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[svn-r24163] Purpose: More on HDFFV-7520 and HDFFV-533

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Description:
    - Improved the changes in revisions r22836 and r23438, mainly on the
      wrappers of reference, dereference, get region, and set/getcomment.
    - Added more tests.

Platforms tested:
    Linux/32 2.6 (jam)
    SunOS 5.11 (emu)
    Linux/ppc64 (ostrich)
This commit is contained in:
Binh-Minh Ribler 2013-09-18 22:08:28 -05:00
parent d95f5e293a
commit 4182c81add
17 changed files with 906 additions and 376 deletions
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1
c++/src/H5Attribute.cpp
View File

@ -44,6 +44,7 @@ namespace H5 {
#endif // H5_NO_STD
#endif
class H5_DLLCPP H5Object; // forward declaration for UserData4Aiterate
//--------------------------------------------------------------------------
// Function: Attribute default constructor
///\brief Default constructor: Creates a stub attribute

131
c++/src/H5CommonFG.cpp
View File

@ -459,137 +459,6 @@ H5std_string CommonFG::getLinkval( const H5std_string& name, size_t size ) const
return( getLinkval( name.c_str(), size ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::setComment
///\brief Sets or resets the comment for an object specified by its name.
///\param name - IN: Name of the object
///\param comment - IN: New comment
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// If \a comment is an empty string or a null pointer, the comment
/// message is removed from the object.
/// Comments should be relatively short, null-terminated, ASCII
/// strings. They can be attached to any object that has an
/// object header, e.g., data sets, groups, named data types,
/// and data spaces, but not symbolic links.
// Programmer Binh-Minh Ribler - 2000
// Modification
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
void CommonFG::setComment( const char* name, const char* comment ) const
{
herr_t ret_value = H5Oset_comment_by_name( getLocId(), name, comment, H5P_DEFAULT );
if( ret_value < 0 )
throwException("setComment", "H5Oset_comment_by_name failed");
}
//--------------------------------------------------------------------------
// Function: CommonFG::setComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name and \a comment.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::setComment( const H5std_string& name, const H5std_string& comment ) const
{
setComment( name.c_str(), comment.c_str() );
}
//--------------------------------------------------------------------------
// Function: CommonFG::removeComment
///\brief Removes the comment from an object specified by its name.
///\param name - IN: Name of the object
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - May 2005
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
void CommonFG::removeComment(const char* name) const
{
herr_t ret_value = H5Oset_comment_by_name(getLocId(), name, NULL, H5P_DEFAULT);
if( ret_value < 0 )
throwException("removeComment", "H5Oset_comment_by_name failed");
}
//--------------------------------------------------------------------------
// Function: CommonFG::removeComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - May 2005
//--------------------------------------------------------------------------
void CommonFG::removeComment(const H5std_string& name) const
{
removeComment (name.c_str());
}
//--------------------------------------------------------------------------
// Function: CommonFG::getComment
///\brief Retrieves comment for the specified object and its comment's
/// length.
///\param name - IN: Name of the object
///\param bufsize - IN: Length of the comment to retrieve
///\return Comment string
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
H5std_string CommonFG::getComment( const char* name, size_t bufsize ) const
{
// bufsize is default to 256
// temporary variable
hid_t loc_id = getLocId(); // temporary variable
// temporary C-string for the object's comment; bufsize already including
// null character
char* comment_C = new char[bufsize];
ssize_t ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, bufsize, H5P_DEFAULT);
// if the actual length of the comment is longer than bufsize and bufsize
// was the default value, i.e., not given by the user, then call
// H5Oget_comment_by_name again with the correct value.
// If the call to H5Oget_comment_by_name returned an error, skip this block
// and throw an exception below.
if (ret_value >= 0 && (size_t)ret_value > bufsize && bufsize == 256)
{
size_t new_size = ret_value;
delete []comment_C;
comment_C = new char[new_size]; // new_size including null terminator
ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, new_size, H5P_DEFAULT);
}
// if H5Oget_comment_by_name returns SUCCEED, return the string comment,
// otherwise, throw an exception
if( ret_value < 0 ) {
delete []comment_C;
throwException("getComment", "H5Oget_comment_by_name failed");
}
H5std_string comment = H5std_string(comment_C);
delete []comment_C;
return (comment);
}
//--------------------------------------------------------------------------
// Function: CommonFG::getComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5std_string CommonFG::getComment( const H5std_string& name, size_t bufsize ) const
{
return( getComment( name.c_str(), bufsize ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::mount
///\brief Mounts the file \a child onto this group.

12
c++/src/H5CommonFG.h
View File

@ -49,18 +49,6 @@ class H5_DLLCPP CommonFG {
DataSet openDataSet(const char* name) const;
DataSet openDataSet(const H5std_string& name) const;
// Retrieves comment for the HDF5 object specified by its name.
H5std_string getComment(const char* name, size_t bufsize=256) const;
H5std_string getComment(const H5std_string& name, size_t bufsize=256) const;
// Removes the comment for the HDF5 object specified by its name.
void removeComment(const char* name) const;
void removeComment(const H5std_string& name) const;
// Sets the comment for an HDF5 object specified by its name.
void setComment(const char* name, const char* comment) const;
void setComment(const H5std_string& name, const H5std_string& comment) const;
// Returns the value of a symbolic link.
H5std_string getLinkval(const char* link_name, size_t size=0) const;
H5std_string getLinkval(const H5std_string& link_name, size_t size=0) const;

48
c++/src/H5DataSet.cpp
View File

@ -79,57 +79,29 @@ DataSet::DataSet(const DataSet& original) : AbstractDs(original), H5Object(origi
//--------------------------------------------------------------------------
// Function: DataSet overload constructor - dereference
///\brief Given a reference, ref, to an hdf5 dataset, creates a
///\brief Given a reference, ref, to an hdf5 location, creates a
/// DataSet object
///\param obj - IN: Dataset reference object is in or location of
///\param loc - IN: Dataset reference object is in or location of
/// object that the dataset is located within.
///\param ref - IN: Reference pointer
///\param ref_type - IN: Reference type - default to H5R_OBJECT
///\exception H5::DataSetIException
///\par Description
/// \c obj can be DataSet, Group, H5File, or named DataType, that
/// \c loc can be DataSet, Group, H5File, or named DataType, that
/// is a datatype that has been named by DataType::commit.
// Programmer Binh-Minh Ribler - Oct, 2006
// Modification
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
DataSet::DataSet(H5Object& obj, const void* ref, H5R_type_t ref_type) : AbstractDs(), H5Object()
DataSet::DataSet(const H5Location& loc, const void* ref, H5R_type_t ref_type, const PropList& plist) : AbstractDs(), H5Object()
{
try {
id = p_dereference(obj.getId(), ref, ref_type);
} catch (ReferenceException deref_error) {
throw ReferenceException("DataSet constructor - located by object",
deref_error.getDetailMsg());
}
H5Location::dereference(loc, ref, ref_type, plist);
}
//--------------------------------------------------------------------------
// Function: DataSet overload constructor - dereference
///\brief Given a reference, ref, to an hdf5 dataset, creates a
/// DataSet object
///\param h5file - IN: Location referenced object is in
///\param ref - IN: Reference pointer
///\param ref_type - IN: Reference type - default to H5R_OBJECT
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Oct, 2006
// Modification
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
DataSet::DataSet(H5File& h5file, const void* ref, H5R_type_t ref_type) : AbstractDs(), H5Object()
{
try {
id = p_dereference(h5file.getId(), ref, ref_type);
} catch (ReferenceException deref_error) {
throw ReferenceException("DataSet constructor - located by HDF5 file",
deref_error.getDetailMsg());
}
}
//--------------------------------------------------------------------------
// Function: DataSet overload constructor - dereference
///\brief Given a reference, ref, to an hdf5 dataset, creates a
///\brief Given a reference, ref, to an hdf5 attribute, creates a
/// DataSet object
///\param attr - IN: Specifying location where the referenced object is in
///\param ref - IN: Reference pointer
@ -140,12 +112,12 @@ DataSet::DataSet(H5File& h5file, const void* ref, H5R_type_t ref_type) : Abstrac
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
DataSet::DataSet(Attribute& attr, const void* ref, H5R_type_t ref_type) : AbstractDs(), H5Object()
DataSet::DataSet(const Attribute& attr, const void* ref, H5R_type_t ref_type, const PropList& plist) : AbstractDs(), H5Object()
{
try {
id = p_dereference(attr.getId(), ref, ref_type);
try {
id = p_dereference(attr.getId(), ref, ref_type, plist);
} catch (ReferenceException deref_error) {
throw ReferenceException("DataSet constructor - located by attribute",
throw ReferenceException("DataSet constructor - by dereferenced",
deref_error.getDetailMsg());
}
}

