void MyThread::DealImage(cv::Mat &frame, cv::Mat &mask, cv::Mat &bgmodle) //DealImage作为BgsMOG的友元类才能访问私有成员
{
HANDLE handle[NUM_THREADS];
MyThreadPra *threadPra[NUM_THREADS];
int patch_h = frame.rows/2;
int patch_w = frame.cols/2;
int x = 0, y = 0 ;
int height = 0, width = 0;
for (int i=0; i < NUM_THREADS; i++)
{
switch(i)
{
case 0:
x = 0;
y= 0;
height = patch_h;
width = patch_w;
break;
case 1:
x = patch_w;
y = 0;
height = patch_h;
width = frame.cols-patch_w;
break;
case 2:
x = 0;
y = patch_h;
height = frame.rows-patch_h;
width = patch_w;
break;
case 3:
x = patch_w;
y = patch_h;
height = frame.rows-patch_h;
width = frame.cols-patch_w;
break;
}
cv::Rect imgRoi(x,y,width,height);
cv::Mat img(frame, imgRoi);
cv::Mat msk(mask, imgRoi);
cv::Mat bg(bgmodle, imgRoi);
threadPra[i] = new MyThreadPra(&mog[i], img, msk, bg);
}
for (int i=0; i < NUM_THREADS; i++)
{
handle[i] = (HANDLE)_beginthreadex(NULL, 0, SetImage, threadPra[i], 0, NULL);
WaitForSingleObject(g_hThreadEvent, INFINITE);
}
WaitForMultipleObjects(NUM_THREADS, handle, TRUE, INFINITE);
//delete[] threadPra;
}
void DProgressCircle::resizeEvent(QResizeEvent *) {
if (parentWidget() != 0) return;
QBitmap msk( size() );
msk.clear();
QPainter painter(&msk);
painter.setPen(Qt::color1);
painter.setBrush(Qt::color1);
painter.drawRoundRect( QRectF(0.0, 0.0, width()-1, height()-1), 20, 20 );
setMask(msk);
}
void QFEvalBeadScanPSFItem::doEvaluation(QFRawDataRecord* record, double deltaXY, double deltaZ, int ROIxy, int ROIz, int pixels_per_frame, double est_psf_width, double est_psf_height, double fitXY_Z_fraction, bool medianFilterBeforeFindBeads, bool useMask, QFListProgressDialog *dlgEvaluationProgress) {
QApplication::processEvents();
if (dlgEvaluationProgress&& dlgEvaluationProgress->wasCanceled()) return; // canceled by user ?
QString evalID=getEvaluationResultID();
QFRDRImageStackInterface* data=dynamic_cast<QFRDRImageStackInterface*>(record);
QFRDRImageMaskInterface* maskI=qobject_cast<QFRDRImageMaskInterface*>(record);
int stack=0;
int channels=qMin(2,data->getImageStackChannels(stack));
int size_z=data->getImageStackFrames(stack);
int width=data->getImageStackWidth(stack);
int height=data->getImageStackHeight(stack);
int zsteps=qMax(4, ROIz/4);
double min_distance=double(ROIxy)/2.0;
QString fitalgID="fit_lmfit";
QString fitalgIRLSID="fit_irls_lmfit";
QFFitAlgorithm* alg=QFPluginServices::getInstance()->getFitAlgorithmManager()->createAlgorithm(fitalgID);
if (!alg) return;
QFFitAlgorithm* algIRLS=QFPluginServices::getInstance()->getFitAlgorithmManager()->createAlgorithm(fitalgIRLSID);
if (!algIRLS) {
algIRLS=QFPluginServices::getInstance()->getFitAlgorithmManager()->createAlgorithm(fitalgID);
}
if (!algIRLS) return;
// fit function object for 1D Gaussian fits:
QFFitFunction* ff1D=new QFFitFunctionPSFGaussian();
if (!ff1D) return;
QFFitFunction* ffGBwidth=new QFFitFunctionPSFGaussianBeamWidth();
if (!ffGBwidth) return;
QVector<double> ff1Dmin=ff1D->getInitialParamMins();
QVector<double> ff1Dmax=ff1D->getInitialParamMaxs();
QVector<double> ffGBwidthmin=ffGBwidth->getInitialParamMins();
QVector<double> ffGBwidthmax=ffGBwidth->getInitialParamMaxs();
// fit function object for 3D Gaussian fits:
QFFitFunction3D* ff3D=new QFFitFunctionPSF3DGaussian();
