def plot_allan_variance(xs: np.ndarray, ys: np.ndarray) -> plt.axes:
from mpl_toolkits.axes_grid.inset_locator import (inset_axes,
InsetPosition,
mark_inset)
_, _ax = plt.subplots()
_ax.plot(xs, ys, '.')
_ax.set_ylabel(f'Variance' +
r' $\langle [x(t + \delta t) - x(t)]^2 \rangle$ $[nm^2]$',
fontsize=font_size)
# _ax.set_ylabel(f'Distance' + r' $abs(x(t + \delta t) - x(t))$ $[nm]$', fontsize=font_size)
_ax.set_xlabel(f'Time step' + r' $\delta t[s]$', fontsize=font_size)
_ax.set_yscale('log')
# _ax.set_xscale('log')
_ax.grid(True)
# Inset
_ax2 = plt.axes([0, 0, 1, 1])
# Manually set the position and relative size of the inset axes within ax1
ip = InsetPosition(_ax, [0.6, 0.1, 0.3, 0.3])
_ax2.set_axes_locator(ip)
# Mark the region corresponding to the inset axes on ax1 and draw lines
# in grey linking the two axes.
mark_inset(_ax, _ax2, loc1=2, loc2=4, fc="none", ec='0.5')
xs2 = []
ys2 = []
for i, x in enumerate(xs):
if x < 0.007:
xs2.append(xs[i])
ys2.append(ys[i])
_ax2.plot(xs2, ys2, '.')
_ax2.set_yscale('log')
_ax2.set_xscale('log')
_ax2.set_ylim(_ax.get_ylim())
_ax2.grid(True)
return _ax
def zoommap(vals, title, label):
fig = plt.figure(figsize=(12,8))
plt.subplots_adjust(left=0.05,right=0.95,top=0.90,bottom=0.05,
wspace=0.15,hspace=0.05)
ax = plt.subplot(211)
m = Basemap(projection = 'mill', llcrnrlat = -45, llcrnrlon = -160,
urcrnrlat= 82, urcrnrlon = 170, resolution = 'c')
m.drawcoastlines(linewidth = 0.5)
plt.subplots_adjust(left=0.05,right=0.95,top=0.90,bottom=0.05,
wspace=0.15,hspace=0.05)
for row in vals:
x,y = m(vals.lon.values, vals.lat.values)
m.scatter(x,y, s = 20, color = vals.color.values)
ax.text(0.03,0.95, label, size = 12, horizontalalignment='center',
verticalalignment='center', transform=ax.transAxes)
plt.title(title, fontsize = 12)
#Zoom Europe
axins_1 = zoomed_inset_axes(ax, 2, loc=2, bbox_to_anchor=(0.42, 0.48),
bbox_transform=ax.figure.transFigure)
axins_1.scatter(x, y, s = 20, c = vals.color.values)
m.drawcoastlines(linewidth = 0.5)
x2,y2 = m(-12,35)
x3,y3 = m(40,65)
axins_1.set_xlim(x2,x3)
axins_1.set_ylim(y2,y3)
axes = mark_inset(ax, axins_1, loc1=1, loc2=2, linewidth=1)
#Zoom Australia
axins_2 = zoomed_inset_axes(ax, 2.2, loc=3, bbox_to_anchor=(0.61, 0.255),
bbox_transform=ax.figure.transFigure)
axins_2.scatter(x, y, s = 20, c = vals.color.values)
m.drawcoastlines(linewidth = 0.5)
x2,y2 = m(110,-43)
x3,y3 = m(155,-10)
axins_2.set_xlim(x2,x3)
axins_2.set_ylim(y2,y3)
axes = mark_inset(ax, axins_2, loc1=1, loc2=2,linewidth=1)
#Zoom US
axins_3 = zoomed_inset_axes(ax, 1.6, loc=3, bbox_to_anchor=(0.21, 0.25),
bbox_transform=ax.figure.transFigure)
axins_3.scatter(x, y, s = 20, c = vals.color.values)
m.drawcoastlines(linewidth = 0.5)
x2,y2 = m(-130,22)
x3,y3 = m(-60,63)
axins_3.set_xlim(x2,x3)
axins_3.set_ylim(y2,y3)
axes = mark_inset(ax, axins_3, loc1=1, loc2=2, linewidth=1)
return(fig, axes)
#%%
# Plot all the baselines
sns.set_style("white")
sns.set_context("paper", font_scale=3)
fig, ax1 = plt.subplots(figsize=(15, 10))
pt_colors = ["r", "b", "g", "k", "m", "c"]
ax2 = plt.axes([0, 0, 1, 1])
# Manually set the position and relative size of the inset axes within ax1
ip = InsetPosition(ax1, [0.1, 0.1, 0.7, 0.4])
ax2.set_axes_locator(ip)
# Mark the region corresponding to the inset axes on ax1 and draw lines
# in grey linking the two axes.
mark_inset(ax1, ax2, loc1=2, loc2=4, fc="none", ec="0.5", linestyle="dotted")
for pp, pt in enumerate(pt_list):
do_condit = do_presence[pt][0]
do_rec_side = do_presence[pt][1]
stim_side = "Bilateral"
print(f"{pt} with {condit}")
t_vect = SGs[pt][condit][do_rec_side]["T"]
f_vect = SGs[pt][condit][do_rec_side]["F"]
sg_data = SGs[pt][do_condit][do_rec_side]["SG"]
# find indices for times
baseline_start_idx = ephys_meta[pt][do_condit]["Configurations"][stim_side][
"Baseline"
][0]
data /= 8.
data = data ** .25
data[np.isnan(data)] = 0
extent = [0., 192., 0., 192.]
im = grid[i].imshow(data, extent=extent, interpolation="nearest")
grid[i].text(10, 170, letters[i], fontsize=20, color="white")
data_zoom = data[135:155, 80:100,]
axins = zoomed_inset_axes(grid[i], 2, loc=3) # zoom = 6
extent = [80., 100., 192. - 155., 192. - 135, ]
im2 = axins.imshow(data_zoom, extent=extent, interpolation="nearest")
im2.set_clim([data.min(), data.max()])
plt.xticks(visible=False)
plt.yticks(visible=False)
im.set_clim([0., .3])
im2.set_clim([0., .15])
mark_inset(grid[i], axins, loc1=2, loc2=4, fc="none", ec="0.5")
fontsize=20
posx = 10
posy = 170
grid[-1].text(posx, posy, "(a): PL", fontsize=fontsize, color="black")
posy -= 25
grid[-1].text(posx, posy, "(b): PLI", fontsize=fontsize, color="black")
posy -= 25
grid[-1].text(posx, posy, "(c): ACI", fontsize=fontsize, color="black")
posy -= 25
grid[-1].text(posx, posy, "(d): HCI", fontsize=fontsize, color="black")
posy -= 25
grid[-1].text(posx, posy, "(e): NOC", fontsize=fontsize, color="black")
grid[0].set_xticks(())
axis.text(i + subextent[0] + 0.5, j + subextent[2] + 0.5, c,
weight='demibold',
horizontalalignment='center',
verticalalignment='center',
color=_determine_ideal_value(c, ma=array.max()))
if __name__ == '__main__':
tux = skimage.io.imread('./tux_icon-33px.png')
fig, ax = plt.subplots(figsize=(5, 5))
extent0 = [0, 33, 0, 36]
ax.imshow(tux, extent=extent0, interpolation='nearest')
axins = zoomed_inset_axes(ax, 3.4, loc=3)
extent1 = [18, 23, 18, 23]
overlay_numbers(axins, tux, extent0, extent1, interpolation='none')
axins.set_xlim(*extent1[:2])
axins.set_ylim(*extent1[2:])
plt.xticks(visible=False)
plt.yticks(visible=False)
plt.gca().xaxis.set_major_locator(plt.NullLocator())
plt.gca().yaxis.set_major_locator(plt.NullLocator())
mark_inset(ax, axins, loc1=2, loc2=4, fc="none", ec="0.5")
ax.axis('off')
fig.tight_layout()
fig.savefig('./tux_inset.png', dpi=150)
# plt.show()
def show_coord_topo_zoom(windpark, show = True):
"""Plot the topology of a given windpark
Topographic Map with farms
see: http://matplotlib.org/basemap/users/examples.html
Basemap
Parameters
----------
windpark : Windpark
A given windpark to show the topology.
"""
plt.clf()
turbines = windpark.get_turbines()
target = windpark.get_target()
radius = windpark.get_radius()
#pack latitude and longitude in lists
rel_input_lat = []
rel_input_lon = []
for row in turbines:
rel_input_lat.append(np.float64(row.latitude))
rel_input_lon.append(np.float64(row.longitude))
targetcoord = [0.0, 0.0]
targetcoord[0] = np.float64(target.latitude)
targetcoord[1] = np.float64(target.longitude)
graddiff = (800/111.0) + 0.5 # degree in km... 800km
fig = plt.figure(figsize=(11.7,8.3))
plt.title("Location of the farm")
#Custom adjust of the subplots
plt.subplots_adjust(left=0.05,right=0.95,top=0.90,bottom=0.05,wspace=0.15,hspace=0.05)
ax = plt.subplot(111)
m = Basemap(projection='lcc', lon_0=targetcoord[1], lat_0=targetcoord[0],\
llcrnrlon = targetcoord[1]-graddiff*2, llcrnrlat = targetcoord[0]-graddiff ,\
urcrnrlon = targetcoord[1]+graddiff, urcrnrlat = targetcoord[0]+graddiff ,\
rsphere=6371200., resolution = None, area_thresh=1000)
# Target
x_target,y_target = m(targetcoord[1],targetcoord[0])
# Input Farms
rel_inputs_lon, rel_inputs_lat = m(rel_input_lon, rel_input_lat)
# labels = [left,right,top,bottom]
parallels = np.arange(int(targetcoord[0]-7), int(targetcoord[0]+7), 2.)
m.drawparallels(parallels,labels=[False,True,True,False])
meridians = np.arange(int(targetcoord[1]-7), int(targetcoord[1]+7), 2.)
