The Technology Partnership / Mbed OS LEX_Threaded_Programming_V3

LEX_Threaded_Programming

Dependencies:   Heater_V2 MODSERIAL Nanopb FastPWM ADS8568_ADC

main.cpp@7:a4fc853feb30, 2019-09-04 (annotated)

Committer:
justinbuckland
Date:
Wed Sep 04 10:18:33 2019 +0000
Revision:
7:a4fc853feb30
Parent:
6:ef2bcc5fe3af
Child:
8:58c6d51957df
PC output format updated

Who changed what in which revision?

UserRevisionLine numberNew contents of line
omatthews 0:54bedd3964e2 1 #include "mbed.h"
omatthews 0:54bedd3964e2 2 #include "pb.h"
omatthews 0:54bedd3964e2 3 #include "pb_decode.h"
omatthews 0:54bedd3964e2 4 #include "pb_encode.h"
omatthews 0:54bedd3964e2 5 #include "MODSERIAL.h"
omatthews 0:54bedd3964e2 6 #include "ADS8568_ADC.h"
omatthews 0:54bedd3964e2 7 #include "Heater.h"
omatthews 0:54bedd3964e2 8 #include "FastPWM.h"
omatthews 0:54bedd3964e2 9 #include "memspcr.pb.h"
omatthews 0:54bedd3964e2 10 #include <vector>
omatthews 0:54bedd3964e2 11 #include <iterator>
omatthews 0:54bedd3964e2 12
omatthews 0:54bedd3964e2 13 Heater * heater;
intrinseca 4:63d7f2a0dec6 14 float r_gradient; //setpoint setting
omatthews 5:702b32ead94e 15
omatthews 0:54bedd3964e2 16
omatthews 0:54bedd3964e2 17 MODSERIAL pc(PA_9, PA_10, 512); //mcu TX, RX, 512 byte TX and RX buffers
omatthews 0:54bedd3964e2 18 ADS8568_ADC adc(PB_15, PB_14, PB_13, PB_12, PC_15, PC_0, PC_1, PC_2, PC_3);
omatthews 0:54bedd3964e2 19 I2C i2c(PB_7, PB_8); //SDA, SCL
omatthews 0:54bedd3964e2 20 Timer timer;
omatthews 0:54bedd3964e2 21 DigitalIn adc_busy(PA_8); //Busy interrupt sig#
omatthews 5:702b32ead94e 22
omatthews 0:54bedd3964e2 23
omatthews 0:54bedd3964e2 24 //Heater Control
omatthews 5:702b32ead94e 25 FastPWM drive_main(PC_9);
omatthews 5:702b32ead94e 26 FastPWM drive_lysis(PC_8);
omatthews 5:702b32ead94e 27 FastPWM guard_main(PC_7);
omatthews 5:702b32ead94e 28 FastPWM guard_lysis(PC_6);
justinbuckland 7:a4fc853feb30 29
justinbuckland 7:a4fc853feb30 30 int heater_ID_main = 1;
justinbuckland 7:a4fc853feb30 31 int heater_ID_lysis = 2;
omatthews 5:702b32ead94e 32 int i_port_main = 0;
omatthews 5:702b32ead94e 33 int i_port_lysis = 2;
omatthews 5:702b32ead94e 34 int v_port_main = 1;
omatthews 5:702b32ead94e 35 int v_port_lysis = 3;
omatthews 0:54bedd3964e2 36
justinbuckland 7:a4fc853feb30 37 int heater_ID = 0;
omatthews 0:54bedd3964e2 38
omatthews 0:54bedd3964e2 39
justinbuckland 7:a4fc853feb30 40 //Indicator LEDs
omatthews 0:54bedd3964e2 41 DigitalOut hb_led(PC_13); //Green
omatthews 0:54bedd3964e2 42 DigitalOut led_0(PC_4); //Red
omatthews 0:54bedd3964e2 43 DigitalOut led_1(PC_5); //Green
omatthews 0:54bedd3964e2 44
justinbuckland 7:a4fc853feb30 45 //Camera and LED drive
justinbuckland 7:a4fc853feb30 46 DigitalOut camTrigger(PB_2); //Trigger camera
justinbuckland 7:a4fc853feb30 47 DigitalOut ledDrive(PB_4); //Drive LED for fluorescence detection
justinbuckland 7:a4fc853feb30 48
omatthews 0:54bedd3964e2 49 //User buttons
omatthews 0:54bedd3964e2 50 DigitalIn user_0(PB_0);
omatthews 0:54bedd3964e2 51 DigitalIn user_1(PB_1);
