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Merge DataSet::operator= and H5Dchunk_iter to Hdf5 1 12 1 (#664)
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* Hdf5 1 12 doxygen version correction (#658)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Attempt format uniformity in RELEASE.txt.

* BUG: DataSet assignment operator is missing (#503)

* BUG: DataSet assignment operator is missing

* Some compilers complain if the copy constructor is given explicitly
  but the assignment operator is implicitly set to default.

* Explicitly defining the assignment operator allows us to properly
  handle reference counters for shared resources.

* BUG: DataSet assignment operator is missing.

* Mimicking code of H5DataType::operator() as suggested by @bmribler.

* Added test

Description:
    Added test for DataSet::operator= that Leengit added
Platform tested:
    Linux/64 (jelly)

* Removed Author field.

* Commit clang format changes.

* Entry for Leengit's github PR #503

* Removed lines left by mistake

Co-authored-by: Binh-Minh Ribler <[email protected]>
Co-authored-by: Larry Knox <[email protected]>

* Add H5Dchunk_iter method for iterating over chunks (#6)

* Add H5Dchunk_iter method for iterating over chunks

This method iterates over all chunks in dataset, calling a user-supplied
callback with the chunk information and optional user supplied data.

The iterator is stopped when ITER_STOP is returned by the user-supplied
callback or the iterator is exhausted.

Existing methods to get chunk_info performs an iteration each time, so
to get many or all chunks causes SUM(i) for i = 0 -> N operations for N
chunks, as opposed to N operations when using this iterator for this use case.

* H5Dchunk_iter: test iterating all chunks, some chunks and failing iteration.

* H5D: move H5Dchunk_iter private methods to specific

* trace: add H5D_chunk_iter_op_t and trace H5D.c

* chunks-iter: document chunk_iter

* chunk-iter: chunk add FUNC_ENTER/FUNC_LEAVE macros

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Set initial doxygen version for H5Dchunk_iter().

Co-authored-by: Allen Byrne <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Lee Newberg <[email protected]>
Co-authored-by: Binh-Minh Ribler <[email protected]>
Co-authored-by: Gaute Hope <[email protected]>
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@lrknox @byrnHDF
@github-actions @Leengit @bmribler @gauteh
6 people authored May 20, 2021
1 parent 0fe13fc commit 3b6565c
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1 change: 1 addition & 0 deletions bin/trace
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@ $Source = "";
"H5D_vds_view_t" => "Dv",
"H5FD_mpio_xfer_t" => "Dt",
"H5FD_splitter_vfd_config_t" => "Dr",
"H5D_chunk_iter_op_t" => "x",
"herr_t" => "e",
"H5E_direction_t" => "Ed",
"H5E_error_t" => "Ee",
Expand Down
62 changes: 22 additions & 40 deletions c++/src/H5DataSet.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,6 @@ using std::endl;
//--------------------------------------------------------------------------
// Function: DataSet default constructor
///\brief Default constructor: creates a stub DataSet.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet::DataSet() : H5Object(), AbstractDs(), id(H5I_INVALID_HID)
{
Expand All @@ -52,7 +51,6 @@ DataSet::DataSet() : H5Object(), AbstractDs(), id(H5I_INVALID_HID)
// Function: DataSet overloaded constructor
///\brief Creates an DataSet object using the id of an existing dataset.
///\param existing_id - IN: Id of an existing dataset
// Programmer Binh-Minh Ribler - 2000
// Description
// incRefCount() is needed here to prevent the id from being closed
// prematurely. That is, when application uses the id of an
Expand All @@ -69,13 +67,26 @@ DataSet::DataSet(const hid_t existing_id) : H5Object(), AbstractDs(), id(existin
// Function: DataSet copy constructor
///\brief Copy constructor: same HDF5 object as \a original
///\param original - IN: DataSet instance to copy
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet::DataSet(const DataSet &original) : H5Object(), AbstractDs(), id(original.id)
{
incRefCount(); // increment number of references to this id
}

