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kirchhausenlab / incasem

Automated Segmentation of cellular substructures in Electron Microscopy
BSD 3-Clause "New" or "Revised" License
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data_formatting #8

Closed che1219 closed 1 year ago

che1219 commented 1 year ago

Hi,

I have installed all the modules and code. I am at the part to convert the tiff to Zarr.

python 00_image_sequences_to_zarr.py -i ~/incasem/data/my_new_data -f ~/incasem/data/my_new_data.zarr

However, I got the error:

ds = daisy.prepare_ds(output_file,
                      output_dataset,
                      total_roi=metric_roi,
                      voxel_size=voxel_size,
                      write_size=voxel_size * daisy.Coordinate(chunks),
                      dtype=dtype,
                      compressor={'id': 'zlib', 'level': 3})

Traceback (most recent call last): File "00_image_sequences_to_zarr.py", line 135, in main() File "00_image_sequences_to_zarr.py", line 119, in main fos.utils.image_sequence_to_zarr( File "/home/chongyuh/incasem/incasem/utils/image_sequence_to_zarr.py", line 255, in image_sequence_to_zarr ds = daisy.prepare_ds(output_file, AttributeError: module 'daisy' has no attribute 'prepare_ds'

I wonder if there is a way to solve this problem. Thank you!

bentaculum commented 1 year ago

Thanks for filing the issue. I pinned the dependency on daisy to version 0.2.1 in 5d4d337 to solve it.

You can either update incasem with git pull and go through the installation process one more time in a fresh conda environment, or simply downgrade your daisy installation using pip.