def test_plot_instantaneous_measure(tsig_comb):
times = create_times(N_SECONDS, FS)
plot_instantaneous_measure(
times,
amp_by_time(tsig_comb, FS, F_RANGE),
'amplitude',
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_instantaneous_measure_amplitude.png')
plot_instantaneous_measure(
times,
phase_by_time(tsig_comb, FS, F_RANGE),
'phase',
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_instantaneous_measure_phase.png')
plot_instantaneous_measure(
times,
freq_by_time(tsig_comb, FS, F_RANGE),
'frequency',
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_instantaneous_measure_frequency.png')
# Check the error for bad measure
with raises(ValueError):
plot_instantaneous_measure(times, tsig_comb, 'BAD')
def test_plot_bursts(tsig_burst):
times = create_times(N_SECONDS, FS)
bursts = detect_bursts_dual_threshold(tsig_burst, FS, (0.75, 1.5), F_RANGE)
plot_bursts(times,
tsig_burst,
bursts,
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_bursts.png')
def test_plot_timefrequency(tsig_comb):
times = create_times(N_SECONDS, FS)
freqs = np.array([5, 10, 15, 20, 25])
mwt = compute_wavelet_transform(tsig_comb, FS, freqs)
plot_timefrequency(times,
freqs,
mwt,
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_timefrequency1.png')
plot_timefrequency(times,
freqs,
mwt,
x_ticks=[2.5, 7.5],
y_ticks=[5, 15],
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_timefrequency2.png')
def test_plot_time_series(tsig_comb, tsig_burst):
times = create_times(N_SECONDS, FS)
# Check single time series plot
plot_time_series(times,
tsig_comb,
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_time_series-1.png')
# Check multi time series plot, labels
plot_time_series(times, [tsig_comb, tsig_comb[::-1]],
labels=['signal', 'signal reversed'],
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_time_series-2.png')
# Test 2D arrays
plot_time_series(times,
np.array([tsig_comb, tsig_burst]),
save_fig=True,
file_path=TEST_PLOTS_PATH,
file_name='test_plot_time_series-2arr.png')
# Often, we want to simulate noise that is comparable to what we see in neural recordings. # # Neural signals display 1/f-like activity, whereby power decreases linearly across # increasing frequencies, when plotted in log-log. # # Let's start with a powerlaw signal, specifically a brown noise process, or a signal # for which the power spectrum is distributed as 1/f^2. # ################################################################################################### # Setting for the simulation exponent = -2 # Simulate powerlaw activity, specifically brown noise times = create_times(n_seconds, fs) br_noise = sim.sim_powerlaw(n_seconds, fs, exponent) ################################################################################################### # Plot the simulated data, in the time domain plot_time_series(times, br_noise) ################################################################################################### # Plot the simulated data, in the frequency domain freqs, psd = spectral.compute_spectrum(br_noise, fs) plot_power_spectra(freqs, psd) ################################################################################################### #
###################################################################################################
# Simulation settings
fs = 1000
n_seconds = 5
# Define simulation components
components = {'sim_synaptic_current' : {'n_neurons':1000, 'firing_rate':2,
't_ker':1.0, 'tau_r':0.002, 'tau_d':0.02},
'sim_bursty_oscillation' : {'freq' : 10,
'prob_enter_burst' : .2, 'prob_leave_burst' : .2}}
# Simulate a signal with a bursty oscillation with an aperiodic component & a time vector
sig = sim_combined(n_seconds, fs, components)
times = create_times(n_seconds, fs)
###################################################################################################
# Plot the simulated data
plot_time_series(times, sig, 'Simulated EEG')
###################################################################################################
#
# In the simulated signal above, we can see some bursty 10 Hz oscillations.
#
###################################################################################################
# Dual Amplitude Threshold Algorithm
# ----------------------------------
#
###################################################################################################
# Load example neural signal
# --------------------------
#
# First, we will load an example neural signal to use for our time-frequency measures.
#
###################################################################################################
# Load a neural signal, as well as a filtered version of the same signal
sig = load_ndsp_data('sample_data_1.npy', folder='data')
sig_filt_true = load_ndsp_data('sample_data_1_filt.npy', folder='data')
# Set sampling rate, and create a times vector for plotting
fs = 1000
times = create_times(len(sig) / fs, fs)
# Set the frequency range to be used
f_range = (13, 30)
###################################################################################################
#
# Throughout this example, we will use
# :func:`~neurodsp.plts.time_series.plot_time_series` to plot time series, and
# :func:`~neurodsp.plts.time_series.plot_instantaneous_measure`
# to plot instantaneous measures.
#
###################################################################################################
