def day_plot(time_idx,
x,
title='',
step=1,
color='k',
scale_sig=True,
savefig=False):
if time_idx is 'default':
time_idx = list(range(len(x)))
plt.figure()
plt.rc('text', usetex=True)
for ri, row in enumerate(x):
current_step = ri * step
y = x[ri, :]
scaled = scale1(y)
shifted = scaled + current_step
if (x.shape[1] == len(time_idx)):
plt.plot(time_idx, shifted, color)
else:
plt.plot(shifted, color)
plt.ylim([-1, x.shape[0] * step])
plt.ylabel('Channels')
plt.xlabel('Time (s)')
plt.title(title)
plt.show()
if savefig:
plt.savefig('%s.pdf' % title)
plt.close()
def partial_autocorrelation(self):
plt.rc('font', family='serif', serif='Times')
plt.rc('text', usetex=True)
plt.rc('xtick', labelsize=8)
plt.rc('ytick', labelsize=8)
plt.rc('axes', labelsize=8)
# width as measured in inkscape
width = 2.987
height = width / 1.618
fig, ax = plt.subplots()
fig.subplots_adjust(left=.18, bottom=.19, right=.99, top=.97)
# Plot PACF:
lag_pacf = pacf(self.test, nlags=20, method='ols')
# plt.subplot(122)
plt.plot(lag_pacf)
plt.axhline(y=0, linestyle='--', color='gray')
plt.axhline(y=-1.96 / np.sqrt(len(self.test)),
linestyle='--',
color='gray')
plt.axhline(y=1.96 / np.sqrt(len(self.test)),
linestyle='--',
color='gray')
# plt.title('Partial Autocorrelation Function')
# ax.grid(zorder=0)
ax.set_ylabel('Partial Autocorrelation')
ax.set_xlabel('Lag')
fig.set_size_inches(width, height)
fig.savefig('partial.pdf')
def plot_barhist(df, y):
plt.rc('font', family='serif')
# matplotlib.rcParams['ps.useafm'] = True
# matplotlib.rcParams['pdf.use14corefonts'] = True
# matplotlib.rcParams['text.usetex'] = True
matplotlib.rcParams['pdf.fonttype'] = 42
col_order = _PROBLEMS
order = [rename_scheme(s) for s in _SCHEMES]
g = sns.catplot(x='scheme',
y=y,
col=None,
data=df,
kind='bar',
col_order=col_order,
order=order,
palette=sns.color_palette(['orangered'] * 4 +
['dodgerblue'] * 3))
g.set_xticklabels(rotation=30, ha='right')
plt.ylim(bottom=.75, top=1.)
locs, _ = plt.yticks()
labels = []
for l in locs:
labels.append('{:.0f}%'.format(l * 100.))
plt.yticks(locs, labels)
plt.tight_layout()
def FeaturesRelationsLoop(Relationships, Features):
"""Function to plot the correlations between the classifiers features
-Inputs:
Relationships: Features correlations
Features: Name of the feautures used, string."""
#Plotting
SMALL_SIZE = 17
MEDIUM_SIZE = 10
BIGGER_SIZE = 12
plt.rc('font', size=SMALL_SIZE) # controls default text sizes
plt.rc('axes', titlesize=SMALL_SIZE) # fontsize of the axes title
for n in range(4):
for m in range(3):
plt.subplots()
axes = plt.gca()
tempvar='subject' + str((m+1)+(n*3))
axes.set_xlim([0,Relationships[tempvar].shape[0]-1])
axes.set_ylim([0,Relationships[tempvar].shape[0]-1])
plt.grid()
plt.ylabel('EEG ' + Features + ' features')
plt.xlabel('EEG ' + Features + ' features')
plt.title('Subject ' + str((m+1)+(n*3)) + ' features correlation')
gra = plt.imshow(abs(Relationships[tempvar]), cmap='jet')
cbar = plt.colorbar(gra, ticks=[0, 1], orientation='vertical')
plt.show()
def plot_corr_btw_walc_n_dalc(df):
'''
Walc & Dalc
Also, we find the correlation coefficient between 'Walc' and 'Dalc' was high.
We used the bar chart to visualize their distribution,
and found although both Walc and Dalc had an increase pattern,
the distribution seemed to be a little different.
After level 2, the Dalc dropped dramatically than Walc.
Therefore, we chose to keep both variables.
'''
fname = 'corr_btw_walc_n_dalc.png'
print('(2) Save ' + fname + ': correlation between walc and dalc\n')\
# Bar charts of Walc & Dalc
plt.rc('figure', figsize=(10, 5))
fig = plt.figure()
ax1 = fig.add_subplot(1, 2, 1)
walc = df['Walc'].value_counts()
walc = pd.DataFrame(walc)
ax1.set_title('Weekly Alchocol Consumption Distribution')
plt.ylabel('Count of Walc')
plt.xlabel('Walc')
ax1.bar(walc.index, walc['Walc'], color='Brown')
ax2 = fig.add_subplot(1, 2, 2)
dalc = df['Dalc'].value_counts()
dalc = pd.DataFrame(dalc)
ax2.set_title('Daily Alchocol Consumption Distribution')
plt.ylabel('Count of Dalc')
plt.xlabel('Dalc')
ax2.bar(dalc.index, dalc['Dalc'], color='indianred')
plt.savefig(fname)
def plot_Scat_function_candidates(self):
allThetas = GetThetas.returnallThetas()
angles = np.arange(0, 179, 0.5)
val90 = self.Scat_function_value(500, 90)
SvalsNorm = [self.Scat_function_value(500, i) / val90 for i in angles]
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
plt.plot(angles, SvalsNorm, color='g')
plt.axvline(x=153.6, color='b')
plt.axvline(x=143.1, color='b')
plt.axvline(x=144.4, color='b')
plt.axvline(x=155.7, color='b')
plt.axvline(x=164, color='b', label='Candidates')
plt.axvline(x=48,
linestyle='dashed',
color='r',
label=r'Brightnest Known SNR LE Example')
#plt.axvspan(30,110,color='k',alpha=0.25,label='Observed LEs from Literature')
plt.hist(allThetas)
plt.xlabel(r'$\theta$', fontsize=20)
plt.ylabel(r'Scattering Efficiency (Norm. to 90$^o$)', fontsize=20)
plt.legend(loc='upper right', fontsize=16)
plt.yscale('log')
def display_TwoHopSchemes(two_hop_schemes, pathString):
'''
Produce a graph that compare ...
'''
self = two_hop_schemes
pylab.rc('axes', linewidth=2) # make the axes boundary lines bold
#fig, ax = plt.subplots()
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.7, 0.7]) # left, bottom, width, height (range 0 to 1)
rr.plot( self.region_CF_ICFsch3, 'red', lw=8, axes=ax, label='CF + ICF')
rr.plot( self.region_DFIntegerCoeff_FCo, 'c', lw=4, axes=ax, label='DF + FCo')
rr.plot( self.region_noInterference, 'blue', lw=2, axes=ax, label='Free Interf.')
fig.suptitle('$g ={},{},{},{}$'.format(self.g13, self.g14, self.g23, self.g24), fontsize=14, fontweight='bold')
ax.set_title(r'$P_s=P_1=P_2={}, \, P_3={}, \, P_4={}, \, N=1$'.format(self.Ps, self.P3, self.P4),fontdict=self.font)
ax.set_xlabel('$R_1$', fontdict=self.font)
ax.set_ylabel('$R_2$', fontdict=self.font)
#ax.set_xlim(xmin=0, xmax=3.5)
#ax.set_ylim(ymin=0, ymax=3.5)
ax.legend(loc=0)
# savefig.save(path='{}compare_TwoHop_Schemes/PsP3P4_{}_{}_{}_g_{}_{}_{}_{}'.format(pathString, self.Ps, self.P3, self.P4, self.g13, self.g14, self.g23, self.g24), ext='pdf', close=False, verbose=True)
nameStr = 'PsP3P4_{}_{}_{}_g13g14g23g24_{}_{}_{}_{}'.format(self.Ps, self.P3, self.P4, self.g13, self.g14, self.g23, self.g24)
savefig.save(path='{}compare_TwoHop_Schemes/{}'.format(pathString, nameStr), ext='pdf', close=False, verbose=True)
def plotpowerspectrum(t, y, t1, t2, Fs, fileprefix):
'''
plot powerspectrum of time-series data between t1 and t2 and save plot to .png file
'''
filename = fileprefix + '_powerspectrum.png'
# find indices for tlow, thigh
n1 = np.where(t>=t1)[0]
n2 = np.where(t>=t2)[0]
# calculate welch estimate of power spectrum
N = n2[0]-n1[0]+1;
seglength = np.int(N/8.)
