def setup(sim):
dim = (32,32,4)
size = (5,5,5)
orig = (-0.5*(dim[0]-1)*size[0],-0.5*(dim[1]-1)*size[1],-0.5*(dim[2]-1)*size[2])
# Set biophysics, signalling, and regulation models
sig = GridDiffusion(sim, 2, dim, size, orig, [1e-1,1e-1], [1.0,1.0])
#integ = ScipyODEIntegrator(sim, 0, 3, max_cells, sig, True)
integ = CLCrankNicIntegrator(sim, 2, 3, max_cells, sig)
#integ = CrankNicIntegrator(sim, 2, 3, max_cells, sig)
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64**2)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.75)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-2)
regul = ModuleRegulator(sim, __file__) # use this file for reg too
sim.init(biophys, regul, sig, integ)
sim.addCell(cellType=0, pos=(-20,1,0))
sim.addCell(cellType=1, pos=(20,0,1))
# Add some objects to draw the models
sigrenderer = Renderers.GLGridRenderer(sig, integ)
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrenderer)
sim.addRenderer(therenderer)
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
#integ = ScipyODEIntegrator(sim, 1, 4, max_cells, sig, True)
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig, boundcond='reflect')
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64*64, jitter_z=True, reg_param=2, gamma=5.0)
biophys.addPlane((0,0,-0.5), (0,0,1), 1.0)
biophys.addPlane((0,0,0.5), (0,0,-1), 5e-4)
reg = ModuleRegulator(sim, __file__)
sim.init(biophys, reg, sig, integ)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
#for i in range(4):
# for j in range(4):
# sim.addCell(cellType=0, pos=(i*16-32,j*16-32,0))
# sim.addCell(cellType=1, pos=(i*16-32-8,j*16-32-8,0))
sim.addCell(cellType=1, pos=(-20.0,0,0), len=2.0)
sim.addCell(cellType=0, pos=(20.0,0,0), len=2.0)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False, max_planes=9)
sim.dt = 0.025
#biophys.addPlane((0,0,-0.5), (0,0,1), 1.0)
#biophys.addPlane((0,0,0.5), (0,0,-1), math.sqrt(7.5e-4))
angs = [i*math.pi/4 for i in range(8)]
for a in angs:
x = math.cos(a)
y = math.sin(a)
p = (50*x,50*y,0)
n = (-x,-y,0)
biophys.addPlane(p,n, 1.0)
regul = ModuleRegulator(sim) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#ct = 0
#for x in range(-4,5):
# for y in range(-4,5):
sim.addCell(cellType=0, pos=(0,-10,0), color=(1,0,0)) #x*40,y*40,0))
sim.addCell(cellType=1, pos=(0,10,0), color=(0,0,1)) #x*40,y*40,0))
# ct += 1
#sim.addCell(cellType=1, pos=(20,0,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 1
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
# add the planes to set physical boundaries of cell growth
biophys.addPlane((0,-16,0), (0,1,0), 1)
biophys.addPlane((0,16,0), (0,-1,0), 1)
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
# Here we set up the numerical integration:
# Crank-Nicholson method:
#integ = CLCrankNicIntegrator(sim, 1, 2, max_cells, sig, boundcond='reflect')
# Alternative is to use the simple forward Euler method:
integ = CLEulerSigIntegrator(sim, 1, 2, max_cells, sig, boundcond='reflect')
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, sig, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sigrend = Renderers.GLGridRenderer(sig, integ) # Add
sim.addRenderer(sigrend) #Add
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
# add the planes to set physical boundaries of cell growth
biophys.addPlane((0,-16,0), (0,1,0), 1)
biophys.addPlane((0,16,0), (0,-1,0), 1)
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim, 1, 1, max_cells, sig, boundcond='reflect')
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, sig, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sigrend = Renderers.GLGridRenderer(sig, integ) # Add
sim.addRenderer(sigrend) #Add
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, \
max_cells=max_cells, \
max_contacts=32, \
max_sqs=128**2, \
jitter_z=False, \
reg_param=2, \
gamma=10)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.2)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-4)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#load data from pickle file
dataFileName = '' # Edit to include your filename here
# Or pop up a dialog to choose a pickle
if dataFileName=='':
print "Please edit the model file to specify a pickle file."
print " -- No data was loaded and there are no cells in this simulation!"
