careamics 0.0.15__py3-none-any.whl → 0.0.17__py3-none-any.whl

{careamics-0.0.15.dist-info → careamics-0.0.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.15
+Version: 0.0.17
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -10,33 +10,30 @@ License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
-Requires-Python: >=3.10
-Requires-Dist: bioimageio-core==0.9.0
-Requires-Dist: matplotlib<=3.10.3
-Requires-Dist: numpy<2.0.0
-Requires-Dist: pillow<=11.2.1
-Requires-Dist: psutil<=7.0.0
-Requires-Dist: pydantic<=2.12,>=2.11
-Requires-Dist: pytorch-lightning<=2.5.2,>=2.2
-Requires-Dist: pyyaml!=6.0.0,<=6.0.2
+Requires-Python: >=3.11
+Requires-Dist: bioimageio-core>=0.9.0
+Requires-Dist: matplotlib<=3.10.7
+Requires-Dist: numpy>=1.21
+Requires-Dist: numpy>=2.1.0; python_version >= '3.13'
+Requires-Dist: pillow<=11.3.0
+Requires-Dist: psutil<=7.1.0
+Requires-Dist: pydantic<=2.12.2,>=2.11
+Requires-Dist: pytorch-lightning<=2.5.5,>=2.2
+Requires-Dist: pyyaml!=6.0.0,<=6.0.3
 Requires-Dist: scikit-image<=0.25.2
-Requires-Dist: tifffile<=2025.5.10
-Requires-Dist: torch<=2.7.1,>=2.0
-Requires-Dist: torchvision<=0.22.1
-Requires-Dist: typer<=0.16.0,>=0.12.3
-Requires-Dist: zarr<3.0.0
+Requires-Dist: tifffile<=2025.10.4
+Requires-Dist: torch<=2.8.0,>=2.0
+Requires-Dist: torchmetrics<1.5.0,>=0.11.0
+Requires-Dist: torchvision<=0.23.0
+Requires-Dist: typer<=0.19.2,>=0.12.3
+Requires-Dist: validators<=0.35.0
+Requires-Dist: zarr<4.0.0,>=3.0.0
 Provides-Extra: czi
 Requires-Dist: pylibczirw<6.0.0,>=4.1.2; extra == 'czi'
-Provides-Extra: dev
-Requires-Dist: onnx; extra == 'dev'
-Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: pytest; extra == 'dev'
-Requires-Dist: pytest-cov; extra == 'dev'
-Requires-Dist: sybil; extra == 'dev'
 Provides-Extra: examples
 Requires-Dist: careamics-portfolio; extra == 'examples'
 Requires-Dist: jupyter; extra == 'examples'

{careamics-0.0.15.dist-info → careamics-0.0.17.dist-info}/RECORD

@@ -1,36 +1,44 @@
 careamics/__init__.py,sha256=eHsl7oE8HTKmi7yLMj8Yyp0RbdtN3QDmQQb-4Sn9d8M,475
-careamics/careamist.py,sha256=DeOt9u_EvRtRkzQ9NzBoyMxSNb8vO1tFHVwopI_37TY,38172
+careamics/careamist.py,sha256=e9kXTVF9ECdSDI9QVVNjk1DbuJHvq7uJIdTevIffETU,37939
 careamics/conftest.py,sha256=Od4WcaaP0UP-XUMrFr_oo4e6c2hi_RvNbuaRTopwlmI,911
 careamics/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
 careamics/cli/__init__.py,sha256=LbM9bVtU1dy-khmdiIDXwvKy2v8wPBCEUuWqV_8rosA,106
-careamics/cli/conf.py,sha256=ePp0hxcP3vUQWr5m2bgsxNBw7sS6eMu8F6pGhV8TvAU,13049
+careamics/cli/conf.py,sha256=pEVyoU2Yawjplct773xmMtYnIC_5jy4OOh6ok6tmGYo,13577
 careamics/cli/main.py,sha256=21UcqLOP0tM7x25pslw0zRAfJMMEZEzG1xeJZI-QfN0,6533
 careamics/cli/utils.py,sha256=DJvHKpZB6LSSnABKxK6i15ITAyIdyaiAnSdpBPZhuuk,626
-careamics/config/__init__.py,sha256=K0N1GIqFCYhpPjalZG-Ygap6Ew_dDAC0uw5Npzhg9Lk,1524
-careamics/config/callback_model.py,sha256=lxytx4rwqOI-UxW8eHTdfLE3K4eIlg907w4Xk9Nul7Y,4065
-careamics/config/configuration.py,sha256=gNBKxeHqAQLa8_btGuQ4-X4987cRPr5L6RI6hOv179Q,13345
-careamics/config/configuration_factories.py,sha256=P_VWHOJEjW-s_yAOKul9TV41yufsQLzRyCPSKJrjUjc,45959
+careamics/config/__init__.py,sha256=QRI7byEt82B36foRhHXybWdG7xKAgrUJalIcP4hg_MQ,1752
+careamics/config/callback_model.py,sha256=VT0NyM8R1Mhtsm8SnZqk-0CK1WVaZXbCFJZCRq5DoXI,4108
+careamics/config/configuration.py,sha256=6By2zlql29r8ka6EZFfND-8BlPpcQmnf3hMr4metyic,11352
+careamics/config/configuration_factories.py,sha256=UjjCsYPs30j5mG3FqaLSWW-3i9C8eEh9GDoQsl7N-Zc,77597
 careamics/config/configuration_io.py,sha256=P-bP1kzkXxJWOEFP02dEZFNmpuLAPJfJtYhX4bFeaKk,2324
-careamics/config/inference_model.py,sha256=OiNLR4srvbaNcsvA5_Zwc3tqr7yQAXXeSxm5aAEpySM,6978
-careamics/config/likelihood_model.py,sha256=mxyhEHC6wS02t5lqFE3l-8N1DpzrTqEiQSswEy3DJgs,2246
-careamics/config/loss_model.py,sha256=yYcUBS90Qyon1MxeaHiVP3dJHPJFC0GUvWKGcAb3IHk,2036
-careamics/config/nm_model.py,sha256=M_YE2fiYgJT1pGF7JpzhDvgTnd8CP6DxZXIjxG9q5Qg,4722
-careamics/config/optimizer_models.py,sha256=9qxcLjtDp5LjYX52u21Rom4F3_GZUV2GJimrK3un574,5717
