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tdm_reaper: process submatrices, localcolumns

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This commit is contained in:
Mario Fink 2021-01-20 12:24:45 +01:00
parent 6179bf01f7
commit 616ceaf326
4 changed files with 125 additions and 327 deletions
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7
lib/tdm_datamodel.hpp
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@ -292,7 +292,7 @@ struct localcolumn {
std::string values_; // -> refers to usi:data -> _sequence
const std::string get_info(int width = 20)
const std::string get_info(int width = 25)
{
std::stringstream ss;
ss<<std::setw(width)<<std::left<<"id:"<<id_<<"\n"
@ -303,8 +303,9 @@ struct localcolumn {
<<std::setw(width)<<std::left<<"minimum:"<<std::to_string(minimum_)<<"\n"
<<std::setw(width)<<std::left<<"maximum:"<<std::to_string(maximum_)<<"\n"
<<std::setw(width)<<std::left<<"sequence_representation:"<<sequence_representation_<<"\n"
<<std::setw(width)<<std::left<<"generation_parameters_:"<<"{"<<generation_parameters_[0]
<<","<<generation_parameters_[1]<<"}"<<"\n"
// TODO
// <<std::setw(width)<<std::left<<"generation_parameters_:"<<"{"<<generation_parameters_[0]
// <<","<<generation_parameters_[1]<<"}"<<"\n"
<<std::setw(width)<<std::left<<"values:"<<values_<<"\n";
return ss.str();
}

