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anim_substrate_grid_step5.py
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anim_substrate_grid_step5.py
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import sys,pathlib
import xml.etree.ElementTree as ET
import math
import scipy.io
import matplotlib
#import matplotlib.pyplot as plt # NB! do this AFTER the TkAgg line below!
#import matplotlib.colors as mplc
from matplotlib.colors import BoundaryNorm
from matplotlib.ticker import MaxNLocator
from matplotlib.collections import LineCollection
import numpy as np
from numpy.random import randn
try:
# apparently we need mpl's Qt backend to do keypresses
# matplotlib.use("Qt5Agg")
matplotlib.use("TkAgg")
import matplotlib.pyplot as plt
except:
print("\n---Error: cannot use matplotlib's TkAgg backend")
# print("Consider installing Anaconda's Python 3 distribution.")
raise
current_idx = 0
if (len(sys.argv) < 3):
current_idx = 0
field_idx = 4
fix_cmap = 0
print("Usage: %s start_idx field_idx fix_cmap(0/1) vmin vmax" % sys.argv[0])
print("e.g. %s start_idx field_idx fix_cmap(0/1) vmin vmax\n" % sys.argv[0])
else:
kdx = 1
current_idx = int(sys.argv[kdx]); kdx += 1
field_idx = int(sys.argv[kdx]); kdx += 1
fix_cmap = int(sys.argv[kdx]); kdx += 1
vmin = float(sys.argv[kdx]); kdx += 1
vmax = float(sys.argv[kdx]); kdx += 1
print('current_idx, field_idx = ',current_idx, field_idx)
# figure out the domain sizes (might not be square)
ifname = "initial.xml"
tree = ET.parse(ifname)
xml_root = tree.getroot()
xcoord_vals = xml_root.find(".//x_coordinates").text.split()
ycoord_vals = xml_root.find(".//y_coordinates").text.split()
xmin = float(xcoord_vals[0])
xmax = float(xcoord_vals[-1]) # should be 999.0
ymin = float(ycoord_vals[0])
ymax = float(ycoord_vals[-1]) # should be 999.0
# numx = int((xmax - xmin) / xdel) # need to also round maybe?
# numy = int((ymax - ymin) / ydel)
numx = len(xcoord_vals)
numy = len(ycoord_vals)
print("numx, numy = ",numx,numy)
fig = plt.figure(figsize=(7,5.8))
#ax = fig.gca()
time_delay = 0.1
count = -1
cbar = None
def plot_substrate():
global current_idx, axes_max, cbar
# select whichever substrate index you want, e.g., for one model:
# 4=tumor cells field, 5=blood vessel density, 6=growth substrate
xml_file = "output%08d.xml" % current_idx
print('xml_file = ',xml_file)
tree = ET.parse(xml_file)
root = tree.getroot()
print('time=' + root.find(".//current_time").text)
mins = float(root.find(".//current_time").text)
hrs = int(mins/60.)
days = int(hrs/24.)
title_str = '%d days, %d hrs, %d mins' % (int(days),(hrs%24), mins - (hrs*60))
print(title_str)
fname = "output%08d_microenvironment0.mat" % current_idx
output_dir_str = '.'
fullname = output_dir_str + "/" + fname
if not pathlib.Path(fullname).is_file():
print("file not found",fullname)
return
info_dict = {}
scipy.io.loadmat(fullname, info_dict)
M = info_dict['multiscale_microenvironment']
print('plot_substrate: field_idx=',field_idx)
f = M[field_idx,:] #
#N = int(math.sqrt(len(M[0,:])))
#grid2D = M[0,:].reshape(N,N)
xgrid = M[0, :].reshape(numy, numx)
ygrid = M[1, :].reshape(numy, numx)
# xvec = grid2D[0,:]
#xvec.size
#xvec.shape
num_contours = 30
num_contours = 10
# vmin = 30.
# vmax = 38.
levels = MaxNLocator(nbins=30).tick_values(vmin, vmax)
# cmap = plt.get_cmap('PiYG')
cmap = plt.get_cmap('viridis')
norm = BoundaryNorm(levels, ncolors=cmap.N, clip=True)
# my_plot = plt.contourf(xvec,xvec,M[field_idx,:].reshape(N,N), num_contours, cmap='viridis') #'viridis'
if fix_cmap > 0:
# my_plot = plt.contourf(xvec,xvec,M[field_idx,:].reshape(N,N), levels=levels, cmap=cmap)
my_plot = plt.contourf(xgrid, ygrid, M[field_idx, :].reshape(numy, numx), levels=levels, extend='both', cmap=cmap)
else:
# my_plot = plt.contourf(xvec,xvec,M[field_idx,:].reshape(N,N), cmap=cmap)
my_plot = plt.contourf(xgrid, ygrid, M[field_idx, :].reshape(numy, numx), cmap=cmap)
if cbar == None:
# cbar = plt.colorbar(my_plot, boundaries=np.arange(vmin, vmax, 1.0))
cbar = plt.colorbar(my_plot)
else:
cbar = plt.colorbar(my_plot, cax=cbar.ax)
xs = np.linspace(xmin,xmax,numx)
ys = np.linspace(ymin,ymax,numy)
hlines = np.column_stack(np.broadcast_arrays(xs[0], ys, xs[-1], ys))
vlines = np.column_stack(np.broadcast_arrays(xs, ys[0], xs, ys[-1]))
grid_lines = np.concatenate([hlines, vlines]).reshape(-1, 2, 2)
line_collection = LineCollection(grid_lines, color="red", linewidths=0.5)
ax = plt.gca()
ax.add_collection(line_collection)
ax.set_xlim(xs[0], xs[-1])
ax.set_ylim(ys[0], ys[-1])
# plt.axis('equal')
plt.title(title_str)
# plt.show()
png_file = "aaa%08d.png" % current_idx
fig.savefig(png_file)
plt.pause(time_delay)
step_value = 1
def press(event):
global current_idx, step_value
# print('press', event.key)
sys.stdout.flush()
if event.key == 'escape':
sys.exit(1)
elif event.key == 'h': # help
print('esc: quit')
print('right arrow: increment by step_value')
print('left arrow: decrement by step_value')
print('up arrow: increment step_value by 1')
print('down arrow: decrement step_value by 1')
print('0: reset to 0th frame')
print('h: help')
elif event.key == 'left': # left arrow key
# print('go backwards')
# fig.canvas.draw()
current_idx -= step_value
if (current_idx < 0):
current_idx = 0
plot_substrate()
elif event.key == 'right': # right arrow key
# print('go forwards')
# fig.canvas.draw()
current_idx += step_value
plot_substrate()
elif event.key == 'up': # up arrow key
step_value += 1
print('step_value=',step_value)
elif event.key == 'down': # down arrow key
step_value -= 1
if (step_value <= 0):
step_value = 1
print('step_value=',step_value)
elif event.key == '0': # reset to 0th frame/file
current_idx = 0
plot_substrate()
else:
print('press', event.key)
plot_substrate()
print("\nNOTE: click in plot window to give it focus before using keys.")
fig.canvas.mpl_connect('key_press_event', press)
#plot_substrate(frame_idx)
plt.show()