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_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 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 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_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 show_signal(r,S,gradients,offset=np.zeros(3)):
PS = np.dot(np.diag(S),gradients)
#for (i,s) in enumerate(S):
fvtk.add(r,fvtk.point(offset+PS/np.max(PS),fvtk.cyan,point_radius=0.05,theta=8,phi=8))
fvtk.add(r,fvtk.point([offset],fvtk.green,point_radius=0.1,theta=8,phi=8))
fvtk.add(r,fvtk.axes((1,1,1)))
lines = fvtk.line([1.5*np.row_stack((needles3d[0],-needles3d[0])), \
1.5*np.row_stack((needles3d[1],-needles3d[1]))], \
colors=np.row_stack((fvtk.golden,fvtk.aquamarine)),linewidth=10)
fvtk.add(r,lines)
def investigate_pca():
data,bvals,bvecs=get_data(name='118_32')
deg_angles=rotate_needles(needles=[(0,0),(90,0),(90,90)],angles=(0,0,0))
S0,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=deg_angles,fractions=[100,0,0],snr=None)
X0=diffusivitize(S0,bvals,bvecs,invert=False)
D0=np.sqrt(np.sum(X0**2,axis=1))
print 'D0 shape',D0.shape
deg_angles=rotate_needles(needles=[(0,0),(90,0),(90,90)],angles=(0,0,0))
S1,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=deg_angles,fractions=[0,100,0],snr=None)
X1=diffusivitize(S1,bvals,bvecs,invert=False)
D1=np.sqrt(np.sum(X1**2,axis=1))
deg_angles=rotate_needles(needles=[(0,0),(90,0),(90,90)],angles=(0,0,0))
S2,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=deg_angles,fractions=[0,0,100],snr=None)
X2=diffusivitize(S2,bvals,bvecs,invert=False)
D2=np.sqrt(np.sum(X2**2,axis=1))
deg_angles=rotate_needles(needles=[(0,0),(90,0),(90,90)],angles=(0,0,0))
SM,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=deg_angles,fractions=[33,33,33],snr=None)
XM=diffusivitize(SM,bvals,bvecs,invert=False)
DM=np.sqrt(np.sum(XM**2,axis=1))
deg_angles=rotate_needles(needles=[(0,0),(90,0),(90,90)],angles=(0,0,0))
SM2,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=deg_angles,fractions=[50,50,0],snr=None)
XM2=diffusivitize(SM2,bvals,bvecs,invert=False)
DM2=np.sqrt(np.sum(XM2**2,axis=1))
X012=(X0+X1+X2)/3.
S012=(S0+S1+S2)/3.
D012=(D0+D1+D2)/3.
X01=(X0+X1)/2.
print 'D', np.corrcoef(DM,D012)
print 'X', np.corrcoef(np.sqrt(np.sum(XM**2,axis=1)), np.sqrt(np.sum(X012**2,axis=1)))
r=fvtk.ren()
fvtk.add(r,fvtk.point(X01,fvtk.yellow,1,.2,16,16))
fvtk.add(r,fvtk.point(XM2,fvtk.red,1,.2,16,16))
fvtk.show(r)
def show_signals(r,Signals,bvecs,offset=0):
#r=fvtk.ren()
global CNT
Bvecs=np.concatenate([bvecs[1:],-bvecs[1:]])
for (i,S) in enumerate(Signals):
X=np.dot(np.diag(np.concatenate([50*S,50*S])),Bvecs)
mX=np.mean(np.sqrt(X[:,0]**2+X[:,1]**2+X[:,2]**2))
print CNT,mX,np.var(S)
CNT=CNT+1
fvtk.add(r,fvtk.point(X+np.array([(i+1)*200,offset,0]),fvtk.green,1,2,6,6))
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 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 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)
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 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 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 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 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 simulations_marta():
#gq_tn_calc_save()
#a_few_phantoms()
#sd=['fibres_2_SNR_100_angle_60_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
#sd=['fibres_2_SNR_60_angle_60_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
#sd=['fibres_2_SNR_100_angle_60_l1_1.4_l2_0.35_l3_0.35_iso_1_diso_0.7']
sd=['fibres_2_SNR_100_angle_90_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
#sd=['fibres_1_SNR_100_angle_00_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
#sd=['fibres_2_SNR_20_angle_90_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
#for simfile in simdata:
np.set_printoptions(2)
dotpow=6
width=6
sincpow=2
sampling_length=1.2
print dotpow,width,sincpow
print sampling_length
verts,faces=get_sphere('symmetric362')
for simfile in sd:
data=np.loadtxt(simdir+simfile)
sf=simfile.split('_')
b_vals_dirs=np.loadtxt(simdir+'Dir_and_bvals_DSI_marta.txt')
bvals=b_vals_dirs[:,0]*1000
gradients=b_vals_dirs[:,1:]
data2=data[::1000,:]
