def display_folds(folds_file, labels, weights, white_file=None,
interactive=True, snap=False, animate=False, outdir=None,
name="folds", actor_ang=(0., 0., 0.)):
""" Display the folds computed by morphologist.
The scene supports one feature activated via the keystroke:
* 'p': Pick the data at the current mouse point. This will pop-up a window
with information on the current pick (ie. the fold name).
Parameters
----------
folds_file: str( mandatory)
the folds '.gii' file.
labels: dict (mandatory)
a mapping between a mesh id and its label.
weights: dict (mandatory)
a mapping between a mesh label and its wheight in [0, 1].
white_file: str (optional, default None)
if specified the white surface will be displayed.
interactive: bool (optional, default True)
if True display the renderer.
snap: bool (optional, default False)
if True create a snap of the scene: need a valid outdir.
animate: bool (optional, default False)
if True create a gif 360 degrees animation of the scene: need a valid
outdir.
outdir: str (optional, default None)
an existing directory.
name: str (optional, default 'folds')
the basename of the generated files.
actor_ang: 3-uplet (optinal, default (0, 0, 0))
the actors x, y, z position (in degrees).
"""
# Load the folds file
image = gio.read(folds_file)
nb_of_surfs = len(image.darrays)
if nb_of_surfs % 2 != 0:
raise ValueError("Need an odd number of arrays (vertices, triangles).")
# Create an actor for each fold
ren = pvtk.ren()
ren.SetBackground(1, 1, 1)
for vertindex in range(0, nb_of_surfs, 2):
vectices = image.darrays[vertindex].data
triangles = image.darrays[vertindex + 1].data
labelindex = image.darrays[vertindex].get_metadata()["Timestep"]
if labelindex != image.darrays[vertindex + 1].get_metadata()[
"Timestep"]:
raise ValueError("Gifti arrays '{0}' and '{1}' do not share the "
"same label.".format(vertindex, vertindex + 1))
labelindex = int(labelindex)
if labelindex in labels:
label = labels[labelindex]
if label in weights:
weight = weights[label] * 256.
else:
weight = 0
else:
label = "NC"
weight = 0
surf = TriSurface(vectices, triangles, labels=None)
actor = pvtk.surface(surf.vertices, surf.triangles,
surf.labels + weight)
actor.label = label
actor.RotateX(actor_ang[0])
actor.RotateY(actor_ang[1])
actor.RotateZ(actor_ang[2])
pvtk.add(ren, actor)
# Add the white surface if specified
if white_file is not None:
image = gio.read(white_file)
nb_of_surfs = len(image.darrays)
if nb_of_surfs != 2:
raise ValueError("'{0}' does not a contain a valid white "
"mesh.".format(white_file))
vectices = image.darrays[0].data
triangles = image.darrays[1].data
surf = TriSurface(vectices, triangles, labels=None)
actor = pvtk.surface(surf.vertices, surf.triangles, surf.labels,
opacity=1, set_lut=False)
actor.label = "white"
actor.RotateX(actor_ang[0])
actor.RotateY(actor_ang[1])
actor.RotateZ(actor_ang[2])
pvtk.add(ren, actor)
# Show the renderer
if interactive:
actor = pvtk.text("!!!!", font_size=15, position=(10, 10),
is_visible=False)
pvtk.add(ren, actor)
obs = LabelsOnPick(actor, static_position=True,
to_keep_actors=["white"])
pvtk.show(ren, title="morphologist folds", observers=[obs])
# Create a snap
if snap:
if not os.path.isdir(outdir):
raise ValueError("'{0}' is not a valid directory.".format(outdir))
pvtk.record(ren, outdir, name, n_frames=1)
# Create an animation
if animate:
if not os.path.isdir(outdir):
raise ValueError("'{0}' is not a valid directory.".format(outdir))
pvtk.record(ren, outdir, name, n_frames=36, az_ang=10, animate=True,
delay=25)
track_filtered_file, as_generator=False, points_space="voxel")
fibers = [track_item[0] for track_item in trackvis_fibers]
if use_vtk:
ren = pvtk.ren()
colors = line_colors(fibers)
actor = pvtk.tubes(fibers, colors)
actor.RotateX(actor_ang[0])
actor.RotateY(actor_ang[1])
actor.RotateZ(actor_ang[2])
pvtk.add(ren, actor)
ren.SetBackground(1, 1, 1)
pvtk.record(ren, qcdir, "fibers", az_ang=45, n_frames=2)
pvtk.record(ren, qcdir, "fibers", n_frames=36, az_ang=10, animate=True,
delay=25)
pvtk.show(ren)
pvtk.clear(ren)
"""
Fiber clustering
----------------
Based on an agglomerative clustering, and a geometric distance.
