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Merge 6e730fa5a into 72bc8feb8

Pull Request Pull Request #222: Upgrade to C++17 and various enhancements

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/dynadjust/dynadjust/dnasegment/dnasegment.cpp

//============================================================================
// Name         : dnasegment.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  : DynAdjust Network Segmentation library
//============================================================================

#include <dynadjust/dnasegment/dnasegment.hpp>
#ifdef _MSDEBUG
#include <include/ide/trace.hpp>
#endif

namespace dynadjust { namespace networksegment {

dna_segment::dna_segment()
        : isProcessing_(false)
{
        network_name_ = "";
}

dna_segment::~dna_segment()
{

}
        

double dna_segment::GetProgress() const
{ 
        return ((bstBinaryRecords_.size() - vfreeStnList_.size()) * 100. / bstBinaryRecords_.size()); 
}

void dna_segment::LoadNetFile()
{
        // Get stations listed in net file
        std::ifstream net_file;
        try {
                // Load net file.  Throws runtime_error on failure.
                file_opener(net_file, projectSettings_.s.net_file, 
                        ios::in, ascii, true);
        }
        catch (const runtime_error& e) {
                SignalExceptionSerialise(e.what(), 0, NULL);
        }

        string station;
        char line[PROGRAM_OPTIONS_LINE_LENGTH];
        
        // read header lines
        net_file.ignore(PRINT_LINE_LENGTH, '\n');                                        // -------------------------------------------
        net_file.getline(line, PROGRAM_OPTIONS_LINE_LENGTH);                //            DYNADJUST BLOCK 1 STATIONS FILE

        vinitialStns_.clear();

        try {

                while (!net_file.eof())
                {
                        net_file.getline(line, PROGRAM_OPTIONS_LINE_LENGTH);                // Stations
                        station = line;
                        if ((station = trimstr(station)).empty())
                                continue;
                        // add this station to the list
                        vinitialStns_.push_back(station);
                }
        }
        catch (const ios_base::failure& f) {

                if (!net_file.eof())
                {
                        stringstream ss;
                        ss << "ParseStartingStations(): An error was encountered when reading " << projectSettings_.s.net_file << "." << endl << f.what();
                        SignalExceptionSerialise(ss.str(), 0, "i", &net_file);        
                }
        }

        net_file.close();
}

void dna_segment::ParseStartingStations()
{
        // Get stations listed in net file (if it exists)
        // Rememeber, calling app should make sure that 
        // projectSettings_.s.net_file contains a valid path if
        // the user wants to use a net file.
        if (exists(projectSettings_.s.net_file.c_str()))
                LoadNetFile();

        // OK, now get the additionalstations on the command line
        if (projectSettings_.s.seg_starting_stns.empty())
                return;

        vstring cmd_line_stations;

        try {
                // Extract stations from comma delimited string
                SplitDelimitedString<string>(
                        projectSettings_.s.seg_starting_stns,        // the comma delimited string
                        string(","),                                                        // the delimiter
                        &cmd_line_stations);                                                // the respective values
        }
        catch (...) {
                return;
        }

        if (!cmd_line_stations.empty())
                vinitialStns_.insert(vinitialStns_.end(), cmd_line_stations.begin(), cmd_line_stations.end());
                
        if (!vinitialStns_.empty())
                strip_duplicates(vinitialStns_);
}
        

void dna_segment::PrepareSegmentation(project_settings* p)
{
        projectSettings_ = *p;

        ParseStartingStations();

        network_name_ = p->g.network_name;

        LoadBinaryFiles(p->s.bst_file, p->s.bms_file);
        LoadAssociationFiles(p->s.asl_file, p->s.aml_file);
        LoadStationMap(p->s.map_file);
        BuildFreeStationAvailabilityList();
        
        SortbyMeasurementCount(&vfreeStnList_);
}


void dna_segment::InitialiseSegmentation()
{
        segmentStatus_ = SEGMENT_SUCCESS;
        isProcessing_ = false;        
        currentBlock_ = 0;

        network_name_ = "network_name";                // network name
        
        vinitialStns_.clear();
        vCurrJunctStnList_.clear();
        vCurrInnerStnList_.clear();
        vCurrMeasurementList_.clear();
        
        bstBinaryRecords_.clear();
        bmsBinaryRecords_.clear();
        vAssocStnList_.clear();
        vAssocMsrList_.clear();
        vfreeStnList_.clear();
        vfreeMsrList_.clear();
        stnsMap_.clear();

        vJSL_.clear();
        vISL_.clear();
        vCML_.clear();
}
        

_SEGMENT_STATUS_ dna_segment::SegmentNetwork(project_settings* p)
{
        isProcessing_ = true;        

        output_folder_ = p->g.output_folder;

        if ((debug_level_ = p->g.verbose) > 2)
        {
                string s(p->s.seg_file + ".trace");
                try {
                        // Create trace file.  Throws runtime_error on failure.
                        file_opener(trace_file, s);
                        print_file_header(trace_file, "DYNADJUST SEGMENTATION TRACE FILE");
                        trace_file << OUTPUTLINE << endl << endl;
                }
                catch (const runtime_error& e) {
                        SignalExceptionSerialise(e.what(), 0, NULL);
                }
        }
        
        if ((debug_level_ = p->g.verbose) > 1)
        {
                string s(p->s.seg_file + ".debug");
                        
                try {
                        // Create debug file.  Throws runtime_error on failure.
                        file_opener(debug_file, s);
                }
                catch (const ios_base::failure& f) {
                        SignalExceptionSerialise(f.what(), 0, NULL);
                }
        }

        segmentStatus_ = SEGMENT_SUCCESS;
        ostringstream ss;

        if (debug_level_ > 2)
                WriteFreeStnListSortedbyASLMsrCount();

        currentBlock_ = 1;

        if (debug_level_ > 2)
                trace_file << "Block " << currentBlock_ << "..." << endl;
        
        cpu_timer time;

        v_ContiguousNetList_.clear();
        v_ContiguousNetList_.push_back(currentNetwork_ = 0);

        if (bstBinaryRecords_.empty())
                SignalExceptionSerialise("SegmentNetwork(): the binary stations file has not been loaded into memory yet.", 0, NULL);
        if (bmsBinaryRecords_.empty())
                SignalExceptionSerialise("SegmentNetwork(): the binary measurements file has not been loaded into memory yet.", 0, NULL);
        if (vAssocStnList_.empty())
                SignalExceptionSerialise("SegmentNetwork(): the Associated Station List (ASL) has not been loaded into memory yet.", 0, NULL);
        if (vAssocFreeMsrList_.empty())
                SignalExceptionSerialise("SegmentNetwork(): the Associated Measurements List (AML) has not been loaded into memory yet.", 0, NULL);
        if (stnsMap_.empty())
                SignalExceptionSerialise("SegmentNetwork(): the station map has not been loaded into memory yet.", 0, NULL);

