import copy
import warnings
from typing import Any, Optional, Union
import numpy as np
import pandas as pd
from napari.layers.base import Layer
from napari.layers.intensity_mixin import IntensityVisualizationMixin
from napari.layers.surface._surface_constants import Shading
from napari.layers.surface._surface_utils import (
calculate_barycentric_coordinates,
)
from napari.layers.surface.normals import SurfaceNormals
from napari.layers.surface.wireframe import SurfaceWireframe
from napari.layers.utils.interactivity_utils import (
nd_line_segment_to_displayed_data_ray,
)
from napari.layers.utils.layer_utils import _FeatureTable, calc_data_range
from napari.utils.colormaps import AVAILABLE_COLORMAPS
from napari.utils.events import Event
from napari.utils.events.event_utils import connect_no_arg
from napari.utils.geometry import find_nearest_triangle_intersection
from napari.utils.translations import trans
# Mixin must come before Layer
[docs]
class Surface(IntensityVisualizationMixin, Layer):
"""
Surface layer renders meshes onto the canvas.
Surfaces may be colored by:
* setting `vertex_values`, which colors the surface with the selected
`colormap` (default is uniform ones)
* setting `vertex_colors`, which replaces/overrides any color from
`vertex_values`
* setting both `texture` and `texcoords`, which blends a the value from
a texture (image) with the underlying color from `vertex_values` or
`vertex_colors`. Blending is achieved by multiplying the texture
color by the underlying color - an underlying value of "white" will
result in the unaltered texture color.
Parameters
----------
data : 2-tuple or 3-tuple of array
The first element of the tuple is an (N, D) array of vertices of
mesh triangles.
The second is an (M, 3) array of int of indices of the mesh triangles.
The optional third element is the (K0, ..., KL, N) array of values
(vertex_values) used to color vertices where the additional L
dimensions are used to color the same mesh with different values. If
not provided, it defaults to ones.
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.
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', and 'additive'}.
cache : bool
Whether slices of out-of-core datasets should be cached upon retrieval.
Currently, this only applies to dask arrays.
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.
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.
feature_defaults : dict[str, Any] or Dataframe-like
The default value of each feature in a table with one row.
features : dict[str, array-like] or Dataframe-like
Features table where each row corresponds to a shape and each column
is a feature.
gamma : float
Gamma correction for determining colormap linearity. Defaults to 1.
metadata : dict
Layer metadata.
name : str
Name of the layer.
normals : None, dict or SurfaceNormals
Whether and how to display the face and vertex normals of the surface mesh.
opacity : float
Opacity of the layer visual, between 0.0 and 1.0.
projection_mode : str
How data outside the viewed dimensions but inside the thick Dims slice will
be projected onto the viewed dimenions.
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
One of a list of preset shading modes that determine the lighting model
using when rendering the surface in 3D.
* ``Shading.NONE``
Corresponds to ``shading='none'``.
* ``Shading.FLAT``
Corresponds to ``shading='flat'``.
* ``Shading.SMOOTH``
Corresponds to ``shading='smooth'``.
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.
texcoords: (N, 2) array
2D coordinates for each vertex, mapping into the texture.
The number of texture coords must match the number of vertices (N).
Coordinates should be in [0.0, 1.0] and are scaled to sample the 2D
texture. Coordinates outside this range will wrap, but this behavior
should be considered an implementation detail: there are no plans to
change it, but it's a feature of the underlying vispy visual.
texture: (I, J) or (I, J, C) array
A 2D texture to be mapped onto the mesh using `texcoords`.
C may be 3 (RGB) or 4 (RGBA) channels for a color texture.
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.
vertex_colors: (N, C) or (K0, ..., KL, N, C) array of color values
Take care that the (optional) L additional dimensions match those of
vertex_values for proper slicing.
C may be 3 (RGB) or 4 (RGBA) channels..
visible : bool
Whether the layer visual is currently being displayed.
wireframe : None, dict or SurfaceWireframe
Whether and how to display the edges of the surface mesh with a wireframe.
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.
axis_labels : tuple of str
Dimension names of the layer data.
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.
features : DataFrame-like
Features table where each row corresponds to a vertex and each column
is a feature.
feature_defaults : DataFrame-like
Stores the default value of each feature in a table with one row.
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.
shading: str
One of a list of preset shading modes that determine the lighting model
using when rendering the surface.
