"""Module that provide actors to render."""
from functools import partial
import os
import warnings
import numpy as np
from fury import layout as lyt
from fury.actors.odf import sh_odf
from fury.actors.odf_slicer import OdfSlicerActor
from fury.actors.peak import PeakActor
from fury.actors.tensor import (
double_cone,
main_dir_uncertainty,
tensor_ellipsoid,
)
from fury.colormap import colormap_lookup_table
from fury.decorators import warn_on_args_to_kwargs
from fury.io import load_image
from fury.lib import (
VTK_UNSIGNED_CHAR,
Actor,
ArrowSource,
Assembly,
ButterflySubdivisionFilter,
CellArray,
CellPicker,
CleanPolyData,
ConeSource,
ContourFilter,
CylinderSource,
DiskSource,
FloatArray,
Follower,
ImageActor,
ImageData,
ImageMapToColors,
ImageReslice,
LODActor,
LinearExtrusionFilter,
LookupTable,
LoopSubdivisionFilter,
Matrix4x4,
OutlineFilter,
Points,
PolyData,
PolyDataMapper,
PolyDataMapper2D,
PolyDataNormals,
ScalarBarActor,
SphereSource,
SplineFilter,
TextActor3D,
Texture,
TextureMapToPlane,
TexturedActor2D,
TexturedSphereSource,
Transform,
TransformPolyDataFilter,
TriangleFilter,
TubeFilter,
VectorText,
numpy_support,
)
import fury.primitive as fp
from fury.shaders import (
add_shader_callback,
attribute_to_actor,
compose_shader,
import_fury_shader,
replace_shader_in_actor,
shader_to_actor,
)
from fury.utils import (
apply_affine,
color_check,
fix_winding_order,
get_actor_from_primitive,
lines_to_vtk_polydata,
numpy_to_vtk_colors,
repeat_sources,
rgb_to_vtk,
set_input,
set_polydata_primitives_count,
set_polydata_triangles,
set_polydata_vertices,
shallow_copy,
)
[docs]
@warn_on_args_to_kwargs()
def slicer(
data,
*,
affine=None,
value_range=None,
opacity=1.0,
lookup_colormap=None,
interpolation="linear",
picking_tol=0.025,
):
"""Cut 3D scalar or rgb volumes into 2D images.
Parameters
----------
data : array, shape (X, Y, Z) or (X, Y, Z, 3)
A grayscale or rgb 4D volume as a numpy array. If rgb then values
expected on the range [0, 255].
affine : array, shape (4, 4)
Grid to space (usually RAS 1mm) transformation matrix. Default is None.
If None then the identity matrix is used.
value_range : None or tuple (2,)
If None then the values will be interpolated from (data.min(),
data.max()) to (0, 255). Otherwise from (value_range[0],
value_range[1]) to (0, 255).
opacity : float, optional
Opacity of 0 means completely transparent and 1 completely visible.
lookup_colormap : vtkLookupTable, optional
If None (default) then a grayscale map is created.
interpolation : string, optional
If 'linear' (default) then linear interpolation is used on the final
texture mapping. If 'nearest' then nearest neighbor interpolation is
used on the final texture mapping.
picking_tol : float, optional
The tolerance for the vtkCellPicker, specified as a fraction of
rendering window size.
Returns
-------
image_actor : ImageActor
An object that is capable of displaying different parts of the volume
as slices. The key method of this object is ``display_extent`` where
one can input grid coordinates and display the slice in space (or grid)
coordinates as calculated by the affine parameter.
"""
if value_range is None:
value_range = (data.min(), data.max())
if data.ndim != 3:
if data.ndim == 4:
if data.shape[3] != 3:
raise ValueError("Only RGB 3D arrays are currently supported.")
else:
nb_components = 3
else:
raise ValueError("Only 3D arrays are currently supported.")
else:
nb_components = 1
vol = data
im = ImageData()
i, j, k = vol.shape[:3]
im.SetDimensions(i, j, k)
# for now setting up for 1x1x1 but transformation comes later.
voxsz = (1.0, 1.0, 1.0)
# im.SetOrigin(0,0,0)
im.SetSpacing(voxsz[2], voxsz[0], voxsz[1])
vtk_type = numpy_support.get_vtk_array_type(vol.dtype)
im.AllocateScalars(vtk_type, nb_components)
# im.AllocateScalars(VTK_UNSIGNED_CHAR, nb_components)
# copy data
# what I do below is the same as what is
# commented here but much faster
# for index in ndindex(vol.shape):
# i, j, k = index
# im.SetScalarComponentFromFloat(i, j, k, 0, vol[i, j, k])
vol = np.swapaxes(vol, 0, 2)
vol = np.ascontiguousarray(vol)
if nb_components == 1:
vol = vol.ravel()
else:
vol = np.reshape(vol, [np.prod(vol.shape[:3]), vol.shape[3]])
uchar_array = numpy_support.numpy_to_vtk(vol, deep=0)
im.GetPointData().SetScalars(uchar_array)
if affine is None:
affine = np.eye(4)
# Set the transform (identity if none given)
transform = Transform()
transform_matrix = Matrix4x4()
transform_matrix.DeepCopy(
(
affine[0][0],
affine[0][1],
affine[0][2],
affine[0][3],
affine[1][0],
affine[1][1],
affine[1][2],
affine[1][3],
affine[2][0],
affine[2][1],
affine[2][2],
affine[2][3],
affine[3][0],
affine[3][1],
affine[3][2],
affine[3][3],
)
)
transform.SetMatrix(transform_matrix)
transform.Inverse()
# Set the reslicing
image_resliced = ImageReslice()
set_input(image_resliced, im)
image_resliced.SetResliceTransform(transform)
image_resliced.AutoCropOutputOn()
# Adding this will allow to support anisotropic voxels
# and also gives the opportunity to slice per voxel coordinates
RZS = affine[:3, :3]
zooms = np.sqrt(np.sum(RZS * RZS, axis=0))
image_resliced.SetOutputSpacing(*zooms)
image_resliced.SetInterpolationModeToLinear()
image_resliced.Update()
vtk_resliced_data = image_resliced.GetOutput()
ex1, ex2, ey1, ey2, ez1, ez2 = vtk_resliced_data.GetExtent()
resliced = numpy_support.vtk_to_numpy(vtk_resliced_data.GetPointData().GetScalars())
# swap axes here
if data.ndim == 4:
if data.shape[-1] == 3:
resliced = resliced.reshape(ez2 + 1, ey2 + 1, ex2 + 1, 3)
if data.ndim == 3:
resliced = resliced.reshape(ez2 + 1, ey2 + 1, ex2 + 1)
class ImActor(ImageActor):
def __init__(self):
self.picker = CellPicker()
self.output = None
self.shape = None
self.outline_actor = None
def input_connection(self, output):
# outline only
outline = OutlineFilter()
outline.SetInputData(vtk_resliced_data)
outline_mapper = PolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
self.outline_actor = Actor()
self.outline_actor.SetMapper(outline_mapper)
self.outline_actor.GetProperty().SetColor(1, 0.5, 0)
self.outline_actor.GetProperty().SetLineWidth(5)
self.outline_actor.GetProperty().SetRenderLinesAsTubes(True)
# crucial
self.GetMapper().SetInputConnection(output.GetOutputPort())
self.output = output
self.shape = (ex2 + 1, ey2 + 1, ez2 + 1)
def display_extent(self, x1, x2, y1, y2, z1, z2):
self.SetDisplayExtent(x1, x2, y1, y2, z1, z2)
self.Update()
# bounds = self.GetBounds()
# xmin, xmax, ymin, ymax, zmin, zmax = bounds
# line = np.array([[xmin, ymin, zmin]])
# self.outline_actor = actor.line()
@warn_on_args_to_kwargs()
def display(self, *, x=None, y=None, z=None):
if x is None and y is None and z is None:
self.display_extent(ex1, ex2, ey1, ey2, ez2 // 2, ez2 // 2)
if x is not None:
self.display_extent(x, x, ey1, ey2, ez1, ez2)
if y is not None:
self.display_extent(ex1, ex2, y, y, ez1, ez2)
if z is not None:
self.display_extent(ex1, ex2, ey1, ey2, z, z)
def resliced_array(self):
"""Return resliced array as numpy array."""
resliced = numpy_support.vtk_to_numpy(
vtk_resliced_data.GetPointData().GetScalars()
)
# swap axes here
if data.ndim == 4:
if data.shape[-1] == 3:
resliced = resliced.reshape(ez2 + 1, ey2 + 1, ex2 + 1, 3)
if data.ndim == 3:
resliced = resliced.reshape(ez2 + 1, ey2 + 1, ex2 + 1)
resliced = np.swapaxes(resliced, 0, 2)
resliced = np.ascontiguousarray(resliced)
return resliced
def opacity(self, value):
self.GetProperty().SetOpacity(value)
def tolerance(self, value):
self.picker.SetTolerance(value)
def copy(self):
im_actor = ImActor()
im_actor.input_connection(self.output)
im_actor.SetDisplayExtent(*self.GetDisplayExtent())
im_actor.opacity(self.GetOpacity())
im_actor.tolerance(self.picker.GetTolerance())
if interpolation == "nearest":
im_actor.SetInterpolate(False)
else:
im_actor.SetInterpolate(True)
im_actor.GetMapper().BorderOn()
return im_actor
def shallow_copy(self):
# TODO rename copy to shallow_copy
self.copy()
r1, r2 = value_range
image_actor = ImActor()
if nb_components == 1:
lut = lookup_colormap
if lookup_colormap is None:
# Create a black/white lookup table.
lut = colormap_lookup_table(
scale_range=(r1, r2),
hue_range=(0, 0),
saturation_range=(0, 0),
value_range=(0, 1),
)
plane_colors = ImageMapToColors()
plane_colors.SetOutputFormatToRGB()
plane_colors.SetLookupTable(lut)
plane_colors.SetInputConnection(image_resliced.GetOutputPort())
plane_colors.Update()
image_actor.input_connection(plane_colors)
else:
image_actor.input_connection(image_resliced)
image_actor.display()
image_actor.opacity(opacity)
image_actor.tolerance(picking_tol)
if interpolation == "nearest":
image_actor.SetInterpolate(False)
else:
image_actor.SetInterpolate(True)
image_actor.GetMapper().BorderOn()
return image_actor
[docs]
@warn_on_args_to_kwargs()
def surface(vertices, *, faces=None, colors=None, smooth=None, subdivision=3):
"""Generate a surface actor from an array of vertices.
The color and smoothness of the surface can be customized by specifying
the type of subdivision algorithm and the number of subdivisions.
Parameters
----------
vertices : array, shape (X, Y, Z)
The point cloud defining the surface.
faces : array
An array of precomputed triangulation for the point cloud.
It is an optional parameter, it is computed locally if None.
colors : (N, 3) array
Specifies the colors associated with each vertex in the
vertices array. Range should be 0 to 1.
Optional parameter, if not passed, all vertices
are colored white.
smooth : string - "loop" or "butterfly"
Defines the type of subdivision to be used
for smoothing the surface.
subdivision : integer, default = 3
Defines the number of subdivisions to do for
each triangulation of the point cloud.
The higher the value, smoother the surface
but at the cost of higher computation.
Returns
-------
surface_actor : Actor
An Actor visualizing the final surface
computed from the point cloud is returned.
"""
from scipy.spatial import Delaunay
points = Points()
points.SetData(numpy_support.numpy_to_vtk(vertices))
triangle_poly_data = PolyData()
triangle_poly_data.SetPoints(points)
if colors is not None:
triangle_poly_data.GetPointData().SetScalars(numpy_to_vtk_colors(255 * colors))
if faces is None:
tri = Delaunay(vertices[:, [0, 1]])
faces = np.array(tri.simplices, dtype="i8")
set_polydata_triangles(triangle_poly_data, faces)
clean_poly_data = CleanPolyData()
clean_poly_data.SetInputData(triangle_poly_data)
mapper = PolyDataMapper()
surface_actor = Actor()
if smooth is None:
mapper.SetInputData(triangle_poly_data)
surface_actor.SetMapper(mapper)
elif smooth == "loop":
smooth_loop = LoopSubdivisionFilter()
smooth_loop.SetNumberOfSubdivisions(subdivision)
smooth_loop.SetInputConnection(clean_poly_data.GetOutputPort())
mapper.SetInputConnection(smooth_loop.GetOutputPort())
surface_actor.SetMapper(mapper)
elif smooth == "butterfly":
smooth_butterfly = ButterflySubdivisionFilter()
smooth_butterfly.SetNumberOfSubdivisions(subdivision)
smooth_butterfly.SetInputConnection(clean_poly_data.GetOutputPort())
mapper.SetInputConnection(smooth_butterfly.GetOutputPort())
surface_actor.SetMapper(mapper)
return surface_actor
[docs]
@warn_on_args_to_kwargs()
def contour_from_roi(data, *, affine=None, color=None, opacity=1):
"""Generate surface actor from a binary ROI.
The color and opacity of the surface can be customized.
Parameters
----------
data : array, shape (X, Y, Z)
An ROI file that will be binarized and displayed.
affine : array, shape (4, 4)
Grid to space (usually RAS 1mm) transformation matrix. Default is None.
If None then the identity matrix is used.
color : (1, 3) ndarray
RGB values in [0,1].
opacity : float
Opacity of surface between 0 and 1.
