File content as of revision 16:32b598af6f86:

#include "mbed.h"
#include "pb.h"
#include "pb_decode.h"
#include "pb_encode.h"
#include "MODSERIAL.h"
#include "ADS8568_ADC.h"
#include "Heater.h"
#include "FastPWM.h"
#include "memspcr.pb.h"
#include <vector>
#include <iterator>

#define BUFFER_SIZE 8192
#define LED_PULSE_PERIOD 1000    // ticks, 84kHz when CPU clock is 84MHz
#define LED_PULSE_WIDTH   100    // ticks, 10% duty cycle

Heater * heater;
float r_gradient; //setpoint setting


MODSERIAL pc(PA_9, PA_10, BUFFER_SIZE); //mcu TX, RX, BUFFER_SIZE byte TX and RX buffers
ADS8568_ADC adc(PB_15, PB_14, PB_13, PB_12, PC_15, PC_0, PC_1, PC_2, PC_3);
I2C i2c(PB_7, PB_8);            //SDA, SCL
Timer timer;
DigitalIn adc_busy(PA_8);                   //Busy interrupt sig#

//Pressure Control
DigitalOut pump(PA_2);
AnalogIn pressure_1(PA_5);
//set up pressure read averaging

float pressure_fAvg = 0.1;    // rolling average

float pressure_in = 0.0;
float pressure_out = 0.0;

float pressure_set = 0.46;
float pressure_hys = 0.02;
float pressure_set_low = pressure_set - pressure_hys/2;
float pressure_set_high = pressure_set + pressure_hys/2;

//Heater Control
FastPWM drive_main(PC_9);
FastPWM drive_lysis(PC_8);
FastPWM guard_main(PC_7);
FastPWM guard_lysis(PC_6);

int heater_ID_main = 1;
int heater_ID_lysis = 2;
int i_port_main = 0;
int i_port_lysis = 2;
int v_port_main = 1;
int v_port_lysis = 3;

int heater_ID = 0;

//Illumination LED Control

//Indicator LEDs
DigitalOut hb_led(PC_13);       //Red
DigitalOut led_0(PC_4);         //Green
DigitalOut led_1(PC_5);         //Red

//Camera and LED drive
DigitalOut camTrigger(PB_2);     //Trigger camera
DigitalOut ledDrive(PB_4);       //Drive LED for fluorescence detection

//User buttons
DigitalIn user_0(PB_0);
DigitalIn user_1(PB_1);

BusOut converts(PC_0, PC_1, PC_2, PC_3);

//Threads
Thread heater_control(osPriorityHigh);
Thread logging_thread(osPriorityAboveNormal);
Thread pressure_thread(osPriorityAboveNormal);

//Tickers
Ticker heat_tick;
Ticker pressure_tick;
Ticker log_tick;


//Flags
EventFlags flags; //Flags:
                  //        0 => update heater
                  //        1 => log state
                  //        2 => read pressure
bool triggered_flag;
bool status = true;

//Configuration data
memspcr_ExperimentConfiguration exp_config = memspcr_ExperimentConfiguration_init_zero;
int buffer_length;
size_t message_length;
uint8_t buffer[BUFFER_SIZE];


//Functions for reading and decoding the message__________________________________________________

void read_message()
{
    if (pc.scanf("%d",&message_length) < 0){pc.printf("# Error reading message length");}
    size_t buffer_length = sizeof(buffer);
    if (message_length > buffer_length) 
    {
        pc.printf("# Message length exceeds buffer. \n Input configuration file\n");
        read_message();
        return;
    }
    pc.printf("# Message is %d chars long, buffer length is %d\n",message_length,buffer_length);
    unsigned int c;
    for (int i = 0; i < message_length; i++) 
    {
        pc.scanf("%02X",&c);
        buffer[i] = (char) c;
    }   
}         

void decode_message()
{
    // Create a stream that reads from the buffer.
    pb_istream_t istream = pb_istream_from_buffer(buffer, message_length);

    //Now we are ready to decode the message.
    status = pb_decode(&istream, memspcr_ExperimentConfiguration_fields, &exp_config);

    // Check for errors...
    if (!status) {
        pc.printf("# Decoding failed: %s\n", PB_GET_ERROR(&istream));
    }
}

bool decode_callback(pb_istream_t *stream, const pb_field_t *field, void **arg)
{
    vector <memspcr_ThermalStep> * dest = (vector <memspcr_ThermalStep> *)(*arg);
    memspcr_ThermalStep result = memspcr_ThermalStep_init_zero;
    status = pb_decode(stream, memspcr_ThermalStep_fields, & result);

    if (!status) {
        pc.printf("# Decode callback failed\n");
    }

    dest->push_back(result); //CHECK: Does result get copied into the vector?
    return true;
}


