def test_scale_space():
num_levels = 3
for test_class in [ScaleSpace, IsotropicScaleSpace]:
for dim in [2, 3]:
print(dim, test_class)
if dim == 2:
moving, static = get_synthetic_warped_circle(1)
else:
moving, static = get_synthetic_warped_circle(30)
input_spacing = np.array([1.1, 1.2, 1.5])[:dim]
grid2world = np.diag(tuple(input_spacing) + (1.0,))
original = moving
if test_class is ScaleSpace:
ss = test_class(
original,
num_levels,
grid2world,
input_spacing)
elif test_class is IsotropicScaleSpace:
factors = [4, 2, 1]
sigmas = [3.0, 1.0, 0.0]
ss = test_class(
original,
factors,
sigmas,
grid2world,
input_spacing)
for level in range(num_levels):
# Verify sigmas and images are consistent
sigmas = ss.get_sigmas(level)
expected = sp.ndimage.filters.gaussian_filter(original, sigmas)
expected = ((expected - expected.min()) /
(expected.max() - expected.min()))
actual = ss.get_image(level)
assert_array_almost_equal(actual, expected)
# Verify scalings and spacings are consistent
spacings = ss.get_spacing(level)
scalings = ss.get_scaling(level)
expected = ss.get_spacing(0) * scalings
actual = ss.get_spacing(level)
assert_array_almost_equal(actual, expected)
# Verify affine and affine_inv are consistent
affine = ss.get_affine(level)
affine_inv = ss.get_affine_inv(level)
expected = np.eye(1 + dim)
actual = affine.dot(affine_inv)
assert_array_almost_equal(actual, expected)
# Verify affine consistent with spacings
exp_dir, expected_sp = get_direction_and_spacings(affine, dim)
actual_sp = spacings
assert_array_almost_equal(actual_sp, expected_sp)
def test_scale_space():
num_levels = 3
for test_class in [ScaleSpace, IsotropicScaleSpace]:
for dim in [2, 3]:
print(dim, test_class)
if dim == 2:
moving, static = get_synthetic_warped_circle(1)
else:
moving, static = get_synthetic_warped_circle(30)
moving = cp.asarray(moving)
static = cp.asarray(static)
input_spacing = np.array([1.1, 1.2, 1.5])[:dim]
grid2world = np.diag(tuple(input_spacing) + (1.0, ))
original = moving
if test_class is ScaleSpace:
ss = test_class(original, num_levels, grid2world,
input_spacing)
elif test_class is IsotropicScaleSpace:
factors = [4, 2, 1]
sigmas = [3.0, 1.0, 0.0]
ss = test_class(original, factors, sigmas, grid2world,
input_spacing)
for level in range(num_levels):
# Verify sigmas and images are consistent
sigmas = ss.get_sigmas(level)
expected = ndi.gaussian_filter(original, sigmas)
expected = (expected - expected.min()) / (expected.max() -
expected.min())
actual = ss.get_image(level)
cp.testing.assert_array_almost_equal(actual, expected)
# Verify scalings and spacings are consistent
spacings = ss.get_spacing(level)
scalings = ss.get_scaling(level)
expected = ss.get_spacing(0) * scalings
actual = ss.get_spacing(level)
cp.testing.assert_array_almost_equal(actual, expected)
# Verify affine and affine_inv are consistent
affine = ss.get_affine(level)
affine_inv = ss.get_affine_inv(level)
expected = np.eye(1 + dim)
actual = affine.dot(affine_inv)
cp.testing.assert_array_almost_equal(actual, expected)
# Verify affine consistent with spacings
exp_dir, expected_sp = get_direction_and_spacings(affine, dim)
actual_sp = spacings
cp.testing.assert_array_almost_equal(actual_sp, expected_sp)
def test_get_direction_and_spacings():
xrot = 0.5
yrot = 0.75
zrot = 1.0
direction_gt = eulerangles.euler2mat(zrot, yrot, xrot)
spacings_gt = np.array([1.1, 1.2, 1.3])
scaling_gt = np.diag(spacings_gt)
translation_gt = np.array([1,2,3])
affine = np.eye(4)
