#include <HDF_fwd.hpp>

Detailed Description

Simplified HDF5 I/O utilities.

This class is a wrapper around the HDF5 C library, for simplified reading and writing.

This class represents a HDF reader and writer: it knows which file (open or closed) and which group (open or closed) are the ones that are to be read from/written to. Any calls to read* or write* methods write to that group in that file. The file and group can be opened, closed or changed during the lifetime of the object, with user's responsibility being that they are open when writing to/reading from it.

In addition atomic() method can be used to perform open/read/close or open/write/close cycle in one line.

Raw C identifiers are exposed with getFileID() and getGroupID() methods and can be used to perform any action not directly supported by this class.

All write methods create the datasets or attributes required. They also have an overwrite parameter which is set to false by default. This means that any attempt to write to an existing object will fail an assertion to prevent accidental deletions of existing data. This can be disabled by setting overwrite = true, allowing one to overwrite existing data.

All open objects are closed upon destruction.

Note: To enable support for Eigen types, HDF_Eigen.hpp must be included.

Usage example:

    // open new empty file and group '/' automatically
    HDF hdf("test/testdata/filename.h5", HDF::DESTROY);
    hdf.writeStringAttribute("text", "This is the content");  // written to group '/'
 
    hdf.openGroup("group1");
    std::vector<double> a = {1.2, -4.5, 4.5};
    hdf.writeDoubleArray("a", a);
    hdf.close();
 
    hdf.reopen();  // reopen previously closed file and group
    hdf.openGroup("/");
    std::string s = hdf.readStringAttribute("text");
    hdf.writeStringAttribute("text", "New content", true);  // enable overwrite
 
    hdf.setFilename("test/testdata/new_file.h5");
    hdf.setGroupName("group_name");  // set current group name and filename, but do not open yet
 
    std::vector<std::vector<double>> b(5, a);  // written as dataset of size 5x3
    hdf.atomic().writeFloat2DArray("b", b);  // opens, writes and closes, the value is cast to float
 
    Eigen::MatrixXd M(5, 3);
    M << 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15;
    hdf.atomic().writeEigen("M", M);
    auto M2 = hdf.atomic().readEigen("M");  // opens, reads, closes
 
    std::cout << hdf << std::endl;
    // Timer, DomainDiscretization and XML classes can also be written directly

Examples: test/end2end/poisson_explicit.cpp.

Definition at line 75 of file HDF_fwd.hpp.

Public Member Functions
	HDF ()
	Construct an empty HDF reader. More...

	HDF (std::string filename, Mode mode=APPEND)
	Construct a HDF reader and open `filename` with given `mode`. More...

	~HDF ()
	Closes all opened objects, by using close(). More...

void	open (const std::string &filename, const std::string &group_name="/", Mode mode=APPEND)
	Opens given file and group. More...

void	openFile (const std::string &filename, Mode mode=APPEND)
	Opens a given file with a given mode. More...

void	reopenFile (Mode mode=APPEND)
	Reopens the current file. More...

void	openGroup (std::string group_name)
	Open given group, closing any previously opened group(). More...

void	reopenGroup ()
	Reopens current group. More...

void	reopen (Mode mode=APPEND)
	Reopens current file and group. More...

bool	isFileOpen () const
	Returns `true` is currently specified file is open and `false` otherwise. More...

bool	isGroupOpen () const
	Returns `true` is currently specified group is open and `false` otherwise. More...

void	flush () const
	Flush opened file, if it is open. More...

void	closeGroup () const
	Closes current group, if open. More...

void	closeFile () const
	Closes current file and all objects associated with it (e.g. the group), if open. More...

void	close () const
	Closes all open objects. Alias of closeFile(). More...

const std::string &	filename () const
	Get current filename. More...

const std::string &	fileName () const
	Alias of filename(). More...

void	setFilename (const std::string &filename)
	Sets new filename without opening the new file. Any previously opened file is closed. More...

void	setFileName (const std::string &filename)
	Alias of setFilename(). More...

const std::string &	groupName () const
	Get current group name. More...

void	setGroupName (const std::string &group_name)
	Set new group name without opening the new group. Any previously opened group is closed. More...

template<class T >
T	readAttribute (const std::string &attr_name) const
	Read attribute given by `attr_name`. More...

template<class T >
void	writeAttribute (const std::string &attr_name, const T &value, const hid_t &type, bool overwrite=false) const
	Writes given attribute with given value and type to file. More...

template<typename T >
std::pair< std::vector< hsize_t >, std::vector< T > >	readLinearArray (const std::string &dataset_name) const
	Read given dataset into linear `dim`-D array. More...

template<typename T >
std::vector< T >	read1DArray (const std::string &dataset_name) const
	Read 1D dataset given by `dataset_name`. More...

template<typename T >
std::vector< std::vector< T > >	read2DArray (const std::string &dataset_name) const
	Read given dataset into 2D array of vectors. More...