Returns
-------
contour_assembly : vtkAssembly
ROI surface object displayed in space
coordinates as calculated by the affine parameter.
"""
if data.ndim != 3:
raise ValueError("Only 3D arrays are currently supported.")
if color is None:
color = np.array([1, 0, 0])
nb_components = 1
data = (data > 0) * 1
vol = np.interp(data, xp=[data.min(), data.max()], fp=[0, 255])
vol = vol.astype("uint8")
im = ImageData()
di, dj, dk = vol.shape[:3]
im.SetDimensions(di, dj, dk)
voxsz = (1.0, 1.0, 1.0)
# im.SetOrigin(0,0,0)
im.SetSpacing(voxsz[2], voxsz[0], voxsz[1])
im.AllocateScalars(VTK_UNSIGNED_CHAR, nb_components)
# copy data
vol = np.swapaxes(vol, 0, 2)
vol = np.ascontiguousarray(vol)
vol = vol.ravel()
uchar_array = numpy_support.numpy_to_vtk(vol, deep=0)
im.GetPointData().SetScalars(uchar_array)
if affine is None:
affine = np.eye(4)
# Set the transform (identity if none given)
transform = Transform()
transform_matrix = Matrix4x4()
transform_matrix.DeepCopy(
(
affine[0][0],
affine[0][1],
affine[0][2],
affine[0][3],
affine[1][0],
affine[1][1],
affine[1][2],
affine[1][3],
affine[2][0],
affine[2][1],
affine[2][2],
affine[2][3],
affine[3][0],
affine[3][1],
affine[3][2],
affine[3][3],
)
)
transform.SetMatrix(transform_matrix)
transform.Inverse()
# Set the reslicing
image_resliced = ImageReslice()
set_input(image_resliced, im)
image_resliced.SetResliceTransform(transform)
image_resliced.AutoCropOutputOn()
# Adding this will allow to support anisotropic voxels
# and also gives the opportunity to slice per voxel coordinates
rzs = affine[:3, :3]
zooms = np.sqrt(np.sum(rzs * rzs, axis=0))
image_resliced.SetOutputSpacing(*zooms)
image_resliced.SetInterpolationModeToLinear()
image_resliced.Update()
skin_extractor = ContourFilter()
skin_extractor.SetInputData(image_resliced.GetOutput())
skin_extractor.SetValue(0, 1)
skin_normals = PolyDataNormals()
skin_normals.SetInputConnection(skin_extractor.GetOutputPort())
skin_normals.SetFeatureAngle(60.0)
skin_mapper = PolyDataMapper()
skin_mapper.SetInputConnection(skin_normals.GetOutputPort())
skin_mapper.ScalarVisibilityOff()
skin_actor = Actor()
skin_actor.SetMapper(skin_mapper)
skin_actor.GetProperty().SetColor(color[0], color[1], color[2])
skin_actor.GetProperty().SetOpacity(opacity)
return skin_actor
[docs]
@warn_on_args_to_kwargs()
def contour_from_label(data, *, affine=None, color=None):
"""Generate surface actor from a labeled Array.
The color and opacity of individual surfaces can be customized.
Parameters
----------
data : array, shape (X, Y, Z)
A labeled array file that will be binarized and displayed.
affine : array, shape (4, 4)
Grid to space (usually RAS 1mm) transformation matrix. Default is None.
If None then the identity matrix is used.
color : (N, 3) or (N, 4) ndarray
RGB/RGBA values in [0,1]. Default is None.
If None then random colors are used.
Alpha channel is set to 1 by default.
Returns
-------
contour_assembly : vtkAssembly
Array surface object displayed in space
coordinates as calculated by the affine parameter
in the order of their roi ids.
"""
unique_roi_id = np.delete(np.unique(data), 0)
nb_surfaces = len(unique_roi_id)
unique_roi_surfaces = Assembly()
if color is None:
color = np.random.rand(nb_surfaces, 3)
elif color.shape != (nb_surfaces, 3) and color.shape != (nb_surfaces, 4):
raise ValueError("Incorrect color array shape")
if color.shape == (nb_surfaces, 4):
opacity = color[:, -1]
color = color[:, :-1]
else:
opacity = np.ones((nb_surfaces, 1)).astype(float)
for i, roi_id in enumerate(unique_roi_id):
roi_data = np.isin(data, roi_id).astype(int)
roi_surface = contour_from_roi(
roi_data, affine=affine, color=color[i], opacity=opacity[i]
)
unique_roi_surfaces.AddPart(roi_surface)
return unique_roi_surfaces
[docs]
@warn_on_args_to_kwargs()
def streamtube(
lines,
*,
colors=None,
opacity=1,
linewidth=0.1,
tube_sides=9,
lod=True,
lod_points=10**4,
lod_points_size=3,
spline_subdiv=None,
lookup_colormap=None,
replace_strips=False,
):
"""Use streamtubes to visualize polylines.
Parameters
----------
lines : list
list of N curves represented as 2D ndarrays
colors : array (N, 3), list of arrays, tuple (3,), array (K,)
If None or False, a standard orientation colormap is used for every
line.
If one tuple of color is used. Then all streamlines will have the same
colour.
If an array (N, 3) is given, where N is equal to the number of lines.
Then every line is coloured with a different RGB color.
If a list of RGB arrays is given then every point of every line takes
a different color.
If an array (K, 3) is given, where K is the number of points of all
lines then every point is colored with a different RGB color.
If an array (K,) is given, where K is the number of points of all
lines then these are considered as the values to be used by the
colormap.
If an array (L,) is given, where L is the number of streamlines then
these are considered as the values to be used by the colormap per
streamline.
If an array (X, Y, Z) or (X, Y, Z, 3) is given then the values for the
colormap are interpolated automatically using trilinear interpolation.
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque). Default is 1.
linewidth : float, optional
Default is 0.01.
tube_sides : int, optional
Default is 9.
lod : bool, optional
Use LODActor(level of detail) rather than Actor. Default is True.
Level of detail actors do not render the full geometry when the
frame rate is low.
lod_points : int, optional
Number of points to be used when LOD is in effect. Default is 10000.
lod_points_size : int, optional
Size of points when lod is in effect. Default is 3.
spline_subdiv : int, optional
Number of splines subdivision to smooth streamtubes. Default is None.
lookup_colormap : vtkLookupTable, optional
Add a default lookup table to the colormap. Default is None which calls
:func:`fury.actor.colormap_lookup_table`.
replace_strips : bool, optional
If True it changes streamtube representation from triangle strips to
triangles. Useful with SelectionManager or PickingManager.
Default False.
Examples
--------
>>> import numpy as np
>>> from fury import actor, window
>>> scene = window.Scene()
>>> lines = [np.random.rand(10, 3), np.random.rand(20, 3)]
>>> colors = np.random.rand(2, 3)
>>> c = actor.streamtube(lines, colors=colors)
>>> scene.add(c)
>>> #window.show(scene)
Notes
-----
Streamtubes can be heavy on GPU when loading many streamlines and
therefore, you may experience slow rendering time depending on system GPU.
A solution to this problem is to reduce the number of points in each
streamline. In Dipy we provide an algorithm that will reduce the number of
points on the straighter parts of the streamline but keep more points on
the curvier parts. This can be used in the following way::
from dipy.tracking.distances import approx_polygon_track
lines = [approx_polygon_track(line, 0.2) for line in lines]
Alternatively we suggest using the ``line`` actor which is much more
efficient.
See Also
--------
:func:`fury.actor.line`
"""
# Poly data with lines and colors
poly_data, color_is_scalar = lines_to_vtk_polydata(lines, colors=colors)
next_input = poly_data
# set primitives count
prim_count = len(lines)
set_polydata_primitives_count(poly_data, prim_count)
# Set Normals
poly_normals = set_input(PolyDataNormals(), next_input)
poly_normals.ComputeCellNormalsOn()
poly_normals.ComputePointNormalsOn()
poly_normals.ConsistencyOn()
poly_normals.AutoOrientNormalsOn()
poly_normals.Update()
next_input = poly_normals.GetOutputPort()
# Spline interpolation
if (spline_subdiv is not None) and (spline_subdiv > 0):
spline_filter = set_input(SplineFilter(), next_input)
spline_filter.SetSubdivideToSpecified()
spline_filter.SetNumberOfSubdivisions(spline_subdiv)
spline_filter.Update()
next_input = spline_filter.GetOutputPort()
# Add thickness to the resulting lines
tube_filter = set_input(TubeFilter(), next_input)
tube_filter.SetNumberOfSides(tube_sides)
tube_filter.SetRadius(linewidth)
# TODO using the line above we will be able to visualize
# streamtubes of varying radius
# tube_filter.SetVaryRadiusToVaryRadiusByScalar()
tube_filter.CappingOn()
tube_filter.Update()
next_input = tube_filter.GetOutputPort()
# Poly mapper
poly_mapper = set_input(PolyDataMapper(), next_input)
if replace_strips:
triangle_filter = set_input(TriangleFilter(), next_input)
poly_mapper = set_input(PolyDataMapper(), triangle_filter.GetOutputPort())
else:
poly_mapper = set_input(PolyDataMapper(), next_input)
poly_mapper.ScalarVisibilityOn()
poly_mapper.SetScalarModeToUsePointFieldData()
poly_mapper.SelectColorArray("colors")
poly_mapper.Update()
# Color Scale with a lookup table
if color_is_scalar:
if lookup_colormap is None:
lookup_colormap = colormap_lookup_table()
poly_mapper.SetLookupTable(lookup_colormap)
poly_mapper.UseLookupTableScalarRangeOn()
poly_mapper.Update()
# Set Actor
if lod:
actor = LODActor()
actor.SetNumberOfCloudPoints(lod_points)
actor.GetProperty().SetPointSize(lod_points_size)
else:
actor = Actor()
actor.SetMapper(poly_mapper)
actor.GetProperty().SetInterpolationToPhong()
actor.GetProperty().BackfaceCullingOn()
actor.GetProperty().SetOpacity(opacity)
return actor
[docs]
@warn_on_args_to_kwargs()
def line(
lines,
*,
colors=None,
opacity=1,
linewidth=1,
spline_subdiv=None,
lod=True,
lod_points=10**4,
lod_points_size=3,
lookup_colormap=None,
depth_cue=False,
fake_tube=False,
):
"""Create an actor for one or more lines.
Parameters
----------
lines : list of arrays
colors : array (N, 3), list of arrays, tuple (3,), array (K,)
If None or False, a standard orientation colormap is used for every
line.
If one tuple of color is used. Then all streamlines will have the same
colour.
If an array (N, 3) is given, where N is equal to the number of lines.
Then every line is coloured with a different RGB color.
If a list of RGB arrays is given then every point of every line takes
a different color.
If an array (K, 3) is given, where K is the number of points of all
lines then every point is colored with a different RGB color.
If an array (K,) is given, where K is the number of points of all
lines then these are considered as the values to be used by the
colormap.
If an array (L,) is given, where L is the number of streamlines then
these are considered as the values to be used by the colormap per
streamline.
If an array (X, Y, Z) or (X, Y, Z, 3) is given then the values for the
colormap are interpolated automatically using trilinear interpolation.
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque). Default is 1.
linewidth : float, optional
Line thickness. Default is 1.
spline_subdiv : int, optional
Number of splines subdivision to smooth streamtubes. Default is None
which means no subdivision.
lod : bool, optional
Use LODActor(level of detail) rather than Actor. Default is True.
Level of detail actors do not render the full geometry when the
frame rate is low.
lod_points : int, optional
Number of points to be used when LOD is in effect. Default is 10000.
lod_points_size : int
Size of points when lod is in effect. Default is 3.
lookup_colormap : vtkLookupTable, optional
Add a default lookup table to the colormap. Default is None which calls
:func:`fury.actor.colormap_lookup_table`.
depth_cue : boolean, optional
Add a size depth cue so that lines shrink with distance to the camera.
Works best with linewidth <= 1.
fake_tube: boolean, optional
Add shading to lines to approximate the look of tubes.
Returns
-------
v : Actor or LODActor object
Line.
Examples
--------
>>> from fury import actor, window
>>> scene = window.Scene()
>>> lines = [np.random.rand(10, 3), np.random.rand(20, 3)]
>>> colors = np.random.rand(2, 3)
>>> c = actor.line(lines, colors=colors)
>>> scene.add(c)
>>> #window.show(scene)
"""
# Poly data with lines and colors
poly_data, color_is_scalar = lines_to_vtk_polydata(lines, colors=colors)
next_input = poly_data
# set primitives count
prim_count = len(lines)
set_polydata_primitives_count(poly_data, prim_count)
# use spline interpolation
if (spline_subdiv is not None) and (spline_subdiv > 0):
spline_filter = set_input(SplineFilter(), next_input)
spline_filter.SetSubdivideToSpecified()
spline_filter.SetNumberOfSubdivisions(spline_subdiv)
spline_filter.Update()
next_input = spline_filter.GetOutputPort()
poly_mapper = set_input(PolyDataMapper(), next_input)
poly_mapper.ScalarVisibilityOn()
poly_mapper.SetScalarModeToUsePointFieldData()
poly_mapper.SelectColorArray("colors")
poly_mapper.Update()
# Color Scale with a lookup table
if color_is_scalar:
if lookup_colormap is None:
lookup_colormap = colormap_lookup_table()
poly_mapper.SetLookupTable(lookup_colormap)
poly_mapper.UseLookupTableScalarRangeOn()
poly_mapper.Update()
# Set Actor
if lod:
actor = LODActor()
actor.SetNumberOfCloudPoints(lod_points)
actor.GetProperty().SetPointSize(lod_points_size)
else:
actor = Actor()
actor.SetMapper(poly_mapper)
actor.GetProperty().SetLineWidth(linewidth)
actor.GetProperty().SetOpacity(opacity)
if depth_cue:
@warn_on_args_to_kwargs()
def callback(_caller, _event, *, calldata=None):
program = calldata
if program is not None:
program.SetUniformf("linewidth", linewidth)
replace_shader_in_actor(actor, "geometry", import_fury_shader("line.geom"))
add_shader_callback(actor, callback)
if fake_tube:
actor.GetProperty().SetRenderLinesAsTubes(True)
return actor
[docs]
@warn_on_args_to_kwargs()
def scalar_bar(*, lookup_table=None, title=" "):
"""Default scalar bar actor for a given colormap (colorbar).
