def main(file_to_denoise, param, output_file_name):
path, file, ext = sct.extract_fname(file_to_denoise)
img = nib.load(file_to_denoise)
hdr_0 = img.get_header()
data = img.get_data()
aff = img.get_affine()
mask = data[:, :, :] > 80
data = data[:, :, :]
print("vol size", data.shape)
t = time()
sigma = np.std(data[~mask])
if param.parameter == 'Rician':
den = nlmeans(data, sigma=sigma, mask=mask, rician=True)
else:
den = nlmeans(data, sigma=sigma, mask=mask, rician=False)
print("total time", time() - t)
print("vol size", den.shape)
axial_middle = data.shape[2] / 2
before = data[:, :, axial_middle].T
after = den[:, :, axial_middle].T
diff_3d = np.absolute(den.astype('f8') - data.astype('f8'))
difference = np.absolute(after.astype('f8') - before.astype('f8'))
difference[~mask[:, :, axial_middle].T] = 0
if param.verbose == 2:
fig, ax = plt.subplots(1, 3)
ax[0].imshow(before, cmap='gray', origin='lower')
ax[0].set_title('before')
ax[1].imshow(after, cmap='gray', origin='lower')
ax[1].set_title('after')
ax[2].imshow(difference, cmap='gray', origin='lower')
ax[2].set_title('difference')
for i in range(3):
ax[i].set_axis_off()
plt.show()
plt.savefig('denoised_S0.png', bbox_inches='tight')
#Save files
img_denoize = nib.Nifti1Image(den, None, hdr_0)
img_diff = nib.Nifti1Image(diff_3d, None, hdr_0)
if output_file_name != None:
output_file_name = output_file_name
else:
output_file_name = file + '_denoised' + ext
nib.save(img_denoize, output_file_name)
nib.save(img_diff, file + '_difference' + ext)
def main(file_to_denoize, param, output_file_name) :
path, file, ext = sct.extract_fname(file_to_denoize)
img = nib.load(file_to_denoize)
hdr_0 = img.get_header()
data = img.get_data()
aff = img.get_affine()
mask = data[:, :, :] > 80
data = data[:, :, :]
print("vol size", data.shape)
t = time()
sigma = np.std(data[~mask])
if param.parameter == 'Rician':
den = nlmeans(data, sigma=sigma, mask=mask, rician=True)
else : den = nlmeans(data, sigma=sigma, mask=mask, rician=False)
print("total time", time() - t)
print("vol size", den.shape)
axial_middle = data.shape[2] / 2
before = data[:, :, axial_middle].T
after = den[:, :, axial_middle].T
diff_3d = np.absolute(den.astype('f8') - data.astype('f8'))
difference = np.absolute(after.astype('f8') - before.astype('f8'))
difference[~mask[:, :, axial_middle].T] = 0
if param.verbose == 2 :
fig, ax = plt.subplots(1, 3)
ax[0].imshow(before, cmap='gray', origin='lower')
ax[0].set_title('before')
ax[1].imshow(after, cmap='gray', origin='lower')
ax[1].set_title('after')
ax[2].imshow(difference, cmap='gray', origin='lower')
ax[2].set_title('difference')
for i in range(3):
ax[i].set_axis_off()
plt.show()
plt.savefig('denoised_S0.png', bbox_inches='tight')
#Save files
img_denoize = nib.Nifti1Image(den, None, hdr_0)
img_diff = nib.Nifti1Image(diff_3d, None, hdr_0)
if output_file_name != None :
output_file_name =output_file_name
else: output_file_name = file + '_denoized' + ext
nib.save(img_denoize,output_file_name)
nib.save(img_diff, file + '_difference' +ext)
def test_nlmeans_dtype():
S0 = 200 * np.ones((20, 20, 20, 3), dtype='f4')
mask = np.zeros((20, 20, 20))
mask[10:14, 10:14, 10:14] = 1
S0n = nlmeans(S0, sigma=1, mask=mask, rician=True)
assert_equal(S0.dtype, S0n.dtype)
S0 = 200 * np.ones((20, 20, 20), dtype=np.uint16)
mask = np.zeros((20, 20, 20))
mask[10:14, 10:14, 10:14] = 1
S0n = nlmeans(S0, sigma=1, mask=mask, rician=True)
assert_equal(S0.dtype, S0n.dtype)
def test_nlmeans_dtype():
S0 = 200 * np.ones((20, 20, 20, 3), dtype='f4')
mask = np.zeros((20, 20, 20))
mask[10:14, 10:14, 10:14] = 1
S0n = nlmeans(S0, sigma=1, mask=mask, rician=True)
assert_equal(S0.dtype, S0n.dtype)
S0 = 200 * np.ones((20, 20, 20), dtype=np.uint16)
mask = np.zeros((20, 20, 20))
mask[10:14, 10:14, 10:14] = 1
S0n = nlmeans(S0, sigma=np.ones((20, 20, 20)), mask=mask, rician=True)
assert_equal(S0.dtype, S0n.dtype)
def test_denoise():
"""
"""
fdata, fbval, fbvec = dpd.get_fnames()
# Test on 4D image:
data = nib.load(fdata).get_data()
sigma1 = estimate_sigma(data)
nlmeans(data, sigma=sigma1)
# Test on 3D image:
data = data[..., 0]
sigma2 = estimate_sigma(data)
nlmeans(data, sigma=sigma2)
def nlmeans_denoise_img(img, mask, N=4):
""" Apply dipy nlmeans denoising to the img. Useful for diffusion images.
Parameters
----------
img: nibabel.Nifti1Image
The diffusion image
mask: nibabel.Nifti1Image
A brain mask image.
N: int
Number of arrays of the head coil used to acquired the image.
Returns
-------
den_img: nibabel.Nifti1Image
A denoised nifti image object with the same headers
and affine as `img`.
