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Nektar::LibUtilities::CsvIO Class Reference

#include <CsvIO.h>

Inheritance diagram for Nektar::LibUtilities::CsvIO:
[legend]

Public Member Functions

 CsvIO (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem=false)
 
virtual ~CsvIO ()
 
void Write (const std::string &outFile, const PtsFieldSharedPtr &ptsField, const bool backup=false)
 Save a pts field to a file. More...
 
- Public Member Functions inherited from Nektar::LibUtilities::PtsIO
 PtsIO (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem=false)
 
virtual ~PtsIO ()
 
void Import (const std::string &inFile, PtsFieldSharedPtr &ptsField, FieldMetaDataMap &fieldmetadatamap=NullFieldMetaDataMap, DomainRangeShPtr &Range=NullDomainRangeShPtr)
 Import a pts field from file. More...
 
void Write (const std::string &outFile, const PtsFieldSharedPtr &ptsField, const bool backup=false)
 Save a pts field to a file. More...
 
void ImportFieldData (const std::string inFile, PtsFieldSharedPtr &ptsField, DomainRangeShPtr &Range=NullDomainRangeShPtr)
 
- Public Member Functions inherited from Nektar::LibUtilities::FieldIOXml
 FieldIOXml (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
 Default constructor. More...
 
virtual ~FieldIOXml ()
 
void ImportFieldDefs (DataSourceSharedPtr dataSource, std::vector< FieldDefinitionsSharedPtr > &fielddefs, bool expChild)
 Import field definitions from the target file. More...
 
void ImportFieldData (DataSourceSharedPtr dataSource, const std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata)
 Import field data from a target file. More...
 
void WriteMultiFldFileIDs (const std::string &outfile, const std::vector< std::string > fileNames, std::vector< std::vector< unsigned int > > &elementList, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap)
 Write out a file containing element ID to partition mapping. More...
 
void SetUpFieldMetaData (const std::string &outname, const std::vector< FieldDefinitionsSharedPtr > &fielddefs, const FieldMetaDataMap &fieldmetadatamap)
 Set up field meta data map. More...
 
void ImportMultiFldFileIDs (const std::string &inFile, std::vector< std::string > &fileNames, std::vector< std::vector< unsigned int > > &elementList, FieldMetaDataMap &fieldmetadatamap)
 Read file containing element ID to partition mapping. More...
 
- Public Member Functions inherited from Nektar::LibUtilities::FieldIO
 FieldIO (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
 Constructor for FieldIO base class. More...
 
virtual ~FieldIO ()
 
void Write (const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const bool backup=false)
 Write out the field information to the file outFile. More...
 
void Import (const std::string &infilename, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata=NullVectorNekDoubleVector, FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const Array< OneD, int > &ElementIDs=NullInt1DArray)
 Read field information from the file infilename. More...
 
DataSourceSharedPtr ImportFieldMetaData (const std::string &filename, FieldMetaDataMap &fieldmetadatamap)
 Import the metadata from a field file. More...
 
const std::string & GetClassName () const
 
std::string GetFileEnding () const
 Helper function that determines default file extension. More...
 

Protected Member Functions

virtual void v_ImportFieldData (const std::string inFile, PtsFieldSharedPtr &ptsField, DomainRangeShPtr &Range) override
 
virtual std::string v_GetFileEnding () const override
 
- Protected Member Functions inherited from Nektar::LibUtilities::PtsIO
virtual void v_ImportFieldData (const std::string inFile, PtsFieldSharedPtr &ptsField, DomainRangeShPtr &Range=NullDomainRangeShPtr)
 
virtual std::string v_GetFileEnding () const override
 
void SetUpFieldMetaData (const std::string outname)
 
- Protected Member Functions inherited from Nektar::LibUtilities::FieldIOXml
virtual void v_Write (const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const bool backup=false) override
 Write an XML file to outFile given the field definitions fielddefs, field data fielddata and metadata fieldmetadatamap. More...
 
void v_Import (const std::string &infilename, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata=NullVectorNekDoubleVector, FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const Array< OneD, int > &ElementIDs=NullInt1DArray) override
 Import an XML format file. More...
 
virtual DataSourceSharedPtr v_ImportFieldMetaData (const std::string &filename, FieldMetaDataMap &fieldmetadatamap) override
 Import field metadata from filename and return the data source which wraps filename. More...
 
virtual const std::string & v_GetClassName () const override
 Returns the class name. More...
 
