ngio 0.5.0a1__py3-none-any.whl → 0.5.0a3__py3-none-any.whl

{ngio-0.5.0a1.dist-info → ngio-0.5.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0a1
+Version: 0.5.0a3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -17,8 +17,8 @@ Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata
-Requires-Dist: dask[array]
-Requires-Dist: dask[distributed]
+Requires-Dist: dask[array]<2025.11.0
+Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models
@@ -31,7 +31,6 @@ Requires-Dist: pydantic
 Requires-Dist: requests
 Requires-Dist: zarr>3
 Provides-Extra: dev
-Requires-Dist: devtools; extra == 'dev'
 Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
 Requires-Dist: napari; extra == 'dev'
@@ -60,8 +59,13 @@ Requires-Dist: rich; extra == 'docs'
 Requires-Dist: scikit-image; extra == 'docs'
 Requires-Dist: tabulate; extra == 'docs'
 Provides-Extra: test
+Requires-Dist: boto; extra == 'test'
+Requires-Dist: devtools; extra == 'test'
+Requires-Dist: moto[server]; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-httpserver; extra == 'test'
+Requires-Dist: s3fs; extra == 'test'
 Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 

{ngio-0.5.0a1.dist-info → ngio-0.5.0a3.dist-info}/RECORD

@@ -1,56 +1,56 @@
-ngio/__init__.py,sha256=rEgnXuU6TCejUUGsxt4eKmjMhxjYh0fYBxWF4o5YjbE,1435
-ngio/common/__init__.py,sha256=aPSuUbdGryrxbnlWrsVNe3LZoBAWC4GijR1BNH1UwuU,612
+ngio/__init__.py,sha256=A7o63AVFPNbhOpePPOb-BZvszc52tNqp2NW277h3rAo,1433
+ngio/common/__init__.py,sha256=F3zAHQIhwig1xUA-SpmFVRtMeOrEj926-nHWhj-wS6c,684
 ngio/common/_dimensions.py,sha256=w8PYgyWxA8hgJETjFbw5CXf7WrasCL5FbzgfL1in86M,11361
-ngio/common/_masking_roi.py,sha256=ZZTXordEZoq_ADk0OzADvq-5dPOwUBSuNobzFR8fpTw,5697
-ngio/common/_pyramid.py,sha256=186eQSCxP_x2heYKmMP_Edl4Aml9Eo1bBmIHlwslqy8,8699
-ngio/common/_roi.py,sha256=9fKFTHoUiP0xmxvQiFkNmIuwWg3bFuRaAx-froCSqvA,11487
+ngio/common/_masking_roi.py,sha256=YSEZ5nv3-TqMrQ04cI70U9NGx3LSy7Z1_cbw_NE-78k,4831
+ngio/common/_pyramid.py,sha256=vPlxHUWBmfw6BtRoZeA7YNu3ft1YdAzyW1tWG8gA_to,14117
+ngio/common/_roi.py,sha256=UMr7ie7dIZ6gMcM0_AlFMev_PRKxBdzUy_1WKRZ4zQU,11403
 ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
 ngio/common/_zoom.py,sha256=U01c-vqXjzZkrpd9Yvs24frVfTls_xPJeeaFCGmUwYI,6727
 ngio/experimental/__init__.py,sha256=3pmBtHi-i8bKjTsvrOJM56ZyRX3Pv_dceCdt88-8COQ,147
 ngio/experimental/iterators/__init__.py,sha256=TECOMGb5PEEZ0yXxt8pqIGvLKG41g_L1fTJU-zGPeV8,488
 ngio/experimental/iterators/_abstract_iterator.py,sha256=7aAoMI-6vYGCMKxO3M10WpuBMTdqX4zr0K-TutAOp88,13195
-ngio/experimental/iterators/_feature.py,sha256=g03yHIzYpTVeD3KUq2a4TwX29Dt48XaaGdZNSykYy7M,6749
+ngio/experimental/iterators/_feature.py,sha256=OnqeSP-UMWku7AIBcutsDsAWqnFqPrjCJiMvMGM96fk,6714
 ngio/experimental/iterators/_image_processing.py,sha256=cM7sL7xgdcjSOKAu-6367Aov89o6wgiJ_wqCGkU2Bsw,5091
