void *BkgFitWorkerCpu(void *arg)
{
ProcessorQueue* pq = static_cast<ProcessorQueue*>(arg);
assert(pq);
WorkerInfoQueue* curQ = NULL;
bool done = false;
WorkerInfoQueueItem item;
while (!done)
{
//item = TryGettingFittingJobForCpuFromQueue(pq, &curQ);
item = pq->TryGettingFittingJob(&curQ);
if (item.finished == true)
{
// we are no longer needed...go away!
done = true;
curQ->DecrementDone();
continue;
}
int event = * ( (int *) item.private_data);
if (event == MULTI_FLOW_REGIONAL_FIT)
{
DoMultiFlowRegionalFit(item);
}
else if (event == INITIAL_FLOW_BLOCK_ALLBEAD_FIT)
{
DoInitialBlockOfFlowsAllBeadFit(item);
}
else if (event == INITIAL_FLOW_BLOCK_REMAIN_REGIONAL_FIT)
{
DoInitialBlockOfFlowsRemainingRegionalFit(item);
}
else if (event == SINGLE_FLOW_FIT) {
DoSingleFlowFitAndPostProcessing(item);
}
else if (event == POST_FIT_STEPS) {
DoPostFitProcessing(item);
}
else if (event == imageInitBkgModel)
{
DoConstructSignalProcessingFitterAndData (item);
}
// indicate we finished that bit of work
curQ->DecrementDone();
}
return (NULL);
}
void *FileSDatLoadWorker ( void *arg )
{
WorkerInfoQueue *q = static_cast<WorkerInfoQueue *> ( arg );
assert ( q );
bool done = false;
while ( !done )
{
WorkerInfoQueueItem item = q->GetItem();
if ( item.finished == true )
{
// we are no longer needed...go away!
done = true;
q->DecrementDone();
continue;
}
ClockTimer timer;
ImageLoadWorkInfo *one_img_loader = ( ImageLoadWorkInfo * ) item.private_data;
SynchDat &sdat = one_img_loader->sdat[one_img_loader->cur_buffer];
// int flow_buffer_for_flow = one_img_loader->cur_buffer;
if ( one_img_loader->inception_state->img_control.col_flicker_correct ) {
ComparatorNoiseCorrector cnc;
Mask &mask = *(one_img_loader->mask);
for (size_t rIx = 0; rIx < sdat.GetNumBin(); rIx++) {
TraceChunk &chunk = sdat.GetChunk(rIx);
// Copy over temp mask for normalization
Mask m(chunk.mWidth, chunk.mHeight);
for (size_t r = 0; r < chunk.mHeight; r++) {
for (size_t c = 0; c < chunk.mWidth; c++) {
m[r*chunk.mWidth+c] = mask[(r+chunk.mRowStart) * mask.W() + (c+chunk.mColStart)];
}
}
cnc.CorrectComparatorNoise(&chunk.mData[0], chunk.mHeight, chunk.mWidth, chunk.mDepth,
&m, one_img_loader->inception_state->img_control.col_flicker_correct_verbose);
}
}
// @todo output trace and dc offset info
sdat.SubDcOffset();
SetReadCompleted(one_img_loader);
size_t usec = timer.GetMicroSec();
fprintf ( stdout, "FileLoadWorker: ImageProcessing time for flow %d: %0.5lf sec\n", one_img_loader->flow, usec / 1.0e6);
q->DecrementDone();
}
return ( NULL );
}
void *FileLoadWorker ( void *arg )
{
WqInfo_t *wqinfo = (WqInfo_t *)arg;
int threadNum=wqinfo->threadNum;
WorkerInfoQueue *q = wqinfo->wq;
assert ( q );
bool done = false;
char dateStr[256];
struct tm newtime;
time_t ltime;
double T1=0,T2=0,T3,T4;
char name[20];
sprintf(name,"FileLdWkr%d",threadNum);
prctl(PR_SET_NAME,name,0,0,0);
const double noiseThreshold = 0.; // to be set by command line option
FluidPotentialCorrector fpCorr(noiseThreshold);
while ( !done )
{
WorkerInfoQueueItem item = q->GetItem();
if ( item.finished == true )
{
// we are no longer needed...go away!