m.drawmeridians(meridians,labels=[True,False,False,True])
# plot farms in the radius
m.plot(x_target, y_target, 'bo')
# m.plot(rel_inputs_lon, rel_inputs_lat, 'r*')
#m.bluemarble()
m.shadedrelief()
# we define the inset_axes, with a zoom of 2 and at location 2 (upper left corner)
# axins = zoomed_inset_axes(ax, 40, loc=2)
axins = inset_axes(ax,
width="65%", # width = 30% of parent_bbox
height="65%", # height : 1 inch
loc=3)
# plot farms in the radius
m.plot(x_target, y_target, 'bo')
m.plot(rel_inputs_lon, rel_inputs_lat, 'r*')
#m.bluemarble()
m.shadedrelief()
#m.etopo()
#m.drawcoastlines()
graddiff_park = (radius/(111.0*0.7)) # degree in km
x,y = m(targetcoord[1]-graddiff_park,targetcoord[0]-graddiff_park)
x2,y2 = m(targetcoord[1]+graddiff_park,targetcoord[0]+graddiff_park)
axins.set_xlim(x,x2) # and we apply the limits of the zoom plot to the inset axes
axins.set_ylim(y,y2) # idem
plt.xticks(visible=False) # we hide the ticks
plt.yticks(visible=False)
mark_inset(ax, axins, loc1=1, loc2=4, fc="none", ec="0.9", linewidth = 3) # we draw the "zoom effect" on the main map (ax), joining cornder 1 & 3
plt.title("Selected Wind Farms")
if(show):
plt.show()
def displacement(ofile, timestep, Natoms, matrix0, Type, Time, frontname,
pathtodatabase, systemsize):
'''
timestep,system_size,matrix0 contain the initial information about the system.
we have to go through sortedfiles to find information about the particles at
later timesteps.
'''
factor = 10**(-8) # conversionfactor from [A^2/ps] -> [m^2/s]
Lx = systemsize[1] - systemsize[0]
Ly = systemsize[3] - systemsize[2]
Lz = systemsize[5] - systemsize[4]
halfsystemsize = 0.5 * (Lx + Ly + Lz) / 3.0 # half of average system size
time = []
for t in Time:
time.append(timestep * t / 1000.0) # to picoseconds
#time.append(t)
MSDX = []
MSDY = []
MSDZ = []
MSD = []
D_local = []
dt = (time[1] - time[0])
for T in Time:
path = frontname + '.%r.txt' % (T)
print path
msdx = 0
msdy = 0
msdz = 0
msd = 0
filename = os.path.abspath(os.path.join(pathtodatabase, path))
t, Natoms, system_size, matrix, readstructure, entries, types = readfile(
filename)
counter = 0
for i in range(Natoms):
if (matrix['type'][i] == Type):
ID = matrix['id'][i]
initial_index = None
for j in range(Natoms):
k = matrix0['id'][j]
if (k == ID):
initial_index = j
break
dx = matrix['x'][i] - matrix0['x'][initial_index]
dy = matrix['y'][i] - matrix0['y'][initial_index]
dz = matrix['z'][i] - matrix0['z'][initial_index]
msdx += (dx)**2
msdy += (dy)**2
msdz += (dz)**2
########################################
# MINIMUM IMAGE CONVENTION #
if (dx < -halfsystemsize): dx = dx + Lx
if (dx > halfsystemsize): dx = dx - Lx
if (dy < -halfsystemsize): dy = dy + Ly
if (dy > halfsystemsize): dy = dy - Ly
if (dz < -halfsystemsize): dz = dz + Lz
if (dz > halfsystemsize): dz = dz - Lz
########################################
msd += dx**2 + dy**2 + dz**2
counter += 1
D_local.append((msd / (counter * 6 * T)))
MSDX.append(msdx / (6 * counter))
MSDY.append(msdy / (6 * counter))
MSDZ.append(msdz / (6 * counter))
MSD.append(msd / (6 * counter))
# ballistic_end = 100ps
degree = 1
start = int(round(len(MSD) / 5.0))
p = np.polyfit(time[start:], MSD[start:],
degree) # last 4/5 of the dataset
f = np.polyval(p, time)
d_mean_lastpart = p[
0] #*10**(-8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
p1 = np.polyfit(time[0:start], MSD[0:start], degree)
f1 = np.polyval(p1, time)
d_mean_firstpart = p1[
0] #*10**(8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
p2 = np.polyfit(time[0:int(round(start / 2.0))],
MSD[0:int(round(start / 2.0))], degree)
f2 = np.polyval(p2, time)
d_mean_initpart = p2[
0] #*10**(8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
p3 = np.polyfit(time[0:100], MSD[0:100], degree)
f3 = np.polyval(p3, time)
d_mean_actual = p3[
0] #*10**(8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
print "#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#"
print " Nvalues in estimate 1 = 100"
print " Nvalues in estimate 2 = %g" % (int(round(start / 2.0)))
print " Nvalues in estimate 3 = %g" % (int(round(start)))
print " Nvalues in estimate 4 = %g" % (len(time[start:]))
###############################################################################
# plotting
#plt.close('all')
plt.figure() # Figure 1
Title = 'Mean square displacement'
legends = ['$msd_{x}$', '$msd_{y}$', '$msd_{z}$', '$msd$'] #['$msd$']#
Ylabel = 'mean square displacement $ [A^2] $'
Xlabel = 'time $ [ps] $'
pltname = 'MSD_bulkwater'
linestyles = ['--r', '--y', '--k', 'o-b'] #['--r'] #
plt.hold(True)
plt.plot(time, MSDX, linestyles[0])
plt.plot(time, MSDY, linestyles[1])
plt.plot(time, MSDZ, linestyles[2])
plt.plot(time, MSD, linestyles[3], markevery=10)
plt.title(Title)
plt.xlabel(Xlabel)
plt.ylabel(Ylabel)
plt.legend(legends, loc='lower right')
plt.hold(False)
write_to_file(ofile, Title, Xlabel, Ylabel, pltname, legends, linestyles,
[time], [MSDX, MSDY, MSDZ, MSD])
from mpl_toolkits.axes_grid.inset_locator import zoomed_inset_axes, inset_axes, mark_inset
plt.figure()
ax = plt.axes() # Figure 2
Title = 'Mean square displacement'
legends = [
'MSD',
'$f_1 %.3f $' % (d_mean_actual),
'$f_2 %.3f $' % (d_mean_initpart),
'$f_3 %.3f $' % (d_mean_firstpart),
'$f_4 %.3f $' % (d_mean_lastpart)
]
pltname = 'MSD_bulkwater_mean'
Xlabel = 'time $ [ps] $'
Ylabel = 'mean square displacement $ [A^2] $'
linestyles = ['b-', '--y', '--r', '--m', '--y']
plt.hold(True)
plt.plot(time, MSD, linestyles[0])
plt.plot(time[0:int(round(len(f) / 8.0))], f3[0:int(round(len(f) / 8.0))],
linestyles[1]) # very first part
plt.plot(time[0:int(round(len(f) / 6.0))], f2[0:int(round(len(f) / 6.0))],
linestyles[2]) # initpart
plt.plot(time[0:int(round(len(f) / 5.0))], f1[0:int(round(len(f) / 5.0))],
linestyles[3]) # firstpart
plt.plot(time, f, linestyles[4]) # lastpart
plt.hold(False)
plt.xlabel(Xlabel)
plt.ylabel(Ylabel)
plt.legend(legends, loc='lower right')
plt.title(Title)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.get_xaxis().tick_bottom()
ax.get_yaxis().tick_left()
axin = inset_axes(ax, width="30%", height="35%", loc=8)
plt.hold(True)
axin.plot(time, MSD, linestyles[0])
axin.plot(time, f3, linestyles[1], linewidth=3.0)
axin.plot(time, f2, linestyles[2])
#axin.plot(time,f1,linestyles[3])
plt.hold(False)
axin.set_xlim(500, 520)
ya = 0.0
yb = 4.0
Npoints = 4
points = np.linspace(ya, yb, Npoints)
axin.set_ylim(ya, yb)
axin.set_xticks([])
axin.set_yticks(points)
mark_inset(ax, axin, loc1=3, loc2=4, fc="none", ec="0.5")
write_to_file(ofile, Title, Xlabel, Ylabel, pltname, legends, linestyles,
[time], [MSD, f])
print "#################################################################"
print "# Diffusion estimate f1 : D = %.10f " % (d_mean_actual)
print "# Diffusion estimate f2 : D = %.10f " % (d_mean_initpart)
print "# Diffusion estimate f3 : D = %.10f " % (d_mean_firstpart)
print "# Diffusion estimate f4 : D = %.10f " % (d_mean_lastpart)
plt.figure() # Figure 3
Title = 'Time evolution of the local diffusion constant. $ D=(msd/6dt) $'
legends = ['$D(t)$']
linestyles = ['-y']
pltname = 'Diffusion_bulkwater'
Ylabel = 'displacement $ [ %g m^2/s]$' % factor
plt.hold(True)
plt.plot(time, D_local, linestyles[0])
plt.hold(False)
plt.legend(legends, loc='upper right')
plt.title(Title)
plt.xlabel(Xlabel)
plt.ylabel(Ylabel)
write_to_file(ofile, Title, Xlabel, Ylabel, pltname, legends, linestyles,
[time], [D_local])
plt.show()
fontsize=12,
color='black',
transform=plt.gcf().transFigure,
bbox=dict(facecolor='white', edgecolor='blue', pad=8.0),
ha='center',
va='center')
# Create a set of inset Axes: these should fill the bounding box allocated to
# them.
ax2 = plt.axes([0, 0, 1, 1])
# Manually set the position and relative size of the inset axes within ax1
ip = InsetPosition(ax1, [0.75, 0.7, 0.3, 0.4])
ax2.set_axes_locator(ip)
