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PySimpleEChem.py
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#!/usr/bin/python3
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pyqtgraph as pg
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtWidgets import QApplication, QMainWindow, QVBoxLayout, QWidget, QSlider, QLabel, QPushButton, QFileDialog, QDialog, QHBoxLayout, QGridLayout, QComboBox, QLineEdit, QScrollArea, QTableWidget, QTableWidgetItem, QFrame, QCheckBox, QMenu, QAction, QSplitter
from PyQt5.QtCore import Qt
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from function_collection import battery_xls2df, get_CV_init, cy_idx_state_range, read_cv_format, get_peak_CV, search_pattern, ir_compen_func, diffusion, reaction_rate, peak_2nd_deriv, find_alpha, min_max_peak, check_val, switch_val, RDE_kou_lev, linear_fit, data_poly_inter,open_battery_data, df_select_column, read_cv_versastat
from superqt import QRangeSlider
# from numba import jit
# @jit
class PySimpleEChem_main(QMainWindow):
def __init__(self):
super().__init__()
self.setWindowTitle("PySimpleEChem")
self.setGeometry(100, 100, 800, 600)
self.central_widget = QWidget(self)
self.setCentralWidget(self.central_widget)
self.layout = QVBoxLayout(self.central_widget) # Use QVBoxLayout for vertical arrangement
self.create_widgets()
self.cv_setup_plot()
def create_widgets(self):
self.cv_concat_list_df = pd.DataFrame()
self.cv_df_ir_currden = pd.DataFrame()
self.cv_param_concat_df = pd.DataFrame()
self.cv_2nd_deriv_concat_list_df = pd.DataFrame()
self.cv_baseline_df = pd.DataFrame()
self.cv_lines = None
self.cv_plot_baseline_1 = None
self.cv_plot_baseline_2 = None
self.cv_plot_baseline_fit_1 = None
self.cv_plot_baseline_fit_2 = None
self.cv_plot_peak_1 = None
self.cv_plot_peak_2 = None
self.cv_plot_range_1 = None
self.cv_plot_range_2 = None
self.cv_chosen_volt = None
self.cv_chosen_current = None
self.cv_peak_range = None
self.cv_peak_pos_1_value = None
self.cv_peak_pos_2_value = None
self.cv_line_artist_list = []
self.cv_plot_defl = None
self.baseline_start_1 = None
self.baseline_start_2 = None
self.baseline_end_1 = None
self.baseline_end_2 = None
self.user_edit = True
# Top section (horizontal)
top_layout = QHBoxLayout()
# Top left section (vertical)
top_left_layout = QVBoxLayout()
self.cv_plot = pg.PlotWidget()
top_left_layout.addWidget(self.cv_plot)
top_right_layout = QVBoxLayout() # Top right section (vertical)
top_right_cv_open = QHBoxLayout() #First top-right CV layout
self.cvaddopenbutton = QPushButton("Add/Open CV file", self)
self.cvaddopenbutton.setMenu(self.create_cv_menu())
self.cvloadbutton = QPushButton("Load CV file", self)
self.cvchoosecombo = QComboBox(self)
self.cvchoosecombo.setFixedSize(300, 35)
self.cvchoosecombo.setEditable(False)
self.cvchoosecombo.setInsertPolicy(QComboBox.NoInsert)
self.cvdeletebutton = QPushButton("Delete CV", self)
top_right_cv_open.addWidget(self.cvaddopenbutton)
top_right_cv_open.addWidget(self.cvloadbutton)
top_right_cv_open.addWidget(self.cvchoosecombo)
top_right_cv_open.addWidget(self.cvdeletebutton)
top_right_layout.addLayout(top_right_cv_open)
# Create a vertical layout for the top right section
top_right_IR = QHBoxLayout()
self.ircompenlabel = QLabel("IR compensation (ohm):")
self.cv_ircompen_box = QLineEdit(self)
self.cv_ircompen_box.setText("0")
self.cv_ircompen_box.setEnabled(False)
self.elec_arealabel = QLabel("Electrode area (cm<sup>2</sup>):")
self.cv_elec_area_box = QLineEdit(self)
self.cv_elec_area_box.setText("1")
self.cv_elec_area_box.setEnabled(False)
self.scan_rate_label = QLabel("Scan rate (V/s):")
self.cv_scan_rate_box = QLineEdit(self)
self.cv_scan_rate_box.setText("0")
self.cv_scan_rate_box.setEnabled(False)
top_right_IR.addWidget(self.ircompenlabel)
top_right_IR.addWidget(self.cv_ircompen_box)
top_right_IR.addWidget(self.elec_arealabel)
top_right_IR.addWidget(self.cv_elec_area_box)
top_right_IR.addWidget(self.scan_rate_label)
top_right_IR.addWidget(self.cv_scan_rate_box)
top_right_layout.addLayout(top_right_IR)
top_right_trim = QHBoxLayout()
self.cv_trim_label = QLabel("Trim:")
self.cv_trim_slider = QRangeSlider(Qt.Horizontal)
self.cv_trim_slider.setRange(0, 1)
self.cv_trim_slider.setValue((0, 1))
self.cv_trim_slider.setDisabled(True)
self.cv_pos_trim_label = QLabel("Position:")
self.cv_pos_trim_start_box = QLineEdit(self)
self.cv_pos_trim_start_box.setFixedSize(50, 30)
self.cv_pos_trim_start_box.setDisabled(True)