affine[:3, :3] = direction_gt.dot(scaling_gt)
affine[:3, 3] = translation_gt
direction, spacings = imwarp.get_direction_and_spacings(affine, 3)
assert_array_almost_equal(direction, direction_gt)
assert_array_almost_equal(spacings, spacings_gt)
def changeFoV(image_nib, new_FOV, com=False):
if isinstance(new_FOV, list):
try:
new_FOV = np.array(new_FOV)
except:
raise IOError("list of fields of view")
image_shape = np.array(image_nib.shape)
direction, spacing = get_direction_and_spacings(image_nib.affine,
image_nib.ndim)
old_fov = image_shape * spacing
print("Input Image has:"
"FOVs: {} "
"Our New FOVs: {}".format(old_fov, new_FOV))
doit = False
for f, fov in enumerate(old_fov):
if (abs(fov - new_FOV[f]) >= 2 * spacing[f]):
doit = True
else:
doit = False
break
if not doit:
return image_nib.get_data(), image_nib.affine
arr = image_nib.get_data()
# Assume B_0 image is always the first vol
if image_nib.ndim > 3:
b0_image = arr[:, :, :, 0]
else:
b0_image = arr
nVols = image_shape[-1]
if com:
new_image, new_affine = crop4D(image_nib, new_FOV, b0_image)
else:
new_image, new_affine = changeFOVimage(image_nib, new_FOV)
return new_image, new_affine
static = ((static.astype(np.float64) - static.min()) /
(static.max() - static.min()))
moving = ((moving.astype(np.float64) - moving.min()) /
(moving.max() - moving.min()))
static = np.array(static).astype(np.float64)
moving = np.array(moving).astype(np.float64)
import numpy.linalg as npl
moving_world2grid = npl.inv(moving_grid2world)
from dipy.align.imwarp import get_direction_and_spacings
dim = len(static.shape)
moving_direction, moving_spacing = \
get_direction_and_spacings(moving_grid2world, dim)
from dipy.align.vector_fields import _gradient_3d
out_shape = static.shape
ftype = moving.dtype.type
out = np.empty(tuple(out_shape) + (dim, ), dtype=ftype)
inside = np.empty(tuple(out_shape), dtype=np.int32)
_gradient_3d(moving, moving_world2grid, moving_spacing, static_grid2world, out,
inside)
mgrad = np.asarray(out)
from dipy.align.imaffine import AffineMap
dim = len(static.shape)
starting_affine = np.eye(dim + 1)
affine_map = AffineMap(starting_affine, static.shape, static_grid2world,
def changeFOVimage(image, new_FOV):
arr = image.get_data()
affine = image.affine
n = 3
if isinstance(new_FOV, list):
try:
new_FOV = np.array(new_FOV)
except:
raise IOError("list of fields of view")
direction, spacing = get_direction_and_spacings(affine, arr.ndim)
print(direction, spacing)
arr_size = arr.size
arr_shape = np.array(arr.shape)
old_fov = np.abs(spacing.dot(direction) * arr_shape)
origin = affine[:3, 3]
print("Input Image has:"
"FOVs: {} "
"Our New FOVs: {}".format(old_fov, new_FOV))
doit = False
for f, fov in enumerate(old_fov):
if (abs(fov - new_FOV[f]) >= 2 * spacing[f]):
doit = True
else:
doit = False
break
if not doit:
print("Can't Change FOV - Return original image")
return image, affine
total_add_3D, total_remove_3D = np.zeros(n).astype(int), np.zeros(
n).astype(int)
new_origin_index = np.zeros(n).astype(int)
new_size = np.zeros(n).astype(int)
start_from = np.zeros(n).astype(int)
start_from_new, from_old_size = np.zeros(n).astype(int), np.zeros(
n).astype(int)
for d, fov in enumerate(old_fov[:n]):
print(d)
if new_FOV[d] > fov:
# print("Dimension {} process add".format(d))
total_add_3D[d] = (np.ceil((new_FOV[d] - fov) / spacing[d]))
if ((total_add_3D[d] % 2) == 1):
total_add_3D[d] += 1
new_origin_index[d] = -(total_add_3D[d] / 2)
