careamics 0.0.8__py3-none-any.whl → 0.0.10__py3-none-any.whl

{careamics-0.0.8.dist-info → careamics-0.0.10.dist-info}/RECORD

@@ -1,39 +1,35 @@
-careamics/__init__.py,sha256=WF2JpQmC-MmuSB0L81XRo67NwaN_0qjyywcpRlbVJVE,569
-careamics/careamist.py,sha256=rakSaDSGRR0Pr0o1s8ejwIrjWknOQs4DgljukqfyWu0,37635
+careamics/__init__.py,sha256=eHsl7oE8HTKmi7yLMj8Yyp0RbdtN3QDmQQb-4Sn9d8M,475
+careamics/careamist.py,sha256=OhBkchHIVIvLyk57R5UXt2Euy4e_EDSbNp5NXJ53hS8,37588
 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=oixGRZNylW-NTM_rkDtQkSRw8KUYwtmUC_hK5BEeLnA,13074
 careamics/cli/main.py,sha256=S4B3c1ZN-OQK0l2_W42CaW0KmF_Pe_y4pKgn_UOuyDg,6564
 careamics/cli/utils.py,sha256=q_dmG7lxg_FT62qX9fPilIWL1M8ibhLnnhUKqa4knPI,660
-careamics/config/__init__.py,sha256=c5FXtcQrtROHdLRl4cHpKo6V4_E4yr6HxYgNwqH9CHg,1917
+careamics/config/__init__.py,sha256=K0N1GIqFCYhpPjalZG-Ygap6Ew_dDAC0uw5Npzhg9Lk,1524
 careamics/config/callback_model.py,sha256=EeYHqpMIPQwyNxLRzzX32Uncl5mZuB1bJO76RHpNymg,4555
-careamics/config/care_configuration.py,sha256=hSfNJ-dooHm4ujG6Q3Hawr8zDeYy1HNiebtM7gxsh7s,2714
-careamics/config/configuration.py,sha256=KmLeXHkFhQTrcru1erhfVf3tHvQdoi12ls_u254rtDw,11114
-careamics/config/configuration_factories.py,sha256=9civH9r1yfXcYeXJS61ft3Wsn8PoODNeqzGU45CTFCs,35460
-careamics/config/configuration_io.py,sha256=ks9R8lRCBY_m0sdy1k4ZWFPKEFSp7K9X47jCG4d0FY4,2353
+careamics/config/configuration.py,sha256=D7i_g48P7d4H4_YSFyvDh9tRM7vLhM1mnU_XMeCC1HU,11193
+careamics/config/configuration_factories.py,sha256=NhheOPkVhIF1cwz0FGNLQrxOByRQGrw-aZ_vGNIE8UE,34599
+careamics/config/configuration_io.py,sha256=P-bP1kzkXxJWOEFP02dEZFNmpuLAPJfJtYhX4bFeaKk,2324
 careamics/config/inference_model.py,sha256=UE_-ZmCX6LFCbDBOwyGnvuAboF_JNX2m2LcF0WiwgCI,6961
 careamics/config/likelihood_model.py,sha256=VorUtc0_-xIWNxwVrd1kBba-003ICdVMtxpcDCxH4Io,2259
 careamics/config/loss_model.py,sha256=yYcUBS90Qyon1MxeaHiVP3dJHPJFC0GUvWKGcAb3IHk,2036
-careamics/config/n2n_configuration.py,sha256=QoHnEak0LiG6rBIXnmx61Chkz-Q0jr2Qt9I0NnmgZo4,2667
-careamics/config/n2v_configuration.py,sha256=5MagUFaVZ-9VGIiaKD-4RRkFpJen2imMoR3Lu07BD14,8489
 careamics/config/nm_model.py,sha256=5dAhDBLa4WPfKaNEK6ATNsSUwtlH8u8gYweEA4gZP6g,4758
 careamics/config/optimizer_models.py,sha256=OWpTydRBBR8wt_af1mZHNNwvL_RtnRFopAOdgjzLo30,5750
 careamics/config/tile_information.py,sha256=c-_xrVPOgcnjiEzQ-9A_GhNPamObkMANbeHaRP29R-4,2059
 careamics/config/training_model.py,sha256=67_ipo_-LxhT4-WqAs40Sg8PjU--my43Qn3BhjvlXxM,3212
 careamics/config/algorithms/__init__.py,sha256=on5D6zBO9Lu-Tf5To8xpF6owIFqdN7RSmZdpyXDOaNw,404
-careamics/config/algorithms/care_algorithm_model.py,sha256=-AEfzrA4HugYwMdDHqcc_i1H9kycXKS0YyRwT_MCCPo,951
-careamics/config/algorithms/n2n_algorithm_model.py,sha256=aWG6-YYB9T2e-QirxC-YijosO3QNA0rJRPIQZrorSi0,799
