TEST(MergeAcq_Test, TopMergeTest) {
Image top;
Image bottom;
Image combo;
MergeAcq merger;
// Load up our test files
const char *file = "test.dat";
ION_ASSERT(top.LoadRaw(file), "Couldn't load file.");
ION_ASSERT(bottom.LoadRaw(file), "Couldn't load file.");
merger.SetFirstImage(&bottom);
merger.SetSecondImage(&top, bottom.GetRows(), 0); // starting vertically raised but columns the same.
// Merge the two images into a single image
merger.Merge(combo);
cout << "Done." << endl;
// Write out the merged image for some testing
Acq acq;
acq.SetData(&combo);
acq.WriteVFC("combo.dat", 0, 0, combo.GetCols(), combo.GetRows());
Image test;
ION_ASSERT(test.LoadRaw("combo.dat"), "Couldn't load file.");
// Check to make sure that the combined file has same values as original
for (int row = 0; row < top.GetRows(); row++) {
for (int col = 0; col < top.GetCols(); col++) {
for (int frame = 0; frame < top.GetFrames(); frame++) {
EXPECT_EQ(top.At(row, col, frame), bottom.At(row,col,frame));
short orig = top.At(row, col, frame);
short combined = test.At(row+top.GetRows(),col,frame);
EXPECT_EQ(orig, combined);
combined = test.At(row,col,frame);
EXPECT_EQ(orig, combined);
}
}
}
}
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::FilterRegionOutliers(Image &bfImg, Mask &mask, float iqrThreshold,
int rowStart, int rowEnd, int colStart, int colEnd) {
const RawImage *raw = bfImg.GetImage();
/* Figure out how many wells are not pinned/excluded right out of the gate. */
int okCount = 0;
for (int r = rowStart; r < rowEnd; r++) {
for (int c = colStart; c < colEnd; c++) {
int idx = r * raw->cols + c;
if (!mask.Match(c, r, MaskPinned) && !mask.Match(c,r,MaskExclude) &&
mWells[idx] != Exclude && mWells[idx] != Filtered) {
okCount++;
}
}
}
/* If not enough, just mark them all as bad. */
if (okCount <= MIN_OK_WELLS || (mNumEmptiesPerRegion > 0 && okCount < mNumEmptiesPerRegion)) {
for (int r = rowStart; r < rowEnd; r++) {
for (int c = colStart; c < colEnd; c++) {
mWells[r * raw->cols + c] = Exclude;
}
}
return;
}
// Make a mtrix for our region
mTraces.set_size(okCount, raw->frames ); // wells in row major order by frames
int count = 0;
vector<int> mapping(mTraces.n_rows, -1);
for (int r = rowStart; r < rowEnd; r++) {
for (int c = colStart; c < colEnd; c++) {
int idx = r * raw->cols + c;
if (!mask.Match(c, r, MaskPinned) && !mask.Match(c,r,MaskExclude) &&
mWells[idx] != Exclude && mWells[idx] != Filtered) {
for (int f = 0; f < raw->frames; f++) {
mTraces.at(count,f) = bfImg.At(r,c,f) - bfImg.At(r,c,0);
}
mapping[count++] = r * raw->cols + c;
}
}
}
for (size_t r = 0; r < mTraces.n_rows; r++) {
for (size_t c = 0; c < mTraces.n_cols; c++) {
assert(isfinite(mTraces.at(r,c)));
}
}
assert(mapping.size() == (size_t)count);
/* Subtract off the median. */
fmat colMed = median(mTraces);
frowvec colMedV = colMed.row(0);
for(size_t i = 0; i < mTraces.n_rows; i++) {
mTraces.row(i) = mTraces.row(i) - colMedV;
}
/* Get the quantiles of the mean difference for well and exclude outliers */
fmat mad = mean(mTraces, 1);
fvec madV = mad.col(0);
mMadSample.Clear();
mMadSample.Init(1000);
mMadSample.AddValues(madV.memptr(), madV.n_elem);
float minVal = mMadSample.GetQuantile(.25) - iqrThreshold * mMadSample.GetIQR();
float maxVal = mMadSample.GetQuantile(.75) + iqrThreshold * mMadSample.GetIQR();
for (size_t i = 0; i < madV.n_rows; i++) {
if (madV[i] <= minVal || madV[i] >= maxVal) {
mWells[mapping[i]] = Filtered;
}
}
}
