Index: firmware/App/Controllers/BloodFlow.c
===================================================================
diff -u -rf2fc3885d55b51a6201c8f4f38e57cf7bcf3ee46 -r15f9827c863812cfd1f891d22342103fe9a72abc
--- firmware/App/Controllers/BloodFlow.c	(.../BloodFlow.c)	(revision f2fc3885d55b51a6201c8f4f38e57cf7bcf3ee46)
+++ firmware/App/Controllers/BloodFlow.c	(.../BloodFlow.c)	(revision 15f9827c863812cfd1f891d22342103fe9a72abc)
@@ -123,6 +123,7 @@
 #define BP_FLOW_WEAR_A_TERM                 0.000000001     ///< A term used for wear portion of alpha flow coefficient.
 #define BP_FLOW_WEAR_B_TERM                 0.00055         ///< B term used for wear portion of alpha flow coefficient.
 #define BP_MAX_ROTOR_COUNT_FOR_WEAR         25000           ///< Maximum rotor count for determining wear of the cartridge (negligible affect beyond this threshold).
+#define DATA_PUBLISH_COUNTER_START_COUNT    9               ///< Data publish counter start count.
 
 /// Enumeration of blood pump controller states.
 typedef enum BloodPump_States
@@ -155,7 +156,7 @@
 // ********** private data **********
 
 static BLOOD_PUMP_STATE_T bloodPumpState = BLOOD_PUMP_OFF_STATE;                    ///< Current state of blood flow controller state machine
-static U32 bloodFlowDataPublicationTimerCounter = 0;                                ///< Used to schedule blood flow data publication to CAN bus
+static U32 bloodFlowDataPublicationTimerCounter;                                    ///< Used to schedule blood flow data publication to CAN bus
 static BOOL isBloodPumpOn = FALSE;                                                  ///< Blood pump is currently running
 static F32 bloodPumpPWMDutyCyclePct = 0.0;                                          ///< Initial blood pump PWM duty cycle
 static F32 bloodPumpPWMDutyCyclePctSet = 0.0;                                       ///< Currently set blood pump PWM duty cycle
@@ -220,12 +221,14 @@
  * @brief
  * The initBloodFlow function initializes the BloodFlow module.
  * @details Inputs: none
- * @details Outputs: BloodFlow module initialized.
+ * @details Outputs: bloodFlowDataPublicationTimerCounter
  * @return none
  *************************************************************************/
 void initBloodFlow( void )
 {
     U32 i;
+
+    bloodFlowDataPublicationTimerCounter = DATA_PUBLISH_COUNTER_START_COUNT;
 
     signalBloodPumpHardStop();
     setBloodPumpDirection( MOTOR_DIR_FORWARD );
@@ -502,11 +505,14 @@
  *************************************************************************/
 void resetBloodPumpRotorCount( void )
 {
-#ifndef WORN_OUT_CARTRIDGE
-    bloodPumpRotorCounter.data = 0;
-#else
-    bloodPumpRotorCounter.data = BP_MAX_ROTOR_COUNT_FOR_WEAR;
-#endif
+    if ( getSoftwareConfigStatus( SW_CONFIG_ENABLE_WORN_OUT_CARTRIDGE ) != SW_CONFIG_ENABLE_VALUE )
+    {
+        bloodPumpRotorCounter.data = 0;
+    }
+    else
+    {
+        bloodPumpRotorCounter.data = BP_MAX_ROTOR_COUNT_FOR_WEAR;
+    }
 }
 
 /*********************************************************************//**
@@ -1065,33 +1071,31 @@
         BOOL isDirIncorrect;
         U08 dirErrorCnt = getFPGABloodPumpHallSensorStatus() & PUMP_DIR_ERROR_COUNT_MASK;
 
