File content as of revision 36:966a86937e17:

#include "StateMachine.hpp"
#include "StaticDefs.hpp"
 
StateMachine::StateMachine() {
    _timeout = 20;            // generic timeout for every state, seconds
    
    _pitchTolerance = 5.0;     // pitch angle tolerance for FLOAT_LEVEL state
 
    _bceFloatPosition = bce().getTravelLimit();      // bce position for "float" states                  (max travel limit for BCE is 320 mm)
    _battFloatPosition = batt().getTravelLimit();    // batt position tail high for "broadcast" state    (max travel limit for battery is 75 mm)
 
    _depth_command = 2.0;                        // user keyboard depth (default)
    _pitch_command = -20.0;                      // user keyboard pitch (default)
    
    _neutral_timer        = 0;                  //timer used in FIND_NEUTRAL sub-FSM
 
    _state = SIT_IDLE;                          // select starting state here
    _isTimeoutRunning = false;                  // default timer to not running
    _isSubStateTimerRunning = false;            // default timer to not running
    
    _multi_dive_counter = 0;
    
    _neutral_sub_state_active = false;
    
    _depth_KP = depthLoop().getControllerP();  // load current depth value
    _depth_KI = depthLoop().getControllerI();  // load current depth value
    _depth_KD = depthLoop().getControllerD();  // load current depth value
    
    _pitch_KP = pitchLoop().getControllerP();  // load current pitch value
    _pitch_KI = pitchLoop().getControllerI();  // load current pitch value
    _pitch_KD = pitchLoop().getControllerD();  // load current pitch value
    
    _neutral_bce_pos_mm = depthLoop().getOutputOffset(); //load current neutral buoyancy position offset
    _neutral_batt_pos_mm = pitchLoop().getOutputOffset(); //load current neutral buoyancy position offset
    
    _state_array_counter = 1;                   //used to iterate through and record states
    _substate_array_counter = 0;                //used to iterate through and record substates

    _state_array[0] = SIT_IDLE;  //system starts in the SIT_IDLE state, record this
    
    _substate = NEUTRAL_SINKING;                //start sub-FSM in NEUTRAL_SINKING
    _previous_substate = -1;                    //to start sub-FSM
    _previous_state = -1;                       //for tracking FSM states
    
    _max_recorded_depth_neutral = -99;          //float to record max depth
    _max_recorded_depth_dive = -99;             //float to record max depth
    
    _neutral_sink_command_mm = -2.5;            //defaults for neutral finding sub-FSM
    _neutral_rise_command_mm = 2.0;
    _neutral_pitch_command_mm = 0.5;
    
    _max_recorded_auto_neutral_depth = -99;
    
    _file_closed = true;
}
 
//Finite State Machine (FSM)
int StateMachine::runStateMachine() {         
    // finite state machine ... each state has at least one exit criteria
    switch (_state) {
    case SIT_IDLE :
    case KEYBOARD:
        // there actually is no timeout for SIT_IDLE, but this enables some one-shot actions
        if (!_isTimeoutRunning) {
            showMenu();
            pc().printf("\r\n\nstate: SIT_IDLE\r\n");
            _isTimeoutRunning = true; 
 
            // what is active?
            bce().pause();
            batt().pause();
                     
            //reset sub FSM
            _isSubStateTimerRunning = false;
            
            //close the MBED file
            _file_closed = true;
        }
        
        // how exit?
        keyboard(); // keyboard function will change the state if needed
        break;
 
    case EMERGENCY_CLIMB :
        // start local state timer and init any other one-shot actions
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: EMERGENCY_CLIMB\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
            
            // what needs to be started?
            bce().unpause();
            batt().unpause();
 
            // what are the commands?
            bce().setPosition_mm(bce().getTravelLimit());
            batt().setPosition_mm(0.0);
            
            //create the log file (works only if the file is closed)
            ////////createNewFile();
            
            //show that this is the start of a new EMERGENCY_CLIMB sequence            
            recordState(_state);
            
            //this was missing
            _is_log_timer_running = true; // reset the sub state timer to do one-shot actions again
            recordData(_state);
        }
        
        // how exit?
        if (timer > _timeout) {
            pc().printf("EC: timed out\r\n");
            _state = FLOAT_BROADCAST;
            timer.reset();
            _isTimeoutRunning = false;
        }
        else if (depthLoop().getPosition() < 2.0) { //if the depth is greater than 0.2 feet, go to float broadcast
            _state = FLOAT_BROADCAST;
            timer.reset();
            _isTimeoutRunning = false;
        }
        
        //print status to screen continuously
        pc().printf("EC: depth: %3.1f (BCE_cmd: %0.1f), pitch: %0.1f deg [%0.1f sec]\r",depthLoop().getPosition(),bce().getPosition_mm(),pitchLoop().getPosition(),timer.read());
        
        //record data every 5 seconds
        recordData(_state);
        
        break;
 
    case FIND_NEUTRAL :
        // start local state timer and init any other one-shot actions
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: FIND_NEUTRAL\n\r");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true;
            
            // what needs to be started?
            bce().unpause();
            batt().unpause();
            bce().setPosition_mm(_bceFloatPosition);
            batt().setPosition_mm(_neutral_batt_pos_mm);    //set battery to close-to-neutral setting from config file 
            
            //first iteration goes into Neutral Finding Sub-FSM 
            //set the first state of the FSM, and start the sub-FSM
            _substate = NEUTRAL_SINKING;        //first state in neutral sub-FSM is the pressure vessel sinking
            _previous_substate = -1;
            
            //save this state to the array
            _substate_array[_substate_array_counter] = NEUTRAL_SINKING;  //save to state array
            _substate_array_counter++;     
                   
            runNeutralStateMachine(); 
            
            //create the log file (works only if the file is closed)
            //createNewFile();       
            
            //show that this is the start of a new FIND_NEUTRAL sequence            
            recordState(_state);  
            
            //this was missing
            _is_log_timer_running = true; // reset the sub state timer to do one-shot actions again     
            recordData(_state);
        }
 
        // how exit? (exit with the timer, if timer still running continue processing sub FSM)
        if (timer > _timeout) {
            pc().printf("FN: timed out [time: %0.1f sec]\r\n", timer.read());
            _state = EMERGENCY_CLIMB;         //new behavior (if this times out it emergency surfaces)
            timer.reset();
            _isTimeoutRunning = false;
            
            //record this to the NEUTRAL sub-FSM tracker
            _substate_array[_substate_array_counter] = EMERGENCY_CLIMB;  //save to state array
            _substate_array_counter++;
        }
        
        //what is active? (neutral finding sub-function runs until completion)        
        //check if substate returned exit state, if so stop running the sub-FSM
        else if (runNeutralStateMachine() == NEUTRAL_EXIT) { 
            //if successful, FIND_NEUTRAL then goes to RISE
            pc().printf("*************************************** FIND_NEUTRAL sequence complete.  Rising.\n\n\r");
            _state = RISE;
            _isTimeoutRunning = false;
        }
        
        //record data every 5 seconds
        recordData(_state);
        
        break;   
        
    case DIVE :
        // start local state timer and init any other one-shot actions
               
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: DIVE\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
            
            // what needs to be started?
            bce().unpause();
            batt().unpause();
 
            // what are the commands?
            depthLoop().setCommand(_depth_command);
            pitchLoop().setCommand(_pitch_command);
            
            pc().printf("DIVE: depth cmd: %3.1f\r\n",depthLoop().getCommand());
            pc().printf("DIVE: pitch cmd: %3.1f\r\n",pitchLoop().getCommand());
            
            //reset max dive depth
            _max_recorded_depth_dive = -99;            //float to record max depth
            
            //create the log file (works only if the file is closed)
            //createNewFile();
            
            //show that this is the start of new dive sequence            
            recordState(_state);
            
            //this was missing
            _is_log_timer_running = false; // reset the sub state timer to do one-shot actions again
            recordData(_state);
        }
 
        // how exit?
        if (timer.read() > _timeout) {
            pc().printf("DIVE: timed out\n\n\r");
            _state = RISE; //new behavior 11/17/2017
            timer.reset();
            _isTimeoutRunning = false;
        }
        else if (depthLoop().getPosition() > depthLoop().getCommand() - 0.5) { // including offset for low momentum approaches
            pc().printf("DIVE: actual depth: %3.1f (cmd: %3.1f)\r\n", depthLoop().getPosition(), depthLoop().getCommand());
            _state = RISE;
            timer.reset();
            _isTimeoutRunning = false;
        }
 
        // what is active?
        pc().printf("DIVE: bce pos: %3.1f mm, batt pos: %3.1f mm (depth: %3.1f ft) (pitch: %3.1f deg)[%0.2f sec]\r", bce().getPosition_mm(), batt().getPosition_mm(), depthLoop().getPosition(), pitchLoop().getPosition(), timer.read());
        bce().setPosition_mm(depthLoop().getOutput());  //constantly checking the Outer Loop output to move the motors
        batt().setPosition_mm(pitchLoop().getOutput());
        
        if (depthLoop().getPosition() > _max_recorded_depth_dive) {  //debug
            _max_recorded_depth_dive = depthLoop().getPosition();    //new max depth recorded
        }
        
