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svg2npy.py
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svg2npy.py
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#
# svg2npy.py: convert svg (asccii) output files to numpy's "npy" (binary) formatted files.
#
# Input:
# SVG output files from PhysiCell: snapshot%08d.svg
#
# Output:
# xyzr_*.npy - cells' centers (x,y,z) and radii (r)
# rgb_*.npy - associated colors (RGB, normalized [0,1])
#
# Author: Randy Heiland
#
import sys
import glob
import os
import xml.etree.ElementTree as ET
import math
try:
import matplotlib
import matplotlib.colors as mplc
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
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
step_value = 1
axes_min = 0.0
axes_max = 2000
#axes_max = 1000
print("current_idx=",current_idx)
def convert_svg():
global current_idx, axes_max, rvals, markers_size
# global vec_xyzr, vec_rgb
fname = "snapshot%08d.svg" % current_idx
if (os.path.isfile(fname) == False):
print("File does not exist: ",fname)
return
vec_xyzr = np.empty(shape=(0,4))
vec_rgb = np.empty(shape=(0,3))
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"
# title_str = "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'])
vec_xyzr = np.append(vec_xyzr, np.array([[xval,yval,0.0,rval]]), axis=0)
# print(xval,yval)
vec_rgb = np.append(vec_rgb, np.array([[rgb[0],rgb[1],rgb[2]]]), axis=0)
# print('rgb=',rgb[0],rgb[1],rgb[2])
# 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)
cell_file = "xyzr_%04d" % current_idx
rgb_file = "rgb_%04d" % current_idx
np.save(cell_file, vec_xyzr)
np.save(rgb_file, vec_rgb)
for current_idx in range(0,505):
convert_svg()