This is the currently provided APIs available in C. More...

Classes
struct	_HL_Node
	Represents a HDF5 object/attribute/reference/... More...

struct	_HL_NodeList
	Represents a HDF5 file. More...

struct	HL_PropertyVersion
	See hdf5 documentation for H5Pget_version for purpose. More...

struct	HL_PropertySize
	See hdf5 documentation for H5Pset_sizes and H5Pget_sizes for purpose. More...

struct	HL_PropertySymK
	See hdf5 documentation for H5Pset_sym_k and H5Pget_sym_k for purpose. More...

struct	HL_FileCreationProperty
	Properties that can be finely tuned when creating a HDF5 file. More...

struct	HL_Compression
	Compression properties. More...

struct	HL_CompoundTypeAttribute
	This type is designed to describe an individual node with a complicated structure, ie. More...

struct	HL_CompoundTypeDescription
	This type is a list of HL_CompoundTypeAttributes. More...

Typedefs
typedef enum HL_Debug	HL_Debug
	Debug levels.

typedef enum HL_CompressionType	HL_CompressionType
	Defines what type of compression that should be used.

typedef enum HL_Type	HL_Type
	This is an enumeration variable designed to identify the type of a given node.

typedef enum HL_DataType	HL_DataType
	This is an enumeration variable designed to identify the type of data in a given node.

typedef enum HL_NodeMark	HL_NodeMark
	This is an enumeration variable designed to keep track of the status of a given node.

typedef struct _HL_Node	HL_Node
	Each entry and type in a HDF5 file is represented by a HL_Node.

typedef struct _HL_NodeList	HL_NodeList
	Represents a HDF5 file.

Enumerations
enum	HL_Debug { HLHDF_SPEWDEBUG =0 , HLHDF_DEBUG , HLHDF_DEPRECATED , HLHDF_INFO , HLHDF_WARNING , HLHDF_ERROR , HLHDF_CRITICAL , HLHDF_SILENT }
	Debug levels. More...

enum	HL_CompressionType { CT_NONE =0 , CT_ZLIB , CT_SZLIB }
	Defines what type of compression that should be used. More...

enum	HL_Type { UNDEFINED_ID =-1 , ATTRIBUTE_ID =0 , GROUP_ID , DATASET_ID , TYPE_ID , REFERENCE_ID }
	This is an enumeration variable designed to identify the type of a given node. More...

enum	HL_DataType { DTYPE_UNDEFINED_ID =-1 , HL_SIMPLE =0 , HL_ARRAY }
	This is an enumeration variable designed to identify the type of data in a given node. More...

enum	HL_NodeMark { NMARK_UNDEFINED =-1 , NMARK_ORIGINAL =0 , NMARK_CREATED , NMARK_CHANGED , NMARK_SELECT , NMARK_SELECTMETA }
	This is an enumeration variable designed to keep track of the status of a given node. More...

Functions
void	HL_disableErrorReporting (void)
	Disables error reporting.

void	HL_enableErrorReporting (void)
	Enables error reporting.

int	HL_isErrorReportingEnabled (void)
	Returns if error reporting is enabled or not.

void	HL_init (void)
	Initializes the HLHDF handler functions.

void	HL_setDebugMode (int flag)
	Toggles the debug mode for HLHDF.

int	HL_isHDF5File (const char *filename)
	Verifies if the provided filename is a valid HDF5 file or not.

HL_FileCreationProperty *	HLFileCreationProperty_new (void)
	Creates a file property instance that can be passed on to createHlHdfFile when creating a HDF5 file.

void	HLFileCreationProperty_free (HL_FileCreationProperty *prop)
	Deallocates the HL_FileCreationProperty instance.

int	HL_sizeOfFormat (const char *format)
	Calculates the size in bytes of the provided format specifiers.

int	HL_isFormatSupported (const char *format)
	Verifies if the format name is supported by HLHDF.

