def repeat_sources(centers,
colors,
active_scalars=1.,
directions=None,
source=None,
vertices=None,
faces=None,
orientation=None):
"""Transform a vtksource to glyph."""
if source is None and faces is None:
raise IOError("A source or faces should be defined")
if np.array(colors).ndim == 1:
colors = np.tile(colors, (len(centers), 1))
pts = numpy_to_vtk_points(np.ascontiguousarray(centers))
cols = numpy_to_vtk_colors(255 * np.ascontiguousarray(colors))
cols.SetName('colors')
if isinstance(active_scalars, (float, int)):
active_scalars = np.tile(active_scalars, (len(centers), 1))
if isinstance(active_scalars, np.ndarray):
ascalars = numpy_support.numpy_to_vtk(np.asarray(active_scalars),
deep=True,
array_type=VTK_DOUBLE)
ascalars.SetName('active_scalars')
if directions is not None:
directions_fa = numpy_support.numpy_to_vtk(np.asarray(directions),
deep=True,
array_type=VTK_DOUBLE)
directions_fa.SetName('directions')
polydata_centers = PolyData()
polydata_geom = PolyData()
if faces is not None:
set_polydata_vertices(polydata_geom, vertices)
set_polydata_triangles(polydata_geom, faces)
polydata_centers.SetPoints(pts)
polydata_centers.GetPointData().AddArray(cols)
if directions is not None:
polydata_centers.GetPointData().AddArray(directions_fa)
polydata_centers.GetPointData().SetActiveVectors('directions')
if isinstance(active_scalars, np.ndarray):
polydata_centers.GetPointData().AddArray(ascalars)
polydata_centers.GetPointData().SetActiveScalars('active_scalars')
glyph = Glyph3D()
if faces is None:
if orientation is not None:
transform = Transform()
transform.SetMatrix(numpy_to_vtk_matrix(orientation))
rtrans = TransformPolyDataFilter()
rtrans.SetInputConnection(source.GetOutputPort())
rtrans.SetTransform(transform)
source = rtrans
glyph.SetSourceConnection(source.GetOutputPort())
else:
glyph.SetSourceData(polydata_geom)
glyph.SetInputData(polydata_centers)
glyph.SetOrient(True)
glyph.SetScaleModeToScaleByScalar()
glyph.SetVectorModeToUseVector()
glyph.Update()
mapper = PolyDataMapper()
mapper.SetInputData(glyph.GetOutput())
mapper.SetScalarModeToUsePointFieldData()
mapper.SelectColorArray('colors')
actor = Actor()
actor.SetMapper(mapper)
return actor
class PeakActor(Actor):
"""VTK actor for visualizing slices of ODF field.
Parameters
----------
directions : ndarray
Peak directions. The shape of the array should be (X, Y, Z, D, 3).
indices : tuple
Indices given in tuple(x_indices, y_indices, z_indices)
format for mapping 2D ODF array to 3D voxel grid.
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.
colors : None or string ('rgb_standard') or tuple (3D or 4D) or
array/ndarray (N, 3 or 4) or array/ndarray (K, 3 or 4) or
array/ndarray(N, ) or array/ndarray (K, )
If None a standard orientation colormap is used for every line.
If one tuple of color is used. Then all streamlines will have the same
color.
If an array (N, 3 or 4) is given, where N is equal to the number of
points. Then every point is colored with a different RGB(A) color.
If an array (K, 3 or 4) is given, where K is equal to the number of
lines. Then every line is colored with a different RGB(A) color.
If an array (N, ) is given, where N is the number of points then these
are considered as the values to be used by the colormap.
If an array (K,) is given, where K is the number of lines then these
are considered as the values to be used by the colormap.
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.
"""
def __init__(self,
directions,
indices,
values=None,
affine=None,
colors=None,
lookup_colormap=None,
linewidth=1,
symmetric=True):
if affine is not None:
w_pos = apply_affine(affine, np.asarray(indices).T)
valid_dirs = directions[indices]
num_dirs = len(np.nonzero(np.abs(valid_dirs).max(axis=-1) > 0)[0])
pnts_per_line = 2
points_array = np.empty((num_dirs * pnts_per_line, 3))
centers_array = np.empty_like(points_array, dtype=int)
diffs_array = np.empty_like(points_array)
line_count = 0
for idx, center in enumerate(zip(indices[0], indices[1], indices[2])):
if affine is None:
xyz = np.asarray(center)
else:
xyz = w_pos[idx, :]
valid_peaks = np.nonzero(
np.abs(valid_dirs[idx, :, :]).max(axis=-1) > 0.)[0]
for direction in valid_peaks:
if values is not None:
pv = values[center][direction]
else:
pv = 1.