        // The inner stations for the first block are created from segmentCriteria._initialStns
        // Junction stations are retrieved from measurements connected to the inner stations
        BuildFirstBlock();
        
        while (!vfreeStnList_.empty())
        {
                isProcessing_ = true;

                currentBlock_++;

                if (debug_level_ > 2)
                        trace_file << "Block " << currentBlock_ << "..." << endl;

                v_ContiguousNetList_.push_back(currentNetwork_);

                // The inner stations for the next block are the junction stations from the previous block
                // The junction stations are retrieved from measurements connected to the inner stations
                // BuildNextBlock applies the min and max station constraints using segmentCriteria
                BuildNextBlock();
        
                if (vfreeStnList_.empty())
                        break;
        }

        milliseconds elapsed_time(milliseconds(0));
        if (debug_level_ > 1)
                elapsed_time = milliseconds(time.elapsed().wall/MILLI_TO_NANO);
        
        isProcessing_ = false;        

        CalculateAverageBlockSize();

        char valid_stations(0);
        char valid_measurements_not_included(0);
        if (vfreeStnList_.size())
        {
                valid_stations = 1;
                ss.str("");
                ss << endl << "- Warning: The following stations were not used:" << endl;
                ss << "  ";
                it_vUINT32_const _it_freestn(vfreeStnList_.begin());
                for (; _it_freestn!=vfreeStnList_.end(); ++_it_freestn)
                        ss << bstBinaryRecords_.at(*_it_freestn).stationName << " ";
                ss << endl;
                ss << "- Possible reasons why these stations were not used include:" << endl;
                ss << "  - No measurements to these stations were found," << endl;
                ss << "  - The network is made up of non-contiguous blocks," << endl;
                ss << "  - There is a bug in this program." << endl;

                if (debug_level_ > 1)
                        debug_file << ss.str();
        }

        if (debug_level_ > 1)
        {
                debug_file << formatedElapsedTime<string>(&elapsed_time, "+ Network segmentation took ") <<
                        " The network is now ready for adjustment." << endl;
                debug_file.close();
        }

        isProcessing_ = false;        

        if (valid_measurements_not_included || valid_stations)
                return (segmentStatus_ = SEGMENT_BLOCK_ERROR);

        return (segmentStatus_ = SEGMENT_SUCCESS);
}
        

void dna_segment::CalculateAverageBlockSize()
{
        vUINT32 blockSizes;
        blockSizes.resize(vISL_.size());

        it_vUINT32 _it_count;
        it_vvUINT32 _it_isl, _it_jsl;
        for (_it_count=blockSizes.begin(), _it_isl=vISL_.begin(), _it_jsl=vJSL_.begin(); 
                _it_isl!=vISL_.end(); 
                ++_it_count, ++_it_isl, ++_it_jsl)
                *_it_count = static_cast<UINT32>(_it_isl->size() + _it_jsl->size());

        averageBlockSize_ = average<double, UINT32, it_vUINT32>(blockSizes.begin(), blockSizes.end(), stationSolutionCount_);

        maxBlockSize_ = *(max_element(blockSizes.begin(), blockSizes.end()));
        minBlockSize_ = *(min_element(blockSizes.begin(), blockSizes.end()));
}


string dna_segment::DefaultStartingStation()
{
        if (vfreeStnList_.empty())
                return "";
        if (bstBinaryRecords_.empty())
                return "";
        return bstBinaryRecords_.at(vfreeStnList_.at(0)).stationName;
}
        

vstring dna_segment::StartingStations()
{
        return vinitialStns_;
}
        

// throws NetSegmentException on failure
void dna_segment::BuildFirstBlock()
{        
        vCurrJunctStnList_.clear();
        vCurrInnerStnList_.clear();
        vCurrMeasurementList_.clear();

        if (vinitialStns_.empty())
                // no station specified? then pick the first one on the free list
                // Remember, vfreeStnList_ is not sorted alphabetically, but according
                // to the number of measurements connected to each station
                vinitialStns_.push_back(bstBinaryRecords_.at(vfreeStnList_.at(0)).stationName);
        else        
                RemoveDuplicateStations(&vinitialStns_);                // remove duplicates
        
        // First pass to validate stations
        VerifyStationsandBuildBlock(true);

        // Second pass to build the block
        VerifyStationsandBuildBlock();

        FinaliseBlock();
}

void dna_segment::VerifyStationsandBuildBlock(bool validationOnly)
{
#ifdef _MSDEBUG
        UINT32 stn_index;
#endif

        it_vUINT32 _it_freeisl;
        _it_vstr_const _it_name(vinitialStns_.begin());
        it_pair_string_vUINT32 it_stnmap_range;
        v_string_uint32_pair::iterator _it_stnmap(stnsMap_.begin());

        // For each station name specified as the initial stations
        for (_it_name=vinitialStns_.begin(); _it_name!=vinitialStns_.end(); ++_it_name)
        {
                // Retrieve the ASL index
                it_stnmap_range = equal_range(stnsMap_.begin(), stnsMap_.end(), *_it_name, StationNameIDCompareName());
                
                if (it_stnmap_range.first == it_stnmap_range.second)
                {
                        // If this point is reached, _it_stnmap->second is not a known network station
                        stringstream ss;
                        ss << "VerifyStationsandBuildBlock(): " << *_it_name << " is not in the list of network stations.";
                        SignalExceptionSerialise(ss.str(), 0, NULL);
                }

                _it_stnmap = it_stnmap_range.first;

#ifdef _MSDEBUG
                stn_index = _it_stnmap->second;
#endif
                // add this station to inner station list if it is on the free stations list only.
                // vfreeStnList_ is sorted according to the number of measurements connected to each station
                // hence, a binary_search (or lower_bound or similar) cannot be used here

                // Check if this station is available before trying to find it.  Why?
                // find_if over a large vector is not fast like binary_search
                if (vfreeStnAvailability_.at(_it_stnmap->second).isfree())
                {                        
                        // Ok, find it and remove it
                        //if ((_it_freeisl = find_if(vfreeStnList_.begin(), vfreeStnList_.end(),
                        //        bind1st(std::equal_to<UINT32>(), _it_stnmap->second))) != vfreeStnList_.end())
                        if ((_it_freeisl = find_if(vfreeStnList_.begin(), vfreeStnList_.end(),
                                [&_it_stnmap](const UINT32& freeStn) {
                                        return freeStn == _it_stnmap->second; } )) != vfreeStnList_.end())
                        {
                                if (!validationOnly)
                                        MoveFreeStnToInnerList(_it_freeisl, _it_stnmap->second);
                        }
                }
                else
                {
                        if (validationOnly)
                        {
                                // If this point is reached, _it_stnmap->second is a known network station but is 
                                // invalid or has no measurements connected to it.
                                stringstream ss;
                                ss << "VerifyStationsandBuildBlock(): " << bstBinaryRecords_.at(_it_stnmap->second).stationName << " does not have any measurements connected to it.";
                                SignalExceptionSerialise(ss.str(), 0, NULL);
                        }
                }
        
                if (!validationOnly)
                        // Retrieve JSL (all stations connected to this station) and
                        // add AML indices to CML for all measurements connected to this station
                        GetInnerMeasurements(_it_stnmap->second);
        }
}

