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|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifdef OLD_HEADER_FILENAME
#include <iostream.h>
#else
#include <iostream>
#endif
#include <string>
#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 "H5LaccProp.h"
#include "H5Location.h"
#include "H5Object.h"
#include "H5CommonFG.h"
#include "H5Group.h"
#include "H5File.h"
namespace H5 {
#ifndef H5_NO_STD
using std::cerr;
using std::endl;
#endif // H5_NO_STD
//--------------------------------------------------------------------------
// Function H5File default constructor
///\brief Default constructor: creates a stub H5File object.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5File::H5File() : Group(), id(H5I_INVALID_HID) {}
//--------------------------------------------------------------------------
// 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
/// FileAccPropList::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_RDONLY - Open file as read-only, if it already
/// exists, and fail, otherwise
/// \li \c H5F_ACC_RDWR - Open file for read/write, if it already
/// exists, and fail, otherwise
///\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://www.hdfgroup.org/HDF5/doc/RM/RM_H5F.html#File-Create
// Notes With a PGI compiler (~2012-2013), the exception thrown by p_get_file
// could not be caught in the applications. Added try block here
// to catch then re-throw it. -BMR 2013/03/21
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5File::H5File(const char* name, unsigned int flags, const FileCreatPropList& create_plist, const FileAccPropList& access_plist) : Group(), id(H5I_INVALID_HID)
{
try {
p_get_file(name, flags, create_plist, access_plist);
} catch (FileIException& open_file) {
throw open_file;
}
}
//--------------------------------------------------------------------------
// 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 H5std_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
/// FileAccPropList::DEFAULT
// Notes With a PGI compiler (~2012-2013), the exception thrown by p_get_file
// could not be caught in the applications. Added try block here
// to catch then re-throw it. -BMR 2013/03/21
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5File::H5File(const H5std_string& name, unsigned int flags, const FileCreatPropList& create_plist, const FileAccPropList& access_plist) : Group(), id(H5I_INVALID_HID)
{
try {
p_get_file(name.c_str(), flags, create_plist, access_plist);
} catch (FileIException& open_file) {
throw open_file;
}
}
#ifndef DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// This function is private and contains common code between the
// constructors taking a string or a char*
// Programmer Binh-Minh Ribler - 2000
// Modification
// - removed H5F_ACC_CREAT because H5Fcreate will fail with
// H5F_ACC_CREAT. - BMR, Sep 17, 2014
//--------------------------------------------------------------------------
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_EXCL|H5F_ACC_TRUNC))
{
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 overloaded constructor
///\brief Creates an H5File object using an existing file id.
///\param existing_id - IN: Id of an existing file
// Programmer Binh-Minh Ribler - 2015
// Description
// Mar 29, 2015
// Added in responding to a request from user Jason Newton.
// However, it is not recommended to use the private member "id"
// in applications. Unlike other situations, where similar
// constructor is needed by the library in order to return
// an object, H5File doesn't need it. -BMR (HDFFV-8766 partially)
//--------------------------------------------------------------------------
H5File::H5File(hid_t existing_id) : Group()
{
id = existing_id;
incRefCount(); // increment number of references to this id
}
#endif // DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// 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) : Group()
{
id = original.getId();
incRefCount(); // increment number of references to this id
}
//--------------------------------------------------------------------------
// Function: H5File::isHdf5 (static)
///\brief Determines whether a file in HDF5 format. (Static)
///\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 (static)
///\brief This is an overloaded member function, provided for convenience.
/// It takes an \c H5std_string for \a name. (Static)
///\param name - IN: Name of the file - \c H5std_string
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
bool H5File::isHdf5(const H5std_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
/// FileAccPropList::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)
{
try {
close();
}
catch (Exception& close_error) {
throw FileIException("H5File::openFile", close_error.getDetailMsg());
}
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 H5std_string for \a name.
