philipp/hdf5
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

[svn-r22836] Purpose: Fix bug HDFFV-533 and add other missing functions

Browse Source 
Description:
    In this bug, H5File doesn't have the ability to create attribute.  The
    following changes will provide that functionality and several others that
    were also missing:
    - Added an abstract class H5Location in between IdComponent and H5Object.
    - New class structure of IdComponent, H5Location, H5Object, H5File
                                IdComponent
                                     |
                                H5Location
                                /        \
                        H5Object        H5File
    - Wrappers in H5Object were moved to H5Location because the related C
      functions take either file, group, dataset, or named datatype ID.
    - Added wrapper for H5Rget_obj_type2
    - Added tests for file attributes and H5Rget_obj_type2 wrapper
Platforms tested:
    Linux/32 2.6 (jam)
    Linux/64 2.6 (koala)
    SunOS 5.10 (linew)
This commit is contained in:
Binh-Minh Ribler
2012-09-27 18:26:16 -05:00
parent e488529430
commit 5fcec401bd
23 changed files with 1148 additions and 924 deletions
Download Patch File Download Diff File Expand all files Collapse all files

501
c++/src/H5Object.cpp
View File

@@ -40,7 +40,7 @@ namespace H5 {
// userAttrOpWrpr simply interfaces between the user's function and the
// C library function H5Aiterate2; used to resolve the different prototype
// problem. May be moved to Iterator later.
extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
extern "C" herr_t userAttrOpWrpr1(hid_t loc_id, const char *attr_name,
const H5A_info_t *ainfo, void *op_data)
{
H5std_string s_attr_name = H5std_string( attr_name );
@@ -49,18 +49,18 @@ extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
#else
UserData4Aiterate* myData = static_cast <UserData4Aiterate *> (op_data);
#endif
myData->op( *myData->object, s_attr_name, myData->opData );
myData->op( *myData->location, s_attr_name, myData->opData );
return 0;
}
//--------------------------------------------------------------------------
// Function: H5Object default constructor (protected)
// Description
// The id is set by IdComponent() but subclass constructor will
// The id is set by H5Location() but subclass constructor will
// set it to a valid HDF5 id.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5Object::H5Object() : IdComponent(0) {}
H5Object::H5Object() : H5Location(0) {}
//--------------------------------------------------------------------------
// Function: H5Object overloaded constructor (protected)
@@ -69,7 +69,7 @@ H5Object::H5Object() : IdComponent(0) {}
// Parameters object_id - IN: Id of an existing HDF5 object
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5Object::H5Object( const hid_t object_id ) : IdComponent( object_id ) {}
H5Object::H5Object( const hid_t object_id ) : H5Location( object_id ) {}
#endif // DOXYGEN_SHOULD_SKIP_THIS
@@ -80,496 +80,7 @@ H5Object::H5Object( const hid_t object_id ) : IdComponent( object_id ) {}
///\param original - IN: H5Object instance to copy
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5Object::H5Object( const H5Object& original ) : IdComponent( original ) {}
//--------------------------------------------------------------------------
// Function: H5Object::createAttribute
///\brief Creates an attribute for a group, dataset, or named datatype.
///\param name - IN: Name of the attribute
///\param data_type - IN: Datatype for the attribute
///\param data_space - IN: Dataspace for the attribute - only simple
/// dataspaces are allowed at this time
///\param create_plist - IN: Creation property list - default to
/// PropList::DEFAULT
///\return Attribute instance
///\exception H5::AttributeIException
///\par Description
/// The attribute name specified in \a name must be unique.
/// Attempting to create an attribute with the same name as an
/// existing attribute will raise an exception, leaving the
/// pre-existing attribute intact. To overwrite an existing
/// attribute with a new attribute of the same name, first
/// delete the existing one with \c H5Object::removeAttr, then
/// recreate it with this function.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::createAttribute( const char* name, const DataType& data_type, const DataSpace& data_space, const PropList& create_plist ) const
{
hid_t type_id = data_type.getId();
hid_t space_id = data_space.getId();
hid_t plist_id = create_plist.getId();
hid_t attr_id = H5Acreate2(getId(), name, type_id, space_id, plist_id, H5P_DEFAULT );
// If the attribute id is valid, create and return the Attribute object
if( attr_id > 0 )
{
Attribute attr( attr_id );
return( attr );
}
else
throw AttributeIException(inMemFunc("createAttribute"), "H5Acreate2 failed");
}
//--------------------------------------------------------------------------
// Function: H5Object::createAttribute
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes
/// a reference to an \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::createAttribute( const H5std_string& name, const DataType& data_type, const DataSpace& data_space, const PropList& create_plist ) const
{
return( createAttribute( name.c_str(), data_type, data_space, create_plist ));
}
//--------------------------------------------------------------------------
// Function: H5Object::openAttribute
///\brief Opens an attribute given its name.