UINT32 dna_segment::SelectInner()
{
        // Sort the list of junction stations by the number of measurements 
        // connected to them, and begin with the station that has the lowest 
        // number of measurements
        SortbyMeasurementCount(&vCurrJunctStnList_);
        
        it_vUINT32 it_currjsl(vCurrJunctStnList_.begin());
        UINT32 stn_index = *it_currjsl;

        if (debug_level_ > 2)
                trace_file << " + Inner '" << bstBinaryRecords_.at(stn_index).stationName << "'" << endl;

#ifdef _MSDEBUG
        string station_name =  bstBinaryRecords_.at(stn_index).stationName;
#endif

        // add this junction station to inner station list
        MoveStation(vCurrJunctStnList_, it_currjsl, vCurrInnerStnList_, stn_index);

        return stn_index;
}
        

// Get the next free station and push it to the junction list
// This method should only be reached when the junction list is empty,
// but measurements still remain and stations exist in the free list.
void dna_segment::SelectJunction()
{
        SortbyMeasurementCount(&vfreeStnList_);
        
        it_vUINT32 it_newjsl(vfreeStnList_.begin());

        MoveFreeStnToJunctionList(it_newjsl, *it_newjsl);
}


it_vUINT32 dna_segment::MoveStation(vUINT32& fromList, it_vUINT32 it_from, vUINT32& toList, const UINT32& stn_index)
{
        // Move a station from one list to another list
        toList.push_back(stn_index);        
        return fromList.erase(it_from);
}
        

void dna_segment::MoveFreeStn(it_vUINT32 it_freeisl, vUINT32& toList, const UINT32& stn_index, const string& type)
{
        if (debug_level_ > 2)
                trace_file << " + New " << type << " station (" << stn_index << ") '" << 
                        bstBinaryRecords_.at(stn_index).stationName << "'" << endl;
        
#ifdef _MSDEBUG
        string station_name =  bstBinaryRecords_.at(stn_index).stationName;
#endif

        // Mark this station as unavailable
        vfreeStnAvailability_.at(stn_index).consume();

        // Move a station from the free station list to the specified list
        // stnList may be either inner or junction list
        MoveStation(vfreeStnList_, it_freeisl, toList, stn_index);
}
        

void dna_segment::MoveFreeStnToJunctionList(it_vUINT32 it_freeisl, const UINT32& stn_index)
{
        // Move a station from the free station list to the junction list
        MoveFreeStn(it_freeisl, vCurrJunctStnList_, stn_index, "junction");        
}
        

void dna_segment::MoveFreeStnToInnerList(it_vUINT32 it_freeisl, const UINT32& stn_index)
{
        // Move a station from the free station list to the junction list
        MoveFreeStn(it_freeisl, vCurrInnerStnList_, stn_index, "inner");
}
        

// throws NetSegmentException on failure
void dna_segment::BuildNextBlock()
{
        // vCurrJunctStnList_ carries the previous block's junction stations. Thus,
        // don't clear it as these stations will become the inners for the next block
        vCurrInnerStnList_.clear();
        vCurrMeasurementList_.clear();

#ifdef _MSDEBUG
        string station_name;
#endif

        // Select a new junction station if there are none on the JSL
        // that have free measurements left
        if (vCurrJunctStnList_.empty() && !vfreeStnList_.empty())
        {
                if (!projectSettings_.s.force_contiguous_blocks)
                        v_ContiguousNetList_.back() = ++currentNetwork_;

                if (debug_level_ > 1)
                {
                        debug_file << "+ Non-contiguous block found... creating a new block using " << bstBinaryRecords_.at(vfreeStnList_.at(0)).stationName << endl;
                        if (debug_level_ > 2)
                                trace_file << " + Non-contiguous block found... creating a new block using " << bstBinaryRecords_.at(vfreeStnList_.at(0)).stationName << endl;
                }

                // Select a new junction from the free station list
                SelectJunction();
        }
        
        if (vCurrJunctStnList_.empty())
        {
                coutSummary();
                SignalExceptionSerialise("BuildNextBlock(): An invalid junction list has been created.  This is most likely a bug.", 0, NULL);
        }

        UINT32 stn_index;
        UINT32 currentTotalSize;
        bool block_threshold_reached = false;

        // Until the threshold is reached...
        //  - Go through the list of junction stations (copied from the previous block) and
        //    make them inner stations if there are new stations connected to them
        //  - If the list is exhausted, add new junctions
        while (!block_threshold_reached)
        {
                // Attempt to add non-contiguous blocks to this block if the 
                // station limit hasn't been reached
                if (vfreeStnList_.empty() /*|| vfreeMsrList_.empty()*/)
                        break;

                // Is the junction list empty?  force_contiguous_blocks determines what to 
                // do in this instance.
                if (projectSettings_.s.force_contiguous_blocks)
                {
                        // Add non-contiguous blocks to this block if the 
                        // station limit hasn't been reached
                        if (vCurrJunctStnList_.empty())
                                SelectJunction();
                }
                else if (vCurrJunctStnList_.empty())
                        break;

                // Get next station from current junction list
                stn_index = SelectInner();

                // Retrieve JSL (all stations connected to this station) and
                // add AML indices to CML for all measurements connected to this station
                GetInnerMeasurements(stn_index);

                currentTotalSize = static_cast<UINT32>(vCurrInnerStnList_.size() + vCurrJunctStnList_.size());

                // Has the station count threshold been exceeded?
                //if (currentTotalSize >= seg_max_total_stations_)
                if (currentTotalSize >= projectSettings_.s.max_total_stations)
                {
                        if (vCurrInnerStnList_.size() < projectSettings_.s.min_inner_stations)
                                continue;
                        block_threshold_reached = true;
                        break;
                }
        }

        if (debug_level_ > 2)
        {
                if (block_threshold_reached)
                        trace_file << " + Block size threshold exceeded... finishing block." << endl;
                else
                        trace_file << " + Block " << currentBlock_ << " complete." << endl;
        }

        FinaliseBlock();
}
        
void dna_segment::FinaliseBlock()
{
        FindCommonMeasurements();
        MoveJunctiontoISL();

        // Sort lists
        sort(vCurrInnerStnList_.begin(), vCurrInnerStnList_.end());
        sort(vCurrJunctStnList_.begin(), vCurrJunctStnList_.end());
        strip_duplicates(vCurrMeasurementList_);                // remove duplicates and sort

        vISL_.push_back(vCurrInnerStnList_);
        vJSL_.push_back(vCurrJunctStnList_);
        vCML_.push_back(vCurrMeasurementList_);

        if (debug_level_ > 1)
        {
                coutCurrentBlockSummary(debug_file);

                if (debug_level_ > 2)
                {
                        UINT32 currentISLSize, currentJSLSize, currentTotalSize, currentMsrSize;
                        currentISLSize = static_cast<UINT32>(vCurrInnerStnList_.size());
                        currentJSLSize = static_cast<UINT32>(vCurrJunctStnList_.size());
                        currentTotalSize = currentISLSize + currentJSLSize;
                        currentMsrSize = static_cast<UINT32>(vCurrMeasurementList_.size());
                
