def test_rigid_real_bundles():
bundle_initial = fornix_streamlines()[:20]
bundle, shift = center_streamlines(bundle_initial)
mat = compose_matrix44([0, 0, 20, 45., 0, 0])
bundle2 = transform_streamlines(bundle, mat)
bundle_sum_distance = BundleSumDistanceMatrixMetric()
srr = StreamlineLinearRegistration(bundle_sum_distance,
x0=np.zeros(6),
method='Powell')
new_bundle2 = srr.optimize(bundle, bundle2).transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
bundle_min_distance = BundleMinDistanceMatrixMetric()
srr = StreamlineLinearRegistration(bundle_min_distance,
x0=np.zeros(6),
method='Powell')
new_bundle2 = srr.optimize(bundle, bundle2).transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
assert_raises(ValueError, StreamlineLinearRegistration, method='Whatever')
def test_rigid_real_bundles():
bundle_initial = fornix_streamlines()[:20]
bundle, shift = center_streamlines(bundle_initial)
mat = compose_matrix44([0, 0, 20, 45., 0, 0])
bundle2 = transform_streamlines(bundle, mat)
bundle_sum_distance = BundleSumDistanceMatrixMetric()
srr = StreamlineLinearRegistration(bundle_sum_distance,
x0=np.zeros(6),
method='Powell')
new_bundle2 = srr.optimize(bundle, bundle2).transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
bundle_min_distance = BundleMinDistanceMatrixMetric()
srr = StreamlineLinearRegistration(bundle_min_distance,
x0=np.zeros(6),
method='Powell')
new_bundle2 = srr.optimize(bundle, bundle2).transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
assert_raises(ValueError, StreamlineLinearRegistration, method='Whatever')
def test_rigid_partial_real_bundles():
static = fornix_streamlines()[:20]
moving = fornix_streamlines()[20:40]
static_center, shift = center_streamlines(static)
moving_center, shift2 = center_streamlines(moving)
print(shift2)
mat = compose_matrix(translate=np.array([0, 0, 0.]),
angles=np.deg2rad([40, 0, 0.]))
moved = transform_streamlines(moving_center, mat)
srr = StreamlineLinearRegistration()
srm = srr.optimize(static_center, moved)
print(srm.fopt)
print(srm.iterations)
print(srm.funcs)
moving_back = srm.transform(moved)
print(srm.matrix)
static_center = set_number_of_points(static_center, 100)
moving_center = set_number_of_points(moving_back, 100)
vol = np.zeros((100, 100, 100))
spts = np.concatenate(static_center, axis=0)
spts = np.round(spts).astype(np.int) + np.array([50, 50, 50])
mpts = np.concatenate(moving_center, axis=0)
mpts = np.round(mpts).astype(np.int) + np.array([50, 50, 50])
for index in spts:
i, j, k = index
vol[i, j, k] = 1
vol2 = np.zeros((100, 100, 100))
for index in mpts:
i, j, k = index
vol2[i, j, k] = 1
overlap = np.sum(np.logical_and(vol, vol2)) / float(np.sum(vol2))
assert_equal(overlap * 100 > 40, True)
def test_rigid_partial_real_bundles():
static = fornix_streamlines()[:20]
moving = fornix_streamlines()[20:40]
static_center, shift = center_streamlines(static)
moving_center, shift2 = center_streamlines(moving)
print(shift2)
mat = compose_matrix(translate=np.array([0, 0, 0.]),
angles=np.deg2rad([40, 0, 0.]))
