Performs data IO to VDF files. More...

#include <AMRIO.h>

Inheritance diagram for VAPoR::AMRIO:

Public Member Functions
	AMRIO (const MetadataVDC &metadata)

	AMRIO (const string &metafile)

virtual	~AMRIO ()

int	VariableExists (size_t ts, const char *varname, int reflevel=0, int lod=0) const

int	OpenTreeWrite (size_t timestep)

int	OpenTreeRead (size_t timestep)

int	CloseTree ()

int	TreeRead (AMRTree *tree)

int	TreeWrite (const AMRTree *tree)

int	OpenVariableWrite (size_t timestep, const char *varname, int reflevel=-1, int lod=-1)

virtual int	BlockWriteRegion (const float *region, const size_t bmin[3], const size_t bmax[3], bool block=true)

virtual int	WriteRegion (const float *region, const size_t min[3], const size_t max[3])

virtual int	WriteRegion (const float *region)

virtual int	WriteSlice (const float *slice)

int	OpenVariableRead (size_t timestep, const char *varname, int reflevel=0, int lod=0)

virtual int	BlockReadRegion (const size_t bmin[3], const size_t bmax[3], float *region, bool unblock=true)

virtual int	ReadRegion (const size_t min[3], const size_t max[3], float *region)

virtual int	ReadRegion (float *region)

virtual int	ReadSlice (float *slice)

virtual int	CloseVariable ()

int	VariableRead (AMRData *data)

int	VariableWrite (AMRData *data)

int	GetBlockMins (const float **mins, int reflevel) const

int	GetBlockMaxs (const float **maxs, int reflevel) const

const float *	GetDataRange () const

void	GetValidRegion (size_t min[3], size_t max[3], int reflevel) const

Public Member Functions inherited from VAPoR::VDFIOBase
	VDFIOBase (const MetadataVDC &metadata)

	VDFIOBase (const string &metafile)

virtual	~VDFIOBase ()

double	GetReadTimer () const

double	GetSeekTimer () const

void	SeekTimerReset ()

void	SeekTimerStart ()

void	SeekTimerStop ()

double	GetWriteTimer () const

double	GetXFormTimer () const

Public Member Functions inherited from VAPoR::MetadataVDC
	MetadataVDC (const size_t dim[3], size_t numTransforms, const size_t bs[3], int nFilterCoef=1, int nLiftingCoef=1, int msbFirst=1, int vdfVersion=VDF_VERSION)

	MetadataVDC (const size_t dim[3], const size_t bs[3], const vector< size_t > &cratios, string wname, string wmode)

	MetadataVDC (const string &metafile)

	MetadataVDC (const MetadataVDC &node)

virtual	~MetadataVDC ()

int	Merge (const MetadataVDC &metadata, size_t ts=0)

int	Merge (const string &path, size_t ts=0)

int	MakeCurrent () const

const string &	GetParentDir () const

const string &	GetMetafileName () const

const string &	GetDataDirName () const

int	ConstructFullVBase (size_t ts, const string &var, string *path) const

int	ConstructFullAuxBase (size_t ts, string *path) const

int	Write (const string &path, int relative_path=1)

virtual const size_t *	GetBlockSize () const

virtual void	GetBlockSize (size_t bs[3], int) const

virtual void	GetGridDim (size_t dim[3]) const

const size_t *	GetDimension () const

int	GetFilterCoef () const

int	GetLiftingCoef () const

virtual int	GetNumTransforms () const

int	GetMSBFirst () const

int	GetVDFVersion () const

string	GetWaveName () const

string	GetBoundaryMode () const

virtual vector< size_t >	GetCRatios () const

int	GetVDCType () const

int	SetGridType (const string &value)

string	GetGridType () const

int	IsValidGridType (const string &value) const

int	SetCoordSystemType (const string &value)

