`ValueError`: `module://matplotlib_inline.backend_inline is not a valid value` when running SCT scripts in Jupyter notbooks about spinalcordtoolbox HOT 11 CLOSED

Thank you for the detailed investigation! Taking a look now. :)

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I tried to checkout an older version of SCT (I wanted to specifically checkout 6.3, but ran into #4524, so I ended up randomly picking 8f2b0e0, which was before the introduction of LazyImport):

I still observe an error, so in the end this issue is likely not related to the LazyImports:

👉 PROCESSING: sub-MGH
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_label_utils.py", line 24, in <module>
    from spinalcordtoolbox.reports.qc import generate_qc
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/qc.py", line 22, in <module>
    from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/matplotlib/__init__.py", line 1270, in <module>
    rcParams['backend'] = os.environ.get('MPLBACKEND')
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/matplotlib/__init__.py", line 738, in __setitem__
    raise ValueError(f"Key {key}: {ve}") from None
ValueError: Key backend: 'module://matplotlib_inline.backend_inline' is not a valid value for backend; supported values are ['gtk3agg', 'gtk3cairo', 'gtk4agg', 'gtk4cairo', 'macosx', 'nbagg', 'notebook', 'qtagg', 'qtcairo', 'qt5agg', 'qt5cairo', 'tkagg', 'tkcairo', 'webagg', 'wx', 'wxagg', 'wxcairo', 'agg', 'cairo', 'pdf', 'pgf', 'ps', 'svg', 'template']
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 34, in <module>
    from spinalcordtoolbox.reports import qc2
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/qc2.py", line 20, in <module>
    from matplotlib.axes import Axes
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/matplotlib/__init__.py", line 1270, in <module>
    rcParams['backend'] = os.environ.get('MPLBACKEND')
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/matplotlib/__init__.py", line 738, in __setitem__
    raise ValueError(f"Key {key}: {ve}") from None
ValueError: Key backend: 'module://matplotlib_inline.backend_inline' is not a valid value for backend; supported values are ['gtk3agg', 'gtk3cairo', 'gtk4agg', 'gtk4cairo', 'macosx', 'nbagg', 'notebook', 'qtagg', 'qtcairo', 'qt5agg', 'qt5cairo', 'tkagg', 'tkcairo', 'webagg', 'wx', 'wxagg', 'wxcairo', 'agg', 'cairo', 'pdf', 'pgf', 'ps', 'svg', 'template']

Next suspicion: the declaration of %matplotlib inline in the notebook.

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I removed the declaration %matplotlib inline, but I still get the same error.

Googling around:

• matplotlib/matplotlib#19848
• ipython/ipython#14368
• https://stackoverflow.com/questions/59123880/valueerror-unrecognized-backend-string-gtkagg-valid-strings-are-gtk3agg
• Particularly relevant, MPL doc: https://matplotlib.org/stable/users/explain/figure/backends.html

I manually set: %matplotlib notebook (as suggested in MPL doc), but I still get the same error. My suspicion is that inside SCT's sct_register_multimodal, we re-set MPL's backend.

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When I comment out this line, the notebook runs without error:

Which suggests that one solution (probably not the best...) would consist in not running this line if QC report is not asked for.

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What I find strange, however, is how come we're only seeing this issue now... we've been using notebooks in other projects lately, and it included sct_register_multimodal, example here

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Hum, it's getting weirder-- if I run another sct_register_multimodal syntax (with other data and parameters), there is no crash:

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Ah! Interesting! When commenting out the SCT's call that comes before the call to sct_register_multimodal, there is no crash either:

OK, so... maybe running sct_label_utils somehow changes something about the state of MPL backend???

Nevermind... now it works even if I put back the sct_label_utils line...

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re-starting the notebook, re-running the cells, now it works without crash... i don't understand.

AH! ok, nevermind.. I had forgotten that I commented out the problematic import in sct_register_multimodal... ok starting the experiments again...

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ok, crash is consistent:

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also consistent when running it in ANOTHER notebook (the rf-shimming one):

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Briefly looking at issues in other repos, I see a few things:

• module://matplotlib_inline.backend_inline should be a valid backend.
• However, 2 other people are reporting this same error (1, 2), and their reports are relatively recent (18-19 days ago). This seems to suggest that this error may be due a recent change in matplotlib/jupyter/etc. Maybe the issue was always present, but matplotlib only started throwing the error in recent versions?

I was able to reproduce the issue depending on the state of the SCT repo:

• If matplotlib-inline is installed in SCT's environment, there is no error.
• If matplotlib-inline is uninstalled, then the error is thrown:

Traceback (most recent call last):
  File "/home/joshua/repos/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 34, in <module>
    from spinalcordtoolbox.reports import qc2
  File "/home/joshua/repos/spinalcordtoolbox/spinalcordtoolbox/reports/qc2.py", line 30, in <module>
    import matplotlib
  File "/home/joshua/repos/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/matplotlib/__init__.py", line 1270, in <module>
    rcParams['backend'] = os.environ.get('MPLBACKEND')
  File "/home/joshua/repos/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/matplotlib/__init__.py", line 738, in __setitem__
    raise ValueError(f"Key {key}: {ve}") from None
ValueError: Key backend: 'module://matplotlib_inline.backend_inline' is not a valid value for backend; supported values are ['gtk3agg', 'gtk3cairo', 'gtk4agg', 'gtk4cairo', 'macosx', 'nbagg', 'notebook', 'qtagg', 'qtcairo', 'qt5agg', 'qt5cairo', 'tkagg', 'tkcairo', 'webagg', 'wx', 'wxagg', 'wxcairo', 'agg', 'cairo', 'pdf', 'pgf', 'ps', 'svg', 'template']

I'm not 100% sure why you only encountered this error sporadically. Perhaps the "sporadic" part was due to the LazyLoading? But, nonetheless, we should be able to fix this by adding matplotlib-inline to SCT's requirements.txt.

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