<filename>starfish/core/imagestack/parser/crop.py<gh_stars>100-1000
from collections import OrderedDict
from typing import Collection, List, Mapping, MutableSequence, Optional, Set, Tuple, Union

import numpy as np
from slicedimage import Tile, TileSet

from starfish.core.imagestack.parser import TileCollectionData, TileData, TileKey
from starfish.core.types import ArrayLike, Axes, Coordinates, Number


class CropParameters:
    """Parameters for cropping an ImageStack at load time."""
    def __init__(
            self,
            *,
            permitted_rounds: Optional[Collection[int]]=None,
            permitted_chs: Optional[Collection[int]]=None,
            permitted_zplanes: Optional[Collection[int]]=None,
            x_slice: Optional[Union[int, slice]]=None,
            y_slice: Optional[Union[int, slice]]=None,
    ):
        """
        Parameters
        ----------
        permitted_rounds : Optional[Collection[int]]
            The rounds in the original dataset to load into the ImageStack.  If this is not set,
            then all rounds are loaded into the ImageStack.
        permitted_chs : Optional[Collection[int]]
            The channels in the original dataset to load into the ImageStack.  If this is not set,
            then all channels are loaded into the ImageStack.
        permitted_zplanes : Optional[Collection[int]]
            The z-layers in the original dataset to load into the ImageStack.  If this is not set,
            then all z-layers are loaded into the ImageStack.
        x_slice : Optional[Union[int, slice]]
            The x-range in the x-y tile that is loaded into the ImageStack.  If this is not set,
            then the entire x-y tile is loaded into the ImageStack.
        y_slice : Optional[Union[int, slice]]
            The y-range in the x-y tile that is loaded into the ImageStack.  If this is not set,
            then the entire x-y tile is loaded into the ImageStack.
        """
        self._permitted_rounds = set(permitted_rounds) if permitted_rounds else None
        self._permitted_chs = set(permitted_chs) if permitted_chs else None
        self._permitted_zplanes = set(permitted_zplanes) if permitted_zplanes else None
        self._x_slice = x_slice
        self._y_slice = y_slice

    def _add_permitted_axes(self, axis_type: Axes, permitted_axis: int) -> None:
        """
        Add a value to one of the permitted axes sets.
        """
        if axis_type == Axes.ROUND and self._permitted_rounds:
            self._permitted_rounds.add(permitted_axis)
        if axis_type == Axes.CH and self._permitted_chs:
            self._permitted_chs.add(permitted_axis)
        if axis_type == Axes.ZPLANE and self._permitted_zplanes:
            self._permitted_zplanes.add(permitted_axis)

    def filter_tilekeys(self, tilekeys: Collection[TileKey]) -> Collection[TileKey]:
        """
        Filters tilekeys for those that should be included in the resulting ImageStack.
        """
        results: MutableSequence[TileKey] = list()
        for tilekey in tilekeys:
            if self._permitted_rounds is not None and tilekey.round not in self._permitted_rounds:
                continue
            if self._permitted_chs is not None and tilekey.ch not in self._permitted_chs:
                continue
            if self._permitted_zplanes is not None and tilekey.z not in self._permitted_zplanes:
                continue

            results.append(tilekey)

        return results

    @staticmethod
    def _crop_axis(size: int, crop: Optional[Union[int, slice]]) -> Tuple[int, int]:
        """
        Given the size of along an axis, and an optional cropping, return the start index
        (inclusive) and end index (exclusive) of the crop.  If no crop is specified, then the
        original size (0, size) is returned.
        """
        # convert int crops to a slice operation.
        if isinstance(crop, int):
            if crop < 0 or crop >= size:
                raise IndexError("crop index out of range")
            return crop, crop + 1

