From 0794b515212fac906cf137d4329b4bcce068d7a2 Mon Sep 17 00:00:00 2001
From: Julien Staub <atsju2@yahoo.fr>
Date: Thu, 14 Aug 2025 18:28:56 +0200
Subject: [PATCH 1/6] move zapm.cpp to dedicated folder as it's not our code

---
 DFTFringe.pro                | 2 +-
 DFTFringe_Dale.pro           | 2 +-
 DFTFringe_QT5.pro            | 2 +-
 zapm.cpp => zernike/zapm.cpp | 0
 4 files changed, 3 insertions(+), 3 deletions(-)
 rename zapm.cpp => zernike/zapm.cpp (100%)

diff --git a/DFTFringe.pro b/DFTFringe.pro
index d3b3dc7c..6a75aa0c 100644
--- a/DFTFringe.pro
+++ b/DFTFringe.pro
@@ -147,6 +147,7 @@ INCLUDEPATH += ./bezier ./SingleApplication
 
 SOURCES += SingleApplication/singleapplication.cpp \
     SingleApplication/singleapplication_p.cpp \
+    zernike/zapm.cpp \
     annulushelpdlg.cpp \
     arbitrarywavefronthelp.cpp \
     arbitrarywavwidget.cpp \
@@ -261,7 +262,6 @@ SOURCES += SingleApplication/singleapplication.cpp \
     wavefrontloader.cpp \
     wftexaminer.cpp \
     wftstats.cpp \
-    zapm.cpp \
     zernikedlg.cpp \
     zernikeeditdlg.cpp \
     zernikepolar.cpp \
diff --git a/DFTFringe_Dale.pro b/DFTFringe_Dale.pro
index de04bf23..b5f9a31e 100644
--- a/DFTFringe_Dale.pro
+++ b/DFTFringe_Dale.pro
@@ -59,7 +59,6 @@ SOURCES += main.cpp \
     dftcolormap.cpp \
     surfaceanalysistools.cpp \
     surfacemanager.cpp \
-    zapm.cpp \
     zernikedlg.cpp \
     zernikepolar.cpp \
     zernikeprocess.cpp \
@@ -147,6 +146,7 @@ SOURCES += main.cpp \
     psitiltoptions.cpp \
     contourrulerparams.cpp \
     zernikesmoothingdlg.cpp \
+    zernike/zapm.cpp \
     SingleApplication/singleapplication.cpp \
     SingleApplication/singleapplication_p.cpp
 
diff --git a/DFTFringe_QT5.pro b/DFTFringe_QT5.pro
index 0271d3fc..854b959f 100644
--- a/DFTFringe_QT5.pro
+++ b/DFTFringe_QT5.pro
@@ -146,6 +146,7 @@ INCLUDEPATH += ./bezier ./SingleApplication
 
 SOURCES += SingleApplication/singleapplication.cpp \
     SingleApplication/singleapplication_p.cpp \
+    zernike/zapm.cpp \
     annulushelpdlg.cpp \
     arbitrarywavefronthelp.cpp \
     arbitrarywavwidget.cpp \
@@ -260,7 +261,6 @@ SOURCES += SingleApplication/singleapplication.cpp \
     wavefrontloader.cpp \
     wftexaminer.cpp \
     wftstats.cpp \
-    zapm.cpp \
     zernikedlg.cpp \
     zernikeeditdlg.cpp \
     zernikepolar.cpp \
diff --git a/zapm.cpp b/zernike/zapm.cpp
similarity index 100%
rename from zapm.cpp
rename to zernike/zapm.cpp

From 73ed28ff35971f835f4a07439b0687587380f43f Mon Sep 17 00:00:00 2001
From: Julien Staub <atsju2@yahoo.fr>
Date: Sun, 17 Aug 2025 08:29:52 +0200
Subject: [PATCH 2/6] adding licence file to be extra clear about code origin

---
 zernike/LICENSE.txt | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 zernike/LICENSE.txt

diff --git a/zernike/LICENSE.txt b/zernike/LICENSE.txt
new file mode 100644
index 00000000..b58b53b3
--- /dev/null
+++ b/zernike/LICENSE.txt
@@ -0,0 +1,22 @@
+The MIT License (MIT)
+
+Copyright (c) 2024 M.L. Peck
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+

