ngio 0.1.6__py3-none-any.whl → 0.2.0a2__py3-none-any.whl

ngio/ngff_meta/fractal_image_meta.py

@@ -1,1267 +0,0 @@
-"""Image metadata models.
-
-This module contains the models for the image metadata.
-These metadata models are not adhering to the OME standard.
-But they can be built from the OME standard metadata, and the
-can be converted to the OME standard.
-"""
-
-from collections.abc import Collection
-from difflib import SequenceMatcher
-from enum import Enum
-from typing import Any, TypeVar
-
-import numpy as np
-from pydantic import BaseModel, Field, field_validator
-from typing_extensions import Self
-
-from ngio.utils._pydantic_utils import BaseWithExtraFields
-
-T = TypeVar("T")
-
-
-class NgffVersion(str, Enum):
-    """Allowed NGFF versions."""
-
-    v04 = "0.4"
-
-
-################################################################################################
-#
-# Omero Section of the Metadata is used to store channel information and visualisation
-# settings.
-# This section is transitory and will be likely changed in the future.
-#
-#################################################################################################
-
-
-class NgioColors(str, Enum):
-    """Default colors for the channels."""
-
-    dapi = "0000FF"
-    hoechst = "0000FF"
-    gfp = "00FF00"
-    cy3 = "FFFF00"
-    cy5 = "FF0000"
-    brightfield = "808080"
-    red = "FF0000"
-    yellow = "FFFF00"
-    magenta = "FF00FF"
-    cyan = "00FFFF"
-    gray = "808080"
-    green = "00FF00"
-
-    @staticmethod
-    def semi_random_pick(channel_name: str | None = None) -> "NgioColors":
-        """Try to fuzzy match the color to the channel name.
-
-        - If a channel name is given will try to match the channel name to the color.
-        - If name has the paatern 'channel_x' cyclic rotate over a list of colors
-            [cyan, magenta, yellow, green]
-        - If no channel name is given will return a random color.
-        """
-        available_colors = NgioColors._member_names_
-
-        if channel_name is None:
-            # Purely random color
-            color_str = available_colors[np.random.randint(0, len(available_colors))]
-            return NgioColors.__members__[color_str]
-
-        if channel_name.startswith("channel_"):
-            # Rotate over a list of colors
-            defaults_colors = [
-                NgioColors.cyan,
-                NgioColors.magenta,
-                NgioColors.yellow,
-                NgioColors.green,
-            ]
-
-            try:
-                index = int(channel_name.split("_")[-1]) % len(defaults_colors)
-                return defaults_colors[index]
-            except ValueError:
-                # If the name of the channel is something like
-                # channel_dapi this will fail an proceed to the
-                # standard fuzzy match
-                pass
-
-        similarity = {}
-        for color in available_colors:
-            # try to match the color to the channel name
-            similarity[color] = SequenceMatcher(None, channel_name, color).ratio()
-        color_str = max(similarity, key=similarity.get)
-        return NgioColors.__members__[color_str]
-
-
-def valid_hex_color(v: str) -> bool:
-    """Validate a hexadecimal color.
-
-    Check that `color` is made of exactly six elements which are letters
-    (a-f or A-F) or digits (0-9).
-    If fail, raise a ValueError.
-
-    Implementation source:
-    https://github.com/fractal-analytics-platform/fractal-tasks-core/fractal_tasks_core/channels.py#L87
-    Original authors:
-     - Tommaso Comparin <tommaso.comparin@exact-lab.it>
-    """
-    if len(v) != 6:
-        return False
-    allowed_characters = "abcdefABCDEF0123456789"
-    for character in v:
-        if character not in allowed_characters:
-            return False
-    return True
-
-
-class ChannelVisualisation(BaseWithExtraFields):
-    """Channel visualisation model.
-
-    Contains the information about the visualisation of a channel.
-
-    Attributes:
-        color(str): The color of the channel in hexadecimal format or a color name.
-        min(int | float): The minimum value of the channel.
-        max(int | float): The maximum value of the channel.
-        start(int | float): The start value of the channel.
-        end(int | float): The end value of the channel.
-        active(bool): Whether the channel is active.
-    """
-
-    color: str | NgioColors | None = Field(default=None, validate_default=True)
-    min: int | float = 0
-    max: int | float = 65535
-    start: int | float = 0
-    end: int | float = 65535
-    active: bool = True
-
-    @field_validator("color", mode="after")
-    @classmethod
-    def validate_color(cls, value: str | NgioColors) -> str:
-        """Color validator.
-
-        There are three possible values to set a color:
-         - A hexadecimal string.
-         - A color name.
-         - A NgioColors element.
-        """
-        if value is None:
-            return NgioColors.semi_random_pick().value
-        if isinstance(value, str) and valid_hex_color(value):
-            return value
-        elif isinstance(value, str):
-            value_lower = value.lower()
-            return NgioColors.semi_random_pick(value_lower).value
-        elif isinstance(value, NgioColors):
-            return value.value
-        else:
-            raise ValueError("Invalid color value.")
