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Nektar::LibUtilities::FieldIO Class Reference

Class for operating on FLD files. More...

#include <FieldIO.h>

Public Member Functions

 FieldIO (LibUtilities::CommSharedPtr pComm)
 Constructor.
void Write (const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap)
 Write data in FLD format.
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)
 Imports an FLD file.
void ImportFieldMetaData (std::string filename, FieldMetaDataMap &fieldmetadatamap)
 Imports the definition of the meta data.
void ImportFieldMetaData (TiXmlDocument &doc, FieldMetaDataMap &fieldmetadatamap)
 Imports the definition of the meta data.
void ImportFieldDefs (TiXmlDocument &doc, std::vector< FieldDefinitionsSharedPtr > &fielddefs, bool expChild)
 Imports the definition of the fields.
void ImportFieldData (TiXmlDocument &doc, const std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata)
 Imports the data fileds.
void WriteMultiFldFileIDs (const std::string &outfile, const std::vector< std::string > fileNames, std::vector< std::vector< unsigned int > > &elementList, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap)

Private Member Functions

void AddInfoTag (TiXmlElement *root, const FieldMetaDataMap &fieldmetadatamap)
 add information about provenance and fieldmetadata
void GenerateSeqString (const std::vector< unsigned int > &elmtids, std::string &idString)
std::string SetUpOutput (const std::string outname, const std::vector< FieldDefinitionsSharedPtr > &fielddefs, const FieldMetaDataMap &fieldmetadatamap)
void ImportMultiFldFileIDs (const std::string &inFile, std::vector< std::string > &fileNames, std::vector< std::vector< unsigned int > > &elementList, FieldMetaDataMap &fieldmetadatamap)
int CheckFieldDefinition (const FieldDefinitionsSharedPtr &fielddefs)
int Deflate (std::vector< NekDouble > &in, string &out)
int Inflate (string &in, std::vector< NekDouble > &out)

Private Attributes

LibUtilities::CommSharedPtr m_comm
 Communicator to use when writing parallel format.

Detailed Description

Class for operating on FLD files.

Definition at line 151 of file FieldIO.h.

Constructor & Destructor Documentation

Nektar::LibUtilities::FieldIO::FieldIO ( LibUtilities::CommSharedPtr  pComm)

Constructor.

Definition at line 140 of file FieldIO.cpp.

: m_comm(pComm)
{
}

Member Function Documentation

void Nektar::LibUtilities::FieldIO::AddInfoTag ( TiXmlElement *  root,
const FieldMetaDataMap &  fieldmetadatamap 
)
private

add information about provenance and fieldmetadata

Definition at line 1005 of file FieldIO.cpp.

References Nektar::NekConstants::kGitBranch, Nektar::NekConstants::kGitSha1, NEKTAR_VERSION, and Nektar::LibUtilities::NullFieldMetaDataMap.

Referenced by Write(), and WriteMultiFldFileIDs().

{
FieldMetaDataMap ProvenanceMap;
// Nektar++ release version from VERSION file
ProvenanceMap["NektarVersion"] = string(NEKTAR_VERSION);
// Date/time stamp
ptime::time_facet *facet = new ptime::time_facet("%d-%b-%Y %H:%M:%S");
std::stringstream wss;
wss.imbue(locale(wss.getloc(), facet));
wss << ptime::second_clock::local_time();
ProvenanceMap["Timestamp"] = wss.str();
// Hostname
boost::system::error_code ec;
ProvenanceMap["Hostname"] = ip::host_name(ec);
// Git information
// If built from a distributed package, do not include this
if (NekConstants::kGitSha1 != "GITDIR-NOTFOUND")
{
ProvenanceMap["GitSHA1"] = NekConstants::kGitSha1;
ProvenanceMap["GitBranch"] = NekConstants::kGitBranch;
}
TiXmlElement * infoTag = new TiXmlElement("Metadata");
root->LinkEndChild(infoTag);
TiXmlElement * v;
FieldMetaDataMap::const_iterator infoit;
TiXmlElement * provTag = new TiXmlElement("Provenance");
infoTag->LinkEndChild(provTag);
for (infoit = ProvenanceMap.begin(); infoit != ProvenanceMap.end(); ++infoit)
{
v = new TiXmlElement( (infoit->first).c_str() );
v->LinkEndChild(new TiXmlText((infoit->second).c_str()));
provTag->LinkEndChild(v);
}
//---------------------------------------------
// write field info section
if(fieldmetadatamap != NullFieldMetaDataMap)
{
for(infoit = fieldmetadatamap.begin(); infoit != fieldmetadatamap.end(); ++infoit)
{
v = new TiXmlElement( (infoit->first).c_str() );
v->LinkEndChild(new TiXmlText((infoit->second).c_str()));
infoTag->LinkEndChild(v);
}
}
}
int Nektar::LibUtilities::FieldIO::CheckFieldDefinition ( const FieldDefinitionsSharedPtr &  fielddefs)
private

Definition at line 1336 of file FieldIO.cpp.

References ASSERTL0, Nektar::LibUtilities::eHexahedron, Nektar::LibUtilities::ePrism, Nektar::LibUtilities::ePyramid, Nektar::LibUtilities::eQuadrilateral, Nektar::LibUtilities::eSegment, Nektar::LibUtilities::eTetrahedron, Nektar::LibUtilities::eTriangle, and Nektar::LibUtilities::StdSegData::getNumberOfCoefficients().

Referenced by ImportFieldData(), and Write().

