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RubyNetCDF Reference Manual

Method Index

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Overview

RubyNetCDF is the Ruby interface of the NetCDF library. Ruby is a free object-oriented scripting language and is available from http://www.ruby-lang.org/. To handle numeric data, RubyNetCDF uses NArray, which is the standard numeric multi-dimensional array class for Ruby (http://www.ruby-lang.org/en/raa-list.rhtml?name=NArray). An NArray object holds numeric data in a consecutive memory area pointed by a C pointer. Thus, it is computationally efficient. NArray is similar to NumPy for Python, but results of some benchmark tests suggests that NArray is more efficient than NumPy.

Structure

RubyNetCDF consists of the four class in the following.

class NetCDF -- the file class

An NetCDF object represents a NetCDF file
class NetCDFDim -- the dimension class

Although in its C version a NetCDF dimension is represented by a combination of a file ID and a dimension ID, it is represented by only one NetCDFDim object in RubyNetCDF.
class NetCDFVar -- the variable class

Although in its C version a NetCDF variable is represented by a combination of a file ID and a variable ID, it is represented by only one NetCDFVar object in RubyNetCDF.
class NetCDFAtt -- the attribute class

Although in its C version a NetCDF attribute is represented by a combination of file ID, variable ID, and its name, it is represented by only one NetCDFAtt object in RubyNetCDF.

Data type

All the NetCDF variable types char, byte, short, int, float, and double are supported in this Ruby interface. These types are called, however, differently in it to adhere to the convention of Ruby, or, more specifically, of NArray. These types are named to as "char", "byte", "sint", "int", "sfloat", and "float", respectively. Therefore, the vartype (=ntype) method of the NetCDFVar class returns one of these strings. The def_var method of the NetCDF class also accepts one of them to define a variable. It should be noted especially that "float" in this library means the double in the NetCDF terminology. This is due to the convention of Ruby -- the predefined Float class corresponds to the double in C, not the float.

The "get" method of NetCDFVar class reads a variable in a NArray of the same type as in the file, except for the "char" type which is read into a "byte". This is because NArray does not have a "char" type. However, it not is not supposed to be a problem, since a byte NArray can easily handle string data.

Error handling

Errors are basically handled by raising exceptions. However, light errors in value-returning methods are handled by returning nil (e.g., if a non-existent attribute name is specified in attribute reading). Those methods that returns nil on error are explicitly written as such in the following.

Security features

Security handling is done just as in the pre-defined File class.

Usage

To use the RubyNetCDF library, load the library first by placing the following line in your Ruby program to load the library:

require 'numru/netcdf'

Here, 'numru', which is taken from "Numerical Ruby", is the name of the subdirectory in the user's load path where the RubyNetCDF library is placed (by default). Then, it can be used as in the following:

file = NumRu::NetCDF.create('tmp.nc')
x = file.def_dim('x',10)
y = file.def_dim('y',10)
v = file.def_var('v','float',[x,y])
file.close

Here, NumRu is the module that has the library in it. The reason why NetCDF library is wrapped in such a module is to avoid conflicts in the name space. Without this kind of treatment, problems happen if the user wants to use a library that happens to have a class or module with the same name as even one of the classes in this library.

If such a problem is not expected to happen, the prefix "NumRu::" can be eliminated by "including" the NumRu module as in the following, so that to place "NumRu::" is not needed anymore in the current scope:

include NumRu
file = NetCDF.create('tmp.nc')
...

For more examples, see demo and test programs included in the distribution package.

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How to read this manual

method_name(argument1, argument2, ...) -- arguments that can be omitted are expressed as Argument_name=Default_value

Explanation of its function

Arguments

name of argument1 (its class or possible values): explanation
name of argument2 (its class or possible values): explanation
...

Return value

Explanation of the return value

Corresponding (dependent) function(s) in the C library of NetCDF

Name(s) in NetCDF ver 3. The function equivalent to the current method, if not in parenthesis. If no direct correspondence, dependent functions are listed in parentheses.

