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 HiKinectApp::update()
{
if( mKinect.checkNewDepthFrame() ) {
mDepthTexture = mKinect.getDepthImage();
mDepthSurface = Surface32f( mKinect.getDepthImage() );
mKinectReady = true;
if ( !mKinectIR ) {
mKinectIR = true;
mKinect.setVideoInfrared( true );
}
ci::Surface captureSurface = Surface8u( mKinect.getDepthImage() );
ci::Surface outputSurface = captureSurface;
mContours->clear();
mSilhouetteDetector->processSurface(&captureSurface, mContours, &outputSurface);
}
if( mKinect.checkNewColorFrame() )
mColorTexture = mKinect.getVideoImage();
if( mIsMouseDown ) // using small number instead of 0.0 because lights go black after a few seconds when going to 0.0f
mDirectional -= ( mDirectional - 0.00001f ) * 0.1f;
else
mDirectional -= ( mDirectional - 1.0f ) * 0.1f;
if (mKinectReady)
mGridMesh.updateKinect(mKinect);
else
mGridMesh.update();
}
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();
}
int TraceStoreCol::CalcMedianReference (size_t row, size_t col,
GridMesh<std::vector<float> > ®ionMed,
std::vector<double> &dist,
std::vector<std::vector<float> *> &values,
std::vector<float> &reference) {
int retVal = TraceStore::TS_OK;
reference.resize(mFrames);
std::fill(reference.begin(), reference.end(), 0.0);
regionMed.GetClosestNeighbors (row, col, mUseMeshNeighbors, dist, values);
int num_good = 0;
size_t valSize = values.size();
for (size_t i =0; i < valSize; i++) {
if (values[i]->size() > 0) {
num_good++;
}
}
// try reaching a little farther if no good reference close by
if (num_good == 0) {
regionMed.GetClosestNeighbors (row, col, 2*mUseMeshNeighbors, dist, values);
}
size_t size = 0;
double maxDist = 0;
for (size_t i = 0; i < values.size(); i++) {
size = max (values[i]->size(), size);
maxDist = max(dist[i], maxDist);
}
reference.resize (size);
std::fill (reference.begin(), reference.end(), 0.0);
double distWeight = 0;
valSize = values.size();
for (size_t i = 0; i < valSize; i++) {
if (values[i]->size() == 0) {
continue;
}
double w = TraceStore::WeightDist (dist[i], mRowRefStep); //1/sqrt(dist[i]+1);
distWeight += w;
size_t vSize = values[i]->size();
for (size_t j = 0; j < vSize; j++) {
reference[j] += w * values[i]->at (j);
}
}
// Divide by our total weight to get weighted mean
if (distWeight > 0) {
for (size_t i = 0; i < reference.size(); i++) {
reference[i] /= distWeight;
}
retVal = TraceStore::TS_OK;
}
else {
retVal = TraceStore::TS_BAD_DATA;
}
return retVal;
}
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 TraceChunkSerializer::ArrangeDataForWriting(GridMesh<TraceChunk> &dataMesh, struct FlowChunk *chunks) {
if (dataMesh.GetNumBin() == 0) {
return;
}
size_t maxSize = dataMesh.mBins[0].mDepth * dataMesh.mBins[0].mHeight * dataMesh.mBins[1].mWidth * 3;
int8_t *compressed = new int8_t[maxSize];
compressMicroSec = 0;
for (size_t bIx = 0; bIx < dataMesh.GetNumBin(); bIx++) {
TraceChunk &tc = dataMesh.GetItem(bIx);
struct FlowChunk &fc = chunks[bIx];
fc.CompressionType = mCompressor->GetCompressionType();
fc.RowStart = tc.mRowStart;
fc.ColStart = tc.mColStart;
fc.FrameStart = tc.mFrameStart;
fc.FrameStep = tc.mFrameStep;
fc.ChipRow = tc.mChipRow;
fc.ChipCol = tc.mChipCol;
fc.ChipFrame = tc.mChipFrame;
fc.StartDetailedTime = tc.mStartDetailedTime;