-
-    @classmethod
-    def lazy_init(
-        cls,
-        color: str | NgioColors | None = None,
-        start: int | float | None = None,
-        end: int | float | None = None,
-        active: bool = True,
-        data_type: Any = np.uint16,
-    ) -> "ChannelVisualisation":
-        """Create a ChannelVisualisation object with the default unit.
-
-        Args:
-            color(str): The color of the channel in hexadecimal format or a color name.
-            start(int | float | None): The start value of the channel.
-            end(int | float | None): The end value of the channel.
-            data_type(Any): The data type of the channel.
-            active(bool): Whether the channel should be shown by default.
-        """
-        for func in [np.iinfo, np.finfo]:
-            try:
-                min_value = func(data_type).min
-                max_value = func(data_type).max
-                break
-            except ValueError:
-                continue
-        else:
-            raise ValueError(f"Invalid data type {data_type}.")
-
-        start = start if start is not None else min_value
-        end = end if end is not None else max_value
-        return ChannelVisualisation(
-            color=color,
-            min=min_value,
-            max=max_value,
-            start=start,
-            end=end,
-            active=active,
-        )
-
-
-class Channel(BaseModel):
-    """Information about a channel in the image.
-
-    Attributes:
-        label(str): The label of the channel.
-        wavelength_id(str): The wavelength ID of the channel.
-        extra_fields(dict): To reduce the api surface, extra fields are stored in the
-            the channel attributes will be stored in the extra_fields attribute.
-    """
-
-    label: str
-    wavelength_id: str | None = None
-    channel_visualisation: ChannelVisualisation
-
-    @classmethod
-    def lazy_init(
-        cls,
-        label: str,
-        wavelength_id: str | None = None,
-        color: str | NgioColors | None = None,
-        start: int | float | None = None,
-        end: int | float | None = None,
-        active: bool = True,
-        data_type: Any = np.uint16,
-    ) -> "Channel":
-        """Create a Channel object with the default unit.
-
-        Args:
-            label(str): The label of the channel.
-            wavelength_id(str | None): The wavelength ID of the channel.
-            color(str): The color of the channel in hexadecimal format or a color name.
-                If None, the color will be picked based on the label.
-            start(int | float | None): The start value of the channel.
-            end(int | float | None): The end value of the channel.
-            active(bool): Whether the channel should be shown by default.
-            data_type(Any): The data type of the channel.
-        """
-        if color is None:
-            # If no color is provided, try to pick a color based on the label
-            # See the NgioColors.semi_random_pick method for more details.
-            color = label
-
-        channel_visualization = ChannelVisualisation.lazy_init(
-            color=color, start=start, end=end, active=active, data_type=data_type
-        )
-
-        if wavelength_id is None:
-            # TODO Evaluate if a better default value can be used
-            wavelength_id = label
-
-        return cls(
-            label=label,
-            wavelength_id=wavelength_id,
-            channel_visualisation=channel_visualization,
-        )
-
-
-def _check_elements(elements: Collection[T], expected_type: Any) -> Collection[T]:
-    """Check that the elements are of the same type."""
-    if len(elements) == 0:
-        raise ValueError("At least one element must be provided.")
-
-    for element in elements:
-        if not isinstance(element, expected_type):
-            raise ValueError(
-                f"All elements must be of the same type {expected_type}. Got {element}."
-            )
-
-    return elements
-
-
-def _check_unique(elements: Collection[T]) -> Collection[T]:
-    """Check that the elements are unique."""
-    if len(set(elements)) != len(elements):
-        raise ValueError("All elements must be unique.")
-    return elements
-
-
-class Omero(BaseWithExtraFields):
-    """Information about the OMERO metadata.
-
-    Attributes:
-        channels(list[Channel]): The list of channels in the image.
-        extra_fields(dict): To reduce the api surface, extra fields are stored in the
-            the omero attributes will be stored in the extra_fields attribute.
-    """
-
-    channels: list[Channel] = Field(default_factory=list)
-
-    @classmethod
-    def lazy_init(
-        cls,
-        labels: Collection[str] | int,
-        wavelength_id: Collection[str] | None = None,
-        colors: Collection[str | NgioColors] | None = None,
-        start: Collection[int | float] | int | float | None = None,
-        end: Collection[int | float] | int | float | None = None,
-        active: Collection[bool] | None = None,
-        data_type: Any = np.uint16,
-        **omero_kwargs: dict,
-    ) -> "Omero":
-        """Create an Omero object with the default unit.
-
-        Args:
-            labels(Collection[str] | int): The list of channels names in the image.
-                If an integer is provided, the channels will be named "channel_i".
-            wavelength_id(Collection[str] | None): The wavelength ID of the channel.
-                If None, the wavelength ID will be the same as the channel name.
-            colors(Collection[str, NgioColors] | None): The list of colors for the
-                channels. If None, the colors will be random.
-            start(Collection[int | float] | int | float | None): The start value of the
-                channel. If None, the start value will be the minimum value of the
-                data type.
-            end(Collection[int | float] | int | float | None): The end value of the
-                channel. If None, the end value will be the maximum value of the
-                data type.
-            data_type(Any): The data type of the channel. Will be used to set the
-                min and max values of the channel.