self.cv_pos_trim_end_box = QLineEdit(self)
self.cv_pos_trim_end_box.setFixedSize(50, 30)
self.cv_pos_trim_end_box.setDisabled(True)
top_right_trim.addWidget(self.cv_trim_label)
top_right_trim.addWidget(self.cv_trim_slider)
top_right_trim.addWidget(self.cv_pos_trim_label)
top_right_trim.addWidget(self.cv_pos_trim_start_box)
top_right_trim.addWidget(self.cv_pos_trim_end_box)
top_right_layout.addLayout(top_right_trim)
top_right_baseline_1 = QHBoxLayout()
self.cv_baseline_1_label = QLabel("Baseline 1:")
self.cv_baseline_1_slider = QRangeSlider(Qt.Horizontal)
self.cv_baseline_1_slider.setRange(0, 1)
self.cv_baseline_1_slider.setValue((0, 1))
self.cv_baseline_1_slider.setDisabled(True)
self.cv_baseline_1_slider.barMovesAllHandles = True
self.cv_baseline_1_pos_label = QLabel("Position:")
self.cv_pos_baseline_start_1_box = QLineEdit(self)
self.cv_pos_baseline_start_1_box.setFixedSize(50, 30)
self.cv_pos_baseline_start_1_box.setDisabled(True)
self.cv_pos_baseline_end_1_box = QLineEdit(self)
self.cv_pos_baseline_end_1_box.setFixedSize(50, 30)
self.cv_pos_baseline_end_1_box.setDisabled(True)
top_right_baseline_1.addWidget(self.cv_baseline_1_label)
top_right_baseline_1.addWidget(self.cv_baseline_1_slider)
top_right_baseline_1.addWidget(self.cv_baseline_1_pos_label)
top_right_baseline_1.addWidget(self.cv_pos_baseline_start_1_box)
top_right_baseline_1.addWidget(self.cv_pos_baseline_end_1_box)
top_right_layout.addLayout(top_right_baseline_1)
top_right_baseline_2 = QHBoxLayout()
self.cv_baseline_2_label = QLabel("Baseline 2:")
self.cv_baseline_2_slider = QRangeSlider(Qt.Horizontal)
self.cv_baseline_2_slider.setRange(0, 1)
self.cv_baseline_2_slider.setValue((0, 1))
self.cv_baseline_2_slider.setDisabled(True)
self.cv_baseline_2_slider.barMovesAllHandles = True
self.cv_baseline_2_pos_label = QLabel("Position:")
self.cv_pos_baseline_start_2_box = QLineEdit(self)
self.cv_pos_baseline_start_2_box.setFixedSize(50, 30)
self.cv_pos_baseline_start_2_box.setDisabled(True)
self.cv_pos_baseline_end_2_box = QLineEdit(self)
self.cv_pos_baseline_end_2_box.setFixedSize(50, 30)
self.cv_pos_baseline_end_2_box.setDisabled(True)
top_right_baseline_2.addWidget(self.cv_baseline_2_label)
top_right_baseline_2.addWidget(self.cv_baseline_2_slider)
top_right_baseline_2.addWidget(self.cv_baseline_2_pos_label)
top_right_baseline_2.addWidget(self.cv_pos_baseline_start_2_box)
top_right_baseline_2.addWidget(self.cv_pos_baseline_end_2_box)
top_right_layout.addLayout(top_right_baseline_2)
top_right_peak_search = QHBoxLayout()
self.cv_peak_search_range_label = QLabel("Peak search range:")
self.cv_peak_range_slider = QSlider(Qt.Horizontal)
self.cv_peak_range_slider.setDisabled(True)
self.cv_pos_search_range_label = QLabel("Range:")
self.cv_pos_search_range_box = QLineEdit(self)
self.cv_pos_search_range_box.setFixedSize(50, 30)
self.cv_pos_search_range_box.setDisabled(True)
top_right_peak_search.addWidget(self.cv_peak_search_range_label)
top_right_peak_search.addWidget(self.cv_peak_range_slider)
top_right_peak_search.addWidget(self.cv_pos_search_range_label)
top_right_peak_search.addWidget(self.cv_pos_search_range_box)
top_right_layout.addLayout(top_right_peak_search)
top_right_pos_1 = QHBoxLayout()
self.cv_peak_pos_1_label = QLabel("Peak position 1:")
self.cv_peak_pos_1_slider = QSlider(Qt.Horizontal)
self.cv_peak_pos_1_slider.setDisabled(True)
self.cv_peak_pos_mode_1_label = QLabel("Mode:")
self.cv_peak_pos_1_combo = QComboBox(self)
self.cv_peak_pos_1_combo.addItems(['max','min','exact','2nd derivative'])
self.cv_peak_pos_1_combo.setCurrentText('max')
self.cv_peak_pos_1_combo.setFixedSize(100, 35)
self.cv_peak_pos_1_combo.setEditable(False)
self.cv_peak_pos_1_combo.setInsertPolicy(QComboBox.NoInsert)
self.cv_peak_pos_1_combo.setDisabled(True)
self.cv_peak_pos_1_val_label = QLabel("Position:")
self.cv_peak_pos_1_box = QLineEdit(self)
self.cv_peak_pos_1_box.setFixedSize(50, 30)
self.cv_peak_pos_1_box.setDisabled(True)
top_right_pos_1.addWidget(self.cv_peak_pos_1_label)
top_right_pos_1.addWidget(self.cv_peak_pos_1_slider)
top_right_pos_1.addWidget(self.cv_peak_pos_mode_1_label)
top_right_pos_1.addWidget(self.cv_peak_pos_1_combo)
top_right_pos_1.addWidget(self.cv_peak_pos_1_val_label)
top_right_pos_1.addWidget(self.cv_peak_pos_1_box)
top_right_layout.addLayout(top_right_pos_1)
top_right_pos_2 = QHBoxLayout()
self.cv_peak_pos_2_label = QLabel("Peak position 2:")
self.cv_peak_pos_2_slider = QSlider(Qt.Horizontal)
self.cv_peak_pos_2_slider.setDisabled(True)
