HDF5Reader Class Reference

#include <hdf5reader.h>

Inheritance diagram for HDF5Reader:

Collaboration diagram for HDF5Reader:

Public Member Functions
	HDF5Reader ()
	~HDF5Reader ()
void	open (std::string strFileName)
void	close ()
std::string	getAttribute (std::string datasetName, std::string attributeName)
std::vector< std::string >	getMeshList ()
std::vector< std::string >	getFieldList ()
std::vector< std::string >	ls (std::string path)
std::string	getDataSetTriangulation (std::string dataset)
VecIndex	getDataSetDim (std::string path)
std::string	readAtt (std::string strPath, std::string attName, bool mustexist=true)
std::string	getFileName ()
Protected Member Functions
hid_t	openGroup (std::string groupName)
hid_t	openId (hid_t rootId, std::string path, hsize_t type)
void	closeId (hid_t id)
std::string	printType (hsize_t type)
Protected Attributes
hid_t	m_file
Private Attributes
std::string	_fileName

Detailed Description

HDF5Reader

Definition at line 13 of file hdf5reader.h.

Constructor & Destructor Documentation

HDF5Reader::HDF5Reader ( )

Definition at line 90 of file hdf5reader.cpp.

00091 {
00092   m_file = -1;
00093 }

HDF5Reader::~HDF5Reader ( )

Definition at line 116 of file hdf5reader.cpp.

00117 {
00118   close();
00119 }

Member Function Documentation

void HDF5Reader::close ( )

Definition at line 106 of file hdf5reader.cpp.

00107 {
00108   if (m_file >=0)
00109   {
00110     H5Fclose(m_file);
00111   }
00112   m_file=-1;
00113 }

void HDF5Reader::closeId ( hid_t id ) [protected]

Definition at line 159 of file hdf5reader.cpp.

00160 {
00161   switch(H5Iget_type(id))
00162   {
00163   case H5I_ATTR:
00164     H5Aclose(id);
00165     break;
00166   case H5I_GROUP:
00167     H5Gclose(id);
00168     break;
00169   case H5I_DATASET:
00170     H5Dclose(id);
00171     break;
00172   default:
00173     throw new Exception("HDF5Read::openId Data type not recognized");
00174   }
00175 
00176 }

std::string HDF5Reader::getAttribute	(	std::string	datasetName,
		std::string	attributeName
	)

VecIndex HDF5Reader::getDataSetDim ( std::string path )

Definition at line 218 of file hdf5reader.cpp.

00219 {
00220   if (m_file == -1)
00221     throw new Exception("HDF5Reader::getDataSetDim: Open the file first");
00222   VecIndex resp;
00223   int rank;
00224   H5LTget_dataset_ndims(m_file,path.c_str(),&rank);
00225   resp.resize(rank);
00226 
00227   hsize_t dims[rank];
00228   H5T_class_t class_id;
00229   size_t type_size;
00230   H5LTget_dataset_info(m_file,path.c_str(),dims,&class_id,&type_size);
00231 
00232   for (int i=0;i<rank;i++)
00233     resp[i]=(Index) dims[i];
00234   return resp;
00235 }

std::string HDF5Reader::getDataSetTriangulation ( std::string dataset )

Definition at line 17 of file hdf5reader.cpp.

00018 {
00019   char strTria[1000];
00020   if (H5LTget_attribute_string(m_file, datasetName.c_str(), "Triangulation",  strTria) < 0)
00021     throw new Exception("Dataset %s not found\n", datasetName.c_str());
00022   else
00023     return strTria;
00024 }

std::vector< std::string > HDF5Reader::getFieldList ( )

Definition at line 49 of file hdf5reader.cpp.

00050 {
00051   std::vector<std::string>  stringList;
00052   //Open group
00053   hid_t group_id = H5Gopen1(m_file,"/DataSets");
00054 
00055   //Get group info
00056   H5G_info_t group_info;
00057   H5Gget_info( group_id, &group_info ); 
00058 
00059   char name[1000];
00060   for (hsize_t i=0;i<group_info.nlinks;i++)
00061   {
00062     H5Lget_name_by_idx(group_id,".",H5_INDEX_NAME,H5_ITER_INC,i,name,1000,H5P_DEFAULT);
00063     stringList.push_back(name);
00064   }
00065   return stringList;
00066 }

std::string HDF5Reader::getFileName ( ) [inline]

Definition at line 36 of file hdf5reader.h.

00036 {return _fileName;}

std::vector< std::string > HDF5Reader::getMeshList ( )

Definition at line 27 of file hdf5reader.cpp.

00028 {
00029   std::vector<std::string> stringList;
00030   //Open group
00031   hid_t group_id = H5Gopen1(m_file,"/Triangulations");
00032 
00033   //Get group info
00034   H5G_info_t group_info;
00035   H5Gget_info( group_id, &group_info ); 
00036 
00037   char name[1000];
00038   for (hsize_t i=0;i<group_info.nlinks;i++)
00039   {
00040     H5Lget_name_by_idx(group_id,".",H5_INDEX_NAME,H5_ITER_INC,i,name,1000,H5P_DEFAULT);
00041     stringList.push_back(name);
00042   }
00043   return stringList;
00044 }

std::vector< std::string > HDF5Reader::ls ( std::string path )

Definition at line 69 of file hdf5reader.cpp.

