Obs container class for IODA. More...

#include <ObsSpaceContainer.h>

Inheritance diagram for ioda::ObsSpaceContainer< ContType >:

Collaboration diagram for ioda::ObsSpaceContainer< ContType >:

Classes
struct	by_group

struct	by_variable

struct	VarRecord
	elemental struct of the obs container More...

Public Types
typedef boost::multi_index::index< VarRecord_set, by_variable >::type	VarIndex
	index by variable More...

typedef VarIndex::iterator	VarIter
	variable iterator More...

typedef VarRecord_set::iterator	DbIter
	container iterator More...

Public Member Functions
	ObsSpaceContainer ()

	~ObsSpaceContainer ()

VarIter	var_iter_begin ()

VarIter	var_iter_end ()

std::string	var_iter_vname (VarIter)

std::string	var_iter_gname (VarIter)

std::string	var_iter_mode (VarIter)

std::size_t	var_iter_size (VarIter)

std::vector< std::size_t >	var_iter_shape (VarIter)

DbIter	find (const std::string &, const std::string &) const

DbIter	begin () const

DbIter	end () const

const std::type_info &	dtype (const DbIter) const

const std::type_info &	dtype (const std::string &, const std::string &) const

bool	has (const std::string &group, const std::string &variable) const

std::size_t	nlocs () const
	Return the number of uniqure observation locations on this PE. More...

std::size_t	nvars () const
	Return the number of observational variables. More...

void	LoadFromDb (const std::string &GroupName, const std::string &VarName, const std::vector< std::size_t > &VarShape, std::vector< ContType > &VarData, const std::size_t Start=0, const std::size_t Count=0) const
	load data from the obs container More...

void	StoreToDb (const std::string &GroupName, const std::string &VarName, const std::vector< std::size_t > &VarShape, const std::vector< ContType > &VarData, const bool Append=false)
	store data into the obs container More...

Private Types
using	VarRecord_set = multi_index_container< VarRecord, indexed_by< ordered_unique< composite_key< VarRecord, member< VarRecord, std::string, &VarRecord::group >, member< VarRecord, std::string, &VarRecord::variable > > >, ordered_non_unique< tag< by_group >, member< VarRecord, std::string, &VarRecord::group > >, ordered_non_unique< tag< by_variable >, member< VarRecord, std::string, &VarRecord::variable > > > >
	Multi Index container for obs data. More...

Private Member Functions
void	print (std::ostream &) const
	Print. More...

Static Private Member Functions
static std::size_t	SetSegmentEnd (std::size_t Start, std::size_t Count, std::size_t VarSize)
	set end of vector segment More...

Private Attributes
VarRecord_set	DataContainer
	obs container instance More...

std::size_t	nlocs_
	number of locations on this PE More...

std::size_t	nvars_
	number of observational variables More...

Detailed Description

template<typename ContType>
class ioda::ObsSpaceContainer< ContType >

Obs container class for IODA.

This class provides a container to hold obs data in memory for use by the ObsSpace class. The container is a Boost Multi Index container (header-only implementation from Boost) which essentially creates indexing structures that point to a set of C structs. Each structure holds the keys that identify that structure and the data the are associated with those keys. There are two keys, group and variable, which identify each struct. The group corresponds to collections of variables such as "ObsValue", "ObsError", "PreQC" and "MetaData". The variables are individual quantities such as "air_temperature" and "brightness_temperature".

Author: Xin Zhang (JCSDA)

Definition at line 64 of file src/core/ObsSpaceContainer.h.

Member Typedef Documentation

◆ DbIter

template<typename ContType >

typedef VarRecord_set::iterator ioda::ObsSpaceContainer< ContType >::DbIter

container iterator

This typedef defines an iterator that can walk through the obs container using the primary indexing (by group and variable).

Definition at line 185 of file src/core/ObsSpaceContainer.h.

