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Import NetCDF Files and OPeNDAP Data

MATLAB NetCDF Capabilities

Network Common Data Form (NetCDF) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. NetCDF is used by a wide range of engineering and scientific fields that want a standard way to store data so that it can be shared.

MATLAB® high-level functions simplify the process of importing data from a NetCDF file or an OPeNDAP NetCDF data source. MATLAB low-level functions enable more control over the importing process, by providing access to the routines in the NetCDF C library. To use the low-level functions effectively, you should be familiar with the NetCDF C Interface. The NetCDF documentation is available at the Unidata website.

Read from NetCDF File Using High-Level Functions

This example shows how to display and read the contents of a NetCDF file, using high-level functions.

Display the contents of the sample NetCDF file, example.nc.

ncdisp('example.nc')
Source:
           \\matlabroot\toolbox\matlab\demos\example.nc
Format:
           netcdf4
Global Attributes:
           creation_date = '29-Mar-2010'
Dimensions:
           x = 50
           y = 50
           z = 5
Variables:
    avagadros_number
           Size:       1x1
           Dimensions: 
           Datatype:   double
           Attributes:
                       description = 'this variable has no dimensions'
    temperature     
           Size:       50x1
           Dimensions: x
           Datatype:   int16
           Attributes:
                       scale_factor = 1.8
                       add_offset   = 32
                       units        = 'degrees_fahrenheight'
    peaks           
           Size:       50x50
           Dimensions: x,y
           Datatype:   int16
           Attributes:
                       description = 'z = peaks(50);'
Groups:
    /grid1/
        Attributes:
                   description = 'This is a group attribute.'
        Dimensions:
                   x    = 360
                   y    = 180
                   time = 0     (UNLIMITED)
        Variables:
            temp
                   Size:       []
                   Dimensions: x,y,time
                   Datatype:   int16
    
    /grid2/
        Attributes:
                   description = 'This is another group attribute.'
        Dimensions:
                   x    = 360
                   y    = 180
                   time = 0     (UNLIMITED)
        Variables:
            temp
                   Size:       []
                   Dimensions: x,y,time
                   Datatype:   int16

ncdisp displays all the groups, dimensions, and variable definitions in the file. Unlimited dimensions are identified with the label, UNLIMITED.

Read data from the peaks variable.

peaksData  = ncread('example.nc','peaks');

Display information about the peaksData output.

whos peaksData
  Name            Size            Bytes  Class    Attributes

  peaksData      50x50             5000  int16  

Read the description attribute associated with the variable.

peaksDesc  = ncreadatt('example.nc','peaks','description')
peaksDesc =

z = peaks(50);

Create a three-dimensional surface plot of the variable data. Use the value of the description attribute as the title of the figure.

surf(double(peaksData))
title(peaksDesc);

Read the description attribute associated with the /grid1/ group. Specify the group name as the second input to the ncreadatt function.

g = ncreadatt('example.nc','/grid1/','description')
g =

This is a group attribute.

Read the global attribute, creation_date. For global attributes, specify the second input argument to ncreadatt as '/'.

creation_date = ncreadatt('example.nc','/','creation_date')
creation_date =

29-Mar-2010

Find All Unlimited Dimensions in NetCDF File

This example shows how to find all unlimited dimensions in a group in a NetCDF file, using high-level functions.

Get information about the /grid2/ group in the sample file, example.nc, using the ncinfo function.

ginfo = ncinfo('example.nc','/grid2/')
ginfo = 

      Filename: '\\matlabroot\toolbox\matlab\demos\example.nc'
          Name: 'grid2'
    Dimensions: [1x3 struct]
     Variables: [1x1 struct]
    Attributes: [1x1 struct]
        Groups: []
        Format: 'netcdf4'

ncinfo returns a structure array containing information about the group.

Get a vector of the Boolean values that indicate the unlimited dimensions for this group.

unlimDims = [ginfo.Dimensions.Unlimited]
unlimDims =

     0     0     1

Use the unlimDims vector to display the unlimited dimension.

disp(ginfo.Dimensions(unlimDims))
         Name: 'time'
       Length: 0
    Unlimited: 1

Read from NetCDF File Using Low-Level Functions

This example shows how to get information about the dimensions, variables, and attributes in a NetCDF file using MATLAB low-level functions in the netcdf package. To use these functions effectively, you should be familiar with the NetCDF C Interface.