omatthews 0:54bedd3964e2 52
omatthews 0:54bedd3964e2 53 BusOut converts(PC_0, PC_1, PC_2, PC_3);
omatthews 0:54bedd3964e2 54
omatthews 0:54bedd3964e2 55 //Threads
omatthews 6:ef2bcc5fe3af 56 Thread heater_control(osPriorityHigh);
omatthews 6:ef2bcc5fe3af 57 Thread logging_thread(osPriorityAboveNormal);
omatthews 0:54bedd3964e2 58
omatthews 0:54bedd3964e2 59 //Tickers
omatthews 0:54bedd3964e2 60 Ticker heat_tick;
omatthews 0:54bedd3964e2 61 Ticker pressure_tick;
omatthews 0:54bedd3964e2 62 Ticker log_tick;
omatthews 0:54bedd3964e2 63
omatthews 0:54bedd3964e2 64
omatthews 0:54bedd3964e2 65 //Flags
omatthews 5:702b32ead94e 66 EventFlags flags; //Flags:
omatthews 5:702b32ead94e 67 // 0 => update heater
omatthews 5:702b32ead94e 68 // 1 => log state
omatthews 5:702b32ead94e 69 bool triggered_flag;
omatthews 0:54bedd3964e2 70 bool status = true;
omatthews 0:54bedd3964e2 71
omatthews 0:54bedd3964e2 72 //Configuration data
omatthews 0:54bedd3964e2 73 memspcr_ExperimentConfiguration exp_config = memspcr_ExperimentConfiguration_init_zero;
omatthews 0:54bedd3964e2 74 int buffer_length;
omatthews 0:54bedd3964e2 75 size_t message_length;
omatthews 5:702b32ead94e 76 uint8_t buffer[512]; //FIXME: Needs to be longer
omatthews 0:54bedd3964e2 77
omatthews 0:54bedd3964e2 78
omatthews 0:54bedd3964e2 79 //Functions for reading and decoding the message__________________________________________________
omatthews 0:54bedd3964e2 80
omatthews 0:54bedd3964e2 81 void read_message()
omatthews 0:54bedd3964e2 82 {
justinbuckland 7:a4fc853feb30 83 if (pc.scanf("%d",&message_length) < 0){pc.printf("# Error reading message length");}
omatthews 5:702b32ead94e 84 size_t buffer_length = sizeof(buffer);
omatthews 5:702b32ead94e 85 if (message_length > buffer_length)
omatthews 5:702b32ead94e 86 {
justinbuckland 7:a4fc853feb30 87 pc.printf("# Message length exceeds buffer. \n Input configuration file\n");
omatthews 5:702b32ead94e 88 read_message();
omatthews 5:702b32ead94e 89 return;
omatthews 5:702b32ead94e 90 }
justinbuckland 7:a4fc853feb30 91 pc.printf("# Message is %d chars long, buffer length is %d\n",message_length,buffer_length);
omatthews 5:702b32ead94e 92 unsigned int c;
omatthews 5:702b32ead94e 93 for (int i = 0; i < message_length; i++)
omatthews 0:54bedd3964e2 94 {
omatthews 0:54bedd3964e2 95 pc.scanf("%02X",&c);
omatthews 0:54bedd3964e2 96 buffer[i] = (char) c;
omatthews 0:54bedd3964e2 97 }
omatthews 0:54bedd3964e2 98 }
omatthews 0:54bedd3964e2 99
omatthews 0:54bedd3964e2 100 void decode_message()
omatthews 0:54bedd3964e2 101 {
omatthews 5:702b32ead94e 102 // Create a stream that reads from the buffer.
omatthews 5:702b32ead94e 103
omatthews 0:54bedd3964e2 104 pb_istream_t istream = pb_istream_from_buffer(buffer, message_length);
omatthews 0:54bedd3964e2 105
omatthews 5:702b32ead94e 106 //Now we are ready to decode the message.
omatthews 0:54bedd3964e2 107 status = pb_decode(&istream, memspcr_ExperimentConfiguration_fields, &exp_config);
omatthews 0:54bedd3964e2 108
omatthews 5:702b32ead94e 109 // Check for errors...