        //record data every 5 seconds
        recordData(_state);
        
        break;
    
    case RISE :
        // start local state timer and init any other one-shot actions
        
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: RISE\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
            
            // what needs to be started?
            bce().unpause();
            batt().unpause();
 
            // what are the commands?
            depthLoop().setCommand(-1.0);           //make sure to get towards the surface (saw issues at LASR pool)
            pitchLoop().setCommand(-_pitch_command);
                        
            pc().printf("RISE: depth cmd: %0.1f\r\n",depthLoop().getCommand());
            pc().printf("RISE: pitch cmd: %0.1f\r\n",pitchLoop().getCommand());
            
            //create the log file (works only if the file is closed)
            //createNewFile();
            
            //show that this is the start of new rise sequence            
            recordState(_state);
            
            //this was missing
            _is_log_timer_running = false; // reset the sub state timer to do one-shot actions again
            recordData(_state);
        }
 
        // how exit?
        if (timer.read() > _timeout) {
            pc().printf("RISE: timed out\r\n");
            _state = EMERGENCY_CLIMB;
            timer.reset();
            _isTimeoutRunning = false;
        }
        
        //modified from (depthLoop().getPosition() < depthLoop().getCommand() + 0.5) 
        //did not work correctly in bench test (stuck in rise state)
        else if (depthLoop().getPosition() < 0.5) {
            pc().printf("RISE: actual depth: %3.1f (cmd: %3.1f)\r\n", depthLoop().getPosition(), depthLoop().getCommand());
            _state = FLOAT_BROADCAST;
            timer.reset();
            _isTimeoutRunning = false;
        }
 
        // what is active?
        pc().printf("RISE: bce pos: %3.1f mm, batt pos: %3.1f mm (depthLoop POS: %3.1f ft) [%0.1f sec]\r", bce().getPosition_mm(), batt().getPosition_mm(), depthLoop().getPosition(), timer.read());
        bce().setPosition_mm(depthLoop().getOutput());  //constantly checking the Outer Loop output to move the motors
        batt().setPosition_mm(pitchLoop().getOutput());
        
        //record data every 5 seconds
        recordData(_state);
         
        break;  
    
    case FLOAT_LEVEL :
        // start local state timer and init any other one-shot actions
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: FLOAT_LEVEL\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
            
            // what needs to be started?
            bce().unpause();
            batt().unpause();
 
            // what are the commands?
            bce().setPosition_mm(_bceFloatPosition);
            pitchLoop().setCommand(0.0);
            
            //create the log file (works only if the file is closed)
            //createNewFile();
            
            //show that this is the start of a new float level sequence            
            recordState(_state);
            
            //this was missing
            _is_log_timer_running = true; // reset the sub state timer to do one-shot actions again
            recordData(_state);
        }
        
        // how exit?
        if (timer > _timeout) {
            pc().printf("FL: timed out\r\n");
            _state = FLOAT_BROADCAST;
            timer.reset();
            _isTimeoutRunning = false;
        }
        else if (fabs(imu().getPitch() - pitchLoop().getCommand()) < fabs(_pitchTolerance)) {         //current tolerance is 5 degrees
            pc().printf("FL: pitch: %3.1f mm, set pos: %3.1f mm, deadband: %3.1f mm\r\n",imu().getPitch(), pitchLoop().getCommand(), _pitchTolerance);
            _state = FLOAT_BROADCAST;
            timer.reset();
            _isTimeoutRunning = false;
        }
        
        // what is active?
        pc().printf("FL: pitchLoop output: %3.1f, batt pos: %3.1f, piston pos: %3.1f [%0.1f sec]\r", pitchLoop().getOutput(), batt().getPosition_mm(), bce().getPosition_mm(), timer.read());
        batt().setPosition_mm(pitchLoop().getOutput());
        
        //record data every 5 seconds
        recordData(_state);
        
        break;
    
    case FLOAT_BROADCAST :
        // start local state timer and init any other one-shot actions
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: FLOAT_BROADCAST\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
            
            // what needs to be started?
            bce().unpause();
            batt().unpause();
 
            // what are the commands?
            bce().setPosition_mm(_bceFloatPosition);
            batt().setPosition_mm(_battFloatPosition);
            
            //create the log file (works only if the file is closed)
            //createNewFile();
            
            //show that this is the start of a new float broadcast sequence            
            recordState(_state);
            
            //this was missing
            _is_log_timer_running = false; // reset the sub state timer to do one-shot actions again
            recordData(_state);
        }
        
        // how exit?
        if (timer > _timeout) {
            pc().printf("FB: timed out\r\n");
            _state = SIT_IDLE;
            timer.reset();
            
            //stop recording data
            //mbedLogger().closeFile();
            
            _isTimeoutRunning = false;
        }
        else if ( (fabs(bce().getPosition_mm() - bce().getSetPosition_mm()) < bce().getDeadband()) and
                  (fabs(batt().getPosition_mm() - batt().getSetPosition_mm()) < batt().getDeadband()) ) {
            pc().printf("FB: position: %3.1f mm, set pos: %3.1f mm, deadband: %3.1f mm\r\n",bce().getPosition_mm(), bce().getSetPosition_mm(), bce().getDeadband());
            _state = SIT_IDLE;
            timer.reset();
            
            //stop recording data
            //mbedLogger().closeFile();
            
            _isTimeoutRunning = false;
        }
        
        // what is active?
        pc().printf("FB: bce pos: %0.1f mm, batt pos: %0.1f mm (depthLoop POS: %3.1f ft) [%0.1f sec] (CMD batt: %0.1f bce: %0.1f)\r", bce().getPosition_mm(), batt().getPosition_mm(), depthLoop().getPosition(), timer.read(), bce().getSetPosition_mm(),batt().getSetPosition_mm());
        
        //record data every 5 seconds
        recordData(_state);
        
        break;
        
    case MULTI_DIVE :
        // start local state timer and init any other one-shot actions        
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: MULTI-DIVE\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
                
            // what needs to be started?
            bce().unpause();
            batt().unpause();
            
            //retrieve commands from structs (loaded from sequence.cfg file)
            float sequence_depth_command = currentStateStruct.depth;
            float sequence_pitch_command = currentStateStruct.pitch;
    
            // what are the commands?            
            depthLoop().setCommand(sequence_depth_command);
            pitchLoop().setCommand(sequence_pitch_command);
            pc().printf("MULTI-DIVE: depth cmd: %3.1f ft, pitch cmd: %3.1f deg\r\n",depthLoop().getCommand(), pitchLoop().getCommand());
            
            //create the log file (works only if the file is closed)
            //createNewFile();
            
            //show that this is the start of a new MULTI_DIVE sequence            
            recordState(_state);  
            
            //no max depth recording right now
            
            //this was missing
            _is_log_timer_running = false; // reset the sub state timer to do one-shot actions again
            recordData(_state);
        }
        
        // how exit?
        if (timer > _timeout) {
            pc().printf("\n\n\rMULTI-DIVE: timed out [time: %0.1f]\n\n\r", timer.read());
            _state = MULTI_RISE; //new behavior 11/17/2017
            timer.reset();
            _isTimeoutRunning = false;
        }
        else if (depthLoop().getPosition() > depthLoop().getCommand()) {
            pc().printf("MULTI-DIVE: depth: %3.1f, cmd: %3.1f\r\n", depthLoop().getPosition(), depthLoop().getCommand());
            _state = MULTI_RISE;
            timer.reset();
            _isTimeoutRunning = false;
        }
        
        // what is active?
        pc().printf("MULTI-DIVE: bce pos: %3.1f mm, batt pos: %3.1f mm (depthLoop POS: %3.1f ft) [%0.1f sec]\r", bce().getPosition_mm(), batt().getPosition_mm(), depthLoop().getPosition(), timer.read());
        bce().setPosition_mm(depthLoop().getOutput());
        batt().setPosition_mm(pitchLoop().getOutput());
        
        //record data every 5 seconds
        recordData(_state);
        
        break;
    
    case MULTI_RISE :
        // start local state timer and init any other one-shot actions
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: MULTI-RISE\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
            
            // what needs to be started?
            bce().unpause();
            batt().unpause();
 
            //NEW: retrieve depth and pitch commands from config file struct
            // concept is to load this each time the multi-dive restarts
            stateMachine().getDiveSequence();
            
            //retrieve just pitch command from struct
            float sequence_pitch_command = currentStateStruct.pitch;
 
            // what are the commands? (send back to 0.5 feet, not surface) // 11/21/2017
            depthLoop().setCommand(0.5);
            pitchLoop().setCommand(-sequence_pitch_command);            
            pc().printf("MULTI-RISE: depth cmd: 0.0 ft, pitch cmd: %3.1f deg\r\n",depthLoop().getCommand(), pitchLoop().getCommand());
            
            //create the log file (works only if the file is closed)
            //createNewFile();
            