From 5f03c2738f14f318147f3ce816e4ff8de3ab95cd Mon Sep 17 00:00:00 2001
From: Julien Staub <atsju2@yahoo.fr>
Date: Sun, 17 Aug 2025 12:00:20 +0200
Subject: [PATCH 3/6] remove unused files and code

---
 dftarea.cpp             |   5 +-
 mikespsiinterface.h_    |  10 --
 mikespsirinterface.cpp_ | 260 ----------------------------------------
 zernikeprocess.cpp      | 131 --------------------
 zernikeprocess.h        |   1 -
 5 files changed, 4 insertions(+), 403 deletions(-)
 delete mode 100644 mikespsiinterface.h_
 delete mode 100644 mikespsirinterface.cpp_

diff --git a/dftarea.cpp b/dftarea.cpp
index 757ffe1d..bd024da9 100644
--- a/dftarea.cpp
+++ b/dftarea.cpp
@@ -1271,7 +1271,9 @@ cv::Mat atan2Mat(cv::Mat y, cv::Mat x){
 }
 #include <armadillo>
 
-
+// zpmCxx commented out, not used, might be needed in doPSIstep4
+// I (atsju) recommend deleting this part and add original or modified file from Mike when/if needed
+/*
 arma::mat zpmCxx(double rho, double theta, int maxorder) {
 
   int m, n, n0, mmax = maxorder/2;
@@ -1345,6 +1347,7 @@ arma::mat zpmCxx(double rho, double theta, int maxorder) {
   }
   return zm;
 }
+*/
 
