void xmlBranchSave::FillLODs( const dataBranch &_data , TiXmlElement* root )
{
//формирование записей LOD'ов
//создать запись для вершин
TiXmlElement *pLods = NULL;
pLods = new TiXmlElement( m_BranchNames.m_sLODs.c_str() );
//количество LOD's
pLods->SetAttribute( m_BranchNames.m_sNum.c_str() , _data.m_vLOD.size() );
for( int i = 0 ; i < _data.m_vLOD.size() ; ++i )
{
//создать запись для вершин
TiXmlElement *pLod = NULL;
pLod = new TiXmlElement( m_BranchNames.m_sLOD.c_str() );
//номер LOD's
pLod->SetAttribute( m_BranchNames.m_sNum.c_str() , i );
//номер LOD's
pLod->SetDoubleAttribute( m_BranchNames.m_sAlfaTest.c_str() , _data .m_vLOD[ i ].m_fAlphaTestValue );
//заполнить данными о координатах
FillVertex( _data .m_vLOD[ i ] , pLod );
//заполнить индексами
FillIndexes( _data .m_vLOD[ i ] , pLod );
pLods->LinkEndChild( pLod );
}
root->LinkEndChild( pLods );
}
TiXmlElement* xmlFrondsSave::GetXmlData()
{
//получить xml тег с сформированными данными
//получить ссылку на данные веток
dataFronds &_data = xmlRoot::Instance().GetDataFronds();
//формируем корневой узел данных
TiXmlElement *pFronds = NULL;
pFronds = new TiXmlElement( m_FrondsNames.m_sFronds.c_str() );
//значение альфа теста
pFronds->SetDoubleAttribute( m_FrondsNames.m_sAlfaTest.c_str() , _data.m_fAlphaTestValue );
//заполнить данными о текстурах
FillTextures( _data , pFronds );
//заполнить данными о координатах
FillVertex( _data , pFronds );
//заполнить индексами
FillIndexes( _data , pFronds );
return pFronds;
}
bool RecalibrationModel::InitializeModel(string model_file_name, int model_threshold)
{
is_enabled_ = false;
if (model_file_name.empty() or model_file_name == "off") {
printf("RecalibrationModel: disabled\n\n");
return false;
}
ifstream model_file;
model_file.open(model_file_name.c_str());
if (model_file.fail()) {
printf("RecalibrationModel: disabled (cannot open %s)\n\n", model_file_name.c_str());
model_file.close();
return false;
}
if (model_threshold < 0 or model_threshold > MAX_HPXLEN) {
cout << "RecalibrationModel: disabled (invalid model threshold of "<< model_threshold <<")" << endl;
return false;
} else
recalModelHPThres = model_threshold;
string comment_line;
getline(model_file, comment_line); //skip the comment time
int flowStart, flowEnd, flowSpan, xMin, xMax, xSpan, yMin, yMax, ySpan, max_hp_calibrated;
model_file >> flowStart >> flowEnd >> flowSpan >> xMin >> xMax >> xSpan >> yMin >> yMax >> ySpan >> max_hp_calibrated;
stratification.SetupChipRegions(xMin, xMax, xSpan, yMin, yMax, ySpan);
stratification.SetupFlowRegions(flowStart,flowEnd, flowSpan);
//calculate number of partitions and initialize the stratifiedAs and stratifiedBs
SetupStratification(flowStart,flowEnd, flowSpan,xMin,xMax,xSpan,yMin,yMax,ySpan,max_hp_calibrated);
//TODO: parse model_file into stratifiedAs and stratifiedBs
while (model_file.good()) {
float paramA, paramB;
int refHP;
char flowBase;
model_file >> flowBase >> flowStart >> flowEnd >> xMin >> xMax >> yMin >> yMax >> refHP >> paramA >> paramB;
//populate it to stratifiedAs and startifiedBs
int offsetRegion = stratification.OffsetRegion(xMin,yMin);
FillIndexes(offsetRegion, NuctoInt(flowBase), refHP, flowStart, flowEnd, paramA, paramB);
}
model_file.close();
cout << "Recalibration Model: enabled (using calibration file " << model_file_name << ")" << endl;
cout << " - using calibration model for HPs " << recalModelHPThres << " and up in a "
<< stratification.xCuts << 'x' << stratification.yCuts << 'x' << stratification.flowCuts << " grid." << endl << endl;
is_enabled_ = true;
return is_enabled_;
}
void RecalibrationModel::Initialize(OptArgs& opts)
{
is_enabled_ = false;
string model_file_name = opts.GetFirstString ('-', "model-file", "");
if (model_file_name.empty() or model_file_name == "off") {
printf("RecalibrationModel: disabled\n\n");
return;
}
ifstream model_file;
model_file.open(model_file_name.c_str());
if (model_file.fail()) {
printf("RecalibrationModel: disabled (cannot open %s)\n\n", model_file_name.c_str());
model_file.close();
return;
}
recalModelHPThres = opts.GetFirstInt('-', "recal-model-hp-thres", 4);