moved = transform_streamlines(moving_center, mat)
srr = StreamlineLinearRegistration()
srm = srr.optimize(static_center, moved)
print(srm.fopt)
print(srm.iterations)
print(srm.funcs)
moving_back = srm.transform(moved)
print(srm.matrix)
static_center = set_number_of_points(static_center, 100)
moving_center = set_number_of_points(moving_back, 100)
vol = np.zeros((100, 100, 100))
spts = np.concatenate(static_center, axis=0)
spts = np.round(spts).astype(np.int) + np.array([50, 50, 50])
mpts = np.concatenate(moving_center, axis=0)
mpts = np.round(mpts).astype(np.int) + np.array([50, 50, 50])
for index in spts:
i, j, k = index
vol[i, j, k] = 1
vol2 = np.zeros((100, 100, 100))
for index in mpts:
i, j, k = index
vol2[i, j, k] = 1
overlap = np.sum(np.logical_and(vol, vol2)) / float(np.sum(vol2))
assert_equal(overlap * 100 > 40, True)
def test_stream_rigid():
static = fornix_streamlines()[:20]
moving = fornix_streamlines()[20:40]
center_streamlines(static)
mat = compose_matrix44([0, 0, 0, 0, 40, 0])
moving = transform_streamlines(moving, mat)
srr = StreamlineLinearRegistration()
sr_params = srr.optimize(static, moving)
moved = transform_streamlines(moving, sr_params.matrix)
srr = StreamlineLinearRegistration(verbose=True)
srm = srr.optimize(static, moving)
moved2 = transform_streamlines(moving, srm.matrix)
moved3 = srm.transform(moving)
assert_array_almost_equal(moved[0], moved2[0], decimal=3)
assert_array_almost_equal(moved2[0], moved3[0], decimal=3)
def test_stream_rigid():
static = fornix_streamlines()[:20]
moving = fornix_streamlines()[20:40]
center_streamlines(static)
mat = compose_matrix44([0, 0, 0, 0, 40, 0])
moving = transform_streamlines(moving, mat)
srr = StreamlineLinearRegistration()
sr_params = srr.optimize(static, moving)
moved = transform_streamlines(moving, sr_params.matrix)
srr = StreamlineLinearRegistration(verbose=True)
srm = srr.optimize(static, moving)
moved2 = transform_streamlines(moving, srm.matrix)
moved3 = srm.transform(moving)
assert_array_almost_equal(moved[0], moved2[0], decimal=3)
assert_array_almost_equal(moved2[0], moved3[0], decimal=3)
def test_center_and_transform():
A = np.array([[1, 2, 3], [1, 2, 3.]])
streamlines = [A for _ in range(10)]
streamlines2, center = center_streamlines(streamlines)
B = np.zeros((2, 3))
assert_array_equal(streamlines2[0], B)
assert_array_equal(center, A[0])
affine = np.eye(4)
affine[0, 0] = 2
affine[:3, -1] = -np.array([2, 1, 1]) * center
streamlines3 = transform_streamlines(streamlines, affine)
assert_array_equal(streamlines3[0], B)
def test_center_and_transform():
A = np.array([[1, 2, 3], [1, 2, 3.]])
streamlines = [A for i in range(10)]
streamlines2, center = center_streamlines(streamlines)
B = np.zeros((2, 3))
assert_array_equal(streamlines2[0], B)
assert_array_equal(center, A[0])
affine = np.eye(4)
affine[0, 0] = 2
affine[:3, -1] = - np.array([2, 1, 1]) * center
streamlines3 = transform_streamlines(streamlines, affine)
assert_array_equal(streamlines3[0], B)
def test_rigid_parallel_lines():
bundle_initial = simulated_bundle()
bundle, shift = center_streamlines(bundle_initial)
mat = compose_matrix44([20, 0, 10, 0, 40, 0])
bundle2 = transform_streamlines(bundle, mat)
bundle_sum_distance = BundleSumDistanceMatrixMetric()
options = {'maxcor': 100, 'ftol': 1e-9, 'gtol': 1e-16, 'eps': 1e-3}
srr = StreamlineLinearRegistration(metric=bundle_sum_distance,
x0=np.zeros(6),
method='L-BFGS-B',
bounds=None,
options=options)
new_bundle2 = srr.optimize(bundle, bundle2).transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
def test_rigid_parallel_lines():
bundle_initial = simulated_bundle()
bundle, shift = center_streamlines(bundle_initial)
mat = compose_matrix44([20, 0, 10, 0, 40, 0])
bundle2 = transform_streamlines(bundle, mat)
bundle_sum_distance = BundleSumDistanceMatrixMetric()
options = {'maxcor': 100, 'ftol': 1e-9, 'gtol': 1e-16, 'eps': 1e-3}
srr = StreamlineLinearRegistration(metric=bundle_sum_distance,
x0=np.zeros(6),
method='L-BFGS-B',
bounds=None,
options=options)
new_bundle2 = srr.optimize(bundle, bundle2).transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
def test_affine_real_bundles():
bundle_initial = fornix_streamlines()
bundle_initial, shift = center_streamlines(bundle_initial)
bundle = bundle_initial[:20]
xgold = [0, 4, 2, 0, 10, 10, 1.2, 1.1, 1., 0., 0.2, 0.]
