def show_gradients(gtab):
renderer = window.Renderer()
renderer.add(fvtk.point(gtab.gradients, (1,0,0), point_radius=100))
renderer.add(fvtk.point(-gtab.gradients, (1,0,0), point_radius=100))
window.show(renderer)
def visualize(fibers, outf=None):
"""
Takes fiber streamlines and visualizes them using DiPy
Required Arguments:
- fibers:
fiber streamlines in a list as returned by DiPy
Optional Arguments:
- save:
flag indicating whether or not you want the image saved
to disk after being displayed
"""
# Initialize renderer
renderer = window.Renderer()
# Add streamlines as a DiPy viz object
stream_actor = actor.line(fibers)
# Set camera orientation properties
# TODO: allow this as an argument
renderer.set_camera() # args are: position=(), focal_point=(), view_up=()
# Add streamlines to viz session
renderer.add(stream_actor)
# Display fibers
# TODO: allow size of window as an argument
window.show(renderer, size=(600, 600), reset_camera=False)
# Saves file, if you're into that sort of thing...
if outf is not None:
window.record(renderer, out_path=outf, size=(600, 600))
def simple_viewer(streamlines, vol, affine):
from dipy.viz import actor, window
renderer = window.Renderer()
renderer.add(actor.line(streamlines))
renderer.add(actor.slicer(vol, affine))
window.show(renderer)
def test_peak_slicer(interactive=False):
_peak_dirs = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype='f4')
# peak_dirs.shape = (1, 1, 1) + peak_dirs.shape
peak_dirs = np.zeros((11, 11, 11, 3, 3))
peak_values = np.random.rand(11, 11, 11, 3)
peak_dirs[:, :, :] = _peak_dirs
renderer = window.Renderer()
peak_actor = actor.peak_slicer(peak_dirs)
renderer.add(peak_actor)
renderer.add(actor.axes((11, 11, 11)))
if interactive:
window.show(renderer)
renderer.clear()
renderer.add(peak_actor)
renderer.add(actor.axes((11, 11, 11)))
for k in range(11):
peak_actor.display_extent(0, 10, 0, 10, k, k)
for j in range(11):
peak_actor.display_extent(0, 10, j, j, 0, 10)
for i in range(11):
peak_actor.display(i, None, None)
renderer.rm_all()
peak_actor = actor.peak_slicer(
peak_dirs,
peak_values,
mask=None,
affine=np.diag([3, 2, 1, 1]),
colors=None,
opacity=1,
linewidth=3,
lod=True,
lod_points=10 ** 4,
lod_points_size=3)
renderer.add(peak_actor)
renderer.add(actor.axes((11, 11, 11)))
if interactive:
window.show(renderer)
report = window.analyze_renderer(renderer)
ex = ['vtkLODActor', 'vtkOpenGLActor', 'vtkOpenGLActor', 'vtkOpenGLActor']
npt.assert_equal(report.actors_classnames, ex)
def test_labels(interactive=False):
text_actor = actor.label("Hello")
renderer = window.Renderer()
renderer.add(text_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer, reset_camera=False)
npt.assert_equal(renderer.GetActors().GetNumberOfItems(), 1)
def show_both_bundles(bundles, colors=None, show=True, fname=None):
ren = window.Renderer()
ren.SetBackground(1., 1, 1)
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines_actor = actor.streamtube(bundle, color, linewidth=0.3)
lines_actor.RotateX(-90)
lines_actor.RotateZ(90)
ren.add(lines_actor)
if show:
window.show(ren)
if fname is not None:
sleep(1)
window.record(ren, n_frames=1, out_path=fname, size=(900, 900))
def show_two_images(vol1, affine1, vol2, affine2, shift=50):
""" Show 2 images side by side"""
renderer = window.Renderer()
mean, std = vol1[vol1 > 0].mean(), vol1[vol1 > 0].std()
value_range1 = (mean - 0.5 * std, mean + 1.5 * std)
mean, std = vol2[vol2 > 0].mean(), vol2[vol2 > 0].std()
value_range2 = (mean - 0.5 * std, mean + 1.5 * std)
slice_actor1 = actor.slicer(vol1, affine1, value_range1)
slice_actor2 = actor.slicer(vol2, affine2, value_range2)
renderer.add(slice_actor1)
renderer.add(slice_actor2)
slice_actor2.SetPosition(slice_actor1.shape[0] + shift, 0, 0)
window.show(renderer)
def show_bundles(bundles, colors=None, size=(1080, 600),
show=False, fname=None):
ren = window.Renderer()
ren.background((1., 1, 1))
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines = actor.line(bundle, color, linewidth=1.5)
ren.add(lines)
ren.reset_clipping_range()
ren.reset_camera()
# if show:
window.show(ren, size=size, reset_camera=True)
if fname is not None:
window.record(ren, n_frames=1, out_path=fname, size=size)
def test_points(interactive=False):
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
points_actor = actor.point(points, colors)
renderer = window.Renderer()
renderer.add(points_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer, reset_camera=False)
npt.assert_equal(renderer.GetActors().GetNumberOfItems(), 1)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=colors)