table={'fibres':sf[1],'snr':sf[3],'angle':sf[5],'l1':sf[7],'l2':sf[9],\
'l3':sf[11],'iso':sf[13],'diso':sf[15],\
'data':data2,'bvals':bvals,'gradients':gradients}
print table['data'].shape
pdi=ProjectiveDiffusivity(table['data'],table['bvals'],table['gradients'],dotpow,width,sincpow)
gqs=GeneralizedQSampling(table['data'],table['bvals'],table['gradients'],sampling_length)
ten=Tensor(table['data'],table['bvals'],table['gradients'])
r=fvtk.ren()
for i in range(10):#range(len(sdi.xa())):
print 'No:',i
print 'simulation fibres ',table['fibres'], ' snr ',table['snr'],' angle ', table['angle']
pdiind=pdi.ind()[i]
gqsind=gqs.ind()[i]
print 'indices',pdiind,gqsind,\
np.rad2deg(np.arccos(np.dot(verts[pdiind[0]],verts[pdiind[1]]))),\
np.rad2deg(np.arccos(np.dot(verts[gqsind[0]],verts[gqsind[1]])))
#ten.ind()[i],
print 'peaks', pdi.xa()[i]*10**3,gqs.qa()[i]
pd=pdi.spherical_diffusivity(table['data'][i])#*10**3
#print 'pd stat',pd.min(),pd.max(),pd.mean(),pd.std()
#colors=fvtk.colors(sdf,'jet')
sdfcol=np.interp(pd,[pd.mean()-4*pd.std(),pd.mean()+4*pd.std()],[0,1])
colors=fvtk.colors(sdfcol,'jet',False)
fvtk.add(r,fvtk.point(5*pdi.odf_vertices+np.array([12*i,0,0]),colors,point_radius=.6,theta=10,phi=10))
odf=gqs.odf(table['data'][i])
colors=fvtk.colors(odf,'jet')
fvtk.add(r,fvtk.point(5*gqs.odf_vertices+np.array([12*i,-12,0]),colors,point_radius=.6,theta=10,phi=10))
fvtk.show(r)
R2=(np.trace(np.dot(X0,XM.T))**2)/(np.trace(np.dot(X0,X0.T))*np.trace(np.dot(XM,XM.T)))
print R2
fvtk.show(r)
"""
if __name__=='__main__':
data,bvals,bvecs=get_data('515_32')
D=[0,-1,1,-2,2,-3,3,-4,4,-5,5,-6,6]
cnt=0
for a in D:
for b in D:
for c in D:
if a**2+b**2+c**2<=36:
cnt+=1
print cnt
for (i,g) in enumerate(bvecs[2:]):
if np.sum((bvecs[1]+g)**2)<0.0001:
print 2+i,g
bvecs[0]=np.array([0,0,0])
qtable=np.vstack((bvals,bvals,bvals)).T * bvecs
r=fvtk.ren()
fvtk.add(r,fvtk.point(qtable/qtable.max(),fvtk.red,1,0.01,6,6))
fvtk.show(r)
#print grad3.shape
#vertices = grad3*gradients
vertices = gradients
if omit > 0:
vertices = vertices[omit:,:]
if entry['hemi']:
vertices = np.vstack([vertices, -vertices])
return vertices[omit:,:]
print sphere_dic.keys()
#vertices = get_vertex_set('create5')
#vertices = get_vertex_set('siem64')
#vertices = get_vertex_set('dsi102')
vertices = get_vertex_set('fy362')
gradients = get_vertex_set('siem64')
gradients = gradients[:gradients.shape[0]/2]
print gradients.shape
from dipy.viz import fvtk
sph=-np.sinc(np.dot(gradients[1],vertices.T))
r=fvtk.ren()
#sph = np.arange(vertices.shape[0])
print sph.shape
cols=fvtk.colors(sph,'jet')
fvtk.add(r,fvtk.point(vertices,cols,point_radius=.1,theta=10,phi=10))
fvtk.show(r)
# Extract feature of every streamline.
centers = np.asarray(map(feature.extract, streamlines))
# Color each center of mass according to the cluster they belong to.
rng = np.random.RandomState(42)
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
# Visualization
ren = fvtk.ren()
fvtk.clear(ren)
ren.SetBackground(0, 0, 0)
fvtk.add(ren, fvtk.streamtube(streamlines, fvtk.colors.white, opacity=0.05))
fvtk.add(ren, fvtk.point(centers[:, 0, :], colormap_full, point_radius=0.2))
fvtk.record(ren,
n_frames=1,
out_path='center_of_mass_feature.png',
size=(600, 600))
"""
.. figure:: center_of_mass_feature.png
:align: center
**Showing the center of mass of each streamline and colored according to
the QuickBundles results**.
.. _clustering-examples-MidpointFeature:
Midpoint Feature
================
# Extract feature of every streamline.
centers = np.asarray(map(feature.extract, streamlines))
# Color each center of mass according to the cluster they belong to.
rng = np.random.RandomState(42)
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
# Visualization
ren = fvtk.ren()
fvtk.clear(ren)
ren.SetBackground(0, 0, 0)
fvtk.add(ren, fvtk.streamtube(streamlines, fvtk.colors.white, opacity=0.05))
fvtk.add(ren, fvtk.point(centers[:, 0, :], colormap_full, point_radius=0.2))
fvtk.record(ren, n_frames=1, out_path='center_of_mass_feature.png', size=(600, 600))
"""
.. figure:: center_of_mass_feature.png
:align: center
**Showing the center of mass of each streamline and colored according to
the QuickBundles results**.
