(i,0) = mirrorY;
qDebug() << "Mirror astigs " << mirrorX << mirrorY;
+ QApplication::processEvents();
}
Circle fittedcircle1;
@@ -2095,7 +2096,7 @@ qDebug() << "circle fit"<< avgRadius << fittedcircle1.r << fittedcircle2.r;
"| " + QString().number(yval,'f',3) + " | "
"" + QString().number(mag,'f',3) + " | "
"" + QString().number((180./ M_PI) * atan2(yval,xval)/2.,'f',1) + " | ");
-
+ QApplication::processEvents();
}
html.append("| MEAN | " + QString().number(fittedcircle.a,'f',3) + " | " +
QString().number(fittedcircle.b,'f',3) + " | " + QString().number(sqrt(fittedcircle.a * fittedcircle.a + fittedcircle.b * fittedcircle.b),'f',3) + " |
");
@@ -2178,6 +2179,7 @@ qDebug() << "circle fit"<< avgRadius << fittedcircle1.r << fittedcircle2.r;
cnt = 0;
imagesHtml.append("");
}
+ QApplication::processEvents();
}
mirrorAstigRadius /= list.size();
@@ -2446,6 +2448,8 @@ void SurfaceManager::computeStandAstig(define_input *wizPage, QListfname;
+ wizPage->m_log->append("Loading " + list[i]->fname);
+ QApplication::processEvents();
loadWavefront(list[i]->fname);
wavefront * wf = m_wavefronts[m_currentNdx];
inputs.append(wf);
@@ -2461,7 +2465,9 @@ void SurfaceManager::computeStandAstig(define_input *wizPage, QList ![](" +imageName + ")
" + angle + " | ");
// counter rotate it
- wizPage->runpb->setText(QString("Counter Rotating ") + list[i]->fname.right(list[i]->fname.size() - list[i]->fname.lastIndexOf("/")-1));
+
+ wizPage->m_log->setText(QString("Counter Rotating ") + list[i]->fname.right(list[i]->fname.size() - list[i]->fname.lastIndexOf("/")-1));
+ QApplication::processEvents();
QList l;
l.append(ndx);
ndx = m_wavefronts.size();
@@ -2492,7 +2498,8 @@ void SurfaceManager::computeStandAstig(define_input *wizPage, QListsetDocument(doc);
//editor->show();
-
+ wizPage->m_log->append("averaging rotated wave fronts");
+ QApplication::processEvents();
// Now average all the rotated ones.
QList wlist;
for (int i = 0; i < rotated.size(); ++i){
@@ -2539,7 +2546,8 @@ void SurfaceManager::computeStandAstig(define_input *wizPage, QListrunpb->setText("computing stand astigs");
+ wizPage->m_log->setText("computing stand astigs");
+ QApplication::processEvents();
textres page3res = Phase2(list, inputs, avgNdx);
QTabWidget *tabw = new QTabWidget();
tabw->setTabShape(QTabWidget::Triangular);
diff --git a/zernikeprocess.cpp b/zernikeprocess.cpp
index f0a53d10..ecdba249 100644
--- a/zernikeprocess.cpp
+++ b/zernikeprocess.cpp
@@ -53,6 +53,8 @@ int Zw[] = { /* n */
// [[Rcpp::export]]
+
+
arma::mat zapm(const arma::vec& rho, const arma::vec& theta,
const double& eps, const int& maxorder=12) ;
cv::Mat zpmCx(QVector rho, QVector theta, int maxorder) {
@@ -1094,6 +1096,7 @@ void spectral_color(double &R,double &G,double &B,double wavelength)
cv::Mat zernikeProcess::makeSurfaceFromZerns(int border, bool doColor){
+
simIgramDlg &dlg = *simIgramDlg::get_instance();
double obs = .01 * dlg.getObs();
int wx = dlg.size + 2 * border;
@@ -1106,7 +1109,7 @@ cv::Mat zernikeProcess::makeSurfaceFromZerns(int border, bool doColor){
initGrid(wx, rad, (wx-1)/2, (wx-1)/2, m_maxOrder, 0);
double spacing = 1.;
mirrorDlg *md = mirrorDlg::get_Instance();
- qDebug() << "fringe spacing" << md->fringeSpacing;
+
double r,g,b;
spectral_color(r,g,b, md->lambda);
if (doColor) {
@@ -1118,7 +1121,6 @@ cv::Mat zernikeProcess::makeSurfaceFromZerns(int border, bool doColor){
if (dlg.m_doArbitrary)
dlg_arbitrary->prepare(dlg.size);
-
for (std::size_t i = 0; i < m_rhoTheta.n_cols; ++i)
{
@@ -1154,6 +1156,8 @@ cv::Mat zernikeProcess::makeSurfaceFromZerns(int border, bool doColor){
int x = m_col[i];
int y = m_row[i];
+
+
if (doColor){
if (rho < obs)
@@ -1174,82 +1178,6 @@ cv::Mat zernikeProcess::makeSurfaceFromZerns(int border, bool doColor){
return result;
}
-#define TSIZE 450 // number of points in zern generator
-void ZernikeSmooth(cv::Mat wf, cv::Mat mask)
-{
- // given a wavefront generate arbitrary number of zernikes from it. Then create wavefront from the zernikies.
