#include <Has_Variables.h>

Inheritance diagram for ioda::detail::Has_Variables_Base:

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Public Member Functions
virtual	~Has_Variables_Base ()

virtual void	setLayout (std::shared_ptr< const detail::DataLayoutPolicy >)

virtual Type_Provider *	getTypeProvider () const
	Query the backend and get the type provider. More...

virtual FillValuePolicy	getFillValuePolicy () const
	Get the fill value policy used for Variables within this Group. More...

General Functions
virtual bool	exists (const std::string &name) const
	Does a Variable with the specified name exist? More...

virtual void	remove (const std::string &name)
	Delete an Attribute with the specified name. More...

virtual Variable	open (const std::string &name) const
	Open a Variable by name. More...

Variable	operator[] (const std::string &name) const
	Open a Variable by name. More...

virtual std::vector< std::string >	list () const

std::vector< std::string >	operator() () const

void	stitchComplementaryVariables (bool removeOriginals=true)
	Combines all complementary variables as specified in the mapping file, opens them, and optionally removes the originals from the ObsGroup. More...

void	convertVariableUnits (std::ostream &out=std::cerr)
	Converts unit to SI for all eligible variables. If conversion function not defined, stores unit as attribute. More...

virtual Variable	create (const std::string &name, const Type &in_memory_dataType, const std::vector< Dimensions_t > &dimensions={1}, const std::vector< Dimensions_t > &max_dimensions={}, const VariableCreationParameters &params=VariableCreationParameters())
	Create a Variable without setting its data. More...

Variable	_create_py (const std::string &name, BasicTypes dataType, const std::vector< Dimensions_t > &cur_dimensions={1}, const std::vector< Dimensions_t > &max_dimensions={}, const std::vector< Variable > &dimension_scales={}, const VariableCreationParameters &params=VariableCreationParameters())

Variable	create (const std::string &name, const Type &in_memory_dataType, const ioda::Dimensions &dims, const VariableCreationParameters &params=VariableCreationParameters())

template<class DataType >
Variable	create (const std::string &name, const std::vector< Dimensions_t > &dimensions={1}, const std::vector< Dimensions_t > &max_dimensions={}, const VariableCreationParameters &params=VariableCreationParameters::defaulted< DataType >())
	Create a Variable without setting its data. More...

template<class DataType >
Variable	create (const std::string &name, const ioda::Dimensions &dims, const VariableCreationParameters &params=VariableCreationParameters::defaulted< DataType >())

template<class DataType >
Variable	createWithScales (const std::string &name, const std::vector< Variable > &dimension_scales, const VariableCreationParameters &params=VariableCreationParameters::defaulted< DataType >())
	Convenience function to create a Variable from certain dimension scales. More...

void	createWithScales (const NewVariables_t &newvars)
	Collective function optimized to mass-construct variables and attach scales. More...

Collective functions
These functions apply the an operation to a set of variables in situations where such an operation would produce better performance results than a loop of serial function calls.
virtual void	attachDimensionScales (const std::vector< std::pair< Variable, std::vector< Variable >>> &mapping)
	Attach dimension scales to many Dimension Numbers in a set of Variables. More...

Protected Member Functions
	Has_Variables_Base (std::shared_ptr< Has_Variables_Backend >, std::shared_ptr< const DataLayoutPolicy >=nullptr)

Private Member Functions
ComplementaryVariableCreationParameters	createDerivedVariableParameters (const std::string &inputName, const std::string &outputName, size_t position)

std::vector< std::vector< std::string > >	loadComponentVariableData (const ComplementaryVariableCreationParameters &derivedVariableParams)

Static Private Member Functions
static void	_py_fvp_helper (BasicTypes dataType, FillValuePolicy &fvp, VariableCreationParameters &params)
	FillValuePolicy helper. More...