HL_Compression *	HLCompression_new (HL_CompressionType type)
	Creates an allocated and initialized instance of HL_Compression.

HL_Compression *	HLCompression_clone (HL_Compression *inv)
	Creates a copy of the provided HL_Compression instance.

void	HLCompression_init (HL_Compression *inv, HL_CompressionType type)
	Initializes a HL_Compressiosn instance.

void	HLCompression_free (HL_Compression *inv)
	Deallocates the HL_Compression instance.

HL_CompoundTypeDescription *	newHL_CompoundTypeDescription (void)
	Creates a compound type description list.

void	freeHL_CompoundTypeDescription (HL_CompoundTypeDescription *typelist)
	Frees the compound type, including all members.

HL_CompoundTypeAttribute *	newHL_CompoundTypeAttribute (char attrname, size_t offset, const char format, size_t size, int ndims, size_t *dims)
	Creates a compound attribute member node.

void	freeHL_CompoundTypeAttribute (HL_CompoundTypeAttribute *attr)
	Frees one compound type attribute.

int	addHL_CompoundTypeAttribute (HL_CompoundTypeDescription typelist, HL_CompoundTypeAttribute attribute)
	Adds a compound type attribute to the type description.

HL_CompoundTypeDescription *	copyHL_CompoundTypeDescription (HL_CompoundTypeDescription *descr)
	Copies the compound type descriptor.

hid_t	createCompoundType (size_t size)
	Creates a new compound type.

herr_t	addAttributeToCompoundType (hid_t loc_id, const char *name, size_t offset, hid_t type_id)
	Adds one attribute to a compound type.

herr_t	addAttributeToCompoundType_fmt (hid_t loc_id, const char name, size_t offset, const char fmt)
	Same as addAttributeToCompoundType, but instead of a type as hid_t a format specifier is provided.

herr_t	addArrayToCompoundType (hid_t loc_id, const char name, size_t offset, int ndims, size_t dims, hid_t type_id)
	Adds an array attribute to a compound type.

herr_t	addArrayToCompoundType_fmt (hid_t loc_id, const char name, size_t offset, int ndims, size_t dims, const char *fmt)
	Same as addArrayToCompoundType, but instead of a type as hid_t, the format is specified with a format specifier.

void	HL_InitializeDebugger (void)
	Initializes the debugger structure, must have been called before executing the code.

void	HL_setDebugLevel (HL_Debug lvl)
	Sets the debug level.

void	HL_setDebugFunction (void(dbgfun)(char filename, int lineno, HL_Debug lvl, const char *fmt,...))
	Sets the debug function where the debug printouts should be routed.

void	HL_setHdf5ErrorFunction (void(hdf5fun)(unsigned n, const H5E_error_t val))
	Sets the HDF5 error reporting function.

void	HL_disableHdf5ErrorReporting (void)
	Disables the HDF5 error reporting.

void	HL_enableHdf5ErrorReporting (void)
	Enables the HDF5 error reporting.

HL_Node *	HLNode_new (const char *name)
	Creates a new HL_Node instance.

void	HLNode_free (HL_Node *node)
	Deallocates the provided node.

HL_Node *	HLNode_newGroup (const char *name)
	Creates an empty group HL_Node of type HL_Type::GROUP_ID.

HL_Node *	HLNode_newAttribute (const char *name)
	Creates an empty attribute HL_Node of type HL_Type::ATTRIBUTE_ID.

HL_Node *	HLNode_newDataset (const char *name)
	Creates an empty data set HL_Node of type HL_Type::DATASET_ID.

HL_Node *	HLNode_newDatatype (const char *name)
	Creates an empty data type HL_Node of type HL_Type::TYPE_ID.

HL_Node *	HLNode_newReference (const char *name)
	Creates an empty reference HL_Node of type HL_Type::REFERENCE_ID.