self.cv_peak_pos_mode_2_label = QLabel("Mode:")
self.cv_peak_pos_2_combo = QComboBox(self)
self.cv_peak_pos_2_combo.addItems(['max','min','exact','2nd derivative'])
self.cv_peak_pos_2_combo.setCurrentText('min')
self.cv_peak_pos_2_combo.setFixedSize(100, 35)
self.cv_peak_pos_2_combo.setEditable(False)
self.cv_peak_pos_2_combo.setInsertPolicy(QComboBox.NoInsert)
self.cv_peak_pos_2_combo.setDisabled(True)
self.cv_peak_pos_2_val_label = QLabel("Position:")
self.cv_peak_pos_2_box = QLineEdit(self)
self.cv_peak_pos_2_box.setFixedSize(50, 30)
self.cv_peak_pos_2_box.setDisabled(True)
top_right_pos_2.addWidget(self.cv_peak_pos_2_label)
top_right_pos_2.addWidget(self.cv_peak_pos_2_slider)
top_right_pos_2.addWidget(self.cv_peak_pos_mode_2_label)
top_right_pos_2.addWidget(self.cv_peak_pos_2_combo)
top_right_pos_2.addWidget(self.cv_peak_pos_2_val_label)
top_right_pos_2.addWidget(self.cv_peak_pos_2_box)
top_right_layout.addLayout(top_right_pos_2)
# Add Nicholson Frame
self.nicholson_position_box = QLineEdit(self)
self.nicholson_position_box.setFixedSize(50, 30)
self.cv_nicholson_frame = QFrame(self)
self.cv_nicholson_frame.setFrameShape(QFrame.Box) # Set the frame shape to Box for a rectangular frame
self.cv_nicholson_frame.setLineWidth(1) # Set the width of the frame lines
right_nicholson_frame = QVBoxLayout(self.cv_nicholson_frame)
cv_nicholson_slider_layout = QHBoxLayout()
self.nicholson_checkbox = QCheckBox("Nicholson method (if baseline cannot be determine)")
self.nicholson_checkbox.setDisabled(True)
self.switch_potential_label = QLabel("Switching potential current (Jps0)")
self.nicholson_slider = QSlider(Qt.Horizontal, minimum=1, maximum=10, tickInterval=1)
self.nicholson_slider.setDisabled(True)
self.nicholson_position_label = QLabel("Position:")
right_nicholson_frame.addWidget(self.nicholson_checkbox)
right_nicholson_frame.addLayout(cv_nicholson_slider_layout)
cv_nicholson_slider_layout.addWidget(self.switch_potential_label)
cv_nicholson_slider_layout.addWidget(self.nicholson_slider)
cv_nicholson_slider_layout.addWidget(self.nicholson_position_label)
cv_nicholson_slider_layout.addWidget(self.nicholson_position_box)
top_right_layout.addWidget(self.cv_nicholson_frame)
self.cv_conc_frame = QFrame(self)
self.cv_conc_frame.setFrameShape(QFrame.Box) # Set the frame shape to Box for a rectangular frame
self.cv_conc_frame.setLineWidth(1) # Set the width of the frame lines
right_result_frame = QVBoxLayout(self.cv_conc_frame)
cv_result_layout = QHBoxLayout()
self.cv_bulk_conc = QLabel("Bulk concentration")
self.cv_bulk_conc_unit = QLabel("mol/cm<sup>2</sup>")
right_result_frame.addLayout(cv_result_layout)
cv_result_layout.addWidget(self.cv_bulk_conc)
cv_result_layout.addWidget(self.cv_bulk_conc_unit)
top_right_layout.addWidget(self.cv_conc_frame)
#Add Help
top_right_help = QHBoxLayout()
self.help_label = QPushButton("Help", self)
self.about_label = QPushButton("About", self)
self.help_label.setFixedSize(50, 30)
self.about_label.setFixedSize(50, 30)
top_right_help.addWidget(self.help_label)
top_right_help.addWidget(self.about_label)
top_right_layout.addLayout(top_right_help)
# Wrap top left and top right sections in QWidgets and add them to QSplitter
top_left_widget = QWidget()
top_left_widget.setLayout(top_left_layout)
top_right_widget = QWidget()
top_right_widget.setLayout(top_right_layout)
# Wrap top layout in a QSplitter to make it adjustable
top_splitter = QSplitter(Qt.Horizontal)
top_splitter.addWidget(top_left_widget)
top_splitter.addWidget(top_right_widget)
# Add top splitter to main layout
self.layout.addWidget(top_splitter)
# Bottom section (vertical)
bottom_layout = QVBoxLayout()
#################### Create Table #####################
self.cv_result_table = QtWidgets.QTableView()
# self.cv_result_display = pd.DataFrame()
self.cv_result_display = pd.DataFrame(columns = ['file name', 'scan rate', 'Jp1', 'Jp2', 'Jp1/Jp2', 'Ep1', 'Ep2',"E\u00bd", "ΔE\u209a", "alpha1", "alpha2", "Jpc0"])
self.cv_result_table.setModel(TableModel(self.cv_result_display))
#######################################################
bottom_layout.addWidget(self.cv_result_table)
# Add bottom section to main layout
self.layout.addLayout(bottom_layout)
self.cv_ircompen_box.textChanged.connect(self.cv_modify_cv_trim)
self.cv_elec_area_box.textChanged.connect(self.cv_modify_cv_trim)
self.cv_scan_rate_box.textChanged.connect(self.cv_modify_cv_trim)
self.cv_trim_slider.sliderMoved.connect(self.cv_draw_all_cv)
