ncempy.algo.distortion module

Module to handle distortions in diffraction patters.

ncempy.algo.distortion.filter_ring(points, center, rminmax)[source]

Filter points to be in a certain radial distance range from center.

Parameters:
  • points (np.ndarray) – Candidate points.
  • center (np.ndarray/tuple) – Center position.
  • rminmax (tuple) – Tuple of min and max radial distance.
Returns:

List of filtered points, two column array.
Return type:

(np.ndarray)
ncempy.algo.distortion.optimize_center(points, center, maxfev=1000, verbose=None)[source]

Optimize the center by minimizing the sum of square deviations from the mean radial distance.

Parameters:
  • points (np.ndarray) – The points to which the optimization is done (x,y coords in org image).
  • center (np.ndarray/tuple) – Initial center guess.
  • maxfev (int) – Max number of iterations forwarded to scipy.optimize.leastsq().
  • verbose (bool) – Set to get verbose output.
Returns:

The optimized center.
Return type:

(np.ndarray)
ncempy.algo.distortion.optimize_distortion(points, ns, maxfev=1000, verbose=False)[source]

Optimize distortions.

The orders in the list ns are first fitted subsequently and the result is refined in a final fit simultaneously fitting all orders.

Parameters:
  • points (np.ndarray) – Points to optimize to (in polar coords).
  • ns (tuple) – List of orders to correct for.
  • maxfev (int) – Max number of iterations forwarded to scipy.optimize.leastsq().
  • verbose (bool) – Set for verbose output.
Returns:

Optimized parameters according to ns.
Return type:

(np.ndarray)
ncempy.algo.distortion.plot_distpolar(points, dims, dists, ns, show=False)[source]

Plot the results of distortion fitting in polar coordinates.

Parameters:
  • points (np.ndarray) – Points in polar coords.
  • dims (tuple) – Dimensions, necessary to have unit information.
  • dists (np.ndarray) – Results of dist fitting, length according to ns.
  • ns (list) – List of used orders.
  • show (bool) – Set to directly show the plot in interactive mode.
Returns:

Image of the plot.
Return type:

(np.ndarray)
ncempy.algo.distortion.plot_ringpolar(points, dims, show=False)[source]

Plot points in polar coordinate system.

Parameters:
  • points (np.ndarrad) – Positions in polar coords.
  • dims (tuple) – Dimension information to plot labels.
  • show (bool) – Set to directly show plot in interactive mode.
Returns:

Image of the plot.
Return type:

(np.ndarray)
ncempy.algo.distortion.points_topolar(points, center)[source]

Convert points to polar coordinate system.

Can be either in pixel or real dim, but should be the same for points and center.

Parameters:
  • points (np.ndarray) – Positions as two column array.
  • center (np.ndarray/tuple) – Origin of the polar coordinate system.
Returns:

Positions in polar coordinate system as two column array (r, theta).
Return type:

(np.ndarray)
ncempy.algo.distortion.rad_dis(theta, alpha, beta, order=2)[source]

Radial distortion due to ellipticity or higher order distortion.

Relative distortion, to be multiplied with radial distance.

Parameters:
  • theta (np.ndarray/float) – Angles at which to evaluate.
  • alpha (float) – Orientation of major axis.
  • beta (float) – Strength of distortion (beta = (1-r_min/r_max)/(1+r_min/r_max).
  • order (int) – Order of distortion.
Returns:

Distortion factor.
Return type:

(np.ndarray/float)
ncempy.algo.distortion.residuals_center(param, data)[source]

Residual function for minimizing the deviations from the mean radial distance.

Parameters:
  • param (np.ndarray) – The center to optimize.
  • data (np.ndarray) – The points in x,y coordinates of the original image.
Returns:

Residuals.
Return type:

(np.ndarray)
ncempy.algo.distortion.residuals_dis(param, points, ns)[source]

Residual function for distortions.

Parameters:
  • param (np.ndarray) – Parameters for distortion.
  • points (np.ndarray) – Points to fit to.
  • ns (tuple) – List of orders to account for.
Returns:

Residuals.
Return type:

(np.ndarray)