kaiko-eva 0.2.2__py3-none-any.whl → 0.3.1__py3-none-any.whl

eva/vision/models/wrappers/from_timm.py

@@ -4,12 +4,13 @@ from typing import Any, Callable, Dict, Tuple
 from urllib import parse
 
 import timm
+import torch
 from typing_extensions import override
 
-from eva.core.models import wrappers
+from eva.core.models.wrappers import base
 
 
-class TimmModel(wrappers.BaseModel):
+class TimmModel(base.BaseModel[torch.Tensor, torch.Tensor]):
     """Model wrapper for `timm` models.
 
     Note that only models with `forward_intermediates`
@@ -23,7 +24,7 @@ class TimmModel(wrappers.BaseModel):
         checkpoint_path: str = "",
         out_indices: int | Tuple[int, ...] | None = None,
         model_kwargs: Dict[str, Any] | None = None,
-        tensor_transforms: Callable | None = None,
+        transforms: Callable | None = None,
     ) -> None:
         """Initializes the encoder.
 
@@ -34,10 +35,10 @@ class TimmModel(wrappers.BaseModel):
             out_indices: Returns last n blocks if `int`, all if `None`, select
                 matching indices if sequence.
             model_kwargs: Extra model arguments.
-            tensor_transforms: The transforms to apply to the output tensor
+            transforms: The transforms to apply to the output tensor
                 produced by the model.
         """
-        super().__init__(tensor_transforms=tensor_transforms)
+        super().__init__(transforms=transforms)
 
         self._model_name = model_name
         self._pretrained = pretrained

{kaiko_eva-0.2.2.dist-info → kaiko_eva-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kaiko-eva
-Version: 0.2.2
+Version: 0.3.1
 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>
@@ -242,6 +242,9 @@ 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: language
+Requires-Dist: datasets<4.0.0,>=2.19.0; extra == "language"
+Requires-Dist: litellm>=1.61.8; extra == "language"
 Provides-Extra: all
 Requires-Dist: h5py>=3.10.0; extra == "all"
 Requires-Dist: nibabel>=4.0.1; extra == "all"
@@ -255,6 +258,8 @@ 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"
+Requires-Dist: datasets<4.0.0,>=2.19.0; extra == "all"
+Requires-Dist: litellm>=1.61.8; extra == "all"
 Description-Content-Type: text/markdown
 
 <div align="center">
@@ -293,7 +298,7 @@ Check out the [documentation](https://kaiko-ai.github.io/eva/) for more informat
 
 ### Highlights:
 - Easy and reliable benchmark of Oncology FMs
-- Supports patch-level classification, slide-level classification and semantic segmentation downstream tasks
+- Supports patch-level classification, slide-level classification, semantic segmentation, and text classification 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
@@ -308,6 +313,9 @@ pip install kaiko-eva
 # to install the expanded `vision` version
 pip install 'kaiko-eva[vision]'
 
+# to install the expanded `language` version
+pip install 'kaiko-eva[language]'
+
 # to install everything
 pip install 'kaiko-eva[all]'
 ```

{kaiko_eva-0.2.2.dist-info → kaiko_eva-0.3.1.dist-info}/RECORD