# Mark the region corresponding to the inset axes on ax1 and draw lines
# in grey linking the two axes.
mark_inset(ax1, ax2, loc1=2, loc2=4, fc="none", ec='0.5')
# The data into the ax2
ax2.hist(data_14_degrees['M'][condition_mass_14],
bins=1000,
weights=None,
histtype='step',
align='mid',
orientation='vertical',
color='r',
label='M measured')
ax2.hist(data_14_degrees['Qi'][condition_mass_14] *
data_14_degrees['M_Q'][condition_mass_14],
bins=1000,
weights=None,
histtype='step',
# formatting the plot
ax.xaxis.set_minor_locator(pylab.MultipleLocator(5))
ax.yaxis.set_minor_locator(pylab.MultipleLocator(0.1))
ax.grid(b=True,which="minor",axis='x')
ax.grid(b=True,which="minor",axis='y')
ax.set_xticks(range(1850,2030,10))
ax.set_xlim(1843,2021)
ax.set_ylim(-1.03,0.89)
ax.set_xlabel("Year")
legend = ax.legend(loc="upper left",fontsize=14)
frame = legend.get_frame()
frame.set_facecolor('1.0')
ax.set_ylabel("Anomaly")
# adding an inset axis to view the downturn at the end better
inset_axes = zoomed_inset_axes(ax, 3, loc=4)
inset_axes.scatter(df2.Date,df2.Anomaly,s=15,marker='o',facecolor="1.0",lw=0.5,edgecolor="0.0")
inset_axes.plot(df2.Date[s12:-e12],yr1LP2,'-y',label='Annual LP')
inset_axes.plot(df2.Date[s152:-e152],yr15LP2,'-g',label='>15 yr LP')
inset_axes.plot(df2.Date[s752:-e752],yr75LP2,'-b',label='>30 yr LP')
inset_axes.plot(df2.Date,yr15SG2,'--r',label='S-G 15 yr')
x1, x2, y1, y2 = 2000, 2015, 0.3, 0.6
inset_axes.set_xlim(x1, x2)
inset_axes.set_ylim(y1, y2)
inset_axes.set_xticks([])
inset_axes.set_yticks([])
inset_axes.set_axis_bgcolor("1.0")
ax.set_title("HadCrut4 Monthly Anomaly Smoothing by CTRM and Savitsky-Golay")
mark_inset(ax, inset_axes, loc1=1, loc2=2, fc="none", ec="0.0");
pylab.show()
def plots(XX, XF, X_update, up_a, xposition, mode, mode_title):
font_size = 18
font = {'size': font_size}
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
matplotlib.rc('font', **font)
plt.rc('xtick', labelsize=30)
plt.rc('ytick', labelsize=30)
plt.figure(figsize=(13, 10))
ax = plt.subplot(111)
if mode == 'Longitudinal':
lb = ['$u$', '$w$', '$q$', '$\\theta$']
elif mode == 'Lateral_directional':
lb = ['$v$', '$p$', '$r$', '$\phi$']
line1 = []
for i in range(4):
line1.append(0)
line1[i], = ax.plot(XX[i, :], alpha=0.35, label=lb[i])
l4, = ax.plot(la.norm(X_update, axis=0),
color='b',
linewidth=2.5,
label='$\|x_t\|$ LQR for $\hat{A}$')
l1, = ax.plot(la.norm(XX, axis=0),
color='k',
linewidth=2.5,
label='$\|x_t\|$ DGR ON')
l2, = ax.plot(la.norm(XF, axis=0),
color='r',
linewidth=2.5,
label='$\|x_t\|$ DGR OFF')
l3, = ax.plot(up_a, color='g', linewidth=2.5, label='Upper Bound')
box = ax.get_position()
first_legend = plt.legend(handles=[l1, l2, l3, l4],
loc='upper right',
prop={'size': 24})
leg = plt.gca().add_artist(first_legend)
second_legend = plt.legend(handles=line1,
prop={'size': 24},
loc='lower right',
bbox_to_anchor=(0.98, 0.39),
borderaxespad=0)
leg = plt.gca().add_artist(second_legend)
ax.axvline(x=xposition, color='gray', linestyle='--', linewidth=3.0)
plt.xlim(0, 130)
plt.ylim(-10, 75)
plt.xlabel('Iteration $t$', fontsize=30)
plt.title(mode_title, fontsize=30)
plt.grid()
plt.show()
# Inner Plot
# Create a set of inset Axes: these should fill the bounding box allocated to
# them.
ax2 = plt.axes([0, 0, 1, 1])
# Manually set the position and relative size of the inset axes within ax1
ip = InsetPosition(ax, [0.32, 0.43, 0.5, 0.2])
ax2.set_axes_locator(ip)
# Mark the region corresponding to the inset axes on ax1 and draw lines
# in grey linking the two axes.
mark_inset(ax, ax2, loc1=3, loc2=4, fc="none", ec='y', linewidth=2.0)
ax2.set_title('zoom in', size=25)
ax2.set(ylim=([-0.5, 3]), xlim=([xposition, 130]))
ax2.plot(la.norm(X_update, axis=0), color='b', linewidth=2.5)
ax2.plot(la.norm(XX, axis=0), color='k', linewidth=2.5)
ax2.plot(up_a, color='g', linewidth=2.5, label='Upper Bound')
line1 = []
lb = ['$u$', '$w$', '$q$', '$\\theta$', '$v$', '$p$', '$r$', '$\phi$']
for i in range(4):
line1.append(0)
line1[i], = ax2.plot(XX[i, :], alpha=0.35, label=lb[i])
ax2.plot(vtx[2, 0], vtx[2, 1], 'bs', markersize=10)
plt.axis('equal')
plt.axis('off')
# plt.title('Grain %d \n'%grain_id+r' $\Delta$g = %.3f$^\circ$'%(mis_ang_deg[-1]),fontsize=22)
plt.title(r' $\Delta$g = %.3f$^\circ$' % (mis_ang_deg[-1]), fontsize=22)
plt.text(-0.08, -0.08, '(0001)', fontsize=16)
plt.text(0.9, -0.08, r'(10$\bar{1}$0)', fontsize=16)
plt.text(0.65, 0.49, r'(11$\bar{2}$0)', fontsize=16)
ax_in = plt.axes([0, 0, 1, 1])
ip = InsetPosition(ax2, [0.25, -0.5, 0.5, 0.5])
ax_in.set_axes_locator(ip)
for i in range(len(pts)):
ax_in.plot(pts[i, 0], pts[i, 1], 'o', color=cmaplist[colornums[i]])
# plt.axis([0.29,0.32,0.02,0.035])
mark_inset(ax2, ax_in, loc1=1, loc2=2, fc="none", ec='0.5')
plt.axis('equal')
ax_in.set_xticklabels('')
ax_in.set_yticklabels('')
#%%
# fig2.savefig('/Users/rachellim/Documents/Research/CHESS_Jun17/2020-08-03/figs/ipfs/grain%d_ipf.jpg'%grain_id,
# bbox_inches='tight',dpi=300)
data[np.isnan(data)] = 0
extent = [0., 192., 0., 192.]
im = grid[i].imshow(data, extent=extent, interpolation="nearest")
grid[i].text(10, 170, letters[i], fontsize=20, color="white")
data_zoom = data[135:155, 80:100, ]
axins = zoomed_inset_axes(grid[i], 2, loc=3) # zoom = 6
extent = [
80.,
100.,
192. - 155.,
192. - 135,
]
im2 = axins.imshow(data_zoom, extent=extent, interpolation="nearest")
im2.set_clim([data.min(), data.max()])
plt.xticks(visible=False)
plt.yticks(visible=False)
im.set_clim([0., .3])
im2.set_clim([0., .3])
mark_inset(grid[i], axins, loc1=2, loc2=4, fc="none", ec="0.5")
grid[0].set_xticks(())
grid[0].set_yticks(())
plt.subplots_adjust(left=0.,
right=1.,
top=.99,
bottom=.01,
wspace=0.,
hspace=0.)
plt.show()
fig.savefig(out_fname)
def show_coord_topo_zoom(windpark, show=True):
"""Plot the topology of a given windpark
Topographic Map with farms
see: http://matplotlib.org/basemap/users/examples.html
Basemap
Parameters
----------
windpark : Windpark
A given windpark to show the topology.
"""
plt.clf()
turbines = windpark.get_turbines()
target = windpark.get_target()
radius = windpark.get_radius()
#pack latitude and longitude in lists
rel_input_lat = []
rel_input_lon = []
for row in turbines:
rel_input_lat.append(np.float64(row.latitude))
rel_input_lon.append(np.float64(row.longitude))
targetcoord = [0.0, 0.0]
targetcoord[0] = np.float64(target.latitude)
targetcoord[1] = np.float64(target.longitude)
graddiff = (800 / 111.0) + 0.5 # degree in km... 800km
fig = plt.figure(figsize=(11.7, 8.3))
plt.title("Location of the farm")
#Custom adjust of the subplots
plt.subplots_adjust(left=0.05,
right=0.95,
top=0.90,
bottom=0.05,
wspace=0.15,
hspace=0.05)
ax = plt.subplot(111)
m = Basemap(projection='lcc', lon_0=targetcoord[1], lat_0=targetcoord[0],\
llcrnrlon = targetcoord[1]-graddiff*2, llcrnrlat = targetcoord[0]-graddiff ,\
urcrnrlon = targetcoord[1]+graddiff, urcrnrlat = targetcoord[0]+graddiff ,\
rsphere=6371200., resolution = None, area_thresh=1000)
# Target
x_target, y_target = m(targetcoord[1], targetcoord[0])
# Input Farms
rel_inputs_lon, rel_inputs_lat = m(rel_input_lon, rel_input_lat)
# labels = [left,right,top,bottom]
parallels = np.arange(int(targetcoord[0] - 7), int(targetcoord[0] + 7), 2.)
m.drawparallels(parallels, labels=[False, True, True, False])
meridians = np.arange(int(targetcoord[1] - 7), int(targetcoord[1] + 7), 2.)
