#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright 2015 by Bruno Silva <bruno.phoenix@gmail.com>, Björn Johansson.
# All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license.  Please see the LICENSE.txt file that should have been included
# as part of this package.

#from pint import UnitRegistry #, DimensionalityError
# Hacky fix for a python3 problem I don't understand
# https://github.com/pallets/flask/issues/1680
#UnitRegistry.__wrapped__ = None
#ureg = UnitRegistry()

"""Provides the class `Gel` for the simulation of agarose slab-gel
electrophoresis of DNA at constant electric field.

Note
----
This code is at an early stage of development and documentation.

"""


import numpy as np

from matplotlib import pyplot as plt, cm
import matplotlib.ticker as mtick
from matplotlib.ticker import FixedLocator

from mpldatacursor import datacursor #, HighlightingDataCursor  # version 0.5.0

from scipy.interpolate import griddata
from scipy.optimize import leastsq, fsolve
from scipy import stats

from pint import UnitRegistry

#from numbers import Number
from io import BytesIO
#from random import randint


from .dsdna import Dseq, Dseqrecord


# Hacky fix for a python3 problem I don't understand
# https://github.com/pallets/flask/issues/1680
UnitRegistry.__wrapped__ = None

# Unit registry
ureg = UnitRegistry()
Q_ = ureg.Quantity
ureg.define('base_pair = [] = bp = basepair')
# ureg.define('base_pair = 3.4 angstrom = bp = basepair')
ureg.define('pixel = [] = px')
ureg.default_format = '~'


# Variable mapping
Vars = {'E': {'synonyms': ('field', 'electric field'), 'units': 'V/cm',
              'details': ("Electric field intensity as given by the applied "
                          "voltage divided by the distance between the "
                          "electrodes.")},
        'quantities': {'synonyms': (), 'units': 'ng',
                       'details': "Mass of DNA in a sample or a band."},
        'volume': {'synonyms': (), 'units': 'ul',
                   'details': ""}
        }


# Weight standards
weight_standards = {
    '1kb_GeneRuler': {
        'sizes': Q_([10000, 8000, 6000, 5000, 4000, 3500, 3000, 2500, 2000,
                     1500, 1000, 750, 500, 250], 'bp'),
        'percent': Q_([0.06, 0.06, 0.14, 0.06, 0.06, 0.06, 0.14, 0.05, 0.05,
                       0.05, 0.12, 0.05, 0.05, 0.05])
        },
    '1kb+_GeneRuler': {
        'sizes': Q_([20000, 10000, 7000, 5000, 4000, 3000, 2000, 1500, 1000,
                     700, 500, 400, 300, 200, 75], 'bp'),
        'percent': Q_([0.04, 0.04, 0.04, 0.15, 0.04, 0.04, 0.04, 0.16, 0.05,
                       0.05, 0.15, 0.05, 0.05, 0.05, 0.05])
        },
    'Mix_GeneRuler': {
        'sizes': Q_([10000, 8000, 6000, 5000, 4000, 3500, 3000, 2500, 2000,
                     1500, 1200, 1000, 900, 800, 700, 600, 500, 400, 300, 200,
                     100], 'bp'),
        'percent': Q_([0.036, 0.036, 0.036, 0.036, 0.036, 0.036, 0.12, 0.032,
                       0.032, 0.032, 0.032, 0.12, 0.034, 0.034, 0.034, 0.034,
                       0.12, 0.04, 0.04, 0.04, 0.04])
        },
    'High_Range_GeneRuler': {
        'sizes': Q_([48502, 24508, 20555, 17000, 15258, 13825, 12119, 10171],
                    'bp'),
        'percent': Q_([0.16, 0.176, 0.16, 0.118, 0.118, 0.1, 0.094, 0.074])
        }
    }


# Data
hor_str = '''
+------+-----+-------+-------+-----------+-----------+----------+--------+-------+--------+
|  E   | %T  | L_max | L_min | mu_S*10^8 | mu_L*10^8 |   gamma  |  chi^2 | L'max | chi^2' |
|(V/cm)|     | (bp)  | (bp)  |(m^2/V.sec)|(m^2/V.sec)|   (kbp)  |        | (bp)  |        |
+------+-----+-------+-------+-----------+-----------+----------+--------+-------+--------+
| 0.71 | 0.5 | 35000 | 1000  |    2.61   |    0.42   |   29.70  | 0.9999 |       |        |
| 0.71 | 1.0 | 20000 |  300  |    2.54   |  1.64E-07 | 2.81E+07 | 0.9981 |  5000 | 0.9992 |
| 0.71 | 1.3 | 20000 |  200  |    2.49   |  2.60E-09 | 1.06E+09 | 0.9647 |  2600 | 0.9990 |
| 1.00 | 1.0 | 48502 |  400  |    2.37   |    0.23   |   29.99  | 0.9997 |       |        |
| 1.00 | 1.1 | 30000 |  200  |    2.21   |    0.05   |   74.08  | 0.9987 | 25000 | 0.9991 |
| 1.00 | 1.2 | 27500 |  200  |    2.14   |    0.01   |  144.40  | 0.9964 |  1300 | 0.9990 |
| 1.23 | 0.7 | 47500 | 1000  |    2.60   |    0.66   |   19.86  | 0.9997 |       |        |
| 1.23 | 0.8 | 35000 |  200  |    2.55   |    0.23   |   23.84  | 0.9988 | 27500 | 0.9990 |
| 1.23 | 0.9 | 25000 |  200  |    2.44   |    0.08   |   49.58  | 0.9971 |  3000 | 0.9992 |
| 1.31 | 0.5 | 35000 |  400  |    2.54   |    0.39   |   19.69  | 0.9999 |       |        |
| 1.31 | 1.0 | 25000 |  200  |    2.52   |    0.15   |   25.75  | 0.9986 | 17500 | 0.9992 |
| 1.31 | 1.3 | 48502 |  200  |    2.48   |    0.05   |   46.75  | 0.9967 | 14000 | 0.9991 |
| 1.51 | 1.0 | 35000 |  200  |    2.24   |    0.29   |   17.86  | 0.9997 |       |        |
| 1.51 | 1.1 | 32500 |  300  |    2.26   |    0.14   |   23.78  | 0.9980 | 20000 | 0.9989 |
| 1.51 | 1.2 | 48502 |  200  |    2.17   |    0.04   |   64.31  | 0.9974 | 15000 | 0.9991 |
| 1.80 | 0.5 | 47500 |  300  |    2.48   |    0.51   |   17.23  | 0.9998 |       |        |
| 1.80 | 1.3 | 30000 |  200  |    2.39   |    0.22   |   11.93  | 0.9980 | 13000 | 0.9991 |
| 2.00 | 1.0 | 48502 |  200  |    2.22   |    0.23   |   13.96  | 0.9982 | 20000 | 0.9992 |
| 2.00 | 1.1 | 48502 |  200  |    2.24   |    0.16   |   13.06  | 0.9971 | 10000 | 0.9991 |
| 2.00 | 1.2 | 17500 |  200  |    2.15   |    0.07   |   30.99  | 0.9979 | 10000 | 0.9990 |
| 2.22 | 0.5 | 35000 |  300  |    2.68   |    0.65   |   12.90  | 0.9995 |       |        |
| 2.22 | 1.0 | 35000 |  200  |    2.64   |    0.43   |    9.56  | 0.9994 |       |        |
| 2.22 | 1.3 | 32500 |  200  |    2.56   |    0.29   |    8.42  | 0.9981 | 17500 | 0.9991 |
| 2.47 | 0.7 | 32500 |  200  |    2.59   |    0.51   |    9.50  | 0.9997 |       |        |
| 2.47 | 0.8 | 35000 |  500  |    2.64   |    0.47   |    8.77  | 0.9998 |       |        |
| 2.47 | 0.9 | 48502 |  200  |    2.57   |    0.39   |    8.98  | 0.9992 |       |        |
| 2.51 | 0.7 | 35000 |  200  |    2.44   |    0.45   |   14.19  | 0.9999 |       |        |
| 2.51 | 0.8 | 35000 |  200  |    2.44   |    0.39   |   12.41  | 0.9996 |       |        |
| 2.51 | 0.9 | 48502 |  200  |    2.43   |    0.27   |   11.03  | 0.9986 | 15000 | 0.9991 |
| 2.78 | 0.5 | 10000 |  200  |    3.32   |    0.92   |    9.30  | 0.9999 |       |        |
| 2.78 | 0.6 | 10000 |  200  |    3.25   |    0.80   |    8.47  | 1.0000 |       |        |
| 2.78 | 0.7 | 10000 |  200  |    3.18   |    0.66   |    9.80  | 0.9998 |       |        |
| 2.78 | 0.8 | 10000 |  200  |    3.06   |    0.55   |    9.84  | 0.9997 |       |        |
| 2.78 | 0.9 | 10000 |  200  |    2.93   |    0.46   |    9.64  | 0.9997 |       |        |
| 2.78 | 1.0 | 10000 |  200  |    2.93   |    0.39   |   10.40  | 0.9997 |       |        |
| 2.78 | 1.1 | 10000 |  200  |    2.93   |    0.33   |   10.35  | 0.9993 |       |        |
| 2.78 | 1.2 | 10000 |  200  |    2.85   |    0.30   |   10.82  | 0.9995 |       |        |
| 2.78 | 1.3 | 10000 |  200  |    2.84   |    0.25   |   11.14  | 0.9996 |       |        |
| 2.78 | 1.4 | 10000 |  200  |    2.79   |    0.22   |   11.52  | 0.9994 |       |        |
| 2.78 | 1.5 | 10000 |  200  |    2.70   |    0.19   |   11.63  | 0.9993 |       |        |
| 3.10 | 1.0 | 32500 |  200  |    2.65   |    0.58   |    8.61  | 0.9999 |       |        |
| 3.10 | 1.1 | 30000 |  200  |    2.62   |    0.55   |    7.99  | 0.9998 |       |        |
| 3.10 | 1.2 | 27500 |  200  |    2.56   |    0.33   |    6.06  | 0.9980 |  5000 | 0.9994 |
| 3.51 | 0.5 | 35000 |  900  |    2.58   |    0.75   |   13.34  | 0.9993 |       |        |
| 3.51 | 1.0 | 48502 |  200  |    2.58   |    0.52   |    6.82  | 0.9997 |       |        |
| 3.51 | 1.3 | 25000 |  200  |    2.51   |    0.38   |    6.05  | 0.9989 |  8000 | 0.9990 |
| 5.00 | 0.5 | 22500 | 1000  |    2.53   |    0.75   |   18.15  | 0.9996 |       |        |
| 5.00 | 1.0 | 20000 |  400  |    2.55   |    0.67   |    5.78  | 0.9995 |       |        |
| 5.00 | 1.3 | 17500 |  200  |    2.51   |    0.50   |    4.22  | 0.9995 |       |        |
+------+-----+-------+-------+-----------+-----------+----------+--------+-------+--------+
'''

