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| import Tkinter
import random
import math
import time
import rules #That's "TedsWorkspace2"
winwidth = 1000
winheight = 700
randinterp = False
num_morphogens = 1
class morphogen:
def __init__(self, diffcoeff, prodrate,decayrate, initconc, mr):
self.diffcoeff = diffcoeff
self.prodrate = prodrate
self.decayrate = decayrate
self.conc = initconc
self.newc = initconc
self.rule = mr
class cell:
def __init__(self, idnum, type, xcor, ycor):
self.idnum = idnum
self.type = type # 0 = nonwing, 1 = scalecell, 2+ = vein
self.xcor = xcor
self.ycor = ycor
self.mrph = []
self.cnxn = [] # list of idnums of neighbors
self.colr = 0
def connect_to(self, clist): # accepts list of cells focal should be connected to and creates one-way connections
for i in range(len(clist)):
self.cnxn.append(clist[i])
def update_concs(self):
area= 1.0/6.0
aa = 1.0
bb = 1.0
cc = 1.0
for m in range(len(self.mrph)):
if self.mrph[m].conc != -1:
self.mrph[m].newc -= self.mrph[m].conc * self.mrph[m].decayrate
self.mrph[m].newc += self.mrph[m].prodrate
self.mrph[m].newc += self.mrph[m].rule.evaluate(self)
for n in range(len(self.cnxn)):
if self.mrph[m].conc > self.cnxn[n].mrph[m].conc:
self.mrph[m].newc -= (self.mrph[m].conc - self.cnxn[n].mrph[m].conc) * area * self.mrph[m].diffcoeff / self.length_to(self.cnxn[n])
self.cnxn[n].mrph[m].newc += (self.mrph[m].conc - self.cnxn[n].mrph[m].conc) * area * self.mrph[m].diffcoeff / self.length_to(self.cnxn[n])
# if m == 0: # because we only want these done once -- the hard-coded 0 and 1 are just for reproducing turing result sloppily
# # later should try to generalize code and make code more elegant
# self.mrph[0].newc += aa * self.mrph[0].conc*self.mrph[0].conc / len(self.cnxn)
# self.mrph[0].newc -= bb * self.mrph[1].conc / len(self.cnxn)
# self.mrph[0].newc -= 12.0 / len(self.cnxn)
# self.mrph[0].newc += self.mrph[0].prodrate / len(self.cnxn)
# self.mrph[0].newc -= self.mrph[0].conc * self.mrph[0].decayrate / len(self.cnxn)
# self.mrph[1].newc += self.mrph[0].conc / len(self.cnxn)
# self.mrph[1].newc -= self.mrph[1].conc * self.mrph[0].conc / len(self.cnxn)
# self.mrph[1].newc += 16.0 / len(self.cnxn)
# self.mrph[1].newc -= self.mrph[1].conc * self.mrph[1].decayrate / len(self.cnxn)
if self.mrph[m].newc < 0.0:
self.mrph[m].newc = 0.0
#if self.type > 1:
#self.mrph[m].newc = 100.0
def length_to(self, other):
x0 = float(self.xcor)
y0 = float(self.ycor)
x1 = float(other.xcor)
y1 = float(other.ycor)
return math.sqrt((x0 - x1)*(x0 - x1) + (y0 - y1) * (y0 - y1))
def define_morphogen(mrphnum, morphogenlist, celllist,morphname,diffcoeff,prodrate,decayrate,initconc):
mr = rules.random_proteinrule(mrphnum)
morphogenlist.append([morphname,diffcoeff,prodrate,decayrate, mr])
for i in range(len(celllist)):
celllist[i].mrph.append(morphogen(diffcoeff,prodrate,decayrate,initconc, mr))
return morphogenlist
def colorToType(r,g,b):
c = (r,g,b)
if c == (0,0,255):
tmp = 2
elif c == (255,0,0):
tmp = 3
elif c == (255,0,107):
tmp = 4
elif c == (255,0,255):
tmp = 5
elif c in ((115,0,107),(90,0,90),(82,0,99)):
tmp = 6
elif c == (49,0,99):
tmp = 7
elif c in ((90,0,57), (123,0,49), (66,0,57), (90,0,41)):
tmp = 8
elif c == (247,0,49):
tmp = 9
elif c == (49, 0, 255):
tmp = 10
elif c in ((255,33,0), (255,74,0)):
tmp = 11
elif c in ((247,90,0)): # also (255,255,0), but only in solitary pixels
tmp = 12
elif c == (0, 99, 255):
tmp = 13
elif c == (0, 255, 0):
tmp = 14
elif c == (0, 255, 255):
tmp = 15
elif c == (0, 247, 99):
tmp = 16
elif c == (0,99,0):
tmp = 17
elif c == (255,255,0):
tmp = 18
elif c == (99,0,0):
tmp = 19
elif c == (255,255,255):
tmp = 0
else:
tmp = 1
return tmp
def make_honeycomb(width, height):
print "Creating wing."