-careamics/config/algorithms/n2v_algorithm_model.py,sha256=b1M1ab9D8rhCG7RmhmaDi5rjHJjaQXebTdUEewJBnNg,709
+careamics/config/algorithms/care_algorithm_model.py,sha256=ncf89BC2aFPFSquJ65-Y7NpwVbvgPE0BKH6Up1OHa1s,3238
+careamics/config/algorithms/n2n_algorithm_model.py,sha256=OZbRis9jhRKWNK1-Z_aw2tfJRuGdlJiYEYlH4Hr1FRs,3066
+careamics/config/algorithms/n2v_algorithm_model.py,sha256=ROeVsFVY2JDMtQEZWOZc75Muh1SnOxww7_Z2BzB9bZ8,9470
 careamics/config/algorithms/unet_algorithm_model.py,sha256=OaBFVlhsb9YhF3f2x1ImazvfnZ4_DPWvYWihRwurkeg,2587
 careamics/config/algorithms/vae_algorithm_model.py,sha256=1ZrShUGHA7zbjSiCQwhUSv7l7Hr7MbpcLOw8ucM27p8,4680
 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/unet_model.py,sha256=HJJWf-wuYTv8KXMwikdjeB8htg1QOt0IyQbMuBt1LUI,3556
-careamics/config/data/__init__.py,sha256=ijFNSRKkKVF8fw6ym8kXq_wNhdwkWXxuNj2XKtD3KjE,218
-careamics/config/data/data_model.py,sha256=Z-sy6bJ_JYT5fzbVwLOH1PnjRkVY0YAmNG5OnQAd-SQ,12635
-careamics/config/data/n2v_data_model.py,sha256=-n5cncmcrd4-KUSmEk8rXAONMC7sfbYfGmshVNuySCU,5915
+careamics/config/data/__init__.py,sha256=ijNcvrKQtKljmBuZ6DDxh86PMzpRob2l2JMqbPQLqPk,111
+careamics/config/data/data_model.py,sha256=0YFN_NXL10f8h_Wr7ce6xsfOy86iZOPIkgLK-KIpeEU,12181
 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
@@ -44,29 +40,29 @@ careamics/config/support/supported_losses.py,sha256=2x5sZuxRbWJzodoL35I1mMYUUDMz
 careamics/config/support/supported_optimizers.py,sha256=_2XmwzYENB6xpTedyWHUdWuGcDzdlfEAJjzm_qI3yRM,1392
 careamics/config/support/supported_pixel_manipulations.py,sha256=rFiktUlvoFU7s1NAKEMqsXOzLw5eaw9GtCKUznvq6xc,432
 careamics/config/support/supported_struct_axis.py,sha256=alZMA5Y-BpDymLPUEd1zqVY0xMkgl9Rv1d4ujED6sco,424
-careamics/config/support/supported_transforms.py,sha256=ODvmoTywvJWG_5-SJJZu-X1FNtKGhkNWQc-t26IFZWI,311
-careamics/config/transformations/__init__.py,sha256=jMTUX15n8ZF4Nc9gQp-qbXfhj-iEsEa65lzNbHwzyfY,631
-careamics/config/transformations/n2v_manipulate_model.py,sha256=Mdxc4J3vxe_dM2CIhmTwwGOIirQvrQXLoa2vRsTzoYI,1855
+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=1Rkk6IkF-7ytGU6HSzP-TpOi4RRWiQJ6fOd8zammXcg,1936
 careamics/config/transformations/transform_model.py,sha256=6UVbXnxm-LLZOQQ-ZBwWwgmS_99DiBuERLfMxrta3-8,990
-careamics/config/transformations/transform_unions.py,sha256=uqlI8Nm827bKfMbDQLVhKFtT9e7TJ_zIYDBdHlOuQ1I,1137
+careamics/config/transformations/transform_unions.py,sha256=lOwwX2LZPhfb0GR8B1jtJeuoDa9jIbOmh_W0rlebS1g,784
 careamics/config/transformations/xy_flip_model.py,sha256=zU-uZ1b1zNZWckbho3onN-B7BHKhN7jbgbNZyRQhv2s,1025
 careamics/config/transformations/xy_random_rotate90_model.py,sha256=6sYKmtCLvz0SV1qZgBSHUTH-CUjwvHnohq1HyPntbyE,894
 careamics/config/validators/__init__.py,sha256=zRrIse0O3ImwG97NphEupFVm3Ib9nEJhpNNrKGyDTps,423
