def dPDF(pts,mu,sigma, distribuition, outlier = 0, data = 0, n=10, seed = None):
import numpy as np
from scipy.interpolate import interp1d
from distAnalyze import dpdf, mediaMovel
from scipy.stats import norm, lognorm
eps = 5e-5
ngrid = int(1e6)
if distribuition == 'normal':
outlier_inf = outlier_sup = outlier
if not data:
inf, sup = norm.interval(0.9999, loc = mu, scale = sigma)
x = np.linspace(inf-outlier_inf,sup+outlier_sup,ngrid)
y = dpdf(x,mu,sigma,distribuition)
else:
np.random.set_state(seed)
d = np.random.normal(mu,sigma,data)
inf,sup = min(d)-outlier_inf,max(d)+outlier_sup
y,x = np.histogram(d,bins = 'fd',normed = True)
x = np.mean(np.array([x[:-1],x[1:]]),0)
y = abs(np.diff(mediaMovel(y,n)))
x = x[:-1]+np.diff(x)[0]/2
elif distribuition == 'lognormal':
outlier_inf = 0
outlier_sup = outlier
if not data:
inf, sup = lognorm.interval(0.9999, sigma, loc = 0, scale = np.exp(mu))
x = np.linspace(inf-outlier_inf,sup+outlier_sup,ngrid)
y = dpdf(x,mu,sigma,distribuition)
else:
np.random.set_state(seed)
d = np.random.lognormal(mu,sigma,data)
inf,sup = min(d)-outlier_inf,max(d)+outlier_sup
y,x = np.histogram(d,bins = 'fd',normed = True)
x = np.mean(np.array([x[:-1],x[1:]]),0)
y = abs(np.diff(mediaMovel(y,n)))
x = x[:-1]+np.diff(x)[0]/2
y = y/(np.diff(x)[0]*sum(y))
#dy = lambda x,u,s : abs(1/(s**3*sqrt(2*pi))*(u-x)*np.exp(-0.5*((u-x)/s)**2))
cdf = np.cumsum(y)
#cdf = np.sum(np.tri(len(x))*y,1)
#cdf = np.concatenate(cdf)
cdf = cdf/max(cdf)
#time.time()-t
interp = interp1d(cdf,x, fill_value = 'extrapolate')
Y = np.linspace(eps,1-eps,pts)
X = interp(Y)
return X,Y
def logs(sigma=1, mu=0, area=0.9999):
from scipy.stats import lognorm
import numpy as np
import matplotlib.pyplot as plt
from numpy import log, exp
scale = median = exp(mu)
mode = exp(mu - sigma**2)
mean = exp(mu + (sigma**2 / 2))
shape = sigma
a, b = lognorm.interval(area, shape, loc=0, scale=np.exp(mu))
x = np.linspace(a, b, 1000000)
mode = exp(mu - shape**2)
mean = exp(mu + (shape**2 / 2))
pdf = lognorm.pdf(x, shape, loc=0, scale=scale)
plt.figure(figsize=(12, 8), dpi=200)
plt.plot(x, pdf, label='PDF ($\sigma = %.2f$)' % shape)
plt.vlines(mode, 0, pdf.max(), linestyle=':', label='Mode = %.2f' % mode)
plt.vlines(mean,
0,
lognorm.pdf(mean, shape, loc=0, scale=scale),
color='green',
linestyle='--',
label='Mean = %.2f' % mean)
plt.vlines(median,
0,
lognorm.pdf(median, shape, loc=0, scale=scale),
color='blue',
label='Median = %.2f' % median)
plt.legend(loc=1)
plt.legend(prop={'size': 18})
plt.xlabel('x', fontsize=45)
plt.ylabel('Probability', fontsize=45)
plt.xticks(size=18)
plt.yticks(size=18)
plt.tight_layout()
def plot_prob_density(mu, la, predsData, testData, xmin, xmax):
from scipy.stats import lognorm
fig, axes = plt.subplots(1, 1, figsize=(5, 4), sharey=True, dpi=120)
font = "Times New Roman"
f3 = lambda x, mu, la: (1 / x * la * (2 * math.pi)**0.5) * np.exp(-(
(np.log(x) - mu)**2) / (2 * la**2))
x2 = np.linspace(0, xmax, 300)
axes.plot(x2, f3(x2, mu, la))
ymin, ymax = axes.get_ylim()
x_bounds = lognorm.interval(alpha=0.95, s=la, scale=np.exp(mu))
x_bounds_std = lognorm.interval(alpha=0.68, s=la, scale=np.exp(mu))
axes.axvline(x=testData.sum(), color='red', linestyle=':')
ymaxes = f3(np.asarray(x_bounds), mu, la) / ymax + 0.01
axes.axvline(x=x_bounds[0], color='blue', alpha=0.3, linestyle=':')
axes.axvline(x=x_bounds[1], color='blue', alpha=0.3, linestyle=':')
xfill = np.linspace(x_bounds[0], x_bounds[1], 100)
xfill_std = np.linspace(x_bounds_std[0], x_bounds_std[1], 100)
