ngio 0.5.0a2__py3-none-any.whl → 0.5.0a3__py3-none-any.whl

ngio/images/_create.py

@@ -1,287 +0,0 @@
-"""Utility functions for working with OME-Zarr images."""
-
-from collections.abc import Sequence
-from typing import Literal, TypeVar
-
-from zarr.core.array import CompressorLike
-
-from ngio.common._pyramid import init_empty_pyramid
-from ngio.ome_zarr_meta import (
-    NgioImageMeta,
-    NgioLabelMeta,
-    PixelSize,
-    get_image_meta_handler,
-    get_label_meta_handler,
-)
-from ngio.ome_zarr_meta.ngio_specs import (
-    DefaultNgffVersion,
-    DefaultSpaceUnit,
-    DefaultTimeUnit,
-    NgffVersions,
-    SpaceUnits,
-    TimeUnits,
-    canonical_axes_order,
-    canonical_label_axes_order,
-)
-from ngio.utils import NgioValueError, StoreOrGroup, ZarrGroupHandler
-
-_image_or_label_meta = TypeVar("_image_or_label_meta", NgioImageMeta, NgioLabelMeta)
-
-
-def _init_generic_meta(
-    meta_type: type[_image_or_label_meta],
-    pixelsize: float,
-    axes_names: Sequence[str],
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    yx_scaling_factor: float | tuple[float, float] = 2.0,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
-    time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    name: str | None = None,
-    ngff_version: NgffVersions = DefaultNgffVersion,
-) -> tuple[_image_or_label_meta, list[float]]:
-    """Initialize the metadata for an image or label."""
-    scaling_factors = []
-    for ax in axes_names:
-        if ax == "z":
-            scaling_factors.append(z_scaling_factor)
-        elif ax in ["x"]:
-            if isinstance(yx_scaling_factor, tuple):
-                scaling_factors.append(yx_scaling_factor[1])
-            else:
-                scaling_factors.append(yx_scaling_factor)
-        elif ax in ["y"]:
-            if isinstance(yx_scaling_factor, tuple):
-                scaling_factors.append(yx_scaling_factor[0])
-            else:
-                scaling_factors.append(yx_scaling_factor)
-        else:
-            scaling_factors.append(1.0)
-
-    pixel_sizes = PixelSize(
-        x=pixelsize,
-        y=pixelsize,
-        z=z_spacing,
-        t=time_spacing,
-        space_unit=space_unit,
-        time_unit=time_unit,
-    )
-
-    meta = meta_type.default_init(
-        name=name,
-        levels=levels,
-        axes_names=axes_names,
-        pixel_size=pixel_sizes,
-        scaling_factors=scaling_factors,
-        version=ngff_version,
-    )
-    return meta, scaling_factors
-
-
-def create_empty_label_container(
-    store: StoreOrGroup,
-    shape: Sequence[int],
-    pixelsize: float,
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    yx_scaling_factor: float | tuple[float, float] = 2.0,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
-    time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    axes_names: Sequence[str] | None = None,
-    name: str | None = None,
-    chunks: Sequence[int] | Literal["auto"] = "auto",
-    dtype: str = "uint32",
-    dimension_separator: Literal[".", "/"] = "/",
-    compressors: CompressorLike = "auto",
-    overwrite: bool = False,
-    ngff_version: NgffVersions = DefaultNgffVersion,
-) -> ZarrGroupHandler:
-    """Create an empty label with the given shape and metadata.
-
-    Args:
-        store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Sequence[int]): The shape of the image.
-        pixelsize (float): The pixel size in x and y dimensions.
-        z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
-        time_spacing (float, optional): The spacing between time points.
-            Defaults to 1.0.
-        levels (int | list[str], optional): The number of levels in the pyramid or a
-            list of level names. Defaults to 5.
-        yx_scaling_factor (float, optional): The down-scaling factor in x and y
-            dimensions. Defaults to 2.0.
-        z_scaling_factor (float, optional): The down-scaling factor in z dimension.
-            Defaults to 1.0.
-        space_unit (SpaceUnits, optional): The unit of space. Defaults to
-            DefaultSpaceUnit.
-        time_unit (TimeUnits, optional): The unit of time. Defaults to
-            DefaultTimeUnit.
-        axes_names (Sequence[str] | None, optional): The names of the axes.
-            If None the canonical names are used. Defaults to None.
-        name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Sequence[int] | Literal["auto"]): The chunk shape. If None the shape
-            is used. Defaults to None.
