Cython extension: working setup
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@ -1,17 +1,18 @@
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# distutils: language = c++
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from tdm_reaper cimport tdmreaper
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import numpy as np
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import re
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import os
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from tdm_reaper cimport tdm_reaper
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# import numpy as np
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# import re
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# import os
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cdef class tdm_reaper:
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cdef class tdmreaper:
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# C++ instance of class => stack allocated (requires nullary constructor!)
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cdef tdm_reaper tdmrip
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cdef tdm_reaper cpp_tdm
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# constructor
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def __cinit__(self):
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self.tdmrip = tdm_reaper()
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def __cinit__(self, string tdmfile, string tdxfile):
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self.cpp_tdm = tdm_reaper(tdmfile,tdxfile)
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# def set_file(self, string rawfile):
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# if not os.path.isfile(rawfile) :
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@ -4,7 +4,7 @@ from Cython.Build import cythonize
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extensions = Extension(
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name="tdm_reaper",
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sources=["cython/tdm_reaper.pyx"],
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sources=["cython/py_tdm_reaper.pyx"],
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# libraries=[""],
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# library_dirs=["lib"],
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include_dirs=["lib","pugixml"],
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@ -1,15 +1,18 @@
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# cython: language_level = 3
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# distutils: language = c++
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# use some C++ STL libraries
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from libcpp.string cimport string
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from libcpp.vector cimport vector
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from libcpp cimport bool
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# from libcpp.vector cimport vector
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# from libcpp cimport bool
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cdef extern from "tdm_reaper.cpp":
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pass
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cdef extern from "tdm_reaper.hpp":
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cdef cppclass tdmreaper:
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# constructor(s)
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tdmreaper() except +
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cdef cppclass tdm_reaper:
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# constructor(s)
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tdm_reaper() except +
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tdm_reaper(string tdmfile, string tdxfile) except +
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# set new file for decoding
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# void set_file(string)
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# # perform conversion (pass any C++ exceptions to Python)
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@ -40,93 +40,62 @@ void tdm_reaper::process_tdm(bool showlog)
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}
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// set up xml-parser and load tdm-file
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pugi::xml_document xml_doc;
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pugi::xml_parse_result xml_result;
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try {
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// load XML document from stream
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std::ifstream fin(tdmfile_.c_str());
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xml_result_ = xml_doc_.load(fin);
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xml_result = xml_doc.load(fin);
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fin.close();
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// xml_result_ = xml_doc_.load_file(tdmfile_.c_str());
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// xml_result = xml_doc_.load_file(tdmfile_.c_str());
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if ( showlog )
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{
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std::cout<<"\nloading "<<tdmfile_<<": "<<xml_result_.description()<<"\n";
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std::cout<<"encoding: "<<(pugi::xml_encoding)xml_result_.encoding<<"\n\n";
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std::cout<<"\nloading "<<tdmfile_<<": "<<xml_result.description()<<"\n";
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std::cout<<"encoding: "<<(pugi::xml_encoding)xml_result.encoding<<"\n\n";
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}
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// check XML parse result
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if ( xml_result_.status != 0 )
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if ( xml_result.status != 0 )
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{
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throw std::runtime_error( std::string("failed to parse XML tree: " )
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+ xml_result_.description() );
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+ xml_result.description() );
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}
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} catch (const std::exception& e) {
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throw std::runtime_error(std::string("failed to load tdm file: ") + e.what());
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}
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// collect meta-data
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pugi::xml_node tdmdocu = xml_doc_.child("usi:tdm").child("usi:documentation");
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pugi::xml_node tdmdocu = xml_doc.child("usi:tdm").child("usi:documentation");
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meta_data_.docu_expo_ = tdmdocu.child_value("usi:exporter");
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meta_data_.docu_expover_ = tdmdocu.child_value("usi:exporterVersion");
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pugi::xml_node tdmmodel = xml_doc_.child("usi:tdm").child("usi:model");
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pugi::xml_node tdmmodel = xml_doc.child("usi:tdm").child("usi:model");
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meta_data_.model_name_ = tdmmodel.attribute("modelName").value();
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meta_data_.model_version_ = tdmmodel.attribute("modelVersion").value();
