def main():
parameterFile = "parameters.json"
params = readParams.fromJSON(capmd.Parameters(), parameterFile)
sim = capmd.interface(params)
N = sim.popSize()
NB = sim.getBoundarySize()
lx = params.Lx
ly = params.Ly
nmax = params.t_final
save_at = params.output_time
steps_between_check = params.popdynfreq
Nzaplist = 50
for n in tqdm(range(nmax)):
sim.move()
if (n % steps_between_check == 0):
sim.populationDynamics(steps_between_check)
if (n % save_at == 0):
sim.saveData('vtp')
sim.saveData('text')
print('Simulation Complete\n\n')
def main():
parameterFile = "parameters.json"
params = readParams.fromJSON(capmd.Parameters(), parameterFile)
# setting some of ours here
params.N = 20
params.Lx = 30
params.Ly = 30
params.poly = 0.3
params.maxZ = 6
params.divrate = 0
params.deathrate = 0
sim = capmd.interface(params)
N = sim.popSize()
NB = sim.getBoundarySize()
nmax = params.t_final
save_at = params.output_time
steps_between_check = params.popdynfreq
Nzaplist = 50
for n in tqdm(range(nmax)):
sim.move()
if (n % save_at == 0):
sim.saveData('vtp')
sim.saveData('text')
print('Simulation Complete\n\n')
def calculate_msd():
parameterFile = "parameters.json"
parser = argparse.ArgumentParser()
parser.add_argument("-d",
"--directory",
type=str,
default="./",
help="input directory")
#parser.add_argument("-o", "--output", type=str, help="output directory")
#parser.add_argument("-p", "--prefix", type=str, default="cornea",help="prefix for output file")
parser.add_argument("-s",
"--skip",
type=int,
default=1100,
help="skip this many samples")
parser.add_argument("-m",
"--howmany",
type=int,
default=30,
help="read this many samples")
parser.add_argument("-t",
"--step",
type=int,
default=4,
help="step snapshots with this spacing in flow field")
parser.add_argument("-a",
"--average",
type=int,
default=5,
help="average over these many samples in flow field")
args = parser.parse_args()
param = read_param_CAPMD.Param(
p.paramsFromFile(capmd.Parameters(), parameterFile))
sheet = Dynamics(initype="fromCSV",
param=param,
datapath='output/',
multiopt="many")
skip = 0
step = 1
howmany = 500
sheet.readDataMany("CAPMD", skip, step, howmany, False, readtypes=[1])
sheet.validate_initialise()
sheet.getMSD(False)
plt.show()
return 0
def main():
parameterFile = "parameters.json"
params = readParams.fromJSON(capmd.Parameters(), parameterFile)
sim = capmd.interface(params)
N = sim.popSize()
NB = sim.getBoundarySize()
lx = params.Lx
ly = params.Ly
nmax = params.t_final
save_at = params.output_time
steps_between_check = 100
zap_time = 1000
Nzaplist = 50
for n in tqdm(range(nmax)):
sim.move()
if (n == zap_time):
#getting system info for zapping
pop = sim.popSize()
idxs = capmd.VectorInt(range(NB, NB + N))
popId = sim.getPopulationId(idxs)
popPosn = sim.getPopulationPosition(idxs)
#list of cells to be zapped
zapList = capmd.VectorInt(np.random.choice(list(popId), Nzaplist))
sim.setCellTypes(zapList, 2)
print("Cell zapping stage completed")
if (n % save_at == 0):
sim.saveData('vtp')
sim.saveData('text')
print('Simulation Complete\n\n')
import pycapmd as capmd import parameters as p import read_param_CAPMD as read_param parameterFile = "parameters.json" params = p.paramsFromFile(capmd.Parameters(), parameterFile) read_param.Param(params)
def main():
parameterFile = "parameters.json"
params = readParams.fromJSON(capmd.Parameters(), parameterFile)
#sim = config.simulation(params)
sim = capmd.interface(params)
N = sim.popSize()
NB = sim.getBoundarySize()
# Choosing the opposing corners of the rectangle to be killed
lx = params.Lx
ly = params.Ly
wound = [(-lx / 4, -ly), (lx / 4, ly)]
nmax = params.t_final
# death_time = 1000000 # <- 50 such that it is far from the death causing holes in popDyn
save_at = params.output_time
steps_between_check = params.popdynfreq
for n in tqdm(range(nmax)):
sim.move()
if (n % steps_between_check == 0):
sim.populationDynamics(steps_between_check)
if (n == death_time):
N = sim.popSize()
NB = sim.getBoundarySize()
idxs = capmd.VectorInt(range(NB, N + NB))
pop_id = sim.getPopulationId(idxs) #<- get id
pop_pos = sim.getPopulationPosition(idxs) # <- get position
# [kc.kill_cell_in_rect(x, i, rect, sim) for (x,i) in zip(pop_pos, pop_id)]
killList = capmd.VectorInt(kc.select_cells(pop_pos, pop_id, wound))
sim.killCells(killList)
print('Finished killing')
# elif (n >= death_time) and (n <= death_time + 1): # Only after wounding occurs (limit is in place as atm we plot the result)
# N = sim.popSize()
# NB = sim.getBoundarySize()
# idxs = config.VectorInt(range(N, N+NB))
# pop_pos = sim.getPopulationPosition(idxs)
# edges = border.alpha_shape(pop_pos, alpha = 3)
# plt.figure()
# plt.axis('equal')
# xs = []
# ys = []
# # separate xs and ys since pop_pos[:,0] and pop_pos[:,1] dont agree since its a list of tuples
# for pos in pop_pos:
# xs.append(pos[0])
# ys.append(pos[1])
# plt.plot(xs, ys, '.')
# for i, j in edges:
# print("edges: ",i,j)
# plt.plot([xs[i],xs[j]], [ys[i],ys[j]])
# plt.show()
if (n % save_at == 0):
sim.saveData('vtp')
sim.saveData('text')
print('Simulation Complete\n\n')
return 0