Index: firmware/App/Controllers/SyringePump.c
===================================================================
diff -u -rc1e18c14a172586f47ebcf027bce9669beded986 -rf8d418646b4dae23ed7694dfc5597dc5a5abf7ed
--- firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision c1e18c14a172586f47ebcf027bce9669beded986)
+++ firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision f8d418646b4dae23ed7694dfc5597dc5a5abf7ed)
@@ -294,7 +294,6 @@
 static void calcMeasRate( void );
 static void calcSafetyVolumeDelivered( void );
 
-static BOOL sendHeparinCommandResponse( U32 accepted, U32 rejReason );
 static void publishSyringePumpData( void );
 
 /*********************************************************************//**
@@ -446,6 +445,8 @@
  * @brief
  * The execSyringePumpSelfTest function executes the state machine for the
  * syringe pump self-test.
+ * @details \b Alarms: ALARM_ID_TD_HEPARIN_FORCE_SENSOR_INVALID_CAL_RECORD
+ * if the force sensor calibration record is invalid
  * @details \b Inputs: none
  * @details \b Outputs: forceSensorCalRecord
  * @return TRUE if the self test passed otherwise, FALSE
@@ -478,16 +479,20 @@
 /*********************************************************************//**
  * @brief
  * The userHeparinRequest function handles a command request from the user
- * to pause or resume Heparin delivery.
+ * to pause or resume heparin delivery.
+ * @details \b Message \b Sent: MSG_ID_TD_HEPARIN_PAUSE_RESUME_RESPONSE
+ * if changing heaprin delivery status
  * @details \b Inputs: none
- * @details \b Outputs: heparinDeliveryState, syringePumpState, syringePumpContinuousRequested
+ * @details \b Outputs: heparinDeliveryState, syringePumpState,
+ * syringePumpContinuousRequested
  * @param cmd command from user
  * @return TRUE if request accepted, FALSE if not
  *************************************************************************/
 BOOL userHeparinRequest( HEPARIN_CMD_T cmd )
 {
     BOOL accepted = FALSE;
     REQUEST_REJECT_REASON_CODE_T rejReason = REQUEST_REJECT_REASON_NONE;
+    UI_RESPONSE_PAYLOAD_T payload;
 
     // Check if the current mode is treatment mode.
     if ( MODE_TREA == getCurrentOperationMode() )
@@ -540,7 +545,10 @@
         rejReason = REQUEST_REJECT_REASON_NOT_IN_TREATMENT_MODE;
     }
 
-    sendHeparinCommandResponse( (U32)accepted, (U32)rejReason );
+    payload.accepted = accepted;
+    payload.rejectionReason = rejReason;
+    result = sendMessage( MSG_ID_TD_HEPARIN_PAUSE_RESUME_RESPONSE, COMM_BUFFER_OUT_CAN_TD_2_UI,
+                          (U08*)(&payload), sizeof( UI_RESPONSE_PAYLOAD_T ) );
 
