kaiko-eva 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

{kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kaiko-eva
-Version: 0.2.0
+Version: 0.2.2
 Summary: Evaluation Framework for oncology foundation models.
 Keywords: machine-learning,evaluation-framework,oncology,foundation-models
 Author-Email: Ioannis Gatopoulos <ioannis@kaiko.ai>, =?utf-8?q?Nicolas_K=C3=A4nzig?= <nicolas@kaiko.ai>, Roman Moser <roman@kaiko.ai>
@@ -241,6 +241,7 @@ Requires-Dist: scikit-image>=0.24.0; extra == "vision"
 Requires-Dist: imagesize>=1.4.1; extra == "vision"
 Requires-Dist: scipy>=1.14.0; extra == "vision"
 Requires-Dist: monai>=1.3.2; extra == "vision"
+Requires-Dist: einops>=0.8.1; extra == "vision"
 Provides-Extra: all
 Requires-Dist: h5py>=3.10.0; extra == "all"
 Requires-Dist: nibabel>=4.0.1; extra == "all"
@@ -253,6 +254,7 @@ Requires-Dist: scikit-image>=0.24.0; extra == "all"
 Requires-Dist: imagesize>=1.4.1; extra == "all"
 Requires-Dist: scipy>=1.14.0; extra == "all"
 Requires-Dist: monai>=1.3.2; extra == "all"
+Requires-Dist: einops>=0.8.1; extra == "all"
 Description-Content-Type: text/markdown
 
 <div align="center">
@@ -291,7 +293,7 @@ Check out the [documentation](https://kaiko-ai.github.io/eva/) for more informat
 
 ### Highlights:
 - Easy and reliable benchmark of Oncology FMs
-- Supports path-level classification, slide-level classification and semantic segmentation downstream tasks
+- Supports patch-level classification, slide-level classification and semantic segmentation downstream tasks
 - Automatic embedding inference and evaluation of a downstream task
 - Native support of popular medical [datasets](https://kaiko-ai.github.io/eva/dev/datasets/) and models
 - Produce statistics over multiple evaluation fits and multiple metrics
@@ -446,26 +448,28 @@ input, resulting in a faster evaluation.
 Here are some examples to get you started:
 
 - Perform a downstream offline **classification** evaluation of `DINO ViT-S/16`
-on the `BACH` dataset with linear probing by first inferring the embeddings
-and then performing 5 sequential fits:
+on the `BACH` dataset with linear probing by first pre-calculating the embeddings:
   ```sh
-  export DOWNLOAD_DATA=true
-  eva predict_fit --config https://raw.githubusercontent.com/kaiko-ai/eva/main/configs/vision/dino_vit/offline/bach.yaml
+  DOWNLOAD_DATA=true \
+  MODEL_NAME=universal/vit_small_patch16_224_dino \
+  eva predict_fit --config https://raw.githubusercontent.com/kaiko-ai/eva/main/configs/vision/pathology/offline/classification/bach.yaml
   ```
 
-- Perform a downstream online **segmentation** evaluation of `DINO ViT-S/16` on the
-`MoNuSAC` dataset with the `ConvDecoderMS` decoder:
+- Perform a downstream online **segmentation** evaluation of `DINO ViT-S/16` on the `MoNuSAC` dataset with the `ConvDecoderWithImage` decoder:
   ```sh
-  export DOWNLOAD_DATA=true
-  eva fit --config https://raw.githubusercontent.com/kaiko-ai/eva/main/configs/vision/dino_vit/online/monusac.yaml
+  DOWNLOAD_DATA=true \
+  MODEL_NAME=universal/vit_small_patch16_224_dino \
+  eva fit --config https://raw.githubusercontent.com/kaiko-ai/eva/main/configs/vision/pathology/online/segmentation/monusac.yaml
   ```
 
+By default `eva` will perform 5 evaluation runs using different seeds, however, you can control the number of runs through the `N_RUNS` environment variable or in the configuration file. The results will be saved to `./logs` by default, or to `OUTPUT_ROOT` if specified.
+
 For more examples, take a look at the [configs](https://github.com/kaiko-ai/eva/tree/main/configs)
-and [tutorials](https://kaiko-ai.github.io/eva/dev/user-guide/advanced/replicate_evaluations/).
+and [tutorials](https://kaiko-ai.github.io/eva/main/user-guide/advanced/replicate_evaluations/).
 
 > [!NOTE]
 > All the datasets that support automatic download in the repo have by default the option to automatically download set to false.
-> For automatic download you have to manually set the environmental variable `DOWNLOAD_DATA=true` or in the configuration file `download=true`.
+> For automatic download you have to manually set the environment variable `DOWNLOAD_DATA=true` or in the configuration file `download=true`.
 
