def test_generate_signal():
# Inputs for generate_signal
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [3]
feature_type = ['cube']
feature_coordinates = np.array([[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
assert np.all(volume.shape == dimensions), "Check signal shape"
assert np.max(volume) == signal_magnitude, "Check signal magnitude"
assert np.sum(volume > 0) == math.pow(feature_size[0],
3), ("Check feature size")
assert volume[5, 5, 5] == signal_magnitude, "Check signal location"
assert volume[5, 5, 1] == 0, "Check noise location"
feature_coordinates = np.array([[5, 5, 5], [3, 3, 3], [7, 7, 7]])
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[3],
signal_magnitude=signal_magnitude)
assert volume[5, 5, 5] == 0, "Loop is empty"
assert volume[3, 3, 3] == 0, "Cavity is empty"
assert volume[7, 7, 7] != 0, "Sphere is not empty"
def test_mask_brain():
# Inputs for generate_signal
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[4, 4, 4]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Mask the volume to be the same shape as a brain
mask, _ = sim.mask_brain(dimensions, mask_self=None,)
brain = volume * mask
assert np.sum(brain != 0) == np.sum(volume != 0), "Masking did not work"
assert brain[0, 0, 0] == 0, "Masking did not work"
assert brain[4, 4, 4] != 0, "Masking did not work"
feature_coordinates = np.array(
[[1, 1, 1]])
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Mask the volume to be the same shape as a brain
mask, _ = sim.mask_brain(dimensions, mask_self=None, )
brain = volume * mask
assert np.sum(brain != 0) < np.sum(volume != 0), "Masking did not work"
# Test that you can load the default
dimensions = np.array([100, 100, 100])
mask, template = sim.mask_brain(dimensions, mask_self=False)
assert mask[20, 80, 50] == 0, 'Masking didn''t work'
assert mask[25, 80, 50] == 1, 'Masking didn''t work'
assert int(template[25, 80, 50] * 100) == 57, 'Template not correct'
# Check that you can mask self
mask_self, template_self = sim.mask_brain(template, mask_self=True)
assert (template_self - template).sum() < 1e2, 'Mask self error'
assert (mask_self - mask).sum() == 0, 'Mask self error'
def test_mask_brain():
# Inputs for generate_signal
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array([[4, 4, 4]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Mask the volume to be the same shape as a brain
mask = sim.mask_brain(volume)[:, :, :, 0]
brain = volume * (mask > 0)
assert np.sum(brain != 0) == np.sum(volume != 0), "Masking did not work"
assert brain[0, 0, 0] == 0, "Masking did not work"
assert brain[4, 4, 4] != 0, "Masking did not work"
feature_coordinates = np.array([[1, 1, 1]])
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Mask the volume to be the same shape as a brain
mask = sim.mask_brain(volume)[:, :, :, 0]
brain = volume * (mask > 0)
assert np.sum(brain != 0) < np.sum(volume != 0), "Masking did not work"
def test_mask_brain():
# Inputs for generate_signal
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[4, 4, 4]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Mask the volume to be the same shape as a brain
mask, _ = sim.mask_brain(volume)
brain = volume * mask
assert np.sum(brain != 0) == np.sum(volume != 0), "Masking did not work"
assert brain[0, 0, 0] == 0, "Masking did not work"
assert brain[4, 4, 4] != 0, "Masking did not work"
feature_coordinates = np.array(
[[1, 1, 1]])
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Mask the volume to be the same shape as a brain
mask, _ = sim.mask_brain(volume)
brain = volume * mask
assert np.sum(brain != 0) < np.sum(volume != 0), "Masking did not work"
def test_apply_signal():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array([[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(
onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.double_gamma_hrf(
stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(
signal_function=signal_function,
volume_static=volume,
)
assert signal.shape == (dimensions[0], dimensions[1], dimensions[2],
duration / tr_duration), "The output is the " \
"wrong size"
signal = sim.apply_signal(
signal_function=stimfunction,
volume_static=volume,
)
assert np.any(signal == signal_magnitude), "The stimfunction is not binary"
def test_generate_signal():