"""
from dipy.denoise.nlmeans import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
data = img.get_data()
msk = mask.get_data()
sigma = estimate_sigma(data, N=N)
return nlmeans(data, sigma=sigma, mask=msk)
def nlmeans_proxy(in_file, settings, noise_mask=None, out_file=None):
"""
Uses non-local means to denoise 4D datasets
"""
package_check('dipy', version='0.8.0.dev')
from dipy.denoise.nlmeans import nlmeans
if out_file is None:
fname, fext = op.splitext(op.basename(in_file))
if fext == '.gz':
fname, fext2 = op.splitext(fname)
fext = fext2 + fext
out_file = op.abspath('./%s_denoise%s' % (fname, fext))
img = nb.load(in_file)
hdr = img.header
data = img.get_data()
aff = img.affine
nmask = data[..., 0] > 80
if noise_mask is not None:
nmask = noise_mask > 0
sigma = np.std(data[nmask == 1])
den = nlmeans(data, sigma, **settings)
nb.Nifti1Image(den.astype(hdr.get_data_dtype()), aff,
hdr).to_filename(out_file)
return out_file, sigma
def _run_interface(self, runtime): import nibabel as nib import numpy as np from dipy.denoise.nlmeans import nlmeans from nipype.utils.filemanip import split_filename fname = self.inputs.in_file img = nib.load(fname) data = img.get_data() affine = img.get_affine() mask = data[..., 0] > 80 a = data.shape denoised_data = np.ndarray(shape=data.shape) for image in range(0,a[3]): print(str(image + 1) + '/' + str(a[3] + 1)) dat = data[...,image] sigma = np.std(dat[~mask]) # Calculating the standard deviation of the noise den = nlmeans(dat, sigma=sigma, mask=mask) denoised_data[:,:,:,image] = den _, base, _ = split_filename(fname) nib.save(nib.Nifti1Image(denoised_data, affine), base + '_denoised.nii') return runtime
def nlmeans_denoise_img(img, mask, N=4):
""" Apply dipy nlmeans denoising to the img. Useful for diffusion images.
Parameters
----------
img: nibabel.Nifti1Image
The diffusion image
mask: nibabel.Nifti1Image
A brain mask image.
N: int
Number of arrays of the head coil used to acquired the image.
Returns
-------
den_img: nibabel.Nifti1Image
A denoised nifti image object with the same headers
and affine as `img`.
"""
from dipy.denoise.nlmeans import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
data = img.get_data()
msk = mask.get_data()
sigma = estimate_sigma(data, N=N)
return nlmeans(data, sigma=sigma, mask=msk)
def preprocess(nifti, name):
"""Preprocess the 3D MRI image before image segmentation"""
image = nifti.get_fdata()
sigma = estimate_sigma(image, N=16) # N: number of coils in the receiver of the MRI scanner
denoised = nlmeans(image, sigma)
denoised_nifti = nib.Nifti1Image(denoised, nifti.affine)
nib.save(denoised_nifti, f'lab4/data/clean_{name}.nii.gz')
def _run_interface(self, runtime): import nibabel as nib import numpy as np import matplotlib.pyplot as plt from dipy.denoise.nlmeans import nlmeans from nipype.utils.filemanip import split_filename fname = self.inputs.in_file img = nib.load(fname) data = img.get_data() affine = img.get_affine() mask = data[..., 0] > 80 a = data.shape denoised_data = np.ndarray(shape=data.shape) for image in range(0,a[3]): print(str(image + 1) + '/' + str(a[3] + 1)) dat = data[...,image] sigma = np.std(dat[~mask]) # Calculating the standard deviation of the noise den = nlmeans(dat, sigma=sigma, mask=mask) denoised_data[:,:,:,image] = den _, base, _ = split_filename(fname) nib.save(nib.Nifti1Image(denoised_data, affine), base + '_denoised.nii') return runtime
def nlmeans_proxy(in_file, settings,
noise_mask=None, out_file=None):
"""
Uses non-local means to denoise 4D datasets
"""
package_check('dipy', version='0.8.0.dev')
from dipy.denoise.nlmeans import nlmeans
if out_file is None:
fname, fext = op.splitext(op.basename(in_file))
if fext == '.gz':
fname, fext2 = op.splitext(fname)
fext = fext2 + fext
out_file = op.abspath('./%s_denoise%s' % (fname, fext))
img = nb.load(in_file)
hdr = img.get_header()
data = img.get_data()
aff = img.get_affine()
nmask = data[..., 0] > 80
if noise_mask is not None:
nmask = noise_mask > 0
sigma = np.std(data[nmask == 1])
den = nlmeans(data, sigma, **settings)
nb.Nifti1Image(den.astype(hdr.get_data_dtype()), aff,
hdr).to_filename(out_file)
return out_file, sigma
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.input])
assert_outputs_exists(parser, args, [args.output],
[args.logfile, args.save_piesno_mask])
logging.basicConfig()
log = logging.getLogger(__name__)
if args.verbose:
log.setLevel(level=logging.INFO)
else:
log.setLevel(level=logging.WARNING)
if args.logfile is not None:
log.addHandler(logging.FileHandler(args.logfile, mode='w'))
vol = nib.load(args.input)
data = vol.get_data()
if args.mask is None:
mask = np.ones(data.shape[:3], dtype=np.bool)
else:
mask = nib.load(args.mask).get_data().astype(np.bool)
sigma = args.sigma
noise_method = args.noise_method
if args.N == 0 and sigma is None and noise_method == PIESNO:
raise ValueError('PIESNO is not designed for Gaussian noise, but you '
'specified N = 0.')
