napari.layers.Points

class napari.layers.Points(data=None, *, ndim=None, properties=None, text=None, symbol='o', size=10, edge_width=1, edge_color='black', edge_color_cycle=None, edge_colormap='viridis', edge_contrast_limits=None, face_color='white', face_color_cycle=None, face_colormap='viridis', face_contrast_limits=None, n_dimensional=False, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=1, blending='translucent', visible=True, cache=True, property_choices=None, experimental_clipping_planes=None)[source]¶

Bases: napari.layers.base.base.Layer

Points layer.

Parameters

data (array (N, D)) – Coordinates for N points in D dimensions.
ndim (int) – Number of dimensions for shapes. When data is not None, ndim must be D. An empty points layer can be instantiated with arbitrary ndim.
properties (dict {str: array (N,)}, DataFrame) – Properties for each point. Each property should be an array of length N, where N is the number of points.
property_choices (dict {str: array (N,)}) – possible values for each property.
text (str, dict) – Text to be displayed with the points. If text is set to a key in properties, the value of that property will be displayed. Multiple properties can be composed using f-string-like syntax (e.g., ‘{property_1}, {float_property:.2f}). A dictionary can be provided with keyword arguments to set the text values and display properties. See TextManager.__init__() for the valid keyword arguments. For example usage, see /napari/examples/add_points_with_text.py.
symbol (str) – Symbol to be used for the point markers. Must be one of the following: arrow, clobber, cross, diamond, disc, hbar, ring, square, star, tailed_arrow, triangle_down, triangle_up, vbar, x.
size (float, array) – Size of the point marker. If given as a scalar, all points are made the same size. If given as an array, size must be the same broadcastable to the same shape as the data.
edge_width (float) – Width of the symbol edge in pixels.
edge_color (str, array-like, dict) – Color of the point marker border. Numeric color values should be RGB(A).
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 edge_color if a continuous attribute is used to set face_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())
face_color (str, array-like, dict) – Color of the point marker body. Numeric color values should be RGB(A).
face_color_cycle (np.ndarray, list) – Cycle of colors (provided as string name, RGB, or RGBA) to map to face_color if a categorical attribute is used color the vectors.
face_colormap (str, napari.utils.Colormap) – Colormap to set face_color if a continuous attribute is used to set face_color.
face_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())
n_dimensional (bool) – If True, renders points not just in central plane but also in all n-dimensions 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¶

Coordinates for N points in D dimensions.

Type: array (N, D)

properties¶

Annotations for each point. Each property should be an array of length N, where N is the number of points.

Type: dict {str: array (N,)} or DataFrame

text¶

Text to be displayed with the points. If text is set to a key in properties, the value of that property will be displayed. Multiple properties can be composed using f-string-like syntax (e.g., ‘{property_1}, {float_property:.2f}). For example usage, see /napari/examples/add_points_with_text.py.

Type: str

symbol¶

Symbol used for all point markers.

Type: str

size¶

Array of sizes for each point in each dimension. Must have the same shape as the layer data.

Type: array (N, D)

edge_width¶

Width of the marker edges in pixels for all points

Type: float

edge_color¶

Array of edge color RGBA values, one for each point.

Type: Nx4 numpy array

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 edge_color if a continuous attribute is used to set face_color.

Type: str, napari.utils.Colormap

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())

Type: None, (float, float)

face_color¶

Array of face color RGBA values, one for each point.

Type: Nx4 numpy array

face_color_cycle¶

Cycle of colors (provided as string name, RGB, or RGBA) to map to face_color if a categorical attribute is used color the vectors.

Type: np.ndarray, list

face_colormap¶

Colormap to set face_color if a continuous attribute is used to set face_color.

Type: str, napari.utils.Colormap

face_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())

Type: None, (float, float)

current_size¶

Size of the marker for the next point to be added or the currently selected point.

Type: float

current_edge_color¶

Size of the marker edge for the next point to be added or the currently selected point.

Type: str

current_face_color¶

Size of the marker edge for the next point to be added or the currently selected point.

Type: str

n_dimensional¶

If True, renders points not just in central plane but also in all n-dimensions according to specified point marker size.

Type: bool

selected_data¶

Integer indices of any selected points.

Type: set

mode¶

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

In ADD mode clicks of the cursor add points at the clicked location.

In SELECT mode the cursor can select points by clicking on them or by dragging a box around them. Once selected points can be moved, have their properties edited, or be deleted.

