savety commit

fishgrid.cfg

@@ -5,6 +5,7 @@
       RecordMode1      : standalone
       Columns1         : 2
       Rows1            : 4
+      Extra1           : 0
       ColumnDistance1  : 50.0cm
       RowDistance1     : 50.0cm
       ElectrodeType1   : headstage

rasp_grid.py

@@ -1,5 +1,6 @@
 from __future__ import print_function
 import os
+import sys
 import glob
 import datetime
 from shutil import copyfile
@@ -9,10 +10,9 @@ except:
     pass
 import subprocess
 import numpy as np
-import matplotlib.pyplot as plt
+import threading
+import multiprocessing as mp
 from time import sleep, time
-from os import system
-from sys import stdout
 from IPython import embed
 
 from uldaq import (get_daq_device_inventory, DaqDevice, AInScanFlag, ScanStatus,
@@ -56,35 +56,37 @@ def read_cfg(cfg_file, now, init_read=False):
                 path_format = ':'.join(line.split(':')[1:]).strip().replace('"', '').replace("'", "")
                 cfg_f.close()
                 return path_format
+    else:
+        for line in cfg:
+            if 'Columns1' in line:
+                n_cols = int(line.split(':')[1].strip())
+            elif 'Rows1' in line:
+                n_rows = int(line.split(':')[1].strip())
+            elif 'Extra1' in line:
+                n_extra = int(line.split(':')[1].strip())
+            elif "AISampleRate" in line:
+                samplerate = int(float(line.split(':')[-1].strip().replace('kHz', '')) * 1000)
+            elif "AIMaxVolt" in line:
+                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 ###
+        for enu, line in enumerate(cfg):
+            if "StartDate" in line:
+                cfg[enu] = ('          StartDate        : %s\n' % now.strftime('%Y-%m-%d'))
+            elif "StartTime" in line:
+                cfg[enu] = ('          StartTime        : %s\n' % (now.strftime('%H:%M:%S') + now.strftime(".%f")[:4]))
+        cfg_f.close()
+
+        cfg_f = open(cfg_file, 'w+')
+        for line in cfg:
+            cfg_f.write(line)
+        cfg_f.close()
 
-    for line in cfg:
+        return channels, samplerate, n_cols, n_rows, max_v, gain
-        if 'Columns1' in line:
-            n_cols = int(line.split(':')[1].strip())
-        elif 'Rows1' in line:
-            n_rows = int(line.split(':')[1].strip())
-        elif "AISampleRate" in line:
-            samplerate = int(float(line.split(':')[-1].strip().replace('kHz', '')) * 1000)
-        elif "AIMaxVolt" in line:
-            max_v = float(line.split(':')[1].strip().replace('mV', ''))
-        elif 'Gain' in line:
-            gain = int(line.split(':')[1].strip())
-    channels = n_rows * n_cols
-
-    ### alter information and re-write ###
-    for enu, line in enumerate(cfg):
-        if "StartDate" in line:
-            cfg[enu] = ('          StartDate        : %s\n' % now.strftime('%Y-%m-%d'))
-        elif "StartTime" in line:
-            cfg[enu] = ('          StartTime        : %s\n' % (now.strftime('%H:%M:%S') + now.strftime(".%f")[:4]))
-    cfg_f.close()
-
-    cfg_f = open(cfg_file, 'w+')
-    for line in cfg:
-        cfg_f.write(line)
-    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())
@@ -156,9 +158,165 @@ def read_cfg(cfg_file, now, init_read=False):
     #         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 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 main():
+    LED1_pin = 11
+    LED2_pin = 13
+    LED_out_pin = 35
+    Button1_pin = 16
+    Button2_pin = 18
+    power_controll_pin = 37
+
+    LED_status = GPIO_setup(LED1_pin, LED2_pin, LED_out_pin, Button1_pin, Button2_pin, power_controll_pin)
+
+    # switch LEDs off
+    GPIO.output(LED1_pin, GPIO.LOW)
+    LED_status[0] = False
+    GPIO.output(LED2_pin, GPIO.LOW)
+    LED_status[1] = False
+
+    last_button_2_t = time()
+
     now = datetime.datetime.now()
 
