ngio 0.2.0b3__py3-none-any.whl → 0.2.2__py3-none-any.whl

ngio/ome_zarr_meta/ngio_specs/_pixel_size.py

@@ -5,7 +5,12 @@ from functools import total_ordering
 
 import numpy as np
 
-from ngio.ome_zarr_meta.ngio_specs import SpaceUnits, TimeUnits
+from ngio.ome_zarr_meta.ngio_specs import (
+    DefaultSpaceUnit,
+    DefaultTimeUnit,
+    SpaceUnits,
+    TimeUnits,
+)
 
 ################################################################################################
 #
@@ -33,8 +38,8 @@ class PixelSize:
         y: float,
         z: float,
         t: float = 1,
-        space_unit: SpaceUnits = SpaceUnits.micrometer,
-        time_unit: TimeUnits | None = TimeUnits.s,
+        space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
+        time_unit: TimeUnits | str | None = DefaultTimeUnit,
     ):
         """Initialize the pixel size."""
         self.x = _validate_type(x, "x")
@@ -42,13 +47,8 @@ class PixelSize:
         self.z = _validate_type(z, "z")
         self.t = _validate_type(t, "t")
 
-        if not isinstance(space_unit, SpaceUnits):
-            raise TypeError("space_unit must be of type SpaceUnits.")
-        self.space_unit = space_unit
-
-        if time_unit is not None and not isinstance(time_unit, TimeUnits):
-            raise TypeError("time_unit must be of type TimeUnits.")
-        self.time_unit = time_unit
+        self._space_unit = space_unit
+        self._time_unit = time_unit
 
     def __repr__(self) -> str:
         """Return a string representation of the pixel size."""
@@ -74,13 +74,30 @@ class PixelSize:
         """Check if one pixel size is less than the other."""
         if not isinstance(other, PixelSize):
             raise TypeError("Can only compare PixelSize with PixelSize.")
-        ref = PixelSize(0, 0, 0, 0, self.space_unit, self.time_unit)
+        ref = PixelSize(
+            0,
+            0,
+            0,
+            0,
+            space_unit=self.space_unit,
+            time_unit=self.time_unit,  # type: ignore
+        )
         return self.distance(ref) < other.distance(ref)
 
     def as_dict(self) -> dict:
         """Return the pixel size as a dictionary."""
         return {"t": self.t, "z": self.z, "y": self.y, "x": self.x}
 
+    @property
+    def space_unit(self) -> SpaceUnits | str | None:
+        """Return the space unit."""
+        return self._space_unit
+
+    @property
+    def time_unit(self) -> TimeUnits | str | None:
+        """Return the time unit."""
+        return self._time_unit
+
     @property
     def tzyx(self) -> tuple[float, float, float, float]:
         """Return the voxel size in t, z, y, x order."""

ngio/ome_zarr_meta/v04/_custom_models.py

@@ -0,0 +1,18 @@
+from typing import Annotated
+
+from ome_zarr_models.v04.well import WellAttrs as WellAttrs04
+from ome_zarr_models.v04.well_types import WellImage as WellImage04
+from ome_zarr_models.v04.well_types import WellMeta as WellMeta04
+from pydantic import SkipValidation
+
+
+class CustomWellImage(WellImage04):
+    path: Annotated[str, SkipValidation]
+
+
+class CustomWellMeta(WellMeta04):
+    images: list[CustomWellImage]  # type: ignore[valid-type]
+
+
+class CustomWellAttrs(WellAttrs04):
+    well: CustomWellMeta  # type: ignore[valid-type]

ngio/ome_zarr_meta/v04/_v04_spec_utils.py

@@ -23,7 +23,6 @@ from ome_zarr_models.v04.multiscales import Multiscale as MultiscaleV04
 from ome_zarr_models.v04.omero import Channel as ChannelV04
 from ome_zarr_models.v04.omero import Omero as OmeroV04
 from ome_zarr_models.v04.omero import Window as WindowV04
-from ome_zarr_models.v04.well import WellAttrs as WellAttrsV04
 from pydantic import ValidationError
 
 from ngio.ome_zarr_meta.ngio_specs import (
@@ -41,7 +40,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     NgioWellMeta,
     default_channel_name,
 )
-from ngio.ome_zarr_meta.ngio_specs._ngio_image import NgffVersion
+from ngio.ome_zarr_meta.v04._custom_models import CustomWellAttrs as WellAttrsV04
 