template<typename T >
std::vector< std::vector< std::vector< T > > >	read3DArray (const std::string &dataset_name) const
	Read given dataset into 3D array of vectors. More...

template<int dim, typename T >
void	writeLinearArray (const std::string &dataset_name, const T *value, const std::array< hsize_t, dim > &sizes, hid_t type, bool overwrite) const
	Writes a `dim`-dimensional dataset stored in 1D array in col-major fashion. More...

template<typename T , typename array_t >
void	write1DArray (const std::string &dataset_name, const array_t &value, hid_t type, bool overwrite) const
	Writes given 1D array with given value and type to file. More...

template<typename T , class array_t >
void	write2DArray (const std::string &dataset_name, const array_t &value, hid_t type, bool overwrite) const
	Writes given 2D array of given value and type to file. More...

template<typename T , class array_t >
void	write3DArray (const std::string &dataset_name, const array_t &value, hid_t type, bool overwrite) const
	Writes given 3D array of given value and type to file. More...

int	readIntAttribute (const std::string &attr_name) const
	Reads `int` attribute. More...

bool	readBoolAttribute (const std::string &attr_name) const
	Reads `bool` attribute. More...

double	readDoubleAttribute (const std::string &attr_name) const
	Reads `double` attribute. More...

float	readFloatAttribute (const std::string &attr_name) const
	Reads `float` attribute. More...

std::string	readStringAttribute (const std::string &attr_name) const
	Reads non-null-terminated `string` attribute. More...

std::string	readNullTerminatedStringAttribute (const std::string &attr_name) const
	Reads null-terminated `string` attribute. More...

void	writeIntAttribute (const std::string &attr_name, int value, bool overwrite=false) const
	Write `int` attribute. More...

void	writeBoolAttribute (const std::string &attr_name, bool value, bool overwrite=false) const
	Write `bool` attribute. More...

void	writeDoubleAttribute (const std::string &attr_name, double value, bool overwrite=false) const
	Write `double` attribute. More...

void	writeFloatAttribute (const std::string &attr_name, float value, bool overwrite=false) const
	Write `float` attribute. More...

void	writeStringAttribute (const std::string &attr_name, const std::string &value, bool overwrite=false) const
	Write `string` attribute. More...

std::vector< int >	readIntArray (const std::string &dataset_name) const
	Read given dataset into vector of `int`s. More...

std::vector< double >	readDoubleArray (const std::string &dataset_name) const
	Read given dataset into vector of `double`s. More...

std::vector< float >	readFloatArray (const std::string &dataset_name) const
	Read given dataset into vector of `float`s. More...

template<typename array_t >
void	writeIntArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 1D array of `int`s. More...

template<typename array_t >
void	writeDoubleArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 1D array of `double`s. More...

template<typename array_t >
void	writeFloatArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 1D array of `floats`s. More...

std::vector< std::vector< int > >	readInt2DArray (const std::string &dataset_name) const
	Read given dataset into 2D vector of `int`s. More...

std::vector< std::vector< double > >	readDouble2DArray (const std::string &dataset_name) const
	Read given dataset into 2D vector of `double`s. More...

std::vector< std::vector< float > >	readFloat2DArray (const std::string &dataset_name) const
	Read given dataset into 2D vector of `float`s. More...

template<typename array_t >
void	writeInt2DArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 2D array of `int`s. More...

template<typename array_t >
void	writeDouble2DArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 2D array of `double`s. More...

template<typename array_t >
void	writeFloat2DArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 2D array of `float`s. More...

std::vector< std::vector< std::vector< int > > >	readInt3DArray (const std::string &dataset_name) const
	Read given dataset into 3D vector of `int`s. More...

std::vector< std::vector< std::vector< double > > >	readDouble3DArray (const std::string &dataset_name) const
	Read given dataset into 3D vector of `double`s. More...

std::vector< std::vector< std::vector< float > > >	readFloat3DArray (const std::string &dataset_name) const
	Read given dataset into 3D vector of `float`s. More...

template<typename array_t >
void	writeInt3DArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 3D array of `int`s. More...

template<typename array_t >
void	writeDouble3DArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 3D array of `double`s. More...

template<typename array_t >
void	writeFloat3DArray (const std::string &dataset_name, const array_t &value, bool overwrite=false) const
	Write given value as a 3D array of `float`s. More...

template<typename scalar_t = double>
Eigen::Matrix< scalar_t, -1, -1, 0, -1, -1 >	readEigen (const std::string &dataset_name) const
	Reads data as an Eigen matrix of type `scalar_t`. More...

template<typename Derived >
void	writeEigen (const std::string &dataset_name, const Eigen::MatrixBase< Derived > &value, bool overwrite=false) const
	Write given Eigen expression as a 2D array of its type (either `int`, `double` or `float`). More...

template<typename SparseMatrixType >
void	writeSparseMatrix (const std::string &name, SparseMatrixType &matrix, bool one_based=true, bool overwrite=false)
	Writes a sparse matrix. More...

template<typename domain_t >
void	writeDomain (const std::string &name, const domain_t &domain, bool overwrite=false)
	Writes given domain discretization to file. More...

template<typename timer_t >
void	writeTimer (const std::string &name, const timer_t &timer, bool overwrite=false)
	Writes given timer to file. More...

template<typename conf_t >
void	writeXML (const std::string &name, const conf_t &conf, bool overwrite=false)
	Writes given XML object to file. More...

