import numbers
import typing
import warnings
from collections.abc import Callable, Iterable, Sequence, Set as AbstractSet
from copy import copy, deepcopy
from itertools import cycle
from typing import (
TYPE_CHECKING,
Any,
ClassVar,
Literal,
Optional,
)
import numpy as np
import numpy.typing as npt
import pandas as pd
from psygnal.containers import Selection
from scipy.stats import gmean
from napari.layers.base import Layer, no_op
from napari.layers.base._base_constants import ActionType
from napari.layers.base._base_mouse_bindings import (
highlight_box_handles,
transform_with_box,
)
from napari.layers.points._points_constants import (
Mode,
PointsProjectionMode,
Shading,
)
from napari.layers.points._points_mouse_bindings import add, highlight, select
from napari.layers.points._points_utils import (
_create_box_from_corners_3d,
coerce_symbols,
create_box,
fix_data_points,
points_to_squares,
)
from napari.layers.points._slice import _PointSliceRequest, _PointSliceResponse
from napari.layers.utils._color_manager_constants import ColorMode
from napari.layers.utils._slice_input import _SliceInput, _ThickNDSlice
from napari.layers.utils.color_manager import ColorManager
from napari.layers.utils.color_transformations import ColorType
from napari.layers.utils.interactivity_utils import (
displayed_plane_from_nd_line_segment,
)
from napari.layers.utils.layer_utils import (
_features_to_properties,
_FeatureTable,
_unique_element,
)
from napari.layers.utils.text_manager import TextManager
from napari.utils.colormaps import Colormap, ValidColormapArg
from napari.utils.colormaps.standardize_color import hex_to_name, rgb_to_hex
from napari.utils.events import Event
from napari.utils.events.custom_types import Array
from napari.utils.geometry import project_points_onto_plane, rotate_points
from napari.utils.transforms import Affine
from napari.utils.translations import trans
if TYPE_CHECKING:
from napari.components.dims import Dims
DEFAULT_COLOR_CYCLE = np.array([[1, 0, 1, 1], [0, 1, 0, 1]])
[docs]
class Points(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.
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.
antialiasing: float
Amount of antialiasing in canvas pixels.
axis_labels : tuple of str, optional
Dimension names of the layer data.
If not provided, axis_labels will be set to (..., 'axis -2', 'axis -1').
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', 'additive', and 'minimum'}.
border_color : str, array-like, dict
Color of the point marker border. Numeric color values should be RGB(A).
border_color_cycle : np.ndarray, list
Cycle of colors (provided as string name, RGB, or RGBA) to map to border_color if a
categorical attribute is used color the vectors.
border_colormap : str, napari.utils.Colormap
Colormap to set border_color if a continuous attribute is used to set face_color.
border_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())
border_width : float, array
Width of the symbol border in pixels.
border_width_is_relative : bool
If enabled, border_width is interpreted as a fraction of the point size.
cache : bool
Whether slices of out-of-core datasets should be cached upon retrieval.
Currently, this only applies to dask arrays.
canvas_size_limits : tuple of float
Lower and upper limits for the size of points in canvas pixels.
experimental_clipping_planes : list of dicts, list of ClippingPlane, or ClippingPlaneList
Each dict defines a clipping plane in 3D in data coordinates.
Valid dictionary keys are {'position', 'normal', and 'enabled'}.
Values on the negative side of the normal are discarded if the plane is enabled.
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())
feature_defaults : dict[str, Any] or DataFrame
The default value of each feature in a table with one row.
features : dict[str, array-like] or DataFrame
Features table where each row corresponds to a point and each column
is a feature.
metadata : dict
Layer metadata.
n_dimensional : bool
This property will soon be deprecated in favor of 'out_of_slice_display'.
Use that instead.
name : str
Name of the layer. If not provided then will be guessed using heuristics.
opacity : float
Opacity of the layer visual, between 0.0 and 1.0.
out_of_slice_display : bool
If True, renders points not just in central plane but also slightly out of slice
according to specified point marker size.
projection_mode : str
How data outside the viewed dimensions but inside the thick Dims slice will
be projected onto the viewed dimensions. Must fit to cls._projectionclass.
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.
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.
scale : tuple of float
Scale factors for the layer.
shading : str, Shading
Render lighting and shading on points. Options are:
* 'none'
No shading is added to the points.
* 'spherical'
Shading and depth buffer are changed to give a 3D spherical look to the points
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.
shown : 1-D array of bool
Whether to show each point.
size : float, array
Size of the point marker in data pixels. If given as a scalar, all points are made
the same size. If given as an array, size must be the same or broadcastable
to the same shape as the data.
symbol : str, array
Symbols 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.
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.
translate : tuple of float
Translation values for the layer.
units : tuple of str or pint.Unit, optional
Units of the layer data in world coordinates.
If not provided, the default units are assumed to be pixels.
visible : bool
Whether the layer visual is currently being displayed.
Attributes
----------
data : array (N, D)
Coordinates for N points in D dimensions.
axis_labels : tuple of str
Dimension names of the layer data.
features : DataFrame-like
Features table where each row corresponds to a point and each column
is a feature.
feature_defaults : DataFrame-like
Stores the default value of each feature in a table with one row.
properties : dict {str: array (N,)} or DataFrame
Annotations for each point. Each property should be an array of length N,
where N is the number of points.
text : str
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.
symbol : array of str
Array of symbols for each point.
size : array (N,)
Array of sizes for each point. Must have the same shape as the layer `data`.
border_width : array (N,)
Width of the marker borders in pixels for all points
border_width : array (N,)
Width of the marker borders for all points as a fraction of their size.
border_color : Nx4 numpy array
Array of border color RGBA values, one for each point.
border_color_cycle : np.ndarray, list
Cycle of colors (provided as string name, RGB, or RGBA) to map to border_color if a
categorical attribute is used color the vectors.
border_colormap : str, napari.utils.Colormap
Colormap to set border_color if a continuous attribute is used to set face_color.
border_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 : Nx4 numpy array
Array of face color RGBA values, one for each point.
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())
current_symbol : Symbol
Symbol for the next point to be added or the currently selected points.
current_size : float
Size of the marker for the next point to be added or the currently
selected point.
current_border_width : float
Border width of the marker for the next point to be added or the currently
selected point.
current_border_color : str
Border color of the marker border for the next point to be added or the currently
selected point.
current_face_color : str
Face color of the marker border for the next point to be added or the currently
selected point.
out_of_slice_display : bool
If True, renders points not just in central plane but also slightly out of slice
according to specified point marker size.
selected_data : Selection
Integer indices of any selected points.
mode : str
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.
face_color_mode : str
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
border_color_mode : str
Border 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
shading : Shading
Shading mode.
antialiasing: float
Amount of antialiasing in canvas pixels.
canvas_size_limits : tuple of float
Lower and upper limits for the size of points in canvas pixels.
shown : 1-D array of bool
Whether each point is shown.
units: tuple of pint.Unit
Units of the layer data in world coordinates.
Notes
-----
_view_data : array (M, D)
coordinates of points in the currently viewed slice.
_view_size : array (M, )
Size of the point markers in the currently viewed slice.
_view_symbol : array (M, )
Symbols of the point markers in the currently viewed slice.
_view_border_width : array (M, )
Border width of the point markers in the currently viewed slice.
_indices_view : array (M, )
Integer indices of the points in the currently viewed slice and are shown.
_selected_view :
Integer indices of selected points in the currently viewed slice within
the `_view_data` array.
_selected_box : array (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_start : list or None
Coordinates of first cursor click during a drag action. Gets reset to
None after dragging is done.
