def test_fvtk_functions():
# Create a renderer
r=fvtk.ren()
# Create 2 lines with 2 different colors
lines=[np.random.rand(10,3),np.random.rand(20,3)]
colors=np.random.rand(2,3)
c=fvtk.line(lines,colors)
fvtk.add(r,c)
# Create a volume and return a volumetric actor using volumetric rendering
vol=100*np.random.rand(100,100,100)
vol=vol.astype('uint8')
r = fvtk.ren()
v = fvtk.volume(vol)
fvtk.add(r,v)
# Remove all objects
fvtk.rm_all(r)
# Put some text
l=fvtk.label(r,text='Yes Men')
fvtk.add(r,l)
# Show everything
#fvtk.show(r)
def test_fvtk_functions():
# Create a renderer
r = fvtk.ren()
# Create 2 lines with 2 different colors
lines = [np.random.rand(10, 3), np.random.rand(20, 3)]
colors = np.random.rand(2, 3)
c = fvtk.line(lines, colors)
fvtk.add(r, c)
# create streamtubes of the same lines and shift them a bit
c2 = fvtk.streamtube(lines, colors)
c2.SetPosition(2, 0, 0)
fvtk.add(r, c2)
# Create a volume and return a volumetric actor using volumetric rendering
vol = 100 * np.random.rand(100, 100, 100)
vol = vol.astype('uint8')
r = fvtk.ren()
v = fvtk.volume(vol)
fvtk.add(r, v)
# Remove all objects
fvtk.rm_all(r)
# Put some text
l = fvtk.label(r, text='Yes Men')
fvtk.add(r, l)
# Slice the volume
fvtk.add(r, fvtk.slicer(vol, plane_i=[50]))
# Change the position of the active camera
fvtk.camera(r, pos=(0.6, 0, 0), verbose=False)
def test_fvtk_functions():
# This tests will fail if any of the given actors changed inputs or do
# not exist
# Create a renderer
r = fvtk.ren()
# Create 2 lines with 2 different colors
lines = [np.random.rand(10, 3), np.random.rand(20, 3)]
colors = np.random.rand(2, 3)
c = fvtk.line(lines, colors)
fvtk.add(r, c)
# create streamtubes of the same lines and shift them a bit
c2 = fvtk.streamtube(lines, colors)
c2.SetPosition(2, 0, 0)
fvtk.add(r, c2)
# Create a volume and return a volumetric actor using volumetric rendering
vol = 100 * np.random.rand(100, 100, 100)
vol = vol.astype('uint8')
r = fvtk.ren()
v = fvtk.volume(vol)
fvtk.add(r, v)
# Remove all objects
fvtk.rm_all(r)
# Put some text
l = fvtk.label(r, text='Yes Men')
fvtk.add(r, l)
# Slice the volume
slicer = fvtk.slicer(vol)
slicer.display(50, None, None)
fvtk.add(r, slicer)
# Change the position of the active camera
fvtk.camera(r, pos=(0.6, 0, 0), verbose=False)
fvtk.clear(r)
# Peak directions
p = fvtk.peaks(np.random.rand(3, 3, 3, 5, 3))
fvtk.add(r, p)
p2 = fvtk.peaks(np.random.rand(3, 3, 3, 5, 3),
np.random.rand(3, 3, 3, 5),
colors=(0, 1, 0))
fvtk.add(r, p2)
def test_fvtk_functions():
# This tests will fail if any of the given actors changed inputs or do
# not exist
# Create a renderer
r = fvtk.ren()
# Create 2 lines with 2 different colors
lines = [np.random.rand(10, 3), np.random.rand(20, 3)]
colors = np.random.rand(2, 3)
c = fvtk.line(lines, colors)
fvtk.add(r, c)
# create streamtubes of the same lines and shift them a bit
c2 = fvtk.streamtube(lines, colors)
c2.SetPosition(2, 0, 0)
fvtk.add(r, c2)
# Create a volume and return a volumetric actor using volumetric rendering
vol = 100 * np.random.rand(100, 100, 100)
vol = vol.astype('uint8')
r = fvtk.ren()
v = fvtk.volume(vol)
fvtk.add(r, v)
# Remove all objects
fvtk.rm_all(r)
# Put some text
l = fvtk.label(r, text='Yes Men')
fvtk.add(r, l)
# Slice the volume
slicer = fvtk.slicer(vol)
slicer.display(50, None, None)
fvtk.add(r, slicer)
# Change the position of the active camera
fvtk.camera(r, pos=(0.6, 0, 0), verbose=False)
fvtk.clear(r)
# Peak directions
p = fvtk.peaks(np.random.rand(3, 3, 3, 5, 3))
fvtk.add(r, p)
p2 = fvtk.peaks(np.random.rand(3, 3, 3, 5, 3),
np.random.rand(3, 3, 3, 5),
colors=(0, 1, 0))
fvtk.add(r, p2)
def visualize_bundles(trk, ren=None, inline=True, interact=False):
"""
Visualize bundles in 3D using fvtk
"""
if isinstance(trk, str):
trk = nib.streamlines.load(trk)
if ren is None:
ren = fvtk.ren()
for b in np.unique(trk.tractogram.data_per_streamline['bundle']):
idx = np.where(trk.tractogram.data_per_streamline['bundle'] == b)[0]
this_sl = list(trk.streamlines[idx])
