File content as of revision 16:577cb22cec99:

#include "mbed.h"
#include "SDFileSystem.h"
#include "Adafruit_ADS1015.h"
#include "MCP40D17.h"
#include "STC3100.h"
#include "LSM303.h"
#include "BME280.h"
#include "SI1145.h"
#include "NCP5623BMUTBG.h"
#include "CronoDot.h"
#include "EEPROM.h"
#include "Calibration.h"
#include "MAX_M8.h" 
#include "DRV8830.h"


/////////////////////////////////////////////
//General Items
/////////////////////////////////////////////
I2C                 i2c(PB_9, PB_8);//(D14, D15); SDA,SCL
Serial              pc(USBTX, USBRX);
DigitalOut          blower(PA_9, 0);//(D8, 0);
DigitalOut          pbKill(PC_12, 1); // Digital input pin that conncect to the LTC2950 battery charger used to shutdown the UPAS 
DigitalIn           nINT(PA_15); //Connected but currently unused is a digital ouput pin from LTC2950 battery charger. http://cds.linear.com/docs/en/datasheet/295012fd.pdf
MCP40D17            DigPot(&i2c);
BME280              bmesensor(PB_9, PB_8);//(D14, D15);
NCP5623BMUTBG       RGB_LED(PB_9, PB_8);//(D14, D15);
//CronoDot            RTC_UPAS(PB_9, PB_8);//(D14, D15);
EEPROM              E2PROM(PB_9, PB_8);//(D14, D15);
Calibration         calibrations(1);     //Default serial/calibration if there are no values for the selected option


/////////////////////////////////////////////
//RN4677 BT/BLE Module
/////////////////////////////////////////////
Serial microChannel(PB_10, PB_11); // tx, rx
DigitalOut          bleRTS(PB_14, 0);
DigitalOut          bleCTS(PB_13, 0);
/*
DigitalOut          BT_IRST(PC_8, 0);
DigitalOut          BT_SW(PA_12, 0);
*/

/////////////////////////////////////////////
//Analog to Digital Converter
/////////////////////////////////////////////
Adafruit_ADS1115    ads(&i2c);
//DigitalIn           ADS_ALRT(PA_10); //Connected but currently unused. (ADS1115) http://www.ti.com/lit/ds/symlink/ads1115.pdf

/////////////////////////////////////////////
//Battery Monitoring
/////////////////////////////////////////////
STC3100             gasG(PB_9, PB_8);//(D14, D15);  // http://www.st.com/web/en/resource/technical/document/datasheet/CD00219947.pdf
DigitalIn           bcs1(PC_9); //Charge complete if High. Connected but currently unused. (MCP73871) http://www.mouser.com/ds/2/268/22090a-52174.pdf
DigitalIn           bcs2(PA_8); //Batt charging if High. Connected but currently unused. (MCP73871) http://www.mouser.com/ds/2/268/22090a-52174.pdf

/////////////////////////////////////////////
//Accelerometer and Magnometer
/////////////////////////////////////////////
LSM303              movementsensor(PB_9, PB_8);//(D14, D15); // http://www.st.com/web/en/resource/technical/document/datasheet/DM00027543.pdf
//DigitalIn           ACC_INT1(PC_7); //Connected but currently unused. (LSM303)
//DigitalIn           ACC_INT2(PC_6); //Connected but currently unused. (LSM303)
//DigitalIn           ACC_DRDY(PC_11); //Connected but currently unused. (LSM303)

/////////////////////////////////////////////
//UV and Visible Light Sensor
/////////////////////////////////////////////
SI1145              lightsensor(PB_9, PB_8);//(D14, D15);
//DigitalIn           UV_INT(PD_2); //Connected but currently unused nor configured (interupt). (SI1145) https://www.silabs.com/Support%20Documents/TechnicalDocs/Si1145-46-47.pdf

/////////////////////////////////////////////
//GPS
/////////////////////////////////////////////
DigitalOut      gpsEN(PB_15, 1);
Max_M8 gps(PB_9, PB_8,(66<<1));   // this must be defnined in the int main (? Not sure if this is true)

