ZERNFUN.m and ZERNFUN2.m compute the Zernike functions Znm(r,theta). These functions, which form an orthogonal basis on the unit circle, are used in disciplines such as astronomy, optics, optometry, and ophthalmology to characterize functions and data on a circular domain. ZERNPOL.m computes the Zernike polynomials Znm(r), which are the radial portion of the Zernike functions.
A MATLAB Digest article describing the use of the Zernike functions for analyzing optics data (using a LASIK surgery data as an example) also is available, on the File Exchange as a PDF,
and in HTML at:
Paul Fricker (2020). Zernike polynomials (https://www.mathworks.com/matlabcentral/fileexchange/7687-zernike-polynomials), MATLAB Central File Exchange. Retrieved .
Your concerns are valid. The issues seem to lie in the published Newsletter (https://www.mathworks.com/company/newsletters/articles/analyzing-lasik-optical-data-using-zernike-functions.html) and not with the code.
1. The values in Table 2 in the Newsletter are swapped for positive and negative values of "m" and are not normalized.
2. Figure 3 has mode numbers which are also swapped and does not correspond exactly to the example that the author is discussing.
Thank you for supporting this example but I found several problems as follows:
(1) "Table 2. The first ten Zernike radial functions and their common names."in the HTML link of the lasik example has incorrect numbering of Z compared to Wikipedia (https://en.wikipedia.org/wiki/Zernike_polynomials).
(2) "Figure 3. Spectrum of Zernike coefficients for the pre-operative eye data shown in Figure 2..." looks wrong ordering of mode number when exactly reproduced by capturing the image.
I have already asked these things and I received the reference number : (Case: #03909269) [ ref:_00Di0Ha1u._5003q1I7j50:ref ] and I'm waiting for your reply.
Please check these again and post a new undate.
Hi, I am also wondering where can one find the eyedata used --Joseph
I am trying to do a reconstruction on the Corneal Topographer. Is the 'eyedata' that is used in 'Analyzing LASIK Optical Data Using Zernike Functions' the image from the topographer itself?
If not, what is it and where can I find it?
Thanks in Advance!
Dear Dr Fricker,
I really enjoyed reading your document "Analyzing LASIK Optical Data Using Zernike Functions". Amazing work!
I am trying to understand the format which your eyedata matrix should be and how to plot it. You probably use something fancier than imagesc here?
Is eye data simply a m x n image? I did save the topo from your example as a jpeg and cropped the axes to try to replicate your example, but I had trouble doing it. Is the raw data and code for your example available somewhere? Thanks!
Where can I find the eyedata for "Analyzing LASIK Optical Data Using Zernike Functions" Everywhere online points to it being found here. HELP!
Hello. I think that the help of ZERNFUN has a typo. It states that "Each element k of M must be a positive integer, with possible values M(k) = -N(k) to +N(k)", which is a contradiction. Even in the examples after that, negative values are used. After examining the code, I have arrived to the conclusion that is merely the help that has a typo. Am I right?
On the other hand, the help for the ZERNPOL function does indeed use strictly positive values for M(k). Perhaps this is the source of the problem.
Thanks for providing these files to the comunity !
However, did you check the othogonality of the functions created?
It seems to me that something's wrong there.
I generated 2 polynoms like it is shown in the doc :
z(idx) = zernfun(3,1,r(idx),theta(idx));
z2(idx) = zernfun(4,0,r(idx),theta(idx));
When I check the orthogonality by simply doing :
the result is not 0.
Am I doing someting wrong or is there a pb here?
Thanks in adavnce
12 Jun 2012 @JUAN CARDENAS
n = floor((-1+sqrt(1+8*p))/2);
Very good solution for using any p but
I think you were missing a '-'sign for your definition of m. (can be seen when plotting the Zernike-Polynomials)
Thank you Paul.
An update for enabling any P order, in zernfun2, instead of:
n = ceil((-3+sqrt(9+8*p))/2);
m = 2*p - n.*(n+2);
change it by:
n = floor((-1+sqrt(1+8*p))/2);
Does anybody know about the discrete Zernike Transform (DZT)?