+careamics/config/inference_model.py,sha256=E0s9wjPr3xEOllkf_oyROngq_BBe8Yc3l0Br4ygNFac,6949
+careamics/config/likelihood_model.py,sha256=oXRwY2wGHUNLWqIdYtpo1KfxJxyWvDcRE-6dCVs7DgU,2241
+careamics/config/loss_model.py,sha256=V_JyOCyFAxJIl7RGHqW_7mFBNq5GLOpYwWwU-WsUyKk,2166
+careamics/config/nm_model.py,sha256=HrQJ49PDmi3dhCm7m4sbYiQ5nF54xYZ0KwJ-8uK7zGw,5524
+careamics/config/optimizer_models.py,sha256=8PR9rRwoghGU3-Bz904sFqD1Ee4mTXtMsXOkekxVcIk,5688
 careamics/config/tile_information.py,sha256=c-_xrVPOgcnjiEzQ-9A_GhNPamObkMANbeHaRP29R-4,2059
-careamics/config/training_model.py,sha256=6XvXMIT2H8vxyGfb9L4cSRqpmlurBPeyWYS6RYhDZaA,3095
-careamics/config/algorithms/__init__.py,sha256=on5D6zBO9Lu-Tf5To8xpF6owIFqdN7RSmZdpyXDOaNw,404
+careamics/config/training_model.py,sha256=kMKPe5M2KHLNS3FFZczOUydKekNXERXWYnbm31D-8eg,1932
+careamics/config/algorithms/__init__.py,sha256=4DjB62MBYyAhbF9IhQy2z4Z0Oz-3ImJGfUlBYI2GF8o,557
 careamics/config/algorithms/care_algorithm_model.py,sha256=ncf89BC2aFPFSquJ65-Y7NpwVbvgPE0BKH6Up1OHa1s,3238
+careamics/config/algorithms/hdn_algorithm_model.py,sha256=tbXPv2l4zKNv1Gq6kVXKVCZ8YV13jhr39R77X1hPopQ,2618
+careamics/config/algorithms/microsplit_algorithm_model.py,sha256=iWfjsOADH6kct21aFVDTG8FOwjyymSZUpjCwG278wAY,2705
 careamics/config/algorithms/n2n_algorithm_model.py,sha256=OZbRis9jhRKWNK1-Z_aw2tfJRuGdlJiYEYlH4Hr1FRs,3066
-careamics/config/algorithms/n2v_algorithm_model.py,sha256=IkHsTj-IkWq--mlWjBHfH18CGK_3p2uaC3Zz2tfieaA,9469
+careamics/config/algorithms/n2v_algorithm_model.py,sha256=MSBkeHaIoFQlZhPxSUnZO-pFKeeq-OmVmx8q00pcmv8,9440
 careamics/config/algorithms/unet_algorithm_model.py,sha256=OaBFVlhsb9YhF3f2x1ImazvfnZ4_DPWvYWihRwurkeg,2587
-careamics/config/algorithms/vae_algorithm_model.py,sha256=JFHWtoLEKt0PthJYiDq3TfBl7fJudODUvtCyTeFZvvg,4661
+careamics/config/algorithms/vae_algorithm_model.py,sha256=o7Weqxyk4idZIp3dpDa7f7CqmvrJJ4UD4tsuj-RW73c,6100
 careamics/config/architectures/__init__.py,sha256=lYUz56R7LDqVQWQDLkLgJL8VtOyxc_ege1r4bXGEBqA,220
 careamics/config/architectures/architecture_model.py,sha256=gXn4gdLrQP3bmTQxIhzkEHYlodPaIp6LI-kwZl23W-Y,911
-careamics/config/architectures/lvae_model.py,sha256=lwOiJYNUqPrZFl9SpPLYon77EiRbe2eI7pmpx45rO78,7606
+careamics/config/architectures/lvae_model.py,sha256=4EScBNA33WZzyuU0vGFlP3UJcX2GmKuKlklH0v9wgTw,7769
 careamics/config/architectures/unet_model.py,sha256=Aqc_KPf2VKMhNrYwOdmr_ez3iIQz8ZRtsA6t5FFT354,3686
 careamics/config/data/__init__.py,sha256=YS04_USNswKL7kpSn_6BeTvhobAiUVst46_SlCztCxs,171
-careamics/config/data/data_model.py,sha256=4zqLKfH1dhOl7CDHvIANrfSbJnUhnkfrCvAJF5F7MdQ,13374
-careamics/config/data/ng_data_model.py,sha256=0RSUvSMoIVcQY4a1drCMHMcOBp15xHchtnEk-nUiTvU,12244
+careamics/config/data/data_model.py,sha256=FQqSFkqeBHyIHqmMPCh27rTgiSVW40BlIlUCuewxUbg,14616
+careamics/config/data/ng_data_model.py,sha256=Zi8RO1AymoPXjLzU0VSxV-o2at_7W9qKruKVtwzb-v8,17480
+careamics/config/data/patch_filter/__init__.py,sha256=TXTGxvAKsEeB-IYTaIFaI-zWFix5McNLxBD7TQ7inL0,433
+careamics/config/data/patch_filter/filter_model.py,sha256=feNi7fXSC9GS8UZqXxf3f-c405KUmF4k-2aA4yqd_FI,472
+careamics/config/data/patch_filter/mask_filter_model.py,sha256=yGRv6j0Dg_CQ1FzI4m-WXiSwS14s3HjzWIchQaNtaE4,423
+careamics/config/data/patch_filter/max_filter_model.py,sha256=fpLhtDAiVTFPDMHtDom5JLv86SNCZ9hlinIz6v59bYA,351
+careamics/config/data/patch_filter/meanstd_filter_model.py,sha256=mblErVTYX9xbF0TVzaRCDTMNoNK8f4zVJmYiX__0uyQ,479
+careamics/config/data/patch_filter/shannon_filter_model.py,sha256=JDfcmw-O1hC6rtB8jWNCbv4EwPFFncG-dq_QoG9wvJ4,384
 careamics/config/data/patching_strategies/__init__.py,sha256=6ZUors-WzBBQCwMyaSojYJzdXeleFRBlrFls1r-Otdo,394
 careamics/config/data/patching_strategies/_overlapping_patched_model.py,sha256=ysGd8QNNdNzLD6NITmvyjVETG6ohhEFLgWPCS_CYSxE,3030
 careamics/config/data/patching_strategies/_patched_model.py,sha256=wmhM1Qt5qDuMCs76ab7dPoNTjy_lLVIL8TD5AzaIoak,1429
@@ -40,11 +48,12 @@ careamics/config/data/patching_strategies/tiled_patching_model.py,sha256=5lltbA9
 careamics/config/data/patching_strategies/whole_patching_model.py,sha256=HCPiWFrYk_ICWvlmddJYW9YjCzZUc7ijGJlLP1WxvjU,272
