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anim_svg2.py
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anim_svg2.py
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#
# anim_svg2.py: render/animate PhysiCell .svg files, non-stop (cycle through all .svg files in a directory)
#
# Usage:
# python anim_svg2.py <show_nucleus start_index axes_min axes_max>
# i.e., the arguments <...> are optional and have defaults.
#
# Dependencies include matplotlib and numpy. We recommend installing the Anaconda Python3 distribution.
#
# Examples (run from directory containing the .svg files):
# python anim_svg2.py
# python anim_svg2.py 0 5 700 1300
#
# Author: Randy Heiland (except for the circles() function)
#
#
__author__ = "Randy Heiland"
import sys
import glob
import os
import xml.etree.ElementTree as ET
import math
join_our_list = "(Join/ask questions at https://groups.google.com/forum/#!forum/physicell-users)\n"
try:
import matplotlib
import matplotlib.colors as mplc
from matplotlib.patches import Circle, Ellipse, Rectangle
from matplotlib.collections import PatchCollection
except:
print("\n---Error: cannot import matplotlib")
print("---Try: python -m pip install matplotlib")
print(join_our_list)
# print("---Consider installing Anaconda's Python 3 distribution.\n")
raise
try:
import numpy as np # if mpl was installed, numpy should have been too.
except:
print("\n---Error: cannot import numpy")
print("---Try: python -m pip install numpy\n")
print(join_our_list)
raise
from collections import deque
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(join_our_list)
# print("Consider installing Anaconda's Python 3 distribution.")
raise
current_idx = 0
print("# args=",len(sys.argv)-1)
#for idx in range(len(sys.argv)):
use_defaults = True
show_nucleus = 0
current_idx = 0
axes_min = 0.0
axes_max = 1000 # but overridden by "width" attribute in .svg
if (len(sys.argv) == 5):
use_defaults = False
kdx = 1
show_nucleus = int(sys.argv[kdx])
kdx += 1
current_idx = int(sys.argv[kdx])
kdx += 1
axes_min = float(sys.argv[kdx])
kdx += 1
axes_max = float(sys.argv[kdx])
elif (len(sys.argv) != 1):
print("Please provide either no args or 4 args:")
usage_str = "show_nucleus start_index axes_min axes_max"
print(usage_str)
print("e.g.,")
eg_str = "%s 0 0 0 2000" % (sys.argv[0])
print(eg_str)
sys.exit(1)
#"""
print("show_nucleus=",show_nucleus)
print("current_idx=",current_idx)
print("axes_min=",axes_min)
print("axes_max=",axes_max)
#"""
"""
if (len(sys.argv) > 1):
current_idx = int(sys.argv[1])
if (len(sys.argv) > 2):
axes_min = float(sys.argv[2])
axes_max = float(sys.argv[3])
if (len(sys.argv) > 4):
usage_str = "[<start_index> [<axes_min axes_max>]]"
print(usage_str)
print("e.g.,")
eg_str = "%s 1 10 700 1300" % (sys.argv[0])
print(eg_str)
sys.exit(1)
"""
print("current_idx=",current_idx)
#d={} # dictionary to hold all (x,y) positions of cells
"""
--- for example ---
In [141]: d['cell1599'][0:3]
Out[141]:
array([[ 4900. , 4900. ],
[ 4934.17, 4487.91],
[ 4960.75, 4148.02]])
"""
fig = plt.figure(figsize=(7,7))
ax = fig.gca()
#ax.set_aspect("equal")
#plt.ion()
time_delay = 0.1
count = -1
#while True:
#-----------------------------------------------------
def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
"""
See https://gist.github.com/syrte/592a062c562cd2a98a83
Make a scatter plot of circles.
Similar to plt.scatter, but the size of circles are in data scale.
Parameters
----------
x, y : scalar or array_like, shape (n, )
Input data
s : scalar or array_like, shape (n, )
Radius of circles.
c : color or sequence of color, optional, default : 'b'
`c` can be a single color format string, or a sequence of color
specifications of length `N`, or a sequence of `N` numbers to be
mapped to colors using the `cmap` and `norm` specified via kwargs.
Note that `c` should not be a single numeric RGB or RGBA sequence
because that is indistinguishable from an array of values
to be colormapped. (If you insist, use `color` instead.)
`c` can be a 2-D array in which the rows are RGB or RGBA, however.
vmin, vmax : scalar, optional, default: None
`vmin` and `vmax` are used in conjunction with `norm` to normalize
luminance data. If either are `None`, the min and max of the
color array is used.
kwargs : `~matplotlib.collections.Collection` properties
Eg. alpha, edgecolor(ec), facecolor(fc), linewidth(lw), linestyle(ls),
norm, cmap, transform, etc.
Returns
-------
paths : `~matplotlib.collections.PathCollection`
Examples
--------
a = np.arange(11)
circles(a, a, s=a*0.2, c=a, alpha=0.5, ec='none')
plt.colorbar()
License
--------
This code is under [The BSD 3-Clause License]
(http://opensource.org/licenses/BSD-3-Clause)
"""
if np.isscalar(c):
kwargs.setdefault('color', c)
c = None
if 'fc' in kwargs:
kwargs.setdefault('facecolor', kwargs.pop('fc'))
if 'ec' in kwargs:
kwargs.setdefault('edgecolor', kwargs.pop('ec'))
if 'ls' in kwargs:
kwargs.setdefault('linestyle', kwargs.pop('ls'))
if 'lw' in kwargs:
kwargs.setdefault('linewidth', kwargs.pop('lw'))
