napari.layers.Layer¶

class napari.layers.Layer(data, ndim, *, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=1, blending='translucent', visible=True, multiscale=False, cache=True, experimental_clipping_planes=None)[source]¶

Bases: napari.utils.key_bindings.KeymapProvider, napari.utils.mouse_bindings.MousemapProvider, abc.ABC

Base layer class.

Parameters

name (str) – Name of the layer.
metadata (dict) – Layer metadata.
scale (tuple of float) – Scale factors for the layer.
translate (tuple of float) – Translation values for the layer.
rotate (float, 3-tuple of float, or n-D array.) – If a float convert into a 2D rotation matrix using that value as an angle. If 3-tuple convert into a 3D rotation matrix, using a yaw, pitch, roll convention. Otherwise assume an nD rotation. Angles are assumed to be in degrees. They can be converted from radians with np.degrees if needed.
shear (1-D array or n-D array) – Either a vector of upper triangular values, or an nD shear matrix with ones along the main diagonal.
affine (n-D array or napari.utils.transforms.Affine) – (N+1, N+1) affine transformation matrix in homogeneous coordinates. The first (N, N) entries correspond to a linear transform and the final column is a length N translation vector and a 1 or a napari Affine transform object. Applied as an extra transform on top of the provided scale, rotate, and shear values.
opacity (float) – Opacity of the layer visual, between 0.0 and 1.0.
blending (str) – One of a list of preset blending modes that determines how RGB and alpha values of the layer visual get mixed. Allowed values are {‘opaque’, ‘translucent’, ‘translucent_no_depth’, and ‘additive’}.
visible (bool) – Whether the layer visual is currently being displayed.
multiscale (bool) – Whether the data is multiscale or not. Multiscale data is represented by a list of data objects and should go from largest to smallest.

name¶

Unique name of the layer.

Type: str

opacity¶

Opacity of the layer visual, between 0.0 and 1.0.

Type: float

visible¶

Whether the layer visual is currently being displayed.

Type: bool

blending¶

Determines how RGB and alpha values get mixed.

Blending.OPAQUE Allows for only the top layer to be visible and corresponds to depth_test=True, cull_face=False, blend=False.
Blending.TRANSLUCENT Allows for multiple layers to be blended with different opacity and corresponds to depth_test=True, cull_face=False, blend=True, blend_func=('src_alpha', 'one_minus_src_alpha').
Blending.TRANSLUCENT_NO_DEPTH Allows for multiple layers to be blended with different opacity, but no depth testing is performed. Corresponds to depth_test=False, cull_face=False, blend=True, blend_func=('src_alpha', 'one_minus_src_alpha').
Blending.ADDITIVE Allows for multiple layers to be blended together with different colors and opacity. Useful for creating overlays. It corresponds to depth_test=False, cull_face=False, blend=True, blend_func=('src_alpha', 'one').

Type: Blending

scale¶

Scale factors for the layer.

Type: tuple of float

translate¶

Translation values for the layer.

Type: tuple of float

rotate¶

If a float convert into a 2D rotation matrix using that value as an angle. If 3-tuple convert into a 3D rotation matrix, using a yaw, pitch, roll convention. Otherwise assume an nD rotation. Angles are assumed to be in degrees. They can be converted from radians with np.degrees if needed.

Type: float, 3-tuple of float, or n-D array.

shear¶

Either a vector of upper triangular values, or an nD shear matrix with ones along the main diagonal.

Type: 1-D array or n-D array

affine¶

(N+1, N+1) affine transformation matrix in homogeneous coordinates. The first (N, N) entries correspond to a linear transform and the final column is a length N translation vector and a 1 or a napari Affine transform object. Applied as an extra transform on top of the provided scale, rotate, and shear values.

Type: n-D array or napari.utils.transforms.Affine

multiscale¶

Whether the data is multiscale or not. Multiscale data is represented by a list of data objects and should go from largest to smallest.

Type: bool

cache¶

Whether slices of out-of-core datasets should be cached upon retrieval. Currently, this only applies to dask arrays.

Type: bool

z_index¶

Depth of the layer visual relative to other visuals in the scenecanvas.

Type: int

coordinates¶

Cursor position in data coordinates.

Type: tuple of float

corner_pixels¶

Coordinates of the top-left and bottom-right canvas pixels in the data coordinates of each layer. For multiscale data the coordinates are in the space of the currently viewed data level, not the highest resolution level.

Type: array

position¶

Cursor position in world coordinates.