{
int i;
if(fielddefs->m_elementIDs.size() == 0) // empty partition
{
return 0;
}
//ASSERTL0(fielddefs->m_elementIDs.size() > 0, "Fielddefs vector must contain at least one element of data .");
unsigned int numbasis = 0;
// Determine nummodes vector lists are correct length
switch(fielddefs->m_shapeType)
{
case eSegment:
numbasis = 1;
if(fielddefs->m_numHomogeneousDir)
{
numbasis += fielddefs->m_numHomogeneousDir;
}
break;
case eTriangle:
case eQuadrilateral:
if(fielddefs->m_numHomogeneousDir)
{
numbasis = 3;
}
else
{
numbasis = 2;
}
break;
case eTetrahedron:
case ePyramid:
case ePrism:
case eHexahedron:
numbasis = 3;
break;
default:
ASSERTL0(false, "Unsupported shape type.");
break;
}
unsigned int datasize = 0;
ASSERTL0(fielddefs->m_basis.size() == numbasis, "Length of basis vector is incorrect");
if(fielddefs->m_uniOrder == true)
{
unsigned int cnt = 0;
// calculate datasize
switch(fielddefs->m_shapeType)
{
case eSegment:
{
int l = fielddefs->m_numModes[cnt++];
if(fielddefs->m_numHomogeneousDir == 1)
{
datasize += l*fielddefs->m_numModes[cnt++];
}
else if(fielddefs->m_numHomogeneousDir == 2)
{
int m = fielddefs->m_numModes[cnt++];
datasize += l*m*fielddefs->m_numModes[cnt++];
}
else
{
datasize += l;
}
}
break;
case eTriangle:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
if(fielddefs->m_numHomogeneousDir == 1)
{
datasize += StdTriData::getNumberOfCoefficients(l,m)*
fielddefs->m_homogeneousZIDs.size();
}
else
{
datasize += StdTriData::getNumberOfCoefficients(l,m);
}
}
break;
case eQuadrilateral:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
if(fielddefs->m_numHomogeneousDir == 1)
{
datasize += l*m*fielddefs->m_homogeneousZIDs.size();
}
else
{
datasize += l*m;
}
}
break;
case eTetrahedron:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += StdTetData::getNumberOfCoefficients(l,m,n);
}
break;
case ePyramid:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += StdPyrData::getNumberOfCoefficients(l,m,n);
}
break;
case ePrism:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += StdPrismData::getNumberOfCoefficients(l,m,n);
}
break;
case eHexahedron:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += l*m*n;
}
break;
default:
ASSERTL0(false, "Unsupported shape type.");
break;
}
datasize *= fielddefs->m_elementIDs.size();
}
else
{
unsigned int cnt = 0;
// calculate data length
for(i = 0; i < fielddefs->m_elementIDs.size(); ++i)
{
switch(fielddefs->m_shapeType)
{
case eSegment:
datasize += fielddefs->m_numModes[cnt++];
break;
case eTriangle:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
datasize += StdTriData::getNumberOfCoefficients(l,m);
}
break;
case eQuadrilateral:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
datasize += l*m;
}
break;
case eTetrahedron:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += StdTetData::getNumberOfCoefficients(l,m,n);
}
break;
case ePyramid:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += StdPyrData::getNumberOfCoefficients(l,m,n);
}
break;
case ePrism:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += StdPrismData::getNumberOfCoefficients(l,m,n);
}
break;
case eHexahedron:
{
int l = fielddefs->m_numModes[cnt++];
int m = fielddefs->m_numModes[cnt++];
int n = fielddefs->m_numModes[cnt++];
datasize += l*m*n;
}
break;
default:
ASSERTL0(false, "Unsupported shape type.");
break;
}
}
}
return datasize;
}
int Nektar::LibUtilities::FieldIO::Deflate ( std::vector< NekDouble > &  in,
string &  out 
)
private

Compress a vector of NekDouble values into a string using zlib.

Definition at line 1221 of file FieldIO.cpp.

References ASSERTL0, CHUNK, and Nektar::void.

Referenced by Write().

{
int ret;
unsigned have;
z_stream strm;
unsigned char* input = (unsigned char*)(&in[0]);
string buffer;
buffer.resize(CHUNK);
/* allocate deflate state */
strm.zalloc = Z_NULL;
strm.zfree = Z_NULL;
strm.opaque = Z_NULL;
ret = deflateInit(&strm, Z_DEFAULT_COMPRESSION);
ASSERTL0(ret == Z_OK, "Error initializing Zlib.");
strm.avail_in = in.size() * sizeof(NekDouble) / sizeof(char);
strm.next_in = input;
// Deflate input until output buffer is no longer full.
do {
strm.avail_out = CHUNK;
strm.next_out = (unsigned char*)(&buffer[0]);
ret = deflate(&strm, Z_FINISH);
// Deflate can return Z_OK, Z_STREAM_ERROR, Z_BUF_ERROR or
// Z_STREAM_END. All, except Z_STREAM_ERROR are ok.
ASSERTL0(ret != Z_STREAM_ERROR, "Zlib stream error");
have = CHUNK - strm.avail_out;
out += buffer.substr(0, have);
} while (strm.avail_out == 0);
// Check all input was processed.
ASSERTL0(strm.avail_in == 0, "Not all input was used.");
// Check stream is complete.
ASSERTL0(ret == Z_STREAM_END, "Stream not finished");
// Clean-up and return
(void)deflateEnd(&strm);
return Z_OK;
}
void Nektar::LibUtilities::FieldIO::GenerateSeqString ( const std::vector< unsigned int > &  elmtids,
std::string &  idString 
)
private

Definition at line 1064 of file FieldIO.cpp.

Referenced by Write(), and WriteMultiFldFileIDs().