axes.fill_between(xfill, f3(xfill, mu, la), alpha=0.1, color='blue')
axes.fill_between(xfill_std,
f3(xfill_std, mu, la),
alpha=0.1,
color='blue')
#axes.fill_between(xfill,)
axes.text(x=testData.sum() + 1,
y=.03 * ymax,
s='Actual: ' + str(int(testData.sum())),
color='red')
#axes.text(x=x_bounds[1]+1,y=ymax*.9,s='Upper 95%:',color='blue')
#axes.text(x=x_bounds[1]+1,y=ymax*.82,s=str(round(x_bounds[1],1)),color='blue')
#axes.text(x=x_bounds[0]-10,y=ymax*.9,s='Lower 95%:',color='blue')
#axes.text(x=x_bounds[0]-10,y=ymax*.82,s=str(round(x_bounds[0],1)),color='blue')
axes.set_xlabel('Number of days exceeding threshold',
fontname=font,
fontweight="heavy",
fontsize=12)
axes.set_ylabel('Probability density function (-)',
fontname=font,
fontweight="heavy",
fontsize=12)
axes.set_ylim(0, ymax)
axes.set_xlim(0, xmax)
labels = axes.get_xticklabels() + axes.get_yticklabels()
[label.set_fontname(font) for label in labels]
fig.show()
print('**********************************')
print('Expected number of days exceeding thermal comfort criteria: ' +
str(round(lognorm.mean(s=la, scale=np.exp(mu)), 1)) + ' +/- ' +
str(round(lognorm.std(s=la, scale=np.exp(mu)), 1)))
print('Most likely number of days exceeding thermal comfort criteria: ' +
str(round(np.exp(mu - la**2))) + ' +/- ' +
str(round(lognorm.std(s=la, scale=np.exp(mu)), 1)))
print(
'Predicted number of days exceeding thermal comfort criteria (deterministic): '
+ str(int(np.sum(predsData))))
print('Actual number of days exceeding thermal comfort criteria: ' +
str(int(testData.sum())))
print('**********************************')
from sklearn.metrics import accuracy_score, precision_score, recall_score, roc_auc_score
acc_score = accuracy_score(predsData, testData)
prec_score = precision_score(predsData, testData)
rec_score = recall_score(predsData, testData)
roc_auc_score = roc_auc_score(predsData, testData)
print("Test Accuracy score: ", acc_score)
print("Test Precision score: ", prec_score)
print("Test Recall score: ", rec_score)
print("Test ROC AUC score: ", roc_auc_score)
def ddPDF(pts, mu, sigma, distribuition, outlier=0, data=0, n=10, seed=None):
import numpy as np
from scipy.interpolate import interp1d
from distAnalyze import ddpdf, mediaMovel
from scipy.stats import norm, lognorm
from someFunctions import ash
eps = 5e-5
ngrid = int(1e6)
#ddy = lambda x,u,s: abs(-(s**2-u**2+2*u*x-x**2)/(s**5*sqrt(2*pi))*np.exp(-0.5*((u-x)/s)**2))
if distribuition == 'normal':
outlier_inf = outlier_sup = outlier
if not data:
inf, sup = norm.interval(0.9999, loc=mu, scale=sigma)
x = np.linspace(inf - outlier_inf, sup + outlier_sup, ngrid)
y = ddpdf(x, mu, sigma, distribuition)
else:
np.random.set_state(seed)
d = np.random.normal(mu, sigma, data)
inf, sup = min(d) - outlier_inf, max(d) + outlier_sup
#y,x = np.histogram(d,bins = 'fd',normed = True)
#x = np.mean(np.array([x[:-1],x[1:]]),0)
x, y = ash(d)
y = abs(np.diff(y, 2))
x = x[:-2] + np.diff(x)[0]
#y = abs(np.diff(mediaMovel(y,n),2))
#x = x[:-2]+np.diff(x)[0]
y = y / (np.diff(x)[0] * sum(y))
elif distribuition == 'lognormal':
outlier_inf = 0
outlier_sup = outlier
inf, sup = lognorm.interval(0.9999, sigma, loc=0, scale=np.exp(mu))
inf = lognorm.pdf(sup, sigma, loc=0, scale=np.exp(mu))
inf = lognorm.ppf(inf, sigma, loc=0, scale=np.exp(mu))
if not data:
x = np.linspace(inf - outlier_inf, sup + outlier_sup, ngrid)
y = ddpdf(x, mu, sigma, distribuition)
else:
np.random.set_state(seed)
d = np.random.lognormal(mu, sigma, data)
#inf,sup = min(d)-outlier_inf,max(d)+outlier_sup