string	GetCoordSystemType () const

int	IsValidCoordSystemType (const string &value) const

int	SetExtents (const vector< double > &value)

vector< double >	GetExtents (size_t ts=0) const

int	IsValidExtents (const vector< double > &value) const

int	SetNumTimeSteps (long value)

long	GetNumTimeSteps () const

int	IsValidTimeStep (long value) const

int	SetVariableNames (const vector< string > &value)

int	SetVariables3D (const vector< string > &value)

vector< string >	GetVariables3D () const

vector< string >	GetCoordinateVariables () const

int	SetCoordinateVariables (const vector< string > &value)

int	SetVariables2DXY (const vector< string > &value)

int	SetVariables2DXZ (const vector< string > &value)

int	SetVariables2DYZ (const vector< string > &value)

vector< string >	GetVariables2DXY () const

vector< string >	GetVariables2DXZ () const

vector< string >	GetVariables2DYZ () const

int	SetComment (const string &value)

string	GetComment () const

int	SetPeriodicBoundary (const vector< long > &value)

vector< long >	GetPeriodicBoundary () const

int	SetGridPermutation (const vector< long > &value)

int	SetMissingValue (double value)

int	SetMissingValue ()

vector< double >	GetMissingValue () const

vector< long >	GetGridPermutation () const

int	SetMapProjection (const string &value)

virtual string	GetMapProjection () const

int	SetTSUserTime (size_t ts, const vector< double > &value)

double	GetTSUserTime (size_t ts) const

int	SetTSUserTimeStamp (size_t ts, const string &s)

void	GetTSUserTimeStamp (size_t ts, string &s) const

string	GetTSAuxBasePath (size_t ts) const

int	HasTSUserTime (size_t ts) const

int	IsValidUserTime (const vector< double > &value) const

int	SetTSXCoords (size_t ts, const vector< double > &value)

vector< double >	GetTSXCoords (size_t ts) const

int	SetTSYCoords (size_t ts, const vector< double > &value)

vector< double >	GetTSYCoords (size_t ts) const

int	SetTSZCoords (size_t ts, const vector< double > &value)

vector< double >	GetTSZCoords (size_t ts) const

int	SetTSComment (size_t ts, const string &value)
	Set a comment for the time step indicated by `ts`. More...

string	GetTSComment (size_t ts) const
	Return the comment for the indicated time step, `ts`, if it exists. More...

int	SetTSExtents (size_t ts, const vector< double > &value)

vector< double >	GetTSExtents (size_t ts) const

int	SetTSMissingValue (size_t ts, double v)

vector< double >	GetTSMissingValue (size_t ts) const
	Returns the time-varying missing value, if any. More...

int	SetVComment (size_t ts, const string &var, const string &value)

string	GetVComment (size_t ts, const string &var) const

string	GetVBasePath (size_t ts, const string &var) const

int	SetVBasePath (size_t ts, const string &var, const string &value)

int	SetVDataRange (size_t ts, const string &var, const vector< double > &value)

vector< double >	GetVDataRange (size_t ts, const string &var) const

int	IsValidVDataRange (const vector< double > &value) const

int	SetVMissingValue (size_t ts, const string &var, double v)

vector< double >	GetVMissingValue (size_t ts, const string &var) const

vector< string >	GetUserDataLongTags () const

int	SetUserDataLong (const string &tag, const vector< long > &value)

vector< long >	GetUserDataLong (const string &tag) const

vector< string >	GetUserDataDoubleTags () const

int	SetUserDataDouble (const string &tag, const vector< double > &value)

vector< double >	GetUserDataDouble (const string &tag) const

vector< string >	GetUserDataStringTags () const

int	SetUserDataString (const string &tag, const string &value)

string	GetUserDataString (const string &tag) const

int	SetUserDataStringVec (const string &tag, const vector< string > &value)

vector< string >	GetUserDataStringVec (const string &tag) const

vector< string >	GetTSUserDataLongTags () const

int	SetTSUserDataLong (size_t ts, const string &tag, const vector< long > &value)

