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R9123/Functions/display_parameters.py
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display_parameters.py
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# -*- coding: utf-8 -*-
""""""""""""""""""""" MODULE IMPORT """""""""""""""""""""
import seaborn as sn
import matplotlib
matplotlib.rcParams['pdf.fonttype'] = 42
from mpl_toolkits import axes_grid1
import numpy as np
import matplotlib.pyplot as plt
import pickle
import sys
import os
import matplotlib.colors as mcolors
sys.path.insert(0, os.path.realpath('..'))
from Functions.create_hidden_variables import create_hidden_variables
from Functions.make_colormap import make_colormap
#colormap
c = mcolors.ColorConverter().to_rgb
bwr = make_colormap( [c('blue'), c('white'), 0.48, c('white'),
0.52,c('white'), c('red')])
#nice plotting style
sn.set_style("whitegrid", { 'xtick.direction': 'out', 'xtick.major.size': 6.0,
'xtick.minor.size': 3.0, 'ytick.color': '.15',
'ytick.direction': 'out', 'ytick.major.size': 6.0,
'ytick.minor.size': 3.0})
""""""""""""""""""""" FUNCTION """""""""""""""""""""
def load_path(type_sim = 'Real', type_param = 'init', type_cell = 'NIH3T3',
temperature = '37', type_div = 'nodiv', local = False):
"""
Return the correct path for the file of parameters given a set of
conditions.
Parameters
----------
type_sim : string
Simulation type. 'Real' or 'Silico'.
type_param : string
Parameters type. 'init' or 'opt' for initial or optimal.
type_cell : string
Cell type. 'NIH3T3' or 'U2OS'.
temperature : integer
Temperature condition . 34, 37 or 40.
type_div : string
Dividing cells or not. 'div' or 'nodiv'.
local : bool
Specify it the script is launched locally or not (to have the correct
path)
Returns
-------
The desired path.
"""
if local:
pref = "../"
else:
pref =''
try:
with open(pref+'Parameters/'+type_sim+'/'+type_param+'_parameters_'\
+type_div+'_'+str(temperature)+"_"+type_cell+'.p', 'rb') as f:
path = pref+'Parameters/'+type_sim+'/'+type_param+'_parameters_'\
+type_div+'_'+str(temperature)+"_"+type_cell+'.p'
except:
print("Error, file " + pref+'Parameters/'+type_sim+'/'+type_param+\
'_parameters_'+type_div+'_'+str(temperature)+"_"+type_cell+'.p'\
+ "doesn't exist")
path = None
return path
def display_parameters_from_file(path, show = False, temperature = None,
cell = None):
"""
Display all the parameters from a given file.
Parameters
----------
path : string
Path for the parameters file.
show : bool
Display the figures (e.g. coupling function, intial condition) or not.
temperature : integer
Temperature condition . 34, 37 or 40.
cell : string
Cell type. 'NIH3T3' or 'U2OS'.
"""
with open(path, 'rb') as f:
l_parameters = [dt, sigma_em_circadian, W, pi,
N_theta, std_theta, period_theta, l_boundaries_theta, w_theta,
N_phi, std_phi, period_phi, l_boundaries_phi, w_phi,
N_amplitude_theta, mu_amplitude_theta, std_amplitude_theta,
gamma_amplitude_theta, l_boundaries_amplitude_theta,
N_background_theta, mu_background_theta, std_background_theta,
gamma_background_theta, l_boundaries_background_theta,
F] = pickle.load(f)
display_parameters(l_parameters, show, temperature, cell)
def display_parameters(l_parameters, show, temperature = None, cell = None):
"""
Display all the parameters from a list.
Parameters
----------
l_parameters : list
List of parameters.
show : bool
Display the figures (e.g. coupling function, intial condition) or not.
temperature : integer
Temperature condition . 34, 37 or 40.
cell : string
Cell type. 'NIH3T3' or 'U2OS'.
