172 lines
14 KiB
Python
172 lines
14 KiB
Python
# Copyright (c) 2019 Esben Rossel
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# All rights reserved.
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#
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# Author: Esben Rossel <esbenrossel@gmail.com>
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions
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# are met:
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# 1. Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# 2. Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
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# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL AUTHOR OR CONTRIBUTORS BE LIABLE
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# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
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# OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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# SUCH DAMAGE.
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import os
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import tkinter as tk
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from tkinter.constants import END
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from PIL import Image,ImageTk
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def center_window(size, window) :
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window_width = size[0] #Fetches the width you gave as arg. Alternatively window.winfo_width can be used if width is not to be fixed by you.
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window_height = size[1] #Fetches the height you gave as arg. Alternatively window.winfo_height can be used if height is not to be fixed by you.
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if window==None:
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window_x = 200
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window_y = 200
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else:
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window_x = int((window.winfo_screenwidth() / 2) - (window_width / 2)) #Calculates the x for the window to be in the centre
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window_y = int((window.winfo_screenheight() / 2) - (window_height / 2)) #Calculates the y for the window to be in the centre
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window_geometry = str(window_width) + 'x' + str(window_height) + '+' + str(window_x) + '+' + str(window_y) #Creates a geometric string argument
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window.geometry(window_geometry) #Sets the geometry accordingly.
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return
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def get_icon_image(xx):
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directory_path = os.path.dirname(__file__)
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file_path = os.path.join(directory_path, 'images\\')
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image =Image.open(file_path+xx)
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photo = ImageTk.PhotoImage(image)
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return photo
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def jfshelpme(win,helpfor):
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top = tk.Toplevel(win)
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scrolling = tk.Scrollbar(top)
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scrolling.pack(side=tk.RIGHT, fill=tk.Y)
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frame = tk.Frame(top)
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frame.pack()
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text = tk.Text(frame, height=30, width=100, wrap=tk.WORD)
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text.pack(side=tk.LEFT, fill=tk.Y)
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scrolling.config(command=text.yview)
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text.config(yscrollcommand=scrolling.set)
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photoImg = get_icon_image('nm405.gif')
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photoImg2= get_icon_image('methods.gif')
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photoImg3= get_icon_image('kinetics.gif')
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photoImg4= get_icon_image('xenon.gif')
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text.tag_configure('it', font=('Arial', 10, 'italic'))
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text.tag_configure('h1', font=('Verdana', 16, 'bold'))
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text.tag_configure('h2', font=('Verdana', 12, 'bold'))
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text.tag_configure('h3', font=('Verdana', 10, 'bold'))
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if (helpfor == 0): #do you need help with the device?
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text.image_create(tk.END,image=photoImg)
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text.insert(tk.END, " Calibration\n", 'h1')
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text.insert(tk.END, "\nTo calibrate the Instrument we need two laserpointer of different colors und known wavelength.\nFor example a blue [405nm] and red [650nm] one.\n")
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text.insert(tk.END, "1) First take two measurements with your device und save the files with the [Save] button under a comprehensible name (e.g. 405nm.data) \n")
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text.insert(tk.END, "2) Open the calibration dialog and insert the wavelength in [nm] and afterwards select the respective file. <first peak> stands for the lower and <second peak> for the higher wavelength.\n")
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text.insert(tk.END, "3) Now you can use the [Calibrate] button to calibrate the instrument and [Save Config] will the store the configuration.\n")
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text.insert(tk.END,"\nAfter this procedure you can switch the [nm] scale on and use other option:\n")
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text.insert(tk.END,'\nMethods\n','h2')
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text.insert(tk.END,"\nAs a Photometer to messure the transmittance or absorbance depending on the concentration of colored compounds.\n\n")
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text.image_create(tk.END,image=photoImg2)
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text.insert(tk.END,"\n\nKinetic\n",'h2')
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text.insert(tk.END,"\nThe instrument can messure in specific intervalls over time the change in absorbance. From this data it is possible to determine the rate of the reaction.\n")
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text.image_create(tk.END,image=photoImg3)
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text.insert(tk.END,"\n Baseline\n",'h1')
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text.insert(tk.END,"\nIn order to messure the absorption of a compound in the cuvette, you have to messure the intensity of the the light passing through the reference cell.\n")
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text.insert(tk.END,"The intensity of the light at a specific wavelength depends on the kind of light source. The spectrum of a tungstone lamp is different from a LED etc.\n")
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text.insert(tk.END,"\nTo make things easy: the value <threshold for the baseline> cuts off the beginning and the end where the light source is not strong enought to give reasonable results ")
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text.image_create(tk.END,image=photoImg4)
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text.insert(tk.END,"\nFor example xenon-lamp as a source. If the value of the threshold is set to 100 (green), the baseline will start at 380nm and end at 510nm\n")
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text.insert(tk.END,"If the value of the threshold is set to 50 (red), the baseline will start at 370nm and end at 695nm. The baseline determines the range of messurement\n")
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elif (helpfor == 1): #do you need help with the device?
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text.image_create(tk.END,image=photoImg)
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text.insert(tk.END, " Calibration\n", 'h1')
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text.insert(tk.END, "\nTo calibrate the Instrument we need two laserpointer of different colors und known wavelength.\nFor example a blue [405nm] and red [650nm] one.\n")
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text.insert(tk.END, "1) First take two measurements with your device und save the files with the [Save] button under a comprehensible name (e.g. 405nm.data) \n")
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text.insert(tk.END, "2) Open the calibration dialog and insert the wavelength in [nm] and afterwards select the respective file. <first peak> stands for the lower and <second peak> for the higher wavelength.\n")
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text.insert(tk.END, "3) Now you can use the [Calibrate] button to calibrate the instrument and [Save Config] will the store the configuration.\n")
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text.insert(tk.END,"\nAfter this procedure you can switch the [nm] scale on and use other option:\n")
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text.insert(tk.END,'\nMethods\n','h2')
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text.insert(tk.END,"\nAs a Photometer to messure the transmittance or absorbance depending on the concentration of colored compounds.\n\n")
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text.image_create(tk.END,image=photoImg2)
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text.insert(tk.END,"\n\nKinetic\n",'h2')
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text.insert(tk.END,"\nThe instrument can messure in specific intervalls over time the change in absorbance. From this data it is possible to determine the rate of the reaction.\n")
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text.image_create(tk.END,image=photoImg3)
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elif (helpfor == 2):
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text.insert(tk.END," Dark spectrum\n",'h1')
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text.insert(tk.END,"\nPlease turn off the light source and take a messurement with the actual parameter. Afterwards save this spektrum of the dark noise\n")
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text.insert(tk.END,"\nClick the checkbutton of [Darkline] to proceed")
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elif (helpfor == 3):
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text.insert(tk.END," Zero solution \n",'h1')
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text.insert(tk.END,"\nIn order to messure the absorbance or transmittance of a sample, you need to messure a zero solution first\n")
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text.insert(tk.END,"\n1) Check the darkline checkbutton\n2) Turn on the light source and insert a cuvette with a solution without a compound -> \'zero solution\'\n")
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text.insert(tk.END,"3) Save the messurement with [save Base]. This will also cut the range of messurement depending of the lightsoure -> Baseline\n" )
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text.insert(tk.END,"4) Click the checkbutton of [Baseline] to proceed\n")
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text.insert(tk.END,"Now you can messure the absorbance or transmittance of different compounds by using the radiobuttons \n")
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text.insert(tk.END,"\nWith the Dialog [Calibration] you can change the range of the light source\n\n")
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text.insert(tk.END,"\n Baseline\n",'h2')
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text.insert(tk.END,"\nIn order to messure the absorption of a compound in the cuvette, you have to messure the intensity of the the light passing through the reference cell.\n")
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text.insert(tk.END,"The intensity of the light at a specific wavelength depends on the kind of light source. The spectrum of a tungstone lamp is different from a LED etc.\n")
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text.insert(tk.END,"\nTo make things easy: the value <threshold for the baseline> cuts off the beginning and the end where the light source is not strong enought to give reasonable results ")
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text.image_create(tk.END,image=photoImg4)
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text.insert(tk.END,"\nFor example xenon-lamp as a source. If the value of the threshold is set to 100 (green), the baseline will start at 380nm and end at 510nm\n")
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text.insert(tk.END,"If the value of the threshold is set to 50 (red), the baseline will start at 370nm and end at 695nm. The baseline determines the range of messurement\n")
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elif (helpfor == 4):
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text.insert(tk.END," Load / Save \n",'h1')
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text.insert(tk.END,"\nThese Buttons save und load the photometer data of the absorbance of a compound. The baseline of the light source and the dark spectrum of the instrument will also be saved\n")
