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Copy pathSpotitPy_GUI.py
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SpotitPy_GUI.py
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# -*- coding: utf-8 -*-
from tkinter import *
from tkinter import ttk
from tkinter import filedialog
from tkinter.filedialog import askopenfilename,asksaveasfilename
import matplotlib.pyplot as plt
from matplotlib.backends.backend_tkagg import (FigureCanvasTkAgg, NavigationToolbar2Tk)
import os
os.environ["KMP_DUPLICATE_LIB_OK"]="TRUE"
from readlif.reader import LifFile
import pylab
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import seaborn as sns
import PIL
from PIL import Image
import read_lif
import skimage # Library for image manipulation
from skimage import io
from skimage.io import imread # sublibrary from skimage
import trackpy as tp # Library for particle tracking
from scipy.ndimage import gaussian_filter
from collections import Counter, OrderedDict
from pywt import wavedecn, waverecn
import tifffile as tif
from scipy.ndimage import gaussian_filter
from joblib import Parallel, delayed
import matplotlib.backends.backend_pdf
from matplotlib.backends.backend_pdf import PdfPages
import PyPDF2
from fpdf import FPDF
from PyPDF2 import PdfFileMerger
from reportlab.pdfgen import canvas
from datetime import datetime
import multiprocessing
import seaborn as sns
import tkinter as tk
from cellpose import models
from cellpose import plot
#---------------------------------------------------------------------------------------------------------------------------------------------------
# GLOBAL LISTS
#---------------------------------------------------------------------------------------------------------------------------------------------------
sizes=[]
particle_sizes=[]
image=[]
number=[]
fp2=[]
number_of_parti=[]
number_of_part_in_Green=[]
number_of_part_in_Blue=[]
inpu_cell_size=[]
inpu_part_size=[]
negative_cells=[]
cells=[]
clean_div=[]
use_GPU = models.use_gpu()
model = models.Cellpose(gpu=use_GPU, model_type='cyto')
pdf_files=[]
noise_l=[]
gaus_f=[]
persentil=[]
persentil2=[]
#---------------------------------------------------------------------------------------------------------------------------------------------------
# FORMAT GUI
#---------------------------------------------------------------------------------------------------------------------------------------------------
# contrast border thumbnail
root = Tk()
root.title(" Channel Colocalization Tool")
root.geometry("1040x1040+0+0")#
root.configure(background='#4B637F')
root.attributes('-alpha',0.98)
my_img = tk.PhotoImage(file = r".\bio2.png")
root.iconphoto(False, my_img)
root2 = Tk()
root2.title("Viewer")
root2.geometry("200x250+1050+0")#
root2.configure(background='#4B637F')
root2.attributes('-alpha',0.95)
root3 = Toplevel()
root3.title("Channel selection")
root3.geometry("200x150+1050+305")#
root3.configure(background='#4B637F')
root3.attributes('-alpha',0.92)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Channels ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold ", 10))
l.place(x=106,y=3)
T =Text(root3, height = 5, width = 5)
l = Label(root3, text = "Nucleus ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=30)
var_n = IntVar()
var_c2= IntVar()
var_c3= IntVar()
var_c4= IntVar()
def test1():
global nucleus_channel
nucleus_channel=var_n.get()
c1=Checkbutton(root3, text="1",variable=var_n,onvalue = 1,bg='#4B637F',command = test1).place(x=85, y=30)
c2=Checkbutton(root3, text="2",variable=var_n,onvalue = 2,bg='#4B637F',command = test1).place(x=123, y=30)
c3=Checkbutton(root3, text="3",variable=var_n,onvalue = 3,bg='#4B637F',command = test1).place(x=160, y=30)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Cutoplasm ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=55)
var_c1= IntVar()
def test2():
global channel1
channel1=var_c1.get()
d1=Checkbutton(root3, text="1",variable=var_c1,onvalue = 1,bg='#4B637F',command = test2).place(x=85, y=55)
d2=Checkbutton(root3, text="2",variable=var_c1,onvalue = 2,bg='#4B637F',command = test2).place(x=123, y=55)
d3=Checkbutton(root3, text="3",variable=var_c1,onvalue = 3,bg='#4B637F',command = test2).place(x=160, y=55)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Colocalized ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=80)
def test3():
global channel2
channel2=var_c2.get()
def test4():
global channel3
channel3=var_c3.get()
def test5():
global channel4
channel4=var_c4.get()
da1=Checkbutton(root3, text="1",variable=var_c2,onvalue = 1,bg='#4B637F',command = test3).place(x=85, y=80)
da2=Checkbutton(root3, text="2",variable=var_c3,onvalue = 2,bg='#4B637F',command = test4).place(x=123, y=80)
da3=Checkbutton(root3, text="3",variable=var_c4,onvalue = 3,bg='#4B637F',command = test5).place(x=160, y=80)
def on():
line = Frame(root3, height=3, width=454, relief='groove',background='#4B637F')
line.place(x=0, y=1)
line = Frame(root3, height=3, width=454, relief='groove',background='#4B637F')
line.place(x=0, y=146)
line = Frame(root3, height=165, width=3, relief='groove',background='#4B637F')
line.place(x=1, y=1)
line = Frame(root3, height=165, width=3, relief='groove',background='#4B637F')
line.place(x=196, y=1)
btn33 = Button(root3, text="Done", width=20, bg='#142841', fg='white', font=('ariel 11 bold'), relief=GROOVE, command=on)
btn33.place(x=5, y=110)
def impo(event=None):
import matplotlib
import matplotlib.pyplot as plt
def plotting_tocheck():
matplotlib.use('TkAgg') # <-- THIS MAKES IT FAST!
