/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * 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 files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifdef OLD_HEADER_FILENAME #include #else #include #endif #include #ifndef H5_NO_NAMESPACE #endif #include "H5Include.h" #include "H5Exception.h" #include "H5IdComponent.h" #include "H5PropList.h" #include "H5Object.h" #include "H5FaccProp.h" #include "H5FcreatProp.h" #include "H5DxferProp.h" #include "H5DcreatProp.h" #include "H5CommonFG.h" #include "H5Group.h" #include "H5AbstractDs.h" #include "H5DataSpace.h" #include "H5DataSet.h" #include "H5File.h" #include "H5Alltypes.h" #ifndef H5_NO_NAMESPACE namespace H5 { #ifndef H5_NO_STD using std::cerr; using std::endl; #endif // H5_NO_STD #endif //-------------------------------------------------------------------------- // Function H5File default constructor ///\brief Default constructor: creates a stub H5File object. // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- H5File::H5File() : IdComponent() {} //-------------------------------------------------------------------------- // Function: H5File overloaded constructor ///\brief Creates or opens an HDF5 file depending on the parameter flags. ///\param name - IN: Name of the file ///\param flags - IN: File access flags ///\param create_plist - IN: File creation property list, used when /// modifying default file meta-data. Default to /// FileCreatPropList::DEFAULT ///\param access_plist - IN: File access property list. Default to /// FileCreatPropList::DEFAULT ///\par Description /// Valid values of \a flags include: /// \li \c H5F_ACC_TRUNC - Truncate file, if it already exists, /// erasing all data previously stored in /// the file. /// \li \c H5F_ACC_EXCL - Fail if file already exists. /// \c H5F_ACC_TRUNC and \c H5F_ACC_EXCL are mutually exclusive /// \li \c H5F_ACC_DEBUG - print debug information. This flag is /// used only by HDF5 library developers; it is neither /// tested nor supported for use in applications. ///\par /// For info on file creation in the case of an already-open file, /// please refer to the \b Special \b case section in the C layer /// Reference Manual at: /// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5F.html#File-Create // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- H5File::H5File( const char* name, unsigned int flags, const FileCreatPropList& create_plist, const FileAccPropList& access_plist ) : IdComponent() { p_get_file(name, flags, create_plist, access_plist); } //-------------------------------------------------------------------------- // Function: H5File overloaded constructor ///\brief This is another overloaded constructor. It differs from the /// above constructor only in the type of the \a name argument. ///\param name - IN: Name of the file - \c std::string ///\param flags - IN: File access flags ///\param create_plist - IN: File creation property list, used when /// modifying default file meta-data. Default to /// FileCreatPropList::DEFAULT ///\param access_plist - IN: File access property list. Default to /// FileCreatPropList::DEFAULT // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- H5File::H5File( const H5_std::string& name, unsigned int flags, const FileCreatPropList& create_plist, const FileAccPropList& access_plist ) : IdComponent() { p_get_file(name.c_str(), flags, create_plist, access_plist); } //-------------------------------------------------------------------------- // This function is private and contains common code between the // constructors taking a string or a char* // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- void H5File::p_get_file(const char* name, unsigned int flags, const FileCreatPropList& create_plist, const FileAccPropList& access_plist) { // These bits only set for creation, so if any of them are set, // create the file. if( flags & (H5F_ACC_CREAT|H5F_ACC_EXCL|H5F_ACC_TRUNC|H5F_ACC_DEBUG)) { hid_t create_plist_id = create_plist.getId(); hid_t access_plist_id = access_plist.getId(); id = H5Fcreate( name, flags, create_plist_id, access_plist_id ); if( id < 0 ) // throw an exception when open/create fail { throw FileIException("H5File constructor", "H5Fcreate failed"); } } // Open the file if none of the bits above are set. else { hid_t access_plist_id = access_plist.getId(); id = H5Fopen( name, flags, access_plist_id ); if( id < 0 ) // throw an exception when open/create fail { throw FileIException("H5File constructor", "H5Fopen failed"); } } } //-------------------------------------------------------------------------- // Function: H5File copy constructor ///\brief Copy constructor: makes a copy of the original /// H5File object. ///\param original - IN: H5File instance to copy // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- H5File::H5File( const