done = true;
q->DecrementDone();
continue;
}
ImageLoadWorkInfo *one_img_loader = ( ImageLoadWorkInfo * ) item.private_data;
ClockTimer timer;
Timer tmr;
Image *img = &one_img_loader->img[one_img_loader->cur_buffer];
if (one_img_loader->inception_state->img_control.threaded_file_access)
{
tmr.restart();
if ( !img->LoadRaw ( one_img_loader->name) )
{
fprintf ( stdout, "ERROR: Failed to load raw image %s\n", one_img_loader->name );
exit ( EXIT_FAILURE );
}
T1=tmr.elapsed();
tmr.restart();
if(img->raw->imageState & IMAGESTATE_QuickPinnedPixelDetect)
one_img_loader->pinnedInFlow->QuickUpdate ( one_img_loader->flow, img);
else
one_img_loader->pinnedInFlow->Update ( one_img_loader->flow, img,(ImageTransformer::gain_correction?ImageTransformer::gain_correction:0));
T2=tmr.elapsed();
}
tmr.restart();
// correct in-channel electrical cross-talk
ImageTransformer::XTChannelCorrect ( one_img_loader->img[one_img_loader->cur_buffer].raw, one_img_loader->img[one_img_loader->cur_buffer].results_folder ); // buffer_ix
// testing of lossy compression
if(ImageTransformer::PCATest[0]) {
AdvComprTest(one_img_loader->name,&one_img_loader->img[one_img_loader->cur_buffer],ImageTransformer::PCATest,false/*one_img_loader->inception_state->img_control.col_flicker_correct*/ );
}
// col noise correction (if done during lossy compression will already have happened.
else if ( !(img->raw->imageState & IMAGESTATE_ComparatorCorrected) &&
one_img_loader->inception_state->img_control.col_flicker_correct )
{
if( one_img_loader->inception_state->img_control.col_pair_pixel_xtalk_correct ){
PairPixelXtalkCorrector xtalkCorrector;
float xtalk_fraction = one_img_loader->inception_state->img_control.pair_xtalk_fraction;
xtalkCorrector.Correct(one_img_loader->img[one_img_loader->cur_buffer].raw, xtalk_fraction);
}
if (one_img_loader->inception_state->img_control.corr_noise_correct){
CorrNoiseCorrector rnc;
rnc.CorrectCorrNoise(one_img_loader->img[one_img_loader->cur_buffer].raw,3,one_img_loader->inception_state->bfd_control.beadfindThumbnail );
}
if(one_img_loader->inception_state->bfd_control.beadfindThumbnail)
{
//ComparatorNoiseCorrector
ComparatorNoiseCorrector cnc;
cnc.CorrectComparatorNoiseThumbnail(one_img_loader->img[one_img_loader->cur_buffer].raw, one_img_loader->mask, one_img_loader->inception_state->loc_context.regionXSize,one_img_loader->inception_state->loc_context.regionYSize, one_img_loader->inception_state->img_control.col_flicker_correct_verbose);
} else {
ComparatorNoiseCorrector cnc;
cnc.CorrectComparatorNoise(one_img_loader->img[one_img_loader->cur_buffer].raw, one_img_loader->mask, one_img_loader->inception_state->img_control.col_flicker_correct_verbose, one_img_loader->inception_state->img_control.aggressive_cnc,false,threadNum );
}
}
//#define DEBUG_IMAGE_CORR_ISSUES 1
#ifdef DEBUG_IMAGE_CORR_ISSUES
char newName[1024];
char *nptr,*ptr=one_img_loader->name;
while((nptr = strstr(ptr,"/")))ptr=nptr+1;
if(*ptr == '/')
ptr++;
sprintf(newName,"%s_proc",one_img_loader->name);
Acq saver;
saver.SetData ( &one_img_loader->img[one_img_loader->cur_buffer] );
saver.WriteVFC(newName, 0, 0, one_img_loader->img[one_img_loader->cur_buffer].raw->cols, one_img_loader->img[one_img_loader->cur_buffer].raw->rows);
#endif
T3=tmr.elapsed();
tmr.restart();
// Fluid potential corrector
const bool correctFluidPotential = one_img_loader->inception_state->img_control.fluid_potential_correct;
const double noiseThreshold = (double) one_img_loader->inception_state->img_control.fluid_potential_threshold;
if (correctFluidPotential){
fpCorr.setThreshold(noiseThreshold);
// parse rowsum file name to load
const std::string datFileName = one_img_loader->name;
