Welcome to the AOtools Documentation!

Introduction

AOtools is an attempt to gather together many common tools, equations and functions for Adaptive Optics. The idea is to provide an alternative to the current model, where a new AO researcher must write their own library of tools, many of which implement theory and ideas that have been in existance for over 20 years. AOtools will hopefully provide a common place to put these tools, which through use and bug fixes, should become reliable and well documented.

Installation

AOtools uses mainly standard library functions, and all attempts have been made to avoid adding unneccessary dependencies. Currently, the library requires only

  • numpy
  • scipy
  • astropy
  • matplotlib

Contents

Introduction

AOtools is an attempt to gather together many common tools, equations and functions for Adaptive Optics. The idea is to provide an alternative to the current model, where a new AO researcher must write their own library of tools, many of which implement theory and ideas that have been in existance for over 20 years. AOtools will hopefully provide a common place to put these tools, which through use and bug fixes, should become reliable and well documented.

Installation

AOtools uses mainly standard library functions, and all attempts have been made to avoid adding unneccessary dependencies. Currently, the library requires only

  • numpy
  • scipy
  • astropy
  • matplotlib

Atmospheric Turbulence

Finite Phase Screens

Creation of phase screens of a defined size with Von Karmen Statistics.

aotools.turbulence.phasescreen.ft_phase_screen(r0, N, delta, L0, l0, FFT=None, seed=None)[source]

Creates a random phase screen with Von Karmen statistics. (Schmidt 2010)

Parameters:
  • r0 (float) – r0 parameter of scrn in metres
  • N (int) – Size of phase scrn in pxls
  • delta (float) – size in Metres of each pxl
  • L0 (float) – Size of outer-scale in metres
  • l0 (float) – inner scale in metres
Returns:

numpy array representing phase screen
Return type:

ndarray
aotools.turbulence.phasescreen.ft_sh_phase_screen(r0, N, delta, L0, l0, FFT=None, seed=None)[source]

Creates a random phase screen with Von Karmen statistics with added sub-harmonics to augment tip-tilt modes. (Schmidt 2010)

Parameters:
  • r0 (float) – r0 parameter of scrn in metres
  • N (int) – Size of phase scrn in pxls
  • delta (float) – size in Metres of each pxl
  • L0 (float) – Size of outer-scale in metres
  • l0 (float) – inner scale in metres
Returns:

numpy array representing phase screen
Return type:

ndarray

Infinite Phase Screens

An implementation of the “infinite phase screen”, as deduced by Francois Assemat and Richard W. Wilson, 2006.

class aotools.turbulence.infinitephasescreen.PhaseScreenVonKarman(nx_size, pixel_scale, r0, L0, random_seed=None, n_columns=2)[source]

Bases: aotools.turbulence.infinitephasescreen.PhaseScreen

A “Phase Screen” for use in AO simulation with Von Karmon statistics.

This represents the phase addition light experiences when passing through atmospheric turbulence. Unlike other phase screen generation techniques that translate a large static screen, this method keeps a small section of phase, and extends it as necessary for as many steps as required. This can significantly reduce memory consumption at the expense of more processing power required.

The technique is described in a paper by Assemat and Wilson, 2006. It essentially assumes that there are two matrices, “A” and “B”, that can be used to extend an existing phase screen. A single row or column of new phase can be represented by

X = A.Z + B.b

where X is the new phase vector, Z is some number of columns of the existing screen, and b is a random vector with gaussian statistics.

This object calculates the A and B matrices using an expression of the phase covariance when it is initialised. Calculating A is straightforward through the relationship:

A = Cov_xz . (Cov_zz)^(-1).

B is less trivial.

BB^t = Cov_xx - A.Cov_zx

(where B^t is the transpose of B) is a symmetric matrix, hence B can be expressed as

B = UL,

where U and L are obtained from the svd for BB^t

U, w, U^t = svd(BB^t)

L is a diagonal matrix where the diagonal elements are w^(1/2).

On initialisation an initial phase screen is calculated using an FFT based method. When add_row is called, a new vector of phase is added to the phase screen using nCols columns of previous phase. Assemat & Wilson claim that two columns are adequate for good atmospheric statistics. The phase in the screen data is always accessed as <phasescreen>.scrn and is in radians.

Parameters:
  • nx_size (int) – Size of phase screen (NxN)
  • pixel_scale (float) – Size of each phase pixel in metres
  • r0 (float) – fried parameter (metres)
  • L0 (float) – Outer scale (metres)
  • n_columns (int, optional) – Number of columns to use to continue screen, default is 2
add_row()

Adds a new row to the phase screen and removes old ones.

scrn

The current phase map held in the PhaseScreen object in radians.

class aotools.turbulence.infinitephasescreen.PhaseScreenKolmogorov(nx_size, pixel_scale, r0, L0, random_seed=None, stencil_length_factor=4)[source]

Bases: aotools.turbulence.infinitephasescreen.PhaseScreen

A “Phase Screen” for use in AO simulation using the Fried method for Kolmogorov turbulence.

This represents the phase addition light experiences when passing through atmospheric turbulence. Unlike other phase screen generation techniques that translate a large static screen, this method keeps a small section of phase, and extends it as neccessary for as many steps as required. This can significantly reduce memory consuption at the expense of more processing power required.

The technique is described in a paper by Assemat and Wilson, 2006 and expanded upon by Fried, 2008. It essentially assumes that there are two matrices, “A” and “B”, that can be used to extend an existing phase screen. A single row or column of new phase can be represented by

X = A.Z + B.b

where X is the new phase vector, Z is some data from the existing screen, and b is a random vector with gaussian statistics.