{
std::stringstream idStringStream;
bool setdash = true;
unsigned int endval;
idStringStream << elmtids[0];
for (int i = 1; i < elmtids.size(); ++i)
{
if(elmtids[i] == elmtids[i-1]+1)
{
if(setdash)
{
idStringStream << "-";
setdash = false;
}
if(i == elmtids.size()-1) // last element
{
idStringStream << elmtids[i];
}
else
{
endval = elmtids[i];
}
}
else
{
if(setdash == false) // finish off previous dash sequence
{
idStringStream << endval;
setdash = true;
}
idStringStream << "," << elmtids[i];
}
}
idString = idStringStream.str();
}
void Nektar::LibUtilities::FieldIO::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 
)

Imports an FLD file.

Definition at line 383 of file FieldIO.cpp.

References ASSERTL0, ImportFieldData(), ImportFieldDefs(), ImportFieldMetaData(), ImportMultiFldFileIDs(), Nektar::iterator, Nektar::NullInt1DArray, Nektar::LibUtilities::NullVectorNekDoubleVector, and Nektar::LibUtilities::PortablePath().

Referenced by Nektar::MultiRegions::ExpList::ExtractFileBCs(), and Nektar::LibUtilities::Import().

{
std::string infile = infilename;
fs::path pinfilename(infilename);
if(fs::is_directory(pinfilename)) // check to see that infile is a directory
{
fs::path infofile("Info.xml");
fs::path fullpath = pinfilename / infofile;
infile = PortablePath(fullpath);
std::vector<std::string> filenames;
std::vector<std::vector<unsigned int> > elementIDs_OnPartitions;
ImportMultiFldFileIDs(infile,filenames, elementIDs_OnPartitions,
fieldmetadatamap);
if(ElementIDs == NullInt1DArray) //load all fields
{
for(int i = 0; i < filenames.size(); ++i)
{
fs::path pfilename(filenames[i]);
fullpath = pinfilename / pfilename;
string fname = PortablePath(fullpath);
TiXmlDocument doc1(fname);
bool loadOkay1 = doc1.LoadFile();
std::stringstream errstr;
errstr << "Unable to load file: " << fname << std::endl;
errstr << "Reason: " << doc1.ErrorDesc() << std::endl;
errstr << "Position: Line " << doc1.ErrorRow() << ", Column " << doc1.ErrorCol() << std::endl;
ASSERTL0(loadOkay1, errstr.str());
ImportFieldDefs(doc1, fielddefs, false);
if(fielddata != NullVectorNekDoubleVector)
{
ImportFieldData(doc1, fielddefs, fielddata);
}
}
}
else // only load relevant partitions
{
int i,j;
map<int,vector<int> > FileIDs;
map<int,vector<int> >::iterator it;
set<int> LoadFile;
for(i = 0; i < elementIDs_OnPartitions.size(); ++i)
{
for(j = 0; j < elementIDs_OnPartitions[i].size(); ++j)
{
FileIDs[elementIDs_OnPartitions[i][j]].push_back(i);
}
}
for(i = 0; i < ElementIDs.num_elements(); ++i)
{
it = FileIDs.find(ElementIDs[i]);
if (it != FileIDs.end())
{
for (j = 0; j < it->second.size(); ++j)
{
LoadFile.insert(it->second[j]);
}
}
}
set<int>::iterator iter;
for(iter = LoadFile.begin(); iter != LoadFile.end(); ++iter)
{
fs::path pfilename(filenames[*iter]);
fullpath = pinfilename / pfilename;
string fname = PortablePath(fullpath);
TiXmlDocument doc1(fname);
bool loadOkay1 = doc1.LoadFile();
std::stringstream errstr;
errstr << "Unable to load file: " << fname << std::endl;
errstr << "Reason: " << doc1.ErrorDesc() << std::endl;
errstr << "Position: Line " << doc1.ErrorRow() << ", Column " << doc1.ErrorCol() << std::endl;
ASSERTL0(loadOkay1, errstr.str());
ImportFieldDefs(doc1, fielddefs, false);
if(fielddata != NullVectorNekDoubleVector)
{
ImportFieldData(doc1, fielddefs, fielddata);
}
}
}
}
else // serial format case
{
TiXmlDocument doc(infile);
bool loadOkay = doc.LoadFile();
std::stringstream errstr;
errstr << "Unable to load file: " << infile << std::endl;
errstr << "Reason: " << doc.ErrorDesc() << std::endl;
errstr << "Position: Line " << doc.ErrorRow() << ", Column " <<
doc.ErrorCol() << std::endl;
ASSERTL0(loadOkay, errstr.str());
ImportFieldMetaData(doc,fieldmetadatamap);
ImportFieldDefs(doc, fielddefs, false);
if(fielddata != NullVectorNekDoubleVector)
{
ImportFieldData(doc, fielddefs, fielddata);
}
}
}
void Nektar::LibUtilities::FieldIO::ImportFieldData ( TiXmlDocument &  doc,
const std::vector< FieldDefinitionsSharedPtr > &  fielddefs,
std::vector< std::vector< NekDouble > > &  fielddata 
)

Imports the data fileds.

Definition at line 947 of file FieldIO.cpp.

References ASSERTL0, CheckFieldDefinition(), and Inflate().

Referenced by Import().

