#include <ObsFrame.h>

Inheritance diagram for ioda::ObsFrame:

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Public Member Functions
	ObsFrame (const ObsSpaceParameters &params)

	~ObsFrame ()

Dimensions_t	ioMaxVarSize () const
	return number of maximum variable size (along first dimension) from ObsIo More...

Dimensions_t	ioNumLocs () const
	return number of locations from ObsIo More...

Dimensions_t	ioNumVars () const
	return number of regular variables from ObsIo More...

Dimensions_t	ioNumDimVars () const
	return number of dimension scale variables from ObsIo More...

Has_Variables &	vars () const
	return variables container from ObsIo More...

Has_Attributes &	atts () const
	return attributes container from ObsIo More...

const VarNameObjectList &	ioVarList () const
	return list of regular variables from ObsIo More...

const VarNameObjectList &	ioDimVarList () const
	return list of dimension scale variables from ObsIo More...

VarDimMap	ioVarDimMap () const
	return map from variables to their attached dimension scales More...

void	ioUpdateVarDimInfo () const
	update variable, dimension info in the ObsIo object More...

bool	ioIsVarDimByNlocs (const std::string &varName) const
	return true if variable is dimensioned by nlocs More...

virtual std::size_t	frameNumLocs () const
	return number of locations More...

virtual std::size_t	frameNumRecs () const
	return number of records More...

Dimensions_t	globalNumLocs () const
	return number of locations that were selected from ObsIo More...

Dimensions_t	globalNumLocsOutsideTimeWindow () const
	return number of locations from obs source that were outside the time window More...

virtual std::vector< std::size_t >	index () const
	return list of indices indicating which locations were selected from ObsIo More...

virtual std::vector< std::size_t >	recnums () const
	return list of record numbers from ObsIo More...

virtual void	frameInit ()
	initialize frame for a read frame object More...

virtual void	frameInit (const VarNameObjectList &varList, const VarNameObjectList &varDimList, const VarDimMap &varDimMap, const Dimensions_t maxVarSize)
	initialize for a write frame object More...

virtual void	frameNext ()
	move to the next frame for a read frame object More...

virtual void	frameNext (const VarNameObjectList &varList)
	move to the next frame for a write frame object More...

virtual bool	frameAvailable ()=0
	true if a frame is available (not past end of frames) More...

virtual Dimensions_t	frameStart ()=0
	return current frame starting index More...

virtual Dimensions_t	frameCount (const std::string &varName)=0
	return current frame count for variable More...

virtual Dimensions_t	adjNlocsFrameStart () const
	return adjusted nlocs frame start More...

virtual Dimensions_t	adjNlocsFrameCount () const
	return adjusted nlocs frame count More...

Selection	createMemSelection (const std::vector< Dimensions_t > &varShape, const Dimensions_t frameCount)
	create selection object for accessing a memory buffer More...

Selection	createEntireFrameSelection (const std::vector< Dimensions_t > &varShape, const Dimensions_t frameCount)
	create selection object for accessing the entire frame variable More...

Selection	createVarSelection (const std::vector< Dimensions_t > &varShape, const Dimensions_t frameStart, const Dimensions_t frameCount)
	create selection object for accessing a frame from a whole variable More...

Protected Member Functions
Selection	createObsIoSelection (const std::vector< Dimensions_t > &varShape, const Dimensions_t frameStart, const Dimensions_t frameCount)
	create selection object for accessing an ObsIo variable More...

void	createFrameFromObsGroup (const VarNameObjectList &varList, const VarNameObjectList &dimVarList, const VarDimMap &varDimMap)
	create a frame object based on dimensions and variables from a source ObsGroup More...

virtual void	print (std::ostream &os) const =0
	print() for oops::Printable base class More...

Protected Attributes
std::shared_ptr< ObsIo >	obs_io_
	ObsIo object. More...

ObsGroup	obs_frame_
	ObsGroup object (temporary storage for a single frame) More...

Dimensions_t	nrecs_
	number of records from source (file or generator) More...

Dimensions_t	nlocs_
	number of locations from source (file or generator) More...

Dimensions_t	gnlocs_
	total number of locations from source (file or generator) that were selected after the timing window filtering More...

Dimensions_t	gnlocs_outside_timewindow_
	number of nlocs from the file (gnlocs) that are outside the time window More...

ObsSpaceParameters	params_
	ObsIo parameter specs. More...

Dimensions_t	max_frame_size_
	maximum frame size More...

Dimensions_t	max_var_size_
	maximum variable size More...