@@ -16,8 +16,10 @@ eva/core/cli/cli.py,sha256=AZ4B4OP3D2af9H2RYBd5nxoy5I9DlaClZaadSWpPEPI,422
 eva/core/cli/logo.py,sha256=x6-vGWI0s9gza-xxQrBDi2wneb2wFU_mQGHgpAiq2MQ,786
 eva/core/cli/setup.py,sha256=kR-7l4X5Hu8kSLoQZGYGIeLXtn9S_EU52dauDy6fm0w,2663
 eva/core/data/__init__.py,sha256=yG3BeOWhp1EjVYMFqx8M_TBWFDyfIwwksQGQmMdSPaI,340
-eva/core/data/dataloaders/__init__.py,sha256=fbNClVZ8J3QoGi4qiPq635ig1j9GdI7six3RhfwDbjY,110
-eva/core/data/dataloaders/dataloader.py,sha256=Ek_OqlOuQSiipFjBJ39DFyWvW3CdqAB2bufOcEs0ChU,2525
+eva/core/data/dataloaders/__init__.py,sha256=0AvpsPOdh4NX5rwkX9Th1M_rzxZVVzTPTdC5oTGFd5w,194
+eva/core/data/dataloaders/collate_fn/__init__.py,sha256=CfSAVrPD36shpyYAkob2ny05VWymb95MutawQcZkbuo,134
+eva/core/data/dataloaders/collate_fn/collate.py,sha256=oBdxaDCIaXBB6H8LB90Qsi2Inw1tyHGF4kAFBINPOeQ,689
+eva/core/data/dataloaders/dataloader.py,sha256=amRIwbmI6Hi2qS-ciKkv7ehgkBbMCHx7XUaEMlttWkw,2688
 eva/core/data/datamodules/__init__.py,sha256=qZchYbgxo9lxYnGoqdk0C6MfS2IbF0WItO0kCdP9Mqc,229
 eva/core/data/datamodules/call.py,sha256=jjj9w3UXYuQB-qyCcw1EZpRJW10OC1I3dvgvsuQWLck,940
 eva/core/data/datamodules/datamodule.py,sha256=_pK59oXDe53oDkmv6eoJUvfl44WlFkrbC8KXSRMs_20,5533
@@ -46,7 +48,7 @@ eva/core/data/transforms/padding/pad_2d_tensor.py,sha256=J4maGFmeQf9IHRxt5kU-6eI
 eva/core/data/transforms/sampling/__init__.py,sha256=BFKbvRjlZrwS0GcNrM54ZSWt6PrQARfFlXM1jJ-wpvo,149
 eva/core/data/transforms/sampling/sample_from_axis.py,sha256=Zbhp94lVa70WQKmSOKMTsOMe2c7wLqNZto7JqWhSdtI,1229
 eva/core/interface/__init__.py,sha256=chdpKXipxe1NP-Fgr_d9r6X1gMna0XiEa38waJ6FzTM,98
-eva/core/interface/interface.py,sha256=GzjneNHhTIEuLbydUG9cSmpHjJ4_IENGM-glN8RaRxY,2741
+eva/core/interface/interface.py,sha256=VNagHKsr2T7Ufm1rpA0NCnMi6F2qpKEmMBq_3eGZIRE,3826
 eva/core/loggers/__init__.py,sha256=4YMLNlN9LnuKqhBI1R1keh69dmMD-2lcH3HKwwyn380,266
 eva/core/loggers/dummy.py,sha256=Y7ypH0ecSAIkkZ5LzTmNNEzlKkqeaHfUNMCDKVOg6D4,1204
 eva/core/loggers/experimental_loggers.py,sha256=p5uCK_9QCYufRhE-LZQUJWbhGElyobX_zRM78yX4p2o,230
@@ -64,7 +66,7 @@ eva/core/metrics/binary_balanced_accuracy.py,sha256=MabsXAtVfLqSaSIIpE0HIM6bo8uR
 eva/core/metrics/defaults/__init__.py,sha256=IeqLcoxLNddtuuFao5r85ZVxTyFP6iFsj1K8iXCTSes,255
 eva/core/metrics/defaults/classification/__init__.py,sha256=xMzE4yV8NoUdcmk2FCKohEUav1GJcxYn60S1KNgXbJY,316
 eva/core/metrics/defaults/classification/binary.py,sha256=9ll6ZOcNGQdsg7ln9DAQ0u-OzsXSzEbueXe-dVJkJZ8,2322
-eva/core/metrics/defaults/classification/multiclass.py,sha256=8Aesy_rKtp4KxfXJtDCmk6FsGxIFS4Ywu2CH1VIRL7M,2518
+eva/core/metrics/defaults/classification/multiclass.py,sha256=i5Oimxps3kjIwGAHKIdylOPJUUkzo6_wfG5JAw6vyAc,2796
 eva/core/metrics/structs/__init__.py,sha256=cvn7E4k5vJmpwJj_zezmtZa_Nl_RddDM1G-MO8TP0po,422
 eva/core/metrics/structs/collection.py,sha256=bNfCekHN8pzD49-YTqVxrmxFtiQfNxnv-RwkxCL6rbc,149
 eva/core/metrics/structs/metric.py,sha256=zdnE0ZVTSYAMl7rW_OL6e1XiZDvLTirYqV0lgJCleXY,109
@@ -72,10 +74,11 @@ eva/core/metrics/structs/module.py,sha256=pHpIAt5HQDoYWvyFXxYTZleTKMW1iaTCgwAkty
 eva/core/metrics/structs/schemas.py,sha256=ZaSrx0j_NfIwT7joMUD1LyrKdAXTLaeSzWYTHDsc6h0,1641
