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Merge pull request #95 from PhasicFlow/develop 

pFlowToVTK enhanced
This commit is contained in:
Hamidreza Norouzi 2024-03-30 19:08:56 +03:30 committed by GitHub
parent cab49ef036 ef0e752929
commit 89c7be0a20
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
15 changed files with 898 additions and 789 deletions
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10
src/phasicFlow/fileSystem/fileSystem.cpp
View File

@ -33,7 +33,6 @@ bool pFlow::fileSystem::checkFileName(const word& name)
"Invalid file name supplied " << name <<
"the following characters are not allowd: " <<
notPermittedCharsFile << endl;
fatalExit;
return false;
}
@ -57,9 +56,9 @@ pFlow::fileSystem::fileSystem( const word& dir, const word& file)
{
isDir_ = file.empty();
if( !isDir_)
if( !isDir_ && !checkFileName(file))
{
checkFileName(file);
fatalExit;
}
try
@ -240,7 +239,10 @@ pFlow::fileSystem pFlow::fileSystem::operator()
void pFlow::fileSystem::operator += (const word& fileName)
{
checkFileName(fileName);
if(!checkFileName(fileName))
{
fatalExit;
}
if( isDir())
{

25
src/phasicFlow/streams/Fstream/fileStream.cpp
View File

@ -69,14 +69,31 @@ void pFlow::fileStream::openOutFile
}
if(binary_)
{
if(append_)
{
outStream_ = makeUnique< std::ofstream>(
path.wordPath(), std::ios_base::out| std::ios::binary|std::ios::app);
}
else
{
outStream_ = makeUnique< std::ofstream>(
path.wordPath(), std::ios_base::out| std::ios::binary);
}
}
else
{
if(append_)
{
outStream_ = makeUnique< std::ofstream>(
path.wordPath(), std::ios_base::out|std::ios::app);
}
else
{
outStream_ = makeUnique< std::ofstream>(
path.wordPath(), std::ios_base::out);
}
}
if(!outStream_->is_open())
{
@ -103,12 +120,14 @@ pFlow::fileStream::fileStream
(
const fileSystem& path,
bool outStream,
bool binary
bool binary,
bool append
)
:
inStream_(nullptr),
outStream_(nullptr),
binary_(binary)
binary_(binary),
append_(append)
{
if(outStream)

4
src/phasicFlow/streams/Fstream/fileStream.hpp
View File

@ -52,6 +52,8 @@ protected:
bool binary_ = false;
bool append_ = false;
/// open input file
void openInFile(const fileSystem& path);
@ -66,7 +68,7 @@ public:
//// - Constructors
/// From file path and input type and format.
fileStream( const fileSystem& path, bool outStream = false, bool binary = false);
fileStream( const fileSystem& path, bool outStream = false, bool binary = false, bool append = false);
/// No copy
fileStream(const fileStream&)= delete;

4
src/phasicFlow/streams/Fstream/oFstream.cpp
View File

@ -22,9 +22,9 @@ Licence:
#include "oFstream.hpp"
pFlow::oFstream::oFstream (const fileSystem& path, bool binary)
pFlow::oFstream::oFstream (const fileSystem& path, bool binary, bool append)
:
fileStream(path, true, binary),
fileStream(path, true, binary, append),
Ostream
(
fileStream::outStream(),

2
src/phasicFlow/streams/Fstream/oFstream.hpp
View File

@ -45,7 +45,7 @@ public:
//// - Constructors
/// From file path and format
oFstream (const fileSystem& path, bool binary = false);
oFstream (const fileSystem& path, bool binary = false, bool append = false);
/// No copy constructor
oFstream( const oFstream& src) = delete;

15
utilities/Utilities/vtkFile/vtkFile.cpp
View File

@ -21,11 +21,14 @@ Licence:
#include "vtkFile.hpp"
bool pFlow::vtkFile::openStream()
bool pFlow::vtkFile::openStream(bool wHeader)
{
oStream_ = makeUnique<oFstream>( fileName() );
oStream_ = makeUnique<oFstream>( fileName(), false, append_ );
if( !oStream_ )return false;
if(wHeader)
return writeHeader();
else
return true;
}
bool pFlow::vtkFile::vtkFile::writeHeader()
@ -49,15 +52,17 @@ pFlow::vtkFile::vtkFile
(
const fileSystem dir,
const word& bName,
real time
real time,
bool append
)
:
dirPath_(dir),
baseName_(bName),
time_(time)
time_(time),
append_(append)
{
if(!openStream())
if(!openStream(!append))
{
fatalErrorInFunction <<
" error in creating vtkFile "<<fileName()<<endl;

12
utilities/Utilities/vtkFile/vtkFile.hpp
View File

@ -40,15 +40,21 @@ protected:
real time_ = 0.0;
bool append_=false;
uniquePtr<oFstream> oStream_= nullptr;
bool openStream();
bool openStream(bool wHeader);
virtual bool writeHeader();
public:
vtkFile(const fileSystem dir, const word& bName, real time);
vtkFile(
const fileSystem dir,
const word& bName,
real time,
bool append = false);
virtual ~vtkFile() = default;
@ -56,7 +62,7 @@ public:
{
if(!oStream_)
{
if(!openStream())
if(!openStream(!append_))
{
fatalErrorInFunction<<
" error in opening vtkFile "<< fileName() <<endl;

2
utilities/pFlowToVTK/CMakeLists.txt
View File

@ -1,5 +1,7 @@
set(source_files
pointFieldToVTK.cpp
triSurfaceFieldToVTK.cpp
pFlowToVTK.cpp
#geometric.cpp
)