.. _clustering-examples-MidpointFeature:
Midpoint Feature
================
**What:** Instances of `MidpointFeature` extract the middle point of a
streamline. If there is an even number of points, the feature will then
def codebook_invest():
data,bvals,bvecs=get_data(name='118_32',par=0)
CBK,STK,FRA,REG=codebook(bvals,bvecs,fractions=True)
Bvecs=np.concatenate([bvecs[1:],-bvecs[1:]])
S0,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=[(0,0),(90,0),(90,90)],fractions=[0,100,0],snr=None)
#S0=S0*bvals/1000
#S0=S0[0]-S0
#S0=100*S0/S0[0]
SIN=CBK[:33]
SIN_STK=STK[:33]
#SIN=S0-SIN
ASIN=np.sum(SIN,axis=1)
print '#####################'
print ASIN.min(), ASIN.argmin(), SIN_STK[ASIN.argmin()]
print ASIN.max(), ASIN.argmax(), SIN_STK[ASIN.argmax()]
print '#####################'
#S0=np.abs(S0-SIN[ASIN.argmax()])
X0=np.dot(np.diag(np.concatenate([S0[1:],S0[1:]])),Bvecs)
#P0=np.fft.ifftn(X0)
#P0=P0/np.sqrt(np.sum(P0[:,0]**2+P0[:,1]**2+P0[:,2]**2,axis=1))
#S0=CBK[2000]
#S0=S0[0]-S0
#X0=np.dot(np.diag(np.concatenate([S0[1:],S0[1:]])),Bvecs)
S0MF0=match_codebook(S0,CBK,REG,type=0)
S0MF1=match_codebook(S0,CBK,REG,type=1)
S0MF2=match_codebook(S0,CBK,REG,type=2)
S0MF3=match_codebook(S0,CBK,REG,type=3)
#S0M=S0M[0]-S0M
X0M=np.dot(np.diag(np.concatenate([S0MF0[1:],S0MF0[1:]])),Bvecs)
r=fvtk.ren()
fvtk.add(r,fvtk.point(X0,fvtk.yellow,1,2,16,16))
draw_needles(r,sticks0,100,2)
l=[]
for i in range(len(SIN)):
S=S0-SIN[i]
print '>>>>'
print SIN_STK[i]
print i, np.sum(S[1:]),np.mean(S[1:]),np.var(S[1:])
l.append(np.var(S[1:]))
"""
X=np.dot(np.diag(np.concatenate([S[1:],S[1:]])),Bvecs)
fvtk.add(r,fvtk.point(X+(i+1-14)*np.array([200,0,0]),fvtk.green,1,2,8,8))
XSIN=np.dot(np.diag(np.concatenate([SIN[i][1:],SIN[i][1:]])),Bvecs)
fvtk.add(r,fvtk.point(XSIN+np.array([(i+1-14)*200,-200,0]),fvtk.yellow,1,2,8,8))
draw_needles(r,sticks0,100,2,off=(i+1-14)*np.array([200,0,0]))
"""
print np.array(l).argmin()
print '#=<>'
print np.argsort(l)
#fvtk.add(r,fvtk.point(0.01*P0,fvtk.green,1,2,16,16))
#fvtk.add(r,fvtk.point(100*P0,fvtk.green,1,2,16,16))
#fvtk.add(r,fvtk.point(X0M,fvtk.cyan,1,2,16,16))
fvtk.show(r)
"""
from dipy.viz import fvtk
from prepare_phantoms import get_data,codebook,simulations_dipy
data,bvals,bvecs=get_data(name='118_32',par=0)
CBK,STK,FRA,REG=codebook(bvals,bvecs,fractions=True)
Bvecs=np.concatenate([bvecs[1:],-bvecs[1:]])
#S0,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=[(0,0),(45,0),(90,90)],fractions=[100,0,0],snr=None)
SIN=CBK[:33]
ST0=SIN[0]
ST1=SIN[2]
ST2=SIN[4]
XST0=np.dot(np.diag(np.concatenate([ST0[1:],ST0[1:]])),Bvecs)
XST1=np.dot(np.diag(np.concatenate([ST1[1:],ST1[1:]])),Bvecs)
XST2=np.dot(np.diag(np.concatenate([ST2[1:],ST2[1:]])),Bvecs)
r=fvtk.ren()
#fvtk.add(r,fvtk.point(.5*XST0-1.*XST1,fvtk.green,1,2,8,8))
the_vals = XST0*0.5+XST1*0.5
fvtk.add(r,fvtk.point(XST0,fvtk.green,1,2,8,8))
fvtk.add(r,fvtk.point(XST1,fvtk.red,1,2,8,8))
fvtk.add(r,fvtk.point(the_vals,fvtk.yellow,1,2,8,8))
fvtk.add(r,fvtk.point(XST0-XST1,fvtk.cyan,1,2,8,8))
#fvtk.add(r,fvtk.point(-XST0,fvtk.green,1,2,8,8))
fvtk.show(r)
pointA = [0.48412286, 0.97713726, 0.74590314]
pointB = [0.07821987, 0.13495185, 0.7239567]
pointC = [0.79723847, 0.06467979, 0.45524464]
pointD = [0.25058964, 0.83944661, 0.16528851]
pointE = [0.61336066, 0.28185135, 0.94522671]
example_xyz = np.array([pointA,
pointB,
pointC,
pointD,
pointE])
ren = fvtk.ren()
point_actor = fvtk.point(example_xyz, fvtk.colors.blue_light)
fvtk.add(ren, point_actor)
lineAB = np.array([pointA, pointB])
lineBC = np.array([pointB, pointC])
lineCD = np.array([pointC, pointD])
lineCE = np.array([pointC, pointE])
line_color = [0.9, 0.97, 1.0]
line_actor_AB = fvtk.line(lineAB, line_color)
line_actor_BC = fvtk.line(lineBC, line_color)
line_actor_CD = fvtk.line(lineCD, line_color)
line_actor_CE = fvtk.line(lineCE, line_color)
fvtk.add(ren, line_actor_AB)
#print grad3.shape
#vertices = grad3*gradients
vertices = gradients