self.cvchoosecombo.textActivated.connect(self.cv_open_switch_cv)
# self.cvaddopenbutton.clicked.connect(self.show_hello_window)
self.cv_baseline_1_slider.sliderMoved.connect(self.cv_draw_baseline_plot)
self.cv_baseline_2_slider.sliderMoved.connect(self.cv_draw_baseline_plot)
self.cv_peak_range_slider.sliderMoved.connect(self.cv_draw_marker_plot)
self.cv_peak_pos_1_slider.sliderMoved.connect(self.cv_draw_marker_plot)
self.cv_peak_pos_2_slider.sliderMoved.connect(self.cv_draw_marker_plot)
# self.cv_peak_range_slider.sliderMoved.connect(self.cv_draw_marker_plot)
self.cv_peak_pos_1_combo.currentIndexChanged.connect(self.cv_draw_marker_plot)
self.cv_peak_pos_2_combo.currentIndexChanged.connect(self.cv_draw_marker_plot)
def cv_setup_plot(self):
self.cv_plot.setLabel('left', text='Current density')
self.cv_plot.setLabel('bottom', text='Voltage')
def create_cv_menu(self):
cv_addload_menu = QMenu(self)
cv_par_action = QAction('VersaSTAT(.par)', self)
cv_par_action.triggered.connect(lambda: self.cv_open_file('.par'))
cv_cor_action = QAction('CorrWare(.cor)', self)
cv_cor_action.triggered.connect(lambda: self.cv_open_file('.cor'))
cv_csv_action = QAction('Comma-separated values(.csv)', self)
cv_csv_action.triggered.connect(lambda: self.cv_open_file('.csv'))
cv_txt_action = QAction('Text(.txt)', self)
cv_txt_action.triggered.connect(lambda: self.cv_open_file('.txt'))
cv_biologic_action = QAction('Biologic(.txt)', self)
cv_biologic_action.triggered.connect(lambda: self.cv_open_file('.txt'))
cv_addload_menu.addAction(cv_par_action)
cv_addload_menu.addAction(cv_cor_action)
cv_addload_menu.addAction(cv_csv_action)
cv_addload_menu.addAction(cv_txt_action)
cv_addload_menu.addAction(cv_biologic_action)
return cv_addload_menu
def cv_open_file(self, cv_file_type):
print("def cv_open_file enter")
if cv_file_type == ".par":
cv_file_format = "VersaSTAT"
elif cv_file_type == ".cor":
cv_file_format = "CorrWare"
elif cv_file_type == ".csv":
cv_file_format = "CorrWare"
elif cv_file_type == ".txt": # TODO
if self.sender() == self.cv_txt_action:
cv_file_format = "text"
elif self.sender() == self.cv_biologic_action:
cv_file_format = "biologic"
file_dialog = QFileDialog()
file_dialog.setNameFilter(f'{cv_file_type} Files (*{cv_file_type})')
cv_file_path, _ = file_dialog.getOpenFileNames(self, "Open File", "", f'{cv_file_type} Files (*{cv_file_type})')
if cv_file_path == []:
pass
else:
for cv_file in cv_file_path:
self.cv_df,self.cv_param_df, self.cv_2nd_deriv_concat_df = read_cv_format(cv_file,cv_file_format)
self.cv_df_ir_currden = pd.concat([self.cv_df_ir_currden,self.cv_df],axis=1) #Simply a copy of cv_df but will be the CV that ir compensation and current density applied
self.cv_concat_list_df = pd.concat([self.cv_concat_list_df,self.cv_df],axis=1)
self.cv_param_concat_df = pd.concat([self.cv_param_concat_df,self.cv_param_df],axis=0)
self.cv_2nd_deriv_concat_list_df = pd.concat([self.cv_2nd_deriv_concat_list_df,self.cv_2nd_deriv_concat_df],axis=1)
self.cv_result_null = pd.DataFrame([['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-']],columns = ['file name', 'scan rate', 'Jp1', 'Jp2', 'Jp1/Jp2', 'Ep1', 'Ep2',"E\u00bd", "ΔE\u209a", "alpha1", "alpha2", "Jpc0"])
self.cv_result_display = pd.concat([self.cv_result_display,self.cv_result_null],axis=0,ignore_index=True)
self.cvchoosecombo.clear()
self.cvchoosecombo.addItems(self.cv_param_concat_df['file name'].astype(str).tolist()) #Update cv combo box
print(self.cv_concat_list_df)
if len(self.cv_concat_list_df.columns) == 0:
#Check if we have cv to work with
self.empty_cv = True
else:
self.empty_cv = False
self.cv_trim_slider.setDisabled(False)
self.cv_pos_trim_start_box.setDisabled(False)
self.cv_pos_trim_end_box.setDisabled(False)
self.cv_baseline_1_slider.setDisabled(False)
self.cv_pos_baseline_start_1_box.setDisabled(False)
self.cv_pos_baseline_end_1_box.setDisabled(False)
self.cv_baseline_2_slider.setDisabled(False)
self.cv_pos_baseline_start_2_box.setDisabled(False)
self.cv_pos_baseline_end_2_box.setDisabled(False)
self.cv_peak_range_slider.setDisabled(False)
self.cv_pos_search_range_box.setDisabled(False)
self.cv_peak_pos_1_slider.setDisabled(False)
self.cv_peak_pos_1_box.setDisabled(False)
self.cv_peak_pos_1_combo.setDisabled(False)
self.cv_peak_pos_2_slider.setDisabled(False)
self.cv_peak_pos_2_box.setDisabled(False)
self.cv_peak_pos_2_combo.setDisabled(False)
self.nicholson_checkbox.setDisabled(False)
self.cv_result_display.reset_index(drop=True, inplace=True)
