def plot(self, count, fit_args):
fig = plt.figure(figsize=[11, 10])
ax = fig.add_subplot(111)
ax.set_yscale("log")
for i in range(len(self.labels)):
ax.plot([s[0] for s in self.data], [s[1][i] for s in self.data],
label=self.labels[i])
ax.legend()
savefig("losses_Count_{}.png".format(count), fit_args)
plt.close(fig)
def main():
if not os.path.exists("../img"):
os.mkdir("../img", 0755)
fs = 44100 # in Hz
length = 0.01 # in seconds
t = np.linspace(0, length, num=length * fs)
h_function = lambda t: b * np.exp(-t / tau)
h = h_function(t)
plt.plot(h, t, fs, 3, "h(t)", "Signal h(t)")
plt.savefig("../img/4.1-transfer_function.png")
x_function = lambda t: a1 * np.cos(2 * np.pi * f1 * t) + a2 * np.sin(
2 * np.pi * f2 * t) + a3 * np.cos(2 * np.pi * f3 * t)
x = x_function(t)
plt.plot(x, t, fs, 10, "x(t)", "Signal x(t)")
yx = np.convolve(h, x)
plt.plot(np.array([x, yx[0:len(t)]]), t, fs, 10, "yx(t)", "Signal yx(t)")
plt.savefig("../img/4.2-sines.png")
z_function = lambda t: A * (abs((t - T / 2) / T) < 1.0)
z = z_function(t)
yz = np.convolve(h, z)
plt.plot(np.array([z, yz[0:len(t)]]), t, fs, 10, "yz(t)", "Signal yz(t)")
plt.savefig("../img/4.3-rect.png")
w, tw, rate, size, max = wav.readWav("../3-audio/af2.wav")
h = h_function(tw) # new sample rate and time vector
yw = np.convolve(h, w)
plt.plot(np.array([w, yw[0:len(tw)]]), tw, rate, 10, "yw(t)",
"Signal yw(t)")
rel_max = np.amax(yw) if np.amax(yw) > abs(np.amin(yw)) else abs(
np.amin(yw))
yw = yw * (max / rel_max)
wav.write("convoluted.wav", rate, yw.astype(np.dtype('i2')))
plt.savefig("../img/4.4-audio.png")
def main():
w, tw, rate, size, max = wav.readWav("af2.wav")
Ew = np.sum(np.square(w)) / rate
Pw = np.sum(np.square(w)) / size
# Get 10 random intervals and measure the power of the signal
for i in range(10):
interval = [random.randint(0, size)]
interval.append(random.randint(0, size))
interval.sort()
Pwi = np.sum(np.square(
w[interval[0]:interval[1] + 1])) / (interval[1] - interval[0])
print("Power for " + str(round(interval[0] / float(rate), 5)) +
"s - " + str(round(interval[1] / float(rate), 5)) + "s = " +
str(round(Pwi, 5)) + "W")
# Plot the audio signal
plt.plot(
w, tw, rate, 10, "w(t)", "Signal w(t)", "Energy: " +
str(round(Ew, 3)) + " W, Power: " + str(round(Pw, 3)) + " J")
# Save the plot into an image file
if not os.path.exists("img"):
os.mkdir("img", 0755)
plt.savefig("img/3-AudioSignal.png")
plt.show()
ax.text(d+s/2.0, d+s/2.0, '$H_{z(i+1/2,j+1/2,k)}$', color = 'blue', verticalalignment = 'bottom', horizontalalignment = 'center')
# E arrows x y dx dy
ax.add_patch(plt.Arrow(d+s/2.0, d, d, 0.0, width = d/2.0, edgecolor='none', facecolor = 'red'))
ax.add_patch(plt.Arrow(d, d+s/2.0, 0, d, width = d/2.0, edgecolor='none', facecolor = 'red'))
ax.add_patch(plt.Arrow(d/2.0, d/2.0, -d/3.0, -d/3.0, width = d/2.0, edgecolor='none', facecolor = 'red'))
# E text
ax.text(d+s/2.0, d, '$E_{x(i+1/2,j,k)}$', color = 'red', verticalalignment = 'bottom', horizontalalignment = 'left')
ax.text(d, d+s/2.0, '$E_{y(i,j+1/2,k)}$', color = 'red', verticalalignment = 'bottom', horizontalalignment = 'right')
ax.text(d/3.0, d/3.0, '$E_{z(i,j,k+1/2)}$', color = 'red', verticalalignment = 'top', horizontalalignment = 'left')
ax.set_xlim((-d/7.0, s+d+d/7.0))
ax.set_ylim((-d/7.0, s+d+d/7.0))
# ******************************************************************************************
# QFDTD cell
fig_qfdtd = plot.figure()
ax = fig_qfdtd.add_subplot(1,1,1, aspect = 'equal', xticks=[], yticks=[], frameon=False)
plot_cell(ax)
ax.plot([d], [d], 'o', markeredgecolor = 'green', markerfacecolor = 'green', markersize = 14)
ax.text(1.1*d, 0.9*d, '$\psi_{i,j,k}$', color = 'green', verticalalignment = 'top', horizontalalignment = 'left')
ax.set_xlim((-d/7.0, s+d+d/7.0))
ax.set_ylim((-d/7.0, s+d+d/7.0))
for ext in ['pdf', 'svg']:
plot.savefig(['fdtd_cell_yee.' + ext, 'fdtd_cell_qfdtd.' + ext])
plot.show()
def main():
# setup output directory
d = datetime.datetime.today()
output_folder = "out/{}-{}-{}_{}:{}:{}".format(d.year, d.month, d.day, d.hour, d.minute, d.second)
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
os.chdir(output_folder)
# load dataset
datasets = load_data()