     return accepted;
 }
@@ -754,6 +762,8 @@
  * @brief
  * The checkForPrimeOcclusion function checks the force sensor for excessive
  * pressure.  Would indicate occlusion or jam or empty syringe.
+ * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_OCCLUSION
+ * if occlusion is detected
  * @details \b Inputs: syringePumpMeasForce.data, syringePumpPosition.data,
  * forceAtEndOfSeek, syringePumpState
  * @details \b Outputs: alarm triggered if max force detected
@@ -801,6 +811,8 @@
 /*********************************************************************//**
  * @brief
  * The startHeparinBolus function requests Heparin bolus delivery.
+ * @details \b Alarms: ALARM_ID_TD_SOFTWARE_FAULT
+ * if heparin bolus command is invalid
  * @details \b Inputs: syringePumpState, syringePumpPrimeCompleted
  * @details \b Outputs: syringePumpSetRate, syringePumpBolusRequested,
  * heparinDeliveryState
@@ -849,6 +861,8 @@
 /*********************************************************************//**
  * @brief
  * The startHeparinContinuous function requests Heparin continuous delivery.
+ * @details \b Alarms: ALARM_ID_TD_SOFTWARE_FAULT
+ * if heparin continuous command is invalid
  * @details \b Inputs: syringePumpState
  * @details \b Outputs: syringePumpSetRate, syringePumpContinuousRequested,
  * heparinDeliveryState
@@ -894,6 +908,8 @@
 /*********************************************************************//**
  * @brief
  * The setSyringePumpDACVref function requests to set the DAC Vref setting.
+ * @details \b Alarms: ALARM_ID_TD_SOFTWARE_FAULT
+ * if force sensor vref value invalid
  * @details \b Inputs: forceSensorCalRecord.tdHeparinForceSensorDACVoltage,
  * syringePumpState
  * @details \b Outputs: syringePumpDACVrefSetRequested, syringePumpDACVref
@@ -925,6 +941,8 @@
  * syringe pump force sensor DAC has been calibrated and is reporting no force
  * as would be expected when fully retracted (caller should not call this function
  * until the syringe pump is homed first).
+ * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_SELF_TEST_FAILURE
+ * if force sensor calibration value is invalid
  * @details \b Inputs: forceSensorCalRecord.tdHeparinForceSensorDACVoltage
  * @details \b Outputs:
  * @return none
@@ -1066,8 +1084,9 @@
 /*********************************************************************//**
  * @brief
  * The execSyringePumpMonitor function executes the syringe pump monitor.
- * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_RUNNING_WHILE_BP_OFF_ERROR,
- * ALARM_ID_TD_SYRINGE_PUMP_FAULT
+ * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_RUNNING_WHILE_BP_OFF_ERROR
+ * if syringe pump is running while the blood pump is off
+ * ALARM_ID_TD_SYRINGE_PUMP_FAULT is syringe pump status is invalid
  * @details \b Inputs: FPGA syringe pump readings
  * @details \b Outputs: Alarm(s) may be triggered
  * @return none
@@ -1167,6 +1186,7 @@
  * The handleSyringePumpOffState function handles the off state
  * of the syringe pump control state machine.
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_NOT_STOPPED_ERROR
+ * if the syringe pump is still running
  * @details \b Inputs: syringePumpRetractRequested, syringePumpPreloadRequested,
  * syringePumpSeekRequested, syringePumpPrimeRequested, syringePumpBolusRequested,
  * syringePumpContinuousRequested, syringePumpDACVrefSetRequested,
@@ -1292,6 +1312,8 @@
  * @brief
  * The handleSyringePumpRetractState function handles the retract state
  * of the syringe pump control state machine.
+ * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_OVER_TRAVEL_ERROR
+ * if the syringe pump retracts beyond the minimum position
  * @details \b Inputs: syringePumpMeasHome.data, syringePumpPositionKnown, syringePumpPosition
  * @details \b Outputs: Syringe pump ramped up to retract rate, alarm conditions checked,
  * syringePumpPosition, syringePumpVolumeStartPosition, syringePumpPositionKnown,
@@ -1416,6 +1438,8 @@
  * @brief
  * The handleSyringePumpSeekState function handles the seek plunger state
  * of the syringe pump control state machine.
+ * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_NOT_ENOUGH_HEPARIN_ALARM
+ * if the heaprin volume is if insufficient for the treatment needs
  * @details \b Inputs: syringePumpMeasForce.data, syringePumpPosition, syringePumpMeasForce,
  * treatmentParameters,
  * @details \b Outputs: Syringe pump ramped up to seek rate, alarm conditions checked,
@@ -1487,7 +1511,7 @@
  * @brief
  * The handleSyringePumpPrimeState function handles the prime state
  * of the syringe pump control state machine.
- * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_PRIME_TIMEOUT
+ * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_PRIME_TIMEOUT if priming state timeouts
  * @details \b Inputs: syringePumpVolumeDelivered, syringePumpStateStartTime,
  * syringePumpPosition
  * @details \b Outputs: Syringe pump ramped up to prime rate, alarm conditions checked,
@@ -1511,7 +1535,9 @@
         syringePumpVolumeDelivered.data = 0.0;
         syringePumpSafetyVolumeDelivered = 0.0;
         syringePumpVolumeStartPosition = syringePumpPosition.data;
-        resetPersistentAlarmTimer( ALARM_ID_TD_SYRINGE_PUMP_OCCLUSION ); // reset persistence after prime so ensured fresh start before continuous state
+
+        // reset persistence after prime so ensured fresh start before continuous state
+        resetPersistentAlarmTimer( ALARM_ID_TD_SYRINGE_PUMP_OCCLUSION );
     }
 