 careamics/config/validators/model_validators.py,sha256=9OCdlf7rmndtTpmQ8COLaEjURYYmszic_RjY9mzS-k4,1941
 careamics/config/validators/validator_utils.py,sha256=NVkEOr5AQK4JXWNtmgeQgAaJOyieJNb5PHCjlcqNeew,2611
 careamics/dataset/__init__.py,sha256=31vop67zbtGesENEIig-LLw1q2lCydMFc_YWgfK2Yt4,547
-careamics/dataset/in_memory_dataset.py,sha256=MV_Vf4siIP-g7VKhxN4rU7MZXpaHKvfwr8ZXqk44Qhs,9958
-careamics/dataset/in_memory_pred_dataset.py,sha256=VvwW5D8TjgO_kR8eZinP-9qepSiI6ZsUN7FZ0Rvc8Bs,2161
-careamics/dataset/in_memory_tiled_pred_dataset.py,sha256=DANmlnlV1ysXKdwGvmJoOYKcjlgoMhnSGSDRpeK79ZA,3552
-careamics/dataset/iterable_dataset.py,sha256=pqtm-AWhDbuZTnXf0roAHWVxGPRTekAzVcJHLzaSyFU,9797
-careamics/dataset/iterable_pred_dataset.py,sha256=jee4b8bZOyvSS5qfIsb6Jkk1EV_MKEU2SyZ0m7p0p9k,3767
-careamics/dataset/iterable_tiled_pred_dataset.py,sha256=2j_kLMB6DfSKXPszZPYgsB08TVgcf1V5HY_kZVozrFM,4560
+careamics/dataset/in_memory_dataset.py,sha256=Snbq7N8lYB06m018Yz0Mgx1PE3hHLh6__DeaArKPBvs,9665
+careamics/dataset/in_memory_pred_dataset.py,sha256=0f_lS8APDmA7KPaZjF9NmD9kjB0tGwUefALu1MEiWB8,2141
+careamics/dataset/in_memory_tiled_pred_dataset.py,sha256=fKg3_Mmx0hXlOjuWU6lhTVRsm02D21J-IOYmTIm4UsE,3561
+careamics/dataset/iterable_dataset.py,sha256=QsrriN62jUQ7OPbGJoyBP9z9MkJV9kipp8maWb9aIfk,9783
+careamics/dataset/iterable_pred_dataset.py,sha256=fgrVC-jdJf8fY8WnZe4QWTAkcKz6xKcw4Zlf5DpqB34,3750
+careamics/dataset/iterable_tiled_pred_dataset.py,sha256=062FVJyj4RQhVdne6HreKgAeBdK9UFi--BXzK76tlBk,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
-careamics/dataset/dataset_utils/iterate_over_files.py,sha256=Jun35Qn9XevHOb_DixYBMHDAOykLmiwciA5Q2MzSUK8,2912
+careamics/dataset/dataset_utils/iterate_over_files.py,sha256=zsNhIDMHUsPMbqwG7cfuSc26Svg5hERHcrXfftKaUoY,2898
 careamics/dataset/dataset_utils/running_stats.py,sha256=kWorioMH4S5uZj2cvUpjHB6cIUhMFa1XXwDQrrKIWdI,5752
 careamics/dataset/patching/__init__.py,sha256=7-s12oUAZNlMOwSkxSwbD7vojQINWYFzn_4qIJ87WBg,37
 careamics/dataset/patching/patching.py,sha256=deAxY34Iz-mguBlHQ-5EO4vRhPpR9I3LQ9onV1K_KqA,8858
@@ -77,6 +73,24 @@ careamics/dataset/tiling/__init__.py,sha256=aW_AMB9rzm0VmooUpjcyqv6sQP69RlPQMEdP
 careamics/dataset/tiling/collate_tiles.py,sha256=XK0BsDQE7XwIwmOoCHJIpVC3kqjSN6nDhrJ4POVeHS8,965
 careamics/dataset/tiling/lvae_tiled_patching.py,sha256=LYEEdjKuKaxIGFtOkhfpsE7hruBnIsD5HcW9aVH6WHI,13019
 careamics/dataset/tiling/tiled_patching.py,sha256=6vxsqlccUqIl4Ys92JWIPs0Kn95VzaHoAYMSGcp2dh8,5956
+careamics/dataset_ng/demo_dataset.ipynb,sha256=gAWQnodNga5I6TrjsJspjeAGWCHiy23SFE5dPvKnETE,7130
+careamics/dataset_ng/demo_patch_extractor.py,sha256=8iCAdvmfGdTJSR59yu0WOb_4r3HshRDDMrSiOpxoh5o,1510
+careamics/dataset_ng/demo_patch_extractor_factory.py,sha256=4NRtb9hOL0bXz2f8PHOmjoltbMhoMl8UkFXIJTf8f5Y,981
+careamics/dataset_ng/dataset/__init__.py,sha256=V8fSRAnabpo706OVLn6l9UtQCyp5Kc5CDwD1hMOjRAA,70