HDF	atomic () const
	Allows for "atomic" read and write operations to HDF5 files. More...

hid_t	getFileID () const
	Return raw HDF C file identifier. More...

hid_t	getGroupID () const
	Return raw HDF C group identifier. More...

Members	members () const
	Returns an object with categorized names of all members of current group. More...

std::vector< std::string >	groups () const
	Returns names of all subgroups in current group in alphabetical order. More...

std::vector< std::string >	datasets () const
	Returns names of all datasets in current group in alphabetical order. More...

Public Types
enum	Mode : unsigned { APPEND = 256, DESTROY = 128, READONLY = 64 }
	Possible file opening modes. More...

Classes
struct	Members
	Holds categorized names for all members of a group. More...

Friends
std::ostream &	operator<< (std::ostream &os, const HDF &hdf)
	Output basic info about HDF reader, such as current group and file. More...

Private Member Functions
template<typename T , class array_t >
void	write2DArray (const std::string &, const array_t &, hid_t, bool, std::false_type) const
	Overload for static_assert for Eigen due to different `size` method. More...

template<typename T , class array_t >
void	write2DArray (const std::string &, const array_t &, hid_t, bool, std::true_type) const
	Overload for static_assert for Eigen due to different `size` method. More...

Static Private Member Functions
static std::string	str (Mode mode)
	Convert HDF::Mode enum to string. More...

static hid_t	openFileHelper (const std::string &filename, Mode mode)
	Opens given file with given mode. More...

static herr_t	memberIterateCallback (hid_t loc_id, const char name, const H5L_info_t , void *data)
	Callback required by HDF `Literate` function when getting a list of members. More...

Private Attributes
std::string	filename_
	Current file name. More...

std::string	group_name_
	Current group name. More...

hid_t	file
	Currently open file identifier. More...

hid_t	group
	Currently open group identifier. More...

Member Enumeration Documentation

◆ Mode

enum mm::HDF::Mode : unsigned

Possible file opening modes.

Enumerator
APPEND	Appends to the existing contents, if any exist.
DESTROY	Removes old contents, if any exist.
READONLY	Read only open, the file must exist.

Definition at line 84 of file HDF_fwd.hpp.

Constructor & Destructor Documentation

◆ HDF() [1/2]

mm::HDF::HDF ( )

inline

Construct an empty HDF reader.

Definition at line 95 of file HDF_fwd.hpp.

◆ HDF() [2/2]

mm::HDF::HDF	(	std::string	filename,
		Mode	mode = `APPEND`
	)

inlineexplicit

Construct a HDF reader and open filename with given mode.

It also opens group / by default, so it is immediately ready for reading / writing.

Exceptions

Assertion fails if mode was READONLY and the file can not be read.

Definition at line 101 of file HDF_fwd.hpp.

◆ ~HDF()

mm::HDF::~HDF ( )

inline

Closes all opened objects, by using close().

See also: close

Definition at line 107 of file HDF_fwd.hpp.

Member Function Documentation

◆ atomic()

HDF mm::HDF::atomic ( ) const

Allows for "atomic" read and write operations to HDF5 files.

This means that read and write functions open the file and group, before reading/writing and close them afterwards. The filename and group name must be set before use.

See also: setFilename, setGroupName

Examples: test/end2end/poisson_explicit.cpp.

Definition at line 250 of file HDF.cpp.

◆ close()

void mm::HDF::close ( ) const

inline

Closes all open objects. Alias of closeFile().

Examples: test/end2end/poisson_explicit.cpp.

Definition at line 164 of file HDF_fwd.hpp.

◆ closeFile()

void mm::HDF::closeFile ( ) const

Closes current file and all objects associated with it (e.g. the group), if open.

Definition at line 243 of file HDF.cpp.

◆ closeGroup()

void mm::HDF::closeGroup ( ) const

Closes current group, if open.

Definition at line 236 of file HDF.cpp.

◆ datasets()

std::vector<std::string> mm::HDF::datasets ( ) const

inline

Returns names of all datasets in current group in alphabetical order.

See also: members

Definition at line 558 of file HDF_fwd.hpp.

◆ filename()

const std::string& mm::HDF::filename ( ) const

inline

Get current filename.

Definition at line 166 of file HDF_fwd.hpp.

◆ fileName()

const std::string& mm::HDF::fileName ( ) const

inline

Alias of filename().

Definition at line 168 of file HDF_fwd.hpp.

◆ flush()

void mm::HDF::flush ( ) const

Flush opened file, if it is open.

Definition at line 229 of file HDF.cpp.

