how to stop data being skipped when recording over long intervals?

Question

I'm using an arduino to log the temperature from ten PT100s in real time.

My code works fine over short intervals (e.g. 10 minutes), but over longer intervals (e.g. 2-7 hours), specifically on the 63rd temperature logged, Matlab doesn't pick up the full string from the serial print It doesn't matter what sample rate i set it at (I have tried 2.5 mins, 1 min and 5 mins), it always stops working at the 63rd piece of data - specifically the y variable from fscanf only has 2 values in it - one normal looking temperature value and 2.

I changed the code so that when the y string isn't the expected 10 temperature values, it just plots 10 NaN values and keeps going. From this point onwards, it fails to log 10 temperature values exactly once every 4 samples, no matter what I set the sample rate to.

clear all;
clc;
delete(instrfindall); %pre-emptively close all ports
b = serial('COM7','BaudRate',1000000); % COM is the COM port of the Arduino
 %flush input buffer
flushinput(b);

fopen(b);  % initiate arduino communication


%% Create a figure window to monitor the live data
Tmax = 24*60*60; % Total time for data collection (s)
figure,
grid on,
xlabel ('Time (s)'), ylabel('Tempeature (K)'),
%axis([0 Tmax+1]),

%% Read and plot the data from Arduino
Ts = 150; % Sampling time (s)
ii = 0;
dataa = 0;
datab = 0;
t = 0;
tic % Start timer
mData = [];
while toc <= Tmax
    ii = ii + 1;
    %% Read buffer data

    datab = fscanf(b);
    y = strsplit(datab, ',')
    if(length(str2double(y))<10)
        disp("Output length mismatch");
        y = NaN(10,1);
        t1(ii,1) = str2double(y(1));
        t2(ii,1) = str2double(y(2));
        t3(ii,1) = str2double(y(3));
        t4(ii,1) = str2double(y(4));
        t5(ii,1) = str2double(y(5));
        t6(ii,1) = str2double(y(6));
        t7(ii,1) = str2double(y(7));
        t8(ii,1) = str2double(y(8));
        t9(ii,1) = str2double(y(9));
        t10(ii,1) = str2double(y(10));
    else
        t1(ii,1) = str2double(y(1));
        t2(ii,1) = str2double(y(2));
        t3(ii,1) = str2double(y(3));
        t4(ii,1) = str2double(y(4));
        t5(ii,1) = str2double(y(5));
        t6(ii,1) = str2double(y(6));
        t7(ii,1) = str2double(y(7));
        t8(ii,1) = str2double(y(8));
        t9(ii,1) = str2double(y(9));
        t10(ii,1) = str2double(y(10));
        %sTemp = smooth(data,25);
        %% Read time stamp
        % If reading faster than sampling rate, force sampling time.
        % If reading slower than sampling rate, nothing can be done. Consider
        % decreasing the set sampling time Ts

