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authorBinh-Minh Ribler <bmribler@hdfgroup.org>2009-07-27 04:00:17 (GMT)
committerBinh-Minh Ribler <bmribler@hdfgroup.org>2009-07-27 04:00:17 (GMT)
commitc1ad3676c4b56b80663d271ac367a65cc41c39ab (patch)
tree42f19502941ff1d02d45b92a7f8a0a3f6945002e
parent405ea51bb7728dc696e29694b22e81dc4b6ce2c1 (diff)
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[svn-r17238] Purpose: Fix bug and improve readability
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)
-rw-r--r--c++/src/H5AbstractDs.cpp5
-rw-r--r--c++/src/H5AbstractDs.h3
-rw-r--r--c++/src/H5Attribute.cpp14
-rw-r--r--c++/src/H5Attribute.h6
-rw-r--r--c++/src/H5DataSet.cpp203
-rw-r--r--c++/src/H5DataSet.h9
-rw-r--r--c++/test/tvlstr.cpp369
7 files changed, 432 insertions, 177 deletions
diff --git a/c++/src/H5AbstractDs.cpp b/c++/src/H5AbstractDs.cpp
index a61cc88..19eeb33 100644
--- a/c++/src/H5AbstractDs.cpp
+++ b/c++/src/H5AbstractDs.cpp
@@ -25,6 +25,11 @@
#include "H5CommonFG.h"
#include "H5Alltypes.h"
+#include <iostream> // remove when done
+
+ using std::cerr;
+ using std::endl;
+
#ifndef H5_NO_NAMESPACE
namespace H5 {
#endif
diff --git a/c++/src/H5AbstractDs.h b/c++/src/H5AbstractDs.h
index c98e5e1..1d04d6c 100644
--- a/c++/src/H5AbstractDs.h
+++ b/c++/src/H5AbstractDs.h
@@ -51,6 +51,9 @@ class H5_DLLCPP AbstractDs {
StrType getStrType() const;
VarLenType getVarLenType() const;
+ // Gets the size in memory of this abstract dataset.
+ virtual size_t getInMemDataSize() const = 0;
+
// Gets the dataspace of this abstract dataset - pure virtual.
virtual DataSpace getSpace() const = 0;
diff --git a/c++/src/H5Attribute.cpp b/c++/src/H5Attribute.cpp
index b1ab73e..6de5e63 100644
--- a/c++/src/H5Attribute.cpp
+++ b/c++/src/H5Attribute.cpp
@@ -198,35 +198,37 @@ void Attribute::read(const DataType& mem_type, H5std_string& strg) const
//--------------------------------------------------------------------------
size_t Attribute::getInMemDataSize() const
{
+ char *func = "Attribute::getInMemDataSize";
+
// Get the data type of this attribute
hid_t mem_type_id = H5Aget_type(id);
- if (mem_type_id <= 0)
+ if( mem_type_id < 0 )
{
- throw AttributeIException("Attribute::getInMemDataSize", "H5Aget_type failed");
+ throw AttributeIException(func, "H5Aget_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 AttributeIException("Attribute::getInMemDataSize", "H5Tget_native_type failed");
+ throw AttributeIException(func, "H5Tget_native_type failed");
}
size_t type_size = H5Tget_size(native_type);
if (type_size == 0)
{
- throw AttributeIException("Attribute::getInMemDataSize", "H5Tget_size failed");
+ throw AttributeIException(func, "H5Tget_size failed");
}
// Get number of elements of the attribute
hid_t space_id = H5Aget_space(id);
if (space_id < 0)
{
- throw AttributeIException("Attribute::getInMemDataSize", "H5Aget_space failed");
+ throw AttributeIException(func, "H5Aget_space failed");
}
hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
if (num_elements < 0)
{
- throw AttributeIException("Attribute::getInMemDataSize", "H5Sget_simple_extent_npoints failed");
+ throw AttributeIException(func, "H5Sget_simple_extent_npoints failed");
}
// Calculate and return the size of the data
diff --git a/c++/src/H5Attribute.h b/c++/src/H5Attribute.h
index abece10..284e5bc 100644
--- a/c++/src/H5Attribute.h
+++ b/c++/src/H5Attribute.h
@@ -38,10 +38,10 @@ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent {
virtual DataSpace getSpace() const;
// Returns the amount of storage size required for this attribute.