+careamics/dataset_ng/dataset/dataset.py,sha256=g0-uBKxLHVUEuRtIQnKseiExhc_yb0-pfS4icTdOFkE,6406
+careamics/dataset_ng/patch_extractor/__init__.py,sha256=X_UBCKi_5py0HfBAGiRMcTaqEu3EdJNVRI7eSG2wmlo,298
+careamics/dataset_ng/patch_extractor/demo_custom_image_stack_loader.py,sha256=fv-izzYW5QyMQ2Oki2sDGzXLAt51uzxxphu-NdrQMOA,2884
+careamics/dataset_ng/patch_extractor/image_stack_loader.py,sha256=0jSF-uM05kv-nqY3tB_bcbpC0Cb7qB1CBDDqkfTvjNs,4690
+careamics/dataset_ng/patch_extractor/patch_extractor.py,sha256=CLexpuFQ_GiNWhzRSa3HoepbBj3lvCHu9ZU5PVfYWas,748
+careamics/dataset_ng/patch_extractor/patch_extractor_factory.py,sha256=rIEuCMUhqslzd-7DHueOAQ13y8rgxjtvjlVX3dql0zk,6017
+careamics/dataset_ng/patch_extractor/image_stack/__init__.py,sha256=xTGRg2W_CpxsTgyiG-cHSFuXh7hwA0fGrEPm61GrsBI,225
+careamics/dataset_ng/patch_extractor/image_stack/image_stack_protocol.py,sha256=8QLpKEVqw3Edz-hL7lmKW_06x6DcbQo20feN8XkTnsY,1543
+careamics/dataset_ng/patch_extractor/image_stack/in_memory_image_stack.py,sha256=FS9dEY5GXKEf0oeNe7Vb005HTby4thUvzTzWwCxe3Zk,1927
+careamics/dataset_ng/patch_extractor/image_stack/zarr_image_stack.py,sha256=hmNOl6-FMUNQS65YMSa4eAz3Rp_2es98p1_UY6S8B50,6590
+careamics/dataset_ng/patching_strategies/__init__.py,sha256=NLSjecNI_BOhkfznjogBEkq8BP74aixjpLhhRdkS9Bo,366
+careamics/dataset_ng/patching_strategies/patching_strategy_protocol.py,sha256=gcbprNfRxG5gEBQzqZyJIhjCfwsC80PQvx0JQ-iunJg,2308
+careamics/dataset_ng/patching_strategies/random_patching.py,sha256=AGlvn1NsjPJY5Ku8DEn92DaKkvAjX293coqMnwi7_UY,13410
+careamics/dataset_ng/patching_strategies/sequential_patching.py,sha256=fngTPpY6D93guFwSdHuCakDebin7eEtK7Y2OFmJ1IG8,2485
 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/get_func.py,sha256=O_pdymjh2mc-JZ1je3ZnPAcsHc7Je3a005AMgAa0xuw,1388
@@ -86,9 +100,9 @@ careamics/file_io/write/__init__.py,sha256=CUt33cRjG9hm18L9a7XqaUKWQ_3xiuQ9ztz4A
 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=3nzRcjv7dlWmWjoWmGaBV7D6d698xMp3XO7fpIrZhwA,22630
+careamics/lightning/lightning_module.py,sha256=_gMGKGSHOEoh00jblCX5egMI91Z0UJpIjEQ74AaVGss,24177
 careamics/lightning/predict_data_module.py,sha256=JNwujK6QwObSx6P25ghpGl2f2gGT3KVgYMTlonZzH20,12745
-careamics/lightning/train_data_module.py,sha256=LeTyjNtAJw8nNiw2k6Ifuw0fAgppyZyRxyEGbDq30Fo,28309
+careamics/lightning/train_data_module.py,sha256=HyXeDZ_u3JLzyh1tqRBIH93spMj0iQhAP4nmHPEI4aM,26554
 careamics/lightning/callbacks/__init__.py,sha256=eA5ltzYNzuO0uMEr1jG4wP01b0s29s5I03WGJ290qkw,312
 careamics/lightning/callbacks/hyperparameters_callback.py,sha256=u45knOZHwoVHz6yYfrnERQuozT_SfZ1OrKP0QjeU4EM,1495
 careamics/lightning/callbacks/progress_bar_callback.py,sha256=w-j_nk2ysyc4THKfwWbpkiKGeqNUpLGtm-8dYBgla2c,2443
@@ -100,13 +114,13 @@ careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.
