def run_method_usage(methods,cases):
methods = [m[0] for m in methods]
# Bootstrap the percentage error bars:
percents =[]
for i in range(10000):
nc = resample(cases)
percents.append(100*np.sum(nc,axis=0)/len(nc))
percents=np.array(percents)
mean_percents = np.mean(percents,axis=0)
std_percents = np.std(percents,axis=0)*1.96
inds=np.argsort(mean_percents).tolist()
inds.reverse()
avg_usage = np.mean(mean_percents)
fig = plt.figure()
ax = fig.add_subplot(111)
x=np.arange(len(methods))
ax.plot(x,[avg_usage]*len(methods),'-',color='0.25',lw=1,alpha=0.2)
ax.bar(x, mean_percents[inds], 0.6, color=paired[0],linewidth=0,
yerr=std_percents[inds],ecolor=paired[1])
#ax.set_title('Method Occurrence')
ax.set_ylabel('Occurrence %',fontsize=30)
ax.set_xlabel('Method',fontsize=30)
ax.set_xticks(np.arange(len(methods)))
ax.set_xticklabels(np.array(methods)[inds],fontsize=8)
fig.autofmt_xdate()
fix_axes()
plt.tight_layout()
fig.savefig(figure_path+'method_occurrence.pdf', bbox_inches=0)
fig.show()
return inds,mean_percents[inds]
def do_plot_extras(self, extra):
""" Plot other observed quantities as a function of time.
Parameters
----------
extra: string
One of the quantities available in system.extras
"""
# import pyqtgraph as pg
colors = 'bgrcmykw' # lets hope for less than 9 data-sets
t = self.time
# handle inexistent field
if extra not in self.extras._fields:
from shell_colors import red
msg = red('ERROR: ') + 'The name "%s" is not available in extras.\n' % extra
clogger.fatal(msg)
return
i = self.extras._fields.index(extra) # index corresponding to this quantity
plt.figure()
# p = pg.plot()
plt.plot(t, self.extras[i], 'o', label=extra)
plt.xlabel('Time [days]')
plt.ylabel(extra + ' []')
plt.legend(loc='upper center', bbox_to_anchor=(0.5, 1.05))
plt.minorticks_on()
plt.tight_layout()
plt.show()
def _plot(self, doFAP=None):
"""
Create a plot.
"""
xlabel = 'Period [d]'
ylabel = 'Power'
self.fig = plt.figure()
self.ax = self.fig.add_subplot(1,1,1)
self.ax.set_title("Normalized periodogram")
self.ax.set_xlabel(xlabel)
self.ax.set_ylabel(ylabel)
self.ax.semilogx(1./self.freq, self.power, 'b-')
# plot FAPs
if doFAP is None:
pass
elif doFAP is True: # do default FAPs of 10%, 1% and 0.1%
pmin = 1./self.freq.min()
pmax = 1./self.freq.max()
plvl1 = self.powerLevel(0.1) # 10% FAP
plvl2 = self.powerLevel(0.01) # 1% FAP
plvl3 = self.powerLevel(0.001) # 0.1% FAP
self.ax.semilogx([pmin, pmax],[plvl1, plvl1],'k-')
self.ax.semilogx([pmin, pmax],[plvl2, plvl2],'k--')
self.ax.semilogx([pmin, pmax],[plvl3, plvl3],'k:')
plt.tight_layout()
plt.show()
def do_plot_obs(self):
""" Plot the observed radial velocities as a function of time.
Data from each file are color coded and labeled.
"""
# import pyqtgraph as pg
colors = 'bgrcmykw' # lets hope for less than 9 data-sets
t, rv, err = self.time, self.vrad, self.error # temporaries
plt.figure()
# p = pg.plot()
# plot each files' values
for i, (fname, [n, nout]) in enumerate(sorted(self.provenance.iteritems())):
m = n-nout # how many values are there after restriction
# e = pg.ErrorBarItem(x=t[:m], y=rv[:m], \
# height=err[:m], beam=0.5,\
# pen=pg.mkPen(None))
# pen={'color': 0.8, 'width': 2})
# p.addItem(e)
# p.plot(t[:m], rv[:m], symbol='o')
plt.errorbar(t[:m], rv[:m], yerr=err[:m], \
fmt='o'+colors[i], label=fname)
t, rv, err = t[m:], rv[m:], err[m:]
plt.xlabel('Time [days]')
plt.ylabel('RV [km/s]')
plt.legend()
plt.tight_layout()
plt.show()
def save(self, plot_filename, max_col=2):
fig = plt.figure()
fig.suptitle(self.title, fontsize=8)
if len(self.datastore) <= max_col:
colsz = len(self.datastore)
rowsz = 1
for i, d in enumerate(self.datastore):
if len(d) == 0:
continue # empty space
ax = fig.add_subplot(rowsz, colsz, i + 1)
self._plot(i, ax)
else:
sz = len(self.datastore)
colsz = max_col
rowsz = sz / max_col
rowsz = rowsz if sz % max_col == 0 else rowsz + 1
for i, d in enumerate(self.datastore):
if len(d) == 0:
continue # empty space
ax = fig.add_subplot(rowsz, colsz, i + 1)
self._plot(i, ax)
#plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=1.0)
plt.tight_layout()
plt.savefig(plot_filename)
return self
def plot_ss_scatter(steadies):
""" Plot scatter plots of steady states
"""
def do_scatter(i, j, ax):
""" Draw single scatter plot
"""
xs, ys = utils.extract(i, j, steadies)
ax.scatter(xs, ys)
ax.set_xlabel(r"$S_%d$" % i)
ax.set_ylabel(r"$S_%d$" % j)
cc = utils.get_correlation(xs, ys)
ax.set_title(r"Corr: $%.2f$" % cc)
dim = steadies.shape[1]
fig, axarr = plt.subplots(1, int((dim ** 2 - dim) / 2), figsize=(20, 5))
axc = 0
for i in range(dim):
for j in range(dim):
if i == j:
break
do_scatter(i, j, axarr[axc])
axc += 1
plt.suptitle("Correlation overview")
plt.tight_layout()
save_figure("images/correlation_scatter.pdf", bbox_inches="tight")
plt.close()
def plot(rho, u, uLB, tau, rho_history, zdjecia, image, nx, maxIter ):
# plt.figure(figsize=(15,15))
# plt.subplot(4, 1, 1)
# plt.imshow(u[1,:,0:50],vmin=-uLB*.15, vmax=uLB*.15, interpolation='none')#,cmap=cm.seismic
# plt.colorbar()
plt.rcParams["figure.figsize"] = (15,15)
plt.subplot(5, 1, 1)
plt.imshow(sqrt(u[0]**2+u[1]**2),vmin=0, vmax=uLB*1.6)#,cmap=cm.seismic
plt.colorbar()
plt.title('tau = {:f}'.format(tau))
plt.subplot(5, 1, 2)
plt.imshow(u[0,:,:30], interpolation='none')#,cmap=cm.seismicvmax=uLB*1.6,
plt.colorbar()
plt.title('tau = {:f}'.format(tau))
plt.subplot(5, 1, 3)
plt.imshow(rho, interpolation='none' )#,cmap=cm.seismic
plt.title('rho')
plt.subplot(5, 1,4)
plt.title(' history rho')
plt.plot(linspace(0,len(rho_history),len(rho_history)),rho_history)
plt.xlim([0,maxIter])
plt.subplot(5, 1,5)
plt.title(' u0 middle develop')
plt.plot(linspace(0,nx,len(u[0,20,:])), u[1,20,:])
plt.tight_layout()
plt.savefig(path.join(zdjecia,'f{0:06d}.png'.format(image)))
plt.clf();
def plot_confusion_matrix(cm, title='', cmap=plt.cm.Blues):
#print cm
#display vehicle, idle, walking accuracy respectively
#display overall accuracy
print type(cm)
# plt.figure(index
plt.imshow(cm, interpolation='nearest', cmap=cmap)
#plt.figure("")
plt.title("Confusion Matrix")
plt.colorbar()
tick_marks = [0,1,2]
target_name = ["driving","idling","walking"]
plt.xticks(tick_marks,target_name,rotation=45)
plt.yticks(tick_marks,target_name,rotation=45)
print len(cm[0])
for i in range(0,3):
for j in range(0,3):
plt.text(i,j,str(cm[i,j]))
plt.tight_layout()
plt.ylabel("Actual Value")
plt.xlabel("Predicted Outcome")
def plot_batch(color_model, q_ab, X_batch_black, X_batch_color, batch_size, h, w, nb_q, epoch):
# Format X_colorized
X_colorized = color_model.predict(X_batch_black / 100.)[:, :, :, :-1]
X_colorized = X_colorized.reshape((batch_size * h * w, nb_q))
X_colorized = q_ab[np.argmax(X_colorized, 1)]
X_a = X_colorized[:, 0].reshape((batch_size, 1, h, w))
X_b = X_colorized[:, 1].reshape((batch_size, 1, h, w))
X_colorized = np.concatenate((X_batch_black, X_a, X_b), axis=1).transpose(0, 2, 3, 1)
X_colorized = [np.expand_dims(color.lab2rgb(im), 0) for im in X_colorized]
X_colorized = np.concatenate(X_colorized, 0).transpose(0, 3, 1, 2)
X_batch_color = [np.expand_dims(color.lab2rgb(im.transpose(1, 2, 0)), 0) for im in X_batch_color]
X_batch_color = np.concatenate(X_batch_color, 0).transpose(0, 3, 1, 2)
list_img = []
for i, img in enumerate(X_colorized[:min(32, batch_size)]):
arr = np.concatenate([X_batch_color[i], np.repeat(X_batch_black[i] / 100., 3, axis=0), img], axis=2)
list_img.append(arr)
plt.figure(figsize=(20,20))
list_img = [np.concatenate(list_img[4 * i: 4 * (i + 1)], axis=2) for i in range(len(list_img) / 4)]
arr = np.concatenate(list_img, axis=1)
plt.imshow(arr.transpose(1,2,0))
ax = plt.gca()
ax.get_xaxis().set_ticks([])
ax.get_yaxis().set_ticks([])
plt.tight_layout()
plt.savefig("../../figures/fig_epoch%s.png" % epoch)
plt.clf()
plt.close()
def plot_ga_cnn(data, save=False, save_dest=None):
plt.figure()
# generation and all time best score plot
# plt.subplot(211)
# plt.title("GA CNN tuner on dataset D2")
# plt.plot(data["dataset1"]["gen_best_score"], label="Generation Best")
# plt.plot(data["dataset1"]["all_time_best_score"], label="All Time best")
# plt.xlabel("Generation")
# plt.ylabel("Score")
# plt.xticks(range(0, 20))
# plt.xlim([0, 9])
# plt.ylim([0, 0.01])
# plt.legend(loc=0)
# plt.subplot(212)
# plt.title("GA CNN tuner on dataset D3")
plt.plot(data["gen_best_score"], label="Generation Best")
plt.plot(data["all_time_best_score"], label="All Time best")
plt.xlabel("Generation")
plt.ylabel("Score")
plt.xticks(range(0, 20))
plt.xlim([0, 9])
plt.ylim([0, 0.01])
plt.legend(loc=0)
# show plot or save as picture
if save is False:
plt.show()
else:
if save_dest is None:
raise RuntimeError("save_dest not set!!")
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=1.0)
plt.savefig(save_dest, dpi=200)
def ACF_PACF_plot(self):
#plot ACF and PACF to find the number of terms needed for the AR and MA in ARIMA
# ACF finds MA(q): cut off after x lags
# and PACF finds AR (p): cut off after y lags
# in ARIMA(p,d,q)
lag_acf = acf(self.ts_log_diff, nlags=20)
lag_pacf = pacf(self.ts_log_diff, nlags=20, method='ols')
#Plot ACF:
ax=plt.subplot(121)
plt.plot(lag_acf)
ax.set_xlim([0,5])
plt.axhline(y=0,linestyle='--',color='gray')
plt.axhline(y= -1.96/np.sqrt(len(ts_log_diff)),linestyle='--',color='gray')
plt.axhline(y= 1.96/np.sqrt(len(ts_log_diff)),linestyle='--',color='gray')
plt.title('Autocorrelation Function')
#Plot PACF:
plt.subplot(122)
plt.plot(lag_pacf)
plt.axhline(y=0,linestyle='--',color='gray')
plt.axhline(y= -1.96/np.sqrt(len(ts_log_diff)),linestyle='--',color='gray')
plt.axhline(y=1.96/np.sqrt(len(ts_log_diff)),linestyle='--',color='gray')
plt.title('Partial Autocorrelation Function')
plt.tight_layout()
def plotRttDistribution(rttEstimates, ip, filename, nbBins=500, logscale=False):
"""Plot the RTT distribution of an IP address
:rttEstimates: pandas DataFrame containing the RTT estimations
:ip: IP address to plot
:filename: Filename for the plot
:nbBins: Number of bins in the histogram
:logscale: Plot RTTs in logscale if set to True
:returns: None
"""
if logscale:
data = np.log10(rttEstimates[rttEstimates.index == ip].rtt)
else:
data = rttEstimates[rttEstimates.index == ip].rtt
h, b=np.histogram(data, nbBins, normed=True)
plt.figure(1, figsize=(9, 3))
plt.clf()
ax = plt.subplot()
x = b[:-1]
ax.plot(x, h, "k")
ax.grid(True)
plt.title("%s (%s RTTs)" % (ip, len(data)))
if logscale:
plt.xlabel("log10(RTT)")
else:
plt.xlabel("RTT")
plt.ylabel("pdf")
minorLocator = mpl.ticker.MultipleLocator(10)
ax.xaxis.set_minor_locator(minorLocator)
plt.tight_layout()
plt.savefig(filename)
def test(args):
data = multivariate_normal([0, 0], [[1, 2], [2, 5]], int(args[1]))
print(data)
# PCA
result = pca(data, base_num=int(args[2]))
pc_base = result[0]
print(pc_base)
# Plotting
fig = plt.figure()
fig.add_subplot(1, 1, 1)
plt.axvline(x=0, color="#000000")
plt.axhline(y=0, color="#000000")
# Plot data
plt.scatter(data[:, 0], data[:, 1])
# Draw the 1st principal axis
pc_line = sp.array([-3.0, 3.0]) * (pc_base[1] / pc_base[0])
plt.arrow(0, 0, -pc_base[0] * 2, -pc_base[1] * 2, fc="r", width=0.15, head_width=0.45)
plt.plot([-3, 3], pc_line, "r")
# Settings
plt.xticks(size=15)
plt.yticks(size=15)
plt.xlim([-3, 3])
plt.tight_layout()
plt.show()
plt.savefig("image.png")
return 0
def plot_corner_posteriors(self, savefile=None, labels=["T1", "R1", "Av", "T2", "R2"]):
'''
Plots the corner plot of the MCMC results.
'''
ndim = len(self.sampler.flatchain[0,:])
chain = self.sampler
samples = chain.flatchain
samples = samples[:,0:ndim]
plt.figure(figsize=(8,8))
fig = corner.corner(samples, labels=labels[0:ndim])
plt.title("MJD: %.2f"%self.mjd)
name = self._get_save_path(savefile, "mcmc_posteriors")
plt.savefig(name)
plt.close("all")
plt.figure(figsize=(8,ndim*3))
for n in range(ndim):
plt.subplot(ndim,1,n+1)
chain = self.sampler.chain[:,:,n]
nwalk, nit = chain.shape
for i in np.arange(nwalk):
plt.plot(chain[i], lw=0.1)
plt.ylabel(labels[n])
plt.xlabel("Iteration")
name_walkers = self._get_save_path(savefile, "mcmc_walkers")
plt.tight_layout()
plt.savefig(name_walkers)
plt.close("all")
def PSTH(self):
TimeRes = np.array([0.1,0.25,0.5,1,2.5,5.0,10.0,25.0,50.0,100.0])
Projection_PSTH = np.zeros((2,len(TimeRes)))
for i in range(0,len(TimeRes)):
Data_Hist,STA_Hist,Model_Hist,B = Hist(TimeRes[i])
data = Data_Hist/np.linalg.norm(Data_Hist)
sta = STA_Hist/np.linalg.norm(STA_Hist)
model = Model_Hist/np.linalg.norm(Model_Hist)
Projection_PSTH[0,i] = np.dot(data,sta)
Projection_PSTH[1,i] = np.dot(data,model)
import matplotlib.font_manager as fm
plt.figure()
plt.semilogx(TimeRes,Projection_PSTH[0,:],'gray',TimeRes,Projection_PSTH[1,:],'k',
linewidth=3, marker='o', markersize = 12)
plt.xlabel('Time Resolution, ms',fontsize=25)
plt.xticks(fontsize=25)
#plt.axis["right"].set_visible(False)
plt.ylabel('Projection onto PSTH',fontsize=25)
plt.yticks(fontsize=25)
prop = fm.FontProperties(size=20)
plt.legend(('1D model','2D model'),loc='upper left',prop=prop)
plt.tight_layout()
plt.show()
def plot_graph(self):
'''
plots a matplotlib graph from the stocks data. Dates on the x axis and
Closing Prices on the y axis. Then adds it to the graph_win in the
display frame as a tk widget()
'''
x_axis = [
dt.datetime.strptime(self.daily_data[day][0], '%Y-%m-%d')
for day in range(1, len(self.daily_data) - 1)
]
y_axis = [
self.daily_data[cls_adj][-1]
for cls_adj in range(1, len(self.daily_data) - 1)
]
fig = plt.figure()
ax = fig.add_subplot("111")
ax.plot(
x_axis,
y_axis,
marker='h',
linestyle='-.',
color='r',
label='Daily Adjusted Closing Prices'
)
labels = ax.get_xticklabels()
for label in labels:
label.set_rotation(15)
plt.xlabel('Dates')
plt.ylabel('Close Adj')
plt.legend()
plt.tight_layout() # adjusts the graph to fit in the space its limited to
self.data_plot = FigureCanvasTkAgg(fig, master=self.display)
self.data_plot.show()
self.graph_win = self.data_plot.get_tk_widget()
def behavioral_analysis(self):
"""some analysis of the behavioral data, such as mean percept duration,
dominance ratio etc"""
self.assert_data_intern()
# only do anything if this is not a no report trial
if 'RP' in self.file_alias:
all_percepts_and_durations = [[],[]]
else:
all_percepts_and_durations = [[],[],[]]
if not 'NR' in self.file_alias: # and not 'RP' in self.file_alias
for x in range(len(self.trial_indices)):
if len(self.events) != 0:
events_this_trial = self.events[(self.events['EL_timestamp'] > self.timestamps_pt[x][0]) & (self.events['EL_timestamp'] < self.timestamps_pt[x][-1])]
for sc, scancode in enumerate(self.scancode_list):
percept_start_indices = np.arange(len(events_this_trial))[np.array(events_this_trial['scancode'] == scancode)]
percept_end_indices = percept_start_indices + 1
# convert to times
start_times = np.array(events_this_trial['EL_timestamp'])[percept_start_indices] - self.timestamps_pt[x,0]
if len(start_times) > 0:
if percept_end_indices[-1] == len(events_this_trial):
end_times = np.array(events_this_trial['EL_timestamp'])[percept_end_indices[:-1]] - self.timestamps_pt[x,0]
end_times = np.r_[end_times, len(self.from_zero_timepoints)]
else:
end_times = np.array(events_this_trial['EL_timestamp'])[percept_end_indices] - self.timestamps_pt[x,0]
these_raw_event_times = np.array([start_times + self.timestamps_pt[x,0], end_times + self.timestamps_pt[x,0]]).T
these_event_times = np.array([start_times, end_times]).T + x * self.trial_duration * self.sample_rate
durations = np.diff(these_event_times, axis = -1)
all_percepts_and_durations[sc].append(np.hstack((these_raw_event_times, these_event_times, durations)))
self.all_percepts_and_durations = [np.vstack(apd) for apd in all_percepts_and_durations]
# last element is duration, sum inclusive and exclusive of transitions
total_percept_duration = np.concatenate([apd[:,-1] for apd in self.all_percepts_and_durations]).sum()
total_percept_duration_excl = np.concatenate([apd[:,-1] for apd in [self.all_percepts_and_durations[0], self.all_percepts_and_durations[-1]]]).sum()
self.ratio_transition = 1.0 - (total_percept_duration_excl / total_percept_duration)
self.ratio_percept_red = self.all_percepts_and_durations[0][:,-1].sum() / total_percept_duration_excl
self.red_durations = np.array([np.mean(self.all_percepts_and_durations[0][:,-1]), np.median(self.all_percepts_and_durations[0][:,-1])])
self.green_durations = np.array([np.mean(self.all_percepts_and_durations[-1][:,-1]), np.median(self.all_percepts_and_durations[-1][:,-1])])
self.transition_durations = np.array([np.mean(self.all_percepts_and_durations[1][:,-1]), np.median(self.all_percepts_and_durations[1][:,-1])])
self.ratio_percept_red_durations = self.red_durations / (self.red_durations + self.green_durations)
plot_mean_or_median = 0 # mean
f = pl.figure(figsize = (8,4))
s = f.add_subplot(111)
for i in range(len(self.colors)):
pl.hist(self.all_percepts_and_durations[i][:,-1], bins = 20, color = self.colors[i], histtype='step', lw = 3.0, alpha = 0.4, label = ['Red', 'Trans', 'Green'][i])
pl.hist(np.concatenate([self.all_percepts_and_durations[0][:,-1], self.all_percepts_and_durations[-1][:,-1]]), bins = 20, color = 'k', histtype='step', lw = 3.0, alpha = 0.4, label = 'Percepts')
pl.legend()
s.set_xlabel('time [ms]')
s.set_ylabel('count')
sn.despine(offset=10)
s.annotate("""ratio_transition: %1.2f, \nratio_percept_red: %1.2f, \nduration_red: %2.2f,\nduration_green: %2.2f, \nratio_percept_red_durations: %1.2f"""%(self.ratio_transition, self.ratio_percept_red, self.red_durations[plot_mean_or_median], self.green_durations[plot_mean_or_median], self.ratio_percept_red_durations[plot_mean_or_median]), (0.5,0.65), textcoords = 'figure fraction')
pl.tight_layout()
pl.savefig(os.path.join(self.analyzer.fig_dir, self.file_alias + '_dur_hist.pdf'))
def plot_abc(self, uarg, param):
"""Plot a() and b() functions on the same plot.
