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plot.py
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import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
from matplotlib.patches import Wedge
from matplotlib.collections import PatchCollection
import matplotlib
from mpl_toolkits.axes_grid1 import make_axes_locatable
# from mpl_toolkits.axes_grid1.colorbar import colorbar
from copy import copy
def determine_cut_time(a):
if np.all(a >= 0):
cut_time = 0
else:
cut_time = 0
while all(a[:,cut_time] >= 0):
cut_time += 1
return cut_time
def fill_removed_portion(number_of_cells, cut_time, a_ax, b_ax, c_ax, v_ax, a, a_ymax, b_ymax, c_ymax, v_ymax):
x_fill = np.arange(0, number_of_cells, 1)
fill_bool = a[:,cut_time] < 0
fill_alpha = 0.35
a_ax.fill_between(x_fill, a_ymax, where=fill_bool, color="tab:gray", alpha=fill_alpha, step='mid')
b_ax.fill_between(x_fill, b_ymax, where=fill_bool, color="tab:gray", alpha=fill_alpha, step='mid')
c_ax.fill_between(x_fill, c_ymax, where=fill_bool, color="tab:gray", alpha=fill_alpha, step='mid')
v_ax.fill_between(x_fill, v_ymax, where=fill_bool, color="tab:gray", alpha=fill_alpha, step='mid')
return a_ax, b_ax, c_ax, v_ax,
def create_animated_output(number_of_cells, t, a, b, v, c, params, save_directory):
a_over_time = a
timepoints_N = a.shape[1]
streak_count = np.zeros((timepoints_N,),dtype=int)
for col_idx in range(timepoints_N):
unique, counts = np.unique(a[:,col_idx], return_counts=True)
count_dict = dict(zip(unique, counts))
try:
one_count = count_dict[1.0]
except KeyError:
one_count = 0
streak_count[col_idx] = one_count
number_of_frames = timepoints_N
sample_rate = int(round(len(t) / timepoints_N))
# print('sample_rate = ' + str(sample_rate))
# print('t shape = ' + str(t.shape))
# print('a shape = ' + str(a.shape))
# fig = plt.figure(figsize=(4,8))
#
# ax_a = fig.add_subplot(4,1,1)
# ax_v = fig.add_subplot(4,1,2)
# ax_b = fig.add_subplot(4,1,3)
# ax_c = fig.add_subplot(4,1,4)
fig, (ax_a, ax_v, ax_b, ax_c) = plt.subplots(nrows=4, ncols=1, sharex=True, figsize=(4,8))
# ax.plot(a[:,100])
# ax_a.set_title('streak')
# ax_b.set_title('bmp')
# ax_c.set_title('calcium')
a_ymax = np.max(a)*1.5 # 0.01
c_ymax = 10
ant_c_ymax = (10/11) * c_ymax
ax_a.set_ylim([0,a_ymax])
ax_b.set_ylim([0,np.max(b)*1.1])
ax_c.set_ylim([0,c_ymax])
# ax_c.set_ylim([0,np.max(c)*1.1])
ax_v.set_ylim([0,np.max(v)*1.1])
ax_a.set_yticks([0,1])
ax_a.set_yticklabels(['OFF','ON'])
anterior_cell = (number_of_cells - 1) / 2
ax_a.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_b.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_c.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_v.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_a.set_xticklabels([])
ax_b.set_xticklabels([])
ax_v.set_xticklabels([])
ax_c.set_xticklabels(['pos.', 'ant.', 'pos.'])
