void OutputTraceChunks(GridMesh<TraceChunk> &traceChunks, const char *fileName) {
//ofstream out("flow_0_data_chunks.txt");
ofstream out(fileName);
int rowStart,rowEnd,colStart, colEnd;
// for (size_t bIx = 0; bIx < traceChunks.GetNumBin(); bIx++) {
for (size_t bIx = 0; bIx < 1; bIx++) {
traceChunks.GetBinCoords(bIx, rowStart, rowEnd, colStart, colEnd);
TraceChunk &tc = traceChunks.GetItem(bIx);
float sum = 0;
for (int i = 0; i < tc.mTime.npts(); i++) {
sum += tc.mTime.deltaFrameSeconds[i];
}
for (int row = rowStart; row < rowEnd; row++) {
for (int col = colStart; col < colEnd; col++) {
out << row << "\t" << col;
for (size_t frame = 0; frame < tc.mDepth; frame++) {
out << "\t" << tc.At(row, col, frame);
}
out << endl;
}
}
}
out.close();
}
void Traces::CalcReference(int rowStep, int colStep, GridMesh<std::vector<float> > &gridReference) {
gridReference.Init(mRow, mCol, rowStep, colStep);
int numBin = gridReference.GetNumBin();
int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1;
for (int binIx = 0; binIx < numBin; binIx++) {
gridReference.GetBinCoords(binIx, rowStart, rowEnd, colStart, colEnd);
vector<float> &trace = gridReference.GetItem(binIx);
CalcRegionReference(MaskEmpty, rowStart, rowEnd, colStart, colEnd, trace);
}
}
void OutputSigmaTmidEstimates(GridMesh<SigmaEst> &sigmaTMid, const char *fileName) {
ofstream out(fileName);
int rowStart,rowEnd,colStart, colEnd;
out << "rowStar" << "\t" << "rowEnd" << "\t" << "colStart" << "\t" << "colEnd" << "\t" << "sigma.t0.est" << "\t" << "tmidnuc.t0.est" << "\t" << "t0.est" << "\t" << "rate" <<endl;
for (size_t bIx = 0; bIx < sigmaTMid.GetNumBin(); bIx++) {
sigmaTMid.GetBinCoords(bIx, rowStart, rowEnd, colStart, colEnd);
SigmaEst &est = sigmaTMid.GetItem(bIx);
out << rowStart << "\t" << rowEnd << "\t" << colStart << "\t" << colEnd << "\t" << est.mSigma << "\t" << est.mTMidNuc << "\t" << est.mT0 << "\t" << est.mRate << endl;
}
out.close();
}
void BFReference::FilterForOutliers(Image &bfImg, Mask &mask, float iqrThreshold, int rowStep, int colStep) {
const RawImage *raw = bfImg.GetImage();
GridMesh<float> grid;
grid.Init(raw->rows, raw->cols, rowStep, colStep);
int numBin = grid.GetNumBin();
int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1;
for (int binIx = 0; binIx < numBin; binIx++) {
grid.GetBinCoords(binIx, rowStart, rowEnd, colStart, colEnd);
FilterRegionOutliers(bfImg, mask, iqrThreshold, rowStart, rowEnd, colStart, colEnd);
}
}
void BFReference::FillInReference(std::vector<char> &wells,
std::vector<float> &metric,
GridMesh<int> &grid,
double minQuantile,
double maxQuantile,
int numWells) {
int rStart = -1, rEnd = -1, cStart = -1, cEnd = -1;
for (size_t bIx = 0; bIx < grid.GetNumBin(); bIx++) {
grid.GetBinCoords(bIx, rStart, rEnd, cStart, cEnd);
FillInRegionRef(rStart, rEnd, cStart, cEnd,
metric, minQuantile, maxQuantile,numWells, wells);
}
}
void Traces::CalcIncorporationStartReference(int nRowStep, int nColStep,
GridMesh<SampleStats<float> > &grid) {
grid.Init(mRow, mCol, nRowStep, nColStep);
int numBin = grid.GetNumBin();
int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1;
for (int binIx = 0; binIx < numBin; binIx++) {
SampleStats<float> &startStat = grid.GetItem(binIx);
grid.GetBinCoords(binIx, rowStart, rowEnd, colStart, colEnd);
CalcIncorpBreakRegionStart(rowStart, rowEnd,
colStart, colEnd,
startStat);
}
}
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;
}
}
}
void BFReference::CalcReference(const std::string &datFile, Mask &mask, std::vector<float> &metric) {
Image bfImg;
bfImg.SetImgLoadImmediate (false);
bool loaded = bfImg.LoadRaw(datFile.c_str());
if (!loaded) {
ION_ABORT("*Error* - No beadfind file found, did beadfind run? are files transferred? (" + datFile + ")");
}
const RawImage *raw = bfImg.GetImage();
assert(raw->cols == GetNumCol());
assert(raw->rows == GetNumRow());
assert(raw->cols == mask.W());
assert(raw->rows == mask.H());
if (!mDebugFile.empty()) {
DebugTraces(mDebugFile, mask, bfImg);
}
bfImg.FilterForPinned(&mask, MaskEmpty, false);
// int StartFrame= bfImg.GetFrame((GetDcStart()*1000/15)-1000);
// int EndFrame = bfImg.GetFrame((GetDcEnd()*1000/15)-1000);
int StartFrame = bfImg.GetFrame(-663); //5
int EndFrame = bfImg.GetFrame(350); //20
cout << "DC start frame: " << StartFrame << " end frame: " << EndFrame << endl;
bfImg.XTChannelCorrect();
FilterForOutliers(bfImg, mask, mIqrOutlierMult, mRegionYSize, mRegionXSize);
bfImg.Normalize(StartFrame, EndFrame);
// bfImg.XTChannelCorrect(&mask);
int NNinnerx = 1, NNinnery = 1, NNouterx = 12, NNoutery = 8;
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++) {
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);
}
Region region;
region.col = 0;
region.row = 0;
region.w = GetNumCol(); //mGrid.GetColStep();
region.h = GetNumRow(); // mGrid.GetRowStep();
int startFrame = bfImg.GetFrame(12); // frame 15 on uncompressed 314
// int endFrame = bfImg.GetFrame(raw->timestamps[bfImg.Ge]5300); // frame 77 or so
int endFrame = bfImg.GetFrame(5000); // frame 77 or so
bfImg.CalcBeadfindMetric_1(&mask, region, "pre", startFrame, endFrame);
const double *results = bfImg.GetResults();
int length = GetNumRow() * GetNumCol();
metric.resize(length);
copy(&results[0], &results[0] + (length), metric.begin());
bfImg.Close();
}