def simulate():
tstop = 75
rownb = 10
colnb = 10
c = sKCSD_utils.simulate(fname_base,
morphology=7,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=1000,
simulate_what='oscillatory',
electrode_distribution=1,
electrode_orientation=3,
xmin=-400,
xmax=400,
ymin=-400,
ymax=400,
colnb=colnb,
rownb=rownb,
dt=0.5)
return c.return_paths_skCSD_python()
scale_factor_LFP = 1000
R_inits = np.array([(2**(i - .5)) / scale_factor for i in range(3, 9)])
lambdas = np.array([(10**(-i)) for i in range(5)])
colnb = 10
rownb = 10
fname = '%s_rows_%d' % (fname_base, rownb)
dt = .5
if sys.version_info < (3, 0):
c = sKCSD_utils.simulate(fname,
morphology=6,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=1000,
simulate_what='oscillatory',
electrode_distribution=1,
electrode_orientation=3,
xmin=-400,
xmax=400,
ymin=-400,
ymax=400,
colnb=colnb,
rownb=rownb,
dt=dt)
data_dir = c.return_paths_skCSD_python()
else:
data_dir = os.path.join('simulation', fname)
data = utils.LoadData(data_dir)
ele_pos = data.ele_pos / scale_factor
data.LFP = data.LFP / scale_factor_LFP
morphology = data.morphology
morphology[:, 2:6] = morphology[:, 2:6] / scale_factor
R_inits = [2**i*1e-6/np.sqrt(2) for i in range(3,8)]
lambdas = [10**(-i) for i in range(-3, 6, 1)]
electrode_number = [8, 32 , 128]
data_dir = []
xmin, xmax = -100, 600
ymin, ymax = 0, 200
orientation = 1
for rownb in electrode_number:
fname = "Figure_3"
c = sKCSD_utils.simulate(fname,
morphology=1,
simulate_what="random",
colnb=1,
rownb=rownb,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
tstop=tstop,
seed=1988,
weight=0.05,
n_syn=100,
dt=0.125)
data_dir.append(c.return_paths_skCSD_python())
seglen = np.loadtxt(os.path.join(data_dir[0], 'seglength'))
ground_truth = np.loadtxt(os.path.join(data_dir[0], 'membcurr'))
ground_truth = ground_truth/seglen[:, None]*1e-3
gvmax, gvmin = pl.get_min_max(ground_truth)
data_paths = []
fig = plt.figure(figsize=(20, 6))
for i in range(7):
colnb = different_trials_parameters[i]['colnb']
rownb = different_trials_parameters[i]['rownb']
xmin = different_trials_parameters[i]['xmin']
xmax = different_trials_parameters[i]['xmax']
ymin = different_trials_parameters[i]['ymin']
ymax = different_trials_parameters[i]['ymax']
c = sKCSD_utils.simulate(fname_base,
morphology=7,
tstop=tstop,
seed=1988,
weight=0.01,
n_syn=1000,
simulate_what='oscillatory',
electrode_distribution=1,
electrode_orientation=3,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
colnb=colnb,
rownb=rownb,
dt=dt)
c.save_for_R_kernel()
data_dir.append(c.return_paths_skCSD_python())
data = utils.LoadData(data_dir[0])
ele_pos = data.ele_pos/scale_factor
data.LFP = data.LFP/scale_factor_LFP
morphology = data.morphology
morphology[:, 2:6] = morphology[:, 2:6]/scale_factor
scaling_factor_LFP = 1000
data_dir = []
colnb = 4
rownb = 8
xmin, xmax = 0, 500
ymin, ymax = -80, 80
t1 = int(5.5 / dt)
fname = "Figure_9"
c = sKCSD_utils.simulate(fname,
morphology=2,
simulate_what="symmetric",
colnb=colnb,
rownb=rownb,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=100,
electrode_distribution=1,
dt=dt)
data_dir = c.return_paths_skCSD_python()
seglen = np.loadtxt(os.path.join(data_dir, 'seglength'))
ground_truth = np.loadtxt(os.path.join(data_dir, 'membcurr'))
ground_truth = ground_truth / seglen[:, None] * 1e-3