◆ VarIndex

template<typename ContType >

typedef boost::multi_index::index<VarRecord_set, by_variable>::type ioda::ObsSpaceContainer< ContType >::VarIndex

index by variable

This typedef defines the index mechanism that allows access to the obs container through the secondary indexing by variable.

Definition at line 169 of file src/core/ObsSpaceContainer.h.

◆ VarIter

template<typename ContType >

typedef VarIndex::iterator ioda::ObsSpaceContainer< ContType >::VarIter

variable iterator

This typedef defines an iterator that can walk through the obs container by variable. It utilizes the secondary indexing by variable.

Definition at line 177 of file src/core/ObsSpaceContainer.h.

◆ VarRecord_set

template<typename ContType >

using ioda::ObsSpaceContainer< ContType >::VarRecord_set = multi_index_container< VarRecord, indexed_by< ordered_unique< composite_key< VarRecord, member<VarRecord, std::string, &VarRecord::group>, member<VarRecord, std::string, &VarRecord::variable> > >, ordered_non_unique< tag<by_group>, member<VarRecord, std::string, &VarRecord::group> >, ordered_non_unique< tag<by_variable>, member<VarRecord, std::string, &VarRecord::variable> > > >

private

Multi Index container for obs data.

This typedef defines the indexing structure of the obs data container. The primary index is a composite key (tuple) consisting of the group and variable names. The iterator of the container itself uses this primary index, as well as the typical container methods such as find and insert. Two more secondary indexes are provided, one by group and the other by variable. These secondary indexes have their own iterators associated with them. See the boost::multiindex documentation for more details.

Definition at line 134 of file src/core/ObsSpaceContainer.h.

Constructor & Destructor Documentation

◆ ObsSpaceContainer()

template<typename ContType >

ioda::ObsSpaceContainer< ContType >::ObsSpaceContainer

Definition at line 241 of file src/core/ObsSpaceContainer.h.

◆ ~ObsSpaceContainer()

template<typename ContType >

ioda::ObsSpaceContainer< ContType >::~ObsSpaceContainer

Definition at line 248 of file src/core/ObsSpaceContainer.h.

Member Function Documentation

◆ begin()

template<typename ContType >

ObsSpaceContainer< ContType >::DbIter ioda::ObsSpaceContainer< ContType >::begin

This method returns the begin iterator for the obs container.

Definition at line 422 of file src/core/ObsSpaceContainer.h.

◆ dtype() [1/2]

template<typename ContType >

const std::type_info & ioda::ObsSpaceContainer< ContType >::dtype ( const DbIter Idb ) const

This method returns the data type associated with the obs container entry pointed to by Idb.

Parameters

[in] Idb Iterator pointing to the current element of the obs container.

Definition at line 446 of file src/core/ObsSpaceContainer.h.

◆ dtype() [2/2]

template<typename ContType >

const std::type_info & ioda::ObsSpaceContainer< ContType >::dtype	(	const std::string &	group,
		const std::string &	variable
	)		const

This method returns the data type associated with the obs container entry defined by the given group and variable. If the entry does not exist, the typeid for void is returned.

Parameters

[in]	group	Name of obs container group
[in]	variable	Name of obs container variable

Definition at line 461 of file src/core/ObsSpaceContainer.h.

◆ end()

template<typename ContType >

ObsSpaceContainer< ContType >::DbIter ioda::ObsSpaceContainer< ContType >::end

This method returns the end iterator for the obs container.

Definition at line 433 of file src/core/ObsSpaceContainer.h.

◆ find()

template<typename ContType >

ObsSpaceContainer< ContType >::DbIter ioda::ObsSpaceContainer< ContType >::find	(	const std::string &	group,
		const std::string &	variable
	)		const

This method returns an obs container iterator that indicates if the given group, variable entry exists. If the entry exists, then the iterator value that is returned will point to that entry. Otherwise, the iterator is set to the end() value to indicate the entry does is not found.