This object calculates the A and B matrices using an expression of the phase covariance when it is initialised. Calculating A is straightforward through the relationship:

A = Cov_xz . (Cov_zz)^(-1).

B is less trivial.

BB^t = Cov_xx - A.Cov_zx

(where B^t is the transpose of B) is a symmetric matrix, hence B can be expressed as

B = UL,

where U and L are obtained from the svd for BB^t

U, w, U^t = svd(BB^t)

L is a diagonal matrix where the diagonal elements are w^(1/2).

The Z data is taken from points in a “stencil” defined by Fried that samples the entire screen. An additional “reference point” is also considered, that is picked from a point separate from teh stencil and applied on each iteration such that the new phase equation becomes:

On initialisation an initial phase screen is calculated using an FFT based method. When add_row is called, a new vector of phase is added to the phase screen. The phase in the screen data is always accessed as <phasescreen>.scrn and is in radians.

Parameters:
  • nx_size (int) – Size of phase screen (NxN)
  • pixel_scale (float) – Size of each phase pixel in metres
  • r0 (float) – fried parameter (metres)
  • L0 (float) – Outer scale (metres)
  • random_seed (int, optional) – seed for the random number generator
  • stencil_length_factor (int, optional) – How much longer is the stencil than the desired phase? default is 4
add_row()

Adds a new row to the phase screen and removes old ones.

scrn

The current phase map held in the PhaseScreen object in radians.

Slope Covariance Matrix Generation

Slope covariance matrix routines for AO systems observing through Von Karmon turbulence. Such matrices have a variety of uses, though they are especially useful for creating ‘tomographic reconstructors’ that can reconstruct some ‘psuedo’ WFS measurements in a required direction (where there might be an interesting science target but no guide stars), given some actual measurements in other directions (where the some suitable guide stars are).

Warning

This code has been tested qualitatively and seems OK, but needs more rigorous testing.

class aotools.turbulence.slopecovariance.CovarianceMatrix(n_wfs, pupil_masks, telescope_diameter, subap_diameters, gs_altitudes, gs_positions, wfs_wavelengths, n_layers, layer_altitudes, layer_r0s, layer_L0s, threads=1)[source]

Bases: object

A creator of slope covariance matrices in Von Karmon turbulence, based on the paper by Martin et al, SPIE, 2012.

Given a list of paramters describing an AO WFS system and the atmosphere above the telescope, this class can compute the covariance matrix between all the WFS measurements. This can support LGS sources that exist at a finite altitude. When computing the covariance matrix, Python’s multiprocessing module is used to spread the work between different processes and processing cores.

On initialisation, this class performs some initial calculations and parameter sorting. To create the covariance matrix run the make_covariace_matrix method. This may take some time depending on your paramters…

Parameters:
  • n_wfs (int) – Number of wavefront sensors present.
  • pupil_masks (ndarray) – A map of the pupil for each WFS which is nx_subaps by ny_subaps. 1 if subap active, 0 if not.
  • telescope_diameter (float) – Diameter of the telescope
  • subap_diameters (ndarray) – The diameter of the sub-apertures for each WFS in metres
  • gs_altitudes (ndarray) – Reciprocal (1/metres) of the Guide star alitude for each WFS
  • gs_positions (ndarray) – X,Y position of each WFS in arcsecs. Array shape (Wfs, 2)
  • wfs_wavelengths (ndarray) – Wavelength each WFS observes
  • n_layers (int) – The number of atmospheric turbulence layers
  • layer_altitudes (ndarray) – The altitude of each turbulence layer in meters
  • layer_r0s (ndarray) – The Fried parameter of each turbulence layer
  • layer_L0s (ndarray) – The outer-scale of each layer in metres
  • threads (int, optional) – Number of processes to use for calculation. default is 1
make_covariance_matrix()[source]

Calculate and build the covariance matrix

Returns:Covariance Matrix
Return type:ndarray
make_tomographic_reconstructor(svd_conditioning=0)[source]

Creats a tomohraphic reconstructor from the covariance matrix as in Vidal, 2010. See the documentation for the function create_tomographic_covariance_reconstructor in this module. Assumes the 1st WFS given is the one for which reconstruction is required to.

Parameters:svd_conditioning (float) – Conditioning for the SVD used in inversion.
Returns:A tomohraphic reconstructor.
Return type:ndarray
aotools.turbulence.slopecovariance.calculate_structure_function(phase, nbOfPoint=None, step=None)[source]

Compute the structure function of an 2D array, along the first dimension. SF defined as sf[j]= < (phase - phase_shifted_by_j)^2 > Translated from a YAO function.

Parameters:
  • phase (ndarray, 2d) – 2d-array
  • nbOfPoint (int) – final size of the structure function vector. Default is phase.shape[1] / 4
  • step (int) – step in pixel when computing the sf. (step * sampling_phase) gives the sf sampling in meters. Default is 1
Returns:

values for the structure function of the data.
Return type:

ndarray, float
aotools.turbulence.slopecovariance.calculate_wfs_seperations(n_subaps1, n_subaps2, wfs1_positions, wfs2_positions)[source]

Calculates the seperation between all sub-apertures in two WFSs

Parameters:
  • n_subaps1 (int) – Number of sub-apertures in WFS 1
  • n_subaps2 (int) – Number of sub-apertures in WFS 2
  • wfs1_positions (ndarray) – Array of the X, Y positions of the centre of each sub-aperture with respect to the centre of the telescope pupil
  • wfs2_positions (ndarray) – Array of the X, Y positions of the centre of each sub-aperture with respect to the centre of the telescope pupil
Returns:

2-D Array of sub-aperture seperations
Return type:

ndarray
aotools.turbulence.slopecovariance.create_tomographic_covariance_reconstructor(covariance_matrix, n_onaxis_subaps, svd_conditioning=0)[source]

Calculates a tomographic reconstructor using the method of Vidal, JOSA A, 2010.