else:
# Import the data and load into Simulator
print "Loading data from pickle file: %s"%(dataFileName)
import cPickle
data = cPickle.load(open(dataFileName,'r'))
sim.loadFromPickle(data)
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(
sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=50**2,
jitter_z=False,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=10.0)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
#biophys.addPlane((0,0,-radiusD/2.0), (0,0,+1), planeWeight) # front of box
#biophys.addPlane((0,0,+radiusD/2.0), (0,0,-1), planeWeight) # back of box
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
solverParams = None
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# initialise 2 cells with different lengths, radii
sim.addCell(
cellType=0,
len=lengthD,
rad=radiusD,
pos=(+init_sep / 2.0, radiusD, 0),
dir=(1, 0, 0))
sim.addCell(
cellType=1,
len=lengthD,
rad=radiusD,
pos=(-init_sep / 2.0, radiusD, 0),
dir=(1, 0, 0))
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [1.0])
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig)
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64**2, jitter_z=False, reg_param=2)
biophys.addPlane((0,-16,0),(0,1,0),0.2)
biophys.addPlane((0,16,0),(0,-1,0),0.2)
reg = ModuleRegulator(sim, __file__)
sim.init(biophys, reg, sig, integ)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GL2DBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.addCell(pos=(0,0,0), len=2.0)
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(
sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=Num_x * Num_y,
jitter_z=False,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=meshParam,
L_x=Len_x,
L_y=Len_y,
)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
# what happens if we add some sides?
biophys.addPlane((0, 0, 0), (+1, 0, 0), planeWeight) # left side
biophys.addPlane((Len_x, 0, 0), (-1, 0, 0), planeWeight) # right side
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
""" CASE 1 - HIGH NUTRIENTS """
solverParams = dict(
h=0.5 * meshParam,
origin=[0.0, 0.0, 0.0],
N_x=2 * Num_x,
L_x=Len_x,
u0=1.0,
K=0.0033,
mu_eff=0.001,
pickleSteps=10,
rel_tol=1e-6,
mesh_type="crossed",
delta=40.0,
)
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# randomly initialise a line of cells along the bottom
RandomSeedOnLine(sim, Len_x, num_initial_cells, initialVola, initialVola, radius)
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
# sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
biophys = CLBacterium(sim, jitter_z=False)
reg = ModuleRegulator(sim, sim.moduleName)
sim.init(biophys, reg, None, None)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therend)
sim.addCell(cellType=0, pos=(0, 0, 0), len=2.0)
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=True)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
sim.addCell(cellType=0, pos=(0,0,0))
biophys.addPlane((0,0,0),(0,0,-1),1.0)
biophys.addPlane((0,0,0),(0,0,1),5e-2)
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0], initLevels=[5e-3])
#integ = ScipyODEIntegrator(sim, 1, 4, max_cells, sig, True)
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig)
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=32**2, jitter_z=True, reg_param=2)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.2)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-3)
reg = ModuleRegulator(sim, __file__)
sim.init(biophys, reg, sig, integ)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.addCell(cellType=0, pos=(0,0,0))
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig, boundcond='reflect')
biophys = CLBacterium(sim, max_cells=max_cells, jitter_z=False)
biophys.addPlane((0,-16,0), (0,1,0), 1)
biophys.addPlane((0,16,0), (0,-1,0), 1)
reg = ModuleRegulator(sim)
sim.init(biophys, reg, sig, integ)
sim.addCell(cellType=1, pos=(-20.0,0,0), len=2.0)
sim.addCell(cellType=0, pos=(20.0,0,0), len=2.0)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=100**2,
jitter_z=True,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=10.0)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
solverParams = None
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# initialise 2 cells with different lengths, radii
sim.addCell(cellType=type,
len=length,
rad=radius,
pos=(0, 0, radius),
dir=(1, 0, 0))
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, \
max_cells=max_cells, \
max_contacts=32, \
max_sqs=128**2, \
jitter_z=False, \
reg_param=2, \
gamma=10)
biophys.addPlane((0, 0, -0.5), (0, 0, 1), 0.2)
biophys.addPlane((0, 0, 0.5), (0, 0, -1), 1e-4)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#load data from pickle file
dataFileName = '' # Edit to include your filename here
# Or pop up a dialog to choose a pickle
if dataFileName == '':
print "Please edit the model file to specify a pickle file."
print " -- No data was loaded and there are no cells in this simulation!"