                        trace_file << " + Done." << endl;
                        trace_file << " + BLOCK " << currentBlock_ << " SUMMARY:" << endl;
                        trace_file << "   - " << currentISLSize << " inner stations, " << currentJSLSize << " junction stations, ";
                        trace_file << currentTotalSize << " total stations, " << currentMsrSize << " measurements." << endl;
                
                        trace_file << "   - Inners (" << currentISLSize << "):" << endl << "     ";
                        it_vUINT32_const _it_freeisl(vfreeStnList_.end());
                        for (_it_freeisl=vCurrInnerStnList_.begin(); _it_freeisl!=vCurrInnerStnList_.end(); ++_it_freeisl)
                                trace_file << "'" << bstBinaryRecords_.at(*_it_freeisl).stationName << "' ";
                        trace_file << endl;

                        trace_file << "   - Junctions (" << currentJSLSize << "):" << endl << "     ";
                        for (_it_freeisl=vCurrJunctStnList_.begin(); _it_freeisl!=vCurrJunctStnList_.end(); ++_it_freeisl)
                                trace_file << "'" << bstBinaryRecords_.at(*_it_freeisl).stationName << "' ";
                
                        trace_file << endl << " + ------------------------------------------" << endl;
                }
        }
}
        

//bool dna_segment::IncrementNextAvailableAMLIndex(UINT32& amlIndex, const UINT32& lastamlIndex)
//{
//        // Already at the last measurement?
//        if (amlIndex > lastamlIndex)
//                return false;
//
//        while (!vAssocFreeMsrList_.at(amlIndex).available)
//        {
//                // Already at the last measurement?
//                if (amlIndex == lastamlIndex)
//                        return false;
//
//                // Get the next measurement record tied 
//                // to this measurement
//                ++amlIndex;                        
//        }
//        return true;
//}
//        
//
//bool dna_segment::IncrementNextAvailableAMLIndex(it_aml_pair& _it_aml, const it_aml_pair& _it_lastaml)
//{
//        // Already at the last measurement?
//        if (_it_aml > _it_lastaml)
//                return false;
//
//        while (!_it_aml->available)
//        {
//                // Already at the last measurement?
//                if (_it_aml == _it_lastaml)
//                        return false;
//
//                // Get the next measurement record tied 
//                // to this measurement
//                ++_it_aml;                        
//        }
//        return true;
//}
        

// Name:                                GetInnerMeasurements
// Purpose:                                Gets all measurements tied to the subject station (innerStation) and stations tied to
//                      those measurements
// Called by:                        BuildFirstBlock(), BuildNextBlock()
// Calls:                                AddtoCurrentMsrList(), AddtoJunctionStnList()
void dna_segment::GetInnerMeasurements(const UINT32& innerStation)
{
        if (debug_level_ > 2)
                trace_file << " + GetInnerMeasurements()" << endl;
                
#ifdef _MSDEBUG
        string from, to, to2;
#endif

        measurement_t measRecord;
        vUINT32 msrStations;

        // Get the original measurement count
        UINT32 m, msrCount(vASLCount_.at(innerStation));
        // Get the aml index, initialised to the last measurement for this station
        UINT32 amlIndex(
                vAssocStnList_.at(innerStation).GetAMLStnIndex()        // beginning of the measurements associated with this station
                + msrCount - 1);                                                                        // the number of associated measurements

        for (m=0; m<msrCount; ++m, --amlIndex)
        {
                // is this measurement ignored or already used?
                if (!vAssocFreeMsrList_.at(amlIndex).available)
                        continue;
                
                measRecord = bmsBinaryRecords_.at(vAssocFreeMsrList_.at(amlIndex).bmsr_index);

                if (measRecord.ignore)
                        continue;

#ifdef _MSDEBUG
                from = bstBinaryRecords_.at(measRecord.station1).stationName;
                if (MsrTally::Stations(measRecord.measType) >= TWO_STATION)
                {
                        to = bstBinaryRecords_.at(measRecord.station2).stationName;
                        if (MsrTally::Stations(measRecord.measType) == THREE_STATION)
                                to2 = bstBinaryRecords_.at(measRecord.station3).stationName;
                }
#endif

                // When a non-measurement element is found (i.e. Y or Z or covariance component),
                // continue to next element.  Hence, only pointers to the starting element of each
                // measurement are kept. See declaration of measRecord.measStart for more info.
                switch (measRecord.measType)
                {
                case 'G':
                case 'X':
                case 'Y':
                        if (measRecord.measStart != xMeas)
                                continue;
                }                

                // Get all the stations associated with this measurement
                GetMsrStations(bmsBinaryRecords_, vAssocFreeMsrList_.at(amlIndex).bmsr_index, msrStations);

                // Add this measurement to the current measurement list
                AddtoCurrentMsrList(amlIndex, msrStations);

                // if this station is not on JSL, move it from the freestnlist to JSL
                AddtoJunctionStnList(msrStations);
        }
}

// If this measurement is "available", then:
//        - consume this measurement and all other occurences of it on the AML
//        - add this measurement to the current list of measurements for this block.
bool dna_segment::AddtoCurrentMsrList(const UINT32& amlIndex, const vUINT32& msrStations)
{
        if (!vAssocFreeMsrList_.at(amlIndex).available)
                return false;
        
        UINT32 m, msrCount, bmsrindex(vAssocFreeMsrList_.at(amlIndex).bmsr_index);

#ifdef _MSDEBUG
        measurement_t msr(bmsBinaryRecords_.at(bmsrindex));
        char measType(msr.measType);
        string station;
        UINT32 stn_index;
#endif

        UINT32 firstIndex(GetFirstMsrIndex<UINT32>(bmsBinaryRecords_, bmsrindex));

        // Add the index of the first binary measurement record to the measurement list
        vCurrMeasurementList_.push_back(firstIndex);

        if (debug_level_ > 2)
        {
                trace_file << "   - Measurement '" << bmsBinaryRecords_.at(bmsrindex).measType << "' ";
                if (bmsBinaryRecords_.at(bmsrindex).ignore)
                        trace_file << "(ignored) ";
                trace_file << "associated with station(s): ";
        }

        it_aml_pair _it_aml;
        it_vUINT32_const _it_stn, _it_msr;
        
        // 1) consume each occurrence of this measurement (and all other
        //          measurements within a cluster) on the AML, then
        // 2) Decrement the measurement count for all stations associated 
        //          with this measurement.
        for (_it_stn=msrStations.begin(); _it_stn!=msrStations.end(); ++_it_stn)
        {
                // Consume the occurrences of this measurement (and other measurements in a cluster)
                // in the aml for the stations in msrStations

#ifdef _MSDEBUG
                stn_index = *_it_stn;
                station = bstBinaryRecords_.at(*_it_stn).stationName;
#endif

                if (debug_level_ > 2)
                        trace_file << bstBinaryRecords_.at(*_it_stn).stationName << " ";
        
                // set _it_aml to point to the first aml entry for station *_it_stn
                _it_aml = vAssocFreeMsrList_.begin() + vAssocStnList_.at(*_it_stn).GetAMLStnIndex();
                msrCount = vASLCount_.at(*_it_stn);
                