ax_c.set_xlabel("Cell position")
ant_x = [anterior_cell, anterior_cell]
threshold_streak = [params["c_b_threshold"], params["c_b_threshold"]]
threshold_vg1 = [params["v_b_threshold"], params["v_b_threshold"]]
ant_a, = ax_a.plot( ant_x, [0,np.max(a)], lw=1, c='k', linestyle='dashed')
ant_b, = ax_b.plot( ant_x, [0,np.max(b)], lw=1, c='k', linestyle='dashed')
ant_c, = ax_c.plot( ant_x, [0,ant_c_ymax], lw=1, c='k', linestyle='dashed')
ant_v, = ax_v.plot( ant_x, [0,np.max(v)], lw=1, c='k', linestyle='dashed')
threshold_streak_line, = ax_b.plot( [0, number_of_cells - 1],threshold_streak, lw=1, c='C0', linestyle='dashed')
threshold_vg1_line, = ax_b.plot( [0, number_of_cells - 1], threshold_vg1, lw=1, c='C9', linestyle='dashed')
line_a, = ax_a.plot( a_over_time[:,0], lw=3, c='C0', label="'Streak'")
line_b, = ax_b.plot( b[:,0], lw=3, c='C3', label='BMP4')
line_c, = ax_c.plot( c[:,0], lw=3, c='C1',label='Ca2+\nactivity')
line_v, = ax_v.plot( v[:,0], lw=3, c='C9',label='cVG1')
time_x_loc = number_of_cells/3
time_y_loc = 0.87*a_ymax
time_text = ax_a.text(time_x_loc, time_y_loc,'t = ', fontsize=16)
streak_x_loc = (number_of_cells/3) - (number_of_cells * 0.03)
streak_y_loc = 0.73*a_ymax
# streak_text = ax_a.text(streak_x_loc, streak_y_loc,'Streak cells: ', fontsize=12)
ax_a.legend(loc=2)
ax_b.legend(loc=2)
ax_c.legend(loc=2)
ax_v.legend(loc=2)
cut_time = determine_cut_time(a)
plt.tight_layout()
# plt.show()
def init():
line_a, = ax_a.plot([],[], lw=3, c='C0', label="'Streak'")
line_b, = ax_b.plot([],[], lw=3, c='C3', label='BMP4')
line_c, = ax_c.plot([],[],lw=3, c='C1',label='Ca2+\nactivity')
line_v, = ax_v.plot([],[],lw=3, c='C9',label='cVG1')
time_text.set_text('t = ')
# streak_text.set_text('Streak cells: ')
return line_a, line_b, line_c, line_v, time_text, # streak text,
def animate(i):
line_a.set_data(range(number_of_cells), a_over_time[:,i])
line_b.set_data(range(number_of_cells), b[:,i])
line_c.set_data(range(number_of_cells), c[:,i])
line_v.set_data(range(number_of_cells), v[:,i])
if i == cut_time:
out = fill_removed_portion(number_of_cells, cut_time, ax_a, ax_b, ax_c, ax_v, a, np.max(a), np.max(b), ant_c_ymax, np.max(v))
# time_text.set_text('t = ' + "{:.1f}".format(t[i]) +'h')
time_text.set_text('t = ' + "{:.2f}".format(t[i*sample_rate]) +'h')
# streak_text.set_text('Streak cells: ' + str(int(streak_count[i])))
return line_a, line_b, line_c, line_v, time_text, # streak text,
anim = FuncAnimation(fig, animate, init_func=init, frames=number_of_frames, blit=False)
anim.save(save_directory + '.mp4', writer='ffmpeg', fps=10)
return
def create_animated_output_extra_calcium(number_of_cells, sample_rate, t, a, b, v, c, params, save_directory):
a_over_time = a
streak_count = np.sum(a, axis=0)
number_of_frames = int(len(t) / sample_rate)
fig, (ax_a, ax_v, ax_b, ax_c_low, ax_c_high) = plt.subplots(nrows=5, ncols=1, sharex=True, figsize=(3.5,8))
a_ymax = np.max(a)*1.5 # 0.01
c_low_max = 10
c_high_max = 110
ax_a.set_ylim([0,a_ymax])
ax_b.set_ylim([0,np.max(b)*1.1])
ax_c_low.set_ylim([0,c_low_max])
ax_c_high.set_ylim([0,c_high_max])
ax_v.set_ylim([0,np.max(v)*1.1])
ax_a.set_yticks([0,1])
ax_a.set_yticklabels(['OFF','ON'])
anterior_cell = (number_of_cells - 1) / 2
ax_a.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_b.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_c_low.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_c_high.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_v.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_a.set_xticklabels([])
ax_b.set_xticklabels([])
ax_v.set_xticklabels([])
ax_c_low.set_xticklabels([])
ax_c_high.set_xticklabels(['pos.', 'ant.', 'pos.'])
