def configure_ax(ax):
plot_polygon(ax, pughpolygon(rmem=100.), linewidth=lw)
ax.set_aspect("equal")
ax.set_xlim([-20., 20.])
ax.set_ylim([-33., 40])
ax.set_axis_off() # <=> plt.axis("off")
ax.get_xaxis().set_visible(False) # so that white space disappears!
ax.get_yaxis().set_visible(False)
gs=gridspec.GridSpec(1, 2, width_ratios=[1,1])
ax0=plt.subplot(gs[0])
plt.title('Current')
ax=plt.gca()
ax.set_aspect('equal')
ax.set_xlim([-20.,20.])
ax.set_ylim([-23.,24.])
ax.set_xticks(np.arange(-20.,20.,2.))
ax.set_yticks(np.arange(-23.,24.,2.))
ax.grid()
data = ax0.imshow(matrix1,cmap=plt.cm.viridis,interpolation='none',**args)
cbar = fig.colorbar(data)
plot_polygon(ax,poly)
ax1=plt.subplot(gs[1])
plt.title('Drop')
ax=plt.gca()
ax.set_aspect('equal')
ax.set_xlim([-20.,20.])
ax.set_ylim([-23.,24.])
ax.set_xticks(np.arange(-20.,20.,2.))
ax.set_yticks(np.arange(-23.,24.,2.))
ax.grid()
data = ax1.imshow(matrix2,cmap=plt.cm.viridis,interpolation='none',**args)
cbar = fig.colorbar(data)
plt.legend(patches, labels, scatterpoints=1, loc=(.43, .12))
ax = plt.gca()
ax.set_aspect("equal")
ax.set_xlim([-20., 60.])
ax.set_ylim([-25., 35.5])
ax.set_axis_off() # <=> plt.axis("off")
ax.get_xaxis().set_visible(False) # so that white space disappears!
ax.get_yaxis().set_visible(False)
#ax.set_xticks([])
#ax.set_yticks([])
#plt.axis('off')
plot_polygon(ax, pughpolygon(rmem=100.), linewidth=lw)
plt.axes([.6, .45, .3, .3])
#plt.title('Current $A/I_0$')
plt.title("Current signal")
ax = plt.gca()
if tau_off < 1e3:
#t = np.linspace(0., tau_off, 3)
fac = 1.
#ax.set_xlabel("Time [ns]")
elif tau_off < 1e6 and tau_off >= 1e3:
#t = np.linspace(0., tau_off*1e-3, 3)
fac = 1e-3
#ax.set_xlabel(u"Time [µs]")
else:
# obtain 2D mesh where we will evaluate field
rx, ry = pughpore.params["R"], 0.5 * pughpore.params["H"]
rx, ry = 15, 28
Nx, Ny = 201, 401
#mesh2D = RectangleMesh([-R,-H/2.], [R, H/2.], int(4*R), int(2*H))
Y, X = np.mgrid[-ry:ry:Ny * 1j, -rx:rx:Nx * 1j]
U = np.zeros((Ny, Nx))
for y in range(Ny):
for x in range(Nx):
U[y][x] = F(X[y][x], Y[y][x])
fig, ax = plt.subplots(figsize=(1.73, 1.9)) #, dpi=300)
pc = plt.pcolor(X, Y, U, cmap=plt.get_cmap("bone"), vmin=0, vmax=1)
plot_polygon(ax, pughpolygon(diamPore=6., rmem=15), linewidth=0.2)
plt.xlim(-15, 15)
plt.ylim(-25, 28)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
bbox = ax.get_position()
l, b, h = bbox.x0, bbox.y0, bbox.height
w = 0.05
cbaxes = fig.add_axes([l - w - 0.07, b, w, h])
cb = plt.colorbar(pc, cax=cbaxes, ax=ax)
cbaxes.set_ylabel("Rel. diffusivity") # (r"$D_{zz} / D_0$")
cb.set_ticks([0., 1.])
cb.set_ticklabels([0, 1])
cbaxes.yaxis.set_ticks_position('left')
cbaxes.yaxis.set_label_position('left')
cbaxes.yaxis.labelpad = -3.