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Method Index

class NetCDF

Class Methods
- NetCDF.open Opens a file (class method). If mode="w" and non-existent, a new
- NetCDF.new Aliased to NetCDF.open
- NetCDF.create Creates a NetCDF file (class method)
- NetCDF.create_tmp Creates a temporary NetCDF file (class method)
Instance Methods
- close Closes the file.
- ndims Returns the number of dimensions in the file
- nvars Returns the number of variables in the file
- natts Returns the number of global attributes in the file
- unlimited Returns the unlimited dimension in the file
- path Returns the path of the file (contents of the filename specified when opened/created)
- redef Switches to the define mode. Does nothing if already in it.
- enddef Switches to the data mode. Does nothing if already in it.
- sync Synchronizes the disk copy of a netCDF dataset with in-memory buffer
- def_dim Define a dimension
- put_att Sets a global attribute
- def_var Defines a variable
- def_var_with_dim Same as def_var but defines dimensions first if needed
- var Opens an existing variable in the file
- dim Opens an existing dimension in the file
- att Opens an existing global attribute in the file
- fill= Sets a fill mode. (Default behavior of NetCDF is FILL.)
- each_dim Iterator regarding the dimensions in the file.
- each_var Iterator regarding the variables in the file.
- each_att Iterator regarding the global attributes of the file.
- dim_names Returns the names of all dimensions in the file
- var_names Returns the names of all variables in the file
- att_names Returns the names of all the global attributes of the file
class NetCDFDim

Class Methods

Instance Methods
- length Returns the length of the dimension
- length_ul0 Same as length but returns 0 for the unlimited dimension
- name= Rename the dimension
- name Returns the name of the dimension
- unlimited? Inquires whether the dimension is unlimited or not
class NetCDFVar

Class Methods
- NetCDFVar.new Combines NetCDF.open and NetCDF#Var to open a variable with one line (no need to use this).
Instance Methods
- dim Inquires the dim_num-th dimension of the variable (dim_num=0,1,2,..)
- dims Returns an array of all the dimensions of the variable
- shape_ul0 Returns the shape of the variable, but the length of the unlimited dimension is set to zero.
- shape_current Returns the current shape of the variable.
- url Returns a combination of filename (path) and variable name as path+'?var='+varname
- each_att Iterator regarding the global attributes of the variables.
- dim_names Returns the names of all the dimensions of the variable
- att_names Returns the names of all the attributes of the variable
- name Returns the name of the variable
- name= Rename the variable
- ndims Number of dimensions of the variable (which is rank of the variable).
- ntype Aliased to vartype
- vartype Data value type of the variable
- natts Returns the number of the attributes of the variable
- file Inquires the file that the variable is in
- att Returns the attribute specified by its name
- put_att Sets an attribute
- put Set the values of the variable
- scaled_put Same as put but interprets the attributes scale_factor and add_offset
- get Returns values of the variable
- scaled_get Same as get but interprets the attributes scale_factor and add_offset
class NetCDFAtt

Class Methods

Instance Methods
- name Returns the name of the attribute
- name= Rename the attribute
- copy Copies an attribute to a variable or a file. If file, becomes an global attribute
- delete Delete an attribute
- put Sets the value of the attribute
- get Returns the values of the attribute
- atttype Inquires the type of attribute values

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class NetCDF

Class Methods

NetCDF.open(filename, mode="r", share=false)

Opens a file (class method). If mode="w" and non-existent, a new file is created.

Arguments

filename (String): file name (path)
mode (String) : IO mode "r"(read only), "w"(writable)
share (true or false) : Whether to use the "shared" mode or not (set true if a file being written may be read from other processes. See nc_open in Ch.5 of users' guide of the C version)

Return value

a NetCDF object

Corresponding (dependent) function(s) in the C library of NetCDF

nc_open, nc_create

NetCDF.new

Aliased to NetCDF.open

NetCDF.create(filename, noclobber=false, share=false)

Creates a NetCDF file (class method)

Arguments

filename (String) : file name (path)
noclobber (true or false) : overwrite or not if the file exists
share (true or false) : Whether to use the shared mode or not

Return value

a NetCDF object

Corresponding (dependent) function(s) in the C library of NetCDF

nc_create

NetCDF.create_tmp(tmpdir=ENV['TMPDIR']||ENV['TMP']||ENV['TEMP']||'.', share=false)

Creates a temporary NetCDF file (class method). Its name is automatically generated, and it is deleted when closed.

Arguments

tmpdir (String) : directory to place the temporary file. By default, "." or a directory specified by an environmental vairable (TMPDIR or TMP oe TEMP) is used. In a secure mode, theses environmental variable is NOT used, and the default value is '.'.
share (true or false) : Whether to use the shared mode or not

Return value

a NetCDF object

Corresponding (dependent) function(s) in the C library of NetCDF

nc_create

Instance Methods

close

Closes the file.