 ## Leaderboards
 

{kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.2.dist-info}/RECORD

@@ -23,7 +23,7 @@ eva/core/data/datamodules/call.py,sha256=jjj9w3UXYuQB-qyCcw1EZpRJW10OC1I3dvgvsuQ
 eva/core/data/datamodules/datamodule.py,sha256=_pK59oXDe53oDkmv6eoJUvfl44WlFkrbC8KXSRMs_20,5533
 eva/core/data/datamodules/schemas.py,sha256=rzcf3uow6T6slVSwxEGDVmpi3QUvkiDoT_gCF3aMAEE,2262
 eva/core/data/datasets/__init__.py,sha256=jWPxT3gjQjwS6HqVZAb7KhMgzgklPgHeH51iPxDh_Tg,493
-eva/core/data/datasets/base.py,sha256=BLzlRFuByhrGmI7NFwn7-Tw0vpSYSRhl2Y65iX4KaMw,2526
+eva/core/data/datasets/base.py,sha256=w8c9Jh3DiXVfBEdLfWpdE190lPAeOFqCQlXl7RqlDOU,2671
 eva/core/data/datasets/classification/__init__.py,sha256=wJ2jD9YODftt-dMcMf0TbCjJt47qXYBKkD4-XXajvRQ,340
 eva/core/data/datasets/classification/embeddings.py,sha256=hBO6dIRHAhoCaYb3ANc9fgvdBjyQNKPTrIhjc9y8-Ys,1108
 eva/core/data/datasets/classification/multi_embeddings.py,sha256=4hQy4741NDKqWCpm3kGq7aC28DF5gcwUuIpYhnbTyeM,4601
@@ -73,21 +73,22 @@ eva/core/metrics/structs/schemas.py,sha256=ZaSrx0j_NfIwT7joMUD1LyrKdAXTLaeSzWYTH
 eva/core/metrics/structs/typings.py,sha256=qJd-FiD2IhJgBeo8FyP0vpVUIH4RKb1k6zYvHtjUA04,388
 eva/core/models/__init__.py,sha256=T6Fo886LxMj-Y58_ylzkPkFSnFR2aISiMIbuO_weC4s,430
 eva/core/models/modules/__init__.py,sha256=QJWJ42BceXZBzDGgk5FHBcCaRrB9egTFKVF6gDsBYfM,255
-eva/core/models/modules/head.py,sha256=2rPlo2Osuq77gjrJmvQKCvNTaawvQRirK2CM2o24_xs,5184
+eva/core/models/modules/head.py,sha256=bZ45RBPi3N8sjvKyt2_TeKWI1eB6GyBeGzV6J11ERO8,5225
 eva/core/models/modules/inference.py,sha256=ih-0Rr2oNf2N6maiXPOW7XH5KVwUT1_MOxnJKOhJ1uQ,978
 eva/core/models/modules/module.py,sha256=LtjYxTZb7UY0owonmt_yQ5EySw3sX-xD9HLN2io8EK4,6697
-eva/core/models/modules/typings.py,sha256=yFMJCE4Nrfd8VEXU1zk8p6Sz5M7UslwitYPVC2OPLSY,776
+eva/core/models/modules/typings.py,sha256=LPR8JdIid2gJZpjMG1FcH5OZ60JlFOj_LupIh__2k_8,803
 eva/core/models/modules/utils/__init__.py,sha256=ScLCHwQfzlg_UsHVi5sf_SavUkh9secwtRn_umC_qA8,325
 eva/core/models/modules/utils/batch_postprocess.py,sha256=RwnDcjJy3uvVirpgx_80Q2CUYKfJKipVwjyX7AF2CKw,3088
 eva/core/models/modules/utils/checkpoint.py,sha256=Zp42rtmjgUC4VUMwFyG5aar-E0Hc5i7qUsxkV7AVKkE,700
 eva/core/models/modules/utils/grad.py,sha256=bl8qb8g4Nhg1KAGfbEV_9HTKkoT0azRwfs9KGX9swGs,706
 eva/core/models/networks/__init__.py,sha256=yqx6UmG1Eg3vb1O_tnK_axnJWabEl9ULkDWiPN440Xc,85
 eva/core/models/networks/mlp.py,sha256=thk-x4pviE3fCaMW9k3I2Oe5_DxfC-CqUrtolvVdXug,2418
-eva/core/models/transforms/__init__.py,sha256=oYL3gNUUKZFViTu6GT1jVE2Kv1xFYPuyiYp-sErtVVg,257
+eva/core/models/transforms/__init__.py,sha256=AOy_2VY3ITLRk2PMqe6xfErvV7V2_XsnPQwEMhovxOU,333
+eva/core/models/transforms/as_discrete.py,sha256=1w2NmcLzEuyPhaoVXl6jZTdblk7DPf6W6gQ_qi96hQM,1901
 eva/core/models/transforms/extract_cls_features.py,sha256=tFRd4H-eGFIGCfZt6wuZGibDmAoNXKSsn15bBw0IDdc,1482
 eva/core/models/transforms/extract_patch_features.py,sha256=k50jTLPWxbfvciH9QZSzTAGqWwDSVpXAteme_Qg2d6E,2202
 eva/core/models/wrappers/__init__.py,sha256=jaiANQdbO-IPgH8U-Y0ftFsuuCAM5i5KuYRHauKw5k8,450
-eva/core/models/wrappers/_utils.py,sha256=HXUyGcILaa8GK31ViIHCKRU4f9kbjAPYQmhvN2N7jSc,957
+eva/core/models/wrappers/_utils.py,sha256=ZWe9Ih_0kH5Wg_AQAtAn77LZ_CODAve5u3G12ifLNsc,4902
 eva/core/models/wrappers/base.py,sha256=xKMUSXk93wI67p_wmh7jujK-bxvIefO1noYaAJN_5Ak,1359
 eva/core/models/wrappers/from_function.py,sha256=_vKBwtfilCNCnOaJTofE6l5bM2K3qJ8GyBT-0CM5FXY,1831
 eva/core/models/wrappers/from_torchhub.py,sha256=OAImGKRG4pfDXHsoriykC_iiO8QvK3nAWnQCE0mIGuk,3285
@@ -95,7 +96,7 @@ eva/core/models/wrappers/huggingface.py,sha256=5CoNieivdjwvoawo7dZtWfYZkW-Mey1j0