m.drawmeridians(meridians, labels=[True, False, False, True])
# plot farms in the radius
m.plot(x_target, y_target, 'bo')
# m.plot(rel_inputs_lon, rel_inputs_lat, 'r*')
#m.bluemarble()
m.shadedrelief()
# we define the inset_axes, with a zoom of 2 and at location 2 (upper left corner)
# axins = zoomed_inset_axes(ax, 40, loc=2)
axins = inset_axes(
ax,
width="65%", # width = 30% of parent_bbox
height="65%", # height : 1 inch
loc=3)
# plot farms in the radius
m.plot(x_target, y_target, 'bo')
m.plot(rel_inputs_lon, rel_inputs_lat, 'r*')
#m.bluemarble()
m.shadedrelief()
#m.etopo()
#m.drawcoastlines()
graddiff_park = (radius / (111.0 * 0.7)) # degree in km
x, y = m(targetcoord[1] - graddiff_park, targetcoord[0] - graddiff_park)
x2, y2 = m(targetcoord[1] + graddiff_park, targetcoord[0] + graddiff_park)
axins.set_xlim(
x, x2) # and we apply the limits of the zoom plot to the inset axes
axins.set_ylim(y, y2) # idem
plt.xticks(visible=False) # we hide the ticks
plt.yticks(visible=False)
mark_inset(
ax, axins, loc1=1, loc2=4, fc="none", ec="0.9", linewidth=3
) # we draw the "zoom effect" on the main map (ax), joining cornder 1 & 3
plt.title("Selected Wind Farms")
if (show):
plt.show()
def make_rq(data_dir):
# set plotting style
mpl.rcParams['font.size']=10
mpl.rcParams['legend.fontsize']='small'
mpl.rcParams['figure.autolayout']=True
mpl.rcParams['figure.figsize']=[8.0,6.0]
# ==================================================================
# define DAQ and other parameters
#wsize = 12500 # size of event window in samples. 1 sample = 2 ns.
#read event window width from the folder name
if data_dir.find("3us") != -1:
event_window = 3
if data_dir.find("25us") != -1:
event_window = 25 # in us.
wsize = int(500 * event_window) # samples per waveform # 12500 for 25 us
vscale = (2000.0/16384.0) # = 0.122 mV/ADCC, vertical scale
tscale = (8.0/4096.0) # = 0.002 µs/sample, time scale
save_avg_wfm = False # get the average waveform passing some cut and save to file
post_trigger = 0.5 # Was 0.2 for data before 11/22/19
trigger_time_us = event_window*(1-post_trigger)
trigger_time = int(trigger_time_us/tscale)
n_sipms = 8
n_channels = n_sipms+1 # includes sum
# define top, bottom channels
n_top = int((n_channels-1)/2)
top_channels=np.array(range(n_top),int)
bottom_channels=np.array(range(n_top,2*n_top),int)
# sphe sizes in mV*sample
ns_to_sample = 1024./2000. #convert spe size unit from mV*ns to mV*sample
spe = {}
with open(data_dir+"spe.txt", 'r') as file:
for line in file:
(key, val) = line.split()
spe[key] = float(val)*ns_to_sample
chA_spe_size = spe["ch0"]#29.02
chB_spe_size = spe["ch1"]#30.61
chC_spe_size = spe["ch2"]#28.87
chD_spe_size = spe["ch3"]#28.86*1.25 # scale factor (0.7-1.4) empirical as of Dec 9, 2020
chE_spe_size = spe["ch4"]#30.4
chF_spe_size = spe["ch5"]#30.44
chG_spe_size = spe["ch6"]#30.84
chH_spe_size = spe["ch7"]#30.3*1.8 # scale factor (1.6-2.2) empirical as of Dec 9, 2020
spe_sizes = [chA_spe_size, chB_spe_size, chC_spe_size, chD_spe_size, chE_spe_size, chF_spe_size, chG_spe_size, chH_spe_size]
# ==================================================================
#load in raw data
t_start = time.time()
block_size = 3000
n_block = 500
max_evts = n_block*block_size#5000 # 25000 # -1 means read in all entries; 25000 is roughly the max allowed in memory on the DAQ computer
max_pts = -1 # do not change
if max_evts > 0:
max_pts = wsize * max_evts
load_dtype = "int16"
# pulse RQs to save
# RQs to add:
# Pulse level: channel areas (fracs; max fracs), TBA, rise time? (just difference of AFTs...)
# Event level: drift time; S1, S2 area
# Pulse class (S1, S2, other)
# max number of pulses per event
max_pulses = 4
p_start = np.zeros(( max_evts, max_pulses), dtype=int)
p_end = np.zeros(( max_evts, max_pulses), dtype=int)
p_found = np.zeros(( max_evts, max_pulses), dtype=int)
#center of mass
center_top_x = np.zeros(( max_evts, max_pulses))
center_top_y = np.zeros(( max_evts, max_pulses))
center_bot_x = np.zeros(( max_evts, max_pulses))
center_bot_y = np.zeros(( max_evts, max_pulses))
p_area = np.zeros(( max_evts, max_pulses))
p_max_height = np.zeros(( max_evts, max_pulses))
p_min_height = np.zeros(( max_evts, max_pulses))
p_width = np.zeros(( max_evts, max_pulses))
p_afs_2l = np.zeros((max_evts, max_pulses) )
p_afs_2r = np.zeros((max_evts, max_pulses) )
p_afs_1 = np.zeros((max_evts, max_pulses) )
p_afs_25 = np.zeros((max_evts, max_pulses) )
p_afs_50 = np.zeros((max_evts, max_pulses) )
p_afs_75 = np.zeros((max_evts, max_pulses) )
p_afs_99 = np.zeros((max_evts, max_pulses) )
p_hfs_10l = np.zeros((max_evts, max_pulses) )
p_hfs_50l = np.zeros((max_evts, max_pulses) )
p_hfs_10r = np.zeros((max_evts, max_pulses) )
p_hfs_50r = np.zeros((max_evts, max_pulses) )
p_mean_time = np.zeros((max_evts, max_pulses) )
p_rms_time = np.zeros((max_evts, max_pulses) )
# Channel level (per event, per pulse, per channel)
p_start_ch = np.zeros((max_evts, max_pulses, n_channels-1), dtype=int)
p_end_ch = np.zeros((max_evts, max_pulses, n_channels-1), dtype=int )
p_area_ch = np.zeros((max_evts, max_pulses, n_channels-1) )
p_area_ch_frac = np.zeros((max_evts, max_pulses, n_channels-1) )
p_area_top = np.zeros((max_evts, max_pulses))
p_area_bottom = np.zeros((max_evts, max_pulses))
p_tba = np.zeros((max_evts, max_pulses))
p_class = np.zeros((max_evts, max_pulses), dtype=int)
# Event-level variables
n_pulses = np.zeros(max_evts, dtype=int)
n_s1 = np.zeros(max_evts, dtype=int)
n_s2 = np.zeros(max_evts, dtype=int)
sum_s1_area = np.zeros(max_evts)
sum_s2_area = np.zeros(max_evts)
drift_Time = np.zeros(max_evts)
drift_Time_AS = np.zeros(max_evts) # for multi-scatter drift time, defined by the first S2.
