void CumulativeLostHydrogens ( float **model_trace, float **incorporation_rise,
TimeCompression &time_c, RegionTracker &my_regions,
bool use_vectorization,
float *vec_tau_top )
{
// Now solve the top of the well cumulative lost hydrogen ions
// happen faster, hence tau_top
#ifdef __INTEL_COMPILER
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
RedSolveHydrogenFlowInWell ( model_trace[fnum],incorporation_rise[fnum],time_c.npts(),my_regions.cache_step.i_start_coarse_step[fnum],&time_c.deltaFrame[0],vec_tau_top[fnum] ); // we lose hydrogen ions fast!
}
}
#else
if ( use_vectorization )
{
RedSolveHydrogenFlowInWell_Vec ( NUMFB,model_trace,incorporation_rise,time_c.npts(),&time_c.deltaFrame[0],vec_tau_top ); // we lose hydrogen ions fast!
}
else
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
RedSolveHydrogenFlowInWell ( model_trace[fnum],incorporation_rise[fnum],time_c.npts(),my_regions.cache_step.i_start_coarse_step[fnum],&time_c.deltaFrame[0],vec_tau_top[fnum] ); // we lose hydrogen ions fast!
}
}
#endif
for ( int fnum=0; fnum<NUMFB; fnum++ )
DiminishVector ( incorporation_rise[fnum],model_trace[fnum],time_c.npts() ); // cumulative lost hydrogen ions instead of retained hydrogen ions
}
void single_flow_optimizer::AllocLevMar (TimeCompression &time_c, PoissonCDFApproxMemo *_math_poiss, float damp_kmult, bool _var_kmult_only, float kmult_low_limit, float kmult_hi_limit, float AmplLowerLimit)
{
//@TODO: All these fitters share the curried calc_trace object, so we can do something useful by sharing it
math_poiss = _math_poiss;
// one parameter fit
oneFlowFit = new BkgModSingleFlowFit (time_c.npts(),&time_c.frameNumber[0],&time_c.deltaFrame[0],&time_c.deltaFrameSeconds[0],math_poiss,1);
// two parameter fit
oneFlowFitKrate = new BkgModSingleFlowFit (time_c.npts(),&time_c.frameNumber[0],&time_c.deltaFrame[0],&time_c.deltaFrameSeconds[0], math_poiss, 2);
// set up levmar state before going off on a wild adventure
oneFlowFit->SetLambdaThreshold (10.0);
oneFlowFitKrate->SetLambdaThreshold (1.0);
SetLowerLimitAmplFit (AmplLowerLimit,kmult_low_limit);
SetUpperLimitAmplFit (LAST_POISSON_TABLE_COL,kmult_hi_limit);
float my_prior[2] = {0.0, 1.0}; // amplitude, kmult
float my_damper[2] = {0.0,damp_kmult*time_c.npts()}; // must make a difference to change kmult
oneFlowFitKrate->SetPrior (&my_prior[0]);
oneFlowFitKrate->SetDampers (&my_damper[0]);
var_kmult_only = _var_kmult_only;
// boot up the new projection fit >which is not an instance of LevMar<
ProjectionFit = new ProjectionSearchOneFlow (time_c.npts(), &time_c.deltaFrame[0], &time_c.deltaFrameSeconds[0], math_poiss);
ProjectionFit->max_paramA = LAST_POISSON_TABLE_COL;
ProjectionFit->min_paramA = AmplLowerLimit;
AltFit = new AlternatingDirectionOneFlow (time_c.npts(), &time_c.deltaFrame[0], &time_c.deltaFrameSeconds[0], math_poiss);
}
void MathModel::AccumulateSingleNeighborExcessHydrogenOneParameter ( float *my_xtflux, float *neighbor_signal,
BeadParams *p, reg_params *reg_p,
BeadScratchSpace &my_scratch,
buffer_params_block_flows &my_cur_buffer_block,
TimeCompression &time_c,
RegionTracker &my_regions, const FlowBufferInfo & my_flow,
bool use_vectorization,
float multiplier, bool rescale_flag,
int flow_block_size, int flow_block_start )
{
FillBufferParamsBlockFlows ( &my_cur_buffer_block,p,reg_p,my_flow.flow_ndx_map, flow_block_start,
flow_block_size );
float block_model_trace[my_scratch.bead_flow_t], block_incorporation_rise[my_scratch.bead_flow_t];
// "In parallel, across flows"
float* model_trace[flow_block_size];
float* scratch_trace[flow_block_size];
float* incorporation_rise[flow_block_size];
float* lost_hydrogens[flow_block_size];
float* neighbor_local[flow_block_size];
// should this be using cur_buffer_block as usual?
