You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
When I run the tutorial, affine alignment functions, I got this error.
But I am not sure what is wrong.
Can I ask you to suggest some possible problems?
I did not change any code and just run the provided jupyter code.
This was reproducible on my laptop and a remote cluster.
Best,
Error message:
Getting key points
FIXED image: found 74 key points
MOVING image: found 184 key points
TypeError Traceback (most recent call last)
TypeError: only size-1 arrays can be converted to Python scalars
The above exception was the direct cause of the following exception:
ValueError Traceback (most recent call last)
in
3
4 # see below for explanation of parameters
----> 5 global_affine = affine.ransac_affine(
6 fix_lowres_data, mov_lowres_data,
7 fix_lowres_spacing, mov_lowres_spacing,
~/.local/lib/python3.8/site-packages/bigstream/features.py in pairwise_correlation(A, B)
59
60 # get means and std for all contexts, center contexts
---> 61 a_mean, a_std = _stats(a_con)
62 b_mean, b_std = _stats(b_con)
63 a_con = a_con - a_mean[..., None]
~/.local/lib/python3.8/site-packages/bigstream/features.py in _stats(arr)
43
44 # compute mean and standard deviation along columns
---> 45 arr = arr.astype(np.float64)
46 means = np.mean(arr, axis=1)
47 sqr_means = np.mean(np.square(arr), axis=1)
ValueError: setting an array element with a sequence.
The text was updated successfully, but these errors were encountered:
When I run the tutorial, affine alignment functions, I got this error.
But I am not sure what is wrong.
Can I ask you to suggest some possible problems?
I did not change any code and just run the provided jupyter code.
This was reproducible on my laptop and a remote cluster.
Best,
Error message:
Getting key points
FIXED image: found 74 key points
MOVING image: found 184 key points
TypeError Traceback (most recent call last)
TypeError: only size-1 arrays can be converted to Python scalars
The above exception was the direct cause of the following exception:
ValueError Traceback (most recent call last)
in
3
4 # see below for explanation of parameters
----> 5 global_affine = affine.ransac_affine(
6 fix_lowres_data, mov_lowres_data,
7 fix_lowres_spacing, mov_lowres_spacing,
~/.local/lib/python3.8/site-packages/bigstream/affine.py in ransac_affine(fix, mov, fix_spacing, mov_spacing, min_radius, max_radius, match_threshold, cc_radius, nspots, align_threshold, num_sigma_max, verbose, fix_spots, mov_spots, default, **kwargs)
73
74 # get point correspondences
---> 75 correlations = features.pairwise_correlation(
76 fix_spots, mov_spots,
77 )
~/.local/lib/python3.8/site-packages/bigstream/features.py in pairwise_correlation(A, B)
59
60 # get means and std for all contexts, center contexts
---> 61 a_mean, a_std = _stats(a_con)
62 b_mean, b_std = _stats(b_con)
63 a_con = a_con - a_mean[..., None]
~/.local/lib/python3.8/site-packages/bigstream/features.py in _stats(arr)
43
44 # compute mean and standard deviation along columns
---> 45 arr = arr.astype(np.float64)
46 means = np.mean(arr, axis=1)
47 sqr_means = np.mean(np.square(arr), axis=1)
ValueError: setting an array element with a sequence.
The text was updated successfully, but these errors were encountered: