File content as of revision 7:2ef0c6032296:

#include "mbed.h"
#include "flow.h"
#include <math.h>
/////////////////////////
// In this version of the program developed for the Breath project, flow and CO2, as well as 8 channel sensors,
// are measured in a separate .h file called: "flow.h" which is included in the
// main code. So 10 sets of data is streamed using a serial connection (TTL cable or Bluetooth)
// without any intruption.
// This version is especially suitable to be used for KST.
// Also, a solenoid would be turned on and off based on calculating the standard deviation in CO2 profile.
//
// START POINT: calculates SD for 9 samples of CO2, if it's grater than 0.02 it enables the solenoid.
// END POINT: calculates SD for 9 samples of CO2, if it's grater thatn 0.05 it disables the solenoid.
//
// You can easily change the threshold of Standard deviation to detect plateau
//
// Generated by: Mehrnaz Javadipour
//////////////////////////

Serial ttl(PC_12,PD_2);  //TTL cable TX,RX
DigitalOut sol(PC_5);   //Solenoid: Digital Output
PwmOut led(PB_6);
Timer stream;

int main()
{
    ttl.baud(115200); //baudrate for the serial connection, 9600 for hc05 115200 for rn

    ttl.printf("$");//enter command mode only for rn
    wait(0.1);
    ttl.printf("$$");//enter command mode
    wait(0.5);
    ttl.printf("SN,POC Breath\r");//set new name
    wait(0.5);
    ttl.printf("SS,C0\r");//set transparent uart
    wait(0.5);
    ttl.printf("&,6146DB234067\r");//Assign mac
    wait(0.5);
    ttl.printf("---\r");//enter data mode
    wait(0.5);

    flow();         //calling flow from flow.h
    carbon();       //calling CO2 from flow.h
    s1();           //calling 8 channels from flow.h
    s2();
    s3();
    s4();
    s5();
    s6();
    s7();
    s8();
    getTemp();      //calling Temperature from flow.h

    //////////////////////////////
    // I defined a flag for each section of specific functions, so by enabling the
    // flag the section starts and by disabling the flag it finishes the section.
    // at the end of the program, I reset the flags so it would be ready for the next loop.
    /////////////////////////////

    int bf=0;         //FLAG for detecting base flow
    int i=0;
    float bfArray[4]; //sampling flow for finding the average base flow
    float sf=0;       //sum of flow samples for calculating base flow
    float fv=0;       //final value of base flow

    int measurement_started=0; //FLAG for starting calculations after detecting breath

    int solstart=0;         //FLAG for starting calculations for detecting plateau
    int m=0;
    int myArray[9];         //sampling 9 values of CO2
    unsigned int sum=0;     //sum of 9 samples of CO2
    int avg=0;              //average of 9 samples of CO2
    int difSum=0;           //used for the Standard deviation algorithm
    long double var=0.0;    //used for the Standard deviation algorithm
    float sigma=0.0;        //final value for standar deviation
    int flags=0;            //FLAG for keep taking samples from CO2 profile when it's too early to detect plateau

    int solend=0;           //FLAG for ending calculations for detecting plateau
    unsigned int sum2=0;    //same as before; used for finding standard deviation
    long double var2=0.0;
    float sigma2=0.0;
    int difSum2=0;
    int avg2=0;
    int flage=0;            //FLAG for keep taking samples from CO2 profile when it's too early to finish plateau

    int fin=0;
    wait(1);
    sol=1;//sol off 1

    while(1) {
        
        led=0.2f;      //LED turned on at 20% power
        ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
        //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
        wait(0.01);
        if (bf==0) {    //finding base flow before breath
            for(i=0; i<4; i++) {
                bfArray[i]=flow();
                sf+=bfArray[i];
            }
            fv=sf/4;
            //fv=fv+0.2;
            fv=0.4;
            //ttl.printf("set\n");
            bf=1;
        }

        //Starts calculations when it detects breathing into the device:

        if ((flow()>fv) and (measurement_started ==0)) {
            stream.start(); 
            measurement_started = 1;
        }