s1_before_s2 = np.zeros(max_evts, dtype=bool)
n_wfms_summed = 0
avg_wfm = np.zeros(wsize)
# Temporary, for testing low area, multiple-S1 events
dt = np.zeros(max_evts)
small_weird_areas = np.zeros(max_evts)
big_weird_areas = np.zeros(max_evts)
n_golden = 0
inn=""
inn="" # used to control hand scan
empty_evt_ind = np.zeros(max_evts)
for j in range(n_block):
ch_data = []
for ch_ind in range(n_sipms):
ch_data.append(np.fromfile(data_dir + "wave"+str(ch_ind)+".dat", dtype=load_dtype, offset = block_size*wsize*j, count=wsize*block_size))
#t_end_load = time.time()
#print("Time to load files: ", t_end_load-t_start)
# scale waveforms to get units of mV/sample
# then for each channel ensure we
# have an integer number of events
array_dtype = "float32" # using float32 reduces memory for big files, otherwise implicitly converts to float64
# matrix of all channels including the sum waveform
v_matrix_all_ch = []
for ch_ind in range(n_sipms):
V = vscale * ch_data[ch_ind].astype(array_dtype) / spe_sizes[ch_ind]
V = V[:int(len(V) / wsize) * wsize]
V = V.reshape(int(V.size / wsize), wsize) # reshape to make each channel's matrix of events
v_matrix_all_ch.append(V)
if ch_ind==0: v_sum = np.copy(V)
else: v_sum += V
v_matrix_all_ch.append(v_sum)
# create a time axis in units of µs:
x = np.arange(0, wsize, 1)
t = tscale*x
t_matrix = np.repeat(t[np.newaxis,:], V.size/wsize, 0)
# Note: if max_evts != -1, we won't load in all events in the dataset
n_events = int(v_matrix_all_ch[0].shape[0])
if n_events == 0: break
# perform baseline subtraction for full event (separate from pulse-level baseline subtraction):
baseline_start = int(0./tscale)
baseline_end = np.min((int(wsize*0.2), 1000))
# baseline subtracted (bls) waveforms saved in this matrix:
v_bls_matrix_all_ch = np.zeros( np.shape(v_matrix_all_ch), dtype=array_dtype) # dims are (chan #, evt #, sample #)
#t_end_wfm_fill = time.time()
#print("Time to fill all waveform arrays: ", t_end_wfm_fill - t_end_load)
#print("Events to process: ",n_events)
for i in range(0, n_events):
sum_baseline = np.mean( v_matrix_all_ch[-1][i,baseline_start:baseline_end] ) #avg ~us, avoiding trigger
baselines = [ np.mean( ch_j[i,baseline_start:baseline_end] ) for ch_j in v_matrix_all_ch ]
sum_data = v_matrix_all_ch[-1][i,:] - sum_baseline
ch_data = [ch_j[i,:]-baseline_j for (ch_j,baseline_j) in zip(v_matrix_all_ch,baselines)]
v_bls_matrix_all_ch[:,i,:] = ch_data
# ==================================================================
# ==================================================================
# now setup for pulse finding on the baseline-subtracted sum waveform
#check mark
#print("Running pulse finder on {:d} events...".format(n_events))
# use for coloring pulses
pulse_class_colors = np.array(['blue', 'green', 'red', 'magenta', 'darkorange'])
pulse_class_labels = np.array(['Other', 'S1-like LXe', 'S1-like gas', 'S2-like', 'Merged S1/S2'])
pc_legend_handles=[]
for class_ind in range(len(pulse_class_labels)):
pc_legend_handles.append(mpl.patches.Patch(color=pulse_class_colors[class_ind], label=str(class_ind)+": "+pulse_class_labels[class_ind]))
for i in range(j*block_size, j*block_size+n_events):
if (i)%2000==0: print("Event #",i)
# Find pulse locations; other quantities for pf tuning/debugging
start_times, end_times, peaks, data_conv, properties = pf.findPulses( v_bls_matrix_all_ch[-1,i-j*block_size,:], max_pulses , SPEMode=False)
# Sort pulses by start times, not areas
startinds = np.argsort(start_times)
n_pulses[i] = len(start_times)
if (n_pulses[i] < 1):
#print("No pulses found for event {0}; skipping".format(i))
empty_evt_ind[i] = i
#continue
for m in startinds:
if m >= max_pulses:
continue
p_start[i,m] = start_times[m]
p_end[i,m] = end_times[m]
# Individual channel pulse locations, in case you want this info
# Can't just ":" the the first index in data, findPulses doesn't like it, so have to loop
#for j in range(n_channels-1):
# start_times_ch, end_times_ch, peaks_ch, data_conv_ch, properties_ch = pf.findPulses( v_bls_matrix_all_ch[j,i,:], max_pulses )
# Sorting by start times from the sum of channels, not each individual channel
# for k in startinds:
# if k >= len(start_times_ch):
# continue
# p_start_ch[i,k,j] = start_times_ch[k]
# p_end_ch[i,k,j] = end_times_ch[k]
# More precisely estimate baselines immediately before each pulse
baselines_precise = pq.GetBaselines(p_start[i,:n_pulses[i]], p_end[i,:n_pulses[i]], v_bls_matrix_all_ch[:,i-j*block_size,:])
# Calculate interesting quantities, only for pulses that were found
for pp in range(n_pulses[i]):
# subtract out more precise estimate of baseline for better RQ estimates
baselines_pulse = baselines_precise[pp] # array of baselines per channel, for this pulse
v_pulse_bls = np.array([ch_j - baseline_j for (ch_j, baseline_j) in zip(v_bls_matrix_all_ch[:,i-j*block_size,:], baselines_pulse)])
# Version w/o pulse-level baseline subtraction
#v_pulse_bls = v_bls_matrix_all_ch[:,i-j*block_size,:]
# copied from above, for reference
#sum_data = v_matrix_all_ch[-1][i, :] - sum_baseline
#ch_data = [ch_j[i, :] - baseline_j for (ch_j, baseline_j) in zip(v_matrix_all_ch, baselines)]
# Area, max & min heights, width, pulse mean & rms
p_area[i,pp] = pq.GetPulseArea(p_start[i,pp], p_end[i,pp], v_pulse_bls[-1] )
p_max_height[i,pp] = pq.GetPulseMaxHeight(p_start[i,pp], p_end[i,pp], v_pulse_bls[-1] )
p_min_height[i,pp] = pq.GetPulseMinHeight(p_start[i,pp], p_end[i,pp], v_pulse_bls[-1] )
p_width[i,pp] = p_end[i,pp] - p_start[i,pp]
#(p_mean_time[i,pp], p_rms_time[i,pp]) = pq.GetPulseMeanAndRMS(p_start[i,pp], p_end[i,pp], v_bls_matrix_all_ch[-1,i,:])
# Area and height fractions
(p_afs_2l[i,pp], p_afs_1[i,pp], p_afs_25[i,pp], p_afs_50[i,pp], p_afs_75[i,pp], p_afs_99[i,pp]) = pq.GetAreaFraction(p_start[i,pp], p_end[i,pp], v_pulse_bls[-1] )
(p_hfs_10l[i,pp], p_hfs_50l[i,pp], p_hfs_10r[i,pp], p_hfs_50r[i,pp]) = pq.GetHeightFractionSamples(p_start[i,pp], p_end[i,pp], v_pulse_bls[-1] )
# Areas for individual channels and top bottom
p_area_ch[i,pp,:] = pq.GetPulseAreaChannel(p_start[i,pp], p_end[i,pp], v_pulse_bls )
p_area_ch_frac[i,pp,:] = p_area_ch[i,pp,:]/p_area[i,pp]
p_area_top[i,pp] = sum(p_area_ch[i,pp,top_channels])
p_area_bottom[i,pp] = sum(p_area_ch[i,pp,bottom_channels])
p_tba[i, pp] = (p_area_top[i, pp] - p_area_bottom[i, pp]) / (p_area_top[i, pp] + p_area_bottom[i, pp])
center_top_x[i,pp] = (p_area_ch[i,pp,1]+p_area_ch[i,pp,3]-p_area_ch[i,pp,0]-p_area_ch[i,pp,2])/p_area_top[i,pp]
center_top_y[i,pp] = (p_area_ch[i,pp,0]+p_area_ch[i,pp,1]-p_area_ch[i,pp,2]-p_area_ch[i,pp,3])/p_area_top[i,pp]
center_bot_x[i,pp] = (p_area_ch[i,pp,5]+p_area_ch[i,pp,7]-p_area_ch[i,pp,4]-p_area_ch[i,pp,6])/p_area_bottom[i,pp]
center_bot_y[i,pp] = (p_area_ch[i,pp,4]+p_area_ch[i,pp,5]-p_area_ch[i,pp,6]-p_area_ch[i,pp,7])/p_area_bottom[i,pp]
# Pulse classifier, work in progress
p_class[i,:] = pc.ClassifyPulses(p_tba[i, :], (p_afs_50[i, :]-p_afs_2l[i, :])*tscale, n_pulses[i], p_area[i,:])
# Event level analysis. Look at events with both S1 and S2.
index_s1 = (p_class[i,:] == 1) + (p_class[i,:] == 2) # S1's
index_s2 = (p_class[i,:] == 3) + (p_class[i,:] == 4) # S2's
n_s1[i] = np.sum(index_s1)
n_s2[i] = np.sum(index_s2)
if n_s1[i] > 0:
sum_s1_area[i] = np.sum(p_area[i, index_s1])
if n_s2[i] > 0:
sum_s2_area[i] = np.sum(p_area[i, index_s2])
if n_s1[i] == 1:
if n_s2[i] == 1:
drift_Time[i] = tscale*(p_start[i, np.argmax(index_s2)] - p_start[i, np.argmax(index_s1)])
drift_Time_AS[i] = tscale*(p_start[i, np.argmax(index_s2)] - p_start[i, np.argmax(index_s1)])
if n_s2[i] > 1:
s1_before_s2[i] = np.argmax(index_s1) < np.argmax(index_s2)
drift_Time_AS[i] = tscale*(p_start[i, np.argmax(index_s2)] - p_start[i, np.argmax(index_s1)]) #For multi-scatter events.
if drift_Time[i]>0:
n_golden += 1
# =============================================================
# draw the waveform and the pulse bounds found
# Code to allow skipping to another event index for plotting
plot_event_ind = i
try:
plot_event_ind = int(inn)
if plot_event_ind < i:
inn = ''
plot_event_ind = i
print("Can't go backwards! Continuing to next event.")
