NetCDF
From BAWiki
General Aspects
Purpose of these BAWiki Pages
These BAWiki pages do describe all NetCDF conventions required to store baw-specific data in NetCDF data files (see network common data form). I. e. all local conventions are listed, which go beyond the international agreed-upon CF-metadata convention.
In cases where the international agreed-upon CF conventions are insufficient, essentially the Unstructured Grid Metadata Conventions for Scientific Datasets (UGRID Conventions) published on GITHUB are used.
Further activities related with OpenDAP to extract a selection of data defined on unstructured grids can be found on e. g. OPULS.
Some further widely spread templates known are the NODC NetCDF Templates. The NODC data center has been recently merged with other data centers and is now part of National Centers for Environmental Information (NCEI).
The BAW instance of a NetCDF file developed since 2010 is a file of type CF-NETCDF.NC.
Since version NetCDF-4.0 HDF (Hierarchical Data File, see HDF5 Group) is used as the underlying file format. Due to the use of HDF concepts like online compression of data stored in NetCDF files is supported as well as chunking of variables to balance read performance in case of different access to data, e.g. time-series vs. synoptic data set access.
Important NetCDF Utilities
Important (helpful) NetCDF Utilities are:
- NCDUMP create (selective) text representation of the contents of a NetCDF file;
- NCCOPY (selective) copy an existing NetCDF file to another, change level of compression, change internal file structure (File Chunking); and
- NCGEN create NetCDF file from a CDL text file; optionally also C or FORTRAN code can be automatically generated.
File Chunking
The chunk size of variables stored in a CF NetCDF file may have significant influence on read performance in case data have to be read along different dimensions, e.g. spatial versus time-series access. Chunk size can be individually tuned using the NetCDF API. As a simple alternative, already helpful in many situations, you can also make use of the NCCOPY program. For further informations about chunking please read the following informations:
NetCDF vs. GRIB
Besides NetCDF GRIB is also widely used. Concerning problems of interoperability between NetCDF and GRIB a workshop was held at ECMWF in September 2014 . Further informatioins can be found on the website of the workshop on Closing the GRIB/NetCDF gap.
Literature
Signell, R. P. und Snowden, D. P. (2014) Advances in a Distributed Approach for Ocean Model Data Interoperability. J. Mar. Sci. Eng. 2014, 2, 194-208. Describes also the benefits using UGRID CF metadata standard to store data in netCDF files.
How to acknowledge Unidata
"Software and technologies developed and distributed by the Unidata Program Center are (with very few exceptions) Free and Open Source, and you can use them in your own work with no restrictions. In order to continue developing software and providing services to the Unidata community, it is important that the Unidata Program Center be able to demonstrate the value of the technologies we develop and services we provide to our sponsors — most notably the National Science Foundation. Including an acknowledgement in your publication or web site helps us do this."
"It helps even more if we are aware of what you're doing. If you're using Unidata technologies and citing them in a paper, poster, thesis, or other venue, we'd be grateful if you would let us know about it by sending a short message to support@unidata.ucar.edu. Thanks!"
Informal
- This project took advantage of netCDF software developed by UCAR/Unidata (www.unidata.ucar.edu/software/netcdf/).
Citation
- Unidata, (year): Package name version number [software]. Boulder, CO: UCAR/Unidata Program Center. Available from URL-to-software-page.
Where is NetCDF used?
Wo wird NetCDF verwendet?
For an overview please visit Where is NetCDF used?.
Terminology
Global Attributes
Grids
- NetCDF multiple locations: several (point) locations, e. g. equivalent to contents of file location_grid.dat;
- NetCDF multiple profiles: several longitudinal and cross-sectional profiles, e. g. equivalent to contents of file profil05.bin;
- NetCDF triangular grid: triangular grid, e. g. equivalent to contents of file gitter05.dat and gitter05.bin;
- NetCDF unstructured grid: unstructured grid, e. g. equivalent to contents of file untrim_grid.dat;
- NetCDF unstructured grid with subgrid: unstructured grid with additional subgrid data, e. g. equivalent to contents of file utrsub_grid.dat.
Time Coordinate
- NetCDF time coordinate: date and time, calendar.
Vertical Coordinate
- NetCDF vertical coordinate: dimensional vertical coordinate (height, depth).
Horizontal Coordinate Reference System
Reduction of Dataset Size
Traditionally, up to the availability of NetCDF-4 (HDF),
were the only ways to reduce data set sizes. Now, with the availability of NetCDF-4 (HDF), it is recommended to use online compression instead. Online compression can be activated on a per variable basis via the NetCDF API. For existing NetCDF files NCCOPY also allows you to (online-) compress the file after it has been created.
Data
Synoptic Data
- NetCDF synoptic data at multiple locations,
- NetCDF synoptic data for multiple profiles,
- NetCDF cross section integral synoptic data for multiple profiles,
- NetCDF synoptic data for triangular grid,
- NetCDF synoptic (morphological) data for triangular grid,
- NetCDF synoptic data for unstructured grid,
- NetCDF synoptic data for unstructured grid with subgrid, and
- NetCDF DelWAQ data.
Time Series Data
Analysis Data
- NetCDF tidal characteristic numbers of water level, and
- NetCDF differences for tidal characteristic numbers of water level.
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