void Run() {
Image datImg;
datImg.LoadRaw(input.c_str());
const RawImage *datRaw = datImg.GetImage();
// ShiftTraces(*bfT0, *wellT0, datRaw->frames, datRaw->baseFrameRate, datRaw->timestamps, datRaw->image);
SynchDat sdat; //GridMesh<TraceChunk> traceChunks;
AddMetaData(sdat, datRaw, acqNum);
GenerateDataChunks(*config, *bfT0, datRaw, config->row_step, config->col_step, *sigmaTMid, sdat.mChunks, datImg);
serializer.Write(output.c_str(), sdat);
if (config->doDebug) {
char buffer[2048];
string tmp = input.substr(input.size()-8,8);
snprintf(buffer, sizeof(buffer), "comIn_%s", tmp.c_str());
OutputTraceChunks(sdat.mChunks,buffer);
TraceChunkSerializer readSer;
// GridMesh<TraceChunk> traceIn;
SynchDat sdatIn;
readSer.Read(output.c_str(),sdatIn);
snprintf(buffer, sizeof(buffer), "decomOut_%s", tmp.c_str());
OutputTraceChunks(sdatIn.mChunks,buffer);
}
datImg.Close();
}
//@TODO: Bad to have side effects on every image load from now on
// should be >explicit< pass of gain correction information to image loader
void ImageTransformer::CalculateGainCorrectionFromBeadfindFlow (char *_datDir, bool gain_debug_output)
{
// calculate gain of each well from the beadfind and use for correction of all images thereafter
Mask *gainCalcMask;
std::string datdir = _datDir;
std::string preBeadFind = datdir + "/beadfind_pre_0003.dat";
Image bfImg;
bfImg.SetImgLoadImmediate (false);
bool loaded = bfImg.LoadRaw (preBeadFind.c_str());
if (!loaded)
{
ION_ABORT ("*Error* - No beadfind file found, did beadfind run? are files transferred? (" + preBeadFind + ")");
}
gainCalcMask = new Mask (bfImg.GetCols(),bfImg.GetRows());
bfImg.FilterForPinned (gainCalcMask, MaskEmpty, false);
bfImg.SetMeanOfFramesToZero (1,3);
//@TODO: implicit global variable->explicit global variable-> explicit variable
GainCalculationFromBeadfind (gainCalcMask,bfImg.raw);
printf ("Computed gain for each pixel using beadind image\n");
if (gain_debug_output)
{
DumpTextGain(bfImg.GetCols(),bfImg.GetRows());
}
bfImg.Close();
delete gainCalcMask;
}
void ImageSpecClass::DeriveSpecsFromDat ( SystemContext &sys_context, ImageControlOpts &img_control, SpatialContext &loc_context )
{
Image img;
ReadFirstImage(img, sys_context, img_control, loc_context);
TimeStampsFromImage(img,img_control);
DimensionsFromImage(img,loc_context);
img.Close();
}
void LoadTraces(Mask &mask, vector<string> &files, vector<Traces> &flows) {
flows.resize(files.size());
for (size_t i = 0; i < files.size(); i++) {
Image img;
bool loaded = img.LoadRaw(files[i].c_str());
if (!loaded) {
ION_ABORT("Couldn't load file: " + files[i]);
}
flows[i].Init(&img, &mask, FRAMEZERO, FRAMELAST, FIRSTDCFRAME,LASTDCFRAME);
img.Close();
flows[i].CalcT0(true);
flows[i].FillCriticalFrames();
flows[i].CalcReference(50,50,flows[i].mGridMedian);
}
}
void ChkFile(char *fname, size_t maxX=0, size_t maxY=0, size_t maxF=0, bool verbose=false)
{
Image loader;
if (loader.LoadRaw(fname))
{
// this one is ok
//printf("File %s OK\n",fname);
cout << fname << " rows=" << loader.GetRows() << " cols=" << loader.GetCols() << " fames=" << loader.GetFrames() << endl << flush;
const RawImage *raw = loader.GetImage();
if (verbose)
{
size_t frames = loader.GetFrames();
