careamics 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

{careamics-0.0.2.dist-info → careamics-0.0.4.dist-info}/RECORD

@@ -1,41 +1,48 @@
 careamics/__init__.py,sha256=xBCerWN66hv3T7dRGiUYLflmbJtJt1HqbSg9JCWp8pY,391
-careamics/careamist.py,sha256=Mi6a4aUAUPH0YCQm2kObQepG5OFpjlHT0qm6GxAiq58,27496
+careamics/careamist.py,sha256=eZttleBmhu649kkVj7spfBw7DLUuGjx58S2fTPem7g4,28351
 careamics/conftest.py,sha256=Od4WcaaP0UP-XUMrFr_oo4e6c2hi_RvNbuaRTopwlmI,911
 careamics/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
-careamics/config/__init__.py,sha256=qaR98bVRFnEHYGG5EgGBIa9P9AtMRmKzpXuc1exdteo,913
-careamics/config/algorithm_model.py,sha256=-Nx4E6M2EyBDozSTkXeYaj9b0KcIli0Gy6DE3P1WVfE,5443
+careamics/cli/__init__.py,sha256=LbM9bVtU1dy-khmdiIDXwvKy2v8wPBCEUuWqV_8rosA,106
+careamics/cli/conf.py,sha256=1MRSzKcIL--IbYiNixW2aA58GC0ptQHWbBtp7b5eRwQ,13370
+careamics/cli/main.py,sha256=EAWBQoCxcNv-4t3h8_YLCXNjWWU08cOzFj5DYam5e6g,3441
+careamics/config/__init__.py,sha256=M_Y0sGIVr1lQF4IpDeVkWkspbUNlbdH-iDjapMSGOoc,1127
 careamics/config/callback_model.py,sha256=EeYHqpMIPQwyNxLRzzX32Uncl5mZuB1bJO76RHpNymg,4555
-careamics/config/configuration_factory.py,sha256=Ckkv4ber2WSaa-BaoDNuyvpVMd02Q-9T27yziXJ-1Ak,18538
-careamics/config/configuration_model.py,sha256=4LbAt3zUtx05mfTRrXBqD57iQn2s0Y93f81M8Gce4zo,18698
-careamics/config/data_model.py,sha256=dpRthXU8lINT3laJygqka-fmUDT7U34QUHZYBX95oY8,15070
+careamics/config/configuration_factory.py,sha256=vHwRuYasELdZQv0KpX3fxPPUBbJfguBOOtPgqQJ3oks,30193
+careamics/config/configuration_model.py,sha256=pvANQOkWpA-bB60bzI40z_tTnk1zt1l8pfXg7KsDsRs,18843
+careamics/config/data_model.py,sha256=MOXnX6dmI-08b4H_43xOrnSlwdbCtO1UuI9YqOT8djA,15370
+careamics/config/fcn_algorithm_model.py,sha256=eBBjkoyavhvDJFTrjJDkNrWSP_-YaK0cy7qo0lCdBQ0,5105
 careamics/config/inference_model.py,sha256=UE_-ZmCX6LFCbDBOwyGnvuAboF_JNX2m2LcF0WiwgCI,6961
-careamics/config/optimizer_models.py,sha256=p6gDYtO-jFtL7zVX0-Id-rGJWkkyhbU3EBrWD_4TxZE,5726
+careamics/config/likelihood_model.py,sha256=CZtkaMqwGZLW5PWModv-tDDjjLxqGhhTkWpk27V3ERU,2274
+careamics/config/nm_model.py,sha256=lscJb31g3w2H_AY-PL2nL06KuknbaLAftZsVNYNDmxA,4742
+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=9dfCcEcdPsGDW1Q0OIR_PmKjkWbZjeOmGIKuIyRd-0E,1875
-careamics/config/architectures/__init__.py,sha256=CdnViydyTdQixus3uWHBIgbgxmu9t1_ADehqpjN_57U,444
-careamics/config/architectures/architecture_model.py,sha256=4WvQQJGz5DLFjOUryZx0fqPuEMlF2RhtlV5XudJTIbc,922
-careamics/config/architectures/custom_model.py,sha256=IRaequRi5BXMPL14gLr1B_27_XWPeWxQwgHF9_EJMaU,4664
+careamics/config/training_model.py,sha256=67_ipo_-LxhT4-WqAs40Sg8PjU--my43Qn3BhjvlXxM,3212
+careamics/config/vae_algorithm_model.py,sha256=p4OSLCDokw2ADYKP6LvUy9eAHfapqKpcO5LE2RMkiT4,4678
+careamics/config/architectures/__init__.py,sha256=VyuBIopbqpR0KPq6cAeX3qPCrlbY8ZB_rGXwa2ApNvc,447
+careamics/config/architectures/architecture_model.py,sha256=qqPpmkNLwTBC3nwOmXpl33UAvpDFsAxFRBw9MIsQgws,921
+careamics/config/architectures/custom_model.py,sha256=-ROcKn_Ai7SZqzQLoEUc2BLAalgjyvoOnyDKUiY_cp0,4876
+careamics/config/architectures/lvae_model.py,sha256=erySFyLStHX-jUXPLYAEZ2q9bPhWzsMRdU6VFLZobpE,4585
