Example #1
0
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();
}
Example #2
0
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;
    }
  }
}