 careamics/losses/__init__.py,sha256=nSWbkBcFhkyUkIT2wVcULqpieyY2Oro39NXZTtfQpXo,351
 careamics/losses/loss_factory.py,sha256=oPacrkwiabsmiW_r--IxX-XPRbzezZUvOuWKbUw5LiI,1518
 careamics/losses/fcn/__init__.py,sha256=kf92MKFGHr6upiztZVgWwtGPf734DZyub92Rn8uEq8o,18
-careamics/losses/fcn/losses.py,sha256=NdOz29hzJ7D26p13q-g0NWoYwNauIWrP2xWww6YPbB8,2360
+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=wHT1dx04BZ_OI-_S7cFQ5hFmMetm6FSnuZfwZBBtIpY,17977
 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=2Ij1L1enIwjox16cPrhGzkcVQooBzN_mcC9ma94mJrE,30180
+careamics/lvae_training/eval_utils.py,sha256=FxZmmT6vMRluLYnnCEQtLcz5Q45OAqmxXbQo6KPbQEk,30372
 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
@@ -124,13 +138,13 @@ careamics/lvae_training/dataset/utils/empty_patch_fetcher.py,sha256=OFjeqhZ6vFUL
 careamics/lvae_training/dataset/utils/index_manager.py,sha256=Gt1I-7lBaQDBgqguOmofAFDdAsJQfz7ktvq4_I80F9c,10084
 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=0fL0cz_80nsu_Jgk-ImXKTNbn_WSdrXB9flvLm2g3Is,7792
-careamics/model_io/model_io_utils.py,sha256=HCSoNvaOo55kI7teZleN57riqNK2fLq77zMadBKXCyc,2777
+careamics/model_io/bmz_io.py,sha256=XQvRUxM4keEiYlnWNTZUxeLgLl3_c-_drOZcH4mjEDo,7801
+careamics/model_io/model_io_utils.py,sha256=ZSBO1MEFBh--GwUqmK1iW7Vf57MgdQtxmucNBdXkHBw,2748
 careamics/model_io/bioimage/__init__.py,sha256=dKm-UluVwa_7EHQB0ukx-Qk8JVWtuT-OUinY8hE9EIw,298
 careamics/model_io/bioimage/_readme_factory.py,sha256=sRfHbuwhfYmpwsG0keXFCSK3qCS4VI4GQhX6OhSKLjY,3440
-careamics/model_io/bioimage/bioimage_utils.py,sha256=YVr75SDfafOiuYGonPbcsO-xVS0wI1WkmWQQZx6DXYQ,1246
+careamics/model_io/bioimage/bioimage_utils.py,sha256=aX0rZny3OPaZZGGE-5Y3qXgnOAhyAQOtN15Ri0EVMTk,1297
 careamics/model_io/bioimage/cover_factory.py,sha256=8URrpEfJvdHBJeSrh5H2IQHSUybsTyAOR3_A-YYAAlw,4583
-careamics/model_io/bioimage/model_description.py,sha256=HwjWT77nIt6LkLvIBRxwgPOsL0ffrCMtDUjim39qgqE,10071
+careamics/model_io/bioimage/model_description.py,sha256=caC9O0xyXEIMyCHW5j37HMX4IhMtNk0QWCF05VdPCQE,10050
 careamics/models/__init__.py,sha256=Xui2BLJd1I2r_E3Sj24fJALFTi2FGtfNscUWj_0c9Hk,93
 careamics/models/activation.py,sha256=nu3sDgd7Lsyw8rvmUwxNN-7SM09cEMfxZ9DRDzdSKns,1049
 careamics/models/layers.py,sha256=tpsxbolRWYycZGxS3hKlDRtMf6HpNdZs98uwx5K8lls,13757
@@ -148,11 +162,13 @@ careamics/prediction_utils/lvae_prediction.py,sha256=ZwPFCSeUGsULIMoMQWRYKHfLFaD
 careamics/prediction_utils/lvae_tiling_manager.py,sha256=SI-JaJvLrKWBSHdm-FjcqWdbhlcflTRiKxYF7CSGzvA,13736
 careamics/prediction_utils/prediction_outputs.py,sha256=fw-bJ2szWJD7BgZlECmxy5sgeXGFJl4T8cRNzLR1aUQ,4069
 careamics/prediction_utils/stitch_prediction.py,sha256=8YRW2rea-is5tYI0Q1bw3bpX7VMFmbpxSP_y6x9Yfug,3893
-careamics/transforms/__init__.py,sha256=WtgpSFL_CJwpa47XzqS7bVXHPJ4qW0TamEymy_kgWQQ,483
-careamics/transforms/compose.py,sha256=ZSVwKg3LT2PrwtSBKtkb6AHsVSSlZIdv9wTYl4To1s4,5682
+careamics/transforms/__init__.py,sha256=n7D3SbcVSRaMOl5F5Rozo2_lY8dn0DH28ywYIdbXxBo,561
+careamics/transforms/compose.py,sha256=QMCuqp0C5mJ5N6xh3ISKY7HfjfKp6NqDwQiKXoxEjug,5326
 careamics/transforms/n2v_manipulate.py,sha256=t9rtMbYV6P1IVp4yzuJfq5-giWyfGrxL8ZhzP29Pp8k,5686
+careamics/transforms/n2v_manipulate_torch.py,sha256=Lxi94cbE0aEZ1fFD0m4T7VDrDSt3cbHPdYISa8XYemw,4830
 careamics/transforms/normalize.py,sha256=fxs813ydCWrIzrxFzkbk1gW8OGSr0esQSrNUFSJuGL0,7715
-careamics/transforms/pixel_manipulation.py,sha256=38NsxY8ARvz7GSNDKx5g67Hv5qciBzadiELAg5OcUSU,13355