-#ifndef DISABLE_PUMP_DIRECTION_CHECKS
         // Check pump direction error count
-        if ( lastBloodPumpDirectionCount != dirErrorCnt )
+        if ( ( lastBloodPumpDirectionCount != dirErrorCnt ) &&
+             ( getSoftwareConfigStatus( SW_CONFIG_DISABLE_PUMP_DIRECTION_CHECKS ) != SW_CONFIG_ENABLE_VALUE ) )
         {
             lastBloodPumpDirectionCount = dirErrorCnt;
 #ifndef DISABLE_PUMP_DIRECTION_CHECKS
             SET_ALARM_WITH_1_U32_DATA( ALARM_ID_HD_PUMP_DIRECTION_STATUS_ERROR, (U32)HD_PUMP_BLOOD_PUMP )
 #endif
         }
-#endif
         bpMCDir = ( getMeasuredBloodPumpMCSpeed() >= 0.0 ? MOTOR_DIR_FORWARD : MOTOR_DIR_REVERSE );
         bpDir = ( getMeasuredBloodPumpSpeed() >= 0.0 ? MOTOR_DIR_FORWARD : MOTOR_DIR_REVERSE );
 
         // Check set direction vs. direction from hall sensors vs. direction from sign of motor controller speed
         isDirIncorrect = ( bloodPumpDirectionSet != bpDir ) || ( bloodPumpDirectionSet != bpMCDir );
-        if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_MC_DIRECTION_CHECK, isDirIncorrect ) )
+        if ( ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_MC_DIRECTION_CHECK, isDirIncorrect ) ) &&
+             ( getSoftwareConfigStatus( SW_CONFIG_DISABLE_PUMP_DIRECTION_CHECKS ) != SW_CONFIG_ENABLE_VALUE ) )
         {
-#ifndef DISABLE_PUMP_DIRECTION_CHECKS
-            if ( bloodPumpDirectionSet != bpDir  )
+            if ( bloodPumpDirectionSet != bpDir )
             {
                 SET_ALARM_WITH_2_U32_DATA( ALARM_ID_BLOOD_PUMP_MC_DIRECTION_CHECK, (U32)bloodPumpDirectionSet, (U32)bpDir )
             }
             else
             {
                 SET_ALARM_WITH_2_U32_DATA( ALARM_ID_BLOOD_PUMP_MC_DIRECTION_CHECK, (U32)bloodPumpDirectionSet, (U32)bpMCDir )
             }
-#endif
         }
     }
     else
@@ -1118,12 +1122,12 @@
     F32 measMCMotorSpeed = fabs( getMeasuredBloodPumpMCSpeed() );
 
     // Check for pump running while commanded off
-    if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_OFF_CHECK, ( 0 == targetBloodFlowRate ) && ( measMotorSpeed > BP_MAX_MOTOR_SPEED_WHILE_OFF_RPM ) ) )
+    if ( ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_OFF_CHECK,
+                                               ( 0 == targetBloodFlowRate ) && ( measMotorSpeed > BP_MAX_MOTOR_SPEED_WHILE_OFF_RPM ) ) ) &&
+         ( getSoftwareConfigStatus( SW_CONFIG_DISABLE_PUMP_SPEED_CHECKS ) != SW_CONFIG_ENABLE_VALUE ) )
     {
-#ifndef DISABLE_PUMP_SPEED_CHECKS
         SET_ALARM_WITH_1_F32_DATA( ALARM_ID_BLOOD_PUMP_OFF_CHECK, measMotorSpeed );
         activateSafetyShutdown();
-#endif
     }
 
     // Checks that only occur when pump is running (and beyond ramp).
@@ -1137,20 +1141,18 @@
         F32 deltaRotorSpeed = fabs( measRotorSpeed - measMotorSpeedInRotorRPM );
 