            //show that this is the start of a new MULTI_DIVE sequence            
            recordState(_state); 
            
            //this was missing
            _is_log_timer_running = false; // reset the sub state timer to do one-shot actions again
            recordData(_state);
        }
        
        // how exit?
        if (timer > _timeout) {
            pc().printf("MULTI-RISE: timed out [time: %0.1f]\n\n\r", timer.read());
            _state = EMERGENCY_CLIMB;
            timer.reset();
            _isTimeoutRunning = false;
            
            //reset multi-dive sequence to start
            _multi_dive_counter = 0;
        }
        else if (depthLoop().getPosition() < 0.5) { // depth is less than 0.5 (zero is surface level)
            pc().printf("MULTI-RISE: depth: %3.1f, cmd: %3.1f\r\n", depthLoop().getPosition(), depthLoop().getCommand());
            
            //going to next state            
            _isTimeoutRunning = false;
            
            //successful dive-rise sequence CONTINUES the multi-dive sequence
            _multi_dive_counter++;
            
            //UPDATE THE SEQUENCE DATA HERE
            stateMachine().getDiveSequence();
            
            //check if this is the end of the dive sequence
            //CHECK BEFORE ANYTHING ELSE that you have reached the "exit" state (FLOAT_BROADCAST)
            if (currentStateStruct.state == FLOAT_BROADCAST) {
                _state = FLOAT_BROADCAST;
            }
            
            else 
                _state = MULTI_DIVE;
            
            //have to stop this with the _multi_dive_counter variable!
        }
        
        // what is active?
        pc().printf("MULTI-RISE: bce pos: %3.1f mm, batt pos: %3.1f mm (depthLoop POS: %3.1f ft) [%0.1f sec]\r", bce().getPosition_mm(), batt().getPosition_mm(), depthLoop().getPosition(), timer.read());
        bce().setPosition_mm(depthLoop().getOutput());  //constantly checking the Outer Loop output to move the motors
        batt().setPosition_mm(pitchLoop().getOutput()); 
        
        //record data every 5 seconds
        recordData(_state);
        
        break; 
        
    case TRANSMIT_DATA :               
        if (!_isTimeoutRunning) {
            pc().printf("\r\n\nstate: TRANSMIT_DATA\r\n");
            timer.reset(); // timer goes back to zero
            timer.start(); // background timer starts running
            _isTimeoutRunning = true; 
            
            // what needs to be started?
 
            // what are the commands?
            recordData(_state);
        }
 
        // how exit?
        if (timer.read() > _timeout) {
            pc().printf("TRANSMIT_DATA: timed out\n\n\r");
            _state = SIT_IDLE;
            timer.reset();
            _isTimeoutRunning = false;
        }
        
        //action
        transmitData();
        
        break;
    
    default :
        pc().printf("DEBUG: SIT_IDLE\n\r");
        _state = SIT_IDLE;
    }
    
    //save the state to print to user
    if (_previous_state != _state) {
        _state_array[_state_array_counter] = _state;  //save to state array
        _state_array_counter++;
        
        _previous_state = _state;
    }
    
    return _state;
//    //if the state is SIT_IDLE, return 0 / false (for recording)
//    if (_state == SIT_IDLE)
//        return 0;
//    else
//        return 1;   //return true to indicate that you're recording
}
 
// output the keyboard menu for user's reference
void StateMachine::showMenu() {
    pc().printf("\r\r\n\nKEYBOARD MENU:\r\r\n");
    pc().printf(" G to initiate auto-neutral sequence\r\n");
    pc().printf(" F to jump to auto-neutral FIND PITCH state\r\n");
    pc().printf(" N to find neutral\r\n");
    pc().printf(" M to initiate multi-dive cycle\r\n");
    pc().printf(" D to initiate dive cycle\r\n");
    pc().printf(" R to initiate rise\r\n");
    pc().printf(" L to float level\r\n");
    pc().printf(" B to float at broadcast pitch\r\n");
    pc().printf(" E to initiate emergency climb\r\n");
    //pc().printf(" H to run homing sequence on both BCE and Batt\r\n");
    pc().printf(" T to tare the depth sensor\r\n");
    pc().printf(" Z to show FSM and sub-FSM states.\r\n");
    pc().printf(" P to print the current log file.\r\n");
    pc().printf(" X to print the list of log files.\r\n");
    pc().printf(" V to transmit data (work in progress).\r\n");
    pc().printf("[/] to change bce neutral position: %0.1f\r\n", _neutral_bce_pos_mm);
    pc().printf("</> to change batt neutral position: %0.1f\r\n", _neutral_batt_pos_mm);
    pc().printf("Q/W to decrease/increase pitch setpoint: %3.1f\r\n",_pitch_command);
    pc().printf("A/S to decrease/increase depth setpoint: %3.1f\r\n",_depth_command);
    pc().printf("+/- to decrease/increase timeout: %d s\r\n",_timeout);
    pc().printf(" 1 BCE PID sub-menu\r\n");
    pc().printf(" 2 BATT PID sub-menu\r\n");
    pc().printf(" 3 Depth PID sub-menu\r\n");
    pc().printf(" 4 Pitch PID sub-menu\r\n");
    pc().printf(" C See sensor readings (and max recorded depth of dive & neutral sequences)\r\n");
    pc().printf(" ? to reset mbed\r\n");
}
 
//Find Neutral sub finite state machine
// Note: the sub-fsm only moves the pistons once at the start of each timer loop
//  (timer completes, move piston, timer completes, move piston, etc)
int StateMachine::runNeutralStateMachine() {                
    switch (_substate) {
        case NEUTRAL_SINKING :
            //start the 10 second timer
            if (!_isSubStateTimerRunning) {                
                _neutral_timer = timer.read() + 5; //record the time when this block is first entered and add 5 seconds
                
                pc().printf("\r\n\nNEUTRAL_SINKING: Next retraction at %0.1f sec [current time: %0.1f] (pitch: %0.1f)\n\r", _neutral_timer, timer.read(), pitchLoop().getPosition());
                
                // what are the commands? (BCE linear actuator active, no pitch movement)
                //move piston at start of sequence (default: retract 2.5 mm)
                bce().setPosition_mm(bce().getSetPosition_mm() - _neutral_sink_command_mm);  //no depth command
                
                pc().printf("NEUTRAL_SINKING: Retracting piston %0.1f mm [BCE CMD : %0.1f] [pitch cmd: %0.1f] (pitch: %0.1f)\n\r", _neutral_sink_command_mm, bce().getSetPosition_mm(), pitchLoop().getCommand(), pitchLoop().getPosition());
                
                _isSubStateTimerRunning = true;    //disable this block after one iteration
            }
 
            // how exit?
            //once reached the travel limit, no need to keep trying, so exit
            if (bce().getPosition_mm() <= 0) {
                pc().printf("\n\rDEBUG: BCE current position is %0.1f mm (NEXT SUBSTATE NEUTRAL EXIT)\n\r", bce().getPosition_mm());
                _substate = NEUTRAL_EXIT;
                _isSubStateTimerRunning = false; // reset the sub state timer
            }         
            //once deeper than the commanded setpoint...
            else if (depthLoop().getPosition() > _depth_command) {
                _substate = NEUTRAL_SLOWLY_RISE; // next state
                _isSubStateTimerRunning = false; //reset the sub state timer
            }
 
            // what is active?
            //once the 10 second timer is complete, reset the timeout so the state one-shot entry will move the setpoint
            if (timer.read() >= _neutral_timer) {
                pc().printf("\r\n\n NEUTRAL_SINKING TIMER COMPLETE! [current time: %0.1f]\r\n", timer.read());
                
                _isSubStateTimerRunning = false; // reset the sub state timer to do one-shot actions again
            }
            // what is active? (only the buoyancy engine moved every 5 seconds)
            pc().printf("depthLoop getOutput (position): %0.1f (current depth: %0.1f ft)\r", depthLoop().getOutput(), depthLoop().getPosition()); //debug
            bce().setPosition_mm(depthLoop().getOutput()); // (DID NOT WORK ON BENCH)
            break;
            
        case NEUTRAL_SLOWLY_RISE:
            if (!_isSubStateTimerRunning) {                                
                _neutral_timer = timer.read()+ 5; //record the time when this block is first entered and add 5 seconds
                
                pc().printf("\r\n\nNEUTRAL_SLOWLY_RISE: Next extension at %0.1f sec) [current time: %0.1f]\r\n",_neutral_timer,timer.read());
                
                // what are the commands?
                //move piston at start of sequence (default: extend 2.0 mm)
                bce().setPosition_mm(bce().getSetPosition_mm() + _neutral_rise_command_mm);  //no depth command
                
                // it's okay to run the pitch outer loop now since we've already found pitch level in the previous state
                pitchLoop().setCommand(0.0);
                
                pc().printf("NEUTRAL_SLOWLY_RISE: Extending BCE piston %0.1f mm [BCE CMD : %0.1f] [pitch cmd: %0.1f]\n\r", _neutral_rise_command_mm, bce().getSetPosition_mm(), pitchLoop().getCommand());

