def streamline2rgb(streamline):
"""Compute orientation of a streamline and retrieve and appropriate RGB
color to represent it.
"""
# simplest implementation:
tmp = orient2rgb(streamline[0] - streamline[-1])
return tmp
def track2rgb(track):
"""Compute orientation of a track and retrieve and appropriate RGB
color to represent it.
"""
# simplest implementation:
#return orient2rgb(track[0] - track[-1])
v=track[0]-track[-1]
v=v/np.linalg.norm(v)
#return boys2rgb(v)
return orient2rgb(v)
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 track2rgb(track):
"""Compute orientation of a track and retrieve and appropriate RGB
color to represent it.
"""
# simplest implementation:
return orient2rgb(track[0] - track[-1])
fvtk.add(r, fvtk.line(no_cross_shift, fvtk.blue, linewidth=5.))
fvtk.add(r, fvtk.line(cross_shift, fvtk.indigo, linewidth=5.))
fvtk.add(r, fvtk.line(dcross_shift, fvtk.red, linewidth=5.))
from dipy.viz import colormap as cm
all_shift = [c + np.array([10, 0, 0]) for c in all]
all_shift2 = [c + np.array([20, 0, 0]) for c in all]
colors = np.zeros((len(all), 3))
colors2 = np.zeros((len(all), 3))
for (i, a) in enumerate(all):
#print a[0]
colors[i] = cm.boys2rgb(allo[i])
colors2[i] = cm.orient2rgb(allo[i])
fvtk.add(r, fvtk.line(all_shift, colors, linewidth=1.))
fvtk.add(r, fvtk.line(all_shift2, colors2, linewidth=2.))
"""
.. figure:: visualize_cross1000000.png
:align: center
**The crossings of a region of interest shown with one color, or boy2rgb or standard orient2rgb colormap**.
.. include:: ../links_names.inc
"""
# To show the figure
def track2rgb(track):
"""Compute orientation of a track and retrieve and appropriate RGB
color to represent it.
"""
# simplest implementation:
return orient2rgb(track[0] - track[-1])
fvtk.add(r,fvtk.line(no_cross_shift,fvtk.blue,linewidth=5.))
fvtk.add(r,fvtk.line(cross_shift,fvtk.indigo,linewidth=5.))
fvtk.add(r,fvtk.line(dcross_shift,fvtk.red,linewidth=5.))
from dipy.viz import colormap as cm
all_shift=[c+np.array([10,0,0]) for c in all]
all_shift2=[c+np.array([20,0,0]) for c in all]
colors=np.zeros((len(all),3))
colors2=np.zeros((len(all),3))
for (i,a) in enumerate(all):
#print a[0]
colors[i]=cm.boys2rgb(allo[i])
colors2[i]=cm.orient2rgb(allo[i])
fvtk.add(r,fvtk.line(all_shift,colors,linewidth=1.))
fvtk.add(r,fvtk.line(all_shift2,colors2,linewidth=2.))
"""
.. figure:: visualize_cross1000000.png
:align: center
**The crossings of a region of interest shown with one color, or boy2rgb or standard orient2rgb colormap**.
.. include:: ../links_names.inc
"""
#3,8,6 double crossing
dcross=fvtk.crossing(QA[3,8,6],IN[3,8,6],verts,1)
all=fvtk.crossing(QA,IN,verts,1)
fvtk.add(r,fvtk.line(all,fvtk.azure,linewidth=1.))
no_cross_shift=[c+np.array([3,8,4]) for c in no_cross]
cross_shift=[c+np.array([3,8,5]) for c in cross]
dcross_shift=[c+np.array([3,8,6]) for c in dcross]
fvtk.add(r,fvtk.line(no_cross_shift,fvtk.blue,linewidth=5.))
fvtk.add(r,fvtk.line(cross_shift,fvtk.indigo,linewidth=5.))
fvtk.add(r,fvtk.line(dcross_shift,fvtk.red,linewidth=5.))
from dipy.viz import colormap as cm
all_shift=[c+np.array([10,0,0]) for c in all]
all_shift2=[c+np.array([20,0,0]) for c in all]
colors=np.zeros((len(all),3))
colors2=np.zeros((len(all),3))
for (i,a) in enumerate(all):
#print a[0]
colors[i]=cm.boys2rgb(a[0])
colors2[i]=cm.orient2rgb(a[0])
fvtk.add(r,fvtk.line(all_shift,colors,linewidth=1.))
fvtk.add(r,fvtk.line(all_shift2,colors2,linewidth=2.))
fvtk.show(r)
