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BscanFFT.cpp
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BscanFFT.cpp
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#ifdef _WIN64
#include "stdafx.h"
#include "windows.h"
// anything before a precompiled header is ignored,
// so no endif here! add #endif to compile on __unix__ !
#endif
#ifdef _WIN64
#include <qhyccd.h>
#endif
/*
* modified from ASKlive2.cpp
* and LiveFrameSampleFFT.cpp
*
*
* Implementing line scan FFT
* for SD OCT
* with binning
* and inputs from ini file.
*
* Captures (background) spectrum on receipt of b key
* Captures pi shifted or J0 frame on receipt of p key
* Saves frames on receipt of s key or spacebar
* Saves J0 null frame for subtraction on receipt of j key
* Clears the J0 thresholding mask on c key
*
* Do manual frame by frame averaging with ini file option
*
* Save individual frames on averaging if option chosen in ini file
*
* + (or =) key increases exposure time by 0.1 ms
* - (or _) key decreases exposure time by 0.1 ms
* u key increases exposure time by 1 ms
* d key decreases exposure time by 1 ms
* U key increases exposure time by 10 ms
* D key decreases exposure time by 10 ms
* A key toggles averaging
* Q key toggles clamping upper bound of displayed Bscan to 50 dB
* ] key increases thresholding in final Bscan
* [ key decreases thresholding in final Bscan
* 9 or ( key decreases the index of the reported ascan max value
* 0 or ) key increases the index of the reported ascan max value
*
* w decreases width of ROI for which avg val is reported, W increases width
* h decreases the height (position), H increases
* location of ROI is to the right of the index of reported ascan
* e toggles rEporting/plotting of ROI average intensity
*
* ESC, x or X key quits
*
*
*
* Hari Nandakumar
* 15 Sep 2018 *
*
*
*/
//#define _WIN64
//#define __unix__
#include <stdio.h>
#include <stdlib.h>
#ifdef __unix__
#include <unistd.h>
#include <libqhy/qhyccd.h>
#endif
#include <string.h>
#include <time.h>
#include <sys/stat.h>
// this is for mkdir
#include <opencv2/opencv.hpp>
// used the above include when imshow was being shown as not declared
// removing
// #include <opencv/cv.h>
// #include <opencv/highgui.h>
using namespace cv;
inline void normalizerows(Mat& src, Mat& dst, double lowerlim, double upperlim)
{
// https://stackoverflow.com/questions/10673715/how-to-normalize-rows-of-an-opencv-mat-without-a-loop
// for syntax _OutputArray(B.ptr(i), B.cols))
for (uint ii = 0; ii<src.rows; ii++)
{
normalize(src.row(ii), dst.row(ii), lowerlim, upperlim, NORM_MINMAX);
}
}
inline void printAvgROI(Mat bscandb, uint ascanat, uint vertposROI, uint widthROI, Mat& ROIplot, uint& ROIploti, Mat& statusimg)
{
Mat AvgROI;
Scalar meanVal;
uint heightROI = 3;
char textbuffer[80];
Mat lastrowofstatusimg = statusimg(Rect(0, 250, 600, 50)); // x,y,width,height
if (ascanat + widthROI<bscandb.cols)
{
bscandb(Rect(ascanat, vertposROI, widthROI, heightROI)).copyTo(AvgROI);
//imshow("ROI",AvgROI);
AvgROI.reshape(0, 1); // make it into a 1D array
meanVal = mean(AvgROI);
//printf("Mean of ROI at %d = %f dB\n", ascanat, meanVal(0));
sprintf(textbuffer, "Mean of ROI at %d = %f dB", ascanat, meanVal(0));
lastrowofstatusimg = Mat::zeros(cv::Size(600, 50), CV_64F);
putText(statusimg, textbuffer, Point(0, 280), FONT_HERSHEY_SIMPLEX, 1, Scalar(255, 255, 255), 3, 1);
imshow("Status", statusimg);
// in ROIplot, we take the range to be 0 to 50 dB
// this is mapped to 0 to 300 vertical pixels
uint vertindex = uint(abs(6 * floor(meanVal(0))));
if (vertindex < 300)