size_t rows = loader.GetRows();
size_t cols = loader.GetCols();
size_t stride = rows*cols;
cout << "flow\tx(col)\ty(row)\tvalue" << endl << flush;
for (size_t f = 0; f < frames; f++) {
if (maxF>0 && f>=maxF)
break;
// First image copied in for this frame
for (size_t r = 0; r < rows; r++) {
if (maxY>0 && r>=maxY)
break;
for (size_t c = 0; c < cols; c++) {
if (maxX>0 && c>=maxX)
break;
cout << f << "\t" << c << "\t" << r << "\t" << raw->image[r * cols + c + stride * f] << endl << flush;
}
}
}
}
loader.Close();
}
else
{
printf("File %s FAILED\n",fname);
Error=1;
exit(-1);
}
}
int main(int argc, const char *argv[]) {
OptArgs opts;
TraceConfig config;
string inputDir;
string outputDir;
bool help;
opts.ParseCmdLine(argc, argv);
opts.GetOption(inputDir, "", '-', "source-dir");
opts.GetOption(outputDir, "", '-', "output-dir");
opts.GetOption(config.precision, "5", '-', "precision");
opts.GetOption(config.numEvec, "7", '-', "num-evec");
opts.GetOption(config.doDebug, "false", '-', "debug-files");
opts.GetOption(config.compressionType, "delta", '-', "compression");
opts.GetOption(config.numFlows, "-1", '-', "num-flows");
opts.GetOption(config.numCores, "6", '-', "num-cores");
opts.GetOption(config.errCon,"0",'-',"err-con");
opts.GetOption(config.rankGood,"0",'-',"rank-good");
opts.GetOption(config.pivot,"0",'-',"pivot");
opts.GetOption(help, "false", 'h', "help");
opts.GetOption(config.isThumbnail, "false", '-', "thumbnail");
opts.GetOption(config.use_hard_est, "false",'-', "use-hard-est");
opts.GetOption(config.t0_hard, "0", '-', "t0-hard");
opts.GetOption(config.tmid_hard, "0", '-', "tmid-hard");
opts.GetOption(config.sigma_hard, "0", '-', "sigma-hard");
opts.GetOption(config.row_step, "100", '-', "row-step");
opts.GetOption(config.col_step, "100", '-', "col-step");
opts.GetOption(config.bg_param, "", '-', "region-param");
opts.GetOption(config.grind_acq_0, "0", '-', "grind-acq0");
if(help || inputDir.empty() || outputDir.empty()) {
usage();
}
char *explog_path = NULL;
explog_path = MakeExpLogPathFromDatDir(inputDir.c_str());
int numFlows = config.numFlows;
if (numFlows < 0) {
numFlows = GetTotalFlows(explog_path);
}
// Check and setup our compression type
TraceChunkSerializer serializer;
serializer.SetRecklessAbandon(true);
if (config.compressionType == "svd") {
SvdDatCompress *dc = new SvdDatCompress(config.precision, config.numEvec);
serializer.SetCompressor(dc);
cout << "Doing lossy svd compression. (" << serializer.GetCompressionType() << ")" << endl;
}
// else if (config.compressionType == "svd+") {
// SvdDatCompressPlus *dc = new SvdDatCompressPlus();
// serializer.SetCompressor(dc);
// cout << "Doing lossy svd compression. (" << serializer.GetCompressionType() << ")" << endl;
// }
// else if (config.compressionType == "svd++") {
// SvdDatCompressPlusPlus *dc = new SvdDatCompressPlusPlus();
// if (config.errCon >0 )
// dc->SetErrCon(config.errCon);
// if (config.rankGood > 0 )
// dc->SetRankGood(config.rankGood);
// if (config.pivot > 0)
// dc->SetPivot(config.pivot);
// serializer.SetCompressor(dc);
// cout << "Doing lossy svd compression for good traces and delta for bad ones. (" << serializer.GetCompressionType() << ")" << endl;
// }