Type: tuple

ndim¶

Dimensionality of the layer.

Type: int

thumbnail¶

Array of thumbnail data for the layer.

Type: (N, M, 4) array

status¶

Displayed in status bar bottom left.

Type: str

help¶

Displayed in status bar bottom right.

Type: str

interactive¶

Determine if canvas pan/zoom interactivity is enabled.

Type: bool

cursor¶

String identifying which cursor displayed over canvas.

Type: str

cursor_size¶

Size of cursor if custom. None yields default size

Type: int | None

scale_factor¶

Conversion factor from canvas coordinates to image coordinates, which depends on the current zoom level.

Type: float

source¶

source of the layer (such as a plugin or widget)

Type: Source

Notes

Must define the following:

_extent_data: property
data property (setter & getter)

May define the following:

_set_view_slice(): called to set currently viewed slice
_basename(): base/default name of the layer

Methods

`as_layer_data_tuple`()
`bind_key`(key[, func, overwrite])	Bind a key combination to a keymap.
`block_update_properties`()
`click_plane_from_click_data`(click_position, ...)	Calculate a (point, normal) plane parallel to the canvas in data coordinates, centered on the centre of rotation of the camera.
`create`(data[, meta, layer_type])	Create layer from data of type layer_type.
`data_to_world`(position)	Convert from data coordinates to world coordinates.
`get_ray_intersections`(position, ...[, world])	Get the start and end point for the ray extending from a point through the data bounding box.
`get_status`(position, *[, view_direction, ...])	Status message of the data at a coordinate position.
`get_value`(position, *[, view_direction, ...])	Value of the data at a position.
`projected_distance_from_mouse_drag`(...)	Calculate the length of the projection of a line between two mouse clicks onto a vector (or array of vectors) in data coordinates.
`refresh`([event])	Refresh all layer data based on current view slice.
`save`(path[, plugin])	Save this layer to `path` with default (or specified) plugin.
`set_view_slice`()
`world_to_data`(position)	Convert from world coordinates to data coordinates.

Attributes

`affine`	Extra affine transform to go from physical to world coordinates.
`blending`	Determines how RGB and alpha values get mixed.
`class_keymap`
`cursor`	String identifying cursor displayed over canvas.
`cursor_size`	Size of cursor if custom.
`data`
`editable`	Whether the current layer data is editable from the viewer.
`experimental_clipping_planes`
`extent`	Extent of layer in data and world coordinates.
`help`	displayed in status bar bottom right.
`interactive`	Determine if canvas pan/zoom interactivity is enabled.
`loaded`	Return True if this layer is fully loaded in memory.
`metadata`	Key/value map for user-stored data.
`name`	Unique name of the layer.
`ndim`	Number of dimensions in the data.
`opacity`	Opacity value between 0.0 and 1.0.
`rotate`	Rotation matrix in world coordinates.
`scale`	Anisotropy factors to scale data into world coordinates.
`shear`	Shear matrix in world coordinates.
`source`
`thumbnail`	Integer array of thumbnail for the layer
`translate`	Factors to shift the layer by in units of world coordinates.
`translate_grid`
`visible`	Whether the visual is currently being displayed.

Details

property affine¶

Extra affine transform to go from physical to world coordinates.

Type: napari.utils.transforms.Affine

bind_key(key, func=<object object>, *, overwrite=False)¶

Bind a key combination to a keymap.

Parameters

keymap (dict of str: callable) – Keymap to modify.
key (str or ...) – Key combination. ... acts as a wildcard if no key combinations can be matched in the keymap (this will overwrite all key combinations further down the lookup chain).
func (callable, None, or ...) – Callable to bind to the key combination. If None is passed, unbind instead. ... acts as a blocker, effectively unbinding the key combination for all keymaps further down the lookup chain.
overwrite (bool, keyword-only, optional) – Whether to overwrite the key combination if it already exists.

Returns

unbound – Callable unbound by this operation, if any.

Return type

callable or None

Notes

Key combinations are represented in the form [modifier-]key, e.g. a, Control-c, or Control-Alt-Delete. Valid modifiers are Control, Alt, Shift, and Meta.

Letters will always be read as upper-case. Due to the native implementation of the key system, Shift pressed in certain key combinations may yield inconsistent or unexpected results. Therefore, it is not recommended to use Shift with non-letter keys. On OSX, Control is swapped with Meta such that pressing Command reads as Control.

