Add _roi_response_denoised to store denoised traces

[alessandratrapani]

Denoised calcium traces should be distinguished from raw calcium traces. See discussion in https://github.com/catalystneuro/roiextractors/issues/287#issuecomment-1956837952

This implementation should also fix #249.

TODO

• [x] Add background spatial components
• [x] Add raw traces as C+Yr
• [x] Add testing

[pauladkisson]

For neuroconv #783, I need

• [x] get_background_ids() following the example of get_roi_ids
• [x] get_background_image_masks() following the example of get_roi_image_masks()
• [x] get_background_pixel_masks() following the example of get_roi_pixels_masks()

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 71.87500% with 9 lines in your changes are missing coverage. Please review.

Project coverage is 79.25%. Comparing base (94691a4) to head (7ad05f5).

Additional details and impacted files

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[pauladkisson]

I noticed that CaimanSegmentationExtractor doesn't have any dedicated unit tests -- maybe this would be a good time to put that together?

I'm still pretty torn about whether we should go for a rolling refactor or an intensive refactor for the testing. @CodyCBakerPhD maybe you can weigh in?

Also, perhaps it is time to add a deprecation warning to the write_segmentation method since we are moving the api away from write support.

[EricThomson]

Note away on vacation until end of next week but I should be able to start looking more then. Very exciting stuff!

[CodyCBakerPhD]

I noticed that CaimanSegmentationExtractor doesn't have any dedicated unit tests -- maybe this would be a good time to put that together?

Looks like it's a part of the general roundtrip tests: https://github.com/catalystneuro/roiextractors/blob/main/tests/test_io.py

From that perspective, dedicated tests would only be for specific assertions of specific structures unique to Caiman that can't be easily included as params in the generic testing framework

I'm still pretty torn about whether we should go for a rolling refactor or an intensive refactor for the testing. @CodyCBakerPhD maybe you can weigh in?

Rolling in small iterative steps is always appreciated for review - for tests as well, there's nothing wrong with keeping the current infrastructure, adding a new one, then remove the old one after the new one is completely done

I'd be in favor of a refactor to something akin to the mixin style of NeuroConv interface tests, which allow you to define format-specific tests pretty easily

Also, perhaps it is time to add a deprecation warning to the write_segmentation method since we are moving the api away from write support.

Yeah, I share the philosophy of SpikeInterface that supporting format-specific writing methods is beyond our scope in this package