Parameters
----------
lookup_table : vtkLookupTable or None
If None then ``colormap_lookup_table`` is called with default options.
title : str
Returns
-------
scalar_bar : vtkScalarBarActor
See Also
--------
:func:`fury.actor.colormap_lookup_table`
"""
lookup_table_copy = LookupTable()
if lookup_table is None:
lookup_table = colormap_lookup_table()
# Deepcopy the lookup_table because sometimes vtkPolyDataMapper deletes it
lookup_table_copy.DeepCopy(lookup_table)
scalar_bar = ScalarBarActor()
scalar_bar.SetTitle(title)
scalar_bar.SetLookupTable(lookup_table_copy)
scalar_bar.SetNumberOfLabels(6)
return scalar_bar
[docs]
@warn_on_args_to_kwargs()
def axes(
*,
scale=(1, 1, 1),
colorx=(1, 0, 0),
colory=(0, 1, 0),
colorz=(0, 0, 1),
opacity=1,
):
"""Create an actor with the coordinate's system axes where
red = x, green = y, blue = z.
Parameters
----------
scale : tuple (3,)
Axes size e.g. (100, 100, 100). Default is (1, 1, 1).
colorx : tuple (3,)
x-axis color. Default red (1, 0, 0).
colory : tuple (3,)
y-axis color. Default green (0, 1, 0).
colorz : tuple (3,)
z-axis color. Default blue (0, 0, 1).
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque). Default is 1.
Returns
-------
arrow_actor: Actor
"""
centers = np.zeros((3, 3))
dirs = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
colors = np.array([colorx + (opacity,), colory + (opacity,), colorz + (opacity,)])
scales = np.asarray(scale)
arrow_actor = arrow(centers, dirs, colors, scales=scales, repeat_primitive=False)
return arrow_actor
[docs]
@warn_on_args_to_kwargs()
def odf_slicer(
odfs,
*,
affine=None,
mask=None,
sphere=None,
scale=0.5,
norm=True,
radial_scale=True,
opacity=1.0,
colormap=None,
global_cm=False,
B_matrix=None,
):
"""Create an actor for rendering a grid of ODFs given an array of
spherical function (SF) or spherical harmonics (SH) coefficients.
Parameters
----------
odfs : ndarray
4D ODFs array in SF or SH coefficients. If SH coefficients,
`B_matrix` must be supplied.
affine : array
4x4 transformation array from native coordinates to world coordinates.
mask : ndarray
3D mask to apply to ODF field.
sphere : dipy Sphere
The sphere used for SH to SF projection. If None, a default sphere
of 100 vertices will be used.
scale : float
Multiplicative factor to apply to ODF amplitudes.
norm : bool
Normalize SF amplitudes so that the maximum
ODF amplitude per voxel along a direction is 1.
radial_scale : bool
Scale sphere points by ODF values.
opacity : float
Takes values from 0 (fully transparent) to 1 (opaque).
colormap : None or str or tuple
The name of the colormap to use. Matplotlib colormaps are supported
(e.g., 'inferno'). A plain color can be supplied as a RGB tuple in
range [0, 255]. If None then a RGB colormap is used.
global_cm : bool
If True the colormap will be applied in all ODFs. If False
it will be applied individually at each voxel.
B_matrix : ndarray (n_coeffs, n_vertices)
Optional SH to SF matrix for projecting `odfs` given in SH
coefficients on the `sphere`. If None, then the input is assumed
to be expressed in SF coefficients.
Returns
-------
actor : OdfSlicerActor
Actor representing the ODF field.
"""
# first we check if the input array is 4D
n_dims = len(odfs.shape)
if n_dims != 4:
raise ValueError(
"Invalid number of dimensions for odfs. Expected 4 "
"dimensions, got {0} dimensions.".format(n_dims)
)
# we generate indices for all nonzero voxels
valid_odf_mask = np.abs(odfs).max(axis=-1) > 0.0
if mask is not None:
valid_odf_mask = np.logical_and(valid_odf_mask, mask)
indices = np.nonzero(valid_odf_mask)
shape = odfs.shape[:-1]
if sphere is None:
# Use a default sphere with 100 vertices
vertices, faces = fp.prim_sphere(name="repulsion100")
else:
vertices = sphere.vertices
faces = fix_winding_order(vertices, sphere.faces, clockwise=True)
if B_matrix is None:
if len(vertices) != odfs.shape[-1]:
raise ValueError(
"Invalid number of SF coefficients. " "Expected {0}, got {1}.".format(
len(vertices), odfs.shape[-1]
)
)
else:
if len(vertices) != B_matrix.shape[1]:
raise ValueError(
"Invalid number of SH coefficients. " "Expected {0}, got {1}.".format(
len(vertices), B_matrix.shape[1]
)
)
# create and return an instance of OdfSlicerActor
return OdfSlicerActor(
odfs[indices],
vertices,
faces,
indices,
scale,
norm,
radial_scale,
shape,
global_cm,
colormap,
opacity,
affine=affine,
B=B_matrix,
)
def _makeNd(array, ndim):
"""Pad as many 1s at the beginning of array's shape as are need to give
array ndim dimensions.
"""
new_shape = (1,) * (ndim - array.ndim) + array.shape
return array.reshape(new_shape)
@warn_on_args_to_kwargs()
def _roll_evals(evals, *, axis=-1):
"""Check evals shape.
Helper function to check that the evals provided to functions calculating
tensor statistics have the right shape.
Parameters
----------
evals : array-like
Eigenvalues of a diffusion tensor. shape should be (...,3).
axis : int
The axis of the array which contains the 3 eigenvals. Default: -1
Returns
-------
evals : array-like
Eigenvalues of a diffusion tensor, rolled so that the 3 eigenvals are
the last axis.
"""
if evals.shape[-1] != 3:
msg = "Expecting 3 eigenvalues, got {}".format(evals.shape[-1])
raise ValueError(msg)
evals = np.rollaxis(evals, axis)
return evals
@warn_on_args_to_kwargs()
def _fa(evals, *, axis=-1):
r"""Return Fractional anisotropy (FA) of a diffusion tensor.
Parameters
----------
evals : array-like
Eigenvalues of a diffusion tensor.
axis : int
Axis of `evals` which contains 3 eigenvalues.
Returns
-------
fa : array
Calculated FA. Range is 0 <= FA <= 1.
Notes
-----
FA is calculated using the following equation:
.. math::
FA = \sqrt{\frac{1}{2}\frac{(\lambda_1-\lambda_2)^2+(\lambda_1-
\lambda_3)^2+(\lambda_2-\lambda_3)^2}{\lambda_1^2+
\lambda_2^2+\lambda_3^2}}
"""
evals = _roll_evals(evals, axis=axis)
# Make sure not to get nans
all_zero = (evals == 0).all(axis=0)
ev1, ev2, ev3 = evals
fa = np.sqrt(
0.5
* ((ev1 - ev2) ** 2 + (ev2 - ev3) ** 2 + (ev3 - ev1) ** 2)
/ ((evals * evals).sum(0) + all_zero)
)
return fa
def _color_fa(fa, evecs):
r"""Color fractional anisotropy of diffusion tensor.
Parameters
----------
fa : array-like
Array of the fractional anisotropy (can be 1D, 2D or 3D).
evecs : array-like
eigen vectors from the tensor model.
Returns
-------
rgb : Array with 3 channels for each color as the last dimension.
Colormap of the FA with red for the x value, y for the green
value and z for the blue value.
Notes
-----
It is computed from the clipped FA between 0 and 1 using the following
formula.
.. math::
rgb = abs(max(\vec{e})) \times fa
"""
if (fa.shape != evecs[..., 0, 0].shape) or ((3, 3) != evecs.shape[-2:]):
raise ValueError("Wrong number of dimensions for evecs")
return np.abs(evecs[..., 0]) * np.clip(fa, 0, 1)[..., None]
[docs]
@warn_on_args_to_kwargs()
def tensor_slicer(
evals,
evecs,
*,
affine=None,
mask=None,
sphere=None,
scale=2.2,
norm=True,
opacity=1.0,
scalar_colors=None,
):
"""Slice many tensors as ellipsoids in native or world coordinates.
Parameters
----------
evals : (3,) or (X, 3) or (X, Y, 3) or (X, Y, Z, 3) ndarray
eigenvalues
evecs : (3, 3) or (X, 3, 3) or (X, Y, 3, 3) or (X, Y, Z, 3, 3) ndarray
eigenvectors
affine : array
4x4 transformation array from native coordinates to world coordinates*
mask : ndarray
3D mask
sphere : Sphere
a sphere
scale : float
Distance between spheres.
norm : bool
Normalize `sphere_values`.
opacity : float
Takes values from 0 (fully transparent) to 1 (opaque). Default is 1.
scalar_colors : (3,) or (X, 3) or (X, Y, 3) or (X, Y, Z, 3) ndarray
RGB colors used to show the tensors
Default None, color the ellipsoids using ``color_fa``
Returns
-------
tensor_actor : Actor
Ellipsoid
"""
if not evals.shape == evecs.shape[:-1]:
raise RuntimeError(
"Eigenvalues shape {} is incompatible with eigenvectors' {}."
" Please provide eigenvalue and"
" eigenvector arrays that have compatible dimensions.".format(
evals.shape, evecs.shape
)
)
if mask is None:
mask = np.ones(evals.shape[:3], dtype=bool)
else:
mask = mask.astype(bool)
szx, szy, szz = evals.shape[:3]
class TensorSlicerActor(LODActor):
def __init__(self):
self.mapper = None
def display_extent(self, x1, x2, y1, y2, z1, z2):
tmp_mask = np.zeros(evals.shape[:3], dtype=bool)
tmp_mask[x1 : x2 + 1, y1 : y2 + 1, z1 : z2 + 1] = True
tmp_mask = np.bitwise_and(tmp_mask, mask)
self.mapper = _tensor_slicer_mapper(
evals=evals,
evecs=evecs,
affine=affine,
mask=tmp_mask,
sphere=sphere,
scale=scale,
norm=norm,
scalar_colors=scalar_colors,
)
self.SetMapper(self.mapper)
@warn_on_args_to_kwargs()
def display(self, *, x=None, y=None, z=None):
if x is None and y is None and z is None:
self.display_extent(
0,
szx - 1,
0,
szy - 1,
int(np.floor(szz / 2)),
int(np.floor(szz / 2)),
)
if x is not None:
self.display_extent(x, x, 0, szy - 1, 0, szz - 1)
if y is not None:
self.display_extent(0, szx - 1, y, y, 0, szz - 1)
if z is not None:
self.display_extent(0, szx - 1, 0, szy - 1, z, z)
tensor_actor = TensorSlicerActor()
tensor_actor.display_extent(
0, szx - 1, 0, szy - 1, int(np.floor(szz / 2)), int(np.floor(szz / 2))
)
tensor_actor.GetProperty().SetOpacity(opacity)
return tensor_actor
@warn_on_args_to_kwargs()
def _tensor_slicer_mapper(
evals,
evecs,
*,
affine=None,
mask=None,
sphere=None,
scale=2.2,
norm=True,
scalar_colors=None,
):
"""Return Helper function for slicing tensor fields.