# y,x = np.histogram(d,bins = 'fd',normed = True)
#x = np.mean(np.array([x[:-1],x[1:]]),0)
x, y = ash(d)
y = y[x < sup]
x = x[x < sup]
y = abs(np.diff(y, 2))
#y = abs(np.diff(mediaMovel(y,n),2))
x = x[:-2] + np.diff(x)[0]
y = y / (np.diff(x)[0] * sum(y))
#cdf = np.sum(np.tri(len(x))*y,1)
cdf = np.cumsum(y)
# =============================================================================
# for i in range(1,ngrid):
# cdf.append(y[i]+cdf[i-1])
cdf = cdf / max(cdf)
#
# =============================================================================
interp = interp1d(cdf, x, fill_value='extrapolate')
Y = np.linspace(eps, 1 - eps, pts)
X = interp(Y)
return X, Y
def PDF(pts, mu, sigma, distribuition, outlier=0, data=0, seed=None):
from scipy.stats import norm, lognorm
import numpy as np
from scipy.interpolate import interp1d
from someFunctions import ash
eps = 5e-5
if distribuition == 'normal':
outlier_inf = outlier_sup = outlier
if not data:
inf, sup = norm.interval(0.9999, loc=mu, scale=sigma)
X1 = np.linspace(inf - outlier, mu, int(1e6))
Y1 = norm.pdf(X1, loc=mu, scale=sigma)
interp = interp1d(Y1, X1)
y1 = np.linspace(Y1[0], Y1[-1], pts // 2 + 1)
x1 = interp(y1)
X2 = np.linspace(mu, sup + outlier, int(1e6))
Y2 = norm.pdf(X2, loc=mu, scale=sigma)
interp = interp1d(Y2, X2)
y2 = np.flip(y1, 0)
x2 = interp(y2)
else:
np.random.set_state(seed)
d = np.random.normal(mu, sigma, data)
inf, sup = min(d) - outlier_inf, max(d) + outlier_sup
#yest,xest = np.histogram(d,bins = 'fd',normed = True)
xest, yest = ash(d)
xest = np.mean(np.array([xest[:-1], xest[1:]]), 0)
M = np.where(yest == max(yest))[0][0]
m = np.where(yest == min(yest))[0][0]
interpL = interp1d(yest[:M + 1],
xest[:M + 1],
assume_sorted=False,
fill_value='extrapolate')
interpH = interp1d(yest[M:],
xest[M:],
assume_sorted=False,
fill_value='extrapolate')
y1 = np.linspace(yest[m] + eps, yest[M], pts // 2 + 1)
x1 = interpL(y1)
y2 = np.flip(y1, 0)
x2 = interpH(y2)
elif distribuition == 'lognormal':
outlier_inf = 0
outlier_sup = outlier
inf, sup = lognorm.interval(0.9999, sigma, loc=0, scale=np.exp(mu))
inf = lognorm.pdf(sup, sigma, loc=0, scale=np.exp(mu))
inf = lognorm.ppf(inf, sigma, loc=0, scale=np.exp(mu))
if not data:
mode = np.exp(mu - sigma**2)
X1 = np.linspace(inf - outlier_inf, mode, int(1e6))
Y1 = lognorm.pdf(X1, sigma, loc=0, scale=np.exp(mu))
interp = interp1d(Y1, X1)
y1 = np.linspace(Y1[0], Y1[-1], pts // 2 + 1)
x1 = interp(y1)
X2 = np.linspace(mode, sup + outlier_sup, int(1e6))
Y2 = lognorm.pdf(X2, sigma, loc=0, scale=np.exp(mu))
interp = interp1d(Y2, X2)
y2 = np.flip(y1, 0)
x2 = interp(y2)
else:
np.random.set_state(seed)
d = np.random.lognormal(mu, sigma, data)
#inf,sup = min(d)-outlier_inf,max(d)+outlier_sup
#yest,xest = np.histogram(d,bins = 'fd',normed = True)
#xest = np.mean(np.array([xest[:-1],xest[1:]]),0)
xest, yest = ash(d)
yest = yest[xest < sup]
xest = xest[xest < sup]
M = np.where(yest == max(yest))[0][0]
m = np.where(yest == min(yest))[0][0]
interpL = interp1d(yest[:M + 1],
xest[:M + 1],
fill_value='extrapolate')
interpH = interp1d(yest[M:], xest[M:])
y1 = np.linspace(yest[m] + eps, yest[M], pts // 2 + 1)
x1 = interpL(y1)
y2 = np.flip(y1, 0)
x2 = interpH(y2)
X = np.concatenate([x1[:-1], x2])
Y = np.concatenate([y1[:-1], y2])
return X, Y
def diffArea(nest,
outlier=0,
data=0,
kinds='all',
axis='probability',
ROI=20,
mu=0,
sigma=1,
weight=False,
interpolator='linear',
distribuition='normal',
seed=None,
plot=True):
"""
Return an error area between a analitic function and a estimated discretization from a distribuition.