"""
[dt, sigma_em_circadian, W, pi,
N_theta, std_theta, period_theta, l_boundaries_theta, w_theta,
N_phi, std_phi, period_phi, l_boundaries_phi, w_phi,
N_amplitude_theta, mu_amplitude_theta, std_amplitude_theta,
gamma_amplitude_theta, l_boundaries_amplitude_theta,
N_background_theta, mu_background_theta, std_background_theta,
gamma_background_theta, l_boundaries_background_theta,
F] = l_parameters
print("")
print("########## SIMULATION PARAMETERS ##########")
print("dt = ", dt)
print("sigma_em_circadian = ", sigma_em_circadian)
print("")
print("########## THETA PARAMETERS ##########")
print("N_theta = ", N_theta)
print("std_theta = ", std_theta)
print("period_theta = ", period_theta)
print("l_boundaries_theta = ", l_boundaries_theta)
print("w_theta = ", w_theta)
print("")
print("########## PHI PARAMETERS ##########")
print("N_phi = ", N_phi)
print("std_phi = ", std_phi)
print("period_phi = ", period_phi)
print("l_boundaries_phi = ", l_boundaries_phi)
print("w_phi = ", w_phi)
print("")
print("########## AMPLITUDE PARAMETERS ##########")
print("N_amplitude_theta = ", N_amplitude_theta)
print("mu_amplitude_theta = ", mu_amplitude_theta)
print("std_amplitude_theta = ", std_amplitude_theta)
print("gamma_amplitude_theta = ", gamma_amplitude_theta)
print("l_boundaries_amplitude_theta = ", l_boundaries_amplitude_theta)
print("")
print("########## BACKGROUND PARAMETERS ##########")
print("N_background_theta = ", N_background_theta)
print("mu_background_theta = ", mu_background_theta)
print("std_background_theta = ", std_background_theta)
print("gamma_background_theta = ", gamma_background_theta)
print("l_boundaries_background_theta = ", l_boundaries_background_theta)
print("")
theta_var_coupled, amplitude_var, background_var = \
create_hidden_variables(l_parameters = l_parameters)
if show:
if W is None:
print("No waveform recorded, default waveform used")
W= [((1+np.cos( np.array(theta)))/2)**1.6 for theta \
in theta_var_coupled.domain]
plt.plot(theta_var_coupled.domain, W)
plt.xlabel(r'$\theta$')
plt.ylabel(r'$s(\theta)$')
plt.title('circadian waveform')
plt.show()
plt.close()
W = np.append(W[int(N_theta/2):], W[:int(N_theta/2)])
plt.plot(theta_var_coupled.domain, W)
plt.xlabel(r'$\theta$')
plt.ylabel(r'$s(\theta)$')
plt.title('circadian waveform')
plt.show()
plt.close()
if F is None:
print("No coupling recorded, blank coupling used")
F = np.zeros((N_theta, N_phi))
def add_colorbar(im, aspect=20, pad_fraction=0.5, **kwargs):
"""Add a vertical color bar to an image plot."""
divider = axes_grid1.make_axes_locatable(im.axes)
width = axes_grid1.axes_size.AxesY(im.axes, aspect=1./aspect)
pad = axes_grid1.axes_size.Fraction(pad_fraction, width)
current_ax = plt.gca()
cax = divider.append_axes("right", size=width, pad=pad)
plt.sca(current_ax)
return im.axes.figure.colorbar(im, cax=cax, **kwargs)
plt.figure(figsize=(5*1.2,5*1.2))
ax = plt.gca()
#ax.grid(False)
im = plt.imshow(F.T, cmap=bwr, vmin=-0.3, vmax=0.3, \
interpolation='spline16', origin='lower',
extent=[0, 1,0, 1])
add_colorbar(im, label = r'Acceleration ($rad.h^{-1}$)')
plt.xlabel(r'Circadian phase $\theta$')
plt.ylabel(r'Cell-cycle phase $\phi$')
plt.plot([0,1],[0.22,0.22], '--', color = 'grey')
plt.text(x = 0.05, y = 0.14, s='G1', color = 'grey', fontsize=12)
plt.text(x = 0.06, y = 0.27, s='S', color = 'grey', fontsize=12)
plt.plot([0,1],[0.84,0.84], '--', color = 'grey')
plt.text(x = 0.05, y = 0.84-0.08, s='S/G2', color = 'grey', fontsize=12)
plt.text(x = 0.06, y = 0.84+0.05, s='M', color = 'grey', fontsize=12)
#plt.xlabel("Circadian phase")
#plt.ylabel("Cell-cycle phase")
#plt.title('Coupling Function')
plt.tight_layout()
try:
plt.savefig("../Results/Disp/F_inferred_"+str(temperature)+"_"\
+cell+'.pdf')
except:
pass
plt.show()
plt.close()
theta_domain = theta_var_coupled.domain
amplitude_domain = amplitude_var.domain
background_domain = background_var.domain
if pi is None:
print("No pi recorded, uniform distribution used")
pi_theta = theta_var_coupled.pi
pi_amplitude = amplitude_var.pi
pi_background = background_var.pi
else:
pi_theta = np.sum(pi, axis = (1,2))
pi_amplitude = np.sum(pi, axis = (0,2))
pi_background = np.sum(pi, axis = (0,1))
plt.plot(theta_domain, pi_theta)
plt.xlabel(r'$\theta$')
plt.ylabel(r'$pi(\theta)$')
plt.title('Initial circadian phase distribution')
plt.show()
plt.close()
plt.plot(amplitude_domain, pi_amplitude)
plt.xlabel(r'$A$')
plt.ylabel(r'$pi(A)$')
plt.title('Initial amplitude distribution')
plt.show()
plt.close()
plt.plot(background_domain, pi_background)
plt.xlabel(r'$B$')
plt.ylabel(r'$pi(B)$')
plt.title('Initial background distribution')
plt.show()
plt.close()
""""""""""""""""""""" TEST """""""""""""""""""""
if __name__ == '__main__':
type_sim = 'Real'
type_param = 'opt'
temperature = None
type_cell = 'NIH3T3'
type_div = 'div'
path = load_path (type_sim = type_sim, type_param = type_param, \
type_cell = type_cell, temperature = temperature,
type_div = type_div, local = True)
print(path)
display_parameters_from_file(path, show = True, temperature = temperature,
cell = type_cell)
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