# Check if dataset is 3D. If so, ensure the user didn't ask for PIESNO.
# This is unsupported.
if data.ndim == 3 and noise_method == PIESNO:
parser.error('Cannot use PIESNO noise estimation with a 3D dataset. '
'Please use the basic estimation')
if sigma is not None:
log.info('User supplied noise standard deviation is %s', sigma)
# Broadcast the single value to a whole 3D volume for nlmeans
sigma = np.ones(data.shape[:3]) * sigma
else:
log.info('Estimating noise with method %s', args.noise_method)
if args.noise_method == PIESNO:
sigma = _get_piesno_sigma(vol, log, args)
else:
sigma = _get_basic_sigma(vol.get_data(), log)
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=DeprecationWarning)
data_denoised = nlmeans(data,
sigma,
mask=mask,
rician=args.N > 0,
num_threads=args.nbr_processes)
nib.save(nib.Nifti1Image(data_denoised, vol.affine, vol.header),
args.output)
def denoise(x, mask):
subjectid = x[0][0]
from dipy.denoise import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
sigma = estimate_sigma(x[1])
#return(x[0], nlmeans.nlmeans(x[1], num_threads=1, sigma=sigma, mask=mask.value[str(subjectid)]))
return (x[0],
nlmeans.nlmeans(x[1], sigma=sigma,
mask=mask.value[str(subjectid)]))
def run(self, input_files, sigma=0, patch_radius=1, block_radius=5,
rician=True, out_dir='', out_denoised='dwi_nlmeans.nii.gz'):
"""Workflow wrapping the nlmeans denoising method.
It applies nlmeans denoise on each file found by 'globing'
``input_files`` and saves the results in a directory specified by
``out_dir``.
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
sigma : float, optional
Sigma parameter to pass to the nlmeans algorithm
(default: auto estimation).
patch_radius : int, optional
patch size is ``2 x patch_radius + 1``. Default is 1.
block_radius : int, optional
block size is ``2 x block_radius + 1``. Default is 5.
rician : bool, optional
If True the noise is estimated as Rician, otherwise Gaussian noise
is assumed.
out_dir : string, optional
Output directory (default input file directory)
out_denoised : string, optional
Name of the resulting denoised volume (default: dwi_nlmeans.nii.gz)
References
----------
.. [Descoteaux08] Descoteaux, Maxime and Wiest-Daesslé, Nicolas and
Prima, Sylvain and Barillot, Christian and Deriche, Rachid.
Impact of Rician Adapted Non-Local Means Filtering on
HARDI, MICCAI 2008
"""
io_it = self.get_io_iterator()
for fpath, odenoised in io_it:
if self._skip:
shutil.copy(fpath, odenoised)
logging.warning('Denoising skipped for now.')
else:
logging.info('Denoising %s', fpath)
data, affine, image = load_nifti(fpath, return_img=True)
if sigma == 0:
logging.info('Estimating sigma')
sigma = estimate_sigma(data)
logging.debug('Found sigma {0}'.format(sigma))
denoised_data = nlmeans(data, sigma=sigma,
patch_radius=patch_radius,
block_radius=block_radius,
rician=rician)
save_nifti(odenoised, denoised_data, affine, image.header)
logging.info('Denoised volume saved as %s', odenoised)
def test_nlmeans_boundary():
# nlmeans preserves boundaries
S0 = 100 + np.zeros((20, 20, 20))
noise = 2 * np.random.standard_normal((20, 20, 20))
S0 += noise
S0[:10, :10, :10] = 300 + noise[:10, :10, :10]
nlmeans(S0, sigma=np.ones((20, 20, 20)) * np.std(noise), rician=False)
print(S0[9, 9, 9])
print(S0[10, 10, 10])
assert_(S0[9, 9, 9] > 290)
assert_(S0[10, 10, 10] < 110)
def test_nlmeans_4D_and_mask():
S0 = 200 * np.ones((20, 20, 20, 3), dtype='f8')
mask = np.zeros((20, 20, 20))
mask[10, 10, 10] = 1
S0n = nlmeans(S0, sigma=1, mask=mask, rician=True)
assert_equal(S0.shape, S0n.shape)
assert_equal(np.round(S0n[10, 10, 10]), 200)
assert_equal(S0n[8, 8, 8], 0)
def test_nlmeans_boundary():
# nlmeans preserves boundaries
S0 = 100 + np.zeros((20, 20, 20))
noise = 2 * np.random.standard_normal((20, 20, 20))
S0 += noise
S0[:10, :10, :10] = 300 + noise[:10, :10, :10]
nlmeans(S0, sigma=np.ones((20, 20, 20)) * np.std(noise),
rician=False)
print(S0[9, 9, 9])
print(S0[10, 10, 10])
assert_(S0[9, 9, 9] > 290)
assert_(S0[10, 10, 10] < 110)
def denoise_image(self, image, mask):
sigma = estimate_sigma(image, N=4)
den = nlmeans(image,
sigma=sigma,
mask=mask,
patch_radius=1,
block_radius=1,
rician=True)
diff = np.abs(den.astype('f8') - image.astype('f8'))
return den, diff
def test_nlmeans_4D_and_mask():
S0 = 200 * np.ones((20, 20, 20, 3), dtype='f8')
mask = np.zeros((20, 20, 20))
mask[10, 10, 10] = 1
S0n = nlmeans(S0, sigma=1, mask=mask, rician=True)
assert_equal(S0.shape, S0n.shape)
assert_equal(np.round(S0n[10, 10, 10]), 200)
assert_equal(S0n[8, 8, 8], 0)
def test_nlmeans_random_noise():
S0 = 100 + 2 * np.random.standard_normal((22, 23, 30))
S0n = nlmeans(S0, sigma=np.ones((22, 23, 30)) * np.std(S0), rician=False)
print(S0.mean(), S0.min(), S0.max())
print(S0n.mean(), S0n.min(), S0n.max())
assert_(S0n.min() > S0.min())
assert_(S0n.max() < S0.max())
assert_equal(np.round(S0n.mean()), 100)
def denoiser(X, method='gaussian'):
#ss = X.shape
X = X.reshape(X.shape[1:])
assert method in ['gaussian', 'nlmean', 'none']
s = X.std()
if method == 'gaussian':
return scipy.ndimage.filters.gaussian_filter(X, sigma=s).reshape(
1, *X.shape)
if method == 'nlmean':
return nlmeans(X, sigma=s / 10, block_radius=1).reshape(1, *X.shape)
