ngio 0.5.0b7__py3-none-any.whl → 0.5.1__py3-none-any.whl

ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -1,6 +1,6 @@
 """HCS (High Content Screening) specific metadata classes for NGIO."""
 
-import warnings
+import logging
 from typing import Annotated
 
 from ome_zarr_models.common.plate import (
@@ -16,16 +16,17 @@ from pydantic import BaseModel, SkipValidation, field_serializer
 from ngio.ome_zarr_meta.ngio_specs._ngio_image import DefaultNgffVersion, NgffVersions
 from ngio.utils import NgioValueError
 
+logger = logging.getLogger(f"ngio:{__name__}")
+
 
 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(
+        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
 
@@ -147,23 +148,58 @@ class NgioWellMeta(BaseModel):
         raise NgioValueError(f"Image at path {path} not found in the well.")
 
 
-def _stringify_column(column: str | int) -> str:
+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:
     """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, str):
-        return column
+    if isinstance(column, int):
+        return _format_int_column(column, num_digits=num_digits)
 
-    # Maybe we should pad the column with zeros
-    return str(column)
+    elif isinstance(column, str):
+        try:
+            column_int = int(column)
+            return _format_int_column(column_int, num_digits=num_digits)
+        except ValueError:
+            pass
+        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.
+
+    Args:
+        rows: List of row names.
+        row: The row name to find.
+
+    Returns:
+        The index of the row, or None if not found.
+    """
     try:
         return rows.index(row)
     except ValueError:
@@ -171,8 +207,17 @@ def _find_row_index(rows: list[str], row: str) -> int | None:
 
 
 def _find_column_index(columns: list[str], column: str | int) -> int | None:
-    _num_columns = [int(columns) for columns in columns]
-    column = int(column)
+    """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)
     try:
         return _num_columns.index(column)
     except ValueError:
@@ -182,6 +227,16 @@ 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]
@@ -286,23 +341,8 @@ class NgioPlateMeta(BaseModel):
         Returns:
             str: The path of the well.
         """
-        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)
+        row_idx = _find_row_index(self.rows, row)
+        column_idx = _find_column_index(self.columns, column)
 
         for well in self.plate.wells:
             if well.columnIndex == column_idx and well.rowIndex == row_idx:
@@ -365,7 +405,7 @@ class NgioPlateMeta(BaseModel):
 
         columns_names.append(_stringify_column(column))
         # sort as numbers
-        columns_names.sort(key=lambda x: int(x))
+        columns_names.sort(key=lambda x: _stringify_column(x))
         column_idx = columns_names.index(_stringify_column(column))
         relabel_wells = True
 
@@ -392,11 +432,14 @@ class NgioPlateMeta(BaseModel):
         row: str,
         column: str | int,
     ) -> "NgioPlateMeta":
-        """Add an image to the well.
+        """Add a well to the plate.
 
         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)
@@ -509,10 +552,13 @@ class NgioPlateMeta(BaseModel):
         """Derive the plate metadata.
 
         Args:
-            name (str): The name of the derived plate.
-            ngff_version (NgffVersion | None): The version of the derived plate.
+            name (str | None): The name of the derived plate.
+            ngff_version (NgffVersions | 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

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -129,6 +129,42 @@ 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."""

ngio/ome_zarr_meta/v04/_v04_spec.py

@@ -119,8 +119,6 @@ def _compute_scale_translation(
 def _v04_to_ngio_datasets(
     v04_multiscale: MultiscaleV04,
     axes_setup: AxesSetup,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
 ) -> list[Dataset]:
     """Convert a v04 multiscale to a list of ngio datasets."""
     datasets = []
@@ -151,8 +149,6 @@ def _v04_to_ngio_datasets(
     axes_handler = AxesHandler(
         axes=axes,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
     )
 
     for v04_dataset in v04_multiscale.datasets:
@@ -172,9 +168,7 @@ def _v04_to_ngio_datasets(
 
 def v04_to_ngio_image_meta(
     metadata: dict,
-    axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
+    axes_setup: AxesSetup,
 ) -> NgioImageMeta:
     """Convert a v04 image metadata to a ngio image metadata.
 