 careamics/config/architectures/register_model.py,sha256=lHH0aUPmXtI3Bq_76zkhg07_Yb_nOJZkZJLCC_G-rZM,2434
 careamics/config/architectures/unet_model.py,sha256=8F2KosNkrXUP2bxlm-D1mowS9x3GOjyXjsEo1Kf-05k,3497
-careamics/config/architectures/vae_model.py,sha256=iLPwjI4B_Ivv_qQNUJc4-Gwm4z8UA3P5BsKQucRFEMI,962
 careamics/config/references/__init__.py,sha256=rZAQzmrciX5cNICcXaBH6sbE6N6L7_qYQUkasNy9y-c,763
 careamics/config/references/algorithm_descriptions.py,sha256=wR3hIoeg5eiUEPbwTxMpQYLTKQyRl_5naSDbBZOZESU,3541
 careamics/config/references/references.py,sha256=AXx08FJQxHb7SYOluCr_eQn_mbOris5dXqhKrCnhBTE,1573
 careamics/config/support/__init__.py,sha256=pKqk76kyBraiSC1SQos-cyiQwsfOLLkLuWj6Hw60LZ4,1041
-careamics/config/support/supported_activations.py,sha256=O27_dGDgw2P-DslKJsXGVAyS2NUQM6Ta4jeo2uTQlW0,519
-careamics/config/support/supported_algorithms.py,sha256=GCkauFDlmb2hJwFSdoIpGmpLjPeYFHOGy2NweKdw8T4,358
-careamics/config/support/supported_architectures.py,sha256=LLD6hyje9Q0BcvA7p2E8WW_cY5yEgMI_NAP4HBi27UU,540
+careamics/config/support/supported_activations.py,sha256=CqOWoziIK5jZZXJO7G7cGg3TTid1POqv8FXqxjXxyME,535
+careamics/config/support/supported_algorithms.py,sha256=Tt5PaV1mwSZdrc4XpW9M4-ofExoHnMgfebCSN6ns0AQ,953
+careamics/config/support/supported_architectures.py,sha256=f93cRyeBOu5rYzvYrvWPVpjyK54GhyVTzCT1GNSdhI8,494
 careamics/config/support/supported_data.py,sha256=T_mDiWLFMVji_EpjBABUObAJcnv-XBnqp9XUZP37Tdk,2902
 careamics/config/support/supported_loggers.py,sha256=ubSOkGoYabGbm_jmyc1R3eFcvcP-sHmuyiBi_d3_wLg,197
-careamics/config/support/supported_losses.py,sha256=TPsMCuDdgb64TRyDwonnwHb1R-rkn3OzhtHimyVtrOY,540
-careamics/config/support/supported_optimizers.py,sha256=xxbJsyohJTlHeUz2I4eRwcE3BeACs-6PH8cpX6w2wX8,1394
+careamics/config/support/supported_losses.py,sha256=2x5sZuxRbWJzodoL35I1mMYUUDMzk8UFiFdbyPwbJ4E,583
+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=4uob-bnZ5aqpN5aEI67-aa7bsmVCrKxEknzf2BAZ3W4,283
-careamics/config/transformations/__init__.py,sha256=oqwBAL2XXbPRZZ5iOzNqalX6SyJ1M-S0lkfbDGZOzyE,378
-careamics/config/transformations/n2v_manipulate_model.py,sha256=UTyfpm1mmMvYg_HoMzXilZhJGx_muiV-lLQ4UThCFJ0,1854
+careamics/config/support/supported_transforms.py,sha256=ODvmoTywvJWG_5-SJJZu-X1FNtKGhkNWQc-t26IFZWI,311
+careamics/config/transformations/__init__.py,sha256=lW9DcsCfemnlcmECyw5Id28nIuwg1YPKWhGgdfzcv5s,493
+careamics/config/transformations/n2v_manipulate_model.py,sha256=Mdxc4J3vxe_dM2CIhmTwwGOIirQvrQXLoa2vRsTzoYI,1855
 careamics/config/transformations/normalize_model.py,sha256=1Rkk6IkF-7ytGU6HSzP-TpOi4RRWiQJ6fOd8zammXcg,1936
 careamics/config/transformations/transform_model.py,sha256=i7KAtSv4nah2H7uyJFKqg7RdKF68OHIPMNNvDo0HxGY,1000
+careamics/config/transformations/transform_union.py,sha256=3PnzsWlD2ymIgRPrUDZzPT9vMOVLVDtUcEorZTYx_-I,574
 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=iv0nVI0W7j9DxFPwh0DjRCzM9P8oLQn4Gwi5rfuFrrI,180
@@ -60,81 +67,99 @@ careamics/dataset/patching/sequential_patching.py,sha256=_l3Q2uYIhjMJMaxDdSbHC9_
 careamics/dataset/patching/validate_patch_dimension.py,sha256=sQQ0-4b4uu60MNKkoWv95KxQ80J7Ku0CEk0-kAXlKeI,2134