-            active (Collection[bool] | None):active(bool): Whether the channel should
-                be shown by default.
-            omero_kwargs(dict): Extra fields to store in the omero attributes.
-        """
-        if isinstance(labels, int):
-            labels = [f"channel_{i}" for i in range(labels)]
-
-        labels = _check_elements(labels, str)
-        labels = _check_unique(labels)
-
-        _wavelength_id: Collection[str | None] = [None] * len(labels)
-        if isinstance(wavelength_id, Collection):
-            _wavelength_id = _check_elements(wavelength_id, str)
-            _wavelength_id = _check_unique(wavelength_id)
-
-        _colors: Collection[str | NgioColors] = ["random"] * len(labels)
-        if isinstance(colors, Collection):
-            _colors = _check_elements(colors, str | NgioColors)
-
-        _start: Collection[int | float | None] = [None] * len(labels)
-        if isinstance(start, Collection):
-            _start = _check_elements(start, (int, float))
-
-        _end: Collection[int | float | None] = [None] * len(labels)
-        if isinstance(end, Collection):
-            _end = _check_elements(end, (int, float))
-
-        _active: Collection[bool] = [True] * len(labels)
-        if isinstance(active, Collection):
-            _active = _check_elements(active, bool)
-
-        omero_channels = []
-        for ch_name, w_id, color, s, e, a in zip(
-            labels, _wavelength_id, _colors, _start, _end, _active, strict=True
-        ):
-            omero_channels.append(
-                Channel.lazy_init(
-                    label=ch_name,
-                    wavelength_id=w_id,
-                    color=color,
-                    start=s,
-                    end=e,
-                    active=a,
-                    data_type=data_type,
-                )
-            )
-        return cls(channels=omero_channels, **omero_kwargs)
-
-
-################################################################################################
-#
-# Axis Types and Units
-# We define a small set of axis types and units that can be used in the metadata.
-# This axis types are more restrictive than the OME standard.
-# We do that to simplify the data processing.
-#
-#################################################################################################
-
-
-class AxisType(str, Enum):
-    """Allowed axis types."""
-
-    channel = "channel"
-    time = "time"
-    space = "space"
-
-
-class SpaceUnits(str, Enum):
-    """Allowed space units."""
-
-    nanometer = "nanometer"
-    nm = "nm"
-    micrometer = "micrometer"
-    um = "um"
-    millimeter = "millimeter"
-    mm = "mm"
-    centimeter = "centimeter"
-    cm = "cm"
-
-    @classmethod
-    def allowed_names(self) -> list[str]:
-        """Get the allowed space axis names."""
-        return list(SpaceUnits.__members__.keys())
-
-
-class SpaceNames(str, Enum):
-    """Allowed space axis names."""
-
-    z = "z"
-    y = "y"
-    x = "x"
-
-    @classmethod
-    def allowed_names(self) -> list[str]:
-        """Get the allowed space axis names."""
-        return list(SpaceNames.__members__.keys())
-
-
-class ChannelNames(str, Enum):
-    """Allowed channel axis names."""
-
-    c = "c"
-
-    @classmethod
-    def allowed_names(self) -> list[str]:
-        """Get the allowed channel axis names."""
-        return list(ChannelNames.__members__.keys())
-
-
-class TimeUnits(str, Enum):
-    """Allowed time units."""
-
-    seconds = "seconds"
-    s = "s"
-
-    @classmethod
-    def allowed_names(self) -> list[str]:
-        """Get the allowed time axis names."""
-        return list(TimeUnits.__members__.keys())
-
-
-class TimeNames(str, Enum):
-    """Allowed time axis names."""
-
-    t = "t"
-
-    @classmethod
-    def allowed_names(self) -> list[str]:
-        """Get the allowed time axis names."""
-        return list(TimeNames.__members__.keys())
-
-
-################################################################################################
-#
-# PixelSize model
-# The PixelSize model is used to store the pixel size in 3D space.
-# The model does not store scaling factors and units for other axes.
-#
-#################################################################################################
-
-
-class PixelSize(BaseModel):
-    """PixelSize class to store the pixel size in 3D space."""
-
-    x: float = Field(..., ge=0)
-    y: float = Field(..., ge=0)
-    z: float = Field(1.0, ge=0)
-    unit: SpaceUnits = SpaceUnits.micrometer
-    virtual: bool = False
-
-    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})"
-
-    @classmethod
-    def from_list(
-        cls, sizes: list[float], unit: SpaceUnits = SpaceUnits.micrometer
-    ) -> "PixelSize":
-        """Build a PixelSize object from a list of sizes.
-
-        Order of the sizes:
-            - for 2d: [y, x]
-            - for 3d: [z, y, x]
-
-        Note: The order of the sizes must be z, y, x.
-
-        Args:
-            sizes(list[float]): The list of sizes.
-            unit(SpaceUnits): The unit of the sizes.
-        """
-        if len(sizes) == 2:
-            return cls(y=sizes[0], x=sizes[1], z=1, unit=unit)
-        elif len(sizes) == 3:
-            return cls(z=sizes[0], y=sizes[1], x=sizes[2], unit=unit)
-        else:
-            raise ValueError("Invalid pixel size list. Must have 2 or 3 elements.")
