void extern_links::DumpRegionFitParamsH5 ( int region_ndx, int flow, reg_params &rp )
{
if ( ( mPtrs->m_regional_param !=NULL ) & ( mPtrs->m_derived_param!=NULL ) )
{
int iBlk = CurComputeBlock ( flow );
///------------------------------------------------------------------------------------------------------------
/// regionalParams, per compute block
///------------------------------------------------------------------------------------------------------------
SpecificRegionParamDump ( rp, region_ndx, iBlk );
///------------------------------------------------------------------------------------------------------------
/// regionalParamsExtra, per compute block
///------------------------------------------------------------------------------------------------------------
// This is allowed here because they are "derived" parmaeters associated with the FitParams and not individual data blocks
// although I may regret this
mPtrs->m_derived_param->At ( region_ndx, 0 ,iBlk ) = GetModifiedMidNucTime ( &rp.nuc_shape,TNUCINDEX,0 );
mPtrs->m_derived_param->At ( region_ndx, 1 ,iBlk ) = GetModifiedMidNucTime ( &rp.nuc_shape,ANUCINDEX,0 );
mPtrs->m_derived_param->At ( region_ndx, 2 ,iBlk ) = GetModifiedMidNucTime ( &rp.nuc_shape,CNUCINDEX,0 );
mPtrs->m_derived_param->At ( region_ndx, 3 ,iBlk ) = GetModifiedMidNucTime ( &rp.nuc_shape,GNUCINDEX,0 );
mPtrs->m_derived_param->At ( region_ndx, 4 ,iBlk ) = GetModifiedSigma ( &rp.nuc_shape,TNUCINDEX );
mPtrs->m_derived_param->At ( region_ndx, 5 ,iBlk ) = GetModifiedSigma ( &rp.nuc_shape,ANUCINDEX );
mPtrs->m_derived_param->At ( region_ndx, 6 ,iBlk ) = GetModifiedSigma ( &rp.nuc_shape,CNUCINDEX );
mPtrs->m_derived_param->At ( region_ndx, 7 ,iBlk ) = GetModifiedSigma ( &rp.nuc_shape,GNUCINDEX );
}
}
void reg_params::DumpRegionParamsLine(FILE *my_fp,int my_row, int my_col, int flow_block_size)
{
// officially the wrong way to do this
fprintf(my_fp,"%4d\t%4d\t", my_row,my_col);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",d[TNUCINDEX],d[ANUCINDEX],d[CNUCINDEX],d[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",krate[TNUCINDEX],krate[ANUCINDEX],krate[CNUCINDEX],krate[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",kmax[TNUCINDEX],kmax[ANUCINDEX],kmax[CNUCINDEX],kmax[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t",nuc_shape.AccessTMidNuc()[0]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",GetModifiedMidNucTime(&nuc_shape,TNUCINDEX,0),GetModifiedMidNucTime(&nuc_shape,ANUCINDEX,0),GetModifiedMidNucTime(&nuc_shape,CNUCINDEX,0),GetModifiedMidNucTime(&nuc_shape,GNUCINDEX,0));
fprintf(my_fp,"%5.3f\t",nuc_shape.sigma);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",GetModifiedSigma(&nuc_shape,TNUCINDEX),GetModifiedSigma(&nuc_shape,ANUCINDEX),GetModifiedSigma(&nuc_shape,CNUCINDEX),GetModifiedSigma(&nuc_shape,GNUCINDEX));
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",NucModifyRatio[TNUCINDEX],NucModifyRatio[ANUCINDEX],NucModifyRatio[CNUCINDEX],NucModifyRatio[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t%5.3f\t%5.3f\t",tau_R_m,tau_R_o,tauE,RatioDrift,CopyDrift,tshift);
for (int i=0; i<flow_block_size; i++)
fprintf(my_fp,"%5.3f\t",nuc_shape.t_mid_nuc_shift_per_flow[i]);
fprintf(my_fp,"\n");
}
void DumpRegionParamsLine(FILE *my_fp,int my_row, int my_col, reg_params &rp)
{
// officially the wrong way to do this
fprintf(my_fp,"%4d\t%4d\t", my_row,my_col);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",rp.d[TNUCINDEX],rp.d[ANUCINDEX],rp.d[CNUCINDEX],rp.d[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",rp.krate[TNUCINDEX],rp.krate[ANUCINDEX],rp.krate[CNUCINDEX],rp.krate[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",rp.kmax[TNUCINDEX],rp.kmax[ANUCINDEX],rp.kmax[CNUCINDEX],rp.kmax[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t",rp.nuc_shape.t_mid_nuc[0]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",GetModifiedMidNucTime(&rp.nuc_shape,TNUCINDEX,0),GetModifiedMidNucTime(&rp.nuc_shape,ANUCINDEX,0),GetModifiedMidNucTime(&rp.nuc_shape,CNUCINDEX,0),GetModifiedMidNucTime(&rp.nuc_shape,GNUCINDEX,0));