Parameters
----------
nest: int
The number of estimation points.
outlier: int, optional
Is the point of an outlier event, e.g outlier = 50 will put an event in -50 and +50 if mu = 0.
Defaut is 0
data: int, optional
If data > 0, a randon data will be inserted insted analitcs data.
Defaut is 0.
kinds: str or array, optional
specifies the kind of distribuition to analize.
('Linspace', 'CDFm', 'PDFm', 'iPDF1', 'iPDF2', 'all').
Defaut is 'all'.
axis: str, optional
specifies the x axis to analize
('probability', 'derivative', '2nd_derivative', 'X').
Defaut is 'probability'.
ROI: int, optional
Specifies the number of regions of interest.
Defaut is 20.
mu: int, optional
Specifies the mean of distribuition.
Defaut is 0.
sigma: int, optional
Specifies the standard desviation of a distribuition.
Defaut is 1.
weight: bool, optional
if True, each ROI will have a diferent weight to analyze.
Defaut is False
interpolator: str, optional
Specifies the kind of interpolation as a string
('linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic'
where 'zero', 'slinear', 'quadratic' and 'cubic' refer to a spline
interpolation of zeroth, first, second or third order) or as an
integer specifying the order of the spline interpolator to use.
Default is 'linear'.
distribuition: str, optional
Select the distribuition to analyze.
('normal', 'lognormal')
Defaut is 'normal'
plot: bool, optional
If True, a plot will be ploted with the analyzes
Defaut is True
Returns
-------
a, [b,c]: float and float of ndarray. area,[probROIord,areaROIord]
returns the sum of total error area and the 'x' and 'y' values.
"""
import numpy as np
from scipy.stats import norm, lognorm
from scipy.interpolate import interp1d
from numpy import exp
import matplotlib.pyplot as plt
from statsmodels.distributions import ECDF
from distAnalyze import pdf, dpdf, ddpdf, PDF, dPDF, ddPDF
area = []
n = []
data = int(data)
if distribuition == 'normal':
outlier_inf = outlier_sup = outlier
elif distribuition == 'lognormal':
outlier_inf = 0
outlier_sup = outlier
ngrid = int(1e6)
truth = pdf
if axis == 'probability':
truth1 = pdf
elif axis == 'derivative':
truth1 = dpdf
elif axis == '2nd_derivative':
truth1 = ddpdf
elif axis == 'X':
truth1 = lambda x, mu, sigma, distribuition: x
#else: return 'No valid axis'
probROIord = {}
areaROIord = {}
div = {}
if seed is not None:
np.random.set_state(seed)
if data:
if distribuition == 'normal':
d = np.random.normal(mu, sigma, data)
elif distribuition == 'lognormal':
d = np.random.lognormal(mu, sigma, data)
if kinds == 'all':
kinds = ['Linspace', 'CDFm', 'PDFm', 'iPDF1', 'iPDF2']
elif type(kinds) == str:
kinds = [kinds]
for kind in kinds:
if distribuition == 'normal':
inf, sup = norm.interval(0.9999, loc=mu, scale=sigma)
elif distribuition == 'lognormal':
inf, sup = lognorm.interval(0.9999, sigma, loc=0, scale=exp(mu))
inf = lognorm.pdf(sup, sigma, loc=0, scale=np.exp(mu))
inf = lognorm.ppf(inf, sigma, loc=0, scale=np.exp(mu))
xgrid = np.linspace(inf, sup, ngrid)
xgridROI = xgrid.reshape([ROI, ngrid // ROI])
dx = np.diff(xgrid)[0]
if kind == 'Linspace':
if not data:
xest = np.linspace(inf - outlier_inf, sup + outlier_sup, nest)
else:
if distribuition == 'normal':
#d = np.random.normal(loc = mu, scale = sigma, size = data)
inf, sup = min(d), max(d)
