PostProcessor#

class cdiutils.process.PostProcessor[source]#

Bases: object

A class to bundle all functions needed to post-process BCDI data.

Structural Properties

`get_displacement`(phase, g_vector)	Calculate the displacement from phase and g_vector.
`get_het_normal_strain`(displacement, ...[, ...])	Compute the heterogeneous normal strain, i.e. the gradient of the displacement projected along the measured Bragg peak direction.
`get_structural_properties`(complex_object, ...)	Main method used in the post-processing workflow.

Phase Manipulation

`unwrap_phase`(phase[, support])	Unwrap phase for voxels that belong to the given support.
`remove_phase_ramp`(phase)	Remove the phase ramp of a 2 \| 3D phase object.

Post-processing

`apodize`(direct_space_data[, window_type, scale])	Apodization in the direct space data using Blackman window.
`flip_reconstruction`(data)	Flip a direct space reconstruction.

static prepare_volume(complex_object, isosurface, support_parameters=None, final_shape=None)[source]#

Prepare the volume by finding a smaller array shape, centering at the center of mass of the support, and cropping

Parameters:

complex_object (np.ndarray) – the complex object
phi}) ((rho e^{i)
isosurface (bool) – the isosurface that determines the
support
final_shape (np.ndarray | tuple | list, optional) – the
None. (final shape of the array requested. Defaults to)

Returns:

the cropped complex_object and the associated support.

Return type:

tuple[np.ndarray, np.ndarray]

static flip_reconstruction(data)[source]#

Flip a direct space reconstruction.

Parameters:: data (np.ndarray) – the 3D direct space reconstruction
Returns:: the flipped reconstruction
Return type:: np.ndarray

static apodize(direct_space_data, window_type='blackman', scale=1)[source]#

Apodization in the direct space data using Blackman window.

Parameters:

direct_space_data (np.ndarray) – the 3D volume data to
apodize.
scale (float, optional) – value of the integral of the
None. (Blackman window. Defaults to)

Returns:

Apodized 3D array.

Return type:

np.ndarray

static unwrap_phase(phase, support=None)[source]#

Unwrap phase for voxels that belong to the given support.

Parameters:

phase (np.ndarray) – the phase to unwrap
support (np.ndarray) – the support where voxels of interest are

Returns:

the unwrapped phase

Return type:

np.ndarray

static remove_phase_ramp(phase)[source]#

Remove the phase ramp of a 2 | 3D phase object.

Parameters:: phase (np.ndarray) – the 2 | 3D phase object
Returns:: the phase without the computed ramp.
Return type:: np.ndarray

static phase_offset_to_zero(phase, support=None)[source]#

Set the phase offset to the mean phase value.

static get_displacement(phase, g_vector)[source]#

Calculate the displacement from phase and g_vector.

static get_displacement_gradient(displacement, voxel_size, gradient_method='hybrid')[source]#

Calculate the gradient of the displacement.

Parameters:

displacement (np.ndarray) – displacement array.
voxel_size (np.ndarray | tuple | list) – the voxel size of
array. (the)
gradient_method (str, optional) – the method employed to
gradient. (compute the gradient. "numpy" is the traditional)
and ("hybrid" compute first order gradient at the surface)
reconstruction. (second order within the bulk of the)
"hybrid". (Defaults to)

Raises:

ValueError – If parsed method is unknown.

Returns:

the gradient of the volume in the three directions.

Return type:

np.ndarray

classmethod get_het_normal_strain(displacement, g_vector, voxel_size, gradient_method='hybrid')[source]#

Compute the heterogeneous normal strain, i.e. the gradient of the displacement projected along the measured Bragg peak direction.

Parameters:

displacement (np.ndarray) – the displacement array
g_vector (np.ndarray | tuple | list) – the position of the
peak (measured Bragg)
voxel_size (np.ndarray | tuple | list) – voxel size of the
array
gradient_method (str, optional) – the method employed to
gradient. (compute the gradient. "numpy" is the traditional)
and ("hybrid" compute first order gradient at the surface)
reconstruction. (second order within the bulk of the)
"hybrid". (Defaults to)

Returns:

the heterogeneous normal strain

Return type:

np.ndarray

classmethod get_structural_properties(complex_object, isosurface, g_vector, hkl, voxel_size, phase_factor=-1, handle_defects=False, support_parameters=None)[source]#

Main method used in the post-processing workflow. The method computes all the structural properties of interest in BCDI (amplitude, phase, displacement, displacement gradient, heterogeneous strain d-spacing and lattice parameter maps.)

Parameters:

complex_object (np.ndarray) – the reconstructed object (rho e^(i phi))
g_vector (np.ndarray | tuple | list) – the reciprocal space node on which the displacement gradient must be projected.
hkl (tuple | list) – the probed Bragg reflection. voxel_size (np.ndarray | tuple | list): the voxel size of the 3D array.
phase_factor (int, optional) – the factor the phase should should be multiplied by, depending on the FFT convention used. Defaults to -1 (PyNX convention in Phase Retrieval, in PyNX scattering, use 1).
handle_defects (bool, optional) – whether a defect is present in the reconstruction, in this case phasing processing and strain computation is different. Defaults to False.

Returns:

the structural properties of the object in the form of: a dictionary. Each key corresponds to one quantity of’ interest, including: amplitude, support, phase, displacement, displacement_gradient (in all three directions), het. (heterogeneous) strain using various methods, d-spacing, lattice parameter 3D maps. hkl, g_vector and voxel size are also returned.

Return type:

dict

Examples#

Post-processing is typically handled by BcdiPipeline:

from cdiutils.pipeline import BcdiPipeline

pipeline = BcdiPipeline(param_file_path="config.yml")
pipeline.preprocess()
pipeline.phase_retrieval()

# Post-processing includes strain, displacement calculation
pipeline.postprocess()

PostProcessor#

Examples#

See Also#

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