         // Check measured motor speed vs. commanded motor speed while controlling to target
-        if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_MOTOR_SPEED_CHECK,
-             ( deltaMotorSpeed > BP_MAX_MOTOR_SPEED_ERROR_RPM ) || ( deltaMCMotorSpeed > BP_MAX_MOTOR_SPEED_ERROR_RPM ) ) )
+        if ( ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_MOTOR_SPEED_CHECK,
+             ( deltaMotorSpeed > BP_MAX_MOTOR_SPEED_ERROR_RPM ) || ( deltaMCMotorSpeed > BP_MAX_MOTOR_SPEED_ERROR_RPM ) ) ) &&
+             ( getSoftwareConfigStatus( SW_CONFIG_DISABLE_PUMP_SPEED_CHECKS ) != SW_CONFIG_ENABLE_VALUE ) )
         {
-#ifndef DISABLE_PUMP_SPEED_CHECKS
             SET_ALARM_WITH_2_F32_DATA( ALARM_ID_BLOOD_PUMP_MOTOR_SPEED_CHECK, cmdMotorSpeed, measMotorSpeed );
-#endif
         }
 
         // Check measured rotor speed vs. measured motor speed while controlling to target
-        if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_ROTOR_SPEED_CHECK, deltaRotorSpeed > BP_MAX_ROTOR_VS_MOTOR_DIFF_RPM ) )
+        if ( ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_ROTOR_SPEED_CHECK, deltaRotorSpeed > BP_MAX_ROTOR_VS_MOTOR_DIFF_RPM ) ) &&
+             ( getSoftwareConfigStatus( SW_CONFIG_DISABLE_PUMP_SPEED_CHECKS ) != SW_CONFIG_ENABLE_VALUE ) )
         {
-#ifndef DISABLE_PUMP_SPEED_CHECKS
             SET_ALARM_WITH_2_F32_DATA( ALARM_ID_BLOOD_PUMP_ROTOR_SPEED_CHECK, measRotorSpeed, measMotorSpeed );
-#endif
         }
     }
     else
@@ -1176,11 +1178,10 @@
     // Check blood pump current during running state
     BOOL const isRunningMCCurrentBad = ( BLOOD_PUMP_OFF_STATE != bloodPumpState ) && ( bpCurr > BP_MAX_CURR_WHEN_RUNNING_MA );
 
-    if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_MC_CURRENT_CHECK, isOffMCCurrentBad || isRunningMCCurrentBad ) )
+    if ( ( TRUE == isPersistentAlarmTriggered( ALARM_ID_BLOOD_PUMP_MC_CURRENT_CHECK, isOffMCCurrentBad || isRunningMCCurrentBad ) ) &&
+         ( getSoftwareConfigStatus( SW_CONFIG_DISABLE_MOTOR_CURRNT_CHECKS ) != SW_CONFIG_ENABLE_VALUE ) )
     {
-#ifndef DISABLE_MOTOR_CURRENT_CHECKS
         SET_ALARM_WITH_1_F32_DATA( ALARM_ID_BLOOD_PUMP_MC_CURRENT_CHECK, bpCurr );
-#endif
     }
 }
 
@@ -1194,15 +1195,16 @@
  *************************************************************************/
 static void checkBloodPumpFlowRate( void )
 {
-#ifndef DISABLE_PUMP_FLOW_CHECKS
-    F32 flow = getMeasuredBloodFlowRate();
-
-    // Range check on measure BP flow rate.
-    if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_HD_BLOOD_FLOW_OUT_OF_RANGE, ( flow > BP_MAX_FLOW_RATE ) || ( flow < BP_MIN_FLOW_RATE ) ) )
+    if ( getSoftwareConfigStatus( SW_CONFIG_DISABLE_PUMP_FLOW_CHECKS ) != SW_CONFIG_ENABLE_VALUE )
     {
-        SET_ALARM_WITH_1_F32_DATA( ALARM_ID_HD_BLOOD_FLOW_OUT_OF_RANGE, flow );
+        F32 flow = getMeasuredBloodFlowRate();
+
+        // Range check on measure BP flow rate.
+        if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_HD_BLOOD_FLOW_OUT_OF_RANGE, ( flow > BP_MAX_FLOW_RATE ) || ( flow < BP_MIN_FLOW_RATE ) ) )
+        {
+            SET_ALARM_WITH_1_F32_DATA( ALARM_ID_HD_BLOOD_FLOW_OUT_OF_RANGE, flow );
+        }
     }
-#endif
 }
 
 /*********************************************************************//**