gmHdf5.h

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/************************************************************************
**
** Copyright (C) 2014 by Carlos Augusto Teixera Mendes
** All rights reserved.
**
** This file is part of the "GeMA" software. It's use should respect
** the terms in the license agreement that can be found together 
** with this source code.
** It is provided AS IS, with NO WARRANTY OF ANY KIND, 
** INCLUDING THE WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR 
** A PARTICULAR PURPOSE.
**
************************************************************************/

#ifndef _GEMA_HDF5_H_
#define _GEMA_HDF5_H_

#include <QString>
#include <functional>

#include "gmValueInfo.h"
#include "gmFileIO.h"

class GmLogCategory;

namespace H5 {
  class H5File;
  class H5Object;
  class PredType;
}

class GmSimulationData;
class GmMesh;
class GmCellMesh;
class GmElementMesh;
class GmCell;
class GmValueAccessor;
class GmCellAccessor;
class GmGaussAccessor;
class GmDiscontinuitySet;

class GmFileFormat;
class GmFileFilter;

class UnitConverter;

class GmHdf5
{
public:
  GmHdf5(const GmLogCategory& logger);
        ~GmHdf5();

  bool create(QString fileName, const GmFileFormat* fileFormat, const GmSimulationData* simData,
              bool singlePrecision, int sequenceNumber);

  static bool addSequenceInfo(QString fileName, int numSequenceFiles, double startTime, double endTime, QString timeUnit, const GmLogCategory& logger);

  bool createGroups(const QStringList& groups);
  bool createGroup (QString group, double time, QString timeUnit);

  bool adjustTimeInfo(int sequenceNum, bool multiTime, double startTime, double endTime, QString timeUnit);

  bool saveMeshNodeCoord(QString dsName, const GmMesh* mesh, const GmFileFilter* filter, 
                         GmValueAccessor* nodeAc, const double* scaleFactor, const double* offset);

  bool saveMeshGaussNodeCoord(QString dsName, const GmElementMesh* mesh, const GmFileFilter* filter, int ruleIndex,
                              GmValueAccessor* nodeAc, const double* scaleFactor, const double* offset);

  bool saveMeshTopology(QString dsName, const GmCellMesh* mesh, const GmFileFilter* filter);

  bool saveMeshPointCloudTopology(QString dsName, const GmMesh* mesh, const GmFileFilter* filter, int ruleIndex = -1);

  bool saveMeshNodeData(QString dsName, const GmMesh* mesh, const GmFileFilter* filter,
                        GmValueAccessor* dataAc, int dimFilter);

  bool saveMeshNodeIdColumn(QString dsName, const GmMesh* mesh, const GmFileFilter* filter);

  bool saveMeshCellData(QString dsName, const GmCellMesh* mesh, const GmFileFilter* filter,
                        GmCellAccessor* dataAc, int dimFilter);

  bool saveMeshGaussData(QString dsName, const GmElementMesh* mesh, const GmFileFilter* filter, int ruleIndex,
                         GmGaussAccessor* dataAc, int dimFilter);

  bool saveDiscontinuitySetData(QString coordDsName, QString cellDsName, const GmDiscontinuitySet* discSet, bool original,
                                const UnitConverter* conv, const double* scaleFactor, const double* offset, 
                                int* numNodes, int* numSegments, int* dataSize);

  bool saveMeshCellExtraColumn(QString dsName, const GmCellMesh* mesh, const GmFileFilter* filter,
                               GmFileIO::ExtraColumns column, int propertySet);

  bool saveMeshGaussIdColumn(QString dsName, const GmElementMesh* mesh, const GmFileFilter* filter, int ruleIndex);

private:
  bool saveNodeData(QString dsName, const GmMesh* mesh, const GmFileFilter* filter, GmValueAccessor* dataAc,
                    int dimFilter, std::function<void(const double*, int, double*)> transformFunc);

  template <class T>
  bool fillDiscontinuityPolylineData(const GmDiscontinuitySet* discSet, bool original, const UnitConverter* conv, 
                                     const double* scaleFactor, const double* offset, 
                                     QVector<T>& nodes, QVector<int>& topology, int* nsegments) const;

  const char* dataBuffer(GmValueAccessor* ac, const GmValueInfo* info) const;

  const H5::PredType& hdf5Type(GmStorageType type) const;

  void addTableAttributes(H5::H5Object* obj, const GmMesh* mesh,      const char* type, const GmDiscontinuitySet* discSet = NULL);
  void addNodeAttributes (H5::H5Object* obj, const GmMesh* mesh,      const GmFileFilter* filter);
  void addCellAttributes (H5::H5Object* obj, const GmCellMesh* mesh,  const GmFileFilter* filter, int ruleIndex = -1);
  void addAcAttributes   (H5::H5Object* obj, const GmValueInfo* info, QString unit, int dimFilter, const double* scaleFactor = NULL, const double* offset = NULL);
  void addPropertySetAttributes(H5::H5Object* obj, const GmCellMesh* mesh, int propertySet);
  void addDiscSetNodeAttributes(H5::H5Object* obj, const GmDiscontinuitySet* discSet, bool original, const UnitConverter* conv,
                                const double* scaleFactor, const double* offset);
  void addDiscSetTopologyAttributes(H5::H5Object* obj, const GmDiscontinuitySet* discSet, bool original);

  static void addAttribute(H5::H5Object* obj, QString name, int         value);
  static void addAttribute(H5::H5Object* obj, QString name, unsigned    value);
  static void addAttribute(H5::H5Object* obj, QString name, double      value);
  static void addAttribute(H5::H5Object* obj, QString name, bool        value);
  static void addAttribute(H5::H5Object* obj, QString name, const char* value);
  static void addAttribute(H5::H5Object* obj, QString name, QString     value);
  static void addAttribute(H5::H5Object* obj, QString name, const QStringList& value);
  static void addAttribute(H5::H5Object* obj, QString name, unsigned n, const int*      values);
  static void addAttribute(H5::H5Object* obj, QString name, unsigned n, const unsigned* values);
  static void addAttribute(H5::H5Object* obj, QString name, unsigned n, const double*   values);

  template<class T> static void addScalarAttribute(H5::H5Object* obj, QString name, const H5::PredType& type, T value);
  template<class T> static void addVectorAttribute(H5::H5Object* obj, QString name, const H5::PredType& type, unsigned n, const T* values);

  const GmLogCategory& _logger;          
        QString                          _fileName;        
        H5::H5File*              _fileh;           
  const GmFileFormat*  _fileFormat;      
  bool                 _singlePrecision; 
};

#endif