/////////////////////////////////////////////
//Hbridge Valve Control
/////////////////////////////////////////////
/*
DRV8830    motor1(PB_9, PB_8, 0xC4); 
DRV8830    motor2(PB_9, PB_8, 0xCA); 
DRV8830    motor3(PB_9, PB_8, 0xCC); 
DRV8830    motor4(PB_9, PB_8, 0xCE); 
DigitalIn  hb_fault1(PA_6);
DigitalIn  hb_fault2(PA_7);
DigitalIn  hb_fault3(PA_5);
DigitalIn  hb_fault4(PA_4);
*/
/////////////////////////////////////////////
//SD Card
/////////////////////////////////////////////
char filename[] = "/sd/XXXX0000LOG000000000000---------------.txt";
SDFileSystem sd(PB_5, PB_4, PB_3, PB_6, "sd");//(D4, D5, D3, D10, "sd"); // (MOSI, MISO, SCK, SEL)
DigitalIn    sdCD(PA_11);

/////////////////////////////////////////////
//Callbacks
/////////////////////////////////////////////
Ticker          stop;     //This is the stop callback object
Ticker          logg;     //This is the logging callback object
Ticker          flowCtl;  //This is the control loop callback object

/////////////////////////////////////////////
//Varible Definitions
/////////////////////////////////////////////
uint16_t serial_num = 1;                // Default serial/calibration number
int RunReady =0;

struct tm STtime;
char timestr[32];

float press;
float temp;
float rh;

int uv;
int vis;
int ir;

float compass;
float accel_x;
float accel_y;
float accel_z;
float accel_comp;
float angle_x;
float angle_y;
float angle_z;
float mag_x;
float mag_y;
float mag_z;

int vInReading;
int vBlowerReading;
int omronDiff;
float omronVolt; //V
int omronReading;
float atmoRho; //g/L

float massflow; //g/min
float volflow; //L/min
float volflowSet = 1.0; //L/min
int   logInerval = 5;//seconds
double secondsD = 0;
double lastsecondD = 0;
float massflowSet;
float deltaVflow = 0.0;
float deltaMflow = 0.0;
float gainFlow;
float sampledVol; //L, total sampled volume

int digital_pot_setpoint = 100; //min = 0x7F, max = 0x00
int digital_pot_set;
int digital_pot_change;
int digitalpotMax = 127;
int digitalpotMin = 10;

int dutyUp;
int dutyDown;

float flat = 0;
float flon = 0;

uint8_t gpssatellites = 0;
double gpsspeed = 0.0;
double gpslatitude = 0.0;
double gpslongitude = 0.0;
float gpsaltitude = 0.0;
char gpslat = 'W';
char gpslon = 'N';


float home_lat  = 40.580508;
float home_lon  = -105.081823;
float work_lat  = 40.594062; //40.569136;
float work_lon  = -105.075683; //-105.081966;
int location = 0;

float homeDistance = 99999;
float workDistance = 99999;

//*************************************************//

void sendData(); 


void pc_recv(){
    while(pc.readable()){
        pc.getc();
    }
}

static uint8_t rx_buf[20];
static uint8_t rx_len=0;
static int haltBLE = 1;
static int transmissionValue = 0;
uint8_t writeData[20] = {0,};
static uint8_t dataLength = 0;
static int runReady = 0;
static uint8_t startAndEndTime[12] = {0,};

//////////////////////////////////////////////////////////////
//BLE Functions
//////////////////////////////////////////////////////////////

void uartMicro(){
    if(runReady!=1){
        haltBLE = 2;
        while(microChannel.readable()){
            rx_buf[rx_len++] = microChannel.getc();
            
            //Code block to verify what is being transmitted.  To function correctly, all data must terminate with \0 or \n
            if(transmissionValue==0){
                
                if     (rx_buf[0] == 0x01)transmissionValue = 1; //rtc
                else if(rx_buf[0] == 0x02)transmissionValue = 2; //sample start and end times
                else if(rx_buf[0] == 0x03)transmissionValue = 3; //sample name
                else if(rx_buf[0] == 0x04)transmissionValue = 4; //Send Data Check
    