return X.reshape(1, *X.shape)
def test_nlmeans_random_noise():
S0 = 100 + 2 * np.random.standard_normal((22, 23, 30))
S0n = nlmeans(S0, sigma=np.std(S0), rician=False)
print(S0.mean(), S0.min(), S0.max())
print(S0n.mean(), S0n.min(), S0n.max())
assert_(S0n.min() > S0.min())
assert_(S0n.max() < S0.max())
assert_equal(np.round(S0n.mean()), 100)
def test_nlmeans_4d_3dsigma_and_threads():
# Input is 4D data and 3D sigma
data = np.ones((50, 50, 50, 5))
sigma = np.ones(data.shape[:3])
mask = np.zeros(data.shape[:3])
# mask[25-10:25+10] = 1
mask[:] = 1
print('cpu count %d' % (cpu_count(), ))
print('1')
t = time()
new_data = nlmeans(data, sigma, mask, num_threads=1)
duration_1core = time() - t
print(duration_1core)
print('All')
t = time()
new_data2 = nlmeans(data, sigma, mask, num_threads=None)
duration_all_core = time() - t
print(duration_all_core)
print('2')
t = time()
new_data3 = nlmeans(data, sigma, mask, num_threads=2)
duration_2core = time() - t
print(duration_all_core)
assert_array_almost_equal(new_data, new_data2)
assert_array_almost_equal(new_data2, new_data3)
if cpu_count() > 2:
assert_equal(duration_all_core < duration_2core, True)
assert_equal(duration_2core < duration_1core, True)
if cpu_count() == 2:
assert_equal(duration_2core < duration_1core, True)
def test_nlmeans_4d_3dsigma_and_threads():
# Input is 4D data and 3D sigma
data = np.ones((50, 50, 50, 5))
sigma = np.ones(data.shape[:3])
mask = np.zeros(data.shape[:3])
# mask[25-10:25+10] = 1
mask[:] = 1
print('cpu count %d' % (cpu_count(),))
print('1')
t = time()
new_data = nlmeans(data, sigma, mask, num_threads=1)
duration_1core = time() - t
print(duration_1core)
print('All')
t = time()
new_data2 = nlmeans(data, sigma, mask, num_threads=None)
duration_all_core = time() - t
print(duration_all_core)
print('2')
t = time()
new_data3 = nlmeans(data, sigma, mask, num_threads=2)
duration_2core = time() - t
print(duration_all_core)
assert_array_almost_equal(new_data, new_data2)
assert_array_almost_equal(new_data2, new_data3)
if cpu_count() > 2:
assert_equal(duration_all_core < duration_2core, True)
assert_equal(duration_2core < duration_1core, True)
if cpu_count() == 2:
assert_equal(duration_2core < duration_1core, True)
def _run_interface(self, runtime):
import nibabel as nib
from dipy.denoise.nlmeans import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
import numpy as np
img = nib.load(self.inputs.in_file)
data = img.get_data()
affine = img.affine
if len(data.shape) > 3:
den = np.zeros(data.shape)
for i in range(data.shape[-1]):
print('direction # ' + str(i))
sigma = estimate_sigma(data[..., i], N=4)
den[..., i] = nlmeans(data[..., i],
sigma=sigma,
patch_radius=1,
block_radius=5,
rician=True)
nib.save(nib.Nifti1Image(den.astype(np.float32), img.affine),
'denoised.nii.gz')
else:
sigma = estimate_sigma(data, N=4)
den = nlmeans(data,
sigma=sigma,
patch_radius=1,
block_radius=5,
rician=True)
nib.save(nib.Nifti1Image(den, affine), 'denoised.nii.gz')
return runtime
def Nonlocal(data,
affine,
keep=False,
filt=100): #Preguntar! #No usan denoise images PCA
if len(data.shape) == 3:
mask = data > filt
else:
mask = data[..., 1] > filt
data2 = data #Preguntar
sigma = np.std(data2[~mask])
den = nlmeans(data2, sigma=sigma, mask=mask)
if keep:
nib.save(nib.Nifti1Image(den.astype(np.float32), affine), "Nonlocal")
return den
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_image)
assert_outputs_exist(parser, args, args.out_image, args.logfile)
logging.basicConfig()
log = logging.getLogger(__name__)
if args.verbose:
log.setLevel(level=logging.INFO)
else:
log.setLevel(level=logging.WARNING)
if args.logfile is not None:
log.addHandler(logging.FileHandler(args.logfile, mode='w'))
vol = nib.load(args.in_image)
data = vol.get_fdata(dtype=np.float32)
if args.mask is None:
mask = np.zeros(data.shape[0:3], dtype=bool)
if data.ndim == 4:
mask[np.sum(data, axis=-1) > 0] = 1
else:
mask[data > 0] = 1
else:
mask = get_data_as_mask(nib.load(args.mask), dtype=bool)
sigma = args.sigma
if sigma is not None:
log.info('User supplied noise standard deviation is {}'.format(sigma))
# Broadcast the single value to a whole 3D volume for nlmeans
sigma = np.ones(data.shape[:3]) * sigma
else:
log.info('Estimating noise')
sigma = _get_basic_sigma(vol.get_fdata(dtype=np.float32), log)
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=DeprecationWarning)
data_denoised = nlmeans(data,
sigma,
mask=mask,
rician=args.number_coils > 0,
num_threads=args.nbr_processes)
nib.save(nib.Nifti1Image(data_denoised, vol.affine, header=vol.header),
args.out_image)
def example_output():
data, sigma = load_data(flat=False, name=dataset_name)
for b in range(1, 8):
for p in range(1, 4):
global B
B = b
global P
P = p
t_start = time.time()
dipynlmeans = nlmeans.nlmeans(np.copy(data), sigma, mask=None,
patch_radius=P, block_radius=B, rician=False)
t_dipy = time.time()-t_start
print("%d, %d, Time: %.3fs" % (b, p, t_dipy))
imsave(path_to_folder + "/images/den_dipy_b%d_p%d_%s.png" % (b, p, dataset_name),
dipynlmeans[:, :, int(sh[2]/2)])
def run(self,
input_files,
sigma=0,
out_dir='',
out_denoised='dwi_nlmeans.nii.gz'):
""" Workflow wrapping the nlmeans denoising method.