fc.StopDetailedTime = tc.mStopDetailedTime;
fc.LeftAvg = tc.mLeftAvg;
fc.OrigFrames = tc.mOrigFrames;
fc.T0 = tc.mT0;
fc.Sigma = tc.mSigma;
fc.TMidNuc = tc.mTMidNuc;
fc.Height = tc.mHeight;
fc.Width = tc.mWidth;
fc.Depth = tc.mDepth;
fc.BaseFrameRate = tc.mBaseFrameRate;
size_t outsize;
ClockTimer timer;
mCompressor->Compress(tc, &compressed, &outsize, &maxSize);
compressMicroSec += timer.GetMicroSec();
//cout <<"Doing: " << fc.CompressionType << " Bytes per wells: " << outsize/(float) (tc.mHeight * tc.mWidth) <<" Compression ratio: "<< tc.mData.size()*2/(float)outsize << endl;
fc.Data.p = (int8_t *)malloc(outsize*sizeof(int8_t));
memcpy(fc.Data.p, compressed, outsize*sizeof(int8_t));
fc.Data.len = outsize;
if (0 == outsize) {
cout << "How can there be zero blocks." << endl;
}
float * tmp = (float *)malloc(tc.mTimePoints.size() * sizeof(float));
copy(tc.mTimePoints.begin(), tc.mTimePoints.end(), tmp);
fc.DeltaFrame.p = tmp;
fc.DeltaFrame.len = tc.mTimePoints.size() * sizeof(float);
}
delete [] compressed;
}
bool Traces::CalcStartFrame(size_t row, size_t col,
GridMesh<SampleStats<float> > ®ionStart, float &start) {
std::vector<double> dist(7);
std::vector<SampleStats<float> *> values;
bool allOk = false;
regionStart.GetClosestNeighbors(row, col, mUseMeshNeighbors, dist, values);
double distWeight = 0;
double startX = 0;
start = 0;
for (size_t i = 0; i < values.size(); i++) {
if (values[i]->GetCount() > 0) {
double w = WeightDist(dist[i]); //1/sqrt(dist[i] + 1);
distWeight += w;
startX += w * values[i]->GetMean();
}
}
if (distWeight > 0 && start >= 0) {
start = startX / distWeight;
if (startX >= 0 && isfinite(startX)) {
allOk = true;
}
}
return allOk;
}
void GenerateDataChunks(TraceConfig &config, T0Calc &t0, const struct RawImage *raw,
int rowStep, int colStep, GridMesh<SigmaEst> &sigmaTMid,
GridMesh<TraceChunk> &mTraceChunks, Image &img) {
mTraceChunks.Init(raw->rows, raw->cols, rowStep, colStep);
int rowStart,rowEnd,colStart, colEnd;
size_t frameStep = raw->rows * raw->cols;
int16_t *frameBuff[raw->frames];
for (int i = 0; i < raw->frames; i++) {
frameBuff[i] = raw->image + (i * frameStep);
}
for (size_t bIx = 0; bIx < t0.GetNumRegions(); bIx++) {
SigmaEst &est = sigmaTMid.GetItem(bIx);
t0.GetRegionCoords(bIx, rowStart, rowEnd, colStart, colEnd);
TraceChunk &chunk = mTraceChunks.GetItem(bIx);
float t0Time = t0.GetT0(bIx);
chunk.mSigma = est.mSigma;
chunk.mTMidNuc = est.mTMidNuc;
t0Time -= config.time_start_slop;
chunk.mStartDetailedTime = config.start_detailed_time;
chunk.mStopDetailedTime = config.stop_detailed_time;
chunk.mLeftAvg = config.left_avg;
chunk.mOrigFrames = raw->frames;
chunk.mT0 = t0Time/raw->baseFrameRate;
// Old style using t0 instead of tmid nuc
chunk.mTime.SetUpTime(raw->uncompFrames, chunk.mT0, chunk.mStartDetailedTime, chunk.mStopDetailedTime, chunk.mLeftAvg);
chunk.mBaseFrameRate = raw->baseFrameRate;
chunk.mTimePoints.resize(chunk.mTime.mTimePoints.size());
copy(chunk.mTime.mTimePoints.begin(), chunk.mTime.mTimePoints.end(), chunk.mTimePoints.begin());
chunk.mTime.SetupConvertVfcTimeSegments(raw->frames, raw->timestamps, raw->baseFrameRate, raw->rows * raw->cols);
// if (bIx == t0.GetNumRegions() /2) {
// cout << "Setup Frames: ";
// float deltaFrame = 0;
