예제 #1
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def test_interp_rbf():
    from dipy.core.sphere import Sphere, interp_rbf
    from dipy.core.subdivide_octahedron import create_unit_hemisphere
    import numpy as np

    s0 = create_unit_hemisphere(2)
    s1 = create_unit_hemisphere(3)

    data = np.cos(s0.theta) + np.sin(s0.phi)
    expected = np.cos(s1.theta) + np.sin(s1.phi)
    interp_data_en = interp_rbf(data, s0, s1, norm="euclidean_norm")
    interp_data_a = interp_rbf(data, s0, s1, norm="angle")

    nt.assert_(np.mean(np.abs(interp_data_en - expected)) < 0.1)
    nt.assert_(np.mean(np.abs(interp_data_a - expected)) < 0.1)
예제 #2
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def test_interp_rbf():
    from dipy.core.sphere import Sphere, interp_rbf
    from dipy.core.subdivide_octahedron import create_unit_hemisphere
    import numpy as np

    s0 = create_unit_hemisphere(2)
    s1 = create_unit_hemisphere(3)

    data = np.cos(s0.theta) + np.sin(s0.phi)
    expected = np.cos(s1.theta) + np.sin(s1.phi)
    interp_data_en = interp_rbf(data, s0, s1, norm = "euclidean_norm")
    interp_data_a = interp_rbf(data, s0, s1, norm = "angle")

    nt.assert_(np.mean(np.abs(interp_data_en - expected)) < 0.1)
    nt.assert_(np.mean(np.abs(interp_data_a - expected)) < 0.1)
예제 #3
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    def odf(self, sphere):
        ## Override the odf method to subclass OdfFit

        bvec = self.model.bvec[self.model.bval > 0]
        data = self.data[self.model.bval > 0]
        origin_sphere = Sphere(xyz=bvec)
        discrete_odf = 1. / data
        return interp_rbf(discrete_odf, origin_sphere, sphere)
예제 #4
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def test_interp_rbf():
    def data_func(s, a, b):
        return a * np.cos(s.theta) + b * np.sin(s.phi)

    from dipy.core.sphere import Sphere, interp_rbf
    import numpy as np
    s0 = create_unit_sphere(3)
    s1 = create_unit_sphere(4)
    for a, b in zip([1, 2, 0.5], [1, 0.5, 2]):
        data = data_func(s0, a, b)
        expected = data_func(s1, a, b)
        interp_data_a = interp_rbf(data, s0, s1, norm="angle")
        nt.assert_(np.mean(np.abs(interp_data_a - expected)) < 0.1)

    # Test that using the euclidean norm raises a warning
    # (following https://docs.python.org/2/library/warnings.html#testing-warnings)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter("always")
        interp_data_en = interp_rbf(data, s0, s1, norm ="euclidean_norm")
        nt.assert_(len(w) == 1)
        nt.assert_(issubclass(w[-1].category, DeprecationWarning))
        nt.assert_("deprecated" in str(w[-1].message))
예제 #5
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def test_interp_rbf():
    def data_func(s, a, b):
        return a * np.cos(s.theta) + b * np.sin(s.phi)

    from dipy.core.sphere import Sphere, interp_rbf
    import numpy as np
    s0 = create_unit_sphere(3)
    s1 = create_unit_sphere(4)
    for a, b in zip([1, 2, 0.5], [1, 0.5, 2]):
        data = data_func(s0, a, b)
        expected = data_func(s1, a, b)
        interp_data_a = interp_rbf(data, s0, s1, norm="angle")
        nt.assert_(np.mean(np.abs(interp_data_a - expected)) < 0.1)

    # Test that using the euclidean norm raises a warning
    # (following
    # https://docs.python.org/2/library/warnings.html#testing-warnings)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter("always")
        interp_data_en = interp_rbf(data, s0, s1, norm="euclidean_norm")
        nt.assert_(len(w) == 1)
        nt.assert_(issubclass(w[-1].category, DeprecationWarning))
        nt.assert_("deprecated" in str(w[-1].message))
예제 #6
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 def odf(self, sphere, interp_kwargs=dict(function='multiquadric', smooth=0)):
     """
     Interpolate the fiber odf into a provided sphere class instance (from
     dipy)
     """
     s0 = dps.Sphere(xyz=self.bvecs[:, self.b_idx].T)
     s1 = sphere
     params_flat = self.model_params[self.mask]
     out_flat = np.empty((self._n_vox, len(sphere.x)))
     if self._n_vox==1:
        this_params = params_flat
        this_params[np.isnan(this_params)] = 0
        out = dps.interp_rbf(this_params, s0, s1, **interp_kwargs)
        return np.squeeze(out)
     else:
         for vox in range(self._n_vox):
             this_params = params_flat[vox]
             this_params[np.isnan(this_params)] = 0
             out_flat[vox] = dps.interp_rbf(this_params, s0, s1,
                                        **interp_kwargs)
         
         out = ozu.nans(self.model_params.shape[:3] + (len(sphere.x),))
         out[self.mask] = out_flat
         return out
예제 #7
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파일: maya.py 프로젝트: qytian/osmosis
def plot_signal_interp(bvecs, signal, origin=[0,0,0], maya=True, cmap='jet',
                       file_name=None, colorbar=False, figure=None, vmin=None,
                       vmax=None, offset=0, azimuth=60, elevation=90, roll=0,
                       points=False, cmap_points=None, scale_points=False,
                       non_neg=False,
                       interp_kwargs=dict(function='thin_plate', smooth=0)):

    """

    Interpolate a measured signal, using RBF interpolation.

