diff options
Diffstat (limited to 'c++/src/H5DataSet.cpp')
| -rw-r--r-- | c++/src/H5DataSet.cpp | 203 |
1 files changed, 187 insertions, 16 deletions
diff --git a/c++/src/H5DataSet.cpp b/c++/src/H5DataSet.cpp index 494d3ea..cddb5d4 100644 --- a/c++/src/H5DataSet.cpp +++ b/c++/src/H5DataSet.cpp @@ -37,6 +37,7 @@ #include "H5File.h" #include "H5Attribute.h" #include "H5DataSet.h" +#include "H5private.h" // for HDfree #ifndef H5_NO_NAMESPACE namespace H5 { @@ -220,6 +221,53 @@ hsize_t DataSet::getStorageSize() const } //-------------------------------------------------------------------------- +// Function: DataSet::getInMemDataSize +///\brief Gets the size in memory of the dataset's data. +///\return Size of data (in memory) +///\exception H5::DataSetIException +// Programmer Binh-Minh Ribler - Apr 2009 +//-------------------------------------------------------------------------- +size_t DataSet::getInMemDataSize() const +{ + char *func = "DataSet::getInMemDataSize"; + + // Get the data type of this dataset + hid_t mem_type_id = H5Dget_type(id); + if( mem_type_id < 0 ) + { + throw DataSetIException(func, "H5Dget_type failed"); + } + + // Get the data type's size + hid_t native_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT); + if (native_type < 0) + { + throw DataSetIException(func, "H5Tget_native_type failed"); + } + size_t type_size = H5Tget_size(native_type); + if (type_size == 0) + { + throw DataSetIException(func, "H5Tget_size failed"); + } + + // Get number of elements of the dataset + hid_t space_id = H5Dget_space(id); // first get its data space + if (space_id < 0) + { + throw DataSetIException(func, "H5Dget_space failed"); + } + hssize_t num_elements = H5Sget_simple_extent_npoints(space_id); + if (num_elements < 0) + { + throw DataSetIException(func, "H5Sget_simple_extent_npoints failed"); + } + + // Calculate and return the size of the data + size_t data_size = type_size * num_elements; + return(data_size); +} + +//-------------------------------------------------------------------------- // Function: DataSet::getOffset ///\brief Returns the address of this dataset in the file. ///\return Address of dataset @@ -364,20 +412,45 @@ void DataSet::read( void* buf, const DataType& mem_type, const DataSpace& mem_sp // Function: DataSet::read ///\brief This is an overloaded member function, provided for convenience. /// It takes a reference to a \c std::string for the buffer. +///\param buf - IN: Buffer for read data +///\param mem_type - IN: Memory datatype +///\param mem_space - IN: Memory dataspace +///\param file_space - IN: Dataset's dataspace in the file +///\param xfer_plist - IN: Transfer property list for this I/O operation +///\exception H5::DataSetIException // Programmer Binh-Minh Ribler - 2000 -//-------------------------------------------------------------------------- -void DataSet::read( H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const +// Modification +// Jul 2009 +// Follow the change to Attribute::read and use the following +// private functions to read datasets with fixed- and +// variable-length string: +// DataSet::p_read_fixed_len and +// DataSet::p_read_variable_len +//-------------------------------------------------------------------------- +void DataSet::read(H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist) const { - // Allocate C character string for reading - size_t size = mem_type.getSize(); - char* strg_C = new char[size+1]; // temporary C-string for C API + // Check if this dataset has variable-len string or fixed-len string and + // proceed appropriately. + htri_t is_variable_len = H5Tis_variable_str(mem_type.getId()); + if (is_variable_len < 0) + { + throw DataSetIException("DataSet::read", "H5Tis_variable_str failed"); + } - // Use the overloaded member to read - read(strg_C, mem_type, mem_space, file_space, xfer_plist); + // Obtain identifiers for C API + hid_t mem_type_id = mem_type.getId(); + hid_t mem_space_id = mem_space.getId(); + hid_t file_space_id = file_space.getId(); + hid_t xfer_plist_id = xfer_plist.getId(); - // Get the String and clean up - strg = strg_C; - delete []strg_C; + if (!is_variable_len) // only allocate for fixed-len string + { + p_read_fixed_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg); + } + else + { + p_read_variable_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg); + } } //-------------------------------------------------------------------------- @@ -416,15 +489,46 @@ void DataSet::write( const void* buf, const