File content as of revision 94:c57720890e76:

#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 "US_Menu.h"
#include "BLEDevice.h"
#include "Calibration.h"
#include "UPAS_Service.h"


#define SERIAL_BAUD_RATE    9600
#define SCL         20
#define SDA         22





uint8_t startAndEndTime[12] = {0,}; 
const static char     DEVICE_NAME[] = "UPAS"; //Will hold the actual name of the whichever UPAS is being connected to
static const uint16_t uuid16_list[] = {UPAS_Service::UPAS_SERVICE_UUID}; //Currently a custom 16-bit representation of 128-bit UUID
BLEDevice   ble;
UPAS_Service *upasServicePtr;
//BLE_Menu    bleMenu(ble, txPayload, rxPayload, uart_base_uuid_rev, uart_base_uuid, uartService);

I2C                 i2c(p22, p20);
Adafruit_ADS1115    ads(&i2c);
MCP40D17            DigPot(&i2c);
BME280              bmesensor(p22, p20);
STC3100             gasG(p22, p20);
Serial              pc(USBTX, USBRX);
DigitalOut          blower(p29, 0);
DigitalOut          pbKill(p18, 1);
LSM303              movementsensor(p22, p20);
SI1145              lightsensor(p22, p20);
NCP5623BMUTBG       RGB_LED(p22, p20);
CronoDot            RTC(p22, p20);
EEPROM              E2PROM(p22, p20);
US_Menu             Menu;
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;
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 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;
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 = 2;

int dutyUp;
int dutyDown;

// variables are only place holders for the US_Menu //
int refreshtime;
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 device_name[] = "---------------";
char filename[] = "/sd/XXXX0000LOG000000000000---------------.txt";
SDFileSystem sd(SPIS_PSELMOSI, SPIS_PSELMISO, SPIS_PSELSCK, SPIS_PSELSS, "sd"); // I believe this matches Todd's pinout, let me know if this doesn't work. (p12, p13, p15, p14)


void disconnectionCallback(Gap::Handle_t handle, Gap::DisconnectionReason_t reason)
{
    ble.startAdvertising();
}

void WrittenHandler(const GattCharacteristicWriteCBParams *Handler) // called any time the phone sends a message
{
   uint8_t *writeData =  const_cast<uint8_t*>(Handler->data);
    // check to see what characteristic was written, by handle
    if(Handler->charHandle == upasServicePtr->rtcCharacteristic.getValueAttribute().getHandle()) {


        
        E2PROM.write(0x00015, writeData+6, 12);
        RTC.set_time(writeData[0],writeData[1],writeData[2],writeData[3],writeData[3],writeData[4],writeData[5]);
   
    }else if(Handler->charHandle == upasServicePtr->sampleTimeCharacteristic.getValueAttribute().getHandle()){
        
        E2PROM.write(0x00015, writeData, 12);
    
    }else if(Handler->charHandle == upasServicePtr->subjectLabelCharacteristic.getValueAttribute().getHandle()){
        E2PROM.write(0x00001,writeData,15);
    
    }else if(Handler->charHandle == upasServicePtr->runReadyCharacteristic.getValueAttribute().getHandle()){
        uint8_t runData = writeData[0];
        
        if(runData == 10){
             RunReady = 10;
             RGB_LED.set_led(1,2,3);
        }else{ 
             RunReady = 2;
        }
    
    }else if(Handler->charHandle == upasServicePtr->runModeCharacteristic.getValueAttribute().getHandle()){
        /* Trigger demo mode*/
        RGB_LED.set_led(3,1,0);
        E2PROM.write(0x00036,writeData,1);
    }
}

void check_stop()   // this checks if it's time to stop and shutdown
{
    
    if(RTC.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);
}


void log_data()
{
    logg.detach();

    logg.attach(&log_data, logInerval);     // reading and logging data must take significintly less than 0.5s. This can be increased.

    RTC.get_time();

    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 if(digital_pot_change+digital_pot_set>=digitalpotMax&abs(digital_pot_change)<50) {
            digital_pot_set = digitalpotMax;
            RGB_LED.set_led(1,0,0);
        } else if(digital_pot_change+digital_pot_set<=digitalpotMin&abs(digital_pot_change)<50) {
            digital_pot_set = digitalpotMin;
            RGB_LED.set_led(1,0,0);
        } else {
            digital_pot_set = (digital_pot_set+ digital_pot_change);
            RGB_LED.set_led(1,1,0);
        }

        DigPot.writeRegister(digital_pot_set);

    } else {
        RGB_LED.set_led(0,1,0);
    }
    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;
    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
    press = bmesensor.getPressure();
    temp = bmesensor.getTemperature()-5.0;
    rh = bmesensor.getHumidity();
    uv =  lightsensor.getUV();
    vis = lightsensor.getVIS();
    ir = lightsensor.getIR();
    FILE *fp = fopen(filename, "a");
    fprintf(fp, "%02d,%02d,%02d,%02d,%02d,%02d,%1.3f,%1.3f,%2.2f,%4.2f,%2.1f,%1.3f,%1.3f,%5.1f,%1.1f,%1.1f,%1.1f,%1.1f,%d,%d,%d,%d,%d,%d,%d,%d,%d,%1.3f,%1.3f,%f\r\n",RTC.year, RTC.month,RTC.date,RTC.hour,RTC.minutes,RTC.seconds,omronVolt,massflow,temp,press,rh,atmoRho,volflow,sampledVol,accel_x,accel_y,accel_z,accel_comp,uv,omronReading, vInReading, vBlowerReading, omronDiff,gasG.getAmps(), gasG.getVolts(), gasG.getCharge(),digital_pot_set, deltaMflow, deltaVflow, compass);
    fclose(fp);
    //wait_ms(5);
    
