void BkgParamH5::Init ( const char *results_folder, const SpatialContext &loc_context,
const ImageSpecClass &my_image_spec,
int numFlows,
int write_params_flag,
int _max_frames,
int _flow_block_size,
int num_flow_blocks
)
{
cout << "BkgParamH5::Init... _max_frames = " << _max_frames << ", MAX_COMPRESSED_FRAMES = " << MAX_COMPRESSED_FRAMES << endl;
//max_frames = MAX_COMPRESSED_FRAMES;
max_frames = _max_frames;
if ( write_params_flag>0 )
{
local_results_directory=results_folder;
flow_block_size = _flow_block_size;
datacube_numflows = numFlows;
nFlowBlks = num_flow_blocks;
bead_col = loc_context.cols;
bead_row = loc_context.rows;
region_total = loc_context.numRegions;
ConstructOneFile ( h5BeadDbg, hgBeadDbgFile,local_results_directory, "bead_param.h5" );
TryInitBeads ( h5BeadDbg, write_params_flag ); //write_params_flag: 1-only important params, small file; 2-all params (very large file, use for debugging only)
ConstructOneFile ( h5RegionDbg, hgRegionDbgFile,local_results_directory, "region_param.h5" );
TryInitRegionParams ( h5RegionDbg,my_image_spec );
///------------------------------------------------------------------------------------------------------------
/// savePointers to be passed to BkgModel::WriteBeadParameterstoDataCubes
///------------------------------------------------------------------------------------------------------------
/// WARNING: these pointers determine >individual< behavior of data cubes
/// just because one cube exists doesn't mean any others exists - see different logging levels
/// if a cube exists, the >exporting< function in GlobalWriter needs to handle it correctly.
savePointers();
}
else
{
hgBeadDbgFile = "";
hgRegionDbgFile="";
}
}
std::string BkgParamH5::Init(SystemContext &sys_context, SpatialContext &loc_context, int numFlows, ImageSpecClass &my_image_spec) {
//wells_output_directory is a better choice than basecaller_output_directory
//hgBgDbgFile = ToStr(sys_context.dat_source_directory) + "/bg_param.h5";
//cout << "dat_source_directory:" << sys_context.dat_source_directory << endl;
//cout << "basecaller_output_directory:" << sys_context.basecaller_output_directory << endl;
//cout << "wells_output_directory:" << sys_context.wells_output_directory << endl;
if (ToStr(sys_context.wells_output_directory)=="")
hgBgDbgFile = sys_context.experimentName;
else
hgBgDbgFile = ToStr(sys_context.wells_output_directory);
if (hgBgDbgFile[hgBgDbgFile.length()-1] != '/')
hgBgDbgFile += '/';
hgBgDbgFile += "bg_param.h5";
cout << "hgBgDbgFile:" << hgBgDbgFile << endl;
h5BgDbg.Init();
h5BgDbg.SetFile(hgBgDbgFile);
h5BgDbg.Open(true);
int blocksOfFlow = NUMFB;
int nFlowBlks = ceil(float(numFlows)/NUMFB);
//int numParam = sizeof(reg_params)/sizeof(float); // +1 not necessary
int numParam = sizeof(reg_params_H5)/sizeof(float); // +1 not necessary
hsize_t rp_dims[2], rp_chunks[2];
char s[128];
string str;
///------------------------------------------------------------------------------------------------------------
/// bead parameters
///------------------------------------------------------------------------------------------------------------
try {
beadDC.Init(loc_context.cols, loc_context.rows, numFlows);
beadDC.SetRange(0,loc_context.cols, 0, loc_context.rows, 0, blocksOfFlow);
beadDC.AllocateBuffer();