//--------------------------------------------------------------------------
// Function: DataSet assignment operator
///\brief Assignment operator: same HDF5 object as \a original
///\param original - IN: DataSet instance to copy
//--------------------------------------------------------------------------
DataSet &
DataSet::operator=(const DataSet &original)
{
if (this != &original) {
setId(original.id);
}
return (*this);
}

//--------------------------------------------------------------------------
// Function: DataSet overload constructor - dereference
///\brief Given a reference, ref, to an hdf5 location, creates a
Expand All @@ -89,7 +100,6 @@ DataSet::DataSet(const DataSet &original) : H5Object(), AbstractDs(), id(origina
///\par Description
/// \c loc can be DataSet, Group, H5File, or named DataType, that
/// is a datatype that has been named by DataType::commit.
// Programmer Binh-Minh Ribler - Oct, 2006
//--------------------------------------------------------------------------
DataSet::DataSet(const H5Location &loc, const void *ref, H5R_type_t ref_type, const PropList &plist)
: H5Object(), AbstractDs(), id(H5I_INVALID_HID)
Expand All @@ -106,7 +116,6 @@ DataSet::DataSet(const H5Location &loc, const void *ref, H5R_type_t ref_type, co
///\param ref_type - IN: Reference type - default to H5R_OBJECT
///\param plist - IN: Property list - default to PropList::DEFAULT
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - Oct, 2006
//--------------------------------------------------------------------------
DataSet::DataSet(const Attribute &attr, const void *ref, H5R_type_t ref_type, const PropList &plist)
: H5Object(), AbstractDs(), id(H5I_INVALID_HID)
Expand All @@ -119,7 +128,6 @@ DataSet::DataSet(const Attribute &attr, const void *ref, H5R_type_t ref_type, co
///\brief Gets a copy of the dataspace of this dataset.
///\return DataSpace instance
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSpace
DataSet::getSpace() const
Expand Down Expand Up @@ -156,7 +164,6 @@ DataSet::p_get_type() const
///\brief Gets the dataset creation property list.
///\return DSetCreatPropList instance
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DSetCreatPropList
DataSet::getCreatePlist() const
Expand Down Expand Up @@ -200,7 +207,6 @@ DataSet::getAccessPlist() const
///\exception H5::DataSetIException
// Note: H5Dget_storage_size returns 0 when there is no data. This
// function should have no failure. (from SLU)
// Programmer Binh-Minh Ribler - Mar, 2005
//--------------------------------------------------------------------------
hsize_t
DataSet::getStorageSize() const
Expand All @@ -214,7 +220,6 @@ DataSet::getStorageSize() const
///\brief Gets the size in memory of the dataset's data.
///\return Size of data (in memory)
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Apr 2009
//--------------------------------------------------------------------------
size_t
DataSet::getInMemDataSize() const
Expand Down Expand Up @@ -272,7 +277,6 @@ DataSet::getInMemDataSize() const
///\brief Returns the address of this dataset in the file.
///\return Address of dataset
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
haddr_t
DataSet::getOffset() const
Expand All @@ -291,7 +295,6 @@ DataSet::getOffset() const
///\brief Determines whether space has been allocated for a dataset.
///\param status - OUT: Space allocation status
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::getSpaceStatus(H5D_space_status_t &status) const
Expand All @@ -309,7 +312,6 @@ DataSet::getSpaceStatus(H5D_space_status_t &status) const
///\param space - IN: Selection for the memory buffer
///\return Amount of storage
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
hsize_t
DataSet::getVlenBufSize(const DataType &type, const DataSpace &space) const
Expand All @@ -334,7 +336,6 @@ DataSet::getVlenBufSize(const DataType &type, const DataSpace &space) const
// misses const's. This wrapper will be removed in future release.
// Return Amount of storage
// Exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Modified to call its replacement. -BMR, 2014/04/16
// Removed from documentation. -BMR, 2016/03/07 1.8.17 and 1.10.0
Expand All @@ -354,7 +355,6 @@ DataSet::getVlenBufSize(const DataType &type, const DataSpace &space) const
///\param xfer_plist - IN: Property list used to create the buffer
///\param buf - IN: Pointer to the buffer to be reclaimed
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::vlenReclaim(const DataType &type, const DataSpace &space, const DSetMemXferPropList &xfer_plist,
Expand All @@ -380,7 +380,6 @@ DataSet::vlenReclaim(const DataType &type, const DataSpace &space, const DSetMem