{
int cntdumps = 0;
TiXmlHandle docHandle(&doc);
TiXmlElement* master = NULL; // Master tag within which all data is contained.
master = doc.FirstChildElement("NEKTAR");
ASSERTL0(master, "Unable to find NEKTAR tag in file.");
// Loop through all nektar tags, finding all of the element tags.
while (master)
{
TiXmlElement* element = master->FirstChildElement("ELEMENTS");
ASSERTL0(element, "Unable to find ELEMENTS tag within nektar tag.");
while (element)
{
// Extract the body, which the "data".
TiXmlNode* elementChild = element->FirstChild();
ASSERTL0(elementChild, "Unable to extract the data from the element tag.");
std::string elementStr;
while(elementChild)
{
if (elementChild->Type() == TiXmlNode::TEXT)
{
elementStr += elementChild->ToText()->ValueStr();
}
elementChild = elementChild->NextSibling();
}
// Convert from base64 to binary.
typedef boost::archive::iterators::transform_width<
boost::archive::iterators::binary_from_base64<
std::string::const_iterator>, 8, 6 > binary_t;
std::string vCompressed(binary_t(elementStr.begin()),
binary_t(elementStr.end()));
std::vector<NekDouble> elementFieldData;
ASSERTL0(Z_OK == Inflate(vCompressed, elementFieldData),
"Failed to decompress field data.");
fielddata.push_back(elementFieldData);
int datasize = CheckFieldDefinition(fielddefs[cntdumps]);
ASSERTL0(fielddata[cntdumps].size() == datasize*fielddefs[cntdumps]->m_fields.size(),"Input data is not the same length as header infoarmation");
cntdumps++;
element = element->NextSiblingElement("ELEMENTS");
}
master = master->NextSiblingElement("NEKTAR");
}
}
void Nektar::LibUtilities::FieldIO::ImportFieldDefs ( TiXmlDocument &  doc,
std::vector< FieldDefinitionsSharedPtr > &  fielddefs,
bool  expChild 
)

Imports the definition of the fields.

The bool decides if the FieldDefs are in <EXPANSIONS> or in <NEKTAR>.

Definition at line 697 of file FieldIO.cpp.

References ASSERTL0, ASSERTL1, Nektar::LibUtilities::BasisTypeMap, Nektar::ParseUtils::GenerateOrderedStringVector(), Nektar::ParseUtils::GenerateOrderedVector(), Nektar::ParseUtils::GenerateSeqVector(), Nektar::ParseUtils::GenerateUnOrderedVector(), Nektar::LibUtilities::kPointsTypeStr, Nektar::LibUtilities::ShapeTypeMap, Nektar::LibUtilities::SIZE_BasisType, Nektar::LibUtilities::SIZE_PointsType, and Nektar::LibUtilities::SIZE_ShapeType.

Referenced by Import(), and Nektar::SpatialDomains::MeshGraph::ReadExpansions().