except ValueError:
plot_event_ind = i
# Condition to plot now includes this rise time calc, not necessary
riseTimeCondition = ((p_afs_50[i,:n_pulses[i]]-p_afs_2l[i,:n_pulses[i]] )*tscale < 0.6)*((p_afs_50[i,:n_pulses[i]]-p_afs_2l[i,:n_pulses[i]] )*tscale > 0.2)
po_test = np.any((p_area[i,:]>5.0e4)*((p_afs_50[i,:]-p_afs_2l[i,:] )*tscale<1.0))
# Condition to skip the individual plotting, hand scan condition
#plotyn = drift_Time[i]<2 and drift_Time[i]>0 and np.any((p_tba[i,:]>-0.75)*(p_tba[i,:]<-0.25)*(p_area[i,:]<3000)*(p_area[i,:]>1400))#np.any((p_tba[i,:]>-0.91)*(p_tba[i,:]<-0.82)*(p_area[i,:]<2800)*(p_area[i,:]>1000))# True#np.any(p_class[i,:]==4)#False#np.any(p_area[i,:]>1000) and
#plotyn = drift_Time[i]>2.5 and (center_bot_y[i,0]**2+center_bot_x[i,0]**2) <0.1
plotyn = drift_Time[i]>1 #np.any((p_class[i,:] == 3) + (p_class[i,:] == 4))#np.any((p_tba[i,:]>-0.75)*(p_tba[i,:]<-0.25)*(p_area[i,:]<3000)*(p_area[i,:]>1000))
#plotyn = np.any((p_tba[i,:]>-1)*(p_tba[i,:]<-0.25)*(p_area[i,:]<30000)*(p_area[i,:]>3000))#np.any((np.log10(p_area[i,:])>3.2)*(np.log10(p_area[i,:])<3.4) )#False#
# Pulse area condition
areaRange = np.sum((p_area[i,:] < 50)*(p_area[i,:] > 5))
if areaRange > 0:
dt[i] = abs(p_start[i,1] - p_start[i,0]) # For weird double s1 data
weird_areas =[p_area[i,0], p_area[i,1] ]
small_weird_areas[i] = min(weird_areas)
big_weird_areas[i] = max(weird_areas)
# Condition to include a wfm in the average
add_wfm = np.any((p_area[i,:]>5000)*(p_tba[i,:]<-0.75))*(n_s1[i]==1)*(n_s2[i]==0)
if add_wfm and save_avg_wfm:
plotyn = add_wfm # in avg wfm mode, plot the events which will go into the average
avg_wfm += v_bls_matrix_all_ch[-1,i-j*block_size,:]
n_wfms_summed += 1
# Both S1 and S2 condition
s1s2 = (n_s1[i] == 1)*(n_s2[i] == 1)
if inn == 's': sys.exit()
if not inn == 'q' and plot_event_ind == i and plotyn:
fig = pl.figure(1,figsize=(10, 3.5))
pl.rc('xtick', labelsize=10)
pl.rc('ytick', labelsize=10)
ax = pl.subplot()
ch_labels = ['A','B','C','D','E','F','G','H']
ch_colors = [pl.cm.tab10(ii) for ii in range(n_channels)]
#pl.plot(t,v_bls_matrix_all_ch[-1,i,:],'blue')
#pl.plot( x*tscale, v_bls_matrix_all_ch[-1,i-j*block_size,:],'blue' )
#pl.xlim([0,wsize])
#pl.xlim([0,event_window])
trigger_time_us = 12 # for some reason seems to be consistently closer to 12 than 12.5
pl.xlim([start_times[0]*tscale-3-trigger_time_us,end_times[1]*tscale+1.5-trigger_time_us])
#pl.ylim( [-1, 1.01*np.max(v_bls_matrix_all_ch[-1,i-j*block_size,:])])
pl.ylim( [-1, 1.1*np.max(v_bls_matrix_all_ch[:-1,i-j*block_size,:])])
pl.xlabel('Time ($\mu$s)')
#pl.xlabel('Samples')
pl.ylabel('phd/sample')
#pl.title("Sum, event "+ str(i))
pl.grid(b=True,which='major',color='lightgray',linestyle='--')
#pl.legend(handles=pc_legend_handles)
dead_channels = [2,7]
for i_chan in range(n_channels - 1):
if i_chan in dead_channels: continue
pl.plot(t-trigger_time_us, v_bls_matrix_all_ch[i_chan, i - j * block_size, :], color=ch_colors[i_chan],
label=ch_labels[i_chan])
# pl.plot( x, v_bls_matrix_all_ch[i_chan,i,:],color=ch_colors[i_chan],label=ch_labels[i_chan] )
#pl.xlim([trigger_time_us - 8, trigger_time_us + 8])
# pl.xlim([wsize/2-4000,wsize/2+4000])
#pl.ylim([-5, 3000 / chA_spe_size])
#pl.xlabel('Time (us)')
# pl.xlabel('Samples')
#pl.ylabel('phd/sample')
#pl.legend()
for pulse in range(len(start_times)):
class_name = "S1"
if p_class[i,pulse] == 3 or p_class[i,pulse] == 4: class_name = "S2"
ax.axvspan(start_times[pulse] * tscale-trigger_time_us, end_times[pulse] * tscale-trigger_time_us, alpha=0.1, color=pulse_class_colors[p_class[i, pulse]])
ax.text((end_times[pulse]) * tscale+0.1-trigger_time_us, 0.9 * ax.get_ylim()[1], class_name,
fontsize=10, color=pulse_class_colors[p_class[i, pulse]])
ax.text((end_times[pulse]) * tscale+0.1-trigger_time_us, 0.84 * ax.get_ylim()[1], 'Area = {:.1f} phd'.format(p_area[i, pulse]),
fontsize=10, color=pulse_class_colors[p_class[i, pulse]])
ax.text((end_times[pulse]) * tscale+0.1-trigger_time_us, 0.73 * ax.get_ylim()[1], '$A_{{TB}}$ = {:.1f}'.format(p_tba[i, pulse]),
fontsize=10, color=pulse_class_colors[p_class[i, pulse]])
#ax.axhline( 0.276, 0, wsize, linestyle='--', lw=1, color='orange')
# Draw drift time w/ arrow
arrow_alpha = 0.8
head_length = 0.1
pl.arrow(start_times[0] * tscale-trigger_time_us, 0.5 * ax.get_ylim()[1], drift_Time[i]-head_length, 0, head_width=1.2, head_length=head_length, width=0.05, color='b', alpha=arrow_alpha)
ax.text(start_times[0] * tscale-trigger_time_us + drift_Time[i]/5, 0.57 * ax.get_ylim()[1], r'Drift time={:.1f} $\mu$s'.format(drift_Time[i]),
fontsize=10, color='b')
# Create a set of inset Axes: these should fill the bounding box allocated to
# them.
from mpl_toolkits.axes_grid.inset_locator import (inset_axes, InsetPosition,
mark_inset)
ax2 = pl.axes([0, 0, 1, 1])
# Manually set the position and relative size of the inset axes within ax1
ip = InsetPosition(ax, [0.05, 0.43, 0.25, 0.5])
ax2.set_axes_locator(ip)
#ax2.set_ylabel('phd/sample')
#ax2.set_xlabel('Time (us)')
# Mark the region corresponding to the inset axes on ax1 and draw lines
# in grey linking the two axes.
mark_inset(ax, ax2, loc1=1, loc2=3, fc="none", ec='0.5')
ax2.grid(b=True,which='major',color='lightgray',linestyle='--')
# Plot data in inset
inset_start = start_times[0]
inset_end = end_times[0]
for i_chan in range(n_channels - 1):
if i_chan in dead_channels: continue
ax2.plot(t[inset_start:inset_end]-trigger_time_us, v_bls_matrix_all_ch[i_chan, i - j * block_size, inset_start:inset_end], color=ch_colors[i_chan],
label=ch_labels[i_chan])
#ax2.plot(t[inset_start:inset_end],v_bls_matrix_all_ch[-1,i,inset_start:inset_end],'blue')
#ax2.xlim((start_times[0]*tscale-1,end_times[0]*tscale+1))
#ax2.ylim((start_times[0]*tscale-1,end_times[0]*tscale+1))
#ax2.legend(loc=0)
# Debugging of pulse finder
debug_pf = False
if debug_pf and n_pulses[i]>0:
pl.plot(t_matrix[i-j*block_size, :], data_conv, 'red')
pl.plot(t_matrix[i-j*block_size, :], np.tile(0., np.size(data_conv)), 'gray')
pl.vlines(x=peaks*tscale, ymin=data_conv[peaks] - properties["prominences"],
ymax=data_conv[peaks], color="C1")
pl.hlines(y=properties["width_heights"], xmin=properties["left_ips"]*tscale,
xmax=properties["right_ips"]*tscale, color="C1")
#print("pulse heights: ", data_conv[peaks] )
#print("prominences:", properties["prominences"])
pl.draw()
pl.show(block=0)
inn = input("Press enter to continue, q to stop plotting, evt # to skip to # (forward only)")
fig.clf()
# end of pulse finding and plotting event loop
if save_avg_wfm:
avg_wfm /= n_wfms_summed
np.savetxt(data_dir+'average_waveform.txt',avg_wfm)
print("Average waveform saved")
n_events = i
t_end = time.time()
print("total number of events processed:", n_events)
print("Time used: {}".format(t_end-t_start))
print("empty events: {0}".format(np.sum(empty_evt_ind>0)))
# pl.hist(empty_evt_ind[empty_evt_ind>0], bins=1000)
# pl.xlabel('Empty event index')
# pl.show()
#create a dictionary with all RQs
list_rq = {}
list_rq['center_top_x'] = center_top_x
list_rq['center_top_y'] = center_top_y
list_rq['center_bot_x'] = center_bot_x
list_rq['center_bot_y'] = center_bot_y
list_rq['n_s1'] = n_s1
list_rq['n_s2'] = n_s2
list_rq['s1_before_s2'] = s1_before_s2
list_rq['n_pulses'] = n_pulses
list_rq['n_events'] = n_events
list_rq['p_area'] = p_area
list_rq['p_class'] = p_class
list_rq['drift_Time'] = drift_Time
list_rq['drift_Time_AS'] = drift_Time_AS
list_rq['p_max_height'] = p_max_height
list_rq['p_min_height'] = p_min_height
list_rq['p_width'] = p_width
list_rq['p_afs_2l'] = p_afs_2l
list_rq['p_afs_50'] = p_afs_50
list_rq['p_area_ch'] = p_area_ch
list_rq['p_area_ch_frac'] = p_area_ch_frac
list_rq['p_area_top'] = p_area_top
list_rq['p_area_bottom'] = p_area_bottom
list_rq['p_tba'] = p_tba
list_rq['p_start'] = p_start
list_rq['p_end'] = p_end
list_rq['sum_s1_area'] = sum_s1_area
list_rq['sum_s2_area'] = sum_s2_area
#list_rq[''] = #add more rq
#remove zeros in the end of each RQ array.
for rq in list_rq.keys():
if rq != 'n_events':
list_rq[rq] = list_rq[rq][:n_events]
rq = open(data_dir + "rq.npz",'wb')
np.savez(rq, **list_rq)
rq.close()
figure()
d = NormalDistr(2, 1) * NormalDistr(2, 1)
demo_distr(d)
#show()
figure()
d = NormalDistr(3, 1) * NormalDistr(3, 1)
d.plot()
d.hist()
ax = gca()
axins = zoomed_inset_axes(ax, 6, loc=1)
d.plot(xmin=-1.5, xmax=1.5)
axins.set_xlim(-1.5, 1.5)
xticks(rotation="vertical")
axins.set_ylim(0, 0.01)
mark_inset(ax, axins, loc1=2, loc2=4, fc="none", ec="0.5")
#show()
figure()
d = NormalDistr(4, 1) * NormalDistr(4, 1)
d.plot()
d.hist()
ax = gca()
axins = zoomed_inset_axes(ax, 12000, loc=1)
d.plot(xmin=-.001, xmax=.001)
axins.set_xlim(-.001, .001)
xticks(rotation="vertical")
axins.set_ylim(0.000072, 0.000075)
mark_inset(ax, axins, loc1=2, loc2=4, fc="none", ec="0.5")
#show()
## just passing transform=ax.transAxes as an argument to add_axes() does nothing.
## So you need to do some complicated jugglery
## (from http://matplotlib.1069221.n5.nabble.com/Adding-custom-axes-within-a-subplot-td20316.html)
Bbox = matplotlib.transforms.Bbox.from_bounds(.75, .6, .5, .5)
trans = ax1.transAxes + fig.transFigure.inverted()
l, b, w, h = matplotlib.transforms.TransformedBbox(Bbox,trans).bounds
axinset = fig.add_axes([l, b, w, h])
axinset.plot(timevec,mit_responses[1][0]*1e3,color='r',linewidth=plot_linewidth,label='Lateral')
## thin frame
for loc, spine in axinset.spines.items(): # items() returns [(key,value),...]
