careamics 0.0.14__py3-none-any.whl → 0.0.16__py3-none-any.whl

{careamics-0.0.14.dist-info → careamics-0.0.16.dist-info}/RECORD

@@ -1,38 +1,40 @@
 careamics/__init__.py,sha256=eHsl7oE8HTKmi7yLMj8Yyp0RbdtN3QDmQQb-4Sn9d8M,475
-careamics/careamist.py,sha256=GhT6Ue3HZGnc0-TIJkR8izgTc3ip3DPO-f0GPJtAthk,38326
+careamics/careamist.py,sha256=-CSwSAW9Nupd31zXUxaecC99mKGlMSwuLFJZUlNsib8,37780
 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=ESeKm86je_6dzJNNEMI6LHYkHEMff0OMvzP5bnxotYk,661
-careamics/config/__init__.py,sha256=K0N1GIqFCYhpPjalZG-Ygap6Ew_dDAC0uw5Npzhg9Lk,1524
-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/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=QRI7byEt82B36foRhHXybWdG7xKAgrUJalIcP4hg_MQ,1752
+careamics/config/callback_model.py,sha256=VT0NyM8R1Mhtsm8SnZqk-0CK1WVaZXbCFJZCRq5DoXI,4108
+careamics/config/configuration.py,sha256=EmamCrBF_4CyA-gJ0VbPVcAvEFArNQkJ_VW5kzUkFt4,13452
+careamics/config/configuration_factories.py,sha256=FFjsht4ZUqrN98CHM_v3zejzUK8IsNZBQlHbHIGysD4,77230
 careamics/config/configuration_io.py,sha256=P-bP1kzkXxJWOEFP02dEZFNmpuLAPJfJtYhX4bFeaKk,2324
-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=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=VfK2bk_1FHaamKZw5S8UDPVxasyUqz1rY1ahcaxYZ7s,3114
-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=1ZrShUGHA7zbjSiCQwhUSv7l7Hr7MbpcLOw8ucM27p8,4680
+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=d_7_bDdLCzl0HgykpObbBYM1-NLBycJ5iOXN1JYS2SI,13444
-careamics/config/data/ng_data_model.py,sha256=DKmNY84KQLwFsLem3RZJBJYq54FdSfQYlI3NnXhIsTQ,12317
+careamics/config/data/data_model.py,sha256=FOZcO6pemGCus8h27iDDGJ0j1ZiCOewKBDg1mTZLjCA,13345
+careamics/config/data/ng_data_model.py,sha256=2d47_FbNCVYC5VLaq_XqpfS3JqookLUOc1F6rTOkm04,12215
 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/_overlapping_patched_model.py,sha256=ysGd8QNNdNzLD6NITmvyjVETG6ohhEFLgWPCS_CYSxE,3030
 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
@@ -40,11 +42,11 @@ 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_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
@@ -52,39 +54,38 @@ 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=1Rkk6IkF-7ytGU6HSzP-TpOi4RRWiQJ6fOd8zammXcg,1936
+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=zU-uZ1b1zNZWckbho3onN-B7BHKhN7jbgbNZyRQhv2s,1025
-careamics/config/transformations/xy_random_rotate90_model.py,sha256=6sYKmtCLvz0SV1qZgBSHUTH-CUjwvHnohq1HyPntbyE,894
+careamics/config/transformations/xy_flip_model.py,sha256=2k4tiUZK3GVn9hEjFlWi0ypz-k5C2XKKO6elU7HlKmI,1012
+careamics/config/transformations/xy_random_rotate90_model.py,sha256=Z0vhD9Hal_rpwWHlOA53ADDcUrrApESzZBa50HD7gRc,881
 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=7wBQzf4YcxiL0h9yOEaFM4RoeOtLPEBp4W7ZVabfqBA,2609
+careamics/config/validators/validator_utils.py,sha256=NUmH_NheVwbx3rQi_pKTjMqX-_k89UIAlKBc7RlQLls,2578
 careamics/dataset/__init__.py,sha256=31vop67zbtGesENEIig-LLw1q2lCydMFc_YWgfK2Yt4,547
-careamics/dataset/in_memory_dataset.py,sha256=INiamRPZGKf0yWIyLds1ZQlBiK4A86XVijOJ65BSH1A,9692
+careamics/dataset/in_memory_dataset.py,sha256=Grt9w4QuhJrTbcHmEJeifmTm06-U09M-6FGyaFw_UXU,9679
 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=ZBiQh96TgThcOB0flRGZmh0arFn30fX3shAafvetq3s,9783