{
TiXmlHandle docHandle(&doc);
TiXmlElement* master = NULL; // Master tag within which all data is contained.
master = doc.FirstChildElement("NEKTAR");
ASSERTL0(master, "Unable to find NEKTAR tag in file.");
std::string strLoop = "NEKTAR";
TiXmlElement* loopXml = master;
TiXmlElement *expansionTypes;
if(expChild)
{
expansionTypes = master->FirstChildElement("EXPANSIONS");
ASSERTL0(expansionTypes, "Unable to find EXPANSIONS tag in file.");
loopXml = expansionTypes;
strLoop = "EXPANSIONS";
}
// Loop through all nektar tags, finding all of the element tags.
while (loopXml)
{
TiXmlElement* element = loopXml->FirstChildElement("ELEMENTS");
ASSERTL0(element, "Unable to find ELEMENTS tag within nektar tag.");
while (element)
{
// Extract the attributes.
std::string idString;
std::string shapeString;
std::string basisString;
std::string homoLengthsString;
std::string homoZIDsString;
std::string homoYIDsString;
std::string numModesString;
std::string numPointsString;
std::string fieldsString;
std::string pointsString;
bool pointDef = false;
bool numPointDef = false;
TiXmlAttribute *attr = element->FirstAttribute();
while (attr)
{
std::string attrName(attr->Name());
if (attrName == "FIELDS")
{
fieldsString.insert(0, attr->Value());
}
else if (attrName == "SHAPE")
{
shapeString.insert(0, attr->Value());
}
else if (attrName == "BASIS")
{
basisString.insert(0, attr->Value());
}
else if (attrName == "HOMOGENEOUSLENGTHS")
{
homoLengthsString.insert(0,attr->Value());
}
else if (attrName == "HOMOGENEOUSZIDS")
{
homoZIDsString.insert(0,attr->Value());
}
else if (attrName == "HOMOGENEOUSYIDS")
{
homoYIDsString.insert(0,attr->Value());
}
else if (attrName == "NUMMODESPERDIR")
{
numModesString.insert(0, attr->Value());
}
else if (attrName == "ID")
{
idString.insert(0, attr->Value());
}
else if (attrName == "POINTSTYPE")
{
pointsString.insert(0, attr->Value());
pointDef = true;
}
else if (attrName == "NUMPOINTSPERDIR")
{
numPointsString.insert(0, attr->Value());
numPointDef = true;
}
else
{
std::string errstr("Unknown attribute: ");
errstr += attrName;
ASSERTL1(false, errstr.c_str());
}
// Get the next attribute.
attr = attr->Next();
}
// Check to see if homogeneous expansion and if so
// strip down the shapeString definition
int numHomoDir = 0;
size_t loc;
//---> This finds the first location of 'n'!
if((loc = shapeString.find_first_of("-"))!=string::npos)
{
if(shapeString.find("Exp1D")!=string::npos)
{
numHomoDir = 1;
}
else // HomogeneousExp1D
{
numHomoDir = 2;
}
shapeString.erase(loc,shapeString.length());
}
// Reconstruct the fielddefs.
std::vector<unsigned int> elementIds;
{
bool valid = ParseUtils::GenerateSeqVector(idString.c_str(), elementIds);
ASSERTL0(valid, "Unable to correctly parse the element ids.");
}
// Get the geometrical shape
ShapeType shape;
bool valid = false;
for (unsigned int j = 0; j < SIZE_ShapeType; j++)
{
if (ShapeTypeMap[j] == shapeString)
{
shape = (ShapeType) j;
valid = true;
break;
}
}
ASSERTL0(valid, std::string("Unable to correctly parse the shape type: ").append(shapeString).c_str());
// Get the basis
std::vector<std::string> basisStrings;
std::vector<BasisType> basis;
valid = ParseUtils::GenerateOrderedStringVector(basisString.c_str(), basisStrings);
ASSERTL0(valid, "Unable to correctly parse the basis types.");
for (std::vector<std::string>::size_type i = 0; i < basisStrings.size(); i++)
{
valid = false;
for (unsigned int j = 0; j < SIZE_BasisType; j++)
{
if (BasisTypeMap[j] == basisStrings[i])
{
basis.push_back((BasisType) j);
valid = true;
break;
}
}
ASSERTL0(valid, std::string("Unable to correctly parse the basis type: ").append(basisStrings[i]).c_str());
}
// Get homoLengths
std::vector<NekDouble> homoLengths;
if(numHomoDir)
{
valid = ParseUtils::GenerateUnOrderedVector(homoLengthsString.c_str(), homoLengths);
ASSERTL0(valid, "Unable to correctly parse the number of homogeneous lengths.");
}
// Get Homogeneous points IDs
std::vector<unsigned int> homoZIDs;
std::vector<unsigned int> homoYIDs;
if(numHomoDir == 1)
{
valid = ParseUtils::GenerateSeqVector(homoZIDsString.c_str(), homoZIDs);
ASSERTL0(valid, "Unable to correctly parse homogeneous planes IDs.");
}
if(numHomoDir == 2)
{
valid = ParseUtils::GenerateSeqVector(homoZIDsString.c_str(), homoZIDs);
ASSERTL0(valid, "Unable to correctly parse homogeneous lines IDs in z-direction.");
valid = ParseUtils::GenerateSeqVector(homoYIDsString.c_str(), homoYIDs);
ASSERTL0(valid, "Unable to correctly parse homogeneous lines IDs in y-direction.");
}
// Get points type
std::vector<PointsType> points;
if(pointDef)
{
std::vector<std::string> pointsStrings;
valid = ParseUtils::GenerateOrderedStringVector(pointsString.c_str(), pointsStrings);
ASSERTL0(valid, "Unable to correctly parse the points types.");
for (std::vector<std::string>::size_type i = 0; i < pointsStrings.size(); i++)
{
valid = false;
for (unsigned int j = 0; j < SIZE_PointsType; j++)
{
if (kPointsTypeStr[j] == pointsStrings[i])
{
points.push_back((PointsType) j);
valid = true;
break;
}
}
ASSERTL0(valid, std::string("Unable to correctly parse the points type: ").append(pointsStrings[i]).c_str());
}
}
// Get numModes
std::vector<unsigned int> numModes;
bool UniOrder = false;
if(strstr(numModesString.c_str(),"UNIORDER:"))
{
UniOrder = true;
}
valid = ParseUtils::GenerateOrderedVector(numModesString.c_str()+9, numModes);
ASSERTL0(valid, "Unable to correctly parse the number of modes.");
// Get numPoints
std::vector<unsigned int> numPoints;
if(numPointDef)
{
valid = ParseUtils::GenerateOrderedVector(numPointsString.c_str(), numPoints);
ASSERTL0(valid, "Unable to correctly parse the number of points.");
}
// Get fields names
std::vector<std::string> Fields;
valid = ParseUtils::GenerateOrderedStringVector(fieldsString.c_str(), Fields);
ASSERTL0(valid, "Unable to correctly parse the number of fields.");
FieldDefinitionsSharedPtr fielddef = MemoryManager<FieldDefinitions>::AllocateSharedPtr(shape, elementIds, basis, UniOrder, numModes, Fields, numHomoDir, homoLengths, homoZIDs, homoYIDs, points, pointDef, numPoints, numPointDef);
fielddefs.push_back(fielddef);
element = element->NextSiblingElement("ELEMENTS");
}
loopXml = loopXml->NextSiblingElement(strLoop);
}
}
void Nektar::LibUtilities::FieldIO::ImportFieldMetaData ( std::string  filename,
FieldMetaDataMap &  fieldmetadatamap 
)

Imports the definition of the meta data.

Definition at line 608 of file FieldIO.cpp.

References ASSERTL0.

Referenced by Import().

{
TiXmlDocument doc(filename);
bool loadOkay = doc.LoadFile();
std::stringstream errstr;
errstr << "Unable to load file: " << filename << std::endl;
errstr << "Reason: " << doc.ErrorDesc() << std::endl;
errstr << "Position: Line " << doc.ErrorRow() << ", Column " << doc.ErrorCol() << std::endl;
ASSERTL0(loadOkay, errstr.str());
ImportFieldMetaData(doc,fieldmetadatamap);
}
void Nektar::LibUtilities::FieldIO::ImportFieldMetaData ( TiXmlDocument &  doc,
FieldMetaDataMap &  fieldmetadatamap 
)

Imports the definition of the meta data.

Definition at line 624 of file FieldIO.cpp.

References ASSERTL0.

