Data preprocessing for CHAOS dataset can break.

[patmjen]

First, thanks a lot for releasing the code!

During preprocessing of the CHAOS dataset, the xy-slices may get loaded out-of-order since os.listdir does not necessarily sort the file names. Specifically, L104 and L152 in data/chaos.py:

voxel2mesh/data/chaos.py

Line 104 in 050a851

images_path = [dir for dir in os.listdir('{}/{}/DICOM_anon'.format(data_root, sample)) if 'dcm' in dir]

voxel2mesh/data/chaos.py

Line 152 in 050a851

images_path = [dir for dir in os.listdir('{}/{}/Ground'.format(data_root, sample)) if 'png' in dir]

This messes up the data since the xy-slices are then in the wrong order. Calling sorted on images_path seems to fix it.

[udaranga3001]

I agree that this can cause an issue. Thank you for pointing it out. I will update the code.

In our experiments, it didn't cause any problems. If it did, we would have noticed it since we save image volumes and ground truth volumes in the experiments.

[patmjen]

Great, thank you!
Just to be clear, the reason for my issue was that I did run the code and had this exact issue.

[Polaris112027]

So, the solution to this problem is still not updated in the code. Can you post the exact code for your solution? I also encountered this problem

[patmjen]

Sure, I changed it to

images_path = [dir for dir in os.listdir('{}/{}/DICOM_anon'.format(data_root, sample)) if 'dcm' in dir]
images_path = sorted(images_path)

at L104, and

images_path = [dir for dir in os.listdir('{}/{}/DICOM_anon'.format(data_root, sample)) if 'png' in dir]
images_path = sorted(images_path)

at L152.

This sorts the images by name, which puts them in the correct order.

[Polaris112027]

I run the code but meet the error:No such file or directory: '/content/drive/My Drive/voxel2mesh/Chaos/Train_Sets/DICOM_anon' . I checked the path but found that the correct format of path should be like "voxel2mesh/Chaos/Train_Sets/CT(or MR)/1(or 2,3,4...)/DICOM_anon" .Have you ever met the same error?Do you have any suggestion to deal with this error?