# Plot signal
# Simulate an Example Signal
# --------------------------
#
# First, we'll simulate an example signal that starts with a burst of alpha activity, followed
# by a period of only aperiodic activity.
#
###################################################################################################
# Set time and sampling rate
n_seconds_burst = 1
n_seconds_noise = 2
fs = 1000
# Create a times vector
times = create_times(n_seconds_burst + n_seconds_noise, fs)
# Simulate a signal component with an oscillation
components = {'sim_powerlaw': {'exponent': 0}, 'sim_oscillation': {'freq': 10}}
s1 = sim_combined(n_seconds_burst, fs, components, [0.1, 1])
# Simulate a signal component with just noise
s2 = sim_powerlaw(n_seconds_noise, fs, 0, variance=0.1)
# Join signals together to approximate a 'burst'
sig = np.append(s1, s2)
###################################################################################################
# Plot example signal
plot_time_series(times, sig)
# Set the random seed, for consistency simulating data np.random.seed(0) ################################################################################################### # # 1. Bandpass filter # ------------------ # # Extract signal within a specific frequency range (e.g. theta, 4-8 Hz). # ################################################################################################### # Generate an oscillation with noise fs = 1000 times = create_times(4, 1000) sig = np.random.randn(len(times)) + 5 * np.sin(times * 2 * np.pi * 6) ################################################################################################### # Filter the data, across a frequency band of interest f_range = (4, 8) sig_filt = filt.filter_signal(sig, fs, 'bandpass', f_range) ################################################################################################### # Plot filtered signal plot_time_series(times, [sig, sig_filt], ['Raw', 'Filtered']) ################################################################################################### #
#
###################################################################################################
# Parameters for simulated signal
n_samples = 5000
fs = 1000
burst_freq = 10
burst_starts = [0, 3000]
burst_seconds = 1
burst_samples = burst_seconds*fs
###################################################################################################
# Design burst kernel
burst_kernel_t = create_times(burst_seconds, fs)
burst_kernel = 2*np.sin(burst_kernel_t*2*np.pi*burst_freq)
# Generate random signal with bursts
times = create_times(n_samples/fs, fs)
sig = np.random.randn(n_samples)
for ind in burst_starts:
sig[ind:ind+burst_samples] += burst_kernel
###################################################################################################
# Plot example signal
plot_time_series(times, sig)
###################################################################################################
#
# Set the sampling rate
fs = 1000
# Set time for each segment of the simulated signal, in seconds
t_osc = 1 # oscillation
t_ap = 2 # aperiodic
# Set the frequency of the oscillation
freq = 10
# Set the exponent value for the aperiodic activity
exp = -1
# Create a times vector
times = create_times(t_osc + t_ap, fs)
###################################################################################################
# Create the simulated data
# ~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Next, we will create our simulated data, by concatenating simulated segments of data
# with and without a rhythm.
#
###################################################################################################
# Simulate a signal component with an oscillation
components = {
'sim_oscillation': {
'freq': freq
'high_gamma' : [50, 150]}) ################################################################################################### # Simulating Data # ~~~~~~~~~~~~~~~ # # We will use simulated data for this example, to create some example aperiodic signals, # that we can then apply filters to. First, let's simulate some data. # ################################################################################################### # Simulation settings s_rate = 1000 n_seconds = 4 times = create_times(n_seconds, s_rate) # Set random seed, for consistency generating simulated data set_random_seed(21) ################################################################################################### # Simulate a signal of aperiodic activity: pink noise sig = sim_powerlaw(n_seconds, s_rate, exponent=-1) ################################################################################################### # Plot our simulated time series plot_time_series(times, sig) ###################################################################################################
import matplotlib.pyplot as plt
from neurodsp.sim import sim_oscillation, sim_bursty_oscillation
