def visualize_signals_testing(gen, sig_type_source):
'''
visualize the estimated and target signals on a minibatch of testing data
:param gen: test generator
:param sig_type_source: list of str of source signals: e.g. ['aX', 'aY', 'aZ'] for all three axes of the acceleroemter
:return: -
'''
torch.cuda.empty_cache()
finished, X_batch, Y_batch, subject_id_list = next(gen)
if finished:
print('Generator Finished')
else:
X_batch = torch.from_numpy(X_batch)
X_batch = network_models.cuda(X_batch)
X_batch = X_batch.type(torch.cuda.FloatTensor)
Y_batch_predicted = sig_model.forward(
X_batch).squeeze().detach().cpu().numpy()
X_batch = X_batch.detach().cpu().numpy()
no_sigs = X_batch.shape[1]
for v in range(0, Y_batch.shape[0], 4):
fig = plt.figure(figsize=(12, 8))
plt.subplot(no_sigs + 1, 1, 1)
plt.plot((Y_batch[v, 0, :] - np.mean(Y_batch[v, 0, :])) / (np.sqrt(
np.sum(
np.power(Y_batch[v, 0, :] - np.mean(Y_batch[v, 0, :]),
2)))), '-r')
plt.plot(
(Y_batch_predicted[v, :] - np.mean(Y_batch_predicted[v, :])) /
(np.sqrt(
np.sum(
np.power(
Y_batch_predicted[v, :] -
np.mean(Y_batch_predicted[v, :]), 2)))), '-b')
plt.title('Subject: ' + str(subject_id_list[v]) +
' Index in batch: ' + str(v))
for k in range(2, no_sigs + 2):
plt.subplot(no_sigs + 1, 1, k)
plt.plot(X_batch[v, k - 2, :], '-g')
plt.plot(
(Y_batch_predicted[v, :] - np.min(Y_batch_predicted[v, :]))
/ (np.max(Y_batch_predicted[v, :]) -
np.min(Y_batch_predicted[v, :])), '-b')
#plt.plot(Y_batch_predicted[v,:] , '-b')
plt.title(sig_type_source[k - 2])
plt.tight_layout()
plt.show()
if save_true:
fig.savefig(directory + '/Code Output/' + file_name_pre +
'_waveforms_testing_hf_' + str(v) + '.png')
del X_batch
del Y_batch_predicted
del Y_batch
def visualize_signals(gen, sig_type_source):
'''
plots target signal segments, source signal segments and the estimated target signal segments together
:param gen: data generator
:param sig_type_source: list of source signals e.g. ['aX', 'aY', 'aZ'] for all three axes of the accelerometer as source signals
:return: -
'''
torch.cuda.empty_cache()
X_batch, Y_batch, list_subjects = next(gen)
X_batch = torch.from_numpy(X_batch)
X_batch = network_models.cuda(X_batch)
X_batch = X_batch.type(torch.cuda.FloatTensor)
Y_batch_predicted = sig_model.forward(
X_batch).squeeze().detach().cpu().numpy()
X_batch = X_batch.detach().cpu().numpy()
# Y_batch_predicted=-Y_batch_predicted
no_sigs = X_batch.shape[1]
for v in range(Y_batch.shape[0]):
fig = plt.figure(figsize=(12, 8))
plt.subplot(no_sigs + 1, 1, 1)
#plt.plot(Y_batch[v,0,:] , '-r')
plt.plot((Y_batch[v, 0, :] - np.mean(Y_batch[v, 0, :])) / (np.sqrt(
np.sum(np.power(Y_batch[v, 0, :] - np.mean(Y_batch[v, 0, :]),
2)))), '-r')
#plt.plot((Y_batch_predicted[v,:]-np.min(Y_batch_predicted[v,:]) )/(np.max(Y_batch_predicted[v,:])-np.min(Y_batch_predicted[v,:])) , '-b')
plt.plot((Y_batch_predicted[v, :] - np.mean(Y_batch_predicted[v, :])) /
(np.sqrt(
np.sum(
np.power(
Y_batch_predicted[v, :] -
np.mean(Y_batch_predicted[v, :]), 2)))), '-b')
#plt.plot(Y_batch_predicted[v, :] , '-b')
plt.title('Subject Number: ' + str(list_subjects[v]))
for k in range(2, no_sigs + 2):
plt.subplot(no_sigs + 1, 1, k)
plt.plot(X_batch[v, k - 2, :], '-g')
plt.plot(
(Y_batch_predicted[v, :] - np.min(Y_batch_predicted[v, :])) /