"""
plt.figure(figsize=(8, 4))
plt.subplot(1, 3, 1)
plt.plot(uarg, self.afun(uarg, param))
plt.axhline(0)
plt.axvline(0)
plt.ylabel('$a(u)$')
plt.xlabel('$u$')
plt.subplot(1, 3, 2)
plt.plot(uarg, self.bfun(uarg, param))
plt.axhline(0)
plt.axvline(0)
plt.ylabel('$b(u)$')
plt.xlabel('$u$')
plt.subplot(1, 3, 3)
plt.plot(uarg, self.cfun(uarg, param))
plt.axhline(0)
plt.axvline(0)
plt.ylabel('$c(u)$')
plt.xlabel('$u$')
plt.tight_layout()
plt.show()
def plmyfig(df, bgname, dirname, tar, count=10):
#plot fig!
print("Starting Plot %s %s" % (dirname, bgname))
if len(df) > count:
df = df.head(count)
pos = plt.arange(len(df)) + 0.5
ytick = _getTerm(df['Term_description'], df['Term_ID'], bgname)
xs = [float(n) for n in df[' -log10(pvalue)']]
ytick.reverse()
xs.reverse()
plt.barh(pos, xs, align = 'center', height = 0.5, alpha = 1, color='orange')
plt.yticks(pos, ytick, size = 'x-small')
plt.xlabel('$-Log10(pValue)$')
plt.title('%s' % bgname)
ax = plt.gca()
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_ticks_position('bottom')
try:
plt.tight_layout()
except ValueError:
pass
filename = os.path.join(tar, dirname, dirname + '_' + bgname)
plt.savefig(filename + '.png', dpi = 72)
plt.savefig(filename + '.pdf')
plt.close()
def plot(self,file):
cds = CaseDataset(file, 'bson')
data = cds.data.driver('driver').by_variable().fetch()
cds2 = CaseDataset('../output/therm_mc_20141110173851.bson', 'bson')
data2 = cds2.data.driver('driver').by_variable().fetch()
#temp
temp_boundary_k = data['hyperloop.temp_boundary']
temp_boundary_k.extend(data2['hyperloop.temp_boundary'])
temp_boundary = [((x-273.15)*1.8 + 32) for x in temp_boundary_k]
#histogram
n, bins, patches = plt.hist(temp_boundary, 100, normed=1, histtype='stepfilled')
plt.setp(patches, 'facecolor', 'b', 'alpha', 0.75)
#stats
mean = np.average(temp_boundary)
std = np.std(temp_boundary)
percentile = np.percentile(temp_boundary,99.5)
print "mean: ", mean, " std: ", std, " 99.5percentile: ", percentile
x = np.linspace(50,170,150)
plt.plot(x,mlab.normpdf(x,mean,std), color='black', lw=2)
plt.xlim([60,160])
plt.ylabel('Probability', fontsize=18)
plt.xlabel(u'Equilibrium Temperature, \N{DEGREE SIGN}F', fontsize=18)
#plt.show()
plt.tight_layout()
plt.savefig('../output/histo.pdf', dpi=300)
def plot_reconstruction_result(res):
""" Plot original and reconstructed graph plus time series
"""
fig = plt.figure(figsize=(32, 8))
gs = mpl.gridspec.GridSpec(1, 4)
# original graph
orig_ax = plt.subplot(gs[0])
plot_graph(nx.from_numpy_matrix(res.A.orig), orig_ax)
orig_ax.set_title('Original graph')
# time series
ax = plt.subplot(gs[1:3])
sns.tsplot(
time='time', value='theta',
unit='source', condition='oscillator',
estimator=np.mean, legend=False,
data=compute_solutions(res),
ax=ax)
ax.set_title(r'$A_{{err}} = {:.2}, B_{{err}} = {:.2}$'.format(*compute_error(res)))
# reconstructed graph
rec_ax = plt.subplot(gs[3])
tmp = res.A.rec
tmp[abs(tmp) < 1e-1] = 0
plot_graph(nx.from_numpy_matrix(tmp), rec_ax)
rec_ax.set_title('Reconstructed graph')
plt.tight_layout()
save(fig, 'reconstruction_overview')
def save(self, out_path):
'''Saves a figure for the monitor
Args:
out_path: str
'''
plt.clf()
np.set_printoptions(precision=4)
font = {
'size': 7
}
matplotlib.rc('font', **font)
y = 2
x = ((len(self.d) - 1) // y) + 1
fig, axes = plt.subplots(y, x)
fig.set_size_inches(20, 8)
for j, (k, v) in enumerate(self.d.iteritems()):
ax = axes[j // x, j % x]
ax.plot(v, label=k)
if k in self.d_valid.keys():
ax.plot(self.d_valid[k], label=k + '(valid)')
ax.set_title(k)
ax.legend()
plt.tight_layout()
plt.savefig(out_path, facecolor=(1, 1, 1))
plt.close()
def plot(self, show=True, filename=None):
"""
Plots the windows for the object's channel.
:param show: Calls ``plt.show()`` before returning if True.
:param filename: If given, a picture will be saved to this path.
:return: The possibly created axes object.
"""
if self.comm is None:
raise ValueError("Operation only possible with an active "
"communicator instance.")
import matplotlib.pylab as plt
ax = self.comm.visualizations.plot_data_and_synthetics(
self.event, self.iteration, self.channel_id, show=False)
ylim = ax.get_ylim()
st = self.event["origin_time"]
for window in self.windows:
ax.fill_between((window.starttime - st, window.endtime - st),
[ylim[0] - 10] * 2, [ylim[1] + 10] * 2,
alpha=0.3, lw=0, zorder=-10)
ax.set_ylim(*ylim)
if show:
plt.tight_layout()
plt.show()
plt.close()
elif filename:
plt.tight_layout()
plt.savefig(filename)
plt.close()
return ax
def zsview(im, cmap=pl.cm.gray, figsize=(8,5), contours=False, ccolor='r'):
z1, z2 = zscale(im)
pl.figure(figsize=figsize)
pl.imshow(im, vmin=z1, vmax=z2, origin='lower', cmap=cmap, interpolation='none')
if contours:
pl.contour(im, levels=[z2], origin='lower', colors=ccolor)
pl.tight_layout()
def expt3():
"""
Experiment 2: Chooses the result files and generates figures
"""
result_file = "./expt3.txt"
input_threads, input_sizes, throughputs, resp_times \
= parse_output(result_file)
throughputs_MiB = [tp/2**20 for tp in throughputs]
fig1, (ax0, ax1) = pl.subplots(ncols=2, figsize=(6, 3))
fig1.set_tight_layout(True)
ax0.plot(input_threads, throughputs_MiB,
'bo-', ms=MARKER_SIZE, mew=0, mec='b')
ax0.set_xlabel("threads")
ax0.set_ylabel("throughput (MiB/sec)")
ax0.set_xlim(0,25)
ax0.text(1, 85, "(A)")
ax1.plot(input_threads, resp_times,
'mo-', ms=MARKER_SIZE, mew=0, mec='m')
ax1.set_xlabel("threads")
ax1.set_ylabel("response time (sec)")
ax1.set_xlim(0,25)
ax1.set_ylim(0,400)
ax1.text(1, 375, "(B)")
pl.tight_layout()
pl.savefig("./figures/%s" % result_file.replace(".txt", ".pdf"))
def plot_ra(s1, s2, idxs=None, epsilon=0.25, fig=None):
"""Computes the RA plot of two groups of samples"""
## compute log2 values
l1 = np.log2(s1 + epsilon)
l2 = np.log2(s2 + epsilon)
## compute A and R
r = l1 - l2
a = (l1 + l2) * 0.5
fig = pl.figure() if fig is None else fig
pl.figure(fig.number)
if idxs is None:
pl.plot(a, r, '.k', markersize=2)
else:
pl.plot(a[~idxs], r[~idxs], '.k', markersize=2)
pl.plot(a[idxs], r[idxs], '.r')
pl.axhline(0, linestyle='--', color='k')
pl.xlabel('(log2 sample1 + log2 sample2) / 2')
pl.ylabel('log2 sample1 - log2 sample2')
pl.tight_layout()
def test_pix_positions(self):
image.sex(os.path.join(self.args.output_path, 'output.fits'))
inputcat=catalog.read(os.path.join(self.args.tmp_path, 'ccd_1.cat'))
outputcat=catalog.readfits(os.path.join(self.args.output_path, 'output.cat'))
ouputcat=outputcat[outputcat["FLAGS"]==0]
mergedcat=catalog.mergecatpix(inputcat,outputcat, delta=3, poskeys1=['X_IMAGE','Y_IMAGE'], poskeys2=['X_IMAGE','Y_IMAGE'])
catalog.add_diff_column(mergedcat,'X_IMAGE_2','X_IMAGE_1',outputfield='DELTAX')
catalog.add_diff_column(mergedcat,'Y_IMAGE_2','Y_IMAGE_1',outputfield='DELTAY')
#p.figure()
#p.scatter(mergedcat['DELTAX'],mergedcat['DELTAY'])
#p.xlabel('Delta X (pixels)')
#p.ylabel('Delta Y (pixels)')
catalog.scattercols(mergedcat,'DELTAX','DELTAY',xlab='Delta X (pixels)',ylab='Delta Y (pixels)',show=False)
p.grid()
p.legend()
p.tight_layout()
p.savefig(os.path.join(self.figdir,"wcs_test_pix_positions_1.png"))
p.figure()
f, axarr = p.subplots(2, sharex=True)
axarr[0].hist(mergedcat['DELTAX'],bins=np.linspace(-0.5,0.5,101))
axarr[0].set_title('Delta X (pixels)')
axarr[1].hist(mergedcat['DELTAY'],bins=np.linspace(-0.5,0.5,101))
axarr[1].set_title('Delta Y (pixels)')
p.grid()
p.legend()
p.tight_layout()
p.savefig(os.path.join(self.figdir,"wcs_test_pix_positions_2.png"))
tol = 0.15
assert (np.mean(mergedcat['DELTAX']) < tol) and (np.mean(mergedcat['DELTAY']) < tol)
def plot_data(self,full_fname=None, dpi=300, ys=None, yhat=None):
name = self.test_name
if ys is not None : ys_data = ys
else : ys_data = self.results.series[name]['ys']
if yhat is not None : yhat_data = yhat
else: yhat_data = self.results.series[name]['yhat']
fig = plt.figure()
ax = fig.add_subplot(111)
plt.plot(ys_data)
plt.plot(yhat_data)
if ys is None :
fig.suptitle("%s | wp:%s,lc:%s" % (name,self.tm.winners_percent,self.tm.loopy_cols))
y = 0.998
for m in ['mape','nll', 'mae', 'rmse', 'r2'] :
metric = "%s: %.3f" % (str(m).upper(), self.results.metrics[name][m])
plt.text(0.998,y, metric, horizontalalignment='right', verticalalignment='top', transform=ax.transAxes)
y -= 0.03
plt.tight_layout()
if full_fname is not None :
fig.savefig(full_fname,bbox_inches='tight',dpi=dpi)
plt.close(fig)
def measure_psf(vignet, pixscale=1., show=False, mask_value=None):
y, x = np.mgrid[-vignet.shape[0]/2:vignet.shape[0]/2, -vignet.shape[1]/2:vignet.shape[1]/2]*pixscale
if mask_value :
vignet = ma.masked_values(vignet, mask_value).filled(0)
# Fit the data using astropy.modeling
p_init=models.Gaussian2D(amplitude=vignet.max(), x_mean=0., y_mean=0.,
x_stddev=2*pixscale, y_stddev=2*pixscale, theta=0, cov_matrix=None)
fit_p = fitting.LevMarLSQFitter()
p = fit_p(p_init, x, y, vignet)
barycenter=measure_barycenter(vignet, pixscale=pixscale)
# Plot the data with the best-fit model
P.figure(figsize=(8, 2.5))
P.subplot(1, 3, 1)
P.imshow(vignet, origin='lower', interpolation='nearest', vmin=vignet.min(), vmax=vignet.max())
P.title("Data")
P.subplot(1, 3, 2)
P.imshow(p(x, y), origin='lower', interpolation='nearest', vmin=vignet.min(), vmax=vignet.max())
P.scatter(vignet.shape[0]/2, vignet.shape[1]/2,marker="+")
P.annotate("({:.3f},{:.3f})".format(*barycenter), (vignet.shape[0]/3, vignet.shape[1]/3))
P.title("Model - psf = {:.2f}".format(2.3548*np.mean([p.x_stddev.value, p.y_stddev.value])))
P.subplot(1, 3, 3)
P.imshow(vignet - p(x, y), origin='lower', interpolation='nearest', vmin=-vignet.max()/10,vmax=vignet.max()/10)
P.title("Residual")
P.tight_layout()
if show :
P.show()
return p
def plot_fitted_model(self, sample, data, fig=None, xmin=-1, xmax=12, npoints=1000, nbins=100, epsilon=0.25):
"""Plot fitted model"""
# fetch group
group = [i for i, item in enumerate(data.groups.items()) if sample in item[1]][0]
# fetch data
counts = data.counts_norm[sample].values.astype('float')
counts[counts < 1] = epsilon
counts = np.log(counts)
# compute fitted model
x = np.reshape(np.linspace(xmin, xmax, npoints), (-1, 1))
xx = np.exp(x)
loglik = _compute_loglik(xx, self.log_phi, self.log_mu, self.beta[self.z[group]])
y = xx * np.exp(loglik) / self.nfeatures
# plot
fig = pl.figure() if fig is None else fig
pl.figure(fig.number)
pl.hist(counts, nbins, histtype='stepfilled', linewidth=0, normed=True, color='gray')
pl.plot(x, np.sum(y, 1), 'r')
pl.grid()
pl.xlabel('log counts')
pl.ylabel('density')
pl.legend(['model', 'data'], loc=0)
pl.tight_layout()
def plot(self, **kwargs):
"""
plot artifact rejection averaged signals for ECG and EOG onsets
Parameters
----------
raw :
raw_clean :
ch_name :
events :
event_id :
picks :
tmin :
tmax :
title :
colors :
alpha :
grid :
scale :
offset :
fontsize :
Returns
-------
"""
self._update_from_kwargs(**kwargs)
title = kwargs.get("title")
evt = kwargs.get("events")
counts = evt.shape[0]
# init figure
sig_raw, sig_clean, range, t = self._calc_data(self.raw,
self.raw_clean,
evt,
event_id=self.event_id,
tmin=self.tmin,
tmax=self.tmax,
picks=self.picks)
#--- ref channel e.g.: ECG
sig_picks = self.labels2picks(labels=self.ch_name)
sig_ref, _, _ = self._calc_signal(self.raw,
evt,
event_id=self.event_id,
tmin=self.tmin,
tmax=self.tmax,
picks=sig_picks)
if not isinstance(self.figures, (list)):
self.figures = []
# if self.idx == 1:
if not self._fig:
self.figures.append(plt.figure(self.fig_nr))
self._fig = self.figures[-1]
if title:
self.figure.suptitle(title, fontsize=12)
suptitle = kwargs.get("suptitle")
self.suptitle = suptitle
else:
self._fig = plt.figure(self.fig_nr)
#--- subplot(nrows,ncols,idx)
ax1 = plt.subplot(self.n_rows, self.n_cols, self.idx)
#--- sig raw
scl = self.scale.get("raw")
ylim = self._calc_ylimits(ranges=range,
factor=scl.get("factor"),
offset=self.offset)
self._plot(ax1, t, sig_raw * scl.get("factor"), scl.get("unit"),
"black")
#--- sig clean
ax2 = plt.subplot(self.n_rows, self.n_cols, self.idx + self.n_cols)
self._plot(ax2, t, sig_clean * scl.get("factor"), scl.get("unit"),
"black")
#---
scl = self.scale.get("ref")
ax3 = ax1.twinx(
) # instantiate a second axes that shares the same x-axis
color = 'tab:blue'
self._plot(ax3, t, sig_ref * scl.get("factor"), scl.get("unit"), "red")
ax3.tick_params(axis='y', labelcolor=color)
ax3.legend([self.ch_name + " cnts {}".format(counts)],
loc=2,
prop={'size': 8})
ax4 = ax2.twinx(
) # instantiate a second axes that shares the same x-axis
color = 'tab:blue'
self._plot(ax4, t, sig_ref * scl.get("factor"), scl.get("unit"),
"green")
ax4.tick_params(axis='y', labelcolor=color)
ax4.legend(["Clean " + self.ch_name + " cnts {}".format(counts)],
loc=2,
prop={'size': 8})
try:
ax1.set_ylim(ylim[0], ylim[1])
ax2.set_ylim(ylim[0], ylim[1])
except:
ax1.set_ylim(-1.0, 1.0)
ax2.set_ylim(-1.0, 1.0)
logger.error(
"ERROR in performance plot : can not set ylim : {}".format(
title))
plt.tight_layout()
def sample_of_trajectories(model, path, agent_ids=range(100), secveg_dynamics=False):
fig, (ax1, ax2, ax3) = plt.subplots(3, sharex='all', figsize=(6, 6))
ax1b = ax2.twinx()
if agent_ids == "all":
agent_ids = range(model.no_agents)
for inspect_id in agent_ids:
print("plotting trajectory %d" % inspect_id )
# print(sv_traj[0:dim])
plot_P, plot_qp, plot_k, plot_F, plot_S, plot_qs, *aux_vars = np.copy(
model.sv_traj.T[inspect_id * model.dim:(inspect_id + 1) * model.dim])
ax1.plot(model.t, plot_F, color='darkgreen', linewidth=.5, label='F', alpha=0.3)
ax1.plot(model.t, plot_P, color='lawngreen', linewidth=.5, label='P', alpha=0.3)
ax1.plot(model.t, plot_S, color='m', linewidth=.5, label='S', alpha=0.3)
ax2.plot(model.t, plot_qp, color='saddlebrown', linewidth=.5, label='q', alpha=0.3)
if secveg_dynamics:
ax2.plot(model.t, plot_qs, color='m', linewidth=.5, label=r'qs', alpha=0.3)
ax1b.plot(model.t, plot_k, 'b', linewidth=.5, label=r'$k$', alpha=0.3) # , marker='o', fillstyle = 'none')
plot_d, plot_a, plot_r, plot_l, plot_m = np.copy(
model.cv_traj.T[inspect_id * model.no_controls:(inspect_id + 1) * model.no_controls])
ax3.plot(model.t, plot_d, label='d', color='b', linewidth=.5, alpha=0.3)
ax3.plot(model.t, plot_a, label='a', color='r', linewidth=.5, alpha=0.3)
ax3.plot(model.t, plot_r, label='r', color='g', linewidth=.5, alpha=0.3)
ax3.plot(model.t, plot_l, label='l', color='m', linewidth=.5, alpha=0.3)
ax3.plot(model.t, plot_m, label='m', color='c', linewidth=.5, alpha=0.3)
