Python ProbabilisticDirectionGetter.from_pmf方法代碼示例

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_pmf [as 別名]
def test_ProbabilisticDirectionGetter():
    # Test the constructors and errors of the ProbabilisticDirectionGetter

    class SillyModel(SphHarmModel):

        sh_order = 4

        def fit(self, data, mask=None):
            coeff = np.zeros(data.shape[:-1] + (15,))
            return SphHarmFit(self, coeff, mask=None)

    model = SillyModel(gtab=None)
    data = np.zeros((3, 3, 3, 7))

    # Test if the tracking works on different dtype of the same data.
    for dtype in [np.float32, np.float64]:
        fit = model.fit(data.astype(dtype))

        # Sample point and direction
        point = np.zeros(3)
        dir = unit_octahedron.vertices[0].copy()

        # make a dg from a fit
        dg = ProbabilisticDirectionGetter.from_shcoeff(fit.shm_coeff, 90,
                                                       unit_octahedron)
        state = dg.get_direction(point, dir)
        npt.assert_equal(state, 1)

        # Make a dg from a pmf
        N = unit_octahedron.theta.shape[0]
        pmf = np.zeros((3, 3, 3, N))
        dg = ProbabilisticDirectionGetter.from_pmf(pmf, 90, unit_octahedron)
        state = dg.get_direction(point, dir)
        npt.assert_equal(state, 1)

        # pmf shape must match sphere
        bad_pmf = pmf[..., 1:]
        npt.assert_raises(ValueError, ProbabilisticDirectionGetter.from_pmf,
                          bad_pmf, 90, unit_octahedron)

        # pmf must have 4 dimensions
        bad_pmf = pmf[0, ...]
        npt.assert_raises(ValueError, ProbabilisticDirectionGetter.from_pmf,
                          bad_pmf, 90, unit_octahedron)
        # pmf cannot have negative values
        pmf[0, 0, 0, 0] = -1
        npt.assert_raises(ValueError, ProbabilisticDirectionGetter.from_pmf,
                          pmf, 90, unit_octahedron)

        # Check basis_type keyword
        dg = ProbabilisticDirectionGetter.from_shcoeff(fit.shm_coeff, 90,
                                                       unit_octahedron,
                                                       basis_type="mrtrix")

        npt.assert_raises(ValueError,
                          ProbabilisticDirectionGetter.from_shcoeff,
                          fit.shm_coeff, 90, unit_octahedron,
                          basis_type="not a basis")

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_pmf [as 別名]
distribution of small fiber bundles within each voxel. We can use this
distribution for probabilistic fiber tracking. One way to do this is to
represent the FOD using a discrete sphere. This discrete FOD can be used by the
Probabilistic Direction Getter as a PMF for sampling tracking directions. We
need to clip the FOD to use it as a PMF because the latter cannot have negative
values. (Ideally the FOD should be strictly positive, but because of noise
and/or model failures sometimes it can have negative values).
"""

from dipy.direction import ProbabilisticDirectionGetter
from dipy.data import small_sphere
from dipy.io.trackvis import save_trk

fod = csd_fit.odf(small_sphere)
pmf = fod.clip(min=0)
prob_dg = ProbabilisticDirectionGetter.from_pmf(pmf, max_angle=30.,
                                                sphere=small_sphere)
streamlines = LocalTracking(prob_dg, classifier, seeds, affine, step_size=.5)
save_trk("probabilistic_small_sphere.trk", streamlines, affine, labels.shape)

"""
One disadvantage of using a discrete PMF to represent possible tracking
directions is that it tends to take up a lot of memory (RAM). The size of the
PMF, the FOD in this case, must be equal to the number of possible tracking
directions on the hemisphere, and every voxel has a unique PMF. In this case
the data is ``(81, 106, 76)`` and ``small_sphere`` has 181 directions so the
FOD is ``(81, 106, 76, 181)``. One way to avoid sampling the PMF and holding it
in memory is to build the direction getter directly from the spherical harmonic
representation of the FOD. By using this approach, we can also use a larger
sphere, like ``default_sphere`` which has 362 directions on the hemisphere,
without having to worry about memory limitations.
"""

