909 IO factory - develop ITKReader, NibabelReader, LoadImage

[Nic-Ma]

part of #856 #909 .

Description

This PR refactor the image loader of MONAI to support different loaders.
It can support most of common medical image format, so no need to use different loader for different images.
It's just a beginner PR, also need to change NiftiWriter, NiftiSaver, PNGWriter, PNGSaver, Spacing transform, Orientation transform, etc.
I didn't delete LoadNifti, LoadPNG for compatibility and many examples and tests use them.

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 --codeformat --coverage.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[Nic-Ma]

/black

[Nic-Ma]

/black

[thewtex]

@Nic-Ma this looks great! 🥇

I added a few suggestions inline that may be helpful.

[Nic-Ma]

Hi @thewtex ,

Thanks for your review here!
I updated the code according to your comments.
I will try to add more features in this PR and complete it as the first step of the IO factory soon.

Thanks.

[Nic-Ma]

/black

[Nic-Ma]

/black

[Nic-Ma]

/black

[Nic-Ma]

/black

[Nic-Ma]

/black

[Nic-Ma]

Hi @wyli ,

I updated PR according to your comments.
Could you please help review it again?

Thanks.

[aylward]

Looks good to me! If MONAI starts using Brad G's idea of an "experiment" file (perhaps quite similar to the MONAI global configuration file mentioned in this PR), then that experiment file might also influence which readers are used, but I think it could be easily added and is conceptually consistent with what was done here. Overall, this looks outstanding!!!

[Nic-Ma]

/black

[Nic-Ma]

/black

[Nic-Ma]

/black

[wyli]

thanks @Nic-Ma

[Nic-Ma]

Hi @wyli ,

Thanks for your fix for the typehints issue.