87
utilities/pFlowToVTK/geometric.cpp
View File

@ -1,87 +0,0 @@
/*------------------------------- phasicFlow ---------------------------------
O C enter of
O O E ngineering and
O O M ultiscale modeling of
OOOOOOO F luid flow
------------------------------------------------------------------------------
Copyright (C): www.cemf.ir
email: hamid.r.norouzi AT gmail.com
------------------------------------------------------------------------------
Licence:
This file is part of phasicFlow code. It is a free software for simulating
granular and multiphase flows. You can redistribute it and/or modify it under
the terms of GNU General Public License v3 or any other later versions.
phasicFlow is distributed to help others in their research in the field of
granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-----------------------------------------------------------------------------*/
#include "geometric.hpp"
template<>
bool pFlow::dataToVTK( vtkFile& vtk, const triSurface& surface )
{
auto nP = surface.numPoints();
auto hPoints = surface.points().hostVector();
vtk() << "DATASET POLYDATA" << endl;
vtk() << "POINTS " << nP << " float" << endl;
for ( auto i=0; i<nP; i++ )
{
vtk() << hPoints[i].x() << " " << hPoints[i].y() << " " << hPoints[i].z() << endl;
if (!vtk) return false;
}
auto nV = surface.numTriangles();
auto hVertices = surface.vertices().hostVector();
vtk() << "POLYGONS " << nV << " " << 4*nV << endl;
for(auto i=0; i<nV; i++)
{
vtk()<< 3 <<" "<< hVertices[i].x() << " " << hVertices[i].y() <<" "<<hVertices[i].z()<<endl;
if (!vtk) return false;
}
return true;
}
template<>
bool pFlow::dataToVTK( vtkFile& vtk, const multiTriSurface& surface )
{
auto nP = surface.numPoints();
auto hPoints = surface.points().hostVector();
vtk() << "DATASET POLYDATA" << endl;
vtk() << "POINTS " << nP << " float" << endl;
for ( auto i=0; i<nP; i++ )
{
vtk() << hPoints[i].x() << " " << hPoints[i].y() << " " << hPoints[i].z() << endl;
if (!vtk) return false;
}
auto nV = surface.numTriangles();
auto hVertices = surface.vertices().hostVector();
vtk() << "POLYGONS " << nV << " " << 4*nV << endl;
for(auto i=0; i<nV; i++)
{
vtk()<< 3 <<" "<< hVertices[i].x() << " " << hVertices[i].y() <<" "<<hVertices[i].z()<<endl;
if (!vtk) return false;
}
return true;
}

78
utilities/pFlowToVTK/geometric.hpp
View File

@ -1,78 +0,0 @@
/*------------------------------- phasicFlow ---------------------------------
O C enter of
O O E ngineering and
O O M ultiscale modeling of
OOOOOOO F luid flow
------------------------------------------------------------------------------
Copyright (C): www.cemf.ir
email: hamid.r.norouzi AT gmail.com
------------------------------------------------------------------------------
Licence:
This file is part of phasicFlow code. It is a free software for simulating
granular and multiphase flows. You can redistribute it and/or modify it under
the terms of GNU General Public License v3 or any other later versions.
phasicFlow is distributed to help others in their research in the field of
granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-----------------------------------------------------------------------------*/
#ifndef __geometric_hpp__
#define __geometric_hpp__
#include "vtkFile.hpp"
#include "triSurface.hpp"
#include "multiTriSurface.hpp"
#include "IOobject.hpp"
namespace pFlow
{
template<typename ObjType>
bool geomObjectToVTK(IOfileHeader& header, real time, fileSystem destPath, word bName)
{
if( ObjType::TYPENAME() != header.objectType() )return false;
auto ioObjPtr = IOobject::make<ObjType>(header);
auto& data = ioObjPtr().template getObject<ObjType>();
vtkFile vtk(destPath, bName, time);
if(!vtk) return false;
REPORT(1)<<"Converting geometry to vtk."<<endREPORT;
if(!dataToVTK(vtk, data) )
{
fatalErrorInFunction<<
" error in writing object "<<ioObjPtr().typeName() << " to folder " << destPath<<endl;
fatalExit;
}
return true;
}
template<typename Type>
bool dataToVTK(vtkFile& vtk, const Type& dataEntity)
{
fatalErrorInFunction<<
"not implemented function!";
fatalExit;
return false;
}
template<>
bool dataToVTK( vtkFile& vtk, const triSurface& surface );
template<>
bool dataToVTK( vtkFile& vtk, const multiTriSurface& surface );
}
#endif //__geometric_hpp__

28
utilities/pFlowToVTK/pFlowToVTK.cpp
View File

@ -26,7 +26,7 @@ Licence:
#include "Vectors.hpp"
#include "phasicFlowKokkos.hpp"
#include "pointFieldToVTK.hpp"
//#include "triSurfaceFieldToVTK.hpp"
#include "triSurfaceFieldToVTK.hpp"
//#include "readControlDict.hpp"
@ -60,10 +60,10 @@ int main(int argc, char** argv )
"path");
bool separateSurfaces = false;
cmds.addOption(
cmds.add_flag(
"-s,--separate-surfaces",
separateSurfaces,
"surfaces in the geometry are converted separatedly");
"use this when you want to have sub-surfaces in separate files");
wordVector fields;
bool allFields = true;
@ -78,7 +78,7 @@ int main(int argc, char** argv )
"a space separated lists of time folders, or a strided range begin:stride:end, or an interval begin:end",
" ");
bool isCoupling = false;
//bool isCoupling = false;
if(!cmds.parse(argc, argv)) return 0;
@ -88,8 +88,8 @@ int main(int argc, char** argv )
timeFolder folders(Control);
fileSystem destFolder = fileSystem(outFolder)/word(geometryFolder__);
fileSystem destFolderField = fileSystem(outFolder);
auto destFolder = fileSystem(outFolder)/word(geometryFolder__);
auto destFolderField = fileSystem(outFolder);
wordList geomfiles{"triSurface"};
@ -117,15 +117,16 @@ int main(int argc, char** argv )
if( !validRange.isMember( folders.time() ) )continue;
output<< "time: " << Cyan_Text( folders.time() )<<" s" <<endl;
/*if(!noGoem)
if(!noGoem)
{
fileSystem geomFolder = folders.folder()/geometryFolder__;
if(!pFlow::TSFtoVTK::convertTimeFolderTriSurfaceFields(geomFolder, folders.time(), destFolder, "surface"))
if(!pFlow::TSFtoVTK::convertTimeFolderTriSurfaceFields(
Control, destFolder, "surface", separateSurfaces))
{
fatalExit;
return 1;
}
}*/
}
if(!noParticle)
{
@ -141,9 +142,8 @@ int main(int argc, char** argv )
}
}else
{
/*if(!pFlow::PFtoVTK::convertTimeFolderPointFieldsSelected(
folders.folder(),
folders.time(),
if(!pFlow::PFtoVTK::convertTimeFolderPointFieldsSelected(
Control,
destFolderField,
"sphereFields",
fields,
@ -151,7 +151,7 @@ int main(int argc, char** argv )
)
{
fatalExit;
}*/
}
}
}

