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MainGui.py
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MainGui.py
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# -*- coding: utf-8 -*-
"""
Created on Fri Jun 25 22:03:01 2021
@author: yonghui
"""
import tkinter as tk
from tkinter import ttk
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.figure import Figure
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
# from matplotlib.backends.figure import Figure
# from t2nnls import T2NNLS
from fitTikhonovReg import T2NNLS
from rotateT2phase import rotate_T2phase
import LoadNMRData_rca
import pltRawData_rca
import pltLcurve
from getLambdaFromRMSE import get_lambda_from_Lcurve
import pltRTD
class ControlFrame(tk.Frame):
def __init__(self, parent=None):
self.parent = parent
tk.Frame.__init__(self,self.parent)
self.container = tk.Frame(self.parent)
self.container.pack(side="top", fill="both", expand=True)
self.frames = {}
self.fr_open_file = OpenFilePanel(self.container, self)
self.fr_invert_setting = InversionSettingPanel(self.container, self)
self.fr_logs_print_out = LogsPrintOut(self.container, self)
self.fr_view = CanvasView(self.container, self)
# make class instance(or the controller)
self.frames[OpenFilePanel.__name__] = self.fr_open_file
self.frames[InversionSettingPanel.__name__] = self.fr_invert_setting
self.frames[CanvasView.__name__] = self.fr_view
self.frames[LogsPrintOut.__name__] = self.fr_logs_print_out
self.fr_open_file.grid(row=0, column=0, pady=5, sticky="nsew")
self.fr_invert_setting.grid(row=1, column=0, sticky="nsew")
self.fr_logs_print_out.grid(row=2, column=0, rowspan=2, pady=5,sticky="nsew")
self.fr_view.grid(row=0, column=1, rowspan=4, columnspan=2, pady=5, sticky='nsew')
self.container.columnconfigure(0, weight=1)
self.container.columnconfigure((1,2), weight=2)
#self.container.rowconfigure((0,1), weight=1)
self.container.rowconfigure(2, weight=2)
self.fr_open_file.open_csv_button['command'] = lambda:[self.open_csv_file(),
self.plot_raw_RCA()]
self.fr_invert_setting.start_button['command'] = lambda:[self.start_inversion(),
self.clear_canvas(),
self.plot_fitted_raw_RCA(),
self.plot_reg_curve(),
self.plot_T2()]
self.fr_invert_setting.reset_button['command'] = lambda:[self.set_default_lambda_T2_par(),
self.clear_canvas()]
self.invT2NNLS = InversionT2NNLS()
self.openCSVFile = OpenCSVFile()
# show default settings in each entry
self.set_default_lambda_T2_par()
self.array_raw_data = None
self.dir_csv_file = None
def open_csv_file(self):
self.openCSVFile.open_csv_file()
self.dir_csv_file = self.openCSVFile.get_dir_csv_file()
self.fr_open_file.open_csv_entry.insert(0, self.dir_csv_file)
self.array_raw_data = self.openCSVFile.get_array_raw_data()
# plot raw RCA data
def plot_raw_RCA(self):
self.fr_view.ax_raw.clear()
pltRawData_rca.plt_raw_rca(self.array_raw_data, self.fr_view.ax_raw)
self.fr_view.canvas_raw.draw()
# start inversion using the input-settings
def start_inversion(self):
if self.array_raw_data is None:
tk.messagebox.showerror(message = "No RCA data was imported")
else:
self.set_manu_lambda_T2_par()
self.invT2NNLS.initial_inversion(self.array_raw_data)
self.invT2NNLS.get_optimize_lambda()
# plot the fitted raw RCA data
def plot_fitted_raw_RCA(self):
self.fr_view.ax_raw.clear()
pltRawData_rca.plt_raw_rca(self.array_raw_data, self.fr_view.ax_raw)