                // consume measurement and decrement measurement count
                for (m=0; m<msrCount; ++m, ++_it_aml)
                {
                        // is this measurement ignored or already used?
                        if (!_it_aml->available)
                                continue;
                        
                        if (_it_aml->bmsr_index == bmsrindex)
                        {
                                // Consume the measurement
                                _it_aml->consume();

                                // Decrement the measurement count.
                                vAssocStnList_.at(*_it_stn).DecrementMsrCount();
                                break;
                        }
                }
        }        

        if (debug_level_ > 2)
                trace_file << endl;

        return true;
}
        

// Name:                                FindCommonMeasurements
// Purpose:                                Gets all measurements tied only to junction stations.
//                                                Measurements between two inners, and between an inner
//                      and a junction are captured by GetInnerMeasurements()
// Called by:                        BuildFirstBlock(), BuildNextBlock()
void dna_segment::FindCommonMeasurements()
{
        // Create a temporary vector
        vUINT32 vCurrBlockStnList(vCurrJunctStnList_), msrStations;
        
        sort(vCurrBlockStnList.begin(), vCurrBlockStnList.end());

        it_vUINT32 _it_stn, _it_mstn;
        measurement_t measRecord;
        bool inList;

        if (debug_level_ > 2)
                trace_file << " + FindCommonMeasurements()" << endl;

#ifdef _MSDEBUG
        string stn;
#endif

        UINT32 m, msrCount, amlIndex;

        for (_it_stn=vCurrBlockStnList.begin(); _it_stn!=vCurrBlockStnList.end(); ++_it_stn)
        {
                // Get the original measurement count
                msrCount = vASLCount_.at(*_it_stn);
                amlIndex = vAssocStnList_.at(*_it_stn).GetAMLStnIndex();

#ifdef _MSDEBUG
                stn = bstBinaryRecords_.at(*_it_stn).stationName;
#endif

                for (m=0; m<msrCount; ++m, ++amlIndex)
                {
                        // is this measurement ignored or already used?
                        if (!vAssocFreeMsrList_.at(amlIndex).available)
                                continue;
                        
                        measRecord = bmsBinaryRecords_.at(vAssocFreeMsrList_.at(amlIndex).bmsr_index);

                        if (measRecord.ignore)
                                continue;

                        // Get all the stations associated with this measurement
                        GetMsrStations(bmsBinaryRecords_, vAssocFreeMsrList_.at(amlIndex).bmsr_index, msrStations);

                        // Since a single station measurement is not associated with other stations,
                        // add the measurement to the list
                        if (msrStations.size() == 1)
                        {
                                // Add this measurement to the current measurement list
                                AddtoCurrentMsrList(amlIndex, msrStations);
                                continue;
                        }
                        
                        // Assume this measurement is common to the stations on vCurrBlockStnList.
                        // inList will be set to false if a measurement station is not found on 
                        // the list
                        inList = true;
                        
                        // Two or more station measurements
                        for (_it_mstn=msrStations.begin(); _it_mstn!=msrStations.end(); ++_it_mstn)
                        {
                                // If one station in msrStations (which are all stations 
                                // associated with the current measurement) is not in the junction list,
                                // then this cannot be a "common measurement".
                                if (!binary_search(vCurrBlockStnList.begin(), vCurrBlockStnList.end(), *_it_mstn))
                                {
                                        // The station at _it_mstn is not in vCurrBlockStnList, so this is not a
                                        // "common measurement" - break out of loop.
                                        inList = false;
                                        break;
                                }
                        }
                
                        // If all stations in msrStations are found within vCurrBlockStnList, then
                        // add this measurement to the current measurement list
                        if (inList)
                                AddtoCurrentMsrList(amlIndex, msrStations);
                }
        }
}

UINT32 dna_segment::GetAvailableMsrCount(const UINT32& stn_index)
{
        return vAssocStnList_.at(stn_index).GetAvailMsrCount();
}


// Name:                                MoveJunctiontoISL
// Purpose:                                Moves stations on the inner list to the junction list.  The
//                                                condition for moving a station is that there are no more
//                                                available measurements connected to the junction station.
// Called by:                        BuildFirstBlock(), BuildNextBlock()
// Calls:                                
void dna_segment::MoveJunctiontoISL()
{
        // Move stations on the current junction station list to the inner station list if
        // there are no more measurements tied to this station
        if (debug_level_ > 2)
                trace_file << " + MoveJunctiontoISL()" << endl;        
        
#ifdef _MSDEBUG
        string station_name;
#endif

        it_vUINT32 _it_currjsl(vCurrJunctStnList_.begin());
        UINT32 stn_index;

        while (!vCurrJunctStnList_.empty())
        {
                stn_index = *_it_currjsl;

#ifdef _MSDEBUG                
                station_name = bstBinaryRecords_.at(stn_index).stationName;
#endif

                // Are there no more available measurements connected to this station?
                if (GetAvailableMsrCount(stn_index) == 0)
                {
                        if (debug_level_ > 2)
                                trace_file << "   - Junction station '" << 
                                        bstBinaryRecords_.at(static_cast<UINT32>(stn_index)).stationName << 
                                        "' was moved to inner list (no more available measurements)." << endl;

                        // Move this station from the junctions list to inners list
                        _it_currjsl = MoveStation(vCurrJunctStnList_, _it_currjsl, 
                                vCurrInnerStnList_, stn_index);

                        // Have all JSLs been removed?
                        if (vCurrJunctStnList_.empty())
                                // end the while loop
                                break;
                        else if (_it_currjsl == vCurrJunctStnList_.end())
                                // reset the iterator to the previous junction station
                                --_it_currjsl;

                        continue;
                }
                
                // move to the next junction, unless the iterator is 
                // pointing to the last
                if (++_it_currjsl == vCurrJunctStnList_.end())
                        break;
        }
}

void dna_segment::AddtoJunctionStnList(const vUINT32& msrStations)
{
        it_vUINT32_const _it_stn;
        it_vUINT32 _it_freeisl;
        for (_it_stn=msrStations.begin(); _it_stn!=msrStations.end(); ++_it_stn)
        {
                // If First station is not already in the junction list...
                //if (find_if(vCurrJunctStnList_.begin(), vCurrJunctStnList_.end(),
                //        bind1st(equal_to<UINT32>(), *_it_stn)) == vCurrJunctStnList_.end())
                if (find_if(vCurrJunctStnList_.begin(), vCurrJunctStnList_.end(),
                        [&_it_stn](const UINT32& junctionStn) {
                                return junctionStn == *_it_stn; }) == vCurrJunctStnList_.end())
                {
                        // If the first station is available, get an iterator to it and move it
                        if (vfreeStnAvailability_.at(*_it_stn).isfree())
                        {
                                // Move it to the list of junctions
                                //if ((_it_freeisl = find_if(vfreeStnList_.begin(), vfreeStnList_.end(),
                                //        bind1st(equal_to<UINT32>(), *_it_stn))) != vfreeStnList_.end())
                                if ((_it_freeisl = find_if(vfreeStnList_.begin(), vfreeStnList_.end(),
                                        [&_it_stn](const UINT32& freeStn) {
                                                return freeStn == *_it_stn; })) != vfreeStnList_.end())
                                {
                                        MoveFreeStnToJunctionList(_it_freeisl, *_it_stn);
                                }
                        }
                }
        }
}