I am so eager to implement that.
thank you in advance
Thanks for the code! I have a question about the unit of the zernike polynomials generated by this code, is it in [number of waves] or [micrometer]?
I was running into problems when using my fitted terms in another program: the same coefficients did not give the same surface.
I found the cause: the cosine and sine terms are inverted in zernfun. M>0 should be a cosine, while M<0 should be a sine.
I've corrected this, starting at line 193
z(:,idx_pos) = y(:,idx_pos).*cos(theta*m(idx_pos)');
z(:,idx_neg) = y(:,idx_neg).*sin(theta*-m(idx_neg)');
% note the required sign change "-m" in the sine term
Very great functions! But the normalization with the 'norm' - option seems to be wrong. I've changed in:
% For the normalized polynomials the line 177:
y(:,j) = y(:,j)*sqrt((1+(m(j)~=0))*(n(j)+1)/pi);
% I have to replaced by:
y(:,j) = y(:,j)*sqrt((n(j)+1));
y(:,j) = y(:,j)*sqrt(2*(n(j)+1));
I am still becoming accustomed to MATLAB. When I run the zernfun.m by itself without any modifications, I get this error
??? Input argument "n" is undefined.
Error in ==> zernfun at 88
if ( ~any(size(n)==1) ) || ( ~any(size(m)==1) ).
However, when I initialized n, m, r, & theta, I get this error
??? Maximum recursion limit of 500 reached. Use set(0,'RecursionLimit',N)
to change the limit. Be aware that exceeding your available stack space can
crash MATLAB and/or your computer.
Error in ==> meshgrid
Does anybody have any thoughts about making zernfun.m to work? Any help would be greatly appreciated.
Paul, Thanks very much for this code. It is very much appreciated.
I think, however, that you have a bug in how you are normalizing your Zernike polynomials. Noll's paper shows that for terms with m=0 the normalization term should be (n+1)**0.5 and for terms with m!=0 the normalization term should be (2*(n+1))**0.5. In the routine zernpol.m you are normalizing all terms (including those with m=0) by (2*(n+1))**0.5.
Perhaps you have already fixed this? I have just downloaded it on 1-21-10 from this site. The creation date for the file I'm looking at is on Nov 13, 2006 12:56:48 PM.
I am interested in extracting the 3D Zernike descriptors of 3D shapes? Do you happen to know if there is any Matlab code?
Looks promising but I'm having a problem duplicating the LASIK example...I copied the lasik image and edited out the the lasik portion -- but all I get from the following is a big red blob -- not a decent reconstructed image...anybody know what's wrong?
% make grid coordinate matrices expressed in polar coordinates
L = size(I,1);
X = -1:2/(L-1):1;
[x,y] = meshgrid(X);
[theta,r] = cart2pol(x,y);
% Compute the required degree and order values from n=0-7, inclusive
N = ;
M = ;
N = [N n*ones(1,n+1)];
M = [M -n:2:n];
is_in_circle = ( r <= 1);
Z = zernfun(N,M,r(is_in_circle),theta(is_in_circle));
a = Z\I(is_in_circle);
% Reconstruct image using Zernike coefficients
r(is_in_circle) = Z*a;
% rescale to 0-255 to display image
r = im2uint8(im2double(r));
Valuable work, thank you.
very helpful!It will be perfect if include the zernike annular polynomials
Why this error? Thank you!
??? Error: File: E:\zernike\zernpol.m Line: 151 Column: 25
"identifier" expected, "(" found.
Very helpful, fast, and complete. Examples in the comments are very helpful too.
thank you very much
this the function i was looking for past few weeks
Removed an unneeded intermediate variable from the code.
Updated Help documentation and screenshot.
Need to point to a MATLAB Digest article which is based on this submission.
Update to the algorithm for computing powers of R (vector of radius values).
Inspired: Zernike decomposition, Zernike Polynomial Coefficients for a given Wavefront using Matrix Inversion in Matlab, zernike3, Fast computation of Zernike Radial Polynomials, Zernfun2a.m, showregions.m, quadcc, iahncajigas/nSTAT