-
-    def as_dict(self) -> dict:
-        """Return the pixel size as a dictionary."""
-        return {"z": self.z, "y": self.y, "x": self.x}
-
-    @property
-    def zyx(self) -> tuple[float, float, float]:
-        """Return the voxel size in z, y, x order."""
-        return self.z, self.y, self.x
-
-    @property
-    def yx(self) -> tuple[float, float]:
-        """Return the xy plane pixel size in y, x order."""
-        return self.y, self.x
-
-    @property
-    def voxel_volume(self) -> float:
-        """Return the volume of a voxel."""
-        return self.y * self.x * self.z
-
-    @property
-    def xy_plane_area(self) -> float:
-        """Return the area of the xy plane."""
-        return self.y * self.x
-
-    def distance(self, other: "PixelSize") -> float:
-        """Return the distance between two pixel sizes."""
-        return float(np.linalg.norm(np.array(self.zyx) - np.array(other.zyx)))
-
-
-################################################################################################
-#
-# Axis and Dataset models are the two core components of the OME-NFF
-#  multiscale metadata.
-# The Axis model is used to store the information about an axis (name, unit, type).
-# The Dataset model is used to store the information about a
-#  dataset (path, axes, scale).
-#
-# The Dataset and Axis have two representations:
-#  - on_disk: The representation of the metadata as stored on disk. This representation
-#   preserves the order of the axes and the scale transformation.
-#  - canonical: The representation of the metadata in the canonical order.
-#   This representation is used to simplify the data processing.
-#
-#################################################################################################
-
-
-class Axis:
-    """Axis infos model."""
-
-    def __init__(
-        self,
-        name: str | TimeNames | SpaceNames,
-        unit: SpaceUnits | TimeUnits | None = None,
-    ) -> None:
-        """Initialize the Axis object.
-
-        Args:
-            name(str): The name of the axis.
-            unit(SpaceUnits | TimeUnits | None): The unit of the axis.
-        """
-        if name is None:
-            raise ValueError("Axis name cannot be None.")
-
-        if isinstance(name, Enum):
-            name = name.value
-
-        self._name = name
-        self._unit = unit
-
-        if name in TimeNames.allowed_names():
-            self._type = AxisType.time
-
-            if unit is None:
-                self._unit = TimeUnits.s
-            elif unit not in TimeUnits.allowed_names():
-                raise ValueError(f"Invalid time unit {unit}.")
-            else:
-                self._unit = unit
-
-        elif name in SpaceNames.allowed_names():
-            self._type = AxisType.space
-
-            if unit is None:
-                self._unit = SpaceUnits.um
-            elif unit not in SpaceUnits.allowed_names():
-                raise ValueError(f"Invalid space unit {unit}.")
-            else:
-                self._unit = unit
-
-        elif name in ChannelNames.allowed_names():
-            self._type = AxisType.channel
-            if unit is not None:
-                raise ValueError("Channel axis cannot have a unit.")
-            self._unit = None
-        else:
-            raise ValueError(f"Invalid axis name {name}.")
-
-    @classmethod
-    def lazy_create(
-        cls,
-        name: str | TimeNames | SpaceNames,
-        time_unit: TimeUnits | None = None,
-        space_unit: SpaceUnits | None = None,
-    ) -> "Axis":
-        """Create an Axis object with the default unit."""
-        if name in TimeNames.allowed_names():
-            return cls(name=name, unit=time_unit)
-        elif name in SpaceNames.allowed_names():
-            return cls(name=name, unit=space_unit)
-        else:
-            return cls(name=name, unit=None)
-
-    @classmethod
-    def batch_create(
-        cls,
-        axes_names: Collection[str | SpaceNames | TimeNames],
-        time_unit: TimeUnits | None = None,
-        space_unit: SpaceUnits | None = None,
-    ) -> list["Axis"]:
-        """Create a list of Axis objects from a list of dictionaries."""
-        axes = []
-        for name in axes_names:
-            axes.append(
-                cls.lazy_create(name=name, time_unit=time_unit, space_unit=space_unit)
-            )
-        return axes
-
-    @property
-    def name(self) -> str:
-        """Get the name of the axis."""
-        return self._name
-
-    @property
-    def unit(self) -> SpaceUnits | TimeUnits | None:
-        """Get the unit of the axis."""
-        return self._unit
-
-    @unit.setter
-    def unit(self, unit: SpaceUnits | TimeUnits | None) -> None:
-        """Set the unit of the axis."""
-        self._unit = unit
-
-    @property
-    def type(self) -> AxisType:
-        """Get the type of the axis."""
-        return self._type
-
-    def model_dump(self) -> dict:
-        """Return the axis information in a dictionary."""
-        _dict = {"name": self.name, "unit": self.unit, "type": self.type}
-        # Remove None values
-        return {k: v for k, v in _dict.items() if v is not None}
-
-
-class Dataset:
-    """Model for a dataset in the multiscale.
-
-    To initialize the Dataset object, the path, the axes, scale, and translation list
-    can be provided with on_disk order.
