void BkgTrace::GenerateAllBeadTrace (Region *region, BeadTracker &my_beads, SynchDat &chunk, int iFlowBuffer, bool matchSdat)
{
// ION_ASSERT(chunk.NumFrames(my_beads.params_nn[0].x,my_beads.params_nn[0].y) >= (size_t)time_cp->npts(), "Wrong data points.");
ION_ASSERT(chunk.NumFrames(region->row, region->col) >= (size_t)time_cp->npts(), "Wrong data points.");
for (int nbd = 0;nbd < my_beads.numLBeads;nbd++) // is this the right iterator here?
{
int rx = my_beads.params_nn[nbd].x; // should x,y be stored with traces instead?
int ry = my_beads.params_nn[nbd].y;
FG_BUFFER_TYPE *fg = &fg_buffers[bead_flow_t*nbd+time_cp->npts()*iFlowBuffer];
if (matchSdat) {
for (int i = 0; i < time_cp->npts(); i++) {
fg[i] = chunk.At(ry + region->row, rx + region->col, i);
}
}
else {
std::vector<float> tmp(time_cp->npts(), 0);
chunk.InterpolatedAt(ry + region->row, rx + region->col, time_cp->mTimePoints, tmp);
for (int i = 0; i < time_cp->npts(); i++) {
fg[i] = tmp[i];
}
}
float offset = BkgTrace::ComputeDcOffset(fg, *time_cp, 0.0f, time_cp->t0-2);
for (int i = 0; i < time_cp->npts(); i++) {
fg[i] = round(fg[i] - offset);
}
}
KeepEmptyScale(region, my_beads,chunk, iFlowBuffer);
}
void ImageSpecClass::ReadFirstImage(Image &img, SystemContext &sys_context, ImageControlOpts &img_control, SpatialContext &loc_context )
{
img.SetImgLoadImmediate ( false );
img.SetNumAcqFiles ( 1 );
img.SetIgnoreChecksumErrors ( img_control.ignoreChecksumErrors );
bool datIsSdat = false;
char *firstAcqFile = ( char * ) malloc ( strlen ( sys_context.dat_source_directory ) + strlen (
img_control.acqPrefix ) + 10 );
sprintf ( firstAcqFile, "%s/%s%04d.dat", sys_context.dat_source_directory, img_control.acqPrefix, 0 );
/* Check to see if our dat file is really an sdat file in disguise, if so updat our suffix and doing sdats. */
if (H5File::IsH5File(firstAcqFile)) {
datIsSdat = true;
img_control.sdatSuffix = "dat";
img_control.doSdat = true;
}
char *firstSdatAcqFile = ( char * ) malloc ( strlen ( sys_context.dat_source_directory ) + strlen (
img_control.acqPrefix ) + 11 );
sprintf ( firstSdatAcqFile, "%s/%s%04d.%s", sys_context.dat_source_directory, img_control.acqPrefix, 0, img_control.sdatSuffix.c_str() );
if (isFile(firstAcqFile) && !datIsSdat) {
if ( !img.LoadRaw ( firstAcqFile, 0, true, false ) )
{
exit ( EXIT_FAILURE );
}
}
else if(isFile(firstSdatAcqFile)) {
TraceChunkSerializer reader;
SynchDat sdat;
reader.Read(firstSdatAcqFile, sdat);
img.InitFromSdat(&sdat);
if (loc_context.regionXSize == 0){ // not explicitly set, set now
loc_context.regionXSize = sdat.GetColStep();
loc_context.regionYSize = sdat.GetRowStep();
}
if ((sdat.GetColStep() != (size_t)loc_context.regionXSize) ||
(sdat.GetRowStep() != (size_t)loc_context.regionYSize)) {
fprintf(stdout, "Warning: Analysis region sizes width=%d, height=%d do not match sdat region sizes width=%d, height=%d\n", loc_context.regionXSize, loc_context.regionYSize, (int)sdat.GetColStep(), (int)sdat.GetRowStep());
}
}
else {
exit ( EXIT_FAILURE );
}
img.SetOffsetFromChipOrigin ( firstAcqFile );
free ( firstAcqFile );
free ( firstSdatAcqFile );
if ( !loc_context.IsSetRegionXYSize() ){ // not yet set, has to be set now
loc_context.SetRegionXYSize(50, 50);
}
img.SetDir ( sys_context.results_folder );
img.SetFlowOffset ( img_control.flowTimeOffset );
}
void RegionalizedData::UpdateTracesFromImage (SynchDat &chunk, int flow)
{
ION_ASSERT(my_trace.time_cp->npts() <= (int)chunk.NumFrames(region->row, region->col), "Wrong number of frames.")