// for (int i = 0; i < chunk.mTime.npts(); i++) {
// deltaFrame += chunk.mTime.deltaFrame[i];
// cout << "\t" << deltaFrame;
// }
// cout << endl;
// chunk.mTime.WriteLinearTransformation(raw->rows * raw->cols);
// }
chunk.SetChipInfo(raw->rows, raw->cols, raw->frames);
chunk.SetDimensions(rowStart, rowEnd-rowStart, colStart, colEnd-colStart, 0, chunk.mTime.npts());
chunk.ZeroData();
chunk.mTime.ConvertVfcSegmentsOpt(rowStart, rowEnd, colStart, colEnd,
raw->rows, raw->cols, raw->frames,
frameBuff, &chunk.mData[0]);
}
}
void HiKinectApp::draw3D() {
gl::setMatrices( mCamUI.getCamera() );
if (mWireframe) gl::enableWireframe();
else gl::disableWireframe();
if (mLighting) {
glEnable( GL_LIGHTING );
glEnable( GL_LIGHT0 );
}
// GLfloat light_position[] = { mMousePos.x, mMousePos.y, -275.0f, 0.0f };
GLfloat light_position[] = { 0, 0, 1.0f, 0.0f };
glLightfv( GL_LIGHT0, GL_POSITION, light_position );
if( DIFFUSE ){
ci::ColorA color( CM_RGB, 1.0f, 1.0f, 1.0f, 1.0f );
glMaterialfv( GL_FRONT, GL_DIFFUSE, color );
} else {
glMaterialfv( GL_FRONT, GL_DIFFUSE, no_mat );
}
if( AMBIENT )
glMaterialfv( GL_FRONT, GL_AMBIENT, mat_ambient );
else
glMaterialfv( GL_FRONT, GL_AMBIENT, no_mat );
if( SPECULAR ){
glMaterialfv( GL_FRONT, GL_SPECULAR, mat_specular );
glMaterialfv( GL_FRONT, GL_SHININESS, mat_shininess );
} else {
glMaterialfv( GL_FRONT, GL_SPECULAR, no_mat );
glMaterialfv( GL_FRONT, GL_SHININESS, no_shininess );
}
if( EMISSIVE )
glMaterialfv( GL_FRONT, GL_EMISSION, mat_emission );
else
glMaterialfv( GL_FRONT, GL_EMISSION, no_mat );
if (mDepthTexture)
mDepthTexture.bind(0);
mFbo.bindTexture(1);
if (mColorTexture)
mColorTexture.bind(2);
mGridMesh.draw( lmap(mMousePos.x, 0.0f, (float)getWindowWidth(), 0.0f, 1.0f) );
if (mLighting) {
glDisable( GL_LIGHTING );
glDisable( GL_LIGHT0 );
}
gl::disableWireframe();
}
void TraceChunkSerializer::DecompressFromReading(const struct FlowChunk *chunks, GridMesh<TraceChunk> &dataMesh) {
compressMicroSec = 0;
for (size_t bIx = 0; bIx < dataMesh.GetNumBin(); bIx++) {
TraceChunk &tc = dataMesh.GetItem(bIx);
const struct FlowChunk &fc = chunks[bIx];
if (mCompressor == NULL) {
if (mDebugMsg) { cout << "Got compression type: " << chunks[bIx].CompressionType << endl;}
mCompressor = CompressorFactory::MakeCompressor((TraceCompressor::CodeType)chunks[bIx].CompressionType);
}
ION_ASSERT(chunks[bIx].CompressionType == (size_t)mCompressor->GetCompressionType(), "Wrong compression type: " + ToStr(chunks[bIx].CompressionType) + " vs: " + ToStr(mCompressor->GetCompressionType()));
tc.mRowStart = fc.RowStart;
tc.mColStart = fc.ColStart;
tc.mFrameStart = fc.FrameStart;
tc.mFrameStep = fc.FrameStep;
tc.mChipRow = fc.ChipRow;
tc.mChipCol = fc.ChipCol;
tc.mChipFrame = fc.ChipFrame;
tc.mStartDetailedTime = fc.StartDetailedTime;
tc.mStopDetailedTime = fc.StopDetailedTime;
tc.mLeftAvg = fc.LeftAvg;
tc.mOrigFrames = fc.OrigFrames;
tc.mT0 = fc.T0;
tc.mSigma = fc.Sigma;
tc.mTMidNuc = fc.TMidNuc;
tc.mHeight = fc.Height;
tc.mWidth = fc.Width;
tc.mDepth = fc.Depth;
tc.mBaseFrameRate = fc.BaseFrameRate;
size_t outsize = fc.Height * fc.Width * fc.Depth;
tc.mData.resize(outsize);
tc.mTimePoints.resize(tc.mDepth);
float * tmp = (float *)fc.DeltaFrame.p;
copy(tmp,tmp+fc.Depth, tc.mTimePoints.begin());