 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/__init__.py,sha256=_4VjN9Qs4_mftEVgt0KqVxCRAtDcKYbUnBA3Ox1Pzis,350
 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/scheduler.py,sha256=orv5TDq9vEItxE7rTj0sQlzdChpx5jHx-3ypnHjUyr4,1650
 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
@@ -85,23 +88,24 @@ eva/core/models/networks/__init__.py,sha256=yqx6UmG1Eg3vb1O_tnK_axnJWabEl9ULkDWi
 eva/core/models/networks/mlp.py,sha256=thk-x4pviE3fCaMW9k3I2Oe5_DxfC-CqUrtolvVdXug,2418
 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/transforms/extract_cls_features.py,sha256=A-oNNiGYBkMLK_E9DrzJUJuTZETERX75w0lg35-rj0g,1498
+eva/core/models/transforms/extract_patch_features.py,sha256=5UsHjZnh3Uk2jAfi3GLtxoJ14ALTrfVoWUy8nTspRDY,2218
 eva/core/models/wrappers/__init__.py,sha256=jaiANQdbO-IPgH8U-Y0ftFsuuCAM5i5KuYRHauKw5k8,450
 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
-eva/core/models/wrappers/huggingface.py,sha256=5CoNieivdjwvoawo7dZtWfYZkW-Mey1j0EjazuxDaqU,1302
-eva/core/models/wrappers/onnx.py,sha256=-iV-IlczTvTTEQuJycZeSVWdSl2kVJXc1eeRLgQQZ7Q,1834
+eva/core/models/wrappers/base.py,sha256=S3LGbb_wo2ZTeDvoLvSlaymBsRN6UAuKrCmVAGasHWY,1452
+eva/core/models/wrappers/from_function.py,sha256=LVnfW3bL1mRtO8kL1D0MLJOiAiyiHkM7RX6-JIJzI0E,1844
+eva/core/models/wrappers/from_torchhub.py,sha256=-saKMxYq4KvVpaJL6BdHmUcEYHuaNvm2-0O_eQMg3GA,3250
+eva/core/models/wrappers/huggingface.py,sha256=-_fA81YRnoMc7O7SbrnCEj1dM_xArpQ8WdsZk9z_f1E,1449
+eva/core/models/wrappers/onnx.py,sha256=34li_xSwPryN8nJDrFyif_Hve1AEH7Ry9E_lZmf7JJM,1834
 eva/core/trainers/__init__.py,sha256=jhsKJF7HAae7EOiG3gKIAHH_h3dZlTE2JRcCHJmOzJc,208
 eva/core/trainers/_logging.py,sha256=gi4FqPy2GuVmh0WZY6mYwF7zMPvnoFA050B0XdCP6PU,2571
 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/functional.py,sha256=tsBfpXjEQ8BiBJ9wZWp0AUUOOxy7UUrLX4GSjQZTeCs,4510
 eva/core/trainers/trainer.py,sha256=a3OwLWOZKDqxayrd0ugUmxJKyQx6XDb4GHtdL8-AEV0,4826
 eva/core/utils/__init__.py,sha256=cndVBvtYxEW7hykH39GCNVI86zkXNn8Lw2A0sUJHS04,237
 eva/core/utils/clone.py,sha256=qcThZOuAs1cs0uV3BL5eKeM2VIBjuRPBe1t-NiUFM5Y,569
+eva/core/utils/factory.py,sha256=upWPWkWW7p3_ZoePAzbkkZvEPiAY4OaOQkwNvh0oa-E,2397
 eva/core/utils/io/__init__.py,sha256=Py03AmoxhmTHkro6CzNps27uXKkXPzdA18mG97xHhWI,172
 eva/core/utils/io/dataframe.py,sha256=CIHFowljH17waDkJ9YJVEVXAIcxMwoLjUgoBttiNk8w,509
 eva/core/utils/io/gz.py,sha256=xxDkOUV2TFEK8pT7j6S_6iSzUUUmXN-sTum-gRuhij0,919
@@ -110,8 +114,27 @@ 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/registry.py,sha256=iEDVsQ7DdPXhzfW32z3lWNgwjagR_jh_g4VkvajjRK4,1348
+eva/core/utils/requirements.py,sha256=u01QPnBDu0YApncxgvg7xEANubyGSptqja12cycg3k0,909
 eva/core/utils/suppress_logs.py,sha256=pOk1076J0mKWn2lgDqEVC1g65FXhA_2IkC4LBEWhnwQ,902
 eva/core/utils/workers.py,sha256=hfx63M82qNg0Dwhre2tl53MnhtRsV7APaDONM9nhVB8,634
+eva/language/__init__.py,sha256=EQxtGM6zT3y-6EGecGAo2IXKS6J8dyWNOGP2mvD7fZ0,360
+eva/language/data/__init__.py,sha256=ONF-CLBK2HO2p1bMCAbdvaHfSsYjdSE9-O3lWgwQQGk,89
+eva/language/data/datasets/__init__.py,sha256=AeGw3EVyz5w8Ja2m8Hd3FoKkCeG68M0BwtF64VCvOk4,211