* ``'none'``
* ``'flat'``
* ``'smooth'``
gamma : float
Gamma correction for determining colormap linearity.
wireframe : SurfaceWireframe
Whether and how to display the edges of the surface mesh with a wireframe.
normals : SurfaceNormals
Whether and how to display the face and vertex normals of the surface mesh.
units: tuple of pint.Unit
Units of the layer data in world coordinates.
Notes
-----
_data_view : (M, 2) or (M, 3) array
The coordinates of the vertices given the viewed dimensions.
_view_faces : (P, 3) array
The integer indices of the vertices that form the triangles
in the currently viewed slice.
_colorbar : array
Colorbar for current colormap.
"""
_colormaps = AVAILABLE_COLORMAPS
def __init__(
self,
data,
*,
affine=None,
axis_labels=None,
blending='translucent',
cache=True,
colormap='gray',
contrast_limits=None,
experimental_clipping_planes=None,
feature_defaults=None,
features=None,
gamma=1.0,
metadata=None,
name=None,
normals=None,
opacity=1.0,
projection_mode='none',
rotate=None,
scale=None,
shading='flat',
shear=None,
texcoords=None,
texture=None,
translate=None,
units=None,
vertex_colors=None,
visible=True,
wireframe=None,
) -> None:
ndim = data[0].shape[1]
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(
interpolation=Event,
rendering=Event,
shading=Event,
wireframe=Event,
normals=Event,
texture=Event,
texcoords=Event,
features=Event,
feature_defaults=Event,
)
# assign mesh data and establish default behavior
if len(data) not in (2, 3):
raise ValueError(
trans._(
'Surface data tuple must be 2 or 3, specifying vertices, faces, and optionally vertex values, instead got length {length}.',
deferred=True,
length=len(data),
)
)
self._vertices = data[0]
self._faces = data[1]
if len(data) == 3:
self._vertex_values = data[2]
else:
self._vertex_values = np.ones(len(self._vertices))
self._feature_table = _FeatureTable.from_layer(
features=features,
feature_defaults=feature_defaults,
num_data=len(data[0]),
)
self._texture = texture
self._texcoords = texcoords
self._vertex_colors = vertex_colors
# Set contrast_limits and colormaps
self._gamma = gamma
if contrast_limits is not None:
self._contrast_limits_range = contrast_limits
else:
self._contrast_limits_range = calc_data_range(self._vertex_values)
self._contrast_limits = 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._slice_input.ndisplay))
self._view_faces = np.zeros((0, 3), dtype=int)
self._view_vertex_values: Union[list[Any], np.ndarray] = []
self._view_vertex_colors: Union[list[Any], np.ndarray] = []
# Trigger generation of view slice and thumbnail.
# Use _update_dims instead of refresh here because _get_ndim is
# dependent on vertex_values as well as vertices.
self._update_dims()
# Shading mode
self._shading = shading
# initialize normals and wireframe
self._wireframe = SurfaceWireframe()
self._normals = SurfaceNormals()
connect_no_arg(self.wireframe.events, self.events, 'wireframe')
connect_no_arg(self.normals.events, self.events, 'normals')
self.wireframe = wireframe
self.normals = normals
def _calc_data_range(self, mode='data'):
return calc_data_range(self.vertex_values)
@property
def dtype(self) -> np.dtype:
return self.vertex_values.dtype
@property
def data(self):
return (self.vertices, self.faces, self.vertex_values)
@data.setter
def data(self, data):
if len(data) not in (2, 3):
raise ValueError(
trans._(
'Surface data tuple must be 2 or 3, specifying vertices, faces, and optionally vertex values, instead got length {data_length}.',
deferred=True,
data_length=len(data),
)
)
self._vertices = data[0]
self._faces = data[1]
if len(data) == 3:
self._vertex_values = data[2]
else:
self._vertex_values = np.ones(len(self._vertices))
self._update_dims()
self.events.data(value=self.data)
self._reset_editable()
if self._keep_auto_contrast:
self.reset_contrast_limits()
@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.events.data(value=self.data)
self._reset_editable()
@property
def vertex_values(self) -> np.ndarray:
return self._vertex_values
@vertex_values.setter
def vertex_values(self, vertex_values: np.ndarray) -> None:
"""Array of values (n, 1) used to color vertices with a colormap."""
if vertex_values is None:
vertex_values = np.ones(len(self._vertices))
self._vertex_values = vertex_values
self._update_dims()
self.events.data(value=self.data)
self._reset_editable()
@property
def vertex_colors(self) -> Optional[np.ndarray]:
return self._vertex_colors
@vertex_colors.setter
def vertex_colors(self, vertex_colors: Optional[np.ndarray]) -> None:
"""Values used to directly color vertices.
