def test_affine_subvolume_3d(self):
from elf.transformation import compute_affine_matrix
# TODO test more orders once implemented
orders = [0, 1]
matrices = [compute_affine_matrix(scale=(1, 2, 1), rotation=(15, 30, 0)),
compute_affine_matrix(scale=(3, 2, .5), rotation=(24, 33, 99)),
compute_affine_matrix(scale=(1., 1.3, .79), rotation=(12, -4, 8),
translation=(10.5, 18., -33.2))]
for mat in matrices:
for order in orders:
self._test_3d(mat, order=order)
def test_affine_subvolume_2d(self):
from elf.transformation import compute_affine_matrix
# TODO test more orders once implemented
orders = [0, 1]
matrices = [compute_affine_matrix(scale=(2, 2), rotation=(45,)),
compute_affine_matrix(scale=(1, 2), rotation=(33,)),
compute_affine_matrix(scale=(3, 2), rotation=(137,)),
compute_affine_matrix(scale=(.5, 1.5), rotation=(23,),
translation=(23., -14.))]
for mat in matrices:
for order in orders:
self._test_2d(mat, order=order)
def bench_affine_2d(affine_function, N=5):
times = []
im = astronaut()[..., 0]
matrix = compute_affine_matrix(scale=(.5, .5), rotation=(45,))
for _ in range(N):
t0 = time.time()
affine_function(im, matrix)
t0 = time.time() - t0
times.append(t0)
print(np.min(times), "s")
def test_toy(self):
from elf.transformation import compute_affine_matrix
from elf.transformation import transform_subvolume_affine
mat = compute_affine_matrix(scale=(2, 2), rotation=(45,), translation=(-1, 1))
x = np.random.rand(10, 10)
bb = np.s_[0:3, 0:3]
res = transform_subvolume_affine(x, mat, bb, order=1)
exp = affine_transform(x, mat, order=1)[bb]
self.assertTrue(np.allclose(res, exp))
def bench_affine_3d(affine_function, N=5):
path = '/home/pape/Work/data/isbi/isbi_train_volume.h5'
with h5py.File(path, 'r') as f:
data = f['raw'][:]
times = []
matrix = compute_affine_matrix(scale=(1., 2., 1.5), rotation=(16, 32, 7))
for _ in range(N):
t0 = time.time()
affine_function(data, matrix)
t0 = time.time() - t0
times.append(t0)
print(np.min(times), "s")
def test_presmoothing(self):
from elf.transformation import compute_affine_matrix
mat = compute_affine_matrix(scale=(2, 2), rotation=(45, ))
self._test_2d(mat, order=1, out_file='tmp.n5', sigma=1.)
def _test_affine_subvolume_2d_chunked(self, out_file):
from elf.transformation import compute_affine_matrix
mat = compute_affine_matrix(scale=(2, 2), rotation=(45, ))
self._test_2d(mat, order=0, out_file=out_file)
def _test_affine_subvolume_3d_chunked(self, out_file):
from elf.transformation import compute_affine_matrix
mat = compute_affine_matrix(scale=(1, 2, 1), rotation=(15, 30, 0))
self._test_3d(mat, order=0, out_file=out_file)