ax1.set_ylabel(r'$F, P, S$', fontsize=16)
if not model.pars["absolute_area"]:
ax1.set_ylim([-0.1, 1.1])
handles, labels = ax1.get_legend_handles_labels()
ax1.legend(handles[0:3], labels[0:3], loc='upper left')
ax2.set_ylabel(r'$q$', fontsize=16, color='saddlebrown')
for tl in ax2.get_yticklabels():
tl.set_color('saddlebrown')
ax1b.set_ylabel(r'$k$', color='b', fontsize=16)
for tick_label in ax1b.get_yticklabels():
tick_label.set_color('b')
ax3.set_xlabel(r't', fontsize=16)
ax3.set_ylim([-0.2, 1])
handles, labels = ax3.get_legend_handles_labels()
ax3.legend(handles[0:5], labels[0:5], loc='upper left')
ax3.text(-1., -0.1, 'strategy', horizontalalignment='right',
verticalalignment='center')
plt.tight_layout()
fig.savefig(path, dpi=model.plot_pars["dpi_saving"])
fig.clf()
plt.close(fig)
return 0
def plot_single_agent(model, path, node_id=1,
plot_areas=True,
plot_qk=True,
plot_controls=False,
plot_aux=False,
secveg_dynamics=False,
):
axis_label_fontsize = 14
# print(sv_traj[0:dim])
plot_p, plot_qp, plot_k, plot_f, plot_s, plot_qs, *aux_vars = np.copy(model.sv_traj.T[node_id * model.dim:(node_id + 1) * model.dim])
no_plots = sum([plot_areas, plot_qk, plot_controls, plot_aux])
fig, ax = plt.subplots(no_plots, sharex='all', figsize=(6, no_plots * 2 + 1))
if no_plots == 1:
ax = [ax]
# current axis
axis_counter = 0
# plot labels
plot_labels = ["(a)", "(b)", "(c)", "(d)", "(e)", "(f)"]
annotation_pos = (-0.15, 1)
annotation_offset = (1, -1)
if plot_areas:
cax = ax[axis_counter]
cax.plot(model.t, plot_f, color='darkgreen', linewidth=2., label='Forest F')
cax.plot(model.t, plot_p, color='lawngreen', linewidth=2., label='Pasture P')
cax.plot(model.t, plot_s, color='m', linewidth=2., label='Sec. Vegetation S')
cax.set_ylabel(r'$F, P, S$ [ha]', fontsize=axis_label_fontsize)
if not model.pars["absolute_area"]:
cax.set_ylim([-0.1, 1.1])
cax.legend(loc='right')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
if plot_qk:
cax = ax[axis_counter]
cax.plot(model.t, plot_qp, color='saddlebrown', linewidth=2., label='pasture productivity q')
if secveg_dynamics:
cax.plot(model.t, plot_qs, color='m', linewidth=2., label='soil quality (on S) v')
if secveg_dynamics:
cax.set_ylabel(r'$q, v$ [a.u.]', fontsize=axis_label_fontsize, color='k')
else:
cax.set_ylabel(r'$q$ [a.u.]', fontsize=axis_label_fontsize, color='saddlebrown')
for tl in cax.get_yticklabels():
tl.set_color('saddlebrown')
#cax.set_zorder(100)
axt = cax.twinx()
if max(plot_k) > 10000000:
rescale_k = 1000000
elif max(plot_k) > 10000:
rescale_k = 1000
else:
rescale_k = 1
axt.plot(model.t, plot_k/rescale_k, 'b', linewidth=2., label=r'savings $k$') # , marker='o', fillstyle = 'none')
if rescale_k == 1:
axt.set_ylabel(r'savings [BRL]', color='b', fontsize=axis_label_fontsize)
else:
axt.set_ylabel(r'savings [{} BRL]'.format(rescale_k), color='b', fontsize=axis_label_fontsize)
for tick_label in axt.get_yticklabels():
tick_label.set_color('b')
if secveg_dynamics:
cax.legend(loc='lower right') # loc='upper/lower right'
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
if plot_controls:
cax = ax[axis_counter]
plot_d, plot_a, plot_r, plot_l, plot_m = np.copy(model.cv_traj.T[node_id * model.no_controls:(node_id + 1)
* model.no_controls])
cax.plot(model.t, plot_d, label='d', color='b')
cax.plot(model.t, plot_a, label='a', color='r')
cax.plot(model.t, plot_r, label='r', color='g')
cax.plot(model.t, plot_l, label='l', color='m')
cax.plot(model.t, plot_m, label='m', color='c')
max_plot = np.array([plot_d, plot_a, plot_r, plot_l, plot_m]).max().max()
cax.set_ylim([-0.2*max_plot, 1.1 * max_plot])
# print(strategy_traj.T[inspect_id])
# visualize strategy
for i, strategy_t in enumerate(model.strategy_traj.T[node_id]):
if strategy_t == 0:
color = 'g'
else:
color = 'r'
cax.plot((i - 0.5, i + 0.5), (-0.1*max_plot, -0.1*max_plot), linewidth=10, color=color, solid_capstyle='butt')
cax.legend(loc='upper right')
cax.text(-1., -0.1*max_plot, 'strategy', horizontalalignment='right',
verticalalignment='center')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
if plot_aux:
cax = ax[axis_counter]
for i, aux_var in enumerate(aux_vars):
cax.plot(model.t, aux_var, label=model.state_variables[model.dim - model.no_aux_vars + i])
cax.legend(loc='upper right')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
cax.set_xlabel(r'time [years]', fontsize=axis_label_fontsize)
plt.tight_layout()
fig.savefig(path, dpi=model.plot_pars["dpi_saving"])
fig.clf()
plt.close(fig)
return 0
def plot_trajectory_stat(
stats_df,
path,
measure="median",
bounds=None,
percentiles=None,
plot_areas=True,
plot_controls=False,
plot_strategy=True,
plot_active_ranches=False,
plot_qk=True,
plot_price=False,
plot_gini=False,
secveg_dynamics=False,
t_min=None,
dpi=150,
ensemble_stats=False):
axis_label_fontsize = 14
# show also standard deviation/percentiles of aggregate variables
# with the following alpha
range_alpha = 0.2
t = stats_df.index.values
if t_min is None:
t_min = min(t)
t_max = max(t)
t = t[t_min:t_max]
no_plots = sum([plot_areas, plot_controls, plot_strategy, plot_qk, plot_price, plot_gini])
fig, ax = plt.subplots(no_plots, sharex='all', figsize=(6, no_plots * 2 + 1))
# plot labels
plot_labels = ["(a)", "(b)", "(c)", "(d)", "(e)", "(f)"]
annotation_pos = (-0.19, 1)
annotation_offset = (1, -1)
# current axis
axis_counter = 0
if bounds is 'percentiles':
if type(percentiles) is not list:
print("Error: Need percentiles for plotting!")
return 1
lb_label = "perc" + str(percentiles[0])
ub_label = "perc" + str(percentiles[1])
elif bounds is 'minmax':
lb_label = 'min'
ub_label = 'max'
elif bounds is 'std' or bounds is None:
pass
else:
print("No valid bounds chosen for plotting")
if plot_areas:
cax = ax[axis_counter]
if bounds is 'std':
cax.fill_between(t, stats_df['F', measure][t_min:t_max]
- stats_df['F', 'std'][t_min:t_max],
stats_df['F', measure][t_min:t_max]
+ stats_df['F', 'std'][t_min:t_max],
color='darkgreen',
alpha=range_alpha)
cax.fill_between(t, stats_df['P', measure][t_min:t_max]
- stats_df['P', 'std'][t_min:t_max],
stats_df['P', measure][t_min:t_max]
+ stats_df['P', 'std'][t_min:t_max], color='lawngreen',
alpha=range_alpha)
cax.fill_between(t, stats_df['S', measure][t_min:t_max]
- stats_df['S', 'std'][t_min:t_max],
stats_df['S', measure][t_min:t_max]
+ stats_df['S', 'std'][t_min:t_max], color='m', alpha=range_alpha)
elif bounds in ['percentiles', 'minmax']:
cax.fill_between(t, stats_df['F', lb_label][t_min:t_max],
stats_df['F', ub_label][t_min:t_max], color='darkgreen',
alpha=range_alpha)
cax.fill_between(t, stats_df['P', lb_label][t_min:t_max],
stats_df['P', ub_label][t_min:t_max], color='lawngreen',
alpha=range_alpha)
cax.fill_between(t, stats_df['S', lb_label][t_min:t_max],
stats_df['S', ub_label][t_min:t_max], color='m', alpha=range_alpha)
cax.plot(t, stats_df['F', measure][t_min:t_max], color='darkgreen',
linewidth=2., label='Forest F')
cax.plot(t, stats_df['P', measure][t_min:t_max], color='lawngreen',
linewidth=2., label='Pasture P')
cax.plot(t, stats_df['S', measure][t_min:t_max], color='m',
linewidth=2., label='Sec. vegetation S')
cax.set_ylabel(r'$F, P, S$ [ha]', fontsize=axis_label_fontsize)
if stats_df['F', measure].max() < 1:
cax.set_ylim([-0.1, 1.1])
cax.set_xlim([t_min, t_max])
cax.legend(loc='right')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
if plot_qk:
cax = ax[axis_counter]
cax.plot(t, stats_df['q', measure][t_min:t_max], color='saddlebrown',
linewidth=2., label='pasture productivity q')
if bounds is 'std':
cax.fill_between(t, stats_df['q', measure][t_min:t_max]
- stats_df['q', 'std'][t_min:t_max],
stats_df['q', measure][t_min:t_max]
+ stats_df['q', 'std'][t_min:t_max], color='saddlebrown',
alpha=range_alpha)
elif bounds in ['percentiles', 'minmax']:
cax.fill_between(t, stats_df['q', lb_label][t_min:t_max],
stats_df['q', ub_label][t_min:t_max], color='saddlebrown',
alpha=range_alpha)
if secveg_dynamics:
cax.plot(t, stats_df['v', measure][t_min:t_max], color='m',
linewidth=2., label='soil quality on S v')
if bounds is 'std':
cax.fill_between(t, stats_df['v', measure][t_min:t_max]
- stats_df['v', 'std'][t_min:t_max],
stats_df['v', measure][t_min:t_max]
+ stats_df['v', 'std'][t_min:t_max], color='m',
alpha=range_alpha)
elif bounds in ['percentiles', 'minmax']:
cax.fill_between(t, stats_df['v', lb_label][t_min:t_max],
stats_df['v', ub_label][t_min:t_max], color='m',
alpha=range_alpha)
cax.set_ylabel(r'$q$, $v$ [a.u.]',
fontsize=axis_label_fontsize, color='k')
else:
cax.set_ylabel(r'$q$ [a.u.]', fontsize=axis_label_fontsize,
color='saddlebrown')
if not secveg_dynamics:
for tl in cax.get_yticklabels():
tl.set_color('saddlebrown')
# plot k
if max(stats_df['k', measure][t_min:t_max]) > 500000:
rescale_k = 1000000
rescale_k_label = "million "
elif max(stats_df['k', measure][t_min:t_max]) > 1000:
rescale_k = 1000
rescale_k_label = "1000 "
else:
rescale_k = 1
rescale_k_label = ""
cax2 = cax.twinx()
cax2.set_xlim([t_min, t_max])
cax2.plot(t, stats_df['k', measure][t_min:t_max]/rescale_k, 'b', linewidth=2., label=r'savings $k$')
# , marker='o', fillstyle = 'none')
label_str = 'savings\n[{}BRL]'.format(rescale_k_label)
cax2.set_ylabel(label_str, color='b', fontsize=axis_label_fontsize)
if bounds is 'std':
cax2.fill_between(t, (stats_df['k', measure][t_min:t_max]
- stats_df['k', 'std'][t_min:t_max])/rescale_k,
(stats_df['k', measure][t_min:t_max]
+ stats_df['k', 'std'][t_min:t_max])/rescale_k,
color='b', alpha=range_alpha)
elif bounds in ['percentiles', 'minmax']:
cax2.fill_between(t, stats_df['k', lb_label][t_min:t_max]/rescale_k,
stats_df['k', ub_label][t_min:t_max]/rescale_k, color='b', alpha=range_alpha)
for tick_label in cax2.get_yticklabels():
tick_label.set_color('b')
if secveg_dynamics:
cax.legend(loc='lower right') # loc='upper right')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
if plot_strategy:
cax = ax[axis_counter]
if ensemble_stats:
if bounds is 'std':
cax.fill_between(t, stats_df["strategy", measure][t_min:t_max]
- stats_df["strategy", "std"][t_min:t_max],
stats_df["strategy", measure][t_min:t_max]
+ stats_df["strategy", "std"][t_min:t_max],
color='k', alpha=range_alpha)
elif bounds in ['percentiles', 'minmax']:
cax.fill_between(t, stats_df["strategy", lb_label][t_min:t_max],
stats_df["strategy", ub_label][t_min:t_max], color='k', alpha=range_alpha)
cax.plot(t, stats_df["strategy", measure][t_min:t_max], linewidth=2., color='k')
else:
cax.plot(t, stats_df["strategy", "mean"][t_min:t_max], linewidth=2., color='k')
cax.set_ylim([0., 1.])
cax.set_ylabel(r'intensification', fontsize=axis_label_fontsize)
if plot_active_ranches:
cax.plot(t, stats_df["active_ranches", "mean"][t_min:t_max], linewidth=2., color='b')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
if plot_price:
cax = ax[axis_counter]
if ensemble_stats:
if bounds is 'std':
cax.fill_between(t, (stats_df["cattle_price", measure][t_min:t_max]
- stats_df["cattle_price", "std"][t_min:t_max])/1000,
(stats_df["cattle_price", measure][t_min:t_max]
+ stats_df["cattle_price", "std"][t_min:t_max])/1000,
color='k', alpha=range_alpha)
elif bounds in ['percentiles', 'minmax']:
cax.fill_between(t, stats_df["cattle_price", lb_label][t_min:t_max]/1000,
stats_df["cattle_price", ub_label][t_min:t_max]/1000, color='k', alpha=range_alpha)
cax.plot(t, stats_df["cattle_price", measure][t_min:t_max]/1000, linewidth=2., color='k')
else:
cax.plot(t, stats_df["cattle_price", "mean"][t_min:t_max]/1000, linewidth=2., color='k')
cax.set_ylabel("cattle price\n[1000 BRL]", fontsize=axis_label_fontsize)
cax.set_ylim(bottom=0.9, top=3.7)
cax2 = cax.twinx()
if stats_df["cattle_quantity", measure][t_min:t_max].max() > 500000:
rescale_cattle_quantity = 1000000
print_rescale_cattle_quantity = "million"
elif stats_df["cattle_quantity", measure][t_min:t_max].max() > 1000:
rescale_cattle_quantity = 1000
print_rescale_cattle_quantity = "1000"
else:
rescale_cattle_quantity = 1
print_rescale_cattle_quantity = ""
if ensemble_stats:
if bounds is 'std':
cax2.fill_between(t, (stats_df["cattle_quantity", measure][t_min:t_max]
- stats_df["cattle_quantity", "std"][t_min:t_max])
/ rescale_cattle_quantity,
(stats_df["cattle_quantity", measure][t_min:t_max]
+ stats_df["cattle_quantity", "std"][t_min:t_max])
/ rescale_cattle_quantity,
color='r', alpha=range_alpha)
elif bounds in ['percentiles', 'minmax']:
cax2.fill_between(t, stats_df["cattle_quantity", lb_label][t_min:t_max]/rescale_cattle_quantity,
stats_df["cattle_quantity", ub_label][t_min:t_max]/rescale_cattle_quantity,
color='r', alpha=range_alpha)
cax2.plot(t, stats_df["cattle_quantity", measure][t_min:t_max]/rescale_cattle_quantity, linewidth=2., color='r')
else:
cax2.plot(t, stats_df["cattle_quantity", "mean"][t_min:t_max], linewidth=2., color='r')
if rescale_cattle_quantity == 1:
cax2.set_ylabel('cattle production\n[heads]', fontsize=axis_label_fontsize, color='r')
else:
cax2.set_ylabel('cattle production\n[{} heads]'.format(print_rescale_cattle_quantity), fontsize=axis_label_fontsize, color='r')
for tl in cax2.get_yticklabels():
tl.set_color('r')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
if plot_controls:
cax = ax[axis_counter]
cax.plot(t, stats_df['d', measure][t_min:t_max],
label=r'$\left\langle d \right\rangle$',
color='b')
cax.plot(t, stats_df['a', measure][t_min:t_max],
label=r'$\left\langle a \right\rangle$',
color='r')
cax.plot(t, stats_df['r', measure][t_min:t_max],
label=r'$\left\langle r \right\rangle$',
color='g')
# ax4.plot(t, plot_l, label=r'$\left\langle l \right\rangle$',
# color='m')
cax.plot(t, stats_df['m', measure][t_min:t_max],
label=r'$\left\langle m \right\rangle$',
color='c')
cax.set_xlim([t_min, t_max])
cax.legend(loc='upper right')
cax.annotate(plot_labels[axis_counter], xy=annotation_pos, xycoords='axes fraction', fontsize=axis_label_fontsize,
xytext=annotation_offset, textcoords='offset points',
horizontalalignment='left', verticalalignment='top')
axis_counter += 1
cax.set_xlim([t_min, t_max])
cax.set_xlabel(r'time [years]', fontsize=axis_label_fontsize)
plt.tight_layout()
if type(path) is not list:
path = [path]
for p in path:
fig.savefig(p, dpi=dpi)
fig.clf()
plt.close(fig)
return 0
def plot_data(data,
name='',
date=[0, 0],
smas=var.default_smas,
emas=var.default_emas,
entry_points=None,
exit_points=None,
market_name='',
to_file=False,
show_smas=False,
show_emas=False,
show_bbands=False):
'''
Plots selected data.
