def plot_field(self,x,y,u=None,v=None,F=None,contour=False,outdir=None,plot='quiver',figname='_field',format='eps'):
outdir = self.set_dir(outdir)
p = 64
if F is None: F=self.calc_F(u,v)
plt.close('all')
plt.figure()
#fig, axes = plt.subplots(nrows=1)
if contour:
plt.hold(True)
plt.contourf(x,y,F)
if plot=='quiver':
plt.quiver(x[::p],y[::p],u[::p],v[::p],scale=0.1)
if plot=='pcolor':
plt.pcolormesh(x[::4],y[::4],F[::4],cmap=plt.cm.Pastel1)
plt.colorbar()
if plot=='stream':
speed = F[::16]
plt.streamplot(x[::16], y[::16], u[::16], v[::16], density=(1,1),color='k')
plt.xlabel('$x$ (a.u.)')
plt.ylabel('$y$ (a.u.)')
plt.savefig(os.path.join(outdir,figname+'.'+format),format=format,dpi=320,bbox_inches='tight')
plt.close()
def plot_mesh(mesh, result_path):
plt.figure()
plt.hold(True)
# change the font
matplotlib.rcParams.update({'font.size': 10, 'font.family': 'serif'})
n_vert = mesh.num_vertices()
n_cells = mesh.num_cells()
d = mesh.geometry().dim()
plotting.plot(mesh)
# Create the triangulation
# mesh_coordinates = mesh.coordinates().reshape((n_vert, d))
# triangles = np.asarray([cell.entities(0) for cell in cells(mesh)])
# triangulation = tri.Triangulation(mesh_coordinates[:, 0],
# mesh_coordinates[:, 1],
# triangles)
# Plot the mesh
# plt.triplot(triangulation)
plt.xlabel("x")
plt.ylabel("y")
# Saving the mesh into the file
fig = plt.gcf()
fig.savefig(result_path + '-cells-%d-vertices-%d' % (n_cells, n_vert) +
".eps")
plt.close('all')
def plot_waveforms(time,voltage,APTimes,titlestr):
"""
plot_waveforms takes four arguments - the recording time array, the voltage
array, the time of the detected action potentials, and the title of your
plot. The function creates a labeled plot showing the waveforms for each
detected action potential
"""
plt.figure()
## Your Code Here
indices = []
for x in range(len(APTimes)):
for i in range(len(time)):
if(time[i]==APTimes[x]):
indices.append(i)
##print indices
Xval = np.linspace(-.003,.003,200)
print len(Xval)
for x in range(len(APTimes)):
plt.plot(Xval, voltage[indices[x]-100:indices[x]+100])
plt.title(titlestr)
plt.xlabel('Time (s)')
plt.ylabel('Voltage (uV)')
plt.hold(True)
plt.show()
def plot_svc(X, y, mysvc, bounds=None, grid=50):
if bounds is None:
xmin = np.min(X[:, 0], 0)
xmax = np.max(X[:, 0], 0)
ymin = np.min(X[:, 1], 0)
ymax = np.max(X[:, 1], 0)
else:
xmin, ymin = bounds[0], bounds[0]
xmax, ymax = bounds[1], bounds[1]
aspect_ratio = (xmax - xmin) / (ymax - ymin)
xgrid, ygrid = np.meshgrid(np.linspace(xmin, xmax, grid),
np.linspace(ymin, ymax, grid))
plt.gca(aspect=aspect_ratio)
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
plt.xticks([])
plt.yticks([])
plt.hold(True)
plt.plot(X[y == 1, 0], X[y == 1, 1], 'bo')
plt.plot(X[y == -1, 0], X[y == -1, 1], 'ro')
box_xy = np.append(xgrid.reshape(xgrid.size, 1), ygrid.reshape(ygrid.size, 1), 1)
if mysvc is not None:
scores = mysvc.decision_function(box_xy)
else:
print 'You must have a valid SVC object.'
return None;
CS=plt.contourf(xgrid, ygrid, scores.reshape(xgrid.shape), alpha=0.5, cmap='jet_r')
plt.contour(xgrid, ygrid, scores.reshape(xgrid.shape), levels=[0], colors='k', linestyles='solid', linewidths=1.5)
plt.contour(xgrid, ygrid, scores.reshape(xgrid.shape), levels=[-1,1], colors='k', linestyles='dashed', linewidths=1)
plt.plot(mysvc.support_vectors_[:,0], mysvc.support_vectors_[:,1], 'ko', markerfacecolor='none', markersize=10)
CB = plt.colorbar(CS)
def plot_completion_graph_complete_vs_failed(result_list,
colors=['b', 'm'],
figure=1,
labels=['complete', 'failed']):
n = len(result_list) # number of trials
times = []
percents = []
for rl in ['complete', 'failed']:
t = [i.time for i in result_list if i.tag == rl]
t.sort()
times.append(np.array(t))
p = np.array(range(1, len(t) + 1))
p = 100 * p / n
percents.append(p)
# the last data points of each type should sum to 1.0 if all trajectories either fail or complete (rather than time out)
plt.figure(figure)
plt.hold(False)
for t, p, c, label in zip(times, percents, colors, labels):
plt.plot(t, p, color=c, linewidth=2.0, label=label)
plt.hold(True)
plt.xlabel("Simulation Time (s)", fontsize='larger')
plt.ylabel("% of Trajectories Complete", fontsize='larger')
plt.yticks([0, 20, 40, 60, 80, 100],
("0%", "20%", "40%", "60%", "80%", "100%"),
fontsize='larger',
va='bottom')
plt.xticks(fontsize='larger')
plt.title(
"Percentage of Total Trajectories Complete by a Given Time, Design A")
plt.legend(loc=0)
plt.show()
def plotConn():
# Create plot
figh = figure(figsize=(8,6))
figh.subplots_adjust(left=0.02) # Less space on left
figh.subplots_adjust(right=0.98) # Less space on right
figh.subplots_adjust(top=0.96) # Less space on bottom
figh.subplots_adjust(bottom=0.02) # Less space on bottom
figh.subplots_adjust(wspace=0) # More space between
figh.subplots_adjust(hspace=0) # More space between
h = axes()
totalconns = zeros(shape(f.connprobs))
for c1 in range(size(f.connprobs,0)):
for c2 in range(size(f.connprobs,1)):
for w in range(f.nreceptors):
totalconns[c1,c2] += f.connprobs[c1,c2]*f.connweights[c1,c2,w]*(-1 if w>=2 else 1)
imshow(totalconns,interpolation='nearest',cmap=bicolormap(gap=0))
# Plot grid lines
hold(True)
for pop in range(f.npops):
plot(array([0,f.npops])-0.5,array([pop,pop])-0.5,'-',c=(0.7,0.7,0.7))
plot(array([pop,pop])-0.5,array([0,f.npops])-0.5,'-',c=(0.7,0.7,0.7))
# Make pretty
h.set_xticks(range(f.npops))
h.set_yticks(range(f.npops))
h.set_xticklabels(f.popnames)
h.set_yticklabels(f.popnames)
h.xaxis.set_ticks_position('top')
xlim(-0.5,f.npops-0.5)
ylim(f.npops-0.5,-0.5)
clim(-abs(totalconns).max(),abs(totalconns).max())
colorbar()
def startAnim(x, m, th, Tsim, inter=1, Tstart=0, h=0.002):
# fig, axM = subplo1ts()
# axX = axM.twinx()
fig = figure()
axM = subplot(211)
axX = subplot(212, sharex=axM)
anim = MyAnim(x, m, th, Tsim, inter, Tstart/h, h)
anim.line1, = axM.plot([], [], 'b')
anim.line2, = axX.plot([], [], 'g')
setp(axM.get_xticklabels(), visible=False)
axM.set_xlim([-pi, pi])
axX.set_xlim([-pi, pi])