vertindex = 300 - vertindex; // since Mat is shown 0th row on top with imshow
ROIplot.col(ROIploti) = Scalar::all(0);
for (int smalloopi = -2; smalloopi < 4; smalloopi++)
{
if ((vertindex + smalloopi) > 0)
if ((vertindex + smalloopi) < 300)
ROIplot.at<double>(vertindex + smalloopi, ROIploti) = 1;
}
imshow("ROI intensity", ROIplot);
if (ROIploti < 599)
ROIploti++;
else
ROIploti = 0;
}
else
sprintf(textbuffer, "ascanat+widthROI > width of image!");
lastrowofstatusimg = Mat::zeros(cv::Size(600, 50), CV_64F);
putText(statusimg, textbuffer, Point(0, 280), FONT_HERSHEY_SIMPLEX, 1, Scalar(255, 255, 255), 3, 1);
imshow("Status", statusimg);
}
inline void printMinMaxAscan(Mat bscandb, uint ascanat, int numdisplaypoints, Mat& statusimg)
{
Mat ascan, ascandisp;
double minVal, maxVal;
char textbuffer[80];
Mat thirdrowofstatusimg = statusimg(Rect(0, 150, 600, 50));
Mat fourthrowofstatusimg = statusimg(Rect(0, 200, 600, 50));
bscandb.col(ascanat).copyTo(ascan);
ascan.row(4).copyTo(ascan.row(1)); // masking out the DC in the display
ascan.row(4).copyTo(ascan.row(0));
ascan.row(4).copyTo(ascan.row(2));
ascan.row(4).copyTo(ascan.row(3));
ascandisp = ascan.rowRange(0, numdisplaypoints);
//debug
//normalize(ascan, ascandebug, 0, 1, NORM_MINMAX);
//imshow("debug", ascandebug);
minMaxLoc(ascandisp, &minVal, &maxVal);
sprintf(textbuffer, "Max of Ascan%d = %f dB", ascanat, maxVal);
thirdrowofstatusimg = Mat::zeros(cv::Size(600, 50), CV_64F);
putText(statusimg, textbuffer, Point(0, 180), FONT_HERSHEY_SIMPLEX, 1, Scalar(255, 255, 255), 3, 1);
sprintf(textbuffer, "Min of Ascan%d = %f dB", ascanat, minVal);
fourthrowofstatusimg = Mat::zeros(cv::Size(600, 50), CV_64F);
putText(statusimg, textbuffer, Point(0, 230), FONT_HERSHEY_SIMPLEX, 1, Scalar(255, 255, 255), 3, 1);
imshow("Status", statusimg);
}
inline void makeonlypositive(Mat& src, Mat& dst)
{
// from https://stackoverflow.com/questions/48313249/opencv-convert-all-negative-values-to-zero
max(src, 0, dst);
}
inline Mat zeropadrowwise(Mat sm, int sn)
{
// increase fft points sn times
// newnumcols = numcols*sn;
// by fft, zero padding, and then inv fft
// returns CV_64F
// guided by https://stackoverflow.com/questions/10269456/inverse-fourier-transformation-in-opencv
// inspired by Drexler & Fujimoto 2nd ed Section 5.1.10
// needs fftshift implementation for the zero pad to work correctly if done on borders.
// or else adding zeros directly to the higher frequencies.
// freqcomplex=fftshift(fft(signal));
// zp2=4*ifft(ifftshift(zpfreqcomplex));
// result of this way of zero padding in the fourier domain is to resample the same min / max range
// at a higher sampling rate in the initial domain.
// So this improves the k linear interpolation.
Mat origimage;
Mat fouriertransform, fouriertransformzp;
Mat inversefouriertransform;
int numrows = sm.rows;
int numcols = sm.cols;
int newnumcols = numcols * sn;
sm.convertTo(origimage, CV_32F);
dft(origimage, fouriertransform, DFT_SCALE | DFT_COMPLEX_OUTPUT | DFT_ROWS);
// implementing fftshift row-wise
// like https://docs.opencv.org/2.4/doc/tutorials/core/discrete_fourier_transform/discrete_fourier_transform.html
int cx = fouriertransform.cols / 2;
// here we assume fouriertransform.cols is even
Mat LHS(fouriertransform, Rect(0, 0, cx, fouriertransform.rows)); // Create a ROI per half
Mat RHS(fouriertransform, Rect(cx, 0, cx, fouriertransform.rows)); // Rect(topleftx, toplefty, w, h),
// OpenCV typically assumes that the top and left boundary of the rectangle are inclusive, while the right and bottom boundaries are not.