float vec_tau_well[flow_block_size];
float vec_tau_empty[flow_block_size];
for ( int fnum=0; fnum<flow_block_size; fnum++ )
{
vec_tau_well[fnum] = my_cur_buffer_block.tauB[fnum];
vec_tau_empty[fnum] = my_cur_buffer_block.etbR[fnum]*vec_tau_well[fnum];
}
// setup parallel pointers into the structure
for ( int fnum=0; fnum<flow_block_size; fnum++ )
{
scratch_trace[fnum] = model_trace[fnum] = &block_model_trace[fnum*time_c.npts() ];
lost_hydrogens[fnum] = incorporation_rise[fnum] = &block_incorporation_rise[fnum*time_c.npts() ]; // set up each flow information
neighbor_local[fnum] = &neighbor_signal[fnum*time_c.npts() ];
}
IncorporationRiseFromNeighborSignal ( incorporation_rise,neighbor_local, time_c,my_regions, my_scratch, my_cur_buffer_block, flow_block_size );
// uses a scratch buffer here [recycles model_trace as we don't need it yet],
// turns incorporation_rise into lost_hydrogens
CumulativeLostHydrogens ( incorporation_rise, scratch_trace, time_c, my_regions, use_vectorization, vec_tau_well, flow_block_size );
// lost_hydrogens=incorporation_rise returned as lost_hydrogens above
// now we generate the real model_trace we're accumulating
IonsFromBulk ( model_trace,lost_hydrogens, time_c, my_regions, my_flow, use_vectorization, vec_tau_empty, flow_block_size );
if (rescale_flag)
RescaleTraceByBuffering(model_trace, vec_tau_well, vec_tau_empty,time_c.npts(), flow_block_size);
// universal
MultiplyVectorByScalar ( block_model_trace,multiplier,my_scratch.bead_flow_t ); // scale down the quantity of ions
// add to the bulk cross-talk we're creating
AccumulateVector ( my_xtflux, block_model_trace,my_scratch.bead_flow_t );
}
void IonsFromBulk ( float **model_trace, float **incorporation_rise,
TimeCompression &time_c, RegionTracker &my_regions, flow_buffer_info my_flow,
bool use_vectorization,
float *vec_tau_bulk )
{
// finally solve the way hydrogen ions diffuse out of the bulk
#ifdef __INTEL_COMPILER
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
// Now solve the bulk
RedSolveHydrogenFlowInWell ( model_trace[fnum],incorporation_rise[fnum],time_c.npts(),
my_regions.cache_step.i_start_coarse_step[my_flow.flow_ndx_map[fnum]],&time_c.deltaFrame[0],vec_tau_bulk[fnum] ); // we retain hydrogen ions variably in the bulk depending on direction
}
}
#else
if ( use_vectorization )
{
// Now solve the bulk
RedSolveHydrogenFlowInWell_Vec ( NUMFB,model_trace,incorporation_rise,time_c.npts(),&time_c.deltaFrame[0],vec_tau_bulk );
}
else
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
// Now solve the bulk
RedSolveHydrogenFlowInWell ( model_trace[fnum],incorporation_rise[fnum],time_c.npts(),
my_regions.cache_step.i_start_coarse_step[fnum],&time_c.deltaFrame[0],vec_tau_bulk[fnum] ); // we retain hydrogen ions variably in the bulk depending on direction
}
}
#endif
}
void EmptyTrace::ShiftMe (
float tshift, const TimeCompression &time_cp, const float *my_buff, float *out_buff,
int flow_block_size ) const
{
for (int fnum=0;fnum<flow_block_size;fnum++)
{
float *fbkg = out_buff + fnum*time_cp.npts();
const float *bg = &my_buff[fnum*imgFrames]; // get ptr to start of neighbor background
memset (fbkg,0,sizeof (float[time_cp.npts()])); // on general principles
//fprintf(stdout, "tshift %f\n", tshift);
for (int i=0;i < time_cp.npts();i++){
// get the frame number of this data point (might be fractional because this point could be
// the average of several frames of data. This number is the average time of all the averaged
// data points
float t=time_cp.frameNumber[i];
float fn=t-tshift;
if (fn < 0.0f) fn = 0.0f;
if (fn > (imgFrames-2)) fn = imgFrames-2;
int ifn= (int) fn;
float frac = fn - ifn;
fbkg[i] = ( (1-frac) *bg[ifn] + frac*bg[ifn+1]);
assert ( !isnan(fbkg[i]) );
}
}
}
// Multiflow: Solve incorporation
// Solve lost hydrogens to bulk
// solve bulk resistance to lost hydrogens
// this function too large, should be componentized
void AccumulateSingleNeighborXtalkTrace ( float *my_xtflux, bead_params *p, reg_params *reg_p,
BeadScratchSpace &my_scratch, TimeCompression &time_c, RegionTracker &my_regions, flow_buffer_info my_flow,
PoissonCDFApproxMemo *math_poiss, bool use_vectorization,
float tau_top, float tau_bulk, float multiplier )
{
// Compute the hydrogen signal of xtalk in the bulk fluid above the affected well
// 1) Xtalk happens fast -> we compute the cumulative lost hydrogen ions at the top of the bead instead of at the bottom (tau_top)
// 1a) xtalk happens as the well loses hydrogen ions so the cumulative lost = cumulative total generated - number in well currently
// 2) hydrogen ions are "retained" by the bulk for a finite amount of time as they are swept along
// 2a) this 'retainer' may be asymmetric (tau_bulk) models the decay rate
// 3) multiplier: hydrogen ions spread out, so are of different proportion to the original signal
// this is pre-calculated outside for the current region parameters
//my_regions.cache_step.CalculateNucRiseCoarseStep(reg_p,time_c);
// over-ride buffering parameters for bead
// use the same incorporation parameters, though
FillIncorporationParamsBlockFlows ( &my_scratch.cur_bead_block, p,reg_p,my_flow.flow_ndx_map,my_flow.buff_flow );
//params_IncrementHits(p);
float block_model_trace[my_scratch.bead_flow_t], block_incorporation_rise[my_scratch.bead_flow_t];
// "In parallel, across flows"
float* nuc_rise_ptr[NUMFB];
float* model_trace[NUMFB];
float* incorporation_rise[NUMFB];
// should this be using cur_buffer_block as usual?