                else if(rx_buf[0] == 0x05)transmissionValue = 5; //log interval
                else if(rx_buf[0] == 0x06)transmissionValue = 6; //Flow Rate
                else if(rx_buf[0] == 0x07)transmissionValue = 7; //Serial Number
                else if(rx_buf[0] == 0x08)transmissionValue = 8; //Run Enable
                else                      transmissionValue = 100; //Not useful data
            }
            
            if(rx_buf[rx_len-1]=='\0' || rx_buf[rx_len-1]=='\n' || rx_buf[rx_len-1] == 0xff){
                if((transmissionValue == 1 || transmissionValue == 2 || transmissionValue == 3 || transmissionValue == 4 || transmissionValue == 5 ||
                    transmissionValue == 6 || transmissionValue == 7) &&  rx_buf[rx_len-1] != 0xff)
                {}else{
                    //if(transmissionValue == 4 ) sendData();
                    if(transmissionValue == 8){
                         runReady = 1;
                         microChannel.attach(NULL,microChannel.RxIrq);
                     }
                    haltBLE = 1;
                    transmissionValue = 0;
                    dataLength = 0;

                }
            }
        }
       
        if(haltBLE!=1){
            
            if((transmissionValue!=100) && (dataLength!= 0)) writeData[dataLength-1] = rx_buf[0];
            
            if(transmissionValue ==100){
                pc.putc(rx_buf[0]); 
            
            }else if(transmissionValue ==1){ //process and store RTC values
                
                //if(dataLength==6)RTC_UPAS.set_time(writeData[0],writeData[1],writeData[2],writeData[3],writeData[3],writeData[4],writeData[5]);//sets chronodot RTC
                if(dataLength==6){
                        //RTC_UPAS.set_time(writeData[0],writeData[1],writeData[2],writeData[3],writeData[3],writeData[4],writeData[5]);//sets chronodot RTC
                        ///////////////////////
                        //sets ST RTC
                        //////////////////////
                        STtime.tm_sec = writeData[0];    // 0-59
                        STtime.tm_min = writeData[1];    // 0-59
                        STtime.tm_hour = writeData[2];   // 0-23
                        STtime.tm_mday = writeData[3];   // 1-31
                        STtime.tm_mon = writeData[4]-1;     // 0-11
                        STtime.tm_year = 100+writeData[5];  // year since 1900 (116 = 2016)
                        time_t STseconds = mktime(&STtime);
                        set_time(STseconds); // Set RTC time 
                    }
    
            }
            else if(transmissionValue ==2){ //process and store sample start/end 
                if(dataLength ==12)E2PROM.write(0x00015, writeData, 12);
                
            }else if(transmissionValue ==3){ //process and store sample name
                if(dataLength ==8)E2PROM.write(0x00001,writeData,8);  
    
            }else if(transmissionValue ==5){ //process and store Log Interval
                 if(dataLength ==1)E2PROM.write(0x00014,writeData,1);
            
            }else if(transmissionValue ==6){ //process and store Flow Rate
                if(dataLength ==4)E2PROM.write(0x00010,writeData,4);
                
            }else if(transmissionValue ==7){ //process and store Serial Number
                if(dataLength ==2)E2PROM.write(0x00034,writeData,2);
            }
            
            dataLength++;        
        }

        rx_len = 0;
    }else{
        while(microChannel.readable())
         uint8_t extract = microChannel.getc();
    }  
    
    
}

void sendData(){
    
    uint8_t sampleTimePassValues[13] = {0x01,};
    uint8_t subjectLabelOriginal[9] = {0x02,};
    uint8_t dataLogOriginal[2] = {0x03,};
    uint8_t flowRateOriginal[5] = {0x04,};
    //uint8_t presetRunModeCheck[1] = {0,}; Commented and currently unused to prevent mem issues
    E2PROM.read(0x00015, sampleTimePassValues+1, 12);
    E2PROM.read(0x00001, subjectLabelOriginal+1,8);
    E2PROM.read(0x00014,dataLogOriginal+1,1);
    E2PROM.read(0x00010,flowRateOriginal+1,4);
    
    for(int i=0; i<13; i++){
         microChannel.putc(sampleTimePassValues[i]);        
    }  
    wait(.25);
        
    for(int i=0; i<9; i++){
        microChannel.putc(subjectLabelOriginal[i]);        
    }  
    wait(.25);
    
    for(int i=0; i<2; i++){
        microChannel.putc(dataLogOriginal[i]);        
    }  
    wait(.25);
    
    for(int i=0; i<5; i++){
        microChannel.putc(flowRateOriginal[i]);        
    } 