npt.assert_equal(report.objects, 3)
def show_mosaic(data, affine, border=70):
""" Show a simple mosaic of the given image
"""
renderer = window.Renderer()
mean, std = data[data > 0].mean(), data[data > 0].std()
value_range = (mean - 0.5 * std, mean + 1.5 * std)
slice_actor = actor.slicer(data, affine, value_range)
renderer.clear()
renderer.projection('parallel')
cnt = 0
X, Y, Z = slice_actor.shape[:3]
rows = 10
cols = 15
border = 70
for j in range(rows):
for i in range(cols):
slice_mosaic = slice_actor.copy()
slice_mosaic.display(None, None, cnt)
slice_mosaic.SetPosition(
(X + border) * i,
0.5 * cols * (Y + border) - (Y + border) * j,
0)
renderer.add(slice_mosaic)
cnt += 1
if cnt > Z:
break
if cnt > Z:
break
renderer.reset_camera()
renderer.zoom(1.6)
window.show(renderer, size=(900, 600), reset_camera=False)
def test_dots(interactive=False):
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
dots_actor = actor.dots(points, color=(0, 255, 0))
renderer = window.Renderer()
renderer.add(dots_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer, reset_camera=False)
npt.assert_equal(renderer.GetActors().GetNumberOfItems(), 1)
extent = renderer.GetActors().GetLastActor().GetBounds()
npt.assert_equal(extent, (0.0, 1.0, 0.0, 1.0, 0.0, 0.0))
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=(0, 255, 0))
npt.assert_equal(report.objects, 3)
# Test one point
points = np.array([0, 0, 0])
dot_actor = actor.dots(points, color=(0, 0, 255))
renderer.clear()
renderer.add(dot_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=(0, 0, 255))
npt.assert_equal(report.objects, 1)
def simple_viewer(streamlines, vol, affine):
renderer = window.Renderer()
renderer.add(actor.line(streamlines))
renderer.add(actor.slicer(vol, affine))
window.show(renderer)
n = len(vert_list)
vert_list.append([a * np.sin(np.deg2rad(v)), 0.0, z_new])
vert_list.append([0.0, b * np.sin(np.deg2rad(v)), z_new])
vert_list.append([-1 * a * np.sin(np.deg2rad(v)), 0.0, z_new])
vert_list.append([0.0, -1 * b * np.sin(np.deg2rad(v)), z_new])
edge_list.append([n - 4, n, n - 3])
edge_list.append([n, n + 1, n - 3])
edge_list.append([n - 3, n + 1, n - 2])
edge_list.append([n + 1, n + 2, n - 2])
edge_list.append([n - 2, n + 2, n - 1])
edge_list.append([n + 2, n + 3, n - 1])
edge_list.append([n - 1, n + 3, n - 4])
edge_list.append([n + 3, n, n - 4])
my_vertices = np.array(vert_list)
my_triangles = np.array(edge_list)
ut_vtk.set_polydata_vertices(my_polydata, my_vertices)
ut_vtk.set_polydata_triangles(my_polydata, my_triangles.astype('i8'))
sphere_vertices = ut_vtk.get_polydata_vertices(my_polydata)
colors = sphere_vertices * 255
ut_vtk.set_polydata_colors(my_polydata, colors)
sphere_actor = ut_vtk.get_actor_from_polydata(my_polydata)
# renderer and scene
renderer = window.Renderer()
renderer.add(sphere_actor)
window.show(renderer, size=(600, 600), reset_camera=False)
ren = window.Renderer()
evals = response[0]
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
response_odf = single_tensor_odf(default_sphere.vertices, evals, evecs)
# transform our data from 1D to 4D
response_odf = response_odf[None, None, None, :]
response_actor = actor.odf_slicer(response_odf,
sphere=default_sphere,
colormap='plasma')
ren.add(response_actor)
print('Saving illustration as csd_response.png')
window.record(ren, out_path='csd_response.png', size=(200, 200))
if interactive:
window.show(ren)
"""
.. figure:: csd_response.png
:align: center
Estimated response function.
"""
ren.rm(response_actor)
"""
**Strategy 2 - data-driven calibration of response function** Depending
on the dataset, FA threshold may not be the best way to find the best possible
response function. For one, it depends on the diffusion tensor
(FA and first eigenvector), which has lower accuracy at high
b-values. Alternatively, the response function can be calibrated in a
print(mcsd_odf.shape)
print(mcsd_odf[40, 40, 0])
fodf_spheres = actor.odf_slicer(mcsd_odf, sphere=sphere, scale=1,
norm=False, colormap='plasma')
interactive = False
scene = window.Scene()
scene.add(fodf_spheres)
scene.reset_camera_tight()
print('Saving illustration as msdodf.png')
window.record(scene, out_path='msdodf.png', size=(600, 600))
if interactive:
window.show(scene)
"""
.. figure:: msdodf.png
:align: center
MSMT-CSD Peaks and ODFs.
References
----------
.. [Jeurissen2014] B. Jeurissen, et al., "Multi-tissue constrained spherical
deconvolution for improved analysis of multi-shell
diffusion MRI data." NeuroImage 103 (2014): 411-426.
