def __init__(self, num_samples, fs, data=None):
self.__steps = 0
self.__num_samples = num_samples
self.__fs = fs
self.__l1 = CircularList(data, num_samples)
self.__filtered = CircularList([], num_samples)
self.__b, self.__a = filt.create_filter(3, 1.2, "lowpass", fs)
self.__peak_arr = []
def __init__(self, num_samples, fs, times=[], data=[]):
self.__hr = 0
self.__num_samples = num_samples
self.__fs = fs
self.__time = CircularList(times, num_samples)
self.__ppg = CircularList(data, num_samples)
self.__filtered = CircularList([], num_samples)
def collect_samples():
num_samples = 500 # 10 seconds of data @ 50Hz
times = CircularList([], num_samples)
ppg = CircularList([], num_samples)
comms = Communication("/dev/cu.usbserial-1420", 115200)
try:
comms.clear() # just in case any junk is in the pipes
# wait for user and then count down
input("Ready to collect data? Press [ENTER] to begin.\n")
print("Start measuring in...")
for k in range(3,0,-1):
print(k)
sleep(1)
print("Begin!")
comms.send_message("wearable") # begin sending data
sample = 0
while(sample < num_samples):
message = comms.receive_message()
if(message != None):
try:
(m1, _, _, _, m2) = message.split(',')
except ValueError: # if corrupted data, skip the sample
continue
# add the new values to the circular lists
times.add(int(m1))
ppg.add(int(m2))
sample += 1
print("Collected {:d} samples".format(sample))
# a single ndarray for all samples for easy file I/O
data = np.column_stack([times, ppg])
except(Exception, KeyboardInterrupt) as e:
print(e) # exiting the program due to exception
finally:
comms.send_message("sleep") # stop sending data
comms.close()
return data
from matplotlib import pyplot as plt
from time import time
from time import sleep
import numpy as np
if __name__ == "__main__":
fs = 50 # sampling rate
num_samples = 500 # 10 seconds of data @ 50Hz
process_time = 1 # compute the heart beat every second
MAX_HEART_RATE = 200
hr = HRMonitor(num_samples, 50)
comms = Communication("/dev/cu.ag-ESP32SPP", 115200)
comms.clear() # just in case any junk is in the pipes
comms.send_message("wearable") # begin sending data
print("Ready!")
hr_plot = CircularList([], num_samples)
t = CircularList([], num_samples)
# Live data
try:
previous_time = time()
while(True):
message = comms.receive_message()
if (message != None):
try:
(m1, _, _, _, m2) = message.split(',')
except ValueError: # if corrupted data, skip the sample
continue
# Collect data in the pedometer
hr.add(int(m1)/1e3, int(m2))
t.add(int(m1)/1e3)
t_plot = np.array(t)
if __name__ == "__main__":
num_samples = 100 # 2 seconds of data @ 50Hz
refresh_time = 0.1 # update the plot every 0.1s (10 FPS)
# This is a predefined dictionary I will use to decide what transformation method to call
transform_dict = {
0: average_value,
1: sample_difference,
2: l2_norm_calculation,
3: l1_norm_calculation,
4: max_acceleration
}
transform_method = transform_dict[0]
times = CircularList([], num_samples)
ax = CircularList([], num_samples)
ay = CircularList([], num_samples)
az = CircularList([], num_samples)
# These will contain data for the transformation data
transform_x = CircularList([], num_samples)
transform_y = CircularList([], num_samples)
transform_z = CircularList([], num_samples)
fig = plt.figure()
ax1 = fig.add_subplot(311)
ax2 = fig.add_subplot(312)
ax3 = fig.add_subplot(313)
comms = Communication("/dev/cu.AkshayBluetooth-ESP32SPP", 115200)
class Pedometer:
"""
Encapsulated class attributes (with default values)
"""
__steps = 0 # the current step count
__l1 = None # CircularList containing L1-norm
__filtered = None # CircularList containing filtered signal
__num_samples = 0 # The length of data maintained
__new_samples = 0 # How many new samples exist to process
__fs = 0 # Sampling rate in Hz
__b = None # Low-pass coefficients
__a = None # Low-pass coefficients
__thresh_low = 1.5 # Threshold from Tutorial 2
__thresh_high = 15 # Threshold from Tutorial 2
"""
Initialize the class instance
"""
def __init__(self, num_samples, fs, data=None):
self.__steps = 0
self.__num_samples = num_samples
self.__fs = fs
self.__l1 = CircularList(data, num_samples)
self.__filtered = CircularList([], num_samples)
self.__b, self.__a = filt.create_filter(3, 1.2, "lowpass", fs)
self.__peak_arr = []
"""
Sets the upper and threshold for detecting steps
"""
def set_thresholds(self, low_thresh, high_thresh):
self.__thresh_low = low_thresh
self.__thresh_high = high_thresh
"""
Add new samples to the data buffer
Handles both integers and vectors!