{
TiXmlHandle docHandle(&doc);
TiXmlElement* master = 0; // Master tag within which all data is contained.
TiXmlElement* metadata = 0;
master = doc.FirstChildElement("NEKTAR");
ASSERTL0(master, "Unable to find NEKTAR tag in file.");
std::string strLoop = "NEKTAR";
// Retain original metadata structure for backwards compatibility
// TODO: Remove old metadata format
metadata = master->FirstChildElement("FIELDMETADATA");
if(metadata)
{
TiXmlElement *param = metadata->FirstChildElement("P");
while (param)
{
TiXmlAttribute *paramAttr = param->FirstAttribute();
std::string attrName(paramAttr->Name());
std::string paramString;
if(attrName == "PARAM")
{
paramString.insert(0,paramAttr->Value());
}
else
{
ASSERTL0(false,"PARAM not provided as an attribute in FIELDMETADATA section");
}
// Now read body of param
std::string paramBodyStr;
TiXmlNode *paramBody = param->FirstChild();
paramBodyStr += paramBody->ToText()->Value();
fieldmetadatamap[paramString] = paramBodyStr;
param = param->NextSiblingElement("P");
}
}
// New metadata format
metadata = master->FirstChildElement("Metadata");
if(metadata)
{
TiXmlElement *param = metadata->FirstChildElement();
while (param)
{
std::string paramString = param->Value();
if (paramString != "Provenance")
{
// Now read body of param
TiXmlNode *paramBody = param->FirstChild();
std::string paramBodyStr = paramBody->ToText()->Value();
fieldmetadatamap[paramString] = paramBodyStr;
}
param = param->NextSiblingElement();
}
}
}
void Nektar::LibUtilities::FieldIO::ImportMultiFldFileIDs ( const std::string &  inFile,
std::vector< std::string > &  fileNames,
std::vector< std::vector< unsigned int > > &  elementList,
FieldMetaDataMap &  fieldmetadatamap 
)
private

Definition at line 548 of file FieldIO.cpp.

References ASSERTL0, and Nektar::ParseUtils::GenerateSeqVector().

Referenced by Import().

{
TiXmlDocument doc(inFile);
bool loadOkay = doc.LoadFile();
std::stringstream errstr;
errstr << "Unable to load file: " << inFile<< std::endl;
errstr << "Reason: " << doc.ErrorDesc() << std::endl;
errstr << "Position: Line " << doc.ErrorRow() << ", Column " << doc.ErrorCol() << std::endl;
ASSERTL0(loadOkay, errstr.str());
// Handle on XML document
TiXmlHandle docHandle(&doc);
// Retrieve main NEKTAR tag - XML specification states one
// top-level element tag per file.
TiXmlElement* master = doc.FirstChildElement("NEKTAR");
ASSERTL0(master, "Unable to find NEKTAR tag in file.");
// Partition element tag name
std::string strPartition = "Partition";
// First attempt to get the first Partition element
TiXmlElement* fldfileIDs = master->FirstChildElement(strPartition.c_str());
if (!fldfileIDs)
{
// If this files try previous name
strPartition = "MultipleFldFiles";
fldfileIDs = master->FirstChildElement("MultipleFldFiles");
}
ASSERTL0(fldfileIDs,
"Unable to find 'Partition' or 'MultipleFldFiles' tag "
"within nektar tag.");
while (fldfileIDs)
{
// Read file name of partition file
const char *attr = fldfileIDs->Attribute("FileName");
ASSERTL0(attr, "'FileName' not provided as an attribute of '"
+ strPartition + "' tag.");
fileNames.push_back(std::string(attr));
const char* elementIDs = fldfileIDs->GetText();
ASSERTL0(elementIDs, "Element IDs not specified.");
std::string elementIDsStr(elementIDs);
std::vector<unsigned int> idvec;
ParseUtils::GenerateSeqVector(elementIDsStr.c_str(),idvec);
elementList.push_back(idvec);
fldfileIDs = fldfileIDs->NextSiblingElement(strPartition.c_str());
}
}
int Nektar::LibUtilities::FieldIO::Inflate ( std::string &  in,
std::vector< NekDouble > &  out 
)
private

Decompress a zlib-compressed string into a vector of NekDouble values.

Definition at line 1274 of file FieldIO.cpp.

References ASSERTL0, CHUNK, and Nektar::void.

Referenced by ImportFieldData().

{
int ret;
unsigned have;
z_stream strm;
string buffer;
buffer.resize(CHUNK);
string output;
strm.zalloc = Z_NULL;
strm.zfree = Z_NULL;
strm.opaque = Z_NULL;
strm.avail_in = 0;
strm.next_in = Z_NULL;
ret = inflateInit(&strm);
ASSERTL0(ret == Z_OK, "Error initializing zlib decompression.");
strm.avail_in = in.size();
strm.next_in = (unsigned char*)(&in[0]);
do {
strm.avail_out = CHUNK;
strm.next_out = (unsigned char*)(&buffer[0]);
ret = inflate(&strm, Z_NO_FLUSH);
ASSERTL0(ret != Z_STREAM_ERROR, "Stream error occured.");
switch (ret) {
case Z_NEED_DICT:
ret = Z_DATA_ERROR; /* and fall through */
case Z_DATA_ERROR:
case Z_MEM_ERROR:
(void)inflateEnd(&strm);
return ret;
}
have = CHUNK - strm.avail_out;
output += buffer.substr(0, have);
} while (strm.avail_out == 0);
(void)inflateEnd(&strm);
if (ret == Z_STREAM_END)
{
NekDouble* readFieldData = (NekDouble*) output.c_str();
unsigned int len = output.size() * sizeof(*output.c_str())
/ sizeof(NekDouble);
out.assign( readFieldData, readFieldData + len);
return Z_OK;
}
else
{
return Z_DATA_ERROR;
}
}
std::string Nektar::LibUtilities::FieldIO::SetUpOutput ( const std::string  outname,
const std::vector< FieldDefinitionsSharedPtr > &  fielddefs,
const FieldMetaDataMap &  fieldmetadatamap 
)
private

Definition at line 1110 of file FieldIO.cpp.

References ASSERTL0, m_comm, Nektar::LibUtilities::PortablePath(), Nektar::LibUtilities::ReduceMax, and WriteMultiFldFileIDs().

Referenced by Write().