plt.figure(figsize=(10,10))
plt.imshow(z_0,cmap='Reds')
plt.show()
impo()
def plotting_tocheck2():
matplotlib.use('TkAgg') # <-- THIS MAKES IT FAST!
plt.figure(figsize=(10,10))
plt.imshow(z_1,cmap='Blues')
plt.show()
impo()
def plotting_tocheck3():
matplotlib.use('TkAgg') # <-- THIS MAKES IT FAST!
plt.figure(figsize=(10,10))
plt.imshow(z_2,cmap='Greens')
plt.show()
impo()
root4 = Tk()
root4.title("Channel selection")
root4.geometry("200x138+1050+510")
root4.configure(background='#4B637F')
root4.attributes('-alpha',0.92)
line = Frame(root4, height=3, width=20, relief='groove',background='#142841')
line.place(x=14, y=25)
btn1 = Button(root4, text="View Channel1", width=18,height=1,bg='#57CAC8', fg='WHITE',font=('ariel 9 bold'), relief=GROOVE, command=plotting_tocheck)
btn1.place(x=50, y=12)
line = Frame(root4, height=3, width=20, relief='groove',background='#142841')
line.place(x=14, y=62)
line = Frame(root4, height=3, width=20, relief='groove',background='#142841')
line.place(x=14, y=68)
btn1 = Button(root4, text="View Channel2", width=18,height=1,bg='#57CAC8', fg='WHITE',font=('ariel 9 bold'), relief=GROOVE, command=plotting_tocheck2)
btn1.place(x=50, y=55)
line = Frame(root4, height=3, width=20, relief='groove',background='#142841')
line.place(x=14, y=103)
line = Frame(root4, height=3, width=20, relief='groove',background='#142841')
line.place(x=14, y=109)
line = Frame(root4, height=3, width=20, relief='groove',background='#142841')
line.place(x=14, y=115)
btn1 = Button(root4, text="View Channel3", width=18,height=1,bg='#57CAC8', fg='WHITE',font=('ariel 9 bold'), relief=GROOVE, command=plotting_tocheck3)
btn1.place(x=50, y=98)
#---------------------------------------------------------------------------------------------------------------------------------------------------
# CANVASES
#---------------------------------------------------------------------------------------------------------------------------------------------------
canvas22 = Canvas(root2, width="165", height= "150", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas22.place(x=10, y=28)
canvas2 = Canvas(root, width="447", height= "490", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas2.place(x=540, y=80)
canvas3 = Canvas(root, width="395", height= "490" , bg='#263A55',highlightbackground='#263A55',highlightthickness=5)
canvas3.place(x=50, y=80)
canvas4 = Canvas(root, width="395", height= "120" , bg='#142841',highlightbackground='#142841',highlightthickness=5)
canvas4.place(x=50, y=450)
canvas5 = Canvas(root, width="395", height= "130" , bg='#263A55',highlightbackground='#263A55',highlightthickness=5)
canvas5.place(x=50, y=310)
#---------------------------------------------------------------------------------------------------------------------------------------------------
# LINES
#---------------------------------------------------------------------------------------------------------------------------------------------------
line = Frame(root, height=140, width=1, relief='groove')
line.place(x=302, y=310)
line = Frame(root, height=3, width=454, relief='groove',background='#1A507B')
line.place(x=540, y=414)
line = Frame(root, height=165, width=4, relief='groove',background='#1A507B')
line.place(x=770, y=414)
line = Frame(root, height=16, width=3, relief='groove')
line.place(x=62, y=344)
line =Frame(root, height=16, width=3, relief='groove')
line.place(x=62, y=392)
line = Frame(root, height=633, width=1, relief='groove')
line.place(x=490, y=7)
line = Frame(root, height=1, width=405, relief='groove')
line.place(x=50, y=450)
line = Frame(root, height=1, width=405, relief='groove')
line.place(x=50, y=250)
line = Frame(root, height=1, width=405, relief='groove')
line.place(x=50, y=50)
line = Frame(root3, height=1, width=100, relief='groove',background='#142841')
line.place(x=88, y=25)
line = Frame(root, height=140, width=4, relief='groove',background='#142841')
line.place(x=50, y=310)
line = Frame(root, height=140, width=4, relief='groove',background='#142841')
line.place(x=452, y=310)
line = Frame(root, height=137, width=4, relief='groove',background='#142841')
line.place(x=50, y=110)
line = Frame(root, height=137, width=4, relief='groove',background='#142841')
line.place(x=450, y=110)
line = Frame(root, height=4, width=400, relief='groove',background='#142841')
line.place(x=52, y=242)