"""
def add(self, ax, ay, az):
l1 = filt.l1_norm(ax, ay, az)
if isinstance(ax, int):
num_add = 1
else:
num_add = len(ax)
l1 = l1.tolist()
self.__l1.add(l1)
self.__new_samples += num_add
"""
Process the new data to update step count
"""
def process(self):
# Grab only the new samples into a NumPy array
x = np.array(self.__l1[-self.__new_samples:])
# Filter the signal (detrend, LP, MA, etc…)
# ...
# ...
# ...
# Store the filtered data
ma = filt.moving_average(x, 20) # Compute Moving Average
dt = filt.detrend(ma) # Detrend the Signal
lp = filt.filter(self.__b, self.__a, dt) # Low-pass Filter Signal
grad = filt.gradient(lp) # Compute the gradient
x = filt.moving_average(
grad, 20) # Compute the moving average of the gradient
self.__filtered.add(x.tolist())
# Count the number of peaks in the filtered data
count, peaks = filt.count_peaks(x, self.__thresh_low,
self.__thresh_high)
# Update the step count and reset the new sample count
self.__steps += count
self.__new_samples = 0
# Return the step count, peak locations, and filtered data
return self.__steps, peaks, np.array(self.__filtered)
"""
Clear the data buffers and step count
"""
def reset(self):
self.__steps = 0
def collect_samples():
num_samples = 500 # 10 seconds of data @ 50Hz
times = CircularList([], num_samples)
ax = CircularList([], num_samples)
ay = CircularList([], num_samples)
az = CircularList([], num_samples)
comms = Communication("/dev/cu.ag-ESP32SPP", 115200)
try:
comms.clear() # just in case any junk is in the pipes
# wait for user to start walking before starting to collect data
input(
"Walk for 10 seconds to calibrate the pedometer. Press [ENTER] to begin.\n"
)
sleep(3)
comms.send_message("wearable") # begin sending data
sample = 0
while sample < num_samples:
message = comms.receive_message()
if (message != None):
try:
(m1, m2, m3, m4) = message.split(',')
except ValueError: # if corrupted data, skip the sample
continue
# add the new values to the circular lists
times.add(int(m1))
ax.add(int(m2))
ay.add(int(m3))
az.add(int(m4))
sample += 1
print("Collected {:d} samples".format(sample))
# a single ndarray for all samples for easy file I/O
data = np.column_stack([times, ax, ay, az])
except (Exception, KeyboardInterrupt) as e:
print(e) # exiting the program due to exception
finally:
comms.send_message("sleep") # stop sending data
comms.close()
return data
num_samples = 500 # 10 seconds of data @ 50Hz
process_time = 1 # compute the heart beat every second
MAX_HEART_RATE = 200 # the maximum heart rate possible
initial_period = num_samples / fs # set initial period in seconds
hr = HRMonitor(num_samples, fs)
hr.train()
input("Ready to start monitoring? Press [ENTER] to begin.\n")
comms = Communication("/dev/cu.ag-ESP32SPP", 115200)
comms.clear() # just in case any junk is in the pipes
comms.send_message("wearable") # begin sending data
# Used for plotting data
t = CircularList([], num_samples)
peaks = CircularList([], num_samples)
# Live data
try:
previous_time = time()
while True:
message = comms.receive_message()
if message != None:
try:
(m1, _, _, _, m2) = message.split(',')
except ValueError: # if corrupted data, skip the sample
continue
# Collect data in the pedometer
hr.add(int(m1) / 1e3, int(m2))
t.add(int(m1) / 1e3)
class Pedometer:
"""
Encapsulated class attributes (with default values)
"""
__steps = 0 # the current step count
__l1 = None # CircularList containing L1-norm
__filtered = None # CircularList containing filtered signal
__num_samples = 0 # The length of data maintained
__new_samples = 0 # How many new samples exist to process
__fs = 0 # Sampling rate in Hz
__b = None # Low-pass coefficients
__a = None # Low-pass coefficients
__thresh_low = 3 # Threshold from Tutorial 2
__thresh_high = 15 # Threshold from Tutorial 2
__xi = None # Initial conditions for filter
__yi = None # Initial conditions for filter
"""
Initialize the class instance
"""
def __init__(self, num_samples, fs, data=None):
self.__steps = 0
self.__num_samples = num_samples
self.__fs = fs
self.__l1 = CircularList(data, num_samples)
self.__filtered = CircularList([], num_samples)
self.__b, self.__a = filt.create_filter(3, 1.2, "lowpass", fs)
self.__xi = np.zeros(4)
self.__yi = np.zeros(4)
"""
Add new samples to the data buffer
Handles both integers and vectors!
