File content as of revision 3:122bfc998c4c:

#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(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(D9, 0);
DigitalOut          pbKill(D7, 1);
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

Timeout         stop;   //This is the stop call back object
Timeout         logg;   //This is the logging call back object

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


float press = 1.1;
float temp = 75.5;
float rh = 12.1;

int uv = 8;
int vis = 7;
int ir = 6;

float compass = 0.1;
float accel_x = 0.2;
float accel_y = 0.3;
float accel_z = 0.4;
float accel_comp = 0.5;
float angle_x = 0.6;
float angle_y = 0.7;
float angle_z = 0.8;
float mag_x = 0.9;
float mag_y = 1.0;
float mag_z = 1.2;

int vInReading = 18;
int vBlowerReading = 19;
int omronDiff = 20;
float omronVolt = 1.2; //V
int omronReading = 100;
float atmoRho = 1.5; //g/L

float massflow = 87.6; //g/min
float volflow = 88.8; //L/min
float volflowSet = 1.0; //L/min
int   logInerval = 10; //seconds
double secondsD = 0;
double lastsecondD = 0;
float massflowSet = 19.2;
float deltaVflow = 0.0;
float deltaMflow = 0.0;
float gainFlow = 98.1;
float sampledVol = 2.0; //L, total sampled volume

int digital_pot_setpoint = 5 ; //min = 0x7F, max = 0x00
int digital_pot_set = 6;
int digital_pot_change = 7;
int digitalpotMax = 127;
int digitalpotMin = 2;

int dutyUp = 4;
int dutyDown = 3;

// variables are only place holders for the US_Menu //
int refreshtime = 6;
float home_lat, home_lon, work_lat, work_lon;
//*************************************************//

//int refresh_Time = 10;   // refresh time in s, note calling read_GPS()(or similar) will still take how ever long it needs(hopefully < 1s)

char filename[] = "/sd/XXXX0000LOG000000000000---------------.txt";

SDFileSystem sd(D11, D12, D13, D10, "sd"); // I believe this matches Todd's pinout, let me know if this doesn't work. (p12, p13, p15, p14)

void sendData(); 

//int timeout = 2;

//void pc_recv(void){
//    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,};

void uartMicro(void){
    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]);
    
            }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]);        
    } 

    
} 

void check_stop()   // this checks if it's time to stop and shutdown
{
    
    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.");
    }
    stop.detach();
    stop.attach(&check_stop, 9);
    
}
    int r = 1;
    int g = 0;
    int b = 1;

void log_data()
{


    RGB_LED.set_led(r,g,b);
    logg.detach();
    logg.attach(&log_data, logInerval);     // reading and logging data must take significintly less than 0.5s. This can be increased.
    
    RTC_UPAS.get_time();
    
    secondsD = RTC_UPAS.seconds;
    lastsecondD = secondsD;

    omronVolt = (omronReading*4.096)/(32768*2);

    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, "%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);
    //wait_ms(5);
    
}
 
int main(){
    
    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);
    //timeout=2;
    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;

    //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");
    
    }
    
    
    //wait(1);
    
    E2PROM.read(0x00015, startAndEndTime, 12); //Grab start and end times from EEPROM
    RGB_LED.set_led(0,1,0);
    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];
    
    stop.attach(&check_stop, 30);    // check if we should shut down every 9 seconds, starting 60s after the start.

    //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;
    //Digtal pot tf from file: UPAS v2 OSU-PrimaryFlowData FullSet 2015-05-29 CQ mods.xlsx




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

    uint8_t subjectLabelOriginal[8] = {0,};
    E2PROM.read(0x00001, subjectLabelOriginal,8);        
    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]);
    FILE *fp = fopen(filename, "w");
    fclose(fp);

    //---------------------------------------------------------------------------------------------//
    //Following lines are needed to enter into the initiallization flow control loop

    wait(5);


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



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


    //logg.attach(&log_data, 30); // uses callbacks or block Interrupts for anything that uses i2c
    while(!RTC_UPAS.compare(startAndEndTime[6], startAndEndTime[7], startAndEndTime[8], startAndEndTime[9], startAndEndTime[10], startAndEndTime[11])){
        wait(logInerval);
        RGB_LED.set_led(1,1,0);
        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, "%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);
    }
    RGB_LED.set_led(1,0,0);

}