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////////////////////////////////////////////////////////////////////////////////
//
// File: FieldIO.cpp
//
// For more information, please see: http://www.nektar.info/
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: I/O routines relating to Fields
//
////////////////////////////////////////////////////////////////////////////////
#include <boost/date_time/posix_time/posix_time.hpp>
#include <boost/date_time/posix_time/posix_time_io.hpp>
#include <boost/asio/ip/host_name.hpp>
#include <LibUtilities/BasicUtils/FieldIO.h>
#include <LibUtilities/BasicUtils/FileSystem.h>
#include <LibUtilities/BasicConst/GitRevision.h>
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#include "zlib.h"
#include <set>
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#ifdef NEKTAR_USE_MPI
#include <mpi.h>
#endif
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// Buffer size for zlib compression/decompression
#define CHUNK 16384
#ifndef NEKTAR_VERSION
#define NEKTAR_VERSION "Unknown"
#endif
namespace ptime = boost::posix_time;
namespace ip = boost::asio::ip;
namespace Nektar
{
namespace LibUtilities
{
/**
* This function allows for data to be written to an FLD file when a
* session and/or communicator is not instantiated. Typically used in
* utilities which do not take XML input and operate in serial only.
*/
void Write( const std::string &outFile,
std::vector<FieldDefinitionsSharedPtr> &fielddefs,
std::vector<std::vector<NekDouble> > &fielddata,
const FieldMetaDataMap &fieldinfomap)
#ifdef NEKTAR_USE_MPI
int size;
MPI_Comm_size( MPI_COMM_WORLD, &size );
ASSERTL0(size == 1, "This function is not available in parallel.");
CommSharedPtr c = GetCommFactory().CreateInstance("Serial", 0, 0);
FieldIO f(c);
f.Write(outFile, fielddefs, fielddata, fieldinfomap);
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}
/**
* This function allows for data to be imported from an FLD file when
* a session and/or communicator is not instantiated. Typically used in
* utilities which only operate in serial.
*/
LIB_UTILITIES_EXPORT void Import(
const std::string& infilename,
std::vector<FieldDefinitionsSharedPtr> &fielddefs,
std::vector<std::vector<NekDouble> > &fielddata,
FieldMetaDataMap &fieldinfomap,
const Array<OneD, int> ElementiDs)
{
#ifdef NEKTAR_USE_MPI
int size;
MPI_Comm_size( MPI_COMM_WORLD, &size );
ASSERTL0(size == 1, "This function is not available in parallel.");
#endif
CommSharedPtr c = GetCommFactory().CreateInstance("Serial", 0, 0);
FieldIO f(c);
f.Import(infilename, fielddefs, fielddata, fieldinfomap, ElementiDs);
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}
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*
*/
FieldIO::FieldIO(
LibUtilities::CommSharedPtr pComm)
: m_comm(pComm)
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{
}
/**
*
*/
void FieldIO::Write(const std::string &outFile,
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std::vector<FieldDefinitionsSharedPtr> &fielddefs,
std::vector<std::vector<NekDouble> > &fielddata,
const FieldMetaDataMap &fieldmetadatamap)
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{
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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.");
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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)
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TiXmlDocument doc;
TiXmlDeclaration * decl = new TiXmlDeclaration("1.0", "utf-8", "");
doc.LinkEndChild(decl);
cout << "Writing outfile: " << filename << endl;
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TiXmlElement * root = new TiXmlElement("NEKTAR");
doc.LinkEndChild(root);
AddInfoTag(root,fieldmetadatamap);
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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;
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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)
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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));
}
}
/**
*
*/
void FieldIO::Import(const std::string& infilename,
std::vector<FieldDefinitionsSharedPtr> &fielddefs,
std::vector<std::vector<NekDouble> > &fielddata,
FieldMetaDataMap &fieldmetadatamap,
const Array<OneD, int> ElementIDs)
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);
ImportFieldData(doc1, fielddefs, fielddata);
}
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}
else // only load relevant partitions
{
int i,j;
map<int,int> FileIDs;
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]] = i;
}
}
for(i = 0; i < ElementIDs.num_elements(); ++i)
{
ASSERTL1(FileIDs.count(ElementIDs[i]) != 0,
"ElementIDs not found in partitions");
LoadFile.insert(FileIDs[ElementIDs[i]]);
}
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);
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);
ImportFieldData(doc, fielddefs, fielddata);
}
}
/**
*
*/
void FieldIO::WriteMultiFldFileIDs(const std::string &outFile,
const std::vector<std::string> fileNames,
std::vector<std::vector<unsigned int> > &elementList,
const FieldMetaDataMap &fieldmetadatamap)
{
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");
cout << "Writing multi-file data: " << outFile << endl;
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TiXmlElement * root = new TiXmlElement("NEKTAR");
doc.LinkEndChild(root);
AddInfoTag(root,fieldmetadatamap);
for (int t = 0; t < fileNames.size(); ++t)
{
ASSERTL1(elementList[t].size() > 0,
"Element list must contain at least one value.");
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);
}
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/**
*
*/
void FieldIO::ImportMultiFldFileIDs(const std::string &inFile,
std::vector<std::string> &fileNames,
std::vector<std::vector<unsigned int> > &elementList,
FieldMetaDataMap &fieldmetadatamap)
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());
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)
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// 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());
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void FieldIO::ImportFieldMetaData(std::string filename,
FieldMetaDataMap &fieldmetadatamap)
{
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 FieldIO::ImportFieldMetaData(TiXmlDocument &doc,
FieldMetaDataMap &fieldmetadatamap)
{
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();
}
/**
* The bool decides if the FieldDefs are in <EXPANSIONS> or in <NEKTAR>.
*/
void FieldIO::ImportFieldDefs(TiXmlDocument &doc, std::vector<FieldDefinitionsSharedPtr> &fielddefs,
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bool expChild)
{
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 FieldIO::ImportFieldData(TiXmlDocument &doc, const std::vector<FieldDefinitionsSharedPtr> &fielddefs, std::vector<std::vector<NekDouble> > &fielddata)
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{
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;
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committed
std::string vCompressed(binary_t(elementStr.begin()),
binary_t(elementStr.end()));
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committed
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");
}
}
/**
* \brief add information about provenance and fieldmetadata
*/
void FieldIO::AddInfoTag(TiXmlElement * root,
const FieldMetaDataMap &fieldmetadatamap)
{
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
ProvenanceMap["GitSHA1"] = NekConstants::kGitSha1;
ProvenanceMap["GitBranch"] = NekConstants::kGitBranch;
TiXmlElement * infoTag = new TiXmlElement("Metadata");
root->LinkEndChild(infoTag);
TiXmlElement * v;
FieldMetaDataMap::const_iterator infoit;