332
utilities/pFlowToVTK/pointFieldToVTK.cpp Normal file
View File

@ -0,0 +1,332 @@
#include <regex>
#include "vtkFile.hpp"
#include "vocabs.hpp"
#include "pointFieldToVTK.hpp"
bool pFlow::PFtoVTK::convertTimeFolderPointFields(
systemControl &control,
const fileSystem &destPath,
const word &bName)
{
fileSystem timeFolder = control.time().path();
// check if pointStructure exist in this folder
IOfileHeader pStructHeader(
objectFile(
pointStructureFile__,
timeFolder,
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS));
if (!pStructHeader.headerOk(true))
{
output << yellowColor << "Time folder " <<
control.time().path() << " does not contain any pStructure data file."<<
" Skipping this folder . . ."<< defaultColor << nl;
return true;
}
vtkFile vtk(destPath, bName, control.time().currentTime());
if (!vtk)
return false;
auto pStruct = pointStructure(control);
// get a list of files in this timeFolder;
auto posVec = pStruct.pointPositionHost();
auto *pos = posVec.data();
REPORT(1) << "Writing pointStructure to vtk file with " <<
Yellow_Text(pStruct.numActive())<<
" active particles" << END_REPORT;
addUndstrcuturedGridField(
vtk(),
pos,
pStruct.numActive());
auto fileList = containingFiles(timeFolder);
for (const auto &file : fileList)
{
IOfileHeader fieldHeader(
objectFile(
file.fileName(),
file.dirPath(),
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS));
if (fieldHeader.headerOk(true))
{
if(
convertRealx3TypePointField(vtk(), fieldHeader, pStruct) ||
convertRealTypePointField(vtk(), fieldHeader, pStruct) ||
convertIntPointField<uint32>(vtk(), fieldHeader, pStruct) ||
convertIntPointField<uint64>(vtk(), fieldHeader, pStruct) ||
convertIntPointField<int32>(vtk(), fieldHeader, pStruct) ||
convertIntPointField<int64>(vtk(), fieldHeader, pStruct)||
fieldHeader.objectName() == pointStructureFile__ )
{
continue;
}
else
{
WARNING << " This object type, " <<
fieldHeader.objectType() << " is not supported" <<
END_WARNING;
}
}
output << endl;
}
return true;
}
bool pFlow::PFtoVTK::convertTimeFolderPointFieldsSelected(
systemControl &control,
const fileSystem &destPath,
const word &bName,
const wordVector &fieldsName,
bool mustExist)
{
fileSystem timeFolder = control.time().path();
// check if pointStructure exist in this folder
IOfileHeader pStructHeader(
objectFile(
pointStructureFile__,
timeFolder,
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS));
if (!pStructHeader.headerOk(true))
{
output << yellowColor << "Time folder " <<
control.time().path() <<
" does not contain any pStructure data file."<<
" Skipping this folder . . ."<< defaultColor << nl;
return true;
}
vtkFile vtk(destPath, bName, control.time().currentTime());
if (!vtk)
return false;
auto pStruct = pointStructure(control);
// get a list of files in this timeFolder;
auto posVec = pStruct.pointPositionHost();
auto *pos = posVec.data();
REPORT(1) << "Writing pointStructure to vtk file with " <<
Yellow_Text(pStruct.numActive())
<< " active particles" << END_REPORT;
addUndstrcuturedGridField(
vtk(),
pos,
pStruct.numActive());
auto fileList = containingFiles(timeFolder);
for (const auto &fname : fieldsName)
{
fileSystem fieldAddress = timeFolder + fname;
IOfileHeader fieldHeader(
objectFile(
fname,
timeFolder,
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS));
if (fieldHeader.headerOk(true))
{
if (
convertRealx3TypePointField(vtk(), fieldHeader, pStruct) ||
convertRealTypePointField(vtk(), fieldHeader, pStruct) ||
convertIntPointField<uint32>(vtk(), fieldHeader, pStruct) ||
convertIntPointField<uint64>(vtk(), fieldHeader, pStruct) ||
convertIntPointField<int32>(vtk(), fieldHeader, pStruct) ||
convertIntPointField<int64>(vtk(), fieldHeader, pStruct) ||
fieldHeader.objectName() == pointStructureFile__ )
{
continue;
}
else
{
WARNING << " This object type, " <<
fieldHeader.objectType() << " is not supported" <<
END_WARNING;
}
}
else
{
if (mustExist)
{
fatalErrorInFunction << "Field " << fieldAddress <<
" does not exist." << endl;
return false;
}
else
{
REPORT(1) << "Could not find " << Yellow_Text(fieldAddress) <<
". Skipping this field . . ." << END_REPORT;
}
}
}
return true;
}
bool pFlow::PFtoVTK::addUndstrcuturedGridField(
iOstream &os,
realx3 *position,
uint32 numPoints)
{
os << "DATASET UNSTRUCTURED_GRID\n";
os << "POINTS " << numPoints << " float\n";
if (numPoints == 0)
return true;
for (uint32 i = 0; i < numPoints; i++)
{
os << position[i].x() <<
' ' << position[i].y() <<
' ' << position[i].z() << '\n';
}
os << "CELLS " << numPoints << ' ' << 2 * numPoints << '\n';
for (uint32 i = 0; i < numPoints; i++)
{
os << 1 << ' ' << i << '\n';
}
os << "CELL_TYPES " << numPoints << '\n';
for (int32 i = 0; i < numPoints; i++)
{
os << 1 << '\n';
}
os << "POINT_DATA " << numPoints << endl;
return true;
}
bool pFlow::PFtoVTK::convertRealTypePointField(
iOstream &os,
const IOfileHeader &header,
pointStructure &pStruct)
{
word objectType = header.objectType();
if (!checkFieldType<real>(objectType))
return false;
auto field = realPointField_H(
header,
pStruct,
static_cast<real>(0));
real const *data = field.deviceViewAll().data();
REPORT(1) << "writing " << Green_Text(header.objectName()) <<
" field to vtk." << END_REPORT;
return addRealPointField(
os,
header.objectName(),
data,
pStruct.numActive());
}
bool pFlow::PFtoVTK::convertRealx3TypePointField(
iOstream &os,
const IOfileHeader &header,
pointStructure &pStruct)
{
word objectType = header.objectType();
if (!checkFieldType<realx3>(objectType))
return false;
auto field = realx3PointField_H(
header,
pStruct,
{0.0, 0.0, 0.0});
realx3 const *data = field.deviceViewAll().data();
REPORT(1) << "writing " << Green_Text(header.objectName()) <<
" field to vtk." << END_REPORT;
return addRealx3PointField(
os,
header.objectName(),
data,
pStruct.numActive());
}
bool pFlow::PFtoVTK::addRealPointField(
iOstream &os,
const word &fieldName,
const real *field,
uint32 numData)
{
if (numData == 0)
return true;
os << "FIELD FieldData 1\n"
<< fieldName << " 1 " << numData << " float\n";
for (uint32 i = 0; i < numData; ++i)
{
os << field[i] << '\n';
}
return true;
}
bool pFlow::PFtoVTK::addRealx3PointField(
iOstream &os,
const word &fieldName,
const realx3 *field,
uint32 numData)
{
if (numData == 0)
return true;
os << "FIELD FieldData 1\n"
<< fieldName << " 3 " << numData << " float\n";
for (uint32 i = 0; i < numData; ++i)
{
os << field[i].x() <<
' ' << field[i].y() <<
' ' << field[i].z() << '\n';
}
return true;
}
bool pFlow::PFtoVTK::regexCheck(const word &TYPENAME, const word &fieldType)
{
std::regex match("pointField\\<([A-Za-z1-9_]*)\\,([A-Za-z1-9_]*)\\>");
std::smatch search1;
std::smatch search2;
if (!std::regex_match(fieldType, search1, match))
return false;
if (!std::regex_match(TYPENAME, search2, match))
return false;
if (search1.size() != 3)
return false;
if (search1.size() != search2.size())
return false;
return search1[1] == search2[1];
}

