napari.layers.Vectors¶
- class napari.layers.Vectors(data=None, *, ndim=None, features=None, properties=None, property_choices=None, edge_width=1, edge_color='red', edge_color_cycle=None, edge_colormap='viridis', edge_contrast_limits=None, out_of_slice_display=False, length=1, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=0.7, blending='translucent', visible=True, cache=True, experimental_clipping_planes=None)[source]¶
Bases:
napari.layers.base.base.Layer
Vectors layer renders lines onto the canvas.
- Parameters
data ((N, 2, D) or (N1, N2, ..., ND, D) array) – An (N, 2, D) array is interpreted as “coordinate-like” data and a list of N vectors with start point and projections of the vector in D dimensions. An (N1, N2, …, ND, D) array is interpreted as “image-like” data where there is a length D vector of the projections at each pixel.
ndim (int) – Number of dimensions for vectors. When data is not None, ndim must be D. An empty vectors layer can be instantiated with arbitrary ndim.
features (dict[str, array-like] or DataFrame) – Features table where each row corresponds to a vector and each column is a feature.
properties (dict {str: array (N,)}, DataFrame) – Properties for each vector. Each property should be an array of length N, where N is the number of vectors.
property_choices (dict {str: array (N,)}) – possible values for each property.
edge_width (float) – Width for all vectors in pixels.
length (float) – Multiplicative factor on projections for length of all vectors.
edge_color (str) – Color of all of the vectors.
edge_color_cycle (np.ndarray, list) – Cycle of colors (provided as string name, RGB, or RGBA) to map to edge_color if a categorical attribute is used color the vectors.
edge_colormap (str, napari.utils.Colormap) – Colormap to set vector color if a continuous attribute is used to set edge_color.
edge_contrast_limits (None, (float, float)) – clims for mapping the property to a color map. These are the min and max value of the specified property that are mapped to 0 and 1, respectively. The default value is None. If set the none, the clims will be set to (property.min(), property.max())
out_of_slice_display (bool) – If True, renders vectors not just in central plane but also slightly out of slice according to specified point marker size.
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’}.
visible (bool) – Whether the layer visual is currently being displayed.
cache (bool) – Whether slices of out-of-core datasets should be cached upon retrieval. Currently, this only applies to dask arrays.
- data¶
The start point and projections of N vectors in D dimensions.
- Type
(N, 2, D) array
- features¶
Features table where each row corresponds to a vector and each column is a feature.
- Type
Dataframe-like
- feature_defaults¶
Stores the default value of each feature in a table with one row.
- Type
DataFrame-like
- properties¶
Properties for each vector. Each property should be an array of length N, where N is the number of vectors.
- Type
dict {str: array (N,)}, DataFrame
- edge_color_cycle¶
Cycle of colors (provided as string name, RGB, or RGBA) to map to edge_color if a categorical attribute is used color the vectors.
- Type
np.ndarray, list
- edge_colormap¶
Colormap to set vector color if a continuous attribute is used to set edge_color.
- Type
- edge_contrast_limits¶
clims for mapping the property to a color map. These are the min and max value of the specified property that are mapped to 0 and 1, respectively. The default value is None. If set the none, the clims will be set to (property.min(), property.max())
- out_of_slice_display¶
If True, renders vectors not just in central plane but also slightly out of slice according to specified point marker size.
- Type
Notes
- _view_data(M, 2, 2) array
The start point and projections of N vectors in 2D for vectors whose start point is in the currently viewed slice.
- _view_face_color(M, 4) np.ndarray
colors for the M in view vectors
- _view_indices(1, M) array
indices for the M in view vectors
- _view_vertices(4M, 2) or (8M, 2) np.ndarray
the corner points for the M in view faces. Shape is (4M, 2) for 2D and (8M, 2) for 3D.
- _view_faces(2M, 3) or (4M, 3) np.ndarray
indices of the _mesh_vertices that form the faces of the M in view vectors. Shape is (2M, 2) for 2D and (4M, 2) for 3D.
- _view_alphas(M,) or float
relative opacity for the M in view vectors
- _property_choicesdict {str: array (N,)}
Possible values for the properties in Vectors.properties.
- _mesh_vertices(4N, 2) array
The four corner points for the mesh representation of each vector as as rectangle in the slice that it starts in.
- _mesh_triangles(2N, 3) array
The integer indices of the _mesh_vertices that form the two triangles for the mesh representation of the vectors.
