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Merge pull request #213 from icsm-au/1.2.7

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/dynadjust/include/io/dnaiodna.cpp

//============================================================================
// Name         : dnaiodna.cpp
// Author       : Roger Fraser
// Contributors :
// Version      : 1.00
// Copyright    : Copyright 2017 Geoscience Australia
//
//                Licensed under the Apache License, Version 2.0 (the "License");
//                you may not use this file except in compliance with the License.
//                You may obtain a copy of the License at
//               
//                http ://www.apache.org/licenses/LICENSE-2.0
//               
//                Unless required by applicable law or agreed to in writing, software
//                distributed under the License is distributed on an "AS IS" BASIS,
//                WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
//                See the License for the specific language governing permissions and
//                limitations under the License.
//
// Description  : DNA file io helper
//============================================================================

#include <include/io/dnaiodna.hpp>
#include <include/parameters/dnaepsg.hpp>
#include <include/measurement_types/dnameasurement_types.hpp>

using namespace dynadjust::measurements;
using namespace dynadjust::epsg;

namespace dynadjust { 
namespace iostreams {

void dna_io_dna::write_dna_files(vdnaStnPtr* vStations, vdnaMsrPtr* vMeasurements, 
                        const string& stnfilename, const string& msrfilename, const string& networkname,
                        const CDnaDatum& datum, const CDnaProjection& projection, bool flagUnused,
                        const string& stn_comment, const string& msr_comment)
{

        write_stn_file(vStations, stnfilename, networkname, datum, projection, flagUnused, stn_comment);
        write_msr_file(vMeasurements, msrfilename, networkname, datum, msr_comment);
}

void dna_io_dna::write_dna_files(pvstn_t vbinary_stn, pvmsr_t vbinary_msr, 
                        const string& stnfilename, const string& msrfilename, const string& networkname,
                        const CDnaDatum& datum, const CDnaProjection& projection, bool flagUnused,
                        const string& stn_comment, const string& msr_comment)
{
        write_stn_file(vbinary_stn, stnfilename, networkname, datum, projection, flagUnused, stn_comment);
        write_msr_file(*vbinary_stn, vbinary_msr, msrfilename, networkname, datum, msr_comment);
}
        
void dna_io_dna::create_file_stn(std::ofstream* ptr, const string& filename)
{
        determineDNASTNFieldParameters<UINT16>("3.01", dsl_, dsw_);
        create_file_pointer(ptr, filename);
}
        
void dna_io_dna::create_file_msr(std::ofstream* ptr, const string& filename)
{
        determineDNAMSRFieldParameters<UINT16>("3.01", dml_, dmw_);
        create_file_pointer(ptr, filename);
}

void dna_io_dna::prepare_sort_list(const UINT32 count)
{
        vStationList_.resize(count);

        // initialise vector with 0,1,2,...,n-2,n-1,n
        initialiseIncrementingIntegerVector<UINT32>(vStationList_, count);
}
        
void dna_io_dna::create_file_pointer(std::ofstream* ptr, const string& filename)
{
        try {
                // Create file pointer to DNA file. 
                file_opener(*ptr, filename);
        }
        catch (const runtime_error& e) {
                throw boost::enable_current_exception(runtime_error(e.what()));
        }
}
        
void dna_io_dna::open_file_pointer(std::ifstream* ptr, const string& filename)
{
        try {
                // Open DNA file.
                file_opener(*ptr, filename, ios::in, ascii, true);
        }
        catch (const runtime_error& e) {
                throw boost::enable_current_exception(runtime_error(e.what()));
        }
}

void dna_io_dna::write_stn_header_data(std::ofstream* ptr, const string& networkname, const string& datum,
        const string& epoch, const size_t& count, const string& comment)
{
        // Write version line
        dna_header(*ptr, "3.01", "STN", datum, epoch, count);

        // Write comments
        dna_comment(*ptr, "File type:    Station file");
        dna_comment(*ptr, "Project name: " + networkname);

        // Write header comment line, e.g. "Coordinates exported from reftran."
        dna_comment(*ptr, comment);
}

void dna_io_dna::write_stn_header(std::ofstream* ptr, vdnaStnPtr* vStations, const string& networkname,
                        const CDnaDatum& datum, bool flagUnused, const string& comment)
{
        // print stations
        // Has the user specified --flag-unused-stations, in which case, do not
        // print stations marked unused?
        size_t count(0);
        if (flagUnused) 
        {
                for_each(vStations->begin(), vStations->end(),
                        [&count](const dnaStnPtr& stn) {
                                if (stn.get()->IsNotUnused())
                                        count++;
                });
        }
        else
                count = vStations->size();