+    # defined start and end time
+    valid = False
+    if len(sys.argv) == 3:
+        if len(sys.argv[1]) == 4 and len(sys.argv[2]) == 4:
+            start_clock = [int(sys.argv[1][:2]), int(sys.argv[1][2:])]
+            end_clock = [int(sys.argv[2][:2]), int(sys.argv[2][2:])]
+            valid = True
+    if not valid:
+        start_clock = [10, 00]
+        end_clock = [16, 00]
+
+
     # get init cfg
     if os.path.exists('/media/pi/data1'):
         init_path = '/media/pi/data1'
@@ -179,38 +337,28 @@ def main():
     cfgfile = os.path.join(path, 'fishgrid.cfg')
 
     # read and edit config file
-    channels, rate, n_cols, n_rows, max_v, gain = read_cfg(init_cfgfile, now)
+    channels, rate, n_cols, n_rows, max_v, gain = read_cfg(cfgfile, now)
-
     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')
 
+    # find w1bus for temp
     record_temp = False
+    temp_f = None
     w1_bus_path = glob.glob('/sys/bus/w1/devices/28*/w1_slave')
     if len(w1_bus_path) > 0:
         w1_bus_path = w1_bus_path[0]
         record_temp = True
+        temp_f = open(temp_file, 'w')
+        temp_f.write('%-6s; %-7s\n' % ('time/s', 'T/C'))
+
     f = open(file, 'wb')
-    temp_f = open(temp_file, 'w')
+    led_f = open(led_file, 'w')
-    temp_f.write('%-6s; %-7s\n' % ('time/s', 'T/C'))
 
     # f.close()
 
-    LED1_pin = 11
-    LED2_pin = 13
-    LED_out_pin = 35
-    Button1_pin = 16
-    Button2_pin = 18
-    power_controll_pin = 37
-
-    LED_status = GPIO_setup(LED1_pin, LED2_pin, LED_out_pin, Button1_pin, Button2_pin, power_controll_pin)
-
-    last_button_1_t = time()
-    last_button_2_t = time()
-
     # DAQ setup
     if True:
-        # channels = 16
-
         status = ScanStatus.IDLE
 
         descriptor_index = 0  # ToDo: ????
@@ -218,9 +366,11 @@ def main():
 
         interface_type = InterfaceType.USB
         low_channel = 0
-        high_channel = channels
+        high_channel = channels - 1
 
         samples_per_channel = rate * 20  # * channels = Buffer size
+        buffer_size = samples_per_channel * channels
+        print('channels: %.0f' % channels)
         # rate = 20000
         scan_options = ScanOption.CONTINUOUS
         flags = AInScanFlag.DEFAULT
@@ -238,7 +388,7 @@ def main():
         # Create the DAQ device object associated with the specified descriptor index.
         daq_device = None
         daq_device = DaqDevice(devices[descriptor_index])
-        
+
         # Get the AiDevice object and verify that it is valid.
         ai_device = None
         ai_device = daq_device.get_ai_device()
@@ -279,133 +429,138 @@ def main():
                 break
         print(ranges[range_index])
 
-        # Allocate a buffer to receive the data.
-        # f = open('/media/pi/data1/test_file.raw', 'wb')
 
+    GPIO.output(LED1_pin, GPIO.HIGH)
+    LED_status[0] = True
+    GPIO.output(LED2_pin, GPIO.HIGH)
+    LED_status[0] = True
+    sleep(.5)
+
+    GPIO.output(LED1_pin, GPIO.LOW)
+    LED_status[0] = False
+    GPIO.output(LED2_pin, GPIO.LOW)
+    LED_status[0] = False
+    sleep(.5)
 
-    # LED on when here ... wait for switch to start data aquisition
     GPIO.output(LED1_pin, GPIO.HIGH)
     LED_status[0] = True
-    while GPIO.input(Button1_pin) == GPIO.LOW:
+    GPIO.output(LED2_pin, GPIO.HIGH)
-        sleep(.1)
+    LED_status[0] = True
+    sleep(.5)
+
     GPIO.output(LED1_pin, GPIO.LOW)
     LED_status[0] = False
-    sleep(2.)
+
+    disp_eth_power = True
+    stop_flag = False
+
+    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]:
+            h = datetime.datetime.now().hour
+            m = datetime.datetime.now().minute
+            start_clock = [h, m]
+            end_clock = [h + 6, m]
+
+    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()
+
+    print('go')
     data = create_float_buffer(channel_count, samples_per_channel)
-    # system('clear')
+    print('----')
+    print(len(data))
+    print(samples_per_channel)
+    print(channel_count)
+    print('----')
 