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_pmf [as 別名]
def test_particle_filtering_tractography():
    """This tests that the ParticleFilteringTracking produces
    more streamlines connecting the gray matter than LocalTracking.
    """
    sphere = get_sphere('repulsion100')
    step_size = 0.2

    # Simple tissue masks
    simple_wm = np.array([[0, 0, 0, 0, 0, 0],
                          [0, 0, 1, 0, 0, 0],
                          [0, 1, 1, 1, 0, 0],
                          [0, 1, 1, 1, 0, 0],
                          [0, 0, 0, 0, 0, 0]])
    simple_wm = np.dstack([np.zeros(simple_wm.shape),
                           simple_wm,
                           simple_wm,
                           simple_wm,
                           np.zeros(simple_wm.shape)])
    simple_gm = np.array([[1, 1, 0, 0, 0, 0],
                          [1, 1, 0, 0, 0, 0],
                          [0, 1, 0, 0, 1, 0],
                          [0, 0, 0, 0, 1, 0],
                          [0, 0, 0, 0, 0, 0]])
    simple_gm = np.dstack([np.zeros(simple_gm.shape),
                           simple_gm,
                           simple_gm,
                           simple_gm,
                           np.zeros(simple_gm.shape)])
    simple_csf = np.ones(simple_wm.shape) - simple_wm - simple_gm
    tc = ActTissueClassifier.from_pve(simple_wm, simple_gm, simple_csf)
    seeds = seeds_from_mask(simple_wm, density=2)

    # Random pmf in every voxel
    shape_img = list(simple_wm.shape)
    shape_img.extend([sphere.vertices.shape[0]])
    np.random.seed(0)  # Random number generator initialization
    pmf = np.random.random(shape_img)

    # Test that PFT recover equal or more streamlines than localTracking
    dg = ProbabilisticDirectionGetter.from_pmf(pmf, 60, sphere)
    local_streamlines_generator = LocalTracking(dg, tc, seeds, np.eye(4),
                                                step_size, max_cross=1,
                                                return_all=False)
    local_streamlines = Streamlines(local_streamlines_generator)

    pft_streamlines_generator = ParticleFilteringTracking(
        dg, tc, seeds, np.eye(4), step_size, max_cross=1, return_all=False,
        pft_back_tracking_dist=1, pft_front_tracking_dist=0.5)
    pft_streamlines = Streamlines(pft_streamlines_generator)

    npt.assert_(np.array([len(pft_streamlines) > 0]))
    npt.assert_(np.array([len(pft_streamlines) >= len(local_streamlines)]))

    # Test that all points are equally spaced
    for l in [1, 2, 5, 10, 100]:
        pft_streamlines = ParticleFilteringTracking(dg, tc, seeds, np.eye(4),
                                                    step_size, max_cross=1,
                                                    return_all=True, maxlen=l)
        for s in pft_streamlines:
            for i in range(len(s) - 1):
                npt.assert_almost_equal(np.linalg.norm(s[i] - s[i + 1]),
                                        step_size)
    # Test that all points are within the image volume
    seeds = seeds_from_mask(np.ones(simple_wm.shape), density=1)
    pft_streamlines_generator = ParticleFilteringTracking(
        dg, tc, seeds, np.eye(4), step_size, max_cross=1, return_all=True)
    pft_streamlines = Streamlines(pft_streamlines_generator)

    for s in pft_streamlines:
        npt.assert_(np.all((s + 0.5).astype(int) >= 0))
        npt.assert_(np.all((s + 0.5).astype(int) < simple_wm.shape))

    # Test that the number of streamline return with return_all=True equal the
    # number of seeds places
    npt.assert_(np.array([len(pft_streamlines) == len(seeds)]))