entry_points is a tuple of lists: (entry_points_x,entry_points_y)
'''
#plt.clf()
# For when it's called outside backtest.
if date != [0, 0]:
if len(data) != date[1] - date[0]:
data = data[date[0]:date[1]]
f, (ax1, ax2, ax3) = plt.subplots(3,
sharex=True,
figsize=(9, 4),
gridspec_kw={'height_ratios': [3, 1, 1]})
ax1.grid(True)
ax2.grid(True)
ax3.grid(True)
# var date is causing conflicts. using name date.
if date[1] == 0:
end_date = len(data)
else:
end_date = date[1]
x = range(date[0], end_date)
ax1.plot(x, data.Last, color='black', linewidth=1, alpha=0.65)
if show_bbands:
bb_upper, bb_lower, bb_sma = bollinger_bands(data.Last, 10, 2)
#ax1.plot(x, bb_upper, color='red', linestyle='none', linewidth=1)
#ax1.plot(x, bb_lower, color='green', linestyle='none', linewidth=1)
ax1.fill_between(x, bb_sma, bb_upper, color='green', alpha=0.3)
ax1.fill_between(x, bb_lower, bb_sma, color='red', alpha=0.3)
if show_smas:
for sma in smas:
ax1.plot(x, data.Last.rolling(sma).mean())
if show_emas:
for ema in emas:
ax1.plot(x, data.Last.ewm(ema).mean())
if entry_points:
ax1.plot(entry_points[0],
entry_points[1],
marker='o',
linestyle='None',
color='green',
alpha=0.75)
if exit_points:
ax1.plot(exit_points[0],
exit_points[1],
marker='o',
linestyle='None',
color='red',
alpha=0.75)
ax2.bar(x, data.BaseVolume.iloc[:], 1, color='black', alpha=0.55)
try:
ax3.plot(x, data.OpenSell.iloc[:])
except Exception as e:
ax3.plot(x, data.High.iloc[:])
plt.xlim(date[0], end_date)
plt.tight_layout()
f.subplots_adjust(hspace=0)
if to_file:
if not name:
name = 'fig_test' + str(time())
f.savefig(var.fig_dir + name + '.pdf', bbox_inches='tight')
plt.close(f)
#plt.show()
return True
def make_model_evaluation(df_nonnan, model_path, ls_pred_dt, cfg_tds, cfg_op):
X_test_ls = []
y_test_ls = []
cmap_pred_dt = plt.cm.get_cmap('viridis_r')
## Import dictionary with selected models:
train_path_name = os.path.join(
model_path, "model_dict_t0diff_maxdepth6_selfeat_gain.pkl")
with open(train_path_name, "rb") as file:
dict_sel_model = pickle.load(file)
plt.close()
fig = plt.figure(num=1, figsize=(7, 6))
## Loop over lead times:
for i, pred_dt in enumerate(ls_pred_dt):
if i == 0:
xgb_model_ls = []
pred_model_ls = []
Rank_obs_ls = []
top_features_ls = []
df_param_ls_diff = []
df_param_ls_rank = []
df_param_ls_rank_PM = []
df_param_ls_rank_pers = []
Rank_pred_XGB_ls = []
Rank_pred_XGB_PM_ls = []
if len(X_test_ls) == len(ls_pred_dt) and len(y_test_ls) == len(
ls_pred_dt):
X_test = X_test_ls[i]
y_test = y_test_ls[i]
else:
if i == 0:
X_test_ls = []
y_test_ls = []
X_train, X_test, y_train, y_test = ipt.get_model_input(
df_nonnan,
del_TRTeqZero_tpred=True,
split_Xy_traintest=True,
X_normalise=False,
pred_dt=pred_dt,
check_for_nans=False,
verbose=True)
del (X_train, y_train)
X_test_ls.append(X_test)
y_test_ls.append(y_test)
## Load XGB model fitted to all features:
with open(
os.path.join(model_path,
"model_%i_t0diff_maxdepth6.pkl" % pred_dt),
"rb") as file:
xgb_model_feat = pickle.load(file)
xgb_model_ls.append(xgb_model_feat)
top_features = pd.DataFrame.from_dict(
xgb_model_feat.get_booster().get_score(importance_type='gain'),
orient="index",
columns=["F_score"]).sort_values(by=['F_score'], ascending=False)
top_features_ls.append(top_features)
## Get specific predictive model for this leadtime:
pred_model = dict_sel_model["pred_mod_%i" % pred_dt]
pred_model_ls.append(pred_model)
## Check that features agree:
features_pred_model = pred_model.get_booster().feature_names
n_features = len(features_pred_model)
if set(features_pred_model) != set(top_features.index[:n_features]):
raise ValueError(
"Features of predictive model and top features of model fitted with all features do not agree"
)
## Make prediction of TRT Rank differences:
TRT_diff_pred = pred_model.predict(X_test[features_pred_model])
## Get set of different TRT Rank predictions:
Rank_obs, Rank_pred_XGB, Rank_pred_XGB_PM, Rank_pred_pers, Rank_pred_pers_PM, \
Rank_pred_diff, Diff_pred_XGB = get_obs_fcst_TRT_Rank(X_test["TRT_Rank|0"], TRT_diff_pred, y_test, X_test["TRT_Rank|-5"])
Rank_obs_ls.append(Rank_obs)
Rank_pred_XGB_ls.append(Rank_pred_XGB)
Rank_pred_XGB_PM_ls.append(Rank_pred_XGB_PM)
## Plot scatterplots obs vs. predicted:
plot_pred_vs_obs_core(y_test,
Diff_pred_XGB.values,
pred_dt,
"_XGB%i" % n_features,
cfg_tds,
outtype="TRT_Rank_diff")
plot_pred_vs_obs_core(Rank_obs,
Rank_pred_XGB.values,
pred_dt,
"_XGB%i" % n_features,
cfg_tds,
outtype="TRT_Rank")
plot_pred_vs_obs_core(Rank_obs,
Rank_pred_XGB_PM.values,
pred_dt,
"_XGB%i-ProbMatch" % n_features,
cfg_tds,
outtype="TRT_Rank")
plot_pred_vs_obs_core(Rank_obs,
Rank_pred_pers.values,
pred_dt,
"_Pers",
cfg_tds,
outtype="TRT_Rank")
plot_pred_vs_obs_core(Rank_obs,
Rank_pred_pers_PM.values,
pred_dt,
"_Pers-ProbMatch",
cfg_tds,
outtype="TRT_Rank")
plot_pred_vs_obs_core(Rank_obs,
Rank_pred_diff.values,
pred_dt,
"_ConstDiff",
cfg_tds,
outtype="TRT_Rank")
## Calculate different term elements for R^2 / Brier Score calculation:
df_param_ls_diff.append(
get_R2_param(y_test.values, Diff_pred_XGB.values))
df_param_ls_rank.append(
get_R2_param(Rank_obs.values, Rank_pred_XGB.values))
df_param_ls_rank_PM.append(
get_R2_param(Rank_obs.values, Rank_pred_XGB_PM.values))
df_param_ls_rank_pers.append(
get_R2_param(Rank_obs.values, Rank_pred_pers.values))
## Calculate statistics for Taylor Diagram:
stat_pred_XGB = sm.taylor_statistics(predicted=Rank_pred_XGB.values,
reference=Rank_obs.values)
stat_pred_XGB_PM = sm.taylor_statistics(
predicted=Rank_pred_XGB_PM.values, reference=Rank_obs.values)
stat_pred_pred_pers = sm.taylor_statistics(
predicted=Rank_pred_pers.values, reference=Rank_obs.values)
stat_pred_pred_diff = sm.taylor_statistics(
predicted=Rank_pred_diff.values, reference=Rank_obs.values)
stat_pred_pred_pers_PM = sm.taylor_statistics(
predicted=Rank_pred_pers_PM.values, reference=Rank_obs.values)
sdev = np.array([
stat_pred_XGB['sdev'][0], stat_pred_XGB['sdev'][1],
stat_pred_XGB_PM['sdev'][1], stat_pred_pred_pers['sdev'][1]
])
crmsd = np.array([
stat_pred_XGB['crmsd'][0], stat_pred_XGB['crmsd'][1],
stat_pred_XGB_PM['crmsd'][1], stat_pred_pred_pers['crmsd'][1]
])
ccoef = np.array([
stat_pred_XGB['ccoef'][0], stat_pred_XGB['ccoef'][1],
stat_pred_XGB_PM['ccoef'][1], stat_pred_pred_pers['ccoef'][1]
])
#sdev = np.array([stat_pred_XGB['sdev'][0], stat_pred_XGB['sdev'][1], stat_pred_XGB_PM['sdev'][1], stat_pred_pred_pers['sdev'][1], stat_pred_pred_diff['sdev'][1]])
#crmsd = np.array([stat_pred_XGB['crmsd'][0], stat_pred_XGB['crmsd'][1], stat_pred_XGB_PM['crmsd'][1], stat_pred_pred_pers['crmsd'][1], stat_pred_pred_diff['crmsd'][1]])
#ccoef = np.array([stat_pred_XGB['ccoef'][0], stat_pred_XGB['ccoef'][1], stat_pred_XGB_PM['ccoef'][1], stat_pred_pred_pers['ccoef'][1], stat_pred_pred_diff['ccoef'][1]])
## Plot Taylor Diagram:
col_point = cmap_pred_dt(float(i) / len(ls_pred_dt))
col_point = (col_point[0], col_point[1], col_point[2], 0.8)
plot_markerLabel = ["Obs", "+%imin" % pred_dt, "", ""]
plot_markerLabelColor = "black"
if i == 0:
plot_markerLegend = 'on'
plot_overlay = 'off'
else:
plot_markerLegend = "on"
plot_overlay = 'on'
#plot_markerLabelColor = None
if i == len(ls_pred_dt) - 1:
plot_markerLabelColor = None
plot_markerLabel = ["Obs", "XGB", "XGB (PM)", "Persistance"]
sm.taylor_diagram(
sdev / sdev[0],
crmsd,
ccoef,
styleOBS='-',
colOBS='darkred',
markerobs='o',
titleOBS='Obs',
markerLabel=plot_markerLabel,
markerLabelColor=plot_markerLabelColor,
alpha=0.1,
markerColor=col_point,
markerLegend=plot_markerLegend,
axismax=1.2,
markerSize=5,
colRMS='grey',
styleRMS='--',
widthRMS=0.8,
rincRMS=0.25,
tickRMS=np.arange(0.25, 1.5, 0.25), #titleRMSangle = 110,
colSTD='grey',
styleSTD='-.',
widthSTD=0.8,
colCOR='grey',
styleCOR=':',
widthCOR=0.8,
overlay=plot_overlay)
## Save Taylor Diagram:
get_time_delta_colorbar(fig, ls_pred_dt, cmap_pred_dt,
[0.7, 0.5, 0.05, 0.3])
plt.savefig(
os.path.join(cfg_tds["fig_output_path"], "Taylor_Diagram_cmap.pdf"))
plt.close()
## Plot histogram showing the effect of probability matching:
print(
"Save dataframe with observed, predicted, and predicted & PM TRT Ranks"
)
Rank_obs_df = pd.concat(Rank_obs_ls, axis=1, sort=True)
Rank_obs_df.columns = [
"TRT_Rank_obs|%i" % pred_dt for pred_dt in ls_pred_dt
]
Rank_pred_XGB_df = pd.concat(Rank_pred_XGB_ls, axis=1, sort=True)
Rank_pred_XGB_df.columns = [
"TRT_Rank_pred|%i" % pred_dt for pred_dt in ls_pred_dt
]
Rank_pred_XGB_PM_df = pd.concat(Rank_pred_XGB_PM_ls, axis=1, sort=True)
Rank_pred_XGB_PM_df.columns = [
"TRT_Rank_pred_PM|%i" % pred_dt for pred_dt in ls_pred_dt
]
#plot_hist_probmatch(Rank_pred_XGB_df, Rank_pred_XGB_PM_df)
Rank_obs_pred_df = pd.concat(
[Rank_obs_df, Rank_pred_XGB_df, Rank_pred_XGB_PM_df],
axis=1,
sort=True)
## Get dataframe with observed, predicted, and predicted & PM TRT Ranks for operational PM:
op_path_name = os.path.join(cfg_op["XGB_model_path"],
"TRT_Rank_obs_pred.pkl")
with open(op_path_name, "wb") as file:
pickle.dump(Rank_obs_pred_df, file, protocol=2)
print(" saved dict to 'XGB_model_path' location:\n %s" % op_path_name)
prt_txt = """
---------------------------------------------------------------------------------
The file 'TRT_Rank_obs_pred.pkl' in the
directory '%s'
is now used for the operational probability matching procedure, be aware of
that!
