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main-file.py
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main-file.py
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from __future__ import division
from visual import *
from visual.controls import *
from visual.graph import *
from random import uniform
from random import choice
from random import randrange
import pprint
class Cells:
def __init__(self, n = 20, ms=1.5):
d = display(x=800, center=(n/5,n/5,n/5), title = "Tumor Growth v1.0")
d.forward = (-0.8,-0.65,-1)
self.num = n #Number of cells = n^3
self.array = [[[0 for k in xrange(n)] for j in xrange(n)] for i in xrange(n)] #Creating a 3D array to store all the positions
self.radius = ms/2 #Radius of a cell
self.MINX = -1-ms/2 #left
self.MINY = -1-ms/2 #bottom
self.MINZ = -1-ms/2 #back
self.MAXX = n-ms/2 #right
self.MAXY = n-ms/2 #top
self.MAXZ = n-ms/2 #front
self.ProbCellMove = .05 # Probability for a cell to Move
self.ProbCellDivide = .1 # Probability for a cell to Divide
self.ProbCelltoCancer = 0.001 # Probability for a cell to become Cancer cell
self.ProbCancerDivide = .30 # Probability for a Cancer cell to Divide
self.ProbCancerCellDie = 0 # Probability for a Cancer cell to Die
self.ProbCancerDivideChemo = 0.05 # Probability for a Cancer cell to Divide during Chemo
self.ProbCancerCellDieChemo = 0.50 # Probability for a Cancer cell to Die during Chemo
self.ProbCelltoCancerChemo = 0 # Probability for a Cancer cell to become Cancer cell during Chemo
self.ProbCellDieChemo = .08 # Probability for a cell to Die under Chemo
self.ProbCellDieNorm = .01 # Probability for a cell to Die under Normal condition
self.NoOfCellsBeforeCancerAppears = n^2 # Approximate number of cells before a cancer cell should appear ~ It's an approximation
self.PercentageCellsHitByChemo = 85 # Percentage of cancer cells hit by chemo
self.t = 0 # Time
self.timechemostart = 9999 # Time the chemo doze was started
self.chemodozecheck = 0 # Check to see whether the chemo doze has been given or not
self.NoOfCells = n^3 # Number of Cells
self.NoOfCancer = 0 # Number of Cancer Cells
self.f = frame() # frame for all the healthy cells
self.c = frame() # frame for all the cancer cells
self.CanTurn = self.ProbCelltoCancer # don't change
self.CanDivide = self.ProbCancerDivide # don't change
self.ProbCellDie = self.ProbCellDieNorm # don't change
self.state = 0 # Check to see the state of chemo
self.cells()
def cells(self):
self.initializePositions()
gd = gdisplay(y=360, xtitle='Time', ytitle='No. of cells') # Creating a Graph Display
f1 = gcurve(color=color.cyan)
f2 = gcurve(color=color.red)
delta = 0.001
while (1==1):
rate(1000)
self.Grow()
f1.plot(pos=(self.t, self.NoOfCells))
f2.plot(pos=(self.t, self.NoOfCancer))
self.t = self.t+delta
if self.chemodozecheck == 1:
if (self.t > (self.timechemostart+1)):
self.state = 0
self.chemodozecheck = 0
self.CanTurn = self.ProbCelltoCancer
self.CanDivide = self.ProbCancerDivide
self.ProbCellDie = self.ProbCellDieNorm
for obj in self.c.objects:
obj.color = color.red
def initializePositions(self):
#wire frame of space
backBottom = curve(pos=[(self.MINX, self.MINY, self.MINZ), (self.MAXX, self.MINY, self.MINZ)], color=color.white)
backTop = curve(pos=[(self.MINX, self.MAXY, self.MINZ), (self.MAXX, self.MAXY, self.MINZ)], color=color.white)
frontBottom = curve(pos=[(self.MINX, self.MINY, self.MAXZ), (self.MAXX, self.MINY, self.MAXZ)], color=color.white)
frontTop = curve(pos=[(self.MINX, self.MAXY, self.MAXZ), (self.MAXX, self.MAXY, self.MAXZ)], color=color.white)
leftBottom = curve(pos=[(self.MINX, self.MINY, self.MINZ), (self.MINX, self.MINY, self.MAXZ)], color=color.white)
leftTop = curve(pos=[(self.MINX, self.MAXY, self.MINZ), (self.MINX, self.MAXY, self.MAXZ)], color=color.white)
rightBottom = curve(pos=[(self.MAXX, self.MINY, self.MINZ), (self.MAXX, self.MINY, self.MAXZ)], color=color.white)
rightTop = curve(pos=[(self.MAXX, self.MAXY, self.MINZ), (self.MAXX, self.MAXY, self.MAXZ)], color=color.white)
backLeft = curve(pos=[(self.MINX, self.MINY, self.MINZ), (self.MINX, self.MAXY, self.MINZ)], color=color.white)
backRight = curve(pos=[(self.MAXX, self.MINY, self.MINZ), (self.MAXX, self.MAXY, self.MINZ)], color=color.white)
frontLeft = curve(pos=[(self.MINX, self.MINY, self.MAXZ), (self.MINX, self.MAXY, self.MAXZ)], color=color.white)