    # Test non WM seed position
    seeds = [[0, 5, 4], [0, 0, 1], [50, 50, 50]]
    pft_streamlines_generator = ParticleFilteringTracking(
        dg, tc, seeds, np.eye(4), step_size, max_cross=1, return_all=True)
    pft_streamlines = Streamlines(pft_streamlines_generator)

    npt.assert_equal(len(pft_streamlines[0]), 3)  # INVALIDPOINT
    npt.assert_equal(len(pft_streamlines[1]), 3)  # ENDPOINT
    npt.assert_equal(len(pft_streamlines[2]), 1)  # OUTSIDEIMAGE

    # Test with wrong tissueclassifier type
    tc_bin = BinaryTissueClassifier(simple_wm)
    npt.assert_raises(ValueError,
                      lambda: ParticleFilteringTracking(dg, tc_bin, seeds,
                                                        np.eye(4), step_size))
    # Test with invalid back/front tracking distances
    npt.assert_raises(
        ValueError,
        lambda: ParticleFilteringTracking(dg, tc, seeds, np.eye(4), step_size,
                                          pft_back_tracking_dist=0,
                                          pft_front_tracking_dist=0))
    npt.assert_raises(
        ValueError,
        lambda: ParticleFilteringTracking(dg, tc, seeds, np.eye(4), step_size,
#.........這裏部分代碼省略.........

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_pmf [as 別名]
def test_stop_conditions():
    """This tests that the Local Tracker behaves as expected for the
    following tissue types.
    """
    # TissueTypes.TRACKPOINT = 1
    # TissueTypes.ENDPOINT = 2
    # TissueTypes.INVALIDPOINT = 0
    tissue = np.array([[2, 1, 1, 2, 1],
                       [2, 2, 1, 1, 2],
                       [1, 1, 1, 1, 1],
                       [1, 1, 1, 2, 2],
                       [0, 1, 1, 1, 2],
                       [0, 1, 1, 0, 2],
                       [1, 0, 1, 1, 1]])
    tissue = tissue[None]

    sphere = HemiSphere.from_sphere(unit_octahedron)
    pmf_lookup = np.array([[0., 0., 0., ],
                           [0., 0., 1.]])
    pmf = pmf_lookup[(tissue > 0).astype("int")]

    # Create a seeds along
    x = np.array([0., 0, 0, 0, 0, 0, 0])
    y = np.array([0., 1, 2, 3, 4, 5, 6])
    z = np.array([1., 1, 1, 0, 1, 1, 1])
    seeds = np.column_stack([x, y, z])

    # Set up tracking
    endpoint_mask = tissue == TissueTypes.ENDPOINT
    invalidpoint_mask = tissue == TissueTypes.INVALIDPOINT
    tc = ActTissueClassifier(endpoint_mask, invalidpoint_mask)
    dg = ProbabilisticDirectionGetter.from_pmf(pmf, 60, sphere)

    # valid streamlines only
    streamlines_generator = LocalTracking(direction_getter=dg,
                                          tissue_classifier=tc,
                                          seeds=seeds,
                                          affine=np.eye(4),
                                          step_size=1.,
                                          return_all=False)
    streamlines_not_all = iter(streamlines_generator)

    # all streamlines
    streamlines_all_generator = LocalTracking(direction_getter=dg,
                                              tissue_classifier=tc,
                                              seeds=seeds,
                                              affine=np.eye(4),
                                              step_size=1.,
                                              return_all=True)
    streamlines_all = iter(streamlines_all_generator)

    # Check that the first streamline stops at 0 and 3 (ENDPOINT)
    y = 0
    sl = next(streamlines_not_all)
    npt.assert_equal(sl[0], [0, y, 0])
    npt.assert_equal(sl[-1], [0, y, 3])
    npt.assert_equal(len(sl), 4)

    sl = next(streamlines_all)
    npt.assert_equal(sl[0], [0, y, 0])
    npt.assert_equal(sl[-1], [0, y, 3])
    npt.assert_equal(len(sl), 4)

    # Check that the first streamline stops at 0 and 4 (ENDPOINT)
    y = 1
    sl = next(streamlines_not_all)
    npt.assert_equal(sl[0], [0, y, 0])
    npt.assert_equal(sl[-1], [0, y, 4])
    npt.assert_equal(len(sl), 5)

    sl = next(streamlines_all)
    npt.assert_equal(sl[0], [0, y, 0])
    npt.assert_equal(sl[-1], [0, y, 4])
    npt.assert_equal(len(sl), 5)

