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Gcsv.py
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Gcsv.py
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import os
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
from matplotlib.backends.backend_tkagg import (FigureCanvasTkAgg, NavigationToolbar2Tk)
import matplotlib.patches as patches
from scipy import integrate
from scipy.signal import find_peaks
import csv
import potterIntegrate as pint
import tkinter as tk
from tkinter.filedialog import askopenfilename
from tkinter import messagebox
class App(object):#swapped out object, tk.Frame
def __init__(self, master):
self.rt = master
self.rt.protocol("WM_DELETE_WINDOW", self.onClosing)
self.menu = tk.Menu(self.rt)
self.rt.title('NMR GUI - Potter')
self.rt.config(menu = self.menu)
self.filemenu = tk.Menu(self.menu)
self.menu.add_cascade(label = 'File', menu = self.filemenu)
self.Master = master
self.filemenu.add_command(label = 'New')
self.filemenu.add_command(label = 'Open', command = self.openFile)
self.filemenu.add_separator()
self.filemenu.add_command(label = 'Exit', command = lambda:[root.quit(), root.destroy()])
self.helpmenu = tk.Menu(self.menu)
self.menu.add_cascade(label = 'Help', menu = self.helpmenu)
self.helpmenu.add_command(label = 'About', command = self.launchHelpWindow)
self.analysismenu = tk.Menu(self.menu)
self.menu.add_cascade(label = 'Analysis', menu = self.analysismenu)
self.analysismenu.add_command(label = 'Integrate', command = self.openIntegrationModule)
self.analysismenu.add_command(label = 'EditIntegralList', command = self.showIntegralList)
self.analysismenu.add_command(label = 'Calibrate', command = self.calibrate)
self.xShift = 0.0
self.showIntVar1 = tk.IntVar()
self.calOn = 0
self.intVar1 = tk.IntVar()
self.showPeakVar1 = tk.IntVar()
self.calVar1 = tk.IntVar()
self.startCoords = []
self.endCoords = []
self.integrals = []
self.intListVar = []
self.intGraphics1 = []
self.intGraphics2 = []
self.peakList = []
self.peakGraphics1 = []
self.intCheckBoxes = []
self.intDeleteButtons = []
self.rt.mainloop()
def openFile(self):
self.filename = askopenfilename(parent = self.rt)
with open(self.filename, mode = 'r') as file:
self.data = pd.read_csv(file, names = ['x', 'y'])
self.th = 0.0
self.t1Top = tk.Frame(self.rt)
self.t1Bottom = tk.Frame(self.rt)
self.t1Top.pack(side = tk.TOP)
self.t1Bottom.pack(side = tk.BOTTOM)
self.t1Left = tk.Frame(self.t1Top)
self.t1Right = tk.Frame(self.t1Top)
self.t1Left.pack(side = tk.LEFT)
self.t1Right.pack(side = tk.RIGHT)
self.fig = plt.figure()
self.ax = self.fig.add_subplot(111)
self.ax.set_xlim(self.data['x'].max(), self.data['x'].min())
self.ax.plot(self.data['x'], self.data['y'])
self.canvas = FigureCanvasTkAgg(self.fig, master = self.rt)
self.canvas.draw()
#self.canvas.get_tk_widget().pack(in_ = self.t1Right, fill = tk.BOTH, expand = 1)
self.canvas.get_tk_widget().pack(in_ = self.t1Right, fill = tk.BOTH, expand = True)
self.toolbar = NavigationToolbar2Tk(self.canvas, self.rt)
self.toolbar.update()
#self.canvas.get_tk_widget().pack(in_ = self.t1Right, fill = tk.BOTH, expand = 1)
self.canvas.get_tk_widget().pack(in_ = self.t1Right, fill = tk.BOTH, expand = True)
self.xShiftScale = tk.Scale(self.rt, from_ = self.data['y'].max(), to_ = self.data['y'].min())
self.xShiftScale.pack(in_ = self.t1Left)
self.showIntToggle = tk.Checkbutton(self.rt, text = 'Show Integrals', variable = self.showIntVar1, command = self.showIntegrals)
self.showIntToggle.pack(in_ = self.t1Bottom, side = tk.RIGHT)
self.showPeaksToggle = tk.Checkbutton(self.rt, text = 'Show Peaks', variable = self.showPeakVar1, command = self.showPeaks)
self.showPeaksToggle.pack(in_ = self.t1Bottom, side = tk.RIGHT)
def openIntegrationModule(self):
self.t = tk.Toplevel(self.rt)
self.t.protocol("WM_DELETE_WINDOW", self.onIntClosing)
self.t.wm_title("Integration Module")
self.intFig = plt.figure()
self.intAx = self.intFig.add_subplot(111)