 #include "outlinedialog.h"
 void DFTArea::doPSIstep4(cv::Mat images, QVector<double> phases){
diff --git a/mikespsiinterface.h_ b/mikespsiinterface.h_
deleted file mode 100644
index fcc07e46..00000000
--- a/mikespsiinterface.h_
+++ /dev/null
@@ -1,10 +0,0 @@
-#ifndef MIKESPSIINTERFACE_H
-#define MIKESPSIINTERFACE_H
-#include "armadillo"
-arma::mat zpmC(arma::vec rho, arma::vec theta, int maxorder);
-
-typedef struct { arma::mat phi; arma::mat mod; arma::mat phase; arma::mat zcx; int iter; arma::vec sse;} psitiltReturn;
-arma::mat pxls(const arma::mat& im, const arma::rowvec& phases, const arma::mat& zcs, const arma::mat& coords);
-arma::mat pwrap(const arma::mat& phase);
-arma::mat rhotheta(const double rows, const double cols, double obspercent=0);
-#endif // MIKESPSIINTERFACE_H
diff --git a/mikespsirinterface.cpp_ b/mikespsirinterface.cpp_
deleted file mode 100644
index 83ede20d..00000000
--- a/mikespsirinterface.cpp_
+++ /dev/null
@@ -1,260 +0,0 @@
-// portions of this code are
-//	Copyright (C) 2016 Michael Peck <mpeck1 -at- ix.netcom.com>
-//
-//	License: MIT <https://opensource.org/licenses/MIT>
-//
-#include <cmath>
-#include <iostream>
-#include "mikespsiinterface.h"
-#include <stdlib.h>
-//#include <armadillo>
-#include <QMessageBox>
-#include "qmath.h"
-#include <QDebug>
-#include <QMap>
-// create two row vectors containing rho and theta values of the inclosed circular pupil
-// return them as two columns of a mat.
-
-
-
-
-// [[Rcpp::export]]
-
-
-typedef struct {arma::vec x; bool convergence; int iter;} lmreturn;
-
-/**************
- *
- * A stupidly simple implementation of a Levenberg-Marquardt
- * algorithm for nonlinear least squares.
- *
- * Adapted directly from the algorithm description on p. 27
- * of the booklet "Methods for Non-Linear Least Squares
- * Problems" by Madsen, Nielsen & Tingleff (2004)
- * download from http://www2.imm.dtu.dk/pubdb/views/edoc_download.php/3215/pdf/imm3215.pdf
- *
-*/
-
-lmreturn mylevmar(arma::vec (*res_fun)(const arma::vec&, const QMap<const char*, arma::mat>&, double abar, double bbar),
-             arma::mat (*jac_fun)(const arma::vec&, const QMap<const char *, arma::mat>&, double bbar),
-             unsigned int m, int n, arma::vec x0, QMap<const char *, arma::mat> adata, double abar, double bbar,
-             int itmax = 100, arma::vec control= {1.e-3, 2., sqrt(arma::datum::eps), sqrt(arma::datum::eps)}) {
-
-  int k=0;
-  double tau = control(0);
-  double nu = control(1);
-  double eps1 = control(2);
-  double eps2 = control(3);
-
-  arma::mat A(n, n);
-  arma::vec g(n);
-  arma::vec feval(m);
-  arma::vec fnew(m);
-  arma::mat Jac(m, n);
-  arma::mat In = arma::eye<arma::mat>(n, n);
-  arma::vec x = x0;
-  arma::vec hx(n), xnew(n);
-  bool found;
-  double mu;
-  double F, Fnew, dL, rho;
-  lmreturn retvals;
-
-  Jac = jac_fun(x, adata,bbar);
-  feval = res_fun(x, adata, abar, bbar);
-  A = Jac.t() * Jac;
-  g = Jac.t() * feval;
-  mu = tau * max(A.diag());
-  found = (norm(g, "Inf") <= eps1);
-
-  while (!found && k<itmax) {
-    k++;
-    hx = -arma::solve(A + mu*In, g);
-    if (arma::norm(hx, 2) <= eps2 * (arma::norm(x, 2) + eps2)) {
-      found = true;
-      break;
-    }
-    xnew = x + hx;
-    F = 0.5 * dot(feval, feval);
-    fnew = res_fun(xnew, adata, abar,bbar);
-    Fnew = 0.5 * arma::dot(fnew, fnew);
-    dL = 0.5 * arma::dot(hx, (mu*hx - g));
-    rho = (F-Fnew)/dL;
-    if (rho > 0.) {
-      x = xnew;
-      Jac = jac_fun(x, adata,bbar);
-      A = Jac.t() * Jac;
-      g = Jac.t() * fnew;
-      feval = fnew;
-      mu *= fmax(1./3., 1 - pow(2.*rho -1., 3));
-      nu = control(1);
-      found = (arma::norm(g, "Inf") <= eps1);
-    } else {
-      mu *= nu;
-      nu *= 2.;
-    }
-  }
-
-  retvals.x = x;
-  retvals.convergence = found;
-  retvals.iter = k;
-
-  return retvals;
-
-}
-
-// pixel-wise least squares with known phases, tilts, etc.
-
-arma::mat pxls(const arma::mat& im, const arma::rowvec& phases, const arma::mat& zcs, const arma::mat& coords) {
-  unsigned int nr = im.n_rows;
-  unsigned int nf = im.n_cols;
-
-  arma::rowvec ph(nf);
-  arma::mat A(3, nf);
-  arma::rowvec b(3);
-  arma::mat B(nr, 3);
-
-  for (unsigned int n=0; n<nr; n++) {
-    ph = phases + coords.row(n) * zcs;
-    A = arma::join_cols(arma::join_cols(arma::ones<arma::rowvec>(nf), arma::cos(ph)), arma::sin(ph));
-    b = im.row(n) * pinv(A);
-    B.row(n) = b;
-  }