new_size[d] = (arr_shape[d] + total_add_3D[d])
start_from[d] = 0
start_from_new[d] = total_add_3D[d] / 2
from_old_size[d] = arr_shape[d]
else:
# print("Dimension {} process remove".format(d))
total_remove_3D[d] = (np.floor((fov - new_FOV[d]) / spacing[d]))
if ((total_remove_3D[d] % 2) == 1):
total_remove_3D[d] -= 1
new_origin_index[d] = (total_remove_3D[d] / 2)
new_size[d] = (arr_shape[d] - total_remove_3D[d])
start_from[d] = total_remove_3D[d] / 2
start_from_new[d] = 0
from_old_size[d] = arr_shape[d] - total_remove_3D[d]
# new_origin = origin + spacing * new_origin_index
# new_origin = _transformIndextoPhysicalPoint(new_origin_index, spacing, direction, origin)
new_origin = _transformIndextoPhysicalPoint_with_affine(
affine, new_origin_index)
new_affine = affine.copy()
new_affine[0:3, 3] = new_origin
if arr.ndim > 3:
new_image = arr[start_from[0]:start_from[0] + from_old_size[0],
start_from[1]:start_from[1] + from_old_size[1],
start_from[2]:start_from[2] + from_old_size[2], :]
else:
new_image = arr[start_from[0]:start_from[0] + from_old_size[0],
start_from[1]:start_from[1] + from_old_size[1],
start_from[2]:start_from[2] + from_old_size[2]]
return new_image, new_affine
def crop4D(image, new_FOV, b0_image):
arr = image.get_data()
affine = image.affine
n = arr.ndim
if isinstance(new_FOV, list):
try:
new_FOV = np.array(new_FOV)
except:
raise IOError("list of fields of view")
direction, spacing = get_direction_and_spacings(affine, arr.ndim)
# print(direction, spacing)
arr_size = arr.size
arr_shape = np.array(arr.shape)
old_fov = np.abs(spacing.dot(direction) * arr_shape)
origin = affine[:3, 3]
print("Input Image has:"
"FOVs: {} "
"Our New FOVs: {}".format(old_fov, new_FOV))
doit = False
for f, fov in enumerate(old_fov):
if (abs(fov - new_FOV[f]) >= 2 * spacing[f]):
doit = True
if not doit:
return image.get_data(), image.affine
# get center of mass index and point
center_index = _get_centerOfGravityPt(b0_image)
center_pt = _transformIndextoPhysicalPoint(center_index, spacing,
direction, origin)
scl = direction[:3, :3] * np.diag(spacing)
new_size = np.ceil(new_FOV / spacing)
new_center_index = (new_size - 1) // 2
new_origin = np.zeros(3)
# Find new_origin
for r in range(3):
sm = np.sum(scl[r, :] * new_center_index)
new_origin[r] = center_pt[r] - sm
spc4 = np.zeros(4)
spc4[:-1] = spacing
spc4[-1] = 1
dir4 = np.eye(4, 4)
dir4[:3, :3] = direction[:3, :3]
new_origin4 = np.zeros(4)
new_origin4[:3] = new_origin
destination_index = np.zeros(3).astype(int)
source_start = np.zeros(3).astype(int)
source_size = np.zeros(3).astype(int)
for d in range(3):
if (new_center_index[d] < center_index[d]):
destination_index[d] = 0
source_start[d] = center_index[d] - new_center_index[d]
if (source_start[d] + new_size[d] > arr.shape[d]):
source_size[d] = arr.shape[d] - source_start[d] - 1
else:
source_size[d] = new_size[d]
else:
destination_index[d] = new_center_index[d] - center_index[d]
source_start[d] = 0
if (arr.shape[d] > new_size[d]):
source_size[d] = new_size[d]
else:
source_size[d] = arr.shape[d]
if arr.ndim > 3:
new_image = arr[source_start[0]:source_start[0] + source_size[0],
source_start[1]:source_start[1] + source_size[1],
source_start[2]:source_start[2] + source_size[2], :]
else:
new_image = arr[source_start[0]:source_start[0] + source_size[0],
source_start[1]:source_start[1] + source_size[1],
source_start[2]:source_start[2] + source_size[2]]
new_affine = affine
new_affine[0:3, 3] = new_origin
return new_image, new_affine