else if (config.compressionType == "delta") {
VencoLossless *venco = new VencoLossless();
serializer.SetCompressor(venco);
cout << "Doing lossless delta compression. (" << serializer.GetCompressionType() << ")" << endl;
}
else if (config.compressionType == "delta-plain") {
DeltaComp *delta = new DeltaComp();
serializer.SetCompressor(delta);
cout << "Doing lossless delta plain compression. (" << serializer.GetCompressionType() << ")" << endl;
}
else if (config.compressionType == "delta-plain-fst") {
DeltaCompFst *delta = new DeltaCompFst();
serializer.SetCompressor(delta);
cout << "Doing lossless delta plain fast compression. (" << serializer.GetCompressionType() << ")" << endl;
}
else if (config.compressionType == "delta-plain-fst-smx") {
DeltaCompFstSmX *delta = new DeltaCompFstSmX();
serializer.SetCompressor(delta);
cout << "Doing lossless delta plain fast compression. (" << serializer.GetCompressionType() << ")" << endl;
}
else if (config.compressionType == "none") {
TraceCompressor *vanilla = new TraceNoCompress();
serializer.SetCompressor(vanilla);
cout << "Doing no compression. (" << serializer.GetCompressionType() << ")" << endl;
}
else {
ION_ABORT("Don't recognize compression type: " + config.compressionType);
}
const char *id = GetChipId(explog_path);
if (explog_path) free (explog_path);
ChipIdDecoder::SetGlobalChipId(id);
ImageTransformer::CalibrateChannelXTCorrection(inputDir.c_str(), "lsrowimage.dat");
Image bfImg1;
string bfFile = inputDir + "/beadfind_pre_0003.dat";
bfImg1.LoadRaw(bfFile.c_str());
const RawImage *bf1raw = bfImg1.GetImage();
Mask mask(bf1raw->cols, bf1raw->rows);
ImageTransformer::XTChannelCorrect(bfImg1.raw,bfImg1.results_folder);
bfImg1.FilterForPinned (&mask, MaskEmpty, false);
Image bfImg2;
string bfFile2 = inputDir + "/beadfind_pre_0001.dat";
bfImg2.LoadRaw(bfFile2.c_str());
ImageTransformer::XTChannelCorrect(bfImg2.raw,bfImg1.results_folder);
bfImg2.FilterForPinned (&mask, MaskEmpty, false);
const RawImage *bf2raw = bfImg2.GetImage();
GridMesh<T0Prior> t0Prior;
T0Calc bfT0;
/* Calc t0 and get prior. */
cout << "Doing beadfind t0" << endl;
GenerateBfT0Prior(config, bf1raw->image, bf1raw->baseFrameRate, bf1raw->rows, bf1raw->cols,
bf1raw->frames, bf1raw->timestamps,
config.row_step, config.col_step, &mask, bfT0, t0Prior);
GridMesh<T0Prior> t0Prior2;
T0Calc bfT02;
GenerateBfT0Prior(config, bf2raw->image, bf2raw->baseFrameRate, bf2raw->rows, bf2raw->cols,
bf2raw->frames, bf2raw->timestamps,
config.row_step, config.col_step, &mask, bfT02, t0Prior2);
SigmaTMidNucEstimation sigmaEst;
sigmaEst.Init(config.rate_sigma_intercept, config.rate_sigma_slope,
config.t0_tmid_intercept, config.t0_tmid_slope, bf1raw->baseFrameRate);
GridMesh<SigmaEst> sigmaTMid;
bfImg1.Close();
bfImg2.Close();
// Calculate individual well t0 by looking at neighboring regions
vector<float> wellT0;
bfT0.CalcIndividualT0(wellT0, 0);
vector<float> wellT02;
bfT02.CalcIndividualT0(wellT02, 0);
for (size_t i =0; i< wellT0.size();i++) {
if (wellT0[i] > 0 && wellT02[i] > 0) {
wellT0[i] = (wellT0[i] + wellT02[i])/2.0f;
}
else {
wellT0[i] = max(wellT0[i], wellT02[i]);
}
}
// Average the region level t0, should we do this first and then just do sinle well level?
