def plot_fig_low(calcAna, calcAnaAll, figname=None):
plt.rcParams['figure.figsize'] = (3.346, 2.55)
plt.rcParams['ytick.labelsize'] = 10
plt.rcParams['xtick.labelsize'] = 10
plt.rcParams['font.size'] = 12
plt.rcParams['legend.fontsize'] = 6
# intialise figure
fig = plt.figure()
fig.subplots_adjust(wspace=0.2,
hspace=0.6,
top=0.85,
bottom=0.09,
left=0.18,
right=0.83)
ax = plt.subplot2grid((1, 1), (0, 0))
# get data
data = get_sensitivity_measure(calcAna,
calcAnaAll,
mode='low',
eig_index=6)
fmax, Z, Z_amp, Z_freq, vec, vec_per, eigc = data
# plot figure
M_plot = [ph.reorder_matrix(Z_amp), ph.reorder_matrix(Z_freq)]
M_title = [
r'$\mathbf{Z}^{\mathrm{amp}}(0\mathrm{Hz})$',
r'$\mathbf{Z}^{\mathrm{freq}}(0\mathrm{Hz})$'
]
zmin = np.min([Z_amp, Z_freq])
zmax = np.max([Z_amp, Z_freq])
z = np.max([abs(zmin), abs(zmax)])
im1 = ax.pcolor(M_plot[0], vmin=-z, vmax=z, cmap=plt.cm.coolwarm)
ax.xaxis.tick_top()
ax.set_xticks([0.5 + i for i in range(8)])
tpops = ph.populations
tpops[0] = '2/3E '
ax.set_xticklabels(tpops, fontsize=9)
ax.set_yticks([0.5 + i for i in range(8)])
ax.set_xlabel(M_title[0])
ax.set_title('sources\n', fontsize=12)
ax.set_yticklabels(ph.populations[::-1], fontsize=9)
ax.set_ylabel('targets', fontsize=12)
per = 0.9
box = ax.get_position()
ax.set_position([box.x0, box.y0, box.width * per, box.height])
cbar_ax = fig.add_axes([box.x0 + box.width, box.y0, 0.04, box.height])
fig.colorbar(im1, cax=cbar_ax, ticks=[-2.0, -1.0, 0, 1.0, 2.0])
if figname is None:
figname = 'sensitivity_measure_low.eps'
plt.savefig(figname)
def plot_connectivity_matrix(Mred, ax):
M = ph.reorder_matrix(Mred)
im1 = ax.pcolor(M, cmap='Greys')
ax.xaxis.tick_top()
ax.set_xticks([0.5 + i for i in range(8)])
ax.set_xticklabels(ph.populations, fontsize=7)
ax.set_yticks([0.5 + i for i in range(8)])
ax.set_yticklabels(ph.populations[::-1], fontsize=7)
ax.set_title('sources\n', fontsize=10)
ax.set_ylabel('targets', fontsize=10)
def plot_matrices_gamma(M_title,
Z,
ax,
fig,
panel,
fontsize_pops=7,
fontsize_title=9):
M_plot = [ph.reorder_matrix(Z[0]), ph.reorder_matrix(Z[1])]
zmin = np.min(Z)
zmax = np.max(Z)
z = np.max([abs(zmin), abs(zmax)])
for j, k in enumerate([3 * panel, 3 * panel + 1]):
im1 = ax[k].pcolor(M_plot[j], vmin=-z, vmax=z, cmap=plt.cm.coolwarm)
ax[k].xaxis.tick_top()
ax[k].set_xticks([0.5 + i for i in range(8)])
ax[k].set_xticklabels(ph.populations, fontsize=fontsize_pops)
ax[k].set_yticks([0.5 + i for i in range(8)])
ax[k].set_xlabel(M_title[j])
ax[k].set_title('sources\n', fontsize=fontsize_title)
ax[0 + 3 * panel].set_yticklabels(ph.populations[::-1],
fontsize=fontsize_pops)
ax[1 + 3 * panel].set_yticklabels([])
ax[0 + 3 * panel].set_ylabel('targets', fontsize=fontsize_title)
per = 0.9
dMx = 0.07
box = ax[0 + 3 * panel].get_position()
ax[0 + 3 * panel].set_position(
[box.x0, box.y0, box.width * per, box.height])
box = ax[1 + 3 * panel].get_position()
ax[1 + 3 * panel].set_position([
box.x0 - box.width * (1 - per) - dMx, box.y0, box.width * per,
box.height
])
box = ax[1 + 3 * panel].get_position()
cbar_ax = fig.add_axes(
[box.x0 + box.width + 0.1 * box.width, box.y0, 0.015, box.height])
fig.colorbar(im1, cax=cbar_ax, ticks=[-0.8, -0.4, 0, 0.4, 0.8])
def plot_fig_high_gamma(calcAna, calcAnaAll, figname=None):
plt.rcParams['figure.figsize'] = (6.929, 3)
plt.rcParams['ytick.labelsize'] = 8.5
plt.rcParams['xtick.labelsize'] = 8.5
plt.rcParams['font.size'] = 9
plt.rcParams['legend.fontsize'] = 6
nx = 2
ny = 4