    # This streamline should be the same as above. This row does not have
    # ENDPOINTs, but the streamline should stop at the edge and not include
    # OUTSIDEIMAGE points.
    y = 2
    sl = next(streamlines_not_all)
    npt.assert_equal(sl[0], [0, y, 0])
    npt.assert_equal(sl[-1], [0, y, 4])
    npt.assert_equal(len(sl), 5)

    sl = next(streamlines_all)
    npt.assert_equal(sl[0], [0, y, 0])
    npt.assert_equal(sl[-1], [0, y, 4])
    npt.assert_equal(len(sl), 5)

    # If we seed on the edge, the first (or last) point in the streamline
    # should be the seed.
    y = 3
    sl = next(streamlines_not_all)
    npt.assert_equal(sl[0], seeds[y])

    sl = next(streamlines_all)
    npt.assert_equal(sl[0], seeds[y])

    # The last 3 seeds should not produce streamlines,
    # INVALIDPOINT streamlines are rejected (return_all=False).
#.........這裏部分代碼省略.........

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_pmf [as 別名]
def test_probabilistic_odf_weighted_tracker():
    """This tests that the Probabalistic Direction Getter plays nice
    LocalTracking and produces reasonable streamlines in a simple example.
    """
    sphere = HemiSphere.from_sphere(unit_octahedron)

    # A simple image with three possible configurations, a vertical tract,
    # a horizontal tract and a crossing
    pmf_lookup = np.array([[0., 0., 1.],
                           [1., 0., 0.],
                           [0., 1., 0.],
                           [.6, .4, 0.]])
    simple_image = np.array([[0, 1, 0, 0, 0, 0],
                             [0, 1, 0, 0, 0, 0],
                             [0, 3, 2, 2, 2, 0],
                             [0, 1, 0, 0, 0, 0],
                             [0, 1, 0, 0, 0, 0],
                             ])

    simple_image = simple_image[..., None]
    pmf = pmf_lookup[simple_image]

    seeds = [np.array([1., 1., 0.])] * 30

    mask = (simple_image > 0).astype(float)
    tc = ThresholdTissueClassifier(mask, .5)

    dg = ProbabilisticDirectionGetter.from_pmf(pmf, 90, sphere,
                                               pmf_threshold=0.1)
    streamlines = LocalTracking(dg, tc, seeds, np.eye(4), 1.)

    expected = [np.array([[0., 1., 0.],
                          [1., 1., 0.],
                          [2., 1., 0.],
                          [2., 2., 0.],
                          [2., 3., 0.],
                          [2., 4., 0.],
                          [2., 5., 0.]]),
                np.array([[0., 1., 0.],
                          [1., 1., 0.],
                          [2., 1., 0.],
                          [3., 1., 0.],
                          [4., 1., 0.]])]

    def allclose(x, y):
        return x.shape == y.shape and np.allclose(x, y)

    path = [False, False]
    for sl in streamlines:
        if allclose(sl, expected[0]):
            path[0] = True
        elif allclose(sl, expected[1]):
            path[1] = True
        else:
            raise AssertionError()
    npt.assert_(all(path))

    # The first path is not possible if 90 degree turns are excluded
    dg = ProbabilisticDirectionGetter.from_pmf(pmf, 80, sphere,
                                               pmf_threshold=0.1)
    streamlines = LocalTracking(dg, tc, seeds, np.eye(4), 1.)

    for sl in streamlines:
        npt.assert_(np.allclose(sl, expected[1]))

    # The first path is not possible if pmf_threshold > 0.67
    # 0.4/0.6 < 2/3, multiplying the pmf should not change the ratio
    dg = ProbabilisticDirectionGetter.from_pmf(10*pmf, 90, sphere,
                                               pmf_threshold=0.67)
    streamlines = LocalTracking(dg, tc, seeds, np.eye(4), 1.)