Open NetCDF File

Open the sample NetCDF file, example.nc, using the netcdf.open function, with read-only access.

ncid = netcdf.open('example.nc','NC_NOWRITE')
ncid =

       65536

netcdf.open returns a file identifier.

Get Information About NetCDF File

Get information about the contents of the file using the netcdf.inq function. This function corresponds to the nc_inq function in the NetCDF library C API.

[ndims,nvars,natts,unlimdimID] = netcdf.inq(ncid)
ndims =

     3


nvars =

     3


natts =

     1


unlimdimID =

    -1

netcdf.inq returns the number of dimensions, variables, and global attributes in the file, and returns the identifier of the unlimited dimension in the file. An unlimited dimension can grow.

Get the name of the global attribute in the file using the netcdf.inqAttName function. This function corresponds to the nc_inq_attname function in the NetCDF library C API. To get the name of an attribute, you must specify the ID of the variable the attribute is associated with and the attribute number. To access a global attribute, which is not associated with a particular variable, use the constant 'NC_GLOBAL' as the variable ID.

global_att_name = netcdf.inqAttName(ncid,...
    netcdf.getConstant('NC_GLOBAL'),0)
global_att_name =

creation_date

Get information about the data type and length of the attribute using the netcdf.inqAtt function. This function corresponds to the nc_inq_att function in the NetCDF library C API. Again, specify the variable ID using netcdf.getConstant('NC_GLOBAL').

[xtype,attlen] = netcdf.inqAtt(ncid,...
    netcdf.getConstant('NC_GLOBAL'),global_att_name)
xtype =

     2


attlen =

    11

Get the value of the attribute, using the netcdf.getAtt function.

global_att_value = netcdf.getAtt(ncid,...
    netcdf.getConstant('NC_GLOBAL'),global_att_name)
global_att_value =

29-Mar-2010

Get information about the first dimension in the file, using the netcdf.inqDim function. This function corresponds to the nc_inq_dim function in the NetCDF library C API. The second input to netcdf.inqDim is the dimension ID, which is a zero-based index that identifies the dimension. The first dimension has the index value 0.

[dimname,dimlen] = netcdf.inqDim(ncid,0)
dimname =

x


dimlen =

    50

netcdf.inqDim returns the name and length of the dimension.

Get information about the first variable in the file using the netcdf.inqVar function. This function corresponds to the nc_inq_var function in the NetCDF library C API. The second input to netcdf.inqVar is the variable ID, which is a zero-based index that identifies the variable. The first variable has the index value 0.

[varname,vartype,dimids,natts] = netcdf.inqVar(ncid,0)
varname =

avagadros_number


vartype =

     6


dimids =

     []


natts =

     1

netcdf.inqVar returns the name, data type, dimension ID, and the number of attributes associated with the variable. The data type information returned in vartype is the numeric value of the NetCDF data type constants, such as, NC_INT and NC_BYTE. See the NetCDF documentation for information about these constants.

Read Data from NetCDF File

Read the data associated with the variable, avagadros_number, in the example file, using the netcdf.getVar function. The second input to netcdf.getVar is the variable ID, which is a zero-based index that identifies the variable. The avagadros_number variable has the index value 0.

A_number = netcdf.getVar(ncid,0)
A_number =

   6.0221e+23

View the data type of A_number.

whos A_number
  Name          Size            Bytes  Class     Attributes

  A_number      1x1                 8  double              

The functions in the netcdf package automatically choose the MATLAB class that best matches the NetCDF data type, but you can also specify the class of the return data by using an optional argument to netcdf.getVar.

Read the data associated with avagadros_number and return the data as class single.

A_number = netcdf.getVar(ncid,0,'single');
whos A_number
  Name          Size            Bytes  Class     Attributes

  A_number      1x1                 4  single              

Close NetCDF File

Close the NetCDF file, example.nc.

netcdf.close(ncid)

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