def noise_std(self):
def _compute_noise_std():
if self._noise_std is None:
try:
return estimate_noise_std(self)
except NoiseStdEstimationNotPossible:
self._logger.warning('Failed to obtain a noise std for this subject. '
'We will continue with an std of 1.')
return 1
if isinstance(self._noise_std, (numbers.Number, np.ndarray)):
return self._noise_std
if isinstance(self._noise_std, str):
filename = str(self._noise_std)
if filename[-4:] == '.txt':
with open(filename, 'r') as f:
return float(f.read())
return load_nifti(filename).get_data()
self._logger.warning('Failed to obtain a noise std for this subject. We will continue with an std of 1.')
return 1
self._noise_std = _compute_noise_std()
if is_scalar(self._noise_std):
return self._noise_std
else:
return create_roi(self._noise_std, self.mask)
def _get_bounds(self, bounds, roi_indices):
return_values = []
for el in bounds:
if is_scalar(el):
return_values.append(el)
else:
return_values.append(el[roi_indices])
return tuple(return_values)
def get_subset(self, volumes_to_keep=None, volumes_to_remove=None):
if (volumes_to_keep is not None) and (volumes_to_remove is not None):
raise ValueError('You can not specify both the list with volumes to keep and volumes to remove. Choose one.')
if (volumes_to_keep is None) and (volumes_to_remove is None):
raise ValueError('Please specify either the list with volumes to keep or the list with volumes to remove.')
if volumes_to_keep is not None:
if is_scalar(volumes_to_keep):
volumes_to_keep = [volumes_to_keep]
elif volumes_to_remove is not None:
if is_scalar(volumes_to_remove):
volumes_to_remove = [volumes_to_remove]
volumes_to_keep = list(range(self.nmr_observations))
volumes_to_keep = [ind for ind in volumes_to_keep if ind not in volumes_to_remove]
new_protocol = self.protocol
if self.protocol is not None:
new_protocol = self.protocol.get_new_protocol_with_indices(volumes_to_keep)
new_dwi_volume = self.signal4d
if self.signal4d is not None:
new_dwi_volume = self.signal4d[..., volumes_to_keep]
new_volume_weights = self._volume_weights
if self._volume_weights is not None:
new_volume_weights = new_volume_weights[..., volumes_to_keep]
new_gradient_deviations = self._gradient_deviations
if self._gradient_deviations is not None:
if self._gradient_deviations.ndim > 4 and self._gradient_deviations.shape[3] == self.protocol.length:
if self._gradient_deviations.ndim == 5:
new_gradient_deviations = self._gradient_deviations[..., volumes_to_keep, :]
else:
new_gradient_deviations = self._gradient_deviations[..., volumes_to_keep, :, :]
new_extra_protocol = {}
for key, value in self._extra_protocol.items():
value = np.array(value, copy=False)
if value.ndim > 3 and value.shape[3] == self.protocol.length:
value = value[:, :, :, volumes_to_keep, ...]
new_extra_protocol[key] = value
return self.copy_with_updates(protocol=new_protocol, signal4d=new_dwi_volume,
gradient_deviations=new_gradient_deviations,
volume_weights=new_volume_weights, extra_protocol=new_extra_protocol)