# Inputs for generate_signal
dimensions = np.array([64, 64, 36]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array([[32, 32, 18]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume_static = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
assert np.all(volume_static.shape == dimensions), "Check signal shape"
assert np.max(volume_static) == signal_magnitude, "Check signal magnitude"
assert np.sum(volume_static>0) == math.pow(feature_size[0], 3), "Check " \
"feature size"
assert volume_static[32, 32,
18] == signal_magnitude, "Check signal location"
assert volume_static[32, 32, 10] == 0, "Check noise location"
feature_coordinates = np.array([[32, 32, 18], [32, 28, 18], [28, 32, 18]])
volume_static = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[9],
signal_magnitude=signal_magnitude,
)
assert volume_static[32, 32, 18] == 0, "Loop is empty"
assert volume_static[32, 28, 18] == 0, "Cavity is empty"
assert volume_static[28, 32, 18] != 0, "Sphere is not empty"
def test_generate_signal():
# Inputs for generate_signal
dimensions = np.array([64, 64, 36]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[32, 32, 18]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume_static = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
assert np.all(volume_static.shape == dimensions), "Check signal shape"
assert np.max(volume_static) == signal_magnitude, "Check signal magnitude"
assert np.sum(volume_static>0) == math.pow(feature_size[0], 3), "Check " \
"feature size"
assert volume_static[32,32,18] == signal_magnitude, "Check signal location"
assert volume_static[32,32,10] == 0, "Check noise location"
feature_coordinates = np.array(
[[32, 32, 18], [32, 28, 18], [28, 32, 18]])
volume_static = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[9],
signal_magnitude=signal_magnitude,
)
assert volume_static[32, 32, 18] == 0, "Loop is empty"
assert volume_static[32, 28, 18] == 0, "Cavity is empty"
assert volume_static[28, 32, 18] != 0, "Sphere is not empty"
def test_generate_signal():
# Inputs for generate_signal
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [3]
feature_type = ['cube']
feature_coordinates = np.array(
[[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
assert np.all(volume.shape == dimensions), "Check signal shape"
assert np.max(volume) == signal_magnitude, "Check signal magnitude"
assert np.sum(volume>0) == math.pow(feature_size[0], 3), "Check feature " \
"size"
assert volume[5, 5, 5] == signal_magnitude, "Check signal location"
assert volume[5, 5, 1] == 0, "Check noise location"
feature_coordinates = np.array(
[[5, 5, 5], [3, 3, 3], [7, 7, 7]])
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[3],
signal_magnitude=signal_magnitude,
)
assert volume[5, 5, 5] == 0, "Loop is empty"
assert volume[3, 3, 3] == 0, "Cavity is empty"
assert volume[7, 7, 7] != 0, "Sphere is not empty"
def test_apply_signal():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.convolve_hrf(stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(signal_function=signal_function,
volume_signal=volume,
)
assert signal.shape == (dimensions[0], dimensions[1], dimensions[2],
duration / tr_duration), "The output is the " \
"wrong size"
signal = sim.apply_signal(signal_function=stimfunction,
volume_signal=volume,
)
assert np.any(signal == signal_magnitude), "The stimfunction is not binary"
# Inputs for generate_stimfunction
onsets_A = [10, 30, 50, 70, 90]
onsets_B = [0, 20, 40, 60, 80]
event_durations = [6]
tr_duration = 2
temporal_res = 1000.0 # How many elements per second are there
duration = 100
# Specify a name to save this generated volume.
savename = 'examples/utils/example.nii'
# Generate a volume representing the location and quality of the signal
volume_signal_A = sim.generate_signal(dimensions=dimensions,
feature_coordinates=coordinates_A,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
volume_signal_B = sim.generate_signal(dimensions=dimensions,
feature_coordinates=coordinates_B,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Visualize the signal that was generated for condition A
fig = plt.figure()
sim.plot_brain(fig,
volume_signal_A)
plt.show()
# Inputs for generate_stimfunction
onsets_A = [10, 30, 50, 70, 90]
onsets_B = [0, 20, 40, 60, 80]
event_durations = [6]