- double *m = (double *)(wf.data);
-
-
- int size = wf.cols;
- int step = (double)size/200.; // 200 samples across the wavefront
- double delta = (double)TSIZE/size; // scale factor from wavefront to zernike generator
-
- double* tmp = new double[TSIZE * TSIZE];
- memset(tmp, 0,sizeof(double) * TSIZE * TSIZE);
-
- zern_generator zg(TSIZE);
- zg.set_spec(6);
- zg.zpoly_list();
-
-
-
- //'calculate LSF matrix elements
-
- int terms = zg.get_terms_cnt();
- int am_size = terms* terms;
- double* Am = new double[am_size];
- double* Bm = new double[terms];
- for (int i = 0; i < am_size; ++i)
- {
- Am[i] = 0.;
- }
- for (int i = 0; i < terms; ++i)
- Bm[i] = 0;
-
- //calculate LSF right hand side
- for(int y = 0; y < size; y += step) //for each point on the surface
- {
- for(int x = 0; x < size; x += step)
- {
- int xx = x* delta;
- int yy = y * delta;
- if (mask.at(x,y))
- {
- int sndx = x + y* size;
-
- tmp[xx+yy * TSIZE] = m[sndx];
- for (int i = 0; i < terms; ++i)
- {
- double ipoly = zg.get_zpoly(i,xx,yy);
- int dy = i * terms;
- for (int j = 0; j < terms; ++j)
- {
- int ndx = j + dy;
- Am[ndx] = Am[ndx] +
- ipoly * zg.get_zpoly(j, xx, yy);
- }
- Bm[i] = Bm[i] + m[sndx] * ipoly;
-
- }
-
- }
- }
-
- }
- // compute coefficients
- gauss_jordan (terms, Am, Bm);
-
- zg.set_zcoefs(Bm);
-
- for (int i = 0; i < terms; ++i){
- qDebug() << i << " " << Bm[i];
- }
- delete[] Am;
- delete[] Bm;
- delete[] tmp;
-}
-
arma::mat zernikeProcess::rhotheta( int width, double radius, double cx, double cy,
const wavefront *wf){
@@ -1277,8 +1205,8 @@ arma::mat zernikeProcess::rhotheta( int width, double radius, double cx, double
for (int y = 0; y < rows; ++y){
double uy = (y -cy)/radius;
- if (!m_bDontProcessEvents)
- QApplication::processEvents();
+// if (!m_bDontProcessEvents)
+// QApplication::processEvents();
for (int x = 0; x< rows; ++x){
double ux = (x -cx)/radius;
@@ -1351,6 +1279,7 @@ arma::mat zernikeProcess::zpmC(arma::rowvec rho, arma::rowvec theta, int maxorde
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
@@ -1433,60 +1362,12 @@ arma::mat zernikeProcess::zapmC(const arma::rowvec& rho, const arma::rowvec& the
return annzm;
}
-void dumpArma(arma::mat mm, QString title = "", QVector colHeading = QVector(0),
- QVector RowLable = QVector(0)){
- arma::mat theMat = mm;
- QString transposed(" ");
-
-
- QString log;
-
- QString s;
- QTextStream out(&s);
-
- out << "" << transposed << title <<" zern matrix size "<< mm.n_rows <<"X" << mm.n_cols << "
";
-
- log.append(s);