f, P = scipy.signal.welch(y[n1[0]:n2[0]], fs=Fs, window='hanning', nperseg=seglength)
# plot power spectrum
plt.figure()
plt.rc('text', usetex=True)
plt.tick_params(labelsize=20)
plt.loglog(f, P, linewidth=2)
plt.xlabel('frequency (Hz)', size=22)
plt.ylabel('power spectral density (1/Hz)', size=22)
plt.grid(True)
plt.savefig(filename, bbox_inches='tight', dpi=400)
return
def plot_param_by_run(self, bins, h, lbl, logscale=False, ax=None):
#runs = np.linspace(self.runs[0]-0.5, self.runs[-1]+0.5, self.nrun+1)
runs = np.linspace(0.5, self.nrun + 0.5, self.nrun + 1)
hmn = np.min(h[h > 0])
hmn = 1e-4
y, x = np.meshgrid(runs, bins, indexing='ij')
plt.rc('text', usetex=True)
plt.rc('font', family='serif', size=16)
if ax is None:
fig = plt.figure(figsize=(16, 4))
ax = fig.gca()
cmap = plt.get_cmap()
cmap.set_bad(cmap(0))
ax.pcolor(x, y, h, norm=LogNorm(), vmin=hmn, cmap=cmap)
if logscale:
ax.set_xscale('log')
ax.set_ylim(self.nrun + 0.5, 0.5)
ax.set_xlabel(lbl)
ax.set_ylabel("run")
#ax.get_xaxis().set_major_formatter(LogFormatterExponent())
#ax.get_xaxis().set_minor_formatter(ScalarFormatter())
ax.set_yticks(runs[:-1] + 0.5)
ax.set_yticklabels(self.runs, fontsize=14)
def make_plot(path_input, path_graph, proc, name, x_val):
file = open(path_input)
i = 0
regret1 = []
regret2 = []
while i < MAX_VAL:
line = file.readline()
if not line:
break
regret1.append(float(line.split()[0]))
regret2.append(float(line.split()[1]))
i = i + 1
file.close()
if x_val == -1:
x_val = i
plt.rc('font', size=BIGGER_SIZE, family='serif')
plt.figure()
plt.title(proc + ': ' + name)
plt.xlim(1, x_val)
plt.xscale('log')
plt.plot(regret1, label='Jugador 1')
plt.plot(regret2, label='Jugador 2')
if (proc == 'A'):
plt.ylabel('Regret (max)')
plt.xlabel('Iteraciones')
plt.legend()
plt.subplots_adjust(bottom=0.15, left=0.15, right=0.85)
plt.savefig(path_graph)
return x_val
def display(oneSimulation,pathString, separate=False ,saveOnly=True):
'''
show/save figures
'''
self = oneSimulation
pylab.rc('axes', linewidth=2) # make the axes boundary lines bold
#fig, ax = plt.subplots()
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.7, 0.7]) # left, bottom, width, height (range 0 to 1)
if separate:
rr.plot( self.df_Region, 'red', lw=6, axes=ax, label='DF')
rr.plot( self.cf_Region, 'blue', lw=4, axes=ax, label='CF')
rr.plot( self.fco_Region, 'red', lw=6, axes=ax, label='DF')
rr.plot( self.icf_Region_bigR1, 'blue', lw=4, axes=ax, label='ICF')
rr.plot( self.icf_Region_bigR2, 'blue', lw=4, axes=ax)
rr.plot(self.df_fco_region, 'red', lw=6, label='DF+FCo')
rr.plot(self.cf_icf_region, 'blue', lw=4, label='CF+ICF')
fig.suptitle('$g ={},{},{},{}$'.format(self.g13, self.g14, self.g23, self.g24), fontsize=14, fontweight='bold')
ax.set_title(r'$P_s=P_1=P_2={}, \, P_3={}, \, P_4={}, \, N=1$'.format(self.Ps,
self.P3, self.P4),fontdict=self.font)
ax.set_xlabel('$R_1$', fontdict=self.font)
ax.set_ylabel('$R_2$', fontdict=self.font)
#ax.set_xlim(xmin=0, xmax=3.5)
#ax.set_ylim(ymin=0, ymax=3.5)
ax.legend(loc=0)
nameStr = 'PsP3P4_{}_{}_{}_g13g14g23g24_{}_{}_{}_{}'.format(self.Ps, self.P3, self.P4,
self.g13, self.g14, self.g23, self.g24)
savefig.save(path='{}/plots_CF_ICF__DF_FCo/{}'.format(pathString, nameStr), ext='pdf', close=saveOnly, verbose=True)
def Plotting_ROCcurve(events, fpr, tpr, roc_auc):
"""Function to plot the ROC curves and the area under the ROC curves
-Inputs:
events -> Name of the events of interst to classify
fpr -> False positive rate
tpr -> True positive rate
roc_auc -> ROC area under the curves """
#Plotting
SMALL_SIZE = 10
MEDIUM_SIZE = 15
BIGGER_SIZE = 12
plt.rc('font', size=MEDIUM_SIZE) # controls default text sizes
plt.rc('axes', titlesize=MEDIUM_SIZE) # fontsize of the axes title
plt.rc('xtick', labelsize=MEDIUM_SIZE) # fontsize of the axes title
plt.rc('ytick', labelsize=MEDIUM_SIZE) # fontsize of the axes title
plt.rc('legend', fontsize=SMALL_SIZE) # controls default text sizes
plt.figure()
lw = 2
for k in range(len(events)):
plt.plot(fpr[k], tpr[k], lw=lw, label='ROC curve ' + events[k] + ' (area = %0.2f)' % roc_auc[k])
plt.plot([0, 1], [0, 1], color='navy', lw=lw, linestyle='--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.0])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Receiver operating characteristic curves')
plt.legend(loc="lower right")
plt.show()
def makeAnimation(Simulation=None,
diagsXT=None,
fps=60,
repeat=True,
dx=50,
dt=60):
if Simulation == None:
return
if diagsXT == None:
from .diagXT import calcXTOnAllLinks
diagsXT = calcXTOnAllLinks(Simulation, dx, dt)
# get prj
NEWdiagsXT = getPointsProjection(Simulation, diagsXT)
fig = plt.figure(figsize=(9.6, 5.4), dpi=200, facecolor=[0.1, 0.1, 0.1])
#...
plt.rc('font', family='Cambria', size=6, style='normal', weight='light')
#...
# setup animation
ani = FuncAnimation(fig,
_plotTraficolorNetwork,
fargs=(NEWdiagsXT, ),
frames=diagsXT[list(diagsXT)[0]]["T"].shape[1],
interval=int(1000 / fps),
repeat=repeat)
return ani
def dynamic_range_main(folder_name_dict, plot_settings):
if not plot_settings['only_plot']:
plot_settings['savefolder_name'] = 'genotype_phenotype_plot_{}_{}' \
.format(time.strftime("%Y%m%d-%H%M%S"), plot_settings['varying_parameter'])
os.makedirs('save/{}'.format(plot_settings['savefolder_name']))
sim_data_list_each_folder = prepare_data(folder_name_dict,
plot_settings)
save_plot_data(sim_data_list_each_folder, plot_settings)
# Save settings:
settings_folder = 'save/{}/settings/'.format(
plot_settings['savefolder_name'])
save_settings(settings_folder, plot_settings)
else:
sim_data_list_each_folder = load_plot_data(
plot_settings['only_plot_folder_name'])
plot_settings['savefolder_name'] = plot_settings[
'only_plot_folder_name']
# if plot_settings['load_dynamic_range_parameter'] or not plot_settings['only_plot']:
# sim_data_list_each_folder = load_dynamic_range_parameter(sim_data_list_each_folder, plot_settings)
# save_plot_data(sim_data_list_each_folder, plot_settings)
plot_axis(sim_data_list_each_folder, plot_settings)
font = {'family': 'serif', 'size': 32, 'serif': ['computer modern roman']}
plt.rc('font', **font)
def plot_transition_ratio(df1, df2):
"""
plot stage transitions
df1: normal sleep (df1 = analyse(base))
df2: sleep depravation (df2 = analyse(depr))
"""
N = 5
ind = np.arange(N) # the x locations for the groups
width = 0.2 # he width of the bars
plt.close()
plt.rc('font', family='Arial')
fig, ax = plt.subplots(nrows=6, ncols=6, sharex='col', sharey='row')
fig.suptitle("Comparison of the number of stage transitions (% of total transitions) (origin stage " + u'\u2192' + " dest. stage)", fontsize=20)
plt.subplots_adjust(wspace = 0.2,hspace = 0.4 )
for i in range(0,6): # do not care about stage transitions > 5
for j in range(0,6):
clef = '%t' + str(i) + '-' + str(j)
normal = df1[clef].tolist()
mean = sum(normal) / len(normal)
normal.extend([mean])
rects1 = ax[i,j].bar(ind, normal, width, color='b')
depravation = df2[clef].tolist()
mean = sum(depravation) / len(depravation)
depravation.extend([mean])
rects2 = ax[i,j].bar(ind+width, depravation, width, color='r')
for label in (ax[i,j].get_xticklabels() + ax[i,j].get_yticklabels()):
label.set_fontname('Arial')
label.set_fontsize(8)
ax[i,j].set_title(str(i) + ' ' + u'\u2192' + ' ' + str(j))
ax[i,j].set_xticks(ind+width)
ax[i,j].set_xticklabels( ('1', '2', '3', '4', 'Avg') )
ax[i,j].set_yticks(np.arange(0, 6, 2))
ax[i,j].set_ylim([0,6])
fig.legend( (rects1[0], rects2[0]), ('Baseline', 'Recovery'), loc = 'lower right', fontsize=10)
def plotsignalsignalnoisetimeseries(t, s1, s2, d, t1, t2, fileprefix):
'''
plot two signal components and data between t1 and t2 and save plot to .png file
'''
filename = fileprefix + '.png'
# find indices for tlow, thigh
n1 = np.where(t >= t1)[0]
n2 = np.where(t >= t2)[0]
plt.figure()
plt.rc('text', usetex=True)
plt.tick_params(labelsize=20)
plt.plot(t[n1[0]:n2[0]], d[n1[0]:n2[0]], color='k')
plt.plot(t[n1[0]:n2[0]], s1[n1[0]:n2[0]], color='r')
plt.plot(t[n1[0]:n2[0]], s2[n1[0]:n2[0]], color='g')
# set symmetric ylimits if both positive and negative
axes = plt.gca()
y1, y2 = axes.get_ylim()
if y1 < 0. and y2 > 0.:
ymin = -max(np.abs(y1), np.abs(y2))
ymax = max(np.abs(y1), np.abs(y2))
axes.set_ylim([ymin, ymax])
plt.xlabel('time (s)', size=22)
plt.ylabel('data', size=22)
plt.legend(['data', 'signal 1', 'signal 2'])
plt.savefig(filename, bbox_inches='tight', dpi=400)
return
def plot_scattering_function_for_obsangles(self, obsangle1, obsangle2,
obsangle3, obsangle4, obsangle5,
obsangle6, obsangle7, tmin,
tmax, step):
tvals = np.arange(tmin, tmax, step)
plt.figure(figsize=(6, 6))
plt.rc('axes', linewidth=2)
plt.plot(tvals,
self.scattering_function(obsangle1, tmin, tmax, step)[0],
label=r'Obs Angle =%s$^o$' % obsangle1)
plt.plot(tvals,
self.scattering_function(obsangle2, tmin, tmax, step)[0],
label=r'Obs Angle =%s$^o$' % obsangle2)
plt.plot(tvals,
self.scattering_function(obsangle3, tmin, tmax, step)[0],
label=r'Obs Angle =%s$^o$' % obsangle3)
plt.plot(tvals,
self.scattering_function(obsangle4, tmin, tmax, step)[0],
label=r'Obs Angle =%s$^o$' % obsangle4)
plt.plot(tvals,
self.scattering_function(obsangle5, tmin, tmax, step)[0],
label=r'Obs Angle =%s$^o$' % obsangle5)
plt.plot(tvals,
self.scattering_function(obsangle6, tmin, tmax, step)[0],
label=r'Obs Angle =%s$^o$' % obsangle6)
plt.plot(tvals,
self.scattering_function(obsangle7, tmin, tmax, step)[0],
label=r'Obs Angle =%s$^o$' % obsangle7)
plt.xlabel('Age', fontsize=18)
plt.ylabel('Vega Magnitude / arcsec^2', fontsize=18)
plt.tight_layout()
plt.legend()
def plot_corr_btw_fedu_n_medu(df):
'''
FEdu & Medu
In this correlation chart, we find the correlation efficient between 'Fedu' and 'Medu' was high,
and we can take a closer look at the reltionship.