---------------------------------------------------------------------------------\n""" % (
cfg_op["XGB_model_path"])
print(prt_txt)
## Plot skill scores as function of lead-time:
df_R2_param_rank = pd.concat(df_param_ls_rank,
axis=0).set_index(np.array(ls_pred_dt))
df_R2_param_rank_PM = pd.concat(df_param_ls_rank_PM,
axis=0).set_index(np.array(ls_pred_dt))
df_R2_param_diff = pd.concat(df_param_ls_diff,
axis=0).set_index(np.array(ls_pred_dt))
df_R2_param_rank_pers = pd.concat(df_param_ls_rank_pers,
axis=0).set_index(np.array(ls_pred_dt))
plot_stats(df_R2_param_rank, "TRT_Rank", cfg_tds)
plot_stats(df_R2_param_diff, "TRT_Rank_diff", cfg_tds)
plot_stats_nice(df_R2_param_rank, "TRT_Rank", cfg_tds)
plot_stats_nice(df_R2_param_diff, "TRT_Rank_diff", cfg_tds)
plot_stats_nice(df_R2_param_rank_pers, "TRT_Rank_pers", cfg_tds)
plot_stats_nice(df_R2_param_rank_PM, "TRT_Rank_PM", cfg_tds)
## Print IDs of long TRT cells in testing dataset:
print(
"\nThese are the IDs of long TRT cells (>25 time steps) in the testing dataset:"
)
TRT_ID = X_test_ls[-1].index
TRT_ID = [TRT_ID_i[13:] for TRT_ID_i in TRT_ID.values]
TRT_ID_count = Counter(TRT_ID)
TRT_ID_count_sort = [
(k, TRT_ID_count[k])
for k in sorted(TRT_ID_count, key=TRT_ID_count.get, reverse=True)
]
TRT_ID_count_sort_pd = pd.DataFrame(np.array(TRT_ID_count_sort),
columns=["TRT_ID", "Count"])
TRT_ID_count_sort_pd["Count"] = TRT_ID_count_sort_pd["Count"].astype(
np.uint16, inplace=True)
TRT_ID_long = TRT_ID_count_sort_pd.loc[TRT_ID_count_sort_pd["Count"] > 25]
print(TRT_ID_long)
TRT_ID_casestudy = [
"2018080721250094", "2018080721300099", "2018080711400069",
"2018080710200036"
]
print(" Making analysis for TRT IDs (hardcoded!): %s" % TRT_ID_casestudy)
TRT_ID_long_sel = TRT_ID_long.loc[TRT_ID_long['TRT_ID'].isin(
TRT_ID_casestudy)]
df_feature_ts_plot = pd.DataFrame.from_dict({
"Radar":
["CZC_lt57dBZ|-45|SUM", "CZC_lt57dBZ|-45|SUM", "CZC_lt57dBZ|-45|SUM"],
"Satellite": [
"IR_097_stat|-20|PERC05", "IR_097_stat|-15|PERC01",
"IR_097_stat|-20|MIN"
],
"COSMO": [
"CAPE_MU_stat|-10|PERC50", "CAPE_MU_stat|-5|PERC75",
"CAPE_ML_stat|0|SUM"
],
"Lightning": [
"THX_densIC_stat|-30|SUM", "THX_curr_pos_stat|-40|SUM",
"THX_curr_pos_stat|-30|SUM"
]
})
for i_sel in range(len(TRT_ID_long_sel)):
print(" Working on cell %s" % TRT_ID_long_sel.iloc[i_sel]["TRT_ID"])
plot_pred_time_series(TRT_ID_long_sel.iloc[i_sel], df_nonnan,
Rank_pred_XGB_ls, ls_pred_dt, cfg_tds)
plot_pred_time_series(TRT_ID_long_sel.iloc[i_sel],
df_nonnan,
Rank_pred_XGB_PM_ls,
ls_pred_dt,
cfg_tds,
path_addon="PM",
title_addon=" (PM)")
plot_var_time_series_dt0_multiquant(TRT_ID_long_sel.iloc[i_sel],
df_nonnan, cfg_tds)
for i_pred_dt, pred_dt in enumerate([10, 20, 30]):
fig = plt.figure(figsize=[10, 6])
ax_rad = fig.add_subplot(2, 2, 1)
ax_sat = fig.add_subplot(2, 2, 2)
ax_cos = fig.add_subplot(2, 2, 3)
ax_thx = fig.add_subplot(2, 2, 4)
ax_ls = [ax_rad, ax_sat, ax_cos, ax_thx]
#fig, axes = plt.subplots(2,2)
#fig.set_size_inches(8,6)
for i_source, source in enumerate(
["Radar", "Satellite", "COSMO", "Lightning"]):
ls_feat_param = df_feature_ts_plot[source].iloc[
i_pred_dt].split("|")
past_dt = np.arange(-45, 0,
5) if int(ls_feat_param[1]) != 0 else [0]
ax_ls[i_source] = plot_var_time_series(
TRT_ID_long_sel.iloc[i_sel],
df_nonnan,
ls_feat_param[0],
ls_feat_param[2],
past_dt=past_dt,
dt_highlight=int(ls_feat_param[1]),
ax=ax_ls[i_source])
plt.tight_layout()
plt.savefig(
os.path.join(
cfg_tds["fig_output_path"], "Feat_series_%i_%s.pdf" %
(pred_dt, TRT_ID_long_sel.iloc[i_sel]["TRT_ID"])))
plt.close()
ax2.errorbar(xlocs,
binned_correlation_times,
yerr=2 * errs,
marker='o',
markersize=5)
#ax6.plot(xlocs,binned_correlation_times,marker='o',markersize=4)
ax1.set_xlabel(r'Cell speed ($\mu$m/min)')
ax1.set_ylabel('Persistence time (min)')
ax4.set_ylabel('Persistence time (min)')
ax1.set_title('Zebrafish T cells', fontsize=10)
ax3.set_xlabel(r'Cell speed ($\mu$m/min)')
ax4.set_xlabel(r'Cell speed ($\mu$m/min)')
ax5.set_xlabel(r'Cell speed ($\mu$m/min)')
ax6.set_xlabel(r'Cell speed ($\mu$m/min)')
ax2.set_xlabel(r'Cell speed ($\mu$m/min)')
ax3.set_title('UPT', fontsize=10)
ax4.set_title('UPT with noise', fontsize=10)
ax5.set_title('S and P uncorrelated', fontsize=10)
ax6.set_title('S and P uncorrelated with noise', fontsize=10)
ax2.set_title('SPC with noise', fontsize=10)
ax1.text(-.1, 1.1, 'A', fontsize=12, transform=ax1.transAxes)
ax2.text(-.1, 1.1, 'B', fontsize=12, transform=ax2.transAxes)
ax3.text(-.1, 1.1, 'C', fontsize=12, transform=ax3.transAxes)
ax4.text(-.1, 1.1, 'D', fontsize=12, transform=ax4.transAxes)
ax5.text(-.1, 1.1, 'E', fontsize=12, transform=ax5.transAxes)
ax6.text(-.1, 1.1, 'F', fontsize=12, transform=ax6.transAxes)
pt.tight_layout()
pt.savefig(
'/Users/ejerison/Dropbox/imaging_data/figures/empirical_sims_v2.pdf')
def flat_corr_matrix(df,
pdf=None,
tight=False,
labels=None,
label_size=None,
size=12,
n_labels=3,
fontsize='auto',
draw_cbar=False,
tick_label_rotation=45,
formatter='%.2e',
label_rotation=45,
cmap='PiYG'):
""" Draws a flat correlation matrix of df
Args:
df:
pdf:
tight:
col_numbers:
labels:
label_size:
size:
n_labels:
fontsize:
draw_cbar:
rotation:
formatter:
Returns:
"""
assert isinstance(
df, pd.DataFrame), 'Argument of wrong type! Needs pd.DataFrame'
n_vars = np.shape(df)[1]
fontsize = np.interp(n_vars, (0, 10),
(22, 10)) if fontsize is 'auto' else fontsize
if labels is None:
labels = df.columns
else:
assert len(labels) == len(
df.columns
), "Numbers of labels not matching the numbers of coulums in the df"
im = None
fig, axes = plt.subplots(nrows=n_vars, ncols=n_vars, figsize=(size, size))
# Plotting the matrix, iterate over the columns in 2D
for i, row in zip(range(n_vars), axes):
for j, ax in zip(range(n_vars), row):
if i is j - 1000:
plt.sca(ax)
ax.hist(df.iloc[:, i].values, label='data', color='gray')
ax.set_yticklabels([])
else:
im = flat_correlation(df.iloc[:, j],
df.iloc[:, i],
ax=ax,
draw_labels=False,
get_im=True,
cmap=cmap)
ax.xaxis.set_major_locator(plt.NullLocator())
ax.yaxis.set_major_locator(plt.NullLocator())
if tight:
plt.tight_layout()
# Common outer label
for i, row in zip(range(n_vars), axes):
for j, ax in zip(range(n_vars), row):
if i == n_vars - 1:
if label_size is not None:
set_flat_labels(ax,
df.iloc[:, j],
axis=1,
n_labels=n_labels,
labelsize=label_size,
rotation=90 if tick_label_rotation is 0
else tick_label_rotation,
formatter=formatter)
ax.set_xlabel(labels[j],
fontsize=fontsize,
rotation=label_rotation,
ha='right',
va='top')
if j == 0:
if label_size is not None:
set_flat_labels(ax,
df.iloc[:, i],
axis=0,
n_labels=n_labels,
labelsize=label_size,
rotation=tick_label_rotation,
formatter=formatter)
ax.set_ylabel(labels[i],
fontsize=fontsize,
rotation=label_rotation,
ha='right',
va='bottom')
if pdf is None:
# plt.show()
pass
else:
pdf.savefig()
plt.close()
if draw_cbar:
cbar_ax = fig.add_axes([0.92, 0.15, 0.02, 0.7])
cbar = plt.colorbar(
im,
cax=cbar_ax,
)
cbar.ax.set_ylabel('$\sigma$',
rotation=0,
fontsize=fontsize * 1.2,
va='center')
cbar.ax.tick_params(labelsize=fontsize)
def plot_intrarater_stats(dbcon, savedir: str, clsgroup: str):
""""""
_maybe_mkdir(savedir)
_maybe_mkdir(opj(savedir, 'csv'))
_maybe_mkdir(opj(savedir, 'plots'))
# read intrarater stats
evalsets = ['B-control', 'E']
stats = read_sql_query(f"""
SELECT "participant", "second_evalset" AS "evalset"
, "detection_and_classification", "classification"
, "n_anchors_second_evalset" AS "n_anchors"
, "n_clicks_second_evalset" AS "n_clicks"
FROM "intra-rater_{clsgroup}ClassGroup"
WHERE "participant" IN ({ir._get_sqlite_usrstr_for_who('All')})
AND "first_evalset" = "U-control"
AND "second_evalset" IN ({ir._get_sqlitestr_for_list(evalsets)})
;""", dbcon)
stats.loc[:, 'psegmented'] = stats.loc[
:, 'n_clicks'] / stats.loc[:, 'n_anchors']
# to save raw values for calculating p-values later
overalldf = []
# reorder evalsets
tmp = []
for evalset in ir.EVALSET_NAMES:
tmp.append(stats.loc[stats.loc[:, 'evalset'] == evalset, :])
stats = concat(tmp, axis=0)
# organize canvas and plot
nperrow = 3
nrows = 1
fig, ax = plt.subplots(nrows, nperrow, figsize=(5 * nperrow, 5.5 * nrows))
scprops = {'alpha': 0.7, 's': 7 ** 2, 'edgecolor': 'k'}
axno = -1
metrics = ['psegmented', 'detection_and_classification', 'classification']
mdict = {
'psegmented': 'N. segmentations / N. anchors',
'detection_and_classification': "Kappa vs U-control (det. & classif.)",
'classification': "Kappa vs U-control (classif.)",
}
for axis in ax.ravel():
axno += 1
metric = metrics[axno]
dfslice = stats.copy()
dfslice.index = dfslice.loc[:, 'participant']
dfslice.loc[:, 'who'] = 'NPs'
for who in ['JPs', 'SPs']:
for p in dfslice.index:
if p in ir.who[who]:
dfslice.loc[p, 'who'] = who
dfslice.loc[:, 'swho'] = dfslice.loc[:, 'who'].copy()
dfslice.loc[dfslice.loc[:, 'swho'] == 'SPs', 'swho'] = 'Ps'
dfslice.loc[dfslice.loc[:, 'swho'] == 'JPs', 'swho'] = 'Ps'
dfslice = dfslice.loc[:, ['evalset', metric, 'who', 'swho']]
overalldf.append(dfslice)
# annotate agreement ranges
if axno > 0:
_annotate_krippendorph_ranges(
axis=axis, minx=0, maxx=2, shades=False)
# main boxplots
bppr = {'alpha': 0.5}
sns.boxplot(
ax=axis, data=dfslice, x='evalset', y=metric, hue='swho',
palette=[ir.PARTICIPANT_STYLES[who]['c'] for who in ['Ps', 'NPs']],
boxprops=bppr, whiskerprops=bppr, capprops=bppr, medianprops=bppr,
showfliers=False, notch=False, bootstrap=5000)
# scatter each participant group
for who in ['NPs', 'JPs', 'SPs']:
pstyle = ir.PARTICIPANT_STYLES[who]
scprops.update({k: pstyle[k] for k in ['c', 'marker']})
plotme = dfslice.loc[dfslice.loc[:, 'who'] == who, :].copy()
offset = -0.2 if who in ['JPs', 'SPs'] else 0.2
plotme.loc[:, 'x'] = plotme.loc[:, 'evalset'].apply(
lambda x: evalsets.index(x) + offset)
plotme = np.array(plotme.loc[:, ['x', metric]])
# add jitter
plotme[:, 0] += 0.05 * np.random.randn(plotme.shape[0])
# now scatter
axis.scatter(
plotme[:, 0], plotme[:, 1], label=f'{who}', **scprops)
axis.set_ylim(0., 1.)
axis.set_title(mdict[metric], fontsize=14, fontweight='bold')
axis.set_ylabel(metric.capitalize(), fontsize=11)
axis.legend()
plt.tight_layout(pad=0.3, w_pad=0.5, h_pad=0.3)
savename = f'intra-rater_comparison'
plt.savefig(opj(savedir, 'plots', savename + '.svg'))
plt.close()
# save raw numbers
overalldf = concat(overalldf, axis=0)
overalldf.to_csv(opj(savedir, 'csv', savename + '.csv'))
plt.plot(Utils.movingAverage(average),
label=str(2 * numOptionsToUse) + ' opt.',
color=Utils.colors[color_idx])
else:
plt.plot(Utils.movingAverage(average),
label=str(numOptionsToUse) + ' opt.',
color=Utils.colors[color_idx])
plt.fill_between(range(len(Utils.movingAverage(average))),
Utils.movingAverage(minConfInt),
Utils.movingAverage(maxConfInt),
alpha=0.5,
color=Utils.colors[color_idx])
plt.legend(loc='upper left', prop={'size': 10}, bbox_to_anchor=(1, 1))
plt.tight_layout(pad=7)
plt.show()
elif taskToPerform == 7: #Solve for a given goal w/ primitive actions (q-learning)
#following discovered AND loaded options This one is for comparison.
numOptionsLoadedToConsider = 4
numOptionsDiscoveredToConsider = 128
returnsEvalPrimitive1, returnsEvalDiscovered, totalOptionsToUseDiscovered = qLearningWithOptions(
env=env,
alpha=0.1,
gamma=0.9,
options_eps=0.0,
epsilon=1.0,
nSeeds=num_seeds,
maxLengthEp=max_length_episode,
def eval(**kwargs):
# Roll out the parameters
batch_size = kwargs["batch_size"]
generator = kwargs["generator"]
model_name = kwargs["model_name"]
image_data_format = kwargs["image_data_format"]
img_dim = kwargs["img_dim"]
cont_dim = (kwargs["cont_dim"],)
cat_dim = (kwargs["cat_dim"],)
noise_dim = (kwargs["noise_dim"],)
bn_mode = kwargs["bn_mode"]
noise_scale = kwargs["noise_scale"]
dset = kwargs["dset"]
eval_epoch = kwargs["eval_epoch"]
# Setup environment (logging directory etc)
general_utils.setup_logging(**kwargs)
# Load and rescale data
if dset == "RGZ":
X_real_train = data_utils.load_RGZ(img_dim, image_data_format)
if dset == "mnist":
X_real_train, _, _, _ = data_utils.load_mnist(image_data_format)
img_dim = X_real_train.shape[-3:]
# Load generator model
generator_model = models.load("generator_%s" % generator,
cat_dim,
cont_dim,
noise_dim,
img_dim,
bn_mode,
batch_size,
dset=dset)
# Load colorization model
generator_model.load_weights("../../models/%s/gen_weights_epoch%05d.h5" %
(model_name, eval_epoch))
X_plot = []
# Vary the categorical variable
for i in range(cat_dim[0]):
X_noise = data_utils.sample_noise(noise_scale, batch_size, noise_dim)
X_cont = data_utils.sample_noise(noise_scale, batch_size, cont_dim)
X_cont = np.repeat(X_cont[:1, :], batch_size, axis=0) # fix continuous noise
X_cat = np.zeros((batch_size, cat_dim[0]), dtype='float32')
X_cat[:, i] = 1 # always the same categorical value
X_gen = generator_model.predict([X_cat, X_cont, X_noise])
X_gen = data_utils.inverse_normalization(X_gen)
if image_data_format == "channels_first":
X_gen = X_gen.transpose(0,2,3,1)
X_gen = [X_gen[i] for i in range(len(X_gen))]
X_plot.append(np.concatenate(X_gen, axis=1))
X_plot = np.concatenate(X_plot, axis=0)
plt.figure(figsize=(8,10))
if X_plot.shape[-1] == 1:
plt.imshow(X_plot[:, :, 0], cmap="gray")
else:
plt.imshow(X_plot)
plt.xticks([])
plt.yticks([])
plt.ylabel("Varying categorical factor", fontsize=28, labelpad=60)
plt.annotate('', xy=(-0.05, 0), xycoords='axes fraction', xytext=(-0.05, 1),
arrowprops=dict(arrowstyle="-|>", color='k', linewidth=4))
plt.tight_layout()
plt.savefig(os.path.join("../../figures", model_name, "varying_categorical.png"))
plt.clf()
plt.close()
# Vary the continuous variables
X_plot = []
# First get the extent of the noise sampling
x = np.ravel(data_utils.sample_noise(noise_scale, batch_size * 20000, cont_dim))
# Define interpolation points
x = np.linspace(x.min(), x.max(), num=batch_size)
for i in range(batch_size):
X_noise = data_utils.sample_noise(noise_scale, batch_size, noise_dim)
X_cont = np.concatenate([np.array([x[i], x[j]]).reshape(1, -1) for j in range(batch_size)], axis=0)
X_cat = np.zeros((batch_size, cat_dim[0]), dtype='float32')
X_cat[:, 1] = 1 # always the same categorical value
X_gen = generator_model.predict([X_cat, X_cont, X_noise])
X_gen = data_utils.inverse_normalization(X_gen)
if image_data_format == "channels_first":
X_gen = X_gen.transpose(0,2,3,1)
X_gen = [X_gen[i] for i in range(len(X_gen))]
X_plot.append(np.concatenate(X_gen, axis=1))
X_plot = np.concatenate(X_plot, axis=0)
plt.figure(figsize=(10,10))
if X_plot.shape[-1] == 1:
plt.imshow(X_plot[:, :, 0], cmap="gray")
else:
plt.imshow(X_plot)
plt.xticks([])
plt.yticks([])
plt.ylabel("Varying continuous factor 1", fontsize=28, labelpad=60)
plt.annotate('', xy=(-0.05, 0), xycoords='axes fraction', xytext=(-0.05, 1),
arrowprops=dict(arrowstyle="-|>", color='k', linewidth=4))
plt.xlabel("Varying continuous factor 2", fontsize=28, labelpad=60)
plt.annotate('', xy=(1, -0.05), xycoords='axes fraction', xytext=(0, -0.05),
arrowprops=dict(arrowstyle="-|>", color='k', linewidth=4))
plt.tight_layout()
plt.savefig(os.path.join("../../figures", model_name, "varying_continuous.png"))
plt.clf()
plt.close()
def make_all_plots(df_plotting_container,
specific_plots=[],
backend='matplotlib',
grid_of_plots=(2, 2),
kde=False,
plot_params=None,
figsize=(9, 7),
norm_hist=False,
xlabelfontsize=12,
ignorePID=False,
stacked=False,
alpha=0.5,
decay=None,
tag='default'):
if plot_params is None:
plot_params = get_variable_parameters_for_plotting()
sps_in_container = list(df_plotting_container.keys())
print(sps_in_container)
tempdf = df_plotting_container[sps_in_container[0]]['df']
tempnames = None
if type(tempdf) is list:
tempnames = tempdf[0].columns
else:
tempnames = tempdf.columns
#tempnames = df_plotting_container[sps_in_container[0]]['dfs'][0].columns
names = []
if ignorePID:
for name in tempnames:
if name.find('Is') >= 0 or name.find('BDT') >= 0 or name.find(
'KM') >= 0:
1
else:
names.append(name)
nplots = len(names)
nplots_per_figure = grid_of_plots[0] * grid_of_plots[1]
grid_count = 0
i = 0
if len(specific_plots) == 0:
specific_plots = list(names)
figcount = 0
sps_for_labels = []
#for icount,name in enumerate(names):
for icount, name in enumerate(specific_plots):
#if len(specific_plots)>0 and name not in specific_plots:
if name not in names:
continue
if i % nplots_per_figure == 0:
plt.figure(figsize=figsize)
grid_count = 0
plt.subplot(grid_of_plots[0], grid_of_plots[1], grid_count + 1)
plotrange = None
xlabel = None
bins = 100
if name in plot_params.keys():
xlabel = plot_params[name]['xlabel']
plotrange = plot_params[name]['range']
if 'bins' in list(plot_params[name].keys()):
bins = plot_params[name]['bins']
if name.find('Is') >= 0 or name.find('BDT') >= 0 or name.find(
'KM') >= 0:
plotrange = (0, 1)
bins = 2
########################################################################
'''
if backend=='seaborn':
if plotrange is not None:
for j,df in enumerate(dfs):
label = None
if labels is not None:
label = labels[j]
weight=np.ones(len(df[name]))
if type(weights) == list:
weight *= weights[j]
sns.distplot(df[name],bins=bins,hist_kws={"range": plotrange, "weights":weight, "stacked":stacked,'alpha':alpha},kde=kde,norm_hist=norm_hist,label=label)
plt.xlim(plotrange[0],plotrange[1])
else:
for j,df in enumerate(dfs):
label = None
if labels is not None:
label = labels[j]
weight=np.ones(len(df[name]))
if type(weights) == list:
weight *= weights[j]
sns.distplot(df[name],bins=bins,kde=kde,norm_hist=norm_hist,label=label,hist_kws={"weights":weight, "stacked":stacked})
if xlabel is not None:
plt.xlabel(xlabel,fontsize=xlabelfontsize)
else:
plt.xlabel(name,fontsize=xlabelfontsize)
if labels is not None:
plt.legend(fontsize=8)
'''
########################################################################
if backend == 'matplotlib':
#if plotrange is not None:
allvals = []
allweights = []
#last_df = len(dfs)
backgroundMC = {
'values': [],
'weights': [],
'colors': [],
'labels': []
}
signalMC = {
'values': [],
'weights': [],
'colors': [],
'labels': []
}
data = {'values': [], 'weights': [], 'colors': [], 'labels': []}
totweights = 0
for sp in sps_in_container:
c = df_plotting_container[sp]
if c['isSignalMC'] is True:
signalMC['values'] = c['df'][name]
signalMC['colors'] = c['color']
signalMC['weights'] = np.ones(len(
c['df'][name])) * c['weights']
signalMC['labels'] = c['label']
elif c['isData'] is True:
data['values'] = c['df'][name]
data['colors'] = c['color']
data['weights'] = np.ones(len(
c['df'][name])) * c['weights']
data['labels'] = c['label']
else:
backgroundMC['values'].append(c['df'][name])
backgroundMC['colors'].append(c['color'])
backgroundMC['weights'].append(
np.ones(len(c['df'][name])) * c['weights'])
backgroundMC['labels'].append(c['label'])
totweights += c['weights'] * np.sum(len(c['df'][name]))
#print(backgroundMC)
#print(backgroundMC['values'])
#print(backgroundMC['weights'])
#print(len(backgroundMC['values']))
#print(len(backgroundMC['weights']))
# Background
#print(backgroundMC['colors'])
#print(backgroundMC['labels'])
plt.hist(backgroundMC['values'],
bins=bins,
range=plotrange,
weights=backgroundMC['weights'],
stacked=stacked,
alpha=alpha,
label=backgroundMC['labels'],
color=backgroundMC['colors'],
histtype='stepfilled',
density=norm_hist)
# Signal
if len(signalMC['values']) > 0:
nentries = len(signalMC['values'])
#print(f"totweights: {totweights}")
signalMC['weights'] = np.ones(nentries) * (totweights /
nentries) * 0.15
plt.hist(signalMC['values'],
bins=bins,
range=plotrange,
weights=signalMC['weights'],
lw=2,
ls='--',
alpha=1.0,
label=signalMC['labels'],
color='b',
histtype='step',
density=norm_hist)
# Data
if len(data['values']) > 0:
hist_with_errors(data['values'],
bins=bins,
range=plotrange,
label='Data')
if plotrange is not None:
plt.xlim(plotrange[0], plotrange[1])
if xlabel is not None:
plt.xlabel(xlabel, fontsize=xlabelfontsize)
else:
plt.xlabel(name, fontsize=xlabelfontsize)
#plt.legend(fontsize=8,loc='upper left')
plt.legend(fontsize=8, loc='best')
########################################################################
if i % nplots_per_figure == nplots_per_figure - 1 or i == nplots - 1:
print("Here!")