8
c++/src/H5DataSet.h
View File

@ -76,16 +76,12 @@ class H5_DLLCPP DataSet : public H5Object, public AbstractDs {
// Iterates the selected elements in the specified dataspace - not implemented in C++ style yet
int iterateElems( void* buf, const DataType& type, const DataSpace& space, H5D_operator_t op, void* op_data = NULL );
// Retrieves a dataspace with the region pointed to selected.
DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
///\brief Returns this class name.
virtual H5std_string fromClass () const { return("DataSet"); }
// Creates a dataset by way of dereference.
DataSet(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
DataSet(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
DataSet(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
DataSet(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
DataSet(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
// Default constructor.
DataSet();

2
c++/src/H5DataSpace.cpp
View File

@ -446,7 +446,7 @@ void DataSpace::getSelectBounds ( hsize_t* start, hsize_t* end ) const
}
//--------------------------------------------------------------------------
// Function: DataSpace::H5Sselect_elements
// Function: DataSpace::selectElements
///\brief Selects array elements to be included in the selection for
/// this dataspace.
///\param op - IN: Operator specifying how the new selection is to be

13
c++/src/H5DataType.cpp
View File

@ -100,7 +100,7 @@ DataType::DataType( const H5T_class_t type_class, size_t size ) : H5Object()
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
DataType::DataType(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Object()
/* DataType::DataType(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Object()
{
try {
id = p_dereference(obj.getId(), ref, ref_type);
@ -109,6 +109,7 @@ DataType::DataType(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Obje
deref_error.getDetailMsg());
}
}
*/
//--------------------------------------------------------------------------
// Function: DataType overload constructor - dereference
@ -123,14 +124,16 @@ DataType::DataType(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Obje
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
DataType::DataType(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Object()
DataType::DataType(const H5Location& loc, const void* ref, H5R_type_t ref_type, const PropList& plist) : H5Object()
{
try {
H5Location::dereference(loc, ref, ref_type, plist);
/* try {
id = p_dereference(h5file.getId(), ref, ref_type);
} catch (ReferenceException deref_error) {
throw ReferenceException("DataType constructor - located by an H5File",
deref_error.getDetailMsg());
}
*/
}
//--------------------------------------------------------------------------
@ -146,10 +149,10 @@ DataType::DataType(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Obj
// Jul, 2008
// Added for application convenience.
//--------------------------------------------------------------------------
DataType::DataType(Attribute& attr, const void* ref, H5R_type_t ref_type) : H5Object()
DataType::DataType(const Attribute& attr, const void* ref, H5R_type_t ref_type, const PropList& plist) : H5Object()
{
try {
id = p_dereference(attr.getId(), ref, ref_type);
id = p_dereference(attr.getId(), ref, ref_type, plist);
} catch (ReferenceException deref_error) {
throw ReferenceException("DataType constructor - located by an Attribute",
deref_error.getDetailMsg());

8
c++/src/H5DataType.h
View File

@ -30,9 +30,8 @@ class H5_DLLCPP DataType : public H5Object {
DataType( const DataType& original );
// Creates a datatype by way of dereference.
DataType(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
DataType(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
DataType(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
DataType(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
DataType(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
// Closes this datatype.
virtual void close();
@ -101,9 +100,6 @@ class H5_DLLCPP DataType : public H5Object {
// Checks whether this datatype is a variable-length string.
bool isVariableStr() const;
// Retrieves a dataspace with the region pointed to selected.
DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
///\brief Returns this class name.
virtual H5std_string fromClass () const { return("DataType"); }

3
c++/src/H5File.h
View File

@ -61,9 +61,6 @@ class H5_DLLCPP H5File : public H5Location, public CommonFG {
// and datatypes) in the same file.
void getObjIDs(unsigned types, size_t max_objs, hid_t *oid_list) const;
// Retrieves a dataspace with the region pointed to selected.
DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
// Returns the pointer to the file handle of the low-level file driver.
void getVFDHandle(FileAccPropList& fapl, void **file_handle) const;
void getVFDHandle(void **file_handle) const;

17
c++/src/H5Group.cpp
View File

@ -99,14 +99,18 @@ Group::Group(const hid_t existing_id) : H5Object()
/// is a datatype that has been named by DataType::commit.
// Programmer Binh-Minh Ribler - Oct, 2006
//--------------------------------------------------------------------------
Group::Group(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Object()
/* Group::Group(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Object()
*/
Group::Group(const H5Location& loc, const void* ref, H5R_type_t ref_type, const PropList& plist) : H5Object()
{
try {
id = p_dereference(obj.getId(), ref, ref_type);
H5Location::dereference(loc, ref, ref_type, plist);
/* try {
id = p_dereference(loc.getId(), ref, ref_type);
} catch (ReferenceException deref_error) {
throw ReferenceException("Group constructor - located by an H5Object",
deref_error.getDetailMsg());
}
*/
}
//--------------------------------------------------------------------------
@ -118,7 +122,7 @@ Group::Group(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Object()
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
//--------------------------------------------------------------------------
Group::Group(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Object()
/* Group::Group(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Object()
{
try {
id = p_dereference(h5file.getId(), ref, ref_type);
@ -127,6 +131,7 @@ Group::Group(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Object()
deref_error.getDetailMsg());
}
}
*/
//--------------------------------------------------------------------------
// Function: Group overload constructor - dereference
@ -137,10 +142,10 @@ Group::Group(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Object()
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
//--------------------------------------------------------------------------
Group::Group(Attribute& attr, const void* ref, H5R_type_t ref_type) : H5Object()
Group::Group(const Attribute& attr, const void* ref, H5R_type_t ref_type, const PropList& plist) : H5Object()
{
try {
id = p_dereference(attr.getId(), ref, ref_type);
id = p_dereference(attr.getId(), ref, ref_type, plist);
} catch (ReferenceException deref_error) {
throw ReferenceException("Group constructor - located by an Attribute",
deref_error.getDetailMsg());

10
c++/src/H5Group.h
View File

@ -26,9 +26,6 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
// Close this group.
virtual void close();
// Retrieves a dataspace with the region pointed to selected.
DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
///\brief Returns this class name.
virtual H5std_string fromClass () const { return("Group"); }
@ -39,9 +36,10 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
virtual hid_t getLocId() const;
// Creates a group by way of dereference.
Group(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
Group(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
Group(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
Group(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
/* Group(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
*/
Group(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
// default constructor
Group();