"""
_modeclass = Mode
_projectionclass = PointsProjectionMode
_drag_modes: ClassVar[dict[Mode, Callable[['Points', Event], Any]]] = {
Mode.PAN_ZOOM: no_op,
Mode.TRANSFORM: transform_with_box,
Mode.ADD: add,
Mode.SELECT: select,
}
_move_modes: ClassVar[dict[Mode, Callable[['Points', Event], Any]]] = {
Mode.PAN_ZOOM: no_op,
Mode.TRANSFORM: highlight_box_handles,
Mode.ADD: no_op,
Mode.SELECT: highlight,
}
_cursor_modes: ClassVar[dict[Mode, str]] = {
Mode.PAN_ZOOM: 'standard',
Mode.TRANSFORM: 'standard',
Mode.ADD: 'crosshair',
Mode.SELECT: 'standard',
}
# TODO write better documentation for border_color and face_color
# The max number of points that will ever be used to render the thumbnail
# If more points are present then they are randomly subsampled
_max_points_thumbnail = 1024
def __init__(
self,
data=None,
ndim=None,
*,
affine=None,
antialiasing=1,
axis_labels=None,
blending='translucent',
border_color='dimgray',
border_color_cycle=None,
border_colormap='viridis',
border_contrast_limits=None,
border_width=0.05,
border_width_is_relative=True,
cache=True,
canvas_size_limits=(2, 10000),
experimental_clipping_planes=None,
face_color='white',
face_color_cycle=None,
face_colormap='viridis',
face_contrast_limits=None,
feature_defaults=None,
features=None,
metadata=None,
n_dimensional=None,
name=None,
opacity=1.0,
out_of_slice_display=False,
projection_mode='all',
properties=None,
property_choices=None,
rotate=None,
scale=None,
shading='none',
shear=None,
shown=True,
size=10,
symbol='o',
text=None,
translate=None,
units=None,
visible=True,
) -> None:
if ndim is None:
if scale is not None:
ndim = len(scale)
elif (
data is not None
and hasattr(data, 'shape')
and len(data.shape) == 2
):
ndim = data.shape[1]
data, ndim = fix_data_points(data, ndim)
# Indices of selected points
self._selected_data_stored = set()
self._selected_data_history = set()
self._selected_data: Selection[int] = Selection()
# Indices of selected points within the currently viewed slice
self._selected_view = []
# Index of hovered point
self._value = None
self._value_stored = None
self._highlight_index = []
self._highlight_box = None
self._mode = Mode.PAN_ZOOM
self._status = self.mode
self._drag_start: Optional[np.ndarray] = None
self._drag_normal: Optional[np.ndarray] = None
self._drag_up: Optional[np.ndarray] = None
# initialize view data
self.__indices_view = np.empty(0, int)
self._view_size_scale = []
self._drag_box: Optional[np.ndarray] = None
self._drag_box_stored: Optional[np.ndarray] = None
self._is_selecting = False
self._clipboard = {}
super().__init__(
data,
ndim,
affine=affine,
axis_labels=axis_labels,
blending=blending,
cache=cache,
experimental_clipping_planes=experimental_clipping_planes,
metadata=metadata,
name=name,
opacity=opacity,
projection_mode=projection_mode,
rotate=rotate,
scale=scale,
shear=shear,
translate=translate,
units=units,
visible=visible,
)
self.events.add(
size=Event,
current_size=Event,
border_width=Event,
current_border_width=Event,
border_width_is_relative=Event,
face_color=Event,
current_face_color=Event,
border_color=Event,
current_border_color=Event,
properties=Event,
current_properties=Event,
symbol=Event,
current_symbol=Event,
out_of_slice_display=Event,
n_dimensional=Event,
highlight=Event,
shading=Event,
antialiasing=Event,
canvas_size_limits=Event,
features=Event,
feature_defaults=Event,
)
# Save the point coordinates
self._data = np.asarray(data)
self._feature_table = _FeatureTable.from_layer(
features=features,
feature_defaults=feature_defaults,
properties=properties,
property_choices=property_choices,
num_data=len(self.data),
)
self._text = TextManager._from_layer(
text=text,
features=self.features,
)
self._border_width_is_relative = False
self._shown = np.empty(0).astype(bool)
# The following point properties are for the new points that will
# be added. For any given property, if a list is passed to the
# constructor so each point gets its own value then the default
# value is used when adding new points
self._current_size = np.asarray(size) if np.isscalar(size) else 10
self._current_border_width = (
np.asarray(border_width) if np.isscalar(border_width) else 0.1
)
self.current_symbol = (
np.asarray(symbol) if np.isscalar(symbol) else 'o'
)
color_properties = (
self._feature_table.properties()
if self._data.size > 0
else self._feature_table.currents()
)
self._border = ColorManager._from_layer_kwargs(
n_colors=len(data),
colors=border_color,
continuous_colormap=border_colormap,
contrast_limits=border_contrast_limits,
categorical_colormap=border_color_cycle,
properties=color_properties,
)
self._face = ColorManager._from_layer_kwargs(
n_colors=len(data),
colors=face_color,
continuous_colormap=face_colormap,
contrast_limits=face_contrast_limits,
categorical_colormap=face_color_cycle,
properties=color_properties,
)
if n_dimensional is not None:
self._out_of_slice_display = n_dimensional
else:
self._out_of_slice_display = out_of_slice_display
# Save the point style params
self.size = size
self.shown = shown
self.symbol = symbol
self.border_width = border_width
self.border_width_is_relative = border_width_is_relative
self.canvas_size_limits = canvas_size_limits
self.shading = shading
self.antialiasing = antialiasing
# Trigger generation of view slice and thumbnail
self.refresh(extent=False)
@property
def data(self) -> np.ndarray:
"""(N, D) array: coordinates for N points in D dimensions."""
return self._data
@data.setter
def data(self, data: np.ndarray | None) -> None:
"""Set the data array and emit a corresponding event."""
prior_data = len(self.data) > 0
data_not_empty = (
data is not None
and (isinstance(data, np.ndarray) and data.size > 0)
) or (isinstance(data, list) and len(data) > 0)
kwargs = {
'value': self.data,
'vertex_indices': ((),),
'data_indices': tuple(i for i in range(len(self.data))),
}
if prior_data and data_not_empty:
kwargs['action'] = ActionType.CHANGING
elif data_not_empty:
kwargs['action'] = ActionType.ADDING
kwargs['data_indices'] = tuple(i for i in range(len(data)))
else:
kwargs['action'] = ActionType.REMOVING
self.events.data(**kwargs)
self._set_data(data)
kwargs['data_indices'] = tuple(i for i in range(len(self.data)))
kwargs['value'] = self.data
if prior_data and data_not_empty:
kwargs['action'] = ActionType.CHANGED
elif data_not_empty:
kwargs['data_indices'] = tuple(i for i in range(len(data)))
kwargs['action'] = ActionType.ADDED
else:
kwargs['action'] = ActionType.REMOVED
self.events.data(**kwargs)
self.events.features()
def _set_data(self, data: np.ndarray | None) -> None:
"""Set the .data array attribute, without emitting an event."""
