Output handling

class mumott.output_handling.OrientationImageMapper(colormap='cet_cyclic_isoluminant')

property colormap: Colormap

Returns the colormap used by the wheel.

property wheel_properties: list

Returns wheel properties as a list. The entry at wheel_properties[0] contains the angles. wheel_properties[1] contains the radius. wheel_properties[2] contains the RGBA values mapped to the angles.

class mumott.output_handling.ProjectionViewer(data_container, data=None, orientation_symmetry='longitudinal', mean_colormap='cet_linear_bmy_10_95_c71', std_colormap='cet_gouldian', phase_colormap='cet_CET_C10', mean_range=None, std_range=None)

Class for viewing data and synthetic projections in a scrollable plot. The viewed projection can be changed with either the arrow keys or with the mouse scrolling wheel.

Parameters

• data_container (DataContainer) – A DataContainer object, containing the necessary dimension and rotation information to show orientations correctly.

• data (numpy.ndarray(dtype=numpy.float64), optional) – A flat array of data from e.g. reconstruction output. If not given, data will be loaded from the provided data_container. Provide if you e.g. want to look at synthetic projections from a reconstruction.

• orientation_symmetry ('longitudinal', 'transversal', optional) – Specifies the assumed three-dimensional symmetry of the reciprocal space map, which determines whether the minimum or the maximum of the cos(phi) ** 2 component of the of the intensity is interpreted as the orientation angle. The default is 'longitudinal', which interprets the angle of maximum scattering as the orientation, corresponding to an assumed three-dimensional symmetry of polar caps of intensity. The other option is transversal, which corresponds to a symmetry of a great circle of intensity (also known as fiber symmetry), corresponding to a phase shift of 90 degrees.

• mean_colormap (str or matplotlib.colors.Colormap) – Specifies the colormap of the mean intensity across all angles. The default is 'cet_linear_bmy_10_95_c71', a linear high-contrast with blue, magenta and yellow.

• std_colormap (str or matplotlib.colors.Colormap) – Specifies the colormap of the standar deviation of the data across all angles. The default is 'cet_gouldian', a linear high-contrast map with blue, green and yellow.

• phase_colormap (str or matplotlib.colors.Colormap) – Specifies the colormap of the phase of the cos(detector_angles) ** 2 fit of the data. The default is 'cet_CET_C10', an isoluminant cyclic map.

• mean_range (tuple(float, float)) – Specifies the range of the colormap of the mean.

• std_range (tuple(float, float)) – Specifies the range of the colormap of the standard deviation.

change_projection(ind)

Method for updating the projection shown when the projection slider changes.

Parameters

ind (int) – The index of the projection to be shown.

Return type

None

class mumott.output_handling.ReconstructionDerivedQuantities(volume_shape, mean_intensity, fractional_anisotropy, eigenvector_1, eigenvector_2, eigenvector_3, eigenvalue_1, eigenvalue_2, eigenvalue_3, second_moment_tensor)

A number of useful quantities that have been computed from the coefficients of a reconstruction.

volume_shape

The shape if the reconstructed volume.

Type

tuple

mean_intensity

The mean intensity of the reconstructed functions over the unit sphere for each voxel.

Type

np.array

fractional_anisostropy

A measure of the relative amount of anisotropic scattering in each voxel.

Type

np.array

eigenvector_1

eigenvector_2

eigenvector_3

The eingenvectors of the second order tensor component of the function. Sorted by ascending eigenvalue.

Type

np.array

eigenvalue_1

eigenvalue_2

eigenvalue_3

The eingenvalues of the second order tensor component of the function. Sorted by ascending eigenvalue.

Type

np.array

second_moment_tensor

The second-moment tensor, which includes both the zero-th and second-order parts of the reconstructed functions.

Type

np.array