Note that dims sliders for this layer are based on vertex_values, so
make sure the shape of vertex_colors matches the shape of vertex_values
for proper slicing. That is: vertex_colors should be None, one set
(N, C), or completely match the dimensions of vertex_values
(K0, ..., KL, N, C).
"""
if vertex_colors is not None and not isinstance(
vertex_colors, np.ndarray
):
msg = (
f'texture should be None or ndarray; got {type(vertex_colors)}'
)
raise ValueError(msg)
self._vertex_colors = vertex_colors
self._update_dims()
self.events.data(value=self.data)
self._reset_editable()
@property
def faces(self) -> np.ndarray:
return self._faces
@faces.setter
def faces(self, faces: np.ndarray) -> None:
"""Array of indices of mesh triangles."""
self.faces = faces
self.refresh(extent=False)
self.events.data(value=self.data)
self._reset_editable()
def _get_ndim(self) -> int:
"""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 = [n - 1 for n in self.vertex_values.shape[:-1]] + list(
maxs
)
extrema = np.vstack([mins, maxs])
return extrema
@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: Union[dict[str, np.ndarray], pd.DataFrame],
) -> None:
self._feature_table.set_values(features, num_data=len(self.data[0]))
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: Union[dict[str, Any], pd.DataFrame]
) -> None:
self._feature_table.set_defaults(defaults)
self.events.feature_defaults()
@property
def shading(self) -> str:
return str(self._shading)
@shading.setter
def shading(self, shading: Union[str, Shading]) -> None:
if isinstance(shading, Shading):
self._shading = shading
else:
self._shading = Shading(shading)
self.events.shading(value=self._shading)
@property
def wireframe(self) -> SurfaceWireframe:
return self._wireframe
@wireframe.setter
def wireframe(
self, wireframe: Union[dict, SurfaceWireframe, None]
) -> None:
if wireframe is None:
self._wireframe.reset()
elif isinstance(wireframe, (SurfaceWireframe, dict)):
self._wireframe.update(wireframe)
else:
raise ValueError(
f'wireframe should be None, a dict, or SurfaceWireframe; got {type(wireframe)}'
)
self.events.wireframe(value=self._wireframe)
@property
def normals(self) -> SurfaceNormals:
return self._normals
@normals.setter
def normals(self, normals: Union[dict, SurfaceNormals, None]) -> None:
if normals is None:
self._normals.reset()
elif not isinstance(normals, (SurfaceNormals, dict)):
raise ValueError(
f'normals should be None, a dict, or SurfaceNormals; got {type(normals)}'
)
else:
if isinstance(normals, SurfaceNormals):
normals = {k: dict(v) for k, v in normals.dict().items()}
# ignore modes, they are unmutable cause errors
for norm_type in ('face', 'vertex'):
normals.get(norm_type, {}).pop('mode', None)
self._normals.update(normals)
self.events.normals(value=self._normals)
@property
def texture(self) -> Optional[np.ndarray]:
return self._texture
@texture.setter
def texture(self, texture: np.ndarray) -> None:
if texture is not None and not isinstance(texture, np.ndarray):
msg = f'texture should be None or ndarray; got {type(texture)}'
raise ValueError(msg)
self._texture = texture
self.events.texture(value=self._texture)
@property
def texcoords(self) -> Optional[np.ndarray]:
return self._texcoords
@texcoords.setter
def texcoords(self, texcoords: np.ndarray) -> None:
if texcoords is not None and not isinstance(texcoords, np.ndarray):
msg = f'texcoords should be None or ndarray; got {type(texcoords)}'
raise ValueError(msg)
self._texcoords = texcoords
self.events.texcoords(value=self._texcoords)
@property
def _has_texture(self) -> bool:
"""Whether the layer has sufficient data for texturing"""
return bool(
self.texture is not None
and self.texcoords is not None
and len(self.texcoords)
)
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(
{
'colormap': self.colormap.dict(),
'contrast_limits': self.contrast_limits,
'gamma': self.gamma,
'shading': self.shading,
'data': self.data,
'features': self.features,
'feature_defaults': self.feature_defaults,
'wireframe': self.wireframe.dict(),
'normals': self.normals.dict(),
'texture': self.texture,
'texcoords': self.texcoords,
'vertex_colors': self.vertex_colors,
}
)
return state
def _slice_associated_data(
self,
data: np.ndarray,
vertex_ndim: int,
dims: int = 1,
) -> Union[list[Any], np.ndarray]:
"""Return associated layer data (e.g. vertex values, colors) within
the current slice.