Private Attributes
std::shared_ptr< Has_Variables_Backend >	backend_
	Using an opaque object to implement the backend. More...

std::shared_ptr< const detail::DataLayoutPolicy >	layout_
	Set by ObsGroup. More...

std::vector< ComplementaryVariableCreationParameters >	complementaryVariables_

Detailed Description

Definition at line 199 of file Has_Variables.h.

Constructor & Destructor Documentation

◆ Has_Variables_Base()

ioda::detail::Has_Variables_Base::Has_Variables_Base	(	std::shared_ptr< Has_Variables_Backend >	b,
		std::shared_ptr< const DataLayoutPolicy >	layoutPolicy = `nullptr`
	)

protected

Definition at line 22 of file Has_Variables.cpp.

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◆ ~Has_Variables_Base()

ioda::detail::Has_Variables_Base::~Has_Variables_Base ( )

virtualdefault

Member Function Documentation

◆ _create_py()

Variable ioda::detail::Has_Variables_Base::_create_py	(	const std::string &	name,
		BasicTypes	dataType,
		const std::vector< Dimensions_t > &	cur_dimensions = `{1}`,
		const std::vector< Dimensions_t > &	max_dimensions = `{}`,
		const std::vector< Variable > &	dimension_scales = `{}`,
		const VariableCreationParameters &	params = `VariableCreationParameters()`
	)

Python compatability function

Note: Multiple ways to specify dimensions to match possible Python function signatures.

Todo:: Extend collective variable creation interface to Python.

Definition at line 261 of file Has_Variables.cpp.

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◆ _py_fvp_helper()

void ioda::detail::Has_Variables_Base::_py_fvp_helper	(	BasicTypes	dataType,
		FillValuePolicy &	fvp,
		VariableCreationParameters &	params
	)

staticprivate

FillValuePolicy helper.

Hides the template function calls, so that the headers are smaller.

Definition at line 301 of file Has_Variables.cpp.

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◆ attachDimensionScales()

void ioda::detail::Has_Variables_Base::attachDimensionScales ( const std::vector< std::pair< Variable, std::vector< Variable >>> & mapping )

virtual

Attach dimension scales to many Dimension Numbers in a set of Variables.

Parameters

DimensionNumber
mapping	is the scale mappings for each variable. The first part of the pair refers to the variable that you are attaching scales to. The second part is a sequence of scales that are attached along each dimension (indexed by the vector).

For some backends, particularly HDF5, attaching a dimension scale to a variable is a slow procedure when you have many variables. This function batches low-level calls and avoids loops.

Reimplemented in ioda::detail::Has_Variables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 335 of file Has_Variables.cpp.

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◆ convertVariableUnits()

void ioda::detail::Has_Variables_Base::convertVariableUnits ( std::ostream & out = std::cerr )

Converts unit to SI for all eligible variables. If conversion function not defined, stores unit as attribute.

Makes the conversion if the variable's unit is defined in the mapping file and the unit conversion is defined in UnitConversions.h.

Definition at line 177 of file Has_Variables.cpp.

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◆ create() [1/4]

template<class DataType >

Variable ioda::detail::Has_Variables_Base::create	(	const std::string &	name,
		const ioda::Dimensions &	dims,
		const VariableCreationParameters &	params = `VariableCreationParameters::defaulted<DataType>()`
	)

inline

Definition at line 332 of file Has_Variables.h.

◆ create() [2/4]

template<class DataType >

Variable ioda::detail::Has_Variables_Base::create	(	const std::string &	name,
		const std::vector< Dimensions_t > &	dimensions = `{1}`,
		const std::vector< Dimensions_t > &	max_dimensions = `{}`,
		const VariableCreationParameters &	params = `VariableCreationParameters::defaulted<DataType>()`
	)

inline

Create a Variable without setting its data.

Template Parameters

DataType is the type of the data. I.e. float, int32_t, uint16_t, std::string, etc.

Parameters

name	is the name of the Variable.
dimensions	is a vector representing the size of the metadata. Each element of the vector is a dimension with a certain size.

Returns: A Variable that can be written to.

Definition at line 316 of file Has_Variables.h.