 
 def _is_v04_image_meta(metadata: dict) -> ImageAttrsV04 | ValidationError:
@@ -290,7 +289,7 @@ def v04_to_ngio_label_meta(
         else:
             image_label_source = source.image
         image_label_source = ImageLabelSource(
-            version=NgffVersion.v04,
+            version="0.4",
             source={"image": image_label_source},
         )
     name = v04_muliscale.name
@@ -322,7 +321,7 @@ def _ngio_to_v04_multiscale(name: str | None, datasets: list[Dataset]) -> Multis
             AxisV04(
                 name=axis.on_disk_name,
                 type=axis.axis_type.value if axis.axis_type is not None else None,
-                unit=axis.unit.value if axis.unit is not None else None,
+                unit=axis.unit if axis.unit is not None else None,
             )
         )
 

ngio/tables/__init__.py

@@ -4,7 +4,7 @@ from ngio.tables.backends import ImplementedTableBackends
 from ngio.tables.tables_container import (
     FeatureTable,
     GenericRoiTable,
-    MaskingROITable,
+    MaskingRoiTable,
     RoiTable,
     Table,
     TablesContainer,
@@ -19,7 +19,7 @@ __all__ = [
     "GenericRoiTable",
     "GenericTable",
     "ImplementedTableBackends",
-    "MaskingROITable",
+    "MaskingRoiTable",
     "RoiTable",
     "Table",
     "TablesContainer",

ngio/tables/tables_container.py

@@ -2,7 +2,7 @@
 
 from typing import Literal, Protocol
 
-from ngio.tables.v1 import FeatureTableV1, MaskingROITableV1, RoiTableV1
+from ngio.tables.v1 import FeatureTableV1, MaskingRoiTableV1, RoiTableV1
 from ngio.tables.v1._generic_table import GenericTable
 from ngio.tables.v1._roi_table import _GenericRoiTableV1
 from ngio.utils import (
@@ -15,7 +15,7 @@ from ngio.utils import (
 
 GenericRoiTable = _GenericRoiTableV1
 RoiTable = RoiTableV1
-MaskingROITable = MaskingROITableV1
+MaskingRoiTable = MaskingRoiTableV1
 FeatureTable = FeatureTableV1
 
 
@@ -253,7 +253,7 @@ class TablesContainer:
 
 
 ImplementedTables().add_implementation(RoiTableV1)
-ImplementedTables().add_implementation(MaskingROITableV1)
+ImplementedTables().add_implementation(MaskingRoiTableV1)
 ImplementedTables().add_implementation(FeatureTableV1)
 
 ###################################################################################

ngio/tables/v1/__init__.py

@@ -2,6 +2,6 @@
 
 from ngio.tables.v1._feature_table import FeatureTableV1
 from ngio.tables.v1._generic_table import GenericTable
-from ngio.tables.v1._roi_table import MaskingROITableV1, RoiTableV1
+from ngio.tables.v1._roi_table import MaskingRoiTableV1, RoiTableV1
 
-__all__ = ["FeatureTableV1", "GenericTable", "MaskingROITableV1", "RoiTableV1"]
+__all__ = ["FeatureTableV1", "GenericTable", "MaskingRoiTableV1", "RoiTableV1"]

ngio/tables/v1/_feature_table.py

@@ -49,7 +49,6 @@ class FeatureTableV1:
             path = f"../labels/{reference_label}"
             self._meta = FeatureTableMeta(region=RegionMeta(path=path))
 
-        self._reference_label = reference_label
         self._instance_key = "label"
         if dataframe is None:
             self._dataframe = None
@@ -59,6 +58,15 @@ class FeatureTableV1:
             )
         self._table_backend = None
 
+    def __repr__(self) -> str:
+        """Return a string representation of the table."""
+        num_rows = len(self.dataframe) if self.dataframe is not None else 0
+        num_columns = len(self.dataframe.columns) if self.dataframe is not None else 0
+        properties = f"num_rows={num_rows}, num_columns={num_columns}"
+        if self.reference_label is not None:
+            properties += f", reference_label={self.reference_label}"
+        return f"FeatureTableV1({properties})"
+
     @staticmethod
     def type() -> str:
         """Return the type of the table."""
@@ -79,6 +87,17 @@ class FeatureTableV1:
             return None
         return self._table_backend.backend_name()
 
+    @property
+    def reference_label(self) -> str | None:
+        """Return the reference label."""
+        path = self._meta.region
+        if path is None:
+            return None
+
+        path = path.path
+        path = path.split("/")[-1]
+        return path
+
     @property
     def dataframe(self) -> pd.DataFrame:
         """Return the table as a DataFrame."""

