Blame for functions.py

import math
import numpy as np
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import io
import base64
from scipy import special
from scipy.optimize import bisect

def SigFigs(number, n):
    if number == 0: return number
    return round(number, n - int(math.floor(math.log10(math.fabs(number)))) - 1)

def HtmlNumber(number,n):
    number_str = f'{number:.{n}e}'
    base, exponent = number_str.split('e')
    html_output = f'{base} × 10<sup>{exponent[0] if exponent[0]=="-" else ""}{int(exponent[1:]):d}</sup>'
    return html_output

def Piringer(Mw, Ap, T=310.):
    # Semi-empirical model for D(Mw) given polymer property Ap- Toxicol. Sci. 2019, 172 (1), 201–212.
    if Mw > 1100.: # if molecule is greater than 1100 g/mol, default to that value as worst case
        Mw = 1100.
    return 1e4 * np.exp(Ap - 0.1351 * Mw ** (2. / 3.) + 0.003 * Mw - 10454. / T)

def WilkeChang(Mw):
    # Semi-empirical model for D(Mw) assuming diffusion in water
    Va = 4.21 + 1.58 * Mw # molecular volume as a function of Mw assuming linear alkanes as worst case
    T = 310.
    MwH2O = 18.
    viscosity = 0.6913
    alpha = 2.6

    return 7.4e-8 * (MwH2O * alpha) ** 0.5 * T / viscosity / Va ** 0.6

def SheetRelease(amount, vol, area, time, D):

    # analytical solution(s) to Fick's law for a plane sheet
    L = vol / area
    D = D * 3600. # convert seconds to hours
    tau = D * time / L ** 2. # dimensionless time
    if tau <= 0.2:
        release = 2. * amount * np.sqrt(tau / np.pi)
    else:
        release = amount * (1. - (8. / (np.pi ** 2.)) * np.exp(-tau * np.pi ** 2. / 4.))

    return release

def SheetRates(amount, vol, area, time, D):

    D = D * 86400.
    L = vol / area

    rates = np.zeros(len(time))
    tau = D * time[0] / L ** 2.
    if tau < 0.2:
        rates[0] = 2. * amount * np.sqrt(tau / np.pi)
    else:
        rates[0] = amount * (1. - (8. / (np.pi ** 2.)) * np.exp(-tau * np.pi ** 2. / 4.))

    for i in range(1, len(time)):
        tau = D * time[i] / L ** 2.
        if tau < 0.2:
            rates[i] = 2. * amount * np.sqrt(tau / np.pi) - np.sum(rates[:i])
        else:
            rates[i] = amount * (1. - (8. / (np.pi ** 2.)) * np.exp(-tau * np.pi ** 2. / 4.)) - np.sum(rates[:i])

    return rates

def RatePlot(tarray, rates):

    fig, ax = plt.subplots(figsize=(6, 4))
    ax.plot(tarray, rates, 'o')
    ax.set(
        xlabel='time (days)',
        ylabel='release rate (mg/day)',
    )
    plt.tight_layout()
    pngImage = io.BytesIO()
    FigureCanvas(fig).print_png(pngImage)
    pngImageB64String = "data:image/png;base64,"
    pngImageB64String += base64.b64encode(pngImage.getvalue()).decode('utf8')

    return pngImageB64String


def CdfPlot(vals, units=None):

    xlabel = 'Total quantity' if units is None else f'Total quantity ({units})'
    fig, ax = plt.subplots(figsize=(6, 4))
    ax.ecdf(vals, c='b', lw=3)
    q50 = np.nanquantile(vals,0.5)
    ax.plot([q50,q50],[0,0.5],'k--',[q50],[0.5],'ko',[ax.get_xlim()[0],q50],[0.5,0.5],'k--',lw=2,ms=10)
    ax.set_xscale('log')
    ax.set(
        xlabel=xlabel,
        ylabel='Cumulative probability',
    )
    plt.tight_layout()
    pngImage = io.BytesIO()
    FigureCanvas(fig).print_png(pngImage)
    pngImageB64String = "data:image/png;base64,"
    pngImageB64String += base64.b64encode(pngImage.getvalue()).decode('utf8')

    return pngImageB64String


def PlaneSheetFiniteBathMass(M0, D, K, PolymerVolume, SurfaceArea, SolventVolume, ExtractionTime, nterms):
    L = PolymerVolume / SurfaceArea  # effective length scale of the component
    alpha = SolventVolume / PolymerVolume / K