Arguments

(none)

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_close

ndims

Returns the number of dimensions in the file

Arguments

(none)

Return value

Integer

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_ndims

nvars

Returns the number of variables in the file

Arguments

(none)

Return value

Integer

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_nvars

natts

Returns the number of global attributes in the file

Arguments

(none)

Return value

Integer

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_natts

unlimited

Returns the unlimited dimension in the file

Arguments

(none)

Return value

a NetCDFDim if it exists; nil if not

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_unlimdim

path

Returns the path of the file (contents of the filename specified when opened/created)

Arguments

(none)

Return value

String

Corresponding (dependent) function(s) in the C library of NetCDF

(none)

redef

Switches to the define mode. Does nothing if already in it.

Arguments

(none)

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_redef

enddef

Switches to the data mode. Does nothing if already in it.

Arguments

(none)

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_enddef

sync

Synchronizes the disk copy of a netCDF dataset with in-memory buffer

Arguments

(none)

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_sync

def_dim(dimension_name, length)

Define a dimension

Arguments

dimension_name (String) : Name of the dimension to be defined
length (Integer) : length of the dimension. 0 for unlimited.

Return value

defined dimension (NetCDFDim object)

Corresponding (dependent) function(s) in the C library of NetCDF

nc_def_dim

put_att(attribute_name, value, atttype=nil)

Sets a global attribute

Arguments

attribute_name (String) : name of the global attribute
value (Numeric, String, Array of Numeric, or NArray) : value of the attribute
atttype (nil or String) : data type of the attribute value. nil lets it automatically determined from the value. "char" (or "string"), "byte", "sint", "int", "sfloat", or "float" specifies the type explicitly (1,1,2,4,4,8 bytes, respectively)

Return value

created attribute (NetCDFAtt object)

Corresponding (dependent) function(s) in the C library of NetCDF

nc_put_att_<type>

def_var(name, vartype, dimensions)

Defines a variable

Arguments

name (String) : Name of the variable to define
vartype (String) : data type of the variable ("char", "byte", "sint", "sint", "int", "sfloat", or "float")
dimensions (Array) : Dimensions of the variable. An Array of NetCDFDim, in the order from the fastest varying dimension to the slowliest varying one; its length becomes the rank of the variable.

Return value

defined variable (NetCDFVar object)

Corresponding (dependent) function(s) in the C library of NetCDF

nc_def_var

def_var_with_dim(name, vartype, shape_ul0, dimnames)

Same as def_var but defines dimensions first if needed. Raise exception if it conflicts with the lengths of exisiting dimensions.

Arguments

name (String) : Name of the variable to define
vartype (String) : data type of the variable ("char", "byte", "sint", "sint", "int", "sfloat", or "float")
shape_ul0 (Array of Integer) : Shape of the variable, i.e., lengths of dimensions. The unlimited dimension is specified by zero. The length of shape_ul0 determines the rank of the variable.
dimnames (Array of String) : Names of the dimensions. Its length (=>rank) must be equal to that of shape_ul0

Return value

defined variable (NetCDFVar object)

Corresponding (dependent) function(s) in the C library of NetCDF

(nc_def_var)

var(var_name)

Opens an existing variable in the file

Arguments

var_name (String) : Name of the variable to open

Return value

a NetCDFVar object if the variable exists; nil if not

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_varid

dim(dimension_name)

Opens an existing dimension in the file

Arguments

dimension_name (String) : Name of the dimension to open

Return value

a NetCDFDim object if the dimension exists; nil if not

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_dimid

att(attribute_name)

Opens an existing global attribute in the file

Arguments

attribute_name (String) : Name of the global attribute to open

Return value

a NetCDFAtt object if the attribute exists; nil if not

Corresponding (dependent) function(s) in the C library of NetCDF

(nc_inq_attid used for inquiry)

fill=(filemode)

Sets a fill mode. (Default behavior of NetCDF is FILL.)

Arguments

fillmode (true or false)

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_set_fill

each_dim{ ... }

Iterator regarding the dimensions in the file. Ex.: {|i| print i.name,"\n"} prints names of all dimensions

Arguments

{ ... } : Block for the iterator. A "do end" block is the alternative.

Return value

self

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_ndims)

each_var{ ... }

Iterator regarding the variables in the file. Ex.: {|i| print i.name,"\n"} prints names of all variables

Arguments

{ ... } : Block for the iterator. A "do end" block is the alternative.

Return value

self

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_nvars)

each_att{ ... }

Iterator regarding the global attributes of the file. Ex.: {|i| print i.name,"\n"} prints names of all of them.

Arguments

{ ... } : Block for the iterator. A "do end" block is the alternative.