if omit > 0:
vertices = vertices[omit:, :]
if entry['hemi']:
vertices = np.vstack([vertices, -vertices])
return vertices[omit:, :]
print sphere_dic.keys()
#vertices = get_vertex_set('create5')
#vertices = get_vertex_set('siem64')
#vertices = get_vertex_set('dsi102')
vertices = get_vertex_set('fy362')
gradients = get_vertex_set('siem64')
gradients = gradients[:gradients.shape[0] / 2]
print gradients.shape
from dipy.viz import fvtk
sph = -np.sinc(np.dot(gradients[1], vertices.T))
r = fvtk.ren()
#sph = np.arange(vertices.shape[0])
print sph.shape
cols = fvtk.colors(sph, 'jet')
fvtk.add(r, fvtk.point(vertices, cols, point_radius=.1, theta=10, phi=10))
fvtk.show(r)
label_coords = np.loadtxt('labels_coords_86.txt')
labelsConnectivity = np.loadtxt('allconnectivityMatrix.txt')
lines_color = [205 / 255.0, 247 / 255.0, 255 / 255.0]
points_color = [2 / 255.0, 128 / 255.0, 232 / 255.0]
lines = []
for columnNumber in range(86):
for rowNumber in range(86):
if labelsConnectivity[columnNumber][rowNumber] > 20:
lines.append([label_coords[columnNumber], label_coords[rowNumber]])
ren = fvtk.ren()
pointActors = fvtk.point(label_coords,
points_color,
opacity=0.8,
point_radius=3)
lineActors = fvtk.line(lines, lines_color, opacity=0.2, linewidth=2)
fvtk.add(ren, pointActors)
fvtk.add(ren, lineActors)
# to explore the data in 3D interactive way
# fvtk.show(ren)
# save figure
fvtk.camera(ren, [-1, -1, 0], [0, 0, 0], viewup=[0, 0, 1])
fvtk.record(ren,
n_frames=1,
out_path='brain_network_example.png',
def playing_with_diffusivities_and_simulations():
data,bvals,bvecs=get_data(name='101_32')
#S=data[:,:,42]
#drange=np.linspace(0,40,5)
S1,sticks1=simulations_dipy(bvals,bvecs,d=0.0015,S0=200,angles=[(0,0),(90,0)],fractions=[50,50],snr=None)
S2,sticks2=simulations_dipy(bvals,bvecs,d=0.0015,S0=200,angles=[(0,0),(90,0),(90,90)],fractions=[33,33,33],snr=None)
scale=10**4
ob=-1/bvals[1:]
D1=ob*(np.log(S1[1:])-np.log(S1[0]))*scale
D2=ob*(np.log(S2[1:])-np.log(S2[0]))*scale
Bvecs=np.concatenate([bvecs[1:],-bvecs[1:]])
SS1=np.concatenate([S1[1:],S1[1:]])
SS2=np.concatenate([S2[1:],S2[1:]])
DD1=np.concatenate([D1,D1])
DD2=np.concatenate([D2,D2])
X1=np.dot(np.diag(DD1),Bvecs)
X2=np.dot(np.diag(DD2),Bvecs)
U,s,V=np.linalg.svd(np.dot(X1.T,X2),full_matrices=True)
R=np.dot(U,V.T)
print np.round(R,2)
print np.sum(np.dot(X1,R)-X2,axis=0)
r=fvtk.ren()
fvtk.add(r,fvtk.point(X1,fvtk.red,1,.5,16,16))
fvtk.add(r,fvtk.point(X2,fvtk.green,1,.5,16,16))
fvtk.add(r,fvtk.axes((10,10,10)))
fvtk.show(r)
U1,s1,V1=np.linalg.svd(np.dot(X1.T,X1),full_matrices=True)
U2,s2,V2=np.linalg.svd(np.dot(X2.T,X2),full_matrices=True)
u1=U1[:,2]
u2=U2[:,2]
R2=vec2vecrotmat(u1,u2)
print np.round(R2,2)
print np.rad2deg(np.arccos(np.dot(u1,u2)))
uu1=np.zeros((2,3))
uu1[1]=u1
uu2=np.zeros((2,3))
uu2[1]=u2
kX1=online_kurtosis(X1)
kX2=online_kurtosis(X2)
print 's1',s1
print 's2',s2
print 'kX1',kX1
print 'kX2',kX2
print 'average diffusivity 1',np.mean(np.linalg.norm(X1))
print 'average diffusivity 2',np.mean(np.linalg.norm(X2))
Next, we call `disperse_charges` which will iteratively move the points so that
the electrostatic potential energy is minimized.
"""
hsph_updated, potential = disperse_charges(hsph_initial, 5000)
"""
In ``hsph_updated` we have the updated HemiSphere with the points nicely
distributed on the hemisphere. Let's visualize them.
"""
from dipy.viz import fvtk
ren = fvtk.ren()
ren.SetBackground(1, 1, 1)
fvtk.add(ren,
fvtk.point(hsph_initial.vertices, fvtk.colors.red, point_radius=0.05))
fvtk.add(
ren, fvtk.point(hsph_updated.vertices,
fvtk.colors.green,
point_radius=0.05))
print('Saving illustration as initial_vs_updated.png')
fvtk.record(ren, out_path='initial_vs_updated.png', size=(300, 300))
"""
.. figure:: initial_vs_updated.png
:align: center
**Example of electrostatic repulsion of red points which become green points**.
We can also create a sphere from the hemisphere and show it in the following way.