# axM.set_ylim([0., 3])
# axX.set_ylim([0., 1.])
axM.set_ylim([amin(m), amax(m)])
axX.set_ylim([amin(x), amax(x)])
axM.set_ylabel(r"$m$")
axX.set_ylabel(r"$x$")
axX.set_xlabel(r"$\theta$")
hold(False)
for tl in axM.get_yticklabels():
tl.set_color('b')
for tl in axX.get_yticklabels():
tl.set_color('g')
anim.axM = axM
anim.axX = axX
fig.canvas.mpl_connect('button_press_event', anim.onClick)
a = FuncAnimation(fig, anim, frames=anim.dataGen, init_func=anim.init,
interval=0, blit=True, repeat=True)
show()
return a
def mark_cross(center, **kwargs):
"""Mark a cross. Correct for matplotlib imshow funny coordinate system.
"""
N = 20
plt.hold(1)
plt.axhline(y=center[1]-0.5, **kwargs)
plt.axvline(x=center[0]-0.5, **kwargs)
def plot_waveforms(time,voltage,APTimes,titlestr):
"""
plot_waveforms takes four arguments - the recording time array, the voltage
array, the time of the detected action potentials, and the title of your
plot. The function creates a labeled plot showing the waveforms for each
detected action potential
"""
plt.figure()
## Your Code Here
for n in range(0,APTimes.size):
ind = time[(time>(APTimes[n] - 0.003)) & (time<(APTimes[n] + 0.003))]
sp = np.zeros(ind.size)
for i in range(0,ind.size):
sp[i] = plt.find(time == ind[i])
sp=sp.astype(np.int64)
x = np.linspace(-3.0e-3, 3.0e-3, sp.size)
plt.plot(x,voltage[sp])
plt.hold(True)
plt.xlabel('Time (s)')
plt.ylabel('Voltages (s)')
plt.title(titlestr)
plt.show()
def plot_histograms(result_lists, figure=1, labels=None):
times = []
for n in range(len(result_lists)):
times.append(
1e6 * np.array([i.time for i in result_lists[n]
])) # convert from seconds to microseconds units.
min_time = np.min([np.min(times[n]) for n in range(len(result_lists))])
max_time = np.max([np.max(times[n]) for n in range(len(result_lists))])
plt.figure(figure)
plt.hold(False)
for n in range(len(result_lists)):
plt.hist(times[n],
50,
range=(min_time, max_time),
color=colors[n],
label=labels[n],
rwidth=(1 - n * 1.0 / len(result_lists)))
plt.hold(True)
plt.title("Migration time for different sequences")
plt.xlabel("First Passage Time (us)", fontsize='larger')
plt.ylabel("# of Trajectories", fontsize='larger')
plt.yticks(fontsize='larger', va='bottom')
plt.xticks(fontsize='larger')
plt.legend(loc=0)
plt.show()
def mark_cross(center, **kwargs):
"""Mark a cross. Correct for matplotlib imshow funny coordinate system.
"""
N = 20
plt.hold(1)
plt.axhline(y=center[1] - 0.5, **kwargs)
plt.axvline(x=center[0] - 0.5, **kwargs)
def question1():
"""
Function compute the runing times of the functions slow_closest_pairs
and fast_closest_pair for lists of clusters of size 2 to 200.
"""
slow_time_list = []
fast_time_list = []
for cluster_size in xrange(2, 201):
random_cluster = gen_random_clusters(cluster_size)
#For the slow_time_list
start_time = time.time()
slow_closest_pairs(random_cluster)
slow_time_list.append(time.time() - start_time)
#For the fast_time_list
start_time = time.time()
fast_closest_pair(random_cluster)
fast_time_list.append(time.time() - start_time)
plt.figure()
plt.hold(True)
plt.plot(range(2, 201), slow_time_list, 'r', label='Slow Closest Pairs')
plt.plot(range(2, 201), fast_time_list, 'b', label='Fast Closest Pair')
plt.legend(loc='upper right')
plt.title('Running Time Comparision')
plt.xlabel('The size of clusters')
plt.ylabel('Runing Time(s)')
plt.hold(False)
plt.show()
def plot_completion_graph(result_lists, figure=1, labels=None):
times = []
percents = []
if labels == None:
labels = [str(n) for n in range(1, 1 + len(result_lists))]
# if len(labels) < len(colors):
# colors = colors[:len(labels)]
for rl in result_lists:
n = len(rl)
t = [i.time for i in rl]
t.sort()
times.append(np.array(t))
p = np.array(range(1, len(t) + 1))
p = 100 * p / n # percentage of all trials
percents.append(p)
plt.figure(figure)
plt.hold(False)
for t, p, c, label in zip(times, percents, colors, labels):
plt.plot(1e6 * t, p, color=c, linewidth=2.0, label=label)
plt.hold(True)
plt.xlabel("Simulation Time (us)", fontsize='larger')
plt.ylabel("% of Trajectories Complete", fontsize='larger')
plt.yticks([0, 20, 40, 60, 80, 100],
("0%", "20%", "40%", "60%", "80%", "100%"),
fontsize='larger',
va='bottom')
plt.xticks(fontsize='larger')
plt.title("Percentage of Total Trajectories Complete by a Given Time")
plt.legend(loc=0)
plt.show()
def ensemble_demo():
utc = Calendar()
t_start = utc.time(YMDhms(2011, 9, 1))
t_fc_ens_start = utc.time(YMDhms(2015, 7, 26))
disp_start = utc.time(YMDhms(2015, 7, 20))
dt = deltahours(1)
n_obs = int(round((t_fc_ens_start - t_start) / dt))
n_fc_ens = 30
n_disp = int(round(t_fc_ens_start - disp_start) / dt) + n_fc_ens + 24 * 7
obs_time_axis = Timeaxis(t_start, dt, n_obs + 1)
fc_ens_time_axis = Timeaxis(t_fc_ens_start, dt, n_fc_ens)
display_time_axis = Timeaxis(disp_start, dt, n_disp)
q_obs_m3s_ts = observed_tistel_discharge(obs_time_axis.total_period())
ptgsk = create_tistel_simulator(
PTGSKOptModel, tistel.geo_ts_repository(tistel.grid_spec.epsg()))
initial_state = burn_in_state(ptgsk, t_start, utc.time(YMDhms(2012, 9, 1)),
q_obs_m3s_ts)
ptgsk.run(obs_time_axis, initial_state)
current_state = adjust_simulator_state(ptgsk, t_fc_ens_start, q_obs_m3s_ts)
q_obs_m3s_ts = observed_tistel_discharge(display_time_axis.total_period())
ens_repos = tistel.arome_ensemble_repository(tistel.grid_spec)
ptgsk_fc_ens = create_tistel_simulator(PTGSKModel, ens_repos)
sims = ptgsk_fc_ens.create_ensembles(fc_ens_time_axis, t_fc_ens_start,
current_state)
for sim in sims:
sim.simulate()
plt.hold(1)
percentiles = [10, 25, 50, 75, 90]
plot_percentiles(sims, percentiles, obs=q_obs_m3s_ts)
#plt.interactive(1)
plt.show()
def plot_fits(direction_rates,fit_curve,title):
"""
This function takes the x-values and the y-values in units of spikes/s
(found in the two columns of direction_rates and fit_curve) and plots the
actual values with circles, and the curves as lines in both linear and
polar plots.