-        dimension_separator (DIMENSION_SEPARATOR): The separator to use for
-            dimensions. Defaults to "/".
-        compressors (CompressorLike): The compressors to use. Defaults to "auto".
-        dtype (str, optional): The data type of the image. Defaults to "uint16".
-        overwrite (bool, optional): Whether to overwrite an existing image.
-            Defaults to True.
-        ngff_version (str, optional): The version of the OME-Zarr specification.
-            Defaults to DefaultVersion.
-
-    """
-    if axes_names is None:
-        axes_names = canonical_label_axes_order()[-len(shape) :]
-
-    if len(axes_names) != len(shape):
-        raise NgioValueError(
-            f"Number of axes names {axes_names} does not match the number of "
-            f"dimensions {shape}."
-        )
-
-    meta, scaling_factors = _init_generic_meta(
-        meta_type=NgioLabelMeta,
-        pixelsize=pixelsize,
-        z_spacing=z_spacing,
-        time_spacing=time_spacing,
-        levels=levels,
-        yx_scaling_factor=yx_scaling_factor,
-        z_scaling_factor=z_scaling_factor,
-        space_unit=space_unit,
-        time_unit=time_unit,
-        axes_names=axes_names,
-        name=name,
-        ngff_version=ngff_version,
-    )
-
-    mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(
-        store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
-    )
-    image_handler = get_label_meta_handler(
-        version=ngff_version, group_handler=group_handler
-    )
-    image_handler.write_meta(meta)
-
-    init_empty_pyramid(
-        store=store,
-        paths=meta.paths,
-        scaling_factors=scaling_factors,
-        ref_shape=shape,
-        chunks=chunks,
-        axes=axes_names,
-        dtype=dtype,
-        mode="a",
-        dimension_separator=dimension_separator,
-        compressors=compressors,
-    )
-    group_handler._mode = "r+"
-    return group_handler
-
-
-def create_empty_image_container(
-    store: StoreOrGroup,
-    shape: Sequence[int],
-    pixelsize: float,
-    z_spacing: float = 1.0,
-    time_spacing: float = 1.0,
-    levels: int | list[str] = 5,
-    yx_scaling_factor: float | tuple[float, float] = 2,
-    z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
-    time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    axes_names: Sequence[str] | None = None,
-    name: str | None = None,
-    chunks: Sequence[int] | Literal["auto"] = "auto",
-    dtype: str = "uint16",
-    dimension_separator: Literal[".", "/"] = "/",
-    compressors: CompressorLike = "auto",
-    overwrite: bool = False,
-    ngff_version: NgffVersions = DefaultNgffVersion,
-) -> ZarrGroupHandler:
-    """Create an empty OME-Zarr image with the given shape and metadata.
-
-    Args:
-        store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Sequence[int]): The shape of the image.
-        pixelsize (float): The pixel size in x and y dimensions.
-        z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
-        time_spacing (float, optional): The spacing between time points.
-            Defaults to 1.0.
-        levels (int | list[str], optional): The number of levels in the pyramid or a
-            list of level names. Defaults to 5.
-        yx_scaling_factor (float, optional): The down-scaling factor in x and y
-            dimensions. Defaults to 2.0.
-        z_scaling_factor (float, optional): The down-scaling factor in z dimension.
-            Defaults to 1.0.
-        space_unit (SpaceUnits, optional): The unit of space. Defaults to
-            DefaultSpaceUnit.
-        time_unit (TimeUnits, optional): The unit of time. Defaults to
-            DefaultTimeUnit.
-        axes_names (Sequence[str] | None, optional): The names of the axes.
-            If None the canonical names are used. Defaults to None.
-        name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Sequence[int] | Literal["auto"]): The chunk shape. If None the shape
-            is used. Defaults to None.
-        dtype (str, optional): The data type of the image. Defaults to "uint16".
-        dimension_separator (DIMENSION_SEPARATOR): The separator to use for
-            dimensions. Defaults to "/".
-        compressors (CompressorLike): The compressors to use. Defaults to "auto".
-        overwrite (bool, optional): Whether to overwrite an existing image.
-            Defaults to True.
-        ngff_version (str, optional): The version of the OME-Zarr specification.
-            Defaults to DefaultVersion.
-
-    """
-    if axes_names is None:
-        axes_names = canonical_axes_order()[-len(shape) :]
-
-    if len(axes_names) != len(shape):
-        raise NgioValueError(
-            f"Number of axes names {axes_names} does not match the number of "
-            f"dimensions {shape}."