plt.tight_layout()
filename = 'plots/stacked_cut_summary_files_{0}_{1}_{2}.png'.format(
decay, tag, figcount)
plt.savefig(filename)
figcount += 1
i += 1
plt.tight_layout()
grid_count += 1
filename = 'plots/stacked_cut_summary_files_{0}_{1}_{2}.png'.format(
decay, tag, figcount)
plt.savefig(filename)
def combine_all(self,
filepath,
savename,
directory,
skiprows,
column_names,
show=True):
dir = directory + '/%s' % (savename.strip('.yaml'))
if not os.path.exists(dir):
os.makedirs(dir)
if filepath.endswith('.yaml') == True:
with open(filepath, 'r') as stream:
data_file = yaml.load(stream)
stream.close()
data = data_file['data']
# parameters = data_file['parameters']
else:
# parameters = open(filepath, "r").readlines()[:33]
data = np.loadtxt(filepath, delimiter=',', skiprows=skiprows)
length = len(data[0]) - (len(column_names) + 3)
L_length = int(data[0][-1])
R_length = int(data[0][-2])
for i in range(R_length):
column_names = np.append(column_names, "R_%i" % (i + 1))
for i in range(L_length):
column_names = np.append(column_names, "L_%i" % (i + 1))
column_names = np.append(column_names, "Accepted")
column_names = np.append(column_names, "Rayleigh_length")
column_names = np.append(column_names, "Love_length")
par = Get_Paramters()
REAL = par.get_unkown()
df = pd.DataFrame(data, columns=column_names)
df_select = df[["Epi", "Depth", "Strike", "Dip", "Rake", "M0"]]
fig = plt.figure(figsize=(20, 20))
ax1 = plt.subplot2grid((5, 2), (0, 0), colspan=2)
# ax1.axhline(y = REAL['epi'] ,linewidth = 0.3 , linestyle =':', color = 'b')
ax1.plot(df_select['Epi'], label="Epi", c='b')
ax1.tick_params("y", colors='b')
ax1.set_ylabel('Epicentral distance [degree]', color='b')
ax2 = ax1.twinx()
ax2.plot(df_select['Depth'], label="Depth", c='r')
# ax2.axhline(y=REAL['depth_s'], linewidth=0.3, linestyle=':', color='r')
ax2.tick_params('y', colors='r')
ax2.set_ylabel('Depth [m]', color='r')
plt.tight_layout()
ax3 = plt.subplot2grid((5, 2), (1, 0), colspan=2)
ax3.plot(df_select['Strike'], label="Strike", color="b")
# ax3.axhline(y=REAL['strike'], linewidth=0.3, linestyle=':', color='b')
# ax3.axhline(y=REAL['dip'], linewidth=0.3, linestyle=':', color='g')
# ax3.axhline(y=REAL['rake'], linewidth=0.3, linestyle=':', color='r')
ax3.plot(df_select['Dip'], label="Dip", color='g')
ax3.plot(df_select['Rake'], label="Rake", color='r')
ax3.set_ylabel('Moment tensor angle [degree]', color='k')
plt.legend(loc='center left', bbox_to_anchor=(1, 0.5))
plt.tight_layout()
axes = ax3.twinx()
axes.plot(df_select['M0'], label="M0", c='m')
# ax2.axhline(y=REAL['depth_s'], linewidth=0.3, linestyle=':', color='r')
axes.tick_params('y', colors='m')
axes.set_ylabel('M0', color='r')
plt.yscale('log')
plt.tight_layout()
R_select = df.filter(like='R_')
L_select = df.filter(like='L_')
df_select_xi = df[[
"Total_misfit", "S_z", "S_r", "S_t", "P_z", "P_r", "BW_misfit",
"Rtot", "Ltot"
]]
ax4 = plt.subplot2grid((5, 2), (2, 0), colspan=2)
ax4.plot(df_select_xi['Total_misfit'], label="Total_misfit", c='r')
# ax4.plot(df_select_xi['S_z'], label = "S_z")
# ax4.plot(df_select_xi['S_r'], label = "S_r")
# ax4.plot(df_select_xi['S_t'], label = "S_t")
# ax4.plot(df_select_xi['P_z'], label = "P_z")
# ax4.plot(df_select_xi['P_r'], label = "P_r")
ax4.plot(df_select_xi['BW_misfit'], label="BW_tot")
ymin, ymax = ax4.get_ylim()
plt.yscale('log')
# plt.ylim((pow(10, 0), pow(10, 3)))
plt.legend(loc='center left', bbox_to_anchor=(1, 0.5))
plt.tight_layout()
ax5 = plt.subplot2grid((5, 2), (3, 0), colspan=2)
# for i in R_select:
# ax5.plot(R_select[i],label = i)
ax5.plot(df_select_xi['Rtot'], label="Rtot")
plt.yscale('log')
# plt.ylim((pow(10, 0), pow(10, 4)))
plt.legend(loc='center left', bbox_to_anchor=(1, 0.5))
plt.tight_layout()
ax6 = plt.subplot2grid((5, 2), (4, 0), colspan=2)
# for i in L_select:
# ax6.plot(L_select[i],label = i)
ax6.plot(df_select_xi['Ltot'], label="Ltot")
plt.yscale('log')
# plt.ylim((pow(10, 0), pow(10, 4)))
plt.legend(loc='center left', bbox_to_anchor=(1, 0.5))
plt.tight_layout()
plt.savefig(dir + '/combined_all_par.pdf')
plt.close()
def createPlot(name, xlabel, ylabel, xlist, \
list1, list1_5, list1_95, label1, \
list2, list2_5, list2_95, label2, \
list3, list3_5, list3_95, label3, \
list4, list4_5, list4_95, label4, \
list5, list5_5, list5_95, label5, \
list6, list6_5, list6_95, label6, \
list7, list7_5, list7_95, label7, \
list8, list8_5, list8_95, label8):
# collecting the data separately in case there are all timeouts for one
# particular algorithm for one case
xlist_list7, new_list7, new_list7_5, new_list7_95 = [], [], [], []
xlist_list8, new_list8, new_list8_5, new_list8_95 = [], [], [], []
for i, n in enumerate(xlist):
if not list7[i] == -1:
xlist_list7.append(n)
new_list7.append(list7[i])
new_list7_5.append(list7_5[i])
new_list7_95.append(list7_95[i])
if not list8[i] == -1:
xlist_list8.append(n)
new_list8.append(list8[i])
new_list8_5.append(list8_5[i])
new_list8_95.append(list8_95[i])
list7 = new_list7
list7_5 = new_list7_5
list7_95 = new_list7_95
list8 = new_list8
list8_5 = new_list8_5
list8_95 = new_list8_95
matplotlib.rcParams.update({'font.size': 14})
plt.figure(facecolor='w', edgecolor='k', figsize=(7, 5))
plt.xlabel(xlabel)
plt.ylabel(ylabel)
xlist = np.array(xlist)
# curve for median best fit
score1CV, _ = curve_fit(func2D, xlist, list1)
score2CV, _ = curve_fit(func2D, xlist, list2)
score3CV, _ = curve_fit(func2D, xlist, list3)
score4CV, _ = curve_fit(func2D, xlist, list4)
score5CV, _ = curve_fit(func2D, xlist, list5)
score6CV, _ = curve_fit(func2D, xlist, list6)
score7CV, _ = curve_fit(func2D, xlist_list7, list7)
score8CV, _ = curve_fit(func2D, xlist_list8, list8)
# curve for 5% CI best fit
score1_5_CV, _ = curve_fit(func2D, xlist, list1_5)
score2_5_CV, _ = curve_fit(func2D, xlist, list2_5)
score3_5_CV, _ = curve_fit(func2D, xlist, list3_5)
score4_5_CV, _ = curve_fit(func2D, xlist, list4_5)
score5_5_CV, _ = curve_fit(func2D, xlist, list5_5)
score6_5_CV, _ = curve_fit(func2D, xlist, list6_5)
score7_5_CV, _ = curve_fit(func2D, xlist_list7, list7_5)
score8_5_CV, _ = curve_fit(func2D, xlist_list8, list8_5)
# curve for 95% CI best fit
score1_95_CV, _ = curve_fit(func2D, xlist, list1_95)
score2_95_CV, _ = curve_fit(func2D, xlist, list2_95)
score3_95_CV, _ = curve_fit(func2D, xlist, list3_95)
score4_95_CV, _ = curve_fit(func2D, xlist, list4_95)
score5_95_CV, _ = curve_fit(func2D, xlist, list5_95)
score6_95_CV, _ = curve_fit(func2D, xlist, list6_95)
score7_95_CV, _ = curve_fit(func2D, xlist_list7, list7_95)
score8_95_CV, _ = curve_fit(func2D, xlist_list8, list8_95)
# confidence interval
# plt.fill_between(xlist, func2D(xlist, score2_5_CV[0], score2_5_CV[1], score2_5_CV[2]), \
# func2D(xlist, score2_95_CV[0], score2_95_CV[1], score2_95_CV[2]), color='blue', alpha=.5)
# plt.fill_between(xlist, func2D(xlist, score3_5_CV[0], score3_5_CV[1], score3_5_CV[2]), \
# func2D(xlist, score3_95_CV[0], score3_95_CV[1], score3_95_CV[2]), color='seagreen', alpha=.5)
# plt.fill_between(xlist, func2D(xlist, score1_5_CV[0], score1_5_CV[1], score1_5_CV[2]), \
# func2D(xlist, score1_95_CV[0], score1_95_CV[1], score1_95_CV[2]), color='orangered', alpha=.5)
# plt.fill_between(xlist, func2D(xlist, score4_5_CV[0], score4_5_CV[1], score4_5_CV[2]), \
# func2D(xlist, score4_95_CV[0], score4_95_CV[1], score4_95_CV[2]), color='skyblue', alpha=.5)
# plt.fill_between(xlist, func2D(xlist, score5_5_CV[0], score5_5_CV[1], score5_5_CV[2]), \
# func2D(xlist, score5_95_CV[0], score5_95_CV[1], score5_95_CV[2]), color='gold', alpha=.5)
# plt.fill_between(xlist, func2D(xlist, score6_5_CV[0], score6_5_CV[1], score6_5_CV[2]), \
# func2D(xlist, score6_95_CV[0], score6_95_CV[1], score6_95_CV[2]), color='purple', alpha=.5)
newx = np.linspace(10, 1000, 250)
# best fit lines
plt.plot(newx,
func2D(np.array(newx), score3CV[0], score3CV[1], score3CV[2]),
'-',
color='darkgreen')
plt.plot(newx,
func2D(np.array(newx), score6CV[0], score6CV[1], score6CV[2]),
'-',
color='navy')
plt.plot(newx,
func2D(np.array(newx), score2CV[0], score2CV[1], score2CV[2]),
'-',
color='mediumseagreen')
plt.plot(newx,
func2D(np.array(newx), score5CV[0], score5CV[1], score5CV[2]),
'-',
color='royalblue')
plt.plot(newx,
func2D(np.array(newx), score1CV[0], score1CV[1], score1CV[2]),
'-',
color='lightgreen')
plt.plot(newx,
func2D(np.array(newx), score4CV[0], score4CV[1], score4CV[2]),
'-',
color='skyblue')
plt.plot(newx,
func2D(np.array(newx), score7CV[0], score7CV[1], score7CV[2]),
'-',
color='orange')
if not paper:
plt.plot(newx,
func2D(np.array(newx), score8CV[0], score8CV[1], score8CV[2]),
'-',
color='red')
# points
plt.plot(xlist, list3, "s", markersize=4, label=label3, color='darkgreen')
plt.plot(xlist, list6, "d", markersize=4, label=label6, color='navy')
plt.plot(xlist,
list2,
'o',
markersize=4,
label=label2,
color='mediumseagreen')
plt.plot(xlist, list5, '^', markersize=4, label=label5, color='royalblue')
plt.plot(xlist, list1, '+', markersize=4, label=label1, color='lightgreen')
plt.plot(xlist, list4, '*', markersize=4, label=label4, color='skyblue')
plt.plot(xlist_list7,
list7,
'3',
markersize=4,
label=label7,
color='orange')
if not paper:
plt.plot(xlist_list8,
list8,
'4',
markersize=4,
label=label8,
color='red')
handles, labels = plt.gca().get_legend_handles_labels()
order = [4, 2, 0, 5, 3, 1, 6]
if not paper:
order = [4, 2, 0, 5, 3, 1, 6, 7]
plt.xlim(xmin=0, xmax=1000)
plt.ylim(ymin=0)
plt.grid()
plt.legend([handles[idx] for idx in order], [labels[idx] for idx in order])
# plt.legend()
plt.tight_layout()
filename = dir_name + "/" + name + ".pdf"
if paper:
filename = dir_name + "/paper_" + name + ".pdf"
plt.savefig(filename)
plt.close()
plt.rcParams.update(plt.rcParamsDefault)
def createHistograms():
# mean num optimal matchings per optimal matching type
fig, ax = plt.subplots()
ind = np.arange(6)
width = 0.2
exps = ['S100', 'S400', 'S700', 'S1000']
exp_bars = []
for i, exp in enumerate(exps):
numMinRegret = float(d[exp + 'Av_MinRegret_num'][0])
numEgalitarian = float(d[exp + 'Av_Egalitarian_num'][0])
numBalanced = float(d[exp + 'Av_Balanced_num'][0])
numSeqEqual = float(d[exp + 'Av_SexEqual_num'][0])
numRegretEqual = float(d[exp + 'Av_RegretEqual_num'][0])
numMinSumRegret = float(d[exp + 'Av_MinSumRegret_num'][0])
av_counts = [
numBalanced, numSeqEqual, numEgalitarian, numMinRegret,
numRegretEqual, numMinSumRegret
]
exp_bars.append(
ax.bar(ind + i * width, av_counts, width, color=blues[i]))
objects = [
'Balanced', 'Sex-equal', 'Egalitarian', 'Minimum\nregret',
'Regret-\nequal', 'Min-regret\nsum'
]
y_pos = np.arange(len(objects))
plt.grid()
plt.xticks(y_pos + 0.3, objects)
plt.ylabel('Mean number of stable matchings')
plt.xlabel('Type of optimal stable matching')
plt.ylim(ymin=0.7)
plt.ylim(ymax=100)
plt.yscale('log')
ax.legend(exp_bars, exps)
plt.tight_layout()
plt.savefig(dir_name + "/paper_bar_optimal_nums.pdf")
plt.close()
# average number of matchings which exhibit different numbers of optimal
# matchings
fig, ax = plt.subplots()
ind = np.arange(7)
width = 0.2
exps = ['S100', 'S400', 'S700', 'S1000']
exp_bars = []
for i, exp in enumerate(exps):
num0 = float(d[exp + 'Av_0_matchingCount'][0])
num1 = float(d[exp + 'Av_1_matchingCount'][0])
num2 = float(d[exp + 'Av_2_matchingCount'][0])
num3 = float(d[exp + 'Av_3_matchingCount'][0])
num4 = float(d[exp + 'Av_4_matchingCount'][0])
num5 = float(d[exp + 'Av_5_matchingCount'][0])
num6 = float(d[exp + 'Av_6_matchingCount'][0])
av_counts = [num0, num1, num2, num3, num4, num5, num6]
exp_bars.append(
ax.bar(ind + i * width, av_counts, width, color=blues[i]))
objects = ['0', '1', '2', '3', '4', '5', '6']
y_pos = np.arange(len(objects))
plt.grid()
plt.xticks(y_pos + 0.3, objects)
plt.ylabel('Mean number of stable matchings')
plt.xlabel('Number of optimal matching criteria satisfied')
plt.ylim(ymin=0.07)
plt.ylim(ymax=1300)
plt.yscale('log')
ax.legend(exp_bars, exps)
plt.tight_layout()
plt.savefig(dir_name + "/paper_bar_num_matchings_num_opt.pdf")
plt.close()
def trace_density(self,
filepath,
savename,
directory,
skiprows,
column_names,
show=True):
dir = directory + '/%s' % (savename.strip('.yaml'))
if not os.path.exists(dir):
os.makedirs(dir)
if filepath.endswith('.yaml') == True:
with open(filepath, 'r') as stream:
data_file = yaml.load(stream)
stream.close()
data = data_file['data']
# parameters = data_file['parameters']
else:
# parameters = open(filepath, "r").readlines()[:33]
data = np.loadtxt(filepath, delimiter=',', skiprows=skiprows)
length = len(data[0]) - (len(column_names) + 3)
L_length = 4 #int(data[0][-1])
R_length = 4 #int(data[0][-2])
for i in range(R_length):
column_names = np.append(column_names, "R_%i" % (i + 1))
for i in range(L_length):
column_names = np.append(column_names, "L_%i" % (i + 1))
column_names = np.append(column_names, "Accepted")
# column_names = np.append(column_names,"Rayleigh_length")
# column_names = np.append(column_names,"Love_length")
params = {
'legend.fontsize': 'x-large',
'figure.figsize': (15, 15),
'axes.labelsize': 25,
'axes.titlesize': 'x-large',
'xtick.labelsize': 25,
'ytick.labelsize': 25
}
pylab.rcParams.update(params)
#
df = pd.DataFrame(data, columns=column_names)
df_select = df[["Epi", "Depth", "Strike", "Dip", "Rake"]]
par = Get_Paramters()
REAL = par.get_unkown()
real_v = np.array([
REAL['epi'], REAL['depth_s'], REAL['strike'], REAL['dip'],
REAL['rake']
])
# real_v=np.array([35.2068855191,16848.1405882,99.88000245897199, 77.02994881296266,68.80551508147109])
# real_v=np.array([73.8059395565,26247.7456326,158.92744919732135, 47.46909146946276,-45.69139707143311])
strike, dip, rake = aux_plane(REAL['strike'], REAL['dip'],
REAL['rake'])