◆ create() [3/4]

Variable ioda::detail::Has_Variables_Base::create	(	const std::string &	name,
		const Type &	in_memory_dataType,
		const ioda::Dimensions &	dims,
		const VariableCreationParameters &	params = `VariableCreationParameters()`
	)

inline

Definition at line 303 of file Has_Variables.h.

◆ create() [4/4]

Variable ioda::detail::Has_Variables_Base::create	(	const std::string &	name,
		const Type &	in_memory_dataType,
		const std::vector< Dimensions_t > &	dimensions = `{1}`,
		const std::vector< Dimensions_t > &	max_dimensions = `{}`,
		const VariableCreationParameters &	params = `VariableCreationParameters()`
	)

virtual

Create a Variable without setting its data.

Parameters

attrname	is the name of the Variable.
dimensions	is a vector representing the size of the metadata. Each element of the vector is a dimension with a certain size.
in_memory_datatype	is the runtime description of the Attribute's data type.

Returns: A Variable that can be written to.

Reimplemented in ioda::Engines::ObsStore::ObsStore_HasVariables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 362 of file Has_Variables.cpp.

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◆ createDerivedVariableParameters()

ComplementaryVariableCreationParameters ioda::detail::Has_Variables_Base::createDerivedVariableParameters	(	const std::string &	inputName,
		const std::string &	outputName,
		size_t	position
	)

private

Definition at line 208 of file Has_Variables.cpp.

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◆ createWithScales() [1/2]

void ioda::detail::Has_Variables_Base::createWithScales ( const NewVariables_t & newvars )

Collective function optimized to mass-construct variables and attach scales.

Parameters

newvars is a vector of the new variables to be created.

See also: NewVariable for the signature of the objects to add.

Definition at line 392 of file Has_Variables.cpp.

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◆ createWithScales() [2/2]

template<class DataType >

Variable ioda::detail::Has_Variables_Base::createWithScales	(	const std::string &	name,
		const std::vector< Variable > &	dimension_scales,
		const VariableCreationParameters &	params = `VariableCreationParameters::defaulted<DataType>()`
	)

inline

Convenience function to create a Variable from certain dimension scales.

Template Parameters

DataType is the type of the data. I.e. int, int32_t, uint16_t, std::string, etc.

Parameters

name	is the name of the Variable.
dimensions	is a vector representing the size of the metadata. Each element of the vector is a dimension with a certain size.

Returns: A Variable that can be written to.

Definition at line 351 of file Has_Variables.h.

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◆ exists()

bool ioda::detail::Has_Variables_Base::exists ( const std::string & name ) const

virtual

Does a Variable with the specified name exist?

Parameters

name	is the name of the Variable that we are looking for.

Returns: true if it exists.; false otherwise.

Reimplemented in ioda::Engines::ObsStore::ObsStore_HasVariables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 70 of file Has_Variables.cpp.

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◆ getFillValuePolicy()

FillValuePolicy ioda::detail::Has_Variables_Base::getFillValuePolicy ( ) const

virtual

Get the fill value policy used for Variables within this Group.

The backend has to be consulted for this operation. Storage of this policy is backend-dependent.

Reimplemented in ioda::detail::Has_Variables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 42 of file Has_Variables.cpp.

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◆ getTypeProvider()

Type_Provider * ioda::detail::Has_Variables_Base::getTypeProvider ( ) const

virtual

Query the backend and get the type provider.

Reimplemented in ioda::Engines::ObsStore::ObsStore_HasVariables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 58 of file Has_Variables.cpp.

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◆ list()

std::vector< std::string > ioda::detail::Has_Variables_Base::list ( ) const

virtual

List all Variables under this group (one-level search).

See also: Group_Base::listObjects if you need to enumerate both Groups and Variables, or if you need recursion.

Reimplemented in ioda::Engines::ObsStore::ObsStore_HasVariables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 248 of file Has_Variables.cpp.