tr_duration = 2
temporal_res = 1000.0 # How many elements per second are there
duration = 100
# Specify a name to save this generated volume.
savename = 'examples/utils/example.nii'
# Generate a volume representing the location and quality of the signal
volume_static_A = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=coordinates_A,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
volume_static_B = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=coordinates_B,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Visualize the signal that was generated for condition A
fig = plt.figure()
sim.plot_brain(fig, volume_static_A)
def test_generate_noise():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[5, 5, 5]])
signal_magnitude = [1]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 200
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.convolve_hrf(stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(signal_function=signal_function,
volume_signal=volume,
)
# Generate the mask of the signal
mask, template = sim.mask_brain(signal, mask_threshold=0.1)
assert min(mask[mask > 0]) > 0.1, "Mask thresholding did not work"
assert len(np.unique(template) > 2), "Template creation did not work"
stimfunction_tr = stimfunction[::int(tr_duration * 100)]
# Create the noise volumes (using the default parameters)
noise = sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
)
assert signal.shape == noise.shape, "The dimensions of signal and noise " \
"the same"
assert np.std(signal) < np.std(noise), "Noise was not created"
noise = sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={'sfnr': 10000, 'snr': 10000},
)
system_noise = np.std(noise[mask > 0], 1).mean()
assert system_noise <= 0.1, "Noise strength could not be manipulated"
# Store these start and end times
onsets[cond_counter] += list(range(start_idx, end_idx, tr_duration))
epoch[cond_counter, idx * conds + cond_counter, start_idx:end_idx] = 1
# The pattern of activity for each trial
weight = ([1] * int(np.floor(stim_dur / 2))) + ([-1]*int(np.ceil(
stim_dur / 2)))
weights[cond_counter] += weight
# Iterate through the conditions to make the necessary functions
for cond in list(range(conds)):
# Generate a volume representing the location and quality of the signal
volume_static = sim.generate_signal(dimensions=dimensions,
feature_coordinates=coordinates[cond],
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Create the time course for the signal to be generated
stimfunction_cond = sim.generate_stimfunction(onsets=onsets[cond],
event_durations=
event_durations,
total_time=duration,
weights=weights[cond],
)
# Convolve the HRF with the stimulus sequence
signal_function = sim.double_gamma_hrf(stimfunction=stimfunction_cond,
tr_duration=tr_duration,
)
def test_generate_noise():
dimensions = np.array([64, 64, 36]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[32, 32, 18]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume_static = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(onsets=onsets,
event_durations=event_durations,
total_time=duration,
tr_duration=tr_duration,
)
signal_function = sim.double_gamma_hrf(stimfunction=stimfunction,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(signal_function=signal_function,
volume_static=volume_static,
)
# Create the noise volumes (using the default parameters)
noise = sim.generate_noise(dimensions=dimensions,
stimfunction=stimfunction,
tr_duration=tr_duration,
)
assert signal.shape == noise.shape, "The dimensions of signal " \
"and noise the same"
Z_noise = sim._generate_noise_temporal(stimfunction, tr_duration, 1)
noise = sim._generate_noise_temporal(stimfunction, tr_duration, 0)
assert np.std(Z_noise) < np.std(noise), "Z scoring is not working"
# Combine the signal and the noise
volume = signal + noise
assert np.std(signal) < np.std(noise), "Noise was not created"
noise = sim.generate_noise(dimensions=dimensions,
stimfunction=stimfunction,
tr_duration=tr_duration,
noise_strength=[0, 0, 0]
)
assert np.sum(noise) == 0, "Noise strength could not be manipulated"
assert np.std(noise) == 0, "Noise strength could not be manipulated"
def test_apply_signal():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.convolve_hrf(stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Check that you can compute signal change appropriately
# Preset a bunch of things
stimfunction_tr = stimfunction[::int(tr_duration * 100)]
mask, template = sim.mask_brain(dimensions, mask_self=False)
noise_dict = sim._noise_dict_update({})
noise = sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict=noise_dict,
iterations=[0, 0]
)
coords = feature_coordinates[0]
noise_function_a = noise[coords[0], coords[1], coords[2], :]