    for sl in streamlines:
        npt.assert_(np.allclose(sl, expected[1]))

    # Test non WM seed position
    seeds = [[0, 0, 0], [5, 5, 5]]
    streamlines = LocalTracking(dg, tc, seeds, np.eye(4), 0.2, max_cross=1,
                                return_all=True)
    streamlines = Streamlines(streamlines)
    npt.assert_(len(streamlines[0]) == 3)  # INVALIDPOINT
    npt.assert_(len(streamlines[1]) == 1)  # OUTSIDEIMAGE

    # Test that all points are within the image volume
    seeds = seeds_from_mask(np.ones(mask.shape), density=2)
    streamline_generator = LocalTracking(dg, tc, seeds, np.eye(4), 0.5,
                                         return_all=True)
    streamlines = Streamlines(streamline_generator)
    for s in streamlines:
        npt.assert_(np.all((s + 0.5).astype(int) >= 0))
        npt.assert_(np.all((s + 0.5).astype(int) < mask.shape))
    # Test that the number of streamline return with return_all=True equal the
    # number of seeds places

    npt.assert_(np.array([len(streamlines) == len(seeds)]))

    # Test reproducibility
    tracking_1 = Streamlines(LocalTracking(dg, tc, seeds, np.eye(4),
                                           0.5,
                                           random_seed=0)).data
    tracking_2 = Streamlines(LocalTracking(dg, tc, seeds, np.eye(4),
#.........這裏部分代碼省略.........

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_pmf [as 別名]
def test_ProbabilisticOdfWeightedTracker():
    """This tests that the Probabalistic Direction Getter plays nice
    LocalTracking and produces reasonable streamlines in a simple example.
    """
    sphere = HemiSphere.from_sphere(unit_octahedron)

    # A simple image with three possible configurations, a vertical tract,
    # a horizontal tract and a crossing
    pmf_lookup = np.array([[0., 0., 1.],
                           [1., 0., 0.],
                           [0., 1., 0.],
                           [.5, .5, 0.]])
    simple_image = np.array([[0, 1, 0, 0, 0, 0],
                             [0, 1, 0, 0, 0, 0],
                             [0, 3, 2, 2, 2, 0],
                             [0, 1, 0, 0, 0, 0],
                             [0, 1, 0, 0, 0, 0],
                             ])

    simple_image = simple_image[..., None]
    pmf = pmf_lookup[simple_image]

    seeds = [np.array([1., 1., 0.])] * 30

    mask = (simple_image > 0).astype(float)
    tc = ThresholdTissueClassifier(mask, .5)

    dg = ProbabilisticDirectionGetter.from_pmf(pmf, 90, sphere)
    streamlines = LocalTracking(dg, tc, seeds, np.eye(4), 1.)

    expected = [np.array([[ 0.,  1.,  0.],
                          [ 1.,  1.,  0.],
                          [ 2.,  1.,  0.],
                          [ 2.,  2.,  0.],
                          [ 2.,  3.,  0.],
                          [ 2.,  4.,  0.],
                          [ 2.,  5.,  0.]]),
                np.array([[ 0.,  1.,  0.],
                          [ 1.,  1.,  0.],
                          [ 2.,  1.,  0.],
                          [ 3.,  1.,  0.],
                          [ 4.,  1.,  0.]])
               ]

    def allclose(x, y):
        return x.shape == y.shape and np.allclose(x, y)

    path = [False, False]
    for sl in streamlines:
        dir = ( -sphere.vertices[0] ).copy()
        if allclose(sl, expected[0]):
            path[0] = True
        elif allclose(sl, expected[1]):
            path[1] = True
        else:
            raise AssertionError()
    npt.assert_(all(path))

    # The first path is not possible if 90 degree turns are excluded
    dg = ProbabilisticDirectionGetter.from_pmf(pmf, 80, sphere)
    streamlines = LocalTracking(dg, tc, seeds, np.eye(4), 1.)

    for sl in streamlines:
        npt.assert_(np.allclose(sl, expected[1]))