ngio 0.5.0__py3-none-any.whl → 0.5.0a1__py3-none-any.whl

ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -1,31 +1,32 @@
 """HCS (High Content Screening) specific metadata classes for NGIO."""
 
-import warnings
 from typing import Annotated
 
-from ome_zarr_models.common.plate import (
+from ome_zarr_models.v04.hcs import HCSAttrs
+from ome_zarr_models.v04.plate import (
     Acquisition,
     Column,
-    PlateBase,
+    Plate,
     Row,
     WellInPlate,
 )
-from ome_zarr_models.common.well_types import WellImage as WellImageCommon
+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 BaseModel, SkipValidation, field_serializer
 
 from ngio.ome_zarr_meta.ngio_specs._ngio_image import DefaultNgffVersion, NgffVersions
-from ngio.utils import NgioValueError
+from ngio.utils import NgioValueError, ngio_logger
 
 
 def path_in_well_validation(path: str) -> str:
     """Validate the path in the well."""
     # Check if the value contains only alphanumeric characters
     if not path.isalnum():
-        warnings.warn(
+        ngio_logger.warning(
             f"Path '{path}' contains non-alphanumeric characters. "
             "This may cause issues with some tools. "
-            "Consider using only alphanumeric characters in the path.",
-            stacklevel=2,
+            "Consider using only alphanumeric characters in the path."
         )
     return path
 
@@ -40,7 +41,7 @@ class ImageInWellPath(BaseModel):
     acquisition_name: str | None = None
 
 
-class CustomWellImage(WellImageCommon):
+class CustomWellImage(WellImage04):
     path: Annotated[str, SkipValidation]
 
     @field_serializer("path")
@@ -49,29 +50,32 @@ class CustomWellImage(WellImageCommon):
         return path_in_well_validation(value)
 
 
-class PlateWithVersion(PlateBase):
-    version: NgffVersions
+class CustomWellMeta(WellMeta04):
+    images: list[CustomWellImage]  # type: ignore (override of WellMeta04.images)
 
 
-class NgioWellMeta(BaseModel):
-    """HCS well metadata."""
+class CustomWellAttrs(WellAttrs04):
+    well: CustomWellMeta  # type: ignore (override of WellAttrs04.well)
 
-    images: list[CustomWellImage]  # type: ignore (override of WellMeta04.images)
-    version: NgffVersions
+
+class NgioWellMeta(CustomWellAttrs):
+    """HCS well metadata."""
 
     @classmethod
     def default_init(
         cls,
-        ngff_version: NgffVersions = DefaultNgffVersion,
+        version: NgffVersions | None = None,
     ) -> "NgioWellMeta":
-        well = cls(images=[], version=ngff_version)
+        if version is None:
+            version = DefaultNgffVersion
+        well = cls(well=CustomWellMeta(images=[], version=version))
         return well
 
     @property
     def acquisition_ids(self) -> list[int]:
         """Return the acquisition ids in the well."""
         acquisitions = []
-        for images in self.images:
+        for images in self.well.images:
             if (
                 images.acquisition is not None
                 and images.acquisition not in acquisitions
@@ -81,7 +85,7 @@ class NgioWellMeta(BaseModel):
 
     def get_image_acquisition_id(self, image_path: str) -> int | None:
         """Return the acquisition id for the given image path."""
-        for images in self.images:
+        for images in self.well.images:
             if images.path == image_path:
                 return images.acquisition
         raise NgioValueError(f"Image at path {image_path} not found in the well.")
@@ -96,9 +100,11 @@ class NgioWellMeta(BaseModel):
             acquisition (int | None): The acquisition id to filter the images.
         """
         if acquisition is None:
-            return [images.path for images in self.images]
+            return [images.path for images in self.well.images]
         return [
-            images.path for images in self.images if images.acquisition == acquisition
+            images.path
+            for images in self.well.images
+            if images.acquisition == acquisition
         ]
 
     def add_image(
@@ -112,7 +118,7 @@ class NgioWellMeta(BaseModel):
             strict (bool): If True, check if the image already exists in the well.
                 If False, do not check if the image already exists in the well.
         """
-        list_of_images = self.images
+        list_of_images = self.well.images
         for image in list_of_images:
             if image.path == path:
                 raise NgioValueError(
@@ -131,7 +137,9 @@ class NgioWellMeta(BaseModel):
 
         new_image = CustomWellImage(path=path, acquisition=acquisition)
         list_of_images.append(new_image)
-        return NgioWellMeta(images=list_of_images, version=self.version)
+        return NgioWellMeta(
+            well=CustomWellMeta(images=list_of_images, version=self.well.version)
+        )
 