"""
import numpy as np
from dipy.viz import fvtk
from prepare_phantoms import get_data,codebook,simulations_dipy,draw_needles
data,bvals,bvecs=get_data(name='118_32',par=0)
CBK,STK,FRA,REG=codebook(bvals,bvecs,fractions=True)
Bvecs=np.concatenate([bvecs[1:],-bvecs[1:]])
S0,sticks0=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=[(0,0),(90,0),(90,90)],fractions=[100,0,0],snr=None)
S1,sticks1=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=[(0,0),(90,0),(90,90)],fractions=[50,50,0],snr=None)
S2,sticks2=simulations_dipy(bvals,bvecs,d=0.0015,S0=100,angles=[(0,0),(45,0),(90,90)],fractions=[50,50,0],snr=None)
SIN=CBK[:33]
r=fvtk.ren()
X0=np.dot(np.diag(np.concatenate([S0[1:],S0[1:]])),Bvecs)
fvtk.add(r,fvtk.point(X0,fvtk.red,1,2,8,8))
X1=np.dot(np.diag(np.concatenate([S1[1:],S1[1:]])),Bvecs)
fvtk.add(r,fvtk.point(X1+np.array([200,0,0]),fvtk.green,1,2,8,8))
X2=np.dot(np.diag(np.concatenate([S2[1:],S2[1:]])),Bvecs)
fvtk.add(r,fvtk.point(X2+np.array([400,0,0]),fvtk.blue,1,2,8,8))
for i in range(0,10):#len(SIN)):
S=SIN[i]
X=np.dot(np.diag(np.concatenate([S[1:],S[1:]])),Bvecs)
fvtk.add(r,fvtk.point(X+np.array([i*200,-200,0]),fvtk.green,1,2,8,8))
#draw_needles(r,sticks0,100,2,off=(i+1)*np.array([200,0,0]))
fvtk.show(r)
def show_graph_values(rt, bundle, show_final=True):
#r.add(streamlines_actor)
#actor_slicer = actor.slicer(FA, interpolation='nearest')
#r.add(actor_slicer)
if not show_final:
window.show(r)
colors2 = np.array((0, 1, 1))
color3 = np.array((1, 1, 1))
colors = np.array((1, 0, 0))
colors1 = np.array((0, 1, 0))
goal_point = np.array([35, 67, 41])
#goal_point = np.array([37,53,59])
starting_point = np.array([53, 65, 40])
#starting_point = np.array([42,55,20])
goal_point = goal_point[None, :]
#r.add(point_actor1)
#r.AddActor(point_actor1)
#r.add(point_actor2)
#r.AddActor(point_actor2)
r = window.Renderer()
r.add(actor.line(bundle))
#def time_event(obj, ev):
#time.sleep(20)
for i in range(len(rt.seeds_nodes_graph)):
#print(i)
#r.clear()
#node_actor = actor.streamtube([nodes[100]])
if len(rt.seeds_nodes_graph[i].graph.shape) == 1:
#colors = np.random.rand(1,3)
colors = np.array((1, 1, 1))
if np.array(rt.seeds_nodes_graph[i].value) > 0:
colors = np.array(
(1, 1 - rt.seeds_nodes_graph[i].value[0] / 100,
1 - rt.seeds_nodes_graph[i].value[0] / 100))
else:
max_value = np.abs(rt.seeds_nodes_graph[i].value.max())
ss = np.where(rt.seeds_nodes_graph[i].value < 0)[0]
colors = np.ones((rt.seeds_nodes_graph[i].graph.shape[0], 3))
#colors[:,2] = 1 - seeds_nodes_graph[i].value/max_value
#colors[:,1] = 1 - seeds_nodes_graph[i].value/max_value
colors[ss, 2] = 1
colors[ss, 1] = 1
sss = np.where(rt.seeds_nodes_graph[i].value > 0)[0]
colors[sss, 1] = 0
colors[sss, 2] = 0
#if rt.seeds_nodes_graph[i].value.max()>0:
#colors = np.zeros((seeds_nodes_graph[i].graph.shape[0],3))
#colors[:,0] = 1
#streamlines_sub.append(rt.seeds_nodes_graph[i].graph)
if len(rt.seeds_nodes_graph[i].graph.shape) == 1:
point_actor = fvtk.point(rt.seeds_nodes_graph[i].graph[None, :],
colors,
point_radius=0.3)
else:
point_actor = fvtk.point(rt.seeds_nodes_graph[i].graph,
colors,
point_radius=0.3)
r.add(point_actor)
#r.AddActor(point_actor)
#iren = obj
#iren.GetRenderWindow().Render()
if not show_final:
window.show(r)
#peak_slicer = actor.line(streamlines_sub)
#r.add(peak_slicer)
if show_final:
window.show(r)
label_coords = np.loadtxt('labels_coords_86.txt')
labelsConnectivity = np.loadtxt('allconnectivityMatrix.txt')
lines_color = [205/255.0,247/255.0,255/255.0]
points_color = [2/255.0, 128/255.0, 232/255.0]
lines = []
for columnNumber in range(86):
for rowNumber in range(86):
if labelsConnectivity[columnNumber][rowNumber] > 20 :
lines.append([label_coords[columnNumber],label_coords[rowNumber]])
ren = fvtk.ren()
pointActors = fvtk.point(label_coords, points_color, opacity=0.8, point_radius=3)
lineActors = fvtk.line(lines, lines_color, opacity=0.2, linewidth=2)
fvtk.add(ren, pointActors)
fvtk.add(ren, lineActors)
# to explore the data in 3D interactive way
# fvtk.show(ren)
# save figure
fvtk.camera(ren, [-1, -1, 0], [0, 0, 0], viewup=[0, 0, 1])
fvtk.record(ren, n_frames=1,
out_path='brain_network_example.png',
Next, we call `disperse_charges` which will iteratively move the points so that
the electrostatic potential energy is minimized.
"""
hsph_updated, potential = disperse_charges(hsph_initial, 5000)
"""
In ``hsph_updated` we have the updated HemiSphere with the points nicely
distributed on the hemisphere. Let's visualize them.