◆ getFileID()

hid_t mm::HDF::getFileID ( ) const

inline

Return raw HDF C file identifier.

Definition at line 523 of file HDF_fwd.hpp.

◆ getGroupID()

hid_t mm::HDF::getGroupID ( ) const

inline

Return raw HDF C group identifier.

Definition at line 525 of file HDF_fwd.hpp.

◆ groupName()

const std::string& mm::HDF::groupName ( ) const

inline

Get current group name.

Definition at line 174 of file HDF_fwd.hpp.

◆ groups()

std::vector<std::string> mm::HDF::groups ( ) const

inline

Returns names of all subgroups in current group in alphabetical order.

See also: members

Definition at line 555 of file HDF_fwd.hpp.

◆ isFileOpen()

bool mm::HDF::isFileOpen ( ) const

inline

Returns true is currently specified file is open and false otherwise.

Definition at line 154 of file HDF_fwd.hpp.

◆ isGroupOpen()

bool mm::HDF::isGroupOpen ( ) const

inline

Returns true is currently specified group is open and false otherwise.

Definition at line 156 of file HDF_fwd.hpp.

◆ memberIterateCallback()

herr_t mm::HDF::memberIterateCallback	(	hid_t	loc_id,
		const char *	name,
		const H5L_info_t *	,
		void *	data
	)

staticprivate

Callback required by HDF Literate function when getting a list of members.

Definition at line 277 of file HDF.cpp.

◆ members()

HDF::Members mm::HDF::members ( ) const

Returns an object with categorized names of all members of current group.

The names within each category are guaranteed to be in alphabetical order.

Definition at line 298 of file HDF.cpp.

◆ open()

void mm::HDF::open	(	const std::string &	filename,
		const std::string &	group_name = `"/"`,
		Mode	mode = `APPEND`
	)

inline

Opens given file and group.

Parameters

filename	Name of the file to open.
group_name	Name of the group to open.
mode	Specifies the mode to open the file in, see HDF::Mode.

Definition at line 120 of file HDF_fwd.hpp.

◆ openFile()

void mm::HDF::openFile	(	const std::string &	filename,
		Mode	mode = `APPEND`
	)

inline

Opens a given file with a given mode.

Any previously opened file is closed. No group is opened.

Definition at line 130 of file HDF_fwd.hpp.

◆ openFileHelper()

hid_t mm::HDF::openFileHelper	(	const std::string &	filename,
		HDF::Mode	mode
	)

staticprivate

Opens given file with given mode.

See also: open, openFile, openGroup

Definition at line 21 of file HDF.cpp.

◆ openGroup()

void mm::HDF::openGroup ( std::string group_name )

Open given group, closing any previously opened group().

Parameters

group_name Name of the group to open. The name must be / separated and can be either absolute or relative. Absolute names such as /a/b/c open groups staring from / group and relative names such as a/b/c open groups staring from current group. The groups are created automatically if they do not exist.

Definition at line 48 of file HDF.cpp.

◆ read1DArray()

template<typename T >

std::vector< T > mm::HDF::read1DArray ( const std::string & dataset_name ) const

Read 1D dataset given by dataset_name.

Parameters

dataset_name Name of the dataset.

Returns: A vector containing all dataset elements.

Exceptions

Assertion fails if the dataset does not exists or cannot be read.

Warning: If the element type is not compatible with type T, the function will still attempt to read it the behavior is undefined. Most often the return value is garbage.

Definition at line 95 of file HDF.hpp.

◆ read2DArray()

template<typename T >

std::vector< std::vector< T > > mm::HDF::read2DArray ( const std::string & dataset_name ) const

Read given dataset into 2D array of vectors.

Parameters

dataset_name Name of the dataset.

Returns: A vector of vectors containing all dataset elements.

Exceptions

Assertion fails if the dataset does not exists or cannot be read.

Warning: If the element type is not compatible with type T, the function will still attempt to read it the behavior is undefined. Most often the return value is garbage.

Definition at line 105 of file HDF.hpp.

◆ read3DArray()

template<typename T >

std::vector< std::vector< std::vector< T > > > mm::HDF::read3DArray ( const std::string & dataset_name ) const

Read given dataset into 3D array of vectors.

Parameters

dataset_name Name of the dataset.

Returns: A vector of vectors containing all dataset elements.

Exceptions

Assertion fails if the dataset does not exists or cannot be read.

Warning: If the element type is not compatible with type T, the function will still attempt to read it the behavior is undefined. Most often the return value is garbage.

Definition at line 123 of file HDF.hpp.

◆ readAttribute()

template<class T >

T mm::HDF::readAttribute ( const std::string & attr_name ) const

Read attribute given by attr_name.

Template Parameters

T	The type to which to read the attribute.

Parameters

attr_name Name of the attribute

Returns: Attribute value, converted to type T.

Exceptions

Assertion fails if the attribute does not exists or cannot be read.

Warning: If the attribute type is not compatible with type T, the function will still attempt to read it the behavior is undefined. Most often the return value is garbage.

