HeartBeatDetection.ino

// Heart Beat Detection - BioAmp EXG Pill
// https://github.com/upsidedownlabs/BioAmp-EXG-Pill

// Upside Down Labs invests time and resources providing this open source code,
// please support Upside Down Labs and open-source hardware by purchasing
// products from Upside Down Labs!

// Copyright (c) 2021 Upside Down Labs - contact@upsidedownlabs.tech

// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:

// The above copyright notice and this permission notice shall be included in all
// copies or substantial portions of the Software.

// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.

#include <math.h>

#define SAMPLE_RATE 125
#define BAUD_RATE 115200
#define INPUT_PIN A0
#define OUTPUT_PIN 13
#define DATA_LENGTH 16

int data_index = 0;
bool peak = false;


void setup() {
	// Serial connection begin
	Serial.begin(BAUD_RATE);
	// Setup Input & Output pin
	pinMode(INPUT_PIN, INPUT);
	pinMode(OUTPUT_PIN, OUTPUT);
}

void loop() {
	// Calculate elapsed time
	static unsigned long past = 0;
	unsigned long present = micros();
	unsigned long interval = present - past;
	past = present;

	// Run timer
	static long timer = 0;
	timer -= interval;

	// Sample
	if(timer < 0){
		timer += 1000000 / SAMPLE_RATE;
    	// Sample and Nomalize input data (-1 to 1)
		float sensor_value = analogRead(INPUT_PIN);
		float signal = ECGFilter(sensor_value)/512;
    	// Get peak
    	peak = Getpeak(signal);
    	// Print sensor_value and peak
    	Serial.print(signal);
    	Serial.print(",");
    	Serial.println(peak);
    	// Blink LED on peak
    	digitalWrite(OUTPUT_PIN, peak);
	}
}

bool Getpeak(float new_sample) {
	// Buffers for data, mean, and standard deviation
	static float data_buffer[DATA_LENGTH];
	static float mean_buffer[DATA_LENGTH];
	static float standard_deviation_buffer[DATA_LENGTH];
  
	// Check for peak
	if (new_sample - mean_buffer[data_index] > (DATA_LENGTH/2) * standard_deviation_buffer[data_index]) {
		data_buffer[data_index] = new_sample + data_buffer[data_index];
		peak = true;
	} else {
		data_buffer[data_index] = new_sample;
		peak = false;
	}

	// Calculate mean
	float sum = 0.0, mean, standard_deviation = 0.0;
	for (int i = 0; i < DATA_LENGTH; ++i){
		sum += data_buffer[(data_index + i) % DATA_LENGTH];
	}
	mean = sum/DATA_LENGTH;

	// Calculate standard deviation
	for (int i = 0; i < DATA_LENGTH; ++i){
		standard_deviation += pow(data_buffer[(i) % DATA_LENGTH] - mean, 2);
	}

	// Update mean buffer
	mean_buffer[data_index] = mean;

	// Update standard deviation buffer
	standard_deviation_buffer[data_index] =  sqrt(standard_deviation/DATA_LENGTH);

	// Update data_index
	data_index = (data_index+1)%DATA_LENGTH;

	// Return peak
	return peak;
}

// Band-Pass Butterworth IIR digital filter, generated using filter_gen.py.
// Sampling rate: 125.0 Hz, frequency: [0.5, 44.5] Hz.
// Filter is order 4, implemented as second-order sections (biquads).
// Reference:
// https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.butter.html
// https://courses.ideate.cmu.edu/16-223/f2020/Arduino/FilterDemos/filter_gen.py
float ECGFilter(float input)
{
  float output = input;
  {
    static float z1, z2; // filter section state
    float x = output - 0.70682283*z1 - 0.15621030*z2;
    output = 0.28064917*x + 0.56129834*z1 + 0.28064917*z2;
    z2 = z1;
    z1 = x;
  }
  {
    static float z1, z2; // filter section state
    float x = output - 0.95028224*z1 - 0.54073140*z2;
    output = 1.00000000*x + 2.00000000*z1 + 1.00000000*z2;
    z2 = z1;
    z1 = x;
  }
  {
    static float z1, z2; // filter section state
    float x = output - -1.95360385*z1 - 0.95423412*z2;
    output = 1.00000000*x + -2.00000000*z1 + 1.00000000*z2;
    z2 = z1;
    z1 = x;
  }
  {
    static float z1, z2; // filter section state
    float x = output - -1.98048558*z1 - 0.98111344*z2;
    output = 1.00000000*x + -2.00000000*z1 + 1.00000000*z2;
    z2 = z1;
    z1 = x;
  }
  return output;
}