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🆕 Integrate Foundation Models Available VIA timm: UNI, Prov-GigaPath, H-optimus-0 #856

Merged
merged 54 commits into from
Nov 15, 2024
Merged

🆕 Integrate Foundation Models Available VIA timm: UNI, Prov-GigaPath, H-optimus-0 #856

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5bf228f
add `_get_timm_architecture()` and `TimmBackbone`
GeorgeBatch Sep 2, 2024
1bc3424
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 2, 2024
f1ec821
inherit `TimmBackbone` from `CNNBackbone`
GeorgeBatch Sep 3, 2024
d823c1e
update link: change GitHub to HuggingDace for UNI model
GeorgeBatch Sep 3, 2024
7aa3ca3
Merge branch 'develop' into enhance-add-timm-feature-extractors
shaneahmed Sep 20, 2024
934bd9a
Merge branch 'TissueImageAnalytics:develop' into enhance-add-timm-fea…
GeorgeBatch Sep 24, 2024
c4bbb40
Apply suggestions from code review: prov-gigapath version of timm
GeorgeBatch Sep 24, 2024
2c9a47f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 24, 2024
6ec9ca1
remove explicit assert statement re prov-gigapath version of `timm`
GeorgeBatch Sep 24, 2024
5445ff5
Merge branch 'TissueImageAnalytics:develop' into enhance-add-timm-fea…
GeorgeBatch Oct 16, 2024
142eaf6
remove unused arguments in ; fix formatting
GeorgeBatch Oct 16, 2024
36126c5
remove unused arguments from docstring of _get_timm_architecture
GeorgeBatch Oct 16, 2024
1b666b8
improve error message in _get_timm_architecture()
GeorgeBatch Oct 16, 2024
9c494a2
simplify inheretance code of TimmBackbone
GeorgeBatch Oct 16, 2024
5b5f674
add TimmModel class inheriting from CNNModel
GeorgeBatch Oct 16, 2024
7f51fec
add tests for TimmModel - fail because backbone argument in not speci…
GeorgeBatch Oct 16, 2024
40f7f95
TEMPORARY FIX: pass backbone="alexnet" for TimmModel and TimmBackbone…
GeorgeBatch Oct 16, 2024
7ec12b7
Make consistent with `_get_architecture` error message
GeorgeBatch Oct 17, 2024
4eb7f8c
fix `__init__` methods of `TimmModel` and `TimmBackbone`
GeorgeBatch Oct 17, 2024
7b0c0e8
add `timm>=1.0.3` as a requirement, otherwise the build is failing
GeorgeBatch Oct 17, 2024
deea74f
introduce a keyword-only `pretrained` argument for `timm` models
GeorgeBatch Oct 17, 2024
3437c1a
add support for `H-optimus-0`
GeorgeBatch Oct 17, 2024
a47300c
add a comment with HuggingFace link for H-Optimus-0
GeorgeBatch Oct 17, 2024
373ee8a
replace "uni_v1" with "UNI" for consistency with HuggingFace name
GeorgeBatch Oct 17, 2024
3263e3c
add "efficientnet_b{i}" for i in [0, 1, ..., 7]
GeorgeBatch Oct 18, 2024
d037dda
fix typo and shorten ProViT-GigaPath comments
GeorgeBatch Oct 18, 2024
e2f4a9d
Merge branch 'TissueImageAnalytics:develop' into enhance-add-timm-fea…
GeorgeBatch Oct 19, 2024
6afecd2
:fire: No need to check for timm version
shaneahmed Oct 24, 2024
2b5f9ce
:fire: No need to check for timm version
shaneahmed Oct 24, 2024
dad9f8e
:recycle: Define `postproc` and `infer_batch` used commonly by CNNMod…
shaneahmed Oct 24, 2024
f893a83
:recycle: Refactor `CNNBackBone` and `TimmBackbone`.
shaneahmed Oct 24, 2024
4293044
:bug: Fix deepsource error
shaneahmed Oct 24, 2024
cc31dc7
:pushpin: Pin `numpy` version <2.0
shaneahmed Oct 24, 2024
9ae4d6e
:white_check_mark: Skip Coverage for `UNI`, `Prov-GigaPath`, `H-Opti…
shaneahmed Oct 24, 2024
0166e61
Merge branch 'TissueImageAnalytics:develop' into enhance-add-timm-fea…
GeorgeBatch Oct 24, 2024
617c93f
🔥 No need to check for timm version
GeorgeBatch Oct 25, 2024
d30d7d8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 25, 2024
d08127f
add test for TimmBackbone
GeorgeBatch Oct 29, 2024
85ad67b
show how thumbnails and masks can be saved using `tiatoolbox.utils.mi…
GeorgeBatch Nov 4, 2024
961a9ba
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 4, 2024
18070c5
fix typo
GeorgeBatch Nov 4, 2024
c270d7d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 4, 2024
ad9053d
add Google Colab link
GeorgeBatch Nov 5, 2024
9eebbb4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 5, 2024
dabf9a9
add TimmBackbone example as a comment under `model = CNNBackbone("res…
GeorgeBatch Nov 5, 2024
5c93e9a
add TimmBackbone example as a comment under model = CNNBackbone("resn…
GeorgeBatch Nov 5, 2024
1ab884e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 5, 2024
276da9c
Attempt to fix ruff error: commented code (TimmBackbone)
GeorgeBatch Nov 5, 2024
eba8d16
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 5, 2024
6450d01
Attempt to fix ruff error: commented code (TimmBackbone) - inference …
GeorgeBatch Nov 5, 2024
ce2ef64
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 5, 2024
3631b34
[skip ci] :memo: Update 03-tissue-masking.ipynb
shaneahmed Nov 15, 2024
6f476c1
Merge branch 'develop' into enhance-add-timm-feature-extractors
shaneahmed Nov 15, 2024
c159182
[skip ci] :memo: Update the jupyter notebooks.
shaneahmed Nov 15, 2024
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86 changes: 57 additions & 29 deletions examples/03-tissue-masking.ipynb
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