- if (!colHeading.empty()){
- log.append("");
- for (int c = 0; c < colHeading.size(); ++c){
- log.append("| "+colHeading[c] + " | ");
- }
- log.append("
\n");
- }
-
- for (arma::uword row =0; row < theMat.n_rows; ++row){
- if (row > 20) break;
- log.append(" | ");
- if (!RowLable.empty()){
-
- if (row < static_cast(RowLable.size())){
- log.append(QString("%1").arg(RowLable[row]));
- }
-
- }
- log.append(" | ");
-
- for (arma::uword c = 0; c< theMat.n_cols; ++c){
- log.append(QString("%1 | ").arg(theMat(row,c), 6, 'f', 5));
- }
- log.append("
\n");
-
- }
- log.append("
");
- QTextEdit *display = new QTextEdit();
- display->resize(2500,1000);
- display->insertHtml(log);
-
- display->show();
-
-}
void zernikeProcess::initGrid(int width, double radius, double cx, double cy, int maxOrder,
double insideRad){
- qDebug() << "initGrid width " << width << radius << cx << cy << maxOrder << insideRad;
+
// if grid or maxOrder is different then update values.
double obsPercent = 0.;
bool shouldUseAnnulus = false;
@@ -1583,17 +1464,18 @@ std::vector zernikeProcess::ZernFitWavefront(wavefront &wf){
if (i%5000 == 0) {
prg->setValue(i);
QApplication::processEvents();
-// if (prg->wasCanceled()){
-// throw 42;
-// }
+ if (prg->wasCanceled()){
+ std::vector dummy;
+ return dummy; // a zero lengh vector signals cancelation.
+
+ }
}
if ( rho <= 1. && (wf.mask.at( m_row[i], m_col[i]) != 0)){
for ( int zi = 0; zi < ztermCnt; ++zi)
{
double t = m_zerns(i,zi);
- //if (zi == 0)
- // qDebug() << "z0" << t << "rho:"< zernikeProcess::ZernFitWavefront(wavefront &wf){
wf.InputZerns = std::vector(ztermCnt,0);
for (std::size_t z = 0; z < static_cast(X.rows); ++z){
- if (z < wf.InputZerns.size()){
- //qDebug() << z << X(z) << wf.InputZerns[z] << (QString("%1").arg(X(z) - wf.InputZerns[z], 6, 'f', 4)).toDouble();
- }
- else {
- //qDebug() << z << X(z);
- }
+
wf.InputZerns[z] = X(z);
}
@@ -1626,148 +1503,54 @@ std::vector zernikeProcess::ZernFitWavefront(wavefront &wf){
X.col(0).copyTo(r);
return r;
}
-void make3DPsf(cv::Mat surface){
-
- QWidget *plotWindow = new QWidget;
- Q3DSurface *m_PSF_3Dgraph;
- m_PSF_3Dgraph = new Q3DSurface();
- QWidget *container = QWidget::createWindowContainer(m_PSF_3Dgraph);
- QHBoxLayout *hLayout = new QHBoxLayout();
- QVBoxLayout *vLayout = new QVBoxLayout();
- hLayout->addWidget(container, 1);
- hLayout->addLayout(vLayout);
- plotWindow->setLayout(hLayout);
-
- cv::Mat data = surface.clone();//(cv::Rect(start,start,nx/2,nx/2));
-
+//debug routine to see what is matrix values.
