ImageData ReadLUTFile(const char *lutfile)
{
PathSeperator sep(lutfile);
if(sep.extension == "jpg") {
return ReadJPEGFile(lutfile);
}
else {
std::string fn = lutfile;
fn = std::string(fn.begin(), fn.begin()+fn.find('#'));
std::string num( ++( sep.extension.begin() + sep.extension.find('#') ), sep.extension.end());
int lutIndex = atoi(num.c_str());
int nbeads, nplanes, nsteps;
FILE *f = fopen(fn.c_str(), "rb");
if (!f)
throw std::runtime_error("Can't open " + fn);
fread(&nbeads, 4, 1, f);
fread(&nplanes, 4, 1, f);
fread(&nsteps, 4, 1, f);
fseek(f, 12 + 4* (nsteps*nplanes * lutIndex), SEEK_SET);
ImageData lut = ImageData::alloc(nsteps,nplanes);
fread(lut.data, 4, nsteps*nplanes,f);
fclose(f);
lut.normalize();
return lut;
}
}
int main(int argc, char** argv)
{
timer *tic, *toc;
CImage *cimg=NULL;
Image *mask=NULL;
Histogram *hist=NULL;
if (argc != 4) {
fprintf(stderr,"usage: extrai_bic <image> <mask> <outputfile>\n");
exit(-1);
}
cimg = ReadJPEGFile(argv[1]);
mask = ReadImage(argv[2]);
tic = Tic();
hist = BIC(cimg, mask);
toc = Toc();
printf("BIC extracted in %f milliseconds\n\n",CTime(tic, toc));
FILE *fp;
fp = fopen(argv[3],"w");
if (fp == NULL) {
fprintf(stderr,"Cannot open %s\n",argv[3]);
exit(-1);
}
WriteFHist(hist, fp);
DestroyCImage(&cimg);
DestroyHistogram(&hist);
DestroyImage(&mask);
fclose(fp);
return(0);
}
void CorrectedRadialProfileTest()
{
// read image
const char* imgname = "SingleBead.jpg";
ImageData img = ReadJPEGFile(imgname);
// localize
CPUTracker trk(img.w,img.h);
trk.SetImageFloat(img.data);
vector2f com = trk.ComputeMeanAndCOM();
bool boundaryHit;
vector2f qi = trk.ComputeQI(com, 4, 64, 64,ANGSTEPF, 1, 30, boundaryHit);
dbgprintf("%s: COM: %f, %f. QI: %f, %f\n", imgname, com.x, com.y, qi.x, qi.y);
std::vector<float> angularProfile(128);
float asym = trk.ComputeAsymmetry(qi, 64, angularProfile.size(), 1, 30, &angularProfile[0]);
// ComputeAngularProfile(&angularProfile[0], 64, angularProfile.size(), 1, 30, qi, &img, trk.mean);
WriteImageAsCSV("angprof.csv", &angularProfile[0], angularProfile.size(), 1);
dbgprintf("Asymmetry value: %f\n", asym);
std::vector<float> crp(128);
float* crpmap = new float[angularProfile.size()*crp.size()];
ComputeCRP(&crp[0], crp.size(), angularProfile.size(), 1, 30, qi, &img, 0.0f);
WriteImageAsCSV("crpmap.csv", crpmap, crp.size(), angularProfile.size());
delete[] crpmap;
delete[] img.data;
//CRP_TestGeneratedData();
// GenerateImageFromLUT(ImageData(img,w,h), ImageData
}
// load jpeg file
BOOL CJpeg::Load(LPCSTR lpstrFileName)
{
UINT uWidth, uHeight, uWidthDW;
// read the jpeg to a packed buffer of RGB bytes
BYTE *lpTmpBuffer = ReadJPEGFile(lpstrFileName, &uWidth, &uHeight);
if (lpTmpBuffer == NULL)
return FALSE;
// do this before DWORD-alignment!!!
