hdf5reader.cpp

Go to the documentation of this file.

#include "hdf5reader.h"
#include <hdf5_hl.h>
#include "exception.h"



std::string getFileNameFromPath(std::string path)
{
  unsigned i=path.size()-1;
  while (i>=0 && path[i]!='/')
    i--;
  return path.substr(i,path.size());

}


std::string HDF5Reader::getDataSetTriangulation(std::string datasetName) 
{
  char strTria[1000];
  if (H5LTget_attribute_string(m_file, datasetName.c_str(), "Triangulation",  strTria) < 0)
    throw new Exception("Dataset %s not found\n", datasetName.c_str());
  else
    return strTria;
}


  std::vector<std::string> HDF5Reader::getMeshList() 
{
  std::vector<std::string> stringList;
  //Open group
  hid_t group_id = H5Gopen1(m_file,"/Triangulations");

  //Get group info
  H5G_info_t group_info;
  H5Gget_info( group_id, &group_info ); 

  char name[1000];
  for (hsize_t i=0;i<group_info.nlinks;i++)
  {
    H5Lget_name_by_idx(group_id,".",H5_INDEX_NAME,H5_ITER_INC,i,name,1000,H5P_DEFAULT);
    stringList.push_back(name);
  }
  return stringList;
}




std::vector<std::string> HDF5Reader::getFieldList() 
{
  std::vector<std::string>  stringList;
  //Open group
  hid_t group_id = H5Gopen1(m_file,"/DataSets");

  //Get group info
  H5G_info_t group_info;
  H5Gget_info( group_id, &group_info ); 

  char name[1000];
  for (hsize_t i=0;i<group_info.nlinks;i++)
  {
    H5Lget_name_by_idx(group_id,".",H5_INDEX_NAME,H5_ITER_INC,i,name,1000,H5P_DEFAULT);
    stringList.push_back(name);
  }
  return stringList;
}


std::vector<std::string> HDF5Reader::ls(std::string path) 
{
  std::vector<std::string>  stringList;
  //Open group
  hid_t group_id = H5Gopen1(m_file,path.c_str());

  //Get group info
  H5G_info_t group_info;
  H5Gget_info( group_id, &group_info ); 

  char name[1000];
  for (hsize_t i=0;i<group_info.nlinks;i++)
  {
    H5Lget_name_by_idx(group_id,".",H5_INDEX_NAME,H5_ITER_INC,i,name,1000,H5P_DEFAULT);
    stringList.push_back(name);
  }
  return stringList;

}


 HDF5Reader::HDF5Reader() 
{
  m_file = -1;
}

void  HDF5Reader::open(std::string strFileName) 
{
  close();
  _fileName=strFileName;
  m_file = H5Fopen(strFileName.c_str(),H5F_ACC_RDONLY,H5P_DEFAULT);
  if (m_file < 0)
    throw new Exception("File name \"%s\" not found",strFileName.c_str());
}



void HDF5Reader::close() 
{
  if (m_file >=0)
  {
    H5Fclose(m_file);
  }
  m_file=-1;
}


 HDF5Reader::~HDF5Reader() 
{
  close();
}



hid_t HDF5Reader::openGroup(std::string groupName) 
{
  hid_t grp = H5Gopen1(m_file,groupName.c_str());
  if (grp <= 0)
    throw new Exception("HDF5OrthoReader::openGroup Fail to open group %s",groupName.c_str());
  return grp;
}


hid_t HDF5Reader::openId(hid_t rootId, std::string path,hsize_t type) 
{
  hid_t result;
  switch(type)
  {
  case H5I_ATTR:
    result= H5Aopen(rootId,path.c_str(),H5P_DEFAULT);
    break;
  case H5I_GROUP:
    result= H5Gopen1(rootId,path.c_str());
    break;
  case H5I_DATASET:
    result= H5Dopen1(rootId,path.c_str());
    break;
  case H5I_BADID:
    throw new Exception("HDF5OrthoRead::openId Invalid object at \"%s\" not recognized",path.c_str());
  default:
    throw new Exception("HDF5OrthoRead::openId Data type \"%s %d\" in path \"%s\" not recognized",printType(type).c_str(),type,path.c_str());
    result=-1;
  }
  if (result <= 0)
    throw new Exception("HDF5OrthoRead::openId Can't open %s",path.c_str());
  return result;
   
}


void HDF5Reader::closeId(hid_t id) 
{
  switch(H5Iget_type(id))
  {
  case H5I_ATTR:
    H5Aclose(id);
    break;
  case H5I_GROUP:
    H5Gclose(id);
    break;
  case H5I_DATASET:
    H5Dclose(id);
    break;
  default:
    throw new Exception("HDF5Read::openId Data type not recognized");
  }

}


std::string HDF5Reader::readAtt(std::string strPath,std::string attName,bool mustexist) 
{
  //open the attribute
  if (m_file == -1)
  {
    throw new Exception("HDF5Reader::readAtt error, open the file first.");
  }
    
  hid_t att = H5Aopen_by_name(m_file,strPath.c_str(), attName.c_str(),H5P_DEFAULT,H5P_DEFAULT);
  if (att < 0 && mustexist)
    throw new Exception("Attribute %s/%s not found",strPath.c_str(),attName.c_str());
  if (att<0 && !mustexist)
    return std::string();
  
  //check Type
  hid_t datatype = H5Aget_type(att);
  if (H5Tget_class(datatype) != H5T_STRING)
    throw new Exception("Attribute %s/%s expected to be a string",strPath.c_str(),attName.c_str());

  size_t size=H5Tget_size(datatype);
  char value[size];
  H5Aclose(att);
  H5Tclose(datatype);

  hid_t error=H5LTget_attribute_string(m_file,strPath.c_str(),attName.c_str(),value);
  if (error>=0)
    return value;
  else
    return "";
}


VecIndex HDF5Reader::getDataSetDim(std::string path) 
{
  if (m_file == -1)
    throw new Exception("HDF5Reader::getDataSetDim: Open the file first");
  VecIndex resp;
  int rank;
  H5LTget_dataset_ndims(m_file,path.c_str(),&rank);
  resp.resize(rank);

  hsize_t dims[rank];
  H5T_class_t class_id;
  size_t type_size;
  H5LTget_dataset_info(m_file,path.c_str(),dims,&class_id,&type_size);

  for (int i=0;i<rank;i++)
    resp[i]=(Index) dims[i];
  return resp;
}

---