def subsample(bvecs, n_dirs, elec_points=None):
"""
Generate a sub-sample of size n of directions from the provided bvecs
Parameters
----------
bvecs: int array (n by 3), a set of cartesian coordinates for a set of
bvecs
n_dirs: int, how many bvecs to sub-sample from this set.
elec_points: optional, a set of points read from the camino points, using
Jones (2003) algorithm for electro-static repulsion
Returns
-------
[x,y,z]: The coordinates of the sub-sample
bvec_idx: The indices into the original bvecs that would give this
sub-sample
Notes
-----
Directions are chosen from the camino-generated electro-static repulsion
points in the directory camino_pts.
"""
if elec_points is None:
# We need a n by 3 here:
xyz = ozu.get_camino_pts(n_dirs).T
else:
xyz = elec_points.copy()
# Rotate all the points to align with the seed, the bvec relative to which
# all the rest are chosen (lots going on in this one line):
new_points = np.array(bvecs *
ozu.calculate_rotation(
bvecs[np.ceil(np.random.rand() *
xyz.shape[0]).astype(int)],
xyz[0]))
sample_bvecs = np.zeros((3, n_dirs))
bvec_idx = []
for vec in xrange(n_dirs):
this = new_points[vec]
delta = np.zeros(bvecs.shape[0])
for j in xrange(bvecs.shape[0]):
delta[j] = ozu.vector_angle(this, bvecs[j])
this_idx = np.where(delta==np.min(delta))
bvec_idx.append(this_idx)
sample_bvecs[:, vec] = bvecs[this_idx]
return sample_bvecs, np.array(bvec_idx).squeeze()
def test_subsample():
"""
Test subsampling
"""
# Sub-sampling 100 out of a random collection of 150 unit-vectors:
bvecs = np.array([ozu.unit_vector(x) for x in np.random.randn(3,150)])
# The following runs through most of the module w/o verifying correctness:
sub_sample = ozb.subsample(bvecs, 100)
# optionally, you can provide elec_points as input. Here we test this with
# the same points
sub_sample = ozb.subsample(bvecs, 100, elec_points=ozu.get_camino_pts(100).T)
def test_subsample():
"""
Test subsampling
"""
# Sub-sampling 100 out of a random collection of 150 unit-vectors:
bvecs = np.array([ozu.unit_vector(x) for x in np.random.randn(3, 150)])
# The following runs through most of the module w/o verifying correctness:
sub_sample = ozb.subsample(bvecs, 100)
# optionally, you can provide elec_points as input. Here we test this with
# the same points
sub_sample = ozb.subsample(bvecs,
100,
elec_points=ozu.get_camino_pts(100).T)
def test_fodf_emd():
"""
Test EMD on fODFs
"""
bvecs = ozu.get_camino_pts(150)
fodf1 = np.zeros(bvecs.shape[-1])
fodf2 = np.zeros(bvecs.shape[-1])
ii = np.random.randint(0, fodf1.shape[0])
jj = np.random.randint(0, fodf2.shape[0])
fodf1[ii] = 1
fodf2[jj] = 1
emd1 = pn.fODF_EMD(fodf1, fodf2, bvecs1=bvecs, bvecs2=bvecs)
angles = np.arccos(np.dot(bvecs.T, bvecs))
angles[np.isnan(angles)] = 0
angles = np.min(np.array([angles, np.pi - angles]), 0)
angles = angles.ravel()
emd2 = pn.fODF_EMD(fodf1, fodf2, bvecs1=bvecs, dist=angles)
npt.assert_equal(emd1, emd2)
def test_fodf_emd():
"""
Test EMD on fODFs
"""
bvecs = ozu.get_camino_pts(150)
fodf1 = np.zeros(bvecs.shape[-1])
fodf2 = np.zeros(bvecs.shape[-1])
ii = np.random.randint(0, fodf1.shape[0])
jj = np.random.randint(0, fodf2.shape[0])
fodf1[ii] = 1
fodf2[jj] = 1
emd1 = pn.fODF_EMD(fodf1, fodf2, bvecs1=bvecs, bvecs2=bvecs)
angles = np.arccos(np.dot(bvecs.T, bvecs))
angles[np.isnan(angles)] = 0
angles = np.min(np.array([angles, np.pi - angles]), 0)
angles = angles.ravel()
emd2 = pn.fODF_EMD(fodf1, fodf2, bvecs1=bvecs, dist=angles)
npt.assert_equal(emd1, emd2)
def subsample(bvecs, n_dirs, elec_points=None):
"""
Generate a sub-sample of size n of directions from the provided bvecs
Parameters
----------
bvecs: int array (n by 3), a set of cartesian coordinates for a set of
bvecs
n_dirs: int, how many bvecs to sub-sample from this set.
