tdm_reaper: process submatrices, localcolumns
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parent
6179bf01f7
commit
616ceaf326
@ -292,7 +292,7 @@ struct localcolumn {
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std::string values_; // -> refers to usi:data -> _sequence
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std::string values_; // -> refers to usi:data -> _sequence
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const std::string get_info(int width = 20)
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const std::string get_info(int width = 25)
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{
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{
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std::stringstream ss;
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std::stringstream ss;
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ss<<std::setw(width)<<std::left<<"id:"<<id_<<"\n"
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ss<<std::setw(width)<<std::left<<"id:"<<id_<<"\n"
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@ -303,8 +303,9 @@ struct localcolumn {
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<<std::setw(width)<<std::left<<"minimum:"<<std::to_string(minimum_)<<"\n"
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<<std::setw(width)<<std::left<<"minimum:"<<std::to_string(minimum_)<<"\n"
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<<std::setw(width)<<std::left<<"maximum:"<<std::to_string(maximum_)<<"\n"
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<<std::setw(width)<<std::left<<"maximum:"<<std::to_string(maximum_)<<"\n"
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<<std::setw(width)<<std::left<<"sequence_representation:"<<sequence_representation_<<"\n"
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<<std::setw(width)<<std::left<<"sequence_representation:"<<sequence_representation_<<"\n"
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<<std::setw(width)<<std::left<<"generation_parameters_:"<<"{"<<generation_parameters_[0]
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// TODO
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<<","<<generation_parameters_[1]<<"}"<<"\n"
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// <<std::setw(width)<<std::left<<"generation_parameters_:"<<"{"<<generation_parameters_[0]
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// <<","<<generation_parameters_[1]<<"}"<<"\n"
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<<std::setw(width)<<std::left<<"values:"<<values_<<"\n";
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<<std::setw(width)<<std::left<<"values:"<<values_<<"\n";
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return ss.str();
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return ss.str();
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}
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}
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@ -71,6 +71,8 @@ void tdm_reaper::process_tdm(bool showlog)
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this->process_root(showlog);
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this->process_root(showlog);
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this->process_channelgroups(showlog);
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this->process_channelgroups(showlog);
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this->process_channels(showlog);
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this->process_channels(showlog);
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this->process_submatrices(showlog);
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this->process_localcolumns(showlog);
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}
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}
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void tdm_reaper::process_include(bool showlog)
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void tdm_reaper::process_include(bool showlog)
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@ -181,7 +183,7 @@ void tdm_reaper::process_channelgroups(bool showlog)
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}
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}
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else
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else
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{
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{
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throw std::runtime_error("tdm_channelgroup without root id");
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throw std::runtime_error("tdm_channelgroup with out/multiple root id(s)");
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}
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}
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tdmchannelgroup.channels_ = this->extract_ids(group.child_value("channels"));
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tdmchannelgroup.channels_ = this->extract_ids(group.child_value("channels"));
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tdmchannelgroup.submatrices_ = this->extract_ids(group.child_value("submatrices"));
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tdmchannelgroup.submatrices_ = this->extract_ids(group.child_value("submatrices"));
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@ -214,8 +216,12 @@ void tdm_reaper::process_channels(bool showlog)
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tdmchannel.description_ = channel.child_value("description");
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tdmchannel.description_ = channel.child_value("description");
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tdmchannel.unit_string_ = channel.child_value("unit_string");
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tdmchannel.unit_string_ = channel.child_value("unit_string");
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tdmchannel.datatype_ = channel.child_value("datatype");
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tdmchannel.datatype_ = channel.child_value("datatype");
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tdmchannel.minimum_ = std::stod(channel.child_value("minimum"));
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std::string chmin = channel.child_value("minimum");
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tdmchannel.maximum_ = std::stod(channel.child_value("maximum"));
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chmin = chmin.empty() ? std::string("0.0") : chmin;
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tdmchannel.minimum_ = std::stod(chmin);
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std::string chmax = channel.child_value("maximum");
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chmax = chmax.empty() ? std::string("0.0") : chmax;
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tdmchannel.maximum_ = std::stod(chmax);
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std::vector<std::string> cg = this->extract_ids(channel.child_value("group"));
