Wrapper class for dealing with output to matlab. More...

#include <wrapper_o_hdf.h>

Inheritance diagram for utilities::Wrapper_o_hdf:

Collaboration diagram for utilities::Wrapper_o_hdf:

Public Types
enum	FILE_T { APPEND_FILE =0, NEW_FILE, NEW_FILE_OVR, FILL_FILE }

typedef enum utilities::Wrapper_o_hdf::FILE_T	FILE_T

Public Member Functions
	Wrapper_o_hdf (const std::string &file_name, const std::set< D_TYPE > &d_add, int comp_number, Wrapper_o_hdf::FILE_T file_type, const std::string &group_prefix="frame")
	Constructor. More...

void	initialize_wrapper ()
	preforms any initialization that needs to be done the logic for this is to not needlessly open and close files, or creat matlab arrays if they arn't going to be used. More...

void	open_group (int, int, int)
	Opens a group to put particles into. More...

void	set_all_values (const tracking::particle *)
	sets all of the values that the wrapper knows about by asking the particle More...

void	set_all_values (const tracking::Track_box *, const utilities::Tuple< float, 3 > &)
	sets all of the values that the wrapper knows about by asking the particle. More...

void	set_value (D_TYPE, const tracking::particle *)

void	add_meta_store (const Md_store *md_in)
	Adds all the meta data in a Md_store object. More...

void	close_group ()
	Closes the currently open group. More...

void	finalize_wrapper ()
	Performs any clean up. More...

void	print () const

int	num_entries () const

const std::set< D_TYPE > &	get_content_tpyes () const
	Returns a set containing the D_TYPES that the wrapper can cope with. More...

void	add_meta_data (const std::string &key, float val)
	Adds a float meta-data. More...

void	add_meta_data (const std::string &key, const Tuple< float, 2 > &val)
	Adds a Pair meta-data. More...

void	add_meta_data (const std::string &key, const Tuple< float, 3 > &val)
	Adds a Triple meta-data. More...

void	add_meta_data (const std::string &key, const std::string &val)
	Adds a string meta-data. More...

void	add_meta_data (const std::string &key, int val)
	Adds an integer meta-data. More...

void	add_meta_data_root (const std::string &key, float val)
	Adds a float meta-data. More...

void	add_meta_data_root (const std::string &key, const Tuple< float, 2 > &val)
	Adds a Pair meta-data. More...

void	add_meta_data_root (const std::string &key, const Tuple< float, 3 > &val)
	Adds a Triple meta-data. More...

void	add_meta_data_root (const std::string &key, const std::string &val)
	Adds a string meta-data. More...

void	add_meta_data_root (const std::string &key, int val)
	Adds an integer meta-data. More...

void	add_meta_data_comp (const std::string &key, float val)
	Adds a float meta-data. More...

void	add_meta_data_comp (const std::string &key, const Tuple< float, 2 > &val)
	Adds a Pair meta-data. More...

void	add_meta_data_comp (const std::string &key, const Tuple< float, 3 > &val)
	Adds a Triple meta-data. More...

void	add_meta_data_comp (const std::string &key, const std::string &val)
	Adds a string meta-data. More...

void	add_meta_data_comp (const std::string &key, int val)
	Adds an integer meta-data. More...

void	add_meta_data (const std::string &key, float val, D_TYPE dset_type)
	Adds metadata for datasets. More...

void	add_meta_data (const std::string &key, const Tuple< float, 2 > &val, D_TYPE dset_type)
	Adds a Pair meta-data for a data set. More...

void	add_meta_data (const std::string &key, const Tuple< float, 3 > &val, D_TYPE dset_type)
	Adds a Triple meta-data for a data set. More...

void	add_meta_data (const std::string &key, const std::string &val, D_TYPE dset_type)
	Adds a string meta-data for a data set. More...

void	add_meta_data (const std::string &key, int val, D_TYPE dset_type)
	Adds an integer meta-data for a data set. More...

void	add_meta_data_list (const Read_config &, const std::set< D_TYPE > &)
	Adds all parameters from the Read_config object to the data sets in the set. More...

	~Wrapper_o_hdf ()

Private Member Functions
std::string	format_name_ (int in) const
	formats group names More...

Private Attributes
int	part_count_
	Count of the number of particles that have been added. More...

bool	wrapper_open_
	if the wrapper is 'open' to get additional particles More...

bool	group_open_
	if there is a 'open' group More...

int	group_index_
	index of current group More...

bool	new_indexing_
	Parameter to control behavior of indexing. More...

Wrapper_o_hdf::FILE_T	file_type_
	Parameter to control file creation and over writing. More...