                _isSubStateTimerRunning = true;    //disable this block after one iteration
            }
            
            // how exit?
            //once at full travel limit (setPosition) and haven't yet risen, time to give up and exit
            if (bce().getSetPosition_mm() >= bce().getTravelLimit()) {
                _substate = NEUTRAL_EXIT;     
                _isSubStateTimerRunning = false; // reset the sub state timer
            }
            //depth rate or sink rate < 0 ft/s, go to the next substate the next iteration
            else if (depthLoop().getVelocity() < 0) { //less than zero ft/s
                pc().printf("\r\n\nNEUTRAL_SLOWLY_RISE: Sink Rate < 0 ft/s [time: %0.1f]\r\n", timer.read());
                _substate = NEUTRAL_CHECK_PITCH;
                _isSubStateTimerRunning = false; // reset the sub state timer
            }
            
            // what is active?
            //once 5 second timer complete, reset the timeout so the state one-shot entry will move the setpoint
            if (timer.read() >= _neutral_timer) {
                pc().printf("\r\n\n NEUTRAL_SLOWLY_RISE TIMER COMPLETE! [timer: %0.1f]\r\n", timer.read());
   
                _isSubStateTimerRunning = false; // reset the sub state timer to do one-shot actions again
            }
                        
            // what is active? (only the buoyancy engine moved every 5 seconds)
            pc().printf("depthLoop getOutput: %0.1f\r", depthLoop().getOutput()); //debug
            bce().setPosition_mm(depthLoop().getOutput());    // (DID NOT WORK ON BENCH)
            break;   
                
        case NEUTRAL_CHECK_PITCH : // fall thru to next state is desired
            // start local state timer and init any other one-shot actions
            
            if (!_isSubStateTimerRunning) {                    
                _neutral_timer = timer.read() + 10; // record time when this block is entered and add several seconds
                pc().printf("\r\nNEUTRAL_CHECK_PITCH: Next move in %0.1f sec \r\n",_neutral_timer - timer.read());
                
                // what are the commands? (default: retract or extend 0.5 mm)
                if (pitchLoop().getPosition() > 2) { // nose is high
                    batt().setPosition_mm(batt().getSetPosition_mm() + _neutral_pitch_command_mm); // move battery forward (using setpoint from linear actuator)
                    pc().printf("\n\rNeutral Check Pitch: moving battery FWD in %0.1f mm increments\n\n\r", _neutral_pitch_command_mm);
                }
                else if (pitchLoop().getPosition() < -2) { // nose is low
                    batt().setPosition_mm(batt().getSetPosition_mm() - _neutral_pitch_command_mm); // move battery aft (using setpoint from linear actuator)
                    pc().printf("\n\rNeutral Check Pitch: moving battery AFT in %0.1f mm increments\n\n\r", _neutral_pitch_command_mm);
                }

                _isSubStateTimerRunning = true;    //disable this block after one iteration
            }
 
            // how exit?            
            //pitch angle and pitch rate within small tolerance
            //benchtop tests confirm angle needs to be around 2 degrees
            if ((fabs(pitchLoop().getPosition()) < 2.0) and (fabs(pitchLoop().getVelocity()) < 5.0)) { 
                pc().printf("Debug: Found Level (NEUTRAL_CHECK_PITCH or NEUTRAL_FIRST_PITCH)\n\r");    //debug
                // found level, but don't need to save anything this time
                
                if (depthLoop().getPosition() > _max_recorded_depth_neutral) {  //debug
                    _max_recorded_depth_neutral = depthLoop().getPosition();    //new max depth recorded
                }
                
                // found level and at depth too, so save it all now               
                if (_substate == NEUTRAL_CHECK_PITCH) {
                    //save positions locally
                    _neutral_batt_pos_mm = batt().getPosition_mm();
                    _neutral_bce_pos_mm = bce().getPosition_mm();
                    
                    //set the neutral positions in each outer loop
                    depthLoop().setOutputOffset(_neutral_bce_pos_mm);
                    pitchLoop().setOutputOffset(_neutral_batt_pos_mm);
                    
                    // save into the depth.txt and pitch.txt files
                    configFileIO().savePitchData(_pitch_KP, _pitch_KI, _pitch_KD, _neutral_batt_pos_mm); //P,I,D,batt zeroOffset
                    configFileIO().saveDepthData(_depth_KP, _depth_KI, _depth_KD, _neutral_bce_pos_mm); //P,I,D, bce zeroOffset
                    
                    pc().printf("\n\n\r>>> Saving Positions: BCE: %0.1f mm, BATT: %0.1f <<<\n\n\r",_neutral_bce_pos_mm,_neutral_batt_pos_mm);
                    
                    _substate = NEUTRAL_EXIT;
                    _isSubStateTimerRunning = false; // reset the sub state timer to do one-shot actions again
                }
                
                else {
                    pc().printf("\n\rDid not find NEUTRAL_CHECK_PITCH or NEUTRAL_FIRST_PITCH, how did I get here?!\n\r");
                    _substate = NEUTRAL_EXIT;
                }
            }
            
            // what is active?
            //once timer complete, reset the timeout so the state one-shot entry will move the setpoint
            if (timer.read() >= _neutral_timer) {
                pc().printf("\r\n\nlevel timer COMPLETE!");
                pc().printf("\r\n\n (BATT POS: %0.1f) moving 1 mm [timer: %0.1f]\r\n", batt().getPosition_mm(), timer.read());
                _isSubStateTimerRunning = false; // reset the sub state timer to do one-shot actions again
            }
            break;
             
        //this state could be removed, it is only used as a transition but is needed to stop entering this function
        case NEUTRAL_EXIT :
            pc().printf("substate: NEUTRAL_EXIT\n\r");            
            break;
            
        default :
            pc().printf("how did we get to substate: default?\n\r"); //debug
            //a default within the sub-state machine
            _substate = NEUTRAL_EXIT;            
            break;
    }
    
    // reset the sub-FSM if needed (useful if you need to redo the neutral-finding sequence)
    if (_substate == NEUTRAL_EXIT) {
        pc().printf("********************************  EXITING sub-FSM! *******************************\n\n\r");

        //reset internal sub-state back to first entry conditions (first state is immediately sinking)
        _substate = NEUTRAL_SINKING;
        _isSubStateTimerRunning = false; // reset the sub state timer
        
        //record sub-states to view after sequence
        _substate_array[_substate_array_counter] = NEUTRAL_EXIT;  //save exit to state array
        _substate_array_counter++;
        
        //reset _previous_substate on exit (has to be done in FIND_NEUTRAL if emergency exit)
        _previous_substate = -1;

        //NEUTRAL_EXIT state is used to tell the greater FSM that this sub-FSM has completed
        return NEUTRAL_EXIT; // message to calling function we just exited
    }
    else {
        //record sub-states to view after sequence (when changed)
        if (_previous_substate != _substate) {
            _substate_array[_substate_array_counter] = _substate;  //save current state to state array
            _substate_array_counter++;
            
            //record the current substate for comparison 
            _previous_substate = _substate;
        }       
        
        return _substate; // message to calling function of what sub-state it's in
    }
}