pltRawData_rca.plt_fitted_rca(self.invT2NNLS.optimize_dsyn, self.array_raw_data, self.fr_view.ax_raw)
self.fr_view.canvas_raw.draw()
# plot lambda vs residual norm
def plot_reg_curve(self):
pltLcurve.plt_lambda_rmse(self.invT2NNLS.coef_lambda, self.invT2NNLS.rmse,
self.invT2NNLS.optimize_index, self.fr_view.ax_reg)
self.fr_view.canvas_reg.draw()
# plot residual norm vs model norm
pltLcurve.plt_rmse_model_norm(self.invT2NNLS.rmse, self.invT2NNLS.model_norm,
self.invT2NNLS.optimize_index, self.fr_view.ax_model)
self.fr_view.canvas_model.draw()
# plot the T2-distribution
"""pltT2dist(T2, m, ax)"""
def plot_T2(self):
pltRTD.pltT2dist(self.invT2NNLS.T2, self.invT2NNLS.optimize_m, self.fr_view.ax_T2)
self.fr_view.canvas_T2.draw()
# default value assigned to each entry
# lambda_vars = [1, 10000, 20]
# time_vars = [-4, 1, 160]
def set_default_lambda_T2_par(self):
for i in range(3):
self.fr_invert_setting.lambda_vars[i].set([1, 10000, 20][i])
self.fr_invert_setting.time_vars[i].set([-4, 1, 160][i])
# set inversion parameters with values got from the input of each entry
def set_manu_lambda_T2_par(self):
for i in range(3):
self.invT2NNLS.lambda_vars[i] = self.fr_invert_setting.lambda_vars[i].get()
self.invT2NNLS.time_vars[i] = self.fr_invert_setting.time_vars[i].get()
def clear_canvas(self):
# self.fr_view.ax_raw.clear()
# self.fr_view.canvas_raw.draw()
self.fr_view.ax_reg.clear()
# self.fr_view.canvas_reg.draw()
self.fr_view.ax_model.clear()
# self.fr_view.canvas_model.draw()
self.fr_view.ax_T2.clear()
# self.fr_view.canvas_T2.draw()
class OpenFilePanel(tk.Frame):
""" Open the NMR data file
"""
def __init__(self, parent, controller):
self.parent = parent
tk.LabelFrame.__init__(self, self.parent, text = "Open", borderwidth=2, relief="ridge")
self.controller = controller
self.browse_label = tk.Label(self, text = "Select file to open:")
self.open_csv_button = tk.Button(self, text="Load RCA data", relief= "raised", bg='lightgray')
# self.open_csv_button.bind("<Button>", self.open_plot_csv_file)
self.open_csv_entry = tk.Entry(self)
self.browse_label.grid(row=0, column=1, padx=5, pady=10, sticky='ew')
self.open_csv_button.grid(row=1, column=0, padx=5, sticky='ew')
self.open_csv_entry.grid(row=1, column=1, columnspan=3, padx=5, sticky='ew')
self.columnconfigure(1, weight=2)
self.columnconfigure(0, weight=1)
class OpenCSVFile():
def __init__(self):
self.dir_csv_file = None
self.array_raw_data = None
def open_csv_file(self):
self.dir_csv_file = tk.filedialog.askopenfilename(initialdir = "/D:",
title = "Open RCA file",
filetypes = (("csv files","*.csv"),("all files","*.*")))
# browse the csv file
if self.dir_csv_file.rsplit(".")[-1] !="csv":
return
self.array_raw_data = LoadNMRData_rca.read_csv(self.dir_csv_file)
def get_array_raw_data(self):
return self.array_raw_data
def get_dir_csv_file(self):
return self.dir_csv_file
class InversionT2NNLS():
def __init__(self):
# initial inversion parameters
self.data = None
self.time = None
self.noise = None
# predefined lambda values - min|max|length
self.lambda_vars = [1, 10000, 20]
self.coef_lambda = np.geomspace(self.lambda_vars[0],self.lambda_vars[1], self.lambda_vars[2])
# predefined T2 values - min|max\length
self.time_vars = [-4, 1, 160]
self.T2 = np.logspace(self.time_vars[0], self.time_vars[1], num = self.time_vars[2]).transpose()
# the size to clip the data in T2NNLS
self.winsize = 100