- Protected Member Functions inherited from Nektar::LibUtilities::FieldIO
int CheckFieldDefinition (const FieldDefinitionsSharedPtr &fielddefs)
 Check field definitions for correctness and return storage size. More...
 
std::string SetUpOutput (const std::string outname, bool perRank, bool backup=false)
 Set up the filesystem ready for output. More...
 
virtual void v_Write (const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, const FieldMetaDataMap &fieldinfomap, const bool backup=false)=0
 Write out the field information to the file outFile. More...
 
virtual void v_Import (const std::string &infilename, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata=NullVectorNekDoubleVector, FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const Array< OneD, int > &ElementIDs=NullInt1DArray)=0
 Read field information from the file infilename. More...
 
virtual DataSourceSharedPtr v_ImportFieldMetaData (const std::string &filename, FieldMetaDataMap &fieldmetadatamap)=0
 Import the metadata from a field file. More...
 
virtual std::string v_GetFileEnding () const
 
virtual const std::string & v_GetClassName () const =0
 
bool ParallelInTime ()
 Check if solver use Parallel-in-Time. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from Nektar::LibUtilities::FieldIOXml
static FieldIOSharedPtr create (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
 Creates an instance of this class. More...
 
- Static Public Member Functions inherited from Nektar::LibUtilities::FieldIO
static const std::string GetFileType (const std::string &filename, CommSharedPtr comm)
 Determine file type of given input file. More...
 
static std::shared_ptr< FieldIO > CreateDefault (const LibUtilities::SessionReaderSharedPtr session)
 Returns an object for the default FieldIO method. More...
 
static std::shared_ptr< FieldIO > CreateForFile (const LibUtilities::SessionReaderSharedPtr session, const std::string &filename)
 Construct a FieldIO object for a given input filename. More...
 
static void AddInfoTag (TagWriterSharedPtr root, const FieldMetaDataMap &fieldmetadatamap)
 Add provenance information to the field metadata map. More...
 
- Static Public Attributes inherited from Nektar::LibUtilities::FieldIOXml
static std::string className
 Name of class. More...
 
- Protected Attributes inherited from Nektar::LibUtilities::FieldIO
LibUtilities::CommSharedPtr m_comm
 Communicator to use when writing parallel format. More...
 
bool m_sharedFilesystem
 Boolean dictating whether we are on a shared filesystem. More...
 

Detailed Description

Definition at line 54 of file CsvIO.h.

Constructor & Destructor Documentation

◆ CsvIO()

Nektar::LibUtilities::CsvIO::CsvIO ( LibUtilities::CommSharedPtr  pComm,
bool  sharedFilesystem = false 
)

Definition at line 59 of file CsvIO.cpp.

60 : PtsIO(pComm, sharedFilesystem)
61{
62}
Nektar::LibUtilities::PtsIO::PtsIO
PtsIO(LibUtilities::CommSharedPtr pComm, bool sharedFilesystem=false)
Definition: PtsIO.cpp:57

◆ ~CsvIO()

virtual Nektar::LibUtilities::CsvIO::~CsvIO ( )
inlinevirtual

Definition at line 60 of file CsvIO.h.

61 {
62 }

Member Function Documentation

◆ v_GetFileEnding()

std::string Nektar::LibUtilities::CsvIO::v_GetFileEnding ( ) const
overrideprotectedvirtual

Reimplemented from Nektar::LibUtilities::PtsIO.

Definition at line 274 of file CsvIO.cpp.

275{
276 return "csv";
277}

◆ v_ImportFieldData()

void Nektar::LibUtilities::CsvIO::v_ImportFieldData ( const std::string  inFile,
PtsFieldSharedPtr &  ptsField,
DomainRangeShPtr &  Range 
)
overrideprotectedvirtual

Reimplemented from Nektar::LibUtilities::PtsIO.

Definition at line 110 of file CsvIO.cpp.