if (!ff3D) return;
QVector<double> ff3Dmin=ff3D->getInitialParamMins();
QVector<double> ff3Dmax=ff3D->getInitialParamMaxs();
/*qDebug()<<"channels="<<channels;
qDebug()<<"size_z="<<size_z;
qDebug()<<"width="<<width;
qDebug()<<"height="<<height;
qDebug()<<"zsteps="<<zsteps;
qDebug()<<"est_psf_width="<<est_psf_width;
qDebug()<<"est_psf_height="<<est_psf_height;
qDebug()<<"deltaXY="<<deltaXY;
qDebug()<<"deltaZ="<<deltaZ;
qDebug()<<"ROIxy="<<ROIxy;
qDebug()<<"ROIz="<<ROIz;
qDebug()<<"pixels_per_frame="<<pixels_per_frame;
qDebug()<<"min_distance="<<min_distance;*/
bool* mask=NULL;
int maskedPixels=0;
if (useMask && maskI && (int64_t)maskI->maskGetHeight()==height && (int64_t)maskI->maskGetWidth()==width) {
mask=maskI->maskGet();
for (int i=0; i<width*height; i++) {
if (mask[i]) maskedPixels++;
}
}
//if (mask) qDebug()<<mask[0]<<mask[1];
int updateCounter=0;
QList<int> initial_beads_x, initial_beads_y, initial_beads_z;
QVector<double> segmentation_levels;
// FIND INITIAL BEAD POSITIONS
updateCounter=0;
if (dlgEvaluationProgress) {
dlgEvaluationProgress->setMinorPrgressLabel(tr("finding beads in 3D stack ... "));
dlgEvaluationProgress->setMinorProgressRange(ROIz/2, (size_z-ROIz/2)*2);
dlgEvaluationProgress->addMessage(tr("evaluating stacke '%1'").arg(record->getName()));
dlgEvaluationProgress->addMessage(tr(" * searching for beads ..."));
}
for (int z=ROIz/2+2; z<size_z-ROIz/2-2; z=z+zsteps) {
if (dlgEvaluationProgress) dlgEvaluationProgress->setMinorProgress(z);
double* frame=data->getImageStack(stack, z, 0);
// DETERMINE level for SEGMENTATION
double level=0;
if (mask && useMask) level=statisticsQuantileMasked(mask, frame, width*height, 1.0-double(pixels_per_frame)/double(width*height), false);
else level=statisticsQuantile(frame, width*height, 1.0-double(pixels_per_frame)/double(width*height));
//qDebug()<<"step "<<z<<" level="<<level<<mask<<useMask<<frame<<width*height<<1.0-double(pixels_per_frame)/double(width*height);
segmentation_levels<<level;
const int lx=ceil(double(ROIxy)/2.0);
const int ly=lx;
double* frame2=frame;
if (medianFilterBeforeFindBeads) {
double *median=qfMallocT<double>(width*height);
double *locals=qfMallocT<double>((2*lx+1)*(2*ly+1));
for (int y=0; y<height; y++) {
for (int x=0; x<width; x++) {
const int i=y*width+x;
unsigned int count=0;
for (int dy=0-ly;dy<ly; dy++) {
for (int dx=0-lx; dx<lx; dx++) {
const int nx=x+dx;
const int ny=y+dy;
const int ni=ny*width+nx;
if((nx>=0)&&(nx<width)&&(ny>=0)&&(ny<height)){
locals[count]=frame[ni];
count++;
}
}
}
median[i]=statisticsMedian(locals,count);
}
}
qfFree(locals);
frame2=qfMallocT<double>(width*height);
for (int y=0; y<height; y++) {
for (int x=0; x<width; x++) {
const int i=y*width+x;
frame2[i]=frame[i]/(0.1+median[i]);
}
}
qfFree( median);
level=statisticsQuantile(frame2, width*height, 1.0-double(pixels_per_frame)/double(width*height));
}
// FIND INITIAL BEADS by SEGMENTATION with level
QVector<int> pixs_x, pixs_y;
QVector<bool> ignored;
for (int y=0; y<height; y++) {
for (int x=0; x<width; x++) {
const int i=y*width+x;
if ((!useMask || !mask || !mask[i]) && x>ROIxy/2 && x<width-ROIxy/2 && y>ROIxy/2 && y<height-ROIxy/2) {
if(frame2[i]>=level){
pixs_x<<x;
pixs_y<<y;
ignored<<false;