///\param name - IN: Name of the attribute
///\return Attribute instance
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::openAttribute( const char* name ) const
{
hid_t attr_id = H5Aopen(getId(), name, H5P_DEFAULT);
if( attr_id > 0 )
{
Attribute attr( attr_id );
return( attr );
}
else
{
throw AttributeIException(inMemFunc("openAttribute"), "H5Aopen failed");
}
}
//--------------------------------------------------------------------------
// Function: H5Object::openAttribute
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes
/// a reference to an \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::openAttribute( const H5std_string& name ) const
{
return( openAttribute( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: H5Object::openAttribute
///\brief Opens an attribute given its index.
///\param idx - IN: Index of the attribute, a 0-based, non-negative integer
///\return Attribute instance
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::openAttribute( const unsigned int idx ) const
{
hid_t attr_id = H5Aopen_by_idx(getId(), ".", H5_INDEX_CRT_ORDER,
H5_ITER_INC, (hsize_t)idx, H5P_DEFAULT, H5P_DEFAULT);
if( attr_id > 0 )
{
Attribute attr( attr_id );
return( attr );
}
else
{
throw AttributeIException(inMemFunc("openAttribute"), "H5Aopen_by_idx failed");
}
}
//--------------------------------------------------------------------------
// Function: H5Object::iterateAttrs
///\brief Iterates a user's function over all the attributes of an H5
/// object, which may be a group, dataset or named datatype.
///\param user_op - IN: User's function to operate on each attribute
///\param _idx - IN/OUT: Starting (IN) and ending (OUT) attribute indices
///\param op_data - IN: User's data to pass to user's operator function
///\return Returned value of the last operator if it was non-zero, or
/// zero if all attributes were processed
///\exception H5::AttributeIException
///\par Description
/// The signature of user_op is
/// void (*)(H5::H5Object&, H5std_string, void*).
/// For information, please refer to the C layer Reference Manual
/// at:
/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-Iterate
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int H5Object::iterateAttrs( attr_operator_t user_op, unsigned *_idx, void *op_data )
{
// store the user's function and data
UserData4Aiterate* userData = new UserData4Aiterate;
userData->opData = op_data;
userData->op = user_op;
userData->object = this;
// call the C library routine H5Aiterate2 to iterate the attributes
hsize_t idx = _idx ? (hsize_t)*_idx : 0;
int ret_value = H5Aiterate2(getId(), H5_INDEX_NAME, H5_ITER_INC, &idx,
userAttrOpWrpr, (void *) userData);
// release memory
delete userData;
if( ret_value >= 0 ) {
/* Pass back update index value to calling code */
if (_idx)
*_idx = (unsigned)idx;
return( ret_value );
}
else // raise exception when H5Aiterate returns a negative value
throw AttributeIException(inMemFunc("iterateAttrs"), "H5Aiterate2 failed");
}
//--------------------------------------------------------------------------
// Function: H5Object::getNumAttrs
///\brief Returns the number of attributes attached to this HDF5 object.
///\return Number of attributes
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int H5Object::getNumAttrs() const
{
H5O_info_t oinfo; /* Object info */
if(H5Oget_info(getId(), &oinfo) < 0)
throw AttributeIException(inMemFunc("getNumAttrs"), "H5Oget_info failed");
else
return( (int)oinfo.num_attrs );
}
//--------------------------------------------------------------------------
// Function: H5Object::removeAttr
///\brief Removes the named attribute from this object.
///\param name - IN: Name of the attribute to be removed
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5Object::removeAttr( const char* name ) const
{
herr_t ret_value = H5Adelete(getId(), name);
if( ret_value < 0 )
throw AttributeIException(inMemFunc("removeAttr"), "H5Adelete failed");
}
//--------------------------------------------------------------------------
// Function: H5Object::removeAttr
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes
/// a reference to an \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5Object::removeAttr( const H5std_string& name ) const
{
removeAttr( name.c_str() );
}
//--------------------------------------------------------------------------
// Function: H5Object::renameAttr
///\brief Renames the named attribute from this object.
///\param oldname - IN: Name of the attribute to be renamed
///\param newname - IN: New name ame of the attribute
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - Mar, 2005
//--------------------------------------------------------------------------
void H5Object::renameAttr(const char* oldname, const char* newname) const
{
herr_t ret_value = H5Arename(getId(), oldname, newname);
if (ret_value < 0)
throw AttributeIException(inMemFunc("renameAttr"), "H5Arename failed");
}
//--------------------------------------------------------------------------
// Function: H5Object::renameAttr
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes
/// a reference to an \c H5std_string for the names.
// Programmer Binh-Minh Ribler - Mar, 2005
//--------------------------------------------------------------------------
void H5Object::renameAttr(const H5std_string& oldname, const H5std_string& newname) const
{
renameAttr (oldname.c_str(), newname.c_str());
}
//--------------------------------------------------------------------------
// Function: H5Object::flush
///\brief Flushes all buffers associated with a file to disk.
///\param scope - IN: Specifies the scope of the flushing action,
/// 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::AttributeIException
///\par Description
/// This object is used to identify the file to be flushed.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5Object::flush(H5F_scope_t scope) const
{
herr_t ret_value = H5Fflush(getId(), scope);
if( ret_value < 0 )
{
throw FileIException(inMemFunc("flush"), "H5Fflush failed");
}
}
//--------------------------------------------------------------------------
// Function: H5Object::getFileName
///\brief Gets the name of the file, in which this HDF5 object belongs.