 careamics/config/support/__init__.py,sha256=ktWvxbTkRXnQPS_N84l9E2B5kTZVdd64SIjsJIQKB-k,1041
 careamics/config/support/supported_activations.py,sha256=CqOWoziIK5jZZXJO7G7cGg3TTid1POqv8FXqxjXxyME,535
-careamics/config/support/supported_algorithms.py,sha256=w6YzcIqGZ_bS85Tw1s7TEltBDXLt4SzgN3Tc6s19dGU,946
+careamics/config/support/supported_algorithms.py,sha256=FKluIBTLQyFZauhMC-mCN7w6w4FdotvFPd8DOl4umko,1090
 careamics/config/support/supported_architectures.py,sha256=pOxvHOAIUkc7HCO0IIg4K22h-Ti5ErtcIkGOjN-zh1s,340
 careamics/config/support/supported_data.py,sha256=rVcBOBUosyvYWZJAofJ66_DucnkkPfPhZMXU6KXugsM,3079
+careamics/config/support/supported_filters.py,sha256=fl2LXGaB0EMXpFurTKskPi28kZOBHtmka_7BqHffjvI,354
 careamics/config/support/supported_loggers.py,sha256=ubSOkGoYabGbm_jmyc1R3eFcvcP-sHmuyiBi_d3_wLg,197
-careamics/config/support/supported_losses.py,sha256=2x5sZuxRbWJzodoL35I1mMYUUDMzk8UFiFdbyPwbJ4E,583
+careamics/config/support/supported_losses.py,sha256=EQompJiL_F4ZHPVORDZf_dAXHBeVikaxfykT6mOnnwQ,671
 careamics/config/support/supported_optimizers.py,sha256=_2XmwzYENB6xpTedyWHUdWuGcDzdlfEAJjzm_qI3yRM,1392
 careamics/config/support/supported_patching_strategies.py,sha256=3Ngth0bna6ibabmg73y-1Hq7MebFNFq2MqE8sUB7UO8,635
 careamics/config/support/supported_pixel_manipulations.py,sha256=rFiktUlvoFU7s1NAKEMqsXOzLw5eaw9GtCKUznvq6xc,432
@@ -52,7 +61,7 @@ careamics/config/support/supported_struct_axis.py,sha256=alZMA5Y-BpDymLPUEd1zqVY
 careamics/config/support/supported_transforms.py,sha256=ylTiS8fUFKFwfn85gh7kKF4Trb9Q4ENPKm-XDWCe-SY,311
 careamics/config/transformations/__init__.py,sha256=6THr9oNI06umw_cchXW9sCeBLpFIcJfGC4hdq3WvUsI,577
 careamics/config/transformations/n2v_manipulate_model.py,sha256=IJ_MeNbVzwnmvLhBjAVZPj5fxPzUXYGYYRe5PHcWIzQ,2428
-careamics/config/transformations/normalize_model.py,sha256=_gQmUTlrPlMx5fptoZbB0Ov7PdJQoeDAw81XMCtQRr4,1920
+careamics/config/transformations/normalize_model.py,sha256=OAQryxDDCm8s_e_XW-McGhnGE0LjEV84CuNiAA48a6E,1891
 careamics/config/transformations/transform_model.py,sha256=6UVbXnxm-LLZOQQ-ZBwWwgmS_99DiBuERLfMxrta3-8,990
 careamics/config/transformations/transform_unions.py,sha256=lOwwX2LZPhfb0GR8B1jtJeuoDa9jIbOmh_W0rlebS1g,784
 careamics/config/transformations/xy_flip_model.py,sha256=2k4tiUZK3GVn9hEjFlWi0ypz-k5C2XKKO6elU7HlKmI,1012
@@ -67,7 +76,6 @@ careamics/dataset/in_memory_tiled_pred_dataset.py,sha256=fKg3_Mmx0hXlOjuWU6lhTVR
 careamics/dataset/iterable_dataset.py,sha256=xDt2985m-K1P5G2EaNHOHg54-fjRI6MfZTdNB4NdSJI,9752
 careamics/dataset/iterable_pred_dataset.py,sha256=4OsyDQv9udIh7R8UixTLeB_jVtaG-6z38bMqWRqxMxI,3750
 careamics/dataset/iterable_tiled_pred_dataset.py,sha256=4553dDF9_yQkb--g2wWD8rempMk_DTLYgRgt5T03mW0,4594
-careamics/dataset/zarr_dataset.py,sha256=lojnK5bhiF1vyjuPtWXBrZ9sy5fT_rBvZJbbbnE-H_I,5665
 careamics/dataset/dataset_utils/__init__.py,sha256=MJ3xriL6R4ZtmzbvLsASUWLb85Hk5AdeRaYnHpNELJQ,507
 careamics/dataset/dataset_utils/dataset_utils.py,sha256=X83DzaOWmHdl4eOPac2IQJH3bPA43RVq0hPrFrzvIXQ,2630
 careamics/dataset/dataset_utils/file_utils.py,sha256=ru6AtQ9LCmo6raN1-GnJEN4UyP1PbmSdR9MEys3CuHo,4094
@@ -83,8 +91,8 @@ careamics/dataset/tiling/collate_tiles.py,sha256=XK0BsDQE7XwIwmOoCHJIpVC3kqjSN6n
 careamics/dataset/tiling/lvae_tiled_patching.py,sha256=2oOXnVsZ_L2jtA02Jw7bLfkugZ2ZO8lF105cjxGADoY,13210
 careamics/dataset/tiling/tiled_patching.py,sha256=985vlz9hJdBNKP6z9hL0hU6lXSUPmGpXutdcbyBtv_o,6000
 careamics/dataset_ng/README.md,sha256=489sMnra-cVotBBWNL-jhb9H4eLO1FFa3b5zhfkK34g,9856
-careamics/dataset_ng/dataset.py,sha256=2R7jMUJFBECI-MBROg4QhGM3vJ8EEIpwOMDoBYEQhN8,8810
-careamics/dataset_ng/factory.py,sha256=bjzolF1k9iTj6cY75licyGYielZZvpp3xJwLbw8t5uU,14723
+careamics/dataset_ng/dataset.py,sha256=wpOSTqAWPfl6oB-M9NTGsjZId7BZgSp6kjzptjJSUvw,11007
+careamics/dataset_ng/factory.py,sha256=SKEhEuy0Stdj13815C8La2OSip-71RkkWlPgymGF6F4,17198
 careamics/dataset_ng/legacy_interoperability.py,sha256=K8u7MZRUkrG-gTX-COIykEejTHDxPET4H2oxKhQ_UTw,5559
 careamics/dataset_ng/demos/bsd68_demo.ipynb,sha256=UdpxKq198IV_xqJLcGR_C5rnX95G_zktnfmbltfEw60,10628