noise_function_a = noise_function_a.reshape(duration // tr_duration, 1)
noise_function_b = noise[coords[0] + 1, coords[1], coords[2], :]
noise_function_b = noise_function_b.reshape(duration // tr_duration, 1)
# Create the calibrated signal with PSC
method = 'PSC'
sig_a = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
sig_b = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[1.0],
method,
)
assert sig_b.max() / sig_a.max() == 2, 'PSC modulation failed'
# Create the calibrated signal with SFNR
method = 'SFNR'
sig_a = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = sig_a / (noise_function_a.mean() / noise_dict['sfnr'])
sig_b = sim.compute_signal_change(signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = sig_b / (noise_function_b.mean() / noise_dict['sfnr'])
assert scaled_b.max() / scaled_a.max() == 2, 'SFNR modulation failed'
# Create the calibrated signal with CNR_Amp/Noise-SD
method = 'CNR_Amp/Noise-SD'
sig_a = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = sig_a / noise_function_a.std()
sig_b = sim.compute_signal_change(signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = sig_b / noise_function_b.std()
assert scaled_b.max() / scaled_a.max() == 2, 'CNR_Amp modulation failed'
# Create the calibrated signal with CNR_Amp/Noise-Var_dB
method = 'CNR_Amp2/Noise-Var_dB'
sig_a = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = np.log(sig_a.max() / noise_function_a.std())
sig_b = sim.compute_signal_change(signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = np.log(sig_b.max() / noise_function_b.std())
assert np.round(scaled_b / scaled_a) == 2, 'CNR_Amp dB modulation failed'
# Create the calibrated signal with CNR_Signal-SD/Noise-SD
method = 'CNR_Signal-SD/Noise-SD'
sig_a = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = sig_a.std() / noise_function_a.std()
sig_b = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[1.0],
method,
)
scaled_b = sig_b.std() / noise_function_a.std()
assert (scaled_b / scaled_a) == 2, 'CNR signal modulation failed'
# Create the calibrated signal with CNR_Amp/Noise-Var_dB
method = 'CNR_Signal-Var/Noise-Var_dB'
sig_a = sim.compute_signal_change(signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = np.log(sig_a.std() / noise_function_a.std())
sig_b = sim.compute_signal_change(signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = np.log(sig_b.std() / noise_function_b.std())
assert np.round(scaled_b / scaled_a) == 2, 'CNR signal dB modulation ' \
'failed'
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(signal_function=signal_function,
volume_signal=volume,
)
assert signal.shape == (dimensions[0], dimensions[1], dimensions[2],
duration / tr_duration), "The output is the " \
"wrong size"
signal = sim.apply_signal(signal_function=stimfunction,
volume_signal=volume,
)
assert np.any(signal == signal_magnitude), "The stimfunction is not binary"
# Check that there is an error if the number of signal voxels doesn't
# match the number of non zero brain voxels
with pytest.raises(IndexError):
sig_vox = (volume > 0).sum()
vox_pattern = np.tile(stimfunction, (1, sig_vox - 1))
sim.apply_signal(signal_function=vox_pattern,
volume_signal=volume,
)
def test_generate_signal():
# Inputs for generate_signal
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [3]
feature_type = ['cube']
feature_coordinates = np.array([[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
assert np.all(volume.shape == dimensions), "Check signal shape"
assert np.max(volume) == signal_magnitude, "Check signal magnitude"
assert np.sum(volume > 0) == math.pow(feature_size[0], 3), (
"Check feature size")
assert volume[5, 5, 5] == signal_magnitude, "Check signal location"
assert volume[5, 5, 1] == 0, "Check noise location"
feature_coordinates = np.array(
[[5, 5, 5], [3, 3, 3], [7, 7, 7]])
# Check feature size is correct
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[3],
signal_magnitude=signal_magnitude)
assert volume[5, 5, 5] == 0, "Loop is empty"
assert volume[3, 3, 3] == 0, "Cavity is empty"
assert volume[7, 7, 7] != 0, "Sphere is not empty"
# Check feature size manipulation
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[1],
signal_magnitude=signal_magnitude)
assert volume[5, 6, 6] == 0, "Loop is too big"
assert volume[3, 5, 5] == 0, "Cavity is too big"
assert volume[7, 9, 9] == 0, "Sphere is too big"
# Check that out of bounds feature coordinates are corrected
feature_coordinates = np.array([0, 2, dimensions[2]])
x, y, z = sim._insert_idxs(feature_coordinates, feature_size[0],
dimensions)
assert x[1] - x[0] == 2, "x min not corrected"
assert y[1] - y[0] == 3, "y was corrected when it shouldn't be"
assert z[1] - z[0] == 1, "z max not corrected"
# Check that signal patterns are created
feature_coordinates = np.array([[5, 5, 5]])