Uses a slope covariance matrix to generate a reconstruction matrix that will convert a collection of measurements from WFSs observing in a variety of directions (the “off-axis” directions) to the measurements that would have been observed by a WFS observing in a different direction (the “on-axis” direction. The given covariance matrix must include the covariance between all WFS measurements, including the “psuedo” WFS pointing in the on-axis direction. It is assumed that the covariance of measurements from this on-axis direction are first in the covariance matrix.

To create the tomographic reconstructor it is neccessary to invert the covariance matrix between off-axis WFS measurements. An SVD based psueod inversion is used for this (numpy.linalg.pinv). A conditioning to this SVD may be required to filter potentially unwanted modes.

Parameters:
  • covariance_matrix (ndarray) – A covariance matrix between WFSs
  • n_onaxis_subaps (int) – Number of sub-aperture in on-axis WFS
  • svd_conditioning (float, optional) – Conditioning for SVD inversion (default is 0)

Returns:

aotools.turbulence.slopecovariance.mirror_covariance_matrix(cov_mat)[source]

Mirrors a covariance matrix around the axis of the diagonal.

Parameters:
  • cov_mat (ndarray) – The covariance matrix to mirror
  • n_subaps (ndarray) – Number of sub-aperture in each WFS
aotools.turbulence.slopecovariance.structure_function_kolmogorov(separation, r0)[source]

Compute the Kolmogorov phase structure function

Parameters:
  • separation (ndarray, float) – float or array of data representing separations between points
  • r0 (float) – Fried parameter for atmosphere
Returns:

Structure function for separation(s)
Return type:

ndarray, float
aotools.turbulence.slopecovariance.structure_function_vk(seperation, r0, L0)[source]

Computes the Von Karmon structure function of atmospheric turbulence

Parameters:
  • seperation (ndarray, float) – float or array of data representing seperations between points
  • r0 (float) – Fried parameter for atmosphere
  • L0 (float) – Outer scale of turbulence
Returns:

Structure function for seperation(s)
Return type:

ndarray, float
aotools.turbulence.slopecovariance.wfs_covariance(n_subaps1, n_subaps2, wfs1_positions, wfs2_positions, wfs1_diam, wfs2_diam, r0, L0)[source]

Calculates the covariance between 2 WFSs

Parameters:
  • n_subaps1 (int) – number of sub-apertures in WFS 1
  • n_subaps2 (int) – number of sub-apertures in WFS 1
  • wfs1_positions (ndarray) – Central position of each sub-apeture from telescope centre for WFS 1
  • wfs2_positions (ndarray) – Central position of each sub-apeture from telescope centre for WFS 2
  • wfs1_diam – Diameter of WFS 1 sub-apertures
  • wfs2_diam – Diameter of WFS 2 sub-apertures
  • r0 – Fried parameter of turbulence
  • L0 – Outer scale of turbulence
Returns:

slope covariance of X with X , slope covariance of Y with Y, slope covariance of X with Y
aotools.turbulence.slopecovariance.wfs_covariance_mpwrap(args)[source]

Temporal Power Spectra

Turbulence gradient temporal power spectra calculation and plotting

author:Andrew Reeves
date:September 2016
aotools.turbulence.temporal_ps.calc_slope_temporalps(slope_data)[source]

Calculates the temporal power spectra of the loaded centroid data.

Calculates the Fourier transform over the number frames of the centroid data, then returns the square of the mean of all sub-apertures, for x and y. This is a temporal power spectra of the slopes, and should adhere to a -11/3 power law for the slopes in the wind direction, and -14/3 in the direction tranverse to the wind direction. See Conan, 1995 for more.

The phase slope data should be split into X and Y components, with all X data first, then Y (or visa-versa).

Parameters:slope_data (ndarray) – 2-d array of shape (…, nFrames, nCentroids)
Returns:The temporal power spectra of the data for X and Y components.
Return type:ndarray
aotools.turbulence.temporal_ps.fit_tps(tps, t_axis, D, V_guess=10, f_noise_guess=20, A_guess=9, tps_err=None, plot=False)[source]

Runs minimization routines to get t0.

Parameters:
  • tps (ndarray) – The temporal power spectrum to fit
  • axis (str) – fit parallel (‘par’) or perpendicular (‘per’) to wind direction
  • D (float) – (Sub-)Aperture diameter

Returns:

aotools.turbulence.temporal_ps.get_tps_time_axis(frame_rate, n_frames)[source]
Parameters:
  • frame_rate (float) – Frame rate of detector observing slope gradients (Hz)
  • n_frames – (int): Number of frames used for temporal power spectrum
Returns:

Time values for temporal power spectra plots
Return type:

ndarray
aotools.turbulence.temporal_ps.plot_tps(slope_data, frame_rate)[source]

Generates a plot of the temporal power spectrum/a for a data set of phase gradients

Parameters:
  • slope_data (ndarray) – 2-d array of shape (…, nFrames, nCentroids)
  • frame_rate (float) – Frame rate of detector observing slope gradients (Hz)
Returns:

The computed temporal power spectrum/a, and the time axis data
Return type:

tuple

Atmospheric Parameter Conversions

Functions for converting between different atmospheric parameters,

aotools.turbulence.atmos_conversions.cn2_to_r0(cn2, lamda=5e-07)[source]