        t(ii) = toc;
        if ii > 1
            T = toc - t(ii-1);
            while T < Ts
                T = toc - t(ii-1);
            end
        end
        t(ii) = toc;
        grid on
        grid minor
        %% Plot live data
        if ii > 1
            x = [t(ii-1) t(ii)];
            %the two values output by the arduino when the sensor is not
            %attached are 38.98 and 1261.79 - changed these values to 0 using
            %logic
            y1 = [(t1(ii-1)*(t1(ii-1)~=30.98)*(t1(ii-1)~=1261.79)) (t1(ii)*(t1(ii)~=30.98)*(t1(ii)~=1261.79))];
            y2 = [(t2(ii-1)*(t2(ii-1)~=30.98)*(t2(ii-1)~=1261.79)) (t2(ii)*(t2(ii)~=30.98)*(t2(ii)~=1261.79))];
            y3 = [(t3(ii-1)*(t3(ii-1)~=30.98)*(t3(ii-1)~=1261.79)) (t3(ii)*(t3(ii)~=30.98)*(t3(ii)~=1261.79))];
            y4 = [(t4(ii-1)*(t4(ii-1)~=30.98)*(t4(ii-1)~=1261.79)) (t4(ii)*(t4(ii)~=30.98)*(t4(ii)~=1261.79))];
            y5 = [(t5(ii-1)*(t5(ii-1)~=30.98)*(t5(ii-1)~=1261.79)) (t5(ii)*(t5(ii)~=30.98)*(t5(ii)~=1261.79))];
            y6 = [(t6(ii-1)*(t6(ii-1)~=30.98)*(t6(ii-1)~=1261.79)) (t6(ii)*(t6(ii)~=30.98)*(t6(ii)~=1261.79))];
            y7 = [(t7(ii-1)*(t7(ii-1)~=30.98)*(t7(ii-1)~=1261.79)) (t7(ii)*(t7(ii)~=30.98)*(t7(ii)~=1261.79))];
            y8 = [(t8(ii-1)*(t8(ii-1)~=30.98)*(t8(ii-1)~=1261.79)) (t8(ii)*(t8(ii)~=30.98)*(t8(ii)~=1261.79))];
            y9 = [(t9(ii-1)*(t9(ii-1)~=30.98)*(t9(ii-1)~=1261.79)) (t9(ii)*(t9(ii)~=30.98)*(t9(ii)~=1261.79))];
            y10 = [(t10(ii-1)*(t10(ii-1)~=30.98)*(t10(ii-1)~=1261.79)) (t10(ii)*(t10(ii)~=30.98)*(t10(ii)~=1261.79))];
            %replace zero values with nan so they will not be plotted
            y1(y1==0) = nan;
            y2(y2==0) = nan;
            y3(y3==0) = nan;
            y4(y4==0) = nan;
            y5(y5==0) = nan;
            y6(y6==0) = nan;
            y7(y7==0) = nan;
            y8(y8==0) = nan;
            y9(y9==0) = nan;
            y10(y10==0) = nan;
            line(x, y1, 'Color', 'red')
            line(x, y2, 'Color', 'blue')
            line(x, y3, 'Color', 'black')
            line(x, y4, 'Color', 'magenta')
            line(x, y5, 'Color', 'green')
            line(x, y6, 'Color', 'blue')
            line(x, y7, 'Color', 'red')
            line(x, y8, 'Color', 'cyan')
            line(x, y9, 'Color', 'black')
            line(x, y10, 'Color', 'magenta')
            legend ('T1','T2','T3','T4', 'T5', 'T6', 'T7', 'T8', 'T9', 'T10')
            drawnow
        end
    end
end
fclose(b);

The actual results are below. Any help is really appreciated!

(https://www.mathworks.com/matlabcentral/answers/uploaded_files/235007/Capture.png)

(https://www.mathworks.com/matlabcentral/answers/uploaded_files/235006/Capture1.png)

(edit: the images are from mathworks because I posted the same question there last week but didn't receive any responses)


#include <Adafruit_MAX31865.h>
#include<SPI.h>
#include <Wire.h>



// Use software SPI: CS, DI, DO, CLK
//Adafruit_MAX31865 max_1 = Adafruit_MAX31865(A0,12,11,13);
//Adafruit_MAX31865 max_2 = Adafruit_MAX31865(2,12,11,13);
//Adafruit_MAX31865 max_3 = Adafruit_MAX31865(3,12,11,13);
//Adafruit_MAX31865 max_4 = Adafruit_MAX31865(4,12,11,13);
//Adafruit_MAX31865 max_5 = Adafruit_MAX31865(5,12,11,13);
//Adafruit_MAX31865 max_6 = Adafruit_MAX31865(6,12,11,13);
//Adafruit_MAX31865 max_7 = Adafruit_MAX31865(7,12,11,13);
//Adafruit_MAX31865 max_8 = Adafruit_MAX31865(8,12,11,13);
//Adafruit_MAX31865 max_9 = Adafruit_MAX31865(9,12,11,13);
//Adafruit_MAX31865 max_10 = Adafruit_MAX31865(10,12,11,13);

// use hardware SPI, just pass in the CS pin
Adafruit_MAX31865 max_1 = Adafruit_MAX31865(A0);
Adafruit_MAX31865 max_2 = Adafruit_MAX31865(2);
Adafruit_MAX31865 max_3 = Adafruit_MAX31865(3);
Adafruit_MAX31865 max_4 = Adafruit_MAX31865(4);
Adafruit_MAX31865 max_5 = Adafruit_MAX31865(5);
Adafruit_MAX31865 max_6 = Adafruit_MAX31865(6);
Adafruit_MAX31865 max_7 = Adafruit_MAX31865(7);
Adafruit_MAX31865 max_8 = Adafruit_MAX31865(8);
Adafruit_MAX31865 max_9 = Adafruit_MAX31865(9);
Adafruit_MAX31865 max_10 = Adafruit_MAX31865(10);