    
} 

//////////////////////////////////////////////////////////////
// GPS: Degree-minute format to decimal-degrees
//////////////////////////////////////////////////////////////
double convertDegMinToDecDeg (float degMin)
{
    double min = 0.0;
    double decDeg = 0.0;

    //get the minutes, fmod() requires double
    min = fmod((double)degMin, 100.0);

    //rebuild coordinates in decimal degrees
    degMin = (int) ( degMin / 100 );
    decDeg = degMin + ( min / 60 );

    return decDeg;
}

//////////////////////////////////////////////////////////////
// GPS: Calculate distance from target location
//////////////////////////////////////////////////////////////
double GPSdistanceCalc (float tlat, float tlon)
{
    


float tlatrad, flatrad;
float sdlong,  cdlong;
float sflat, cflat;
float stlat, ctlat;
float delta, denom;

    double distance;
    delta = (flon-tlon)*0.0174532925;
    sdlong = sin(delta);
    cdlong = cos(delta);
    flatrad = (flat)*0.0174532925;
    tlatrad = (tlat)*0.0174532925;
    sflat = sin(flatrad);
    cflat = cos(flatrad);
    stlat = sin(tlatrad);
    ctlat = cos(tlatrad);
    delta = (cflat * stlat) - (sflat * ctlat * cdlong);
    delta = pow(delta,2);
    delta += pow(ctlat * sdlong,2);
    delta = sqrt(delta);
    denom = (sflat * stlat) + (cflat * ctlat * cdlong);
    delta = atan2(delta, denom);
    distance = delta * 6372795;
    return distance;
}


//////////////////////////////////////////////////////////////
//Shutdown Function
//////////////////////////////////////////////////////////////
void check_stop()   // this checks if it's time to stop and shutdown
{
    //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    //UPDATE THIS TO WORK WITH ST RTC INSTEAD
    //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 /*  
    if(RTC_UPAS.compare(startAndEndTime[6], startAndEndTime[7], startAndEndTime[8], startAndEndTime[9], startAndEndTime[10], startAndEndTime[11])) {
        pbKill = 0; // this is were we shut everything down
        //pc.printf("If you're reading this something has gone very wrong.");
    }
*/ 
}

//////////////////////////////////////////////////////////////
//SD Logging Function
//////////////////////////////////////////////////////////////
void log_data()
{

    RGB_LED.set_led(1,1,1);
        
    time_t seconds = time(NULL);
    strftime(timestr, 32, "%y%m%d%H%M%S", localtime(&seconds));

    //RTC_UPAS.get_time(); 
    press = bmesensor.getPressure();
    temp = bmesensor.getTemperature()-5.0;
    rh = bmesensor.getHumidity();
    uv =  lightsensor.getUV();
    movementsensor.getACCEL();
    movementsensor.getCOMPASS();
    compass = movementsensor.getCOMPASS_HEADING();
    accel_x = movementsensor.AccelData.x;
    accel_y = movementsensor.AccelData.y;
    accel_z = movementsensor.AccelData.z;
    accel_comp = pow(accel_x,(float)2)+pow(accel_y,(float)2)+pow(accel_z,(float)2)-1.0;
    mag_x = movementsensor.MagData.x;
    mag_y = movementsensor.MagData.y;
    mag_z = movementsensor.MagData.z;
        
    omronReading = ads.readADC_SingleEnded(0, 0xC583); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
    omronVolt = (omronReading*4.096)/(32768*2);
    
    if(omronVolt<=calibrations.omronVMin) {
            massflow = calibrations.omronMFMin;
    } else if(omronVolt>=calibrations.omronVMax) {
            massflow = calibrations.omronMFMax;
    } else {
            massflow = calibrations.MF4*pow(omronVolt,(float)4)+calibrations.MF3*pow(omronVolt,(float)3)+calibrations.MF2*pow(omronVolt,(float)2)+calibrations.MF1*omronVolt+calibrations.MF0;
    }
    
