Using magicgui in napari

magicgui

magicgui is a python package that assists in building small, composable graphical user interfaces (widgets). It is a general abstraction layer on GUI toolkit backends (like Qt), with an emphasis on mapping python types to widgets. In particular, it makes building widgets to represent function inputs easy:

from magicgui import magicgui
import datetime
import pathlib

@magicgui(
    call_button="Calculate",
    slider_float={"widget_type": "FloatSlider", 'max': 10},
    dropdown={"choices": ['first', 'second', 'third']},
)
def widget_demo(
    maybe: bool,
    some_int: int,
    spin_float=3.14159,
    slider_float=4.5,
    string="Text goes here",
    dropdown='first',
    date=datetime.datetime.now(),
    filename=pathlib.Path('/some/path.ext')
):
    ...

widget_demo.show()

Add caption here

For more information on the features and usage of magicgui, see the magicgui documentation. magicgui does not require napari, but napari does provide support for using magicgui within napari. The purpose of this page is to document some of the conveniences provided by napari when using magicgui with napari-specific type annotations.

magicgui and type annotations

magicgui uses type hints to infer the appropriate widget type for a given function parameter, and to indicate a context-dependent action for the object returned from the function (in the absence of a type hint, the type of the default value will be used). Third party packages (like napari in this case) may provide support for their types using magicgui.register_type. This is how using the type annotations described below leads to widgets and/or “actions” in napari.

Important

All of the type annotations described below require that the resulting widget be added to a napari viewer (either via viewer.window.add_dock_widget, or by providing a magicgui-based widget via the napari_experimental_provide_dock_widget() plugin hook specification).

Parameter annotations

The following napari types may be used as parameter type annotations in magicgui functions to get information from the napari viewer into your magicgui function. The consequence of each type annotation is described below:

• any napari Layer type, such as Image or Points

• any of the <LayerType>Data types from napari.types, such as napari.types.ImageData or napari.types.LabelsData

• napari.Viewer

Annotating as a Layer subclass

If you annotate one of your function parameters as a Layer subclass (such as Image or Points), it will be rendered as a ComboBox widget (i.e. “dropdown menu”), where the options in the dropdown box are the layers of the corresponding type currently in the viewer.

from napari.layers import Image

@magicgui
def my_widget(image: Image):
    # do something with whatever image layer the user has selected
    # note: it *may* be None! so your function should handle the null case
    ...

Here’s a complete example:

import napari
import numpy as np
from napari.layers import Image

@magicgui(image={'label': 'Pick an Image'})
def my_widget(image: Image):
    ...

viewer = napari.view_image(np.random.rand(64, 64), name="My Image")
viewer.window.add_dock_widget(my_widget)

Note the widget at the bottom with “My Image” as the currently selected option

Annotating as Layer

In the previous example, the dropdown menu will only show Image layers, because the parameter was annotated as an Image. If you’d like a dropdown menu that allows the user to pick from all layers in the layer list, annotate your parameter as Layer

from napari.layers import Layer

@magicgui
def my_widget(layer: Layer):
    # do something with whatever layer the user has selected
    # note: it *may* be None! so your function should handle the null case
    ...

Annotating as napari.types.*Data

In the previous example, the object passed to your function will be the actual Layer instance, meaning you will need to access any attributes (like layer.data) on your own. If your function is designed to accept a numpy array, you can use any of the special <LayerType>Data types from napari.types to indicate that you only want the data attribute from the layer (where <LayerType> is one of the available layer types). Here’s an example using napari.types.ImageData

from napari.types import ImageData
import numpy as np

@magicgui
def my_widget(array: ImageData):
    # note: it *may* be None! so your function should handle the null case
    if array is not None:
      assert isinstance(array, np.ndarray)  # it will be!

Annotating as napari.Viewer

Lastly, if you need to access the actual Viewer instance in which the widget is docked, you can annotate one of your parameters as a napari.Viewer.

from napari import Viewer

@magicgui
def my_widget(viewer: Viewer):
  ...

Caution

Please use this sparingly, as a last resort. If you need to add layers to the viewer from your function, prefer one of the return-annotation methods described below. If you find that you require the viewer instance because of functionality that is otherwise missing here, please consider opening an issue in the napari issue tracker, describing your use case.