     def remove_image(self, path: str) -> "NgioWellMeta":
         """Remove an image from the well.
@@ -139,66 +147,35 @@ class NgioWellMeta(BaseModel):
         Args:
             path (str): The path of the image.
         """
-        list_of_images = self.images
+        list_of_images = self.well.images
         for image in list_of_images:
             if image.path == path:
                 list_of_images.remove(image)
-                return NgioWellMeta(images=list_of_images, version=self.version)
+                return NgioWellMeta(
+                    well=CustomWellMeta(
+                        images=list_of_images, version=self.well.version
+                    )
+                )
         raise NgioValueError(f"Image at path {path} not found in the well.")
 
 
-def _format_int_column(column: int, num_digits: int = 2) -> str:
-    """Format the column as a string.
-
-    We make sure to pad the column with zeros
-    to have a consistent format.
-
-    Args:
-        column (int): The column to format.
-        num_digits (int): The number of digits to pad the column.
-
-    Returns:
-        str: The column as a string.
-    """
-    return f"{column:0{num_digits}d}"
-
-
-def _stringify_column(column: str | int, num_digits: int = 2) -> str:
+def _stringify_column(column: str | int) -> str:
     """Convert the column to a string.
 
-    This will ensure that columns are always strings.
-    and will help with sorting and comparison.
-
     Args:
         column (str | int): The column to convert.
-        num_digits (int): The number of digits to pad the column.
 
     Returns:
         str: The column as a string.
     """
-    if isinstance(column, int):
-        return _format_int_column(column, num_digits=num_digits)
-
-    elif isinstance(column, str):
-        try:
-            column_int = int(column)
-            return _format_int_column(column_int, num_digits=num_digits)
-        except ValueError:
-            pass
+    if isinstance(column, str):
         return column
-    raise NgioValueError(f"Column {column} must be a string or an integer.")
-
 
-def _find_row_index(rows: list[str], row: str) -> int | None:
-    """Find the index of a row in the list of rows.
+    # Maybe we should pad the column with zeros
+    return str(column)
 
-    Args:
-        rows: List of row names.
-        row: The row name to find.
 
-    Returns:
-        The index of the row, or None if not found.
-    """
+def _find_row_index(rows: list[str], row: str) -> int | None:
     try:
         return rows.index(row)
     except ValueError:
@@ -206,17 +183,8 @@ def _find_row_index(rows: list[str], row: str) -> int | None:
 
 
 def _find_column_index(columns: list[str], column: str | int) -> int | None:
-    """Find the index of a column in the list of columns.
-
-    Args:
-        columns: List of column names.
-        column: The column name or number to find.
-
-    Returns:
-        The index of the column, or None if not found.
-    """
-    _num_columns = [_stringify_column(columns) for columns in columns]
-    column = _stringify_column(column)
+    _num_columns = [int(columns) for columns in columns]
+    column = int(column)
     try:
         return _num_columns.index(column)
     except ValueError:
@@ -226,16 +194,6 @@ def _find_column_index(columns: list[str], column: str | int) -> int | None:
 def _relabel_wells(
     wells: list[WellInPlate], rows: list[Row], columns: list[Column]
 ) -> list[WellInPlate]:
-    """Relabel well indices after rows or columns have been added.
-
-    Args:
-        wells: List of wells to relabel.
-        rows: Updated list of rows.
-        columns: Updated list of columns.
-
-    Returns:
-        List of wells with updated row and column indices.
-    """
     new_wells = []
     _rows = [row.name for row in rows]
     _columns = [column.name for column in columns]
@@ -260,30 +218,26 @@ def _relabel_wells(
     return new_wells
 
 
-class NgioPlateMeta(BaseModel):
+class NgioPlateMeta(HCSAttrs):
     """HCS plate metadata."""
 