- hsize_t getStorageSize() const;
+ virtual hsize_t getStorageSize() const;
// Returns the in memory size of this attribute's data.
- size_t getInMemDataSize() const;
+ virtual size_t getInMemDataSize() const;
// Reads data from this attribute.
void read( const DataType& mem_type, void *buf ) const;
@@ -82,7 +82,7 @@ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent {
// sub-types
virtual hid_t p_get_type() const;
- // Reads variable or fixed len strings
+ // Reads variable or fixed len strings from this attribute.
void p_read_variable_len(const DataType& mem_type, H5std_string& strg) const;
void p_read_fixed_len(const DataType& mem_type, H5std_string& strg) const;
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
diff --git a/c++/src/H5DataSet.h b/c++/src/H5DataSet.h
index f26d775..3d9183d 100644
--- a/c++/src/H5DataSet.h
+++ b/c++/src/H5DataSet.h
@@ -49,7 +49,10 @@ class H5_DLLCPP DataSet : public H5Object, public AbstractDs {
void getSpaceStatus(H5D_space_status_t& status) const;
// Returns the amount of storage size required for this dataset.
- hsize_t getStorageSize() const;
+ virtual hsize_t getStorageSize() const;
+
+ // Returns the in memory size of this attribute's data.
+ virtual size_t getInMemDataSize() const;
// Returns the number of bytes required to store VL data.
hsize_t getVlenBufSize( DataType& type, DataSpace& space ) const;
@@ -113,6 +116,10 @@ class H5_DLLCPP DataSet : public H5Object, public AbstractDs {
// sub-types
virtual hid_t p_get_type() const;
+ // Reads variable or fixed len strings from this dataset.
+ void 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;
+ void 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;
+
protected:
// Sets the dataset id.
virtual void p_setId(const hid_t new_id);
diff --git a/c++/test/tvlstr.cpp b/c++/test/tvlstr.cpp
index 0abab1b..01033be 100644
--- a/c++/test/tvlstr.cpp
+++ b/c++/test/tvlstr.cpp
@@ -18,7 +18,6 @@
tvlstr.cpp - HDF5 C++ testing the Variable-Length String functionality
EXTERNAL ROUTINES/VARIABLES:
- These routines are in the test directory of the C library:
***************************************************************************/
@@ -52,7 +51,7 @@ const H5std_string FILENAME("tvlstr.h5");
const int SPACE1_RANK = 1;
const hsize_t SPACE1_DIM1 = 4;
-// Utility functions
+// Utility functions - not used now, later though.
void *test_vlstr_alloc_custom(size_t size, void *info);
void test_vlstr_free_custom(void *mem, void *info);
@@ -119,9 +118,9 @@ void test_vlstr_free_custom(void *_mem, void *info)
}
/*-------------------------------------------------------------------------
- * Function: test_vlstrings_basic
+ * Function: test_vlstring_dataset
*
- * Purpose: Test simple VL string I/O.
+ * Purpose: Test writing/reading VL strings on datasets.
*
* Return: None
*
@@ -130,98 +129,171 @@ void test_vlstr_free_custom(void *_mem, void *info)
*
*-------------------------------------------------------------------------
*/
-static void test_vlstrings_basic()
+// String for testing datasets
+static char *dynstring_ds_write=NULL;
+static char stastring_ds_write[1]={'A'};
+
+// Info for a string dataset
+const H5std_string DSET1_NAME("String_ds");
+const H5std_string DSET1_DATA("String Dataset");
+
+static void test_vlstring_dataset()
+{
+ // Output message about test being performed
+ SUBTEST("Testing VL String on Datasets");
+
+ try {
+ // Open the file
+ H5File file1(FILENAME, H5F_ACC_TRUNC);
+
+ // Create a datatype to refer to.
+ StrType vlst(0, H5T_VARIABLE);
+
+ // Open the root group.
+ Group root = file1.openGroup("/");
+
+ // Create dataspace for the dataset.
+ DataSpace ds_space (H5S_SCALAR);
+
+ // Create an dataset in the root group.
+ DataSet dset1 = root.createDataSet(DSET1_NAME, vlst, ds_space);
+
+ // Write data to the dataset.
+ dset1.write(DSET1_DATA, vlst);
+
+ // Read and verify the dataset string as a string of chars.