train_set_x, train_set_y = util.shared_dataset(datasets[0])
valid_set_x, valid_set_y = util.shared_dataset(datasets[1])
test_set_x, test_set_y = util.shared_dataset(datasets[2])
train_set = (train_set_x, train_set_y)
valid_set = (valid_set_x, valid_set_y)
test_set = (test_set_x, test_set_y)
n_input = train_set_x.get_value(borrow=True).shape[1]
n_output = train_set_y.get_value(borrow=True).shape[1]
# compute number of minibatches for training, validation and testing
n_train_batches = train_set_x.get_value(borrow=True).shape[0]
n_train_batches /= batch_size
# numpy random generator
# start-snippet-3
numpy_rng = numpy.random.RandomState(89677)
print '... building the model'
# construct the stacked denoising autoencoder class
sda = SdA(
numpy_rng=numpy_rng,
n_ins=n_input,
hidden_layers_sizes=[1000, 1000, 1000],
n_outs=n_output
)
predict_fn = sda.build_predict_function()
#########################
# PRETRAINING THE MODEL #
#########################
print '... getting the pretraining functions'
pretraining_fns = sda.pretraining_functions(train_set_x=train_set_x, batch_size=batch_size)
print '... pre-training the model'
start_time = time.clock()
## Pre-train layer-wise
corruption_levels = [.1, .2, .3]
for i in xrange(sda.n_layers):
# go through pretraining epochs
for epoch in xrange(pretraining_epochs):
# go through the training set
c = []
for batch_index in xrange(n_train_batches):
c.append(pretraining_fns[i](index=batch_index,
corruption=corruption_levels[i],
lr=pretrain_lr))
print("Pre-training layer {}, epoch {}, cost ".format(i, epoch)),
print("{}".format(numpy.mean(c)))
end_time = time.clock()
print >> sys.stderr, ('The pretraining code for file ' + os.path.split(__file__)[1] + ' ran for %.2fm' % ((end_time - start_time) / 60.))
########################
# FINETUNING THE MODEL #
########################
# get the training, validation and testing function for the model
print '... getting the finetuning functions'
train_fn, validate_model, test_model = sda.build_finetune_functions(
datasets=(train_set, valid_set, test_set),
batch_size=batch_size,
learning_rate=finetune_lr
)
print '... finetunning the model'
# early-stopping parameters
patience = 10 * n_train_batches # look as this many examples regardless
patience_increase = 2. # wait this much longer when a new best is
# found
improvement_threshold = 0.995 # a relative improvement of this much is
# considered significant
validation_frequency = min(n_train_batches, patience / 2)
# go through this many
# minibatche before checking the network
# on the validation set; in this case we
# check every epoch
best_validation_loss = numpy.inf
test_score = 0.
start_time = time.clock()
done_looping = False
epoch = 0
while (epoch < training_epochs) and (not done_looping):
epoch = epoch + 1
for minibatch_index in xrange(n_train_batches):
minibatch_avg_cost = train_fn(minibatch_index)
iter = (epoch - 1) * n_train_batches + minibatch_index
if (iter + 1) % validation_frequency == 0:
validation_losses = validate_model()
this_validation_loss = numpy.mean(validation_losses)
print('epoch %i, minibatch %i/%i, validation error %f %%' %
(epoch, minibatch_index + 1, n_train_batches,
this_validation_loss * 100.))
# if we got the best validation score until now
if this_validation_loss < best_validation_loss:
#improve patience if loss improvement is good enough
if (
this_validation_loss < best_validation_loss *
improvement_threshold
):
patience = max(patience, iter * patience_increase)
# save best validation score and iteration number
best_validation_loss = this_validation_loss
best_iter = iter
# test it on the test set
test_losses = test_model()
test_score = numpy.mean(test_losses)
print((' epoch %i, minibatch %i/%i, test error of '
'best model %f %%') %
(epoch, minibatch_index + 1, n_train_batches,
test_score * 100.))
if patience <= iter:
done_looping = True
break
end_time = time.clock()
print(
(
'Optimization complete with best validation score of %f %%, '
'on iteration %i, '
'with test performance %f %%'
)
% (best_validation_loss * 100., best_iter + 1, test_score * 100.)
)
print >> sys.stderr, ('The training code for file ' +
os.path.split(__file__)[1] +
' ran for %.2fm' % ((end_time - start_time) / 60.))