        # convert start and stop to absolute values.
        start: int
        if crop is None or crop.start is None:
            start = 0
        elif crop.start is not None and crop.start < 0:
            start = max(0, size + crop.start)
        else:
            start = min(size, crop.start)

        stop: int
        if crop is None or crop.stop is None:
            stop = size
        elif crop.stop is not None and crop.stop < 0:
            stop = max(0, size + crop.stop)
        else:
            stop = min(size, crop.stop)

        return start, stop

    @staticmethod
    def parse_aligned_groups(tileset: TileSet,
                             rounds: Optional[Collection[int]] = None,
                             chs: Optional[Collection[int]] = None,
                             zplanes: Optional[Collection[int]] = None,
                             x: Optional[Union[int, slice]] = None,
                             y: Optional[Union[int, slice]] = None
                             ) -> List["CropParameters"]:

        """Takes a tileset and any optional selected axes lists compares the physical coordinates on each
         tile to create aligned coordinate groups (groups of tiles that have the same physical
         coordinates)

        Parameters
        ----------
        tileset: TileSet
            The TileSet to parse
        rounds: Optional[Collection[int]]
            The rounds in the tileset to include in the final aligned groups. If this is not set,
            then all rounds are included.
        chs: Optional[Collection[int]]
            The chs in the tileset to include in the final aligned groups. If this is not set,
            then all chs are included.
        zplanes: Optional[Collection[int]]
            The zplanes in the tileset to include in the final aligned groups. If this is not set,
            then all zplanes are included.
        x: Optional[Union[int, slice]]
            The x-range in the x-y tile to include in the final aligned groups.  If this is not set,
            then the entire x-y tile is included.
        y: Optional[Union[int, slice]]
            The y-range in the x-y tile to include in the final aligned groups.  If this is not set,
            then the entire x-y tile is included.

         Returns
         -------
         List["CropParameters"]
             A list of CropParameters. Each entry describes the r/ch/z values of tiles that are
             aligned (have matching coordinates) and are within the selected_axes if provided.
         """
        coord_groups: OrderedDict[tuple, CropParameters] = OrderedDict()
        for tile in tileset.tiles():
            if CropParameters.tile_in_selected_axes(tile, rounds, chs, zplanes):
                x_y_coords = (
                    tile.coordinates[Coordinates.X][0], tile.coordinates[Coordinates.X][1],
                    tile.coordinates[Coordinates.Y][0], tile.coordinates[Coordinates.Y][1]
                )
                # A tile with this (x, y) has already been seen, add tile's indices to
                # CropParameters
                if x_y_coords in coord_groups:
                    crop_params = coord_groups[x_y_coords]
                    crop_params._add_permitted_axes(Axes.CH, tile.indices[Axes.CH])
                    crop_params._add_permitted_axes(Axes.ROUND, tile.indices[Axes.ROUND])
                    if Axes.ZPLANE in tile.indices:
                        crop_params._add_permitted_axes(Axes.ZPLANE, tile.indices[Axes.ZPLANE])
                else:
                    coord_groups[x_y_coords] = CropParameters(
                        permitted_chs=[tile.indices[Axes.CH]],
                        permitted_rounds=[tile.indices[Axes.ROUND]],
                        permitted_zplanes=[tile.indices[Axes.ZPLANE]]
                        if Axes.ZPLANE in tile.indices else None,
                        x_slice=x,
                        y_slice=y)
        return list(coord_groups.values())

    @staticmethod
    def tile_in_selected_axes(tile: Tile,
                              rounds: Optional[Collection[int]] = None,
                              chs: Optional[Collection[int]] = None,
                              zplanes: Optional[Collection[int]] = None) -> bool:
        """
        Return True if a tile belongs in a list of selected axes.

        Parameters
        ----------
        tile:
            The tile in question
        rounds: Optional[Collection[int]]
            The allowed rounds.
        chs: Optional[Collection[int]]
            The allowed chs.
        zplanes: Optional[Collection[int]]
            The allowed zplanes.