////Find Neutral sub finite state machine
//// Note: the sub-fsm only moves the pistons once at the start of each timer loop
////  (timer completes, move piston, timer completes, move piston, etc)
//int StateMachine::runActiveNeutralStateMachine() {                
//    switch (_substate) {
//        case NEUTRAL_AUTO_DEPTH :
//            //start the 10 second timer
//            if (!_isSubStateTimerRunning) {                
//                _neutral_timer = timer.read() + 5; //record the time when this block is first entered and add 5 seconds
//                
//                pc().printf("\r\n\nNEUTRAL_SINKING: Next retraction at %0.1f sec [current time: %0.1f] (pitch: %0.1f)\n\r", _neutral_timer, timer.read(), pitchLoop().getPosition());
//                
//                // what are the commands? (BCE linear actuator active, no pitch movement)
//                //move piston at start of sequence (default: retract 2.5 mm)
//                bce().setPosition_mm(bce().getSetPosition_mm() - _neutral_sink_command_mm);  //no depth command
//                
//                pc().printf("NEUTRAL_SINKING: Retracting piston %0.1f mm [BCE CMD : %0.1f] [pitch cmd: %0.1f] (pitch: %0.1f)\n\r", _neutral_sink_command_mm, bce().getSetPosition_mm(), pitchLoop().getCommand(), pitchLoop().getPosition());
//                
//                _isSubStateTimerRunning = true;    //disable this block after one iteration
//            }
// 
//            // how exit?
//            //once reached the travel limit, no need to keep trying, so exit
//            if (bce().getPosition_mm() <= 0) {
//                pc().printf("\n\rDEBUG: BCE current position is %0.1f mm (NEXT SUBSTATE NEUTRAL EXIT)\n\r", bce().getPosition_mm());
//                _substate = NEUTRAL_EXIT;
//                _isSubStateTimerRunning = false; // reset the sub state timer
//            }         
//            //once deeper than the commanded setpoint...
//            else if (depthLoop().getPosition() > _depth_command) {
//                _substate = NEUTRAL_SLOWLY_RISE; // next state
//                _isSubStateTimerRunning = false; //reset the sub state timer
//            }
// 
//            // what is active?
//            //once the 10 second timer is complete, reset the timeout so the state one-shot entry will move the setpoint
//            if (timer.read() >= _neutral_timer) {
//                pc().printf("\r\n\n NEUTRAL_SINKING TIMER COMPLETE! [current time: %0.1f]\r\n", timer.read());
//                
//                _isSubStateTimerRunning = false; // reset the sub state timer to do one-shot actions again
//            }
//            // what is active? (only the buoyancy engine moved every 5 seconds)
//            break;  
//                
//        case NEUTRAL_CHECK_PITCH : // fall thru to next state is desired
//            // start local state timer and init any other one-shot actions
//            
//            if (!_isSubStateTimerRunning) {                    
//                _neutral_timer = timer.read() + 10; // record time when this block is entered and add several seconds
//                pc().printf("\r\nNEUTRAL_CHECK_PITCH: Next move in %0.1f sec \r\n",_neutral_timer - timer.read());
//                
//                // what are the commands? (default: retract or extend 0.5 mm)
//                if (pitchLoop().getPosition() > 2) { // nose is high
//                    batt().setPosition_mm(batt().getSetPosition_mm() + _neutral_pitch_command_mm); // move battery forward (using setpoint from linear actuator)
//                    pc().printf("\n\rNeutral Check Pitch: moving battery FWD in %0.1f mm increments\n\n\r", _neutral_pitch_command_mm);
//                }
//                else if (pitchLoop().getPosition() < -2) { // nose is low
//                    batt().setPosition_mm(batt().getSetPosition_mm() - _neutral_pitch_command_mm); // move battery aft (using setpoint from linear actuator)
//                    pc().printf("\n\rNeutral Check Pitch: moving battery AFT in %0.1f mm increments\n\n\r", _neutral_pitch_command_mm);
//                }
//
//                _isSubStateTimerRunning = true;    //disable this block after one iteration
//            }
// 
//            // how exit?            
//            //pitch angle and pitch rate within small tolerance
//            //benchtop tests confirm angle needs to be around 2 degrees
//            if ((fabs(pitchLoop().getPosition()) < 2.0) and (fabs(pitchLoop().getVelocity()) < 5.0)) { 
//                pc().printf("Debug: Found Level (NEUTRAL_CHECK_PITCH or NEUTRAL_FIRST_PITCH)\n\r");    //debug
//                // found level, but don't need to save anything this time
//                
//                if (depthLoop().getPosition() > _max_recorded_depth_neutral) {  //debug
//                    _max_recorded_depth_neutral = depthLoop().getPosition();    //new max depth recorded
//                }
//                
//                // found level and at depth too, so save it all now               
//                if (_substate == NEUTRAL_CHECK_PITCH) {
//                    //save positions locally
//                    _neutral_batt_pos_mm = batt().getPosition_mm();
//                    _neutral_bce_pos_mm = bce().getPosition_mm();
//                    
//                    //set the neutral positions in each outer loop
//                    depthLoop().setOutputOffset(_neutral_bce_pos_mm);
//                    pitchLoop().setOutputOffset(_neutral_batt_pos_mm);
//                    
//                    // save into the depth.txt and pitch.txt files
//                    configFileIO().savePitchData(_pitch_KP, _pitch_KI, _pitch_KD, _neutral_batt_pos_mm); //P,I,D,batt zeroOffset
//                    configFileIO().saveDepthData(_depth_KP, _depth_KI, _depth_KD, _neutral_bce_pos_mm); //P,I,D, bce zeroOffset
//                    
//                    pc().printf("\n\rSaving Positions: BCE: %0.1f mm, BATT: %0.1f\n\n\r",_neutral_bce_pos_mm,_neutral_batt_pos_mm);
//                    
//                    _substate = NEUTRAL_EXIT;
//                    _isSubStateTimerRunning = false; // reset the sub state timer to do one-shot actions again
//                }
//                
//                else {
//                    pc().printf("\n\rDid not find NEUTRAL_CHECK_PITCH or NEUTRAL_FIRST_PITCH, how did I get here?!\n\r");
//                    _substate = NEUTRAL_EXIT;
//                }
//            }
//            
//            // what is active?
//            //once timer complete, reset the timeout so the state one-shot entry will move the setpoint
//            if (timer.read() >= _neutral_timer) {
//                pc().printf("\r\n\nlevel timer COMPLETE!");
//                pc().printf("\r\n\n (BATT POS: %0.1f) moving 1 mm [timer: %0.1f]\r\n", batt().getPosition_mm(), timer.read());
//                _isSubStateTimerRunning = false; // reset the sub state timer to do one-shot actions again
//            }
//            break;
//             
//        //this state could be removed, it is only used as a transition but is needed to stop entering this function
//        case NEUTRAL_EXIT :
//            pc().printf("substate: NEUTRAL_EXIT\n\r");            
//            break;
//            
//        default :
//            pc().printf("how did we get to substate: default?\n\r"); //debug
//            //a default within the sub-state machine
//            _substate = NEUTRAL_EXIT;            
//            break;
//    }
//    
//    // reset the sub-FSM if needed (useful if you need to redo the neutral-finding sequence)
//    if (_substate == NEUTRAL_EXIT) {
//        pc().printf("********************************  EXITING sub-FSM! *******************************\n\n\r");
//
//        //reset internal sub-state back to first entry conditions (first state is immediately sinking)
//        _substate = NEUTRAL_SINKING;
//        _isSubStateTimerRunning = false; // reset the sub state timer
//        
//        //record sub-states to view after sequence
//        _substate_array[_substate_array_counter] = NEUTRAL_EXIT;  //save exit to state array
//        _substate_array_counter++;
//        
//        //reset _previous_substate on exit (has to be done in FIND_NEUTRAL if emergency exit)
//        _previous_substate = -1;
//
//        //NEUTRAL_EXIT state is used to tell the greater FSM that this sub-FSM has completed
//        return NEUTRAL_EXIT; // message to calling function we just exited
//    }
//    else {
//        //record sub-states to view after sequence (when changed)
//        if (_previous_substate != _substate) {
//            _substate_array[_substate_array_counter] = _substate;  //save current state to state array
//            _substate_array_counter++;
//            
//            //record the current substate for comparison 
//            _previous_substate = _substate;
//        }       
//        
//        return _substate; // message to calling function of what sub-state it's in
//    }
//}
 
// keyboard runs independently of the state machine, handling one key at a time
//keyboard updates the desired _keyboard_state that is used in the state machine
//and only allows input when the state is "idle"
void StateMachine::keyboard() {
    char userInput;
 
    // check keyboard and make settings changes as requested
    // states can be changed only at the start of a sequence (when the system is in SIT_IDLE)
    
    int _keyboard_state = -1;   //made this a local variable because it was retaining the last keyboard state
    
    if (pc().readable() && (_state == SIT_IDLE || _state == KEYBOARD)) {        
        // get the key
        userInput = pc().getc();    
        
        //record that the keyboard was used
        _state_array[_state_array_counter] = KEYBOARD;
        _state_array_counter++;
        
        // keyboard has to reset timer each time it's used
        _isTimeoutRunning = false;
        
        // check command against desired control buttons
        if (userInput == 'D' or userInput == 'd') {
            _keyboard_state = DIVE;
        }
        else if (userInput == 'G') {
            _keyboard_state = FIND_AUTO_NEUTRAL_DEPTH;      //new test 12/7/2017
        }
        else if (userInput == 'F') {
            _keyboard_state = FIND_AUTO_NEUTRAL_PITCH;      //new test 12/7/2017
        }
        else if (userInput == 'N' or userInput == 'n') {
            _keyboard_state = FIND_NEUTRAL;
        }
        else if (userInput == 'M' or userInput == 'm') {
            //currently does not run if there is no file.
            