+ char *string_ds_check;
+ dset1.read(&string_ds_check, vlst);
+ if(HDstrcmp(string_ds_check, DSET1_DATA.c_str())!=0)
+ TestErrPrintf("Line %d: Attribute data different: DSET1_DATA=%s,string_ds_check=%s\n",__LINE__, DSET1_DATA.c_str(), string_ds_check);
+
+ HDfree(string_ds_check); // note: no need for std::string test
+
+ // Read and verify the dataset string as an std::string.
+ H5std_string read_str;
+ dset1.read(read_str, vlst);
+ if (read_str != DSET1_DATA)
+ TestErrPrintf("Line %d: Attribute data different: DSET1_DATA=%s,read_str=%s\n",__LINE__, DSET1_DATA.c_str(), read_str.c_str());
+
+ // Close the dataset.
+ dset1.close();
+
+ // Test scalar type dataset with 1 value.
+ dset1 = root.createDataSet("test_scalar_small", vlst, ds_space);
+
+ dynstring_ds_write = (char*)HDcalloc(1, sizeof(char));
+ HDmemset(dynstring_ds_write, 'A', 1);
+
+ // Write data to the dataset, then read it back.
+ dset1.write(&dynstring_ds_write, vlst);
+ dset1.read(&string_ds_check, vlst);
+
+ // Verify data read.
+ if(HDstrcmp(string_ds_check,dynstring_ds_write)!=0)
+ TestErrPrintf("VL string datasets don't match!, dynstring_ds_write=%s, string_ds_check=%s\n",dynstring_ds_write,string_ds_check);
+ HDfree(string_ds_check);
+ dset1.close();
+
+ // Open dataset DSET1_NAME again.
+ dset1 = root.openDataSet(DSET1_NAME);
+
+ // Close dataset and file
+ dset1.close();
+ file1.close();
+
+ PASSED();
+ } // end try block
+
+ // Catch all exceptions.
+ catch (Exception E) {
+ issue_fail_msg("test_vlstring_dataset()", __LINE__, __FILE__, E.getCDetailMsg());
+ }
+} // test_vlstring_dataset()
+
+/*-------------------------------------------------------------------------
+ * Function: test_vlstring_array_dataset
+ *
+ * Purpose: Test writing/reading VL string array to/from datasets.
+ *
+ * Return: None
+ *
+ * Programmer: Binh-Minh Ribler
+ * July, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+const H5std_string DSSTRARR_NAME("StringArray_dset");
+static void test_vlstring_array_dataset()
{
- const char *wdata[SPACE1_DIM1]= {
- "Four score and seven years ago our forefathers brought forth on this continent a new nation,",
- "conceived in liberty and dedicated to the proposition that all men are created equal.",
- "Now we are engaged in a great civil war,",
- "testing whether that nation or any nation so conceived and so dedicated can long endure."
+ const char *string_ds_array[SPACE1_DIM1]= {
+ "Line 1", "Line 2", "Line 3", "Line 4"
}; // Information to write
// Output message about test being performed
- SUBTEST("Testing Basic VL String Functionality");
+ SUBTEST("Testing VL String Array on Datasets");
- H5File* file1 = NULL;
+ H5File* file1;
try {
// Create file.
- file1 = new H5File (FILENAME, H5F_ACC_TRUNC);
+ file1 = new H5File (FILENAME, H5F_ACC_RDWR);
- // Create dataspace for datasets.
- hsize_t dims1[] = {SPACE1_DIM1};
- DataSpace sid1(SPACE1_RANK, dims1);
+ // Create dataspace for datasets.
+ hsize_t dims1[] = {SPACE1_DIM1};
+ DataSpace ds_space(SPACE1_RANK, dims1);
// Create a datatype to refer to.
- StrType tid1(0, H5T_VARIABLE);
+ StrType vlst(0, H5T_VARIABLE);
// Create and write a dataset.
- DataSet dataset(file1->createDataSet("Dataset1", tid1, sid1));
- dataset.write(wdata, tid1);
+ DataSet dataset(file1->createDataSet(DSSTRARR_NAME, vlst, ds_space));
+ dataset.write(string_ds_array, vlst);
+
+ // Read and verify the dataset using strings of chars as buffer.
+ // Note: reading by array of H5std_string doesn't work yet.