Calculates r0 from the integrated Cn2 value

Parameters:
  • cn2 (float) – integrated Cn2 value in m^2/3
  • lamda – wavelength
Returns:

r0 in cm
aotools.turbulence.atmos_conversions.cn2_to_seeing(cn2, lamda=5e-07)[source]

Calculates the seeing angle from the integrated Cn2 value

Parameters:
  • cn2 (float) – integrated Cn2 value in m^2/3
  • lamda – wavelength
Returns:

seeing angle in arcseconds
aotools.turbulence.atmos_conversions.coherenceTime(cn2, v, lamda=5e-07)[source]

Calculates the coherence time from profiles of the Cn2 and wind velocity

Parameters:
  • cn2 (array) – Cn2 profile in m^2/3
  • v (array) – profile of wind velocity, same altitude scale as cn2
  • lamda – wavelength
Returns:

coherence time in seconds
aotools.turbulence.atmos_conversions.isoplanaticAngle(cn2, h, lamda=5e-07)[source]

Calculates the isoplanatic angle from the Cn2 profile

Parameters:
  • cn2 (array) – Cn2 profile in m^2/3
  • h (Array) – Altitude levels of cn2 profile in m
  • lamda – wavelength
Returns:

isoplanatic angle in arcseconds
aotools.turbulence.atmos_conversions.r0_from_slopes(slopes, wavelength, subapDiam)[source]

Measures the value of R0 from a set of WFS slopes.

Uses the equation in Saint Jaques, 1998, PhD Thesis, Appendix A to calculate the value of atmospheric seeing parameter, r0, that would result in the variance of the given slopes.

Parameters:
  • slopes (ndarray) – A 3-d set of slopes in radians, of shape (dimension, nSubaps, nFrames)
  • wavelength (float) – The wavelegnth of the light observed
  • subapDiam (float) –
Returns:

An estimate of r0 for that dataset.
Return type:

float
aotools.turbulence.atmos_conversions.r0_to_cn2(r0, lamda=5e-07)[source]

Calculates integrated Cn2 value from r0

Parameters:
  • r0 (float) – r0 in cm
  • lamda – wavelength
Returns:

integrated Cn2 value in m^2/3
Return type:

cn2 (float)
aotools.turbulence.atmos_conversions.r0_to_seeing(r0, lamda=5e-07)[source]

Calculates the seeing angle from r0

Parameters:
  • r0 (float) – Freid’s parameter in cm
  • lamda – wavelength
Returns:

seeing angle in arcseconds
aotools.turbulence.atmos_conversions.seeing_to_cn2(seeing, lamda=5e-07)[source]

Calculates the integrated Cn2 value from the seeing

Parameters:
  • seeing (float) – seeing in arcseconds
  • lamda – wavelength
Returns:

integrated Cn2 value in m^2/3
aotools.turbulence.atmos_conversions.seeing_to_r0(seeing, lamda=5e-07)[source]

Calculates r0 from seeing

Parameters:
  • seeing (float) – seeing angle in arcseconds
  • lamda – wavelength
Returns:

Freid’s parameter in cm
Return type:

r0 (float)
aotools.turbulence.atmos_conversions.slope_variance_from_r0(r0, wavelength, subapDiam)[source]

Uses the equation in Saint Jaques, 1998, PhD Thesis, Appendix A to calculate the slope variance resulting from a value of r0.

Parameters:
  • r0 (float) – Fried papamerter of turubulence in metres
  • wavelength (float) – Wavelength of light in metres (where 1e-9 is 1nm)
  • subapDiam (float) – Diameter of the aperture in metres
Returns:

The expected slope variance for a given r0 ValueError

Image Processing

Centroiders

Functions for centroiding images.

aotools.image_processing.centroiders.brightest_pixel(img, threshold, **kwargs)[source]

Centroids using brightest Pixel Algorithm (A. G. Basden et al, MNRAS, 2011)

Finds the nPxlsth brightest pixel, subtracts that value from frame, sets anything below 0 to 0, and finally takes centroid.

Parameters:
  • img (ndarray) – 2d or greater rank array of imgs to centroid
  • threshold (float) – Fraction of pixels to use for centroid
Returns:

Array of centroid values
Return type:

ndarray
aotools.image_processing.centroiders.centre_of_gravity(img, threshold=0, min_threshold=0, **kwargs)[source]

Centroids an image, or an array of images. Centroids over the last 2 dimensions. Sets all values under “threshold*max_value” to zero before centroiding Origin at 0,0 index of img.

Parameters:
  • img (ndarray) – ([n, ]y, x) 2d or greater rank array of imgs to centroid
  • threshold (float) – Percentage of max value under which pixels set to 0
Returns:

Array of centroid values (2[, n])
Return type:

ndarray
aotools.image_processing.centroiders.correlation_centroid(im, ref, threshold=0.0, padding=1)[source]

Correlation Centroider, currently only works for 3d im shape. Performs a simple thresholded COM on the correlation.

Parameters:
  • im – sub-aperture images (t, y, x)
  • ref – reference image (y, x)
  • threshold – fractional threshold for COM (0=all pixels, 1=brightest pixel)
  • padding – factor to zero-pad arrays in Fourier transforms
Returns:

centroids of im (2, t), given in order x, y
Return type:

ndarray
aotools.image_processing.centroiders.cross_correlate(x, y, padding=1)[source]

2D convolution using FFT, use to generate cross-correlations.

Parameters:
  • x (array) – subap image
  • y (array) – reference image
  • padding (int) – Factor to zero-pad arrays in Fourier transforms
Returns:

cross-correlation of x and y
Return type:

ndarray
aotools.image_processing.centroiders.quadCell(img, **kwargs)[source]

Centroider to be used for 2x2 images.

