# -*- coding: utf-8 -*-
import numpy as np
from fury.colormap import create_colormap
from fury.decorators import warn_on_args_to_kwargs
from fury.lib import Actor, PolyData, PolyDataMapper
from fury.utils import (
apply_affine,
set_polydata_colors,
set_polydata_triangles,
set_polydata_vertices,
)
[docs]
class OdfSlicerActor(Actor):
"""VTK actor for visualizing slices of ODF field.
Parameters
----------
odfs : ndarray
SF or SH coefficients 2-dimensional array.
vertices: ndarray
The sphere vertices used for SH to SF projection.
faces: ndarray
Indices of sphere vertices forming triangles. Should be
ordered clockwise (see fury.utils.fix_winding_order).
indices: tuple
Indices given in tuple(x_indices, y_indices, z_indices)
format for mapping 2D ODF array to 3D voxel grid.
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.
global_cm : bool
If True the colormap will be applied in all ODFs. If False
it will be applied individually at each voxel.
colormap : None or str
The name of the colormap to use. Matplotlib colormaps are supported
(e.g., 'inferno'). If None then a RGB colormap is used.
opacity : float
Takes values from 0 (fully transparent) to 1 (opaque).
affine : array
optional 4x4 transformation array from native
coordinates to world coordinates.
B : 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.
"""
@warn_on_args_to_kwargs()
def __init__(
self,
odfs,
vertices,
faces,
indices,
scale,
norm,
radial_scale,
shape,
global_cm,
colormap,
opacity,
*,
affine=None,
B=None,
):
self.vertices = vertices
self.faces = faces
self.odfs = odfs
self.indices = indices
self.B = B
self.radial_scale = radial_scale
self.colormap = colormap
self.grid_shape = shape
self.global_cm = global_cm
# declare a mask to be instantiated in slice_along_axis
self.mask = None
# If a B matrix is given, odfs are expected to
# be in SH basis coefficients.
if self.B is not None:
# In that case, we need to save our normalisation and scale
# to apply them after conversion from SH to SF.
self.norm = norm
self.scale = scale
else:
# If our input is in SF coefficients, we can normalise and
# scale it only once, here.
if norm:
self.odfs /= np.abs(self.odfs).max(axis=-1, keepdims=True)
self.odfs *= scale
# Compute world coordinates of an affine is supplied
self.affine = affine
if self.affine is not None:
self.w_verts = self.vertices.dot(affine[:3, :3])
self.w_pos = apply_affine(affine, np.asarray(self.indices).T)
# Initialize mapper and slice to the
# middle of the volume along Z axis
self.mapper = PolyDataMapper()
self.SetMapper(self.mapper)
self.slice_along_axis(self.grid_shape[-1] // 2)
self.set_opacity(opacity)
[docs]
def set_opacity(self, opacity):
"""Set opacity value of ODFs to display."""
self.GetProperty().SetOpacity(opacity)
[docs]
def display_extent(self, x1, x2, y1, y2, z1, z2):
"""Set visible volume from x1 (inclusive) to x2 (inclusive),
y1 (inclusive) to y2 (inclusive), z1 (inclusive) to z2
(inclusive).
"""
mask = np.zeros(self.grid_shape, dtype=bool)
mask[x1 : x2 + 1, y1 : y2 + 1, z1 : z2 + 1] = True
self.mask = mask
self._update_mapper()
[docs]
@warn_on_args_to_kwargs()
def slice_along_axis(self, slice_index, *, axis="zaxis"):
"""Slice ODF field at given `slice_index` along axis
in ['xaxis', 'yaxis', zaxis'].
"""
if axis == "xaxis":
self.display_extent(
slice_index,
slice_index,
0,
self.grid_shape[1] - 1,
0,
self.grid_shape[2] - 1,
)
elif axis == "yaxis":
self.display_extent(
0,
self.grid_shape[0] - 1,
slice_index,
slice_index,
0,
self.grid_shape[2] - 1,
)
elif axis == "zaxis":
self.display_extent(
0,
self.grid_shape[0] - 1,
0,
self.grid_shape[1] - 1,
slice_index,
slice_index,
)
else:
raise ValueError("Invalid axis name {0}.".format(axis))
[docs]
@warn_on_args_to_kwargs()
def display(self, *, x=None, y=None, z=None):
"""Display a slice along x, y, or z axis."""
