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AMOS no longer works with the originally published data #73

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BorisShirokikh opened this issue Aug 15, 2024 · 0 comments
Open

AMOS no longer works with the originally published data #73

BorisShirokikh opened this issue Aug 15, 2024 · 0 comments

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@BorisShirokikh
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Originally, the AMOS' authors published only 600 labeled images in the "amos22.zip" archive. After supplementing the dataset code with the newest published data, e.g., "amos22_unlabeled_ct_5000_5399.zip", it stops working if only the initial data archive is provided.

Download instructions are also outdated, since they recommend to download only the initially published data, https://zenodo.org/record/7262581/files/amos22.zip. If I follow the instructions or just want to use labeled data only, I obtain the following error:

$ python
Python 3.10.4 (main, Mar 31 2022, 08:41:55) [GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from amid.amos import AMOS
>>> ds = AMOS("/gpfs/gpfs0/m.belyaev/data/amos22")
>>> ds.ids
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/beegfs/home/b.shirokikh/amid/amid/amos/dataset.py", line 66, in ids
    unlabelled = sorted(self._ids_unlabelled)
  File "/trinity/home/b.shirokikh/miniconda3/lib/python3.10/functools.py", line 981, in __get__
    val = self.func(instance)
  File "/trinity/home/b.shirokikh/miniconda3/lib/python3.10/site-packages/jboc/_main.py", line 41, in wrapper
    return func(decorated(*args_, **kwargs_), *args, **kwargs)
  File "/beegfs/home/b.shirokikh/amid/amid/amos/dataset.py", line 182, in _ids_unlabelled
    with ZipFile(self.root / archive) as zf:
  File "/trinity/home/b.shirokikh/miniconda3/lib/python3.10/zipfile.py", line 1249, in __init__
    self.fp = io.open(file, filemode)
FileNotFoundError: [Errno 2] No such file or directory: '/gpfs/gpfs0/m.belyaev/data/amos22/amos22_unlabeled_ct_5000_5399.zip'
>>> 

It does not work both for amid-0.14.0 and amid-0.13.0.

First, we need to update download instructions. Secondly, do we need two versions of amid? or maybe optional behavior of one AMID class?

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