Type: str

face_color_mode¶

Face color setting mode.

DIRECT (default mode) allows each point 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: str

edge_color_mode¶

Edge color setting mode.

DIRECT (default mode) allows each point 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: str

Notes

_property_choicesdict {str: array (N,)}: Possible values for the properties in Points.properties.
_view_dataarray (M, 2): 2D coordinates of points in the currently viewed slice.
_view_sizearray (M, ): Size of the point markers in the currently viewed slice.
_indices_viewarray (M, ): Integer indices of the points in the currently viewed slice.
_selected_view :: Integer indices of selected points in the currently viewed slice within the _view_data array.
_selected_boxarray (4, 2) or None: Four corners of any box either around currently selected points or being created during a drag action. Starting in the top left and going clockwise.
_drag_startlist or None: Coordinates of first cursor click during a drag action. Gets reset to None after dragging is done.

Methods

`add`(coord)	Adds point at coordinate.
`as_layer_data_tuple`()
`bind_key`(key[, func, overwrite])	Bind a key combination to a keymap.
`block_update_properties`()
`create`(data[, meta, layer_type])	Create layer from data of type layer_type.
`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.
`interaction_box`(index)	Create the interaction box around a list of points in view.
`refresh`([event])	Refresh all layer data based on current view slice.
`refresh_colors`([update_color_mapping])	Calculate and update face and edge colors if using a cycle or color map :type update_color_mapping: `bool` :param update_color_mapping: 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 points and want them to be colored with the same mapping as the other points (i.e., the new points shouldn’t affect the color cycle map or colormap), set update_color_mapping=False. Default value is False. :type update_color_mapping: bool.
`refresh_text`()	Refresh the text values.
`remove_selected`()	Removes selected points if any.
`save`(path[, plugin])	Save this layer to `path` with default (or specified) plugin.
`set_view_slice`()
`to_mask`(*, shape[, data_to_world, …])	Return a binary mask array of all the points as balls.
`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`
`current_edge_color`	Edge color of marker for the next added point or the selected point(s).
`current_face_color`	Face color of marker for the next added point or the selected point(s).
`current_properties`	properties for the next added point.
`current_size`	size of marker for the next added point.
`cursor`	String identifying cursor displayed over canvas.
`cursor_size`	Size of cursor if custom.
`data`	coordinates for N points in D dimensions.
`edge_color`	Array of RGBA edge colors for each point
`edge_color_cycle`	Color cycle for edge_color.
`edge_color_mode`	Edge color setting mode
`edge_colormap`	Return the colormap to be applied to a property to get the edge color.
`edge_contrast_limits`	contrast limits for mapping the edge_color colormap property to 0 and 1
`edge_width`	width used for all point markers.
`editable`	Whether the current layer data is editable from the viewer.
`experimental_clipping_planes`
`extent`	Extent of layer in data and world coordinates.
`face_color`	Array of RGBA face colors for each point
`face_color_cycle`	Color cycle for face_color Can be a list of colors defined by name, RGB or RGBA
`face_color_mode`	Face color setting mode
`face_colormap`	Return the colormap to be applied to a property to get the face color.
`face_contrast_limits`	clims for mapping the face_color colormap property to 0 and 1
`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.
`mode`	Interactive mode
`n_dimensional`	renders points as n-dimensionsal.
`name`	Unique name of the layer.
`ndim`	Number of dimensions in the data.
`opacity`	Opacity value between 0.0 and 1.0.
`properties`	Annotations for each point
`property_choices`	rtype `Dict`[`str`, `ndarray`]
`rotate`	Rotation matrix in world coordinates.
`scale`	Anisotropy factors to scale data into world coordinates.
`selected_data`	set of currently selected points.
`shear`	Shear matrix in world coordinates.
`size`	size of all N points in D dimensions.
`source`
`symbol`	symbol used for all point markers.
`text`	the TextManager object containing containing the text properties
`thumbnail`	Integer array of thumbnail for the layer
`translate`	Factors to shift the layer by in units of world coordinates.
`translate_grid`	Factors to shift the layer by.
`visible`	Whether the visual is currently being displayed.

Details

add(coord)[source]¶

Adds point at coordinate.

Parameters: coord (sequence of indices to add point at) –

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

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 current_edge_color¶

Edge color of marker for the next added point or the selected point(s).

Type: str
Return type: str

property current_face_color¶

Face color of marker for the next added point or the selected point(s).