It applies nlmeans denoise on each file found by 'globing'
``input_files`` and saves the results in a directory specified by
``out_dir``.
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
sigma : float, optional
Sigma parameter to pass to the nlmeans algorithm
(default: auto estimation).
out_dir : string, optional
Output directory (default input file directory)
out_denoised : string, optional
Name of the resuting denoised volume (default: dwi_nlmeans.nii.gz)
"""
io_it = self.get_io_iterator()
for fpath, odenoised in io_it:
if self._skip:
shutil.copy(fpath, odenoised)
logging.warning('Denoising skipped for now.')
else:
logging.info('Denoising {0}'.format(fpath))
image = nib.load(fpath)
data = image.get_data()
if sigma == 0:
logging.info('Estimating sigma')
sigma = estimate_sigma(data)
logging.debug('Found sigma {0}'.format(sigma))
denoised_data = nlmeans(data, sigma)
denoised_image = nib.Nifti1Image(denoised_data,
image.get_affine(),
image.get_header())
denoised_image.to_filename(odenoised)
logging.info('Denoised volume saved as {0}'.format(odenoised))
def denoise_nlmeans(data_in, patch_radius=1, block_radius=5):
"""
:param data_in: nd_array to denoise
.. note::
for more info about patch_radius and block radius, please refer to the dipy website: http://dipy.org/dipy/reference/dipy.denoise.html#dipy.denoise.nlmeans.nlmeans
"""
data_in = np.asarray(data_in)
block_radius_max = min(data_in.shape) - 1
block_radius = block_radius_max if block_radius > block_radius_max else block_radius
sigma = estimate_sigma(data_in)
denoised = nlmeans(data_in, sigma, patch_radius=patch_radius, block_radius=block_radius)
return denoised
def denoise_nlmeans(data_in, patch_radius=1, block_radius=5):
"""
data_in: nd_array to denoise
for more info about patch_radius and block radius, please refer to the dipy website: http://nipy.org/dipy/reference/dipy.denoise.html#dipy.denoise.nlmeans.nlmeans
"""
from dipy.denoise.nlmeans import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
from numpy import asarray
data_in = asarray(data_in)
block_radius_max = min(data_in.shape)-1
block_radius = block_radius_max if block_radius > block_radius_max else block_radius
sigma = estimate_sigma(data_in)
denoised = nlmeans(data_in, sigma, patch_radius=patch_radius, block_radius=block_radius)
return denoised
def denoise_nlmeans(data_in, patch_radius=1, block_radius=5):
"""
data_in: nd_array to denoise
for more info about patch_radius and block radius, please refer to the dipy website: http://nipy.org/dipy/reference/dipy.denoise.html#dipy.denoise.nlmeans.nlmeans
"""
from dipy.denoise.nlmeans import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
from numpy import asarray
data_in = asarray(data_in)
block_radius_max = min(data_in.shape) - 1
block_radius = block_radius_max if block_radius > block_radius_max else block_radius
sigma = estimate_sigma(data_in)
denoised = nlmeans(data_in,
sigma,
patch_radius=patch_radius,
block_radius=block_radius)
return denoised
def run_nonLocalMean(path_input,path_output):
print(' - running NonLocal Mean algoritm...')
finalFileName = os.path.join(path_output, utils.to_extract_filename(path_input) + d.id_non_local_mean + d.extension)
if not (os.path.exists(finalFileName)):
img = nib.load(path_input)
data = img.get_data()
newData = np.zeros(data.shape)
gradientDirections = data.shape[-1]
for index in range(gradientDirections):
print(index)
sigma = estimate_sigma(data[:, :, :, index], N=8)
newData[:, :, :, index] = nlmeans(data[:, :, :, index], sigma=sigma)
nib.save(nib.Nifti1Image(newData.astype(np.float32), img.affine), finalFileName)
return finalFileName
def _run_interface(self, runtime): import nibabel as nib import numpy as np from dipy.denoise.nlmeans import nlmeans from nipype.utils.filemanip import split_filename fname = self.inputs.in_file img = nib.load(fname) data = img.get_data() affine = img.get_affine() mask = data > 20 sigma = np.std(data[~mask]) # Calculating the standard deviation of the noise denoised_data = nlmeans(data, sigma=sigma, mask=mask) _, base, _ = split_filename(fname) nib.save(nib.Nifti1Image(denoised_data, affine), base + '_denoised.nii') return runtime
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.input])
assert_outputs_exists(parser, args, [args.output], [args.logfile])
logging.basicConfig()
log = logging.getLogger(__name__)
if args.verbose:
log.setLevel(level=logging.INFO)
else:
log.setLevel(level=logging.WARNING)
if args.logfile is not None:
log.addHandler(logging.FileHandler(args.logfile, mode='w'))
vol = nb.load(args.input)
data = vol.get_data()
if args.mask is None:
mask = np.ones(data.shape[:3], dtype=np.bool)
else:
mask = nb.load(args.mask).get_data().astype(np.bool)
sigma = args.sigma
if sigma is not None:
log.info('User supplied noise standard deviation is %s', sigma)
# Broadcast the single value to a whole 3D volume for nlmeans
sigma = np.ones(data.shape[:3]) * sigma
else:
log.info('Estimating noise')
sigma = _get_basic_sigma(vol.get_data(), log)
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=DeprecationWarning)
data_denoised = nlmeans(data,
sigma,
mask=mask,
rician=args.N > 0,
num_threads=args.nbr_processes)
nb.save(nb.Nifti1Image(data_denoised, vol.affine, vol.header), args.output)
def run(self, input_files, sigma=0, out_dir='',
out_denoised='dwi_nlmeans.nii.gz'):
""" Workflow wrapping the nlmeans denoising method.
It applies nlmeans denoise on each file found by 'globing'
``input_files`` and saves the results in a directory specified by
``out_dir``.
