modified so no threads are used anymore. data will be devided by gain when saved.

This commit is contained in:
till 2020-05-04 15:20:49 +02:00
parent 01640f6bdf
commit 9418ab96df

View File

@ -45,7 +45,7 @@ def GPIO_setup(LED1_pin, LED2_pin, LED_out_pin, Button1_pin, Button2_pin, power_
return LED_status
def read_cfg(cfg_file, now, init_read=False):
def read_cfg(cfg_file, now, start_time=None, init_read=False):
cfg_f = open(cfg_file, 'r+')
cfg = cfg_f.readlines()
@ -70,7 +70,6 @@ def read_cfg(cfg_file, now, init_read=False):
max_v = float(line.split(':')[1].strip().replace('mV', ''))
elif 'Gain' in line:
gain = int(line.split(':')[1].strip())
gain = int(line.split(':')[1].strip())
channels = n_rows * n_cols + n_extra
### alter information and re-write ###
@ -78,7 +77,10 @@ def read_cfg(cfg_file, now, init_read=False):
if "StartDate" in line:
cfg[enu] = (' StartDate : %s\n' % now.strftime('%Y-%m-%d'))
elif "StartTime" in line:
if start_time == None:
cfg[enu] = (' StartTime : %s\n' % (now.strftime('%H:%M:%S') + now.strftime(".%f")[:4]))
else:
cfg[enu] = (' StartTime : %s\n' % ('%2.f:%2.f:00' % (start_time[0], start_time[1])))
cfg_f.close()
cfg_f = open(cfg_file, 'w+')
@ -87,139 +89,8 @@ def read_cfg(cfg_file, now, init_read=False):
cfg_f.close()
return channels, samplerate, n_cols, n_rows, max_v, gain
# for line in cfg:
# if 'Columns1' in line:
# self.Grid.columns_val = int(line.split(':')[1].strip())
# elif 'Rows1' in line:
# self.Grid.rows_val = int(line.split(':')[1].strip())
# elif "ColumnDistance1" in line:
# self.Grid.col_dist_val = float(line.split(':')[-1].strip().replace('cm', ''))
# elif "RowDistance1" in line:
# self.Grid.row_dist_val = float(line.split(':')[-1].strip().replace('cm', ''))
# elif "ChannelOffset1" in line:
# self.Grid.channel_offset_val = int(line.split(':')[-1].strip())
# elif "ElectrodeType1" in line:
# self.Grid.elec_type_val = line.split(':')[-1].strip()
# elif "RefElectrodeType1" in line:
# self.Grid.ref_elec_type_val = line.split(":")[-1].strip()
# elif "RefElectrodePosX1" in line:
# self.Grid.ref_elec_posx_val = float(line.split(':')[-1].strip().replace('m', ''))
# elif 'RefElectrodePosY1' in line:
# self.Grid.ref_elec_posy_val = float(line.split(':')[-1].strip().replace('m', ''))
# elif 'WaterDepth1' in line:
# self.Grid.water_depth_val = float(line.split(':')[-1].strip().replace('m', ''))
#
# elif "AISampleRate" in line:
# self.HardWare.ai_sr_val = float(line.split(':')[-1].strip().replace('kHz', ''))
# elif "AIMaxVolt" in line:
# self.HardWare.ai_max_vol_val = float(line.split(':')[-1].strip().replace('mV', ''))
# elif "AmplName" in line:
# self.HardWare.amp_name_val = line.split(':')[-1].strip()
# elif "AmplModel" in line:
# self.HardWare.amp_model_val = line.split(':')[-1].strip()
# elif ' Type ' in line:
# self.HardWare.amp_type_val = line.split(':')[-1].strip()
# elif 'Gain' in line:
# self.HardWare.gain_val = line.split(':')[-1].strip()
# elif "HighpassCutoff" in line:
# self.HardWare.highpass_cutoff_val = int(line.split(':')[-1].strip().replace('Hz', ''))
# elif 'LowpassCutoff' in line:
# self.HardWare.lowpass_cutoff_val = float(line.split(':')[-1].strip().replace('kHz', ''))
#
# elif "Experiment.Name" in line:
# self.Recording.experiment_name_val = line.split(':')[-1].strip()
# elif "StartDate" in line:
# self.Recording.startdate_val = line.split(':')[-1].strip()
# elif "StartTime" in line:
# self.Recording.starttime_val = ':'.join(line.split(':')[1:]).strip()
# elif "Location" in line:
# self.Recording.location_val = line.split(':')[-1].strip()
# elif "Position" in line:
# self.Recording.position_val = line.split(':')[-1].strip()
# elif "WaterTemperature" in line:
# self.Recording.water_temp_val = float(line.split(':')[-1].strip().replace('C', ''))
# elif "WaterConductivity" in line:
# self.Recording.water_cond_val = float(line.split(':')[-1].strip().replace('uS/cm', ''))
# elif 'WaterpH' in line:
# self.Recording.water_ph_val = float(line.split(':')[-1].strip().replace('pH', ''))
# elif "WaterOxygen" in line:
# self.Recording.water_oxy_val = float(line.split(':')[-1].strip().replace('mg/l', ''))
# elif "Comment" in line:
# self.Recording.comment_val = ':'.join(line.split(':')[1:]).strip()
# elif "Experimenter" in line:
# self.Recording.experimenter_val = ':'.join(line.split(':')[1:]).strip()
# elif "DataTime" in line:
# self.Recording.datatime_val = int(line.split(':')[-1].strip().replace('ms', ''))
# elif "DataInterval" in line:
# self.Recording.datainterval_val = int(line.split(':')[-1].strip().replace('ms', ''))
# elif "BufferTime" in line:
# self.Recording.buffertime_val = int(line.split(':')[-1].strip().replace('s', ''))
# else:
# continue
# def led_controll(pin, t0, dt, stop_flag, save_f=None):
# next = t0
#
# while True:
# if stop_flag():
# break
# if time() > next:
# save_t = next + time() - next
# GPIO.output(pin, GPIO.HIGH)
# sleep(0.1)
# GPIO.output(pin, GPIO.LOW)
#
# if save_f != None:
# save_f.write('%.4f' % (save_t))
# save_f.flush()
# next += dt
#
#
#
# def temp_rec(w1_bus_path, temp_f, t0, dt, stop_flag):
# next = t0
# while True:
# if stop_flag():
# break
# if time() > next:
# w1_f = open(w1_bus_path, 'r')
# w1_file = w1_f.readlines()
# for line in w1_file:
# if 't=' in line:
# temp = float((line.split('=')[-1].strip())) / 1000
# temp_f.write('%6.0f; %7.3f\n' % (next, temp))
# temp_f.flush()
# break
# w1_f.close()
# next += dt
#
# def clock_controll(end_clock, run_led_pin, sync_led_pin, w1_bus_path, temp_f, led_f, stop_flag):
# t0 = time()
# sub_stop_flag = False
#
# run_led_interval = 2
# run_thread = threading.Thread(target=led_controll, args=(run_led_pin, t0, run_led_interval, lambda: sub_stop_flag, None))
#
# sync_led_interval = 1
# sync_thread = threading.Thread(target=led_controll, args=(sync_led_pin, t0, sync_led_interval, lambda: sub_stop_flag, led_f))
#
# temp_interval = 300
# temp_thread = threading.Thread(target=temp_rec, args=(w1_bus_path, temp_f, t0, temp_interval, lambda: sub_stop_flag))
#
# run_thread.start()
# sync_thread.start()
# temp_thread.start()
#
# while True:
# if stop_flag():
# sub_stop_flag = True
# sync_thread.join()
# run_thread.join()
# break
# if datetime.datetime.now().hour == end_clock[0] and datetime.datetime.now().minute == end_clock[1]:
# break
def clock_process(end_clock, run_led_pin, sync_led_pin, w1_bus_path, temp_f, led_f):
t0 = time()
run_led_interval = 2
@ -236,10 +107,10 @@ def clock_process(end_clock, run_led_pin, sync_led_pin, w1_bus_path, temp_f, led
print('\nEnd time reached ...')
