def edit_file(ui):
"""
Initializes the 'Edit config file' window.
Parameters
------
ui: the Ui_mainwindow object
Instance is created in the main.py
"""
if ui.experiment_queue.currentItem():
filename = ui.experiment_queue.currentItem().data(3)
config_data = parse_config_file(filename)
else:
warning(
'Do you want to edit a existing config file? If so, please load it!'
)
return
exp = None
if 'CA' in filename:
exp = CA_main(ui, config_data)
CA_window_writer(exp, config_data)
elif 'CV' in filename:
exp = CV_main(ui, config_data)
CV_window_writer(exp, config_data)
elif 'LSV' in filename:
exp = LSV_main(ui, config_data)
LSV_window_writer(exp, config_data)
if exp is None:
warning('Please rename the file with experiment type: CA/CV/LSV!')
ui.experiment_queue.clearSelection()
def find_port_main(ui):
"""
This function is connected with 'Find Potentiostat' button.
Parameters
----------
ui: the mainwindow object.
Instance is created in the main.py
Returns
-------
com : string, the name of the port with the potentiostat on it
Instance is created in the main.py
board_objects = (board, a0, a2, d9).
board : serial communication for board
a0 : location of analog read pin 0
a2 : location of analog read pin 2
d9 : location of digital pwm pin 9
Instance is created in the main.py
"""
com, board, a0, a2, d9 = startup_routine(ui)
board_objects = (board, a0, a2, d9)
icon_true = QIcon("../pics/icon_connected.ico")
if com and board:
ui.arduino_connection_indicator.setIcon(icon_true)
if not com:
warning('Please connect potentiostat!')
return com, board_objects
def preview_CA(exp, grid):
"""
This function is to show the preview and the experiment type.
Parameters
------
exp: the Ui_experiment object
grid: QGridLayout object
"""
stp_num = exp.experiment_step_number.text()
ca_v = exp.experiment_voltage.text()
ca_time = exp.experiment_time.text()
if check(stp_num) and check(ca_v) and check(ca_time):
stp_num = int(stp_num)
ca_v = float(ca_v)
ca_time = int(ca_time)
else:
warning(
'Please make sure all the experiment parameters are either integer or float.'
)
return
steps_list = np.linspace(ca_v, ca_v, stp_num + 1)
times_step_list = np.linspace(0, ca_time, num=stp_num + 1)
while grid.count() > 0:
item = grid.takeAt(0)
w = item.widget()
if w:
w.deleteLater()
grid.addWidget(plot(times_step_list, steps_list))
exp.experiment_duration.setText(time_converter(ca_time))
def preview_LSV(exp, grid):
"""
This function is to show the preview and the experiment type.
Parameters
------
exp: the Ui_experiment object
grid: QGridLayout object
"""
stp_num = exp.experiment_step_number.text()
lsv_sv = exp.experiment_start_voltage.text()
lsv_ev = exp.experiment_end_voltage.text()
lsv_sr = exp.experiment_sweep_rate.text()
if check(stp_num) and check(lsv_sv) and check(lsv_ev) and check(lsv_sr):
stp_num = int(stp_num)
lsv_sv = float(lsv_sv)
lsv_ev = float(lsv_ev)
lsv_sr = float(lsv_sr)
else:
warning(
'Please make sure all the experiment parameters are either integer or float.'
)
return
voltage_range = abs(lsv_ev - lsv_sv) # V
time_for_range = voltage_range / (lsv_sr / 1000) # s
steps_list = np.linspace(lsv_sv, lsv_ev, num=stp_num + 1)
times_step_list = np.linspace(0, time_for_range, num=stp_num + 1)
while grid.count() > 0:
item = grid.takeAt(0)
w = item.widget()
if w:
w.deleteLater()
grid.addWidget(plot(times_step_list, steps_list))
exp.experiment_duration.setText(time_converter((times_step_list[-1])))
def write_to_file_CA(ui, CA, CA_window, AP_params):
"""
This function is connect to save file button.
Parameters
------
CA : the Ui_CA object
CA_window: the CA QMainWindow object
AP_parameters: list that contains the advanced parameters
"""
config_params = get_parameters(CA, 'CA', AP_params)
data_out_name = config_params[3]
data_out_path = config_params[4]
filename_list = os.listdir(
data_out_path) # list all the filename in the folder
config_writer_CA(*config_params)
filename = os.path.join(data_out_path, data_out_name + "_CA_config.yml")
filename_parse = filename.split('/')[-1].strip(
) # this contains the filename without the path,e.g. 0_CA_config.yml
# list all the filename in the experiment queue, stored in queue_filename
queue_filename = []
for x in range(ui.experiment_queue.count()):
queue_filename.append(
ui.experiment_queue.item(x).data(2).split('.yml')[0] + '.yml')
if filename_parse in filename_list:
if warning('The filename exists. Do you want to overwrite it?'):
CA_window.close()
if filename_parse not in queue_filename:
item = QListWidgetItem()
icon = QIcon("../pics/icon_ca.ico")
item.setData(1, icon)
item.setData(2, filename_parse)
item.setData(3, filename)
ui.experiment_queue.addItem(item)
return
else: # if the filename is already in the experiment queue,
return # we don't need to show it on the queue again
else:
return
if warning('The file is saved. Do you want to exit the window?'):
CA_window.close()
item = QListWidgetItem()
icon = QIcon("../pics/icon_ca.ico")
item.setData(1, icon)
item.setData(2, filename_parse)
item.setData(3, filename)
ui.experiment_queue.addItem(item)
def get_parameters(exp, exp_type, AP_parameters):
"""
This function is to get all the parameters from the window
Parameters
------
exp : the Ui_Experiment object
exp_type: string, experiment type
AP_parameters: list that contains the advanced parameters
Return
------
config_params: list that contain all the experiment parameters
"""
data_out_name = exp.experiment_file_name.text()
data_out_path = exp.experiment_file_path.text()
rt = exp.experiment_rest_time.text()
stp_num = exp.experiment_step_number.text()
if check(stp_num) and check(rt):
move_on = True
stp_num = int(stp_num)
rt = int(rt)
else:
move_on = False
warning('Please input all the parameters with the correct data type.')