-
-    The Dataset object will reorder the scale and translation lists according to the
-    following canonical order of the axes:
-        * Time axis (if present)
-        * Channel axis (if present)
-        * Z axis (if present)
-        * Y axis (Mandatory)
-        * X axis (Mandatory)
-    """
-
-    def __init__(
-        self,
-        *,
-        path: str,
-        on_disk_axes: list[Axis],
-        on_disk_scale: list[float],
-        on_disk_translation: list[float] | None = None,
-        canonical_order: list[str] | None = None,
-    ):
-        """Initialize the Dataset object.
-
-        Args:
-            path(str): The path of the dataset.
-            on_disk_axes(list[Axis]): The list of axes in the multiscale.
-            on_disk_scale(list[float]): The list of scale transformation.
-                The scale transformation must have the same length as the axes.
-            on_disk_translation(list[float] | None): The list of translation.
-            canonical_order(list[str] | None): The canonical order of the axes.
-                If None, the default order is ["t", "c", "z", "y", "x"].
-        """
-        self._path = path
-
-        # Canonical order validation
-        if canonical_order is None:
-            self._canonical_order = ["t", "c", "z", "y", "x"]
-        else:
-            self._canonical_order = canonical_order
-
-        for ax in on_disk_axes:
-            if ax.name not in self._canonical_order:
-                raise ValueError(f"Axis {ax.name} not found in the canonical order.")
-
-        if len(set(self._canonical_order)) != len(self._canonical_order):
-            raise ValueError("Canonical order must have unique elements.")
-
-        if len(set(on_disk_axes)) != len(on_disk_axes):
-            raise ValueError("on_disk axes must have unique elements.")
-
-        self._on_disk_axes = on_disk_axes
-
-        # Scale transformation validation
-        if len(on_disk_scale) != len(on_disk_axes):
-            raise ValueError(
-                "Inconsistent scale transformation. "
-                "The scale transformation must have the same length."
-            )
-        self._scale = on_disk_scale
-
-        # Translation transformation validation
-        if on_disk_translation is not None and len(on_disk_translation) != len(
-            on_disk_axes
-        ):
-            raise ValueError(
-                "Inconsistent translation transformation. "
-                "The translation transformation must have the same length."
-            )
-
-        self._translation = on_disk_translation
-
-        # Compute the index mapping between the canonical order and the actual order
-        _map = {ax.name: i for i, ax in enumerate(on_disk_axes)}
-
-        self._index_mapping = {}
-        for name in self._canonical_order:
-            _index = _map.get(name, None)
-            if _index is not None:
-                self._index_mapping[name] = _index
-
-        self._ordered_axes = [
-            on_disk_axes[i] for i in self._index_mapping.values() if i is not None
-        ]
-
-    @property
-    def path(self) -> str:
-        """Get the path of the dataset."""
-        return self._path
-
-    @property
-    def index_mapping(self) -> dict[str, int]:
-        """Get the mapping between the canonical order and the actual order."""
-        return self._index_mapping
-
-    @property
-    def axes(self) -> list[Axis]:
-        """Get the axes in the canonical order."""
-        return self._ordered_axes
-
-    @property
-    def on_disk_axes_names(self) -> list[str]:
-        """Get the axes in the on-disk order."""
-        return [ax.name for ax in self._on_disk_axes]
-
-    @property
-    def axes_order(self) -> list[int]:
-        """Get the mapping between the canonical order and the on-disk order.
-
-        Example:
-            on_disk_order = ["z", "c", "y", "x"]
-            canonical_order = ["c", "z", "y", "x"]
-            axes_order = [1, 0, 2, 3]
-        """
-        on_disk_axes = self.on_disk_axes_names
-        canonical_axes = self.axes_names
-        return [on_disk_axes.index(ax) for ax in canonical_axes]
-
-    @property
-    def reverse_axes_order(self) -> list[int]:
-        """Get the mapping between the on-disk order and the canonical order.
-
-        It is the inverse of the axes_order.
-        """
-        sorted_order = np.argsort(self.axes_order).tolist()
-        return sorted_order  # type: ignore
-
-    @property
-    def scale(self) -> list[float]:
-        """Get the scale transformation of the dataset in the canonical order."""
-        return [self._scale[i] for i in self._index_mapping.values() if i is not None]
-
-    @property
-    def time_spacing(self) -> float:
-        """Get the time spacing of the dataset."""
-        t = self.index_mapping.get("t")
-        if t is None:
-            return 1.0
-
-        scale_t = self.scale[t]
-        return scale_t
-
-    @property
-    def on_disk_scale(self) -> list[float]:
-        """Get the scale transformation of the dataset in the on-disk order."""
-        return self._scale
-
-    @property
-    def translation(self) -> list[float] | None:
-        """Get the translation transformation of the dataset in the canonical order."""
-        if self._translation is None:
-            return None
-        return [self._translation[i] for i in self._index_mapping.values()]
-
-    @property
-    def axes_names(self) -> list[str]:
-        """Get the axes names in the canonical order."""
-        return [ax.name for ax in self.axes]
-
-    @property
-    def space_axes_names(self) -> list[str]:
-        """Get the spatial axes names in the canonical order."""