omatthews 5:702b32ead94e 110 if (!status) {
justinbuckland 7:a4fc853feb30 111 pc.printf("# Decoding failed: %s\n", PB_GET_ERROR(&istream));
omatthews 0:54bedd3964e2 112 }
omatthews 0:54bedd3964e2 113 }
omatthews 0:54bedd3964e2 114
omatthews 0:54bedd3964e2 115 bool decode_callback(pb_istream_t *stream, const pb_field_t *field, void **arg)
omatthews 0:54bedd3964e2 116 {
omatthews 0:54bedd3964e2 117 vector <memspcr_ThermalStep> * dest = (vector <memspcr_ThermalStep> *)(*arg);
omatthews 0:54bedd3964e2 118 memspcr_ThermalStep result = memspcr_ThermalStep_init_zero;
omatthews 0:54bedd3964e2 119 status = pb_decode(stream, memspcr_ThermalStep_fields, & result);
omatthews 5:702b32ead94e 120
omatthews 5:702b32ead94e 121 if (!status) {
justinbuckland 7:a4fc853feb30 122 pc.printf("# Decode callback failed\n");
omatthews 0:54bedd3964e2 123 }
omatthews 0:54bedd3964e2 124
intrinseca 4:63d7f2a0dec6 125 dest->push_back(result); //CHECK: Does result get copied into the vector?
omatthews 0:54bedd3964e2 126 return true;
omatthews 0:54bedd3964e2 127 }
omatthews 0:54bedd3964e2 128
omatthews 0:54bedd3964e2 129
omatthews 0:54bedd3964e2 130 //Ticking functions_________________________________________________________________
omatthews 0:54bedd3964e2 131
omatthews 6:ef2bcc5fe3af 132
omatthews 5:702b32ead94e 133 void temp_trigger()
omatthews 0:54bedd3964e2 134 {
omatthews 5:702b32ead94e 135 //This function triggers a temperature update.
omatthews 5:702b32ead94e 136 //N.B. update cannot be called directly from a ticker as tickers and
omatthews 0:54bedd3964e2 137 //reading the ADC both rely on interrupts.
omatthews 5:702b32ead94e 138 flags.set(0x1);
omatthews 0:54bedd3964e2 139 }
omatthews 0:54bedd3964e2 140
omatthews 6:ef2bcc5fe3af 141
omatthews 6:ef2bcc5fe3af 142
omatthews 2:b27d8f9a6e49 143 void log_trigger()
omatthews 2:b27d8f9a6e49 144 {
omatthews 5:702b32ead94e 145 flags.set(0x2);
omatthews 2:b27d8f9a6e49 146 }
justinbuckland 7:a4fc853feb30 147
omatthews 5:702b32ead94e 148 void pressure_control()
omatthews 0:54bedd3964e2 149 {
omatthews 0:54bedd3964e2 150 //Input pressure control function here
omatthews 0:54bedd3964e2 151 //i.e.
omatthews 0:54bedd3964e2 152 //read_pressure();
omatthews 0:54bedd3964e2 153 //if (pressure < lower_bound) {
omatthews 5:702b32ead94e 154 //pump_turn_on();
omatthews 5:702b32ead94e 155 //}
omatthews 0:54bedd3964e2 156 //else if (pressure > upper_bound) {
omatthews 5:702b32ead94e 157 //pump_turn_off();
omatthews 5:702b32ead94e 158 //}
omatthews 0:54bedd3964e2 159 led_1 = !led_1;
omatthews 0:54bedd3964e2 160 }
omatthews 0:54bedd3964e2 161
omatthews 2:b27d8f9a6e49 162
omatthews 0:54bedd3964e2 163
omatthews 0:54bedd3964e2 164
omatthews 5:702b32ead94e 165 //Other functions__________________________________________________________________
omatthews 0:54bedd3964e2 166
omatthews 0:54bedd3964e2 167
omatthews 0:54bedd3964e2 168 void temp_control() {
omatthews 0:54bedd3964e2 169 while(1){
omatthews 6:ef2bcc5fe3af 170 flags.wait_any(0x1,osWaitForever,true);
omatthews 0:54bedd3964e2 171 heater->read();
omatthews 0:54bedd3964e2 172 heater->update();
omatthews 0:54bedd3964e2 173 }
omatthews 0:54bedd3964e2 174 }
omatthews 5:702b32ead94e 175
omatthews 2:b27d8f9a6e49 176 void log_state()