.. [Tournier2007] J-D. Tournier, F. Calamante and A. Connelly, "Robust
vol_actor2.display(z=35)
# Add display objects to canvas
r = window.Renderer()
r.add(vol_actor)
r.add(vol_actor2)
r.add(cc_streamlines_actor)
r.add(cc_ROI_actor)
# Save figures
window.record(r,
n_frames=1,
out_path='corpuscallosum_axial.png',
size=(800, 800))
if interactive:
window.show(r)
r.set_camera(position=[-1, 0, 0], focal_point=[0, 0, 0], view_up=[0, 0, 1])
window.record(r,
n_frames=1,
out_path='corpuscallosum_sagittal.png',
size=(800, 800))
if interactive:
window.show(r)
"""
.. figure:: corpuscallosum_axial.png
:align: center
**Corpus Callosum Axial**
.. include:: ../links_names.inc
def test_tensor_slicer(interactive=False):
evals = np.array([1.4, .35, .35]) * 10**(-3)
evecs = np.eye(3)
mevals = np.zeros((3, 2, 4, 3))
mevecs = np.zeros((3, 2, 4, 3, 3))
mevals[..., :] = evals
mevecs[..., :, :] = evecs
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
affine = np.eye(4)
renderer = window.Renderer()
tensor_actor = actor.tensor_slicer(mevals,
mevecs,
affine=affine,
sphere=sphere,
scale=.3)
I, J, K = mevals.shape[:3]
renderer.add(tensor_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
tensor_actor.display_extent(0, 1, 0, J, 0, K)
tensor_actor.GetProperty().SetOpacity(1.0)
if interactive:
window.show(renderer, reset_camera=False)
npt.assert_equal(renderer.GetActors().GetNumberOfItems(), 1)
# Test extent
big_extent = renderer.GetActors().GetLastActor().GetBounds()
big_extent_x = abs(big_extent[1] - big_extent[0])
tensor_actor.display(x=2)
if interactive:
window.show(renderer, reset_camera=False)
small_extent = renderer.GetActors().GetLastActor().GetBounds()
small_extent_x = abs(small_extent[1] - small_extent[0])
npt.assert_equal(big_extent_x > small_extent_x, True)
# Test empty mask
empty_actor = actor.tensor_slicer(mevals,
mevecs,
affine=affine,
mask=np.zeros(mevals.shape[:3]),
sphere=sphere,
scale=.3)
npt.assert_equal(empty_actor.GetMapper(), None)
# Test mask
mask = np.ones(mevals.shape[:3])
mask[:2, :3, :3] = 0
cfa = color_fa(fractional_anisotropy(mevals), mevecs)
tensor_actor = actor.tensor_slicer(mevals,
mevecs,
affine=affine,
mask=mask,
scalar_colors=cfa,
sphere=sphere,
scale=.3)
renderer.clear()
renderer.add(tensor_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer, reset_camera=False)
mask_extent = renderer.GetActors().GetLastActor().GetBounds()
mask_extent_x = abs(mask_extent[1] - mask_extent[0])
npt.assert_equal(big_extent_x > mask_extent_x, True)
# test display
tensor_actor.display()
current_extent = renderer.GetActors().GetLastActor().GetBounds()
current_extent_x = abs(current_extent[1] - current_extent[0])
npt.assert_equal(big_extent_x > current_extent_x, True)
if interactive:
window.show(renderer, reset_camera=False)
tensor_actor.display(y=1)
current_extent = renderer.GetActors().GetLastActor().GetBounds()
current_extent_y = abs(current_extent[3] - current_extent[2])
big_extent_y = abs(big_extent[3] - big_extent[2])
npt.assert_equal(big_extent_y > current_extent_y, True)
if interactive:
window.show(renderer, reset_camera=False)
tensor_actor.display(z=1)
current_extent = renderer.GetActors().GetLastActor().GetBounds()
current_extent_z = abs(current_extent[5] - current_extent[4])
big_extent_z = abs(big_extent[5] - big_extent[4])
npt.assert_equal(big_extent_z > current_extent_z, True)
if interactive:
window.show(renderer, reset_camera=False)
def test_odf_slicer(interactive=False):
sphere = get_sphere('symmetric362')
shape = (11, 11, 11, sphere.vertices.shape[0])
fid, fname = mkstemp(suffix='_odf_slicer.mmap')
print(fid)
print(fname)
odfs = np.memmap(fname, dtype=np.float64, mode='w+', shape=shape)
odfs[:] = 1
affine = np.eye(4)
renderer = window.Renderer()
mask = np.ones(odfs.shape[:3])
mask[:4, :4, :4] = 0
odfs[..., 0] = 1
odf_actor = actor.odf_slicer(odfs,
affine,
mask=mask,
sphere=sphere,
scale=.25,
colormap='jet')
fa = 0. * np.zeros(odfs.shape[:3])
fa[:, 0, :] = 1.
fa[:, -1, :] = 1.
fa[0, :, :] = 1.
fa[-1, :, :] = 1.
fa[5, 5, 5] = 1
k = 5
I, J, K = odfs.shape[:3]
fa_actor = actor.slicer(fa, affine)
fa_actor.display_extent(0, I, 0, J, k, k)
renderer.add(odf_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
odf_actor.display_extent(0, I, 0, J, k, k)
odf_actor.GetProperty().SetOpacity(1.0)
if interactive:
window.show(renderer, reset_camera=False)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr, find_objects=True)
npt.assert_equal(report.objects, 11 * 11)
renderer.clear()
renderer.add(fa_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer)
mask[:] = 0
mask[5, 5, 5] = 1
fa[5, 5, 5] = 0
fa_actor = actor.slicer(fa, None)
fa_actor.display(None, None, 5)
odf_actor = actor.odf_slicer(odfs,
None,
mask=mask,
sphere=sphere,
scale=.25,
colormap='jet',
norm=False,
global_cm=True)
renderer.clear()
renderer.add(fa_actor)
renderer.add(odf_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer)
renderer.clear()
renderer.add(odf_actor)
renderer.add(fa_actor)
odfs[:, :, :] = 1
mask = np.ones(odfs.shape[:3])
odf_actor = actor.odf_slicer(odfs,
None,
mask=mask,
sphere=sphere,
scale=.25,
colormap='jet',
norm=False,
global_cm=True)
renderer.clear()
renderer.add(odf_actor)
renderer.add(fa_actor)
renderer.add(actor.axes((11, 11, 11)))
for i in range(11):
odf_actor.display(i, None, None)
fa_actor.display(i, None, None)
if interactive:
window.show(renderer)
for j in range(11):
odf_actor.display(None, j, None)
