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Reading multiple supported files using 'addfiles'

addfiles

The addfiles function allows the user to open multiple supported files and read variables across all files.

You have two options for how the variable is structured, when reading the same variable across multiple files:

Option 1: "cat" mode

When a variable is read from a series of files in "cat" mode, then the leftmost dimension of each variable will be concatenated to form a new leftmost dimension whose size is the sum of the sizes of the leftmost dimension in each individual file.

For example, if you have 5 files, each with a variable "temp" that has dimensions ntim x nlat x nlon (10 x 64 x 128), then the new "temp" variable will be of size 50 x 64 x 128.

Option 1: "join" mode

When a variable is read from a series of files in "join" mode, then a new leftmost dimension is added to the variable that represents the number of files.

In the example above, then, you would end up with a new "temp" variable of size 5 x 10 x 64 x 128.

"cat" versus "join"

Under what conditions should the "cat" (default) and "join" options be used?

Generally speaking, if the leftmost dimension of a variable is a "record" dimension (say, "time") with successive coordinates in each file, then the "cat" option is best. If, however, there is no record dimension (e.g. [lev,lat,lon] where the existing dimensions have the same size and coordinate values in all files), then the "join" option is appropriate.

addfiles_1.ncl - This example illustrates reading a variable off a series of files in "cat" mode.

Assume you have a directory containing several files called pottmp.YYYY.nc, where YYYY represents a year. Each file has a variable called "pottmp" which contains monthly data and is dimensioned time x level x lat x lon (12 x 40 x 418 x 360). Further assume that you only want to read the data for years 1980 to 2008.

This script creates a list of files using ispan to indicate the desired years.

Results:

Variable: pottmp
Type: short
Total Size: 4189363200 bytes
            2094681600 values
Number of Dimensions: 4
Dimensions and sizes: [time | 348] x [level | 40] x [lat | 418] x [lon | 360]
Coordinates: 
            time: [28854..39416]
            level: [ 5..4478]
            lat: [-74.5..64.499]
            lon: [0.5..359.5]
Number Of Attributes: 19
long_name : Potential temperature
units : K
_FillValue : 32766
. . .
addfiles_2.ncl - This example illustrates reading a variable off a series of files in "join" mode. It uses the same data files described in the previous example.

This script is identical to the previous one, except we use the special ListSetType procedure to indicate we want to read the variable in "join" mode.

Results:

Note that you now have a new leftmost dimension called "ncl_join", which is equal to 29 (the number of files):

Variable: pottmp
Type: short
Total Size: 4189363200 bytes
            2094681600 values
Number of Dimensions: 5
Dimensions and sizes: [ncl_join | 29] x [time | 12] x [level | 40] x [lat | 418] x [lon | 360]
Coordinates: 
            time: [28854..29189]
            level: [ 5..4478]
            lat: [-74.5..64.499]
            lon: [0.5..359.5]
Number Of Attributes: 19
long_name : Potential temperature
units : K
_FillValue : 32766
. . .
fao56_1.ncl - This example shows how to read a series of CLM NetCDF files, this time using the systemfunc command to get the list of desired files via the UNIX "ls" command.

 diri = "./"
 fili = systemfunc("cd "+diri+" ; ls BCL_NOTILE_SE_CAM5_1.00.clm2.h0*.nc")

A full description of this script can be found on the Crop and Evapotranspiration examples page.

animate_3_1.ncl - This script illustrates reading a series of WRF output files, each with one time step, to create an animated GIF image (click on thumbnail).

The wrf_user_getvar allows you to input a list of files opened with addfiles, making it easy to calculate WRF diagnostics across a series of files.

A full description of this script can be found on the Animation examples page.