printf("dat file name %s\n", datFileName.c_str());
const size_t pos1 = datFileName.find_last_of('/');
const size_t pos2 = datFileName.find_last_of('.');
const std::string rowsumFileName = datFileName.substr(0, pos1) + "/../rowsum/" + datFileName.substr(pos1+1, pos2-pos1-1) + ".hwsum";
// printf("rowsum file name %s pos1 %u pos2 %u\n", rowsumFileName.c_str(), (uint32_t) pos1, (uint32_t) pos2);
// determine if the data file is thumbnail or block
const bool isThumbnail = one_img_loader->inception_state->bfd_control.beadfindThumbnail;
if(isThumbnail){
fpCorr.setIsThumbnail();
}
// set image
const unsigned int regionXSize = one_img_loader->inception_state->loc_context.regionXSize;
const unsigned int regionYSize = one_img_loader->inception_state->loc_context.regionYSize;
const char nucChar = one_img_loader->inception_state->flow_context.ReturnNucForNthFlow(one_img_loader->flow);
fpCorr.setImage(one_img_loader->img[one_img_loader->cur_buffer].raw, one_img_loader->mask, regionYSize, regionXSize, nucChar);
//printf("nucChar is %c\n", nucChar);
// load sensing electrode data
if (isThumbnail){
const unsigned int numRows = one_img_loader->img[one_img_loader->cur_buffer].raw->rows;
fpCorr.loadSensingElectrodeDataThumbnail(rowsumFileName, numRows);
} else {
// determine startRow and endRow
one_img_loader->img[one_img_loader->cur_buffer].SetOffsetFromChipOrigin(one_img_loader->name);
const unsigned int startRow = one_img_loader->img[one_img_loader->cur_buffer].raw->chip_offset_y;
const unsigned int endRow = startRow + one_img_loader->img[one_img_loader->cur_buffer].raw->rows;
// printf("offset x y = %d %d, start and end rows are %u,%u\n", one_img_loader->img[one_img_loader->cur_buffer].raw->chip_offset_x,one_img_loader->img[one_img_loader->cur_buffer].raw->chip_offset_y, startRow, endRow);
fpCorr.loadSensingElectrodeData(rowsumFileName, startRow, endRow);
}
// correct fluid potential
if (fpCorr.readRowSumIsSuccess()){
fpCorr.doCorrection();
} else {
printf("fluidPotentialCorrector skipped: Cannot find rowsum file %s \n", rowsumFileName.c_str());
}
}
// dump dc offset one_img_loaderrmation before we do any normalization
DumpDcOffset ( one_img_loader );
int buffer_ix = one_img_loader->cur_buffer;
// setting the mean of frames to zero will be done by the bkgmodel as soon as its loaded.
// the traces will be zero'd by the bknd model loader anyway, no need to do them here.
// img->SetMeanOfFramesToZero ( one_img_loader->normStart, one_img_loader->normEnd,0 );
// calculate the smooth pH step amplitude in empty wells across the whole image
if ( one_img_loader->doEmptyWellNormalization )
{
// this is redundant with what's in the EmptyTrace class, but this method of spatial normalization
// is going to go away soon, so not worth fixing
MaskType referenceMask = MaskReference;
if ( one_img_loader->inception_state->bkg_control.trace_control.use_dud_and_empty_wells_as_reference )
referenceMask = ( MaskType ) ( MaskReference | MaskDud );
one_img_loader->img[buffer_ix].CalculateEmptyWellLocalScaleForFlow ( * ( one_img_loader->pinnedInFlow ),one_img_loader->mask,one_img_loader->flow,referenceMask,one_img_loader->smooth_span );
#if 0
char fname[512];
sprintf ( fname,"ewampimg_%04d.txt",one_img_loader->flow );
FILE *ewampfile = fopen ( fname,"w" );
for ( int row=0;row < one_img_loader->img[buffer_ix].GetRows();row++ )
{
int col;
for ( col=0;col < ( one_img_loader->img[buffer_ix].GetCols()-1 ); col++ )
fprintf ( ewampfile,"%9.5f\t",one_img_loader->img[buffer_ix].getEmptyWellAmplitude ( row,col ) );
fprintf ( ewampfile,"%9.5f\n",one_img_loader->img[buffer_ix].getEmptyWellAmplitude ( row,col ) );
}
fclose ( ewampfile );
#endif
}
// dump pH step debug one_img_loader to file (its really fast, don't worry)
