napari.layers.Image

class napari.layers.Image(data, *, rgb=None, colormap='gray', contrast_limits=None, gamma=1, interpolation='nearest', rendering='mip', iso_threshold=0.5, attenuation=0.05, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=1, blending='translucent', visible=True, multiscale=None, cache=True, experimental_slicing_plane=None, experimental_clipping_planes=None)[source]

Bases: napari.layers.image.image._ImageBase

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.

reset_contrast_limits([mode])

Scale contrast limits to data range

reset_contrast_limits_range()

Scale contrast limits range to data type.

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.

attenuation

attenuation rate for attenuated_mip rendering.

blending

Determines how RGB and alpha values get mixed.

class_keymap

colormap

colormap for luminance images.

colormaps

names of available colormaps.

contrast_limits

Limits to use for the colormap.

contrast_limits_range

The current valid range of the contrast limits.

cursor

String identifying cursor displayed over canvas.

cursor_size

Size of cursor if custom.

data

Data, possibly in multiscale wrapper.

data_level

Current level of multiscale, or 0 if image.

data_raw

Data, exactly as provided by the user.

downsample_factors

Downsample factors for each level of the multiscale.

dtype

editable

Whether the current layer data is editable from the viewer.

experimental_clipping_planes

experimental_slicing_plane

extent

Extent of layer in data and world coordinates.

gamma

help

displayed in status bar bottom right.

interactive

Determine if canvas pan/zoom interactivity is enabled.

interpolation

Return current interpolation mode.

iso_threshold

threshold for isosurface.

level_shapes

Shapes of each level of the multiscale or just of image.

loaded

Has the data for this layer been loaded yet.

metadata

Key/value map for user-stored data.

mode

Interactive mode

name

Unique name of the layer.

ndim

Number of dimensions in the data.

opacity

Opacity value between 0.0 and 1.0.

rendering

Return current rendering mode.

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

property attenuation

attenuation rate for attenuated_mip rendering.

Type

float

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, view_direction, dims_displayed)

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]

property colormap

colormap for luminance images.

Type

napari.utils.Colormap

property colormaps

names of available colormaps.

Type

tuple of str

property contrast_limits

Limits to use for the colormap.

Type

list of float

property contrast_limits_range

The current valid range of the contrast limits.

classmethod create(data, meta=None, layer_type=None)

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)
Return type

Layer

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

property data: napari.layers._data_protocols.LayerDataProtocol

Data, possibly in multiscale wrapper. Obeys LayerDataProtocol.

Return type

LayerDataProtocol

property data_level

Current level of multiscale, or 0 if image.

Type

int

property data_raw

Data, exactly as provided by the user.

data_to_world(position)

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 downsample_factors

Downsample factors for each level of the multiscale.

Type

list

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, view_direction, dims_displayed, world=True)

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

Parameters
  • position (List[float]) – 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 (List[int]) – 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.

Return type

Union[Tuple[ndarray, ndarray], Tuple[None, None]]

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, *, view_direction=None, dims_displayed=None, world=False)

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=None, dims_displayed=None, world=False)

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 interpolation

Return current interpolation mode.

Selects a preset interpolation mode in vispy that determines how volume is displayed. Makes use of the two Texture2D interpolation methods and the available interpolation methods defined in vispy/gloo/glsl/misc/spatial_filters.frag

Options include: ‘bessel’, ‘bicubic’, ‘bilinear’, ‘blackman’, ‘catrom’, ‘gaussian’, ‘hamming’, ‘hanning’, ‘hermite’, ‘kaiser’, ‘lanczos’, ‘mitchell’, ‘nearest’, ‘spline16’, ‘spline36’

Returns

The current interpolation mode

Return type

str

property iso_threshold

threshold for isosurface.

Type

float

property level_shapes

Shapes of each level of the multiscale or just of image.

Type

array

property loaded

Has the data for this layer been loaded yet.

With asynchronous loading the layer might exist but its data for the current slice has not been loaded.

property metadata: dict

Key/value map for user-stored data.

Return type

dict

property mode: str

Interactive mode

Interactive mode. The normal, default mode is PAN_ZOOM, which allows for normal interactivity with the canvas.

TRANSFORM allows for manipulation of the layer transform.

Type

str

Return type

str

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, end_position, view_direction, vector, dims_displayed)

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)

Refresh all layer data based on current view slice.

property rendering

Return current rendering mode.

Selects a preset rendering mode in vispy that determines how volume is displayed. Options include:

  • translucent: voxel colors are blended along the view ray until

    the result is opaque.

  • mip: maximum intensity projection. Cast a ray and display the

    maximum value that was encountered.

  • minip: minimum intensity projection. Cast a ray and display the

    minimum value that was encountered.

  • attenuated_mip: attenuated maximum intensity projection. Cast a

    ray and attenuate values based on integral of encountered values, display the maximum value that was encountered after attenuation. This will make nearer objects appear more prominent.

  • additive: voxel colors are added along the view ray until

    the result is saturated.

  • iso: isosurface. Cast a ray until a certain threshold is

    encountered. At that location, lighning calculations are performed to give the visual appearance of a surface.

  • average: average intensity projection. Cast a ray and display the

    average of values that were encountered.

Returns

The current rendering mode

Return type

str

reset_contrast_limits(mode=None)

Scale contrast limits to data range

reset_contrast_limits_range()

Scale contrast limits range to data type.

Currently, this only does something if the data type is an unsigned integer… otherwise it’s unclear what the full range should be.

property rotate

Rotation matrix in world coordinates.

Type

array

save(path, plugin=None)

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)

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