//qDebug()<<" possible: "<<x<<y<<", level="<<level;
}
}
}
}
if (frame2!=frame && frame2) qfFree( frame2);
// SETUP DISTANCE MATRIX OF INITIAL BEADS
double* distance_matrix=qfCallocT<double>(pixs_x.size()*pixs_x.size());
for (int i=0; i<pixs_x.size(); i++) {
for (int j=0; j<pixs_x.size(); j++) {
distance_matrix[i*pixs_x.size()+j]=sqrt(qfSqr((double)pixs_x[i]-(double)pixs_x[j])+qfSqr((double)pixs_y[i]-(double)pixs_y[j]));
}
}
// FILTER DISTANCE MATRIX FOR MINIMUM DISTANCE
bool done=false;
while (!done) {
done=true;
// determine the nextPix to look at
int nextPix=0;
while (nextPix<pixs_x.size() && ignored[nextPix]) {
nextPix++;
}
//qDebug()<<" nextPix="<<nextPix;
if (nextPix<pixs_x.size()) {
int count=0;
// count beads in vicinity of the nextPix
double maxI=0;
int brightestIdx=-1;
QList<int> nearPixels;
for (int i=0; i<pixs_x.size(); i++) {
if (i!=nextPix && !ignored[i] && distance_matrix[nextPix*pixs_x.size()+i]<min_distance) {
count++;
if (brightestIdx<0) {
maxI=frame[i];
brightestIdx=i;
nearPixels<<i;
} else if (frame[i]>maxI) {
maxI=frame[i];
brightestIdx=i;
nearPixels<<i;
}
}
}
//qDebug()<<" count="<<count;
//qDebug()<<" brightestIdx="<<brightestIdx;
//qDebug()<<" maxI="<<maxI;
//qDebug()<<" nearPixels="<<nearPixels;
// if count==0: add bead
if (count==0) {
initial_beads_x<<pixs_x[nextPix];
initial_beads_y<<pixs_y[nextPix];
initial_beads_z<<z;
ignored[nextPix]=true;
done=false;
//qDebug()<<" added single-pix: "<<nextPix;
} else if (count>0 && brightestIdx>=0) { // if more beads: add the brightest and ignore the rest
initial_beads_x<<pixs_x[brightestIdx];
initial_beads_y<<pixs_y[brightestIdx];
initial_beads_z<<z;
ignored[brightestIdx]=true;
ignored[nextPix]=true;
for (int i=0; i<nearPixels.size(); i++) {
ignored[nearPixels[i] ]=true;
}
//qDebug()<<" added more-pix: "<<brightestIdx<<" ( "<<nearPixels.size()<<" more)";
done=false;
}
}
}
// filter output beads once again:
for (int i=initial_beads_x.size()-1; i>=0; i--) {
for (int j=0; j<i; j++) {
const double maxZ=double(ROIz)/2.0*deltaZ;
double d=sqrt(qfSqr(deltaXY*(initial_beads_x[i]-initial_beads_x[j]))+qfSqr(deltaXY*(initial_beads_y[i]-initial_beads_y[j]))+qfSqr(deltaZ*(initial_beads_z[i]-initial_beads_z[j])));
double dxy=sqrt(qfSqr(deltaXY*(initial_beads_x[i]-initial_beads_x[j]))+qfSqr(deltaXY*(initial_beads_y[i]-initial_beads_y[j])));
double dz=fabs(deltaZ*(initial_beads_z[i]-initial_beads_z[j]));
if (i!=j && ((d<min_distance*deltaXY) || (dz<maxZ && dxy<min_distance*deltaXY))) {
initial_beads_x.removeAt(i);
initial_beads_y.removeAt(i);
initial_beads_z.removeAt(i);
//qDebug()<<"removed bead i="<<i<<d<<min_distance*deltaXY<<double(ROIz)/2.0*deltaZ;
break;
}
}
}
qfFree(distance_matrix);
if (updateCounter%5==0) {
if (dlgEvaluationProgress) {
dlgEvaluationProgress->setMinorPrgressLabel(tr("finding beads in 3D stack ... found %1").arg(initial_beads_x.size()));
}
QApplication::processEvents();
}
if (dlgEvaluationProgress&& dlgEvaluationProgress->wasCanceled()) break;
updateCounter++;
}
//qDebug()<<"beads: "<<initial_beads_x.size();
if (!dlgEvaluationProgress || !dlgEvaluationProgress->wasCanceled()) {
if (dlgEvaluationProgress) dlgEvaluationProgress->addMessage(tr(" * found %1 beads.").arg(initial_beads_x.size()));
// write back fit results to record!
