def test_track_volumes():
# simplest case
vol_dims = (1, 2, 3)
tracks = ([[0, 0, 0], [0, 1, 1]], )
tracks = [np.array(t) for t in tracks]
ex_counts, ex_els = tracks_to_expected(tracks, vol_dims)
tcs, tes = tv.track_counts(tracks, vol_dims, [1, 1, 1])
yield assert_array_equal, tcs, ex_counts
yield assert_array_equal, tes, ex_els
# check only counts returned for return_elements=False
tcs = tv.track_counts(tracks, vol_dims, [1, 1, 1], False)
yield assert_array_equal, tcs, ex_counts
# non-unique points, non-integer points, points outside
vol_dims = (5, 10, 15)
tracks = ([[-1, 0, 1], [0, 0.1, 0], [1, 1, 1], [1, 1, 1],
[2, 2, 2]], [[0.7, 0, 0], [1, 1, 1], [1, 2, 2], [1, 11, 0]])
tracks = [np.array(t) for t in tracks]
ex_counts, ex_els = tracks_to_expected(tracks, vol_dims)
tcs, tes = tv.track_counts(tracks, vol_dims, [1, 1, 1])
yield assert_array_equal, tcs, ex_counts
yield assert_array_equal, tes, ex_els
# points with non-unit voxel sizes
vox_sizes = [1.4, 2.1, 3.7]
float_tracks = []
for t in tracks:
float_tracks.append(t * vox_sizes)
tcs, tes = tv.track_counts(float_tracks, vol_dims, vox_sizes)
yield assert_array_equal, tcs, ex_counts
yield assert_array_equal, tes, ex_els
def load_template_tes_and_tracks(path,brain,scan):
volpath=path+'/ICBM_WMPM_tweaked_'+str(brain) +'_'+str(scan)+'.nii'
print volpath
template,voxsz,aff=pbc.loadvol(volpath)
tracks=pbc.load_approximate_tracks(path,brain,scan)
print 'template shape', template.shape
tcs,tes = tv.track_counts(tracks, template.shape, vox_sizes=(1,1,1), return_elements=True)
print 'tcs shape', tcs.shape
return template,tcs,tes,tracks
def test_track_volumes():
# simplest case
vol_dims = (1, 2, 3)
tracks = ([[0, 0, 0],
[0, 1, 1]],)
tracks = [np.array(t) for t in tracks]
ex_counts, ex_els = tracks_to_expected(tracks, vol_dims)
tcs, tes = tv.track_counts(tracks, vol_dims, [1,1,1])
yield assert_array_equal, tcs, ex_counts
yield assert_array_equal, tes, ex_els
# check only counts returned for return_elements=False
tcs = tv.track_counts(tracks, vol_dims, [1,1,1], False)
yield assert_array_equal, tcs, ex_counts
# non-unique points, non-integer points, points outside
vol_dims = (5, 10, 15)
tracks = ([[-1, 0, 1],
[0, 0.1, 0],
[1, 1, 1],
[1, 1, 1],
[2, 2, 2]],
[[0.7, 0, 0],
[1, 1, 1],
[1, 2, 2],
[1, 11, 0]])
tracks = [np.array(t) for t in tracks]
ex_counts, ex_els = tracks_to_expected(tracks, vol_dims)
tcs, tes = tv.track_counts(tracks, vol_dims, [1,1,1])
yield assert_array_equal, tcs, ex_counts
yield assert_array_equal, tes, ex_els
# points with non-unit voxel sizes
vox_sizes = [1.4, 2.1, 3.7]
float_tracks = []
for t in tracks:
float_tracks.append(t * vox_sizes)
tcs, tes = tv.track_counts(float_tracks, vol_dims, vox_sizes)
yield assert_array_equal, tcs, ex_counts
yield assert_array_equal, tes, ex_els
