module 'monai.transforms' has no attribute 'AddChannel'

[slefcourt27]

I am using the most recent version of monai - monai_weekly-1.4.dev2413 because other versions give me an error of

AttributeError: 'FileFinder' object has no attribute 'find_module'

Trying to migrate to the most recent version and am met with this issue

module 'monai.transforms' has no attribute 'AddChannel'

Is there documentation somewhere which explains which functions are deprecated and their replacements? I tried reading the official documentation but did not see this anywhere.

[KumoLiu]

Hi @slefcourt27,

AttributeError: 'FileFinder' object has no attribute 'find_module'

Fixed in this PR.
Project-MONAI/MONAI#7458

module 'monai.transforms' has no attribute 'AddChannel'

AddChannel has been removed since 1.3.
https://github.com/Project-MONAI/MONAI/releases

Please check your version or perhaps reinstall it in a fresh environment.
Hope it helps, thanks.

[slefcourt27]

Hi @KumoLiu,

One more question - What has AddChannel been replaced with? To confirm, the AddChannel has been removed and the
corresponding code is

Original
transforms.AddChanneld(keys=["image"]),

Updated
transforms.EnsureChannelFirstd(keys=["image"])

Is this correct? Thank you for your help and those previous references were helpful.

[KumoLiu]

Will be equal to:
transforms.EnsureChannelFirstd(keys=["image"], channel_dim="no_channel")
https://github.com/Project-MONAI/MONAI/blob/c0b9cc0b00459563196b9ce1d430f5d86406c5e6/monai/transforms/utility/array.py#L188

[slefcourt27]

Thank you for your response. You have answered my question!

As an aside, I found this tutorial also https://github.com/Project-MONAI/tutorials/blob/main/modules/3d_image_transforms.ipynb and it seems that both

ensure_channel_first_no_channel = EnsureChannelFirstd(keys=["image", "label"], channel_dim="no_channel")

and

ensure_channel_first = EnsureChannelFirstd(keys=["image", "label"])

return the same shape of

torch.Size([1, 512, 512, 55])

[ebaldelomar]

Hi,

I'm trying to address a similar issue and it's not clear to me how one goes about implementing this edit. I'm pretty new to Monai and monailabel.

I’m trying to test out the case 2 example in the Quickstart documentation (Quickstart — MONAI Label 0.8.5 Documentation).

I got all things installed, downloaded the test data set, and started the server. Below is the error I get when trying to hit 'run' on the Auto Segmentation:

raise ModuleNotFoundError(f"Cannot locate class or function path: ‘{__path}’.")
ModuleNotFoundError: Cannot locate class or function path: ‘AddChanneld’.

I have searched both the monai/ and monailabel/ folders for 'AddChanneld'

grep --include=*.{py} -rnw '/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/' -e "AddChanneld"

Output:

/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/monailabel/tasks/infer/basic_infer.py:171: monai.transforms.AddChanneld(keys='image'),
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/monailabel/tasks/infer/basic_infer.py:211: monai.transforms.AddChanneld(keys='pred'),
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/tests/unit/deepedit/test_deepedit_transforms.py:16:from monai.transforms import AddChanneld
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/tests/unit/deepedit/test_deepedit_transforms.py:184: add_ch = AddChanneld(keys=["image", "label"])(input_data)
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/tests/unit/deepedit/test_deepedit_transforms.py:193: add_ch = AddChanneld(keys=["image", "label"])(input_data)
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/tests/unit/deepedit/test_deepedit_transforms.py:202: add_ch = AddChanneld(keys=["image", "label"])(input_data)
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/tests/unit/deepedit/test_deepedit_transforms.py:211: add_ch = AddChanneld(keys=["image", "label"])(input_data)
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/tests/unit/activelearning/test_epistemic.py:24: AddChanneld,
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/tests/unit/activelearning/test_epistemic.py:73: AddChanneld(keys),
/bmr207/nmrgrp/nmr141/.local/lib/python3.8/site-packages/monai/transforms/transform.py:443: except for example: AddChanneld expects (spatial_dim_1[, spatial_dim_2, ...])

The only two files that actually use 'AddChanneld' (not commented out) are:

• tests/unit/activelearning/test_epistemic.py:73
• tests/unit/deepedit/test_deepedit_transforms.py

I found this thread but it's not clear to me how one goes about properly editing it; and if it's still the appropriate issue.

When checking version of things using:

python -c "import monai; monai.config.print_config()"

I get the following output if helpful:

MONAI version: 1.3.2
Numpy version: 1.23.4
Pytorch version: 2.4.1+cu121
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 59a7211070538586369afd4a01eca0a7fe2e742e
MONAI file: /bmr207/nmrgrp//.local/lib/python3.8/site-packages/monai/init.py

Optional dependencies:
Pytorch Ignite version: 0.4.11
ITK version: 5.4.3
Nibabel version: 4.0.2
scikit-image version: 0.21.0
scipy version: 1.10.1
Pillow version: 9.3.0
Tensorboard version: 2.14.0
gdown version: 5.2.0
TorchVision version: 0.19.1+cu121
tqdm version: 4.64.1
lmdb version: 1.6.2
psutil version: 7.0.0
pandas version: 1.5.1
einops version: 0.7.0
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: 2.17.2
pynrrd version: 1.0.0
clearml version: NOT INSTALLED or UNKNOWN VERSION.

[slefcourt27]

Hi @ebaldelomar, as @KumoLiu mentioned, the AddChannelD function has been removed since MONAI version 1.3. I suggest that you uninstall the MONAI package and reinstall through specifying an earlier version.

[ebaldelomar]

Ah! I didn't think of that. A few questions to follow up to help my understanding if you happen to know:

1. This is likely an issue with the specific bundle/model I'm trying to implement, thus why I may need an older version?

2. When you say uninstall monai package; would that include monai and monailabel? or just monai?

Thanks so much for the response and help!