ver_str = '''
+------+-----+--------+-------+-----------+-----------+----------+--------+-------+--------+
|  E   | %T  | L_max  | L_min | mu_S*10^8 | mu_L*10^8 |   gamma  |  chi^2 | L'max | chi^2' |
|(V/cm)|     |  (bp)  | (bp)  |(m^2/V.sec)|(m^2/V.sec)|   (kbp)  |        | (bp)  |        |
+------+-----+--------+-------+-----------+-----------+----------+--------+-------+--------+
| 0.62 | 0.4 |  48502 | 1000  |    2.67   |    0.21   |  52.799  | 0.9993 |       |        |
| 0.93 | 0.4 | 194000 | 1000  |    2.54   |    0.34   |  25.304  | 0.9992 |       |        |
| 1.24 | 0.4 |  48502 |  200  |    3.67   |    0.81   |  14.922  | 0.9997 |       |        |
| 1.55 | 0.4 | 194000 |  200  |    3.18   |    0.77   |  14.488  | 0.9992 |       |        |
| 1.86 | 0.4 | 194000 |  200  |    3.12   |    0.78   |  12.603  | 0.9990 |       |        |
| 2.17 | 0.4 | 194000 |  200  |    3.07   |    0.89   |  11.911  | 0.9971 | 17500 | 0.9992 |
| 2.48 | 0.4 | 194000 |  200  |    3.13   |    0.90   |  12.648  | 0.9979 | 15000 | 0.9991 |
| 3.10 | 0.4 | 194000 |  200  |    3.14   |    0.98   |   9.423  | 0.9964 | 12000 | 0.9991 |
| 4.97 | 0.4 | 194000 |  200  |    3.34   |    1.22   |   9.630  | 0.9983 |  8000 | 0.9990 |
| 6.21 | 0.4 | 194000 |  200  |    3.11   |    1.20   |   9.214  | 0.9959 |  4400 | 0.9993 |
| 0.62 | 0.7 |  48502 |  200  |    2.86   |  8.36E-06 | 7.32E+05 | 0.9973 |  2700 | 0.9990 |
| 0.93 | 0.7 | 194000 |  200  |    2.38   |    0.09   |  54.264  | 0.9968 | 25000 | 0.9990 |
| 1.24 | 0.7 |  48502 |  200  |    3.71   |    0.49   |  15.255  | 0.9993 |       |        |
| 1.55 | 0.7 | 194000 |  200  |    3.61   |    0.53   |  13.125  | 0.9994 |       |        |
| 1.86 | 0.7 |  47500 |  300  |    3.61   |    0.62   |   9.834  | 0.9997 |       |        |
| 2.17 | 0.7 | 194000 |  200  |    3.07   |    0.55   |  10.151  | 0.9998 |       |        |
| 2.48 | 0.7 | 194000 |  200  |    3.42   |    0.72   |   9.036  | 0.9997 |       |        |
| 3.10 | 0.7 | 194000 |  200  |    3.14   |    0.69   |   7.713  | 0.9996 |       |        |
| 4.97 | 0.7 | 194000 |  200  |    3.08   |    0.93   |   6.188  | 0.9984 | 15000 | 0.9990 |
| 6.21 | 0.7 | 194000 |  200  |    3.24   |    1.03   |   6.371  | 0.9987 | 10000 | 0.9991 |
| 0.62 | 1.0 |  48502 |  200  |    2.48   |  1.82E-14 | 1.83E+14 | 0.9938 |  2900 | 0.9990 |
| 0.93 | 1.0 | 194000 |  300  |    2.41   |  1.37E-13 | 2.33E+13 | 0.9947 |  2900 | 0.9990 |
| 1.24 | 1.0 |  48502 |  200  |    3.34   |    0.17   |  25.855  | 0.9974 | 14000 | 0.9990 |
| 1.55 | 1.0 |  47500 |  200  |    3.25   |    0.33   |  12.773  | 0.9977 | 14000 | 0.9990 |
| 1.86 | 1.0 |  47500 |  400  |    3.69   |    0.47   |   8.502  | 0.9984 | 10000 | 0.9991 |
| 2.17 | 1.0 | 194000 |  200  |    2.87   |    0.38   |   9.372  | 0.9989 | 15000 | 0.9990 |
| 2.48 | 1.0 | 194000 |  200  |    3.39   |    0.52   |   7.209  | 0.9990 |       |        |
| 3.10 | 1.0 |  19400 |  300  |    3.36   |    0.61   |   5.852  | 0.9994 |       |        |
| 4.97 | 1.0 |  48502 |  200  |    3.04   |    0.77   |   4.749  | 0.9989 | 48502 | 0.9991 |
| 6.21 | 1.0 | 194000 |  200  |    3.13   |    0.88   |   4.417  | 0.9975 | 12500 | 0.9991 |
| 0.62 | 1.3 |  48502 |  200  |    2.12   |  1.87E-10 | 1.11E+10 | 0.9904 |  1800 | 0.9991 |
| 0.93 | 1.3 | 194000 |  300  |    1.96   |  3.80E-06 | 6.10E+05 | 0.9928 |  2600 | 0.9992 |
| 1.24 | 1.3 |  48502 |  300  |    3.32   |    0.02   | 179.189  | 0.9967 |  2600 | 0.9991 |
| 1.55 | 1.3 | 194000 |  200  |    3.47   |    0.27   |  11.920  | 0.9958 |  9000 | 0.9990 |
| 1.86 | 1.3 |  47500 |  400  |    3.97   |    0.36   |   8.594  | 0.9970 |  7000 | 0.9991 |
| 2.17 | 1.3 | 194000 |  200  |    2.76   |    0.21   |  12.412  | 0.9966 | 10000 | 0.9990 |
| 2.48 | 1.3 | 194000 |  200  |    3.26   |    0.45   |   7.464  | 0.9985 | 11000 | 0.9990 |
| 3.10 | 1.3 |  47500 |  200  |    3.37   |    0.50   |   5.159  | 0.9984 |  6000 | 0.9992 |
| 4.97 | 1.3 |  48502 |  200  |    2.68   |    0.49   |   4.048  | 0.9983 |  4000 | 0.9993 |
| 6.21 | 1.3 | 194000 |  200  |    2.70   |    0.59   |   3.555  | 0.9991 |       |        |
+------+-----+--------+-------+-----------+-----------+----------+--------+-------+--------+
'''

# Strings of data as text files
data_as_file = {'horizontal':
                BytesIO(hor_str.replace('\n|', '\n').replace('|\n', '\n').encode()),
                'vertical':
                BytesIO(ver_str.replace('\n|', '\n').replace('|\n', '\n').encode())
                }

# Load data into numpy arrays
datasets = {}
for name in data_as_file:
    datasets[name] = {}
    data_source = data_as_file[name]
    temp_dset = np.genfromtxt(data_source, delimiter='|', dtype=None,
                              skip_header=5, skip_footer=1,
                              usecols=(0, 1, 4, 5, 6),
                              names=('E', 'T', 'muS', 'muL', 'gamma'))
    datasets[name]['E'] = temp_dset['E'] * ureg('V/cm')
    datasets[name]['T'] = temp_dset['T'] * ureg('(g/(100 mL))*100')
    datasets[name]['muS'] = temp_dset['muS'] * ureg('1.0E-8 m**2/(V*s)')
    datasets[name]['muL'] = temp_dset['muL'] * ureg('1.0E-8 m**2/(V*s)')
    datasets[name]['gamma'] = temp_dset['gamma'] * ureg('kbp')
del hor_str, ver_str, data_as_file, data_source, temp_dset


# vWBR equation
def vWBR(muS, muL, gamma):
    """vWBR equation"""
    alpha = 1/muL - 1/muS
    beta = 1/muS
    return lambda L: 1/(beta + alpha * (1 - np.exp(-L/gamma)))

# Mobility function: mu(L) = f(muS, muL, gamma)
mu_funcs = {}
for name in datasets:
    mu_funcs[name] = vWBR(datasets[name]['muS'].to('cm**2/V/s'),
                          datasets[name]['muL'].to('cm**2/V/s'),
                          datasets[name]['gamma'].to('bp')
                          )
del name

# Constants
kB = (1 * ureg.boltzmann_constant).to('m**2 * kg / s**2 / K')  # Boltzmann constant
lp = 50 * ureg('nm')  # persistence length of dsDNA (nm)
l = 2 * lp            # Kuhn length (nm)
b = 0.34 * ureg('nm/bp')  # curvilinear length dsDNA (nm/bp)
e = (1 * ureg.e).to('A*s')  # elementary charge (1.602176565E-19 A.s)
qeff = e/Q_(7, 'bp')  # effective charge per dsDNA base pair (A.s/bp)
constants = {'kB': kB, 'lp': lp, 'l': l, 'b': b, 'qeff': qeff}

# mobility = distance/(time*field)
runtime = lambda distance, mobility, field: distance/(mobility*field)

rundistance = lambda time, mobility, field: time*mobility*field

# Intrinsic band broadening as function of the diffusion coefficient and time
bandbroadening = lambda D, time: np.sqrt(2*D*time)

pore_size = lambda gamma, muL, mu0, lp, b: (gamma*muL*lp*b/mu0)**(1/2)

pore_size_fit = lambda C: 143*ureg('nm*g**0.59/mL**0.59')*C**(-0.59)

radius_gyration = lambda L, lp: (lp*L/3*(1-lp/L+lp/L*np.exp(-L/lp)))**(1/2)