vector< long >	GetTSUserDataLong (size_t ts, const string &tag) const

int	SetTSUserDataDouble (size_t ts, const string &tag, const vector< double > &value)

vector< double >	GetTSUserDataDouble (size_t ts, const string &tag) const

vector< string >	GetTSUserDataDoubleTags () const

int	SetTSUserDataString (size_t ts, const string &tag, const string &value)

string	GetTSUserDataString (size_t ts, const string &tag) const

vector< string >	GetTSUserDataStringTags () const

vector< string >	GetVUserDataLongTags () const

int	SetVUserDataLong (size_t ts, const string &var, const string &tag, const vector< long > &value)

vector< long >	GetVUserDataLong (size_t ts, const string &var, const string &tag) const

vector< string >	GetVUserDataDoubleTags () const

int	SetVUserDataDouble (size_t ts, const string &var, const string &tag, const vector< double > &value)

vector< double >	GetVUserDataDouble (size_t ts, const string &var, const string &tag) const

int	SetVUserDataString (size_t ts, const string &var, const string &tag, const string &value)

string	GetVUserDataString (size_t ts, const string &var, const string &tag) const

vector< string >	GetVUserDataStringTags () const

Public Member Functions inherited from VAPoR::Metadata
	Metadata ()

virtual	~Metadata ()

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

virtual void	GetTSUserTimeStamp (size_t ts, std::string &s) const =0

virtual void	GetDim (size_t dim[3], int reflevel=0) const

virtual void	GetDimBlk (size_t bdim[3], int reflevel=0) const

virtual bool	GetMissingValue (std::string varname, float &value) const

virtual void	MapVoxToBlk (const size_t vcoord[3], size_t bcoord[3], int reflevel=-1) const

virtual void	MapVoxToUser (size_t timestep, const size_t vcoord0[3], double vcoord1[3], int ref_level=0) const

void	MapUserToVox (size_t timestep, const double vcoord0[3], size_t vcoord1[3], int reflevel) const

virtual VarType_T	GetVarType (const std::string &varname) const

virtual int	IsValidRegion (const size_t min[3], const size_t max[3], int reflevel=0) const

virtual int	IsValidRegionBlk (const size_t min[3], const size_t max[3], int reflevel=0) const

virtual bool	IsCoordinateVariable (std::string varname) const

Public Member Functions inherited from VetsUtil::MyBase
	MyBase ()

const string &	getClassName () const

Public Member Functions inherited from VAPoR::ParsedXml
virtual	~ParsedXml ()

virtual bool	charHandler (ExpatParseMgr , const XML_Char , int)

Additional Inherited Members
Public Types inherited from VAPoR::Metadata
enum	VarType_T { VARUNKNOWN = -1, VAR3D, VAR2D_XY, VAR2D_XZ, VAR2D_YZ }

Public Types inherited from VetsUtil::MyBase
typedef void(*	ErrMsgCB_T )(const char *msg, int err_code)

typedef void(*	DiagMsgCB_T )(const char *msg)

Static Public Member Functions inherited from VetsUtil::MyBase
static void	SetErrMsg (const char *format,...)
	Record a formatted error message. More...

static void	SetErrMsg (int errcode, const char *format,...)
	Record a formatted error message and an error code. More...

static const char *	GetErrMsg ()

static void	SetErrCode (int err_code)
	Record an error code. More...

static int	GetErrCode ()
	Retrieve the current error code. More...

static void	SetErrMsgCB (ErrMsgCB_T cb)

static ErrMsgCB_T	GetErrMsgCB ()

static void	SetErrMsgFilePtr (FILE *fp)

static const FILE *	SetErrMsgFilePtr ()

static void	SetDiagMsg (const char *format,...)
	Record a formatted diagnostic message. More...