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
signal_constant=0,
)
assert volume[4:7, 4:7, 4:7].std() > 0, "Signal is constant"
def test_generate_noise():
dimensions = np.array([64, 64, 36]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array([[32, 32, 18]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume_static = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(
onsets=onsets,
event_durations=event_durations,
total_time=duration,
tr_duration=tr_duration,
)
signal_function = sim.double_gamma_hrf(stimfunction=stimfunction, )
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(
signal_function=signal_function,
volume_static=volume_static,
)
# Create the noise volumes (using the default parameters)
noise = sim.generate_noise(
dimensions=dimensions,
stimfunction=stimfunction,
tr_duration=tr_duration,
)
assert signal.shape == noise.shape, "The dimensions of signal " \
"and noise the same"
Z_noise = sim._generate_noise_temporal(stimfunction, tr_duration, 1)
noise = sim._generate_noise_temporal(stimfunction, tr_duration, 0)
assert np.std(Z_noise) < np.std(noise), "Z scoring is not working"
# Combine the signal and the noise
volume = signal + noise
assert np.std(signal) < np.std(noise), "Noise was not created"
noise = sim.generate_noise(dimensions=dimensions,
stimfunction=stimfunction,
tr_duration=tr_duration,
noise_strength=[0, 0, 0])
assert np.sum(noise) == 0, "Noise strength could not be manipulated"
assert np.std(noise) == 0, "Noise strength could not be manipulated"
def test_generate_noise():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array([[5, 5, 5]])
signal_magnitude = [1]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 200
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(
onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.convolve_hrf(
stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(
signal_function=signal_function,
volume_signal=volume,
)
# Generate the mask of the signal
mask, template = sim.mask_brain(signal, mask_self=None)
assert min(mask[mask > 0]) > 0.1, "Mask thresholding did not work"
assert len(np.unique(template) > 2), "Template creation did not work"
stimfunction_tr = stimfunction[::int(tr_duration * 100)]
# Create the noise volumes (using the default parameters)
noise = sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
iterations=[1, 0],
)
assert signal.shape == noise.shape, "The dimensions of signal and noise " \
"the same"
noise_high = sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={
'sfnr': 50,
'snr': 25
},
iterations=[1, 0],
)
noise_low = sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={
'sfnr': 100,
'snr': 25
},
iterations=[1, 0],
)
system_high = np.std(noise_high[mask > 0], 1).mean()
system_low = np.std(noise_low[mask > 0], 1).mean()
assert system_low < system_high, "SFNR noise could not be manipulated"
# Check that you check for the appropriate template values
with pytest.raises(ValueError):
sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template * 2,
mask=mask,
noise_dict={},
)
# Check that iterations does what it should
sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={},
iterations=[0, 0],
)
sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={},
iterations=None,
)
# Test drift noise
trs = 1000
period = 100
drift = sim._generate_noise_temporal_drift(
trs,
tr_duration,
'sine',
period,
)
# Check that the max frequency is the appropriate frequency
power = abs(np.fft.fft(drift))[1:trs // 2]
freq = np.linspace(1, trs // 2 - 1, trs // 2 - 1) / trs
period_freq = np.where(freq == 1 / (period // tr_duration))
max_freq = np.argmax(power)
assert period_freq == max_freq, 'Max frequency is not where it should be'
# Do the same but now with cosine basis functions, answer should be close
drift = sim._generate_noise_temporal_drift(
trs,
tr_duration,
'discrete_cos',
period,
)
# Check that the appropriate frequency is peaky (may not be the max)
power = abs(np.fft.fft(drift))[1:trs // 2]
freq = np.linspace(1, trs // 2 - 1, trs // 2 - 1) / trs
period_freq = np.where(freq == 1 / (period // tr_duration))[0][0]
assert power[period_freq] > power[period_freq + 1], 'Power is low'
assert power[period_freq] > power[period_freq - 1], 'Power is low'
# Check it runs fine
drift = sim._generate_noise_temporal_drift(
50,
tr_duration,
'discrete_cos',
period,
)
# Check it runs fine
drift = sim._generate_noise_temporal_drift(
300,
tr_duration,
'cos_power_drop',
period,
)
# Check that when the TR is greater than the period it errors
with pytest.raises(ValueError):
sim._generate_noise_temporal_drift(30, 10, 'cos_power_drop', 5)
# Test physiological noise (using unrealistic parameters so that it's easy)
timepoints = list(np.linspace(0, (trs - 1) * tr_duration, trs))
