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Fix nonlinear transformations #12

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merged 5 commits into from
May 9, 2020
+31 −14
Merged

Fix nonlinear transformations #12

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1cad786
Fix non_parametric and use time.perf_counter
sumanthratna Apr 26, 2020
649ee03
Fix wendland
sumanthratna Apr 26, 2020
b8ad9c5
Slightly reduce loss of microarchitectural details in wendland
sumanthratna Apr 26, 2020
82312f5
Comment out bspline constant_flow
sumanthratna May 1, 2020
312a973
Comment out B-spline constant flow for each iteration
sumanthratna May 8, 2020
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Fix wendland
@sumanthratna
sumanthratna committed Apr 26, 2020
commit 649ee034a6b9682b41acbb57c77dd2051fb9f956
12 changes: 4 additions & 8 deletions pathflow_mixmatch/cli.py
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Original file line number Diff line number Diff line change
@@ -145,9 +145,7 @@ def affine_register(im1, im2, iterations=1000, lr=0.01, transform_type='similari
if transform_type == 'non_parametric':
transform_args[0]=mov_im_level[0].size
elif transform_type in ['bspline','wendland']:
transform_args[0]=mov_im_level.size
# transform_args[0]=tuple(mov_im_level.size)
# transform_opts['sigma'] = (11, 11, 3)
transform_opts['sigma'] = (11, 11)

transformation = transforms[transform_type](*transform_args,**transform_opts)

@@ -200,9 +198,9 @@ def affine_register(im1, im2, iterations=1000, lr=0.01, transform_type='similari
print("=================================================================")

print("Registration done in:", end - start, "s")
if transform_type != 'non_parametric':
if transform_type in ['similarity', 'affine', 'rigid']:
print("Result parameters:")
transformation.print() # only works with rigid?
transformation.print()

# plot the results
plt.subplot(131)
@@ -217,9 +215,7 @@ def affine_register(im1, im2, iterations=1000, lr=0.01, transform_type='similari
plt.imshow(warped_image.numpy(), cmap='gray')
plt.title('Warped Moving Image')

if transform_type == 'similarity' or transform_type == 'affine' or transform_type == 'rigid':
# TODO: check if transformation has parent class
# airlab.transformation.pairwise.RigidTransformation
if transform_type in ['similarity', 'affine', 'rigid']:
transformation_param = transformation._phi_z
elif transform_type == 'non_parametric':
transformation_param = transformation.trans_parameters