// https://docs.opencv.org/3.2.0/d2/d44/classcv_1_1Rect__.html
Mat tmp; // swap LHS & RHS
LHS.copyTo(tmp);
RHS.copyTo(LHS);
tmp.copyTo(RHS);
copyMakeBorder(fouriertransform, fouriertransformzp, 0, 0, floor((newnumcols - numcols) / 2), floor((newnumcols - numcols) / 2), BORDER_CONSTANT, 0.0);
// this does the zero pad - copyMakeBorder(src, dest, top, bottom, left, right, borderType, value)
// Now we do the ifftshift before ifft
cx = fouriertransformzp.cols / 2;
Mat LHSzp(fouriertransformzp, Rect(0, 0, cx, fouriertransformzp.rows)); // Create a ROI per half
Mat RHSzp(fouriertransformzp, Rect(cx, 0, cx, fouriertransformzp.rows)); // Rect(topleftx, toplefty, w, h)
LHSzp.copyTo(tmp);
RHSzp.copyTo(LHSzp);
tmp.copyTo(RHSzp);
dft(fouriertransformzp, inversefouriertransform, DFT_INVERSE | DFT_REAL_OUTPUT | DFT_ROWS);
inversefouriertransform.convertTo(inversefouriertransform, CV_64F);
return inversefouriertransform;
}
inline Mat smoothmovavg(Mat sm, int sn)
{
// smooths each row of Mat m using 2n+1 point weighted moving average
// x(p) = ( x(p-n) + x(p-n+1) + .. + 2*x(p) + x(p+1) + ... + x(p+n) ) / 2*(n+1)
// The window size is truncated at the edges.
// can see https://docs.opencv.org/2.4/doc/tutorials/core/how_to_scan_images/how_to_scan_images.html#howtoscanimagesopencv
// for efficient ways
// accept only double type matrices
// sm needs to be CV_64FC1
CV_Assert(sm.depth() == CV_64F);
Mat sresult;
sm.copyTo(sresult); // initializing size of result
int smaxcols = sm.cols;
int smaxrows = sm.rows;
double ssum;
int sindexi;
double* srcptr;
double* destptr;
for (int si = 0; si < smaxrows; si++)
{
srcptr = sm.ptr<double>(si);
destptr = sresult.ptr<double>(si);
for (int sj = 0; sj < smaxcols; sj++)
{
ssum = 0;
for (int sk = -sn; sk < (sn + 1); sk++)
{
// address as m.at<double>(y, x); ie (row,column)
sindexi = sj + sk;
if ((sindexi > -1) && (sindexi < smaxcols)) // truncate window
ssum = ssum + srcptr[sindexi]; //equivalent to ssum = ssum + sm.at<double>(si,sindexi);
else
ssum = ssum + srcptr[sj]; // when window is truncated,
// weight of original point increases
}
// we want to add m.at<double>(i,j) once again, since its weight is 2
ssum = ssum + srcptr[sj];
destptr[sj] = ssum / 2 / (sn + 1); //equivalent to sresult.at<double>(si,sj) = ssum / (2 * (sn+1) );
}
}
return sresult;
}
inline void savematasimage(char* p, char* d, char* f, Mat m)
{
// saves a Mat m using imwrite as filename f appending .png, both windows and unix versions
// p=pathname, d=dirname, f=filename
#ifdef __unix__
strcpy(p, d);
strcat(p, "/");
strcat(p, f);
strcat(p, ".png");
imwrite(p, m);
#else
strcpy(p, d);
strcat(p, "\\"); // imwrite needs path with \\ separators, not /, on windows
strcat(p, f);
strcat(p, ".png");
imwrite(p, m);
#endif
}
// the next function saves a Mat m as variablename f by dumping to outfile o, both windows and unix versions
#ifdef __unix__
inline void savematasdata(std::ofstream& o, char* f, Mat m)
{
// saves a Mat m as variable named f in Matlab m file format
o << f << "=";
o << m;
o << ";" << std::endl;
}
#else
inline void savematasdata(cv::FileStorage& o, char* f, Mat m)
{
// saves Mat m by serializing to xml as variable named f
o << f << m;
}
#endif
