def compute_voxel_measures(args):
bundle_filename, bundle_reference = args[0]
tracking_mask = args[1]
gs_binary_3d = args[2]
bundle_sft = load_tractogram(bundle_filename, bundle_reference)
bundle_sft.to_vox()
bundle_sft.to_corner()
bundle_streamlines = bundle_sft.streamlines
_, bundle_dimensions, _, _ = bundle_sft.space_attributes
if not bundle_streamlines:
logging.info('{} is empty'.format(bundle_filename))
return None
binary_3d = compute_tract_counts_map(bundle_streamlines, bundle_dimensions)
binary_3d[binary_3d > 0] = 1
binary_3d_indices = np.where(binary_3d.flatten() > 0)[0]
gs_binary_3d_indices = np.where(gs_binary_3d.flatten() > 0)[0]
voxels_binary = binary_classification(
binary_3d_indices,
gs_binary_3d_indices,
int(np.prod(tracking_mask.shape)),
mask_count=np.count_nonzero(tracking_mask))
return dict(
zip([
'sensitivity_voxels', 'specificity_voxels', 'precision_voxels',
'accuracy_voxels', 'dice_voxels', 'kappa_voxels', 'youden_voxels'
], voxels_binary))
def compute_streamlines_measures(args):
bundle_filename, bundle_reference = args[0]
wb_streamlines = args[1]
gs_streamlines_indices = args[2]
if not os.path.isfile(bundle_filename):
logging.info('{} does not exist'.format(bundle_filename))
return None
bundle_sft = load_tractogram(bundle_filename, bundle_reference)
bundle_sft.to_vox()
bundle_sft.to_corner()
bundle_streamlines = bundle_sft.streamlines
_, bundle_dimensions, _, _ = bundle_sft.space_attributes
if not bundle_streamlines:
logging.info('{} is empty'.format(bundle_filename))
return None
_, streamlines_indices = perform_streamlines_operation(
intersection, [wb_streamlines, bundle_streamlines], precision=0)
streamlines_binary = binary_classification(streamlines_indices,
gs_streamlines_indices,
len(wb_streamlines))
return dict(
zip([
'sensitivity_streamlines', 'specificity_streamlines',
'precision_streamlines', 'accuracy_streamlines',
'dice_streamlines', 'kappa_streamlines', 'youden_streamlines'
], streamlines_binary))