-        )
-
-    meta, scaling_factors = _init_generic_meta(
-        meta_type=NgioImageMeta,
-        pixelsize=pixelsize,
-        z_spacing=z_spacing,
-        time_spacing=time_spacing,
-        levels=levels,
-        yx_scaling_factor=yx_scaling_factor,
-        z_scaling_factor=z_scaling_factor,
-        space_unit=space_unit,
-        time_unit=time_unit,
-        axes_names=axes_names,
-        name=name,
-        ngff_version=ngff_version,
-    )
-    mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(
-        store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
-    )
-    image_handler = get_image_meta_handler(
-        version=ngff_version, group_handler=group_handler
-    )
-    image_handler.write_meta(meta)
-
-    init_empty_pyramid(
-        store=store,
-        paths=meta.paths,
-        scaling_factors=scaling_factors,
-        ref_shape=shape,
-        chunks=chunks,
-        axes=axes_names,
-        dtype=dtype,
-        mode="a",
-        dimension_separator=dimension_separator,
-        compressors=compressors,
-        zarr_format=meta.zarr_format,
-    )
-
-    group_handler._mode = "r+"
-    return group_handler

ngio/tables/backends/_non_zarr_backends.py

@@ -1,196 +0,0 @@
-import io
-from collections.abc import Callable
-from typing import Any
-
-from pandas import DataFrame
-from polars import DataFrame as PolarsDataFrame
-from polars import LazyFrame
-from zarr.storage import FsspecStore, LocalStore
-
-from ngio.tables.backends._abstract_backend import AbstractTableBackend
-from ngio.tables.backends._utils import normalize_pandas_df, normalize_polars_lf
-from ngio.utils import NgioFileNotFoundError, NgioValueError
-
-
-class NonZarrBaseBackend(AbstractTableBackend):
-    """A class to load and write small tables in CSV format."""
-
-    def __init__(
-        self,
-        df_reader: Callable[[Any], DataFrame],
-        lf_reader: Callable[[Any], LazyFrame],
-        df_writer: Callable[[str, DataFrame], None],
-        lf_writer: Callable[[str, PolarsDataFrame], None],
-        table_name: str,
-    ):
-        self.df_reader = df_reader
-        self.lf_reader = lf_reader
-        self.df_writer = df_writer
-        self.lf_writer = lf_writer
-        self.table_name = table_name
-
-    @staticmethod
-    def implements_anndata() -> bool:
-        """Whether the handler implements the anndata protocol."""
-        return False
-
-    @staticmethod
-    def implements_pandas() -> bool:
-        """Whether the handler implements the dataframe protocol."""
-        return True
-
-    @staticmethod
-    def implements_polars() -> bool:
-        """Whether the handler implements the polars protocol."""
-        return True
-
-    @staticmethod
-    def backend_name() -> str:
-        """Return the name of the backend."""
-        raise NotImplementedError(
-            "The backend_name method must be implemented in the subclass."
-        )
-
-    def _load_from_directory_store(self, reader):
-        """Load the table from a directory store."""
-        url = self._group_handler.full_url
-        if url is None:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support reading a {ext} table from a "
-                f"store of type {type(self._group_handler)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore."
-            )
-        table_path = f"{url}/{self.table_name}"
-        dataframe = reader(table_path)
-        return dataframe
-
-    def _load_from_fs_store_df(self, reader):
-        """Load the table from an FS store."""
-        path = self._group_handler.group.path
-        table_path = f"{path}/{self.table_name}"
-        bytes_table = self._group_handler.store.get(table_path)
-        if bytes_table is None:
-            raise NgioFileNotFoundError(f"No table found at {table_path}. ")
-        dataframe = reader(io.BytesIO(bytes_table))
-        return dataframe
-
-    def _load_from_fs_store_lf(self, reader):
-        """Load the table from an FS store."""
-        full_url = self._group_handler.full_url
-        parquet_path = f"{full_url}/{self.table_name}"
-        store_fs = self._group_handler.store.fs  # type: ignore (in this context, store_fs is a fs.FSStore)
-        with store_fs.open(parquet_path, "rb") as f:
-            dataframe = reader(f)
-        return dataframe
-
-    def load_as_pandas_df(self) -> DataFrame:
-        """Load the table as a pandas DataFrame."""