From the following bar chart, we can see Father's education had a different distribution compared to mother's education.
Most father's education were 2, while mothers tended to have higher education level.
Therefore, we choose to keep both FEdu and MEdu.
'''
fname = 'corr_btw_fedu_n_medu.png'
print('(1) Save ' + fname + ': correlation between FEdu and Medu\n')\
# Bar charts of FEdu & Medu
plt.rc('figure', figsize=(10, 5))
fig = plt.figure()
ax1 = fig.add_subplot(1, 2, 1)
fedu = df['Fedu'].value_counts()
fedu = pd.DataFrame(fedu)
ax1.set_title('Father\'s Education Distribution')
plt.ylabel('count of Fedu')
plt.xlabel('Fedu')
ax1.bar(fedu.index, fedu['Fedu'], color='cornflowerblue')
ax2 = fig.add_subplot(1, 2, 2)
medu = df['Medu'].value_counts()
medu = pd.DataFrame(medu)
ax2.set_title('Mother\'s Education Distribution')
plt.ylabel('count of Medu')
plt.xlabel('Medu')
ax2.bar(medu.index, medu['Medu'], color='pink')
plt.savefig(fname)
def plothistogram(t, y, t1, t2, fileprefix):
'''
plot histogram of time-series data between t1 and t2 and save plot to .png file
'''
filename = fileprefix + '_hist.png'
# find indices for tlow, thigh
n1 = np.where(t>=t1)[0]
n2 = np.where(t>=t2)[0]
# histogram and best fit gaussian of h
(mu, sigma) = norm.fit(y[n1[0]:n2[0]])
plt.figure()
plt.rc('text', usetex=True)
plt.tick_params(labelsize=20)
n, bins, patches = plt.hist(y[n1[0]:n2[0]], bins=50, normed='true')
z = mlab.normpdf(bins, mu, sigma)
l = plt.plot(bins, z, 'r--', linewidth=2)
plt.xlabel('data', size=22)
plt.savefig(filename, bbox_inches='tight', dpi=400)
return
def run_demo():
plt.rc('font', size=25)
fig,axes = plt.subplots(2,3)
alphas = [1.,5.,10.]
linear_spaced = get_linear_spaced()
axes[0,0].set_ylabel("Unnormalized")
axes[1,0].set_ylabel("Normalized")
lines = []
for index in range(len(alphas)):
alpha = alphas[index]
current_normalizer = quadrature_normalizer(alpha)
standard = target(alpha, linear_spaced)
normalized = standard / current_normalizer
laplace_normalized, laplace_raw = laplace_approx(alpha, linear_spaced)
if index==0:
lines = lines + axes[0,index].plot( linear_spaced, standard, 'b', label = 'Exact')
lines = lines + axes[0,index].plot( linear_spaced, laplace_raw, 'g', label = 'Laplace')
else:
axes[0,index].plot( linear_spaced, standard, 'b')
axes[0,index].plot( linear_spaced, laplace_raw, 'g')
axes[0,index].set_title('Alpha = '+str(alpha))
axes[1,index].plot( linear_spaced, normalized, 'b')
axes[1,index].plot( linear_spaced, laplace_normalized, 'g')
axes[1,index].set_ylim( [0.,2.21])
plt.subplots_adjust(right=0.7)
plt.legend( handles = lines, loc= 7, bbox_to_anchor=(1.75, 1.1) )
plt.show()
def triage(par, weights, parnames, figsize=[5,5], nbins = 30, figname=None, fontsize=8):
npar = np.size(par[1,:])
f, ax = plt.subplots(npar, npar, figsize=(figsize), sharex='col')
# f, ax = plt.subplots(figsize=(10,10), sharex='col', sharey='row')
plt.rc('font',size=fontsize)
for h,v in it.product(range(npar), range(npar)) :
if v < h :
hvals, xedges, yedges = np.histogram2d(par[:,v], par[:,h], weights=weights[:,0], bins = nbins)
hvals = np.rot90(hvals)
hvals = np.flipud(hvals)
Hmasked = np.ma.masked_where(hvals==0, hvals)
hvals = hvals / np.sum(hvals)
X,Y = np.meshgrid(xedges,yedges)
sig1 = opt.brentq( conf_interval, 0., 1., args=(hvals,0.683) )
sig2 = opt.brentq( conf_interval, 0., 1., args=(hvals,0.953) )
sig3 = opt.brentq( conf_interval, 0., 1., args=(hvals,0.997) )
lvls = [sig3, sig2, sig1]
ax[h,v].pcolor(X, Y, (Hmasked), cmap=plt.cm.BuPu, norm = LogNorm())
ax[h,v].contour(hvals, linewidths=(1.0, 0.5, 0.25), colors='lavender', levels = lvls, norm = LogNorm(), extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]])
if v > 0:
ax[h,v].get_yaxis().set_ticklabels([])
elif v == h :
ax[h,v].hist(par[:,h],bins = nbins,color='mediumslateblue',histtype='step',lw=1.5)
ax[h,v].yaxis.tick_right()
ax[h,v].get_yticklabels()
conf_lims = np.percentile(par[:,h], [2.5, 16, 50, 84, 97.5])
hmean = np.mean(par[:,h])
hstd = np.std(par[:,h])
print(parnames[h] + '\t%.3f +- %.3f'%(hmean, hstd)+ '; [2.5, 16, 50, 84, 97.5] %-tiles: ' + ' '.join(['%.3f'%(p) for p in conf_lims]))
#textable.write( parnames[h] + ' & %.4f & %.4f'%(hmean, hstd)+ ' & ' + ' & '.join(['%.4f'%(p) for p in conf_lims]) + '\\\\\n')
#for i in range(len(conf_lims)) : ax[h,v].axvline(conf_lims[i], color='lavender', lw = (3. - np.abs(2-i))/2. )
else :
ax[h,v].axis('off')
if v == 0:
ax[h,v].set_ylabel(parnames[h])
ax[h,v].get_yaxis().set_label_coords(-0.35,0.5)
if h == npar-1:
ax[h,v].set_xlabel(parnames[v])
ax[h,v].get_xaxis().set_label_coords(0.5,-0.35)
labels = ax[h,v].get_xticklabels()
for label in labels:
label.set_rotation(90)
plt.tight_layout(pad=1.5, w_pad=-4, h_pad=-0.6)
if figname:
plt.savefig(figname, bbox_inches='tight')
def display70(oneSimulation,pathString, separate=False ,saveOnly=True):
'''
show/save figures
'''
self = oneSimulation
tmp = np.asarray(oneSimulation.cf_icf01_region._geometry.boundary)
tmp01= tmp[(0,1,3), :]
tmp = np.asarray(oneSimulation.cf_icf_region._geometry.boundary)
tmp03= tmp[(1,2,3,4), :]
tmp = np.asarray(oneSimulation.df_fco_region._geometry.boundary)
tmpDF = tmp[(0,1,2,3), :]
pylab.rc('axes', linewidth=2) # make the axes boundary lines bold
# fig, ax = plt.subplots()
fig = plt.figure()
fig.set( size_inches=(8.8, 6) )
ax = fig.add_axes([0.1, 0.1, 0.7, 0.7]) # left, bottom, width, height (range 0 to 1)
# if separate:
# rr.plot( self.df_region, 'red', lw=6, axes=ax, label='DF')
# rr.plot( self.cf_region, 'blue', lw=4, axes=ax, label='CF')
# rr.plot( self.fco_region, 'red', lw=6, axes=ax, label='DF')
# rr.plot( self.icf_region_bigR1, 'blue', lw=4, axes=ax, label='ICF')
# rr.plot( self.icf_region_bigR2, 'blue', lw=4, axes=ax)
# rr.plot(self.df_fco_region, 'blue', lw=6, label='DF+FCo')
# rr.plot(self.cf_icf_region, 'red', lw=4, label='CF+ICF Scheme 3')
# rr.plot(self.cf_icf01_region, 'green', lw=2, label='CF+ICF Scheme 1' )
ax.plot(tmpDF[:,0], tmpDF[:,1], 'blue', lw=6, label='DF+FCo')
ax.plot(tmp03[:,0], tmp03[:,1], 'red', lw=4, label='CF+ICF Scheme 3')
ax.plot(tmp01[:,0], tmp01[:,1], 'green', lw=2, label='CF+ICF Scheme 1' )
# fig.suptitle('$g ={},{},{},{}$'.format(self.g13, self.g14, self.g23, self.g24), fontsize=14, fontweight='bold')
ax.set_title(r'$P_s=P_1=P_2={}, \, P_3={}, \, P_4={}, \, N=1$'.format(self.Ps,
self.P3, self.P4),fontdict=self.font)
ax.set_xlabel('$R_1$', fontdict=self.font)
ax.set_ylabel('$R_2$', fontdict=self.font)
#ax.set_xlim(xmin=0, xmax=3.5)
#ax.set_ylim(ymin=0, ymax=3.5)
ax.legend(loc=0)
nameStr = 'PsP3P4_{}_{}_{}_g13g14g23g24_{}_{}_{}_{}'.format(self.Ps, self.P3, self.P4,
self.g13, self.g14, self.g23, self.g24)
savefig.save(path='{}/plots_CF_ICF03__CF_ICF01__DF_FCo/{}'.format(pathString, nameStr), ext='pdf', close=saveOnly, verbose=True)
def newCreateAndSaveMultilineFig(xDataList, yDataList, xLabel="", yLabel="",
figFileRoot="", fileExt='.png', xMin=0,
xMax=0, yMin=0, yMax=0, legendFlag=1,
legendFont=12, traceNameList=[],
legLoc=(0, 0)):
"""This subroutine saves a figure with multiple lines."""
