def __init__(self,
data,
bvecs,
bvals,
params_file=None,
axial_diffusivity=AD,
radial_diffusivity=RD,
affine=None,
mask=None,
scaling_factor=SCALE_FACTOR,
sub_sample=None,
over_sample=None,
verbose=True,
mode='relative_signal',
n_canonicals=2):
"""
Initialize a MultiCanonicalTensorModel class instance.
"""
# Initialize the super-class:
CanonicalTensorModel.__init__(self,
data,
bvecs,
bvals,
params_file=params_file,
axial_diffusivity=axial_diffusivity,
radial_diffusivity=radial_diffusivity,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
over_sample=over_sample,
mode=mode,
verbose=verbose)
self.n_canonicals = n_canonicals
def __init__(self,
data,
bvecs,
bvals,
params_file=None,
axial_diffusivity=AD,
radial_diffusivity=RD,
affine=None,
mask=None,
scaling_factor=SCALE_FACTOR,
sub_sample=None,
over_sample=None,
verbose=True,
mode='relative_signal',
n_canonicals=2):
"""
Initialize a MultiCanonicalTensorModel class instance.
"""
# Initialize the super-class:
CanonicalTensorModel.__init__(self,
data,
bvecs,
bvals,
params_file=params_file,
axial_diffusivity=axial_diffusivity,
radial_diffusivity=radial_diffusivity,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
over_sample=over_sample,
mode=mode,
verbose=verbose)
self.n_canonicals = n_canonicals
def __init__(self,
data,
bvecs,
bvals,
calibration_roi,
params_file=None,
affine=None,
mask=None,
scaling_factor=SCALE_FACTOR,
sub_sample=None,
over_sample=None,
verbose=True):
"""
Initialize a CalibratedCanonicalTensorModel instance.
Parameters
----------
calibration_roi: full path to a nifti file containing zeros everywhere,
except ones where the calibration ROI is defined. Should be already
registered and xformed to the DWI data resolution/alignment.
"""
# Initialize the super-class, we set AD and RD to None, to prevent
# things from going forward before calibration has occurred. This will
# probably cause an error to be thrown, if calibration doesn't
# happen. We might want to catch that error and explain it to the
# user...
CanonicalTensorModel.__init__(self,
data,
bvecs,
bvals,
params_file=params_file,
axial_diffusivity=None,
radial_diffusivity=None,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
over_sample=over_sample,
verbose=verbose)
# This is used to initialize the optimization in each voxel.
# The orientation parameters are chosen to be close to horizontal.
self.start_params = np.pi/2, 0, 0.5, 1.5, 0
#theta, phi, beta, lambda1, lambda2
self.calibration_roi = calibration_roi
def __init__(self,
data,
bvecs,
bvals,
calibration_roi,
params_file=None,
affine=None,
mask=None,
scaling_factor=SCALE_FACTOR,
sub_sample=None,
over_sample=None,
verbose=True):
"""
Initialize a CalibratedCanonicalTensorModel instance.
Parameters
----------
calibration_roi: full path to a nifti file containing zeros everywhere,
except ones where the calibration ROI is defined. Should be already
registered and xformed to the DWI data resolution/alignment.
"""
# Initialize the super-class, we set AD and RD to None, to prevent
# things from going forward before calibration has occurred. This will
# probably cause an error to be thrown, if calibration doesn't
# happen. We might want to catch that error and explain it to the
# user...
CanonicalTensorModel.__init__(self,
data,
bvecs,
bvals,
params_file=params_file,
axial_diffusivity=None,
radial_diffusivity=None,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
over_sample=over_sample,
verbose=verbose)
# This is used to initialize the optimization in each voxel.
# The orientation parameters are chosen to be close to horizontal.
self.start_params = np.pi / 2, 0, 0.5, 1.5, 0
#theta, phi, beta, lambda1, lambda2
self.calibration_roi = calibration_roi
def test_predict():
"""
Test the CanonicalTensorModel predict method
"""
# 1000 'voxels' with constant data in each one in all directions (+b0):
data = (np.random.rand(10 * 10 * 10).reshape(10 * 10 * 10, 1) + np.zeros(
(10 * 10 * 10, 160))).reshape(10, 10, 10, 160)
CTM = CanonicalTensorModel(data,
data_path + 'dwi.bvecs',
data_path + 'dwi.bvals',
params_file=tempfile.NamedTemporaryFile().name)
bvecs = CTM.bvecs[:, CTM.b_idx]
new_bvecs = bvecs[:, :4]
prediction = CTM.predict(new_bvecs)
npt.assert_array_equal(prediction, CTM.fit[..., :4])
def test_predict():
"""
Test the CanonicalTensorModel predict method
"""
# 1000 'voxels' with constant data in each one in all directions (+b0):
data = (np.random.rand(10 * 10 * 10).reshape(10 * 10 * 10, 1) +
np.zeros((10 * 10 * 10, 160))).reshape(10,10,10,160)
CTM = CanonicalTensorModel(data,
data_path + 'dwi.bvecs',
data_path + 'dwi.bvals',
params_file=tempfile.NamedTemporaryFile().name)
bvecs = CTM.bvecs[:, CTM.b_idx]
new_bvecs = bvecs[:,:4]
prediction = CTM.predict(new_bvecs)
npt.assert_array_equal(prediction, CTM.fit[...,:4])
def __init__(self,
tissue_fraction,
data,
bvecs,
bvals,
alpha1,
alpha2,
water_D=3,
gray_D=1,
params_file=None,
axial_diffusivity=AD,
radial_diffusivity=RD,
affine=None,
mask=None,
scaling_factor=SCALE_FACTOR,
sub_sample=None,
over_sample=None,
verbose=True):
# Initialize the super-class:
CanonicalTensorModel.__init__(self,
data,
bvecs,
bvals,
params_file=params_file,
axial_diffusivity=axial_diffusivity,
radial_diffusivity=radial_diffusivity,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
over_sample=over_sample,
verbose=verbose)
self.tissue_fraction = ni.load(tissue_fraction).get_data()
# Convert the diffusivity constants to signal attenuation:
self.gray_D = np.exp(-self.bvals[self.b_idx][0] * gray_D)
self.water_D = np.exp(-self.bvals[self.b_idx][0] * water_D)
# We're going to grid-search over these:
self.alpha1 = alpha1
self.alpha2 = alpha2
def __init__(self,
data,
bvecs,
bvals,
solver=None,
solver_params=None,
params_file=None,
axial_diffusivity=AD,
radial_diffusivity=RD,
affine=None,
mask=None,
scaling_factor=SCALE_FACTOR,
sub_sample=None,
over_sample=None,
mode='relative_signal',
verbose=True,
force_recompute=False):
"""
Initialize SparseDeconvolutionModel class instance.