// The value of the Rref resistor. Use 430.0 for PT100 and 4300.0 for PT1000
#define RREF      430.0
// The 'nominal' 0-degrees-C resistance of the sensor
// 100.0 for PT100, 1000.0 for PT1000
#define RNOMINAL  100.0
float kelvin1;
float kelvin2;
float kelvin3;
float kelvin4;
float kelvin5;
float kelvin6;
float kelvin7;
float kelvin8;
float kelvin9;
float kelvin10;

void setup() {
  Serial.begin(115200);
  Wire.begin();


  //Serial.println("Adafruit MAX31865 PT100 Sensor Test!");
  max_1.begin(MAX31865_4WIRE);  // set to 2WIRE or 4WIRE as necessary
  max_2.begin(MAX31865_4WIRE);
  max_3.begin(MAX31865_4WIRE);
  max_4.begin(MAX31865_4WIRE);
  max_5.begin(MAX31865_4WIRE);
  max_6.begin(MAX31865_4WIRE);
  max_7.begin(MAX31865_4WIRE);
  max_8.begin(MAX31865_4WIRE);
  max_9.begin(MAX31865_4WIRE);
  max_10.begin(MAX31865_4WIRE);
}


void loop() {

  uint16_t rtd1 = max_1.readRTD();
  uint16_t rtd2 = max_2.readRTD();
  uint16_t rtd3 = max_3.readRTD();
  uint16_t rtd4 = max_4.readRTD();
  uint16_t rtd5 = max_5.readRTD();
  uint16_t rtd6 = max_6.readRTD();
  uint16_t rtd7 = max_7.readRTD();
  uint16_t rtd8 = max_8.readRTD();
  uint16_t rtd9 = max_9.readRTD();
  uint16_t rtd10 = max_10.readRTD();

  //  Serial.print("RTD value: "); Serial.println(rtd);
  float ratio1 = rtd1;
  ratio1 /= 32768;
  float ratio2 = rtd2;
    ratio2 /= 32768;
    float ratio3 = rtd3;
    ratio3 /= 32768;
    float ratio4 = rtd4;
    ratio4 /= 32768;
    float ratio5 = rtd5;
    ratio5 /= 32768;
    float ratio6 = rtd6;
    ratio6 /= 32768;
    float ratio7 = rtd7;
    ratio7 /= 32768;
    float ratio8 = rtd8;
    ratio8 /= 32768;
    float ratio9 = rtd9;
    ratio9 /= 32768;
    float ratio10 = rtd10;
    ratio10 /= 32768;

  kelvin1 = (max_1.temperature(RNOMINAL, RREF)) + 273;
  kelvin2 = (max_2.temperature(RNOMINAL, RREF))+273;
    kelvin3 = (max_3.temperature(RNOMINAL, RREF))+273;
    kelvin4 = (max_4.temperature(RNOMINAL, RREF))+273;
    kelvin5 = (max_5.temperature(RNOMINAL, RREF))+273;
    kelvin6 = (max_6.temperature(RNOMINAL, RREF))+273;
    kelvin7 = (max_7.temperature(RNOMINAL, RREF))+273;
    kelvin8 = (max_8.temperature(RNOMINAL, RREF))+273;
    kelvin9 = (max_9.temperature(RNOMINAL, RREF))+273;
    kelvin10 = (max_10.temperature(RNOMINAL, RREF))+273;

  //Serial.print("Ratio = "); Serial.println(ratio1,8);
  Serial.print(kelvin1);
  Serial.print(", ");
  Serial.print(kelvin2);
    Serial.print(", ");
    Serial.print(kelvin3);
    Serial.print(", ");
    Serial.print(kelvin4);
    Serial.print(", ");
    Serial.print(kelvin5);
    Serial.print(", ");
    Serial.print(kelvin6);
    Serial.print(", ");
    Serial.print(kelvin7);
    Serial.print(", ");
    Serial.print(kelvin8);
    Serial.print(", ");
    Serial.print(kelvin9);
    Serial.print(", ");
    Serial.print(kelvin10);
    Serial.print(", ");


