void BkgParamH5::IncrementalWriteParam(DataCube<float> &cube, H5DataSet *set, int flow, int saveWellsFrequency,int numFlows)
{
int testWellFrequency = saveWellsFrequency*NUMFB; // block size
if (((flow+1) % (saveWellsFrequency*NUMFB) == 0 && (flow != 0)) || (flow+1) >= numFlows) {
fprintf(stdout, "Writing incremental wells at flow: %d\n", flow);
MemUsage("BeforeWrite");
size_t starts[3];
size_t ends[3];
cube.SetStartsEnds(starts, ends);
set->WriteRangeData(starts, ends, cube.GetMemPtr());
cube.SetRange(0, cube.GetNumX(), 0, cube.GetNumY(), flow+1, flow + 1 + min(testWellFrequency,numFlows-(flow+1)));
MemUsage("AfterWrite");
}
}
void BkgParamH5::WriteOneFlowBlock ( DataCube<int> &cube, H5DataSet *set, int flow, int chunksize )
{
// fprintf ( stdout, "Writing incremental H5-diagnostics at flow: %d\n", flow );
MemUsage ( "BeforeWrite" );
size_t starts[3];
size_t ends[3];
cube.SetStartsEnds ( starts, ends );
// here's the actual write
set->WriteRangeData ( starts, ends, cube.GetMemPtr() );
// set for next iteration
int nextflow = flow+1;
int nextchunk = min ( chunksize,datacube_numflows- ( flow+1 ) );
cube.SetRange ( 0, cube.GetNumX(), 0, cube.GetNumY(), nextflow, nextflow+nextchunk );
MemUsage ( "AfterWrite" );
}
// set to write one compute block
void BkgParamH5::WriteOneBlock ( DataCube<int> &cube, H5DataSet *set, int iBlk )
{
if ( set!=NULL )
{
// fprintf ( stdout, "Writing incremental H5-diagnostics at compute block: %d\n", iBlk );
MemUsage ( "BeforeWrite" );
size_t starts[3];
size_t ends[3];
cube.SetStartsEnds ( starts, ends );
// here's the actual write
set->WriteRangeData ( starts, ends, cube.GetMemPtr() );
// set for next iteration
int nextBlk = iBlk+1;
int nextChunk = min ( 1,nFlowBlks-nextBlk );
cube.SetRange ( 0, cube.GetNumX(), 0, cube.GetNumY(), nextBlk, nextBlk+nextChunk );
MemUsage ( "AfterWrite" );
}
}
int GenerateCourantNumberRestabFile::CourantRestab(std::vector<Real>cour_numb){
DataCube datacube;
///====================================
/// Set Description
///====================================
{
IndexDescription index;
index.label = "timeStep";
index.name = "iTimeStep";
datacube.list_of_index_description.add(index);
}
{
Restab::VariableDescription var;
var.label = "Courant_number";
datacube.list_of_variable_description.add(var);
}
///====================================
/// Add Step Values
///====================================
MapInteger step_index_values;
MapReal step_var_values;
Integer num_solution = cour_numb.size();
//!Steps
for(Integer i = 1; i < num_solution; i++){
step_index_values.clear();
step_var_values.clear();
step_index_values.insert(KeyInteger("timeStep",i));
Real cour = cour_numb[i];
step_var_values.insert(KeyReal("Courant_number" ,cour));
datacube.table_of_index_values.add(step_index_values);
datacube.table_of_variable_values.add(step_var_values);
}
///======================================
/// Write Results
///======================================
String filename = "Courantresult";
//! Description
String filenameDesc = filename + ".restab.desc";
String text_desc = datacube.toStringDescription();
//std::cout << text_desc << "\n";
datacube.writeDescription(filenameDesc);
//! Data
String filenameData = filename + ".restab";
String text_data = datacube.toStringData();
//std::cout << text_data << "\n";
datacube.writeData(filenameData);
//======================================
return 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;
}
int GenerateNumbComponentsRestabFile::ComponentsRestab( std::vector<std::unique_ptr<ISolverData>>&& vect_solution){
DataCube datacube;
///====================================
/// Set Description
///====================================
{
IndexDescription index;
index.label = "timeStep";
index.name = "iTimeStep";
datacube.list_of_index_description.add(index);
}
{
Restab::VariableDescription var;
var.label = "number_of_components";
datacube.list_of_variable_description.add(var);
}
///====================================
/// Add Step Values
///====================================
MapInteger step_index_values;
MapReal step_var_values;
Integer num_solution = vect_solution.size();
//!Steps
for(Integer i = 1; i < num_solution; i++){
step_index_values.clear();
step_var_values.clear();
step_index_values.insert(KeyInteger("timeStep",i));
IntegerVector ref = vect_solution[i]->getNumbComponentsSolve();
Integer numb_comp = ref.sum();
step_var_values.insert(KeyReal("number_of_components" ,numb_comp));
datacube.table_of_index_values.add(step_index_values);
datacube.table_of_variable_values.add(step_var_values);
}
///======================================
/// Write Results
///======================================
String filename = "Componentsresult";
//! Description
String filenameDesc = filename + ".restab.desc";
String text_desc = datacube.toStringDescription();
//std::cout << text_desc << "\n";
datacube.writeDescription(filenameDesc);
//! Data
String filenameData = filename + ".restab";
String text_data = datacube.toStringData();
//std::cout << text_data << "\n";
datacube.writeData(filenameData);
//======================================
return 0;
}