Note: This function is specialized for std::string.

Definition at line 16 of file HDF.hpp.

◆ readBoolAttribute()

bool mm::HDF::readBoolAttribute ( const std::string & attr_name ) const

Reads bool attribute.

See also: readAttribute

Definition at line 122 of file HDF.cpp.

◆ readDouble2DArray()

std::vector< std::vector< double > > mm::HDF::readDouble2DArray ( const std::string & dataset_name ) const

Read given dataset into 2D vector of doubles.

See also: read2DArray

Definition at line 206 of file HDF.cpp.

◆ readDouble3DArray()

std::vector< std::vector< std::vector< double > > > mm::HDF::readDouble3DArray ( const std::string & dataset_name ) const

Read given dataset into 3D vector of doubles.

See also: read2DArray

Definition at line 220 of file HDF.cpp.

◆ readDoubleArray()

std::vector< double > mm::HDF::readDoubleArray ( const std::string & dataset_name ) const

Read given dataset into vector of doubles.

See also: readArray

Definition at line 194 of file HDF.cpp.

◆ readDoubleAttribute()

double mm::HDF::readDoubleAttribute ( const std::string & attr_name ) const

Reads double attribute.

See also: readAttribute

Definition at line 126 of file HDF.cpp.

◆ readEigen()

template<typename scalar_t = double>

Eigen::Matrix<scalar_t, -1, -1, 0, -1, -1> mm::HDF::readEigen ( const std::string & dataset_name ) const

Reads data as an Eigen matrix of type scalar_t.

Template Parameters

scalar_t The of the data to read. Set to double by default.

Parameters

dataset_name Name of the dataset to read from.

Warning: If the supplied data type does not match the actual type of the data, the behavior is undefined. Most likely, the returned matrix will have garbage contents.

Note: To use this function, the file HDF_Eigen.hpp must be included.

◆ readFloat2DArray()

std::vector< std::vector< float > > mm::HDF::readFloat2DArray ( const std::string & dataset_name ) const

Read given dataset into 2D vector of floats.

See also: read2DArray

Definition at line 210 of file HDF.cpp.

◆ readFloat3DArray()

std::vector< std::vector< std::vector< float > > > mm::HDF::readFloat3DArray ( const std::string & dataset_name ) const

Read given dataset into 3D vector of floats.

See also: read2DArray

Definition at line 225 of file HDF.cpp.

◆ readFloatArray()

std::vector< float > mm::HDF::readFloatArray ( const std::string & dataset_name ) const

Read given dataset into vector of floats.

See also: readArray

Definition at line 198 of file HDF.cpp.

◆ readFloatAttribute()

float mm::HDF::readFloatAttribute ( const std::string & attr_name ) const

Reads float attribute.

See also: readAttribute

Definition at line 130 of file HDF.cpp.

◆ readInt2DArray()

std::vector< std::vector< int > > mm::HDF::readInt2DArray ( const std::string & dataset_name ) const

Read given dataset into 2D vector of ints.

See also: read2DArray

Definition at line 202 of file HDF.cpp.

◆ readInt3DArray()

std::vector< std::vector< std::vector< int > > > mm::HDF::readInt3DArray ( const std::string & dataset_name ) const

Read given dataset into 3D vector of ints.

See also: read2DArray

Definition at line 215 of file HDF.cpp.

◆ readIntArray()

std::vector< int > mm::HDF::readIntArray ( const std::string & dataset_name ) const

Read given dataset into vector of ints.

See also: readArray

Definition at line 190 of file HDF.cpp.

◆ readIntAttribute()

int mm::HDF::readIntAttribute ( const std::string & attr_name ) const

Reads int attribute.

See also: readAttribute

Definition at line 118 of file HDF.cpp.

◆ readLinearArray()

template<typename T >

std::pair< std::vector< hsize_t >, std::vector< T > > mm::HDF::readLinearArray ( const std::string & dataset_name ) const

Read given dataset into linear dim-D array.

Parameters

dataset_name Name of the dataset.

Returns: A vector containing all dataset elements in col-major fashion.

Exceptions

Assertion fails if the dataset does not exists or cannot be read.

Warning: If the element type is not compatible with type T, the function will still attempt to read it the behavior is undefined. Most often the return value is garbage.

Definition at line 68 of file HDF.hpp.

◆ readNullTerminatedStringAttribute()

std::string mm::HDF::readNullTerminatedStringAttribute ( const std::string & attr_name ) const

Reads null-terminated string attribute.

See also: readAttribute

Definition at line 113 of file HDF.cpp.

◆ readStringAttribute()

std::string mm::HDF::readStringAttribute ( const std::string & attr_name ) const

Reads non-null-terminated string attribute.

Any null characters are read as part of the string.

See also: readAttribute

Definition at line 134 of file HDF.cpp.

◆ reopen()

void mm::HDF::reopen ( Mode mode = APPEND )

inline

Reopens current file and group.

Examples: test/end2end/poisson_explicit.cpp.