 eva/core/models/wrappers/onnx.py,sha256=-iV-IlczTvTTEQuJycZeSVWdSl2kVJXc1eeRLgQQZ7Q,1834
 eva/core/trainers/__init__.py,sha256=jhsKJF7HAae7EOiG3gKIAHH_h3dZlTE2JRcCHJmOzJc,208
 eva/core/trainers/_logging.py,sha256=gi4FqPy2GuVmh0WZY6mYwF7zMPvnoFA050B0XdCP6PU,2571
-eva/core/trainers/_recorder.py,sha256=y6i5hfXftWjeV3eQHmMjUOkWumnZ2QNv_u275LLmvPA,7702
+eva/core/trainers/_recorder.py,sha256=uD17l_WVveFuWuann59VU9iJ-Jumdh9F6vnAcL3M_FU,7855
 eva/core/trainers/_utils.py,sha256=M3h8lVhUmkeSiEXpX9hRdMvThGFCnTP15gv-hd1CZkc,321
 eva/core/trainers/functional.py,sha256=rLtQZw8TcAa4NYIf901TmoQiJDNm4RGVLN-64nku3Jo,4445
 eva/core/trainers/trainer.py,sha256=a3OwLWOZKDqxayrd0ugUmxJKyQx6XDb4GHtdL8-AEV0,4826
@@ -109,6 +110,7 @@ eva/core/utils/multiprocessing.py,sha256=BWX8AW_KPLgIIlbsPG1kYdtbHPx6Dklw13bu4u8
 eva/core/utils/operations.py,sha256=eoC_ScuHUMDCuk08j1bosiQZdPrgiIODqqheR9MtJHQ,641
 eva/core/utils/parser.py,sha256=2czmwEGJJ6PtmaD86s9I14P-_sek4DmDCkEatRGT5sI,725
 eva/core/utils/progress_bar.py,sha256=KvvsM_v3_Fhb4JvbEEPHb4PJMokg6mNLj-o6dkfzcMc,499
+eva/core/utils/suppress_logs.py,sha256=pOk1076J0mKWn2lgDqEVC1g65FXhA_2IkC4LBEWhnwQ,902
 eva/core/utils/workers.py,sha256=hfx63M82qNg0Dwhre2tl53MnhtRsV7APaDONM9nhVB8,634
 eva/vision/__init__.py,sha256=oUZXFYjwtkWzi8An0uS5Xc84pLKintlXe2iti8zW6BQ,480
 eva/vision/callbacks/__init__.py,sha256=su1V73L0dDVYWSyvV_lnWbszDi2KikRraF7OsgeaKl4,139
@@ -116,46 +118,58 @@ eva/vision/callbacks/loggers/__init__.py,sha256=td1JRJbE08nsGIZdO64_yLC3FUuMDp0k
 eva/vision/callbacks/loggers/batch/__init__.py,sha256=DVYP7Aonbi4wg_ERHRj_8kb87Ee_75wRZzdduJ_icQk,173
 eva/vision/callbacks/loggers/batch/base.py,sha256=hcAd5iiHvjZ0DIf4Qt4ENT54D6ky_1OO4rKQZqeo-1k,3628
 eva/vision/callbacks/loggers/batch/segmentation.py,sha256=GYh2kfexW5pUZ0BdApYJI3e8xsuNkjIzkj5jnuKtHR4,6886
-eva/vision/data/__init__.py,sha256=aoKPmX8P2Q2k2W3nlq8vFU41FV6Sze-0SDuWtU-ETh4,111
-eva/vision/data/datasets/__init__.py,sha256=wvbkhBv_yS7hHMdMR-QpNHMkGoGzSL0L33XaXUwXTpM,1040
+eva/vision/data/__init__.py,sha256=zuLOC8ExyeQGlwib1LB70RedrTC9w0siOhFTQIRb0V8,137
+eva/vision/data/dataloaders/__init__.py,sha256=7AOD_UF3hMokrGxJ2tbawH44ujQaesDsaW-3HWorYv8,128
+eva/vision/data/dataloaders/collate_fn/__init__.py,sha256=GCvJaeILmAc_-lhGw8yzj2cC2KG4i1PvSWAyVzPKvVo,146
+eva/vision/data/dataloaders/collate_fn/collection.py,sha256=45s9fKjVBnqfnuGWmJZMtt_DDGnfuf7qkWe0QmxXMKo,611
+eva/vision/data/datasets/__init__.py,sha256=NW034jrOnpDwYBQfsTjWG6jDJY_dPWKV-cq37HkBm10,1014
 eva/vision/data/datasets/_utils.py,sha256=epPcaYE4w2_LtUKLLQJh6qQxUNVBe22JA06k4WUerYQ,1430
 eva/vision/data/datasets/_validators.py,sha256=77WZj8ewsuxUjW5WegJ-7zDuR6WdF5JbaOYdywhKIK4,2594
 eva/vision/data/datasets/classification/__init__.py,sha256=5fOGZxKGPeMCf3Jd9qAOYADPrkZnYg97_QE4DC79AMI,1074
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 eva/vision/data/datasets/segmentation/_total_segmentator.py,sha256=DTaQaAisY7j1h0-zYk1_81Sr4b3D9PTMieYX0PMPtIc,3127
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 eva/vision/data/datasets/segmentation/embeddings.py,sha256=RsTuAwGEJPnWPY7q3pwcjmqtEj0wtRBNRBD4a0RcGtA,1218
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 eva/vision/data/datasets/structs.py,sha256=RaTDW-B36PumcR5gymhCiX-r8GiKqIFcjqoEEjjFyUE,389
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+eva/vision/data/transforms/common/__init__.py,sha256=ZHzpdr-THc9CgFFbAVMWUiZrUNUiHnCDM8GYhM7tMfU,138
 eva/vision/data/transforms/common/resize_and_crop.py,sha256=GI1HTkbJ9qg4p8c6vk_XkXO0Qi6mBeUeiZIA0jVtmAw,1360
-eva/vision/data/transforms/normalization/__init__.py,sha256=0MZ1KphOr6LxBCOBn7LZ8H8M6-0CuFqvynTON5pedxg,240