 careamics/dataset/tiling/__init__.py,sha256=XynyAz85hVfkLtrG0lrMr_aBQm_YEwfu5uFcXMGHlOA,190
 careamics/dataset/tiling/collate_tiles.py,sha256=OrPZ-n-V3uGOc_7CcPnyEJqdbEVDlTfJfWmZnyBZ-HA,978
+careamics/dataset/tiling/lvae_tiled_patching.py,sha256=AOS_1m1q74YhfLgWeUx1xkRNvgw1dq6Vi7yJhmMR-A0,12992
 careamics/dataset/tiling/tiled_patching.py,sha256=ouxUWvttzmTY310CuiR25IGNVWgksVQAXoN4IXSi_G0,5942
 careamics/file_io/__init__.py,sha256=vdIx5JV3JwoyOeWnY_0tY6aekwPFy_8hBqe0Yj-aOH8,334
 careamics/file_io/read/__init__.py,sha256=I2Ios3fOoe_7f1nYT88qt2hcl0107aJCvA8yPfdpVIA,259
 careamics/file_io/read/get_func.py,sha256=yGXD0rTFD7u70FR0axrQtWies0aYW3iQ6f0Wfcd8z-8,1394
-careamics/file_io/read/tiff.py,sha256=_WVqUycI4NMk2GzDBEOWcGuSr1293673A1vs7WvZbS4,1358
+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=syy-e55OKPqa2Fn7G6szJrAmmJ4JUJyr4Y4ZSnKK0zg,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=IAhfuveylgTdwIqynRqmGNOGrBlNmsXNgK3TuPDqU-o,572
-careamics/lightning/lightning_module.py,sha256=n8aQmHmjnztUTm5eob_MwcDw4W6pHMiUra1WNsvcVug,8951
-careamics/lightning/predict_data_module.py,sha256=rgHhS5fKoa5wscWyvmPP_FHHdVnDnLbF4sG7y_C7ZOM,12747
-careamics/lightning/train_data_module.py,sha256=XVLeFTfB5IQFdh9LnuvDNOMqqloRMH-miQxk8cVybjU,27897
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 careamics/lightning/callbacks/__init__.py,sha256=neTWqF6EbBRVf0FqtBkPHeGIR3j1yTk0OASraEVN0Pg,312
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 careamics/lightning/callbacks/progress_bar_callback.py,sha256=8HvNSWZldixd6pjz0dLDo0apIbzTovv5smKmZ6tZQ8U,2444
 careamics/lightning/callbacks/prediction_writer_callback/__init__.py,sha256=tATV4kFZ8h4ZpN866URsf2vbEfY9HlHN4VALJcDySCY,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=HGDyYLSak9puGEs42cI_08peAuOMaFyZaRkcpv_n0iY,8183
 careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py,sha256=aqc6DDewD4n3tbLfqS4y-FfNKV9zy3-CZ0K2Mu16Mms,12567
-careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py,sha256=yki7H3_11nGOpCmjVqI5KY_kItHkQj3JQhLsnledT2A,7115
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 careamics/lvae_training/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 careamics/lvae_training/lightning_module.py,sha256=ryr7iHqCMzCl5esi6_gEcnKFDQkMrw0EXK9Zfgv1Nek,27186
 careamics/lvae_training/metrics.py,sha256=KTDAKhe3vh-YxzGibjtkIG2nnUyujbnwqX4xGwaRXwE,6718
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 careamics/lvae_training/train_utils.py,sha256=e-d4QsF-li8MmAPkAmB1daHpkuU16nBTnQFZYqpTjn4,3567
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 careamics/model_io/__init__.py,sha256=HITzjiuZQwo-rQ2_Ma3bz9l7PDANv1_S489E-tffV9s,155
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 careamics/model_io/bioimage/__init__.py,sha256=r94nu8WDAvj0Fbu4C-iJXdOhfSQXeZBvN3UKsLG0RNI,298
 careamics/model_io/bioimage/_readme_factory.py,sha256=LZAuEiWNBTPaD8KrLPMq16yJuOPKDZiGQuTMHKLvoT4,3514
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-careamics/models/activation.py,sha256=xdqz4-yKV7oElG_dDrYuibS8HOiYvKdV_r9FwWPvaDE,977
