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#include <fstream>
#include <BALL/QSAR/registry.h>
#include <BALL/QSAR/featureSelection.h>
#include <BALL/QSAR/configIO.h>
using namespace BALL::QSAR;
using namespace BALL;
void startFeatureSelection(std::ifstream& in, QSARData* q, String* data_filename)
{
FeatureSelectionConfiguration conf = ConfigIO::readFeatureSelectionConfiguration(&in);
if(conf.done) return; // stop processing this section
bool created_data_object=0;
if(q==NULL || data_filename==NULL || conf.data_file!=*data_filename)
{
if(q==NULL)
{
q = new QSARData;
created_data_object=1;
}
q->readFromFile(conf.data_file);
if(data_filename) *data_filename = conf.data_file;
}
else
{
std::cout<<"[FeatureSelector debug-info:] QSARData object for file "<<conf.data_file<<" already in memory; not reading it again."<<std::endl;
}
Registry reg;
Model* m;
String model_type;
std::ifstream model_input(conf.model.c_str()); // read model-abbreviation
if(!model_input)
{
std::cout<<"Error: Model-file '"<<conf.model<<"' does not exist!!"<<std::endl;
return;
}
std::getline(model_input,model_type);
std::getline(model_input,model_type);
model_type = model_type.getField(0,"\t");
model_input.close();
RegistryEntry* entry = reg.getEntry(model_type);
bool regression = entry->regression;
if(!entry->kernel)
{
m = (*entry->create)(*q);
}
else
{
// parameters irrelevant; will be overwritten by those read from file
m = (*entry->createKernel1)(*q,1,1, -1);
}
std::cout<<" using "<<conf.statistic_name<<" to assess qualitiy of the model ... "<<std::endl;
m->model_val->selectStat(conf.statistic);
m->readFromFile(conf.model.c_str());
FeatureSelection fs(*m);
if(conf.quality_increase_cutoff!=-1)
{
fs.setQualityIncreaseCutoff(conf.quality_increase_cutoff);
}
if(conf.remove_correlated || conf.feat_type==0)
{
fs.removeHighlyCorrelatedFeatures(conf.cor_threshold);
}
if(conf.feat_type==1)
{
fs.forwardSelection(conf.k_fold,conf.opt);
}
else if(conf.feat_type==2)
{
fs.backwardSelection(conf.k_fold,conf.opt);
}
else if(conf.feat_type==3)
{
fs.stepwiseSelection(conf.k_fold,conf.opt);
}
else if(conf.feat_type==4)
{
fs.removeLowResponseCorrelation(conf.cor_threshold);
}
else if(conf.feat_type==6)
{
fs.twinScan(conf.k_fold,conf.opt);
}
if(conf.opt_model_after_fs)
{
m->optimizeParameters(conf.opt_k_fold);
}
KernelModel* km = dynamic_cast<KernelModel*>(m);
if(km && conf.opt_kernel_after_fs)
{
/// search locally around current kernel parameters
try
{
// specifing start-values for grid search now obsolete; grid search will automatically search locally around current kernel parameter(s)
km->kernel->gridSearch(conf.grid_search_stepwidth, conf.grid_search_steps,conf.grid_search_recursions,conf.opt_k_fold,conf.opt/*,start_par1,start_par2*/);
}
catch(BALL::Exception::GeneralException e)
{
std::cout<<e.getName()<<" : "<<e.getMessage()<<std::endl;
return;
}
}
m->readTrainingData();
m->train();
m->saveToFile(conf.output);
if(created_data_object) delete q;
delete m;
}
#ifndef EXT_MAIN
int main(int argc, char* argv[])
{
if(argc<2)
{
std::cout<<"Please specify configuration file!"<<std::endl;
return 0;
}
std::ifstream in(argv[1]);
if(!in)
{
std::cout<<"Configuration file '"<<argv[1]<<"' not found!"<<std::endl;
return 0;
}
String line;
for(int i=0;!in.eof();i++) // read ALL FeatureSelector sections
{
for(int j=0;!in.eof();j++) // skip everthing until the beginning of the next FeatureSelector-section
{
std::getline(in,line);
if(!line.hasPrefix("[FeatureSelector]")) continue;
else break;
}
if(!line.hasPrefix("[FeatureSelector]")) break; // there are no (more) FS-sections!
ConfigIO::putbackLine(&in,line);
startFeatureSelection(in, NULL, NULL);
}
}
#endif
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