xest = np.linspace(inf - outlier_inf, sup + outlier_sup,
nest)
elif distribuition == 'lognormal':
#d = np.random.lognormal(mean = mu, sigma = sigma, size = data)
inf, sup = min(d), max(d)
xest = np.linspace(inf - outlier_inf, sup + outlier_sup,
nest)
yest = pdf(xest, mu, sigma, distribuition)
elif kind == 'CDFm':
eps = 5e-5
yest = np.linspace(0 + eps, 1 - eps, nest)
if distribuition == 'normal':
if not data:
xest = norm.ppf(yest, loc=mu, scale=sigma)
yest = pdf(xest, mu, sigma, distribuition)
else:
#d = np.random.normal(loc = mu, scale = sigma, size = data)
ecdf = ECDF(d)
inf, sup = min(d), max(d)
xest = np.linspace(inf, sup, data)
yest = ecdf(xest)
interp = interp1d(yest,
xest,
fill_value='extrapolate',
kind='nearest')
yest = np.linspace(eps, 1 - eps, nest)
xest = interp(yest)
elif distribuition == 'lognormal':
if not data:
xest = lognorm.ppf(yest, sigma, loc=0, scale=exp(mu))
yest = pdf(xest, mu, sigma, distribuition)
else:
#d = np.random.lognormal(mean = mu, sigma = sigma, size = data)
ecdf = ECDF(d)
inf, sup = min(d), max(d)
xest = np.linspace(inf, sup, nest)
yest = ecdf(xest)
interp = interp1d(yest,
xest,
fill_value='extrapolate',
kind='nearest')
yest = np.linspace(eps, 1 - eps, nest)
xest = interp(yest)
elif kind == 'PDFm':
xest, yest = PDF(nest, mu, sigma, distribuition, outlier, data,
seed)
elif kind == 'iPDF1':
xest, yest = dPDF(nest, mu, sigma, distribuition, outlier, data,
10, seed)
elif kind == 'iPDF2':
xest, yest = ddPDF(nest, mu, sigma, distribuition, outlier, data,
10, seed)
YY = pdf(xest, mu, sigma, distribuition)
fest = interp1d(xest,
YY,
kind=interpolator,
bounds_error=False,
fill_value=(YY[0], YY[-1]))
#fest = lambda x: np.concatenate([fest1(x)[fest1(x) != -1],np.ones(len(fest1(x)[fest1(x) == -1]))*fest1(x)[fest1(x) != -1][-1]])
yestGrid = []
ytruthGrid = []
ytruthGrid2 = []
divi = []
for i in range(ROI):
yestGrid.append([fest(xgridROI[i])])
ytruthGrid.append([truth(xgridROI[i], mu, sigma, distribuition)])
ytruthGrid2.append([truth1(xgridROI[i], mu, sigma, distribuition)])
divi.append(
len(
np.intersect1d(
np.where(xest >= min(xgridROI[i]))[0],
np.where(xest < max(xgridROI[i]))[0])))
diff2 = np.concatenate(
abs((np.array(yestGrid) - np.array(ytruthGrid)) * dx))
#diff2[np.isnan(diff2)] = 0
areaROI = np.sum(diff2, 1)
divi = np.array(divi)
divi[divi == 0] = 1
try:
probROI = np.mean(np.sum(ytruthGrid2, 1), 1)
except:
probROI = np.mean(ytruthGrid2, 1)
probROIord[kind] = np.sort(probROI)
index = np.argsort(probROI)
areaROIord[kind] = areaROI[index]
#deletes = ~np.isnan(areaROIord[kind])
#areaROIord[kind] = areaROIord[kind][deletes]
#probROIord[kind] = probROIord[kind][deletes]
area = np.append(area, np.sum(areaROIord[kind]))
n = np.append(n, len(probROIord[kind]))
div[kind] = divi[index]
if plot:
if weight:
plt.logy(probROIord[kind],
areaROIord[kind] * div[kind],
'-o',
label=kind,
ms=3)
else:
plt.plot(probROIord[kind],
areaROIord[kind],
'-o',
label=kind,
ms=3)
plt.yscale('log')
plt.xlabel(axis)
plt.ylabel('Error')
plt.legend()
#plt.title('%s - Pontos = %d, div = %s - %s' %(j,nest, divs,interpolator))
return area, [probROIord, areaROIord]
sigma, loc, scale = lognorm.fit(data, floc=0)
# print sigma, loc, scale
# print lognorm.mean(sigma, loc=loc, scale=scale)
read_length_count = 0
"""