mat = compose_matrix44(xgold)
bundle2 = transform_streamlines(bundle_initial[:20], mat)
x0 = np.array([0, 0, 0, 0, 0, 0, 1., 1., 1., 0, 0, 0])
x = 25
bounds = [(-x, x), (-x, x), (-x, x),
(-x, x), (-x, x), (-x, x),
(0.1, 1.5), (0.1, 1.5), (0.1, 1.5),
(-1, 1), (-1, 1), (-1, 1)]
options = {'maxcor': 10, 'ftol': 1e-7, 'gtol': 1e-5, 'eps': 1e-8}
metric = BundleMinDistanceMatrixMetric()
slr = StreamlineLinearRegistration(metric=metric,
x0=x0,
method='L-BFGS-B',
bounds=bounds,
verbose=True,
options=options)
slm = slr.optimize(bundle, bundle2)
new_bundle2 = slm.transform(bundle2)
slr2 = StreamlineLinearRegistration(metric=metric,
x0=x0,
method='Powell',
bounds=None,
verbose=True,
options=None)
slm2 = slr2.optimize(bundle, new_bundle2)
new_bundle2 = slm2.transform(new_bundle2)
evaluate_convergence(bundle, new_bundle2)
def test_similarity_real_bundles():
bundle_initial = fornix_streamlines()
bundle_initial, shift = center_streamlines(bundle_initial)
bundle = bundle_initial[:20]
xgold = [0, 0, 10, 0, 0, 0, 1.5]
mat = compose_matrix44(xgold)
bundle2 = transform_streamlines(bundle_initial[:20], mat)
metric = BundleMinDistanceMatrixMetric()
x0 = np.array([0, 0, 0, 0, 0, 0, 1], 'f8')
slr = StreamlineLinearRegistration(metric=metric,
x0=x0,
method='Powell',
bounds=None,
verbose=False)
slm = slr.optimize(bundle, bundle2)
new_bundle2 = slm.transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
def test_similarity_real_bundles():
bundle_initial = fornix_streamlines()
bundle_initial, shift = center_streamlines(bundle_initial)
bundle = bundle_initial[:20]
xgold = [0, 0, 10, 0, 0, 0, 1.5]
mat = compose_matrix44(xgold)
bundle2 = transform_streamlines(bundle_initial[:20], mat)
metric = BundleMinDistanceMatrixMetric()
x0 = np.array([0, 0, 0, 0, 0, 0, 1], 'f8')
slr = StreamlineLinearRegistration(metric=metric,
x0=x0,
method='Powell',
bounds=None,
verbose=False)
slm = slr.optimize(bundle, bundle2)
new_bundle2 = slm.transform(bundle2)
evaluate_convergence(bundle, new_bundle2)
def optimize(self, static, moving, mat=None):
""" Find the minimum of the provided metric.
Parameters
----------
static : streamlines
Reference or fixed set of streamlines.
moving : streamlines
Moving set of streamlines.
mat : array
Transformation (4, 4) matrix to start the registration. ``mat``
is applied to moving. Default value None which means that initial
transformation will be generated by shifting the centers of moving
and static sets of streamlines to the origin.