"""
def add(self, ax, ay, az):
l1 = filt.l1_norm(ax, ay, az)
if isinstance(ax, int):
num_add = 1
else:
num_add = len(ax)
l1 = l1.tolist()
self.__l1.add(l1)
self.__new_samples += num_add
"""
Process the new data to update step count
"""
def process(self):
# Grab only the new samples into a NumPy array
x = np.array(self.__l1[-self.__new_samples:])
# Filter the signal (detrend, LP, MA, etc…)
x = filt.detrend(x)
# x = filt.filter(self.__b, self.__a, x)
x, self.__xi, self.__yi = filt.filter_ic(self.__b, self.__a, x,
self.__xi, self.__yi)
x = filt.gradient(x)
x = filt.moving_average(x, 25)
# Store the filtered data
self.__filtered.add(x.tolist())
# Count the number of peaks in the filtered data
count, peaks = filt.count_peaks(x, self.__thresh_low,
self.__thresh_high)
# Update the step count and reset the new sample count
self.__steps += count
self.__new_samples = 0
# Return the step count, peak locations, and filtered data
return self.__steps, peaks, np.array(self.__filtered)
"""
Clear the data buffers and step count
"""
def reset(self):
self.__steps = 0
self.__l1.clear()
self.__filtered = np.zeros(self.__num_samples)
class Processing():
__num_samples = 250 # 2 seconds of data @ 50Hz
__refresh_time = 0.5 # update the plot every 0.1s (10 FPS)
# Thresholds for idle detection
__ax_idle_threshold = 1935
__ay_idle_threshold = 1918
__az_idle_threshold = 2430
"""
Initializes the processing object and sets the field variables
@:param transformation_method: the type of transformation that will be plotted and computed
@:param port_name: The Serial port name used for Serial communication
"""
def __init__(self, transformation_method, port_name):
self.comms = Communication(port_name, 115200)
__transform_dict = {
"average acceleration": self.__average_value,
"sample difference": self.__sample_difference,
"L2 norm": self.__l2_norm_calculation,
"L1 norm": self.__l1_norm_calculation,
"Maximum acceleration:": self.__max_acceleration
}
# This will keep track of the transformation method to be called
self.__transformation_method = __transform_dict[transformation_method]
self.transform_x = CircularList([], self.__num_samples)
self.transform_y = CircularList([], self.__num_samples)
self.transform_z = CircularList([], self.__num_samples)
# These will contain the acceleration values read from the accelerometer
self.times = CircularList([], self.__num_samples)
self.ax = CircularList([], self.__num_samples)
self.ay = CircularList([], self.__num_samples)
self.az = CircularList([], self.__num_samples)
# Set up the plotting
fig = plt.figure()
self.ax1 = fig.add_subplot(311)
self.ax2 = fig.add_subplot(312)
self.ax3 = fig.add_subplot(313)
self.graph_type = transformation_method
# times to keep track of when
self.__last_idlecheck_time = 0
self.__idle_state = False
self.__last_active_time = 0
"""
Updates the plot, displaying the acceeleration values as well as the
transformation values
"""
def __plot(self):
# Clears the plots and resets them
self.ax1.cla()
self.ax2.cla()
self.ax3.cla()
# Sets the title of the plot
self.ax1.set_title("X acceleration (Red) and " + self.graph_type +
" (Blue)")
self.ax2.set_title("Y acceleration (Red) and " + self.graph_type +
" (Blue)")
self.ax3.set_title("X acceleration (Red) and " + self.graph_type +
" (Blue)")
# Plots the acceleration values along with the transformation
self.ax1.plot(self.transform_x, 'b', self.ax, 'r')
self.ax2.plot(self.transform_y, 'b', self.ay, 'r')
self.ax3.plot(self.transform_z, 'b', self.az, 'r')
plt.show(block=False)
plt.pause(0.0001)
"""
Determines whether the device is inactive or not
@:param average_x: The average x-acceleration
@:param average_y: The average y-acceleration
@:param average_z: The average z-acceleration
@:return: a boolean representing whether the device is inactive or not
"""
def __is_inactive(self, average_x, average_y, average_z):