"""
curve_xs = np.arange(direction_rates[0,0], direction_rates[-1,0])
fit_ys2 = normal_fit(curve_xs,fit_curve[0],fit_curve[1],fit_curve[2])
plt.subplot(2,2,3)
plt.plot(direction_rates[:,0],direction_rates[:,1],'o',hold=True)
plt.plot(curve_xs,fit_ys2,'-')
plt.xlabel('Direction of Motions (Degrees)')
plt.ylabel('Firing Rates (Spikes/sec)')
plt.title(title)
plt.axis([0, 360, 0, 40])
plt.xticks(direction_rates[:,0])
fit_ys = normal_fit(direction_rates[:,0],fit_curve[0],fit_curve[1],fit_curve[2])
plt.subplot(2,2,4,polar=True)
spkiecount = np.append(direction_rates[:,1],direction_rates[0,1])
plt.polar(np.arange(0,361,45)*np.pi/180,spkiecount,'o',label='Firing Rate (spike/s)')
plt.hold(True)
spkiecount_y = np.append(fit_ys,fit_ys[0])
plt.plot(np.arange(0,361,45)*np.pi/180,spkiecount_y,'-')
plt.legend(loc=8)
plt.title(title)
fit_ys2 = np.transpose(np.vstack((curve_xs,fit_ys2)))
return(fit_ys2)
def plot(self):
Ns = 1
h = 0.1
m = []
for i in range(len(self.l)):
for s in range(Ns):
m.append(ml_to_xy((i, float(s)/Ns, 0), self.kappa, self.l, self.x0, self.theta0))
m.append(ml_to_xy((len(self.l)-1, 1., 0), self.kappa, self.l, self.x0, self.theta0))
plt.clf()
plt.hold(True)
x=[p[0] for p in m]
y=[p[1] for p in m]
bp, angles, tangents= breakpoints(self.kappa, self.l, self.x0, self.theta0)
x=[p[0] for p in bp]
y=[p[1] for p in bp]
plt.plot(x[::10],y[::10],'k-')
# xm = [p[0] for i, p in enumerate(bp) if self.markers[i]==1]
# ym = [p[1] for i, p in enumerate(bp) if self.markers[i]==1]
# plt.plot(xm,ym,'kx')
plt.xlim((-100, 3000))
plt.ylim((-3000, 100))
plt.draw()
def plotVWavelet(self, width=30):
plt.close()
fig, figInds = plt.subplots(nrows=self.nCell, sharex=True)
# 周波数
widths = np.arange(1, width + 1)
for figInd in np.arange(len(figInds)):
# continuous waveletをかけて、係数マップと周波数を出力
cwtmatr, freqs = pywt.cwt(self.yV[:, figInd], widths, 'mexh')
# 係数マップのプロット
figInds[figInd].imshow(
cwtmatr,
extent=[1, self.nYear, widths[-1], widths[0]],
cmap='gray',
aspect='auto',
vmax=abs(cwtmatr).max(),
vmin=-abs(cwtmatr).max())
plt.hold(True)
fullPath = os.path.join(self.visualPath,
"{}_cwt.png".format(self.logName))
plt.savefig(fullPath)
fig.show()
plt.show()
def plot_completion_graph(result_lists,
colors=['b', 'r'],
figure=1,
labels=['Design A', 'Design B']):
times = []
percents = []
for rl in result_lists:
n = len(rl)
t = [i.time for i in rl if i.tag == 'complete']
t.sort()
times.append(np.array(t))
p = np.array(range(1, len(t) + 1))
p = 100 * p / n # percentage of all trials, including ones that don't complete
percents.append(p)
plt.figure(figure)
plt.hold(False)
for t, p, c, label in zip(times, percents, colors, labels):
plt.plot(t, p, color=c, linewidth=2.0, label=label)
plt.hold(True)
plt.xlabel("Simulation Time (s)", fontsize='larger')
plt.ylabel("% of Trajectories Complete", fontsize='larger')
plt.yticks([0, 20, 40, 60, 80, 100],
("0%", "20%", "40%", "60%", "80%", "100%"),
fontsize='larger',
va='bottom')
plt.xticks(fontsize='larger')
plt.title("Percentage of Total Trajectories Complete by a Given Time")
plt.legend(loc=0)
plt.show()
def plot_histograms_two_designs(result_lists,
colors=['magenta', 'b'],
figure=1):
times = []
times.append(
np.array([i.time for i in result_lists[0] if i.tag == 'complete']))
times.append(
np.array([i.time for i in result_lists[1] if i.tag == 'complete']))
min_time = np.min([np.min(times[0]), np.min(times[1])])
max_time = np.max([np.max(times[0]), np.max(times[1])])
# the above might fail if any list is empty; min, max of empty is undefined
plt.figure(figure)
plt.hold(False)
plt.hist(times[1],
50,
range=(min_time, max_time),
color=colors[1],
label="Design B")
plt.hold(True)
plt.hist(times[0],
50,
range=(min_time, max_time),
color=colors[0],
label="Design A",
rwidth=.5)
plt.title("Successful trajectories in two designs")
plt.xlabel("First Passage Time (s)", fontsize='larger')
plt.ylabel("# of Trajectories", fontsize='larger')
plt.yticks(fontsize='larger', va='bottom')
plt.xticks(fontsize='larger')
plt.legend(loc=0)
plt.show()
def ensemble_demo():
utc = Calendar()
t_start = utc.time(YMDhms(2011, 9, 1))
t_fc_ens_start = utc.time(YMDhms(2015, 7, 26))
disp_start = utc.time(YMDhms(2015, 7, 20))
dt = deltahours(1)
n_obs = int(round((t_fc_ens_start - t_start)/dt))
n_fc_ens = 30
n_disp = int(round(t_fc_ens_start - disp_start)/dt) + n_fc_ens + 24*7
obs_time_axis = Timeaxis(t_start, dt, n_obs + 1)
fc_ens_time_axis = Timeaxis(t_fc_ens_start, dt, n_fc_ens)
display_time_axis = Timeaxis(disp_start, dt, n_disp)
q_obs_m3s_ts = observed_tistel_discharge(obs_time_axis.total_period())
ptgsk = create_tistel_simulator(PTGSKOptModel, tistel.geo_ts_repository(tistel.grid_spec.epsg()))
initial_state = burn_in_state(ptgsk, t_start, utc.time(YMDhms(2012, 9, 1)), q_obs_m3s_ts)
ptgsk.run(obs_time_axis, initial_state)
current_state = adjust_simulator_state(ptgsk, t_fc_ens_start, q_obs_m3s_ts)
q_obs_m3s_ts = observed_tistel_discharge(display_time_axis.total_period())
ens_repos = tistel.arome_ensemble_repository(tistel.grid_spec)