record->disableEmitResultsChanged();
record->resultsSetString(evalID, "dataorder", "beadslists");
record->resultsSetNumber(evalID, "pixel_size", deltaXY);
record->resultsSetNumber(evalID, "step_size", deltaZ);
record->resultsSetBoolean(evalID, "mask_use", useMask);
record->resultsSetInteger(evalID, "initial_beads_found", initial_beads_x.size());
record->resultsSetInteger(evalID, "roi_size_xy", ROIxy);
record->resultsSetInteger(evalID, "roi_size_z", ROIz);
record->resultsSetInteger(evalID, "beadsearch_zstep_size", zsteps);
record->resultsSetInteger(evalID, "beadsearch_pixels_per_frame", pixels_per_frame);
record->resultsSetInteger(evalID, "masked_pixels_per_frame", maskedPixels);
record->resultsSetNumberList(evalID, "beadsearch_segmentation_levels", segmentation_levels);
record->resultsSetNumberList(evalID, "beadsearch_initial_positions_x", initial_beads_x);
record->resultsSetNumberList(evalID, "beadsearch_initial_positions_y", initial_beads_y);
record->resultsSetNumberList(evalID, "beadsearch_initial_positions_z", initial_beads_z);
record->enableEmitResultsChanged();
if (dlgEvaluationProgress) {
dlgEvaluationProgress->setMinorProgressRange(0, channels*initial_beads_x.size());
dlgEvaluationProgress->setMinorPrgressLabel(tr("evaluating %1 beads ...").arg(initial_beads_x.size()));
}
QApplication::processEvents();
// EVALUATE BEADS IN STACK
updateCounter=0;
for (int c=0; c<channels; c++) {
cimg_library::CImg<double> image(data->getImageStack(stack, 0, c), width, height, size_z, true);
if (dlgEvaluationProgress) dlgEvaluationProgress->addMessage(tr(" * evaluating beads in channel %1 ...").arg(c+1));
for (int b=0; b<initial_beads_x.size(); b++) {
if (dlgEvaluationProgress) dlgEvaluationProgress->setMinorProgress(c*initial_beads_x.size()+b);
// CUT ROI AROUND PIXEL
cimg_library::CImg<double> roi=image.get_crop(initial_beads_x[b]-ROIxy/2, initial_beads_y[b]-ROIxy/2, initial_beads_z[b]-ROIz/2, initial_beads_x[b]+ROIxy/2, initial_beads_y[b]+ROIxy/2, initial_beads_z[b]+ROIz/2);
QVector<bool> msk(roi.width()*roi.height(), false);
if (mask && useMask) {
int iy=0;
for (int y=initial_beads_y[b]-ROIxy/2; y<=initial_beads_y[b]+ROIxy/2; y++) {
int ix=0;
for (int x=initial_beads_x[b]-ROIxy/2; x<=initial_beads_x[b]+ROIxy/2; x++) {
msk[iy*roi.width()+ix]=mask[y*image.width()+x];
ix++;
}
iy++;
}
}
//roi.save_tiff(QString("c:\\temp\\roi_c%1_b%2.tif").arg(c).arg(b).toLatin1().data());
// COORDINATES OF TOP-LEFT CORNER OF ROI
const double x0tl=double(initial_beads_x[b]-ROIxy/2)*deltaXY;
const double y0tl=double(initial_beads_y[b]-ROIxy/2)*deltaXY;
const double z0tl=double(initial_beads_z[b]-ROIz/2)*deltaZ;
// COORDINATES OF THE CENTER OF ROI in absolute nanometers
const double x0=double(initial_beads_x[b])*deltaXY;
const double y0=double(initial_beads_y[b])*deltaXY;
const double z0=double(initial_beads_z[b])*deltaZ;
// COORDINATES OF THE CENTER OF ROI as index into ROI
const int x0i=ROIxy/2;
const int y0i=ROIxy/2;
const int z0i=ROIz/2;
// absolute X,Y,Z coordinates (in nanometers) of the ROI
QVector<double> X, Y, Z, roiXYZ;
//qfGridXYZ(X, Y, Z, x0tl, y0tl, z0tl, roi.width(), roi.height(), roi.depth(), deltaXY, deltaXY, deltaZ);