data_dir = []
colnb = 16
lfps = []
extent = [-200, 200, -200, 600]
xmin = [50, -200]
dt = 0.15
for i, rownb in enumerate(electrode_number):
fname = '%s_%d' % (fname_base, rownb)
if sys.version_info < (3, 0):
c = sKCSD_utils.simulate(fname,
morphology=2,
colnb=colnb,
rownb=rownb,
xmin=-200,
xmax=600,
ymin=xmin[i],
ymax=200,
tstop=tstop,
seed=1988,
weight=0.01,
n_syn=100,
simulate_what="symmetric",
dt=dt)
new_dir = c.return_paths_skCSD_python()
else:
new_dir = os.path.join('simulation', fname)
data_dir.append(new_dir)
seglen = np.loadtxt(os.path.join(data_dir[0], 'seglength'))
ground_truth = np.loadtxt(os.path.join(data_dir[0], 'membcurr'))
ground_truth = ground_truth / seglen[:, None] * 1e-3
ground_truth_grid = []
ground_truth_t1 = None
lambdas = [10**(-i) for i in range(6)]
electrode_number = [8, 32, 128]
data_dir = []
xmin, xmax = -100, 600
ymin, ymax = 0, 200
orientation = 1
for rownb in electrode_number:
fname = '%s_rows_%d' % (fname_base, rownb)
if sys.version_info < (3, 0):
c = sKCSD_utils.simulate(fname,
morphology=1,
simulate_what="random",
colnb=1,
rownb=rownb,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
tstop=tstop,
seed=1988,
weight=0.1,
n_syn=100)
new_dir = c.return_paths_skCSD_python()
else:
new_dir = os.path.join('simulation', fname)
data_dir.append(new_dir)
seglen = np.loadtxt(os.path.join(data_dir[0], 'seglength'))
ground_truth = np.loadtxt(os.path.join(data_dir[0], 'membcurr'))
ground_truth = ground_truth / seglen[:, None] * 1e-3
gvmax, gvmin = pl.get_min_max(ground_truth)
data_paths = []
scaling_factor_LFP = 1000
data_dir = []
colnb = 4
rownb = 8
xmin, xmax = 0, 500
ymin, ymax = -80, 80
t1 = int(5.5/dt)
fname = "Figure_9"
c = sKCSD_utils.simulate(fname,
morphology=2,
simulate_what="symmetric",
colnb=colnb,
rownb=rownb,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=100,
electrode_distribution=1,
dt=dt)
data_dir = c.return_paths_skCSD_python()
seglen = np.loadtxt(os.path.join(data_dir,
'seglength'))
ground_truth = np.loadtxt(os.path.join(data_dir,
'membcurr'))
dt = 2**(-4)
rows = [2, 4, 8, 16]
xmin, xmax = -100, 600
ymin, ymax = -100, 100
sim_type = {'1': "grid", '2': "random"}
for i, rownb in enumerate(rows):
for orientation in [1, 2]:
fname = "Figure_6_" + sim_type[str(orientation)]
c = sKCSD_utils.simulate(fname,
morphology=2,
simulate_what="symmetric",
colnb=rownb,
rownb=colnb,
xmin=-100,
xmax=500,
ymin=-100,
ymax=100,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=100,
electrode_distribution=orientation,
electrode_orientation=2,
dt=2**(-4))
data_dir.append(c.return_paths_skCSD_python())
seglen = np.loadtxt(os.path.join(data_dir[0], 'seglength'))
ground_truth = np.loadtxt(os.path.join(data_dir[0], 'membcurr'))
ground_truth = ground_truth / seglen[:, None] * 1e-3
t1 = int(42 / dt)
t2 = int(5 / dt)
atstart = t2
atstop = int(t2 + 10 / dt)
colnb = [4, 16]
lfps = []
xmax = [100, 500]
ymax = [500, 100]
cell_itself = []
for i, electrode_orientation in enumerate([1, 2]):
fname = fname_base
c = sKCSD_utils.simulate(fname,
morphology=2,
colnb=rownb[i],
rownb=colnb[i],
xmin=-100,
xmax=xmax[i],
ymin=-100,
ymax=ymax[i],
tstop=tstop,
seed=1988,
weight=0.01,
n_syn=100,
simulate_what="symmetric",
electrode_orientation=electrode_orientation,
dt=dt)
data_dir.append(c.return_paths_skCSD_python())