HL_Node *	HLNode_copy (HL_Node *node)
	Copies an HL_Node.

int	HLNode_setScalarValue (HL_Node node, size_t sz, unsigned char value, const char *fmt, hid_t typid)
	Sets a scalar value in the specified node.

int	HLNode_setArrayValue (HL_Node node, size_t sz, int ndims, hsize_t dims, unsigned char value, const char fmt, hid_t typid)
	Sets an array value in the specified node.

int	HLNode_commitType (HL_Node *node, hid_t typid)
	Will mark the node to be committed, only applicable on type nodes.

HL_NodeList *	HLNodeList_new (void)
	Creates a new HL_NodeList instance.

void	HLNodeList_free (HL_NodeList *nodelist)
	Releasing all resources associated with this node list including the node list itself.

int	HLNodeList_addNode (HL_NodeList nodelist, HL_Node node)
	Adds a node to the nodelist.

HL_Node *	HLNodeList_getNodeByName (HL_NodeList nodelist, const char nodeName)
	Locates a node called nodeName in the nodelist and returns a pointer to this node.

HL_CompoundTypeDescription *	HLNodeList_findCompoundDescription (HL_NodeList *nodelist, unsigned long objno0, unsigned long objno1)
	Searches the nodelist for any type node, that has got the same object id as objno0 and objno1.

HL_NodeList *	HLNodeList_readFrom (const char filename, const char fromPath)
	Reads an HDF5 file with name filename from the group fromPath and downwards.

HL_NodeList *	HLNodeList_read (const char *filename)
	Reads an HDF5 file with name filename from the root group ("/") and downwards.

int	HLNodeList_selectNode (HL_NodeList nodelist, const char name)
	Selects the node named 'name' from which to fetch data.

int	HLNodeList_selectAllNodes (HL_NodeList *nodelist)
	Marks all nodes in the nodelist for retrival.

int	HLNodeList_selectMetadataNodes (HL_NodeList *nodelist)
	Selects all metadata nodes in the nodelist to be fetched, ie.

int	HLNodeList_selectAllMetadataNodes (HL_NodeList *nodelist)
	Selects all metadata including metadata about datasets but will exclude data for datasets.

int	HLNodeList_selectOnlyDatasetNodes (HL_NodeList *nodelist)
	Only select data set nodes for fetching.

int	HLNodeList_deselectNode (HL_NodeList nodelist, const char name)
	De-selects the node named 'name' to be retrived when fetching data from the nodelist file.

int	HLNodeList_fetchMarkedNodes (HL_NodeList *nodelist)
	Fills all nodes (marked as select) with data.

HL_Node *	HLNodeList_fetchNode (HL_NodeList nodelist, const char name)
	Behaves as a combination of HLNodeList_selectNode()/fetch()/getNode().

int	HLNodeList_write (HL_NodeList nodelist, HL_FileCreationProperty property, HL_Compression *compr)
	Writes a HDF5 file from a nodelist with the specified file properties and compression level/type.

int	HLNodeList_update (HL_NodeList nodelist, HL_Compression compr)
	Updates a HDF5 file from a nodelist.

Detailed Description

This is the currently provided APIs available in C.

This group is a subset of all defined functions and if more information on all source code is wanted, please refer to the files section of the documentation.

Typedef Documentation

◆ HL_CompressionType

typedef enum HL_CompressionType HL_CompressionType

Defines what type of compression that should be used.

◆ HL_DataType

typedef enum HL_DataType HL_DataType

This is an enumeration variable designed to identify the type of data in a given node.

When new nodes are initiated, they are initialized with DTYPE_UNDEFINED_ID.

◆ HL_Debug

typedef enum HL_Debug HL_Debug

Debug levels.

The levels are defined so that if HLHDF_INFO debug level is turned on, all higher levels will also be printed except HLHDF_SILENT which means turn of logging.

◆ HL_Node

typedef struct _HL_Node HL_Node

Each entry and type in a HDF5 file is represented by a HL_Node.

◆ HL_NodeList

typedef struct _HL_NodeList HL_NodeList

Represents a HDF5 file.