fa_actor.display(None, j, None)
if interactive:
window.show(renderer)
# with mask equal to zero everything should be black
mask = np.zeros(odfs.shape[:3])
odf_actor = actor.odf_slicer(odfs,
None,
mask=mask,
sphere=sphere,
scale=.25,
colormap='plasma',
norm=False,
global_cm=True)
renderer.clear()
renderer.add(odf_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors, 1)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
del odf_actor
odfs._mmap.close()
del odfs
os.close(fid)
os.remove(fname)
def test_tensor_slicer(interactive=False):
evals = np.array([1.4, .35, .35]) * 10 ** (-3)
evecs = np.eye(3)
mevals = np.zeros((3, 2, 4, 3))
mevecs = np.zeros((3, 2, 4, 3, 3))
mevals[..., :] = evals
mevecs[..., :, :] = evecs
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
affine = np.eye(4)
renderer = window.Renderer()
tensor_actor = actor.tensor_slicer(mevals, mevecs, affine=affine,
sphere=sphere, scale=.3)
I, J, K = mevals.shape[:3]
renderer.add(tensor_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
tensor_actor.display_extent(0, 1, 0, J, 0, K)
tensor_actor.GetProperty().SetOpacity(1.0)
if interactive:
window.show(renderer, reset_camera=False)
npt.assert_equal(renderer.GetActors().GetNumberOfItems(), 1)
# Test extent
big_extent = renderer.GetActors().GetLastActor().GetBounds()
big_extent_x = abs(big_extent[1] - big_extent[0])
tensor_actor.display(x=2)
if interactive:
window.show(renderer, reset_camera=False)
small_extent = renderer.GetActors().GetLastActor().GetBounds()
small_extent_x = abs(small_extent[1] - small_extent[0])
npt.assert_equal(big_extent_x > small_extent_x, True)
# Test empty mask
empty_actor = actor.tensor_slicer(mevals, mevecs, affine=affine,
mask=np.zeros(mevals.shape[:3]),
sphere=sphere, scale=.3)
npt.assert_equal(empty_actor.GetMapper(), None)
# Test mask
mask = np.ones(mevals.shape[:3])
mask[:2, :3, :3] = 0
cfa = color_fa(fractional_anisotropy(mevals), mevecs)
tensor_actor = actor.tensor_slicer(mevals, mevecs, affine=affine, mask=mask,
scalar_colors=cfa, sphere=sphere, scale=.3)
renderer.clear()
renderer.add(tensor_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer, reset_camera=False)
mask_extent = renderer.GetActors().GetLastActor().GetBounds()
mask_extent_x = abs(mask_extent[1] - mask_extent[0])
npt.assert_equal(big_extent_x > mask_extent_x, True)
# test display
tensor_actor.display()
current_extent = renderer.GetActors().GetLastActor().GetBounds()
current_extent_x = abs(current_extent[1] - current_extent[0])
npt.assert_equal(big_extent_x > current_extent_x, True)
if interactive:
window.show(renderer, reset_camera=False)
tensor_actor.display(y=1)
current_extent = renderer.GetActors().GetLastActor().GetBounds()
current_extent_y = abs(current_extent[3] - current_extent[2])
big_extent_y = abs(big_extent[3] - big_extent[2])
npt.assert_equal(big_extent_y > current_extent_y, True)
if interactive:
window.show(renderer, reset_camera=False)
tensor_actor.display(z=1)
current_extent = renderer.GetActors().GetLastActor().GetBounds()
current_extent_z = abs(current_extent[5] - current_extent[4])
big_extent_z = abs(big_extent[5] - big_extent[4])
npt.assert_equal(big_extent_z > current_extent_z, True)
if interactive:
window.show(renderer, reset_camera=False)
polydata_in = load_polydata(fib_file_name)
streamlines_in = get_streamlines(polydata_in)
streamlines = []
for line in streamlines_in:
dist = line[:-1] - line[1:]
line_length = np.sum(np.sqrt(np.sum(np.square(dist), axis=1)))
if line_length > min_length:
streamlines.append(line)
#streamlines_sub = streamlines
streamlines_sub = streamlines[::100]
print len(streamlines_in), len(streamlines_sub)
actor = streamtube(streamlines_sub, linewidth=linewidth, tube_sides=tube_sides, spline_subdiv=spline_subdiv)
renderer = window.Renderer()
renderer.add(actor)
my_window = window.show(renderer)
#objexporter = vtk.vtkOBJExporter()
#objexporter.SetInput(my_window)
#objexporter.SetFileName(save_file)
#objexporter.SetFileName("/home/eti/home_mint/Nic/s100_s100_tube_flow.obj")
#objexporter.Write()
#save_polydata(actor.GetMapper().GetInput(), save_file)
"""
seeds = random_seeds_from_mask(fa > 0.3, seeds_count=1)
"""
For quality assurance we can also visualize a slice from the direction field
which we will use as the basis to perform the tracking.
"""
ren = window.Renderer()
ren.add(actor.peak_slicer(csd_peaks.peak_dirs,
csd_peaks.peak_values,
colors=None))
if interactive:
window.show(ren, size=(900, 900))
else:
window.record(ren, out_path='csd_direction_field.png', size=(900, 900))
"""
.. figure:: csd_direction_field.png
:align: center
**Direction Field (peaks)**
``EuDX`` [Garyfallidis12]_ is a fast algorithm that we use here to generate
streamlines. This algorithm is what is used here and the default option
when providing the output of peaks directly in LocalTracking.
"""
streamline_generator = LocalTracking(csd_peaks, tissue_classifier,
"""
`actor.line` creates a streamline actor for streamline visualization
and `ren.add` adds this actor to the scene
"""
ren.add(actor.streamtube(tensor_streamlines, line_colors(tensor_streamlines)))
print('Saving illustration as tensor_tracks.png')
ren.SetBackground(1, 1, 1)
window.record(ren, out_path='tensor_tracks.png', size=(600, 600))
# Enables/disables interactive visualization
interactive = False
if interactive:
window.show(ren)
"""
.. figure:: tensor_tracks.png
:align: center
Deterministic streamlines with EuDX on a Tensor Field.