-eva/vision/data/transforms/normalization/clamp.py,sha256=B-QyMCFEJPiJagpPr7JhrzOJMVuUB-D_qrmjvthJTyE,1412
-eva/vision/data/transforms/normalization/functional/__init__.py,sha256=ICg611_heHCiNxTNoteFX2MTav59fv7vLkTM8c4eS3w,194
-eva/vision/data/transforms/normalization/functional/rescale_intensity.py,sha256=ihJdDRogrJbvFpb8LcPdRzCFWdlMcBTpWD5RY2MOPbE,844
-eva/vision/data/transforms/normalization/rescale_intensity.py,sha256=BNzDeyzT0GG_FBtlZauCL-K4E_KVWH9SzTSN1SsFNJw,1756
+eva/vision/data/transforms/croppad/__init__.py,sha256=d36WGe9x39p-d7VymRM29qdquv8YEa0RfsTfwt7Cou4,375
+eva/vision/data/transforms/croppad/crop_foreground.py,sha256=3o27nOgxfRo8ap45lpmnaiAIZ08kdyp14vYpr4BC8zc,4865
+eva/vision/data/transforms/croppad/rand_crop_by_pos_neg_label.py,sha256=8CwMYAOQgOIb1Uw1jc219aqY3s2tCWd6r-2nU7kqOLc,5538
+eva/vision/data/transforms/croppad/spatial_pad.py,sha256=j5V2vvgGcf75GzGyAT7mGgpvlEOS2BnAcThRdt7Und4,2857
+eva/vision/data/transforms/intensity/__init__.py,sha256=mNp6pi0pnHcA24kQuiGHzMb4XLRaR0Lgi-Vb7Nl-Aoo,408
+eva/vision/data/transforms/intensity/rand_scale_intensity.py,sha256=DDcFWTmq5UbwISO9qGIPOQJ72rx7JQWtVi2OxggLzyE,2041
+eva/vision/data/transforms/intensity/rand_shift_intensity.py,sha256=9YNREhRoCzLOt2C21daum62cbB53ZRcYOSuSW_Jz7eQ,1974
+eva/vision/data/transforms/intensity/scale_intensity_ranged.py,sha256=VLvYZYG6jQCuR5poJsAlhIFjw6VjPEpcDPKBlJTjYBM,1873
+eva/vision/data/transforms/spatial/__init__.py,sha256=k7C_p4fMZd7A00ikldAMsprYDedKrlMjKQB6BLA5InA,284
+eva/vision/data/transforms/spatial/flip.py,sha256=jfRc-wPBvG58OtCNU3GrOkb57kcRddRqpwcAdCB0_No,2553
+eva/vision/data/transforms/spatial/rotate.py,sha256=FpMTAPWtgrG10yQ3R1_Ii6obPcn3boNWOuLhsblxUbQ,1793
+eva/vision/data/transforms/spatial/spacing.py,sha256=T1UhqK-OhhbLQxzejMyI8BQzYRF44PNc02Qap4nk1hY,2695
+eva/vision/data/transforms/utility/__init__.py,sha256=TjncS2aOgRJwjjRuIvmr4eRz2nKVg6b76tThp4UlzII,163
+eva/vision/data/transforms/utility/ensure_channel_first.py,sha256=jpnV7oWel1ZSL2VUf3wUdbB8xM2OFD8R6xpHcPCJVgw,1945
+eva/vision/data/tv_tensors/__init__.py,sha256=qla_QYWN52vP0IlTmHlTZF4kLh9xj-Zy-WxQgXakYyk,125
+eva/vision/data/tv_tensors/volume.py,sha256=VlWTIbswNv-aUqEWd1EJgoqEH60d-gNALPG815TD_W8,2381
 eva/vision/data/wsi/__init__.py,sha256=vfSfyogsj4OS1sGKfsYWyj2O5ZMT9iqkc1lvcuZJVGI,422
 eva/vision/data/wsi/backends/__init__.py,sha256=wX7cjeT7ktX8sH6lRDEEU5cgRKLH6RhPyey16aJthJ4,2251
 eva/vision/data/wsi/backends/base.py,sha256=0oFzMc3zklLyqyD_kzDKekydeFyDReqjBBj1qJLdM9Y,4094
@@ -177,45 +191,47 @@ eva/vision/metrics/__init__.py,sha256=zXOc1Idgfk86CGE5yBHn3B22iD5tRyfl4H-kTSB2dC
 eva/vision/metrics/defaults/__init__.py,sha256=ncQ9uH5q5SpfalyPX6dINPRLk34HLw6z9u8ny_HHbFQ,174
 eva/vision/metrics/defaults/segmentation/__init__.py,sha256=ve6dwyfhJGYBYKS6l6OySCBs32JnEBFnvhAyNvj-Uqo,191
 eva/vision/metrics/defaults/segmentation/multiclass.py,sha256=MUBp-PIyiJB2VVV_NintRrP7Ha2lJ75_3xvqSdeDYwE,2855
-eva/vision/metrics/segmentation/BUILD,sha256=Nf7BYWWe1USoFEIsIiEVZ8sa05J5FPkMJ-UIMDLrU8o,17
 eva/vision/metrics/segmentation/__init__.py,sha256=7iz3fFNd-iBuNyxdeSfsgp6D7oZtmPsbyA0ZKRzzRCw,402
 eva/vision/metrics/segmentation/_utils.py,sha256=_ubv2sP1-f_dLKy8Y4wLkj5ed56fAFLURfv1shQWVcs,2402
 eva/vision/metrics/segmentation/dice.py,sha256=H_U6XSZcieX0xb6aptxxW1s-Jshs8Lp4P1SAwjdwntM,2905
 eva/vision/metrics/segmentation/generalized_dice.py,sha256=T57An-lBVefnlv6dIWVRNghFxy0e0K470xwla0TbCSk,2436
 eva/vision/metrics/segmentation/mean_iou.py,sha256=2PjqTa_VAtnW4nxHzT93uBKgnml7INU-wt_jR68RM54,2104
-eva/vision/metrics/segmentation/monai_dice.py,sha256=febnvA2gtTyydLZMwjQBS1zq2NjZcsXf0EcV0eRn8Aw,2117
+eva/vision/metrics/segmentation/monai_dice.py,sha256=I_DX6r4y5d9QzxI3WyMV14uwt1uqrKlRqbNHqGMtmy0,2421