config_params = [exp_type, rt, stp_num, data_out_name, data_out_path
] + AP_parameters
cv_sv = exp.experiment_start_voltage.text()
cv_ftv = exp.experiment_first_vertex_voltage.text()
cv_stv = exp.experiment_second_vertex_voltage.text()
cv_sr = exp.experiment_sweep_rate.text()
cyc_num = exp.experiment_cycle_number.text()
if check(cv_sv) and check(cv_ftv) and check(cv_stv) and check(
cv_sr) and check(cyc_num):
cv_sv = float(cv_sv)
cv_ftv = float(cv_ftv)
cv_stv = float(cv_stv)
cv_sr = float(cv_sr)
cyc_num = int(cyc_num)
elif move_on:
warning(
'Please make sure all the experiment parameters are either integer or float.'
)
data = [cv_sv, cv_ftv, cv_stv, cv_sr, cyc_num]
config_params += data
return config_params
def write_to_file_LSV(ui, LSV, LSV_window, AP_params):
"""
This function is connect to save file button.
Parameters
------
LSV : the Ui_LSV object
LSV_window: the LSV QMainWindow object
AP_parameters: list that contains the advanced parameters
"""
config_params = get_parameters(LSV, 'LSV', AP_params)
data_out_name = config_params[3]
data_out_path = config_params[4]
filename_list = os.listdir(data_out_path)
config_writer_LSV(*config_params)
filename = os.path.join(data_out_path, data_out_name + "_LSV_config.yml")
filename_parse = filename.split('/')[-1].strip()
queue_filename = []
for x in range(ui.experiment_queue.count()):
queue_filename.append(
ui.experiment_queue.item(x).data(2).split('.yml')[0] + '.yml')
if filename_parse in filename_list:
if warning('The filename exists. Do you want to overwrite it?'):
LSV_window.close()
if filename_parse not in queue_filename:
item = QListWidgetItem()
icon = QIcon("../pics/icon_lsv.ico")
item.setData(1, icon)
item.setData(2, filename_parse)
item.setData(3, filename)
ui.experiment_queue.addItem(item)
return
else:
return
else:
return
if warning('The file is saved. Do you want to exit the window?'):
LSV_window.close()
item = QListWidgetItem()
icon = QIcon("../pics/icon_lsv.ico")
item.setData(1, icon)
item.setData(2, filename_parse)
item.setData(3, filename)
ui.experiment_queue.addItem(item)
def change_params():
"""
This function is connected to 'Save' button to save changed parameters.
"""
AP_params[0:7] = get_AP_parameters(AP)
if warning('The file has been saved. Do you want to exit the window?'):
AP_window.close()
def startup_routine(ui):
"""
Initializes the communication port with the JUAMI potentistat
Parameters
----------
ui: the mainwindow object.
Instance is created in the main.py
Returns
-------
Map of hardware
com : string, the name of the port with the potentiostat on it
board : serial communication for board
a0 : location of analog read pin 0
a2 : location of analog read pin 2
d9 : location of digital pwm pin 9
"""
com = ui.arduino_connection_name.currentText()
curr_ports = []
for p in list(serial.tools.list_ports.comports()
): # Checking if com still connected
curr_ports.append(p.device)
if com:
if com in curr_ports:
board = _initialize_arduino(com)
it = util.Iterator(board)
it.start()
# Setup Arduino pins
a0 = board.get_pin("a:0:i")
a2 = board.get_pin("a:2:i")
d9 = board.get_pin("d:9:p")
return com, board, a0, a2, d9
else:
warning('Current port not connected!')
return com, None, None, None, None
def preview_CV(exp, grid):
"""
This function is to show the preview and the experiment type.
Parameters
------
exp : the Ui_experiment object
grid : QGridLayout object
"""
stp_num = exp.experiment_step_number.text()
cv_sv = exp.experiment_start_voltage.text()
cv_ftv = exp.experiment_first_vertex_voltage.text()
cv_stv = exp.experiment_second_vertex_voltage.text()
cv_sr = exp.experiment_sweep_rate.text()
cyc_num = exp.experiment_cycle_number.text()
if check(stp_num) and check(cv_sv) and check(cv_ftv) and check(
cv_stv) and check(cv_sr) and check(cyc_num):
stp_num = int(stp_num)
cv_sv = float(cv_sv)
cv_ftv = float(cv_ftv)
cv_stv = float(cv_stv)
cv_sr = float(cv_sr)
cyc_num = int(cyc_num)
else:
warning(
'Please make sure all the experiment parameters are either integer or float.'
)
return
x, y = CV_data(stp_num, cv_sv, cv_ftv, cv_stv, cv_sr)
while grid.count() > 0:
item = grid.takeAt(0)
w = item.widget()
if w:
w.deleteLater()
grid.addWidget(plot(x, y))
exp.experiment_duration.setText(time_converter((x[-1] * cyc_num)))