    Parameters
    ----------
    signal:

    bvecs: array (3,n)
        the x,y,z locations where the signal was measured 

    offset : float
        where to place the plotted voxel (on the z axis)

    points : bool
       whether to show the sampling points on the interpolated
       surface. Default: False.
    
    """

    bvecs_new = np.hstack([bvecs, -bvecs])
    new_signal = np.hstack([signal, signal])

    s0 = Sphere(xyz=bvecs_new.T)
    s1 = create_unit_sphere(7)

    signal[np.isnan(signal)] = 0
    
    interp_signal = interp_rbf(new_signal, s0, s1, **interp_kwargs)
    vertices = s1.vertices

    if non_neg:
        interp_signal[interp_signal<0] = 0
        
    faces = s1.faces
    x,y,z = vertices.T 

    r, phi, theta = geo.cart2sphere(x,y,z)
    x_plot, y_plot, z_plot = geo.sphere2cart(interp_signal, phi, theta)

    if points:
        r, phi, theta = geo.cart2sphere(s0.x, s0.y, s0.z)
        x_p, y_p, z_p =  geo.sphere2cart(signal, phi, theta)
        figure = _display_maya_voxel(x_p, y_p, z_p, faces,
                                     signal, origin, cmap=cmap,
                                     colorbar=colorbar, figure=figure,
                                     vmin=vmin, vmax=vmax, file_name=file_name,
                                     azimuth=azimuth, elevation=elevation,
                                     points=True, cmap_points=cmap_points,
                                     scale_points=scale_points)

    # Call and return straightaway:
    return _display_maya_voxel(x_plot, y_plot, z_plot, faces,
                               interp_signal, origin,
                               cmap=cmap, colorbar=colorbar, figure=figure,
                               vmin=vmin, vmax=vmax, file_name=file_name,
                               azimuth=azimuth, elevation=elevation)
예제 #8
0
파일: maya.py 프로젝트: zhangerjun/osmosis
def plot_signal_interp(bvecs,
                       signal,
                       origin=[0, 0, 0],
                       maya=True,
                       cmap='jet',
                       file_name=None,
                       colorbar=False,
                       figure=None,
                       vmin=None,
                       vmax=None,
                       offset=0,
                       azimuth=60,
                       elevation=90,
                       roll=0,
                       points=False,
                       cmap_points=None,
                       scale_points=False,
                       non_neg=False,
                       interp_kwargs=dict(function='thin_plate', smooth=0)):
    """

    Interpolate a measured signal, using RBF interpolation.

    Parameters
    ----------
    signal:

    bvecs: array (3,n)
        the x,y,z locations where the signal was measured 

    offset : float
        where to place the plotted voxel (on the z axis)

    points : bool
       whether to show the sampling points on the interpolated
       surface. Default: False.
    
    """

    bvecs_new = np.hstack([bvecs, -bvecs])
    new_signal = np.hstack([signal, signal])

    s0 = Sphere(xyz=bvecs_new.T)
    s1 = create_unit_sphere(7)

    signal[np.isnan(signal)] = 0

    interp_signal = interp_rbf(new_signal, s0, s1, **interp_kwargs)
    vertices = s1.vertices

    if non_neg:
        interp_signal[interp_signal < 0] = 0

    faces = s1.faces
    x, y, z = vertices.T

    r, phi, theta = geo.cart2sphere(x, y, z)
    x_plot, y_plot, z_plot = geo.sphere2cart(interp_signal, phi, theta)

    if points:
        r, phi, theta = geo.cart2sphere(s0.x, s0.y, s0.z)
        x_p, y_p, z_p = geo.sphere2cart(signal, phi, theta)
        figure = _display_maya_voxel(x_p,
                                     y_p,
                                     z_p,
                                     faces,
                                     signal,
                                     origin,
                                     cmap=cmap,
                                     colorbar=colorbar,
                                     figure=figure,
                                     vmin=vmin,
                                     vmax=vmax,
                                     file_name=file_name,
                                     azimuth=azimuth,
                                     elevation=elevation,
                                     points=True,
                                     cmap_points=cmap_points,
                                     scale_points=scale_points)

    # Call and return straightaway:
    return _display_maya_voxel(x_plot,
                               y_plot,
                               z_plot,
                               faces,
                               interp_signal,
                               origin,
                               cmap=cmap,
                               colorbar=colorbar,
                               figure=figure,
                               vmin=vmin,
                               vmax=vmax,
                               file_name=file_name,
                               azimuth=azimuth,
                               elevation=elevation)