ngio 0.3.1__py3-none-any.whl → 0.3.2__py3-none-any.whl

ngio/common/_roi.py

@@ -57,6 +57,7 @@ class Roi(BaseModel):
             x_length=_to_raster(self.x_length, pixel_size.x, dim_x),
             y_length=_to_raster(self.y_length, pixel_size.y, dim_y),
             z_length=_to_raster(self.z_length, pixel_size.z, dim_z),
+            **self.model_extra,
         )
 
     def zoom(self, zoom_factor: float = 1) -> "Roi":
@@ -94,6 +95,7 @@ class RoiPixels(BaseModel):
             y_length=_to_world(self.y_length, pixel_size.y),
             z_length=_to_world(self.z_length, pixel_size.z),
             unit=pixel_size.space_unit,
+            **self.model_extra,
         )
 
     def to_slices(self) -> dict[str, slice]:

ngio/hcs/_plate.py

@@ -27,6 +27,7 @@ from ngio.ome_zarr_meta import (
 )
 from ngio.tables import (
     ConditionTable,
+    DefaultTableBackend,
     FeatureTable,
     GenericRoiTable,
     MaskingRoiTable,
@@ -944,7 +945,7 @@ class OmeZarrPlate:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the image."""

ngio/images/_ome_zarr_container.py

@@ -23,6 +23,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
 )
 from ngio.tables import (
     ConditionTable,
+    DefaultTableBackend,
     FeatureTable,
     GenericRoiTable,
     MaskingRoiTable,
@@ -501,7 +502,7 @@ class OmeZarrContainer:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the image."""
@@ -831,7 +832,7 @@ def create_ome_zarr_from_array(
         axes_names=axes_names,
         name=name,
         chunks=chunks,
-        dtype=array.dtype,
+        dtype=str(array.dtype),
         overwrite=overwrite,
         version=version,
     )

ngio/tables/__init__.py

@@ -15,6 +15,7 @@ from ngio.tables._tables_container import (
     open_tables_container,
 )
 from ngio.tables.backends import (
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -23,6 +24,7 @@ from ngio.tables.v1._generic_table import GenericTable
 
 __all__ = [
     "ConditionTable",
+    "DefaultTableBackend",
     "FeatureTable",
     "GenericRoiTable",
     "GenericTable",

ngio/tables/_abstract_table.py

@@ -10,6 +10,7 @@ from anndata import AnnData
 
 from ngio.tables.backends import (
     BackendMeta,
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -203,7 +204,7 @@ class AbstractBaseTable(ABC):
     def set_backend(
         self,
         handler: ZarrGroupHandler | None = None,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
     ) -> None:
         """Set the backend of the table."""
         if handler is None:

ngio/tables/_tables_container.py

@@ -8,6 +8,7 @@ import polars as pl
 
 from ngio.tables.backends import (
     BackendMeta,
+    DefaultTableBackend,
     TableBackend,
     TabularData,
 )
@@ -90,7 +91,7 @@ class Table(Protocol):
     def set_backend(
         self,
         handler: ZarrGroupHandler | None = None,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
     ) -> None:
         """Set the backend store and path for the table.
 
@@ -314,7 +315,7 @@ class TablesContainer:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the group."""
@@ -406,7 +407,7 @@ def open_table_as(
 def write_table(
     store: StoreOrGroup,
     table: Table,
-    backend: TableBackend = "anndata",
+    backend: TableBackend = DefaultTableBackend,
     cache: bool = False,
     mode: AccessModeLiteral = "a",
     parallel_safe: bool = False,

ngio/tables/backends/__init__.py

@@ -6,6 +6,7 @@ from ngio.tables.backends._csv import CsvTableBackend
 from ngio.tables.backends._json import JsonTableBackend
 from ngio.tables.backends._parquet import ParquetTableBackend
 from ngio.tables.backends._table_backends import (
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -32,6 +33,7 @@ __all__ = [
     "AnnDataBackend",
     "BackendMeta",
     "CsvTableBackend",
+    "DefaultTableBackend",
     "ImplementedTableBackends",
     "JsonTableBackend",
     "ParquetTableBackend",

ngio/tables/backends/_abstract_backend.py

@@ -19,7 +19,7 @@ from ngio.utils import NgioValueError, ZarrGroupHandler
 class BackendMeta(BaseModel):
     """Metadata for the backend."""
 