float vec_tau_top[NUMFB];
float vec_tau_bulk[NUMFB];
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
vec_tau_top[fnum] = tau_top;
vec_tau_bulk[fnum] = tau_bulk;
}
// setup parallel pointers into the structure
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
nuc_rise_ptr[fnum] = my_regions.cache_step.NucCoarseStep ( fnum );
model_trace[fnum] = &block_model_trace[fnum*time_c.npts() ];
incorporation_rise[fnum] = &block_incorporation_rise[fnum*time_c.npts() ]; // set up each flow information
}
IncorporationRiseFromNeighborParameters ( incorporation_rise, nuc_rise_ptr, p, time_c, my_regions, my_scratch, math_poiss );
CumulativeLostHydrogens ( model_trace,incorporation_rise, time_c, my_regions, use_vectorization, vec_tau_top );
IonsFromBulk ( model_trace,incorporation_rise, time_c, my_regions, my_flow, use_vectorization, vec_tau_bulk );
// universal
MultiplyVectorByScalar ( block_model_trace,multiplier,my_scratch.bead_flow_t ); // scale down the quantity of ions
// add to the bulk cross-talk we're creating
AccumulateVector ( my_xtflux, block_model_trace,my_scratch.bead_flow_t );
}
void MathModel::AccumulateSingleNeighborExcessHydrogen ( float *my_xtflux, float *neighbor_signal, BeadParams *p, reg_params *reg_p,
BeadScratchSpace &my_scratch,
buffer_params_block_flows &my_cur_buffer_block,
TimeCompression &time_c,
RegionTracker &my_regions, const FlowBufferInfo & my_flow,
bool use_vectorization,
float tau_top, float tau_bulk, float multiplier,
int flow_block_size, int flow_block_start )
{
// over-ride buffering parameters for bead
FillBufferParamsBlockFlows ( &my_cur_buffer_block,p,reg_p,my_flow.flow_ndx_map,flow_block_start,
flow_block_size );
float block_model_trace[my_scratch.bead_flow_t], block_incorporation_rise[my_scratch.bead_flow_t];
// "In parallel, across flows"
float* model_trace[flow_block_size];
float* scratch_trace[flow_block_size];
float* incorporation_rise[flow_block_size];
float* lost_hydrogens[flow_block_size];
float* neighbor_local[flow_block_size];
// should this be using cur_buffer_block as usual?
float vec_tau_top[flow_block_size];
float vec_tau_bulk[flow_block_size];
for ( int fnum=0; fnum<flow_block_size; fnum++ )
{
vec_tau_top[fnum] = tau_top;
vec_tau_bulk[fnum] = tau_bulk;
}
// setup parallel pointers into the structure
for ( int fnum=0; fnum<flow_block_size; fnum++ )
{
scratch_trace[fnum]=model_trace[fnum] = &block_model_trace[fnum*time_c.npts() ];
lost_hydrogens[fnum]=incorporation_rise[fnum] = &block_incorporation_rise[fnum*time_c.npts() ]; // set up each flow information
neighbor_local[fnum] = &neighbor_signal[fnum*time_c.npts() ];
}
// make incorporation_rise
IncorporationRiseFromNeighborSignal ( incorporation_rise,neighbor_local, time_c,my_regions, my_scratch, my_cur_buffer_block, flow_block_size );
// use scratch_trace to hold temporary trace - same memory as model_trace because we don't need it yet
// turn incorporation_rise into lost_hydrogens
CumulativeLostHydrogens ( incorporation_rise, scratch_trace,time_c, my_regions, use_vectorization, vec_tau_top, flow_block_size );
// lost_hydrogens = incorporation_rise
// now get model_trace for real in cross-talk and overwrite any temporary uses of that space
IonsFromBulk ( model_trace,lost_hydrogens, time_c, my_regions, my_flow, use_vectorization, vec_tau_bulk, flow_block_size );
// universal
MultiplyVectorByScalar ( block_model_trace,multiplier,my_scratch.bead_flow_t ); // scale down the quantity of ions
// add to the bulk cross-talk we're creating
AccumulateVector ( my_xtflux, block_model_trace,my_scratch.bead_flow_t );
}
// 2nd-order background function with non-uniform bead well
void MultiFlowComputeTraceGivenIncorporationAndBackground ( float *fval,struct bead_params *p,struct reg_params *reg_p, float *ival, float *sbg,
RegionTracker &my_regions, buffer_params_block_flows &cur_buffer_block,
TimeCompression &time_c, flow_buffer_info &my_flow, bool use_vectorization, int bead_flow_t )
{
float *vb_out[NUMFB];
float *bkg_for_flow[NUMFB];
float *new_hydrogen_for_flow[NUMFB];
//@TODO: the natural place for vectorization is here at the flow level
// flows are logically independent: apply "compute trace" to all flows
// this makes for an obvious fit to solving 4 at once using the processor vectorization routines
// parallel fill one bead parameter for block of flows
FillBufferParamsBlockFlows ( &cur_buffer_block,p,reg_p,my_flow.flow_ndx_map,my_flow.buff_flow );
// parallel compute across flows