- _max_vectors_thumbnailint
The maximum number of vectors that will ever be used to render the thumbnail. If more vectors are present then they are randomly subsampled.
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.
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.
refresh_colors
([update_color_mapping])Calculate and update edge colors if using a cycle or color map
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
Extra affine transform to go from physical to world coordinates.
Determines how RGB and alpha values get mixed.
class_keymap
String identifying cursor displayed over canvas.
Size of cursor if custom.
start point and projections of vectors.
Array of RGBA edge colors (applied to all vectors)
Color cycle for edge_color.
Edge color setting mode
Return the colormap to be applied to a property to get the edge color.
contrast limits for mapping the edge_color colormap property to 0 and 1
Width for all vectors in pixels.
Whether the current layer data is editable from the viewer.
experimental_clipping_planes
Extent of layer in data and world coordinates.
Dataframe-like with one row of feature default values.
Dataframe-like features table.
displayed in status bar bottom right.
Determine if canvas pan/zoom interactivity is enabled.
Multiplicative factor for length of all vectors.
Return True if this layer is fully loaded in memory.
Key/value map for user-stored data.
Unique name of the layer.
Number of dimensions in the data.
Opacity value between 0.0 and 1.0.
renders vectors slightly out of slice.
Annotations for each point
property_choices
Rotation matrix in world coordinates.
Anisotropy factors to scale data into world coordinates.
Shear matrix in world coordinates.
source
Integer array of thumbnail for the layer
Factors to shift the layer by in units of world coordinates.
translate_grid
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
, orControl-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] ¶
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 ¶
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 data: numpy.ndarray¶
start point and projections of vectors.
- Type
(N, 2, D) array
- data_to_world(position)¶
Convert from data coordinates to world coordinates.
- property edge_color: numpy.ndarray¶
Array of RGBA edge colors (applied to all vectors)
- Type
(1 x 4) np.ndarray
- property edge_color_cycle: numpy.ndarray¶
Color cycle for edge_color. Can be a list of colors defined by name, RGB or RGBA
- Type
list, np.ndarray
- property edge_color_mode: napari.layers.utils._color_manager_constants.ColorMode¶
Edge color setting mode
DIRECT (default mode) allows each vector to be set arbitrarily
CYCLE allows the color to be set via a color cycle over an attribute
COLORMAP allows color to be set via a color map over an attribute
- Type
- property edge_colormap: Tuple[str, napari.utils.colormaps.colormap.Colormap]¶
Return the colormap to be applied to a property to get the edge color.
- Returns
colormap – The Colormap object.
- Return type
- property edge_contrast_limits: Tuple[float, float]¶
contrast limits for mapping the edge_color colormap property to 0 and 1
- property extent: napari.layers.base.base.Extent¶
Extent of layer in data and world coordinates.
- property feature_defaults¶
Dataframe-like with one row of feature default values.
See features for more details on the type of this property.
- property features¶
Dataframe-like features table.
It is an implementation detail that this is a pandas.DataFrame. In the future, we will target the currently-in-development Data API dataframe protocol [1]. This will enable us to use alternate libraries such as xarray or cuDF for additional features without breaking existing usage of this.
If you need to specifically rely on the pandas API, please coerce this to a pandas.DataFrame using features_to_pandas_dataframe.
References
- 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]] ¶
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)¶
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)¶
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 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.
- 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])¶
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
- property properties: Dict[str, numpy.ndarray]¶
Annotations for each point
- Type
dict {str
- Type
array (N,)}, DataFrame
- refresh(event=None)¶
Refresh all layer data based on current view slice.
- refresh_colors(update_color_mapping: bool = False)[source]¶
Calculate and update edge colors if using a cycle or color map
- Parameters
update_color_mapping (bool) – If set to True, the function will recalculate the color cycle map or colormap (whichever is being used). If set to False, the function will use the current color cycle map or color map. For example, if you are adding/modifying vectors and want them to be colored with the same mapping as the other vectors (i.e., the new vectors shouldn’t affect the color cycle map or colormap), set update_color_mapping=False. Default value is False.
- property rotate¶
Rotation matrix in world coordinates.
- Type
array
- save(path: str, plugin: Optional[str] = None) List[str] ¶
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 shear¶
Shear matrix in world coordinates.
- Type
array
- property thumbnail¶
Integer array of thumbnail for the layer
- Type
array