spine.set_linewidth(axes_linewidth)
axinset.set_xlim(910,975)
axinset.set_ylim(-71.5,-70)
axinset.set_xticks([])
axinset.set_yticks([])
mark_inset(ax1, axinset, loc1=2, loc2=4, fc="none", ec="0.5", linewidth=axes_linewidth)
## mitral B
ax1 = fig.add_subplot(2,2,2)
ax1.plot((tmin,tmax),(Vrest,Vrest),linestyle='dashed',linewidth=plot_linewidth,color=(0.5,0.5,0.5))
ax1.plot(timevec,mit_responses[1][1]*1e3,color='g',linewidth=plot_linewidth,label='Lateral')
beautify_plot(ax1,x0min=False,y0min=False,xticksposn='none',yticksposn='none')
ax1.set_xlim(tmin,tmax)
ax1.set_ylim(Vmin,Vmax)
ax1.set_yticks([])
axes_labels(ax1,'','')
ax2 = fig.add_subplot(2,2,4)
ax2.plot((tmin,tmax),(Vrest,Vrest),linestyle='dashed',linewidth=plot_linewidth,color=(0.5,0.5,0.5))
ax2.plot(timevec,mit_responses[0][1]*1e3,color='g',linewidth=plot_linewidth,label='Recurrent')
beautify_plot(ax2,x0min=False,y0min=False,xticksposn='bottom',yticksposn='none')
ax2.set_xlim(tmin,tmax)
fig, ax = plt.subplots(figsize=(8,6))
axin1 = ax.inset_axes(
[20, 12, 8, 4], transform=ax.transData)
axin1.plot(col_x_arr,col_y_arr, "r--")
#axin1.plot(col_x_arr,col_y2_arr,'b--')
axin1.set_xlim(0 , 5.0)
axin1.set_ylim(0, 2.0)
axin1.set(facecolor='white')
#axin1.grid(which='major', color='gray',linestyle='-') #Plot Gridlines in Subgrid
axin1.spines['bottom'].set_color('black')
axin1.spines['top'].set_color('black')
axin1.spines['right'].set_color('black')
axin1.spines['left'].set_color('black')
#Marklines to trace inset
mark_inset(ax, axin1, loc1=2, loc2=4, fc="none", ec='0.5')
#Main Plot
line1=ax.plot(col_x_arr,col_y_arr)
#line2=ax.plot(col_x_arr,col_y2_arr)
ax.set_title('Matplotlib')
ax.set(facecolor='white')
ax.grid(which='major', color='lightgray',linestyle='-')
ax.spines['bottom'].set_color('black')
ax.spines['top'].set_color('black')
ax.spines['right'].set_color('black')
ax.spines['left'].set_color('black')
#ax.legend(loc=0) #Legend if available
plt.setp(line1, color='r', linewidth=2.0)
#plt.setp(line2, color='b', linewidth=2.0)
def zoommap(vals, title, label):
fig = plt.figure(figsize=(12, 8))
plt.subplots_adjust(left=0.05,
right=0.95,
top=0.90,
bottom=0.05,
wspace=0.15,
hspace=0.05)
ax = plt.subplot(211)
m = Basemap(projection='mill',
llcrnrlat=-45,
llcrnrlon=-160,
urcrnrlat=82,
urcrnrlon=170,
resolution='c')
x, y = m(lons, lats)
m.drawcoastlines(linewidth=0.5)
plt.subplots_adjust(left=0.05,
right=0.95,
top=0.90,
bottom=0.05,
wspace=0.15,
hspace=0.05)
cmap = matplotlib.colors.ListedColormap(
['#d73027', '#fc8d59', '#fee090', '#e0f3f8', '#91bfdb', '#4575b4'])
bounds = [0, 0.3, 0.5, 0.7, 0.8, 0.9, 1.0]
norm = matplotlib.colors.BoundaryNorm(bounds, cmap.N)
m.scatter(x, y, s=40, c=vals, cmap=cmap, norm=norm)
plt.colorbar(orientation="vertical",
boundaries=bounds,
spacing='proportional',
ticks=bounds)
ax.text(0.03,
0.95,
label,
size=12,
horizontalalignment='center',
verticalalignment='center',
transform=ax.transAxes)
plt.title(title, fontsize=14)
#Zoom Europe
axins_1 = zoomed_inset_axes(ax,
2,
loc=2,
bbox_to_anchor=(0.396, 0.48),
bbox_transform=ax.figure.transFigure)
axins_1.scatter(x, y, s=20, c=vals, cmap=cmap, norm=norm)
m.drawcoastlines(linewidth=0.5)
x2, y2 = m(-12, 35)
x3, y3 = m(40, 65)
axins_1.set_xlim(x2, x3)
axins_1.set_ylim(y2, y3)
axes = mark_inset(ax, axins_1, loc1=1, loc2=2, linewidth=1)
#Zoom Australia
axins_2 = zoomed_inset_axes(ax,
2.2,
loc=3,
bbox_to_anchor=(0.59, 0.255),
bbox_transform=ax.figure.transFigure)
axins_2.scatter(x, y, s=20, c=vals, cmap=cmap, norm=norm)
m.drawcoastlines(linewidth=0.5)
x2, y2 = m(110, -43)
x3, y3 = m(155, -10)
axins_2.set_xlim(x2, x3)
axins_2.set_ylim(y2, y3)
axes = mark_inset(ax, axins_2, loc1=1, loc2=2, linewidth=1)
#Zoom US
axins_3 = zoomed_inset_axes(ax,
1.6,
loc=3,
bbox_to_anchor=(0.19, 0.25),
bbox_transform=ax.figure.transFigure)
axins_3.scatter(x, y, s=20, c=vals, cmap=cmap, norm=norm)
m.drawcoastlines(linewidth=0.5)
x2, y2 = m(-130, 22)
x3, y3 = m(-60, 63)
axins_3.set_xlim(x2, x3)
axins_3.set_ylim(y2, y3)
axes = mark_inset(ax, axins_3, loc1=1, loc2=2, linewidth=1)
return (fig, axes)
ax1 = plt.gca()
x_max = 4.0
x_min = 2.0
ann_mask = numpy.logical_and(r_ann >= x_min, r_ann <= x_max)
gfmc_mask = numpy.logical_and(r_gfmc >= x_min, r_gfmc <= x_max)
# bottom, left, width, height
ax2 = plt.axes([0, 2., 2., 0.2])
# Manually set the position and relative size of the inset axes within ax1
ip = InsetPosition(ax1, [0.35, 0.25, 0.5, 0.5])
ax2.set_axes_locator(ip)
# Mark the region corresponding to the inset axes on ax1 and draw lines
# in grey linking the two axes.
mark_inset(ax1, ax2, loc1=3, loc2=1, fc="black", alpha=0.5, ec='black')
ax2.fill_between(r_gfmc[gfmc_mask],
rho_gfmc[gfmc_mask] - drho_gfmc[gfmc_mask],
rho_gfmc[gfmc_mask] + drho_gfmc[gfmc_mask],
alpha=0.75)
ax2.plot(r_gfmc[gfmc_mask], rho_gfmc[gfmc_mask], lw=3)
ax2.errorbar(
r_ann[ann_mask],
rho_ann[ann_mask],
yerr=drho_ann[ann_mask],
# label="Error x10",
ls="none",
marker='o',
ms=7,
# color='orange'
## just passing transform=ax.transAxes as an argument to add_axes() does nothing.
## So you need to do some complicated jugglery
## (from http://matplotlib.1069221.n5.nabble.com/Adding-custom-axes-within-a-subplot-td20316.html)
Bbox = matplotlib.transforms.Bbox.from_bounds(0.75, 0.6, 0.5, 0.5)
trans = ax1.transAxes + fig.transFigure.inverted()
l, b, w, h = matplotlib.transforms.TransformedBbox(Bbox, trans).bounds
axinset = fig.add_axes([l, b, w, h])
axinset.plot(timevec, mit_responses[1][0] * 1e3, color="r", linewidth=plot_linewidth, label="Lateral")
## thin frame
for loc, spine in axinset.spines.items(): # items() returns [(key,value),...]
spine.set_linewidth(axes_linewidth)
axinset.set_xlim(910, 975)
axinset.set_ylim(-71.5, -70)
axinset.set_xticks([])
axinset.set_yticks([])
mark_inset(ax1, axinset, loc1=2, loc2=4, fc="none", ec="0.5", linewidth=axes_linewidth)
## mitral B
ax1 = fig.add_subplot(2, 2, 2)
ax1.plot((tmin, tmax), (Vrest, Vrest), linestyle="dashed", linewidth=plot_linewidth, color=(0.5, 0.5, 0.5))
ax1.plot(timevec, mit_responses[1][1] * 1e3, color="g", linewidth=plot_linewidth, label="Lateral")
beautify_plot(ax1, x0min=False, y0min=False, xticksposn="none", yticksposn="none")
ax1.set_xlim(tmin, tmax)
ax1.set_ylim(Vmin, Vmax)
ax1.set_yticks([])
axes_labels(ax1, "", "")
ax2 = fig.add_subplot(2, 2, 4)
ax2.plot((tmin, tmax), (Vrest, Vrest), linestyle="dashed", linewidth=plot_linewidth, color=(0.5, 0.5, 0.5))
ax2.plot(timevec, mit_responses[0][1] * 1e3, color="g", linewidth=plot_linewidth, label="Recurrent")
beautify_plot(ax2, x0min=False, y0min=False, xticksposn="bottom", yticksposn="none")
ax2.set_xlim(tmin, tmax)
def displacement(ofile,timestep,Natoms,matrix0,Type,Time,frontname,pathtodatabase,systemsize):
'''
timestep,system_size,matrix0 contain the initial information about the system.
we have to go through sortedfiles to find information about the particles at
later timesteps.