data, _ = fix_data_points(data, self.ndim)
cur_npoints = len(self._data)
self._data = data
# Add/remove property and style values based on the number of new points.
with (
self.events.blocker_all(),
self._border.events.blocker_all(),
self._face.events.blocker_all(),
):
self._feature_table.resize(len(data))
self.text.apply(self.features)
if len(data) < cur_npoints:
# If there are now fewer points, remove the size and colors of the
# extra ones
if len(self._border.colors) > len(data):
self._border._remove(
np.arange(len(data), len(self._border.colors))
)
if len(self._face.colors) > len(data):
self._face._remove(
np.arange(len(data), len(self._face.colors))
)
self._shown = self._shown[: len(data)]
self._size = self._size[: len(data)]
self._border_width = self._border_width[: len(data)]
self._symbol = self._symbol[: len(data)]
elif len(data) > cur_npoints:
# If there are now more points, add the size and colors of the
# new ones
adding = len(data) - cur_npoints
size = np.repeat(self.current_size, adding, axis=0)
new_border_width = self.current_border_width
border_width = np.repeat([new_border_width], adding, axis=0)
new_symbol = self.current_symbol
symbol = np.repeat([new_symbol], adding, axis=0)
# Add new colors, updating the current property value before
# to handle any in-place modification of feature_defaults.
# Also see: https://github.com/napari/napari/issues/5634
current_properties = self._feature_table.currents()
self._border._update_current_properties(current_properties)
self._border._add(n_colors=adding)
self._face._update_current_properties(current_properties)
self._face._add(n_colors=adding)
shown = np.repeat([True], adding, axis=0)
self._shown = np.concatenate((self._shown, shown), axis=0)
self.size = np.concatenate((self._size, size), axis=0)
self.border_width = np.concatenate(
(self._border_width, border_width), axis=0
)
self.symbol = np.concatenate((self._symbol, symbol), axis=0)
self._update_dims()
self._reset_editable()
def _on_selection(self, selected: bool) -> None:
if selected:
self._set_highlight()
else:
self._highlight_box = None
self._highlight_index = []
self.events.highlight()
@property
def features(self) -> pd.DataFrame:
"""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
----------
.. [1]: https://data-apis.org/dataframe-protocol/latest/API.html
"""
return self._feature_table.values
@features.setter
def features(
self,
features: dict[str, np.ndarray] | pd.DataFrame,
) -> None:
self._feature_table.set_values(features, num_data=len(self.data))
self._update_color_manager(
self._face, self._feature_table, 'face_color'
)
self._update_color_manager(
self._border, self._feature_table, 'border_color'
)
self.text.refresh(self.features)
self.events.properties()
self.events.features()
@property
def feature_defaults(self) -> pd.DataFrame:
"""Dataframe-like with one row of feature default values.
See `features` for more details on the type of this property.
"""
return self._feature_table.defaults
@feature_defaults.setter
def feature_defaults(
self, defaults: dict[str, Any] | pd.DataFrame
) -> None:
self._feature_table.set_defaults(defaults)
current_properties = self.current_properties
self._border._update_current_properties(current_properties)
self._face._update_current_properties(current_properties)
self.events.current_properties()
self.events.feature_defaults()
@property
def property_choices(self) -> dict[str, np.ndarray]:
return self._feature_table.choices()
@property
def properties(self) -> dict[str, np.ndarray]:
"""dict {str: np.ndarray (N,)}, DataFrame: Annotations for each point"""
return self._feature_table.properties()
@staticmethod
def _update_color_manager(color_manager, feature_table, name):
if color_manager.color_properties is not None:
color_name = color_manager.color_properties.name
if color_name not in feature_table.values:
color_manager.color_mode = ColorMode.DIRECT
color_manager.color_properties = None
warnings.warn(
trans._(
'property used for {name} dropped',
deferred=True,
name=name,
),
RuntimeWarning,
)
else:
color_manager.color_properties = {
'name': color_name,
'values': feature_table.values[color_name].to_numpy(),
'current_value': feature_table.defaults[color_name][0],
}
@properties.setter
def properties(
self, properties: dict[str, Array] | pd.DataFrame | None
) -> None:
self.features = properties
@property
def current_properties(self) -> dict[str, np.ndarray]:
"""dict{str: np.ndarray(1,)}: properties for the next added point."""
return self._feature_table.currents()
@current_properties.setter
def current_properties(self, current_properties):
update_indices = None
if self._update_properties and len(self.selected_data) > 0:
update_indices = list(self.selected_data)
self._feature_table.set_currents(
current_properties, update_indices=update_indices
)
current_properties = self.current_properties
self._border._update_current_properties(current_properties)
self._face._update_current_properties(current_properties)
self.events.current_properties()
self.events.feature_defaults()
if update_indices is not None:
self.events.properties()
self.events.features()
@property
def text(self) -> TextManager:
"""TextManager: the TextManager object containing containing the text properties"""
return self._text
@text.setter
def text(self, text):
self._text._update_from_layer(
text=text,
features=self.features,
)
[docs]
def refresh_text(self) -> None:
"""Refresh the text values.
This is generally used if the features were updated without changing the data
"""
self.text.refresh(self.features)
def _get_ndim(self) -> int:
"""Determine number of dimensions of the layer."""
return self.data.shape[1]
@property
def _extent_data(self) -> np.ndarray:
"""Extent of layer in data coordinates.
Returns
-------
extent_data : array, shape (2, D)
"""
if len(self.data) == 0:
extrema = np.full((2, self.ndim), np.nan)
else:
maxs = np.max(self.data, axis=0)
mins = np.min(self.data, axis=0)
extrema = np.vstack([mins, maxs])
return extrema.astype(float)
@property
def _extent_data_augmented(self) -> npt.NDArray:
# _extent_data is a property that returns a new/copied array, which
# is safe to modify below
extent = self._extent_data
if len(self.size) == 0:
return extent
max_point_size = np.max(self.size)
extent[0] -= max_point_size / 2
extent[1] += max_point_size / 2
return extent
@property
def out_of_slice_display(self) -> bool:
"""bool: renders points slightly out of slice."""
return self._out_of_slice_display
@out_of_slice_display.setter
def out_of_slice_display(self, out_of_slice_display: bool) -> None:
self._out_of_slice_display = bool(out_of_slice_display)
self.events.out_of_slice_display()
self.events.n_dimensional()
self.refresh(extent=False)
@property
def n_dimensional(self) -> bool:
"""
This property will soon be deprecated in favor of `out_of_slice_display`. Use that instead.
"""
return self._out_of_slice_display
@n_dimensional.setter
def n_dimensional(self, value: bool) -> None:
self.out_of_slice_display = value
@property
def symbol(self) -> np.ndarray:
"""str: symbol used for all point markers."""
return self._symbol
@symbol.setter
def symbol(self, symbol: str | np.ndarray | list) -> None:
coerced_symbols = coerce_symbols(symbol)
# If a single symbol has been converted, this will broadcast it to
# the number of points in the data. If symbols is already an array,
# this will check that it is the correct length.
if coerced_symbols.size == 1:
coerced_symbols = np.full(
self.data.shape[0], coerced_symbols[0], dtype=object
)
else:
coerced_symbols = np.array(coerced_symbols)
if coerced_symbols.size != self.data.shape[0]:
raise ValueError(
'Symbol array must be the same length as data.'