-    # Start the acquisition.
     rate = ai_device.a_in_scan(low_channel, high_channel, input_mode, ranges[range_index], samples_per_channel,
-                                   rate, scan_options, flags, data)
+                               rate, scan_options, flags, data)
-    last_idx = 0 
-    
-    
 
-    emergency_LED_t = time()
+    status, transfer_status = ai_device.get_scan_status()
-    emergency_LED_interval = 0.5
 
-    LED_t = time()
+    save_ranges = np.array([[int(buffer_size / 2), len(data)], [0, int(buffer_size / 2)]])
-    LED_t_interval = 2
+    save_range = save_ranges[0]
 
-    out_LED_t = time()
-    out_LED_interval = 1
-    
-    temp_t0 = time()
-    next_temp_t = 0
-    temp_interval = 300  # sec --> 5 min
 
-    disp_eth_power = True
+    cont_t = time()
-    #while True:
+    while GPIO.input(Button1_pin) == GPIO.LOW and clock_thread.is_alive():
-    while GPIO.input(Button1_pin) == GPIO.LOW:
+
-        if record_temp == True:
+        if GPIO.input(Button2_pin) == GPIO.HIGH:
-            if time() - temp_t0 > next_temp_t:
+            if (time() - last_button_2_t) > 5:
-                w1_f = open(w1_bus_path, 'r')
+                if disp_eth_power == True:
-                w1_file = w1_f.readlines()
+                    subprocess.run(['tvservice', '-o'])
-                for line in w1_file:
+                    subprocess.run(['vcgencmd', 'display_power', '0'])#
-                    if 't=' in line:
+
-                        temp = float((line.split('=')[-1].strip())) / 1000
+                    subprocess.run(['sudo', 'ip', 'link', 'set', 'eth0', 'down'])
-                        temp_f.write('%6.0f; %7.3f\n' % (next_temp_t, temp))
+                    GPIO.output(LED2_pin, GPIO.LOW)
-                        temp_f.flush()
+                    disp_eth_power = False
-                        break
+                    last_button_2_t = time()
-
+
-                w1_f.close()
+                elif disp_eth_power == False:
-                next_temp_t += temp_interval
+                    subprocess.run(['tvservice', '-p'])
-
+                    subprocess.run(['vcgencmd', 'display_power', '1'])
-        # blinking LED for rec
+                    subprocess.run(['sudo', '/bin/chvt', '6'])
-        if time() - LED_t < .1 and LED_status[0] == False:
+                    subprocess.run(['sudo', '/bin/chvt', '7'])#
-            LED_status[0] = True
+
-            GPIO.output(LED1_pin, GPIO.HIGH)
+                    subprocess.run(['sudo', 'ip', 'link', 'set', 'eth0', 'up'])
-        if time() - LED_t >= .1 and LED_status[0] == True:
+                    GPIO.output(LED2_pin, GPIO.HIGH)
-            LED_status[0] = False
+                    disp_eth_power = True
-            GPIO.output(LED1_pin, GPIO.LOW)
+                    last_button_2_t = time()
-        if time() - LED_t >= LED_t_interval:
-            LED_t = time() - (time() - LED_t - LED_t_interval)
-
-        if len(LED_status) == 3:
-            if time() - out_LED_t < .1 and LED_status[2] == False:
-                LED_status[2] = True
-                GPIO.output(LED_out_pin, GPIO.HIGH)
-            elif time() - out_LED_t >= .1 and LED_status[2] == True:
-                LED_status[2] = False
-                GPIO.output(LED_out_pin, GPIO.LOW)
-            else:
-                pass
-
-            if time() - out_LED_t >= out_LED_interval:
-                out_LED_t = time() - (time() - out_LED_t - out_LED_interval )
-            
-            
-        # dist & eth0 controll
-        if GPIO.input(Button2_pin) == GPIO.HIGH and (time() - last_button_2_t) > 5:
-            if disp_eth_power == True:
-                subprocess.run(['tvservice', '-o'])
-                subprocess.run(['vcgencmd', 'display_power', '0'])#
-
-                subprocess.run(['sudo', 'ip', 'link', 'set', 'eth0', 'down'])
-                GPIO.output(LED2_pin, GPIO.LOW)
-                disp_eth_power = False
-                last_button_2_t = time()
-
-            elif disp_eth_power == False:
-                subprocess.run(['tvservice', '-p'])
-                subprocess.run(['vcgencmd', 'display_power', '1'])
-                subprocess.run(['sudo', '/bin/chvt', '6'])
-                subprocess.run(['sudo', '/bin/chvt', '7'])#
-
-                subprocess.run(['sudo', 'ip', 'link', 'set', 'eth0', 'up'])
-                GPIO.output(LED2_pin, GPIO.HIGH)
-                disp_eth_power = True
-                last_button_2_t = time()
 