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
sigma : float, optional
Sigma parameter to pass to the nlmeans algorithm
(default: auto estimation).
out_dir : string, optional
Output directory (default input file directory)
out_denoised : string, optional
Name of the resuting denoised volume (default: dwi_nlmeans.nii.gz)
"""
io_it = self.get_io_iterator()
for fpath, odenoised in io_it:
if self._skip:
shutil.copy(fpath, odenoised)
logging.warning('Denoising skipped for now.')
else:
logging.info('Denoising {0}'.format(fpath))
image = nib.load(fpath)
data = image.get_data()
if sigma == 0:
logging.info('Estimating sigma')
sigma = estimate_sigma(data)
logging.debug('Found sigma {0}'.format(sigma))
denoised_data = nlmeans(data, sigma)
denoised_image = nib.Nifti1Image(
denoised_data, image.affine, image.header)
denoised_image.to_filename(odenoised)
logging.info('Denoised volume saved as {0}'.format(odenoised))
def calc(triple):
""" Calculation of one chunk - "Core-Function"
"""
values = triple[1][0]
sigmas = triple[1][1]
new_values = np.zeros([SB, SB, SB], np.float64)
ts = time.time()
if use_cython:
if use_dipy:
new_values = nlmeans.nlmeans(values, (sigmas[0],), mask=None,
patch_radius=P, block_radius=B,
rician=False, add_padding=False,
num_threads=1)
else:
new_values = denspeed.nlmeans_3d_single(values, None, sigmas,
P, B, False, None, SB)
new_values = np.sqrt(new_values)
else:
sumw = np.zeros([SB, SB, SB], np.float64)
patch_vol_size = (2*P+1)**3
add_filter = np.ones([2*P+1, 2*P+1, 2*P+1])
center_block = values[B-P: B+SB+P, B-P: B+SB+P, B-P: B+SB+P]
for m in range(P, 2*B+1-P):
for n in range(P, 2*B+1-P):
for o in range(P, 2*B+1-P):
d = (center_block - values[m-P: m+SB+P, n-P: n+SB+P, o-P: o+SB+P])**2
summs = convolve(d, add_filter, mode="constant")[P:-P, P:-P, P:-P]
sigm = convolve(sigmas[m-P: m+SB+P, n-P: n+SB+P, o-P: o+SB+P],
add_filter, mode="constant")[P:-P, P:-P, P:-P]
denom = np.sqrt(2) * (sigm / patch_vol_size)**2
ws = np.exp(-(summs / patch_vol_size) / denom)
sumw += ws
new_values += ws*values[m: m+SB, n: n+SB, o: o+SB]**2
new_values[sumw != 0] /= sumw[sumw != 0]
new_values[sumw == 0] = 0
new_values = np.sqrt(new_values)
return triple[0], new_values, time.time()-ts
def denoise(dt):
from dipy.denoise import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
import itertools
item = dt[0]
image = item[1]
mask = item[2]
sigma = estimate_sigma(image)
denoised_data = nlmeans.nlmeans(image, sigma=sigma, mask=mask)
[xp,yp,zp] = [4,4,4]
[xSize,ySize,zSize] = [denoised_data.shape[0]/xp, denoised_data.shape[1]/yp, denoised_data.shape[2]/zp]
datalist = []
for x,y,z in itertools.product(range(xp), range(yp), range(zp)):
[xS, yS, zS] = [x*xSize, y*ySize, z*zSize]
[xE, yE, zE] = [denoised_data.shape[0] if x == xp - 1 else (x+1)*xSize, \
denoised_data.shape[1] if y == yp - 1 else (y+1)*ySize, \
denoised_data.shape[2] if z == zp - 1 else (z+1)*zSize]
tup =(denoised_data[xS:xE, yS:yE, zS:zE],mask[xS:xE, yS:yE, zS:zE])
datalist.append(tup)
return datalist
def img_denoise(data, patch_rad=3, block_rad=4, n_sigma=4):
#data = np.load(img)['vol_data']
new_data = np.zeros((data.shape[1], data.shape[2], data.shape[0]))
for ch in range(data.shape[0]):
new_data[:, :, ch] = data[ch, :, :]
sigma = estimate_sigma(new_data, N=n_sigma)
#den = nlmeans(data, sigma=sigma, mask=mask, patch_radius= 1, block_radius = 1, rician= True)
den = nlmeans(new_data,
sigma=sigma,
patch_radius=patch_rad,
block_radius=block_rad,
rician=True)
#print("total time", time() - t)
res_data = np.zeros(data.shape)
for ch in range(data.shape[0]):
res_data[ch, :, :] = den[:, :, ch]
return res_data
def execution(self, context):
data_vol = aims.read(self.dwi_data.fullPath())
header = data_vol.header()
data = vol_to_array(data_vol)
sigma_vol = aims.read(self.sigma.fullPath())
sigma = vol_to_array(sigma_vol)
if self.brain_mask is not None:
brain_mask_vol = aims.read(self.brain_mask.fullPath())
brain_mask = vol_to_array(brain_mask_vol)
else:
brain_mask = None
denoised_data = nlmeans(data,
sigma,
mask=brain_mask,
patch_radius=self.patch_radius,
block_radius=self.block_radius,
rician=self.rician_noise)
denoised_data_vol = array_to_vol(denoised_data, header=header)
aims.write(denoised_data_vol, self.denoised_dwi_data.fullPath())
def denoise_dipy(input_dwi, input_bval, input_bvec, mask_image, output_dwi):
#This function uses nlmeans as part of dipy to remove noise from images
img = nib.load(input_dwi)
data = img.get_data()
mask = nib.load(mask_image).get_data()
aff = img.get_affine()
sform = img.get_sform()
qform = img.get_qform()
bvals, bvecs = read_bvals_bvecs(input_bval, input_bvec)
values = np.array(bvals)
ii = np.where(values == bvals.min())[0]
sigma = estimate_sigma(data)
sigma = np.mean(sigma[ii])
den = nlmeans(data, sigma=sigma, mask=mask)
den_img = nib.Nifti1Image(den.astype(np.float32), aff, img.header)
den_img.set_sform(sform)
den_img.set_qform(qform)
nib.save(den_img, output_dwi)
def main(file_to_denoise, param, output_file_name) :
path, file, ext = sct.extract_fname(file_to_denoise)
img = nib.load(file_to_denoise)
hdr_0 = img.get_header()
data = img.get_data()
# aff = img.get_affine()
if min(data.shape) <= 5:
sct.printv('One of the image dimensions is <= 5 : reducing the size of the block radius.')