fprintf(my_fp,"%5.3f\t",rp.nuc_shape.sigma);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",GetModifiedSigma(&rp.nuc_shape,TNUCINDEX),GetModifiedSigma(&rp.nuc_shape,ANUCINDEX),GetModifiedSigma(&rp.nuc_shape,CNUCINDEX),GetModifiedSigma(&rp.nuc_shape,GNUCINDEX));
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t",rp.NucModifyRatio[TNUCINDEX],rp.NucModifyRatio[ANUCINDEX],rp.NucModifyRatio[CNUCINDEX],rp.NucModifyRatio[GNUCINDEX]);
fprintf(my_fp,"%5.3f\t%5.3f\t%5.3f\t%5.3f\t%5.3f\t%5.3f\t",rp.tau_R_m,rp.tau_R_o,rp.tauE,rp.RatioDrift,rp.CopyDrift,rp.tshift);
for (int i=0; i<NUMFB; i++)
fprintf(my_fp,"%5.3f\t",rp.nuc_shape.t_mid_nuc_shift_per_flow[i]);
fprintf(my_fp,"\n");
}
void BkgParamH5::DumpBkgModelRegionInfoH5(BkgFitterTracker &GlobalFitter, int flow, bool last_flow)
// DumpBkgModelRegionInfoH5() called by IncrementalWrite() for every flow in ProcessImageToWell.cpp
{
int numRegions = GlobalFitter.numFitters;
for (int r = 0; r<numRegions; r++) {
///------------------------------------------------------------------------------------------------------------
/// emptyTrace
// use copyCube_element to copy DataCube element to mEmptyOnceParam in BkgParamH5::DumpBkgModelRegionInfoH5
///------------------------------------------------------------------------------------------------------------
int imgFrames = GlobalFitter.BkgModelFitters[r]->get_emptytrace_imgFrames();
float *buff = GlobalFitter.BkgModelFitters[r]->get_emptytrace_bg_buffers();
float *bg_bead_dc = GlobalFitter.BkgModelFitters[r]->get_emptytrace_bg_dc_offset();
for (int j=0; j<imgFrames; j++) {
ptrs.copyCube_element(ptrs.mEmptyOnceParam,r,j,flow,buff[j]);
}
///------------------------------------------------------------------------------------------------------------
/// bg_bead_DC
///------------------------------------------------------------------------------------------------------------
ptrs.copyMatrix_element(ptrs.mBeadDC_bg,r,flow,bg_bead_dc[flow]);
}
if (CheckFlowForWrite(flow, last_flow) ) {
struct reg_params rp;
struct reg_params_H5 rp5;
//int numParam = sizeof(reg_params)/sizeof(float); // +1 naot necessary
int numParam = sizeof(reg_params_H5)/sizeof(float); // +1 not necessary
//cout << "DumpBkgModelRegionInfoH5... numParam=" << numParam << ", sizeof(reg_params) " << sizeof(reg_params) << " / size(float)" << sizeof(float) << endl;
for (int r = 0; r<numRegions; r++) {
GlobalFitter.BkgModelFitters[r]->GetRegParams(rp);
int iFlow1 = flow%NUMFB + 1;
///------------------------------------------------------------------------------------------------------------
/// darkMatter
// use copyCube_element to copy DataCube element to mDarkOnceParam in BkgParamH5::DumpBkgModelRegionInfoH5
///------------------------------------------------------------------------------------------------------------
int npts = GlobalFitter.BkgModelFitters[r]->get_tim_c_npts();
for (int i=0; i<NUMNUC; i++) {
float * missingMass = GlobalFitter.BkgModelFitters[r]->get_region_darkMatter(i);
for (int j=0; j<npts; j++)
ptrs.copyCube_element(ptrs.mDarkOnceParam,r,i,j,missingMass[j]);
for (int j=npts; j<MAX_COMPRESSED_FRAMES; j++)
ptrs.copyCube_element(ptrs.mDarkOnceParam,r,i,j,0); // pad 0's
}
///------------------------------------------------------------------------------------------------------------
/// darkness
// use copyMatrix_element to copy Matrix element to mDarknessParam in BkgParamH5::DumpBkgModelRegionInfoH5
///------------------------------------------------------------------------------------------------------------
for (int i=0; i<iFlow1; i++)
ptrs.copyMatrix_element(ptrs.mDarknessParam,r,i,rp.darkness[i]);
for (int i=iFlow1; i<NUMFB; i++)