        Returns
        -------
        Boolean
            True if tile belongs with selected axes, False if not.
        """
        if rounds and tile.indices[Axes.ROUND] not in rounds:
            return False
        if chs and tile.indices[Axes.CH] not in chs:
            return False
        if zplanes and tile.indices[Axes.ZPLANE] not in zplanes:
            return False
        return True

    def crop_shape(self, shape: Mapping[Axes, int]) -> Mapping[Axes, int]:
        """
        Given the shape of the original tile, return the shape of the cropped tile.
        """
        output_x_shape = CropParameters._crop_axis(shape[Axes.X], self._x_slice)
        output_y_shape = CropParameters._crop_axis(shape[Axes.Y], self._y_slice)
        width = output_x_shape[1] - output_x_shape[0]
        height = output_y_shape[1] - output_y_shape[0]

        return {Axes.Y: height, Axes.X: width}

    def crop_image(self, image: np.ndarray) -> np.ndarray:
        """
        Given the original image, return the cropped image.
        """
        output_x_shape = CropParameters._crop_axis(image.shape[1], self._x_slice)
        output_y_shape = CropParameters._crop_axis(image.shape[0], self._y_slice)

        return image[output_y_shape[0]:output_y_shape[1], output_x_shape[0]:output_x_shape[1]]

    def crop_coordinates(
            self, coordinates: Mapping[Coordinates, ArrayLike[Number]],
    ) -> Mapping[Coordinates, ArrayLike[Number]]:
        """
        Given a mapping of coordinate to coordinate values, return a mapping of the coordinate to
        cropped coordinate values.
        """
        output_x_shape = CropParameters._crop_axis(len(coordinates[Coordinates.X]), self._x_slice)
        output_y_shape = CropParameters._crop_axis(len(coordinates[Coordinates.Y]), self._y_slice)

        return_coords = {
            Coordinates.X: coordinates[Coordinates.X][output_x_shape[0]:output_x_shape[1]],
            Coordinates.Y: coordinates[Coordinates.Y][output_y_shape[0]:output_y_shape[1]],
        }

        if Coordinates.Z in coordinates:
            return_coords[Coordinates.Z] = coordinates[Coordinates.Z]

        return return_coords


class CroppedTileData(TileData):
    """Represent a cropped view of a TileData object."""
    def __init__(self, tile_data: TileData, cropping_parameters: CropParameters):
        self.backing_tile_data = tile_data
        self.cropping_parameters = cropping_parameters

    @property
    def tile_shape(self) -> Mapping[Axes, int]:
        return self.cropping_parameters.crop_shape(self.backing_tile_data.tile_shape)

    @property
    def numpy_array(self) -> np.ndarray:
        return self.cropping_parameters.crop_image(self.backing_tile_data.numpy_array)

    @property
    def coordinates(self) -> Mapping[Coordinates, ArrayLike[Number]]:
        return self.cropping_parameters.crop_coordinates(self.backing_tile_data.coordinates)

    @property
    def selector(self) -> Mapping[Axes, int]:
        return self.backing_tile_data.selector


class CroppedTileCollectionData(TileCollectionData):
    """Represent a cropped view of a TileCollectionData object."""
    def __init__(
            self,
            backing_tile_collection_data: TileCollectionData,
            crop_parameters: CropParameters,
    ) -> None:
        self.backing_tile_collection_data = backing_tile_collection_data
        self.crop_parameters = crop_parameters

    def __getitem__(self, tilekey: TileKey) -> dict:
        return self.backing_tile_collection_data[tilekey]

    def keys(self) -> Collection[TileKey]:
        return self.crop_parameters.filter_tilekeys(self.backing_tile_collection_data.keys())

    @property
    def group_by(self) -> Set[Axes]:
        """Returns the axes to group by when we load the data."""
        return self.backing_tile_collection_data.group_by

    @property
    def tile_shape(self) -> Mapping[Axes, int]:
        return self.crop_parameters.crop_shape(self.backing_tile_collection_data.tile_shape)