for (int z=0; z<roi.depth(); z++) {
for (int y=0; y<roi.height(); y++) {
for (int x=0; x<roi.width(); x++) {
if (!useMask || !msk[y*roi.width()+x]){
X<<(x0tl+double(x)*deltaXY);
Y<<(y0tl+double(y)*deltaXY);
Z<<(z0tl+double(z)*deltaZ);
roiXYZ<<roi(x,y,z);
}
}
}
}
// cuts through center pixel with x-coordinate vectors
QVector<double> cutX(roi.width()); //=image.get_crop(0, y0i, z0i, roi.width()-1, y0i, z0i).unroll('x');
QVector<double> cutXX;
qfGridX(cutXX, x0tl, roi.width(), deltaXY);
int cutXN=0;
for (int i=0; i<cutX.size(); i++) {
if (!useMask || !msk[y0i*roi.width()+i]){
cutX[cutXN]=roi(i, y0i, z0i);
cutXX[cutXN]=cutXX[i];
cutXN++;
}
}
QVector<double> cutY(roi.height()); //=image.get_crop(x0i, 0, z0i, x0i, roi.height()-1, z0i).unroll('x');
QVector<double> cutYX;
int cutYN=0;
qfGridX(cutYX, y0tl, roi.height(), deltaXY);
for (int i=0; i<cutY.size(); i++) {
if (!useMask || !msk[i*roi.width()+x0i]){
cutY[cutYN]=roi(x0i, i, z0i);
cutYX[cutYN]=cutYX[i];
cutYN++;
}
}
QVector<double> cutZ(roi.depth()); //=image.get_crop(x0i, y0i, 0, x0i, y0i, roi.depth()-1).unroll('x');
QVector<double> cutZX;
qfGridX(cutZX, z0tl, roi.depth(), deltaZ);
int cutZN=0;
for (int i=0; i<cutZ.size(); i++) {
if (!useMask || !msk[y0i*roi.width()+x0i]){
cutZ[cutZN]=roi(x0i, y0i, i);
cutZX[cutZN]=cutZX[i];
cutZN++;
}
}
// estimate initial params
double init_background=qfstatisticsAverage(constructQVectorFromItems(
statisticsQuantile(cutX.data(), cutXN, 0.1),
statisticsQuantile(cutY.data(), cutYN, 0.1),
statisticsQuantile(cutZ.data(), cutZN, 0.1))
);
double init_amplitude=qfstatisticsAverage(constructQVectorFromItems(
statisticsMax(cutX.data(), cutXN),
statisticsMax(cutY.data(), cutYN),
statisticsMax(cutZ.data(), cutZN))
)-init_background;
double init_w12=est_psf_width;
double init_w3=est_psf_height;
// fit X-cut
QVector<double> cutXP=ff1D->getInitialParamValues();
int cutXi=-1;
for (int i=0; i<cutXP.size(); i++) {
if (ff1D->getParameterID(i)=="offset") cutXP[i]=init_background;
else if (ff1D->getParameterID(i)=="amplitude") cutXP[i]=init_amplitude;
else if (ff1D->getParameterID(i)=="position") cutXP[i]=x0;
else if (ff1D->getParameterID(i)=="width") { cutXi=i; cutXP[i]=init_w12; }
}
alg->fit(cutXP.data(), NULL, cutXX.data(), cutX.data(), NULL, cutXN, ff1D, cutXP.data(), NULL, ff1Dmin.data(), ff1Dmax.data());
// fit Y-cut
QVector<double> cutYP=ff1D->getInitialParamValues();
int cutYi=-1;
for (int i=0; i<cutYP.size(); i++) {
if (ff1D->getParameterID(i)=="offset") cutYP[i]=init_background;
else if (ff1D->getParameterID(i)=="amplitude") cutYP[i]=init_amplitude;
else if (ff1D->getParameterID(i)=="position") cutYP[i]=y0;
else if (ff1D->getParameterID(i)=="width") {cutYi=i; cutYP[i]=init_w12; }
}
alg->fit(cutYP.data(), NULL, cutYX.data(), cutY.data(), NULL, cutYN, ff1D, cutYP.data(), NULL, ff1Dmin.data(), ff1Dmax.data());
// fit Z-cut
QVector<double> cutZP=ff1D->getInitialParamValues();
int cutZi=-1;
for (int i=0; i<cutZP.size(); i++) {
if (ff1D->getParameterID(i)=="offset") cutZP[i]=init_background;
else if (ff1D->getParameterID(i)=="amplitude") cutZP[i]=init_amplitude;