    atmoRho = ((press-((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)))*100)/(287.0531*(temp+273.15))+((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)*100)/(461.4964*(temp+273.15));
    volflow = massflow/atmoRho;
    sampledVol = sampledVol + ((((float)logInerval)/60.0)*volflow);
    deltaVflow = volflow-volflowSet;
    massflowSet = volflowSet*atmoRho;
    deltaMflow = massflow-massflowSet;    
        
    vInReading = ads.readADC_SingleEnded(1, 0xD583); // read channel 0
    vBlowerReading = ads.readADC_SingleEnded(2, 0xE783); // read channel 0
    omronDiff = ads.readADC_Differential(0x8583); // differential channel 2-3
        
    gps.read(1);
        RGB_LED.set_led(1,1,0);
        gpsspeed = gps.speed;
        gpssatellites =  gps.satellites;
        gpslatitude = gps.lat;
       // gpslat = 'N'; //gps.lat; need to fix this (if statement?)
        gpslongitude = gps.lon;
       // gpslon = 'W'; //gps.lon; need to fix this (if statement?)
        gpsaltitude = gps.altitude;
        
          /*  
            if (abs(gpslatitude) > 0 && abs(gpslongitude) > 0) {
      
            if(gpslat == 'S')
              {
              flat = convertDegMinToDecDeg (gpslatitude) * -1;
              }
              else
              {
              flat = convertDegMinToDecDeg (gpslatitude);
              }
              
              if(gpslon == 'W')
              {
              flon = convertDegMinToDecDeg (gpslongitude) * -1;
              }
              else
              {
              flon = convertDegMinToDecDeg (gpslongitude);
              }
          
                workDistance = GPSdistanceCalc (work_lat, work_lon);
                homeDistance = GPSdistanceCalc (home_lat, home_lon);
              }
              
              if (homeDistance == 99999 && workDistance == 99999) {
            //    digitalWrite (work_yellow_led, HIGH);
            //    digitalWrite (home_green_led, HIGH);
            //    digitalWrite (travel_red_led, HIGH);
                location = 0;
              }
              
              else if (workDistance < 30) {
            //    digitalWrite (work_yellow_led, HIGH);
            //    digitalWrite (home_green_led, LOW);
            //    digitalWrite (travel_red_led, LOW);
                location = 1;
              }
               
              else if (homeDistance < 20) {
            //    digitalWrite (work_yellow_led, LOW);
            //    digitalWrite (home_green_led, HIGH);
            //    digitalWrite (travel_red_led, LOW);
                location = 2;
              }
              
              else {
            //    digitalWrite (work_yellow_led, LOW);
            //    digitalWrite (home_green_led, LOW);
            //    digitalWrite (travel_red_led, HIGH);
                location = 3;
              }
*/
     
    FILE *fp = fopen(filename, "a");
    //fprintf(fp, "%02d,%02d,%02d,%02d,%02d,%02d,",RTC_UPAS.year, RTC_UPAS.month,RTC_UPAS.date,RTC_UPAS.hour,RTC_UPAS.minutes,RTC_UPAS.seconds);
    fprintf(fp, "%s,", timestr);
    fprintf(fp, "%1.3f,%1.3f,%2.2f,%4.2f,%2.1f,%1.3f,", omronVolt,massflow,temp,press,rh,atmoRho);
    fprintf(fp, "%1.3f,%5.1f,%1.1f,%1.1f,%1.1f,%1.1f,", volflow, sampledVol, accel_x, accel_y, accel_z, accel_comp);
    fprintf(fp, "%.1f,%.1f,%.1f,%.3f,%.3f,%.3f,%.1f,", angle_x,angle_y,angle_z,mag_x, mag_y, mag_z,compass);
    fprintf(fp, "%d,%d,%d,%d,%d,%d," ,uv,omronReading, vInReading, vBlowerReading, omronDiff,gasG.getAmps());
    fprintf(fp, "%d,%d,%d,%1.3f,%1.3f,", gasG.getVolts(), gasG.getCharge(),digital_pot_set, deltaMflow, deltaVflow);
    //fprintf(fp, "%f,%f,%06d,%06d\r\n",  gps.lat, gps.lon, (long)gps.date, (long)gps.utc); // test and add in speed, etc that Josh added in to match the adafruit GPS
    fprintf(fp, "%f,%f,%06d,%06d,%f,%d,%f\r\n",  gps.lat, gps.lon, (long)gps.date, (long)gps.utc, gpsspeed, gpssatellites,  gpsaltitude); // test and add in speed, etc that Josh added in to match the adafruit GPS
    fclose(fp);
    free(fp);
    RGB_LED.set_led(0,1,0);


pc.printf("%s,", timestr);