break
if (time() - t0) % temp_interval <= 0.1:
GPIO.output(run_led_pin, GPIO.HIGH)
#GPIO.output(run_led_pin, GPIO.HIGH)
GPIO.output(sync_led_pin, GPIO.HIGH)
sleep(0.1)
GPIO.output(run_led_pin, GPIO.LOW)
#GPIO.output(run_led_pin, GPIO.LOW)
GPIO.output(sync_led_pin, GPIO.LOW)
w1_f = open(w1_bus_path, 'r')
@ -254,10 +125,10 @@ def clock_process(end_clock, run_led_pin, sync_led_pin, w1_bus_path, temp_f, led
next_t_t += temp_interval
elif (time() - t0) % run_led_interval <= 0.1:
GPIO.output(run_led_pin, GPIO.HIGH)
#GPIO.output(run_led_pin, GPIO.HIGH)
GPIO.output(sync_led_pin, GPIO.HIGH)
sleep(0.1)
GPIO.output(run_led_pin, GPIO.LOW)
#GPIO.output(run_led_pin, GPIO.LOW)
GPIO.output(sync_led_pin, GPIO.LOW)
elif (time() - t0) % sync_led_interval <= 0.1:
@ -284,70 +155,17 @@ def save_process(q, f, gain):
Cdata.tofile(f)
f.flush()
# def duration_control(end_clock, stop_flag):
# while True:
# if stop_flag():
# break
#
# if datetime.datetime.now().hour == end_clock[0] and datetime.datetime.now().minute == end_clock[1]:
# break
#
# def led_controll_box(LED_t, LED1_pin, LED_out_pin, led_f, stop_flag):
# LED_t_interval = 2
# out_LED_interval = 1
#
# led_on_times = []
#
# status0 = False
# status1 = False
# while True:
# if stop_flag():
# GPIO.output(LED1_pin, GPIO.LOW)
# GPIO.output(LED_out_pin, GPIO.LOW)
# break
#
# if (time() - LED_t) % LED_t_interval < .1:
# status0 = True
# GPIO.output(LED1_pin, GPIO.HIGH)
# elif (time() - LED_t) % LED_t_interval >= .1 and status0 == True:
# status0 = False
# GPIO.output(LED1_pin, GPIO.LOW)
# else:
# pass
#
# if (time() - LED_t) % out_LED_interval < .1:
# status1 = True
# GPIO.output(LED_out_pin, GPIO.HIGH)
#
# led_on_times.append(time() - LED_t)
# led_f.write('%.4f' % (time() - LED_t))
# led_f.flush()
# elif (time() - LED_t) % out_LED_interval >= .1 and status1 == True:
# GPIO.output(LED_out_pin, GPIO.LOW)
# status1 = False
# else:
# pass
# def record_temperature(temp_t0, w1_bus_path, temp_f, stop_flag):
# next_temp_t = 0
# temp_interval = 300
#
# while True:
# if stop_flag():
# break
#
# if time() - temp_t0 > next_temp_t:
# w1_f = open(w1_bus_path, 'r')
# w1_file = w1_f.readlines()
# for line in w1_file:
# if 't=' in line:
# temp = float((line.split('=')[-1].strip())) / 1000
# temp_f.write('%6.0f; %7.3f\n' % (next_temp_t, temp))
# temp_f.flush()
# break
#
# w1_f.close()
# next_temp_t += temp_interval
def save_controll(q, pin):
while True:
if q.empty():
sleep(0.1)
pass
else:
trigger = q.get()
GPIO.output(pin, GPIO.HIGH)
sleep(0.5)
GPIO.output(pin, GPIO.LOW)
def main():
LED1_pin = 11
@ -378,14 +196,23 @@ def main():
valid = True
if not valid:
start_clock = [10, 00]
end_clock = [16, 00]
end_clock = [10, 30]
# get init cfg
if os.path.exists('/media/pi/data1'):
init_path = '/media/pi/data1'
else:
elif os.path.exists('/home/raab/data/rasp_test'):
init_path = '/home/raab/data/rasp_test'
else:
for i in range(10):
GPIO.output(LED1_pin, GPIO.HIGH)
sleep(0.5)
GPIO.output(LED1_pin, GPIO.LOW)
sleep(0.5)
print('got no path')
quit()
init_cfgfile = os.path.join(init_path, 'fishgrid.cfg')
if os.path.exists(init_cfgfile):
@ -395,16 +222,22 @@ def main():
quit()