elec_points: optional, a set of points read from the camino points, using
Jones (2003) algorithm for electro-static repulsion
Returns
-------
[x,y,z]: The coordinates of the sub-sample
bvec_idx: The indices into the original bvecs that would give this
sub-sample
Notes
-----
Directions are chosen from the camino-generated electro-static repulsion
points in the directory camino_pts.
"""
if elec_points is None:
# We need a n by 3 here:
xyz = ozu.get_camino_pts(n_dirs).T
else:
xyz = elec_points.copy()
# Rotate all the points to align with the seed, the bvec relative to which
# all the rest are chosen (lots going on in this one line):
rot_to_first = ozu.calculate_rotation(
bvecs[:, np.ceil(np.random.randint(xyz.shape[0]))],
xyz[0])
new_points = np.dot(rot_to_first, bvecs).T
sample_bvecs = np.zeros((3, n_dirs))
bvec_idx = []
potential_indices = np.arange(bvecs.shape[-1])
for vec in xrange(n_dirs):
this = new_points[vec]
delta = np.zeros(potential_indices.shape)
for j in range(delta.shape[0]):
delta[j] = ozu.vector_angle(this, bvecs[:, j])
this_idx = np.where(delta==np.min(delta))
bvec_idx.append(potential_indices[this_idx])
sample_bvecs[:, vec] = np.squeeze(bvecs[:, this_idx])
# Remove bvecs that you've used, so that you don't have them more than
# once:
bvecs = np.hstack([bvecs[:, :this_idx[0]],bvecs[:, this_idx[0]+1:]])
potential_indices = np.hstack([potential_indices[:this_idx[0]],
potential_indices[this_idx[0]+1:]])
return sample_bvecs, np.array(bvec_idx).squeeze()
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,
mode='relative_signal',
iso_diffusivity=None,
verbose=True):
"""
Initialize a CanonicalTensorModel class instance.
Parameters
----------
params_file: str, optional
full path to the name of the file in which to save the model
parameters, once a model is fit.
over_sample: optional, int.
Sometimes you might want to probe the sphere at a higher resolution
than that provided by the measurement. You can do that using two
possible sources of information. The first is the camino points,
which ship together with osmosis and are used for the boot-strapping
(see osmosis.boot). These are used for integers smaller than 150,
for 246 and for 755. The other sources of information are the
symmetric spheres provided as part of dipy. These are used if 362 or
642 are provided. Note that these might be problematic, because they
contain polar opposite points, so use with caution.
mode: string, optional
This can take one of several values, determining the form of the
regressors and the form of the signal to fit to.