H5File& original ) : IdComponent( original ) {} //-------------------------------------------------------------------------- // Function: H5File::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::FileIException // Programmer Binh-Minh Ribler - Dec. 2005 //-------------------------------------------------------------------------- void H5File::flush(H5F_scope_t scope) const { herr_t ret_value = H5Fflush( id, scope ); if( ret_value < 0 ) { throw FileIException("H5File::flush", "H5Fflush failed"); } } //-------------------------------------------------------------------------- // Function: H5File::isHdf5 ///\brief Determines whether a file in HDF5 format. ///\param name - IN: Name of the file ///\return true if the file is in HDF5 format, and false, otherwise ///\exception H5::FileIException // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- bool H5File::isHdf5(const char* name) { // Calls C routine H5Fis_hdf5 to determine whether the file is in // HDF5 format. It returns positive value, 0, or negative value htri_t ret_value = H5Fis_hdf5( name ); if( ret_value > 0 ) return true; else if( ret_value == 0 ) return false; else // Raise exception when H5Fis_hdf5 returns a negative value { throw FileIException("H5File::isHdf5", "H5Fis_hdf5 returned negative value"); } } //-------------------------------------------------------------------------- // Function: H5File::isHdf5 ///\brief This is an overloaded member function, provided for convenience. /// It takes an \c std::string for \a name. ///\param name - IN: Name of the file - \c std::string // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- bool H5File::isHdf5(const H5_std::string& name ) { return( isHdf5( name.c_str()) ); } //-------------------------------------------------------------------------- // Function: openFile ///\brief Opens an HDF5 file ///\param name - IN: Name of the file ///\param flags - IN: File access flags ///\param access_plist - IN: File access property list. Default to /// FileCreatPropList::DEFAULT ///\par Description /// Valid values of \a flags include: /// H5F_ACC_RDWR: Open with read/write access. If the file is /// currently open for read-only access then it /// will be reopened. Absence of this flag /// implies read-only access. /// /// H5F_ACC_RDONLY: Open with read only access. - default /// // Programmer Binh-Minh Ribler - Oct, 2005 //-------------------------------------------------------------------------- void H5File::openFile(const char* name, unsigned int flags, const FileAccPropList& access_plist) { hid_t access_plist_id = access_plist.getId(); id = H5Fopen (name, flags, access_plist_id); if (id < 0) // throw an exception when open fails { throw FileIException("H5File::openFile", "H5Fopen failed"); } } //-------------------------------------------------------------------------- // Function: H5File::openFile ///\brief This is an overloaded member function, provided for convenience. /// It takes an \c std::string for \a name. ///\param name - IN: Name of the file - \c std::string ///\param flags - IN: File access flags ///\param access_plist - IN: File access property list. Default to /// FileAccPropList::DEFAULT // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- void H5File::openFile(const H5_std::string& name, unsigned int flags, const FileAccPropList& access_plist) { openFile(name.c_str(), flags, access_plist); } //-------------------------------------------------------------------------- // Function: H5File::reOpen ///\brief Reopens this file. /// ///\exception H5::FileIException // Description // If this object has represented another HDF5 file, the previous // HDF5 file need to be closed first. // Programmer Binh-Minh Ribler - 2000 // Note: This wrapper doesn't seem right regarding the 'id' and should // be investigated. BMR - 2/20/2005 // Modification // Replaced resetIdComponent with decRefCount to use C library // ID reference counting mechanism - June 1, 2004 //-------------------------------------------------------------------------- void H5File::reOpen() { // If this object has a valid id, appropriately decrement reference // counter and close the id. try { decRefCount(); } catch (Exception close_error) { throw FileIException("H5File::reOpen", close_error.getDetailMsg()); } // call C routine to reopen the file - Note: not sure about this // does id need to be closed later? which id to be the parameter? id = H5Freopen( id ); if( id < 0 ) // Raise exception when H5Freopen returns a neg value throw FileIException("H5File::reOpen", "H5Freopen failed"); } //-------------------------------------------------------------------------- // Function: H5File::reopen ///\brief Reopens this file. /// ///\exception H5::FileIException ///\par Description /// This function will be replaced by the above function \c reOpen /// in future releases. // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- void H5File::reopen() { H5File::reOpen(); } //-------------------------------------------------------------------------- // Function: H5File::getCreatePlist ///\brief Returns the creation property list of this file ///\return FileCreatPropList object ///\exception H5::FileIException // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- FileCreatPropList H5File::getCreatePlist() const { hid_t create_plist_id = H5Fget_create_plist( id ); // if H5Fget_create_plist returns a valid id, create and return // the FileCreatPropList object for this property list if( create_plist_id > 0 ) { FileCreatPropList create_plist( create_plist_id ); return( create_plist ); } else { throw FileIException("H5File::getCreatePlist", "H5Fget_create_plist failed"); } } //-------------------------------------------------------------------------- // Function: H5File::getAccessPlist ///\brief Returns the access property list of this file ///\return FileAccPropList object ///\exception H5::FileIException // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- FileAccPropList H5File::getAccessPlist() const { hid_t access_plist_id = H5Fget_access_plist( id ); // if H5Fget_access_plist returns a valid id, create and return // the FileAccPropList object for this property list if( access_plist_id > 0 ) { FileAccPropList access_plist( access_plist_id ); return access_plist; } else // Raise an exception { throw FileIException("H5File::getAccessPlist", "H5Fget_access_plist failed"); } } //-------------------------------------------------------------------------- // Function: H5File::getFreeSpace ///\brief Returns the amount of free space in the file. ///\return Amount of free space ///\exception H5::FileIException // Programmer Binh-Minh Ribler - May 2004 //-------------------------------------------------------------------------- hssize_t H5File::getFreeSpace() const { hssize_t free_space = H5Fget_freespace(id); if( free_space < 0 ) { throw FileIException("H5File::getFreeSpace", "H5Fget_freespace failed"); } return (free_space); } //-------------------------------------------------------------------------- // Function: H5File::getObjCount ///\brief Returns the number of opened object IDs (files, datasets, /// groups and datatypes) in the same file. ///\param types - Type of object to retrieve the count ///\return Number of opened object IDs ///\exception H5::FileIException ///\par Description /// The valid values for \a types include: /// \li \c H5F_OBJ_FILE - Files only /// \li \c H5F_OBJ_DATASET - Datasets only /// \li \c H5F_OBJ_GROUP - Groups only /// \li \c H5F_OBJ_DATATYPE - Named datatypes only /// \li \c H5F_OBJ_ATTR - Attributes only /// \li \c H5F_OBJ_ALL - All of the above, i.e., \c H5F_OBJ_FILE /// | \c H5F_OBJ_DATASET | \c H5F_OBJ_GROUP /// | \c H5F_OBJ_DATATYPE | \c H5F_OBJ_ATTR ///\par /// Multiple object types can be combined with the logical OR operator (|). // Programmer Binh-Minh Ribler - May 2004 //-------------------------------------------------------------------------- int H5File::getObjCount(unsigned types) const { int num_objs = H5Fget_obj_count(id, types); if( num_objs < 0 ) { throw FileIException("H5File::getObjCount", "H5Fget_obj_count failed"); } return (num_objs); } //-------------------------------------------------------------------------- // Function: H5File::getObjCount ///\brief This is an overloaded member function, provided for convenience. /// It takes no parameter and returns the object count of all /// object types. ///\return Number of opened object IDs ///\exception H5::FileIException // Programmer Binh-Minh Ribler - May 2004 //-------------------------------------------------------------------------- int H5File::getObjCount() const { int num_objs = H5Fget_obj_count(id, H5F_OBJ_ALL); if( num_objs < 0 ) { throw FileIException("H5File::getObjCount", "H5Fget_obj_count failed"); } return (num_objs); } //-------------------------------------------------------------------------- // Function: H5File::getObjIDs ///\brief Retrieves a list of opened object IDs (files, datasets, /// groups and datatypes) in the same file. ///\param types - Type of object to retrieve the count ///\param max_objs - Maximum number of object identifiers to place /// into obj_id_list. ///\param oid_list - List of open object identifiers ///\exception H5::FileIException ///\par Description /// The valid values for \a types include: /// \li \c H5F_OBJ_FILE - Files only /// \li \c H5F_OBJ_DATASET - Datasets only /// \li \c H5F_OBJ_GROUP - Groups only /// \li \c H5F_OBJ_DATATYPE - Named datatypes only /// \li \c H5F_OBJ_ATTR - Attributes only /// \li \c H5F_OBJ_ALL - All of the above, i.e., \c H5F_OBJ_FILE /// | \c H5F_OBJ_DATASET | \c H5F_OBJ_GROUP /// | \c H5F_OBJ_DATATYPE | \c H5F_OBJ_ATTR ///\par /// Multiple object types can be combined with the logical OR operator (|). // // Notes: will do the overload for this one after hearing from Quincey??? // Programmer Binh-Minh Ribler - May 2004 //-------------------------------------------------------------------------- void H5File::getObjIDs(unsigned types, int max_objs, hid_t *oid_list) const { herr_t ret_value = H5Fget_obj_ids(id, types, max_objs, oid_list); if( ret_value < 0 ) { throw FileIException("H5File::getObjIDs", "H5Fget_obj_ids failed"); } } //-------------------------------------------------------------------------- // Function: H5File::getVFDHandle ///\brief Returns the pointer to the file handle of the low-level file /// driver. ///\param fapl - File access property list ///\param file_handle - Pointer to the file handle being used by /// the low-level virtual file driver ///\exception H5::FileIException ///\par Description /// For the \c FAMILY or \c MULTI drivers, \a fapl should be /// defined through the property list functions: /// \c FileAccPropList::setFamilyOffset for the \c FAMILY driver /// and \c FileAccPropList::setMultiType for the \c MULTI driver. /// /// The obtained file handle is dynamic and is valid only while /// the file remains open; it will be invalid if the file is /// closed and reopened or opened during a subsequent session. // Programmer Binh-Minh Ribler - May 2004 //-------------------------------------------------------------------------- void H5File::getVFDHandle(FileAccPropList& fapl, void **file_handle) const { hid_t fapl_id = fapl.getId(); herr_t ret_value = H5Fget_vfd_handle(id, fapl_id, file_handle); if( ret_value < 0 ) { throw FileIException("H5File::getVFDHandle", "H5Fget_vfd_handle failed"); } } //-------------------------------------------------------------------------- // Function: H5File::getVFDHandle ///\brief This is an overloaded member function, provided for convenience. /// It differs from the above function only in what arguments it /// accepts. ///\param file_handle - Pointer to the file handle being used by /// the low-level virtual file driver ///\exception H5::FileIException // Programmer Binh-Minh Ribler - May 2004 //-------------------------------------------------------------------------- void H5File::getVFDHandle(void **file_handle) const { herr_t ret_value = H5Fget_vfd_handle(id, H5P_DEFAULT, file_handle); if( ret_value < 0 ) { throw FileIException("H5File::getVFDHandle", "H5Fget_vfd_handle failed"); } } //-------------------------------------------------------------------------- // Function: H5File::getFileName ///\brief Gets the name of this file. ///\return File name ///\exception H5::IdComponentException // Programmer Binh-Minh Ribler - Jul, 2004 //-------------------------------------------------------------------------- H5_std::string H5File::getFileName() const { try { return(p_get_file_name()); } catch (IdComponentException E) { throw FileIException("H5File::getFileName", E.getDetailMsg()); } } //-------------------------------------------------------------------------- // Function: H5File::Reference ///\brief Creates a reference to an Hdf5 object or a dataset region. ///\param name - IN: Name of the object to be referenced ///\param dataspace - IN: Dataspace with selection ///\param ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION ///\return A reference ///\exception H5::IdComponentException ///\par Description /// Note that name must be an absolute path to the object in the file. // Programmer Binh-Minh Ribler - May, 2004 //-------------------------------------------------------------------------- void* H5File::Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type) const { try { return(p_reference(name, dataspace.getId(), ref_type)); } catch (IdComponentException E) { throw FileIException("H5File::Reference", E.getDetailMsg()); } } //-------------------------------------------------------------------------- // Function: H5File::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 name - IN: Name of the object to be referenced ///\return A reference ///\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. ///\par /// Note that, for H5File, name must be an absolute path to the /// object in the file. // Programmer Binh-Minh Ribler - May, 2004 //-------------------------------------------------------------------------- void* H5File::Reference(const char* name) const { try { return(p_reference(name, -1, H5R_OBJECT)); } catch (IdComponentException E) { throw FileIException("H5File::Reference", E.getDetailMsg()); } } //-------------------------------------------------------------------------- // Function: H5File::Reference ///\brief This is an overloaded function, provided for your convenience. /// It differs from the above function in that it takes an /// \c std::string for the object's name. ///\param name - IN: Name of the object to be referenced - \c std::string // Programmer Binh-Minh Ribler - May, 2004 //-------------------------------------------------------------------------- void* H5File::Reference(const H5_std::string& name) const { return(Reference(name.c_str())); } //-------------------------------------------------------------------------- // Function: H5File::getObjType ///\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 ///\return Object type, which can be one of the following: /// \li \c H5G_LINK - Object is a symbolic link. /// \li \c H5G_GROUP - Object is a group. /// \li \c H5G_DATASET - Object is a dataset. /// \li \c H5G_TYPE - Object is a named datatype ///\exception H5::IdComponentException // Programmer Binh-Minh Ribler - May, 2004 //-------------------------------------------------------------------------- H5G_obj_t H5File::getObjType(void *ref, H5R_type_t ref_type) const { try { return(p_get_obj_type(ref, ref_type)); } catch (IdComponentException E) { throw FileIException("H5File::getObjType", E.getDetailMsg()); } } //-------------------------------------------------------------------------- // Function: H5File::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 ///\return DataSpace instance ///\exception H5::IdComponentException // Programmer Binh-Minh Ribler - May, 2004 //-------------------------------------------------------------------------- DataSpace H5File::getRegion(void *ref, H5R_type_t ref_type) const { try { DataSpace dataspace(p_get_region(ref, ref_type)); return(dataspace); } catch (IdComponentException E) { throw FileIException("H5File::getRegion", E.getDetailMsg()); } } //-------------------------------------------------------------------------- // Function: H5File::getFileSize ///\brief Returns the file size of the HDF5 file. ///\return File size ///\exception H5::FileIException ///\par Description /// This function is called after an existing file is opened in /// order to learn the true size of the underlying file. // Programmer Raymond Lu - June 24, 2004 //-------------------------------------------------------------------------- hsize_t H5File::getFileSize() const { hsize_t file_size; herr_t ret_value = H5Fget_filesize(id, &file_size); if (ret_value < 0) { throw FileIException("H5File::getFileSize", "H5Fget_filesize failed"); } return (file_size); } //-------------------------------------------------------------------------- // Function: H5File::getLocId // Purpose: Get the id of this file // Description // This function is a redefinition of CommonFG::getLocId. It // is used by CommonFG member functions to get the file id. // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- hid_t H5File::getLocId() const { return( getId() ); } //-------------------------------------------------------------------------- // Function: H5File::close ///\brief Closes this HDF5 file. /// ///\exception H5::FileIException // Programmer Binh-Minh Ribler - Mar 9, 2005 //-------------------------------------------------------------------------- void H5File::close() { herr_t ret_value = H5Fclose( id ); if( ret_value < 0 ) { throw FileIException("H5File::close", "H5Fclose failed"); } // reset the id because the file that it represents is now closed id = 0; } //-------------------------------------------------------------------------- // Function: H5File::throwException ///\brief Throws file exception - initially implemented for CommonFG ///\param func_name - Name of the function where failure occurs ///\param msg - Message describing the failure ///\exception H5::FileIException // Description // This function is used in CommonFG implementation so that // proper exception can be thrown for file or group. The // argument func_name is a member of CommonFG and "H5File::" // will be inserted to indicate the function called is an // implementation of H5File. // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- void H5File::throwException(const H5_std::string func_name, const H5_std::string msg) const { H5_std::string full_name = func_name; full_name.insert(0, "H5File::"); throw FileIException(full_name, msg); } //-------------------------------------------------------------------------- // Function: H5File destructor ///\brief Properly terminates access to this file. // Programmer Binh-Minh Ribler - 2000 // Modification // Replaced resetIdComponent with decRefCount to use C library // ID reference counting mechanism - June 1, 2004 //-------------------------------------------------------------------------- H5File::~H5File() { // The HDF5 file id will be closed properly try { decRefCount(); } catch (Exception close_error) { cerr << "H5File::~H5File - " << close_error.getDetailMsg() << endl; } } #ifndef H5_NO_NAMESPACE } // end namespace #endif