H2Oviscosity = lambda T: 2.414E-5*ureg('kg/m/s')*10**(247.8*ureg.K/(T-140*ureg.K))  # (Pa.s)=(kg/(m.s)) accurate to within 2.5% from 0 °C to 370 °C

contour_length = lambda Nbp, b: Nbp*b

reduced_field = lambda eta, a, mu0, E, kB, T: eta*a**2*mu0*E/(kB*T)

reduced_field_Kuhn = lambda eta, l, mu0, E, kB, T: eta*l**2*mu0*E/(kB*T)

# Diffusion coefficient of a blob
Dblob = lambda kB, T, eta, a: kB*T/(eta*a)

# Diffusion coefficient of a Kuhn segment
DKuhn = lambda kB, T, eta, l: kB*T/(eta*l)

# Relations between basepairs (Nbp), Kuhn segments (NKuhn) and blobs (N)
Nbp_to_NKuhn = lambda Nbp, b, l: Nbp*b/l  # number of Kuhn segments (~= Nbp/300)
NKuhn_to_Nbp = lambda NKuhn, b, l: NKuhn*l/b  # number of base pairs (bp)
NKuhn_to_N = lambda NKuhn, l, a: NKuhn*(l/a)**2  # number of occupied pores
N_to_NKuhn = lambda N, a, l: N*(a/l)**2  # number of Kuhn segments
N_to_Nbp = lambda N, a, b, l: N*(l/b)*(a/l)**2  # number of base pairs (bp)
Nbp_to_N = lambda Nbp, a, b, l: Nbp*(b/l)*(l/a)**2  # number of occupied pores

# Individual diffusion regimes
reptation_equilibrium = lambda Dblob, N: Dblob/N**2
reptation_accelerated = lambda Dblob, epsilon, N: Dblob*epsilon*N**(-1/2)
reptation_plateau = lambda Dblob, epsilon: Dblob*epsilon**(3/2)
free_solution = lambda kB, T, eta, Rh: kB*T/(6*np.pi*eta*Rh)
Zimm_g = lambda Nbp, DRouse, qeff, mu0, kB, T: DRouse*Nbp*qeff/(mu0*kB*T)
Ogston_Zimm = lambda D0, g: D0 * g
Ogston_Rouse = lambda Nbp, kB, T, a, eta, b, l: kB*T*a**3/(eta*b**2*l**2*Nbp**2)

# Diffusion regime frontiers (in number of occupied pores)
Zimm_Rouse = lambda x0, args: (
    Nbp_to_N(fsolve(diff_Zimm_Rouse, x0, args)[0] * ureg.bp,
             args[5], args[6], args[7]))
equil_accel = lambda epsilon: epsilon**(-2/3)
accel_plateau = lambda epsilon: epsilon**(-1)


def diff_Zimm_Rouse(Nbp, args):
    kB, T, qeff, eta, mu0, a, b, l, lp = args
    Nbp = Q_(Nbp[0], 'bp')
    L = contour_length(Nbp, b)
    Rg = radius_gyration(L, lp)
    D0 = free_solution(kB, T, eta, Rg)
    DRouse = Ogston_Rouse(Nbp, kB, T, a, eta, b, l)
    g = Zimm_g(Nbp, DRouse, qeff, mu0, kB, T)
    g = g.to_base_units()
    DZimm = Ogston_Zimm(D0, g)
#    print 'Nbp =\t', Nbp
#    print 'kB =\t', kB
#    print 'T =\t', T
#    print 'qeff =\t', qeff
#    print 'eta =\t', eta
#    print 'mu0 =\t', mu0
#    print 'a =\t', a
#    print 'b =\t', b
#    print 'l =\t', l
#    print 'lp =\t', lp
#    print 'L =\t', L
#    print 'Rg =\t', Rg
#    print 'D0 =\t', D0
#    print 'DRouse =\t', DRouse
#    print 'g =\t', g
#    print 'DZimm =\t', DZimm
#    print 'DZimm - DRouse =\t', DZimm - DRouse
#    print 70*'#'
    return DZimm - DRouse


# Diffusion coefficient
def diffusion_coefficient(Nbp, N_lim1, N_lim2, N_lim3, args):
    kB, T, qeff, eta, mu0, a, b, l, lp = args
    N = Nbp_to_N(Nbp, a, b, l)
    if N < N_lim3:
        # Ogston-Zimm
        L = contour_length(Nbp, b)
        Rg = radius_gyration(L, lp)
        D0 = free_solution(kB, T, eta, Rg)
        DRouse = Ogston_Rouse(Nbp, kB, T, a, eta, b, l)
        g = Zimm_g(Nbp, DRouse, qeff, mu0, kB, T)
        D = Ogston_Zimm(D0, g)
    elif N < N_lim2:
        # Rouse/Reptation-equilibrium
        D = Db/N**2
    elif N > N_lim1:
        # Reptation-plateau (reptation with orientation)
        D = Db*epsilon**(3/2)
    else:
        # Accelerated-reptation
        D = Db*epsilon*N**(-1/2)
    return D


#def rand_str(sample, length):
#    """
#    Return a random string of given length built from the chars in sample.
#    """
#    rnd_str = ''
#    for i in xrange(length):
#        r = randint(0, len(sample)-1)
#        rnd_str += sample[r]
#    return rnd_str


def random_Dseqs(sizes):
    """
    Return a list of pydna Dseqs of given sizes and random sequences.
    """
    sample = []
    for size in sizes:
        seq = Dseq("n"*size) #Dseq(rand_str('actg', size))
        sample.append(seq)
    return sample



class Fakeseq(object):

    def __init__(self, l, n=10E-12):
        self._length = l
        self.n = n

    def __len__(self):
        return self._length


def gen_sample(sizes, quantities):
    """Return list of pydna Dseqrecords of given size and quantity.

    If a single quantity is given it is divided by the DNA fragments
    in proportion to their length.

    Parameters
    ----------

    sizes : iterable of pint.unit.Quantity objects or ints
        List of DNA sizes in base pairs (bp).

    quantities : iterable of pint.unit.Quantity objects, floats or ints
        List of DNA weights in nanograms (ng).
        If a single quantity is given (pint.unit.Quantity object, float
        or int) it is divided linearly by the DNA fragments length.

    Examples
    --------

    Direct quantity assignment without declared units.

    >>> sizes = [3000, 500, 1500]  # bp
    >>> qts = [70.0, 11.7, 35.0]  # ng
    >>> sample = gen_sample(sizes, qts)
    >>> sample
    [Dseqrecord(-3000), Dseqrecord(-500), Dseqrecord(-1500)]
    >>> sample[0].m()  # g
    7.0000000000000005e-08
    >>> Q_([dna.m() for dna in sample], 'g').to('ng')
    <Quantity([ 70.   11.7  35. ], 'nanogram')>
    >>> Q_([dna.n for dna in sample], 'mol').to('pmol')
    <Quantity([ 0.03776682  0.03786665  0.03776521], 'picomole')>

    Direct quantity assignment with declared units.

    >>> sizes = Q_([3000, 500, 1500], 'bp')
    >>> qts = Q_([70.0, 11.7, 35.0],  'ng')
    >>> sample = gen_sample(sizes, qts)
    >>> sample
    [Dseqrecord(-3000), Dseqrecord(-500), Dseqrecord(-1500)]
    >>> Q_([dna.m() for dna in sample], 'g').to('ng')
    <Quantity([ 70.   11.7  35. ], 'nanogram')>
    >>> Q_([dna.n for dna in sample], 'mol').to('pmol')
    <Quantity([ 0.03776682  0.03786665  0.03776521], 'picomole')>

    Assignment of total quantity (with declared units).

    >>> sample = gen_sample(Q_([3000, 500, 1500], 'bp'), Q_(200, 'ng'))
    >>> sample
    [Dseqrecord(-3000), Dseqrecord(-500), Dseqrecord(-1500)]
    >>> Q_([dna.m() for dna in sample], 'g').to('ng')
    <Quantity([ 120.   20.   60.], 'nanogram')>
    >>> Q_([dna.n for dna in sample], 'mol').to('pmol')
    <Quantity([ 0.06474311  0.06472932  0.06474035], 'picomole')>

    """
    frags = random_Dseqs([int(s.magnitude) for s in to_units(sizes, 'bp')])
    quantities = to_units(quantities, 'ng')
    quantities = quantities.to('g').magnitude
    if not hasattr(quantities, '__iter__'):
        quantities = lin_div_Qty(frags, quantities, criteria=len)
    return [Dseqrecord(seq, n=quantities[i]/seq.mw()) for i, seq in
            enumerate(frags)]


def weight_standard_sample(key, qty=Q_(500, 'ng')):
    assert key in weight_standards, ("Key not recognized. Choose from: %s"
                                     % list(weight_standards.keys()))
    qty = to_units(qty, Vars['quantities']['units'], var_name='qty')
    sizes = weight_standards[key]['sizes']
    fracs = weight_standards[key]['percent']
    quantities = qty * fracs
    return gen_sample(sizes, quantities)


def logspace_int(minimum, maximum, divs):
    space = np.logspace(np.log10(minimum), np.log10(maximum), divs)
    return np.array([int(round(val, 0)) for val in space])


def flatten(List):
    if List == []:
        return List
    flatL = []
    for elem in List:
        if not isinstance(elem, Q_) and hasattr(elem, '__iter__'):
            flatE = flatten(elem)
            [flatL.append(E) for E in flatE]
        else:
            flatL.append(elem)
    return flatL