int main(int argc, char *argv[])
{
int num = 0;
qhyccd_handle *camhandle = NULL;
int ret;
char id[32];
//char camtype[16];
int found = 0;
unsigned int w, h, bpp = 8, channels, cambitdepth = 16;
unsigned int offsetx = 0, offsety = 0;
unsigned int indexi, manualindexi, averages = 1, opw, oph;
uint indextemp;
//uint indextempl;
uint ascanat = 20;
uint averagestoggle = 1;
int camtime = 1, camgain = 1, camspeed = 1, cambinx = 2, cambiny = 2, usbtraffic = 10;
int camgamma = 1, binvalue = 1, normfactor = 1, normfactorforsave = 25;
int numfftpoints = 1024;
int numdisplaypoints = 512;
bool saveframes = 0;
bool manualaveraging = 0, saveinterferograms = 0;
unsigned int manualaverages = 1;
int movavgn = 0;
bool clampupper = 0;
bool ROIreport = 0;
bool doneflag = 0, skeypressed = 0, bkeypressed = 0, pkeypressed = 0;
bool jlockin = 0, jkeypressed = 0, ckeypressed = 0;
Mat jmask, jmaskt;
double lambdamin, lambdamax;
lambdamin = 816e-9;
lambdamax = 884e-9;
int mediann = 5;
uint increasefftpointsmultiplier = 1;
double bscanthreshold = -30.0;
bool rowwisenormalize = 0;
bool donotnormalize = 1;
w = 640;
h = 480;
int fps, key;
int t_start, t_end;
std::ifstream infile("BscanFFT.ini");
std::string tempstring;
char dirdescr[60];
sprintf(dirdescr, "_");
//namedWindow("linearized",0); // 0 = WINDOW_NORMAL
//moveWindow("linearized", 20, 500);
//namedWindow("Bscanl",0); // 0 = WINDOW_NORMAL
//moveWindow("Bscanl", 400, 0);
char dirname[80];
char filename[20];
char filenamec[20];
char pathname[140];
char lambdamaxstr[40];
char lambdaminstr[40];
struct tm *timenow;
time_t now = time(NULL);
// inputs from ini file
if (infile.is_open())
{
infile >> tempstring;
infile >> tempstring;
infile >> tempstring;
// first three lines of ini file are comments
infile >> camgain;
infile >> tempstring;
infile >> camtime;
infile >> tempstring;
infile >> bpp;
infile >> tempstring;
infile >> w;
infile >> tempstring;
infile >> h;
infile >> tempstring;
infile >> offsetx;
infile >> tempstring;
infile >> offsety;
infile >> tempstring;
infile >> camspeed;
infile >> tempstring;
infile >> cambinx;
infile >> tempstring;
infile >> cambiny;
infile >> tempstring;
infile >> usbtraffic;
infile >> tempstring;
infile >> binvalue;
infile >> tempstring;
infile >> dirdescr;
infile >> tempstring;
infile >> averages;
infile >> tempstring;
infile >> numfftpoints;
infile >> tempstring;
infile >> saveframes;
infile >> tempstring;
infile >> manualaveraging;
infile >> tempstring;
infile >> manualaverages;
infile >> tempstring;
infile >> saveinterferograms;
infile >> tempstring;
infile >> movavgn;
infile >> tempstring;
infile >> numdisplaypoints;
infile >> tempstring;
infile >> lambdaminstr;
infile >> tempstring;
infile >> lambdamaxstr;
infile >> tempstring;
infile >> mediann;
infile >> tempstring;
infile >> increasefftpointsmultiplier;
infile >> tempstring;
infile >> rowwisenormalize;
infile >> tempstring;
infile >> donotnormalize;
infile.close();
lambdamin = atof(lambdaminstr);
lambdamax = atof(lambdamaxstr);
averagestoggle = averages;
}
else std::cout << "Unable to open ini file, using defaults.";
namedWindow("show", 0); // 0 = WINDOW_NORMAL
moveWindow("show", 0, 0);
namedWindow("Bscan", 0); // 0 = WINDOW_NORMAL
moveWindow("Bscan", 800, 0);