beadDCDS = h5BgDbg.CreateDataSet("/bead/fg_bead_DC", beadDC, 3);
h5BgDbg.CreateAttribute(beadDCDS->getDataSetId(),"description","bead_DC per flow");
h5BgDbg.makeParamNames("fg_beadDC_",numFlows,str);
h5BgDbg.CreateAttribute(beadDCDS->getDataSetId(),"paramNames",str.c_str());
amplMultiplier.Init(loc_context.cols, loc_context.rows, numFlows);
amplMultiplier.SetRange(0,loc_context.cols, 0, loc_context.rows, 0, blocksOfFlow);
amplMultiplier.AllocateBuffer();
amplDS = h5BgDbg.CreateDataSet("/bead/ampl_multiplier", amplMultiplier, 3);
h5BgDbg.CreateAttribute(amplDS->getDataSetId(),"description","Amplitude-multiplier per flow");
h5BgDbg.makeParamNames("ampl_",numFlows,str);
h5BgDbg.CreateAttribute(amplDS->getDataSetId(),"paramNames",str.c_str());
kRateMultiplier.Init(loc_context.cols, loc_context.rows, numFlows);
kRateMultiplier.SetRange(0,loc_context.cols, 0, loc_context.rows, 0, blocksOfFlow);
kRateMultiplier.AllocateBuffer();
kRateDS = h5BgDbg.CreateDataSet("/bead/k_rate_multiplier", kRateMultiplier, 3);
h5BgDbg.CreateAttribute(kRateDS->getDataSetId(),"description","K-rate-multiplier per flow");
h5BgDbg.makeParamNames("kRate_",numFlows,str);
h5BgDbg.CreateAttribute(kRateDS->getDataSetId(),"paramNames",str.c_str());
bgResidualError.Init(loc_context.cols, loc_context.rows, numFlows);
bgResidualError.SetRange(0,loc_context.cols, 0, loc_context.rows, 0, blocksOfFlow);
bgResidualError.AllocateBuffer();
resErrorDS = h5BgDbg.CreateDataSet("/bead/res_error", bgResidualError, 3);
h5BgDbg.CreateAttribute(resErrorDS->getDataSetId(),"description","Residual-error per flow");
h5BgDbg.makeParamNames("resErr_",numFlows,str);
h5BgDbg.CreateAttribute(resErrorDS->getDataSetId(),"paramNames",str.c_str());
beadInitParam.Init(loc_context.cols, loc_context.rows, 4);
beadInitParam.SetRange(0,loc_context.cols, 0, loc_context.rows, 0, beadInitParam.GetNumZ());
beadInitParam.AllocateBuffer();
beadInitParamDS = h5BgDbg.CreateDataSet("/bead/bead_init_param", beadInitParam, 3);
h5BgDbg.CreateAttribute(beadInitParamDS->getDataSetId(),"description","Bead-init-param, same for all flows, 4 data points: Copies, R, dmult, gain");
h5BgDbg.CreateAttribute(beadInitParamDS->getDataSetId(),"paramNames","Copies, R, dmult, gain");
beadFblk_avgErr.set_size(loc_context.cols, loc_context.rows);
beadFblk_clonal.set_size(loc_context.cols, loc_context.rows);
beadFblk_corrupt.set_size(loc_context.cols, loc_context.rows);
rp_dims[0] = rp_chunks[0] = loc_context.cols;
rp_dims[1] = rp_chunks[1] = loc_context.rows;
for (int i=0; i<nFlowBlks; i++) {
int f = (i+1)*NUMFB;
if (i==nFlowBlks-1)
f = numFlows;
sprintf(s,"/bead/flowBlkParams/avgErr/flow_%04d",f);
H5DataSet *ptr = h5BgDbg.CreateDataSet(s, 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(beadFblk_avgErr.at(0,0)));
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"description","avg-err per flow-block");
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"paramNames","avgErr");
beadFblk_avgErrDS.push_back(ptr);
sprintf(s,"/bead/flowBlkParams/clonal/flow_%04d",f);
ptr = h5BgDbg.CreateDataSet(s, 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(beadFblk_clonal.at(0,0)));
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"description","clonal flag per flow-block");
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"paramNames","clonal");
