ngio 0.3.1__tar.gz → 0.3.2__tar.gz

ngio-0.3.2/.github/pull_request_template.md

@@ -0,0 +1,3 @@
+
+## Checklist before merging
+- [ ] I added an appropriate entry to `CHANGELOG.md`

ngio-0.3.2/CHANGELOG.md

@@ -0,0 +1,12 @@
+# Changelog
+
+## [v0.3.2]
+
+### API Changes
+
+- change table backend default to `anndata_v1` for backward compatibility. This will be chaanged again when ngio `v0.2.x` is no longer supported.
+
+### Bug Fixes
+
+- fix [#13](https://github.com/fractal-analytics-platform/fractal-converters-tools/issues/13) (converters tools)
+- fix [#88](https://github.com/fractal-analytics-platform/ngio/issues/88)

{ngio-0.3.1 → ngio-0.3.2}/PKG-INFO

@@ -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 → ngio-0.3.2}/docs/table_specs/table_types/roi_table.md

@@ -33,7 +33,7 @@ Moreover the ROI table must include the following columns:
 
 Additionally, each ROI can include the following optional columns:
 
-- `x_micrometer_original` and `y_micrometer_original` which are the original coordinates of the ROI in micrometers. These are typically used when the data is saved in different coordinates during conversion, e.g. to avoid overwriting data from overlapping ROIs.
+- `x_micrometer_original`, `y_micrometer_original` and `z_micrometer_original` which are the original coordinates of the ROI in micrometers. These are typically used when the data is saved in different coordinates during conversion, e.g. to avoid overwriting data from overlapping ROIs.
 - `translation_x`, `translation_y` and `translation_z`, which are used during registration of multiplexing acquisitions.
 
 The user can also add additional columns to the ROI table, but these columns will not be exposed in the ROI table API.

{ngio-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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-0.3.1 → ngio-0.3.2}/src/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 → ngio-0.3.2}/tests/unit/common/test_roi.py

@@ -41,3 +41,4 @@ def test_rois():
     assert world_roi_2.x_length == 1.0
     assert world_roi_2.y_length == 1.0
     assert world_roi_2.z_length == 1.0
+    assert world_roi_2.other == "other"

{ngio-0.3.1 → ngio-0.3.2}/tests/unit/tables/test_masking_roi_table_v1.py

@@ -24,6 +24,8 @@ def test_masking_roi_table_v1(tmp_path: Path):
     table = MaskingRoiTableV1(rois=rois.values(), reference_label="label")
     assert isinstance(table.__repr__(), str)
     assert table.reference_label == "label"
+    assert table.meta.region is not None
+    assert table.meta.region.path == "../labels/label"
 
     table.add(
         roi=Roi(

ngio-0.3.1/CHANGELOG.md

@@ -1,7 +0,0 @@
-# Changelog
-
-## [Unreleased]
-
-### Added
-
-- Initial version of the changelog.