-  return B;
-}
-
-// residuals and analytic Jacobian for mylevmar. Exported just in case I want to use minpack.lm
-
-// [[Rcpp::export]]
-
-arma::vec res_frame(const arma::vec& pars, const QMap<const char*, arma::mat> & adata, double abar, double bbar) {
-  arma::vec img = adata["img"];
-  arma::mat coords = adata["coords"];
-
-  arma::vec phi = adata["phi"];
-  int np = pars.n_elem;
-  arma::vec ph(img.n_elem);
-  ph = pars[0] + coords * pars.tail(np-1);
-  return img - abar - bbar * cos(phi + ph);
-}
-
-// [[Rcpp::export]]
-
-arma::mat jac_frame(const arma::vec& pars, const QMap<const char*, arma::mat> & adata, double bbar) {
-  arma::vec img = adata["img"];
-  arma::mat coords = adata["coords"];
-
-  arma::vec phi = adata["phi"];
-  int np = pars.n_elem;
-  unsigned int m = img.n_elem;
-  arma::vec ph(m);
-  arma::vec sp(m);
-  arma::mat jac(m, np);
-  ph = phi + pars[0] + coords * pars.tail(np-1);
-  sp = sin(ph);
-  jac = arma::join_rows(arma::ones(m), coords);
-  jac.each_col() %= sp;
-  return bbar*jac;
-}
-
-/************
- *
- * wrap phase into [-pi, pi)
- * This is slower than R version
- * but export it anyway with a different name.
- *
-*/
-
-//[[Rcpp::export]]
-
-arma::mat pwrap(const arma::mat& phase) {
-  unsigned int nr = phase.n_rows;
-  unsigned int nc = phase.n_cols;
-  unsigned int ne = phase.n_elem;
-  arma::mat wphase(nr, nc);
-
-  for (unsigned int i=0; i<ne; i++) {
-    wphase(i) = fmod(phase(i) + M_PI, 2.*M_PI) - M_PI;
-  }
-
-  return wphase;
-}
-
-
-
-// The main routine. This is what gets called from R
-
-//[[Rcpp::export]]
-
-psitiltReturn tiltpsiC(const arma::mat& images, const arma::rowvec& phases_init, const arma::mat& coords,
-              const double& ptol, const int& maxiter, const bool& trace) {
-  int N = images.n_cols;
-  unsigned int M = images.n_rows;
-  int np = coords.n_cols + 1;
-
-  //if (np < 3) stop("It doesn't make sense to use this algorithm without at least variable tilts.\nUse AIA or PC instead");
-  //if (phases_init.n_elem != N) stop("# phases must match # of images");
-  //if (coords.n_rows != M) stop("coordinates must have same # rows as image matrix");
-
-  arma::rowvec phases = phases_init - phases_init(0);
-
-  arma::mat S(3, N);
-  arma::mat Phi(M, 3);
-  arma::vec phi(M);
-  arma::vec mod(M);
-  arma::vec res(M);
-  arma::mat zcs = arma::zeros<arma::mat>(np-1, N);
-  arma::vec t0(np-1);
-  arma::vec sse = arma::zeros<arma::vec>(maxiter);
-  double abar, bbar;
-  QMap<const char*,arma::mat> adata;
-  adata["coords"] = coords;
-  arma::vec pars(np);
-  arma::mat pt_last = join_cols(phases, zcs);
-  arma::mat pt = pt_last;
-  double dpt;
-  int i;
-  lmreturn lmrets;
-
-  S = arma::join_cols(arma::join_cols(arma::ones<arma::rowvec>(N), arma::cos(phases)), arma::sin(phases));
-  Phi = images * pinv(S);
-
-  for (i=0; i<maxiter; i++) {
-    abar = arma::mean(Phi.col(0));
-    bbar = arma::mean(arma::sqrt(arma::square(Phi.col(1)) + arma::square(Phi.col(2))));
-    phi = arma::atan2(-Phi.col(2), Phi.col(1));
-
-    adata["phi"] = phi;
-
-    for (int n=0; n<N; n++) {
-      pars(0) = phases(n);
-      pars.tail(np-1) = zcs.col(n);
-      adata["img"] = images.col(n);
-      lmrets = mylevmar((*res_frame),
-                      (*jac_frame),
-                      M, np, pars, adata, abar, bbar);
-      if (!lmrets.convergence) QMessageBox::warning(0, "","lm convergence reported failed");
-      pars = lmrets.x;
-      res = res_frame(pars, adata, abar, bbar);
-      sse(i) = sse(i) + pow((double) arma::norm(res, 2), 2);
-      phases(n) = pars(0);
-      zcs.col(n) = pars.tail(np-1);
-    }
-    phases = phases - phases(0);
-    t0 = zcs.col(0);
-    zcs.each_col() -= t0;
-    pt = join_cols(phases, zcs);
-    dpt = norm(pt - pt_last, 2);
-    if (trace) {
-      qDebug() << "Iteration " << i << " sse = " << sse(i) << " dpt = " << dpt << Qt::endl;
-    }
-    if (dpt < ptol) break;
-    Phi = pxls(images, phases, zcs, coords);
-    pt_last = pt;
-  }
-  Phi = pxls(images, phases, zcs, coords);
-  phi = atan2(-Phi.col(2), Phi.col(1));
-  mod = sqrt(square(Phi.col(1)) + square(Phi.col(2)));
-  mod = mod/max(mod);
-  psitiltReturn list  = { phi, mod, pwrap(phases), zcs/(2.*M_PI),i, sse};
-  return list;
-}
diff --git a/zernikeprocess.cpp b/zernikeprocess.cpp
index 538cae5a..7cc7bc82 100644
--- a/zernikeprocess.cpp
+++ b/zernikeprocess.cpp
@@ -49,80 +49,6 @@ std::vector<double> zNulls;
 