img = Tkinter.PhotoImage(file="/Users/twong/Desktop/VeinWing.gif")
imgwidth = img.width()
imgheight = img.height()
tmpM = [] # a 1-dim list of cells
tmpT = [] # a 2-dim list for looking up cells by xy location and finding tmpM address corresponding to cell with that location
i = 0
for col in range(width):
tmp = []
for row in range(height):
irow = int(row * (float(imgheight) / float(height)))
if row % 2 == 0:
icol = int(col * (float(imgwidth) / float(width)))
r, g, b = map(int, img.get(icol, irow).split(" "))
ttype = colorToType(r,g,b)
if ttype == 18:
tr, tg, tb = map(int, img.get(icol, irow-1).split(" "))
if colorToType(tr,tg,tb) == 12:
ttype = 12
tmpM.append(cell(i,ttype,col,row))
else:
icol = int((col+.5) * (float(width) / float(imgwidth)))
r, g, b = map(int, img.get(icol, irow).split(" "))
ttype = colorToType(r,g,b)
if ttype == 18:
tr, tg, tb = map(int, img.get(icol, irow-1).split(" "))
if colorToType(tr,tg,tb) == 12:
ttype = 12
tmpM.append(cell(i,ttype,col+.5,row))
tmp.append(i)
i += 1
if i % 5000 == 0:
print " ", i, "cells created."
tmpT.append(tmp)
print len(tmpM), "cells created."
print "Creating neighbor connections."
cnxnnum = 0
for col in range(len(tmpT)):
for row in range(len(tmpT[0])):
if tmpM[tmpT[col][row]].type > 0:
if row % 2 == 0 and row < len(tmpT[0]) - 1: # even, not bottom
if tmpM[tmpT[col][row+1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col][row+1]]]) # connect to straight down, is to right
cnxnnum += 1
if col > 0: # connect down to left
if tmpM[tmpT[col-1][row+1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col-1][row+1]]])
cnxnnum += 1
if row % 2 == 0 and row > 0: # even, not top
if col < len(tmpT) - 1:
if tmpM[tmpT[col][row-1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col][row-1]]]) # connect to straight up, is to right
cnxnnum += 1
if col > 0: # connect up to left
if tmpM[tmpT[col-1][row-1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col-1][row-1]]])
cnxnnum += 1
if row % 2 == 1 and row < len(tmpT[0]) - 1: # odd, not bottom
if tmpM[tmpT[col][row+1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col][row+1]]]) # connect to straight down, is to left
cnxnnum += 1
if col < len(tmpT) - 1: # connect down to rt
if tmpM[tmpT[col+1][row+1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col+1][row+1]]])
cnxnnum += 1
if row % 2 == 1 and row > 0: # odd, not top
if tmpM[tmpT[col][row-1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col][row-1]]]) # connect to straight up, is to left
cnxnnum += 1
if col < len(tmpT) - 1: # connect up to left
if tmpM[tmpT[col+1][row-1]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col+1][row-1]]])
cnxnnum += 1
if col > 0:
if tmpM[tmpT[col-1][row]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col-1][row]]])
cnxnnum += 1
if col< len(tmpT) - 1:
if tmpM[tmpT[col+1][row]].type > 0:
tmpM[tmpT[col][row]].connect_to([tmpM[tmpT[col+1][row]]])
cnxnnum += 1
if cnxnnum % 5000 == 0 and cnxnnum > 0:
print " ", cnxnnum,"neighbor-pairs connected."
print " ", cnxnnum,"neighbor-pairs connected."
print "Deleting non-wing cells."
deletednum = 0
deletelist = []
k = 0
for l in range(len(tmpM) / 5000):
deletelist.append(tmpM[(l * 5000):((l+1)*5000)])
deletelist.append(tmpM[(len(tmpM) / 5000)*5000:len(tmpM)])
tmpM = []
for l in range(len(deletelist)):
m = len(deletelist[l]) - 1
while m >= 0:
if deletelist[l][m].type == 0:
del(deletelist[l][m])
deletednum += 1
if deletednum % 2500 == 0:
print " Deleted", deletednum, "cells."
m -= 1
for l in range(len(deletelist)):
tmpM += deletelist[l]
# j = len(tmpM) - 1
# while j >= 0:
# if tmpM[j].type == 0:
# del(tmpM[j])
# deletednum += 1
# j -= 1
# if deletednum % 2500 == 0:
# print " Deleted", deletednum, "cells."
print "Wing created. Final cell number", str(len(tmpM))+"."