(np.max(Y_batch_predicted[v, :]) -
np.min(Y_batch_predicted[v, :])), '-b')
#plt.plot(Y_batch_predicted[v,:] , '-b')
plt.title(sig_type_source[k - 2])
plt.tight_layout()
plt.show()
if save_true:
fig.savefig(directory + '/Code Output/' + file_name_pre +
'_waveforms_' + str(v) + '.png')
del X_batch
del Y_batch_predicted
del Y_batch
def visualize_signals(gen , sig_type_source ):
torch.cuda.empty_cache()
X_batch, tt, freq_vector = next(gen)
X_batch = torch.from_numpy(X_batch)
X_batch = network_models.cuda(X_batch)
X_batch = X_batch.type(torch.cuda.FloatTensor)
Y_batch_predicted= sig_model.forward(X_batch).squeeze().detach().cpu().numpy()
X_batch = X_batch.detach().cpu().numpy()
offset = len(tt)//2
no_sigs = X_batch.shape[1]
for v in range(X_batch.shape[0]):
plt.figure()
for k in range(1,no_sigs+1):
inp = X_batch[v,k-2,:]
out = (Y_batch_predicted[v, :] - np.min(Y_batch_predicted[v, :])) / (
np.max(Y_batch_predicted[v, :]) - np.min(Y_batch_predicted[v, :]))
time_ax=tt
time_ax = time_ax if freq_vector[v]<3 else time_ax[ offset:offset+ int(len(tt)//freq_vector[v]) ]
inp = inp if freq_vector[v]<3 else inp[ offset:offset+ int(len(tt)//freq_vector[v]) ]
out = out if freq_vector[v] < 3 else out[offset:offset + int(len(tt) // freq_vector[v])]
plt.subplot( no_sigs , 1 , k )
plt.plot(time_ax,inp , '-g')
plt.plot(time_ax,out, '-b')
#plt.plot(Y_batch_predicted[v,:] , '-b')
plt.title(sig_type_source[k-2] + ' , ' + str(freq_vector[v]))
plt.tight_layout()
plt.show()
del X_batch
del Y_batch_predicted
def test_model(gen, sig_model):
'''
function tests a model by running it over the test data and calculating error metrics
:param gen: test generator
:param sig_model: model
:return: list_pearson_r_loss: list of pearson correlations between target and estimated segments
:return: list_subject_ids: subject ID for each segment
:return: list_i_errors: list of R-I interval errors between each target and estimated signal segment
:return: list_j_errors: list of R-J interval errors between each target and estimated signal segment
:return: list_k_errors: list of R-K interval errors between each target and estimated signal segment
'''
criterion = network_models.PearsonRLoss()
with torch.no_grad():
finished = False
list_pearson_r_loss = []
list_i_errors = []
list_j_errors = []
list_k_errors = []
list_subject_ids = []
list_noise_var_target = []
list_noise_var_estimate = []
list_target_i_points = []
list_target_j_points = []
list_target_k_points = []
list_sdr = []
while not finished:
print('Running Testing')
torch.cuda.empty_cache()
finished, X_batch, Y_batch, subject_id_list= next(gen)
if finished:
print('Generator Finished')
else:
#get ecg
ecg = X_batch[:, -1, :]
#calculate pearson correlation
X_batch = torch.from_numpy(X_batch[:, :-1, :]).contiguous()
X_batch = network_models.cuda(X_batch)
X_batch = X_batch.type(torch.cuda.FloatTensor)
Y_batch_predicted= sig_model.forward(X_batch).squeeze()
Y_batch = torch.from_numpy(Y_batch)
Y_batch = network_models.cuda(Y_batch)
Y_batch = Y_batch.type(torch.cuda.FloatTensor)
Y_batch = Y_batch.squeeze()
if len(Y_batch.size())==1:
Y_batch=Y_batch.view(1,-1)
if len(Y_batch_predicted.size())==1:
Y_batch_predicted=Y_batch_predicted.view(1,-1)
