careamics 0.0.11__py3-none-any.whl → 0.0.13__py3-none-any.whl

{careamics-0.0.11.dist-info → careamics-0.0.13.dist-info}/RECORD

@@ -1,43 +1,52 @@
 careamics/__init__.py,sha256=eHsl7oE8HTKmi7yLMj8Yyp0RbdtN3QDmQQb-4Sn9d8M,475
-careamics/careamist.py,sha256=OhBkchHIVIvLyk57R5UXt2Euy4e_EDSbNp5NXJ53hS8,37588
+careamics/careamist.py,sha256=GhT6Ue3HZGnc0-TIJkR8izgTc3ip3DPO-f0GPJtAthk,38326
 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/cli/utils.py,sha256=ESeKm86je_6dzJNNEMI6LHYkHEMff0OMvzP5bnxotYk,661
 careamics/config/__init__.py,sha256=K0N1GIqFCYhpPjalZG-Ygap6Ew_dDAC0uw5Npzhg9Lk,1524
-careamics/config/callback_model.py,sha256=EeYHqpMIPQwyNxLRzzX32Uncl5mZuB1bJO76RHpNymg,4555
-careamics/config/configuration.py,sha256=D7i_g48P7d4H4_YSFyvDh9tRM7vLhM1mnU_XMeCC1HU,11193
-careamics/config/configuration_factories.py,sha256=NhheOPkVhIF1cwz0FGNLQrxOByRQGrw-aZ_vGNIE8UE,34599
+careamics/config/callback_model.py,sha256=YRXE-qgnTrI-KInYQK4UwxC55ttY6eg_eb1wvrGhCDU,4096
+careamics/config/configuration.py,sha256=gNBKxeHqAQLa8_btGuQ4-X4987cRPr5L6RI6hOv179Q,13345
+careamics/config/configuration_factories.py,sha256=lg3tG4LYzMsanoiD_c2jX2hY50fXIk1d6ALsRTny1uM,46113
 careamics/config/configuration_io.py,sha256=P-bP1kzkXxJWOEFP02dEZFNmpuLAPJfJtYhX4bFeaKk,2324
-careamics/config/inference_model.py,sha256=UE_-ZmCX6LFCbDBOwyGnvuAboF_JNX2m2LcF0WiwgCI,6961
+careamics/config/inference_model.py,sha256=NEgRN-VZulMKNwY42fecnK0shLh75xVnrY-odMJpwHA,7034
 careamics/config/likelihood_model.py,sha256=VorUtc0_-xIWNxwVrd1kBba-003ICdVMtxpcDCxH4Io,2259
 careamics/config/loss_model.py,sha256=yYcUBS90Qyon1MxeaHiVP3dJHPJFC0GUvWKGcAb3IHk,2036
 careamics/config/nm_model.py,sha256=5dAhDBLa4WPfKaNEK6ATNsSUwtlH8u8gYweEA4gZP6g,4758
-careamics/config/optimizer_models.py,sha256=OWpTydRBBR8wt_af1mZHNNwvL_RtnRFopAOdgjzLo30,5750
+careamics/config/optimizer_models.py,sha256=9qxcLjtDp5LjYX52u21Rom4F3_GZUV2GJimrK3un574,5717
 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/training_model.py,sha256=VfK2bk_1FHaamKZw5S8UDPVxasyUqz1rY1ahcaxYZ7s,3114
 careamics/config/algorithms/__init__.py,sha256=on5D6zBO9Lu-Tf5To8xpF6owIFqdN7RSmZdpyXDOaNw,404
 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/n2v_algorithm_model.py,sha256=IkHsTj-IkWq--mlWjBHfH18CGK_3p2uaC3Zz2tfieaA,9469
 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=ijNcvrKQtKljmBuZ6DDxh86PMzpRob2l2JMqbPQLqPk,111
-careamics/config/data/data_model.py,sha256=0YFN_NXL10f8h_Wr7ce6xsfOy86iZOPIkgLK-KIpeEU,12181
+careamics/config/architectures/unet_model.py,sha256=Aqc_KPf2VKMhNrYwOdmr_ez3iIQz8ZRtsA6t5FFT354,3686
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+careamics/config/data/ng_data_model.py,sha256=DKmNY84KQLwFsLem3RZJBJYq54FdSfQYlI3NnXhIsTQ,12317
+careamics/config/data/patching_strategies/__init__.py,sha256=6ZUors-WzBBQCwMyaSojYJzdXeleFRBlrFls1r-Otdo,394
+careamics/config/data/patching_strategies/_overlapping_patched_model.py,sha256=Qyz4qlFzhZ6e-1aPlV89heKINIaoHfVIBO3dCTyBbOE,3073
