import warnings
import numpy as np
from ...utils.colormaps import AVAILABLE_COLORMAPS
from ...utils.events import Event
from ..base import Layer
from ..intensity_mixin import IntensityVisualizationMixin
from ..utils.layer_utils import calc_data_range
# Mixin must come before Layer
[docs]class Surface(IntensityVisualizationMixin, Layer):
"""
Surface layer renders meshes onto the canvas.
Parameters
----------
data : 3-tuple of array
The first element of the tuple is an (N, D) array of vertices of
mesh triangles. The second is an (M, 3) array of int of indices
of the mesh triangles. The third element is the (K0, ..., KL, N)
array of values used to color vertices where the additional L
dimensions are used to color the same mesh with different values.
colormap : str, napari.utils.Colormap, tuple, dict
Colormap to use for luminance images. If a string must be the name
of a supported colormap from vispy or matplotlib. If a tuple the
first value must be a string to assign as a name to a colormap and
the second item must be a Colormap. If a dict the key must be a
string to assign as a name to a colormap and the value must be a
Colormap.
contrast_limits : list (2,)
Color limits to be used for determining the colormap bounds for
luminance images. If not passed is calculated as the min and max of
the image.
gamma : float
Gamma correction for determining colormap linearity. Defaults to 1.
name : str
Name of the layer.
metadata : dict
Layer metadata.
scale : tuple of float
Scale factors for the layer.
translate : tuple of float
Translation values for the layer.
rotate : float, 3-tuple of float, or n-D array.
If a float convert into a 2D rotation matrix using that value as an
angle. If 3-tuple convert into a 3D rotation matrix, using a yaw,
pitch, roll convention. Otherwise assume an nD rotation. Angles are
assumed to be in degrees. They can be converted from radians with
np.degrees if needed.
shear : 1-D array or n-D array
Either a vector of upper triangular values, or an nD shear matrix with
ones along the main diagonal.
affine : n-D array or napari.utils.transforms.Affine
(N+1, N+1) affine transformation matrix in homogeneous coordinates.
The first (N, N) entries correspond to a linear transform and
the final column is a lenght N translation vector and a 1 or a napari
AffineTransform object. If provided then translate, scale, rotate, and
shear values are ignored.
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.
Attributes
----------
data : 3-tuple of array
The first element of the tuple is an (N, D) array of vertices of
mesh triangles. The second is an (M, 3) array of int of indices
of the mesh triangles. The third element is the (K0, ..., KL, N)
array of values used to color vertices where the additional L
dimensions are used to color the same mesh with different values.
vertices : (N, D) array
Vertices of mesh triangles.
faces : (M, 3) array of int
Indices of mesh triangles.
vertex_values : (K0, ..., KL, N) array
Values used to color vertices.
colormap : str, napari.utils.Colormap, tuple, dict
Colormap to use for luminance images. If a string must be the name
of a supported colormap from vispy or matplotlib. If a tuple the
first value must be a string to assign as a name to a colormap and
the second item must be a Colormap. If a dict the key must be a
string to assign as a name to a colormap and the value must be a
Colormap.
contrast_limits : list (2,)
Color limits to be used for determining the colormap bounds for
luminance images. If not passed is calculated as the min and max of
the image.
gamma : float
Gamma correction for determining colormap linearity.
Extended Summary
----------
_data_view : (M, 2) or (M, 3) array
The coordinates of the vertices given the viewed dimensions.
_view_faces : (P, 3) array
The integer indices of the vertices that form the triangles
in the currently viewed slice.
_colorbar : array
Colorbar for current colormap.
"""
_colormaps = AVAILABLE_COLORMAPS
def __init__(
self,
data,
*,
colormap='gray',
contrast_limits=None,
gamma=1,
name=None,
metadata=None,
scale=None,
translate=None,
rotate=None,
shear=None,
affine=None,
opacity=1,
blending='translucent',
visible=True,
):
ndim = data[0].shape[1]
super().__init__(
data,
ndim,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
rotate=rotate,
shear=shear,
affine=affine,
opacity=opacity,
blending=blending,
visible=visible,
)
self.events.add(interpolation=Event, rendering=Event)
# Set contrast_limits and colormaps
self._gamma = gamma
if contrast_limits is None:
self._contrast_limits_range = calc_data_range(data[2])
else:
self._contrast_limits_range = contrast_limits
self._contrast_limits = tuple(self._contrast_limits_range)
self.colormap = colormap
self.contrast_limits = self._contrast_limits
# Data containing vectors in the currently viewed slice
self._data_view = np.zeros((0, self._ndisplay))
self._view_faces = np.zeros((0, 3))
self._view_vertex_values = []
# assign mesh data and establish default behavior
self._vertices = data[0]
self._faces = data[1]
self._vertex_values = data[2]
# Trigger generation of view slice and thumbnail
self._update_dims()
def _calc_data_range(self):
return calc_data_range(self.vertex_values)
@property
def dtype(self):
return self.vertex_values.dtype
@property
def data(self):
return (self.vertices, self.faces, self.vertex_values)
@property
def vertices(self):
return self._vertices
@vertices.setter
def vertices(self, vertices):
"""Array of vertices of mesh triangles."""