for ( int fnum=0;fnum<NUMFB;fnum++ )
{
vb_out[fnum] = fval + fnum*time_c.npts(); // get ptr to start of the function evaluation for the current flow
bkg_for_flow[fnum] = &sbg[fnum*time_c.npts() ]; // get ptr to pre-shifted background
new_hydrogen_for_flow[fnum] = &ival[fnum*time_c.npts() ];
}
// do the actual computation
#ifdef __INTEL_COMPILER
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
PurpleSolveTotalTrace ( vb_out[fnum],bkg_for_flow[fnum], new_hydrogen_for_flow[fnum], time_c.npts(),
&time_c.deltaFrame[0], cur_buffer_block.tauB[fnum], cur_buffer_block.etbR[fnum] );
}
#else // assumed to be GCC
if ( use_vectorization )
{
PurpleSolveTotalTrace_Vec ( NUMFB, vb_out, bkg_for_flow, new_hydrogen_for_flow, time_c.npts(),
&time_c.deltaFrame[0], cur_buffer_block.tauB, cur_buffer_block.etbR, p->gain );
}
else
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
PurpleSolveTotalTrace ( vb_out[fnum],bkg_for_flow[fnum], new_hydrogen_for_flow[fnum],time_c.npts(),
&time_c.deltaFrame[0], cur_buffer_block.tauB[fnum], cur_buffer_block.etbR[fnum] );
}
#endif
// adjust for well sensitivity, unexplained systematic effects
// gain naturally parallel across flows
MultiplyVectorByScalar ( fval,p->gain,bead_flow_t );
// Dark Matter is extra background term of unexplained origin
// Possibly should be applied directly to the observed signal rather than synthesized here inside a loop.
if (my_regions.missing_mass.mytype == PerNucAverage)
ApplyDarkMatter ( fval,reg_p,my_regions.missing_mass.dark_matter_compensator,my_flow.flow_ndx_map,time_c.npts() );
else
ApplyPCADarkMatter ( fval,p,my_regions.missing_mass.dark_matter_compensator,time_c.npts() );
}
void MultiCorrectBeadBkg ( float *block_signal_corrected, bead_params *p,
BeadScratchSpace &my_scratch, flow_buffer_info &my_flow, TimeCompression &time_c, RegionTracker &my_regions, float *sbg, bool use_vectorization )
{
float vb[my_scratch.bead_flow_t];
float* vb_out[my_flow.numfb];
float* sbgPtr[my_flow.numfb];
float block_bkg_plus_xtalk[my_scratch.bead_flow_t]; // set up instead of shifted background
memset ( vb,0,sizeof ( float[my_scratch.bead_flow_t] ) );
// add cross-talk for this bead to the empty-trace
CopyVector ( block_bkg_plus_xtalk,sbg,my_scratch.bead_flow_t );
AccumulateVector ( block_bkg_plus_xtalk,my_scratch.cur_xtflux_block,my_scratch.bead_flow_t );
// compute the zeromer
// setup pointers into the arrays
for ( int fnum=0; fnum<my_flow.numfb; fnum++ )
{
// remove zeromer background - just like oneFlowFit.
// should include xtalk (0) so I can reuse this routine
sbgPtr[fnum] = &block_bkg_plus_xtalk[fnum*time_c.npts() ];
vb_out[fnum] = &vb[fnum*time_c.npts() ];
}
// do the actual calculation in parallel or not
#ifdef __INTEL_COMPILER
{
for ( int fnum=0; fnum<my_flow.numfb; fnum++ )
BlueSolveBackgroundTrace ( vb_out[fnum],sbgPtr[fnum],time_c.npts(),&time_c.deltaFrame[0],
my_scratch.cur_buffer_block.tauB[fnum],my_scratch.cur_buffer_block.etbR[fnum] );
}
#else
if ( use_vectorization )
{
BlueSolveBackgroundTrace_Vec ( my_flow.numfb, vb_out, sbgPtr, time_c.npts(), &time_c.deltaFrame[0],
my_scratch.cur_buffer_block.tauB, my_scratch.cur_buffer_block.etbR );
}
else
{
for ( int fnum=0; fnum<my_flow.numfb; fnum++ )
BlueSolveBackgroundTrace ( vb_out[fnum],sbgPtr[fnum],time_c.npts(),&time_c.deltaFrame[0],
my_scratch.cur_buffer_block.tauB[fnum],my_scratch.cur_buffer_block.etbR[fnum] );
}
#endif
MultiplyVectorByScalar ( vb,p->gain,my_scratch.bead_flow_t );
ApplyDarkMatter ( vb,&my_regions.rp, my_regions.missing_mass.dark_matter_compensator,my_flow.flow_ndx_map,time_c.npts() );
// zeromer computed, now remove from observed
DiminishVector ( block_signal_corrected,vb,my_scratch.bead_flow_t ); // remove calculated background to produce corrected signal
}
void AccumulateSingleNeighborExcessHydrogenOneParameter ( float *my_xtflux, float *neighbor_signal,
bead_params *p, reg_params *reg_p,
BeadScratchSpace &my_scratch, TimeCompression &time_c,
RegionTracker &my_regions, flow_buffer_info my_flow,
bool use_vectorization,
float multiplier, bool rescale_flag )
{
FillBufferParamsBlockFlows ( &my_scratch.cur_buffer_block,p,reg_p,my_flow.flow_ndx_map,my_flow.buff_flow );
float block_model_trace[my_scratch.bead_flow_t], block_incorporation_rise[my_scratch.bead_flow_t];
// "In parallel, across flows"
float* model_trace[NUMFB];
float* incorporation_rise[NUMFB];
float* neighbor_local[NUMFB];
// should this be using cur_buffer_block as usual?
