Jupyter Utilities

[ericspod]

Description

This includes some utilities to help use MONAI in Jupyter. I will have an example notebook shortly for the tutorials repo. One issue is that the type checking was difficult to fully include and make work with Matplotlib so some values are untyped, and optional_import cause circular dependency issues in the utility file.

Status

Ready

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[ericspod]

/black

[rijobro]

Could be:

Suggested change

	def _get_loss_from_output(output):
	return output["loss"].item()
	def _get_loss_from_output(output, loss_key = "loss"):
	return output[loss_key].item()

[rijobro]

Might be overkill but could be:

Suggested change

	loss_transform: Callable = _get_loss_from_output,
	loss_transform: Callable = partial(_get_loss_from_output, loss_key=MetricLoggerKeys.LOSS),

[rijobro]

Could you call the other implementation to reduce duplication?

[rijobro]

Looks good. I really like plotting losses with live updates, which makes my tutorials more bloated than necessary. Would be great if that functionality could be incorporated somehow (see use of plot_range in https://app.reviewnb.com/Project-MONAI/tutorials/pull/129/).

[ericspod]

plot_range and the other plotting functions should be consolidated in one place, I have other plot functions to add later on.

[wyli]

could you create a few tests for the plotting method and MetricLogger? came across this util not sure how reliable it is https://github.com/matplotlib/matplotlib/blob/6fe34e72d2b7daf8586a08a8611cc73b3c0ad60c/lib/matplotlib/testing/decorators.py#L393

[wyli]

I forgot to request changes for unit tests, could you please have a follow-up PR, thank you! @ericspod

[wyli]

without tests it's difficult for the other maintainers to understand the intended behaviour and ensure the quality...
as we have a tight schedule for v0.5, If we don't have proper tests for this PR within this week, I'll try to exclude it from the upcoming release to avoid any issues

[wyli]

followup testing addressed by #1826