-    backend: str = "anndata"
+    backend: str = "anndata_v1"
     index_key: str | None = None
     index_type: Literal["int", "str"] | None = None
 

ngio/tables/backends/_table_backends.py

@@ -223,3 +223,4 @@ ImplementedTableBackends().add_backend(
 )
 
 TableBackend = Literal["anndata", "json", "csv", "parquet"] | str | TableBackendProtocol
+DefaultTableBackend = "anndata_v1"

ngio/tables/v1/_roi_table.py

@@ -47,11 +47,20 @@ REQUIRED_COLUMNS = [
 ORIGIN_COLUMNS = [
     "x_micrometer_original",
     "y_micrometer_original",
+    "z_micrometer_original",
 ]
 
 TRANSLATION_COLUMNS = ["translation_x", "translation_y", "translation_z"]
 
-PLATE_COLUMNS = ["plate_name", "row", "column", "path", "acquisition"]
+PLATE_COLUMNS = [
+    "plate_name",
+    "row",
+    "column",
+    "path_in_well",
+    "path_in_plate",
+    "acquisition_id",
+    "acquisition_name",
+]
 
 INDEX_COLUMNS = [
     "FieldIndex",
@@ -390,7 +399,8 @@ class MaskingRoiTableV1(GenericRoiTableV1):
             meta = MaskingRoiTableV1Meta()
 
         if reference_label is not None:
-            meta.region = RegionMeta(path=reference_label)
+            path = f"../labels/{reference_label}"
+            meta.region = RegionMeta(path=path)
 
         if meta.index_key is None:
             meta.index_key = "label"

{ngio-0.3.1.dist-info → ngio-0.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.1
+Version: 0.3.2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
 Project-URL: repository, https://github.com/fractal-analytics-platform/ngio