ax_c_high.set_xlabel("Cell position")
ant_x = [anterior_cell, anterior_cell]
threshold_streak = [params["c_b_threshold"], params["c_b_threshold"]]
threshold_vg1 = [params["v_b_threshold"], params["v_b_threshold"]]
ant_a, = ax_a.plot( ant_x, [0,np.max(a)], lw=1, c='k', linestyle='dashed')
ant_b, = ax_b.plot( ant_x, [0,np.max(b)], lw=1, c='k', linestyle='dashed')
ant_c_low, = ax_c_low.plot( ant_x, [0,c_low_max], lw=1, c='k', linestyle='dashed')
ant_c_high, = ax_c_high.plot( ant_x, [0,c_high_max], lw=1, c='k', linestyle='dashed')
ant_v, = ax_v.plot( ant_x, [0,np.max(v)], lw=1, c='k', linestyle='dashed')
threshold_streak_line, = ax_b.plot( [0, number_of_cells - 1],threshold_streak, lw=1, c='C0', linestyle='dashed')
threshold_vg1_line, = ax_b.plot( [0, number_of_cells - 1], threshold_vg1, lw=1, c='C9', linestyle='dashed')
line_a, = ax_a.plot( a_over_time[:,0], lw=3, c='C0', label="'Streak'")
line_b, = ax_b.plot( b[:,0], lw=3, c='C3', label='BMP4')
line_c_low, = ax_c_low.plot( c[:,0], lw=3, c='C1',label='Ca2+\nactivity')
line_c_high, = ax_c_high.plot( c[:,0], lw=3, c='C1',label='Ca2+\nactivity')
line_v, = ax_v.plot( v[:,0], lw=3, c='C9',label='cVG1')
text_x_loc = number_of_cells * 0.68
# text_x_loc = number_of_cells * 0.33
time_x_loc = text_x_loc
time_y_loc = 0.85*a_ymax
time_text = ax_a.text(time_x_loc, time_y_loc,'t = ', fontsize=14)
streak_x_loc = text_x_loc - number_of_cells*0.05
streak_y_loc = 0.74*a_ymax
streak_text = ax_a.text(streak_x_loc, streak_y_loc,'Streak cells: ', fontsize=10)
ax_a.legend(loc=2)
ax_b.legend(loc=2)
# ax_c_low.legend(loc=2)
ax_c_high.legend(loc=2)
ax_v.legend(loc=2)
plt.tight_layout()
# plt.show()
def init():
line_a, = ax_a.plot([],[], lw=3, c='C0', label="'Streak'")
line_b, = ax_b.plot([],[], lw=3, c='C3', label='BMP4')
line_c_low, = ax_c_low.plot([],[],lw=3, c='C1',label='Ca2+\nactivity')
line_c_high, = ax_c_high.plot([],[],lw=3, c='C1',label='Ca2+\nactivity')
line_v, = ax_v.plot([],[],lw=3, c='C9',label='cVG1')
time_text.set_text('t = ')
streak_text.set_text('Streak cells: ')
return line_a, line_b, line_c_low, line_c_high, line_v, time_text, streak_text,
def animate(i):
line_a.set_data(range(number_of_cells), a_over_time[:,i * sample_rate])
line_b.set_data(range(number_of_cells), b[:,i * sample_rate])
line_c_low.set_data(range(number_of_cells), c[:,i * sample_rate])
line_c_high.set_data(range(number_of_cells), c[:,i * sample_rate])
line_v.set_data(range(number_of_cells), v[:,i * sample_rate])
time_text.set_text('t = ' + "{:.1f}".format(t[i * sample_rate]) +'h')
streak_text.set_text('Streak cells: ' + str(int(streak_count[i * sample_rate])))
return line_a, line_b, line_c_low,line_c_high, line_v, time_text, streak_text,
anim = FuncAnimation(fig, animate, init_func=init, frames=number_of_frames, blit=False)
anim.save(save_directory + 'hello.mp4', writer='ffmpeg', fps=10)
return
def create_stills_array(time_indices, number_of_cells, t, a, b, v, c, params, filename):
matplotlib.rcParams['font.family'] = 'sans-serif'
# matplotlib.rcParams['font.sans-serif'] = ['Arial']
# matplotlib.rcParams['font.sans-serif'] = ['Clear Sans']
timepointsN = len(time_indices)
streak_count = np.sum(a, axis=0)
a_ymax = np.max(a)*1.1
b_ymax = np.max(b)*1.1
c_ymax = np.max(c)*1.1
v_ymax = np.max(v)*1.1