    @property
    def extras(self) -> dict:
        return self.backing_tile_collection_data.extras

    def get_tile_by_key(self, tilekey: TileKey) -> TileData:
        return CroppedTileData(
            self.backing_tile_collection_data.get_tile_by_key(tilekey),
            self.crop_parameters,
        )

    def get_tile(self, r: int, ch: int, z: int) -> TileData:
        return CroppedTileData(
            self.backing_tile_collection_data.get_tile(r, ch, z),
            self.crop_parameters,
        )

<filename>starfish/core/imagestack/parser/crop.py<gh_stars>100-1000
from collections import OrderedDict
from typing import Collection, List, Mapping, MutableSequence, Optional, Set, Tuple, Union

import numpy as np
from slicedimage import Tile, TileSet

from starfish.core.imagestack.parser import TileCollectionData, TileData, TileKey
from starfish.core.types import ArrayLike, Axes, Coordinates, Number


class CropParameters:
    """Parameters for cropping an ImageStack at load time."""
    def __init__(
            self,
            *,
            permitted_rounds: Optional[Collection[int]]=None,
            permitted_chs: Optional[Collection[int]]=None,
            permitted_zplanes: Optional[Collection[int]]=None,
            x_slice: Optional[Union[int, slice]]=None,
            y_slice: Optional[Union[int, slice]]=None,
    ):
        """
        Parameters
        ----------
        permitted_rounds : Optional[Collection[int]]
            The rounds in the original dataset to load into the ImageStack.  If this is not set,
            then all rounds are loaded into the ImageStack.
        permitted_chs : Optional[Collection[int]]
            The channels in the original dataset to load into the ImageStack.  If this is not set,
            then all channels are loaded into the ImageStack.
        permitted_zplanes : Optional[Collection[int]]
            The z-layers in the original dataset to load into the ImageStack.  If this is not set,
            then all z-layers are loaded into the ImageStack.
        x_slice : Optional[Union[int, slice]]
            The x-range in the x-y tile that is loaded into the ImageStack.  If this is not set,
            then the entire x-y tile is loaded into the ImageStack.
        y_slice : Optional[Union[int, slice]]
            The y-range in the x-y tile that is loaded into the ImageStack.  If this is not set,
            then the entire x-y tile is loaded into the ImageStack.
        """
        self._permitted_rounds = set(permitted_rounds) if permitted_rounds else None
        self._permitted_chs = set(permitted_chs) if permitted_chs else None
        self._permitted_zplanes = set(permitted_zplanes) if permitted_zplanes else None
        self._x_slice = x_slice
        self._y_slice = y_slice

    def _add_permitted_axes(self, axis_type: Axes, permitted_axis: int) -> None:
        """
        Add a value to one of the permitted axes sets.
        """
        if axis_type == Axes.ROUND and self._permitted_rounds:
            self._permitted_rounds.add(permitted_axis)
        if axis_type == Axes.CH and self._permitted_chs:
            self._permitted_chs.add(permitted_axis)
        if axis_type == Axes.ZPLANE and self._permitted_zplanes:
            self._permitted_zplanes.add(permitted_axis)

    def filter_tilekeys(self, tilekeys: Collection[TileKey]) -> Collection[TileKey]:
        """
        Filters tilekeys for those that should be included in the resulting ImageStack.
        """
        results: MutableSequence[TileKey] = list()
        for tilekey in tilekeys:
            if self._permitted_rounds is not None and tilekey.round not in self._permitted_rounds:
                continue
            if self._permitted_chs is not None and tilekey.ch not in self._permitted_chs:
                continue
            if self._permitted_zplanes is not None and tilekey.z not in self._permitted_zplanes:
                continue

            results.append(tilekey)

        return results

    @staticmethod
    def _crop_axis(size: int, crop: Optional[Union[int, slice]]) -> Tuple[int, int]:
        """
        Given the size of along an axis, and an optional cropping, return the start index
        (inclusive) and end index (exclusive) of the crop.  If no crop is specified, then the
        original size (0, size) is returned.
        """
        # convert int crops to a slice operation.
        if isinstance(crop, int):
            if crop < 0 or crop >= size:
                raise IndexError("crop index out of range")
            return crop, crop + 1