{
ASSERTL0(!outname.empty(), "Empty path given to SetUpOutput()");
int nprocs = m_comm->GetSize();
int rank = m_comm->GetRank();
// Directory name if in parallel, regular filename if in serial
fs::path specPath (outname);
// Remove any existing file which is in the way
if(m_comm->RemoveExistingFiles())
{
try
{
fs::remove_all(specPath);
}
catch (fs::filesystem_error& e)
{
ASSERTL0(e.code().value() == berrc::no_such_file_or_directory,
"Filesystem error: " + string(e.what()));
}
}
// serial processing just add ending.
if(nprocs == 1)
{
cout << "Writing: " << specPath << endl;
return LibUtilities::PortablePath(specPath);
}
// Compute number of elements on this process and share with other
// processes. Also construct list of elements on this process from
// available vector of field definitions.
std::vector<unsigned int> elmtnums(nprocs,0);
std::vector<unsigned int> idlist;
int i;
for (i = 0; i < fielddefs.size(); ++i)
{
elmtnums[rank] += fielddefs[i]->m_elementIDs.size();
idlist.insert(idlist.end(), fielddefs[i]->m_elementIDs.begin(),
fielddefs[i]->m_elementIDs.end());
}
m_comm->AllReduce(elmtnums,LibUtilities::ReduceMax);
// Create the destination directory
try
{
fs::create_directory(specPath);
}
catch (fs::filesystem_error& e)
{
ASSERTL0(false, "Filesystem error: " + string(e.what()));
}
// Collate per-process element lists on root process to generate
// the info file.
if (rank == 0)
{
std::vector<std::vector<unsigned int> > ElementIDs(nprocs);
// Populate the list of element ID lists from all processes
ElementIDs[0] = idlist;
for (i = 1; i < nprocs; ++i)
{
std::vector<unsigned int> tmp(elmtnums[i]);
m_comm->Recv(i, tmp);
ElementIDs[i] = tmp;
}
// Set up output names
std::vector<std::string> filenames;
for(int i = 0; i < nprocs; ++i)
{
boost::format pad("P%1$07d.fld");
pad % i;
filenames.push_back(pad.str());
}
// Write the Info.xml file
string infofile = LibUtilities::PortablePath(
specPath / fs::path("Info.xml"));
cout << "Writing: " << specPath << endl;
WriteMultiFldFileIDs(infofile, filenames, ElementIDs,
fieldmetadatamap);
}
else
{
// Send this process's ID list to the root process
m_comm->Send(0, idlist);
}
// Pad rank to 8char filenames, e.g. P0000000.fld
boost::format pad("P%1$07d.fld");
pad % m_comm->GetRank();
// Generate full path name
fs::path poutfile(pad.str());
fs::path fulloutname = specPath / poutfile;
// Return the full path to the partition for this process
return LibUtilities::PortablePath(fulloutname);
}
void Nektar::LibUtilities::FieldIO::Write ( const std::string &  outFile,
std::vector< FieldDefinitionsSharedPtr > &  fielddefs,
std::vector< std::vector< NekDouble > > &  fielddata,
const FieldMetaDataMap &  fieldinfomap = NullFieldMetaDataMap 
)

Write data in FLD format.

Definition at line 150 of file FieldIO.cpp.

References AddInfoTag(), ASSERTL0, ASSERTL1, Nektar::LibUtilities::BasisTypeMap, CheckFieldDefinition(), Deflate(), GenerateSeqString(), SetUpOutput(), and Nektar::LibUtilities::ShapeTypeMap.

Referenced by main(), and Nektar::LibUtilities::Write().