block_radius = min(data.shape) - 1
else:
block_radius = 5 # default value
# Process for manual detecting of background
# mask = data[:, :, :] > noise_threshold
# data = data[:, :, :]
if '-std' in arguments:
sigma = std_noise
# Application of NLM filter to the image
print 'Applying Non-local mean filter...'
if param.parameter == 'Rician':
den = nlmeans(data, sigma=sigma, mask=None, rician=True, block_radius=block_radius)
else : den = nlmeans(data, sigma=sigma, mask=None, rician=False, block_radius=block_radius)
else:
# # Process for manual detecting of background
mask = data > noise_threshold
sigma = np.std(data[~mask])
# Application of NLM filter to the image
print 'Applying Non-local mean filter...'
if param.parameter == 'Rician':
den = nlmeans(data, sigma=sigma, mask=mask, rician=True, block_radius=block_radius)
else: den = nlmeans(data, sigma=sigma, mask=mask, rician=False, block_radius=block_radius)
t = time()
print("total time", time() - t)
print("vol size", den.shape)
axial_middle = data.shape[2] / 2
before = data[:, :, axial_middle].T
after = den[:, :, axial_middle].T
diff_3d = np.absolute(den.astype('f8') - data.astype('f8'))
difference = np.absolute(after.astype('f8') - before.astype('f8'))
if '-std' not in arguments:
difference[~mask[:, :, axial_middle].T] = 0
if param.verbose == 2 :
fig, ax = plt.subplots(1, 3)
ax[0].imshow(before, cmap='gray', origin='lower')
ax[0].set_title('before')
ax[1].imshow(after, cmap='gray', origin='lower')
ax[1].set_title('after')
ax[2].imshow(difference, cmap='gray', origin='lower')
ax[2].set_title('difference')
for i in range(3):
ax[i].set_axis_off()
plt.show()
#Save files
img_denoise = nib.Nifti1Image(den, None, hdr_0)
img_diff = nib.Nifti1Image(diff_3d, None, hdr_0)
if output_file_name != None :
output_file_name =output_file_name
else: output_file_name = file + '_denoised' + ext
nib.save(img_denoise,output_file_name)
nib.save(img_diff, file + '_difference' +ext)
saving_mask_start = time()
nib.save(nib.Nifti1Image(mask.astype(int), affine), mask_file)
print("[{0}] Saved mask to {2} in {1}s".format(datetime.datetime.now(),
time() - saving_mask_start,
mask_file))
else:
print("[{0}] Skipping mask save - already exists".format(
datetime.datetime.now()))
print("[{0}] Denoising".format(datetime.datetime.now()))
denoise_start = time()
from dipy.denoise import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
sigma = estimate_sigma(data)
denoised_data = nlmeans.nlmeans(data, num_threads=8, sigma=sigma, mask=mask)
print("[{0}] Finished denoising in {1}s".format(datetime.datetime.now(),
time() - denoise_start))
denoised_file = file_prefix + 'denoised_data.nii.gz'
if not op.exists(denoised_file):
print("[{0}] Saving denoising result".format(datetime.datetime.now()))
saving_denoise_start = time()
nib.save(nib.Nifti1Image(denoised_data, affine), denoised_file)
print("[{0}] Saved denoised file to {1} in {2}s".format(
datetime.datetime.now(), denoised_file,
time() - saving_denoise_start))
else:
print("[{0}] Skipping denoised file save - already exists".format(
datetime.datetime.now()))
data pre-processing step for diffusion kurtosis fitting is to denoise our data. For this, we use Dipy's non-local mean filter (see :ref:`example-denoise-nlmeans`). Note that, since the HCP-like data has a large number of diffusion-weigthed volumes, this procedure can take a couple of hours to compute the entire dataset. Therefore, to speed the run time in this example we only denoise an axial slice of the data. """ axial_slice = 40 sigma = estimate_sigma(data, N=4) mask_roi = np.zeros(data.shape[:-1], dtype=bool) mask_roi[:, :, axial_slice] = mask[:, :, axial_slice] den = nlmeans(data, sigma=sigma, mask=mask_roi) den = den[:, :, axial_slice, :] """ Now that we have loaded and prepared the voxels to process we can go forward with the voxel reconstruction. This can be done by first instantiating the DiffusionKurtosisModel in the following way: """ dkimodel = dki.DiffusionKurtosisModel(gtab) """ To fit the data using the defined model object, we call the ``fit`` function of this object: """
"""
Calling the main function ``non_local_means``
"""
den = non_local_means(
data,
sigma=sigma,
mask=mask,
patch_radius=1,
block_radius=1,
rician=True)
print("total time", time() - t)
t = time()
den = nlmeans(data, sigma=sigma, mask=mask, patch_radius= 1, block_radius = 1, rician= True)
print("total time", time() - t)
"""
Let us plot the axial slice of the denoised output
"""
axial_middle = data.shape[2] / 2
before = data[:, :, axial_middle].T
after = den[:, :, axial_middle].T
difference = np.abs(after.astype('f8') - before.astype('f8'))
difference[~mask[:, :, axial_middle].T] = 0
def nlmeans_proxy(in_file, settings,
snr=None,
smask=None,
nmask=None,
out_file=None):
"""
Uses non-local means to denoise 4D datasets
"""
from dipy.denoise.nlmeans import nlmeans
from scipy.ndimage.morphology import binary_erosion
from scipy import ndimage
if out_file is None:
fname, fext = op.splitext(op.basename(in_file))
if fext == '.gz':