            //need to add method to Sequence Controller that returns -1 
            //   or some check that insures you cannot run the dive sequence without a file
            
            stateMachine().getDiveSequence();               //get first sequence on keyboard press
            _keyboard_state = currentStateStruct.state;
            
            pc().printf("Starting Dive Sequence Controller! (state: %d)\n\r", _keyboard_state);  //neutral sequence and dive cycles
        }
        else if (userInput == 'R' or userInput == 'r') {
            _keyboard_state = RISE;
        }
        else if (userInput == 'L' or userInput == 'l') {
            _keyboard_state = FLOAT_LEVEL;
        }
        else if (userInput == 'B' or userInput == 'b') {
            _keyboard_state = FLOAT_BROADCAST;
        }
        else if (userInput == 'E' or userInput == 'e') {
            _keyboard_state = EMERGENCY_CLIMB;
        }
        else if (userInput == 'P') {
            //Print current SD card log file
            //printCurrentSdLog();
            mbedLogger().printCurrentLogFile();        //print the current log file to the screen
        }
        else if (userInput == 'X') {
            printDirectory();
            //mbedLogger().printDirectory();        //print all log files to the screen
        }
        else if (userInput == 'V') {
            _keyboard_state = TRANSMIT_DATA;      //Transmit data (work in progress)
        }
//        else if (userInput == 'H' or userInput == 'h') {
//            pc().printf("running homing procedure\r\n");
//            bce().unpause();  bce().homePiston();  bce().pause();
//            batt().unpause(); batt().homePiston(); batt().pause();
//        }
        else if (userInput == 'z' or userInput == 'Z') {
            pc().printf("FSG FSM States: \n\r");
            string string_state;
            
            for (int i = 0; i < _state_array_counter; i++) {
                if (_state_array[i] == SIT_IDLE)
                    string_state = "SIT_IDLE              <END>";
                else if (_state_array[i] == FIND_NEUTRAL)
                    string_state = "FIND_NEUTRAL";
                else if (_state_array[i] == DIVE)
                    string_state = "DIVE";
                else if (_state_array[i] == RISE)
                    string_state = "RISE";
                else if (_state_array[i] == FLOAT_LEVEL)
                    string_state = "FLOAT_LEVEL";
                else if (_state_array[i] == FLOAT_BROADCAST)
                    string_state = "FLOAT_BROADCAST";          
                else if (_state_array[i] == EMERGENCY_CLIMB)
                    string_state = "EMERGENCY_CLIMB";
                else if (_state_array[i] == MULTI_DIVE)
                    string_state = "MULTI_DIVE";
                else if (_state_array[i] == MULTI_RISE)
                    string_state = "MULTI_RISE";
                else if (_state_array[i] == KEYBOARD)
                    string_state = "KEYBOARD";                    
                pc().printf("State #%d: %d (%s)\n\r", i, _state_array[i], string_state.c_str());
            }
            
            pc().printf("\n\rNeutral sub-FSM States: \n\r");
            string string_substate;
            
            for (int i = 0; i < _substate_array_counter; i++) {
                if (_substate_array[i] == NEUTRAL_SINKING)
                    string_substate = "NEUTRAL_SINKING";
                else if (_substate_array[i] == NEUTRAL_SLOWLY_RISE)
                    string_substate = "NEUTRAL_SLOWLY_RISE";
                else if (_substate_array[i] == NEUTRAL_CHECK_PITCH)
                    string_substate = "NEUTRAL_CHECK_PITCH";
                else if (_substate_array[i] == NEUTRAL_EXIT)
                    string_substate = "NEUTRAL_EXIT                  <--   ";
                else if (_substate_array[i] == EMERGENCY_CLIMB)
                    string_substate = " -- > EMERGENCY_CLIMB  <-- ";                
                pc().printf("Neutral Substate #%d: %d (%s)\n\r", i, _state_array[i], string_substate.c_str());
            }
            pc().printf("\n\r");  //make space between printouts
        }
        else if (userInput == 'T' or userInput == 't') {
            pc().printf("taring depth sensor\r\n");
            pc().printf("Pre-tare:  press: %3.3f psi, depth: %3.3f ft\r\n", depth().getPsi(), depth().getDepthFt());
            wait(0.1);
            depth().tare(); // tares to ambient (do on surface)
            pc().printf("Post-tare: press: %3.3f psi, depth: %3.3f ft\r\n", depth().getPsi(), depth().getDepthFt());
        }
        
        else if (userInput == '[' or userInput == '{') {
            _neutral_bce_pos_mm = depthLoop().getOutputOffset() - 1;
            depthLoop().setOutputOffset(_neutral_bce_pos_mm); // decrease the bce neutral setpoint
            pc().printf("Adjusting bce neutral position. new offset: %0.1f\r\n",depthLoop().getOutputOffset());
            // save neutral depth value to config file
            configFileIO().saveDepthData(_depth_KP, _depth_KI, _depth_KD, _neutral_bce_pos_mm);
        }
        else if (userInput == ']' or userInput == '}') {
            _neutral_bce_pos_mm = depthLoop().getOutputOffset() + 1;
            depthLoop().setOutputOffset(_neutral_bce_pos_mm); // increase the bce neutral setpoint
            pc().printf("Adjusting bce neutral position. new offset: %0.1f\r\n",depthLoop().getOutputOffset());
            // save neutral depth value to config file
            configFileIO().saveDepthData(_depth_KP, _depth_KI, _depth_KD, _neutral_bce_pos_mm);
        }
        else if (userInput == '<' or userInput == ',') {
            _neutral_batt_pos_mm = pitchLoop().getOutputOffset() - 1;
            pitchLoop().setOutputOffset(_neutral_batt_pos_mm); // decrease the batt neutral setpoint
            pc().printf("Adjusting batt neutral position. new offset: %0.1f\r\n",pitchLoop().getOutputOffset());
            // save neutral pitch value to config file
            configFileIO().savePitchData(_pitch_KP, _pitch_KI, _pitch_KD, _neutral_batt_pos_mm);
        }
        else if (userInput == '>' or userInput == '.') {
            _neutral_batt_pos_mm = pitchLoop().getOutputOffset() + 1;
            pitchLoop().setOutputOffset(_neutral_batt_pos_mm); // increase the batt neutral setpoint
            pc().printf("Adjusting batt neutral position. new offset: %0.1f\r\n",pitchLoop().getOutputOffset());
            // save neutral pitch value to config file
            configFileIO().savePitchData(_pitch_KP, _pitch_KI, _pitch_KD, _neutral_batt_pos_mm);
        }
        
        else if (userInput == '?') {
            pc().printf("\n\n\n>>> Resetting MBED <<<\n\n\n");
            wait(0.5);
            mbed_reset();
        }
 
        // change settings        
        else if (userInput == 'Q' or userInput == 'q') {
            _pitch_command -= 0.5;         //decrement the pitch setpoint
            pitchLoop().setCommand(_pitch_command);
            pc().printf(">>> new pitch angle setpoint: %0.3f deg (decreased)\r\n", pitchLoop().getCommand());
        }
        else if (userInput == 'W' or userInput == 'w') {
            _pitch_command += 0.5;         //increment the pitch setpoint
            pitchLoop().setCommand(_pitch_command);
            pc().printf(">>> new pitch angle setpoint: %0.3f deg (increased)\r\n", pitchLoop().getCommand());
        }
        else if (userInput == 'A' or userInput == 'a') {
            _depth_command -= 0.5;         //decrement the depth setpoint
            depthLoop().setCommand(_depth_command);
            pc().printf(">>> new depth (ft) setpoint: %0.3f ft (sink)\r\n", depthLoop().getCommand());
        }
        else if (userInput == 'S' or userInput == 's') {
            _depth_command += 0.5;         //increment the depth setpoint
            depthLoop().setCommand(_depth_command);
            pc().printf(">>> new depth setpoint: %0.3f ft (rise)\r\n", depthLoop().getCommand());
        }
        else if (userInput == '-') {
            _timeout -= 10.0;               //decrement the timeout
            pc().printf(">>> timeout decreased: %d\r\n", _timeout);
        }
        else if (userInput == '=' or userInput == '+') {
            _timeout += 10.0;               //increment the timeout
            pc().printf(">>> timeout increased: %d\r\n", _timeout);
        }
        
        // go to sub-menus for the PID gains (this is blocking)
        else if (userInput == '1') {
            keyboard_menu_BCE_PID_settings();
        }
        else if (userInput == '2') {
            keyboard_menu_BATT_PID_settings();
        }
        else if (userInput == '3') {
            keyboard_menu_DEPTH_PID_settings();
        }
        else if (userInput == '4') {
            keyboard_menu_PITCH_PID_settings();
        }
        
        else if (userInput == 'C' or userInput == 'c') {
            
            pc().printf("\n\n\rCURRENT STATUS AND PARAMETERS:\n\r");
            pc().printf("depth: %3.1f ft\r\n",depthLoop().getPosition());
            pc().printf("pitch: %3.1f deg\r\n",imu().getPitch());
            pc().printf("bce().getPosition_mm(): %3.1f\r\n",bce().getPosition_mm());
            pc().printf("bce().getSetPosition_mm(): %3.1f\r\n",bce().getSetPosition_mm());
            pc().printf("batt().getPosition_mm(): %3.1f\r\n",batt().getPosition_mm());
            pc().printf("batt().getSetPosition_mm(): %3.1f\r\n",batt().getSetPosition_mm());
            pc().printf("depthLoop().getCommand(): %3.1f\r\n",depthLoop().getCommand());
            pc().printf("pitchLoop().getCommand(): %3.1f\r\n",pitchLoop().getCommand());
            
            pc().printf("\n\rNeutral Buoyancy Positions: bce: %0.1f, batt: %0.1f\r\n",_neutral_bce_pos_mm,_neutral_batt_pos_mm);
            pc().printf("depthLoop().getOutputOffset(): %0.1f\r\n",depthLoop().getOutputOffset());
            pc().printf("pitchLoop().getOutputOffset(): %0.1f\r\n",pitchLoop().getOutputOffset());
            pc().printf("Max recorded depth: neutral: %0.1f, dive: %0.1f, auto_neutral_depth: %0.1f\n\n\r",_max_recorded_depth_neutral, _max_recorded_depth_dive, _max_recorded_auto_neutral_depth);
        }
        
