TODO
%matplotlib inline
import matplotlib.pyplot as plt
import matplotlib
import pandas as pd
import numpy as np
from kt_simul.core import Metaphase
from kt_simul.core import load_metaphase
from kt_simul.core import parameters
from kt_simul.visu import SpindleViewer
from kt_simul.visu import SpindleWidget
params = parameters.get_default_params()
params.loc['dt', 'value'] = 0.1
params.loc['span', 'value'] = 10
params.loc['t_A', 'value'] = 10
params.loc['d_alpha', 'value'] = 0.05 # 0.05
params.loc['k_a', 'value'] = 0.06 # 0.06
params.loc['orientation', 'value'] = 1 # 1
params.loc['N', 'value'] = 2 # 3
params.loc['Mk', 'value'] = 1 # 3
params.loc['L0', 'value'] = 0.3 # 0.3
params.loc['ldep', 'value'] = 0 # 0.2
measures = parameters.get_default_measures()
meta = Metaphase(verbose=False,
params=params,
measures=measures,
initial_plug='null',
keep_same_random_seed=False,
force_parameters=[])
meta.simul(progress=True)
meta.project(progress=True)
Save simulation for later re-use.
meta.save("/home/hadim/test.h5")
Visualize spindle elements trajectories
fig = meta.show()
Visualize points trajectories in 3D with vispy.
%matplotlib qt
# Pure vispy
v = SpindleViewer(metaphase=meta)
v.play()
v.quit()
# Vispy + Qt
w = SpindleWidget(metaphase=meta)
w.show()