}

//////////////////////////////////////////////////////////////
//Flow Control Function
//////////////////////////////////////////////////////////////
void flowControl()
{
/*        
        RGB_LED.set_led(0,1,0);
        omronReading = ads.readADC_SingleEnded(0, 0xC583); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
        omronVolt = (omronReading*4.096)/(32768*2);
    
        if(omronVolt<=calibrations.omronVMin) {
            massflow = calibrations.omronMFMin;
        } else if(omronVolt>=calibrations.omronVMax) {
            massflow = calibrations.omronMFMax;
        } else {
            massflow = calibrations.MF4*pow(omronVolt,(float)4)+calibrations.MF3*pow(omronVolt,(float)3)+calibrations.MF2*pow(omronVolt,(float)2)+calibrations.MF1*omronVolt+calibrations.MF0;
        }
    
        atmoRho = ((press-((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)))*100)/(287.0531*(temp+273.15))+((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)*100)/(461.4964*(temp+273.15));
        volflow = massflow/atmoRho;
        sampledVol = sampledVol + ((((float)logInerval)/60.0)*volflow);
        deltaVflow = volflow-volflowSet;
        massflowSet = volflowSet*atmoRho;
        deltaMflow = massflow-massflowSet;
        
        if(abs(deltaMflow)>.025) {
            digital_pot_change = (int)(gainFlow*deltaMflow);
    
    
            if(abs(digital_pot_change)>=10) {
                digital_pot_set = (int)(digital_pot_set+ (int)(1*deltaMflow));
                RGB_LED.set_led(1,0,0);
            } else {
                digital_pot_set = (digital_pot_set+ digital_pot_change);
                RGB_LED.set_led(1,1,0);
            }
            
            if(digital_pot_set>=digitalpotMax) {
                 digital_pot_set = digitalpotMax;
                 RGB_LED.set_led(1,0,0);
            } else if(digital_pot_set<=digitalpotMin) {
                 digital_pot_set = digitalpotMin;
                 RGB_LED.set_led(1,0,0);
            }
    
            DigPot.writeRegister(digital_pot_set);
                
        } else {
            RGB_LED.set_led(0,1,0);
        }
        
*/
}
//////////////////////////////////////////////////////////////
//Main Function
//////////////////////////////////////////////////////////////
int main(){
    
    RGB_LED.set_led(0,0,1);
    STtime.tm_sec = 10;    // 0-59
    STtime.tm_min = 30;    // 0-59
    STtime.tm_hour = 9;   // 0-23
    STtime.tm_mday = 22;   // 1-31
    STtime.tm_mon = 2;     // 0-11
    STtime.tm_year = 116;  // year since 1900
    time_t seconds = mktime(&STtime);
    set_time(seconds); // Set RTC time to 16 December 2013 10:05:23 UTC
    wait(5);

/*
motor1.getFault();
    wait(5);
    RGB_LED.set_led(0,0,0);
motor2.getFault();
    wait(5);
    RGB_LED.set_led(1,0,0);
motor3.getFault();
    wait(5);
    RGB_LED.set_led(0,0,0);
motor4.getFault();
    wait(5);
    RGB_LED.set_led(1,0,0);

    RGB_LED.set_led(1,0,0);
    motor1.drive(254); //closed = 253, open = 254
        wait(10);
    motor1.stop();
    RGB_LED.set_led(0,0,0);
        

    motor2.drive(254); //closed = 253, open = 254
        wait(10);
    motor2.stop();
    RGB_LED.set_led(1,0,0);

    motor3.drive(254); //closed = 253, open = 254
        wait(10);
    motor3.stop();
    RGB_LED.set_led(0,0,0);


    motor4.drive(254); //closed = 253, open = 254
        wait(10);
    motor4.stop();
    RGB_LED.set_led(0,0,1);




    pc.baud(115200);  // set what you want here depending on your terminal program speed
    pc.printf("\f\n\r-------------Startup-------------\n\r");
    wait(0.5);
    
    
    uint8_t serialNumberAndType[6] = {0x50,0x53};
    
