Commit 68f60676 authored by Rahix's avatar Rahix
Browse files

Merge 'ECG-App Settings Menu'

See merge request card10/firmware!337
parents 27777266 c91b74c7
......@@ -7,12 +7,13 @@ import max30001
import math
import struct
import itertools
from ecg.settings import *
config = ecg_settings()
WIDTH = 160
HEIGHT = 80
OFFSET_Y = 49
ECG_RATE = 128
HISTORY_MAX = ECG_RATE * 4
HISTORY_MAX = WIDTH * 4
DRAW_AFTER_SAMPLES = 5
SCALE_FACTOR = 30
MODE_USB = "USB"
......@@ -26,24 +27,18 @@ COLOR_MODE_USB = [0, 0, 255]
COLOR_WRITE_FG = [255, 255, 255]
COLOR_WRITE_BG = [255, 0, 0]
current_mode = MODE_FINGER
modes = itertools.cycle(
[
({"bar", "pulse"}, {"text": "Top + Pulse", "posx": 0}),
({}, {"text": "off", "posx": 55}),
({"bar"}, {"text": "Top Only", "posx": 25}),
({"pulse"}, {"text": "Pulse Only", "posx": 5}),
]
)
led_mode = next(modes)[0]
history = []
# variables for file output
filebuffer = bytearray()
write = 0
bias = True
write_time_string = ""
samples_since_start_of_write = 0
update_screen = 0
pause_screen = 0
pause_histogram = False
histogram_offset = 0
pause_graph = False
graph_offset = 0
sensor = 0
disp = display.open()
last_sample_count = 1
......@@ -64,7 +59,7 @@ def update_history(datasets):
global history, moving_average, alpha, beta, last_sample_count
last_sample_count = len(datasets)
for val in datasets:
if current_mode == MODE_FINGER:
if "HP" in config.get_option("Filter"):
history.append(val - moving_average)
moving_average += betadash * (val - moving_average)
# identical to: moving_average = (alpha * moving_average + beta * val) / (alpha + beta)
......@@ -81,7 +76,7 @@ samples_since_last_pulse = 0
last_pulse_blink = 0
q_threshold = -1
r_threshold = 1
q_spike = -ECG_RATE
q_spike = -500 # just needs to be long ago
def neighbours(n, lst):
......@@ -103,6 +98,8 @@ def detect_pulse(num_new_samples):
# consider ["CDE", "DEF"]
# new samples: "GHI" => "ABCDEFGHI"
# consider ["EFG", "FGH", "GHI"]
ecg_rate = config.get_option("Rate")
for [prev, cur, next_] in neighbours(3, history[-(num_new_samples + 2) :]):
samples_since_last_pulse += 1
......@@ -113,33 +110,37 @@ def detect_pulse(num_new_samples):
elif (
prev < cur > next_
and cur > r_threshold
and samples_since_last_pulse - q_spike < ECG_RATE // 10
and samples_since_last_pulse - q_spike < ecg_rate // 10
):
# the full QRS complex is < 0.1s long, so the q and r spike in particular cannot be more than ECG_RATE//10 samples apart
pulse = 60 * ECG_RATE // samples_since_last_pulse
samples_since_last_pulse = 0
q_spike = -ECG_RATE
# the full QRS complex is < 0.1s long, so the q and r spike in particular cannot be more than ecg_rate//10 samples apart
pulse = 60 * ecg_rate // samples_since_last_pulse
q_spike = -ecg_rate
if pulse < 30 or pulse > 210:
pulse = -1
elif write > 0 and "pulse" in config.get_option("Log"):
write_pulse()
# we expect the next r-spike to be at least 60% as high as this one
r_threshold = (cur * 3) // 5
elif samples_since_last_pulse > 2 * ECG_RATE:
samples_since_last_pulse = 0
elif samples_since_last_pulse > 2 * ecg_rate:
q_threshold = -1
r_threshold = 1
pulse = -1
def callback_ecg(datasets):
global update_screen, history, filebuffer, write
global update_screen, history, filebuffer, write, samples_since_start_of_write
update_screen += len(datasets)
if write > 0:
samples_since_start_of_write += len(datasets)
# update histogram datalist
if not pause_histogram:
