File content as of revision 2:2b7eb44d597d:

//include relevant libraries
#include "mbed.h"
#include "stdio.h"
#include "math.h"
#include "ADXL362.h"

//define constants high and low for entire program
#define HIGH 1
#define LOW 0

//Define LED to be used to show mbed is operational
DigitalOut myled1(LED1);
//Define serial connection 
Serial pc(USBTX, USBRX);
//Define accelerometer
ADXL362 adxl362(p11, p12, p13, p10);
//Set up local file system to allow writing of txt files
LocalFileSystem local("local"); 

//???
int matlabdata;
char usercmd;

//Define paramater strings for communication over USB
char N[1000]; //Number of samples
char T [1000]; //Sample period 


int main()
{
    //Create file with pointer
    FILE *samplesettings; 
    FILE *timesettings;
    
    char res[100];//String to store user command
        
    matlabdata=pc.scanf("%s",res);//Get user command from matlab
   
    while(1)
    {    
        if(!strcmp(res,"1")==0)//if user command in matlab is 1 write the sample settings into a file 
        {  
            myled1 = HIGH;
            char N[1000];//To store the number of samples which is received from the matlab
            pc.scanf("%s\n",&N);//to get the number of  samples input from the matlab
            samplesettings = fopen("/local/samplesettings.txt", "w");//Open file for writing
            fprintf(samplesettings,"%s\n",N); //Writes settings values onto file
            fclose(samplesettings);//close file
            break;
        }
        else if(!strcmp(res,"2")==0)//If user command is 2 search the file for sample settings
        {
            //Define variables for output
            char value1[1000];
            samplesettings = fopen("/local/samplesettings.txt" , "r"); //Open file for reading
            fseek(samplesettings, 0 ,SEEK_SET); //Sets cursor to start of file
            fscanf(samplesettings,"%s\n", value1);//Scans fo the value of N
            pc.printf("%s\n", value1);//Prints the value of N
            fclose(samplesettings); //Close file
            break;
        }
        else if(!strcmp(res,"3")==0)//If user command recieved is 3 then write the time settings into a file
        {
            char T[1000];//To store value of T recieved from matlab
            pc.scanf("%s\n",&T);//To scan value of T from matlab
            timesettings = fopen("/local/timesettings.txt", "w");//Open file for writing
            fprintf(timesettings,"%s\n",T); //Writes settings values onto file                
            fclose(timesettings);//Close file
            break; 
        }
        else if(!strcmp(res,"4")==0)//If 4 is recieved as a user command then read the time settings 
        {
            //Define variables for output
            char value2[100];
            samplesettings = fopen("/local/timesettings.txt" , "r"); //Open file for reading
            fseek(timesettings, 0 ,SEEK_SET); //Sets cursor to start of file
            fscanf(timesettings,"%s\n", value2);//Reads the time period from the file
            pc.printf("%s\n", value2);//Outsputs the time period 
            fclose(timesettings); //Close file
            break; 
        }
        else if(!strcmp(res,"5")==0)//If the user command is 5 then we collect data 
        {
            //Initialise accelerometer
            adxl362.init_spi();
            adxl362.init_adxl362();
            wait(0.1);
            int8_t xdata, ydata, zdata;
            for(int i=0; i<atoi(N); i++)
            {
                adxl362.ACC_GetXYZ8(&xdata,&ydata,&zdata);//Fetch readings from accelerometer
                pc.printf("%+04d\n", xdata);
                pc.printf("%+04d\n", ydata);
                pc.printf("%+04d\n", zdata);
                wait(atoi(T));
                                        
                //Open data file
                FILE *data;
                data = fopen("/local/data.txt", "w");
                //Data collection loop using sample rate and number of samples 
                for(int i=0; i<atoi(N); i++)
                {
                    //Get accelerometer data
                    adxl362.ACC_GetXYZ8(&xdata,&ydata,&zdata);
                    //Print data to data file
                    fprintf(data, "%+04d", xdata);
                    fprintf(data, "%+04d", ydata);
                    fprintf(data, "%+04d", zdata);
                    //Attempt to print same data to MATLAB if connection is not null
                    if(pc != NULL)
                    {
                        pc.printf("%+04d\n", xdata);
                        pc.printf("%+04d\n", ydata);
                        pc.printf("%+04d\n", zdata);
                    }
                    //Pause to ensure sample rate
                    wait(atoi(T));
                }
                fclose(data);
                break;
            }
        }
    }                                               
}