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std::vector<std::string> cg = this->extract_ids(channel.child_value("group"));
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if ( cg.size() == 1 )
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if ( cg.size() == 1 )
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{
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{
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@ -223,7 +229,7 @@ void tdm_reaper::process_channels(bool showlog)
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}
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}
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else
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else
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{
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{
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throw std::runtime_error("tdm_channel without group id");
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throw std::runtime_error("tdm_channel with out/multiple group id(s)");
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}
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}
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tdmchannel.local_columns_ = this->extract_ids(channel.child_value("local_columns"));
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tdmchannel.local_columns_ = this->extract_ids(channel.child_value("local_columns"));
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@ -236,5 +242,107 @@ void tdm_reaper::process_channels(bool showlog)
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if ( showlog ) std::cout<<"number of channels: "<<tdmchannels_.size()<<"\n\n";
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if ( showlog ) std::cout<<"number of channels: "<<tdmchannels_.size()<<"\n\n";
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}
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}
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void tdm_reaper::process_submatrices(bool showlog)
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{
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// get XML node <usi:data>
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pugi::xml_node tdmdata = xml_doc_.child("usi:tdm").child("usi:data");
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// find all its <submatrix> elements
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for ( pugi::xml_node subm = tdmdata.child("submatrix"); subm;
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subm = subm.next_sibling("submatrix") )
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{
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// declare new submatrix
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submatrix submat;
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// extract properties
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submat.id_ = subm.attribute("id").value();
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submat.name_ = subm.child_value("name");
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submat.description_ = subm.child_value("description");
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std::vector<std::string> mid = this->extract_ids(subm.child_value("measurement"));
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if ( mid.size() == 1 )
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{
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submat.measurement_ = mid.at(0);
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}
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else
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{
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throw std::runtime_error("submatrix with out/multiple measurement id(s)");
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}
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submat.local_columns_ = this->extract_ids(subm.child_value("local_columns"));
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std::string numrows = subm.child_value("number_of_rows");
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numrows = numrows.empty() ? std::string("0") : numrows;
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submat.number_of_rows_ = std::stoul(numrows);
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// add submatrix to map
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submatrices_.insert( std::pair<std::string,submatrix>(submat.id_,submat) );
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if ( showlog ) std::cout<<submat.get_info()<<"\n";
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}
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if ( showlog ) std::cout<<"number of submatrices: "<<submatrices_.size()<<"\n\n";
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}
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void tdm_reaper::process_localcolumns(bool showlog)
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{
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// get XML node <usi:data>
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pugi::xml_node tdmdata = xml_doc_.child("usi:tdm").child("usi:data");
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// find all its <localcolumn> elements
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for ( pugi::xml_node loccol = tdmdata.child("localcolumn"); loccol;
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loccol = loccol.next_sibling("localcolumn") )
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{
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// declare new localcolumn
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localcolumn locc;
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// extract properties
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locc.id_ = loccol.attribute("id").value();
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locc.name_ = loccol.child_value("name");
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locc.description_ = loccol.child_value("description");
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std::vector<std::string> mq = this->extract_ids(loccol.child_value("measurement_quantity"));
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if ( mq.size() == 1 )
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{
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locc.measurement_quantity_ = mq.at(0);
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}
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else
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{
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throw std::runtime_error("localcolumn with out/multiple measurement quantity id(s)");
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}
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std::vector<std::string> sm = this->extract_ids(loccol.child_value("submatrix"));
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if ( sm.size() == 1 )