self.intAx.set_xlim(self.data['x'].max(), self.data['x'].min())
self.intAx.plot(self.data['x'], self.data['y'])
self.canvas2 = FigureCanvasTkAgg(self.intFig, master = self.t)
self.canvas2.draw()
self.canvas2.get_tk_widget().pack(side = tk.TOP, fill = tk.BOTH, expand = 1)
self.toolbar2 = NavigationToolbar2Tk(self.canvas2, self.t)
self.toolbar2.update()
self.canvas2.get_tk_widget().pack(side = tk.TOP, fill = tk.BOTH, expand = 1)
self.intToggle = tk.Checkbutton(self.t, text="Integration Mode", variable=self.intVar1, command = self.integrate)
self.intToggle.pack(side = tk.LEFT)
def onclick(self, event):
ix = event.xdata
self.startCoords.append(ix)
def onrelease(self, event):
ix = event.xdata
self.endCoords.append(ix)
pint.drawTraps(self.data, min([self.startCoords[-1], self.endCoords[-1]]), max([self.startCoords[-1], self.endCoords[-1]]), self.intAx)
self.canvas2.draw()
def integrate(self):
if self.intVar1.get() == 1:
self.cid1 = self.canvas2.mpl_connect('button_press_event', self.onclick)
self.cid2 = self.canvas2.mpl_connect('button_release_event', self.onrelease)
else:
self.canvas2.mpl_disconnect(self.cid1)
self.canvas2.mpl_disconnect(self.cid2)
def onClosing(self):
if messagebox.askokcancel("Quit", "Do you want to quit?"):
self.rt.quit()
self.rt.destroy()
def onIntClosing(self):
if messagebox.askokcancel("Quit", "Save integrals?"):
tempInts = []
for i in range(len(self.startCoords)):
tempInts.append(min([self.startCoords[i], self.endCoords[i]]))
tempInts.append(max([self.startCoords[i], self.endCoords[i]]))
tempInts.append(pint.trapInt(self.data, tempInts[0], tempInts[1]))
tempInts.append(1)
self.integrals.append(tempInts.copy())
tempInts.clear()
self.startCoords.clear()
self.endCoords.clear()
self.t.destroy()
def showIntegrals(self):
if self.showIntVar1.get() == 1:
for i in range(len(self.integrals)): #this is the region marker
if (self.integrals[i][3] == 1 and not self.intListVar) or (self.integrals[i][3] == 1 and self.intListVar[i].get() == 1):
self.intGraphics1.append(self.ax.annotate('', xy = (self.integrals[i][0], 0), xytext = (self.integrals[i][1], 0), arrowprops = dict(arrowstyle = '<->', facecolor = 'red'),
annotation_clip = False))
for i in range(len(self.integrals)): #this is the line connecting the integral value
if (self.integrals[i][3] == 1 and not self.intListVar) or (self.integrals[i][3] == 1 and self.intListVar[i].get() == 1):
self.intGraphics2.append(self.ax.annotate('{:.2f}'.format(self.integrals[i][2]), xy = (self.integrals[i][0] + ((self.integrals[i][1] - self.integrals[i][0])/2), 0), xytext = (self.integrals[i][0] + ((self.integrals[i][1] - self.integrals[i][0])/2), -3), arrowprops = dict(arrowstyle = '-', facecolor = 'red'),
annotation_clip = False))
self.canvas.draw()
else:
for i in self.intGraphics1:
i.remove()
for i in self.intGraphics2:
i.remove()
self.intGraphics1.clear()
self.intGraphics2.clear()
self.canvas.draw()
def showIntegralList(self):
self.t2 = tk.Toplevel(self.rt)
self.t2.protocol("WM_DELETE_WINDOW", self.onCloseIntegralListWindow)
self.t2.wm_title("Integrals")
self.t2Top = tk.Frame(self.t2)
self.t2Bottom = tk.Frame(self.t2)
self.t2Top.pack(side=tk.TOP)
self.t2Bottom.pack(side = tk.BOTTOM)
self.t2Left = tk.Frame(self.t2Bottom)
self.t2Right = tk.Frame(self.t2Bottom)
self.t2Left.pack(side = tk.LEFT)
self.t2Right.pack(side = tk.RIGHT)
for i in range(len(self.integrals)):
self.intListVar.append(tk.IntVar(value = 1))
self.intCheckBoxes.append(tk.Checkbutton(self.t2Left, text = str(len(self.integrals)-i) + '\t' + '{:.2f}'.format(self.integrals[i][0]) +
'\t' + '{:.2f}'.format(self.integrals[i][1]) + '\t' + '{:.2f}'.format(self.integrals[i][2]),
variable = self.intListVar[i], width = 40))
self.intDeleteButtons.append(tk.Button(self.t2Right, text = 'Delete: ' + str((len(self.integrals)-i)),
command = lambda c=i:self.deleteInt(self.integrals, c))) # why not lambda:self.integrals[len(self.integrals)-i-1] ????