# create save folder and copy cfg file
path = os.path.join(init_path, now.strftime(path_format))
start_str = ('%2.f_%2.f' % (start_clock[0], start_clock[1])).replace(' ', '0')
path = os.path.join(init_path, now.strftime(path_format[:-9]) + start_str) #ToDo: Edit here
if not os.path.exists(path):
os.makedirs(path)
copyfile(os.path.join(os.path.split(path)[0], 'fishgrid.cfg'), os.path.join(path, 'fishgrid.cfg'))
cfgfile = os.path.join(path, 'fishgrid.cfg')
# read and edit config file
channels, rate, n_cols, n_rows, max_v, gain = read_cfg(cfgfile, now)
channels, rate, n_cols, n_rows, max_v, gain = read_cfg(cfgfile, now, start_clock)
file = os.path.join(path, 'traces-grid1.raw')
temp_file = os.path.join(path, 'temperatures.csv')
led_file = os.path.join(path, 'led_times.csv')
led_file2 = os.path.join(path, 'led_idxs.csv')
# find w1bus for temp
record_temp = False
@ -418,6 +251,7 @@ def main():
f = open(file, 'wb')
led_f = open(led_file, 'w')
led_f2 = open(led_file2, 'w')
# f.close()
@ -497,24 +331,30 @@ def main():
GPIO.output(LED1_pin, GPIO.HIGH)
LED_status[0] = True
GPIO.output(LED2_pin, GPIO.HIGH)
LED_status[0] = True
GPIO.output(LED2_pin, GPIO.LOW)
LED_status[1] = False
sleep(.5)
GPIO.output(LED1_pin, GPIO.LOW)
LED_status[0] = False
GPIO.output(LED2_pin, GPIO.LOW)
LED_status[0] = False
GPIO.output(LED2_pin, GPIO.HIGH)
LED_status[1] = True
sleep(.5)
GPIO.output(LED1_pin, GPIO.HIGH)
LED_status[0] = True
GPIO.output(LED2_pin, GPIO.HIGH)
LED_status[0] = True
GPIO.output(LED2_pin, GPIO.LOW)
LED_status[1] = False
sleep(.5)
GPIO.output(LED1_pin, GPIO.LOW)
LED_status[0] = False
GPIO.output(LED2_pin, GPIO.HIGH)
LED_status[1] = True
sleep(.5)
GPIO.output(LED2_pin, GPIO.LOW)
LED_status[1] = False
disp_eth_power = True
stop_flag = False
@ -522,21 +362,28 @@ def main():
while True:
if datetime.datetime.now().hour == start_clock[0] and datetime.datetime.now().minute == start_clock[1]:
break
elif datetime.datetime.now().hour > start_clock[0] or datetime.datetime.now().minute > start_clock[1]:
elif datetime.datetime.now().hour * 60 + datetime.datetime.now().minute >= start_clock[0] * 60 + start_clock[1]:
# elif datetime.datetime.now().hour >= start_clock[0] and datetime.datetime.now().minute >= start_clock[1]:
h = datetime.datetime.now().hour
m = datetime.datetime.now().minute
start_clock = [h, m]
end_clock = [h + 6, m]
# end_clock = [h + 6, m]
GPIO.output(LED2_pin, GPIO.HIGH)
LED_status[1] = True
#clock_thread = threading.Thread(target=clock_controll, args=(end_clock, LED1_pin, LED_out_pin, w1_bus_path, temp_f, led_f, lambda: stop_flag))
#clock_thread.start()
clock_thread = mp.Process(target=clock_process, args=(end_clock, LED1_pin, LED_out_pin, w1_bus_path, temp_f, led_f))
clock_thread.start()
q = mp.Queue()
save_thread = mp.Process(target=save_process, args=(q, f, gain))
save_thread.start()
# clock_thread = mp.Process(target=clock_process, args=(end_clock, LED1_pin, LED_out_pin, w1_bus_path, temp_f, led_f))
# clock_thread.start()
#
# q = mp.Queue()
# # save_thread = mp.Process(target=save_process, args=(q, f, gain))
# # save_thread.start()
# save_thread = mp.Process(target=save_controll, args=(q, LED1_pin))
# save_thread.start()
print('\nRecording started.')