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{
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locc.submatrix_ = sm.at(0);
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}
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else
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{
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throw std::runtime_error("localcolumn with out/multiple submatrix id(s)");
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}
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std::string lcmin = loccol.child_value("minimum");
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lcmin = lcmin.empty() ? std::string("0.0") : lcmin;
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locc.minimum_ = std::stod(lcmin);
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std::string lcmax = loccol.child_value("maximum");
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lcmax = lcmax.empty() ? std::string("0.0") : lcmax;
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locc.maximum_ = std::stod(lcmax);
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locc.sequence_representation_ = loccol.child_value("sequence_representation");
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// TODO
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// .... loccal.child_value("generation_parameters");
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std::vector<std::string> vl = this->extract_ids(loccol.child_value("values"));
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if ( vl.size() == 1 )
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{
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locc.values_ = vl.at(0);
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}
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else
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{
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throw std::runtime_error("localcolumn with out/multiple values id(s)");
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}
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// add localcolumn to map
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localcolumns_.insert( std::pair<std::string,localcolumn>(locc.id_,locc) );
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if ( showlog ) std::cout<<locc.get_info()<<"\n";
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}
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if ( showlog ) std::cout<<"number of localcolumns: "<<localcolumns_.size()<<"\n\n";
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}
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// -------------------------------------------------------------------------- //
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// -------------------------------------------------------------------------- //
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@ -51,38 +51,10 @@ class tdm_reaper
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// tdm channels
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// tdm channels
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std::map<std::string,tdm_channel> tdmchannels_;
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std::map<std::string,tdm_channel> tdmchannels_;
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// // number/names/ids of channels, channelgroups and channels's assignment to groups
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// submatrices and local_columns
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// int num_channels_, num_groups_;
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std::map<std::string,submatrix> submatrices_;
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// std::vector<std::string> channel_id_, inc_id_, units_, channel_name_;
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std::map<std::string,localcolumn> localcolumns_;
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// std::vector<std::string> group_id_, group_name_;
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// std::vector<std::pair<std::string,std::string>> group_timestamp_;
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// std::vector<int> num_channels_group_;
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// std::vector<int> channels_group_;
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// std::vector<int> channel_ext_;
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//
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// // neglect empty groups
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// bool neglect_empty_groups_;
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// int num_empty_groups_;
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//
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// // minimum/maximum value in particular channel (is provided in .tdm file as float)
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// std::vector<std::pair<double,double>> minmax_;
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//
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// // use xpointers and ids to assign channels to byteoffsets
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// std::map<std::string,std::string> xml_local_columns_, xml_values_, xml_double_sequence_;
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//
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// // byteoffset, length and datatype of channels
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// std::vector<int> byteoffset_;
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// std::vector<int> length_;
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// std::vector<std::string> type_;
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// std::vector<std::string> external_id_;
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//
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// // NI datatypes ( )
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// std::map<std::string, int> datatypes_;
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//
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// // .tdm-file eventually contains some meta information (about measurement)
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// std::map<std::string,std::string> root_info_;
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// std::map<std::string,std::string> meta_info_;
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//
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// // binary data container
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// // binary data container
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// std::vector<unsigned char> tdxbuf_;
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// std::vector<unsigned char> tdxbuf_;
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@ -129,293 +101,9 @@ public:
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void process_channelgroups(bool showlog);
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void process_channelgroups(bool showlog);