if x is None and y is None and z is None:
self.slice_along_axis(self.grid_shape[2] // 2)
elif x is not None:
self.slice_along_axis(x, axis="xaxis")
elif y is not None:
self.slice_along_axis(y, axis="yaxis")
elif z is not None:
self.slice_along_axis(z, axis="zaxis")
[docs]
def update_sphere(self, vertices, faces, B):
"""Dynamically change the sphere used for SH to SF projection."""
if self.B is None:
raise ValueError("Can't update sphere when using " "SF coefficients.")
self.vertices = vertices
if self.affine is not None:
self.w_verts = self.vertices.dot(self.affine[:3, :3])
self.faces = faces
self.B = B
# draw ODFs with new sphere
self._update_mapper()
def _update_mapper(self):
"""Map vtkPolyData to the actor."""
polydata = PolyData()
offsets = self._get_odf_offsets(self.mask)
if len(offsets) == 0:
self.mapper.SetInputData(polydata)
return None
sph_dirs = self._get_sphere_directions()
sf = self._get_sf(self.mask)
all_vertices = self._get_all_vertices(offsets, sph_dirs, sf)
all_faces = self._get_all_faces(len(offsets), len(sph_dirs))
all_colors = self._generate_color_for_vertices(sf)
# TODO: There is a lot of deep copy here.
# Optimize (see viz_network.py example).
set_polydata_triangles(polydata, all_faces)
set_polydata_vertices(polydata, all_vertices)
set_polydata_colors(polydata, all_colors)
self.mapper.SetInputData(polydata)
def _get_odf_offsets(self, mask):
"""Get the position of non-zero voxels inside `mask`."""
if self.affine is not None:
return self.w_pos[mask[self.indices]]
return np.asarray(self.indices).T[mask[self.indices]]
def _get_sphere_directions(self):
"""Get the sphere directions onto which is projected the signal."""
if self.affine is not None:
return self.w_verts
return self.vertices
def _get_sf(self, mask):
"""Get SF coefficients inside `mask`."""
# when odfs are expressed in SH coefficients
if self.B is not None:
sf = self.odfs[mask[self.indices]].dot(self.B)
# normalisation and scaling is done on SF coefficients
if self.norm:
sf /= np.abs(sf).max(axis=-1, keepdims=True)
return sf * self.scale
# when odfs are in SF coefficients, the normalisation and scaling
# are done during initialisation. We simply return them:
return self.odfs[mask[self.indices]]
def _get_all_vertices(self, offsets, sph_dirs, sf):
"""Get array of all the vertices of the ODFs to display."""
if self.radial_scale:
# apply SF amplitudes to all sphere
# directions and offset each voxel
return np.tile(sph_dirs, (len(offsets), 1)) * sf.reshape(-1, 1) + np.repeat(
offsets, len(sph_dirs), axis=0
)
# return scaled spheres offsetted by `offsets`
return np.tile(sph_dirs, (len(offsets), 1)) * self.scale + np.repeat(
offsets, len(sph_dirs), axis=0
)
def _get_all_faces(self, nb_odfs, nb_dirs):
"""Get array of all the faces of the ODFs to display."""
return np.tile(self.faces, (nb_odfs, 1)) + np.repeat(
np.arange(nb_odfs) * nb_dirs, len(self.faces)
).reshape(-1, 1)
def _generate_color_for_vertices(self, sf):
"""Get array of all vertices colors."""
if self.global_cm:
if self.colormap is None:
raise IOError("if global_cm=True, colormap must be defined.")
else:
all_colors = create_colormap(sf.ravel(), name=self.colormap) * 255
elif self.colormap is not None:
if isinstance(self.colormap, str):
# Map ODFs values [min, max] to [0, 1] for each ODF
range_sf = sf.max(axis=-1) - sf.min(axis=-1)
rescaled = sf - sf.min(axis=-1, keepdims=True)
rescaled[range_sf > 0] /= range_sf[range_sf > 0][..., None]
all_colors = create_colormap(rescaled.ravel(), name=self.colormap) * 255
else:
all_colors = np.tile(
np.array(self.colormap).reshape(1, 3),
(sf.shape[0] * sf.shape[1], 1),
)
else:
all_colors = np.tile(np.abs(self.vertices) * 255, (len(sf), 1))
return all_colors.astype(np.uint8)