)
self._symbol = coerced_symbols
self.events.symbol()
self.events.highlight()
@property
def current_symbol(self) -> int | float:
"""float: symbol of marker for the next added point."""
return self._current_symbol
@current_symbol.setter
def current_symbol(self, symbol: None | float) -> None:
symbol = coerce_symbols(np.array([symbol]))[0]
self._current_symbol = symbol
if self._update_properties and len(self.selected_data) > 0:
self.symbol[list(self.selected_data)] = symbol
self.events.symbol()
self.events.current_symbol()
@property
def size(self) -> np.ndarray:
"""(N,) array: size of all N points."""
return self._size
@size.setter
def size(self, size: float | np.ndarray | list) -> None:
try:
self._size = np.broadcast_to(size, len(self.data)).copy()
except ValueError as e:
raise ValueError(
trans._(
'Size is not compatible for broadcasting (may be anisotropic)',
deferred=True,
)
) from e
# TODO: technically not needed to cleat the non-augmented extent... maybe it's fine like this to avoid complexity
self.refresh(highlight=False)
@property
def current_size(self) -> int | float:
"""float: size of marker for the next added point."""
return self._current_size
@current_size.setter
def current_size(self, size: None | float) -> None:
if isinstance(size, list | tuple | np.ndarray):
size = size[-1]
if not isinstance(size, numbers.Number):
raise TypeError(
trans._(
'currrent size must be a number',
deferred=True,
)
)
if size < 0:
raise ValueError(
trans._(
'current_size value must be positive.',
deferred=True,
),
)
self._current_size = size
if self._update_properties and len(self.selected_data) > 0:
idx = np.fromiter(self.selected_data, dtype=int)
self.size[idx] = size
# TODO: also here technically no need to clear base extent
self.refresh(highlight=False)
self.events.size()
self.events.current_size()
@property
def antialiasing(self) -> float:
"""Amount of antialiasing in canvas pixels."""
return self._antialiasing
@antialiasing.setter
def antialiasing(self, value: float) -> None:
"""Set the amount of antialiasing in canvas pixels.
Values can only be positive.
"""
if value < 0:
warnings.warn(
message=trans._(
'antialiasing value must be positive, value will be set to 0.',
deferred=True,
),
category=RuntimeWarning,
)
self._antialiasing = max(0, value)
self.events.antialiasing(value=self._antialiasing)
@property
def shading(self) -> Shading:
"""shading mode."""
return self._shading
@shading.setter
def shading(self, value):
self._shading = Shading(value)
self.events.shading()
@property
def canvas_size_limits(self) -> tuple[float, float]:
"""Limit the canvas size of points"""
return self._canvas_size_limits
@canvas_size_limits.setter
def canvas_size_limits(self, value):
self._canvas_size_limits = float(value[0]), float(value[1])
self.events.canvas_size_limits()
@property
def shown(self) -> npt.NDArray:
"""
Boolean array determining which points to show
"""
return self._shown
@shown.setter
def shown(self, shown):
self._shown = np.broadcast_to(shown, self.data.shape[0]).astype(bool)
self.refresh(extent=False, highlight=False)
@property
def border_width(self) -> np.ndarray:
"""(N, D) array: border_width of all N points."""
return self._border_width
@border_width.setter
def border_width(self, border_width: float | np.ndarray | list) -> None:
# broadcast to np.array
border_width = np.broadcast_to(border_width, self.data.shape[0]).copy()
# border width cannot be negative
if np.any(border_width < 0):
raise ValueError(
trans._(
'All border_width must be > 0',
deferred=True,
)
)
# if relative border width is enabled, border_width must be between 0 and 1
if self.border_width_is_relative and np.any(border_width > 1):
raise ValueError(
trans._(
'All border_width must be between 0 and 1 if border_width_is_relative is enabled',
deferred=True,
)
)
self._border_width = border_width
self.events.border_width(value=border_width)
self.refresh(extent=False)
@property
def border_width_is_relative(self) -> bool:
"""bool: treat border_width as a fraction of point size."""
return self._border_width_is_relative
@border_width_is_relative.setter
def border_width_is_relative(self, border_width_is_relative: bool) -> None:
if border_width_is_relative and np.any(
(self.border_width > 1) | (self.border_width < 0)
):
raise ValueError(
trans._(
'border_width_is_relative can only be enabled if border_width is between 0 and 1',
deferred=True,
)
)
self._border_width_is_relative = border_width_is_relative
self.events.border_width_is_relative()
@property
def current_border_width(self) -> int | float:
"""float: border_width of marker for the next added point."""
return self._current_border_width
@current_border_width.setter
def current_border_width(self, border_width: None | float) -> None:
self._current_border_width = border_width
if self._update_properties and len(self.selected_data) > 0:
idx = np.fromiter(self.selected_data, dtype=int)
self.border_width[idx] = border_width
self.refresh(highlight=False)
self.events.border_width()
self.events.current_border_width()
@property
def border_color(self) -> np.ndarray:
"""(N x 4) np.ndarray: Array of RGBA border colors for each point"""
return self._border.colors
@border_color.setter
def border_color(self, border_color):
self._border._set_color(
color=border_color,
n_colors=len(self.data),
properties=self.properties,
current_properties=self.current_properties,
)
self.events.border_color()
@property
def border_color_cycle(self) -> np.ndarray:
"""Union[list, np.ndarray] : Color cycle for border_color.
Can be a list of colors defined by name, RGB or RGBA
"""
return self._border.categorical_colormap.fallback_color.values
@border_color_cycle.setter
def border_color_cycle(
self, border_color_cycle: list | np.ndarray
) -> None:
self._border.categorical_colormap = border_color_cycle
@property
def border_colormap(self) -> Colormap:
"""Return the colormap to be applied to a property to get the border color.
Returns
-------
colormap : napari.utils.Colormap
The Colormap object.
"""
return self._border.continuous_colormap
@border_colormap.setter
def border_colormap(self, colormap: ValidColormapArg) -> None:
self._border.continuous_colormap = colormap
@property
def border_contrast_limits(self) -> tuple[float, float]:
"""None, (float, float): contrast limits for mapping
the border_color colormap property to 0 and 1
"""
return self._border.contrast_limits
@border_contrast_limits.setter
def border_contrast_limits(
self, contrast_limits: None | tuple[float, float]
) -> None:
self._border.contrast_limits = contrast_limits
@property
def current_border_color(self) -> str:
"""str: border color of marker for the next added point or the selected point(s)."""
hex_ = rgb_to_hex(self._border.current_color)[0]
return hex_to_name.get(hex_, hex_)
@current_border_color.setter
def current_border_color(self, border_color: ColorType) -> None:
if self._update_properties and len(self.selected_data) > 0:
update_indices = list(self.selected_data)
else:
update_indices = []
self._border._update_current_color(
border_color, update_indices=update_indices
)
self.events.current_border_color()
@property
def border_color_mode(self) -> str:
"""str: border 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
"""
return self._border.color_mode
@border_color_mode.setter
def border_color_mode(self, border_color_mode: str | ColorMode) -> None:
self._set_color_mode(border_color_mode, 'border')
@property
def face_color(self) -> np.ndarray:
"""(N x 4) np.ndarray: Array of RGBA face colors for each point"""
return self._face.colors
@face_color.setter
def face_color(self, face_color):
self._face._set_color(
color=face_color,
n_colors=len(self.data),
properties=self.properties,
current_properties=self.current_properties,
)
self.events.face_color()
@property
def face_color_cycle(self) -> np.ndarray:
"""Union[np.ndarray, cycle]: Color cycle for face_color
Can be a list of colors defined by name, RGB or RGBA
"""
return self._face.categorical_colormap.fallback_color.values
@face_color_cycle.setter
def face_color_cycle(self, face_color_cycle: np.ndarray | cycle) -> None:
self._face.categorical_colormap = face_color_cycle
@property
def face_colormap(self) -> Colormap:
"""Return the colormap to be applied to a property to get the face color.
Returns
-------
colormap : napari.utils.Colormap
The Colormap object.
