algotom.util.calibration

Module of calibration methods: - Correcting the non-uniform background of an image. - Binarizing an image. - Calculating the distance between two point-like objects segmented from

two images. Useful for determining pixel-size in helical scans.

Functions:

algotom.util.calibration.binarize_image(mat, threshold=None, bgr='bright', norm=False, denoise=True, invert=True)[source]

Binarize an image.

Parameters

  • mat (array_like) – 2D array.

  • threshold (float, optional) – Threshold value for binarization. Automatically calculated using Algorithm 4 in Ref. [1] if None.

  • bgr ({“bright”, “dark”}) – To indicate the brightness of the background against image features.

  • norm (bool, optional) – Apply normalization if True.

  • denoise (bool, optional) – Apply denoising if True.

  • invert (bool, optional) – Invert the contrast if needed.

Returns

array_like – 2D binary array.

References

1

https://doi.org/10.1364/OE.26.028396

algotom.util.calibration.calculate_distance(mat1, mat2, size_opt='max', threshold=None, bgr='bright', norm=False, denoise=True, invert=True)[source]

Calculate the distance between two point-like objects segmented from two images. Useful for measuring pixel-size in helical scans (Ref. [1]).

Parameters

  • mat1 (array_like) – 2D array.

  • mat2 (array_like) – 2D array.

  • size_opt ({“max”, “min”, “median”, “mean”}) – Options to select binary objects based on their size.

  • threshold (float, optional) – Threshold value for binarization. Automatically calculated using Algorithm 4 in Ref. [2] if None.

  • bgr ({“bright”, “dark”}) – To indicate the brightness of the background against image features.

  • norm (bool, optional) – Apply normalization if True.

  • denoise (bool, optional) – Apply denoising if True.

  • invert (bool, optional) – Invert the contrast if needed.

References

1

https://doi.org/10.1364/OE.418448

2

https://doi.org/10.1364/OE.26.028396

algotom.util.calibration.calculate_threshold(mat, bgr='bright')[source]

Calculate threshold value based on Algorithm 4 in Ref. [1].

Parameters

  • mat (array_like) – 2D array.

  • bgr ({“bright”, “dark”}) – To indicate the brightness of the background against image features.

Returns

float – Threshold value.

References

1

https://doi.org/10.1364/OE.26.028396

algotom.util.calibration.check_dot_size(mat, min_size, max_size)[source]

Check if the size of a dot is in a range.

Parameters

  • mat (array_like) – 2D array.

  • min_size (float) – Minimum size.

  • max_size (float) – Maximum size.

Returns

bool

algotom.util.calibration.get_dot_size(mat, size_opt='max')[source]

Get size of binary dots given the option.

Parameters

  • mat (array_like) – 2D binary array.

  • size_opt ({“max”, “min”, “median”, “mean”}) – Select options.

Returns

dot_size (float) – Size of the dot.

algotom.util.calibration.invert_dot_contrast(mat)[source]

Invert the contrast of a 2D binary array to make sure that a dot is white.

Parameters

mat (array_like) – 2D binary array.

Returns

array_like – 2D array.

algotom.util.calibration.normalize_background(mat, radius=51)[source]

Correct a non-uniform background of an image using the median filter.

Parameters

  • mat (array_like) – 2D array.

  • radius (int) – Size of the median filter.

Returns

array_like – 2D array. Corrected image.

algotom.util.calibration.normalize_background_based_fft(mat, sigma=5, pad=None, mode='reflect')[source]

Correct a non-uniform background of an image using a Fourier Gaussian filter.

Parameters

  • mat (array_like) – 2D array.

  • sigma (int) – Sigma of the Gaussian.

  • pad (int) – Padding for the Fourier transform.

  • mode (str, list of str, or tuple of str) – Padding method. One of options : ‘reflect’, ‘edge’, ‘constant’. Full list is at: https://numpy.org/doc/stable/reference/generated/numpy.pad.html

Returns

array_like – 2D array. Corrected image.

algotom.util.calibration.select_dot_based_size(mat, dot_size, ratio=0.01)[source]

Select dots having a certain size.

Parameters

  • mat (array_like) – 2D array.

  • dot_size (float) – Size of the standard dot.

  • ratio (float) – Used to calculate the acceptable range. [dot_size - ratio*dot_size; dot_size + ratio*dot_size]

Returns

array_like – 2D array. Selected dots.