{ngio-0.3.1.dist-info → ngio-0.3.2.dist-info}/RECORD

@@ -6,19 +6,19 @@ ngio/common/_common_types.py,sha256=OkAYNSNjZkixL1MI-HPBVuXamheFBr862uJ4PvTxmhk,
 ngio/common/_dimensions.py,sha256=UV2XulWaROb3Y2f4fv27ZkTIu-MoS53U26aDkrv-_lk,3900
 ngio/common/_masking_roi.py,sha256=-o6meGP17iTXEbkO9aGh1VX2drkc2laIcRJvCy_pRRM,4919
 ngio/common/_pyramid.py,sha256=SJzPauuduuqcm9B7nFCJhMTzIg6Knjsnp4CY4lN61Is,7411
-ngio/common/_roi.py,sha256=dq1iVT8-G_zWuxcYWJeHfviBSbPgsyKUcDL3Vg6jx6I,5122
+ngio/common/_roi.py,sha256=xJZ3vSusxhM1wXOizyjPbgzYhneva4IlhaWQc13Kuk4,5186
 ngio/common/_slicer.py,sha256=AKpwXRncOmF9nhjKYma0C_41WqAgSv860beKGx-aw-0,3075
 ngio/common/_table_ops.py,sha256=ToNR7F053l1dubVv-gvBD-523T10HnE2UzqeU2BuNy8,15494
 ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
-ngio/hcs/_plate.py,sha256=Z8M3slG5t16MYvPwvAzj-e9O4yAswWZp7_EDBlAxiHc,44225
+ngio/hcs/_plate.py,sha256=o8g4WkbFPABV8mBRqyVLbLrKhwFvsf94LwwcBZac_7A,44260
 ngio/images/__init__.py,sha256=PlYvbHOMvZLDgn_PeGrytOEU3e_-AO8GWpRjEqoX_Gw,536
 ngio/images/_abstract_image.py,sha256=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
 ngio/images/_create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
 ngio/images/_image.py,sha256=B9MTk3Cei-FBR4jbhSujTSNcKM_ySape28yXR_JlY0A,17980
 ngio/images/_label.py,sha256=Q1vPrXDcjJ7Gdd0wDz6NCVYQLNe1Ae6YDI4iK0oq31s,10557
 ngio/images/_masked_image.py,sha256=sd6aQetNVwtDkwUvKX-lssQyHzt5m-CYZL8ZFkwDSn8,8533
-ngio/images/_ome_zarr_container.py,sha256=hRx_8CPtFpxQUcprTT4_k5L5pjMUJ6t4wJaYr1tyljw,31181
+ngio/images/_ome_zarr_container.py,sha256=CygzzFMYFT35ztLSPKe6iKLzCtgCnVWk8M9xOj6Tc5U,31221
 ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=ctknNDT8jxwyvxQf9on5gW31H1tRRsnneO38GT2UXoE,25880
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImGSAOK3D3Bg-Js,1786
@@ -31,31 +31,31 @@ ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=5TT8250XdCKUnk3OwZeyXIMNFKOg
 ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
 ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R0R_9rSaa85A,530
 ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=05tEr2eEP_XVIfBMOAWLT7lzJV4KS5eYrpK8l94tn3w,15876
-ngio/tables/__init__.py,sha256=rJGcyQUlHQb_ZbeMM9ICD8_mhTE2X9H5nKp0J-z9tMM,825
-ngio/tables/_abstract_table.py,sha256=naAeDsPTVjDUOnAxj_57UWXApg_nyWCsWdZ0f7bm740,8169
-ngio/tables/_tables_container.py,sha256=a2NNExiP1HqFVJ6HPLn0nEkYHLdf2LONVz5OxoH7OkY,12118
-ngio/tables/backends/__init__.py,sha256=tx97ZkK5kF_sAGU2kf_ZI9JxbOXn8GVjE0rUUq9h-QM,1525
-ngio/tables/backends/_abstract_backend.py,sha256=jtai3AqcLNZyxYyK0rernbMtcwxWhWAahCS0fPlMNls,7454
+ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
+ngio/tables/_abstract_table.py,sha256=rwGa47TzbFmosucBWVfFq6JEXtgGvOdUVtU9DIelV88,8204
+ngio/tables/_tables_container.py,sha256=w1rT_5kMh23OHXpFJI3edTH1-tul0YLIYY6x5lMn2k4,12173
+ngio/tables/backends/__init__.py,sha256=nQZVazwTL1IHU08gL-BZcFZd7Cehhbc_AsJ3t3XSps0,1577
+ngio/tables/backends/_abstract_backend.py,sha256=tsbHzSPTX88fiCbVc8khXv5aN68ck6HKG8r5OHkY3S8,7457
 ngio/tables/backends/_anndata.py,sha256=8RX2NO15CLxys3p6gw54Nd-_0WATU4WBlNndX06wvzI,2587
 ngio/tables/backends/_anndata_utils.py,sha256=DBWIcR0btnH-DIvDvzlcnMXoYhhtXc9DstryiOP0Qsg,3122
 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=SvPPhT6n5TrKUOyV1mNcdHQK49huZ5lwR8EVe9MdydM,7254
 ngio/tables/backends/_parquet.py,sha256=ic-p86h8lce8q9luBJGRzy6vxlWyJvA0-2l5cUD6OqY,1398
-ngio/tables/backends/_table_backends.py,sha256=E4b1p_ZqRmEf3JK_Wp05r2J-q-PZQU_B1qFluBrjU9Q,7232
+ngio/tables/backends/_table_backends.py,sha256=QUS59VU395966AEul2SNJQAzklSitvISL0wnZTKWZa0,7267
 ngio/tables/backends/_utils.py,sha256=tJBSWN6OhO_1ybxl4vT2l3ImB028Fb6h0vaitPRcr8A,19668
 ngio/tables/v1/__init__.py,sha256=Wr1_9RZFpaN8FYMTnxT9Yjkw4AS7y9FMWailmB_uj5g,617
 ngio/tables/v1/_condition_table.py,sha256=IMU3sds8wrKGqU-C20HbpFCVGZX1L_V7Sh8f7CHB_x0,1781
 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=Q1dBQqPvxqBOqatGzYTAbxmgEnEkBawpSbCL38YBnE0,13456
+ngio/tables/v1/_roi_table.py,sha256=DgXhp-DHTeEJwzSsSRSlnPghjMhYGa3IGSpwTt5LKZU,13603
 ngio/utils/__init__.py,sha256=r3nuLWgp6-cQlS4ODjYSBrfgdTLkCOVke9jKbn1NpkA,1129
 ngio/utils/_datasets.py,sha256=EdYJHIifpRou4f43dIuiKsdxe4K6FaeS4f1_e_EYrcI,1727
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
 ngio/utils/_logger.py,sha256=HIuqD_2ShfFGDswBddcouStbKfL0Vz_ah8cAIFGhbS8,888
 ngio/utils/_zarr_utils.py,sha256=qOI-HL2HsfFLCj_yxsTR-aq4oHpSqS9KR13aEIvhGDY,13593
-ngio-0.3.1.dist-info/METADATA,sha256=6KnWDNEe6TWTYu4kKvT9uJR6D6uikMu0W6VOgXoNXcw,5868
-ngio-0.3.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.3.1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.3.1.dist-info/RECORD,,
+ngio-0.3.2.dist-info/METADATA,sha256=lTCmsFw4q7EZUvjlH6aSpnqVDnUnP025vdUrp1o7pyY,5868
+ngio-0.3.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.3.2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.3.2.dist-info/RECORD,,