figFileName = figFileRoot + fileExt
colorDict = createColorDictWithDashes()
if xMax == 0:
curMax = 0
for n in range(0, len(xDataList)):
if type(xDataList[n]) == list:
if max(xDataList[n]) > curMax:
curMax = max(xDataList[n])
else:
if xDataList[n].any() > curMax:
curMax = max(xDataList[n])
xMax = curMax
if yMax == 0:
curMax = 0
for n in range(0, len(yDataList)):
if type(yDataList[n]) == list:
if max(yDataList[n]) > curMax:
curMax = max(yDataList[n])
else:
if yDataList[n].any() > curMax:
curMax = max(yDataList[n])
yMax = curMax
plt.axes([0.1, 0.1, 0.71, 0.8])
if traceNameList == []:
for n in range(0, len(xDataList)):
traceNameList.append("Trace_" + str(n))
for n in range(0, len(xDataList)):
xData = convert_list_to_array(xDataList[n])
yData = convert_list_to_array(yDataList[n])
tempPlot = plt.plot(
xData, yData, colorDict[str(n + 1)], hold="True",
label=traceNameList[n])
plt.xlabel(xLabel)
plt.ylabel(yLabel)
plt.xlim(xMin, xMax)
plt.ylim(yMin, yMax)
plt.rc("legend", fontsize=legendFont)
if legendFlag == 1:
if legLoc != (0, 0):
print(legLoc)
plt.legend(loc=legLoc)
else:
plt.legend()
plt.savefig(figFileName, dpi=300)
plt.clf()
def __init__(self, model_name):
""" Inits SimulationPlotter with loading the simulation results. """
# Load the data of the simulation results.
self.__save_dir = 'models/' + model_name + '/simulation_result/'
self.__file_header = self.__save_dir + model_name
self.__state_data = np.genfromtxt(self.__file_header + '_state' +
'.dat')
self.__control_input_data = np.genfromtxt(self.__file_header +
'_control_input' + '.dat')
self.__error_data = np.genfromtxt(self.__file_header + '_error' +
'.dat')
self.__sim_conditions = simcon.SimulationConditions(self.__file_header)
self.__time_sequence = np.linspace(
0, self.__sim_conditions.simulation_time(),
self.__state_data.shape[0])
# Replace NaN with 0.
self.__state_data[np.isnan(self.__state_data)] = 0
self.__control_input_data[np.isnan(self.__control_input_data)] = 0
self.__error_data[np.isnan(self.__error_data)] = 0
# Set dimensions of the state and the control input.
if self.__state_data.shape[0] == self.__state_data.size:
self.__dim_state = 1
else:
self.__dim_state = self.__state_data.shape[1]
if self.__control_input_data.shape[
0] == self.__control_input_data.size:
self.__dim_control_input = 1
else:
self.__dim_control_input = self.__control_input_data.shape[1]
# Set the layout of the graphs.
self.__num_plots = self.__dim_state + self.__dim_control_input + 1
self.__num_plot_x = int(
np.floor(self.__num_plots / np.sqrt(self.__num_plots)))
self.__num_plot_y = int(np.ceil(self.__num_plots / self.__num_plot_x))
# Set default figure scales.
self.__figure_scale = 1
self.__font_scale = 1
self.__space_scale = 1
# Set format of the graphs.
sns.set_style("ticks")
sns.set_palette("deep")
sns.set_context("paper")
plt.rc(
'mathtext', **{
'rm': 'serif',
'it': 'serif:itelic',
'bf': 'serif:bold',
'fontset': 'cm'
})
plt.rcParams['xtick.direction'] = 'in'
plt.rcParams['ytick.direction'] = 'in'
plt.rcParams['pdf.fonttype'] = 42
plt.rcParams['ps.fonttype'] = 42
# Set the width of lines and axes.
plt.rcParams['lines.linewidth'] = 1
plt.rcParams['axes.linewidth'] = 0.5
def show_cavity_step(title):
plt.title(title, fontsize=40, y=1.02)
plt.xlabel('Time [s]', fontsize=30)
plt.ylabel(r'$| \vec V_{\rm acc}|$ [V]', fontsize=30)
plt.ticklabel_format(style='sci', axis='y', scilimits=(1, 0))
plt.rc('font', **{'size': 20})
plt.legend(loc='upper right')
plt.show()
def plot_many_thetas(self, theta1, theta2, theta3, tmin, tmax, step):
plt.figure(figsize=(6, 6))
plt.rc('axes', linewidth=2)
self.plot_mags_vs_age(theta1, tmin, tmax, step)
self.plot_mags_vs_age(theta2, tmin, tmax, step)
self.plot_mags_vs_age(theta3, tmin, tmax, step)
plt.xlabel('Age', fontsize=18)
plt.ylabel('Vega Magnitude / arcsec^2', fontsize=18)
plt.tight_layout()
plt.legend()
def plot_z_vs_obsangle_for_given_age(self, t1, t2, t3, t4, t5, t6, t7,
obsanglemin, obsanglemax, step):
obsangles = np.arange(obsanglemin, obsanglemax, step)
plt.figure(figsize=(6, 6))
plt.rc('axes', linewidth=2)
plt.plot(obsangles,
self.get_SB_vs_obsangle_for_given_age(t1, obsanglemin,
obsanglemax, step)[5],
color='r',
label='%s yrs' % t1)
plt.plot(obsangles,
self.get_SB_vs_obsangle_for_given_age(t2, obsanglemin,
obsanglemax, step)[5],
color='orange',
label='%s yrs' % t2)
plt.plot(obsangles,
self.get_SB_vs_obsangle_for_given_age(t3, obsanglemin,
obsanglemax, step)[5],
color='y',
label='%s yrs' % t3)
plt.plot(obsangles,
self.get_SB_vs_obsangle_for_given_age(t4, obsanglemin,
obsanglemax, step)[5],
color='g',
label='%s yrs' % t4)
plt.plot(obsangles,
self.get_SB_vs_obsangle_for_given_age(t5, obsanglemin,
obsanglemax, step)[5],
color='b',
label='%s yrs' % t5)
plt.plot(obsangles,
self.get_SB_vs_obsangle_for_given_age(t6, obsanglemin,
obsanglemax, step)[5],
color='purple',
label='%s yrs' % t6)
plt.plot(obsangles,
self.get_SB_vs_obsangle_for_given_age(t7, obsanglemin,
obsanglemax, step)[5],
color='m',
label='%s yrs' % t7)
#plt.axhline(y=1630,linestyle='--',color='k',label='Edge of LMC')
#plt.axhline(y=-1630,linestyle='--',color='k')
plt.axhspan(-1630,
1630,
color='skyblue',
alpha=0.5,
label='Thickness of LMC')
#plt.axhline(y=2000,linestyle='-.',color='k',label='Edge of 30 Dor')
plt.xlabel('Observed Angular Separation', fontsize=18)
plt.ylabel('z (lyrs)', fontsize=18)
plt.tight_layout()
plt.legend(loc='upper left', prop={'size': 15})
def font_setup(size=13, weight='normal', family='serif', color='None'):
''' Set-up font for Matplotlib plots
'family':'Times New Roman','weight':'heavy','size': 18
'''
import matplotlib.pylab as plt
font = {'family': family, 'weight': weight, 'size': size}
plt.rc('font', **font)
plt.rcParams.update({
'mathtext.default': 'regular',
'figure.facecolor': color,
})
def init_plot_parameter(self):
#--- A4 landscape
plt.rc('figure', figsize=self.figsize, autolayout=True)
plt.rcParams.update({'font.size': self.fontsize})
plt.subplots_adjust(left=0.1,
right=0.95,
bottom=0.05,
top=0.95,
hspace=0.35)
plt.rcParams['savefig.facecolor'] = "0.9"
if not self.fig_nr:
self.fig_nr = 1
def font_setup(size=13, weight="normal", family="serif", color="None"):
""" Set-up font for Matplotlib plots
'family':'Times New Roman','weight':'heavy','size': 18
"""
import matplotlib.pylab as plt
font = {"family": family, "weight": weight, "size": size}
plt.rc("font", **font)
plt.rcParams.update({
"mathtext.default": "regular",
"figure.facecolor": color,
})
def plot_visibility(ts, target_alts, sun_alts, hrs_visible_per_night, min_alt):
"""Function to plot a chart of the target and solar altitude above the
horizon at the LSST site as a function of time"""
ts = np.array(ts)
target_alts = np.array(target_alts)
(fig, ax1) = plt.subplots(figsize=(10, 10))
plt.rcParams.update({'font.size': 18})
plt.rc('xtick', labelsize=18)
plt.rc('ytick', labelsize=18)
plt.xticks(rotation=45.0)
idx = np.where(target_alts > -1e5)
ax1.plot((ts - 2450000)[idx],
target_alts[idx],
'b-',
label='Target altitude')
ax1.set_xlabel('JD')
ax1.set_ylabel('Maximum altitude [$^{\circ}$]', color='b')
ax1.xaxis.label.set_fontsize(18)
ax1.yaxis.label.set_fontsize(18)
for label in ax1.get_xticklabels():
label.set_fontsize(18)
for label in ax1.get_yticklabels():
label.set_fontsize(18)
t = [(ts - 2450000).min(), (ts - 2450000).max()]
ax1.plot(t, [min_alt] * len(t), 'g-.')