}

int main()
{
    uint8_t temp_crr;
    RGB_LED.set_led(1,1,1);
// Setup and Initialization
//---------------------------------------------------------------------------------------------//
    Menu.read_menu(E2PROM, logInerval,refreshtime, volflowSet, device_name, dutyUp, dutyDown, home_lat, home_lon, work_lat, work_lon, RunReady, serial_num);   //Read all data from the EEPROM here
    if(Menu.crr == 255) {
        Menu.factory_reset(E2PROM, logInerval,refreshtime, volflowSet, device_name, dutyUp, dutyDown, home_lat, home_lon, work_lat, work_lon, RunReady, serial_num);
    }
    //**************//BLE initialization//**************//
    RTC.get_time();
    uint8_t rtcPassValues[6] = {RTC.seconds, RTC.minutes,RTC.hour,RTC.date,RTC.month,RTC.year};
    uint8_t sampleTimePassValues[12] = {0,};
    uint8_t subjectLabelOriginal[15] = {0,};
    E2PROM.read(0x00015, sampleTimePassValues, 12);
    E2PROM.read(0x00001, subjectLabelOriginal,15);
    
    
    ble.init();
    ble.onDisconnection(disconnectionCallback);
    ble.onDataWritten(WrittenHandler); //add writeCharCallback (custom function) to whenever data is being written to device
    UPAS_Service upasService(ble, false,rtcPassValues,sampleTimePassValues,subjectLabelOriginal); //Create a GattService that is defined in UPAS_Service.h
    upasServicePtr = &upasService; //Create a pointer to the service (Allows advertisement without specifically adding the service

    /* setup advertising 
    Following lines do the follow:
        1:Declare the device as Bluetooth Smart(Low-Energy)
        2.Advertise the UPAS service that will send and receive the 57-bits of settable values in the UPAS EEPROM
        3.Advertise the name that will be associated with the UPAS
        4.Allow the UPAS to advertise unrestricted (this might change) */
        
    ble.accumulateAdvertisingPayload(GapAdvertisingData::BREDR_NOT_SUPPORTED | GapAdvertisingData::LE_GENERAL_DISCOVERABLE);
    ble.accumulateAdvertisingPayload(GapAdvertisingData::COMPLETE_LIST_16BIT_SERVICE_IDS, (uint8_t *)uuid16_list, sizeof(uuid16_list));
    ble.accumulateAdvertisingPayload(GapAdvertisingData::COMPLETE_LOCAL_NAME, (uint8_t *)DEVICE_NAME, sizeof(DEVICE_NAME));
    ble.setAdvertisingType(GapAdvertisingParams::ADV_CONNECTABLE_UNDIRECTED);
    ble.setAdvertisingInterval(160); /* 160ms. */
    ble.startAdvertising();

    //**************//BLE initialization//**************//
    while (1) {
        ble.waitForEvent();
        if(RunReady==2 && blower ==0){ //Code used to see if one-click run should begin
            calibrations.initialize(serial_num);
            RGB_LED.set_led(3,0,2);
            blower=1;
            RunReady=0;
         }
         if(RunReady==2 && blower ==1){ //Code used to see if one-click run is done.
            blower=0;
            RunReady=0;
         }
         
        if(RunReady==10){ //Check to see if app is done with configurations
           blower = 0;
           ble.stopAdvertising();
           break;
       }
    }

    E2PROM.read(0x00015, startAndEndTime, 12); //Grab start and end times from EEPROM
    while(!RTC.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.get_time(); 

        }
    calibrations.initialize(serial_num);
    blower=1;
    
   // while(!RTC.compare(startAndEndTime[6], startAndEndTime[7], startAndEndTime[8], startAndEndTime[9], startAndEndTime[10], startAndEndTime[11])) { //Waits for end time
//        wait(0.5);
//        RTC.get_time(); 
//
//    }
    //pbKill = 0; // this is were we shut everything down









    
    pc.printf("You're done, you can now disconect the USB cable.\r\n");
    RunReady = 0;
    Menu.save_menu(E2PROM, logInerval, refreshtime, volflowSet, device_name, dutyUp, dutyDown, home_lat, home_lon, work_lat, work_lon, RunReady, serial_num);       //Save all data to the EEPROM
    
    RGB_LED.set_led(1,1,0);


    calibrations.initialize(serial_num);


    stop.attach(&check_stop, 60);    // check if we should shut down every 9 seconds, starting 60s after the start.

    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;
    }

    DigPot.writeRegister(digital_pot_setpoint);
    wait(1);
    blower = 1;
   
    //Menu.save_menu(E2PROM, logInerval, refreshtime, volflowSet, device_name, dutyUp, dutyDown, home_lat, home_lon, work_lat, work_lon, RunReady, serial_num);       //Save all data to the EEPROM
            
    sprintf(filename, "/sd/UPAS%04dLOG_%02d-%02d-%02d_%02d=%02d=%02d_%s.txt",serial_num,RTC.year,RTC.month,RTC.date,RTC.hour,RTC.minutes,RTC.seconds,device_name);
    FILE *fp = fopen(filename, "w");
    fclose(fp);

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

    wait(10);

    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)>.015) {

        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);
        wait(1);


    }

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



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


    logg.attach(&log_data, logInerval); // uses callbacks or block Interrupts for anything that uses i2c

}