DumpStep ( one_img_loader );
if ( one_img_loader->doRawBkgSubtract )
{
one_img_loader->img[buffer_ix].SubtractLocalReferenceTrace ( one_img_loader->mask, MaskBead, MaskReference, one_img_loader->NNinnerx,
one_img_loader->NNinnery,one_img_loader->NNouterx,one_img_loader->NNoutery, false, true, true );
if ( one_img_loader->flow==0 ) // absolute first flow,not flow buffer
printf ( "Notify user: NN empty subtraction in effect. No further warnings will be given. %d \n",one_img_loader->flow );
}
T4=tmr.elapsed();
// printf ( "Allow model to go %d \n", one_img_loader->flow );
SetReadCompleted(one_img_loader);
size_t usec = timer.GetMicroSec();
ltime=time(<ime);
localtime_r(<ime, &newtime);
strftime(dateStr,sizeof(dateStr),"%H:%M:%S", &newtime);
fprintf ( stdout, "FileLoadWorker: ImageProcessing time for flow %d: %0.2lf(ld=%.2f pin=%.2f cnc=%.2f xt=%.2f sem=%.2lf cache=%.2lf) sec %s\n",
one_img_loader->flow , usec / 1.0e6, T1, T2, T3, T4, img->SemaphoreWaitTime, img->CacheAccessTime, dateStr);
fflush(stdout);
fprintf(stdout, "File: %s\n", one_img_loader->name);
fflush(stdout);
q->DecrementDone();
}
return ( NULL );
}
void *FileSDatLoadWorker ( void *arg )
{
WorkerInfoQueue *q = static_cast<WorkerInfoQueue *> ( arg );
assert ( q );
bool done = false;
TraceChunkSerializer serializer;
while ( !done )
{
WorkerInfoQueueItem item = q->GetItem();
if ( item.finished == true )
{
// we are no longer needed...go away!
done = true;
q->DecrementDone();
continue;
}
ClockTimer timer;
ImageLoadWorkInfo *one_img_loader = ( ImageLoadWorkInfo * ) item.private_data;
bool ok = serializer.Read ( one_img_loader->name, one_img_loader->sdat[one_img_loader->cur_buffer] );
if (!ok) {
ION_ABORT("Couldn't load file: " + ToStr(one_img_loader->name));
}
one_img_loader->pinnedInFlow->Update ( one_img_loader->flow, &one_img_loader->sdat[one_img_loader->cur_buffer],(ImageTransformer::gain_correction?ImageTransformer::gain_correction:0));
// one_img_loader->pinnedInFlow->Update ( one_img_loader->flow, &one_img_loader->sdat[one_img_loader->cur_buffer] );
SynchDat &sdat = one_img_loader->sdat[one_img_loader->cur_buffer];
// if ( ImageTransformer::gain_correction != NULL )
// ImageTransformer::GainCorrectImage ( &sdat );
// ImageTransformer::GainCorrectImage ( &one_img_loader->sdat[one_img_loader->cur_buffer] );
// int buffer_ix = one_img_loader->cur_buffer;
if ( one_img_loader->inception_state->img_control.col_flicker_correct ) {
ComparatorNoiseCorrector cnc;
Mask &mask = *(one_img_loader->mask);
for (size_t rIx = 0; rIx < sdat.GetNumBin(); rIx++) {
TraceChunk &chunk = sdat.GetChunk(rIx);
// Copy over temp mask for normalization
Mask m(chunk.mWidth, chunk.mHeight);
for (size_t r = 0; r < chunk.mHeight; r++) {
for (size_t c = 0; c < chunk.mWidth; c++) {
m[r*chunk.mWidth+c] = mask[(r+chunk.mRowStart) * mask.W() + (c+chunk.mColStart)];
}
}
cnc.CorrectComparatorNoise(&chunk.mData[0], chunk.mHeight, chunk.mWidth, chunk.mDepth,
&m, one_img_loader->inception_state->img_control.col_flicker_correct_verbose,
one_img_loader->inception_state->img_control.aggressive_cnc);
}
}
// @todo output trace and dc offset info
sdat.AdjustForDrift();
sdat.SubDcOffset();
SetReadCompleted(one_img_loader);
size_t usec = timer.GetMicroSec();
fprintf ( stdout, "FileLoadWorker: ImageProcessing time for flow %d: %0.5lf sec\n", one_img_loader->flow, usec / 1.0e6);
q->DecrementDone();
}
return ( NULL );
}
void *FileLoadWorker ( void *arg )
{
WorkerInfoQueue *q = static_cast<WorkerInfoQueue *> ( arg );
assert ( q );
bool done = false;
while ( !done )
{
WorkerInfoQueueItem item = q->GetItem();
if ( item.finished == true )
{
// we are no longer needed...go away!
