#!/usr/bin/env python

__author__ = "Sreenivas Bhattiprolu"

__license__ = "Feel free to copy, I appreciate if you acknowledge Python for Microscopists"

# https://www.youtube.com/watch?v=jcUx-TQpcM8

#Scratch Assay on time series images

import matplotlib.pyplot as plt

from skimage import io

from skimage.filters.rank import entropy

from skimage.morphology import disk

import numpy as np

from skimage.filters import threshold_otsu

import glob

time = 0

time_list=[]

area_list=[]

path = "images/scratch_assay/*.*"

for file in glob.glob(path):

dict={}

img=io.imread(file)

entropy_img = entropy(img, disk(3))

thresh = threshold_otsu(entropy_img)

binary = entropy_img <= thresh

scratch_area = np.sum(binary == 1)

print("time=", time, "hr ", "Scratch area=", scratch_area, "pix\N{SUPERSCRIPT TWO}")

time_list.append(time)

area_list.append(scratch_area)

time += 1

#print(time_list, area_list)

plt.plot(time_list, area_list, 'bo') #Print blue dots scatter plot

#Print slope, intercept

from scipy.stats import linregress

#print(linregress(time_list, area_list))

slope, intercept, r_value, p_value, std_err = linregress(time_list, area_list)

print("y = ",slope, "x", " + ", intercept )

print("R\N{SUPERSCRIPT TWO} = ", r_value**2)

#print("r-squared: %f" % r_value**2)