-    plate: PlateWithVersion
-    version: NgffVersions
-
     @classmethod
     def default_init(
         cls,
         images: list[ImageInWellPath] | None = None,
         name: str | None = None,
-        ngff_version: NgffVersions = DefaultNgffVersion,
+        version: NgffVersions | None = None,
     ) -> "NgioPlateMeta":
         plate = cls(
-            plate=PlateWithVersion(
+            plate=Plate(
                 rows=[],
                 columns=[],
                 acquisitions=None,
                 wells=[],
                 field_count=None,
+                version=version,
                 name=name,
-                version=ngff_version,
-            ),
-            version=ngff_version,
+            )
         )
 
         if images is None:
@@ -340,8 +294,23 @@ class NgioPlateMeta(BaseModel):
         Returns:
             str: The path of the well.
         """
-        row_idx = _find_row_index(self.rows, row)
-        column_idx = _find_column_index(self.columns, column)
+        if row not in self.rows:
+            raise NgioValueError(
+                f"Row {row} not found in the plate. Available rows are {self.rows}."
+            )
+
+        row_idx = self.rows.index(row)
+
+        _num_columns = [int(columns) for columns in self.columns]
+
+        try:
+            _column = int(column)
+        except ValueError:
+            raise NgioValueError(
+                f"Column {column} must be an integer or convertible to an integer."
+            ) from None
+
+        column_idx = _num_columns.index(_column)
 
         for well in self.plate.wells:
             if well.columnIndex == column_idx and well.rowIndex == row_idx:
@@ -377,16 +346,16 @@ class NgioPlateMeta(BaseModel):
         else:
             wells = self.plate.wells
 
-        new_plate = PlateWithVersion(
+        new_plate = Plate(
             rows=rows,
             columns=self.plate.columns,
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.version,
+            version=self.plate.version,
         )
-        return NgioPlateMeta(plate=new_plate, version=self.version), row_idx
+        return NgioPlateMeta(plate=new_plate), row_idx
 
     def add_column(self, column: str | int) -> "tuple[NgioPlateMeta, int]":
         """Add a column to the plate.
@@ -404,7 +373,7 @@ class NgioPlateMeta(BaseModel):
 
         columns_names.append(_stringify_column(column))
         # sort as numbers
-        columns_names.sort(key=lambda x: _stringify_column(x))
+        columns_names.sort(key=lambda x: int(x))
         column_idx = columns_names.index(_stringify_column(column))
         relabel_wells = True
 
@@ -415,30 +384,27 @@ class NgioPlateMeta(BaseModel):
         else:
             wells = self.plate.wells
 
-        new_plate = PlateWithVersion(
+        new_plate = Plate(
             rows=self.plate.rows,
             columns=columns,
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.version,
+            version=self.plate.version,
         )
-        return NgioPlateMeta(plate=new_plate, version=self.version), column_idx
+        return NgioPlateMeta(plate=new_plate), column_idx
 
     def add_well(
         self,
         row: str,
         column: str | int,
     ) -> "NgioPlateMeta":
-        """Add a well to the plate.
+        """Add an image to the well.
 
         Args:
             row (str): The row of the well.
             column (str | int): The column of the well.
-
-        Returns:
-            NgioPlateMeta: Updated plate metadata with the new well.
         """
         plate, row_idx = self.add_row(row=row)
         plate, column_idx = plate.add_column(column=column)
@@ -456,16 +422,16 @@ class NgioPlateMeta(BaseModel):
                 )
             )
 
-        new_plate = PlateWithVersion(
+        new_plate = Plate(
             rows=plate.plate.rows,
             columns=plate.plate.columns,
             acquisitions=plate.plate.acquisitions,
             wells=wells,
             field_count=plate.plate.field_count,
             name=plate.plate.name,
-            version=plate.version,
+            version=plate.plate.version,
         )
-        return NgioPlateMeta(plate=new_plate, version=plate.version)
+        return NgioPlateMeta(plate=new_plate)
 
     def add_acquisition(
         self,
@@ -495,16 +461,16 @@ class NgioPlateMeta(BaseModel):
             Acquisition(id=acquisition_id, name=acquisition_name, **acquisition_kwargs)
         )
 
-        new_plate = PlateWithVersion(
+        new_plate = Plate(
             rows=self.plate.rows,
             columns=self.plate.columns,
             acquisitions=acquisitions,
             wells=self.plate.wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.version,
+            version=self.plate.version,
         )
-        return NgioPlateMeta(plate=new_plate, version=self.version)
+        return NgioPlateMeta(plate=new_plate)
 
     def remove_well(self, row: str, column: str | int) -> "NgioPlateMeta":
         """Remove a well from the plate.
@@ -531,33 +497,30 @@ class NgioPlateMeta(BaseModel):
                 f"Well at row {row} and column {column} not found in the plate."
             )
 
-        new_plate = PlateWithVersion(
+        new_plate = Plate(
             rows=self.plate.rows,
             columns=self.plate.columns,
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.version,
+            version=self.plate.version,
         )
-        return NgioPlateMeta(plate=new_plate, version=self.version)
+        return NgioPlateMeta(plate=new_plate)
 
     def derive(
         self,
         name: str | None = None,
-        ngff_version: NgffVersions | None = None,
+        version: NgffVersions | None = None,
         keep_acquisitions: bool = False,
     ) -> "NgioPlateMeta":
         """Derive the plate metadata.
 