459
utilities/pFlowToVTK/pointFieldToVTK.hpp
View File

@ -18,426 +18,125 @@ Licence:
-----------------------------------------------------------------------------*/
#ifndef __pointFieldToVTK_hpp__
#define __pointFieldToVTK_hpp__
#include <regex>
#include "vtkFile.hpp"
#include "systemControl.hpp"
#include "pointStructure.hpp"
#include "pointFields.hpp"
namespace pFlow::PFtoVTK
{
/*template<typename IntType, typename IncludeMaskType>
bool addIntPointField(
iOstream& os,
word fieldName,
int32 numActivePoints,
IntType* field,
IncludeMaskType includeMask );
bool convertTimeFolderPointFields(
systemControl &control,
const fileSystem &destPath,
const word &bName);
template<typename IncludeMaskType>
bool addRealPointField(
iOstream& os,
word fieldName,
int32 numActivePoints,
real* field,
IncludeMaskType includeMask );
bool convertTimeFolderPointFieldsSelected(
systemControl &control,
const fileSystem &destPath,
const word &bName,
const wordVector &fieldsName,
bool mustExist);
template<typename IncludeMaskType>
bool addRealx3PointField(
iOstream& os,
word fieldName,
int32 numActivePoints,
realx3* field,
IncludeMaskType includeMask );*/
bool addUndstrcuturedGridField(
iOstream &os,
realx3 *position,
uint32 numPoints);
bool regexCheck(word TYPENAME, word fieldType)
{
std::regex match("pointField\\<([A-Za-z1-9_]*)\\,([A-Za-z1-9_]*)\\>");
std::smatch search1, search2;
if(!std::regex_match(fieldType, search1, match))return false;
if(!std::regex_match(TYPENAME, search2, match))return false;
if(search1.size()!=3)return false;
if(search1.size()!=search2.size())return false;
return search1[1] == search2[1];
}
bool convertRealTypePointField(
iOstream &os,
const IOfileHeader &header,
pointStructure &pStruct);
template<typename Type>
bool checkFieldType(word objectType)
{
bool convertRealx3TypePointField(
iOstream &os,
const IOfileHeader &header,
pointStructure &pStruct);
template <typename IntType>
bool addIntPointField(
iOstream &os,
const word &fieldName,
IntType *field,
uint32 numData);
bool addRealPointField(
iOstream &os,
const word &fieldName,
const real *field,
uint32 numData);
bool addRealx3PointField(
iOstream &os,
const word &fieldName,
const realx3 *field,
uint32 numData);
template <typename Type>
bool checkFieldType(word objectType);
bool regexCheck(const word &TYPENAME, const word &fieldType);
template <typename Type>
inline bool checkFieldType(word objectType)
{
return regexCheck(pointField<Type>::TYPENAME(), objectType);
}
}
/*template<typename T>
bool convertIntPointField
(
iOstream& os,
const IOfileHeader& header,
const pointStructure& pStruct
)
{
template <typename IntType>
inline bool convertIntPointField(
iOstream &os,
const IOfileHeader &header,
pointStructure &pStruct)
{
using PointFieldType = pointField<VectorSingle, T, HostSpace>;
using PointFieldType = pointField<IntType, HostSpace>;
word objectType = header.objectType();
if(!checkFieldType<T>(objectType))
if (!checkFieldType<IntType>(objectType))
{
return false;
}
auto objField = IOobject::make<PointFieldType>
(
auto field = PointFieldType(
header,
pStruct,
static_cast<T>(0)
);
static_cast<IntType>(0));
auto& Field = objField().template getObject<PointFieldType>();
const IntType *data = field.deviceViewAll().data();
T* data = Field.deviceVectorAll().data();
REPORT(2)<<"writing "<< greenColor <<header.objectName()<<defaultColor<<" field to vtk.\n";
REPORT(1) << "writing " << Green_Text(header.objectName()) << " field to vtk.\n";
return addIntPointField(
os,
header.objectName(),
pStruct.numActive(),
data,
pStruct.activePointsMaskH() );
}*/
/*bool convertRealTypePointField(
iOstream& os,
const IOfileHeader& header,
const pointStructure& pStruct)
{
word objectType = header.objectType();
if(!checkFieldType<real>(objectType))return false;
auto objField = IOobject::make<realPointField_H>
(
header,
pStruct,
static_cast<real>(0)
);
auto& Field = objField().getObject<realPointField_H>();
real* data = Field.hostVectorAll().data();
REPORT(2)<<"writing "<< greenColor <<header.objectName()<<defaultColor<<" field to vtk."<<endREPORT;
return addRealPointField(
os,
header.objectName(),
pStruct.numActive(),
data,
pStruct.activePointsMaskH() );
}*/
/*bool convertRealx3TypePointField(
iOstream& os,
const IOfileHeader& header,
const pointStructure& pStruct)
{
word objectType = header.objectType();
if(!checkFieldType<realx3>(objectType))return false;
auto objField = IOobject::make<realx3PointField_H>
(
header,
pStruct,
static_cast<real>(0)
);
auto& Field = objField().getObject<realx3PointField_H>();
realx3* data = Field.hostVectorAll().data();
REPORT(2)<<"writing "<< greenColor <<header.objectName()<<defaultColor<<" field to vtk."<<endREPORT;
return addRealx3PointField(
os,
header.objectName(),
pStruct.numActive(),
data,
pStruct.activePointsMaskH() );
}*/
bool addUndstrcuturedGridField(
iOstream& os,
realx3* position,
uint32 numPoints)
{
os<< "DATASET UNSTRUCTURED_GRID\n";
os<< "POINTS "<< numPoints << " float\n";
if(numPoints==0) return true;
for(uint32 i=0; i<numPoints; i++)
{
os<< position[i].x()<<' '<< position[i].y()<<' '<<position[i].z()<<'\n';
}
os<<"CELLS "<< numPoints<<' '<< 2*numPoints<<'\n';
for(uint32 i=0; i<numPoints; i++)
{
