Our testing setup utilizes the raw data provided. We found that each .tif file contains one frame and the downsampling expects multiple frames as it has a for loop to run through each of the frames in a .tif file. Clarification on the downsampling process or any potential configuration adjustments needed would be highly beneficial.
We are getting this "IndexError: cannot do a non-empty take from an empty axes." which can be traced back to the downsample list being empty.
Output:
Loading config.json
Transformed paths in config file.
Making /data/output/04_atlas_alignment/collection/
Our testing setup utilizes the raw data provided. We found that each .tif file contains one frame and the downsampling expects multiple frames as it has a for loop to run through each of the frames in a .tif file. Clarification on the downsampling process or any potential configuration adjustments needed would be highly beneficial.
We are getting this "IndexError: cannot do a non-empty take from an empty axes." which can be traced back to the downsample list being empty.
Output: Loading config.json
Transformed paths in config file.
Making /data/output/04_atlas_alignment/collection/
HOOK:OVERALL:6
Masking
HOOK:1:6:0:717
2024-05-16 16:08:20.035569 : Defining downsampling folders
2024-05-16 16:08:20.035569 : Downsampling
2024-05-16 16:08:25.995693 : Saving downsampled stacks
Downsampled list empty!
C:\ProgramData\anaconda3\envs\DELIVR\lib\site-packages\tifffile\tifffile.py:2151: UserWarning: <tifffile.TiffWriter 'stack_resampled.tif'> writing zero-size array to nonconformant TIFF
warnings.warn(
Traceback (most recent call last):
File "main.py", line 95, in
File "[PATH NAME]\downsample_and_mask.py", line 671, in downsample_mask
File "[PATH NAME]\downsample_and_mask.py", line 571, in histogram_equalization_8b
File "<__array_function__ internals>", line 200, in percentile
File "[PATH NAME]\function_base.py", line 4205, in percentile
File "[PATH NAME]\function_base.py", line 4473, in _quantile_unchecked
File "[PATH NAME]\function_base.py", line 3752, in _ureduce
File "[PATH NAME]\function_base.py", line 4639, in _quantile_ureduce_func
File "[PATH NAME]\function_base.py", line 4745, in _quantile
File "<__array_function__ internals>", line 200, in take
File "[PATH NAME]\fromnumeric.py", line 190, in take
File "[PATH NAME]\fromnumeric.py", line 57, in _wrapfunc
IndexError: cannot do a non-empty take from an empty axes.