"""
if data is None:
return []
data_ndim = data.ndim - 1
if data_ndim >= dims:
# Get indices for axes corresponding to data dimensions
data_indices: tuple[Union[int, slice], ...] = tuple(
slice(None) if np.isnan(idx) else int(np.round(idx))
for idx in self._data_slice.point[:-vertex_ndim]
)
data = data[data_indices]
if data.ndim > dims:
warnings.warn(
trans._(
'Assigning multiple data per vertex after slicing '
'is not allowed. All dimensions corresponding to '
'vertex data must be non-displayed dimensions. Data '
'may not be visible.',
deferred=True,
),
category=UserWarning,
stacklevel=2,
)
return []
return data
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
self._view_vertex_values = self._slice_associated_data(
self.vertex_values,
vertex_ndim,
)
self._view_vertex_colors = self._slice_associated_data(
self.vertex_colors,
vertex_ndim,
dims=2,
)
if len(self._view_vertex_values) == 0:
self._data_view = np.zeros((0, self._slice_input.ndisplay))
self._view_faces = np.zeros((0, 3), dtype=int)
return
if values_ndim > 0:
indices = np.array(self._data_slice.point[-vertex_ndim:])
disp = [
d
for d in np.subtract(self._slice_input.displayed, values_ndim)
if d >= 0
]
not_disp = [
d
for d in np.subtract(
self._slice_input.not_displayed, values_ndim
)
if d >= 0
]
else:
indices = np.array(self._data_slice.point)
not_disp = list(self._slice_input.not_displayed)
disp = list(self._slice_input.displayed)
self._data_view = self.vertices[:, disp]
if len(self.vertices) == 0:
self._view_faces = np.zeros((0, 3), dtype=int)
elif vertex_ndim > self._slice_input.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), dtype=int)
else:
self._view_faces = self.faces[matches]
else:
self._view_faces = self.faces
if self._keep_auto_contrast:
self.reset_contrast_limits()
def _update_thumbnail(self) -> None:
"""Update thumbnail with current surface."""
def _get_value(self, position) -> None:
"""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
def _get_value_3d(
self,
start_point: Optional[np.ndarray],
end_point: Optional[np.ndarray],
dims_displayed: list[int],
) -> tuple[Union[None, float, int], Optional[int]]:
"""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
The data value along the supplied ray.
vertex : None
Index of vertex if any that is at the coordinates.
"""
if len(dims_displayed) != 3:
# only applies to 3D
return None, None
if (start_point is None) or (end_point is None):
# return None if the ray doesn't intersect the data bounding box
return None, None
start_position, ray_direction = nd_line_segment_to_displayed_data_ray(
start_point=start_point,
end_point=end_point,
dims_displayed=dims_displayed,
)
# get the mesh triangles
mesh_triangles = self._data_view[self._view_faces]
# get the triangles intersection
intersection_index, intersection = find_nearest_triangle_intersection(
ray_position=start_position,
ray_direction=ray_direction,
triangles=mesh_triangles,
)
if intersection_index is None or intersection is None:
return None, None
# add the full nD coords to intersection
intersection_point = start_point.copy()
intersection_point[dims_displayed] = intersection
# calculate the value from the intersection
triangle_vertex_indices = self._view_faces[intersection_index]
triangle_vertices = self._data_view[triangle_vertex_indices]
barycentric_coordinates = calculate_barycentric_coordinates(
intersection, triangle_vertices
)
vertex_values = self._view_vertex_values[triangle_vertex_indices]
intersection_value = (barycentric_coordinates * vertex_values).sum()
return intersection_value, intersection_index
def __copy__(self):
"""Create a copy of this layer.
Returns
-------
layer : napari.layers.Layer
Copy of this layer.
Notes
-----
This method is defined for purpose of asv memory benchmarks.
The copy of data is intentional for properly estimating memory
usage for layer.
If you want a to copy a layer without coping the data please use
`layer.create(*layer.as_layer_data_tuple())`
If you change this method, validate if memory benchmarks are still
working properly.
"""
data, meta, layer_type = self.as_layer_data_tuple()
return self.create(
tuple(copy.copy(x) for x in self.data),
meta=meta,
layer_type=layer_type,
)