+eva/language/data/datasets/classification/__init__.py,sha256=HXtgJpMt9CgqvdeWc147bOn-9YeUMcL8v-0UHHkY_A4,144
+eva/language/data/datasets/classification/base.py,sha256=53Tbu8dRSMuNfRB_xEBk_3wSe0jRqd_S-IwE9WIpgW0,1669
+eva/language/data/datasets/classification/pubmedqa.py,sha256=AxqW5OQAtDBLVX-Sr0WIt3E7GBbkGMUPOvhOlKLTLh8,5439
+eva/language/data/datasets/language.py,sha256=Kjy1X9xZBIfjjEYJKMikgKhLaquugRSjXTYM_HWiHmw,305
+eva/language/models/__init__.py,sha256=ggL8uDv_J8vQTr5fc5j8UENoPA24h2Bo3uNSdd_vRU0,606
+eva/language/models/modules/__init__.py,sha256=UWO_yq7kPzTrptl6iWTFy07E_Cyzf-sTu-zAK-sN3CI,112
+eva/language/models/modules/text.py,sha256=wknEnS_t8IToLTo_F9AG4EXkt0_6o4n6dYm-8AVxgOY,2906
+eva/language/models/modules/typings.py,sha256=dWq3FTbvGZGoIMTEIX1yWBk_VFKIHsvxaTvBXlbJfCA,379
+eva/language/models/wrappers/__init__.py,sha256=syKHBqX3MRD2oq_MjDjvoNC6W0F8TdmGYqhwrGLBahI,402
+eva/language/models/wrappers/huggingface.py,sha256=l3wVOB4QOe2_yeG4xwNm0imP_kWbjM8RG0ISE4ANAyE,2396
+eva/language/models/wrappers/litellm.py,sha256=0GSo3gxUv1Ah6FQ6VqTiiu_0TVx-h4xUkZqdOAGbKTM,2619
+eva/language/models/wrappers/vllm.py,sha256=LXadfveGSHmjWAlOBrJm1QHkKzB_O-s3M8U7bnKfW-E,5684
+eva/language/utils/__init__.py,sha256=jqrU3o80NAwt6HbNDWSM3e3B1-65vw811DqiUWT0Bys,150
+eva/language/utils/str_to_int_tensor.py,sha256=YlNppLlAoX0ZRVfcDX4BStCQPbS1NNParcwptxH0_wE,3143
 eva/vision/__init__.py,sha256=oUZXFYjwtkWzi8An0uS5Xc84pLKintlXe2iti8zW6BQ,480
 eva/vision/callbacks/__init__.py,sha256=su1V73L0dDVYWSyvV_lnWbszDi2KikRraF7OsgeaKl4,139
 eva/vision/callbacks/loggers/__init__.py,sha256=td1JRJbE08nsGIZdO64_yLC3FUuMDp0kma0HjpUdXT4,161
@@ -119,10 +142,11 @@ eva/vision/callbacks/loggers/batch/__init__.py,sha256=DVYP7Aonbi4wg_ERHRj_8kb87E
 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=zuLOC8ExyeQGlwib1LB70RedrTC9w0siOhFTQIRb0V8,137
-eva/vision/data/dataloaders/__init__.py,sha256=7AOD_UF3hMokrGxJ2tbawH44ujQaesDsaW-3HWorYv8,128
+eva/vision/data/dataloaders/__init__.py,sha256=9ykBD4vyZ-Yv3IEnqvVcSMURS-gXWjOunA43brQK6Hg,207
 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/dataloaders/worker_init.py,sha256=lFWywHGCC4QxHeDXrneF8DQ45XG3WmVltEELJrPyLz0,1182
+eva/vision/data/datasets/__init__.py,sha256=s3h4w71LiM6dT6AYWzCG2-nexkSuuTWixw4KrCGAhS8,1026
 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
@@ -137,30 +161,37 @@ eva/vision/data/datasets/classification/panda.py,sha256=HVfCvByyajdo5o_waqTpzZWC
 eva/vision/data/datasets/classification/patch_camelyon.py,sha256=1yXkfP680qxkQUFAPKRFbZv0cHAFx23s2vvT9th2nKM,7149
 eva/vision/data/datasets/classification/unitopatho.py,sha256=IO3msEsuOnmdcYZxF-eBpo0K97y54rWFmCb_KxuF4bk,5129
 eva/vision/data/datasets/classification/wsi.py,sha256=YMGxU8ECjudizt_uXUevuPS8k66HxtEQ7M2IZJmL6kE,4079
-eva/vision/data/datasets/segmentation/__init__.py,sha256=YA7qx4B-pfsILfONa2AfIQHKzDnv8l0sHwjsSXa5-vQ,765
-eva/vision/data/datasets/segmentation/_total_segmentator.py,sha256=DTaQaAisY7j1h0-zYk1_81Sr4b3D9PTMieYX0PMPtIc,3127