###########
# PREDICT #
###########
y_pred = predict_fn(test_set_x.get_value(borrow=True))
mae, mre = util.calculate_error_indexes(test_set_y, y_pred)
print("-*-*RESULT*-*-")
print("mae={}".format(mae))
print("mre={}".format(mre))
# plot
for i in xrange(n_output):
filename = "{}.png".format(str(i))
plot.savefig(filename, test_set_x, y_pred, indexes=[i])
axes = [ax1, ax2]
coulombic.Plot( axes, ':k', 'Coulomb')
harmonic.Plot( axes, '-b', 'Harmonic')
sg_one.Plot( axes, '-r', 'Super-Gaussian (m=1)')
sg_three.Plot( axes, '-c', 'Super-Gaussian (m=3)')
cs.Plot( axes, '-m', 'Charge distribution')
ax1.grid()
ax1.set_ylabel('Potential [Eh]')
ax2.grid()
ax2.set_ylabel('Field [a.u.]')
ax2.set_xlabel('r [Bohr]')
ax1.set_ylim((0.0, 1.25*phi0))
ax2.set_ylim((-2.0, 0.05))
plot.setp(ax1.get_xticklabels(), visible=False)
leg = ax1.legend(loc = "best")
leg.get_frame().set_alpha(0.6)
#leg.set_zorder(100)
ax2.set_zorder(-100)
plot.savefig('potential_shapes.pdf')
plot.savefig('potential_shapes.svg')
plot.show()
cooling_indices = np.where(NumericalHeating[:, index1, index2] <= 0.0)
if (len(cooling_indices[0]) >= 1):
ax2_eV.plot(base_potentials[cooling_indices], abs(NumericalHeating[:, index1, index2][cooling_indices]),
'.' + colors_and_symbols.symb_col(c))
c += 1
ax1_eV.set_xlabel(r"$\Delta t$ [as]")
ax1_eV.set_xlim((dts[0], dts[-1]))
plt.setp(ax1_Eh.get_xticklabels(), visible=False)
ax2_eV.set_xlabel("Potential depth [Hartree]")
ax2_eV.set_xlim((base_potentials[0], base_potentials[-1]))
for ax in [ax1_eV, ax2_eV]:
leg = ax.legend(loc = "best")
leg.get_frame().set_alpha(0.75)
ax.grid(True)
ax.set_ylabel("Energy change [eV]")
ax.set_xscale('log')
ax.set_yscale('log')
for ax in [ax1_Eh, ax2_Eh]:
ax.set_xscale('log')
ax.set_yscale('log')
ax.set_ylabel("Energy change [Hartree]")
for ext in ['pdf', 'svg']:
plot.savefig(['numerical_heating_dt.' + ext, 'numerical_heating_D.' + ext])
plot.show()
## Bound electron, now free
ax4.plot([0.0], [Xe_Z0_es_E[0]], 'og', ms = 14, alpha = 0.4)
ax4.plot([0.0], [Ke2+Xe_Z0_es_E[0]], 'og', ms = 14)
ar1Ke = fleches.arrow('', [0.0, Xe_Z0_es_E[0]], [0.0, Ke2+Xe_Z0_es_E[0]]) # Vertical (Ke)
ar1Ke.Plot(ax4, color = 'g')
ar2Ke = fleches.arrow('', [0.0, Ke2+Xe_Z0_es_E[0]], [0.0+2.5, Ke2+Xe_Z0_es_E[0]]) # Horizontal (v)
ar2Ke.Plot(ax4, color = 'g', label = "$v_{e,3}$", verticalalignment = 'top')
for ax in [ax1, ax2, ax3, ax4]:
ax.set_xlabel('r [bohr]')
ax.set_ylabel('Energy [Hartree]')
#ax.set_ylim((Umin, 0.05*abs(Umin)))
ax.set_ylim((0.97*Umin, 1.05*Ke))
#leg = ax.legend(loc = "lower right")
ax.axhline(0.0, linestyle = ':', color = 'k')
ax1.text(0.9*r[0], 0.9*Umin, 'a)')
ax2.text(0.9*r[0], 0.9*Umin, 'b)')
ax3.text(0.9*r[0], 0.9*Umin, 'c)')
ax4.text(0.9*r[0], 0.9*Umin, 'd)')
# Remove overlapping labels
ax3.get_xticklabels()[-1].set_visible(False)
ax4.get_xticklabels()[0].set_visible(False)
for ext in ['pdf', 'svg']:
plot.savefig('ionization_aci.' + ext)
plot.show()
def main():
# setup output directory
d = datetime.datetime.today()
output_folder = "out/{}-{}-{}_{}:{}:{}".format(d.year, d.month, d.day,
d.hour, d.minute, d.second)
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
os.chdir(output_folder)
# load dataset
datasets = load_data()
train_set_x, train_set_y = util.shared_dataset(datasets[0])
valid_set_x, valid_set_y = util.shared_dataset(datasets[1])
test_set_x, test_set_y = util.shared_dataset(datasets[2])
train_set = (train_set_x, train_set_y)
valid_set = (valid_set_x, valid_set_y)
test_set = (test_set_x, test_set_y)
n_input = train_set_x.get_value(borrow=True).shape[1]
n_output = train_set_y.get_value(borrow=True).shape[1]
# compute number of minibatches for training, validation and testing
n_train_batches = train_set_x.get_value(borrow=True).shape[0]
n_train_batches /= batch_size
# numpy random generator
# start-snippet-3
numpy_rng = numpy.random.RandomState(89677)
print '... building the model'
# construct the stacked denoising autoencoder class
sda = SdA(numpy_rng=numpy_rng,
n_ins=n_input,
hidden_layers_sizes=[1000, 1000, 1000],
n_outs=n_output)
predict_fn = sda.build_predict_function()
#########################
# PRETRAINING THE MODEL #
#########################
print '... getting the pretraining functions'
pretraining_fns = sda.pretraining_functions(train_set_x=train_set_x,
batch_size=batch_size)
print '... pre-training the model'
start_time = time.clock()
## Pre-train layer-wise
corruption_levels = [.1, .2, .3]
for i in xrange(sda.n_layers):
# go through pretraining epochs
for epoch in xrange(pretraining_epochs):
# go through the training set
c = []
for batch_index in xrange(n_train_batches):
c.append(pretraining_fns[i](index=batch_index,
corruption=corruption_levels[i],
lr=pretrain_lr))
print("Pre-training layer {}, epoch {}, cost ".format(i, epoch)),
print("{}".format(numpy.mean(c)))
end_time = time.clock()
print >> sys.stderr, ('The pretraining code for file ' +
os.path.split(__file__)[1] + ' ran for %.2fm' %
((end_time - start_time) / 60.))