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text.insert(tk.END,"\nThis will not work with with simple spetra saves over the [Save] button")
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elif (helpfor == 5):
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text.image_create(tk.END,image=photoImg3)
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text.insert(tk.END,"\nKinetic\n",'h1')
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text.insert(tk.END,"\nTo run kinetic measurements with this photometer, make sure that:\n")
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text.insert(tk.END,"1) The instrument is calibrated\n2) A dark spektrum is taken/saved [save Dark]\n3) A zero solution is messured a saved [save Base].\n\n")
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text.insert(tk.END,"If all parameters a ok. Adjust the numbers of repetitions and the time between the messurement in the dialog.\nThe [start Kinetic] Button will start the process.\n")
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text.insert(tk.END,"When the messurement is finished the [Math] Dialog appears and the data can be saved and inspected.\n")
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elif (helpfor == 6):
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#text.image_create(tk.END,image=photoImg3)
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text.insert(tk.END,"\nMath on Kinetics\n",'h1')
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text.insert(tk.END,"\nRaw - Absorbanz\n\n",'h2')
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text.insert(tk.END,"- Raw: is the raw output of the instrument\n- Raw + Baseline: is raw plus the darkline und the baseline of the lighsource\n")
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text.insert(tk.END,"- Transmission: is the relation of the intensity of the light absorpt by the sample and the intensity of the light source.\n")
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text.insert(tk.END,"- Absorbanz: is the relation of the log(I of light source/I of transmitted)\n-- For more information please look for Beer-Lambert law\n")
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text.insert(tk.END,"\nSlicing\n\n",'h2')
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text.insert(tk.END,"If you move the mouse in the left diagram, the coordinats will be displayed in the bottom of the diagram < x=.. and y=.. > x means the point of the nmscale.\n")
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text.insert(tk.END,"Clicking with the left mousebutton will select a slice through the curves at the x-value. This slice is displayed in the upper left window. This function works only if the [3 D Print] is not toggled.\n")
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text.insert(tk.END,"To check the kinetic order the log(absorbance) is displayed in the lower left window. This can be toggled with the [ln[A] 1/[A]]-button to display 1/[A]\n")
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text.insert(tk.END,"\nSelection\n\n",'h2')
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text.insert(tk.END,"It is possible to display only parts of the measurements by selecting with the mouse. All other functions should work.\n")
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elif (helpfor == 7):
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text.image_create(tk.END,image=photoImg2)
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text.insert(tk.END," Methods\n",'h1')
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text.insert(tk.END,"\nIn this part of the programm it is possible to determine the concentration of a compound with the spectrometer.\n")
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text.insert(tk.END,"1) Try out concentration of the compount, ICG, SH, light source etc. that works fine and give an absorbance of approx 1.\nCheck [nm], [Darkline] and [Baseline]\n")
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text.insert(tk.END,"2) Dilute the solution for the standard curve.\nFor example if the last concentration in 30mmol and 5 solution are made. You have to prepare 6mmol,12mmol,18mmol,24mmol and 30mmol.\n")
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text.insert(tk.END,"3) Complete the dialog <Edit the method> and [add Method]. The method will appear in the methods window, with a line for each concentration.\n")
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text.insert(tk.END,"4) Now insert the cuvette with the specific concentration and select the line.\nThe measurement takes place and the absorbance will be stored\n")
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text.insert(tk.END,"5) If everything is ok, you can save the method and it's values.\n")
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text.insert(tk.END,"\nThe fitting curve is determined by numpy's polyfit and the r2_score and displayed.\n")
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text.insert(tk.END,"\nAfterwards an unknown concentration of a compound can be determined over the dialog <Do measurements>")
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### at the end
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text.config(state=tk.DISABLED)
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top.focus_set()
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top.grab_set()
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top.wait_window() |