{
// Check everything seems sensible
ASSERTL1(fielddefs.size() == fielddata.size(),
"Length of fielddefs and fielddata incompatible");
for (int f = 0; f < fielddefs.size(); ++f)
{
ASSERTL1(fielddata[f].size() > 0,
"Fielddata vector must contain at least one value.");
ASSERTL1(fielddata[f].size() ==
fielddefs[f]->m_fields.size() *
CheckFieldDefinition(fielddefs[f]),
"Invalid size of fielddata vector.");
}
// Prepare to write out data. In parallel, we must create directory
// and determine the full pathname to the file to write out.
// Any existing file/directory which is in the way is removed.
std::string filename = SetUpOutput(outFile, fielddefs, fieldmetadatamap);
// Create the file (partition)
TiXmlDocument doc;
TiXmlDeclaration * decl = new TiXmlDeclaration("1.0", "utf-8", "");
doc.LinkEndChild(decl);
TiXmlElement * root = new TiXmlElement("NEKTAR");
doc.LinkEndChild(root);
AddInfoTag(root,fieldmetadatamap);
for (int f = 0; f < fielddefs.size(); ++f)
{
//---------------------------------------------
// Write ELEMENTS
TiXmlElement * elemTag = new TiXmlElement("ELEMENTS");
root->LinkEndChild(elemTag);
// Write FIELDS
std::string fieldsString;
{
std::stringstream fieldsStringStream;
bool first = true;
for (std::vector<int>::size_type i = 0; i
< fielddefs[f]->m_fields.size(); i++)
{
if (!first)
fieldsStringStream << ",";
fieldsStringStream << fielddefs[f]->m_fields[i];
first = false;
}
fieldsString = fieldsStringStream.str();
}
elemTag->SetAttribute("FIELDS", fieldsString);
// Write SHAPE
std::string shapeString;
{
std::stringstream shapeStringStream;
shapeStringStream << ShapeTypeMap[fielddefs[f]->m_shapeType];
if(fielddefs[f]->m_numHomogeneousDir == 1)
{
shapeStringStream << "-HomogenousExp1D";
}
else if (fielddefs[f]->m_numHomogeneousDir == 2)
{
shapeStringStream << "-HomogenousExp2D";
}
shapeString = shapeStringStream.str();
}
elemTag->SetAttribute("SHAPE", shapeString);
// Write BASIS
std::string basisString;
{
std::stringstream basisStringStream;
bool first = true;
for (std::vector<BasisType>::size_type i = 0; i < fielddefs[f]->m_basis.size(); i++)
{
if (!first)
basisStringStream << ",";
basisStringStream
<< BasisTypeMap[fielddefs[f]->m_basis[i]];
first = false;
}
basisString = basisStringStream.str();
}
elemTag->SetAttribute("BASIS", basisString);
// Write homogeneuous length details
if(fielddefs[f]->m_numHomogeneousDir)
{
std::string homoLenString;
{
std::stringstream homoLenStringStream;
bool first = true;
for (int i = 0; i < fielddefs[f]->m_numHomogeneousDir; ++i)
{
if (!first)
homoLenStringStream << ",";
homoLenStringStream
<< fielddefs[f]->m_homogeneousLengths[i];
first = false;
}
homoLenString = homoLenStringStream.str();
}
elemTag->SetAttribute("HOMOGENEOUSLENGTHS", homoLenString);
}
// Write homogeneuous planes/lines details
if(fielddefs[f]->m_numHomogeneousDir)
{
if(fielddefs[f]->m_homogeneousYIDs.size() > 0)
{
std::string homoYIDsString;
{
std::stringstream homoYIDsStringStream;
bool first = true;
for(int i = 0; i < fielddefs[f]->m_homogeneousYIDs.size(); i++)
{
if (!first)
homoYIDsStringStream << ",";
homoYIDsStringStream << fielddefs[f]->m_homogeneousYIDs[i];
first = false;
}
homoYIDsString = homoYIDsStringStream.str();
}
elemTag->SetAttribute("HOMOGENEOUSYIDS", homoYIDsString);
}
if(fielddefs[f]->m_homogeneousZIDs.size() > 0)
{
std::string homoZIDsString;
{
std::stringstream homoZIDsStringStream;
bool first = true;
for(int i = 0; i < fielddefs[f]->m_homogeneousZIDs.size(); i++)
{
if (!first)
homoZIDsStringStream << ",";
homoZIDsStringStream << fielddefs[f]->m_homogeneousZIDs[i];
first = false;
}
homoZIDsString = homoZIDsStringStream.str();
}
elemTag->SetAttribute("HOMOGENEOUSZIDS", homoZIDsString);
}
}
// Write NUMMODESPERDIR
std::string numModesString;
{
std::stringstream numModesStringStream;
if (fielddefs[f]->m_uniOrder)
{
numModesStringStream << "UNIORDER:";
// Just dump single definition
bool first = true;
for (std::vector<int>::size_type i = 0; i
< fielddefs[f]->m_basis.size(); i++)
{
if (!first)
numModesStringStream << ",";
numModesStringStream << fielddefs[f]->m_numModes[i];
first = false;
}
}
else
{
numModesStringStream << "MIXORDER:";
bool first = true;
for (std::vector<int>::size_type i = 0; i
< fielddefs[f]->m_numModes.size(); i++)
{
if (!first)
numModesStringStream << ",";
numModesStringStream << fielddefs[f]->m_numModes[i];
first = false;
}
}
numModesString = numModesStringStream.str();
}
elemTag->SetAttribute("NUMMODESPERDIR", numModesString);
// Write ID
// Should ideally look at ways of compressing this stream
// if just sequential;
std::string idString;
{
std::stringstream idStringStream;
GenerateSeqString(fielddefs[f]->m_elementIDs,idString);
}
elemTag->SetAttribute("ID", idString);
std::string compressedDataString;
ASSERTL0(Z_OK == Deflate(fielddata[f], compressedDataString),
"Failed to compress field data.");
// If the string length is not divisible by 3,
// pad it. There is a bug in transform_width
// that will make it reference past the end
// and crash.
switch (compressedDataString.length() % 3)
{
case 1:
compressedDataString += '\0';
case 2:
compressedDataString += '\0';
break;
}
// Convert from binary to base64.
typedef boost::archive::iterators::base64_from_binary<
boost::archive::iterators::transform_width<
std::string::const_iterator, 6, 8> > base64_t;
std::string base64string(base64_t(compressedDataString.begin()),
base64_t(compressedDataString.end()));
elemTag->LinkEndChild(new TiXmlText(base64string));
}
doc.SaveFile(filename);
}
void Nektar::LibUtilities::FieldIO::WriteMultiFldFileIDs ( const std::string &  outfile,
const std::vector< std::string >  fileNames,
std::vector< std::vector< unsigned int > > &  elementList,
const FieldMetaDataMap &  fieldinfomap = NullFieldMetaDataMap 
)

Definition at line 508 of file FieldIO.cpp.

References AddInfoTag(), ASSERTL0, and GenerateSeqString().

Referenced by SetUpOutput().

{
TiXmlDocument doc;
TiXmlDeclaration * decl = new TiXmlDeclaration("1.0", "utf-8", "");
doc.LinkEndChild(decl);
ASSERTL0(fileNames.size() == elementList.size(),"Outfile names and list of elements ids does not match");
TiXmlElement * root = new TiXmlElement("NEKTAR");
doc.LinkEndChild(root);
AddInfoTag(root,fieldmetadatamap);
for (int t = 0; t < fileNames.size(); ++t)
{
if(elementList[t].size())
{
TiXmlElement * elemIDs = new TiXmlElement("Partition");
root->LinkEndChild(elemIDs);
elemIDs->SetAttribute("FileName",fileNames[t]);
string IDstring;
GenerateSeqString(elementList[t],IDstring);
elemIDs->LinkEndChild(new TiXmlText(IDstring));
}
}
doc.SaveFile(outFile);
}

Member Data Documentation

LibUtilities::CommSharedPtr Nektar::LibUtilities::FieldIO::m_comm
private

Communicator to use when writing parallel format.

Definition at line 204 of file FieldIO.h.

Referenced by SetUpOutput().

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