# update graph datalist
if not pause_graph:
update_history(datasets)
detect_pulse(len(datasets))
# buffer for writes
if write > 0:
if write > 0 and "graph" in config.get_option("Log"):
for value in datasets:
filebuffer.extend(struct.pack("h", value))
if len(filebuffer) >= FILEBUFFERBLOCK:
......@@ -147,20 +148,18 @@ def callback_ecg(datasets):
# don't update on every callback
if update_screen >= DRAW_AFTER_SAMPLES:
draw_histogram()
draw_graph()
def write_filebuffer():
global write, filebuffer
def append_to_file(fileprefix, content):
global write, pause_screen
# write to file
chars = ""
lt = utime.localtime(write)
filename = "/ecg-{:04d}-{:02d}-{:02d}_{:02d}{:02d}{:02d}.log".format(*lt)
filename = "/ecg_logs/{}-{}.log".format(fileprefix, write_time_string)
# write stuff to disk
try:
f = open(filename, "ab")
f.write(filebuffer)
f.write(content)
f.close()
except OSError as e:
print("Please check the file or filesystem", e)
......@@ -174,18 +173,28 @@ def write_filebuffer():
disp.update()
close_sensor()
except:
print("Unexpected error, stop writeing logfile")
print("Unexpected error, stop writing logfile")
write = 0
def write_pulse():
# estimates timestamp as calls to utime.time() take too much time
approx_timestamp = write + samples_since_start_of_write // config.get_option("Rate")
append_to_file("pulse", struct.pack("ib", approx_timestamp, pulse))
def write_filebuffer():
global filebuffer
append_to_file("ecg", filebuffer)
filebuffer = bytearray()
def open_sensor():
global sensor
sensor = max30001.MAX30001(
usb=(current_mode == MODE_USB),
bias=bias,
sample_rate=ECG_RATE,
usb=(config.get_option("Mode") == "USB"),
bias=config.get_option("Bias"),
sample_rate=config.get_option("Rate"),
callback=callback_ecg,
)
......@@ -195,36 +204,8 @@ def close_sensor():
sensor.close()
def toggle_mode():
global current_mode, disp, pause_screen
if write > 0:
pause_screen = utime.time_ms() + 500
disp.clear(COLOR_BACKGROUND)
disp.print("Locked", posx=30, posy=30, fg=COLOR_TEXT)
disp.update()
return
close_sensor()
current_mode = MODE_USB if current_mode == MODE_FINGER else MODE_FINGER
open_sensor()
def toggle_bias():
global bias, disp, pause_screen
if write > 0:
pause_screen = utime.time_ms() + 500
disp.clear(COLOR_BACKGROUND)
disp.print("Locked", posx=30, posy=30, fg=COLOR_TEXT)
disp.update()
return
close_sensor()
bias = not bias
open_sensor()
def toggle_write():
global write, disp, pause_screen
global write, disp, pause_screen, filebuffer, samples_since_start_of_write, write_time_string
pause_screen = utime.time_ms() + 1000
disp.clear(COLOR_BACKGROUND)
if write > 0:
......@@ -235,6 +216,13 @@ def toggle_write():
else:
filebuffer = bytearray()
write = utime.time()
lt = utime.localtime(write)
write_time_string = "{:04d}-{:02d}-{:02d}_{:02d}{:02d}{:02d}".format(*lt)
samples_since_start_of_write = 0
try:
os.mkdir("ecg_logs")
except:
pass
disp.print("Start", posx=45, posy=20, fg=COLOR_TEXT)
disp.print("logging", posx=30, posy=40, fg=COLOR_TEXT)
......@@ -242,25 +230,13 @@ def toggle_write():
def toggle_pause():
global pause_histogram, histogram_offset, history, leds
if pause_histogram:
pause_histogram = False
global pause_graph, graph_offset, history, leds
if pause_graph:
pause_graph = False
history = []
else:
pause_histogram = True
histogram_offset = 0
leds.clear()
def toggle_leds():
global led_mode, disp, pause_screen, leds, modes