else if (ff1D->getParameterID(i)=="position") cutZP[i]=z0;
else if (ff1D->getParameterID(i)=="width") { cutZi=i; cutZP[i]=init_w3; }
}
alg->fit(cutZP.data(), NULL, cutZX.data(), cutZ.data(), NULL, cutZN, ff1D, cutZP.data(), NULL, ff1Dmin.data(), ff1Dmax.data());
// fit X/Y-cuts along Z-axis
QVector<double> zpos, fitZX_width, fitZY_width;
for (int z=z0i-ceil(double(ROIz)*fitXY_Z_fraction/2.0); z<=z0i+ceil(double(ROIz)*fitXY_Z_fraction/2.0); z++) {
zpos<<(z0+double(z)*deltaZ);
// fit X-cut
cutXN=0;
for (int i=0; i<cutX.size(); i++) {
if (!useMask || !msk[y0i*roi.width()+i]){
cutX[cutXN]=roi(i, y0i, z);
cutXN++;
}
}
QVector<double> cutZXP=ff1D->getInitialParamValues();
int wid=-1;
for (int i=0; i<cutZXP.size(); i++) {
if (ff1D->getParameterID(i)=="offset") cutZXP[i]=init_background;
else if (ff1D->getParameterID(i)=="amplitude") cutZXP[i]=init_amplitude;
else if (ff1D->getParameterID(i)=="position") cutZXP[i]=x0;
else if (ff1D->getParameterID(i)=="width") { wid=i; cutZXP[i]=init_w12; }
}
alg->fit(cutZXP.data(), NULL, cutXX.data(), cutX.data(), NULL, cutXN, ff1D, cutZXP.data(), NULL, ff1Dmin.data(), ff1Dmax.data());
fitZX_width<<cutZXP[wid];
// fit Y-cut
cutYN=0;
for (int i=0; i<cutY.size(); i++) {
if (!useMask || !msk[i*roi.width()+x0i]){
cutY[cutYN]=roi(x0i, i, z);
cutYN++;
}
}
QVector<double> cutZYP=ff1D->getInitialParamValues();
wid=-1;
for (int i=0; i<cutZYP.size(); i++) {
if (ff1D->getParameterID(i)=="offset") cutZYP[i]=init_background;
else if (ff1D->getParameterID(i)=="amplitude") cutZYP[i]=init_amplitude;
else if (ff1D->getParameterID(i)=="position") cutZYP[i]=y0;
else if (ff1D->getParameterID(i)=="width") {wid=i; cutZYP[i]=init_w12; }
}
alg->fit(cutZYP.data(), NULL, cutYX.data(), cutY.data(), NULL, cutYN, ff1D, cutZYP.data(), NULL, ff1Dmin.data(), ff1Dmax.data());
fitZY_width<<cutZYP[wid];
}
// fit gaussian beam width to X/Y cut results
QVector<double> fitXZCutResults=ffGBwidth->getInitialParamValues();
QVector<double> fitYZCutResults=ffGBwidth->getInitialParamValues();
ffGBwidth->estimateInitial(fitXZCutResults.data(), zpos.data(), fitZX_width.data(), zpos.size(), NULL);
ffGBwidth->estimateInitial(fitYZCutResults.data(), zpos.data(), fitZY_width.data(), zpos.size(), NULL);
for (int i=0; i<fitXZCutResults.size(); i++) {
if (ffGBwidth->getParameterID(i)=="zR") { fitXZCutResults[i]=init_w3; fitYZCutResults[i]=init_w3; }
else if (ffGBwidth->getParameterID(i)=="position") { fitXZCutResults[i]=z0; fitYZCutResults[i]=z0; }
else if (ffGBwidth->getParameterID(i)=="w0") { fitXZCutResults[i]=init_w12; fitYZCutResults[i]=init_w12; }
}
alg->fit(fitXZCutResults.data(), NULL, zpos.data(), fitZX_width.data(), NULL, zpos.size(), ffGBwidth, fitXZCutResults.data(), NULL, ffGBwidthmin.data(), ffGBwidthmax.data());
alg->fit(fitYZCutResults.data(), NULL, zpos.data(), fitZY_width.data(), NULL, zpos.size(), ffGBwidth, fitYZCutResults.data(), NULL, ffGBwidthmin.data(), ffGBwidthmax.data());
// fit XYZ-stack to 3D model
QVector<double> fit3DP=ff3D->getInitialParamValues();
int xposi=-1, yposi=-1, zposi=-1;
int widi1=-1, widi2=-1, widi3=-1;
for (int i=0; i<fit3DP.size(); i++) {