for (size_t bIx = 0; bIx < bfT0.GetNumRegions(); bIx++) {
double t1 = bfT0.GetT0(bIx);
double t2 = bfT02.GetT0(bIx);
if (t1 > 0 && t2 > 0) {
t1 = (t1 + t2)/2.0;
}
else {
t1 = max(t1,t2);
}
bfT0.SetT0(bIx, t1);
}
// Single thread first dat
for (size_t datIx = 0; datIx < 1; ++datIx) {
cout << "Doing: " << datIx << endl;
char buffer[2048];
snprintf(buffer, sizeof(buffer), "%s/acq_%.4d.dat", inputDir.c_str(), (int) datIx);
string datFile = buffer;
/* Use prior to calculate t0 and slope. */
Image datImg;
T0Calc t0;
datImg.LoadRaw(datFile.c_str());
// ImageTransformer::XTChannelCorrect(datImg.raw,datImg.results_folder);
const RawImage *datRaw = datImg.GetImage();
/* Estimate sigma and t_mid_nuc */
if (datIx == 0) {
cout << "Doing acquisition t0" << endl;
GenerateAcqT0Prior(config, datRaw->image, datRaw->baseFrameRate, datRaw->rows, datRaw->cols,
datRaw->frames, datRaw->timestamps,
config.row_step, config.col_step, &mask, t0, t0Prior);
ClockTimer timer;
cout << "Estimating sigma." << endl;
sigmaTMid.Init(datRaw->rows, datRaw->cols, config.row_step, config.col_step);
for (size_t bIx = 0; bIx < t0.GetNumRegions(); bIx++) {
t0.SetT0(bIx, bfT0.GetT0(bIx));
}
int neighbors = 2;
if (config.isThumbnail) {
cout << "Doing thumbnail version of slope." << endl;
neighbors = 1;
}
EstimateSigmaValue(t0, sigmaEst, sigmaTMid, neighbors);
timer.PrintMilliSeconds(cout,"Sigma Est took:");
string sigmaFile = outputDir + "/sigma_tmid_est.txt";
OutputSigmaTmidEstimates(sigmaTMid, sigmaFile.c_str());
}
/* For each region do shifting */
ClockTimer timer;
cout << "Shifting traces" << endl;
timer.StartTimer();
// ShiftTraces(bfT0, wellT0, datRaw->frames, datRaw->baseFrameRate, datRaw->timestamps, datRaw->image);
timer.PrintMilliSeconds(cout,"Shift took:");
if (!config.bg_param.empty()) {
DataCube<int> rowsCols;
DataCube<float> tmidSigma;
DataCube<float> fitTmidSigma;
string path = config.bg_param + ":/region/region_location";
if (!H5File::ReadDataCube(path, rowsCols)) {
ION_ABORT("Couldn't read file: " + path);
}
path = config.bg_param + ":/region/region_init_param";
if (!H5File::ReadDataCube(path, fitTmidSigma)) {
ION_ABORT("Couldn't read file: " + path);
}
for (size_t i = 0; i < rowsCols.GetNumX(); i++) {
int row = rowsCols.At(i,1,0);
int col = rowsCols.At(i,0,0);
SigmaEst &est = sigmaTMid.GetItemByRowCol(row, col);
float tmid_est = fitTmidSigma.At(i,0,0);
float sigma_est = fitTmidSigma.At(i,1,0);
est.mTMidNuc = tmid_est;
est.mSigma = sigma_est;
}
string fitSigmaFile = outputDir + "/bg_fit_sigma_tmid_est.txt";
OutputSigmaTmidEstimates(sigmaTMid, fitSigmaFile.c_str());
// path = config.bg_param + ":/region/region_init_param";
// if (!H5File::ReadMatrix(path, tmidSigma)) {