sl_actor = fvtk.line(this_sl, Tableau_20.colors[int(b)])
fvtk.add(ren, sl_actor)
if inline:
tdir = tempfile.gettempdir()
fname = op.join(tdir, "fig.png")
fvtk.record(ren, out_path=fname)
display.display_png(display.Image(fname))
if interact:
fvtk.show(ren)
return ren
def prepare_odfplot(data, params, dipy_sph, p_slice=None):
p_slice = params['slice'] if p_slice is None else p_slice
data = (data, ) if type(data) is np.ndarray else data
slicedims = data[0][p_slice].shape[:-1]
l_labels = data[0].shape[-1]
camera_params, long_ax, view_ax, stack_ax = \
prepare_plot_camera(slicedims, datalen=len(data), scale=params['scale'])
stack = [u[p_slice] for u in data]
if params['spacing']:
uniform_odf = np.ones((1, 1, 1, l_labels), order='C') / (4 * np.pi)
tile_descr = [1, 1, 1, 1]
tile_descr[long_ax] = slicedims[long_ax]
spacing = np.tile(uniform_odf, tile_descr)
for i in reversed(range(1, len(stack))):
stack.insert(i, spacing)
if stack_ax == max(long_ax, stack_ax):
stack = list(reversed(stack))
plotdata = np.concatenate(stack, axis=stack_ax)
r = fvtk.ren()
r_data = fvtk.sphere_funcs(plotdata,
dipy_sph,
colormap='jet',
norm=params['norm'],
scale=params['scale'])
fvtk.add(r, r_data)
r.set_camera(**camera_params)
return r
def draw_ellipsoid(data, gtab, outliers, data_without_noise):
bvecs = gtab.bvecs
raw_data = bvecs * np.array([data, data, data]).T
ren = fvtk.ren()
# Draw Sphere of predicted data
new_sphere = sphere.Sphere(xyz=bvecs[~gtab.b0s_mask, :])
sf1 = fvtk.sphere_funcs(data_without_noise[~gtab.b0s_mask],
new_sphere,
colormap=None,
norm=False,
scale=1)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
# Draw Raw Data as points, Red means outliers
good_values = [index for index, voxel in enumerate(outliers) if voxel == 0]
bad_values = [index for index, voxel in enumerate(outliers) if voxel == 1]
point_actor_good = fvtk.point(raw_data[good_values, :],
fvtk.colors.yellow,
point_radius=.05)
point_actor_bad = fvtk.point(raw_data[bad_values, :],
fvtk.colors.red,
point_radius=0.05)
fvtk.add(ren, point_actor_good)
fvtk.add(ren, point_actor_bad)
fvtk.show(ren)
def show_all_bundles(start, end):
ren = fvtk.ren()
ren.SetBackground(1, 1, 1.)
from dipy.viz.fvtk import colors as c
colors = [c.alice_blue, c.maroon, c.alizarin_crimson, c.mars_orange, c.antique_white,
c.mars_yellow, c.aquamarine, c.melon, c.aquamarine_medium, c.midnight_blue,
c.aureoline_yellow, c.mint, c.azure, c.mint_cream, c.banana, c.misty_rose,
c.beige]
print(len(colors))
for (i, bundle) in enumerate(bundle_names[start:end]):
bun = load_bundle(bundle)
bun_actor = vtk_a.streamtube(bun, colors[i], linewidth=0.5, tube_sides=9)
fvtk.add(ren, bun_actor)
fvtk.show(ren, size=(1800, 1000))
#fvtk.record(ren, n_frames=100, out_path='test.png',
# magnification=1)
fvtk.record(ren, size=(1800, 1000), n_frames=100, out_path='test.png',
path_numbering=True, magnification=1)
def plot_tract(bundle, affine, num_class=1, pred=[], ignore=[]):
# Visualize the results
from dipy.viz import fvtk, actor
from dipy.tracking.streamline import transform_streamlines
# Create renderer
r = fvtk.ren()
if len(pred) > 0:
colors = get_spaced_colors(num_class)
for i in range(num_class):
if i in ignore:
continue
idx = np.argwhere(pred == i).squeeze()
bundle_native = transform_streamlines(
bundle[idx], np.linalg.inv(affine))
if len(bundle_native) == 0:
continue
lineactor = actor.line(
bundle_native, colors[i], linewidth=0.2)
fvtk.add(r, lineactor)
elif num_class == 1:
bundle_native = transform_streamlines(bundle, np.linalg.inv(affine))
lineactor = actor.line(bundle_native, linewidth=0.2)
fvtk.add(r, lineactor)
# Show original fibers
fvtk.camera(r, pos=(-264, 285, 155), focal=(0, -14, 9),
viewup=(0, 0, 1), verbose=False)
fvtk.show(r)
def plot_proj_shell(ms,
use_sym=True,
use_sphere=True,
same_color=False,
rad=0.025):
ren = fvtk.ren()
ren.SetBackground(1, 1, 1)
if use_sphere:
sphere = get_sphere('symmetric724')
sphere_actor = fvtk.sphere_funcs(np.ones(sphere.vertices.shape[0]),
sphere,
colormap='winter',
scale=0)
fvtk.add(ren, sphere_actor)