Return annotations

The following napari types may be used as return type annotations in magicgui functions to add layers to napari from your magicgui function. The consequence of each type is described below:

• any napari Layer type, such as Image or Points

• any of the <LayerType>Data types from napari.types, such as napari.types.ImageData or napari.types.LabelsData

• napari.types.LayerDataTuple

• Lists of napari.layers.Layer or napari.types.LayerDataTuple

Returning a Layer subclass

If you use a Layer subclass as a return annotation on a magicgui function, napari will interpet it to mean that the layer returned from the function should be added to the viewer. The object returned from the function must be an actual Layer instance.

from napari.layers import Image
import numpy as np

@magicgui
def my_widget(ny: int=64, nx: int=64) -> Image:
  return Image(np.random.rand(ny, nx), name='my Image')

Here’s a complete example

@magicgui(call_button='Add Image')
def my_widget(ny: int=64, nx: int=64) -> Image:
  return Image(np.random.rand(ny, nx), name='My Image')

viewer = napari.Viewer()
viewer.window.add_dock_widget(my_widget, area='right')
my_widget()  # "call the widget" to call the function.
             # Normally this would be caused by some user UI interaction

Note the new “My Image” layer in the viewer as a result of having called the widget function.

Note

With this method, a new layer will be added to the layer list each time the function is called. To update an existing layer, you must use the LayerDataTuple approach described below

Returning List[napari.layers.Layer]

You can create multiple layers by returning a list of Layer.

from typing import List

@magicgui
def make_points(...) -> List[napari.layers.Layer]:
  ...

Note

Note: the List[] syntax here is optional from the perspective of napari. You can return either a single Layer or a list of Layers and they will all be added to the viewer as long as you use either List[napari.layers.Layer] or napari.layers.Layer. If you want your code to be properly typed, however, your return type must match your return annotation.

Returning napari.types.*Data

In the previous example, the object returned by the function had to be an actual Layer instance (in keeping with the return type annotation). In many cases, you may only be interested in receiving and returning the layer data itself. (There are many functions already written that accept and return a numpy.ndarray, for example). In this case, you may use a return type annotation of one the special <LayerType>Data types from napari.types to indicate that you want data returned by your function to be turned into the corresponding Layer type, and added to the viewer.

For example, in combination with the ImageData paramater annotation described above:

from napari.types import LabelsData, ImageData

@magicgui(call_button='Run Threshold')
def threshold(image: ImageData, threshold: int = 75) -> LabelsData:
    """Threshold an image and return a mask."""
    return (image > threshold).astype(int)

viewer = napari.view_image(np.random.randint(0, 100, (64, 64)))
viewer.window.add_dock_widget(threshold)
threshold()  # "call the widget" to call the function.
             # Normally this would be caused by some user UI interaction

Returning napari.types.LayerDataTuple

The most flexible return type annotation is napari.types.LayerDataTuple: it gives you full control over the layer that will be created and added to the viewer. (It also lets you update an existing layer with a matching name).

A LayerDataTuple is a tuple in one of the following three forms:

1. (layer_data,)

   • a single item tuple containing only layer data (will be interpreted as an image).

2. (layer_data, {})

   • a 2-tuple of layer_data and a metadata dict. the keys in the metadata dict must be valid keyword arguments to the corresponding napari.layers.Layer constructor.

3. (layer_data, {}, 'layer_type')

   • a 3-tuple of data, metadata, and layer type string.layer_type should be a lowercase string form of one of the layer types (like 'points', 'shapes', etc…). If omitted, the layer type is assumed to be 'image'.

The following are all valid napari.types.LayerDataTuple examples:

# an image array
(np.random.rand(64, 64),) 

# an image with name and custom blending mode
(np.random.rand(64, 64), {'name': 'My Image', 'blending': 'additive'})

# an empty points layer
(None, {}, 'points')

# points with properties
(np.random.rand(20, 2), {'properties': {'values': np.random.rand(20)}}, 'points')

An example of using a LayerDataTuple return annotation in a magicgui function:

import napari.types

@magicgui(call_button='Make Points')
def make_points(n_points=40) -> napari.types.LayerDataTuple:
  data = 500 * np.random.rand(n_points, 2)
  props = {'values': np.random.rand(n_points)}
  return (data, {'properties': props}, 'points')

viewer = napari.Viewer()
viewer.window.add_dock_widget(make_points)
make_points()  # "call the widget" to call the function.
               # Normally this would be caused by some user UI interaction

Returning List[napari.types.LayerDataTuple]

You can also create multiple layers by returning a list of LayerDataTuple.

from typing import List

@magicgui
def make_points(...) -> List[napari.types.LayerDataTuple]:
  ...

