File content as of revision 35:e0bdd6389a75:

#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          pumps(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
InterruptIn           bcs1(PC_9); //Charge complete if High. Connected but currently unused. (MCP73871) http://www.mouser.com/ds/2/268/22090a-52174.pdf
InterruptIn           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, 0);
Max_M8 gps(PB_9, PB_8,(0x84));   

/////////////////////////////////////////////
//Hbridge Valve Control
/////////////////////////////////////////////


DRV8830    schoolF1(PB_9, PB_8, 0xC4); //Work/School Filter
DRV8830    homeF2(PB_9, PB_8, 0xCA); //Home Filter
DRV8830    transitF3(PB_9, PB_8, 0xCC); //Transit Filter
DRV8830    blankF4(PB_9, PB_8, 0xCE); //Blank Filter
DigitalIn  hb1_school(PA_6);
DigitalIn  hb2_home(PA_7);
DigitalIn  hb3_transit(PA_5);
DigitalIn  hb4_blank(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, PullUp);

/////////////////////////////////////////////
//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;

bool ledOn = 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 vInReadingLast;
int vBlowerReading;
int omronDiff;
float omronVolt; //V
int omronReading;
float atmoRho; //g/L

int amps;
int bVolt;
int bFuel;
//bool pumpOn;
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 = 30; //min = 0x7F, max = 0x00
int digital_pot_set;
int digital_pot_change;
int digitalpotMax = 127;
int digitalpotMin = 10;

int dutyUp;
int dutyDown;

bool    gpsFix;
uint8_t gpssatellites = 0;
double  gpsspeed = 0.0;
double  gpscourse = 0.0;
double  gpslatitude = 0.0;
double  gpslongitude = 0.0;
float   gpsaltitude = 0.0;

float home_lat  = 40.00000;    //40.580508;
float home_lon  = -105.000000; //-105.081823;
float work_lat  = 40.100000;   //40.594062; //40.569136;
float work_lon  = -105.100000; //-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 if(rx_buf[0] == 0x0A)transmissionValue = 10; //GPS Coordinates
                else if(rx_buf[0] == 0x0B)transmissionValue = 11; //GPS Coordinates (Second Set)
                //else if(rx_buf[0] == 0x30)RGB_LED.set_led(1,0,0);
                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 || transmissionValue ==10) &&  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(fileWrite == 1){
                        //FILE *fp = fopen(gpsConfigFilename, "a");    
                        //fprintf(fp,"HELLO");
                        //fclose(fp); 
                        //free(fp);
                        //fileWrite=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);
            }else if (transmissionValue == 10){
                if(dataLength == 16)E2PROM.write(0x00050,writeData,16);
            }else if (transmissionValue == 11){
                if(dataLength == 8)E2PROM.write(0x00060,writeData,8);
            }
        
            dataLength++;        
        }

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

void sendData(){
    
    //First byte is designator for the App
    uint8_t sampleTimePassValues[13] = {0x01,0x00,0x00,0x0A,0x01,0x01,0x10,0x00,0x00,0x0A,0x01,0x01,0x10};
    uint8_t subjectLabelOriginal[9] = {0x02,0x52,0x45,0x53,0x45,0x54,0x5F,0x5F,0x5f};
    uint8_t dataLogOriginal[2] = {0x03,0x0A,};
    uint8_t flowRateOriginal[5] = {0x04,0x00,0x00,0x80,0x3F};
    uint8_t serialBytes[3] = {0x07,0x00,0x00};
    uint8_t latLongSchoolOriginal[17] = {0x0A,0x00,0x00,0x80,0x3F,0x00,0x00,0x80,0x3F,0x00,0x00,0x80,0x3F,0x00,0x00,0x80,0x3F};
    uint8_t latLongHome2[9] = {0x0B,0x00,0x00,0x80,0x3F,0x00,0x00,0x80,0x3F};
    // Latitude School EEPROM = 0x50-0x53
    // Longitude School EEPROM = 0x54-0x57
    // Latitude Home EEPROM = 0x58-0x5B
    // Longitude Home EEPROM = 0x5C-0x5F
    uint8_t NEW_EEPROM_CHECK[1] = {0,}; //THIS IS USED TO ENSURE COOPERATION WITH MOBILE APPS
    uint8_t TERMINATE_BYTE[1] = {0xff,}; //used for compatibility with android app
    