+ char *string_ds_check[SPACE1_DIM1];
+ dataset.read(string_ds_check, vlst);
+
+ int ii;
+ for (ii = 0; ii < SPACE1_DIM1; ii++)
+ {
+ if(HDstrcmp(string_ds_check[ii], string_ds_array[ii])!=0)
+ TestErrPrintf("Line %d: Dataset data different: written=%s,read=%s\n",__LINE__, string_ds_array[ii], string_ds_check[ii]);
+
+ HDfree(string_ds_check[ii]);
+ }
+
+ // Close objects that are no longer needed.
+ dataset.close();
+ ds_space.close();
+
+ //
+ // Test with scalar data space.
+ //
// Create H5S_SCALAR data space.
DataSpace scalar_space;
// Create and write another dataset.
- DataSet dataset2(file1->createDataSet("Dataset2", tid1, scalar_space));
+ DataSet dataset2(file1->createDataSet("Dataset2", vlst, scalar_space));
char *wdata2 = (char*)HDcalloc(65534, sizeof(char));
HDmemset(wdata2, 'A', 65533);
- dataset2.write(&wdata2, tid1);
+ dataset2.write(&wdata2, vlst);
+
+ char *rdata2 = (char*)HDcalloc(65534, sizeof(char));
+ HDmemset(rdata2, 0, 65533);
+ dataset2.read(&rdata2, vlst);
+ if (HDstrcmp(wdata2, rdata2)!=0)
+ TestErrPrintf("Line %d: Dataset data different: written=%s,read=%s\n",__LINE__, wdata2, rdata2);
// Release resources from second dataset operation.
scalar_space.close();
dataset2.close();
HDfree(wdata2);
-
- // Change to the custom memory allocation routines for reading
- // VL string.
- DSetMemXferPropList xfer;
- size_t mem_used = 0; // Memory used during allocation
- xfer.setVlenMemManager(test_vlstr_alloc_custom, &mem_used, test_vlstr_free_custom, &mem_used);
-
- // Make certain the correct amount of memory will be used.
- hsize_t vlsize = dataset.getVlenBufSize(tid1, sid1);
-
- // Count the actual number of bytes used by the strings.
- size_t str_used; // String data in memory
- hsize_t i; // counting variable
- for (i=0,str_used=0; i<SPACE1_DIM1; i++)
- str_used+=HDstrlen(wdata[i])+1;
-
- // Compare against the strings actually written.
- verify_val((int)vlsize,str_used,"DataSet::getVlenBufSize", __LINE__, __FILE__);
-
- // Read dataset from disk.
- char *rdata[SPACE1_DIM1]; // Data read in
- dataset.read(rdata, tid1, DataSpace::ALL, DataSpace::ALL, xfer);
-
- // Make certain the correct amount of memory has been used.
- verify_val(mem_used, str_used, "DataSet::read", __LINE__, __FILE__);
-
- // Compare data read in.
- for(i = 0; i < SPACE1_DIM1; i++) {
- size_t wlen = HDstrlen(wdata[i]);
- size_t rlen = HDstrlen(rdata[i]);
- if(wlen != rlen) {
- TestErrPrintf("VL data lengths don't match!, strlen(wdata[%d])=%u, strlen(rdata[%d])=%u\n", (int)i, (unsigned)wlen, (int)i, (unsigned)rlen);
- continue;
- } // end if
- if(HDstrcmp(wdata[i], rdata[i]) != 0) {
- TestErrPrintf("VL data values don't match!, wdata[%d]=%s, rdata[%d]=%s\n", (int)i, wdata[i], (int)i, rdata[i]);
- continue;
- } // end if
- } // end for
-
- // Reclaim the read VL data.
- DataSet::vlenReclaim((void *)rdata, tid1, sid1, xfer);
-
- // Make certain the VL memory has been freed.
- verify_val(mem_used, 0, "DataSet::vlenReclaim", __LINE__, __FILE__);
+ HDfree(rdata2);
// Close objects and file.
- dataset.close();
- tid1.close();
- sid1.close();
- xfer.close();
+ dataset2.close();
+ vlst.close();
file1->close();
PASSED();
@@ -230,11 +302,10 @@ static void test_vlstrings_basic()
// Catch all exceptions.
catch (Exception E)
{
- issue_fail_msg("test_vlstrings_basic()", __LINE__, __FILE__, E.getCDetailMsg());
- if (file1 != NULL) // clean up
- delete file1;
+ issue_fail_msg("test_vlstring_array_dataset()", __LINE__, __FILE__, E.getCDetailMsg());
+ delete file1;
}
-} // end test_vlstrings_basic()
+} // end test_vlstring_array_dataset()
/*-------------------------------------------------------------------------
* Function: test_vlstrings_special
@@ -267,13 +338,13 @@ static void test_vlstrings_special()
DataSpace sid1(SPACE1_RANK, dims1);
// Create a datatype to refer to.