         Args:
-            name (str | None): The name of the derived plate.
-            ngff_version (NgffVersions | None): The version of the derived plate.
+            name (str): The name of the derived plate.
+            version (NgffVersion | None): The version of the derived plate.
                 If None, use the version of the original plate.
             keep_acquisitions (bool): If True, keep the acquisitions in the plate.
-
-        Returns:
-            NgioPlateMeta: The derived plate metadata.
         """
         columns = self.plate.columns
         rows = self.plate.rows
@@ -567,18 +530,17 @@ class NgioPlateMeta(BaseModel):
         else:
             acquisitions = None
 
-        if ngff_version is None:
-            ngff_version = self.version
+        if version is None:
+            version = self.plate.version  # type: ignore (version is NgffVersions or None)
 
         return NgioPlateMeta(
-            plate=PlateWithVersion(
+            plate=Plate(
                 rows=rows,
                 columns=columns,
                 acquisitions=acquisitions,
                 wells=[],
                 field_count=self.plate.field_count,
+                version=version,
                 name=name,
-                version=ngff_version,
-            ),
-            version=ngff_version,
+            )
         )

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -13,11 +13,11 @@ import numpy as np
 from pydantic import BaseModel
 
 from ngio.ome_zarr_meta.ngio_specs._axes import (
-    AxesHandler,
     DefaultSpaceUnit,
     DefaultTimeUnit,
     SpaceUnits,
     TimeUnits,
+    build_canonical_axes_handler,
 )
 from ngio.ome_zarr_meta.ngio_specs._channels import ChannelsMeta
 from ngio.ome_zarr_meta.ngio_specs._dataset import Dataset
@@ -41,13 +41,6 @@ class ImageLabelSource(BaseModel):
         return cls(version=version, source={"image": "../../"})
 
 
-class NgioLabelsGroupMeta(BaseModel):
-    """Metadata model for the /labels group in OME-NGFF."""
-
-    version: NgffVersions
-    labels: list[str]
-
-
 class AbstractNgioImageMeta:
     """Base class for ImageMeta and LabelMeta."""
 
@@ -73,23 +66,42 @@ class AbstractNgioImageMeta:
     @classmethod
     def default_init(
         cls,
-        levels: Sequence[str],
-        axes_handler: AxesHandler,
-        scales: Sequence[tuple[float, ...]],
-        translations: Sequence[tuple[float, ...] | None],
+        levels: int | Sequence[str],
+        axes_names: Sequence[str],
+        pixel_size: PixelSize,
+        scaling_factors: Sequence[float] | None = None,
         name: str | None = None,
         version: NgffVersions = DefaultNgffVersion,
     ):
         """Initialize the ImageMeta object."""
+        axes_handler = build_canonical_axes_handler(
+            axes_names,
+            space_units=pixel_size.space_unit,
+            time_units=pixel_size.time_unit,
+        )
+
+        px_size_dict = pixel_size.as_dict()
+        scale = [px_size_dict.get(name, 1.0) for name in axes_handler.axes_names]
+
+        if scaling_factors is None:
+            _default = {"x": 2.0, "y": 2.0}
+            scaling_factors = [
+                _default.get(name, 1.0) for name in axes_handler.axes_names
+            ]
+
+        if isinstance(levels, int):
+            levels = [str(i) for i in range(levels)]
+
         datasets = []
-        for level, scale, translation in zip(levels, scales, translations, strict=True):
+        for level in levels:
             dataset = Dataset(
                 path=level,
                 axes_handler=axes_handler,
                 scale=scale,
-                translation=translation,
+                translation=None,
             )
             datasets.append(dataset)
+            scale = [s * f for s, f in zip(scale, scaling_factors, strict=True)]
 
         return cls(
             version=version,
@@ -129,42 +141,6 @@ class AbstractNgioImageMeta:
             datasets=new_datasets,
         )
 