Parameters
----------
evals : (3,) or (X, 3) or (X, Y, 3) or (X, Y, Z, 3) ndarray
eigenvalues.
evecs : (3, 3) or (X, 3, 3) or (X, Y, 3, 3) or (X, Y, Z, 3, 3) ndarray
eigenvectors.
affine : array
4x4 transformation array from native coordinates to world coordinates.
mask : ndarray
3D mask.
sphere : Sphere
a sphere.
scale : float
Distance between spheres.
norm : bool
Normalize `sphere_values`.
scalar_colors : (3,) or (X, 3) or (X, Y, 3) or (X, Y, Z, 3) ndarray
RGB colors used to show the tensors
Default None, color the ellipsoids using ``color_fa``
Returns
-------
mapper : vtkPolyDataMapper
Ellipsoid mapper
"""
mask = np.ones(evals.shape[:3]) if mask is None else mask
ijk = np.ascontiguousarray(np.array(np.nonzero(mask)).T)
if len(ijk) == 0:
return None
if affine is not None:
ijk = np.ascontiguousarray(apply_affine(affine, ijk))
faces = np.asarray(sphere.faces, dtype=int)
vertices = sphere.vertices
if scalar_colors is None:
# from dipy.reconst.dti import color_fa, fractional_anisotropy
cfa = _color_fa(_fa(evals), evecs)
else:
cfa = _makeNd(scalar_colors, 4)
cols = np.zeros((ijk.shape[0],) + sphere.vertices.shape, dtype="f4")
all_xyz = []
all_faces = []
for k, center in enumerate(ijk):
ea = evals[tuple(center.astype(int))]
if norm:
ea /= ea.max()
ea = np.diag(ea.copy())
ev = evecs[tuple(center.astype(int))].copy()
xyz = np.dot(ev, np.dot(ea, vertices.T))
xyz = xyz.T
all_xyz.append(scale * xyz + center)
all_faces.append(faces + k * xyz.shape[0])
cols[k, ...] = np.interp(
cfa[tuple(center.astype(int))], [0, 1], [0, 255]
).astype("ubyte")
all_xyz = np.ascontiguousarray(np.concatenate(all_xyz))
all_xyz_vtk = numpy_support.numpy_to_vtk(all_xyz, deep=True)
points = Points()
points.SetData(all_xyz_vtk)
all_faces = np.concatenate(all_faces)
cols = np.ascontiguousarray(
np.reshape(cols, (cols.shape[0] * cols.shape[1], cols.shape[2])), dtype="f4"
)
vtk_colors = numpy_support.numpy_to_vtk(
cols, deep=True, array_type=VTK_UNSIGNED_CHAR
)
vtk_colors.SetName("colors")
polydata = PolyData()
polydata.SetPoints(points)
set_polydata_triangles(polydata, all_faces)
polydata.GetPointData().SetScalars(vtk_colors)
mapper = PolyDataMapper()
mapper.SetInputData(polydata)
return mapper
[docs]
@warn_on_args_to_kwargs()
def peak_slicer(
peaks_dirs,
*,
peaks_values=None,
mask=None,
affine=None,
colors=(1, 0, 0),
opacity=1.0,
linewidth=1,
lod=False,
lod_points=10**4,
lod_points_size=3,
symmetric=True,
):
"""Visualize peak directions as given from ``peaks_from_model``.
Parameters
----------
peaks_dirs : ndarray
Peak directions. The shape of the array can be (M, 3) or (X, M, 3) or
(X, Y, M, 3) or (X, Y, Z, M, 3).
peaks_values : ndarray
Peak values. The shape of the array can be (M, ) or (X, M) or
(X, Y, M) or (X, Y, Z, M).
affine : array
4x4 transformation array from native coordinates to world coordinates.
mask : ndarray
3D mask.
colors : tuple or None
Default red color. If None then every peak gets an orientation color
in similarity to a DEC map.
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque).
linewidth : float, optional
Line thickness. Default is 1.
lod : bool
Use LODActor(level of detail) rather than Actor.
Default is False. Level of detail actors do not render the full
geometry when the frame rate is low.
lod_points : int
Number of points to be used when LOD is in effect. Default is 10000.
lod_points_size : int
Size of points when lod is in effect. Default is 3.
symmetric: bool, optional
If True, peaks are drawn for both peaks_dirs and -peaks_dirs. Else,
peaks are only drawn for directions given by peaks_dirs. Default is
True.
Returns
-------
peak_actor: Actor
See Also
--------
:func:`fury.actor.odf_slice`
"""
peaks_dirs = np.asarray(peaks_dirs)
if peaks_dirs.ndim > 5:
raise ValueError("Wrong shape")
peaks_dirs = _makeNd(peaks_dirs, 5)
if peaks_values is not None:
peaks_values = _makeNd(peaks_values, 4)
grid_shape = np.array(peaks_dirs.shape[:3])
if mask is None:
mask = np.ones(grid_shape).astype(bool)
class PeakSlicerActor(LODActor):
def __init__(self):
self.line = None
def display_extent(self, x1, x2, y1, y2, z1, z2):
tmp_mask = np.zeros(grid_shape, dtype=bool)
tmp_mask[x1 : x2 + 1, y1 : y2 + 1, z1 : z2 + 1] = True
tmp_mask = np.bitwise_and(tmp_mask, mask)
ijk = np.ascontiguousarray(np.array(np.nonzero(tmp_mask)).T)
if len(ijk) == 0:
self.SetMapper(None)
return
if affine is not None:
ijk_trans = np.ascontiguousarray(apply_affine(affine, ijk))
list_dirs = []
for index, center in enumerate(ijk):
# center = tuple(center)
if affine is None:
xyz = center[:, None]
else:
xyz = ijk_trans[index][:, None]
xyz = xyz.T
for i in range(peaks_dirs[tuple(center)].shape[-2]):
if peaks_values is not None:
pv = peaks_values[tuple(center)][i]
else:
pv = 1.0
if symmetric:
dirs = np.vstack(
(
-peaks_dirs[tuple(center)][i] * pv + xyz,
peaks_dirs[tuple(center)][i] * pv + xyz,
)
)
else:
dirs = np.vstack((xyz, peaks_dirs[tuple(center)][i] * pv + xyz))
list_dirs.append(dirs)
self.line = line(
list_dirs,
colors=colors,
opacity=opacity,
linewidth=linewidth,
lod=lod,
lod_points=lod_points,
lod_points_size=lod_points_size,
)
self.SetProperty(self.line.GetProperty())
self.SetMapper(self.line.GetMapper())
@warn_on_args_to_kwargs()
def display(self, *, x=None, y=None, z=None):
if x is None and y is None and z is None:
self.display_extent(
0,
szx - 1,
0,
szy - 1,
int(np.floor(szz / 2)),
int(np.floor(szz / 2)),
)
if x is not None:
self.display_extent(x, x, 0, szy - 1, 0, szz - 1)
if y is not None:
self.display_extent(0, szx - 1, y, y, 0, szz - 1)
if z is not None:
self.display_extent(0, szx - 1, 0, szy - 1, z, z)
peak_actor = PeakSlicerActor()
szx, szy, szz = grid_shape
peak_actor.display_extent(
0, szx - 1, 0, szy - 1, int(np.floor(szz / 2)), int(np.floor(szz / 2))
)
return peak_actor
[docs]
@warn_on_args_to_kwargs()
def peak(
peaks_dirs,
*,
peaks_values=None,
mask=None,
affine=None,
colors=None,
linewidth=1,
lookup_colormap=None,
symmetric=True,
):
"""Visualize peak directions as given from ``peaks_from_model``.
Parameters
----------
peaks_dirs : ndarray
Peak directions. The shape of the array should be (X, Y, Z, D, 3).
peaks_values : ndarray, optional
Peak values. The shape of the array should be (X, Y, Z, D).
affine : array, optional
4x4 transformation array from native coordinates to world coordinates.
mask : ndarray, optional
3D mask
colors : tuple or None, optional
Default None. If None then every peak gets an orientation color
in similarity to a DEC map.
lookup_colormap : vtkLookupTable, optional
Add a default lookup table to the colormap. Default is None which calls
:func:`fury.actor.colormap_lookup_table`.
linewidth : float, optional
Line thickness. Default is 1.
symmetric : bool, optional
If True, peaks are drawn for both peaks_dirs and -peaks_dirs. Else,
peaks are only drawn for directions given by peaks_dirs. Default is
True.
Returns
-------
peak_actor : PeakActor
Actor or LODActor representing the peaks directions and/or
magnitudes.
Examples
--------
>>> from fury import actor, window
>>> import numpy as np
>>> scene = window.Scene()
>>> peak_dirs = np.random.rand(3, 3, 3, 3, 3)
>>> c = actor.peak(peak_dirs)
>>> scene.add(c)
>>> #window.show(scene)
"""
if peaks_dirs.ndim != 5:
raise ValueError(
"Invalid peak directions. The shape of the structure "
"must be (XxYxZxDx3). Your data has {} dimensions."
"".format(peaks_dirs.ndim)
)
if peaks_dirs.shape[4] != 3:
raise ValueError(
"Invalid peak directions. The shape of the last "
"dimension must be 3. Your data has a last dimension "
"of {}.".format(peaks_dirs.shape[4])
)
dirs_shape = peaks_dirs.shape
if peaks_values is not None:
if peaks_values.ndim != 4:
raise ValueError(
"Invalid peak values. The shape of the structure "
"must be (XxYxZxD). Your data has {} dimensions."
"".format(peaks_values.ndim)
)
vals_shape = peaks_values.shape
if vals_shape != dirs_shape[:4]:
raise ValueError(
"Invalid peak values. The shape of the values "
"must coincide with the shape of the directions."
)
valid_mask = np.abs(peaks_dirs).max(axis=(-2, -1)) > 0
if mask is not None:
if mask.ndim != 3:
warnings.warn(
"Invalid mask. The mask must be a 3D array. The "
"passed mask has {} dimensions. Ignoring passed "
"mask.".format(mask.ndim),
UserWarning,
stacklevel=2,
)
elif mask.shape != dirs_shape[:3]:
warnings.warn(
"Invalid mask. The shape of the mask must coincide "
"with the shape of the directions. Ignoring passed "
"mask.",
UserWarning,
stacklevel=2,
)
else:
valid_mask = np.logical_and(valid_mask, mask)
indices = np.nonzero(valid_mask)
return PeakActor(
peaks_dirs,
indices,
values=peaks_values,
affine=affine,
colors=colors,
lookup_colormap=lookup_colormap,
linewidth=linewidth,
symmetric=symmetric,
)
[docs]
@warn_on_args_to_kwargs()
def dot(points, *, colors=None, opacity=None, dot_size=5):
"""Create one or more 3d points.
Parameters
----------
points : ndarray, (N, 3)
dots positions.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque).
If a value is given, each dot will have the same opacity otherwise
opacity is set to 1 by default, or is defined by Alpha parameter
in colors if given.
dot_size : int
Returns
-------
dot_actor: Actor
See Also
--------
:func:`fury.actor.point`
"""
if points.ndim != 2:
raise ValueError(
"Invalid points. The shape of the structure must be "
"(Nx3). Your data has {} dimensions.".format(points.ndim)
)
if points.shape[1] != 3:
raise ValueError(
"Invalid points. The shape of the last dimension "
"must be 3. Your data has a last dimension of {}.".format(points.shape[1])
)
vtk_vertices = Points()
vtk_faces = CellArray()
# Add points
for i in range(len(points)):
p = points[i]
idd = vtk_vertices.InsertNextPoint(p)
vtk_faces.InsertNextCell(1)
vtk_faces.InsertCellPoint(idd)
color_tuple = color_check(len(points), colors=colors)
color_array, global_opacity = color_tuple
# Create a polydata object
polydata = PolyData()
polydata.SetPoints(vtk_vertices)
polydata.SetVerts(vtk_faces)
polydata.GetPointData().SetScalars(color_array)
# set primitives count
prim_count = len(points)
set_polydata_primitives_count(polydata, prim_count)
# Visualize
mapper = PolyDataMapper()
mapper.SetInputData(polydata)
# Create an actor
poly_actor = Actor()
poly_actor.SetMapper(mapper)
if opacity is not None:
poly_actor.GetProperty().SetOpacity(opacity)
elif global_opacity >= 0:
poly_actor.GetProperty().SetOpacity(global_opacity)
poly_actor.GetProperty().SetPointSize(dot_size)
return poly_actor
[docs]
@warn_on_args_to_kwargs()
def point(points, colors, *, point_radius=0.1, phi=8, theta=8, opacity=1.0):
"""Visualize points as sphere glyphs.
Parameters
----------
points : ndarray, shape (N, 3)
colors : ndarray (N,3) or tuple (3,)
point_radius : float
phi : int
theta : int
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque). Default is 1.
Returns
-------
point_actor: Actor
See Also
--------
:func:`fury.actor.dot`
:func:`fury.actor.sphere`
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> pts = np.random.rand(5, 3)
>>> point_actor = actor.point(pts, window.colors.coral)
>>> scene.add(point_actor)
>>> # window.show(scene)
"""
return sphere(
centers=points,
colors=colors,
radii=point_radius,
phi=phi,
theta=theta,
vertices=None,
faces=None,
opacity=opacity,
)
[docs]
@warn_on_args_to_kwargs()
def sphere(
centers,
colors,
*,
radii=1.0,
phi=16,
theta=16,
vertices=None,
faces=None,
opacity=1,
use_primitive=False,
):
"""Visualize one or many spheres with different colors and radii.
Parameters
----------
centers : ndarray, shape (N, 3)
Spheres positions.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
radii : float or ndarray, shape (N,)
Sphere radius.
phi : int, optional
Set the number of points in the latitude direction.
theta : int, optional
Set the number of points in the longitude direction.
vertices : ndarray, shape (N, 3)
The point cloud defining the sphere.
faces : ndarray, shape (M, 3)
If faces is None then a sphere is created based on theta and phi angles
If not then a sphere is created with the provided vertices and faces.
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque). Default is 1.
use_primitive : boolean, optional
If True, uses primitives to create an actor.
Returns
-------
sphere_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> sphere_actor = actor.sphere(centers, window.colors.coral)
>>> scene.add(sphere_actor)
>>> # window.show(scene)
"""
if not use_primitive:
src = SphereSource() if faces is None else None
if src is not None:
src.SetRadius(1)
src.SetThetaResolution(theta)
src.SetPhiResolution(phi)
sphere_actor = repeat_sources(
centers=centers,
colors=colors,
active_scalars=radii,
source=src,
vertices=vertices,
faces=faces,
)
sphere_actor.GetProperty().SetOpacity(opacity)
return sphere_actor
scales = radii
directions = (1, 0, 0)
if faces is None and vertices is None:
vertices, faces = fp.prim_sphere(phi=phi, theta=theta)
res = fp.repeat_primitive(
vertices,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
sphere_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
sphere_actor.GetProperty().SetOpacity(opacity)
return sphere_actor
[docs]
@warn_on_args_to_kwargs()
def cylinder(
centers,
directions,
colors,
*,
radius=0.05,
heights=1,
capped=False,
resolution=8,
vertices=None,
faces=None,
repeat_primitive=True,
):
"""Visualize one or many cylinder with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Cylinder positions.
directions : ndarray, shape (N, 3)
The orientation vector of the cylinder.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
radius : float
cylinder radius.
heights : ndarray, shape (N)
The height of the cylinder.
capped : bool
Turn on/off whether to cap cylinder with polygons. Default (False).
resolution: int
Number of facets/sectors used to define cylinder.
vertices : ndarray, shape (N, 3)
The point cloud defining the sphere.
faces : ndarray, shape (M, 3)
If faces is None then a sphere is created based on theta
and phi angles.
If not then a sphere is created with the provided vertices and faces.
repeat_primitive: bool
If True, cylinder will be generated with primitives
If False,
repeat_sources will be invoked to use VTK filters for cylinder.
Returns
-------
cylinder_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> dirs = np.random.rand(5, 3)
>>> heights = np.random.rand(5)
>>> actor = actor.cylinder(centers, dirs, (1, 1, 1), heights=heights)
>>> scene.add(actor)
>>> # window.show(scene)
"""
if repeat_primitive:
if resolution < 8:
# Sectors parameter should be greater than 7 in fp.prim_cylinder()
raise ValueError("resolution parameter should be greater than 7")
verts, faces = fp.prim_cylinder(
radius=radius,
sectors=resolution,
capped=capped,
)
res = fp.repeat_primitive(
verts,
faces,
centers=centers,
directions=directions,
colors=colors,
scales=heights,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
cylinder_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
else:
if faces is None:
src = CylinderSource()
src.SetCapping(capped)
src.SetResolution(resolution)
src.SetRadius(radius)
rotate = np.array([[0, 1, 0, 0], [-1, 0, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]])
else:
src = None
rotate = None
cylinder_actor = repeat_sources(
centers=centers,
colors=colors,
directions=directions,
active_scalars=heights,
source=src,
vertices=vertices,
faces=faces,
orientation=rotate,
)
return cylinder_actor
[docs]
@warn_on_args_to_kwargs()
def disk(
centers,
directions,
colors,
*,
rinner=0.3,
router=0.7,
cresolution=6,
rresolution=2,
vertices=None,
faces=None,
):
"""Visualize one or many disks with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Disk positions.
directions : ndarray, shape (N, 3)
The orientation vector of the disk.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
rinner : float
disk inner radius, default: 0.3
router : float
disk outer radius, default: 0.5
cresolution: int, optional
Number of facets used to define perimeter of disk, default: 6
rresolution: int, optional
Number of facets used radially, default: 2
vertices : ndarray, shape (N, 3)
The point cloud defining the disk.
faces : ndarray, shape (M, 3)
If faces is None then a disk is created based on theta and phi angles.
If not then a disk is created with the provided vertices and faces.
Returns
-------
disk_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> import numpy as np
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> dirs = np.random.rand(5, 3)
>>> colors = np.random.rand(5, 4)
>>> actor = actor.disk(centers, dirs, colors,
... rinner=.1, router=.8, cresolution=30)
>>> scene.add(actor)
>>> # window.show(scene)
"""
if faces is None:
src = DiskSource()
src.SetCircumferentialResolution(cresolution)
src.SetRadialResolution(rresolution)
src.SetInnerRadius(rinner)
src.SetOuterRadius(router)
rotate = np.array([[0, 0, -1, 0], [0, 1, 0, 0], [1, 0, 0, 0], [0, 0, 0, 1]])
else:
src = None
rotate = None
disk_actor = repeat_sources(
centers=centers,
colors=colors,
directions=directions,
source=src,
vertices=vertices,
faces=faces,
orientation=rotate,
)
return disk_actor
[docs]
@warn_on_args_to_kwargs()
def square(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
"""Visualize one or many squares with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Square positions.
directions : ndarray, shape (N, 3), optional
The orientation vector of the square.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,), optional
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Square size on each direction (x, y), default(1)
Returns
-------
sq_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> dirs = np.random.rand(5, 3)
>>> sq_actor = actor.square(centers, directions=dirs)
>>> scene.add(sq_actor)
>>> # window.show(scene)
"""
verts, faces = fp.prim_square()
res = fp.repeat_primitive(
verts,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
sq_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
sq_actor.GetProperty().BackfaceCullingOff()
return sq_actor
[docs]
@warn_on_args_to_kwargs()
def rectangle(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=(1, 2, 0)):
"""Visualize one or many rectangles with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Rectangle positions.
directions : ndarray, shape (N, 3), optional
The orientation vector of the rectangle.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,), optional
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Rectangle size on each direction (x, y), default(1)
Returns
-------
rect_actor: Actor
See Also
--------
:func:`fury.actor.square`
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> dirs = np.random.rand(5, 3)
>>> rect_actor = actor.rectangle(centers, directions=dirs)
>>> scene.add(rect_actor)
>>> # window.show(scene)
"""
return square(centers=centers, directions=directions, colors=colors, scales=scales)
[docs]
@warn_on_args_to_kwargs()
def box(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=(1, 2, 3)):
"""Visualize one or many boxes with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Box positions.
directions : ndarray, shape (N, 3), optional
The orientation vector of the box.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,), optional
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Box size on each direction (x, y), default(1)
Returns
-------
box_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> dirs = np.random.rand(5, 3)
>>> box_actor = actor.box(centers, directions=dirs, colors=(1, 1, 1))
>>> scene.add(box_actor)
>>> # window.show(scene)
"""
verts, faces = fp.prim_box()
res = fp.repeat_primitive(
verts,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
box_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return box_actor
[docs]
@warn_on_args_to_kwargs()
def cube(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
"""Visualize one or many cubes with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Cube positions.
directions : ndarray, shape (N, 3), optional
The orientation vector of the cube.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,), optional
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Cube size, default: 1
Returns
-------
cube_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> dirs = np.random.rand(5, 3)
>>> cube_actor = actor.cube(centers, directions=dirs)
>>> scene.add(cube_actor)
>>> # window.show(scene)
"""
return box(centers=centers, directions=directions, colors=colors, scales=scales)
[docs]
@warn_on_args_to_kwargs()
def arrow(
centers,
directions,
colors,
*,
heights=1.0,
resolution=10,
tip_length=0.35,
tip_radius=0.1,
shaft_radius=0.03,
scales=1,
vertices=None,
faces=None,
repeat_primitive=True,
):
"""Visualize one or many arrows with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Arrow positions.
directions : ndarray, shape (N, 3)
The orientation vector of the arrow.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
heights : ndarray, shape (N)
The height of the arrow.
resolution : int
The resolution of the arrow.
tip_length : float
The tip size of the arrow (default: 0.35)
tip_radius : float
the tip radius of the arrow (default: 0.1)
shaft_radius : float
The shaft radius of the arrow (default: 0.03)
vertices : ndarray, shape (N, 3)
The point cloud defining the arrow.
faces : ndarray, shape (M, 3)
If faces is None then a arrow is created based on directions, heights
and resolution. If not then a arrow is created with the provided
vertices and faces.
Returns
-------
arrow_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> directions = np.random.rand(5, 3)
>>> heights = np.random.rand(5)
>>> arrow_actor = actor.arrow(centers, directions, (1, 1, 1), heights=heights)
>>> scene.add(arrow_actor)
>>> # window.show(scene)
"""
if repeat_primitive:
vertices, faces = fp.prim_arrow()
res = fp.repeat_primitive(
vertices,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_vertices, big_faces, big_colors, _ = res
prim_count = len(centers)
arrow_actor = get_actor_from_primitive(
big_vertices, big_faces, colors=big_colors, prim_count=prim_count
)
return arrow_actor
src = ArrowSource() if faces is None else None
if src is not None:
src.SetTipResolution(resolution)
src.SetShaftResolution(resolution)
src.SetTipLength(tip_length)
src.SetTipRadius(tip_radius)
src.SetShaftRadius(shaft_radius)
arrow_actor = repeat_sources(
centers=centers,
directions=directions,
colors=colors,
active_scalars=heights,
source=src,
vertices=vertices,
faces=faces,
)
return arrow_actor
[docs]
@warn_on_args_to_kwargs()
def cone(
centers,
directions,
colors,
*,
heights=1.0,
resolution=10,
vertices=None,
faces=None,
use_primitive=True,
):
"""Visualize one or many cones with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Cone positions.
directions : ndarray, shape (N, 3)
The orientation vector of the cone.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
heights : ndarray, shape (N)
The height of the cone.
resolution : int
The resolution of the cone.
vertices : ndarray, shape (N, 3)
The point cloud defining the cone.
faces : ndarray, shape (M, 3)
If faces is None then a cone is created based on directions, heights
and resolution. If not then a cone is created with the provided.
vertices and faces.
use_primitive : boolean, optional
If True uses primitives to create the cone actor.
Returns
-------
cone_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(5, 3)
>>> directions = np.random.rand(5, 3)
>>> heights = np.random.rand(5)
>>> cone_actor = actor.cone(centers, directions, (1, 1, 1), heights=heights)
>>> scene.add(cone_actor)
>>> # window.show(scene)
"""
if not use_primitive:
src = ConeSource() if faces is None else None
if src is not None:
src.SetResolution(resolution)
cone_actor = repeat_sources(
centers=centers,
directions=directions,
colors=colors,
active_scalars=heights,
source=src,
vertices=vertices,
faces=faces,
)
return cone_actor
if faces is None and vertices is None:
vertices, faces = fp.prim_cone(sectors=resolution)
res = fp.repeat_primitive(
vertices, faces, centers, directions=directions, colors=colors, scales=heights
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
cone_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return cone_actor
[docs]
@warn_on_args_to_kwargs()
def triangularprism(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
"""Visualize one or many regular triangular prisms with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Triangular prism positions.
directions : ndarray, shape (N, 3)
The orientation vector(s) of the triangular prism(s).
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Triangular prism size on each direction (x, y), default(1)
Returns
-------
tprism_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(3, 3)
>>> dirs = np.random.rand(3, 3)
>>> colors = np.random.rand(3, 3)
>>> scales = np.random.rand(3, 1)
>>> actor = actor.triangularprism(centers, directions=dirs, colors=colors, scales=scales)
>>> scene.add(actor)
>>> # window.show(scene)
""" # noqa: E501
verts, faces = fp.prim_triangularprism()
res = fp.repeat_primitive(
verts,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
tprism_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return tprism_actor
[docs]
@warn_on_args_to_kwargs()
def rhombicuboctahedron(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
"""Visualize one or many rhombicuboctahedron with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Rhombicuboctahedron positions.
directions : ndarray, shape (N, 3)
The orientation vector(s) of the Rhombicuboctahedron(s).
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Rhombicuboctahedron size on each direction (x, y), default(1)
Returns
-------
rcoh_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(3, 3)
>>> dirs = np.random.rand(3, 3)
>>> colors = np.random.rand(3, 3)
>>> scales = np.random.rand(3, 1)
>>> actor = actor.rhombicuboctahedron(centers, directions=dirs, colors=colors, scales=scales)
>>> scene.add(actor)
>>> # window.show(scene)
""" # noqa: E501
verts, faces = fp.prim_rhombicuboctahedron()
res = fp.repeat_primitive(
verts,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
rcoh_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return rcoh_actor
[docs]
@warn_on_args_to_kwargs()
def pentagonalprism(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
"""Visualize one or many pentagonal prisms with different features.