data = create_float_buffer(channel_count, samples_per_channel)
@ -546,17 +393,32 @@ def main():
print('Samples per channel: %.0f' % samples_per_channel)
print('----')
LED_t0 = time()
LED_t_interval = 5
sync_LED_t_interval = 5
temp_t0 = time()
next_temp_t = 0
temp_interval = 300 # sec --> 5 min
next_l_t = 0
disp_eth_power = True
rate = ai_device.a_in_scan(low_channel, high_channel, input_mode, ranges[range_index], samples_per_channel,
rate, scan_options, flags, data)
status, transfer_status = ai_device.get_scan_status()
save_ranges = np.array([[int(buffer_size / 2), len(data)], [0, int(buffer_size / 2)]])
save_range = save_ranges[0]
last_idx = 0
# while GPIO.input(Button1_pin) == GPIO.LOW and clock_thread.is_alive():
#while GPIO.input(Button1_pin) == GPIO.LOW and datetime.datetime.now().hour * 60 + datetime.datetime.now().minute < end_clock[0] * 60 + end_clock[1]:
buffer_no = 0
cont_t = time()
while GPIO.input(Button1_pin) == GPIO.LOW and clock_thread.is_alive():
while GPIO.input(Button1_pin) == GPIO.LOW:
if GPIO.input(Button2_pin) == GPIO.HIGH:
if (time() - last_button_2_t) > 5:
@ -580,58 +442,118 @@ def main():
disp_eth_power = True
last_button_2_t = time()
#################
if record_temp == True:
if time() - temp_t0 > next_temp_t:
w1_f = open(w1_bus_path, 'r')
w1_file = w1_f.readlines()
for line in w1_file:
if 't=' in line:
temp = float((line.split('=')[-1].strip())) / 1000
temp_f.write('%6.0f; %7.3f\n' % (next_temp_t, temp))
temp_f.flush()
break
w1_f.close()
next_temp_t += temp_interval
# blinking LED (run)
if (time() - LED_t0) % LED_t_interval < .5 and LED_status[0] == False:
# if (time() - LED_t0) % LED_t_interval < .5:
LED_status[0] = True
GPIO.output(LED1_pin, GPIO.HIGH)
elif (time() - LED_t0) % LED_t_interval >= .5 and LED_status[0] == True:
# elif (time() - LED_t0) % LED_t_interval >= .5:
LED_status[0] = False
GPIO.output(LED1_pin, GPIO.LOW)
else:
pass
if (time() - LED_t0) % sync_LED_t_interval < .5 and LED_status[2] == False:
if led_f != None:
Cidx = int((buffer_size * buffer_no + last_idx) / channels)
led_f.write('%.4f\n' % (time()-LED_t0))
led_f.flush()
led_f2.write('%.0f\n' % Cidx)
led_f2.flush()
LED_status[2] = True
GPIO.output(LED_out_pin, GPIO.HIGH)
elif (time() - LED_t0) % sync_LED_t_interval >= .5 and LED_status[2] == True:
LED_status[2] = False
GPIO.output(LED_out_pin, GPIO.LOW)
else:
pass
# if time() - LED_t < .1 and LED_status[0] == False:
# LED_status[0] = True
# GPIO.output(LED1_pin, GPIO.HIGH)
# if time() - LED_t >= .1 and LED_status[0] == True:
# LED_status[0] = False
# GPIO.output(LED1_pin, GPIO.LOW)
# if time() - LED_t >= LED_t_interval:
# LED_t = time()
##########################################
