void BFReference::CalcSignalReference(const std::string &datFile, const std::string &bgFile,
Mask &mask, int traceFrame) {
Image bfImg;
Image bfBkgImg;
bfImg.SetImgLoadImmediate (false);
bfBkgImg.SetImgLoadImmediate (false);
bool loaded = bfImg.LoadRaw(datFile.c_str());
bool bgLoaded = bfBkgImg.LoadRaw(bgFile.c_str());
if (!loaded) {
ION_ABORT("*Error* - No beadfind file found, did beadfind run? are files transferred? (" + datFile + ")");
}
if (!bgLoaded) {
ION_ABORT("*Error* - No beadfind background file found, did beadfind run? are files transferred? (" + bgFile + ")");
}
const RawImage *raw = bfImg.GetImage();
assert(raw->cols == GetNumCol());
assert(raw->rows == GetNumRow());
assert(raw->cols == mask.W());
assert(raw->rows == mask.H());
bfImg.FilterForPinned(&mask, MaskEmpty, false);
bfBkgImg.FilterForPinned(&mask, MaskEmpty, false);
// bfImg.XTChannelCorrect(&mask);
bfImg.XTChannelCorrect();
// bfBkgImg.XTChannelCorrect(&mask);
bfBkgImg.XTChannelCorrect();
Traces trace;
trace.Init(&bfImg, &mask, FRAMEZERO, FRAMELAST, FIRSTDCFRAME,LASTDCFRAME);
bfImg.Close();
Traces bgTrace;
bgTrace.Init(&bfBkgImg, &mask, FRAMEZERO, FRAMELAST, FIRSTDCFRAME,LASTDCFRAME);
bfBkgImg.Close();
if (mDoRegionalBgSub) {
trace.SetMeshDist(0);
bgTrace.SetMeshDist(0);
}
trace.SetT0Step(mRegionXSize);
bgTrace.SetT0Step(mRegionXSize);
trace.CalcT0(true);
size_t numWells = trace.GetNumRow() * trace.GetNumCol();
for (size_t i = 0; i < numWells; i++) {
trace.SetT0(max(trace.GetT0(i) - 3, 0.0f), i);
}
bgTrace.SetT0(trace.GetT0());
trace.T0DcOffset(0,4);
trace.FillCriticalFrames();
trace.CalcReference(mRegionXSize,mRegionYSize,trace.mGridMedian);
bgTrace.T0DcOffset(0,4);
bgTrace.FillCriticalFrames();
bgTrace.CalcReference(mRegionXSize,mRegionYSize,bgTrace.mGridMedian);
int length = GetNumRow() * GetNumCol();
mBfMetric.resize(length, std::numeric_limits<double>::signaling_NaN());
vector<double> rawTrace(trace.GetNumFrames());
vector<double> bgRawTrace(bgTrace.GetNumFrames());
int pinned =0, excluded = 0;
for (int i = 0; i < length; i++) {
if (mask[i] & MaskExclude || mask[i] & MaskPinned) {
continue;
if (mask[i] & MaskExclude) {
excluded++;
}
else if (mask[i] & MaskPinned) {
pinned++;
}
}
trace.GetTraces(i, rawTrace.begin());
bgTrace.GetTraces(i, bgRawTrace.begin());
mBfMetric[i] = 0;
for (int s = 3; s < 15; s++) {
mBfMetric[i] += rawTrace[s] - bgRawTrace[s];
}
}
cout << "Pinned: " << pinned << " excluded: " << excluded << endl;
for (int i = 0; i < length; i++) {
if (mask[i] & MaskExclude || mask[i] & MaskPinned || mask[i] & MaskIgnore) {
mWells[i] = Exclude;
}
else {
mask[i] = MaskIgnore;
}
}
cout << "Filling reference. " << endl;
FillInReference(mWells, mBfMetric, mGrid, mMinQuantile, mMaxQuantile, mNumEmptiesPerRegion);
for (int i = 0; i < length; i++) {
if (mWells[i] == Reference) {
mask[i] = MaskEmpty;
}
}
bfImg.Close();