    E2PROM.read(0x00034,serialNumberAndType+2,2);
   
    int tempSerialNum = serialNumberAndType[2]+serialNumberAndType[3];
    int serialNumDigits[4];
    serialNumDigits[0] = tempSerialNum / 1000 % 10;
    serialNumDigits[1] = tempSerialNum / 100 % 10;
    serialNumDigits[2] = tempSerialNum / 10 % 10;
    serialNumDigits[3] = tempSerialNum  % 10;
    
    serialNumberAndType[2] = serialNumDigits[0]+48;
    serialNumberAndType[3] = serialNumDigits[1]+48;
    serialNumberAndType[4] = serialNumDigits[2]+48;
    serialNumberAndType[5] = serialNumDigits[3]+48;
    
    RGB_LED.set_led(0,1,0);
    
    pc.attach(pc_recv);
    microChannel.attach(uartMicro,microChannel.RxIrq);
    microChannel.baud(115200);  
    microChannel.printf("$$$");
    wait(0.5);
    microChannel.printf("SN,");
    for(int i=0;i<6;i++)microChannel.putc(serialNumberAndType[i]);
    microChannel.printf("\r");
    wait(0.5);
    microChannel.printf("A\r");
    wait(0.5);
    microChannel.printf("---\r");
    wait(0.5);
    
    //RGB_LED.set_led(1,1,1);
    while(runReady!=1) {
        wait(1);
        pc.printf("Waiting for BLE instruction");
    
    }
    
   
    E2PROM.read(0x00015, startAndEndTime, 12); //Grab start and end times from EEPROM
    RGB_LED.set_led(0,1,0);
    
    //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    //UPDATE THIS TO WORK WITH ST RTC INSTEAD
    //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

    while(!RTC_UPAS.compare(startAndEndTime[0], startAndEndTime[1], startAndEndTime[2], startAndEndTime[3], startAndEndTime[4], startAndEndTime[5])) {  // this while waits for the start time by looping until the start time
            wait(0.5);
            
            RTC_UPAS.get_time(); 

    }


    
    //Get the proper serial number
    uint8_t serialBytes[2] = {0,};
    E2PROM.read(0x00034, serialBytes,2);    
    serial_num = ((uint16_t)serialBytes[1] << 8) | serialBytes[0];
    calibrations.initialize(serial_num);
    
    uint8_t logByte[1] = {0,};
    E2PROM.read(0x00014,logByte,1);
    logInerval = logByte[0];
    
    //Use the flow rate value stored in eeprom
    uint8_t flowRateBytes[4] = {0,};
    E2PROM.read(0x00010,flowRateBytes,4);
    E2PROM.byteToFloat(flowRateBytes, &volflowSet);
    
    if(volflowSet<=1.0) {
        gainFlow = 100;
    } else if(volflowSet>=2.0) {
        gainFlow = 25;
    } else {
        gainFlow = 25;
    }
*/
    RGB_LED.set_led(1,0,0);
    press = bmesensor.getPressure();
    temp = bmesensor.getTemperature();
    rh = bmesensor.getHumidity();

    atmoRho = ((press-((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)))*100)/(287.0531*(temp+273.15))+((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)*100)/(461.4964*(temp+273.15));
    massflowSet = volflowSet*atmoRho;

    DigPot.writeRegister(digital_pot_setpoint);
    wait(1);
    blower = 1;

    uint8_t subjectLabelOriginal[8] = {0,};
    E2PROM.read(0x00001, subjectLabelOriginal,8); 


        
    seconds = time(NULL);
    strftime(timestr, 32, "%y-%m-%d-%H=%M=%S", localtime(&seconds));