        //when you read the keyboard successfully, change the state
        _state = _keyboard_state;   //set state at the end of this function
    }
}
 
 
void StateMachine::keyboard_menu_BCE_PID_settings() {    
    char PID_key;
    float gain_step_size = 0.01;    // modify this to change gain step size
    float KP = bce().getControllerP();  // load current value
    float KI = bce().getControllerI();  // load current global value
    float KD = bce().getControllerD();  // load current global value
 
    // show the menu
    pc().printf("\n\r1: Buoyancy Engine PID gain settings (MENU)");
    pc().printf("\n\r(Adjust PID settings with the following keys: -= and [] and ;'");
    pc().printf("\n\r(Hit shift + X to exit w/o saving.  Hit shift + S to save.)\n\n\n\r");
    pc().printf("bce    P: %3.2f, I: %3.2f, D %3.2f, zero %d, limit %3.0f mm, slope %3.3f  \r\n", bce().getControllerP(), bce().getControllerI(), bce().getControllerD(), bce().getZeroCounts(), bce().getTravelLimit(), bce().getPotSlope());
    
    // handle the key presses
    while(1) {
        // get the user's keystroke from either of the two inputs
        if (pc().readable()) {
            PID_key = pc().getc();
        }
        else {
            continue; // didn't get a user input, so keep waiting for it
        }
    
        // handle the user's key input
        if (PID_key == '-') {
            KP -= gain_step_size;
            pc().printf("P gain: %0.5f               \r\n", KP);
        }
        else if (PID_key == '=') {
            KP += gain_step_size;
            pc().printf("P gain: %0.5f               \r\n", KP);
        }
        else if (PID_key == '[') {
            KI -= gain_step_size;
            pc().printf("I gain: %0.5f               \r\n", KI);
        }
        else if (PID_key == ']') {
            KI += gain_step_size;
            pc().printf("I gain: %0.5f               \r\n", KI);
        }
        else if (PID_key == ';') {
            KD -= gain_step_size;
            pc().printf("D gain: %0.5f               \r\n", KD);
        }
        else if (PID_key == '\'') {
            KD += gain_step_size;
            pc().printf("D gain: %0.5f               \r\n", KD);
        }
        else if (PID_key == 'S') { // user wants to save these modified values
            // set values
            bce().setControllerP(KP);
            bce().setControllerI(KI);
            bce().setControllerD(KD);  
 
            // save into "PID.cfg"
            //Config_File_IO().write_manual_position_PID_values_to_config(batt_position_P,batt_position_I,batt_position_D,bce_position_P,bce_position_I,bce_position_D);
            break;  //exit the while loop
        }
        else if (PID_key == 'X') {    
            break;  //exit the while loop
        }
        else {
            pc().printf("\n\rThis key does nothing here.                              ");
        }
    }
}
 
void StateMachine::keyboard_menu_BATT_PID_settings() {    
    char PID_key;
    float gain_step_size = 0.01;    // modify this to change gain step size
    float KP = batt().getControllerP(); // load current global value
    float KI = batt().getControllerI(); // load current global value
    float KD = batt().getControllerD(); // load current global value
 
    // print the menu
    pc().printf("\n\r2: Battery Motor PID gain settings (MENU)");
    pc().printf("\n\r(Adjust PID settings with the following keys: -= and [] and ;'");
    pc().printf("\n\r(Hit shift + X to exit w/o saving.  Hit shift + S to save.\n\r");
    pc().printf("batt   P: %3.2f, I: %3.2f, D %3.2f, zero %d, limit %3.0f mm, slope %3.3f  \r\n", batt().getControllerP(), batt().getControllerI(), batt().getControllerD(), batt().getZeroCounts(), batt().getTravelLimit(), batt().getPotSlope());
 
    // handle the key presses
    while(1) {
        // get the user's keystroke from either of the two inputs
        if (pc().readable()) {
            PID_key = pc().getc();
        }
        else {
            continue; // didn't get a user input, so keep waiting for it
        }
 
        // handle the user's key input
        if (PID_key == '-') {
            KP -= gain_step_size;
            pc().printf("\rP gain: %0.5f               ", KP);
        }
        else if (PID_key == '=') {
            KP += gain_step_size;
            pc().printf("\rP gain: %0.5f               ", KP);
        }
        else if (PID_key == '[') {
            KI -= gain_step_size;
            pc().printf("\rI gain: %0.5f               ", KI);
        }
        else if (PID_key == ']') {
            KI += gain_step_size;
            pc().printf("\rI gain: %0.5f               ", KI);
        }
        else if (PID_key == ';') {
            KD -= gain_step_size;
            pc().printf("\rD gain: %0.5f               ", KD);
        }
        else if (PID_key == '\'') {
            KD += gain_step_size;
            pc().printf("\rD gain: %0.5f               ", KD);
        }
        else if (PID_key == 'S') { // user wants to save the modified values
            // set global values
            batt().setControllerP(KP);
            batt().setControllerI(KI);
            batt().setControllerD(KD);
            
            // save to "PID.cfg" file
            //Config_File_IO().write_manual_position_PID_values_to_config(batt_position_P,batt_position_I,batt_position_D,bce_position_P,bce_position_I,bce_position_D);
            break;  //exit the while loop
        }
        else if (PID_key == 'X') {    
            break;  //exit the while loop
        }
        else {
            pc().printf("This key does nothing here.\r");
        }
    }
}
 
void StateMachine::keyboard_menu_DEPTH_PID_settings() {    
    char PID_key;
    float gain_step_size = 0.01;    // modify this to change gain step size
 
    // show the menu
    pc().printf("\n\r1: Buoyancy Engine PID gain settings (MENU)");
    pc().printf("\n\r(Adjust PID settings with the following keys: -= and [] and ;'");
    pc().printf("\n\r(Hit shift + X to exit w/o saving.  Hit shift + S to save.\n\n\n\r");
    pc().printf("depth  P: %3.2f, I: %3.2f, D %3.2f, offset: %3.1f mm \r\n", depthLoop().getControllerP(), depthLoop().getControllerI(), depthLoop().getControllerD(), depthLoop().getOutputOffset());
    
    // handle the key presses
    while(1) {
        // get the user's keystroke from either of the two inputs
        if (pc().readable()) {
            PID_key = pc().getc();
        }
        else {
            continue; // didn't get a user input, so keep waiting for it
        }
    
        // handle the user's key input
        if (PID_key == '-') {
            _depth_KP -= gain_step_size;
            pc().printf("P gain: %0.5f               \r\n", _depth_KP);
        }
        else if (PID_key == '=') {
            _depth_KP += gain_step_size;
            pc().printf("P gain: %0.5f               \r\n", _depth_KP);
        }
        else if (PID_key == '[') {
            _depth_KI -= gain_step_size;
            pc().printf("I gain: %0.5f               \r\n", _depth_KI);
        }
        else if (PID_key == ']') {
            _depth_KI += gain_step_size;
            pc().printf("I gain: %0.5f               \r\n", _depth_KI);
        }
        else if (PID_key == ';') {
            _depth_KD -= gain_step_size;
            pc().printf("D gain: %0.5f               \r\n", _depth_KD);
        }
        else if (PID_key == '\'') {
            _depth_KD += gain_step_size;
            pc().printf("D gain: %0.5f               \r\n", _depth_KD);
        }
        else if (PID_key == 'S') { // user wants to save these settings
            // set global values
            depthLoop().setControllerP(_depth_KP);
            depthLoop().setControllerI(_depth_KI);
            depthLoop().setControllerD(_depth_KD);
            
            // save depth PID values for outer loop
            configFileIO().saveDepthData(_depth_KP, _depth_KI, _depth_KD, _neutral_bce_pos_mm);
            break;  //exit the while loop
        }
        else if (PID_key == 'X') {    
            break;  //exit the while loop
        }
        else {
            pc().printf("\n\rThis key does nothing here.                              ");
        }
    }
}
 
void StateMachine::keyboard_menu_PITCH_PID_settings() {    
    char PID_key;
    float gain_step_size = 0.01;    // modify this to change gain step size
 
    // print the menu
    pc().printf("\n\r2: Battery Motor PID gain settings (MENU)");
    pc().printf("\n\r(Adjust PID settings with the following keys: -= and [] and ;'");
    pc().printf("\n\r(Hit shift + X to exit w/o saving.  Hit shift + S to save.\n\r");
    pc().printf("pitch  P: %3.2f, I: %3.2f, D %3.2f, offset: %3.1f mm \r\n", pitchLoop().getControllerP(), pitchLoop().getControllerI(), pitchLoop().getControllerD(), pitchLoop().getOutputOffset());
 
