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Introduction to NetCDF

Introduction to NetCDF. Ernesto Munoz. Outline. Overview of NetCDF NetCDF file information CDL utilities: ncdump, ncgen Reading NetCDF file with Fortran with GrADS with Matlab Writing NetCDF file. What is NetCDF?. Network Common Data Form (NetCDF)

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Introduction to NetCDF

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  1. Introduction to NetCDF Ernesto Munoz

  2. Outline • Overview of NetCDF • NetCDF file information • CDL utilities: ncdump, ncgen • Reading NetCDF file • with Fortran • with GrADS • with Matlab • Writing NetCDF file

  3. What is NetCDF? • Network Common Data Form (NetCDF) • An interface for (array-oriented) data access • A collection of libraries of data-access routines (for Fortran, C++, etc.) • A machine-independent format for scientific data • Developed at Unidata UCAR • More information at: • www.unidata.ucar.edu/software/netcdf/

  4. Positive Attributes of NetCDF • Self-describing – includes information about the data it contains • Portable - A machine-independent binary data format • Direct-access – can access efficiently a subset of the dataset

  5. NetCDF file contents • Dimensions Information about its name and length At most one unlimited dimension (i.e., a dimension with no maximum size) • Variables Information about its name, type, shape, attributes & values • Coordinate variable: 1-D array with the same name as its dimension (e.g., latitude) • Primary variable: the data • Fixed-length variable: primary variable with fixed dimensions • Record variable: primary variable with an unlimited dimension • Attributes –“metadata” Information about its name, type, values & length • Variable attributes • Global attributes

  6. Example of NetCDF file contents • Data values on a 2-D latitude/longitude grid • E.g., zonal and meridional wind data • Information about the dimensions • Latitudes, longitudes, vertical levels and times • The units of the data values • Scaling factor and offset to be applied to data

  7. CDL - Common Data Language • NetCDF ↔ ASCII translator • Its two main utilities: 1. ncdump (from netcdf to ascii) • to get overview of NetCDF file contents 2. ncgen (from ascii to netcdf) • to create NetCDF files • to create Fortran (or C) programs to write NetCDF files

  8. ncdump For quick glimpse at file’s “metadata” • To view header info: ncdump -h myfile.nc • To view header info plus values of coordinate variables: ncdump -c myfile.nc • To output data values in ascii form: ncdump –v varname myfile.nc

  9. Exercise Look at description of file with ncdump • Compare -c and -h options ncdump -h myfile.nc > filehdr.txt ncdump -c myfile.nc > filehdrdim.txt

  10. Reading NetCDF with Fortran Typical order of calls to read a NetCDF file NF_OPEN ! open NetCDF dataset . . . . . NF_INQ_DIMID ! get dimensions IDs . . . . . NF_INQ_DIMLEN ! get dimensions lengths . . . . . NF_INQ_VARID ! get variables IDs . . . . . NF_GET_ATT ! get attribute values . . . . . NF_GET_VAR ! get values of variables . . . . . NF_CLOSE ! close NetCDF dataset

  11. Reading NetCDF • With Matlab • Read Takemasa’s memo at: • http://www.atmos.umd.edu/~miyoshi/memorandum/memo_netcdf.html • With GrADS • Open GrADS with gradsnc command (instead of grads) • Open NetCDF file with sdfopen command (instead of open) • For more information refer to: http://grads.iges.org/grads/gadoc/SDFdescriptorfile.html

  12. Writing a NetCDF file with ncgen • ncgen can be used to: • Generate code that will produce a NetCDF file Fortran: ncgen -f mydata.cdl > mydata.f C: ncgen -c mydata.cdl > mydata.c • Generate a NetCDF file ncgen -o mydata.nc mydata.cdl • Best practices to writing NetCDF files: • www.unidata.ucar.edu/software/netcdf/docs/BestPractices.html

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