float vec_tau_well[NUMFB];
float vec_tau_empty[NUMFB];
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
vec_tau_well[fnum] = my_scratch.cur_buffer_block.tauB[fnum];
vec_tau_empty[fnum] = my_scratch.cur_buffer_block.etbR[fnum]*vec_tau_well[fnum];
}
// setup parallel pointers into the structure
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
model_trace[fnum] = &block_model_trace[fnum*time_c.npts() ];
incorporation_rise[fnum] = &block_incorporation_rise[fnum*time_c.npts() ]; // set up each flow information
neighbor_local[fnum] = &neighbor_signal[fnum*time_c.npts() ];
}
IncorporationRiseFromNeighborSignal ( incorporation_rise,neighbor_local, time_c,my_regions, my_scratch );
CumulativeLostHydrogens ( model_trace,incorporation_rise, time_c, my_regions, use_vectorization, vec_tau_well );
IonsFromBulk ( model_trace,incorporation_rise, time_c, my_regions, my_flow, use_vectorization, vec_tau_empty );
if (rescale_flag)
RescaleTraceByBuffering(model_trace, vec_tau_well, vec_tau_empty,time_c.npts());
// universal
MultiplyVectorByScalar ( block_model_trace,multiplier,my_scratch.bead_flow_t ); // scale down the quantity of ions
// add to the bulk cross-talk we're creating
AccumulateVector ( my_xtflux, block_model_trace,my_scratch.bead_flow_t );
}
void MultiFlowComputeCumulativeIncorporationSignal ( struct bead_params *p,struct reg_params *reg_p, float *ivalPtr,
NucStep &cache_step, incorporation_params_block_flows &cur_bead_block,
TimeCompression &time_c, flow_buffer_info &my_flow, PoissonCDFApproxMemo *math_poiss )
{
// only side effect should be new values in ivalPtr
// this is region wide
//This will short-circuit if has been computed
cache_step.CalculateNucRiseCoarseStep ( reg_p,time_c,my_flow );
// pretend I'm making a parallel process
FillIncorporationParamsBlockFlows ( &cur_bead_block, p,reg_p,my_flow.flow_ndx_map,my_flow.buff_flow );
// "In parallel, across flows"
float* nuc_rise_ptr[NUMFB];
float* incorporation_rise[NUMFB];
int my_start[NUMFB];
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
nuc_rise_ptr[fnum] = cache_step.NucCoarseStep ( fnum );
incorporation_rise[fnum]= &ivalPtr[fnum*time_c.npts() ];
my_start[fnum] = cache_step.i_start_coarse_step[fnum];
}
// this is >almost< a parallel operation by flows now
bool use_my_parallel=true;
if ( use_my_parallel )
{
//@TODO handle cases of fewer than 4 flows remaining
for ( int fnum=0; fnum<NUMFB; fnum+=4 )
{
ParallelSimpleComputeCumulativeIncorporationHydrogens ( &incorporation_rise[fnum], time_c.npts(), &time_c.deltaFrameSeconds[0],&nuc_rise_ptr[fnum],
ISIG_SUB_STEPS_MULTI_FLOW, &my_start[fnum], &p->Ampl[fnum],
&cur_bead_block.SP[fnum],&cur_bead_block.kr[fnum], &cur_bead_block.kmax[fnum], &cur_bead_block.d[fnum], &cur_bead_block.molecules_to_micromolar_conversion[fnum], math_poiss );
for ( int q=0; q<4; q++ )
MultiplyVectorByScalar ( incorporation_rise[fnum+q], cur_bead_block.sens[fnum+q],time_c.npts() ); // transform hydrogens to signal
}
}
else
{
for ( int fnum=0;fnum<NUMFB;fnum++ )
{
ComputeCumulativeIncorporationHydrogens ( incorporation_rise[fnum], time_c.npts(),
&time_c.deltaFrameSeconds[0], nuc_rise_ptr[fnum], ISIG_SUB_STEPS_MULTI_FLOW, my_start[fnum],
cur_bead_block.C[fnum], p->Ampl[fnum], cur_bead_block.SP[fnum], cur_bead_block.kr[fnum], cur_bead_block.kmax[fnum], cur_bead_block.d[fnum],cur_bead_block.molecules_to_micromolar_conversion[fnum], math_poiss );
MultiplyVectorByScalar ( incorporation_rise[fnum], cur_bead_block.sens[fnum],time_c.npts() ); // transform hydrogens to signal
}
}
}
void extern_links::DumpTimeAndEmphasisByRegionH5 ( int reg, TimeCompression &time_c, EmphasisClass &emphasis_data )
{
if ( mPtrs->mEmphasisParam!=NULL )
{
ION_ASSERT ( emphasis_data.numEv <= MAX_HPLEN+1, "emphasis_data.numEv > MAX_HPLEN+1" );
//ION_ASSERT(time_c.npts <= MAX_COMPRESSED_FRAMES, "time_c.npts > MAX_COMPRESSED_FRAMES");
int npts = std::min ( time_c.npts(), MAX_COMPRESSED_FRAMES );
if ( mPtrs->mEmphasisParam!=NULL )
{
// use copyCube_element to copy DataCube element to mEmphasisParam in BkgModel::DumpTimeAndEmphasisByRegionH5
for ( int hp=0; hp<emphasis_data.numEv; hp++ )
{
for ( int t=0; t< npts; t++ )