+careamics/config/data/patching_strategies/_patched_model.py,sha256=wmhM1Qt5qDuMCs76ab7dPoNTjy_lLVIL8TD5AzaIoak,1429
+careamics/config/data/patching_strategies/random_patching_model.py,sha256=HZfPLkkhwYNQ11O-ahmoaE1bTw7rXg2mIIqsBNkY4WE,533
+careamics/config/data/patching_strategies/sequential_patching_model.py,sha256=sS1h-sHUGvlh41b4kc_3B858ZCPDMJlPb6roAhDL63Y,865
+careamics/config/data/patching_strategies/tiled_patching_model.py,sha256=5lltbA9dqZlo8-yxJWlAAWqZbPRg5gw0PS6752Nr1ec,1295
+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_architectures.py,sha256=pOxvHOAIUkc7HCO0IIg4K22h-Ti5ErtcIkGOjN-zh1s,340
-careamics/config/support/supported_data.py,sha256=T_mDiWLFMVji_EpjBABUObAJcnv-XBnqp9XUZP37Tdk,2902
+careamics/config/support/supported_data.py,sha256=rVcBOBUosyvYWZJAofJ66_DucnkkPfPhZMXU6KXugsM,3079
 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_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
 careamics/config/support/supported_struct_axis.py,sha256=alZMA5Y-BpDymLPUEd1zqVY0xMkgl9Rv1d4ujED6sco,424
 careamics/config/support/supported_transforms.py,sha256=ylTiS8fUFKFwfn85gh7kKF4Trb9Q4ENPKm-XDWCe-SY,311
@@ -50,59 +59,68 @@ careamics/config/transformations/xy_flip_model.py,sha256=zU-uZ1b1zNZWckbho3onN-B
 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
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+careamics/config/validators/validator_utils.py,sha256=7wBQzf4YcxiL0h9yOEaFM4RoeOtLPEBp4W7ZVabfqBA,2609
 careamics/dataset/__init__.py,sha256=31vop67zbtGesENEIig-LLw1q2lCydMFc_YWgfK2Yt4,547
-careamics/dataset/in_memory_dataset.py,sha256=Snbq7N8lYB06m018Yz0Mgx1PE3hHLh6__DeaArKPBvs,9665
+careamics/dataset/in_memory_dataset.py,sha256=INiamRPZGKf0yWIyLds1ZQlBiK4A86XVijOJ65BSH1A,9692
 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
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 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
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 careamics/dataset/dataset_utils/running_stats.py,sha256=clnSs4TR-lUiQNIYs1ay1_n3wUoeRQqY83V2K70ZBtM,5897
 careamics/dataset/patching/__init__.py,sha256=7-s12oUAZNlMOwSkxSwbD7vojQINWYFzn_4qIJ87WBg,37
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 careamics/dataset/patching/random_patching.py,sha256=gm1jxye9yvHbdijLzCtDSzRU_9j110GRLMnJaUwLAHQ,6487
 careamics/dataset/patching/sequential_patching.py,sha256=4F5E1Ta0M5kFXGwI2-QXRxeOx0CyUwbFaB5awkMCN_Q,5890
 careamics/dataset/patching/validate_patch_dimension.py,sha256=mC2bZWBpU44NEvXxEfR7ULUKwWPuZPjmBWpHYJxNDWc,2121
 careamics/dataset/tiling/__init__.py,sha256=aW_AMB9rzm0VmooUpjcyqv6sQP69RlPQMEdP2sVjdz8,190
 careamics/dataset/tiling/collate_tiles.py,sha256=XK0BsDQE7XwIwmOoCHJIpVC3kqjSN6nDhrJ4POVeHS8,965
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 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
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+careamics/dataset_ng/patching_strategies/sequential_patching.py,sha256=T65DszwUmCvLBZXbMmTYYWFn702tuECkPKJ_x8ps00A,2491