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void process_channels(bool showlog);
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void process_channels(bool showlog);
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// void parse_structure();
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// process submatrices and localcolumns
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//
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void process_submatrices(bool showlog);
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// void list_channels(std::ostream& gout = std::cout, int width = 15, int maxshow = 50);
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void process_localcolumns(bool showlog);
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// void list_groups(std::ostream& gout = std::cout, int width = 15, int maxshow = 50);
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//
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// void show_structure();
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//
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// // count number of occurences of substring in string
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// int count_occ_string(std::string s, std::string sub)
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// {
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// int num_occs = 0;
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// std::string::size_type pos = 0;
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//
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// while ( ( pos = s.find(sub,pos) ) != std::string::npos )
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// {
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// num_occs++;
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// pos += sub.length();
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// }
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//
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// return num_occs;
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// }
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//
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// // obtain substring of 'entirestr' in between starting and stopping delimiter
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// std::string get_str_between(std::string entirestr, std::string startlim, std::string stoplim)
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// {
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// std::size_t apos = entirestr.find(startlim);
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// std::size_t bpos = entirestr.find_last_of(stoplim);
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// assert( apos != std::string::npos && bpos != std::string::npos );
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// return entirestr.substr(apos+startlim.length(),bpos-(apos+startlim.length()));
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// }
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//
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// void print_hash_local(const char* filename, int width = 20)
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// {
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// std::ofstream fout(filename);
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//
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// std::map<std::string,std::string>::iterator it;
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// int count = 0;
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// for ( it = xml_local_columns_.begin(); it != xml_local_columns_.end(); it++ )
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// {
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// count++;
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// fout<<std::setw(width)<<count;
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// fout<<std::setw(width)<<it->first;
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// fout<<std::setw(width)<<it->second;
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// fout<<"\n";
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// }
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// fout.close();
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// }
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//
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// void print_hash_values(const char* filename, int width = 20)
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// {
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// std::ofstream fout(filename);
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//
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// std::map<std::string,std::string>::iterator it;
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// int count = 0;
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// for ( it = xml_values_.begin(); it != xml_values_.end(); it++ )
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// {
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// count++;
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// fout<<std::setw(width)<<count;
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// fout<<std::setw(width)<<it->first;
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// fout<<std::setw(width)<<it->second;
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// fout<<"\n";
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// }
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// fout.close();
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// }
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//
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// void print_hash_double(const char* filename, int width = 20)
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// {
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// std::ofstream fout(filename);
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//
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// std::map<std::string,std::string>::iterator it;
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// int count = 0;
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// for ( it = xml_double_sequence_.begin(); it != xml_double_sequence_.end(); it++ )
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// {
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// count++;
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// fout<<std::setw(width)<<count;
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// fout<<std::setw(width)<<it->first;
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// fout<<std::setw(width)<<it->second;
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// fout<<"\n";
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// }
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// fout.close();
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// }
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//
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// void print_extid(const char* filename, int width = 20)