mPtrs->copyCube_element ( mPtrs->mEmphasisParam,reg,hp,t,emphasis_data.EmphasisVectorByHomopolymer[hp][t] );
for ( int t=npts; t< MAX_COMPRESSED_FRAMES; t++ )
mPtrs->copyCube_element ( mPtrs->mEmphasisParam,reg,hp,t,0 ); // pad 0's, memset faster here?
}
for ( int hp=emphasis_data.numEv; hp<MAX_HPLEN+1; hp++ )
{
for ( int t=0; t< MAX_COMPRESSED_FRAMES; t++ )
{
mPtrs->copyCube_element ( mPtrs->mEmphasisParam,reg,hp,t,0 ); // pad 0's, memset faster here?
}
}
}
}
}
// note: input is incorporation_rise, returns lost_hydrogens in the same buffer, recycling the memory
void CumulativeLostHydrogens ( float **incorporation_rise_to_lost_hydrogens, float **scratch_trace,
TimeCompression &time_c, RegionTracker &my_regions,
bool use_vectorization,
float *vec_tau_top )
{
// Put the model trace from buffering the incorporation_rise into scratch_trace
#ifdef __INTEL_COMPILER
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
RedSolveHydrogenFlowInWell ( scratch_trace[fnum],incorporation_rise_to_lost_hydrogens[fnum],time_c.npts(),my_regions.cache_step.i_start_coarse_step[fnum],&time_c.deltaFrame[0],vec_tau_top[fnum] ); // we lose hydrogen ions fast!
}
}
#else
if ( use_vectorization )
{
RedSolveHydrogenFlowInWell_Vec ( NUMFB,scratch_trace,incorporation_rise_to_lost_hydrogens,time_c.npts(),&time_c.deltaFrame[0],vec_tau_top ); // we lose hydrogen ions fast!
}
else
{
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
RedSolveHydrogenFlowInWell ( scratch_trace[fnum],incorporation_rise_to_lost_hydrogens[fnum],time_c.npts(),my_regions.cache_step.i_start_coarse_step[fnum],&time_c.deltaFrame[0],vec_tau_top[fnum] ); // we lose hydrogen ions fast!
}
}
#endif
// return lost_hydrogens in the incorporation_rise variables by subtracting the trace from the cumulative
for ( int fnum=0; fnum<NUMFB; fnum++ )
DiminishVector ( incorporation_rise_to_lost_hydrogens[fnum],scratch_trace[fnum],time_c.npts() ); // cumulative lost hydrogen ions instead of retained hydrogen ions
}
void extern_links::DumpTimeCompressionH5 ( int reg, TimeCompression &time_c )
{
if ( mPtrs->m_time_compression!=NULL )
{
int npts = time_c.npts();
//@TODO: copy/paste bad, but I have 3 different operations for 4 variables
// frameNumber
for ( int j=0; j<npts; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,0,j,time_c.frameNumber[j] );
for ( int j=npts; j<MAX_COMPRESSED_FRAMES; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,0,j,0.0f ); // pad 0's
//deltaFrame
for ( int j=0; j<npts; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,1,j,time_c.deltaFrame[j] );
for ( int j=npts; j<MAX_COMPRESSED_FRAMES; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,1,j,0.0f ); // pad 0's
//frames_per_point
for ( int j=0; j<npts; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,2,j, ( float ) time_c.frames_per_point[j] );
for ( int j=npts; j<MAX_COMPRESSED_FRAMES; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,2,j,0.0f ); // pad 0's
// npts = which time points are weighted
for ( int j=0; j<npts; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,3,j,1.0f );
for ( int j=npts; j<MAX_COMPRESSED_FRAMES; j++ )
mPtrs->copyCube_element ( mPtrs->m_time_compression,reg,3,j,0.0f ); // pad 0's
}
}
static void IncorporationRiseFromNeighborParameters (
float **incorporation_rise, const float * const *nuc_rise_ptr,
BeadParams *p,
TimeCompression &time_c, RegionTracker &my_regions,
BeadScratchSpace &my_scratch,
incorporation_params_block_flows &my_cur_bead_block,
PoissonCDFApproxMemo *math_poiss, int hydrogenModelType,
int flow_block_size)
{
// fill in each flow incorporation
for ( int fnum=0; fnum<flow_block_size; fnum++ )
{
// compute newly generated ions for the amplitude of each flow
MathModel::ComputeCumulativeIncorporationHydrogens ( incorporation_rise[fnum],
time_c.npts(), &time_c.deltaFrameSeconds[0], nuc_rise_ptr[fnum], ISIG_SUB_STEPS_MULTI_FLOW, my_regions.cache_step.i_start_coarse_step[fnum],
my_cur_bead_block.C[fnum], p->Ampl[fnum], my_cur_bead_block.SP[fnum], my_cur_bead_block.kr[fnum], my_cur_bead_block.kmax[fnum], my_cur_bead_block.d[fnum],my_cur_bead_block.molecules_to_micromolar_conversion[fnum], math_poiss, hydrogenModelType );
