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 = vtk.vtkLookupTable()
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 = vtk.vtkScalarBarActor()
scalar_bar.SetTitle(title)
scalar_bar.SetLookupTable(lookup_table_copy)
scalar_bar.SetNumberOfLabels(6)
return scalar_bar
def __init__(self,
directions,
indices,
values=None,
affine=None,
colors=None,
lookup_colormap=None,
linewidth=1):
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.
point_i = directions[center][direction] * pv + xyz
point_e = -directions[center][direction] * pv + 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 = vtk.vtkPolyData()
poly_data.SetPoints(vtk_points)
poly_data.SetLines(vtk_cells)
poly_data.GetPointData().SetScalars(vtk_colors)
self.__mapper = vtk.vtkPolyDataMapper()
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 = load('peak_dec.vert')
vs_impl_code = load('peak_impl.vert')
fs_dec_code = load('peak_dec.frag')
fs_impl_code = load('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(vtk.vtkCommand.UpdateShaderEvent,
self.__display_peaks_vtk_callback)
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):
"""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,), None
If None then 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, ) 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
Takes values from 0 (fully transparent) to 1 (opaque). Default is 1.
linewidth : float
Default is 0.01.
tube_sides : int
Default is 9.
lod : bool
Use vtkLODActor(level of detail) rather than vtkActor. Default is True.
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.
spline_subdiv : int
Number of splines subdivision to smooth streamtubes. Default is None.
lookup_colormap : vtkLookupTable
Add a default lookup table to the colormap. Default is None which calls
:func:`fury.actor.colormap_lookup_table`.
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)
>>> 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, is_colormap = lines_to_vtk_polydata(lines, colors)
next_input = poly_data
# Set Normals
poly_normals = set_input(vtk.vtkPolyDataNormals(), 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(vtk.vtkSplineFilter(), 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(vtk.vtkTubeFilter(), 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(vtk.vtkPolyDataMapper(), next_input)
poly_mapper.ScalarVisibilityOn()
poly_mapper.SetScalarModeToUsePointFieldData()
poly_mapper.SelectColorArray("Colors")
poly_mapper.Update()
# Color Scale with a lookup table
if is_colormap:
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 = vtk.vtkLODActor()
actor.SetNumberOfCloudPoints(lod_points)
actor.GetProperty().SetPointSize(lod_points_size)
else:
actor = vtk.vtkActor()
actor.SetMapper(poly_mapper)
actor.GetProperty().SetInterpolationToPhong()
actor.GetProperty().BackfaceCullingOn()
actor.GetProperty().SetOpacity(opacity)
return actor
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):
""" Create an actor for one or more lines.
Parameters
------------
lines : list of arrays
colors : array (N, 3), list of arrays, tuple (3,), array (K,), None
If None then 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, ) 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
Use vtkLODActor(level of detail) rather than vtkActor. Default is True.
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.
lookup_colormap : bool, optional
Add a default lookup table to the colormap. Default is None which calls
:func:`fury.actor.colormap_lookup_table`.
Returns
----------
v : vtkActor or vtkLODActor 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)
>>> scene.add(c)
>>> #window.show(scene)
"""
# Poly data with lines and colors
poly_data, is_colormap = lines_to_vtk_polydata(lines, colors)
next_input = poly_data
# use spline interpolation
if (spline_subdiv is not None) and (spline_subdiv > 0):
spline_filter = set_input(vtk.vtkSplineFilter(), next_input)
spline_filter.SetSubdivideToSpecified()
spline_filter.SetNumberOfSubdivisions(spline_subdiv)
spline_filter.Update()
next_input = spline_filter.GetOutputPort()
poly_mapper = set_input(vtk.vtkPolyDataMapper(), next_input)
poly_mapper.ScalarVisibilityOn()
poly_mapper.SetScalarModeToUsePointFieldData()
poly_mapper.SelectColorArray("Colors")
poly_mapper.Update()
# Color Scale with a lookup table
if is_colormap:
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 = vtk.vtkLODActor()
actor.SetNumberOfCloudPoints(lod_points)
actor.GetProperty().SetPointSize(lod_points_size)
else:
actor = vtk.vtkActor()
# actor = vtk.vtkActor()
actor.SetMapper(poly_mapper)
actor.GetProperty().SetLineWidth(linewidth)
actor.GetProperty().SetOpacity(opacity)
return actor
def slicer(data,
affine=None,
value_range=None,
opacity=1.,
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.
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
If None (default) then a grayscale map is created.
interpolation : string
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
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 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
if value_range is None:
vol = np.interp(data, xp=[data.min(), data.max()], fp=[0, 255])
else:
vol = np.interp(data, xp=[value_range[0], value_range[1]], fp=[0, 255])
vol = vol.astype('uint8')
im = vtk.vtkImageData()
I, J, K = vol.shape[:3]
im.SetDimensions(I, J, K)
voxsz = (1., 1., 1.)
# im.SetOrigin(0,0,0)
im.SetSpacing(voxsz[2], voxsz[0], voxsz[1])
im.AllocateScalars(vtk.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 = vtk.vtkTransform()
transform_matrix = vtk.vtkMatrix4x4()
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 = vtk.vtkImageReslice()
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()
ex1, ex2, ey1, ey2, ez1, ez2 = image_resliced.GetOutput().GetExtent()
class ImageActor(vtk.vtkImageActor):
def __init__(self):
self.picker = vtk.vtkCellPicker()
def input_connection(self, output):
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()
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 opacity(self, value):
self.GetProperty().SetOpacity(value)
def tolerance(self, value):
self.picker.SetTolerance(value)
def copy(self):
im_actor = ImageActor()
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
image_actor = ImageActor()
if nb_components == 1:
lut = lookup_colormap
if lookup_colormap is None:
# Create a black/white lookup table.
lut = colormap_lookup_table((0, 255), (0, 0), (0, 0), (0, 1))
plane_colors = vtk.vtkImageMapToColors()
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