ptgsk_fc_ens = create_tistel_simulator(PTGSKModel, ens_repos)
sims = ptgsk_fc_ens.create_ensembles(fc_ens_time_axis, t_fc_ens_start, current_state)
for sim in sims:
sim.simulate()
plt.hold(1)
percentiles = [10, 25, 50, 75, 90]
plot_percentiles(sims, percentiles, obs=q_obs_m3s_ts)
#plt.interactive(1)
plt.show()
def waterfall_plot(q,x,sampling=10,cmap=None,num_colors=100,outdir='./',outname='waterfall',format='eps',cbar_label='$|q| (a.u.)$'):
plt.figure()
plt.hold(True)
colorVal = 'b'
vmax = q[:,:].max()
print vmax,len(q)
for n in range(0,len(q),sampling):
if cmap is not None:
print q[n,:].max()
colorVal = get_color(value=q[n,:].max(),cmap=cmap,vmax=vmax+.1,num_colors=num_colors)
plt.plot(x,q[n,:]+n/10.0,label=str(n),color=colorVal,alpha=0.7)
ax = plt.gca()
for tic in ax.yaxis.get_major_ticks():
tic.tick1On = tic.tick2On = False
tic.label1On = tic.label2On = False
if cmap is not None:
scalar = get_smap(vmax=q[:,:].max()+.1,num_colors=sampling)
cbar = plt.colorbar(scalar)
plt.xlabel('$x\quad (a.u.)$')
cbar.set_label(cbar_label)
plt.draw()
plt.savefig(os.path.join(outdir,outname+'.'+format),format=format,dpi=320,bbox_inches='tight')
plt.close()
return
def saveCMDataFig(CMdata, trialDuration, trialReps, saveDir, plotName, timeStr):
plt.figure(1, figsize=(14, 11), dpi=80)
plt.clf()
numFreq = len(CMdata.freqArray)
numAmp = len(CMdata.ampArray)
nGraphs = numFreq + 1
numRows = int(np.ceil(nGraphs ** 0.5))
numCols = int(np.ceil(nGraphs / numRows))
numSD = 2.5
for n in range(0, numFreq):
CMresp = CMdata.CMResp[n, :]
noise_mean = CMdata.noise_mean[n, :]
noise_std = CMdata.noise_std[n, :]
noise = noise_mean + (numSD * noise_std)
plt.subplot(numRows, numCols, n+1)
plt.plot(CMdata.ampArray, 1e6*CMresp,'-bo', label='Response (uV)')
plt.hold('on')
plt.plot(CMdata.ampArray, 1e6*(noise_mean + 3*noise_std), '-ro', label='Noise')
plt.plot(CMdata.ampArray, noise_mean, ':r', label='Noise mean')
# plt.plot(CMdata.ampArray, noise, '-rs', label='+ %g SD' % numSD)
plt.xlabel('Amplitude (dB)', fontsize=10)
if n == (numFreq-1):
plt.legend(loc='upper left', fontsize=10)
#plt.pcolormesh(t, f, Sxx)
plt.ylabel('dB SPL', fontsize=10)
plt.title('%0.2f kHz' % (CMdata.freqArray[n]/1e3), x=0.15, fontsize=10)
plt.show()
fname = os.path.join(saveDir, plotName)
plt.savefig(fname)
def saveABRDataFig(ABRdata, ABRparams, saveDir, plotName, timeStr):
plt.figure(1, figsize=(14, 11), dpi=80)
plt.clf()
numFreq = len(ABRdata.freqArray)
numAmp = len(ABRdata.ampArray)
numSD = 5
# clr_lbls = ['b', 'g', 'r', 'c', 'm', 'y', 'k']
nGraphs = numFreq + 1
numRows = int(np.ceil(nGraphs ** 0.5))
numCols = int(np.ceil(nGraphs / numRows))
for n in range(0, numFreq):
plt.subplot(numRows, numCols, n+1)
ABRresp = 1e6*ABRdata.ABRResp[n, :]
noise = 1e6*numSD*ABRdata.noise_std[n, :]
plt.plot(ABRdata.ampArray, ABRresp, '-bo', label='Signal')
plt.hold('on')
plt.plot(ABRdata.ampArray, noise, '-r', label='Noise (%0.1f SD)' % numSD)
if n == (0):
plt.ylabel('Resp PP (uV)', fontsize=10)
if n == (numFreq-1):
plt.legend(loc='upper left', fontsize=10)
plt.xlabel('Amplitude (dB)', fontsize=10)
#plt.pcolormesh(t, f, Sxx)
plt.title('%0.2f kHz' % (ABRdata.freqArray[n]/1e3), x=0.15, fontsize=10)
plt.show()
fname = os.path.join(saveDir, plotName)
plt.savefig(fname)
plt.figure(2, figsize=(14, 11), dpi=80)
plt.clf()
# clr_lbls = ['b', 'g', 'r', 'c', 'm', 'y', 'k']
t = ABRdata.t
for n in range(0, numFreq):
plt.subplot(numRows, numCols, n+1)
offset = 0
for a in range(numAmp):
tr = 1e6*ABRdata.tracings[n, a, :]
if a > 0:
offset = offset + np.abs(np.min(tr))
plt.plot(t*1e3, tr+offset, '-b', label='Signal')
plt.hold('on')
offset = offset + np.max(tr)
if n == (0):
plt.ylabel('Resp (uV)', fontsize=10)
if n == (numFreq-1):
plt.xlabel('Time (ms)', fontsize=10)
#plt.pcolormesh(t, f, Sxx)
plt.title('%0.2f kHz' % (ABRdata.freqArray[n]/1e3), x=0.15, fontsize=10)
plt.show()
fname = os.path.join(saveDir, plotName + ' tracings')
plt.savefig(fname)
def gasket(pa, pb, pc, level, col):
if level == 0:
plt.fill([pa[0], pb[0], pc[0]], [pa[1], pb[1], pc[1]], col)
plt.hold(True)
else:
gasket(pa, (pa + pb) / 2., (pa + pc) / 2., level - 1, col)
gasket(pb, (pb + pa) / 2., (pb + pc) / 2., level - 1, col)
gasket(pc, (pc + pa) / 2., (pc + pb) / 2., level - 1, col)
def gasket(pa, pb, pc, level, color):
if level == 0:
plt.fill([pa[0], pb[0], pc[0]], [pa[1], pb[1], pc[1]], color)
plt.hold(True)
else:
gasket(pa, (pa + pb) / 2., (pa + pc) / 2., level - 1, color)
gasket(pb, (pb + pa) / 2., (pb + pc) / 2., level - 1, color)
gasket(pc, (pc + pa) / 2., (pc + pb) / 2., level - 1, color)
def Sierpinski(a, b, c, k, iteration):
if iteration == 0:
plt.fill([a[0], b[0], c[0]], [a[1], b[1], c[1]], 'b')
plt.hold(True)
else:
Sierpinski(a, bis(a, b, k), bis(a, c, k), k, iteration - 1)
Sierpinski(b, bis(a, b, k), bis(b, c, k), k, iteration - 1)
Sierpinski(c, bis(a, c, k), bis(b, c, k), k, iteration - 1)
plt.hold(True)
def Sierpinski(a,b,c,k,iteration):
if iteration==0:
plt.fill([a[0], b[0], c[0]], [a[1], b[1], c[1]],'b')