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 eva/vision/data/datasets/segmentation/_utils.py,sha256=aXUHrnbefP6-OgSvDQHqssFKhUwETul_8aosqYiOfm8,3065
 eva/vision/data/datasets/segmentation/bcss.py,sha256=rqk6VqK0QCHLFnMnDuHd1JPJVK5_C6WnsmnNSKBw6Uo,8230
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 eva/vision/data/datasets/segmentation/embeddings.py,sha256=RsTuAwGEJPnWPY7q3pwcjmqtEj0wtRBNRBD4a0RcGtA,1218
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 eva/vision/data/datasets/segmentation/monusac.py,sha256=iv9-MFaTsGfGV1u6_lQNcSEeSpmVBDQC1Oa123iEtu0,8410
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 eva/vision/data/datasets/structs.py,sha256=RaTDW-B36PumcR5gymhCiX-r8GiKqIFcjqoEEjjFyUE,389
 eva/vision/data/datasets/vision.py,sha256=-_WRiyICMgqABR6Ay_RKBMfsPGwgx9MQfCA7WChHo24,3219
 eva/vision/data/datasets/wsi.py,sha256=dEAT_Si_Qb3qdSovUPeoiWeoPb7m-NGYqq44e3UXHk8,8384
-eva/vision/data/transforms/__init__.py,sha256=Bv1aPvjahteAZzVGSuxzHz2LRwa63NV7IcoPzKUt_fY,720
-eva/vision/data/transforms/common/__init__.py,sha256=ZHzpdr-THc9CgFFbAVMWUiZrUNUiHnCDM8GYhM7tMfU,138
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 eva/vision/data/transforms/common/resize_and_crop.py,sha256=GI1HTkbJ9qg4p8c6vk_XkXO0Qi6mBeUeiZIA0jVtmAw,1360
-eva/vision/data/transforms/croppad/__init__.py,sha256=d36WGe9x39p-d7VymRM29qdquv8YEa0RfsTfwt7Cou4,375
+eva/vision/data/transforms/common/squeeze.py,sha256=N9G2XRKOCuqaaLc27jWy8a-x1kgxez0hM2fDPH4w5Ak,726
+eva/vision/data/transforms/croppad/__init__.py,sha256=sa-M4JMdZGB39JqWOLAJvoun4YK3N4hBFuM--DZ8SnE,606
 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/rand_crop_by_label_classes.py,sha256=9oRY1ZuvUGuJNRkAT7JEquWBrYmNAD82FebrbvwVEtc,2587
+eva/vision/data/transforms/croppad/rand_crop_by_pos_neg_label.py,sha256=5omKDSECPdnWEt-AXlu8oeN7N-qa1MXekEggZ08KeIQ,5670
+eva/vision/data/transforms/croppad/rand_spatial_crop.py,sha256=yKAW5GN1B1vac74REYpBbrRhKxI2BhGA_LDEJ_AcO5w,3769
 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/rand_scale_intensity.py,sha256=x3gYRRAFbZXFWgqvoUjT0sDFWT6zbhja3PJLXbOBtTg,2184
+eva/vision/data/transforms/intensity/rand_shift_intensity.py,sha256=5ngSHfHgJOR9KQykNKJhQMWhQYj781Mj_JKJ_ADchbM,2117
 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
@@ -201,42 +232,42 @@ eva/vision/metrics/wrappers/__init__.py,sha256=V4z3hradMa6CQgTkk1bc2cbZzCgcoIYw7
 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=f04QwxSt8x9oVHf5JMeN5b_PMPmfLcso_icDBma1ToE,7930
+eva/vision/models/modules/semantic_segmentation.py,sha256=57sfKU6AAaWp8qTTYwcDFNwrTCMpVVbJtOdbGUmXb7Y,8308
 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=mvYVtmJOvYLCXDX52hP6dzQxj9cQikwSeBZvEDNyNmU,347
-eva/vision/models/networks/backbones/_utils.py,sha256=V7xeod4mElEuuO1TRW0xJE051cUyS1Saraw3-KcK1Mw,1667
+eva/vision/models/networks/backbones/__init__.py,sha256=oczI7-IyKWyrkM-tIDYIrw01sCVJoWvxrDjvCcVU_vg,301
+eva/vision/models/networks/backbones/_utils.py,sha256=sF9y7vRBc1nFLLGmxramzMQmVwf3oiMMI7XcpKDiBss,1660
 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/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/pathology/bioptimus.py,sha256=N14sD2LMHKO_V8frN8FpXfPc2p6k8tnZAiAQhEw1dOs,2646