 ngio/experimental/iterators/_mappers.py,sha256=VVVsjems57wJUnWeufUFcgqa23k7VPeFL4Nc04HVw4o,1399
-ngio/experimental/iterators/_rois_utils.py,sha256=Q-8lQ26neYn63h_RvfypYqvrq2UUN2O3xqVe57k_ufU,4363
+ngio/experimental/iterators/_rois_utils.py,sha256=5foGjt3qrACNrO29LlvSUbJ4yfI0z6MhU2oVCzEU214,4363
 ngio/experimental/iterators/_segmentation.py,sha256=xzotGvTn04HPeMeXZ_URnQqWco6d2lH6Ng6vkCUh9NM,9153
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
-ngio/hcs/_plate.py,sha256=qfRwbCKaoz_AWTi8RDFFwOxy5geSknfJrPcqFVno9zI,44288
+ngio/hcs/_plate.py,sha256=-8Ffx07s73jKTDKBj11yrJTtfNfwBP0DwUbzJQKPCWM,43503
 ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
-ngio/images/_abstract_image.py,sha256=hrB9xn4MFRxnxE1d7HKnM8SXVPUGhMD9u32yBHTsFiU,18517
-ngio/images/_create.py,sha256=OirIKg843CCSiwy_oUolX2UHlROR_iO4rN_IK47jDWc,10448
-ngio/images/_create_synt_container.py,sha256=D3SkjYN_AZ5fSefjEX0iQ3ZGEuBTWZvuPQIwHc6l-CU,5519
-ngio/images/_image.py,sha256=JWN7qmNVZxAzm9zmaImYseDt8xzYtOw-N0olR6VQo_8,33483
-ngio/images/_label.py,sha256=sJUB8of7t1YErZRu3t7jzGjlRn3KAAs0EL5nFrbvvlc,11921
+ngio/images/_abstract_image.py,sha256=xCpI--oe9B81s3A99JGSYNiZzN-DaYheUJoP19n9Uwg,31915
+ngio/images/_create_synt_container.py,sha256=Cvg_J0KSxK0PH8IBzlKLIcCwH2vRTuBj-nZo5uOKXXk,5182
+ngio/images/_create_utils.py,sha256=hXVbFM8D_0mZTfBAhcZiuGX2lLXSJCep8THuxpH4d4E,14374
+ngio/images/_image.py,sha256=YSO6dzEKdrgh4AE-cE4j_hxsU4QBpxUc_j6-Xpq5YqM,33664
+ngio/images/_label.py,sha256=Y7Y0yLgoRUJtRzqgNPWc1yZ3HgDu4bbXbwhQJlnPKA8,14047
 ngio/images/_masked_image.py,sha256=YhbBzgPZMav6rX0WYue1BaxAzEIsfaQrxUIOK6ZWZcw,18848
-ngio/images/_ome_zarr_container.py,sha256=tfG40PLNfyfaR2pVAmGINlkKJRoQ4W0L0melFotMcP8,38737
+ngio/images/_ome_zarr_container.py,sha256=_fI23IHb1iuhgLUqWdVvOwbFKtFpLY3J6y_k_i6mkjA,46044
 ngio/images/_table_ops.py,sha256=jFv_AMqoB4JBpoWsMtZppZVW7dAOC_u-JpfNm8b33kY,15292
 ngio/io_pipes/__init__.py,sha256=arW_7GWzZs82kPNKdm_6B1sIDFV0lWwp-ZaORr9Q1FQ,2412
-ngio/io_pipes/_io_pipes.py,sha256=KuwMYofE11EKx0iplWXBQZ-eE1A9YpGDprWh98cUlAI,10710
-ngio/io_pipes/_io_pipes_masked.py,sha256=077j1XNgyCNOHlOsbjPOWcLtb2ccFvbLp-cPzWL1j3c,16999
-ngio/io_pipes/_io_pipes_roi.py,sha256=cu_vd4MTDuyiabCWQ5ieMLI4v3tu_twSEe4X5-3bp84,4543
-ngio/io_pipes/_io_pipes_types.py,sha256=xCeUd9rZe2wsgoZR1pUq6L4LSeawoPsb-9pmz5C6ztA,1393
-ngio/io_pipes/_match_shape.py,sha256=eDy_Eqzld08m9zDuIjAvJnIhWh_HVjQS-5Pw9BMjdbw,13200
+ngio/io_pipes/_io_pipes.py,sha256=l85mmjj1l0uYU3qzsSHg9l8cMIEevInm_MTD-8MlXgw,10603
+ngio/io_pipes/_io_pipes_masked.py,sha256=uvfNIuW8prWux3fZ-a25l44zDfZW4qBaXZEm0TkhloA,16916
+ngio/io_pipes/_io_pipes_roi.py,sha256=HJHlItx2nsFYcE4OjvVR-W0lFMMK8CcyYK23dKUrP8w,4472
+ngio/io_pipes/_io_pipes_types.py,sha256=PcRdnjBJIsXcDT1_dbH2LZiH6d3z6D7y48cmybyZCXk,1358
+ngio/io_pipes/_match_shape.py,sha256=e3cQM6BI8n2YODmU6wgnFoaguwRVZw9bk5eafzmcTBM,13185