+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/get_func.py,sha256=O_pdymjh2mc-JZ1je3ZnPAcsHc7Je3a005AMgAa0xuw,1388
+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=_gMGKGSHOEoh00jblCX5egMI91Z0UJpIjEQ74AaVGss,24177
-careamics/lightning/predict_data_module.py,sha256=JNwujK6QwObSx6P25ghpGl2f2gGT3KVgYMTlonZzH20,12745
-careamics/lightning/train_data_module.py,sha256=HyXeDZ_u3JLzyh1tqRBIH93spMj0iQhAP4nmHPEI4aM,26554
+careamics/lightning/lightning_module.py,sha256=C7BylX4uMok7q_ioAsptrWpFt-INIxaLjLFOjz0usSw,24384
+careamics/lightning/predict_data_module.py,sha256=Ve_ADYLo67yoFlY-04xofkt8KvbJXKIkviF_9bZ3fVc,12772
+careamics/lightning/train_data_module.py,sha256=A4nVrL5tXQTCeeXlGD_oGlAMPEWryykVKElnSmDhmjQ,26581
 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
@@ -111,8 +129,14 @@ careamics/lightning/callbacks/prediction_writer_callback/file_path_utils.py,sha2
 careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py,sha256=8HHUSKcG7G0FSCVPnpGQHLfpara5mnKAwsiiyWp2wzo,8210
 careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py,sha256=lxsLjLskRpYnzdyWCdOICUJxF9YzuUi1RH0LJnOCVgo,12594
 careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py,sha256=F1IpbNNgkv5eK8Xpqp7wqv2lsqEdP1wMRlBL7RBn93U,7114
+careamics/lightning/dataset_ng/__init__.py,sha256=5913hBQ5FRn4K-zzPtrqh-2zN4iie9bD-KXm0-_FNXY,49
+careamics/lightning/dataset_ng/data_module.py,sha256=acRjHcJSUEb9Unmc6n_BvyBOwMEnCaHr8wl0UH52wQU,26365
+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=oPacrkwiabsmiW_r--IxX-XPRbzezZUvOuWKbUw5LiI,1518
+careamics/losses/loss_factory.py,sha256=IVcvSWLnbMuoLG_4SmZ4s_hfinB-olu44PL9lhDEGEM,1545
 careamics/losses/fcn/__init__.py,sha256=kf92MKFGHr6upiztZVgWwtGPf734DZyub92Rn8uEq8o,18
 careamics/losses/fcn/losses.py,sha256=KuoXqL24QbTxDdRmQJbERC95x0f3u4T0S77dqBZRarQ,2513
 careamics/losses/lvae/__init__.py,sha256=0FNtMLHrOMfagtWkaBdz1NTjyf2y0QLgysxJv5jq5uw,19
@@ -120,33 +144,35 @@ careamics/losses/lvae/loss_utils.py,sha256=QxzA2N1TglR4H0X0uyTWWytDagE1lA9IB_TK1
 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=FxZmmT6vMRluLYnnCEQtLcz5Q45OAqmxXbQo6KPbQEk,30372
+careamics/lvae_training/eval_utils.py,sha256=PWKlG2XrvdfZTG0_brcADaAA0owTeNRT1g673gYtk5k,34410
 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=dvdHHaRA9ZfOt_uOnXkYyra2_b0Wsxs8qmrze6zxJAE,377
-careamics/lvae_training/dataset/config.py,sha256=hGIggj5uOZrFBK54o9vii0sG5WGhF_E32URKIIzQMec,4342
+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/multich_dataset.py,sha256=5yMC6bgEIYHBsjFj5gXlc68xJQz8A05TYbYfOo-TdUQ,41672
+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/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/types.py,sha256=SQ99hV9R3iwrRLJs-aRkL3OlmrWWkCrca2JqkntoWZs,633
+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
 careamics/lvae_training/dataset/utils/empty_patch_fetcher.py,sha256=OFjeqhZ6vFULJsF5tnoByhEhE8aLHujFToU_yyqMCP4,2266