 eva/vision/metrics/wrappers/__init__.py,sha256=V4z3hradMa6CQgTkk1bc2cbZzCgcoIYw7-hufMK3D_4,128
 eva/vision/metrics/wrappers/monai.py,sha256=FNa1yHN2U3vO6BGqS0BFm8uJAL6DCzSE4XOFCV4aBjg,885
 eva/vision/models/__init__.py,sha256=a-P6JL73A3miHQnqgqUz07XtVmQB_o4DqPImk5rEATo,275
 eva/vision/models/modules/__init__.py,sha256=vaM_V6OF2s0lYjralP8dzv8mAtv_xIMZItfXgz0NZg8,156
-eva/vision/models/modules/semantic_segmentation.py,sha256=PSeqm5h6YgbzQ0jA9lUexGYUE3ehfWx-LH1NgZ7cGhw,7300
+eva/vision/models/modules/semantic_segmentation.py,sha256=f04QwxSt8x9oVHf5JMeN5b_PMPmfLcso_icDBma1ToE,7930
 eva/vision/models/networks/__init__.py,sha256=j43IurizNlAyKPH2jwDHaeq49L2QvwbHWqUaptA1mG4,100
 eva/vision/models/networks/abmil.py,sha256=N1eH4fn1nXmgXurSQyQIxxonv7nsqeeuPWaQSHeltfs,6796
-eva/vision/models/networks/backbones/__init__.py,sha256=CvK0sHKufUq4chwX-p2cFVBZFReMuwmeHFTG5LUA6CM,318
+eva/vision/models/networks/backbones/__init__.py,sha256=mvYVtmJOvYLCXDX52hP6dzQxj9cQikwSeBZvEDNyNmU,347
 eva/vision/models/networks/backbones/_utils.py,sha256=V7xeod4mElEuuO1TRW0xJE051cUyS1Saraw3-KcK1Mw,1667
-eva/vision/models/networks/backbones/pathology/__init__.py,sha256=goR59h8bfzd-Wa3rxPPdaSlAOH_df8SHBkTSKi08TS8,1147
-eva/vision/models/networks/backbones/pathology/bioptimus.py,sha256=wUSKjYgxcRV3FRHGaPwF1uRAQcGO0rHNHGmK1QDJXk4,991
+eva/vision/models/networks/backbones/pathology/__init__.py,sha256=JZ1mhKm4w89JTrXDfTM02OyFWtDuxRhhvpytDk_t500,1386
+eva/vision/models/networks/backbones/pathology/bioptimus.py,sha256=NrS0WJqiJKjDYT3odQGLPgnzMuCbJfWoW1Dal-L9F50,2626
 eva/vision/models/networks/backbones/pathology/gigapath.py,sha256=mfGXtKhY7XLpKQQAFNVZYsM-aeHCEbOVUrxpAEOr-l8,955
 eva/vision/models/networks/backbones/pathology/histai.py,sha256=X_we3U7GK91RrXyOX2PJB-YFDF2ozdL2fzZhNxm9SVU,1914
-eva/vision/models/networks/backbones/pathology/kaiko.py,sha256=GSdBG4WXrs1PWB2hr-sy_dFe2riwpPKwHx71esDoVfE,3952
+eva/vision/models/networks/backbones/pathology/hkust.py,sha256=bZpzx7EvK4CVefNnJmyz-2Ta-WdYDwEDzf-zWoZkoCQ,2308
+eva/vision/models/networks/backbones/pathology/kaiko.py,sha256=lVzgWhgFn1iOlfSSxsX2cH16rrFQFjzdaF6_HS1y-6c,4517
 eva/vision/models/networks/backbones/pathology/lunit.py,sha256=ku4lr9pWeeHatHN4x4OVgwlve9sVqiRqIbgI0PXLiqg,2160
 eva/vision/models/networks/backbones/pathology/mahmood.py,sha256=VYoVWrMNkoaEqa0och-GbwGd0VISQmbtzk1dSBZ1M0I,2464
 eva/vision/models/networks/backbones/pathology/owkin.py,sha256=uWJV5fgY7UZX6ilgGzkPY9fnlOiF03W7E8rc9TmlHGg,1231
 eva/vision/models/networks/backbones/pathology/paige.py,sha256=MjOLgdEKk8tdAIpCiHelasGwPE7xgzaooW6EE7IsuEE,1642
+eva/vision/models/networks/backbones/radiology/__init__.py,sha256=pD8ijQZRaX_Lu3tPBV73qUVaAURDrB_2pEyyBdRZmis,294
+eva/vision/models/networks/backbones/radiology/swin_unetr.py,sha256=n5lJkoKjxKogs5Q_XuKh7Q5J96Bgln5W4ShL-VwSZXs,7976
+eva/vision/models/networks/backbones/radiology/voco.py,sha256=sICZnsxQYnqYEmauhB6CBmaqpzBoAB6CpXJjNm5FesI,2464
 eva/vision/models/networks/backbones/registry.py,sha256=anjILtEHHB6Ltwiw22h1bsgWtIjh_l5_fkPh87K7-d0,1631
 eva/vision/models/networks/backbones/timm/__init__.py,sha256=cZH3av9gIZcvEVD0rwKsI-MEq7zPqaW4dQ0E05CksvQ,128
 eva/vision/models/networks/backbones/timm/backbones.py,sha256=fCTiwqU6NhQ-ccAMzmpPDddXkFzRAB3mw4lcQ9um_PU,1646
-eva/vision/models/networks/backbones/torchhub/__init__.py,sha256=zBLJBvkwKJ1jD7M3Wt5BE6Cx-R8G2YRoyPG7p2V-3nQ,147
-eva/vision/models/networks/backbones/torchhub/backbones.py,sha256=hgCCoP8AdRSsli0w9a_PRNB-UR36-SLLhBIW0BFrkdE,1911
 eva/vision/models/networks/backbones/universal/__init__.py,sha256=MAlkALSJ2_w6spSbB7NmKlL0Jsk1YKEycatdI0xO0_I,252