MultiplyVectorByScalar ( incorporation_rise[fnum], my_cur_bead_block.sens[fnum],time_c.npts() ); // transform hydrogens to signal // variables used for solving background signal shape
}
}
void extern_links::DumpDarkMatterH5 ( int reg, TimeCompression &time_c, RegionTracker &my_reg_tracker )
{
if ( mPtrs->mDarkOnceParam!=NULL )
{
int npts = time_c.npts();
for ( int i=0; i<NUMNUC; i++ )
{
float *missingMass = my_reg_tracker.missing_mass.dark_nuc_comp[i];
for ( int j=0; j<npts; j++ )
mPtrs->copyCube_element ( mPtrs->mDarkOnceParam,reg,i,j,missingMass[j] );
for ( int j=npts; j<MAX_COMPRESSED_FRAMES; j++ )
mPtrs->copyCube_element ( mPtrs->mDarkOnceParam,reg,i,j,0 ); // pad 0's
}
}
}
void IncorporationRiseFromNeighborSignal ( float **incorporation_rise, float **neighbor_local,
TimeCompression &time_c, RegionTracker &my_regions,
BeadScratchSpace &my_scratch
)
{
// fill in each flow incorporation
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
// grab my excess hydrogen ions from the observed signal
IntegrateRedFromObservedTotalTrace ( incorporation_rise[fnum], neighbor_local[fnum], &my_scratch.shifted_bkg[fnum*time_c.npts() ], time_c.npts(),&time_c.deltaFrame[0], my_scratch.cur_buffer_block.tauB[fnum], my_scratch.cur_buffer_block.etbR[fnum] );
// variables used for solving background signal shape
}
// construct the incorporation in the neighbor well just for research purposes
for ( int fnum=0; fnum<NUMFB; fnum++ )
{
// bad! put trace back in neighbor signal
RedSolveHydrogenFlowInWell ( neighbor_local[fnum],incorporation_rise[fnum],time_c.npts(),my_regions.cache_step.i_start_coarse_step[fnum],&time_c.deltaFrame[0],my_scratch.cur_buffer_block.tauB[fnum] ); // we lose hydrogen ions fast!
}
}
void MathModel::MultiFlowComputeCumulativeIncorporationSignal (
struct BeadParams *p,struct reg_params *reg_p, float *ivalPtr,
NucStep &cache_step, incorporation_params_block_flows &cur_bead_block,
const TimeCompression &time_c, const FlowBufferInfo &my_flow,
PoissonCDFApproxMemo *math_poiss, int flow_block_size,
int flow_block_start )
{
// only side effect should be new values in ivalPtr
// this is region wide
//This will short-circuit if has been computed
cache_step.CalculateNucRiseCoarseStep ( reg_p,time_c,my_flow );
// pretend I'm making a parallel process
FillIncorporationParamsBlockFlows ( &cur_bead_block, p,reg_p,my_flow.flow_ndx_map,
flow_block_start, flow_block_size );
// "In parallel, across flows"
const float** nuc_rise_ptr = new const float *[flow_block_size];
float** incorporation_rise = new float *[flow_block_size];
int* my_start = new int[flow_block_size];
for ( int fnum=0; fnum<flow_block_size; fnum++ )
{
nuc_rise_ptr[fnum] = cache_step.NucCoarseStep ( fnum );
incorporation_rise[fnum] = &ivalPtr[fnum*time_c.npts() ];
my_start[fnum] = cache_step.i_start_coarse_step[fnum];
}
// this is >almost< a parallel operation by flows now
bool use_my_parallel= (flow_block_size%4 == 0);
if ( use_my_parallel )
{
//@TODO handle cases of fewer than 4 flows remaining
for ( int fnum=0; fnum<flow_block_size; fnum+=4 )
{
MathModel::ParallelSimpleComputeCumulativeIncorporationHydrogens (
&incorporation_rise[fnum], time_c.npts(), &time_c.deltaFrameSeconds[0],
&nuc_rise_ptr[fnum],
ISIG_SUB_STEPS_MULTI_FLOW, &my_start[fnum], &p->Ampl[fnum],
&cur_bead_block.SP[fnum],&cur_bead_block.kr[fnum], &cur_bead_block.kmax[fnum],
&cur_bead_block.d[fnum], &cur_bead_block.molecules_to_micromolar_conversion[fnum],
math_poiss, reg_p->hydrogenModelType );
}
}
else
{
for ( int fnum=0;fnum<flow_block_size;fnum++ )
{
MathModel::ComputeCumulativeIncorporationHydrogens ( incorporation_rise[fnum], time_c.npts(),
&time_c.deltaFrameSeconds[0], nuc_rise_ptr[fnum], ISIG_SUB_STEPS_MULTI_FLOW,
my_start[fnum], cur_bead_block.C[fnum], p->Ampl[fnum], cur_bead_block.SP[fnum],
cur_bead_block.kr[fnum], cur_bead_block.kmax[fnum],
cur_bead_block.d[fnum],cur_bead_block.molecules_to_micromolar_conversion[fnum],
math_poiss, reg_p->hydrogenModelType );
}
}
// transform hydrogens to signal
for ( int fnum=0;fnum<flow_block_size;fnum++ )
MultiplyVectorByScalar ( incorporation_rise[fnum], cur_bead_block.sens[fnum],time_c.npts() );
// Cleanup.
