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[svn-r17238] Purpose: Fix bug and improve readability

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Description:
    - Revised DataSet::write to pass in correct string buffer
    - Added member function DataSet::getInMemDataSize() to simplify
      getting the dataset's data size in memory.
    - Added private functions for reading fixed- and variable-length
      string data: p_read_fixed_len and p_read_variable_len.
    - Added tests to write/read array of strings to datasets.

Platforms tested:
    Linux/32 2.6 (jam)
    FreeBSD/64 6.3 (liberty)
    SunOS 5.10 (linew)
This commit is contained in:
Binh-Minh Ribler
2009-07-26 23:00:17 -05:00
parent 405ea51bb7
commit c1ad3676c4
7 changed files with 431 additions and 176 deletions
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201
c++/src/H5DataSet.cpp
View File

@@ -37,6 +37,7 @@
#include "H5File.h"
#include "H5Attribute.h"
#include "H5DataSet.h"
#include "H5private.h" // for HDfree
#ifndef H5_NO_NAMESPACE
namespace H5 {
@@ -219,6 +220,53 @@ hsize_t DataSet::getStorageSize() const
return(storage_size);
}
//--------------------------------------------------------------------------
// 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.
@@ -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
// 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
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");
}
// Use the overloaded member
write(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();
// 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;
// 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