-        store = self._group_handler.store
-        if isinstance(store, LocalStore):
-            dataframe = self._load_from_directory_store(reader=self.df_reader)
-        elif isinstance(store, FsspecStore):
-            dataframe = self._load_from_fs_store_df(reader=self.df_reader)
-        else:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support reading a {ext} table from a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-
-        dataframe = normalize_pandas_df(
-            dataframe,
-            index_key=self.index_key,
-            index_type=self.index_type,
-            reset_index=False,
-        )
-        return dataframe
-
-    def load(self) -> DataFrame:
-        """Load the table as a pandas DataFrame."""
-        return self.load_as_pandas_df()
-
-    def load_as_polars_lf(self) -> LazyFrame:
-        """Load the table as a polars LazyFrame."""
-        store = self._group_handler.store
-        if isinstance(store, LocalStore):
-            lazy_frame = self._load_from_directory_store(reader=self.lf_reader)
-        elif isinstance(store, FsspecStore):
-            lazy_frame = self._load_from_fs_store_lf(reader=self.lf_reader)
-        else:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support reading a {ext} from a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-        if not isinstance(lazy_frame, LazyFrame):
-            raise NgioValueError(
-                "Table is not a lazy frame. Please report this issue as an ngio bug."
-                f" {type(lazy_frame)}"
-            )
-
-        lazy_frame = normalize_polars_lf(
-            lazy_frame,
-            index_key=self.index_key,
-            index_type=self.index_type,
-        )
-        return lazy_frame
-
-    def _get_store_url(self) -> str:
-        """Get the store URL."""
-        store = self._group_handler.store
-        if isinstance(store, LocalStore):
-            full_url = self._group_handler.full_url
-        else:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support writing a {ext} file to a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-        if full_url is None:
-            ext = self.table_name.split(".")[-1]
-            raise NgioValueError(
-                f"Ngio does not support writing a {ext} file to a "
-                f"store of type {type(store)}. "
-                "Please make sure to use a compatible "
-                "store like a zarr.DirectoryStore or "
-                "zarr.FSStore."
-            )
-        return full_url
-
-    def write_from_pandas(self, table: DataFrame) -> None:
-        """Write the table from a pandas DataFrame."""
-        table = normalize_pandas_df(
-            table,
-            index_key=self.index_key,
-            index_type=self.index_type,
-            reset_index=True,
-        )
-        full_url = self._get_store_url()
-        table_path = f"{full_url}/{self.table_name}"
-        self.df_writer(table_path, table)
-
-    def write_from_polars(self, table: PolarsDataFrame | LazyFrame) -> None:
-        """Write the table from a polars DataFrame or LazyFrame."""
-        table = normalize_polars_lf(
-            table,
-            index_key=self.index_key,
-            index_type=self.index_type,
-        )
-
-        if isinstance(table, LazyFrame):
-            table = table.collect()
-
-        full_url = self._get_store_url()
-        table_path = f"{full_url}/{self.table_name}"
-        self.lf_writer(table_path, table)

ngio/utils/_logger.py

@@ -1,50 +0,0 @@
-import logging
-import time
-from functools import cache
-
-from ngio.utils._errors import NgioValueError
-
-# Configure the logger
-ngio_logger = logging.getLogger("NgioLogger")
-ngio_logger.setLevel(logging.ERROR)
-
-# Set up a console handler with a custom format
-console_handler = logging.StreamHandler()
-formatter = logging.Formatter(
-    "%(asctime)s - %(levelname)s - %(name)s - "
-    "[%(module)s.%(funcName)s:%(lineno)d]: %(message)s"
-)
-console_handler.setFormatter(formatter)
-
-# Add the handler to the logger
-ngio_logger.addHandler(console_handler)
-
-
-def set_logger_level(level: str) -> None:
-    """Set the logger level.
-
-    Args:
-        level: The level to set the logger to.
-            Must be one of "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL".
-    """
-    if level not in ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]:
-        raise NgioValueError(f"Invalid log level: {level}")
-
-    ngio_logger.setLevel(level)
-
-
-@cache
-def _warn(message: str, ttl_hash: int) -> None:
-    """Log a warning message with a time-to-live (TTL) hash."""
-    ngio_logger.warning(message, stacklevel=3)
-
-
-def ngio_warn(message: str, cooldown: int = 2) -> None:
-    """Log a warning message.
-
-    Args:
-        message: The warning message to log.
-        cooldown: The cooldown period in seconds to avoid repeated logging.
-    """
-    ttl_hash = time.time() // cooldown
-    _warn(message, ttl_hash)