# indices of dominant eigenmodes
eig_index = [0, 1, 2, 3]
# peak frequencies of dominant eigenmodes
fps = [284, 267, 263, 241]
# intialise figure
fig = plt.figure()
fig.subplots_adjust(wspace=0.2,
hspace=0.6,
top=0.9,
bottom=0.07,
left=0.065,
right=0.97)
ax = []
# panel A
ax.append([plt.subplot2grid((nx, ny), (0, i)) for i in [0, 1]])
# panel B
ax.append([plt.subplot2grid((nx, ny), (0, i)) for i in [2, 3]])
# panel C
ax.append([plt.subplot2grid((nx, ny), (1, i)) for i in [0, 1]])
# panel D
ax.append([plt.subplot2grid((nx, ny), (1, i)) for i in [2, 3]])
# loop over panels
for n in range(4):
data = get_sensitivity_measure(calcAna,
calcAnaAll,
mode='high_gamma',
eig_index=eig_index[n])
fmax, Z, Z_amp, Z_freq, vec, vec_per, eigc = data
M_plot = [ph.reorder_matrix(Z_amp), ph.reorder_matrix(Z_freq)]
M_title = [
r'$\mathbf{Z}^{\mathrm{amp}}($' + str(fps[n]) + r'$\mathrm{Hz})$',
r'$\mathbf{Z}^{\mathrm{freq}}($' + str(fps[n]) + r'$\mathrm{Hz})$'
]
# normalise plots to dominant mode
if n == 0:
zmin = np.min([Z_amp, Z_freq])
zmax = np.max([Z_amp, Z_freq])
z = np.max([abs(zmin), abs(zmax)])
tax = ax[n]
for k in [1, 0]:
im1 = tax[k].pcolor(M_plot[k],
vmin=-z,
vmax=z,
cmap=plt.cm.coolwarm)
tax[k].xaxis.tick_top()
tax[k].set_xticks([0.5 + i for i in range(8)])
tax[k].set_xticklabels(ph.populations, fontsize=6)
tax[k].set_yticks([0.5 + i for i in range(8)])
tax[k].set_xlabel(M_title[k])
tax[k].set_title('sources\n', fontsize=9)
tax[0].set_yticklabels(ph.populations[::-1], fontsize=6)
tax[1].set_yticklabels([])
tax[0].set_ylabel('targets', fontsize=9)
per = 0.9
dMx = 0.02
box = tax[0].get_position()
tax[0].set_position([box.x0, box.y0, box.width * per, box.height])
box = tax[1].get_position()
tax[1].set_position([
box.x0 - box.width * (1 - per) - dMx, box.y0, box.width * per,
box.height
])
box = tax[1].get_position()
if n % 2 == 1:
cbar_ax = fig.add_axes([
box.x0 + box.width + 0.1 * box.width, box.y0, 0.015, box.height
])
fig.colorbar(im1, cax=cbar_ax, ticks=[-0.8, -0.4, 0, 0.4, 0.8])
for i, label in enumerate(['A', 'B', 'C', 'D']):
box = ax[i][0].get_position()
fig.text(box.x0 - 0.04,
box.y0 + box.height + 0.03,
label[0],
fontsize=13,
fontweight='bold')
if figname is None:
figname = 'sensitivity_measure_high_gamma.eps'
plt.savefig(figname)
def plot_fig(calcData=False, calcAna=False, calcAnaAll=False):
plt.rcParams['figure.figsize'] = (6.929, 6.0)
plt.rcParams['ytick.labelsize'] = 12
plt.rcParams['xtick.labelsize'] = 12
plt.rcParams['font.size'] = 12
plt.rcParams['legend.fontsize'] = 10
nr_windows = 20
bin_size = 1.0
colors = ph.get_parameter_plot()
nx = 5
ny = 4
fig = plt.figure()
fig.subplots_adjust(wspace=0.1, hspace=0.1, top=0.93,
bottom=0.185, left=0.1, right=0.97)
ax = []
ax.append(plt.subplot2grid((nx,ny), (0,0),rowspan=3)) # column
ax.append(plt.subplot2grid((nx,ny), (0,3),rowspan=2)) # in-degrees
ax.append(plt.subplot2grid((nx,ny), (2,3))) # firing rates
ax.append(plt.subplot2grid((nx,ny), (0,1), rowspan=3,
colspan=2)) # dotplot
ax.append([plt.subplot2grid((nx,ny), (nx-(2-i%2),i/2))
for i in range(8)]) # spectra
### panel A ###
ax[0].axis('off')
### panel B ###
times, gids = get_dotplot(calcData)
box = ax[3].get_position()
ax[3].set_position([box.x0+box.width*0.05, box.y0,
box.width*0.85, box.height])
clrs=['0','0.5','0','0.5','0','0.5','0','0.5']
pop_sizes = circuit_params['N']
N_temp = 0
for j in range(8):
# pick a gid in the middle
green_gids = gids[j][np.argmin(abs(abs(gids[j]-77169)-
(N_temp+pop_sizes[j]/2.)))]
