Brian K
Published © CC BY

Accelerometer and Data Logger for Small Animal Research

This is a low-cost, low-power, customizable data logger for animal research.

IntermediateWork in progress1 hour2,023
Accelerometer and Data Logger for Small Animal Research

Things used in this project

Hardware components

TinyZero
TinyCircuits TinyZero
×1
TinyShield MicroSD
TinyCircuits TinyShield MicroSD
×1
Lithium Ion Polymer Battery
TinyCircuits Lithium Ion Polymer Battery
×1
Generic micro SD card
×1

Software apps and online services

Arduino IDE
Arduino IDE

Story

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Code

sdlogger.ino

Arduino
Main Arduino script for collecting data and saving to SD card using as little power as possible
//Libraries
#include <Wire.h>
#include <BMA250.h>
#include <RTCZero.h>            // Can only go into sleep on second intervals
                                // Does not have power down flash or SYSTICK modifications
#include <Adafruit_SleepyDog.h> //Has power down flash correct, but not SYSTICK
                                //Allows you to do millisecond sleep, but limited to WDT limit ~18s
#include <SdFat.h>
#include <SPI.h>
#include <ArduinoLowPower.h>    //Use RTC library for timing, therefore can only sleep in second intervals
                                //Has power down flash and SYSTICK correct
// Parameters to change:
char fileName[] = "logfile.csv";

#define INITIAL_SLEEP_TIME 240 //hours; How long to sleep on power, allows to delay start of recording to save power
#define RECORD_INTERVAL 15 //seconds; How long to collect data for during each recording interval
#define SLEEP_BETWEEN_INTERVAL 900 //seconds; How long to sleep between recording intervals
#define SAVE_INTERVAL 14400 //seconds; How long to delay between SD card saves. Each save uses a lot of power, so we only save occasionally
#define SLEEP_BETWEEN_SAMPLES 60 //milliseconds; Time between samples, determined by data rate of accelerometer
#define TIME_BETWEEN_SAMPLES 64 //milliseconds; Adjustment factor to keep timestamp accurate after sleep
#define DATA_COUNT 4 //Number of data fields you are collecting. For x,y,z accelerations + temperature -> DATA_COUNT=4

#define CHIP_SELECT 10
#define SECONDS_IN_MIN 60
#define SECONDS_IN_HOUR 3600
#define SECONDS_IN_DAY 86400
#define EPOCH_OFFSET 946684800 //Convert Y2K to epoch time, allows timestamp to start at 0
#define error(msg) sd.errorPrint(&SerialUSB)

int wakeupTime; //Records RTC time when processor wakes up
int prevTime; //Records RTC time (second) at each sample
int lastSave; //Record last time data was stored (synced) on SD card
int iteration = 0;

RTCZero rtc; //create RTC object
BMA250 accelSensor; //create BMA250 accelerometer object
SdFat sd; //create file system object
SdFile file; //create file object

void setup() {
  //If SD initialization fails, light LED
  if (!sd.begin(CHIP_SELECT, SD_SCK_MHZ(50))) {
    SPI.end();
    lightLED();
  }
  //If file creation fails light LED
  if (!file.open(fileName, O_WRONLY | O_CREAT | O_APPEND)) {
    SPI.end();
    lightLED();
  }

  detectReset(); //Checks reason for reset, for debugging
  file.sync();

  //Initialize RTC
  rtc.begin();
  rtc.setEpoch(0);

  //Initialize Sensor
  Wire.begin();
  accelSensor.begin(BMA250_range_2g, BMA250_update_time_64ms);

  //Set alarm for initial sleep - allows for to delay recording
  rtc.setAlarmEpoch(rtc.getEpoch() + INITIAL_SLEEP_TIME * SECONDS_IN_HOUR);
  rtc.enableAlarm(rtc.MATCH_YYMMDDHHMMSS);
  LowPower.sleep();

  // Record time at wakeup, record initial timestamp time
  wakeupTime = rtc.getEpoch();
  prevTime = rtc.getEpoch() - EPOCH_OFFSET;

}

void loop() {

  // Data array
  double data[DATA_COUNT];

  //Get data
  getAccel(data);

  //Create timestamp
  String timeStampNow = getTimestamp(&prevTime);

  //Record timestamp and data
  writeData(timeStampNow, data);

