nc_io.cc File Reference

This file contains basic functions to handle NetCDF data files. More...

#include "arts.h"
#include "exceptions.h"
#include "file.h"
#include "messages.h"
#include "nc_io.h"
#include "nc_io_types.h"
#include "nc_io_instantiation.h"

Go to the source code of this file.

Functions
void	nca_filename (String &filename, const String &varname)
	Gives the default filename for the NetCDF formats. More...
void	nca_filename_with_index (String &filename, const Index &file_index, const String &varname)
	Gives the default filename, with file index, for the NetCDF formats. More...
template<typename T >
void	nca_read_from_file (const String &filename, T &type, const Verbosity &verbosity)
	Reads a variable from a NetCDF file. More...
template<typename T >
void	nca_write_to_file (const String &filename, const T &type, const Verbosity &verbosity)
	Writes a variable to a NetCDF file. More...
void	nca_def_dim (const int ncid, const String &name, const Index nelem, int *ncdim)
	Define NetCDF dimension. More...
void	nca_def_var (const int ncid, const String &name, const nc_type type, const int ndims, const int *dims, int *varid)
	Define NetCDF variable. More...
int	nca_def_ArrayOfIndex (const int ncid, const String &name, const ArrayOfIndex &a)
	Define NetCDF dimensions and variable for an ArrayOfIndex. More...
int	nca_def_Vector (const int ncid, const String &name, const Vector &v)
	Define NetCDF dimensions and variable for a Vector. More...
int	nca_def_Matrix (const int ncid, const String &name, const Matrix &m)
	Define NetCDF dimensions and variable for a Matrix. More...
int	nca_def_Tensor4 (const int ncid, const String &name, const Tensor4 &t)
	Define NetCDF dimensions and variable for a Tensor4. More...
Index	nc_get_dim (const int ncid, const String &name, const bool noerror)
	Read a dimension from NetCDF file. More...
void	nca_get_data_int (const int ncid, const String &name, int *data)
	Read variable of type int from NetCDF file. More...
void	nca_get_data_long (const int ncid, const String &name, long *data)
	Read variable of type long from NetCDF file. More...
void	nca_get_data_double (const int ncid, const String &name, Numeric *data)
	Read variable of type double from NetCDF file. More...
void	nca_get_dataa_double (const int ncid, const String &name, size_t start, size_t count, Numeric *data)
	Read variable of type array of double from NetCDF file. More...
void	nca_get_data_text (const int ncid, const String &name, char *data)
	Read variable of type array of char from NetCDF file. More...
void	nca_get_data_ArrayOfIndex (const int ncid, const String &name, ArrayOfIndex &aoi, const bool noerror)
	Read variable of type ArrayOfIndex from NetCDF file. More...
void	nca_get_data_ArrayOfArrayOfSpeciesTag (const int ncid, const String &name, ArrayOfArrayOfSpeciesTag &aast, const bool noerror)
	Read variable of type ArrayOfArrayOfSpeciesTag from NetCDF file. More...
void	nca_get_data_Vector (const int ncid, const String &name, Vector &v, const bool noerror)
	Read variable of type Vector from NetCDF file. More...
void	nca_get_data_Matrix (const int ncid, const String &name, Matrix &m, const bool noerror)
	Read variable of type Matrix from NetCDF file. More...
void	nca_get_data_Tensor4 (const int ncid, const String &name, Tensor4 &t, const bool noerror)
	Read variable of type Tensor4 from NetCDF file. More...
bool	nca_put_var_ArrayOfIndex (const int ncid, const int varid, const ArrayOfIndex &a)
	Write variable of type ArrayOfIndex to NetCDF file. More...
bool	nca_put_var_Vector (const int ncid, const int varid, const Vector &v)
	Write variable of type Vector to NetCDF file. More...
bool	nca_put_var_Matrix (const int ncid, const int varid, const Matrix &m)
	Write variable of type Matrix to NetCDF file. More...
bool	nca_put_var_Tensor4 (const int ncid, const int varid, const Tensor4 &t)
	Write variable of type Tensor4 to NetCDF file. More...
void	nca_error (const int e, const String s)
	Throws a runtime error for the given NetCDF error code. More...

Detailed Description

This file contains basic functions to handle NetCDF data files.

Author

Oliver Lemke olemk.nosp@m.e@co.nosp@m.re-du.nosp@m.mp.i.nosp@m.nfo

Date

2008-09-12

Definition in file nc_io.cc.