plt.hold(True)
else:
Sierpinski(a,bis(a,b,k),bis(a,c,k),k,iteration-1)
Sierpinski(b,bis(a,b,k),bis(b,c,k),k,iteration-1)
Sierpinski(c,bis(a,c,k),bis(b,c,k),k,iteration-1)
plt.hold(True)
def run(self):
plt.figure()
plt.ion()
plt.hold(True)
while not rospy.is_shutdown():
self.plotTrajectory()
time.sleep(0.5 / self.update_rate)
def display_multiple_egg_carton(u0,s0,s1,ds,C,s):
X = solve_multiple(C,u0,s0,s1,ds,s)
plt.hold('on')
# plot the parametrized data on to the egg carton
u,v = X[:,0], X[:,2]
x = u
y = v
z = np.sin(u)*np.cos(v)
ax.plot(x,y,z,'--r')
return plt
def display_multiple_torus(u0,s0,s1,ds,C,s):
X = solve_multiple(C,u0,s0,s1,ds,s)
plt.hold('on')
# plot the parametrized data on to the sphere
u,v = X[:,0], X[:,2]
x = (2 + 1*np.cos(v))*np.cos(u)
y = (2 + 1*np.cos(v))*np.sin(u)
z = np.sin(v)
ax.plot(x,y,z,'--r')
return plt
def display_multiple_egg_carton(u0, s0, s1, ds, C, s):
X = solve_multiple(C, u0, s0, s1, ds, s)
plt.hold('on')
# plot the parametrized data on to the egg carton
u, v = X[:, 0], X[:, 2]
x = u
y = v
z = np.sin(u) * np.cos(v)
ax.plot(x, y, z, '--r')
return plt
def display_multiple_catenoid(u0, s0, s1, ds, C, s):
X = solve_multiple(C, u0, s0, s1, ds, s)
plt.hold('on')
# plot the parametrized data on to the catenoid
u, v = X[:, 0], X[:, 2]
x = np.cos(u) - v * np.sin(u)
y = np.sin(u) + v * np.cos(u)
z = v
ax.plot(x, y, z, '--r')
return plt
def display_multiple_torus(u0, s0, s1, ds, C, s):
X = solve_multiple(C, u0, s0, s1, ds, s)
plt.hold('on')
# plot the parametrized data on to the sphere
u, v = X[:, 0], X[:, 2]
x = (2 + 1 * np.cos(v)) * np.cos(u)
y = (2 + 1 * np.cos(v)) * np.sin(u)
z = np.sin(v)
ax.plot(x, y, z, '--r')
return plt
def display_multiple_catenoid(u0,s0,s1,ds,C,s):
X = solve_multiple(C,u0,s0,s1,ds,s)
plt.hold('on')
# plot the parametrized data on to the catenoid
u,v = X[:,0], X[:,2]
x = np.cos(u) - v*np.sin(u)
y = np.sin(u) + v*np.cos(u)
z = v
ax.plot(x,y,z,'--r')
return plt
def plotPolygon(lat,lon,poly,regnum,plotFile):
fig = plt.figure(figsize=(6,6))
px = [pol[0] for pol in poly]
py = [pol[1] for pol in poly]
plt.plot(px,py,'b')
plt.hold(True)
plt.plot(lon,lat,'rx')
plt.title('%.4f,%.4f in Region %i' % (lat,lon,regnum))
plt.savefig(plotFile)
plt.close()
def plotPolygon(lat,lon,poly,regnum,plotFile):
fig = plt.figure(figsize=(6,6))
px = [pol[0] for pol in poly]
py = [pol[1] for pol in poly]
plt.plot(px,py,'b')
plt.hold(True)
plt.plot(lon,lat,'rx')
plt.title('%.4f,%.4f in Region %i' % (lat,lon,regnum))
plt.savefig(plotFile)
plt.close()
def sierpinski(a, b, c, iterations):
x=(random.random(),random.random(),random.random())
if iterations == 0:
plt.fill([a[0], b[0], c[0]], [a[1], b[1], c[1]], color=x,alpha=0.9)
plt.hold(True)
else:
sierpinski(a, (a + b) / 2., (a + c) / 2., iterations - 1)
sierpinski(b, (b + a) / 2., (b + c) / 2., iterations - 1)
sierpinski(c, (c + a) / 2., (c + b) / 2., iterations - 1)
plt.fill([(a[0] + b[0]) / 2., (a[0] + c[0]) / 2., (b[0] + c[0]) / 2.], [(a[1] + b[1]) / 2., (a[1] + c[1]) / 2., (b[1] + c[1]) / 2.], color=x,alpha=0.9)
def display_toroid(u0,
s0,
s1,
ds,
u_val=1,
v_val=None,
a=1,
solver=None,
show=False):
C = toroid(u_val, v_val, a) # Find the Christoffel tensor for toroid
X = solve(C, u0, s0, s1, ds, solver)
import matplotlib.pylab as plt
from mpl_toolkits.mplot3d import Axes3D
from math import pi
if v_val is None:
u = u_val # toroids
v, w = plt.meshgrid(np.linspace(-pi, pi, 250),
np.linspace(0, 2 * pi, 250))
else:
v = v_val # spherical bowls
u, w = plt.meshgrid(np.linspace(0, 2, 250),
np.linspace(0, 2 * pi, 250))
x = (a * np.sinh(u) * np.cos(w)) / (np.cosh(u) - np.cos(v))
y = (a * np.sinh(u) * np.sin(w)) / (np.cosh(u) - np.cos(v))
z = (a * np.sin(v)) / (np.cosh(u) - np.cos(v))
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.view_init(elev=90., azim=0)
# use transparent colormap
import matplotlib.cm as cm
theCM = cm.get_cmap()
theCM._init()
alphas = -.5 * np.ones(theCM.N)
theCM._lut[:-3, -1] = alphas
ax.plot_surface(x, y, z, linewidth=0, cmap=theCM)
plt.hold('on')
# plot the parametrized data on to the toroid
if v_val is None:
w, v = X[:, 0], X[:, 2]
else:
w, u = X[:, 0], X[:, 2]
x = (a * np.sinh(u) * np.cos(w)) / (np.cosh(u) - np.cos(v))
y = (a * np.sinh(u) * np.sin(w)) / (np.cosh(u) - np.cos(v))
z = (a * np.sin(v)) / (np.cosh(u) - np.cos(v))
s1_ = s1 / pi
ax.plot(x, y, z, '--r')
fig.suptitle('$s\in[%.1f\pi \, , \,%2.1f\pi]$' % (s0, s1_))
if show == True:
plt.show()
return X, plt
def plot_histograms_complete_vs_failed(result_list,
colors=['b', 'm'],
figure=1):
# separate based on which stop condition ended the simulation ((( what if simulation ran out of time? )))
times_complete = np.array(
[i.time for i in result_list if i.tag == 'complete'])
times_failed = np.array([i.time for i in result_list if i.tag == 'failed'])
neither = [
i for i in result_list
if not i.tag == 'complete' and not i.tag == 'failed'
]
if len(neither) > 0:
print "some trajectories did not finish, one way nor the other..."