// Name:                                SignalExceptionSerialise
// Purpose:                                Closes all files (if file pointers are passed in) and throws NetSegmentException
// Called by:                        Any
// Calls:                                NetSegmentException()
void dna_segment::SignalExceptionSerialise(const string& msg, const int& i, const char *streamType, ...)
{
        isProcessing_ = false;
        segmentStatus_ = SEGMENT_EXCEPTION_RAISED;

        if (debug_level_ > 1)
                if (debug_file.is_open())
                        debug_file.close();

        if (debug_level_ > 2)
                if (trace_file.is_open())
                        trace_file.close();

        if (streamType == NULL)
                throw NetSegmentException(msg, i);
        
        std::ofstream* ofsDynaML;
        std::ifstream* ifsbinaryFile;

        va_list argptr; 
        va_start(argptr, streamType);

        while (*streamType != '\0')
        {
                //ifstream
                if (*streamType == 'i' )
                {
                        ifsbinaryFile = va_arg(argptr, std::ifstream*);
                        ifsbinaryFile->close();
                }
                //ofstream
                if (*streamType == 'o' )
                {
                        ofsDynaML = va_arg(argptr, std::ofstream*);
                        ofsDynaML->close();
                }
                streamType++;
        }

        va_end(argptr);

        throw NetSegmentException(msg, i);
}

void dna_segment::LoadAssociationFiles(const string& aslfileName, const string& amlfileName)
{
        UINT32 stn, stnCount(0);
        
        try {
                dna_io_asl asl;
                stnCount = asl.load_asl_file(aslfileName, &vAssocStnList_, &vfreeStnList_);
        }
        catch (const runtime_error& e) {
                SignalExceptionSerialise(e.what(), 0, NULL);
        }

        // Dertmine original measurement count for each station
        vASLCount_.clear();
        vASLCount_.resize(stnCount);
        
        _it_vasl _it_asl;
        for (stn=0, _it_asl=vAssocStnList_.begin();
                _it_asl!=vAssocStnList_.end();
                ++_it_asl, ++stn)
        {
                vASLCount_.at(stn) = _it_asl->GetAssocMsrCount();                // original measurement count
        }

        // remove stations from the free list that are invalid
        RemoveInvalidFreeStations();

        // Load associated measurements list.  Throws runtime_error on failure.
        try {
                dna_io_aml aml;
                aml.load_aml_file(amlfileName, &vAssocFreeMsrList_, &bmsBinaryRecords_);
        }
        catch (const runtime_error& e) {
                SignalExceptionSerialise(e.what(), 0, NULL);
        }

        // set available msr count
        SetAvailableMsrCount();
}

        
void dna_segment::LoadStationMap(const string& stnmap_file)
{
        try {
                dna_io_map map;
                map.load_map_file(stnmap_file, &stnsMap_);
        }
        catch (const runtime_error& e) {
                SignalExceptionSerialise(e.what(), 0, NULL);
        }
}

void dna_segment::LoadBinaryFiles(const string& bstrfileName, const string& bmsrfileName)
{
        binary_file_meta_t        bst_meta_, bms_meta_;
        try {
                // Load binary stations data.  Throws runtime_error on failure.
                dna_io_bst bst;
                bst.load_bst_file(bstrfileName, &bstBinaryRecords_, bst_meta_);
        
                // Load binary measurements data.  Throws runtime_error on failure.
                dna_io_bms bms;
                bms.load_bms_file(bmsrfileName, &bmsBinaryRecords_, bms_meta_);
        }
        catch (const runtime_error& e) {
                SignalExceptionSerialise(e.what(), 0, NULL);
        }
        
        // Update the Cluster comparison functor with the AML binary vector
        clusteridCompareFunc_.SetAMLPointer(const_cast<pvmsr_t>(&bmsBinaryRecords_));

        // count the number of measurements not ignored
        MsrTally msrTally;
        UINT32 m = msrTally.CreateTally(bmsBinaryRecords_, true);

        // throw an exception if no measurements are available        
        if (m == 0)
        {
                stringstream ss;
                ss << "No measurements were found." << endl << 
                        "  If measurements were successfully loaded on import, ensure that\n  all measurements have not been ignored." << endl;
                SignalExceptionSerialise(ss.str(), 0, NULL);
        }
}
        

void dna_segment::IdentifyInnerMsrsandAssociatedStns(const UINT32& innerStation, vUINT32& totalStations)
{
        it_vmsr_t measRecord;
        vUINT32 msrStations;
        
        // Get the original measurement count
        UINT32 m, msrCount(vASLCount_.at(innerStation));
        // Get the aml index, initialised to the last measurement for this station
        UINT32 amlIndex(
                vAssocStnList_.at(innerStation).GetAMLStnIndex()        // beginning of the measurements associated with this station
                + msrCount - 1);                                                                        // the number of associated measurements

        for (m=0; m<msrCount; ++m, --amlIndex)
        {
                // is this measurement ignored or already used?
                if (!vAssocFreeMsrList_.at(amlIndex).available)
                        continue;
                
                measRecord = bmsBinaryRecords_.begin() + vAssocFreeMsrList_.at(amlIndex).bmsr_index;

                if (measRecord->ignore)
                        continue;

                // When a non-measurement element is found (i.e. Y or Z or covariance component),
                // continue to next element.  Hence, only pointers to the starting element of each
                // measurement are kept. See declaration of measRecord.measStart for more info.
                switch (measRecord->measType)
                {
                case 'G':
                case 'X':
                case 'Y':
                        if (measRecord->measStart != xMeas)
                                continue;
                }

                // Get all the stations associated with this measurement
                GetMsrStations(bmsBinaryRecords_, vAssocFreeMsrList_.at(amlIndex).bmsr_index, msrStations);

                totalStations.insert(totalStations.end(), msrStations.begin(), msrStations.end());
        }

        strip_duplicates(totalStations);
}

void dna_segment::IdentifyLowestStationAssociation(pvUINT32 vStnList, vUINT32& totalStations, const int currentLevel, const int maxLevel, pvUINT32 vStnCount)
{
        it_vUINT32 it_stn;
        vUINT32 msrStations, subStations;

        //if (currentLevel == 0)
        //{
        //        TRACE("Stations to examine:\n");
        //        for_each(vStnList->begin(), vStnList->end(),
        //                [this] (UINT32& stn) { 
        //                        TRACE("%d ", stn);
        //        });
        //        TRACE("\n");
        //}

        for (it_stn=vStnList->begin(); it_stn!=vStnList->end(); ++it_stn)
        {
                if (currentLevel == 0)
                        vStnCount->push_back(0);

                //TRACE("Level %d  Station %d: ", currentLevel, *it_stn);
                IdentifyInnerMsrsandAssociatedStns(*it_stn, msrStations);