self._vertices = vertices
self._update_dims()
self.refresh()
self.events.data(value=self.data)
self._set_editable()
@property
def vertex_values(self) -> np.ndarray:
return self._vertex_values
@vertex_values.setter
def vertex_values(self, vertex_values: np.ndarray):
"""Array of values used to color vertices.."""
self._vertex_values = vertex_values
self.refresh()
self.events.data(value=self.data)
self._set_editable()
@property
def faces(self) -> np.ndarray:
return self._faces
@faces.setter
def faces(self, faces: np.ndarray):
"""Array of indices of mesh triangles.."""
self.faces = faces
self.refresh()
self.events.data(value=self.data)
self._set_editable()
def _get_ndim(self):
"""Determine number of dimensions of the layer."""
return self.vertices.shape[1] + (self.vertex_values.ndim - 1)
@property
def _extent_data(self) -> np.ndarray:
"""Extent of layer in data coordinates.
Returns
-------
extent_data : array, shape (2, D)
"""
if len(self.vertices) == 0:
extrema = np.full((2, self.ndim), np.nan)
else:
maxs = np.max(self.vertices, axis=0)
mins = np.min(self.vertices, axis=0)
# The full dimensionality and shape of the layer is determined by
# the number of additional vertex value dimensions and the
# dimensionality of the vertices themselves
if self.vertex_values.ndim > 1:
mins = [0] * (self.vertex_values.ndim - 1) + list(mins)
maxs = list(self.vertex_values.shape[:-1]) + list(maxs)
extrema = np.vstack([mins, maxs])
return extrema
def _get_state(self):
"""Get dictionary of layer state.
Returns
-------
state : dict
Dictionary of layer state.
"""
state = self._get_base_state()
state.update(
{
'colormap': self.colormap.name,
'contrast_limits': self.contrast_limits,
'gamma': self.gamma,
'data': self.data,
}
)
return state
def _set_view_slice(self):
"""Sets the view given the indices to slice with."""
N, vertex_ndim = self.vertices.shape
values_ndim = self.vertex_values.ndim - 1
# Take vertex_values dimensionality into account if more than one value
# is provided per vertex.
if values_ndim > 0:
# Get indices for axes corresponding to values dimensions
values_indices = self._slice_indices[:-vertex_ndim]
values = self.vertex_values[values_indices]
if values.ndim > 1:
warnings.warn(
"""Assigning multiple values per vertex after slicing is
not allowed. All dimensions corresponding to vertex_values
must be non-displayed dimensions. Data will not be
visible."""
)
self._data_view = np.zeros((0, self._ndisplay))
self._view_faces = np.zeros((0, 3))
self._view_vertex_values = []
return
self._view_vertex_values = values
# Determine which axes of the vertices data are being displayed
# and not displayed, ignoring the additional dimensions
# corresponding to the vertex_values.
indices = np.array(self._slice_indices[-vertex_ndim:])
disp = [
d
for d in np.subtract(self._dims_displayed, values_ndim)
if d >= 0
]
not_disp = [
d
for d in np.subtract(self._dims_not_displayed, values_ndim)
if d >= 0
]
else:
self._view_vertex_values = self.vertex_values
indices = np.array(self._slice_indices)
not_disp = list(self._dims_not_displayed)
disp = list(self._dims_displayed)
self._data_view = self.vertices[:, disp]
if len(self.vertices) == 0:
self._view_faces = np.zeros((0, 3))
elif vertex_ndim > self._ndisplay:
vertices = self.vertices[:, not_disp].astype('int')
triangles = vertices[self.faces]
matches = np.all(triangles == indices[not_disp], axis=(1, 2))
matches = np.where(matches)[0]
if len(matches) == 0:
self._view_faces = np.zeros((0, 3))
else:
self._view_faces = self.faces[matches]
else:
self._view_faces = self.faces
def _update_thumbnail(self):
"""Update thumbnail with current surface."""
pass
def _get_value(self, position):
"""Value of the data at a position in data coordinates.
Parameters
----------
position : tuple
Position in data coordinates.
Returns
-------
value : None
Value of the data at the coord.
"""
return None