fname, fext2 = op.splitext(fname)
fext = fext2 + fext
out_file = op.abspath('./%s_denoise%s' % (fname, fext))
img = nb.load(in_file)
hdr = img.header
data = img.get_data()
aff = img.affine
if data.ndim < 4:
data = data[..., np.newaxis]
data = np.nan_to_num(data)
if data.max() < 1.0e-4:
raise RuntimeError('There is no signal in the image')
df = 1.0
if data.max() < 1000.0:
df = 1000. / data.max()
data *= df
b0 = data[..., 0]
if smask is None:
smask = np.zeros_like(b0)
smask[b0 > np.percentile(b0, 85.)] = 1
smask = binary_erosion(
smask.astype(np.uint8), iterations=2).astype(np.uint8)
if nmask is None:
nmask = np.ones_like(b0, dtype=np.uint8)
bmask = settings['mask']
if bmask is None:
bmask = np.zeros_like(b0)
bmask[b0 > np.percentile(b0[b0 > 0], 10)] = 1
label_im, nb_labels = ndimage.label(bmask)
sizes = ndimage.sum(bmask, label_im, range(nb_labels + 1))
maxidx = np.argmax(sizes)
bmask = np.zeros_like(b0, dtype=np.uint8)
bmask[label_im == maxidx] = 1
nmask[bmask > 0] = 0
else:
nmask = np.squeeze(nmask)
nmask[nmask > 0.0] = 1
nmask[nmask < 1] = 0
nmask = nmask.astype(bool)
nmask = binary_erosion(nmask, iterations=1).astype(np.uint8)
den = np.zeros_like(data)
est_snr = True
if snr is not None:
snr = [snr] * data.shape[-1]
est_snr = False
else:
snr = []
for i in range(data.shape[-1]):
d = data[..., i]
if est_snr:
s = np.mean(d[smask > 0])
n = np.std(d[nmask > 0])
snr.append(s / n)
den[..., i] = nlmeans(d, snr[i], **settings)
den = np.squeeze(den)
den /= df
nb.Nifti1Image(den.astype(hdr.get_data_dtype()), aff,
hdr).to_filename(out_file)
return out_file, snr
def test_nlmeans_4d_3dsigma():
# Input is 4D data and 3D sigma
data = np.ones((10,10,10,5))
sigma = np.ones((10,10,10))
nlmeans(data, sigma)
def sparky(sparki=True, dipyi=False, plot=False, n_cores=8):
"""" Runs the NLMeans on the predefined data
:param sparki: bool
True: spark implementation is used
:param dipyi: bool
True: dipy implementation is used
:param plot: bool
True: images of the processed data is written to the
predefined folder
:param n_cores: int
number of cores of the used system
used for overhead calculation
:return:
sparkyout: result of spark implementation (retransformed out)
dipynlmeans: result of dipy implementation
data: raw data
out: output of spark implementation
t_ov: time overhead of spark implementation
t_core: runtime of calculation of spark implementation
t_core_std: std of calc runtime of calculation spark implementation
t_dipy: runtime of dipy implementation
"""
t_ov = 0
t_core = 0
t_core_std = 0
t_dipy = 0
out = []
data = []
sparkyout = []
dipynlmeans = []
if sparki:
data = load_data(name=dataset_name)
conf = SparkConf()
conf.setMaster("local[*]")
conf.setAppName("NLMeans")
conf.set("spark.default.parallelism", "30")
t_start = time.time()
sc = SparkContext(conf=conf, batchSize=batchSize)
rdd = sc.parallelize(data, 30)
rdd = rdd.flatMap(superblock_mapper).reduceByKey(lambda p, q: p+q)\
.flatMap(stitch_mapper).map(calc)
out = rdd.collect()
sc.stop()
t_ov = time.time()-t_start
sparkyout = retransform_data(out)
data, sigma = load_data(flat=False, name=dataset_name)
if dipyi:
t_start = time.time()
dipynlmeans = nlmeans.nlmeans(np.copy(data), sigma, mask=None,
patch_radius=P, block_radius=B, rician=False)
t_dipy = time.time()-t_start
if sparki:
t_temp = []
for triple in out:
t_temp.append(triple[2])
t_core = np.mean(t_temp)
t_core_std = np.std(t_temp)
print("\n\nTimes-----------------------------")
print("Time pyspark overall: %.2fs" % t_ov)
print("Time pyspark overhead: %.2fs" % (t_ov - t_core * np.product(np.array(sh)/SB)/n_cores))
print("Time dipy: %.2fs" % t_dipy)
# Save images for visual inspection
if plot:
if len(sparkyout):
imsave(path_to_folder + "/images/den_sparky.png", sparkyout[:, :, int(sh[2]/2)])
if len(dipynlmeans):
imsave(path_to_folder + "/images/den_dipy.png", dipynlmeans[:, :, int(sh[2]/2)])
if len(sparkyout) and len(dipynlmeans):
diff = sparkyout-dipynlmeans
print("Mean difference spark/dipy: %.3f" % (np.mean(np.abs(diff))))
diff[diff < 0] = 0
imsave(path_to_folder + "/images/den_diff_sp_di.png", diff[:, :, int(sh[2]/2)])
diff = dipynlmeans-sparkyout
diff[diff < 0] = 0
imsave(path_to_folder + "/images/den_diff_di_sp.png", diff[:, :, int(sh[2]/2)])
if not isinstance(data, list):
imsave(path_to_folder + "/images/den_data.png", data[:, :, int(sh[2]/2)])
if len(sparkyout) and not isinstance(data, list):
diff = np.abs(sparkyout-data)
print("Mean difference spark/data: %.3f" % (np.mean(diff)))
imsave(path_to_folder + "/images/den_data_sp_diff.png", diff[:, :, int(sh[2]/2)])
if len(dipynlmeans) and not isinstance(data, list):
diff = np.abs(dipynlmeans-data)
print("Mean difference dipy/data: %.3f" % (np.mean(diff)))
imsave(path_to_folder + "/images/den_data_di_diff.png", diff[:, :, int(sh[2]/2)])
return sparkyout, dipynlmeans, data, out, t_ov, t_core, t_core_std, t_dipy
def test_nlmeans_static():
S0 = 100 * np.ones((20, 20, 20), dtype='f8')
S0n = nlmeans(S0, sigma=np.ones((20, 20, 20)), rician=False)
assert_array_almost_equal(S0, S0n)