def save_fig_traj(params,fieldsname,i,showtraj):
data=f.get_fields(fieldsname,**params)
b1 =data["b1"]
b2 =data["b2"]
if showtraj:
X = data["X"][i]
Y = data["Y"][i]
Z = data["Z"][i]
T = data["T"][i]
J = data["J"][i]
J=J.load()
T=T.load()
curr = 7.523849e-10
bind1 = np.where(T>1e6)[0]
bind2 = np.intersect1d(np.where(T<=1e6)[0],np.where(T>100.)[0])
amplitude = curr-np.inner(J,T)/np.sum(T)
for k in range(1,T.shape[0]):
T[k]=T[k]+T[k-1]
tau_off=T[-1]
J=J*1e12
figname = fieldsname+'_traj_'+'%.8f'%(tau_off*1e-6)+'_%04d'%i+'_%.1e_%.1e_%.1e_%.1e'%(params["avgbind1"],params["avgbind2"],params["P_bind1"],params["P_bind2"])+str(params["z0"])
else:
figname = fieldsname+'_bindzones'+'_%.1e_%.1e_%.1e_%.1e'%(params["avgbind1"],params["avgbind2"],params["P_bind1"],params["P_bind2"])+str(params["z0"])
if showtraj:
fig=plt.figure(figsize=(8,5),dpi=80)
else:
fig=plt.figure(figsize=(3,5),dpi=80)
color2='#ff0000'
color1='#ff9900'
color3='#00ff00'
#b1 = [[[l1/2.,17.],[l1/2.,19.]],[[l3/2.,-hpore/2.],[l3/2.,hpore/2.-h2],[l2/2.,hpore/2.-h2],[l2/2.,14.]]]
for seq in b1:
x= [p[0] for p in seq]
xm=[-p[0] for p in seq]
y= [p[1] for p in seq]
plt.plot(x,y,color=color1,linewidth=2.)
plt.plot(xm,y,color=color1,linewidth=2.)
#b2 = [[[l3/2.-.5,-3.],[l3/2.-.5,11.]]]
for seq in b2:
x= [p[0] for p in seq]
xm=[-p[0] for p in seq]
y= [p[1] for p in seq]
plt.plot(x,y,color=color2,linewidth=2.)
plt.plot(xm,y,color=color2,linewidth=2.)
if showtraj:
plt.plot(X,Z,linewidth=1.,c='#0000ff')
longer = plt.scatter(X[bind1],Z[bind1],s=200,marker='h',c=color2,linewidth=0.)
shorter = plt.scatter(X[bind2],Z[bind2],s=100,marker='h',c=color1,linewidth=0.)
start = plt.scatter([X[0]],[Z[0]],s=200,marker='x',c=color3,linewidth=2.)
patches=[start]
labels=['Start']
if showtraj and len(bind1)>0:
patches=patches+[longer]
labels+=['Longer bindings']
if showtraj and len(bind2)>0:
patches=patches+[shorter]
labels+=['Shorter bindings']
if showtraj:
plt.legend(patches,labels,scatterpoints=1,loc=(.42,.15))
ax=plt.gca()
ax.set_aspect('equal')
if showtraj:
ax.set_xlim([20.,-55.])
ax.set_ylim([-25.,40.])
else:
ax.set_xlim([20.,-20.])
ax.set_ylim([-25.,40.])
ax.set_xticks([])
ax.set_yticks([])
plt.axis('off')
plot_polygon(ax,polygon(rmem=60.))
if showtraj:
plt.axes([.55,.5,.2,.3])
plt.title('Current signal')
ax=plt.gca()
if tau_off<1e3:
t = np.linspace(0.,tau_off,3)
fac=1.
ax.set_xlabel('time [$ns$]')
elif tau_off<1e6 and tau_off>=1e3:
t = np.linspace(0.,tau_off*1e-3,3)
fac = 1e-3
ax.set_xlabel(r'time [$\mu s$]')
else:
t = np.linspace(0.,tau_off*1e-6,3)
fac = 1e-6
ax.set_xlabel('time [$ms$]')
T=T*fac
plt.plot(T,J,color='#000000')
yt = np.linspace(580.,760,4)
ax.set_ylabel(r'A [$pA$]')
ax.set_yticks(yt)
ax.set_xticks(t)
xfmt=FormatStrFormatter('%.1f')
ax.xaxis.set_major_formatter(xfmt)
ax.set_xlim([-4e-2*tau_off*fac,(1.+4e-2)*tau_off*fac])
plt.tight_layout()
# nano.savefigs(name=figname,DIR='/home/bstadlbau/plots/')
plt.show()
print 'savefig: %s'%figname
plt.close("all")
def save_frame(r, X=X, Z=Z, T=T, J=J, curr=curr * 1e12):
figname = 'frames/' + '%08d' % r
suffix = '.eps'
figname += suffix
fig = plt.figure(figsize=(32, 18), dpi=120)
color2 = '#ff0000'
color1 = '#ff9900'
color3 = '#00ff00'
#b1 = [[[l1/2.,17.],[l1/2.,19.]],[[l3/2.,-hpore/2.],[l3/2.,hpore/2.-h2],[l2/2.,hpore/2.-h2],[l2/2.,14.]]]
for seq in b1:
x = [p[0] for p in seq]
xm = [-p[0] for p in seq]
y = [p[1] for p in seq]
plt.plot(x, y, color=color1, linewidth=3.)
plt.plot(xm, y, color=color1, linewidth=3.)