116
lib/tdm_reaper.cpp
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@ -71,6 +71,8 @@ void tdm_reaper::process_tdm(bool showlog)
this->process_root(showlog);
this->process_channelgroups(showlog);
this->process_channels(showlog);
this->process_submatrices(showlog);
this->process_localcolumns(showlog);
}
void tdm_reaper::process_include(bool showlog)
@ -181,7 +183,7 @@ void tdm_reaper::process_channelgroups(bool showlog)
}
else
{
throw std::runtime_error("tdm_channelgroup without root id");
throw std::runtime_error("tdm_channelgroup with out/multiple root id(s)");
}
tdmchannelgroup.channels_ = this->extract_ids(group.child_value("channels"));
tdmchannelgroup.submatrices_ = this->extract_ids(group.child_value("submatrices"));
@ -214,8 +216,12 @@ void tdm_reaper::process_channels(bool showlog)
tdmchannel.description_ = channel.child_value("description");
tdmchannel.unit_string_ = channel.child_value("unit_string");
tdmchannel.datatype_ = channel.child_value("datatype");
tdmchannel.minimum_ = std::stod(channel.child_value("minimum"));
tdmchannel.maximum_ = std::stod(channel.child_value("maximum"));
std::string chmin = channel.child_value("minimum");
chmin = chmin.empty() ? std::string("0.0") : chmin;
tdmchannel.minimum_ = std::stod(chmin);
std::string chmax = channel.child_value("maximum");
chmax = chmax.empty() ? std::string("0.0") : chmax;
tdmchannel.maximum_ = std::stod(chmax);
std::vector<std::string> cg = this->extract_ids(channel.child_value("group"));
if ( cg.size() == 1 )
{
@ -223,7 +229,7 @@ void tdm_reaper::process_channels(bool showlog)
}
else
{
throw std::runtime_error("tdm_channel without group id");
throw std::runtime_error("tdm_channel with out/multiple group id(s)");
}
tdmchannel.local_columns_ = this->extract_ids(channel.child_value("local_columns"));
@ -236,5 +242,107 @@ void tdm_reaper::process_channels(bool showlog)
if ( showlog ) std::cout<<"number of channels: "<<tdmchannels_.size()<<"\n\n";
}
void tdm_reaper::process_submatrices(bool showlog)
{
// get XML node <usi:data>
pugi::xml_node tdmdata = xml_doc_.child("usi:tdm").child("usi:data");
// find all its <submatrix> elements
for ( pugi::xml_node subm = tdmdata.child("submatrix"); subm;
subm = subm.next_sibling("submatrix") )
{
// declare new submatrix
submatrix submat;
// extract properties
submat.id_ = subm.attribute("id").value();
submat.name_ = subm.child_value("name");
submat.description_ = subm.child_value("description");
std::vector<std::string> mid = this->extract_ids(subm.child_value("measurement"));
if ( mid.size() == 1 )
{
submat.measurement_ = mid.at(0);
}
else
{
throw std::runtime_error("submatrix with out/multiple measurement id(s)");
}
submat.local_columns_ = this->extract_ids(subm.child_value("local_columns"));
std::string numrows = subm.child_value("number_of_rows");
numrows = numrows.empty() ? std::string("0") : numrows;
submat.number_of_rows_ = std::stoul(numrows);
// add submatrix to map
submatrices_.insert( std::pair<std::string,submatrix>(submat.id_,submat) );
if ( showlog ) std::cout<<submat.get_info()<<"\n";
}
if ( showlog ) std::cout<<"number of submatrices: "<<submatrices_.size()<<"\n\n";
}
void tdm_reaper::process_localcolumns(bool showlog)
{
// get XML node <usi:data>
pugi::xml_node tdmdata = xml_doc_.child("usi:tdm").child("usi:data");
// find all its <localcolumn> elements
for ( pugi::xml_node loccol = tdmdata.child("localcolumn"); loccol;
loccol = loccol.next_sibling("localcolumn") )
{
// declare new localcolumn
localcolumn locc;
// extract properties
locc.id_ = loccol.attribute("id").value();
locc.name_ = loccol.child_value("name");
locc.description_ = loccol.child_value("description");
std::vector<std::string> mq = this->extract_ids(loccol.child_value("measurement_quantity"));
if ( mq.size() == 1 )
{
locc.measurement_quantity_ = mq.at(0);
}
else
{
throw std::runtime_error("localcolumn with out/multiple measurement quantity id(s)");
}
std::vector<std::string> sm = this->extract_ids(loccol.child_value("submatrix"));
if ( sm.size() == 1 )
{
locc.submatrix_ = sm.at(0);
}
else
{
throw std::runtime_error("localcolumn with out/multiple submatrix id(s)");
}
std::string lcmin = loccol.child_value("minimum");
lcmin = lcmin.empty() ? std::string("0.0") : lcmin;
locc.minimum_ = std::stod(lcmin);
std::string lcmax = loccol.child_value("maximum");
lcmax = lcmax.empty() ? std::string("0.0") : lcmax;
locc.maximum_ = std::stod(lcmax);
locc.sequence_representation_ = loccol.child_value("sequence_representation");
// TODO
// .... loccal.child_value("generation_parameters");
std::vector<std::string> vl = this->extract_ids(loccol.child_value("values"));
if ( vl.size() == 1 )
{
locc.values_ = vl.at(0);
}
else
{
throw std::runtime_error("localcolumn with out/multiple values id(s)");
}
// add localcolumn to map
localcolumns_.insert( std::pair<std::string,localcolumn>(locc.id_,locc) );
if ( showlog ) std::cout<<locc.get_info()<<"\n";
}
if ( showlog ) std::cout<<"number of localcolumns: "<<localcolumns_.size()<<"\n\n";
}
// -------------------------------------------------------------------------- //