ngio/tables/v1/_generic_table.py

@@ -51,6 +51,16 @@ class GenericTable:
 
         self._table_backend = None
 
+    def __repr__(self) -> str:
+        """Return a string representation of the table."""
+        if self._dataframe is not None:
+            num_rows = len(self.dataframe)
+            num_columns = len(self.dataframe.columns)
+            prop = f"num_rows={num_rows}, num_columns={num_columns}, mode=dataframe"
+        else:
+            prop = "mode=anndata"
+        return f"GenericTable({prop})"
+
     @staticmethod
     def type() -> str:
         """Return the type of the table."""

ngio/tables/v1/_roi_table.py

@@ -12,7 +12,7 @@ from typing import Generic, Literal, TypeVar
 import pandas as pd
 from pydantic import BaseModel
 
-from ngio.common import WorldCooROI
+from ngio.common import Roi
 from ngio.tables._validators import validate_columns
 from ngio.tables.backends import ImplementedTableBackends
 from ngio.utils import NgioValueError, ZarrGroupHandler
@@ -37,7 +37,7 @@ TRANSLATION_COLUMNS = ["translation_x", "translation_y", "translation_z"]
 OPTIONAL_COLUMNS = ORIGIN_COLUMNS + TRANSLATION_COLUMNS
 
 
-def _dataframe_to_rois(dataframe: pd.DataFrame) -> dict[str, WorldCooROI]:
+def _dataframe_to_rois(dataframe: pd.DataFrame) -> dict[str, Roi]:
     """Convert a DataFrame to a WorldCooROI object."""
     rois = {}
     for key, row in dataframe.iterrows():
@@ -47,7 +47,7 @@ def _dataframe_to_rois(dataframe: pd.DataFrame) -> dict[str, WorldCooROI]:
         translation = {col: row.get(col, None) for col in TRANSLATION_COLUMNS}
         translation = dict(filter(lambda x: x[1] is not None, translation.items()))
 
-        roi = WorldCooROI(
+        roi = Roi(
             name=str(key),
             x=row["x_micrometer"],
             y=row["y_micrometer"],
@@ -63,7 +63,7 @@ def _dataframe_to_rois(dataframe: pd.DataFrame) -> dict[str, WorldCooROI]:
     return rois
 
 
-def _rois_to_dataframe(rois: dict[str, WorldCooROI], index_key: str) -> pd.DataFrame:
+def _rois_to_dataframe(rois: dict[str, Roi], index_key: str) -> pd.DataFrame:
     """Convert a list of WorldCooROI objects to a DataFrame."""
     data = []
     for roi in rois.values():
@@ -124,7 +124,7 @@ class _GenericRoiTableV1(Generic[_roi_meta]):
     _meta: _roi_meta
 
     def __init__(
-        self, meta: _roi_meta | None = None, rois: Iterable[WorldCooROI] | None = None
+        self, meta: _roi_meta | None = None, rois: Iterable[Roi] | None = None
     ) -> None:
         """Create a new ROI table."""
         if meta is None:
@@ -225,13 +225,13 @@ class _GenericRoiTableV1(Generic[_roi_meta]):
         self._meta.backend = backend_name
         self._table_backend = backend
 
-    def rois(self) -> list[WorldCooROI]:
+    def rois(self) -> list[Roi]:
         """List all ROIs in the table."""
         return list(self._rois.values())
 
-    def add(self, roi: WorldCooROI | Iterable[WorldCooROI]) -> None:
+    def add(self, roi: Roi | Iterable[Roi]) -> None:
         """Append ROIs to the current table."""
-        if isinstance(roi, WorldCooROI):
+        if isinstance(roi, Roi):
             roi = [roi]
 
         for _roi in roi:
@@ -266,10 +266,15 @@ class RoiTableV1(_GenericRoiTableV1[RoiTableV1Meta]):
     https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
     """
 
-    def __init__(self, rois: Iterable[WorldCooROI] | None = None) -> None:
+    def __init__(self, rois: Iterable[Roi] | None = None) -> None:
         """Create a new ROI table."""
         super().__init__(RoiTableV1Meta(), rois)
 
+    def __repr__(self) -> str:
+        """Return a string representation of the table."""
+        prop = f"num_rois={len(self._rois)}"
+        return f"RoiTableV1({prop})"
+
     @staticmethod
     def type() -> Literal["roi_table"]:
         """Return the type of the table."""
@@ -290,14 +295,14 @@ class RoiTableV1(_GenericRoiTableV1[RoiTableV1Meta]):
         """Return the metadata type of the table."""
         return RoiTableV1Meta
 
-    def get(self, roi_name: str) -> WorldCooROI:
+    def get(self, roi_name: str) -> Roi:
         """Get an ROI from the table."""
         if roi_name not in self._rois:
             raise NgioValueError(f"ROI {roi_name} not found in the table.")
         return self._rois[roi_name]
 
 
-class MaskingROITableV1(_GenericRoiTableV1[MaskingRoiTableV1Meta]):
+class MaskingRoiTableV1(_GenericRoiTableV1[MaskingRoiTableV1Meta]):
     """Class to handle fractal ROI tables.
 
