🆕 Use Annotations as a Filter for Patch Extraction

[measty]

This PR is something i've been thinking about from a conversation with Daan when he was here from Radboud doing a seminar a while back. His comment was that one thing some of his colleges felt was missing in TIAtoolbox was ability to get patches filtered by class/label.

Its not that hard to set up tiatoolbox patch extractor to allow this, which is what i've added in this PR.

it allows you to provide a path to an annotation store as the mask. By default the mask will then be built out of all the annotations, but you can also provide any filter that works in the annotation store, and have only those annotations make the mask. So for example, if you have some pathologist annotations with some regions, and you only want to extract patches which have some overlap with regions labelled 'tumor' or whatever, you would just have to provide the appropriate string ("props['label'] == 'tumor'" for example).

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Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 99.86%. Comparing base (52792bc) to head (62f3566). Report is 17 commits behind head on develop.

Additional details and impacted files

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  Coverage    99.86%   99.86%           
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  Files           69       69           
  Lines         8656     8664    +8     
  Branches      1653     1654    +1     
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+ Hits          8644     8652    +8     
  Misses           4        4           
  Partials         8        8           

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[shaneahmed]

Thanks @measty

@mostafajahanifar Please can you review this PR so we can merge this.

[shaneahmed]

@mostafajahanifar I have updated the file.

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mostafajahanifar commented on 2024-08-30T18:02:03Z ----------------------------------------------------------------

Link of documentaiotn is better to be to the main repo instead of the develop

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mostafajahanifar commented on 2024-08-30T18:02:04Z ----------------------------------------------------------------

Line #3.    pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@patch-extractor-filter | tail -n 1

Just make sure you change this installation back to the main repo before merging.

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mostafajahanifar commented on 2024-08-30T18:02:05Z ----------------------------------------------------------------

if you want, you can also add a reference to tissue masking example notebook here in the paranthesis in the first sentence.

... wsi through a simple otsu threshold approach (for more information on tissue masking, please see tiatoolbox/examples/03-tissue-masking.ipynb at master · TissueImageAnalytics/tiatoolbox (github.com))