 ngio/io_pipes/_ops_axes.py,sha256=Geg4ZXxB0njWWopX9YeiwRJJ9Ef2GKfG0NIUafOmi2c,10043
 ngio/io_pipes/_ops_slices.py,sha256=hHMIOQ_niUSK9uFl8P2-10dP_K4GX3Do6vivN4fGRE0,14520
-ngio/io_pipes/_ops_slices_utils.py,sha256=xjDaCVGmtME5Q0XSmGrY3nUKYgw5jOBQZW4YDq5s4vE,6580
+ngio/io_pipes/_ops_slices_utils.py,sha256=mps_I0eTI4gdBVM9MCKsd8rCyefdo9bIK9fEmqwr23E,6633
 ngio/io_pipes/_ops_transforms.py,sha256=uITs6v6sZ7DQ_Hpw3JdX8MuPOzir-bihvGzY84Qn4wY,2934
 ngio/io_pipes/_zoom_transform.py,sha256=WBY1tO6_Qhf8FaDujfTdipuuqFf7PSi204wx5VKKs88,6884
-ngio/ome_zarr_meta/__init__.py,sha256=tzxW2oVhfeMBVuv3XkcbOLzMnbDvUnie-AVsvSxRkdE,1265
-ngio/ome_zarr_meta/_meta_handlers.py,sha256=P2Edraf2MlTMlwFOpXCkUqD1QTN2nTwGv5Ff0ab5csw,26715
+ngio/ome_zarr_meta/__init__.py,sha256=3_QbSt-Ta8MXL8R_tGmgrYMGePgawI96Hc5msrbZCgM,1139
+ngio/ome_zarr_meta/_meta_handlers.py,sha256=70R0waA1BNX7yNOZnvVuNBeIIxkzGQN6xEKebFpYFx0,13673
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=U2FqZR91Ob2N6CqKdyw-_Ll-wMgmGuPZGVRCr6wuRFY,1698
-ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=gNzxCddn53m9dlNJlV5CL-aQS-nGJrbCDGfAp5L97LY,16412
+ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=CY63mWf7_ALoi7o_1QDVK1lAG56xN0gvgwfcuNRmMIg,16446
 ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=TDxIy-yVc2YaWPIFJRYnYwZbA8O5Ee_OiWppHYrEdpU,16647
-ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=CrHnjVWBGYPqErKkHR-E2DKrE3DmGznXMkd3Y9Z4uYo,3434
-ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=N1CGPOubwf0pvm8tiTnh-C1cOu9lToyDe3WagnEnPN4,17207
-ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=y44AVdB7IQD9t5yiZV6cXSvV9_-CGDiYrCfX3PeaclQ,16231
+ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=5YdAplk90koX3vjoIJimms-CJYxt095rJ9YagZSQg88,2872
+ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=_KM9Ql-sBL1zV_OLhDiFBj9QhEjwVcW8W5sMUA7xtzM,16944
+ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=kjlC2Otz7z__ojrSHYsFJaQW_OKNQoevVlAn1cZYNJs,14442
 ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=4VF1djY9T5tp6GCJXppFrUJwALI1XgIm0imoM5rNvdE,3876
-ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
+ngio/ome_zarr_meta/v04/__init__.py,sha256=WHT8RFLxqx9QBtm8wwg8tZ_EBuC1l8PG_JxwFl02Tk4,577
 ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R0R_9rSaa85A,530
-ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=xa3DT7VJJZyd-4EB-KGjlPcKkTmst_izTcoWj30mLiY,15766
-ngio/ome_zarr_meta/v05/__init__.py,sha256=j6YuIKu2bxmhlhFCbhXg5UA4qD7V8CpyTAHl1vnIpq8,583
+ngio/ome_zarr_meta/v04/_v04_spec.py,sha256=qmp9xAfA2z9UErrs4xvS0qmO5G8Dli-CenAL3rO4TFo,14348
+ngio/ome_zarr_meta/v05/__init__.py,sha256=zGWjeVCXQX7ezs4hEmmLrgOcQNhR6nZJ4LXKpj1oCfE,577
 ngio/ome_zarr_meta/v05/_custom_models.py,sha256=ZN3bE9nwx4y3tElhsYafI4S2zp_WzdkQKcyuuBiaXXo,530
-ngio/ome_zarr_meta/v05/_v05_spec_utils.py,sha256=vd9-EiZZjBpCXmwgLj8a1RWiwFpSjjxKBfbH8OpsG9M,16493