"""
return self._face.continuous_colormap
@face_colormap.setter
def face_colormap(self, colormap: ValidColormapArg) -> None:
self._face.continuous_colormap = colormap
@property
def face_contrast_limits(self) -> None | tuple[float, float]:
"""None, (float, float) : clims for mapping the face_color
colormap property to 0 and 1
"""
return self._face.contrast_limits
@face_contrast_limits.setter
def face_contrast_limits(
self, contrast_limits: None | tuple[float, float]
) -> None:
self._face.contrast_limits = contrast_limits
@property
def current_face_color(self) -> str:
"""Face color of marker for the next added point or the selected point(s)."""
hex_ = rgb_to_hex(self._face.current_color)[0]
return hex_to_name.get(hex_, hex_)
@current_face_color.setter
def current_face_color(self, face_color: ColorType) -> None:
if self._update_properties and len(self.selected_data) > 0:
update_indices = list(self.selected_data)
else:
update_indices = []
self._face._update_current_color(
face_color, update_indices=update_indices
)
self.events.current_face_color()
@property
def face_color_mode(self) -> str:
"""str: 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
"""
return self._face.color_mode
@face_color_mode.setter
def face_color_mode(self, face_color_mode):
self._set_color_mode(face_color_mode, 'face')
def _set_color_mode(
self,
color_mode: ColorMode | str,
attribute: Literal['border', 'face'],
) -> None:
"""Set the face_color_mode or border_color_mode property
Parameters
----------
color_mode : str, ColorMode
The value for setting border or face_color_mode. If color_mode is a string,
it should be one of: 'direct', 'cycle', or 'colormap'
attribute : str in {'border', 'face'}
The name of the attribute to set the color of.
Should be 'border' for border_color_mode or 'face' for face_color_mode.
"""
color_mode = ColorMode(color_mode)
color_manager = getattr(self, f'_{attribute}')
if color_mode == ColorMode.DIRECT:
color_manager.color_mode = color_mode
elif color_mode in (ColorMode.CYCLE, ColorMode.COLORMAP):
if color_manager.color_properties is not None:
color_property = color_manager.color_properties.name
else:
color_property = ''
if color_property == '':
if self.features.shape[1] > 0:
new_color_property = next(iter(self.features))
color_manager.color_properties = {
'name': new_color_property,
'values': self.features[new_color_property].to_numpy(),
'current_value': np.squeeze(
self.current_properties[new_color_property]
),
}
warnings.warn(
trans._(
'_{attribute}_color_property was not set, setting to: {new_color_property}',
deferred=True,
attribute=attribute,
new_color_property=new_color_property,
)
)
else:
raise ValueError(
trans._(
'There must be a valid Points.properties to use {color_mode}',
deferred=True,
color_mode=color_mode,
)
)
# ColorMode.COLORMAP can only be applied to numeric properties
color_property = color_manager.color_properties.name
if (color_mode == ColorMode.COLORMAP) and not issubclass(
self.features[color_property].dtype.type, np.number
):
raise TypeError(
trans._(
'selected property must be numeric to use ColorMode.COLORMAP',
deferred=True,
)
)
color_manager.color_mode = color_mode
[docs]
def refresh_colors(self, update_color_mapping: bool = False) -> None:
"""Calculate and update face and border 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 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.
"""
self._border._refresh_colors(self.properties, update_color_mapping)
self._face._refresh_colors(self.properties, update_color_mapping)
def _get_state(self) -> dict[str, Any]:
"""Get dictionary of layer state.
Returns
-------
state : dict of str to Any
Dictionary of layer state.
"""
state = self._get_base_state()
state.update(
{
'symbol': (
self.symbol if self.data.size else [self.current_symbol]
),
'border_width': self.border_width,
'border_width_is_relative': self.border_width_is_relative,
'face_color': (
self.face_color
if self.data.size
else [self.current_face_color]
),
'face_color_cycle': self.face_color_cycle,
'face_colormap': self.face_colormap.dict(),
'face_contrast_limits': self.face_contrast_limits,
'border_color': (
self.border_color
if self.data.size
else [self.current_border_color]
),
'border_color_cycle': self.border_color_cycle,
'border_colormap': self.border_colormap.dict(),
'border_contrast_limits': self.border_contrast_limits,
'properties': self.properties,
'property_choices': self.property_choices,
'text': self.text.dict(),
'out_of_slice_display': self.out_of_slice_display,
'n_dimensional': self.out_of_slice_display,
'size': self.size,
'ndim': self.ndim,
'data': self.data,
'features': self.features,
'feature_defaults': self.feature_defaults,
'shading': self.shading,
'antialiasing': self.antialiasing,
'canvas_size_limits': self.canvas_size_limits,
'shown': self.shown,
}
)
return state
@property
def selected_data(self) -> Selection[int]:
"""set: set of currently selected points."""
return self._selected_data
@selected_data.setter
def selected_data(self, selected_data: Iterable[int]) -> None:
self._selected_data.clear()
self._selected_data.update(set(selected_data))
self._selected_view = list(
np.intersect1d(
np.array(list(self._selected_data)),
self._indices_view,
return_indices=True,
)[2]
)
# Update properties based on selected points
if not len(self._selected_data):
self._set_highlight()
return
index = list(self._selected_data)
with self.block_update_properties():
if (
unique_border_color := _unique_element(
self.border_color[index]
)
) is not None:
self.current_border_color = unique_border_color
if (
unique_face_color := _unique_element(self.face_color[index])
) is not None:
self.current_face_color = unique_face_color
if (unique_size := _unique_element(self.size[index])) is not None:
self.current_size = unique_size
if (
unique_border_width := _unique_element(
self.border_width[index]
)
) is not None:
self.current_border_width = unique_border_width
if (
unique_symbol := _unique_element(self.symbol[index])
) is not None:
self.current_symbol = unique_symbol
unique_properties = {}
for k, v in self.properties.items():
unique_properties[k] = _unique_element(v[index])
if all(p is not None for p in unique_properties.values()):
self.current_properties = unique_properties
self._set_highlight()
[docs]
def interaction_box(self, index: list[int]) -> np.ndarray | None:
"""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 : np.ndarray or None
4x2 array of corners of the interaction box in clockwise order
starting in the upper-left corner.
"""
if len(index) > 0:
data = self._view_data[index]
size = self._view_size[index]
data = points_to_squares(data, size)
return create_box(data)
return None
@Layer.mode.getter
def mode(self) -> str:
"""str: 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.
"""
return str(self._mode)
def _mode_setter_helper(self, mode):
mode = super()._mode_setter_helper(mode)
if mode == self._mode:
return mode
if mode == Mode.ADD:
self.selected_data = set()
self.mouse_pan = True
elif mode != Mode.SELECT or self._mode != Mode.SELECT:
self._selected_data_stored = set()
self._set_highlight()
return mode
@property
def _indices_view(self):
return self.__indices_view
@_indices_view.setter
def _indices_view(self, value):
if len(self._shown) == 0:
self.__indices_view = np.empty(0, int)
else:
self.__indices_view = value[self.shown[value]]
@property
def _view_data(self) -> np.ndarray:
"""Get the coords of the points in view
Returns
-------
view_data : (N x D) np.ndarray
Array of coordinates for the N points in view
"""
if len(self._indices_view) > 0:
data = self.data[
np.ix_(self._indices_view, self._slice_input.displayed)
]
else:
# if no points in this slice send dummy data
data = np.zeros((0, self._slice_input.ndisplay))
return data
@property
def _view_text(self) -> np.ndarray:
"""Get the values of the text elements in view
Returns
-------
text : (N x 1) np.ndarray
Array of text strings for the N text elements in view
"""
# This may be triggered when the string encoding instance changed,
# in which case it has no cached values, so generate them here.
self.text.string._apply(self.features)
return self.text.view_text(self._indices_view)
@property
def _view_text_coords(self) -> tuple[np.ndarray, str, str]:
"""Get the coordinates of the text elements in view
Returns
-------
text_coords : (N x D) np.ndarray
Array of coordinates for the N text elements in view
anchor_x : str
The vispy text anchor for the x axis
anchor_y : str
The vispy text anchor for the y axis
"""
return self.text.compute_text_coords(
self._view_data,
self._slice_input.ndisplay,
self._slice_input.order,
)
@property
def _view_text_color(self) -> np.ndarray:
"""Get the colors of the text elements at the given indices."""