delete [] nuc_rise_ptr;
delete [] incorporation_rise;
delete [] my_start;
}
// 2nd-order background function with non-uniform bead well
void MathModel::MultiFlowComputeTraceGivenIncorporationAndBackground (
float *fval, BeadParams *p,const reg_params *reg_p, float *ival, float *sbg,
RegionTracker &my_regions, buffer_params_block_flows &cur_buffer_block,
const TimeCompression &time_c, const FlowBufferInfo &my_flow,
bool use_vectorization, int bead_flow_t,
int flow_block_size, int flow_block_start )
{
// Save on allocation complexity; allocate enough to get to the end.
float **vb_out = new float*[ flow_block_size ];
float **bkg_for_flow = new float*[ flow_block_size ];
float **new_hydrogen_for_flow = new float*[ flow_block_size ];
//@TODO: the natural place for vectorization is here at the flow level
// flows are logically independent: apply "compute trace" to all flows
// this makes for an obvious fit to solving 4 at once using the processor vectorization routines
// parallel fill one bead parameter for block of flows
FillBufferParamsBlockFlows ( &cur_buffer_block,p,reg_p,my_flow.flow_ndx_map, flow_block_start,
flow_block_size );
// parallel compute across flows
for ( int fnum=0;fnum<flow_block_size;fnum++ )
{
vb_out[fnum] = fval + fnum*time_c.npts(); // get ptr to start of the function evaluation for the current flow
bkg_for_flow[fnum] = &sbg[fnum*time_c.npts() ]; // get ptr to pre-shifted background
new_hydrogen_for_flow[fnum] = &ival[fnum*time_c.npts() ];
}
// do the actual computation
#ifdef __INTEL_COMPILER
{
for ( int fnum=0; fnum<flow_block_size; fnum++ )
PurpleSolveTotalTrace ( vb_out[fnum],bkg_for_flow[fnum], new_hydrogen_for_flow[fnum], time_c.npts(),
&time_c.deltaFrame[0], cur_buffer_block.tauB[fnum], cur_buffer_block.etbR[fnum] );
}
#else // assumed to be GCC
if ( use_vectorization )
{
MathModel::PurpleSolveTotalTrace_Vec ( vb_out, bkg_for_flow, new_hydrogen_for_flow,
time_c.npts(), &time_c.deltaFrame[0],
cur_buffer_block.tauB, cur_buffer_block.etbR, p->gain, flow_block_size );
}
else
{
for ( int fnum=0; fnum<flow_block_size; fnum++ )
PurpleSolveTotalTrace ( vb_out[fnum],bkg_for_flow[fnum], new_hydrogen_for_flow[fnum],time_c.npts(),
&time_c.deltaFrame[0], cur_buffer_block.tauB[fnum], cur_buffer_block.etbR[fnum] );
}
#endif
// adjust for well sensitivity, unexplained systematic effects
// gain naturally parallel across flows
MultiplyVectorByScalar ( fval,p->gain,bead_flow_t );
// Dark Matter is extra background term of unexplained origin
// Possibly should be applied directly to the observed signal rather than synthesized here inside a loop.
if (my_regions.missing_mass.mytype == PerNucAverage)
{
// used to rely on "darkness" being 0.0 when this happened.
// making this trap more explicit.
if (!my_regions.missing_mass.training_only)
ApplyDarkMatter ( fval,reg_p,my_regions.missing_mass.dark_matter_compensator,my_flow.flow_ndx_map,time_c.npts(), flow_block_size );
}
if (my_regions.missing_mass.mytype==PCAVector)
ApplyPCADarkMatter ( fval,p,my_regions.missing_mass.dark_matter_compensator,time_c.npts(), flow_block_size );
// Cleanup.
delete [] vb_out;
delete [] bkg_for_flow;
delete [] new_hydrogen_for_flow;
}