113{
114 std::stringstream errstr;
115 errstr << "Unable to load file: " << inFile << std::endl;
116 std::ifstream in(inFile.c_str());
117 ASSERTL0(in.is_open(), errstr.str());
118
119 std::string line;
120 std::getline(in, line);
121 boost::erase_first(line, "#");
122
123 std::vector<std::string> fieldNames;
124 bool valid = ParseUtils::GenerateVector(line, fieldNames);
125 ASSERTL0(valid, "Unable to process list of fields from line: " + line);
126
127 int dim = 0;
128 for (auto &it : fieldNames)
129 {
130 if (it == "x" || it == "y" || it == "z")
131 {
132 dim++;
133 }
134 }
135
136 ASSERTL0(dim, "Failed to find a paramater labelled \"x\",\"y\" or \"z\" "
137 "in file" +
138 inFile + ". Is the coordinated labelled something else?");
139
140 size_t totvars = fieldNames.size();
141 std::vector<std::string> dimNames = {"x", "y", "z"};
142 Array<OneD, int> loc_coord(dim);
143 for (int i = 0; i < dim; ++i)
144 {
145 auto p = std::find(fieldNames.begin(), fieldNames.end(), dimNames[i]);
146 if (p != fieldNames.end())
147 {
148 auto j = std::distance(fieldNames.begin(), p);
149
150 loc_coord[i] = j;
151 }
152 }
153
154 std::vector<NekDouble> ptsSerial;
155 typedef boost::tokenizer<boost::escaped_list_separator<char>> Tokenizer;
156 Tokenizer tok(line);
157 while (getline(in, line))
158 {
159 tok.assign(line);
160
161 ASSERTL0(std::distance(tok.begin(), tok.end()) ==
162 std::iterator_traits<Tokenizer::iterator>::difference_type(
163 totvars),
164 "wrong number of columns in line: " + line);
165
166 bool ReadValue = true;
167
168 if (Range != NullDomainRangeShPtr)
169 {
170 int cnt = 0;
171 for (auto &it : tok)
172 {
173 for (int j = 0; j < dim; ++j)
174 {
175 if (cnt == loc_coord[j])
176 {
177 NekDouble CoordVal = boost::lexical_cast<NekDouble>(
178 boost::trim_copy(std::string(it)));
179 switch (j)
180 {
181 case 0:
182 {
183 if ((CoordVal < Range->m_xmin) ||
184 (CoordVal > Range->m_xmax))
185 {
186 ReadValue = false;
187 }
188 }
189 break;
190 case 1:
191 {
192 if ((CoordVal < Range->m_ymin) ||
193 (CoordVal > Range->m_ymax))
194 {
195 ReadValue = false;
196 }
197 }
198 break;
199 case 2:
200 {
201 if ((CoordVal < Range->m_zmin) ||
202 (CoordVal > Range->m_zmax))
203 {
204 ReadValue = false;
205 }
206 }
207 }
208 }
209 }
210 cnt++;
211 }
212 }
213 if (ReadValue)
214 {
215 for (auto &it : tok)
216 {
217 try
218 {
219 ptsSerial.push_back(boost::lexical_cast<NekDouble>(
220 boost::trim_copy(std::string(it))));
221 }
222 catch (const boost::bad_lexical_cast &)
223 {
224 NEKERROR(ErrorUtil::efatal,
225 "could not convert line: " + line);
226 }
227 }
228 }
229 }
230
231 size_t npts = ptsSerial.size() / totvars;
232
233 Array<OneD, Array<OneD, NekDouble>> pts(totvars);
234 for (size_t i = 0; i < totvars; ++i)
235 {
236 pts[i] = Array<OneD, NekDouble>(npts);
237 }
238
239 for (size_t i = 0; i < npts; ++i)
240 {
241 for (size_t j = 0; j < totvars; ++j)
242 {
243 pts[j][i] = ptsSerial[i * totvars + j];
244 }
245 }
246
247 // reorder pts to make x,y,z the first columns
248 for (int i = 0; i < dim; ++i)
249 {
250 auto p = std::find(fieldNames.begin(), fieldNames.end(), dimNames[i]);
251 if (p != fieldNames.end())
252 {
253 auto j = std::distance(fieldNames.begin(), p);
254
255 if (i == j)
256 {
257 continue;
258 }
259
260 Array<OneD, NekDouble> tmp = pts[i];
261 pts[i] = pts[j];
262 pts[j] = tmp;
263
264 std::string tmp2 = fieldNames[i];
265 fieldNames[i] = fieldNames[j];
266 fieldNames[j] = tmp2;
267 }
268 }
269 fieldNames.erase(fieldNames.begin(), fieldNames.begin() + dim);
270
271 ptsField = MemoryManager<PtsField>::AllocateSharedPtr(dim, fieldNames, pts);
272}
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:215
NEKERROR
#define NEKERROR(type, msg)
Assert Level 0 – Fundamental assert which is used whether in FULLDEBUG, DEBUG or OPT compilation mode...
Definition: ErrorUtil.hpp:209
Nektar::MemoryManager::AllocateSharedPtr
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:168
Nektar::ParseUtils::GenerateVector
static bool GenerateVector(const std::string &str, std::vector< T > &out)
Takes a comma-separated string and converts it to entries in a vector.
Definition: ParseUtils.cpp:131
CellMLToNektar.cellml_metadata.p
p
Definition: cellml_metadata.py:350
Nektar::LibUtilities::NullDomainRangeShPtr
static DomainRangeShPtr NullDomainRangeShPtr
Definition: DomainRange.h:67
Nektar::StdRegions::find
InputIterator find(InputIterator first, InputIterator last, InputIterator startingpoint, const EqualityComparable &value)
Definition: StdRegions.hpp:453
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::ErrorUtil::efatal, Nektar::StdRegions::find(), Nektar::ParseUtils::GenerateVector(), NEKERROR, Nektar::LibUtilities::NullDomainRangeShPtr, and CellMLToNektar.cellml_metadata::p.