# Gaussian function
Gaussian = lambda x, hgt, ctr, dev: hgt*np.exp(-(x-ctr)**2/(2*dev**2))
Gauss_hgt = lambda auc, dev: auc/(dev*np.sqrt(2*np.pi))
Gauss_dev = lambda FWHM: FWHM/(2*np.sqrt(2*np.log(2)))
# Gauss_dev = lambda FWTM: FWTM/(2*np.sqrt(2*np.log(10)))
Gauss_FWHM = lambda FWTM: FWTM * np.sqrt(2*np.log(2))/np.sqrt(2*np.log(10))


def _to_units(quantity, units, var_name=None):
    """Asserts that the quantity has the proper dimensions
    (inferred from the default units) if the quantity is an instance of
    pint.unit.Quantity or assigns the default units if it's not.
    """
    if isinstance(quantity, Q_):
        try:
            quantity = quantity.to(units)
        except TypeError as error:
            quantity = [q.to(units) for q in quantity]
        except Exception as error:
            if var_name:
                error.extra_msg = " for variable '%s'" % var_name
            raise error
    else:
        quantity = Q_(quantity, units)
    return quantity


def to_units(quantity, units, var_name=None):
    """Asserts that the quantity has the proper dimensions
    (inferred from the default units) if the quantity is an instance of
    pint.unit.Quantity or assigns the default units if it's not.
    """
    if (not isinstance(quantity, Q_) and hasattr(quantity, '__iter__') and
            len(quantity) > 0 and
            sum([isinstance(q, Q_) for q in flatten(quantity)]) > 0):
        temp_qty = [to_units(q, units, var_name) for q in quantity]
        quantity = Q_([q.magnitude for q in temp_qty], units)
    else:
        quantity = _to_units(quantity, units, var_name)
    return quantity


def dim_or_units(quantity, reference):
    """If <quantity> is not an instance of <Quantity>, instantiate a <Quantity>
    object with <quantity> as magnitude and as <reference.units> as units.
    If <quantity> is an instance of <Quantity>, check whether it has the same
    dimensionality as <reference>.
    """
    if not isinstance(quantity, Q_):
        quantity = to_units(quantity, reference.units)
    else:
        assert quantity.dimensionality == reference.dimensionality, (
            "Dimension mismatch: (%s) != (%s)" % (quantity.dimensionality,
                                                  reference.dimensionality))
    return quantity

def assign_quantitiesB(samples, maxdef=Q_(150, 'ng')):
    """
    Assigns quantities (masses in nanograms) to the DNA fragments without
    corresponding quantity assuming a linear relationship between the DNA
    length (in basepairs) and its mass. As if the fragments originated in
    a restriction procedure.
    For each sample takes the maximum quantity (either from the other samples
    or from the default) and assigns it to the fragment with greater length.
    """
    quantities = []
    units = Vars['quantities']['units']
    maxQ = Q_(0, units)
    # Preprocessing and straightforward cases
    for sample in samples:
        sample_qts = []
        for qty in sample.quantities:
            if not np.isnan(qty.magnitude) and qty.magnitude is not None:
                sample_qts.append(qty)
                if qty > maxQ:
                    maxQ = qty
        quantities.append(sample_qts)
    # Quantity assignment - missing values
    if maxQ.magnitude == 0:
        maxQ = to_units(maxdef, units, 'maxdef')
    maxQ = maxQ.magnitude
    for i, sample in enumerate(samples):
        if quantities[i] == []:
            # Linearly extrapolates each DNA fragment's quantity taking as
            # reference the maximum quantity registered (or the default)
            sizes = [len(dna) for dna in sample.solutes]
            maxL = max(sizes)
            quantities[i] = [size*maxQ/maxL for size in sizes]
    quantities = to_units(quantities, units, 'quantities')
    return quantities


def lin_div_Qty(sample, quantity, criteria=len):
    """
    Linearly divides a quantity by the elements of sample considering a
    criteria. Criteria must by a function that returns a number upon being
    applied to each element of sample.
    """
    sizes = [criteria(dna) for dna in sample]
    return [size*quantity/sum(sizes) for size in sizes]


def size_to_mobility(dna_len, field, percentage,
                     mu_func=mu_funcs['vertical'],
                     dataset=datasets['vertical'],
                     method='linear',
                     replNANs=True):
    mobility = griddata((dataset['E'], dataset['T']), mu_func(dna_len),
                        (field, percentage), method)
    if replNANs and np.isnan(mobility):
        # Replace NANs by 'nearest' interpolation
        print("WARNING: NAN replaced by 'nearest' interpolation.")  # #### ! ###
        mobility = griddata((dataset['E'], dataset['T']), mu_func(dna_len),
                            (field, percentage), method='nearest')
    return mobility.item()


def vWBRfit(field, percentage, DNAvals=np.linspace(100, 50000, 100),
            dataset=datasets['vertical'], mu_func=mu_funcs['vertical'],
            method='linear', replNANs=True, plot=True):
    mu = np.zeros(len(DNAvals))
    vWBR = lambda L, muS, muL, gamma: (1/muS+(1/muL-1/muS)*(1-np.exp(-L/gamma)))**-1
    for i, Li in enumerate(DNAvals):
        mu[i] = size_to_mobility(Li, field, percentage, mu_func,
                                 dataset, method, replNANs)

    def residuals(pars, L, mu):
        return mu - vWBR(L, *pars)
    muS0 = 3.5E-4  # cm^2/(V.sec)  ############################################
    muL0 = 1.0E-4  # cm^2/(V.sec)  ############################################
    gamma0 = 8000  # bp            ############################################
    pars, cov, infodict, mesg, ier = leastsq(residuals, [muS0, muL0, gamma0],
                                             args=(DNAvals, mu),
                                             full_output=True)
    muS, muL, gamma = pars
    # print ('E=%.2f V/cm, T=%.1f %%, muS=%.3e, muL=%.3e cm^2/(V.s), '
    #        'gamma=%s bp' % (field, percentage, muS, muL, gamma))
    if plot:
        DNAmin = min(DNAvals)
        DNAmax = max(DNAvals)
        fig = plt.figure()
        ax = fig.add_subplot(111)
        ax.scatter(DNAvals, mu*1E4, color='blue')
        ax.plot(DNAvals, vWBR(DNAvals, muS, muL, gamma)*1E4, label='fit',
                linestyle='--', color='red')
        ax.set_xlim(DNAmin-0.1*DNAmin, DNAmax+0.1*DNAmax)
        ax.set_ylim((min(mu)-0.1*min(mu))*1E4, (max(mu)+0.1*max(mu))*1E4)
        ax.set_xscale('log')
        ax.xaxis.set_major_formatter(mtick.FormatStrFormatter('%d'))
        ax.tick_params(which='both', top='off', right='off')
        ax.set_xlabel('$\mathrm{DNA\,length\,(bp)}$', fontsize=14)
        ax.set_ylabel(r'$\mu\times{10^{8}}\,(\mathrm{m^{2}/V\cdot s})$',
                      fontsize=14)
        ax.set_title('$\mu_S=%.2e,\,\mu_L=%.2e\,\mathrm{cm^2/(V.s)},\,'
                     '\gamma=%d \mathrm{bp}$' % (muS, muL, gamma))
        ax.legend().draggable()
        plt.show()
    return pars, cov, infodict, mesg, ier


def ferguson_to_mu0(field, Tvals, DNAvals, dataset, mu_func,
                    adjmethod='linear', replNANs=True, plot=True):
    """
    This function extrapolates the free solution mobility (mu0)
    for a specified electric field intensity (field), via Ferguson plot
    (ln(mobility) vs. %agarose).

    Mobiliy calculation method:
    [E,T,muS,muL,gamma] -> [E,T,mu(L)] -(L*)-> [E,T,mu] -(E*,T*,interp.)-> mu*
    """
    # Mobility dependence on size (mu(L)) for each agarose percentage (Ti)
    ln_mu_LxT = []
    for Lj in DNAvals:
        ln_mu_T = []
        for Ti in Tvals:
            mu = size_to_mobility(Lj, field, Ti, mu_func,
                                  dataset, adjmethod, replNANs)
            ln_mu_T.append(np.log(mu))
        ln_mu_LxT.append(ln_mu_T)
    ln_mu_LxT = np.array(ln_mu_LxT)
    # Linear regression for each DNA size
    lregr_stats = []
    exclude = []
    for l in range(len(DNAvals)):
        not_nan = np.logical_not(np.isnan(ln_mu_LxT[l]))
        if sum(not_nan) > 1:
            # (enough points for linear regression)
            gradient, intercept, r_value, p_value, std_err =\
                      stats.linregress(Tvals[not_nan], ln_mu_LxT[l][not_nan])
            lregr_stats.append((gradient, intercept, r_value, p_value,
                                std_err))
            exclude.append(False)
        else:
            exclude.append(True)
    exclude = np.array(exclude)
    DNAvals = DNAvals[~exclude]
    ln_mu_LxT = ln_mu_LxT[~exclude]
    if len(lregr_stats) > 0:
        # Free solution mobility determination
        ln_mu0 = np.mean([row[1] for row in lregr_stats])  # mean of intercepts
        mu0 = np.exp(ln_mu0)  # cm^2/(V.seg)
    else:
        mu0 = None
    if plot and len(ln_mu_LxT) > 0:
        # Ferguson Plot (ln(mu) vs. %T) --> mu0
        regline = lambda m, b, x: m*x+b  # Line function (for the plot)
        colors = cm.rainbow(np.linspace(0, 1, len(DNAvals)))
        Tvals0 = np.concatenate([[0], Tvals])
        fig = plt.figure()
        ax = fig.add_subplot(111)
        for l in range(len(DNAvals)):
            ax.scatter(Tvals, ln_mu_LxT[l], label=DNAvals[l],
                       color=colors[l])
            m = lregr_stats[l][0]
            b = lregr_stats[l][1]
            ax.plot(Tvals0, [regline(m, b, t) for t in Tvals0],
                    color=colors[l])
        ax.set_xlim(0)
        # ax.set_ylim(-10, -7.5)
        ax.legend(title='$\mathrm{DNA size (bp)}$',
                  prop={'size': 10}).draggable()
        ax.tick_params(which='both', top='off', right='off')
        ax.set_xlabel('$\%\,agarose$', fontsize=14)
        ax.set_ylabel('$\mathrm{ln(mobility\,[cm^{2}/V sec])}$',
                      fontsize=14)
        ax.set_title('$\mathrm{Ferguson\,plot}$'+'\n'+\
                     '$\mathrm{ln(mobility)\,vs.\,\%\,agarose\,}$'+\
                     '$\mathrm{(field=%.3f\,V/cm)}$' %field.magnitude)
        plt.show()
    return mu0  # cm^2/(V.seg)