os<< 1 <<' '<< i<<'\n';
}
os<<"CELL_TYPES "<< numPoints<<'\n';
for(int32 i=0; i<numPoints; i++)
{
os<< 1 <<'\n';
}
os << "POINT_DATA " << numPoints << endl;
return true;
}
/*template<typename IntType, typename IncludeMaskType>
bool addIntPointField(
iOstream& os,
word fieldName,
int32 numActivePoints,
IntType* field,
IncludeMaskType includeMask )
{
if(numActivePoints==0) return true;
auto [iFirst, iLast] = includeMask.activeRange();
os << "FIELD FieldData 1\n"<<
fieldName << " 1 " << numActivePoints << " int\n";
for(int32 i=iFirst; i<iLast; ++i)
{
if(includeMask(i))
os<< field[i] <<'\n';
}
return true;
}*/
/*template<typename IncludeMaskType>
bool addRealPointField(
iOstream& os,
word fieldName,
int32 numActivePoints,
real* field,
IncludeMaskType includeMask )
{
if(numActivePoints==0) return true;
auto [iFirst, iLast] = includeMask.activeRange();
os << "FIELD FieldData 1\n"<<
fieldName << " 1 " << numActivePoints << " float\n";
for(int32 i=iFirst; i<iLast; ++i)
{
if(includeMask(i))
os<< field[i] <<'\n';
}
return true;
}*/
/*template<typename IncludeMaskType>
bool addRealx3PointField(
iOstream& os,
word fieldName,
int32 numActivePoints,
realx3* field,
IncludeMaskType includeMask )
{
if(numActivePoints==0) return true;
auto [iFirst, iLast] = includeMask.activeRange();
os << "FIELD FieldData 1\n"<<
fieldName << " 3 " << numActivePoints << " float\n";
for(int32 i=iFirst; i<iLast; ++i)
{
if(includeMask(i))
os<< field[i].x()<<' '<< field[i].y()<<' '<<field[i].z()<<'\n';
}
return true;
}*/
bool convertTimeFolderPointFields(
systemControl& control,
fileSystem destPath,
word bName)
{
fileSystem timeFolder = control.time().path();
// check if pointStructure exist in this folder
IOfileHeader pStructHeader(
objectFile(
pointStructureFile__,
timeFolder,
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS)
);
if( !pStructHeader.headerOk(true) )
{
output<<yellowColor<<"Time folder "<< control.time().path() <<
" does not contain any pStructure data file. Skipping this folder . . ."
<<defaultColor<<nl;
return true;
}
vtkFile vtk(destPath, bName, control.time().currentTime());
if(!vtk) return false;
auto pStruct = pointStructure(control);
// get a list of files in this timeFolder;
auto posVec = pStruct.pointPositionHost();
auto* pos = posVec.data();
REPORT(1)<<"Writing pointStructure to vtk file with "<< Yellow_Text(pStruct.numActive())
<<" active particles"<<END_REPORT;
addUndstrcuturedGridField(
vtk(),
pos,
pStruct.numActive());
//auto fileList = containingFiles(timeFolder);
/*for(auto& file:fileList)
{
IOfileHeader fieldHeader(
objectFile(
file.wordPath(),
"",
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS) );
if( fieldHeader.headerOk(true) )
{
convertIntPointField<int32>(vtk(), fieldHeader, pStruct);
convertIntPointField<int64>(vtk(), fieldHeader, pStruct);
convertIntPointField<int8>(vtk(), fieldHeader, pStruct);
convertRealTypePointField(vtk(), fieldHeader, pStruct);
convertRealx3TypePointField(vtk(), fieldHeader, pStruct);
}
}*/
return true;
}
bool convertTimeFolderPointFieldsSelected(
fileSystem timeFolder,
real time,
fileSystem destPath,
word bName,
wordVector fieldsName,
bool mustExist)
{
// check if pointStructure exist in this folder
/*IOfileHeader pStructHeader(
objectFile(
pointStructureFile__,
timeFolder,
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS)
);
if( !pStructHeader.headerOk(true) )
template <typename IntType>
inline bool addIntPointField(
iOstream &os,
const word &fieldName,
IntType *field,
uint32 numData)
{
output<<yellowColor<<"Time folder "<< timeFolder <<
" does not contain any pStructure data file. Skipping this folder . . ."
<<defaultColor<<nl;
if (numData == 0)
return true;
os << "FIELD FieldData 1\n"
<< fieldName << " 1 " << numData << " int\n";
for (uint32 i = 0; i < numData; ++i)
{
os << field[i] << '\n';
}
return true;
}
vtkFile vtk(destPath, bName, time);
if(!vtk) return false;
auto pStructObjPtr = IOobject::make<pointStructure>(pStructHeader);
auto& pStruct = pStructObjPtr().getObject<pointStructure>();
// get a list of files in this timeFolder;
auto posVec = std::as_const(pStruct).pointPosition().hostVectorAll();
auto* pos = posVec.data();
REPORT(1)<<"Writing pointStructure to vtk file with "<< yellowText(pStruct.numActive())
<<" active particles"<<endREPORT;
addUndstrcuturedGridField(
vtk(),
pStruct.numActive(),
pos,
pStruct.activePointsMaskH());
auto fileList = containingFiles(timeFolder);
for(auto& fname:fieldsName)
{
fileSystem fieldAddress = timeFolder+fname;
IOfileHeader fieldHeader(
objectFile(
fieldAddress.wordPath(),
"",
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS) );
if( fieldHeader.headerOk(true) )
{
convertIntPointField<int32>(vtk(), fieldHeader, pStruct);
convertIntPointField<int64>(vtk(), fieldHeader, pStruct);
convertIntPointField<int8>(vtk(), fieldHeader, pStruct);
convertRealTypePointField(vtk(), fieldHeader, pStruct);
convertRealx3TypePointField(vtk(), fieldHeader, pStruct);
}
else
{
if(mustExist)
{
fatalErrorInFunction<<"Field " << fieldAddress <<
" does not exist."<<endl;
return false;
}
else
{
REPORT(1)<<"Could not find "<<yellowText(fieldAddress) <<" skipping . . ."<<endREPORT;
}
}
}*/
return true;
}
}
#endif