resp_freq = 0.2
heart_freq = 1.17
phys = sim._generate_noise_temporal_phys(
timepoints,
resp_freq,
heart_freq,
)
# Check that the max frequency is the appropriate frequency
power = abs(np.fft.fft(phys))[1:trs // 2]
freq = np.linspace(1, trs // 2 - 1, trs // 2 - 1) / (trs * tr_duration)
peaks = (power > (power.mean() + power.std())) # Where are the peaks
peak_freqs = freq[peaks]
assert np.any(resp_freq == peak_freqs), 'Resp frequency not found'
assert len(peak_freqs) == 2, 'Two peaks not found'
# Test task noise
sim._generate_noise_temporal_task(
stimfunction_tr,
motion_noise='gaussian',
)
sim._generate_noise_temporal_task(
stimfunction_tr,
motion_noise='rician',
)
# Test ARMA noise
with pytest.raises(ValueError):
noise_dict = {'fwhm': 4, 'auto_reg_rho': [1], 'ma_rho': [1, 1]}
sim._generate_noise_temporal_autoregression(
stimfunction_tr,
noise_dict,
dimensions,
mask,
)
# Generate spatial noise
vol = sim._generate_noise_spatial(np.array([10, 10, 10, trs]))
assert len(vol.shape) == 3, 'Volume was not reshaped to ignore TRs'
# Switch some of the noise types on
noise_dict = dict(physiological_sigma=1,
drift_sigma=1,
task_sigma=1,
auto_reg_sigma=0)
sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict=noise_dict,
iterations=[0, 0],
)
def test_generate_signal():
# Inputs for generate_signal
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [3]
feature_type = ['cube']
feature_coordinates = np.array([[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
assert np.all(volume.shape == dimensions), "Check signal shape"
assert np.max(volume) == signal_magnitude, "Check signal magnitude"
assert np.sum(volume > 0) == math.pow(feature_size[0],
3), ("Check feature size")
assert volume[5, 5, 5] == signal_magnitude, "Check signal location"
assert volume[5, 5, 1] == 0, "Check noise location"
feature_coordinates = np.array([[5, 5, 5], [3, 3, 3], [7, 7, 7]])
# Check feature size is correct
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[3],
signal_magnitude=signal_magnitude)
assert volume[5, 5, 5] == 0, "Loop is empty"
assert volume[3, 3, 3] == 0, "Cavity is empty"
assert volume[7, 7, 7] != 0, "Sphere is not empty"
# Check feature size manipulation
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=['loop', 'cavity', 'sphere'],
feature_size=[1],
signal_magnitude=signal_magnitude)
assert volume[5, 6, 6] == 0, "Loop is too big"
assert volume[3, 5, 5] == 0, "Cavity is too big"
assert volume[7, 9, 9] == 0, "Sphere is too big"
# Check that out of bounds feature coordinates are corrected
feature_coordinates = np.array([0, 2, dimensions[2]])
x, y, z = sim._insert_idxs(feature_coordinates, feature_size[0],
dimensions)
assert x[1] - x[0] == 2, "x min not corrected"
assert y[1] - y[0] == 3, "y was corrected when it shouldn't be"
assert z[1] - z[0] == 1, "z max not corrected"
# Check that signal patterns are created
feature_coordinates = np.array([[5, 5, 5]])
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
signal_constant=0,
)
assert volume[4:7, 4:7, 4:7].std() > 0, "Signal is constant"
def test_apply_signal():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array([[5, 5, 5]])
signal_magnitude = [30]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(
onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.convolve_hrf(
stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Check that you can compute signal change appropriately
# Preset a bunch of things
stimfunction_tr = stimfunction[::int(tr_duration * 100)]
mask, template = sim.mask_brain(dimensions, mask_self=False)
noise_dict = sim._noise_dict_update({})
noise = sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict=noise_dict,
iterations=[0, 0])
coords = feature_coordinates[0]
noise_function_a = noise[coords[0], coords[1], coords[2], :]
noise_function_a = noise_function_a.reshape(duration // tr_duration, 1)
noise_function_b = noise[coords[0] + 1, coords[1], coords[2], :]
noise_function_b = noise_function_b.reshape(duration // tr_duration, 1)
# Create the calibrated signal with PSC
method = 'PSC'
sig_a = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
sig_b = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[1.0],
method,
)
assert sig_b.max() / sig_a.max() == 2, 'PSC modulation failed'
# Create the calibrated signal with SFNR
method = 'SFNR'
sig_a = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = sig_a / (noise_function_a.mean() / noise_dict['sfnr'])
sig_b = sim.compute_signal_change(
signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = sig_b / (noise_function_b.mean() / noise_dict['sfnr'])
assert scaled_b.max() / scaled_a.max() == 2, 'SFNR modulation failed'
# Create the calibrated signal with CNR_Amp/Noise-SD
method = 'CNR_Amp/Noise-SD'