+void dumpArma(arma::mat mm, QString title = "", QVector colHeading = QVector(0),
+ QVector RowLable = QVector(0)){
+ arma::mat theMat = mm;
+ QString transposed(" ");
- double xmin,xmax;
- cv::minMaxLoc(data, &xmin,&xmax);
- data/=xmax;
+ QString log;
- QSurfaceDataProxy *m_sqrtSinProxy = new QSurfaceDataProxy();
- QSurface3DSeries *m_sqrtSinSeries = new QSurface3DSeries(m_sqrtSinProxy);
+ QString s;
+ QTextStream out(&s);
- //draw surfaced
- {
+ out << "" << transposed << title <<" zern matrix size "<< mm.n_rows <<"X" << mm.n_cols << "
";
- int sampleCountX = data.size[1];
- int sampleCountZ = data.size[0];
- int width = sampleCountX;
- QSurfaceDataArray *dataArray = new QSurfaceDataArray;
- QSurfaceDataArray *dataArray2 = new QSurfaceDataArray;
- dataArray->reserve(sampleCountZ);
- dataArray2->reserve(sampleCountZ);
- for (int i = 0 ; i < sampleCountZ ; i++) {
- QSurfaceDataRow *newRow = new QSurfaceDataRow(sampleCountX);
- QSurfaceDataRow *backRow = new QSurfaceDataRow(sampleCountX);
- float z = -(sampleCountZ/2. - i);
- int index = 0;
- for (int j = 0; j < sampleCountX; j++) {
- float x = -(sampleCountX/2. -j);
-
- float y = data.at(i,j);
- (*newRow)[index].setPosition(QVector3D(x, y, z));
- (*backRow)[index++].setPosition(QVector3D(x, y, width/2));
- }
- *dataArray << newRow;
- *dataArray2 << backRow;
+ log.append(s);
+ if (!colHeading.empty()){
+ log.append("");
+ for (int c = 0; c < colHeading.size(); ++c){
+ log.append("| "+colHeading[c] + " | ");
}
+ log.append("
\n");
+ }
- QSurfaceDataProxy *m_sqrtSinProxy2 = new QSurfaceDataProxy();
- QSurface3DSeries *m_sqrtSinSeries2 = new QSurface3DSeries(m_sqrtSinProxy2);
-
-
- m_sqrtSinProxy->resetArray(dataArray);
- m_sqrtSinSeries->setDrawMode(QSurface3DSeries::DrawSurface);
- m_sqrtSinSeries->setFlatShadingEnabled(false);
-
- m_sqrtSinProxy2->resetArray(dataArray2);
- m_sqrtSinSeries2->setDrawMode(QSurface3DSeries::DrawSurfaceAndWireframe);
- m_sqrtSinSeries2->setFlatShadingEnabled(false);
-
- QLinearGradient gr;
- gr.setColorAt(0.0, Qt::darkGray);
- gr.setColorAt(0.01,Qt::cyan);
- gr.setColorAt(0.33, Qt::blue);
- gr.setColorAt(0.67, Qt::lightGray);
- gr.setColorAt(1.0, Qt::red);
- m_PSF_3Dgraph->activeTheme()->setType(Q3DTheme::Theme(3));
+ for (arma::uword row =0; row < theMat.n_rows; ++row){
+ if (row > 20) break;
+ log.append(" | ");
+ if (!RowLable.empty()){
+ if (row < static_cast(RowLable.size())){
+ log.append(QString("%1").arg(RowLable[row]));
+ }
+ }
+ log.append(" | ");
- m_PSF_3Dgraph->axisX()->setRange(-width/2, width/2);
- m_PSF_3Dgraph->axisZ()->setRange(-width/2, width/2);
+ for (arma::uword c = 0; c< theMat.n_cols; ++c){
+ log.append(QString("%1 | ").arg(theMat(row,c), 6, 'f', 5));
+ }
+ log.append("
\n");
- m_PSF_3Dgraph->addSeries(m_sqrtSinSeries);
- m_PSF_3Dgraph->addSeries(m_sqrtSinSeries2);
- m_PSF_3Dgraph->seriesList().at(0)->setBaseGradient(gr);
- m_PSF_3Dgraph->seriesList().at(0)->setColorStyle(Q3DTheme::ColorStyleRangeGradient);
- }
- plotWindow->show();
-}
-#include
-#include
-#include "zernikesmoothingdlg.h"
-using namespace cv;
-void debugZernRoutines(wavefront &wf){
- int cols = 4;
- for (int i = 0; i < 10; ++i) {
- qDebug() << i << i/cols << i%cols;
}
- return;
- zernikeProcess &zp = *zernikeProcess::get_Instance();