+ngio/ome_zarr_meta/v05/_v05_spec.py,sha256=JBZrm3BRZVbxHB29UFsfo3tuedhpMdy8KuWf4vDL3_g,15134
 ngio/resources/__init__.py,sha256=4E4TXTNYEgRHt26C1XcC4pPobJJsmZRYm1Ml4uAuAkE,1664
 ngio/resources/resource_model.py,sha256=eE1m0dyk-2psPC4X8Ifyan524QHUOd52TEQdvoU0m8I,861
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/mask.png,sha256=g3QmxQdmeciAtBe5cTCRfR6yw3keG9cBYfjizMo6EGo,11890
@@ -58,31 +58,31 @@ ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/nuclei.png,sha
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/raw.jpg,sha256=82lejQAIokj5w9g-qqhysDTWpHtNvJTkdURG_BjqIxQ,37743
 ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
 ngio/tables/_abstract_table.py,sha256=rwGa47TzbFmosucBWVfFq6JEXtgGvOdUVtU9DIelV88,8204
-ngio/tables/_tables_container.py,sha256=3xmpREaN671l40MPprnl1BD-VoOb6xfjECb5mNoMW0w,12173
+ngio/tables/_tables_container.py,sha256=DV_uX_bf3kCcmWLFKjY9FhKX8iBewbHkZSECqKjsCIw,12333
 ngio/tables/backends/__init__.py,sha256=MwSRXNF1rWQBFOTDA_vT3oGoNZpviVgytsL5Txnu08I,1619
 ngio/tables/backends/_abstract_backend.py,sha256=M1ogsBpWBiQMV65YweZhA845PAtkzG2BsZCPN_7Xp8U,7613
-ngio/tables/backends/_anndata.py,sha256=KBzXVxaXstVx3ofcLYYFm8ECVFDaHxfUWcKdg5vQPqY,2992
-ngio/tables/backends/_anndata_utils.py,sha256=g0mIfihXd4p75bvMvCYTljBKTP13EZ9p_SVMifDKE3Y,3208
-ngio/tables/backends/_csv.py,sha256=Ev61D-AUKo4LIhXRmWPJgYbHI7eQdxiajQR574DevEM,932
-ngio/tables/backends/_json.py,sha256=1ZsEuXDJm1rOZV_KjFm8CB0qhv7L1W7L2EGWPf4q_p0,3137
-ngio/tables/backends/_non_zarr_backends.py,sha256=5a1fbxiVnUXt1tiA025BqN0T7SQJvIERFtQHp4PhFHw,7294
-ngio/tables/backends/_parquet.py,sha256=ic-p86h8lce8q9luBJGRzy6vxlWyJvA0-2l5cUD6OqY,1398
+ngio/tables/backends/_anndata.py,sha256=brJaTZCBe_ipexWbGQgFM2-B30sRKI1kxNLuSTcY2uE,4546
+ngio/tables/backends/_anndata_utils.py,sha256=PoHiLkGeDhBgPsEMJi9QH-NejHmfrfILcwj1CYubyCM,3095
+ngio/tables/backends/_csv.py,sha256=iZJNLHOXYysV_2iq6Lmekq0XXYsVE7OYrKz2HP2TU9w,479
+ngio/tables/backends/_json.py,sha256=A4iaKOIc5Q_XKDOm321QNqAN4DAOuA-dEinnfTlk1Fk,3091
+ngio/tables/backends/_parquet.py,sha256=Fi3VZlTH5UTykk0eqr43_e_Qt_GQcEN-3pHK07XFBwk,503
+ngio/tables/backends/_py_arrow_backends.py,sha256=lxxI5TN4lFYwpsjD1g1xAxEt4lZ9Mu7YW3-m3nIuo2g,8587
 ngio/tables/backends/_table_backends.py,sha256=ksP2NAosXZkNMZf-IMrLx7bjQgp_eKfvPYK4vMdT1A8,7250
 ngio/tables/backends/_utils.py,sha256=t4dLXSPxx2AnJvVtj0GIwrLoO11h4Ges6U7hj4md0hY,19730
 ngio/tables/v1/__init__.py,sha256=Wr1_9RZFpaN8FYMTnxT9Yjkw4AS7y9FMWailmB_uj5g,617
 ngio/tables/v1/_condition_table.py,sha256=T0Uq5BKkmMoEspt_Rx0U99Ow6S9GAMZDHqvUO5obCAM,1780
 ngio/tables/v1/_feature_table.py,sha256=n9uMHwoBh-_dlOhUXCFbmAjXFVXncNCR3SjE2qzXI68,3821
 ngio/tables/v1/_generic_table.py,sha256=1ktJHeuv7U1g5Z8PFUuTkCjOzcYMQd8xegKHKUedJB8,1240
-ngio/tables/v1/_roi_table.py,sha256=g7UpMmpf3uAfaG59WYRnimUBgiB_T1qUJRwMZpMt9cI,17099