static const char *	GetDiagMsg ()

static void	SetDiagMsgCB (DiagMsgCB_T cb)

static DiagMsgCB_T	GetDiagMsgCB ()

static void	SetDiagMsgFilePtr (FILE *fp)

static bool	EnableErrMsg (bool enable)

Public Attributes inherited from VAPoR::ParsedXml
ParsedXml *	previousClass

Static Public Attributes inherited from VetsUtil::MyBase
static char *	ErrMsg

static int	ErrCode

static int	ErrMsgSize

static FILE *	ErrMsgFilePtr

static ErrMsgCB_T	ErrMsgCB

static char *	DiagMsg

static int	DiagMsgSize

static FILE *	DiagMsgFilePtr

static DiagMsgCB_T	DiagMsgCB

static bool	Enabled

Protected Member Functions inherited from VAPoR::VDFIOBase
void	_ReadTimerReset ()

void	_ReadTimerStart ()

void	_ReadTimerStop ()

void	_WriteTimerReset ()

void	_WriteTimerStart ()

void	_WriteTimerStop ()

void	_XFormTimerReset ()

void	_XFormTimerStart ()

void	_XFormTimerStop ()

int	_MaskOpenWrite (size_t timestep, string varname, int reflevel)

int	_MaskOpenRead (size_t timestep, string varname, int reflevel)

int	_MaskClose ()

int	_MaskWrite (const float *srcblk, const size_t bmin_p[3], const size_t bmax_p[3], bool block)

int	_MaskRead (const size_t bmin_p[3], const size_t bmax_p[3])

void	_MaskRemove (float *blk, bool &valid_data) const

void	_MaskReplace (size_t bx, size_t by, size_t bz, float *blk) const

Protected Member Functions inherited from VetsUtil::MyBase
void	SetClassName (const string &name)

Static Protected Member Functions inherited from VAPoR::VDFIOBase
static void	_UnpackCoord (VarType_T vtype, const size_t src[3], size_t dst[3], size_t fill)

static void	_PackCoord (VarType_T vtype, const size_t src[3], size_t dst[3], size_t fill)

static void	_FillPackedCoord (VarType_T vtype, const size_t src[3], size_t dst[3], size_t fill)

Protected Attributes inherited from VAPoR::Metadata
bool	_deprecated_get_dim

Static Protected Attributes inherited from VAPoR::ParsedXml
static const string	_stringType

static const string	_longType

static const string	_doubleType

static const string	_typeAttr

Detailed Description

Performs data IO to VDF files.

Author: John Clyne

Version: $$

Date: $$

This class provides an API for performing IO on AMR data sets to/from Vapor Data Collections (VDCs)

Definition at line 45 of file AMRIO.h.

Constructor & Destructor Documentation

VAPoR::AMRIO::AMRIO ( const MetadataVDC & metadata )

Constructor for the AMRIO class.

Parameters

[in]	metadata	Pointer to a metadata class object for which all future class operations will apply. The metadata class object identifies the VDC for all subsequent data operations
[in]	nthreads	Number of execution threads that may be used by the class for parallel execution.

Note: The success or failure of this constructor can be checked with the GetErrCode() method.

See also: MetadataVDC, GetErrCode(),

VAPoR::AMRIO::AMRIO ( const string & metafile )

Constructor for the AMRIO class.

Parameters

[in] metafile Path to a metadata file for which all future class operations will apply. The metadata class object identifies the VDC for all subsequent data operations

Note: The success or failure of this constructor can be checked with the GetErrCode() method.

See also: MetadataVDC, GetErrCode(),

virtual VAPoR::AMRIO::~AMRIO ( )

virtual

Member Function Documentation

virtual int VAPoR::AMRIO::BlockReadRegion	(	const size_t	bmin[3],
		const size_t	bmax[3],
		float *	region,
		bool	unblock = `true`
	)

inlinevirtual

Implements VAPoR::VDFIOBase.