2
c++/src/H5IdComponent.cpp
View File

@ -269,7 +269,7 @@ IdComponent::IdComponent() {}
// Description:
// This function is protected so that the user applications can
// only have access to its code via allowable classes, namely,
// H5File and H5Object subclasses.
// Attribute and H5Location subclasses.
// Programmer Binh-Minh Ribler - Jul, 2004
//--------------------------------------------------------------------------
H5std_string IdComponent::p_get_file_name() const

420
c++/src/H5Location.cpp
View File

@ -55,17 +55,17 @@ extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
}
//--------------------------------------------------------------------------
// Function: H5Location default constructor (protected)
// Programmer Binh-Minh Ribler - 2000
// Function: H5Location default constructor (protected)
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5Location::H5Location() : IdComponent(0) {}
//--------------------------------------------------------------------------
// Function: H5Location overloaded constructor (protected)
// Purpose Creates an H5Location object using the id of an existing HDF5
// object.
// Parameters object_id - IN: Id of an existing HDF5 object
// Programmer Binh-Minh Ribler - 2000
// Function: H5Location overloaded constructor (protected)
// Purpose Creates an H5Location object using the id of an existing HDF5
// object.
// Parameters object_id - IN: Id of an existing HDF5 object
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5Location::H5Location(const hid_t object_id) : IdComponent(object_id) {}
@ -78,6 +78,30 @@ H5Location::H5Location(const hid_t object_id) : IdComponent(object_id) {}
//--------------------------------------------------------------------------
H5Location::H5Location( const H5Location& original ) : IdComponent( original ) {}
//--------------------------------------------------------------------------
// Function: H5Location constructor
///\brief Dereferences into an HDF5 object, given an HDF5 location.
///\param loc - IN: H5Location instance to copy
///\param ref - IN: Name of the object to be referenced
///\param ref_type - IN: Dataspace with selection
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
// Dereferences into an HDF5 object, given an HDF5 location.
/* H5Location::H5Location(const H5Location& loc, const void* ref, H5R_type_t ref_type, const PropList& plist)
{
hid_t temp_id;
try {
temp_id = p_dereference(loc.getId(), ref, ref_type, plist);
}
catch (ReferenceException deref_error) {
throw ReferenceException("H5Location constructor - by dereferenced",
deref_error.getDetailMsg());
}
setId(temp_id);
}
*/
#endif // DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
@ -342,7 +366,7 @@ void H5Location::renameAttr(const H5std_string& oldname, const H5std_string& new
/// which can be either of these values:
/// \li \c H5F_SCOPE_GLOBAL - Flushes the entire virtual file
/// \li \c H5F_SCOPE_LOCAL - Flushes only the specified file
///\exception H5::FileIException
///\exception H5::Exception
///\par Description
/// This location is used to identify the file to be flushed.
// Programmer Binh-Minh Ribler - 2012
@ -355,7 +379,7 @@ void H5Location::flush(H5F_scope_t scope) const
herr_t ret_value = H5Fflush(getId(), scope);
if( ret_value < 0 )
{
throw FileIException(inMemFunc("flush"), "H5Fflush failed");
throw Exception(inMemFunc("flush"), "H5Fflush failed");
}
}
@ -376,17 +400,147 @@ H5std_string H5Location::getFileName() const
}
}
//--------------------------------------------------------------------------
// Function: H5Location::setComment
///\brief Sets or resets the comment for an object specified by its name.
///\param name - IN: Name of the object
///\param comment - IN: New comment
///\exception H5::Exception
///\par Description
/// If \a comment is an empty string or a null pointer, the comment
/// message is removed from the object.
/// Comments should be relatively short, null-terminated, ASCII
/// strings. They can be attached to any object that has an
/// object header, e.g., data sets, groups, named data types,
/// and data spaces, but not symbolic links.
// Programmer Binh-Minh Ribler - 2000 (moved from CommonFG, Sep 2013)
// Modification
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
void H5Location::setComment(const char* name, const char* comment) const
{
herr_t ret_value = H5Oset_comment_by_name(getId(), name, comment, H5P_DEFAULT);
if( ret_value < 0 )
throw Exception("setComment", "H5Oset_comment_by_name failed");
}
//--------------------------------------------------------------------------
// Function: H5Location::setComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name and \a comment.
// Programmer Binh-Minh Ribler - 2000 (moved from CommonFG, Sep 2013)
//--------------------------------------------------------------------------
void H5Location::setComment(const H5std_string& name, const H5std_string& comment) const
{
setComment(name.c_str(), comment.c_str());
}
//--------------------------------------------------------------------------
// Function: H5Location::removeComment
///\brief Removes the comment from an object specified by its name.
///\param name - IN: Name of the object
///\exception H5::Exception
// Programmer Binh-Minh Ribler - May 2005 (moved from CommonFG, Sep 2013)
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
void H5Location::removeComment(const char* name) const
{
herr_t ret_value = H5Oset_comment_by_name(getId(), name, NULL, H5P_DEFAULT);
if( ret_value < 0 )
throw Exception("removeComment", "H5Oset_comment_by_name failed");
}
//--------------------------------------------------------------------------
// Function: H5Location::removeComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - May 2005 (moved from CommonFG, Sep 2013)
//--------------------------------------------------------------------------
void H5Location::removeComment(const H5std_string& name) const
{
removeComment (name.c_str());
}
//--------------------------------------------------------------------------
// Function: H5Location::getComment
///\brief Retrieves comment for the specified object and its comment's
/// length.
///\param name - IN: Name of the object
///\param bufsize - IN: Length of the comment to retrieve
///\return Comment string
///\exception H5::Exception
// Programmer Binh-Minh Ribler - 2000 (moved from CommonFG, Sep 2013)
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
H5std_string H5Location::getComment(const char* name, size_t bufsize) const
{
// bufsize is default to 256
// temporary variable
hid_t loc_id = getId(); // temporary variable
// temporary C-string for the object's comment; bufsize already including
// null character
char* comment_C = new char[bufsize];
ssize_t ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, bufsize, H5P_DEFAULT);
// if the actual length of the comment is longer than bufsize and bufsize
// was the default value, i.e., not given by the user, then call
// H5Oget_comment_by_name again with the correct value.
// If the call to H5Oget_comment_by_name returned an error, skip this block
// and throw an exception below.
if (ret_value >= 0 && (size_t)ret_value > bufsize && bufsize == 256)
{
size_t new_size = ret_value;
delete []comment_C;
comment_C = new char[new_size]; // new_size including null terminator
ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, new_size, H5P_DEFAULT);
}
// if H5Oget_comment_by_name returns SUCCEED, return the string comment,
// otherwise, throw an exception
if (ret_value < 0) {
delete []comment_C;
throw Exception("getComment", "H5Oget_comment_by_name failed");
}
H5std_string comment = H5std_string(comment_C);
delete []comment_C;
return (comment);
}
//--------------------------------------------------------------------------
// Function: H5Location::getComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000 (moved from CommonFG, Sep 2013)
