def calculate_average_rgtpase_activity(cell_index, storefile_path):
rac_data = hardio.get_data(cell_index, None, 'rac_membrane_active',
storefile_path)
sum_rac_over_nodes = np.sum(rac_data, axis=1)
avg_sum_rac_over_nodes = np.average(sum_rac_over_nodes)
rho_data = hardio.get_data(cell_index, None, 'rho_membrane_active',
storefile_path)
sum_rho_over_nodes = np.sum(rho_data, axis=1)
avg_sum_rho_over_nodes = np.average(sum_rho_over_nodes)
return avg_sum_rac_over_nodes, avg_sum_rho_over_nodes
def graph_data_label_average_node_over_time(ax, a_cell, data_label):
data = hardio.get_data(a_cell, None, data_label)
average_data_over_nodes = np.average(data, axis=1)
ax.plot(average_data_over_nodes, label=data_label)
return ax
def graph_data_label_over_time(ax, a_cell, data_label):
data = hardio.get_data(a_cell, None, data_label)
sum_data_over_nodes = np.sum(data, axis=1)
ax.plot(sum_data_over_nodes, label=data_label)
return ax
def score_distance_travelled(cell_index, storefile_path):
xs = hardio.get_data(cell_index, None, 'x', storefile_path)
ys = hardio.get_data(cell_index, None, 'y', storefile_path)
x_disps = xs[1:] - xs[:-1]
y_disps = ys[1:] - ys[:-1]
dists = np.sqrt(x_disps * x_disps + y_disps * y_disps)
total_dist_magnitude = np.sum(dists)
sum_x_disps = np.sum(x_disps)
sum_y_disps = np.sum(y_disps)
total_disp_magnitude = np.sqrt(sum_x_disps * sum_x_disps +
sum_y_disps * sum_y_disps)
return total_dist_magnitude, total_disp_magnitude
def get_ic_contact_data(cell_index, storefile_path, max_tstep=None):
if max_tstep == None:
ic_contact_data = hardio.get_data(
cell_index, None, "intercellular_contact_factor_magnitudes",
storefile_path)
else:
ic_contact_data = hardio.get_data_until_timestep(
cell_index, max_tstep, "intercellular_contact_factor_magnitudes",
storefile_path)
return np.array(np.any(ic_contact_data > 1, axis=1), dtype=np.int64)
def calculate_migry_boundary_violation_score(num_nodes, num_timesteps,
cell_index, storefile_path):
migr_bdry_contact_data = hardio.get_data(cell_index, None,
'migr_bdry_contact',
storefile_path)
x = migr_bdry_contact_data - 1.0
y = x > 1e-10
y = np.array(y, dtype=np.int64)
return np.sum(y) / (num_timesteps * num_nodes)
def get_event_tsteps(event_type, cell_index, storefile_path):
relevant_data_per_tstep = None
if event_type == "ic-contact":
ic_mags = hardio.get_data(cell_index, None,
"intercellular_contact_factor_magnitudes",
storefile_path)
relevant_data_per_tstep = np.any(ic_mags > 1, axis=1)
elif event_type == "randomization":
polarity_loss_occurred = hardio.get_data(cell_index, None,
"polarity_loss_occurred",
storefile_path)
relevant_data_per_tstep = np.any(polarity_loss_occurred, axis=1)
if relevant_data_per_tstep == None:
raise StandardError("Unknown event type given!")
event_tsteps = [
n for n in xrange(relevant_data_per_tstep.shape[0])
if relevant_data_per_tstep[n] == 1
]
return event_tsteps