◆ HL_NodeMark

typedef enum HL_NodeMark HL_NodeMark

This is an enumeration variable designed to keep track of the status of a given node.

◆ HL_Type

typedef enum HL_Type HL_Type

This is an enumeration variable designed to identify the type of a given node.

Enumeration Type Documentation

◆ HL_CompressionType

enum HL_CompressionType

Defines what type of compression that should be used.

Enumerator
CT_NONE	No compression.
CT_ZLIB	ZLIB compression.
CT_SZLIB	SZLIB compression.

◆ HL_DataType

enum HL_DataType

This is an enumeration variable designed to identify the type of data in a given node.

When new nodes are initiated, they are initialized with DTYPE_UNDEFINED_ID.

Enumerator
DTYPE_UNDEFINED_ID	Undefined data type.
HL_SIMPLE	If the value is a scalar.
HL_ARRAY	If the value is of array type.

◆ HL_Debug

enum HL_Debug

Debug levels.

The levels are defined so that if HLHDF_INFO debug level is turned on, all higher levels will also be printed except HLHDF_SILENT which means turn of logging.

Enumerator
HLHDF_SPEWDEBUG	The most verbose printouts is turned on here. Like entering functions and similar
HLHDF_DEBUG	Basic debug functions.
HLHDF_DEPRECATED	Print outs deprecated warnings.
HLHDF_INFO	Informational messages.
HLHDF_WARNING	Warnings.
HLHDF_ERROR	Errors can be when memory not could be allocated or a file not could be created.
HLHDF_CRITICAL	If this occurs, then something has gone very wrong or the code contains a bug, please report it to the HLHDF dev group for investigation.
HLHDF_SILENT	Turns of debugging.

◆ HL_NodeMark

enum HL_NodeMark

This is an enumeration variable designed to keep track of the status of a given node.

Enumerator
NMARK_UNDEFINED	Undefined type.
NMARK_ORIGINAL	Nothing has been done on the node, e.g. it has been read but nothing else
NMARK_CREATED	If a node has been created but not been written.
NMARK_CHANGED	If a nodes value has been changed and needs to be written.
NMARK_SELECT	The node has been marked for fetching but the read has not been performed yet.
NMARK_SELECTMETA	Special variant for marking datasets that we are only interested in the metadata.

◆ HL_Type

enum HL_Type

This is an enumeration variable designed to identify the type of a given node.

Enumerator
UNDEFINED_ID	An undefined type.
ATTRIBUTE_ID	Attribute type (corresponds to H5A)
GROUP_ID	Group type (corresponds to H5G)
DATASET_ID	Data set type (corresponds to H5D)
TYPE_ID	Type type (corresponds to H5T)
REFERENCE_ID	Reference type (corresponds to H5R)

Function Documentation

◆ addArrayToCompoundType()

herr_t addArrayToCompoundType	(	hid_t	loc_id,
		const char *	name,
		size_t	offset,
		int	ndims,
		size_t *	dims,
		hid_t	type_id )

Adds an array attribute to a compound type.

Parameters

[in]	loc_id	The type this attribute should be inserted in
[in]	name	The name of the attribute
[in]	offset	Offset of this attribute
[in]	ndims	The rank of the array attribute (max 4)
[in]	dims	The dimension of the array attribute
[in]	type_id	The type of the array attribute

Returns: <0 on failure, otherwise ok.

◆ addArrayToCompoundType_fmt()

herr_t addArrayToCompoundType_fmt	(	hid_t	loc_id,
		const char *	name,
		size_t	offset,
		int	ndims,
		size_t *	dims,
		const char *	fmt )

Same as addArrayToCompoundType, but instead of a type as hid_t, the format is specified with a format specifier.

Parameters

[in]	loc_id	The type this attribute should be inserted in
[in]	name	The name of the attribute
[in]	offset	Offset of this attribute
[in]	ndims	The rank of the array attribute (max 4)
[in]	dims	The dimension of the array attribute
[in]	fmt	The type of the attribute. See format specifiers. Returns: <0 is failure, otherwise ok.