H5::H5File *	file_
	Pointer to hdf file. More...

std::string	file_name_
	file name More...

std::string	group_name_
	name of currently open group More...

std::set< D_TYPE >	d_types_add_
	A set of the data types that are to be added to the file. More...

std::set< D_TYPE >	d_types_check_
	A set of the data types to be checked to make sure there isn't a mismatch. More...

std::set< D_TYPE >	d_types_already_
	The set of data that the file already contains. More...

std::string	group_prefix_
	prefix for use in formatting the group name More...

Wrapper_o_hdf_group *	current_group_
	object for current group More...

int	comp_number_
	computation number More...

H5::Group *	dset_pram_group_

Static Private Attributes
static const int	format_padding_ = 6
	the number if digits in the formatted group name More...

Detailed Description

Wrapper class for dealing with output to matlab.

Member Typedef Documentation

typedef enum utilities::Wrapper_o_hdf::FILE_T utilities::Wrapper_o_hdf::FILE_T

Member Enumeration Documentation

enum utilities::Wrapper_o_hdf::FILE_T

Enumerator
APPEND_FILE
NEW_FILE
NEW_FILE_OVR
FILL_FILE

Constructor & Destructor Documentation

Wrapper_o_hdf::Wrapper_o_hdf	(	const std::string &	file_name,
		const std::set< D_TYPE > &	d_add,
		int	comp_number,
		Wrapper_o_hdf::FILE_T	file_type,
		const std::string &	group_prefix = `"frame"`
	)

Constructor.

Parameters

file_name	full name of the file to open
d_add	a set of the data types to add
group_prefix	the prefix used for building group names
file_type	Enum to control if a new file is created, indexing, etc
comp_number	the computation number to use during name clashes

References APPEND_FILE, file_type_, and new_indexing_.

Wrapper_o_hdf::~Wrapper_o_hdf ( )

References finalize_wrapper().

Member Function Documentation

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		float	val
	)

virtual

Adds a float meta-data.

Implements utilities::Wrapper_out.

References current_group_, group_open_, and local_add_meta_data().

Referenced by add_meta_data_list(), and main().

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		const Tuple< float, 2 > &	val
	)

virtual

Adds a Pair meta-data.

Implements utilities::Wrapper_out.

References current_group_, group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		const Tuple< float, 3 > &	val
	)

virtual

Adds a Triple meta-data.

Implements utilities::Wrapper_out.

References current_group_, group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		const std::string &	val
	)

virtual

Adds a string meta-data.

Implements utilities::Wrapper_out.

References current_group_, group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		int	val
	)

virtual

Adds an integer meta-data.

Implements utilities::Wrapper_out.

References current_group_, group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		float	val,
		D_TYPE	dset_type
	)

virtual

Adds metadata for datasets.

Adds a float meta-data for a data set

Implements utilities::Wrapper_out.

References comp_number_, dset_pram_group_, local_add_meta(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		const Tuple< float, 2 > &	val,
		D_TYPE	dset_type
	)

virtual

Adds a Pair meta-data for a data set.

Implements utilities::Wrapper_out.

References comp_number_, dset_pram_group_, local_add_meta(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		const Tuple< float, 3 > &	val,
		D_TYPE	dset_type
	)

virtual

Adds a Triple meta-data for a data set.

Implements utilities::Wrapper_out.

References comp_number_, dset_pram_group_, local_add_meta(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		const std::string &	val,
		D_TYPE	dset_type
	)

virtual

Adds a string meta-data for a data set.

Implements utilities::Wrapper_out.

References comp_number_, dset_pram_group_, local_add_meta(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data	(	const std::string &	key,
		int	val,
		D_TYPE	dset_type
	)

virtual

Adds an integer meta-data for a data set.

Implements utilities::Wrapper_out.

References comp_number_, dset_pram_group_, local_add_meta(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data_comp	(	const std::string &	key,
		float	val
	)

virtual

Adds a float meta-data.

Implements utilities::Wrapper_out.

References comp_number_, current_group_, utilities::format_name(), group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data_comp	(	const std::string &	key,
		const Tuple< float, 2 > &	val
	)

virtual

Adds a Pair meta-data.

Implements utilities::Wrapper_out.

References comp_number_, current_group_, utilities::format_name(), group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data_comp	(	const std::string &	key,
		const Tuple< float, 3 > &	val
	)

virtual

Adds a Triple meta-data.

Implements utilities::Wrapper_out.

References comp_number_, current_group_, utilities::format_name(), group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data_comp	(	const std::string &	key,
		const std::string &	val
	)

virtual

Adds a string meta-data.

Implements utilities::Wrapper_out.