         # Get the status of the background operation
         status, transfer_status = ai_device.get_scan_status()
 
         index = transfer_status.current_index
-        #print(last_idx - index)
+        # print(index)
-        #embed()
+
-        #quit()
+        if index >= save_range[0] and index < save_range[1]:
-        if index < 0 or index == last_idx:
+            dt = time() - cont_t
-            continue
+            cont_t = time()
-
-        if index > last_idx:
-            (np.array(data[last_idx:index], dtype=np.float32) / gain).tofile(f)
-        else:
-            (np.array(data[last_idx:], dtype=np.float32) / gain).tofile(f)
-            (np.array(data[:index], dtype=np.float32) / gain).tofile(f)
-            f.flush()
 
-        last_idx = index
+            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))
+
+            (np.array(data[save_range[0]:save_range[1]], dtype=np.float32) / gain).tofile(f)
+            f.flush()
+            save_ranges = np.roll(save_ranges, 1, axis=0)
+            save_range = save_ranges[0]
+
+        # 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('end')
 
     f.close()
     temp_f.close()
+    led_f.close()
 
-    if LED_status[0] == False:
+    GPIO.output(LED1_pin, GPIO.HIGH)
-        GPIO.output(LED1_pin, GPIO.HIGH)
+    GPIO.output(LED2_pin, GPIO.HIGH)
-    if LED_status[1] == False:
-        GPIO.output(LED2_pin, GPIO.HIGH)
 
     sleep(2)
 
+    GPIO.output(LED1_pin, GPIO.LOW)
+    GPIO.output(LED2_pin, GPIO.LOW)
+
     if daq_device:
         # Stop the acquisition if it is still running.
         if status == ScanStatus.RUNNING:

rasp_grid_cfg.py

@@ -14,6 +14,7 @@ class Grid_tab(QWidget):
         self.rec_mode_val = 'standalone'
         self.columns_val = 8
         self.rows_val = 8
+        self.extra_val = 0
         self.col_dist_val = 50
         self.row_dist_val = 50
         self.channel_offset_val = 0
@@ -57,53 +58,60 @@ class Grid_tab(QWidget):
         self.gridlayout.addWidget(self.row_elecs, 3, 1)
         self.gridlayout.addWidget(row_elecsU, 3, 2)
 
+        ext_elecsU = QLabel('n', self)
+        ext_elecsL = QLabel('Extra electrodes:', self)
+        self.extra_elecs = QLineEdit(str(self.extra_val), self)
+        self.gridlayout.addWidget(ext_elecsL, 4, 0)
+        self.gridlayout.addWidget(self.extra_elecs, 4, 1)
+        self.gridlayout.addWidget(ext_elecsU, 4, 2)
+
         col_spaceU = QLabel('cm', self)
         col_spaceL = QLabel('Column spacing:', self)
         self.col_space = QLineEdit(str(self.col_dist_val), self)
-        self.gridlayout.addWidget(col_spaceL, 4, 0)
+        self.gridlayout.addWidget(col_spaceL, 5, 0)
-        self.gridlayout.addWidget(self.col_space, 4, 1)
+        self.gridlayout.addWidget(self.col_space, 5, 1)
-        self.gridlayout.addWidget(col_spaceU, 4, 2)
+        self.gridlayout.addWidget(col_spaceU, 5, 2)
 
         row_spaceU = QLabel('cm', self)
         row_spaceL = QLabel('Row spacing:', self)
         self.row_space = QLineEdit(str(self.row_dist_val), self)
-        self.gridlayout.addWidget(row_spaceL, 5, 0)
+        self.gridlayout.addWidget(row_spaceL, 6, 0)
-        self.gridlayout.addWidget(self.row_space, 5, 1)
+        self.gridlayout.addWidget(self.row_space, 6, 1)
-        self.gridlayout.addWidget(row_spaceU, 5, 2)
+        self.gridlayout.addWidget(row_spaceU, 6, 2)
 