for i, shell in enumerate(ms):
if same_color:
i = 0
pts_actor = fvtk.point(shell, vtkcolors[i], point_radius=rad)
fvtk.add(ren, pts_actor)
if use_sym:
pts_actor = fvtk.point(-shell, vtkcolors[i], point_radius=rad)
fvtk.add(ren, pts_actor)
fvtk.show(ren)
def show_many_fractions(name):
data,bvals,bvecs=get_data(name)
S0s=[];S1s=[];S2s=[];
X0s=[];X1s=[];X2s=[];
U0s=[];U1s=[];U2s=[];
Fractions=[0,10,20,30,40,50,60,70,80,90,100]
#Fractions=[90,100]
for f in Fractions:
S0,sticks=simulations_dipy(bvals,bvecs,d=0.0015,S0=200,angles=[(0,0)],fractions=[f],snr=None)
X0=diffusivitize(S0,bvals,bvecs);S0s.append(S0);X0s.append(X0)
S1,sticks=simulations_dipy(bvals,bvecs,d=0.0015,S0=200,angles=[(0,0),(90,0)],fractions=[f/2.,f/2.],snr=None)
X1=diffusivitize(S1,bvals,bvecs);S1s.append(S1);X1s.append(X1)
S2,sticks=simulations_dipy(bvals,bvecs,d=0.0015,S0=200,angles=[(0,0),(90,0),(90,90)],fractions=[f/3.,f/3.,f/3.],snr=None)
X2=diffusivitize(S2,bvals,bvecs);S2s.append(S2);X2s.append(X2)
U,s,V=np.linalg.svd(np.dot(X2.T,X2),full_matrices=True)
U2s.append(U)
r=fvtk.ren()
for i in range(len(Fractions)):
fvtk.add(r,fvtk.point(X0s[i]+np.array([30*i,0,0]),fvtk.red,1,.5,8,8))
fvtk.add(r,fvtk.point(X1s[i]+np.array([30*i,30,0]),fvtk.green,1,.5,8,8))
fvtk.add(r,fvtk.point(X2s[i]+np.array([30*i,60,0]),fvtk.yellow,1,.5,8,8))
fvtk.show(r)
def visualize(streamlines_A, streamlines_B, mappingAB, line='line', shift=np.array([0.0, 0.0, 200.0]), color_A=fvtk.colors.white, color_B=fvtk.colors.green, color_line=fvtk.colors.yellow):
assert(len(mappingAB) == len(streamlines_A))
assert(mappingAB.max() <= len(streamlines_B))
if line == 'line':
line = fvtk.line
linewidth = 2.0
linekwargs = {'linewidth':linewidth}
elif line == 'tube':
line = fvtk.streamtube
linewidth = 1.0
linekwargs = {'linewidth':linewidth, 'lod':False}
else:
raise Exception
if color_A == 'auto':
color_A = line_colors(streamlines_A)
if color_B == 'auto':
color_B = line_colors(streamlines_B)
streamlines_B_shifted = np.array([s + shift for s in streamlines_B])
midpointA = [s[int(s.shape[0] / 2)] for s in streamlines_A]
midpointB = [s[int(s.shape[0] / 2)] for s in streamlines_B_shifted]
ren = fvtk.ren()
fvtk.add(ren, line(streamlines_A.tolist(), colors=color_A, **linekwargs))
fvtk.add(ren, line(streamlines_B_shifted.tolist(), colors=color_B, **linekwargs))
fvtk.add(ren, fvtk.line(zip(midpointA, midpointB), colors=color_line, opacity=0.5, linewidth=0.5))
fvtk.show(ren)
def show_signals(data,bvals,gradients,sticks=None):
s=data[1:]
s0=data[0]
ls=np.log(s)-np.log(s0)
ind=np.arange(1,data.shape[-1])
ob=-1/bvals[1:]
#lg=np.log(s[1:])-np.log(s0)
d=ob*(np.log(s)-np.log(s0))
r=fvtk.ren()
all=fvtk.crossing(s,ind,gradients,scale=1)
#fvtk.add(r,fvtk.line(all,fvtk.coral))
#d=d-d.min()
#all3=fvtk.crossing(d,ind,gradients,scale=10**4)
#fvtk.add(r,fvtk.line(all3,fvtk.red))
#d=d-d.min()
all2=fvtk.crossing(d,ind,gradients,scale=10**4)
fvtk.add(r,fvtk.line(all2,fvtk.green))
#"""
#d2=d*10**4
#print d2.min(),d2.mean(),d2.max(),d2.std()
for a in all2:
fvtk.label(r,str(np.round(np.linalg.norm(a[0]),2)),pos=a[0],scale=(.2,.2,.2),color=(1,0,0))
if sticks!=None:
for s in sticks:
ln=np.zeros((2,3))
ln[1]=s
fvtk.add(r,fvtk.line(d.max()*10**4*ln,fvtk.blue))
#data2=data.reshape(1,len(data))
#pdi=ProjectiveDiffusivity(data2,bvals,gradients,dotpow=6,width=6,sincpow=2)
#pd=pdi.spherical_diffusivity(data)
#print pd
#"""
fvtk.show(r)
def show_sim_odfs(peaks, sphere, title):
ren = fvtk.ren()
odf = np.dot(peaks.shm_coeff, peaks.invB)
odf2 = peaks.odf
print(np.sum( np.abs(odf - odf2)))
sfu = fvtk.sphere_funcs(odf, sphere, norm=True)
fvtk.add(ren, sfu)
fvtk.show(ren, title=title)
def viz_vol(vol):
ren = fvtk.ren()
vl = 100*vol
v = fvtk.volume(vl)
fvtk.add(ren, v)
fvtk.show(ren)
def plotODF(ODF, sphere):
r = fvtk.ren()
sfu = fvtk.sphere_funcs(ODF, sphere, scale=2.2, norm=True)
sfu.RotateY(90)
# sfu.RotateY(180)
fvtk.add(r, sfu)
# outname = 'screenshot_signal_r.png'
# fvtk.record(r, n_frames=1, out_path = outname, size=(3000, 1500), magnification = 2)
fvtk.show(r)