-        return [ax.name for ax in self.axes if ax.type == AxisType.space]
-
-    @property
-    def space_axes_unit(self) -> SpaceUnits:
-        """Get the unit of the spatial axes."""
-        types = [ax.unit for ax in self.axes if ax.type == AxisType.space]
-        if len(set(types)) > 1:
-            raise ValueError("Inconsistent spatial axes units.")
-        return_type = types[0]
-        if return_type is None:
-            raise ValueError("Spatial axes must have a unit.")
-        if return_type not in SpaceUnits.allowed_names():
-            raise ValueError(f"Invalid space unit {return_type}.")
-        return SpaceUnits(return_type)
-
-    @property
-    def pixel_size(self) -> PixelSize:
-        """Get the pixel size of the dataset."""
-        pixel_sizes = {}
-
-        for ax, scale in zip(self.axes, self.scale, strict=True):
-            if ax.type == AxisType.space:
-                pixel_sizes[ax.name] = scale
-
-        return PixelSize(
-            x=pixel_sizes["x"],
-            y=pixel_sizes["y"],
-            z=pixel_sizes.get("z", 1.0),
-            unit=self.space_axes_unit,
-        )
-
-    @property
-    def time_axis_unit(self) -> TimeUnits | None:
-        """Get the unit of the time axis."""
-        types = [ax.unit for ax in self.axes if ax.type == AxisType.time]
-        if len(types) == 0:
-            return None
-        elif len(types) == 1:
-            return TimeUnits(types[0])
-        else:
-            raise ValueError("Multiple time axes found. Only one time axis is allowed.")
-
-    def remove_axis(self, axis_name: str) -> "Dataset":
-        """Remove an axis from the dataset.
-
-        Args:
-            axis_name(str): The name of the axis to remove.
-        """
-        if axis_name not in self.axes_names:
-            raise ValueError(f"Axis {axis_name} not found in the dataset.")
-
-        if axis_name in ["x", "y"]:
-            raise ValueError("Cannot remove mandatory axes x and y.")
-
-        axes_idx = self.index_mapping[axis_name]
-
-        new_on_disk_axes = self._on_disk_axes.copy()
-        new_on_disk_axes.pop(axes_idx)
-
-        new_scale = self._scale.copy()
-        new_scale.pop(axes_idx)
-
-        if self._translation is not None:
-            new_translation = self._translation.copy()
-            new_translation.pop(axes_idx)
-        else:
-            new_translation = None
-
-        return Dataset(
-            path=self.path,
-            on_disk_axes=new_on_disk_axes,
-            on_disk_scale=new_scale,
-            on_disk_translation=new_translation,
-            canonical_order=self._canonical_order,
-        )
-
-
-################################################################################################
-#
-# BaseMeta, ImageMeta and LabelMeta are the core models to represent the multiscale the
-#  OME-NGFF spec on memory. The are the only interfaces to interact with
-#  the metadata on-disk and the metadata in memory.
-#
-#################################################################################################
-class BaseMeta:
-    """Base class for ImageMeta and LabelMeta."""
-
-    def __init__(self, version: str, name: str | None, datasets: list[Dataset]) -> None:
-        """Initialize the ImageMeta object."""
-        self._version = NgffVersion(version)
-        self._name = name
-
-        if len(datasets) == 0:
-            raise ValueError("At least one dataset must be provided.")
-
-        self._datasets = datasets
-
-    @property
-    def version(self) -> NgffVersion:
-        """Version of the OME-NFF metadata used to build the object."""
-        return self._version
-
-    @property
-    def name(self) -> str | None:
-        """Name of the image."""
-        return self._name
-
-    @property
-    def datasets(self) -> list[Dataset]:
-        """List of datasets in the multiscale."""
-        return self._datasets
-
-    @property
-    def num_levels(self) -> int:
-        """Number of levels in the multiscale."""
-        return len(self.datasets)
-
-    @property
-    def levels_paths(self) -> list[str]:
-        """List of paths of the datasets."""
-        return [dataset.path for dataset in self.datasets]
-
-    @property
-    def index_mapping(self) -> dict[str, int]:
-        """Get the mapping between the canonical order and the actual order."""
-        return self.datasets[0].index_mapping
-
-    @property
-    def axes(self) -> list[Axis]:
-        """List of axes in the canonical order."""
-        return self.datasets[0].axes
-
-    @property
-    def axes_names(self) -> list[str]:
-        """List of axes names in the canonical order."""
-        return self.datasets[0].axes_names
-
-    @property
-    def space_axes_names(self) -> list[str]:
-        """List of spatial axes names in the canonical order."""
-        return self.datasets[0].space_axes_names
-
-    @property
-    def space_axes_unit(self) -> SpaceUnits:
-        """Get the unit of the spatial axes."""
-        return self.datasets[0].space_axes_unit
-
-    @property
-    def time_axis_unit(self) -> TimeUnits | None:
-        """Get the unit of the time axis."""
-        return self.datasets[0].time_axis_unit
-
-    def _get_dataset_by_path(self, path: str) -> Dataset:
-        """Get a dataset by its path."""
