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MIC-DKFZ / MITK-Diffusion

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit
http://mitk.org/wiki/MITK
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Documentation missing on docs.mitk.org #5

Open benoit-dubreuil opened 2 years ago

benoit-dubreuil commented 2 years ago

The MITK Diffusion plugin's documentation is missing on docs.mitk.org.

A linkless org_mitk_gui_qt_diffusionimaging list item is present in the List of Plugins for End User Use on the MITK Plugin Manuals web page for diffusion imaging. I tried to enter the following URL manually in my web browser, but in vain : https://docs.mitk.org/diffusion/nightly/org_mitk_gui_qt_diffusionimaging.html.

Also, there is no entry for diffusion imaging on the API Reference for MITK Plugins page. Is this normal?

However, by searching in the search box on the docs.mitk.org/diffusion website, I was able to find the page private plugins Directory Reference in which the API Reference for org.mitk.gui.qt.diffusionimaging is located. Is it normal that this is private and difficult to find?

benoit-dubreuil commented 2 years ago

Actually, what I'm looking for is how to use FiberFox using Python code. Is there documentation about this?

The only thing I found was this : https://github.com/PennBBL/fiberfox-wrapper.

Thank you

peterneher commented 2 years ago

Hi Benoît. Since mitk diffusion moved from the core mitk repository to it's own repo and is now an extension of mitk, the documentation is unfortunately not building anymore. This is a known issue and will hopefully be addressed soonish.

Regarding your Fiberfox question. FIberfox or MITK DIffusion in general has no python interface. Nevertheless, you can of course simply call the Fiberfox command line app from python, e.g. using os.system('/path/to/MitkDiffusion/MitkFiberfox.sh')

peterneher commented 2 years ago

The documentation inside of MITK Diffusion should work though. Simply open the Fiberfox view and press F1

benoit-dubreuil commented 2 years ago

Regarding your Fiberfox question. FIberfox or MITK DIffusion in general has no python interface. Nevertheless, you can of course simply call the Fiberfox command line app from python, e.g. using os.system('/path/to/MitkDiffusion/MitkFiberfox.sh')

That's what I found out whilst looking at the FiberFox Python Wrapper code. For any Internet user reading this, on Windows, it is actually os.system('C:/path/to/MitkDiffusion/MitkFiberfox.bat') (Windows supports "forward" slashes in paths).

The documentation inside of MITK Diffusion should work though. Simply open the Fiberfox view and press F1

I confirm it works, thank you.

@peterneher Should I leave this issue open due to the fact that it is a known issue but there's no official issue on this GitHub repository about it?

peterneher commented 2 years ago

Yeas, leave it ope. Might be useful for others. Thank you and don't hesitate to contact me if there are any more questions!