def test_track_roi_intersection_check():
roi = np.array([[0, 0, 0], [1, 0, 0], [2, 0, 0]], dtype='f4')
t = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2]], dtype='f4')
assert_equal(pf.track_roi_intersection_check(t, roi, 1), True)
t = np.array([[0, 0, 0], [1, 0, 0], [2, 2, 2]], dtype='f4')
assert_equal(pf.track_roi_intersection_check(t, roi, 1), True)
t = np.array([[1, 1, 0], [1, 0, 0], [1, -1, 0]], dtype='f4')
assert_equal(pf.track_roi_intersection_check(t, roi, 1), True)
t = np.array([[4, 0, 0], [4, 1, 1], [4, 2, 0]], dtype='f4')
assert_equal(pf.track_roi_intersection_check(t, roi, 1), False)
def test_track_roi_intersection_check():
roi=np.array([[0,0,0],[1,0,0],[2,0,0]],dtype='f4')
t=np.array([[0,0,0],[1,1,1],[2,2,2]],dtype='f4')
assert_equal( pf.track_roi_intersection_check(t,roi,1), True)
t=np.array([[0,0,0],[1,0,0],[2,2,2]],dtype='f4')
assert_equal(pf.track_roi_intersection_check(t,roi,1), True)
t=np.array([[1,1,0],[1,0,0],[1,-1,0]],dtype='f4')
assert_equal( pf.track_roi_intersection_check(t,roi,1), True)
t=np.array([[4,0,0],[4,1,1],[4,2,0]],dtype='f4')
assert_equal(pf.track_roi_intersection_check(t,roi,1), False)
def spherical_rois(fdpy,fsr,sq_radius=4):
R=atlantic_points()
dpr=Dpy(fdpy,'r')
T=dpr.read_tracks()
dpr.close()
center=R['BCC']
refimg=nib.load(fref)
aff=refimg.get_affine()
SR={}
for key in R:
center=R[key]
#back to world space
centerw=np.dot(aff,np.array(center+(1,)))[:3]
centerw.shape=(1,)+centerw.shape
centerw=centerw.astype(np.float32)
res= [track_roi_intersection_check(t,centerw,sq_radius) for t in T]
res= np.array(res,dtype=np.int)
ind=np.where(res>0)[0]
SR[key]={}
SR[key]['center']=center
SR[key]['centerw']=tuple(np.squeeze(centerw))
SR[key]['radiusw']=np.sqrt(sq_radius)
SR[key]['indices']=ind
save_pickle(fsr,SR)
def roi_intersection(fdpy,fatlas,roi_no,froidpy):
dpr=Dpy(fdpy,'r')
T=dpr.read_tracksi(range(10000))
dpr.close()
Troi=[]
wI=get_roi(fatlas,roi_no,0)
for (i,t) in enumerate(T):
if i%1000==0:
print i
if track_roi_intersection_check(t,wI,.5):
Troi.append(t)
print(len(Troi))
dpw=Dpy(froidpy,'w')
dpw.write_tracks(Troi)
dpw.close()
'''
def compute_intersecting(voxel, R, kdt, max_segment): """ function for finding the streamlines which are inside the specific redius for each ROI """ subset = np.unique(si[kdt.query_radius(voxel, r=R+max_segment)[0]]).astype(np.int) return subset[np.array([track_roi_intersection_check(s, voxel, sq_dist_thr=R**2) for s in tracks[subset]])]