sig_a = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = sig_a / noise_function_a.std()
sig_b = sim.compute_signal_change(
signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = sig_b / noise_function_b.std()
assert scaled_b.max() / scaled_a.max() == 2, 'CNR_Amp modulation failed'
# Create the calibrated signal with CNR_Amp/Noise-Var_dB
method = 'CNR_Amp2/Noise-Var_dB'
sig_a = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = np.log(sig_a.max() / noise_function_a.std())
sig_b = sim.compute_signal_change(
signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = np.log(sig_b.max() / noise_function_b.std())
assert np.round(scaled_b / scaled_a) == 2, 'CNR_Amp dB modulation failed'
# Create the calibrated signal with CNR_Signal-SD/Noise-SD
method = 'CNR_Signal-SD/Noise-SD'
sig_a = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = sig_a.std() / noise_function_a.std()
sig_b = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[1.0],
method,
)
scaled_b = sig_b.std() / noise_function_a.std()
assert (scaled_b / scaled_a) == 2, 'CNR signal modulation failed'
# Create the calibrated signal with CNR_Amp/Noise-Var_dB
method = 'CNR_Signal-Var/Noise-Var_dB'
sig_a = sim.compute_signal_change(
signal_function,
noise_function_a,
noise_dict,
[0.5],
method,
)
scaled_a = np.log(sig_a.std() / noise_function_a.std())
sig_b = sim.compute_signal_change(
signal_function,
noise_function_b,
noise_dict,
[1.0],
method,
)
scaled_b = np.log(sig_b.std() / noise_function_b.std())
assert np.round(scaled_b / scaled_a) == 2, 'CNR signal dB modulation ' \
'failed'
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(
signal_function=signal_function,
volume_signal=volume,
)
assert signal.shape == (dimensions[0], dimensions[1], dimensions[2],
duration / tr_duration), "The output is the " \
"wrong size"
signal = sim.apply_signal(
signal_function=stimfunction,
volume_signal=volume,
)
assert np.any(signal == signal_magnitude), "The stimfunction is not binary"
# Check that there is an error if the number of signal voxels doesn't
# match the number of non zero brain voxels
with pytest.raises(IndexError):
sig_vox = (volume > 0).sum()
vox_pattern = np.tile(stimfunction, (1, sig_vox - 1))
sim.apply_signal(
signal_function=vox_pattern,
volume_signal=volume,
)
def test_generate_noise():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[5, 5, 5]])
signal_magnitude = [1]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 200
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.convolve_hrf(stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(signal_function=signal_function,
volume_signal=volume,
)
# Generate the mask of the signal
mask, template = sim.mask_brain(signal,
mask_self=None)
assert min(mask[mask > 0]) > 0.1, "Mask thresholding did not work"
assert len(np.unique(template) > 2), "Template creation did not work"
stimfunction_tr = stimfunction[::int(tr_duration * 100)]
# Create the noise volumes (using the default parameters)
noise = sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
iterations=[1, 0],
)
assert signal.shape == noise.shape, "The dimensions of signal and noise " \
"the same"
noise_high = sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={'sfnr': 50, 'snr': 25},
iterations=[1, 0],
)
noise_low = sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={'sfnr': 100, 'snr': 25},
iterations=[1, 0],
)
system_high = np.std(noise_high[mask > 0], 1).mean()
system_low = np.std(noise_low[mask > 0], 1).mean()
assert system_low < system_high, "SFNR noise could not be manipulated"
# Check that you check for the appropriate template values
with pytest.raises(ValueError):
sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template * 2,
mask=mask,
noise_dict={},
)
# Check that iterations does what it should
sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={},
iterations=[0, 0],
)
sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict={},
iterations=None,
)
# Test drift noise
trs = 1000
period = 100
drift = sim._generate_noise_temporal_drift(trs,
tr_duration,
'sine',
period,
)
# Check that the max frequency is the appropriate frequency
power = abs(np.fft.fft(drift))[1:trs // 2]
freq = np.linspace(1, trs // 2 - 1, trs // 2 - 1) / trs
period_freq = np.where(freq == 1 / (period // tr_duration))
max_freq = np.argmax(power)
assert period_freq == max_freq, 'Max frequency is not where it should be'
# Do the same but now with cosine basis functions, answer should be close
drift = sim._generate_noise_temporal_drift(trs,
tr_duration,
'discrete_cos',
period,
)
# Check that the appropriate frequency is peaky (may not be the max)
power = abs(np.fft.fft(drift))[1:trs // 2]
freq = np.linspace(1, trs // 2 - 1, trs // 2 - 1) / trs