+eva/vision/models/networks/backbones/pathology/gigapath.py,sha256=YTBYSb1KduwYsFOTFzNkzI9-GtjU7UjPLzqPzwIJEvs,970
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 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
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+eva/vision/models/networks/backbones/radiology/voco.py,sha256=Rzwbk6nMrjnd71KDLf8uyXntGY0YMTLDkHhzP56p_7Q,2519
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 eva/vision/models/networks/backbones/timm/__init__.py,sha256=cZH3av9gIZcvEVD0rwKsI-MEq7zPqaW4dQ0E05CksvQ,128
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 eva/vision/models/networks/decoders/__init__.py,sha256=RXFWmoYw2i6E9VOUCJmU8c72icHannVuo-cUKy6fnLM,200
 eva/vision/models/networks/decoders/segmentation/__init__.py,sha256=SqmxtzxwBRF8g2hsiqe0o3Nr0HFK97azTnWLyqsYigY,652
 eva/vision/models/networks/decoders/segmentation/base.py,sha256=b2TIJKiJR9vejVRpNyedMJLPTrpHhAEXvco8atb9TPU,411
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 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/common.py,sha256=FSf_eI-FaBroxPRJd4TiV97RCreauJh1IznIVzBT2eg,2528
 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/networks/decoders/segmentation/typings.py,sha256=rY4CXp0MNF16SHnx9TgGjXI_r8bVGSqAWdR835hXndg,537
 eva/vision/models/wrappers/__init__.py,sha256=ogmr-eeVuGaOCcsuxSp6PGyauP2QqWTb8dGTtbC7lRU,210
-eva/vision/models/wrappers/from_registry.py,sha256=gdnxyg9drqlxfTNuS3aLbWGbZIwX1VNl0uudfjzVsXM,1614
-eva/vision/models/wrappers/from_timm.py,sha256=Z38Nb1i6OPKkgvFZOvGx-O3AZQuscf1zRVyrEBXQdJg,2320
+eva/vision/models/wrappers/from_registry.py,sha256=2vpKTkoa_CGjVLbhnUclstFzDfkXCqMxjdtxTk212HQ,1729
+eva/vision/models/wrappers/from_timm.py,sha256=Lkdibly4H_XNjl863YFBj10ZbSTN1onT2Bc6yV072m0,2334
 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
@@ -246,8 +277,8 @@ eva/vision/utils/io/image.py,sha256=IdOkr5MYqhYHz8U9drZ7wULTM3YHwCWSjZlu_Qdl4GQ,
 eva/vision/utils/io/mat.py,sha256=qpGifyjmpE0Xhv567Si7-zxKrgkgE0sywP70cHiLFGU,808
 eva/vision/utils/io/nifti.py,sha256=TFMgNhLqIK3sl3RjIRXEABM7FmSQjqVOwk1vXkuvX2w,4983
 eva/vision/utils/io/text.py,sha256=qYgfo_ZaDZWfG02NkVVYzo5QFySqdCCz5uLA9d-zXtI,701
-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-0.3.1.dist-info/METADATA,sha256=gXYGvp6Ap95944atE7L9Dxk8AnmuVhn22sHAC2iIl_g,25704
+kaiko_eva-0.3.1.dist-info/WHEEL,sha256=9P2ygRxDrTJz3gsagc0Z96ukrxjr-LFBGOgv3AuKlCA,90
+kaiko_eva-0.3.1.dist-info/entry_points.txt,sha256=6CSLu9bmQYJSXEg8gbOzRhxH0AGs75BB-vPm3VvfcNE,88
+kaiko_eva-0.3.1.dist-info/licenses/LICENSE,sha256=e6AEzr7j_R-PYr2qLO-JwLn8y70jbVD3U2mxbRmwcI4,11338
+kaiko_eva-0.3.1.dist-info/RECORD,,

{kaiko_eva-0.2.2.dist-info → kaiko_eva-0.3.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: pdm-backend (2.4.4)
+Generator: pdm-backend (2.4.5)
 Root-Is-Purelib: true
 Tag: py3-none-any

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

@@ -1,199 +0,0 @@
-"""LiTS dataset."""
-
-import functools
-import glob
-import os
-from typing import Any, Callable, Dict, List, Literal, Tuple
-
-import numpy as np
-import numpy.typing as npt