//--------------------------------------------------------------------------
H5std_string H5Location::getComment(const H5std_string& name, size_t bufsize) const
{
return(getComment(name.c_str(), bufsize));
}
#ifndef DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: H5Location::p_reference (protected)
// Purpose Creates a reference to an HDF5 object or a dataset region.
// Function: H5Location::p_reference (protected)
// Purpose Creates a reference to an HDF5 object or a dataset region.
// Parameters
// name - IN: Name of the object to be referenced
// dataspace - IN: Dataspace with selection
// ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
// Exception H5::IdComponentException
// Programmer Binh-Minh Ribler - May, 2004
// name - IN: Name of the object to be referenced
// dataspace - IN: Dataspace with selection
// ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
// Exception H5::IdComponentException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Location::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
{
@ -400,17 +554,18 @@ void H5Location::p_reference(void* ref, const char* name, hid_t space_id, H5R_ty
#endif // DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: H5Location::reference
///\brief Creates a reference to an HDF5 object or a dataset region.
///\param ref - IN: Reference pointer
///\param name - IN: Name of the object to be referenced
///\param dataspace - IN: Dataspace with selection
///\param ref_type - IN: Type of reference to query, valid values are:
// Function: H5Location::reference
///\brief Creates a reference to an HDF5 object or a dataset region.
///\param ref - IN: Reference pointer
///\param name - IN: Name of the object to be referenced
///\param dataspace - IN: Dataspace with selection
///\param ref_type - IN: Type of reference to query, valid values are:
/// \li \c H5R_OBJECT - Reference is an object reference.
/// \li \c H5R_DATASET_REGION - Reference is a dataset region
/// reference. - this is the default
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
///\exception H5::ReferenceException
///\notes This method is more suitable for a dataset region reference.
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Location::reference(void* ref, const char* name, const DataSpace& dataspace, H5R_type_t ref_type) const
{
@ -423,23 +578,25 @@ void H5Location::reference(void* ref, const char* name, const DataSpace& dataspa
}
//--------------------------------------------------------------------------
// Function: H5Location::reference
///\brief This is an overloaded function, provided for your convenience.
/// It differs from the above function in that it only creates
/// a reference to an HDF5 object, not to a dataset region.
///\param ref - IN: Reference pointer
///\param name - IN: Name of the object to be referenced - \c char pointer
///\exception H5::ReferenceException
///\par Description
// This function passes H5R_OBJECT and -1 to the protected
// function for it to pass to the C API H5Rcreate
// to create a reference to the named object.
// Programmer Binh-Minh Ribler - May, 2004
// Function: H5Location::reference
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
///\param ref - IN: Reference pointer
///\param name - IN: Name of the object to be referenced
///\param dataspace - IN: Dataspace with selection
///\param ref_type - IN: Type of reference to query, valid values are:
/// \li \c H5R_OBJECT - Reference is an object reference.
/// \li \c H5R_DATASET_REGION - Reference is a dataset region
/// reference. - this is the default
///\exception H5::ReferenceException
///\notes This method is more suitable for a dataset region reference.
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Location::reference(void* ref, const char* name) const
void H5Location::reference(void* ref, const H5std_string& name, const DataSpace& dataspace, H5R_type_t ref_type) const
{
try {
p_reference(ref, name, -1, H5R_OBJECT);
p_reference(ref, name.c_str(), dataspace.getId(), ref_type);
}
catch (ReferenceException E) {
throw ReferenceException("H5Location::reference", E.getDetailMsg());
@ -447,17 +604,45 @@ void H5Location::reference(void* ref, const char* name) const
}
//--------------------------------------------------------------------------
// Function: H5Location::reference
///\brief This is an overloaded function, provided for your convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for the object's name.
///\param ref - IN: Reference pointer
///\param name - IN: Name of the object to be referenced - \c H5std_string
// Programmer Binh-Minh Ribler - May, 2004
// Function: H5Location::reference
///\brief This is an overloaded function, provided for your convenience.
/// It differs from the above function in that it does not take
/// a DataSpace object and the reference type must be specified.
///\param ref - IN: Reference pointer
///\param name - IN: Name of the object to be referenced
///\param ref_type - IN: Type of reference to query, valid values are:
/// \li \c H5R_OBJECT - Reference is an object reference.
/// \li \c H5R_DATASET_REGION - Reference is a dataset region
///\exception H5::ReferenceException
///\notes This method is more suitable for an object reference.
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Location::reference(void* ref, const H5std_string& name) const
void H5Location::reference(void* ref, const char* name, H5R_type_t ref_type) const
{
reference(ref, name.c_str());
try {
p_reference(ref, name, -1, ref_type);
}
catch (ReferenceException E) {
throw ReferenceException("H5Location::reference", E.getDetailMsg());
}
}
//--------------------------------------------------------------------------
// Function: H5Location::reference
///\brief This is an overloaded function, provided for your convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for the object's name.
///\param ref - IN: Reference pointer
///\param name - IN: Name of the object to be referenced - \c H5std_string
///\param ref_type - IN: Type of reference to query, valid values are:
/// \li \c H5R_OBJECT - Reference is an object reference.
/// \li \c H5R_DATASET_REGION - Reference is a dataset region
///\notes This method is more suitable for an object reference.
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Location::reference(void* ref, const H5std_string& name, H5R_type_t ref_type) const
{
reference(ref, name.c_str(), ref_type);
}
#ifndef DOXYGEN_SHOULD_SKIP_THIS
@ -475,10 +660,16 @@ void H5Location::reference(void* ref, const H5std_string& name) const
// May 2008 - BMR
// Moved from IdComponent.
//--------------------------------------------------------------------------
hid_t H5Location::p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_type)
hid_t H5Location::p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_type, const PropList& plist)
{
hid_t plist_id;
if (p_valid_id(plist.getId()))
plist_id = plist.getId();
else
plist_id = H5P_DEFAULT;
hid_t temp_id;
temp_id = H5Rdereference2(loc_id, H5P_DEFAULT, ref_type, ref);
temp_id = H5Rdereference2(loc_id, plist_id, ref_type, ref);
if (temp_id < 0)
{
throw ReferenceException("", "H5Rdereference failed");
@ -496,16 +687,16 @@ hid_t H5Location::p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_ty
///\param ref - IN: Reference pointer
///\param ref_type - IN: Reference type
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
// Programmer Binh-Minh Ribler - Oct, 2006
// Modification
// May, 2008
// Corrected missing parameters. - BMR
//--------------------------------------------------------------------------
void H5Location::dereference(H5Object& obj, const void* ref, H5R_type_t ref_type)
void H5Location::dereference(const H5Location& loc, const void* ref, H5R_type_t ref_type, const PropList& plist)