Definition at line 152 of file HDF_fwd.hpp.

◆ reopenFile()

void mm::HDF::reopenFile ( Mode mode = APPEND )

inline

Reopens the current file.

Definition at line 137 of file HDF_fwd.hpp.

◆ reopenGroup()

void mm::HDF::reopenGroup ( )

inline

Reopens current group.

Definition at line 148 of file HDF_fwd.hpp.

◆ setFilename()

void mm::HDF::setFilename ( const std::string & filename )

inline

Sets new filename without opening the new file. Any previously opened file is closed.

Definition at line 170 of file HDF_fwd.hpp.

◆ setFileName()

void mm::HDF::setFileName ( const std::string & filename )

inline

Alias of setFilename().

Definition at line 172 of file HDF_fwd.hpp.

◆ setGroupName()

void mm::HDF::setGroupName ( const std::string & group_name )

Set new group name without opening the new group. Any previously opened group is closed.

Definition at line 262 of file HDF.cpp.

◆ str()

std::string mm::HDF::str ( HDF::Mode mode )

staticprivate

Convert HDF::Mode enum to string.

Definition at line 12 of file HDF.cpp.

◆ write1DArray()

template<typename T , typename array_t >

void mm::HDF::write1DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		hid_t	type,
		bool	overwrite
	)		const

Writes given 1D array with given value and type to file.

Template Parameters

T	Type to which the elements of value are converted to.
array_t	Type of the given array. It must support `operator[]` and `.size()`.

Parameters

dataset_name	Name of the attribute.
value	Value to be written
type	HDF5 type of the elements to be written.
overwrite	If overwriting existing datasets is allowed. If an attribute with the same name is attempted to be written, it must have the same dimensions and type as current value. Otherwise the overwrite will fail.

Definition at line 190 of file HDF.hpp.

◆ write2DArray() [1/3]

template<typename T , class array_t >

void mm::HDF::write2DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		hid_t	type,
		bool	overwrite,
		std::false_type
	)		const

private

Overload for static_assert for Eigen due to different size method.

Definition at line 199 of file HDF.hpp.

◆ write2DArray() [2/3]

template<typename T , class array_t >

void mm::HDF::write2DArray	(	const std::string &	,
		const array_t &	,
		hid_t	,
		bool	,
		std::true_type
	)		const

inlineprivate

Overload for static_assert for Eigen due to different size method.

Definition at line 309 of file HDF_fwd.hpp.

◆ write2DArray() [3/3]

template<typename T , class array_t >

void mm::HDF::write2DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		hid_t	type,
		bool	overwrite
	)		const

inline

Writes given 2D array of given value and type to file.

Template Parameters

T	Type of `array_t` elements
array_t	Type of the given 2D array. It must support `.size()`, `[i].size()` and `[i][j]` operations.

Parameters

dataset_name	Name of the dataset.
value	Value to be written.
type	HDF5 type of the elements to be written.
overwrite	If overwriting existing datasets is allowed. If an attribute with the same name is attempted to be written, it must have the same dimensions and type as current value. Otherwise the overwrite will fail.

Definition at line 296 of file HDF_fwd.hpp.

◆ write3DArray()

template<typename T , class array_t >

void mm::HDF::write3DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		hid_t	type,
		bool	overwrite
	)		const

Writes given 3D array of given value and type to file.

Template Parameters

T	Type of `array_t` elements
array_t	Type of the given 2D array. It must support `.size()`, `[i].size()`, `[i][j]`, `[i][j].size()` and `[i][j][k]` operations.

Parameters

dataset_name	Name of the dataset.
value	Value to be written.
type	HDF5 type of the elements to be written.
overwrite	If overwriting existing datasets is allowed. If an attribute with the same name is attempted to be written, it must have the same dimensions and type as current value. Otherwise the overwrite will fail.

Definition at line 216 of file HDF.hpp.

◆ writeAttribute()

template<class T >

void mm::HDF::writeAttribute	(	const std::string &	attr_name,
		const T &	value,
		const hid_t &	type,
		bool	overwrite = `false`
	)		const

Writes given attribute with given value and type to file.

Parameters

attr_name	Name of the attribute.
value	Value to be written
type	HDF5 type of the attribute to be written.
overwrite	If overwriting existing attributes is allowed. If an attribute with the same name is attempted to be written, the existing attribute is deleted and a new one is created instead.

Definition at line 38 of file HDF.hpp.

◆ writeBoolAttribute()

void mm::HDF::writeBoolAttribute	(	const std::string &	attr_name,
		bool	value,
		bool	overwrite = `false`
	)		const

Write bool attribute.

See also: writeAttribute

Definition at line 142 of file HDF.cpp.

◆ writeDomain()

template<typename domain_t >

void mm::HDF::writeDomain	(	const std::string &	name,
		const domain_t &	domain,
		bool	overwrite = `false`
	)

Writes given domain discretization to file.