- StrType tid1(0, H5T_VARIABLE);
+ StrType vlst(0, H5T_VARIABLE);
// Create a dataset.
- DataSet dataset(file1.createDataSet("Dataset3", tid1, sid1));
+ DataSet dataset(file1.createDataSet("Dataset3", vlst, sid1));
// Read from the dataset before writing data.
- dataset.read(rdata, tid1);
+ dataset.read(rdata, vlst);
// Check data read in.
hsize_t i; // counting variable
@@ -282,8 +353,8 @@ static void test_vlstrings_special()
TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i,rdata[i]);
// Write dataset to disk, then read it back.
- dataset.write(wdata, tid1);
- dataset.read(rdata, tid1);
+ dataset.write(wdata, vlst);
+ dataset.read(rdata, vlst);
// Compare data read in.
for(i = 0; i < SPACE1_DIM1; i++) {
@@ -300,7 +371,7 @@ static void test_vlstrings_special()
} // end for
// Reclaim the read VL data.
- DataSet::vlenReclaim((void *)rdata, tid1, sid1);
+ DataSet::vlenReclaim((void *)rdata, vlst, sid1);
// Close Dataset.
dataset.close();
@@ -313,14 +384,14 @@ static void test_vlstrings_special()
// dataset.
DSetCreatPropList dcpl;
char *fill = NULL; // Fill value
- dcpl.setFillValue(tid1, &fill);
- dataset = file1.createDataSet("Dataset4", tid1, sid1, dcpl);
+ dcpl.setFillValue(vlst, &fill);
+ dataset = file1.createDataSet("Dataset4", vlst, sid1, dcpl);
// Close dataset creation property list.
dcpl.close();
// Read from dataset before writing data.
- dataset.read(rdata, tid1);
+ dataset.read(rdata, vlst);
// Check data read in.
for (i=0; i<SPACE1_DIM1; i++)
@@ -328,10 +399,10 @@ static void test_vlstrings_special()
TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i, rdata[i]);
// Try to write nil strings to disk.
- dataset.write(wdata2, tid1);
+ dataset.write(wdata2, vlst);
// Read nil strings back from disk.
- dataset.read(rdata, tid1);
+ dataset.read(rdata, vlst);
// Check data read in.
for (i=0; i<SPACE1_DIM1; i++)
@@ -340,7 +411,7 @@ static void test_vlstrings_special()
// Close objects and file.
dataset.close();
- tid1.close();
+ vlst.close();
sid1.close();
file1.close();
@@ -370,7 +441,7 @@ const H5std_string VLSTR_TYPE("vl_string_type");
static void test_vlstring_type()
{
// Output message about test being performed.
- SUBTEST("Testing VL String type");
+ SUBTEST("Testing VL String Type");
H5File* file1 = NULL;
try {
@@ -378,55 +449,55 @@ static void test_vlstring_type()
file1 = new H5File(FILENAME, H5F_ACC_RDWR);
// Create a datatype to refer to.
- StrType vlstr_type(PredType::C_S1);
+ StrType vlst(PredType::C_S1);
// Change padding and verify it.
- vlstr_type.setStrpad(H5T_STR_NULLPAD);
- H5T_str_t pad = vlstr_type.getStrpad();
+ vlst.setStrpad(H5T_STR_NULLPAD);
+ H5T_str_t pad = vlst.getStrpad();
verify_val(pad, H5T_STR_NULLPAD, "StrType::getStrpad", __LINE__, __FILE__);
// Convert to variable-length string.
- vlstr_type.setSize(H5T_VARIABLE);
+ vlst.setSize(H5T_VARIABLE);
// Check if datatype is VL string.
- H5T_class_t type_class = vlstr_type.getClass();
+ H5T_class_t type_class = vlst.getClass();
verify_val(type_class, H5T_STRING, "DataType::getClass", __LINE__, __FILE__);
- bool is_variable_str = vlstr_type.isVariableStr();
+ bool is_variable_str = vlst.isVariableStr();
verify_val(is_variable_str, TRUE, "DataType::isVariableStr", __LINE__, __FILE__);
// Check default character set and padding.