References
----------
.. [Garyfallidis12] Garyfallidis E., "Towards an accurate brain tractography",
PhD thesis, University of Cambridge, 2012.
.. include:: ../links_names.inc
def show_image(data, affine=None):
renderer = window.Renderer()
slicer = actor.slicer(data, affine)
renderer.add(slicer)
window.show(renderer)
be done using the ``fury`` python package
"""
from dipy.viz import window, actor, has_fury
if has_fury:
scene = window.Scene()
scene.add(
actor.peak_slicer(csa_peaks.peak_dirs,
csa_peaks.peak_values,
colors=None))
window.record(scene, out_path='csa_direction_field.png', size=(900, 900))
if interactive:
window.show(scene, size=(800, 800))
"""
.. figure:: csa_direction_field.png
:align: center
**Direction Field (peaks)**
"""
"""
2. Next we need some way of restricting the fiber tracking to areas with good
directionality information. We've already created the white matter mask,
but we can go a step further and restrict fiber tracking to those areas where
the ODF shows significant restricted diffusion by thresholding on
the generalized fractional anisotropy (GFA).
"""
from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion
be done using the ``fury`` python package
"""
from dipy.viz import window, actor, has_fury
if has_fury:
ren = window.Renderer()
ren.add(
actor.peak_slicer(csa_peaks.peak_dirs,
csa_peaks.peak_values,
colors=None))
window.record(ren, out_path='csa_direction_field.png', size=(900, 900))
if interactive:
window.show(ren, size=(800, 800))
"""
.. figure:: csa_direction_field.png
:align: center
**Direction Field (peaks)**
"""
"""
2. Next we need some way of restricting the fiber tracking to areas with good
directionality information. We've already created the white matter mask,
but we can go a step further and restrict fiber tracking to those areas where
the ODF shows significant restricted diffusion by thresholding on
the generalized fractional anisotropy (GFA).
"""
from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion
def visualize(self,
out_path='out/',
outer_box=True,
axes=True,
clip_neg=False,
azimuth=0,
elevation=0,
n_frames=1,
mag=1,
video=False,
viz_type='ODF',
mask=None,
mask_roi=None,
skip_n=1,
skip_n_roi=1,
scale=1,
roi_scale=1,
zoom_start=1.0,
zoom_end=1.0,
top_zoom=1,
interact=False,
save_parallels=False,
my_cam=None,
compress=True,
roi=None,
corner_text='',
scalemap=None,
titles_on=True,
scalebar_on=True,
invert=False,
flat=False,
colormap='bwr',
global_cm=True,
camtilt=False,
axes_on=False,
colors=None,
arrows=None,
arrow_color=np.array([0, 0, 0]),
linewidth=0.1,
mark_slices=None,
z_shift=0,
profiles=[],
markers=[],
marker_colors=[],
marker_scale=1,
normalize_glyphs=True,
gamma=1,
density_max=1):
log.info('Preparing to render ' + out_path)
# Handle scalemap
if scalemap is None:
scalemap = util.ScaleMap(min=np.min(self.f[..., 0]),
max=np.max(self.f[..., 0]))
# Prepare output
util.mkdir(out_path)
# Setup vtk renderers
renWin = vtk.vtkRenderWindow()
if not interact:
renWin.SetOffScreenRendering(1)
if isinstance(viz_type, str):
viz_type = [viz_type]
# Rows and columns
cols = len(viz_type)
if roi is None:
rows = 1
else:
rows = 2
renWin.SetSize(np.int(500 * mag * cols), np.int(500 * mag * rows))
# Select background color
if save_parallels:
bg_color = [1, 1, 1]
line_color = np.array([0, 0, 0])
line_bcolor = np.array([1, 1, 1])
else:
if not invert:
bg_color = [0, 0, 0]
line_color = np.array([1, 1, 1])
line_bcolor = np.array([0, 0, 0])
else:
bg_color = [1, 1, 1]
line_color = np.array([0, 0, 0])
line_bcolor = np.array([1, 1, 1])
# For each viz_type
rens = []
zoom_start = []
zoom_end = []
for row in range(rows):
for col in range(cols):
# Render
ren = window.Scene()
rens.append(ren)
if viz_type[col] is 'Density':
ren.background([0, 0, 0])
line_color = np.array([1, 1, 1])
else:
ren.background(bg_color)
ren.SetViewport(col / cols, (rows - row - 1) / rows,
(col + 1) / cols, (rows - row) / rows)
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Mask
if mask is None:
mask = np.ones((self.X, self.Y, self.Z), dtype=np.bool)
if mask_roi is None:
mask_roi = mask
# Main vs roi
if row == 0:
data = self.f
skip_mask = np.zeros(mask.shape, dtype=np.bool)
skip_mask[::skip_n, ::skip_n, ::skip_n] = 1
my_mask = np.logical_and(mask, skip_mask)
scale = scale
scalemap = scalemap
if np.sum(my_mask) == 0:
my_mask[0, 0, 0] = True
else:
data = self.f[roi[0][0]:roi[1][0], roi[0][1]:roi[1][1],
roi[0][2]:roi[1][2], :]
roi_mask = mask_roi[roi[0][0]:roi[1][0],