def draw_p(p, x, new_sphere):
ren = fvtk.ren()
raw_data = x * np.array([p, p, p])
sf1 = fvtk.sphere_funcs(raw_data, new_sphere, colormap=None, norm=False, scale=0)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
fvtk.show(ren)
def show(fname):
streams, hdr = tv.read(fname)
streamlines = [s[0] for s in streams]
renderer = fvtk.ren()
fvtk_tubes = vtk_a.line(streamlines, opacity=0.2, linewidth=5)
fvtk.add(renderer, fvtk_tubes)
fvtk.show(renderer)
def show_Pi_mapping(streamlines_A, streamlines_B, Pi_ids_A, mapping_Pi):
r = fvtk.ren()
Pi_viz_A = fvtk.streamtube(streamlines_A[Pi_ids_A], fvtk.colors.red)
fvtk.add(r, Pi_viz_A)
# Pi_viz_B = fvtk.streamtube(streamlines_B[Pi_ids_B], fvtk.colors.blue)
# fvtk.add(r, Pi_viz_B)
Pi_viz_A_1nn_B = fvtk.streamtube(streamlines_B[mapping_Pi], fvtk.colors.white)
fvtk.add(r, Pi_viz_A_1nn_B)
fvtk.show(r)
def show_odf_sample(filename):
odf = nib.load(filename).get_data()
sphere = get_sphere('symmetric724')
from dipy.viz import fvtk
r = fvtk.ren()
# fvtk.add(r, fvtk.sphere_funcs(odf[:, :, 25], sphere))
fvtk.add(r, fvtk.sphere_funcs(odf[25 - 10:25 + 10, 25 - 10:25 + 10, 25], sphere))
fvtk.show(r)
def show_odfs(peaks, sphere):
ren = fvtk.ren()
odf = np.dot(peaks.shm_coeff, peaks.invB)
#odf = odf[14:24, 22, 23:33]
#odf = odf[:, 22, :]
odf = odf[:, 0, :]
sfu = fvtk.sphere_funcs(odf[:, None, :], sphere, norm=True)
sfu.RotateX(-90)
fvtk.add(ren, sfu)
fvtk.show(ren)
def show_tract(segmented_tract, color):
"""Visualization of the segmented tract.
"""
ren = fvtk.ren()
fvtk.add(ren, fvtk.line(segmented_tract.tolist(),
colors=color,
linewidth=2,
opacity=0.3))
fvtk.show(ren)
fvtk.clear(ren)
def show_tract(segmented_tract, color):
ren = fvtk.ren()
fvtk.add(
ren,
fvtk.line(segmented_tract.tolist(),
colors=color,
linewidth=2,
opacity=0.3))
fvtk.show(ren)
fvtk.clear(ren)
def show(imgtck, clusters, out_path):
colormap = fvtk.create_colormap(np.ravel(clusters.centroids), name='jet')
colormap_full = np.ones((len(imgtck.streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
ren = fvtk.ren()
ren.SetBackground(1, 1, 1)
fvtk.add(ren, fvtk.streamtube(imgtck.streamlines, colormap_full))
fvtk.record(ren, n_frames=1, out_path=out_path, size=(600, 600))
fvtk.show(ren)
def show_all_bundles_fnames(fnames, colors=None):
ren = fvtk.ren()
for (i, fname) in enumerate(fnames):
streamlines = read_bundles(fname)
if colors is None:
color = np.random.rand(3)
else:
color = colors[i]
fvtk.add(ren, fvtk.line(streamlines, color))
fvtk.show(ren)
def see_skeletons(fskel):
C=load_pickle(fskel)
tracks=[C[c]['most'] for c in C if C[c]['N'] > 10 ]
r=fvtk.ren()
colors=np.array([t[0]-t[-1] for t in tracks])
colors=colormap.orient2rgb(colors)
fvtk.add(r,fvtk.line(tracks,colors))
fvtk.show(r)
def draw_p(p, x):
ren = fvtk.ren()
raw_data = x * np.array([p, p, p])
#point = fvtk.point(raw_data, fvtk.colors.red, point_radius=0.00001)
#fvtk.add(ren, point)
#fvtk.show(ren)
new_sphere = sphere.Sphere(xyz=x)
sf1 = fvtk.sphere_funcs(raw_data, new_sphere, colormap=None, norm=False, scale=0)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
def show_2_generations(C,thr=10.,cthr=0.000442707065162):
r=fvtk.ren()
vs,cinds,ls=bring_virtuals(C)
lvs=len(vs)
vs=[vs[i] for (i,c) in enumerate(cinds) if c>=cthr] #c/ls>=cthr]
#fvtk.add(r,fvtk.line(vs,fvtk.red))
C2=local_skeleton_clustering(vs,thr)
vs2,inds2,ls2=bring_virtuals(C2)
#fvtk.add(r,fvtk.line(vs2,fvtk.green,opacity=0.5))
print 'Initial',lvs,'Thresholded',len(vs),'Recalculated',len(vs2),'Total_Tracks',int(ls)
#fvtk.show(r)
return np.array([lvs,len(vs),len(vs2),int(ls)])
def displaySphericalHist(odf, pts, minmax=False):
# assumes pts and odf are hemisphere
fullsphere = HemiSphere(xyz=pts).mirror()
fullodf = np.concatenate((odf, odf), axis=0)
r = fvtk.ren()
if minmax:
a = fvtk.sphere_funcs(fullodf - fullodf.min(), fullsphere)
else:
a = fvtk.sphere_funcs(fullodf, fullsphere)
fvtk.add(r, a)
fvtk.show(r)
def show_odfs(peaks, sphere, fname):
ren = fvtk.ren()
ren.SetBackground(1, 1, 1.)