if (ff3D->getParameterID(i)=="offset") fit3DP[i]=init_background;
else if (ff3D->getParameterID(i)=="amplitude") fit3DP[i]=init_amplitude;
else if (ff3D->getParameterID(i)=="position_x") {xposi=i; fit3DP[i]=x0;}
else if (ff3D->getParameterID(i)=="position_y") {yposi=i; fit3DP[i]=y0;}
else if (ff3D->getParameterID(i)=="position_z") {zposi=i; fit3DP[i]=z0;}
else if (ff3D->getParameterID(i)=="width1") { widi1=i; fit3DP[i]=init_w12; }
else if (ff3D->getParameterID(i)=="width2") { widi2=i; fit3DP[i]=init_w12; }
else if (ff3D->getParameterID(i)=="width3") { widi3=i; fit3DP[i]=init_w3; }
}
//qDebug()<<"c="<<c<<" b="<<b;
//qDebug()<<"init: "<<fit3DP;
alg->fit3D(fit3DP.data(), NULL, X.data(), Y.data(), Z.data(), roiXYZ.data(), NULL, roiXYZ.size(), ff3D, fit3DP.data(), NULL, ff3Dmin.data(), ff3Dmax.data());
//qDebug()<<"fit: "<<fit3DP<<"\n\n";
QVector<double> axialRatios, axialRatios3D;
if (cutXi>=0 && cutZi>=0) {
axialRatios<<cutZP[cutZi]/cutXP[cutXi];
}
if (cutYi>=0 && cutZi>=0) {
axialRatios<<cutZP[cutZi]/cutYP[cutYi];
}
if (widi1>=0 && widi3>=0) {
axialRatios3D<<fit3DP[widi3]/fit3DP[widi1];
}
if (widi2>=0 && widi3>=0) {
axialRatios3D<<fit3DP[widi3]/fit3DP[widi2];
}
if (updateCounter%1==0) {
if (dlgEvaluationProgress) dlgEvaluationProgress->setMinorPrgressLabel(tr("evaluating beads ... (channel: %1/%4, bead: %2/%3)").arg(c+1).arg(b+1).arg(initial_beads_x.size()+1).arg(channels));
QApplication::processEvents();
}
if (dlgEvaluationProgress&& dlgEvaluationProgress->wasCanceled()) break;
updateCounter++;
record->disableEmitResultsChanged();
record->resultsSetNumber(evalID, QString("channel%1_beads").arg(c), b+1);
record->resultsSetString(evalID, QString("cutx_fitfunction"), ff1D->id());
record->resultsSetStringList(evalID, QString("cutx_fitfunction_parameternames"), ff1D->getParameterIDs());
record->resultsSetString(evalID, QString("cuty_fitfunction"), ff1D->id());
record->resultsSetStringList(evalID, QString("cuty_fitfunction_parameternames"), ff1D->getParameterIDs());
record->resultsSetString(evalID, QString("cutz_fitfunction"), ff1D->id());
record->resultsSetStringList(evalID, QString("cutz_fitfunction_parameternames"), ff1D->getParameterIDs());
record->resultsSetString(evalID, QString("fit3d_fitfunction"), ff3D->id());
record->resultsSetStringList(evalID, QString("fit3d_fitfunction_parameternames"), ff3D->getParameterIDs());
record->resultsSetString(evalID, QString("cutxz_gaussianbeam_fitfunc"), ffGBwidth->id());
record->resultsSetStringList(evalID, QString("cutxz_gaussianbeam_parameternames"), ffGBwidth->getParameterIDs());
record->resultsSetString(evalID, QString("cutyz_gaussianbeam_fitfunc"), ffGBwidth->id());
record->resultsSetStringList(evalID, QString("cutyz_gaussianbeam_parameternames"), ffGBwidth->getParameterIDs());
for (int pi=0; pi<cutXP.size(); pi++) {
record->resultsSetInNumberList(evalID, QString("channel%1_cutx_fitresult_%2").arg(c).arg(ff1D->getParameterID(pi)), b, cutXP[pi]);
record->resultsSetInNumberList(evalID, QString("channel%1_cuty_fitresult_%2").arg(c).arg(ff1D->getParameterID(pi)), b, cutYP[pi]);