self.rmse = [0 for _ in range(self.lambda_vars[2])]
self.model_norm = [0 for _ in range(self.lambda_vars[2])]
self.optimize_index = None
self.optimize_rmse = None
self.optimize_model_norm = None
self.m = [0 for _ in range(self.lambda_vars[2])]
self.r = [0 for _ in range(self.lambda_vars[2])]
self.dsyn = [0 for _ in range(self.lambda_vars[2])]
self.optimize_m = []
self.optimize_dsyn = []
self.optimize_r = [0,0]
def initial_inversion(self, array_raw_data):
if array_raw_data is not None:
self.data, self.time, self.noise = rotate_T2phase(array_raw_data)
else:
tk.messagebox.showerror(message = " 'failure during reading RCA' \n data is none or data is not a numpy array")
for i in range(self.lambda_vars[2]):
(self.m[i], self.r[i], self.dsyn[i]) = T2NNLS(self.data, self.time, self.noise, self.T2, self.coef_lambda[i], self.winsize)
self.rmse[i] = self.r[i][0]
self.model_norm[i] = self.r[i][1]
self.optimize_index = get_lambda_from_Lcurve(self.coef_lambda, self.rmse)
def get_optimize_lambda(self):
self.optimize_rmse = self.r[self.optimize_index][0]
self.optimize_model_norm = self.r[self.optimize_index][1]
self.optimize_m = self.m[self.optimize_index]
self.optimize_r = self.r[self.optimize_index]
self.optimize_dsyn = self.dsyn[self.optimize_index]
# def optimize_inversion(self, array_raw_data):
# (self.optimize_m, self.optimize_r, self.optimize_dsyn, rnorm) = T2NNLS(self.data, self.time, self.noise,
# self.T2, self.coef_lambda[self.optimize_index], 100)
# self.optimize_rmse = self.optimize_r[0]
# self.optimize_model_norm = self.optimize_r[1]
class InversionSettingPanel(tk.Frame):
def __init__(self, parent, controller):
self.parent = parent
tk.LabelFrame.__init__(self, self.parent,text = "Inversion Settings", borderwidth=2, relief="ridge")
self.controller = controller
self.reg_label = tk.Label(self, text = "Regularization")
self.reg_combox = ttk.Combobox(self, values = ["L2", "L1","None"])
self.reg_combox.current(0)
self.reset_button = tk.Button(self, text="Reset Settings",relief= "raised")
self.lambda_label = tk.Label(self, text = "Lambda min|max|#")
self.lambda_vars = []
self.lambda_entries = []
for i in range(3):
var = tk.IntVar()
self.lambda_vars.append(var)
entry = tk.Entry(self, bg='white', textvariable=self.lambda_vars[i], justify=tk.CENTER)
self.lambda_entries.append(entry)
self.time_label = tk.Label(self, text = "Time-T2 min|max|#")
self.time_vars = []
self.time_entries = []
for i in range(3):
var = tk.IntVar()
self.time_vars.append(var)
entry = tk.Entry(self, bg='white',textvariable=self.time_vars[i], justify=tk.CENTER)
self.time_entries.append(entry)
# start inversion button
self.start_button = tk.Button(self, text="Start Inversion",relief= "raised", bg='lightgray')
self.grid(row=0, column=0, sticky='nsew')
self.reg_label.grid(row=0, column=0,pady=10, sticky='nsew')
self.reg_combox.grid(row=0, column=1,pady=10,sticky='ns')
self.reset_button.grid(row=0, column=2, columnspan=2, pady=10, sticky='ns')
self.lambda_label.grid(row=1, column=0,sticky='nsew')
self.lambda_entries[0].grid(row=1, column=1,sticky='nsew')
self.lambda_entries[1].grid(row=1, column=2,sticky='nsew')
self.lambda_entries[2].grid(row=1, column=3,sticky='nsew')
self.time_label.grid(row=2, column=0, pady=10,sticky='nsew')
self.time_entries[0].grid(row=2, column=1,pady=10,sticky='nsew')
self.time_entries[1].grid(row=2, column=2,pady=10,sticky='nsew')