    // handle the key presses
    while(1) {
        // get the user's keystroke from either of the two inputs
        if (pc().readable()) {
            PID_key = pc().getc();
        }
        else {
            continue; // didn't get a user input, so keep waiting for it
        }
 
        // handle the user's key input
        if (PID_key == '-') {
            _pitch_KP -= gain_step_size;
            pc().printf("\rP gain: %0.5f               ", _pitch_KP);
        }
        else if (PID_key == '=') {
            _pitch_KP += gain_step_size;
            pc().printf("\rP gain: %0.5f               ", _pitch_KP);
        }
        else if (PID_key == '[') {
            _pitch_KI -= gain_step_size;
            pc().printf("\rI gain: %0.5f               ", _pitch_KI);
        }
        else if (PID_key == ']') {
            _pitch_KI += gain_step_size;
            pc().printf("\rI gain: %0.5f               ", _pitch_KI);
        }
        else if (PID_key == ';') {
            _pitch_KD -= gain_step_size;
            pc().printf("\rD gain: %0.5f               ", _pitch_KD);
        }
        else if (PID_key == '\'') {
            _pitch_KD += gain_step_size;
            pc().printf("\rD gain: %0.5f               ", _pitch_KD);
        }
        else if (PID_key == 'S') { // user wants to save the modified values
            // set global values
            pitchLoop().setControllerP(_pitch_KP);
            pitchLoop().setControllerI(_pitch_KI);
            pitchLoop().setControllerD(_pitch_KD);
            
            // save pitch PID values for outer loop (must save neutral position also)
            configFileIO().savePitchData(_pitch_KP, _pitch_KI, _pitch_KD, _neutral_batt_pos_mm);
            break;  //exit the while loop
        }
        else if (PID_key == 'X') {    
            break;  //exit the while loop
        }
        else {
            pc().printf("This key does nothing here.\r");
        }
    }
}
 
float StateMachine::getDepthCommand() {
    return _depth_command;
}
 
float StateMachine::getPitchCommand() {
    return _pitch_command;
}

float StateMachine::getDepthReading() {
    return _depth_reading;
}
 
float StateMachine::getPitchReading() {
    return _pitch_reading;
}

float StateMachine::getTimerReading() {
    return _timer_reading;
}

void StateMachine::setState(int input_state) {
    _state = input_state;
}
 
int StateMachine::getState() {
    return _state;  //return the current state of the system
}
 
void StateMachine::setTimeout(float input_timeout) {
    _timeout = input_timeout;
}
 
void StateMachine::setDepthCommand(float input_depth_command) {
    _depth_command = input_depth_command;
}
 
void StateMachine::setPitchCommand(float input_pitch_command) {
    _pitch_command = input_pitch_command;
}
 
void StateMachine::setNeutralPositions(float batt_pos_mm, float bce_pos_mm) {
    _neutral_batt_pos_mm = batt_pos_mm;
    _neutral_bce_pos_mm = bce_pos_mm;
    
    pc().printf("Neutral Buoyancy Positions: batt: %0.1f, bce: %0.1f\n\r",_neutral_batt_pos_mm,_neutral_bce_pos_mm);
}
 
int StateMachine::timeoutRunning() {
    return _isTimeoutRunning;
}
 
//process one state at a time
void StateMachine::getDiveSequence() {
    //iterate through this sequence using the FSM
    currentStateStruct.state = sequenceController().sequenceStructLoaded[_multi_dive_counter].state;
    currentStateStruct.timeout = sequenceController().sequenceStructLoaded[_multi_dive_counter].timeout;
    currentStateStruct.depth = sequenceController().sequenceStructLoaded[_multi_dive_counter].depth;
    currentStateStruct.pitch = sequenceController().sequenceStructLoaded[_multi_dive_counter].pitch;
    
    _timeout = currentStateStruct.timeout;  //set timeout before exiting this function
}

void StateMachine::printDirectory() {
    //create a DirectoryList object that points to the local directory
    DirectoryList mbed_dir( "/local" );
 
    if ( mbed_dir.error_check() ) {
        //error( "MBED directory could not be opened\r\n" );
        pc().printf("MBED directory could not be opened\r\n");
    }
    
    else {
        pc().printf("\n\rFiles in MBED directory:\n\r");
        for ( int i = 0; i < mbed_dir.size(); i++ )
            pc().printf( "%s\r\n", mbed_dir[ i ].c_str() );
    }
    
    //SD CARD DIRECTORY (does not work for openlog)
    DirectoryList sd_dir( "/sd" );
 
    if ( sd_dir.error_check() ) {
        //error( "MBED directory could not be opened\r\n" );
        pc().printf("SD directory could not be opened\r\n");
    }
    else {
        pc().printf("\n\rFiles in SD card directory:\n\r");
        for ( int i = 0; i < sd_dir.size(); i++ )
            pc().printf( "%s\r\n", sd_dir[ i ].c_str() );
    }
}

void StateMachine::printCurrentSdLog() {
    pc().printf("SD card log work in progress\n\r");
    //might be worth saving the last few logs to the MBED...
}

//check if the file is still opened
void StateMachine::createNewFile() {
    if (_file_closed) {
        //mbedLogger().createFile();       //create a new MBED file
        
        _file_closed = false;   //file is still open until you get to SIT_IDLE
    }
}

void StateMachine::transmitData() {
    static float transmit_timer = 0; 
    static bool is_transmit_timer_running = false;
    
    if (!is_transmit_timer_running) {     
        //pc().printf("\n\n\rTRANSMIT timer running...\n\n\r");    //debug
                   
        transmit_timer = timer.read() + 1; //record the time when this block is first entered and add 5 seconds 
        is_transmit_timer_running = true;    //disable this block after one iteration
        
        pc().printf("TESTING to see if this transmits once a second. (timer: %0.1f)\n\r", timer.read());
    }
    if (timer.read() >= transmit_timer) {
        is_transmit_timer_running = false; // reset the sub state timer to do one-shot actions again
    }
}

void StateMachine::recordData(int input_state) {
    string string_state;
    if (input_state == SIT_IDLE)
        string_state = "SIT_IDLE";
    else if (input_state == FIND_NEUTRAL)
        string_state = "FIND_NEUTRAL";
    else if (input_state == DIVE)
        string_state = "DIVE";
    else if (input_state == RISE)
        string_state = "RISE";
    else if (input_state == FLOAT_LEVEL)
        string_state = "FLOAT_LEVEL";
    else if (input_state == FLOAT_BROADCAST)
        string_state = "FLOAT_BROADCAST";          
    else if (input_state == EMERGENCY_CLIMB)
        string_state = "EMERGENCY_CLIMB";
    else if (input_state == MULTI_DIVE)
        string_state = "MULTI_DIVE";
    else if (input_state == MULTI_RISE)
        string_state = "MULTI_RISE";
    else if (input_state == KEYBOARD)
        string_state = "KEYBOARD";
        
    if (!_is_log_timer_running) {     
        //pc().printf("\n\n\rlog timer running...\n\n\r");    //debug
                   
        _log_timer = timer.read() + 1; //record the time when this block is first entered and add 5 seconds 
        _is_log_timer_running = true;    //disable this block after one iteration
        
        _data_log[0] = timer.read();                //timer reading (shouldn't this be constant throughout the state?)
        _data_log[1] = depthLoop().getCommand();    //depth command
        _data_log[2] = depthLoop().getPosition();   //depth reading
        _data_log[3] = pitchLoop().getCommand();    //pitch command
        _data_log[4] = pitchLoop().getPosition();   //pitch reading
        _data_log[5] = bce().getSetPosition_mm();
        _data_log[6] = bce().getPosition_mm();
        _data_log[7] = batt().getSetPosition_mm();
        _data_log[8] = batt().getPosition_mm();
        
        //record data to the MBED every 5 seconds
        //mbedLogger().saveArrayToFile(string_state,input_state,_data_log);
    }
    if (timer.read() >= _log_timer) {
        _is_log_timer_running = false; // reset the sub state timer to do one-shot actions again
    }
}

void StateMachine::recordState(int input_state) {
    string string_state;
            
    if (input_state == SIT_IDLE)
        string_state = "SIT_IDLE";
    else if (input_state == FIND_NEUTRAL)
        string_state = "FIND_NEUTRAL";
    else if (input_state == DIVE)
        string_state = "DIVE";
    else if (input_state == RISE)
        string_state = "RISE";
    else if (input_state == FLOAT_LEVEL)
        string_state = "FLOAT_LEVEL";
    else if (input_state == FLOAT_BROADCAST)
        string_state = "FLOAT_BROADCAST";          
    else if (input_state == EMERGENCY_CLIMB)
        string_state = "EMERGENCY_CLIMB";
    else if (input_state == MULTI_DIVE)
        string_state = "MULTI_DIVE";
    else if (input_state == MULTI_RISE)
        string_state = "MULTI_RISE";
    else if (input_state == KEYBOARD)
        string_state = "KEYBOARD";                    
    //datalogger().printf("%s\n", string_state.c_str());
}

float * StateMachine::dataArray() {
    //return the array to a calling function
    return _data_log;
}