- H5T_cset_t cset = vlstr_type.getCset();
+ H5T_cset_t cset = vlst.getCset();
verify_val(cset, H5T_CSET_ASCII, "StrType::getCset", __LINE__, __FILE__);
- pad = vlstr_type.getStrpad();
+ pad = vlst.getStrpad();
verify_val(pad, H5T_STR_NULLPAD, "StrType::getStrpad", __LINE__, __FILE__);
// Commit variable-length string datatype to storage.
- vlstr_type.commit(*file1, VLSTR_TYPE);
+ vlst.commit(*file1, VLSTR_TYPE);
// Close datatype.
- vlstr_type.close();
+ vlst.close();
// Try opening datatype again.
- vlstr_type = file1->openStrType(VLSTR_TYPE);
+ vlst = file1->openStrType(VLSTR_TYPE);
// Close datatype and file.
- vlstr_type.close();
+ vlst.close();
file1->close();
// Open file.
file1 = new H5File(FILENAME, H5F_ACC_RDWR);
// Open the variable-length string datatype just created
- vlstr_type = file1->openStrType(VLSTR_TYPE);
+ vlst = file1->openStrType(VLSTR_TYPE);
// Verify character set and padding
- cset = vlstr_type.getCset();
+ cset = vlst.getCset();
verify_val(cset, H5T_CSET_ASCII, "StrType::getCset", __LINE__, __FILE__);
- pad = vlstr_type.getStrpad();
+ pad = vlst.getStrpad();
verify_val(pad, H5T_STR_NULLPAD, "StrType::getStrpad", __LINE__, __FILE__);
// Close datatype and file
- vlstr_type.close();
+ vlst.close();
file1->close();
PASSED();
@@ -436,6 +507,7 @@ static void test_vlstring_type()
catch (Exception E)
{
issue_fail_msg("test_vlstring_type()", __LINE__, __FILE__, E.getCDetailMsg());
+ delete file1;
}
} // end test_vlstring_type()
@@ -454,7 +526,7 @@ static void test_vlstring_type()
static void test_compact_vlstring()
{
// Output message about test being performed
- SUBTEST("Testing VL Strings in compact dataset");
+ SUBTEST("Testing VL Strings on Compact Dataset");
try {
// Create file
@@ -465,22 +537,22 @@ static void test_compact_vlstring()
DataSpace sid1(SPACE1_RANK, dims1);
// Create a datatype to refer to
- StrType tid1(0, H5T_VARIABLE);
+ StrType vlst(0, H5T_VARIABLE);
// Create dataset create property list and set layout
DSetCreatPropList plist;
plist.setLayout(H5D_COMPACT);
// Create a dataset
- DataSet dataset(file1.createDataSet("Dataset5", tid1, sid1, plist));
+ DataSet dataset(file1.createDataSet("Dataset5", vlst, sid1, plist));
// Write dataset to disk
const char *wdata[SPACE1_DIM1] = {"one", "two", "three", "four"};
- dataset.write(wdata, tid1);
+ dataset.write(wdata, vlst);
// Read dataset from disk
char *rdata[SPACE1_DIM1]; // Information read in
- dataset.read(rdata, tid1);
+ dataset.read(rdata, vlst);
// Compare data read in
hsize_t i;
@@ -496,11 +568,11 @@ static void test_compact_vlstring()
} // end for
// Reclaim the read VL data
- DataSet::vlenReclaim((void *)rdata, tid1, sid1);
+ DataSet::vlenReclaim((void *)rdata, vlst, sid1);
// Close objects and file
dataset.close();
- tid1.close();
+ vlst.close();
sid1.close();
plist.close();
file1.close();
@@ -516,9 +588,9 @@ static void test_compact_vlstring()
} // test_compact_vlstrings
/*-------------------------------------------------------------------------
- * Function: test_write_vl_string_attribute
+ * Function: test_vlstring_attribute
*
- * Purpose: Test writing VL strings as attributes.
+ * Purpose: Test writing/reading VL strings on attributes.
