[FEATURE] Strain calculation for particules with defects

[ewbellec]

Impossible to completely remove the phase wrapping when you have toppological defect (dislocations).
Solution : Changing the phase by an offset (and not unwrapping) moves the wrapping region. Simply compute the strain for 3 phase offsets. At each positions, at least 2 strain maps should be equal.
Here's a rough try of a function that might work in cdiutils :

def compute_normal_strain_defects(
displacement: np.ndarray,
q_vector: Union[np.ndarray, tuple, list],
voxel_size: Union[np.ndarray, tuple, list],
gradient_method: str="hybrid",
phase_shift=np.pi/2.,
) -> np.ndarray:
factor = ? # factor that you use to go from phase to displacement.
displacement1 = np.mod(displacement, 2.pifactor)
displacement2 = np.mod(displacement + phase_shift, 2.pifactor)
displacement3 = np.mod(displacement + 2. * phase_shift , 2.pifactor)

strain1 = compute_normal_strain(displacement1, q_vector, voxel_size)
strain2 = compute_normal_strain(displacement2, q_vector, voxel_size)
strain3 = compute_normal_strain(displacemen3, q_vector, voxel_size)

strain_clean = np.zeros(strain1.shape)
strain_clean[np.isnan(strain1)] = np.nan # Not sure you need that.

mask = np.isclose(strain1,strain2)
strain_clean[mask==1] = strain1[mask==1]
    
mask = np.isclose(strain1,strain3)
strain_clean[mask==1] = strain1[mask==1]

mask = np.isclose(strain2,strain3)
strain_clean[mask==1] = strain2[mask==1]

return strain_clean

It works fine for me. You may get problems for particles with few pixels or with several defects. You could imagine making more than 3 strain maps in that case. But for me it worked fine on 2 different particles.

If you want to test on a particle with a defect, you can use this one :
/data/visitor/ihhc3936/id01/20231010/RAW_DATA/PtYSZ/PtYSZ_0001/PtYSZ_0001.h5
scan 54