+ngio/tables/v1/_roi_table.py,sha256=DuKJlDmtQtLOfL0g4CSdncfm4hBsKWG6F6fkMUpt4Nk,17821
 ngio/transforms/__init__.py,sha256=JA0-Ui7skbXkm9ofN-AEhU1FTLutkMkwTdVD-310frQ,113
 ngio/transforms/_zoom.py,sha256=otyE-vxFnywUJ8U4mHjat-bNG_7_jv62ckTpqDMxyVQ,550
-ngio/utils/__init__.py,sha256=XPYh8ehC7uXNU2cFFXZAw-S3DpWpX1Yq2xGkffZv5vI,1142
+ngio/utils/__init__.py,sha256=1eIInpFEEWQtMeGaRhAyVjqSKWUCuksMkx2cqg9D9nI,987
+ngio/utils/_cache.py,sha256=Ey9fgc_BTdMyqg6c80C0CuGDhOafln8-3e_1MQ0MFzw,1283
 ngio/utils/_datasets.py,sha256=6GtxfPkjutNaeg5BHuJDBP0GudvQXHLU6mmHp_o0bGA,5650
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
-ngio/utils/_logger.py,sha256=N5W0a_xwze4blS1MolidBkTMbjTbg8GPguJZNun3mAE,1392
-ngio/utils/_zarr_utils.py,sha256=ATehiEALPI__eNQSWdSW5PpJLmI2FECrexA9jTZAI2s,16103
-ngio-0.5.0a1.dist-info/METADATA,sha256=AT0kbnHlYkhiL0_AmZpOm8DagaEPGCkI1xze_cJy3w8,6104
-ngio-0.5.0a1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.5.0a1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.5.0a1.dist-info/RECORD,,
+ngio/utils/_zarr_utils.py,sha256=asAmD4FSFspyAfIDB8ISwHLCZYctsKENyCCAQHEfubA,17817
+ngio-0.5.0a3.dist-info/METADATA,sha256=yvzf4IseuuNv8cAvtQLnrWwrdbZYVl422KnEjnQpyQc,6294
+ngio-0.5.0a3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+ngio-0.5.0a3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.5.0a3.dist-info/RECORD,,

{ngio-0.5.0a1.dist-info → ngio-0.5.0a3.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

ngio/images/_create.py

@@ -1,283 +0,0 @@
-"""Utility functions for working with OME-Zarr images."""
-
-from collections.abc import Sequence
-from typing import Literal, TypeVar
-
-from zarr.core.array import CompressorLike
-
-from ngio.common._pyramid import init_empty_pyramid
-from ngio.ome_zarr_meta import (
-    NgioImageMeta,
-    NgioLabelMeta,
-    PixelSize,
-    get_image_meta_handler,
-    get_label_meta_handler,
-)
-from ngio.ome_zarr_meta.ngio_specs import (
-    DefaultNgffVersion,
-    DefaultSpaceUnit,
-    DefaultTimeUnit,
-    NgffVersions,
-    SpaceUnits,
-    TimeUnits,
-    canonical_axes_order,
-    canonical_label_axes_order,
-)
-from ngio.utils import NgioValueError, StoreOrGroup, ZarrGroupHandler
-
-_image_or_label_meta = TypeVar("_image_or_label_meta", NgioImageMeta, NgioLabelMeta)
-
-
-def _init_generic_meta(
-    meta_type: type[_image_or_label_meta],
-    pixelsize: float,
-    axes_names: Sequence[str],
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    yx_scaling_factor: float | tuple[float, float] = 2.0,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
-    time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    name: str | None = None,
-    version: NgffVersions = DefaultNgffVersion,
-) -> tuple[_image_or_label_meta, list[float]]:
-    """Initialize the metadata for an image or label."""