DataType& mem_type, const DataSpace& ///\brief This is an overloaded member function, provided for convenience. /// It takes a reference to a \c std::string for the buffer. // Programmer Binh-Minh Ribler - 2000 +// Modification +// Jul 2009 +// Modified to pass the buffer into H5Dwrite properly depending +// whether the dataset has variable- or fixed-length string. //-------------------------------------------------------------------------- void DataSet::write( const H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const { - // Convert string to C-string - const char* strg_C; - strg_C = strg.c_str(); // strg_C refers to the contents of strg as a C-str + // Check if this attribute has variable-len string or fixed-len string and + // proceed appropriately. + htri_t is_variable_len = H5Tis_variable_str(mem_type.getId()); + if (is_variable_len < 0) + { + throw DataSetIException("DataSet::write", "H5Tis_variable_str failed"); + } + + // Obtain identifiers for C API + hid_t mem_type_id = mem_type.getId(); + hid_t mem_space_id = mem_space.getId(); + hid_t file_space_id = file_space.getId(); + hid_t xfer_plist_id = xfer_plist.getId(); + + // Convert string to C-string + const char* strg_C; + strg_C = strg.c_str(); // strg_C refers to the contents of strg as a C-str + herr_t ret_value = 0; - // Use the overloaded member - write(strg_C, mem_type, mem_space, file_space, xfer_plist); + // Pass string in differently depends on variable or fixed length + if (!is_variable_len) + { + ret_value = H5Dwrite( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C ); + } + else + { + // passing string argument by address + ret_value = H5Dwrite( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C ); + } + if (ret_value < 0) + { + throw DataSetIException("DataSet::write", "H5Dwrite failed"); + } } //-------------------------------------------------------------------------- @@ -586,7 +690,74 @@ hid_t DataSet::getId() const } //-------------------------------------------------------------------------- -// Function: DataSet::p_setId +// Function: DataSet::p_read_fixed_len (private) +// brief Reads a fixed length \a H5std_string from an dataset. +// param mem_type - IN: DataSet datatype (in memory) +// param strg - IN: Buffer for read string +// exception H5::DataSetIException +// Programmer Binh-Minh Ribler - Jul, 2009 +// Modification +// Jul 2009 +// Added in follow to the change in Attribute::read +//-------------------------------------------------------------------------- +void DataSet::p_read_fixed_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const +{ + // Only allocate for fixed-len string. + + // Get the size of the dataset's data + size_t attr_size = getInMemDataSize(); + + // If there is data, allocate buffer and read it. + if (attr_size > 0) + { + char *strg_C = NULL; + + strg_C = new char [(size_t)attr_size+1]; + herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C); + + if( ret_value < 0 ) + { + delete []strg_C; // de-allocate for fixed-len string + throw DataSetIException("DataSet::read", "H5Dread failed for fixed length string"); + } + + // Get string from the C char* and release resource allocated locally + strg = strg_C; + delete []strg_C; + } +} + +//-------------------------------------------------------------------------- +// Function: DataSet::p_read_variable_len (private) +// brief Reads a variable length \a H5std_string from an dataset. +// param mem_type - IN: DataSet datatype (in memory) +// param strg - IN: Buffer for read string +// exception H5::DataSetIException +// Programmer Binh-Minh Ribler - Jul, 2009 +// Modification +// Jul 2009 +// Added in follow to the change in Attribute::read +//-------------------------------------------------------------------------- +void DataSet::p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const +{ + // Prepare and call C API to read dataset. + char *strg_C; + + // Read dataset, no allocation for variable-len string; C library will + herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C); + + if( ret_value < 0 ) + { + throw DataSetIException("DataSet::read", "H5Dread failed for variable length string"); + } + + // Get string from the C char* and release resource allocated by C API + strg = strg_C; + HDfree(strg_C); +} + +//-------------------------------------------------------------------------- +// Function: DataSet::p_setId (private) ///\brief Sets the identifier of this object to a new value. /// ///\exception H5::IdComponentException when the attempt to close the HDF5 |