<?php
+
+namespace Moserware\Skills\FactorGraphs;
+
+require_once(dirname(__FILE__) . "/Variable.php");
+
+class VariableFactory
+{
+    // using a Func<TValue> to encourage fresh copies in case it's overwritten
+    private $_variablePriorInitializer;
+
+    public function __construct($variablePriorInitializer)
+    {
+        $this->_variablePriorInitializer = &$variablePriorInitializer;
+    }
+
+    public function &createBasicVariable($name)
+    {
+        $initializer = $this->_variablePriorInitializer;
+        $newVar = new Variable($name, $initializer());
+        return $newVar;
+    }
+
+    public function &createKeyedVariable(&$key, $name)
+    {
+        $initializer = $this->_variablePriorInitializer;
+        $newVar = new KeyedVariable($key, $name, $initializer());
+        return $newVar;
+    }
+}
+
+?>