*
* Return: None
*
@@ -534,17 +606,17 @@ static char *string_att_write=NULL;
const H5std_string ATTRSTR_NAME("String_attr");
const H5std_string ATTRSTR_DATA("String Attribute");
-static void test_write_vl_string_attribute()
+static void test_vlstring_attribute()
{
// Output message about test being performed
- SUBTEST("Testing writing VL String as attributes");
+ SUBTEST("Testing VL String on Attributes");
try {
// Open the file
H5File file1(FILENAME, H5F_ACC_RDWR);
// Create a datatype to refer to.
- StrType tid1(0, H5T_VARIABLE);
+ StrType vlst(0, H5T_VARIABLE);
// Open the root group.
Group root = file1.openGroup("/");
@@ -553,14 +625,14 @@ static void test_write_vl_string_attribute()
DataSpace att_space (H5S_SCALAR);
// Create an attribute for the root group.
- Attribute gr_attr = root.createAttribute(ATTRSTR_NAME, tid1, att_space);
+ Attribute gr_attr = root.createAttribute(ATTRSTR_NAME, vlst, att_space);
// Write data to the attribute.
- gr_attr.write(tid1, ATTRSTR_DATA);
+ gr_attr.write(vlst, ATTRSTR_DATA);
// Read and verify the attribute string as a string of chars.
char *string_att_check;
- gr_attr.read(tid1, &string_att_check);
+ gr_attr.read(vlst, &string_att_check);
if(HDstrcmp(string_att_check, ATTRSTR_DATA.c_str())!=0)
TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,string_att_check=%s\n",__LINE__, ATTRSTR_DATA.c_str(), string_att_check);
@@ -568,7 +640,7 @@ static void test_write_vl_string_attribute()
// Read and verify the attribute string as an std::string.
H5std_string read_str;
- gr_attr.read(tid1, read_str);
+ gr_attr.read(vlst, read_str);
if (read_str != ATTRSTR_DATA)
TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,read_str=%s\n",__LINE__, ATTRSTR_DATA.c_str(), read_str.c_str());
@@ -576,28 +648,22 @@ static void test_write_vl_string_attribute()
gr_attr.close();
// Test creating a "large" sized string attribute
- gr_attr = root.createAttribute("test_scalar_large", tid1, att_space);
+ gr_attr = root.createAttribute("test_scalar_large", vlst, att_space);
string_att_write = (char*)HDcalloc(8192, sizeof(char));
HDmemset(string_att_write, 'A', 8191);
// Write data to the attribute, then read it back.
- gr_attr.write(tid1, &string_att_write);
- gr_attr.read(tid1, &string_att_check);
+ gr_attr.write(vlst, &string_att_write);
+ gr_attr.read(vlst, &string_att_check);
// Verify data read.
if(HDstrcmp(string_att_check,string_att_write)!=0)
TestErrPrintf("VL string attributes don't match!, string_att_write=%s, string_att_check=%s\n",string_att_write,string_att_check);
- HDfree(string_att_check);
- gr_attr.close();
-
- // Open attribute ATTRSTR_NAME again.
- gr_attr = root.openAttribute(ATTRSTR_NAME);
- // The attribute string written is freed below, in the
- // test_read_vl_string_attribute() test
-
- // Close attribute and file
+ // Release resources.
+ HDfree(string_att_check);
+ HDfree(string_att_write);
gr_attr.close();
file1.close();
@@ -606,9 +672,9 @@ static void test_write_vl_string_attribute()
// Catch all exceptions.
catch (Exception E) {
- issue_fail_msg("test_string_attr()", __LINE__, __FILE__, E.getCDetailMsg());
+ issue_fail_msg("test_vlstring_attribute()", __LINE__, __FILE__, E.getCDetailMsg());
}
-} // test_string_attr()
+} // test_vlstring_attribute()
/*-------------------------------------------------------------------------
* Function: test_read_vl_string_attribute
@@ -633,7 +699,7 @@ static void test_read_vl_string_attribute()
H5File file1(FILENAME, H5F_ACC_RDONLY);
// Create a datatype to refer to.
- StrType tid1(0, H5T_VARIABLE);
+ StrType vlst(0, H5T_VARIABLE);
// Open the root group and its attribute named ATTRSTR_NAME.