line = Frame(root2, height=400, width=4, relief='groove',background='#142841')
line.place(x=0, y=0)
line = Frame(root3, height=400, width=4, relief='groove',background='#142841')
line.place(x=0, y=0)
line = Frame(root4, height=400, width=4, relief='groove',background='#142841')
line.place(x=0, y=0)
#---------------------------------------------------------------------------------------------------------------------------------------------------
# TEXT
#---------------------------------------------------------------------------------------------------------------------------------------------------
T = Text(root, height = 5, width = 52)
l = Label(root, text = "IMAGE PREVIEW",bg = "WHITE",fg='#666A68',width=45,height=2)
l.config(font =("helvetica", 12,'bold'))
l.place(x=540,y=20)
l = Label(root, text = "SELECT YOUR FILE",bg = "WHITE",fg='#666A68',width=40,height=2)
l.config(font =("helvetica ", 12, 'bold'))
l.place(x=50,y=20)
l = Label(root, text = " ",bg = "#57CAC8",fg='#152635',width=4,height=2)
l.config(font =("helvetica ", 12, 'bold'))
l.place(x=50,y=20)
line =Frame(l, height=3, width=23, relief='flat')
line.place(x=9, y=11)
line = Frame(l, height=3, width=23, relief='flat')
line.place(x=9, y=19)
line = Frame(l, height=3, width=23, relief='flat')
line.place(x=9, y=27)
l = Label(root, text = " ",bg = '#4B637F',fg='WHITE',width=40,height=1)
l.config(font =("helvetica ", 12, 'bold'))
l.place(x=50,y=246)
l = Label(root, text = "SETTING PARAMETERS",bg = "WHITE",fg='#666A68',width=40,height=2)
l.config(font =("helvetica ", 12, 'bold'))
l.place(x=50,y=271)
T = Text(root, height = 5, width = 52)
l = Label(root, text = "What model would you like: ",bg = '#263A55',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=70,y=140)
btt1 = Button(root, text="Cyto", width=6, bg='#57CAC8', fg='white', font=('ariel 9 bold'), relief=GROOVE)
btt1.place(x=310, y=140)
btt2 = Button(root, text="Nuclei", width=6, bg='#57CAC8', fg='white', font=('ariel 9 bold'), relief=GROOVE, command=None)
btt2.place(x=380, y=140)
fp=IntVar()
lp=IntVar()
T = Text(root, height = 5, width = 52)
l = Label(root, text = "Select images From: ",bg = '#263A55',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=70,y=190)
T = Text(root, height = 5, width = 52)
l = Label(root, text = "To ",bg = '#263A55',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=360,y=190)
ei = Entry(root, bd =1, bg="#C3CBCE",textvariable=fp,width=4,highlightbackground='#1A507B',highlightthickness=5)
ei.place(x=312, y=185)
eii = Entry(root, bd =1, bg="#C3CBCE",textvariable=lp,width=4,highlightbackground='#1A507B',highlightthickness=5)
eii.place(x=392, y=185)
ns = IntVar()
T = Text(root, height = 5, width = 52)
l = Label(root, text = "Approxiamte nucleus diameter: ",bg = '#263A55',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=70,y=340)
l = Label(root, text = " ",bg = "#C3CBCE",fg='#152635',width=4)
l.config(font =("arial bold", 10))
l.place(x=392,y=343)
e1 =Entry(root, bd =1, bg='white',textvariable=ns,width=6,highlightbackground='#1A507B',highlightthickness=5)
e1.place(x=320, y=340)
ts = IntVar()
T = Text(root, height = 5, width = 52)
l = Label(root, text = "Define the particle diameter: ",bg = '#263A55',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=70,y=390)
l = Label(root, text = " ",bg = "#C3CBCE",fg='#152635',width=4)
l.config(font =("arial bold", 10))
l.place(x=392,y=394)
e2 = Entry(root, bd =1, bg='white',textvariable=ts,width=6,highlightbackground='#1A507B',highlightthickness=5)
e2.place(x=320, y=390)
ps = IntVar()
T = Text(root, height = 5, width = 52)
l = Label(root, text = "Define 1st persentile: ",bg = '#142841',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=70,y=465)
l = Label(root, text = " ",bg = "#C3CBCE",fg='#152635',width=4)
l.config(font =("arial bold", 10))
l.place(x=392,y=468)
e3 = Entry(root, bd =1, bg='white',textvariable=ps,width=15,highlightbackground='#1A507B',highlightthickness=5)
e3.place(x=245, y=465)
ps2 = IntVar()
T = Text(root, height = 5, width = 52)
l = Label(root, text = "Define 2nd persentile: ",bg = '#142841',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=70,y=505)
l = Label(root, text = " ",bg = "#C3CBCE",fg='#152635',width=4)
l.config(font =("arial bold", 10))
l.place(x=392,y=508)
e4 = Entry(root, bd =1, bg='white',textvariable=ps2,width=15,highlightbackground='#1A507B',highlightthickness=5)