        //Starts detecting plateau:

        if ((measurement_started == 1) and (solstart==0)) {

            //Takes 9 samples of CO2:
            //I have also included printing the values inside the loops so we don't loose any data during calculatins.
            for(m=0; m<9; m++) {
                ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                myArray[m]=carbon();
                wait(0.1);
            }
            while(flags==0) {
                //While "flags" is enabled, keeps calculating the standard deviation.
                for(int m=0; m<9; m++) {
                    ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                    //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                    sum+=myArray[m];
                    wait(0.1);

                }
                avg=sum/9;
                for(int m=0; m<9; m++) {
                    //
                    ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                    //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                    difSum+=(myArray[m]-avg)*(myArray[m]-avg); //Find sum of difference between value X and mean
                    wait(0.1);
                }
                var=difSum/9;
                sigma=sqrt(var);
                if (sigma<0.02) {

                    //if SD is less than 0.02 it means that it is too early to start the plateau
                    //So we shift all but the first sample and define the new set of arrays:

                    for(int m=0; m<8; m++) {
                        ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                        //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                        myArray[m]=myArray[m+1];  //Shift all CO2 values to the left by 1 value
                        wait(0.1);

                    }
                    myArray[8]=carbon();  //assign a new value for the 9th sample
                }
                //The new set of arrays are now generated and is sent back to be used for preveious SD calculations.
                //If sigma for the new set is still small, a newer set will be generated and replaced
                //Otherwise, it's accepted and will turn on the solenoid:
                else {
                    sol=0;      //Solenoid is ON 0
                    ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(),0.00,s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                    //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), 0.00,s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor, CHANGED CO2 TO 0
                    
                    //led=0.4f;  //The brightness is reduced to half during the plateau
                    wait(0.1);
                    flags=1;    //breakes the while loop
                }
            }
            solend=1;   //prepares the next section for finishing the plateau
            solstart =1;
        }
        if ((measurement_started == 1) and (solend==1)) {
            // same process happens for finishing the plateau:

            for(m=0; m<9; m++) {
                ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                myArray[m]=carbon();
                wait(0.1);
            }
            while(flage==0) {
                for(int m=0; m<9; m++) {
                    ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                    //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                    sum2+=myArray[m];
                    wait(0.1);
                }
                avg2=sum2/9;
                for(int m=0; m<9; m++) {
                    ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                    //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                    difSum2+=(myArray[m]-avg2)*(myArray[m]-avg2);
                    wait(0.1);
                }
                var2=difSum2/9;
                sigma2=sqrt(var2);
                if (sigma2<0.05) {
                    // here we defined the end threshold to be 0.05, it can be changed later based on experiment results
                    for(int m=0; m<8; m++) {
                        ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                        //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor, CHANGEC CO2 TO 0
                        myArray[m]=myArray[m+1];
                        wait(0.1);

                    }
                    myArray[8]=carbon();
                } else {
                    sol=1;  //Solenoid is OFF 1
                    ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(), 0.00,s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                    //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), 0.00,s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor
                    wait(0.1);
                    
                    flage=1;    //breakes the loop
                }
            }

            //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(),carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
            //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor            solend =0;  //end of this section
            //led=0.4f;  //LED is back to full brightness
            bf=0;       //reset the detecting base flow flag
            fin=1;      //enables the next section flag



        }

        if(carbon()<2.00 && fin ==1) {
                //User has to wait for the CO2 level to drop less than 1% before testing again.
                //Once it is less than 1%, all the flags and parameters used in calculations are reset

                ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",getTemp(),flow(),carbon(),s1(),s2(),s3(),s4(),s5(),s6(),s7(),s8(),stream.read()); //chemical sensor
                //ttl.printf("tt%.2f,ff%.2f,cc%.2f,sa%i,sb%i,sc%i,sd%i,se%i,sf%i,sg%i,sh%i,ti%.2f\n",0.00,flow(), carbon(),s1(),s2(),s3(),s4(),c2612S1(),c2610S1(),c2620S1(),c2602S1(),stream.read()); //commercial sensor            solend =0;  //end of this section
                stream.reset();
                stream.stop();
                measurement_started =0;
                solstart=0;
                sum=0;
                var=0.0;
                sigma=0.0;
                difSum=0;
                sum2=0;
                var2=0.0;
                sigma2=0.0;
                difSum2=0;
                avg2=0;
                avg=0;
                flags=0;
                flage=0;
                fin=0;
            }

    }
}