    //NEW EEPROM Check bit = 0x75
    E2PROM.read(0x00075,NEW_EEPROM_CHECK,1);
    
    if(NEW_EEPROM_CHECK[0] == 0x0A){
        E2PROM.read(0x00015, sampleTimePassValues+1, 12);
        E2PROM.read(0x00001, subjectLabelOriginal+1,8);
        E2PROM.read(0x00014,dataLogOriginal+1,1);
        E2PROM.read(0x00010,flowRateOriginal+1,4);
        E2PROM.read(0x00034,serialBytes+1,2);
        E2PROM.read(0x00050,latLongSchoolOriginal+1,16);
        E2PROM.read(0x00060,latLongHome2+1,8);
    }else{
        NEW_EEPROM_CHECK[0] = 0x0A;
        E2PROM.write(0x00075,NEW_EEPROM_CHECK,1);
        E2PROM.write(0x00015, sampleTimePassValues+1, 12);
        E2PROM.write(0x00001, subjectLabelOriginal+1,8);
        E2PROM.write(0x00014,dataLogOriginal+1,1);
        E2PROM.write(0x00010,flowRateOriginal+1,4);
        E2PROM.write(0x00034,serialBytes+1,2);
        E2PROM.write(0x00050,latLongSchoolOriginal+1,16);
        E2PROM.write(0x00060,latLongHome2+1,8);
    }

    
    for(int i=0; i<13; i++){
         microChannel.putc(sampleTimePassValues[i]);        
    }  
    wait(.15);
        
    for(int i=0; i<9; i++){
        microChannel.putc(subjectLabelOriginal[i]);        
    }  
    wait(.15);
    
    for(int i=0; i<2; i++){
        microChannel.putc(dataLogOriginal[i]);        
    }  
    wait(.15);
    
    for(int i=0; i<5; i++){
        microChannel.putc(flowRateOriginal[i]);        
    }
    wait(.15);
    
    for(int i=0;i<17;i++){
        microChannel.putc(latLongSchoolOriginal[i]);
    } 
    wait(.15);
    
    for(int i=0;i<9;i++){
        microChannel.putc(latLongHome2[i]);
    } 
    wait(.15);
    microChannel.putc(TERMINATE_BYTE[0]);

    
}

//////////////////////////////////////////////////////////////
// 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 = (gpslongitude-tlon)*0.0174532925;
    sdlong = sin(delta);
    cdlong = cos(delta);
    flatrad = (gpslatitude)*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()
{
    //Get time and set RTC 
    ///////////////////////////
    time_t seconds = time(NULL);
    strftime(timestr, 32, "%y%m%d%H%M%S", localtime(&seconds));
    RTC_UPAS.get_time(); 
    
    //Get Sensor Data except GPS
    ////////////////////////////
    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;
    vInReadingLast = vInReading;
    vInReading = ads.readADC_SingleEnded(1, 0xD583); // read channel 0
    amps = gasG.getAmps();
    bVolt = gasG.getVolts(); 
    bFuel = gasG.getCharge();
    
    //Check for fully charged battery
    if(bVolt > 1750 && amps > 8191) {
               RGB_LED.set_led(0,1,0);
    //Check for battery with ~2 hours left of runtime at 2lpm or if after 8pm to remind user to plug in sampler            
    }else if(amps > 8191 && (RTC_UPAS.hour >=20 || bVolt < 1500)) {
        if(ledOn) {
            RGB_LED.set_led(0,0,0);
            ledOn = 0;
        }else {
            RGB_LED.set_led(1,0,0);
            ledOn = 1;
        }
    //No LED on when not low battery and not fully charged    
    }else{
        RGB_LED.set_led(0,0,0);
    }
    