string comment_line;
getline(model_file, comment_line); //skip the comment time
int flowStart, flowEnd, flowSpan, xMin, xMax, xSpan, yMin, yMax, ySpan, max_hp_calibrated;
model_file >> flowStart >> flowEnd >> flowSpan >> xMin >> xMax >> xSpan >> yMin >> yMax >> ySpan >> max_hp_calibrated;
stratification.SetupRegion(xMin, xMax, xSpan, yMin, yMax, ySpan);
//calculate number of partitions and initialize the stratifiedAs and stratifiedBs
SetupStratification(flowStart,flowEnd, flowSpan,xMin,xMax,xSpan,yMin,yMax,ySpan,max_hp_calibrated);
//TODO: parse model_file into stratifiedAs and stratifiedBs
while (model_file.good()) {
float paramA, paramB;
int refHP;
char flowBase;
model_file >> flowBase >> flowStart >> flowEnd >> xMin >> xMax >> yMin >> yMax >> refHP >> paramA >> paramB;
//populate it to stratifiedAs and startifiedBs
int nucInd = NuctoInt(flowBase);
//boundary check
int offsetRegion = stratification.OffsetRegion(xMin,yMin);
FillIndexes(offsetRegion,nucInd, refHP, flowStart, flowEnd, paramA, paramB);
}
model_file.close();
printf("Recalibration: enabled (using calibration file %s)\n\n", model_file_name.c_str());
is_enabled_ = true;
if (recalModelHPThres > MAX_HPXLEN) is_enabled_ = false;
}
void RecalibrationModel::InitializeFromJSON(Json::Value &recal_params, string &my_block_key, bool spam_enabled) {
// this needs to signal when it fails in some way
int flowStart, flowEnd, flowSpan, xMin, xMax, xSpan, yMin, yMax, ySpan, max_hp_calibrated;
flowStart = rGetParamsInt(recal_params[my_block_key],"flowStart",0);
//cout << flowStart << endl;
flowEnd = rGetParamsInt(recal_params[my_block_key],"flowEnd",0);
//cout << flowEnd << endl;
flowSpan = rGetParamsInt(recal_params[my_block_key],"flowSpan",0);
//cout << flowSpan << endl;
xMin = rGetParamsInt(recal_params[my_block_key],"xMin",0);
//cout << xMin << endl;
xMax =rGetParamsInt(recal_params[my_block_key],"xMax",0);
//cout << xMax << endl;
xSpan =rGetParamsInt(recal_params[my_block_key],"xSpan",0);
//cout << xSpan << endl;
yMin = rGetParamsInt(recal_params[my_block_key],"yMin",0);
//cout << yMin << endl;
yMax =rGetParamsInt(recal_params[my_block_key],"yMax",0);
//cout << yMax << endl;
ySpan = rGetParamsInt(recal_params[my_block_key],"ySpan",0);
//cout << ySpan << endl;
max_hp_calibrated = rGetParamsInt(recal_params[my_block_key],"max_hp_calibrated",0);
stratification.SetupRegion(xMin, xMax, xSpan, yMin, yMax, ySpan);
//calculate number of partitions and initialize the stratifiedAs and stratifiedBs
SetupStratification(flowStart,flowEnd, flowSpan,xMin,xMax,xSpan,yMin,yMax,ySpan,max_hp_calibrated);
// stratification setup done
// now iterate and obtain each line from the JSON
int iter_size = recal_params[my_block_key]["modelParameters"].size();
for (int i_item=0; i_item<iter_size; i_item++) {
// extract my single line
//model_file >> flowBase >> flowStart >> flowEnd >> xMin >> xMax >> yMin >> yMax >> refHP >> paramA >> paramB;
//flowBase is a special extraction
flowStart = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowStart",0);
flowEnd = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowEnd",0);
xMin = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"xMin",0);
xMax =rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"xMax",0);
yMin = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"yMin",0);
yMax =rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"yMax",0);
int refHP;
refHP = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"refHP",0);
float paramA, paramB;
paramA = rGetParamsDbl(recal_params[my_block_key]["modelParameters"][i_item],"paramA",1.0);
paramB = rGetParamsDbl(recal_params[my_block_key]["modelParameters"][i_item],"paramB",0.0);
//string flowBase = recal_params[my_block_key]["modelParameters"][i_item]["flowBase"].asCString();
char flowBase = (char) rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowBase",0);
int nucInd = NuctoInt(flowBase);
// all set with the values
int offsetRegion = stratification.OffsetRegion(xMin,yMin);
FillIndexes(offsetRegion,nucInd, refHP, flowStart, flowEnd, paramA, paramB);
}
// now we're done!