Return value

self

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_natts, nc_inq_attname)

dim_names

Returns the names of all dimensions in the file

Arguments

(none)

Return value

Array of NetCDFDim

Corresponding (dependent) function(s) in the C library of NetCDF

(nc_inq_ndims, nc_inq_dimname)

var_names

Returns the names of all variables in the file

Arguments

(none)

Return value

Array of String

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_nvars, nc_inq_varname)

att_names

Returns the names of all the global attributes of the file

Arguments

(none)

Return value

Array of NetCDFAtt

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_natts, nc_inq_attname)

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class NetCDFDim

Class Methods

Instance Methods

length

Returns the length of the dimension

Arguments

(none)

Return value

Integer

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_dimlen

length_ul0

Same as length but returns 0 for the unlimited dimension

Arguments

(none)

Return value

Integer

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_dimlen

name=(dimension_newname)

Rename the dimension

Arguments

dimension_newname (String) : new name

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_rename_dim

name

Returns the name of the dimension

Arguments

(none)

Return value

String

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_dimname

unlimited?

Inquires whether the dimension is unlimited or not

Arguments

(none)

Return value

true or false

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_unlimdim)

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class NetCDFVar

Class Methods

NetCDFVar.new(file,varname,mode="r",share=false)

open a NetCDF variable. This can also be done with NetCDF#var (instance method of NetCDF class), which is recommended over this method.

Arguments

file (NetCDF or String) : a NetCDF file object (NetCDF) or the path of a NetCDF file (String).
varname (String) : name of the variable in the file
mode (String) : IO mode "r"(read only), "w"(writable)
share (true or false) : Whether to use the "shared" mode or not (set true if a file being written may be read from other processes. See nc_open in Ch.5 of users' guide of the C version)

Return value

a NetCDFVar object

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_open, nc_create, nc_inq_varid etc.)

Instance Methods

dim(dim_num)

Inquires the dim_num-th dimension of the variable (dim_num=0,1,2,..)

Arguments

dim_num (Fixnum) : 0,1,... 0 is the fastest varying dimension.

Return value

a NetCDFDim object

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_vardimid)

dims

Returns an array of all the dimensions of the variable

Arguments

(none)

Return value

Array of NetCDFDim objects.

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_vardimid

shape_ul0

Returns the shape of the variable, but the length of the unlimited dimension is set to zero. Good to define another variable.

Arguments

(none)

Return value

Array. [length of 0th dim, length of 1st dim,.. ]

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_vardimid, nc_inq_unlimdim etc)

shape_current

Returns the current shape of the variable.

Arguments

(none)

Return value

Array. [length of 0th dim, length of 1st dim,.. ]

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_vardimid etc)

each_att{ ... }

Iterator regarding the global attributes of the variables. Ex.: {|i| print i.name,"\n"} prints names of all of them.

Arguments

{ ... } : Block for the iterator. A "do end" block is the alternative.

Return value

self

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_natts, nc_inq_attname)

dim_names

Returns the names of all the dimensions of the variable

Arguments

(none)

Return value

Array of String

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_varndims, nc_inq_vardimid, nc_inq_dimname)

att_names

Returns the names of all the attributes of the variable

Arguments

(none)

Return value

Array of String

Corresponding (dependent) function(s) in the C library of NetCDF

(dependent on nc_inq_natts, nc_inq_attname)

name

Returns the name of the variable

Arguments

(none)

Return value

String

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_varname

name=(variable_newname)

Rename the variable

Arguments

variable_newname (String) : new name

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_rename_var

ndims

Number of dimensions of the variable (which is rank of the variable).

Arguments

(none)

Return value

Integer

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_varndims

ntype

Aliased to vartype

vartype

Data value type of the variable

Arguments

(none)

Return value

String ("char","byte","sint","int","sfloat", or "float")

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_vartype

natts

Returns the number of the attributes of the variable

Arguments

(none)

Return value

Integer

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_varnatts

file

Inquires the file that the variable is in

Arguments

(none)

Return value

a NetCDF object

Corresponding (dependent) function(s) in the C library of NetCDF

(none)

att(attribute_name)

Returns the attribute specified by its name

Arguments

attribute_name (String) : Name of the attribute

Return value

a NetCDFAtt object if the attribute exists; nil if not

Corresponding (dependent) function(s) in the C library of NetCDF

(nc_inq_attid is used for inquiry)

put_att(attribute_name, value, atttype=nil)