#b2 = [[[l3/2.-.5,-3.],[l3/2.-.5,11.]]]
for seq in b2:
x = [p[0] for p in seq]
xm = [-p[0] for p in seq]
y = [p[1] for p in seq]
plt.plot(x, y, color=color2, linewidth=3.)
plt.plot(xm, y, color=color2, linewidth=3.)
plt.plot(X[:r], Z[:r], linewidth=2., c='#0000ff')
molecolor = '#33ff99'
molecule = plt.Circle((X[r - 1], Z[r - 1]), 2.0779, color=molecolor)
mole2 = Line2D(range(1),
range(1),
color='white',
marker='o',
markerfacecolor=molecolor,
markersize=20)
longer = plt.scatter(X[bind1],
Z[bind1],
s=200,
marker='h',
c=color2,
linewidth=0.)
shorter = plt.scatter(X[bind2],
Z[bind2],
s=100,
marker='h',
c=color1,
linewidth=0.)
start = plt.scatter([X[0]], [Z[0]],
s=400,
marker='x',
c=color3,
linewidth=2.)
patches = [start, mole2]
labels = ['Start', 'Molecule']
plt.legend(patches,
labels,
scatterpoints=1,
loc=(.47, .15),
fontsize=fs,
numpoints=1)
ax = plt.gca()
ax.add_artist(molecule)
ax.set_aspect('equal')
ax.set_xlim([47., -82.])
ax.set_ylim([-30., 40.])
ax.set_xticks([])
ax.set_yticks([])
plt.axis('off')
plot_polygon(ax, polygon(rmem=100.))
plt.axes([.55, .5, .3, .4])
plt.title('Current signal', fontsize=fs)
ax = plt.gca()
if tau_off < 1e3:
t = np.linspace(0., tau_off, 3)
fac = 1.
ax.set_xlabel('time [$ns$]', fontsize=fs)
elif tau_off < 1e6 and tau_off >= 1e3:
t = np.linspace(0., tau_off * 1e-3, 3)
fac = 1e-3
ax.set_xlabel(r'time [$\mu s$]', fontsize=fs)
else:
t = np.linspace(0., tau_off * 1e-6, 3)
fac = 1e-6
ax.set_xlabel('time [$ms$]', fontsize=fs)
T = T * fac
plt.plot(T[:r], J[:r], color='#000000', linewidth=2.)
b, a = bessel(3, 2e-5, analog=False)
# sig = filtfilt(b,a,J-curr)+curr
sig = lfilter(b, a, lfilter(b, a, J - curr)) + curr
# plt.plot(T[:r],sig[:r])
yt = np.linspace(580., 760, 4)
ax.set_ylabel(r'A [$pA$]', fontsize=fs)
ax.set_yticks(yt)
ax.set_xticks(t)
xfmt = FormatStrFormatter('%.1f')
ax.xaxis.set_major_formatter(xfmt)
ax.set_xlim([-4e-2 * tau_off * fac, (1. + 4e-2) * tau_off * fac])
plt.tight_layout()
# plt.show()
plt.savefig(figname)
print 'save: ' + figname + ' from %08d' % len
plt.close('all')
return D3D([-x, z]) / D0
#D = uCross(u=D3D, axis=1, degree=1, dim=2)
# obtain 2D mesh where we will evaluate field
rx, ry = pugh.pughpore.params["R"], 0.5 * pugh.pughpore.params["H"]
rx, ry = 13, 28
Nx, Ny = 201, 401
#mesh2D = RectangleMesh([-R,-H/2.], [R, H/2.], int(4*R), int(2*H))
Y, X = np.mgrid[-ry:ry:Ny * 1j, -rx:rx:Nx * 1j]
U = np.zeros((Ny, Nx))
for y in range(Ny):
for x in range(Nx):
U[y][x] = F(X[y][x], Y[y][x])
fig, ax = plt.subplots(figsize=(6.5, 6.5), num="r0.11")
pc = plt.pcolor(X, Y, U, cmap=cm.inferno, vmin=0, vmax=1)
plt.colorbar(pc)
plot_polygon(ax, pugh.polygon(diamPore=6., rmem=13))
plt.xlim(-13, 13)
plt.ylim(-25, 28)
#plt.xlabel("x [nm]")
#plt.ylabel("z [nm]")
fig.axes[1].set_ylabel(r"$D_{zz} / D_0$")
#cb = fig.colorbar(CS, cax=cax, extend="both", orientation="vertical", format=formt)
import folders
nanopores.savefigs("pugh_Dfield_protein", folders.FIGDIR)
plt.show()