improve logging

src/ngio/__init__.py

@@ -1,14 +1,11 @@
 """Next Generation file format IO."""
 
-import os
 from importlib.metadata import PackageNotFoundError, version
 
 from ngio.core import Image, Label, NgffImage
-from ngio.utils import ngio_logger, set_logger_level
 
-__all__ = ["Image", "Label", "NgffImage", "set_logger_level", "ngio_logger"]
+__all__ = ["Image", "Label", "NgffImage"]
 
-set_logger_level(os.getenv("NGIO_LOGGER_LEVEL", "WARNING"))
 
 try:
     __version__ = version("ngio")

src/ngio/core/dimensions.py

@@ -39,6 +39,17 @@ def __init__(
         self._shape = [self._on_disk_shape[i] for i in axes_order]
         self._shape_dict = dict(zip(axes_names, self._shape, strict=True))
 
+    def __str__(self) -> str:
+        """Return the string representation of the object."""
+        _dimensions = ", ".join(
+            [f"{name}={self._shape_dict[name]}" for name in self._axes_names]
+        )
+        return f"Dimensions({_dimensions})"
+
+    def __repr__(self) -> str:
+        """Return the string representation of the object."""
+        return str(self)
+
     @property
     def shape(self) -> tuple[int, ...]:
         """Return the shape as a tuple in the canonical order."""

src/ngio/core/ngff_image.py

@@ -10,6 +10,7 @@
 from ngio.ngff_meta import get_ngff_image_meta_handler
 from ngio.ngff_meta.fractal_image_meta import ImageMeta, PixelSize
 from ngio.tables.tables_group import TableGroup
+from ngio.utils import ngio_logger
 
 
 class NgffImage:
@@ -28,6 +29,8 @@ def __init__(
         self._metadata_cache = cache
         self.table = TableGroup(self.group, mode=self._mode)
         self.label = LabelGroup(self.group, image_ref=self.get_image(), mode=self._mode)
+        ngio_logger.info(f"Opened image located in store: {store}")
+        ngio_logger.info(f"- Image number of levels: {self.num_levels}")
 
     @property
     def image_meta(self) -> ImageMeta:
@@ -68,14 +71,18 @@ def get_image(
         if path is not None or pixel_size is not None:
             highest_resolution = False
 
-        return Image(
+        image = Image(
             store=self.group,
             path=path,
             pixel_size=pixel_size,
             highest_resolution=highest_resolution,
             label_group=LabelGroup(self.group, image_ref=None),
             cache=self._metadata_cache,
         )
+        ngio_logger.info(f"Opened image at path: {image.path}")
+        ngio_logger.info(f"- {image.dimensions}")
+        ngio_logger.info(f"- {image.pixel_size}")
+        return image
 
     def _update_omero_window(
         self, min_percentile: int = 5, max_percentile: int = 95
@@ -103,7 +110,6 @@ def _update_omero_window(
             max_percentile,
             method="nearest",
         ).compute()
-        print(f"Setting window to {start} - {end}")
 
         if meta.omero is None:
             raise ValueError("OMERO metadata is not present in the image.")

src/ngio/io/_zarr.py

@@ -62,7 +62,6 @@ def _open_group_v2_v3(
     Returns:
         zarr.Group: The opened Zarr group.
     """
-    print(mode)
     if ZARR_PYTHON_V == 3:
         return zarr.open_group(store=store, mode=mode, zarr_format=zarr_format)
     else:

src/ngio/io/_zarr_group_utils.py

@@ -10,6 +10,7 @@
     _open_group_v2_v3,
     _pass_through_group,
 )
+from ngio.utils import ngio_logger
 
 # Zarr v3 Imports
 # import zarr.store
@@ -40,8 +41,14 @@ def open_group_wrapper(
         zarr.Group: The opened Zarr group.
     """
     if isinstance(store, zarr.Group):
-        return _pass_through_group(store, mode=mode, zarr_format=zarr_format)
+        _group = _pass_through_group(store, mode=mode, zarr_format=zarr_format)
+        ngio_logger.debug(
+            f"Passing through group: {_group}, "
+            f"located in store: {_group.store.path}"
+        )
+        return _group
 
     store = _check_store(store)
-
-    return _open_group_v2_v3(store=store, mode=mode, zarr_format=zarr_format)
+    _group = _open_group_v2_v3(store=store, mode=mode, zarr_format=zarr_format)
+    ngio_logger.debug(f"Opened located in store: {store}")
+    return _group

src/ngio/ngff_meta/fractal_image_meta.py

@@ -100,7 +100,7 @@ class PixelSize(BaseModel):
     unit: SpaceUnits = SpaceUnits.micrometer
     virtual: bool = False
 
-    def __repr__(self) -> str:
+    def __str__(self) -> str:
         """Return the string representation of the object."""
         return f"PixelSize(x={self.x}, y={self.y}, z={self.z}, unit={self.unit.value})"
 

src/ngio/tables/_utils.py

@@ -197,6 +197,7 @@ def table_ad_to_df(
     index_key: str = "label",
     index_type: Literal["str", "int"] = "int",
     validators: list[Validator] | None = None,
+    validate_index_name: bool = False,
 ) -> pd.DataFrame:
     """Convert a AnnData object representing a fractal table to a pandas DataFrame.
 
@@ -207,16 +208,24 @@ def table_ad_to_df(
         index_type (str): The type of the index column in the DataFrame.
             Either 'str' or 'int'. Default is 'int'.
         validators (list[Validator]): A list of functions to further validate the table.
+        validate_index_name (bool): If True, the index name is validated.
     """
     table_df = table_ad.to_df()
-
     table_df[table_ad.obs_keys()] = table_ad.obs
 
     # Set the index of the DataFrame
-    if table_ad.obs.index.name is not None:
-        table_df.index = table_ad.obs.index
-    elif index_key in table_df.columns:
+    if index_key in table_df.columns:
         table_df = table_df.set_index(index_key)
+    elif table_ad.obs.index.name is not None:
+        if validate_index_name:
+            if table_ad.obs.index.name != index_key:
+                raise TableValidationError(
+                    f"Index key {index_key} not found in AnnData object."
+                )
+        table_df.index = table_ad.obs.index
+    elif table_ad.obs.index.name is None:
+        table_df.index = table_ad.obs.index
+        table_df.index.name = index_key
     else:
         raise TableValidationError(
             f"Index key {index_key} not found in AnnData object."

src/ngio/utils/__init__.py

@@ -1,5 +1,7 @@
 """Various utilities for the ngio package."""
 
+import os
+
 from ngio.utils._common_types import ArrayLike
 from ngio.utils._errors import (
     NgioFileExistsError,
@@ -10,6 +12,8 @@
 from ngio.utils._logger import ngio_logger, set_logger_level
 from ngio.utils._pydantic_utils import BaseWithExtraFields, unique_items_validator
 
+set_logger_level(os.getenv("NGIO_LOGGER_LEVEL", "WARNING"))
+
 __all__ = [
     "ArrayLike",
     # Pydantic