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akashiwo_dist.py
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akashiwo_dist.py
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import numpy as np
import scipy.interpolate
import csv
import matplotlib.pyplot as plt
from matplotlib import rc
rc('text', usetex=True)
def rand_unit_vect_2D():
"""Generate a unit 2-vector with random direction"""
xy = np.random.normal(size=2)
mag = sum(i**2 for i in xy) ** 0.5
return xy / mag
def swim_speed_dist(num_particles, dist='swim_speed_distribution.csv'):
"""Produce a random swim speed for each particle based on the swim speed distribution for H. Akashiwo given in [Durham2013]"""
# import the histogram (contains particle speed dist in um/s)
with open(dist, newline='') as csvfile:
reader = csv.reader(csvfile, delimiter=",", quoting=csv.QUOTE_NONNUMERIC)
bins = []
counts = []
for row in reader:
bins.append(row[0])
counts.append(row[1])
# generate the PDF
cum_counts = np.cumsum(counts)
bin_width = 3
x = cum_counts * bin_width
y = bins
pdf = scipy.interpolate.interp1d(x, y)
b = np.zeros(num_particles)
for i in range(len(b)):
u = np.random.uniform(x[0], x[-1])
b[i] = pdf(u) # could convert in to meters if you want
#plt.figure(figsize=(10, 6))
#plt.hist(b, bins=100, density=True, alpha=1, color='black')
#plt.xlabel('Swim Speed (um/s)')
#plt.ylabel('PDF')
#plt.xlim([0, np.max(b)])
#plt.title('Swim Speed Distribution for H. Akashiwo')
#plt.grid(True)
#median_speed = np.median(b)
# mean_speed = np.mean(b)
#std_speed = np.std(b)
#textbox_content = f'Median: {median_speed:.3f}\nMean: {mean_speed:.3f}\nStd: {std_speed:.3f}'
#plt.text(0.98, 0.95, textbox_content, fontsize=13, horizontalalignment='right', verticalalignment='top', transform=plt.gca().transAxes, bbox=dict(facecolor='white', alpha=1))
#plt.savefig("LB_plankton_figs/PDF_Akashiwo.png",dpi=400)
return b
def ini_swimspeed_cells(width, length, num_cells=1000):
x0 = np.random.rand(num_cells,2) * np.array([width,length])
p0 = np.array([rand_unit_vect_2D() for _ in range(num_cells)])
vc = swim_speed_dist(num_cells)
ini_velocities = np.zeros((num_cells,2))
for i in range(num_cells):
ini_velocities[i] = vc[i] * p0[i]
return x0, vc, ini_velocities, p0