if (spam_enabled)
printf("Recalibration: enabled (using recalibration comment %s)\n\n", my_block_key.c_str());
// if something bad happened above, how do we find out?
is_enabled_ = true;
}
void RecalibrationModel::InitializeFromJSON(Json::Value &recal_params, string &my_block_key, bool spam_enabled, int over_flow_protect) {
// this needs to signal when it fails in some way
verbose_ = spam_enabled;
int flowStart, flowEnd, flowSpan, xMin, xMax, xSpan, yMin, yMax, ySpan, max_hp_calibrated;
flowStart = rGetParamsInt(recal_params[my_block_key],"flowStart",0);
//cout << flowStart << endl;
flowEnd = rGetParamsInt(recal_params[my_block_key],"flowEnd",0);
if (over_flow_protect>flowEnd)
flowEnd = over_flow_protect; // allocate for combined bam files that need to access flows "past the end" without crashing
//cout << flowEnd << endl;
flowSpan = rGetParamsInt(recal_params[my_block_key],"flowSpan",0);
//cout << flowSpan << endl;
xMin = rGetParamsInt(recal_params[my_block_key],"xMin",0);
//cout << xMin << endl;
xMax =rGetParamsInt(recal_params[my_block_key],"xMax",0);
//cout << xMax << endl;
xSpan =rGetParamsInt(recal_params[my_block_key],"xSpan",0);
//cout << xSpan << endl;
yMin = rGetParamsInt(recal_params[my_block_key],"yMin",0);
//cout << yMin << endl;
yMax =rGetParamsInt(recal_params[my_block_key],"yMax",0);
//cout << yMax << endl;
ySpan = rGetParamsInt(recal_params[my_block_key],"ySpan",0);
//cout << ySpan << endl;
max_hp_calibrated = rGetParamsInt(recal_params[my_block_key],"max_hp_calibrated",0);
stratification.SetupChipRegions(xMin, xMax, xSpan, yMin, yMax, ySpan);
stratification.SetupFlowRegions(flowStart,flowEnd, flowSpan);
//calculate number of partitions and initialize the stratifiedAs and stratifiedBs
SetupStratification(flowStart,flowEnd, flowSpan,xMin,xMax,xSpan,yMin,yMax,ySpan,max_hp_calibrated);
// stratification setup done
// now iterate and obtain each line from the JSON
int iter_size = recal_params[my_block_key]["modelParameters"].size();
for (int i_item=0; i_item<iter_size; i_item++) {
// extract my single line
//model_file >> flowBase >> flowStart >> flowEnd >> xMin >> xMax >> yMin >> yMax >> refHP >> paramA >> paramB;
//flowBase is a special extraction
flowStart = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowStart",0);
flowEnd = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowEnd",0);
xMin = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"xMin",0);
xMax =rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"xMax",0);
yMin = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"yMin",0);
yMax =rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"yMax",0);
int refHP;
refHP = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"refHP",0);
float paramA, paramB;
paramA = rGetParamsDbl(recal_params[my_block_key]["modelParameters"][i_item],"paramA",1.0);
paramB = rGetParamsDbl(recal_params[my_block_key]["modelParameters"][i_item],"paramB",0.0);
//string flowBase = recal_params[my_block_key]["modelParameters"][i_item]["flowBase"].asCString();
char flowBase = (char) rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowBase",0);
int nucInd = NuctoInt(flowBase);
// all set with the values
int offsetRegion = stratification.OffsetRegion(xMin,yMin);
// note we only fill >in< flows fit by the recalibration model
FillIndexes(offsetRegion,nucInd, refHP, flowStart, flowEnd, paramA, paramB);
}
// if something bad happened above, how do we find out? - We do some basic sanity checks
CheckArraySize();
// now we're done!
if (verbose_)
cout << "Recalibration: enabled (using recalibration comment " << my_block_key << ") in a "
<< stratification.xCuts << 'x' << stratification.yCuts << 'x' << stratification.flowCuts << " grid." <<endl << endl;
is_enabled_ = true;
}