"""
from dipy.viz import fvtk
ren = fvtk.ren()
ren.SetBackground(1, 1, 1)
fvtk.add(ren, fvtk.point(hsph_initial.vertices, fvtk.colors.red, point_radius=0.05))
fvtk.add(ren, fvtk.point(hsph_updated.vertices, fvtk.colors.green, point_radius=0.05))
print("Saving illustration as initial_vs_updated.png")
fvtk.record(ren, out_path="initial_vs_updated.png", size=(300, 300))
"""
.. figure:: initial_vs_updated.png
:align: center
**Example of electrostatic repulsion of red points which become green points**.
We can also create a sphere from the hemisphere and show it in the following way.
"""
sph = Sphere(xyz=np.vstack((hsph_updated.vertices, -hsph_updated.vertices)))
def main():
parser = _build_arg_parser()
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
assert_inputs_exist(parser, [args.bvecs_in, args.eddyparams])
assert_outputs_exists(parser, args,
[args.bvecs_out, args.trans, args.angles])
_, bvecs = read_bvals_bvecs(None, args.bvecs_in)
eddy = np.loadtxt(args.eddyparams)
eddy_a = np.array(eddy)
bvecs_rotated = np.zeros(bvecs.shape)
norm_diff = np.zeros(bvecs.shape[0])
angle = np.zeros(bvecs.shape[0])
# Documentation here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq
# Will eddy rotate my bvecs for me?
# No, it will not. There is nothing to prevent you from doing that
# yourself though. eddy produces two output files, one with the corrected
# images and another a text file with one row of parameters for each volume
# in the --imain file. Columns 4-6 of these rows pertain to rotation
# (in radians) around around the x-, y- and z-axes respectively.
# eddy uses "pre-multiplication".
# IMPORTANT: from various emails with FSL's people, we couldn't directly
# get the information about the handedness of the system.
# From the FAQ linked earlier, we deduced that the system
# is considered left-handed, and therefore the following
# matrices are correct.
for i in range(len(bvecs)):
theta_x = eddy_a[i, 3]
theta_y = eddy_a[i, 4]
theta_z = eddy_a[i, 5]
Rx = np.array([[1, 0, 0], [0, np.cos(theta_x),
np.sin(theta_x)],
[0, -np.sin(theta_x),
np.cos(theta_x)]])
Ry = np.array([[np.cos(theta_y), 0, -np.sin(theta_y)], [0, 1, 0],
[np.sin(theta_y), 0,
np.cos(theta_y)]])
Rz = np.array([[np.cos(theta_z), np.sin(theta_z), 0],
[-np.sin(theta_z), np.cos(theta_z), 0], [0, 0, 1]])
v = bvecs[i, :]
rotation_matrix = np.linalg.inv(np.dot(np.dot(Rx, Ry), Rz))
v_rotated = np.dot(rotation_matrix, v)
bvecs_rotated[i, :] = v_rotated
norm_diff[i] = np.linalg.norm(v - v_rotated)
if np.linalg.norm(v):
angle[i] = np.arctan2(np.linalg.norm(np.cross(v, v_rotated)),
np.dot(v, v_rotated))
logging.info('%s mm is the maximum translation error', np.max(norm_diff))
logging.info('%s degrees is the maximum rotation error',
np.max(angle) * 180 / np.pi)
if args.vis:
print('Red points are the original & Green points are the motion '
'corrected ones')
ren = fvtk.ren()
sphere_actor = fvtk.point(bvecs,
colors=fvtk.colors.red,
opacity=1,
point_radius=0.01,
theta=10,
phi=20)
fvtk.add(ren, sphere_actor)
sphere_actor_rot = fvtk.point(bvecs_rotated,
colors=fvtk.colors.green,
opacity=1,
point_radius=0.01,
theta=10,
phi=20)
fvtk.add(ren, sphere_actor_rot)
fvtk.show(ren)
fvtk.record(ren,
n_frames=1,
out_path=args.bvecs_out + '.png',
size=(600, 600))
np.savetxt(args.bvecs_out, bvecs_rotated.T)
if args.trans:
np.savetxt(args.trans, norm_diff)
if args.angles:
np.savetxt(args.angles, angle * 180 / np.pi)
def test():
# img=nib.load('/home/eg309/Data/project01_dsi/connectome_0001/tp1/RAWDATA/OUT/mr000001.nii.gz')
btable = np.loadtxt(get_data("dsi515btable"))
# volume size
sz = 16
# shifting
origin = 8
# hanning width
filter_width = 32.0
# number of signal sampling points
n = 515
# odf radius
radius = np.arange(2.1, 6, 0.2)
# create q-table
bv = btable[:, 0]
bmin = np.sort(bv)[1]
bv = np.sqrt(bv / bmin)
qtable = np.vstack((bv, bv, bv)).T * btable[:, 1:]
qtable = np.floor(qtable + 0.5)
# copy bvals and bvecs
bvals = btable[:, 0]
bvecs = btable[:, 1:]
# S=img.get_data()[38,50,20]#[96/2,96/2,20]
S, stics = SticksAndBall(
bvals, bvecs, d=0.0015, S0=100, angles=[(0, 0), (60, 0), (90, 90)], fractions=[0, 0, 0], snr=None
)
S2 = S.copy()
S2 = S2.reshape(1, len(S))