326
lib/tdm_reaper.hpp
View File

@ -51,38 +51,10 @@ class tdm_reaper
// tdm channels
std::map<std::string,tdm_channel> tdmchannels_;
// // number/names/ids of channels, channelgroups and channels's assignment to groups
// int num_channels_, num_groups_;
// std::vector<std::string> channel_id_, inc_id_, units_, channel_name_;
// std::vector<std::string> group_id_, group_name_;
// std::vector<std::pair<std::string,std::string>> group_timestamp_;
// std::vector<int> num_channels_group_;
// std::vector<int> channels_group_;
// std::vector<int> channel_ext_;
//
// // neglect empty groups
// bool neglect_empty_groups_;
// int num_empty_groups_;
//
// // minimum/maximum value in particular channel (is provided in .tdm file as float)
// std::vector<std::pair<double,double>> minmax_;
//
// // use xpointers and ids to assign channels to byteoffsets
// std::map<std::string,std::string> xml_local_columns_, xml_values_, xml_double_sequence_;
//
// // byteoffset, length and datatype of channels
// std::vector<int> byteoffset_;
// std::vector<int> length_;
// std::vector<std::string> type_;
// std::vector<std::string> external_id_;
//
// // NI datatypes ( )
// std::map<std::string, int> datatypes_;
//
// // .tdm-file eventually contains some meta information (about measurement)
// std::map<std::string,std::string> root_info_;
// std::map<std::string,std::string> meta_info_;
//
// submatrices and local_columns
std::map<std::string,submatrix> submatrices_;
std::map<std::string,localcolumn> localcolumns_;
// // binary data container
// std::vector<unsigned char> tdxbuf_;
@ -129,293 +101,9 @@ public:
void process_channelgroups(bool showlog);
void process_channels(bool showlog);
// void parse_structure();
//
// void list_channels(std::ostream& gout = std::cout, int width = 15, int maxshow = 50);
// void list_groups(std::ostream& gout = std::cout, int width = 15, int maxshow = 50);
//
// void show_structure();
//
// // count number of occurences of substring in string
// int count_occ_string(std::string s, std::string sub)
// {
// int num_occs = 0;
// std::string::size_type pos = 0;
//
// while ( ( pos = s.find(sub,pos) ) != std::string::npos )
// {
// num_occs++;
// pos += sub.length();
// }
//
// return num_occs;
// }
//
// // obtain substring of 'entirestr' in between starting and stopping delimiter
// std::string get_str_between(std::string entirestr, std::string startlim, std::string stoplim)
// {
// std::size_t apos = entirestr.find(startlim);
// std::size_t bpos = entirestr.find_last_of(stoplim);
// assert( apos != std::string::npos && bpos != std::string::npos );
// return entirestr.substr(apos+startlim.length(),bpos-(apos+startlim.length()));
// }
//
// void print_hash_local(const char* filename, int width = 20)
// {
// std::ofstream fout(filename);
//
// std::map<std::string,std::string>::iterator it;
// int count = 0;
// for ( it = xml_local_columns_.begin(); it != xml_local_columns_.end(); it++ )
// {
// count++;
// fout<<std::setw(width)<<count;
// fout<<std::setw(width)<<it->first;
// fout<<std::setw(width)<<it->second;
// fout<<"\n";
// }
// fout.close();
// }
//
// void print_hash_values(const char* filename, int width = 20)
// {
// std::ofstream fout(filename);
//
// std::map<std::string,std::string>::iterator it;
// int count = 0;
// for ( it = xml_values_.begin(); it != xml_values_.end(); it++ )
// {
// count++;
// fout<<std::setw(width)<<count;
// fout<<std::setw(width)<<it->first;
// fout<<std::setw(width)<<it->second;
// fout<<"\n";
// }
// fout.close();
// }
//
// void print_hash_double(const char* filename, int width = 20)
// {
// std::ofstream fout(filename);
//
// std::map<std::string,std::string>::iterator it;
// int count = 0;
// for ( it = xml_double_sequence_.begin(); it != xml_double_sequence_.end(); it++ )
// {
// count++;
// fout<<std::setw(width)<<count;
// fout<<std::setw(width)<<it->first;
// fout<<std::setw(width)<<it->second;
// fout<<"\n";
// }
// fout.close();
// }
//
// void print_extid(const char* filename, int width = 20)
// {
// std::ofstream fout(filename);
//
// int count = 0;
// for ( auto extid: channel_ext_ )
// {
// count++;
// fout<<std::setw(width)<<count;
// fout<<std::setw(width)<<extid;
// fout<<"\n";
// }
// fout.close();
// }
//
// // provide number of channels and group
// const int& num_channels()
// {
// return num_channels_;
// }
// const int& num_groups()
// {
// return num_groups_;
// }
//
// // get number of channels in specific group
// const int& no_channels(int groupid)
// {
// assert( groupid >= 0 && groupid < num_groups_ );
//
// return num_channels_group_[groupid];
// }
//
// const std::string& channel_name(int channelid)
// {
// 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);
// process submatrices and localcolumns
void process_submatrices(bool showlog);
void process_localcolumns(bool showlog);
};
#endif

3
src/main.cpp
View File

@ -181,7 +181,8 @@ int main(int argc, char* argv[])
try {
jack.submit_files(cfgopts.at("tdm"),cfgopts.at("tdx"),true);
} 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