def test_sparse_nnls():
# Set up the regression:
beta = np.random.rand(10)
X = np.random.randn(1000, 10)
y = np.dot(X, beta)
beta_hat = sparse_nnls(y, X)
beta_hat_sparse = sparse_nnls(y, sps.csr_matrix(X))
# We should be able to get back the right answer for this simple case
npt.assert_array_almost_equal(beta, beta_hat, decimal=1)
npt.assert_array_almost_equal(beta, beta_hat_sparse, decimal=1)
def test_sparse_nnls():
# Set up the regression:
beta = np.random.rand(10)
X = np.random.randn(1000, 10)
y = np.dot(X, beta)
beta_hat = sparse_nnls(y, X)
beta_hat_sparse = sparse_nnls(y, sps.csr_matrix(X))
# We should be able to get back the right answer for this simple case
npt.assert_array_almost_equal(beta, beta_hat, decimal=1)
npt.assert_array_almost_equal(beta, beta_hat_sparse, decimal=1)
def fit(self, data, streamline, affine=None, evals=[0.001, 0, 0], sphere=None):
"""
Fit the LiFE FiberModel for data and a set of streamlines associated
with this data
Parameters
----------
data : 4D array
Diffusion-weighted data
streamline : list
A bunch of streamlines
affine: 4 by 4 array (optional)
The affine to go from the streamline coordinates to the data
coordinates. Defaults to use `np.eye(4)`
evals : list (optional)
The eigenvalues of the tensor response function used in constructing
the model signal. Default: [0.001, 0, 0]
sphere: `dipy.core.Sphere` instance, or False
Whether to approximate (and cache) the signal on a discrete
sphere. This may confer a significant speed-up in setting up the
problem, but is not as accurate. If `False`, we use the exact
gradients along the streamlines to calculate the matrix, instead of
an approximation.
Returns
-------
FiberFit class instance
"""
if affine is None:
affine = np.eye(4)
life_matrix, vox_coords = self.setup(streamline, affine, evals=evals, sphere=sphere)
to_fit, weighted_signal, b0_signal, relative_signal, mean_sig, vox_data = self._signals(data, vox_coords)
beta = opt.sparse_nnls(to_fit, life_matrix)
return FiberFit(
self,
life_matrix,
vox_coords,
to_fit,
beta,
weighted_signal,
b0_signal,
relative_signal,
mean_sig,
vox_data,
streamline,
affine,
evals,
)
def fit(self,
data,
streamline,
affine=None,
evals=[0.001, 0, 0],
sphere=None):
"""
Fit the LiFE FiberModel for data and a set of streamlines associated
with this data
Parameters
----------
data : 4D array
Diffusion-weighted data
streamline : list
A bunch of streamlines
affine: 4 by 4 array (optional)
The affine to go from the streamline coordinates to the data
coordinates. Defaults to use `np.eye(4)`
evals : list (optional)
The eigenvalues of the tensor response function used in constructing
the model signal. Default: [0.001, 0, 0]
sphere: `dipy.core.Sphere` instance, or False
Whether to approximate (and cache) the signal on a discrete
sphere. This may confer a significant speed-up in setting up the
problem, but is not as accurate. If `False`, we use the exact
gradients along the streamlines to calculate the matrix, instead of
an approximation.
Returns
-------
FiberFit class instance
"""
if affine is None:
affine = np.eye(4)
life_matrix, vox_coords = \
self.setup(streamline, affine, evals=evals, sphere=sphere)
(to_fit, weighted_signal, b0_signal, relative_signal, mean_sig,
vox_data) = self._signals(data, vox_coords)
beta = opt.sparse_nnls(to_fit, life_matrix)
return FiberFit(self, life_matrix, vox_coords, to_fit, beta,
weighted_signal, b0_signal, relative_signal, mean_sig,
vox_data, streamline, affine, evals)
def fit(self, data, streamline, affine, evals=[0.001, 0, 0], sphere=None):
"""
Fit the LiFE FiberModel for data and a set of streamlines associated
with this data
Parameters
----------
data : 4D array
Diffusion-weighted data
streamline : list
A bunch of streamlines
affine : array_like (4, 4)
The mapping from voxel coordinates to streamline points.
The voxel_to_rasmm matrix, typically from a NIFTI file.
evals : list (optional)
The eigenvalues of the tensor response function used in
constructing the model signal. Default: [0.001, 0, 0]
sphere: `dipy.core.Sphere` instance, or False
Whether to approximate (and cache) the signal on a discrete
sphere. This may confer a significant speed-up in setting up the
problem, but is not as accurate. If `False`, we use the exact
gradients along the streamlines to calculate the matrix, instead of
an approximation.
Returns
-------
FiberFit class instance
"""
if affine is None:
affine = np.eye(4)
sl_len = np.array([len(s) for s in streamline])
if np.any(sl_len < 2):
raise ValueError(
"Input contains streamlines with only one node."
" The LiFE model cannot be fit with these streamlines included."
)
life_matrix, vox_coords = \
self.setup(streamline, affine, evals=evals, sphere=sphere)
(to_fit, weighted_signal, b0_signal, relative_signal, mean_sig,
vox_data) = self._signals(data, vox_coords)
beta = opt.sparse_nnls(to_fit, life_matrix)
return FiberFit(self, life_matrix, vox_coords, to_fit, beta,
weighted_signal, b0_signal, relative_signal, mean_sig,
vox_data, streamline, affine, evals)
def fit(self,
data,
streamline,
affine,
evals=[0.001, 0, 0],
sphere=None,
processes=1,
verbose=False):
"""
Fit the LiFE FiberModel for data and a set of streamlines associated
with this data
Parameters
----------
data : 4D array
Diffusion-weighted data
streamline : list
A bunch of streamlines
affine : array_like (4, 4)
The mapping from voxel coordinates to streamline points.
The voxel_to_rasmm matrix, typically from a NIFTI file.
evals : list (optional)
The eigenvalues of the tensor response function used in
constructing the model signal. Default: [0.001, 0, 0]
sphere: `dipy.core.Sphere` instance, or False
Whether to approximate (and cache) the signal on a discrete
sphere. This may confer a significant speed-up in setting up the
problem, but is not as accurate. If `False`, we use the exact
gradients along the streamlines to calculate the matrix, instead of
an approximation.
Returns
-------
FiberFit class instance
"""
if affine is None:
affine = np.eye(4)
life_matrix, vox_coords = \
self.setup(streamline, affine, evals=evals, sphere=sphere, processes=processes, verbose=verbose)
duration1 = time()
(to_fit, weighted_signal, b0_signal, relative_signal, mean_sig,
vox_data) = self._signals(data, vox_coords)
if verbose:
print("Signals computed in " + str(time() - duration1) + "s")
duration2 = time()
beta = opt.sparse_nnls(to_fit, life_matrix)
if verbose:
print("beta matrix computed in " + str(time() - duration2) + "s")
"""
nanvals=0
for i in range(np.shape(relative_signal)[0]):
for j in range(np.shape(relative_signal)[1]):
if math.isnan(relative_signal[i,j]):
nanvals += 1
print(str(nanvals) + " out of " + str(np.size(relative_signal)))
nanvals = 0
for i in range(np.shape(mean_sig)[0]):
if math.isnan(mean_sig[i]):
nanvals += 1
print(str(nanvals) + " out of " + str(np.size(mean_sig)))
"""
return FiberFit(self, life_matrix, vox_coords, to_fit, beta,
weighted_signal, b0_signal, relative_signal, mean_sig,
vox_data, streamline, affine, evals)