Parameters:img – 2d or greater rank array, where centroiding performed over last 2 dimensions
Returns:Array of centroid values
Return type:ndarray

Contrast

Functions for calculating the contrast of an image.

aotools.image_processing.contrast.image_contrast(image)[source]

Calculates the ‘Michelson’ contrast.

Uses a method by Michelson (Michelson, A. (1927). Studies in Optics. U. of Chicago Press.), to calculate the contrast ratio of an image. Uses the formula:
(img_max - img_min)/(img_max + img_min)
Parameters:image (ndarray) – Image array
Returns:Contrast value
Return type:float
aotools.image_processing.contrast.rms_contrast(image)[source]

Calculates the RMS contrast - basically the standard deviation of the image

Parameters:image (ndarray) – Image array
Returns:Contrast value
Return type:float

PSF Analysis

Functions for analysing PSFs.

aotools.image_processing.psf.azimuthal_average(data)[source]

Measure the azimuthal average of a 2d array

Parameters:data (ndarray) – A 2-d array of data
Returns:A 1-d vector of the azimuthal average
Return type:ndarray
aotools.image_processing.psf.encircled_energy(data, fraction=0.5, center=None, eeDiameter=True)[source]

Return the encircled energy diameter for a given fraction (default is ee50d). Can also return the encircled energy function. Translated and extended from YAO.

Parameters:
  • data – 2-d array
  • fraction – energy fraction for diameter calculation default = 0.5
  • center – default = center of image
  • eeDiameter – toggle option for return. If False returns two vectors: (x, ee(x)) Default = True
Returns:

Encircled energy diameter or 2 vectors: diameters and encircled energies

Circular Functions

Zernike Modes

aotools.functions.zernike.makegammas(nzrad)[source]

Make “Gamma” matrices which can be used to determine first derivative of Zernike matrices (Noll 1976).

Parameters:nzrad – Number of Zernike radial orders to calculate Gamma matrices for
Returns:Array with x, then y gamma matrices
Return type:ndarray
aotools.functions.zernike.phaseFromZernikes(zCoeffs, size, norm='noll')[source]

Creates an array of the sum of zernike polynomials with specified coefficeints

Parameters:
  • zCoeffs (list) – zernike Coefficients
  • size (int) – Diameter of returned array
  • norm (string, optional) – The normalisation of Zernike modes. Can be "noll", "p2v" (peak to valley), or "rms". default is "noll".
Returns:

a size x size array of summed Zernike polynomials
Return type:

ndarray
aotools.functions.zernike.zernIndex(j)[source]

Find the [n,m] list giving the radial order n and azimuthal order of the Zernike polynomial of Noll index j.

Parameters:j (int) – The Noll index for Zernike polynomials
Returns:n, m values
Return type:list
aotools.functions.zernike.zernikeArray(J, N, norm='noll')[source]

Creates an array of Zernike Polynomials

Parameters:
  • maxJ (int or list) – Max Zernike polynomial to create, or list of zernikes J indices to create
  • N (int) – size of created arrays
  • norm (string, optional) – The normalisation of Zernike modes. Can be "noll", "p2v" (peak to valley), or "rms". default is "noll".
Returns:

array of Zernike Polynomials
Return type:

ndarray
aotools.functions.zernike.zernikeRadialFunc(n, m, r)[source]

Fucntion to calculate the Zernike radial function

Parameters:
  • n (int) – Zernike radial order
  • m (int) – Zernike azimuthal order
  • r (ndarray) – 2-d array of radii from the centre the array
Returns:

The Zernike radial function
Return type:

ndarray
aotools.functions.zernike.zernike_nm(n, m, N)[source]

Creates the Zernike polynomial with radial index, n, and azimuthal index, m.

Parameters:
  • n (int) – The radial order of the zernike mode
  • m (int) – The azimuthal order of the zernike mode
  • N (int) – The diameter of the zernike more in pixels
Returns:

The Zernike mode
Return type:

ndarray
aotools.functions.zernike.zernike_noll(j, N)[source]

Creates the Zernike polynomial with mode index j, where j = 1 corresponds to piston.

Parameters:
  • j (int) – The noll j number of the zernike mode
  • N (int) – The diameter of the zernike more in pixels
Returns:

The Zernike mode
Return type:

ndarray

Karhunen Loeve Modes

Collection of routines related to Karhunen-Loeve modes.

The theory is based on the paper “Optimal bases for wave-front simulation and reconstruction on annular apertures”, Robert C. Cannon, 1996, JOSAA, 13, 4

The present implementation is based on the IDL package of R. Cannon (wavefront modelling and reconstruction). A closely similar implementation can also be find in Yorick in the YAO package.

Usage

Main routine is ‘make_kl’ to generate KL basis of dimension [dim, dim, nmax].

For Kolmogorov statistics, e.g.

kl, _, _, _ = make_kl(150, 128, ri = 0.2, stf='kolmogorov')

Warning

make_kl with von Karman stf fails. It has been implemented but KL generation failed in ‘while loop’ of gkl_fcom…

date:November 2017
aotools.functions.karhunenLoeve.gkl_azimuthal(nord, npp)[source]

Compute the azimuthal function of the KL basis.

Parameters:
  • nord (int) – number of azimuthal orders
  • npp (int) – grid of point sampling the azimuthal coordinate
Returns:

gklazi – azimuthal function of the KL basis.
Return type:

ndarray
aotools.functions.karhunenLoeve.gkl_basis(ri=0.25, nr=40, npp=None, nfunc=500, stf='kolstf', outerscale=None)[source]

Wrapper to create the radial and azimuthal K-L functions.