    
    // Get GPS Data
    //////////////////////////////
    //if(gpsEN ==1){  
    
        gpsFix = gps.read(1);
        gpsspeed = gps.speed;
        //gpscourse = gps.course;
        gpssatellites =  gps.satellites;
        gpslatitude = gps.lat;
        gpslongitude = gps.lon;
        gpsaltitude = gps.altitude;
      
        if(gpsFix){
            workDistance = GPSdistanceCalc (work_lat, work_lon);
            homeDistance = GPSdistanceCalc (home_lat, home_lon);
            RGB_LED.set_led(0,0,0);
            
            if(workDistance < 50) {
                    location = 1;
                    //RGB_LED.set_led(0,1,1);
            }else if(homeDistance < 50) { // 25 or 30 m instead?
                    location = 2;
                    //RGB_LED.set_led(1,0,1);
            }else{
                    location = 3;
                    //RGB_LED.set_led(1,1,1);
                  }
        
        }else if(homeDistance == 99999 && workDistance == 99999){
                location = 0;
                RGB_LED.set_led(1,1,0);
        }
   
//}
    
    //Check for 3.3V rail cut out and turn off pumps in this event
    if(vInReading > 5950 && amps > 8191) {
        pumps = 0;
        wait(1);
    //Turn pumps back on once the sampler is plugged in and charging after pumps shutoff and 3.3V rail drops out
    } else if(pumps == 0 && amps < 8191) {
        
        // If pumps are plugged in the next morning assume the sampler is at school if after 8 if no GPSfix is available
        if(gpsFix == 0 && RTC_UPAS.hour>8){
            gpslatitude =   work_lat; // specific to Rivendell Study. In case student forgets to plug in and teachers catch this. Assume if plugged in after 8 and no GPS signal will change to proper valve. Hopefully...
            gpslongitude =  work_lon; // specific to Rivendell Study. In case student forgets to plug in and teachers catch this. Assume if plugged in after 8 and no GPS signal will change to proper valve. Hopefully...
        }
            //Adjust valves to ensure everything is in proper place before pumps restart
            /*
            schoolF1.getFault();
            homeF2.getFault();
            transitF3.getFault();
            blankF4.getFault();

            schoolF1.drive(254); //closed = 253, open = 254
            homeF2.drive(253); //closed = 253, open = 254
            transitF3.drive(253); //closed = 253, open = 254
            blankF4.drive(253); //closed = 253, open = 254
            wait(1);
            schoolF1.stop();
            homeF2.stop();
            transitF3.stop();
            blankF4.stop();
            */
            //pumps = 1;
            
    }
          
   
    
    if(pumps == 1){     
        omronReading = ads.readADC_SingleEnded(0, 0xC383); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
        omronVolt = (omronReading*4.096)/(32768*1);
        
        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;    
            
        vBlowerReading = ads.readADC_SingleEnded(2, 0xE783); // read channel 0
        omronDiff = ads.readADC_Differential(0x8583); // differential channel 2-3
    }
    

   
    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,amps);
    fprintf(fp, "%d,%d,%d,%1.3f,%1.3f,", bVolt, bFuel,digital_pot_set, deltaMflow, deltaVflow);
    fprintf(fp, "%f,%f,%06d,%06d,", gpslatitude, gpslongitude, (long)gps.date, (long)gps.utc); 
    //fprintf(fp, "%f,%d,%f,%f,%d,", gpsspeed, gpssatellites, gpscourse, gpsaltitude, gpsFix);
    fprintf(fp, "%f,%d,%f,%d,", gpsspeed, gpssatellites, gpsaltitude, gpsFix);
    fprintf(fp, "%f,%f,%d,%d\r\n", homeDistance, workDistance, location, pumps == 1); // test and add in speed, etc that Josh added in to match the adafruit GPS
    fclose(fp);
    free(fp);
    






}

//////////////////////////////////////////////////////////////
//Flow Control Function
//////////////////////////////////////////////////////////////
void flowControl()
{
        
        //RGB_LED.set_led(0,1,0);
        omronReading = ads.readADC_SingleEnded(0, 0xC383); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
        omronVolt = (omronReading*4.096)/(32768*1);
    
        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);
  