 arma::mat zapm(const arma::vec& rho, const arma::vec& theta,
                const double& eps, const int& maxorder=12) ;
-cv::Mat zpmCx(QVector<double> rho, QVector<double> theta, int maxorder) {
-
-  int m, n, n0, mmax = maxorder/2;
-  int i, imax = rho.size();
-  int order, nm, nm1mm1, nm1mp1, nm2m;
-  int ncol = (mmax+1)*(mmax+1);
-  double a0;
-  double cosmtheta[mmax], sinmtheta[mmax];
-  cv::Mat_<double>  zm(imax, ncol);
-
-  //do some rudimentary error checking
-
-  //if (rho.length() != theta.length()) stop("Numeric vectors must be same length");
-  //if ((maxorder % 2) != 0) stop("maxorder must be even");
-
-  //good enough
-
-
-  for (i=0; i<imax; i++) {
-
-    //cache values of cos and sin
-    cosmtheta[0] = std::cos(theta[i]);
-    sinmtheta[0] = std::sin(theta[i]);
-    for (m=1; m<mmax; m++) {
-      cosmtheta[m] = cosmtheta[m-1]*cosmtheta[0] - sinmtheta[m-1]*sinmtheta[0];
-      sinmtheta[m] = sinmtheta[m-1]*cosmtheta[0] + cosmtheta[m-1]*sinmtheta[0];
-    }
-
-    zm(i, 0) = 1.0;                     //piston term
-    zm(i, 3) = 2. * rho[i] * rho[i] - 1.; //defocus
-
-    // now fill in columns with m=n for n>0
-
-    for (m=1; m <= mmax; m++) {
-      zm(i, m*m) = rho[i] * zm(i, (m-1)*(m-1));
-    }
-
-    // non-symmetric terms
-
-    for (order=4; order<=maxorder; order+=2) {
-      for (m=order/2-1; m>0; m--) {
-        n=order-m;
-        nm = order*order/4 + n - m;
-        nm1mm1 = (order-2)*(order-2)/4 + n - m;
-        nm1mp1 = nm - 2;
-        nm2m = nm1mm1 - 2;
-        zm(i, nm) = rho[i]*(zm(i, nm1mm1) + zm(i, nm1mp1)) - zm(i, nm2m);
-      }
-
-      // m=0 (symmetric) term
-      nm = order*order/4 + order;
-      nm1mp1 = nm-2;
-      nm2m = (order-2)*(order-2)/4+order-2;
-      zm(i, nm) = 2.*rho[i]*zm(i, nm1mp1) - zm(i, nm2m);
-    }
-
-    // now multiply each column by normalizing factor and cos, sin
-
-    n0 = 1;
-    for (order=2; order <= maxorder; order+=2) {
-      for(m=order/2; m>0; m--) {
-        n=order-m;
-        a0 = sqrt(2.*(n+1));
-        zm(i, n0+1) = a0*sinmtheta[m-1]*zm(i, n0);
-        zm(i, n0) *= a0*cosmtheta[m-1];
-        n0 += 2;
-      }
-      n = order;
-      zm(i, n0) *= sqrt(n+1.);
-      n0++;
-    }
-  }
-  return zm;
-}
 