# strike,dip,rake = aux_plane(99.88000245897199,77.02994881296266,68.80551508147109)
# strike,dip,rake = aux_plane(158.92744919732135, 47.46909146946276,-45.69139707143311)
fig = plt.figure(figsize=(20, 20))
row = 0
for i in df_select:
ax1 = plt.subplot2grid((5, 2), (row, 0))
ax1.plot(df_select[i], label=i)
# ax1.axhline(y=REAL[df_select], linewidth=0.3, linestyle=':')
ax1.set_title("Trace %s" % i, color='b', fontsize=20)
ax1.set_xlabel("Iteration")
# ax1.set_ylabel("Epicentral ")
plt.tight_layout()
ax2 = plt.subplot2grid((5, 2), (row, 1))
plt.hist(df_select[i], bins=100)
ymin, ymax = ax2.get_ylim()
plt.vlines(df_select[i][1],
ymin=ymin,
ymax=ymax,
colors='r',
linewidth=3)
plt.vlines(real_v[row],
ymin=ymin,
ymax=ymax,
colors='k',
linewidth=3)
if i == 'Strike':
plt.vlines(strike,
ymin=ymin,
ymax=ymax,
colors='g',
linewidth=3)
if i == 'Dip':
plt.vlines(dip, ymin=ymin, ymax=ymax, colors='g', linewidth=3)
if i == 'Rake':
plt.vlines(rake, ymin=ymin, ymax=ymax, colors='g', linewidth=3)
# y, binEdges = np.histogram(df_select[i], bins=100)
# bincenters = 0.5 * (binEdges[1:] + binEdges[:-1])
# pylab.plot(bincenters, y, '-',label = "%s" % i)
ax2.set_title("Density %s" % i, color='b', fontsize=20)
ax2.set_xlabel("N=%i" % (len(df_select[i])))
plt.tight_layout()
row += 1
plt.savefig(dir + '/Trace_density.pdf')
def visualize_stats(data, out):
f, axs = plt.subplots(2, 2, sharey=False, sharex=False)
X = plt.arange(data.shape[0])
width = 0.4
title_fontsize = 10
label_fontsize = 6
# number of detected clusters
bars3dsize = axs[0][0].bar(X, data[:, 1], width, color=COLOR1)
bars1dsize = axs[0][0].bar(X + width, data[:, 2], width, color=COLOR2)
axs[0][0].legend((bars3dsize[0], bars1dsize[0]), ('3D gene clusters', \
'1D gene clusters'), fontsize=title_fontsize)
axs[0][0].set_xticks(X + width / 2)
axs[0][0].set_xticklabels(map(int, data[:, 0]))
axs[0][0].set_ylabel('count')
# axs[0][0].set_xlabel(r'$\delta$')
axs[0][0].set_title('number of discovered clusters',
fontsize=title_fontsize)
# average size of detected clusters
bars3dsize = axs[0][1].bar(X, data[:, 3], width, color=COLOR1)
bars1dsize = axs[0][1].bar(X + width, data[:, 4], width, color=COLOR2)
axs[0][1].legend((bars3dsize[0], bars1dsize[0]), ('3D gene clusters', \
'1D gene clusters'), fontsize=title_fontsize)
axs[0][1].set_xticks(X + width / 2)
axs[0][1].set_xticklabels(map(int, data[:, 0]))
axs[0][1].set_ylabel('avg. size')
# axs[0][1].set_xlabel(r'$\delta$')
axs[0][1].set_title('average size of discovered clusters',
fontsize=title_fontsize)
axs[0][1].set_yscale('log')
# runtime of GraphTeams
axs[1][1].scatter(X + width / 2, data[:, 5], color=COLOR1)
# axs[1][0].legend(('1D gene clusters', ), fontsize=title_fontsize)
axs[1][1].set_xticks(X + width / 2)
axs[1][1].set_xticklabels(map(int, data[:, 0]))
axs[1][1].set_ylim([0, max(data[:, 5]) + 10])
axs[1][1].set_ylabel('time in mins')
axs[1][1].set_xlabel(r'$\delta$')
axs[1][1].set_title('computation time of 3D clusters',
fontsize=title_fontsize)
# spatial gain 3D clusters
axs[1][0].bar(X + (width / 2), data[:, 6], width, color=COLOR1)
# axs[1][1].legend(('3D gene clusters', ), fontsize=title_fontsize)
axs[1][0].set_xticks(X + width / 2)
axs[1][0].set_xticklabels(map(int, data[:, 0]))
axs[1][0].set_ylabel('avg. number of gained genes')
axs[1][0].set_xlabel(r'$\delta$')
axs[1][0].set_title('spatial gain of 3D clusters', fontsize=title_fontsize)
axs[1][0].set_yscale('log')
for axsx in axs:
for axsy in axsx:
for label in axsy.get_xmajorticklabels():
label.set_rotation(90)
label.set_fontsize(label_fontsize)
#label.set_horizontalalignment('right')
for label in axsy.get_ymajorticklabels():
label.set_fontsize(label_fontsize)
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=1.0)
f.savefig(out, format='pdf')
obs_odd_mean + obs_odd_sem,
color=odd_colour,
alpha=0.2,
linewidth=0)
ax_obs.axhline(0, linewidth=0.5, color="black")
ax_obs.axvline(0, linestyle="--", linewidth=0.5, color="black")
plt.title("Observation phase")
plt.legend(loc=1)
plt.xlabel("Time[s]")
plt.ylabel("fT")
plt.ylim(-10, 10)
plt.xlim(-0.1, 1.0)
ax_subset = figure.add_subplot(gs[1])
mne.viz.plot_topomap(np.zeros(274),
info,
cmap="Greys",
vmin=0,
vmax=0,
mask=ch_selection,
mask_params=mask_params,
axes=ax_subset,
show=False)
plt.title("Channel subset")
plt.tight_layout(w_pad=0.2, h_pad=0.2)
out_path = op.join(img_save, "ERF_ttest_{}.svg".format(key))
plt.savefig(out_path, bbox_inches="tight")
plt.show()
def plot_markers():
from matplotlib.colors import LogNorm
SMALL_SIZE = 15
MEDIUM_SIZE = 22
plt.rc('font', size=MEDIUM_SIZE) # controls default text sizes
plt.rc('axes', titlesize=MEDIUM_SIZE) # fontsize of the axes title
plt.rc('axes', labelsize=MEDIUM_SIZE) # fontsize of the x and y labels
plt.rc('xtick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('ytick', labelsize=SMALL_SIZE) # fontsize of the tick labels
from matplotlib import rcParams
rcParams['font.family'] = 'STIXGeneral' # 'Times New Roman'
rcParams['mathtext.fontset'] = 'custom'
rcParams['mathtext.rm'] = 'Bitstream Vera Sans'
# mpl.rcParams['mathtext.it'] = 'Bitstream Vera Sans:italic'
rcParams['mathtext.bf'] = 'Bitstream Vera Sans:bold'
# with open(LCmapFile, 'rb') as handle:
# LCmap = pickle.load(handle)
# xs = [65, 23, 80, 23]
# ys = [64, 106, 66, 42]
xs = [65, 25, 80, 23]
ys = [64, 103, 66, 42]
fig = plt.figure(figsize=(20, 10))
# im_ax = fig.add_subplot(1,2,1)
im_ax = fig.add_axes([0.00, 0.25, 0.35, 0.55])
interval_map = np.sum(LCmap[:, :, :1], axis=2)
im = im_ax.imshow(np.abs(interval_map) + 1e-9,
interpolation='none',
origin='lower',
vmin=1,
norm=LogNorm(),
cmap="inferno")
plt.colorbar(im)
# annotate_axis(im, im_ax, interval_map.shape[0])
im_ax.axis('off')
im_ax.text(3, 121, 'a', color='w', fontweight='bold', fontsize='30')
labels = ['b', 'c', 'd', 'e']
axes = []
subposes = [[0.1, 0.4, 0.4, 0.4], [0.07, 0.4, 0.4, 0.4],
[0.55, 0.4, 0.4, 0.4], [0.55, 0.4, 0.4, 0.4]]
for i in [2, 3, 5, 6]:
axes.append(fig.add_subplot(2, 3, i))
intses = []
for ia, (ix, iy) in enumerate(zip(xs, ys)):
circle = plt.Circle((ix, iy),
radius=4,
color='w',
fill=False,
linewidth=2)
im_ax.add_artist(circle)
im_ax.text(ix - 2,
iy + 6,
labels[ia],
color='w',
fontweight='bold',
fontsize=25) #fontsize is newly added
ints = LCmap[iy, ix]
intses.append(ints)
ID = pipe.get_intensity_dist(ints)
bincent = (ID['binsS'] + np.roll(ID['binsS'], 1)) / 2.
bincent = np.array(bincent)[1:]
guessIc = np.mean(ints) * 0.7
guessIs = np.mean(ints) * 0.3
barwidth = (bincent[-1] - bincent[0]) / len(bincent)
popt, _ = curve_fit(MR, bincent, ID['histS'], p0=[guessIc, guessIs])
axes[ia].bar(bincent,
ID['histS'],
width=barwidth,
edgecolor='k',
facecolor='lightgrey')
axes[ia].plot(bincent, MR(bincent, *popt), 'r--', linewidth=2)
# Imean = np.mean(ints)
# Istd = np.std(ints)
# Ic= np.sqrt(Imean ** 2 - Istd ** 2)
# Is = Imean - Ic
# axes[ia].plot(bincent, MR(bincent, Ic, Is), 'r--')
axes[ia].set_xlabel('Intensity (counts)')
axes[ia].tick_params(direction='in',
which='both',
right=True,
top=True)
r = popt[0] / popt[1]
print r
axes[ia].set_ylim([0, 0.165])
axes[ia].text(0.03,
0.9,
labels[ia],
transform=axes[ia].transAxes,
fontweight='bold')
props = dict(boxstyle='square', facecolor='w')
axes[ia].text(0.97,
0.9,
r'$I_C=$%.1f $I_S=$%.1f $I_C/I_S=$%.1f' %
(popt[0], popt[1], r),
transform=axes[ia].transAxes,
ha='right',
bbox=props)
print 'in order to put the data at the top in a square make 3 text instances with ha = left center and right. Then do plt.Rectangle around all 3. You will need to add some hspace too after you call tight_layout'
# axes[ia].text(1.1,0.5, r'$I_C=$%.1f $I_S=$%.1f $I_C/I_S=$%.1f' % (popt[0],popt[1],r), transform=axes[ia].transAxes, ha='center', bbox=props)
# if ia <2: axes[ia].text(subposes[ia][0],0.25, r'$\frac{I_C}{I_S}=$%.1f' % r, transform=axes[ia].transAxes)
# else: axes[ia].text(subposes[ia][0] + subposes[ia][3] ,0.25, r'$\frac{I_C}{I_S}=$%.1f' % r, ha='right', transform=axes[ia].transAxes)
# axes[ia].legend([popt[0], popt[1], r], ['$I_C=$%.1f', '$I_S=$%.1f',r'$\frac{I_C}{I_S}=$%.1f'], loc=3)
if ia == 1:
axes[ia].set_xlim([20, 110])
plt.tight_layout()
for ia in range(4):
subax1 = add_subplot_axes(axes[ia], subposes[ia])
subax1.plot(np.linspace(0, 2, len(ints)), intses[ia])
subax1.set_xlabel('Time (s)')
# plt.subplots_adjust(left=0.11, right=0.99, top=0.98, bottom=0.14, wspace=0.2)
plt.show()
def createDurationPlot(xlist, xlabel, ylabel, \
re_alg_duration_median, re_alg_duration_5, re_alg_duration_95, alg_label, \
re_algAlt_duration_median, re_algAlt_duration_5, re_algAlt_duration_95, algAlt_label, \
re_enum_duration_median, re_enum_duration_5, re_enum_duration_95, enum_label):
xlist_alg, xlist_algAlt, xlist_enum = [], [], []
new_re_alg_duration_median, new_re_alg_duration_5, new_re_alg_duration_95 = [], [], []
new_re_algAlt_duration_median, new_re_algAlt_duration_5, new_re_algAlt_duration_95 = [], [], []
new_re_enum_duration_median, new_re_enum_duration_5, new_re_enum_duration_95 = [], [], []
# if paper:
# matplotlib.rcParams.update({'font.size': 14})
# collecting the data separately in case we have all timeouts on one particular algorithm
for i, n in enumerate(xlist):
if not re_alg_duration_median[i] == -1:
xlist_alg.append(n)
new_re_alg_duration_median.append(re_alg_duration_median[i])
new_re_alg_duration_5.append(re_alg_duration_5[i])
new_re_alg_duration_95.append(re_alg_duration_95[i])
if not re_algAlt_duration_median[i] == -1:
xlist_algAlt.append(n)
new_re_algAlt_duration_median.append(re_algAlt_duration_median[i])
new_re_algAlt_duration_5.append(re_algAlt_duration_5[i])
new_re_algAlt_duration_95.append(re_algAlt_duration_95[i])
if not re_enum_duration_median[i] == -1:
xlist_enum.append(n)
new_re_enum_duration_median.append(re_enum_duration_median[i])
new_re_enum_duration_5.append(re_enum_duration_5[i])
new_re_enum_duration_95.append(re_enum_duration_95[i])
re_alg_duration_median = new_re_alg_duration_median
re_algAlt_duration_median = new_re_algAlt_duration_median
re_enum_duration_median = new_re_enum_duration_median
re_alg_duration_5 = new_re_alg_duration_5
re_algAlt_duration_5 = new_re_algAlt_duration_5
re_enum_duration_5 = new_re_enum_duration_5
re_alg_duration_95 = new_re_alg_duration_95
re_algAlt_duration_95 = new_re_algAlt_duration_95
re_enum_duration_95 = new_re_enum_duration_95
# starting the plotting
plt.figure()
plt.figure(facecolor='w', edgecolor='k', figsize=(7, 5))
plt.xlabel(xlabel)
plt.ylabel(ylabel)
xlist_alg = np.array(xlist_alg)
xlist_algAlt = np.array(xlist_algAlt)
xlist_enum = np.array(xlist_enum)
# curves
algCV, _ = curve_fit(func2D, np.log(xlist_alg),
np.log(re_alg_duration_median))
algAltCV, _ = curve_fit(func2D, np.log(xlist_algAlt),
np.log(re_algAlt_duration_median))
enumCV, _ = curve_fit(func2D, np.log(xlist_enum),
np.log(re_enum_duration_median))
alg_5_CV, _ = curve_fit(func2D, np.log(xlist_alg),
np.log(re_alg_duration_5))
algAlt_5_CV, _ = curve_fit(func2D, np.log(xlist_algAlt),
np.log(re_algAlt_duration_5))
enum_5_CV, _ = curve_fit(func2D, np.log(xlist_enum),
np.log(re_enum_duration_5))
alg_95_CV, _ = curve_fit(func2D, np.log(xlist_alg),
np.log(re_alg_duration_95))
algAlt_95_CV, _ = curve_fit(func2D, np.log(xlist_algAlt),
np.log(re_algAlt_duration_95))
enum_95_CV, _ = curve_fit(func2D, np.log(xlist_enum),
np.log(re_enum_duration_95))
newx_alg = np.logspace(1, 3, 250)
newx_algAlt = np.logspace(1, 3, 250)
newx_algenum = np.logspace(1, 3, 250)
if paper:
# plot the best fit curves
plt.plot(newx_alg,
np.exp(func2D(np.log(newx_alg), algCV[0], algCV[1],
algCV[2])),
'-',
color=blues[1])
plt.plot(newx_algenum,
np.exp(
func2D(np.log(newx_algenum), enumCV[0], enumCV[1],
enumCV[2])),
'-',
color=blues[3])
# plot the points
plt.plot(xlist_alg,
re_alg_duration_median,
'o',
markersize=4,
label=alg_label,
color=blues[1])
plt.plot(xlist_enum,
re_enum_duration_median,
's',
markersize=4,
label=enum_label,
color=blues[3])
# plot the confidence intervals
plt.fill_between(newx_alg, np.exp(func2D(np.log(newx_alg), alg_5_CV[0], alg_5_CV[1], alg_5_CV[2])), \
np.exp(func2D(np.log(newx_alg), alg_95_CV[0], alg_95_CV[1], alg_95_CV[2])), color=blues[0], alpha=0.8)
plt.fill_between(newx_algenum, np.exp(func2D(np.log(newx_algenum), enum_5_CV[0], enum_5_CV[1], enum_5_CV[2])), \
np.exp(func2D(np.log(newx_algenum), enum_95_CV[0], enum_95_CV[1], enum_95_CV[2])), color=blues[2], alpha=0.8)
else:
# plot the best fit curves
plt.plot(newx_alg,
np.exp(func2D(np.log(newx_alg), algCV[0], algCV[1],
algCV[2])),
'-',
color='skyblue')
plt.plot(newx_algAlt,
np.exp(
func2D(np.log(newx_algAlt), algAltCV[0], algAltCV[1],
algAltCV[2])),
'-',
color='orangered')
plt.plot(newx_algenum,
np.exp(
func2D(np.log(newx_algenum), enumCV[0], enumCV[1],
enumCV[2])),
'-',
color='seagreen')
# plot the points
plt.plot(xlist_alg,
re_alg_duration_median,
'o',
markersize=4,
label=alg_label,
color='skyblue')
plt.plot(xlist_algAlt,
re_algAlt_duration_median,
'*',
markersize=4,
label=algAlt_label,
color='orangered')
plt.plot(xlist_enum,
re_enum_duration_median,
's',
markersize=4,
label=enum_label,
color='seagreen')
plt.plot([0, 1000], [timeout_ms, timeout_ms],
"--",
label="Timeout",
color='red')
# plot the confidence intervals
plt.fill_between(newx_alg, np.exp(func2D(np.log(newx_alg), alg_5_CV[0], alg_5_CV[1], alg_5_CV[2])), \
np.exp(func2D(np.log(newx_alg), alg_95_CV[0], alg_95_CV[1], alg_95_CV[2])), color='skyblue', alpha=.5)
plt.fill_between(newx_algAlt, np.exp(func2D(np.log(newx_algAlt), algAlt_5_CV[0], algAlt_5_CV[1], algAlt_5_CV[2])), \
np.exp(func2D(np.log(newx_algAlt), algAlt_95_CV[0], algAlt_95_CV[1], algAlt_95_CV[2])), color='orangered', alpha=.5)