self.cv_param_concat_df.reset_index(drop=True, inplace=True)
idx_file_name = 0
for file_name in self.cv_param_concat_df['file name']:
self.cv_result_display.loc[idx_file_name,'file name'] = file_name
idx_file_name += 1
self.cv_ircompen_box.setEnabled(True)
self.cv_elec_area_box.setEnabled(True)
self.cv_scan_rate_box.setEnabled(True)
self.cv_open_switch_cv()
self.cv_draw_all_cv()
print("def cv_open_file end")
def cv_open_switch_cv(self):
print("def cv_open_switch_cv enter")
#Activate this function when new CV is open or change
self.cv_chosen_name = self.cvchoosecombo.currentText()
self.cv_chosen_idx = int(self.cvchoosecombo.currentIndex())
self.cv_chosen_path = self.cv_param_concat_df.loc[self.cv_chosen_idx]['file path']
#Set initial CV volt and current
self.cv_chosen_volt = np.array(self.cv_df_ir_currden[str(self.cv_chosen_path)+' volt'])
self.cv_chosen_current = np.array(self.cv_df_ir_currden[str(self.cv_chosen_path)+' current'])
self.cv_chosen_data_point_num = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['number of data points'])
self.cv_set_slider_val() #Now set slider to correspond to the chosen file
#Set IR compensation, scan rate, and electrode area only when the user
#edit the value rather than copying from saved parameter
self.user_edit = False
self.cv_chosen_elec_area = float(self.cv_param_concat_df.loc[self.cv_chosen_idx]['elec_area'])
self.cv_elec_area_box.setText(str(self.cv_chosen_elec_area))
self.cv_chosen_ircompen = float(self.cv_param_concat_df.loc[self.cv_chosen_idx]['ir_compensation'])
self.cv_ircompen_box.setText(str(self.cv_chosen_ircompen))
self.cv_chosen_scan_rate = float(self.cv_param_concat_df.loc[self.cv_chosen_idx]['scan_rate'])
self.cv_scan_rate_box.setText(str(self.cv_chosen_scan_rate))
self.user_edit = True
# I want to fill in the values in the box and slider first before plotting
self.cv_draw_baseline_plot()
print("def cv_open_switch_cv end")
def cv_set_slider_val(self):
print("def cv_set_slider_val enter")
#When new files are loaded or switch in the combobox, set the value of the slider and boxes.
self.cv_chosen_defl = self.cv_2nd_deriv_concat_list_df[self.cv_chosen_path]
self.cv_trim_slider.setMaximum(self.cv_chosen_data_point_num)
self.trim_start = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['trim_start'])
self.trim_end = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['trim_end'])
self.cv_trim_slider.setValue((self.trim_start,self.trim_end))
self.cv_baseline_1_slider.setMaximum(self.cv_chosen_data_point_num-1)
self.cv_baseline_2_slider.setMaximum(self.cv_chosen_data_point_num-1)
self.cv_peak_pos_1_slider.setMaximum(self.cv_chosen_data_point_num-1)
self.cv_peak_pos_2_slider.setMaximum(self.cv_chosen_data_point_num-1)
self.cv_peak_range_slider.setMaximum(self.cv_chosen_data_point_num-1)
self.baseline_start_1 = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['baseline_start_1'])
self.baseline_end_1 = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['baseline_end_1'])
self.baseline_start_2 = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['baseline_start_2'])
self.baseline_end_2 = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['baseline_end_2'])
self.cv_baseline_1_slider.setValue((self.baseline_start_1,self.baseline_end_1))
self.cv_baseline_2_slider.setValue((self.baseline_start_2,self.baseline_end_2))
self.cv_peak_range = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['peak_range'])
self.cv_peak_range_slider.setValue(self.cv_peak_range)
self.cv_peak_pos_1_value = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['peak_pos_1'])
self.cv_peak_pos_1_slider.setValue(self.cv_peak_pos_1_value)
self.cv_peak_pos_2_value = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['peak_pos_2'])
self.cv_peak_pos_2_slider.setValue(self.cv_peak_pos_2_value)
print("def cv_set_slider_val end")
def cv_modify_cv_trim(self):
print("def cv_modify_cv_trim enter")
#Only calculate this value when user input them rather than programmatically from setText()
if self.user_edit == True:
print("def cv_modify_cv_trim user edited")
#Make sure the value is a number and not negative
try:
self.cv_chosen_ircompen = float(self.cv_ircompen_box.text())
if self.cv_chosen_ircompen < 0:
self.cv_chosen_ircompen = float(0)
except ValueError:
self.cv_chosen_ircompen = float(0)
self.cv_param_concat_df.loc[self.cv_chosen_idx,'ir_compensation'] = self.cv_chosen_ircompen
try:
self.cv_chosen_elec_area = float(self.cv_elec_area_box.text())