-careamics/lvae_training/dataset/utils/index_manager.py,sha256=Gt1I-7lBaQDBgqguOmofAFDdAsJQfz7ktvq4_I80F9c,10084
+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=XQvRUxM4keEiYlnWNTZUxeLgLl3_c-_drOZcH4mjEDo,7801
-careamics/model_io/model_io_utils.py,sha256=ZSBO1MEFBh--GwUqmK1iW7Vf57MgdQtxmucNBdXkHBw,2748
+careamics/model_io/bmz_io.py,sha256=fWuBXKbz2gNQZmZIV7m7M_qF80rQMCR7E448ALIuosU,7802
+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
-careamics/model_io/bioimage/bioimage_utils.py,sha256=aX0rZny3OPaZZGGE-5Y3qXgnOAhyAQOtN15Ri0EVMTk,1297
+careamics/model_io/bioimage/bioimage_utils.py,sha256=VaDF0XCCcvhvqqNXLIWQI-uny45uPstKyw8e0KdjY1A,1297
 careamics/model_io/bioimage/cover_factory.py,sha256=8URrpEfJvdHBJeSrh5H2IQHSUybsTyAOR3_A-YYAAlw,4583
-careamics/model_io/bioimage/model_description.py,sha256=caC9O0xyXEIMyCHW5j37HMX4IhMtNk0QWCF05VdPCQE,10050
+careamics/model_io/bioimage/model_description.py,sha256=4cgbSBnRUwOJDnhk7sds_gooB_HlbHWGSZdhR7vP8NQ,10064
 careamics/models/__init__.py,sha256=Xui2BLJd1I2r_E3Sj24fJALFTi2FGtfNscUWj_0c9Hk,93
-careamics/models/activation.py,sha256=nu3sDgd7Lsyw8rvmUwxNN-7SM09cEMfxZ9DRDzdSKns,1049
+careamics/models/activation.py,sha256=vvoOOuJk_3x8_LsAXl2Utz0r8uRMozFIwgw5GRi0wso,1076
 careamics/models/layers.py,sha256=tpsxbolRWYycZGxS3hKlDRtMf6HpNdZs98uwx5K8lls,13757
 careamics/models/model_factory.py,sha256=GWbouERvEfHj_BrpKHYgrPAj8dpdoh1R-X--Jt09N1Q,1370
 careamics/models/unet.py,sha256=9m8GxsTXX9c0mC-eVe2ZXQn2afose1CG6Z8vIhELb7I,14308
@@ -160,15 +186,15 @@ careamics/models/lvae/utils.py,sha256=EE3paHu3vhCaqfOrGypzUsImZJO94uBhx8q6kZ-R36
 careamics/prediction_utils/__init__.py,sha256=k5hsPGY8FOkwIT0fQgrUz7fVCH2NlwuOdZiISdXjEWg,270
 careamics/prediction_utils/lvae_prediction.py,sha256=ZwPFCSeUGsULIMoMQWRYKHfLFaDm7UKyGaUMVfSUqfs,6210
 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/prediction_utils/prediction_outputs.py,sha256=-rjI6pWEy_29nljG9sLGdI-7VaBH4ZBvJQOxB5UAOi4,4070
+careamics/prediction_utils/stitch_prediction.py,sha256=zWpfUPdJWKoJwHDcOjVyDek2YXmfQb3gHDWrkAb5E_I,3907
 careamics/transforms/__init__.py,sha256=n7D3SbcVSRaMOl5F5Rozo2_lY8dn0DH28ywYIdbXxBo,561
-careamics/transforms/compose.py,sha256=QMCuqp0C5mJ5N6xh3ISKY7HfjfKp6NqDwQiKXoxEjug,5326
+careamics/transforms/compose.py,sha256=ETnI_Z4ZfBWNA12D-KEtr_P8wKeyBQVHvostGG2f_SI,5395
 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/n2v_manipulate_torch.py,sha256=eOSM5Xp7Hm6xrzjlInOMGzdmWhAxRURD1ePTQdIdu7c,5133
+careamics/transforms/normalize.py,sha256=sVa6uiI2vB1CZJBdgJ6KOlujRmsOQ72YXnhPuQ1QGuE,8314
 careamics/transforms/pixel_manipulation.py,sha256=WSx2sqcZ2wUkm6qPi4pG3Ai0sE8ONPOpYLSvkW5M3bY,13393
-careamics/transforms/pixel_manipulation_torch.py,sha256=W2sTQrM00TwmcoFf1bcYapAwE66pKIVVeAtBIW6ovK4,14343
+careamics/transforms/pixel_manipulation_torch.py,sha256=4QhG9ZsITVRKdA_Po6ikw6YGWltNIwP2dAOZClbHRX4,13936
 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