// swap red and blue for display
BGRFromRGB(lpTmpBuffer, uWidth, uHeight);
// now DWORD-align for display
BYTE *lpBuffer = MakeDwordAlign(lpTmpBuffer, uWidth, uHeight, &uWidthDW);
FreeBuffer(lpTmpBuffer);
// flip for display
VertFlipBuf(lpBuffer, uWidthDW, uHeight);
BITMAPINFOHEADER bmiHeader;
bmiHeader.biSize = sizeof(BITMAPINFOHEADER);
bmiHeader.biWidth = uWidth;
bmiHeader.biHeight = uHeight;
bmiHeader.biPlanes = 1;
bmiHeader.biBitCount = 24;
bmiHeader.biCompression = BI_RGB;
bmiHeader.biSizeImage = 0;
bmiHeader.biXPelsPerMeter = 0;
bmiHeader.biYPelsPerMeter = 0;
bmiHeader.biClrUsed = 0;
bmiHeader.biClrImportant = 0;
// Allocate enough memory for the new CF_DIB, and copy bits
DWORD dwHeaderSize = sizeof(BITMAPINFOHEADER);
DWORD dwBitsSize = WIDTHBYTES(uWidth*24) * uHeight;
HDIB hDIB = GlobalAlloc(GHND, dwHeaderSize + dwBitsSize);
if (hDIB == NULL)
return FALSE;
LPBYTE lpDIB = (LPBYTE)GlobalLock(hDIB);
memcpy(lpDIB, (LPBYTE)&bmiHeader, dwHeaderSize);
memcpy(FindDIBBits((LPBYTE)lpDIB), lpBuffer, dwBitsSize);
FreeBuffer(lpBuffer);
if (m_pDib != NULL)
delete m_pDib;
m_pDib = new CDib();
m_pDib->Attach(hDIB);
return TRUE;
}
void CRP_TestGeneratedData()
{
int w=64,h=64;
float* img = new float[w*h];
const char* lutname = "LUTexample25X.jpg";
std::vector<uchar> lutdata = ReadToByteBuffer(lutname);
int lutw,luth;
uchar* lut;
ReadJPEGFile(&lutdata[0], lutdata.size(), &lut, &lutw, &luth);
delete[] img;
}
void AutoBeadFindTest()
{
auto img = ReadJPEGFile("00008153.jpg");
auto smp = ReadJPEGFile("00008153-s.jpg");
BeadFinder::Config cfg;
cfg.img_distance = 0.5f;
cfg.roi = 80;
cfg.similarity = 0.5;
auto results=BeadFinder::Find(&img, smp.data, &cfg);
for (uint i=0;i<results.size();i++) {
dbgprintf("beadpos: x=%d, y=%d\n", results[i].x, results[i].y);
img.at(results[i].x+cfg.roi/2, results[i].y+cfg.roi/2) = 1.0f;
}
dbgprintf("%d beads total\n", results.size());
FloatToJPEGFile("autobeadfind.jpg", img.data, img.w, img.h);
img.free();
smp.free();
}
ImageData ReadJPEGFile(const char*fn)
{
int w, h;
uchar* imgdata;
std::vector<uchar> jpgdata = ReadToByteBuffer(fn);
ReadJPEGFile(&jpgdata[0], jpgdata.size(), &imgdata, &w,&h);
float* fbuf = new float[w*h];
for (int x=0;x<w*h;x++)
fbuf[x] = imgdata[x]/255.0f;
delete[] imgdata;
return ImageData(fbuf,w,h);
}
void GenerateZLUTFittingCurve(const char *lutfile)
{
QTrkSettings settings;
settings.width = settings.height = 80;
QueuedCPUTracker qt(settings);
ImageData lut = ReadJPEGFile(lutfile);
ImageData nlut;
ResampleLUT(&qt, &lut, lut.h, &nlut);
CPUTracker trk(settings.width,settings.height);
ImageData smp = ImageData::alloc(settings.width,settings.height);
trk.SetRadialZLUT(nlut.data, nlut.h, nlut.w, 1, qt.cfg.zlut_minradius, qt.cfg.zlut_maxradius, false, false);
int N=8;
for (int z=0;z<6;z++) {
vector3f pos(settings.width/2,settings.height/2, nlut.h * (1+z) / (float)N + 0.123f);
GenerateImageFromLUT(&smp, &nlut, qt.cfg.zlut_minradius, qt.cfg.zlut_maxradius, pos);
ApplyPoissonNoise(smp, 10000);
WriteJPEGFile( SPrintf("zlutfitcurve-smpimg-z%d.jpg", z).c_str(), smp);
trk.SetImageFloat(smp.data);
std::vector<float> profile(qt.cfg.zlut_radialsteps), cmpProf(nlut.h), fitted(nlut.h);
trk.ComputeRadialProfile(&profile[0], qt.cfg.zlut_radialsteps, qt.cfg.zlut_angularsteps, qt.cfg.zlut_minradius, qt.cfg.zlut_maxradius, pos.xy(), false);
trk.LUTProfileCompare(&profile[0], 0, &cmpProf[0], CPUTracker::LUTProfMaxQuadraticFit, &fitted[0]);
WriteArrayAsCSVRow("zlutfitcurve-profile.txt", &profile[0], profile.size(), z>0);
WriteArrayAsCSVRow("zlutfitcurve-cmpprof.txt", &cmpProf[0], cmpProf.size(), z>0);
WriteArrayAsCSVRow("zlutfitcurve-fitted.txt", &fitted[0], fitted.size(), z>0);
}
smp.free();
nlut.free();
lut.free();
}