self.intCheckBoxes[i].pack(in_ = self.t2Left, side = tk.BOTTOM, fill = tk.X)
self.intDeleteButtons[i].pack(in_ = self.t2Right, side = tk.BOTTOM)
def deleteInt(self, ar, inx):
del self.integrals[int(inx)]
def onCloseIntegralListWindow(self):
self.intCheckBoxes.clear()
self.intDeleteButtons.clear()
self.canvas.draw()
self.t2Left.destroy()
self.t2Right.destroy()
self.t2Bottom.destroy()
self.t2Top.destroy()
self.t2.destroy()
def showPeaks(self): # removed parameter th
self.th = self.xShiftScale.get()
self.peakList = find_peaks(self.data['y'].to_numpy(), self.th)
if self.showPeakVar1.get() == 1:
a = 0
for i in range(len(self.peakList[0])):
if ((self.data.iloc[self.peakList[0][i-1]][1] < self.data.iloc[self.peakList[0][i]][1]) and
((self.data.iloc[self.peakList[0][i-1]][1]) >= (self.data.iloc[self.peakList[0][i]][1] - 0.1)) or
((self.data.iloc[self.peakList[0][i-1]][1] > (self.data.iloc[self.peakList[0][i]][1])) and
((self.data.iloc[self.peakList[0][i-1]][1]) <= (self.data.iloc[self.peakList[0][i]][1] + 0.1)))):
a = a + 1
else:
a = a + 0
self.peakGraphics1.append(self.ax.annotate('{:.2f}'.format(self.data.iloc[self.peakList[0][i]][0]), xy = (self.data.iloc[self.peakList[0][i]][0], self.data.iloc[self.peakList[0][i]][1]), xytext = (self.data.iloc[self.peakList[0][i]][0], self.data.iloc[self.peakList[0][i]][1] + a)))
self.canvas.draw()
else:
for i in self.peakGraphics1:
i.remove()
self.peakGraphics1.clear()
self.canvas.draw()
def onclick2(self, event):
ix = event.xdata
self.xShift = ix
self.data['x'] = self.data['x'] - self.xShift
self.shiftIntegrals(self.integrals, self.xShift)
self.calOn = 0
self.canvas.mpl_disconnect(self.cid3)
self.rt.config(cursor='')
def shiftIntegrals(self, iL, sh):
msgBox = tk.messagebox.askquestion('Shift Integrals', 'Shift integrals along with spectrum?', icon = 'warning')
if msgBox == 'yes':
self.integralShift(iL, sh)
self.ax.cla()
self.ax.set_xlim(self.data['x'].max(), self.data['x'].min())
self.ax.plot(self.data['x'], self.data['y'])
self.canvas.draw()
else:
self.ax.cla()
self.ax.set_xlim(self.data['x'].max(), self.data['x'].min())
self.ax.plot(self.data['x'], self.data['y'])
self.canvas.draw()
def integralShift(self, ints, xsh):
for i in range(len(self.integrals)):
self.integrals[i][0] = self.integrals[i][0] - xsh
self.integrals[i][1] = self.integrals[i][1] - xsh
def calibrate(self):
self.rt.config(cursor = 'cross')
self.calOn = 1
self.cid3 = self.canvas.mpl_connect('button_press_event', self.onclick2)
def onHelpClosing(self):
self.t3.destroy()
def launchHelpWindow(self):
self.t3 = tk.Toplevel(self.rt)
self.t3.protocol("WM_DELETE_HELPWINDOW", self.onHelpClosing)
self.helpText = tk.Text(self.t3, height = 10, width = 30, wrap = 'word')
self.helpText.pack(expand=True, fill = tk.BOTH)
__location__ = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__)))
aboutFile = open(os.path.join(__location__, 'about.rtf'))
self.helpText.insert(tk.END, aboutFile.read())
aboutFile.close()
root = tk.Tk()
app = App(root)