@@ -178,18 +204,18 @@ careamics/utils/__init__.py,sha256=mLwBQ7wTL2EwDwL3NcX53EHPNklojU45Jcc728y4EWQ,4
 careamics/utils/autocorrelation.py,sha256=M_WYzrEOQngc5iSXWar4S3-EOnK6DfYHPC2vVMeu_Bs,945
 careamics/utils/base_enum.py,sha256=bz1D8mDx5V5hdnJ3WAzJXWHJTbgwAky5FprUt9F5cMA,1387
 careamics/utils/context.py,sha256=SoTZfzG6fO4SDOGHOTL2Xlm1n1CSgb9B57GVhrEkFls,1436
-careamics/utils/lightning_utils.py,sha256=DMMmqx-AlNtddBCqm8b_W3h09qUetz32OMPhdDieFwg,1769
+careamics/utils/lightning_utils.py,sha256=vAdcRMu0JzXwhdsf8l4eG4daNi1ZtG8D1-u764x2_ho,2067
 careamics/utils/logging.py,sha256=5U4VsQ4m4OajtirLH6qUjrM1CAc-oXeCsd6JyROjkWE,10337
-careamics/utils/metrics.py,sha256=i9TQNzVF6lUL9c6OwRZFFDhelZfinkEDpWSCKeduscc,10853
+careamics/utils/metrics.py,sha256=dO_46tWuu__F2whndeTFr1zmMYwGY63SOLNVxVu0nos,10880
 careamics/utils/path_utils.py,sha256=8AugiG5DOmzgSnTCJI8vypXaPE0XhnR-9pzeiFUZ-0I,554
 careamics/utils/plotting.py,sha256=cea1GQB932j2UA3IQZnh-0EenQdnjzPOFoGoFKJ4how,2518
 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/utils/torch_utils.py,sha256=IUTxKIqYpUTvN-UDZDGBheF7zgtskH_yDcVvYx0p8zI,3478
 careamics/utils/version.py,sha256=WKtMlrNmXymJqzMfguBX558D6tb6aoAZfbABRh_ViIs,1142
-careamics-0.0.11.dist-info/METADATA,sha256=AKeMVWNP52xha3axDHE2j_y5wn5OroRFbxvQB1GVUVY,3917
-careamics-0.0.11.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-careamics-0.0.11.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
-careamics-0.0.11.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
-careamics-0.0.11.dist-info/RECORD,,
+careamics-0.0.13.dist-info/METADATA,sha256=ryCa_q8gC_8BRa4U8KjKZFItYjzL3MQhOnZXiwgzzgI,3940
+careamics-0.0.13.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+careamics-0.0.13.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
+careamics-0.0.13.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.0.13.dist-info/RECORD,,

careamics/dataset_ng/dataset/__init__.py

@@ -1,3 +0,0 @@
-__all__ = ["CareamicsDataset"]
-
-from .dataset import CareamicsDataset

careamics/dataset_ng/dataset/dataset.py

@@ -1,184 +0,0 @@
-from collections.abc import Sequence
-from enum import Enum
-from pathlib import Path
-from typing import Literal, NamedTuple, Optional, Union
-
-import numpy as np
-from numpy.typing import NDArray
-from torch.utils.data import Dataset
-from typing_extensions import ParamSpec
-
-from careamics.config import DataConfig, InferenceConfig
-from careamics.config.support import SupportedData
-from careamics.dataset.patching.patching import Stats
-from careamics.dataset_ng.patch_extractor import (
-    ImageStackLoader,
-    PatchExtractor,
-    create_patch_extractor,
-)
-from careamics.dataset_ng.patching_strategies import (
-    FixedRandomPatchingStrategy,
-    PatchingStrategy,
-    PatchSpecs,
-    RandomPatchingStrategy,
-)
-from careamics.transforms import Compose
-
-P = ParamSpec("P")
-
-
-class Mode(str, Enum):
-    TRAINING = "training"
-    VALIDATING = "validating"