ax1.grid(True)
ax1.tick_params('y', colors='b')
ax2 = ax1.twinx()
ax2.plot(ts - 2450000,
hrs_visible_per_night,
'm--',
label='Time target visible')
ax2.set_ylabel('Hours per night', color='m')
ax2.yaxis.label.set_fontsize(18)
ax2.grid(False)
ax2.tick_params('y', colors='m')
fig.tight_layout()
plt.legend()
plt.savefig('target_visibility_from_lsst.png')
plt.close()
def violin_plot(ax, values_list, measure_name, group_names, fontsize, color='blue', ttest=False):
'''
This is a little wrapper around the statsmodels violinplot code
so that it looks nice :)
'''
# IMPORTS
import matplotlib.pylab as plt
import statsmodels.api as sm
import numpy as np
# Make your violin plot from the values_list
# Don't show the box plot because it looks a mess to be honest
# we're going to overlay a boxplot on top afterwards
plt.sca(ax)
# Adjust the font size
font = { 'size' : fontsize}
plt.rc('font', **font)
max_value = np.max(np.concatenate(values_list))
min_value = np.min(np.concatenate(values_list))
vp = sm.graphics.violinplot(values_list,
ax = ax,
labels = group_names,
show_boxplot=False,
plot_opts = { 'violin_fc':color ,
'cutoff': True,
'cutoff_val': max_value,
'cutoff_type': 'abs'})
# Now plot the boxplot on top
bp = plt.boxplot(values_list, sym='x')
for key in bp.keys():
plt.setp(bp[key], color='black', lw=fontsize/10)
# Adjust the power limits so that you use scientific notation on the y axis
plt.ticklabel_format(style='sci', axis='y')
ax.yaxis.major.formatter.set_powerlimits((-3,3))
plt.tick_params(axis='both', which='major', labelsize=fontsize)
# Add the y label
plt.ylabel(measure_name, fontsize=fontsize)
# And now turn off the major ticks on the y-axis
for t in ax.yaxis.get_major_ticks():
t.tick1On = False
t.tick2On = False
return ax
def plot_run_correlation(self, C, ticks=None, lbl="", ax=None):
ny, nx = C.shape
i = np.linspace(0.5, ny + 0.5, ny + 1)
j = np.linspace(0.5, nx + 0.5, nx + 1)
if ticks is None:
tx = range(1, nx + 1)
ty = range(1, ny + 1)
elif isinstance(ticks, tuple):
tx, ty = ticks[0], ticks[1]
else:
tx, ty = ticks, ticks
if isinstance(lbl, tuple):
lx, ly = lbl[0], lbl[1]
else:
lx, ly = lbl, lbl
#runs = np.linspace(self.runs[0]-0.5, self.runs[-1]+0.5, self.nrun+1)
plt.rc('text', usetex=True)
plt.rc('font', family='serif', size=16)
if ax is None:
fig = plt.figure(figsize=(8, 8))
ax = fig.gca()
x, y = np.meshgrid(j, i, indexing='ij')
im = ax.pcolor(x, y, C, vmin=0, vmax=1)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.1)
plt.colorbar(im, ax=ax, cax=cax)
ax.set_ylim(i[-1], i[0])
ax.set_xlim(j[0], j[-1])
ax.set_yticks(i[:-1] + 0.5)
ax.set_yticklabels(ty, fontsize=14)
ax.set_xticks(j[:-1] + 0.5)
ax.set_xticklabels(tx, fontsize=14)
ax.tick_params("x",
labelrotation=90,
bottom=False,
top=True,
labelbottom=False,
labeltop=True)
ax.set_xlabel(lx)
ax.set_ylabel(ly)
ax.set_aspect("equal")
def disp(m):
fig, ax = plt.subplots()
ax.matshow(m, cmap=plt.get_cmap('Set3'))
for i in range(m.shape[0]):
for j in range(m.shape[0]):
c = m[j, i]
if c > 0:
ax.text(i, j, str(c), va='center', ha='center', color='black')
plt.rc('font', size=30)
plt.axis('off')
#ax.set_axis_off()
fig.set_size_inches(3, 3)
plt.show()
def p_plot(p_values, intervals, start=0, end=1):
plt.close()
with sns.axes_style("white", {"legend.frameon": True}):
plt.rc("font", weight="bold")
plt.rc("grid", lw=3)
plt.rc("lines", lw=2)
plt.rc("axes", lw=2)
styles = ["--", "-."]
for idx, interval in enumerate(intervals):
p = p_values[:, :, idx, idx].flatten()
p = p[~np.isnan(p)]
p = np.sort(p)
x = np.concatenate([[0], p, [1]])
y = np.concatenate([[0],
(np.arange(p.shape[0]) + 1.0) / p.shape[0],
[1]])
plt.plot(
x,
y,
label="[{},{}]".format(50 - interval, 50 + interval),
lw=2,
ls=styles[idx // 6],
)
plt.plot([0, 1], [0, 1],
color="black",
ls="--",
lw=3,
label="U(0,1)",
alpha=0.7)
plt.xlim([start, end])
plt.ylim([start, end])
plt.xlabel("p-value", fontsize=18, weight="bold")
plt.ylabel("Empirical CDF", fontsize=18, weight="bold")
plt.legend(loc="upper left", ncol=2)
def chi_squared_stats(self, plot_chisq=False):
"""
Compute chi^2 statistics for an X^2 distribution.
This is essentially a chi^2 test for normality being
computed on residual from the fit. I'll rewrite it
into a chi^2 goodness of fit test when I'll get around
to it.
Returns
-------
prob_chisq : probability that X^2 obeys the chi^2 distribution
dof : degrees of freedom for chi^2
"""
# ------------------- TODO --------------------- #
# rewrite it to a real chi-square goodness of fit!
# this is essentially a chi^2 test for normality
from scipy.stats import chisqprob
# TODO: for Pearson's chisq test it would be
# dof = self.xarr.size - self.specfit.fitter.npars - 1
# NOTE: likelihood function should asymptotically approach
# chi^2 distribution too! Given that the whole point
# of calculating chi^2 is to use it for model
# selection I should probably switch to it.
# TODO: derive an expression for this "Astronomer's X^2" dof.
dof = self.xarr.size
prob_chisq = chisqprob(self.chi_squared, dof)
# NOTE: for some reason get_modelcube returns zeros for some
# pixels even if corresponding Cube.parcube[:,y,x] is NaN
prob_chisq[np.isnan(self.parcube.min(axis=0))] = np.nan
if plot_chisq:
if not plt.rcParams['text.usetex']:
plt.rc('text', usetex=True)
if self.mapplot.figure is None:
self.mapplot()
self.mapplot.plane = prob_chisq
self.mapplot(estimator=None, cmap='viridis', vmin=0, vmax=1)
labtxt = r'$\chi^2\mathrm{~probability~(%i~d.o.f.)}$' % dof
self.mapplot.FITSFigure.colorbar.set_axis_label_text(labtxt)
plt.show()
self.prob_chisq = prob_chisq
return prob_chisq, dof
def plot(self):
name = self.get_tag()
Y_list = self.get_geom().get_XYZ()[1,:]
plt.xlim(1.1*Y_list[0], 1.1*Y_list[-1])
plt.xlabel('y')
plt.ylabel('gamma')
plt.plot(Y_list,self.__gamma)
plt.rc("font", size=14)
plt.savefig(name+"_gamma_distrib.png",format='png')
plt.close()
plt.xlim(1.1*Y_list[0], 1.1*Y_list[-1])
plt.xlabel('y')
plt.ylabel('iAoA')
plt.plot(Y_list,self.__iAoA*self.RAD_TO_DEG)
plt.rc("font", size=14)
plt.savefig(name+"_iAoA_distrib.png",format='png')
plt.close()
def AxisFormat(FONTSIZE = 22, TickSize = 10, TickDirection = 'out'):
"""
Format axes to standard design.
:param FONTSIZE: desired fontsize of all fonts.
:type FONTSIZE: int
:param TickSize: size of ticks in pxls.
:type TickSize: int
:param TickDirection: decide whether to plot ticks in or out
:type TickDirection: str
:returns: altered axes.
.. note::
* This function should work if called prior to plot input.