ClockTimer timer;
mCompressor->Decompress(tc, (int8_t *)fc.Data.p, fc.Data.len);
compressMicroSec += timer.GetMicroSec();
outsize = fc.Height * fc.Width * fc.Depth;
}
}
bool TraceChunkSerializer::Write(H5File &h5, GridMesh<TraceChunk> &dataMesh) {
mNumChunks = dataMesh.GetNumBin();
ClockTimer timer;
mChunks = (struct FlowChunk *) malloc(sizeof(struct FlowChunk) * mNumChunks);
ArrangeDataForWriting(dataMesh, mChunks);
computeMicroSec = timer.GetMicroSec();
hsize_t dims1[1];
dims1[0] = mNumChunks;
hid_t fcDataSpace = H5Screate_simple(1, dims1, NULL);
hid_t charArrayType = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t charArrayType2 = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t fcType = H5Tcreate(H5T_COMPOUND, sizeof(struct FlowChunk));
H5Tinsert(fcType, "CompressionType", HOFFSET(struct FlowChunk, CompressionType), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipRow", HOFFSET(struct FlowChunk, ChipRow), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipCol", HOFFSET(struct FlowChunk, ChipCol), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipFrame", HOFFSET(struct FlowChunk, ChipFrame), H5T_NATIVE_B64);
H5Tinsert(fcType, "RowStart", HOFFSET(struct FlowChunk, RowStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "ColStart", HOFFSET(struct FlowChunk, ColStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStart", HOFFSET(struct FlowChunk, FrameStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStep", HOFFSET(struct FlowChunk, FrameStep), H5T_NATIVE_B64);
H5Tinsert(fcType, "Height", HOFFSET(struct FlowChunk, Height), H5T_NATIVE_B64);
H5Tinsert(fcType, "Width", HOFFSET(struct FlowChunk, Width), H5T_NATIVE_B64);
H5Tinsert(fcType, "Depth", HOFFSET(struct FlowChunk, Depth), H5T_NATIVE_B64);
H5Tinsert(fcType, "OrigFrames", HOFFSET(struct FlowChunk, OrigFrames), H5T_NATIVE_B64);
H5Tinsert(fcType, "StartDetailedTime", HOFFSET(struct FlowChunk, StartDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "StopDetailedTime", HOFFSET(struct FlowChunk, StopDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "LeftAvg", HOFFSET(struct FlowChunk, LeftAvg), H5T_NATIVE_INT);
H5Tinsert(fcType, "T0", HOFFSET(struct FlowChunk, T0), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "Sigma", HOFFSET(struct FlowChunk, Sigma), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "TMidNuc", HOFFSET(struct FlowChunk, TMidNuc), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "BaseFrameRate", HOFFSET(struct FlowChunk, BaseFrameRate), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "DeltaFrame", HOFFSET(struct FlowChunk, DeltaFrame), charArrayType2);
H5Tinsert(fcType, "Data", HOFFSET(struct FlowChunk, Data), charArrayType);
timer.StartTimer();
hid_t dataset = H5Dcreate2(h5.GetFileId(), "FlowChunk", fcType, fcDataSpace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
herr_t status = H5Dwrite(dataset, fcType, H5S_ALL, H5S_ALL, H5P_DEFAULT, mChunks);
status = H5Dvlen_reclaim(fcType, fcDataSpace, H5P_DEFAULT, mChunks);
// // delete [] mChunks;
free(mChunks);
mChunks = NULL;
ION_ASSERT(status == 0, "Couldn't write dataset");
H5Tclose(fcType);
H5Tclose(charArrayType);
H5Tclose(charArrayType2);
H5Sclose(fcDataSpace);
H5Dclose(dataset);
ioMicroSec += timer.GetMicroSec();