     To know more about the ROI table format, please refer to the
@@ -307,7 +312,7 @@ class MaskingROITableV1(_GenericRoiTableV1[MaskingRoiTableV1Meta]):
 
     def __init__(
         self,
-        rois: Iterable[WorldCooROI] | None = None,
+        rois: Iterable[Roi] | None = None,
         reference_label: str | None = None,
     ) -> None:
         """Create a new ROI table."""
@@ -316,6 +321,13 @@ class MaskingROITableV1(_GenericRoiTableV1[MaskingRoiTableV1Meta]):
             meta.region = RegionMeta(path=reference_label)
         super().__init__(meta, rois)
 
+    def __repr__(self) -> str:
+        """Return a string representation of the table."""
+        prop = f"num_rois={len(self._rois)}"
+        if self.reference_label is not None:
+            prop += f", reference_label={self.reference_label}"
+        return f"MaskingRoiTableV1({prop})"
+
     @staticmethod
     def type() -> Literal["masking_roi_table"]:
         """Return the type of the table."""
@@ -336,7 +348,17 @@ class MaskingROITableV1(_GenericRoiTableV1[MaskingRoiTableV1Meta]):
         """Return the metadata type of the table."""
         return MaskingRoiTableV1Meta
 
-    def get(self, label: int) -> WorldCooROI:
+    @property
+    def reference_label(self) -> str | None:
+        """Return the reference label."""
+        path = self._meta.region
+        if path is None:
+            return None
+        path = path.path
+        path = path.split("/")[-1]
+        return path
+
+    def get(self, label: int) -> Roi:
         """Get an ROI from the table."""
         _label = str(label)
         if _label not in self._rois:

{ngio-0.2.0b3.dist-info → ngio-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.0b3
+Version: 0.2.2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -41,6 +41,8 @@ Requires-Dist: rich; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: scikit-image; extra == 'dev'
 Provides-Extra: docs
+Requires-Dist: markdown-exec[ansi]; extra == 'docs'
+Requires-Dist: matplotlib; extra == 'docs'
 Requires-Dist: mike; extra == 'docs'
 Requires-Dist: mkdocs; extra == 'docs'
 Requires-Dist: mkdocs-autorefs; extra == 'docs'
@@ -49,7 +51,9 @@ Requires-Dist: mkdocs-git-revision-date-localized-plugin; extra == 'docs'
 Requires-Dist: mkdocs-jupyter; extra == 'docs'
 Requires-Dist: mkdocs-material; extra == 'docs'
 Requires-Dist: mkdocstrings[python]; extra == 'docs'
+Requires-Dist: rich; extra == 'docs'
 Requires-Dist: scikit-image; extra == 'docs'
+Requires-Dist: tabulate; extra == 'docs'
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
@@ -69,9 +73,9 @@ NGIO is a Python library to streamline OME-Zarr image analysis workflows.
 **Main Goals:**
 
 - Abstract object base API for handling OME-Zarr files
-- Powefull iterators for processing data using common access patterns
+- Powerful iterators for processing data using common access patterns
 - Tight integration with [Fractal's Table Fractal](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/)
-- Validate OME-Zarr files
+- Validation of OME-Zarr files
 
 To get started, check out the [Getting Started](https://fractal-analytics-platform.github.io/ngio/getting-started/) guide. Or checkout our [Documentation](https://fractal-analytics-platform.github.io/ngio/)
 
@@ -91,10 +95,9 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | Basic Iterators | Ongoing | End-September | Read and Write Iterators for common access patterns |
 | Base Documentation | ✅ | End-September | API Documentation and Examples |
 | Beta Ready Testing | ✅ | End-September | Beta Testing; Library is ready for testing, but the API is not stable |
-| Streaming from Fractal | Ongoing | December | Ngio can stream ome-zarr from fractal |
+| Streaming from Fractal | Ongoing | December | Ngio can stream OME-Zarr from fractal |
 | Mask Iterators | Ongoing | Early 2025 | Iterators over Masked Tables |
 | Advanced Iterators | Not started | mid-2025 | Iterators for advanced access patterns |
 | Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |
 | Full Documentation | Not started | 2025 | Complete Documentation |
 | Release 1.0 (Commitment to API) | Not started | 2025 | API is stable; breaking changes will be avoided |
-