led_mode, display_args = next(modes)
pause_screen = utime.time_ms() + 250
disp.clear(COLOR_BACKGROUND)
disp.print("LEDs", posx=50, posy=20, fg=COLOR_TEXT)
disp.print(**display_args, posy=40, fg=COLOR_TEXT)
disp.update()
pause_graph = True
graph_offset = 0
leds.clear()
......@@ -269,6 +245,8 @@ def draw_leds(vmin, vmax):
# vmax should be in [0, 1]
global pulse, samples_since_last_pulse, last_pulse_blink
led_mode = config.get_option("LEDs")
# stop blinking
if not bool(led_mode):
return
......@@ -300,8 +278,8 @@ def draw_leds(vmin, vmax):
leds.update()
def draw_histogram():
global disp, history, current_mode, bias, write, pause_screen, update_screen
def draw_graph():
global disp, history, write, pause_screen, update_screen
# skip rendering due to message beeing shown
if pause_screen == -1:
......@@ -315,32 +293,32 @@ def draw_histogram():
disp.clear(COLOR_BACKGROUND)
# offset in pause_histogram mode
window_end = int(len(history) - histogram_offset)
s_start = max(0, window_end - (ECG_RATE * 2))
# offset in pause_graph mode
timeWindow = config.get_option("Window")
window_end = int(len(history) - graph_offset)
s_end = max(0, window_end)
s_draw = max(0, s_end - WIDTH)
s_start = max(0, s_end - WIDTH * timeWindow)
# get max value and calc scale
value_max = max(abs(x) for x in history[s_start:s_end])
scale = SCALE_FACTOR / (value_max if value_max > 0 else 1)
# draw histogram
# draw graph
# values need to be inverted so high values are drawn with low pixel coordinates (at the top of the screen)
draw_points = (int(-x * scale + OFFSET_Y) for x in history[s_draw:s_end])
draw_points = (int(-x * scale + OFFSET_Y) for x in history[s_start:s_end])
prev = next(draw_points)
for x, value in enumerate(draw_points):
disp.line(x, prev, x + 1, value, col=COLOR_LINE)
disp.line(x // timeWindow, prev, (x + 1) // timeWindow, value, col=COLOR_LINE)
prev = value
# draw text: mode/bias/write
if pause_histogram:
if pause_graph:
disp.print(
"Pause"
+ (
" -{:0.1f}s".format(histogram_offset / ECG_RATE)
if histogram_offset > 0
" -{:0.1f}s".format(graph_offset / config.get_option("Rate"))
if graph_offset > 0
else ""
),
posx=0,
......@@ -354,11 +332,14 @@ def draw_histogram():
)
if pulse < 0:
disp.print(
current_mode + ("+Bias" if bias else ""),
config.get_option("Mode")
+ ("+Bias" if config.get_option("Bias") else ""),
posx=0,
posy=0,
fg=(
COLOR_MODE_FINGER if current_mode == MODE_FINGER else COLOR_MODE_USB
COLOR_MODE_FINGER
if config.get_option("Mode") == MODE_FINGER
else COLOR_MODE_USB
),
)
else:
......@@ -367,7 +348,9 @@ def draw_histogram():
posx=0,
posy=0,
fg=(
COLOR_MODE_FINGER if current_mode == MODE_FINGER else COLOR_MODE_USB
COLOR_MODE_FINGER
if config.get_option("Mode") == MODE_FINGER
else COLOR_MODE_USB
),
)
......@@ -382,7 +365,7 @@ def draw_histogram():
def main():
global pause_histogram, histogram_offset
global pause_graph, graph_offset, pause_screen
# show button layout
disp.clear(COLOR_BACKGROUND)
......@@ -392,10 +375,10 @@ def main():
" Pause >", posx=0, posy=28, fg=COLOR_MODE_FINGER, font=display.FONT16
)
disp.print(
" Mode/Bias >", posx=0, posy=44, fg=COLOR_MODE_USB, font=display.FONT16
" Settings >", posx=0, posy=44, fg=COLOR_MODE_USB, font=display.FONT16
)
disp.print(
"< LED/WriteLog", posx=0, posy=64, fg=COLOR_WRITE_BG, font=display.FONT16
"< WriteLog ", posx=0, posy=64, fg=COLOR_WRITE_BG, font=display.FONT16