return status == 0;
}
void HiKinectApp::setup()
{
console() << "There are " << Kinect::getNumDevices() << " Kinects connected." << std::endl;
mKinect = Kinect( Kinect::Device() );
mKinectReady = false;
mKinectIR = false;
mNormalShader = gl::GlslProg( loadResource( "normal_vert.glsl" ), loadResource( "normal_frag.glsl" ) );
mNormalStrength = 20.0f;
gl::Fbo::Format format;
mFbo = gl::Fbo( CAPTURE_WIDTH, CAPTURE_HEIGHT, format );
mSilhouetteDetector = new SilhouetteDetector(640,480);
mContours = new vector<vector<cv::Point> >();
mDoNormalMap = false;
mParams = params::InterfaceGl( "Parameters", Vec2i( 300, 200 ) );
mParams.addParam( "NormalStrength", &mNormalStrength, "min=1.0 max=1000.0 step=1.0 keyIncr=z keyDecr=Z" );
mParams.addParam( "Depth Scale", &mGridMesh.mDepthScale, "min=1.0 max=2000.0" );
mParams.addParam( "Depth Offset", &mGridMesh.mDepthOffset, "min=0.0 max=1000.0" );
mParams.addParam( "Shader Displacement", &mGridMesh.mShaderDisplacement );
mParams.addParam( "Depth Max", &mGridMesh.mDepthMax, "min=0.0 max=1.0 step=0.01" );
mParams.addParam( "Generate Normal Map", &mDoNormalMap );
mGridMesh.init(160, 120, 640, 480, false, true);
mIsMouseDown = false;
mWireframe = true;
DIFFUSE = true;
AMBIENT = false;
SPECULAR = false;
EMISSIVE = false;
mCamera.setEyePoint( Vec3f(0.0f, 0.0f, 750.0f));
mCamera.setCenterOfInterestPoint( Vec3f::zero() );
mCamera.setPerspective( 60, getWindowAspectRatio(), 1, 2000 );
mCamUI.setCurrentCam( mCamera );
gl::enableDepthWrite();
gl::enableDepthRead();
}
int Traces::CalcMedianReference(int row, int col,
GridMesh<std::vector<float> > ®ionMed,
std::vector<double> &dist,
std::vector<std::vector<float> *> &values,
std::vector<float> &reference) {
int retVal = OK;
// vector<float> &binVal = regionMed.GetItemByRowCol(row,col);
// if (binVal.size() > 0) {
// reference.resize(binVal.size());
// copy(binVal.begin(), binVal.end(), reference.begin());
// return OK;
// }
regionMed.GetClosestNeighbors(row, col, mUseMeshNeighbors, dist, values);
size_t size = 0;
for (size_t i = 0; i < values.size(); i++) {
size = max(values[i]->size(), size);
}
reference.resize(size);
fill(reference.begin(), reference.end(), 0.0);
double distWeight = 0;
size_t valSize = values.size();
for (size_t i = 0; i < valSize; i++) {
if (values[i]->size() == 0) {
continue;
}
double w = WeightDist(dist[i]); //1/sqrt(dist[i]+1);
distWeight += w;
size_t vSize = values[i]->size();
for (size_t j = 0; j < vSize; j++) {
reference[j] += w * values[i]->at(j);
}
}
// Divide by our total weight to get weighted mean
if (distWeight > 0) {
for (size_t i = 0; i < reference.size(); i++) {
reference[i] /= distWeight;
}
retVal = OK;
}
else {
retVal = BAD_DATA;
}
return retVal;
}
bool TraceChunkSerializer::Read(H5File &h5, GridMesh<TraceChunk> &dataMesh) {
hid_t dataset = H5Dopen2(h5.GetFileId(), "FlowChunk", H5P_DEFAULT);
// hid_t datatype = H5Dget_type(dataset); /* datatype handle */
static pthread_once_t onceControl = PTHREAD_ONCE_INIT;
int err = pthread_once(&onceControl, InitSdatReadSem);
if (err != 0) { cout << "Error with pthread once." << endl; }
hid_t dataspace = H5Dget_space(dataset);
int rank = H5Sget_simple_extent_ndims(dataspace);
std::vector<hsize_t> dims;
dims.resize(rank);
