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main_ver2_merged_with_live_peak_analysis.py
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main_ver2_merged_with_live_peak_analysis.py
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from piotimer import Piotimer as Timer
from ssd1306 import SSD1306_I2C
from machine import Pin, ADC, I2C, PWM
from fifo import Fifo
import utime
import array
import time
import network
import socket
import urequests as requests
import ujson
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.#
# #
# GPIO PINS #
# #
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*:*.*.*.*.*.*.*.*.*.#
# ADC-converter
adc = ADC(26)
# OLED
i2c = I2C(1, scl = Pin(15), sda = Pin(14))
oled = SSD1306_I2C(128, 64, i2c)
# LEDs
led_onboard = Pin("LED", Pin.OUT)
led21 = PWM(Pin(21))
led21.freq(1000)
# Rotary Encoder
rot_push = Pin(12, mode = Pin.IN, pull = Pin.PULL_UP)
rota = Pin(10, mode = Pin.IN, pull = Pin.PULL_UP)
rotb = Pin(11, mode = Pin.IN, pull = Pin.PULL_UP)
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.#
# #
# VARIABLES #
# #
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*:*.*.*.*.*.*.*.*.*.#
# Sample Rate, Buffer
samplerate = 250
samples = Fifo(32)
# Menu selection variables and switch filtering
mode = 0
count = 0
switch_state = 0
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.#
# #
# FUNCTIONS #
# #
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*:*.*.*.*.*.*.*.*.*.#
#######################################
# Function for reading the signal #
#######################################
def read_adc(tid):
x = adc.read_u16()
samples.put(x)
########################################
# Function to display welcome text #
########################################
def welcome_text():
oled.fill(1)
i = 0
h = 0
for i in range(8):
oled.pixel(5+h, 3, 0)
oled.pixel(9+h, 3, 0)
oled.pixel(5+h, 54, 0)
oled.pixel(9+h, 54, 0)
oled.line(4+h, 4, 6+h, 4, 0)
oled.line(4+h, 55, 6+h, 55, 0)
oled.line(8+h, 4, 10+h, 4, 0)
oled.line(8+h, 55, 10+h, 55, 0)
oled.line(3+h, 5, 11+h, 5, 0)
oled.line(3+h, 56, 11+h, 56, 0)
oled.line(4+h, 6, 10+h, 6, 0)
oled.line(4+h, 57, 10+h, 57, 0)
oled.line(5+h, 7, 9+h, 7, 0)
oled.line(5+h, 58, 9+h, 58, 0)
oled.line(6+h, 8, 8+h, 8, 0)
oled.line(6+h, 59, 8+h, 59, 0)
oled.pixel(7+h, 9, 0)
oled.pixel(7+h, 60, 0)
i += 1
h += 16
oled.text("Welcome to", 26, 17, 0)
oled.text("Group 5's", 29, 27, 0)
oled.text("project!", 33, 37, 0)
oled.show()
utime.sleep_ms(3750)
########################################
# Function to display "Start menu" #
########################################
def press_to_start():
oled.fill(0)
oled.text("Press to start", 4, 7, 1)
oled.text("the measurement", 4, 17, 1)
oled.line(45, 53, 60, 53, 1)
oled.line(60, 53, 63, 50, 1)
oled.line(63, 50, 66, 53, 1)
oled.line(66, 53, 68, 53, 1)
oled.line(68, 53, 70, 57, 1)
oled.line(70, 57, 73, 31, 1)
oled.line(73, 31, 76, 64, 1)
oled.line(76, 64, 78, 53, 1)
oled.line(78, 53, 80, 53, 1)
oled.line(80, 53, 84, 47, 1)
oled.line(84, 47, 88, 53, 1)
oled.line(88, 53, 89, 53, 1)
oled.line(89, 53, 91, 51, 1)
oled.line(91, 51, 93, 53, 1)
oled.line(93, 53, 124, 53, 1)
oled.line(118, 48, 124, 53, 1)
oled.line(118, 58, 124, 53, 1)
oled.show()
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.#
# Functions for HRV calculations #
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*:*.*.*.*.*.*.*.*.*.#
###########################
# Mean PPI Calculator #
###########################
def meanPPI_calculator(data):
sumPPI = 0
for i in data:
sumPPI += i
rounded_PPI = round(sumPPI/len(data), 0)
return int(rounded_PPI)
##########################
# Mean HR Calculator #
##########################
def meanHR_calculator(meanPPI):
rounded_HR = round(60*1000/meanPPI, 0)
return int(rounded_HR)
#######################
# SDNN Calculator #
#######################
def SDNN_calculator(data, PPI):
summary = 0
for i in data:
summary += (i-PPI)**2
SDNN = (summary/(len(data)-1))**(1/2)
rounded_SDNN = round(SDNN, 0)
return int(rounded_SDNN)
########################
# RMSSD Calculator #
########################
def RMSSD_calculator(data):
i = 0
summary = 0
while i < len(data)-1:
summary += (data[i+1]-data[i])**2
i +=1
rounded_RMSSD = round((summary/(len(data)-1))**(1/2), 0)
return int(rounded_RMSSD)
#######################
# SDSD Calculator #
#######################
def SDSD_calculator(data):
PP_array = array.array('l')
i = 0
first_value = 0
second_value = 0
while i < len(data)-1:
PP_array.append(int(data[i+1])-int(data[i]))