     // Check for timeout
@@ -1638,6 +1664,7 @@
  * calibrate force sensor state of the syringe pump control state machine.
  * of the syringe pump control state machine.
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_DAC_WRITE_ERROR
+ * if unable to calibrate the force sensor after retrying 5 times
  * @details \b Inputs: syringePumpADCandDACStatus, syringePumpDACRetryCount
  * @details \b Outputs: syringePumpDACVrefWriteInProgress, ADC read mode restored
  * syringePumpDACRetryCount, syringePumpDACRetryTimer
@@ -1802,8 +1829,10 @@
  * @brief
  * The checkDirection function checks the measured direction of the syringe
  * pump vs. the given expected direction.
- * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_ENCODER_DIRECTION_ERROR,
+ * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_ENCODER_DIRECTION_ERROR
+ * if syringe pump encoder direction is invalid
  * ALARM_ID_TD_SYRINGE_PUMP_CONTROLLER_DIRECTION_ERROR
+ * if syringe pump controller direction is invalid
  * @details \b Inputs: syringePumpMeasForce.data, syringePumpPosition.data,
  * syringePumpEncoderMeasuredDirection, syringePumpControllerMeasuredDirection
  * @details \b Outputs: alarm triggered if max force detected
@@ -1848,6 +1877,7 @@
  * The checkSyringeEmpty function checks the force sensor position
  * to determine if the syringe pump is empty.
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_SYRINGE_EMPTY
+ * if the syringe is empty
  * @details \b Inputs: syringePumpMeasForce.data, syringePumpPosition.data
  * @details \b Outputs: alarm triggered if position is empty.,
  * heparinDeliveryState
@@ -1888,6 +1918,7 @@
  * has been exceeded.  This threshold is state dependent so the calling function
  * must provide the maximum position to apply.
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_OVER_TRAVEL_ERROR
+ * if syringe pump extends beyond the maximum position
  * @details \b Inputs: syringePumpPosition.data
  * @details \b Outputs: alarm triggered if beyond given max position
  * @param stopPump flag passed in by caller indicating whether pump should be stopped
@@ -1913,6 +1944,7 @@
  * The checkMeasRate function checks whether the measured rate is within a
  * given margin of the set rate (in mL/hr).
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_SPEED_ERROR
+ * is the syringe pump speed is invalid
  * @details \b Inputs: syringePumpMeasRate.data, syringePumpSetRate
  * @details \b Outputs: alarm triggered if measured and set rates deviate too much
  * @param stopPump flag passed in by caller indicating whether pump should be stopped
@@ -1951,6 +1983,7 @@
  * is state dependent so the calling function must provide the tolerance (in +/- %)
  * to apply.
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_VOLUME_ERROR
+ * if the heparin volume is invalid
  * @details \b Inputs: syringePumpVolumeDelivered.data, syringePumpSafetyVolumeDelivered
  * @details \b Outputs: alarm triggered if measured and expected volume deviate too much
  * @param stopPump flag passed in by caller indicating whether pump should be stopped
@@ -1982,6 +2015,7 @@
  * If stall detected, the ramp up will be restarted up to 3 times.
  * If cannot resolve the stall within 3 retries, a stall fault is triggered.
  * @details \b Alarms: ALARM_ID_TD_SYRINGE_PUMP_STALL
+ * if the syringe pump stalls
  * @details \b Inputs: syringePumpMeasRate.data, syringePumpState,
  * syringePumpStallCtr, syringePumpStallRetryCount
  * @details \b Outputs: syringePumpStallCtr, syringePumpStallRetryCount,
@@ -2168,30 +2202,6 @@
 
 /*********************************************************************//**
  * @brief
- * The sendHeparinCommandResponse function constructs a Heparin command response
- * to the UI and queues the msg for transmit on the
- * appropriate CAN channel.
- * @details \b Message \b Sent: MSG_ID_TD_HEPARIN_PAUSE_RESUME_RESPONSE
- * @details \b Inputs: none
- * @details  \b Outputs: Heparin command response msg constructed and queued.
- * @param accepted flag indicating whether request was accepted
- * @param rejReason rejection reason code
- * @return TRUE if msg successfully queued for transmit, FALSE if not
- *************************************************************************/
-static BOOL sendHeparinCommandResponse( U32 accepted, U32 rejReason )
-{
-    BOOL result;
-    UI_RESPONSE_PAYLOAD_T payload;
-
-    payload.accepted = accepted;
-    payload.rejectionReason = rejReason;
-    result = sendMessage( MSG_ID_TD_HEPARIN_PAUSE_RESUME_RESPONSE, COMM_BUFFER_OUT_CAN_TD_2_UI, (U08*)(&payload), sizeof( UI_RESPONSE_PAYLOAD_T ) );
-
-    return result;
-}
-
-/*********************************************************************//**
- * @brief
  * The publishSyringePumpData function publishes syringe pump data at the
  * set interval.
  * @details \b Inputs: latest syringe pump data, syringePumpDataPublicationTimerCounter,