{
hid_t temp_id;
try {
temp_id = p_dereference(obj.getId(), ref, ref_type);
temp_id = p_dereference(loc.getId(), ref, ref_type, plist);
}
catch (ReferenceException E) {
throw ReferenceException("H5Location::dereference - located by object", E.getDetailMsg());
@ -513,30 +704,6 @@ void H5Location::dereference(H5Object& obj, const void* ref, H5R_type_t ref_type
p_setId(temp_id);
}
//--------------------------------------------------------------------------
// Function: H5Location::dereference
///\brief Dereferences a reference into an HDF5 object, given an HDF5 file.
///\param h5file - IN: HDF5 file specifying the location of the referenced object
///\param ref - IN: Reference pointer
///\param ref_type - IN: Reference type
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
// Modification
// May, 2008
// Corrected missing parameters. - BMR
//--------------------------------------------------------------------------
void H5Location::dereference(H5File& h5file, const void* ref, H5R_type_t ref_type)
{
hid_t temp_id;
try {
temp_id = p_dereference(h5file.getId(), ref, ref_type);
}
catch (ReferenceException E) {
throw ReferenceException("H5Location::dereference - located by file", E.getDetailMsg());
}
p_setId(temp_id);
}
//--------------------------------------------------------------------------
// Function: H5Location::dereference
///\brief Dereferences a reference into an HDF5 object, given an attribute.
@ -544,16 +711,16 @@ void H5Location::dereference(H5File& h5file, const void* ref, H5R_type_t ref_typ
///\param ref - IN: Reference pointer
///\param ref_type - IN: Reference type
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
// Programmer Binh-Minh Ribler - Oct, 2006
// Modification
// May, 2008
// Corrected missing parameters. - BMR
//--------------------------------------------------------------------------
void H5Location::dereference(Attribute& attr, const void* ref, H5R_type_t ref_type)
void H5Location::dereference(const Attribute& attr, const void* ref, H5R_type_t ref_type, const PropList& plist)
{
hid_t temp_id;
try {
temp_id = p_dereference(attr.getId(), ref, ref_type);
temp_id = p_dereference(attr.getId(), ref, ref_type, plist);
}
catch (ReferenceException E) {
throw ReferenceException("H5Location::dereference - located by attribute", E.getDetailMsg());
@ -593,20 +760,20 @@ H5G_obj_t H5Location::getObjType(void *ref, H5R_type_t ref_type) const
#ifndef DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: H5Location::p_get_obj_type (protected)
// Purpose Retrieves the type of object that an object reference points to.
// Function: H5Location::p_get_obj_type (protected)
// Purpose Retrieves the type of object that an object reference points to.
// Parameters
// ref - IN: Reference to query
// ref_type - IN: Type of reference to query
// Return An object type, which can be one of the following:
// H5G_UNKNOWN \tFailure occurs (-1)
// H5G_GROUP \tObject is a group.
// H5G_DATASET \tObject is a dataset.
// H5G_TYPE Object \tis a named datatype.
// H5G_LINK \tObject is a symbolic link.
// H5G_UDLINK \tObject is a user-defined link.
// Exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
// ref - IN: Reference to query
// ref_type - IN: Type of reference to query
// Return An object type, which can be one of the following:
// H5G_UNKNOWN \tFailure occurs (-1)
// H5G_GROUP \tObject is a group.
// H5G_DATASET \tObject is a dataset.
// H5G_TYPE Object \tis a named datatype.
// H5G_LINK \tObject is a symbolic link.
// H5G_UDLINK \tObject is a user-defined link.
// Exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
H5G_obj_t H5Location::p_get_obj_type(void *ref, H5R_type_t ref_type) const
{
@ -622,20 +789,20 @@ H5G_obj_t H5Location::p_get_obj_type(void *ref, H5R_type_t ref_type) const
#endif /* H5_NO_DEPRECATED_SYMBOLS */
//--------------------------------------------------------------------------
// Function: H5Location::getRefObjType
///\brief Retrieves the type of object that an object reference points to.
///\param ref - IN: Reference to query
///\param ref_type - IN: Type of reference to query, valid values are:
/// \li \c H5R_OBJECT - Reference is an object reference.
/// \li \c H5R_DATASET_REGION - Reference is a dataset region reference.
///\return An object type, which can be one of the following:
/// \li \c H5O_TYPE_UNKNOWN - Unknown object type (-1)
/// \li \c H5O_TYPE_GROUP - Object is a group
/// \li \c H5O_TYPE_DATASET - Object is a dataset
/// \li \c H5O_TYPE_NAMED_DATATYPE - Object is a named datatype
/// \li \c H5O_TYPE_NTYPES - Number of different object types
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
// Function: H5Location::getRefObjType
///\brief Retrieves the type of object that an object reference points to.
///\param ref - IN: Reference to query
///\param ref_type - IN: Type of reference to query, valid values are:
/// \li \c H5R_OBJECT - Reference is an object reference.
/// \li \c H5R_DATASET_REGION - Reference is a dataset region reference.
///\return An object type, which can be one of the following:
/// \li \c H5O_TYPE_UNKNOWN - Unknown object type (-1)
/// \li \c H5O_TYPE_GROUP - Object is a group
/// \li \c H5O_TYPE_DATASET - Object is a dataset
/// \li \c H5O_TYPE_NAMED_DATATYPE - Object is a named datatype
/// \li \c H5O_TYPE_NTYPES - Number of different object types
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type) const
{
@ -649,19 +816,19 @@ H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type) const
#ifndef DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: H5Location::p_get_ref_obj_type (protected)
// Purpose Retrieves the type of object that an object reference points to.
// Function: H5Location::p_get_ref_obj_type (protected)
// Purpose Retrieves the type of object that an object reference points to.
// Parameters
// ref - IN: Reference to query
// ref_type - IN: Type of reference to query
// Return An object type, which can be one of the following:
// ref - IN: Reference to query
// ref_type - IN: Type of reference to query
// Return An object type, which can be one of the following:
// H5O_TYPE_UNKNOWN - Unknown object type (-1)
// H5O_TYPE_GROUP - Object is a group
// H5O_TYPE_DATASET - Object is a dataset
// H5O_TYPE_NAMED_DATATYPE - Object is a named datatype
// H5O_TYPE_NTYPES - Number of object types
// Exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
// Exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
H5O_type_t H5Location::p_get_ref_obj_type(void *ref, H5R_type_t ref_type) const
{
@ -677,24 +844,29 @@ H5O_type_t H5Location::p_get_ref_obj_type(void *ref, H5R_type_t ref_type) const
//--------------------------------------------------------------------------
// Function: H5Location::p_get_region (protected)
// Purpose Retrieves a dataspace with the region pointed to selected.
// Parameters
// ref_type - IN: Type of reference to get region of - default
// to H5R_DATASET_REGION
// ref - IN: Reference to get region of
// Return Dataspace id
// Exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
// Function: H5Location::getRegion
///\brief Retrieves a dataspace with the region pointed to selected.
///\param ref - IN: Reference to get region of
///\param ref_type - IN: Type of reference to get region of - default
// to H5R_DATASET_REGION
///\return DataSpace object
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
hid_t H5Location::p_get_region(void *ref, H5R_type_t ref_type) const
DataSpace H5Location::getRegion(void *ref, H5R_type_t ref_type) const
{
hid_t space_id = H5Rget_region(getId(), ref_type, ref);
if (space_id < 0)
{
throw ReferenceException("", "H5Rget_region failed");
}
return(space_id);
try {
DataSpace dataspace(space_id);
return(dataspace);
}
catch (DataSpaceIException E) {
throw ReferenceException("H5Location::getRegion", E.getDetailMsg());
}
}