        # convert start and stop to absolute values.
        start: int
        if crop is None or crop.start is None:
            start = 0
        elif crop.start is not None and crop.start < 0:
            start = max(0, size + crop.start)
        else:
            start = min(size, crop.start)

        stop: int
        if crop is None or crop.stop is None:
            stop = size
        elif crop.stop is not None and crop.stop < 0:
            stop = max(0, size + crop.stop)
        else:
            stop = min(size, crop.stop)

        return start, stop

    @staticmethod
    def parse_aligned_groups(tileset: TileSet,
                             rounds: Optional[Collection[int]] = None,
                             chs: Optional[Collection[int]] = None,
                             zplanes: Optional[Collection[int]] = None,
                             x: Optional[Union[int, slice]] = None,
                             y: Optional[Union[int, slice]] = None
                             ) -> List["CropParameters"]:

        """Takes a tileset and any optional selected axes lists compares the physical coordinates on each
         tile to create aligned coordinate groups (groups of tiles that have the same physical
         coordinates)

        Parameters
        ----------
        tileset: TileSet
            The TileSet to parse
        rounds: Optional[Collection[int]]
            The rounds in the tileset to include in the final aligned groups. If this is not set,
            then all rounds are included.
        chs: Optional[Collection[int]]
            The chs in the tileset to include in the final aligned groups. If this is not set,
            then all chs are included.
        zplanes: Optional[Collection[int]]
            The zplanes in the tileset to include in the final aligned groups. If this is not set,
            then all zplanes are included.
        x: Optional[Union[int, slice]]
            The x-range in the x-y tile to include in the final aligned groups.  If this is not set,
            then the entire x-y tile is included.
        y: Optional[Union[int, slice]]
            The y-range in the x-y tile to include in the final aligned groups.  If this is not set,
            then the entire x-y tile is included.

         Returns
         -------
         List["CropParameters"]
             A list of CropParameters. Each entry describes the r/ch/z values of tiles that are
             aligned (have matching coordinates) and are within the selected_axes if provided.
         """
        coord_groups: OrderedDict[tuple, CropParameters] = OrderedDict()
        for tile in tileset.tiles():
            if CropParameters.tile_in_selected_axes(tile, rounds, chs, zplanes):
                x_y_coords = (
                    tile.coordinates[Coordinates.X][0], tile.coordinates[Coordinates.X][1],
                    tile.coordinates[Coordinates.Y][0], tile.coordinates[Coordinates.Y][1]
                )
                # A tile with this (x, y) has already been seen, add tile's indices to
                # CropParameters
                if x_y_coords in coord_groups:
                    crop_params = coord_groups[x_y_coords]
                    crop_params._add_permitted_axes(Axes.CH, tile.indices[Axes.CH])
                    crop_params._add_permitted_axes(Axes.ROUND, tile.indices[Axes.ROUND])
                    if Axes.ZPLANE in tile.indices:
                        crop_params._add_permitted_axes(Axes.ZPLANE, tile.indices[Axes.ZPLANE])
                else:
                    coord_groups[x_y_coords] = CropParameters(
                        permitted_chs=[tile.indices[Axes.CH]],
                        permitted_rounds=[tile.indices[Axes.ROUND]],
                        permitted_zplanes=[tile.indices[Axes.ZPLANE]]
                        if Axes.ZPLANE in tile.indices else None,
                        x_slice=x,
                        y_slice=y)
        return list(coord_groups.values())

    @staticmethod
    def tile_in_selected_axes(tile: Tile,
                              rounds: Optional[Collection[int]] = None,
                              chs: Optional[Collection[int]] = None,
                              zplanes: Optional[Collection[int]] = None) -> bool:
        """
        Return True if a tile belongs in a list of selected axes.