        // write header
        write_stn_header_data(ptr, networkname, datum.GetName(), datum.GetEpoch_s(), count, comment);        
}
        

void dna_io_dna::write_stn_header(std::ofstream* ptr, pvstn_t vbinary_stn, const string& networkname,
                        const CDnaDatum& datum, bool flagUnused, const string& comment)
{
        // print stations
        // Has the user specified --flag-unused-stations, in which case, do not
        // print stations marked unused?
        size_t count(0);
        if (flagUnused) 
        {
                for_each(vbinary_stn->begin(), vbinary_stn->end(),
                        [&count](const station_t& stn) {
                                if (stn.unusedStation == 0)
                                        count++;
                });
        }
        else
                count = vbinary_stn->size();

        // write header
        write_stn_header_data(ptr, networkname, datum.GetName(), datum.GetEpoch_s(), count, comment);
}
        

void dna_io_dna::read_ren_file(const string& filename, pv_string_vstring_pair stnRenaming)
{
        std::ifstream renaming_file;

        // create file pointer
        open_file_pointer(&renaming_file, filename);

        string version;
        INPUT_DATA_TYPE idt;
        CDnaDatum datum;
        string geoidVersion, fileEpsg, fileEpoch;
        UINT32 count(0);

        // read header information
        read_dna_header(&renaming_file, version, idt, datum, false, false, fileEpsg, fileEpoch, geoidVersion, count);

        read_ren_data(&renaming_file, stnRenaming);

        renaming_file.close();
}

void dna_io_dna::read_ren_data(std::ifstream* ptr, pv_string_vstring_pair stnRenaming)
{
        string sBuf;

        string_vstring_pair stnNames;
        vstring altStnNames;

        while (!ptr->eof())                        // while EOF not found
        {
                try {
                        getline((*ptr), sBuf);
                }
                catch (...) {
                        if (ptr->eof())
                                return;
                        stringstream ss;
                        ss << "read_ren_data(): Could not read from the renaming file." << endl;
                        boost::enable_current_exception(runtime_error(ss.str()));
                }

                // blank or whitespace?
                if (trimstr(sBuf).empty())                        
                        continue;

                // Ignore lines with blank station name
                if (trimstr(sBuf.substr(dsl_.stn_name, dsw_.stn_name)).empty())                        
                        continue;
                
                // Ignore lines with comments
                if (sBuf.compare(0, 1, "*") == 0)
                        continue;
                
                string tmp;
                
                // Add the preferred name
                try {
                        tmp = trimstr(sBuf.substr(dsl_.stn_name, dsw_.stn_name));
                        stnNames.first = tmp;
                }
                catch (...) {
                        stringstream ss;
                        ss << "read_ren_data(): Could not extract station name from the record:  " << 
                                endl << "    " << sBuf << endl;
                        boost::enable_current_exception(runtime_error(ss.str()));
                }                

                // Alternative names
                altStnNames.clear();
                UINT32 positionEndName(dsw_.stn_name+dsw_.stn_name);
                UINT32 positionNextName(dsw_.stn_name);
                while (sBuf.length() > positionNextName)
                {
                        if (sBuf.length() > positionEndName)
                                tmp = trimstr(sBuf.substr(positionNextName, dsw_.stn_name));
                        else
                                tmp = trimstr(sBuf.substr(positionNextName));

                        if (!tmp.empty())
                                altStnNames.push_back(tmp);

                        positionNextName = positionEndName;
                        positionEndName += dsw_.stn_name;
                }
                
                // sort for faster searching
                sort(altStnNames.begin(), altStnNames.end());

                // Add the alternate names
                stnNames.second = altStnNames;

                // Okay, add the pair to the list
                stnRenaming->push_back(stnNames);
        }
}
        

void dna_io_dna::read_dna_header(std::ifstream* ptr, string& version, INPUT_DATA_TYPE& idt, 
        CDnaDatum& referenceframe, bool user_supplied_frame, bool override_input_frame,
        string& fileEpsg, string& fileEpoch, string& geoidversion, UINT32& count)
{
        string sBuf;
        getline((*ptr), sBuf);
        sBuf = trimstr(sBuf);

        // Set the default version
        version = "1.00";

        // Attempt to get the file's version
        try {
                if (iequals("!#=DNA", sBuf.substr(0, 6)))
                        version = trimstr(sBuf.substr(6, 6));
        }
        catch (const runtime_error& e) {
                throw boost::enable_current_exception(runtime_error(e.what()));
        }