if self.cv_chosen_elec_area < 0:
self.cv_chosen_elec_area = float(1)
except ValueError:
self.cv_chosen_elec_area = float(1)
self.cv_param_concat_df.loc[self.cv_chosen_idx,'elec_area'] = self.cv_chosen_elec_area
try:
self.cv_chosen_scan_rate = float(self.cv_scan_rate_box.text())
if self.cv_chosen_scan_rate < 0:
self.cv_chosen_scan_rate = float(0)
except ValueError:
self.cv_chosen_scan_rate = float(0)
self.cv_param_concat_df.loc[self.cv_chosen_idx,'scan_rate'] = self.cv_chosen_scan_rate
#Calculate new CVs with given values
self.cv_df_ir_currden[self.cv_chosen_path+" volt"] = self.cv_concat_list_df[self.cv_chosen_path+" volt"]+(self.cv_concat_list_df[self.cv_chosen_path+str(" current")]*self.cv_chosen_ircompen)
self.cv_df_ir_currden[self.cv_chosen_path+" current"] = self.cv_concat_list_df[self.cv_chosen_path+" current"]/self.cv_chosen_elec_area
#Save the value
self.cv_param_concat_df.loc[self.cv_chosen_idx,'elec_area'] = self.cv_chosen_elec_area
self.cv_param_concat_df.loc[self.cv_chosen_idx,'ir_compensation'] = self.cv_chosen_ircompen
self.cv_param_concat_df.loc[self.cv_chosen_idx,'scan_rate'] = self.cv_chosen_scan_rate
self.cv_draw_all_cv()
print("def cv_modify_cv_trim end")
def cv_draw_all_cv(self):
print("def cv_draw_all_cv enter")
#Draw all CV with IR drop
# print(self.user_edit)
# print(self.cv_param_concat_df.to_string())
# if self.user_edit_box == True:
self.cv_param_concat_df.loc[self.cv_chosen_idx,'trim_start'] = self.cv_trim_slider.value()[0]
self.cv_param_concat_df.loc[self.cv_chosen_idx,'trim_end'] = self.cv_trim_slider.value()[1]
# self.user_edit_box = False
# Remove all plot when redraw
if self.cv_line_artist_list is not None:
for i in self.cv_line_artist_list:
self.cv_plot.removeItem(i)
self.cv_line_artist_list = []
cv_select_trim_start_val = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['trim_start'])
cv_select_trim_end_val = int(self.cv_param_concat_df.loc[self.cv_chosen_idx]['trim_end'])
for i in range(int(self.cv_param_concat_df.shape[0])):
cv_select_trim_start_val = self.cv_param_concat_df.loc[i]['trim_start']
cv_select_trim_end_val = self.cv_param_concat_df.loc[i]['trim_end']
self.cv_lines = self.cv_plot.plot(np.array(self.cv_df_ir_currden.iloc[:,i*2])[cv_select_trim_start_val:cv_select_trim_end_val],np.array(self.cv_df_ir_currden.iloc[:,(i*2)+1])[cv_select_trim_start_val:cv_select_trim_end_val], width=1.5, pen='white')
self.cv_line_artist_list.append(self.cv_lines)
max_volt = []
min_volt = []
max_current = []
min_current = []
for column in self.cv_df_ir_currden.columns:
if column.endswith('current'):
max_current.append(max(self.cv_df_ir_currden[column]))
min_current.append(min(self.cv_df_ir_currden[column]))
if column.endswith('volt'):
max_volt.append(max(self.cv_df_ir_currden[column]))
min_volt.append(min(self.cv_df_ir_currden[column]))
self.cv_plot.setRange(xRange=[min(min_volt), max(max_volt)])
self.cv_plot.setRange(yRange=[min(min_current), max(max_current)])
print("def cv_draw_all_cv end")
def cv_draw_baseline_plot(self):
print("def cv_draw_baseline_plot enter")
print(self.cv_chosen_volt[10:15])
self.cv_plot.removeItem(self.cv_plot_baseline_1)
self.cv_plot_baseline_1 = 0
self.cv_plot.removeItem(self.cv_plot_baseline_2)
self.cv_plot_baseline_2 = 1
self.baseline_start_1 = self.cv_baseline_1_slider.value()[0]
self.baseline_end_1 = self.cv_baseline_1_slider.value()[1]
self.baseline_start_2 = self.cv_baseline_2_slider.value()[0]
self.baseline_end_2 = self.cv_baseline_2_slider.value()[1]
volt = np.array(self.cv_df_ir_currden[str(self.cv_chosen_path)+' volt'])
current = np.array(self.cv_df_ir_currden[str(self.cv_chosen_path)+' current'])
self.cv_plot_baseline_1 = self.cv_plot.plot(volt[self.baseline_start_1:self.baseline_end_1],current[self.baseline_start_1:self.baseline_end_1],pen=pg.mkPen(color='red', width=4))
self.cv_plot_baseline_2 = self.cv_plot.plot(volt[self.baseline_start_2:self.baseline_end_2],current[self.baseline_start_2:self.baseline_end_2],pen=pg.mkPen(color='skyblue', width=4))
self.cv_draw_marker_plot()
print("def cv_draw_baseline_plot end")
def cv_draw_marker_plot(self):
print("def cv_draw_marker_plot enter")
if self.cv_df_ir_currden is not None:
self.cv_plot.removeItem(self.cv_plot_baseline_fit_1)
self.cv_plot_baseline_fit_1 = None
self.cv_plot.removeItem(self.cv_plot_baseline_fit_2)
self.cv_plot_baseline_fit_2 = None
self.cv_plot.removeItem(self.cv_plot_peak_1)
self.cv_plot_peak_1 = None
self.cv_plot.removeItem(self.cv_plot_peak_2)