//Ticking functions_________________________________________________________________


void temp_trigger()
{
    //This function triggers a temperature update.
    //N.B. update cannot be called directly from a ticker as tickers and
    //reading the ADC both rely on interrupts.
    flags.set(0x1);
}


void log_trigger()
{
    flags.set(0x2);
}

void pressure_trigger()
{
    flags.set(0x3);
}


//Other functions__________________________________________________________________


void temp_control() {
    while(1){
        flags.wait_any(0x1,osWaitForever,true);
        heater->read();
        heater->update();
        } 
    }

void log_state()
{
    while(1){
        flags.wait_any(0x2,osWaitForever,true);
        //Output time, R_ref, R, error, error_integrated
        pc.printf("%10d,%10d,%10.6f,%10.6f,%10.6f,%10.6f\n", heater_ID, timer.read_ms(), heater->Get_R(), heater->Get_R_ref(), pressure_in, pressure_out);
    }
}

void pressure_control() {
    while(1){
        flags.wait_any(0x3,osWaitForever,true);
        pressure_in = pressure_in*(1.0-pressure_fAvg) + pressure_1.read()*pressure_fAvg;
        //pressure_in = 0;
        //for (int i = 0; i < pressure_nAvg; i++) pressure_in += pressure_1.read();  //read pressure
        //pressure_in = pressure_in / pressure_nAvg;
//        pc.printf("%10.6f %10.6f %10.6f\n", pressure_set_low, pressure_set_high, pressure_in);
        if (pressure_in < pressure_set_low) {
            led_1 = 1;
            pump = 1;
//            pc.printf(" pump on\n");
        }
        else if (pressure_in > pressure_set_high) {
            led_1 = 0;
            pump = 0;
//            pc.printf(" pump off\n");
        }
    }
}


void set_point_routine(std::vector<memspcr_ThermalStep> profile) {
    int curr_time;
    vector <memspcr_ThermalStep>::iterator it_prev, it = profile.begin();
    if (it->elapsed_time_ms != 0)
    {
        pc.printf("# Error: the first point in the profile should be at time 0.\n");
        return;
    }
    it++;

    for (it_prev = profile.begin(); it < profile.end(); it ++, it_prev++){
        triggered_flag = false;
        r_gradient = (it->resistance_set_point - it_prev->resistance_set_point)/(it->elapsed_time_ms - it_prev->elapsed_time_ms);
        while ((curr_time = timer.read_ms()) <= it->elapsed_time_ms){
            heater->Set_ref(it_prev->resistance_set_point + r_gradient * (curr_time - it_prev->elapsed_time_ms));   
                             
            if (!triggered_flag && (it->camera_offset_ms != 0) && (curr_time > it_prev->elapsed_time_ms + it->camera_offset_ms))
            {
                //Start camera exposure and turn on LED if camera_offset_ms is non-zero
                camTrigger = 0;
                wait_us(10);
                camTrigger = 1;
                led_0 = 1;
                ledDrive = 1;
                triggered_flag = true;
            }
            wait_us(200);
        }
        //Stop camera exposure and turn off LED at end of time segment
        camTrigger = 0;
        led_0 = 0;
        ledDrive = 0;
    }
}   


int main()
{
    pc.baud(115200);
    adc.init();

    buffer_length = sizeof(buffer)/sizeof(uint8_t);
    pc.printf("# Input configuration file\n");
        
    //set up nanopb
    std::vector<memspcr_ThermalStep> profile;
    exp_config.profile.funcs.decode = decode_callback;
    exp_config.profile.arg = &profile;

    //read and decode configuration
    read_message();
    
    pc.printf("# Message read\n");
    decode_message();
    pc.printf("# Message decoded\n");

    Heater * heater_main = new Heater(i_port_main, v_port_main, & drive_main, & guard_main, & adc, adc_busy, exp_config.thermal);
    Heater * heater_lysis = new Heater(i_port_lysis, v_port_lysis, & drive_lysis, & guard_lysis, & adc, adc_busy, exp_config.thermal);

    //Select heater. Put control times in us for ticker functions
    if (exp_config.selected_heater == memspcr_ExperimentConfiguration_Heater_HEATER_1) {
        heater = heater_main;
        heater_ID = heater_ID_main;
    } else if (exp_config.selected_heater == memspcr_ExperimentConfiguration_Heater_HEATER_2) {
        heater = heater_lysis;
        heater_ID = heater_ID_lysis;
    } else {
        pc.printf("# Error - no heater has been selected\n");
        return 1;
    }

    pc.printf("# Starting pressure control\n");    
    pressure_thread.start(& pressure_control);
    pressure_tick.attach_us(& pressure_trigger, 500000);

    pc.printf("# Waiting for start signal to begin temperature control (type in an s or press button 0)\n");
    heater->Set_ref(0.0);
    heater_control.start(& temp_control);
    heat_tick.attach_us(& temp_trigger,exp_config.thermal.control_loop_interval_ms * 1000);
    
    while (pc.getcNb()!='s' && !user_0);

    pc.printf("# Start signal received\n");

    logging_thread.start(& log_state);
    log_tick.attach_us(& log_trigger,exp_config.logging_interval_ms * 1000);

    pc.printf("# Starting routine\n");
    pc.printf("#   heater,  time(ms),         r,      rSet,       pIn,      pOut\n");
    timer.start();
    set_point_routine(profile);
    
    //Turn off
    heat_tick.detach();
    log_tick.detach();
    wait(1);
    heater->turn_off();
    
    
    pc.printf("# Finished\n");
     
    return 0;
}