data = utils.LoadData(data_dir[i])
ele_pos = data.ele_pos/scaling_factor
morphology = data.morphology
morphology[:, 2:6] = morphology[:, 2:6]/scaling_factor
if i == 0:
cell_itself.append(sKCSDcell(morphology,
ele_pos,
xmax = [100, 500]
ymax = [500, 100]
cell_itself = []
morpho = []
extent = []
for i, electrode_orientation in enumerate([1, 2]):
fname = fname_base
c = sKCSD_utils.simulate(fname,
morphology=2,
colnb=rownb[i],
rownb=colnb[i],
xmin=-100,
xmax=xmax[i],
ymin=-100,
ymax=ymax[i],
tstop=tstop,
seed=1988,
weight=0.01,
n_syn=100,
simulate_what="symmetric",
electrode_orientation=electrode_orientation,
dt=dt)
data_dir.append(c.return_paths_skCSD_python())
data = utils.LoadData(data_dir[i])
ele_pos = data.ele_pos/scaling_factor
morphology = data.morphology
morphology[:, 2:6] = morphology[:, 2:6]/scaling_factor
if i == 0:
cell_itself.append(sKCSDcell(morphology,
ele_pos,
scale_factor_LFP = 1000
R_inits = np.array([(2**(i - .5)) / scale_factor for i in range(3, 7)])
lambdas = np.array([(10**(-i)) for i in range(5, 0, -1)])
n_srcs = np.array([32, 64, 128, 512, 1024])
x_ticklabels = [2**i for i in range(3, 7)]
y_ticklabels = [str(lambd) for lambd in lambdas]
colnb = 4
rownb = 4
c = sKCSD_utils.simulate(fname_base,
morphology=2,
colnb=colnb,
rownb=rownb,
xmin=0,
xmax=500,
ymin=-100,
ymax=100,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=100,
electrode_orientation=2,
simulate_what='symmetric',
dt=dt)
new_path = c.return_paths_skCSD_python()
data = utils.LoadData(new_path)
ele_pos = data.ele_pos / scale_factor
pots = data.LFP / scale_factor_LFP
morphology = data.morphology
morphology[:, 2:6] = morphology[:, 2:6] / scale_factor
ground_truth = np.loadtxt(os.path.join(new_path, 'membcurr'))
dt = 2**(-4)
rows = [2, 4, 8, 16]
xmin, xmax = -100, 600
ymin, ymax = -100, 100
sim_type = {'1': "grid", '2': "random"}
for i, rownb in enumerate(rows):
for orientation in [1, 2]:
fname = "Figure_6_" + sim_type[str(orientation)]
c = sKCSD_utils.simulate(fname,
morphology=2,
simulate_what="symmetric",
colnb=rownb,
rownb=colnb,
xmin=-100,
xmax=500,
ymin=-100,
ymax=100,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=100,
electrode_distribution=orientation,
electrode_orientation=2,
dt=2**(-4))
data_dir.append(c.return_paths_skCSD_python())
seglen = np.loadtxt(os.path.join(data_dir[0],
'seglength'))
ground_truth = np.loadtxt(os.path.join(data_dir[0],
'membcurr'))
ground_truth = ground_truth/seglen[:, None]*1e-3
t1 = int(42/dt)
t2 = int(5/dt)
scale_factor_LFP = 1000
R_inits = np.array([(2**(i - .5))/scale_factor for i in range(3, 7)])
lambdas = np.array([(10**(-i))for i in range(5, 0, -1)])
n_srcs = np.array([32, 64, 128, 512, 1024])
x_ticklabels = [2**i for i in range(3, 7)]
y_ticklabels = [str(lambd) for lambd in lambdas]
colnb = 4
rownb = 4
c = sKCSD_utils.simulate(fname_base,
morphology=2,
colnb=colnb,
rownb=rownb,
xmin=0,
xmax=500,
ymin=-100,
ymax=100,
tstop=tstop,
seed=1988,
weight=0.04,
n_syn=100,
electrode_orientation=2,
simulate_what='symmetric',
dt=dt)
data = utils.LoadData(c.return_paths_skCSD_python())
ele_pos = data.ele_pos/scale_factor
pots = data.LFP/scale_factor_LFP
morphology = data.morphology
morphology[:, 2:6] = morphology[:, 2:6]/scale_factor
ground_truth = np.loadtxt(os.path.join(new_path,
'membcurr'))