// ION_ABORT("Couldn't read file: " + path);
// }
// for (size_t i = 0; i < rowsCols.n_rows; i++) {
// int row = rowsCols.at(i,0);
// int col = rowsCols.at(i,1);
// SigmaEst &est = sigmaTMid.GetItemByRowCol(row, col);
// float tmid_est = tmidSigma.at(i,0);
// float sigma_est = tmidSigma.at(i,1);
// est.mTMidNuc = tmid_est;
// est.mSigma = sigma_est;
// }
// string sigmaFile = outputDir + "/supplied_sigma_tmid_est.txt";
// OutputSigmaTmidEstimates(sigmaTMid, sigmaFile.c_str());
}
else if (config.use_hard_est) {
for (size_t i = 0; i < bfT0.GetNumRegions(); i++) {
bfT0.SetT0(i,config.t0_hard * datRaw->baseFrameRate + config.time_start_slop);
}
for (size_t i = 0; i < sigmaTMid.GetNumBin(); i++) {
SigmaEst &est = sigmaTMid.GetItem(i);
est.mTMidNuc = config.tmid_hard;
est.mSigma = config.sigma_hard;
est.mT0 = config.t0_hard;
}
}
/* Use t0 and sigma to get the time compression bkgModel wants. */
cout << "Generating chunks" << endl;
// GridMesh<TraceChunk> traceChunks;
SynchDat sdat;
if (datIx == 0 && config.grind_acq_0 > 0) {
int nTimes = config.grind_acq_0;
timer.StartTimer();
size_t processMicroSec = 0;
size_t hdf5MicroSec = 0;
size_t compressMicroSec = 0;
size_t convertMicroSec = 0;
for (int i = 0; i <nTimes; i++) {
//GridMesh<TraceChunk> traceChunken;
SynchDat sdatIn;
AddMetaData(sdat, datRaw, datIx);
ClockTimer convTimer;
GenerateDataChunks(config, bfT0, datRaw, config.row_step, config.col_step, sigmaTMid, sdatIn.mChunks,datImg);
convertMicroSec += convTimer.GetMicroSec();
snprintf(buffer, sizeof(buffer), "%s/acq_%.4d.sdat", outputDir.c_str(), (int)datIx);
serializer.Write(buffer, sdatIn);
processMicroSec += serializer.computeMicroSec;
hdf5MicroSec += serializer.ioMicroSec;
compressMicroSec += serializer.compressMicroSec;
}
size_t usec = timer.GetMicroSec();
cout << "Took: " << usec / 1.0e6 << " seconds, " << usec / (nTimes * 1.0f) << " usec per write." << endl;
timer.PrintMilliSeconds(cout,"Chunks took:");
cout << "Read took: " << processMicroSec / (1e3 * nTimes) << " milli seconds per sdat compute." << endl;
cout << "Read took: " << hdf5MicroSec / (1e3 * nTimes) << " milli seconds per sdat hdf5." << endl;
cout << "Read took: " << compressMicroSec / (1e3 * nTimes) << " milli seconds per sdat compressing." << endl;
cout << "Read took: " << convertMicroSec / (1e3 * nTimes) << " milli seconds per sdat converting." << endl;
exit(0);
}
else {
timer.StartTimer();
AddMetaData(sdat, datRaw, datIx);
GenerateDataChunks(config, bfT0, datRaw, config.row_step, config.col_step, sigmaTMid, sdat.mChunks,datImg);
timer.PrintMilliSeconds(cout,"Chunks took:");
if (datIx == 0 && config.doDebug) {
OutputTraceChunks(sdat.mChunks,"flow_0_data_chunks.txt");
}
}
datImg.Close();
/* Serialize onto disk. */