-    scaling_factors = []
-    for ax in axes_names:
-        if ax == "z":
-            scaling_factors.append(z_scaling_factor)
-        elif ax in ["x"]:
-            if isinstance(yx_scaling_factor, tuple):
-                scaling_factors.append(yx_scaling_factor[1])
-            else:
-                scaling_factors.append(yx_scaling_factor)
-        elif ax in ["y"]:
-            if isinstance(yx_scaling_factor, tuple):
-                scaling_factors.append(yx_scaling_factor[0])
-            else:
-                scaling_factors.append(yx_scaling_factor)
-        else:
-            scaling_factors.append(1.0)
-
-    pixel_sizes = PixelSize(
-        x=pixelsize,
-        y=pixelsize,
-        z=z_spacing,
-        t=time_spacing,
-        space_unit=space_unit,
-        time_unit=time_unit,
-    )
-
-    meta = meta_type.default_init(
-        name=name,
-        levels=levels,
-        axes_names=axes_names,
-        pixel_size=pixel_sizes,
-        scaling_factors=scaling_factors,
-        version=version,
-    )
-    return meta, scaling_factors
-
-
-def create_empty_label_container(
-    store: StoreOrGroup,
-    shape: Sequence[int],
-    pixelsize: float,
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    yx_scaling_factor: float | tuple[float, float] = 2.0,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
-    time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    axes_names: Sequence[str] | None = None,
-    name: str | None = None,
-    chunks: Sequence[int] | Literal["auto"] = "auto",
-    dtype: str = "uint32",
-    dimension_separator: Literal[".", "/"] = "/",
-    compressors: CompressorLike = "auto",
-    overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
-) -> ZarrGroupHandler:
-    """Create an empty label with the given shape and metadata.
-
-    Args:
-        store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Sequence[int]): The shape of the image.
-        pixelsize (float): The pixel size in x and y dimensions.
-        z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
-        time_spacing (float, optional): The spacing between time points.
-            Defaults to 1.0.
-        levels (int | list[str], optional): The number of levels in the pyramid or a
-            list of level names. Defaults to 5.
-        yx_scaling_factor (float, optional): The down-scaling factor in x and y
-            dimensions. Defaults to 2.0.
-        z_scaling_factor (float, optional): The down-scaling factor in z dimension.
-            Defaults to 1.0.
-        space_unit (SpaceUnits, optional): The unit of space. Defaults to
-            DefaultSpaceUnit.
-        time_unit (TimeUnits, optional): The unit of time. Defaults to
-            DefaultTimeUnit.
-        axes_names (Sequence[str] | None, optional): The names of the axes.
-            If None the canonical names are used. Defaults to None.
-        name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Sequence[int] | Literal["auto"]): The chunk shape. If None the shape
-            is used. Defaults to None.
-        dimension_separator (DIMENSION_SEPARATOR): The separator to use for
-            dimensions. Defaults to "/".
-        compressors (CompressorLike): The compressors to use. Defaults to "auto".
-        dtype (str, optional): The data type of the image. Defaults to "uint16".
-        overwrite (bool, optional): Whether to overwrite an existing image.
-            Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
-            Defaults to DefaultVersion.
-
-    """
-    if axes_names is None:
-        axes_names = canonical_label_axes_order()[-len(shape) :]
-
-    if len(axes_names) != len(shape):
-        raise NgioValueError(
-            f"Number of axes names {axes_names} does not match the number of "
-            f"dimensions {shape}."
-        )
-
-    meta, scaling_factors = _init_generic_meta(
-        meta_type=NgioLabelMeta,
-        pixelsize=pixelsize,
-        z_spacing=z_spacing,
-        time_spacing=time_spacing,
-        levels=levels,
-        yx_scaling_factor=yx_scaling_factor,
-        z_scaling_factor=z_scaling_factor,
-        space_unit=space_unit,
-        time_unit=time_unit,
-        axes_names=axes_names,
-        name=name,
-        version=version,
-    )
-
-    mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(
-        store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
-    )
-    image_handler = get_label_meta_handler(version=version, group_handler=group_handler)
-    image_handler.write_meta(meta)
-
-    init_empty_pyramid(
-        store=store,
-        paths=meta.paths,
-        scaling_factors=scaling_factors,
-        ref_shape=shape,
-        chunks=chunks,
-        axes=axes_names,
-        dtype=dtype,
-        mode="a",
-        dimension_separator=dimension_separator,
-        compressors=compressors,
-    )
-    group_handler._mode = "r+"
-    return group_handler
-
-
-def create_empty_image_container(
-    store: StoreOrGroup,
-    shape: Sequence[int],
-    pixelsize: float,
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    yx_scaling_factor: float | tuple[float, float] = 2,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
-    time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    axes_names: Sequence[str] | None = None,
-    name: str | None = None,
-    chunks: Sequence[int] | Literal["auto"] = "auto",
-    dtype: str = "uint16",
-    dimension_separator: Literal[".", "/"] = "/",
-    compressors: CompressorLike = "auto",
-    overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
-) -> ZarrGroupHandler:
-    """Create an empty OME-Zarr image with the given shape and metadata.