Dimensions_t	frame_start_
	current frame starting index More...

Detailed Description

The ObsFrame class along with its subclasses are responsible for appying the timing window filtering, record number assignment (according to the obsgrouping specification) and the application of MPI distribution when transferring data from a source (file or generator) into memory. For data transfer in both directions (source to memory, and memory to destination), this class also provides a means for transferring data in chunks (first n locations, followed by second n locations, etc.) which for a transfer from a file to memory can be utilized to avoid reading in the whole file into memory before applying the filtering and distribution.

Author: Stephen Herbener (JCSDA)

Definition at line 40 of file ObsFrame.h.

Constructor & Destructor Documentation

◆ ObsFrame()

ioda::ObsFrame::ObsFrame ( const ObsSpaceParameters & params )

explicit

Definition at line 20 of file ObsFrame.cc.

◆ ~ObsFrame()

ioda::ObsFrame::~ObsFrame ( )

inline

Definition at line 43 of file ObsFrame.h.

Member Function Documentation

◆ adjNlocsFrameCount()

virtual Dimensions_t ioda::ObsFrame::adjNlocsFrameCount ( ) const

inlinevirtual

return adjusted nlocs frame count

Reimplemented in ioda::ObsFrameRead.

Definition at line 136 of file ObsFrame.h.

◆ adjNlocsFrameStart()

virtual Dimensions_t ioda::ObsFrame::adjNlocsFrameStart ( ) const

inlinevirtual

return adjusted nlocs frame start

Reimplemented in ioda::ObsFrameRead.

Definition at line 133 of file ObsFrame.h.

◆ atts()

Has_Attributes& ioda::ObsFrame::atts ( ) const

inline

return attributes container from ObsIo

Definition at line 61 of file ObsFrame.h.

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◆ createEntireFrameSelection()

Selection ioda::ObsFrame::createEntireFrameSelection	(	const std::vector< Dimensions_t > &	varShape,
		const Dimensions_t	frameCount
	)

create selection object for accessing the entire frame variable

Parameters

varShape	dimension sizes for variable being transferred
frameCount	size of current frame

Definition at line 49 of file ObsFrame.cc.

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◆ createFrameFromObsGroup()

void ioda::ObsFrame::createFrameFromObsGroup	(	const VarNameObjectList &	varList,
		const VarNameObjectList &	dimVarList,
		const VarDimMap &	varDimMap
	)

protected

create a frame object based on dimensions and variables from a source ObsGroup

This function is used to set up a temprary ObsGroup based frame in memory which is to be used for processing and transferring data between ObsIo and ObsSpace variables. The two parameters dimVarList and varDimMap can be created with IodaUtils::collectVarDimInfo() in IodaUtils.h.

Parameters

varList	source ObsGroup list of regular variables
dimVarList	source ObsGroup list of dimension variable names
varDimMap	source ObsGroup map showing variables with associated dimensions

Definition at line 109 of file ObsFrame.cc.

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◆ createMemSelection()

Selection ioda::ObsFrame::createMemSelection	(	const std::vector< Dimensions_t > &	varShape,
		const Dimensions_t	frameCount
	)

create selection object for accessing a memory buffer

Parameters

varShape	dimension sizes for variable being transferred
frameCount	size of current frame

Definition at line 26 of file ObsFrame.cc.

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◆ createObsIoSelection()

Selection ioda::ObsFrame::createObsIoSelection	(	const std::vector< Dimensions_t > &	varShape,
		const Dimensions_t	frameStart,
		const Dimensions_t	frameCount
	)

protected

create selection object for accessing an ObsIo variable

Parameters

varShape	dimension sizes for variable being transferred
frameStart	starting index number for current frame
frameCount	size of current frame

Definition at line 91 of file ObsFrame.cc.

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◆ createVarSelection()

Selection ioda::ObsFrame::createVarSelection	(	const std::vector< Dimensions_t > &	varShape,
		const Dimensions_t	frameStart,
		const Dimensions_t	frameCount
	)

create selection object for accessing a frame from a whole variable

Parameters

varShape	dimension sizes for variable being transferred
frameStart	start of current frame for current variable
frameCount	size of current frame

Definition at line 72 of file ObsFrame.cc.

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◆ frameAvailable()

virtual bool ioda::ObsFrame::frameAvailable ( )

pure virtual

true if a frame is available (not past end of frames)

Implemented in ioda::ObsFrameWrite, and ioda::ObsFrameRead.