i += 1
i = 0
while i < len(PP_array)-1:
first_value += float(PP_array[i]**2)
second_value += float(PP_array[i])
i += 1
first = first_value/(len(PP_array)-1)
second = (second_value/(len(PP_array)))**2
rounded_SDSD = round((first - second)**(1/2), 0)
return int(rounded_SDSD)
######################
# SD1 Calculator #
######################
def SD1_calculator(SDSD):
rounded_SD1 = round(((SDSD**2)/2)**(1/2), 0)
return int(rounded_SD1)
######################
# SD2 Calculator #
######################
def SD2_calculator(SDNN, SDSD):
rounded_SD2 = round(((2*(SDNN**2))-((SDSD**2)/2))**(1/2), 0)
return int(rounded_SD2)
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.#
# #
# MAIN PROGRAMME #
# #
#*.*.*.*.*.*.*.*.*.*.*.*.*.*.*.*:*.*.*.*.*.*.*.*.*.#
welcome_text()
avg_size = int(samplerate * 0.5)
buffer = array.array('H',[0]*avg_size)
while True:
press_to_start()
new_state = rot_push.value()
if new_state != switch_state:
count += 1
if count > 3:
if new_state == 0:
if mode == 0:
mode = 1
else:
mode = 0
led_onboard.value(1)
time.sleep(0.15)
led_onboard.value(0)
switch_state = new_state
count = 0
else:
count = 0
utime.sleep(0.01)
if mode == 1:
count = 0
switch_state = 0
oled.fill(0)
oled.show()
x1 = -1
y1 = 32
m0 = 65535/2
a = 1/10
disp_div = samplerate/50
disp_count = 0
capture_length = samplerate*30
index = 0
capture_count = 0
subtract_old_sample = 0
sample_sum = 0
min_bpm = 30
max_bpm = 200
sample_peak = 0
sample_index = 0
previous_peak = 0
previous_index = 0
PPI_array = []
brightness = 0
tmr = Timer(freq = samplerate, callback = read_adc)
#####################################
# Plotting the signal, Sampling #
#####################################
while capture_count < capture_length:
if not samples.empty():
x = samples.get()
disp_count += 1
if disp_count >= disp_div:
disp_count = 0
m0 = (1-a)*m0 + a*x
y2 = int(32*(m0-x)/10000 + 32)
y2 = max(0, min(64, y2))
x2 = x1 + 1
oled.line(x2, 0, x2, 64, 0)
oled.line(x1, y1, x2, y2, 1)
oled.show()
x1 = x2
if x1 > 127:
x1 = -1
y1 = y2
if subtract_old_sample:
old_sample = buffer[index]
else:
old_sample = 0
sample_sum = sample_sum + x - old_sample
######################
# Peak Detection #
######################
if subtract_old_sample:
sample_avg = sample_sum / avg_size
sample_val = x
if sample_val > sample_avg * 1.05:
if sample_val > sample_peak:
sample_peak = sample_val
sample_index = capture_count
else:
if sample_peak > 0:
if (sample_index - previous_index) > (60 * samplerate / min_bpm):
previous_peak = 0
previous_index = sample_index
else:
if sample_peak >= (0.8 * previous_peak):
if (sample_index - previous_index) > (60 * samplerate / max_bpm):
if previous_peak > 0:
interval = sample_index - previous_index
interval_ms = int(interval * 1000 / samplerate)
PPI_array.append(interval_ms)
brightness = 5
led21.duty_u16(3000)
#print("BPM: " + str((samplerate / interval) * 60))
previous_peak = sample_peak
previous_index = sample_index
#print("Sample " + str(sample_index) + " peak: " + str(sample_peak))
sample_peak = 0
if brightness > 0:
brightness -= 1
else:
led21.duty_u16(0)
buffer[index] = x
capture_count += 1
index += 1
if index >= avg_size:
index = 0
subtract_old_sample = 1
tmr.deinit()
while not samples.empty():
x = samples.get()
#print(PPI_array)
#######################
# HRV calculation #
#######################
#PPI_array2 = [754, 854, 968, 796, 785, 983, 1012, 879, 846, 794, 689, 987, 834, 821, 768, 895]
oled.fill(0)
if len(PPI_array) >= 3:
mean_PPI = meanPPI_calculator(PPI_array)
mean_HR = meanHR_calculator(mean_PPI)
SDNN = SDNN_calculator(PPI_array, mean_PPI)
RMSSD = RMSSD_calculator(PPI_array)
SDSD = SDSD_calculator(PPI_array)
SD1 = SD1_calculator(SDSD)
SD2 = SD2_calculator(SDNN, SDSD)
oled.text('MeanPPI:'+ str(int(mean_PPI)) +'ms', 0, 0, 1)
oled.text('MeanHR:'+ str(int(mean_HR)) +'bpm', 0, 9, 1)
oled.text('SDNN:'+str(int(SDNN)) +'ms', 0, 18, 1)
oled.text('RMSSD:'+str(int(RMSSD)) +'ms', 0, 27, 1)
oled.text('SD1:'+str(int(SD1))+' SD2:'+str(int(SD2)), 0, 36, 1)
#oled.text('PNS:'+str(PNS), 0, 45, 1)
#oled.text('SNS:'+str(SNS), 0, 54, 1)
else:
oled.text('Error', 45, 10, 1)
oled.text('Please restart', 8, 30, 1)
oled.text('measurement', 20, 40, 1)
oled.show()
while mode == 1:
new_state = rot_push.value()
if new_state != switch_state:
count += 1
if count > 3:
if new_state == 0:
if mode == 0:
mode = 1
else:
mode = 0
led_onboard.value(1)
time.sleep(0.15)
led_onboard.value(0)
switch_state = new_state
count = 0
else:
count = 0
utime.sleep(0.01)