This class reads and writes a HDF5 file. More...

#include <hdf_file.h>

Inheritance diagram for FullPhysics::HdfFile:

Collaboration diagram for FullPhysics::HdfFile:

Public Types
enum	Mode { READ, CREATE, READ_WRITE }

Public Member Functions
	HdfFile (const std::string &Fname, Mode M=READ)
	Open the given file with the given mode. More...

virtual	~HdfFile ()

void	close ()
	Close the underlying file. More...

void	dimension_metadata (const std::string &Name, const std::string &Description, int Size)
	The SDOS products have a particular metadata convention where the information about each of the Dimensions that appear in the file are documented. More...

const std::string &	file_name () const
	File name. More...

H5::H5File &	h5_file ()

const H5::H5File &	h5_file () const

bool	has_attribute (const std::string &Aname) const
	Check to see if a attribute is in the file. More...

bool	has_object (const std::string &Objname) const
	Check to see if an object (such as a Dataset) is in the file. More...

Mode	mode () const
	Mode file was opened with. More...

template<class T >
H5::PredType	pred_arr () const

template<>
H5::PredType	pred_arr () const

template<>
H5::PredType	pred_arr () const

template<>
H5::PredType	pred_arr () const

template<>
H5::PredType	pred_arr () const

template<class T >
H5::PredType	pred_data () const

template<>
H5::PredType	pred_data () const

template<>
H5::PredType	pred_data () const

template<>
H5::PredType	pred_data () const

template<>
H5::PredType	pred_data () const

void	print (std::ostream &Os) const

std::string	print_to_string () const
	Print to string. More...

template<class T , int D>
blitz::Array< T, D >	read_attribute (const std::string &Aname) const
	Read the given attribute attached to a group or dataset. More...

template<class T >
T	read_attribute (const std::string &Aname) const
	Read the given attribute attached to a group or dataset. More...

template<class T , int D>
blitz::Array< T, D >	read_field (const std::string &Dataname) const
	Read a given field. More...

template<class T , int D>
blitz::Array< T, D >	read_field (const std::string &Dataname, const blitz::TinyVector< int, D > &Start, const blitz::TinyVector< int, D > &Size) const
	Read a given field. More...

template<class T >
T	read_field (const std::string &Dataname) const
	Read a given scalar field. More...

template<>
std::string	read_field (const std::string &Dataname) const

template<class T , int D>
ArrayWithUnit< T, D >	read_field_with_unit (const std::string &Dataname) const
	Read a given field, along with metadata describing the units. More...

template<class T , int D>
ArrayWithUnit< T, D >	read_field_with_unit (const std::string &Dataname, const Unit &Default_unit) const
	Read a given field, along with metadata describing the units. More...

template<class T , int D>
ArrayWithUnit< T, D >	read_field_with_unit (const std::string &Dataname, const blitz::TinyVector< int, D > &Start, const blitz::TinyVector< int, D > &Size) const
	Read a given field, along with metadata describing the units. More...

template<class T , int D>
ArrayWithUnit< T, D >	read_field_with_unit (const std::string &Dataname, const Unit &Default_unit, const blitz::TinyVector< int, D > &Start, const blitz::TinyVector< int, D > &Size) const
	Adds ability to specify Start and Size along with default units. More...

template<int D>
blitz::TinyVector< int, D >	read_shape (const std::string &Dataname) const
	Reads the shape of a dataset. More...

Unit	read_units (const std::string &Dataname) const
	Read the units for a dataset. More...

void	shape_metadata (const std::string &Name, const std::string &Dim1)
	The SDOS products have a particular metadata convention where the information about each of the Shapes that appear in the file are documented. More...

void	shape_metadata (const std::string &Name, const std::string &Dim1, const std::string &Dim2)
	The SDOS products have a particular metadata convention where the information about each of the Shapes that appear in the file are documented. More...

void	shape_metadata (const std::string &Name, const std::string &Dim1, const std::string &Dim2, const std::string &Dim3)
	The SDOS products have a particular metadata convention where the information about each of the Shapes that appear in the file are documented. More...

template<class T , int D>
void	write_attribute (const std::string &Aname, const blitz::Array< T, D > &Data)
	Write attribute to file. More...

template<class T >
void	write_attribute (const std::string &Aname, const T &Data)
	Write attribute to file. More...