def gelplot_imshow(distances, bandwidths, intensities, lanes, names,
                   gel_len, wellx, welly, wellsep, res, cursor_ovr,
                   back_col, band_col, well_col, noise, Itol, detectlim, title,
                   FWTM, show=True):
    nlanes = len(lanes)
    gel_width = sum(wellx) + (nlanes+1)*wellsep  # cm
    res = res.to('px/cm')
    pxl_x = int(round(gel_width * res))
    pxl_y = int(round(gel_len * res))
    lane_centers = [(l+1)*wellsep + sum(wellx[:l]) + 0.5*wellx[l]
                    for l in range(nlanes)]
    rgb_arr = np.zeros(shape=(pxl_y, pxl_x, 3), dtype=np.float32)
    bandlengths = wellx
    bands_pxlXYmid = []
    # Paint the bands
    for i in range(nlanes):
        distXmid = lane_centers[i]
        pxlXmid = int(round(distXmid * res))
        bandlength = bandlengths[i]
        from_x = int(round((distXmid - bandlength/2.0) * res))
        to_x = int(round((distXmid + bandlength/2.0) * res))
        bands_pxlXYmid.append([])
        for j in range(len(lanes[i])):
            distYmid = distances[i][j]
            pxlYmid = int(round(distYmid * res))
            bands_pxlXYmid[i].append((pxlXmid, pxlYmid))
            bandwidth = bandwidths[i][j]  # w=FWHM or w=FWTM ???
            if FWTM:
                FWHM = Gauss_FWHM(bandwidth)
            else:
                FWHM = bandwidth
            std_dev = Gauss_dev(FWHM)
            maxI = intensities[i][j]
            midI = Gaussian(distYmid, maxI, distYmid, std_dev)
            if pxlYmid < len(rgb_arr):  # band within gel frontiers
                rgb_arr[pxlYmid, from_x:to_x] += midI
            bckwdYstop = False if pxlYmid > 0 else True
            forwdYstop = False if pxlYmid < len(rgb_arr)-1 else True
            pxlYbck = pxlYmid-1
            pxlYfor = pxlYmid+1
            while not bckwdYstop or not forwdYstop:
                if not bckwdYstop:
                    distYbck = Q_(pxlYbck, 'px')/res
                    bckYI = Gaussian(distYbck, maxI, distYmid, std_dev)
                    if pxlYbck < len(rgb_arr):
                        rgb_arr[pxlYbck, from_x:to_x] += bckYI
                    pxlYbck -= 1
                    if bckYI <= Itol or pxlYbck == -1:
                        bckwdYstop = True
                if not forwdYstop:
                    distYfor = Q_(pxlYfor, 'px')/res
                    forYI = Gaussian(distYfor, maxI, distYmid, std_dev)
                    rgb_arr[pxlYfor, from_x:to_x] += forYI
                    pxlYfor += 1
                    if forYI <= Itol or pxlYfor == pxl_y:
                        forwdYstop = True
    # Background color
    if noise is None or noise <= 0:
        rgb_arr += back_col
    else:
        bckg = np.random.normal(back_col, noise,
                                (len(rgb_arr), len(rgb_arr[0])))
        rgb_arr += bckg[:, :, np.newaxis]
    # Saturation
    rgb_arr[rgb_arr > 1] = 1
    rgb_arr[rgb_arr < 0] = 0
    # bands_arr = np.ma.masked_where(rgb_arr == back_col, rgb_arr)  ###########
    bands_arr = rgb_arr
    # Plot
    gel_len = gel_len.magnitude
    gel_width = gel_width.magnitude
    wellx = wellx.magnitude
    welly = welly.magnitude
    wellsep = wellsep.magnitude
    lane_centers = [c.magnitude for c in lane_centers]
    bandlengths = bandlengths.magnitude
    bandwidths = [[bw.magnitude for bw in bwlane] for bwlane in bandwidths]
    fig = plt.figure()
    ax1 = fig.add_subplot(111, axisbg=str(back_col))
    ax1.xaxis.tick_top()
    ax1.yaxis.set_ticks_position('left')
    ax1.spines['left'].set_position(('outward', 8))
    ax1.spines['left'].set_bounds(0, gel_len)
    ax1.spines['right'].set_visible(False)
    ax1.spines['bottom'].set_visible(False)
    ax1.spines['top'].set_visible(False)
    ax1.spines['right'].set_color(str(back_col))
    ax1.spines['bottom'].set_color(str(back_col))
    ax1.xaxis.set_label_position('top')
    plt.xticks(lane_centers, names)
    majorLocator = FixedLocator(list(range(int(gel_len+1))))
    minorLocator = FixedLocator([j/10.0 for k in
                                 range(0, int(gel_len+1)*10, 10)
                                 for j in range(1+k, 10+k, 1)])
    ax1.yaxis.set_major_locator(majorLocator)
    ax1.yaxis.set_minor_locator(minorLocator)
    ax1.tick_params(axis='x', which='both', top='off')
    # Gel image
    bands_plt = ax1.imshow(bands_arr, extent=[0, gel_width, gel_len, 0],
                           interpolation='none')
    # Draw wells
    for i in range(nlanes):
        ctr = lane_centers[i]
        wx = wellx[i]
        wy = welly[i]
        ax1.fill_between(x=[ctr-wx/2, ctr+wx/2], y1=[0, 0],
                         y2=[-wy, -wy], color=str(well_col))
    # Invisible rectangles overlapping the bands for datacursor to detect
    bands = []
    for i in range(nlanes):
        bandlength = bandlengths[i]
        center = lane_centers[i]
        x = center - bandlength/2.0
        for j in range(len(lanes[i])):
            dna_frag = lanes[i][j]
            bandwidth = bandwidths[i][j]
            dist = distances[i][j].magnitude
            y = dist - bandwidth/2.0
            pxlX, pxlY = bands_pxlXYmid[i][j]
            band_midI = bands_arr[pxlY, pxlX][0]
            alpha = 0 if abs(band_midI - back_col) >= detectlim else 0.4
            band = plt.Rectangle((x, y), bandlength, bandwidth,
                                 fc='none', ec='w', ls=':', alpha=alpha,
                                 label='{} bp'.format(len(dna_frag)))
            plt.gca().add_patch(band)
            bands.append(band)
    plt.ylim(gel_len, -max(welly))
    xlim = sum(wellx) + (nlanes+1)*wellsep
    plt.xlim(0, xlim)
    plt.ylabel('Distance (cm)')
    plt.xlabel('Lanes')
    bbox_args = dict(boxstyle='round,pad=0.6', fc='none')
    an1 = plt.annotate(title, xy=(0, 0),
                       xytext=(xlim+0.4, (gel_len+max(welly))/2.0),
                       va="center", bbox=bbox_args)
    an1.draggable()
    plt.gca().set_aspect('equal', adjustable='box')
    cursor_args = dict(display='multiple',
                       draggable=True,
                       hover=False,
                       bbox=dict(fc='white'),
                       arrowprops=dict(arrowstyle='simple',
                                       fc='white', alpha=0.5),
                       xytext=(15, -15),
                       formatter='{label}'.format)
    if cursor_ovr:
        for key in cursor_ovr:
            cursor_args[key] = cursor_ovr[key]
    if cursor_args['hover'] == True:
        cursor_args['display'] = 'single'
    datacursor(bands, **cursor_args)
    # fig.savefig('example.png', dpi=300)
    if show:
        plt.show()
    return plt


class Gel:
    """Gel object for DNA slab-gel electrophoresis simulation.

    Class designed to store information regarding an electrophoresis
    experimental setup. Includes gel's and well's dimensions,
    DNA samples loaded, agarose concentration, electric field
    intensity and temperature.

    Parameters
    ----------

    samples : list of lists of pydna.Dseqrecord objects
        List of samples with the DNA fragments to separate.
        Each sample corresponds to a different well.
        Accepts lists of pydna.Dseq objects and converts them to
        Dseqrecords with the default quantity (`n` parameter).

    names : list of str, optional
        List with the identifiers of the samples.
        Defaults to None, in which case the identifiers are of the form
        "lane i" where i is the index.

    percentgel : pint.unit.Quantity object, float or int, optional
        Agarose concentration in the gel.
        Defaults to Q_(1.0, '(g/(100 mL))*100').
        If a float or int is given assumes grams of agarose per milliliter
        of buffer.

    electrfield : pint.unit.Quantity object, float or int, optional
        Electric field intensity.
        Defaults to Q_(5.0, 'V/cm').
        If a float or int is given assumes Volts per centimeter.

    temperature : pint.unit.Quantity object, float or int, optional
        Absolute temperature.
        Defaults to Q_(295.15, 'K').
        If a float or int is given assumes Kelvin.
        The temperature is only considered in the calculation of the
        diffusional component of the band width.

    gel_len : pint.unit.Quantity object, float or int, optional
        Gel length (as measured from the bottom of the well in the
        direction of the DNA migration).
        Defaults to Q_(8, 'cm').
        If a float or int is given assumes centimeters.

    wellxy : iterable of pint.unit.Quantity object, float or int, optional
        Well's dimensions.
        Well's width (perpendicular to the migration direction) and
        well's height (migration direction).
        Defaults to Q_([7, 2], 'mm').
        If a float or int is given assumes millimeters.
        The well's width is merely used for aesthetic purposes.
        The well's height is used to compute the initial band width.

    wellsep : pint.unit.Quantity object, float or int, optional
        Separation between wells.
        Defaults to Q_(2, 'mm').
        Merelly for aestetic purposes.

    Notes
    -----
        * The DNA is diluted in the full volume of the well.
        * The previous implies that the injection size, which relates to
        the initial bandwidth, is assumed to be well height (welly).
        * The DNA electrophoretic mobility in the well is given by the free
        solution mobility and is equal for every fragment.