///\param xfer_plist - IN: Property list used to create the buffer
///\param buf - IN: Pointer to the buffer to be reclaimed
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//\parDescription
// This function has better prototype for the users than the
// other, which might be removed at some point. BMR - 2006/12/20
Expand Down Expand Up @@ -413,7 +412,6 @@ DataSet::vlenReclaim(void *buf, const DataType &type, const DataSpace &space,
/// This function reads raw data from this dataset into the
/// buffer \a buf, converting from file datatype and dataspace
/// to memory datatype \a mem_type and dataspace \a mem_space.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::read(void *buf, const DataType &mem_type, const DataSpace &mem_space, const DataSpace &file_space,
Expand Down Expand Up @@ -441,7 +439,6 @@ DataSet::read(void *buf, const DataType &mem_type, const DataSpace &mem_space, c
///\param file_space - IN: Dataset's dataspace in the file
///\param xfer_plist - IN: Transfer property list for this I/O operation
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Jul 2009
// Follow the change to Attribute::read and use the following
Expand Down Expand Up @@ -490,7 +487,6 @@ DataSet::read(H5std_string &strg, const DataType &mem_type, const DataSpace &mem
/// \a buf to a dataset, converting from memory datatype
/// \a mem_type and dataspace \a mem_space to file datatype
/// and dataspace.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::write(const void *buf, const DataType &mem_type, const DataSpace &mem_space,
Expand All @@ -512,7 +508,6 @@ DataSet::write(const void *buf, const DataType &mem_type, const DataSpace &mem_s
// Function: DataSet::write
///\brief This is an overloaded member function, provided for convenience.
/// It takes a reference to a \c H5std_string for the buffer.
// Programmer Binh-Minh Ribler - 2000
// Modification
// Jul 2009
// Modified to pass the buffer into H5Dwrite properly depending
Expand Down Expand Up @@ -568,7 +563,6 @@ DataSet::write(const H5std_string &strg, const DataType &mem_type, const DataSpa
///\exception H5::DataSetIException
///\note This function may not work correctly yet - it's still
/// under development.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int
DataSet::iterateElems(void *buf, const DataType &type, const DataSpace &space, H5D_operator_t op,
Expand All @@ -594,7 +588,6 @@ DataSet::iterateElems(void *buf, const DataType &type, const DataSpace &space, H
///\par Description
/// For information, please refer to the H5Dset_extent API in
/// the HDF5 C Reference Manual.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::extend(const hsize_t *size) const
Expand All @@ -613,7 +606,6 @@ DataSet::extend(const hsize_t *size) const
///\param buf_type - IN: Datatype of the elements in buffer
///\param space - IN: Dataspace describing memory buffer & containing selection to use
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2014
//--------------------------------------------------------------------------
void
DataSet::fillMemBuf(const void *fill, const DataType &fill_type, void *buf, const DataType &buf_type,
Expand All @@ -639,7 +631,6 @@ DataSet::fillMemBuf(const void *fill, const DataType &fill_type, void *buf, cons
// Param buf_type - IN: Datatype of the elements in buffer
// Param space - IN: Dataspace describing memory buffer & containing selection to use
// Exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Modified to call its replacement. -BMR, 2014/04/16
// Removed from documentation. -BMR, 2016/03/07 1.8.17 and 1.10.0
Expand All @@ -658,7 +649,6 @@ DataSet::fillMemBuf(const void *fill, const DataType &fill_type, void *buf, cons
///\param buf_type - IN: Datatype of the elements in buffer
///\param space - IN: Dataspace describing memory buffer & containing selection to use
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void
DataSet::fillMemBuf(void *buf, const DataType &buf_type, const DataSpace &space) const
Expand All @@ -680,7 +670,6 @@ DataSet::fillMemBuf(void *buf, const DataType &buf_type, const DataSpace &space)
// Param buf_type - IN: Datatype of the elements in buffer
// Param space - IN: Dataspace describing memory buffer & containing selection to use
// Exception H5::DataSetIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// Modified to call its replacement. -BMR, 2014/04/16
// Removed from documentation. -BMR, 2016/03/07 1.8.17 and 1.10.0
Expand All @@ -700,7 +689,6 @@ DataSet::fillMemBuf(void *buf, const DataType &buf_type, const DataSpace &space)
// 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
DataSet::getId() const
Expand All @@ -710,11 +698,10 @@ DataSet::getId() const