-        for dataset in self.datasets:
-            if dataset.path == path:
-                return dataset
-        raise ValueError(f"Dataset with path {path} not found.")
-
-    def _get_dataset_by_index(self, idx: int) -> Dataset:
-        """Get a dataset by its index."""
-        if idx < 0 or idx >= len(self.datasets):
-            raise ValueError(f"Index {idx} out of range.")
-        return self.datasets[idx]
-
-    def _get_dataset_by_pixel_size(
-        self, pixel_size: PixelSize, strict: bool = False, tol: float = 1e-6
-    ) -> Dataset:
-        """Get a dataset with the closest pixel size.
-
-        Args:
-            pixel_size(PixelSize): The pixel size to search for.
-            strict(bool): If True, the pixel size must smaller than tol.
-            tol(float): Any pixel size with a distance less than tol will be considered.
-        """
-        min_dist = np.inf
-
-        for dataset in self.datasets:
-            dist = dataset.pixel_size.distance(pixel_size)
-            if dist < min_dist:
-                min_dist = dist
-                closest_dataset = dataset
-
-        if strict and min_dist > tol:
-            raise ValueError("No dataset with a pixel size close enough.")
-
-        return closest_dataset
-
-    def get_dataset(
-        self,
-        *,
-        path: str | None = None,
-        idx: int | None = None,
-        pixel_size: PixelSize | None = None,
-        highest_resolution: bool = False,
-        strict: bool = False,
-    ) -> Dataset:
-        """Get a dataset by its path, index or pixel size.
-
-        Args:
-            path(str): The path of the dataset.
-            idx(int): The index of the dataset.
-            pixel_size(PixelSize): The pixel size to search for.
-            highest_resolution(bool): If True, the dataset with the highest resolution
-            strict(bool): If True, the pixel size must be exactly the same.
-                If pixel_size is None, strict is ignored.
-        """
-        # Only one of the arguments must be provided
-        if (
-            sum(
-                [
-                    path is not None,
-                    idx is not None,
-                    pixel_size is not None,
-                    highest_resolution,
-                ]
-            )
-            != 1
-        ):
-            raise ValueError("get_dataset must receive only one argument.")
-
-        if path is not None:
-            return self._get_dataset_by_path(path)
-        elif idx is not None:
-            return self._get_dataset_by_index(idx)
-        elif pixel_size is not None:
-            return self._get_dataset_by_pixel_size(pixel_size, strict=strict)
-        elif highest_resolution:
-            return self.get_highest_resolution_dataset()
-        else:
-            raise ValueError("get_dataset has no valid arguments.")
-
-    def get_highest_resolution_dataset(self) -> Dataset:
-        """Get the dataset with the highest resolution."""
-        return self._get_dataset_by_pixel_size(
-            pixel_size=PixelSize(x=0.0, y=0.0, z=0.0, unit=SpaceUnits.um), strict=False
-        )
-
-    def scale(self, path: str | None = None, idx: int | None = None) -> list[float]:
-        """Get the scale transformation of a dataset.
-
-        Args:
-            path(str): The path of the dataset.
-            idx(int): The index of the dataset.
-        """
-        return self.get_dataset(path=path, idx=idx).scale
-
-    def _scaling_factors(self) -> list[float]:
-        scaling_factors = []
-        for d1, d2 in zip(self.datasets[1:], self.datasets[:-1], strict=True):
-            scaling_factors.append(
-                [d1 / d2 for d1, d2 in zip(d1.scale, d2.scale, strict=True)]
-            )
-
-        for sf in scaling_factors:
-            assert (
-                sf == scaling_factors[0]
-            ), "Inconsistent scaling factors not well supported."
-        return scaling_factors[0]
-
-    @property
-    def xy_scaling_factor(self) -> float:
-        """Get the xy scaling factor of the dataset."""
-        scaling_factors = self._scaling_factors()
-        x, y = self.index_mapping.get("x"), self.index_mapping.get("y")
-        if x is None or y is None:
-            raise ValueError("Mandatory axes x and y not found.")
-
-        x_scaling_f = scaling_factors[x]
-        y_scaling_f = scaling_factors[y]
-
-        if not np.allclose(x_scaling_f, y_scaling_f):
-            raise ValueError("Inconsistent xy scaling factor.")
-        return x_scaling_f
-
-    @property
-    def z_scaling_factor(self) -> float:
-        """Get the z scaling factor of the dataset."""
-        scaling_factors = self._scaling_factors()
-        z = self.index_mapping.get("z")
-        if z is None:
-            return 1.0
-
-        z_scaling_f = scaling_factors[z]
-        return z_scaling_f
-
-    def translation(
-        self, path: str | None = None, idx: int | None = None
-    ) -> list[float] | None:
-        """Get the translation transformation of a dataset.
-
-        Args:
-            path(str): The path of the dataset.
-            idx(int): The index of the dataset.
-        """
-        return self.get_dataset(path=path, idx=idx).translation
-
-    def pixel_size(self, path: str | None = None, idx: int | None = None) -> PixelSize:
-        """Get the pixel size of a dataset.
-
-        Args:
-            path(str): The path of the dataset.
-            idx(int): The index of the dataset.