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 careamics/models/layers.py,sha256=oWzpq8OdHFEJqPWC9X8IRPNe0XqAnesSqwoT6V3t1Mw,13712
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 careamics/prediction_utils/__init__.py,sha256=uYKzirlF-unFL9GbDPxFnYgOwSjGAtik9fonU7DfuEY,270
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 careamics/prediction_utils/prediction_outputs.py,sha256=p3Nbw9wRLU_M5uixPbzj_DmfxcSL7Y8rAQ_aTx70KQI,4082
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 careamics/transforms/__init__.py,sha256=VIHIsC8sMAh1TCm67ifB816Zp-LRo6rAONPuT2Qs3bs,483
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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=rG_dnqX7rdyNTFWlDkIdNtDwwMQBpg_ym14ZFeYrWfs,402
 careamics/utils/autocorrelation.py,sha256=M_WYzrEOQngc5iSXWar4S3-EOnK6DfYHPC2vVMeu_Bs,945
 careamics/utils/base_enum.py,sha256=bz1D8mDx5V5hdnJ3WAzJXWHJTbgwAky5FprUt9F5cMA,1387
 careamics/utils/context.py,sha256=Ljf70OR1FcYpsVpxb5Sr2fzmPVIZgDS1uZob_3BcELg,1409
 careamics/utils/logging.py,sha256=coIscjkDYpqcsGnsONuYOdIYd6_gHxdnYIZ-e9Y2Ybg,10322
-careamics/utils/metrics.py,sha256=9YQe5Aj2Pv2h9jnRFeRbDQ_3qXAW0QHpucSqiUtwDcA,2382
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 careamics/utils/path_utils.py,sha256=8AugiG5DOmzgSnTCJI8vypXaPE0XhnR-9pzeiFUZ-0I,554
 careamics/utils/ram.py,sha256=tksyn8dVX_iJXmrDZDGub32hFZWIaNxnMheO5G1p43I,244
 careamics/utils/receptive_field.py,sha256=Y2h4c8S6glX3qcx5KHDmO17Kkuyey9voxfoXyqcAfiM,3296
+careamics/utils/serializers.py,sha256=tovAjYoYjM26FbwjKuMD4xiyiISgqROs7aiCPa_rbVs,1379
 careamics/utils/torch_utils.py,sha256=g1zxdlM7_BA7mMLcCzmrxZX4LmH__KXlJibC95muVaA,3014
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-careamics-0.0.2.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
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-careamics-0.0.2.dist-info/RECORD,,
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+careamics-0.0.4.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.0.4.dist-info/RECORD,,

careamics-0.0.4.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+careamics = careamics.cli.main:run

careamics/config/architectures/vae_model.py

@@ -1,42 +0,0 @@
-"""VAE Pydantic model."""
-
-from typing import Literal
-
-from pydantic import (
-    ConfigDict,
-)
-
-from .architecture_model import ArchitectureModel
-
-
-class VAEModel(ArchitectureModel):
-    """VAE model placeholder."""
-
-    model_config = ConfigDict(
-        use_enum_values=True, protected_namespaces=(), validate_assignment=True
-    )
-
-    architecture: Literal["VAE"]
-    """Name of the architecture."""
-
-    def set_3D(self, is_3D: bool) -> None:
-        """
-        Set 3D model by setting the `conv_dims` parameters.
-
-        Parameters
-        ----------
-        is_3D : bool
-            Whether the algorithm is 3D or not.
-        """
-        raise NotImplementedError("VAE is not implemented yet.")
-
-    def is_3D(self) -> bool:
-        """
-        Return whether the model is 3D or not.
-
-        Returns
-        -------
-        bool
-            Whether the model is 3D or not.
-        """
-        raise NotImplementedError("VAE is not implemented yet.")