Note

Note: the List[] syntax here is optional from the perspective of napari. You can return either a single tuple or a list of tuples and they will all be added to the viewer as long as you use either List[napari.types.LayerDataTuple] or napari.types.LayerDataTuple. If you want your code to be properly typed, however, your return type must match your return annotation.

Updating an existing Layer

The default behavior is to add a new layer to the viewer for each LayerDataTuple returned by a magicgui function. By providing a unique name key in your LayerDataTuple metadata dict, you can update an existing layer, rather than creating a new layer each time the function is called:

@magicgui(call_button='Make Points', n_points={'maximum': 200})
def make_points(n_points=40) -> napari.types.LayerDataTuple:
  data = 500 * np.random.rand(n_points, 2)
  return (data, {'name': 'My Points'}, 'points')

viewer = napari.Viewer()
viewer.window.add_dock_widget(make_points)
# calling this multiple times will just update 'My Points'
make_points()
make_points.n_points.value = 80
make_points()
make_points.n_points.value = 120
make_points()

Avoid imports with forward references

Sometimes, it is undesirable to import and/or depend on napari directly just to provide type annotations. It is possible to avoid importing napari entirely by annotating with the string form of the napari type. This is called a Forward reference:

@magicgui
def my_func(data: 'napari.types.ImageData') -> 'napari.types.ImageData':
    ...

Tip

If you’d like to maintain IDE type support and autocompletion, you can do so by hiding the napari imports inside of a typing.TYPE_CHECKING clause:

from typing import TYPE_CHECKING

if TYPE_CHECKING:
  import napari

@magicgui
def my_func(data: 'napari.types.ImageData') -> 'napari.types.ImageData':
    ...

This will not require napari at runtime, but if it is installed in your development environment, you will still get all the type inference.

Using magicgui in napari plugin widgets

Using magicgui can be an effective way to generate widgets for use in napari Plugins, in particular the napari_experimental_provide_dock_widget() plugin hook specification. There is an important distinction to be made, however, between using magicgui with viewer.window.add_dock_widget, and using it with napari_experimental_provide_dock_widget().

viewer.window.add_dock_widget expects an instance of a widget, like a magicgui.widgets.Widget or a qtpy.QtWidgets.QWidget. napari_experimental_provide_dock_widget(), on the other hand, expects a widget class (or, more broadly, a callable that returns a widget instance). There are two ways to acheive this with magicgui.

@magic_factory

In most cases, the @magicgui decorator used in the preceding examples can simply be replaced with the @magic_factory decorator, to use it as a plugin dock widget.

For example, the threshold widget shown above could be provided as a napari plugin as follows:

from magicgui import magic_factory
from napari_plugin_engine import napari_hook_implementation

@magic_factory(auto_call=True, threshold={'max': 2 ** 16})
def threshold(
    data: 'napari.types.ImageData', threshold: int
) -> 'napari.types.LabelsData':
    return (data > threshold).astype(int)

@napari_hook_implementation
def napari_experimental_provide_dock_widget():
    return threshold

Note

@magic_factory behaves very much like functools.partial(): it returns a callable that “remembers” some or all of the parameters required for a “future” call to magicgui.magicgui(). The parameters provided to @magic_factory can also be overridden when creating a widget from a factory:

@magic_factory(call_button=True)
def my_factory(x: int):
    ...

widget1 = my_factory()
widget2 = my_factory(call_button=False, x={'widget_type': 'Slider'})

magicgui.widgets.FunctionGui

The other option for using magicgui in plugins is to directly subclass magicgui.widgets.FunctionGui (which is the type that is returned by the @magicgui decorator).

from magicgui.widgets import FunctionGui

def my_function(...):
    ...

class MyGui(FunctionGui):
    def __init__(self):
        super().__init__(
          my_function,
          call_button=True,
          layout='vertical',
          param_options={...}
        )
        # do whatever other initialization you want here

@napari_hook_implementation
def napari_experimental_provide_dock_widget():
    return MyGui

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