-
-// QFile inputFile("C:\\Users\\doeas\\Documents\\t.txt");
-// double xc = 487.;
-// double yc = 486.;
-// double rad = 463.;
-// if (inputFile.open(QIODevice::ReadOnly))
-// {
-// QTextStream in(&inputFile);
-// int row = 0;
-// vector tmpRow;
-// vector< vector> data;
-// while (!in.atEnd())
-// {
-// QString line = in.readLine();
-// QStringList fields = line.simplified().split(" ");
-// tmpRow.clear();
-// for (int i = 0; i < fields.size(); ++i){
-// if (fields[i].contains("NA")){
-// tmpRow.push_back(0.0);
-// }
-// else {
-// tmpRow.push_back(fields[i].toDouble());
-// }
-// }
-// data.push_back(tmpRow);
-// }
-// inputFile.close();
-// qDebug() << "data" << data.size() << data[10].size();
-// cv::Mat matd(data.size(),data[1].size(), numType,0.);
-// for(int i=0; i(i, j) = data.at(i).at(j);
-// make3DPsf(matd);
-
-// sm->createSurfaceFromPhaseMap(matd,
-// CircleOutline(QPointF(xc,yc),rad),
-// CircleOutline(QPointF(0,0),0),
-// QString("Mikes wavefront"));
-
-
-
-
- for (int terms = 6; terms < 50; terms += 2) {
-
- zp.initGrid(wf, terms);
- zp.ZernFitWavefront(wf);
- qDebug() << "Max Order" << terms << wf.InputZerns[8]/(sqrt(5.));
- }
+ log.append("
");
+ QTextEdit *display = new QTextEdit();
+ display->resize(2500,1000);
+ display->insertHtml(log);
+ display->show();
- }
+}
diff --git a/zernikesmoothingdlg.cpp b/zernikesmoothingdlg.cpp
index 9bba9d0f..a3ecfddb 100644
--- a/zernikesmoothingdlg.cpp
+++ b/zernikesmoothingdlg.cpp
@@ -20,7 +20,8 @@ ZernikeSmoothingDlg::ZernikeSmoothingDlg(wavefront &wf, QWidget *parent) :
std::vector val(m_noOfTerms,0.);
ui->zernView->setModel(tableModel);
QSettings set;
- m_maxOrder = set.value("Zern maxOrder", 12).toInt();
+
+ m_maxOrder = set.value("Zern maxOrder", 22).toInt();
ui->maxOrder->setValue(m_maxOrder);
ui->termCnt->setText(QString("%1 Terms").arg(m_noOfTerms));
connect(&m_timer, SIGNAL(timeout()), this, SLOT(intiZernTable()));
@@ -52,10 +53,12 @@ void ZernikeSmoothingDlg::on_maxOrder_valueChanged(int arg1)
{
if (arg1 % 2 != 0)
++arg1;
+ QSettings set;
+ set.setValue("Zern maxOrder",arg1);
+
ui->maxOrder->setValue( arg1);
m_maxOrder = arg1;
-
m_zp->setMaxOrder(arg1);
m_noOfTerms = m_zp->getNumberOfTerms();
ui->termCnt->setText(QString("%1 Terms").arg(m_noOfTerms));
@@ -66,25 +69,51 @@ void ZernikeSmoothingDlg::on_maxOrder_valueChanged(int arg1)
m_timer.setSingleShot(true);
m_timer.start(1000);
+
}
-cv::Mat makeSurfaceFromZerns(int width, zernikeProcess &zp, std::vector theZerns){
+
+cv::Mat makeSurfaceFromZerns(int width, zernikeProcess &zp, std::vector theZerns, bool sph = false){
int wx = width;
cv::Mat result = cv::Mat::zeros(wx,wx, numType);
-
- for (unsigned long long i = 0; i < zp.m_zerns.n_rows; ++i){
- double S1 = 0.0;
- for (unsigned int z = 0; z < theZerns.size(); ++z){
- double val = theZerns[z];
- S1 += val * zp.m_zerns(i,z);
+ if (!sph) {
+ for (unsigned long long i = 0; i < zp.m_zerns.n_rows; ++i){
+ double S1 = 0.0;
+ for (unsigned int z = 0; z < theZerns.size(); ++z){
+ double val = theZerns[z];
+ S1 += val * zp.m_zerns(i,z);
+
+ //if (rho < .5) S1 = 0.;
+ }
int x = zp.m_col[i];
int y = zp.m_row[i];
-
if (S1 == 0.0) S1 += .0000001;
- //if (rho < .5) S1 = 0.;
result.at(y,x) = S1;
}
}
+ else { // use only spherical terms.