namedWindow("Status", 0); // 0 = WINDOW_NORMAL
moveWindow("Status", 0, 500);
if (ROIreport)
{
namedWindow("ROI intensity", 0); // 0 = WINDOW_NORMAL
moveWindow("ROI intensity", 800, 500);
}
// debug
/*
char debugwinname[80];
namedWindow("debug1", 0); // 0 = WINDOW_NORMAL
moveWindow("debug1", 100, 600);
namedWindow("debug2", 0); // 0 = WINDOW_NORMAL
moveWindow("debug2", 200, 600);
namedWindow("debug3", 0); // 0 = WINDOW_NORMAL
moveWindow("debug3", 300, 600);
namedWindow("debug4", 0); // 0 = WINDOW_NORMAL
moveWindow("debug4", 400, 600);
namedWindow("debug5", 0); // 0 = WINDOW_NORMAL
moveWindow("debug5", 500, 600);
namedWindow("debug6", 0); // 0 = WINDOW_NORMAL
moveWindow("debug6", 600, 600);
namedWindow("debug7", 0); // 0 = WINDOW_NORMAL
moveWindow("debug7", 700, 600);
namedWindow("debug8", 0); // 0 = WINDOW_NORMAL
moveWindow("debug8", 800, 600);
namedWindow("debug9", 0); // 0 = WINDOW_NORMAL
moveWindow("debug9", 900, 600);
namedWindow("debug0", 0); // 0 = WINDOW_NORMAL
moveWindow("debug0", 0, 600);
* */
if (manualaveraging)
{
namedWindow("Bscanm", 0); // 0 = WINDOW_NORMAL
moveWindow("Bscanm", 800, 400);
}
/////////////////////////////////////
// init camera, variables, etc
cambitdepth = bpp;
opw = w / binvalue;
oph = h / binvalue;
float lambda0 = (lambdamin + lambdamax) / 2;
float lambdabw = lambdamax - lambdamin;
unsigned int vertposROI = 10, widthROI = 10;
Mat data_y(oph, opw, CV_64F); // the Mat constructor Mat(rows,columns,type)
Mat data_ylin(oph, numfftpoints, CV_64F);
Mat data_yb(oph, opw, CV_64F);
Mat data_yp(oph, opw, CV_64F);
Mat padded, paddedn;
Mat barthannwin(1, opw, CV_64F); // the Mat constructor Mat(rows,columns,type);
Mat baccum, manualaccum;
uint baccumcount, manualaccumcount;
// initialize data_yb with zeros
data_yb = Mat::zeros(Size(opw, oph), CV_64F); //Size(cols,rows)
data_yp = Mat::zeros(Size(opw, oph), CV_64F);
baccum = Mat::zeros(Size(opw, oph), CV_64F);
baccumcount = 0;
manualaccumcount = 0;
Mat bscansave0[100]; // allocate buffer to save frames, max 100
Mat bscansave1[100]; // one buffer is active while other is saved on skeypressed
Mat jscansave; // to save j frames
Mat bscanmanualsave0[100];
Mat bscanmanualsave1[100];
Mat interferogramsave0[100];
Mat interferogramsave1[100];
Mat interferogrambsave0[100];
Mat interferogrambsave1[100];
Mat bscansublog, positivediff;
bool zeroisactive = 1;
int nr, nc;
Mat m, opm, opmvector, bscan, bscanlog, bscandb, bscandisp, bscandispmanual, bscantemp, bscantemp2, bscantemp3, bscantransposed, chan[3];
Mat tempmat;
Mat bscandispj;
Mat mraw;
Mat ROIplot = Mat::zeros(cv::Size(600, 300), CV_64F);
uint ROIploti = 0;
Mat statusimg = Mat::zeros(cv::Size(600, 300), CV_64F);
Mat firstrowofstatusimg = statusimg(Rect(0, 0, 600, 50)); // x,y,width,height
Mat secrowofstatusimg = statusimg(Rect(0, 50, 600, 50));
Mat secrowofstatusimgRHS = statusimg(Rect(300, 50, 300, 50));
char textbuffer[80];
//Mat bscanl, bscantempl, bscantransposedl;
Mat magI, cmagI, cmagImanual;
//Mat magIl, cmagIl;
//double minbscan, maxbscan;
//double minbscanl, maxbscanl;
Scalar meanval;
Mat lambdas, k, klinear;
Mat diffk, slopes, fractionalk, nearestkindex;
double kmin, kmax;
double pi = 3.141592653589793;