00070 {
00071   std::vector<std::string>  stringList;
00072   //Open group
00073   hid_t group_id = H5Gopen1(m_file,path.c_str());
00074 
00075   //Get group info
00076   H5G_info_t group_info;
00077   H5Gget_info( group_id, &group_info ); 
00078 
00079   char name[1000];
00080   for (hsize_t i=0;i<group_info.nlinks;i++)
00081   {
00082     H5Lget_name_by_idx(group_id,".",H5_INDEX_NAME,H5_ITER_INC,i,name,1000,H5P_DEFAULT);
00083     stringList.push_back(name);
00084   }
00085   return stringList;
00086 
00087 }

void HDF5Reader::open ( std::string strFileName )

Definition at line 95 of file hdf5reader.cpp.

00096 {
00097   close();
00098   _fileName=strFileName;
00099   m_file = H5Fopen(strFileName.c_str(),H5F_ACC_RDONLY,H5P_DEFAULT);
00100   if (m_file < 0)
00101     throw new Exception("File name \"%s\" not found",strFileName.c_str());
00102 }

hid_t HDF5Reader::openGroup ( std::string groupName ) [protected]

Definition at line 123 of file hdf5reader.cpp.

00124 {
00125   hid_t grp = H5Gopen1(m_file,groupName.c_str());
00126   if (grp <= 0)
00127     throw new Exception("HDF5OrthoReader::openGroup Fail to open group %s",groupName.c_str());
00128   return grp;
00129 }

hid_t HDF5Reader::openId	(	hid_t	rootId,
		std::string	path,
		hsize_t	type
	)			`[protected]`

Definition at line 132 of file hdf5reader.cpp.

00133 {
00134   hid_t result;
00135   switch(type)
00136   {
00137   case H5I_ATTR:
00138     result= H5Aopen(rootId,path.c_str(),H5P_DEFAULT);
00139     break;
00140   case H5I_GROUP:
00141     result= H5Gopen1(rootId,path.c_str());
00142     break;
00143   case H5I_DATASET:
00144     result= H5Dopen1(rootId,path.c_str());
00145     break;
00146   case H5I_BADID:
00147     throw new Exception("HDF5OrthoRead::openId Invalid object at \"%s\" not recognized",path.c_str());
00148   default:
00149     throw new Exception("HDF5OrthoRead::openId Data type \"%s %d\" in path \"%s\" not recognized",printType(type).c_str(),type,path.c_str());
00150     result=-1;
00151   }
00152   if (result <= 0)
00153     throw new Exception("HDF5OrthoRead::openId Can't open %s",path.c_str());
00154   return result;
00155    
00156 }

std::string HDF5Reader::printType ( hsize_t type ) [protected]

Definition at line 156 of file hdf5orthoreader.cpp.

00157 {
00158   switch(type)
00159   {
00160   case H5I_ATTR:
00161     return "ATTRIBUTE";
00162     break;
00163   case H5I_GROUP:
00164     return "GROUP";
00165     break;
00166   case H5I_DATASET:
00167     return "DATASET";
00168     break;
00169   case H5I_FILE:
00170     return "FILE";
00171     break;
00172   case H5I_DATASPACE:
00173     return "DATASPACE";
00174     break;
00175   case H5I_DATATYPE:
00176     return "DATATYPE";
00177     break;
00178   }
00179   return "UNKNOWN";
00180 }

std::string HDF5Reader::readAtt	(	std::string	strPath,
		std::string	attName,
		bool	mustexist = `true`
	)

Read an attribute

Parameters:

	strPath	The path to the link
	attName	The name of the attribute
	mustexist	If 1 throws an Exception if the attribute does not exist. If 0 just return an empty string

Returns:

Definition at line 186 of file hdf5reader.cpp.

00187 {
00188   //open the attribute
00189   if (m_file == -1)
00190   {
00191     throw new Exception("HDF5Reader::readAtt error, open the file first.");
00192   }
00193     
00194   hid_t att = H5Aopen_by_name(m_file,strPath.c_str(), attName.c_str(),H5P_DEFAULT,H5P_DEFAULT);
00195   if (att < 0 && mustexist)
00196     throw new Exception("Attribute %s/%s not found",strPath.c_str(),attName.c_str());
00197   if (att<0 && !mustexist)
00198     return std::string();
00199   
00200   //check Type
00201   hid_t datatype = H5Aget_type(att);
00202   if (H5Tget_class(datatype) != H5T_STRING)
00203     throw new Exception("Attribute %s/%s expected to be a string",strPath.c_str(),attName.c_str());
00204 
00205   size_t size=H5Tget_size(datatype);
00206   char value[size];
00207   H5Aclose(att);
00208   H5Tclose(datatype);
00209 
00210   hid_t error=H5LTget_attribute_string(m_file,strPath.c_str(),attName.c_str(),value);
00211   if (error>=0)
00212     return value;
00213   else
00214     return "";
00215 }

Member Data Documentation

std::string HDF5Reader::_fileName [private]

Definition at line 16 of file hdf5reader.h.

hid_t HDF5Reader::m_file [protected]

Definition at line 23 of file hdf5reader.h.

The documentation for this class was generated from the following files:

HDF5Reader Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation