Merge pull request #88 from rogerfraser/master

Extend discontinuity renaming functionality, bug fix and other enhancements

.gitignore

@@ -22,7 +22,7 @@ dynadjust/bin/
 *.db-wal
 *.user
 /.idea/
-.vscode/launch.json
+.vscode/*
 
 # readme and other files not requiring external contribution
 README.md

dynadjust/CMakeLists.txt

@@ -229,7 +229,12 @@ if (BUILD_TESTING)
     add_test (NAME ref-itrf-pmm-05 COMMAND $<TARGET_FILE:dnaimportwrapper> -n apr -r itrf2008 ${CMAKE_SOURCE_DIR}/../sampleData/apr.ITRF2008.04.06.2020.stn ${CMAKE_SOURCE_DIR}/../sampleData/apr.ITRF2008.04.06.2020.msr)
     add_test (NAME ref-itrf-pmm-06 COMMAND $<TARGET_FILE:dnareftranwrapper> apr -r itrf2008 -e 01.01.2021 --export-dna --verb 2 --plate-model-option 1 -b ${CMAKE_SOURCE_DIR}/../sampleData/MORVEL56_plates.dig -m ${CMAKE_SOURCE_DIR}/../sampleData/NNR-MORVEL56_poles.dat)
     add_test (NAME ref-itrf-pmm-07 COMMAND bash -c "diff <(tail -n +6 apr.ITRF2008.01.01.2021.stn) <(tail -n +4 ${CMAKE_SOURCE_DIR}/../sampleData/apr.ITRF2008.01.01.2021.stn.expected)")
+
+    add_test (NAME imp-discont-01 COMMAND $<TARGET_FILE:dnaimportwrapper> -n discont -r itrf2005 ${CMAKE_SOURCE_DIR}/../sampleData/TEST_ITRF05.SNX --discontinuity-file ${CMAKE_SOURCE_DIR}/../sampleData/disconts20201205.snx)
+    add_test (NAME imp-discont-02 COMMAND $<TARGET_FILE:dnaimportwrapper> -n discont -r itrf2005 ${CMAKE_SOURCE_DIR}/../sampleData/TEST_ITRF05.SNX --discontinuity-file ${CMAKE_SOURCE_DIR}/../sampleData/disconts20201205.snx --split-gnss --include-stn "ALIC" --export-dna)
 
+    add_test (NAME imp-m2s-sort-01 COMMAND $<TARGET_FILE:dnaimportwrapper> -n gnss ${CMAKE_SOURCE_DIR}/../sampleData/gnss-network.stn ${CMAKE_SOURCE_DIR}/../sampleData/gnss-network.msr --output-msr-to-stn --sort-msr-to-stn-field 1 -r GDA94) 
+
     # set execution dependencies (the execution of tests must be sequential)
     set_tests_properties(
         import-gnss-network geoid-gnss-network adjust-gnss-network

dynadjust/dynadjust/dnaadjust/dnaadjust.cpp

@@ -9641,9 +9641,9 @@ void dna_adjust::PrintAdjStation(ostream& os,
 			StringFromTW(sqrt(var_local.get(2, 2)), STDDEV, PRECISION_MTR_STN);
 	else
 		os <<
-			StringFromT(sqrt(var_local.get(0, 0)), PRECISION_MTR_STN) <<
-			StringFromT(sqrt(var_local.get(1, 1)), PRECISION_MTR_STN) <<
-			StringFromT(sqrt(var_local.get(2, 2)), PRECISION_MTR_STN);
+			setw(STDDEV) << right << StringFromT(sqrt(var_local.get(0, 0)), PRECISION_MTR_STN) <<
+			setw(STDDEV) << right << StringFromT(sqrt(var_local.get(1, 1)), PRECISION_MTR_STN) <<
+			setw(STDDEV) << right << StringFromT(sqrt(var_local.get(2, 2)), PRECISION_MTR_STN);
 
 	if (projectSettings_.o._stn_corr)
 	{

dynadjust/dynadjust/dnaimport/dnainterop.cpp

@@ -156,6 +156,46 @@ void dna_import::BuildExtractStationsList(const string& stnList, pvstring vstnLi
 		ss << "BuildExtractStationsList(): An error was encountered when parsing " << stnList << "." << endl;
 		SignalExceptionParse(ss.str(), 0);
 	}
+
+	// Have discontinuities been applied?
+	if (!projectSettings_.i.apply_discontinuities)
+		return;
+
+	if (stn_renamed_.empty())
+		return;
+
+	it_string_pair _it_discont_ren;
+
+	_it_vstr _it_stn;
+	string station_name;
+	vstring renamed_stations;
+
+	// loop through all station names in vstnList
+	for (_it_stn = vstnList->begin();
+		_it_stn != vstnList->end();
+		_it_stn++)
+	{
+		station_name = *_it_stn;
+
+		_it_discont_ren = stn_renamed_.begin();
+
+		// Advance through _it_discont_ren for all occurrences of station_name
+		while ((_it_discont_ren = lower_bound(_it_discont_ren, stn_renamed_.end(), 
+			station_name, ComparePairFirst<string>())) != stn_renamed_.end())
+		{
+			// found a station that has been renamed.			
+			// add the discontinuity name to the list
+			renamed_stations.push_back(_it_discont_ren->second);
+			_it_discont_ren++;
+		}
+	}
+
+	// Add discontinuity sites and remove duplicates
+	if (!renamed_stations.empty())
+	{
+		vstnList->insert(vstnList->end(), renamed_stations.begin(), renamed_stations.end());
+		strip_duplicates(vstnList);
+	}
 }
 
 
@@ -719,25 +759,32 @@ void dna_import::ParseDiscontinuities(const string& fileName)
 	discont_file.close();
 }
 
+// Station names in SINEX files are automatically renamed to account for discontinuities and added
+// to vStations.  For non SINEX files, any renamed stations are tracked in stn_renamed_.  After
+// all files have been loaded, this function is called to (1) find any discontinuity stations not in the 
+// station list and (2) add a duplicate for it, renamed to the respective discontinuity site name.
 void dna_import::AddDiscontinuityStations(vdnaStnPtr* vStations)
 {
 	_it_vdnastnptr _it_stn(vStations->begin());
-	it_string_pair stn_renames_it;
+	it_string_pair stn_renames_it(stn_renamed_.begin());
 
 	dnaStnPtr stn_ptr;
 	string stationName;
 
 	UINT32 i, station_count(static_cast<UINT32>(vStations->size()));
 	UINT32 station_index(station_count);
+
+	sort(vStations->begin(), vStations->end(), CompareStationName<dnaStnPtr>());
 
 	for (i=0; i<station_count; ++i)
 	{
 		stationName = vStations->at(i)->GetName();
-
+	
 		// For each occurrence of stationName in stn_renamed_, create a clone and add it to 
-		// vStations so that the measurement stations renamed by ApplyDiscontinuitiesMeasurements
-		// are supported by corresponding stations
-		while ((stn_renames_it = binary_search_index_pair(stn_renamed_.begin(), stn_renamed_.end(), stationName)) != stn_renamed_.end())
+		// vStations so that the measurement stations in non SINEX files that are
+		// renamed by ApplyDiscontinuitiesMeasurements (via TrackDiscontinuitySite) are 
+		// supported by corresponding stations.
+		while ((stn_renames_it = binary_search_index_pair(stn_renames_it, stn_renamed_.end(), stationName)) != stn_renamed_.end())
 		{
 			// If a sinex file has been loaded and stationName exists in the sinex file, stn_renames_it->second may 
 			// already exist in vStations.  In this case, the following code will add a duplicate station.
@@ -752,15 +799,13 @@ void dna_import::AddDiscontinuityStations(vdnaStnPtr* vStations)
 			stn_ptr->SetfileOrder(++station_index);
 			vStations->push_back(stn_ptr);
 
-			if (!stn_renamed_.empty())
-				stn_renamed_.erase(stn_renames_it);
+			stn_renames_it++;
 		}
 
-		if (stn_renamed_.empty())
-			break;
+		stn_renames_it = stn_renamed_.begin();
 	}
 
-	// Removde duplicates which may have been added through the above process
+	// Remove duplicates which may have been added through the above process
 	sort(vStations->begin(), vStations->end(), CompareStationName<dnaStnPtr>());
 	_it_vdnastnptr _it_stn_newend = unique(vStations->begin(), vStations->end(), EqualStationName<dnaStnPtr>());
 	if (_it_stn_newend != vStations->end())
@@ -771,11 +816,6 @@ void dna_import::AddDiscontinuityStations(vdnaStnPtr* vStations)
 
 void dna_import::ApplyDiscontinuities(vdnaStnPtr* vStations, vdnaMsrPtr* vMeasurements, project_settings* p)
 {
-#ifndef _MSDEBUG
-	// return on release
-	return;
-#endif
-
 	if (stn_discontinuities_.empty())
 		return;
 
@@ -786,11 +826,16 @@ void dna_import::ApplyDiscontinuities(vdnaStnPtr* vStations, vdnaMsrPtr* vMeasur
 		m_discontsSortedbyName = true;
 	}
 
-	// There isn't any need to apply discontinuities to a station file, since those
-	// stations will be introduced via the process of handling a discontinuity file.
-	// DynAdjust should load the stations as normal. If a station becomes renamed
-	// through the process of applying discontinuities to measurements, then it will
-	// be flagged as unused (since it won't be found in the measurements).
+	// If the only input file is a SINEX file, there isn't any need to apply discontinuities 
+	// to a station file, since those stations will be introduced via the process of 
+	// handling a discontinuity file. 
+	// However, if other station and measurement file types are loaded, there may be a case 
+	// where station discontinuities exist but have not been accounted for at this point.  
+	// For this purpose, a call to ApplyDiscontinuitiesStations will be made after all files 
+	// have been imported.
+	// If a station becomes renamed through the process of applying discontinuities to 
+	// measurements, then it will be flagged as unused (since it won't be found in the 
+	// measurements).
 
 	if (!vMeasurements->empty())
 		ApplyDiscontinuitiesMeasurements(vMeasurements, p);
@@ -805,9 +850,10 @@ void dna_import::TrackDiscontinuitySite(const string& site, const string& site_r
 	}
 }
 
+
 // This function renames stations in each measurement based on a discontinuity file
 // NOTE: A fundamental prerequisite for the proper renaming of discontinuity sites
-// in this function is a valid epoch for each measurement!s
+// in this function is a valid epoch for each measurement!
 void dna_import::ApplyDiscontinuitiesMeasurements(vdnaMsrPtr* vMeasurements, project_settings* p)
 {
 	_it_vdiscontinuity_tuple _it_discont(stn_discontinuities_.begin());
@@ -1434,6 +1480,12 @@ void dna_import::ParseDNASTN(vdnaStnPtr* vStations, PUINT32 stnCount, string* su
 			catch (...) {
 				switch (stn_ptr->GetMyCoordTypeC())
 				{
+				case LLh_type_i:
+				case LLH_type_i:
+				case ENU_type_i:
+				case AED_type_i:
+				case XYZ_type_i:
+					break;
 				case UTM_type_i:	// Hemisphere and zone is only essential for UTM types
 					stringstream ss;
 					ss << "ParseDNASTN(): Could not extract station hemisphere and zone from the record:  " << endl << "    " << sBuf << endl;
@@ -3066,7 +3118,7 @@ void dna_import::ExtractStnsAndAssociatedMsrs(const string& stnListInclude, cons
 	// backup station vector
 	vdnaStnPtr bvStations = *vStations;
 
-	const string *stnListIn, *stnListEx;
+	const string *stnListIn;
 
 	vstring vIncludedStns;
 	pvstring pvStnsIn, pvStnsEx;
@@ -3077,15 +3129,13 @@ void dna_import::ExtractStnsAndAssociatedMsrs(const string& stnListInclude, cons
 		pvStnsIn = &vIncludedStns;
 		pvStnsEx = vExcludedStns;		
 		stnListIn = &stnListInclude; 
-		stnListEx = &stnListExclude;
 	}
 	// Has the user provided a list of stations to exclude?
 	else if (!stnListExclude.empty()) 
 	{
 		pvStnsIn = vExcludedStns;
 		pvStnsEx = &vIncludedStns;
 		stnListIn = &stnListExclude; 
-		stnListEx = &stnListInclude;
 	}
 	else
 	{

dynadjust/dynadjust/dnaimport/dnainterop.hpp

@@ -135,7 +135,6 @@ class dna_import {
 	void RenameStations(vdnaStnPtr* vStations, vdnaMsrPtr* vMeasurements, project_settings* p);
 	void ApplyDiscontinuities(vdnaStnPtr* vStations, vdnaMsrPtr* vMeasurements, project_settings* p);
 	void TrackDiscontinuitySite(const string& site, const string& site_renamed);
-	void ApplyDiscontinuitiesStations(vdnaStnPtr* vStations, project_settings* p);
 	void ApplyDiscontinuitiesMeasurements(vdnaMsrPtr* vMeasurements, project_settings* p);
 
 	void ApplyDiscontinuitiesMeasurements_GX(vector<CDnaGpsBaseline>* vGpsBaselines);

dynadjust/dynadjust/dnaimportwrapper/dnaimportwrapper.cpp

@@ -550,6 +550,7 @@ void ExportStationsandMeasurements(dna_import* parserDynaML, const project_setti
 				cout << "Done." << endl;
 				cout.flush();
 			}
+			*imp_file << "Done." << endl;
 		}
 		else
 		{
@@ -584,6 +585,7 @@ void ExportStationsandMeasurements(dna_import* parserDynaML, const project_setti
 				cout << "Done." << endl;
 				cout.flush();
 			}
+			*imp_file << "Done." << endl;
 		}		
 	}
 
@@ -1442,6 +1444,18 @@ int main(int argc, char* argv[])
 		}
 	}
 
+	/////////////////////////////////////////////////////////////////////////
+	// Add discontinuity sites to vStations
+	//
+	// WARNING: If discontinuity sites are present in the renaming file, and
+	// the renaming file changes the name from the four-character id in the 
+	// discontinuity file to another name, this function call will not work
+	// properly. Hence, sites in the discontinuity file must be consistently
+	// named in the station and measurement files and not renamed to another
+	// name.
+	if (p.i.apply_discontinuities && !vstationsTotal.empty())
+		parserDynaML.AddDiscontinuityStations(&vstationsTotal);
+
 	UINT32 stn;
 
 	// Extract user-defined stations and all connected measurements
@@ -1861,24 +1875,11 @@ int main(int argc, char* argv[])
 			imp_file.close();
 			return EXIT_FAILURE;
 		}		
-
-		/////////////////////////////////////////////////////////////////////////
-		// Add discontinuity sites to vStations
-		//
-		// WARNING: If discontinuity sites are present in the renaming file, and
-		// the renaming file changes the name from the four-character id in the 
-		// discontinuity file to another name, this function call will not work
-		// properly. Hence, sites in the discontinuity file must be consistently
-		// named in the station and measurement files and not renamed to another
-		// name.
-		if (p.i.apply_discontinuities && stnCount > 0)
-			parserDynaML.AddDiscontinuityStations(&vstationsTotal);
 
 		/////////////////////////////////////////////////////////////////
 		// Now commence sorting and mapping
 		// 1. Sort stations
-		// 2. Add new discontinuity sites
-		// 3. Create station map
+		// 2. Create station map
 		try {
 			if (!p.g.quiet)
 			{
@@ -2218,8 +2219,7 @@ int main(int argc, char* argv[])
 		}
 	}
 
-	// Create ASL and AML files
-	// Export to text if required
+	// Export ASL and AML to text if required
 	if (measurements_mapped) 
 	{
 		try {

dynadjust/include/functions/dnatemplatefuncs.hpp

@@ -959,15 +959,28 @@ class CompareStnFileOrder
 
 
 // S = CDnaStation
-template<typename S>
+template<typename S, typename T>
 class CompareStnName_CDnaStn
 {
 public:
 	bool operator()(const boost::shared_ptr<S> lhs, const boost::shared_ptr<S> rhs) {
 		if (lhs.get()->GetName() == rhs.get()->GetName())
 			return (lhs.get()->GetfileOrder() < rhs.get()->GetfileOrder());
-		return (lhs.get()->GetName() < rhs.get()->GetName());
-
+		return keyLess(lhs.get()->GetName(), rhs.get()->GetName());
+	}
+
+	bool operator()(const T lhs, const boost::shared_ptr<S> rhs) {
+		return keyLess(lhs, rhs.get()->GetName());
+	}
+
+	bool operator()(const boost::shared_ptr<S> lhs, const T rhs) {
+		return keyLess(lhs.get()->GetName(), rhs);
+	}
+
+private:
+	// the "real" comparison function
+	bool keyLess(const T& k1, const T& k2) const {
+		return k1 < k2;
 	}
 };
 

dynadjust/include/io/dnaiosnx.hpp

@@ -252,7 +252,7 @@ class dna_io_snx : public dna_io_base
 public:
 	dna_io_snx(void) 
 	: blockCount_(0), block_(0), measurementParams_(0), unknownParams_(0)
-	, sigmaZero_(0.), uniqueStationCount_(0)
+	, sigmaZero_(0.), blockStationsMap_(0), uniqueStationCount_(0)
 	, containsVelocities_(false), containsDiscontinuities_(false), applyDiscontinuities_(false)
 	, siteIDsRead_(false), solutionEpochsRead_(false) {
 	}

dynadjust/include/measurement_types/dnastation.hpp

@@ -73,6 +73,7 @@ typedef boost::shared_ptr<CDnaStation> dnaStnPtr;
 typedef vector<dnaStnPtr> vdnaStnPtr;		// vector of dnaStnPtr
 typedef vdnaStnPtr::iterator _it_vdnastnptr;
 typedef vdnaStnPtr::const_iterator _it_vdnastnptr_const;
+typedef pair<_it_vdnastnptr, _it_vdnastnptr> it_pair_dnastnptr;
 
 typedef vector<CAStationList> vASL, *pvASL;
 typedef vASL::iterator _it_vasl;