omatthews 2:b27d8f9a6e49 177 {
omatthews 2:b27d8f9a6e49 178 while(1){
omatthews 6:ef2bcc5fe3af 179 flags.wait_any(0x2,osWaitForever,true);
omatthews 6:ef2bcc5fe3af 180 //Output time, R_ref, R, error, error_integrated
justinbuckland 7:a4fc853feb30 181 pc.printf("%10d,%10d,%10.6f,%10.6f\n", heater_ID, timer.read_ms(), heater->Get_R(), heater->Get_R_ref());
omatthews 2:b27d8f9a6e49 182 }
omatthews 2:b27d8f9a6e49 183 }
omatthews 5:702b32ead94e 184
omatthews 5:702b32ead94e 185 void set_point_routine(std::vector<memspcr_ThermalStep> profile) {
omatthews 5:702b32ead94e 186 int curr_time;
omatthews 5:702b32ead94e 187 vector <memspcr_ThermalStep>::iterator it_prev, it = profile.begin();
omatthews 5:702b32ead94e 188 if (it->elapsed_time_ms != 0)
omatthews 5:702b32ead94e 189 {
justinbuckland 7:a4fc853feb30 190 pc.printf("# Error: the first point in the profile should be at time 0.\n");
omatthews 5:702b32ead94e 191 return;
omatthews 5:702b32ead94e 192 }
omatthews 2:b27d8f9a6e49 193 it++;
omatthews 0:54bedd3964e2 194
omatthews 0:54bedd3964e2 195 for (it_prev = profile.begin(); it < profile.end(); it ++, it_prev++){
omatthews 0:54bedd3964e2 196 triggered_flag = false;
omatthews 0:54bedd3964e2 197 r_gradient = (it->resistance - it_prev->resistance)/(it->elapsed_time_ms - it_prev->elapsed_time_ms);
omatthews 0:54bedd3964e2 198 while ((curr_time = timer.read_ms()) <= it->elapsed_time_ms){
omatthews 5:702b32ead94e 199 heater->Set_ref(it_prev->resistance + r_gradient * (curr_time - it_prev->elapsed_time_ms));
omatthews 0:54bedd3964e2 200
omatthews 5:702b32ead94e 201
omatthews 0:54bedd3964e2 202 if (!triggered_flag && curr_time > it_prev->elapsed_time_ms + it->camera_offset_ms)
omatthews 0:54bedd3964e2 203 {
justinbuckland 7:a4fc853feb30 204 //Start camera exposure and turn on LED
justinbuckland 7:a4fc853feb30 205 camTrigger = 0;
justinbuckland 7:a4fc853feb30 206 wait_us(10);
justinbuckland 7:a4fc853feb30 207 camTrigger = 1;
justinbuckland 7:a4fc853feb30 208 ledDrive = 1;
justinbuckland 7:a4fc853feb30 209 led_0 = 1;
omatthews 0:54bedd3964e2 210 triggered_flag = true;
omatthews 0:54bedd3964e2 211 }
omatthews 5:702b32ead94e 212 else
omatthews 5:702b32ead94e 213 {
justinbuckland 7:a4fc853feb30 214 //Stop camera exposure and turn off LED
justinbuckland 7:a4fc853feb30 215 camTrigger = 0;
justinbuckland 7:a4fc853feb30 216 ledDrive = 0;
justinbuckland 7:a4fc853feb30 217 led_0 = 0;
intrinseca 4:63d7f2a0dec6 218 }
omatthews 0:54bedd3964e2 219
justinbuckland 7:a4fc853feb30 220 wait_us(10000);
omatthews 0:54bedd3964e2 221 }
omatthews 0:54bedd3964e2 222
omatthews 0:54bedd3964e2 223 }
omatthews 0:54bedd3964e2 224 }
omatthews 0:54bedd3964e2 225
omatthews 0:54bedd3964e2 226
omatthews 5:702b32ead94e 227
omatthews 5:702b32ead94e 228 int main()
omatthews 5:702b32ead94e 229 {
omatthews 0:54bedd3964e2 230 pc.baud(115200);
omatthews 0:54bedd3964e2 231 adc.init();
omatthews 5:702b32ead94e 232
omatthews 0:54bedd3964e2 233 buffer_length = sizeof(buffer)/sizeof(uint8_t);
justinbuckland 7:a4fc853feb30 234 pc.printf("# Input configuration file\n");
omatthews 5:702b32ead94e 235
intrinseca 4:63d7f2a0dec6 236 //set up nanopb
omatthews 5:702b32ead94e 237 std::vector<memspcr_ThermalStep> profile;