 /*  
    while(1){
    if(sdCD == 0){
       RGB_LED.set_led(0,1,0);
    }else{
        RGB_LED.set_led(1,0,0);
    }
    
    wait(10); 
    }


    schoolF1.getFault();
    homeF2.getFault();
    transitF3.getFault();
    blankF4.getFault();
    
    schoolF1.drive(253); //closed = 253, open = 254
    homeF2.drive(253); //closed = 253, open = 254
    transitF3.drive(253); //closed = 253, open = 254
    blankF4.drive(253); //closed = 253, open = 254
    
    wait(1);
    schoolF1.stop();
    homeF2.stop();
    transitF3.stop();
    blankF4.stop();
    */
    
    schoolF1.getFault();
    homeF2.getFault();
    transitF3.getFault();
    blankF4.getFault();
    
    schoolF1.drive(253); //closed = 253, open = 254
    homeF2.drive(254); //closed = 253, open = 254
    transitF3.drive(253); //closed = 253, open = 254
    blankF4.drive(253); //closed = 253, open = 254
    
    wait(1);
    schoolF1.stop();
    homeF2.stop();
    transitF3.stop();
    blankF4.stop();
    
      

    gpsEN = 1;
    wait(1);
    BT_SW = 1;
    wait(1);
    BT_IRST = 1;
    wait(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,}; //ex) PS0018 // 0x50,0x53 <- ASCII 80 + 83 (PS) //0x4d,0x53 <- ASCII  77 + 83 (MS) 
   E2PROM.read(0x00034,serialNumberAndType+2,2);
   
    int tempSerialNum = ((serialNumberAndType[2]-48)*10 + serialNumberAndType[3]-48);
    if(tempSerialNum < 18){
        serialNumberAndType[0] = 0x4D;
    }
    
    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;
    
    /*
    serialNumberAndType[2] = serialNumDigits[0];
    serialNumberAndType[3] = serialNumDigits[1];
    serialNumberAndType[4] = serialNumDigits[2];
    serialNumberAndType[5] = serialNumDigits[3];
    */
    
   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\r\n");
    
    }
    
   
    E2PROM.read(0x00015, startAndEndTime, 12); //Grab start and end times from EEPROM
    RGB_LED.set_led(0,1,0);
    
    
    //Pull MicroEnviornment Lat/Lons from EEPROM
    // Latitude School EEPROM = 0x50-0x53
    // Longitude School EEPROM = 0x54-0x57
    // Latitude Home EEPROM = 0x58-0x5B
    // Longitude Home EEPROM = 0x5C-0x5F
    
    uint8_t workLat[4] = {0,};
    E2PROM.read(0x00050,workLat,4);
    E2PROM.byteToFloat(workLat, &work_lat);
    
    uint8_t workLon[4] = {0,};
    E2PROM.read(0x00054,workLon,4);
    E2PROM.byteToFloat(workLon, &work_lon);
    
    uint8_t homeLat[4] = {0,};
    E2PROM.read(0x00058,homeLat,4);
    E2PROM.byteToFloat(homeLat, &home_lat);
    
    uint8_t homeLon[4] = {0,};
    E2PROM.read(0x0005C,homeLon,4);
    E2PROM.byteToFloat(homeLon, &home_lon);
    
    pc.printf("%f,%f\r\n%f,%f\r\n", home_lat, home_lon, work_lat, work_lon);
    
    //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    //UPDATE THIS TO WORK WITH ST RTC INSTEAD
    //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

    BT_SW = 0;
    wait(1);
    BT_IRST = 0;
    wait(1);

    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 subject line information
    uint8_t subjectLabelOriginal[8] = {0,};
    E2PROM.read(0x00001, subjectLabelOriginal,8);
    
    //Get the proper serial number
    uint8_t serialBytes[2] = {0,};
    E2PROM.read(0x00034,serialBytes,2);    
    serial_num = (uint16_t)(((serialBytes[0]-48)*10 + serialBytes[1]-48));
    
    
////////////////////////////////////////////////////////////////////
    //Temporary fix for setting serial_num
////////////////////////////////////////////////////////////////////
    //uint8_t serialsubjectLabelOriginal[2] = {0,};
    //E2PROM.read(0x00001, serialsubjectLabelOriginal,2);
    //uint8_t newserialBytes[2] = {0,};
    
    if(subjectLabelOriginal[2] == 126){ 
            E2PROM.write(0x00034,subjectLabelOriginal,2); 
            serial_num = (uint16_t)(((subjectLabelOriginal[0]-48)*10 + subjectLabelOriginal[1]-48));
    }
     