Parameters

[in]	group	Name of obs container group
[in]	variable	Name of obs container variable

Definition at line 409 of file src/core/ObsSpaceContainer.h.

◆ has()

template<typename ContType >

bool ioda::ObsSpaceContainer< ContType >::has	(	const std::string &	group,
		const std::string &	variable
	)		const

This method returns a boolean that indicates if the given group, variable entry exists in the obs container. If the entry exists, then "true" is returned. Otherwise, "false" is returned.

Parameters

[in]	group	Name of obs container group
[in]	variable	Name of obs container variable

Definition at line 553 of file src/core/ObsSpaceContainer.h.

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◆ LoadFromDb()

template<typename ContType >

void ioda::ObsSpaceContainer< ContType >::LoadFromDb	(	const std::string &	GroupName,
		const std::string &	VarName,
		const std::vector< std::size_t > &	VarShape,
		std::vector< ContType > &	VarData,
		const std::size_t	Start = `0`,
		const std::size_t	Count = `0`
	)		const

load data from the obs container

This method transfers data from the obs container to the caller's memory. The caller needs to allocate the memory that the VarData parameter points to. This method handles the lookup of the container group, variable entry, and checking that the data type in the container matches that of the VarData parameter.

Parameters

[in]	GroupName	Name of container group (ObsValue, ObsError, MetaData, etc.)
[in]	VarName	Name of container variable
[in]	VarShape	Dimension sizes of variable
[in]	VarData	Pointer to memory that will loaded from the container.

Definition at line 317 of file src/core/ObsSpaceContainer.h.

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◆ nlocs()

template<typename ContType >

std::size_t ioda::ObsSpaceContainer< ContType >::nlocs ( ) const

inline

Return the number of uniqure observation locations on this PE.

Definition at line 206 of file src/core/ObsSpaceContainer.h.

◆ nvars()

template<typename ContType >

std::size_t ioda::ObsSpaceContainer< ContType >::nvars ( ) const

inline

Return the number of observational variables.

Definition at line 209 of file src/core/ObsSpaceContainer.h.

◆ print()

template<typename ContType >

void ioda::ObsSpaceContainer< ContType >::print ( std::ostream & os ) const

private

Print.

print method for Printable base class

This method provides a print routine so that the obs container can be used in an output stream. A list of all group, variable combinations present in the obs container is printed out.

Definition at line 568 of file src/core/ObsSpaceContainer.h.

◆ SetSegmentEnd()

template<typename ContType >

std::size_t ioda::ObsSpaceContainer< ContType >::SetSegmentEnd	(	std::size_t	Start,
		std::size_t	Count,
		std::size_t	VarSize
	)

staticprivate

set end of vector segment

This method returns the ending index for the vector segment given the start and count values.

Definition at line 351 of file src/core/ObsSpaceContainer.h.

◆ StoreToDb()

template<typename ContType >

void ioda::ObsSpaceContainer< ContType >::StoreToDb	(	const std::string &	GroupName,
		const std::string &	VarName,
		const std::vector< std::size_t > &	VarShape,
		const std::vector< ContType > &	VarData,
		const bool	Append = `false`
	)

store data into the obs container

This method transfers data from the caller's memory into the obs conatiner. The caller needs to allocate and assign the memory that the VarData parameter points to. This method also handles checking that the varible has write permission if it already exists in the obs container.

Parameters

[in]	GroupName	Name of container group (ObsValue, ObsError, MetaData, etc.)
[in]	VarName	Name of container variable
[in]	VarShape	Dimension sizes of variable
[in]	VarData	Pointer to memory that will be stored in the container

Definition at line 268 of file src/core/ObsSpaceContainer.h.

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◆ var_iter_begin()

template<typename ContType >

ObsSpaceContainer< ContType >::VarIter ioda::ObsSpaceContainer< ContType >::var_iter_begin

This method returns the begin iterator for access by variable in the obs container.