349
utilities/pFlowToVTK/triSurfaceFieldToVTK.cpp Normal file
View File

@ -0,0 +1,349 @@
#include "vocabs.hpp"
#include "vtkFile.hpp"
#include "triSurfaceFieldToVTK.hpp"
bool pFlow::TSFtoVTK::convertTimeFolderTriSurfaceFields(
systemControl &control,
const fileSystem &destPath,
const word &bName,
bool separate)
{
auto timeFolder = control.geometry().path();
// check if pointStructure exist in this folder
IOfileHeader triSurfaeHeader(
objectFile(
triSurfaceFile__,
timeFolder,
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS));
if (!triSurfaeHeader.headerOk(true))
{
WARNING << "Time folder " << timeFolder << " does not contain any triSurface data file."
<< " Skipping this folder . . ." << END_WARNING;
return true;
}
auto triSurfaceObj = multiTriSurface(
objectFile(
triSurfaceFile__,
"",
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS),
&control.geometry());
if(separate)
{
return convertTimeFolderTriSurfaceFieldsSeparate(
triSurfaceObj,
destPath,
control.time().currentTime(),
bName);
}
else
{
return convertTimeFolderTriSurfaceFieldsSingle(
triSurfaceObj,
destPath,
control.time().currentTime(),
bName );
}
}
bool pFlow::TSFtoVTK::triSurfaceToVTK(
iOstream &os,
const realx3 *points,
const uint32x3 *vertices,
const subSurface &subSurf)
{
auto nP = subSurf.numPoints();
os << "DATASET UNSTRUCTURED_GRID" << endl;
os << "POINTS " << nP << " float" << endl;
for ( auto i=subSurf.pointStart(); i<subSurf.pointEnd(); i++ )
{
os << points[i].x() <<
" " << points[i].y() <<
" " << points[i].z() << endl;
if (!os) return false;
}
auto nTri = subSurf.size();
os << "CELLS " << nTri << " " << 4*nTri << endl;
for(auto i=subSurf.start(); i<subSurf.end(); i++)
{
os<< 3 <<
" "<< vertices[i].x()-subSurf.pointStart() <<
" "<< vertices[i].y()-subSurf.pointStart() <<
" "<< vertices[i].z()-subSurf.pointStart()<<endl;
if (!os) return false;
}
os<<"CELL_TYPES "<< nTri<<'\n';
for(uint32 i=0; i<nTri; i++)
{
os<< 5 <<'\n';
}
os << "CELL_DATA " << nTri << endl;
return true;
}
bool pFlow::TSFtoVTK::triSurfaceToVTK(
iOstream &os,
const realx3 *points,
const uint32x3 *vertices,
uint32 numPoints,
uint32 numTris)
{
os << "DATASET UNSTRUCTURED_GRID" << endl;
os << "POINTS " << numPoints << " float" << endl;
for ( auto i=0; i<numPoints; i++ )
{
os << points[i].x() <<
" " << points[i].y() <<
" " << points[i].z() << endl;
if (!os) return false;
}
os << "CELLS " << numTris << " " << 4*numTris << endl;
for(auto i=0; i<numTris; i++)
{
os<< 3 <<
" "<< vertices[i].x()<<
" "<< vertices[i].y()<<
" "<< vertices[i].z()<<endl;
if (!os) return false;
}
os<<"CELL_TYPES "<< numTris<<'\n';
for(uint32 i=0; i<numTris; i++)
{
os<< 5 <<'\n';
}
os << "CELL_DATA " << numTris << endl;
return true;
}
bool pFlow::TSFtoVTK::convertTimeFolderTriSurfaceFieldsSingle
(
multiTriSurface &surface,
const fileSystem &destPath,
real time,
const word &bName
)
{
vtkFile vtk(destPath, bName, time);
if (!vtk)
return false;
auto hPoints = surface.points().hostView();
auto hVertices = surface.vertices().hostView();
realx3 const* pData = hPoints.data();
uint32x3 const* vData = hVertices.data();
REPORT(1) << "Wrting triSurface geometry to vtk file "<<
Green_Text(vtk.fileName()) << END_REPORT;
if (! triSurfaceToVTK(
vtk(),
pData,
vData,
surface.numPoints(),
surface.size()))
{