 careamics/dataset_ng/demos/care_U2OS_demo.ipynb,sha256=fxuiJ0g65Ts7jFUxHgCGbf30Xoz8kIB4dfh9qfpW1D8,9501
@@ -94,15 +102,23 @@ careamics/dataset_ng/demos/demo_dataset.ipynb,sha256=3mNGotUtQ2XMbw4JE5HkOSZXtqc
 careamics/dataset_ng/demos/demo_patch_extractor.py,sha256=2guz1iRqBzue4GLAVh9-K8sXCgsygtsJS-wzeHctY34,1419
 careamics/dataset_ng/demos/mouse_nuclei_demo.ipynb,sha256=Afd-_T848z3ZCDAL8vMfP6CJR8CbUg0xLAurBxg-fuc,8278
 careamics/dataset_ng/patch_extractor/__init__.py,sha256=U27Gxp6dk6DUc-MiDMPvdh2aoWlM7jU-bjueqa7elPg,207
-careamics/dataset_ng/patch_extractor/demo_custom_image_stack_loader.py,sha256=Y6CQyCy-_NcRf9ytOeCsIXjeN8CZBnKpMwcM1H50cNc,2987
-careamics/dataset_ng/patch_extractor/image_stack_loader.py,sha256=Gq1KbqZWCX8fR4ZCcFysXPK6LoJJJvb4Cig_KYeGyqs,2490
+careamics/dataset_ng/patch_extractor/demo_custom_image_stack_loader.py,sha256=UnSBiLCeBruHxuJgbEN2o2LaoNouTcbT2EixYepwbwg,3021
+careamics/dataset_ng/patch_extractor/image_stack_loader.py,sha256=fcEmjFCOy6PNuqHBnf357d11EDhxVz6ni6pdUGzyJbI,2498
 careamics/dataset_ng/patch_extractor/patch_extractor.py,sha256=nGN5TrmmSo5KeQoXJ-wrVQtQlYadaR8onH7TOWXhVy4,824
 careamics/dataset_ng/patch_extractor/patch_extractor_factory.py,sha256=8B3s5n8nEOQ6JCJIANVdckgJGaYm8Y4v69vYn4Zsmdo,5927
 careamics/dataset_ng/patch_extractor/image_stack/__init__.py,sha256=0K4swSw3fmVonjavNyxDtXRDJTNq4P7oMBktsoNO2GI,333
 careamics/dataset_ng/patch_extractor/image_stack/czi_image_stack.py,sha256=5XXbOZoxPY3g8cAcuHgwKFWN5gAC9vAwvuesA2pxF9Q,14420
 careamics/dataset_ng/patch_extractor/image_stack/image_stack_protocol.py,sha256=NnhqyDmZPuQgU_gjNugNWNX9_NetRguwLg9LfTmd7U8,1649
-careamics/dataset_ng/patch_extractor/image_stack/in_memory_image_stack.py,sha256=2eICQjYTzjEaYLh9Wg2IJ6cguo7Ty1p-eXPvTJk0nv0,1941
-careamics/dataset_ng/patch_extractor/image_stack/zarr_image_stack.py,sha256=hmNOl6-FMUNQS65YMSa4eAz3Rp_2es98p1_UY6S8B50,6590
+careamics/dataset_ng/patch_extractor/image_stack/in_memory_image_stack.py,sha256=0Iw2TFASM-28qoJeAkvwt1N1t79QMMwCqlSoLZOUt08,1912
+careamics/dataset_ng/patch_extractor/image_stack/zarr_image_stack.py,sha256=yAOpwifNEXViDgkrbXSgNugSLVx-BDtDqBz6g6pFhBc,7400
+careamics/dataset_ng/patch_filter/__init__.py,sha256=llqhrtVAGyAMutG5dri9tpZvXaNBJrsk4FKTzt3i6rc,624
+careamics/dataset_ng/patch_filter/coordinate_filter_protocol.py,sha256=kGYapdjVdz1yRMMz6kbzVvZEuzhMbdV1pGh_2o2xawU,670
+careamics/dataset_ng/patch_filter/filter_factory.py,sha256=aIvAq0TDXYpZ9C2-udpjgRNgeDo19YTrhmKnGg4ny-U,2902
+careamics/dataset_ng/patch_filter/mask_filter.py,sha256=Ky27Jw7EQbHdq1gwe7P3DBL7-YCvcXRnMYIYetVMPJ4,3068
+careamics/dataset_ng/patch_filter/max_filter.py,sha256=-qHN67RDwcP57ISVXpe-wzxAUVeLqVHmEhNJ0h8dzCk,6425
+careamics/dataset_ng/patch_filter/mean_std_filter.py,sha256=xc_E7FpDzYvQKYiicROyx8LdVvpFsBSBQghKxTDetBk,7498
+careamics/dataset_ng/patch_filter/patch_filter_protocol.py,sha256=wJaHFjEwsuHSOy7hUXmCUxTNg9KBl4_h2DCxuri48Go,1165
+careamics/dataset_ng/patch_filter/shannon_filter.py,sha256=A8AYDe4dD7PMJj4EEPc5xNA1ZijGKR7Yb3Hxiaht8B0,6261
 careamics/dataset_ng/patching_strategies/__init__.py,sha256=2KwdY_TeD9WQju150WbV2IF19TincHU3lbcL0fqZF5o,549
 careamics/dataset_ng/patching_strategies/patching_strategy_protocol.py,sha256=ukw5G9hIOPEJz-DEFDMuJsGYou7wUeRjALNU8qdgn9g,3475
 careamics/dataset_ng/patching_strategies/random_patching.py,sha256=0qEhUgANJAuhnVYeCiCaiW1gwLWOGAIIFcvriW0_byM,13490
@@ -110,18 +126,19 @@ careamics/dataset_ng/patching_strategies/sequential_patching.py,sha256=Qsqqf8D_2
 careamics/dataset_ng/patching_strategies/tiling_strategy.py,sha256=jKug3ocARe-pSqSB3g27T7GGmrrQ6eRYbp_m49BJ4-4,6415
 careamics/dataset_ng/patching_strategies/whole_sample.py,sha256=o1Z4iHKveq9X--LRV-gdUQqB-TPVxr2RvaKHmgDnCx0,1249
 careamics/file_io/__init__.py,sha256=vgMI77X820VOWywAEW5W20FXfmbqBzx4V63D3V3_HhI,334
-careamics/file_io/read/__init__.py,sha256=wf8O_o80ghrlWQ-RGEuSqcc2LU55P1B-oxTacDToygo,259
+careamics/file_io/read/__init__.py,sha256=r8WILkWoBOTLTJiltg1tCozIh-XSq_I33VMIx3ykSKs,231
 careamics/file_io/read/get_func.py,sha256=1UJMfVb6gUCe_5WBRxCEO2Q7pqdVu8u2Sm0aHxXdiak,1415