green_times = times[j][np.where(gids[j]==green_gids)]
if j == 2:
k = 0
while len(green_times) != 2:
green_gid = gids[j][k]
green_gids = [green_gid,green_gid]
green_times = times[j][np.where(gids[j]==green_gid)]
k += 1
if k == len(gids[j]):
green_times = [green_times,green_times]
break
N_temp += pop_sizes[j]
ax[3].plot(times[j], gids[j], 'o', ms=1, mfc=clrs[j], mec=clrs[j])
if len(green_times) >1:
green_gids = [green_gids for i in range(len(green_times))]
ax[3].plot(green_times, green_gids,'o',mfc='red',mec='red')
# position labels
size = 0
layer_labels = []
for layer in [3, 2, 1, 0]:
layer_labels.append(sum(pop_sizes[2*layer:2*layer+2])/2. + size)
size += sum(pop_sizes[2*layer:2*layer+2])
ax[3].set_xlim(0,50)
ax[3].set_ylim(0,77169)
ax[3].set_xlabel(r't (ms)')
ax[3].set_yticks(layer_labels)
ax[3].set_yticklabels(['L2/3','L4','L5','L6'][::-1])
ax[3].tick_params(axis='y',length=0)
box = ax[3].get_position()
ax[3].set_position([box.x0-box.width*0.07, box.y0,
box.width, box.height])
### panel C ###
In = circuit_params['I']
M = ph.reorder_matrix(In)
im1 = ax[1].pcolor(M, vmax=3000, cmap='OrRd')
ax[1].xaxis.tick_top()
ax[1].set_xticks([0.1, 1.45]+[0.5 + j for j in range(2,8)])
ax[1].set_xticklabels(ph.populations, fontsize=6)
ax[1].set_yticks([0.5 + j for j in range(8)])
ax[1].set_yticklabels(ph.populations[::-1], fontsize=6)
ax[1].tick_params(axis='x', which='both', top='off', labelbottom='off')
ax[1].tick_params(axis='y', which='both', right='off', left='off',
labelbottom='off')
ax[1].set_title('sources\n',fontsize=11)
ax[1].set_ylabel('targets',fontsize=11)
box = ax[1].get_position()
per = 0.88
cbar_ax = fig.add_axes([box.x0, box.y0*1.1, box.width, 0.015])
ax[1].set_position([box.x0, box.y0*1.15, box.width, box.height*0.7])
fig.colorbar(im1, orientation="horizontal", cax=cbar_ax, ticks=[0,3000])
### panel D ###
rates_sim, rates_calc = get_rates(calcData, calcAna, calcAnaAll)
ax[2].bar(np.arange(8), rates_sim*1000,0.8,
color=['black','grey','black','grey',
'black','grey','black','grey'])
ax[2].plot(np.arange(8)+0.4, rates_calc, 'x', mew=2.5, ms=5, color='red')
ax[2].set_xticks([1, 3, 5, 7])
ax[2].set_xticklabels(['L2/3', 'L4', 'L5', 'L6'])
ax[2].set_yticks([2, 4, 6, 8])
ax[2].set_yticks([1, 3, 5, 7])
ax[2].set_ylabel(r'$\bar r$ (1/$s$)')
### panel E ###
power, freq = get_spec_sim(calcData, nr_windows, bin_size)
power_1w, freq_1w = get_spec_sim(calcData, 1, bin_size)
freq_ana, power_ana = get_spec_ana(calcAna, calcAnaAll)
for layer in [0, 1, 2, 3]:
for pop in [0, 1]:
j = layer*2+pop
box = ax[4][j].get_position()
ax[4][j].set_position([box.x0, box.y0-box.height*0.58,
box.width, box.height])
ax[4][j].plot(freq_1w, power_1w[j], color=(0.8, 0.8, 0.8))
ax[4][j].plot(freq, power[j], color=(0.5, 0.5, 0.5))
ax[4][j].plot(freq_ana,np.sqrt(power_ana[j]),
color='black', zorder=2)
ax[4][j].set_xlim([10.0, 400.0])
ax[4][j].set_ylim([1e-6, 1e0])
ax[4][j].set_yscale('log')
ax[4][j].set_yticks([])
ax[4][j].set_xticks([100, 200, 300])
ax[4][j].set_title(ph.populations[j])
if pop == 0:
ax[4][j].set_xticklabels([])
else:
box = ax[4][j].get_position()
ax[4][j].set_position([box.x0, box.y0-box.height*0.2,
box.width, box.height])
ax[4][j].set_xlabel(r'frequency (1/$s$)')
ax[4][0].set_yticks([1e-5,1e-3,1e-1])
ax[4][1].set_yticks([1e-5,1e-3,1e-1])
ax[4][0].set_ylabel(r'$|C(\omega)|$')
ax[4][1].set_ylabel(r'$|C(\omega)|$')
for i,label in enumerate(['A','C','D','B','E']):
if label == 'E':
box = ax[i][0].get_position()
else:
box = ax[i].get_position()
fig.text(box.x0-0.04, box.y0+box.height+0.015,
label,fontsize=16, fontweight='bold')
plt.savefig('microcircuit.eps')