my_trace.SetRawTrace(); // buffers treated as raw traces
// populate bead traces from image file, just filling in data already saved
my_trace.GenerateAllBeadTrace (region,my_beads,chunk, my_flow.flowBufferWritePos, regionAndTimingMatchSdat);
// calculate average trace across all empty wells in a region for a flow
// to FileLoadWorker at Image load time, should be able to go here
emptytrace = emptyTraceTracker->GetEmptyTrace (*region);
// sanity check images are what we think
assert ( emptytrace->imgFrames == (int)chunk.NumFrames(region->row, region->col));
}
bool TraceChunkSerializer::Write(const char *filename, SynchDat &data) {
data.mInfo.SetValue(SYNCHDATSERIALIZE_VERSION_KEY, SYNCHDATSERIALIZE_VERSION_VALUE);
int numEntries = data.mInfo.GetCount();
vector<string> keys(numEntries);
vector<string> values(numEntries);
vector<const char *> keysBuff(numEntries);
vector<const char *> valuesBuff(numEntries);
for (int i = 0; i < numEntries; i++) {
data.mInfo.GetEntry(i, keys[i], values[i]);
keysBuff[i] = keys[i].c_str();
valuesBuff[i] = values[i].c_str();
}
ClockTimer timer;
H5File h5(filename);
bool ok = h5.OpenNew();
openMicroSec = timer.GetMicroSec();
if (!ok) { return ok; }
timer.StartTimer();
h5.WriteStringVector(INFO_KEYS, &keysBuff[0], keysBuff.size());
h5.WriteStringVector(INFO_VALUES, &valuesBuff[0], keysBuff.size());
ioMicroSec = timer.GetMicroSec();
ok = Write(h5, data.GetMesh());
timer.StartTimer();
h5.Close();
H5garbage_collect();
ioMicroSec += timer.GetMicroSec();
return ok;
}
void AddMetaData(SynchDat &sdat, const RawImage *raw, int acqNum) {
string s = ToStr(raw->timestamps[0]);
for (int i = 1; i < raw->frames; i++) {
s = s + "," + ToStr(raw->timestamps[i]);
}
sdat.SetValue("x_block", "0");
sdat.SetValue("y_block", "0");
sdat.SetValue("base_frame_rate","66");
sdat.SetValue("experiment_name","unknown");
sdat.SetValue("machine_name", "dat");
sdat.SetValue("serial_number","0");
sdat.SetValue("oversampling", "0");
sdat.SetValue("overclocking", "0");
sdat.SetValue("overclocking", "0");
sdat.SetValue("acq_num", ToStr(acqNum+1)); // +1 as dats are 0 based and acqs are 1 based
sdat.SetValue("orig_timestamps", ToStr(s));
sdat.SetValue("uncompressed_frames", ToStr(raw->uncompFrames));
}
bool TraceChunkSerializer::Read(const char *filename, SynchDat &data) {
data.Clear();
if (!H5File::IsH5File(filename)) {
return false;
}
bool result = true;
try {
if (!mRecklessAbandon) {
uint32_t waitTime = mRetryInterval;
int32_t timeOut = mTotalTimeout;
//--- Wait up to 3600 seconds for a file to be available
while ( timeOut > 0 )
{
//--- Is the file we want available?
if ( Image::ReadyToLoad ( filename ) ) {
break;
}
//DEBUG
fprintf ( stdout, "Waiting to load %s\n", filename );
sleep ( waitTime );
timeOut -= waitTime;
}
}
/* Turn off error printing as we're not sure this is actually an hdf5 file. */
H5File h5(filename);
result = h5.OpenForReading();
if (result) {
h5.SetReadOnly(true);
result &= Read(h5, data.GetMesh());
ReadInfo(h5, data);
}
h5.Close();
}
catch (...) {
result = false;
}
return result;
}
void RegionalizedData::UpdateTracesFromImage (SynchDat &chunk, FlowBufferInfo &my_flow, int flow, int flow_block_size)
{
ION_ASSERT(my_trace.time_cp->npts() <= (int)chunk.NumFrames(region->row, region->col), "Wrong number of frames.")
my_trace.SetRawTrace(); // buffers treated as raw traces
// populate bead traces from image file, just filling in data already saved
my_trace.GenerateAllBeadTrace (region,my_beads,chunk, my_flow.flowBufferWritePos, regionAndTimingMatchSdat, flow_block_size);
float t_mid_nuc = GetTypicalMidNucTime (&my_regions.rp.nuc_shape);
float t_offset_beads = my_regions.rp.nuc_shape.sigma;
my_trace.RezeroBeads(time_c.time_start, t_mid_nuc-t_offset_beads, my_flow.flowBufferWritePos, flow_block_size);
// calculate average trace across all empty wells in a region for a flow
// to FileLoadWorker at Image load time, should be able to go here
emptytrace = emptyTraceTracker->GetEmptyTrace (*region);
}
void SignalProcessingMasterFitter::AllocateRegionDataIfNeeded ( SynchDat &data )
{
if ( region_data->my_trace.NeedsAllocation() )
{
TraceChunk &chunk = data.GetItemByRowCol ( get_region_row(), get_region_col() );
// timing initialized to match chunk timing
SetupTimeAndBuffers ( chunk.mSigma, chunk.mTMidNuc, chunk.mT0 );
// SetupTimeAndBuffers ( chunk.mSigma, chunk.mTMidNuc, chunk.mT0 );
if ( chunk.RegionMatch ( *region_data->region ) )
{
if ( chunk.TimingMatch ( region_data->time_c.mTimePoints ) )
{
// both region and timing match chunk
region_data->regionAndTimingMatchSdat = true;
}
}
}
}