snprintf(buffer, sizeof(buffer), "%s/acq_%.4d.sdat", outputDir.c_str(), (int)datIx);
serializer.Write(buffer, sdat);
/* Read back in first flow for checking */
if (datIx == 0) {
TraceChunkSerializer readSerializer;
readSerializer.SetRecklessAbandon(true);
// GridMesh<TraceChunk> traceChunksIn;
SynchDat sdatIn;
readSerializer.Read(buffer, sdatIn);
if (datIx == 0 && config.doDebug) {
OutputTraceChunks(sdatIn.mChunks, "flow_0_data_chunks_read.txt");
}
SampleQuantiles<float> s(50000);
SampleQuantiles<float> s2(50000);
SampleQuantiles<float> sAbs(50000);
SampleStats<double> ss;
int diffCount = 0;
for (size_t bIx = 0; bIx < sdatIn.mChunks.mBins.size(); bIx++) {
if (sdatIn.mChunks.mBins[bIx].mT0 != sdat.mChunks.mBins[bIx].mT0) {
cout << "Got: " << sdatIn.mChunks.mBins[bIx].mT0 << " vs: " << sdat.mChunks.mBins[bIx].mT0 << endl;
exit(1);
}
for (size_t i = 0; i < sdatIn.mChunks.mBins[bIx].mData.size(); i++) {
double diff = (double)sdatIn.mChunks.mBins[bIx].mData[i] - (double)sdat.mChunks.mBins[bIx].mData[i];
if (!std::isfinite(diff)) {
cout << "NaNs!!" << endl;
}
if (diffCount < 10 && fabs(diff) > .00001) { // != 0) {
diffCount++;
cout << "Bin: " << bIx << " well: " << i << " diff is: " << diff << endl;
}
s.AddValue(diff);
sAbs.AddValue(fabs(diff));
ss.AddValue(sqrt(diff * diff));
s2.AddValue(sqrt(diff * diff));
}
}
cout << "Median rms: " << s2.GetMedian() << " Avg: " << ss.GetMean() << " diff: " << s.GetMedian() << endl;
cout << "Abs(diff) Quantiles:" << endl;
for (size_t i = 0; i <= 100; i+=10) {
cout << i << "\t" << sAbs.GetQuantile(i/100.0) << endl;
}
}
}
// do the next N flows multithreaded
if (numFlows > 1) {
PJobQueue jQueue (config.numCores, numFlows-1);
vector<CreateSDat> jobs(numFlows -1);
// for (int i = 0; i < 4; i++) {
// char buffer[2048];
// snprintf(buffer, sizeof(buffer), "%s/beadfind_pre_%.4d.dat", inputDir.c_str(), (int) i);
// string input = buffer;
// snprintf(buffer, sizeof(buffer), "%s/beadfind_pre_%.4d.sdat", outputDir.c_str(), (int)i);
// string output = buffer;
// jobs[i].Init(&config, input, output, &wellT0, &bfT0, &sigmaTMid);
// jQueue.AddJob(jobs[i]);
// }
// jQueue.WaitUntilDone();
for (int i = 1; i < numFlows; i++) {
char buffer[2048];
snprintf(buffer, sizeof(buffer), "%s/acq_%.4d.dat", inputDir.c_str(), (int) i);
string input = buffer;
snprintf(buffer, sizeof(buffer), "%s/acq_%.4d.sdat", outputDir.c_str(), (int)i);
string output = buffer;
jobs[i-1].Init(&config, input, output, &wellT0, &bfT0, &sigmaTMid, i);
jQueue.AddJob(jobs[i-1]);
}
jQueue.WaitUntilDone();
}
/* Serialize into backbround models */
cout << "Done." << endl;
}
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;
}
}
}
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();
}