self.text.color._apply(self.features)
return self.text._view_color(self._indices_view)
@property
def _view_size(self) -> np.ndarray:
"""Get the sizes of the points in view
Returns
-------
view_size : (N,) np.ndarray
Array of sizes for the N points in view
"""
if len(self._indices_view) > 0:
sizes = self.size[self._indices_view] * self._view_size_scale
else:
# if no points, return an empty list
sizes = np.array([])
return sizes
@property
def _view_symbol(self) -> np.ndarray:
"""Get the symbols of the points in view
Returns
-------
symbol : (N,) np.ndarray
Array of symbol strings for the N points in view
"""
return self.symbol[self._indices_view]
@property
def _view_border_width(self) -> np.ndarray:
"""Get the border_width of the points in view
Returns
-------
view_border_width : (N,) np.ndarray
Array of border_widths for the N points in view
"""
return self.border_width[self._indices_view]
@property
def _view_face_color(self) -> np.ndarray:
"""Get the face colors of the points in view
Returns
-------
view_face_color : (N x 4) np.ndarray
RGBA color array for the face colors of the N points in view.
If there are no points in view, returns array of length 0.
"""
return self.face_color[self._indices_view]
@property
def _view_border_color(self) -> np.ndarray:
"""Get the border colors of the points in view
Returns
-------
view_border_color : (N x 4) np.ndarray
RGBA color array for the border colors of the N points in view.
If there are no points in view, returns array of length 0.
"""
return self.border_color[self._indices_view]
def _reset_editable(self) -> None:
"""Set editable mode based on layer properties."""
# interaction currently does not work for 2D layers being rendered in 3D
self.editable = not (
self.ndim == 2 and self._slice_input.ndisplay == 3
)
def _on_editable_changed(self) -> None:
if not self.editable:
self.mode = Mode.PAN_ZOOM
def _update_draw(
self, scale_factor, corner_pixels_displayed, shape_threshold
):
prev_scale = self.scale_factor
super()._update_draw(
scale_factor, corner_pixels_displayed, shape_threshold
)
# update highlight only if scale has changed, otherwise causes a cycle
self._set_highlight(force=(prev_scale != self.scale_factor))
def _get_value_(
self,
position: npt.ArrayLike,
*,
view_direction: npt.ArrayLike | None = None,
dims_displayed: list[int] | None = None,
world: bool = False,
) -> int | None:
"""Workaround for inconsistency in real return type of get_value"""
return typing.cast(
int,
self.get_value(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
),
)
def _get_value(self, position) -> int | None:
"""Index of the point at a given 2D position in data coordinates.
Parameters
----------
position : tuple
Position in data coordinates.
Returns
-------
value : int or None
Index of point that is at the current coordinate if any.
"""
# Display points if there are any in this slice
view_data = self._view_data
selection = None
if len(view_data) > 0:
displayed_position = [
position[i] for i in self._slice_input.displayed
]
# positions are scaled anisotropically by scale, but sizes are not,
# so we need to calculate the ratio to correctly map to screen coordinates
scale_ratio = (
self.scale[self._slice_input.displayed] / self.scale[-1]
)
# Get the point sizes
# TODO: calculate distance in canvas space to account for canvas_size_limits.
# Without this implementation, point hover and selection (and anything depending
# on self.get_value()) won't be aware of the real extent of points, causing
# unexpected behaviour. See #3734 for details.
sizes = np.expand_dims(self._view_size, axis=1) / scale_ratio / 2
distances = abs(view_data - displayed_position)
in_slice_matches = np.all(
distances <= sizes,
axis=1,
)
indices = np.where(in_slice_matches)[0]
if len(indices) > 0:
selection = self._indices_view[indices[-1]]
return selection
def _get_value_3d(
self,
start_point: np.ndarray,
end_point: np.ndarray,
dims_displayed: list[int],
) -> int | None:
"""Get the layer data value along a ray
Parameters
----------
start_point : np.ndarray
The start position of the ray used to interrogate the data.
end_point : np.ndarray
The end position of the ray used to interrogate the data.
dims_displayed : List[int]
The indices of the dimensions currently displayed in the Viewer.
Returns
-------
value : Union[int, None]
The data value along the supplied ray.
"""
if (start_point is None) or (end_point is None):
# if the ray doesn't intersect the data volume, no points could have been intersected
return None
plane_point, plane_normal = displayed_plane_from_nd_line_segment(
start_point, end_point, dims_displayed
)
# project the in view points onto the plane
projected_points, projection_distances = project_points_onto_plane(
points=self._view_data,
plane_point=plane_point,
plane_normal=plane_normal,
)
# rotate points and plane to be axis aligned with normal [0, 0, 1]
rotated_points, rotation_matrix = rotate_points(
points=projected_points,
current_plane_normal=plane_normal,
new_plane_normal=[0, 0, 1],
)
rotated_click_point = np.dot(rotation_matrix, plane_point)
# positions are scaled anisotropically by scale, but sizes are not,
# so we need to calculate the ratio to correctly map to screen coordinates
scale_ratio = self.scale[self._slice_input.displayed] / self.scale[-1]
# find the points the click intersects
sizes = np.expand_dims(self._view_size, axis=1) / scale_ratio / 2
distances = abs(rotated_points - rotated_click_point)
in_slice_matches = np.all(
distances <= sizes,
axis=1,
)
indices = np.where(in_slice_matches)[0]
if len(indices) > 0:
# find the point that is most in the foreground
candidate_point_distances = projection_distances[indices]
closest_index = indices[np.argmin(candidate_point_distances)]
selection = self._indices_view[closest_index]
else:
selection = None
return selection
[docs]
def get_ray_intersections(
self,
position: list[float],
view_direction: np.ndarray,
dims_displayed: list[int],
world: bool = True,
) -> tuple[np.ndarray, np.ndarray] | tuple[None, None]:
"""Get the start and end point for the ray extending
from a point through the displayed bounding box.
This method overrides the base layer, replacing the bounding box used
to calculate intersections with a larger one which includes the size
of points in view.
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.
"""
if len(dims_displayed) != 3:
return None, None
# create the bounding box in data coordinates
bounding_box = self._display_bounding_box_augmented(dims_displayed)
if bounding_box is None:
return None, None
start_point, end_point = self._get_ray_intersections(
position=position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
bounding_box=bounding_box,
)
return start_point, end_point
def _set_view_slice(self) -> None:
"""Sets the view given the indices to slice with."""
# The new slicing code makes a request from the existing state and
# executes the request on the calling thread directly.
# For async slicing, the calling thread will not be the main thread.
request = self._make_slice_request_internal(
self._slice_input, self._data_slice
)
response = request()
self._update_slice_response(response)
def _make_slice_request(self, dims: 'Dims') -> _PointSliceRequest:
"""Make a Points slice request based on the given dims and these data."""
slice_input = self._make_slice_input(dims)
# See Image._make_slice_request to understand why we evaluate this here
# instead of using `self._data_slice`.
data_slice = slice_input.data_slice(self._data_to_world.inverse)
return self._make_slice_request_internal(slice_input, data_slice)
def _make_slice_request_internal(
self, slice_input: _SliceInput, data_slice: _ThickNDSlice
) -> _PointSliceRequest:
return _PointSliceRequest(
slice_input=slice_input,
data=self.data,
data_slice=data_slice,
projection_mode=self.projection_mode,
out_of_slice_display=self.out_of_slice_display,
size=self.size,
)
def _update_slice_response(self, response: _PointSliceResponse) -> None:
"""Handle a slicing response."""
self._slice_input = response.slice_input
indices = response.indices
scale = response.scale
# Update the _view_size_scale in accordance to the self._indices_view setter.
# If out_of_slice_display is False, scale is a number and not an array.
# Therefore we have an additional if statement checking for
# self._view_size_scale being an integer.
if not isinstance(scale, np.ndarray):
self._view_size_scale = scale
elif len(self._shown) == 0:
self._view_size_scale = np.empty(0, int)
else:
self._view_size_scale = scale[self.shown[indices]]
self._indices_view = np.array(indices, dtype=int)
# get the selected points that are in view
self._selected_view = list(
np.intersect1d(
np.array(list(self._selected_data)),
self._indices_view,
return_indices=True,
)[2]
)
with self.events.highlight.blocker():
self._set_highlight(force=True)
def _set_highlight(self, force: bool = False) -> None:
"""Render highlights of shapes including boundaries, vertices,
interaction boxes, and the drag selection box when appropriate.
