def test_patch_size(self):
""" Test the patch size normalization according to the image anisotropy.
"""
for spacing, patch_size in zip(self.spacings, self.patch_sizes):
half_patch_size, full_patch_size = normalize_patch_size(spacing[0], spacing[1:])
self.assertEqual(half_patch_size.tolist(), patch_size.tolist())
self.assertEqual(full_patch_size.tolist(), (2 * patch_size + 1).tolist())
def test_patch_size(self):
""" Test the patch size normalization according to the image anisotropy.
"""
for spacing, patch_size in zip(self.spacings, self.patch_sizes):
half_patch_size, full_patch_size = normalize_patch_size(
spacing[0], spacing[1:])
self.assertEqual(half_patch_size.tolist(), patch_size.tolist())
self.assertEqual(full_patch_size.tolist(),
(2 * patch_size + 1).tolist())
def __init__(self, to_denoise_array, spacing, mask_array=None,
half_patch_size=1, half_spatial_bandwidth=5,
central_point_strategy="weight", blockwise_strategy="blockwise",
lower_mean_threshold=0.95, lower_variance_threshold=0.5,
beta=1, use_optimized_strategy=True, use_cython=True,
nb_of_threads=1):
""" Initialize the non-local denoising class.
Parameters
----------
array_to_denoise: array
an input n dimensional array to process containing the image
intensities.
spacing: n-uplet
the image spacing in voxel.
half_patch_size: int
the patch size in voxel.
central_point_strategy: str (default 'weight')
the way the central patch is considered, one of 'add', 'remove' or
'weight'.
blockwise_strategy: str (default 'blockwise')
the blockwise denoising strategy, one of 'pointwise', 'blockwise' or
'fastblockwise'.
lower_mean_threshold: float (default 0.95)
threshold to select two patches depending on the mean values.
lower_variance_threshold: float (default 0.5)
threshold to select two patches depending on the variance values.
beta: float
smoothing parameter.
use_optimized_strategy: bool (default True)
use the mean and variance to discard some patches in the neighborhood
based on the mean and variance thresholds.
use_cython: bool (default True)
the cython to speed up the denoised patch creation.
nb_of_threads: int (default 1)
if cython code, defines the number of threads to use.
"""
# Class parameters
self.to_denoise_array = numpy.cast[numpy.single](to_denoise_array)
self.spacing = numpy .asarray(spacing)
self.mask_array = mask_array
self.mean_array = None
self.variance_array = None
self.central_point_strategy = central_point_strategy
self.blockwise_strategy = blockwise_strategy
self.use_optimized_strategy = use_optimized_strategy
self.lower_mean_threshold = lower_mean_threshold
self.lower_variance_threshold = lower_variance_threshold
self.use_cython = use_cython
self.nb_of_threads = nb_of_threads
# Intern parameters
self.shape = self.to_denoise_array.shape
self.size = self.to_denoise_array.size
# Check that the mask array has a valid shape
if self.mask_array is not None:
if self.shape != self.mask_array.shape:
raise ValueError("Input mask array has invalid shape.")
else:
self.mask_array = numpy.ones(self.shape, dtype=numpy.int)
remaining_voxels = len(numpy.where(self.mask_array > 0)[0])
logger.info("Remaining voxels to process '%s' percent.",
int(remaining_voxels / self.size * 100.))
# Check that a valid denoising strategy has been selected.
if self.blockwise_strategy not in self.valid_blockwise_strategies:
raise ValueError(
"Wrong denoising strategy '{0}'. Valid options are '{1}'.".format(
self.blockwise_strategy, self.valid_blockwise_strategies))
# Check that a valid central point strategy has been selected.
if self.central_point_strategy not in self.valid_cental_point_strategies:
raise ValueError(
"Wrong central point strategy '{0}'. Valid options are '{1}'.".format(
self.central_point_strategy, self.valid_cental_point_strategies))
# Intern parameters
# > patch size
self.half_patch_size, self.full_patch_size = normalize_patch_size(
half_patch_size, self.spacing)
# > spatial bandwidth: equivalent to the size of the volume search area
# in non-local means
(self.half_spatial_bandwidth,
self.full_spatial_bandwidth) = normalize_patch_size(
half_spatial_bandwidth, self.spacing)
# > compute mean and variance images
if self.use_optimized_strategy:
if self.use_cython:
self.mean_array, self.variance_array = c_patch_mean_variance(
self.to_denoise_array,
numpy.cast[numpy.single](self.mask_array),
self.full_patch_size)
else:
self.mean_array, self.variance_array = patch_mean_variance(
self.to_denoise_array, self.mask_array, self.full_patch_size)
# > smooth parameter
self.range_bandwidth = self._compute_range_bandwidth(beta)