return average_x <= self.__ax_idle_threshold and average_y <= self.__ay_idle_threshold and average_z <= self.__az_idle_threshold
"""
Computes the average value for an axis
@:param acceleration_list: The acceleration over 5 seconds in either x,y,z direction
@:return: A scalar which is the average from the acceleration list
"""
def __average_value(self, acceleration_list):
return np.average(np.array(acceleration_list))
"""
Computes the difference between each adjacent indexes
@:param acceleration_list: The acceleration over 5 seconds in either x,y,z direction
@:return: a numpy array containing the differences between each point
"""
def __sample_difference(self, acceleration_list):
np.diff(np.array(acceleration_list))
return np.diff(np.array(acceleration_list))
"""
Computes the euclidean distance for the acceleration list
@:param x_acceleration: one sample of the x-acceleration
@:param y_acceleration: one sample of the y-acceleration
@:param z_acceleration: one sample of the z-acceleration
@:return: A scalar which is the square root of the sum of each number in the
"""
def __l2_norm_calculation(self, x_acceleration, y_acceleration,
z_acceleration):
return np.linalg.norm(
np.array([x_acceleration, y_acceleration, z_acceleration]))
"""
Computes the L1 norm for the acceleration lsit
@:param x_acceleration: one sample of the x-acceleration
@:param y_acceleration: one sample of the y-acceleration
@:param z_acceleration: one sample of the z-acceleration
@:return: The sum of the absolute value of each acceleration value
"""
def __l1_norm_calculation(self, x_acceleration, y_acceleration,
z_acceleration):
return np.linalg.norm(np.array(
[x_acceleration, y_acceleration, z_acceleration]),
ord=1)
"""
Finds the max acceleration in one of the accelerations
@:param: acceleration_list: The acceleration over 5 seconds in either x,y,z direction
@:return: The maximum value in the acceleration list
"""
def __max_acceleration(self, acceleration_list):
return int(np.max(np.array(acceleration_list)))
"""
Records the acceleration and times from the accelerometer
@:param time: the time from the Serial monitor
@:param x_acceleration: the x-acceleration
@:param y_acceleration: the y-acceleration
@:param z_acceleration: the z-acceleration
"""
def __record_acceleration(self, time, x_acceleration, y_acceleration,
z_acceleration):
# add the new values to the circular lists
self.times.add(int(time))
self.ax.add(int(x_acceleration))
self.ay.add(int(y_acceleration))
self.az.add(int(z_acceleration))
"""
Records the transformation value based on what transformation type the
instance uses
@:param x_acceleration: one sample of the x-acceleration
@:param y_acceleration: one sample of the y-acceleration
@:param z_acceleration: one sample of the z-acceleration
"""
def __record_transformation(self, x_acceleration, y_acceleration,
z_acceleration):
# These if statements are used because some of these methods have different parameters and return types
if self.__transformation_method == self.__l1_norm_calculation or self.__transformation_method == self.__l2_norm_calculation:
norm_number = self.__transformation_method()
self.transform_x.add(norm_number)
self.transform_y.add(norm_number)
self.transform_z.add(norm_number)
# sets each transformation method to the sample difference array
elif self.__transformation_method == self.__sample_difference:
self.transform_x = self.__transformation_method(self.ax)
self.transform_y = self.__transformation_method(self.ay)
self.transform_z = self.__transformation_method(self.az)
# This will either call average_value or maximum_acceleration
else:
self.transform_x.add(self.__transformation_method(self.ax))
self.transform_y.add(self.__transformation_method(self.ay))
self.transform_z.add(self.__transformation_method(self.az))
"""
Checks if the device has been idle for 5 seconds or if it's been active for 1
second. This will either cause the motor to buzz or another message displaying that the person has
been active.