omatthews 5:702b32ead94e 238 exp_config.profile.funcs.decode = decode_callback;
omatthews 5:702b32ead94e 239 exp_config.profile.arg = &profile;
omatthews 5:702b32ead94e 240
intrinseca 4:63d7f2a0dec6 241 //read and decode configuration
intrinseca 4:63d7f2a0dec6 242 read_message();
justinbuckland 7:a4fc853feb30 243 pc.printf("# Message read\n");
omatthews 0:54bedd3964e2 244 decode_message();
justinbuckland 7:a4fc853feb30 245 pc.printf("# Message decoded\n");
omatthews 5:702b32ead94e 246
omatthews 6:ef2bcc5fe3af 247 Heater * heater_main = new Heater(i_port_main, v_port_main, & drive_main, & guard_main, & adc, adc_busy, exp_config.thermal);
omatthews 6:ef2bcc5fe3af 248 Heater * heater_lysis = new Heater(i_port_lysis, v_port_lysis, & drive_lysis, & guard_lysis, & adc, adc_busy, exp_config.thermal);
omatthews 5:702b32ead94e 249
omatthews 5:702b32ead94e 250 //Select heater. Put control times in us for ticker functions
omatthews 5:702b32ead94e 251 if (exp_config.selected_heater == memspcr_ExperimentConfiguration_Heater_MAIN) {
omatthews 5:702b32ead94e 252 heater = heater_main;
justinbuckland 7:a4fc853feb30 253 heater_ID = heater_ID_main;
omatthews 5:702b32ead94e 254 } else if (exp_config.selected_heater == memspcr_ExperimentConfiguration_Heater_LYSIS) {
omatthews 5:702b32ead94e 255 heater = heater_lysis;
justinbuckland 7:a4fc853feb30 256 heater_ID = heater_ID_lysis;
omatthews 5:702b32ead94e 257 } else {
justinbuckland 7:a4fc853feb30 258 pc.printf("# Error - no heater has been selected");
omatthews 5:702b32ead94e 259 return 1;
omatthews 5:702b32ead94e 260 }
omatthews 5:702b32ead94e 261
justinbuckland 7:a4fc853feb30 262 pc.printf("# Starting pressure control\n");
omatthews 0:54bedd3964e2 263 pressure_tick.attach(& pressure_control, 1);
justinbuckland 7:a4fc853feb30 264 pc.printf("# Waiting for start signal to begin temperature control (type in an s or press button 0)\n");
omatthews 6:ef2bcc5fe3af 265 heater->Set_ref(0.0);
omatthews 6:ef2bcc5fe3af 266 heater_control.start(& temp_control);
omatthews 6:ef2bcc5fe3af 267 heat_tick.attach_us(& temp_trigger,exp_config.thermal.control_loop_interval_ms * 1000);
omatthews 6:ef2bcc5fe3af 268
omatthews 2:b27d8f9a6e49 269 while (pc.getcNb()!='s' && !user_0);
omatthews 5:702b32ead94e 270
justinbuckland 7:a4fc853feb30 271 pc.printf("# Start signal received");
omatthews 0:54bedd3964e2 272
omatthews 2:b27d8f9a6e49 273 logging_thread.start(& log_state);
omatthews 6:ef2bcc5fe3af 274 log_tick.attach_us(& log_trigger,exp_config.logging_interval_ms * 1000);
omatthews 0:54bedd3964e2 275
justinbuckland 7:a4fc853feb30 276 pc.printf("# Starting routine\n");
justinbuckland 7:a4fc853feb30 277 pc.printf("# heater, time(ms), r, rSet\n");
omatthews 2:b27d8f9a6e49 278 timer.start();
omatthews 5:702b32ead94e 279 set_point_routine(profile);
omatthews 6:ef2bcc5fe3af 280
omatthews 6:ef2bcc5fe3af 281 //Turn off
omatthews 5:702b32ead94e 282 heat_tick.detach();
omatthews 5:702b32ead94e 283 log_tick.detach();
omatthews 5:702b32ead94e 284 wait(1);
omatthews 2:b27d8f9a6e49 285 heater->turn_off();
omatthews 5:702b32ead94e 286
justinbuckland 7:a4fc853feb30 287 pc.printf("# Finished\n");
justinbuckland 7:a4fc853feb30 288
omatthews 5:702b32ead94e 289 return 0;
omatthews 5:702b32ead94e 290 }