# Get the status of the background operation
status, transfer_status = ai_device.get_scan_status()
index = transfer_status.current_index
# print(index)
if index >= save_range[0] and index < save_range[1]:
GPIO.output(LED2_pin, GPIO.HIGH)
dt = time() - cont_t
cont_t = time()
print("dt = %.3f sec" % (dt))
print('samples = %.0f' % (len(data[save_range[0]:save_range[1]]) / 15))
print('rate = %.2f Hz\n' % (len(data[save_range[0]:save_range[1]]) / 15 /dt))
### the new way ###
# if index == -1:
# continue
#
# if index > save_range[0] and index <= save_range[1]:
# pass
#
# else:
# GPIO.output(LED1_pin, GPIO.HIGH)
# dt = time() - cont_t
# cont_t = time()
#
# Cdata = np.copy(np.array(data[save_range[0]:save_range[1]], dtype=np.float32) / gain)
# q.put(Cdata)
#
# save_ranges = np.roll(save_ranges, -1, axis=0)
# save_range = save_ranges[0]
#
#
# GPIO.output(LED1_pin, GPIO.LOW)
###---###
# (np.array(data[save_range[0]:save_range[1]], dtype=np.float32) / gain).tofile(f)
# f.flush()
### the old way ###
if index < 0 or index == last_idx:
continue
Cdata = np.copy(np.array(data[save_range[0]:save_range[1]], dtype=np.float32) / gain)
q.put(Cdata)
if index > last_idx:
(np.array(data[last_idx:index] / gain, dtype=np.float32)).tofile(f)
save_ranges = np.roll(save_ranges, 1, axis=0)
save_range = save_ranges[0]
else:
(np.array(data[last_idx:] / gain, dtype=np.float32)).tofile(f)
if datetime.datetime.now().hour * 60 + datetime.datetime.now().minute >= end_clock[0] * 60 + end_clock[1]:
f.flush()
GPIO.output(LED1_pin, GPIO.LOW)
GPIO.output(LED_out_pin, GPIO.LOW)
break
(np.array(data[:index] / gain, dtype=np.float32)).tofile(f)
f.flush()
GPIO.output(LED2_pin, GPIO.LOW)
buffer_no += 1
last_idx = index
# if index < 0 or index == last_idx:
# continue
#
# if index > last_idx:
#
# if index-last_idx > buffer_size / 5:
# (np.array(data[last_idx:index], dtype=np.float32) / gain).tofile(f)
# last_idx = index
# print('save')
# else:
# buffer_size = samples_per_channel * channels
# if buffer_size - last_idx + index > buffer_size / 5:
# (np.array(data[last_idx:], dtype=np.float32) / gain).tofile(f)
# (np.array(data[:index], dtype=np.float32) / gain).tofile(f)
# f.flush()
# print('save n flush')
# last_idx = index
###---###
#stop_flag = True
#clock_thread.join()
print('\nEmpty Queue')
while not q.empty():
sleep(0.01)
clock_thread.terminate()
save_thread.terminate()
# print('\nEmpty Queue')
# while not q.empty():
# sleep(0.01)
# clock_thread.terminate()
# save_thread.terminate()
# save_thread.terminate()
print('\nDone!')
f.close()