########################
# FINETUNING THE MODEL #
########################
# get the training, validation and testing function for the model
print '... getting the finetuning functions'
train_fn, validate_model, test_model = sda.build_finetune_functions(
datasets=(train_set, valid_set, test_set),
batch_size=batch_size,
learning_rate=finetune_lr)
print '... finetunning the model'
# early-stopping parameters
patience = 10 * n_train_batches # look as this many examples regardless
patience_increase = 2. # wait this much longer when a new best is
# found
improvement_threshold = 0.995 # a relative improvement of this much is
# considered significant
validation_frequency = min(n_train_batches, patience / 2)
# go through this many
# minibatche before checking the network
# on the validation set; in this case we
# check every epoch
best_validation_loss = numpy.inf
test_score = 0.
start_time = time.clock()
done_looping = False
epoch = 0
while (epoch < training_epochs) and (not done_looping):
epoch = epoch + 1
for minibatch_index in xrange(n_train_batches):
minibatch_avg_cost = train_fn(minibatch_index)
iter = (epoch - 1) * n_train_batches + minibatch_index
if (iter + 1) % validation_frequency == 0:
validation_losses = validate_model()
this_validation_loss = numpy.mean(validation_losses)
print('epoch %i, minibatch %i/%i, validation error %f %%' %
(epoch, minibatch_index + 1, n_train_batches,
this_validation_loss * 100.))
# if we got the best validation score until now
if this_validation_loss < best_validation_loss:
#improve patience if loss improvement is good enough
if (this_validation_loss <
best_validation_loss * improvement_threshold):
patience = max(patience, iter * patience_increase)
# save best validation score and iteration number
best_validation_loss = this_validation_loss
best_iter = iter
# test it on the test set
test_losses = test_model()
test_score = numpy.mean(test_losses)
print((' epoch %i, minibatch %i/%i, test error of '
'best model %f %%') %
(epoch, minibatch_index + 1, n_train_batches,
test_score * 100.))
if patience <= iter:
done_looping = True
break
end_time = time.clock()
print(('Optimization complete with best validation score of %f %%, '
'on iteration %i, '
'with test performance %f %%') %
(best_validation_loss * 100., best_iter + 1, test_score * 100.))
print >> sys.stderr, ('The training code for file ' +
os.path.split(__file__)[1] + ' ran for %.2fm' %
((end_time - start_time) / 60.))
###########
# PREDICT #
###########
y_pred = predict_fn(test_set_x.get_value(borrow=True))
mae, mre = util.calculate_error_indexes(test_set_y, y_pred)
print("-*-*RESULT*-*-")
print("mae={}".format(mae))
print("mre={}".format(mre))
# plot
for i in xrange(n_output):
filename = "{}.png".format(str(i))
plot.savefig(filename, test_set_x, y_pred, indexes=[i])
pool = Pool(processes=12)
pool.map(norm, range(fres.shape[1]))
# plot
res_tn = exp.load('%s_%s_time_normalized_scales_mean.npy' % (strain, feat),
memmap='r')
dorder = exp.load('%s_%s_order.npy' % (strain, feat))
datplt = alys.scales_to_array(res_tn, worms_first=False, order=dorder)
fig = fplt.plot_array(datplt,
title='%s %s time normalized scales mean' %
(strain, feat))
fplt.savefig(fig,
exp.figname('%s_%s_time_normalized_scales_mean.png' %
(strain, feat)),
width=2500)
datplt = alys.scales_to_array(res_tn, worms_first=True, order=dorder)
fig = fplt.plot_array(datplt,
title='%s %s time normalized scales mean' %
(strain, feat))
fplt.savefig(fig,
exp.figname('%s_%s_time_normalized_scales_mean_2.png' %
(strain, feat)),
width=2500)
#### Test on single worm
#
#from timer import timeit;
#
def save(self):
plot.savefig(self.figpath.joinpath('%05d.png' % rounds_played))
ax_U_Eh.set_xlim(xlim)
if options.vmin != None or options.vmax != None:
if plot_V:
ylim = list(ax_V_Eh.get_ylim())
if options.vmin != None:
ylim[0] = options.vmin
if options.vmax != None:
ylim[1] = options.vmax