# You can set `facecolor` with an array for each patch,
# while you can only set `facecolors` with a value for all.
zipped = np.broadcast(x, y, s)
patches = [Circle((x_, y_), s_)
for x_, y_, s_ in zipped]
collection = PatchCollection(patches, **kwargs)
if c is not None:
c = np.broadcast_to(c, zipped.shape).ravel()
collection.set_array(c)
collection.set_clim(vmin, vmax)
ax = plt.gca()
ax.add_collection(collection)
ax.autoscale_view()
plt.draw_if_interactive()
if c is not None:
plt.sci(collection)
return collection
#-----------------------------------------------------
def plot_svg():
global current_idx, axes_max
fname = "snapshot%08d.svg" % current_idx
if (os.path.isfile(fname) == False):
print("File does not exist: ",fname)
return
xlist = deque()
ylist = deque()
rlist = deque()
rgb_list = deque()
# print('\n---- ' + fname + ':')
tree = ET.parse(fname)
root = tree.getroot()
# print('--- root.tag ---')
# print(root.tag)
# print('--- root.attrib ---')
# print(root.attrib)
# print('--- child.tag, child.attrib ---')
numChildren = 0
for child in root:
# print(child.tag, child.attrib)
# print("keys=",child.attrib.keys())
if use_defaults and ('width' in child.attrib.keys()):
axes_max = float(child.attrib['width'])
# print("--- found width --> axes_max =", axes_max)
if child.text and "Current time" in child.text:
svals = child.text.split()
title_str = "(" + str(current_idx) + ") Current time: " + svals[2] + "d, " + svals[4] + "h, " + svals[7] + "m"
# print("width ",child.attrib['width'])
# print('attrib=',child.attrib)
# if (child.attrib['id'] == 'tissue'):
if ('id' in child.attrib.keys()):
# print('-------- found tissue!!')
tissue_parent = child
break
# print('------ search tissue')
cells_parent = None
for child in tissue_parent:
# print('attrib=',child.attrib)
if (child.attrib['id'] == 'cells'):
# print('-------- found cells, setting cells_parent')
cells_parent = child
break
numChildren += 1
num_cells = 0
# print('------ search cells')
for child in cells_parent:
# print(child.tag, child.attrib)
# print('attrib=',child.attrib)
for circle in child: # two circles in each child: outer + nucleus
# circle.attrib={'cx': '1085.59','cy': '1225.24','fill': 'rgb(159,159,96)','r': '6.67717','stroke': 'rgb(159,159,96)','stroke-width': '0.5'}
# print(' --- cx,cy=',circle.attrib['cx'],circle.attrib['cy'])
xval = float(circle.attrib['cx'])
s = circle.attrib['fill']
# print("s=",s)
# print("type(s)=",type(s))
if (s[0:3] == "rgb"): # if an rgb string, e.g. "rgb(175,175,80)"
rgb = list(map(int, s[4:-1].split(",")))
rgb[:]=[x/255. for x in rgb]
else: # otherwise, must be a color name
rgb_tuple = mplc.to_rgb(mplc.cnames[s]) # a tuple
rgb = [x for x in rgb_tuple]
# test for bogus x,y locations (rwh TODO: use max of domain?)
too_large_val = 10000.
if (math.fabs(xval) > too_large_val):
print("bogus xval=",xval)
break
yval = float(circle.attrib['cy'])
if (math.fabs(yval) > too_large_val):
print("bogus xval=",xval)
break
rval = float(circle.attrib['r'])
# print('rval=',rval)
xlist.append(xval)
ylist.append(yval)
rlist.append(rval)
rgb_list.append(rgb)
# print('rgb_list = ',rgb_list)
# For .svg files with cells that *have* a nucleus, there will be a 2nd
if (show_nucleus == 0):
break
num_cells += 1
# if num_cells > 3: # for debugging
# print(fname,': num_cells= ',num_cells," --- debug exit.")
# sys.exit(1)
# break
print(fname,': num_cells= ',num_cells)
xvals = np.array(xlist)
yvals = np.array(ylist)
rvals = np.array(rlist)
rgbs = np.array(rgb_list)
# print('type(rgbs) = ',type(rgbs))
# print('rgbs = ',rgbs)
#print("xvals[0:5]=",xvals[0:5])
#print("rvals[0:5]=",rvals[0:5])
# print("rvals.min, max=",rvals.min(),rvals.max())
plt.cla()
title_str += " (" + str(num_cells) + " agents)"
plt.title(title_str)
plt.xlim(axes_min,axes_max)
plt.ylim(axes_min,axes_max)
# plt.scatter(xvals,yvals, s=rvals*scale_radius, c=rgbs)
# plt.scatter(xvals,yvals, s=rvals*scale_radius, c=rgbs, alpha=0.5, edgecolor='black')
# plt.scatter(xvals,yvals, s=rvals*scale_radius, c=rgbs, alpha=1.0, edgecolor='black')
# circles(xvals,yvals, s=rvals, c=rgbs, alpha=1.0, edgecolor='black')
# circles(xvals,yvals, s=rvals)
# circles(xvals,yvals, s=rvals, c=rgbs)
circles(xvals,yvals, s=rvals, color=rgbs)
#plt.xlim(0,2000) # TODO - get these values from width,height in .svg at top
#plt.ylim(0,2000)
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_svg()
elif event.key == 'right': # right arrow key
# print('go forwards')
# fig.canvas.draw()
current_idx += step_value
plot_svg()
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_svg()
else:
print('press', event.key)
#for current_idx in range(40):
# fname = "snapshot%08d.svg" % current_idx
# plot_svg(fname)
while True:
svg_files = glob.glob('snap*.svg')
for current_idx in range(len(svg_files)):
plot_svg()
#print("\nNOTE: click in plot window to give it focus before using keys.")
# fig.canvas.mpl_connect('key_press_event', press)
# keep last plot displayed
#plt.ioff()
plt.show()