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

#include "arts.h"
#include <netcdf.h>
#include "mystring.h"
#include "exceptions.h"
#include "messages.h"
#include "abs_species_tags.h"

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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=false)
	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=false)
	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=false)
	Read variable of type Matrix from NetCDF file. More...

void	nca_get_data_Tensor4 (const int ncid, const String &name, Tensor4 &m, const bool noerror=false)
	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 err, const String msg)
	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.h.

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 334 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 234 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 197 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_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 282 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 307 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 216 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 258 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 671 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 55 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 76 of file nc_io.cc.

References 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 480 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 454 of file nc_io.cc.

References nc_get_dim(), and nca_get_data_long().

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 397 of file nc_io.cc.

References 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 361 of file nc_io.cc.

References 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 379 of file nc_io.cc.

References 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 539 of file nc_io.cc.

References MatrixView::get_c_array(), nc_get_dim(), nca_get_data_double(), 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 558 of file nc_io.cc.

References Tensor4View::get_c_array(), nc_get_dim(), nca_get_data_double(), 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 434 of file nc_io.cc.

References 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 521 of file nc_io.cc.

References VectorView::get_c_array(), nc_get_dim(), nca_get_data_double(), 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 415 of file nc_io.cc.

References nca_error().

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 578 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 629 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 651 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 607 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 105 of file nc_io.cc.

References CREATE_OUT2, expand_path(), and nca_read_from_file().

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 151 of file nc_io.cc.

References add_basedir(), CREATE_OUT2, and nca_write_to_file().

Referenced by nca_write_to_file(), and WriteNetCDF().

Functions

Detailed Description

Function Documentation

◆ nc_get_dim()

◆ nca_def_ArrayOfIndex()

◆ nca_def_dim()

◆ nca_def_Matrix()

◆ nca_def_Tensor4()

◆ nca_def_var()

◆ nca_def_Vector()

◆ nca_error()

◆ nca_filename()

◆ nca_filename_with_index()

◆ nca_get_data_ArrayOfArrayOfSpeciesTag()

◆ nca_get_data_ArrayOfIndex()

◆ nca_get_data_double()

◆ nca_get_data_int()

◆ nca_get_data_long()

◆ nca_get_data_Matrix()

◆ nca_get_data_Tensor4()

◆ nca_get_data_text()

◆ nca_get_data_Vector()

◆ nca_get_dataa_double()

◆ nca_put_var_ArrayOfIndex()

◆ nca_put_var_Matrix()

◆ nca_put_var_Tensor4()

◆ nca_put_var_Vector()

◆ nca_read_from_file()

◆ nca_write_to_file()