    """

    def __init__(self,
                 samples,                        # list of lists of Dseqrecords
                 names=None,
                 percentgel=Q_(1.0, '(g/(100 mL))*100'),  # agar/buffer
                 electrfield=Q_(5.0, 'V/cm'),
                 temperature=Q_(295.15, 'K'),
                 gel_len=Q_(8, 'cm'),
                 wellxy=Q_([7, 2], 'mm'),
                 wellsep=Q_(2, 'mm')
                 ):
        #self.samples = [[dna if isinstance(dna, Dseqrecord) else
        #                 Dseqrecord(dna) for dna in sample] for sample in
        #                samples]    # len(DNA) in bp

        self.samples = samples

        self.names = names if names else [str(i) for i in      #
                                          range(1, len(samples)+1)]  #
        self.percent = to_units(percentgel, '(g/(100 mL))*100', 'percentgel')
        self.field = to_units(electrfield, 'V/cm', 'electrfield')
        self.temperature = to_units(temperature, 'K', 'temperature')
        self.gel_len = to_units(gel_len, 'cm', 'gel_len')
        self.wellx = to_units(wellxy[0], 'mm', 'wellx')  # well width
        self.welly = to_units(wellxy[1], 'mm', 'welly')  # well height
        self.wellsep = to_units(wellsep, 'mm', 'wellsep')
        # Quantities
        # defaulQty = Q_(150,'ng')
        quantities = [[Q_(dna.m(), 'g') for dna in sampl] for sampl in
                      self.samples]
        self.quantities = to_units(quantities, 'ng', 'quantities')
        self.quantities
        self.runtime = np.nan                                      # ##########
        self.freesol_mob = None
        self.mobilities = []
        self.distances = []
        self.bandwidths0 = []
        self.bandwidthsI = []
        self.bandwidths = []
        self.intensities = []
        # exponential space of DNA sizes
        self.DNAspace_for_mu0 = logspace_int(100, 3000, 10)*ureg.bp
        self.DNAspace_for_vWBRfit = np.linspace(100, 50000, 100)*ureg.bp
        self.Tvals_for_mu0 = []
        self.H2Oviscosity = None
        self.accel_to_plateau = None
        self.equil_to_accel = None
        self.Zimm_to_Rouse = None
        self.poresize = None
        self.poresize_fit = None
        self.vWBR_muS = None
        self.vWBR_muL = None
        self.vWBR_gamma = None

    def set_field(self, electrfield):
        self.field = to_units(electrfield, 'V/cm', 'electrfield')

    def set_percentgel(self, percentgel):
        self.percent = to_units(percentgel, '(g/(100 mL))*100', 'percentgel')

    def set_temperature(self, temperature):
        self.temperature = to_units(temperature, 'K', 'temperature')

    def set_gelength(self, gel_len):
        self.gel_len = to_units(gel_len, 'cm', 'gel_len')

    def set_wellx(self, wellx):  # set wellxy ???
        self.wellx = to_units(wellx, 'mm', 'wellx')

    def set_welly(self, welly):
        self.welly = to_units(welly, 'mm', 'welly')

    def set_wellsep(self, wellsep):
        self.wellsep = to_units(wellsep, 'mm', 'wellsep')

    def set_DNAspace_for_mu0(self, DNA_space):
        self.DNAspace_for_mu0 = to_units(DNA_space, 'bp', 'DNA_space')

    def set_Tvals_for_mu0(self, Tvals):
        self.Tvals_for_mu0 = to_units(Tvals, '(g/(100 mL))*100', 'Tvals')

    def set_DNAspace_for_vWBRfit(self, DNA_space):
        self.DNAspace_for_vWBRfit = to_units(DNA_space, 'bp', 'DNA_space')

    def run(self,
            till_len=0.75,         # percent of gel_len
            till_time=None,        # hours
            exposure=0.5,          # [0-1]
            plot=True,
            res=Q_(500, 'px/in'),
            cursor_ovr=dict(hover=False),
            back_col=0.3,
            band_col=1,
            well_col=0.05,
            noise=0.015,
            detectlim=0.04,
            interpol='linear',     # 'cubic','nearest'
            dset_name='vertical',  # 'horizontal'
            replNANs=True          # replace NANs by 'nearest' interpolation
            ):
        """Run electrophoresis.

        Run the electrophoresis procedure until a specified time or until
        the quickest band reaches a specified gel length.
        If both conditions are given the most stringent will be respected.

        Parameters
        ----------

        till_len : float (0 to 1), optional
            Fraction of the gel length (measured from the well bottom) to
            serve as finish line.
            Defaults to 0.75.

        till_time : pint.unit.Quantity object, float or int, optional
            Time at which to stop the electrophoresis.
            Defaults to None.
            If float or int is given assumes hours.

        exposure : float (0 to 1)
            Fraction of signal saturation.
            If exposure is set to 0 every band's light intensity will be
            given by a perfect Gaussian curve. Wider bands with lower
            amounts of DNA might be hard to see.
            The closer to 1 the exposure the higher the saturation, which
            favors the weaker bands visualization.
            If exposure is set to 1 only the weakest band will be a
            Gaussian, all others will be saturated.
            Defaults to 0.5.

        plot : {True, False}, optional
            Whether to draw and return the gel picture or not.
            The electrophoresis data (such as migrated distances) will be
            stored in the Gel object either way.

        res : pint.unit.Quantity object, float or int, optional
            Resolution used to construct an array of light intensities
            corresponding to the gel picture.
            The dimensions of the intensities array are given by the gel's
            dimensions multiplied by the resolution.
            A higher resolution implies more calculations and might cause
            the method to become slow.
            A lower resolution might result in a very pixelated image.
            Defaults to Q_(500, 'px/in').
            If float or int is given assumes pixels per inch.
            This resolution won't necessarily convey to the final gel
            picture since the intensity array is processed by
            matplotlib.pyplot.imshow.

        cursor_ovr : dict, optional
            Key arguments to be passed to mpldatacursor.datacursor which
            provides interactive cursor functions to the resulting plot.
            Defaults to dict(hover=False).

        back_col : float or int, optional
            Background color (light intensity).
            Defaults to 0.3.
            Solid black (0) allows the maximum contrast.

        band_col : float or int, optional
            Band color (maximum light intensity).
            Defaults to 1.
            White (1) allows for maximum contrast.

        well_col : float or int, optional
            Well color (light intensity).
            Defaults to 0.05.

        noise : float or int, optional
            Standard deviation used to generate a Normal distribution of
            noise centered in the background color. This effect is purely
            aesthetic.
            Defaults to 0.015.

        detectlim : float, optional
            Minimal light intensity difference between the center of the band
            and the background color (back_col) below which the band is
            considered to be indistinguishable and a white doted outline is
            drawn around it.
            Defaults to 0.04.

        interpol : {'linear', 'cubic', 'nearest'}, optional
            Interpolation method. This is passed to
            scipy.interpolate.griddata for the interpolation of the
            vWBR's parameters from the experimental datasets
            (mu_S, mu_L, gamma = f(field, agarose concentration) [1-3]_.
            Defaults to 'linear' which is more conservative.
            'nearest' is not expected to provide good results.

        dset_name : {'vertical', 'horizontal'}, optional
            Dataset identifier (str). Identifies the dataset to use.
            Currently two datasets are available ('vertical' and
            'horizontal') [1-3]_.
            The names alude to the geometry of the experimental setup.
            The geometry however is not expected to cause significant
            differences on the results.

        replNANs : {True, False}, optional
            Whether to replace NANs (not a number) by 'nearest'
            interpolation. NANs will only be produced if the conditions
            of electric field intensity and agarose concentration go
            beyond the concave space provided by the dataset.

        References
        ----------
        .. [1] Van Winkle, D.H., Beheshti, A., Rill, R.L.: DNA
        electrophoresis in agarose gels: A simple relation describing the
        length dependence of mobility. ELECTROPHORESIS 23(1), 15–19 (2002)

        .. [2] Rill, R.L., Beheshti, A., Van Winkle, D.H.: DNA
        electrophoresis in agarose gels: Effects of field and gel
        concentration on the exponential dependence of reciprocal mobility
        on DNA length. ELECTROPHORESIS 23(16), 2710–2719 (2002)

        .. [3] Beheshti, A.: DNA Electrophoresis in th Agarose Gels: A New
        Mobility vs. DNA Length Dependence. Electronic Theses, Treatises and
        Dissertations (Paper 1207) (2002)

        """
        bandwidth = 2  # {0:'well_only', 1:'intrinsic_only', 2:'both'}
        Itol = 1E-5    # intensity tolerance
        FWTM = False   # bandwidth interpreted as FWTM instead of FWHM
        lanes = self.samples
        names = self.names
        field = self.field              # V/cm
        percentage = self.percent       # %agarose
        temperature = self.temperature  # K
        gel_len = self.gel_len          # cm
        wellx = self.wellx              # mm
        welly = self.welly              # mm
        wellsep = self.wellsep          # mm
        quantities = self.quantities    # ng
        dataset = datasets[dset_name]
        mu_func = mu_funcs[dset_name]
        DNAspace_mu0 = self.DNAspace_for_mu0
        DNAspace_vWBRfit = self.DNAspace_for_vWBRfit
        if self.Tvals_for_mu0 == []:
            self.Tvals_for_mu0 = Q_(np.unique(dataset['T']),
                                    dataset['T'].units).to('(g/(100 mL))*100')
        else:
            self.Tvals_for_mu0 = to_units(self.Tvals_for_mu0,
                                          '(g/(100 mL))*100', 'Tvals_for_mu0')
        Tvals = self.Tvals_for_mu0
        nlanes = len(lanes)
        exposure = 0 if exposure < 0 else 1 if exposure > 1 else exposure  # ##
        if not hasattr(wellx.magnitude, '__iter__'):
            wellx = np.repeat(wellx, nlanes)
        wellx = wellx.to('cm')
        if not hasattr(welly.magnitude, '__iter__'):
            welly = np.repeat(welly, nlanes)
        welly = welly.to('cm')
        wellsep = wellsep.to('cm')
        till_len = abs(till_len) if till_len is not None else 1
        if till_time is not None:
            till_time = to_units(till_time, 'hr', 'till_time').to('s')
        res = to_units(res, 'px/cm', 'res')
        max_dist = till_len * gel_len

        # Electrophoretic Mobilities
        self.mobilities = []
        for lane in lanes:  # # self.mobs=[]+append  ou self.mobs=None + assign
            lane_mobs = []
            for dna_frag in lane:
                dna_size = len(dna_frag) * ureg.bp  # bp assumption ###### ! ##
                frag_mob = size_to_mobility(dna_size, field, percentage,
                                            mu_func, dataset, interpol,
                                            replNANs)
                lane_mobs.append(frag_mob)
            self.mobilities.append(lane_mobs * ureg('cm**2/V/s'))  # ##########
        # self.mobilities = Q_(self.mobilities, 'cm**2/V/s')
        mobilities = self.mobilities
        max_mob = max([max(lane_mobs) for lane_mobs in mobilities])