+careamics/transforms/pixel_manipulation.py,sha256=WSx2sqcZ2wUkm6qPi4pG3Ai0sE8ONPOpYLSvkW5M3bY,13393
+careamics/transforms/pixel_manipulation_torch.py,sha256=W2sTQrM00TwmcoFf1bcYapAwE66pKIVVeAtBIW6ovK4,14343
 careamics/transforms/struct_mask_parameters.py,sha256=jE29Li9sx3olaRnqYfJsSlKi2t0WQzJmCm9aCbIQEsA,421
 careamics/transforms/transform.py,sha256=cEqc4ci8na70i-HIGYC7udRfVa8D_8OjdRVrr3txLvQ,464
 careamics/transforms/tta.py,sha256=78S7Df9rLHmEVSQSI1qDcRrRJGauyG3oaIrXkckCkmw,2335
@@ -171,8 +187,9 @@ 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=_Cf3HdlIRl5hxfpUg9aofCSlcW7GSsIJxsbSORXko0U,3010
-careamics-0.0.8.dist-info/METADATA,sha256=jBK6zEhnACTuo9igH-PT-5sphN-tj2-b20j1E2zE7_w,3967
-careamics-0.0.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-careamics-0.0.8.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
-careamics-0.0.8.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
-careamics-0.0.8.dist-info/RECORD,,
+careamics/utils/version.py,sha256=WKtMlrNmXymJqzMfguBX558D6tb6aoAZfbABRh_ViIs,1142
+careamics-0.0.10.dist-info/METADATA,sha256=-OAGJepthRIcvZVDlc7uhgtipB5vOFb_8p5FTA09Zos,3917
+careamics-0.0.10.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+careamics-0.0.10.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
+careamics-0.0.10.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.0.10.dist-info/RECORD,,

careamics/config/care_configuration.py

@@ -1,100 +0,0 @@
-"""CARE Pydantic configuration."""
-
-from bioimageio.spec.generic.v0_3 import CiteEntry
-
-from careamics.config.algorithms.care_algorithm_model import CAREAlgorithm
-from careamics.config.configuration import Configuration
-from careamics.config.data import DataConfig
-
-CARE = "CARE"
-
-CARE_DESCRIPTION = (
-    "Content-aware image restoration (CARE) is a deep-learning-based "
-    "algorithm that uses a U-Net architecture to restore images. CARE "
-    "is a supervised algorithm that requires pairs of noisy and "
-    "clean images to train the network. The algorithm learns to "
-    "predict the clean image from the noisy image. CARE is "
-    "particularly useful for denoising images acquired in low-light "
-    "conditions, such as fluorescence microscopy images."
-)
-CARE_REF = CiteEntry(
-    text='Weigert, Martin, et al. "Content-aware image restoration: pushing the '
-    'limits of fluorescence microscopy." Nature methods 15.12 (2018): 1090-1097.',
-    doi="10.1038/s41592-018-0216-7",
-)
-
-
-class CAREConfiguration(Configuration):
-    """CARE configuration."""
-
-    algorithm_config: CAREAlgorithm
-    """Algorithm configuration."""
-
-    data_config: DataConfig
-    """Data configuration."""
-
-    def get_algorithm_friendly_name(self) -> str:
-        """
-        Get the algorithm friendly name.
-
-        Returns
-        -------
-        str
-            Friendly name of the algorithm.
-        """
-        return CARE
-
-    def get_algorithm_keywords(self) -> list[str]:
-        """
-        Get algorithm keywords.
-
-        Returns
-        -------
-        list[str]
-            List of keywords.
-        """
-        return [
-            "restoration",
-            "UNet",
-            "3D" if "Z" in self.data_config.axes else "2D",
-            "CAREamics",
-            "pytorch",
-            CARE,
-        ]
-
-    def get_algorithm_references(self) -> str:
-        """
-        Get the algorithm references.