'relative_signal': The fit is to $\frac{S}{S_0}$ and the regressors
are the relative signal predicted for a canonical tensor and the
relative signal predicted for a isotropic diffusivity compartment:
.. math::
\frac{S}{S_0} = \beta_1 e^{-bD} + \beta_2 e^{-b\vec{b}Q\vec{b}^t}
'signal_attenuation': The fit is to $1-\frac{S}{S_0}$ and the
regressors are the signal attenuation for the canonical tensor and the
signal attenuation due to isotropic diffusion:
.. math::
1-\frac{S}{S_0} = \beta_1 (1-e^{-bD}) + \beta_2 (1-e^{-b\vec{b} Q \vec{b}^t})
'normalize': in this case, we fit to $\frac{S}{S_0}$, but our regressor
set is normalized to maximum of 1 in each columns. This affects the
values of the weights, and also the goodness-of-fit (because of the
relative scaling of the regressors in the OLS). The equation in
this case is:
.. math::
\frac{S}{S_0} = \beta_1 + \beta_2 \frac{e^{-b\vec{b} Q \vec{b}^t}}{max(e^{-b\vec{b} Q \vec{b}^t})}
'log': in this case, we fit to $log(\frac{S}{S_0})$ and our regressors
are the exponents:
.. math::
log(\frac{S}{S_0}) = \beta_1 -bD + \beta_1 -b\vec{b}Q\vec{b}^t
iso_diffusivity: optional, float
What the diffusivity of the isotropic component should be set
to. This is irrelevant for the 'normalize' mode. Defaults to be
equal to the axial_diffusivity
"""
# Initialize the super-class:
BaseModel.__init__(self,
data,
bvecs,
bvals,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
params_file=params_file,
verbose=verbose)
self.ad = axial_diffusivity
self.rd = radial_diffusivity
if iso_diffusivity is None:
iso_diffusivity = axial_diffusivity
self.iso_diffusivity = iso_diffusivity
if over_sample is not None:
# Symmetric spheres from dipy:
if over_sample in[362, 642]:
# We want to get these vertices:
verts = dpd.get_sphere('symmetric%s'%over_sample).vertices
# Their convention is transposed relative to ours:
self.rot_vecs = verts.T
elif (isinstance(over_sample, int) and (over_sample<=150 or
over_sample in [246,755])):
self.rot_vecs = ozu.get_camino_pts(over_sample)
elif over_sample== 'quad132':
pp = os.path.split(oz.__file__)[0]+'/data/SparseKernelModel/'
self.rot_vecs = np.loadtxt(pp + 'qsph1-16-132DP.dat')[:,:-1].T
else:
e_s = "You asked to sample the sphere in %s"%over_sample
e_s += " different directions. Can only do that for n<=150"
e_s += " or n in [246, 362, 642, 755]"
raise ValueError(e_s)
else:
self.rot_vecs = self.bvecs[:,self.b_idx]
if mode not in ['relative_signal',
'signal_attenuation',
'normalize',
'log']:
raise ValueError("Not a recognized mode of CanonicalTensorModel")
self.mode = mode
self.iso_diffusivity = iso_diffusivity
def subsample(bvecs, n_dirs, elec_points=None):
"""
Generate a sub-sample of size n of directions from the provided bvecs
Parameters
----------
bvecs: int array (n by 3), a set of cartesian coordinates for a set of
bvecs
n_dirs: int, how many bvecs to sub-sample from this set.
elec_points: optional, a set of points read from the camino points, using
Jones (2003) algorithm for electro-static repulsion
Returns
-------
[x,y,z]: The coordinates of the sub-sample
bvec_idx: The indices into the original bvecs that would give this
sub-sample
Notes
-----
Directions are chosen from the camino-generated electro-static repulsion
points in the directory camino_pts.
"""
if elec_points is None:
# We need a n by 3 here:
xyz = ozu.get_camino_pts(n_dirs).T
else:
xyz = elec_points.copy()
# Rotate all the points to align with the seed, the bvec relative to which
# all the rest are chosen (lots going on in this one line):
rot_to_first = ozu.calculate_rotation(
bvecs[:, np.ceil(np.random.randint(xyz.shape[0]))], xyz[0])
new_points = np.dot(rot_to_first, bvecs).T
sample_bvecs = np.zeros((3, n_dirs))
bvec_idx = []
potential_indices = np.arange(bvecs.shape[-1])
for vec in xrange(n_dirs):
this = new_points[vec]
delta = np.zeros(potential_indices.shape)
for j in range(delta.shape[0]):
delta[j] = ozu.vector_angle(this, bvecs[:, j])
this_idx = np.where(delta == np.min(delta))
bvec_idx.append(potential_indices[this_idx])
sample_bvecs[:, vec] = np.squeeze(bvecs[:, this_idx])
# Remove bvecs that you've used, so that you don't have them more than
# once:
bvecs = np.hstack([bvecs[:, :this_idx[0]], bvecs[:, this_idx[0] + 1:]])
potential_indices = np.hstack([
potential_indices[:this_idx[0]],
potential_indices[this_idx[0] + 1:]
])
return sample_bvecs, np.array(bvec_idx).squeeze()
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,
mode='relative_signal',
iso_diffusivity=None,
verbose=True):
"""
Initialize a CanonicalTensorModel class instance.