//--------------------------------------------------------------------------
// Function: DataSet::p_read_fixed_len (private)
// brief Reads a fixed length \a H5std_string from a dataset.
// param mem_type - IN: DataSet datatype (in memory)
// param strg - IN: Buffer for read string
// exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Jul, 2009
// brief Reads a fixed length \a H5std_string from a dataset.
// param mem_type - IN: DataSet datatype (in memory)
// param strg - IN: Buffer for read string
// exceptio n H5::DataSetIException
// Modification
// Jul 2009
// Added in follow to the change in Attribute::read
Expand Down Expand Up @@ -748,11 +735,10 @@ DataSet::p_read_fixed_len(const hid_t mem_type_id, const hid_t mem_space_id, con

//--------------------------------------------------------------------------
// Function: DataSet::p_read_variable_len (private)
// brief Reads a variable length \a H5std_string from an dataset.
// param mem_type - IN: DataSet datatype (in memory)
// param strg - IN: Buffer for read string
// exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Jul, 2009
// brief Reads a variable length \a H5std_string from an dataset.
// param mem_type - IN: DataSet datatype (in memory)
// param strg - IN: Buffer for read string
// exception H5::DataSetIException
// Modification
// Jul 2009
// Added in follow to the change in Attribute::read
Expand Down Expand Up @@ -787,7 +773,6 @@ DataSet::p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id,
// 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
DataSet::p_setId(const hid_t new_id)
Expand All @@ -811,7 +796,6 @@ DataSet::p_setId(const hid_t new_id)
// Applications shouldn't need to use it.
// param dset - IN/OUT: DataSet object to be changed
// param new_id - IN: New id to set
// Programmer Binh-Minh Ribler - 2015
//--------------------------------------------------------------------------
void
f_PropList_setId(PropList *plist, hid_t new_id)
Expand All @@ -826,7 +810,6 @@ f_PropList_setId(PropList *plist, hid_t new_id)
///\brief Closes this dataset.
///
///\exception H5::DataSetIException
// Programmer Binh-Minh Ribler - Mar 9, 2005
//--------------------------------------------------------------------------
void
DataSet::close()
Expand All @@ -844,7 +827,6 @@ DataSet::close()
//--------------------------------------------------------------------------
// Function: DataSet destructor
///\brief Properly terminates access to this dataset.
// Programmer Binh-Minh Ribler - 2000
// Modification
// - Replaced resetIdComponent() with decRefCount() to use C
// library ID reference counting mechanism - BMR, Jun 1, 2004
Expand Down
3 changes: 3 additions & 0 deletions c++/src/H5DataSet.h
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Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,9 @@ class H5_DLLCPP DataSet : public H5Object, public AbstractDs {
// Copy constructor - same as the original DataSet.
DataSet(const DataSet &original);

// Assignment operator
DataSet &operator=(const DataSet &original);

// Creates a copy of an existing DataSet using its id.
DataSet(const hid_t existing_id);

Expand Down
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