         elec_typeL = QLabel('Electrode Type:', self)
         self.elec_type = QLineEdit(self.elec_type_val, self)
-        self.gridlayout.addWidget(elec_typeL, 6, 0)
+        self.gridlayout.addWidget(elec_typeL, 7, 0)
-        self.gridlayout.addWidget(self.elec_type, 6, 1)
+        self.gridlayout.addWidget(self.elec_type, 7, 1)
 
         ref_elec_typeL = QLabel('Ref. Electrode Type:', self)
         self.ref_elec_type = QLineEdit(self.ref_elec_type_val, self)
-        self.gridlayout.addWidget(ref_elec_typeL, 7, 0)
+        self.gridlayout.addWidget(ref_elec_typeL, 8, 0)
-        self.gridlayout.addWidget(self.ref_elec_type, 7, 1)
+        self.gridlayout.addWidget(self.ref_elec_type, 8, 1)
 
         ref_elec_xU = QLabel('m', self)
         ref_elec_xL = QLabel('Ref. Electrode Pos-x:', self)
         self.ref_elec_x = QLineEdit('%.2f' % self.ref_elec_posx_val, self)
-        self.gridlayout.addWidget(ref_elec_xL, 8, 0)
+        self.gridlayout.addWidget(ref_elec_xL, 9, 0)
-        self.gridlayout.addWidget(self.ref_elec_x, 8, 1)
+        self.gridlayout.addWidget(self.ref_elec_x, 9, 1)
-        self.gridlayout.addWidget(ref_elec_xU, 8, 2)
+        self.gridlayout.addWidget(ref_elec_xU, 9, 2)
 
         ref_elec_yU = QLabel('m', self)
         ref_elec_yL = QLabel('Ref. Electrode Pos-y:', self)
         self.ref_elec_y = QLineEdit('%.2f' % self.ref_elec_posy_val, self)
-        self.gridlayout.addWidget(ref_elec_yL, 9, 0)
+        self.gridlayout.addWidget(ref_elec_yL, 10, 0)
-        self.gridlayout.addWidget(self.ref_elec_y, 9, 1)
+        self.gridlayout.addWidget(self.ref_elec_y, 10, 1)
-        self.gridlayout.addWidget(ref_elec_yU, 9, 2)
+        self.gridlayout.addWidget(ref_elec_yU, 10, 2)
 
         water_depthU = QLabel('cm', self)
         water_depthL = QLabel('Water depth:', self)
         self.water_depth = QLineEdit('%.2f' % self.water_depth_val, self)
-        self.gridlayout.addWidget(water_depthL, 10, 0)
+        self.gridlayout.addWidget(water_depthL, 11, 0)
-        self.gridlayout.addWidget(self.water_depth, 10, 1)
+        self.gridlayout.addWidget(self.water_depth, 11, 1)
-        self.gridlayout.addWidget(water_depthU, 10, 2)
+        self.gridlayout.addWidget(water_depthU, 11, 2)
 
         space = QLabel('', self)
-        self.gridlayout.addWidget(space, 11, 0)
+        self.gridlayout.addWidget(space, 12, 0)
 
 class Hardware_settings_tab(QWidget):
     def __init__(self):
@@ -381,6 +389,8 @@ class MainWindow(QTabWidget):
                 self.Grid.columns_val = int(line.split(':')[1].strip())
             elif 'Rows1' in line:
                 self.Grid.rows_val = int(line.split(':')[1].strip())
+            elif 'Extra1' in line:
+                self.Grid.extra_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:
@@ -459,6 +469,7 @@ class MainWindow(QTabWidget):
         f.write('      RecordMode1      : %s\n' % self.Grid.rec_mode.text())
         f.write('      Columns1         : %.0f\n' % int(self.Grid.col_elecs.text()))
         f.write('      Rows1            : %.0f\n' % int(self.Grid.row_elecs.text()))
+        f.write('      Extra1           : %.0f\n' % int(self.Grid.extra_elecs.text()))
         f.write('      ColumnDistance1  : %.1fcm\n' % float(self.Grid.col_space.text()))
         f.write('      RowDistance1     : %.1fcm\n' % float(self.Grid.row_space.text()))
         # f.write('      ChannelOffset1   : %.0f\n' % int(self.Grid.channel_offset.text()))