roi[0][1]:roi[1][1],
roi[0][2]:roi[1][2]]
skip_mask = np.zeros(roi_mask.shape, dtype=np.bool)
skip_mask[::skip_n_roi, ::skip_n_roi, ::skip_n_roi] = 1
my_mask = np.logical_and(roi_mask, skip_mask)
scale = roi_scale
scalemap = scalemap
# Add visuals to renderer
if viz_type[col] == "ODF":
renWin.SetMultiSamples(4)
log.info('Rendering ' + str(np.sum(my_mask)) + ' ODFs')
fodf_spheres = viz.odf_sparse(data,
self.Binv,
sphere=self.sphere,
scale=skip_n * scale * 0.5,
norm=False,
colormap=colormap,
mask=my_mask,
global_cm=global_cm,
scalemap=scalemap,
odf_sphere=False,
flat=flat,
normalize=normalize_glyphs)
ren.add(fodf_spheres)
elif viz_type[col] == "ODF Sphere":
renWin.SetMultiSamples(4)
log.info('Rendering ' + str(np.sum(my_mask)) + ' ODFs')
fodf_spheres = viz.odf_sparse(data,
self.Binv,
sphere=self.sphere,
scale=skip_n * scale * 0.5,
norm=False,
colormap=colormap,
mask=my_mask,
global_cm=global_cm,
scalemap=scalemap,
odf_sphere=True,
flat=flat)
ren.add(fodf_spheres)
elif viz_type[col] == "Ellipsoid":
renWin.SetMultiSamples(4)
log.info(
'Warning: scaling is not implemented for ellipsoids')
log.info('Rendering ' + str(np.sum(my_mask)) +
' ellipsoids')
fodf_peaks = viz.tensor_slicer_sparse(data,
sphere=self.sphere,
scale=skip_n *
scale * 0.5,
mask=my_mask)
ren.add(fodf_peaks)
elif viz_type[col] == "Peak":
renWin.SetMultiSamples(4)
log.info('Rendering ' + str(np.sum(my_mask)) + ' peaks')
fodf_peaks = viz.peak_slicer_sparse(
data,
self.Binv,
self.sphere.vertices,
linewidth=linewidth,
scale=skip_n * scale * 0.5,
colors=colors,
mask=my_mask,
scalemap=scalemap,
normalize=normalize_glyphs)
fodf_peaks.GetProperty().LightingOn()
fodf_peaks.GetProperty().SetDiffuse(
0.4) # Doesn't work (VTK bug I think)
fodf_peaks.GetProperty().SetAmbient(0.15)
fodf_peaks.GetProperty().SetSpecular(0)
fodf_peaks.GetProperty().SetSpecularPower(0)
ren.add(fodf_peaks)
elif viz_type[col] == "Principal":
log.info(
'Warning: scaling is not implemented for principals')
log.info('Rendering ' + str(np.sum(my_mask)) +
' principals')
fodf_peaks = viz.principal_slicer_sparse(
data,
self.Binv,
self.sphere.vertices,
scale=skip_n * scale * 0.5,
mask=my_mask)
ren.add(fodf_peaks)
elif viz_type[col] == "Density":
renWin.SetMultiSamples(0) # Must be zero for smooth
# renWin.SetAAFrames(4) # Slow antialiasing for volume renders
log.info('Rendering density')
gamma_corr = np.where(data[..., 0] > 0,
data[..., 0]**gamma, data[..., 0])
scalemap.max = density_max * scalemap.max**gamma
volume = viz.density_slicer(gamma_corr, scalemap)
ren.add(volume)
X = np.float(data.shape[0])
Y = np.float(data.shape[1])
Z = np.float(data.shape[2]) - z_shift
# Titles
if row == 0 and titles_on:
viz.add_text(ren, viz_type[col], 0.5, 0.96, mag)
# Scale bar
if col == cols - 1 and not save_parallels and scalebar_on:
yscale = 1e-3 * self.vox_dim[1] * data.shape[1]
yscale_label = '{:.2g}'.format(yscale) + ' um'
viz.add_text(ren, yscale_label, 0.5, 0.03, mag)
viz.draw_scale_bar(ren, X, Y, Z, [1, 1, 1])
# Corner text
if row == rows - 1 and col == 0 and titles_on:
viz.add_text(ren, corner_text, 0.03, 0.03, mag, ha='left')
# Draw boxes
Nmax = np.max([X, Y, Z])
if outer_box:
if row == 0:
viz.draw_outer_box(
ren,
np.array([[0, 0, 0], [X, Y, Z]]) - 0.5, line_color)
if row == 1:
viz.draw_outer_box(
ren,
np.array([[0, 0, 0], [X, Y, Z]]) - 0.5, [0, 1, 1])
# Add colored axes
if axes:
viz.draw_axes(ren, np.array([[0, 0, 0], [X, Y, Z]]) - 0.5)
# Add custom arrows
if arrows is not None:
for i in range(arrows.shape[0]):
viz.draw_single_arrow(ren,
arrows[i, 0, :],
arrows[i, 1, :],
color=arrow_color)
viz.draw_unlit_line(ren, [
np.array([arrows[i, 0, :], [X / 2, Y / 2, Z / 2]])
], [arrow_color],
lw=0.3,
scale=1.0)
# Draw roi box
if row == 0 and roi is not None:
maxROI = np.max([
roi[1][0] - roi[0][0], roi[1][1] - roi[0][1],
roi[1][2] - roi[0][2]
])
maxXYZ = np.max([self.X, self.Y, self.Z])
viz.draw_outer_box(ren,
roi, [0, 1, 1],
lw=0.3 * maxXYZ / maxROI)
viz.draw_axes(ren, roi, lw=0.3 * maxXYZ / maxROI)
# Draw marked slices
if mark_slices is not None:
for slicen in mark_slices:
md = np.max((X, Z))
frac = slicen / data.shape[1]
rr = 0.83 * md
t1 = 0
t2 = np.pi / 2
t3 = np.pi
t4 = 3 * np.pi / 2
points = [
np.array([[
X / 2 + rr * np.cos(t1), frac * Y,
Z / 2 + rr * np.sin(t1)
],
[
X / 2 + rr * np.cos(t2), frac * Y,
Z / 2 + rr * np.sin(t2)
],
[
X / 2 + rr * np.cos(t3), frac * Y,
Z / 2 + rr * np.sin(t3)
],
[
X / 2 + rr * np.cos(t4), frac * Y,