dn = DiffusionNabla(S2, bvals, bvecs, auto=False)
pR = dn.equators
odf = dn.odf(S)
# Xs=dn.precompute_interp_coords()
peaks, inds = peak_finding(odf.astype("f8"), dn.odf_faces.astype("uint16"))
print peaks
print peaks / peaks.min()
# print dn.PK
dn.fit()
print dn.PK
# """
ren = fvtk.ren()
colors = fvtk.colors(odf, "jet")
fvtk.add(ren, fvtk.point(dn.odf_vertices, colors, point_radius=0.05, theta=8, phi=8))
fvtk.show(ren)
# """
stop
# ds=DiffusionSpectrum(S2,bvals,bvecs)
# tpr=ds.pdf(S)
# todf=ds.odf(tpr)
"""
#show projected signal
Bvecs=np.concatenate([bvecs[1:],-bvecs[1:]])
X0=np.dot(np.diag(np.concatenate([S[1:],S[1:]])),Bvecs)
ren=fvtk.ren()
fvtk.add(ren,fvtk.point(X0,fvtk.yellow,1,2,16,16))
fvtk.show(ren)
"""
# qtable=5*matrix[:,1:]
# calculate radius for the hanning filter
r = np.sqrt(qtable[:, 0] ** 2 + qtable[:, 1] ** 2 + qtable[:, 2] ** 2)
# setting hanning filter width and hanning
hanning = 0.5 * np.cos(2 * np.pi * r / filter_width)
# center and index in q space volume
q = qtable + origin
q = q.astype("i8")
# apply the hanning filter
values = S * hanning
"""
#plot q-table
ren=fvtk.ren()
colors=fvtk.colors(values,'jet')
fvtk.add(ren,fvtk.point(q,colors,1,0.1,6,6))
fvtk.show(ren)
"""
# create the signal volume
Sq = np.zeros((sz, sz, sz))
for i in range(n):
Sq[q[i][0], q[i][1], q[i][2]] += values[i]
# apply fourier transform
Pr = fftshift(np.abs(np.real(fftn(fftshift(Sq), (sz, sz, sz)))))
# """
ren = fvtk.ren()
vol = fvtk.volume(Pr)
fvtk.add(ren, vol)
fvtk.show(ren)
# """
"""
from enthought.mayavi import mlab
mlab.pipeline.volume(mlab.pipeline.scalar_field(Sq))
mlab.show()
"""
# vertices, edges, faces = create_unit_sphere(5)
vertices, faces = sphere_vf_from("symmetric362")
odf = np.zeros(len(vertices))
for m in range(len(vertices)):
xi = origin + radius * vertices[m, 0]
yi = origin + radius * vertices[m, 1]
zi = origin + radius * vertices[m, 2]
PrI = map_coordinates(Pr, np.vstack((xi, yi, zi)), order=1)
for i in range(len(radius)):
odf[m] = odf[m] + PrI[i] * radius[i] ** 2
"""
ren=fvtk.ren()
colors=fvtk.colors(odf,'jet')
fvtk.add(ren,fvtk.point(vertices,colors,point_radius=.05,theta=8,phi=8))
fvtk.show(ren)
"""
"""
#Pr[Pr<500]=0
ren=fvtk.ren()
#ren.SetBackground(1,1,1)
fvtk.add(ren,fvtk.volume(Pr))
fvtk.show(ren)
"""
peaks, inds = peak_finding(odf.astype("f8"), faces.astype("uint16"))
Eq = np.zeros((sz, sz, sz))
for i in range(n):
Eq[q[i][0], q[i][1], q[i][2]] += S[i] / S[0]
LEq = laplace(Eq)
# Pr[Pr<500]=0
ren = fvtk.ren()
# ren.SetBackground(1,1,1)
fvtk.add(ren, fvtk.volume(Eq))
fvtk.show(ren)
phis = np.linspace(0, 2 * np.pi, 100)
planars = []
for phi in phis:
planars.append(sphere2cart(1, np.pi / 2, phi))
planars = np.array(planars)
planarsR = []
for v in vertices:
R = vec2vec_rotmat(np.array([0, 0, 1]), v)
planarsR.append(np.dot(R, planars.T).T)
"""
ren=fvtk.ren()
fvtk.add(ren,fvtk.point(planarsR[0],fvtk.green,1,0.1,8,8))
fvtk.add(ren,fvtk.point(2*planarsR[1],fvtk.red,1,0.1,8,8))
fvtk.show(ren)
"""
azimsums = []
for disk in planarsR:
diskshift = 4 * disk + origin
# Sq0=map_coordinates(Sq,diskshift.T,order=1)
# azimsums.append(np.sum(Sq0))
# Eq0=map_coordinates(Eq,diskshift.T,order=1)
# azimsums.append(np.sum(Eq0))
LEq0 = map_coordinates(LEq, diskshift.T, order=1)
azimsums.append(np.sum(LEq0))
azimsums = np.array(azimsums)
# """
ren = fvtk.ren()
colors = fvtk.colors(azimsums, "jet")
fvtk.add(ren, fvtk.point(vertices, colors, point_radius=0.05, theta=8, phi=8))
fvtk.show(ren)
# """
# for p in planarsR[0]:
"""
def show_graph_values(self,
show_final=True,
show_node=True,
show_start=True,
show_node_general=True):
#streamlines_actor = actor.line(streamlines)
time_count = 0
renderwindow = vtk.vtkRenderWindow()
renderwindow.SetSize(1000, 1000)
r = window.Renderer()
#r = vtk.vtkRenderer()
#r.clear()
r.background((1, 1, 1))
#r.SetBackground(1,1,1)
renderwindow.AddRenderer(r)
renderwindowInteractor = vtkRenderWindowInteractor()
#r = vtk.vtkRenderWindowInteractor()
renderwindowInteractor.SetRenderWindow(renderwindow)
camera = vtkCamera()
camera.SetPosition(-50, -50, -50)
camera.SetFocalPoint(0, 0, 0)
#r.SetActiveCamera(camera)
streamlines_sub = []
#r.add(streamlines_actor)
