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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
Sample<T> bootstrapMean(const Index nSample, const SeedType seed);
Sample<T> bootstrapMean(const Index nSample);
void dumpBootstrapSeq(std::ostream &out, const Index nSample,
const SeedType seed);
private:
// mean from pointer vector for resampling
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());
}
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>
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 ////////////////////////////////////////////////////////
OptParser opt;
bool parsed;
bool parsed, dumpBoot;
random_device rd;
SeedType seed = rd();
string manFileName, nameFileName, outDirName;
@@ -56,6 +56,8 @@ int main(int argc, char *argv[])
"output directory", ".");
opt.addOption("f", "format" , OptParser::OptType::value, true,
"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,
"show this help message and exit");
parsed = opt.parse(argc, argv);
@@ -75,6 +77,7 @@ int main(int argc, char *argv[])
}
ext = opt.optionValue("f");
outDirName = opt.optionValue("o");
dumpBoot = opt.gotOption("d");
manFileName = opt.getArgs()[0];
nameFileName = opt.getArgs()[1];
@@ -124,6 +127,15 @@ int main(int argc, char *argv[])
cout << '\r' << ProgressBar(i + 1, name.size());
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);
Io::save<DMatSample>(s, outDirName + "/" + outFileName,
File::Mode::write, outFileName);