A group with given name is created and 4 datasets and 1 attribute are stored inside:

N: int attribute storing number of nodes in the domain,
pos: N x dim double array of positions,
types: int array of length N representing domain types,
bmap: int array of length N mapping nodes to boundary nodes (see DomainDiscretization::bmap),
normals: double array of domain normals for boundary nodes. After the function exists, the same group is opened as before the call.

Parameters

name	Name of the group in which the domain is stored.
domain	Domain to write to file.
overwrite	If `true`, allows overwriting of existing entries.

See also: DomainDiscretization

Examples: test/end2end/poisson_explicit.cpp.

Definition at line 332 of file HDF.hpp.

◆ writeDouble2DArray()

template<typename array_t >

void mm::HDF::writeDouble2DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 2D array of doubles.

See also: write2DArray

Definition at line 264 of file HDF.hpp.

◆ writeDouble3DArray()

template<typename array_t >

void mm::HDF::writeDouble3DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 3D array of doubles.

See also: write3DArray

Definition at line 282 of file HDF.hpp.

◆ writeDoubleArray()

template<typename array_t >

void mm::HDF::writeDoubleArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 1D array of doubles.

See also: write1DArray

Examples: test/end2end/poisson_explicit.cpp.

Definition at line 246 of file HDF.hpp.

◆ writeDoubleAttribute()

void mm::HDF::writeDoubleAttribute	(	const std::string &	attr_name,
		double	value,
		bool	overwrite = `false`
	)		const

Write double attribute.

See also: writeAttribute

Definition at line 146 of file HDF.cpp.

◆ writeEigen()

template<typename Derived >

void mm::HDF::writeEigen	(	const std::string &	dataset_name,
		const Eigen::MatrixBase< Derived > &	value,
		bool	overwrite = `false`
	)		const

Write given Eigen expression as a 2D array of its type (either int, double or float).

Note: To use this function, the file HDF_Eigen.hpp must be included.

Definition at line 46 of file HDF_Eigen.hpp.

◆ writeFloat2DArray()

template<typename array_t >

void mm::HDF::writeFloat2DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 2D array of floats.

See also: write2DArray

Definition at line 270 of file HDF.hpp.

◆ writeFloat3DArray()

template<typename array_t >

void mm::HDF::writeFloat3DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 3D array of floats.

See also: write3DArray

Definition at line 288 of file HDF.hpp.

◆ writeFloatArray()

template<typename array_t >

void mm::HDF::writeFloatArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 1D array of floatss.

See also: write1DArray

Definition at line 252 of file HDF.hpp.

◆ writeFloatAttribute()

void mm::HDF::writeFloatAttribute	(	const std::string &	attr_name,
		float	value,
		bool	overwrite = `false`
	)		const

Write float attribute.

See also: writeAttribute

Definition at line 150 of file HDF.cpp.

◆ writeInt2DArray()

template<typename array_t >

void mm::HDF::writeInt2DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 2D array of ints.

See also: write2DArray

Definition at line 258 of file HDF.hpp.

◆ writeInt3DArray()

template<typename array_t >

void mm::HDF::writeInt3DArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 3D array of ints.

See also: write3DArray

Definition at line 276 of file HDF.hpp.

◆ writeIntArray()

template<typename array_t >

void mm::HDF::writeIntArray	(	const std::string &	dataset_name,
		const array_t &	value,
		bool	overwrite = `false`
	)		const

Write given value as a 1D array of ints.

See also: write1DArray

Definition at line 240 of file HDF.hpp.

◆ writeIntAttribute()

void mm::HDF::writeIntAttribute	(	const std::string &	attr_name,
		int	value,
		bool	overwrite = `false`
	)		const

Write int attribute.

See also: writeAttribute

Definition at line 138 of file HDF.cpp.

◆ writeLinearArray()

template<int dim, typename T >

void mm::HDF::writeLinearArray	(	const std::string &	dataset_name,
		const T *	value,
		const std::array< hsize_t, dim > &	sizes,
		hid_t	type,
		bool	overwrite
	)		const

Writes a dim-dimensional dataset stored in 1D array in col-major fashion.

Template Parameters

dim	Dimension (HDF rank) of the dataset, 2 for matrices, 3 for tensors.

Parameters

dataset_name	Name of the dataset.
value	Pointer to values to be written, stored in a linear col-major fashion. The number of values should be equal to the product of `sizes`.
sizes	Sizes of the dataset along each dimension.
type	HDF5 type of the dataset.
overwrite	See write2DArray()

Definition at line 144 of file HDF.hpp.

◆ writeSparseMatrix()

template<typename SparseMatrixType >

void mm::HDF::writeSparseMatrix	(	const std::string &	name,
		SparseMatrixType &	matrix,
		bool	one_based = `true`,
		bool	overwrite = `false`
	)

Writes a sparse matrix.

Matrix matrix is written as a N x 3 matrix, where the columns represent vectors I, J, V, such that M(I(i), J(i)) = V(i). Matrix values are stored as doubles of native size.

Warning: By default, the indexes of the matrix elements are saved in 1-based format.