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◆ loadComponentVariableData()

std::vector< std::vector< std::string > > ioda::detail::Has_Variables_Base::loadComponentVariableData ( const ComplementaryVariableCreationParameters & derivedVariableParams )

private

Definition at line 228 of file Has_Variables.cpp.

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◆ open()

Variable ioda::detail::Has_Variables_Base::open ( const std::string & name ) const

virtual

Open a Variable by name.

Parameters

name	is the name of the Variable to be opened.

Returns: An instance of a Variable that can be queried (with getDimensions()) and read.

Reimplemented in ioda::Engines::ObsStore::ObsStore_HasVariables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 98 of file Has_Variables.cpp.

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◆ operator()()

std::vector<std::string> ioda::detail::Has_Variables_Base::operator() ( ) const

inline

Convenience function to list all Variables under this group (one-level search).

See also: Group_Base::listObjects if you need to enumerate both Groups and Variables, or if you need recursion.

Definition at line 265 of file Has_Variables.h.

◆ operator[]()

Variable ioda::detail::Has_Variables_Base::operator[] ( const std::string & name ) const

inline

Open a Variable by name.

Parameters

name	is the name of the Variable to be opened.

Returns: An instance of a Variable that can be queried (with getDimensions()) and read.

Definition at line 256 of file Has_Variables.h.

◆ remove()

void ioda::detail::Has_Variables_Base::remove ( const std::string & name )

virtual

Delete an Attribute with the specified name.

Parameters

attname is the name of the Variable that we are deleting.

Exceptions

jedi::xError if no such attribute exists.

Reimplemented in ioda::Engines::ObsStore::ObsStore_HasVariables_Backend, and ioda::detail::Engines::HH::HH_HasVariables.

Definition at line 84 of file Has_Variables.cpp.

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◆ setLayout()

void ioda::detail::Has_Variables_Base::setLayout ( std::shared_ptr< const detail::DataLayoutPolicy > layout )

virtual

Set the mapping policy to determine the Layout of Variables stored under this Group. Usually only set by ObsGroup when we create / open.

Definition at line 38 of file Has_Variables.cpp.

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◆ stitchComplementaryVariables()

void ioda::detail::Has_Variables_Base::stitchComplementaryVariables ( bool removeOriginals = true )

Combines all complementary variables as specified in the mapping file, opens them, and optionally removes the originals from the ObsGroup.

removeOriginals determines if the original complementary variables should be removed from the ObsGroup. Later functionality will ensure that the original complementary variables can be recreated on writing back to the original file.

Definition at line 112 of file Has_Variables.cpp.

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Member Data Documentation

◆ backend_

std::shared_ptr<Has_Variables_Backend> ioda::detail::Has_Variables_Base::backend_

private

Using an opaque object to implement the backend.

Definition at line 203 of file Has_Variables.h.

◆ complementaryVariables_

std::vector<ComplementaryVariableCreationParameters> ioda::detail::Has_Variables_Base::complementaryVariables_

private

Definition at line 206 of file Has_Variables.h.

◆ layout_

std::shared_ptr<const detail::DataLayoutPolicy> ioda::detail::Has_Variables_Base::layout_

private

Set by ObsGroup.

Definition at line 205 of file Has_Variables.h.

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

Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Has_Variables_Base()

◆ ~Has_Variables_Base()

Member Function Documentation

◆ _create_py()

◆ _py_fvp_helper()

◆ attachDimensionScales()

◆ convertVariableUnits()

◆ create() [1/4]

◆ create() [2/4]

◆ create() [3/4]

◆ create() [4/4]

◆ createDerivedVariableParameters()

◆ createWithScales() [1/2]

◆ createWithScales() [2/2]

◆ exists()

◆ getFillValuePolicy()

◆ getTypeProvider()

◆ list()

◆ loadComponentVariableData()

◆ open()

◆ operator()()

◆ operator[]()

◆ remove()

◆ setLayout()

◆ stitchComplementaryVariables()

Member Data Documentation

◆ backend_

◆ complementaryVariables_

◆ layout_