Definition at line 377 of file src/core/ObsSpaceContainer.h.

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◆ var_iter_end()

template<typename ContType >

ObsSpaceContainer< ContType >::VarIter ioda::ObsSpaceContainer< ContType >::var_iter_end

This method returns the end iterator for access by variable in the obs container.

Definition at line 390 of file src/core/ObsSpaceContainer.h.

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◆ var_iter_gname()

template<typename ContType >

std::string ioda::ObsSpaceContainer< ContType >::var_iter_gname ( VarIter )

This method returns the group name associated with the obs container entry pointed to by var_iter.

Parameters

[in] var_iter Iterator of the indexing by variable type.

Definition at line 494 of file src/core/ObsSpaceContainer.h.

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◆ var_iter_mode()

template<typename ContType >

std::string ioda::ObsSpaceContainer< ContType >::var_iter_mode ( VarIter )

This method returns the access mode associated with the obs container entry pointed to by var_iter.

Parameters

[in] var_iter Iterator of the indexing by variable type.

Definition at line 508 of file src/core/ObsSpaceContainer.h.

◆ var_iter_shape()

template<typename ContType >

std::vector< std::size_t > ioda::ObsSpaceContainer< ContType >::var_iter_shape ( VarIter )

This method returns the data shape associated with the obs container entry pointed to by var_iter.

Parameters

[in] var_iter Iterator of the indexing by variable type.

Definition at line 536 of file src/core/ObsSpaceContainer.h.

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◆ var_iter_size()

template<typename ContType >

std::size_t ioda::ObsSpaceContainer< ContType >::var_iter_size ( VarIter )

This method returns the data size associated with the obs container entry pointed to by var_iter.

Parameters

[in] var_iter Iterator of the indexing by variable type.

Definition at line 522 of file src/core/ObsSpaceContainer.h.

◆ var_iter_vname()

template<typename ContType >

std::string ioda::ObsSpaceContainer< ContType >::var_iter_vname ( VarIter )

This method returns the variable name associated with the obs container entry pointed to by var_iter.

Parameters

[in] var_iter Iterator of the indexing by variable type.

Definition at line 480 of file src/core/ObsSpaceContainer.h.

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Member Data Documentation

◆ DataContainer

template<typename ContType >

VarRecord_set ioda::ObsSpaceContainer< ContType >::DataContainer

private

obs container instance

Definition at line 226 of file src/core/ObsSpaceContainer.h.

◆ nlocs_

template<typename ContType >

std::size_t ioda::ObsSpaceContainer< ContType >::nlocs_

private

number of locations on this PE

Definition at line 229 of file src/core/ObsSpaceContainer.h.

◆ nvars_

template<typename ContType >

std::size_t ioda::ObsSpaceContainer< ContType >::nvars_

private

number of observational variables

Definition at line 232 of file src/core/ObsSpaceContainer.h.

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

src/core/ObsSpaceContainer.h

Classes

Public Types

Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

template<typename ContType> class ioda::ObsSpaceContainer< ContType >

Member Typedef Documentation

◆ DbIter

◆ VarIndex

◆ VarIter

◆ VarRecord_set

Constructor & Destructor Documentation

◆ ObsSpaceContainer()

◆ ~ObsSpaceContainer()

Member Function Documentation

◆ begin()

◆ dtype() [1/2]

◆ dtype() [2/2]

◆ end()

◆ find()

◆ has()

◆ LoadFromDb()

◆ nlocs()

◆ nvars()

◆ print()

◆ SetSegmentEnd()

◆ StoreToDb()

◆ var_iter_begin()

◆ var_iter_end()

◆ var_iter_gname()

◆ var_iter_mode()

◆ var_iter_shape()

◆ var_iter_size()

◆ var_iter_vname()

Member Data Documentation

◆ DataContainer

◆ nlocs_

◆ nvars_

template<typename ContType>
class ioda::ObsSpaceContainer< ContType >