loss = criterion.get_induvidual_losses(Y_batch_predicted, Y_batch)
list_pearson_r_loss+=loss.cpu().numpy().reshape(-1).tolist()
list_subject_ids+=subject_id_list
#ijk points
Y_batch_predicted = Y_batch_predicted.detach().cpu().numpy()
Y_batch = Y_batch.detach().cpu().numpy()
for v in range(Y_batch.shape[0]):
r_peaks = signal_processing_modules.get_R_peaks(ecg[v, :])
ensemble_avg_target, ensemble_beats_target = signal_processing_modules.get_ensemble_avg(r_peaks,
(Y_batch[v, :] - np.mean(Y_batch[v, :]) )/( np.sqrt(np.sum(np.power( Y_batch[v, :] - np.mean(Y_batch[v, :]) ,2)))) ,
n_samples=500,upsample_factor=1)
i_point_target, j_point_target, k_point_target = signal_processing_modules.get_IJK_peaks(ensemble_avg_target, upsample_factor=1)
ensemble_avg_estimate, ensemble_beats_estimate = signal_processing_modules.get_ensemble_avg(r_peaks,
( Y_batch_predicted[v,:]-np.mean(Y_batch_predicted[v,:]) )/(np.sqrt(np.sum(np.power( Y_batch_predicted[v,:]-np.mean(Y_batch_predicted[v,:]) , 2 )))) ,
n_samples=500, upsample_factor=1)
i_point_estimate, j_point_estimate, k_point_estimate = signal_processing_modules.get_IJK_peaks(ensemble_avg_estimate, upsample_factor=1)
i_error = 1000 * np.abs(i_point_target - i_point_estimate) / (500) if i_point_target != -1 and i_point_estimate != -1 else -1 # 500 is the sampling rate of the signal segments, 1000* for miliseconds
j_error = 1000 * np.abs(j_point_target - j_point_estimate) / (500) if j_point_target != -1 and j_point_estimate != -1 else -1
k_error = 1000 * np.abs(k_point_target - k_point_estimate) / (500) if k_point_target != -1 and k_point_estimate != -1 else -1
list_i_errors.append(i_error)
list_j_errors.append(j_error)
list_k_errors.append(k_error)
list_noise_var_target.append( signal_processing_modules.get_noise_variance(ensemble_avg_target, ensemble_beats_target) )
list_noise_var_estimate.append( signal_processing_modules.get_noise_variance(ensemble_avg_estimate, ensemble_beats_estimate ) )
list_target_i_points.append(i_point_target)
list_target_j_points.append(j_point_target)
list_target_k_points.append(k_point_target)
list_sdr.append(signal_processing_modules.get_sdr(( Y_batch_predicted[v,:]-np.mean(Y_batch_predicted[v,:]) )/(np.sqrt(np.sum(np.power( Y_batch_predicted[v,:]-np.mean(Y_batch_predicted[v,:]) , 2 ))))
, (Y_batch[v, :] - np.mean(Y_batch[v, :]) )/( np.sqrt(np.sum(np.power( Y_batch[v, :] - np.mean(Y_batch[v, :]) ,2)))) ))
del X_batch
del Y_batch_predicted
del Y_batch
return list_pearson_r_loss, list_subject_ids, list_i_errors, list_j_errors, list_k_errors, list_noise_var_target, list_noise_var_estimate, list_target_i_points, list_target_j_points, list_target_k_points, list_sdr
def visualize_signals_video(gen, sig_type_source, directory,
model_path_for_video, model_type, no_layers,
input_size, kernel_size, filter_number,
video_name):
list_all_files = os.listdir(directory + '/Models for Video/')
list_models = [
file for file in list_all_files
if file.startswith(model_path_for_video[-25::])
]
no_epochs = len(list_models)
torch.cuda.empty_cache()
X_batch, Y_batch, list_subjects = next(gen)
X_batch = torch.from_numpy(X_batch)
X_batch = network_models.cuda(X_batch)
X_batch = X_batch.type(torch.cuda.FloatTensor)
v = np.random.randint(0, Y_batch.shape[0])