        // Attempt to get the file's type
        try {
                determineDNASTNFieldParameters<UINT16>(version, dsl_, dsw_);
                determineDNAMSRFieldParameters<UINT16>(version, dml_, dmw_);
        }
        catch (const runtime_error& e) {
                stringstream ssError;
                ssError << "- Error: Unable to determine DNA file version." << endl <<
                        sBuf << endl << " " << e.what() << endl;
                throw boost::enable_current_exception(runtime_error(ssError.str()));
        }

        // Version 1
        if (iequals(version, "1.00"))
        {
                idt = unknown;                                                        // could be stn or msr
                count = 100;                                                        // set default 100 stations
                return;
        }

        string type;
        // Attempt to get the file's type
        try {
                type = trimstr(sBuf.substr(12, 3));
        }
        catch (const runtime_error& e) {
                stringstream ssError;
                ssError << "- Error: File type has not been provided in the header" << endl <<
                        sBuf << endl << e.what() << endl;
                throw boost::enable_current_exception(runtime_error(ssError.str()));
        }

        // Station file
        if (iequals(type, "stn"))
                idt = stn_data;
        // MEasurement file
        else if (iequals(type, "msr"))
                idt = msr_data;
        // Geoid information file
        else if (iequals(type, "geo"))
                idt = geo_data;
        // Station renaming
        else if (iequals(type, "ren"))
                idt = ren_data;
        else
        {
                idt = unknown;
                stringstream ssError;
                ssError << "The supplied filetype '" << type << "' is not recognised" << endl;
                throw boost::enable_current_exception(runtime_error(ssError.str()));
        }

        if (sBuf.length() < 29)
        {
                count = 100;
                return;
        }

        string file_referenceframe;
        // Attempt to get the default reference frame
        try {
                if (sBuf.length() > 42)
                        file_referenceframe = trimstr(sBuf.substr(29, 14));
                else if (sBuf.length() > 29)
                        file_referenceframe = trimstr(sBuf.substr(29));
                else
                        file_referenceframe = "";
        }
        catch (...) {
                // datum not provided?
                file_referenceframe = "";
        }

        string epoch_version;
        // Attempt to get the default epoch / geoid version
        try {
                if (sBuf.length() > 56)
                        epoch_version = trimstr(sBuf.substr(43, 14));
                else if (sBuf.length() > 43)
                        epoch_version = trimstr(sBuf.substr(43));
                else
                        epoch_version = "";
        }
        catch (...) {
                // epoch / version not provided?
                epoch_version = "";
        }

        // Try to get the reference frame
        try {
                

                switch (idt)
                {
                case stn_data:
                case msr_data:

                        // Capture file epsg
                        if (file_referenceframe.empty())
                                // Get the epsg code from the default datum 
                                fileEpsg = referenceframe.GetEpsgCode_s();
                        else
                                fileEpsg = epsgStringFromName<string>(file_referenceframe);

                        if (epoch_version.empty())
                                // No, so get the epoch from the default datum 
                                fileEpoch = referenceframe.GetEpoch_s();
                        else
                                fileEpoch = epoch_version;

                        // Presently, the logic for handling default reference frame is duplicated for 
                        // each file type, here and in dnaparser_pimpl.cxx:
                        //     void referenceframe_pimpl::post_type(...)

                        // 2. Does the user want to override the default datum?
                        if (override_input_frame)
                                // Do nothing, just return as referenceframe will become 
                                // the default for all stations and measurements loaded
                                // from the file.
                                break;
                        
                        // 3. Does the user want the referenceframe attribute in the file to become the default?
                        if (!user_supplied_frame)
                        {
                                if (!file_referenceframe.empty())
                                        // adopt the reference frame supplied in the file
                                        referenceframe.SetDatumFromName(file_referenceframe, epoch_version);
                        }

                        // Since import doesn't offer an option to capture epoch on the command line,
                        // take the epoch from the file (if not empty).
                        if (!epoch_version.empty())
                                referenceframe.SetEpoch(epoch_version);
                                                
                        break;

                case geo_data:
                        geoidversion = epoch_version;
                        break;
                default:
                        break;
                }
        }
        catch (const runtime_error& e) {
                stringstream ssError;
                ssError << "The supplied frame is not recognised" << endl <<
                        e.what() << endl;
                throw boost::enable_current_exception(runtime_error(ssError.str()));
        }        