  Serial.println();

  /*
      // Check and print any faults
      uint8_t fault = max_1.readFault();
      if (fault) {
        Serial.print("Fault 0x"); Serial.println(fault, HEX);
        if (fault & MAX31865_FAULT_HIGHTHRESH) {
          Serial.println("RTD High Threshold");
        }
        if (fault & MAX31865_FAULT_LOWTHRESH) {
          Serial.println("RTD Low Threshold");
        }
        if (fault & MAX31865_FAULT_REFINLOW) {
          Serial.println("REFIN- > 0.85 x Bias");
        }
        if (fault & MAX31865_FAULT_REFINHIGH) {
          Serial.println("REFIN- < 0.85 x Bias - FORCE- open");
        }
        if (fault & MAX31865_FAULT_RTDINLOW) {
          Serial.println("RTDIN- < 0.85 x Bias - FORCE- open");
        }
        if (fault & MAX31865_FAULT_OVUV) {
          Serial.println("Under/Over voltage");
        }
        max_1.clearFault();
      }
  */
  delay(50);

}

A tip: don't use variables as `t1, t2, t3` etc. This is called dynamic variable naming, and [will eventually get you into trouble](https://stackoverflow.com/a/32467170/5211833). Instead, use a single variable `t`, and give that a 3rd dimension, or, if the matrices are not the same size, use cells or structs. This will result in less hand-copying of lines, more readable code, faster code, and less hard to find bugs. — Adriaan, Aug 27 '19 at 09:28
Whenever I see an issue near a power of 2 (e.g, the 16th/32nd/64th/... *thing*), I start wondering if there is a memory issue somewhere. It's good that you've isolated your issue to concerning every 63rd sample, I suspect somewhere your buffer runs out of space and resets (or something similar), I say this without knowing anything about reading from a serial Arduino port! — Wolfie, Aug 27 '19 at 09:30
Why are you using a `1000000` baudrate ? From the arduino doc: `Supported baud rates are 300, 600, 1200, 2400, 4800, 9600, 14400, 19200, 28800, 31250, 38400, 57600, and 115200.` Also I would avoid using the maximal baudrate if it's not necessary. — obchardon, Aug 27 '19 at 10:10
@obchardon because my supervisor suggested it to see if it made a difference. the problem was the same at lower baud rates — Amy Fawcett, Aug 27 '19 at 10:12
So as explained by @Wolfie there is probably a memory issue. You should also post your arduino code. — obchardon, Aug 27 '19 at 10:33
You are performing quite some floating point calculations on the Arduino, but are not using these variables (`ratio1` etc.) after they are calculated. What happens if you remove this? Use baud rate `115200`. In general, avoid performing floating point calculations on Arduino's, especially if you are transferring data to a pc, which can handle this much better. — rinkert, Aug 27 '19 at 11:57
Do you know for sure if the problem is with Matlab, or whether the Arduino just starts to send zeros after a long time? (easy check just using a serial monitor for a couple hours) If the problem is reading the sensors on the Arduino, you could implement a watchdog timer (/trigger the watchdog), which will reset the Arduino. — rinkert, Aug 27 '19 at 12:09
@rinkert it's definitely matlab, the Arduino is still outputting data once the problem starts occurring (I checked) — Amy Fawcett, Aug 27 '19 at 12:29

score 2 · Accepted Answer · answered Aug 27 '19 at 13:50

2

So, I checked out @Wolfie's suggestion (and found that an Arduino nano's buffer is 64 bits, fitting this theory) and added

flushinput(b);

after reading the values from the serial input, to flush the input buffer. Just tested it out and it works perfectly - thanks for your help!

answered Aug 27 '19 at 13:50

Amy Fawcett

41
5

1

Glad I could help! Once you hit these problems a couple of times, you begin to develop a wariness towards 2^n (or 2^n-1 for 0-based systems) – Wolfie Aug 27 '19 at 15:17

how to stop data being skipped when recording over long intervals?

1 Answers1