                //for_each(msrStations.begin(), msrStations.end(),
                //        [this] (UINT32& stn) { 
                //                TRACE("%d ", stn);
                //});
                //TRACE("\n  ");

                if (currentLevel < maxLevel)
                        IdentifyLowestStationAssociation(&msrStations, subStations, currentLevel + 1, maxLevel, vStnCount);

                subStations.insert(subStations.end(), msrStations.begin(), msrStations.end());

                if (currentLevel == 0)
                {
                        // get total stations associated with this station
                        strip_duplicates(subStations);
                        vStnCount->back() = static_cast<UINT32>(subStations.size());
                }
        }

        if (currentLevel == 0)
                return;

        totalStations.insert(totalStations.end(), subStations.begin(), subStations.end());
        strip_duplicates(totalStations);

        //TRACE("Summary (%d stations): ", totalStations.size());
        //for_each(totalStations.begin(), totalStations.end(),
        //        [this] (UINT32& stn) { 
        //                TRACE("%d ", stn);
        //});
        //TRACE("\n\n");
}

void dna_segment::SortbyMeasurementCount(pvUINT32 vStnList)
{
        if (vStnList->size() < 2)
                return;
        // sort vStnList by number of measurements to each station (held by vAssocStnList
        CompareMeasCount<CAStationList, UINT32> msrcountCompareFunc(&vAssocStnList_);
        sort(vStnList->begin(), vStnList->end(), msrcountCompareFunc);

        // Search lower level
        if (projectSettings_.s.seg_search_level == 0)
                return;

        vUINT32 msrStations;
        vUINT32 stnList, stnCount;
        stnList.insert(stnList.end(), vStnList->begin(), 
                (vStnList->begin() + minVal(vUINT32::size_type(5),vStnList->size())));
        IdentifyLowestStationAssociation(&stnList, msrStations, 0, projectSettings_.s.seg_search_level, &stnCount);

        UINT32 lowestStnCount(*(min_element(stnCount.begin(), stnCount.end())));
        
        if (stnCount.front() == lowestStnCount)
                return;

        it_vUINT32 it_stn(vStnList->begin()), it_count;
        for (it_count=stnCount.begin(); it_count!=stnCount.end(); ++it_stn, ++it_count)
        {
                if (lowestStnCount == *it_count)
                        break;
        }

        if (vStnList->size() < 2)
                return;

        lowestStnCount = *it_stn;
        vStnList->erase(it_stn);
        vStnList->insert(vStnList->begin(), lowestStnCount);

}
        

void dna_segment::SetAvailableMsrCount()
{
        _it_vasl _it_asl;

        UINT32 stn_index, msrCount, amlIndex;

        for (_it_asl=vAssocStnList_.begin();
                _it_asl!=vAssocStnList_.end();
                ++_it_asl)
        {
                stn_index = static_cast<UINT32>(std::distance(vAssocStnList_.begin(), _it_asl));

                _it_asl->SetAvailMsrCount(_it_asl->GetAssocMsrCount());

                if (_it_asl->GetAssocMsrCount() == 0)
                        continue;

                msrCount = vASLCount_.at(stn_index);        // original measurement count
                amlIndex = vAssocStnList_.at(stn_index).GetAMLStnIndex();

                // if a measurement is ignored, it will not be available
                for (UINT32 m(0); m<msrCount; ++m, ++amlIndex)
                {
                        if (!vAssocFreeMsrList_.at(amlIndex).available)
                                _it_asl->DecrementAvailMsrCount();
                }                
        }
}
        

void dna_segment::RemoveInvalidFreeStations()
{
        CompareValidity<CAStationList, UINT32> aslValidityCompareFunc(&vAssocStnList_, FALSE);
        sort(vfreeStnList_.begin(), vfreeStnList_.end(), aslValidityCompareFunc);
        erase_if(vfreeStnList_, aslValidityCompareFunc);
}


void dna_segment::BuildFreeStationAvailabilityList()
{
        dna_io_seg seg;
        seg.build_free_stn_availability(vAssocStnList_, vfreeStnAvailability_);
}                

void dna_segment::RemoveDuplicateStations(pvstring vStations)
{
        if (vStations->size() < 2)
                return;
        
        // A prior sort on name is essential, since the criteria for removing duplicates 
        // is based upon two successive station entries in an ordered vector being equal
        strip_duplicates(vStations);
}
        
//void dna_segment::RemoveNonMeasurements()
//{
//        if (vfreeMsrList_.size() < 2)
//                return;
//        CompareNonMeasStart<measurement_t, UINT32> measstartCompareFunc(&bmsBinaryRecords_, xMeas);
//        sort(vfreeMsrList_.begin(), vfreeMsrList_.end(), measstartCompareFunc);
//        erase_if(vfreeMsrList_, measstartCompareFunc);
//        
//}
        

//void dna_segment::RemoveIgnoredMeasurements()
//{
//        if (vfreeMsrList_.size() < 2)
//                return;
//        CompareIgnoreedMeas<measurement_t, UINT32> ignoremeasCompareFunc(&bmsBinaryRecords_);
//        sort(vfreeMsrList_.begin(), vfreeMsrList_.end(), ignoremeasCompareFunc);
//        erase_if(vfreeMsrList_, ignoremeasCompareFunc);
//        
//}
        

void dna_segment::WriteFreeStnListSortedbyASLMsrCount()
{
        if (!exists(output_folder_))
        {
                stringstream ss("WriteFreeStnListSortedbyASLMsrCount(): Path does not exist... \n\n    ");
                ss << output_folder_ << ".";
                SignalExceptionSerialise(ss.str(), 0, NULL);
        }

        string file(output_folder_ + "/free_stn_sorted_by_msr_count.lst");
        std::ofstream freestnlist(file.c_str());
        UINT32 x(0);
        string s;
        UINT32 u, msrCount, m, amlindex;
        for (; x<vfreeStnList_.size(); ++x)
        {
                u = vfreeStnList_.at(x);
                s = bstBinaryRecords_.at(vfreeStnList_.at(x)).stationName;
                s.insert(0, "'");
                s += "'";
                msrCount = vAssocStnList_.at(vfreeStnList_.at(x)).GetAssocMsrCount();
                freestnlist << left << setw(10) << u << left << setw(14) << s << left << setw(5) << msrCount;

                for (m=0; m<msrCount; m++)
                {
                        // get the measurement record (holds other stations tied to this measurement)
                        amlindex = vAssocStnList_.at(vfreeStnList_.at(x)).GetAMLStnIndex() + m;        // get the AML index
                        freestnlist << left << setw(HEADER_20) << amlindex;
                }
                freestnlist << endl;
        }
        freestnlist.close();
}
        

void dna_segment::coutCurrentBlockSummary(ostream &os)
{
        try {
                dna_io_seg seg;
                seg.write_seg_block(os, 
                        vCurrInnerStnList_, vCurrJunctStnList_, vCurrMeasurementList_, 
                        currentBlock_,
                        &bstBinaryRecords_, &bmsBinaryRecords_, 
                        true);
        }
        catch (const runtime_error& e) {
                SignalExceptionSerialise(e.what(), 0, NULL);
        }
        