ax_V_Eh.set_ylim(ylim)
if options.umin != None or options.umax != None:
if plot_U:
ylim = list(ax_U_eV.get_ylim())
if options.umin != None:
ylim[0] = options.umin
if options.umax != None:
ylim[1] = options.umax
ax_U_Eh.set_ylim(ylim)
if plot_V:
leg = ax_V_Eh.legend(loc="best")
leg.get_frame().set_alpha(0.4)
# if (plot_U):
# leg = ax_U_Eh.legend(loc="best")
# leg.get_frame().set_alpha(0.4)
for ext in ["pdf", "svg"]:
plot.savefig("potential_landscape." + ext)
plot.show()
ar1Ke = fleches.arrow("K_e'", [0.0, 0.0], [0.0, Kep]) # Vertical (Ke)
ar2Ke = fleches.arrow("K_e'", [0.0, Kep*1.3], [5.0, Kep*1.3]) # Horizontal (v)
ar1Ke.Plot(ax2, color = 'b', label = r"$K_e'$ .", horizontalalignment = 'right', bidirectional = True)
ar2Ke.Plot(ax2, color = 'b', verticalalignment = 'bottom')
ax2.plot([0.0], [Kep*1.3], 'ob', ms = 14)
# Bound electron
ax2.plot([0.0], [-Xe_Z0_Ip], 'og', ms = 14, alpha = 0.4)
ax2.plot([0.0], [Kep], 'og', ms = 14)
ar2a = fleches.arrow("", [0.0, 0.0], [0.0, Kep]) # Vertical
ar2a.Plot(ax2, color = 'g', label = r".$K_e'$", horizontalalignment = 'left', bidirectional = True)
ar2b = fleches.arrow("K_e'", [0.0, Kep], [5.0, Kep]) # Horizontal (v)
ar2b.Plot(ax2, color = 'g', verticalalignment = 'bottom')
for ax in [ax1, ax2]:
ax.set_xlabel('r [bohr]')
ax.set_ylabel('Energy [Hartree]')
#ax.set_ylim((Umin, 0.05*abs(Umin)))
ax.set_ylim((0.97*Umin, 1.05*Ke))
#leg = ax.legend(loc = "lower right")
ax.axhline(0.0, linestyle = ':', color = 'k')
ax1.text(0.9*r[0], 0.9*Umin, 'a)')
ax2.text(0.9*r[0], 0.9*Umin, 'b)')
for ext in ['pdf', 'svg']:
plot.savefig('ionization_impact.' + ext)
plot.show()
def test_SdA(state_file=None, output_folder=None):
# load data
datasets = load_data(r=2, d=1)
train_set_x, train_set_y = util.shared_dataset(datasets[0])
valid_set_x, valid_set_y = util.shared_dataset(datasets[1])
test_set_x, test_set_y = util.shared_dataset(datasets[2])
train_set = (train_set_x, train_set_y)
valid_set = (valid_set_x, valid_set_y)
test_set = (test_set_x, test_set_y)
n_input = train_set_x.get_value(borrow=True).shape[1]
n_output = train_set_y.get_value(borrow=True).shape[1]
# prepare output folder
if output_folder is None:
d = datetime.datetime.today()
output_folder = "out/{0:04d}{1:02d}{2:02d}_{3:02d}{4:02d}{5:02d}".format(
d.year, d.month, d.day, d.hour, d.minute, d.second)
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
# instantiate TestBed
if state_file is None:
bed = TestBed.new(n_input, [400, 400, 400], n_output, output_folder)
else:
bed = TestBed.load(state_file)
######################
# PRETRAIN THE MODEL #
######################
bed.pretrain(test_set_x, epochs=1, learning_rate=0.1, batch_size=1)
########################
# FINETUNING THE MODEL #
########################
bed.finetune(train_set,
valid_set,
test_set,
epochs=1000,
learning_rate=0.1,
batch_size=1)
bed.finetune(train_set,
valid_set,
test_set,
epochs=1000,
learning_rate=0.01,
batch_size=1)
bed.finetune(train_set,
valid_set,
test_set,
epochs=1000,
learning_rate=0.001,
batch_size=1)
bed.finetune(train_set,
valid_set,
test_set,
epochs=1000,
learning_rate=0.0001,
batch_size=1)
bed.finetune(train_set,
valid_set,
test_set,
epochs=1000,
learning_rate=0.00001,
batch_size=1)
###########
# PREDICT #
###########
y_pred = bed.predict(test_set_x.get_value(borrow=True))
mae, mre, rmse = util.calculate_error_indexes(
test_set_y.get_value(borrow=True), y_pred)
print("-*-*RESULT*-*-")
print("mae={}".format(mae))
print("mre={}".format(mre))
print("rmse={}".format(rmse))
# plot
os.chdir(output_folder)
cut = min(10 * 144, test_set_x.get_value(borrow=True).shape[0])
plot_y = test_set_x.get_value(borrow=True)[:cut]
plot_y_pred = y_pred[:cut]
for i in xrange(n_output):
filename = "{}.png".format(str(i))
plot.savefig(filename, plot_y, plot_y_pred, indexes=[i])
X,Y = np.meshgrid(y, y)
print "--> The warning 'UserWarning: Images are not supported on non-linear axes.' can be ignored."
