NetCDF for BBMP

• NetCDF is a data file format which is becoming more and more popular in the international oceanogrpahic community
• Self contained files which include data and metadata and can be modified to fit a variety of multi dimensional data types

• Cross platform compatibility, able to be opened, read, edited in most popular programs including python, MATLAB and R

• Contains a large metadata “header” of global attributes describing the entire data set, such as start/ end dates or ship and mission information

• Data sections contains multiple variables, each variable has an individual set of attributes that apply only to the specific data contained within it such as sensor serial number or max/min range

HOW IT WORKS

using R….

library(ncdf4)

ncfname <- 'sample.nc' #name file with .nc extension
ncpath <- './' #set file path

#create dimensions

timedim <- ncdim_def("time", "seconds since 1970-01-01T00:00:00Z", as.double(obj[['time']]))
stationdim <- ncdim_def("station", "counts", as.numeric(obj[['station']]))


#set fill value
FillValue <- 1e35

#define variables

dlname <- 'TEMP_01'
temp_def <- ncvar_def(longname= "temperature", units = 'degrees_celsius', dim = list(stationdim, londim, latdim) , name = dlname, prec = 'double')

#create netCDF shell

ncout <- nc_create(ncfname, vars = temp_def, force_v4 = TRUE)

#insert data into variable slots

ncvar_put(ncout, temp_def, obj[['temperature']])


#metadata

#variable attributes
ncatt_put(ncout, varid = 'TEMP_01', attname = 'sensorID', attval = '010101')

#global attributes
ncatt_put(ncout, varid = 0, attname = 'ship', attval = 'hudson')

#export finished netCDF

nc_close(ncout)

• Potentially useful to BBMP and other monitoring projects for easy storage of data
• easily exported and shared with other institutes, internationally
• self contained metadata is easy to search through (using NCO application or data base like ERDDAP)