-
-        This is used to generate the README of the BioImage Model Zoo export.
-
-        Returns
-        -------
-        str
-            Algorithm references.
-        """
-        return CARE_REF.text + " doi: " + CARE_REF.doi
-
-    def get_algorithm_citations(self) -> list[CiteEntry]:
-        """
-        Return a list of citation entries of the current algorithm.
-
-        This is used to generate the model description for the BioImage Model Zoo.
-
-        Returns
-        -------
-        List[CiteEntry]
-            List of citation entries.
-        """
-        return [CARE_REF]
-
-    def get_algorithm_description(self) -> str:
-        """
-        Get the algorithm description.
-
-        Returns
-        -------
-        str
-            Algorithm description.
-        """
-        return CARE_DESCRIPTION

careamics/config/data/n2v_data_model.py

@@ -1,193 +0,0 @@
-"""Noise2Void specific data configuration model."""
-
-from collections.abc import Sequence
-from typing import Literal
-
-from pydantic import Field, field_validator
-
-from careamics.config.data.data_model import GeneralDataConfig
-from careamics.config.support import SupportedTransform
-from careamics.config.transformations import (
-    N2V_TRANSFORMS_UNION,
-    N2VManipulateModel,
-    XYFlipModel,
-    XYRandomRotate90Model,
-)
-
-
-class N2VDataConfig(GeneralDataConfig):
-    """N2V specific data configuration model."""
-
-    transforms: Sequence[N2V_TRANSFORMS_UNION] = Field(
-        default=[XYFlipModel(), XYRandomRotate90Model(), N2VManipulateModel()],
-        validate_default=True,
-    )
-    """N2V compatible transforms. N2VManpulate should be the last transform."""
-
-    @field_validator("transforms")
-    @classmethod
-    def validate_transforms(
-        cls, transforms: list[N2V_TRANSFORMS_UNION]
-    ) -> list[N2V_TRANSFORMS_UNION]:
-        """
-        Validate N2VManipulate transform position in the transform list.
-
-        Parameters
-        ----------
-        transforms : list of transforms compatible with N2V
-            Transforms.
-
-        Returns
-        -------
-        list of transforms
-            Validated transforms.
-
-        Raises
-        ------
-        ValueError
-            If multiple instances of N2VManipulate are found or if it is not the last
-            transform.
-        """
-        transform_list = [t.name for t in transforms]
-
-        if SupportedTransform.N2V_MANIPULATE in transform_list:
-            # multiple N2V_MANIPULATE
-            if transform_list.count(SupportedTransform.N2V_MANIPULATE.value) > 1:
-                raise ValueError(
-                    f"Multiple instances of "
-                    f"{SupportedTransform.N2V_MANIPULATE} transforms "
-                    f"are not allowed."
-                )
-
-            # N2V_MANIPULATE not the last transform
-            elif transform_list[-1] != SupportedTransform.N2V_MANIPULATE:
-                raise ValueError(
-                    f"{SupportedTransform.N2V_MANIPULATE} transform "
-                    f"should be the last transform."
-                )
-
-        else:
-            raise ValueError(
-                f"{SupportedTransform.N2V_MANIPULATE} transform "
-                f"is required for N2V training."
-            )
-
-        return transforms
-
-    def set_n2v2(self, use_n2v2: bool) -> None:
-        """
-        Set the N2V transform to the N2V2 version.
-
-        Parameters
-        ----------
-        use_n2v2 : bool
-            Whether to use N2V2.
-
-        Raises
-        ------
-        ValueError
-            If the N2V pixel manipulate transform is not found in the transforms.
-        """
-        if use_n2v2:
-            self.set_masking_strategy("median")
-        else:
-            self.set_masking_strategy("uniform")
-
-    def set_masking_strategy(self, strategy: Literal["uniform", "median"]) -> None:
-        """
-        Set masking strategy.
-
-        Parameters
-        ----------
-        strategy : "uniform" or "median"
-            Strategy to use for N2V2.
-
-        Raises
-        ------
-        ValueError
-            If the N2V pixel manipulate transform is not found in the transforms.
-        """
-        found_n2v = False
-
-        for transform in self.transforms:
-            if transform.name == SupportedTransform.N2V_MANIPULATE.value:
-                transform.strategy = strategy
-                found_n2v = True
-
-        if not found_n2v:
-            transforms = [t.name for t in self.transforms]
-            raise ValueError(
-                f"N2V_Manipulate transform not found in the transforms list "
-                f"({transforms})."
-            )
-
-    def get_masking_strategy(self) -> Literal["uniform", "median"]:
-        """
-        Get N2V2 strategy.
-
-        Returns
-        -------
-        "uniform" or "median"
-            Strategy used for N2V2.
