Unable to run example: No module named 'mrml' and cannot import name 'vtkMRMLScene' from 'slicer'

[ddutartr]

Hi,

I followed the installation steps described in the repository,, including installing the vtk_mrml wheel as indicated in the README, but I cannot run the example application (medical_viewer_app.py).

I successfully installed the Windows wheel (vtk_mrml-9.4.0-cp310-cp310-win_amd64.whl).
However, when I run the example application (medical_viewer_app.py) from a clean Python environment, I still get the following errors:

(trame) PS C:\Users\t6dutdan\Documents\dev\trame_slicer_proxy\examples> python .\medical_viewer_app.py
No module named 'mrml'
Traceback (most recent call last):
  File "C:\Users\t6dutdan\Documents\dev\trame_slicer_proxy\examples\medical_viewer_app.py", line 6, in <module>
    from viewer_lib import MedicalViewerLogic, MedicalViewerUI
  File "C:\Users\t6dutdan\Documents\dev\trame_slicer_proxy\examples\viewer_lib\__init__.py", line 1, in <module>
    from .logic import MedicalViewerLogic, SegmentationAppLogic
  File "C:\Users\t6dutdan\Documents\dev\trame_slicer_proxy\examples\viewer_lib\logic\__init__.py", line 1, in <module>
    from .base_logic import BaseLogic
  File "C:\Users\t6dutdan\Documents\dev\trame_slicer_proxy\examples\viewer_lib\logic\base_logic.py", line 3, in <module>
    from slicer import vtkMRMLScene
ImportError: cannot import name 'vtkMRMLScene' from 'slicer' (C:\Users\t6dutdan\AppData\Local\miniconda3\envs\trame\lib\site-packages\slicer\__init__.py)

It looks like the example still expects the full Slicer Python environment (with MRML and vtkMRMLScene), even though the README suggests that installing vtk_mrml should be enough.

Questions

Is the example expected to work in a standalone Python environment using only the vtk_mrml wheel?

If not, should the README clarify that a full 3D Slicer installation and the SlicerPython interpreter are required?

If yes, is there an additional step or dependency missing to expose vtkMRMLScene and MRML nodes from vtk_mrml?

Thanks for your help!

[Thibault-Pelletier]

Hi @ddutartr,

The MRML wheels are for usage in a separate Python environment.
If the wheel doesn't work, it's probably because you are not using a python version compatible with the wheels.

The windows wheel are only compatible with Python 3.10 win64.

I can see you are using miniconda, but I would recommend to download a simple Python version available here :
https://www.python.org/downloads/release/python-31011/

You can then use a virtual environment following the official instructions and installing the libraries there.

If you are looking for a one click start solution without bothering with the install steps, you can also install the Slicer trame 3D Slicer extension available in 3D Slicer 5.10

For this extension, the trame-slicer library can be installed and a server launched.

[ddutartr]

Hi,

I double-checked: my Python (inside miniconda) is Python 3.10 win64.

To be sure I wasn’t making a mistake, I repeated the exact same steps on a Linux machine.
There too I used miniconda to manage the Python version, installed trame-slicer, and installed the corresponding vtk-mrml wheel for Linux.
Everything works correctly on Linux, but not on Windows.

I did not test using the official 3D Slicer application with the Trame extension.

I can work on Linux without any problem, but I’m wondering:
is this difference in behavior between Windows and Linux expected?

Thanks.

[Thibault-Pelletier]

Hi @ddutartr,

Thx for your feedback!
Are you using a dual boot or using Linux from WSL?

The only difference you will get when using from WSL is the markups point size behavior in screen relative mode.
In WSL, with the default config, the screen size will be the width of all screens connected to your computer.
This width is then used by the markups to define the point size and they will be bigger in case of using multiple screens (you can fiddle with WSL to modify this behavior, but I never used it myself).

If you're on a dual boot or normal Linux configuration, everything will be the same as with the Windows version.
We use Linux to deploy on docker / k8s / AWS and everything is working fine.

Note also that the github action CI is running the unit tests on Linux.

[ddutartr]

Hi @Thibault-Pelletier ,

Just to clarify: I tested on another machine that boots directly into Linux (not WSL).
On this Linux system, everything installs and runs without any issue.

However, on Windows, using the exact same steps and the same conda + pip commands, the installation fails due to the MRML import errors mentioned earlier.

So the behavior is:

Linux (native) --> conda env --> works perfectly

Windows (native) --> conda env --> fails, even with Python 3.10 win64

Let me know if I can provide any additional logs or details to help diagnose the Windows-specific issue.

Thanks!

[Thibault-Pelletier]

Thx for the clarification.

Could you test without conda env and a "normal" python 3.10 win64 environment ?
This is the environment I use on a day to day basis and it works as expected with the provided wheels (as well as other developers on Windows using the same wheel).

If you want to dive further into your specific error, you should:

• Try to import directly from the mrml package: from slicer.mrml import vtkMRMLScene -> this should raise a better error
• Check the pyd present in site-packages/vtkmodules/vtkMRML* with executables like DependenciesGui to check for DLL incompatibilities

I suspect your problem is coming from a DLLs resolution problem which can come from :

• The conda setup itself
• Your windows path configuration
• A win32 / win64 compatibility problem

[ddutartr]

@Thibault-Pelletier
Thanks,

I went quite deep into trying to find the problem, but it still hasn’t been resolved.

It looks like I cannot load this module even after fixing some issues with DependenciesGui:
from vtkmodules.vtkSlicerVolumeRenderingModuleLogic import * ImportError: DLL load failed while importing vtkSlicerVolumeRenderingModuleLogic: Le module spécifié est introuvable.

I will continue working on Linux. =)

[hieund4438]

Hello @ddutartr
I was facing the same situation as you on my Windows machine.

I saw you mentioned 'running on Linux'—does that mean you are running it natively? Have you tried using Docker?

I decided to switch to Docker following the instructions on the /docker branch. However, I am now encountering a "missing module" error inside the container.

Here is the error log:
ImportError: cannot import name 'vtkMRMLLayerDMObjectEventObserverScripted' from 'slicer' (/usr/local/lib/python3.10/site-packages/slicer/init.py)

Did you run into this same issue? If so, how did you resolve it?

Thanks!

[ddutartr]

HI @hieund4438
I tried to run on another computer (native linux).
I did'nt try docker version.

On linux it works "out of the box"

Best

[Thibault-Pelletier]

Hi @hieund4438,

Your problem in docker likely comes from an outdated vtk-mrml wheel version.

Please check the latest version on the readme page

For Windows the current wheels only work on x86_x64 architectures (not arm64 / surface devices)

[hieund4438]

Thank you @Thibault-Pelletier . I have tried another way: i mounted the vtk-mrml wheel to docker container and it run well. I think the version of wheel which I downloaded in the dockerfile is outdated.