odf = np.dot(peaks.shm_coeff, peaks.invB)
#odf = odf[14:24, 22, 23:33]
#odf = odf[:, 22, :]
odf = odf[:, 0, :]
sfu = fvtk.sphere_funcs(odf[:, None, :], sphere, norm=True)
sfu.RotateX(-90)
fvtk.add(ren, sfu)
fvtk.show(ren)
fvtk.record(ren, n_frames=1, out_path=fname, size=(600, 600))
def show_odfs_with_map(odf, sphere, map):
ren = fvtk.ren()
sfu = fvtk.sphere_funcs(odf[:, None, :], sphere, norm=True)
sfu.RotateX(-90)
sfu.SetPosition(5, 5, 1)
sfu.SetScale(0.435)
slice = fvtk.slicer(map, plane_i=None, plane_j=[0])
slice.RotateX(-90)
fvtk.add(ren, slice)
fvtk.add(ren, sfu)
fvtk.show(ren)
def label_streamlines(streamlines, labels, labels_Value, affine, hdr, f_name,
data_path):
cc_slice = labels == labels_Value
cc_streamlines = utils.target(streamlines, labels, affine=affine)
cc_streamlines = list(cc_streamlines)
other_streamlines = utils.target(streamlines,
cc_slice,
affine=affine,
include=False)
other_streamlines = list(other_streamlines)
assert len(other_streamlines) + len(cc_streamlines) == len(streamlines)
print("num of roi steamlines is %d", len(cc_streamlines))
# Make display objects
color = line_colors(cc_streamlines)
cc_streamlines_actor = fvtk.line(cc_streamlines,
line_colors(cc_streamlines))
cc_ROI_actor = fvtk.contour(cc_slice,
levels=[1],
colors=[(1., 1., 0.)],
opacities=[1.])
# Add display objects to canvas
r = fvtk.ren()
fvtk.add(r, cc_streamlines_actor)
fvtk.add(r, cc_ROI_actor)
# Save figures
fvtk.record(r, n_frames=1, out_path=f_name + '_roi.png', size=(800, 800))
fvtk.camera(r, [-1, 0, 0], [0, 0, 0], viewup=[0, 0, 1])
fvtk.record(r, n_frames=1, out_path=f_name + '_roi.png', size=(800, 800))
""""""
csd_streamlines_trk = ((sl, None, None) for sl in cc_streamlines)
csd_sl_fname = f_name + '_roi_streamline.trk'
nib.trackvis.write(csd_sl_fname,
csd_streamlines_trk,
hdr,
points_space='voxel')
#nib.save(nib.Nifti1Image(FA, img.get_affine()), 'FA_map2.nii.gz')
print('Saving "_roi_streamline.trk" sucessful.')