int status = H5Sget_simple_extent_dims(dataspace, &dims[0], NULL);
if (mChunks != NULL) {
delete [] mChunks;
}
mChunks = new FlowChunk[dims[0]];
mNumChunks = dims[0];
hid_t fcDataSpace = H5Screate_simple(1, &dims[0], NULL);
hid_t charArrayType = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t charArrayType2 = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t fcType = H5Tcreate(H5T_COMPOUND, sizeof(struct FlowChunk));
H5Tinsert(fcType, "CompressionType", HOFFSET(struct FlowChunk, CompressionType), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipRow", HOFFSET(struct FlowChunk, ChipRow), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipCol", HOFFSET(struct FlowChunk, ChipCol), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipFrame", HOFFSET(struct FlowChunk, ChipFrame), H5T_NATIVE_B64);
H5Tinsert(fcType, "RowStart", HOFFSET(struct FlowChunk, RowStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "ColStart", HOFFSET(struct FlowChunk, ColStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStart", HOFFSET(struct FlowChunk, FrameStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStep", HOFFSET(struct FlowChunk, FrameStep), H5T_NATIVE_B64);
H5Tinsert(fcType, "Height", HOFFSET(struct FlowChunk, Height), H5T_NATIVE_B64);
H5Tinsert(fcType, "Width", HOFFSET(struct FlowChunk, Width), H5T_NATIVE_B64);
H5Tinsert(fcType, "Depth", HOFFSET(struct FlowChunk, Depth), H5T_NATIVE_B64);
H5Tinsert(fcType, "OrigFrames", HOFFSET(struct FlowChunk, OrigFrames), H5T_NATIVE_B64);
H5Tinsert(fcType, "StartDetailedTime", HOFFSET(struct FlowChunk, StartDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "StopDetailedTime", HOFFSET(struct FlowChunk, StopDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "LeftAvg", HOFFSET(struct FlowChunk, LeftAvg), H5T_NATIVE_INT);
H5Tinsert(fcType, "T0", HOFFSET(struct FlowChunk, T0), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "Sigma", HOFFSET(struct FlowChunk, Sigma), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "TMidNuc", HOFFSET(struct FlowChunk, TMidNuc), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "BaseFrameRate", HOFFSET(struct FlowChunk, BaseFrameRate), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "DeltaFrame", HOFFSET(struct FlowChunk, DeltaFrame), charArrayType2);
H5Tinsert(fcType, "Data", HOFFSET(struct FlowChunk, Data), charArrayType);
ClockTimer timer;
IonImageSem::Take();
status = H5Dread(dataset, fcType, H5S_ALL, H5S_ALL, H5P_DEFAULT, mChunks);
IonImageSem::Give();
ioMicroSec = timer.GetMicroSec();
ION_ASSERT(status == 0, "Couldn' read dataset");
timer.StartTimer();
dataMesh.Init(mChunks[0].ChipRow, mChunks[0].ChipCol, mChunks[0].Height, mChunks[0].Width);
ION_ASSERT(dataMesh.GetNumBin() == mNumChunks, "Didn't get number of chunks expected");
DecompressFromReading(mChunks, dataMesh);
computeMicroSec = timer.GetMicroSec();
timer.StartTimer();
status = H5Dvlen_reclaim(fcType, fcDataSpace, H5P_DEFAULT, mChunks);
delete [] mChunks;
mChunks = NULL;
H5Tclose(fcType);
H5Tclose(charArrayType);
H5Tclose(charArrayType2);
H5Sclose(fcDataSpace);
H5Dclose(dataset);
ioMicroSec += timer.GetMicroSec();
return status == 0;
}
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::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();
}