return tmpM
def connect(pairlist, isDirectional): #accept list of two-element lists and connects from first elem to second for each
for i in len(pairlist): # if not isDirectional, also connects from second back to first
pairlist[i][0].connect([pairlist[i][1]])
if not(isDirectional):
pairlist[i][1].connect([pairlist[i][0]])
def distance(a,b):
x0 = float(a.xcor)
y0 = float(a.ycor)
x1 = float(b.xcor)
y1 = float(b.ycor)
return math.sqrt((x0-x1)*(x0-x1)+ (y0-y1)*(y0-y1))
def coin(prob):
if random.random() < prob:
return 1
else:
return 0
random.seed()
win = Tkinter.Tk()
can = Tkinter.Canvas(win,height=winheight,width=winwidth,background="white")
can.pack()
rfile = open("rulefile", "a")
wing = make_honeycomb(400,400)
for rnum in range(2000):
graphicslist = []
if rnum > 0:
for i in range(len(wing)):
for j in range(len(wing[i].mrph)):
wing[i].mrph[j].conc = 0.0
morph = []
define_morphogen(num_morphogens, morph,wing,"activator",0.1,0.4,0.5,0.0) # (morphogenlist, celllist,morphname,diffcoeff,prodrate,decayrate,initconc)
# define_morphogen(num_morphogens, morph,wing,"inhibitor",0.5,0.2,0.5,0.0)
if rnum == 0:
#tg = can.create_text(150+5*wing[len(wing)-1].xcor+10,50, anchor = "w", text="t = 1", fill = "black")
tg = can.create_text(50,500, anchor = "w", text="t = 1", fill = "black")
if randinterp:
iru = rules.random_interprule(num_morphogens)
irstring = iru.rule_string()
pru = rules.random_proteinrule(num_morphogens)
prstring = ""
for i in range(len(morph)):
prstring += str(i) + ": " + morph[i][4].rule_string()
if i != len(morph)-1:
prstring += "\n"
if rnum == 0:
if randinterp:
irs = Tkinter.StringVar()
prs = Tkinter.StringVar()
if randinterp:
irtext = Tkinter.Label(win, textvariable = irs, wraplength = winwidth, font = ("Helvetica", 24))
prtext = Tkinter.Label(win, textvariable = prs, anchor = "w", wraplength = winwidth, font = ("Helvetica", 24))
if randinterp:
irs.set(irstring)
prs.set(prstring)
if randinterp:
irtext.pack()
prtext.pack()
else:
if randinterp:
irs.set(irstring)
prs.set(prstring)
if rnum == 0:
if randinterp:
rb = Tkinter.Button(win, text = "record", width = 12, pady = 2, command = rules.write_curr_rstring(rfile, irstring + "\n"+prstring))
else:
rb = Tkinter.Button(win, text = "record", width = 12, pady = 2, command = rules.write_curr_rstring(rfile, prstring))
rb.pack()
for t in range(10):
can.itemconfig(tg, text = ("t = "+str(t+1)))
can.update()
for i in range(len(wing)):
for j in range(len(wing[i].mrph)):
wing[i].mrph[j].newc = wing[i].mrph[j].conc
for i in range(len(wing)):
wing[i].update_concs()
for i in range(len(wing)):
if wing[i].type > 1:
# Here is where morphogen sources are sources
wing[i].mrph[0].newc = 4.0
wmin = 1e60
wmax = -1
for i in range(len(wing)):
if wing[i].type == 1:
wmin = min(wmin, wing[i].mrph[0].conc)
wmax = max(wmax, wing[i].mrph[0].conc)
for j in range(len(wing[i].mrph)):
wing[i].mrph[j].conc = wing[i].mrph[j].newc
if abs(wing[i].mrph[j].conc) > 1e50:
wing[i].mrph[j].conc = -1
for i in range(len(wing)):
if randinterp:
if iru.evaluate(wing[i]):
wing[i].colr = "#0000ff"
else:
wing[i].colr = "#000000"
else:
if wing[i].mrph[0].conc == -1:
wing[i].colr = "#ff0000"
elif wmax - wmin > .01:
wing[i].colr = "#%02x%02x%02x" % (0, 0, (min(255,max(0,int(wmin+wing[i].mrph[0].conc*256.0/wmax-wmin)))))
else:
wing[i].colr = "#%02x%02x%02x" % (0, 0, (min(255,max(0,int(wmin+wing[i].mrph[0].conc*256.0/.01)))))
d=1
s = 3
if t == 0:
for i in range(len(wing)):
graphicslist.append(can.create_rectangle(s+d*wing[i].xcor-1, s+d*wing[i].ycor-1, s+d*wing[i].xcor+0, s+d*wing[i].ycor+1,width=0,fill=wing[i].colr))
else:
for i in range(len(wing)):
can.itemconfig(graphicslist[i], fill = wing[i].colr)
can.itemconfig(graphicslist[len(graphicslist) - 1], fill = "red")
for i in range(len(graphicslist)):
can.delete(graphicslist[i])
i = len(wing) - 1
while i >= 0:
del wing[i]
i -= 1
# time.sleep(0.5)
rfile.close()
can.mainloop() |