import tractconverter as tc
input_format = tc.detect_format(csd_sl_fname)
input = input_format(csd_sl_fname)
output = tc.FORMATS['vtk'].create(csd_sl_fname + ".vtk", input.hdr)
tc.convert(input, output)
return cc_streamlines
def show_sph_grid():
r=fvtk.ren()
print verts.shape, faces.shape
sph=np.abs(np.dot(gradients[1],verts.T)**2)
print sph.shape
cols=fvtk.colors(sph,'jet')
#fvtk.add(r,fvtk.point(verts,cols,point_radius=.1,theta=10,phi=10))
for (i,v) in enumerate(gradients):
fvtk.label(r,str(i),pos=v,scale=(.02,.02,.02))
if i in [62,76,58]:
fvtk.label(r,str(i),pos=v,scale=(.05,.05,.05),color=(1,0,0))
fvtk.show(r)
def draw_p(p, x, new_sphere):
ren = fvtk.ren()
raw_data = x * np.array([p, p, p])
sf1 = fvtk.sphere_funcs(raw_data,
new_sphere,
colormap=None,
norm=False,
scale=0)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
fvtk.show(ren)
def show_odfs_from_nii(fshm_coeff, finvB, sphere=None):
odf_sh = nib.load(fshm_coeff).get_data()
invB = np.loadtxt(finvB)
odf = np.dot(odf_sh, invB.T)
# odf = odf[14:24, 22, 23:33]
odf = odf[:, 22, :]
if sphere is None:
sphere = get_sphere('symmetric724')
ren = fvtk.ren()
sfu = fvtk.sphere_funcs(odf[:, None, :], sphere, norm=True)
fvtk.add(ren, sfu)
fvtk.show(ren)
def show_odfs(fpng, odf_sh, invB, sphere):
ren = fvtk.ren()
ren.SetBackground(1, 1, 1.0)
odf = np.dot(odf_sh, invB)
print(odf.shape)
odf = odf[14:24, 22, 23:33]
# odf = odf[:, 22, :]
# odf = odf[:, 0, :]
sfu = fvtk.sphere_funcs(odf[:, None, :], sphere, norm=True)
sfu.RotateX(-90)
fvtk.add(ren, sfu)
fvtk.show(ren)
fvtk.record(ren, n_frames=1, out_path=fpng, size=(900, 900))
fvtk.clear(ren)
def test(x,y,z):
fimg,fbvals,fbvecs=get_dataX('small_101D')
img=nib.load(fimg)
data=img.get_data()
print('data.shape (%d,%d,%d,%d)' % data.shape)
bvals=np.loadtxt(fbvals)
bvecs=np.loadtxt(fbvecs).T
S=data[x,y,z,:]
print('S.shape (%d)' % S.shape)
X=diffusivitize(S,bvals,bvecs,scale=10**4)
r=fvtk.ren()
fvtk.add(r,fvtk.point(X,fvtk.green,1,.5,16,16))
fvtk.show(r)
def show_odfs_with_map2(odf, sphere, map, w, fpng):
ren = fvtk.ren()
sfu = fvtk.sphere_funcs(odf, sphere, norm=True)
#sfu.RotateX(-90)
sfu.SetPosition(w, w, 1)
sfu.SetScale(0.435)
sli = fvtk.slicer(map, plane_i=None, plane_k=[0], outline=False)
#sli.RotateX(-90)
fvtk.add(ren, sli)
fvtk.add(ren, sfu)
#fvtk.add(ren, fvtk.axes((20, 20, 20)))
#fvtk.show(ren)
fvtk.record(ren, n_frames=1, out_path=fpng, magnification=2, size=(900, 900))
def draw_odf(data, gtab, odf, sphere_odf):
ren = fvtk.ren()
bvecs = gtab.bvecs
raw_data = bvecs * np.array([data, data, data]).T
# Draw Raw Data as points, Red means outliers
point = fvtk.point(raw_data[~gtab.b0s_mask, :], fvtk.colors.red, point_radius=0.05)
fvtk.add(ren, point)
sf1 = fvtk.sphere_funcs(odf, sphere_odf, colormap=None, norm=False, scale=0)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
fvtk.show(ren)
def show_tracts(estimated_target_tract, target_tract):
"""Visualization of the tracts.
"""
ren = fvtk.ren()
fvtk.add(
ren,
fvtk.line(estimated_target_tract,
fvtk.colors.green,
linewidth=1,
opacity=0.3))
fvtk.add(
ren,
fvtk.line(target_tract, fvtk.colors.white, linewidth=2, opacity=0.3))
fvtk.show(ren)
fvtk.clear(ren)
def show_both_bundles(bundles, colors=None, show=False, fname=None):
ren = fvtk.ren()
ren.SetBackground(1., 1, 1)
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines = fvtk.streamtube(bundle, color, linewidth=0.3)
lines.RotateX(-90)
lines.RotateZ(90)
fvtk.add(ren, lines)
if show:
fvtk.show(ren)
if fname is not None:
sleep(1)
fvtk.record(ren, n_frames=1, out_path=fname, size=(900, 900))
def viz_vol1(vol,color):
ren = fvtk.ren()
ren.SetBackground(255,255,255)
d1, d2, d3 = vol.shape
point = []
for i in np.arange(d1):
for j in np.arange(d2):
for k in np.arange(d3):
if (vol[i, j, k] == 1):
point.append([i,j,k])
pts = fvtk.point(point,color, point_radius=0.85)#0.85)
fvtk.add(ren, pts)
fvtk.show(ren)
def loadPeaksFromMrtrix():
filename='CSD8.nii.gz'
mask='mask.nii.gz'
pkdir,pkval,pkind = getPeaksFromMrtrix(filename, mask)
fodf_peaks = fvtk.peaks(pkdir, pkval, scale=1)
#fodf_spheres = fvtk.sphere_funcs(data_small, sphere, scale=0.6, norm=False)
ren = fvtk.ren()
#fodf_spheres.GetProperty().SetOpacity(0.4)
fvtk.add(ren, fodf_peaks)
#fvtk.add(ren, fodf_peaks)
fvtk.show(ren)
return fodf_peaks
def draw_p(p, x):
ren = fvtk.ren()
raw_data = x * np.array([p, p, p])
#point = fvtk.point(raw_data, fvtk.colors.red, point_radius=0.00001)
#fvtk.add(ren, point)
#fvtk.show(ren)
new_sphere = sphere.Sphere(xyz=x)
sf1 = fvtk.sphere_funcs(raw_data,
new_sphere,
colormap=None,
norm=False,
scale=0)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
def show_both_bundles(bundles, colors=None, show=False, fname=None):
ren = fvtk.ren()
ren.SetBackground(1.0, 1, 1)
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines = fvtk.streamtube(bundle, color, linewidth=0.3)
lines.RotateX(-90)
lines.RotateZ(90)
fvtk.add(ren, lines)
if show:
fvtk.show(ren)
if fname is not None:
sleep(1)
fvtk.record(ren, n_frames=1, out_path=fname, size=(900, 900))
def test_fvtk_functions():
# Create a renderer
r = fvtk.ren()
# Create 2 lines with 2 different colors
lines = [np.random.rand(10, 3), np.random.rand(20, 3)]
colors = np.random.rand(2, 3)
c = fvtk.line(lines, colors)
fvtk.add(r, c)
# Create a volume and return a volumetric actor using volumetric rendering
vol = 100 * np.random.rand(100, 100, 100)
vol = vol.astype('uint8')
r = fvtk.ren()
v = fvtk.volume(vol)
fvtk.add(r, v)
# Remove all objects
fvtk.rm_all(r)
# Put some text
l = fvtk.label(r, text='Yes Men')
fvtk.add(r, l)
def show_tract(segmented_tract_positive, color_positive, color_negative,
segmented_tract_negative):
"""Visualization of the segmented tract.