-import torch
-from torchvision import tv_tensors
-from typing_extensions import override
-
-from eva.core import utils
-from eva.core.data import splitting
-from eva.vision.data.datasets import _validators, vision
-from eva.vision.utils import io
-
-
-class LiTS(vision.VisionDataset[tv_tensors.Image, tv_tensors.Mask]):
-    """LiTS - Liver Tumor Segmentation Challenge.
-
-    Webpage: https://competitions.codalab.org/competitions/17094
-    """
-
-    _train_ratio: float = 0.7
-    _val_ratio: float = 0.15
-    _test_ratio: float = 0.15
-    """Index ranges per split."""
-
-    _fix_orientation: bool = True
-    """Whether to fix the orientation of the images to match the default for radiologists."""
-
-    _sample_every_n_slices: int | None = None
-    """The amount of slices to sub-sample per 3D CT scan image."""
-
-    _expected_dataset_lengths: Dict[str | None, int] = {
-        "train": 38686,
-        "val": 11192,
-        "test": 8760,
-        None: 58638,
-    }
-    """Dataset version and split to the expected size."""
-
-    _license: str = (
-        "Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License "
-        "(https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en)"
-    )
-    """Dataset license."""
-
-    def __init__(
-        self,
-        root: str,
-        split: Literal["train", "val", "test"] | None = None,
-        transforms: Callable | None = None,
-        seed: int = 8,
-    ) -> None:
-        """Initialize dataset.
-
-        Args:
-            root: Path to the root directory of the dataset. The dataset will
-                be downloaded and extracted here, if it does not already exist.
-            split: Dataset split to use.
-            transforms: A function/transforms that takes in an image and a target
-                mask and returns the transformed versions of both.
-            seed: Seed used for generating the dataset splits.
-        """
-        super().__init__(transforms=transforms)
-
-        self._root = root
-        self._split = split
-        self._seed = seed
-        self._indices: List[Tuple[int, int]] = []
-
-    @property
-    @override
-    def classes(self) -> List[str]:
-        return ["background", "liver", "tumor"]
-
-    @functools.cached_property
-    @override
-    def class_to_idx(self) -> Dict[str, int]:
-        return {label: index for index, label in enumerate(self.classes)}
-
-    @override
-    def filename(self, index: int) -> str:
-        sample_index, _ = self._indices[index]
-        volume_file_path = self._volume_files[sample_index]
-        return os.path.relpath(volume_file_path, self._root)
-
-    @override
-    def configure(self) -> None:
-        self._indices = self._create_indices()
-
-    @override
-    def validate(self) -> None:
-        for i in range(len(self._volume_files)):
-            seg_path = self._segmentation_file(i)
-            if not os.path.exists(seg_path):
-                raise FileNotFoundError(
-                    f"Segmentation file {seg_path} not found for volume {self._volume_files[i]}."