print "--> Even though the axes are log-scaled, the rectangle with the colormap should be shown on linear scale."
print ""
#im = ax_eV.imshow(Z, cmap=cm.cool, alpha=.9, interpolation='bilinear', extent=extent)
#im = ax_eV.pcolormesh(x, y, Z, cmap=cm.cool, shading='gouraud')
im = ax_eV.pcolorfast(x, y, Z, cmap=cm.cool, alpha=0.7)
#im = ax_eV.pcolor(x, y, Z, cmap=cm.cool)
draw_text_box(ax_eV, "VUV",
1.0e11, 1.0e15, 6.2, 17,
color = 'none')
draw_text_box(ax_eV, "XUV",
1.0e11, 1.0e15, 47, 124,
color = 'none')
draw_text_box(ax_eV, "XFEL",
1.0e11, 1.0e17, 250, 1000,
color = 'blue')
ax_eV.set_xlim((I_min, I_max))
ax_eV.set_ylim((eV_min, eV_max))
ax_wl.set_ylim((eV_to_nm(eV_min), eV_to_nm(eV_max)))
for ext in ['pdf', 'svg']:
plot.savefig('regimes.' + ext)
plot.show()
linestyle = colors_and_symbols.symbol(ei+5),
color = colors_and_symbols.color(ei),
label = Xe_Z0_es_n[ei])
# 3 electrons
al = 0.09 # arrow length
e1_xy = [0.25*r[0], 0.8*Umax]
e2_xy = [0.20*r[-1], 0.25*Umax]
e3_xy = [0.75*r[0], 0.1*Umax]
ar_e1 = fleches.arrow('e1', e1_xy, [e1_xy[0], e1_xy[1] +al*dU])
ar_e2 = fleches.arrow('e2', e2_xy, [e2_xy[0], e2_xy[1]-2.0*al*dU])
ar_e3 = fleches.arrow('e3', e3_xy, [e3_xy[0], e3_xy[1] +al*dU])
ar_e1.Plot(ax1, color = 'b')
ar_e2.Plot(ax1, color = 'b')
ar_e3.Plot(ax1, color = 'b')
ax1.plot([e1_xy[0]], [e1_xy[1]], 'ob', ms = 14)
ax1.plot([e2_xy[0]], [e2_xy[1]], 'ob', ms = 14)
ax1.plot([e3_xy[0]], [e3_xy[1]], 'ob', ms = 14)
ax1.set_xlabel('r [bohr]')
ax1.set_ylabel('Energy [Hartree]')
#leg = ax1.legend(loc = "lower right")
ax1.axhline(0.0, linestyle = ':', color = 'k')
ax1.set_ylim((0.98*Umin,1.02*Umax))
for ext in ['pdf', 'svg']:
plot.savefig('heating_mbr.' + ext)
plot.show()
for d, daugther in enumerate(daugthers):
alpha = 1.0 - (self.level) / (max_level+2.0)
R = daugther.level / (max_level+2)
#print 'd', d, ' level =', self.level, ' alpha = ', alpha, ' red =', R
if (particles.is_inside(daugther)):
ax.plot([daugther.mins[0], daugther.maxs[0]], daugther.pos[1]*np.ones(2), '-', color = (R, 0, 0), linewidth = linewidth, alpha = alpha)
ax.plot(daugther.pos[0]*np.ones(2), [daugther.mins[1], daugther.maxs[1]], '-', color = (R, 0, 0), linewidth = linewidth, alpha = alpha)
if (self.level < max_level and particles.is_inside(daugther)):
daugther.draw_daugthers(ax, particles)
x = r * np.cos(theta)
y = r * np.sin(theta)
particles = Part(x, y)
cell = Cell(0.0, 0.0, (2.05*abs(x).max(), 2.05*abs(y).max()))
fig = plot.figure()
ax = fig.add_subplot(1,1,1, xticks=[], yticks=[])
#ax = fig.add_subplot(1,1,1)
ax.plot(x[0:N/2], y[0:N/2], 'ob', ms = 14)
ax.plot(x[N/2:], y[N/2:], 'om', ms = 7)
cell.draw_quadtree(ax, particles)
ax.set_ylim(cell.mins[0], cell.maxs[0])
ax.set_ylim(cell.mins[1], cell.maxs[1])
plot.savefig('quadtree.svg')
plot.savefig('quadtree.pdf')
plot.show()
ax2.plot(r, U2)
ax2.plot([-r0, r0], [Uep, Uep], '-m', label = '5p')
# Electron
ax2.plot([0.0], [Uep], 'og', ms = 14, alpha = 0.6)
ax2.plot([0.0], [Uep+gamma], 'og', ms = 14 )
# Photon
gamma = 0.5*Xe_Z0_Ip
ar_e1 = fleches.arrow('e1', [0.0, Uep], [0.0, Uep+gamma])
ar_e1.Plot(ax2, color = 'b', alpha = 0.5)
photon(ax2, [r[0]+lr*0.1, Uep], [0.0, Uep], Xe_Z0_Ip/5.0)
for ax in [ax1, ax2]:
ax.set_xlabel('r [bohr]')
ax.set_ylabel('Energy [Hartree]')
#leg = ax.legend(loc = "lower right")
ax.axhline(0.0, linestyle = ':', color = 'k')
ax1.set_ylim((0.98*Umin,1.02*Umax))
# Remove overlapping labels
ax1.get_xticklabels()[-1].set_visible(False)