@:param current_time: The current time the program is at
"""
def __check_idle(self, current_time):
# If it's been 5 seconds since the last time the person has been inactive
if current_time - self.__last_idlecheck_time >= 5:
# get the average acceleration over 5 seconds
average_x = self.__average_value(self.ax)
average_y = self.__average_value(self.ay)
average_z = self.__average_value(self.az)
print(average_x, ",", average_y, ",", average_z)
self.__last_idlecheck_time = current_time
# if the device has been idle for 5 seconds, buzz the motor
if self.__is_inactive(average_x, average_y, average_z):
self.__idle_state = True
self.comms.send_message("Buzz motor")
else:
self.__idle_state = False
# If the person has been inactive but has become active for 1 second
if self.__idle_state and current_time - self.__last_active_time >= 1:
self.__last_active_time = current_time
# get the average values for the last 1 second
average_x = self.__average_value(self.ax[200:])
average_y = self.__average_value(self.ay[200:])
average_z = self.__average_value(self.az[200:])
if not self.__is_inactive(average_x, average_y, average_z):
print("Active accelerations: ", average_x, average_y,
average_z)
self.__last_idlecheck_time = current_time # this ensures that the person must be inactive for 5 seconds after their activity
self.comms.send_message("Keep it up!")
"""
Runs all the processing for the Serial communication, including plotting the
acceleration values and checking whether the device has been inactive or not.
"""
def run(self):
self.comms.clear() # just in case any junk is in the pipes
self.comms.send_message("wearable") # begin sending data
try:
previous_time = 0
while (True):
message = self.comms.receive_message()
if (message != None):
try:
(m1, m2, m3, m4) = message.split(',')
except ValueError: # if corrupted data, skip the sample
continue
# Record the acceleration and transformation
self.__record_acceleration(m1, m2, m3, m4)
self.__record_transformation(m2, m3, m4)
current_time = time()
if current_time - previous_time > self.__refresh_time:
previous_time = current_time
self.__plot()
self.__check_idle(current_time)
except (Exception, KeyboardInterrupt) as e:
print(e) # Exiting the program due to exception
finally:
print("Closing Connection")
self.comms.send_message("sleep") # stop sending data
self.comms.close()
sleep(1)
def __init__(self, transformation_method, port_name):
self.comms = Communication(port_name, 115200)
__transform_dict = {
"average acceleration": self.__average_value,
"sample difference": self.__sample_difference,
"L2 norm": self.__l2_norm_calculation,
"L1 norm": self.__l1_norm_calculation,
"Maximum acceleration:": self.__max_acceleration
}
# This will keep track of the transformation method to be called
self.__transformation_method = __transform_dict[transformation_method]
self.transform_x = CircularList([], self.__num_samples)
self.transform_y = CircularList([], self.__num_samples)
self.transform_z = CircularList([], self.__num_samples)
# These will contain the acceleration values read from the accelerometer
self.times = CircularList([], self.__num_samples)
self.ax = CircularList([], self.__num_samples)
self.ay = CircularList([], self.__num_samples)
self.az = CircularList([], self.__num_samples)
# Set up the plotting
fig = plt.figure()
self.ax1 = fig.add_subplot(311)
self.ax2 = fig.add_subplot(312)
self.ax3 = fig.add_subplot(313)
self.graph_type = transformation_method
# times to keep track of when
self.__last_idlecheck_time = 0
self.__idle_state = False
self.__last_active_time = 0
from ECE16Lib.Communication import Communication
from ECE16Lib.CircularList import CircularList
from matplotlib import pyplot as plt
from time import time
if __name__ == "__main__":
num_samples = 100 # 2 seconds of data @ 50Hz
refresh_time = 0.1 # update the plot every 0.1s (10 FPS)
times = CircularList([], num_samples)
ax = CircularList([], num_samples)
ay = CircularList([], num_samples)
az = CircularList([], num_samples)
comms = Communication("/dev/cu.ag-ESP32SPP", 115200)
comms.clear() # just in case any junk is in the pipes
comms.send_message("wearable") # begin sending data
fig = plt.figure()
ax1 = fig.add_subplot(311)
ax2 = fig.add_subplot(312)
ax3 = fig.add_subplot(313)
try:
previous_time = 0
while(True):
message = comms.receive_message()
if(message != None):
try:
(m1, m2, m3, m4) = message.split(',')
except ValueError: # if corrupted data, skip the sample
continue
class HRMonitor:
"""
Encapsulated class attributes (with default values)
"""
__hr = 0 # the current heart rate
__time = None # CircularList containing the time vector
__ppg = None # CircularList containing the raw signal
__filtered = None # CircularList containing filtered signal
__num_samples = 0 # The length of data maintained
__new_samples = 0 # How many new samples exist to process
__fs = 0 # Sampling rate in Hz
__thresh = 0.6 # Threshold from Tutorial 2
"""
Initialize the class instance
"""
def __init__(self, num_samples, fs, times=[], data=[]):
self.__hr = 0
self.__num_samples = num_samples
self.__fs = fs
self.__time = CircularList(times, num_samples)
self.__ppg = CircularList(data, num_samples)
self.__filtered = CircularList([], num_samples)
"""
Add new samples to the data buffer
Handles both integers and vectors!