53
c++/src/H5Location.h
View File

@ -36,12 +36,12 @@ typedef void (*attr_operator_t)( H5Location& loc/*in*/,
class UserData4Aiterate { // user data for attribute iteration
public:
attr_operator_t op;
void* opData;
H5Location* location;
attr_operator_t op;
void* opData;
H5Location* location;
};
// An H5Location can be a file, group, dataset, named datatype, or attribute.
// An H5Location can be a file, group, dataset, or committed datatype.
class H5_DLLCPP H5Location : public IdComponent {
public:
@ -85,29 +85,47 @@ class H5_DLLCPP H5Location : public IdComponent {
bool attrExists(const char* name) const;
bool attrExists(const H5std_string& name) const;
// Removes the named attribute from this location.
void removeAttr(const char* name) const;
void removeAttr(const H5std_string& name) const;
// Renames the named attribute to a new name.
void renameAttr(const char* oldname, const char* newname) const;
void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
// Removes the named attribute from this location.
void removeAttr(const char* name) const;
void removeAttr(const H5std_string& name) const;
// Sets the comment for an HDF5 object specified by its name.
void setComment(const char* name, const char* comment) const;
void setComment(const H5std_string& name, const H5std_string& comment) const;
// Retrieves comment for the HDF5 object specified by its name.
H5std_string getComment(const char* name, size_t bufsize=256) const;
H5std_string getComment(const H5std_string& name, size_t bufsize=256) const;
// Removes the comment for the HDF5 object specified by its name.
void removeComment(const char* name) const;
void removeComment(const H5std_string& name) const;
// Creates a reference to a named object or to a dataset region
// in this object.
void reference(void* ref, const char* name,
H5R_type_t ref_type = H5R_OBJECT) const;
void reference(void* ref, const H5std_string& name,
H5R_type_t ref_type = H5R_DATASET_REGION) const;
void reference(void* ref, const char* name, const DataSpace& dataspace,
H5R_type_t ref_type = H5R_DATASET_REGION) const;
void reference(void* ref, const char* name) const;
void reference(void* ref, const H5std_string& name) const;
void reference(void* ref, const H5std_string& name, const DataSpace& dataspace,
H5R_type_t ref_type = H5R_DATASET_REGION) const;
// Open a referenced object whose location is specified by either
// a file, an HDF5 object, or an attribute.
void dereference(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
void dereference(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
void dereference(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
void dereference(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
void dereference(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT);
///\brief Returns an identifier. (pure virtual)
virtual hid_t getId() const = 0;
// Retrieves a dataspace with the region pointed to selected.
DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
///\brief Returns an identifier. (pure virtual)
virtual hid_t getId() const = 0;
protected:
#ifndef DOXYGEN_SHOULD_SKIP_THIS
@ -124,7 +142,7 @@ class H5_DLLCPP H5Location : public IdComponent {
void p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const;
// Dereferences a ref into an HDF5 id.
hid_t p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_type);
hid_t p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_type, const PropList& plist);
#ifndef H5_NO_DEPRECATED_SYMBOLS
// Retrieves the type of object that an object reference points to.
@ -134,9 +152,6 @@ class H5_DLLCPP H5Location : public IdComponent {
// Retrieves the type of object that an object reference points to.
H5O_type_t p_get_ref_obj_type(void *ref, H5R_type_t ref_type) const;
// Retrieves a dataspace with the region pointed to selected.
hid_t p_get_region(void *ref, H5R_type_t ref_type) const;
// Noop destructor.
virtual ~H5Location();

1
c++/src/H5Object.cpp
View File

@ -52,7 +52,6 @@ H5Object::H5Object() : H5Location() {}
//--------------------------------------------------------------------------
H5Object::H5Object( const hid_t object_id ) : H5Location( object_id ) {}
//--------------------------------------------------------------------------
// Function: H5Object copy constructor
///\brief Copy constructor: makes a copy of the original H5Object

5
c++/src/H5PropList.cpp
View File

@ -39,7 +39,7 @@ namespace H5 {
//--------------------------------------------------------------------------
///\brief Constant for default property.
//--------------------------------------------------------------------------
const PropList PropList::DEFAULT( H5P_DEFAULT );
const PropList PropList::DEFAULT;
//--------------------------------------------------------------------------
// Function Default constructor
@ -644,6 +644,9 @@ void PropList::removeProp(const H5std_string& name) const
//--------------------------------------------------------------------------
bool PropList::operator==(const PropList& rhs) const
{
fprintf(stderr, "operator==\n");
H5Eprint2(H5E_DEFAULT, stderr);
htri_t ret_value = H5Pequal(id, rhs.getId());
if( ret_value > 0 )
return true;