ax2.get_xticklabels()[0].set_visible(False)
for ext in ['pdf', 'svg']:
plot.savefig('heating_barrier_sup.' + ext)
plot.show()
import plot as fplt
strain = 'N2'
feat = 'roam'
nbins = 2**13
save_fig = True
data = exp.load_data(strain)
### Bin data
sbins = exp.stage_bins(data, nbins=nbins)
d = getattr(data, feat)
tn = exp.bin_data(d, sbins)
exp.save(tn, '%s_%s_time_normalized.npy' % (strain, feat))
#fig = plt.figure(1); plt.clf();
#plt.imshow(tn, aspect = 'auto');
#plt.tight_layout();
#plt.title('%s %s time normalized' % (strain, feat));
#if save_fig:
# fig.savefig(exp.figname('%s_%s_time_normalized.png'% (strain, feat)));
fig = fplt.plot_array(tn, title='%s %s time normalized' % (strain, feat))
fplt.savefig(fig,
exp.figname('%s_%s_time_normalized.png' % (strain, feat)),
width=2500)
# Photon energy
ar1 = fleches.arrow('GammaE', [0.0, -Xe_Z0_Ip], [0.0, GammaE-Xe_Z0_Ip])
ar1.Plot(ax1, color = 'r', label = r'$E_\gamma$', horizontalalignment = 'left')
ax1.plot([0.0], [-Xe_Z0_Ip], 'ob', ms = 14, alpha = 0.6)
# New electron velocity
ar2 = fleches.arrow('N_e', [0.0, GammaE-Xe_Z0_Ip], [5.0, GammaE-Xe_Z0_Ip])
ar2.Plot(ax1, color = 'b', label = '$v_e$', horizontalalignment = 'center', verticalalignment = 'bottom')
ax1.plot([0.0], [GammaE-Xe_Z0_Ip], 'ob', ms = 14)
# Delta E
x = -1.0
ar3 = fleches.arrow('D_e', [x, 0.0], [x, GammaE-Xe_Z0_Ip])
ar3.Plot(ax1, color = 'g', label = '$\Delta E.$', horizontalalignment = 'right', bidirectional = True)
# Photon
#photon(ax1, [r[0]+lr*0.1, -Xe_Z0_Ip/2.0], [0.0, -Xe_Z0_Ip/2.0], Xe_Z0_Ip/5.0)
photon(ax1, [r[0]+lr*0.1, -Xe_Z0_Ip], [0.0, -Xe_Z0_Ip], Xe_Z0_Ip/5.0)
ax1.set_xlim((r[0], r[-1]))
ax1.set_ylim((Umin, Umax))
ax1.set_xlabel('r [bohr]')
ax1.set_ylabel('Energy [Hartree]')
for ext in ['pdf', 'svg']:
plot.savefig('ionization_single.' + ext)
plot.show()
def draw_histos(vis=False, filepath='/output/evalSave/'):
print(filepath)
if not os.path.exists(filepath):
print('path created')
os.makedirs(filepath)
with open(os.path.join(filepath, 'eval.json'), 'r') as j:
data = json.load(j)
# build precision-recall curves
prec_03, rec_03 = eval_plot.sort_prec_rec(data['evaluation']['prec']['0.3'], data['evaluation']['rec']['0.3'])
eval_plot.plot_prec_rec(rec_03, prec_03, 'Thrs: 0.3', color=(1, 0, 1))
prec_05, rec_05 = eval_plot.sort_prec_rec(data['evaluation']['prec']['0.5'], data['evaluation']['rec']['0.5'])
eval_plot.plot_prec_rec(rec_05, prec_05, 'Thrs: 0.5', color=(0, 1, 0))
# build smoothed precision-recall curves
# smooth PR-curve as described in http://cs229.stanford.edu/section/evaluation_metrics.pdf#
smoothed_prec_03 = [max(prec_03[idx:]) for idx, _ in enumerate(prec_03)]
smoothed_prec_05 = [max(prec_05[idx:]) for idx, _ in enumerate(prec_05)]
eval_plot.plot_prec_rec(rec_03, smoothed_prec_03, 'Thrs_smoothed: 0.3', color=(1, 0, 1), linestyle="--")
eval_plot.plot_prec_rec(rec_05, smoothed_prec_05, 'Thrs_smoothed: 0.5', color=(0, 1, 0), linestyle="--")
#auc_03 = np.trapz(smoothed_prec_03, rec_03)
#auc_05 = np.trapz(smoothed_prec_05, rec_05)
auc_03 = np.trapz(prec_03, rec_03)
auc_05 = np.trapz(prec_05, rec_05)
title = "conf. stride: {:0.2f}, max. conf.: {:0.4f}, AUC_03: {:0.2f}, AUC_05: {:0.2f}".\
format(data['confidence stride'], data['max_conf'], auc_03, auc_05)
eval_plot.config(data['name'], title=title)
eval_plot.savefig(os.path.join(filepath, (data['name'] + '.svg')))
if vis:
eval_plot.show()
else:
eval_plot.clearfig()
# build mean iou - recall curves
postfix = ['', '_low', '_mid', '_high']