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// {
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// std::ofstream fout(filename);
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//
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// int count = 0;
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// for ( auto extid: channel_ext_ )
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// {
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// count++;
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// fout<<std::setw(width)<<count;
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// fout<<std::setw(width)<<extid;
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// fout<<"\n";
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// }
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// fout.close();
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// }
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//
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// // provide number of channels and group
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// const int& num_channels()
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// {
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// return num_channels_;
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// }
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// const int& num_groups()
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// {
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// return num_groups_;
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// }
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//
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// // get number of channels in specific group
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// const int& no_channels(int groupid)
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// {
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// assert( groupid >= 0 && groupid < num_groups_ );
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//
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// return num_channels_group_[groupid];
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// }
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//
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// const std::string& channel_name(int channelid)
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// {
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// assert( channelid >= 0 && channelid < num_channels_ );
|
|
||||||
//
|
|
||||||
// return channel_name_[channelid];
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// // obtain overall channel id from combined group and group-specific channel id
|
|
||||||
// int obtain_channel_id(int groupid, int channelid)
|
|
||||||
// {
|
|
||||||
// assert( groupid >= 0 && groupid < num_groups_ );
|
|
||||||
// assert( channelid >= 0 && channelid < num_channels_group_[groupid] );
|
|
||||||
//
|
|
||||||
// // find cummulative number of channels
|
|
||||||
// int numsum = 0;
|
|
||||||
// for ( int i = 0; i < groupid; i++ )
|
|
||||||
// {
|
|
||||||
// numsum += num_channels_group_[i];
|
|
||||||
// }
|
|
||||||
// assert( (numsum + channelid) >= 0 );
|
|
||||||
// assert( (numsum + channelid) <= num_channels_ );
|
|
||||||
//
|
|
||||||
// return numsum+channelid;
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// const std::string& channel_name(int groupid, int channelid)
|
|
||||||
// {
|
|
||||||
// return channel_name_[obtain_channel_id(groupid,channelid)];
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// const std::string& group_name(int groupid)
|
|
||||||
// {
|
|
||||||
// assert( groupid >= 0 && groupid < num_groups_ );
|
|
||||||
//
|
|
||||||
// return group_name_[groupid];
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// const std::string& channel_unit(int groupid, int channelid)
|
|
||||||
// {
|
|
||||||
// return units_[obtain_channel_id(groupid,channelid)];
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// int channel_exists(int groupid, std::string channel_name)
|
|
||||||
// {
|
|
||||||
// assert( groupid >= 0 && groupid < num_groups_ );
|
|
||||||
//
|
|
||||||
// int channelid = -1;
|
|
||||||
// for ( int i = 0; i < num_channels_group_[groupid]; i++)
|
|
||||||
// {
|
|
||||||
// if ( comparestrings(channel_name_[obtain_channel_id(groupid,i)],channel_name) )
|
|
||||||
// {
|
|
||||||
// channelid = i;
|
|
||||||
// }
|
|
||||||
// }
|
|
||||||
// return channelid;
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// bool comparestrings(std::string s1, std::string s2, bool case_sensitive = false)
|
|
||||||
// {
|
|
||||||
// if ( case_sensitive )
|
|
||||||
// {
|
|
||||||
// return ( s1.compare(s2) == 0 );
|
|
||||||
// }
|
|
||||||
// else
|
|
||||||
// {
|
|
||||||
// std::transform( s1.begin(), s1.end(), s1.begin(), ::tolower);
|
|
||||||
// std::transform( s2.begin(), s2.end(), s2.begin(), ::tolower);
|
|
||||||
// return ( s1.compare(s2) == 0 );
|
|
||||||
// }
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// // get time-stamp of channel-group in .tdm file given in unix format
|
|
||||||
// static std::string unix_timestamp(std::string unixts)
|
|
||||||
// {
|
|
||||||
// // average year of Gregorian calender
|
|
||||||
// const double avgdaysofyear = 365.0 + 1./4 - 1./100 + 1./400
|
|
||||||
// - 8./24561; // gauge timestamp according to DIADEM result
|
|
||||||
//
|
|
||||||
// // convert string to long int = number of seconds since 0000/01/01 00:00
|
|
||||||
// long int ts = atol(unixts.c_str());
|
|
||||||
// assert( ts >= 0 );
|
|
||||||
//
|
|
||||||
// // use STL to convert timestamp (epoch usually starts on 01.01.1970)
|
|
||||||
// std::time_t tstime = ts - 1970*avgdaysofyear*86400;
|
|
||||||
//
|
|
||||||
// // get rid of linebreak character and return the result
|
|
||||||
// return strtok(std::ctime(&tstime),"\n");
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// std::string time_stamp(int groupid, bool startstop = true)
|
|
||||||
// {
|
|
||||||
// assert( groupid >= 0 && groupid < num_groups_ );
|
|
||||||
//
|
|
||||||
// return startstop ? unix_timestamp(group_timestamp_[groupid].first)
|
|
||||||
// : unix_timestamp(group_timestamp_[groupid].second);
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// void list_datatypes();
|
|
||||||
//
|
|
||||||
// // convert array of chars to single integer or floating point double
|
|
||||||
// int convert_int(std::vector<unsigned char> bych);
|
|
||||||
// double convert_double(std::vector<unsigned char> bych);
|
|
||||||
//
|
|
||||||
// // disassemble single integer or double into array of chars
|
|
||||||
// std::vector<unsigned char> convert_int(int number);
|
|
||||||
// std::vector<unsigned char> convert_double(double number);
|
|
||||||
//
|
|
||||||
// // convert entire channel, i.e. expert of .tdx binary file
|
|
||||||
// // std::vector<double> convert_channel(int byteoffset, int length, int typesize);
|
|
||||||
// std::vector<double> convert_channel(int channelid);
|
|
||||||
//
|
|
||||||
// // obtain channel from overall channel id...