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meta_data_.model_include_uri_ = tdmmodel.child("usi:include").attribute("nsUri").value();
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//
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pugi::xml_node tdmincl = xml_doc_.child("usi:tdm").child("usi:include");
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pugi::xml_node tdmincl = xml_doc.child("usi:tdm").child("usi:include");
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meta_data_.byte_order_ = tdmincl.child("file").attribute("byteOrder").value();
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meta_data_.file_url_ = tdmincl.child("file").attribute("url").value();
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if ( showlog ) std::cout<<meta_data_.get_info()<<"\n";
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} catch (const std::exception& e) {
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throw std::runtime_error(std::string("failed to load tdm file: ") + e.what());
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}
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// check datatype consistency, i.e. "local" representation of datatypes
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// and build map(s) for "tdm_datatypes"
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this->check_datatype_consistency();
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for ( tdm_datatype el: tdm_datatypes )
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{
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if ( el.name_ == "eInt16Usi" )
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{
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if ( el.size_ != sizeof(eInt16Usi) ) throw std::logic_error("invalid representation of eInt16Usi");
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}
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else if ( el.name_ == "eInt32Usi" )
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{
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if ( el.size_ != sizeof(eInt32Usi) ) throw std::logic_error("invalid representation of eInt32Usi");
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}
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else if ( el.name_ == "eUInt8Usi" )
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{
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if ( el.size_ != sizeof(eUInt8Usi) ) throw std::logic_error("invalid representation of eUInt8Usi");
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}
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else if ( el.name_ == "eUInt16Usi" )
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{
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if ( el.size_ != sizeof(eUInt16Usi) ) throw std::logic_error("invalid representation of eUInt16Usi");
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}
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else if ( el.name_ == "eUInt32Usi" )
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{
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if ( el.size_ != sizeof(eUInt32Usi) ) throw std::logic_error("invalid representation of eUInt32Usi");
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}
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else if ( el.name_ == "eFloat32Usi" )
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{
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if ( el.size_ != sizeof(eFloat32Usi) ) throw std::logic_error("invalid representation of eFloat32Usi");
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}
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else if ( el.name_ == "eFloat64Usi" )
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{
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if ( el.size_ != sizeof(eFloat64Usi) ) throw std::logic_error("invalid representation of eFloat64Usi");
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}
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else
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{
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throw std::logic_error("missing datatype validation");
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}
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tdmdt_name_.insert(std::pair<std::string,tdm_datatype>(el.name_,el));
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tdmdt_chan_.insert(std::pair<std::string,tdm_datatype>(el.channel_datatype_,el));
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}
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// process elements of XML
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this->process_include(showlog);
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this->process_root(showlog);
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this->process_channelgroups(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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this->process_include(showlog,xml_doc);
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this->process_root(showlog,xml_doc);
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this->process_channelgroups(showlog,xml_doc);
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this->process_channels(showlog,xml_doc);
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this->process_submatrices(showlog,xml_doc);
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this->process_localcolumns(showlog,xml_doc);
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// open .tdx and stream all binary data into buffer
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try {
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@ -147,10 +116,10 @@ void tdm_reaper::process_tdm(bool 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, pugi::xml_document& xml_doc)
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{
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// get XML node
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pugi::xml_node tdmincl = xml_doc_.child("usi:tdm").child("usi:include");
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pugi::xml_node tdmincl = xml_doc.child("usi:tdm").child("usi:include");
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// check endianness
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std::string endianness(tdmincl.child("file").attribute("byteOrder").value());
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@ -201,11 +170,11 @@ void tdm_reaper::process_include(bool showlog)
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if ( showlog ) std::cout<<"number of blocks: "<<tdx_blocks_.size()<<"\n\n";
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}
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void tdm_reaper::process_root(bool showlog)
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void tdm_reaper::process_root(bool showlog, pugi::xml_document& xml_doc)
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{
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// get XML node
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pugi::xml_node tdmdataroot = xml_doc_.child("usi:tdm").child("usi:data")
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.child("tdm_root");
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pugi::xml_node tdmdataroot = xml_doc.child("usi:tdm").child("usi:data")
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.child("tdm_root");
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// extract properties
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tdmroot_.id_ = tdmdataroot.attribute("id").value();
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@ -221,10 +190,10 @@ void tdm_reaper::process_root(bool showlog)
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if ( showlog ) std::cout<<tdmroot_.get_info()<<"\n";