for i in neither:
assert (i.type_name == 'Time')
assert (i.tag == None)
if len(times_complete) > 0 and len(times_failed) > 0:
min_time = np.min([np.min(times_complete), np.min(times_failed)])
max_time = np.max([np.max(times_complete), np.max(times_failed)])
else:
if len(times_complete) > 0:
min_time = np.min(times_complete)
max_time = np.max(times_complete)
if len(times_failed) > 0:
min_time = np.min(times_failed)
max_time = np.max(times_failed)
plt.figure(figure)
plt.hold(False)
if len(times_complete) > 0:
plt.hist(times_complete,
50,
range=(min_time, max_time),
color=colors[0],
label="complete")
plt.hold(True)
if len(times_failed) > 0:
plt.hist(times_failed,
50,
range=(min_time, max_time),
color=colors[1],
rwidth=.5,
label="failed")
plt.title(
"Completion times for successful and failed trajectories, Design A")
plt.xlabel("First Passage Time (s)", fontsize='larger')
plt.ylabel("# of Trajectories", fontsize='larger')
plt.yticks(fontsize='larger', va='bottom')
plt.xticks(fontsize='larger')
plt.legend(loc=0)
plt.show()
def plot_rect_mesh(p,tri):
plt.figure()
tx = p[:,0]; ty = p[:,1]
for t in tri:
t_i = [t[0],t[1],t[2],t[0]]
plt.plot(tx[t_i],ty[t_i],'k')
plt.hold('on')
plt.title('TRIANGULAR MESH')
plt.axis('equal')
plt.hold('off')
plt.show()
def plot_learning_curves(clf, X, y):
train_sizes, train_scores, valid_scores = learning_curve.learning_curve(clf, X, np.ravel(y), scoring = roc_auc_scorer,
cv = 6, train_sizes = np.linspace(.5, 1, 10), n_jobs = -1)
plt.figure()
plt.plot(train_sizes, np.mean(train_scores, axis = 1))
plt.hold(True)
plt.plot(train_sizes, np.mean(valid_scores, axis = 1))
plt.grid(True)
plt.show()
def Sierpinski(a,b,c,k,iteration):
x=(random.random(),random.random(),random.random())
if iteration==0:
plt.fill([a[0], b[0], c[0]], [a[1], b[1], c[1]], color=x,alpha=0.9)
plt.hold(True)
else:
Sierpinski(a,bis(a,b,k),bis(a,c,k),k,iteration-1)
Sierpinski(b,bis(a,b,k),bis(b,c,k),k,iteration-1)
Sierpinski(c,bis(a,c,k),bis(b,c,k),k,iteration-1)
plt.hold(True)
plt.fill([bis(a,b,k)[0], bis(a,c,k)[0], bis(b,c,k)[0]], [bis(a,b,k)[1], bis(a,c,k)[1], bis(b,c,k)[1]], color=x,alpha=0.9)
def plotPORVelocity(velocity, POR, time, xtitle, ytitle, title):
plt.figure()
plt.plot(time, velocity)
plt.hold(True)
plt.plot(time, POR, 'r.')
plt.xlabel(xtitle)
plt.ylabel(ytitle)
plt.title(title)
plt.grid(True)
plt.show()
def update_iq_power_plot_all(self, iq_power_1, iq_power_2):
plt.cla()
plt.plot(np.arange(0, len(iq_power_1), 1), iq_power_1, 'd-', color='b')
plt.hold(True)
plt.plot(np.arange(0, len(iq_power_2), 1), iq_power_2, 'o-', color='r')
plt.hold(False)
plt.grid(True)
plt.ylim([-100, -30])
plt.tight_layout()
plt.show()
plt.pause(0.00001)
def plot_svc(X, y, mysvc, bounds=None, grid=50):
if bounds is None:
xmin = np.min(X[:, 0], 0)
xmax = np.max(X[:, 0], 0)
ymin = np.min(X[:, 1], 0)
ymax = np.max(X[:, 1], 0)
else:
xmin, ymin = bounds[0], bounds[0]
xmax, ymax = bounds[1], bounds[1]
aspect_ratio = (xmax - xmin) / (ymax - ymin)
xgrid, ygrid = np.meshgrid(np.linspace(xmin, xmax, grid),
np.linspace(ymin, ymax, grid))
plt.gca(aspect=aspect_ratio)
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
plt.xticks([])
plt.yticks([])
plt.hold(True)
plt.plot(X[y == 1, 0], X[y == 1, 1], 'bo')
plt.plot(X[y == -1, 0], X[y == -1, 1], 'ro')
box_xy = np.append(xgrid.reshape(xgrid.size, 1),
ygrid.reshape(ygrid.size, 1), 1)
if mysvc is not None:
scores = mysvc.decision_function(box_xy)
else:
print 'You must have a valid SVC object.'
return None
CS = plt.contourf(xgrid,
ygrid,
scores.reshape(xgrid.shape),
alpha=0.5,
cmap='jet_r')
plt.contour(xgrid,
ygrid,
scores.reshape(xgrid.shape),
levels=[0],
colors='k',
linestyles='solid',
linewidths=1.5)
plt.contour(xgrid,
ygrid,
scores.reshape(xgrid.shape),
levels=[-1, 1],
colors='k',
linestyles='dashed',
linewidths=1)
plt.plot(mysvc.support_vectors_[:, 0],
mysvc.support_vectors_[:, 1],
'ko',
markerfacecolor='none',
markersize=10)
CB = plt.colorbar(CS)
def plotPoints(self, TITLE, saveName, xlab, ylab):
plot(self.points[0, :], self.points[1, :], '.')
