// [[Rcpp::export]]
Rcpp::List
GridDiag(const Rcpp::NumericVector & FUNvalues
, const Rcpp::IntegerVector & gridDim
, const int maxdimension
, const std::string & decomposition
, const std::string & library
, const bool location
, const bool printProgress
) {
#ifdef LOGGING
//rlog::RLogInit(argc, argv);
stdoutLog.subscribeTo(RLOG_CHANNEL("topology/persistence"));
//stdoutLog.subscribeTo(RLOG_CHANNEL("topology/chain"));
//stdoutLog.subscribeTo(RLOG_CHANNEL("topology/vineyard"));
#endif
std::vector< std::vector< std::vector< double > > > persDgm;
std::vector< std::vector< std::vector< unsigned > > > persLoc;
std::vector< std::vector< std::vector< std::vector< unsigned > > > > persCycle;
Fltr f;
// Generate simplicial complex from function values and grid
if (decomposition[0] == '5') {
simplicesFromGrid(f, FUNvalues, gridDim, maxdimension + 1);
}
if (decomposition[0] == 'b') {
simplicesFromGridBarycenter(f, FUNvalues, gridDim, maxdimension + 1);
}
if (printProgress) {
Rprintf("# Generated complex of size: %d \n", f.size());
}
// Sort the simplices with respect to function values
f.sort(Smplx::DataComparison());
// Compute the persistence diagram of the complex
if (library[0] == 'D') {
computePersistenceDionysus< Persistence >(f, Smplx::DataEvaluator(),
maxdimension, FUNvalues, location, printProgress,
persDgm, persLoc, persCycle);
}
if (library[0] == 'P') {
computePersistencePhat(f, Smplx::DataEvaluator(), maxdimension,
FUNvalues, location, printProgress, persDgm, persLoc);
}
// Output persistent diagram
return Rcpp::List::create(
concatStlToRcpp< Rcpp::NumericMatrix >(persDgm, true, 3),
concatStlToRcpp< Rcpp::NumericMatrix >(persLoc, false, 2),
StlToRcppMatrixList< Rcpp::List, Rcpp::NumericMatrix >(persCycle));
}
void program_options(int argc, char* argv[], std::string& complex_fn,
std::string& values_fn,
std::string& output_prefix,
bool& skip_infinite_vines,
bool& save_vines,
bool& explicit_events)
{
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
hidden.add_options()
("complex-file", po::value<std::string>(&complex_fn), "file listing the simplices of the complex")
("values-file", po::value<std::string>(&values_fn), "file listing the values at the vertices")
("output-prefix", po::value<std::string>(&output_prefix), "output prefix");
po::options_description visible("Allowed options", 100);
visible.add_options()
("skip-infinite,s", po::bool_switch(&skip_infinite_vines), "skip infinite vines in the output")
("explicit-events,e", po::bool_switch(&explicit_events), "process kinetic sort events one by one")
("save-vines,v", po::bool_switch(&save_vines), "save vines instead of edges")
("help,h", "produce help message");
#if LOGGING
std::vector<std::string> log_channels;
visible.add_options()
("log,l", po::value< std::vector<std::string> >(&log_channels), "log channels to turn on (info, debug, etc)");
#endif
po::positional_options_description pos;
pos.add("complex-file", 1);
pos.add("values-file", 1);
pos.add("output-prefix", 1);
po::options_description all; all.add(visible).add(hidden);
po::variables_map vm;
po::store(po::command_line_parser(argc, argv).
options(all).positional(pos).run(), vm);
po::notify(vm);
#if LOGGING
for (std::vector<std::string>::const_iterator cur = log_channels.begin(); cur != log_channels.end(); ++cur)
stderrLog.subscribeTo( RLOG_CHANNEL(cur->c_str()) );
#endif
if (vm.count("help") || !vm.count("complex-file") || !vm.count("values-file") || !vm.count("output-prefix"))
{
std::cout << "Usage: " << argv[0] << " [options] complex-file values-file output-prefix" << std::endl;
std::cout << visible << std::endl;
std::abort();
}
}
int main(int argc, char **argv) {
rlog::StdioNode client_log(1, rlog::StdioNode::OutputColor);
client_log.subscribeTo( RLOG_CHANNEL("debug") ) ;
client_log.subscribeTo( RLOG_CHANNEL("error") ) ;
client_log.subscribeTo( RLOG_CHANNEL("info") );
client_log.subscribeTo( RLOG_CHANNEL("warning") );
client_log.subscribeTo( RLOG_CHANNEL("fuse/control") ) ;
client_log.subscribeTo( RLOG_CHANNEL("intercom/user_harmony/control") ) ;
//client_log.subscribeTo( RLOG_CHANNEL("sink") ) ;
colony::CSScheduler::SetCSL();
colonyfs_fusexx hello;
// The first 3 parameters are identical to the fuse_main function.
// The last parameter gives a pointer to a class instance, which is
// required for static methods to access instance variables/ methods.
return hello.main(argc, argv, NULL, &hello);
}
// This file os part of FVM
// Copyright (c) 2012 FVM Authors
// See LICENSE file for terms.
#include "RLogInterface.h"
rlog::RLogChannel* RLogInterface::ctorChannel = RLOG_CHANNEL("cdtor/ctor");
rlog::RLogChannel* RLogInterface::dtorChannel = RLOG_CHANNEL("cdtor/dtor");
rlog::RLogChannel* RLogInterface::infoChannel = RLOG_CHANNEL("info");
rlog::RLogChannel* RLogInterface::warningChannel = RLOG_CHANNEL("info/warning");
rlog::RLogChannel* RLogInterface::errorChannel = RLOG_CHANNEL("info/error");
