stemtool.nbed package

Submodules

stemtool.nbed.nbed_strain module

stemtool.nbed.nbed_strain.ROI_from_image(image, med_val, style='over', showfig=True)

stemtool.nbed.nbed_strain.ROI_strain_map(strain_ROI, ROI)

Convert the strain in the ROI array to a strain map

stemtool.nbed.nbed_strain.angle_fun(angle, image_orig, axis=0)

Rotation Sum Finder

Parameters:

• angle (float) – Angle to rotate
• image_orig ((2,2) shape ndarray) – Input Image
• axis (int, optional) – Axis along which to perform sum

Returns:

rotmin – Sum of the rotated image multiplied by -1 along the axis specified

Return type:

float

Notes

This is an internal minimization function for finding the minimum sum of the image at a particular rotation angle.

See also

rotation_finder()

stemtool.nbed.nbed_strain.aperture_image(data4D, center, radius)

Generate Virtual DF image for a given aperture

Parameters:

• data4D (ndarray of shape (4,4)) – the first two dimensions are Fourier space, while the next two dimensions are real space
• center (ndarray of shape (1,2)) – Center of the circular aperture
• radius (float) – Radius of the circular aperture

Returns:

df_image – Generated virtual dark field image from the aperture and 4D data

Return type:

ndarray of shape (2,2)

Notes

We generate the aperture first, and then make copies of the aperture to generate a 4D dataset of the same size as the 4D data. Then we do an element wise multiplication of this aperture 4D data with the 4D data and then sum it along the two Fourier directions.

stemtool.nbed.nbed_strain.custom_detector(data4D, det_inner, det_outer, det_center=(0, 0), mrad_calib=0)

Generate an image with a custom annular detector located anywhere in diffraction space

Parameters:

• data4D (ndarray of shape (4,4)) – the first two dimensions are Fourier space, while the next two dimensions are real space
• center (ndarray of shape (1,2)) – Center of the circular aperture
• radius (float) – Radius of the circular aperture

Returns:

df_image – Generated virtual dark field image from the aperture and 4D data

Return type:

ndarray of shape (2,2)

Notes

We generate the aperture first, and then make copies of the aperture to generate a 4D dataset of the same size as the 4D data. Then we do an element wise multiplication of this aperture 4D data with the 4D data and then sum it along the two Fourier directions.

stemtool.nbed.nbed_strain.data4Dto2D(data4D)

Convert 4D data to 2D data

Parameters:data4D (ndarray of shape (4,4)) – the first two dimensions are Fourier space, while the next two dimensions are real space Returns:data2D – Raveled 2D data where the first two dimensions are positions while the next two dimensions are spectra Return type:ndarray of shape (2,2)

stemtool.nbed.nbed_strain.rotate_and_center_ROI(data4D_ROI, rotangle, xcenter, ycenter)

Rotation Corrector

Parameters:

• data4D_ROI (ndarray) – Region of interest of the 4D-STEM dataset in the form of ROI pixels (scanning), CBED_Y, CBED_x
• rotangle (float) – angle in counter-clockwise direction to rotate individual CBED patterns
• xcenter (float) – X pixel co-ordinate of center of mean pattern
• ycenter (float) – Y pixel co-ordinate of center of mean pattern

Returns:

corrected_ROI – Each CBED pattern from the region of interest first centered and then rotated along the center

Return type:

ndarray

Notes

We start by centering each 4D-STEM CBED pattern and then rotating the patterns with respect to the pattern center

stemtool.nbed.nbed_strain.rotation_finder(image_orig, axis=0)

Angle Finder

Parameters:

• image_orig ((2,2) shape ndarray) – Input Image
• axis (int, optional) – Axis along which to perform sum

Returns:

min_x – Angle by which if the image is rotated by, the sum of the image along the axis specified is maximum

Return type:

float

Notes

Uses the angle_fun function as the minimizer.

See also

angle_fun()

stemtool.nbed.nbed_strain.sobel_filter(image, med_filter=50)

stemtool.nbed.nbed_strain.sort_edges(edge_map, edge_distance=5)

stemtool.nbed.nbed_strain.spectra_finder(data4D, yvals, xvals)

stemtool.nbed.nbed_strain.test_aperture(pattern, center, radius, showfig=True)

Test an aperture position for Virtual DF image

Parameters:

• pattern (ndarray of shape (2,2)) – Diffraction pattern, preferably the mean diffraction pattern for testing out the aperture location
• center (ndarray of shape (1,2)) – Center of the circular aperture
• radius (float) – Radius of the circular aperture
• showfig (bool, optional) – If showfig is True, then the image is displayed with the aperture overlaid

Returns:

aperture – A matrix of the same size of the input image with zeros everywhere and ones where the aperture is supposed to be

Return type:

ndarray of shape (2,2)

Notes

Use the showfig option to visually test out the aperture location with varying parameters

Module contents