hold('on')
plot(self.points[0, :], self.evaluated, '-')
hold('off')
title(TITLE)
xlabel(xlab)
ylabel(ylab)
legend(('datapunkter', 'polynomtilnærming',), loc=1)
savefig(saveName)
show()
def runAllBenchmarks(X, JobQ, ResultQ,
nRepeat=1, methods='all', **kwargs):
methodNames = getMethodNames(methods=methods)
print '======================= ', makeTitle(**kwargs)
print '%16s %15s %15s %15s %10s' % (
' ', 'slice size', 'slice time', 'wallclock time', 'speedup')
Tinfo = defaultdict(dict)
for rep in xrange(nRepeat):
for method in methodNames:
tstart = time.time()
ts = runBenchmark(X, JobQ, ResultQ, method=method, **kwargs)
telapsed = time.time() - tstart
Tinfo[method][rep] = dict()
Tinfo[method][rep]['telapsed'] = telapsed
Tinfo[method][rep]['ts'] = ts
# PRINT RESULTS
if 'monolithic' in Tinfo:
telasped_monolithic = np.median([Tinfo['monolithic'][r]['telapsed']
for r in xrange(nRepeat)])
for rep in xrange(nRepeat):
for method in methodNames:
start, stop = [x for x in sliceGenerator(**kwargs)][0]
msg = "%16s" % (method)
if method == 'monolithic':
msg += " %8d x %2d" % (X.shape[0], 1)
else:
msg += " %8d x %2d" % (stop - start, kwargs['nWorker'])
msg += " %11.3f sec" % (np.median(Tinfo[method][rep]['ts']))
telapsed = Tinfo[method][rep]['telapsed']
msg += " %11.3f sec" % (telapsed)
if 'monolithic' in Tinfo:
msg += " %11.2f" % (telasped_monolithic / telapsed)
print msg
# PLOT RESULTS
pylab.figure(1)
pylab.hold('on')
for method in methodNames:
xs = kwargs['nWorker'] * np.ones(nRepeat)
ys = [Tinfo[method][r]['telapsed'] for r in xrange(nRepeat)]
if kwargs['nWorker'] == 1:
label = method
else:
label = None
pylab.plot(xs, ys, '.',
color=ColorMap[method],
markeredgecolor=ColorMap[method],
label=label)
return Tinfo
def plot_generic(x_values, y_values, plot_func = pyp.plot, hold = True, figure_number = None, *args, **kargs): """ Actual plotting function that passes arguments to the correct plot method. """ if figure_number: pyp.figure(figure_number) pyp.hold(hold) # keeps existing plots on the graph if true plot_func(x_values, y_values, *args, **kargs)
def draw_grid_plot():
if not has_plt:
return
plt.imshow(z_sample, cmap=plt.cm.binary, origin='lower',
interpolation='nearest',
extent=(grid_min, grid_max, grid_min, grid_max))
plt.hold(True) # XXX: restore plt state
plt.contour(np.linspace(grid_min, grid_max, grid_n),
np.linspace(grid_min, grid_max, grid_n),
z_actual)
plt.savefig(grid_filename)
plt.close()
def gasket(pa, pb, pc, level):
x=(random.random(),random.random(),random.random())
if level == 0:
plt.fill([pa[0], pb[0], pc[0]], [pa[1], pb[1], pc[1]], color=x,alpha=0.9)
plt.hold(True)
else:
gasket(pa, (pa + pb) / 2., (pa + pc) / 2., level - 1)
gasket(pb, (pb + pa) / 2., (pb + pc) / 2., level - 1)
gasket(pc, (pc + pa) / 2., (pc + pb) / 2., level - 1)
plt.hold(True)
plt.fill([(pa[0] + pb[0]) / 2.,(pb[0] + pc[0]) / 2.,(pa[0] + pc[0]) / 2.],
[(pa[1] + pb[1]) / 2.,(pb[1] + pc[1]) / 2.,(pa[1] + pc[1]) / 2.],color=x,alpha=0.9)
def plot_comparison(template,
haps,
snps=None,
title=None,
xlabel=None,
x=None,
y=None,
template_y='TEMP',
colors=DEFAULT_COLORS):
'''Generate a recombination coloring plot of the difference between template
and each element in the list haps..'''
# Read or re-generate differences data
num_snps = len(template)
if np.size(haps.shape) == 1:
haps = np.transpose(np.array([haps]))
num_haps = haps.shape[1]
# d = (haps != np.transpose(np.tile(template, (num_haps,1)))).astype('int8')
d = np.transpose(
np.array([
diff.hap_diff(haps[:, j], template).astype('int8')
for j in xrange(0, num_haps)
]))
# Restrict view to snps, if specified
x = x if x is not None else np.arange(0, num_snps)
if snps is not None:
(x, d) = (x[snps], d[snps, :])
# Generate haplotype plots
P.clf()
P.hold(True)
hap_ticks = range(0, num_haps)
for j in hap_ticks:
difference = d[:, j]
for (value, color) in colors.iteritems():
hap = np.where(difference == value)
if hap:
P.plot(x[hap[0]],
np.zeros((np.size(hap), )) + j,
color,
markeredgecolor='gray'
if value == INDETERMINATE else color[0])
if title is not None:
P.title(title)
P.xlim([min(x) - 1, max(x) + 1])
P.ylim([-0.5, num_haps - 0.5])
P.xlabel(xlabel if xlabel else 'SNP #')
P.ylabel('Sample')
if y is not None:
P.yticks(hap_ticks, [template_y] + list(y))
return d
def optimize_char_ngram():
log_reg_clf = LogisticRegression(C = 10)
#svm_clf = svm.SVC(C = 10)
#classifiers = [log_reg_clf, svm_clf]
tfidf_vect = TfidfVectorizer()
estimators = [('vect', tfidf_vect), ('clf', log_reg_clf)]
clf = Pipeline(estimators)
clf.set_params(vect__analyzer = 'char')
n_gram_range = np.array(range(1, 5))
scores_train_vec = np.zeros(n_gram_range.shape)
scores_test_vec = np.zeros(n_gram_range.shape)
for n_gram_ind in range(len(n_gram_range)):
print("%d n_gram:" % n_gram_range[n_gram_ind])
clf.set_params(vect__ngram_range=(1, n_gram_range[n_gram_ind]))
#cv = cross_validation.ShuffleSplit(X_train.shape[0], n_iter = 20, test_size = 0.2)
cv = cross_validation.KFold(X_train.shape[0], n_folds = 6)
scores_train = []
scores_test = []
for train_index, test_index in cv:
clf.fit(X_train[train_index], np.ravel(y_train[train_index]))
y_train_pred = clf.predict(X_train[train_index])
train_score = roc_auc_score_(y_train_pred, np.ravel(y_train[train_index]))
print train_score
scores_train.append(train_score)
y_test_pred = clf.predict(X_train[test_index])
test_score = roc_auc_score_(y_test_pred, np.ravel(y_train[test_index]))
print test_score
scores_test.append(test_score)
scores_train_vec[n_gram_ind] = np.mean(scores_train)
scores_test_vec[n_gram_ind] = np.mean(scores_test)
print(scores_train_vec)
print(scores_test_vec)
plt.figure()
plt.plot(n_gram_range, scores_train_vec)
plt.hold(True)
plt.plot(n_gram_range, scores_test_vec)
plt.grid(True)
plt.show()
def show_image(img_dir, img_name, label_dict):
img_path = os.path.join(img_dir, img_name)
img = scipy.misc.imread(img_path)
plt.figure()
plt.imshow(img)
if len(label_dict[img_name]):
points = np.array(label_dict[img_name]) / 100. * [640., 480.]
plt.hold('on')
plt.scatter(points[:, 0], points[:, 1])
plt.show()
def draw_grid_plot():
if not has_plt:
return
plt.imshow(z_sample,
cmap=plt.cm.binary,
origin='lower',
interpolation='nearest',
extent=(grid_min, grid_max, grid_min, grid_max))
plt.hold(True) # XXX: restore plt state
plt.contour(np.linspace(grid_min, grid_max, grid_n),
np.linspace(grid_min, grid_max, grid_n), z_actual)
plt.savefig(grid_filename)
plt.close()
def plot_data_and_model(x, y, f, knee, title):
'''Generate a plot of the data y(x), fitted curve f, and knee point (knee is the index of that
point into the x-array).'''