Highlighting only occurs in Mode.SELECT.
Parameters
----------
force : bool
Bool that forces a redraw to occur when `True`
"""
# Check if any point ids have changed since last call
if (
self.selected_data == self._selected_data_stored
and self._value == self._value_stored
and np.array_equal(self._drag_box, self._drag_box_stored)
) and not force:
return
self._selected_data_stored = Selection(self.selected_data)
self._value_stored = copy(self._value)
self._drag_box_stored = copy(self._drag_box)
if self._highlight_visible and (
self._value is not None or len(self._selected_view) > 0
):
if len(self._selected_view) > 0:
index = copy(self._selected_view)
# highlight the hovered point if not in adding mode
if (
self._value in self._indices_view
and self._mode == Mode.SELECT
and not self._is_selecting
):
hover_point = list(self._indices_view).index(self._value)
if hover_point not in index:
index.append(hover_point)
index.sort()
else:
# only highlight hovered points in select mode
if (
self._value in self._indices_view
and self._mode == Mode.SELECT
and not self._is_selecting
):
hover_point = list(self._indices_view).index(self._value)
index = [hover_point]
else:
index = []
self._highlight_index = index
else:
self._highlight_index = []
# only display dragging selection box in 2D
if self._highlight_visible and self._is_selecting:
if self._drag_normal is None:
pos = create_box(self._drag_box)
else:
pos = _create_box_from_corners_3d(
self._drag_box, self._drag_normal, self._drag_up
)
pos = pos[[*range(4), 0]]
else:
pos = None
self._highlight_box = pos
self.events.highlight()
def _update_thumbnail(self) -> None:
"""Update thumbnail with current points and colors."""
colormapped = np.zeros(self._thumbnail_shape)
colormapped[..., 3] = 1
view_data = self._view_data
if len(view_data) > 0:
# Get the zoom factor required to fit all data in the thumbnail.
de = self._extent_data
min_vals = [de[0, i] for i in self._slice_input.displayed]
shape = np.ceil(
[de[1, i] - de[0, i] + 1 for i in self._slice_input.displayed]
).astype(int)
zoom_factor = np.divide(
self._thumbnail_shape[:2], shape[-2:]
).min()
# Maybe subsample the points.
if len(view_data) > self._max_points_thumbnail:
thumbnail_indices = np.random.randint(
0, len(view_data), self._max_points_thumbnail
)
points = view_data[thumbnail_indices]
else:
points = view_data
thumbnail_indices = self._indices_view
# Calculate the point coordinates in the thumbnail data space.
thumbnail_shape = np.clip(
np.ceil(zoom_factor * np.array(shape[:2])).astype(int),
1, # smallest side should be 1 pixel wide
self._thumbnail_shape[:2],
)
coords = np.floor(
(points[:, -2:] - min_vals[-2:] + 0.5) * zoom_factor
).astype(int)
coords = np.clip(coords, 0, thumbnail_shape - 1)
# Draw single pixel points in the colormapped thumbnail.
colormapped = np.zeros((*thumbnail_shape, 4))
colormapped[..., 3] = 1
colors = self._face.colors[thumbnail_indices]
colormapped[coords[:, 0], coords[:, 1]] = colors
colormapped[..., 3] *= self.opacity
self.thumbnail = colormapped
[docs]
def add(self, coords: np.ndarray) -> None:
"""Adds points at coordinates.
Parameters
----------
coords : array
Point or points to add to the layer data.
"""
cur_points = len(self.data)
self.events.data(
value=self.data,
action=ActionType.ADDING,
data_indices=(-1,),
vertex_indices=((),),
)
self._set_data(np.append(self.data, np.atleast_2d(coords), axis=0))
self.events.data(
value=self.data,
action=ActionType.ADDED,
data_indices=tuple(np.arange(-len(np.atleast_2d(coords)), 0)),
vertex_indices=((),),
)
self.selected_data = set(np.arange(cur_points, len(self.data)))
self.events.features()
[docs]
def remove(self, indices: list[int]) -> None:
"""Removes any points at the given indices.
Parameters
----------
indices : List[int]
List of indices of points to remove from the layer.
"""
indices = sorted(indices)
if len(indices):
self.events.data(
value=self.data,
action=ActionType.REMOVING,
data_indices=tuple(
indices,
),
vertex_indices=((),),
)
self._shown = np.delete(self._shown, indices, axis=0)
self._size = np.delete(self._size, indices, axis=0)
self._symbol = np.delete(self._symbol, indices, axis=0)
self._border_width = np.delete(self._border_width, indices, axis=0)
with self._border.events.blocker_all():
self._border._remove(indices_to_remove=indices)
with self._face.events.blocker_all():
self._face._remove(indices_to_remove=indices)
self._feature_table.remove(indices)
self.text.remove(indices)
if self._value in indices:
self._value = None
else:
if self._value is not None:
# update the index of self._value to account for the
# data being removed
indices_removed = np.array(indices) < self._value
offset = np.sum(indices_removed)
self._value -= offset
self._value_stored -= offset
self._set_data(np.delete(self.data, indices, axis=0))
if len(self.data) == 0 and self.selected_data:
self.selected_data.clear()
elif self.selected_data:
selected_not_removed = self.selected_data - set(indices)
if selected_not_removed:
indices_array = np.array(indices)
remaining_selected = np.fromiter(
selected_not_removed,
dtype=np.intp,
count=len(selected_not_removed),
)
shifts = np.searchsorted(indices_array, remaining_selected)
new_selected_indices = remaining_selected - shifts
self.selected_data = set(new_selected_indices)
else:
self.selected_data.clear()
self.events.data(
value=self.data,
action=ActionType.REMOVED,
data_indices=tuple(
indices,
),
vertex_indices=((),),
)
self.events.features()
[docs]
def get_point_info(self, index: int) -> dict:
"""
Retrieve all available information about a point at the given index.
Parameters
----------
index : int
Index of the point.
Returns
-------
dict
A dictionary containing all relevant details of the point.
"""
if not (0 <= index < len(self.data)):
return {
'data': None,
'features': {},
'face_color': None,
'border_color': None,
'size': None,
'symbol': None,
'border_width': None,
}
info = {
'data': self.data[index],
'features': self.features.iloc[index].to_dict(),
'face_color': self.face_color[index],
'border_color': self.border_color[index],
'size': self.size[index],
'symbol': self.symbol[index],
'border_width': self.border_width[index],
}
return info
[docs]
def pop(self, index=-1) -> dict[str, Any]:
"""Remove and return the point at the given index.
Parameters
----------
index : int, optional
Index of the point to remove. Default is -1, which removes the last point.
Returns
-------
dict[str, Any]
Dictionary containing the removed point's data.