-    PREDICTING = "predicting"
-
-
-class ImageRegionData(NamedTuple):
-    data: NDArray
-    source: Union[Path, Literal["array"]]
-    data_shape: Sequence[int]
-    dtype: str  # dtype should be str for collate
-    axes: str
-    region_spec: PatchSpecs
-
-
-InputType = Union[Sequence[np.ndarray], Sequence[Path]]
-
-
-class CareamicsDataset(Dataset):
-    def __init__(
-        self,
-        data_config: Union[DataConfig, InferenceConfig],
-        mode: Mode,
-        inputs: InputType,
-        targets: Optional[InputType] = None,
-        image_stack_loader: Optional[ImageStackLoader[P]] = None,
-        *args: P.args,
-        **kwargs: P.kwargs,
-    ):
-        self.config = data_config
-        self.mode = mode
-
-        data_type_enum = SupportedData(self.config.data_type)
-        self.input_extractor = create_patch_extractor(
-            inputs,
-            self.config.axes,
-            data_type_enum,
-            image_stack_loader,
-            *args,
-            **kwargs,
-        )
-        if targets is not None:
-            self.target_extractor: Optional[PatchExtractor] = create_patch_extractor(
-                targets,
-                self.config.axes,
-                data_type_enum,
-                image_stack_loader,
-                *args,
-                **kwargs,
-            )
-        else:
-            self.target_extractor = None
-
-        self.patching_strategy = self._initialize_patching_strategy()
-
-        self.input_stats, self.target_stats = self._initialize_statistics()
-
-        self.transforms = self._initialize_transforms()
-
-    def _initialize_patching_strategy(self) -> PatchingStrategy:
-        patching_strategy: PatchingStrategy
-        if self.mode == Mode.TRAINING:
-            if isinstance(self.config, InferenceConfig):
-                raise ValueError("Inference config cannot be used for training.")
-            patching_strategy = RandomPatchingStrategy(
-                data_shapes=self.input_extractor.shape,
-                patch_size=self.config.patch_size,
-                # TODO: Add random seed to dataconfig
-                seed=getattr(self.config, "random_seed", None),
-            )
-        elif self.mode == Mode.VALIDATING:
-            if isinstance(self.config, InferenceConfig):
-                raise ValueError("Inference config cannot be used for validating.")
-            patching_strategy = FixedRandomPatchingStrategy(
-                data_shapes=self.input_extractor.shape,
-                patch_size=self.config.patch_size,
-                # TODO: Add random seed to dataconfig
-                seed=getattr(self.config, "random_seed", None),
-            )
-        elif self.mode == Mode.PREDICTING:
-            # TODO: patching strategy will be tilingStrategy in upcoming PR
-            raise NotImplementedError(
-                "Prediction mode for the CAREamicsDataset has not been implemented yet."