◆ addAttributeToCompoundType()

herr_t addAttributeToCompoundType	(	hid_t	loc_id,
		const char *	name,
		size_t	offset,
		hid_t	type_id )

Adds one attribute to a compound type.

Parameters

[in]	loc_id	The type the attribute should be inserted in.
[in]	name	The name of the member attribute
[in]	offset	Offset of this attribute
[in]	type_id	The type of the attribute

Returns: <0 on failure, otherwise ok.

◆ addAttributeToCompoundType_fmt()

herr_t addAttributeToCompoundType_fmt	(	hid_t	loc_id,
		const char *	name,
		size_t	offset,
		const char *	fmt )

Same as addAttributeToCompoundType, but instead of a type as hid_t a format specifier is provided.

Parameters

[in]	loc_id	The type the attribute should be inserted in.
[in]	name	The name of the member attribute
[in]	offset	Offset of this attribute
[in]	fmt	The type of the attribute. See format specifiers.

Returns: <0 on failure, otherwise ok.

◆ addHL_CompoundTypeAttribute()

int addHL_CompoundTypeAttribute	(	HL_CompoundTypeDescription *	typelist,
		HL_CompoundTypeAttribute *	attribute )

Adds a compound type attribute to the type description.

Parameters

[in]	typelist	the descriptor that should get the new attribute
[in]	attribute	the attribute that should be added

Returns: 0 on failure, 1 if success

◆ copyHL_CompoundTypeDescription()

HL_CompoundTypeDescription * copyHL_CompoundTypeDescription ( HL_CompoundTypeDescription * descr )

Copies the compound type descriptor.

Parameters

[in] descr the descriptor that should be copied.

Returns: The type description on success, otherwise NULL

◆ createCompoundType()

hid_t createCompoundType ( size_t size )

Creates a new compound type.

Parameters

[in] size The size of the compound type, usually sizeof(struct name).

Returns: <0 on failure, otherwise a reference to the created type.

◆ freeHL_CompoundTypeAttribute()

void freeHL_CompoundTypeAttribute ( HL_CompoundTypeAttribute * attr )

Frees one compound type attribute.

Parameters

[in] attr the attribute that should be deallocated.

◆ freeHL_CompoundTypeDescription()

void freeHL_CompoundTypeDescription ( HL_CompoundTypeDescription * typelist )

Frees the compound type, including all members.

Parameters

[in] typelist the descriptor that should be deleted.

◆ HL_disableErrorReporting()

void HL_disableErrorReporting ( void )

Disables error reporting.

◆ HL_disableHdf5ErrorReporting()

void HL_disableHdf5ErrorReporting ( void )

Disables the HDF5 error reporting.

◆ HL_enableErrorReporting()

void HL_enableErrorReporting ( void )

Enables error reporting.

◆ HL_enableHdf5ErrorReporting()

void HL_enableHdf5ErrorReporting ( void )

Enables the HDF5 error reporting.

◆ HL_init()

void HL_init ( void )

Initializes the HLHDF handler functions.

This always needs to be done before doing anything else when using HLHDF.

◆ HL_InitializeDebugger()

void HL_InitializeDebugger ( void )

Initializes the debugger structure, must have been called before executing the code.

◆ HL_isErrorReportingEnabled()

int HL_isErrorReportingEnabled ( void )

Returns if error reporting is enabled or not.

◆ HL_isFormatSupported()

int HL_isFormatSupported ( const char * format )

Verifies if the format name is supported by HLHDF.

Does not see string and compound as a supported format since they are not possible to determine without a hid.

Parameters

[in] format the format name string

Returns: TRUE if it is supported, otherwise FALSE.

◆ HL_isHDF5File()

int HL_isHDF5File ( const char * filename )

Verifies if the provided filename is a valid HDF5 file or not.