+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
-careamics/dataset/dataset_utils/iterate_over_files.py,sha256=xQJZQhusFiI3oPJmSsL8fFBVVRA3WS8R1TcAXW-xfdE,2898
+careamics/dataset/dataset_utils/iterate_over_files.py,sha256=mVY1PAnLQn-xr8PDfXspiPrsv0k6o8ypor6_1MB59_k,2882
 careamics/dataset/dataset_utils/running_stats.py,sha256=clnSs4TR-lUiQNIYs1ay1_n3wUoeRQqY83V2K70ZBtM,5897
 careamics/dataset/patching/__init__.py,sha256=7-s12oUAZNlMOwSkxSwbD7vojQINWYFzn_4qIJ87WBg,37
 careamics/dataset/patching/patching.py,sha256=InV9Nt9JeRp9xo5W42nPwP_zif_AjC0O5-w2nyH9Qyw,8899
-careamics/dataset/patching/random_patching.py,sha256=gm1jxye9yvHbdijLzCtDSzRU_9j110GRLMnJaUwLAHQ,6487
-careamics/dataset/patching/sequential_patching.py,sha256=4F5E1Ta0M5kFXGwI2-QXRxeOx0CyUwbFaB5awkMCN_Q,5890
+careamics/dataset/patching/random_patching.py,sha256=8ZrC5CygBLnA4e1yXJg4XT3RnsIeN9PMzuTRkO_wPo8,6462
+careamics/dataset/patching/sequential_patching.py,sha256=Dg5C57hO7BqnKP2sJh2xylupzmuV2lvTs4vYe5KTH-Q,5871
 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
-careamics/dataset/tiling/lvae_tiled_patching.py,sha256=rGcUOOL0nC5zv22RLn_WiLV9cxrqCwZc-btJ6zrtAy8,13223
+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=ZrFnB4Xj3mWDYQyP2yMoazRnKs8wrkJYL28pHsOC8Yc,8826
-careamics/dataset_ng/factory.py,sha256=lPh61FIkvXdqW5nH68d5Jvn4vg8wxB7bNmTCvea1_2Q,14787
+careamics/dataset_ng/dataset.py,sha256=2R7jMUJFBECI-MBROg4QhGM3vJ8EEIpwOMDoBYEQhN8,8810
+careamics/dataset_ng/factory.py,sha256=bjzolF1k9iTj6cY75licyGYielZZvpp3xJwLbw8t5uU,14723
 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
@@ -94,54 +95,55 @@ 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/patching_strategies/__init__.py,sha256=2KwdY_TeD9WQju150WbV2IF19TincHU3lbcL0fqZF5o,549
 careamics/dataset_ng/patching_strategies/patching_strategy_protocol.py,sha256=ukw5G9hIOPEJz-DEFDMuJsGYou7wUeRjALNU8qdgn9g,3475
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 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
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 careamics/file_io/read/get_func.py,sha256=1UJMfVb6gUCe_5WBRxCEO2Q7pqdVu8u2Sm0aHxXdiak,1415
 careamics/file_io/read/tiff.py,sha256=UMofW33rvByK9B1zYGhSrWAiAA3uQUV3OVK7cq9d0gQ,1359
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 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
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+careamics/lightning/lightning_module.py,sha256=isLtzxx60JvaNql6CGuKscaU1MwG-sTRbVl65ik5SpQ,28623
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 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
 careamics/lightning/callbacks/prediction_writer_callback/file_path_utils.py,sha256=i4vGGiVLslafi-5iuvkAKzBgZ0BpwTTxSTo31oViFz4,1480
-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
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+careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py,sha256=aWj6TbNmRNSxAL32GjrVQ1TNtK0Jr7t2od33nSgGjW4,8188
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 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/data_module.py,sha256=PyU7igSn22vnrPJLyVn2UYo9szS3NXayRZY5wqo8iu8,26229
 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