Sets an attribute

Arguments

attribute_name (String) : name of the attribute
value (Numeric, String, Array of Numeric, or NArray) : value of the attribute
atttype (nil or String) : data type of the attribute value. nil lets it automatically determined from the value. "char" (="string"), "byte", "sint", "int", "sfloat", or "float" specifies the type explicitly (1,1,2,4,4,8 bytes, respectively)

Return value

a NetCDFAtt object

Corresponding (dependent) function(s) in the C library of NetCDF

nc_put_att_<type>

put(value, option=nil)

Set the values of the variable

Arguments

value : value to set (Numeric, Array of Numeric (1D only), or NArray (possibly multi-D))
option (Hash) : Optional argument to limit the portion of the variable to output values. If omitted, the whole variable is subject to the output. This argument accepts a Hash whose keys contain either "index" or a combination of "start","end", and "stride". The value of "index" points the index of a scalar portion of the variable. The other case is used to designate a regularly ordered subset, where "start" and "end" specifies bounds in each dimension and "stride" specifies intervals in it. As in Array "start", "end", and "index" can take negative values to specify index backward from the end. However, "stride" has to be positive, so reversing the array must be done afterwards if you like.

Example: If the variable is 2D:

{"start"=>[2,5],"end"=>[6,-1],"stride"=>[2,4]} -- Specifies a subset made as follows: the 1st dimension from the element 2 to the element 6 (note that the count starts with 0, so that the element 2 is the 3rd one) with an interval of 2; the 2nd dimension from the element 6 to the last element (designated by -1) with an interval of 5.

{"index"=>[0,0]}: Scalar of the fist element

{"index"=>[0,-2]}: Scalar from the 1st element of with respect to the 1st dimension and the 2nd element from the last with respect to the 2nd dimension

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_put_var_<type>, nc_put_vars_<type>, nc_put_var1_<type>

scaled_put(value, option=nil)

Same as put but interprets the attributes scale_factor and add_offset

If scale_factor and/or add_offest is defined, does (value-add_offset)/scale_factor before writing. (If not, exactly the same as put.) If one of the attributes is not defined, assumes 1 for the factor and 0 for the offset.

See the document for put for arguments etc.

get(option=nil)

Returns values of the variable

Arguments

option (Hash) : Optional argument to limit the portion of the variable to get values. Its usage is the same as in the method put.

Return value

an NArray object

Corresponding (dependent) function(s) in the C library of NetCDF

nc_get_var_<type>, nc_get_vars_<type>, nc_get_var1_<type>

scaled_get(option=nil)

Same as get but interprets the attributes scale_factor and add_offset

If scale_factor and/or add_offest is defined, returns value*scale_factor+add_offset. (If not, exactly the same as get.) If one of the attributes is not defined, assumes 1 for the factor and 0 for the offset. The variable type of the return value (NArray) is float (which is double precision) if the NetCDF variable is int or float; else, it is sfloat (single presision).

See the document for get for arguments etc.

---------------------------------------------

class NetCDFAtt

Class Methods

Instance Methods

name

Returns the name of the attribute

Arguments

(none)

Return value

String

Corresponding (dependent) function(s) in the C library of NetCDF

(none)

name=(attribute_newname)

Rename the attribute

Arguments

attribute_newname (String) : New name

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_rename_att

copy(var_or_file)

Copies an attribute to a variable or a file. If file, becomes an global attribute

Arguments

var_or_file (NetCDFVar or NetCDF)

Return value

Resultant new attribute (NetCDFAtt)

Corresponding (dependent) function(s) in the C library of NetCDF

nc_copy_att

delete

Delete an attribute

Arguments

(none)

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_del_att

put(value, atttype=nil)

Sets the value of the attribute

Arguments

value (Numeric, String, Array of Numeric, or NArray) : value of the attribute
atttype (nil or String) : data type of the attribute value. nil lets it automatically determined from the value. "char" (="string"), "byte", "sint", "int", "sfloat", or "float" specifies the type explicitly (1,1,2,4,4,8 bytes, respectively)

Return value

Corresponding (dependent) function(s) in the C library of NetCDF

nc_put_att_<type>

get

Returns the values of the attribute

Arguments

(none)

Return value

String or an NArray object (NOTE: even a scalar is returned as an NArray of length 1)

Corresponding (dependent) function(s) in the C library of NetCDF

nc_get_att_<type>

atttype

Inquires the type of attribute values

Arguments

(none)

Return value

"char","byte","sint","int","sfloat","float"

Corresponding (dependent) function(s) in the C library of NetCDF

nc_inq_atttype