Index: firmware/App/Controllers/AirTrap.c
===================================================================
diff -u -r37a8a58b766a496b39241dd7ae46dc10dbda35e4 -raf2674758d7b9dbe05e348b318845975b423509f
--- firmware/App/Controllers/AirTrap.c	(.../AirTrap.c)	(revision 37a8a58b766a496b39241dd7ae46dc10dbda35e4)
+++ firmware/App/Controllers/AirTrap.c	(.../AirTrap.c)	(revision af2674758d7b9dbe05e348b318845975b423509f)
@@ -17,7 +17,8 @@
 
 #include "AirTrap.h"
 #include "AlarmMgmt.h"
-#include "FPGA.h"
+#include "FPGA.h"
+#include "ModeTreatmentParams.h"
 #include "OperationModes.h"
 #include "SystemCommMessages.h"
 #include "TaskGeneral.h"
@@ -31,7 +32,9 @@
 
 // ********** private definitions **********
 
-#define AIR_TRAP_DATA_PUB_INTERVAL          ( MS_PER_SECOND / TASK_PRIORITY_INTERVAL )   ///< interval (ms/task time) at which the air trap data is published on the CAN bus.
+#define AIR_TRAP_DATA_PUB_INTERVAL          ( MS_PER_SECOND / TASK_PRIORITY_INTERVAL )      ///< interval (ms/task time) at which the air trap data is published on the CAN bus.
+#define AIR_TRAP_ILLEGAL_LEVELS_PERSISTENCE ( MS_PER_SECOND * 2 / TASK_PRIORITY_INTERVAL )  ///< persistence period for illegal level sensors fault.
+#define VENOUS_LINE_VOLUME_ML               ( 50.0 )                                        ///< TODO volume (in mL) of venous portion of blood circuit line.
 
 /// Defined states for the air trap controller state machine.
 typedef enum AirTrap_States
@@ -65,7 +68,11 @@
 static U32 airTrapSelfTestTimerCount = 0;                                                   ///< timer counter for air trap self-test.
 
 static BOOL pendingStartAirTrapController = FALSE;                                          ///< flag indicates an air trap controller start request is pending.
-static BOOL pendingStopAirTrapController = FALSE;                                           ///< flag indicates an air trap controller stop request is pending.
+static BOOL pendingStopAirTrapController = FALSE;                                           ///< flag indicates an air trap controller stop request is pending.
+
+static U32  fillStartTime = 0;                                                              ///< time stamp for start of air trap fill.
+
+static U32  airTrapIllegalLevelSensorsCtr = 0;                                              ///< timer counter for illegal level sensor fault.
 
 // ********** private function prototypes **********
 
@@ -86,6 +93,7 @@
 {
     resetAirTrap();
     airTrapSelfTestState = AIR_TRAP_SELF_TEST_STATE_START;
+    airTrapIllegalLevelSensorsCtr = 0;
 }
 
 /*********************************************************************//**
@@ -157,8 +165,8 @@
 /*********************************************************************//**
  * @brief
  * The execAirTrapMonitor function executes the air trap monitor.
- * @details Inputs: TBD
- * @details Outputs: airTrapLevels[]
+ * @details Inputs: FPGA air trap levels GPIO pin levels, airTrapIllegalLevelSensorsCtr
+ * @details Outputs: airTrapLevels[], airTrapIllegalLevelSensorsCtr
  * @return none
  *************************************************************************/
 void execAirTrapMonitor( void )
@@ -173,20 +181,73 @@
     // check level readings are valid
     if ( ( TRUE == lower ) && ( FALSE == upper ) )
     {
-        // TODO - fault if illegal level readings persist
-        // TODO - close valve and end valve control
+        if ( ++airTrapIllegalLevelSensorsCtr >= AIR_TRAP_ILLEGAL_LEVELS_PERSISTENCE )
+        {
+            activateAlarmNoData( ALARM_ID_AIR_TRAP_ILLEGAL_LEVELS );
+        }
     }
+    else
+    {
+        airTrapIllegalLevelSensorsCtr--;
+    }
 }
 
 /*********************************************************************//**
  * @brief
+ * The execAirTrapMonitorPriming function executes the air trap monitor
+ * for cartridge priming during pre-treatment mode.
+ * @details Inputs: airTrapLevels[], airTrapFillAlarmCtr
+ * @details Outputs: airTrapFillAlarmCtr
+ * @return none
+ *************************************************************************/
+void execAirTrapMonitorPriming( void )
+{
+    // TODO - implement when priming sub-mode of pre-treatment mode is implemented.
+}
+
+/*********************************************************************//**
+ * @brief
+ * The execAirTrapMonitorTreatment function executes the air trap monitor
+ * for treatment mode.
+ * @details Inputs: airTrapLevels[], airTrapFillAlarmCtr
+ * @details Outputs: airTrapFillAlarmCtr
+ * @return none
+ *************************************************************************/
+void execAirTrapMonitorTreatment( void )
+{
+    // check air trap fill timeout during treatment
+    if ( airTrapControllerState > AIR_TRAP_MANUAL_CONTROL_STATE )
+    {
+        if ( AIR_TRAP_LEVEL_AIR == getAirTrapLevel( AIR_TRAP_LEVEL_SENSOR_LOWER ) )
+        {
+            F32 bldFlowRate = (F32)getTreatmentParameterU32( TREATMENT_PARAM_BLOOD_FLOW );  // function will never return zero
+            F32 fillTimeoutMS = ( VENOUS_LINE_VOLUME_ML / bldFlowRate ) * (F32)SEC_PER_MIN * (F32)MS_PER_SECOND;
+
+            if ( TRUE == didTimeout( fillStartTime, fillTimeoutMS ) )
+            {
+                activateAlarmNoData( ALARM_ID_AIR_TRAP_ILLEGAL_LEVELS );
+                setValveAirTrap( STATE_CLOSED );
+            }
+        }
+    }
+}
+
+/*********************************************************************//**
+ * @brief
  * The execAirTrapController function executes the air trap control state machine.
  * @details Inputs: airTrapControllerState
  * @details Outputs: airTrapControllerState
  * @return none
  *************************************************************************/
 void execAirTrapController( void )
 {
+    // if we've faulted, close valve and go to manual control
+    if ( MODE_FAUL == getCurrentOperationMode() )
+    {
+        airTrapControllerState = AIR_TRAP_MANUAL_CONTROL_STATE;
+        pendingStartAirTrapController = FALSE;
+    }
+
     // execute air trap state machine
     switch( airTrapControllerState )
     {
@@ -261,6 +322,7 @@
     else if ( AIR_TRAP_LEVEL_AIR == getAirTrapLevel( AIR_TRAP_LEVEL_SENSOR_LOWER ) )
     {
         setValveAirTrap( STATE_OPEN );
+        fillStartTime = getMSTimerCount();
         result = AIR_TRAP_VALVE_OPEN_STATE;
     }