NEWS.md

In mlpeck/zernike: Zernike Polynomials and Fringe Analysis tools

Version 3.8.0

• All C code has been removed.
• load.images uses libraries jpeg, png, or tiff to read image files of respective types.
• Reading png format files is now explicitly supported.
• Function rescale to rescale an image matrix is written in C++ using Armadillo's interp2.

Version 3.7.8-3.7.9

• wf_net now does all of the post-processing of phase estimates from any of the fringe analysis routines. Function arguments have changed.
• Removed options sgs and uselm from fitzernikes and return values from psfit_options().
• Changed the way initial guess for phase shifts is made in gpcapsi.
• Use Rcout instead of cout in C++ routines that report progress.

Version 3.7.7

• Return values from functions psifit, vortexfit, fftfit and wf_net have S3 class wf_zfit with plot, summary, and print methods. These were available previously but have been improved and are now more or less documented.
• Added S3Method report for objects of class wf_zfit. This produces an html report and displays in a browser.
• Added some options to list of psi algorithms.
• pcapsi has an additional option pc3 for a new variant of the PCA based PSI analysis. Arguments have been changed.

Version 3.7.6

• Modified wf3d.pupil to be compatible with recent versions of rgl. Also added an optional argument new.window with default value TRUE.
• Bumped required R version to >4.1.0
• Added some graphics to anzern.pdf
• Windows binary will now be 64 bit (x86-64) only.

Version 3.7.5

• Formal writeup of the procedure for recursive generation of Zernike annular polynomials is included with the documentation.
• Added functions rzernike_ann_direct, zapm_direct, zapm_iso_direct to calculate radial and Zernike annular polynomials directly from formulas published by Mahajan.

Version 3.7.4

• Removed functions zapmC and zapm_cart for approximate Zernike Annular polynomials.
• Added C++ functions zapm, zapm_iso, zapm_128, zapm_iso_128 for nominally exact Zernike Annular polynomials, and their R wrappers. These return matrixes of annular Zernikes in extended Fringe or ISO/ANSI ordering. The functions *_128 use 128 bit floats for somewhat higher numerical precision.
• Example code is included for the above functions.
• Also new are rzernike_ann and rzernike_ann_128 to calculate the radial annular Zernikes. Finally, function gol_welsch calculates nodes and weights for Gauss-Legendre quadrature in the interval (eps^2, 1). This would normally not be called by the user, but it is in the namespace and documented. All of these are mostly for testing purposes.
• added boolean variable usecirc to the list of options returned by psfit_options(). If set to TRUE functions that use Zernikes for wavefront representations will use Zernike circle polynomials even for obstructed apertures. For the default value FALSE functions like wf_net() and pupil will toggle between Zernikes and annular Zernikes depending on whether the obstruction fraction is > 0.
• The boost library in package BH is now linked to and therefore must be installed (?? IS THIS TRUE FOR USERS ??)

Version 3.7.2

• crop will return a square matrix with an even number of pixels per side. Side length is optionally specifiable. Interferograms should be completely contained within frames with some padding on all sides. This function does absolutely no error checking.
• added option lpbrcut to list of available phase unwrapping routines set in psfit_options()$puw_alg. This will result in lppuw::brcutpuw being called as the phase unwrapper. Option brcut will result in calling zernike::brcutpuw.
• Consistent calls to phase unwrapping routine in fftfit and vortexfit.

Version 3.7.1

New in this version: support for Zernike Annular polynomials approximated by orthogonalizing a matrix of Zernike polynomials:

• Added C++ functions zapmC and zapm_cart to create matrixes of Annular Zernikes in extended Fringe or ISO/ANSI sequence.
• Modified the functions wf_net, fitzernikes, and pupil to use annular Zernikes for annular (or obstructed) wavefronts. This is done automatically and involves no user visible changes.
• Expanded help for some topics and added examples for wf_net and zpm_cart.

Version 3.7.0

A number of additions and changes have been made for this release, and some of the changes may break previously working code. This list may not be comprehensive:

• Added gradzpm_cart, zpm_cart, and norm_zpm to create matrixes of Zernike polynomials and their derivatives in ISO/ANSI sequence and Cartesian coordinates. See the documentation for further details.
• Added the item isoseq to the list in psfit_options() to tell other routines when to use zpm_cart instead of zpm. This is checked in the function wf_net() and if true zpm_cart is used in the Zernike fitting.
• Added function makezlist.iso to make a list of Zernike polynomial indexes in ISO/ANSI sequence.
• Added print, summary, and plot methods for the return lists from psifit(), vortexfit(), and fftfit(). These have been assigned the S3 class wf_fitted.
• Potentially important! Arguments to pupil have changed: instead of passing zlist as argument I now use maxorder which is in turn passed to zpm or zpm_cart. If the first element of zcoef is the piston term the piston entry in the argument list should be left null, which is the default. If zcoef starts with tilts, which it will be if returned by wf_net or one of the routines that call it, piston must be non-null (usually should be 0). The function pupil.arb() continues to use zlist to provide a list of Zernike indexes since the usual use case would be to create a synthetic wavefront with just a few aberrations.
• The bonus functions startest() and synth.interferogram() have modified arguments and the logic of the code has been improved (maybe).
• I'm continuing the process of splitting out source files organized into topically related functions. This only applies to the source distribution.

Release notes 3.6.0

Several changes were made for the current release. Most of these are "behind the scenes" and mostly made for performance or maintainability reasons. These include:

• C code for phase unwrapping routines has been converted to C++ for use with Rcpp. This mostly involved changing pointers to references in function calls.
• A threaded version of the code for filling matrixes of Zernike polynomials has been added. The number of threads used is set by the argument nthreads to psfit_options(). This is set by default to half the number of cores detected because all of the PCs in my collection have multithreading CPUs that report double the number of physical cores actually present. In practice threading might or might not be beneficial. Speed gains are more likely if very large numbers of ZP values are needed.

Some user visible changes:

• Added function vortexfit() implementing the vortex aka spiral quadrature transform algorithm of Larkin et al. This is the same algorithm with possibly slightly different implementation as used in DFTFringe.
• Added function circle.hough() to detect circular interferogram edges using the Hough circle transform. This is experimental and is not curently used by any other routine.
• The function circle.pars() for automated edge detection now uses the function nlsrob() from package robustbase for circle parameter estimation. An optional but enabled by default refinement step used in previous versions of the algorithm has been removed.

mlpeck/zernike documentation built on Oct. 12, 2024, 1:27 a.m.