X_batch_detached = X_batch.detach().cpu().numpy()
no_sigs = X_batch_detached.shape[1]
fig = plt.figure(figsize=(12, 8))
def animate(i):
#for epoch in range(1,no_epochs+1):
epoch = i + 1
if epoch < 10:
epoch_str = '000' + str(epoch)
elif epoch >= 10 and epoch < 100:
epoch_str = '00' + str(epoch)
elif epoch >= 100 and epoch < 1000:
epoch_str = '0' + str(epoch)
else:
epoch_str = str(epoch)
model_path = model_path_for_video + '_' + epoch_str + '.pt'
print('Loading...' + model_path)
sig_model = network_models.load_saved_model(
model_path,
model_type,
input_size,
kernel_size,
filter_number=filter_number,
signal_number=len(sig_type_source),
no_layers=no_layers)
Y_batch_predicted = sig_model.forward(
X_batch).squeeze().detach().cpu().numpy()
#for v in range(Y_batch.shape[0]):
plt.clf()
plt.subplot(no_sigs + 1, 1, 1)
#plt.plot(Y_batch[v,0,:] , '-r')
plt.plot((Y_batch[v, 0, :] - np.mean(Y_batch[v, 0, :])) / (np.sqrt(
np.sum(np.power(Y_batch[v, 0, :] - np.mean(Y_batch[v, 0, :]),
2)))), '-r')
#plt.plot((Y_batch_predicted[v,:]-np.min(Y_batch_predicted[v,:]) )/(np.max(Y_batch_predicted[v,:])-np.min(Y_batch_predicted[v,:])) , '-b')
plt.plot((Y_batch_predicted[v, :] - np.mean(Y_batch_predicted[v, :])) /
(np.sqrt(
np.sum(
np.power(
Y_batch_predicted[v, :] -
np.mean(Y_batch_predicted[v, :]), 2)))), '-b')
#plt.plot(Y_batch_predicted[v, :] , '-b')
# plt.title('Subject Number: ' + str(list_subjects[v]) +' , Epoch: ' + str(epoch)
# + ', Train Loss=' + str(train_history[epoch-1]['train_loss']) + ', Val Loss=' + str(valid_history[epoch-1]['valid_loss']) )
plt.title(
'Subject Number: {}, Epoch: {}, Train Loss: {:.4f}, Val Loss: {:.4f}'
.format(list_subjects[v], epoch,
train_history[epoch - 1]['train_loss'],
valid_history[epoch - 1]['valid_loss']))
for k in range(2, no_sigs + 2):
plt.subplot(no_sigs + 1, 1, k)
plt.plot(X_batch_detached[v, k - 2, :], '-g')
plt.plot(
(Y_batch_predicted[v, :] - np.min(Y_batch_predicted[v, :])) /
(np.max(Y_batch_predicted[v, :]) -
np.min(Y_batch_predicted[v, :])), '-b')
#plt.plot(Y_batch_predicted[v,:] , '-b')
plt.title(sig_type_source[k - 2])
# plt.tight_layout()
# plt.show()
# if save_true:
# fig.savefig(directory + '/' + file_name_pre + '_waveforms_' + str(v)+ '.png')
del Y_batch_predicted
ani = animation.FuncAnimation(fig, animate, frames=no_epochs, repeat=False)
Writer = animation.writers['ffmpeg']
writer = Writer(fps=fps, metadata=dict(artist='Me'), bitrate=1800)
ani.save(directory + '/Code Output/' + video_name + '.mp4',
writer=writer,
dpi=dpi)
del Y_batch
del X_batch
def visualize_ijk(gen, upsample_factor, no_cycles):
'''
plots target signal segments and estimated target signal segments, ensemble averaged with the i,j,k points
:param gen: data generator
:param sig_type_source: list of source signals e.g. ['aX', 'aY', 'aZ'] for all three axes of the accelerometer as source signals
:return: -
'''
torch.cuda.empty_cache()
X_batch, Y_batch, list_subjects = next(gen)
ecg = X_batch[:, -1, :]
X_batch = torch.from_numpy(X_batch[:, :-1, :]).contiguous()
X_batch = network_models.cuda(X_batch)
X_batch = X_batch.type(torch.cuda.FloatTensor)
Y_batch_predicted = sig_model.forward(
X_batch).squeeze().detach().cpu().numpy()
X_batch = X_batch.detach().cpu().numpy()
list_i_errors = []
list_j_errors = []