Returns
-------
map : StreamlineRegistrationMap
"""
msg = 'need to have the same number of points. Use '
msg += 'set_number_of_points from dipy.tracking.streamline'
if not np.all(np.array(list(map(len, static))) == static[0].shape[0]):
raise ValueError('Static streamlines ' + msg)
if not np.all(np.array(list(map(len, moving))) == moving[0].shape[0]):
raise ValueError('Moving streamlines ' + msg)
if not np.all(np.array(list(map(len, moving))) == static[0].shape[0]):
raise ValueError('Static and moving streamlines ' + msg)
if mat is None:
static_centered, static_shift = center_streamlines(static)
moving_centered, moving_shift = center_streamlines(moving)
static_mat = compose_matrix44([static_shift[0], static_shift[1],
static_shift[2], 0, 0, 0])
moving_mat = compose_matrix44([-moving_shift[0], -moving_shift[1],
-moving_shift[2], 0, 0, 0])
else:
static_centered = static
moving_centered = transform_streamlines(moving, mat)
static_mat = np.eye(4)
moving_mat = mat
self.metric.setup(static_centered, moving_centered)
distance = self.metric.distance
if self.method == 'Powell':
if self.options is None:
self.options = {'xtol': 1e-6, 'ftol': 1e-6, 'maxiter': 1e6}
opt = Optimizer(distance, self.x0.tolist(),
method=self.method, options=self.options,
evolution=self.evolution)
if self.method == 'L-BFGS-B':
if self.options is None:
self.options = {'maxcor': 10, 'ftol': 1e-7,
'gtol': 1e-5, 'eps': 1e-8,
'maxiter': 100}
opt = Optimizer(distance, self.x0.tolist(),
method=self.method,
bounds=self.bounds, options=self.options,
evolution=self.evolution)
if self.verbose:
opt.print_summary()
opt_mat = compose_matrix44(opt.xopt)
mat = compose_transformations(moving_mat, opt_mat, static_mat)
mat_history = []
if opt.evolution is not None:
for vecs in opt.evolution:
mat_history.append(
compose_transformations(moving_mat,
compose_matrix44(vecs),
static_mat))
srm = StreamlineRegistrationMap(mat, opt.xopt, opt.fopt,
mat_history, opt.nfev, opt.nit)
del opt
return srm
def optimize(self, static, moving, mat=None):
""" Find the minimum of the provided metric.
Parameters
----------
static : streamlines
Reference or fixed set of streamlines.
moving : streamlines
Moving set of streamlines.
mat : array
Transformation (4, 4) matrix to start the registration. ``mat``
is applied to moving. Default value None which means that initial
transformation will be generated by shifting the centers of moving
and static sets of streamlines to the origin.
Returns
-------
map : StreamlineRegistrationMap
"""
msg = 'need to have the same number of points. Use '
msg += 'set_number_of_points from dipy.tracking.streamline'
if not np.all(np.array(list(map(len, static))) == static[0].shape[0]):
raise ValueError('Static streamlines ' + msg)
if not np.all(np.array(list(map(len, moving))) == moving[0].shape[0]):
raise ValueError('Moving streamlines ' + msg)
if not np.all(np.array(list(map(len, moving))) == static[0].shape[0]):
raise ValueError('Static and moving streamlines ' + msg)
if mat is None:
static_centered, static_shift = center_streamlines(static)
moving_centered, moving_shift = center_streamlines(moving)
static_mat = compose_matrix44(
[static_shift[0], static_shift[1], static_shift[2], 0, 0, 0])
moving_mat = compose_matrix44([
-moving_shift[0], -moving_shift[1], -moving_shift[2], 0, 0, 0
])
else:
static_centered = static
moving_centered = transform_streamlines(moving, mat)
static_mat = np.eye(4)
moving_mat = mat
self.metric.setup(static_centered, moving_centered)
distance = self.metric.distance
if self.method == 'Powell':
if self.options is None:
self.options = {'xtol': 1e-6, 'ftol': 1e-6, 'maxiter': 1e6}
opt = Optimizer(distance,
self.x0.tolist(),
method=self.method,
options=self.options,
evolution=self.evolution)
if self.method == 'L-BFGS-B':
if self.options is None:
self.options = {
'maxcor': 10,
'ftol': 1e-7,
'gtol': 1e-5,
'eps': 1e-8,
'maxiter': 100
}
opt = Optimizer(distance,
self.x0.tolist(),
method=self.method,
bounds=self.bounds,
options=self.options,
evolution=self.evolution)
if self.verbose:
opt.print_summary()
opt_mat = compose_matrix44(opt.xopt)
mat = compose_transformations(moving_mat, opt_mat, static_mat)
mat_history = []
if opt.evolution is not None:
for vecs in opt.evolution:
mat_history.append(
compose_transformations(moving_mat, compose_matrix44(vecs),
static_mat))
srm = StreamlineRegistrationMap(mat, opt.xopt, opt.fopt, mat_history,
opt.nfev, opt.nit)
del opt
return srm
def test_bundle_maps():
renderer = window.renderer()
bundle = fornix_streamlines()
bundle, shift = center_streamlines(bundle)
mat = np.array([[1, 0, 0, 100],
[0, 1, 0, 100],
[0, 0, 1, 100],
[0, 0, 0, 1.]])