self.cv_plot_peak_2 = None
self.cv_plot.removeItem(self.cv_plot_range_1)
self.cv_plot_range_1 = None
self.cv_plot.removeItem(self.cv_plot_range_2)
self.cv_plot_range_2 = None
self.cv_plot.removeItem(self.cv_plot_defl)
self.cv_plot_defl = None
self.cv_peak_range = self.cv_peak_range_slider.value()
self.cv_peak_pos_1_value = self.cv_peak_pos_1_slider.value()
self.cv_peak_pos_2_value = self.cv_peak_pos_2_slider.value()
# Instead of using instance variable, I think using the local variable for voltage and current variable
volt = np.array(self.cv_df_ir_currden[str(self.cv_chosen_path)+' volt'])
current = np.array(self.cv_df_ir_currden[str(self.cv_chosen_path)+' current'])
self.low_range_1, self.high_range_1, self.cv_peak_volt_1, self.cv_peak_curr_1, self.jp_1, self.jp_1_poly1d = get_peak_CV(self.cv_peak_pos_1_combo.currentText(), volt, current, self.cv_peak_range, self.cv_peak_pos_1_value, self.cv_baseline_1_slider.value(),self.cv_chosen_defl)
self.low_range_2, self.high_range_2, self.cv_peak_volt_2, self.cv_peak_curr_2, self.jp_2, self.jp_2_poly1d = get_peak_CV(self.cv_peak_pos_2_combo.currentText(), volt, current, self.cv_peak_range, self.cv_peak_pos_2_value, self.cv_baseline_2_slider.value(),self.cv_chosen_defl)
# Find alpha
ep12_jp_1, jp12_jp_1, alpha_jp_1 = find_alpha(volt, current,self.cv_baseline_1_slider.value(),self.cv_peak_pos_1_value,self.jp_1_poly1d,self.jp_1,self.cv_peak_volt_1)
ep12_jp_2, jp12_jp_2, alpha_jp_2 = find_alpha(volt, current,self.cv_baseline_2_slider.value(),self.cv_peak_pos_2_value,self.jp_2_poly1d,self.jp_2,self.cv_peak_volt_2)
if self.cv_peak_pos_1_combo.currentText() == "2nd derivative" or self.cv_peak_pos_2_combo.currentText() == "2nd derivative":
cv_chosen_defl_nonan = [int(x) for x in self.cv_chosen_defl.dropna().to_numpy()]
self.cv_plot_defl = self.cv_plot.plot(volt[cv_chosen_defl_nonan],current[cv_chosen_defl_nonan],pen=None,symbol="o", symbolSize=8)
# Flip baseline fitting depending on peak position
baseline_fit_1 = [volt[self.baseline_start_1],volt[self.baseline_end_1]]
baseline_fit_1.sort()
if self.cv_peak_volt_1 > baseline_fit_1[1]:
baseline_fit_1_x1 = baseline_fit_1[0]
baseline_fit_1_x2 = self.cv_peak_volt_1
elif self.cv_peak_volt_1 < baseline_fit_1[0]:
baseline_fit_1_x1 = baseline_fit_1[1]
baseline_fit_1_x2 = self.cv_peak_volt_1
elif self.cv_peak_volt_1 <= baseline_fit_1[1] and self.cv_peak_volt_1 >= baseline_fit_1[0]:
baseline_fit_1_x1 = baseline_fit_1[0]
baseline_fit_1_x2 = baseline_fit_1[1]
# print(baseline_fit_1_x1)
baseline_fit_1_y1 = self.jp_1_poly1d(baseline_fit_1_x1)
baseline_fit_1_y2 = self.jp_1_poly1d(baseline_fit_1_x2)
baseline_fit_2 = [volt[self.baseline_start_2],volt[self.baseline_end_2]]
baseline_fit_2.sort()
if self.cv_peak_volt_2 > baseline_fit_2[1]:
baseline_fit_2_x1 = baseline_fit_2[0]
baseline_fit_2_x2 = self.cv_peak_volt_2
elif self.cv_peak_volt_2 < baseline_fit_2[0]:
baseline_fit_2_x1 = baseline_fit_2[1]
baseline_fit_2_x2 = self.cv_peak_volt_2
elif self.cv_peak_volt_2 <= baseline_fit_2[1] and self.cv_peak_volt_2 >= baseline_fit_2[0]:
baseline_fit_2_x1 = baseline_fit_2[0]
baseline_fit_2_x2 = baseline_fit_2[1]
baseline_fit_2_y1 = self.jp_2_poly1d(baseline_fit_2_x1)
baseline_fit_2_y2 = self.jp_2_poly1d(baseline_fit_2_x2)
# Highlight selected data for baseline fitting
self.cv_plot_baseline_fit_1 = self.cv_plot.plot([baseline_fit_1_x1,baseline_fit_1_x2],[baseline_fit_1_y1,baseline_fit_1_y2],pen=pg.mkPen(color='white', width=1, style=QtCore.Qt.DashLine))
self.cv_plot_baseline_fit_2 = self.cv_plot.plot([baseline_fit_2_x1,baseline_fit_2_x2],[baseline_fit_2_y1,baseline_fit_2_y2],pen=pg.mkPen(color='white', width=1, style=QtCore.Qt.DashLine))
# Plot peak height
self.cv_plot_peak_1 = self.cv_plot.plot([self.cv_peak_volt_1,self.cv_peak_volt_1],[self.jp_1_poly1d(self.cv_peak_volt_1),self.cv_peak_curr_1],pen=pg.mkPen(color='white', width=1, style=QtCore.Qt.DashLine))
self.cv_plot_peak_2 = self.cv_plot.plot([self.cv_peak_volt_2,self.cv_peak_volt_2],[self.jp_2_poly1d(self.cv_peak_volt_2),self.cv_peak_curr_2],pen=pg.mkPen(color='white', width=1, style=QtCore.Qt.DashLine))
self.cv_plot_range_1 = self.cv_plot.plot([volt[int(self.low_range_1)],volt[int(self.high_range_1)]],[current[int(self.low_range_1)],current[int(self.high_range_1)]],pen=None,symbol="|")
self.cv_plot_range_2 = self.cv_plot.plot([volt[int(self.low_range_2)],volt[int(self.high_range_2)]],[current[int(self.low_range_2)],current[int(self.high_range_2)]],pen=None,symbol="|")