-
-    Args:
-        store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Sequence[int]): The shape of the image.
-        pixelsize (float): The pixel size in x and y dimensions.
-        z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
-        time_spacing (float, optional): The spacing between time points.
-            Defaults to 1.0.
-        levels (int | list[str], optional): The number of levels in the pyramid or a
-            list of level names. Defaults to 5.
-        yx_scaling_factor (float, optional): The down-scaling factor in x and y
-            dimensions. Defaults to 2.0.
-        z_scaling_factor (float, optional): The down-scaling factor in z dimension.
-            Defaults to 1.0.
-        space_unit (SpaceUnits, optional): The unit of space. Defaults to
-            DefaultSpaceUnit.
-        time_unit (TimeUnits, optional): The unit of time. Defaults to
-            DefaultTimeUnit.
-        axes_names (Sequence[str] | None, optional): The names of the axes.
-            If None the canonical names are used. Defaults to None.
-        name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Sequence[int] | Literal["auto"]): The chunk shape. If None the shape
-            is used. Defaults to None.
-        dtype (str, optional): The data type of the image. Defaults to "uint16".
-        dimension_separator (DIMENSION_SEPARATOR): The separator to use for
-            dimensions. Defaults to "/".
-        compressors (CompressorLike): The compressors to use. Defaults to "auto".
-        overwrite (bool, optional): Whether to overwrite an existing image.
-            Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
-            Defaults to DefaultVersion.
-
-    """
-    if axes_names is None:
-        axes_names = canonical_axes_order()[-len(shape) :]
-
-    if len(axes_names) != len(shape):
-        raise NgioValueError(
-            f"Number of axes names {axes_names} does not match the number of "
-            f"dimensions {shape}."
-        )
-
-    meta, scaling_factors = _init_generic_meta(
-        meta_type=NgioImageMeta,
-        pixelsize=pixelsize,
-        z_spacing=z_spacing,
-        time_spacing=time_spacing,
-        levels=levels,
-        yx_scaling_factor=yx_scaling_factor,
-        z_scaling_factor=z_scaling_factor,
-        space_unit=space_unit,
-        time_unit=time_unit,
-        axes_names=axes_names,
-        name=name,
-        version=version,
-    )
-    mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(
-        store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
-    )
-    image_handler = get_image_meta_handler(version=version, group_handler=group_handler)
-    image_handler.write_meta(meta)
-
-    init_empty_pyramid(
-        store=store,
-        paths=meta.paths,
-        scaling_factors=scaling_factors,
-        ref_shape=shape,
-        chunks=chunks,
-        axes=axes_names,
-        dtype=dtype,
-        mode="a",
-        dimension_separator=dimension_separator,
-        compressors=compressors,
-        zarr_format=meta.zarr_format,
-    )
-
-    group_handler._mode = "r+"
-    return group_handler

ngio/tables/backends/_non_zarr_backends.py

@@ -1,196 +0,0 @@
-import io
-from collections.abc import Callable
-from typing import Any
-
-from pandas import DataFrame
-from polars import DataFrame as PolarsDataFrame
-from polars import LazyFrame
-from zarr.storage import FsspecStore, LocalStore
-
-from ngio.tables.backends._abstract_backend import AbstractTableBackend
-from ngio.tables.backends._utils import normalize_pandas_df, normalize_polars_lf
-from ngio.utils import NgioFileNotFoundError, NgioValueError
-
-
-class NonZarrBaseBackend(AbstractTableBackend):
-    """A class to load and write small tables in CSV format."""
-
-    def __init__(
-        self,
-        df_reader: Callable[[Any], DataFrame],
-        lf_reader: Callable[[Any], LazyFrame],
-        df_writer: Callable[[str, DataFrame], None],
-        lf_writer: Callable[[str, PolarsDataFrame], None],
-        table_name: str,
-    ):
-        self.df_reader = df_reader
-        self.lf_reader = lf_reader
-        self.df_writer = df_writer
-        self.lf_writer = lf_writer
-        self.table_name = table_name
-
-    @staticmethod
-    def implements_anndata() -> bool:
-        """Whether the handler implements the anndata protocol."""