"""
ren = fvtk.ren()
fvtk.add(
ren,
fvtk.line(segmented_tract_positive.tolist(),
colors=color_positive,
linewidth=2,
opacity=0.3))
# fvtk.add(ren, fvtk.line(segmented_tract_negative.tolist(),
# colors=color_negative,
# linewidth=2,
# opacity=0.3))
fvtk.show(ren)
fvtk.clear(ren)
def show_bundles(streamlines, clusters, show_b=True):
# Color each streamline according to the cluster they belong to.
colormap = fvtk.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
ren = fvtk.ren()
ren.SetBackground(1, 1, 1)
fvtk.add(ren, fvtk.streamtube(streamlines, colormap_full))
fvtk.record(ren,
n_frames=1,
out_path='fornix_clusters_cosine.png',
size=(600, 600))
if show_b:
fvtk.show(ren)
def renderBundles(clusters):
from dipy.viz import fvtk
import numpy as np
ren = fvtk.ren()
ren.SetBackground(0, 0, 0)
colormap = fvtk.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster in clusters:
colormap_full[cluster.indices] = np.random.rand(3)
fvtk.add(ren, fvtk.line(streamlines, colormap_full))
#fvtk.record(ren, n_frames=1, out_path='fornix_clusters.png', size=(600, 600))
fvtk.show(ren)
fvtk.clear(ren)
def renderCentroids(clusters):
from dipy.viz import fvtk
import numpy as np
ren = fvtk.ren()
ren.SetBackground(0, 0, 0)
colormap = fvtk.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster in clusters:
colormap_full[cluster.indices] = np.random.rand(3)
#fvtk.add(ren, fvtk.streamtube(streamlines, fvtk.colors.white, opacity=0.05))
fvtk.add(ren, fvtk.line(clusters.centroids, linewidth=0.4, opacity=1))
#fvtk.record(ren, n_frames=1, out_path='fornix_centroids.png', size=(600, 600))
fvtk.show(ren)
fvtk.clear(ren)
def plot_as_dti(gtab, data, params, dipy_sph, output_dir="."):
logging.info("Fitting data to DTI model...")
tenmodel = dti.TensorModel(gtab)
tenfit = tenmodel.fit(data[params['slice']])
FA = dti.fractional_anisotropy(tenfit.evals)
FA = np.clip(FA, 0, 1)
RGB = dti.color_fa(FA, tenfit.evecs)
cfa = RGB
cfa /= cfa.max()
logging.info("Recording DTI plot...")
camera_params, long_ax, view_ax, stack_ax = \
prepare_plot_camera(data[params['slice']].shape[:-1], scale=2.2)
r = fvtk.ren()
fvtk.add(r, fvtk.tensor(tenfit.evals, tenfit.evecs, cfa, dipy_sph))
r.set_camera(**camera_params)
fname = os.path.join(output_dir, "plot-dti-0.png")
fvtk.snapshot(r, size=(1500, 1500), offscreen=True, fname=fname)
def visualize(streamlines_A,
streamlines_B,
mappingAB,
line='line',
shift=np.array([0.0, 0.0, 200.0]),
color_A=fvtk.colors.white,
color_B=fvtk.colors.green,
color_line=fvtk.colors.yellow):
assert (len(mappingAB) == len(streamlines_A))
assert (mappingAB.max() <= len(streamlines_B))
if line == 'line':
line = fvtk.line
linewidth = 2.0
linekwargs = {'linewidth': linewidth}
elif line == 'tube':
line = fvtk.streamtube
linewidth = 1.0
linekwargs = {'linewidth': linewidth, 'lod': False}
else:
raise Exception
if color_A == 'auto':
color_A = line_colors(streamlines_A)
if color_B == 'auto':
color_B = line_colors(streamlines_B)
streamlines_B_shifted = np.array([s + shift for s in streamlines_B])
midpointA = [s[int(s.shape[0] / 2)] for s in streamlines_A]
midpointB = [s[int(s.shape[0] / 2)] for s in streamlines_B_shifted]
ren = fvtk.ren()
fvtk.add(ren, line(streamlines_A.tolist(), colors=color_A, **linekwargs))
fvtk.add(
ren, line(streamlines_B_shifted.tolist(), colors=color_B,
**linekwargs))
fvtk.add(
ren,
fvtk.line(zip(midpointA, midpointB),
colors=color_line,
opacity=0.5,
linewidth=0.5))
fvtk.show(ren)
def draw_odf(data, gtab, odf, sphere_odf):
ren = fvtk.ren()
bvecs = gtab.bvecs
raw_data = bvecs * np.array([data, data, data]).T
# Draw Raw Data as points, Red means outliers
point = fvtk.point(raw_data[~gtab.b0s_mask, :],
fvtk.colors.red,
point_radius=0.05)
fvtk.add(ren, point)
sf1 = fvtk.sphere_funcs(odf,
sphere_odf,
colormap=None,
norm=False,