 
 long fact( int n1, int n2)
@@ -1145,63 +1071,6 @@ arma::mat zernikeProcess::zpmC(arma::rowvec rho, arma::rowvec theta, int maxorde
     return zm;
 }
 
-arma::mat zernikeProcess::zapmC(const arma::rowvec& rho, const arma::rowvec& theta, const int& maxorder) {
-
-  unsigned int nrow = rho.size();
-  int mmax = maxorder/2;
-  int ncol = (mmax+1)*(mmax+1);
-  int i, j, m, nj;
-  double zpnorm = std::sqrt((double) nrow);
-  arma::mat zm(nrow, ncol), annzm(nrow, ncol);
-
-  //do some rudimentary error checking
-
-//  if (rho.size() != theta.size()) stop("Numeric vectors must be same length");
-//  if ((maxorder % 2) != 0) stop("maxorder must be even");
-
-  //good enough
-
-  zm = zpmC(rho, theta, maxorder);
-
-  // for each azimuthal index m find the column indexes
-  // of the zp matrix having that value of m. That
-  // subset is what we need to orthogonalize.
-  // Note this is done separately for "sine" and "cosine" components.
-
-  nj = maxorder/2 + 1;
-  for (m=0; m<mmax; m++) {
-    arma::uvec jsin(nj);
-    arma::uvec jcos(nj);
-    arma::mat Q(nrow, nj);
-    arma::mat R(nj, nj);
-    arma::vec sgn(nj);
-    for (i=0; i<nj; i++) {
-      jcos(i) = (m+i+1)*(m+i+1) - 2*m -1;
-      jsin(i) = jcos(i) + 1;
-    }
-
-    qr_econ(Q, R, zm.cols(jcos));
-    sgn = sign(R.diag());
-
-    annzm.cols(jcos) = zpnorm * Q * diagmat(sgn);
-    if (m > 0) {
-      qr_econ(Q, R, zm.cols(jsin));
-      sgn = sign(R.diag());
-      annzm.cols(jsin) = zpnorm * Q * diagmat(sgn);
-    }
-    --nj;
-  }
-
-  //  highest order only has one term
-
-  j = mmax*mmax;
-
-  annzm.col(j) = zm.col(j) * zpnorm / norm(zm.col(j));
-  annzm.col(j+1) = zm.col(j+1) * zpnorm / norm(zm.col(j+1));
-
-  return annzm;
-}
-
 
 
 void zernikeProcess::initGrid(int width, double radius, double cx, double cy, int maxOrder,
diff --git a/zernikeprocess.h b/zernikeprocess.h
index 75128cc3..bf3429f2 100644
--- a/zernikeprocess.h
+++ b/zernikeprocess.h
@@ -62,7 +62,6 @@ class zernikeProcess : public QObject
     arma::mat rhotheta( int width, double radius, double cx, double cy, const wavefront *wf = 0);
 
     arma::mat zpmC(arma::rowvec rho, arma::rowvec theta, int maxorder);
-    arma::mat zapmC(const arma::rowvec& rho, const arma::rowvec& theta, const int& maxorder=12);
     void fillVoid(wavefront &wf);
     void setMaxOrder(int n);
     int getNumberOfTerms();

From 71df2845753f69531bdbb115b072919442969f37 Mon Sep 17 00:00:00 2001
From: Julien Staub <atsju2@yahoo.fr>
Date: Sun, 17 Aug 2025 14:50:04 +0200
Subject: [PATCH 4/6] moved wild function declarations

---
 DFTFringe.pro            | 3 ++-
 DFTFringe_Dale.pro       | 3 ++-
 DFTFringe_QT5.pro        | 3 ++-
 mainwindow.cpp           | 8 +++-----
 zernike/zapm.cpp         | 7 ++++---
 zernike/zapm_interface.h | 6 ++++++
 zernikeprocess.cpp       | 6 ++----
 zernikeprocess.h         | 3 +++
 8 files changed, 24 insertions(+), 15 deletions(-)
 create mode 100644 zernike/zapm_interface.h

diff --git a/DFTFringe.pro b/DFTFringe.pro
index 6a75aa0c..e4af46a4 100644
--- a/DFTFringe.pro
+++ b/DFTFringe.pro
@@ -143,7 +143,7 @@ RESOURCES += DFTResources.qrc
 
 TRANSLATIONS += dftfringe_fr.ts
 
-INCLUDEPATH += ./bezier ./SingleApplication
+INCLUDEPATH += ./bezier ./SingleApplication ./zernike
 
 SOURCES += SingleApplication/singleapplication.cpp \
     SingleApplication/singleapplication_p.cpp \
@@ -272,6 +272,7 @@ SOURCES += SingleApplication/singleapplication.cpp \
 HEADERS += bezier/bezier.h \
     SingleApplication/singleapplication_p.h \
     SingleApplication/singleapplication.h \
+    zernike/zapm_interface.h \
     annulushelpdlg.h \
     arbitrarywavefronthelp.h \
     astigpolargraph.h \
diff --git a/DFTFringe_Dale.pro b/DFTFringe_Dale.pro
index b5f9a31e..a88e4fe1 100644
--- a/DFTFringe_Dale.pro
+++ b/DFTFringe_Dale.pro
@@ -275,10 +275,11 @@ HEADERS  += mainwindow.h \
     contourrulerparams.h \
     zernikesmoothingdlg.h \
     bezier/bezier.h \
+    zernike/zapm_interface.h \
     SingleApplication/singleapplication.h \
     SingleApplication/singleapplication_p.h
 