    //----------------------------------------------
    calibrations.initialize(serial_num);
    pc.printf("%d\r\n", serial_num);
    pc.printf("%f\r\n",calibrations.MF4);
    //----------------------------------------------
////////////////////////////////////////////////////////////////////
    
    
    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);
    pumps = 1;
    //pumpOn = 1;


    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;
    
    //Digtal pot tf from file: UPAS v2 OSU-PrimaryFlowData FullSet 2015-05-29 CQ mods.xlsx
    digital_pot_setpoint = (int)floor(calibrations.DP4*pow(massflowSet,4)+calibrations.DP3*pow(massflowSet,3)+calibrations.DP2*pow(massflowSet,2)+calibrations.DP1*massflowSet+calibrations.DP0); //min = 0x7F, max = 0x00

    if(digital_pot_setpoint>=digitalpotMax) {
        digital_pot_setpoint = digitalpotMax;
    } else if(digital_pot_setpoint<=digitalpotMin) {
        digital_pot_setpoint = digitalpotMin;
    }

    pc.printf("%d\r\n", digital_pot_setpoint);
    DigPot.writeRegister(digital_pot_setpoint);
    wait(1);
    pumps = 1;
  
    


        
    time_t seconds = time(NULL);
    strftime(timestr, 32, "%y-%m-%d-%H=%M=%S", localtime(&seconds));
    if(tempSerialNum < 18){
        sprintf(filename, "/sd/MS%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]);
    
    }
    else{
        sprintf(filename, "/sd/PS%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, 0xC383); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
    omronVolt = (omronReading*4.096)/(32768*1);
    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, 0xC383); // read channel 0 PGA = 2 : Full Scale Range = 2.048V
        omronVolt = (omronReading*4.096)/(32768*1);
        //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);
    wait(1);
    RGB_LED.set_led(0,0,0);

    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, 3);




/*    
    wait(60);
    
    schoolF1.getFault();
    homeF2.getFault();
    transitF3.getFault();
    blankF4.getFault();
    
    schoolF1.drive(254); //closed = 253, open = 254
    homeF2.drive(253); //closed = 253, open = 254
    transitF3.drive(253); //closed = 253, open = 254
    blankF4.drive(253); //closed = 253, open = 254
    
    wait(1);
    schoolF1.stop();
    homeF2.stop();
    transitF3.stop();
    blankF4.stop();
            

wait(60);
    
    schoolF1.getFault();
    homeF2.getFault();
    transitF3.getFault();
    blankF4.getFault();
    
    schoolF1.drive(253); //closed = 253, open = 254
    homeF2.drive(254); //closed = 253, open = 254
    transitF3.drive(253); //closed = 253, open = 254
    blankF4.drive(253); //closed = 253, open = 254
    
    wait(1);
    schoolF1.stop();
    homeF2.stop();
    transitF3.stop();
    blankF4.stop();
    
    wait(60);
    
    schoolF1.getFault();
    homeF2.getFault();
    transitF3.getFault();
    blankF4.getFault();
    
    schoolF1.drive(253); //closed = 253, open = 254
    homeF2.drive(253); //closed = 253, open = 254
    transitF3.drive(254); //closed = 253, open = 254
    blankF4.drive(253); //closed = 253, open = 254
    
    wait(1);
    schoolF1.stop();
    homeF2.stop();
    transitF3.stop();
    blankF4.stop();
    
    wait(60);
    
    schoolF1.getFault();
    homeF2.getFault();
    transitF3.getFault();
    blankF4.getFault();
    
    schoolF1.drive(253); //closed = 253, open = 254
    homeF2.drive(253); //closed = 253, open = 254
    transitF3.drive(253); //closed = 253, open = 254
    blankF4.drive(254); //closed = 253, open = 254
    
    wait(1);
    schoolF1.stop();
    homeF2.stop();
    transitF3.stop();
    blankF4.stop();
*/

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

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



}