double minVal, maxVal;
Mat ascan;
//minMaxLoc( m, &minVal, &maxVal, &minLoc, &maxLoc );
double deltalambda = (lambdamax - lambdamin) / data_y.cols;
klinear = Mat::zeros(cv::Size(1, numfftpoints), CV_64F);
fractionalk = Mat::zeros(cv::Size(1, numfftpoints), CV_64F);
nearestkindex = Mat::zeros(cv::Size(1, numfftpoints), CV_32S);
if (increasefftpointsmultiplier > 1)
{
lambdas = Mat::zeros(cv::Size(1, increasefftpointsmultiplier*data_y.cols), CV_64F); //Size(cols,rows)
diffk = Mat::zeros(cv::Size(1, increasefftpointsmultiplier*data_y.cols), CV_64F);
slopes = Mat::zeros(cv::Size(data_y.rows, increasefftpointsmultiplier*data_y.cols), CV_64F);
}
else
{
lambdas = Mat::zeros(cv::Size(1, data_y.cols), CV_64F); //Size(cols,rows)
diffk = Mat::zeros(cv::Size(1, data_y.cols), CV_64F);
slopes = Mat::zeros(cv::Size(data_y.rows, data_y.cols), CV_64F);
}
resizeWindow("Bscan", oph, numdisplaypoints); // (width,height)
for (indextemp = 0; indextemp<(increasefftpointsmultiplier*data_y.cols); indextemp++)
{
// lambdas = linspace(830e-9, 870e-9 - deltalambda, data_y.cols)
lambdas.at<double>(0, indextemp) = lambdamin + indextemp * deltalambda / increasefftpointsmultiplier;
}
k = 2 * pi / lambdas;
kmin = 2 * pi / (lambdamax - deltalambda);
kmax = 2 * pi / lambdamin;
double deltak = (kmax - kmin) / numfftpoints;
for (indextemp = 0; indextemp<(numfftpoints); indextemp++)
{
// klinear = linspace(kmin, kmax, numfftpoints)
klinear.at<double>(0, indextemp) = kmin + (indextemp + 1)*deltak;
}
//for (indextemp=0; indextemp<(data_y.cols); indextemp++)
//{
//printf("k=%f, klin=%f\n", k.at<double>(0,indextemp), klinear.at<double>(0,indextemp));
//}
for (indextemp = 1; indextemp<(increasefftpointsmultiplier*data_y.cols); indextemp++)
{
//find the diff of the non-linear ks
// since this is a decreasing series, RHS is (i-1) - (i)
diffk.at<double>(0, indextemp) = k.at<double>(0, indextemp - 1) - k.at<double>(0, indextemp);
//printf("i=%d, diffk=%f \n", indextemp, diffk.at<double>(0,indextemp));
}
// and initializing the first point separately
diffk.at<double>(0, 0) = diffk.at<double>(0, 1);
for (int f = 0; f < numfftpoints; f++)
{
// find the index of the nearest k value, less than the linear k
for (indextemp = 0; indextemp < increasefftpointsmultiplier*data_y.cols; indextemp++)
{
//printf("Before if k=%f,klin=%f \n",k.at<double>(0,indextemp),klinear.at<double>(0,f));
if (k.at<double>(0, indextemp) < klinear.at<double>(0, f))
{
nearestkindex.at<int>(0, f) = indextemp;
//printf("After if k=%f,klin=%f,nearestkindex=%d\n",k.at<double>(0,indextemp),klinear.at<double>(0,f),nearestkindex.at<int>(0,f));
break;
} // end if
} //end indextemp loop
} // end f loop
for (int f = 0; f < numfftpoints; f++)
{
// now find the fractional amount by which the linearized k value is greater than the next lowest k
fractionalk.at<double>(0, f) = (klinear.at<double>(0, f) - k.at<double>(0, nearestkindex.at<int>(0, f))) / diffk.at<double>(0, nearestkindex.at<int>(0, f));
//printf("f=%d, klinear=%f, diffk=%f, k=%f, nearesti=%d\n",f, klinear.at<double>(0,f), diffk.at<double>(0,nearestkindex.at<int>(0,f)), k.at<double>(0,nearestkindex.at<int>(0,f)),nearestkindex.at<int>(0,f) );
//printf("f=%d, fractionalk=%f\n",f, fractionalk.at<double>(0,f));