        // Attempt to get the data count
        try {
                if (sBuf.length() > 66)
                        count = val_uint<UINT32, string>(trimstr(sBuf.substr(57, 10)));
                else if (sBuf.length() > 57)
                        count = val_uint<UINT32, string>(trimstr(sBuf.substr(57)));
                else 
                        count = 100;
        }
        catch (...) {
                count = 100;
        }
}


void dna_io_dna::write_stn_file(pvstn_t vbinary_stn, const string& stnfilename, const string& networkname,
                                const CDnaDatum& datum, const CDnaProjection& projection, bool flagUnused,
                                const string& comment)
{
        // Print DNA stations from a vector of stn_t
        std::ofstream dna_stn_file;

        try {
                // Create file pointer
                create_file_stn(&dna_stn_file, stnfilename);

                // Write header and comment
                write_stn_header(&dna_stn_file, vbinary_stn, networkname, datum, flagUnused, comment);

                // Sort on original file order
                prepare_sort_list(static_cast<UINT32>(vbinary_stn->size()));
                CompareStnFileOrder<station_t, UINT32> stnorderCompareFunc(vbinary_stn);
                sort(vStationList_.begin(), vStationList_.end(), stnorderCompareFunc);

                dnaStnPtr stnPtr(new CDnaStation(datum.GetName(), datum.GetEpoch_s()));

                // print stations
                // Has the user specified --flag-unused-stations, in wich case, do not
                // print stations marked unused?
                if (flagUnused) 
                {
                        // Print stations in DNA format
                        for_each(vStationList_.begin(), vStationList_.end(),
                                [&dna_stn_file, &stnPtr, &projection, &datum, &vbinary_stn, this](const UINT32& stn) {
                                        if (stnPtr->IsNotUnused())
                                        {
                                                stnPtr->SetStationRec(vbinary_stn->at(stn));
                                                stnPtr->WriteDNAXMLStnCurrentEstimates(&dna_stn_file, datum.GetEllipsoidRef(), 
                                                        const_cast<CDnaProjection*>(&projection), dna, &dsw_);
                                        }
                        });
                }
                else
                {
                        // Print stations in DNA format
                        for_each(vStationList_.begin(), vStationList_.end(),
                                [&dna_stn_file, &stnPtr, &projection, &datum, &vbinary_stn, this](const UINT32& stn) {
                                        stnPtr->SetStationRec(vbinary_stn->at(stn));
                                        stnPtr->WriteDNAXMLStnCurrentEstimates(&dna_stn_file, datum.GetEllipsoidRef(), 
                                                const_cast<CDnaProjection*>(&projection), dna, &dsw_);
                        });
                }

                dna_stn_file.close();
                
        }
        catch (const std::ifstream::failure& f) {
                throw boost::enable_current_exception(runtime_error(f.what()));
        }
}
        

void dna_io_dna::write_stn_file(vdnaStnPtr* vStations, const string& stnfilename, const string& networkname,
                        const CDnaDatum& datum, const CDnaProjection& projection, bool flagUnused,
                        const string& comment)
{
        // Print DNA stations from a vector of dnaStnPtr
        std::ofstream dna_stn_file;

        try {
                // Create file pointer
                create_file_stn(&dna_stn_file, stnfilename);

                // Write header and comment
                write_stn_header(&dna_stn_file, vStations, networkname, datum, flagUnused, comment);

                // Sort on original file order
                sort(vStations->begin(), vStations->end(), CompareStnFileOrder_CDnaStn<CDnaStation>());

                // print stations
                // Has the user specified --flag-unused-stations, in wich case, do not
                // print stations marked unused?
                if (flagUnused) 
                {
                        // Print stations in DNA format
                        for_each(vStations->begin(), vStations->end(),
                                [&dna_stn_file, &projection, &datum, this](const dnaStnPtr& stn) {
                                        if (stn.get()->IsNotUnused())
                                                stn.get()->WriteDNAXMLStnCurrentEstimates(&dna_stn_file, datum.GetEllipsoidRef(), 
                                                        const_cast<CDnaProjection*>(&projection), dna, &dsw_);
                        });
                }
                else
                {
                        // Print stations in DNA format
                        for_each(vStations->begin(), vStations->end(),
                                [&dna_stn_file, &projection, &datum, this](const dnaStnPtr& stn) {
                                        stn.get()->WriteDNAXMLStnCurrentEstimates(&dna_stn_file, datum.GetEllipsoidRef(), 
                                                const_cast<CDnaProjection*>(&projection), dna, &dsw_);
                        });
                }

                dna_stn_file.close();
                