from neurodsp.utils import set_random_seed
from neurodsp.utils import create_times
from neurodsp.plts.time_series import plot_time_series
time = 1.5
sampling_rate = 100
oscillation_freq = 1
set_random_seed(0)
oscillation_sine = sim_oscillation(time,
sampling_rate,
oscillation_freq,
cycle='sine')
timeSequenceMatrix = create_times(time, sampling_rate)
print("TIME : " + str(len(timeSequenceMatrix)))
print(timeSequenceMatrix)
print("OSCILACION : " + str(len(oscillation_sine)))
print(oscillation_sine)
plt.scatter(timeSequenceMatrix, oscillation_sine)
plt.show()
plot_time_series(timeSequenceMatrix, oscillation_sine)
def predict_and_plot_sstaging(data_path, data_file):
print("I am here", os.getcwd())
model = keras.models.load_model('flaskapp/model')
data_path = Path(data_path)
record = data_file
annotation_dict = defaultdict(lambda: 5, {
'1': 0,
'2': 1,
'3': 2,
'4': 2,
'R': 3
})
classes = defaultdict(lambda: '6', {
'1000': '1',
'0100': '2',
'0010': '3',
'0001': '4',
'0000': '5'
})
class_count = defaultdict(lambda: 0, {
'1000': 0,
'0100': 0,
'0010': 0,
'0001': 0,
'0000': 0
})
annsamp = wfdb.rdann(str(data_path / record),
extension='st', summarize_labels=True)
signal = wfdb.rdrecord(str(data_path / record), channels=[2])
physical_signal = signal.p_signal
physical_signal = preprocessing.scale(physical_signal)
number_annotations = len(annsamp.aux_note)
starting_index = int((len(physical_signal) / 7500) -
number_annotations)*7500
physical_signal = physical_signal[starting_index:]
inputs = np.split(physical_signal, number_annotations)
annots = list()
target = [[0]*4 for _ in range(number_annotations)]
for annotation_index in range(number_annotations):
labels = annsamp.aux_note[annotation_index].split(' ')
labels = [_l.strip('\x00') if type(_l) == str else str(_l)
for _l in labels]
for label in labels:
if annotation_dict[label] != 5:
target[annotation_index][annotation_dict[label]] = 1
event_class = ''.join([str(v) for v in target[annotation_index]])
event_class = classes[event_class]
annots.append(event_class)
annots_c = to_categorical(annots)
inputs = np.array(inputs)
y_pred = model.predict(inputs)
y_pred_c = y_pred.argmax(axis=1)
y_pred_c = y_pred_c.tolist()
S1 = 0
S2 = 0
S3 = 0
R = 0
W = 0
for i in y_pred_c:
if i == 1:
S1 += 1
elif i == 2:
S2 += 1
elif i == 3:
S3 += 1
elif i == 4:
R += 1
else:
W += 1
annots = np.array(annots).astype(np.int)
annotation_dict1 = defaultdict(
lambda: 5, {
'S1': 1,
'S2': 2,
'S3': 3,
'R': 4,
'W': 5
}
)
matplotlib.rcParams['agg.path.chunksize'] = 10000
fig, ax = plt.subplots(figsize=(50, 20))
plt.rcParams["axes.linewidth"] = 3
plt.xticks(fontsize=50)
plt.yticks(fontsize=50)
plt.title('Hypno Çizimi', fontsize=50)
plt.tick_params(axis='both', pad=30)
plt.yticks(range(1, len(annotation_dict1.keys())+1),
annotation_dict1.keys())
plt.plot(y_pred_c, color='blue', linewidth=5)
figfile = BytesIO()
plt.savefig(figfile, format='png')
figfile.seek(0)
print(figfile)
global figure
figure = base64.b64encode(figfile.getvalue()).decode('ascii')
plt.savefig("./flaskapp/static/images"+"/" +
record+"_hypno.png", format='png')
plt.clf()
plt.cla()
gc.collect()
fs = 250
times = create_times(len(physical_signal)/fs, fs)
plt.rcParams['axes.linewidth'] = 5
plt.rcParams["figure.figsize"] = (40, 50)
plt.title('Epoch Çizimi', fontsize=50)
plt.tick_params(axis='both', pad=45)
plt.xticks(fontsize=50)
plt.yticks(fontsize=50)
# plt.xlabel('time (s)', fontsize=100, labelpad=50)
# plt.ylabel('Voltage (mV)', fontsize=100, labelpad=50)
plt.gca().yaxis.set_major_locator(MaxNLocator(prune='lower'))
plt.plot(times, physical_signal, linewidth=6)
figfile1 = BytesIO()
plt.savefig(figfile1, format='png')
figfile1.seek(0)
global figure2
figure2 = base64.b64encode(figfile1.getvalue()).decode('ascii')
plt.savefig("./flaskapp/static/images"+"/" +
record + "_epochs.png", format='png')
plt.clf()
plt.cla()
gc.collect()
total = len(annots)
eq = 0
for i in range(len(annots)):
if annots[i] == y_pred_c[i]:
eq += 1
f = open("./flaskapp/"+data_file + ".txt", "w")
f.write("Toplam uyku süresi:" + str(total/2) + " dakika\n")
f.write("S1:" + str(S1) + " dakika\n")
f.write("S2:" + str(S2) + " dakika\n")
f.write("S3:" + str(S3) + " dakika\n")
f.write("R:" + str(R) + " dakika\n")
f.write("W:" + str(W) + " dakika\n")
f.close()
global read_file
read = open("./flaskapp/"+data_file + ".txt")
global info
info = read.read()
read_file = read.readlines()
ss_labels = ["S1", "S2", "S3", "R", "W"]
ss_values = [S1, S2, S3, R, W]
ss_explode = (0, 0, 0.1, 0, 0)
fig1, ax1 = plt.subplots(figsize=(40, 30))
ax1.pie(ss_values, explode=ss_explode, labels=ss_labels, autopct='%1.1f%%',
shadow=False, startangle=90, textprops={'fontsize': 60})
ax1.axis('equal')
figfile2 = BytesIO()
plt.savefig(figfile2, format='png')
figfile2.seek(0)
global figure3
figure3 = base64.b64encode(figfile2.getvalue()).decode('ascii')
plt.savefig("./flaskapp/static/images"+"/" +
record + "_pie.png", format='png')
plt.clf()
plt.cla()
gc.collect()