-        """
-        for transform in self.transforms:
-            if transform.name == SupportedTransform.N2V_MANIPULATE.value:
-                return transform.strategy
-
-        raise ValueError(
-            f"{SupportedTransform.N2V_MANIPULATE} transform "
-            f"is required for N2V training."
-        )
-
-    def set_structN2V_mask(
-        self, mask_axis: Literal["horizontal", "vertical", "none"], mask_span: int
-    ) -> None:
-        """
-        Set structN2V mask parameters.
-
-        Setting `mask_axis` to `none` will disable structN2V.
-
-        Parameters
-        ----------
-        mask_axis : Literal["horizontal", "vertical", "none"]
-            Axis along which to apply the mask. `none` will disable structN2V.
-        mask_span : int
-            Total span of the mask in pixels.
-
-        Raises
-        ------
-        ValueError
-            If the N2V pixel manipulate transform is not found in the transforms.
-        """
-        found_n2v = False
-
-        for transform in self.transforms:
-            if transform.name == SupportedTransform.N2V_MANIPULATE.value:
-                transform.struct_mask_axis = mask_axis
-                transform.struct_mask_span = mask_span
-                found_n2v = True
-
-        if not found_n2v:
-            transforms = [t.name for t in self.transforms]
-            raise ValueError(
-                f"N2V pixel manipulate transform not found in the transforms "
-                f"({transforms})."
-            )
-
-    def is_using_struct_n2v(self) -> bool:
-        """
-        Check if structN2V is enabled.
-
-        Returns
-        -------
-        bool
-            Whether structN2V is enabled or not.
-        """
-        for transform in self.transforms:
-            if transform.name == SupportedTransform.N2V_MANIPULATE.value:
-                return transform.struct_mask_axis != "none"
-
-        raise ValueError(
-            f"N2V pixel manipulate transform not found in the transforms "
-            f"({self.transforms})."
-        )

careamics/config/n2n_configuration.py

@@ -1,101 +0,0 @@
-"""N2N configuration."""
-
-from bioimageio.spec.generic.v0_3 import CiteEntry
-
-from careamics.config.algorithms import N2NAlgorithm
-from careamics.config.configuration import Configuration
-from careamics.config.data import DataConfig
-
-N2N = "Noise2Noise"
-
-N2N_DESCRIPTION = (
-    "Noise2Noise is a deep-learning-based algorithm that uses a U-Net "
-    "architecture to restore images. Noise2Noise is a self-supervised "
-    "algorithm that requires only noisy images to train the network. "
-    "The algorithm learns to predict the clean image from the noisy "
-    "image. Noise2Noise is particularly useful when clean images are "
-    "not available for training."
-)
-
-N2N_REF = CiteEntry(
-    text="Lehtinen, J., Munkberg, J., Hasselgren, J., Laine, S., Karras, T., "
-    'Aittala, M. and Aila, T., 2018. "Noise2Noise: Learning image restoration '
-    'without clean data". arXiv preprint arXiv:1803.04189.',
-    doi="10.48550/arXiv.1803.04189",
-)
-
-
-class N2NConfiguration(Configuration):
-    """Noise2Noise configuration."""
-
-    algorithm_config: N2NAlgorithm
-    """Algorithm configuration."""
-
-    data_config: DataConfig
-    """Data configuration."""
-
-    def get_algorithm_friendly_name(self) -> str:
-        """
-        Get the algorithm friendly name.
-
-        Returns
-        -------
-        str
-            Friendly name of the algorithm.
-        """
-        return N2N
-
-    def get_algorithm_keywords(self) -> list[str]:
-        """
-        Get algorithm keywords.
-
-        Returns
-        -------
-        list[str]
-            List of keywords.
-        """
-        return [
-            "restoration",
-            "UNet",
-            "3D" if "Z" in self.data_config.axes else "2D",
-            "CAREamics",
-            "pytorch",
-            N2N,
-        ]
-
-    def get_algorithm_references(self) -> str:
-        """
-        Get the algorithm references.
-
-        This is used to generate the README of the BioImage Model Zoo export.
-
-        Returns
-        -------
-        str
-            Algorithm references.
-        """
-        return N2N_REF.text + " doi: " + N2N_REF.doi
-
-    def get_algorithm_citations(self) -> list[CiteEntry]:
-        """
-        Return a list of citation entries of the current algorithm.
-
-        This is used to generate the model description for the BioImage Model Zoo.
-
-        Returns
-        -------
-        List[CiteEntry]
-            List of citation entries.
-        """
-        return [N2N_REF]
-
-    def get_algorithm_description(self) -> str:
-        """
-        Get the algorithm description.
-
-        Returns
-        -------
-        str
-            Algorithm description.
-        """
-        return N2N_DESCRIPTION