Parameters
----------
centers : ndarray, shape (N, 3), optional
Pentagonal prism positions.
directions : ndarray, shape (N, 3), optional
The orientation vector of the pentagonal prism.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,), optional
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Pentagonal prism size on each direction (x, y), default(1)
Returns
-------
pent_actor: Actor
Examples
--------
>>> import numpy as np
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(3, 3)
>>> dirs = np.random.rand(3, 3)
>>> colors = np.random.rand(3, 3)
>>> scales = np.random.rand(3, 1)
>>> actor_pentagonal = actor.pentagonalprism(centers, directions=dirs, colors=colors, scales=scales)
>>> scene.add(actor_pentagonal)
>>> # window.show(scene)
""" # noqa: E501
verts, faces = fp.prim_pentagonalprism()
res = fp.repeat_primitive(
verts,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
pent_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return pent_actor
[docs]
@warn_on_args_to_kwargs()
def octagonalprism(centers, *, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
"""Visualize one or many octagonal prisms with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Octagonal prism positions.
directions : ndarray, shape (N, 3)
The orientation vector of the octagonal prism.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Octagonal prism size on each direction (x, y), default(1)
Returns
-------
oct_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(3, 3)
>>> dirs = np.random.rand(3, 3)
>>> colors = np.random.rand(3, 3)
>>> scales = np.random.rand(3, 1)
>>> actor = actor.octagonalprism(centers, directions=dirs, colors=colors, scales=scales)
>>> scene.add(actor)
>>> # window.show(scene)
""" # noqa: E501
verts, faces = fp.prim_octagonalprism()
res = fp.repeat_primitive(
verts,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
oct_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return oct_actor
[docs]
@warn_on_args_to_kwargs()
def frustum(centers, *, directions=(1, 0, 0), colors=(0, 1, 0), scales=1):
"""Visualize one or many frustum pyramids with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Frustum pyramid positions.
directions : ndarray, shape (N, 3)
The orientation vector of the frustum pyramid.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : int or ndarray (N,3) or tuple (3,), optional
Frustum pyramid size on each direction (x, y), default(1)
Returns
-------
frustum_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(4, 3)
>>> dirs = np.random.rand(4, 3)
>>> colors = np.random.rand(4, 3)
>>> scales = np.random.rand(4, 1)
>>> actor = actor.frustum(centers, directions=dirs, colors=colors, scales=scales)
>>> scene.add(actor)
>>> # window.show(scene)
"""
verts, faces = fp.prim_frustum()
res = fp.repeat_primitive(
verts,
faces,
directions=directions,
centers=centers,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
frustum_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return frustum_actor
[docs]
@warn_on_args_to_kwargs()
def superquadric(
centers, *, roundness=(1, 1), directions=(1, 0, 0), colors=(1, 0, 0), scales=1
):
"""Visualize one or many superquadrics with different features.
Parameters
----------
centers : ndarray, shape (N, 3)
Superquadrics positions.
roundness : ndarray, shape (N, 2) or tuple/list (2,), optional
parameters (Phi and Theta) that control the shape of the superquadric.
directions : ndarray, shape (N, 3) or tuple (3,), optional
The orientation vector of the cone.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : ndarray, shape (N) or (N,3) or float or int, optional
The height of the cone.
Returns
-------
spq_actor: Actor
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> centers = np.random.rand(3, 3) * 10
>>> directions = np.random.rand(3, 3)
>>> scales = np.random.rand(3)
>>> colors = np.random.rand(3, 3)
>>> roundness = np.array([[1, 1], [1, 2], [2, 1]])
>>> sq_actor = actor.superquadric(centers, roundness=roundness,
... directions=directions,
... colors=colors, scales=scales)
>>> scene.add(sq_actor)
>>> # window.show(scene)
"""
def have_2_dimensions(arr):
return all(isinstance(i, (list, tuple, np.ndarray)) for i in arr)
# reshape roundness to a valid numpy array
if (
isinstance(roundness, (tuple, list, np.ndarray))
and len(roundness) == 2
and not have_2_dimensions(roundness)
):
roundness = np.array([roundness] * centers.shape[0])
elif isinstance(roundness, np.ndarray) and len(roundness) == 1:
roundness = np.repeat(roundness, centers.shape[0], axis=0)
else:
roundness = np.array(roundness)
res = fp.repeat_primitive_function(
func=fp.prim_superquadric,
centers=centers,
func_args=roundness,
directions=directions,
colors=colors,
scales=scales,
)
big_verts, big_faces, big_colors, _ = res
prim_count = len(centers)
spq_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
return spq_actor
[docs]
@warn_on_args_to_kwargs()
def billboard(
centers,
*,
colors=(0, 1, 0),
scales=1,
vs_dec=None,
vs_impl=None,
gs_prog=None,
fs_dec=None,
fs_impl=None,
bb_type="spherical",
):
"""Create a billboard actor.
-
Billboards are 2D elements placed in a 3D world. They offer possibility to
draw different shapes/elements at the fragment shader level.
Parameters
----------
centers : ndarray, shape (N, 3)
Billboard positions.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : ndarray, shape (N) or (N,3) or float or int, optional
The scale of the billboards.
vs_dec : str or list of str, optional
Vertex Shader code that contains all variable/function declarations.
vs_impl : str or list of str, optional
Vertex Shaders code that contains all variable/function
implementations.
gs_prog : str, optional
Geometry Shader program.
fs_dec : str or list of str, optional
Fragment Shaders code that contains all variable/function declarations.
fs_impl : str or list of str, optional
Fragment Shaders code that contains all variable/function
implementation.
bb_type : str, optional
Type of billboard (spherical, cylindrical_x, cylindrical_y).
If spherical, billboard will always face the camera.
If cylindrical_x or cylindrical_y, billboard will face the camera only
when rotating around x-axis and y-axis respectively.
Returns
-------
billboard_actor: Actor
"""
verts, faces = fp.prim_square()
res = fp.repeat_primitive(
verts, faces, centers=centers, colors=colors, scales=scales
)
big_verts, big_faces, big_colors, big_centers = res
prim_count = len(centers)
bb_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
bb_actor.GetMapper().SetVBOShiftScaleMethod(False)
bb_actor.GetProperty().BackfaceCullingOff()
attribute_to_actor(bb_actor, big_centers, "center")
bb_norm = import_fury_shader(os.path.join("utils", "billboard_normalization.glsl"))
if bb_type.lower() == "cylindrical_x":
bb_type_sd = import_fury_shader(os.path.join("billboard", "cylindrical_x.glsl"))
v_pos_mc = """
vec3 vertexPositionMC = cylindricalXVertexPos(center, MCVCMatrix,
normalizedVertexMCVSOutput, shape);
"""
elif bb_type.lower() == "cylindrical_y":
bb_type_sd = import_fury_shader(os.path.join("billboard", "cylindrical_y.glsl"))
v_pos_mc = """
vec3 vertexPositionMC = cylindricalYVertexPos(center,MCVCMatrix,
normalizedVertexMCVSOutput, shape);
"""
elif bb_type.lower() == "spherical":
bb_type_sd = import_fury_shader(os.path.join("billboard", "spherical.glsl"))
v_pos_mc = """
vec3 vertexPositionMC = sphericalVertexPos(center, MCVCMatrix,
normalizedVertexMCVSOutput, shape);
"""
else:
bb_type_sd = import_fury_shader(os.path.join("billboard", "spherical.glsl"))
v_pos_mc = """
vec3 vertexPositionMC = sphericalVertexPos(center, MCVCMatrix,
normalizedVertexMCVSOutput, shape);
"""
warnings.warn(
"Invalid option. The billboard will be generated "
"with the default spherical option. ",
UserWarning,
stacklevel=2,
)
gl_position = """
gl_Position = MCDCMatrix * vec4(vertexPositionMC, 1.);
"""
billboard_dec_vert = """
/* Billboard vertex shader declaration */
in vec3 center;
out vec3 centerVertexMCVSOutput;
out vec3 normalizedVertexMCVSOutput;
"""
billboard_impl_vert = """
/* Billboard vertex shader implementation */
centerVertexMCVSOutput = center;
normalizedVertexMCVSOutput = bbNorm(vertexMC.xyz, center);
float scalingFactor = 1. / abs(normalizedVertexMCVSOutput.x);
float size = abs((vertexMC.xyz - center).x) * 2;
vec2 shape = vec2(size, size); // Fixes the scaling issue
"""
billboard_dec_frag = """
/* Billboard fragment shader declaration */
in vec3 centerVertexMCVSOutput;
in vec3 normalizedVertexMCVSOutput;
"""
billboard_impl_frag = """
/* Billboard Fragment shader implementation */
// Renaming variables passed from the Vertex Shader
vec3 color = vertexColorVSOutput.rgb;
vec3 point = normalizedVertexMCVSOutput;
fragOutput0 = vec4(color, 1.);
"""
billboard_vert_impl = compose_shader([billboard_impl_vert, v_pos_mc, gl_position])
vs_dec_code = compose_shader(
[billboard_dec_vert, compose_shader(vs_dec), bb_norm, bb_type_sd]
)
vs_impl_code = compose_shader([compose_shader(vs_impl), billboard_vert_impl])
gs_code = compose_shader(gs_prog)
fs_dec_code = compose_shader([billboard_dec_frag, compose_shader(fs_dec)])
fs_impl_code = compose_shader([billboard_impl_frag, compose_shader(fs_impl)])
shader_to_actor(bb_actor, "vertex", impl_code=vs_impl_code, decl_code=vs_dec_code)
replace_shader_in_actor(bb_actor, "geometry", gs_code)
shader_to_actor(bb_actor, "fragment", decl_code=fs_dec_code)
shader_to_actor(bb_actor, "fragment", impl_code=fs_impl_code, block="light")
return bb_actor
[docs]
@warn_on_args_to_kwargs()
def vector_text(
*,
text="Origin",
pos=(0, 0, 0),
scale=(0.2, 0.2, 0.2),
color=(1, 1, 1),
direction=(0, 0, 1),
extrusion=0.0,
align_center=False,
):
"""Create a label actor.
This actor will always face the camera.
Parameters
----------
text : str
Text for the label.
pos : (3,) array_like, optional
Left down position of the label.
scale : (3,) array_like
Changes the size of the label.
color : (3,) array_like
Label color as ``(r,g,b)`` tuple.
direction : (3,) array_like, optional, default: (0, 0, 1)
The direction of the label. If None, label will follow the camera.
extrusion : float, optional
The extrusion amount of the text in Z axis.
align_center : bool, optional, default: True
If `True`, the anchor of the actor will be the center of the text.
If `False`, the anchor will be at the left bottom of the text.
Returns
-------
l : Actor object
Label.
Examples
--------
>>> from fury import window, actor
>>> scene = window.Scene()
>>> l = actor.vector_text(text='Hello')
>>> scene.add(l)
>>> # window.show(scene)
"""
atext = VectorText()
atext.SetText(text)
textm = PolyDataMapper()
if extrusion:
extruded_text = LinearExtrusionFilter()
extruded_text.SetInputConnection(atext.GetOutputPort())
extruded_text.SetExtrusionTypeToNormalExtrusion()
extruded_text.SetVector(0, 0, extrusion)
atext = extruded_text
trans_matrix = Transform()
trans_matrix.PostMultiply()
if direction is None:
# set text to follow the camera if direction is None.
texta = Follower()
def add_to_scene(scene):
texta.SetCamera(scene.GetActiveCamera())
scene.AddActor(texta)
texta.add_to_scene = add_to_scene
else:
texta = Actor()
textm.SetInputConnection(atext.GetOutputPort())
orig_dir = [0, 0, 1]
direction = np.array(direction, dtype=float)
direction /= np.linalg.norm(direction)
normal_vec = np.cross(orig_dir, direction)
angle = np.arccos(np.dot(orig_dir, direction))
trans_matrix.RotateWXYZ(np.rad2deg(angle), *normal_vec)
trans_matrix.Scale(*scale[0:2], 1)
plan = TransformPolyDataFilter()
plan.SetInputConnection(atext.GetOutputPort())
plan.SetTransform(trans_matrix)
textm.SetInputConnection(plan.GetOutputPort())
texta.SetMapper(textm)
texta.GetProperty().SetColor(color)
# Set rotation origin to the center of the text is following the camera
if align_center or direction is None:
trans_matrix.Translate(-np.array(textm.GetCenter()))
texta.SetPosition(*pos)
return texta
[docs]
@warn_on_args_to_kwargs()
def text_3d(
text,
*,
position=(0, 0, 0),
color=(1, 1, 1),
font_size=12,
font_family="Arial",
justification="left",
vertical_justification="bottom",
bold=False,
italic=False,
shadow=False,
):
"""Generate 2D text that lives in the 3D world.
Parameters
----------
text : str
position : tuple
color : tuple
font_size : int
font_family : str
justification : str
Left, center or right (default left).
vertical_justification : str
Bottom, middle or top (default bottom).
bold : bool
italic : bool
shadow : bool
Returns
-------
Text3D
"""
class Text3D(TextActor3D):
def message(self, text):
self.set_message(text)
def set_message(self, text):
self.SetInput(text)
def get_message(self):
return self.GetInput()
def font_size(self, size):
self.GetTextProperty().SetFontSize(24)
text_actor.SetScale((1.0 / 24.0 * size,) * 3)
@warn_on_args_to_kwargs()
def font_family(self, *, _family="Arial"):
self.GetTextProperty().SetFontFamilyToArial()
def justification(self, justification):
tprop = self.GetTextProperty()
if justification == "left":
tprop.SetJustificationToLeft()
elif justification == "center":
tprop.SetJustificationToCentered()
elif justification == "right":
tprop.SetJustificationToRight()
else:
raise ValueError("Unknown justification: '{}'".format(justification))
def vertical_justification(self, justification):
tprop = self.GetTextProperty()
if justification == "top":
tprop.SetVerticalJustificationToTop()
elif justification == "middle":
tprop.SetVerticalJustificationToCentered()
elif justification == "bottom":
tprop.SetVerticalJustificationToBottom()
else:
raise ValueError(
"Unknown vertical justification: '{}'".format(justification)
)
@warn_on_args_to_kwargs()
def font_style(self, *, bold=False, italic=False, shadow=False):
tprop = self.GetTextProperty()
if bold:
tprop.BoldOn()
else:
tprop.BoldOff()
if italic:
tprop.ItalicOn()
else:
tprop.ItalicOff()
if shadow:
tprop.ShadowOn()
else:
tprop.ShadowOff()
def color(self, color):
self.GetTextProperty().SetColor(*color)
def set_position(self, position):
self.SetPosition(position)
def get_position(self):
return self.GetPosition()
text_actor = Text3D()
text_actor.message(text)
text_actor.font_size(font_size)
text_actor.set_position(position)
text_actor.font_family(_family=font_family)
text_actor.font_style(bold=bold, italic=italic, shadow=shadow)
text_actor.color(color)
text_actor.justification(justification)
text_actor.vertical_justification(vertical_justification)
return text_actor
[docs]
class Container:
"""Provides functionalities for grouping multiple actors using a given
layout.
