# -*- coding: utf-8 -*-

"""

Spyder Editor

This is a temporary script file.

"""

from __future__ import division, unicode_literals, print_function

import matplotlib as mpl

import matplotlib.pyplot as plt

import numpy as np

import pandas as pd

from pandas import DataFrame, Series

import pims

import trackpy as tp

from uncertainties import ufloat

T = ufloat(293,1)

eta = 1/1000

a = ufloat(0.00000099, 0.00000003)

frames = pims.TiffStack('C:/Users/Ewout van der Velde/Downloads/Untitled4.tif', as_grey=False)

f = tp.locate(frames[-250:], 21, invert = True, minmass=1000)

f.head()

plt.figure()

tp.annotate(f, frames[0])

fig,ax = plt.subplots()

ax.hist(f['mass'], bins=40)

f = tp.batch(frames[-100:], 21, minmass = 1000, invert=True)

t = tp.link_df(f, 5, memory=3)

t.head()

t1 = tp.filter_stubs(t, 25)

print('before:', t['particle'].nunique())

print('after:', t1['particle'].nunique())

plt.figure()

tp.plot_traj(t1)

d = tp.compute_drift(t1)

d.plot()

plt.show()

plt.savefig("1.pdf")

tm = tp.subtract_drift(t1.copy(),d)

ax = tp.plot_traj(tm)

plt.show()

plt.savefig("2.pdf")

em = tp.emsd(tm, 0.00000119029/1, 30) # microns per pixel = 100/285., frames per second = 24

fig, ax = plt.subplots()

ax.plot(em.index, em, 'o')

ax.set_xscale('log')

ax.set_yscale('log')

ax.set(ylabel=r'$\langle \Delta r^2 \rangle$ [$\mu$m$^2$]',

xlabel='lag time $t$')

ax.set(ylim=(1e-2, 100));

plt.savefig("3.pdf")

plt.figure()

plt.ylabel(r'$\langle \Delta r^2 \rangle$ [$\mu$m$^2$]')

plt.xlabel('lag time $t$');

atre = tp.utils.fit_powerlaw(em) # performs linear best fit in log space, plots]

plt.savefig("4.pdf")

print(atre)

atre_matrix = atre.as_matrix()

Kb = ( (atre_matrix[0,1]) * (6*np.pi*eta*a) ) / (4*T)

print(Kb)