ptrs.copyMatrix_element(ptrs.mDarknessParam,r,i,0); //pad 0's
///------------------------------------------------------------------------------------------------------------
/// region_size, only once at flow+1=NUMFB
///------------------------------------------------------------------------------------------------------------
regionOffset.at(r,0) = GlobalFitter.BkgModelFitters[r]->get_region_row();
regionOffset.at(r,1) = GlobalFitter.BkgModelFitters[r]->get_region_col();
///------------------------------------------------------------------------------------------------------------
/// regionInitParam, only once at flow+1=NUMFB
///------------------------------------------------------------------------------------------------------------
regionInitParam.at(r,0) = GlobalFitter.BkgModelFitters[r]->get_t_mid_nuc_start();
regionInitParam.at(r,1) = GlobalFitter.BkgModelFitters[r]->get_sigma_start();
///------------------------------------------------------------------------------------------------------------
/// regionalParams, many times at each (flow+1)%NUMFB==0
///------------------------------------------------------------------------------------------------------------
//float *rpp = (float *) &rp;
float *rpp5 = (float *) &rp5;
reg_params_copyTo_reg_params_H5(rp,rp5);
for (int i = 0; i < numParam; i++)
regionalParams.at(r, i) = rpp5[i];
///------------------------------------------------------------------------------------------------------------
/// regionalParamsExtra, many times at each (flow+1)%NUMFB==0
///------------------------------------------------------------------------------------------------------------
regionalParamsExtra.at(r, 0) = GetModifiedMidNucTime(&rp.nuc_shape,TNUCINDEX,0);
regionalParamsExtra.at(r, 1) = GetModifiedMidNucTime(&rp.nuc_shape,ANUCINDEX,0);
regionalParamsExtra.at(r, 2) = GetModifiedMidNucTime(&rp.nuc_shape,CNUCINDEX,0);
regionalParamsExtra.at(r, 3) = GetModifiedMidNucTime(&rp.nuc_shape,GNUCINDEX,0);
regionalParamsExtra.at(r, 4) = GetModifiedSigma(&rp.nuc_shape,TNUCINDEX);
regionalParamsExtra.at(r, 5) = GetModifiedSigma(&rp.nuc_shape,ANUCINDEX);
regionalParamsExtra.at(r, 6) = GetModifiedSigma(&rp.nuc_shape,CNUCINDEX);
regionalParamsExtra.at(r, 7) = GetModifiedSigma(&rp.nuc_shape,GNUCINDEX);
regionalParamsExtra.at(r, 8) = rp.nuc_shape.sigma;
}
///------------------------------------------------------------------------------------------------------------
/// write to dataset (DS) in the .h5 output file
///------------------------------------------------------------------------------------------------------------
//note: regionParam only has to allocate enough regionalParam.n_rows per flow-block
// only the DS has to have the right # of rows, as in the CreateDataSet()
//cout << "DumpBkgModelRegionInfoH5... flow= " << flow << endl;
size_t starts[2];
size_t ends[2];
//starts[0] = flow/NUMFB * numRegions;
starts[0] = 0;
ends[0] = starts[0] + numRegions;
if (last_flow && (flow+1) % NUMFB != 0) {
ends[0] = starts[0] + (flow+1) % NUMFB;
//starts[0] = ceil((float) flow / NUMFB);
cout << "DumpBkgModelRegionInfoH5... lastflow= " << flow << endl;
cout << "changing starts[0] from " << (flow/NUMFB)* numRegions << " to " << starts[0] << " at flow " << flow << endl;
}
starts[1] = 0;
ends[1] = regionalParams.n_cols; // numParam, not numParam+1
ION_ASSERT(ends[0] <= regionalParams.n_rows, "ends[0] > regionalParam.n_rows");
ION_ASSERT(ends[1] <= regionalParams.n_cols, "ends[1] > regionalParam.n_cols");
// write matrix to the DS w/ the right start/offset (or the right DS as in the later versions)
int iBlk = ceil(float(flow+1)/NUMFB) - 1;
arma::Mat<float> m = arma::trans(regionalParams);
regionParamDS[iBlk]->WriteRangeData(starts, ends, m.memptr());
ends[1] = regionalParamsExtra.n_cols;
arma::Mat<float> m1 = arma::trans(regionalParamsExtra);
regionParamDSExtra[iBlk]->WriteRangeData(starts, ends, m1.memptr());
}
}