+ unsigned int z = 0;
+ for (unsigned long long i = 4; i < zp.m_zerns.n_rows; ++i){
+
+ double S1 = 0.0;
+ unsigned int z = 8;
+ for (unsigned int j = 6; z < theZerns.size(); j+=2){
+
+ double val = theZerns[z];
+ S1 += val * zp.m_zerns(i,z);
+
+ z = j * j/4 + j;
+ }
+ int x = zp.m_col[i];
+ int y = zp.m_row[i];
+ if (S1 == 0.0) S1 += .0000001;
+ result.at(y,x) = S1;
+ if (y == wx/2.){
+ qDebug() << x << y << S1;
+ }
+
+ }
+ }
return result;
}
@@ -94,16 +123,17 @@ void ZernikeSmoothingDlg::on_createWaveFront_clicked()
QApplication::setOverrideCursor(Qt::WaitCursor);
m_wf = *p_wf;
if (!ui->useCurrentZernySet->isChecked()){
- theZerns = m_zp->ZernFitWavefront(m_wf);
- qDebug() << "the zerns";
- for (int z = 0; z < 8; ++z){
- qDebug() << z << theZerns[z];
+ std::vector tzerns = m_zp->ZernFitWavefront(m_wf);
+ if (tzerns.size() == 0){
+ QApplication::restoreOverrideCursor();
+ return;
}
+ theZerns = tzerns;
}
tableModel->setValues(&theZerns);
- cv::Mat result = makeSurfaceFromZerns(m_wf.data.cols, *m_zp, theZerns);
+ cv::Mat result = makeSurfaceFromZerns(m_wf.data.cols, *m_zp, theZerns, m_spherical_only);
QStringList l = m_wf.name.split("/");
l.back().replace(".wft","");
@@ -123,3 +153,9 @@ void ZernikeSmoothingDlg::on_createWaveFront_clicked()
}
QApplication::restoreOverrideCursor();
}
+
+void ZernikeSmoothingDlg::on_sphereOnly_toggled(bool checked)
+{
+ m_spherical_only = checked;
+}
+
diff --git a/zernikesmoothingdlg.h b/zernikesmoothingdlg.h
index 0ab059e4..b1479e61 100644
--- a/zernikesmoothingdlg.h
+++ b/zernikesmoothingdlg.h
@@ -16,11 +16,14 @@ class ZernikeSmoothingDlg : public QDialog
public:
explicit ZernikeSmoothingDlg(wavefront &wf, QWidget *parent = nullptr);
~ZernikeSmoothingDlg();
-
+ bool m_spherical_only = false;
private slots:
void on_maxOrder_valueChanged(int arg1);
void on_createWaveFront_clicked();
void intiZernTable();
+
+ void on_sphereOnly_toggled(bool checked);
+
private:
Ui::ZernikeSmoothingDlg *ui;
int m_maxOrder;
diff --git a/zernikesmoothingdlg.ui b/zernikesmoothingdlg.ui
index ced903bd..44ea69d9 100644
--- a/zernikesmoothingdlg.ui
+++ b/zernikesmoothingdlg.ui
@@ -65,6 +65,9 @@ p, li { white-space: pre-wrap; }
2
+
+ 22
+