 eva/vision/models/networks/backbones/universal/vit.py,sha256=kpUCoXpefR34hRNlQDFK9lGr4oqS8Mn5vTLKWZ-gaOs,1820
 eva/vision/models/networks/decoders/__init__.py,sha256=RXFWmoYw2i6E9VOUCJmU8c72icHannVuo-cUKy6fnLM,200
-eva/vision/models/networks/decoders/segmentation/__init__.py,sha256=N6jrhXHj0P7i7RptZbZ-JFehT2BM7meFyNIK0owAkaE,517
+eva/vision/models/networks/decoders/segmentation/__init__.py,sha256=SqmxtzxwBRF8g2hsiqe0o3Nr0HFK97azTnWLyqsYigY,652
 eva/vision/models/networks/decoders/segmentation/base.py,sha256=b2TIJKiJR9vejVRpNyedMJLPTrpHhAEXvco8atb9TPU,411
 eva/vision/models/networks/decoders/segmentation/decoder2d.py,sha256=A7vz0LJ_YweftpKeEBJm0Y3N7hbVLDSIkAajaQv1UgE,4456
-eva/vision/models/networks/decoders/segmentation/linear.py,sha256=-i9RVaKM1UsB3AXDDKdMmHiD7y2sr5HfF-WvkB47Fhw,4743
-eva/vision/models/networks/decoders/segmentation/semantic/__init__.py,sha256=Ubs8GXyQpEHs26JUeUuiVP3jfn47eiBZM_UVbu749XU,398
+eva/vision/models/networks/decoders/segmentation/linear.py,sha256=PZeEIH0ybgxgIKtmcflh8jsARo5NQqkgoGbpAZd7yj4,4650
+eva/vision/models/networks/decoders/segmentation/semantic/__init__.py,sha256=2yol7W1ARXL-Ge7gYxjUzaGTjH6nfMBlNqQJHprEWGg,539
 eva/vision/models/networks/decoders/segmentation/semantic/common.py,sha256=fPTb0T-2FiOU-jT81ynASKaW7fJiRk6vQjuPkzHOluc,2530
+eva/vision/models/networks/decoders/segmentation/semantic/swin_unetr.py,sha256=ODUpnJrpDQl0m8CC2SPnE_lpFflzS0GSiCZOmrjL6uQ,3373
 eva/vision/models/networks/decoders/segmentation/semantic/with_image.py,sha256=I5PyGKKo8DcXYcw4xlCFzuavRJNRrzGT-szpDidMPXI,3516
 eva/vision/models/networks/decoders/segmentation/typings.py,sha256=8zAqIJLlQdCjsx-Dl4lnF4BB1VxTg_AyIquBVwpZlHg,537
 eva/vision/models/wrappers/__init__.py,sha256=ogmr-eeVuGaOCcsuxSp6PGyauP2QqWTb8dGTtbC7lRU,210
@@ -224,14 +240,14 @@ eva/vision/models/wrappers/from_timm.py,sha256=Z38Nb1i6OPKkgvFZOvGx-O3AZQuscf1zR
 eva/vision/utils/__init__.py,sha256=vaUovprE743SmyFH8l6uk4pYSWpI4zxn7lN0EwePTJI,96
 eva/vision/utils/colormap.py,sha256=sP1F0JCX3abZfFgdxEjLJO-LhNYKjXZvXxs03ZgrEvI,2876
 eva/vision/utils/convert.py,sha256=fqGmKrg5-JJLrTkTXB4YDcWTudXPrO1gGjsckVRUesU,1881
-eva/vision/utils/io/__init__.py,sha256=XGJ_W94DVEYXJ_tVpr_20NMpR5JLWEWHGF3v9Low79A,610
+eva/vision/utils/io/__init__.py,sha256=Oa4CjmqXN0wzkG1PW79zSsHrN1jlI7_VJ5NSXLKx0eA,652
 eva/vision/utils/io/_utils.py,sha256=JzOt7Frj6ScF_aNjFtfHBn4ROnl6NhUZucmQhLc4Cww,768
 eva/vision/utils/io/image.py,sha256=IdOkr5MYqhYHz8U9drZ7wULTM3YHwCWSjZlu_Qdl4GQ,2053
 eva/vision/utils/io/mat.py,sha256=qpGifyjmpE0Xhv567Si7-zxKrgkgE0sywP70cHiLFGU,808
-eva/vision/utils/io/nifti.py,sha256=4YoKjKuoNdE0qY7tYB_WlnSsYAx2oBzZRZXczc_8HAU,2555
+eva/vision/utils/io/nifti.py,sha256=TFMgNhLqIK3sl3RjIRXEABM7FmSQjqVOwk1vXkuvX2w,4983
 eva/vision/utils/io/text.py,sha256=qYgfo_ZaDZWfG02NkVVYzo5QFySqdCCz5uLA9d-zXtI,701
-kaiko_eva-0.2.0.dist-info/METADATA,sha256=CTFbtAErERl1SU0--56Y5-d1tXrr1vBNtNVkaV3orrA,24899
-kaiko_eva-0.2.0.dist-info/WHEEL,sha256=thaaA2w1JzcGC48WYufAs8nrYZjJm8LqNfnXFOFyCC4,90
-kaiko_eva-0.2.0.dist-info/entry_points.txt,sha256=6CSLu9bmQYJSXEg8gbOzRhxH0AGs75BB-vPm3VvfcNE,88
-kaiko_eva-0.2.0.dist-info/licenses/LICENSE,sha256=e6AEzr7j_R-PYr2qLO-JwLn8y70jbVD3U2mxbRmwcI4,11338
-kaiko_eva-0.2.0.dist-info/RECORD,,
+kaiko_eva-0.2.2.dist-info/METADATA,sha256=hiFFWrNu2fMZd7VLI08q4EDOc0IU6X4T00RGkHC0QT8,25363
+kaiko_eva-0.2.2.dist-info/WHEEL,sha256=tSfRZzRHthuv7vxpI4aehrdN9scLjk-dCJkPLzkHxGg,90
+kaiko_eva-0.2.2.dist-info/entry_points.txt,sha256=6CSLu9bmQYJSXEg8gbOzRhxH0AGs75BB-vPm3VvfcNE,88
+kaiko_eva-0.2.2.dist-info/licenses/LICENSE,sha256=e6AEzr7j_R-PYr2qLO-JwLn8y70jbVD3U2mxbRmwcI4,11338
+kaiko_eva-0.2.2.dist-info/RECORD,,

{kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: pdm-backend (2.4.3)
+Generator: pdm-backend (2.4.4)
 Root-Is-Purelib: true
 Tag: py3-none-any

eva/vision/data/datasets/classification/base.py

@@ -1,96 +0,0 @@
-"""Base for image classification datasets."""
-
-import abc
-from typing import Any, Callable, Dict, List, Tuple
-
-import torch
-from torchvision import tv_tensors
-from typing_extensions import override
-
-from eva.vision.data.datasets import vision
-
-
-class ImageClassification(vision.VisionDataset[Tuple[tv_tensors.Image, torch.Tensor]], abc.ABC):
-    """Image classification abstract dataset."""
-
-    def __init__(
-        self,
-        transforms: Callable | None = None,
-    ) -> None:
-        """Initializes the image classification dataset.
-
-        Args:
-            transforms: A function/transform which returns a transformed
-                version of the raw data samples.
-        """
-        super().__init__()
-
-        self._transforms = transforms
-
-    @property
-    def classes(self) -> List[str] | None:
-        """Returns the list with names of the dataset names."""
-
-    @property
-    def class_to_idx(self) -> Dict[str, int] | None:
-        """Returns a mapping of the class name to its target index."""
-
-    def load_metadata(self, index: int) -> Dict[str, Any] | None:
-        """Returns the dataset metadata.
-
-        Args:
-            index: The index of the data sample to return the metadata of.
-
-        Returns:
-            The sample metadata.
-        """
-
-    @abc.abstractmethod
-    def load_image(self, index: int) -> tv_tensors.Image:
-        """Returns the `index`'th image sample.
-
-        Args:
-            index: The index of the data sample to load.
-
-        Returns:
-            The image as a numpy array.
-        """
-
-    @abc.abstractmethod
-    def load_target(self, index: int) -> torch.Tensor:
-        """Returns the `index`'th target sample.
-
-        Args:
-            index: The index of the data sample to load.
-
-        Returns:
-            The sample target as an array.
-        """
-
-    @abc.abstractmethod
-    @override
-    def __len__(self) -> int:
-        raise NotImplementedError
-
-    @override
-    def __getitem__(self, index: int) -> Tuple[tv_tensors.Image, torch.Tensor, Dict[str, Any]]:
-        image = self.load_image(index)
-        target = self.load_target(index)
-        image, target = self._apply_transforms(image, target)
-        return image, target, self.load_metadata(index) or {}
-
-    def _apply_transforms(
-        self, image: tv_tensors.Image, target: torch.Tensor
-    ) -> Tuple[tv_tensors.Image, torch.Tensor]:
-        """Applies the transforms to the provided data and returns them.
-
-        Args:
-            image: The desired image.
-            target: The target of the image.
-
-        Returns:
-            A tuple with the image and the target transformed.
-        """
-        if self._transforms is not None:
-            image, target = self._transforms(image, target)
-        return image, target