void	write_attribute (const std::string &Aname, const char *Data)

template<class T , int D>
void	write_field (const std::string &Dataname, const blitz::Array< T, D > &Data)
	Write a given field. More...

template<int D>
void	write_field (const std::string &Dataname, const blitz::Array< std::string, D > &Data)

template<int D>
void	write_field (const std::string &Dataname, const blitz::Array< const char *, D > &Data)

template<class T >
void	write_field (const std::string &Dataname, const T &Data)
	Write a given field. More...

void	write_field (const std::string &Dataname, const std::string &Data)

void	write_field (const std::string &Dataname, const char *Data)

template<class T >
void	write_field (const std::string &Dataname, const T &Data, H5::DataType P)
	Write a given field. More...

template<class T , int D>
void	write_field (const std::string &Dataname, const blitz::Array< T, D > &Data, H5::DataType P)
	Write a given field. More...

Static Public Member Functions
static bool	is_hdf (const std::string &Fname)
	Return true if the given file is an HDF file. More...

Detailed Description

This class reads and writes a HDF5 file.

Note that this is just a thin layer on top of the HDF 5 libraries to make the file operations we need to do in Level 2 Full Physics easier. There are many other things that can be done with a HDF 5 than what this class exposes.

Note that because it is what is used by Level 2 product, we produce data in 32 bit (either 32 bit integer or 32 bit floating point). On a 64 bit system, the underlying double and int are larger. We map between these types as needed transparently.

HDF supports both fixed length strings and variable length strings. We have the need to write both variable length strings and fixed length strings. As a convention, if std::string are passed we write as variable length. If const char* is passed, we determine the fixed length needed to accommodate the largest string passed and write the data as fixed strings of that length (padding shorter strings with spaces). This is an arbitrary decision, but it allows us to write both types.

Note that in what is a fairly odd convention, we add a trailing '\0' in our fixed length string, so there is one extra character.

Definition at line 39 of file hdf_file.h.

Member Enumeration Documentation

◆ Mode

enum FullPhysics::HdfFile::Mode

Enumerator
READ
CREATE
READ_WRITE

Definition at line 41 of file hdf_file.h.

Constructor & Destructor Documentation

◆ HdfFile()

HdfFile::HdfFile	(	const std::string &	Fname,
		Mode	M = `READ`
	)

Open the given file with the given mode.

Definition at line 261 of file hdf_file.cc.

◆ ~HdfFile()

virtual FullPhysics::HdfFile::~HdfFile ( )

inlinevirtual

Definition at line 43 of file hdf_file.h.

Member Function Documentation

◆ close()

void FullPhysics::HdfFile::close ( )

inline

Close the underlying file.

This is automatically done by the destructor, so you only need to call this if you want to force a close (e.g., for a unit test)

Definition at line 126 of file hdf_file.h.

◆ dimension_metadata()

void HdfFile::dimension_metadata	(	const std::string &	Name,
		const std::string &	Description,
		int	Size
	)

The SDOS products have a particular metadata convention where the information about each of the Dimensions that appear in the file are documented.

This function takes this metadata for dimension and puts it into the file.

Definition at line 463 of file hdf_file.cc.

◆ file_name()

const std::string& FullPhysics::HdfFile::file_name ( ) const

inline

File name.

Definition at line 131 of file hdf_file.h.

◆ h5_file() [1/2]

H5::H5File& FullPhysics::HdfFile::h5_file ( )

inline

Definition at line 155 of file hdf_file.h.

◆ h5_file() [2/2]

const H5::H5File& FullPhysics::HdfFile::h5_file ( ) const

inline

Definition at line 156 of file hdf_file.h.

◆ has_attribute()

bool HdfFile::has_attribute ( const std::string & Aname ) const

Check to see if a attribute is in the file.

Determine if attribute is present.

Definition at line 363 of file hdf_file.cc.

◆ has_object()

bool FullPhysics::HdfFile::has_object ( const std::string & Objname ) const

inline

Check to see if an object (such as a Dataset) is in the file.

Definition at line 48 of file hdf_file.h.

◆ is_hdf()

static bool FullPhysics::HdfFile::is_hdf ( const std::string & Fname )

inlinestatic

Return true if the given file is an HDF file.

Definition at line 137 of file hdf_file.h.

◆ mode()

Mode FullPhysics::HdfFile::mode ( ) const

inline

Mode file was opened with.

Definition at line 118 of file hdf_file.h.