"""
def add(self, t, x):
if isinstance(t, np.ndarray):
t = t.tolist()
if isinstance(x, np.ndarray):
x = x.tolist()
self.__time.add(t)
self.__ppg.add(x)
self.__new_samples += len(x)
"""
Compute the average heart rate over the peaks
"""
def compute_heart_rate(self, peaks):
t = np.array(self.__time)
return 60 / np.mean(np.diff(t[peaks]))
"""
Process the new data to update step count
"""
def process(self):
# Grab only the new samples into a NumPy array
x = np.array(self.__ppg[-self.__new_samples:])
# Filter the signal (feel free to customize!)
x = filt.detrend(x, 25)
x = filt.moving_average(x, 5)
x = filt.gradient(x)
x = filt.normalize(x)
# Store the filtered data
self.__filtered.add(x.tolist())
# Find the peaks in the filtered data
_, peaks = filt.count_peaks(x, self.__thresh, 1)
# Update the step count and reset the new sample count
self.__hr = self.compute_heart_rate(peaks)
self.__new_samples = 0
# Return the heart rate, peak locations, and filtered data
return self.__hr, peaks, np.array(self.__filtered)
"""
Clear the data buffers and step count
"""
def reset(self):
self.__steps = 0
self.__time.clear()
self.__ppg.clear()
self.__filtered = np.zeros(self.__num_samples)
class HRMonitor:
"""
Encapsulated class attributes (with default values)
"""
__hr = 0 # the current heart rate
__time = None # CircularList containing the time vector
__ppg = None # CircularList containing the raw signal
__filtered = None # CircularList containing filtered signal
__num_samples = 0 # The length of data maintained
__new_samples = 0 # How many new samples exist to process
__fs = 0 # Sampling rate in Hz
__thresh = 0.6 # Threshold from Tutorial 2
__directory = "/Users/akshaygopalkrishnan/Desktop/ECE 16/Python/Lab 7/data/data"
"""
Initialize the class instance
"""
def __init__(self, num_samples, fs, times=[], data=[]):
self.__hr = 0
self.__num_samples = num_samples
self.__fs = fs
self.__time = CircularList(data, num_samples)
self.__ppg = CircularList(data, num_samples)
self.__filtered = CircularList([], num_samples)
self.__gmm = GMM(n_components=2)
"""
Add new samples to the data buffer
Handles both integers and vectors!
