Input error in Relion source file and other fails due to column to row changes #290
Description
Try to run the cov2d analysis using experimental dataset again. The analysis can not go through any more due to input error in Relion source file and other failures from column to row changes. Some of them are listed as below:
File "/tigress/junchaox/software/ASPIRE-Python_git/src/aspire/source/relion.py", line 167, in _images
im[data_indices-start] = data[data_indices-start]
IndexError: index 103 is out of bounds for axis 0 with size 99
File "/tigress/junchaox/software/ASPIRE-Python_git/src/aspire/estimation/covar2d.py", line 627, in get_cwf_coeffs
coeff_k = coeffs[:, ctf_idx == k]
IndexError: boolean index did not match indexed array along dimension 1; dimension is 2474 but corresponding boolean dimension is 512
File "/tigress/junchaox/software/ASPIRE-Python_git/src/aspire/utils/blk_diag_matrix.py", line 609, in solve
raise RuntimeError('Sizes of self and Y are not compatible.')
RuntimeError: Sizes of self and Y are not compatible.
File "/tigress/junchaox/software/ASPIRE-Python_git/src/aspire/denoising/denoiser_cov2d.py", line 83, in images
imgs_denoised = Image(imgs_estim)
File "/tigress/junchaox/software/ASPIRE-Python_git/src/aspire/image/init.py", line 111, in init
assert isinstance(data, np.ndarray), "Image should be instantiated with an ndarray"
AssertionError: Image should be instantiated with an ndarray
File "/tigress/junchaox/software/ASPIRE-Python_git/src/aspire/io/starfile.py", line 206, in save_star
start=i_start, num=num).data.astype('float32'), 0, 2)
ValueError: could not broadcast input array from shape (64,64,512) into shape (512,64,64)
File "/tigress/junchaox/software/ASPIRE-Python_git/src/aspire/io/starfile.py", line 206, in save_star
start=i_start, num=num).data.astype('float32'), 0, 2)
ValueError: could not broadcast input array from shape (64,64,512) into shape (512,64,64)