How to create and run executable of a monai code?

[Bhagii2508]

Hello,
I have a segmentation code with monai architecture running perfectly with python execution, but when I try to create an executable and run it, it doesn't work. Could anyone please let me know how to fix this? Thanks

[rijobro]

What doesn't work? What error?

[Bhagii2508]

It is throwing me an import error on monai. I created the executable with the pyinstaller package. Also, I noticed on a lot of platforms that there is difficulty in creating executables with Pytorch workflow. Whereas the executables created with pyinstaller of Tensorflow architecture are working perfectly fine.

[plaresmedima]

Hi -I have the same problem. My program runs fine when executing from source but throws an error when I am running the executable created with pyinstaller:

ImportError: cannot import name 'CacheDataset' from partially initialized module 'monai.data' (most likely due to a circular import) (.\monai\data_init_.pyc)

Does anyone know how to resolve it? My executable was running fine before adding the monai/pytorch feature.

[KumoLiu]

Hi @plaresmedima, maybe you can try some solutions introduced in https://stackoverflow.com/questions/69739699/pyinstaller-importerror-cannot-import-name-ccompiler-from-partially-initiali.
Hope it can help you, thanks!

[plaresmedima]

Hi thank you for the suggestion, but it seems the errors are specific to monai. It tried adding the modules that have issues to hidden imports but that does not help.

…

On Fri, 16 Jun 2023, 03:30 YunLiu, ***@***.***> wrote: Hi @plaresmedima <https://github.com/plaresmedima>, maybe you can try some solutions introduced in https://stackoverflow.com/questions/69739699/pyinstaller-importerror-cannot-import-name-ccompiler-from-partially-initiali . Hope it can help you, thanks! — Reply to this email directly, view it on GitHub <#4197 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABOFKAYYOILFEDNS64TCJT3XLPAKRANCNFSM5UTJ6FIQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[wyli]

Thanks for raising the issue, could you help create a small example to demonstrate the issue? I can look into it. (Also a potential reason is that this line of load modules is not involved

MONAI/monai/__init__.py

Line 58 in a89a0af

load_submodules(sys.modules[__name__], False, exclude_pattern=excludes)

)

[plaresmedima]

Dear Wenqi - just a quick note to say thank for your kind offer to look into this. I have not had the time to write up a small example for you unfortunately but I am keeping this on my todo list as it remains an unsolved issue for us. Prof. Steven Sourbron, PhD Chair in Medical Imaging Physics University of Sheffield, UK *https <https://www.sheffield.ac.uk/medicine/people/iicd/steven-sourbron>://www.sheffield.ac.uk/medicine/people/iicd/steven-sourbron <https://www.sheffield.ac.uk/medicine/people/iicd/steven-sourbron>* *Sheffield abdominal imaging research page* <https://www.sheffield.ac.uk/medicine/research/research-themes/medical-imaging/medical-imaging-research/abdominal-imaging> *Open source initiative in perfusion imaging* <http://www.osipi.org> *Magnetic resonance imaging biomarkers for chronic kidney disease <https://renalmri.org/>*

…

On Fri, 16 Jun 2023 at 11:39, Wenqi Li ***@***.***> wrote: Thanks for raising the issue, could you help create a small example to demonstrate the issue? I can look into it. (Also a potential reason is that this line of load modules is not involved https://github.com/Project-MONAI/MONAI/blob/a89a0af10e70256fbe8641e71385ad2c2b3fb405/monai/__init__.py#L58 ) — Reply to this email directly, view it on GitHub <#4197 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABOFKA6RCLD7IX5LHDV5JPLXLQZVNANCNFSM5UTJ6FIQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[VenturaFranklin]

I was able to get around this issue with the following code:

import monai
datas = [(str(Path(monai.__file__).parent), "monai"),]
datas += PyInstaller.utils.hooks.collect_data_files("monai")

a = Analysis(
    ["{PATH_TO_YOUR_MAIN_FILE}"],
    pathex=["{PATH_TO_YOUR_MAIN_DIR}"],
    binaries=[],
    datas=datas,
    hiddenimports=hiddenimports,
    hookspath=[],
    hooksconfig={},
    runtime_hooks=[],
    excludes=[],
    win_no_prefer_redirects=False,
    win_private_assemblies=False,
    cipher=None,
    noarchive=False,
)

Then you have your exe and collect configurations.

There might be better ways to do this, but this worked for me.
And of course you need to replace the path sections with the right paths for you.

I have not had the time to write up a small example for you
unfortunately but I am keeping this on my todo list as it remains an
unsolved issue for us.

@plaresmedima Please, when asking for help, include your code even when it's not a small example. Copy and paste whatever you have and that is a million times better than nothing. And a small example is 1000 times better, but any code is better than nothing. I hope this helps, good luck!

[AmirV97]

Could u elaborate where i should add this code snippet? the 'a' part seems like part of the .spec file, but the first 2 lines seem like python code.

[VenturaFranklin]

@AmirV97 correct yes in the .spec file. You can have Python code in that file.

[AmirV97]

The code snippet uses the class Path in line 2, which is not imported. I'm using a .py script to get my exe file:
import PyInstaller.main
PyInstaller.main.run([
'test__.spec',
])

test__.spec contain the code snippet. I'm getting the following error:
NameError: name 'Path' is not defined

I've added the line from pathlib import Path to both test__.spec and the .py script but i'm still getting the error.