else:
# Import the data and load into Simulator
print "Loading data from pickle file: %s" % (dataFileName)
import cPickle
data = cPickle.load(open(dataFileName, 'r'))
sim.loadFromPickle(data)
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim,
jitter_z=False,
periodic=True,
N_x=1,
N_y=1,
grid_spacing=15.0,
max_cells=8,
max_contacts=8)
# add some planes to make the system 1-D
planeWeight = 1.0
biophys.addPlane((0, 7.0, 0), (0, +1, 0),
planeWeight) # bottom channel boundary
biophys.addPlane((0, 8.0, 0), (0, -1, 0),
planeWeight) # top channel boundary
# temporarily add some planes to stop cells leaving the domain
biophys.addPlane((0, 0, 0), (+1, 0, 0),
planeWeight) # left channel boundary
biophys.addPlane((15.0, 0, 0), (-1, 0, 0),
planeWeight) # right channel boundary
# use this file for reg too
regul = ModuleRegulator(sim)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(5, 7.5, 0))
sim.addCell(cellType=1, pos=(10, 7.5, 0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
# add the planes to set physical boundaries of cell growth
biophys.addPlane((0, -16, 0), (0, 1, 0), 1)
biophys.addPlane((0, 16, 0), (0, -1, 0), 1)
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
# Here we set up the numerical integration:
# Crank-Nicholson method:
#integ = CLCrankNicIntegrator(sim, 1, 2, max_cells, sig, boundcond='reflect')
# Alternative is to use the simple forward Euler method:
integ = CLEulerSigIntegrator(sim,
1,
2,
max_cells,
sig,
boundcond='reflect')
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, sig, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0, 0, 0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sigrend = Renderers.GLGridRenderer(sig, integ) # Add
sim.addRenderer(sigrend) #Add
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False, max_cells=30000,max_sqs=192**2)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
sim.addCell(cellType=0, pos=(0,0,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_planes=9)
sim.dt = 0.025
#biophys.addPlane((0,0,-0.5), (0,0,1), 1.0)
#biophys.addPlane((0,0,0.5), (0,0,-1), math.sqrt(7.5e-4))
'''
angs = [i*math.pi/8 for i in range(8)]
for a in angs:
x = math.cos(a)
y = math.sin(a)
p = (30*x,30*y,0)
n = (-x,-y,0)
biophys.addPlane(p,n, 1.0)
'''
biophys.addPlane((0, 0, 0), (0, 0, -1), 1.0)
regul = ModuleRegulator(sim) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#ct = 0
#for x in range(-4,5):
# for y in range(-4,5):
sim.addCell(cellType=0, pos=(0, 0, -5), color=(1, 1, 1)) #x*40,y*40,0))
# ct += 1
#sim.addCell(cellType=1, pos=(20,0,0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim,
1,
5,
max_cells,
sig,
boundcond='reflect')
biophys = CLBacterium(sim, max_cells=max_cells, jitter_z=False)
biophys.addPlane((0, -16, 0), (0, 1, 0), 1)
biophys.addPlane((0, 16, 0), (0, -1, 0), 1)
reg = ModuleRegulator(sim)
sim.init(biophys, reg, sig, integ)
sim.addCell(cellType=1, pos=(-20.0, 0, 0), len=2.0)
sim.addCell(cellType=0, pos=(20.0, 0, 0), len=2.0)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
regul = ModuleRegulator(sim)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0, 0, 0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=Num_x * Num_y,
jitter_z=False,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=meshParam,
L_x=Len_x,
L_y=Len_y)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
# what happens if we add some sides?
biophys.addPlane((0, 0, 0), (+1, 0, 0), planeWeight) # left side
biophys.addPlane((Len_x, 0, 0), (-1, 0, 0), planeWeight) # right side
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
""" CASE 0 - NO NUTRIENTS """
solverParams = None
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# randomly initialise a line of cells along the bottom
RandomSeedOnLine(sim, Len_x, num_initial_cells, initialVola, initialVola,
radius)
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
#sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64**2, jitter_z=False, reg_param=2)
regul = ModuleRegulator(sim, __file__) # use this file for reg too
sim.init(biophys, regul, None, None)
# load from pickle file
import pickle
(cs, lineage) = pickle.load(open('data/biophysCL-01-03-13-04-12/step-02450.pickle','r'))
print "Loading %i cells..."%len(cs)
sim.setCellStates(cs)
biophys.load_from_cellstates(cs)
#for (i,cell) in sim.cellStates.items():
# cell.color = [0.1, 0.1+1000.0*cell.species[3],
# 0.1+200.0*cell.species[4]]
# for (i,cell) in sim.cellStates.items():
# cell.color = [0.1, cell.species[3]*0.1, cell.species[4]*0.1]
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
sim.addCell(cellType=0, pos=(0, 0, 0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_cells=max_cells, jitter_z=False)
integ = CLEulerIntegrator(sim, 2, max_cells)
# use this file for reg too
regul = ModuleRegulator(sim)
# Only biophys and regulation
sim.init(biophys, regul, None, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0, 0, 0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
def setup(sim):
# Set biophysics module
biophys = CLBacterium(sim, jitter_z=False)
# Set up regulation module
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0, 0, 0), dir=(1, 0, 0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
# Specify how often data is saved
sim.pickleSteps = 100
def setup(sim):
# Set biophysics module
biophys = CLBacterium(sim, jitter_z=False, max_cells=50000,gamma=10.0, cgs_tol=1E-5,compNeighbours=True)
# Set up regulation module
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(-5,0,0), dir=(1,0,0), length=delta,rad=0.4) #acceptor