Parameters:
  • ri (float) – normalized internal radius
  • nr (int) – number of radial resolution elements
  • np (int) – number of azimuthal resolution elements
  • nfunc (int) – number of generated K-L function
  • stf (string) – structure function tag describing the atmospheric statistics
Returns:

gklbasis – dictionary containing the radial and azimuthal basis + other relevant information
Return type:

dic
aotools.functions.karhunenLoeve.gkl_fcom(ri, kernels, nfunc, verbose=False)[source]

Computation of the radial eigenvectors of the KL basis.

Obtained by taking the eigenvectors from the matrix L^p. The final function corresponds to the ‘nfunc’ largest eigenvalues. See eq. 16-18 in Cannon 1996.

Parameters:
  • ri (float) – radius of central obscuration radius (normalized by D/2; <1)
  • kernels (ndarray) – kernel L^p of dimension (nr, nr, nth), where nth is the azimuthal discretization (5 * nr)
  • nfunc (int) – number of final KL functions
Returns:

  • evals (1darray) – eigenvalues
  • nord (int) – resulting number of azimuthal orders
  • npo (int)
  • ord (1darray)
  • rabas (ndarray) – radial eigenvectors of the KL basis
aotools.functions.karhunenLoeve.gkl_kernel(ri, nr, rad, stfunc='kolmogorov', outerscale=None)[source]

Calculation of the kernel L^p

The kernel constructed here should be simply a discretization of the continuous kernel. It needs rescaling before it is treated as a matrix for finding the eigen-values

Parameters:
  • ri (float) – radius of central obscuration radius (normalized by D/2; <1)
  • nr (int) – number of resolution elements
  • rad (1d-array) – grid of points where the kernel is evaluated
  • stfunc (string) – string tag of the structure function on which the kernel are computed
  • outerscale (float) – in unit of telescope diameter. Outer-scale for von Karman structure function.
Returns:

L^p – kernel L^p of dimension (nr, nr, nth), where nth is the azimuthal discretization (5 * nr)
Return type:

ndarray
aotools.functions.karhunenLoeve.gkl_radii(ri, nr)[source]

Generate n points evenly spaced in r^2 between r_i^2 and 1

Parameters:
  • nr (int) – number of resolution elements
  • ri (float) – radius of central obscuration radius (normalized; <1)
Returns:

r – grid of point to calculate the appropriate kernels. correspond to ‘sqrt(s)’ wrt the paper.
Return type:

1d-array, float
aotools.functions.karhunenLoeve.gkl_sfi(kl_basis, i)[source]

return the i’th function from the generalized KL basis ‘bas’. ‘bas’ must be generated by ‘gkl_basis’

aotools.functions.karhunenLoeve.make_kl(nmax, dim, ri=0.0, nr=40, stf='kolmogorov', outerscale=None, mask=True)[source]

Main routine to generatre a KL basis of dimension [nmax, dim, dim].

For Kolmogorov statistics, e.g.

kl, _, _, _ = make_kl(150, 128, ri = 0.2, stf='kolmogorov')
As a rule of thumb
nr x npp = 50 x 250 is fine up to 500 functions
60 x 300 for a thousand
80 x 400 for three thousands.
Parameters:
  • nmax (int) – number of KL function to generate
  • dim (int) – size of the KL arrays
  • ri (float) – radial central obscuration normalized by D/2
  • nr (int) – number of point on radius. npp (number of azimuthal pts) is =2 pi * nr
  • stf (string) – structure function tag. Default is ‘kolmogorov’
  • outerscale (float) – outer scale in units of telescope diameter. Releveant if von vonKarman stf. (not implemented yet)
  • mask (bool) – pupil masking. Default is True
Returns:

  • kl (ndarray (nmax, dim, dim)) – KL basis in cartesian coordinates
  • varKL (1darray) – associated variance
  • pupil (2darray) – pupil
  • polar_base (dictionary) – polar base dictionary used for the KL basis computation. as returned by ‘gkl_basis’

See also

gkl_basis(), set_pctr(), pol2car()

aotools.functions.karhunenLoeve.pcgeom(nr, npp, ncp, ri, ncmar)[source]

This routine builds a geom dic.

Parameters:
  • py (px,) – the x, y coordinates of points in the polar arrays.
  • cp (cr,) – the r, phi coordinates of points in the cartesian grids.
  • ncmar – allows the possibility that there is a margin of ncmar points in the cartesian arrays outside the region of interest.
aotools.functions.karhunenLoeve.piston_orth(nr)[source]

Unitary matrix used to filter out piston term. Eq. 19 in Cannon 1996.

Parameters:nr (int) – number of resolution elements
Returns:U – Unitary matrix
Return type:2d array
aotools.functions.karhunenLoeve.pol2car(cpgeom, pol, mask=False)[source]

Polar to cartesian conversion.

(points not in the aperture are treated as though they were at the first or last radial polar value…)

aotools.functions.karhunenLoeve.polang(r)[source]

Generate an array with the same dimensions as r, but containing the azimuthal values for a polar coordinate system.

aotools.functions.karhunenLoeve.radii(nr, npp, ri)[source]

Use to generate a polar coordinate system.

Generate an nr x npp array with npp copies of the radial coordinate array. Radial coordinate span the range from r=ri to r=1 with successive annuli having equal areas.

ie, the area between ri and 1 is divided into nr equal rings, and the points are positioned at the half-area mark on each ring; there are no points on the border

See also

polang()

aotools.functions.karhunenLoeve.rebin(a, newshape)[source]

Rebin an array to a new shape. See scipy cookbook. It is intended to be similar to ‘rebin’ of IDL

aotools.functions.karhunenLoeve.set_pctr(bas, ncp=None, ncmar=None)[source]

call pcgeom to build the dic geom_struct with the right initializtions.

