/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include "H5Include.h" #include "H5Exception.h" #include "H5IdComponent.h" #include "H5PropList.h" #include "H5FaccProp.h" #include "H5FcreatProp.h" #include "H5OcreatProp.h" #include "H5DcreatProp.h" #include "H5DxferProp.h" #include "H5LcreatProp.h" #include "H5LaccProp.h" #include "H5DaccProp.h" #include "H5Location.h" #include "H5Object.h" #include "H5DataType.h" #include "H5DataSpace.h" #include "H5AbstractDs.h" #include "H5CommonFG.h" #include "H5Group.h" #include "H5File.h" #include "H5DataSet.h" #include "H5Attribute.h" namespace H5 { #ifndef DOXYGEN_SHOULD_SKIP_THIS // userAttrOpWrpr interfaces between the user's function and the // C library function H5Aiterate2 extern "C" { static herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name, const H5A_info_t *ainfo, void *op_data) { // Unused (void)loc_id; (void)ainfo; H5std_string s_attr_name = H5std_string(attr_name); UserData4Aiterate *myData = reinterpret_cast(op_data); myData->op(*myData->location, s_attr_name, myData->opData); return 0; } // userVisitOpWrpr interfaces between the user's function and the // C library function H5Ovisit3 static herr_t userVisitOpWrpr(hid_t obj_id, const char *attr_name, const H5O_info2_t *obj_info, void *op_data) { // Unused (void)obj_id; H5std_string s_attr_name = H5std_string(attr_name); UserData4Visit *myData = reinterpret_cast(op_data); int status = myData->op(*myData->obj, s_attr_name, obj_info, myData->opData); return status; } } // extern "C" //-------------------------------------------------------------------------- // Function: H5Object default constructor (protected) // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- H5Object::H5Object() : H5Location() { } //-------------------------------------------------------------------------- // Function: f_Attribute_setId - friend // Purpose: This function is friend to class H5::Attribute so that it // can set Attribute::id in order to work around a problem // described in the JIRA issue HDFFV-7947. // Applications shouldn't need to use it. // param attr - IN/OUT: Attribute object to be changed // param new_id - IN: New id to set // Programmer Binh-Minh Ribler - 2015 //-------------------------------------------------------------------------- void f_Attribute_setId(Attribute *attr, hid_t new_id) { attr->p_setId(new_id); } #endif //-------------------------------------------------------------------------- // 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; f_Attribute_setId(&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; f_Attribute_setId(&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, static_cast(idx), H5P_DEFAULT, H5P_DEFAULT); if (attr_id > 0) { Attribute attr; f_Attribute_setId(&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::H5Location&, H5std_string, void*). // 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->location = this; // call the C library routine H5Aiterate2 to iterate the attributes hsize_t idx = _idx ? static_cast(*_idx) : 0; int ret_value = H5Aiterate2(getId(), H5_INDEX_NAME, H5_ITER_INC, &idx, userAttrOpWrpr, static_cast(userData)); // release memory delete userData; if (ret_value >= 0) { /* Pass back update index value to calling code */ if (_idx) *_idx = static_cast(idx); return (ret_value); } else // raise exception when H5Aiterate returns a negative value throw AttributeIException(inMemFunc("iterateAttrs"), "H5Aiterate2 failed"); } //-------------------------------------------------------------------------- // Function: H5Object::visit ///\brief Recursively visits all HDF5 objects accessible from this object. ///\param idx_type - IN: Type of index; valid values include: /// \li \c H5_INDEX_NAME /// \li \c H5_INDEX_CRT_ORDER ///\param order - IN: Order in which index is traversed; valid values include: /// \li \c H5_ITER_DEC /// \li \c H5_ITER_INC /// \li \c H5_ITER_NATIVE ///\param user_op - IN: Callback function passing data regarding the /// object to the calling application ///\param *op_data - IN: User-defined pointer to data required by the /// application for its processing of the object ///\param fields - IN: Flags specifying the fields to be retrieved /// to the callback op via the H5O_info2_t argument. /// \li \c H5O_INFO_BASIC fileno, addr, type, and rc fields /// \li \c H5O_INFO_TIME atime, mtime, ctime, and btime fields /// \li \c H5O_INFO_NUM_ATTRS num_attrs field /// \li \c H5O_INFO_ALL H5O_INFO_BASIC | H5O_INFO_TIME | H5O_INFO_NUM_ATTRS ///\return /// \li On success: /// \li the return value of the first operator that returns a positive value /// \li zero if all members were processed with no operator returning non-zero /// \li On failure: /// \li an exception Exception will be thrown if something went /// wrong within the library or the operator failed ///\exception H5::Exception ///\par Description /// For information, please refer to the H5Ovisit3 API in the HDF5 /// C Reference Manual. // Programmer Binh-Minh Ribler - Feb, 2019 //-------------------------------------------------------------------------- void H5Object::visit(H5_index_t idx_type, H5_iter_order_t order, visit_operator_t user_op, void *op_data, unsigned int fields) { // Store the user's function and data UserData4Visit *userData = new UserData4Visit; userData->opData = op_data; userData->op = user_op; userData->obj = this; // Call the C API passing in op wrapper and info herr_t ret_value = H5Ovisit3(getId(), idx_type, order, userVisitOpWrpr, static_cast(userData), fields); // Release memory delete userData; // Throw exception if H5Ovisit3 failed, which could be a failure in // the library or in the call back operator if (ret_value < 0) throw Exception(inMemFunc("visit"), "H5Ovisit3 failed"); } //-------------------------------------------------------------------------- // Function: H5Object::objVersion ///\brief Returns the header version of this HDF5 object. ///\return Object version, which can have the following values: /// \li \c H5O_VERSION_1 /// \li \c H5O_VERSION_2 ///\exception H5::ObjHeaderIException /// Exception will be thrown when: /// - an error returned by the C API /// - version number is not one of the valid values above // Programmer Binh-Minh Ribler - December, 2016 //-------------------------------------------------------------------------- unsigned H5Object::objVersion() const { H5O_native_info_t objinfo; unsigned version = 0; // Use C API to get information of the object herr_t ret_value = H5Oget_native_info(getId(), &objinfo, H5O_NATIVE_INFO_HDR); // Throw exception if C API returns failure if (ret_value < 0) throw Exception(inMemFunc("objVersion"), "H5Oget_native_info failed"); // Return a valid version or throw an exception for invalid value else { version = objinfo.hdr.version; if (version != H5O_VERSION_1 && version != H5O_VERSION_2) throw ObjHeaderIException("objVersion", "Invalid version for object"); } return (version); } //-------------------------------------------------------------------------- // 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_info2_t oinfo; /* Object info */ if (H5Oget_info3(getId(), &oinfo, H5O_INFO_NUM_ATTRS) < 0) throw AttributeIException(inMemFunc("getNumAttrs"), "H5Oget_info failed"); else return (static_cast(oinfo.num_attrs)); } //-------------------------------------------------------------------------- // Function: H5Object::attrExists ///\brief Checks whether the named attribute exists at this location. ///\param name - IN: Name of the attribute to be queried ///\exception H5::AttributeIException // Programmer Binh-Minh Ribler - 2013 //-------------------------------------------------------------------------- bool H5Object::attrExists(const char *name) const { // Call C routine H5Aexists to determine whether an attribute exists // at this location, which could be specified by a file, group, dataset, // or named datatype. herr_t ret_value = H5Aexists(getId(), name); if (ret_value > 0) return true; else if (ret_value == 0) return false; else // Raise exception when H5Aexists returns a negative value throw AttributeIException(inMemFunc("attrExists"), "H5Aexists failed"); } //-------------------------------------------------------------------------- // Function: H5Object::attrExists ///\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 //-------------------------------------------------------------------------- bool H5Object::attrExists(const H5std_string &name) const { return (attrExists(name.c_str())); } //-------------------------------------------------------------------------- // 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: getObjName ///\brief Given an id, returns the type of the object. ///\return The name of the object // Programmer Binh-Minh Ribler - Mar, 2014 //-------------------------------------------------------------------------- ssize_t H5Object::getObjName(char *obj_name, size_t buf_size) const { // H5Iget_name will get buf_size-1 chars of the name to null terminate it ssize_t name_size = H5Iget_name(getId(), obj_name, buf_size); // If H5Iget_name returns a negative value, raise an exception if (name_size < 0) { throw Exception(inMemFunc("getObjName"), "H5Iget_name failed"); } else if (name_size == 0) { throw Exception(inMemFunc("getObjName"), "Object must have a name, but name length is 0"); } // Return length of the name return (name_size); } //-------------------------------------------------------------------------- // Function: H5Object::getObjName ///\brief Returns the name of this object as an \a H5std_string. ///\return Name of the object ///\exception H5::Exception // Programmer Binh-Minh Ribler - Mar, 2014 //-------------------------------------------------------------------------- H5std_string H5Object::getObjName() const { H5std_string obj_name; // object name to return // Preliminary call to get the size of the object name ssize_t name_size = H5Iget_name(getId(), NULL, 0); // If H5Iget_name failed, throw exception if (name_size < 0) { throw Exception(inMemFunc("getObjName"), "H5Iget_name failed"); } else if (name_size == 0) { throw Exception(inMemFunc("getObjName"), "Object must have a name, but name length is 0"); } // Object's name exists, retrieve it else if (name_size > 0) { // Create buffer for C string char *name_C = new char[name_size + 1]; memset(name_C, 0, name_size + 1); // Use overloaded function name_size = getObjName(name_C, name_size + 1); // Convert the C object name to return obj_name = name_C; // Clean up resource delete[] name_C; } // Return object's name return (obj_name); } //-------------------------------------------------------------------------- // Function: H5Object::getObjName ///\brief Gets the name of this object, returning its length. ///\param obj_name - OUT: Buffer for the name string as \a H5std_string ///\param len - IN: Desired length of the name, default to 0 ///\return Actual length of the object name ///\exception H5::Exception ///\par Description /// This function retrieves the object's name as an std string. /// buf_size can specify a specific length or default to 0, in /// which case the entire name will be retrieved. // Programmer Binh-Minh Ribler - Mar, 2014 //-------------------------------------------------------------------------- ssize_t H5Object::getObjName(H5std_string &obj_name, size_t len) const { ssize_t name_size = 0; // If no length is provided, get the entire object name if (len == 0) { obj_name = getObjName(); name_size = obj_name.length(); } // If length is provided, get that number of characters in name else { // Create buffer for C string char *name_C = new char[len + 1]; memset(name_C, 0, len + 1); // Use overloaded function name_size = getObjName(name_C, len + 1); // Convert the C object name to return obj_name = name_C; // Clean up resource delete[] name_C; } // Otherwise, keep obj_name intact // Return name size return (name_size); } #ifndef DOXYGEN_SHOULD_SKIP_THIS //-------------------------------------------------------------------------- // Function: H5Object destructor ///\brief Noop destructor. // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- H5Object::~H5Object() { } #endif // DOXYGEN_SHOULD_SKIP_THIS } // namespace H5