ngio-0.2.2.dist-info/RECORD

@@ -0,0 +1,55 @@
+ngio/__init__.py,sha256=zce-RIfRhkiFyfKwO6s7A1-9ZCD3n6RuVuW3GeRj_VA,1309
+ngio/common/__init__.py,sha256=tMKp1eZzGfpdKDkpfHn0iVzSO11dmp-RZARpuxoGGQk,1351
+ngio/common/_array_pipe.py,sha256=we3gZLhgUsiPQwPQqg_XVkyG_9EpQ2xoe0L_nOALDho,7828
+ngio/common/_axes_transforms.py,sha256=kWU0M5erNmgWBXdu5LNv-tLW3jqkT00MMYX7cz-kyHs,2035
+ngio/common/_common_types.py,sha256=OkAYNSNjZkixL1MI-HPBVuXamheFBr862uJ4PvTxmhk,129
+ngio/common/_dimensions.py,sha256=UV2XulWaROb3Y2f4fv27ZkTIu-MoS53U26aDkrv-_lk,3900
+ngio/common/_masking_roi.py,sha256=-o6meGP17iTXEbkO9aGh1VX2drkc2laIcRJvCy_pRRM,4919
+ngio/common/_pyramid.py,sha256=8xTFnrKcldYXSnBqcVtH1E6hzS9_et8NdoPo8zfTCjc,7308
+ngio/common/_roi.py,sha256=dq1iVT8-G_zWuxcYWJeHfviBSbPgsyKUcDL3Vg6jx6I,5122
+ngio/common/_slicer.py,sha256=AKpwXRncOmF9nhjKYma0C_41WqAgSv860beKGx-aw-0,3075
+ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
+ngio/hcs/__init__.py,sha256=5oAYT_454WGhms97kxo8gS4_rKHtFf_x-9uu8M_VeVM,356
+ngio/hcs/plate.py,sha256=Upmq8-1zi0rWtsTVHsZYAma6EwvbgaEF54nHlcL5PBU,26219
+ngio/images/__init__.py,sha256=DYbXAdBgPxyjBRdJrWvU0UnBRI0gUMmx9KaJ-Bucvz4,533
+ngio/images/abstract_image.py,sha256=oR0CeWUdQJkJ8bbI4kegX3xFIRcR3x5F_yaT4Z-mbag,10226
+ngio/images/create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
+ngio/images/image.py,sha256=FSlYvwOk3Fz4ywUZwWcLeCMWLMB4wQ-U0lCGYomVI-o,16108
+ngio/images/label.py,sha256=bmwWuOfZWApjttL_CspiNg-j728ODF1i2zKtKIP_u6k,10120
+ngio/images/masked_image.py,sha256=IBo8x2jHyXBXn7ORo8fSiwBPjV_1JOTb_vatjKNxbJ0,8531
+ngio/images/ome_zarr_container.py,sha256=mEKOtZtZkJbMG02ne0pRIKtlFoi8B1QV8j9WSXDavRs,28705
+ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
+ngio/ome_zarr_meta/_meta_handlers.py,sha256=BLvYt5PONYrWkEb2XgEiAXR_OX9rfeX_C0eEqen0jQA,25549
+ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImGSAOK3D3Bg-Js,1786
+ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=Kqe9T7LWa_9o3UWS5uzALyyNluIhXxWhDGxWY4-GIo8,16707
+ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=ufZuYuTO5PJA1vcBrNAcuZCMgIEwF57buPloTHIzB1Q,14082
+ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=hY8ogPPxvCgVg6k02t3zUr24lasYrvnxBd1iPEigdG4,5892
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+ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=8E38Mgw-l0Ff1nkmCJIzo64G_paAVhM8xktUS_V5egY,17960
+ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=5TT8250XdCKUnk3OwZeyXIMNFKOg_jx4NnoCo9RLsXI,4079
+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=gxvNvAgLePgrngOm06H5qU50Axc6boeIs5iCfrmqTi0,609
+ngio/tables/_validators.py,sha256=RzF09YrlUSb-xdVlosuU-_BaLswtvhpduHfzLaWu2mY,6468
+ngio/tables/tables_container.py,sha256=elOTjpRuC_zsRuZmGeBWfMl2y6OLp2g6FmOe__xLsWE,9845
+ngio/tables/backends/__init__.py,sha256=NlOXmZXDA1kOCVONUyo_aqSjdMHmfqk-3xuKBLXpaUM,217
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