P.figure(1)
P.clf()
P.hold(True)
P.plot(x, y, 'x', label='Data')
P.plot(x, f, 'r-', label='Fit')
P.title(title)
P.xlabel(r'$\beta$')
P.ylabel('Frequency')
P.legend(loc=0)
P.plot(x[knee], y[knee], 'ko', markersize=8)
def SierpinskiTriangle(a, b, c, iterations):
'''
Recursively generated Sierpinski Triangle.
'''
if iterations == 0:
# Fill the triangle with vertices a, b, c.
plt.fill([a[0], b[0], c[0]], [a[1], b[1], c[1]], 'g')
plt.hold(True)
else:
# Recursive calls for the three subtriangles.
SierpinskiTriangle(a, (a + b) / 2., (a + c) / 2., iterations - 1)
SierpinskiTriangle(b, (b + a) / 2., (b + c) / 2., iterations - 1)
SierpinskiTriangle(c, (c + a) / 2., (c + b) / 2., iterations - 1)
def sierpinski(a, b, c, iterations):
x = (random.random(), random.random(), random.random())
if iterations == 0:
plt.fill([a[0], b[0], c[0]], [a[1], b[1], c[1]], color=x, alpha=0.9)
plt.hold(True)
else:
sierpinski(a, (a + b) / 2., (a + c) / 2., iterations - 1)
sierpinski(b, (b + a) / 2., (b + c) / 2., iterations - 1)
sierpinski(c, (c + a) / 2., (c + b) / 2., iterations - 1)
plt.fill([(a[0] + b[0]) / 2., (a[0] + c[0]) / 2., (b[0] + c[0]) / 2.],
[(a[1] + b[1]) / 2., (a[1] + c[1]) / 2., (b[1] + c[1]) / 2.],
color=x,
alpha=0.9)
def SierpinskiTriangle(a, b, c, iterations):
"""
Recursively generated Sierpinski Triangle.
"""
if iterations == 0:
# Fill the triangle with vertices a, b, c.
plt.fill([a[0], b[0], c[0]], [a[1], b[1], c[1]], "g")
plt.hold(True)
else:
# Recursive calls for the three subtriangles.
SierpinskiTriangle(a, (a + b) / 2.0, (a + c) / 2.0, iterations - 1)
SierpinskiTriangle(b, (b + a) / 2.0, (b + c) / 2.0, iterations - 1)
SierpinskiTriangle(c, (c + a) / 2.0, (c + b) / 2.0, iterations - 1)
def show_trajectories(positions,LM_traj,intensities,LM_traj2=None,legend=True):
fig = plt.figure()
if LM_traj2!=None:
plt.subplot(121)
plt.hold(True)
x,y = list(itertools.chain(*[v[0,:] for v in positions])), list(itertools.chain(*[v[1,:] for v in positions]))
plt.scatter(x,y,marker='o',edgecolor='b',linestyle='dashed',alpha=0.3)
for i,idx in enumerate(LM_traj):
pos = [positions[t,:,int(ix)] for t,ix in enumerate(idx) if ix==ix]
x, y = [v[0] for v in pos], [v[1] for v in pos]
plt.plot(x,y,'-',linewidth=2.,alpha=0.4,label=str(i))
plt.hold(False)
if legend: plt.legend(loc=0)
if LM_traj2!=None:
plt.title('traj1')
if LM_traj2!=None:
plt.subplot(122)
plt.hold(True)
x,y = list(itertools.chain(*[v[0,:] for v in positions])), list(itertools.chain(*[v[1,:] for v in positions]))
plt.scatter(x,y,marker='o',edgecolor='b',linestyle='dashed',alpha=0.3)
for i,idx in enumerate(LM_traj2):
pos = [positions[t,:,int(ix)] for t,ix in enumerate(idx) if ix==ix]
x, y = [v[0] for v in pos], [v[1] for v in pos]
plt.plot(x,y,'-',linewidth=2.,alpha=0.4,label=str(i))
plt.hold(False)
if legend: plt.legend(loc=0)
plt.title('traj2')
plt.show()
def watch_sim():
G = nx.complete_graph(40)
G.name = 'K%d'%G.number_of_nodes()
#G = nx.erdos_renyi_graph(20, 0.1)
#G.name = 'ER%d'%G.number_of_nodes()
#lam = 16.
#lam = 10
#lam = 1.
lam = 3
tau = 0.2
Kvals = dict([(node,npr.poisson(lam)) for node in G])
extentDummy,statuses = resMetrics.extentKFleeSIRSim_helper(G=G, startN=0, vaccinated=[], weighted=False, verbose=True,
params={'tau':tau, 'K':Kvals,})
pos = nx.drawing.layout.spring_layout(G, iterations=90)
uninfected_color = 'green' #'black'
infected_color = 'red'
contrarian_color = 'blue'
uninfected_nodes = []
infected_nodes = []
contrarian_nodes = []
for node in G:
status = statuses[node]
if 'UIF' in status:
uninfected_nodes.append(node)
elif 'INF' in status:
infected_nodes.append(node)
elif 'CON' in status:
contrarian_nodes.append(node)
else:
raise ValueError, 'unknown status'
reg_node_size = 200
pylab.figure()
pylab.hold(True)
nx.draw_networkx_nodes(G, pos=pos, nodelist=uninfected_nodes, node_color=uninfected_color, node_size=reg_node_size, alpha=0.4)
nx.draw_networkx_nodes(G, pos=pos, nodelist=infected_nodes, node_color=infected_color, node_size=reg_node_size, alpha=0.4)
nx.draw_networkx_nodes(G, pos=pos, nodelist=contrarian_nodes, node_color=contrarian_color, node_size=reg_node_size, alpha=0.4)
#nx.draw_networkx_edges(G, pos=pos, alpha=0.1)
nx.draw_networkx_labels(G, pos=pos, labels=statuses)
#pylab.grid(b=False)
pylab.axis('off')
#pylab.axes(frameon=False)
pylab.text(-0.2, -0.2, 'nn=%d, tau=%.2f, lam=%.1f'%(G.number_of_nodes(),tau,lam))
pylab.savefig('output/epidemic_final_tau=%.2f_lam=%.1f'%(tau,lam)+timeNow()+'.pdf')