fatalErrorInFunction <<
"error in writing triSurface data to vtk file " <<
vtk.fileName() << endl;
return false;
}
auto fileList = containingFiles(surface.path().dirPath());
for(const auto& file:fileList)
{
IOfileHeader fieldHeader(
objectFile(
file.fileName(),
file.dirPath(),
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS) );
if( fieldHeader.headerOk(true) )
{
convertRealx3TypetriSurfaceField(vtk(), fieldHeader, surface);
}
}
output<<endl;
return true;
}
bool pFlow::TSFtoVTK::convertTimeFolderTriSurfaceFieldsSeparate(
multiTriSurface &surface,
const fileSystem &destPath,
real time,
const word &bName)
{
auto hPoints = surface.points().hostView();
auto hVertices = surface.vertices().hostView();
realx3 const* pData = hPoints.data();
uint32x3 const* vData = hVertices.data();
REPORT(1) << "Wrting triSurface geometry to vtk file . . ."<<
END_REPORT;
auto nSurf = surface.numSurfaces();
for(auto nS=0; nS<nSurf; nS++)
{
auto sName = surface.subSurfaceName(nS);
vtkFile vtk(destPath, groupNames(bName,sName), time);
REPORT(2) << "Wrting sub-surface to "<<
Green_Text(vtk.fileName())<<END_REPORT;
if (!vtk)
return false;
if (! triSurfaceToVTK(
vtk(),
pData,
vData,
surface.subSurfaces()[nS]) )
{
fatalErrorInFunction <<
"error in writing triSurface data to vtk file " <<
vtk.fileName() << endl;
return false;
}
}
auto fileList = containingFiles(surface.path().dirPath());
for(const auto& file:fileList)
{
IOfileHeader fieldHeader(
objectFile(
file.fileName(),
file.dirPath(),
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS) );
if( fieldHeader.headerOk(true) )
{
convertRealx3TypetriSurfaceFieldSeparate(
destPath,
fieldHeader,
surface,
bName,
time);
}
}
output<<endl;
return true;
}
bool pFlow::TSFtoVTK::convertRealx3TypetriSurfaceField(
iOstream& os,
const IOfileHeader& header,
multiTriSurface& tSurface)
{
word objectType = header.objectType();
if(!checkTriFieldType<realx3>(objectType))return false;
auto field = realx3TriSurfaceField_H
(
header,
tSurface,
static_cast<real>(0)
);
const realx3* data = field.deviceViewAll().data();
REPORT(1)<<"writing "<< greenColor <<header.objectName()<<
defaultColor<<" field to vtk."<<END_REPORT;
return pFlow::PFtoVTK::addRealx3PointField
(
os,
header.objectName(),
data,
field.size()
);
}
bool pFlow::TSFtoVTK::convertRealx3TypetriSurfaceFieldSeparate
(
const fileSystem& destPath,
const IOfileHeader& header,
multiTriSurface& tSurface,
const word& bName,
real time
)
{
word objectType = header.objectType();
if(!checkTriFieldType<realx3>(objectType))return false;
auto field = realx3TriSurfaceField_H
(
header,
tSurface,
static_cast<real>(0)
);
const realx3* data = field.deviceViewAll().data();
/*REPORT(1)<<"writing "<< greenColor <<header.objectName()<<
defaultColor<<" field to vtk."<<END_REPORT;*/
auto nSurf = tSurface.numSurfaces();
for(auto nS=0; nS<nSurf; nS++)
{
auto& subSurf = tSurface.subSurfaces()[nS];
auto sName = subSurf.name();
vtkFile vtk(destPath, groupNames(bName,sName), time, true);
REPORT(2) << "Wrting sub-surface to "<<
Green_Text(vtk.fileName())<<END_REPORT;
pFlow::PFtoVTK::addRealx3PointField
(
vtk(),
header.objectName(),
data+subSurf.start(),
subSurf.size()
);
}
return true;
/*return pFlow::PFtoVTK::addRealx3PointField
(
os,
header.objectName(),
data,
field.size()
);*/
}