    Minfty = M0 / (1. + 1. / (alpha))

    qn = np.zeros((nterms))
    for j in range(nterms):
        solved = False
        eps = 1e-8
        while not solved:
            f = lambda x: np.tan(x) + alpha * x
            rts = bisect(f, np.pi / 2. + j * np.pi + eps, np.pi * (1. + j) - eps, xtol=1e-6)
            # print(rts)
            solved = True
        qn[j] = rts

    result = 1.
    for j in range(nterms):
        result = result - (2. * alpha * (1. + alpha)) * np.exp(-D * qn[j] ** 2. * ExtractionTime / L ** 2.) / (
                    1. + alpha + alpha ** 2. * qn[j] ** 2.)
    result = Minfty * result

    return result


def PlaneSheetFiniteBathMassApprox(M0, D, K, PolymerVolume, SurfaceArea, SolventVolume, ExtractionTime):
    L = PolymerVolume / SurfaceArea  # effective length scale of the component
    alpha = SolventVolume / PolymerVolume / K

    Minfty = M0 / (1. + 1. / (alpha))

    T = D * ExtractionTime / L ** 2.

    # if exp will blow up, use asymptotic expansion instead
    if (T / alpha ** 2. < 100.):
        result = Minfty * (1. + alpha) * (1. - np.exp(T / alpha ** 2.) * special.erfc(np.sqrt(T) / alpha))
    else:
        result = Minfty * (1. + alpha) * (1. - alpha / (np.sqrt(np.pi) * np.sqrt(T)) + alpha ** 3. / (
                    2. * np.sqrt(np.pi) * (T) ** 1.5) - 3. * alpha ** 5. / (4. * np.sqrt(np.pi) * (T) ** 2.5))

    return result


def PlaneSheetAnalytical(M0, D, K, PolymerVolume, SurfaceArea, SolventVolume, ExtractionTime, nterms):
    L = PolymerVolume / SurfaceArea  # effective length scale of the component
    tau = D * ExtractionTime / L ** 2.

    if tau > 0.05:
        result = PlaneSheetFiniteBathMass(M0, D, K, PolymerVolume, SurfaceArea, SolventVolume, ExtractionTime, nterms)
    else:
        result = PlaneSheetFiniteBathMassApprox(M0, D, K, PolymerVolume, SurfaceArea, SolventVolume, ExtractionTime)

    return result

def Piecewise(Mw, params):
    mw_cut, func_lo, func_hi, params_lo, params_hi = params
    if Mw <= mw_cut:
        D = func_lo(Mw,*params_lo)
    else:
        D = func_hi(Mw,*params_hi)
    return D

def PowerLaw(Mw, A, B):
    logMw = np.log(Mw)
    logD = A+logMw*B
    return np.exp(logD)

def weight_func(dists):
    """
    Returns the weights, based on the method in OPERA
    Parameter f controls the maximum weight, prevents 1/dist -> inf
    Set f to a very small number to mimic default sklearn behavior when dist = 0
    """
    #f = 1e-15 # OPERA on CompTox?
    #f = 5e-2 # OPERA in Matlab code
    #f = 1e-3 # test
    f = 5e-3
    tmp = 1/(f+dists)
    tmp = tmp/tmp.sum(axis=1)[..., None]
    return tmp

#def func_piringer(Mw,T,Ap):
#    if Mw > 1100.: # if molecule is greater than 1100 g/mol, default to that value as worst case
#        Mw = 1100.
#    D = 1e4*np.exp(Ap-0.1351*Mw**(2/3)+0.003*Mw-10454/T)
#    return D