list_k_errors = []
for _ in range(no_cycles):
for v in range(Y_batch.shape[0]):
r_peaks = signal_processing_modules.get_R_peaks(ecg[v, :])
ensemble_avg_target, ensemble_beats_target = signal_processing_modules.get_ensemble_avg(
r_peaks,
Y_batch[v, 0, :],
n_samples=500,
upsample_factor=upsample_factor)
i_point_target, j_point_target, k_point_target = signal_processing_modules.get_IJK_peaks(
ensemble_avg_target, upsample_factor=upsample_factor)
ensemble_avg_estimate, ensemble_beats_estimate = signal_processing_modules.get_ensemble_avg(
r_peaks,
Y_batch_predicted[v, :],
n_samples=500,
upsample_factor=upsample_factor)
i_point_estimate, j_point_estimate, k_point_estimate = signal_processing_modules.get_IJK_peaks(
ensemble_avg_estimate, upsample_factor=upsample_factor)
i_error = 1000 * np.abs(i_point_target - i_point_estimate) / (
upsample_factor * 500
) if i_point_target != -1 and i_point_estimate != -1 else -1 #500 is the sampling rate of the signal segments, 1000* for miliseconds
j_error = 1000 * np.abs(j_point_target - j_point_estimate) / (
upsample_factor *
500) if j_point_target != -1 and j_point_estimate != -1 else -1
k_error = 1000 * np.abs(k_point_target - k_point_estimate) / (
upsample_factor *
500) if k_point_target != -1 and k_point_estimate != -1 else -1
fig = plt.figure(figsize=(12, 8))
plt.subplot(2, 1, 1)
plt.plot(ensemble_beats_target.T, 'r', alpha=0.3)
plt.plot(ensemble_avg_target, '-r', linewidth=4)
plt.plot(i_point_target, ensemble_avg_target[i_point_target], 'ok')
plt.text(i_point_target,
ensemble_avg_target[i_point_target] + 0.05,
'I',
color='red')
plt.plot(j_point_target, ensemble_avg_target[j_point_target], 'ok')
plt.text(j_point_target,
ensemble_avg_target[j_point_target] + 0.05,
'J',
color='red')
plt.plot(k_point_target, ensemble_avg_target[k_point_target], 'ok')
plt.text(k_point_target,
ensemble_avg_target[k_point_target] + 0.05,
'K',
color='red')
plt.title('Subject Number: ' + str(list_subjects[v]))
plt.subplot(2, 1, 2)
plt.plot(ensemble_beats_estimate.T, 'b', alpha=0.3)
plt.plot(ensemble_avg_estimate, '-b', linewidth=4)
plt.plot(i_point_estimate, ensemble_avg_estimate[i_point_estimate],
'ok')
plt.text(i_point_estimate,
ensemble_avg_estimate[i_point_estimate] + 0.05,
'I',
color='blue')
plt.plot(j_point_estimate, ensemble_avg_estimate[j_point_estimate],
'ok')
plt.text(j_point_estimate,
ensemble_avg_estimate[j_point_estimate] + 0.05,
'J',
color='blue')
plt.plot(k_point_estimate, ensemble_avg_estimate[k_point_estimate],
'ok')
plt.text(k_point_estimate,
ensemble_avg_estimate[k_point_estimate] + 0.05,
'K',
color='blue')
plt.title('I-error=' + str(i_error) + ' | J-error=' +
str(j_error) + ' | K-error=' + str(k_error) + ' in (ms)')
plt.tight_layout()
plt.show()
if save_true:
fig.savefig(directory + '/Code Output/' + file_name_pre +
'_waveforms_ensemble_averaged' + str(v) + '.png')
if i_error != -1:
list_i_errors.append(i_error)
if j_error != -1:
list_j_errors.append(j_error)
if k_error != -1:
list_k_errors.append(k_error)
print('MAE I-Point (ms): ' + str(np.mean(np.array(list_i_errors))))
print('MAE J-Point (ms): ' + str(np.mean(np.array(list_j_errors))))
print('MAE K-Point (ms): ' + str(np.mean(np.array(list_k_errors))))
del X_batch
del Y_batch_predicted
del Y_batch