@@ -182,8 +176,6 @@ def v04_to_ngio_image_meta(
         metadata (dict): The v04 image metadata.
         axes_setup (AxesSetup, optional): The axes setup. This is
             required to convert image with non-canonical axes names.
-        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
-        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
         NgioImageMeta: The ngio image metadata.
@@ -198,12 +190,9 @@ def v04_to_ngio_image_meta(
     v04_muliscale = v04_image.multiscales[0]
 
     channels_meta = _v04_omero_to_channels(v04_image.omero)
-    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v04_to_ngio_datasets(
         v04_muliscale,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
     )
 
     name = v04_muliscale.name
@@ -219,9 +208,7 @@ def v04_to_ngio_image_meta(
 
 def v04_to_ngio_label_meta(
     metadata: dict,
-    axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
+    axes_setup: AxesSetup,
 ) -> NgioLabelMeta:
     """Convert a v04 image metadata to a ngio image metadata.
 
@@ -229,8 +216,6 @@ def v04_to_ngio_label_meta(
         metadata (dict): The v04 image metadata.
         axes_setup (AxesSetup, optional): The axes setup. This is
             required to convert image with non-canonical axes names.
-        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
-        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
         NgioImageMeta: The ngio image metadata.
@@ -243,13 +228,9 @@ def v04_to_ngio_label_meta(
         )
 
     v04_muliscale = v04_label.multiscales[0]
-
-    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v04_to_ngio_datasets(
         v04_muliscale,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
     )
 
     source = v04_label.image_label.source

ngio/ome_zarr_meta/v05/_v05_spec.py

@@ -133,8 +133,6 @@ def _compute_scale_translation(
 def _v05_to_ngio_datasets(
     v05_multiscale: MultiscaleV05,
     axes_setup: AxesSetup,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
 ) -> list[Dataset]:
     """Convert a v05 multiscale to a list of ngio datasets."""
     datasets = []
@@ -165,8 +163,6 @@ def _v05_to_ngio_datasets(
     axes_handler = AxesHandler(
         axes=axes,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
     )
 
     for v05_dataset in v05_multiscale.datasets:
@@ -186,18 +182,14 @@ def _v05_to_ngio_datasets(
 
 def v05_to_ngio_image_meta(
     metadata: dict,
-    axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
+    axes_setup: AxesSetup,
 ) -> NgioImageMeta:
     """Convert a v05 image metadata to a ngio image metadata.
 
     Args:
         metadata (dict): The v05 image metadata.
-        axes_setup (AxesSetup, optional): The axes setup. This is
+        axes_setup (AxesSetup): The axes setup. This is
             required to convert image with non-canonical axes names.
-        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
-        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
         NgioImageMeta: The ngio image metadata.
@@ -212,12 +204,9 @@ def v05_to_ngio_image_meta(
     v05_multiscale = v05_image.multiscales[0]
 
     channels_meta = _v05_omero_to_channels(v05_image.omero)
-    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v05_to_ngio_datasets(
         v05_multiscale,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
     )
 
     name = v05_multiscale.name
@@ -233,18 +222,14 @@ def v05_to_ngio_image_meta(
 
 def v05_to_ngio_label_meta(
     metadata: dict,
-    axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
+    axes_setup: AxesSetup,
 ) -> NgioLabelMeta:
     """Convert a v05 image metadata to a ngio image metadata.
 