Parameters:bas (dic) – gkl_basis dic built with the gkl_bas routine
aotools.functions.karhunenLoeve.setpincs(ax, ay, px, py, ri)[source]

determine a set of squares for interpolating from cartesian to polar coordinates, using only those points with ri <= r <= 1

aotools.functions.karhunenLoeve.stf_kolmogorov(r)[source]

Kolmogorov structure function with r = (D/r0)

aotools.functions.karhunenLoeve.stf_vonKarman(r, L0)[source]

von Karman structure function with r = (D / r0) L0 is in unit of telescope diameter, typically a few (3; or 20m)

aotools.functions.karhunenLoeve.stf_vonKarman_yao(r, L)[source]

Telescope Pupils

Pupil Maps

Functions for the creation of pupil maps and masks.

aotools.functions.pupil.circle(radius, size, circle_centre=(0, 0), origin='middle')[source]

Create a 2-D array: elements equal 1 within a circle and 0 outside.

The default centre of the coordinate system is in the middle of the array: circle_centre=(0,0), origin=”middle” This means: if size is odd : the centre is in the middle of the central pixel if size is even : centre is in the corner where the central 4 pixels meet

origin = “corner” is used e.g. by psfAnalysis:radialAvg()

Examples:

circle(1,5) circle(0,5) circle(2,5) circle(0,4) circle(0.8,4) circle(2,4)
  00000       00000       00100       0000        0000          0110
  00100       00000       01110       0000        0110          1111
  01110       00100       11111       0000        0110          1111
  00100       00000       01110       0000        0000          0110
  00000       00000       00100

circle(1,5,(0.5,0.5))   circle(1,4,(0.5,0.5))
   .-->+
   |  00000               0000
   |  00000               0010
  +V  00110               0111
      00110               0010
      00000
Parameters:
  • radius (float) – radius of the circle
  • size (int) – size of the 2-D array in which the circle lies
  • circle_centre (tuple) – coords of the centre of the circle
  • origin (str) – where is the origin of the coordinate system in which circle_centre is given; allowed values: {“middle”, “corner”}
Returns:

the circle array
Return type:

ndarray (float64)

Wavefront Sensors

aotools.wfs.computeFillFactor(mask, subapPos, subapSpacing)[source]

Calculate the fill factor of a set of sub-aperture co-ordinates with a given pupil mask.

Parameters:
  • mask (ndarray) – Pupil mask
  • subapPos (ndarray) – Set of n sub-aperture co-ordinates (n, 2)
  • subapSpacing – Number of mask pixels between sub-apertures
Returns:

fill factor of sub-apertures
Return type:

list
aotools.wfs.findActiveSubaps(subaps, mask, threshold, returnFill=False)[source]

Finds the subapertures which are “seen” be through the pupil function. Returns the coords of those subapertures

Parameters:
  • subaps (int) – The number of subaps in x (assumes square)
  • mask (ndarray) – A pupil mask, where is transparent when 1, and opaque when 0
  • threshold (float) – The mean value across a subap to make it “active”
  • returnFill (optional, bool) – Return an array of fill-factors
Returns:

An array of active subap coords
Return type:

ndarray
aotools.wfs.make_subaps_2d(data, mask)[source]

Fills in a pupil shape with 2-d sub-apertures

Parameters:
  • data (ndarray) – slope data, of shape, (frames, 2, nSubaps)
  • mask (ndarray) – 2-d array of shape (nxSubaps, nxSubaps), where 1 indicates a valid subap position and 0 a masked subap
aotools.wfs.range

alias of __builtin__.xrange

Optical Propagation

A library of useful optical propagation methods.

Many extracted from the book by Schmidt, 2010: Numerical Methods of optical proagation

aotools.opticalpropagation.angularSpectrum(inputComplexAmp, wvl, inputSpacing, outputSpacing, z)[source]

Propogates light complex amplitude using an angular spectrum algorithm

Parameters:
  • inputComplexAmp (ndarray) – Complex array of input complex amplitude
  • wvl (float) – Wavelength of light to propagate
  • inputSpacing (float) – The spacing between points on the input array in metres
  • outputSpacing (float) – The desired spacing between points on the output array in metres
  • z (float) – Distance to propagate in metres
Returns:

propagated complex amplitude
Return type:

ndarray
aotools.opticalpropagation.lensAgainst(Uin, wvl, d1, f)[source]

Propagates from the pupil plane to the focal plane for an object placed against (and just before) a lens.

Parameters:
  • Uin (ndarray) – Input complex amplitude
  • wvl (float) – Wavelength of light in metres
  • d1 (float) – spacing of input plane
  • f (float) – Focal length of lens
Returns:

Output complex amplitude
Return type:

ndarray
aotools.opticalpropagation.oneStepFresnel(Uin, wvl, d1, z)[source]

Fresnel propagation using a one step Fresnel propagation method.

Parameters:
  • Uin (ndarray) – A 2-d, complex, input array of complex amplitude
  • wvl (float) – Wavelength of propagated light in metres
  • d1 (float) – spacing of input plane
  • z (float) – metres to propagate along optical axis
Returns:

Complex ampltitude after propagation
Return type:

ndarray
aotools.opticalpropagation.twoStepFresnel(Uin, wvl, d1, d2, z)[source]

Fresnel propagation using a two step Fresnel propagation method.