sim.addCell(cellType=1, pos=(5,0,0), dir=(1,0,0), length=delta,rad=0.4) #donor
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
# Specify how often data is saved
sim.pickleSteps = 50
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=True, gamma = 20, max_planes=5)
biophys.addPlane((0,0,0),(0,0,1),1.0) #Base plane
biophys.addPlane((10,0,0),(-1,0,0),1.0)
biophys.addPlane((-10,0,0),(1,0,0),1.0)
biophys.addPlane((0,10,0),(0,-1,0),1.0)
biophys.addPlane((0,-10,0),(0,1,0),1.0)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0.5))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
integ = CLEulerIntegrator(sim, 2, max_cells)
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0, 0, 0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0), dir=(1,0,0))
# Add some objects to draw the models
if sim.is_gui:
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
else:
print "Running in batch mode: no display will be output"
sim.pickleSteps = 10
sim.saveOutput = True
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
sig = GridDiffusion(sim, n_signals, grid_dim, grid_size, grid_orig, [1.0, 1.0])
integ = CLCrankNicIntegrator(sim, n_signals, n_species, max_cells, sig)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, sig, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(-3.0,0,0)) #Add
sim.addCell(cellType=1, pos=(3.0,0,0)) #Add
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sigrend = Renderers.GLGridRenderer(sig, integ) # Add
sim.addRenderer(sigrend) #Add
sim.pickleSteps = 20
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=128**2, jitter_z=False, reg_param=2, gamma=10)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.2)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-4)
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#sim.addCell(cellType=0, pos=(0,0,0))
#load data from pickle file
import cPickle
data = cPickle.load(open('data/BiofilmWallLessCrash_no_alternation_9-12-56-25-09-12/step-00700.pickle','r'))
cellStates = data[0]
print "Loading %i cells"%len(cellStates)
sim.cellStates = cellStates
regul.cellStates = cellStates
biophys.load_from_cellstates(cellStates)
idx_map = {}
for id,state in sim.cellStates.iteritems():
idx_map[state.id] = state.idx
sim.idToIdx = idx_map
# parents = data[1]
# for id,state in sim.cellStates.iteritems():
# p = lineage(parents, [1,2], id)
# if p == 1: state.color = [0, 1, 0]
# elif p == 2: state.color = [0, 0, 1]
#import numpy.random
#cellcols = numpy.random.uniform(0,1,81*3)
#cellcols.shape = (81,3)
#for id,state in sim.cellStates.iteritems():
# state.color = list(cellcols[state.cellType,:])
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=True, gamma = 20, max_planes=5)
biophys.addPlane((0,0,0),(0,0,1),1.0) #Base plane
biophys.addPlane((10,0,0),(-1,0,0),1.0)
biophys.addPlane((-10,0,0),(1,0,0),1.0)
biophys.addPlane((0,10,0),(0,-1,0),1.0)
biophys.addPlane((0,-10,0),(0,1,0),1.0)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0.5))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
def setup(sim):
"""
This function is called when the simulation is initiated.
It specifies which modules are to be used in the simulation, how cells are initially placed, and when to generate output.
"""
global TimeStep
# Use biophys, regulation and T6SS modules
biophys = CLBacterium(sim, jitter_z=False, max_cells=max_population)
regul = ModuleRegulator(sim)
sim.init(biophys, regul, None, None, CDKParams)
# Specify initial cell locations in the simulation
sim.addCell(cellType=0, pos=(-10, 0, 0))
sim.addCell(cellType=1, pos=(10, 0, 0))
# Add some objects to render the cells in the GUI
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
TimeStep = sim.dt
# print output (pickle) files every 10 timesteps
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim,
jitter_z=False,
gamma=100,
max_cells=100000,
max_planes=1)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#biophys.addPlane((0,0,0),(0,0,1),1.0) #Base plane
#biophys.addPlane((10,0,0),(-1,0,0),1.0)
#biophys.addPlane((-10,0,0),(1,0,0),1.0)
#biophys.addPlane((0,10,0),(0,-1,0),1.0)
#biophys.addPlane((0,-10,0),(0,1,0),1.0)
sim.addCell(cellType=0, pos=(0, 0, 0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 1
def setup(sim):
biophys = CLBacterium(sim, jitter_z=False, gamma=10, max_planes=3) #gamme is how the external pressure makes them stop growing (high means they keep growing)
# Set certin planes that limit the simulation
biophys.addPlane( (0, 0, 0), (0, 1, 0), 1.0)
biophys.addPlane( (-8, 0, 0), (1, 0, 0), 1.0)
biophys.addPlane( (8, 0, 0), (-1, 0, 0), 1.0)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-7.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-6.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-5.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-4.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-3.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-2.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-1.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-0.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(0.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(1.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(2.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(3.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(4.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(5.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(6.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(7.5,2,0), dir=(0,1,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