///\return File name
///\exception H5::IdComponentException
// Programmer Binh-Minh Ribler - Jul, 2004
//--------------------------------------------------------------------------
H5std_string H5Object::getFileName() const
{
try {
return(p_get_file_name());
}
catch (IdComponentException E) {
throw FileIException(inMemFunc("getFileName"), E.getDetailMsg());
}
}
//--------------------------------------------------------------------------
// Function: H5Object::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
//--------------------------------------------------------------------------
void H5Object::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
{
herr_t ret_value = H5Rcreate(ref, getId(), name, ref_type, space_id);
if (ret_value < 0)
{
throw IdComponentException("", "H5Rcreate failed");
}
}
//--------------------------------------------------------------------------
// Function: H5Object::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::IdComponentException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Object::reference(void* ref, const char* name, const DataSpace& dataspace, H5R_type_t ref_type) const
{
try {
p_reference(ref, name, dataspace.getId(), ref_type);
}
catch (IdComponentException E) {
throw IdComponentException("H5Object::reference", E.getDetailMsg());
}
}
//--------------------------------------------------------------------------
// Function: H5Object::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::IdComponentException
///\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
//--------------------------------------------------------------------------
void H5Object::reference(void* ref, const char* name) const
{
try {
p_reference(ref, name, -1, H5R_OBJECT);
}
catch (IdComponentException E) {
throw IdComponentException("H5Object::reference", E.getDetailMsg());
}
}
//--------------------------------------------------------------------------
// Function: H5Object::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
//--------------------------------------------------------------------------
void H5Object::reference(void* ref, const H5std_string& name) const
{
reference(ref, name.c_str());
}
//--------------------------------------------------------------------------
// Function: H5Object::p_dereference (protected)
// Purpose Dereference a ref into an hdf5 object.
// Parameters
// loc_id - IN: An hdf5 identifier specifying the location of the
// referenced object
// ref - IN: Reference pointer
// ref_type - IN: Reference type
// Exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
// Modification
// May 2008 - BMR
// Moved from IdComponent.
//--------------------------------------------------------------------------
hid_t H5Object::p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_type)
{
hid_t temp_id;
temp_id = H5Rdereference2(loc_id, H5P_DEFAULT, ref_type, ref);
if (temp_id < 0)
{
throw ReferenceException("", "H5Rdereference failed");
}
// No failure, set id to the object
return(temp_id);
}
//--------------------------------------------------------------------------
// Function: H5Object::dereference
///\brief Dereferences a reference into an HDF5 object, given an HDF5 object.
///\param obj - IN: Object 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 H5Object::dereference(H5Object& obj, const void* ref, H5R_type_t ref_type)
{
hid_t temp_id;
try {
temp_id = p_dereference(obj.getId(), ref, ref_type);
}
catch (ReferenceException E) {
throw ReferenceException("H5Object::dereference - located by object", E.getDetailMsg());
}
p_setId(temp_id);
}
//--------------------------------------------------------------------------
// Function: H5Object::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 H5Object::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("H5Object::dereference - located by file", E.getDetailMsg());
}
p_setId(temp_id);
}
//--------------------------------------------------------------------------
// Function: H5Object::dereference
///\brief Dereferences a reference into an HDF5 object, given an attribute.
///\param attr - IN: Attribute 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 H5Object::dereference(Attribute& attr, const void* ref, H5R_type_t ref_type)
{
hid_t temp_id;
try {
temp_id = p_dereference(attr.getId(), ref, ref_type);
}
catch (ReferenceException E) {
throw ReferenceException("H5Object::dereference - located by attribute", E.getDetailMsg());
}
p_setId(temp_id);
}
#ifndef H5_NO_DEPRECATED_SYMBOLS
//--------------------------------------------------------------------------
// Function: H5Object::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_LINK Object is a symbolic link.
// H5G_GROUP Object is a group.
// H5G_DATASET Object is a dataset.
// H5G_TYPE Object is a named datatype
// Exception H5::IdComponentException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
H5G_obj_t H5Object::p_get_obj_type(void *ref, H5R_type_t ref_type) const
{
H5G_obj_t obj_type = H5Rget_obj_type1(getId(), ref_type, ref);
if (obj_type == H5G_UNKNOWN)
{
throw IdComponentException("", "H5Rget_obj_type failed");
}
return(obj_type);
}
#endif /* H5_NO_DEPRECATED_SYMBOLS */
//--------------------------------------------------------------------------
// Function: H5Object::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::IdComponentException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
hid_t H5Object::p_get_region(void *ref, H5R_type_t ref_type) const
{
hid_t space_id = H5Rget_region(getId(), ref_type, ref);
if (space_id < 0)
{
throw IdComponentException("", "H5Rget_region failed");
}
return(space_id);
}
H5Object::H5Object( const H5Object& original ) : H5Location( original ) {}
//--------------------------------------------------------------------------
// Function: H5Object destructor