        Parameters
        ----------
        tile:
            The tile in question
        rounds: Optional[Collection[int]]
            The allowed rounds.
        chs: Optional[Collection[int]]
            The allowed chs.
        zplanes: Optional[Collection[int]]
            The allowed zplanes.

        Returns
        -------
        Boolean
            True if tile belongs with selected axes, False if not.
        """
        if rounds and tile.indices[Axes.ROUND] not in rounds:
            return False
        if chs and tile.indices[Axes.CH] not in chs:
            return False
        if zplanes and tile.indices[Axes.ZPLANE] not in zplanes:
            return False
        return True

    def crop_shape(self, shape: Mapping[Axes, int]) -> Mapping[Axes, int]:
        """
        Given the shape of the original tile, return the shape of the cropped tile.
        """
        output_x_shape = CropParameters._crop_axis(shape[Axes.X], self._x_slice)
        output_y_shape = CropParameters._crop_axis(shape[Axes.Y], self._y_slice)
        width = output_x_shape[1] - output_x_shape[0]
        height = output_y_shape[1] - output_y_shape[0]

        return {Axes.Y: height, Axes.X: width}

    def crop_image(self, image: np.ndarray) -> np.ndarray:
        """
        Given the original image, return the cropped image.
        """
        output_x_shape = CropParameters._crop_axis(image.shape[1], self._x_slice)
        output_y_shape = CropParameters._crop_axis(image.shape[0], self._y_slice)

        return image[output_y_shape[0]:output_y_shape[1], output_x_shape[0]:output_x_shape[1]]

    def crop_coordinates(
            self, coordinates: Mapping[Coordinates, ArrayLike[Number]],
    ) -> Mapping[Coordinates, ArrayLike[Number]]:
        """
        Given a mapping of coordinate to coordinate values, return a mapping of the coordinate to
        cropped coordinate values.
        """
        output_x_shape = CropParameters._crop_axis(len(coordinates[Coordinates.X]), self._x_slice)
        output_y_shape = CropParameters._crop_axis(len(coordinates[Coordinates.Y]), self._y_slice)

        return_coords = {
            Coordinates.X: coordinates[Coordinates.X][output_x_shape[0]:output_x_shape[1]],
            Coordinates.Y: coordinates[Coordinates.Y][output_y_shape[0]:output_y_shape[1]],
        }

        if Coordinates.Z in coordinates:
            return_coords[Coordinates.Z] = coordinates[Coordinates.Z]

        return return_coords


class CroppedTileData(TileData):
    """Represent a cropped view of a TileData object."""
    def __init__(self, tile_data: TileData, cropping_parameters: CropParameters):
        self.backing_tile_data = tile_data
        self.cropping_parameters = cropping_parameters

    @property
    def tile_shape(self) -> Mapping[Axes, int]:
        return self.cropping_parameters.crop_shape(self.backing_tile_data.tile_shape)

    @property
    def numpy_array(self) -> np.ndarray:
        return self.cropping_parameters.crop_image(self.backing_tile_data.numpy_array)

    @property
    def coordinates(self) -> Mapping[Coordinates, ArrayLike[Number]]:
        return self.cropping_parameters.crop_coordinates(self.backing_tile_data.coordinates)

    @property
    def selector(self) -> Mapping[Axes, int]:
        return self.backing_tile_data.selector


class CroppedTileCollectionData(TileCollectionData):
    """Represent a cropped view of a TileCollectionData object."""
    def __init__(
            self,
            backing_tile_collection_data: TileCollectionData,
            crop_parameters: CropParameters,
    ) -> None:
        self.backing_tile_collection_data = backing_tile_collection_data
        self.crop_parameters = crop_parameters

    def __getitem__(self, tilekey: TileKey) -> dict:
        return self.backing_tile_collection_data[tilekey]

    def keys(self) -> Collection[TileKey]:
        return self.crop_parameters.filter_tilekeys(self.backing_tile_collection_data.keys())