-            )
-        else:
-            raise ValueError(f"Unrecognised dataset mode {self.mode}.")
-
-        return patching_strategy
-
-    def _initialize_transforms(self) -> Optional[Compose]:
-        if isinstance(self.config, DataConfig):
-            return Compose(
-                transform_list=list(self.config.transforms),
-            )
-        # TODO: add TTA
-        return None
-
-    def _initialize_statistics(self) -> tuple[Stats, Optional[Stats]]:
-        # TODO: add running stats
-        # Currently assume that stats are provided in the configuration
-        input_stats = Stats(self.config.image_means, self.config.image_stds)
-        target_stats = None
-        if isinstance(self.config, DataConfig):
-            target_means = self.config.target_means
-            target_stds = self.config.target_stds
-            if target_means is not None and target_stds is not None:
-                target_stats = Stats(target_means, target_stds)
-        return input_stats, target_stats
-
-    def __len__(self):
-        return self.patching_strategy.n_patches
-
-    def _create_image_region(
-        self, patch: np.ndarray, patch_spec: PatchSpecs, extractor: PatchExtractor
-    ) -> ImageRegionData:
-        data_idx = patch_spec["data_idx"]
-        return ImageRegionData(
-            data=patch,
-            source=extractor.image_stacks[data_idx].source,
-            dtype=str(extractor.image_stacks[data_idx].data_dtype),
-            data_shape=extractor.image_stacks[data_idx].data_shape,
-            # TODO: should it be axes of the original image instead?
-            axes=self.config.axes,
-            region_spec=patch_spec,
-        )
-
-    def __getitem__(
-        self, index: int
-    ) -> tuple[ImageRegionData, Optional[ImageRegionData]]:
-        patch_spec = self.patching_strategy.get_patch_spec(index)
-        input_patch = self.input_extractor.extract_patch(**patch_spec)
-
-        target_patch = (
-            self.target_extractor.extract_patch(**patch_spec)
-            if self.target_extractor is not None
-            else None
-        )
-
-        if self.transforms is not None:
-            input_patch, target_patch = self.transforms(input_patch, target_patch)
-
-        input_data = self._create_image_region(
-            patch=input_patch, patch_spec=patch_spec, extractor=self.input_extractor
-        )
-
-        if target_patch is not None and self.target_extractor is not None:
-            target_data = self._create_image_region(
-                patch=target_patch,
-                patch_spec=patch_spec,
-                extractor=self.target_extractor,
-            )
-        else:
-            target_data = None
-
-        return input_data, target_data

careamics/dataset_ng/demo_patch_extractor_factory.py

@@ -1,37 +0,0 @@
-# %%
-import numpy as np
-
-from careamics.config import create_n2n_configuration
-from careamics.config.support import SupportedData
-from careamics.dataset_ng.patch_extractor.patch_extractor_factory import (
-    create_patch_extractors,
-)
-
-rng = np.random.default_rng()
-
-# %%
-# define example data
-array1 = np.arange(36).reshape(1, 6, 6)
-array2 = np.arange(50).reshape(2, 5, 5)
-target1 = rng.integers(0, 1, size=array1.shape, endpoint=True)
-target2 = rng.integers(0, 1, size=array2.shape, endpoint=True)
-
-# %%
-config = create_n2n_configuration(
-    "test_exp",
-    data_type="array",
-    axes="SYX",
-    patch_size=[8, 8],
-    batch_size=1,
-    num_epochs=1,
-)
-data_config = config.data_config
-
-# %%
-data_type = SupportedData(data_config.data_type)
-train_inputs, train_targets = create_patch_extractors(
-    [array1, array2], [target1, target2], axes=data_config.axes, data_type=data_type
-)
-
-# %%
-train_inputs.extract_patch(data_idx=0, sample_idx=0, coords=(2, 2), patch_size=(3, 3))