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option to dump bootstrap sequence while resampling

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This commit is contained in:
Antonin Portelli 2017-10-02 11:54:12 +01:00
parent 3d514ef026
commit 98cf39efda
2 changed files with 32 additions and 1 deletions
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19
lib/Dataset.hpp
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@ -47,6 +47,8 @@ public:
// resampling // resampling
Sample<T> bootstrapMean(const Index nSample, const SeedType seed); Sample<T> bootstrapMean(const Index nSample, const SeedType seed);
Sample<T> bootstrapMean(const Index nSample); Sample<T> bootstrapMean(const Index nSample);
void dumpBootstrapSeq(std::ostream &out, const Index nSample,
const SeedType seed);
private: private:
// mean from pointer vector for resampling // mean from pointer vector for resampling
void ptVectorMean(T &m, const std::vector<const T *> &v); void ptVectorMean(T &m, const std::vector<const T *> &v);
@ -114,6 +116,23 @@ Sample<T> Dataset<T>::bootstrapMean(const Index nSample)
return bootstrapMean(nSample, rd()); return bootstrapMean(nSample, rd());
} }
template <typename T>
void Dataset<T>::dumpBootstrapSeq(std::ostream &out, const Index nSample,
const SeedType seed)
{
std::mt19937 gen(seed);
std::uniform_int_distribution<Index> dis(0, this->size() - 1);
for (Index i = 0; i < nSample; ++i)
{
for (unsigned int j = 0; j < this->size(); ++j)
{
out << dis(gen) << " " << std::endl;
}
out << std::endl;
}
}
template <typename T> template <typename T>
void Dataset<T>::ptVectorMean(T &m, const std::vector<const T *> &v) void Dataset<T>::ptVectorMean(T &m, const std::vector<const T *> &v)
{ {

14
utils/resample.cpp
View File

@ -39,7 +39,7 @@ int main(int argc, char *argv[])
{ {
// argument parsing //////////////////////////////////////////////////////// // argument parsing ////////////////////////////////////////////////////////
OptParser opt; OptParser opt;
bool parsed; bool parsed, dumpBoot;
random_device rd; random_device rd;
SeedType seed = rd(); SeedType seed = rd();
string manFileName, nameFileName, outDirName; string manFileName, nameFileName, outDirName;
@ -56,6 +56,8 @@ int main(int argc, char *argv[])
"output directory", "."); "output directory", ".");
opt.addOption("f", "format" , OptParser::OptType::value, true, opt.addOption("f", "format" , OptParser::OptType::value, true,
"output file format", DEF_FMT); "output file format", DEF_FMT);
opt.addOption("d", "dump-boot" , OptParser::OptType::trigger, true,
"dump bootstrap sequence", DEF_FMT);
opt.addOption("" , "help" , OptParser::OptType::trigger, true, opt.addOption("" , "help" , OptParser::OptType::trigger, true,
"show this help message and exit"); "show this help message and exit");
parsed = opt.parse(argc, argv); parsed = opt.parse(argc, argv);
@ -75,6 +77,7 @@ int main(int argc, char *argv[])
} }
ext = opt.optionValue("f"); ext = opt.optionValue("f");
outDirName = opt.optionValue("o"); outDirName = opt.optionValue("o");
dumpBoot = opt.gotOption("d");
manFileName = opt.getArgs()[0]; manFileName = opt.getArgs()[0];
nameFileName = opt.getArgs()[1]; nameFileName = opt.getArgs()[1];
@ -124,6 +127,15 @@ int main(int argc, char *argv[])
cout << '\r' << ProgressBar(i + 1, name.size()); cout << '\r' << ProgressBar(i + 1, name.size());
data[name[i]].bin(binSize); data[name[i]].bin(binSize);
if (i == 0)
{
ofstream file(outDirName + "/" + manFileName + ".bootseq");
file << "# bootstrap sequences" << endl;
file << "# manifest file: " << manFileName << endl;
file << "# bin size: " << binSize << endl;
data[name[i]].dumpBootstrapSeq(file, nSample, seed);
}
s = data[name[i]].bootstrapMean(nSample, seed); s = data[name[i]].bootstrapMean(nSample, seed);
Io::save<DMatSample>(s, outDirName + "/" + outFileName, Io::save<DMatSample>(s, outDirName + "/" + outFileName,
File::Mode::write, outFileName); File::Mode::write, outFileName);