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}
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void tdm_reaper::process_channelgroups(bool showlog)
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void tdm_reaper::process_channelgroups(bool showlog, pugi::xml_document& xml_doc)
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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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pugi::xml_node tdmdata = xml_doc.child("usi:tdm").child("usi:data");
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// find all its <tdm_channelgroup> elements
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for ( pugi::xml_node group = tdmdata.child("tdm_channelgroup"); group;
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@ -259,10 +228,10 @@ void tdm_reaper::process_channelgroups(bool showlog)
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if ( showlog ) std::cout<<"number of channelgroups: "<<tdmchannelgroups_.size()<<"\n\n";
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}
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void tdm_reaper::process_channels(bool showlog)
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void tdm_reaper::process_channels(bool showlog, pugi::xml_document& xml_doc)
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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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pugi::xml_node tdmdata = xml_doc.child("usi:tdm").child("usi:data");
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// find all its <tdm_channel> elements
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for ( pugi::xml_node channel = tdmdata.child("tdm_channel"); channel;
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@ -303,10 +272,10 @@ 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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}
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void tdm_reaper::process_submatrices(bool showlog)
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void tdm_reaper::process_submatrices(bool showlog, pugi::xml_document& xml_doc)
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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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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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@ -342,10 +311,10 @@ void tdm_reaper::process_submatrices(bool showlog)
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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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void tdm_reaper::process_localcolumns(bool showlog, pugi::xml_document& xml_doc)
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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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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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@ -786,6 +755,79 @@ void tdm_reaper::print_group(std::string &id, const char* filename, bool include
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// -------------------------------------------------------------------------- //
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void tdm_reaper::check_local_datatypes()
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{
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std::cout<<"\nmachine's C++ datatypes:\n";
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std::cout<<std::setw(25)<<std::left<<"char:"
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<<std::setw(5)<<std::left<<sizeof(char)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"uint8_t:"
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<<std::setw(5)<<std::left<<sizeof(uint8_t)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"short int:"
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<<std::setw(5)<<std::left<<sizeof(short int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"unsigned short int:"
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<<std::setw(5)<<std::left<<sizeof(unsigned short int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"int:"
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<<std::setw(5)<<std::left<<sizeof(int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"unsigned int:"
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<<std::setw(5)<<std::left<<sizeof(unsigned int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"long int:"
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<<std::setw(5)<<std::left<<sizeof(long int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"unsigned long int:"
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<<std::setw(5)<<std::left<<sizeof(unsigned long int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"float:"
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<<std::setw(5)<<std::left<<sizeof(float)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"double:"
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<<std::setw(5)<<std::left<<sizeof(double)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"long double:"
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<<std::setw(5)<<std::left<<sizeof(long double)<<"byte(s)\n\n";
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}
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void tdm_reaper::check_datatype_consistency()
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{
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// check datatype consistency, i.e. "local" representation of datatypes
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for ( tdm_datatype el: tdm_datatypes )
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{
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if ( el.name_ == "eInt16Usi" )
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{
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if ( el.size_ != sizeof(eInt16Usi) ) throw std::logic_error("invalid representation of eInt16Usi");
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}
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else if ( el.name_ == "eInt32Usi" )
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{
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if ( el.size_ != sizeof(eInt32Usi) ) throw std::logic_error("invalid representation of eInt32Usi");
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}
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else if ( el.name_ == "eUInt8Usi" )
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{
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if ( el.size_ != sizeof(eUInt8Usi) ) throw std::logic_error("invalid representation of eUInt8Usi");
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}
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else if ( el.name_ == "eUInt16Usi" )
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{
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if ( el.size_ != sizeof(eUInt16Usi) ) throw std::logic_error("invalid representation of eUInt16Usi");
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}
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else if ( el.name_ == "eUInt32Usi" )
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{
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if ( el.size_ != sizeof(eUInt32Usi) ) throw std::logic_error("invalid representation of eUInt32Usi");
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}
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else if ( el.name_ == "eFloat32Usi" )
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{
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if ( el.size_ != sizeof(eFloat32Usi) ) throw std::logic_error("invalid representation of eFloat32Usi");
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}