beadFblk_clonalDS.push_back(ptr);
sprintf(s,"/bead/flowBlkParams/corrupt/flow_%04d",f);
ptr = h5BgDbg.CreateDataSet(s, 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(beadFblk_corrupt.at(0,0)));
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"description","corrupt flag per flow-block");
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"paramNames","corrupt");
beadFblk_corruptDS.push_back(ptr);
}
}
catch( char * str ) {
cout << "Exception raised while creating bead datasets in BkgParamH5::Init(): " << str << '\n';
}
///------------------------------------------------------------------------------------------------------------
/// region parameters
///------------------------------------------------------------------------------------------------------------
try {
//cout << "Init...regionalParams.n_rows,n_cols=" << regionalParams.n_rows << "," << regionalParams.n_cols << endl;
//rp_dims[0] = loc_context.numRegions * nFlowBlks;
char s[128];
rp_dims[0] = rp_chunks[0] = loc_context.numRegions;
rp_dims[1] = rp_chunks[1] = numFlows;
beadDC_bg.set_size(rp_dims[0], rp_dims[1]);
beadDC_bgDS = h5BgDbg.CreateDataSet("/region/bg_bead_DC", 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(beadDC_bg.at(0,0)));
h5BgDbg.CreateAttribute(beadDC_bgDS->getDataSetId(),"description","bg_bead_DC");
h5BgDbg.makeParamNames("bg_beadDC_",numFlows,str);
h5BgDbg.CreateAttribute(beadDC_bgDS->getDataSetId(),"paramNames",str.c_str());
rp_dims[0] = rp_chunks[0] = loc_context.numRegions;
rp_dims[1] = rp_chunks[1] = 2;
regionOffset.set_size(rp_dims[0], rp_dims[1]);
regionOffsetDS = h5BgDbg.CreateDataSet("/region/region_offset_RowCol", 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(regionOffset.at(0,0)));
h5BgDbg.CreateAttribute(regionOffsetDS->getDataSetId(),"description","region-offset-xy");
h5BgDbg.CreateAttribute(regionOffsetDS->getDataSetId(),"paramNames","row,col");
regionalParams.set_size(loc_context.numRegions, numParam);
regionalParamsExtra.set_size(loc_context.numRegions, 9);
emptyOnceParam.Init(loc_context.numRegions, my_image_spec.uncompFrames, numFlows);
emptyOnceParam.SetRange(0,loc_context.numRegions, 0, my_image_spec.uncompFrames, 0, blocksOfFlow);
emptyOnceParam.AllocateBuffer();
emptyOnceParamDS = h5BgDbg.CreateDataSet("/region/emptyTrace", emptyOnceParam, 3);
h5BgDbg.CreateAttribute(emptyOnceParamDS->getDataSetId(),"description","Empty-trace per region, per imgFrame , per flow");
h5BgDbg.makeParamNames("empty_",numFlows,str);
h5BgDbg.CreateAttribute(emptyOnceParamDS->getDataSetId(),"paramNames",str.c_str());
darkOnceParam.Init(loc_context.numRegions, NUMNUC, MAX_COMPRESSED_FRAMES);
darkOnceParam.SetRange(0,loc_context.numRegions, 0, NUMNUC, 0, darkOnceParam.GetNumZ());
darkOnceParam.AllocateBuffer();
darkOnceParamDS = h5BgDbg.CreateDataSet("/region/darkMatter/missingMass", darkOnceParam, 3);
sprintf(s,"Missing-mass per region, per nucleotide, %d data points",MAX_COMPRESSED_FRAMES);
h5BgDbg.CreateAttribute(darkOnceParamDS->getDataSetId(),"description",s);
h5BgDbg.makeParamNames("missingMass_",MAX_COMPRESSED_FRAMES,str);
h5BgDbg.CreateAttribute(darkOnceParamDS->getDataSetId(),"paramNames",str.c_str());
rp_dims[0] = rp_chunks[0] = loc_context.numRegions;
rp_dims[1] = rp_chunks[1] = NUMFB;