Attributes
----------
anchor : 3-tuple of float
Anchor of this container used when laying out items in a container.
The anchor point is relative to the center of the container.
Default: (0, 0, 0).
padding : 6-tuple of float
Padding around this container bounding box. The 6-tuple represents
(pad_x_neg, pad_x_pos, pad_y_neg, pad_y_pos, pad_z_neg, pad_z_pos).
Default: (0, 0, 0, 0, 0, 0).
"""
@warn_on_args_to_kwargs()
def __init__(self, *, layout=None):
"""Parameters
----------
layout : ``fury.layout.Layout`` object
Items of this container will be arranged according to `layout`.
"""
if layout is None:
layout = lyt.Layout()
self.layout = layout
self._items = []
self._need_update = True
self._position = np.zeros(3)
self._visibility = True
self.anchor = np.zeros(3)
self.padding = np.zeros(6)
@property
def items(self):
if self._need_update:
self.update()
return self._items
[docs]
def add(self, *items, **kwargs):
"""Adds some items to this container.
Parameters
----------
items : `vtkProp3D` objects
Items to add to this container.
borrow : bool
If True the items are added as-is, otherwise a shallow copy is
made first. If you intend to reuse the items elsewhere you
should set `borrow=False`. Default: True.
"""
self._need_update = True
for item in items:
if not kwargs.get("borrow", True):
item = shallow_copy(item)
self._items.append(item)
[docs]
def clear(self):
"""Clears all items of this container."""
self._need_update = True
del self._items[:]
[docs]
def update(self):
"""Updates the position of the items of this container."""
self.layout.apply(self._items)
self._need_update = False
[docs]
def add_to_scene(self, scene):
"""Adds the items of this container to a given scene."""
for item in self.items:
if isinstance(item, Container):
item.add_to_scene(scene)
else:
scene.add(item)
[docs]
def remove_from_scene(self, scene):
"""Removes the items of this container from a given scene."""
for item in self.items:
if isinstance(item, Container):
item.remove_from_scene(scene)
else:
scene.rm(item)
[docs]
def GetBounds(self):
"""Get the bounds of the container."""
bounds = np.zeros(6) # x1, x2, y1, y2, z1, z2
bounds[::2] = np.inf # x1, y1, z1
bounds[1::2] = -np.inf # x2, y2, z2
for item in self.items:
item_bounds = item.GetBounds()
bounds[::2] = np.minimum(bounds[::2], item_bounds[::2])
bounds[1::2] = np.maximum(bounds[1::2], item_bounds[1::2])
# Add padding, if any.
bounds[::2] -= self.padding[::2]
bounds[1::2] += self.padding[1::2]
return tuple(bounds)
[docs]
def GetVisibility(self):
return self._visibility
[docs]
def SetVisibility(self, visibility):
self._visibility = visibility
for item in self.items:
item.SetVisibility(visibility)
[docs]
def GetPosition(self):
return self._position
[docs]
def AddPosition(self, position):
self._position += position
for item in self.items:
item.AddPosition(position)
[docs]
def SetPosition(self, position):
self.AddPosition(np.array(position) - self._position)
[docs]
def GetCenter(self):
"""Get the center of the bounding box."""
x1, x2, y1, y2, z1, z2 = self.GetBounds()
return ((x1 + x2) / 2.0, (y1 + y2) / 2.0, (z1 + z2) / 2.0)
[docs]
def GetLength(self):
"""Get the length of bounding box diagonal."""
x1, x2, y1, y2, z1, z2 = self.GetBounds()
width, height, depth = x2 - x1, y2 - y1, z2 - z1
return np.sqrt(np.sum([width**2, height**2, depth**2]))
[docs]
def NewInstance(self):
return Container(layout=self.layout)
[docs]
def ShallowCopy(self, other):
self._position = other._position.copy()
self.anchor = other.anchor
self.clear()
self.add(*other._items, borrow=False)
self.update()
def __len__(self):
return len(self._items)
[docs]
@warn_on_args_to_kwargs()
def grid(
actors,
*,
captions=None,
caption_offset=(0, -100, 0),
cell_padding=0,
cell_shape="rect",
aspect_ratio=16 / 9.0,
dim=None,
):
"""Creates a grid of actors that lies in the xy-plane.
Parameters
----------
actors : list of `vtkProp3D` objects
Actors to be layout in a grid manner.
captions : list of `vtkProp3D` objects or list of str
Objects serving as captions (can be any `vtkProp3D` object, not
necessarily text). There should be one caption per actor. By
default, there are no captions.
caption_offset : tuple of float (optional)
Tells where to position the caption w.r.t. the center of its
associated actor. Default: (0, -100, 0).
cell_padding : tuple of 2 floats or float
Each grid cell will be padded according to (pad_x, pad_y) i.e.
horizontally and vertically. Padding is evenly distributed on each
side of the cell. If a single float is provided then both pad_x and
pad_y will have the same value.
cell_shape : str
Specifies the desired shape of every grid cell.
'rect' ensures the cells are the tightest.
'square' ensures the cells are as wide as high.
'diagonal' ensures the content of the cells can be rotated without
colliding with content of the neighboring cells.
aspect_ratio : float
Aspect ratio of the grid (width/height). Default: 16:9.
dim : tuple of int
Dimension (nb_rows, nb_cols) of the grid. If provided,
`aspect_ratio` will be ignored.
Returns
-------
``fury.actor.Container`` object
Object that represents the grid containing all the actors and
captions, if any.
"""
grid_layout = lyt.GridLayout(
cell_padding=cell_padding,
cell_shape=cell_shape,
aspect_ratio=aspect_ratio,
dim=dim,
)
grid = Container(layout=grid_layout)
if captions is not None:
actors_with_caption = []
for actor, caption in zip(actors, captions):
actor_center = np.array(actor.GetCenter())
# Offset accordingly the caption w.r.t.
# the center of the associated actor.
if isinstance(caption, str):
caption = text_3d(caption, justification="center")
else:
caption = shallow_copy(caption)
caption.SetPosition(actor_center + caption_offset)
actor_with_caption = Container()
actor_with_caption.add(actor, caption)
# We change the anchor of the container so
# the actor will be centered in the
# grid cell.
actor_with_caption.anchor = actor_center - actor_with_caption.GetCenter()
actors_with_caption.append(actor_with_caption)
actors = actors_with_caption
grid.add(*actors)
return grid
[docs]
@warn_on_args_to_kwargs()
def texture(rgb, *, interp=True):
"""Map an RGB or RGBA texture on a plane.
Parameters
----------
rgb : ndarray
Input 2D RGB or RGBA array. Dtype should be uint8.
interp : bool
Interpolate between grid centers. Default True.
Returns
-------
act: Actor
"""
arr = rgb
grid = rgb_to_vtk(np.ascontiguousarray(arr))
Y, X = arr.shape[:2]
# Get vertices and triangles, then scale it
vertices, triangles = fp.prim_square()
vertices *= np.array([[X, Y, 0]])
# Create a polydata
my_polydata = PolyData()
set_polydata_vertices(my_polydata, vertices)
set_polydata_triangles(my_polydata, triangles)
# Create texture object
texture = Texture()
texture.SetInputDataObject(grid)
# texture.UseSRGBColorSpaceOn()
# texture.SetPremultipliedAlpha(True)
if interp:
texture.InterpolateOn()
# Map texture coordinates
map_to_sphere = TextureMapToPlane()
map_to_sphere.SetInputData(my_polydata)
# Create mapper and set the mapped texture as input
mapper = PolyDataMapper()
mapper.SetInputConnection(map_to_sphere.GetOutputPort())
mapper.Update()
# Create actor and set the mapper and the texture
act = Actor()
act.SetMapper(mapper)
act.SetTexture(texture)
return act
[docs]
def texture_update(texture_actor, arr):
"""Updates texture of an actor by updating the vtkImageData
assigned to the vtkTexture object.
Parameters
----------
texture_actor: Actor
Actor whose texture is to be updated.
arr : ndarray
Input 2D image in the form of RGB or RGBA array.
This is the new image to be rendered on the actor.
Dtype should be uint8.
Notes
-----
Check docs/examples/viz_video_on_plane.py
"""
grid = texture_actor.GetTexture().GetInput()
dim = arr.shape[-1]
img_data = np.flip(arr.swapaxes(0, 1), axis=1).reshape((-1, dim), order="F")
vtkarr = numpy_support.numpy_to_vtk(img_data, deep=False)
grid.GetPointData().SetScalars(vtkarr)
@warn_on_args_to_kwargs()
def _textured_sphere_source(*, theta=60, phi=60):
"""Use vtkTexturedSphereSource to set the theta and phi.
Parameters
----------
theta : int, optional
Set the number of points in the longitude direction.
phi : int, optional
Set the number of points in the latitude direction.
Returns
-------
tss : TexturedSphereSource
"""
tss = TexturedSphereSource()
tss.SetThetaResolution(theta)
tss.SetPhiResolution(phi)
return tss
[docs]
@warn_on_args_to_kwargs()
def texture_on_sphere(rgb, *, theta=60, phi=60, interpolate=True):
"""Map an RGB or RGBA texture on a sphere.
Parameters
----------
rgb : ndarray
Input 2D RGB or RGBA array. Dtype should be uint8.
theta : int, optional
Set the number of points in the longitude direction.
phi : int, optional
Set the number of points in the latitude direction.
interpolate : bool, optional
Interpolate between grid centers.
Returns
-------
earthActor : Actor
"""
tss = _textured_sphere_source(theta=theta, phi=phi)
earthMapper = PolyDataMapper()
earthMapper.SetInputConnection(tss.GetOutputPort())
earthActor = Actor()
earthActor.SetMapper(earthMapper)
atext = Texture()
grid = rgb_to_vtk(rgb)
atext.SetInputDataObject(grid)
if interpolate:
atext.InterpolateOn()
earthActor.SetTexture(atext)
return earthActor
[docs]
@warn_on_args_to_kwargs()
def texture_2d(rgb, *, interp=False):
"""Create 2D texture from array.
Parameters
----------
rgb : ndarray
Input 2D RGB or RGBA array. Dtype should be uint8.
interp : bool, optional
Interpolate between grid centers.
Returns
-------
vtkTexturedActor
"""
arr = rgb
Y, X = arr.shape[:2]
size = (X, Y)
grid = rgb_to_vtk(np.ascontiguousarray(arr))
texture_polydata = PolyData()
texture_points = Points()
texture_points.SetNumberOfPoints(4)
polys = CellArray()
polys.InsertNextCell(4)
polys.InsertCellPoint(0)
polys.InsertCellPoint(1)
polys.InsertCellPoint(2)
polys.InsertCellPoint(3)
texture_polydata.SetPolys(polys)
tc = FloatArray()
tc.SetNumberOfComponents(2)
tc.SetNumberOfTuples(4)
tc.InsertComponent(0, 0, 0.0)
tc.InsertComponent(0, 1, 0.0)
tc.InsertComponent(1, 0, 1.0)
tc.InsertComponent(1, 1, 0.0)
tc.InsertComponent(2, 0, 1.0)
tc.InsertComponent(2, 1, 1.0)
tc.InsertComponent(3, 0, 0.0)
tc.InsertComponent(3, 1, 1.0)
texture_polydata.GetPointData().SetTCoords(tc)
texture_points.SetPoint(0, 0, 0, 0.0)
texture_points.SetPoint(1, size[0], 0, 0.0)
texture_points.SetPoint(2, size[0], size[1], 0.0)
texture_points.SetPoint(3, 0, size[1], 0.0)
texture_polydata.SetPoints(texture_points)
texture_mapper = PolyDataMapper2D()
texture_mapper = set_input(texture_mapper, texture_polydata)
act = TexturedActor2D()
act.SetMapper(texture_mapper)
tex = Texture()
tex.SetInputDataObject(grid)
if interp:
tex.InterpolateOn()
tex.Update()
act.SetTexture(tex)
return act
[docs]
@warn_on_args_to_kwargs()
def sdf(
centers, *, directions=(1, 0, 0), colors=(1, 0, 0), primitives="torus", scales=1
):
"""Create a SDF primitive based actor.
Parameters
----------
centers : ndarray, shape (N, 3)
SDF primitive positions.
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,), optional
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
directions : ndarray, shape (N, 3)
The orientation vector of the SDF primitive.
primitives : str, list, tuple, np.ndarray
The primitive of choice to be rendered.
Options are sphere, torus and ellipsoid. Default is torus.
scales : float
The size of the SDF primitive.
