User interfaces¶

to_napari ¶

to_napari(
    runner: Union[AlgorithmRunner, Callable],
    viewer: Optional[Viewer] = None,
) -> Viewer

Add the dock widget of an algorithm, collection, or client to a Napari viewer.

Requires the napari extra.

Parameters:

Name	Type	Description	Default
`runner`	`AlgorithmRunner or callable`	An algorithm, an algorithm collection, or a client. A plain Python function is converted to an algorithm.	required
`viewer`	`Viewer`	The viewer to add the widget to. By default, a new viewer is created.	`None`

Returns:

Type	Description
`Viewer`	The viewer with the dock widget.

Examples:

>>> viewer = sk.to_napari(threshold_algo)

to_qwidget ¶

to_qwidget(
    runner: Union[AlgorithmRunner, Callable], viewer: Viewer
) -> QWidget

Create the Napari widget of an algorithm, collection, or client, without adding it to a viewer.

Useful to ship an algorithm as a Napari plugin of its own. Requires the napari extra.

Parameters:

Name	Type	Description	Default
`runner`	`AlgorithmRunner or callable`	An algorithm, an algorithm collection, or a client. A plain Python function is converted to an algorithm.	required
`viewer`	`Viewer`	The Napari viewer the widget interacts with.	required

Returns:

Type	Description
`QWidget`	The widget, exposing the parameters and results of the runner.

to_qupath ¶

to_qupath(
    runner: Union[AlgorithmRunner, Callable],
    port: int = 25333,
    token: str = "",
    viewer: Optional[Viewer] = None,
) -> Optional[Viewer]

Open a panel to run an algorithm, collection, or client on QuPath images. Experimental.

The panel connects to QuPath through QuBaLab and a Py4J gateway started from QuPath. Computations run inside a selected QuPath annotation (e.g. a rectangular region). Only algorithms that take a single image as input are compatible; that image is interpreted as the current QuPath image. Requires the qupath extra.

Parameters:

Name	Type	Description	Default
`runner`	`AlgorithmRunner or callable`	An algorithm, an algorithm collection, or a client. A plain Python function is converted to an algorithm.	required
`port`	`int`	Port of the Py4J gateway started from QuPath.	`25333`
`token`	`str`	Token of the Py4J gateway started from QuPath.	`""`
`viewer`	`Viewer`	A Napari viewer to collect results that cannot be displayed in QuPath. If given, the panel is added to the viewer as a dock widget, and the viewer is returned. Otherwise, the panel opens in its own window.	`None`

Returns:

Type	Description
`Viewer or None`	The viewer, if one was given.

convert ¶

convert(
    stack: Stack, to: str = "stack"
) -> Union[Stack, Viewer]

Convert a stack into another representation.

Parameters:

Name	Type	Description	Default
`stack`	`Stack`	The stack to convert.	required
`to`	`(stack, napari)`	The target representation.	`"stack"`

Returns:

Type	Description
`Stack or Viewer`	With `to="stack"`, a new stack with the same layers. With `to="napari"`, a new Napari viewer displaying the layers (requires the `napari` extra).

Raises:

Type	Description
`ValueError`	If `to` is not supported.