e4.place(x=245, y=505)
def process3(event=None):
content = e3.get()
l = Label(root, text = content ,bg = "#585E63",fg='#152635',width=4)
global Ps
Ps=ps.get()
print(ps.get())
l.config(font =("arial bold", 10))
l.place(x=392,y=340)
e3.bind('<Return>', process3)
def process4(event=None):
content = e4.get()
l = Label(root, text = content ,bg = "#585E63",fg='#152635',width=4)
global Ps
Ps2=ps2.get()
print(ps.get())
l.config(font =("arial bold", 10))
l.place(x=392,y=440)
e4.bind('<Return>', process4)
T = Text(root2, height = 5, width = 52)
l = Label(root2, text = "Previous Image: ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold", 10))
l.place(x=11,y=5)
#-----------------------------------------------------------------------------------------------------------------------------------------------
#
# FUNCTIONS
#-----------------------------------------------------------------------------------------------------------------------------------------------
def model_selection(event=None):
global img_path,var_model
pdf_files.append('Intro.pdf')
line = Frame(root, height=16, width=3, relief='groove')
line.place(x=62, y=144)
img_path = filedialog.askopenfilename(initialdir=os.getcwd())
line = Frame(root, height=16, width=3, relief='groove',background='#EA6060')
line.place(x=62, y=144)
var_model = tk.IntVar()
btt1 = Button(root, text="Cyto", width=6, bg='#57CAC8', fg='white', font=('ariel 9 bold'), relief=GROOVE, command=lambda: var_model.set(1))
btt1.place(x=310, y=140)
btt2 = Button(root, text="Nuclei", width=6, bg='#57CAC8', fg='white', font=('ariel 9 bold'), relief=GROOVE, command=lambda: var_model.set(2))
btt2.place(x=380, y=140)
root.wait_variable(var_model)
if var_model.get()==1:
btt1 = Button(root, text="Cyto", width=6, bg='#263A55', fg='white', font=('ariel 9 bold'), relief=GROOVE, command=lambda: var_model.set(1))
btt1.place(x=310, y=140)
else :
btt2 = Button(root, text="Nuclei", width=6, bg='#263A55', fg='white', font=('ariel 9 bold'), relief=GROOVE, command=lambda: var_model.set(2))
btt2.place(x=380, y=140)
line = Frame(root, height=19, width=7, relief='flat',background='#263A55')
line.place(x=60, y=142)
if var_model.get()==1:
root3 = Toplevel()
root3.title("Channel selection")
root3.geometry("200x150+1050+305")#
root3.configure(background='#4B637F')
root3.attributes('-alpha',0.99)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Channels ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold ", 10))
l.place(x=106,y=3)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Nucleus ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=30)
line = Frame(root3, height=1, width=100, relief='groove',background='#142841')
line.place(x=88, y=25)
line = Frame(root3, height=3, width=454, relief='groove',background='#EA6060')
line.place(x=0, y=1)
line = Frame(root3, height=3, width=454, relief='groove',background='#EA6060')
line.place(x=0, y=146)
line = Frame(root3, height=165, width=3, relief='groove',background='#EA6060')
line.place(x=1, y=1)
line = Frame(root3, height=165, width=3, relief='groove',background='#EA6060')
line.place(x=196, y=1)
var_n = IntVar()
def test1():
global nucleus_channel
nucleus_channel=var_n.get()
c1=Checkbutton(root3, text="1",variable=var_n,onvalue = 1,bg='#4B637F',command = test1).place(x=85, y=30)
c2=Checkbutton(root3, text="2",variable=var_n,onvalue = 2,bg='#4B637F',command = test1).place(x=123, y=30)
c3=Checkbutton(root3, text="3",variable=var_n,onvalue = 3,bg='#4B637F',command = test1).place(x=160, y=30)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Cutoplasm ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=55)
var_c1= IntVar()
def test2():
global channel1
channel1=var_c1.get()
d1=Checkbutton(root3, text="1",variable=var_c1,onvalue = 1,bg='#4B637F',command = test2).place(x=85, y=55)
d2=Checkbutton(root3, text="2",variable=var_c1,onvalue = 2,bg='#4B637F',command = test2).place(x=123, y=55)
d3=Checkbutton(root3, text="3",variable=var_c1,onvalue = 3,bg='#4B637F',command = test2).place(x=160, y=55)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Colocalized ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=80)
var_c2= IntVar()
var_c3= IntVar()
var_c4= IntVar()
global channel2
global channel3
global channel4
channel2=0
channel3=0
channel4=0
def test3():
global channel2
channel2=0
channel2=var_c2.get()
def test4():
global channel3