Special keys include Shift, Control, Alt, Meta, Up, Down, Left, Right, PageUp, PageDown, Insert, Delete, Home, End, Escape, Backspace, F1, F2, F3, F4, F5, F6, F7, F8, F9, F10, F11, F12, Space, Enter, and Tab

Functions take in only one argument: the parent that the function was bound to.

By default, all functions are assumed to work on key presses only, but can be denoted to work on release too by separating the function into two statements with the yield keyword:

@viewer.bind_key('h')
def hello_world(viewer):
    # on key press
    viewer.status = 'hello world!'

    yield

    # on key release
    viewer.status = 'goodbye world :('

To create a keymap that will block others, bind_key(..., ...)`.

property blending¶

Determines how RGB and alpha values get mixed.

Blending.OPAQUE: Allows for only the top layer to be visible and corresponds to depth_test=True, cull_face=False, blend=False.
Blending.TRANSLUCENT: Allows for multiple layers to be blended with different opacity and corresponds to depth_test=True, cull_face=False, blend=True, blend_func=(‘src_alpha’, ‘one_minus_src_alpha’).
Blending.ADDITIVE: Allows for multiple layers to be blended together with different colors and opacity. Useful for creating overlays. It corresponds to depth_test=False, cull_face=False, blend=True, blend_func=(‘src_alpha’, ‘one’).

Type: Blending mode

click_plane_from_click_data(click_position: numpy.ndarray, view_direction: numpy.ndarray, dims_displayed: List) → Tuple[numpy.ndarray, numpy.ndarray][source]¶

Calculate a (point, normal) plane parallel to the canvas in data coordinates, centered on the centre of rotation of the camera.

Parameters

click_position (np.ndarray) – click position in world coordinates from mouse event.
view_direction (np.ndarray) – view direction in world coordinates from mouse event.
dims_displayed (List) – dimensions of the data array currently in view.

Returns

click_plane – tuple of (plane_position, plane_normal) in data coordinates.

Return type

Tuple[np.ndarray, np.ndarray]

classmethod create(data, meta: Optional[dict] = None, layer_type: Optional[str] = None) → napari.layers.base.base.Layer[source]¶

Create layer from data of type layer_type.

Primarily intended for usage by reader plugin hooks and creating a layer from an unwrapped layer data tuple.

Parameters

data (Any) – Data in a format that is valid for the corresponding layer_type.
meta (dict, optional) – Dict of keyword arguments that will be passed to the corresponding layer constructor. If any keys in meta are not valid for the corresponding layer type, an exception will be raised.
layer_type (str) – Type of layer to add. Must be the (case insensitive) name of a Layer subclass. If not provided, the layer is assumed to be “image”, unless data.dtype is one of (np.int32, np.uint32, np.int64, np.uint64), in which case it is assumed to be “labels”.

Raises

ValueError – If layer_type is not one of the recognized layer types.
TypeError – If any keyword arguments in meta are unexpected for the corresponding add_* method for this layer_type.

Examples

A typical use case might be to upack a tuple of layer data with a specified layer_type.

>>> data = (
...     np.random.random((10, 2)) * 20,
...     {'face_color': 'blue'},
...     'points',
... )
>>> Layer.create(*data)

property cursor¶

String identifying cursor displayed over canvas.

Type: str

property cursor_size¶

Size of cursor if custom. None yields default size.

Type: int | None

data_to_world(position)[source]¶

Convert from data coordinates to world coordinates.

Parameters: position (tuple, list, 1D array) – Position in data coordinates. If longer then the number of dimensions of the layer, the later dimensions will be used.
Returns: Position in world coordinates.
Return type: tuple

property editable¶

Whether the current layer data is editable from the viewer.

Type: bool

property extent: napari.layers.base.base.Extent¶: Extent of layer in data and world coordinates.

get_ray_intersections(position: List[float], view_direction: numpy.ndarray, dims_displayed: List[int], world: bool = True) → Union[Tuple[numpy.ndarray, numpy.ndarray], Tuple[None, None]][source]¶

Get the start and end point for the ray extending from a point through the data bounding box.

Parameters

position – the position of the point in nD coordinates. World vs. data is set by the world keyword argument.
view_direction (np.ndarray) – a unit vector giving the direction of the ray in nD coordinates. World vs. data is set by the world keyword argument.
dims_displayed – a list of the dimensions currently being displayed in the viewer.
world (bool) – True if the provided coordinates are in world coordinates. Default value is True.