eva/vision/data/datasets/segmentation/base.py

@@ -1,96 +0,0 @@
-"""Base for image segmentation datasets."""
-
-import abc
-from typing import Any, Callable, Dict, List, Tuple
-
-from torchvision import tv_tensors
-from typing_extensions import override
-
-from eva.vision.data.datasets import vision
-
-
-class ImageSegmentation(vision.VisionDataset[Tuple[tv_tensors.Image, tv_tensors.Mask]], abc.ABC):
-    """Image segmentation abstract dataset."""
-
-    def __init__(self, transforms: Callable | None = None) -> None:
-        """Initializes the image segmentation base class.
-
-        Args:
-            transforms: A function/transforms that takes in an
-                image and a label and returns the transformed versions of both.
-        """
-        super().__init__()
-
-        self._transforms = transforms
-
-    @property
-    def classes(self) -> List[str] | None:
-        """Returns the list with names of the dataset names."""
-
-    @property
-    def class_to_idx(self) -> Dict[str, int] | None:
-        """Returns a mapping of the class name to its target index."""
-
-    @abc.abstractmethod
-    def load_image(self, index: int) -> tv_tensors.Image:
-        """Loads and returns the `index`'th image sample.
-
-        Args:
-            index: The index of the data sample to load.
-
-        Returns:
-            An image torchvision tensor (channels, height, width).
-        """
-
-    @abc.abstractmethod
-    def load_mask(self, index: int) -> tv_tensors.Mask:
-        """Returns the `index`'th target masks sample.
-
-        Args:
-            index: The index of the data sample target masks to load.
-
-        Returns:
-            The semantic mask as a (H x W) shaped tensor with integer
-            values which represent the pixel class id.
-        """
-
-    def load_metadata(self, index: int) -> Dict[str, Any] | None:
-        """Returns the dataset metadata.
-
-        Args:
-            index: The index of the data sample to return the metadata of.
-                If `None`, it will return the metadata of the current dataset.
-
-        Returns:
-            The sample metadata.
-        """
-
-    @abc.abstractmethod
-    @override
-    def __len__(self) -> int:
-        raise NotImplementedError
-
-    @override
-    def __getitem__(self, index: int) -> Tuple[tv_tensors.Image, tv_tensors.Mask, Dict[str, Any]]:
-        image = self.load_image(index)
-        mask = self.load_mask(index)
-        metadata = self.load_metadata(index) or {}
-        image_tensor, mask_tensor = self._apply_transforms(image, mask)
-        return image_tensor, mask_tensor, metadata
-
-    def _apply_transforms(
-        self, image: tv_tensors.Image, mask: tv_tensors.Mask
-    ) -> Tuple[tv_tensors.Image, tv_tensors.Mask]:
-        """Applies the transforms to the provided data and returns them.
-
-        Args:
-            image: The desired image.
-            mask: The target segmentation mask.
-
-        Returns:
-            A tuple with the image and the masks transformed.
-        """
-        if self._transforms is not None:
-            image, mask = self._transforms(image, mask)
-
-        return image, mask

eva/vision/data/transforms/common/resize_and_clamp.py

@@ -1,51 +0,0 @@
-"""Specialized transforms for resizing, clamping and range normalizing."""
-
-from typing import Callable, Sequence, Tuple
-
-from torchvision.transforms import v2
-
-from eva.vision.data.transforms import normalization
-
-
-class ResizeAndClamp(v2.Compose):
-    """Resizes, crops, clamps and normalizes an input image."""
-
-    def __init__(
-        self,
-        size: int | Sequence[int] = 224,
-        clamp_range: Tuple[int, int] = (-1024, 1024),
-        mean: Sequence[float] = (0.0, 0.0, 0.0),
-        std: Sequence[float] = (1.0, 1.0, 1.0),
-    ) -> None:
-        """Initializes the transform object.
-
-        Args:
-            size: Desired output size of the crop. If size is an `int` instead
-                of sequence like (h, w), a square crop (size, size) is made.
-            clamp_range: The lower and upper bound to clamp the pixel values.
-            mean: Sequence of means for each image channel.
-            std: Sequence of standard deviations for each image channel.
-        """
-        self._size = size
-        self._clamp_range = clamp_range
-        self._mean = mean
-        self._std = std
-
-        super().__init__(transforms=self._build_transforms())
-
-    def _build_transforms(self) -> Sequence[Callable]:
-        """Builds and returns the list of transforms."""
-        transforms = [
-            v2.Resize(size=self._size),
-            v2.CenterCrop(size=self._size),
-            normalization.Clamp(out_range=self._clamp_range),
-            normalization.RescaleIntensity(
-                in_range=self._clamp_range,
-                out_range=(0.0, 1.0),
-            ),
-            v2.Normalize(
-                mean=self._mean,
-                std=self._std,
-            ),
-        ]
-        return transforms

eva/vision/data/transforms/normalization/__init__.py

@@ -1,6 +0,0 @@
-"""Normalization related transformations."""
-
-from eva.vision.data.transforms.normalization.clamp import Clamp
-from eva.vision.data.transforms.normalization.rescale_intensity import RescaleIntensity
-
-__all__ = ["Clamp", "RescaleIntensity"]

eva/vision/data/transforms/normalization/clamp.py

@@ -1,43 +0,0 @@
-"""Image clamp transform."""
-
-import functools
-from typing import Any, Dict, Tuple
-
-import torch
-import torchvision.transforms.v2 as torch_transforms
-from torchvision import tv_tensors
-from typing_extensions import override
-
-
-class Clamp(torch_transforms.Transform):
-    """Clamps all elements in input into a specific range."""
-
-    def __init__(self, out_range: Tuple[int, int]) -> None:
-        """Initializes the transform.
-
-        Args:
-            out_range: The lower and upper bound of the range to
-                be clamped to.
-        """
-        super().__init__()
-
-        self._out_range = out_range
-
-    @functools.singledispatchmethod
-    @override
-    def _transform(self, inpt: Any, params: Dict[str, Any]) -> Any:
-        return inpt
-
-    @_transform.register(torch.Tensor)
-    def _(self, inpt: torch.Tensor, params: Dict[str, Any]) -> Any:
-        return torch.clamp(inpt, min=self._out_range[0], max=self._out_range[1])
-
-    @_transform.register(tv_tensors.Image)
-    def _(self, inpt: tv_tensors.Image, params: Dict[str, Any]) -> Any:
-        inpt_clamp = torch.clamp(inpt, min=self._out_range[0], max=self._out_range[1])
-        return tv_tensors.wrap(inpt_clamp, like=inpt)
-
-    @_transform.register(tv_tensors.BoundingBoxes)
-    @_transform.register(tv_tensors.Mask)
-    def _(self, inpt: tv_tensors.BoundingBoxes | tv_tensors.Mask, params: Dict[str, Any]) -> Any:
-        return inpt

eva/vision/data/transforms/normalization/functional/__init__.py

@@ -1,5 +0,0 @@
-"""Functional normalization related transformations API."""
-
-from eva.vision.data.transforms.normalization.functional.rescale_intensity import rescale_intensity
-
-__all__ = ["rescale_intensity"]