channel3=0
channel3=var_c3.get()
def test5():
global channel4
channel4=0
channel4=var_c4.get()
da1=Checkbutton(root3, text="1",variable=var_c2,onvalue = 1,bg='#4B637F',command = test3).place(x=85, y=80)
da2=Checkbutton(root3, text="2",variable=var_c3,onvalue = 2,bg='#4B637F',command = test4).place(x=123, y=80)
da3=Checkbutton(root3, text="3",variable=var_c4,onvalue = 3,bg='#4B637F',command = test5).place(x=160, y=80)
cha=[]
def on():
channel4a=int(channel4)-1
channel3a=int(channel3)-1
channel2a=int(channel2)-1
ch=[channel4a,channel3a,channel2a]
for x in ch :
if x>=0:
cha.append(x)
global ch_1
global ch_2
ch_1=cha[0]
ch_2=cha[1]
line = Frame(root3, height=3, width=454, relief='groove',background='#4B637F')
line.place(x=0, y=1)
line = Frame(root3, height=3, width=454, relief='groove',background='#4B637F')
line.place(x=0, y=146)
line = Frame(root3, height=165, width=3, relief='groove',background='#4B637F')
line.place(x=1, y=1)
line = Frame(root3, height=165, width=3, relief='groove',background='#4B637F')
line.place(x=196, y=1)
image_params()
btn33 = Button(root3, text="Done", width=20, bg='#142841', fg='white', font=('ariel 11 bold'), relief=GROOVE, command=on)
btn33.place(x=5, y=106)
root3.mainloop()
else :
root3 = Toplevel()
root3.title("Channel selectioooon")
root3.geometry("200x150+1050+305")#
root3.configure(background='#4B637F')
root3.attributes('-alpha',0.99)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Channels ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold ", 10))
l.place(x=106,y=5)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Nucleus ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=40)
var_c2= IntVar()
var_c3= IntVar()
var_c4= IntVar()
line = Frame(root3, height=1, width=100, relief='groove',background='#142841')
line.place(x=88, y=30)
line = Frame(root3, height=3, width=454, relief='groove',background='#EA6060')
line.place(x=0, y=1)
line = Frame(root3, height=3, width=454, relief='groove',background='#EA6060')
line.place(x=0, y=146)
line = Frame(root3, height=165, width=3, relief='groove',background='#EA6060')
line.place(x=1, y=1)
line = Frame(root3, height=165, width=3, relief='groove',background='#EA6060')
line.place(x=196, y=1)
var_n = IntVar()
def test1():
global nucleus_channel
nucleus_channel=var_n.get()
c1=Checkbutton(root3, text="1",variable=var_n,onvalue = 1,bg='#4B637F',command = test1).place(x=85, y=40)
c2=Checkbutton(root3, text="2",variable=var_n,onvalue = 2,bg='#4B637F',command = test1).place(x=123, y=40)
c3=Checkbutton(root3, text="3",variable=var_n,onvalue = 3,bg='#4B637F',command = test1).place(x=160, y=40)
T = Text(root3, height = 5, width = 5)
l = Label(root3, text = "Colocalized ",bg = '#4B637F',fg='#AFB9BF')
l.config(font =("arial bold underline", 10))
l.place(x=5,y=70)
global channel22
global channel32
global channel42
channel22=0
channel32=0
channel42=0
def test3():
global channel22
channel22=0
channel22=var_c2.get()
def test4():
global channel32
channel32=0
channel32=var_c3.get()
def test5():
global channel42
channel42=0
channel42=var_c4.get()
da1=Checkbutton(root3, text="1",variable=var_c2,onvalue = 1,bg='#4B637F',command = test3).place(x=85, y=70)
da2=Checkbutton(root3, text="2",variable=var_c3,onvalue = 2,bg='#4B637F',command = test4).place(x=123, y=70)
da3=Checkbutton(root3, text="3",variable=var_c4,onvalue = 3,bg='#4B637F',command = test5).place(x=160, y=70)
cha=[]
def on():
channel4a=int(channel42)-1
channel3a=int(channel32)-1
channel2a=int(channel22)-1
ch=[channel4a,channel3a,channel2a]
for x in ch :
if x>=0:
cha.append(x)
global ch_1
global ch_2
ch_1=cha[0]
ch_2=cha[1]
line = Frame(root3, height=3, width=454, relief='groove',background='#4B637F')
line.place(x=0, y=1)
line = Frame(root3, height=3, width=454, relief='groove',background='#4B637F')
line.place(x=0, y=146)
line = Frame(root3, height=165, width=3, relief='groove',background='#4B637F')
line.place(x=1, y=1)
line = Frame(root3, height=165, width=3, relief='groove',background='#4B637F')
line.place(x=196, y=1)
image_params2()
btn33 = Button(root3, text="Done", width=20, bg='#142841', fg='white', font=('ariel 11 bold'), relief=GROOVE, command=on)
btn33.place(x=5, y=106)
root3.mainloop()
def pdf_output(img):