anterior_cell = (number_of_cells - 1) / 2
cut_time = determine_cut_time(a)
fig = plt.figure(figsize=(8,4))
for col_idx, time_idx in enumerate(time_indices):
ax_a = fig.add_subplot(4, timepointsN, 1 + col_idx)
ax_v = fig.add_subplot(4, timepointsN, 1 + timepointsN + col_idx)
ax_b = fig.add_subplot(4, timepointsN, 1 + (2*timepointsN) + col_idx)
ax_c = fig.add_subplot(4, timepointsN, 1 + (3*timepointsN) + col_idx)
ax_a.set_ylim([0,a_ymax])
ax_b.set_ylim([0,b_ymax])
ax_c.set_ylim([0,c_ymax])
ax_v.set_ylim([0,v_ymax])
ax_a.set_yticks([0,1])
ax_a.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_b.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_c.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_v.set_xticks([0,anterior_cell, number_of_cells - 1])
ax_a.set_xticklabels([])
ax_b.set_xticklabels([])
ax_v.set_xticklabels([])
ax_c.set_xticklabels(['P', 'A', 'P'])
b_x_min, b_x_max = ax_b.get_xlim()
ax_c.set_xlabel("Cell position")
ant_x = [anterior_cell, anterior_cell]
thresh_v_b = [params["v_b_threshold"], params["v_b_threshold"]]
thresh_c_b = [params["c_b_threshold"], params["c_b_threshold"]]
ant_a, = ax_a.plot( ant_x, [0,np.max(a)], lw=0.5, c='k', linestyle='dashed')
ant_b, = ax_b.plot( ant_x, [0,np.max(b)], lw=0.5, c='k', linestyle='dashed')
ant_c, = ax_c.plot( ant_x, [0,np.max(c)], lw=0.5, c='k', linestyle='dashed')
ant_v, = ax_v.plot( ant_x, [0,np.max(v)], lw=0.5, c='k', linestyle='dashed')
line_thresh_v_b, = ax_b.plot( [b_x_min,b_x_max], thresh_v_b, lw=1, c='C9', linestyle='dashed')
line_thresh_c_b, = ax_b.plot( [b_x_min,b_x_max], thresh_c_b, lw=1, c='C0', linestyle='dashed')
line_a, = ax_a.plot( a[:,time_idx], lw=2, c='C0', label="'Streak'")
line_b, = ax_b.plot( b[:,time_idx], lw=2, c='C3', label='cBMP4')
line_c, = ax_c.plot( c[:,time_idx], lw=2, c='C1',label='Ca2+')
line_v, = ax_v.plot( v[:,time_idx], lw=2, c='C9',label='cVG1')
time_str = str(t[time_idx])
ax_a.set_title('t = ' + time_str + 'h', fontweight='bold')
if col_idx == 0:
ax_a.set_yticklabels(['OFF','ON'])
ax_a.set_ylabel("'Streak'", fontweight='bold')
ax_b.set_ylabel('BMP4\n', fontweight='bold')
ax_c.set_ylabel('Ca2+\nactivity', fontweight='bold')
ax_v.set_ylabel('cVG1\n', fontweight='bold')
else:
ax_a.set_yticklabels([])
ax_b.set_yticklabels([])
ax_c.set_yticklabels([])
ax_v.set_yticklabels([])
if time_idx >= cut_time:
out = fill_removed_portion(number_of_cells, cut_time, ax_a, ax_b, ax_c, ax_v, a, np.max(a), np.max(b), np.max(c), np.max(v))
# if col_idx == timepointsN - 1:
# ax_a.legend(loc=2)
# ax_b.legend(loc=2)
# ax_c.legend(loc=2)
# ax_v.legend(loc=2)
plt.tight_layout()
fig.savefig(filename, dpi=300, orientation='portrait', format='png') #, transparent=True)
def create_circle_animation(var, save_directory):
number_of_cells = var.shape[0]
number_of_steps = var.shape[1] # timesteps
b_max = np.amax(var)
b_min = np.amin(var)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_ylim([1,-1])
ax.set_xlim([1,-1])
ax.set_aspect('equal')
ax.axis('off')
theta_list = np.linspace(90 , 450, 101)
b_patches = []
for i in range(len(theta_list) - 1):
b_patches.append(Wedge((0,0), 0.8, theta_list[i], theta_list[i+1], width=0.1))
b_patch_col = PatchCollection(b_patches)
b_colors = var[:,0]
b_patch_col.set_array(np.array(b_colors))
b_patch_col.set_clim(vmin=b_min, vmax=b_max)