period_freq = np.where(freq == 1 / (period // tr_duration))[0][0]
assert power[period_freq] > power[period_freq + 1], 'Power is low'
assert power[period_freq] > power[period_freq - 1], 'Power is low'
# Check it gives a warning if the duration is too short
drift = sim._generate_noise_temporal_drift(50,
tr_duration,
'discrete_cos',
period,
)
# Test physiological noise (using unrealistic parameters so that it's easy)
timepoints = list(np.linspace(0, (trs - 1) * tr_duration, trs))
resp_freq = 0.2
heart_freq = 1.17
phys = sim._generate_noise_temporal_phys(timepoints,
resp_freq,
heart_freq,
)
# Check that the max frequency is the appropriate frequency
power = abs(np.fft.fft(phys))[1:trs // 2]
freq = np.linspace(1, trs // 2 - 1, trs // 2 - 1) / (trs * tr_duration)
peaks = (power > (power.mean() + power.std())) # Where are the peaks
peak_freqs = freq[peaks]
assert np.any(resp_freq == peak_freqs), 'Resp frequency not found'
assert len(peak_freqs) == 2, 'Two peaks not found'
# Test task noise
sim._generate_noise_temporal_task(stimfunction_tr,
motion_noise='gaussian',
)
sim._generate_noise_temporal_task(stimfunction_tr,
motion_noise='rician',
)
# Test ARMA noise
with pytest.raises(ValueError):
noise_dict = {'fwhm': 4, 'auto_reg_rho': [1], 'ma_rho': [1, 1]}
sim._generate_noise_temporal_autoregression(stimfunction_tr,
noise_dict,
dimensions,
mask,
)
# Generate spatial noise
vol = sim._generate_noise_spatial(np.array([10, 10, 10, trs]))
assert len(vol.shape) == 3, 'Volume was not reshaped to ignore TRs'
# Switch some of the noise types on
noise_dict = dict(physiological_sigma=1, drift_sigma=1, task_sigma=1,
auto_reg_sigma=0)
sim.generate_noise(dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
template=template,
mask=mask,
noise_dict=noise_dict,
iterations=[0, 0],
)
def test_generate_noise():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array([[5, 5, 5]])
signal_magnitude = [1]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(
dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(
onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.double_gamma_hrf(
stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(
signal_function=signal_function,
volume_static=volume,
)
# Generate the mask of the signal
mask = sim.mask_brain(signal, mask_threshold=0.1)
assert min(mask[mask > 0]) > 0.1, "Mask thresholding did not work"
stimfunction_tr = stimfunction[::int(tr_duration * 1000)]
# Create the noise volumes (using the default parameters)
noise = sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
mask=mask,
)
assert signal.shape == noise.shape, "The dimensions of signal and noise " \
"the same"
assert np.std(signal) < np.std(noise), "Noise was not created"
noise = sim.generate_noise(
dimensions=dimensions,
stimfunction_tr=stimfunction_tr,
tr_duration=tr_duration,
mask=mask,
noise_dict={
'temporal_noise': 0,
'sfnr': 10000
},
)
temporal_noise = np.std(noise[mask[:, :, :, 0] > 0], 1).mean()
assert temporal_noise <= 0.1, "Noise strength could not be manipulated"
def test_generate_noise():
dimensions = np.array([10, 10, 10]) # What is the size of the brain
feature_size = [2]
feature_type = ['cube']
feature_coordinates = np.array(
[[5, 5, 5]])
signal_magnitude = [1]
# Generate a volume representing the location and quality of the signal
volume = sim.generate_signal(dimensions=dimensions,
feature_coordinates=feature_coordinates,
feature_type=feature_type,
feature_size=feature_size,
signal_magnitude=signal_magnitude,
)
# Inputs for generate_stimfunction
onsets = [10, 30, 50, 70, 90]
event_durations = [6]
tr_duration = 2
duration = 100
# Create the time course for the signal to be generated
stimfunction = sim.generate_stimfunction(onsets=onsets,
event_durations=event_durations,
total_time=duration,
)
signal_function = sim.double_gamma_hrf(stimfunction=stimfunction,
tr_duration=tr_duration,
)
# Convolve the HRF with the stimulus sequence
signal = sim.apply_signal(signal_function=signal_function,
volume_static=volume,
)
# Generate the mask of the signal
mask = sim.mask_brain(signal, mask_threshold=0.1)
assert min(mask[mask > 0]) > 0.1, "Mask thresholding did not work"
# Create the noise volumes (using the default parameters)
noise = sim.generate_noise(dimensions=dimensions,
stimfunction=stimfunction,
tr_duration=tr_duration,
mask=mask,
)
assert signal.shape == noise.shape, "The dimensions of signal and noise " \
"the same"
assert np.std(signal) < np.std(noise), "Noise was not created"
noise = sim.generate_noise(dimensions=dimensions,
stimfunction=stimfunction,
tr_duration=tr_duration,
mask=mask,
noise_dict={'overall': 0},
)
assert np.sum(noise) == 0, "Noise strength could not be manipulated"
assert np.std(noise) == 0, "Noise strength could not be manipulated"