     Args:
         metadata (dict): The v05 image metadata.
-        axes_setup (AxesSetup, optional): The axes setup. This is
+        axes_setup (AxesSetup): The axes setup. This is
             required to convert image with non-canonical axes names.
-        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
-        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
         NgioLabelMeta: The ngio label metadata.
@@ -259,12 +244,9 @@ def v05_to_ngio_label_meta(
 
     v05_multiscale = v05_label.multiscales[0]
 
-    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v05_to_ngio_datasets(
         v05_multiscale,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
     )
 
     if v05_label.image_label is not None:

ngio/resources/__init__.py

@@ -31,7 +31,7 @@ _resources = {
                 dtype="uint8",
             ),
         ],
-        xy_pixelsize=0.325,
+        pixelsize=0.325,
         z_spacing=1.0,
         time_spacing=1.0,
         name="Cardiomyocyte Differentiation",

ngio/resources/resource_model.py

@@ -27,7 +27,7 @@ class SampleInfo(BaseModel):
 
     img_path: Path
     labels: list[LabelsInfo] = Field(default_factory=list)
-    xy_pixelsize: float
+    pixelsize: float
     z_spacing: float = 1.0
     time_spacing: float = 1.0
     space_unit: SpaceUnits = DefaultSpaceUnit

ngio/tables/_tables_container.py

@@ -229,10 +229,10 @@ class ImplementedTables:
 
 
 class TablesContainer:
-    """A class to handle the /labels group in an OME-NGFF file."""
+    """A class to handle the /tables group in an OME-NGFF file."""
 
     def __init__(self, group_handler: ZarrGroupHandler) -> None:
-        """Initialize the LabelGroupHandler."""
+        """Initialize the TablesContainer."""
         self._group_handler = group_handler
 
         # Validate the group
@@ -252,7 +252,7 @@ class TablesContainer:
             )
 
     def _get_tables_list(self) -> list[str]:
-        """Create the /tables group if it doesn't exist."""
+        """Return the list of table names from the group attributes."""
         attrs = self._group_handler.load_attrs()
         return attrs.get("tables", [])
 
@@ -262,7 +262,14 @@ class TablesContainer:
         return handler
 
     def list(self, filter_types: TypedTable | str | None = None) -> list[str]:
-        """List all labels in the group."""
+        """List all tables in the group.
+
+        Args:
+            filter_types: If provided, only return tables of this type.
+
+        Returns:
+            A list of table names.
+        """
         tables = self._get_tables_list()
         if filter_types is None:
             return tables
@@ -281,7 +288,16 @@ class TablesContainer:
         backend: TableBackend | None = None,
         strict: bool = True,
     ) -> Table:
-        """Get a label from the group."""
+        """Get a table from the group.
+
+        Args:
+            name: The name of the table.
+            backend: The backend to use for reading the table.
+            strict: If True, raise an error if the table type is not implemented.
+
+        Returns:
+            The table object.
+        """
         if name not in self.list():
             raise NgioValueError(f"Table '{name}' not found in the group.")
 
@@ -301,7 +317,16 @@ class TablesContainer:
         table_cls: type[TableType],
         backend: TableBackend | None = None,
     ) -> TableType:
-        """Get a table from the group as a specific type."""
+        """Get a table from the group as a specific type.
+
+        Args:
+            name: The name of the table.
+            table_cls: The table class to use for loading the table.
+            backend: The backend to use for reading the table.
+
+        Returns:
+            The table object of the specified type.
+        """
         if name not in self.list():
             raise NgioValueError(f"Table '{name}' not found in the group.")
 
@@ -339,7 +364,14 @@ class TablesContainer:
         backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
-        """Add a table to the group."""
+        """Add a table to the group.
+
+        Args:
+            name: The name of the table.
+            table: The table object to add.
+            backend: The backend to use for writing the table.
+            overwrite: Whether to overwrite an existing table with the same name.
+        """
         existing_tables = self._get_tables_list()
         if name in existing_tables and not overwrite:
             raise NgioValueError(

ngio/tables/v1/_roi_table.py

@@ -4,7 +4,7 @@ This class follows the roi_table specification at:
 https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
 """
 
-import warnings
+import logging
 from collections.abc import Iterable
 from typing import Literal
 from uuid import uuid4
@@ -29,6 +29,8 @@ from ngio.utils import (
     ZarrGroupHandler,
 )
 
