class napari.layers.Surface(data, *, colormap='gray', contrast_limits=None, gamma=1, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=1, blending='translucent', shading='flat', visible=True, experimental_clipping_planes=None)[source]

Bases: napari.layers.intensity_mixin.IntensityVisualizationMixin, napari.layers.base.base.Layer

Surface layer renders meshes onto the canvas.

Parameters
  • data (2-tuple or 3-tuple of array) – The first element of the tuple is an (N, D) array of vertices of mesh triangles. The second is an (M, 3) array of int of indices of the mesh triangles. The optional third element is the (K0, …, KL, N) array of values used to color vertices where the additional L dimensions are used to color the same mesh with different values. If not provided, it defaults to ones.

  • colormap (str, napari.utils.Colormap, tuple, dict) – Colormap to use for luminance images. If a string must be the name of a supported colormap from vispy or matplotlib. If a tuple the first value must be a string to assign as a name to a colormap and the second item must be a Colormap. If a dict the key must be a string to assign as a name to a colormap and the value must be a Colormap.

  • contrast_limits (list (2,)) – Color limits to be used for determining the colormap bounds for luminance images. If not passed is calculated as the min and max of the image.

  • gamma (float) – Gamma correction for determining colormap linearity. Defaults to 1.

  • 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’, and ‘additive’}.

  • shading (str, Shading) –

    One of a list of preset shading modes that determine the lighting model using when rendering the surface in 3D.

    • Shading.NONE

      Corresponds to shading=’none’.

    • Shading.FLAT

      Corresponds to shading=’flat’.

    • Shading.SMOOTH

      Corresponds to shading=’smooth’.

  • visible (bool) – Whether the layer visual is currently being displayed.

data

The first element of the tuple is an (N, D) array of vertices of mesh triangles. The second is an (M, 3) array of int of indices of the mesh triangles. The third element is the (K0, …, KL, N) array of values used to color vertices where the additional L dimensions are used to color the same mesh with different values.

Type

3-tuple of array

vertices

Vertices of mesh triangles.

Type

(N, D) array

faces

Indices of mesh triangles.

Type

(M, 3) array of int

vertex_values

Values used to color vertices.

Type

(K0, .., KL, N) array

colormap

Colormap to use for luminance images. If a string must be the name of a supported colormap from vispy or matplotlib. If a tuple the first value must be a string to assign as a name to a colormap and the second item must be a Colormap. If a dict the key must be a string to assign as a name to a colormap and the value must be a Colormap.

Type

str, napari.utils.Colormap, tuple, dict

contrast_limits

Color limits to be used for determining the colormap bounds for luminance images. If not passed is calculated as the min and max of the image.

Type

list (2,)

shading

One of a list of preset shading modes that determine the lighting model using when rendering the surface.

  • ‘none’

  • ‘flat’

  • ‘smooth’

Type

str

gamma

Gamma correction for determining colormap linearity.

Type

float

Notes

_data_view(M, 2) or (M, 3) array

The coordinates of the vertices given the viewed dimensions.

_view_faces(P, 3) array

The integer indices of the vertices that form the triangles in the currently viewed slice.

_colorbararray

Colorbar for current colormap.

Methods

Attributes

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

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.

property coordinates

Cursor position in data coordinates.

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 displayed_coordinates

List of currently displayed coordinates.

displayed_coordinates is deprecated and will be removed in version 0.4.9. It should no longer be used as layers should will soon not know which dimensions are displayed. Instead you should use `[layer.coordinates[d] for d in viewer.dims.displayed]

Type

list

property editable

Whether the current layer data is editable from the viewer.

Type

bool

property extent

Extent of layer in data and world coordinates.

Return type

Extent

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 loaded

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.

Return type

bool

property metadata

Key/value map for user-stored data.

Return type

dict

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

property position

Cursor position in world slice coordinates.

Type

tuple

refresh(event=None)

Refresh all layer data based on current view slice.

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 selected

Whether this layer is selected or not.

Type

bool

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 translate_grid

Factors to shift the layer by.

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