        # vWBR eq. parameters muL, muS, gamma
        output = vWBRfit(field, percentage, DNAspace_vWBRfit, dataset, mu_func,
                         interpol, replNANs, plot=False)
        muS, muL, gamma = output[0]
        muS = Q_(muS, 'cm**2/V/s')                                            #
        muL = Q_(muL, 'cm**2/V/s')                                            #
        gamma = Q_(gamma, 'bp')                                               #
        self.vWBR_muS = muS
        self.vWBR_muL = muL
        self.vWBR_gamma = gamma

        # vWBR
        # mu_func = vWBR(muS, muL, gamma)

        # Time limit
        time = runtime(max_dist, max_mob, field)  # sec
        if till_time is not None and till_time < time:
            time = till_time
        self.runtime = time

        # Distances
        distances = [rundistance(time, lane_mobs, field)
                     for lane_mobs in mobilities]
        self.distances = distances

        # Free solution mobility estimate
        mu0 = ferguson_to_mu0(field, Tvals, DNAspace_mu0, dataset, mu_func,
                              interpol, replNANs, plot=False)
        mu0 = Q_(mu0, 'cm**2/V/s')  # #########################################
        self.freesol_mob = mu0

        # Initial bandwidths
        dist0 = welly
        time0 = dist0/(mu0*field)
        bandwidths0 = [mobs*time0[l]*field for l, mobs in
                       enumerate(mobilities)]
        self.bandwidths0 = bandwidths0

        # Intrinsic diffusional bandwidths
        muS = muS.to('m**2/V/s')
        muL = muL.to('m**2/V/s')
        mu0 = mu0.to('m**2/V/s')
        lp = constants['lp'].to('m')
        l = constants['l'].to('m')
        b = constants['b'].to('m/bp')
        kB = constants['kB'].to('m**2*kg/s**2/K')
        qeff = constants['qeff'].to('A*s/bp')
        field = field.to('V/m')
        eta = H2Oviscosity(temperature)
        self.H2Oviscosity = eta
        a = pore_size(gamma, muL, mu0, lp, b)
        a_fit = pore_size_fit(percentage)  # ##################################
        a_fit = a_fit.to('m')              # ##################################
        self.poresize = a
        self.poresize_fit = a_fit
        epsilon = reduced_field(eta, a, mu0, field, kB, temperature)
        Db = Dblob(kB, temperature, eta, a)
        N_lim1 = accel_plateau(epsilon)     # #################################
        N_lim2 = equil_accel(epsilon)       # # ***   Major problem    ***   ##
        N_lim3 = Zimm_Rouse(Q_(2E3, 'bp'),  # #################################
                            [kB, temperature, qeff, eta, mu0, a, b, l, lp])
        # print 'N_lim1 = accel_plateau = %s (%s)' % (N_lim1,
        #                                             N_to_Nbp(N_lim1, a, b,
        #                                                      l))
        # print 'N_lim2 = equil_accel = %s (%s)' %(N_lim2,
        #                                          N_to_Nbp(N_lim2, a, b, l))
        # print 'N_lim3 = Zimm_Rouse = %s (%s)' %(N_lim3,
        #                                         N_to_Nbp(N_lim3, a, b, l))
        self.accel_to_plateau = N_to_Nbp(N_lim1, a, b, l)
        self.equil_to_accel = N_to_Nbp(N_lim2, a, b, l)
        self.Zimm_to_Rouse = N_to_Nbp(N_lim3, a, b, l)
        for lane in lanes:
            lane_widths = []
            for dna_frag in lane:
                Nbp = len(dna_frag) * ureg.bp  # # assumption #################
                N = Nbp_to_N(Nbp, a, b, l)
                if N < N_lim3:
                    # Ogston-Zimm
                    L = contour_length(Nbp, b)   # (m)
                    Rg = radius_gyration(L, lp)  # (m)
                    D0 = free_solution(kB, temperature, eta, Rg)  # (m^2/s)
                    DRouse = Ogston_Rouse(Nbp, kB, temperature,
                                          a, eta, b, l)  # (m^2/s)
                    g = Zimm_g(Nbp, DRouse, qeff, mu0, kB, temperature)  # base
                    D = Ogston_Zimm(D0, g)                               # unit
                elif N < N_lim2:
                    # Rouse/Reptation-equilibrium
                    D = Db/N**2
                elif N > N_lim1:
                    # Reptation-plateau (reptation with orientation)
                    D = Db*epsilon**(3/2)
                else:
                    # Accelerated-reptation
                    D = Db*epsilon*N**(-1/2)
                frag_width = bandbroadening(D, time).to('cm')
                lane_widths.append(frag_width)
            self.bandwidthsI.append(lane_widths)
        bandwidthsI = self.bandwidthsI

        # Total bandwidths
        bandwidths = [[bandwidths0[i][j] + bandwidthsI[i][j] for j in
                       range(len(lanes[i]))] for i in range(nlanes)]
        self.bandwidths = bandwidths
        if bandwidth == 0:
            bandwidths = self.bandwidths0
        if bandwidth == 1:
            bandwidths = self.bandwidthsI

        # Max intensities
        raw_Is = []
        maxI = Q_(-np.inf, 'ng/cm')
        minI = Q_(np.inf, 'ng/cm')
        for i, lane in enumerate(lanes):
            lane_I = []
            for j in range(len(lane)):
                frag_Qty = quantities[i][j]
                frag_Wth = bandwidths[i][j]  # w=FWHM or w=FWTM ???
                if FWTM:
                    FWHM = Gauss_FWHM(frag_Wth)
                else:
                    FWHM = frag_Wth
                std_dev = Gauss_dev(FWHM)
                auc = frag_Qty  # area under curve proportional to DNA quantity
                frag_I = Gauss_hgt(auc, std_dev)  # peak height
                if frag_I > maxI:
                    maxI = frag_I
                if frag_I < minI:
                    minI = frag_I
                lane_I.append(frag_I)
            raw_Is.append(lane_I)

        # max intensity normalization
        satI = maxI+exposure*(minI-maxI)
        intensities = [[(1-back_col)/satI*fragI for fragI in lane]
                       for lane in raw_Is]
        self.intensities = intensities

        # Plot gel
        if plot:
            # Title
            mins, secs = divmod(time.to('s').magnitude, 60)  # time is in secs
            hours, mins = divmod(mins, 60)
            hours = Q_(hours, 'hr')
            mins = Q_(mins, 'min')
            secs = Q_(secs, 's')
            title = ('E = %.2f V/cm\n'
                     'C = %.1f %%\n'
                     'T = %.2f K\n'
                     't = %d h %02d m\n'
                     'expo = %.1f' % (field.to('V/cm').magnitude,
                                      percentage.magnitude,
                                      temperature.magnitude,
                                      hours.magnitude, mins.magnitude,
                                      exposure))
            # Plot
            gelpic = gelplot_imshow(distances, bandwidths, intensities, lanes,
                                    names, gel_len, wellx, welly, wellsep, res,
                                    cursor_ovr, back_col, band_col, well_col,
                                    noise, Itol, detectlim, title, FWTM, False)
            return #gelpic
        return None


if __name__ == "__main__":  
    test_gel = True
    test_mu0 = True
    test_vWBRfit = True
    test_vWBRfit_comprehensive = False  # very time consuming
    check_ladders = True

    # Conditions
    electrfield = 6.21    # V/cm
    percentgel = 1.0      # %agarose
    temperature = 295.15  # K

    # Gel length and geometry
    gel_len = 7.5  # cm

    # Well dimensions
    wellx = 7    # mm
    welly = 2    # mm
    wellsep = 2  # mm

    # Length limit
    till_len = 0.77

    # Time limit
    till_time = None  # 45/60.0

    # Exposure factor
    exposure = 0.4

    # Dataset and interpolation
    dset_name = 'vertical'
    dataset = datasets[dset_name]
    interpol = 'linear'
    replNANs = True

    # Plot
    plot = True
    res = Q_(500, 'px/in')
    cursor_ovr = None  # dict(hover=True)
    back_col = 0.33166993353685043  # 0.332  0.15
    band_col = 1
    well_col = 0.05
    noise = 0.5*0.023400015217741609  # 0.015
    detectlim = 0.04

    # Lane identifiers
    lanenames = ['L1', 'S1', 'S2']

    # Samples
    ladder = weight_standard_sample('1kb_GeneRuler')
    sample1 = gen_sample([561, 1302, 135, 5021], [7.82, 18.15, 1.88, 70.00])
    sample2 = gen_sample([3000, 500, 1500], [70.00, 11.67, 35.00])
    samples = [ladder, sample1, sample2]

    # Quantities
    quantities = []
    # quantities.append([25, 25, 25, 60, 25, 25, 25, 70, 30, 30, 30, 70, 30,
    #                    30])
    # quantities.append([50]*4)
    # quantities.append([])
    # quantities.append(100)
    # quantities.append([120, 20, 60])
    # quantities = None

    # Data
    # DNAmin = 100
    # DNAmax = 20000
    # DNAdivs = 100
    DNAvals = np.linspace(100, 20000, 100) * ureg.bp
    DNAspace = logspace_int(100, 3000, 10) * ureg.bp
    divsE = 10
    divsT = 10
    Evals = sorted(list(set(datasets[dset_name]['E'])))  # why sort and list?
    minE = min(Evals)
    maxE = max(Evals)
    E_space = list(np.linspace(minE.magnitude, maxE.magnitude,
                               divsE)) * ureg(str(minE.units))
    Tvals = sorted(list(set(datasets[dset_name]['T'])))
    minT = min(Tvals)
    maxT = max(Tvals)
    T_space = list(np.linspace(minT.magnitude, maxT.magnitude,
                               divsT)) * ureg(str(minT.units))

    if test_gel:
        # ### Instantiate Gel ###
        G = Gel(samples, lanenames, percentgel, electrfield, temperature,
                gel_len, (wellx, welly), wellsep)