548
c++/test/trefer.cpp
View File

@ -27,13 +27,6 @@
#endif
#include <string>
#ifndef H5_NO_NAMESPACE
#ifndef H5_NO_STD
using std::cerr;
using std::endl;
#endif // H5_NO_STD
#endif
#include "H5Cpp.h" // C++ API header file
#ifndef H5_NO_NAMESPACE
@ -44,11 +37,10 @@
const H5std_string FILE1("trefer1.h5");
const H5std_string FILE2("trefer2.h5");
const H5std_string FILE3("trefer3.h5");
const H5std_string DSET_DEFAULT_NAME("default");
// Dataset 1
const H5std_string DSET1_NAME("Dataset1");
const H5std_string DSET2_NAME("Dataset2");
const int DSET1_LEN = 8;
const H5std_string MEMBER1( "a_name" );
@ -56,15 +48,15 @@ const H5std_string MEMBER2( "b_name" );
const H5std_string MEMBER3( "c_name" );
// 1-D dataset with fixed dimensions
const H5std_string SPACE1_NAME("Space1");
const int SPACE1_RANK = 1;
const int SPACE1_DIM1 = 4;
// 2-D dataset with fixed dimensions
const H5std_string SPACE2_NAME("Space2");
/* Larger 1-D dataset with fixed dimensions */
const int SPACE3_RANK = 1;
const int SPACE3_DIM1 = 100;
// Larger 1-D dataset with fixed dimensions
const H5std_string SPACE3_NAME("Space3");
/* Element selection information */
const int POINT1_NPOINTS = 10;
// Compound datatype
typedef struct s1_t {
@ -75,8 +67,122 @@ typedef struct s1_t {
/****************************************************************
**
** test_reference_obj(): Test basic object reference functionality.
** Tests references to various kinds of objects
** test_reference_params(): Test basic H5R (reference) parameters
** for correct processing
**
****************************************************************/
static void
test_reference_params(void)
{
const char *write_comment = "Foo!"; /* Comments for group */
// Output message about test being performed
SUBTEST("Object Reference Parameters");
H5File* file1 = NULL;
try {
hobj_ref_t *wbuf, // buffer to write to disk
*rbuf, // buffer read from disk
*tbuf; // temp. buffer read from disk
// Allocate write & read buffers
int temp_size = MAX(sizeof(unsigned),sizeof(hobj_ref_t));
wbuf=(hobj_ref_t*)HDmalloc(temp_size*SPACE1_DIM1);
rbuf=(hobj_ref_t*)HDmalloc(temp_size*SPACE1_DIM1);
tbuf=(hobj_ref_t*)HDmalloc(temp_size*SPACE1_DIM1);
// Create file FILE1
file1 = new H5File (FILE1, H5F_ACC_TRUNC);
// Create dataspace for datasets
hsize_t dims1[] = {SPACE1_DIM1};
DataSpace sid1(SPACE1_RANK, dims1);
// Create a group
Group group = file1->createGroup("Group1");
// Set group's comment
group.setComment(".", write_comment);
// Create a dataset (inside /Group1)
DataSet dataset = group.createDataSet(DSET1_NAME, PredType::NATIVE_UINT, sid1);
unsigned *tu32; // Temporary pointer to uint32 data
int i;
for (tu32=(unsigned *)wbuf, i=0; i<SPACE1_DIM1; i++)
*tu32++=i*3; // from C test
// Write selection to disk
dataset.write(wbuf, PredType::NATIVE_UINT);
// Close Dataset
dataset.close();
// Create another dataset (inside /Group1)
dataset = group.createDataSet("Dataset2", PredType::NATIVE_UCHAR, sid1);
// Close Dataset
dataset.close();
// Create a datatype to refer to
CompType dtype1(sizeof(s1_t));
// Insert fields
dtype1.insertMember(MEMBER1, HOFFSET(s1_t, a), PredType::NATIVE_INT);
dtype1.insertMember(MEMBER2, HOFFSET(s1_t, b), PredType::NATIVE_INT);
dtype1.insertMember(MEMBER3, HOFFSET(s1_t, c), PredType::NATIVE_FLOAT);
// Save datatype for later
dtype1.commit(group, "Datatype1");
// Close datatype and group
dtype1.close();
group.close();
// Create a dataset
dataset = file1->createDataSet("Dataset3", PredType::STD_REF_OBJ, sid1);
/* Test parameters to H5Location::reference */
try {
file1->reference(NULL, "/Group1/Dataset1");
} catch (ReferenceException E) {} // We expect this to fail
try {
file1->reference(&wbuf[0], NULL);
} catch (ReferenceException E) {} // We expect this to fail
try {
file1->reference(&wbuf[0], "");
} catch (ReferenceException E) {} // We expect this to fail
try {
file1->reference(&wbuf[0], "/Group1/Dataset1", H5R_MAXTYPE);
} catch (ReferenceException E) {} // We expect this to fail
try {
file1->reference(&wbuf[0], "/Group1/Dataset1", H5R_DATASET_REGION);
} catch (ReferenceException E) {} // We expect this to fail
// Close resources
dataset.close();
file1->close();
// Let sid1 go out of scope
// Free memory buffers
HDfree(wbuf);
HDfree(rbuf);
HDfree(tbuf);
PASSED();
} // end try
catch (Exception E) {
issue_fail_msg("test_reference_obj()", __LINE__, __FILE__, E.getCDetailMsg());
}
if(file1)
delete file1;
} /* test_reference_param() */
/****************************************************************
**
** test_reference_obj(): Test basic object reference functions
** to various kinds of objects
**
****************************************************************/
static void test_reference_obj(void)
@ -321,6 +427,412 @@ static void test_reference_obj(void)
delete file1;
} // test_reference_obj()
/****************************************************************
**
** test_reference_group(): Test object reference functionality
** Tests for correct behavior of various routines on
** dereferenced group
**
****************************************************************/
#define GROUPNAME "/group"
#define GROUPNAME2 "group2"
#define GROUPNAME3 "group3"
#define DSETNAME "/dset"
#define DSETNAME2 "dset2"
#define NAME_SIZE 16
static void
test_reference_group(void)
{
hobj_ref_t wref; /* Reference to write */
hobj_ref_t rref; /* Reference to read */
int i; // counting variables
const H5std_string write_comment="Foo!"; // Comments for group
// Output message about test being performed
SUBTEST("Object Reference to Group");
H5File* file1 = NULL;
try {
// Create file with a group and a dataset containing an object reference to the group
// Create file FILE1
file1 = new H5File (FILE1, H5F_ACC_TRUNC);
// Create scalar dataspace
DataSpace sid1;
// Create a group
Group group = file1->createGroup(GROUPNAME);
/* Create nested groups */
Group group2 = group.createGroup(GROUPNAME2);
group2.close();
group2 = group.createGroup(GROUPNAME3);
group2.close();
// Create bottom dataset
DataSet dset1 = group.createDataSet(DSETNAME2, PredType::NATIVE_INT, sid1);
dset1.close();
// Close group 1
group.close();
// Create dataset
DataSet dset2 = file1->createDataSet(DSETNAME, PredType::STD_REF_OBJ, sid1);
file1->reference(&wref, GROUPNAME);
// Write selection to disk
dset2.write(&wref, PredType::STD_REF_OBJ);
// Close resources
dset2.close();
sid1.close();
file1->close();
/*
* Re-open the file and test deferencing group
*/
// Re-open file
file1->openFile(FILE1, H5F_ACC_RDWR);
// Re-open dataset
dset1 = file1->openDataSet(DSETNAME);
// Read in the reference
dset1.read(&rref, PredType::STD_REF_OBJ);
// Dereference to get the group
Group refgroup(dset1, &rref);
// Dereference group object the other way
group.dereference(dset1, &rref);
/*
* Various queries on the group opened
*/
// Check number of objects in the group dereferenced by constructor
hsize_t nobjs = refgroup.getNumObjs();
verify_val(nobjs, 3, "H5Group::getNumObjs", __LINE__, __FILE__);
// Check number of objects in the group dereferenced by ::reference
nobjs = group.getNumObjs();
verify_val(nobjs, 3, "H5Group::getNumObjs", __LINE__, __FILE__);
// Check getting file name given the group dereferenced via constructor
H5std_string fname = refgroup.getFileName();
verify_val(fname, FILE1, "H5Group::getFileName", __LINE__, __FILE__);
// Check getting file name given the group dereferenced by ::reference
fname = group.getFileName();
verify_val(fname, FILE1, "H5Group::getFileName", __LINE__, __FILE__);
// Unlink one of the objects in the dereferenced group, and re-check
refgroup.unlink(GROUPNAME2);
nobjs = refgroup.getNumObjs();
verify_val(nobjs, 2, "H5Group::getNumObjs", __LINE__, __FILE__);
// Close resources
group.close();
refgroup.close();
dset1.close();
file1->close();
PASSED();
} // end try
catch (Exception E) {
issue_fail_msg("test_reference_group()", __LINE__, __FILE__, E.getCDetailMsg());
}
if(file1)
delete file1;
} /* test_reference_group() */
/****************************************************************
**
** test_reference_region_1D(): Test 1-D reference functionality
** Tests 1-D references to various kinds of objects
**
****************************************************************/
static void
test_reference_region_1D(void)
{
hid_t fid1; /* HDF5 File IDs */
hid_t dset1, /* Dataset ID */
dset3; /* Dereferenced dataset ID */
hid_t sid1, /* Dataspace ID #1 */
sid3; /* Dataspace ID #3 */
hid_t dapl_id; /* Dataset access property list */
hsize_t dims1[] = {SPACE1_DIM1},
dims3[] = {SPACE3_DIM1};
hsize_t start[SPACE3_RANK]; /* Starting location of hyperslab */
hsize_t stride[SPACE3_RANK]; /* Stride of hyperslab */
hsize_t count[SPACE3_RANK]; /* Element count of hyperslab */
hsize_t block[SPACE3_RANK]; /* Block size of hyperslab */
hsize_t coord1[POINT1_NPOINTS][SPACE3_RANK]; /* Coordinates for point selection */
hsize_t * coords; /* Coordinate buffer */
hsize_t low[SPACE3_RANK]; /* Selection bounds */
hsize_t high[SPACE3_RANK]; /* Selection bounds */
uint8_t *tu8; /* Temporary pointer to uint8 data */
H5O_type_t obj_type; /* Object type */
int i; /* counting variables */
herr_t ret; /* Generic return value */
// Output message about test being performed
SUBTEST("1-D Dataset Region Reference Functions");
try {
hdset_reg_ref_t *wbuf, // buffer to write to disk
*rbuf, // buffer read from disk
