def get_pairs(imgs, unique_pairs, offsets, subsample_factor, overlap_pixels,
n_kp):
"""Create inlier keypoint pairs."""
orb = ORB(n_keypoints=n_kp, fast_threshold=0.05)
k = gaussian(offsets * 2 + 1, 1, sym=True)
tf = SimilarityTransform # tf = RigidTransform
tf0 = SimilarityTransform()
# FIXME: is there no rigid model in scikit-image???
# this is needed for input to RANSAC
pairs = []
init_tfs = np.empty([n_slcs, n_tiles, 3])
for p in unique_pairs:
pair_tstart = time()
full_im1, full_im2 = subsample_images(p, imgs, subsample_factor)
part_im1, part_im2 = select_imregions(p[2], full_im1, full_im2,
overlap_pixels)
keyp_im1, desc_im1 = get_keypoints(orb, part_im1)
keyp_im2, desc_im2 = get_keypoints(orb, part_im2)
keyp_im1, keyp_im2 = reset_imregions(p[2], keyp_im1, keyp_im2,
overlap_pixels, full_im1.shape)
matches = match_descriptors(desc_im1, desc_im2, cross_check=True)
dst = keyp_im1[matches[:, 0]][:, ::-1]
src = keyp_im2[matches[:, 1]][:, ::-1]
model, inliers = ransac((src, dst),
tf,
min_samples=4,
residual_threshold=2,
max_trials=300)
w = k[offsets - (p[1][0] - p[0][0])]
pairs.append((p, src[inliers], dst[inliers], model, w))
if (p[0][1] == 0) & (p[0][0] == p[1][0]
): # referenced to tile 0 within the same slice
tf1 = tf0.__add__(model)
itf = [
math.acos(min(tf1.params[0, 0],
1)), # FIXME!!! with RigidTransform
tf1.params[0, 2],
tf1.params[1, 2]
]
init_tfs[p[1][0], p[1][1], :] = np.array(itf)
if (p[0][1] == p[1][1] == 0) & (
p[1][0] - p[0][0] == 1): # if [slcX,tile0] to [slcX-1,tile0]
tf0 = tf0.__add__(model)
plot_pair_ransac(p, full_im1, full_im2, keyp_im1, keyp_im2, matches,
inliers)
print('Pair done in: %.2f s' % (time() - pair_tstart, ))
return pairs, init_tfs
def generate_init_tfs(pairs, n_slcs, n_tiles):
"""Find the transformation of each tile to tile[0,0]."""
tf0 = SimilarityTransform()
init_tfs = np.empty([n_slcs, n_tiles, 3])
for pair in pairs:
p, _, _, model, _ = pair
if (p[0][1] == 0) & (p[0][0] == p[1][0]
): # referenced to tile 0 within the same slice
tf1 = tf0.__add__(model)
itf = [
math.acos(min(tf1.params[0, 0],
1)), # FIXME!!! with RigidTransform
tf1.params[0, 2],
tf1.params[1, 2]
]
init_tfs[p[1][0], p[1][1], :] = np.array(itf)
if (p[0][1] == p[1][1] == 0) & (
p[1][0] - p[0][0] == 1): # if [slcX,tile0] to [slcX-1,tile0]
tf0 = tf0.__add__(model)
return init_tfs
def test_union_differing_types():
tform1 = SimilarityTransform()
tform2 = PolynomialTransform()
with pytest.raises(TypeError):
tform1.__add__(tform2)
def test_union_differing_types():
tform1 = SimilarityTransform()
tform2 = PolynomialTransform()
with testing.raises(TypeError):
tform1.__add__(tform2)
