ZernikeVector

class mmtwfs.zernike.ZernikeVector(coeffs=[], modestart=2, normalized=False, zmap=None, units=Unit('nm'), errorbars=None, **kwargs)

Bases: collections.abc.MutableMapping

Class to wrap and visualize a vector of Zernike polynomial coefficients. We build upon a MutableMapping class to provide a way to access/modify coefficients in a dict-like way.

Attributes

modestartint

Noll mode number of the first included mode.

normalizedbool

If True, coefficients are normalized to unit variance. If False, coefficients reflect the phase amplitude of the mode.

coeffsdict

Contains the Zernike coefficients with keys of form “Z%02d”

ignoreddict

Used to store coefficients that are temporarily ignored. Managed via self.ignore() and self.restore().

Parameters

coeffslist-like (default: [])

Vector of coefficients starting from modestart.

modestartint (default: 2)

Noll mode number of the first included mode.

normalizedbool (default: False)

If True, coefficients are normalized to unit variance (Noll coefficients). If False, coefficients reflect the phase amplitude of the mode (fringe coefficients).

zmapdict

When loading coefficients from an array this maps the coefficient keys to array indices.

unitsIrreducibleUnit or PrefixUnit (default: u.nm - nanometers)

Units of the coefficients.

errorbars = dict (default: None)

Uncertainties for each coefficient.

**kwargskwargs

Keyword arguments for setting terms individually, e.g. Z09=10.0.

Attributes Summary

array	Return coefficients in the form of a 1D np.ndarray.
norm_array	Return coefficients in the form of a 1D np.ndarray with each coefficient normalized to unit variance for its mode.
peak2valley	Return the peak-to-valley amplitude of the Zernike set.
rms	Return the RMS phase displacement of the Zernike set.
units	Return the coefficient units currently being used.

Methods Summary

bar_chart([residual, total, max_c, title, ...])	Plot a bar chart of the coefficients and, optionally, a residual amount not included in the coefficients.
copy()	Make a new ZernikeVector with the same configuration and coefficients
denormalize()	Restore normalized coefficients to fringe coefficients.
frac_error([key])	Calculate fractional size of the error bar for mode, key.
fringe_bar_chart([total, max_c, title, ...])	Plot a bar chart of the fringe amplitudes of the coefficients
from_array(coeffs[, zmap, modestart, ...])	Load coefficients from a provided list/array starting from modestart.
ignore(key)	Set coefficient, key, aside for later recall if needed.
label(key)	If defined, return the descriptive label for mode, 'key'
load([filename])	Load ZernikeVector data from JSON format.
load_lmfit(fit_report)	Load information from a lmfit.minimizer.MinimizerResult that is output from a wavefront fit.
normalize()	Normalize coefficients to unit variance for each mode.
phase_map([n])	Calculate a 2D polar map of total phase displacements with sampling of n points along rho and phi vectors.
plot_map()	Plot 2D map of total phase displacement.
plot_surface()	Plot total phase displacement as a 3D surface along with 2D contour map.
pretty_print([last])	Overload __repr__ to print out coefficients in a nice way including units and descriptive labels.
restore(key)	Restore coefficient, key, back into set of coefficients.
rotate([angle])	Rotate the ZernikeVector by an angle.
save([filename])	Save Zernike vector to JSON format to retain units and normalization info.
shortlabel(key)	If defined, return the short label for mode, 'key'
total_phase(rho, phi)	Calculate total phase displacement at polar coordinates (rho, phi).

Attributes Documentation

array

Return coefficients in the form of a 1D np.ndarray.

norm_array

Return coefficients in the form of a 1D np.ndarray with each coefficient normalized to unit variance for its mode.

peak2valley

Return the peak-to-valley amplitude of the Zernike set.

rms

Return the RMS phase displacement of the Zernike set.

units

Return the coefficient units currently being used.

Methods Documentation

bar_chart(residual=None, total=True, max_c=<Quantity 500. nm>, title=None, last_mode=None)

Plot a bar chart of the coefficients and, optionally, a residual amount not included in the coefficients.

copy()

Make a new ZernikeVector with the same configuration and coefficients

denormalize()

Restore normalized coefficients to fringe coefficients.

frac_error(key=None)

Calculate fractional size of the error bar for mode, key.

fringe_bar_chart(total=True, max_c=<Quantity 2000. nm>, title=None, last_mode=None)

Plot a bar chart of the fringe amplitudes of the coefficients

from_array(coeffs, zmap=None, modestart=None, errorbars=None, normalized=False)

Load coefficients from a provided list/array starting from modestart. Array is assumed to start from self.modestart if modestart is not provided.

ignore(key)

Set coefficient, key, aside for later recall if needed.

label(key)

If defined, return the descriptive label for mode, ‘key’

load(filename='zernike.json')

Load ZernikeVector data from JSON format.

load_lmfit(fit_report)

Load information from a lmfit.minimizer.MinimizerResult that is output from a wavefront fit. If there are reported errorbars, populate those, too.

normalize()

Normalize coefficients to unit variance for each mode.

phase_map(n=400)

Calculate a 2D polar map of total phase displacements with sampling of n points along rho and phi vectors.

plot_map()

Plot 2D map of total phase displacement.

plot_surface()

Plot total phase displacement as a 3D surface along with 2D contour map.

pretty_print(last=22)

Overload __repr__ to print out coefficients in a nice way including units and descriptive labels.

restore(key)

Restore coefficient, key, back into set of coefficients.

rotate(angle=<Quantity 0. deg>)

Rotate the ZernikeVector by an angle. Rotation matrix algorithm taken from https://arxiv.org/pdf/1302.7106.pdf.

save(filename='zernike.json')

Save Zernike vector to JSON format to retain units and normalization info.

shortlabel(key)

If defined, return the short label for mode, ‘key’

total_phase(rho, phi)

Calculate total phase displacement at polar coordinates (rho, phi).