#actor_slicer = actor.slicer(FA, interpolation='nearest')
#r.add(actor_slicer)
if not show_final:
window.show(r)
colors2 = np.array((0, 1, 1))
color3 = np.array((1, 1, 1))
colors = np.array((1, 0, 0))
colors1 = np.array((0, 1, 0))
#goal_point = np.array([35,67,41])
#goal_point = np.array([37,53,59])
#starting_point = np.array([53,65,40])
#starting_point = np.array([42,55,20])
#goal_point = goal_point[None,:]
#point_actor2 = fvtk.point(self.seed[None,:],colors2, point_radius=0.5)#point_radius=self.start_radius)
point_actor2 = fvtk.point(self.start_points, colors2, point_radius=0.5)
#point_actor1 = fvtk.point(self.goal_points[None,:],colors1, point_radius=self.goal_radius)
point_actor1 = fvtk.point(self.goal_points, colors1, point_radius=0.5)
if show_start:
r.add(point_actor1)
#r.AddActor(point_actor1)
r.add(point_actor2)
#r.AddActor(point_actor2)
#def time_event(obj, ev):
#time.sleep(20)
"""Alter
"""
if len(self.exp_graph_general.shape) == 1:
#colors = np.random.rand(1,3)
colors = np.array((1, 1, 1))
if np.array(self.exp_value_general) > 0:
colors = np.array((1, 1 - self.exp_value_general[0] / 100,
1 - self.exp_value_general[0] / 100))
else:
max_value = np.abs(self.exp_value_general.max())
ss = np.where(self.exp_value_general < 0)[0]
colors = np.ones((self.exp_graph_general.shape[0], 3))
#colors[:,2] = 1 - seeds_nodes_graph[i].value/max_value
#colors[:,1] = 1 - seeds_nodes_graph[i].value/max_value
colors[ss, 2] = 1
colors[ss, 1] = 1
sss = np.where(self.exp_value_general > 0)[0]
colors[sss, 1] = 0
colors[sss, 2] = 0
if len(self.exp_graph_general.shape) == 1:
point_actor = fvtk.point(self.exp_graph_general[None, :],
colors,
point_radius=0.3)
else:
point_actor = fvtk.point(self.exp_graph_general,
colors,
point_radius=0.3)
if show_node_general:
r.add(point_actor)
for i in range(len(self.seeds_nodes_graph)):
#print(i)
#r.clear()
#node_actor = actor.streamtube([nodes[100]])
if len(self.seeds_nodes_graph[i].graph.shape) == 1:
#colors = np.random.rand(1,3)
colors = np.array((1, 1, 1))
if np.array(self.seeds_nodes_graph[i].value) > 0:
colors = np.array(
(1, 1 - self.seeds_nodes_graph[i].value[0] / 100,
1 - self.seeds_nodes_graph[i].value[0] / 100))
else:
max_value = np.abs(self.seeds_nodes_graph[i].value.max())
ss = np.where(self.seeds_nodes_graph[i].value < 0)[0]
colors = np.ones((self.seeds_nodes_graph[i].graph.shape[0], 3))
#colors[:,2] = 1 - seeds_nodes_graph[i].value/max_value
#colors[:,1] = 1 - seeds_nodes_graph[i].value/max_value
colors[ss, 2] = 1
colors[ss, 1] = 1
sss = np.where(self.seeds_nodes_graph[i].value > 0)[0]
colors[sss, 1] = 0
colors[sss, 2] = 0
if self.seeds_nodes_graph[i].value.max() > 0:
#colors = np.zeros((seeds_nodes_graph[i].graph.shape[0],3))
#colors[:,0] = 1
streamlines_sub.append(self.seeds_nodes_graph[i].graph)
if len(self.seeds_nodes_graph[i].graph.shape) == 1:
point_actor = fvtk.point(
self.seeds_nodes_graph[i].graph[None, :],
colors,
point_radius=0.3)
else:
point_actor = fvtk.point(self.seeds_nodes_graph[i].graph,
colors,
point_radius=0.3)
if show_node:
r.add(point_actor)
#r.AddActor(point_actor)
#iren = obj
#iren.GetRenderWindow().Render()
if not show_final:
window.show(r)
if not len(self.streamlines) == 0:
peak_slicer = actor.line(self.streamlines)
r.add(peak_slicer)
if show_final:
window.show(r)
import dipy.viz.fvtk as fvtk import numpy as np pointA = [0.48412286, 0.97713726, 0.74590314] pointB = [0.07821987, 0.13495185, 0.7239567] pointC = [0.79723847, 0.06467979, 0.45524464] pointD = [0.25058964, 0.83944661, 0.16528851] pointE = [0.61336066, 0.28185135, 0.94522671] example_xyz = np.array([pointA, pointB, pointC, pointD, pointE]) ren = fvtk.ren() point_actor = fvtk.point(example_xyz, fvtk.colors.blue_light) fvtk.add(ren, point_actor) lineAB = np.array([pointA, pointB]) lineBC = np.array([pointB, pointC]) lineCD = np.array([pointC, pointD]) lineCE = np.array([pointC, pointE]) line_color = [0.9, 0.97, 1.0] line_actor_AB = fvtk.line(lineAB, line_color) line_actor_BC = fvtk.line(lineBC, line_color) line_actor_CD = fvtk.line(lineCD, line_color) line_actor_CE = fvtk.line(lineCE, line_color) fvtk.add(ren, line_actor_AB) fvtk.add(ren, line_actor_BC) fvtk.add(ren, line_actor_CD) fvtk.add(ren, line_actor_CE)