Function Documentation

nc_get_dim()

Index nc_get_dim	(	const int	ncid,
		const String &	name,
		const bool	noerror
	)

Read a dimension from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Dimension name in NetCDF file
[in]	noerror	Return 0 instead of throwing an exception if dimension does not exist in file

Returns

Dimension size

Author

Oliver Lemke

Definition at line 300 of file nc_io.cc.

References nca_error().

Referenced by nca_get_data_ArrayOfArrayOfSpeciesTag(), nca_get_data_ArrayOfIndex(), nca_get_data_Matrix(), nca_get_data_Tensor4(), nca_get_data_Vector(), and nca_read_from_file().

nca_def_ArrayOfIndex()

int nca_def_ArrayOfIndex	(	const int	ncid,
		const String &	name,
		const ArrayOfIndex &	a
	)

Define NetCDF dimensions and variable for an ArrayOfIndex.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	a	ArrayOfIndex

Returns

Variable handle

Author

Oliver Lemke

Definition at line 214 of file nc_io.cc.

References nca_def_dim(), nca_def_var(), and Array< base >::nelem().

Referenced by nca_write_to_file().

nca_def_dim()

void nca_def_dim	(	const int	ncid,
		const String &	name,
		const Index	nelem,
		int *	ncdim
	)

Define NetCDF dimension.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Dimension name
[in]	nelem	Dimension size
[out]	ncdim	NetCDF dimension handle

Author

Oliver Lemke

Definition at line 174 of file nc_io.cc.

References nca_error(), and Absorption::nelem().

Referenced by nca_def_ArrayOfIndex(), nca_def_Matrix(), nca_def_Tensor4(), nca_def_Vector(), and nca_write_to_file().

nca_def_Matrix()

int nca_def_Matrix	(	const int	ncid,
		const String &	name,
		const Matrix &	m
	)

Define NetCDF dimensions and variable for a Matrix.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	m	Matrix

Returns

Variable handle

Author

Oliver Lemke

Definition at line 256 of file nc_io.cc.

References nca_def_dim(), nca_def_var(), ConstMatrixView::ncols(), and ConstMatrixView::nrows().

Referenced by nca_write_to_file().

nca_def_Tensor4()

int nca_def_Tensor4	(	const int	ncid,
		const String &	name,
		const Tensor4 &	t
	)

Define NetCDF dimensions and variable for a Tensor4.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	t	Tensor4

Returns

Variable handle

Author

Oliver Lemke

Definition at line 277 of file nc_io.cc.

References ConstTensor4View::nbooks(), nca_def_dim(), nca_def_var(), ConstTensor4View::ncols(), ConstTensor4View::npages(), and ConstTensor4View::nrows().

Referenced by nca_write_to_file().

nca_def_var()

void nca_def_var	(	const int	ncid,
		const String &	name,
		const nc_type	type,
		const int	ndims,
		const int *	dims,
		int *	varid
	)

Define NetCDF variable.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	type	NetCDF type
[in]	ndims	Number of dimensions
[in]	dims	Pointer to dimensions
[out]	varid	NetCDF variable handle

Author

Oliver Lemke

Definition at line 194 of file nc_io.cc.

References nca_error().

Referenced by nca_def_ArrayOfIndex(), nca_def_Matrix(), nca_def_Tensor4(), nca_def_Vector(), and nca_write_to_file().

nca_def_Vector()

int nca_def_Vector	(	const int	ncid,
		const String &	name,
		const Vector &	v
	)

Define NetCDF dimensions and variable for a Vector.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	v	Vector

Returns

Variable handle

Author

Oliver Lemke

Definition at line 236 of file nc_io.cc.

References nca_def_dim(), nca_def_var(), and ConstVectorView::nelem().

Referenced by nca_write_to_file().

nca_error()

void nca_error	(	const int	e,
		const String	s
	)

Throws a runtime error for the given NetCDF error code.

Parameters

[in]	e	NetCDF error code
[in]	s	Error message string

Author

Oliver Lemke

Definition at line 622 of file nc_io.cc.

Referenced by nc_get_dim(), nca_def_dim(), nca_def_var(), nca_get_data_double(), nca_get_data_int(), nca_get_data_long(), nca_get_data_text(), nca_get_dataa_double(), nca_put_var_ArrayOfIndex(), nca_put_var_Matrix(), nca_put_var_Tensor4(), nca_put_var_Vector(), nca_write_to_file(), and WriteMolTau().

nca_filename()

void nca_filename	(	String &	filename,
		const String &	varname
	)

Gives the default filename for the NetCDF formats.