Definition at line 240 of file AMRIO.h.

virtual int VAPoR::AMRIO::BlockWriteRegion	(	const float *	region,
		const size_t	bmin[3],
		const size_t	bmax[3],
		bool	block = `true`
	)

inlinevirtual

Implements VAPoR::VDFIOBase.

Definition at line 192 of file AMRIO.h.

int VAPoR::AMRIO::CloseTree ( )

Close the currently opened octree.

See also: OpenTreeWrite(), OpenTreeRead()

virtual int VAPoR::AMRIO::CloseVariable ( )

virtual

Close the currently opened variable.

See also: OpenVariableWrite(), OpenVariableRead()

Reimplemented from VAPoR::VDFIOBase.

Referenced by VAPoR::DataMgrAMR::_CloseVariable().

int VAPoR::AMRIO::GetBlockMaxs	(	const float **	maxs,
		int	reflevel
	)		const

Return the maximum data values for each block in the volume

int VAPoR::AMRIO::GetBlockMins	(	const float **	mins,
		int	reflevel
	)		const

Return the minimum data values for each block in the volume

This method returns an a pointer to an internal array containing the minimum data value for each block at the specified refinement level. The serial array is dimensioned nbx by nby by nbz, where nbx, nby, and nbz are the dimensions of the volume in blocks at the requested refinement level.

Parameters

[in]	reflevel	Refinement level requested. The coarsest refinement level is 0 (zero). A value of -1 indicates the finest refinement level contained in the VDC.
[out]	mins	The address of a pointer to float to which will be assigned the address of the internal min data array

The values returned are undefined if the variable is either not open for reading, closed after writing

const float* VAPoR::AMRIO::GetDataRange ( ) const

inlinevirtual

Implements VAPoR::VDFIOBase.

Definition at line 306 of file AMRIO.h.

Referenced by VAPoR::DataMgrAMR::_GetDataRange().

void VAPoR::AMRIO::GetValidRegion	(	size_t	min[3],
		size_t	max[3],
		int	reflevel
	)		const

Referenced by VAPoR::DataMgrAMR::_GetValidRegion().

int VAPoR::AMRIO::OpenTreeRead ( size_t timestep )

Open the specified AMR octree for reading

Prepare a VDC for the reading of an AMR grid topology octree. AMR grids contain two components: a topology octree which describes the cell refinement hierarchy, and the field values associated with the cells in the octree. A single octree is associated with each time step, whereas multiple field variables may be defined for each time step, all associated with the same octree.

Parameters

[in] timestep Time step of the octree to write

Return values

status Returns a non-negative value on success

See also: Metadata::GetVariableNames(), Metadata::GetNumTransforms()

int VAPoR::AMRIO::OpenTreeWrite ( size_t timestep )

Open the specified AMR octree for writing

Prepare a VDC for the storage of an AMR grid topology octree. AMR grids contain two components: a topology octree which describes the cell refinement hierarchy, and the field values associated with the cells in the octree. A single octree is associated with each time step, whereas multiple field variables may be defined for each time step, all associated with the same octree.

Parameters

[in] timestep Time step of the octree to write

Return values

status Returns a non-negative value on success

See also: Metadata::GetVariableNames(), Metadata::GetNumTransforms(); TreeWrite()

int VAPoR::AMRIO::OpenVariableRead	(	size_t	timestep,
		const char *	varname,
		int	reflevel = `0`,
		int	lod = `0`
	)

virtual

Open the named AMR grid for reading

This method prepares the AMR data grid, indicated by a variable name and time step pair, for subsequent read operations by methods of this class. Furthermore, the number of the refinement level parameter, reflevel indicates the resolution of the volume in the multiresolution hierarchy. The valid range of values for reflevel is [0..max_refinement], where max_refinement is the maximum finement level of the data set: Metadata::GetNumTransforms(). volume when the volume was created. A value of zero indicates the coarsest resolution data, a value of max_refinement indicates the finest resolution data.