}
timenow = localtime(&now);
strftime(dirname, sizeof(dirname), "%Y-%m-%d_%H_%M_%S-", timenow);
strcat(dirname, dirdescr);
#ifdef _WIN64
CreateDirectoryA(dirname, NULL);
cv::FileStorage outfile;
sprintf(filename, "BscanFFT.xml");
strcpy(pathname, dirname);
strcat(pathname, "\\");
strcat(pathname, filename);
outfile.open(pathname, cv::FileStorage::WRITE);
#else
mkdir(dirname, 0755);
#endif
#ifdef __unix__
sprintf(filename, "BscanFFT.m");
strcpy(pathname, dirname);
strcat(pathname, "/");
strcat(pathname, filename);
std::ofstream outfile(pathname);
#endif
ret = InitQHYCCDResource();
if (ret != QHYCCD_SUCCESS)
{
printf("Init SDK not successful!\n");
}
num = ScanQHYCCD();
if (num > 0)
{
printf("Found QHYCCD,the num is %d \n", num);
}
else
{
printf("QHYCCD camera not found, please check the usb cable.\n");
goto failure;
}
for (int i = 0; i < num; i++)
{
ret = GetQHYCCDId(i, id);
if (ret == QHYCCD_SUCCESS)
{
//printf("connected to the first camera from the list,id is %s\n",id);
found = 1;
break;
}
}
if (found != 1)
{
printf("The camera is not QHYCCD or other error \n");
goto failure;
}
if (found == 1)
{
camhandle = OpenQHYCCD(id);
if (camhandle != NULL)
{
//printf("Open QHYCCD success!\n");
}
else
{
printf("Open QHYCCD failed \n");
goto failure;
}
ret = SetQHYCCDStreamMode(camhandle, 1);
ret = InitQHYCCD(camhandle);
if (ret == QHYCCD_SUCCESS)
{
//printf("Init QHYCCD success!\n");
}
else
{
printf("Init QHYCCD fail code:%d\n", ret);
goto failure;
}
ret = IsQHYCCDControlAvailable(camhandle, CONTROL_TRANSFERBIT);
if (ret == QHYCCD_SUCCESS)
{
ret = SetQHYCCDBitsMode(camhandle, cambitdepth);
if (ret != QHYCCD_SUCCESS)
{
printf("SetQHYCCDBitsMode failed\n");
getchar();
return 1;
}
}
ret = SetQHYCCDResolution(camhandle, offsetx, offsety, w, h); //handle, xpos,ypos,xwidth,ywidth
if (ret == QHYCCD_SUCCESS)
{
printf("Resolution set - width = %d height = %d\n", w, h);
}
else
{
printf("SetQHYCCDResolution fail\n");
goto failure;
}
ret = SetQHYCCDParam(camhandle, CONTROL_USBTRAFFIC, usbtraffic); //handle, parameter name, usbtraffic (which can be 0..100 perhaps)
if (ret == QHYCCD_SUCCESS)
{
//printf("CONTROL_USBTRAFFIC success!\n");
}
else
{
printf("CONTROL_USBTRAFFIC fail\n");
goto failure;
}
ret = SetQHYCCDParam(camhandle, CONTROL_SPEED, camspeed); //handle, parameter name, speed (which can be 0,1,2)
if (ret == QHYCCD_SUCCESS)
{
//printf("CONTROL_CONTROL_SPEED success!\n");
}
else
{
printf("CONTROL_CONTROL_SPEED fail\n");
goto failure;
}
ret = SetQHYCCDParam(camhandle, CONTROL_EXPOSURE, camtime); //handle, parameter name, exposure time (which is in us)
if (ret == QHYCCD_SUCCESS)
{
//printf("CONTROL_EXPOSURE success!\n");
}
else
{
printf("CONTROL_EXPOSURE fail\n");
goto failure;
}
ret = SetQHYCCDParam(camhandle, CONTROL_GAIN, camgain); //handle, parameter name, gain (which can be 0..99)
if (ret == QHYCCD_SUCCESS)
{
//printf("CONTROL_GAIN success!\n");
}
else
{
printf("CONTROL_GAIN fail\n");
goto failure;
}
ret = SetQHYCCDParam(camhandle, CONTROL_GAMMA, camgamma); //handle, parameter name, gamma (which can be 0..2 perhaps)
if (ret == QHYCCD_SUCCESS)
{
//printf("CONTROL_GAMMA success!\n");
}
else
{
printf("CONTROL_GAMMA fail\n");
goto failure;
}