pdfs = ['GFG.pdf', '1st Channel stacked.pdf', '2nd Channel stacked.pdf', '3rd Channel stacked.pdf', 'Masked nucleus.pdf','Masked cytoplasm.pdf','Calculation area.pdf','Filtered channel 2 image.pdf','Filtered channel 3 image.pdf','Identified particles in 2nd channel.pdf','Identified particles in 3rd channel.pdf']
merger = PdfFileMerger()
for pdf in pdfs:
merger.append(pdf)
merger.write(str(img)+'.pdf')
pdfs_names=str(img)+'.pdf'
pdf_files.append(str(pdfs_names))
merger.close()
pdfs = ['GFG.pdf', '1st Channel stacked.pdf', '2nd Channel stacked.pdf', '3rd Channel stacked.pdf','Masked nucleus.pdf','Masked cytoplasm.pdf','Calculation area.pdf','Filtered channel 2 image.pdf','Filtered channel 3 image.pdf','Identified particles in 2nd channel.pdf','Identified particles in 3rd channel.pdf']
for f in pdfs:
os.remove(os.path.join('./', f))
def pdf_output2(img):
pdfs = ['GFG.pdf', '1st Channel stacked.pdf', '2nd Channel stacked.pdf', '3rd Channel stacked.pdf', 'Masked nucleus.pdf','Calculation area.pdf','Filtered channel 2 image.pdf','Filtered channel 3 image.pdf','Identified particles in 2nd channel.pdf','Identified particles in 3rd channel.pdf']
merger = PdfFileMerger()
for pdf in pdfs:
merger.append(pdf)
merger.write(str(img)+'.pdf')
pdfs_names=str(img)+'.pdf'
pdf_files.append(str(pdfs_names))
merger.close()
pdfs = ['GFG.pdf', '1st Channel stacked.pdf', '2nd Channel stacked.pdf', '3rd Channel stacked.pdf','Masked nucleus.pdf','Masked cytoplasm.pdf','Calculation area.pdf','Filtered channel 2 image.pdf','Filtered channel 3 image.pdf','Identified particles in 2nd channel.pdf','Identified particles in 3rd channel.pdf']
for f in pdfs:
os.remove(os.path.join('./', f))
def final_merging(counter):
merger = PdfFileMerger()
dateTimeObj = datetime.now()
date='This file was created the: '+str(dateTimeObj.year)+'/'+str(dateTimeObj.month)+'/'+str(dateTimeObj.day)
title='IMAGE ANALYSIS REPORT'
per='Persentile: '+str(persentil)+','+str(persentil2)
filt='Sigma Gaussian filter: '+str(gaus_f[0])
num='Number of analyzed images: '+str(counter)
c = canvas.Canvas("Intro.pdf")
c.setFont("Courier", 9) #choose your font type and font size
c.drawString(390, 820, date)
c.setFont("Helvetica", 26) #choose your font type and font size
c.drawString(130, 620, title)
c.setFont("Courier", 9) #choose your font type and font size
c.drawString(30, 80, per)
c.drawString(30, 50, filt)
c.save()
os.remove(os.path.join('./', 'Saturated image'))
os.remove(os.path.join('./', 'Channel 2 Image'))
os.remove(os.path.join('./', 'Channel 3 Image'))
for pdf in pdf_files:
merger.append(pdf)
merger.write(str('Report')+'.pdf')
merger.close()
for x in pdf_files:
os.remove(os.path.join('./', x))
popupmsg('Analysis completed','Terminal')
def get_going():
if var_model.get()==1:
image_analysis()
else:
image_analysis2()
def popupmsg1(msg, title):
root = tk.Tk()
root.title(title)
root.geometry("220x80+550+300")
root.attributes('-alpha',0.80)
root.configure(background='#581845')
label = Label(root, text=msg,background='#581845',fg='white')
label.pack(side="top", fill="x", pady=10)
B1 = tk.Button(root, text="START",activebackground="#142841", command = lambda:[get_going(),root.destroy()])
B1.pack()
root.mainloop()
def popupmsg(msg, title):
root = tk.Tk()
root.title(title)
root.geometry("140x80+550+300")#
root.attributes('-alpha',0.80)
root.configure(background='#581845')
label = Label(root, text=msg,background='#581845',fg='white')
label.pack(side="top", fill="x", pady=10)
B1 = tk.Button(root, text="Okay", command = root.destroy)
B1.pack()
def plot(image,color,plot_title):
matplotlib.use('agg')
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(0.8,0.8))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.show()
plt.figure(figsize=(10,10))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.savefig(plot_title+'.pdf')
def ploting(image,color,plot_title):
matplotlib.use('agg')
import matplotlib.pyplot as plt
canvas22 = Canvas(root2, width="165", height= "150", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas22.place(x=15, y=37)
fig=plt.figure(figsize=(0.8,0.8))
plt.imshow(image,cmap=color)
plt.show()
canvas = FigureCanvasTkAgg(fig, master=canvas22)
canvas.get_tk_widget().grid(row=0, column=0, ipadx=55, ipady=40)
plt.figure(figsize=(10,10))
plt.imshow(image,cmap=color)
plt.savefig(plot_title+'.pdf')
def plotting(image,color,plot_title):
matplotlib.use('agg')
import matplotlib.pyplot as plt
canvas2 = Canvas(root, width="450", height= "490", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas2.place(x=550, y=86)
