Missing dependencies in deepgrow tutorial

[melonipoika]

Describe the bug

Missing reader for nii.gz images

To Reproduce
Steps to reproduce the behavior:

1. Run this notebook
2. Pre Processing fails with:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
/tmp/ipykernel_2246/4005805290.py in <module>
     30 for t in pre_transforms:
     31     tname = type(t).__name__
---> 32     data = t(data)
     33     image = data['image']
     34     label = data.get('label')

/opt/conda/lib/python3.7/site-packages/monai/transforms/io/dictionary.py in __call__(self, data, reader)
    119         d = dict(data)
    120         for key, meta_key, meta_key_postfix in self.key_iterator(d, self.meta_keys, self.meta_key_postfix):
--> 121             data = self._loader(d[key], reader)
    122             if self._loader.image_only:
    123                 if not isinstance(data, np.ndarray):

/opt/conda/lib/python3.7/site-packages/monai/transforms/io/array.py in __call__(self, filename, reader)
    199         if img is None or reader is None:
    200             raise RuntimeError(
--> 201                 f"can not find a suitable reader for file: {filename}.\n"
    202                 "    Please install the reader libraries, see also the installation instructions:\n"
    203                 "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies.\n"

RuntimeError: can not find a suitable reader for file: ('_image.nii.gz',).
    Please install the reader libraries, see also the installation instructions:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies.
   The current registered: [<monai.data.image_reader.ITKReader object at 0x7f123bcb70d0>, <monai.data.image_reader.NumpyReader object at 0x7f123bcb7110>, <monai.data.image_reader.PILReader object at 0x7f123bcb7190>, <monai.data.image_reader.NibabelReader object at 0x7f123bcb71d0>].

Expected behavior

It should be possible to run this cell.

Environment (please complete the following information):

• OS

$ cat /etc/os-release 
PRETTY_NAME="Debian GNU/Linux 10 (buster)"
NAME="Debian GNU/Linux"
VERSION_ID="10"
VERSION="10 (buster)"
VERSION_CODENAME=buster
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"

• Python version

Python 3.7.10

• MONAI version [e.g. git commit hash]

0.8.dev2143
7964d45b3f4fc0323561522462c6fbacc882a3ea

Additional context

Installing all MONAI dependencies fixed the issue:

pip install -q "monai-weekly[all]"
---
LoadImaged => image shape: (392, 392, 210)
Guidance: [[[145, 66, 180], [105, 66, 180]], []]; Slice Idx: 145

AsChannelFirstd => image shape: (210, 392, 392)
Guidance: [[[145, 66, 180], [105, 66, 180]], []]; Slice Idx: 145

<snip>

[rijobro]

thanks for spotting this. I think the solution would be to change the very first line to:

!python -c "import monai" || pip install -q "monai-weekly[gdown, tqdm, nibabel]"

Would you mind giving this a go, and creating a PR if it works?

[melonipoika]

Absolutely! Thanks for the quick response. I will test the fix you suggested and create a PR for it.

[wyli]

thanks, the current ci pipeline runs all notebooks sequentially, it won't detect this kind of dependency error...

[rijobro]

We could be cleverer about it if we wanted. E.g., new virtual env for each test. Think it might be overkill though.

[melonipoika]

I forgot to check the other notebook in this tutorial, it has the same problem :-(

https://github.com/Project-MONAI/tutorials/blob/master/deepgrow/ignite/inference.ipynb

I will make a new PR to fix this one as well.