The default name is only used if the filename is empty.

Parameters

filename	filename
varname	variable name

Author

Oliver Lemke

Definition at line 53 of file nc_io.cc.

References out_basename.

Referenced by WriteNetCDF().

nca_filename_with_index()

void nca_filename_with_index	(	String &	filename,
		const Index &	file_index,
		const String &	varname
	)

Gives the default filename, with file index, for the NetCDF formats.

The default name is only used if the filename is empty.

Parameters

[out]	filename	filename
[in]	file_index	Index appended to the filename
[in]	varname	variable name

Author

Oliver Lemke

Definition at line 70 of file nc_io.cc.

References ARTS::Var::file_index(), and out_basename.

Referenced by WriteNetCDFIndexed().

nca_get_data_ArrayOfArrayOfSpeciesTag()

void nca_get_data_ArrayOfArrayOfSpeciesTag	(	const int	ncid,
		const String &	name,
		ArrayOfArrayOfSpeciesTag &	aast,
		const bool	noerror
	)

Read variable of type ArrayOfArrayOfSpeciesTag from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	aast	Data read from file
[in]	noerror	Return empty variable instead of throwing an exception if variable does not exist in file

Author

Oliver Lemke

Definition at line 438 of file nc_io.cc.

References nc_get_dim(), nca_get_data_ArrayOfIndex(), nca_get_data_text(), and Array< base >::nelem().

Referenced by nca_read_from_file().

nca_get_data_ArrayOfIndex()

void nca_get_data_ArrayOfIndex	(	const int	ncid,
		const String &	name,
		ArrayOfIndex &	aoi,
		const bool	noerror
	)

Read variable of type ArrayOfIndex from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	aoi	Data read from file
[in]	noerror	Return empty variable instead of throwing an exception if variable does not exist in file

Author

Oliver Lemke

Definition at line 413 of file nc_io.cc.

References nc_get_dim(), nca_get_data_long(), and Absorption::nelem().

Referenced by nca_get_data_ArrayOfArrayOfSpeciesTag(), and nca_read_from_file().

nca_get_data_double()

void nca_get_data_double	(	const int	ncid,
		const String &	name,
		Numeric *	data
	)

Read variable of type double from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	data	Data read from file

Author

Oliver Lemke

Definition at line 359 of file nc_io.cc.

References data, and nca_error().

Referenced by nca_get_data_Matrix(), nca_get_data_Tensor4(), nca_get_data_Vector(), and nca_read_from_file().

nca_get_data_int()

void nca_get_data_int	(	const int	ncid,
		const String &	name,
		int *	data
	)

Read variable of type int from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	data	Data read from file

Author

Oliver Lemke

Definition at line 327 of file nc_io.cc.

References data, and nca_error().

nca_get_data_long()

void nca_get_data_long	(	const int	ncid,
		const String &	name,
		long *	data
	)

Read variable of type long from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	data	Data read from file

Author

Oliver Lemke

Definition at line 343 of file nc_io.cc.

References data, and nca_error().

Referenced by nca_get_data_ArrayOfIndex(), and nca_read_from_file().

nca_get_data_Matrix()

void nca_get_data_Matrix	(	const int	ncid,
		const String &	name,
		Matrix &	m,
		const bool	noerror
	)

Read variable of type Matrix from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	m	Data read from file
[in]	noerror	Return empty variable instead of throwing an exception if variable does not exist in file

Author

Oliver Lemke

Definition at line 497 of file nc_io.cc.

References MatrixView::get_c_array(), nc_get_dim(), nca_get_data_double(), ARTS::Var::ncols(), ARTS::Var::nrows(), and Matrix::resize().

Referenced by nca_read_from_file().

nca_get_data_Tensor4()

void nca_get_data_Tensor4	(	const int	ncid,
		const String &	name,
		Tensor4 &	t,
		const bool	noerror
	)

Read variable of type Tensor4 from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	t	Data read from file
[in]	noerror	Return empty variable instead of throwing an exception if variable does not exist in file

Author

Oliver Lemke

Definition at line 517 of file nc_io.cc.

References Tensor4View::get_c_array(), ARTS::Var::nbooks(), nc_get_dim(), nca_get_data_double(), ARTS::Var::ncols(), ARTS::Var::npages(), ARTS::Var::nrows(), and Tensor4::resize().