y_value = lognorm.pdf(data, sigma, loc, scale)
background = np.median(y_value)
"""
end_point = lognorm.interval(0.5, sigma, loc, scale)
print end_point
# calculate the homogenesous distribution as a comparable reference
background = 0.5/(end_point[1] - end_point[0])
print background
record_dict = SeqIO.index("D:/Data/20161125/filtered_subreads_first1k.fastq", "fastq")
target_seq = []
i= 0
id_list = list(record_dict.keys())
seq_num = len(id_list)
while read_length_count <= target_read_length:
print read_length_count
if i == seq_num:
from scipy.stats import lognorm
data2 = []
with open('datafile2.csv') as csvfile2:
reader = csv.reader(csvfile2)
for row in reader:
data2.append(float(row[0]))
plt.figure()
_ = plt.hist(data2, bins=100)
# Parameter estimates for generic data
# the argument floc=0 to ensure that it does not treat the location as a free parameter
shape1, loc1, scale1 = lognorm.fit(data2, floc=0)
mu1 = np.log(scale1)
sigma1 = shape1
print("Estimated mu = " + str(mu1))
print("Estimated sigma = " + str(sigma1))
# 0.95 is the alpha value, which specifies a 95 percentile point, as the corresponding 1.96 standard deviations of the mean is given in the formula.
ci1 = lognorm.interval(0.95, s=sigma1, loc=loc1, scale=scale1)
print("Lognorm function CI = " + str(ci1))
# confidence interval left line
one_x12, one_y12 = [ci1[0], ci1[0]], [0, 20]
# confidence interval right line
two_x12, two_y12 = [ci1[1], ci1[1]], [0, 20]
plt.plot(one_x12, one_y12, two_x12, two_y12, marker='o')
plt.title("Lognormal distribution confidence interval")
plt.show()
def log_normal_distribution(
radius_g: float, sigma_g: float,
n_bins: int) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
"""
Function for returning a log-normal size distribution. See Eq. 9
in Ackerman & Marley (2001).
Parameters
----------
radius_g : float
Mean geometric radius (um).
sigma_g : float
Geometric standard deviation (dimensionless).
n_bins : int
Number of logarithmically-spaced radius bins.
Returns
-------
np.ndarray
Number of grains in each radius bin, normalized to a total of
1 grain.
np.ndarray
Widths of the radius bins (um).
np.ndarray
Grain radii (um).
"""
if sigma_g == 1.0:
# The log-normal distribution is equal to a delta
# function with sigma_g = 1
radii = np.array([radius_g])
r_width = np.array([np.nan])
dn_grains = np.array([1.0])
else:
# Get the radius interval which contains 99.999%
# of the distribution
interval = lognorm.interval(1.0 - 1e-5,
np.log(sigma_g),
loc=0.0,
scale=radius_g)
# Create bin boundaries (um), so +1 because there
# are n_bins+1 bin boundaries
r_bins = np.logspace(np.log10(interval[0]), np.log10(interval[1]),
n_bins + 1)
# Width of the radius bins (um)
r_width = np.diff(r_bins)
# Grain radii (um) at which the size distribution is sampled
radii = (r_bins[1:] + r_bins[:-1]) / 2.0
# Number of grains per radius bin width, normalized to an
# integrated value of 1 grain, that is,
# np.sum(dn_dr*r_width) = 1
# The log-normal distribution from Ackerman & Marley 2001
# gives the same result as scipy.stats.lognorm.pdf with
# s = log(sigma_g) and scale=radius_g
dn_dr = lognorm.pdf(radii, s=np.log(sigma_g), loc=0.0, scale=radius_g)
# Number of grains for each radius bin
dn_grains = dn_dr * r_width
return dn_grains, r_width, radii