**Usage**
.. code-block:: python
:emphasize-lines: 3
fig = plt.figure(figsize=(8,6))
ax = fig.add_subplot(111)
pf.AxisFormat()
ax.plot(np.arange(0,100), np.arange(0,100), 'b-', linewidth =2)
plt.tight_layout()
plt.show()
**Exmaple**
*simple plot without AxisFormat call*
.. plot:: pyplots/AxisFormatDemo1.py
:include-source:
*simple plotnwith AxisFormat call*
.. plot:: pyplots/AxisFormatDemo2.py
:include-source:
"""
font = {'weight': 'norm', 'size': FONTSIZE}
legend = {'frameon': False}
ticks = {'direction': TickDirection, 'major.size': TickSize,
'minor.size': TickSize - 2}
plt.rc('font', **font)
plt.rc('legend', **legend)
plt.rc('xtick', **ticks)
plt.rc('ytick', **ticks)
def __init__(self):
"""
"""
fig = plt.figure(facecolor = 'w', figsize = [12, 12])
fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
ax1 = fig.add_subplot(1, 1, 1, aspect='equal')
self.t = np.arange(0, len(Nodes['age']))
self.x = xx[self.t]
self.y = yy[self.t]
self.age = Nodes['age'][self.t]
plot_eye(Nodes,ax1)
ax1.set_xlabel('mm',fontsize=20)
ax1.set_ylabel('mm',fontsize=20)
self.line1 = Line2D([], [], color='red', linewidth=4)
self.line1e = Line2D([], [], color='red', marker='o', markeredgecolor='r', markersize=10)
self.text = ax1.text(0.05, 0.05, 'Age: %s'%self.age[0] , fontsize=18, animated = True,
transform=ax1.transAxes)
ax1.add_line(self.line1)
ax1.add_line(self.line1e)
ax1.set_xlim(-14, 14)
ax1.set_ylim(-14, 14)
ax1.set_title('eye growth simulation',fontsize=20)
ax1.set_xticks([-10, -5, 0, 5, 10])
ax1.set_yticks([-10, -5, 0, 5, 10])
plt.rc('xtick', labelsize=20)
plt.rc('ytick', labelsize=20)
plt.tight_layout()
animation.TimedAnimation.__init__(self, fig, interval=10, blit=True)
def display(oneSimulation,pathString ,saveOnly=True):
'''
Produce a graph that compare three ICF schemes
'''
self = oneSimulation
# get the union rate region for plotting
icf_sch1 = rr.union( [self.icf_sch1_bigR1, self.icf_sch1_bigR2] )
icf_sch2 = rr.union( [self.icf_sch2_bigR1, self.icf_sch2_bigR2] )
icf_sch3 = rr.union( [self.icf_sch3_bigR1, self.icf_sch3_bigR2] )
pylab.rc('axes', linewidth=2) # make the axes boundary lines bold
fig, ax = plt.subplots()
rr.plot( icf_sch1, 'g', axes=ax, label='Scheme 1')
rr.plot( icf_sch2, 'b', axes=ax, label='Scheme 2')
rr.plot( icf_sch3, 'r', axes=ax, label='Scheme 3')
# plot the line: R2 = R1
tmp = np.asarray(self.icf_sch1_bigR1._geometry.boundary)
tmp2 = [[0, tmp[1, 0]], [0, tmp[1, 1] ] ]
ax.plot( [0, tmp[1, 0]], [0, tmp[1, 1] ] , 'k--', lw=2)
ax.set_title(r'$ P_3={}, \, P_4={}, \, N=1$'.format(self.P3, self.P4) , fontdict=self.font)
ax.set_xlabel('$R_1$', fontdict=self.font)
ax.set_ylabel('$R_2$', fontdict=self.font)
ax.set_xlim(xmin=0, xmax=3.5)
ax.set_ylim(ymin=0, ymax=3.5)
ax.legend(loc='upper right')
savefig.save(path='{}/compare_three_ICF_Schemes/P3P4_{}_{}'.format(pathString, self.P3, self.P4 ), ext='pdf', close=saveOnly, verbose=True)
if (0):
# add annotations for 3 regions
plt.text(0.7, 2.3, 'capacity region by coherent coding with cardinality-bounding', color='red')
plt.text(1, 1.8, 'non-coherent coding with cardinality-bounding', color='blue')
plt.text(1.3, 1.4, 'capacity region by coherent coding with cardinality-bounding', color='green')
bbox_props = dict(boxstyle="round,pad=0.1", fc="white", ec="g", lw=1)
plt.text(1, 0.5, r'$1$', color='black', bbox=bbox_props)
bbox_props = dict(boxstyle="round,pad=0.1", fc="white", ec="b", lw=1)
plt.text(1.7, 0.4, r'$2$', color='black', bbox=bbox_props)
bbox_props = dict(boxstyle="round,pad=0.1", fc="white", ec="r", lw=1)
plt.text(2.2, 0.3, r'$3$', color='black', bbox=bbox_props)
def OrientationPlot(OrientationHist_Data,BINS):
"""
Plot an orienation histogram. For use with OrientationHist function
Input
-----
OrientationHist_Data: computed from OrienationHist function
BINS: bins used to compute OrientationHist
Output
------
Produces a polar plot with the orientation histogram data
"""
RAD_BINS = BINS/(180./np.pi)
## Data Plot
plt.rc('grid', color='gray', linewidth=1, linestyle='-')
plt.rc('xtick', labelsize=25)
plt.rc('ytick', labelsize=20)
width, height = plt.rcParams['figure.figsize']
size = min(width, height)
fig = plt.figure(figsize=(size, size))
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8], polar=True, axisbg='w')
plt.polar(RAD_BINS,OrientationHist_Data/float(sum(OrientationHist_Data)), 'k',linewidth=4, marker='o')
ax.set_rmax(0.2)
plt.show()
def plot_matches(smresbest,lspec):
"""
Plot best matches
Plots the target spectrum along with the top matches
"""
shift = 1
fig,axL = plt.subplots(nrows=2,figsize=(20,12),sharex=True)
plt.sca(axL[0])
targpar = smresbest.rename(columns={'targobs':'obs'})
targpar = dict(targpar['obs ord wlo whi'.split()].iloc[0])
targpar['type'] = 'cps'
targspec = smio.getspec_h5(**targpar)
w = targspec['w']
plt.plot(w,targspec['s'],'k')
plt.rc('axes',color_cycle=['Tomato', 'RoyalBlue'])
for i in smresbest.index:
# Plot target spectrum
plt.sca(axL[0])
y = shift*0.3
plt.plot(w,lspec['lspec'][i]+y)
par = dict(smresbest.ix[i])
par['y'] = y+1
annotate_matches(par)
# Plot residuals
plt.sca(axL[1])
y = shift*0.2
plt.plot(w,lspec['fres'][i]+y)
par['y'] = y
annotate_matches(par)
shift+=1
fig.subplots_adjust(left=.03,bottom=.03,top=0.97,right=.8)
def create_bar_plots(bins, freq_list, height, group_names, colors, xlabel, ylabel, legend=True):
import matplotlib.pylab as plt
import numpy as np
from matplotlib.ticker import MaxNLocator
fig = plt.figure(figsize=(height*1.5, height))
ax = fig.add_subplot(111)
font = { 'size' : 22 * height/8}
plt.rc('font', **font)
range = np.max(bins) - np.min(bins)
w = range/((len(bins)-1) * len(group_names))
for i, group in enumerate(group_names):
bar = plt.bar(bins + w*i, freq_list[i],
width=w, label = group,
color=colors[i],
edgecolor='none')
# Adjust the power limits so that you use scientific notation on the y axis
plt.ticklabel_format(style='sci', axis='y')
ax.yaxis.major.formatter.set_powerlimits((-3,3))
for t in ax.yaxis.get_major_ticks():
t.tick1On = False
t.tick2On = False
if legend:
plt.legend(loc=0)
plt.ylabel(ylabel)
plt.xlabel(xlabel)
# Make sure the layout looks good :)
fig.tight_layout()
return fig
def plot_graphs(df, trending_daily, day_from, day_to, limit, country_code, folder_out=None):
days = pd.DatetimeIndex(start=day_from, end=day_to, freq='D')
for day in days:
fig = plt.figure()
ax = fig.add_subplot(111)
plt.rc('lines', linewidth=2)
data = trending_daily.get_group(str(day.date()))
places, clusters = top_trending(data, limit)
for cluster in clusters:
places.add(max_from_cluster(cluster, data))
ax.set_prop_cycle(plt.cycler('color', ['r', 'b', 'yellow'] + [plt.cm.Accent(i) for i in np.linspace(0, 1, limit-3)]
) + plt.cycler('linestyle', ['-', '-', '-', '-', '-', '--', '--', '--', '--', '--']))
frame = export(places, clusters, data)
frame.sort_values('trending_rank', ascending=False, inplace=True)
for i in range(len(frame)):
item = frame.index[i]
lat, lon, country = item
result_items = ReverseGeoCode().get_address_attributes(lat, lon, 10, 'city', 'country_code')
if 'city' not in result_items.keys():
mark = "%s (%s)" % (manipulate_display_name(result_items['display_name']),
result_items['country_code'].upper() if 'country_code' in result_items.keys() else country)
else:
if check_eng(result_items['city']):
mark = "%s (%s)" % (result_items['city'], result_items['country_code'].upper())
else:
mark = "%.2f %.2f (%s)" % (lat, lon, result_items['country_code'].upper())
gp = df.loc[item].plot(ax=ax, x='date', y='count', label=mark)
ax.tick_params(axis='both', which='major', labelsize=10)
ax.set_yscale("log", nonposy='clip')
plt.xlabel('Date', fontsize='small', verticalalignment='baseline', horizontalalignment='right')
plt.ylabel('Total number of views (log)', fontsize='small', verticalalignment='center', horizontalalignment='center', labelpad=6)
gp.legend(loc='best', fontsize='xx-small', ncol=2)
gp.set_title('Top 10 OSM trending places on ' + str(day.date()), {'fontsize': 'large', 'verticalalignment': 'bottom'})
plt.tight_layout()
db = TrendingDb()
db.update_table_img(plt, str(day.date()), region=country_code)
plt.close()
def plot_histogram(df1, df2):
"""
plot histo for question 1 (Difference in REM sleep?)
result => not concluant
df1: normal sleep (df1 = analyse(base))
df2: sleep depravation (df2 = analyse(depr))
"""
plt.rc('font', family='Arial')
N = 5
normal = df1['%5'].tolist()
mean = sum(normal) / len(normal)
normal.extend([mean])
ind = np.arange(N) # the x locations for the groups
width = 0.35 # the width of the bars
fig, ax = plt.subplots()
rects1 = ax.bar(ind, normal, width, color='b')
depravation = df2['%5'].tolist()
mean = sum(depravation) / len(depravation)
depravation.extend([mean])
rects2 = ax.bar(ind+width, depravation, width, color='r')
ax.set_ylabel('Sleep in REM stage (%)')
ax.set_xlabel('Subjects')
ax.set_title('REM sleep comparison', fontsize=20)
ax.set_xticks(ind+width)
ax.set_xticklabels( ('1', '2', '3', '4', 'Mean') )
for label in (ax.get_xticklabels() + ax.get_yticklabels()):
label.set_fontname('Arial')
label.set_fontsize(8)
ax.legend( (rects1[0], rects2[0]), ('Baseline', 'After sleep depravation') , loc = 'lower right', fontsize=10 )
def plot_sleepTime(df1, df2):
"""
First conclusion - obvious from experience -> sleep time longer after sleep depravation
df1: normal sleep (df1 = analyse(base))
df2: sleep depravation (df2 = analyse(depr))
"""
plt.rc('font', family='Arial')
N = 5
normal = df1['sleep duration'].tolist()
mean = sum(normal) / len(normal)
normal.extend([mean])
ind = np.arange(N) # the x locations for the groups
width = 0.35 # the width of the bars
fig, ax = plt.subplots()
rects1 = ax.bar(ind, normal, width, color='b')
depravation = df2['sleep duration'].tolist()
mean = sum(depravation) / len(depravation)
depravation.extend([mean])
rects2 = ax.bar(ind+width, depravation, width, color='r')
ax.set_ylabel('Sleep time (hours)')
ax.set_xlabel('Subjects')
ax.set_title('Overall sleep duration comparison', fontsize=20)
ax.set_xticks(ind+width)
ax.set_xticklabels( ('1', '2', '3', '4', 'Mean') )
for label in (ax.get_xticklabels() + ax.get_yticklabels()):
label.set_fontname('Arial')
label.set_fontsize(8)
ax.legend( (rects1[0], rects2[0]), ('Baseline', 'Recovery'), loc = 'lower right', fontsize=10 )
def plot_spectrograms(bsl,rec,rate,title):
plt.close()
plt.rc('font', family='Arial')
fig, ax = plt.subplots(nrows=9, ncols=2, sharex='col', sharey='row')
fig.suptitle(title + " - REM stage", fontsize=20)
plt.subplots_adjust(wspace = .05,hspace = 0.4 )
ny_nfft=1024
i=0
plt.tick_params(axis='both', labelsize=8)
while i<9:
Pxx, freq, bins, im = ax[i,0].specgram(bsl[i],NFFT=ny_nfft,Fs=rate)
ax[i,0].set_yticks(np.arange(0, 50, 10))
ax[i,0].set_ylim([0, 40])
if(i==8):
ax[i,0].set_xlabel("Time, seconds", fontsize=10)
ax[i,0].set_ylabel("Freq, Hz", fontsize=8)
ax[i,0].set_title('Baseline, channel:'+str(i+1), fontsize=10)
for label in (ax[i,0].get_xticklabels() + ax[i,0].get_yticklabels()):
label.set_fontname('Arial')
label.set_fontsize(8)
i=i+1
i=0
while i<9:
Pxx, freq, bins, im = ax[i,1].specgram(rec[i],NFFT=ny_nfft,Fs=rate)
ax[i,0].set_yticks(np.arange(0, 50, 10))
ax[i,1].set_ylim([0, 40])
#ax[i,1].set_xlim([0, 10000]) #13000])
if(i==8):
ax[i,1].set_xlabel("Time, seconds", fontsize=10)
#ax[i,1].set_ylabel("Freq, Hz")
ax[i,1].set_title('Recovery, channel:'+str(i+1), fontsize=10)
for label in (ax[i,0].get_xticklabels() + ax[i,0].get_yticklabels()):
label.set_fontname('Arial')
label.set_fontsize(8)
i=i+1
plt.show()
return
pl.axvline(x=51,color='r',ls='dashed')
pl.ylabel('Temp. Dev.')