        }
        catch (const std::ifstream::failure& f) {
                throw boost::enable_current_exception(runtime_error(f.what()));
        }        
}

void dna_io_dna::write_msr_header_data(std::ofstream* ptr, const string& networkname, const string& datum,
        const string& epoch, const size_t& count, const string& comment)
{
        // Write version line
        dna_header(*ptr, "3.01", "MSR", datum, epoch, count);

        // Write comments
        dna_comment(*ptr, "File type:    Measurement file");
        dna_comment(*ptr, "Project name: " + networkname);

        // Write header comment line
        dna_comment(*ptr, comment);

}


void dna_io_dna::write_msr_header(std::ofstream* ptr, vdnaMsrPtr* vMeasurements, const string& networkname,
        const CDnaDatum& datum, const string& comment)
{
        // write header
        write_msr_header_data(ptr, networkname, datum.GetName(), datum.GetEpoch_s(), vMeasurements->size(), comment);
}
        

void dna_io_dna::write_msr_header(std::ofstream* ptr, pvmsr_t vbinary_msrn, const string& networkname,
        const CDnaDatum& datum, const string& comment)
{
        // write header
        write_msr_header_data(ptr, networkname, datum.GetName(), datum.GetEpoch_s(), vbinary_msrn->size(), comment);
}


void dna_io_dna::write_msr_file(const vstn_t& vbinary_stn, pvmsr_t vbinary_msr, const string& msrfilename, const string& networkname,
        const CDnaDatum& datum, const string& comment)
{
        // Print DNA measurements        

        std::ofstream dna_msr_file;

        it_vmsr_t _it_msr(vbinary_msr->begin());
        dnaMsrPtr msrPtr;
        size_t dbindex;
        it_vdbid_t _it_dbid;

        try {
                // Create file pointer
                create_file_msr(&dna_msr_file, msrfilename);

                // Write header and comment
                write_msr_header(&dna_msr_file, vbinary_msr, networkname, datum, comment);

                // print measurements
                for (_it_msr=vbinary_msr->begin(); _it_msr!=vbinary_msr->end(); ++_it_msr)
                {
                        ResetMeasurementPtr<char>(&msrPtr, _it_msr->measType);

                        // Database IDs
                        if (m_databaseIDsSet_)
                        {
                                dbindex = std::distance(vbinary_msr->begin(), _it_msr);
                                _it_dbid = pv_msr_db_map_->begin() + dbindex;
                        }

                        msrPtr->SetMeasurementRec(vbinary_stn, _it_msr, _it_dbid);
                        msrPtr->WriteDNAMsr(&dna_msr_file, dmw_, dml_);
                }

                dna_msr_file.close();

        }
        catch (const std::ifstream::failure& f) {
                throw boost::enable_current_exception(runtime_error(f.what()));
        }
}
        
void dna_io_dna::write_msr_file(vdnaMsrPtr* vMeasurements, const string& msrfilename, const string& networkname,
        const CDnaDatum& datum,        const string& comment)
{
        // Print DNA measurements        
        
        std::ofstream dna_msr_file;
        
        _it_vdnamsrptr _it_msr(vMeasurements->begin());
        size_t dbindex;
        it_vdbid_t _it_dbid;
        
        try {
                // Create file pointer
                create_file_msr(&dna_msr_file, msrfilename);

                // Write header and comment
                write_msr_header(&dna_msr_file, vMeasurements, networkname, datum, comment);

                // print measurements
                for (_it_msr = vMeasurements->begin(); _it_msr != vMeasurements->end(); _it_msr++)
                {
                        // Get database IDs
                        dbindex = std::distance(vMeasurements->begin(), _it_msr);
                        _it_dbid = pv_msr_db_map_->begin() + dbindex;
                        _it_msr->get()->SetDatabaseMaps(_it_dbid);

                        // Write
                        _it_msr->get()->WriteDNAMsr(&dna_msr_file, dmw_, dml_);
                }
                
                dna_msr_file.close();
                
        }
        catch (const std::ifstream::failure& f) {
                throw boost::enable_current_exception(runtime_error(f.what()));
        }
        

}

void dna_io_dna::set_dbid_ptr(pv_msr_database_id_map pv_msr_db_map)
{
        pv_msr_db_map_ = pv_msr_db_map;
        if (pv_msr_db_map->size() > 0)
                m_databaseIDsSet_ = true;
        else
                m_databaseIDsSet_ = false;
}


} // dnaiostreams
} // dynadjust


icsm-au / DynAdjust / 4558854622

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