-INCLUDEPATH += ./bezier ./SingleApplication
+INCLUDEPATH += ./bezier ./SingleApplication ./zernike
 
 FORMS    += mainwindow.ui \
     annulushelpdlg.ui \
diff --git a/DFTFringe_QT5.pro b/DFTFringe_QT5.pro
index 854b959f..72741196 100644
--- a/DFTFringe_QT5.pro
+++ b/DFTFringe_QT5.pro
@@ -142,7 +142,7 @@ RESOURCES += DFTResources.qrc
 
 TRANSLATIONS += dftfringe_fr.ts
 
-INCLUDEPATH += ./bezier ./SingleApplication
+INCLUDEPATH += ./bezier ./SingleApplication ./zernike
 
 SOURCES += SingleApplication/singleapplication.cpp \
     SingleApplication/singleapplication_p.cpp \
@@ -271,6 +271,7 @@ SOURCES += SingleApplication/singleapplication.cpp \
 HEADERS += bezier/bezier.h \
     SingleApplication/singleapplication_p.h \
     SingleApplication/singleapplication.h \
+    zernike/zapm_interface.h \
     annulushelpdlg.h \
     arbitrarywavefronthelp.h \
     astigpolargraph.h \
diff --git a/mainwindow.cpp b/mainwindow.cpp
index 8f267eda..d80c1c55 100644
--- a/mainwindow.cpp
+++ b/mainwindow.cpp
@@ -49,6 +49,8 @@
 #include "colorchannel.h"
 #include "opencv2/opencv.hpp"
 #include <QUrl>
+#include "zapm_interface.h"
+#include "zernikeprocess.h"
 
 using namespace QtConcurrent;
 std::vector<wavefront*> g_wavefronts;
@@ -1845,11 +1847,7 @@ void MainWindow::on_actionCreate_Movie_of_wavefronts_triggered()
     this->setCursor(Qt::ArrowCursor);
     QApplication::restoreOverrideCursor();
 }
-arma::mat zapm(const arma::vec& rho, const arma::vec& theta,
-               const double& eps, const int& maxorder=12) ;
-#include "armadillo"
-void dumpArma(arma::mat mm, QString title = "", QVector<QString> colHeading = QVector<QString>(0),
-              QVector<QString> RowLable = QVector<QString>(0));
+
 void MainWindow::on_actionDebugStuff_triggered()
 {
     zernikeProcess *zp = zernikeProcess::get_Instance();
diff --git a/zernike/zapm.cpp b/zernike/zapm.cpp
index 54504a35..3c737f5a 100644
--- a/zernike/zapm.cpp
+++ b/zernike/zapm.cpp
@@ -13,8 +13,9 @@ THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR I
 
 // [[Rcpp::depends(RcppArmadillo)]]
 
-# include <cmath>
-# include "armadillo"
+#include "zapm_interface.h"
+#include <cmath>
+#include "armadillo"
 #include <QDebug>
 #include <QString>
 
@@ -296,7 +297,7 @@ mat rzernike_ann(const vec& rho, const double& eps, const int& n, const int& m,
 //'
 //' @md
 // [[Rcpp::export]]
-mat zapm(const vec& rho, const vec& theta, const double& eps, const int& maxorder=12) {
+mat zapm(const vec& rho, const vec& theta, const double& eps, const int& maxorder) {
 
   int j, k, nmax, nz, mmax = maxorder/2;
   uword nr = rho.size();
diff --git a/zernike/zapm_interface.h b/zernike/zapm_interface.h
new file mode 100644
index 00000000..c0175cb9
--- /dev/null
+++ b/zernike/zapm_interface.h
@@ -0,0 +1,6 @@
+#include "armadillo"
+#include <QString>
+#include <Qvector>
+
+arma::mat zapm(const arma::vec &rho, const arma::vec &theta, const double &eps,
+               const int &maxorder = 12);
diff --git a/zernikeprocess.cpp b/zernikeprocess.cpp
index 7cc7bc82..f2f558ef 100644
--- a/zernikeprocess.cpp
+++ b/zernikeprocess.cpp
@@ -27,6 +27,7 @@
 #include "myutils.h"
 //#include "arbitrarywavefrontdlg.h"
 #include "userdrawnprofiledlg.h"
+#include "zapm_interface.h"
 
 
 std::vector<bool> zernEnables;
@@ -47,8 +48,6 @@ std::vector<double> zNulls;
 