        if (!vfreeStnList_.empty())
                os << "+ Free stations remaining:     " << setw(10) << right << vfreeStnList_.size() << endl;
        if (!vfreeMsrList_.empty())
                os << "+ Free measurements remaining: " << setw(10) << right<< vfreeMsrList_.size() << endl;
}
        
void dna_segment::coutSummary() const
{
        UINT32 stns(0), msrs(0);
        vvUINT32::const_iterator _it_isl, _it_jsl, _it_cml;

        char BLOCK = 10;
        char INNER = 12;
        char JUNCT = 15;
        char TOTAL = 12;
        char MEASR = 14;

        for (_it_cml = vCML_.begin(); _it_cml!=vCML_.end(); ++_it_cml)
                msrs += static_cast<UINT32>(_it_cml->size());
        for (_it_isl = vISL_.begin(); _it_isl!=vISL_.end(); ++_it_isl)
                stns += static_cast<UINT32>(_it_isl->size());

        cout << "+ Segmentation summary:" << endl << endl;
        cout << setw(BLOCK) << left << "  Block" << setw(JUNCT) << left << "Junction stns" << setw(INNER) << left << "Inner stns" << setw(MEASR) << left << "Measurements" << setw(TOTAL) << left << "Total stns"  << endl;
        cout << "  ";
        for (char dash=BLOCK+NETID+INNER+JUNCT+TOTAL+MEASR; dash>2; dash--)
                cout << "-";
        cout << endl;
        UINT32 b = 1;
        _it_jsl = vJSL_.begin();
        _it_cml = vCML_.begin();
        for (_it_isl=vISL_.begin(); _it_isl!=vISL_.end(); ++_it_isl)
        {
                // block
                cout << "  " << setw(BLOCK-2) << left << b;

                // junction stns
                if (_it_jsl!=vJSL_.end())
                        cout << setw(JUNCT) << left << _it_jsl->size();
                else
                        cout << setw(JUNCT) << " ";
                
                // inner stns
                cout << setw(INNER) << left << _it_isl->size();
                
                // total measurements
                if (_it_cml!=vCML_.end())
                        cout << setw(MEASR) << left << _it_cml->size();
                else
                        cout << setw(MEASR) << " ";

                // total stns
                if (_it_jsl!=vJSL_.end())
                        cout << setw(TOTAL) << left << (_it_isl->size() + _it_jsl->size());
                else
                        cout << setw(TOTAL) << left << _it_isl->size();
                
                cout << endl;

                ++_it_jsl;
                ++_it_cml;
                b++;
        }

        cout << endl;

        cout << "+ Stations used:       " << setw(10) << right << stns << endl;
        cout << "+ Measurements used:   " << setw(10) << right << msrs << endl;
        if (!vfreeStnList_.empty())
                cout << "+ Unused stations:     " << setw(10) << right << vfreeStnList_.size() << endl;
        //if (!vfreeMsrList_.empty())
        //        cout << "+ Unused measurements: " << setw(10) << right << vfreeMsrList_.size() << endl;
}
        
void dna_segment::WriteSegmentedNetwork(const string& segfileName)
{
        if (bstBinaryRecords_.empty())
                SignalExceptionSerialise("WriteSegmentedNetwork(): the binary stations file has not been loaded into memory yet.", 0, NULL);
        if (bmsBinaryRecords_.empty())
                SignalExceptionSerialise("WriteSegmentedNetwork(): the binary measurements file has not been loaded into memory yet.", 0, NULL);
        if (vJSL_.empty())
                SignalExceptionSerialise("WriteSegmentedNetwork(): the junction stations list is empty, most likely because the network has not been segmented yet.", 0, NULL);
        if (vISL_.empty())
                SignalExceptionSerialise("WriteSegmentedNetwork(): the inner stations list is empty, most likely because the network has not been segmented yet.", 0, NULL);
        if (vCML_.empty())
                SignalExceptionSerialise("WriteSegmentedNetwork(): the block measurementslist is empty, most likely because the network has not been segmented yet.", 0, NULL);
        
        try {
                dna_io_seg seg;
                seg.write_seg_file(segfileName, projectSettings_.s.bst_file, projectSettings_.s.bms_file,
                        projectSettings_.s.min_inner_stations, projectSettings_.s.max_total_stations,
                        projectSettings_.s.seg_starting_stns, vinitialStns_,
                        projectSettings_.s.command_line_arguments, 
                        vISL_, vJSL_, vCML_,
                        v_ContiguousNetList_, &bstBinaryRecords_, &bmsBinaryRecords_);
        }
        catch (const runtime_error& e) {
                SignalExceptionSerialise(e.what(), 0, NULL);
        }
        catch (...) {
                SignalExceptionSerialise("WriteSegmentedNetwork(): failed to print segmentation file.", 0, NULL);
        }
}

void dna_segment::VerifyStationConnections()
{
        UINT32 block, blockCount(static_cast<UINT32>(vISL_.size()));

        for (block=0; block<blockCount; ++block)
                VerifyStationConnections_Block(block);
}

void dna_segment::VerifyStationConnections_Block(const UINT32& block)
{
        vUINT32::const_iterator _it_isl, _it_jsl, _it_cml;
        bool stationAssociated;
        vUINT32 unusedStns, msrStations, allmsrStations;

#ifdef _MSDEBUG
        string isl_stn_name;
#endif

        // get all stations connected with measurements
        for (_it_cml=vCML_.at(block).begin(); _it_cml!=vCML_.at(block).end(); ++_it_cml)
        {
                // Get all the stations associated with this measurement
                GetMsrStations(bmsBinaryRecords_, *_it_cml, msrStations);
                // Append to master station list
                allmsrStations.insert(allmsrStations.end(), msrStations.begin(), msrStations.end());
        }

        strip_duplicates(allmsrStations);
        
        // Check all isl stations are associated with a measurement
        // No need to check jsl stations as a junction may appear in a block
        // as a result of being carried forward without any measurements
        for (_it_isl=vISL_.at(block).begin(); _it_isl!=vISL_.at(block).end(); ++_it_isl)
        {
                stationAssociated = false;
                if (binary_search(allmsrStations.begin(), allmsrStations.end(), *_it_isl))
                        stationAssociated = true;
                
                if (!stationAssociated)
                {
                        unusedStns.push_back(*_it_isl);

#ifdef _MSDEBUG
                        isl_stn_name = bstBinaryRecords_.at(*_it_isl).stationName;
#endif
                }
        }

        if (!unusedStns.empty())
        {
                stringstream ss;
                ss << "The following station(s) are not associated with any" << endl <<
                        "  measurements in block " << block+1 << ":" << endl;
                for_each(unusedStns.begin(), unusedStns.end(),
                        [this, &ss](UINT32& stn){
                                ss << "  " << bstBinaryRecords_.at(stn).stationName << " (" << stn << ")" << endl;
                });
                SignalExceptionSerialise(ss.str(), 0, NULL);
        }

}

}        // namespace networksegment
}        // namespace dynadjust


icsm-au / DynAdjust / 5021237816

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