pl.xlabel('Timestamp')
pl.rcParams.update({'font.size':14})
print '\nave_PN:', np.mean(e1_set[ind][:49]), np.mean(e1_set[ind][51:]), np.mean(e1_set[ind])
print '\nave_PN:', np.mean(e2_set[ind][:49]), np.mean(e2_set[ind][51:]), np.mean(e2_set[ind])
print '\nave_PN:', np.mean(e4_set[ind][:49]), np.mean(e4_set[ind][51:]), np.mean(e4_set[ind])
if set_length == 1 and compare == True:
pl.subplot(311)
pl.plot(x, e11, label = comp_with)
pl.subplot(312)
pl.plot(x, e21)
pl.subplot(313)
david2, = pl.semilogy(x, e41)
pl.rc('legend',**{'fontsize':14})
david3 = pl.legend([david1,david2],['TVGL','Baseline'], ncol=2, loc=7, bbox_to_anchor=(1,0.57), columnspacing=0.4)
david3.draw_frame(False)
print '\nave_Naive:', np.mean(e11)
print '\nave_Naive:', np.mean(e21)
print '\nave_Naive:', np.mean(e41)
Data_type = cov_mode + '%s'%(cov_mode_number) + '%s'%(samplesPerStep)
pl.savefig(Data_type)
pl.savefig(Data_type+'.eps', format = 'eps', bbox_inches = 'tight', dpi = 1000)
pl.show()
if set_length > 1:
#print index1, index11, index12, index2, index21, index22
print 'alpha = ', alpha_set[index11], ' beta = ', beta_set[index12], ' FroError = ', FroError[index1]
print 'alpha = ', alpha_set[index21], ' beta = ', beta_set[index22], ' Score = ', Score[index2]
print 'alpha = ', alpha_set[index31], ' beta = ', beta_set[index32], ' AIC = ', AIC[index3]
print 'alpha = ', alpha_set[index41], ' beta = ', beta_set[index42], ' FroThetaDiff = ', FroThetaDiff[index4]
def make_mask(data_file,mask_file='none'):
global key, x, y,lc,data,im,xy,mymask,xx,yy,px,lx,lm,default_mask,maskfig
# determine if a point is inside a given polygon or not
# Polygon is a list of (x,y) pairs.
#read input parameters
print "masking the edf file"
print "use mouse to select a region"
print "m - to mask selected region"
print "u - to unmask selected region"
print "a - to cancel selected region"
print "w - to save mask and exit"
#print "e - to exit"
data=loadedf(data_file)
lx,ly=shape(data)
if os.path.exists(mask_file) is True:
mymask=loadedf(mask_file,0)
automask=loadedf(mask_file,1)
if shape(mymask)!=shape(data):
mymask=zeros((lx,ly))
else:
mymask=zeros((lx,ly))
automask=zeros((lx,ly))
#points=[]
#for i in range(lx):
# for j in range(ly):
# points.append([i,j])
x, y = meshgrid(arange(lx), arange(ly))
x, y = x.flatten(), y.flatten()
points = vstack((x,y)).T
key=[]
x=0
y=0
xy=[]
xx=[]
yy=[]
print "Make Mask"
def on_click(event):
print "On click"
global key, x, y,lc,data,im,xy,mymask,xx,yy,px,lx,lm,default_mask,maskfig
if not event.inaxes:
xy=[]
return
x,y=int(event.xdata), int(event.ydata)
xx.append([x])
yy.append([y])
xy.append([y,x])
lc.set_data(xx,yy)
p.draw()
def on_click_key(event):
global key, x, y,lc,data,im,xy,mymask,xx,yy,px,lx,lm,default_mask,maskfig
key=event.key
if not event.inaxes:
xy=[]
return
if key=='a':
xx=[]
yy=[]
xy=[]
x=0
y=0
lc.set_data(xx,yy)
lm.set_data(xx,yy)
p.draw()
if key=='m':
#print 'masking'
xx.append(xx[0])#xx[-1]=xx[0]
yy.append(yy[0])#yy[-1]=yy[0]
xy.append(xy[0])#xy[-1]=xy[0]
ind=points_inside_poly(points,xy).reshape(lx,ly).T
mymask[ind]=1
data=masked_array(data,mymask+automask)
im.set_data(data)
xx=[]
yy=[]
xy=[]
lc.set_data(xx,yy)
lm.set_data(xx,yy)
p.draw()
x=0
y=0
print "key m pressed"
if key=='u':
xx.append(xx[0])#xx[-1]=xx[0]
yy.append(yy[0])#yy[-1]=yy[0]
xy.append(xy[0])#xy[-1]=xy[0]
ind=points_inside_poly(points,xy).reshape(lx,ly).T
mymask[ind]=0
data=masked_array(data,mymask+automask)
im.set_data(data)
xx=[]
yy=[]
xy=[]
lc.set_data(xx,yy)
lm.set_data(xx,yy)
p.draw()
x=0
y=0
print "key u pressed"
if key=='r':
mymask=0*mymask
mymask=mymask.reshape(lx,ly)
data=masked_array(data,mymask+automask)
im.set_data(data)
xx=[]
yy=[]
xy=[]
lc.set_data(xx,yy)
lm.set_data(xx,yy)
p.draw()
x=0
y=0
print "key r pressed"
if key=='w':
p.close()
saveedf(mask_file,mymask,0)
saveedf(mask_file,automask,1)
print "key w pressed, CLOSING"
return
def on_move(event):
#print"On move"
global lm,x,y
if not event.inaxes: return
xm,ym=int(event.xdata), int(event.ydata)
# update the line positions
if x!=0:
lm.set_data((x,xm),(y,ym))
p.draw()
p.rc('image',origin = 'lower')
p.rc('image',interpolation = 'nearest')
p.figure()
px=p.subplot(111)
data=p.log(data+1)
im=p.imshow(masked_array(data,mymask+automask))
p.title("Select a ROI. Press m to mask or u to unmask it \n w to write mask and exit")
lc,=px.plot((0,0),(0,0),'-+m',linewidth=1,markersize=8,markeredgewidth=1)
lm,=px.plot((0,0),(0,0),'-+m',linewidth=1,markersize=8,markeredgewidth=1)
px.set_xlim(0,ly)
px.set_ylim(0,lx)
#p.ion()
cidb=p.connect('button_press_event',on_click)
cidk=p.connect('key_press_event',on_click_key)
cidm=p.connect('motion_notify_event',on_move)
p.show()
for name in ['x', 'chord', 'rot_z', 'rthick']:
spl_ae.add_spline(name, np.array([0, 0.25, 0.75, 1.]), spline_type='bezier')
# configure
spl_ae.configure()
return p
# --- 5
if __name__ == '__main__':
p = configure_surface()
p.setup()
p.run()
import matplotlib.pylab as plt
plt.rc('lines', linewidth=3)
plt.figure()
plt.axis('equal')
for i in range(p['blade_surface_st'].shape[1]):
plt.plot(p['blade_surface_st'][:,i, 2], p['blade_surface_st'][:,i, 0], 'r-')
plt.plot(p['blade_surface_st'][0, :, 2], p['blade_surface_st'][100, :, 0],'r-')
plt.plot(p['blade_surface_st'][0, :, 2], p['blade_surface_st'][0, :, 0],'r-')
plt.plot(p['z'], p['x'], 'r-', label='Original')
# --- 6
# add sweep to the blade
p['x_C'][-1]=-.05
p.run()
for i in range(p['blade_surface_st'].shape[1]):
Created on Sun Apr 06 18:42:59 2014
@author: lassnech
"""
from sklearn import svm
from sklearn import grid_search
import tmpfertilized as f
import matplotlib.pylab as plt
import matplotlib
import matplotlib.cm as cm
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import numpy as np
from plottools import make_spiral, point_prob_plot, probaproxy
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
np.random.seed(1)
n_classes = 2
n_trees = 200
ploty = [-6, 6, 100]
plotx = [-6, 6, 100]
X, Y = make_spiral(n_arms=n_classes, noise=.4)
##############################################################################
parameters = {'kernel': ['rbf'],
'C': [1, 10, 100, 1000, 10000, 100000],
'gamma': [10 ** x for x in range(-5, 3)],
def make_heated_time_map(sep_array, Nside, width):
print 'generating heated time map ...'