◆ frameCount()

virtual Dimensions_t ioda::ObsFrame::frameCount ( const std::string & varName )

pure virtual

return current frame count for variable

Variables can be of different sizes so it's possible that the frame has moved past the end of some variables but not so for other variables. When the frame is past the end of the given variable, this routine returns a zero to indicate that we're done with this variable.

Parameters

varName variable name

Implemented in ioda::ObsFrameWrite, and ioda::ObsFrameRead.

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◆ frameInit() [1/2]

virtual void ioda::ObsFrame::frameInit ( )

inlinevirtual

initialize frame for a read frame object

Reimplemented in ioda::ObsFrameRead.

Definition at line 99 of file ObsFrame.h.

◆ frameInit() [2/2]

virtual void ioda::ObsFrame::frameInit	(	const VarNameObjectList &	varList,
		const VarNameObjectList &	varDimList,
		const VarDimMap &	varDimMap,
		const Dimensions_t	maxVarSize
	)

inlinevirtual

initialize for a write frame object

Parameters

varList	source ObsGroup list of regular variables
dimVarList	source ObsGroup list of dimension variables
varDimMap	source ObsGroup map showing variables with associated dimensions
maxVarSize	source ObsGroup maximum variable size along the first dimension

Reimplemented in ioda::ObsFrameWrite.

Definition at line 106 of file ObsFrame.h.

◆ frameNext() [1/2]

virtual void ioda::ObsFrame::frameNext ( )

inlinevirtual

move to the next frame for a read frame object

Reimplemented in ioda::ObsFrameRead.

Definition at line 111 of file ObsFrame.h.

◆ frameNext() [2/2]

virtual void ioda::ObsFrame::frameNext ( const VarNameObjectList & varList )

inlinevirtual

move to the next frame for a write frame object

Parameters

varList source ObsGroup list variable names

Reimplemented in ioda::ObsFrameWrite.

Definition at line 115 of file ObsFrame.h.

◆ frameNumLocs()

virtual std::size_t ioda::ObsFrame::frameNumLocs ( ) const

inlinevirtual

return number of locations

Definition at line 81 of file ObsFrame.h.

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◆ frameNumRecs()

virtual std::size_t ioda::ObsFrame::frameNumRecs ( ) const

inlinevirtual

return number of records

Definition at line 84 of file ObsFrame.h.

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◆ frameStart()

virtual Dimensions_t ioda::ObsFrame::frameStart ( )

pure virtual

return current frame starting index

Parameters

varName name of variable

Implemented in ioda::ObsFrameWrite, and ioda::ObsFrameRead.

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◆ globalNumLocs()

Dimensions_t ioda::ObsFrame::globalNumLocs ( ) const

inline

return number of locations that were selected from ObsIo

Definition at line 87 of file ObsFrame.h.

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◆ globalNumLocsOutsideTimeWindow()

Dimensions_t ioda::ObsFrame::globalNumLocsOutsideTimeWindow ( ) const

inline

return number of locations from obs source that were outside the time window

Definition at line 90 of file ObsFrame.h.

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◆ index()

virtual std::vector<std::size_t> ioda::ObsFrame::index ( ) const

inlinevirtual

return list of indices indicating which locations were selected from ObsIo

Reimplemented in ioda::ObsFrameRead.

Definition at line 93 of file ObsFrame.h.

◆ ioDimVarList()

const VarNameObjectList& ioda::ObsFrame::ioDimVarList ( ) const

inline

return list of dimension scale variables from ObsIo

Definition at line 67 of file ObsFrame.h.

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◆ ioIsVarDimByNlocs()

bool ioda::ObsFrame::ioIsVarDimByNlocs ( const std::string & varName ) const

inline

return true if variable is dimensioned by nlocs

Definition at line 76 of file ObsFrame.h.

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◆ ioMaxVarSize()

Dimensions_t ioda::ObsFrame::ioMaxVarSize ( ) const

inline

return number of maximum variable size (along first dimension) from ObsIo

Definition at line 46 of file ObsFrame.h.

◆ ioNumDimVars()

Dimensions_t ioda::ObsFrame::ioNumDimVars ( ) const

inline

return number of dimension scale variables from ObsIo

Definition at line 55 of file ObsFrame.h.

◆ ioNumLocs()

Dimensions_t ioda::ObsFrame::ioNumLocs ( ) const

inline

return number of locations from ObsIo

Definition at line 49 of file ObsFrame.h.

◆ ioNumVars()

Dimensions_t ioda::ObsFrame::ioNumVars ( ) const

inline

return number of regular variables from ObsIo

Definition at line 52 of file ObsFrame.h.