fig=plt.figure(figsize=(5,4))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.show()
canvas = FigureCanvasTkAgg(fig, master=canvas2)
canvas.get_tk_widget().grid(row=0, column=0, ipadx=40, ipady=20)
plt.figure(figsize=(10,10))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.savefig(plot_title+'.pdf')
def plotting2(image,color,plot_title):
matplotlib.use('agg')
import matplotlib.pyplot as plt
canvas2 = Canvas(root, width="450", height= "490", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas2.place(x=549, y=425)
fig=plt.figure(figsize=(1.5,1.5))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.show()
canvas = FigureCanvasTkAgg(fig, master=canvas2)
canvas.get_tk_widget().grid(row=0, column=0, ipadx=30, ipady=20)
plt.figure(figsize=(10,10))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.savefig(plot_title+'.pdf')
def plotting3(image,color,plot_title):
matplotlib.use('agg')
import matplotlib.pyplot as plt
canvas2 = Canvas(root, width="450", height= "490", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas2.place(x=575, y=425)
fig=plt.figure(figsize=(1.5,1.5))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.show()
canvas = FigureCanvasTkAgg(fig, master=canvas2)
canvas.get_tk_widget().grid(row=0, column=0, ipadx=30, ipady=20)
plt.figure(figsize=(10,10))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.savefig(plot_title+'.pdf')
def plotting4(image,color,plot_title):
matplotlib.use('agg')
import matplotlib.pyplot as plt
canvas2 = Canvas(root, width="450", height= "490", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas2.place(x=801, y=425)
fig=plt.figure(figsize=(1.5,1.5))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.show()
canvas = FigureCanvasTkAgg(fig, master=canvas2)
canvas.get_tk_widget().grid(row=0, column=0, ipadx=30, ipady=20)
plt.figure(figsize=(10,10))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.savefig(plot_title+'.pdf')
def plotting5(image,color,plot_title):
matplotlib.use('agg')
import matplotlib.pyplot as plt
canvas2 = Canvas(root, width="450", height= "490", relief=RIDGE, bd=1, bg='white',highlightbackground='#1A507B',highlightthickness=5)
canvas2.place(x=801, y=425)
fig=plt.figure(figsize=(1.5,1.5))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.show()
canvas = FigureCanvasTkAgg(fig, master=canvas2)
canvas.get_tk_widget().grid(row=0, column=0, ipadx=30, ipady=20)
plt.figure(figsize=(10,10))
plt.imshow(image,cmap=color)
plt.title(plot_title)
plt.savefig(plot_title+'.pdf')
def stacking_step(z_list_0,z_list_1,z_list_2):
z_st_0=[]
for x in range(len(z_list_0)):
pic=np.array(z_list_0[x])
z_st_0.append(pic)
if len(z_st_0)==19:
global z_0
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18]])
elif len(z_st_0)==30:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22],z_st_0[23],z_st_0[24],z_st_0[25],z_st_0[26],z_st_0[27],z_st_0[28],z_st_0[29]])
elif len(z_st_0)==29:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22],z_st_0[23],z_st_0[24],z_st_0[25],z_st_0[26],z_st_0[27],z_st_0[28]])
elif len(z_st_0)==28:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22],z_st_0[23],z_st_0[24],z_st_0[25],z_st_0[26],z_st_0[27]])
elif len(z_st_0)==27:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22],z_st_0[23],z_st_0[24],z_st_0[25],z_st_0[26]])
elif len(z_st_0)==26:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22],z_st_0[23],z_st_0[24],z_st_0[25]])
elif len(z_st_0)==25:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22],z_st_0[23],z_st_0[24]])
elif len(z_st_0)==24:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22],z_st_0[23]])
elif len(z_st_0)==23:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21],z_st_0[22]])
elif len(z_st_0)==22:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20],z_st_0[21]])
elif len(z_st_0)==21:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19],z_st_0[20]])
elif len(z_st_0)==20:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17],z_st_0[18],z_st_0[19]])
elif len(z_st_0)==18:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16],z_st_0[17]])
elif len(z_st_0)==17:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15],z_st_0[16]])
elif len(z_st_0)==16:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14],z_st_0[15]])
elif len(z_st_0)==15:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13],z_st_0[14]])