frontRight = curve(pos=[(self.MAXX, self.MINY, self.MAXZ), (self.MAXX, self.MAXY, self.MAXZ)], color=color.white)
# Creating initial 8 cells
for x in range(int(self.num/2),int(self.num/2)+2):
for y in range(int(self.num/2),int(self.num/2)+2):
for z in range(int(self.num/2),int(self.num/2)+2):
self.array[x][y][z] = sphere(frame = self.f,pos=(x,y,z), radius=self.radius, color=color.white)
c = controls(height=360) # Creating the buttons to control the Display
b1 = button(pos=(0,75), height=42, width=110, text='Show All', action=lambda: self.showall())
b2 = button(pos=(0,25), height=42, width=110, text='Show Cancer Cells', action=lambda: self.showcancer())
b5 = button(pos=(0,-25), height=42, width=100, text='Chemo 1 doze', action=lambda: self.chemodoze())
def showcancer(self):
self.f.visible = False
def showall(self):
self.f.visible = True
def chemodoze(self):
self.state = 1
self.CanTurn = self.ProbCelltoCancerChemo
self.CanDivide = self.ProbCancerDivideChemo
self.ProbCellDie = self.ProbCellDieChemo
self.chemodozecheck = 1
self.timechemostart = self.t
for obj in self.c.objects:
a = uniform(0, 100)
if a < self.PercentageCellsHitByChemo :
obj.color = color.cyan
else :
pass
def Grow(self):
count = 0
count1 = 0
for x in range(self.num):
for y in range(self.num):
for z in range(self.num):
if self.array[x][y][z] == 0:
pass
elif self.array[x][y][z].frame == self.f:
count = count+1
a = uniform(0, 100)
if a < self.ProbCellMove :
self.MoveCell(x,y,z)
elif a < self.ProbCellMove+self.ProbCellDivide :
self.CellDivide(x,y,z)
elif a < self.ProbCellMove+self.ProbCellDivide+self.ProbCellDie :
self.array[x][y][z].visible = False
self.array[x][y][z] = 0
elif ((a<self.ProbCellMove+self.ProbCellDivide+self.ProbCellDie+self.CanTurn)&(self.NoOfCells>(self.NoOfCellsBeforeCancerAppears))) :
if self.state==1:
self.array[x][y][z].color = color.cyan
else:
self.array[x][y][z].color = color.red
self.array[x][y][z].frame = self.c
elif self.array[x][y][z].frame == self.c:
count = count+1
count1 = count1+1
a = uniform(0, 100)
if a < self.CanDivide :
self.CancerDivide(x,y,z)
elif self.array[x][y][z].color == color.red :
if a < self.CanDivide+self.ProbCancerCellDie :
self.array[x][y][z].visible = False
self.array[x][y][z] = 0
elif self.array[x][y][z].color == color.cyan :
if a < self.CanDivide+self.ProbCancerCellDieChemo :
self.array[x][y][z].visible = False
self.array[x][y][z] = 0
self.NoOfCells = count
self.NoOfCancer = count1
def MoveCell(self, x, y, z): # Function to move a specific cell
t = []
t = self.FindAdjacentFree(x,y,z)
if t != []:
moveto = choice(t)
i=0
for x1 in range(x-1, x+2):
for y1 in range(y-1, y+2):
for z1 in range(z-1, z+2):
i = i+1
if i==moveto :
self.array[x1][y1][z1] = sphere(frame = self.f, pos=(x1,y1,z1), radius=self.radius, color=color.white)
self.array[x][y][z].visible = False
self.array[x][y][z] = 0
def FindAdjacentFree(self, x, y, z): # Function to find empty adjacent places
t = []
i=0
for x1 in range(x-1, x+2):
for y1 in range(y-1, y+2):
for z1 in range(z-1, z+2):
i = i+1
try:
if self.array[x1][y1][z1]==0:
t.append(i)
except:
pass
return t
def CellDivide(self, x, y, z): # Function to Divide the Cell.
t = []
t = self.FindAdjacentFree(x,y,z)
if t != []:
moveto = choice(t)
i=0
for x1 in range(x-1, x+2):
for y1 in range(y-1, y+2):
for z1 in range(z-1, z+2):
i = i+1
if i==moveto :
self.array[x1][y1][z1] = sphere(frame = self.f, pos=(x1,y1,z1), radius=self.radius, color=color.white)
def CancerDivide(self, x, y, z): # Function to Divide the Cancer Cell.
moveto = randrange(0,28)
i = 0
for x1 in range(x-1, x+2):
for y1 in range(y-1, y+2):
for z1 in range(z-1, z+2):
i = i+1
if i==moveto :
try:
if self.array[x1][y1][z1] == 0:
self.array[x1][y1][z1] = sphere(frame = self.c, pos=(x1,y1,z1), radius=self.radius)
else:
self.array[x1][y1][z1].visible = False
self.array[x1][y1][z1] = sphere(frame = self.c, pos=(x1,y1,z1), radius=self.radius)
if self.state==1:
self.array[x1][y1][z1].color = color.cyan
else:
self.array[x1][y1][z1].color = color.red
except:
pass
################################################################################################################
c = Cells(20, 1.5) ### USED TO RUN THE PROGRAM. GIVE THE NUMBER OF CELLS AND THE SIZE OF EACH CELL HERE ###
################################################################################################################