pypty.se

getvirtualhaadf

Compute a virtual HAADF image from 4D-STEM data.

PARAMETER	DESCRIPTION
pypty_params	Dictionary with keys 'data_path', 'scan_size', 'plot', 'output_folder'. TYPE: dict
save	Whether to save the image. Default is True. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
haadf	HAADF intensities array. TYPE: ndarray

get_aperture

Generate a binary aperture mask from diffraction data.

PARAMETER	DESCRIPTION
params	Dictionary with keys 'data_path', 'data_pad', 'plot', 'bright_threshold', 'flip_ky'. TYPE: dict

RETURNS	DESCRIPTION
params	Updated dict including 'aperture_mask'. TYPE: dict

create_binned_dataset

Downsample a dataset by spatial binning and save to a new file.

PARAMETER	DESCRIPTION
path_orig	Path to the original dataset. TYPE: str
path_new	Path to save the binned dataset. TYPE: str
bin	Binning factor. TYPE: int

RAISES	DESCRIPTION
IOError	If file operations fail.

compensate_pattern_drift

Compensate drift in diffraction patterns via phase correlation.

PARAMETER	DESCRIPTION
aperture	Binary aperture mask. TYPE: ndarray
patterns	4D diffraction patterns. TYPE: ndarray

RETURNS	DESCRIPTION
ndarray	Drift-compensated patterns.

get_virtual_annular_detector

Compute virtual detector signal using annular masks.

PARAMETER	DESCRIPTION
pypty_params	Dictionary with keys 'data_path', 'scan_size', 'plot', 'output_folder'. TYPE: dict
inner_rad	Inner radius in normalized units. Default is 0. TYPE: float DEFAULT: 0
outer_rad	Outer radius in normalized units. Default is 1. TYPE: float DEFAULT: 1
save	Whether to save the signal. Default is False. TYPE: bool DEFAULT: False
offset_x	X-offset. Default is 0. TYPE: float DEFAULT: 0
offset_y	Y-offset. Default is 0. TYPE: float DEFAULT: 0

RETURNS	DESCRIPTION
ndarray	2D detector signal array.

coordinate_transformation_2d

Map coordinates from XY space to UV space using polynomial coefficients.

PARAMETER	DESCRIPTION
xy	Coordinates to transform. Shape (2, N) or (N, 2). TYPE: array_like
ab	Transformation coefficients. Length 3 (linear), 6 (quadratic), or 10 (cubic). TYPE: ndarray

RETURNS	DESCRIPTION
ndarray	Transformed coordinates, shape (N, 2).

Notes

Original implementation by Wouter Van den Broek.

find_ab

Estimate polynomial coefficients for coordinate mapping.

PARAMETER	DESCRIPTION
x	Source x-coordinates. TYPE: array_like
y	Source y-coordinates. TYPE: array_like
u	Target u-coordinates. TYPE: array_like
v	Target v-coordinates. TYPE: array_like
trafo_flag	Transformation order: 0=linear, 1=quadratic, 2=cubic. Default is 2. TYPE: int DEFAULT: 2

RETURNS	DESCRIPTION
ndarray	Transformation coefficients.

Notes

Original implementation by Wouter Van den Broek.

unwarp_im

Correct distortions and illumination in warped images.

PARAMETER	DESCRIPTION
warp_im	Input image(s). TYPE: array_like
ab	Transformation coefficients. TYPE: ndarray
method	Interpolation method. Default is 'linear'. TYPE: str DEFAULT: 'linear'

RETURNS	DESCRIPTION
ndarray	Unwarped image(s).

Notes

Original implementation by Wouter Van den Broek.

coordinate_transformation_2d_areamag

Compute local area magnification of polynomial mapping.

PARAMETER	DESCRIPTION
xy	Coordinates of shape (2, N) or (N, 2). TYPE: array_like
ab	Transformation coefficients. TYPE: ndarray

RETURNS	DESCRIPTION
ndarray	Local magnification values.

Notes

Original implementation by Wouter Van den Broek.

fit_vector_field

Fit a smooth displacement field from calibration points.

PARAMETER	DESCRIPTION
x	Nominal coordinates. TYPE: array_like
y	Nominal coordinates. TYPE: array_like
u	Observed coordinates. TYPE: array_like
v	Observed coordinates. TYPE: array_like
Xi	Grid coordinates for mapping. TYPE: array_like
Yi	Grid coordinates for mapping. TYPE: array_like

RETURNS	DESCRIPTION
tuple of numpy.ndarray	Displacement fields (dV, dU).

warp_image

Warp image(s) based on a displacement field.

PARAMETER	DESCRIPTION
image	Input image(s). TYPE: array_like
vector_field	Displacement fields (U, V). TYPE: tuple of numpy.ndarray
order	Interpolation order. Default is 1. TYPE: int DEFAULT: 1
extra_angle_rotation_compensation	Rotation angle in degrees. Default is 0. TYPE: float DEFAULT: 0

RETURNS	DESCRIPTION
ndarray	Warped image(s).

compose_fields

Compose two displacement fields for use with warp_image.

Resulting field corresponds to: first apply field1, then field2.

PARAMETER	DESCRIPTION
field1	First displacement field. Applied closest to the original image. TYPE: (U1, V1)
field2	Second displacement field. Applied after field1. TYPE: (U2, V2)
order	Interpolation order used to resample field1. TYPE: int DEFAULT: 1
mode	Boundary mode for map_coordinates (e.g. 'nearest', 'constant'). TYPE: str DEFAULT: 'nearest'

RETURNS	DESCRIPTION
U_tot, V_tot : np.ndarray	Composed displacement field such that: warp_image(warp_image(I, field1), field2) ≈ warp_image(I, (U_tot, V_tot))

warp_images_batch

Apply warping to a batch of images using precomputed indices.

PARAMETER	DESCRIPTION
images	Batch of images. TYPE: array_like
vector_field	Not used. TYPE: ignored
batches	Batch indices. TYPE: array_like
warped_rows	Flattened row and column indices. TYPE: array_like
warped_cols	Flattened row and column indices. TYPE: array_like
order	Interpolation order. TYPE: int

RETURNS	DESCRIPTION
ndarray	Warped images.

unwarp_4dstem_batch

Unwarp a 4D-STEM dataset in batches.

PARAMETER	DESCRIPTION
data_old	Input dataset. TYPE: str or ndarray
path_numpy_new	Path to save warped data. TYPE: str DEFAULT: None
vector_field	Displacement fields. TYPE: tuple of numpy.ndarray DEFAULT: None
batch_size	Frames per batch. Default is 20. TYPE: int DEFAULT: 20
order	Interpolation order. Default is 5. TYPE: int DEFAULT: 5
return_data	If True, return data instead of saving. TYPE: bool DEFAULT: False

RETURNS	DESCRIPTION
ndarray or None	Warped dataset or None.

RAISES	DESCRIPTION
ValueError	If total frames not divisible by batch_size.

remove_hot_pixels

Remove hot pixels from 4D-STEM data.

PARAMETER	DESCRIPTION
data	Input dataset. TYPE: ndarray
percentile	Threshold percentile. Default is 99.99. TYPE: float DEFAULT: 99.99

RETURNS	DESCRIPTION
ndarray	Corrected dataset.