*tbuf; // temp. buffer read from disk
uint8_t *dwbuf, // Buffer for writing numeric data to disk
*drbuf; // Buffer for reading numeric data from disk
// Allocate write & read buffers
wbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)SPACE1_DIM1);
rbuf = (hdset_reg_ref_t *)HDmalloc(sizeof(hdset_reg_ref_t) * SPACE1_DIM1);
dwbuf = (uint8_t *)HDmalloc(sizeof(uint8_t) * SPACE3_DIM1);
drbuf = (uint8_t *)HDcalloc(sizeof(uint8_t), (size_t)SPACE3_DIM1);
// Create file FILE1
H5File file1(FILE2, H5F_ACC_TRUNC);
// Create dataspace for datasets
hsize_t dims3[] = {SPACE3_DIM1};
DataSpace sid3(SPACE3_RANK, dims3);
// Create dataset access property list
PropList dapl(H5P_DATASET_ACCESS);
// Create a dataset
DataSet dset3 = file1.createDataSet(DSET2_NAME, PredType::STD_U8LE, sid3);
uint8_t *tu8; // Temporary pointer to uint8 data
for (tu8 = dwbuf, i = 0; i < SPACE3_DIM1; i++)
*tu8++ = i * 3; // from C test
// Write selection to disk
dset3.write(dwbuf, PredType::STD_U8LE);
// Close Dataset
dset3.close();
// Create dataspace for datasets
hsize_t dims1[] = {SPACE1_DIM1};
DataSpace sid1(SPACE1_RANK, dims1);
// Create a dataset (inside /Group1)
DataSet dset1 = file1.createDataSet(DSET1_NAME, PredType::STD_REF_DSETREG, sid1);
/* Create references */
/* Select 15 2x1 hyperslabs for first reference */
start[0] = 2;
stride[0] = 5;
count[0] = 15;
block[0] = 2;
// Select a hyperslab region to add to the current selected region
sid3.selectHyperslab(H5S_SELECT_SET, count, start, stride, block);
// Get and verify the number of elements in a dataspace selection
hssize_t nelms = sid3.getSelectNpoints();
verify_val(nelms, 30, "DataSet::getRefObjType", __LINE__, __FILE__);
// Store first dataset region
file1.reference(&wbuf[0], "/Dataset2", sid3);
// Get and verify object type
H5O_type_t obj_type = dset1.getRefObjType(&wbuf[0], H5R_DATASET_REGION);
verify_val(obj_type, H5O_TYPE_DATASET, "DataSet::getRefObjType", __LINE__, __FILE__);
/* Select sequence of ten points for second reference */
coord1[0][0] = 16;
coord1[1][0] = 22;
coord1[2][0] = 38;
coord1[3][0] = 41;
coord1[4][0] = 52;
coord1[5][0] = 63;
coord1[6][0] = 70;
coord1[7][0] = 89;
coord1[8][0] = 97;
coord1[9][0] = 3;
// Selects array elements to be included in the selection for sid3
sid3.selectElements(H5S_SELECT_SET, (size_t)POINT1_NPOINTS, (const hsize_t *)coord1);
// Get and verify the number of elements in a dataspace selection
nelms = sid3.getSelectNpoints();
verify_val(nelms, 10, "DataSet::getRefObjType", __LINE__, __FILE__);
// Store first dataset region
file1.reference(&wbuf[1], "/Dataset2", sid3);
// Write selection to disk
dset1.write(wbuf, PredType::STD_REF_DSETREG);
// Close disk dataspace, dataset, and file
sid1.close();
dset1.close();
sid3.close();
file1.close();
// Re-open the file
file1.openFile(FILE2, H5F_ACC_RDWR);
// Open the dataset
dset1 = file1.openDataSet("/Dataset1");
// Read selection from disk
dset1.read(rbuf, PredType::STD_REF_DSETREG);
// Dereference dataset object by ctor, from the location where
// 'dset1' is located
dset3.dereference(dset1, &rbuf[0], H5R_DATASET_REGION, dapl);
/* DataSet adset3(dset1, &rbuf[0], H5R_DATASET_REGION, dapl);
*/
// Get and verify object type
obj_type = dset1.getRefObjType(&rbuf[0], H5R_DATASET_REGION);
verify_val(obj_type, H5O_TYPE_DATASET, "DataSet::getRefObjType", __LINE__, __FILE__);
// Check information in the referenced dataset, i.e., adset3
// Get dataspace of adset3 the verify number of elements
sid1 = dset3.getSpace();
nelms = sid1.getSimpleExtentNpoints();
verify_val((long)nelms, 100, "DataSpace::getSimpleExtentNpoints", __LINE__, __FILE__);
// Read from disk
dset3.read(drbuf, PredType::STD_U8LE);
for(tu8 = (uint8_t *)drbuf, i = 0; i < SPACE3_DIM1; i++, tu8++)
verify_val(*tu8, (uint8_t)(i * 3), "DataSpace::getSimpleExtentNpoints", __LINE__, __FILE__);
// Get the referenced region and verify values
// Get region
DataSpace reg_sp = dset1.getRegion(&rbuf[0]);
// Get and verify number of elements in a dataspace selection
nelms = reg_sp.getSelectNpoints();
verify_val((long)nelms, 30, "DataSpace::getSelectNpoints", __LINE__, __FILE__);
// Get and verify number of hyperslab blocks
nelms = reg_sp.getSelectHyperNblocks();
verify_val((long)nelms, 15, "DataSpace::getSelectNpoints", __LINE__, __FILE__);
/* Allocate space for the hyperslab blocks */
coords = (hsize_t *)HDmalloc(nelms * SPACE3_RANK * sizeof(hsize_t) * 2);
// Get the list of hyperslab blocks currently selected
reg_sp.getSelectHyperBlocklist((hsize_t)0, (hsize_t)nelms, coords);
// Verify values in the list
verify_val(coords[0], 2, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[1], 3, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[2], 7, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[3], 8, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[4], 12, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[5], 13, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[6], 17, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[7], 18, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[8], 22, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[9], 23, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[10], 27, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[11], 28, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[12], 32, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[13], 33, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[14], 37, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[15], 38, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[16], 42, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[17], 43, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[18], 47, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[19], 48, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[20], 52, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[21], 53, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[22], 57, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[23], 58, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[24], 62, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[25], 63, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[26], 67, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[27], 68, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[28], 72, "Hyperslab Coordinates", __LINE__, __FILE__);
verify_val(coords[29], 73, "Hyperslab Coordinates", __LINE__, __FILE__);
HDfree(coords);
// Check boundaries
reg_sp.getSelectBounds(low, high);
verify_val(low[0], 2, "DataSpace::getSelectBounds", __LINE__, __FILE__);
verify_val(high[0], 73, "DataSpace::getSelectBounds", __LINE__, __FILE__);
/* Close region space */
reg_sp.close();
// Get the referenced region and verify values
// Get region
DataSpace elm_sp = dset1.getRegion(&rbuf[1]);
// Get and verify number of element points in the current selection
hssize_t nelmspts = elm_sp.getSelectElemNpoints();
verify_val((long)nelmspts, 10, "DataSpace::getSelectNpoints", __LINE__, __FILE__);
/* Allocate space for the hyperslab blocks */
coords = (hsize_t *)HDmalloc(nelmspts * SPACE3_RANK * sizeof(hsize_t));
// Get the list of element points currently selected
elm_sp.getSelectElemPointlist((hsize_t)0, (hsize_t)nelmspts, coords);
// Verify points
verify_val(coords[0], coord1[0][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[1], coord1[1][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[2], coord1[2][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[3], coord1[3][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[4], coord1[4][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[5], coord1[5][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[6], coord1[6][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[7], coord1[7][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[8], coord1[8][0], "Element Coordinates", __LINE__, __FILE__);
verify_val(coords[9], coord1[9][0], "Element Coordinates", __LINE__, __FILE__);
HDfree(coords);
// Check boundaries
elm_sp.getSelectBounds(low, high);
verify_val(low[0], 3, "DataSpace::getSelectBounds", __LINE__, __FILE__);
verify_val(high[0], 97, "DataSpace::getSelectBounds", __LINE__, __FILE__);
// Close element space
elm_sp.close();
// Close resources
sid1.close();
dset3.close();
dset1.close();
file1.close();
// Free memory buffers
HDfree(wbuf);
HDfree(rbuf);
HDfree(dwbuf);
HDfree(drbuf);
PASSED();
} // end try
catch (Exception E) {
issue_fail_msg("test_reference_region_1D()", __LINE__, __FILE__, E.getCDetailMsg());
}
} /* test_reference_region_1D() */
/****************************************************************
**
** test_reference_compat(): Test basic object reference functionality.
@ -346,7 +858,10 @@ void test_reference(void)
// Output message about test being performed
MESSAGE(5, ("Testing References\n"));
test_reference_params(); // Test basic parameters of reference functionality
test_reference_obj(); // Test basic object reference functionality
test_reference_group(); // Test group reference functionality
test_reference_region_1D(); // Test 1-D reference functionality
test_reference_compat(); // Tests deprecated reference routines (not yet)
} // test_reference()
@ -363,5 +878,6 @@ extern "C"
void cleanup_reference(void)
{
HDremove(FILE1.c_str());
HDremove(FILE2.c_str());
}