self.time_entries[2].grid(row=2, column=3,pady=10,sticky='nsew')
self.start_button.grid(row=3, column=0, columnspan = 4, sticky='nsew')
self.columnconfigure((0), weight=1)
class LogsPrintOut(tk.Frame):
def __init__(self, parent, controller):
self.parent = parent
tk.Frame.__init__(self, self.parent, borderwidth=2, relief="ridge")
self.controller = controller
self.logs_label = tk.Label(self,bg='white')
self.logs_label.grid(row=0, column=0, sticky='nsew')
self.columnconfigure(0, weight=1)
self.rowconfigure(0, weight=1)
class CanvasView(tk.Frame):
def __init__(self, parent, controller):
self.parent = parent
tk.Frame.__init__(self, self.parent, borderwidth=2, relief="ridge")
self.controller = controller
self.fr_raw_notebooks = ttk.Notebook(self)
self.fr_raw_data = ttk.Frame(self.fr_raw_notebooks)
self.fr_T2 = ttk.Frame(self.fr_raw_notebooks)
self.fr_raw_notebooks.add(self.fr_raw_data, text = "Raw data")
self.fr_raw_notebooks.add(self.fr_T2, text = "T2 dist")
self.fr_raw_notebooks.grid(row=0, column=0, columnspan=2, pady=5, sticky="nsew")
self.fr_reg_notebooks = ttk.Notebook(self)
self.fr_reg_curve = ttk.Frame(self.fr_reg_notebooks)
self.fr_reg_notebooks.add(self.fr_reg_curve, text="L-curve")
self.fr_reg_notebooks.grid(row=1, column=0, sticky="nsew")
self.rowconfigure((0,1), weight=1)
self.columnconfigure(0, weight=2)
# plot raw data on top
self.fig_raw = Figure(figsize=(8,3), dpi=100)
self.ax_raw = self.fig_raw.add_subplot(111)
self.canvas_raw = FigureCanvasTkAgg(self.fig_raw, self.fr_raw_data)
# self.canvas_raw.get_tk_widget().grid(row=0, column=0,rowspan=2, sticky='nsew')
self.canvas_raw.get_tk_widget().pack(side="top", fill="both", expand=True)
self.canvas_raw.draw()
# plot T2 on top
self.fig_T2 = Figure(figsize=(8,3), dpi=100)
self.ax_T2 = self.fig_T2.add_subplot(111)
self.canvas_T2 = FigureCanvasTkAgg(self.fig_T2, self.fr_T2)
# self.canvas_T2.get_tk_widget().grid(row=0, column=0,rowspan=2, sticky='nsew')
self.canvas_T2.get_tk_widget().pack(side="top", fill="both", expand=True)
self.canvas_T2.draw()
# plot on lambda vs residual norm on bottom-left
self.fig_reg = Figure(figsize=(4,3),dpi=100)
self.ax_reg = self.fig_reg.add_subplot(111)
self.canvas_reg = FigureCanvasTkAgg(self.fig_reg, self.fr_reg_curve)
# self.canvas_reg.get_tk_widget().grid(row=0, column=0, sticky='nsew')
self.canvas_reg.get_tk_widget().pack(side="left", fill="both", expand=True)
self.canvas_reg.draw()
# plot residual norm vs model norm on bottom-right
self.fig_model = Figure(figsize=(4,3),dpi=100)
self.ax_model = self.fig_model.add_subplot(111)
self.canvas_model = FigureCanvasTkAgg(self.fig_model, self.fr_reg_curve)
# self.canvas_model.get_tk_widget().grid(row=0, column=1, sticky='nsew')
self.canvas_model.get_tk_widget().pack(side="left", fill="both", expand=True)
self.canvas_model.draw()
class MainApplication(tk.Tk):
def __init__(self):
tk.Tk.__init__(self)
# put the window in the middle of the screen/monitor
screenWidth = self.winfo_screenwidth()
screenHeight = self.winfo_screenheight()
w = 800
h = 300
x = (screenWidth - w) / 4 # x_position from the top-left corner
y = (screenHeight - h) / 4 # y_distance from the top-left corner
self.geometry("%dx%d+%d+%d" % (w,h,x,y))
# self.geometry("400x300")
self.title("pyNMR-T2 inverstion") # title on the top left
if __name__=="__main__":
app = MainApplication()
ControlFrame(app)
app.mainloop()