    @property
    def group_by(self) -> Set[Axes]:
        """Returns the axes to group by when we load the data."""
        return self.backing_tile_collection_data.group_by

    @property
    def tile_shape(self) -> Mapping[Axes, int]:
        return self.crop_parameters.crop_shape(self.backing_tile_collection_data.tile_shape)

    @property
    def extras(self) -> dict:
        return self.backing_tile_collection_data.extras

    def get_tile_by_key(self, tilekey: TileKey) -> TileData:
        return CroppedTileData(
            self.backing_tile_collection_data.get_tile_by_key(tilekey),
            self.crop_parameters,
        )

    def get_tile(self, r: int, ch: int, z: int) -> TileData:
        return CroppedTileData(
            self.backing_tile_collection_data.get_tile(r, ch, z),
            self.crop_parameters,
        )

Parameters for cropping an ImageStack at load time. Parameters         ----------         permitted_rounds : Optional[Collection[int]]             The rounds in the original dataset to load into the ImageStack.  If this is not set,             then all rounds are loaded into the ImageStack.         permitted_chs : Optional[Collection[int]]             The channels in the original dataset to load into the ImageStack.  If this is not set,             then all channels are loaded into the ImageStack.         permitted_zplanes : Optional[Collection[int]]             The z-layers in the original dataset to load into the ImageStack.  If this is not set,             then all z-layers are loaded into the ImageStack.         x_slice : Optional[Union[int, slice]]             The x-range in the x-y tile that is loaded into the ImageStack.  If this is not set,             then the entire x-y tile is loaded into the ImageStack.         y_slice : Optional[Union[int, slice]]             The y-range in the x-y tile that is loaded into the ImageStack.  If this is not set,             then the entire x-y tile is loaded into the ImageStack. Add a value to one of the permitted axes sets. Filters tilekeys for those that should be included in the resulting ImageStack. Given the size of along an axis, and an optional cropping, return the start index         (inclusive) and end index (exclusive) of the crop.  If no crop is specified, then the         original size (0, size) is returned. # convert int crops to a slice operation. # convert start and stop to absolute values. Takes a tileset and any optional selected axes lists compares the physical coordinates on each          tile to create aligned coordinate groups (groups of tiles that have the same physical          coordinates)          Parameters         ----------         tileset: TileSet             The TileSet to parse         rounds: Optional[Collection[int]]             The rounds in the tileset to include in the final aligned groups. If this is not set,             then all rounds are included.         chs: Optional[Collection[int]]             The chs in the tileset to include in the final aligned groups. If this is not set,             then all chs are included.         zplanes: Optional[Collection[int]]             The zplanes in the tileset to include in the final aligned groups. If this is not set,             then all zplanes are included.         x: Optional[Union[int, slice]]             The x-range in the x-y tile to include in the final aligned groups.  If this is not set,             then the entire x-y tile is included.         y: Optional[Union[int, slice]]             The y-range in the x-y tile to include in the final aligned groups.  If this is not set,             then the entire x-y tile is included.           Returns          -------          List["CropParameters"]              A list of CropParameters. Each entry describes the r/ch/z values of tiles that are              aligned (have matching coordinates) and are within the selected_axes if provided. # A tile with this (x, y) has already been seen, add tile's indices to # CropParameters Return True if a tile belongs in a list of selected axes.          Parameters         ----------         tile:             The tile in question         rounds: Optional[Collection[int]]             The allowed rounds.         chs: Optional[Collection[int]]             The allowed chs.         zplanes: Optional[Collection[int]]             The allowed zplanes.          Returns         -------         Boolean             True if tile belongs with selected axes, False if not. Given the shape of the original tile, return the shape of the cropped tile. Given the original image, return the cropped image. Given a mapping of coordinate to coordinate values, return a mapping of the coordinate to         cropped coordinate values. Represent a cropped view of a TileData object. Represent a cropped view of a TileCollectionData object. Returns the axes to group by when we load the data.