 careamics/file_io/read/tiff.py,sha256=UMofW33rvByK9B1zYGhSrWAiAA3uQUV3OVK7cq9d0gQ,1359
-careamics/file_io/read/zarr.py,sha256=2jzREAnJDQSv0qmsL-v00BxmiZ_sp0ijq667LZSQ_hY,1685
 careamics/file_io/write/__init__.py,sha256=CUt33cRjG9hm18L9a7XqaUKWQ_3xiuQ9ztz4Ab7RYG0,283
 careamics/file_io/write/get_func.py,sha256=hyGHe1RX-lfa9QFAnwRCz_gS0NRiRnXEtg4Bdeh2Esc,1627
 careamics/file_io/write/tiff.py,sha256=tBGIgl-I1sMyBivgx-dOTBykXBODkgwPH8MT3_4KAE8,1050
-careamics/lightning/__init__.py,sha256=ATCVAGnX08Ik4TxbIv0-cXb52UinR42JgvZh_GIMSpc,588
-careamics/lightning/lightning_module.py,sha256=EgRIWOHxZ9FZyS2lGaRSGaVecT8revXjd4mE59se7T0,24311
-careamics/lightning/predict_data_module.py,sha256=yahMMPbEIX0AXNgA2PKIABm9cYEXlyhl0SKc1GCDEZU,12741
-careamics/lightning/train_data_module.py,sha256=028si-InvNHbr78ne1sEudhwKz-ReZGNIoOtr9hUlvc,26541
-careamics/lightning/callbacks/__init__.py,sha256=eA5ltzYNzuO0uMEr1jG4wP01b0s29s5I03WGJ290qkw,312
+careamics/lightning/__init__.py,sha256=NeqZmOgor6EXov6ULmPdGxl5dB39ljibGvjZaA0zkaM,970
+careamics/lightning/lightning_module.py,sha256=5TJyphmITh00SOcrl3-hLx7tr7sHUaXQgmLFCbYAivE,28647
+careamics/lightning/microsplit_data_module.py,sha256=8BSAiuTmsl2p96Drv6Wnz8LBtMg4Qj1SCS-8Jn50Rss,20597
+careamics/lightning/predict_data_module.py,sha256=EQ-X2go-beMIhGD8bbOm3XorTDfMReFUkk9MewmYxuw,13094
+careamics/lightning/train_data_module.py,sha256=wFWO2wC0uXtoBNcNk8xNMCQxsl7eEJ5cXFOl1DXTYNg,27055
+careamics/lightning/callbacks/__init__.py,sha256=sgP-u7FKnrD83cyWidvaIZZHvCIP-3pwrgZsfzPejow,388
+careamics/lightning/callbacks/data_stats_callback.py,sha256=Z4BPbicdwPLLePdXjRPGKC831zgO-YQxCqONAmYFIz4,1183
 careamics/lightning/callbacks/hyperparameters_callback.py,sha256=u45knOZHwoVHz6yYfrnERQuozT_SfZ1OrKP0QjeU4EM,1495
 careamics/lightning/callbacks/progress_bar_callback.py,sha256=w-j_nk2ysyc4THKfwWbpkiKGeqNUpLGtm-8dYBgla2c,2443
 careamics/lightning/callbacks/prediction_writer_callback/__init__.py,sha256=ZVf3vaSU_NjSjrKbI24H0kK9WAiP9oKXfhP670EaWMo,548
@@ -130,33 +147,33 @@ careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callb
 careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py,sha256=BulDaQdXoLYoU39sfKrtdnHjY_TIQ8qOvfDjkSWi13s,12572
 careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py,sha256=WLPWuZbLZ1pJWwAssqK9ObLZsljMhu-lxN0xe7_yCKc,7083
 careamics/lightning/dataset_ng/__init__.py,sha256=5913hBQ5FRn4K-zzPtrqh-2zN4iie9bD-KXm0-_FNXY,49
-careamics/lightning/dataset_ng/data_module.py,sha256=PyU7igSn22vnrPJLyVn2UYo9szS3NXayRZY5wqo8iu8,26229
+careamics/lightning/dataset_ng/data_module.py,sha256=4BHMwcvji0taqA6ga8n-uc0oLjsuEMMD7Y33aO9wC4k,29160
 careamics/lightning/dataset_ng/lightning_modules/__init__.py,sha256=Kx7NkwAS9rqfozxamMWcJa3U8zw47HT5T8R1E0Uk8Rc,164
 careamics/lightning/dataset_ng/lightning_modules/care_module.py,sha256=Mc72uucp8DOObIfK05-LvzFVbXcBQ5IZ7vDUeYoMt1Q,3145
 careamics/lightning/dataset_ng/lightning_modules/n2v_module.py,sha256=DD9JkNDD-nbBNDjmUP-PWTr_sbNaYb8_TKXpUC6FB5Q,3355
 careamics/lightning/dataset_ng/lightning_modules/unet_module.py,sha256=aGN_xZptJ1fxK3J39YLoF_E4UDYNJGeYJETQKVgxRwU,6868
-careamics/losses/__init__.py,sha256=nSWbkBcFhkyUkIT2wVcULqpieyY2Oro39NXZTtfQpXo,351
-careamics/losses/loss_factory.py,sha256=IVcvSWLnbMuoLG_4SmZ4s_hfinB-olu44PL9lhDEGEM,1545
+careamics/losses/__init__.py,sha256=ROBvKNkKpo46e3sgWpLeuPNvTBEas8OHl6GIBr9lWxk,398
+careamics/losses/loss_factory.py,sha256=sZo-pxBgnAcgKrRm0us_6S7hDXi4FdNazSHzC2Y277o,1637
 careamics/losses/fcn/__init__.py,sha256=kf92MKFGHr6upiztZVgWwtGPf734DZyub92Rn8uEq8o,18
 careamics/losses/fcn/losses.py,sha256=KuoXqL24QbTxDdRmQJbERC95x0f3u4T0S77dqBZRarQ,2513
 careamics/losses/lvae/__init__.py,sha256=0FNtMLHrOMfagtWkaBdz1NTjyf2y0QLgysxJv5jq5uw,19
 careamics/losses/lvae/loss_utils.py,sha256=QxzA2N1TglR4H0X0uyTWWytDagE1lA9IB_TK1lms3ao,2720
-careamics/losses/lvae/losses.py,sha256=Bx9oNnFGw9YThVSAn7tznS53_aym1_BPABVcDMH5spY,17943
+careamics/losses/lvae/losses.py,sha256=rzeEnPQnyp0Eej2l8XwpSDeiaD_k5qE63LHdSpfR3Ik,20798
 careamics/lvae_training/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 careamics/lvae_training/calibration.py,sha256=xHbiLcY2csYos3s7rRSqp7P7G-9wzULcSo1JfVzfIjE,7239