'''
factor = 10**(-8) # conversionfactor from [A^2/ps] -> [m^2/s]
Lx = systemsize[1] -systemsize[0]
Ly = systemsize[3] -systemsize[2]
Lz = systemsize[5] -systemsize[4]
halfsystemsize = 0.5*(Lx+Ly+Lz)/3.0 # half of average system size
time = []
for t in Time:
time.append(timestep*t/1000.0) # to picoseconds
#time.append(t)
MSDX = [];MSDY = [];MSDZ = [];MSD = [];D_local = []
dt = (time[1]-time[0])
for T in Time:
path = frontname + '.%r.txt' % (T)
print path
msdx = 0; msdy = 0; msdz = 0; msd = 0
filename = os.path.abspath(os.path.join(pathtodatabase,path))
t, Natoms, system_size, matrix, readstructure, entries, types = readfile(filename)
counter = 0
for i in range(Natoms):
if (matrix['type'][i] == Type):
ID = matrix['id'][i]
initial_index = None
for j in range(Natoms):
k = matrix0['id'][j]
if (k == ID):
initial_index = j
break
dx = matrix['x'][i] - matrix0['x'][initial_index]
dy = matrix['y'][i] - matrix0['y'][initial_index]
dz = matrix['z'][i] - matrix0['z'][initial_index]
msdx += (dx)**2
msdy += (dy)**2
msdz += (dz)**2
########################################
# MINIMUM IMAGE CONVENTION #
if (dx < -halfsystemsize): dx = dx + Lx
if (dx > halfsystemsize): dx = dx - Lx
if (dy < -halfsystemsize): dy = dy + Ly
if (dy > halfsystemsize): dy = dy - Ly
if (dz < -halfsystemsize): dz = dz + Lz
if (dz > halfsystemsize): dz = dz - Lz
########################################
msd += dx**2 + dy**2 + dz**2
counter += 1
D_local.append((msd/(counter*6*T)))
MSDX.append(msdx/(6*counter));MSDY.append(msdy/(6*counter));MSDZ.append(msdz/(6*counter));MSD.append(msd/(6*counter))
# ballistic_end = 100ps
degree = 1
start = int(round(len(MSD)/5.0))
p = np.polyfit(time[start:],MSD[start:],degree) # last 4/5 of the dataset
f = np.polyval(p,time)
d_mean_lastpart = p[0]#*10**(-8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
p1 = np.polyfit(time[0:start],MSD[0:start],degree)
f1 = np.polyval(p1,time)
d_mean_firstpart = p1[0]#*10**(8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
p2 = np.polyfit(time[0:int(round(start/2.0))],MSD[0:int(round(start/2.0))],degree)
f2 = np.polyval(p2,time)
d_mean_initpart = p2[0]#*10**(8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
p3 = np.polyfit(time[0:100],MSD[0:100],degree)
f3 = np.polyval(p3,time)
d_mean_actual = p3[0]#*10**(8) # to get [m^2/s]. [A^2/ps] = 10**(-8)[m^2/s]
print "#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#"
print " Nvalues in estimate 1 = 100"
print " Nvalues in estimate 2 = %g" % (int(round(start/2.0)))
print " Nvalues in estimate 3 = %g" % (int(round(start)))
print " Nvalues in estimate 4 = %g" % (len(time[start:]))
###############################################################################
# plotting
#plt.close('all')
plt.figure() # Figure 1
Title = 'Mean square displacement'
legends = ['$msd_{x}$','$msd_{y}$','$msd_{z}$','$msd$']#['$msd$']#
Ylabel = 'mean square displacement $ [A^2] $'
Xlabel = 'time $ [ps] $'
pltname = 'MSD_bulkwater'
linestyles = ['--r','--y','--k','o-b']#['--r'] #
plt.hold(True)
plt.plot(time,MSDX,linestyles[0])
plt.plot(time,MSDY,linestyles[1])
plt.plot(time,MSDZ,linestyles[2])
plt.plot(time,MSD,linestyles[3],markevery=10)
plt.title(Title)
plt.xlabel(Xlabel)
plt.ylabel(Ylabel)
plt.legend(legends,loc='lower right')
plt.hold(False)
write_to_file(ofile,Title,Xlabel,Ylabel,pltname,legends,linestyles,[time],[MSDX,MSDY,MSDZ,MSD])
from mpl_toolkits.axes_grid.inset_locator import zoomed_inset_axes, inset_axes, mark_inset
plt.figure()
ax = plt.axes() # Figure 2
Title = 'Mean square displacement'
legends = ['MSD','$f_1 %.3f $' % (d_mean_actual),'$f_2 %.3f $' % (d_mean_initpart),'$f_3 %.3f $' % (d_mean_firstpart),'$f_4 %.3f $' % (d_mean_lastpart)]
pltname = 'MSD_bulkwater_mean'
Xlabel = 'time $ [ps] $'
Ylabel = 'mean square displacement $ [A^2] $'
linestyles = ['b-','--y','--r','--m','--y']
plt.hold(True)
plt.plot(time,MSD,linestyles[0])
plt.plot(time[0:int(round(len(f)/8.0))],f3[0:int(round(len(f)/8.0))],linestyles[1]) # very first part
plt.plot(time[0:int(round(len(f)/6.0))],f2[0:int(round(len(f)/6.0))],linestyles[2]) # initpart
plt.plot(time[0:int(round(len(f)/5.0))],f1[0:int(round(len(f)/5.0))],linestyles[3]) # firstpart
plt.plot(time,f,linestyles[4]) # lastpart
plt.hold(False)
plt.xlabel(Xlabel)
plt.ylabel(Ylabel)
plt.legend(legends,loc='lower right')
plt.title(Title)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.get_xaxis().tick_bottom()
ax.get_yaxis().tick_left()
axin = inset_axes(ax, width="30%", height="35%", loc=8)
plt.hold(True)
axin.plot(time,MSD,linestyles[0])
axin.plot(time,f3,linestyles[1],linewidth=3.0)
axin.plot(time,f2,linestyles[2])
#axin.plot(time,f1,linestyles[3])
plt.hold(False)
axin.set_xlim(500, 520)
ya = 0.0
yb = 4.0
Npoints = 4
points = np.linspace(ya,yb,Npoints)
axin.set_ylim(ya, yb)
axin.set_xticks([])
axin.set_yticks(points)
mark_inset(ax, axin, loc1=3, loc2=4, fc="none", ec="0.5")
write_to_file(ofile,Title,Xlabel,Ylabel,pltname,legends,linestyles,[time],[MSD,f])
print "#################################################################"
print "# Diffusion estimate f1 : D = %.10f " % (d_mean_actual)
print "# Diffusion estimate f2 : D = %.10f " % (d_mean_initpart)
print "# Diffusion estimate f3 : D = %.10f " % (d_mean_firstpart)
print "# Diffusion estimate f4 : D = %.10f " % (d_mean_lastpart)
plt.figure() # Figure 3
Title = 'Time evolution of the local diffusion constant. $ D=(msd/6dt) $'
legends = ['$D(t)$']; linestyles = ['-y']
pltname = 'Diffusion_bulkwater'
Ylabel = 'displacement $ [ %g m^2/s]$' % factor
plt.hold(True)
plt.plot(time,D_local,linestyles[0])
plt.hold(False)
plt.legend(legends,loc='upper right')
plt.title(Title)
plt.xlabel(Xlabel)
plt.ylabel(Ylabel)
write_to_file(ofile,Title,Xlabel,Ylabel,pltname,legends,linestyles,[time],[D_local])
plt.show()
ax.plot(t2, np2, c='k', lineStyle='--', label='$\epsilon_p=0.06$')
ax.plot(t3, np3, c='k', lineStyle='-.', label='$\epsilon_p=0.12$')
ax.plot(t4, np4, c='k', lineStyle=':', label='$\epsilon_p=0.18$')
ax.plot(t5, np5, c='k', lineStyle=(0, (5, 5)), label='$\epsilon_p=0.24$')
ip = InsetPosition(ax, [0.2, 0.2, 0.5, 0.45])
ax2 = plt.axes([0, 0, 1, 1])
ax2.set_axes_locator(ip)
ax2.plot(t1[t1 >= 0.6], np1[t1 >= 0.6], c='k', lineStyle='-')
ax2.plot(t2[t2 >= 0.6], np2[t2 >= 0.6], c='k', lineStyle='--')
ax2.plot(t3[t3 >= 0.6], np3[t3 >= 0.6], c='k', lineStyle='-.')
ax2.plot(t4[t4 >= 0.6], np4[t4 >= 0.6], c='k', lineStyle=':')
ax2.plot(t5[t5 >= 0.6], np5[t5 >= 0.6], c='k', lineStyle=(0, (5, 5)))
# inset plot #
mark_inset(ax, ax2, loc1=1, loc2=3, fc="none", ec='r', lw='0.5')
#ax2.plot
#---------------------------axis control------------------------#
ax.set_xlabel("$t\ (s)$")
ax.set_ylabel("Particle number")
#ax[0,0].set_xlim(0,0.6)
ax2.set_xlim(0.6, 1.0)
ax2.axes.get_xaxis().set_visible(False)
ax2.axes.get_yaxis().set_visible(False)
#ax.set_ylim(0.,0.8)
#majorLocator = MultipleLocator(1)
#majorFormatter = FormatStrFormatter('%d')