 
 
-arma::mat zapm(const arma::vec& rho, const arma::vec& theta,
-               const double& eps, const int& maxorder=12) ;
 
 
 long fact( int n1, int n2)
@@ -1213,8 +1212,7 @@ std::vector<double>  zernikeProcess::ZernFitWavefront(wavefront &wf){
 }
 
 //debug routine to see what is matrix values.
-void dumpArma(arma::mat mm, QString title = "", QVector<QString> colHeading = QVector<QString>(0),
-              QVector<QString> RowLable = QVector<QString>(0)){
+void dumpArma(arma::mat mm, QString title, QVector<QString> colHeading, QVector<QString> RowLable){
     arma::mat theMat = mm;
     QString transposed(" ");
 
diff --git a/zernikeprocess.h b/zernikeprocess.h
index bf3429f2..44433a96 100644
--- a/zernikeprocess.h
+++ b/zernikeprocess.h
@@ -32,6 +32,9 @@ extern std::vector<bool> zernEnables;
 //void gauss_jordan(int n, double* Am, double* Bm);
 
 
+void dumpArma(arma::mat mm, QString title = "",
+            QVector<QString> colHeading = QVector<QString>(0),
+            QVector<QString> RowLable = QVector<QString>(0));
 
 class zernikeProcess : public QObject
 {

From e068748a84f840e6e8c9965c8efe8e87a8123a8b Mon Sep 17 00:00:00 2001
From: Julien Staub <atsju2@yahoo.fr>
Date: Sun, 17 Aug 2025 14:54:47 +0200
Subject: [PATCH 5/6] added comments to explain zapm file change

---
 zernike/zapm.cpp | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/zernike/zapm.cpp b/zernike/zapm.cpp
index 3c737f5a..0fe2969a 100644
--- a/zernike/zapm.cpp
+++ b/zernike/zapm.cpp
@@ -338,7 +338,8 @@ mat zapm(const vec& rho, const vec& theta, const double& eps, const int& maxorde
   RZ = rzernike_ann(rho, eps, maxorder, 0, xq, qwts);
   for (int n=0; n<=maxorder; n += 2) {
     k = (n*n)/4 + n;
-    zm.col(k) = RZ.col(n/2);
+    // Dale: normalizers aka m_norms[] are not used here in DFTFringe
+    zm.col(k) = /* std::sqrt(n+1.)* */RZ.col(n/2);
   }
 
   for (int m=1; m<=mmax; m++) {
@@ -349,9 +350,11 @@ mat zapm(const vec& rho, const vec& theta, const double& eps, const int& maxorde
     j = 0;
     for (int n=m; n<= nmax; n += 2) {
       k = ((n+m)*(n+m))/4 + n - m;
-      zm.col(k) = RZ.col(j) % cosmtheta.col(m-1);
+      // Dale: normalizers aka m_norms[] are not used here in DFTFringe
+      zm.col(k) = /* std::sqrt(2.*(n+1.)) * */ RZ.col(j) % cosmtheta.col(m-1);
       k++;
-      zm.col(k) =  RZ.col(j) % sinmtheta.col(m-1);
+      // Dale: normalizers aka m_norms[] are not used here in DFTFringe
+      zm.col(k) = /* std::sqrt(2.*(n+1.)) * */ RZ.col(j) % sinmtheta.col(m-1);
       j++;
     }
   }

From bf6a323e507d6ba2bd2e9d072f024f89bd2a76c0 Mon Sep 17 00:00:00 2001
From: Julien Staub <atsju2@yahoo.fr>
Date: Sun, 17 Aug 2025 16:51:21 +0200
Subject: [PATCH 6/6] fix typo

---
 zernike/zapm_interface.h | 2 --
 1 file changed, 2 deletions(-)

diff --git a/zernike/zapm_interface.h b/zernike/zapm_interface.h
index c0175cb9..7bd39382 100644
--- a/zernike/zapm_interface.h
+++ b/zernike/zapm_interface.h
@@ -1,6 +1,4 @@
 #include "armadillo"
-#include <QString>
-#include <Qvector>
 
 arma::mat zapm(const arma::vec &rho, const arma::vec &theta, const double &eps,
                const int &maxorder = 12);