◆ Write()

void Nektar::LibUtilities::CsvIO::Write ( const std::string &  outFile,
const PtsFieldSharedPtr &  ptsField,
const bool  backup = false 
)

Save a pts field to a file.

Parameters
outFilefilename of the file
ptsFieldthe pts field

Definition at line 70 of file CsvIO.cpp.

73{
74 size_t nTotvars = ptsField->GetNFields() + ptsField->GetDim();
75 size_t np = ptsField->GetNpoints();
76
77 std::string filename = SetUpOutput(outFile, true, backup);
78 SetUpFieldMetaData(outFile);
79
80 std::ofstream ptsFile;
81 ptsFile.open(filename.c_str());
82
83 std::vector<std::string> xyz;
84 xyz.push_back("x");
85 xyz.push_back("y");
86 xyz.push_back("z");
87 xyz.resize(ptsField->GetDim());
88
89 std::string fn = boost::algorithm::join(xyz, ",");
90 ptsFile << "# " << fn << ",";
91 fn = boost::algorithm::join(ptsField->GetFieldNames(), ",");
92 ptsFile << fn;
93 ptsFile << std::endl;
94
95 Array<OneD, Array<OneD, NekDouble>> pts;
96 ptsField->GetPts(pts);
97 for (size_t i = 0; i < np; ++i)
98 {
99 ptsFile << pts[0][i];
100 for (size_t j = 1; j < nTotvars; ++j)
101 {
102 ptsFile << "," << pts[j][i];
103 }
104 ptsFile << std::endl;
105 }
106
107 ptsFile.close();
108}
Nektar::LibUtilities::FieldIO::SetUpOutput
std::string SetUpOutput(const std::string outname, bool perRank, bool backup=false)
Set up the filesystem ready for output.
Definition: FieldIO.cpp:406
Nektar::LibUtilities::PtsIO::SetUpFieldMetaData
void SetUpFieldMetaData(const std::string outname)
Definition: PtsIO.cpp:306

References Nektar::LibUtilities::PtsIO::SetUpFieldMetaData(), and Nektar::LibUtilities::FieldIO::SetUpOutput().

Referenced by Nektar::SolverUtils::CouplingCwipi::DumpRawFields(), and Nektar::FieldUtils::OutputPts::v_OutputFromPts().

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