-careamics/lvae_training/eval_utils.py,sha256=PWKlG2XrvdfZTG0_brcADaAA0owTeNRT1g673gYtk5k,34410
+careamics/lvae_training/eval_utils.py,sha256=D_RmDMVOu-6XAMBogOG6zCL2m7bU0YOXr8p2lLEzm4s,34573
 careamics/lvae_training/get_config.py,sha256=dwVfaQS7nzjQss0E1gGLUpQpjPcOWwLgIhbu3Z0I1rg,3068
 careamics/lvae_training/lightning_module.py,sha256=ryr7iHqCMzCl5esi6_gEcnKFDQkMrw0EXK9Zfgv1Nek,27186
 careamics/lvae_training/metrics.py,sha256=KTDAKhe3vh-YxzGibjtkIG2nnUyujbnwqX4xGwaRXwE,6718
 careamics/lvae_training/train_lvae.py,sha256=lJEBlBGdISVkZBcEnPNRYgJ7VbapYzZHRaFOrZ0xYGE,11080
 careamics/lvae_training/train_utils.py,sha256=e-d4QsF-li8MmAPkAmB1daHpkuU16nBTnQFZYqpTjn4,3567
-careamics/lvae_training/dataset/__init__.py,sha256=TcsPOoeYXWZh2mTEOodYf4u5dd12TzzkxAaxLzBrMyA,538
-careamics/lvae_training/dataset/config.py,sha256=upMx0NvYtKBi0SHH6WHMfVDzwLzgIk3Nw7z5vRoEvj0,4392
-careamics/lvae_training/dataset/lc_dataset.py,sha256=r4PffRXzuTJ0tLWei4B3wq6f1Q34raaZQzZ0IQXi8OI,10762
-careamics/lvae_training/dataset/ms_dataset_ref.py,sha256=uyyz9RjiV3iszQAmavhLhU6PT2B_n6pch3F22ZS4M0o,40892
-careamics/lvae_training/dataset/multich_dataset.py,sha256=kw2gFZPDEp6WdsJwjQ-2EFvxZHe-HI83FhI4C5k39b4,42593
+careamics/lvae_training/dataset/__init__.py,sha256=EM_FjJA1xF74uSo2zZLecRKMWaGLlNoyQGkDItAdnUw,552
+careamics/lvae_training/dataset/config.py,sha256=UoHWg0sQYGI6bPIvUW6SDk18KG7c377r4XSHsvAs3CM,4761
+careamics/lvae_training/dataset/lc_dataset.py,sha256=886JcdPrg1v_3Ks6BP50EdCE118PVCSRAWguxS9PF_0,10991
+careamics/lvae_training/dataset/ms_dataset_ref.py,sha256=Lk-aeyEIYRoM46ZBhQ879W77o_AbRvvZeYtxrhwF9jk,40950
+careamics/lvae_training/dataset/multich_dataset.py,sha256=cLtZ_e-b-qrCaYUkGYp2HdmXwNTv75Fy1Agd2ffRAuA,42814
 careamics/lvae_training/dataset/multicrop_dset.py,sha256=1h5fREkDNxKGBO1vb4d9W_UVMOA105uBTrN6_J-jUs0,6418
-careamics/lvae_training/dataset/multifile_dataset.py,sha256=hJBs6iBrf_FcyUYzg8rDjvKEICHxDYyXVOj-5L0F6FE,10273
+careamics/lvae_training/dataset/multifile_dataset.py,sha256=YEaWVy8X_eGtrz3Q2ixT6olhGG9M56-lDDpdNg4zLQw,10315
 careamics/lvae_training/dataset/types.py,sha256=7uCrbL_FQeQfAPz-mHnqHKpZC1x4sdvq9wswmBvOPO0,616
 careamics/lvae_training/dataset/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 careamics/lvae_training/dataset/utils/data_utils.py,sha256=8PvRPqSbYHPCl87cycZHxXIFOT_EoBV-8XCt3ZLh36s,3125
@@ -164,7 +181,7 @@ careamics/lvae_training/dataset/utils/empty_patch_fetcher.py,sha256=OFjeqhZ6vFUL
 careamics/lvae_training/dataset/utils/index_manager.py,sha256=rihMe5zOfXvPFvM_2paP0EzK4WhaG6RhRFLy8TxnNas,21654
 careamics/lvae_training/dataset/utils/index_switcher.py,sha256=ZoMi8LsaIkm8MFqIFaxN4oQGyzCcwOlCom8SYNus15E,6716
 careamics/model_io/__init__.py,sha256=khMIkk107LL5JGze0OVfl5Lfi14R3_e4W21tW0iJ1kE,155
-careamics/model_io/bmz_io.py,sha256=XMV-a9btKf1bsC7NP7awoN2hrewSQHRbN8K9G4Sfi8E,7788
+careamics/model_io/bmz_io.py,sha256=IlmgOPI-1jPVBgDH1caDf0dTUWyM7uWRt4egm5yhLQU,7964
 careamics/model_io/model_io_utils.py,sha256=mA8y5ZJ2r5vqA3OCgJqB1wxvCCx37x8Yl7nj1zi3_3U,2750
 careamics/model_io/bioimage/__init__.py,sha256=dKm-UluVwa_7EHQB0ukx-Qk8JVWtuT-OUinY8hE9EIw,298
 careamics/model_io/bioimage/_readme_factory.py,sha256=sRfHbuwhfYmpwsG0keXFCSK3qCS4VI4GQhX6OhSKLjY,3440
@@ -178,16 +195,16 @@ careamics/models/model_factory.py,sha256=GWbouERvEfHj_BrpKHYgrPAj8dpdoh1R-X--Jt0
 careamics/models/unet.py,sha256=f7QT_tHilub9y22RF9rki9ISjS6BYA0fJn5ULwHtVAo,14785
 careamics/models/lvae/__init__.py,sha256=6dT6uqgT__V08EjoTGxXguTbTkySZmByS9J2Bj6WWLM,53
 careamics/models/lvae/layers.py,sha256=UPxZiZjgnBnPs_wdSzcP-_s17MEw4P1CoIZzn4OdUA0,57944
-careamics/models/lvae/likelihoods.py,sha256=qRYRewQv6PqzJO-7nDnFkK86-R8dI4HSp1_ilRSc2I4,12233
-careamics/models/lvae/lvae.py,sha256=Jlw3mxVCxMDtjMvBWI9C9javHHyrngm8RfTYPsYhbI4,34767
-careamics/models/lvae/noise_models.py,sha256=lpSygXsJmD_erP0V72u9i5CX51wpopLNCH_YjmEL29s,24095
+careamics/models/lvae/likelihoods.py,sha256=-FtUnqUPNkkNYTQdTSpYMUcxc_QJ_9MJgsndav026lg,12744
+careamics/models/lvae/lvae.py,sha256=0JIX8ylMDO2fshc0m_0vG8WHRlU30cykp5zpCUQJOSI,34754