///\param name - IN: Name of the file - \c H5std_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 H5std_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 - BMR, Feb 20, 2005
// - Replaced decRefCount with close() to let the C library
// handle the reference counting - BMR, Jun 1, 2006
//--------------------------------------------------------------------------
void H5File::reOpen()
{
try {
close();
}
catch (Exception& close_error) {
throw FileIException("H5File::reOpen", close_error.getDetailMsg());
}
// call C routine to reopen the file - Note: not sure about this,
// which id to be the parameter when closing?
id = H5Freopen(id);
if(id < 0) // Raise exception when H5Freopen returns a neg value
throw FileIException("H5File::reOpen", "H5Freopen failed");
}
//--------------------------------------------------------------------------
// 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
//--------------------------------------------------------------------------
ssize_t H5File::getObjCount(unsigned types) const
{
ssize_t num_objs = H5Fget_obj_count(id, types);
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, size_t max_objs, hid_t *oid_list) const
{
ssize_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
// Modification
// Replaced the version without const parameter - Apr, 2014
//--------------------------------------------------------------------------
void H5File::getVFDHandle(const 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
// Purpose This is an overloaded member function, kept for backward
// compatibility. It differs from the above function in that it
// misses const's. This wrapper will be removed in future release.
// 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
// Programmer Binh-Minh Ribler - May 2004
// Modification
// Planned for removal. -BMR, 2014/04/16
// Removed from documentation. -BMR, 2016/03/07 1.8.17 and 1.10.0
// Removed from code. -BMR, 2016/08/11 1.8.18 and 1.10.1
//--------------------------------------------------------------------------
//void H5File::getVFDHandle(FileAccPropList& fapl, void **file_handle) const
//{
// getVFDHandle((const FileAccPropList)fapl, file_handle);
//}
//--------------------------------------------------------------------------
// 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::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::getId
///\brief Get the id of this file
///\return File identifier
// Modification:
// May 2008 - BMR
// Class hierarchy is revised to address bugzilla 1068. Class
// AbstractDS and Attribute are moved out of H5Object. In
// addition, member IdComponent::id is moved into subclasses, and
// IdComponent::getId now becomes pure virtual function.
// Programmer Binh-Minh Ribler - May, 2008
//--------------------------------------------------------------------------
hid_t H5File::getId() const
{
return(id);
}
#ifndef DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: H5File::reopen
// Purpose: Reopens this file.
// Exception H5::FileIException
// Description
// This function is replaced by the above function reOpen.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5File::reopen()
{
H5File::reOpen();
}
//--------------------------------------------------------------------------
// 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::p_setId (protected)
///\brief Sets the identifier of this object to a new value.
///
///\exception H5::IdComponentException when the attempt to close the HDF5
/// object fails
// Description:
// The underlaying reference counting in the C library ensures
// that the current valid id of this object is properly closed.
// Then the object's id is reset to the new id.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5File::p_setId(const hid_t new_id)
{
// handling references to this old id
try {
close();
}
catch (Exception& E) {
throw FileIException("H5File::p_setId", E.getDetailMsg());
}
// reset object's id to the given id
id = new_id;
}
#endif // DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function: H5File::close
///\brief Closes this HDF5 file.
///
///\exception H5::FileIException
// Programmer Binh-Minh Ribler - Mar 9, 2005
//--------------------------------------------------------------------------
void H5File::close()
{
if (p_valid_id(id))
{
herr_t ret_value = H5Fclose(id);
if(ret_value < 0)
{
throw FileIException("H5File::close", "H5Fclose failed");
}
// reset the id
id = H5I_INVALID_HID;
}
}
//--------------------------------------------------------------------------
// 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 H5std_string& func_name, const H5std_string& msg) const
{
H5std_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 - BMR, Feb 20, 2005
// - Replaced decRefCount with close() to let the C library
// handle the reference counting - BMR, Jun 1, 2006
//--------------------------------------------------------------------------
H5File::~H5File()
{
try {
close();
} catch (Exception& close_error) {
cerr << "H5File::~H5File - " << close_error.getDetailMsg() << endl;
}
}
} // end namespace
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