b_patch_col.set_cmap('viridis')
ax.add_collection(b_patch_col)
fig.colorbar(b_patch_col, ax=ax)
# ax.text(-0.9, 0.5, label_string, fontsize=20)
#
# current_time = 0
# time_string = 't = ' + str(current_time) + 's'
# time_text = ax.text(-0.9, -0.5,[],fontsize=16)
# time_text.set_text(time_string)
def init():
b_colors = var[:,0]
b_patch_col.set_array(np.array(b_colors))
b_patch_col.set_clim(vmin=b_min, vmax=b_max)
return b_patch_col,
sample_rate = 1
def animate(i):
sample_rate = 1
b_colors = var[:,sample_rate * i]
b_patch_col.set_array(np.array(b_colors))
b_patch_col.set_clim(vmin=b_min, vmax=b_max)
return b_patch_col,
number_of_frames = int(np.ceil(number_of_steps / sample_rate))
frames_per_second = 24
interval = np.ceil(1000/frames_per_second)
anim = FuncAnimation(fig, animate, init_func=init, interval=interval, frames=number_of_frames, blit=True)
anim.save(save_directory + 'circle' + '.mp4', fps=frames_per_second, extra_args=['-vcodec', 'libx264'])
# def add_colormaps(var):
#
# grey_proportion = 1 / (np.max(var) + 1)
# color_proportion = np.max(var) / (np.max(var) + 1)
#
# cmap_pointsN = 256
#
# grey_pointsN = np.floor(grey_proportion * cmap_pointsN)
# color_pointsN = np.ceil(color_proportion * cmap_pointsN)
#
# grey_points = numpy.linspace(-1, 0, num=50, endpoint=False)
# color_points = numpy.linspace(0, 1, num=50, endpoint=True) # not sure 1 here is what you want
#
# # sample the colormaps that you want to use. Use 128 from each so we get 256
# # colors in total
# colors1 = plt.cm.binary(np.linspace(0., 1, 128))
# colors2 = plt.cm.gist_heat_r(np.linspace(0, 1, 128))
#
# # combine them and build a new colormap
# colors = np.vstack((colors1, colors2))
# mymap = mcolors.LinearSegmentedColormap.from_list('my_colormap', colors)
#
# plt.pcolor(data, cmap=mymap)
# plt.colorbar()
# plt.show()
def concentric_circle_animation(t, a, b, c, v, save_directory):
number_of_cells = a.shape[0]
number_of_steps = a.shape[1] # timesteps
a_max = np.amax(a)
a_min = 0
b_max = np.amax(b)
b_min = 0
c_max = np.amax(c)
c_min = 0
v_max = np.amax(v)
v_min = 0
fig = plt.figure()
ax = fig.add_subplot(122)
ax_bmp = fig.add_subplot(121)
ax.set_ylim([1,-1])
ax.set_xlim([1,-1])
ax.set_aspect('equal')
# ax.axis('off')
ax.set_facecolor('C7')
ax.set_xticks([])
ax.set_yticks([])
ax.plot([-1,1],[0,0],linestyle='dashed', linewidth=0.5, c='k')
ax.plot([0,0],[-1,1],linestyle='dashed', linewidth=0.5, c='k')
ax_bmp.set_ylim([1,-1])
ax_bmp.set_xlim([1,-1])
ax_bmp.set_aspect('equal')
# ax.axis('off')
ax_bmp.set_facecolor('C7')
ax_bmp.set_xticks([])
ax_bmp.set_yticks([])
ax_bmp.plot([-1,1],[0,0],linestyle='dashed', linewidth=0.5, c='k')
ax_bmp.plot([0,0],[-1,1],linestyle='dashed', linewidth=0.5, c='k')
theta_list = np.linspace(90 , 450, 101)
a_patches = []
b_patches = []
c_patches = []
v_patches = []
for i in range(len(theta_list) - 1):
a_patches.append(Wedge((0,0), 0.75, theta_list[i], theta_list[i+1], width=0.08))
b_patches.append(Wedge((0,0), 0.85, theta_list[i], theta_list[i+1], width=0.25))
c_patches.append(Wedge((0,0), 0.65, theta_list[i], theta_list[i+1], width=0.08))
v_patches.append(Wedge((0,0), 0.85, theta_list[i], theta_list[i+1], width=0.08))
a_patch_col = PatchCollection(a_patches)
a_colors = a[:,0]
a_patch_col.set_array(np.array(a_colors))