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 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=wHT1dx04BZ_OI-_S7cFQ5hFmMetm6FSnuZfwZBBtIpY,17977
+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
@@ -150,13 +152,13 @@ careamics/lvae_training/lightning_module.py,sha256=ryr7iHqCMzCl5esi6_gEcnKFDQkMr
 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
@@ -164,58 +166,58 @@ 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=fWuBXKbz2gNQZmZIV7m7M_qF80rQMCR7E448ALIuosU,7802
+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
 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=4cgbSBnRUwOJDnhk7sds_gooB_HlbHWGSZdhR7vP8NQ,10064
+careamics/model_io/bioimage/model_description.py,sha256=gqSZUFlsbaK5RBMyQMfUfYz5AD3LvE9l4bd0sisC_L4,10082
 careamics/models/__init__.py,sha256=Xui2BLJd1I2r_E3Sj24fJALFTi2FGtfNscUWj_0c9Hk,93
 careamics/models/activation.py,sha256=vvoOOuJk_3x8_LsAXl2Utz0r8uRMozFIwgw5GRi0wso,1076
-careamics/models/layers.py,sha256=tpsxbolRWYycZGxS3hKlDRtMf6HpNdZs98uwx5K8lls,13757
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 careamics/models/model_factory.py,sha256=GWbouERvEfHj_BrpKHYgrPAj8dpdoh1R-X--Jt09N1Q,1370
 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
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 careamics/models/lvae/stochastic.py,sha256=wiTrLBSYwOvsF1araKxUHy1CHp1mdH9bazctVo0NchA,16628
 careamics/models/lvae/utils.py,sha256=EE3paHu3vhCaqfOrGypzUsImZJO94uBhx8q6kZ-R36o,11516
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 careamics/prediction_utils/lvae_tiling_manager.py,sha256=SI-JaJvLrKWBSHdm-FjcqWdbhlcflTRiKxYF7CSGzvA,13736
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 careamics/transforms/__init__.py,sha256=n7D3SbcVSRaMOl5F5Rozo2_lY8dn0DH28ywYIdbXxBo,561
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 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
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 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
 careamics/utils/context.py,sha256=SoTZfzG6fO4SDOGHOTL2Xlm1n1CSgb9B57GVhrEkFls,1436
 careamics/utils/lightning_utils.py,sha256=vAdcRMu0JzXwhdsf8l4eG4daNi1ZtG8D1-u764x2_ho,2067
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+careamics/utils/metrics.py,sha256=Mzqh9m7gkzirevgDEt3UosLjtyzEl3GoFUU_HWMYL-Y,10867
 careamics/utils/path_utils.py,sha256=8AugiG5DOmzgSnTCJI8vypXaPE0XhnR-9pzeiFUZ-0I,554
-careamics/utils/plotting.py,sha256=cea1GQB932j2UA3IQZnh-0EenQdnjzPOFoGoFKJ4how,2518
+careamics/utils/plotting.py,sha256=muoN3y5JonZOg_kHSCOa06bJt6PH6a0O8gBFw502i9g,2486
 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-0.0.14.dist-info/METADATA,sha256=jI7wBOg2luJpEUpkYEnLjkpApJPRhJdCSr4QNwzSE2w,3940
-careamics-0.0.14.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-careamics-0.0.14.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
-careamics-0.0.14.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
-careamics-0.0.14.dist-info/RECORD,,
+careamics-0.0.16.dist-info/METADATA,sha256=L2pnu0KFm9PP3OA-riakzhIIM_z_P96O_fPCM3ZaZ-U,4055
+careamics-0.0.16.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+careamics-0.0.16.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
+careamics-0.0.16.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.0.16.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