        # ### Run Gel ###
        pic = G.run(till_len, till_time, exposure, plot, res,
                    cursor_ovr, back_col, band_col, well_col, noise, detectlim,
                    interpol, dset_name, replNANs)
        if plot:
            # pic.savefig('gelplot.jpg', dpi=300)
            # pic.show()
            pass

    if test_mu0:
        # ### Test <ferguson_to_mu0> ### --------------------------------------
        print('\n'+80*'#')
        print('( Free Solution Mobility from Ferguson Plot )'.center(80, '#'))
        print(80*'#'+'\n')
        plot = True
        for Ei in E_space:
            mu0 = ferguson_to_mu0(Ei, T_space, DNAspace, dataset,
                                  mu_funcs[dset_name], interpol, replNANs,
                                  plot)
            if mu0 is None:
                print(mu0)
            else:
                print('mu0= %.3e cm^2/(V.seg)' % mu0)

    if test_vWBRfit:
        # ### Test <vWBRfit> ### ----------------------------------------------
        print('\n'+80*'#')
        print(("( Non-linear Least Squares Fitting"
               " with vWBR's Eq. )".center(80, '#')))
        print(80*'#'+'\n')
        plot = True
        output = vWBRfit(electrfield, percentgel, DNAvals,
                         datasets[dset_name], mu_funcs[dset_name],
                         interpol, replNANs, plot)
        # print output

    if test_vWBRfit_comprehensive:
        # ### Test <vWBRfit comprehensively> ### ------------------------------
        print('\n'+80*'#')
        print(("( Non-linear Least Squares Fitting with vWBR's Eq."
               "- comprehensive )".center(80, '#')))
        print(80*'#'+'\n')
        for Ei in E_space:
            for Ti in T_space:
                output = vWBRfit(Ei, Ti, DNAvals,
                                 dataset=datasets[dset_name],
                                 mu_func=mu_funcs[dset_name],
                                 method=interpol, replNANs=replNANs, plot=plot)

    if check_ladders:
        # ### Verify and print weight_standards info ### ----------------------
        print('\n'+80*'#')
        print('( DNA Ladder Info )'.center(80, '#'))
        print(80*'#')
        store_n = []
        store_m = []
        for k in weight_standards:
            sizes = weight_standards[k]['sizes']
            fracs = weight_standards[k]['percent']
            total = Q_(0.5, 'ug')
            masses = total * fracs
            ladder = weight_standard_sample(k, total)
            ns = Q_([seqrec.n for seqrec in ladder], 'mol').to('pmol')
            [store_n.append(n.to('pmol').magnitude) for n in ns]
            [store_m.append(m.to('ng').magnitude) for m in masses]
            assert len(sizes) == len(fracs), ('ladder: %s, len(sizes)'
                                              ' != len(percent)' % k)
            assert round(sum(fracs), 5) == 1, ('ladder: %s, sum(percent)'
                                               ' != 1' % k)
            print('\n', k, '\n', '-'*80)
            print('size \t\t mass/%s \t fraction \t n/pmol' % total)
            print('-'*80)
            for i in range(len(sizes)):
                print('%s   \t  %.3f  \t  %.3f \t %.4f' % (sizes[i],
                                                           masses[i].magnitude,
                                                           fracs[i].magnitude,
                                                           ns[i].magnitude))
            print('-'*80)
        print("min(m) = %.4f ng" % np.min(store_m))
        print("avg(m) = %.4f ng" % np.mean(store_m))
        print("max(m) = %.4f ng" % np.max(store_m))
        print("min(n) = %.4f pmol" % np.min(store_n))
        print("avg(n) = %.4f pmol" % np.mean(store_n))
        print("max(n) = %.4f pmol" % np.max(store_n))


# References (very incomplete)
# ============================================================================#
# 1. Van Winkle, D.H., Beheshti, A., Rill, R.L.: DNA electrophoresis in       #
# agarose gels: A simple relation describing the length dependence of         #
# mobility. ELECTROPHORESIS 23(1), 15–19 (2002)                               #
#                                                                             #
# 2. Rill, R.L., Beheshti, A., Van Winkle, D.H.: DNA electrophoresis in       #
# agarose gels: Effects of field and gel concentration on the exponential     #
# dependence of reciprocal mobility on DNA length. ELECTROPHORESIS 23(16),    #
# 2710–2719 (2002)                                                            #
#                                                                             #
# 3. Beheshti, A.: DNA Electrophoresis in th Agarose Gels: A New Mobility vs. #
# DNA Length Dependence. Electronic Theses, Treatises and Dissertations       #
# (Paper 1207)(2002)                                                          #
# ============================================================================#

# Bugs
# ============================================================================#
# - Error when zooming and hovering cursor.                                   #
# - Imperfect conversion from array to image!?                                #
#   While in the array the band broadness didn't vary more than one "pixel",  #
#   in the plot the difference was greater and more  noticeable.              #
#       ? imshow options ?                                                    #
#       ? Resolution ?                                                        #
#       ? Only in "show" not in "save" ?                                      #
#       ? Interference of other plot parameters ?                             #
# - The hoovering mode of the datacursor is slow.                             #
# - Error when till_length is 1: IndexError: index 3150 is out of bounds for  #
#   axis 0 with size 3150                                                     #
# ============================================================================#

# Questions for Professor Björn
# ============================================================================#
# - Ask for guidance for the simple SAMPLE objects and basic operations.      #
# - Ask for guidance for the default values.                                  #
# - Ask for guidance for the user friendliness from the standpoint of a       #
#   researcher.                                                               #
# - Would an "excise band" method be useful?                                  #
# ============================================================================#

# To-do list
# ============================================================================#
# - Band convolution (https://en.wikipedia.org/wiki/Convolution);             #
# - Qualitative and quantitative validation;                                  #
# - Comparison with other softwares;                                          #
# - Gather more data (obtained at well controlled conditions);                #
#       + Professor Beheshti's Phd thesis                                     #
#       + Extend the dataset with new experimental data                       #
# - Study extrapolation options beyond the data range:                        #
#       + parameters dependence on gel concentration equations (at low field) #
# - Train and validate a regression predictive model;                         #
# - Interpolation of user's experimental data with vWBR equation;             #
# ----------------------------------------------------------------------------#
# - Documentation (Numpy style);                                              #
# - Code readability and conformity to standards and style guides;            #
# - User friendliness;                                                        #
# - Testing module;                                                           #
# - Sharing on GitHub;                                                        #
# - Integration with pydna;                                                   #
# - Application exemples and guide in IPython Notebook;                       #
# - <mu_func> as module variable??                                            #
# - self.runtime = np.nan??                                                   #
# - Data and mu_funcs as module variables or class variables??                #
# - Keep most values in numpy arrays?? (may be helpful to implement units)    #
# - Experimental conditions on the plot's title;                              #
# - Keep and return the plots objects;                                        #
# - Passing the matplotlib's **keyargs;                                       #
# - Additional plots;                                                         #
# - Variable mapping:                                                         #
#       {'var':'meaning'}{'var':'units'}                                      #
#       {'E':'Electric field intensity (V/cm)', ...}                          #
# - Internal objects to organize information (LANE, BAND, SAMPLE);            #
# - Recognize unequivocal initials: 'v':'vertical', 'h':'horizontal', etc.;   #
# - There should be a single (Pint) UnitRegistry for the entire project.      #
# - Show DNA size in matplotlib coordinate viewer:                            #
#       "http://stackoverflow.com/questions/14754931/matplotlib-values-under- #
#        cursor"                                                              #
# - Click band to print DNA fragment data in console;                         #
# - Defaults, Assertions, warnings, errors, etc.                              #
# - Assert dimension concordance:                                             #
#       if wellx is iterable: len(wellx) == len(lanes)                        #
# - Combine gels;                                                             #
# - Mosaic of gels: same samples, different conditions;                       #
# - Method <save_with_resolution>;                                            #
# - Attention to pixel [0], in pixel->cm / cm->pixel conversions;             #
# - Study more carefully the distance <-> pixel conversion;                   #
# - At this point, the "exposure time" is being optimized so that no band's   #
#   intensity saturates (reaches white color) before it's peak. All curves    #
#   are perfect Gaussians. This benefites the highest curves in detriment of  #
#   the wider ones. It may be better for visualization to allow saturation    #
#   basing the "exposure time" on a parameter, maximizing the average hight   #
#   band or assuring that no peak falls bellow a certain level.               #
# - There is pehaps a wiser way to perform peak convolution.                  #
# - The stoping condition for the evaluation of the intensity function is too #
#   strick. "color <= background" goes till the order of 1E-16. A toletance   #
#   is needed.                                                                #
# - Peak convolution in the perpendicular direction.                          #
# - premade Ladder addition.                                                  #
# - Dimension concordance, data type and missing values verification on input.#
# - Full spell check.                                                         #
# - Most assert statements must be replaced with proper errors.               #
# ============================================================================#

# Random notes
# ============================================================================#
# - Avoid integer division: from __future__ import division                   #
# - Careful: Operations with unitary numpy arrays return numeric data types:  #
#       + type(np.array(2)*np.array(2)) --> <'numpy.int32'>                   #
#       + type(np.array(2)*np.array(2)/np.array(5)) --> <'numpy.int32'>       #
#       + from __future__ import division                                     #
#         type(np.array(2)*np.array(2)/np.array(5)) --> <'numpy.float64'>     #
#       + np.asarray(np.array(2)*np.array(2)/np.array(5)) --> array(0.8)      #
# - The pore size in the diffusion coefficient equations might not be an      #
#   "effective" pore size as that defined by Slater as function of muL, mu0   #
#   and gamma. Note that Viovy defined the interval 200-500 nm as the         #
#   consensus regarding pore size in 1% agarose gel. Yet, using Slater's      #
#   method we arrive at an effective pore size of 135.4 nm.                   #
# - I'm getting a smaller free solution mobility than the muS parameter.      #
#   I think it should be the other way around!...                             #
# - Is it better to never have unused lanes (as it is now) or to build a gel  #
#   with a chosen dimension and number of wells (used or not)?                #
# - The one thing that causes troubles with quantities is to assign a         #
#   quantity to a list of quantities. Ex: Q_([Q_(1, 'nm')], 'nm')             #
#   With that in mind, there might be simpler ways to implement the           #
#   functionality of "to_units".                                              #
# - mpldatacursor use:                                                        #
#       + right-click on annotation box to hide it;                           #
#       + press "d" on the keyboard to hide all annotation boxes;             #
#       + press "t" (toogle) to disable or re-enable interactive datacursors. #
# ============================================================================#