)
disp.update()
utime.sleep(3)
......@@ -410,90 +393,64 @@ def main():
)
# TOP RIGHT
#
# pause
# down
if button_pressed["TOP_RIGHT"] == 0 and v & buttons.TOP_RIGHT != 0:
button_pressed["TOP_RIGHT"] = utime.time_ms()
button_pressed["TOP_RIGHT"] = 1
toggle_pause()
# up
if button_pressed["TOP_RIGHT"] > 0 and v & buttons.TOP_RIGHT == 0:
duration = utime.time_ms() - button_pressed["TOP_RIGHT"]
button_pressed["TOP_RIGHT"] = 0
# BOTTOM LEFT
#
# on pause = shift view left
# long = toggle write
# short = toggle leds
# down, and still pressed
if (
button_pressed["BOTTOM_LEFT"] > 0
and v & buttons.BOTTOM_LEFT != 0
and not pause_histogram
):
duration = utime.time_ms() - button_pressed["BOTTOM_LEFT"]
if duration > 1000:
button_pressed["BOTTOM_LEFT"] = -1
toggle_write()
# register down event
elif button_pressed["BOTTOM_LEFT"] == 0 and v & buttons.BOTTOM_LEFT != 0:
button_pressed["BOTTOM_LEFT"] = utime.time_ms()
# else = toggle write
# register up event but event already called
if button_pressed["BOTTOM_LEFT"] == -1 and v & buttons.BOTTOM_LEFT == 0:
button_pressed["BOTTOM_LEFT"] = 0
# down
if button_pressed["BOTTOM_LEFT"] == 0 and v & buttons.BOTTOM_LEFT != 0:
button_pressed["BOTTOM_LEFT"] = 1
if pause_graph:
l = len(history)
graph_offset += config.get_option("Rate") / 2
if l - graph_offset < WIDTH * config.get_option("Window"):
graph_offset = l - WIDTH * config.get_option("Window")
else:
toggle_write()
# register normal up event
elif button_pressed["BOTTOM_LEFT"] > 0 and v & buttons.BOTTOM_LEFT == 0:
duration = utime.time_ms() - button_pressed["BOTTOM_LEFT"]
# up
if button_pressed["BOTTOM_LEFT"] > 0 and v & buttons.BOTTOM_LEFT == 0:
button_pressed["BOTTOM_LEFT"] = 0
if not pause_histogram:
toggle_leds()
else:
l = len(history)
histogram_offset += ECG_RATE / 2
if l - histogram_offset < WIDTH:
histogram_offset = l - WIDTH
# BOTTOM RIGHT
#
# on pause = shift view right
# long = toggle bias
# short = toggle mode (finger/usb)
# down, and still pressed
if (
button_pressed["BOTTOM_RIGHT"] > 0
and v & buttons.BOTTOM_RIGHT != 0
and not pause_histogram
):
duration = utime.time_ms() - button_pressed["BOTTOM_RIGHT"]
if duration > 1000:
button_pressed["BOTTOM_RIGHT"] = -1
toggle_bias()
# register down event
elif button_pressed["BOTTOM_RIGHT"] == 0 and v & buttons.BOTTOM_RIGHT != 0:
button_pressed["BOTTOM_RIGHT"] = utime.time_ms()
# register up event but event already called
if button_pressed["BOTTOM_RIGHT"] == -1 and v & buttons.BOTTOM_RIGHT == 0:
button_pressed["BOTTOM_RIGHT"] = 0
# else = show settings
# register normal up event
elif button_pressed["BOTTOM_RIGHT"] > 0 and v & buttons.BOTTOM_RIGHT == 0:
duration = utime.time_ms() - button_pressed["BOTTOM_RIGHT"]
button_pressed["BOTTOM_RIGHT"] = 0
if pause_histogram:
histogram_offset -= ECG_RATE / 2
histogram_offset -= histogram_offset % (ECG_RATE / 2)
if histogram_offset < 0:
histogram_offset = 0
# down
if button_pressed["BOTTOM_RIGHT"] == 0 and v & buttons.BOTTOM_RIGHT != 0:
button_pressed["BOTTOM_RIGHT"] = 1
if pause_graph:
graph_offset -= config.get_option("Rate") / 2
graph_offset -= graph_offset % (config.get_option("Rate") / 2)
if graph_offset < 0:
graph_offset = 0
else:
toggle_mode()
pause_screen = -1 # hide graph
leds.clear() # disable all LEDs
config.run() # show config menu
close_sensor() # reset sensor in case mode or bias was changed TODO do not close sensor otherwise?