-        return False
-
-    @staticmethod
-    def implements_pandas() -> bool:
-        """Whether the handler implements the dataframe protocol."""
-        return True
-
-    @staticmethod
-    def implements_polars() -> bool:
-        """Whether the handler implements the polars protocol."""
-        return True
-
-    @staticmethod
-    def backend_name() -> str:
-        """Return the name of the backend."""
-        raise NotImplementedError(
-            "The backend_name method must be implemented in the subclass."
-        )
-
-    def _load_from_directory_store(self, reader):
-        """Load the table from a directory store."""
-        url = self._group_handler.full_url
-        if url is None:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support reading a {ext} table from a "
-                f"store of type {type(self._group_handler)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore."
-            )
-        table_path = f"{url}/{self.table_name}"
-        dataframe = reader(table_path)
-        return dataframe
-
-    def _load_from_fs_store_df(self, reader):
-        """Load the table from an FS store."""
-        path = self._group_handler.group.path
-        table_path = f"{path}/{self.table_name}"
-        bytes_table = self._group_handler.store.get(table_path)
-        if bytes_table is None:
-            raise NgioFileNotFoundError(f"No table found at {table_path}. ")
-        dataframe = reader(io.BytesIO(bytes_table))
-        return dataframe
-
-    def _load_from_fs_store_lf(self, reader):
-        """Load the table from an FS store."""
-        full_url = self._group_handler.full_url
-        parquet_path = f"{full_url}/{self.table_name}"
-        store_fs = self._group_handler.store.fs  # type: ignore (in this context, store_fs is a fs.FSStore)
-        with store_fs.open(parquet_path, "rb") as f:
-            dataframe = reader(f)
-        return dataframe
-
-    def load_as_pandas_df(self) -> DataFrame:
-        """Load the table as a pandas DataFrame."""
-        store = self._group_handler.store
-        if isinstance(store, LocalStore):
-            dataframe = self._load_from_directory_store(reader=self.df_reader)
-        elif isinstance(store, FsspecStore):
-            dataframe = self._load_from_fs_store_df(reader=self.df_reader)
-        else:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support reading a {ext} table from a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-
-        dataframe = normalize_pandas_df(
-            dataframe,
-            index_key=self.index_key,
-            index_type=self.index_type,
-            reset_index=False,
-        )
-        return dataframe
-
-    def load(self) -> DataFrame:
-        """Load the table as a pandas DataFrame."""
-        return self.load_as_pandas_df()
-
-    def load_as_polars_lf(self) -> LazyFrame:
-        """Load the table as a polars LazyFrame."""
-        store = self._group_handler.store
-        if isinstance(store, LocalStore):
-            lazy_frame = self._load_from_directory_store(reader=self.lf_reader)
-        elif isinstance(store, FsspecStore):
-            lazy_frame = self._load_from_fs_store_lf(reader=self.lf_reader)
-        else:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support reading a {ext} from a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-        if not isinstance(lazy_frame, LazyFrame):
-            raise NgioValueError(
-                "Table is not a lazy frame. Please report this issue as an ngio bug."
-                f" {type(lazy_frame)}"
-            )
-
-        lazy_frame = normalize_polars_lf(
-            lazy_frame,
-            index_key=self.index_key,
-            index_type=self.index_type,
-        )
-        return lazy_frame
-
-    def _get_store_url(self) -> str:
-        """Get the store URL."""
-        store = self._group_handler.store
-        if isinstance(store, LocalStore):
-            full_url = self._group_handler.full_url
-        else:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support writing a {ext} file to a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-        if full_url is None:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support writing a {ext} file to a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-        return full_url
-
-    def write_from_pandas(self, table: DataFrame) -> None:
-        """Write the table from a pandas DataFrame."""
-        table = normalize_pandas_df(
-            table,
-            index_key=self.index_key,
-            index_type=self.index_type,
-            reset_index=True,
-        )
-        full_url = self._get_store_url()
-        table_path = f"{full_url}/{self.table_name}"
-        self.df_writer(table_path, table)
-
-    def write_from_polars(self, table: PolarsDataFrame | LazyFrame) -> None:
-        """Write the table from a polars DataFrame or LazyFrame."""
-        table = normalize_polars_lf(
-            table,
-            index_key=self.index_key,
-            index_type=self.index_type,
-        )
-
-        if isinstance(table, LazyFrame):
-            table = table.collect()
-
-        full_url = self._get_store_url()
-        table_path = f"{full_url}/{self.table_name}"
-        self.lf_writer(table_path, table)