bundle = transform_streamlines(bundle, mat)
# metric = np.random.rand(*(200, 200, 200))
metric = 100 * np.ones((200, 200, 200))
# add lower values
metric[100, :, :] = 100 * 0.5
# create a nice orange-red colormap
lut = actor.colormap_lookup_table(scale_range=(0., 100.),
hue_range=(0., 0.1),
saturation_range=(1, 1),
value_range=(1., 1))
line = actor.line(bundle, metric, linewidth=0.1, lookup_colormap=lut)
window.add(renderer, line)
window.add(renderer, actor.scalar_bar(lut, ' '))
report = window.analyze_renderer(renderer)
npt.assert_almost_equal(report.actors, 1)
# window.show(renderer)
renderer.clear()
nb_points = np.sum([len(b) for b in bundle])
values = 100 * np.random.rand(nb_points)
# values[:nb_points/2] = 0
line = actor.streamtube(bundle, values, linewidth=0.1, lookup_colormap=lut)
renderer.add(line)
# window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
renderer.clear()
colors = np.random.rand(nb_points, 3)
# values[:nb_points/2] = 0
line = actor.line(bundle, colors, linewidth=2)
renderer.add(line)
# window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
# window.show(renderer)
arr = window.snapshot(renderer)
report2 = window.analyze_snapshot(arr)
npt.assert_equal(report2.objects, 1)
# try other input options for colors
renderer.clear()
actor.line(bundle, (1., 0.5, 0))
actor.line(bundle, np.arange(len(bundle)))
actor.line(bundle)
colors = [np.random.rand(*b.shape) for b in bundle]
actor.line(bundle, colors=colors)
def test_bundle_maps():
renderer = window.renderer()
bundle = fornix_streamlines()
bundle, shift = center_streamlines(bundle)
mat = np.array([[1, 0, 0, 100],
[0, 1, 0, 100],
[0, 0, 1, 100],
[0, 0, 0, 1.]])
bundle = transform_streamlines(bundle, mat)
# metric = np.random.rand(*(200, 200, 200))
metric = 100 * np.ones((200, 200, 200))
# add lower values
metric[100, :, :] = 100 * 0.5
# create a nice orange-red colormap
lut = actor.colormap_lookup_table(scale_range=(0., 100.),
hue_range=(0., 0.1),
saturation_range=(1, 1),
value_range=(1., 1))
line = actor.line(bundle, metric, linewidth=0.1, lookup_colormap=lut)
window.add(renderer, line)
window.add(renderer, actor.scalar_bar(lut, ' '))
report = window.analyze_renderer(renderer)
npt.assert_almost_equal(report.actors, 1)
# window.show(renderer)
renderer.clear()
nb_points = np.sum([len(b) for b in bundle])
values = 100 * np.random.rand(nb_points)
# values[:nb_points/2] = 0
line = actor.streamtube(bundle, values, linewidth=0.1, lookup_colormap=lut)
renderer.add(line)
# window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
renderer.clear()
colors = np.random.rand(nb_points, 3)
# values[:nb_points/2] = 0
line = actor.line(bundle, colors, linewidth=2)
renderer.add(line)
# window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
# window.show(renderer)
arr = window.snapshot(renderer)
report2 = window.analyze_snapshot(arr)
npt.assert_equal(report2.objects, 1)
# try other input options for colors
renderer.clear()
actor.line(bundle, (1., 0.5, 0))
actor.line(bundle, np.arange(len(bundle)))
actor.line(bundle)
colors = [np.random.rand(*b.shape) for b in bundle]
actor.line(bundle, colors=colors)