plt.fill_between(newx_algenum, np.exp(func2D(np.log(newx_algenum), enum_5_CV[0], enum_5_CV[1], enum_5_CV[2])), \
np.exp(func2D(np.log(newx_algenum), enum_95_CV[0], enum_95_CV[1], enum_95_CV[2])), color='seagreen', alpha=.5)
# plt.plot([100, 1000], [100, 1000000], "--", label="Gradient 4n")
plt.xlim(xmin=0, xmax=1000)
plt.ylim(ymin=100)
plt.yscale('log')
plt.grid()
plt.legend(loc='upper left')
plt.tight_layout()
filename = dir_name + "/duration.pdf"
if paper:
filename = dir_name + "/paper_duration.pdf"
plt.savefig(filename)
plt.close()
plt.rcParams.update(plt.rcParamsDefault)
from matplotlib import pylab
if __name__ == '__main__':
fh = open('read_lengths.txt')
L = [int(x.strip()) for x in fh]
fh.close()
pylab.hist(L,120, histtype='bar')
pylab.tight_layout();
pylab.show()
def plot(index):
ts = 1e-12 # time resolution
tos = 19e-9
tend = 30e-9
wz1 = -2.0 * np.pi * 0.55e9
wp1 = -2.0 * np.pi * 1.2e9
wp2 = -2.0 * np.pi * 3.4e9
gain = -1.0 * wp1 * wp2 / wz1
if index == 1:
simout_filename = 'eq_out1.txt'
gs_filename = 'ctle_pulse_response_1.eps'
elif index == 2:
simout_filename = 'eq_out2.txt'
gs_filename = 'ctle_pulse_response_2.eps'
elif index == 3:
simout_filename = 'eq_out3.txt'
gs_filename = 'ctle_pulse_response_3.eps'
# load verilog simulation data and get 1d interpolator
data1 = np.loadtxt(simout_filename)
t = data1[:, 0]
yv = data1[:, 1]
fn_vlog = interp1d(t, yv)
time = np.arange(t[0], t[-1], ts)
time2 = np.arange(t[0], tend, ts)
time = time[:-1]
time2 = time2[:-1]
no_sample = len(time2) - len(time)
xdata = np.loadtxt('input.txt')
xt = np.append(xdata[:, 0], t[-1])
xy = np.append(xdata[:, 1], xdata[:, 1][-1])
fn_x = interp1d(xt, xy)
x = fn_x(time)
if no_sample > 0:
x2 = np.array(list(x) + no_sample * [x[-1]])
else:
x2 = x[:no_sample]
# ideal transfer function in s-domain
t0, y0, x0 = lsim(zpk2tf([wz1], [wp1, wp2], gain), x2, time2)
# residual error
y_vlog = fn_vlog(time)
if no_sample > 0:
y_vlog = np.array(list(y_vlog) + no_sample * [y_vlog[-1]])
else:
y_vlog = y_vlog[:no_sample]
err = y_vlog - y0
print 'Max. residual error = %.1f [mV]' % (max(abs(err[t0 > tos])) * 1000)
# plot time, value pairs at which events occur
plt.subplot(2, 1, 1)
plt.plot(1e9 * t[t > tos],
yv[t > tos],
'or',
label='Verilog',
markersize=5)
plt.plot(1e9 * t0[t0 > tos], y0[t0 > tos], label='Analytic expression')
plt.xlabel('Time [nsec]')
plt.ylabel('Output [V]')
plt.axis([tos * 1e9, tend * 1e9, -0.20, 0.20])
#plt.title('Pulse response of CTLE ('+r'$e_{tol}$'+'=1 [mV])')
plt.legend(loc=0)
plt.subplot(2, 1, 2)
plt.plot(1e9 * t0[t0 > tos], 1000 * err[t0 > tos], 'r')
plt.xlabel('Time [nsec]')
plt.ylabel('Residual error [mV]')
plt.axis([tos * 1e9, tend * 1e9, -20, 20])
plt.tight_layout()
plt.savefig(gs_filename)
plt.close()
plt.plot(ts, label = 'Original') plt.legend(loc = 'best') plt.subplot(4, 1, 2) plt.plot(tendencia, label = 'Tendencia') plt.legend(loc = 'best') plt.subplot(4, 1, 3) plt.plot(sazonal, label = 'Sazionalidade') plt.legend(loc = 'best') plt.subplot(4, 1, 4) plt.plot(aleatorio, label = 'Aleatorio') plt.legend(loc = 'best') plt.tight_layout() #para mostrar o legends # ============================================================================= # Previsão com media # ============================================================================= ts.mean() # ============================================================================= # Média do ultimo ano # ============================================================================= ts['1960-01-01':'1960-12-01'].mean() # ============================================================================= # Media movel
import numpy as np
import matplotlib.pylab as plt
import pylab
from kernel import KernelBasisDE
from scipy.special import legendre
params = {
'backend': 'ps',
'axes.labelsize': 18,
'text.fontsize': 18,
'axes.titlesize': 18,
'legend.fontsize': 18,
'xtick.labelsize': 18,
'ytick.labelsize': 18,
'text.usetex': True,
}
pylab.rcParams.update(params)
def find_zeros(x, y):
r = []
for i in range(len(y) - 1):
if y[i] * y[i + 1] < 0:
zero = (x[i] * np.abs(y[i + 1]) + x[i + 1] * np.abs(y[i])) / (
np.abs(y[i]) + np.abs(y[i + 1]))
r.append(zero)
return np.array(r)
results = []
N = 1001
il_list = [0, 1, 2]
marker_list = ['o', 'x', '+', 'v']
def quicklook_im(image,
logAmp=False,
show=True,
vmin=None,
vmax=None,
axis=False,
anno=None,
annos=None,
title=None,
pupil=False,
colormap="YlGnBu_r",
mark_star=False,
label=None):
# MEDIUM_SIZE = 27
# plt.rc('font', size=MEDIUM_SIZE) # controls default text sizes
# mgr = plt.get_current_fig_manager()
# mgr.full_screen_toggle()
# py = mgr.canvas.height()
# px = mgr.canvas.width()
# dprint((py,px))
# mgr.window.close()
if pupil:
import Analysis.phot
image = image * Analysis.phot.aperture(
tp.grid_size / 2, tp.grid_size / 2, tp.grid_size / 2)
if show != 'continuous':
fig = plt.figure()
else:
fig = sp.fig
vmax = sp.vmax
vmin = sp.vmin
if title == None:
title = r' $I / I^{*}$'
ax = fig.add_subplot(111)
if logAmp:
if np.min(image) <= 0:
cax = ax.imshow(image,
interpolation='none',
origin='lower',
vmin=vmin,
vmax=vmax,
norm=SymLogNorm(linthresh=1e-5),
cmap="YlGnBu_r")
else:
cax = ax.imshow(image,
interpolation='none',
origin='lower',
vmin=vmin,
vmax=vmax,
norm=LogNorm(),
cmap="YlGnBu_r")
else:
cax = ax.imshow(image,
interpolation='none',
origin='lower',
vmin=vmin,
vmax=vmax,
cmap=colormap)
if axis:
annotate_axis(cax, ax, image.shape[0])
if show == 'continuous':
fig.canvas.draw()
if not sp.cbar:
sp.cbar = plt.colorbar(
cax) #norm=LogNorm(vmin=cax.min(), vmax=cax.max()))
clims = sp.cbar.get_clim()
sp.vmax = clims[1]
sp.vmin = clims[0]
plt.show(block=False)
# import time
# time.sleep(5.0)
else:
# cb = plt.colorbar(cax, format=ticker.FuncFormatter(fmt))
cb = plt.colorbar(cax)
if axis == None:
ax.axis('off')
# ax.text(0.84, 0.9, '0.2"', transform=ax.transAxes, fontweight='bold', color='w', ha='center', fontsize=14, family='serif')
# ax.plot([0.78, 0.9], [0.87, 0.87],transform=ax.transAxes, color='w', linestyle='-', linewidth=3)
# cb.ax.set_title(title, fontsize=16)
# if anno:
# ax.text(0.05, 0.05, anno, transform=ax.transAxes, fontweight='bold', color='w', fontsize=22)
if anno:
props = dict(boxstyle='square', facecolor='k', alpha=0.3)
ax.text(0.05,
0.05,
anno,
transform=ax.transAxes,
fontweight='bold',
color='w',
fontsize=22,
bbox=props)
if label:
props = dict(boxstyle='square', facecolor='k', alpha=0.3)
ax.text(0.05,
0.9,
label,
transform=ax.transAxes,
fontweight='bold',
color='w',
fontsize=22,
family='serif',
bbox=props)
# ax.text(0.84, 0.9, '0.5"', transform=ax.transAxes, fontweight='bold', color='w', ha='center', fontsize=14, family='serif')
# ax.plot([0.78, 0.9], [0.87, 0.87],transform=ax.transAxes, color='w', linestyle='-', linewidth=3)
if mark_star:
ax.plot(image.shape[0] / 2, image.shape[1] / 2, marker='*', color='r')
plt.tight_layout()
# # For plotting on the leftmost screen
# figManager = plt.get_current_fig_manager()
# # if px=0, plot will display on 1st screen
# figManager.window.move(-1920, 0)
# figManager.window.setFocus()
if show == True:
plt.show(block=True)
vi = 100 * 1000 / 3600.
z0 = sp.array([0, 0, vi, vi])
# Viento:
V = 0 #[m/s]
while V <= 20:
sol = odeint(bala, z0, t)
x = sol[:, 0]
y = sol[:, 1]
plt.figure(1)
plt.plot(x, y)
V += 10
# Grafico:
plt.legend(['V=0 m/s', 'V=10 m/s', 'V=20 m/s'])
plt.title('Trayectoria para distintos vientos')
plt.xlabel('X (m)')
plt.ylabel('Y (m)')
plt.axis([0, 150, 0, 50])
plt.grid(True)
plt.tight_layout()
# Guardar grafico como png sin abrir una ventana de visualizacion
plt1.savefig('Trayectoria para distintos vientos')
def view_datacube(datacube,
show=True,
logAmp=False,
axis=True,
vmin=None,
vmax=None,
width=5):
'''axis = anno/None/True'''
fig = plt.figure(figsize=(14, 7))
colors = len(datacube)
print(colors, width)
height = int(np.ceil(colors / float(width)))
print(height)
peak = np.max(datacube)
trough = np.min(datacube)
# print peak, trough, 'max'
if vmin != None:
if peak >= vmin:
vmax = peak
else:
vmin = np.min(datacube)
dprint((vmin, peak))
for w in range(colors):
ax = fig.add_subplot(height, width, w + 1)
if logAmp:
if vmin <= 0:
# datacube[w] = np.abs(datacube[w] + 1e-9)
im = ax.imshow(datacube[w],
interpolation='none',
origin='lower',
vmin=vmin,
vmax=vmax,
norm=SymLogNorm(linthresh=1e-5),
cmap="YlGnBu_r")
else:
im = ax.imshow(datacube[w],
interpolation='none',
origin='lower',
vmin=vmin,
vmax=peak,
norm=LogNorm(),
cmap="YlGnBu_r")
else:
im = ax.imshow(datacube[w],
interpolation='none',
origin='lower',
vmin=vmin,
vmax=peak,
cmap="YlGnBu_r")
if axis == 'anno':
annotate_axis(im, ax, datacube.shape[1])
if axis == None:
plt.axis('off')
# ax.grid(color='w', linestyle='--')
if axis:
# fig.subplots_adjust(bottom=0.1)
cbar_ax = fig.add_axes([0.45, 0.15, 0.4, 0.05])
fig.colorbar(im, cax=cbar_ax, orientation='horizontal')
# # For plotting on the leftmost screen
# figManager = plt.get_current_fig_manager()
# # if px=0, plot will display on 1st screen
# figManager.window.move(-1920, 0)
# figManager.window.setFocus()
if show == True:
plt.tight_layout()
plt.show(block=True)
X_ticks[12] = "Lack of spontaneity (N6)"
cl_mean = np.mean(X_org[X_cl_labels == 0], axis=0)
n_subs = np.sum(X_cl_labels == 0)
ax1 = sns.barplot(X_ticks, cl_mean, palette=my_palette, ax=axarr[0])
ax1.xaxis.set_ticks_position('top')
rotateTickLabels(ax1, 45, 'x')
ax1.xaxis.set_ticklabels(X_ticks, fontsize=12)
ax1.set_xlabel('%i patients' % n_subs, fontsize=16)
ax1.set_ylabel("Group 1", fontsize=16)
cl_mean = np.mean(X_org[X_cl_labels == 1], axis=0)
n_subs = np.sum(X_cl_labels == 1)
ax2 = sns.barplot(X_ticks, cl_mean, palette=my_palette, ax=axarr[1])
ax2.set_xlabel('%i patients' % n_subs, fontsize=16)
ax2.set_ylabel("Group 2", fontsize=16)
cl_mean = np.mean(X_org[X_cl_labels == 2], axis=0)
n_subs = np.sum(X_cl_labels == 2)
ax3 = sns.barplot(X_ticks, cl_mean, palette=my_palette, ax=axarr[2])
ax3.set_xlabel('%i patients' % n_subs, fontsize=16)
ax3.set_ylabel("Group 3", fontsize=16)
ax3.tick_params(axis='x', labelbottom='off')
# sns.despine(bottom=True)
plt.setp(f.axes, ylim=[0, 5.])
# plt.xticks(rotation= 90, fontsize=8)
plt.tight_layout(h_pad=3)
# plt.savefig('plots/kmeans_3cl_noYaxis.png')
plt.show()
axs[3].plot(mjd, df['par_2'], 'o', mec='black')
axs[3].set_ylabel('Disk blackbody\nkT (keV)')
axs[3].set_ylim(0.15, 0.18)
axs[4].plot(mjd, np.sqrt(df['par_3']), 'o', mec='black')
axs[4].set_ylabel('Inner disk radius\n'
r'R$_{in}d_{10 kpc}/\sqrt{\cos {\theta}}$ (km)')
axs[4].set_ylim(380, 900)
axs[5].plot(mjd, df['par_4'], 'o', mec='black', mfc='orange')
axs[5].set_ylabel('Power-law \nPhoton index')
axs[6].plot(mjd, df['par_7'] / 100.0, 'o', mec='black', mfc='orange')
axs[6].set_ylabel(
'Unabsorb PL 2-10 keV flux \n($10^{-10}$ erg s$^{-1}$ cm$^{-2}$) ')
axs[-1].set_xlabel('MJD')
for ax in axs:
ax.label_outer()
#ax.minorticks_on()
ax.xaxis.grid(True)
ax.xaxis.grid(which='major', linestyle='--', color='#000000')
ax.xaxis.grid(which='minor', linestyle='-.')
ax.tick_params(axis="both", which='major', direction='in', length=5)
ax.tick_params(axis="both", which='minor', direction='in', length=3)
outpdf = 'test.pdf'
fig.align_ylabels(axs)
plt.tight_layout(pad=2)
plt.rcParams["font.family"] = "serif"
plt.rcParams["mathtext.fontset"] = "dejavuserif"
plt.savefig(outpdf)
def process(f, i):
path = 'time_series_images/' + os.path.basename(f) + '.png'
if os.path.exists(path):
print('Exists, skipping ...')
return
j = json.loads(open(f).read())
p = j['features'][0]['properties']
# fr = p['water_area_filled_fraction']
t = p['water_area_time']
v1 = p['water_area_value']
v2 = p['water_area_filled']
t_jrc = p['water_area_time_jrc']
v_jrc = p['water_area_value_jrc']
filled_fr = list(zip(v1, v2))
filled_fr = [(o[1] - o[0]) / o[1] for o in filled_fr]
mask = ma.masked_greater_equal(filled_fr, 0.5)
# t = list(ma.masked_array(t, mask).compressed())
# v1 = list(ma.masked_array(v1, mask).compressed())
# v2 = list(ma.masked_array(v2, mask).compressed())
if not len(t):
print('Empty, skipping ...')
return
years = mdates.YearLocator() # every year
v2_filtered = savitzky_golay(np.array(v2), window_size=15, order=4)
# v2_filtered = signal.medfilt(v2, 7)
# v2_filtered = lowess(v2, t)
# v2_filtered = lowess(v2, t, frac=1./50)
t = [datetime.datetime.fromtimestamp(tt / 1000) for tt in t]
t_jrc = [
datetime.datetime.fromtimestamp(tt_jrc / 1000) for tt_jrc in t_jrc
]
s_scale = 'Scale: {:.2f}'.format(p['scale']) + '$m$'
s_area = 'Area: {:.2f}'.format(
p['area'] /
(1000 * 1000)) + '$km^2$, ' + '{:.2f}'.format(100 * p['area'] /
(1000 * 1000)) + '$ha$'
title = s_scale + ', ' + s_area
fig = plt.figure(figsize=(11, 4))
ax = fig.add_subplot(111)
ax.xaxis.set_major_locator(years)
# fig.autofmt_xdate()
ax.set_xlim([datetime.date(1985, 1, 1), datetime.date(2019, 1, 1)])
ax.grid(color='k', linestyle='-', linewidth=1, alpha=0.2)
plt.title(title)
plt.xticks(rotation=90)
ax.plot(t_jrc,
v_jrc,
marker='.',
c='r',
markersize=2,
linewidth=0,
alpha=0.05)
ax.plot(t, v1, marker='.', c='b', markersize=2, linewidth=0, alpha=0.05)
ax.plot(t, v2, marker='.', c='k', markersize=3, linewidth=0, alpha=0.8)
# for SG
if len(t) != len(v2_filtered):
print('Bad, shapes are not equal, skipping line plotting ...')
else:
ax.plot(t,
v2_filtered,
marker='.',
c='k',
markersize=0,
linewidth=2,
alpha=0.1)
# for LOWESS
# v2_filtered_t = [datetime.datetime.fromtimestamp(t / 1000) for t in v2_filtered[:, 0]]
# ax.plot(v2_filtered_t, v2_filtered[:, 1], marker='.', c='k', markersize=0, linewidth=2, alpha=0.1)
path = 'time_series_images/' + os.path.basename(f) + '.png'
print(str(i) + ' ' + path)
plt.tight_layout()
plt.savefig(path, dpi=150)
plt.close()