Parameters:
  • Uin (ndarray) – A 2-d, complex, input array of complex amplitude
  • wvl (float) – Wavelength of propagated light in metres
  • d1 (float) – spacing of input plane
  • d2 (float) – desired output array spacing
  • z (float) – metres to propagate along optical axis
Returns:

Complex ampltitude after propagation
Return type:

ndarray

Astronomical Functions

Magnitude and Flux Calculations

aotools.astronomy.flux_to_magnitude(flux, waveband='V')[source]

Converts incident flux of photons to the apparent magnitude

Parameters:
  • flux (float) – Number of photons received from an object per second per meter squared
  • waveband (string) – Waveband of the measured flux, can be U, B, V, R, I, J, H, K, g, r, i, z
Returns:

Apparent magnitude
Return type:

float
aotools.astronomy.magnitude_to_flux(magnitude, waveband='V')[source]

Converts apparent magnitude to a flux of photons

Parameters:
  • magnitude (float) – Star apparent magnitude
  • waveband (string) – Waveband of the stellar magnitude, can be U, B, V, R, I, J, H, K, g, r, i, z
Returns:

Number of photons emitted by the object per second per meter squared
Return type:

float
aotools.astronomy.photons_per_band(mag, mask, pxlScale, expTime, waveband='V')[source]

Calculates the photon flux for a given aperture, star magnitude and wavelength band

Parameters:
  • mag (float) – Star apparent magnitude
  • mask (ndarray) – 2-d pupil mask array, 1 is transparent, 0 opaque
  • pxlScale (float) – size in metres of each pixel in mask
  • expTime (float) – Exposure time in seconds
  • waveband (string) – Waveband
Returns:

number of photons
Return type:

float
aotools.astronomy.photons_per_mag(mag, mask, pixel_scale, wvlBand, exposure_time)[source]

Calculates the photon flux for a given aperture, star magnitude and wavelength band

Parameters:
  • mag (float) – Star apparent magnitude
  • mask (ndarray) – 2-d pupil mask array, 1 is transparent, 0 opaque
  • pixel_scale (float) – size in metres of each pixel in mask
  • wvlBand (float) – length of wavelength band in nanometres
  • exposure_time (float) – Exposure time in seconds
Returns:

number of photons
Return type:

float

Normalised Fourier Transforms

Module containing useful FFT based function and classes

aotools.fouriertransform.ft(data, delta)[source]

A properly scaled 1-D FFT

Parameters:
  • data (ndarray) – An array on which to perform the FFT
  • delta (float) – Spacing between elements
Returns:

scaled FFT
Return type:

ndarray
aotools.fouriertransform.ft2(data, delta)[source]

A properly scaled 2-D FFT

Parameters:
  • data (ndarray) – An array on which to perform the FFT
  • delta (float) – Spacing between elements
Returns:

scaled FFT
Return type:

ndarray
aotools.fouriertransform.ift(DATA, delta_f)[source]

Scaled inverse 1-D FFT

Parameters:
  • DATA (ndarray) – Data in Fourier Space to transform
  • delta_f (ndarray) – Frequency spacing of grid
Returns:

Scaled data in real space
Return type:

ndarray
aotools.fouriertransform.ift2(DATA, delta_f)[source]

Scaled inverse 2-D FFT

Parameters:
  • DATA (ndarray) – Data in Fourier Space to transform
  • delta_f (ndarray) – Frequency spacing of grid
Returns:

Scaled data in real space
Return type:

ndarray
aotools.fouriertransform.irft(DATA, delta_f)[source]

Scaled real inverse 1-D FFT

Parameters:
  • DATA (ndarray) – Data in Fourier Space to transform
  • delta_f (ndarray) – Frequency spacing of grid
Returns:

Scaled data in real space
Return type:

ndarray
aotools.fouriertransform.irft2(DATA, delta_f)[source]

Scaled inverse real 2-D FFT

Parameters:
  • DATA (ndarray) – Data in Fourier Space to transform
  • delta_f (ndarray) – Frequency spacing of grid
Returns:

Scaled data in real space
Return type:

ndarray
aotools.fouriertransform.rft(data, delta)[source]

A properly scaled real 1-D FFT

Parameters:
  • data (ndarray) – An array on which to perform the FFT
  • delta (float) – Spacing between elements
Returns:

scaled FFT
Return type:

ndarray
aotools.fouriertransform.rft2(data, delta)[source]

A properly scaled, real 2-D FFT

Parameters:
  • data (ndarray) – An array on which to perform the FFT
  • delta (float) – Spacing between elements
Returns:

scaled FFT
Return type:

ndarray

Interpolation

aotools.interpolation.binImgs(data, n)[source]

Bins one or more images down by the given factor bins. n must be a factor of data.shape, who knows what happens otherwise……

aotools.interpolation.zoom(array, newSize, order=3)[source]

A Class to zoom 2-dimensional arrays using interpolation

Uses the scipy Interp2d interpolation routine to zoom into an array. Can cope with real of complex data.

Parameters:
  • array (ndarray) – 2-dimensional array to zoom
  • newSize (tuple) – the new size of the required array
  • order (int, optional) – Order of interpolation to use (1, 3, 5). default is 3
Returns:

zoom array of new size.
Return type:

ndarray
aotools.interpolation.zoom_rbs(array, newSize, order=3)[source]

A Class to zoom 2-dimensional arrays using RectBivariateSpline interpolation

Uses the scipy RectBivariateSpline interpolation routine to zoom into an array. Can cope with real of complex data. May be slower than above zoom, as RBS routine copies data.

Parameters:
  • array (ndarray) – 2-dimensional array to zoom
  • newSize (tuple) – the new size of the required array
  • order (int, optional) – Order of interpolation to use. default is 3
Returns:

zoom array of new size.
Return type:

ndarray

Indices and tables