234
utilities/pFlowToVTK/triSurfaceFieldToVTK.hpp
View File

@ -24,19 +24,51 @@ Licence:
#include <regex>
#include "vtkFile.hpp"
#include "pointFieldToVTK.hpp"
#include "triSurface.hpp"
#include "multiTriSurface.hpp"
#include "triSurfaceFields.hpp"
#include "IOobject.hpp"
namespace pFlow::TSFtoVTK
{
bool regexCheck(word TYPENAME, word fieldType)
bool convertTimeFolderTriSurfaceFields(
systemControl& control,
const fileSystem& destPath,
const word& bName,
bool separate);
bool triSurfaceToVTK(iOstream &os,
const realx3 *points,
const uint32x3 *vertices,
const subSurface &subSurf);
bool triSurfaceToVTK(iOstream &os,
const realx3* points,
const uint32x3* vertices,
uint32 numPoints,
uint32 numTris);
bool convertTimeFolderTriSurfaceFieldsSingle(
multiTriSurface& surface,
const fileSystem& destPath,
real time,
const word& bName);
bool convertTimeFolderTriSurfaceFieldsSeparate(
multiTriSurface& surface,
const fileSystem& destPath,
real time,
const word& bName);
inline
bool regexCheck(const word& TYPENAME, const word& fieldType)
{
std::regex match("triSurfaceField\\<([A-Za-z1-9_]*)\\,([A-Za-z1-9_]*)\\>");
std::smatch search1, search2;
std::smatch search1;
std::smatch search2;
if(!std::regex_match(fieldType, search1, match))return false;
if(!std::regex_match(TYPENAME, search2, match))return false;
if(search1.size()!=3)return false;
@ -45,201 +77,27 @@ bool regexCheck(word TYPENAME, word fieldType)
}
template<typename Type>
bool checkFieldType(word objectType)
inline
bool checkTriFieldType(word objectType)
{
//if( pointField<VectorSingle,Type>::TYPENAME() == objectType )return true;
//if( pointField<VectorSingle,Type, HostSpace>::TYPENAME() == objectType ) return true;
//if( pointField<VectorDual, Type>::TYPENAME() == objectType )return true;
return regexCheck(triSurfaceField<VectorSingle,Type>::TYPENAME(), objectType);
}
template<typename Type>
bool triDataToVTK(iOstream& os, const Type& dataEntity)
{
fatalErrorInFunction<<
"not implemented function!";
fatalExit;
return false;
}
template<>
bool triDataToVTK(iOstream& os, const triSurface& surface )
{
auto nP = surface.numPoints();
auto hPoints = surface.points().hostVector();
os << "DATASET POLYDATA" << endl;
os << "POINTS " << nP << " float" << endl;
for ( auto i=0; i<nP; i++ )
{
os << hPoints[i].x() << " " << hPoints[i].y() << " " << hPoints[i].z() << endl;
}
auto nV = surface.numTriangles();
auto hVertices = surface.vertices().hostVector();
os << "POLYGONS " << nV << " " << 4*nV << endl;
for(auto i=0; i<nV; i++)
{
os<< 3 <<" "<< hVertices[i].x() << " " << hVertices[i].y() <<" "<<hVertices[i].z()<<endl;
}
return true;
}
template<>
bool triDataToVTK(iOstream& os, const multiTriSurface& surface )
{
auto nP = surface.numPoints();
auto hPoints = surface.points().hostVector();
os << "DATASET UNSTRUCTURED_GRID" << endl;
os << "POINTS " << nP << " float" << endl;
for ( auto i=0; i<nP; i++ )
{
os << hPoints[i].x() << " " << hPoints[i].y() << " " << hPoints[i].z() << endl;
}
auto nV = surface.numTriangles();
auto hVertices = surface.vertices().hostVector();
os<<"CELLS "<< nV<<' '<< 4*nV<<'\n';
//os << "POLYGONS " << nV << " " << 4*nV << endl;
for(auto i=0; i<nV; i++)
{
os<< 3 <<" "<< hVertices[i].x() << " " << hVertices[i].y() <<" "<<hVertices[i].z()<<endl;
}
os<<"CELL_TYPES "<< nV<<'\n';
for(int32 i=0; i<nV; i++)
{
os<< 5 <<'\n';
}
os << "CELL_DATA " << nV << endl;
return true;
}
bool addRealx3TriSurfaceField(
iOstream& os,
word fieldName,
int32 size,
realx3* field )
{
if(size==0) return true;
os << "FIELD FieldData 1\n"<<
fieldName << " 3 " << size << " float\n";
for(int32 i=0; i<size; ++i)
{
os<< field[i].x()<<' '<< field[i].y()<<' '<<field[i].z()<<'\n';
}
return true;
return regexCheck(triSurfaceField<Type>::TYPENAME(), objectType);
}
bool convertRealx3TypetriSurfaceField(
iOstream& os,
const IOfileHeader& header,
const multiTriSurface& tSurface)
{
word objectType = header.objectType();
multiTriSurface& tSurface);
if(!checkFieldType<realx3>(objectType))return false;
auto objField = IOobject::make<realx3TriSurfaceField_H>
(
header,
tSurface,
static_cast<real>(0)
);
auto& Field = objField().getObject<realx3TriSurfaceField_H>();
realx3* data = Field.hostVectorAll().data();
REPORT(2)<<"writing "<< greenColor <<header.objectName()<<defaultColor<<" field to vtk."<<endREPORT;
return addRealx3TriSurfaceField(
os,
header.objectName(),
tSurface.size(),
data );
}
bool convertTimeFolderTriSurfaceFields(
fileSystem timeFolder,
real time,
fileSystem destPath,
word bName)
{
// check if pointStructure exist in this folder
IOfileHeader triSurfaeHeader(
objectFile(
triSurfaceFile__,
timeFolder,
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS)
);
if( !triSurfaeHeader.headerOk(true) )
{
output<<yellowText("Time folder "<< timeFolder <<
" does not contain any triSurface data file. Skipping this folder . . ."
)<<nl;
return true;
}
vtkFile vtk(destPath, bName, time);
if(!vtk) return false;
auto triSurfaceObjPtr = IOobject::make<multiTriSurface>(triSurfaeHeader);
auto& tSurface = triSurfaceObjPtr().getObject<multiTriSurface>();
// get a list of files in this timeFolder;
REPORT(1)<<"Wrting triSurface mesh/Geometry to vtk file."<<endREPORT;
if(!triDataToVTK(vtk(), tSurface))
{
fatalErrorInFunction<<
"error in writing triSurface data to vtk file "<< vtk.fileName()<<endl;
return false;
}
bool convertRealx3TypetriSurfaceFieldSeparate(
const fileSystem& destPath,
const IOfileHeader& header,
multiTriSurface& tSurface,
const word& bName,
real time);
auto fileList = containingFiles(timeFolder);
for(auto& file:fileList)
{
IOfileHeader fieldHeader(
objectFile(
file.wordPath(),
"",
objectFile::READ_ALWAYS,
objectFile::WRITE_ALWAYS) );
if( fieldHeader.headerOk(true) )
{
//output<<"object file type is "<<fieldHeader.objectType()<<endl;
convertRealx3TypetriSurfaceField(vtk(), fieldHeader, tSurface);
}
}
return true;
}
}
#endif