WSIReader read by power and mpp

[drbeh]

Fixes #6289

Description

This PR enable WSIReader to be provided with objective power and resolution (micron per pixel) to decide which WSI level to load. It also set absolute and relative tolerances for power and mpp.

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• 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 --disttests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[drbeh]

@Nic-Ma @wyli please let me know if you have any other comments. Otherwise, this PR is ready to be merged. Thanks

[wyli]

this missing piece is an option for handling the resampling e.g. when the requested exact mpp is not available. could you please add this?

@wyli that's correct! We have discussed about it in the pathology working group few weeks ago and we decided not to include resampling in this PR and leave it as a feature request for the future since it requires some decision on how and when exactly to do resampling.

so in that case this PR wouldn't close #4980 as the description suggested?

[drbeh]

this missing piece is an option for handling the resampling e.g. when the requested exact mpp is not available. could you please add this?

@wyli that's correct! We have discussed about it in the pathology working group few weeks ago and we decided not to include resampling in this PR and leave it as a feature request for the future since it requires some decision on how and when exactly to do resampling.

so in that case this PR wouldn't close #4980 as the description suggested?

Fair enough! I'll make it clear in a separate issue.

[wyli]

thanks, it looks good to me now

sorry I thought it was updated

[wyli]

cc @cooperlab @gigony @manthey @shaneahmed from the original feature request in case they are interested in sharing some comments

[drbeh]

cc @cooperlab @gigony @manthey @shaneahmed from the original feature request in case they are interested in sharing some comments

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

[wyli]

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

thanks, I couldn't find any documentation/discussion about the proposed interfaces as recommended in rapidsai/cucim#389

[drbeh]

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

thanks, I couldn't find any documentation/discussion about the proposed interfaces as recommended in rapidsai/cucim#389

I believe what you are referring to is not related to this PR. As you correctly spotted, this PR is not addressing #4980, which is related to that cucim feature request. This PR is now closing this feature request #6289. Please let me know if you have any question.

[wyli]

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

thanks, I couldn't find any documentation/discussion about the proposed interfaces as recommended in rapidsai/cucim#389

I believe what you are referring to is not related to this PR. As you correctly spotted, this PR is not addressing #4980, which is related to that cucim feature request. This PR is now closing this feature request #6289. Please let me know if you have any question.

I saw that you have edited ticket #6289 to have the opposite meaning, I kind of agree more with the previous edit...

[drbeh]

I saw that you have edited ticket #6289 to have the opposite meaning, I kind of agree more with the previous edit...

@wyli I have reverted the update to the issue. Please take another look and let me know if all is good with you for this PR to me merged. Thanks

[drbeh]

@wyli @Nic-Ma if there is not any other comments, we should be able to merge this PR. Thanks

[Nic-Ma]

@wyli @Nic-Ma if there is not any other comments, we should be able to merge this PR. Thanks

I already approved the PR before, @wyli Do you have any other comments?

Thanks.

[wyli]

/build