Parameters
----------
params_file: str, optional
full path to the name of the file in which to save the model
parameters, once a model is fit.
over_sample: optional, int.
Sometimes you might want to probe the sphere at a higher resolution
than that provided by the measurement. You can do that using two
possible sources of information. The first is the camino points,
which ship together with osmosis and are used for the boot-strapping
(see osmosis.boot). These are used for integers smaller than 150,
for 246 and for 755. The other sources of information are the
symmetric spheres provided as part of dipy. These are used if 362 or
642 are provided. Note that these might be problematic, because they
contain polar opposite points, so use with caution.
mode: string, optional
This can take one of several values, determining the form of the
regressors and the form of the signal to fit to.
'relative_signal': The fit is to $\frac{S}{S_0}$ and the regressors
are the relative signal predicted for a canonical tensor and the
relative signal predicted for a isotropic diffusivity compartment:
.. math::
\frac{S}{S_0} = \beta_1 e^{-bD} + \beta_2 e^{-b\vec{b}Q\vec{b}^t}
'signal_attenuation': The fit is to $1-\frac{S}{S_0}$ and the
regressors are the signal attenuation for the canonical tensor and the
signal attenuation due to isotropic diffusion:
.. math::
1-\frac{S}{S_0} = \beta_1 (1-e^{-bD}) + \beta_2 (1-e^{-b\vec{b} Q \vec{b}^t})
'normalize': in this case, we fit to $\frac{S}{S_0}$, but our regressor
set is normalized to maximum of 1 in each columns. This affects the
values of the weights, and also the goodness-of-fit (because of the
relative scaling of the regressors in the OLS). The equation in
this case is:
.. math::
\frac{S}{S_0} = \beta_1 + \beta_2 \frac{e^{-b\vec{b} Q \vec{b}^t}}{max(e^{-b\vec{b} Q \vec{b}^t})}
'log': in this case, we fit to $log(\frac{S}{S_0})$ and our regressors
are the exponents:
.. math::
log(\frac{S}{S_0}) = \beta_1 -bD + \beta_1 -b\vec{b}Q\vec{b}^t
iso_diffusivity: optional, float
What the diffusivity of the isotropic component should be set
to. This is irrelevant for the 'normalize' mode. Defaults to be
equal to the axial_diffusivity
"""
# Initialize the super-class:
BaseModel.__init__(self,
data,
bvecs,
bvals,
affine=affine,
mask=mask,
scaling_factor=scaling_factor,
sub_sample=sub_sample,
params_file=params_file,
verbose=verbose)
self.ad = axial_diffusivity
self.rd = radial_diffusivity
if iso_diffusivity is None:
iso_diffusivity = axial_diffusivity
self.iso_diffusivity = iso_diffusivity
if over_sample is not None:
# Symmetric spheres from dipy:
if over_sample in [362, 642]:
# We want to get these vertices:
verts = dpd.get_sphere('symmetric%s' % over_sample).vertices
# Their convention is transposed relative to ours:
self.rot_vecs = verts.T
elif (isinstance(over_sample, int)
and (over_sample <= 150 or over_sample in [246, 755])):
self.rot_vecs = ozu.get_camino_pts(over_sample)
elif over_sample == 'quad132':
pp = os.path.split(oz.__file__)[0] + '/data/SparseKernelModel/'
self.rot_vecs = np.loadtxt(pp + 'qsph1-16-132DP.dat')[:, :-1].T
else:
e_s = "You asked to sample the sphere in %s" % over_sample
e_s += " different directions. Can only do that for n<=150"
e_s += " or n in [246, 362, 642, 755]"
raise ValueError(e_s)
else:
self.rot_vecs = self.bvecs[:, self.b_idx]
if mode not in [
'relative_signal', 'signal_attenuation', 'normalize', 'log'
]:
raise ValueError("Not a recognized mode of CanonicalTensorModel")
self.mode = mode
self.iso_diffusivity = iso_diffusivity