Referenced by nca_read_from_file().

nca_get_data_text()

void nca_get_data_text	(	const int	ncid,
		const String &	name,
		char *	data
	)

Read variable of type array of char from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	data	Data read from file

Author

Oliver Lemke

Definition at line 395 of file nc_io.cc.

References data, and nca_error().

Referenced by nca_get_data_ArrayOfArrayOfSpeciesTag().

nca_get_data_Vector()

void nca_get_data_Vector	(	const int	ncid,
		const String &	name,
		Vector &	v,
		const bool	noerror
	)

Read variable of type Vector from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	v	Data read from file
[in]	noerror	Return empty variable instead of throwing an exception if variable does not exist in file

Author

Oliver Lemke

Definition at line 478 of file nc_io.cc.

References VectorView::get_c_array(), nc_get_dim(), nca_get_data_double(), Absorption::nelem(), and Vector::resize().

Referenced by nca_read_from_file().

nca_get_dataa_double()

void nca_get_dataa_double	(	const int	ncid,
		const String &	name,
		size_t	start,
		size_t	count,
		Numeric *	data
	)

Read variable of type array of double from NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[out]	data	Data read from file

Author

Oliver Lemke

Definition at line 375 of file nc_io.cc.

References data, nca_error(), and Zeeman::start().

Referenced by nca_read_from_file().

nca_put_var_ArrayOfIndex()

bool nca_put_var_ArrayOfIndex	(	const int	ncid,
		const int	varid,
		const ArrayOfIndex &	a
	)

Write variable of type ArrayOfIndex to NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	a	Data to be written

Returns

True if variable was not empty

Author

Oliver Lemke

Definition at line 539 of file nc_io.cc.

References nca_error(), and Array< base >::nelem().

Referenced by nca_write_to_file().

nca_put_var_Matrix()

bool nca_put_var_Matrix	(	const int	ncid,
		const int	varid,
		const Matrix &	m
	)

Write variable of type Matrix to NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	m	Data to be written

Returns

True if variable was not empty

Author

Oliver Lemke

Definition at line 585 of file nc_io.cc.

References MatrixView::get_c_array(), nca_error(), ConstMatrixView::ncols(), and ConstMatrixView::nrows().

Referenced by nca_write_to_file().

nca_put_var_Tensor4()

bool nca_put_var_Tensor4	(	const int	ncid,
		const int	varid,
		const Tensor4 &	t
	)

Write variable of type Tensor4 to NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	t	Data to be written

Returns

True if variable was not empty

Author

Oliver Lemke

Definition at line 604 of file nc_io.cc.

References Tensor4View::get_c_array(), ConstTensor4View::nbooks(), nca_error(), ConstTensor4View::ncols(), ConstTensor4View::npages(), and ConstTensor4View::nrows().

Referenced by nca_write_to_file().

nca_put_var_Vector()

bool nca_put_var_Vector	(	const int	ncid,
		const int	varid,
		const Vector &	v
	)

Write variable of type Vector to NetCDF file.

Parameters

[in]	ncid	NetCDF file descriptor
[in]	name	Variable name in NetCDF file
[in]	v	Data to be written

Returns

True if variable was not empty

Author

Oliver Lemke

Definition at line 566 of file nc_io.cc.

References VectorView::get_c_array(), nca_error(), and ConstVectorView::nelem().

Referenced by nca_write_to_file().

nca_read_from_file()

template<typename T >

void nca_read_from_file	(	const String &	filename,
		T &	type,
		const Verbosity &	verbosity
	)

Reads a variable from a NetCDF file.

Parameters

[in]	filename	NetCDF filename
[out]	type	Input variable
[in]	verbosity	Verbosity

Author

Oliver Lemke

Definition at line 94 of file nc_io.cc.

References CREATE_OUT2, expand_path(), nca_read_from_file(), and ARTS::Var::verbosity().

Referenced by nca_read_from_file(), and ReadNetCDF().

nca_write_to_file()

template<typename T >

void nca_write_to_file	(	const String &	filename,
		const T &	type,
		const Verbosity &	verbosity
	)

Writes a variable to a NetCDF file.

Parameters

[in]	filename	NetCDF filename
[in]	type	Output variable
[in]	verbosity	Verbosity

Author

Oliver Lemke

Definition at line 134 of file nc_io.cc.

References add_basedir(), CREATE_OUT2, nca_write_to_file(), and ARTS::Var::verbosity().

Referenced by nca_write_to_file(), and WriteNetCDF().