# choose points within specified range. Example plot separations greater than 5 minutes:
# indices = (sep_array[:,0]>5*60) & (sep_array[:,1]>5*60)
indices=range(sep_array.shape[0]) # all time separations
x_pts = np.log(sep_array[indices,0])
y_pts = np.log(sep_array[indices,1])
min_val = np.min([np.min(x_pts), np.min(y_pts)])
x_pts = x_pts - min_val
y_pts = y_pts - min_val
max_val = np.max([np.max(x_pts), np.max(y_pts)])
x_pts *= (Nside-1)/max_val
y_pts *= (Nside-1)/max_val
img=np.zeros((Nside,Nside))
for i in range(len(x_pts)):
img[x_pts[i],y_pts[i]] +=1
img = ndi.gaussian_filter(img,width) # apply Gaussian filter
img = np.sqrt(img) # taking the square root makes the lower values more visible
img=np.transpose(img) # needed so the orientation is the same as scatterplot
plt.imshow(img, origin='lower')
## create custom tick marks. Calculate positions of tick marks on the transformed log scale of the image array
plt.minorticks_off()
## change font, which can also now accept latex: http://matplotlib.org/users/usetex.html
plt.rc('text',usetex=True)
plt.rc('font',family='serif')
my_max = np.max([np.max(sep_array[indices,0]), np.max(sep_array[indices,1])])
my_min = np.max([np.min(sep_array[indices,0]), np.min(sep_array[indices,1])])
pure_ticks = np.array([1e-3,1,10,60*10,2*3600,1*24*3600, 7*24*3600]) # where the tick marks will be placed, in units of seconds. An additional value will be appended to the end for the max
labels = ['1 msec','1 sec','10 sec','10 min','2 hr','1 day','1 week'] # tick labels
index_lower=np.min(np.nonzero(pure_ticks >= my_min)) # index of minimum tick that is greater than or equal to the smallest time interval. This will be the first tick with a non-blank label
index_upper=np.max(np.nonzero(pure_ticks <= my_max))
ticks = pure_ticks[index_lower: index_upper + 1]
ticks = np.log(np.hstack((my_min, ticks, my_max ))) # append values to beginning and end in order to specify the limits
ticks = ticks - min_val
ticks *= (Nside-1)/(max_val)
labels= np.hstack(('',labels[index_lower:index_upper + 1],'')) # append blank labels to beginning and end
plt.xticks(ticks, labels,fontsize=16)
plt.yticks(ticks, labels,fontsize=16)
plt.xlabel('Time Before Tweet',fontsize=18)
plt.ylabel('Time After Tweet' ,fontsize=18)
plt.show()
return None
def mpl_thumbnails(usetex=False):
"""
Make png thumbnails
"""
plt.rcdefaults()
plt.rc('font', family='serif')
plt.rc('xtick', labelsize='x-small')
plt.rc('ytick', labelsize='x-small')
plt.rc('text', usetex=usetex)
plt.rc('savefig', format='pdf', bbox='tight')
plt.rc('savefig', format='png', bbox='tight')
plt.rc('figure', figsize=(4,3))
def mpl_slides(usetex=False):
"""
Set matplotlibrc to make pretty slides
"""
plt.rcdefaults()
plt.rc('font', family='serif', size=24)
# The default PowerPoint page setup
plt.rc('figure', figsize=(7,5.5))
plt.rc('axes', titlesize=24, labelsize=20, linewidth=3)
plt.rc('legend', fontsize=18, numpoints=1, scatterpoints=1)
plt.rc('xtick', labelsize='small')
plt.rc('ytick', labelsize='small')
plt.rc('text', usetex=usetex)
plt.rc('lines', linewidth=5)
plt.rc('savefig', format='pdf', bbox='tight')
def mpl_span_columns(usetex=False):
"""
Set matplotlib to make pretty plots for publishing a full-page figure
"""
plt.rcdefaults()
plt.rc('font', family='serif', size=12.0, style='normal')
plt.rc('figure', figsize=(7, 5.25))
plt.rc('axes', titlesize=12, labelsize=10)
plt.rc('legend', fontsize=8, numpoints=1, scatterpoints=1)
plt.rc('xtick', labelsize='x-small')
plt.rc('ytick', labelsize='x-small')
plt.rc('text', usetex=usetex)
plt.rc('savefig', format='pdf', bbox='tight')
# try a simple spline-based integration (good enough for small scales)
xir[i] = intsp.integral(lnkf[0],(lnkf[-1]))/(2.0*math.pi**2)
#
# for large r, do an expensive integration breaking integral into many pieces
# each integrating between successive zeroes of sin(kr)
#
xir2[i] = integrate.romberg(intfunc,lnk[0],lnk[-1],tol=1.e-14)/(2.0*math.pi**2)
print "%.4f"%rd, "%.5e"%xir[i], "%.5e"%xir2[i]
xiout.write('%.4f %.5e %.5e \n' % (rd, xir[i], xir2[i]))
fig1 = plt.figure()
plt.rc('text', usetex=True)
plt.rc('font',size=16,**{'family':'sans-serif','sans-serif':['Helvetica']})
plt.rc('xtick.major',pad=10); plt.rc('xtick.minor',pad=10)
plt.rc('ytick.major',pad=10); plt.rc('ytick.minor',pad=10)
#rfull,xifull = np.loadtxt('../s2_out.dat',usecols=(0,1),unpack=True)
plt.plot(lr,np.log10(np.abs(xir)),linewidth=1.5,c='b',label=r'$\sigma_2^2(r)$ Gaussian (spline)')
plt.plot(lr,np.log10(np.abs(xir2)),linewidth=1.5,c='m',label=r'$\sigma_2^2(r)$ TH (Romberg)')
plt.ylim(-10.0,8.0)
plt.xlim(-0.99,2.5)
#plt.xlim(8.0,16.0);
plt.xlabel(r'\textbf{$\log_{10}(R/\rm Mpc)$}',labelpad = 5)
plt.ylabel(r'$\log_{10}(\sigma^2_2(R))$',labelpad = 10)
plt.title('power spectrum moment',fontsize=16)
plt.legend(loc='upper right')
def make_time_map(times, times_tot_mins, sep_array, Ncolors):
print 'rendering normal time map ...'
## set up color list
red=Color("red")
blue=Color("blue")
color_list = list(red.range_to(blue, Ncolors)) # range of colors evenly speced on the spectrum between red and blue. Each element is a colour object
color_list = [c.hex for c in color_list] # give hex version
fig=plt.figure()
ax =fig.add_subplot(111)
plt.rc('text',usetex=True)
plt.rc('font',family='serif')
colormap = plt.cm.get_cmap('rainbow') # see color maps at http://matplotlib.org/users/colormaps.html
order=np.argsort(times_tot_mins[1:-1]) # so that the red dots are on top
# order=np.arange(1,len(times_tot_mins)-2) # dots are unsorted
# taken from http://stackoverflow.com/questions/6063876/matplotlib-colorbar-for-scatter
sc= ax.scatter(sep_array[:,0][order],sep_array[:,1][order],c=times_tot_mins[1:-1][order],vmin=0,vmax=24*60,s=25,cmap=colormap,marker='o',edgecolors='none')
color_bar=fig.colorbar(sc,ticks=[0,24*15,24*30,24*45,24*60],orientation='horizontal',shrink=0.5)
color_bar.ax.set_xticklabels(['Midnight','18:00','Noon','6:00','Midnight'])
color_bar.ax.invert_xaxis()
color_bar.ax.tick_params(labelsize=16)
ax.set_yscale('log') # logarithmic axes
ax.set_xscale('log')
plt.minorticks_off()
pure_ticks = np.array([1e-3,1,10,60*10,2*3600,1*24*3600, 7*24*3600]) # where the tick marks will be placed, in units of seconds.
labels = ['1 msec','1 sec','10 sec','10 min','2 hr','1 day','1 week'] # tick labels
max_val = np.max([np.max(sep_array[:,0]), np.max(sep_array[:,1])])
ticks = np.hstack((pure_ticks, max_val))
min_val = np.min([np.min(sep_array[:,0]), np.min(sep_array[:,1])])
plt.xticks(ticks,labels,fontsize=16)
plt.yticks(ticks,labels,fontsize=16)
plt.xlabel('Time Before Tweet',fontsize=18)
plt.ylabel('Time After Tweet',fontsize=18)
plt.xlim((min_val, max_val))
plt.ylim((min_val, max_val))
ax.set_aspect('equal')
plt.tight_layout()
plt.show()
return None
# Run simulation. Make sure to add/remove the moons you want to simulate!
ttv_array, tdv_array = run_sim(
R_star,
transit_duration,
[planet, firstmoon, secondmoon, thirdmoon])
# Output information
print 'TTV amplitude =', numpy.amax(ttv_array), \
'[min] = ', numpy.amax(ttv_array) * 60, '[sec]'
print 'TDV amplitude =', numpy.amax(tdv_array), \
'[min] = ', numpy.amax(tdv_array) * 60, '[sec]'
ax = plt.axes()
plt.plot(ttv_array, tdv_array, color = 'k')
plt.rc('font', **{'family': 'serif', 'serif': ['Computer Modern']})
plt.rc('text', usetex=True)
plt.tick_params(axis='both', which='major', labelsize = 16)
plt.xlabel('transit timing variation [minutes]', fontsize = 16)
plt.ylabel('transit duration variation [minutes]', fontsize = 16)
ax.tick_params(direction='out')
plt.ylim([numpy.amin(tdv_array) * 1.2, numpy.amax(tdv_array) * 1.2])
plt.xlim([numpy.amin(ttv_array) * 1.2, numpy.amax(ttv_array) * 1.2])
plt.plot((0, 0), (numpy.amax(tdv_array) * 10., numpy.amin(tdv_array) * 10.), 'k', linewidth=0.5)
plt.plot((numpy.amin(ttv_array) * 10., numpy.amax(ttv_array) * 10.), (0, 0), 'k', linewidth=0.5)
# Fix axes for comparison with eccentric moon
plt.xlim(-0.15, +0.15)
plt.ylim(-0.65, +0.65)
plt.annotate(r"5:4:3", xy=(-0.145, +0.55), size=16)
#! /usr/bin/python
#!encoding: UTF-8
import matplotlib.pylab as pl
import numpy as np
import newton
import time
pl.rc('text', usetex=True)
pl.rc('font', family='Bookman')
g = (3.45,-5.8,-7.2,2.17)
tol = (10e-4,10e-5, 10e-7,10e-12)
nmax = (10,50,100,10)
X = []
Y = []
for i in range (0, 4):
t0 = time.clock()
for j in range (0, 10000):
sol = newton.newton (g[i], tol[i], nmax[i], 0)
tf = time.clock() - t0
X = X + [i+1]
Y = Y + [tf]
print Y
pl.plot(X,Y,'mp--')
pl.title(r'Costo computacional del m\'etodo de Newton')
pl.xlabel(r'Cantidad de iteraciones (en decenas de miles)')