# Plot range that search for peak
# Can be more efficient?????
self.cv_save_param()
print("def cv_draw_marker_plot end")
def cv_save_param(self):
print("def cv_save_param enter")
# Write the changed parameters in cv_param_concat_df
self.cv_param_concat_df.loc[self.cv_chosen_idx,'trim_start'] = self.trim_start
self.cv_param_concat_df.loc[self.cv_chosen_idx,'trim_end'] = self.trim_end
self.cv_param_concat_df.loc[self.cv_chosen_idx,'baseline_start_1'] = self.baseline_start_1
self.cv_param_concat_df.loc[self.cv_chosen_idx,'baseline_end_1'] = self.baseline_end_1
self.cv_param_concat_df.loc[self.cv_chosen_idx,'baseline_start_2'] = self.baseline_start_2
self.cv_param_concat_df.loc[self.cv_chosen_idx,'baseline_end_2'] = self.baseline_end_2
self.cv_param_concat_df.loc[self.cv_chosen_idx,'peak_range'] = self.cv_peak_range
self.cv_param_concat_df.loc[self.cv_chosen_idx,'peak_pos_1'] = self.cv_peak_pos_1_value
self.cv_param_concat_df.loc[self.cv_chosen_idx,'peak_pos_2'] = self.cv_peak_pos_2_value
self.cv_param_concat_df.loc[self.cv_chosen_idx,'elec_area'] = self.cv_chosen_elec_area
self.cv_param_concat_df.loc[self.cv_chosen_idx,'ir_compensation'] = self.cv_chosen_ircompen
self.cv_param_concat_df.loc[self.cv_chosen_idx,'scan_rate'] = self.cv_chosen_scan_rate
#Display result
self.cv_result_display.loc[self.cv_chosen_idx,'file name'] = self.cv_param_concat_df.loc[self.cv_chosen_idx,'file name']
self.cv_result_display.loc[self.cv_chosen_idx,'scan rate'] = self.cv_param_concat_df.loc[self.cv_chosen_idx,'scan_rate']
self.cv_result_display.loc[self.cv_chosen_idx,'Jp1'] = abs(self.jp_1)
self.cv_result_display.loc[self.cv_chosen_idx,'Jp2'] = abs(self.jp_2)
self.cv_result_display.loc[self.cv_chosen_idx,'Jp1/Jp2'] = abs(self.jp_1)/abs(self.jp_2)
self.cv_result_display.loc[self.cv_chosen_idx,'Ep1'] = self.cv_peak_volt_1
self.cv_result_display.loc[self.cv_chosen_idx,'Ep2'] = self.cv_peak_volt_2
self.cv_result_display.loc[self.cv_chosen_idx,'E\u00bd'] = (self.cv_peak_volt_1+self.cv_peak_volt_2)/2
self.cv_result_display.loc[self.cv_chosen_idx,'ΔE\u209a'] = abs(self.cv_peak_volt_1-self.cv_peak_volt_2)
self.cv_result_table.setModel(TableModel(self.cv_result_display))
print("def cv_save_param end")
# print(self.cv_param_concat_df.to_string())
# def save_result(self):
# # Write the calculated result
# # print(self.cv_chosen_idx)
# jp1 = self.jp_1_poly1d(self.cv_peak_volt_1)-self.cv_peak_curr_1
# jp2 = self.jp_2_poly1d(self.cv_peak_volt_2)-self.cv_peak_curr_2
# # print("jp1",jp1)
# # print("jp2",abs(self.jp_2_poly1d(self.cv_peak_volt_2)-self.cv_peak_curr_2))
# # print(self.cv_result_display)
# self.cv_result_table.setModel(TableModel(self.cv_result_display))
# self.low_range_1, self.high_range_1
# class helloDialog(QDialog):
# def __init__(self, parent):
# super().__init__(parent)
# self.setWindowTitle("hello")
# self.setGeometry(200, 200, 300, 150)
# layout = QVBoxLayout()
# label = QLabel("Say Hello", self)
# layout.addWidget(label)
# self.setLayout(layout)
class TableModel(QtCore.QAbstractTableModel):
# https://www.pythonguis.com/tutorials/qtableview-modelviews-numpy-pandas/
def __init__(self, data):
super(TableModel, self).__init__()
self._data = data
def data(self, index, role):
if role == Qt.DisplayRole:
value = self._data.iloc[index.row(), index.column()]
if isinstance(value, float):
return f"{value:.5f}"
return str(value)
def rowCount(self, index):
return self._data.shape[0]
def columnCount(self, index):
return self._data.shape[1]
def headerData(self, section, orientation, role):
# section is the index of the column/row.
if role == Qt.DisplayRole:
if orientation == Qt.Horizontal:
return str(self._data.columns[section])
if orientation == Qt.Vertical:
return str(self._data.index[section])
if __name__ == '__main__':
app = QApplication(sys.argv)
mainWin = PySimpleEChem_main()
mainWin.show()
sys.exit(app.exec_())