-        """
-        return self.get_dataset(path=path, idx=idx).pixel_size
-
-    def remove_axis(self, axis_name: str) -> Self:
-        """Remove an axis from the metadata.
-
-        Args:
-            axis_name(str): The name of the axis to remove.
-        """
-        new_datasets = [dataset.remove_axis(axis_name) for dataset in self.datasets]
-        return self.__class__(
-            version=self.version, name=self.name, datasets=new_datasets
-        )
-
-
-class LabelMeta(BaseMeta):
-    """Label metadata model."""
-
-    def __init__(self, version: str, name: str | None, datasets: list[Dataset]) -> None:
-        """Initialize the ImageMeta object."""
-        super().__init__(version, name, datasets)
-
-        # Make sure that there are no channel axes
-        for ax in self.datasets[0].axes:
-            if ax.type == AxisType.channel:
-                raise ValueError("Channel axes are not allowed in ImageMeta.")
-
-
-class ImageMeta(BaseMeta):
-    """Image metadata model."""
-
-    def __init__(
-        self,
-        version: str,
-        name: str | None,
-        datasets: list[Dataset],
-        omero: Omero | None = None,
-    ) -> None:
-        """Initialize the ImageMeta object."""
-        super().__init__(version=version, name=name, datasets=datasets)
-        self._omero = omero
-
-    @property
-    def omero(self) -> Omero | None:
-        """Get the OMERO metadata."""
-        return self._omero
-
-    def set_omero(self, omero: Omero) -> None:
-        """Set omero metadata."""
-        self._omero = omero
-
-    def lazy_init_omero(
-        self,
-        labels: list[str] | int,
-        wavelength_ids: list[str] | None = None,
-        colors: list[str] | None = None,
-        active: list[bool] | None = None,
-        start: list[int | float] | None = None,
-        end: list[int | float] | None = None,
-        data_type: Any = np.uint16,
-    ) -> None:
-        """Set the OMERO metadata for the image.
-
-        Args:
-            labels (list[str]|int): The labels of the channels.
-            wavelength_ids (list[str], optional): The wavelengths of the channels.
-            colors (list[str], optional): The colors of the channels.
-            adjust_window (bool, optional): Whether to adjust the window.
-            start_percentile (int, optional): The start percentile.
-            end_percentile (int, optional): The end percentile.
-            active (list[bool], optional): Whether the channel is active.
-            start (list[int | float], optional): The start value of the channel.
-            end (list[int | float], optional): The end value of the channel.
-            end (int): The end value of the channel.
-            data_type (Any): The data type of the channel.
-        """
-        omero = Omero.lazy_init(
-            labels=labels,
-            wavelength_id=wavelength_ids,
-            colors=colors,
-            active=active,
-            start=start,
-            end=end,
-            data_type=data_type,
-        )
-        self.set_omero(omero=omero)
-
-    @property
-    def channels(self) -> list[Channel]:
-        """Get the channels in the image."""
-        if self._omero is None:
-            return []
-        assert self.omero is not None
-        return self.omero.channels
-
-    @property
-    def channel_labels(self) -> list[str]:
-        """Get the labels of the channels in the image."""
-        return [channel.label for channel in self.channels]
-
-    @property
-    def channel_wavelength_ids(self) -> list[str | None]:
-        """Get the wavelength IDs of the channels in the image."""
-        return [channel.wavelength_id for channel in self.channels]
-
-    def _get_channel_idx_by_label(self, label: str) -> int | None:
-        """Get the index of a channel by its label."""
-        if self._omero is None:
-            return None
-
-        if label not in self.channel_labels:
-            raise ValueError(f"Channel with label {label} not found.")
-
-        return self.channel_labels.index(label)
-
-    def _get_channel_idx_by_wavelength_id(self, wavelength_id: str) -> int | None:
-        """Get the index of a channel by its wavelength ID."""
-        if self._omero is None:
-            return None
-
-        if wavelength_id not in self.channel_wavelength_ids:
-            raise ValueError(f"Channel with wavelength ID {wavelength_id} not found.")
-
-        return self.channel_wavelength_ids.index(wavelength_id)
-
-    def get_channel_idx(
-        self, label: str | None = None, wavelength_id: str | None = None
-    ) -> int | None:
-        """Get the index of a channel by its label or wavelength ID."""
-        # Only one of the arguments must be provided
-        if sum([label is not None, wavelength_id is not None]) != 1:
-            raise ValueError("get_channel_idx must receive only one argument.")
-
-        if label is not None:
-            return self._get_channel_idx_by_label(label)
-        elif wavelength_id is not None:
-            return self._get_channel_idx_by_wavelength_id(wavelength_id)
-        else:
-            raise ValueError(
-                "get_channel_idx must receive either label or wavelength_id."
-            )
-
-    def to_label(self, name: str | None = None) -> LabelMeta:
-        """Convert the ImageMeta to a LabelMeta."""
-        image_meta = self.remove_axis("c")
-        name = self.name if name is None else name
-        return LabelMeta(
-            version=self.version, name=self.name, datasets=image_meta.datasets
-        )
-
-
-ImageLabelMeta = ImageMeta | LabelMeta