scale=0)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
fvtk.show(ren)
def show_both_bundles(bundles, colors=None, show_b=False, fname=None):
"""
Show both bundles
bundles: return of --pyfat/algorithm/fiber_math/bundle_registration
example:
show_both_bundles([cb_subj1, cb_subj2_aligned],
colors=[fvtk.colors.orange, fvtk.colors.red],
fname='after_registration.png')
"""
ren = fvtk.ren()
ren.SetBackground(1., 1, 1)
for (i, bundle) in enumerate(bundles):
color = colors[i]
lines = fvtk.streamtube(bundle, color, linewidth=0.3)
lines.RotateX(-90)
lines.RotateZ(90)
fvtk.add(ren, lines)
if show_b:
fvtk.show(ren)
if fname is not None:
sleep(1)
fvtk.record(ren, n_frames=1, out_path=fname, size=(900, 900))
def test_fvtk_ellipsoid():
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')
ren = fvtk.ren()
fvtk.add(ren, fvtk.tensor(mevals, mevecs, sphere=sphere))
fvtk.add(ren,
fvtk.tensor(mevals, mevecs, np.ones(mevals.shape), sphere=sphere))
assert_equal(ren.GetActors().GetNumberOfItems(), 2)
def draw_points(data, gtab, predicted_data):
ren = fvtk.ren()
bvecs = gtab.bvecs
raw_points = bvecs * np.array([data, data, data]).T
predicted_points = bvecs * np.array(
[predicted_data, predicted_data, predicted_data]).T
# Draw Raw Data as points, Red means outliers
point = fvtk.point(raw_points[~gtab.b0s_mask, :],
fvtk.colors.red,
point_radius=0.02)
fvtk.add(ren, point)
new_sphere = sphere.Sphere(xyz=bvecs[~gtab.b0s_mask, :])
sf1 = fvtk.sphere_funcs(predicted_data[~gtab.b0s_mask],
new_sphere,
colormap=None,
norm=False,
scale=0)
sf1.GetProperty().SetOpacity(0.35)
fvtk.add(ren, sf1)
fvtk.show(ren)
def main():
parser = buildArgsParser()
args = parser.parse_args()
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
ren = fvtk.ren()
if args.points:
points = fvtk.point(bvecs * bvals[..., None] * 0.01,
fvtk.colors.red,
point_radius=.5)
fvtk.add(ren, points)
if args.antipod:
points = fvtk.point(-bvecs * bvals[..., None] * 0.01,
fvtk.colors.green,
point_radius=.5)
fvtk.add(ren, points)
else:
for i in range(bvecs.shape[0]):
label = fvtk.label(ren,
text=str(i),
pos=bvecs[i] * bvals[i] * 0.01,
color=fvtk.colors.red,
scale=(0.5, 0.5, 0.5))
fvtk.add(ren, label)
if args.antipod:
label = fvtk.label(ren,
text=str(i),
pos=-bvecs[i] * bvals[i] * 0.01,
color=fvtk.colors.green,
scale=(0.5, 0.5, 0.5))
fvtk.add(ren, label)
fvtk.show(ren)
points_space='voxel')
"""
If you don't want to use Trackvis to visualize the file you can use our
lightweight `fvtk` module.
"""
try:
from dipy.viz import fvtk
except ImportError:
raise ImportError('Python vtk module is not installed')
sys.exit()
"""
Create a scene.
"""
ren = fvtk.ren()
"""
Every streamline will be coloured according to its orientation
"""
from dipy.viz.colormap import line_colors
"""
fvtk.line adds a streamline actor for streamline visualization
and fvtk.add adds this actor in the scene
"""
fvtk.add(ren,
fvtk.streamtube(tensor_streamlines, line_colors(tensor_streamlines)))
print('Saving illustration as tensor_tracks.png')
"""
sphere = get_sphere('symmetric724')
"""
Compute the ODFs
The radial order s can be increased to sharpen the results, but it might
also make the odfs noisier. Always check the results visually.
"""
odf = mapfit_both_iso.odf(sphere, s=2)
print('odf.shape (%d, %d, %d, %d)' % odf.shape)
"""
Display the ODFs
"""
r = fvtk.ren()
sfu = fvtk.sphere_funcs(odf, sphere, colormap='jet')
sfu.RotateX(-90)
fvtk.add(r, sfu)
fvtk.record(r, n_frames=1, out_path='odfs.png', size=(600, 600))
"""
.. figure:: odfs.png
:align: center
**Orientation distribution functions**.
.. [Ozarslan2013]_ Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A
novel diffusion imaging method for mapping tissue
microstructure", NeuroImage, 2013.
.. [Fick2016]_ Fick, Rutger HJ, et al. "MAPL: Tissue microstructure estimation