a_patch_col.set_clim(vmin=a_min, vmax=a_max)
a_patch_col.set_cmap('Purples')
a_cm = copy(a_patch_col.get_cmap())
a_cm.set_under('C7')
a_patch_col.set_cmap(a_cm)
b_patch_col = PatchCollection(b_patches)
b_colors = b[:,0]
b_patch_col.set_array(np.array(b_colors))
b_patch_col.set_clim(vmin=b_min, vmax=b_max)
b_patch_col.set_cmap('viridis')
b_cm = copy(b_patch_col.get_cmap())
b_cm.set_under('C7')
b_patch_col.set_cmap(b_cm)
c_patch_col = PatchCollection(c_patches)
c_colors = c[:,0]
c_patch_col.set_array(np.array(c_colors))
c_patch_col.set_clim(vmin=c_min, vmax=c_max)
c_patch_col.set_cmap('Oranges')
c_cm = copy(c_patch_col.get_cmap())
c_cm.set_under('C7')
c_patch_col.set_cmap(c_cm)
v_patch_col = PatchCollection(v_patches)
v_colors = v[:,0]
v_patch_col.set_array(np.array(v_colors))
v_patch_col.set_clim(vmin=v_min, vmax=v_max)
v_patch_col.set_cmap('Blues')
v_cm = copy(v_patch_col.get_cmap())
v_cm.set_under('C7')
v_patch_col.set_cmap(v_cm)
ax.add_collection(a_patch_col)
ax.add_collection(c_patch_col)
ax.add_collection(v_patch_col)
ax_bmp.add_collection(b_patch_col)
""" colorbars """
# divider = make_axes_locatable(ax)
# b_cax = divider.append_axes("right", size="5%", pad=0.05)
# b_cb = fig.colorbar(b_patch_col, cax=b_cax, orientation='vertical', label='BMP4')
#
# c_cax = divider.append_axes("left", size="5%", pad=0.05)
# c_cb = colorbar(c_patch_col, cax=c_cax, orientation="vertical")
# # c_cb = plt.colorbar(c_patch_col, cax=c_cax, orientation="vertical")
# # c_cb = fig.colorbar(c_patch_col, cax=c_cax, orientation="vertical")
# c_cax.yaxis.set_ticks_position("left")
""" time string """
# ax.text(-0.9, 0.5, label_string, fontsize=20)
#
# current_time = 0
# time_string = 't = ' + str(current_time) + 's'
# time_text = ax.text(-0.9, -0.5,[],fontsize=16)
# time_text.set_text(time_string)
def init():
a_colors = a[:,0]
a_patch_col.set_array(np.array(a_colors))
a_patch_col.set_clim(vmin=a_min, vmax=a_max)
b_colors = b[:,0]
b_patch_col.set_array(np.array(b_colors))
b_patch_col.set_clim(vmin=b_min, vmax=b_max)
c_colors = c[:,0]
c_patch_col.set_array(np.array(c_colors))
c_patch_col.set_clim(vmin=c_min, vmax=c_max)
v_colors = c[:,0]
v_patch_col.set_array(np.array(v_colors))
v_patch_col.set_clim(vmin=v_min, vmax=v_max)
return a_patch_col, b_patch_col, c_patch_col, v_patch_col,
sample_rate = 2
def animate(i):
sample_rate = 2
a_colors = a[:,sample_rate * i]
a_patch_col.set_array(np.array(a_colors))
a_patch_col.set_clim(vmin=a_min, vmax=a_max)
b_colors = b[:,sample_rate * i]
b_patch_col.set_array(np.array(b_colors))
b_patch_col.set_clim(vmin=b_min, vmax=b_max)
c_colors = c[:,sample_rate * i]
c_patch_col.set_array(np.array(c_colors))
c_patch_col.set_clim(vmin=c_min, vmax=c_max)
v_colors = v[:,sample_rate * i]
v_patch_col.set_array(np.array(v_colors))
v_patch_col.set_clim(vmin=v_min, vmax=v_max)
return a_patch_col, b_patch_col, c_patch_col, v_patch_col,
number_of_frames = int(np.ceil(number_of_steps / sample_rate))
frames_per_second = 10
interval = np.ceil(1000/frames_per_second)
anim = FuncAnimation(fig, animate, init_func=init, interval=interval, frames=number_of_frames, blit=True)
anim.save(save_directory + 'circle' + '.mp4', fps=frames_per_second, extra_args=['-vcodec', 'libx264'])
# plt.savefig(save_directory + 'circle' + '.jpg')
# plt.show()