done = true;
q->DecrementDone();
continue;
}
ImageLoadWorkInfo *one_img_loader = ( ImageLoadWorkInfo * ) item.private_data;
ClockTimer timer;
if (one_img_loader->inception_state->img_control.threaded_file_access)
JustLoadOneImageWithPinnedUpdate(one_img_loader);
// col noise correction
if ( one_img_loader->inception_state->img_control.col_flicker_correct )
{
if(one_img_loader->inception_state->bfd_control.beadfindThumbnail)
{
//ComparatorNoiseCorrector
ComparatorNoiseCorrector cnc;
cnc.CorrectComparatorNoiseThumbnail(one_img_loader->img[one_img_loader->cur_buffer].raw, one_img_loader->mask, one_img_loader->inception_state->loc_context.regionXSize,one_img_loader->inception_state->loc_context.regionYSize, one_img_loader->inception_state->img_control.col_flicker_correct_verbose);
} else {
ComparatorNoiseCorrector cnc;
cnc.CorrectComparatorNoise(one_img_loader->img[one_img_loader->cur_buffer].raw, one_img_loader->mask, one_img_loader->inception_state->img_control.col_flicker_correct_verbose);
}
}
// dump dc offset one_img_loaderrmation before we do any normalization
DumpDcOffset ( one_img_loader );
int flow_buffer_for_flow = one_img_loader->cur_buffer;
one_img_loader->img[flow_buffer_for_flow].SetMeanOfFramesToZero ( one_img_loader->normStart, one_img_loader->normEnd );
// correct in-channel electrical cross-talk
ImageTransformer::XTChannelCorrect ( one_img_loader->img[flow_buffer_for_flow].raw, one_img_loader->img[flow_buffer_for_flow].results_folder );
// calculate the smooth pH step amplitude in empty wells across the whole image
if ( one_img_loader->doEmptyWellNormalization )
{
// this is redundant with what's in the EmptyTrace class, but this method of spatial normalization
// is going to go away soon, so not worth fixing
MaskType referenceMask = MaskReference;
if ( one_img_loader->inception_state->bkg_control.use_dud_and_empty_wells_as_reference )
referenceMask = ( MaskType ) ( MaskReference | MaskDud );
one_img_loader->img[flow_buffer_for_flow].CalculateEmptyWellLocalScaleForFlow ( * ( one_img_loader->pinnedInFlow ),one_img_loader->mask,one_img_loader->flow,referenceMask,one_img_loader->smooth_span );
#if 0
char fname[512];
sprintf ( fname,"ewampimg_%04d.txt",one_img_loader->flow );
FILE *ewampfile = fopen ( fname,"w" );
for ( int row=0;row < one_img_loader->img[flow_buffer_for_flow].GetRows();row++ )
{
int col;
for ( col=0;col < ( one_img_loader->img[flow_buffer_for_flow].GetCols()-1 ); col++ )
fprintf ( ewampfile,"%9.5f\t",one_img_loader->img[flow_buffer_for_flow].getEmptyWellAmplitude ( row,col ) );
fprintf ( ewampfile,"%9.5f\n",one_img_loader->img[flow_buffer_for_flow].getEmptyWellAmplitude ( row,col ) );
}
fclose ( ewampfile );
#endif
}
// dump pH step debug one_img_loader to file (its really fast, don't worry)
DumpStep ( one_img_loader );
if ( one_img_loader->doRawBkgSubtract )
{
one_img_loader->img[flow_buffer_for_flow].SubtractLocalReferenceTrace ( one_img_loader->mask, MaskBead, MaskReference, one_img_loader->NNinnerx,
one_img_loader->NNinnery,one_img_loader->NNouterx,one_img_loader->NNoutery, false, true, true );
if ( one_img_loader->flow==0 ) // absolute first flow,not flow buffer
printf ( "Notify user: NN empty subtraction in effect. No further warnings will be given. %d \n",one_img_loader->flow );
}
printf ( "Allow model to go %d\n", one_img_loader->flow );
SetReadCompleted(one_img_loader);
size_t usec = timer.GetMicroSec();
fprintf ( stdout, "FileLoadWorker: ImageProcessing time for flow %d: %0.5lf sec\n", one_img_loader->flow , usec / 1.0e6);
q->DecrementDone();
}
return ( NULL );
}