for p in postfix:
eval_plot.plot_prec_rec(data['evaluation']['rec' + p]['0.3'], data['evaluation']['m_iou' + p]['0.3'], 'halt au', color=(1, 0, 1))
eval_plot.plot_prec_rec(data['evaluation']['rec' + p]['0.5'], data['evaluation']['m_iou' + p]['0.5'], 'halt au', color=(0, 1, 0))
title = "conf. stride: {:0.2f}, max. conf.: {:0.4f},\nAUC_03: {:0.2f}, AUC_05: {:0.2f}".\
format(data['confidence stride'], data['max_conf'], auc_03, auc_05)
eval_plot.config(data['name'], title=title)
eval_plot.savefig(os.path.join(filepath, 'm_iou' + p + '.svg'))
if vis:
eval_plot.show()
else:
eval_plot.clearfig()
classes = ["Background", "Ferry", "Buoy", "Vessel/ship", "Speed boat", "Boat", "Kayak", "Sail boat", "Swimming person", "Flying bird/plane", "Other"]
num_classes = data['evaluation']['conf_mat']["0.3"][0][1]
cm = np.array(data['evaluation']['conf_mat']["0.3"][0][0]).reshape((num_classes, num_classes))
name = os.path.join(filepath, "confusion_matrix_03_05.svg")
eval_plot.plot_confusion_matrix(cm, classes, name)
cm = np.array(data['evaluation']['conf_mat']["0.3"][1][0]).reshape((num_classes, num_classes))
name = os.path.join(filepath, "confusion_matrix_03_075.svg")
eval_plot.plot_confusion_matrix(cm, classes, name)
cm = np.array(data['evaluation']['conf_mat']["0.5"][0][0]).reshape((num_classes, num_classes))
name = os.path.join(filepath, "confusion_matrix_05_05.svg")
eval_plot.plot_confusion_matrix(cm, classes, name)
cm = np.array(data['evaluation']['conf_mat']["0.5"][1][0]).reshape((num_classes, num_classes))
name = os.path.join(filepath, "confusion_matrix_05_075.svg")
eval_plot.plot_confusion_matrix(cm, classes, name)
# Threshold
ax1.axhline(0.0, color="k", ls="-", alpha=0.5)
# U(r)
ax1.plot(r, U, "--k", alpha=0.5, label="Unperturbed ion")
# Laser
ax1.plot(r, laser, "-r", label="Laser")
# U(r) + laser
ax1.plot(r, Ubent, "-k", label="Effective")
# Electron
ax1.plot([0.0], [-Xe_Z0_Ip], "ob", ms=14)
ar1 = fleches.arrow("Tunnel", [0.0, -Xe_Z0_Ip], [0.9 * r[-1], -Xe_Z0_Ip])
ar1.Plot(ax1, color="g")
ax1.set_xlim((r[0], r[-1]))
ax1.set_ylim((0.95 * Umin, Umax))
ax1.set_xlabel("r [bohr]")
ax1.set_ylabel("Energy [Hartree]")
leg = ax1.legend(loc="best")
leg.get_frame().set_alpha(0.75)
for ext in ["pdf", "svg"]:
plot.savefig("ionization_tunnel." + ext)
plot.show()
ax2.add_patch(mpatches.Circle(auger_1_xy, r_e, color='blue', ec="none", alpha = 1.0))
# Arrow for inner shell filling
arrow_end = (auger_1_xy[0], auger_1_xy[1])
arrow_start = (auger_2_xy[0], auger_2_xy[1])
ax2.annotate('', xycoords='data',
xy = arrow_end, xytext = arrow_start, textcoords='data',
size = 20, arrowprops=dict(arrowstyle="simple",
fc="g", ec="none",
connectionstyle="arc3,rad=-0.3"))
# Outer shell electron leaving
auger_3_xy_new = np.array([None]*2)
angle = np.arctan2(auger_3_xy[1], auger_3_xy[0])
auger_3_xy_new[0] = 1.4 * el_r.max() * np.cos(angle)
auger_3_xy_new[1] = 1.4 * el_r.max() * np.sin(angle)
ax2.add_patch(mpatches.Circle(auger_3_xy_new, r_e, color='blue', ec="none", alpha=1.0))
# Arrow showing it
ar = arrow('AuE', auger_3_xy, auger_3_xy_new) # Vertical (Ke)
ar.Plot(ax2, color = 'g')
# *******************************************************************************************
for ax in [ax1, ax2]:
ax.set_xlim((-1.1*el_r.max(), 1.1*el_r.max()))
ax.set_ylim((-1.1*el_r.max(), 1.1*el_r.max()))
for ext in ['pdf', 'svg']:
plot.savefig(['auger_step_1.' + ext, 'auger_step_2.' + ext])
plot.show()
