impy.viewer package

Submodules

impy.viewer.utils module

class impy.viewer.utils.ComplexArrayView(data: _A)

Bases: object

View a complex array in napari.

property data_raw: _A

Return the raw data.

property dtype: dtype

Data type of array.

property nbytes: int

Bytes of array.

property ndim: int

Number of dimensions of array.

property shape: tuple

Shape of array.

impy.viewer.utils.add_dask(viewer: Viewer, img: LazyImgArray, **kwargs)

impy.viewer.utils.add_labeledarray(viewer: Viewer, img: LabeledArray, **kwargs)

Add a LabeledArray to the viewer.

impy.viewer.utils.add_labels(viewer: Viewer, labels: Label, opacity: float = 0.3, name: str | list[str] | None = None, **kwargs)

impy.viewer.utils.add_paths(viewer: napari.Viewer, paths: PathFrame, **kwargs)

impy.viewer.utils.add_points(viewer: napari.Viewer, points: AxesFrame, **kwargs)

impy.viewer.utils.add_rois(viewer: napari.Viewer, rois: Iterable[Roi], **kwargs)

impy.viewer.utils.add_tracks(viewer: napari.Viewer, track: TrackFrame, **kwargs)

impy.viewer.utils.front_image(viewer: Viewer)

From list of image layers return the most front visible image.

impy.viewer.utils.get_a_selected_layer(viewer: Viewer)

impy.viewer.utils.get_viewer_scale(viewer: Viewer)

Get the scale of the viewer.

impy.viewer.utils.iter_layer(viewer: Viewer, layer_type: str)

Iterate over layers and yield only certain type of layers.

Parameters:

layer_type (str, {"shape", "image", "point"}) – Type of layer.

Yields:

napari.layers – Layers specified by layer_type

impy.viewer.utils.iter_selected_layer(viewer: Viewer, layer_type: str | list[str])

Iterate over selected layers and yield only certain type of layers.

impy.viewer.utils.layer_to_impy_object(viewer: Viewer, layer)

Convert layer to real data.

Parameters:

layer (napari.layers.Layer) – Input layer.

Return type:

ImgArray, Label, MarkerFrame or TrackFrame, or Shape features.

impy.viewer.utils.make_world_scale(obj)

impy.viewer.utils.to_labels(layer: Shapes, labels_shape: tuple[int, ...], zoom_factor: float = 1.0)

Convert a Shapes layer to labels, with given zoom factor.

impy.viewer.utils.viewer_imread(viewer: Viewer, path: str)

Read an image into the viewer.

impy.viewer.viewer module

class impy.viewer.viewer.napariViewers

Bases: object

The controller of napari.Viewer``s from ``impy. Always access by ip.gui.

add(obj: ImpyObject, **kwargs)

Add images, points, labels, tracks etc to viewer.

Parameters:

obj (ImpyObject) – Object to add.

add_image(*args, **kwargs)

add_labels(*args, **kwargs)

add_points(*args, **kwargs)

add_shapes(*args, **kwargs)

add_surface(*args, **kwargs)

add_table(table: pd.DataFrame | dict[str, ArrayLike], **kwargs)

add_tracks(*args, **kwargs)

add_vectors(*args, **kwargs)

property axes: Axes

Axes information of current viewer.

Defined to make compatible with ImgArray.

axisof(symbol: str | Axis) → int

property current_slice: tuple[slice | int, ...]

Return a tuple of slicer that corresponds to current field of view.

For instance, when the viewer is displaying yx-plane at t=1, then this property returns (1, slice(None), slice(None)).

property cursor_pos: ndarray

Return cursor position. Scale is considered.

cursor_to_pixel(ref: 'napari.layers.Image' | int | str | LabeledArray | LazyImgArray, ndim: int = None) → np.ndarray

With cursor position and a layer as inputs, this function returns the cursor “pixel” coordinates on the given layer. This function is useful when you want to get such as pixel value at the cursor position.

Parameters:

• ref (napari.layers.Image, int, str, LabeledArray or LazyImgArray) –

  Reference layer or its identifier. To determine the reference layer, this parameter is interpreted in different ways depending on its type:

  • napari.layers.Image … layer itself

  • int … the index of layer list

  • str … the name of layer list

  • LabeledArray or LazyImgArray … layer that has same object as data

• ndim (int, optional) – If specified, the last ndim coordinates will be returned.

Returns:

1-D, int64 array of cursor position along each dimension.

Return type:

np.ndarray

get(kind: str = 'image', layer_state: str = 'visible', returns: str = 'last') → ImpyObject | list[impy.viewer.viewer.ImpyObject]

Simple way to get impy object from viewer.

Parameters:

• kind (str, optional) –

  Kind of layers/shapes to return.

  • ”image”: Image layer.

  • ”labels”: Labels layer

  • ”points”: Points layer.

  • ”shapes”: Shapes layer.

  • ”tracks”: Tracks layer.

  • ”vectors”: Vectors layer.

  • ”surface”: Surface layer.

  • ”line”: Line shapes in Shapes layer.

  • ”rectangle”: Rectangle shapes in Shapes layer.

  • ”path”: Path shapes in Shapes layer.

  • ”polygon”: Polygon shapes in Shapes layer.

  • ”ellipse”: Ellipse shapes in Shapes layer.

• layer_state ({"selected", "visible", "any"}, default is "any") –

  How to filter layer list.

  • ”selected”: Only selected layers will be searched.

  • ”visible”: Only visible layers will be searched.

  • ”any”: All the layers will be searched.

• returns ({"first", "last", "all"}) –

  What will be returned in case that there are multiple layers/shapes.

  • ”first”: Only the first object will be returned.

  • ”last”: Only the last object will be returned.

  • ”all”: All the objects will be returned as a list.

Returns:

impy object(s) that satisfies the options.

Return type:

ImgArray, Label, MarkerFrame or TrackFrame, np.ndarray, or list of one of them.

Examples

1. Get the front image.

   >>> ip.gui.get("image")
   

2. Get all the selected images as a list.

   >>> ip.gui.get("image", layer_state="selected", returns="all")
   

3. Get all the lines from the front visible shapes layer.

   >>> ip.gui.get("line", layer_state="visible")
   

goto(**kwargs) → tuple[int, ...]

Change the current step of the viewer.

Examples

1. Go to t=3.

   >>> ip.gui.goto(t=3)
   

2. Go to t=3 and last z.

   >>> ip.gui.goto(t=3, z=-1)
   

property layers: LayerList

Napari layer list. Identical to ip.gui.viewer.layers.

property scale: ScaleView

Scale information of current viewer.

Defined to make compatible with ImgArray.

property selection: list[impy.viewer.viewer.ImpyObject]

Return selected layers’ data as a list of impy objects.

start(key: str = 'impy')

Create a napari window with name key.

stepof(symbol: str | Axis) → int

Get the current step of certain axis.

Parameters:

symbol (AxisLike) – Axis symbol

property viewer: Viewer

The most front viewer you’re using

Module contents