+careamics/models/lvae/noise_models.py,sha256=X3FzpNPnHsnadW2C4bXUJwUQLtaNoiWwUhhei7lScZ0,24555
 careamics/models/lvae/stochastic.py,sha256=wiTrLBSYwOvsF1araKxUHy1CHp1mdH9bazctVo0NchA,16628
 careamics/models/lvae/utils.py,sha256=EE3paHu3vhCaqfOrGypzUsImZJO94uBhx8q6kZ-R36o,11516
-careamics/prediction_utils/__init__.py,sha256=k5hsPGY8FOkwIT0fQgrUz7fVCH2NlwuOdZiISdXjEWg,270
+careamics/prediction_utils/__init__.py,sha256=u18N8a9MSYa1RRIrJOPBgbiaLwFDDjsKEO8B0zDtMao,401
 careamics/prediction_utils/lvae_prediction.py,sha256=B66w0F5GM95yhD68L9Sg1LqgtxgIgi_a_83WlN4fZu4,6188
 careamics/prediction_utils/lvae_tiling_manager.py,sha256=SI-JaJvLrKWBSHdm-FjcqWdbhlcflTRiKxYF7CSGzvA,13736
-careamics/prediction_utils/prediction_outputs.py,sha256=-rjI6pWEy_29nljG9sLGdI-7VaBH4ZBvJQOxB5UAOi4,4070
-careamics/prediction_utils/stitch_prediction.py,sha256=zWpfUPdJWKoJwHDcOjVyDek2YXmfQb3gHDWrkAb5E_I,3907
+careamics/prediction_utils/prediction_outputs.py,sha256=HH4W9EoAoPX2My5H8tli8uEuLgDpSoaksX2grAtrR5E,5771
+careamics/prediction_utils/stitch_prediction.py,sha256=Y0QQFJdoVSwly-zu2H86qXGqblTArcxkDuVc18VQyes,6723
 careamics/transforms/__init__.py,sha256=n7D3SbcVSRaMOl5F5Rozo2_lY8dn0DH28ywYIdbXxBo,561
 careamics/transforms/compose.py,sha256=8hOfcPDlI9z0kmlsi2QlIyEX3Y7gJxx1typCEdJszq0,5361
 careamics/transforms/n2v_manipulate.py,sha256=pAwGEZW_SFwbbVQGwpfWl6SVIa7slvfSSfve6sIHq_w,5670
@@ -199,7 +216,7 @@ careamics/transforms/struct_mask_parameters.py,sha256=jE29Li9sx3olaRnqYfJsSlKi2t
 careamics/transforms/transform.py,sha256=cEqc4ci8na70i-HIGYC7udRfVa8D_8OjdRVrr3txLvQ,464
 careamics/transforms/tta.py,sha256=78S7Df9rLHmEVSQSI1qDcRrRJGauyG3oaIrXkckCkmw,2335
 careamics/transforms/xy_flip.py,sha256=PlkwWneq5ypLvIcoevZatHMhPXpE2-sTpytziWC1oaw,3804
-careamics/transforms/xy_random_rotate90.py,sha256=o582ktYI2F54OLKZDn4tDMX-aOcD7S955vAHrJvCtNk,3147
+careamics/transforms/xy_random_rotate90.py,sha256=xJJWBxVz227hFM11Dk-ufAsjS7LFsO3AOJoFn2ke8Bk,3152
 careamics/utils/__init__.py,sha256=mLwBQ7wTL2EwDwL3NcX53EHPNklojU45Jcc728y4EWQ,402
 careamics/utils/autocorrelation.py,sha256=M_WYzrEOQngc5iSXWar4S3-EOnK6DfYHPC2vVMeu_Bs,945
 careamics/utils/base_enum.py,sha256=bz1D8mDx5V5hdnJ3WAzJXWHJTbgwAky5FprUt9F5cMA,1387
@@ -213,9 +230,9 @@ careamics/utils/ram.py,sha256=tksyn8dVX_iJXmrDZDGub32hFZWIaNxnMheO5G1p43I,244
 careamics/utils/receptive_field.py,sha256=Y2h4c8S6glX3qcx5KHDmO17Kkuyey9voxfoXyqcAfiM,3296
 careamics/utils/serializers.py,sha256=mILUhz75IMpGKnEzcYu9hlOPG8YIiIW09fk6eZM7Y8k,1427
 careamics/utils/torch_utils.py,sha256=IUTxKIqYpUTvN-UDZDGBheF7zgtskH_yDcVvYx0p8zI,3478
-careamics/utils/version.py,sha256=WKtMlrNmXymJqzMfguBX558D6tb6aoAZfbABRh_ViIs,1142
-careamics-0.0.15.dist-info/METADATA,sha256=1lpIRjfRtM_XPs7eZP-JnV9rYZtRer2XrqK1rykEE84,3911
-careamics-0.0.15.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-careamics-0.0.15.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
-careamics-0.0.15.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
-careamics-0.0.15.dist-info/RECORD,,
+careamics/utils/version.py,sha256=i2d02OGg2dmdVrxk6auomCGDzLxCd8q4540hB7SzXYQ,1152
+careamics-0.0.17.dist-info/METADATA,sha256=AuSVi9CrMMspo0kJ3dne8MSvdEsC7VNJZhzR2PFEjBk,3837
+careamics-0.0.17.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+careamics-0.0.17.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
+careamics-0.0.17.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.0.17.dist-info/RECORD,,

careamics/dataset/zarr_dataset.py

@@ -1,151 +0,0 @@
-"""Zarr dataset."""
-
-# from itertools import islice
-# from typing import Callable, Dict, List, Optional, Tuple, Union
-
-# import numpy as np
-# import torch
-# import zarr
-
-# from careamics.utils import RunningStats
-# from careamics.utils.logging import get_logger
-
-# from ..utils import normalize
-# from .dataset_utils import read_zarr
-# from .patching.patching import (
-#     generate_patches_unsupervised,
-# )
-
-# logger = get_logger(__name__)
-
-
-# class ZarrDataset(torch.utils.data.IterableDataset):
-#     """Dataset to extract patches from a zarr storage.