Group root = file1.openGroup("/");
@@ -641,7 +707,7 @@ static void test_read_vl_string_attribute()
// Test reading "normal" sized string attribute
char *string_att_check;
- att.read(tid1, &string_att_check);
+ att.read(vlst, &string_att_check);
if(HDstrcmp(string_att_check,ATTRSTR_DATA.c_str())!=0)
TestErrPrintf("VL string attributes don't match!, string_att=%s, string_att_check=%s\n",ATTRSTR_DATA.c_str(),string_att_check);
HDfree(string_att_check);
@@ -649,7 +715,7 @@ static void test_read_vl_string_attribute()
// Test reading "large" sized string attribute
att = root.openAttribute("test_scalar_large");
- att.read(tid1, &string_att_check);
+ att.read(vlst, &string_att_check);
if(HDstrcmp(string_att_check,string_att_write)!=0)
TestErrPrintf("VL string attributes don't match!, string_att_write=%s, string_att_check=%s\n",string_att_write,string_att_check);
HDfree(string_att_check);
@@ -657,7 +723,7 @@ static void test_read_vl_string_attribute()
// Close objects and file.
att.close();
- tid1.close();
+ vlst.close();
root.close();
file1.close();
@@ -672,7 +738,7 @@ static void test_read_vl_string_attribute()
/*-------------------------------------------------------------------------
- * Function: test_vl_stringarray_attribute
+ * Function: test_vlstring_array_attribute
*
* Purpose: Test writing/reading VL string array to/from attributes.
*
@@ -685,21 +751,21 @@ static void test_read_vl_string_attribute()
*/
const H5std_string ATTRSTRARR_NAME("StringArray_attr");
-static void test_vl_stringarray_attribute()
+static void test_vlstring_array_attribute()
{
const char *string_att_array[SPACE1_DIM1]= {
"Line 1", "Line 2", "Line 3", "Line 4"
}; // Information to write
// Output message about test being performed
- SUBTEST("Testing writing/reading VL String Array on attribute");
+ SUBTEST("Testing VL String Array on Attributes");
try {
// Open the file
H5File file1(FILENAME, H5F_ACC_RDWR);
// Create a datatype to refer to.
- StrType tid1(0, H5T_VARIABLE);
+ StrType vlst(0, H5T_VARIABLE);
// Open the root group.
Group root = file1.openGroup("/");
@@ -709,15 +775,15 @@ static void test_vl_stringarray_attribute()
DataSpace att_space(SPACE1_RANK, dims1);
// Create an attribute for the root group.
- Attribute gr_attr = root.createAttribute(ATTRSTRARR_NAME, tid1, att_space);
+ Attribute gr_attr = root.createAttribute(ATTRSTRARR_NAME, vlst, att_space);
// Write data to the attribute.
- gr_attr.write(tid1, string_att_array);
+ gr_attr.write(vlst, string_att_array);
// Read and verify the attribute string as a string of chars.
// Note: reading by array of H5std_string doesn't work yet.
char *string_att_check[SPACE1_DIM1];
- gr_attr.read(tid1, &string_att_check);
+ gr_attr.read(vlst, &string_att_check);
int ii;
for (ii = 0; ii < SPACE1_DIM1; ii++)
@@ -737,9 +803,9 @@ static void test_vl_stringarray_attribute()
// Catch all exceptions.
catch (Exception E) {
- issue_fail_msg("test_string_attr()", __LINE__, __FILE__, E.getCDetailMsg());
+ issue_fail_msg("test_vlstring_array_attribute()", __LINE__, __FILE__, E.getCDetailMsg());
}
-} // test_vl_stringarray_attribute()
+} // test_vlstring_array_attribute()
/* Helper routine for test_vl_rewrite() */
static void write_scalar_dset(H5File& file, DataType& type, DataSpace& space,
@@ -885,17 +951,18 @@ void test_vlstrings()
// These tests use the same file
// Test basic VL string datatype
- test_vlstrings_basic();
+ test_vlstring_dataset();
test_vlstrings_special();
test_vlstring_type();
test_compact_vlstring();
// Test using VL strings in attributes
- test_write_vl_string_attribute();
- test_read_vl_string_attribute();
+ test_vlstring_attribute();
+ // test_read_vl_string_attribute();
- // Test using VL string array in attributes
- test_vl_stringarray_attribute();
+ // Test using VL string array in attributes and datasets
+ test_vlstring_array_attribute();
+ test_vlstring_array_dataset();
// Test writing VL datasets in files with lots of unlinking
test_vl_rewrite();