Exemple #1
0
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)
Exemple #3
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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)
Exemple #4
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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]])]