darknessParam.set_size(loc_context.numRegions, NUMFB);
darknessParamDS = h5BgDbg.CreateDataSet("/region/darkMatter/darkness", 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(darknessParam.at(0,0)));
h5BgDbg.CreateAttribute(darknessParamDS->getDataSetId(),"description","Darkness per region, per flowBuffer");
h5BgDbg.makeParamNames("darkness_",NUMFB,str);
h5BgDbg.CreateAttribute(darknessParamDS->getDataSetId(),"paramNames",str.c_str());
rp_dims[1] = rp_chunks[1] = 2;
regionInitParam.set_size(loc_context.numRegions, 2);
regionInitParamDS = h5BgDbg.CreateDataSet("/region/region_init_param", 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(regionInitParam.at(0,0)));
h5BgDbg.CreateAttribute(regionInitParamDS->getDataSetId(),"description","Region-init-param per region, 2 data points: t_mid_nuc_start & sigma_start");
h5BgDbg.CreateAttribute(regionInitParamDS->getDataSetId(),"paramNames","t_mid_nuc_start,sigma_start");
emphasisParam.Init(loc_context.numRegions, MAX_HPLEN+1, MAX_COMPRESSED_FRAMES);
emphasisParam.SetRange(0,loc_context.numRegions, 0, MAX_HPLEN+1, 0, emphasisParam.GetNumZ());
emphasisParam.AllocateBuffer();
for (int i=0; i<nFlowBlks; i++) {
int f = (i+1)*NUMFB;
if (i==nFlowBlks-1)
f = numFlows;
sprintf(s,"/region/emphasis/flow_%04d",f);
H5DataSet *ptr = h5BgDbg.CreateDataSet(s, emphasisParam, 3);
sprintf(s,"Emphasis param per region, per HP length, %d data points per flow-block",MAX_COMPRESSED_FRAMES);
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"description",s);
h5BgDbg.makeParamNames("emphasis_",NUMFB,str);
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"paramNames",str.c_str());
emphasisParamDS.push_back(ptr);
rp_dims[0] = rp_chunks[0] = loc_context.numRegions;
rp_dims[1] = rp_chunks[1] = numParam;
sprintf(s,"/region/region_param/flow_%04d",f);
ptr = h5BgDbg.CreateDataSet(s, 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(regionalParams.at(0,0)));
sprintf(s,"Region_param per region, %d data points per flow-block",numParam);
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"description",s);
h5BgDbg.makeParamNames("regionParam_",numParam,str);
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"paramNames",str.c_str());
regionParamDS.push_back(ptr);
rp_dims[1] = rp_chunks[1] = regionalParamsExtra.n_cols;
sprintf(s,"/region/region_param_extra/flow_%04d",f);
ptr = h5BgDbg.CreateDataSet(s, 2, rp_dims, rp_chunks, 3, h5BgDbg.GetH5Type(regionalParamsExtra.at(0,0)));
sprintf(s,"Region_param_extra per region, %d data points per flow-block",regionalParamsExtra.n_cols);
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"description",s);
h5BgDbg.CreateAttribute(ptr->getDataSetId(),"paramNames","midNucTime_0,midNucTime_1,midNucTime_2,midNucTime_3,sigma_0,sigma_1,sigma_2,sigma_3,sigma");
regionParamDSExtra.push_back(ptr);
}
}
catch( char * str ) {
cout << "Exception raised while creating region datasets in BkgParamH5::Init(): " << str << '\n';
}
///------------------------------------------------------------------------------------------------------------
/// savePointers to be passed to BkgModel::WriteBeadParameterstoDataCubes
///------------------------------------------------------------------------------------------------------------
savePointers();
return hgBgDbgFile;
}