  // Sleep bewteen samples
  Watchdog.sleep(SLEEP_BETWEEN_SAMPLES);

  int currentTime = rtc.getEpoch();
  //If current recording time interval is over, go to sleep for sleep period
  if (currentTime - wakeupTime > RECORD_INTERVAL) {

    //If data has not been saved to SD card recently, save the data
    if (currentTime - lastSave > SAVE_INTERVAL) {

      lastSave = currentTime;
      file.sync();
    }
    
    rtc.setAlarmEpoch(currentTime + SLEEP_BETWEEN_INTERVAL); //Set alarm SLEEP_BETWEEN_INTERVAL seconds from now
    rtc.enableAlarm(rtc.MATCH_YYMMDDHHMMSS);
    LowPower.sleep();
    wakeupTime = rtc.getEpoch();
  }
}

void getAccel(double pdata[]) {
  accelSensor.read();
  pdata[0] = accelSensor.X;
  pdata[1] = accelSensor.Y;
  pdata[2] = accelSensor.Z;
  pdata[3] = ((accelSensor.rawTemp * 0.5) + 24.0);
}

String getTimestamp(int *pprevTime) {
  int timeStamp = rtc.getEpoch() - EPOCH_OFFSET;

  //RTC only returns whole seconds. Therefore to get a timestamp at the millisecond
  //level, we estimate it. We know the sampling rate of the accelerometer. Therefore, each time
  //the RTC changes, for example from second 11 to second 12, we start a counter at 0.
  //This counter increments each time the accelerometer collects data. The millisecond
  //portion of the time stamp is then estimated as (iteration * time_between_samples)
  
  //If the RTC has changed, set prevTime to new second, and reset the counter to 0
  if (timeStamp != *pprevTime) {
    iteration = 0;
    *pprevTime = timeStamp;
  }

  //If RTC is stil on the same second, increment the counter
  else {
    iteration += 1;
  }

  //Calculate timestamp values and concatenate
  int t_ms = iteration * TIME_BETWEEN_SAMPLES;
  int t_sec = timeStamp % SECONDS_IN_MIN;
  int t_min = (timeStamp / SECONDS_IN_MIN) % SECONDS_IN_MIN;
  int t_hr =  (timeStamp % SECONDS_IN_DAY) / SECONDS_IN_HOUR;
  int t_day = (timeStamp / SECONDS_IN_DAY);

  String colon = " : ";
  String dot = ".";

  String timeStampString = t_day + colon + t_hr + colon +
                           t_min + colon + t_sec + dot + t_ms;
  return timeStampString;
}

void writeData(String timeStamp, double pdata[]) {
  file.print(timeStamp);

  for (byte i = 0; i < DATA_COUNT; i = i + 1) {
    file.write(",");
    file.print(pdata[i]);
  }

  file.println();
}

void detectReset() {
  if (REG_PM_RCAUSE == PM_RCAUSE_SYST) {
    file.println(F("Reset requested by system"));
  }
  if (REG_PM_RCAUSE == PM_RCAUSE_WDT) {
    file.println(F("Reset requested by Watchdog"));
  }
  if (REG_PM_RCAUSE == PM_RCAUSE_EXT) {
    file.println(F("External reset requested"));
  }
  if (REG_PM_RCAUSE == PM_RCAUSE_BOD33) {
    file.println(F("Reset brown out 3.3V"));
  }
  if (REG_PM_RCAUSE == PM_RCAUSE_BOD12) {
    file.println(F("Reset brown out 1.2v"));
  }
  if (REG_PM_RCAUSE == PM_RCAUSE_POR) {
    file.println(F("Normal power on reset"));
  }
}

void lightLED() {
  pinMode(LED_BUILTIN, OUTPUT);
  while (1) {
    digitalWrite(LED_BUILTIN, HIGH);
  }
}

BMA250 Library

Library for the BMA250 accelerometer on the TinyZero

(Fixed) Adafruit Sleepy Dog library

Timer and sleep code for saving power

Arduino Low Power Library

Library for putting Arduino to sleep to save power

RTC Zero library

Use the Real Time Clock on the TinyCircuits TinyZero

Credits

Brian K

Brian K

1 project • 3 followers
Dedicated to helping others use technology to help themselves and others.
Thanks to CHAN Wing Sing and SUNG Yik Hei.

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