if (cambitdepth == 8)
{
m = Mat::zeros(cv::Size(w, h), CV_8U);
mraw = Mat::zeros(cv::Size(w, h), CV_8U);
}
else // is 16 bit
{
m = Mat::zeros(cv::Size(w, h), CV_16U);
mraw = Mat::zeros(cv::Size(w, h), CV_16U);
}
ret = BeginQHYCCDLive(camhandle);
if (ret == QHYCCD_SUCCESS)
{
printf("BeginQHYCCDLive success!\n");
key = waitKey(300);
}
else
{
printf("BeginQHYCCDLive failed\n");
goto failure;
}
/////////////////////////////////////////
/////////////////////////////////////////
//outfile<<"%Data cube in MATLAB compatible format - m(h,w,slice)"<<std::endl;
doneflag = 0;
ret = SetQHYCCDParam(camhandle, CONTROL_EXPOSURE, camtime); //handle, parameter name, exposure time (which is in us)
if (ret == QHYCCD_SUCCESS)
{
sprintf(textbuffer, "Exp time = %d ", camtime);
secrowofstatusimg = Mat::zeros(cv::Size(600, 50), CV_64F);
putText(statusimg, textbuffer, Point(0, 80), FONT_HERSHEY_SIMPLEX, 1, Scalar(255, 255, 255), 3, 1);
imshow("Status", statusimg);
}
else
{
sprintf(textbuffer, "CONTROL_EXPOSURE failed");
secrowofstatusimg = Mat::zeros(cv::Size(600, 50), CV_64F);
putText(statusimg, textbuffer, Point(0, 80), FONT_HERSHEY_SIMPLEX, 1, Scalar(255, 255, 255), 3, 1);
imshow("Status", statusimg);
goto failure;
}
t_start = time(NULL);
fps = 0;
indexi = 0;
manualindexi = 0;
indextemp = 0;
bscantransposed = Mat::zeros(Size(numdisplaypoints, oph), CV_64F);
manualaccum = Mat::zeros(Size(oph, numdisplaypoints), CV_64F); // this is transposed version
//bscantransposedl = Mat::zeros(Size(opw/2, oph), CV_64F);
for (uint p = 0; p<(opw); p++)
{
// create modified Bartlett-Hann window
// https://in.mathworks.com/help/signal/ref/barthannwin.html
float nn = p;
float NN = opw - 1;
barthannwin.at<double>(0, p) = 0.62 - 0.48*std::abs(nn / NN - 0.5) + 0.38*std::cos(2 * pi*(nn / NN - 0.5));
}
while (1) //camera frames acquisition loop
{
ret = GetQHYCCDLiveFrame(camhandle, &w, &h, &bpp, &channels, mraw.data);
if (ret == QHYCCD_SUCCESS)
{
//median filter while the numbers are still int
if (mediann>0)
medianBlur(mraw, m, mediann);
else
mraw.copyTo(m);
resize(m, opm, Size(), 1.0 / binvalue, 1.0 / binvalue, INTER_AREA); // binning (averaging)
imshow("show", opm);
if (saveinterferograms)
{
// save mraw to active buffer
// inactive buffer is saved to disk when skeypressed
if (zeroisactive)
{
mraw.copyTo(interferogramsave0[indextemp]);
opm.copyTo(interferogrambsave0[indextemp]);
//printf("Saved to interferogramsave0[%d]\n",indextemp);
//sprintf(debugwinname,"debug%d",baccumcount);
//imshow(debugwinname,interferogramsave0[indextemp]);
//waitKey(30);
}
else
{
mraw.copyTo(interferogramsave1[indextemp]);
opm.copyTo(interferogrambsave1[indextemp]);
//printf("Saved to interferogramsave1[%d]\n",indextemp);
//sprintf(debugwinname,"debug%d",baccumcount);
//imshow(debugwinname,interferogramsave1[indextemp]);
//waitKey(30);
}
}
opm.convertTo(data_y, CV_64F); // initialize data_y
// smoothing by weighted moving average
if (movavgn > 0)
data_y = smoothmovavg(data_y, movavgn);
//transpose(opm, data_y); // void transpose(InputArray src, OutputArray dst)
// because we actually want the columns and not rows
// using DFT_ROWS
// But that has rolling shutter issues, so going back to rows
if (bkeypressed == 1)