Parameters

[in] filename the full path of the file to check

Returns: TRUE if file is an HDF5 file, otherwise FALSE

◆ HL_setDebugFunction()

void HL_setDebugFunction ( void(* dbgfun )(char *filename, int lineno, HL_Debug lvl, const char *fmt,...) )

Sets the debug function where the debug printouts should be routed.

Parameters

[in] dbgfun The debug function.

◆ HL_setDebugLevel()

void HL_setDebugLevel ( HL_Debug lvl )

Sets the debug level.

Parameters

[in] lvl the debug level. See HL_Debug.

◆ HL_setDebugMode()

void HL_setDebugMode ( int flag )

Toggles the debug mode for HLHDF.

Possible values of flag are:

0 = No debugging
1 = Debug only the HLHDF library
2 = Debug both HLHDF and HDF5 library

Parameters

[in] flag the level of debugging

◆ HL_setHdf5ErrorFunction()

void HL_setHdf5ErrorFunction ( void(* hdf5fun )(unsigned n, const H5E_error_t *val) )

Sets the HDF5 error reporting function.

Parameters

[in] hdf5fun the HDF5 error reporting function

◆ HL_sizeOfFormat()

int HL_sizeOfFormat ( const char * format )

Calculates the size in bytes of the provided format specifiers.

The exception is string and compound type since they needs to be analyzed to get the size.

Parameters

[in] format The format specifier.

Returns: the size in bytes or -1 on failure.

◆ HLCompression_clone()

HL_Compression * HLCompression_clone ( HL_Compression * inv )

Creates a copy of the provided HL_Compression instance.

Parameters

[in] inv the instance to be cloned

Returns: the cloned instance or NULL if parameter was NULL or memory not could be allocated.

◆ HLCompression_free()

void HLCompression_free ( HL_Compression * inv )

Deallocates the HL_Compression instance.

Parameters

inv	The instance that should be deallocated

◆ HLCompression_init()

void HLCompression_init	(	HL_Compression *	inv,
		HL_CompressionType	type )

Initializes a HL_Compressiosn instance.

Parameters

[in]	inv	The compression object to be initialized
[in]	type	the type of compression the object should be initialized with

◆ HLCompression_new()

HL_Compression * HLCompression_new ( HL_CompressionType type )

Creates an allocated and initialized instance of HL_Compression.

Parameters

[in] type the compression type to use

Returns: the created instance, NULL on failure.

◆ HLFileCreationProperty_free()

void HLFileCreationProperty_free ( HL_FileCreationProperty * prop )

Deallocates the HL_FileCreationProperty instance.

Parameters

[in] prop The property to be deallocated

◆ HLFileCreationProperty_new()

HL_FileCreationProperty * HLFileCreationProperty_new ( void )

Creates a file property instance that can be passed on to createHlHdfFile when creating a HDF5 file.

Returns: the allocated file property instance, NULL on failure. See HLFileCreationProperty_free for deallocation.

◆ HLNode_commitType()

int HLNode_commitType	(	HL_Node *	node,
		hid_t	typid )

Will mark the node to be committed, only applicable on type nodes.

Parameters

[in]	node	the node that should be commited
[in]	typid	the HDF5 type identifier

Returns: 1 on success, otherwise 0

Deprecated: this function will be removed sooner or later.

◆ HLNode_copy()

HL_Node * HLNode_copy ( HL_Node * node )

Copies an HL_Node.

Parameters

[in] node the node that should be copied

Returns: the allocated node on success, otherwise NULL.

◆ HLNode_free()

void HLNode_free ( HL_Node * node )

Deallocates the provided node.

Parameters

[in] node the node that should be deallocated

◆ HLNode_new()

HL_Node * HLNode_new ( const char * name )

Creates a new HL_Node instance.

Parameters

[in] name the name of this node, should be fully qualified name. I.e. /a/b/c

Returns: the allocated node on success, otherwise NULL.