+logger = logging.getLogger(f"ngio:{__name__}")
+
 REQUIRED_COLUMNS = [
     "x_micrometer",
     "y_micrometer",
@@ -77,9 +79,7 @@ OPTIONAL_COLUMNS = ORIGIN_COLUMNS + TRANSLATION_COLUMNS + PLATE_COLUMNS + INDEX_
 def _check_optional_columns(col_name: str) -> None:
     """Check if the column name is in the optional columns."""
     if col_name not in OPTIONAL_COLUMNS + TIME_COLUMNS:
-        warnings.warn(
-            f"Column {col_name} is not in the optional columns.", stacklevel=2
-        )
+        logger.warning(f"Column {col_name} is not in the optional columns.")
 
 
 def _dataframe_to_rois(

ngio/utils/_zarr_utils.py

@@ -1,7 +1,7 @@
 """Common utilities for working with Zarr groups in consistent ways."""
 
 import json
-import warnings
+import logging
 from pathlib import Path
 from typing import Literal, TypeAlias
 
@@ -22,6 +22,8 @@ from ngio.utils._errors import (
     NgioValueError,
 )
 
+logger = logging.getLogger(f"ngio:{__name__}")
+
 AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
 # StoreLike is more restrictive than it could be
 # but to make sure we can handle the store correctly
@@ -36,12 +38,10 @@ StoreOrGroup: TypeAlias = NgioSupportedStore | zarr.Group
 def _check_store(store) -> NgioSupportedStore:
     """Check the store and return a valid store."""
     if not isinstance(store, NgioSupportedStore):
-        warnings.warn(
+        logger.warning(
             f"Store type {type(store)} is not explicitly supported. "
             f"Supported types are: {NgioSupportedStore}. "
-            "Proceeding, but this may lead to unexpected behavior.",
-            UserWarning,
-            stacklevel=2,
+            "Proceeding, but this may lead to unexpected behavior."
         )
     return store
 
@@ -114,7 +114,6 @@ class ZarrGroupHandler:
 
         Args:
             store (StoreOrGroup): The Zarr store or group containing the image data.
-            meta_mode (str): The mode of the metadata handler.
             zarr_format (int | None): The Zarr format version to use.
             cache (bool): Whether to cache the metadata.
             mode (str | None): The mode of the store.
@@ -154,11 +153,7 @@ class ZarrGroupHandler:
             return (self.store.path / self.group.path).as_posix()
         elif isinstance(self.store, MemoryStore):
             return None
-        warnings.warn(
-            f"Cannot determine full URL for store type {type(self.store)}. ",
-            UserWarning,
-            stacklevel=2,
-        )
+        logger.warning(f"Cannot determine full URL for store type {type(self.store)}.")
         return None
 
     @property
@@ -524,11 +519,9 @@ def copy_group(
         _fsspec_copy(src_group.store, src_group.path, dest_group.store, dest_group.path)
         return
     if not suppress_warnings:
-        warnings.warn(
+        logger.warning(
             "Fsspec copy not possible, falling back to Zarr Python API for the copy. "
             "This will preserve some tabular data non-zarr native (parquet, and csv), "
-            "and it will be slower for large datasets.",
-            UserWarning,
-            stacklevel=2,
+            "and it will be slower for large datasets."
         )
     _zarr_python_copy(src_group, dest_group)

{ngio-0.5.0b7.dist-info → ngio-0.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b7
+Version: 0.5.1
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -23,7 +23,7 @@ Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models
-Requires-Dist: pandas>=1.2.0
+Requires-Dist: pandas<3.0.0,>=1.2.0
 Requires-Dist: pillow
 Requires-Dist: polars
 Requires-Dist: pooch
@@ -58,6 +58,7 @@ 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: ruff; extra == 'docs'
 Requires-Dist: scikit-image; extra == 'docs'
 Requires-Dist: tabulate; extra == 'docs'
 Provides-Extra: test