|
|
||||||
// std::vector<double> get_channel(int channelid);
|
|
||||||
// // ...or from group id and group-specific channel id
|
|
||||||
// std::vector<double> channel(int groupid, int channelid)
|
|
||||||
// {
|
|
||||||
// return get_channel(obtain_channel_id(groupid,channelid));
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// int channel_length(int groupid, int channelid)
|
|
||||||
// {
|
|
||||||
// return length_[channel_ext_[obtain_channel_id(groupid,channelid)]];
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// double get_min(int groupid, int channelid)
|
|
||||||
// {
|
|
||||||
// return minmax_[obtain_channel_id(groupid,channelid)].first;
|
|
||||||
// }
|
|
||||||
// double get_max(int groupid, int channelid)
|
|
||||||
// {
|
|
||||||
// return minmax_[obtain_channel_id(groupid,channelid)].second;
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// void print_channel(int channelid, const char* filename, int width = 15);
|
|
||||||
//
|
|
||||||
// // obtain any meta information about .tdm-file if available
|
|
||||||
// std::string get_meta(std::string attribute_name)
|
|
||||||
// {
|
|
||||||
// // check if key "attribute_name" actually exits
|
|
||||||
// std::map<std::string,std::string>::iterator positer = meta_info_.find(attribute_name);
|
|
||||||
// bool ispresent = ( positer == meta_info_.end() ) ? false : true;
|
|
||||||
//
|
|
||||||
// return ispresent ? meta_info_[attribute_name] : "key does not exist";
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// // prepare meta information file including all available meta-data
|
|
||||||
// void print_meta(const char* filename, std::string sep = ",")
|
|
||||||
// {
|
|
||||||
// // open file
|
|
||||||
// std::ofstream fout(filename);
|
|
||||||
//
|
|
||||||
// for ( const auto& it : root_info_ )
|
|
||||||
// {
|
|
||||||
// fout<<it.first<<sep<<it.second<<"\n";
|
|
||||||
// }
|
|
||||||
// fout<<sep<<"\n";
|
|
||||||
// for ( const auto& it : meta_info_ )
|
|
||||||
// {
|
|
||||||
// fout<<it.first<<sep<<it.second<<"\n";
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// // close down file
|
|
||||||
// fout.close();
|
|
||||||
// }
|
|
||||||
|
|
||||||
// TODO add elements/methods to build .tdm and write .tdx files for your own data
|
|
||||||
// by constructing xml document tree and write data to binary .tdx
|
|
||||||
// void set_channels(std::vector<std::string> channels);
|
|
||||||
// void set_groups(std::vector<std::string> groups);
|
|
||||||
// void set_assigment(std::vector<int> assignment);
|
|
||||||
// void set_channel(int i, std::vector<double> data);
|
|
||||||
|
|
||||||
};
|
};
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
@ -181,7 +181,8 @@ int main(int argc, char* argv[])
|
|||||||
try {
|
try {
|
||||||
jack.submit_files(cfgopts.at("tdm"),cfgopts.at("tdx"),true);
|
jack.submit_files(cfgopts.at("tdm"),cfgopts.at("tdx"),true);
|
||||||
} catch (const std::exception& e) {
|
} catch (const std::exception& e) {
|
||||||
throw std::runtime_error("failed to load and parse tdm/tdx files");
|
throw std::runtime_error( std::string("failed to load and parse tdm/tdx files: ")
|
||||||
|
+ e.what() );
|
||||||
}
|
}
|
||||||
|
|
||||||
// print list of groups or channels to stdout
|
// print list of groups or channels to stdout
|
||||||
|
|||||||
Loading…
x
Reference in New Issue
Block a user