File content as of revision 9:8646fd501832:

#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" 
//Serial pc(USBTX, USBRX);
//Serial microChannel(USBTX, USBRX); // tx, rx Appears there is a conflict in the mbed code (possibly already assigned to SERIAL_TX, SERIAL_RX, USBTX, USBRX need to reassign these values)
// However still an issue with the BLE not reading the EEPROM with the old pin assignments Jake had.
Serial microChannel(D8, D2); // tx, rx
//Timer t;
struct tm tt;

I2C                 i2c(D14, D15);
Adafruit_ADS1115    ads(&i2c);
MCP40D17            DigPot(&i2c);
BME280              bmesensor(D14, D15);
STC3100             gasG(D14, D15);
//DigitalOut          blower(D8, 0);
DigitalOut          pbKill(PC_12, 1);
DigitalOut          bleRTS(PB_14, 0);
DigitalOut          bleCTS(PB_13, 0);
LSM303              movementsensor(D14, D15);
SI1145              lightsensor(D14, D15);
NCP5623BMUTBG       RGB_LED(D14, D15);
CronoDot            RTC_UPAS(D14, D15);
EEPROM              E2PROM(D14, D15);
//DigitalOut          GPS_EN(p4,0);       //pin 4 is used to enable and disable the GPS, in order to recive serial communications
Calibration         calibrations(1);     //Default serial/calibration if there are no values for the selected option


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

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

int dutyUp = 4;
int dutyDown = 3;

// variables are only place holders for the US_Menu //
int refreshtime;
//int refresh_Time = 10;   // refresh time in s, note calling read_GPS()(or similar) will still take how ever long it needs(hopefully < 1s)
float home_lat, home_lon, work_lat, work_lon;
//*************************************************//

char filename[] = "/sd/XXXX0000LOG000000000000---------------.txt";
SDFileSystem sd(D4, D5, D3, D10, "sd"); // I believe this matches Todd's pinout, let me know if this doesn't work. (MOSI, MISO, SCK, SEL)

void sendData(); 
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 to 16 December 2013 10:05:23 UTC
                    }
    
            }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]);        
    } 

    
} 

//////////////////////////////////////////////////////////////
//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(1,1,0);
        
    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();
        
    
    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\r\n", gasG.getVolts(), gasG.getCharge(),digital_pot_set, deltaMflow, deltaVflow);
    fclose(fp);
    free(fp);
    RGB_LED.set_led(1,0,0);

}

//////////////////////////////////////////////////////////////
//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)>=50) {
                digital_pot_set = (int)(digital_pot_set+(int)((10.0*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(){

    //wait(10);
    //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); 
    
    time_t 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/UPASboardtest_%s.txt", timestr);
    FILE *fp = fopen(filename, "w");
    fclose(fp);


    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...
    }
    



}