open_sensor()
pause_screen = 0 # start plotting graph again
# returning from menu was by pressing the TOP_RIGHT button
button_pressed["TOP_RIGHT"] = 1
# up
if button_pressed["BOTTOM_RIGHT"] > 0 and v & buttons.BOTTOM_RIGHT == 0:
button_pressed["BOTTOM_RIGHT"] = 0
if __name__ == "__main__":
......
import color
import simple_menu
import itertools
class Settings(simple_menu.Menu):
color_1 = color.CAMPGREEN
color_2 = color.CAMPGREEN_DARK
selected_options = {}
def __init__(self):
super().__init__([("return", False)])
def on_select(self, value, index):
if index == 0:
self.exit()
else:
self.selected_options[value[0]] = next(value[1])
self.write_to_file()
def entry2name(self, value):
if value[0] == "return":
return value[0]
else:
return "{}: {}".format(value[0], self.selected_options[value[0]][0])
def add_option(self, option):
self.entries.append(option)
self.selected_options[option[0]] = next(option[1])
def get_option(self, name):
return self.selected_options[name][1]
def load_from_file(self):
config_path = "/".join(__file__.split("/")[0:-1])
try:
f = open("{}/config.cfg".format(config_path), "r")
for line in f:
parts = [x.strip() for x in line.split(":")]
if parts[0] in self.selected_options:
# find corresponding entry from menu to get access to the corresponding itertools.cycle
option_cycle = next(x for x in self.entries if x[0] == parts[0])[1]
if self.selected_options[parts[0]][0] != parts[1]:
previous = self.selected_options[parts[0]][0]
self.selected_options[parts[0]] = next(option_cycle)
while self.selected_options[parts[0]][0] not in {
parts[1],
previous,
}:
self.selected_options[parts[0]] = next(option_cycle)
if self.selected_options[parts[0]][0] == previous:
print(
"Settings: unknown option '{}' for key '{}'".format(
parts[1], parts[0]
)
)
else:
print("Settings: unknown key '{}'".format(parts[0]))
f.close()
except OSError:
print("Settings could not be loaded from file. Maybe it did not exist yet?")
def write_to_file(self):
config_path = "/".join(__file__.split("/")[0:-1])
try:
f = open("{}/config.cfg".format(config_path), "w")
for option_name in self.selected_options:
f.write(
"{}:{}\n".format(option_name, self.selected_options[option_name][0])
)
f.close()
except OSError as e:
print("Settings could not be written to file! Error: {}".format(e))
def ecg_settings():
config = Settings()
config.add_option(
(
"LEDs",
itertools.cycle(
[
("off", {}),
("Pulse", {"pulse"}),
("Bar", {"bar"}),
("Full", {"pulse", "bar"}),
]
),
)
)
config.add_option(("Mode", itertools.cycle([("Finger", "Finger"), ("USB", "USB")])))
config.add_option(("Bias", itertools.cycle([("on", True), ("off", False)])))
config.add_option(("Filter", itertools.cycle([("HP", {"HP"}), ("off", {})])))
config.add_option(("Rate", itertools.cycle([("128Hz", 128), ("256Hz", 256)])))
config.add_option(("Window", itertools.cycle([("1x", 1), ("2x", 2), ("3x", 3)])))
config.add_option(
(
"Log",
itertools.cycle(
[
("graph", {"graph"}),
("pulse", {"pulse"}),
("full", {"graph", "pulse"}),
]
),
)
)