}
void BFReference::CalcSignalReference2(const std::string &datFile, const std::string &bgFile,
Mask &mask, int traceFrame) {
Image bfImg;
Image bfBkgImg;
bfImg.SetImgLoadImmediate (false);
bfBkgImg.SetImgLoadImmediate (false);
bool loaded = bfImg.LoadRaw(datFile.c_str());
bool bgLoaded = bfBkgImg.LoadRaw(bgFile.c_str());
if (!loaded) {
ION_ABORT("*Error* - No beadfind file found, did beadfind run? are files transferred? (" + datFile + ")");
}
if (!bgLoaded) {
ION_ABORT("*Error* - No beadfind background file found, did beadfind run? are files transferred? (" + bgFile + ")");
}
const RawImage *raw = bfImg.GetImage();
assert(raw->cols == GetNumCol());
assert(raw->rows == GetNumRow());
assert(raw->cols == mask.W());
assert(raw->rows == mask.H());
int StartFrame = bfImg.GetFrame(-663); //5
int EndFrame = bfImg.GetFrame(350); //20
int NNinnerx = 1, NNinnery = 1, NNouterx = 12, NNoutery = 8;
cout << "DC start frame: " << StartFrame << " end frame: " << EndFrame << endl;
bfImg.FilterForPinned(&mask, MaskEmpty, false);
bfImg.XTChannelCorrect();
// bfImg.XTChannelCorrect(&mask);
Traces trace;
trace.Init(&bfImg, &mask, FRAMEZERO, FRAMELAST, FIRSTDCFRAME,LASTDCFRAME);
bfImg.Normalize(StartFrame, EndFrame);
if (mDoRegionalBgSub) {
trace.SetMeshDist(0);
}
trace.CalcT0(true);
if (mDoRegionalBgSub) {
GridMesh<float> grid;
grid.Init(raw->rows, raw->cols, mRegionYSize, mRegionXSize);
int numBin = grid.GetNumBin();
int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1;
for (int binIx = 0; binIx < numBin; binIx++) {
cout << "BG Subtract Region: " << binIx << endl;
grid.GetBinCoords(binIx, rowStart, rowEnd, colStart, colEnd);
Region reg;
reg.row = rowStart;
reg.h = rowEnd - rowStart;
reg.col = colStart;
reg.w = colEnd - colStart;
bfImg.BackgroundCorrectRegion(&mask, reg, MaskAll, MaskEmpty, NNinnerx, NNinnery, NNouterx, NNoutery, NULL);
}
}
else {
bfImg.BackgroundCorrect(&mask, MaskEmpty, MaskEmpty, NNinnerx, NNinnery, NNouterx, NNoutery, NULL);
}
int length = GetNumRow() * GetNumCol();
mBfMetric.resize(length, std::numeric_limits<double>::signaling_NaN());
for (int wIx = 0; wIx < length; wIx++) {
if (mask[wIx] & MaskExclude || mask[wIx] & MaskPinned)
continue;
int t0 = (int)trace.GetT0(wIx);
mBfMetric[wIx] = 0;
float zSum = 0;
int count = 0;
for (int fIx = min(t0-20, 0); fIx < t0-10; fIx++) {
zSum += bfImg.At(wIx,fIx);
count ++;
}
for (int fIx = t0+3; fIx < t0+15; fIx++) {
mBfMetric[wIx] += (bfImg.At(wIx,fIx) - (zSum / count));
}
}
bfImg.Close();
for (int i = 0; i < length; i++) {
if (mask[i] & MaskExclude || mWells[i] == Exclude) {
mWells[i] = Exclude;
}
else {
mask[i] = MaskIgnore;
}
}
cout << "Filling reference. " << endl;
FillInReference(mWells, mBfMetric, mGrid, mMinQuantile, mMaxQuantile, mNumEmptiesPerRegion);
for (int i = 0; i < length; i++) {
if (mWells[i] == Reference) {
mask[i] = MaskEmpty;
}
}
}