"""
if index == -1:
index = len(self.data) - 1
info = self.get_point_info(index)
self.remove([index])
return info
[docs]
def remove_selected(self) -> None:
"""Remove all selected points."""
self.remove(list(self.selected_data))
def _move(
self,
selection_indices: AbstractSet[int],
position: Sequence[float]
| np.ndarray[tuple[int], np.dtype[np.floating]],
) -> None:
"""Move points relative to drag start location.
Parameters
----------
selection_indices : Sequence[int]
Integer indices of points to move in self.data
position : tuple
Position to move points to in data coordinates.
"""
if len(selection_indices) > 0:
selection_indices = list(selection_indices)
disp = list(self._slice_input.displayed)
self._set_drag_start(selection_indices, position)
center = self.data[np.ix_(selection_indices, disp)].mean(axis=0)
shift = np.array(position)[disp] - center - self._drag_start
self.data[np.ix_(selection_indices, disp)] = (
self.data[np.ix_(selection_indices, disp)] + shift
)
self.refresh()
self.events.data(
value=self.data,
action=ActionType.CHANGED,
data_indices=tuple(selection_indices),
vertex_indices=((),),
)
self.events.features()
def _set_drag_start(
self,
selection_indices: AbstractSet[int],
position: Sequence[float]
| np.ndarray[tuple[int], np.dtype[np.floating]],
center_by_data: bool = True,
) -> None:
"""Store the initial position at the start of a drag event.
Parameters
----------
selection_indices : set of int
integer indices of selected data used to index into self.data
position : Sequence of numbers
position of the drag start in data coordinates.
center_by_data : bool
Center the drag start based on the selected data.
Used for modifier drag_box selection.
"""
selection_indices = list(selection_indices)
dims_displayed = list(self._slice_input.displayed)
if self._drag_start is None:
self._drag_start = np.array(position, dtype=float)[dims_displayed]
if len(selection_indices) > 0 and center_by_data:
center = self.data[
np.ix_(selection_indices, dims_displayed)
].mean(axis=0)
self._drag_start -= center
def _paste_data(self) -> None:
"""Paste any point from clipboard and select them."""
npoints = len(self._view_data)
totpoints = len(self.data)
if len(self._clipboard.keys()) > 0:
not_disp = self._slice_input.not_displayed
data = deepcopy(self._clipboard['data'])
offset = [
self._data_slice[i] - self._clipboard['indices'][i]
for i in not_disp
]
data[:, not_disp] = data[:, not_disp] + np.array(offset)
self._data = np.append(self.data, data, axis=0)
self._shown = np.append(
self.shown, deepcopy(self._clipboard['shown']), axis=0
)
self._size = np.append(
self.size, deepcopy(self._clipboard['size']), axis=0
)
self._symbol = np.append(
self.symbol, deepcopy(self._clipboard['symbol']), axis=0
)
self._feature_table.append(self._clipboard['features'])
self.text._paste(**self._clipboard['text'])
self._border_width = np.append(
self.border_width,
deepcopy(self._clipboard['border_width']),
axis=0,
)
self._border._paste(
colors=self._clipboard['border_color'],
properties=_features_to_properties(
self._clipboard['features']
),
)
self._face._paste(
colors=self._clipboard['face_color'],
properties=_features_to_properties(
self._clipboard['features']
),
)
self._selected_view = list(
range(npoints, npoints + len(self._clipboard['data']))
)
self._selected_data.update(
set(range(totpoints, totpoints + len(self._clipboard['data'])))
)
self.refresh()
def _copy_data(self) -> None:
"""Copy selected points to clipboard."""
if len(self.selected_data) > 0:
index = list(self.selected_data)
self._clipboard = {
'data': deepcopy(self.data[index]),
'border_color': deepcopy(self.border_color[index]),
'face_color': deepcopy(self.face_color[index]),
'shown': deepcopy(self.shown[index]),
'size': deepcopy(self.size[index]),
'symbol': deepcopy(self.symbol[index]),
'border_width': deepcopy(self.border_width[index]),
'features': deepcopy(self.features.iloc[index]),
'indices': self._data_slice,
'text': self.text._copy(index),
}
else:
self._clipboard = {}
[docs]
def to_mask(
self,
*,
shape: tuple,
data_to_world: Affine | None = None,
isotropic_output: bool = True,
) -> npt.NDArray:
"""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
-------
np.ndarray
The output binary mask array of the given shape containing this layer's points as balls.
"""
if data_to_world is None:
data_to_world = self._data_to_world
mask = np.zeros(shape, dtype=bool)
mask_world_to_data = data_to_world.inverse
points_data_to_mask_data = self._data_to_world.compose(
mask_world_to_data
)
points_in_mask_data_coords = np.atleast_2d(
points_data_to_mask_data(self.data)
)
# Calculating the radii of the output points in the mask is complex.
radii = self.size / 2
# Scale each radius by the geometric mean scale of the Points layer to
# keep the balls isotropic when visualized in world coordinates.
# The geometric means are used instead of the arithmetic mean
# to maintain the volume scaling factor of the transforms.
point_data_to_world_scale = gmean(np.abs(self._data_to_world.scale))
mask_world_to_data_scale = (
gmean(np.abs(mask_world_to_data.scale))
if isotropic_output
else np.abs(mask_world_to_data.scale)
)
radii_scale = point_data_to_world_scale * mask_world_to_data_scale
output_data_radii = radii[:, np.newaxis] * np.atleast_2d(radii_scale)
for coords, radii in zip(
points_in_mask_data_coords, output_data_radii, strict=False
):
# Define a minimal set of coordinates where the mask could be present
# by defining an inclusive lower and exclusive upper bound for each dimension.
lower_coords = np.maximum(np.floor(coords - radii), 0).astype(int)
upper_coords = np.minimum(
np.ceil(coords + radii) + 1, shape
).astype(int)
# Generate every possible coordinate within the bounds defined above
# in a grid of size D1 x D2 x ... x Dd x D (e.g. for D=2, this might be 4x5x2).
submask_coords = [
range(lower_coords[i], upper_coords[i])
for i in range(self.ndim)
]
submask_grids = np.stack(
np.meshgrid(*submask_coords, copy=False, indexing='ij'),
axis=-1,
)
# Update the mask coordinates based on the normalized square distance
# using a logical or to maintain any existing positive mask locations.
normalized_square_distances = np.sum(
((submask_grids - coords) / radii) ** 2, axis=-1
)
mask[np.ix_(*submask_coords)] |= normalized_square_distances <= 1
return mask
[docs]
def get_status(
self,
position: tuple | None = None,
*,
view_direction: np.ndarray | None = None,
dims_displayed: list[int] | None = None,
world: bool = False,
) -> dict:
"""Status message information 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
# -------
# source_info : dict
# Dict containing information that can be used in a status update.
#"""
status = super().get_status(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
# if this points layer has properties
properties = self._get_properties(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
if properties:
status['coordinates'] += '; ' + ', '.join(properties)
status['value'] += '; ' + ', '.join(properties)
return status
def _get_tooltip_text(
self,
position,
*,
view_direction: np.ndarray | None = None,
dims_displayed: list[int] | None = None,
world: bool = False,
) -> str:
"""
tooltip 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
String containing a message that can be used as a tooltip.
"""
return '\n'.join(
self._get_properties(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
)
def _get_properties(
self,
position,
*,
view_direction: np.ndarray | None = None,
dims_displayed: list[int] | None = None,
world: bool = False,
) -> list:
if self.features.shape[1] == 0:
return []
value = self.get_value(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
# if the cursor is not outside the image or on the background
if value is None or value > self.data.shape[0]:
return []
return [
f'{k}: {v[value]}'
for k, v in self.features.items()
if k != 'index'
and len(v) > value
and v[value] is not None
and not (isinstance(v[value], float) and np.isnan(v[value]))
]
