Kaggle cryo

[ChristofHenkel]

Description

Added tutorial based on the 1st place solution of kaggles Cryo-ET competition

[KumoLiu]

cc @virginiafdez @garciadias

[garciadias]

Hi @ChristofHenkel,

thank you for your contribution and congratulations on your great achievement.

I am trying to follow your README.md file instructions to run the code myself, but I have encountered some issues.

I leave you some comments. Please let me know if I am on the right track.

Many thanks,

Rafael

[garciadias]

This try statement will defer the error to line 88, where img will not be defined. Consider replacing the print statement with a raise or instantiating img on the exception.

[garciadias]

While debugging the code, I found that it was erroring out because of this error:

  File "/workspace/data/ds_1.py", line 83, in load_one
    img = np.array(zarr.open(img_fp + '/VoxelSpacing10.000/denoised.zarr')[0]).transpose(2,1,0)
  File "/usr/local/lib/python3.10/dist-packages/zarr/hierarchy.py", line 511, in __getitem__
    raise KeyError(item)

I confirmed the img_fp + '/VoxelSpacing10.000/denoised.zarr' path exists and it does, but zf is empty:

> zf
array([], dtype=float64)

I may have downloaded the data incorrectly. @ChristofHenkel, could you please take a look at this?

The contents of my folder are these:

$ ls /data/train/static/ExperimentRuns/TS_86_3/TS_86_3/VoxelSpacing10.000/denoised.zarr/.zgroup -la
-rw-r--r-- 1 root root 24 Mar  7 17:06 /data/train/static/ExperimentRuns/TS_86_3/TS_86_3/VoxelSpacing10.000/denoised.zarr/.zgroup

[ChristofHenkel]

/data/train/static/ExperimentRuns/TS_86_3/TS_86_3/VoxelSpacing10.000/denoised.zarr/.zgroup should not have the experiment (TS_86_3) twice in the filepath. Not sure how you neded up with this

[ChristofHenkel]

I adjusted readme for data settings. Can you try again @garciadias

[garciadias]

Thank you @ChristofHenkel, I proposed some changes at #1969 to simplify the process. Let me know what you think.

[KumoLiu]

Hi @ChristofHenkel, could you please add the license header?
https://github.com/Project-MONAI/tutorials/actions/runs/13538357621/job/38066337184?pr=1947

All the scripts should start with this copyright:

# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#     http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

Thanks.