C++ (Cpp) Image::BackgroundCorrectRegion Examples

Example #1

File: BFReference.cpp Project: golharam/TS

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;
    }
  }
}

Example #2

File: BFReference.cpp Project: golharam/TS

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();
}