Returns
-------
box_actor: Actor
"""
prims = {"sphere": 1, "torus": 2, "ellipsoid": 3, "capsule": 4}
verts, faces = fp.prim_box()
repeated = fp.repeat_primitive(
verts,
faces,
centers=centers,
colors=colors,
directions=directions,
scales=scales,
)
rep_verts, rep_faces, rep_colors, rep_centers = repeated
prim_count = len(centers)
box_actor = get_actor_from_primitive(
rep_verts, rep_faces, colors=rep_colors, prim_count=prim_count
)
box_actor.GetMapper().SetVBOShiftScaleMethod(False)
if isinstance(primitives, (list, tuple, np.ndarray)):
primlist = [prims[prim] for prim in primitives]
if len(primitives) < len(centers):
primlist = primlist + [2] * (len(centers) - len(primitives))
warnings.warn(
"Not enough primitives provided,\
defaulting to torus",
category=UserWarning,
stacklevel=2,
)
rep_prims = np.repeat(primlist, verts.shape[0])
else:
rep_prims = np.repeat(prims[primitives], rep_centers.shape[0], axis=0)
if isinstance(scales, (list, tuple, np.ndarray)):
rep_scales = np.repeat(scales, verts.shape[0])
else:
rep_scales = np.repeat(scales, rep_centers.shape[0], axis=0)
if isinstance(directions, (list, tuple, np.ndarray)) and len(directions) == 3:
rep_directions = np.repeat(directions, rep_centers.shape[0], axis=0)
else:
rep_directions = np.repeat(directions, verts.shape[0], axis=0)
attribute_to_actor(box_actor, rep_centers, "center")
attribute_to_actor(box_actor, rep_prims, "primitive")
attribute_to_actor(box_actor, rep_scales, "scale")
attribute_to_actor(box_actor, rep_directions, "direction")
vs_dec_code = import_fury_shader("sdf_dec.vert")
vs_impl_code = import_fury_shader("sdf_impl.vert")
fs_dec_code = import_fury_shader("sdf_dec.frag")
fs_impl_code = import_fury_shader("sdf_impl.frag")
shader_to_actor(box_actor, "vertex", impl_code=vs_impl_code, decl_code=vs_dec_code)
shader_to_actor(box_actor, "fragment", decl_code=fs_dec_code)
shader_to_actor(box_actor, "fragment", impl_code=fs_impl_code, block="light")
return box_actor
[docs]
@warn_on_args_to_kwargs()
def markers(
centers,
*,
colors=(0, 1, 0),
scales=1,
marker="3d",
marker_opacity=0.8,
edge_width=0.0,
edge_color=(255, 255, 255),
edge_opacity=0.8,
):
"""Create a marker actor with different shapes.
Parameters
----------
centers : ndarray, shape (N, 3)
colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1].
scales : ndarray, shape (N) or (N,3) or float or int, optional
marker : str or a list
Available markers are: '3d', 'o', 's', 'd', '^', 'p', 'h', 's6',
'x', '+', optional.
marker_opacity : float, optional
edge_width : int, optional
edge_color : ndarray, shape (3), optional
edge_opacity : float, optional
Returns
-------
sq_actor: Actor
Examples
--------
>>> import numpy as np
>>> from fury import actor, window
>>> scene = window.Scene()
>>> markers = ['o', 'x', '^', 's'] # some examples
>>> n = len(markers)
>>> centers = np.random.normal(size=(n, 3), scale=10)
>>> colors = np.random.rand(n, 4)
>>> nodes_actor = actor.markers(
... centers,
... marker=markers,
... edge_width=.1,
... edge_color=[255, 255, 0],
... colors=colors,
... scales=10,
... )
>>> center = np.random.normal(size=(1, 3), scale=10)
>>> nodes_3d_actor = actor.markers(
... center,
... marker='3d',
... scales=5,
... )
>>> scene.add(nodes_actor, nodes_3d_actor)
>>> # window.show(scene, size=(600, 600))
"""
n_markers = centers.shape[0]
verts, faces = fp.prim_square()
res = fp.repeat_primitive(
verts, faces, centers=centers, colors=colors, scales=scales
)
big_verts, big_faces, big_colors, big_centers = res
prim_count = len(centers)
sq_actor = get_actor_from_primitive(
big_verts, big_faces, colors=big_colors, prim_count=prim_count
)
sq_actor.GetMapper().SetVBOShiftScaleMethod(False)
sq_actor.GetProperty().BackfaceCullingOff()
attribute_to_actor(sq_actor, big_centers, "center")
marker2id = {
"o": 0,
"s": 1,
"d": 2,
"^": 3,
"p": 4,
"h": 5,
"s6": 6,
"x": 7,
"+": 8,
"3d": 0,
}
bb_impl = """
vec3 vertexPositionMC = sphericalVertexPos(center, MCVCMatrix,
normalizedVertexMCVSOutput, shape);
gl_Position = MCDCMatrix * vec4(vertexPositionMC, 1.);
"""
vs_dec_code = """
/* Billboard vertex shader declaration */
in vec3 center;
out vec3 centerVertexMCVSOutput;
out vec3 normalizedVertexMCVSOutput;
"""
vs_dec_code += f'\n{import_fury_shader("utils/billboard_normalization.glsl")}'
vs_dec_code += f'\n{import_fury_shader("billboard/spherical.glsl")}'
vs_dec_code += f'\n{import_fury_shader("marker_billboard_dec.vert")}'
vs_impl_code = """
/* Billboard vertex shader implementation */
centerVertexMCVSOutput = center;
normalizedVertexMCVSOutput = bbNorm(vertexMC.xyz, center);
float scalingFactor = 1. / abs(normalizedVertexMCVSOutput.x);
float size = abs((vertexMC.xyz - center).x) * 2;
vec2 shape = vec2(size, size); // Fixes the scaling issue
"""
vs_impl_code += f"\n{compose_shader(bb_impl)}"
vs_impl_code += f'\n{import_fury_shader("marker_billboard_impl.vert")}'
fs_dec_code = """
/* Billboard fragment shader declaration */
in vec3 centerVertexMCVSOutput;
in vec3 normalizedVertexMCVSOutput;
"""
fs_dec_code += f'\n{import_fury_shader("marker_billboard_dec.frag")}'
fs_impl_code = """
/* Billboard Fragment shader implementation */
// Renaming variables passed from the Vertex Shader
vec3 color = vertexColorVSOutput.rgb;
vec3 point = normalizedVertexMCVSOutput;
fragOutput0 = vec4(color, 1.);
"""
if marker == "3d":
fs_impl_code += f'{import_fury_shader("billboard_spheres_impl.frag")}'
else:
fs_impl_code += f'{import_fury_shader("marker_billboard_impl.frag")}'
if isinstance(marker, str):
list_of_markers = np.ones(n_markers) * marker2id[marker]
else:
list_of_markers = [marker2id[i] for i in marker]
list_of_markers = np.repeat(list_of_markers, 4).astype("float")
attribute_to_actor(sq_actor, list_of_markers, "marker")
def callback(
_caller,
_event,
calldata=None,
uniform_type="f",
uniform_name=None,
value=None,
):
program = calldata
if program is not None:
program.__getattribute__(f"SetUniform{uniform_type}")(uniform_name, value)
add_shader_callback(
sq_actor,
partial(callback, uniform_type="f", uniform_name="edgeWidth", value=edge_width),
)
add_shader_callback(
sq_actor,
partial(
callback,
uniform_type="f",
uniform_name="markerOpacity",
value=marker_opacity,
),
)
add_shader_callback(
sq_actor,
partial(
callback, uniform_type="f", uniform_name="edgeOpacity", value=edge_opacity
),
)
add_shader_callback(
sq_actor,
partial(
callback, uniform_type="3f", uniform_name="edgeColor", value=edge_color
),
)
shader_to_actor(sq_actor, "vertex", impl_code=vs_impl_code, decl_code=vs_dec_code)
shader_to_actor(sq_actor, "fragment", decl_code=fs_dec_code)
shader_to_actor(sq_actor, "fragment", impl_code=fs_impl_code, block="light")
return sq_actor
[docs]
@warn_on_args_to_kwargs()
def ellipsoid(
centers,
axes,
lengths,
*,
colors=(1, 0, 0),
scales=1.0,
opacity=1.0,
):
"""VTK actor for visualizing ellipsoids.
Parameters
----------
centers : ndarray(N, 3)
Ellipsoid positions.
axes : ndarray (3, 3) or (N, 3, 3)
Axes of the ellipsoid.
lengths : ndarray (3, ) or (N, 3)
Axes lengths.
colors : ndarray (N,3) or tuple (3,), optional
Default red color. R, G and B should be in the range [0, 1].
scales : float or ndarray (N, ), optional
Ellipsoid size, default(1.0).
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque), default(1.0).
Returns
-------
tensor_ellipsoid: Actor
"""
if not isinstance(centers, np.ndarray):
centers = np.array(centers)
if centers.ndim == 1:
centers = np.array([centers])
if not isinstance(axes, np.ndarray):
axes = np.array(axes)
if axes.ndim == 2:
axes = np.array([axes])
if axes.shape[0] != centers.shape[0]:
raise ValueError(
"number of axes defined does not match with number of" "centers"
)
if not isinstance(lengths, np.ndarray):
lengths = np.array(lengths)
if lengths.ndim == 1:
lengths = np.array([lengths])
if lengths.shape[0] != centers.shape[0]:
raise ValueError(
"number of lengths defined does not match with number" "of centers"
)
if not isinstance(scales, np.ndarray):
scales = np.array(scales)
if scales.size == 1:
scales = np.repeat(scales, centers.shape[0])
elif scales.size != centers.shape[0]:
scales = np.concatenate(
(scales, np.ones(centers.shape[0] - scales.shape[0])), axis=None
)
if isinstance(colors, tuple):
colors = np.array([colors])
elif not isinstance(colors, np.ndarray):
colors = np.array(colors)
if colors.shape[1] == 4:
colors = colors[:, :-1]
return tensor_ellipsoid(centers, axes, lengths, colors, scales, opacity)
[docs]
@warn_on_args_to_kwargs()
def uncertainty_cone(
evals,
evecs,
signal,
sigma,
b_matrix,
*,
scales=0.6,
opacity=1.0,
):
"""VTK actor for visualizing the cone of uncertainty representing the
variance of the main direction of diffusion.
Parameters
----------
evals : ndarray (3, ) or (N, 3)
Eigenvalues.
evecs : ndarray (3, 3) or (N, 3, 3)
Eigenvectors.
signal : 3D or 4D ndarray
Predicted signal.
sigma : ndarray
Standard deviation of the noise.
b_matrix : array (N, 7)
Design matrix for DTI.
scales : float or ndarray (N, ), optional
Cones of uncertainty size.
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque), default(1.0).
Returns
-------
double_cone: Actor
"""
valid_mask = np.abs(evecs).max(axis=(-2, -1)) > 0
indices = np.nonzero(valid_mask)
evecs = evecs[indices]
evals = evals[indices]
signal = signal[indices]
centers = np.asarray(indices).T
colors = np.array([107, 107, 107])
x, y, z = evecs.shape
if not isinstance(scales, np.ndarray):
scales = np.array(scales)
if scales.size == 1:
scales = np.repeat(scales, x)
angles = main_dir_uncertainty(evals, evecs, signal, sigma, b_matrix)
return double_cone(centers, evecs, angles, colors, scales, opacity)
[docs]
def odf(centers, coeffs, sh_basis="descoteaux", scales=1.0, opacity=1.0):
"""
FURY actor for visualizing Orientation Distribution Functions (ODFs) given
an array of Spherical Harmonics (SH) coefficients.
Parameters
----------
centers : ndarray(N, 3)
ODFs positions.
coeffs : (N, M) or (N, 6) or (N, 15) or (N, 28) or (N, 45) or (N, 66) or
(N, 91) ndarray.
Corresponding SH coefficients for the ODFs.
sh_basis: str, optional
Type of basis (descoteaux, tournier)
'descoteaux' for the default ``descoteaux07`` DIPY basis.
'tournier' for the default ``tournier07`` DIPY basis.
scales : float or ndarray (N, ), optional
ODFs size.
opacity : float, optional
Takes values from 0 (fully transparent) to 1 (opaque).
Returns
-------
odf: Actor
"""
if not isinstance(centers, np.ndarray):
centers = np.array(centers)
if centers.ndim == 1:
centers = np.array([centers])
if not isinstance(coeffs, np.ndarray):
coeffs = np.array(coeffs)
if coeffs.ndim != 2:
if coeffs.ndim == 1:
coeffs = np.array([coeffs])
else:
raise ValueError("coeffs should be a 2D array.")
if coeffs.shape[0] != centers.shape[0]:
raise ValueError(
"number of odf glyphs defined does not match with number of centers"
)
coeffs_given = coeffs.shape[-1]
degree = int((np.sqrt(8 * coeffs_given + 1) - 3) / 2)
if degree % 2 != 0:
degree -= 1
coeffs = coeffs[:, : int(((degree + 1) * (degree + 2)) / 2)]
if not isinstance(scales, np.ndarray):
scales = np.array(scales)
if scales.size == 1:
scales = np.repeat(scales, centers.shape[0])
elif scales.size != centers.shape[0]:
scales = np.concatenate(
(scales, np.ones(centers.shape[0] - scales.shape[0])), axis=None
)
total = np.sum(abs(coeffs), axis=1)
coeffs = np.dot(np.diag(1 / total * scales), coeffs) * 1.7
return sh_odf(centers, coeffs, degree, sh_basis, scales, opacity)