-                )
-
-        _validators.check_dataset_integrity(
-            self,
-            length=self._expected_dataset_lengths.get(self._split, 0),
-            n_classes=3,
-            first_and_last_labels=("background", "tumor"),
-        )
-
-    @override
-    def load_data(self, index: int) -> tv_tensors.Image:
-        sample_index, slice_index = self._indices[index]
-        volume_path = self._volume_files[sample_index]
-        image_nii = io.read_nifti(volume_path, slice_index)
-        image_array = io.nifti_to_array(image_nii)
-        if self._fix_orientation:
-            image_array = self._orientation(image_array, sample_index)
-        return tv_tensors.Image(image_array.transpose(2, 0, 1))
-
-    @override
-    def load_target(self, index: int) -> tv_tensors.Mask:
-        sample_index, slice_index = self._indices[index]
-        segmentation_path = self._segmentation_file(sample_index)
-        mask_nii = io.read_nifti(segmentation_path, slice_index)
-        mask_array = io.nifti_to_array(mask_nii)
-        if self._fix_orientation:
-            semantic_labels = self._orientation(mask_array, sample_index)
-        return tv_tensors.Mask(semantic_labels.squeeze(), dtype=torch.int64)  # type: ignore[reportCallIssue]
-
-    def _orientation(self, array: npt.NDArray, sample_index: int) -> npt.NDArray:
-        volume_path = self._volume_files[sample_index]
-        orientation = io.fetch_nifti_axis_direction_code(volume_path)
-        array = np.rot90(array, axes=(0, 1))
-        if orientation == "LPS":
-            array = np.flip(array, axis=0)
-        return array.copy()
-
-    @override
-    def load_metadata(self, index: int) -> Dict[str, Any]:
-        _, slice_index = self._indices[index]
-        return {"slice_index": slice_index}
-
-    @override
-    def __len__(self) -> int:
-        return len(self._indices)
-
-    def _get_number_of_slices_per_volume(self, sample_index: int) -> int:
-        """Returns the total amount of slices of a volume."""
-        file_path = self._volume_files[sample_index]
-        volume_shape = io.fetch_nifti_shape(file_path)
-        return volume_shape[-1]
-
-    @functools.cached_property
-    def _volume_files(self) -> List[str]:
-        files_pattern = os.path.join(self._root, "**", "volume-*.nii")
-        files = glob.glob(files_pattern, recursive=True)
-        return utils.numeric_sort(files)
-
-    def _segmentation_file(self, index: int) -> str:
-        volume_file_path = self._volume_files[index]
-        segmentation_file = os.path.basename(volume_file_path).replace("volume", "segmentation")
-        return os.path.join(os.path.dirname(volume_file_path), segmentation_file)
-
-    def _create_indices(self) -> List[Tuple[int, int]]:
-        """Builds the dataset indices for the specified split.
-
-        Returns:
-            A list of tuples, where the first value indicates the
-            sample index which the second its corresponding slice
-            index.
-        """
-        indices = [
-            (sample_idx, slide_idx)
-            for sample_idx in self._get_split_indices()
-            for slide_idx in range(self._get_number_of_slices_per_volume(sample_idx))
-            if slide_idx % (self._sample_every_n_slices or 1) == 0
-        ]
-        return indices
-
-    def _get_split_indices(self) -> List[int]:
-        """Returns the sample indices for the specified dataset split."""
-        indices = list(range(len(self._volume_files)))
-        train_indices, val_indices, test_indices = splitting.random_split(
-            indices, self._train_ratio, self._val_ratio, self._test_ratio, seed=self._seed
-        )
-        split_indices_dict = {
-            "train": train_indices,
-            "val": val_indices,
-            "test": test_indices,
-            None: indices,
-        }
-        if self._split not in split_indices_dict:
-            raise ValueError("Invalid data split. Use 'train', 'val', 'test' or `None`.")
-        return list(split_indices_dict[self._split])
-
-    def _print_license(self) -> None:
-        """Prints the dataset license."""
-        print(f"Dataset license: {self._license}")