An error occurs, indicated by a negative return value, if the volume identified by the {varname, timestep, reflevel} tripple is not present on disk. Note the presence of a volume can be tested for with the VariableExists() method.

Parameters

[in]	timestep	Time step of the variable to read
[in]	varname	Name of the variable to read
[in]	reflevel	Refinement level of the variable. A value of -1 indicates the maximum refinment level defined for the VDC

Return values

status Returns a non-negative value on success

See also: Metadata::GetVariableNames(), Metadata::GetNumTransforms()

Reimplemented from VAPoR::VDFIOBase.

int VAPoR::AMRIO::OpenVariableWrite	(	size_t	timestep,
		const char *	varname,
		int	reflevel = `-1`,
		int	lod = `-1`
	)

virtual

Open the named AMR variable for writing

Prepare a VDC for the storage of an AMR grid via subsequent write operations. The AMR grid is identified by the specfied time step and variable name. The maximum number of refinement level is determined by the Metadata object used to initialize the class. The number of refinement levels actually saved to the data collection are determined by reflevels. If reflevels is zero, the default, only the coarsest approximation is saved. If reflevels is one, the coarsest and first refinement level is saved, and so on. A value of -1 indicates the maximum refinment level permitted by the associated Metadata object

Parameters

[in]	timestep	Time step of the variable to read
[in]	varname	Name of the variable to read
[in]	reflevel	Refinement level of the variable. A value of -1 indicates the maximum refinment level.

Return values

status Returns a non-negative value on success

See also: Metadata::GetVariableNames(), Metadata::GetNumTransforms()

Reimplemented from VAPoR::VDFIOBase.

virtual int VAPoR::AMRIO::ReadRegion	(	const size_t	min[3],
		const size_t	max[3],
		float *	region
	)

inlinevirtual

Implements VAPoR::VDFIOBase.

Definition at line 244 of file AMRIO.h.

virtual int VAPoR::AMRIO::ReadRegion ( float * region )

inlinevirtual

Implements VAPoR::VDFIOBase.

Definition at line 248 of file AMRIO.h.

virtual int VAPoR::AMRIO::ReadSlice ( float * slice )

inlinevirtual

Implements VAPoR::VDFIOBase.

Definition at line 252 of file AMRIO.h.

int VAPoR::AMRIO::TreeRead ( AMRTree * tree )

Read an AMR octree

Read the currently opened octree into the AMRTree structure pointed to tree.

Parameters

[out] tree Upon success the octree pointed to by tree will contain the octree associated with the currently opened time step.

See also: OpenTreeRead()

int VAPoR::AMRIO::TreeWrite ( const AMRTree * tree )

Write an AMR octree

Write the octree pointed to by tree to the VDC at the time step associated with the currently opened tree.

Parameters

[in] tree A pointer to an AMR octree

See also: OpenTreeRead()

int VAPoR::AMRIO::VariableExists	(	size_t	ts,
		const char *	varname,
		int	reflevel = `0`,
		int	lod = `0`
	)		const

Returns true if indicated AMR grid exists on disk

Returns true if the variable identified by the timestep, variable name, and refinement level is present on disk. Returns 0 if the variable is not present.

Parameters

[in]	ts	A valid time step from the Metadata object used to initialize the class
[in]	varname	A valid variable name
[in]	reflevel	Refinement level requested. The coarsest refinement level is 0 (zero). A value of -1 indicates the finest refinement level contained in the VDC.

Referenced by VAPoR::DataMgrAMR::_VariableExists().

int VAPoR::AMRIO::VariableRead ( AMRData * data )

Read an AMR grid

Read the currently opened AMR grid into the AMRData structure pointed to data.

Parameters

[out] data Upon success the AMR grid pointed to by data will contain the AMR Grid associated with the currently opened time step and variable.