if symmetric:
point_i = directions[center][direction] * pv + xyz
point_e = -directions[center][direction] * pv + xyz
else:
point_i = directions[center][direction] * pv + xyz
point_e = xyz
diff = point_e - point_i
points_array[line_count * pnts_per_line, :] = point_e
points_array[line_count * pnts_per_line + 1, :] = point_i
centers_array[line_count * pnts_per_line, :] = center
centers_array[line_count * pnts_per_line + 1, :] = center
diffs_array[line_count * pnts_per_line, :] = diff
diffs_array[line_count * pnts_per_line + 1, :] = diff
line_count += 1
vtk_points = numpy_to_vtk_points(points_array)
vtk_cells = _points_to_vtk_cells(points_array)
colors_tuple = _peaks_colors_from_points(points_array, colors=colors)
vtk_colors, colors_are_scalars, self.__global_opacity = colors_tuple
poly_data = PolyData()
poly_data.SetPoints(vtk_points)
poly_data.SetLines(vtk_cells)
poly_data.GetPointData().SetScalars(vtk_colors)
self.__mapper = PolyDataMapper()
self.__mapper.SetInputData(poly_data)
self.__mapper.ScalarVisibilityOn()
self.__mapper.SetScalarModeToUsePointFieldData()
self.__mapper.SelectColorArray('colors')
self.__mapper.Update()
self.SetMapper(self.__mapper)
attribute_to_actor(self, centers_array, 'center')
attribute_to_actor(self, diffs_array, 'diff')
vs_dec_code = import_fury_shader('peak_dec.vert')
vs_impl_code = import_fury_shader('peak_impl.vert')
fs_dec_code = import_fury_shader('peak_dec.frag')
fs_impl_code = import_fury_shader('peak_impl.frag')
shader_to_actor(self,
'vertex',
decl_code=vs_dec_code,
impl_code=vs_impl_code)
shader_to_actor(self, 'fragment', decl_code=fs_dec_code)
shader_to_actor(self,
'fragment',
impl_code=fs_impl_code,
block='light')
# Color scale with a lookup table
if colors_are_scalars:
if lookup_colormap is None:
lookup_colormap = colormap_lookup_table()
self.__mapper.SetLookupTable(lookup_colormap)
self.__mapper.UseLookupTableScalarRangeOn()
self.__mapper.Update()
self.__lw = linewidth
self.GetProperty().SetLineWidth(self.__lw)
if self.__global_opacity >= 0:
self.GetProperty().SetOpacity(self.__global_opacity)
self.__min_centers = np.min(indices, axis=1)
self.__max_centers = np.max(indices, axis=1)
self.__is_range = True
self.__low_ranges = self.__min_centers
self.__high_ranges = self.__max_centers
self.__cross_section = self.__high_ranges // 2
self.__mapper.AddObserver(Command.UpdateShaderEvent,
self.__display_peaks_vtk_callback)
@calldata_type(VTK_OBJECT)
def __display_peaks_vtk_callback(self, caller, event, calldata=None):
if calldata is not None:
calldata.SetUniformi('isRange', self.__is_range)
calldata.SetUniform3f('highRanges', self.__high_ranges)
calldata.SetUniform3f('lowRanges', self.__low_ranges)
calldata.SetUniform3f('crossSection', self.__cross_section)
def display_cross_section(self, x, y, z):
if self.__is_range:
self.__is_range = False
self.__cross_section = [x, y, z]
def display_extent(self, x1, x2, y1, y2, z1, z2):
if not self.__is_range:
self.__is_range = True
self.__low_ranges = [x1, y1, z1]
self.__high_ranges = [x2, y2, z2]
@property
def cross_section(self):
return self.__cross_section
@property
def global_opacity(self):
return self.__global_opacity
@global_opacity.setter
def global_opacity(self, opacity):
self.__global_opacity = opacity
self.GetProperty().SetOpacity(self.__global_opacity)
@property
def high_ranges(self):
return self.__high_ranges
@property
def is_range(self):
return self.__is_range
@property
def low_ranges(self):
return self.__low_ranges
@property
def linewidth(self):
return self.__lw
@linewidth.setter
def linewidth(self, linewidth):
self.__lw = linewidth
self.GetProperty().SetLineWidth(self.__lw)
@property
def max_centers(self):
return self.__max_centers
@property
def min_centers(self):
return self.__min_centers