"""
clustering_outdir = os.path.join(outdir, "clustering")
cluster_file = os.path.join(clustering_outdir, "clusters.json")
if not os.path.isdir(clustering_outdir):
os.mkdir(clustering_outdir)
if not os.path.isfile(cluster_file):
def display_folds(folds_file,
labels,
weights,
white_file=None,
interactive=True,
snap=False,
animate=False,
outdir=None,
name="folds",
actor_ang=(0., 0., 0.)):
""" Display the folds computed by morphologist.
The scene supports one feature activated via the keystroke:
* 'p': Pick the data at the current mouse point. This will pop-up a window
with information on the current pick (ie. the fold name).
Parameters
----------
folds_file: str( mandatory)
the folds '.gii' file.
labels: dict (mandatory)
a mapping between a mesh id and its label.
weights: dict (mandatory)
a mapping between a mesh label and its wheight in [0, 1].
white_file: str (optional, default None)
if specified the white surface will be displayed.
interactive: bool (optional, default True)
if True display the renderer.
snap: bool (optional, default False)
if True create a snap of the scene: need a valid outdir.
animate: bool (optional, default False)
if True create a gif 360 degrees animation of the scene: need a valid
outdir.
outdir: str (optional, default None)
an existing directory.
name: str (optional, default 'folds')
the basename of the generated files.
actor_ang: 3-uplet (optinal, default (0, 0, 0))
the actors x, y, z position (in degrees).
"""
# Load the folds file
image = gio.read(folds_file)
nb_of_surfs = len(image.darrays)
if nb_of_surfs % 2 != 0:
raise ValueError("Need an odd number of arrays (vertices, triangles).")
# Create an actor for each fold
ren = pvtk.ren()
ren.SetBackground(1, 1, 1)
for vertindex in range(0, nb_of_surfs, 2):
vectices = image.darrays[vertindex].data
triangles = image.darrays[vertindex + 1].data
labelindex = image.darrays[vertindex].get_metadata()["Timestep"]
if labelindex != image.darrays[vertindex +
1].get_metadata()["Timestep"]:
raise ValueError("Gifti arrays '{0}' and '{1}' do not share the "
"same label.".format(vertindex, vertindex + 1))
labelindex = int(labelindex)
if labelindex in labels:
label = labels[labelindex]
if label in weights:
weight = weights[label] * 256.
else:
weight = 0
else:
label = "NC"
weight = 0
surf = TriSurface(vectices, triangles, labels=None)
actor = pvtk.surface(surf.vertices, surf.triangles,
surf.labels + weight)
actor.label = label
actor.RotateX(actor_ang[0])
actor.RotateY(actor_ang[1])
actor.RotateZ(actor_ang[2])
pvtk.add(ren, actor)
# Add the white surface if specified
if white_file is not None:
image = gio.read(white_file)
nb_of_surfs = len(image.darrays)
if nb_of_surfs != 2:
raise ValueError("'{0}' does not a contain a valid white "
"mesh.".format(white_file))
vectices = image.darrays[0].data
triangles = image.darrays[1].data
surf = TriSurface(vectices, triangles, labels=None)
actor = pvtk.surface(surf.vertices,
surf.triangles,
surf.labels,
opacity=1,
set_lut=False)
actor.label = "white"
actor.RotateX(actor_ang[0])
actor.RotateY(actor_ang[1])
actor.RotateZ(actor_ang[2])
pvtk.add(ren, actor)
# Show the renderer
if interactive:
actor = pvtk.text("!!!!",
font_size=15,
position=(10, 10),
is_visible=False)
pvtk.add(ren, actor)
obs = LabelsOnPick(actor,
static_position=True,
to_keep_actors=["white"])
pvtk.show(ren, title="morphologist folds", observers=[obs])
# Create a snap
if snap:
if not os.path.isdir(outdir):
raise ValueError("'{0}' is not a valid directory.".format(outdir))
pvtk.record(ren, outdir, name, n_frames=1)
# Create an animation
if animate:
if not os.path.isdir(outdir):
raise ValueError("'{0}' is not a valid directory.".format(outdir))
pvtk.record(ren,
outdir,
name,
n_frames=36,
az_ang=10,
animate=True,
delay=25)
bvecfile = os.path.join(output_directory, "dwi.bvec")
bvalfile = os.path.join(output_directory, "dwi.bval")
dwi_image.to_filename(dfile)
numpy.savetxt(bvecfile, g)
numpy.savetxt(bvalfile, b.T)
gdtifile = generalized_tensor_estimation(dfile,
bvalfile,
bvecfile,
order,
maskfile=None,
number_of_workers=1,
odf=False,
output_directory=output_directory)
dti_params = nibabel.load(gdtifile).get_data()
print "Tensor:"
for index, params in enumerate(dti_params[0, 0]):
print "nnls:", index
print_tensor(params, order)
for tensor in dti6to33(dti_params)[0, 0]:
vals, vecs = numpy.linalg.eigh(tensor)
print vals
print vecs
# Plot
ren = pvtk.ren()
for index, params in enumerate(dti_params[0, 0]):
actor = pvtk.tensor(params, order, position=(index, 0, 0))
pvtk.add(ren, actor)
pvtk.show(ren)