    //sprintf(filename, "/sd/UPAS%04dLOG_%02d-%02d-%02d_%02d=%02d=%02d_%c%c%c%c%c%c%c%c.txt",serial_num,RTC_UPAS.year,RTC_UPAS.month,RTC_UPAS.date,RTC_UPAS.hour,RTC_UPAS.minutes,RTC_UPAS.seconds,subjectLabelOriginal[0],subjectLabelOriginal[1],subjectLabelOriginal[2],subjectLabelOriginal[3],subjectLabelOriginal[4],subjectLabelOriginal[5],subjectLabelOriginal[6],subjectLabelOriginal[7]);
    //sprintf(filename, "/sd/UPAS_TboardtestLog_%s_%c%c%c%c%c%c%c%c.txt", timestr,subjectLabelOriginal[0],subjectLabelOriginal[1],subjectLabelOriginal[2],subjectLabelOriginal[3],subjectLabelOriginal[4],subjectLabelOriginal[5],subjectLabelOriginal[6],subjectLabelOriginal[7]);
    sprintf(filename, "/sd/UPAS_TboardtestLog_%s.txt", timestr);
    FILE *fp = fopen(filename, "w");
    fclose(fp);

/*
    omronReading = ads.readADC_SingleEnded(0, 0xC583); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
    omronVolt = (omronReading*4.096)/(32768*2);
    if(omronVolt<=calibrations.omronVMin) {
        massflow = calibrations.omronMFMin;
    } else if(omronVolt>=calibrations.omronVMax) {
        massflow = calibrations.omronMFMax;
    } else {
        massflow = calibrations.MF4*pow(omronVolt,(float)4)+calibrations.MF3*pow(omronVolt,(float)3)+calibrations.MF2*pow(omronVolt,(float)2)+calibrations.MF1*omronVolt+calibrations.MF0;
    }
    deltaMflow = massflow-massflowSet;
    digital_pot_set = digital_pot_setpoint;
    wait(5);

    //---------------------------------------------------------------------------------------------//
    //Sets the flow withen +-1.5% of the desired flow rate based on mass flow

    while(abs(deltaMflow)>.025) {

        omronReading = ads.readADC_SingleEnded(0, 0xC583); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
        omronVolt = (omronReading*4.096)/(32768*2);
        //Mass Flow tf from file: UPAS v2 OSU-PrimaryFlowData FullSet 2015-05-29 CQ mods.xlsx
        if(omronVolt<=calibrations.omronVMin) {
            massflow = calibrations.omronMFMin;
        } else if(omronVolt>=calibrations.omronVMax) {
            massflow = calibrations.omronMFMax;
        } else {
            massflow = calibrations.MF4*pow(omronVolt,(float)4)+calibrations.MF3*pow(omronVolt,(float)3)+calibrations.MF2*pow(omronVolt,(float)2)+calibrations.MF1*omronVolt+calibrations.MF0;
        }

        atmoRho = ((press-((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)))*100)/(287.0531*(temp+273.15))+((6.1078*pow((float)10,(float)((7.5*temp)/(237.3+temp))))*(rh/100)*100)/(461.4964*(temp+273.15));
        volflow = massflow/atmoRho;
        massflowSet = volflowSet*atmoRho;
        deltaMflow = massflow-massflowSet;

        digital_pot_set = (int)(digital_pot_set+(int)((gainFlow*deltaMflow)));
        if(digital_pot_set>=digitalpotMax) {
            digital_pot_set = digitalpotMax;
        } else if(digital_pot_set<=digitalpotMin) {
            digital_pot_set = digitalpotMin;
        }

        wait(2);
        DigPot.writeRegister(digital_pot_set);
        pc.printf("%d,\r\n", digital_pot_set);
        wait(1);


    }
*/
    sampledVol = 0.0;
    RGB_LED.set_led(0,1,0);

  //  stop.attach(&check_stop, 9);    // check if we should shut down every 9 number seconds, starting after the start.
    logg.attach(&log_data, logInerval);
    //flowCtl.attach(&flowControl, 1);
            

    //** end of initalization **//
    //---------------------------------------------------------------------------------------------//
    //---------------------------------------------------------------------------------------------//
    // Main Control Loop

    while (1) {
        // Do other things...
        /*
        blower = 1;
        wait(5);
        blower = 0;
        wait(5);
        */
    }
    



}