tolerance=tolerance,
dist_table_density=20,
exact=True,
sigma=0.3)
path = os.path.join('simulation',
'%s_lambda_%f_R_%f' % (fname_base, l, R))
if sys.version_info < (3, 0):
path = os.path.join(path, "preprocessed_data/Python_2")
else:
path = os.path.join(path, "preprocessed_data/Python_3")
if not os.path.exists(path):
print("Creating", path)
os.makedirs(path)
try:
utils.save_sim(path, ker)
except NameError:
pass
skcsd, pot, morphology, ele_pos, n_src = utils.load_sim(path)
cell_obj = sKCSDcell(morphology, ele_pos, n_src)
skcsd = cell_itself.transform_to_3D(skcsd)
ax[(i + 1) // 3, (i + 1) % 3].imshow(morpho,
origin='lower',
aspect='auto',
interpolation='none',
extent=extent)
pl.make_map_plot(ax[(i + 1) // 3, (i + 1) % 3],
skcsd[:, :, :, t0].sum(axis=2),
vmin=vmin,
n_src_init=n_src,
src_type='gauss',
lambd=lambd,
exact=True,
R_init=R,
sigma=0.3)
path = os.path.join(data_dir, 'lambda_%f_R_%f_n_src_%d' % (lambd, R, n_src))
if sys.version_info < (3, 0):
path = os.path.join(path, "preprocessed_data/Python_2")
else:
path = os.path.join(path, "preprocessed_data/Python_3")
if not os.path.exists(path):
print("Creating", path)
os.makedirs(path)
try:
utils.save_sim(path, k)
except NameError:
pass
skcsd, pot, morphology_file, ele_pos, n_src = utils.load_sim(path)
cell_obj = sKCSDcell(morphology_file, ele_pos, n_src)
csd = cell_obj.transform_to_segments(skcsd)
draw_ground_truth_skcsd_segments(ax, ground_truth, csd, time, gvmin, gvmax)
csd_3D = cell_itself.transform_to_3D(skcsd[:, toplot])
gt_3D = cell_itself.transform_to_3D(ground_truth[:, toplot],
what="morpho")
draw_ground_truth_skcsd_3D(ax, gt_3D, csd_3D, data,
gvmin, gvmax, time[toplot])