def load_colony(colony, initial_file, config):
"""Loads the initial colony of cells."""
with open(initial_file, newline='') as fp:
reader = csv.DictReader(fp, skipinitialspace=True)
for row in reader:
name = row['name']
celltype = config['global.cellType'].lower()
if celltype == 'bacilli':
x = float(row['x'])
y = float(row['y'])
width = float(row['width'])
length = float(row['length'])
rotation = float(row['rotation'])
if config["simulation"]["image.type"] == "graySynthetic":
opacity = config["simulation"]["cell.opacity"]
cell = Bacilli(name,
x,
y,
width,
length,
rotation,
opacity=opacity)
else:
cell = Bacilli(name, x, y, width, length, rotation)
colony.add(CellNode(cell))
def perturb_bacilli(node, config, imageshape):
"""Create a new perturbed bacilli cell."""
global badcount # DEBUG
cell = node.cell
prior = node.prior.cell
if node.split:
p1, p2 = node.prior.cell.split(node.alpha)
if p1.name == node.cell.name:
prior = p1
elif p2.name == node.cell.name:
prior = p2
else:
AssertionError('Names not matching')
max_displacement = config['bacilli.maxSpeed'] / config[
'global.framesPerSecond']
max_rotation = config['bacilli.maxSpin'] / config['global.framesPerSecond']
min_growth = config['bacilli.minGrowth']
max_growth = config['bacilli.maxGrowth']
min_width = config['bacilli.minWidth']
max_width = config['bacilli.maxWidth']
min_length = config['bacilli.minLength']
max_length = config['bacilli.maxLength']
perturb_conf = config["perturbation"]
p_x = perturb_conf["prob.x"]
p_y = perturb_conf["prob.y"]
p_width = perturb_conf["prob.width"]
p_length = perturb_conf["prob.length"]
p_rotation = perturb_conf["prob.rotation"]
x_mu = perturb_conf["modification.x.mu"]
y_mu = perturb_conf["modification.y.mu"]
width_mu = perturb_conf["modification.width.mu"]
length_mu = perturb_conf["modification.length.mu"]
rotation_mu = perturb_conf["modification.rotation.mu"]
x_sigma = perturb_conf["modification.x.sigma"]
y_sigma = perturb_conf["modification.y.sigma"]
width_sigma = perturb_conf["modification.width.sigma"]
length_sigma = perturb_conf["modification.length.sigma"]
rotation_sigma = perturb_conf["modification.rotation.sigma"]
simulation_config = config["simulation"]
if simulation_config["image.type"] == "graySynthetic":
p_opacity = perturb_conf["prob.opacity"]
opacity_mu = perturb_conf["modification.opacity.mu"]
opacity_sigma = perturb_conf["modification.opacity.sigma"]
while True:
# set starting properties
x = cell.x
y = cell.y
width = cell.width
length = cell.length
rotation = cell.rotation
cell_opacity = cell.opacity
if simulation_config["image.type"] == "graySynthetic":
p_decision = np.array(
[p_x, p_y, p_width, p_length, p_rotation, p_opacity])
else:
p_decision = np.array([p_x, p_y, p_width, p_length, p_rotation])
p = np.random.uniform(0.0, 1.0, size=p_decision.size)
# generate a sequence such that at least an attribute must be modified
while (p > p_decision).all():
p = np.random.uniform(0.0, 1.0, size=p_decision.size)
if p[0] < p_decision[0]: # perturb x
x = cell.x + random.gauss(mu=x_mu, sigma=x_sigma)
if p[1] < p_decision[1]: # perturb y
y = cell.y + random.gauss(mu=y_mu, sigma=y_sigma)
if p[2] < p_decision[2]: # perturb width
width = cell.width + random.gauss(mu=width_mu, sigma=width_sigma)
if p[3] < p_decision[3]: # perturb length
length = cell.length + random.gauss(mu=length_mu,
sigma=length_sigma)
if p[4] < p_decision[4]: # perturb rotation
rotation = cell.rotation + random.gauss(mu=rotation_mu,
sigma=rotation_sigma)
# if simulation_config["image.type"] == "graySynthetic" and p[5] < p_decision[5]:
# cell_opacity = cell.opacity + (random.gauss(mu=opacity_mu, sigma=opacity_sigma))
displacement = sqrt(np.sum((np.array([x, y, 0] - prior.position))**2))
if not (0 <= x < imageshape[1] and 0 <= y < imageshape[0]) or (displacement > max_displacement) \
or width < min_width or width > max_width or (abs(rotation - prior.rotation) > max_rotation) or \
not (min_length < length < max_length) or not (min_growth < length - prior.length < max_growth):
badcount += 1
elif simulation_config[
"image.type"] == "graySynthetic" and cell_opacity < 0:
badcount += 1
else:
break
# push the new cell over the previous in the node
node.push(
Bacilli(cell.name, x, y, width, length, rotation, cell.split_alpha,
cell_opacity))
def perturb_bacilli(node, config, imageshape):
"""Create a new perturbed bacilli cell."""
global badcount # DEBUG
cell = node.cell
prior = node.prior.cell
if node.split:
p1, p2 = node.prior.cell.split(node.alpha)
if p1.name == node.cell.name:
prior = p1
elif p2.name == node.cell.name:
prior = p2
else:
AssertionError('Names not matching')
max_displacement = config['bacilli.maxSpeed'] / config[
'global.framesPerSecond']
max_rotation = config['bacilli.maxSpin'] / config['global.framesPerSecond']
min_growth = config['bacilli.minGrowth']
max_growth = config['bacilli.maxGrowth']
min_width = config['bacilli.minWidth']
max_width = config['bacilli.maxWidth']
min_length = config['bacilli.minLength']
max_length = config['bacilli.maxLength']
# set starting properties
x = cell.x
y = cell.y
width = cell.width
length = cell.length
rotation = cell.rotation
modified = False
wasbad = False # DEBUG
while not modified:
# randomly make changes
if random.random() < 0.35:
x = cell.x + random.gauss(mu=0, sigma=0.5)
modified = True
if random.random() < 0.35:
y = cell.y + random.gauss(mu=0, sigma=0.5)
modified = True
if random.random() < 0.1:
width = cell.width + random.gauss(mu=0, sigma=0.1)
modified = True
if random.random() < 0.2:
length = cell.length + random.gauss(mu=0, sigma=1)
modified = True
if random.random() < 0.2:
rotation = cell.rotation + random.gauss(mu=0, sigma=0.2)
modified = True
# ensure that those changes fall within constraints
if modified:
displacement = sqrt(
np.sum((np.array([x, y, 0] - prior.position))**2))
bad = False
if not (0 <= x < imageshape[1] and 0 <= y < imageshape[0]):
bad = True
elif displacement > max_displacement:
bad = True
elif width < min_width or width > max_width:
bad = True
elif abs(rotation - prior.rotation) > max_rotation:
bad = True
elif not (min_length < length < max_length):
bad = True
elif not (min_growth < length - prior.length < max_growth):
bad = True
if bad:
wasbad = True # DEBUG
x = cell.x
y = cell.y
width = cell.width
length = cell.length
rotation = cell.rotation
modified = False
if wasbad: # DEBUG
badcount += 1
# push the new cell over the previous in the node
node.push(Bacilli(cell.name, x, y, width, length, rotation))