Z / 2 + rr * np.sin(t4)
],
[
X / 2 + rr * np.cos(t1), frac * Y,
Z / 2 + rr * np.sin(t1)
],
[
X / 2 + rr * np.cos(t2), frac * Y,
Z / 2 + rr * np.sin(t2)
]])
]
viz.draw_unlit_line(ren,
points,
6 * [line_color + 0.6],
lw=0.3,
scale=1.0)
# Draw markers
for i, marker in enumerate(markers):
# Draw sphere
source = vtk.vtkSphereSource()
source.SetCenter(marker)
source.SetRadius(marker_scale)
source.SetThetaResolution(30)
source.SetPhiResolution(30)
# mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(source.GetOutputPort())
# actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(marker_colors[i, :])
actor.GetProperty().SetLighting(0)
ren.AddActor(actor)
# Draw profile lines
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
for i, profile in enumerate(profiles):
import pdb
pdb.set_trace()
n_seg = profile.shape[0]
viz.draw_unlit_line(ren, [profile],
n_seg * [colors[i, :]],
lw=0.5,
scale=1.0)
# Draw sphere
source = vtk.vtkSphereSource()
source.SetCenter(profile[0])
source.SetRadius(1)
source.SetThetaResolution(30)
source.SetPhiResolution(30)
# mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(source.GetOutputPort())
# actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# actor.GetProperty().SetColor(colors[i,:])
actor.GetProperty().SetLighting(0)
# assign actor to the renderer
ren.AddActor(actor)
# Setup cameras
Rmax = np.linalg.norm([Z / 2, X / 2, Y / 2])
Rcam_rad = Rmax / np.tan(np.pi / 12)
Ntmax = np.max([X, Y])
ZZ = Z
if ZZ > Ntmax:
Rcam_edge = np.max([X / 2, Y / 2])
else:
Rcam_edge = np.min([X / 2, Y / 2])
Rcam = Rcam_edge + Rcam_rad
if my_cam is None:
cam = ren.GetActiveCamera()
if camtilt:
cam.SetPosition(
((X - 1) / 2, (Y - 1) / 2, (Z - 1) / 2 + Rcam))
cam.SetViewUp((-1, 0, 1))
if axes_on:
max_dim = np.max((X, Z))
viz.draw_unlit_line(ren, [
np.array([[(X - max_dim) / 2, Y / 2, Z / 2],
[X / 2, Y / 2, +Z / 2],
[X / 2, Y / 2, (Z + max_dim) / 2]])
],
3 * [line_color],
lw=max_dim / 250,
scale=1.0)
else:
cam.SetPosition(
((X - 1) / 2 + Rcam, (Y - 1) / 2, (Z - 1) / 2))
cam.SetViewUp((0, 0, 1))
cam.SetFocalPoint(((X - 1) / 2, (Y - 1) / 2, (Z - 1) / 2))
#ren.reset_camera()
else:
ren.set_camera(*my_cam)
ren.azimuth(azimuth)
ren.elevation(elevation)
# Set zooming
if save_parallels:
zoom_start.append(1.7)
zoom_end.append(1.7)
else:
if row == 0:
zoom_start.append(1.3 * top_zoom)
zoom_end.append(1.3 * top_zoom)
else:
zoom_start.append(1.3)
zoom_end.append(1.3)
# Setup writer
writer = vtk.vtkTIFFWriter()
if not compress:
writer.SetCompressionToNoCompression()
# Execute renders
az = 90
naz = np.ceil(360 / n_frames)
log.info('Rendering ' + out_path)
if save_parallels:
# Parallel rendering for summaries
filenames = ['yz', 'xy', 'xz']
zooms = [zoom_start[0], 1.0, 1.0]
azs = [90, -90, 0]
els = [0, 0, 90]
ren.projection(proj_type='parallel')
ren.reset_camera()
for i in tqdm(range(3)):
ren.zoom(zooms[i])
ren.azimuth(azs[i])
ren.elevation(els[i])
ren.reset_clipping_range()
renderLarge = vtk.vtkRenderLargeImage()
renderLarge.SetMagnification(1)
renderLarge.SetInput(ren)
renderLarge.Update()
writer.SetInputConnection(renderLarge.GetOutputPort())
writer.SetFileName(out_path + filenames[i] + '.tif')
writer.Write()
else:
# Rendering for movies
for j, ren in enumerate(rens):
ren.zoom(zoom_start[j])
for i in tqdm(range(n_frames)):
for j, ren in enumerate(rens):
ren.zoom(1 + ((zoom_end[j] - zoom_start[j]) / n_frames))
ren.azimuth(az)
ren.reset_clipping_range()
renderLarge = vtk.vtkRenderLargeImage()
renderLarge.SetMagnification(1)
renderLarge.SetInput(ren)
renderLarge.Update()
writer.SetInputConnection(renderLarge.GetOutputPort())
if n_frames != 1:
writer.SetFileName(out_path + str(i).zfill(3) + '.tif')
else:
writer.SetFileName(out_path + '.tif')
writer.Write()
az = naz
# Interactive
if interact:
window.show(ren)
# Generate video (requires ffmpeg)
if video:
log.info('Generating video from frames')
fps = np.ceil(n_frames / 12)
subprocess.call([
'ffmpeg', '-nostdin', '-y', '-framerate',
str(fps), '-loglevel', 'panic', '-i',
out_path + '%03d' + '.png', '-pix_fmt', 'yuvj420p', '-vcodec',
'mjpeg', out_path[:-1] + '.avi'
])
# subprocess.call(['rm', '-r', out_path])
return my_cam
def show_seeds(seeds):
renderer = window.Renderer()
points = actor.point(seeds, colors=np.random.rand(*seeds.shape))
renderer.add(points)
window.show(renderer)
seeds. Using ``random_seeds_from_mask`` we can select a specific number of
seeds (``seeds_count``) in each voxel where the mask ``fa > 0.3`` is true.