record->resultsSetInNumberList(evalID, QString("channel%1_cutz_fitresult_%2").arg(c).arg(ff1D->getParameterID(pi)), b, cutZP[pi]);
}
for (int pi=0; pi<fitXZCutResults.size(); pi++) {
record->resultsSetInNumberList(evalID, QString("channel%1_cutxz_gaussianbeam_results_%2").arg(c).arg(ffGBwidth->getParameterID(pi)), b, fitXZCutResults[pi]);
record->resultsSetInNumberList(evalID, QString("channel%1_cutyz_gaussianbeam_results_%2").arg(c).arg(ffGBwidth->getParameterID(pi)), b, fitYZCutResults[pi]);
}
for (int pi=0; pi<axialRatios.size(); pi++) {
record->resultsSetInNumberList(evalID, QString("channel%1_fits_axialratios_%2").arg(c).arg(pi), b, axialRatios[pi]);
}
for (int pi=0; pi<axialRatios3D.size(); pi++) {
record->resultsSetInNumberList(evalID, QString("channel%1_fits_axialratios_3d_%2").arg(c).arg(pi), b, axialRatios3D[pi]);
}
for (int pi=0; pi<fit3DP.size(); pi++) {
record->resultsSetInNumberList(evalID, QString("channel%1_fit3d_results_%2").arg(c).arg(ff3D->getParameterID(pi)), b, fit3DP[pi]);
}
record->resultsSetNumberList(evalID, QString("channel%1_bead%2_cutxz_zpos").arg(c).arg(b), zpos);
record->resultsSetNumberList(evalID, QString("channel%1_bead%2_cutxz_width").arg(c).arg(b), fitZX_width);
record->resultsSetNumberList(evalID, QString("channel%1_bead%2_cutyz_zpos").arg(c).arg(b), zpos);
record->resultsSetNumberList(evalID, QString("channel%1_bead%2_cutyz_width").arg(c).arg(b), fitZY_width);
if (c>0 && xposi>=0 && yposi>=0 && zposi>=0) {
bool ok=true;
QVector<double> fitres0;
for (int pi=0; pi<ff3D->paramCount(); pi++) {
fitres0<<record->resultsGetInNumberList(evalID, QString("channel0_fit3d_results_%1").arg(ff3D->getParameterID(pi)), b, ff3D->getDescription(pi).initialValue);
}
if (ok && xposi<fitres0.size() && yposi<fitres0.size() && zposi<fitres0.size()) {
record->resultsSetInNumberList(evalID, QString("channel%1_fit3d_distc0_x").arg(c), b, (fitres0[xposi]-fit3DP[xposi]));
record->resultsSetInNumberList(evalID, QString("channel%1_fit3d_distc0_y").arg(c), b, (fitres0[yposi]-fit3DP[yposi]));
record->resultsSetInNumberList(evalID, QString("channel%1_fit3d_distc0_z").arg(c), b, (fitres0[zposi]-fit3DP[zposi]));
record->resultsSetInNumberList(evalID, QString("channel%1_fit3d_distc0_abs").arg(c), b, sqrt(qfSqr(fitres0[xposi]-fit3DP[xposi])+qfSqr(fitres0[yposi]-fit3DP[yposi])+qfSqr(fitres0[zposi]-fit3DP[zposi])));
/*QVector<double> d;
d<<(fitres0[xposi]-fit3DP[xposi]);
d<<(fitres0[yposi]-fit3DP[yposi]);
d<<(fitres0[zposi]-fit3DP[zposi]);
d<<sqrt(qfSqr(fitres0[xposi]-fit3DP[xposi])+qfSqr(fitres0[yposi]-fit3DP[yposi])+qfSqr(fitres0[zposi]-fit3DP[zposi]));
record->resultsSetNumberList(evalID, QString("channel%1_bead%2_fit3d_distc0").arg(0).arg(b), d);*/
}
}
record->enableEmitResultsChanged();
}
if (dlgEvaluationProgress&& dlgEvaluationProgress->wasCanceled()) break;
// write back fit results to record!
record->disableEmitResultsChanged();
record->resultsSetNumber(evalID, "channels", c+1);
record->enableEmitResultsChanged();
}
if (dlgEvaluationProgress) dlgEvaluationProgress->addMessage(tr(" * evaluation finished!"));
}
if (alg) delete alg;
alg=NULL;
if (ff1D) delete ff1D;
ff1D=NULL;
if (ff3D) delete ff3D;
ff3D=NULL;
}