elif len(z_st_0)==14:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12],z_st_0[13]])
elif len(z_st_0)==13:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11],z_st_0[12]])
elif len(z_st_0)==12:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10],z_st_0[11]])
elif len(z_st_0)==11:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9],z_st_0[10]])
elif len(z_st_0)==10:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8],z_st_0[9]])
elif len(z_st_0)==9:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7],z_st_0[8]])
elif len(z_st_0)==8:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6],z_st_0[7]])
elif len(z_st_0)==7:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5],z_st_0[6]])
elif len(z_st_0)==6:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4],z_st_0[5]])
elif len(z_st_0)==5:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3],z_st_0[4]])
elif len(z_st_0)==4:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2],z_st_0[3]])
elif len(z_st_0)==3:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1],z_st_0[2]])
elif len(z_st_0)==2:
z_0=np.maximum.reduce([z_st_0[0],z_st_0[1]])
elif len(z_st_0)==1:
z_0=np.maximum.reduce([z_st_0[0]])
plot(z_0,'Reds','1st Channel stacked')
z_st_1=[]
for x in range(len(z_list_1)):
pic=np.array(z_list_1[x])
z_st_1.append(pic)
if len(z_st_1)==19:
global z_1
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18]])
elif len(z_st_1)==30:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22],z_st_1[23],z_st_1[24],z_st_1[25],z_st_1[26],z_st_1[27],z_st_1[28],z_st_1[29]])
elif len(z_st_1)==29:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22],z_st_1[23],z_st_1[24],z_st_1[25],z_st_1[26],z_st_1[27],z_st_1[28]])
elif len(z_st_1)==28:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22],z_st_1[23],z_st_1[24],z_st_1[25],z_st_1[26],z_st_1[27]])
elif len(z_st_1)==27:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22],z_st_1[23],z_st_1[24],z_st_1[25],z_st_1[26]])
elif len(z_st_1)==26:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22],z_st_1[23],z_st_1[24],z_st_1[25]])
elif len(z_st_1)==25:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22],z_st_1[23],z_st_1[24]])
elif len(z_st_1)==24:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22],z_st_1[23]])
elif len(z_st_1)==23:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21],z_st_1[22]])
elif len(z_st_1)==22:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20],z_st_1[21]])
elif len(z_st_1)==21:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19],z_st_1[20]])
elif len(z_st_1)==20:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17],z_st_1[18],z_st_1[19]])
elif len(z_st_1)==18:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16],z_st_1[17]])
elif len(z_st_1)==17:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15],z_st_1[16]])
elif len(z_st_1)==16:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14],z_st_1[15]])
elif len(z_st_1)==15:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13],z_st_1[14]])
elif len(z_st_1)==14:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12],z_st_1[13]])
elif len(z_st_1)==13:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11],z_st_1[12]])
elif len(z_st_1)==12:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10],z_st_1[11]])
elif len(z_st_1)==11:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9],z_st_1[10]])
elif len(z_st_1)==10:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8],z_st_1[9]])
elif len(z_st_1)==9:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7],z_st_1[8]])
elif len(z_st_1)==8:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6],z_st_1[7]])
elif len(z_st_1)==7:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5],z_st_1[6]])
elif len(z_st_1)==6:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4],z_st_1[5]])
elif len(z_st_1)==5:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3],z_st_1[4]])
elif len(z_st_1)==4:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2],z_st_1[3]])
elif len(z_st_1)==3:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1],z_st_1[2]])
elif len(z_st_1)==2:
z_1=np.maximum.reduce([z_st_1[0],z_st_1[1]])
elif len(z_st_1)==1:
z_1=np.maximum.reduce([z_st_1[0]])
plot(z_1,'Greens','2nd Channel stacked')
z_st_2=[]
for x in range(len(z_list_2)):
pic=np.array(z_list_2[x])
z_st_2.append(pic)
if len(z_st_2)==19:
global z_2