"""
seeds = random_seeds_from_mask(fa > 0.3, seeds_count=1)
"""
For quality assurance we can also visualize a slice from the direction field
which we will use as the basis to perform the tracking.
"""
ren = window.Renderer()
ren.add(
actor.peak_slicer(csd_peaks.peak_dirs, csd_peaks.peak_values, colors=None))
if interactive:
window.show(ren, size=(900, 900))
else:
window.record(ren, out_path='csd_direction_field.png', size=(900, 900))
"""
.. figure:: csd_direction_field.png
:align: center
**Direction Field (peaks)**
``EuDX`` [Garyfallidis12]_ is a fast algorithm that we use here to generate
streamlines. This algorithm is what is used here and the default option
when providing the output of peaks directly in LocalTracking.
"""
streamline_generator = LocalTracking(csd_peaks,
tissue_classifier,
def show_lines(streamlines, affine=None):
renderer = window.Renderer()
lines = actor.line(streamlines, affine)
renderer.add(lines)
window.show(renderer)
def test_odf_slicer(interactive=False):
sphere = get_sphere('symmetric362')
shape = (11, 11, 11, sphere.vertices.shape[0])
fid, fname = mkstemp(suffix='_odf_slicer.mmap')
print(fid)
print(fname)
odfs = np.memmap(fname, dtype=np.float64, mode='w+',
shape=shape)
odfs[:] = 1
affine = np.eye(4)
renderer = window.Renderer()
mask = np.ones(odfs.shape[:3])
mask[:4, :4, :4] = 0
odfs[..., 0] = 1
odf_actor = actor.odf_slicer(odfs, affine,
mask=mask, sphere=sphere, scale=.25,
colormap='jet')
fa = 0. * np.zeros(odfs.shape[:3])
fa[:, 0, :] = 1.
fa[:, -1, :] = 1.
fa[0, :, :] = 1.
fa[-1, :, :] = 1.
fa[5, 5, 5] = 1
k = 5
I, J, K = odfs.shape[:3]
fa_actor = actor.slicer(fa, affine)
fa_actor.display_extent(0, I, 0, J, k, k)
renderer.add(odf_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
odf_actor.display_extent(0, I, 0, J, k, k)
odf_actor.GetProperty().SetOpacity(1.0)
if interactive:
window.show(renderer, reset_camera=False)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr, find_objects=True)
npt.assert_equal(report.objects, 11 * 11)
renderer.clear()
renderer.add(fa_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer)
mask[:] = 0
mask[5, 5, 5] = 1
fa[5, 5, 5] = 0
fa_actor = actor.slicer(fa, None)
fa_actor.display(None, None, 5)
odf_actor = actor.odf_slicer(odfs, None, mask=mask,
sphere=sphere, scale=.25,
colormap='jet',
norm=False, global_cm=True)
renderer.clear()
renderer.add(fa_actor)
renderer.add(odf_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer)
renderer.clear()
renderer.add(odf_actor)
renderer.add(fa_actor)
odfs[:, :, :] = 1
mask = np.ones(odfs.shape[:3])
odf_actor = actor.odf_slicer(odfs, None, mask=mask,
sphere=sphere, scale=.25,
colormap='jet',
norm=False, global_cm=True)
renderer.clear()
renderer.add(odf_actor)
renderer.add(fa_actor)
renderer.add(actor.axes((11, 11, 11)))
for i in range(11):
odf_actor.display(i, None, None)
fa_actor.display(i, None, None)
if interactive:
window.show(renderer)
for j in range(11):
odf_actor.display(None, j, None)
fa_actor.display(None, j, None)
if interactive:
window.show(renderer)
# with mask equal to zero everything should be black
mask = np.zeros(odfs.shape[:3])
odf_actor = actor.odf_slicer(odfs, None, mask=mask,
sphere=sphere, scale=.25,
colormap='plasma',
norm=False, global_cm=True)
renderer.clear()
renderer.add(odf_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer)
report = window.analyze_renderer(renderer)
npt.assert_equal(report.actors, 1)
npt.assert_equal(report.actors_classnames[0], 'vtkLODActor')
del odf_actor
odfs._mmap.close()
del odfs
os.close(fid)
os.remove(fname)
streamlines = Streamlines(streamlines_generator)
# Prepare the display objects.
color = line_colors(streamlines)
if window.have_vtk:
streamlines_actor = actor.line(streamlines, line_colors(streamlines))
# Create the 3D display.
r = window.Renderer()
r.add(streamlines_actor)
# Save still images for this static example. Or for interactivity use
window.record(r, n_frames=1, out_path='deterministic.png', size=(800, 800))
if interactive:
window.show(r)
"""
.. figure:: deterministic.png
:align: center
**Corpus Callosum Deterministic**
We've created a deterministic set of streamlines, so called because if you
repeat the fiber tracking (keeping all the inputs the same) you will get
exactly the same set of streamlines. We can save the streamlines as a Trackvis
file so it can be loaded into other software for visualization or further
analysis.
"""
from dipy.io.streamline import save_trk
def show_peaks(pam):
renderer = window.Renderer()
peaks = actor.peak_slicer(pam.peak_dirs, colors=None)
renderer.add(peaks)
window.show(renderer)