-
-#     Parameters
-#     ----------
-#     data_source : Union[zarr.Group, zarr.Array]
-#         Zarr storage.
-#     axes : str
-#         Description of axes in format STCZYX.
-#     patch_extraction_method : Union[ExtractionStrategies, None]
-#         Patch extraction strategy, as defined in extraction_strategy.
-#     patch_size : Optional[Union[List[int], Tuple[int]]], optional
-#         Size of the patches in each dimension, by default None.
-#     num_patches : Optional[int], optional
-#         Number of patches to extract, by default None.
-#     mean : Optional[float], optional
-#         Expected mean of the dataset, by default None.
-#     std : Optional[float], optional
-#         Expected standard deviation of the dataset, by default None.
-#     patch_transform : Optional[Callable], optional
-#         Patch transform callable, by default None.
-#     patch_transform_params : Optional[Dict], optional
-#         Patch transform parameters, by default None.
-#     running_stats_window_perc : float, optional
-#         Percentage of the dataset to use for calculating the initial mean and standard
-#         deviation, by default 0.01.
-#     mode : str, optional
-#         train/predict, controls running stats calculation.
-#     """
-
-#     def __init__(
-#         self,
-#         data_source: Union[zarr.Group, zarr.Array],
-#         axes: str,
-#         patch_extraction_method: Union[SupportedExtractionStrategy, None],
-#         patch_size: Optional[Union[List[int], Tuple[int]]] = None,
-#         num_patches: Optional[int] = None,
-#         mean: Optional[float] = None,
-#         std: Optional[float] = None,
-#         patch_transform: Optional[Callable] = None,
-#         patch_transform_params: Optional[Dict] = None,
-#         running_stats_window_perc: float = 0.01,
-#         mode: str = "train",
-#     ) -> None:
-#         self.data_source = data_source
-#         self.axes = axes
-#         self.patch_extraction_method = patch_extraction_method
-#         self.patch_size = patch_size
-#         self.num_patches = num_patches
-#         self.mean = mean
-#         self.std = std
-#         self.patch_transform = patch_transform
-#         self.patch_transform_params = patch_transform_params
-#         self.sample = read_zarr(self.data_source, self.axes)
-#         self.running_stats_window = int(
-#             np.prod(self.sample._cdata_shape) * running_stats_window_perc
-#         )
-#         self.mode = mode
-#         self.running_stats = RunningStats()
-
-#         self._calculate_initial_mean_std()
-
-#     def _calculate_initial_mean_std(self):
-#         """Calculate initial mean and std of the dataset."""
-#         if self.mean is None and self.std is None:
-#             idxs = np.random.randint(
-#                 0,
-#                 np.prod(self.sample._cdata_shape),
-#                 size=max(1, self.running_stats_window),
-#             )
-#             random_chunks = self.sample[idxs]
-#             self.running_stats.init(random_chunks.mean(), random_chunks.std())
-
-#     def _generate_patches(self):
-#         """Generate patches from the dataset and calculates running stats.
-
-#         Yields
-#         ------
-#         np.ndarray
-#             Patch.
-#         """
-#         patches = generate_patches_unsupervised(
-#             self.sample,
-#             self.patch_extraction_method,
-#             self.patch_size,
-#         )
-
-#         # num_patches = np.ceil(
-#         #     np.prod(self.sample.chunks)
-#         #     / (np.prod(self.patch_size) * self.running_stats_window)
-#         # ).astype(int)
-
-#         for idx, patch in enumerate(patches):
-#             if self.mode != "predict":
-#                 self.running_stats.update(patch.mean())
-#             if isinstance(patch, tuple):
-#                 normalized_patch = normalize(
-#                     img=patch[0],
-#                     mean=self.running_stats.avg_mean.value,
-#                     std=self.running_stats.avg_std.value,
-#                 )
-#                 patch = (normalized_patch, *patch[1:])
-#             else:
-#                 patch = normalize(
-#                     img=patch,
-#                     mean=self.running_stats.avg_mean.value,
-#                     std=self.running_stats.avg_std.value,
-#                 )
-
-#             if self.patch_transform is not None:
-#                 assert self.patch_transform_params is not None
-#                 patch = self.patch_transform(patch, **self.patch_transform_params)
-#             if self.num_patches is not None and idx >= self.num_patches:
-#                 return
-#             else:
-#                 yield patch
-#         self.mean = self.running_stats.avg_mean.value
-#         self.std = self.running_stats.avg_std.value
-
-#     def __iter__(self):
-#         """
-#         Iterate over data source and yield single patch.
-
-#         Yields
-#         ------
-#         np.ndarray
-#         """
-#         worker_info = torch.utils.data.get_worker_info()
-#         num_workers = worker_info.num_workers if worker_info is not None else 1
-#         yield from islice(self._generate_patches(), 0, None, num_workers)

careamics/file_io/read/zarr.py

@@ -1,60 +0,0 @@
-"""Function to read zarr images."""
-
-from typing import Union
-
-from zarr import Group, core, hierarchy, storage
-
-
-def read_zarr(
-    zarr_source: Group, axes: str
-) -> Union[core.Array, storage.DirectoryStore, hierarchy.Group]:
-    """Read a file and returns a pointer.
-
-    Parameters
-    ----------
-    zarr_source : Group
-        Zarr storage.
-    axes : str
-        Axes of the data.
-
-    Returns
-    -------
-    np.ndarray
-        Pointer to zarr storage.
-
-    Raises
-    ------
-    ValueError, OSError
-        if a file is not a valid tiff or damaged.
-    ValueError
-        if data dimensions are not 2, 3 or 4.
-    ValueError
-        if axes parameter from config is not consistent with data dimensions.
-    """
-    if isinstance(zarr_source, hierarchy.Group):
-        array = zarr_source[0]
-
-    elif isinstance(zarr_source, storage.DirectoryStore):
-        raise NotImplementedError("DirectoryStore not supported yet")
-
-    elif isinstance(zarr_source, core.Array):
-        # array should be of shape (S, (C), (Z), Y, X), iterating over S ?
-        if zarr_source.dtype == "O":
-            raise NotImplementedError("Object type not supported yet")
-        else:
-            array = zarr_source
-    else:
-        raise ValueError(f"Unsupported zarr object type {type(zarr_source)}")
-
-    # sanity check on dimensions
-    if len(array.shape) < 2 or len(array.shape) > 4:
-        raise ValueError(
-            f"Incorrect data dimensions. Must be 2, 3 or 4 (got {array.shape})."
-        )
-
-    # sanity check on axes length
-    if len(axes) != len(array.shape):
-        raise ValueError(f"Incorrect axes length (got {axes}).")
-
-    # arr = fix_axes(arr, axes)
-    return array