Parameters

name	Attribute name.
matrix	A sparse matrix.
one_based	Whether to store the indices as one or zero based. One based indexes are ready to be read by Matlab's `spconvert`.
overwrite	See write2DArray().

Definition at line 316 of file HDF.hpp.

◆ writeStringAttribute()

void mm::HDF::writeStringAttribute	(	const std::string &	attr_name,
		const std::string &	value,
		bool	overwrite = `false`
	)		const

Write string attribute.

The string is written as an non-null-terminater array of bytes. It may contain null characters in the middle.

See also: writeAttribute

Definition at line 154 of file HDF.cpp.

◆ writeTimer()

template<typename timer_t >

void mm::HDF::writeTimer	(	const std::string &	name,
		const timer_t &	timer,
		bool	overwrite = `false`
	)

Writes given timer to file.

A group with given name is created and durations (in seconds) between consecutive labels are writen as double attributes named label1-label2. Additionally, total time between first and last label (in seconds) is stored in the double attribute named total. After the function exists, the same group is opened as before the call. If timer has 0 labels, only the group is created. If timer has one label, attribute total with value 0.0 is written.

Parameters

name	Name of the group in which the timer is stored.
timer	Timer to write to file.
overwrite	If `true`, allows overwriting of existing entries.

See also: Timer

Definition at line 346 of file HDF.hpp.

◆ writeXML()

template<typename conf_t >

void mm::HDF::writeXML	(	const std::string &	name,
		const conf_t &	conf,
		bool	overwrite = `false`
	)

Writes given XML object to file.

All attributes in the file, given by XML::getAll, are written in their dot-separated full-path format. They are written either as doubles (if whole value can be parsed as a double) or strings otherwise. After the function exists, the same group is opened as before the call.

Parameters

name	Name of the group in which the XML attributes are stored.
conf	XML object.
overwrite	If `true`, allows overwriting of existing entries.

See also: XML

Definition at line 294 of file HDF.hpp.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const HDF &	hdf
	)

friend

Output basic info about HDF reader, such as current group and file.

Definition at line 561 of file HDF_fwd.hpp.

Member Data Documentation

◆ file

hid_t mm::HDF::file

private

Currently open file identifier.

Definition at line 79 of file HDF_fwd.hpp.

◆ filename_

std::string mm::HDF::filename_

private

Current file name.

Definition at line 76 of file HDF_fwd.hpp.

◆ group

hid_t mm::HDF::group

private

Currently open group identifier.

Definition at line 80 of file HDF_fwd.hpp.

◆ group_name_

std::string mm::HDF::group_name_

private

Current group name.

Definition at line 77 of file HDF_fwd.hpp.

The documentation for this class was generated from the following files:

include/medusa/bits/io/HDF_fwd.hpp
include/medusa/bits/io/HDF.hpp
include/medusa/bits/io/HDF_Eigen.hpp
src/io/HDF.cpp

Detailed Description

Public Member Functions

Public Types

Classes

Friends

Private Member Functions

Static Private Member Functions

Private Attributes

Member Enumeration Documentation

◆ Mode

Constructor & Destructor Documentation

◆ HDF() [1/2]

◆ HDF() [2/2]

◆ ~HDF()

Member Function Documentation

◆ atomic()

◆ close()

◆ closeFile()

◆ closeGroup()

◆ datasets()

◆ filename()

◆ fileName()

◆ flush()

◆ getFileID()

◆ getGroupID()

◆ groupName()

◆ groups()

◆ isFileOpen()

◆ isGroupOpen()

◆ memberIterateCallback()

◆ members()

◆ open()

◆ openFile()

◆ openFileHelper()

◆ openGroup()

◆ read1DArray()

◆ read2DArray()

◆ read3DArray()

◆ readAttribute()

◆ readBoolAttribute()

◆ readDouble2DArray()

◆ readDouble3DArray()

◆ readDoubleArray()

◆ readDoubleAttribute()

◆ readEigen()

◆ readFloat2DArray()

◆ readFloat3DArray()

◆ readFloatArray()

◆ readFloatAttribute()

◆ readInt2DArray()

◆ readInt3DArray()

◆ readIntArray()

◆ readIntAttribute()

◆ readLinearArray()

◆ readNullTerminatedStringAttribute()

◆ readStringAttribute()

◆ reopen()

◆ reopenFile()

◆ reopenGroup()

◆ setFilename()

◆ setFileName()

◆ setGroupName()

◆ str()

◆ write1DArray()

◆ write2DArray() [1/3]

◆ write2DArray() [2/3]

◆ write2DArray() [3/3]

◆ write3DArray()

◆ writeAttribute()

◆ writeBoolAttribute()

◆ writeDomain()

◆ writeDouble2DArray()

◆ writeDouble3DArray()

◆ writeDoubleArray()

◆ writeDoubleAttribute()

◆ writeEigen()

◆ writeFloat2DArray()

◆ writeFloat3DArray()

◆ writeFloatArray()

◆ writeFloatAttribute()