References comp_number_, current_group_, utilities::format_name(), group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data_comp	(	const std::string &	key,
		int	val
	)

virtual

Adds an integer meta-data.

Implements utilities::Wrapper_out.

References comp_number_, current_group_, utilities::format_name(), group_open_, and local_add_meta_data().

void Wrapper_o_hdf::add_meta_data_list	(	const Read_config &	,
		const std::set< D_TYPE > &
	)

virtual

Adds all parameters from the Read_config object to the data sets in the set.

Implements utilities::Wrapper_out.

References add_meta_data(), utilities::Read_config::get_key(), utilities::Read_config::get_type(), utilities::Read_config::get_value(), utilities::Read_config::size(), utilities::V_FLOAT, utilities::V_INT, utilities::V_STRING, and utilities::VT2str_s().

Referenced by main().

void Wrapper_o_hdf::add_meta_data_root	(	const std::string &	key,
		float	val
	)

virtual

Adds a float meta-data.

Implements utilities::Wrapper_out.

References file_, local_add_meta_data_root(), and wrapper_open_.

Referenced by initialize_wrapper().

void Wrapper_o_hdf::add_meta_data_root	(	const std::string &	key,
		const Tuple< float, 2 > &	val
	)

virtual

Adds a Pair meta-data.

Implements utilities::Wrapper_out.

References file_, local_add_meta_data_root(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data_root	(	const std::string &	key,
		const Tuple< float, 3 > &	val
	)

virtual

Adds a Triple meta-data.

Implements utilities::Wrapper_out.

References file_, local_add_meta_data_root(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data_root	(	const std::string &	key,
		const std::string &	val
	)

virtual

Adds a string meta-data.

Implements utilities::Wrapper_out.

References file_, local_add_meta_data_root(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_data_root	(	const std::string &	key,
		int	val
	)

virtual

Adds an integer meta-data.

Implements utilities::Wrapper_out.

References file_, local_add_meta_data_root(), and wrapper_open_.

void Wrapper_o_hdf::add_meta_store ( const Md_store * md_in)

virtual

Adds all the meta data in a Md_store object.

Implements utilities::Wrapper_out.

References utilities::Wrapper_o_hdf_group::add_meta_store(), and current_group_.

void Wrapper_o_hdf::close_group ( )

virtual

Closes the currently open group.

Throws an error if there is no open group.

Implements utilities::Wrapper_out.

References current_group_, group_open_, and utilities::Wrapper_o_hdf_group::write_to_disk().

Referenced by finalize_wrapper().

void Wrapper_o_hdf::finalize_wrapper ( )

virtual

Performs any clean up.

that needs to be done such as closing a file

Implements utilities::Wrapper_out.

References close_group(), dset_pram_group_, file_, group_open_, and wrapper_open_.

Referenced by main(), and ~Wrapper_o_hdf().

string Wrapper_o_hdf::format_name_ ( int in) const

private

formats group names

References format_padding_, and group_prefix_.

Referenced by open_group().

const set< D_TYPE > & Wrapper_o_hdf::get_content_tpyes ( ) const

virtual

Returns a set containing the D_TYPES that the wrapper can cope with.

Implements utilities::Wrapper_out.

References d_types_add_.

void Wrapper_o_hdf::initialize_wrapper ( )

virtual

preforms any initialization that needs to be done the logic for this is to not needlessly open and close files, or creat matlab arrays if they arn't going to be used.

It also allows the wrapper object to be reused (ie, do all the processing, output one subset of data to one place, and another subset to another place

Implements utilities::Wrapper_out.

References add_meta_data_root(), APPEND_FILE, comp_number_, d_types_add_, dset_pram_group_, file_, file_name_, file_type_, FILL_FILE, utilities::format_dset_name(), NEW_FILE, NEW_FILE_OVR, and wrapper_open_.

Referenced by main().

int utilities::Wrapper_o_hdf::num_entries ( ) const

inline

void Wrapper_o_hdf::open_group	(	int	group,
		int	p_count,
		int	wrapper_size
	)

virtual

Opens a group to put particles into.

Parameters

group	the index of the group to be opened
p_count	the number of particles to expect
wrapper_size	the size of the group of the underlying wrapper, if <0, then set equal to p_count

Implements utilities::Wrapper_out.

References APPEND_FILE, utilities::Wrapper_o_hdf_group::APPEND_GROUP, comp_number_, current_group_, d_types_add_, utilities::Wrapper_o_hdf_group::ERROR, file_, file_type_, FILL_FILE, utilities::Wrapper_o_hdf_group::FILL_GROUP, format_name_(), group_open_, NEW_FILE, NEW_FILE_OVR, utilities::Wrapper_o_hdf_group::NEW_GROUP, and wrapper_open_.