Returns

start_point (np.ndarray) – The point on the axis-aligned data bounding box that the cursor click intersects with. This is the point closest to the camera. The point is the full nD coordinates of the layer data. If the click does not intersect the axis-aligned data bounding box, None is returned.
end_point (np.ndarray) – The point on the axis-aligned data bounding box that the cursor click intersects with. This is the point farthest from the camera. The point is the full nD coordinates of the layer data. If the click does not intersect the axis-aligned data bounding box, None is returned.

get_status(position: numpy.ndarray, *, view_direction: Optional[numpy.ndarray] = None, dims_displayed: Optional[List[int]] = None, world=False)[source]¶

Status message of the data at a coordinate position.

Parameters

position (tuple) – Position in either data or world coordinates.
view_direction (Optional[np.ndarray]) – A unit vector giving the direction of the ray in nD world coordinates. The default value is None.
dims_displayed (Optional[List[int]]) – A list of the dimensions currently being displayed in the viewer. The default value is None.
world (bool) – If True the position is taken to be in world coordinates and converted into data coordinates. False by default.

Returns

msg – String containing a message that can be used as a status update.

Return type

string

get_value(position, *, view_direction: Optional[numpy.ndarray] = None, dims_displayed: Optional[List[int]] = None, world=False)[source]¶

Value of the data at a position.

If the layer is not visible, return None.

Parameters

position (tuple) – Position in either data or world coordinates.
view_direction (Optional[np.ndarray]) – A unit vector giving the direction of the ray in nD world coordinates. The default value is None.
dims_displayed (Optional[List[int]]) – A list of the dimensions currently being displayed in the viewer. The default value is None.
world (bool) – If True the position is taken to be in world coordinates and converted into data coordinates. False by default.

Returns

value – Value of the data. If the layer is not visible return None.

Return type

tuple, None

property help¶

displayed in status bar bottom right.

Type: str

property interactive¶

Determine if canvas pan/zoom interactivity is enabled.

Type: bool

property loaded: bool¶

Return True if this layer is fully loaded in memory.

This base class says that layers are permanently in the loaded state. Derived classes that do asynchronous loading can override this.

property metadata: dict¶: Key/value map for user-stored data.

property name¶

Unique name of the layer.

Type: str

property ndim¶

Number of dimensions in the data.

Type: int

property opacity¶

Opacity value between 0.0 and 1.0.

Type: float

projected_distance_from_mouse_drag(start_position: numpy.ndarray, end_position: numpy.ndarray, view_direction: numpy.ndarray, vector: numpy.ndarray, dims_displayed: Union[List, numpy.ndarray])[source]¶

Calculate the length of the projection of a line between two mouse clicks onto a vector (or array of vectors) in data coordinates.

Parameters

start_position (np.ndarray) – Starting point of the drag vector in data coordinates
end_position (np.ndarray) – End point of the drag vector in data coordinates
view_direction (np.ndarray) – Vector defining the plane normal of the plane onto which the drag vector is projected.
vector (np.ndarray) – (3,) unit vector or (n, 3) array thereof on which to project the drag vector from start_event to end_event. This argument is defined in data coordinates.
dims_displayed (Union[List, np.ndarray]) – (3,) list of currently displayed dimensions

Returns

projected_distance

Return type

(1, ) or (n, ) np.ndarray of float

refresh(event=None)[source]¶: Refresh all layer data based on current view slice.

property rotate¶

Rotation matrix in world coordinates.

Type: array

save(path: str, plugin: Optional[str] = None) → List[str][source]¶

Save this layer to path with default (or specified) plugin.

Parameters

path (str) – A filepath, directory, or URL to open. Extensions may be used to specify output format (provided a plugin is available for the requested format).
plugin (str, optional) – Name of the plugin to use for saving. If None then all plugins corresponding to appropriate hook specification will be looped through to find the first one that can save the data.

Returns

File paths of any files that were written.

Return type

list of str

property scale¶

Anisotropy factors to scale data into world coordinates.

Type: list

property shear¶

Shear matrix in world coordinates.

Type: array

property thumbnail¶

Integer array of thumbnail for the layer

Type: array

property translate¶

Factors to shift the layer by in units of world coordinates.

Type: list

property visible¶

Whether the visual is currently being displayed.

Type: bool

world_to_data(position)[source]¶

Convert from world coordinates to data coordinates.

Parameters: position (tuple, list, 1D array) – Position in world coordinates. If longer then the number of dimensions of the layer, the later dimensions will be used.
Returns: Position in data coordinates.
Return type: tuple

napari.layers.Labels

napari.layers.Points