"""
def add(self, t, x):
if isinstance(t, np.ndarray):
t = t.tolist()
if isinstance(x, np.ndarray):
x = x.tolist()
if isinstance(x, int):
self.__new_samples += 1
else:
self.__new_samples += len(x)
self.__time.add(t)
self.__ppg.add(x)
"""
Compute the average heart rate over the peaks
"""
def compute_heart_rate(self, peaks):
t = np.array(self.__time)
if len(np.diff(t[peaks])) > 0:
return 60 / np.mean(np.diff(t[peaks]))
else:
return 0
"""
Removes outlier peaks from the filtered data
@:param peaks: The location of each peak
@:return the peaks with outliers removed
"""
def remove_outliers(self, peaks):
if len(peaks) > 1:
t = np.array(self.__time)
# Calculate peak difference and average/standard deviation
peak_diff = np.diff(t[peaks])
avg_peak_diff = np.mean(peak_diff)
std_peak_diff = np.std(peak_diff)
for i in range(len(peak_diff)):
# If the peak difference is less than 2 deviations from the average, remove the peak (outlier)
if peak_diff[i] < (avg_peak_diff - (1 * std_peak_diff)):
peaks.pop(i + 1)
return peaks
# Filter the signal (as in the prior lab)
def train_process(self, x):
x = filt.detrend(x, 25)
x = filt.moving_average(x, 5)
x = filt.gradient(x)
return filt.normalize(x)
# Retrieve a list of the names of the subjects
def get_subjects(self, directory):
filepaths = glob.glob(directory + "/*")
return [filepath.split("/")[-1] for filepath in filepaths]
# Estimate the heart rate from the user-reported peak count
def get_hr(self, filepath, num_samples, fs):
count = int(filepath.split("_")[-1].split(".")[0])
seconds = num_samples / fs
return count / seconds * 60 # 60s in a minute
# Estimate the sampling rate from the time vector
def estimate_fs(self, times):
return 1 / np.mean(np.diff(times))
# Retrieve a data file, verifying its FS is reasonable
def get_data(self, directory, subject, trial, fs):
search_key = "%s/%s/%s_%02d_*.csv" % (directory, subject, subject,
trial)
filepath = glob.glob(search_key)[0]
t, ppg = np.loadtxt(filepath, delimiter=',', unpack=True)
t = (t - t[0]) / 1e3
hr = self.get_hr(filepath, len(ppg), fs)
fs_est = self.estimate_fs(t)
if (fs_est < fs - 1 or fs_est > fs):
print("Bad data! FS=%.2f. Consider discarding: %s" %
(fs_est, filepath))
return t, ppg, hr, fs_est
"""
Trains the GMM model on offline data
@:return: the trained GMM model
"""
def train(self):
print("Training GMM model... ")
subjects = self.get_subjects(self.__directory)
train_data = np.array([])
for subject in subjects:
for trial in range(1, 11):
t, ppg, hr, fs_est = self.get_data(self.__directory, subject,
trial, self.__fs)
train_data = np.append(train_data, self.train_process(ppg))
# Train the GMM
train_data = train_data.reshape(-1,
1) # convert from (N,1) to (N,) vector
self.__gmm = GMM(n_components=2).fit(train_data)
"""
Estimate the heart rate given GMM output labels
"""
def estimate_hr(self, labels, num_samples, fs):
peaks = np.diff(labels, prepend=0) == 1
count = sum(peaks)
seconds = num_samples / fs
hr = count / seconds * 60 # 60s in a minute
return hr, peaks
"""
Uses the GMM model to estimate the heart rate
@:param filtered: the filtered data
@:param fs: the sampling frequency
@:return: the estimated heart rate and estimated time of each peak
"""
def predict(self):
# Grab only the new samples into a NumPy array
x = np.array(self.__ppg[-self.__new_samples:])
filtered_arr = self.train_process(x)
self.__filtered.add(filtered_arr.tolist())
labels = self.__gmm.predict(np.array(self.__filtered).reshape(-1, 1))
self.__new_samples = 0
hr_est, est_peaks = self.estimate_hr(labels, len(self.__filtered),
self.__fs)
return hr_est, est_peaks, np.array(self.__filtered)
"""
Process the new data to update step count
"""
def process(self):
# Grab only the new samples into a NumPy array
x = np.array(self.__ppg[-self.__new_samples:])
# Filter the signal (feel free to customize!)
x = filt.detrend(x, 25)
x = filt.moving_average(x, 5)
x = filt.gradient(x)
x = filt.normalize(x)
# Store the filtered data
self.__filtered.add(x.tolist())
# Find the peaks in the filtered data
_, peaks = filt.count_peaks(self.__filtered, self.__thresh, 1)
peaks = self.remove_outliers(peaks)
# Update the step count and reset the new sample count
self.__hr = self.compute_heart_rate(peaks)
self.__new_samples = 0
# Return the heart rate, peak locations, and filtered data
return self.__hr, peaks, np.array(self.__filtered)
"""
Clear the data buffers and step count
"""
def reset(self):
self.__steps = 0
self.__time.clear()
self.__ppg.clear()
self.__filtered = np.zeros(self.__num_samples)