"""
# Initialize the super-class:
CanonicalTensorModel.__init__(self,
data,
bvecs,
bvals,
params_file=params_file,
axial_diffusivity=axial_diffusivity,
radial_diffusivity=radial_diffusivity,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
over_sample=over_sample,
mode=mode,
verbose=verbose)
# Name the params file, if needed:
this_class = str(self.__class__).split("'")[-2].split('.')[-1]
self.params_file = params_file_resolver(self,
this_class,
params_file=params_file)
# Deal with the solver stuff:
# For now, the default is ElasticNet:
if solver is None:
this_solver = sklearn_solvers['ElasticNet']
# Assume it's a key into the dict:
elif isinstance(solver, str):
this_solver = sklearn_solvers[solver]
# Assume it's a class:
else:
this_solver = solver
# This will be passed as kwarg to the solver initialization:
if solver_params is None:
# This seems to be good for our data:
alpha = 0.0005
l1_ratio = 0.6
self.solver_params = dict(alpha=alpha,
l1_ratio=l1_ratio,
fit_intercept=True,
positive=True)
else:
self.solver_params = solver_params
# We reuse the same class instance in all voxels:
self.solver = this_solver(**self.solver_params)
# This is only here for now, but should be implemented in the
# base-class (all the way up?) and generalized in a wrapper to model
# params, I believe.
self.force_recompute = force_recompute
def test_CanonicalTensorModel():
"""
Test the simple canonical + sphere model.
"""
# 1000 'voxels' with constant data in each one in all directions (+b0):
data = (np.random.rand(10 * 10 * 10).reshape(10 * 10 * 10, 1) + np.zeros(
(10 * 10 * 10, 160))).reshape(10, 10, 10, 160)
CTM = CanonicalTensorModel(data,
data_path + 'dwi.bvecs',
data_path + 'dwi.bvals',
params_file=tempfile.NamedTemporaryFile().name)
# XXX Smoke testing only
npt.assert_equal(CTM.fit.shape, CTM.signal.shape)
mask_array = np.zeros(ni.load(data_path + 'small_dwi.nii.gz').shape[:3])
# Only two voxels:
mask_array[1:3, 1:3, 1:3] = 1
# Fit this on some real dwi data
for mode in ['signal_attenuation', 'relative_signal', 'normalize', 'log']:
for params_file in [None, tempfile.NamedTemporaryFile().name, 'temp']:
CTM = CanonicalTensorModel(data_path + 'small_dwi.nii.gz',
data_path + 'dwi.bvecs',
data_path + 'dwi.bvals',
mask=mask_array,
params_file=params_file,
mode=mode)
# XXX Smoke testing only:
npt.assert_equal(CTM.fit.shape, CTM.signal.shape)
npt.assert_equal(CTM.principal_diffusion_direction.shape,
CTM.signal.shape[:3] + (3, ))
npt.assert_equal(CTM.fractional_anisotropy.shape,
CTM.signal.shape[:3])
# Test over-sampling:
for over_sample in [362, 246]: # Over-sample from dipy and from
# camino-points
CTM = CanonicalTensorModel(
data_path + 'small_dwi.nii.gz',
data_path + 'dwi.bvecs',
data_path + 'dwi.bvals',
mask=mask_array,
params_file=tempfile.NamedTemporaryFile().name,
over_sample=over_sample,
mode=mode)
# XXX Smoke testing only:
npt.assert_equal(CTM.fit.shape, CTM.signal.shape)
# This shouldn't be possible, because we don't have a sphere with 151
# samples handy:
npt.assert_raises(
ValueError, CanonicalTensorModel, data_path + 'small_dwi.nii.gz',
data_path + 'dwi.bvecs', data_path + 'dwi.bvals',
**dict(mask=mask_array,
params_file=tempfile.NamedTemporaryFile().name,
over_sample=151))
# If you provide an unrecognized mode, you get an error:
npt.assert_raises(
ValueError, CanonicalTensorModel, data_path + 'small_dwi.nii.gz',
data_path + 'dwi.bvecs', data_path + 'dwi.bvals',
**dict(mask=mask_array,
mode='crazy_mode',
params_file=tempfile.NamedTemporaryFile().name))