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else if ( el.name_ == "eFloat64Usi" )
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{
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if ( el.size_ != sizeof(eFloat64Usi) ) throw std::logic_error("invalid representation of eFloat64Usi");
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}
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else
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{
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throw std::logic_error("missing datatype validation");
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}
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}
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}
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// -------------------------------------------------------------------------- //
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template<typename datatype>
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void tdm_reaper::convert_data_to_type(std::vector<unsigned char> &buffer,
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std::vector<tdmdatatype> &channel)
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@ -33,10 +33,6 @@ class tdm_reaper
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// set of .csv files (encoding mode)
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std::vector<std::string> csvfile_;
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// XML parser
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pugi::xml_document xml_doc_;
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pugi::xml_parse_result xml_result_;
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// endianness (true = little, false = big)
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bool endianness_, machine_endianness_;
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@ -84,69 +80,36 @@ class tdm_reaper
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return listofids;
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}
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public:
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// check machine's datatypes
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// https://en.cppreference.com/w/cpp/language/types
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void check_local_datatypes()
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{
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std::cout<<"\nmachine's C++ datatypes:\n";
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std::cout<<std::setw(25)<<std::left<<"char:"
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<<std::setw(5)<<std::left<<sizeof(char)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"uint8_t:"
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<<std::setw(5)<<std::left<<sizeof(uint8_t)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"short int:"
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<<std::setw(5)<<std::left<<sizeof(short int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"unsigned short int:"
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<<std::setw(5)<<std::left<<sizeof(unsigned short int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"int:"
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<<std::setw(5)<<std::left<<sizeof(int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"unsigned int:"
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<<std::setw(5)<<std::left<<sizeof(unsigned int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"long int:"
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<<std::setw(5)<<std::left<<sizeof(long int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"unsigned long int:"
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<<std::setw(5)<<std::left<<sizeof(unsigned long int)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"float:"
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<<std::setw(5)<<std::left<<sizeof(float)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"double:"
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<<std::setw(5)<<std::left<<sizeof(double)<<"byte(s)\n"
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<<std::setw(25)<<std::left<<"long double:"
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<<std::setw(5)<<std::left<<sizeof(long double)<<"byte(s)\n\n";
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}
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public:
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// encoding
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tdm_reaper(std::vector<std::string> csvfile);
|
||||
// tdm_reaper(std::vector<std::string> csvfile);
|
||||
|
||||
// decoding
|
||||
tdm_reaper();
|
||||
tdm_reaper(std::string tdmfile, std::string tdxfile = std::string(""), bool showlog = false);
|
||||
tdm_reaper(std::string tdmfile, std::string tdxfile = std::string(""),
|
||||
bool showlog = false);
|
||||
|
||||
// provide (tdm,tdx) files
|
||||
void submit_files(std::string tdmfile, std::string tdxfile = std::string(""), bool showlog = false);
|
||||
void submit_files(std::string tdmfile, std::string tdxfile = std::string(""),
|
||||
bool showlog = false);
|
||||
|
||||
// process TDM data model in tdm file
|
||||
void process_tdm(bool showlog);
|
||||
|
||||
// process <usi:include> element
|
||||
void process_include(bool showlog);
|
||||
void process_include(bool showlog, pugi::xml_document& xml_doc);
|
||||
|
||||
// extract tdm_root
|
||||
void process_root(bool showlog);
|
||||
void process_root(bool showlog, pugi::xml_document& xml_doc);
|
||||
|
||||
// process/list all channels and groups
|
||||
void process_channelgroups(bool showlog);
|
||||
void process_channels(bool showlog);
|
||||
void process_channelgroups(bool showlog, pugi::xml_document& xml_doc);
|
||||
void process_channels(bool showlog, pugi::xml_document& xml_doc);
|
||||
|
||||
// process submatrices and localcolumns
|
||||
void process_submatrices(bool showlog);
|
||||
void process_localcolumns(bool showlog);
|
||||
void process_submatrices(bool showlog, pugi::xml_document& xml_doc);
|
||||
void process_localcolumns(bool showlog, pugi::xml_document& xml_doc);
|
||||
|
||||
// get meta-data
|
||||
tdm_meta get_meta()
|
||||
@ -218,12 +181,19 @@ public:
|
||||
void print_channel(std::string &id, const char* filename, bool include_meta = true);
|
||||
void print_group(std::string &id, const char* filename, bool include_meta = true, char sep = ' ');
|
||||
|
||||
// check machine's datatypes
|
||||
// https://en.cppreference.com/w/cpp/language/types
|
||||
void check_local_datatypes();
|
||||
|
||||
private:
|
||||
|
||||
template<typename datatype>
|
||||
void convert_data_to_type(std::vector<unsigned char> &buffer,
|
||||
std::vector<tdmdatatype> &channel);
|
||||
|
||||
// check consistency of mapped datatypes between C++ and TDM datatypes
|
||||
void check_datatype_consistency();
|
||||
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
6
makefile
6
makefile
@ -74,7 +74,7 @@ cython-help : cython/setup.py
|
||||
cython-list : cython/setup.py
|
||||
python3 $< --name --description --author --author-email --url
|
||||
|
||||
cython-build : cython/setup.py cython/tdm_reaper.pyx cython/tdm_reaper.pyx
|
||||
cython-build : cython/setup.py cython/tdm_reaper.pxd cython/py_tdm_reaper.pyx $(HPP) lib/tdm_reaper.cpp
|
||||
python3 $< build_ext --inplace
|
||||
# python3 $< build_ext
|
||||
|
||||
@ -82,8 +82,8 @@ cython-install : cython/setup.py cython/tdm_reaper.pyx cython/tdm_reaper.pyx
|
||||
python3 $< install
|
||||
|
||||
clean-cython :
|
||||
rm -vf cython/tdm_reaper.cpp tdm_reaper.cpython-*.so
|
||||
rm -r build
|
||||
rm -vf cython/py_tdm_reaper.cpp tdm_reaper.cpython-*.so
|
||||
rm -rf build
|
||||
|
||||
# --------------------------------------------------------------------------- #
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user