Stacks and domains¶

Stack ¶

Stack(
    layers: Optional[List[Layer]] = None,
    tile_meta: Optional[TileMeta] = None,
    position: Optional[Tuple] = None,
)

An ordered collection of data layers.

Access layers by index (stack[0]) or by name (stack.read("Layer name")). Further indices are spatial, as with NumPy arrays: stack[:, 50:150] selects rows 50 to 150 of all layers.

Parameters:

Name	Type	Description	Default
`layers`	`list of Layer`	Initial layers of the stack.	`None`
`tile_meta`	`TileMeta`	Metadata about the stack's position and role in a set of tiles.	`None`
`position`	`tuple`	Position of the stack in global pixel coordinates.	`None`

Attributes:

Name	Type	Description
`layers`	`list of Layer`	The layers in the stack.
`position`	`tuple`	Position of the stack in global pixel coordinates. Setting it offsets the positions of all layers.
`extent`	`Domain`	Smallest region containing all layers, in global pixel coordinates.
`size`	`tuple`	Size of the extent.
`coords_min`	`tuple`	Lower corner of the extent.
`coords_max`	`tuple`	Upper corner of the extent.
`ndim`	`int`	Number of spatial dimensions of the extent.
`tile_meta`	`TileMeta`	Metadata about the stack's position and role in a set of tiles.

add ¶

add(layer: Layer) -> Layer

Add a layer to the stack.

Parameters:

Name	Type	Description	Default
`layer`	`Layer`	The layer to add. If a layer with the same name already exists, a suffix is appended to the name of the new layer (e.g. `Image-01`).	required

Returns:

Type	Description
`Layer`	The added layer.

read ¶

read(name: str) -> Optional[Layer]

Get a layer by name.

Parameters:

Name	Type	Description	Default
`name`	`str`	Name of the layer.	required

Returns:

Type	Description
`Layer or None`	The layer, or `None` if there is no layer with that name.

delete ¶

delete(name: str) -> None

Delete a layer by name.

Parameters:

Name	Type	Description	Default
`name`	`str`	Name of the layer to delete.	required

select ¶

select(domain: Domain) -> Stack

Select the part of the stack inside a domain.

Parameters:

Name	Type	Description	Default
`domain`	`Domain`	The region to select, in global pixel coordinates.	required

Returns:

Type	Description
`Stack`	A new stack with the selected part of each layer.

merge ¶

merge(
    stack: Optional[Stack],
    reinitialize_domain: Optional[Domain] = None,
) -> None

Merge another stack into this one, in place.

Incoming layers with the same name as an existing layer are merged into that layer, following the merging strategy of the layer type. Other incoming layers are added to the stack.

Parameters:

Name	Type	Description	Default
`stack`	`Stack`	The stack to merge. If `None`, nothing happens.	required
`reinitialize_domain`	`Domain`	A region of the existing layers to reinitialize before merging the first tile of the incoming stack.	`None`

Domain ¶

Domain(
    size: Optional[Union[Tuple, List]] = None,
    position: Optional[Union[Tuple, List]] = None,
)

An n-D box defined by a size and a position in global pixel coordinates.

Domains represent regions of interest and tile extents, and are used to restrict the computation of an algorithm to a region.

Parameters:

Name	Type	Description	Default
`size`	`tuple`	Size of the domain in pixels, one value per dimension.	`None`
`position`	`tuple`	Position of the lower corner of the domain (top-left in 2D), in global pixel coordinates. Defaults to the origin if only `size` is provided.	`None`

Attributes:

Name	Type	Description
`size`	`tuple`	Size of the domain in pixels.
`coords_min`	`tuple`	Lower corner of the domain (top-left in 2D).
`coords_max`	`tuple`	Upper corner of the domain (bottom-right in 2D).
`ndim`	`int`	Number of dimensions.

Examples:

>>> roi = sk.Domain(position=(20, 30), size=(60, 80))
>>> roi.coords_max
(80.0, 110.0)

merge_layers ¶

merge_layers(layers: List[Layer]) -> Layer

Merge a list of data layers of the same kind into a new layer.

The layers are merged as successive tiles, following the merging strategy of the layer type (see the "Merging tiles" section of the documentation). The input layers are not modified.

Parameters:

Name	Type	Description	Default
`layers`	`list of Layer`	The layers to merge. They must all be of the same kind.	required

Returns:

Type	Description
`Layer`	A new layer containing the merged data. If a single layer is given, it is returned as is.

Raises:

Type	Description
`ValueError`	If `layers` is empty, or if the layers are not all of the same kind.