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));
}
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 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);
}