Kaggle cryo #1947
Kaggle cryo #1947
Conversation
for more information, see https://pre-commit.ci
DCO Remediation Commit for christofhenkel <[email protected]> I, christofhenkel <[email protected]>, hereby add my Signed-off-by to this commit: 1db03fd I, christofhenkel <[email protected]>, hereby add my Signed-off-by to this commit: 2ffe23d I, christofhenkel <[email protected]>, hereby add my Signed-off-by to this commit: df958e7 Signed-off-by: christofhenkel <[email protected]> Signed-off-by: ChristofHenkel <[email protected]>
Signed-off-by: ChristofHenkel <[email protected]>
Signed-off-by: ChristofHenkel <[email protected]>
Signed-off-by: ChristofHenkel <[email protected]>
There was a problem hiding this comment.
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
| def load_one(self, experiment_id): | ||
|
|
||
| img_fp = f"{self.data_folder}{experiment_id}" | ||
| try: |
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
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/.zgroupThere was a problem hiding this comment.
/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
There was a problem hiding this comment.
I adjusted readme for data settings. Can you try again @garciadias
|
Hi @ChristofHenkel, could you please add the license header? All the scripts should start with this copyright: Thanks. |
Signed-off-by: ChristofHenkel <[email protected]>
for more information, see https://pre-commit.ci
Description
Added tutorial based on the 1st place solution of kaggles Cryo-ET competition