-    def rename_axes(self, axes_names: Sequence[str]):
-        """Rename axes in the metadata.
-
-        Args:
-            axes_names(Sequence[str]): The new axes names in the order of the current
-                axes.
-        """
-        new_axes_handler = self.axes_handler.rename_axes(axes_names=axes_names)
-        new_datasets = []
-        for dataset in self.datasets:
-            new_dataset = Dataset(
-                path=dataset.path,
-                axes_handler=new_axes_handler,
-                scale=dataset.scale,
-                translation=dataset.translation,
-            )
-            new_datasets.append(new_dataset)
-
-        return type(self)(
-            version=self.version,
-            name=self.name,
-            datasets=new_datasets,
-        )
-
-    def rename_image(self, name: str):
-        """Rename the image in the metadata.
-
-        Args:
-            name(str): The new name of the image.
-        """
-        return type(self)(
-            version=self.version,
-            name=name,
-            datasets=self.datasets,
-        )
-
     @property
     def version(self) -> NgffVersions:
         """Version of the OME-NFF metadata used to build the object."""
@@ -361,15 +337,50 @@ class AbstractNgioImageMeta:
             )
         return dataset, lr_dataset
 
-    def scaling_factor(self, path: str | None = None) -> tuple[float, ...]:
-        """Get the scaling factors to downscale to the next lower resolution dataset."""
+    def scaling_factor(self, path: str | None = None) -> list[float]:
+        """Get the scaling factors from a dataset to its lower resolution."""
+        if self.levels == 1:
+            return [1.0] * len(self.axes_handler.axes_names)
+        dataset, lr_dataset = self._get_closest_datasets(path=path)
+
+        scaling_factors = []
+        for ax_name in self.axes_handler.axes_names:
+            s_d = dataset.get_scale(ax_name)
+            s_lr_d = lr_dataset.get_scale(ax_name)
+            scaling_factors.append(s_lr_d / s_d)
+        return scaling_factors
+
+    def yx_scaling(self, path: str | None = None) -> tuple[float, float]:
+        """Get the scaling factor from a dataset to its lower resolution."""
         if self.levels == 1:
-            return (1.0,) * len(self.axes_handler.axes_names)
+            return 1.0, 1.0
         dataset, lr_dataset = self._get_closest_datasets(path=path)
-        scale = dataset.scale
-        lr_scale = lr_dataset.scale
-        scaling_factors = [s / s_lr for s_lr, s in zip(scale, lr_scale, strict=True)]
-        return tuple(scaling_factors)
+
+        if lr_dataset is None:
+            raise NgioValueError(
+                "No lower resolution dataset found. "
+                "This is the lowest resolution dataset."
+            )
+
+        s_d = dataset.get_scale("y")
+        s_lr_d = lr_dataset.get_scale("y")
+        scale_y = s_lr_d / s_d
+
+        s_d = dataset.get_scale("x")
+        s_lr_d = lr_dataset.get_scale("x")
+        scale_x = s_lr_d / s_d
+
+        return scale_y, scale_x
+
+    def z_scaling(self, path: str | None = None) -> float:
+        """Get the scaling factor from a dataset to its lower resolution."""
+        if self.levels == 1:
+            return 1.0
+        dataset, lr_dataset = self._get_closest_datasets(path=path)
+
+        s_d = dataset.get_scale("z", default=1.0)
+        s_lr_d = lr_dataset.get_scale("z", default=1.0)
+        return s_lr_d / s_d
 
 
 class NgioLabelMeta(AbstractNgioImageMeta):

ngio/ome_zarr_meta/v04/__init__.py

@@ -1,14 +1,12 @@
 """Utility to read/write OME-Zarr metadata v0.4."""
 
-from ngio.ome_zarr_meta.v04._v04_spec import (
+from ngio.ome_zarr_meta.v04._v04_spec_utils import (
     ngio_to_v04_image_meta,
     ngio_to_v04_label_meta,
-    ngio_to_v04_labels_group_meta,
     ngio_to_v04_plate_meta,
     ngio_to_v04_well_meta,
     v04_to_ngio_image_meta,
     v04_to_ngio_label_meta,
-    v04_to_ngio_labels_group_meta,
     v04_to_ngio_plate_meta,
     v04_to_ngio_well_meta,
 )
@@ -16,12 +14,10 @@ from ngio.ome_zarr_meta.v04._v04_spec import (
 __all__ = [
     "ngio_to_v04_image_meta",
     "ngio_to_v04_label_meta",
-    "ngio_to_v04_labels_group_meta",
     "ngio_to_v04_plate_meta",
     "ngio_to_v04_well_meta",
     "v04_to_ngio_image_meta",
     "v04_to_ngio_label_meta",
-    "v04_to_ngio_labels_group_meta",
     "v04_to_ngio_plate_meta",
     "v04_to_ngio_well_meta",
 ]