◆ ioUpdateVarDimInfo()

void ioda::ObsFrame::ioUpdateVarDimInfo ( ) const

inline

update variable, dimension info in the ObsIo object

Definition at line 73 of file ObsFrame.h.

◆ ioVarDimMap()

VarDimMap ioda::ObsFrame::ioVarDimMap ( ) const

inline

return map from variables to their attached dimension scales

Definition at line 70 of file ObsFrame.h.

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◆ ioVarList()

const VarNameObjectList& ioda::ObsFrame::ioVarList ( ) const

inline

return list of regular variables from ObsIo

Definition at line 64 of file ObsFrame.h.

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◆ print()

virtual void ioda::ObsFrame::print ( std::ostream & os ) const

protectedpure virtual

print() for oops::Printable base class

Parameters

ostream output stream

Implemented in ioda::ObsFrameWrite, and ioda::ObsFrameRead.

◆ recnums()

virtual std::vector<std::size_t> ioda::ObsFrame::recnums ( ) const

inlinevirtual

return list of record numbers from ObsIo

Reimplemented in ioda::ObsFrameRead.

Definition at line 96 of file ObsFrame.h.

◆ vars()

Has_Variables& ioda::ObsFrame::vars ( ) const

inline

return variables container from ObsIo

Definition at line 58 of file ObsFrame.h.

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Member Data Documentation

◆ frame_start_

Dimensions_t ioda::ObsFrame::frame_start_

protected

current frame starting index

Definition at line 189 of file ObsFrame.h.

◆ gnlocs_

Dimensions_t ioda::ObsFrame::gnlocs_

protected

total number of locations from source (file or generator) that were selected after the timing window filtering

Definition at line 174 of file ObsFrame.h.

◆ gnlocs_outside_timewindow_

Dimensions_t ioda::ObsFrame::gnlocs_outside_timewindow_

protected

number of nlocs from the file (gnlocs) that are outside the time window

Definition at line 177 of file ObsFrame.h.

◆ max_frame_size_

Dimensions_t ioda::ObsFrame::max_frame_size_

protected

maximum frame size

Definition at line 183 of file ObsFrame.h.

◆ max_var_size_

Dimensions_t ioda::ObsFrame::max_var_size_

protected

maximum variable size

Definition at line 186 of file ObsFrame.h.

◆ nlocs_

Dimensions_t ioda::ObsFrame::nlocs_

protected

number of locations from source (file or generator)

Definition at line 170 of file ObsFrame.h.

◆ nrecs_

Dimensions_t ioda::ObsFrame::nrecs_

protected

number of records from source (file or generator)

Definition at line 167 of file ObsFrame.h.

◆ obs_frame_

ObsGroup ioda::ObsFrame::obs_frame_

protected

ObsGroup object (temporary storage for a single frame)

Definition at line 164 of file ObsFrame.h.

◆ obs_io_

std::shared_ptr<ObsIo> ioda::ObsFrame::obs_io_

protected

ObsIo object.

Definition at line 161 of file ObsFrame.h.

◆ params_

ObsSpaceParameters ioda::ObsFrame::params_

protected

ObsIo parameter specs.

Definition at line 180 of file ObsFrame.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ObsFrame()

◆ ~ObsFrame()

Member Function Documentation

◆ adjNlocsFrameCount()

◆ adjNlocsFrameStart()

◆ atts()

◆ createEntireFrameSelection()

◆ createFrameFromObsGroup()

◆ createMemSelection()

◆ createObsIoSelection()

◆ createVarSelection()

◆ frameAvailable()

◆ frameCount()

◆ frameInit() [1/2]

◆ frameInit() [2/2]

◆ frameNext() [1/2]

◆ frameNext() [2/2]

◆ frameNumLocs()

◆ frameNumRecs()

◆ frameStart()

◆ globalNumLocs()

◆ globalNumLocsOutsideTimeWindow()

◆ index()

◆ ioDimVarList()

◆ ioIsVarDimByNlocs()

◆ ioMaxVarSize()

◆ ioNumDimVars()

◆ ioNumLocs()

◆ ioNumVars()

◆ ioUpdateVarDimInfo()

◆ ioVarDimMap()

◆ ioVarList()

◆ print()

◆ recnums()

◆ vars()

Member Data Documentation

◆ frame_start_

◆ gnlocs_

◆ gnlocs_outside_timewindow_

◆ max_frame_size_

◆ max_var_size_

◆ nlocs_

◆ nrecs_

◆ obs_frame_

◆ obs_io_

◆ params_