Return type: str

property current_properties¶

properties for the next added point.

Type: dict{str
Type: np.ndarray(1,)}
Return type: Dict[str, ndarray]

property current_size¶

size of marker for the next added point.

Type: float
Return type: Union[int, float]

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¶

coordinates for N points in D dimensions.

Type: (N, D) array
Return type: ndarray

property edge_color¶

Array of RGBA edge colors for each point

Type: (N x 4) np.ndarray
Return type: ndarray

property edge_color_cycle¶

Color cycle for edge_color. Can be a list of colors defined by name, RGB or RGBA

Type: Union[list, np.ndarray]
Return type: ndarray

property edge_color_mode¶

Edge color setting mode

DIRECT (default mode) allows each point 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: str
Return type: str

property edge_colormap¶

Return the colormap to be applied to a property to get the edge color.

Returns: colormap – The Colormap object.
Return type: napari.utils.Colormap

property edge_contrast_limits¶

contrast limits for mapping the edge_color colormap property to 0 and 1

Type: None, (float, float)
Return type: Tuple[float, float]

property edge_width¶

width used for all point markers.

Type: float
Return type: Union[None, int, float]

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

property face_color¶

Array of RGBA face colors for each point

Type: (N x 4) np.ndarray
Return type: ndarray

property face_color_cycle¶

Color cycle for face_color Can be a list of colors defined by name, RGB or RGBA

Type: Union[np.ndarray, cycle]
Return type: ndarray

property face_color_mode¶

Face color setting mode

DIRECT (default mode) allows each point 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: str
Return type: str

property face_colormap¶

Return the colormap to be applied to a property to get the face color.

Returns: colormap – The Colormap object.
Return type: napari.utils.Colormap

property face_contrast_limits¶

clims for mapping the face_color colormap property to 0 and 1

Type: None, (float, float)
Return type: Optional[Tuple[float, float]]

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

interaction_box(index)[source]¶

Create the interaction box around a list of points in view.

Parameters: index (list) – List of points around which to construct the interaction box.
Returns: box – 4x2 array of corners of the interaction box in clockwise order starting in the upper-left corner.
Return type: np.ndarray or None

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 mode¶

Interactive mode

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

In ADD mode clicks of the cursor add points at the clicked location.

In SELECT mode the cursor can select points by clicking on them or by dragging a box around them. Once selected points can be moved, have their properties edited, or be deleted.

Type: str
Return type: str

property n_dimensional¶

renders points as n-dimensionsal.

Type: bool
Return type: bool

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 properties¶

Annotations for each point

Type: dict {str
Type: np.ndarray (N,)}, DataFrame
Return type: Dict[str, ndarray]

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

refresh_colors(update_color_mapping=False)[source]¶

Calculate and update face and edge colors if using a cycle or color map :type update_color_mapping: bool :param update_color_mapping: 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 points and want them to be colored with the same mapping as the other points (i.e., the new points shouldn’t affect the color cycle map or colormap), set update_color_mapping=False. Default value is False.

refresh_text()[source]¶

Refresh the text values.

This is generally used if the properties were updated without changing the data

remove_selected()[source]¶: Removes selected points if any.

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_data¶

set of currently selected points.

Type: set
Return type: set

property shear¶

Shear matrix in world coordinates.

Type: array

property size¶

size of all N points in D dimensions.

Type: (N, D) array
Return type: Union[int, float, ndarray, list]

property symbol¶

symbol used for all point markers.

Type: str
Return type: str

property text¶

the TextManager object containing containing the text properties

Type: TextManager
Return type: TextManager

property thumbnail¶

Integer array of thumbnail for the layer

Type: array

to_mask(*, shape, data_to_world=None, isotropic_output=True)[source]¶

Return a binary mask array of all the points as balls.

Parameters

shape (tuple) – The shape of the mask to be generated.
data_to_world (Optional[Affine]) – The data-to-world transform of the output mask image. This likely comes from a reference image. If None, then this is the same as this layer’s data-to-world transform.
isotropic_output (bool) – If True, then force the output mask to always contain isotropic balls in data/pixel coordinates. Otherwise, allow the anisotropy in the data-to-world transform to squash the balls in certain dimensions. By default this is True, but you should set it to False if you are going to create a napari image layer from the result with the same data-to-world transform and want the visualized balls to be roughly isotropic.

Returns

The output binary mask array of the given shape containing this layer’s points as balls.

Return type

np.ndarray

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