R/dbpf_export_nc_chain_ortho.R

In geocryology/PermafrostDB: PermafrostDB

# =============================================================================
#'
#' @title Download ground temperature time series to netCDF
#'
#' @description Downloads one or more time series from the carleton permafrost
#' database and export as a netCDF file. The netCDF file is designed to
#' accommodate many stations with the same measurement depths.  It is possible
#' to group stations with different measurement depths but this is at the cost
#' of wasted space because any non-shared measurement depths will be filled with
#' null values.
#'
#' @details Requires that the PermafrostDB, reshape2 and ncdf4 packages be
#' installed. The file structure is based on H.5.1. "Multidimensional array
#' representations of time series profiles" with  Example H.16 used as a
#' template and a one-dimensional time coordinate variable.
#'
#' @param con Database connection object, as returned by dbpf_con()
#'
#' @param location_name Character, one or more location names to convert. These should
#' correspond to locations with thermistor strings
#'
#' @param file_name character, path to output netCDF file (*.nc)
#'
#' @param freq Character, one of ('daily', 'hourly'). Interval at which data is to
#' be aggregated from the database.
#'
#' @export
#' @author Nick Brown <nick.brown@@carleton.ca>
# =============================================================================

dbpf_export_nc_chain_ortho <- function(con, location_name, file_name, freq='daily'){

  period <- switch(tolower(freq), 'daily'=24, 'hourly'=1)

  ## Get data from DB
  db_dat <- dbpf_observations_agg(con = con,
                                  location_name = location_name,
                                  period = period)

  #reshape and get values
  db_dat$height <- abs(db_dat$height)
  db_dat <- db_dat[,c("loc_name", "height", "agg_avg", "time")]

  m <- reshape2::acast(db_dat,
           formula = height ~ time ~ loc_name,
           value.var = 'agg_avg',
           fun.aggregate = function(x) x[1])

  refdate <- as.POSIXct("1970-01-01 00:00:00", fmt="%Y-%m-%D %T", tz='UTC')

  vals_time <- as.POSIXct(dimnames(m)[[2]], fmt="%Y-%m-%D %T", tz='UTC')
  if (tolower(freq) == 'daily'){
    vals_time <- vals_time - refdate
    time_units <- "days since 1970-01-01 00:00:00"
  }else if(tolower(freq) == 'hourly'){
    vals_time <- as.numeric(vals_time) - as.numeric(refdate)
    time_units <- "seconds since 1970-01-01 00:00:00"
    print(class(utils::head(vals_time)))
  }

  vals_tmp <- m
  vals_name <- dimnames(m)[[3]]
  vals_depths <- -as.numeric(dimnames(m)[[1]])

  n_ts <- dim(m)[2]
  n_depth <- dim(m)[1]
  n_stations <- dim(m)[3]

  ## Get coordinate data
  loc <- dbpf_locations(con)
  coords <- loc[match(location_name, loc$name),
                c('name','lon', 'lat', 'elevation_in_metres')]

  ## Create .nc file
  nc <- createOrthogonalThermistorNCF(file = file_name,
                                      n_timestep = n_ts,
                                      n_stations = n_stations,
                                      n_depth = n_depth,
                                      close_file=F)

  ## Populate data
  ncvar_put(nc, varid='depth', vals=vals_depths)
  ncvar_put(nc, varid='time', vals = vals_time)
  ncvar_put(nc, varid="soil_temperature", vals = vals_tmp) #unique(db_dat$agg_avg))
  ncvar_put(nc, varid="platform_id", vals = vals_name)
  ncvar_put(nc, varid='latitude', vals = coords$lat)
  ncvar_put(nc, varid='longitude', vals = coords$lon)
  ncvar_put(nc, varid='elevation', vals = coords$elevation_in_metres)

  ## Close file
  nc_close(nc)
}

# =============================================================================
#'
#' @title Create empty netCDF file thermistor stations with identical measurement
#' depths
#'
#' @description Creates a netCDF file with specified dimensions. The file has no
#' data within it, but must be added in afterwards.
#'
#' @details The file structure is based on H.5.1. "Multidimensional array of
#'  time series profiles representation of time series"
#' (http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#_multidimensional_array_representations_of_time_series_profiles)
#'
#' @param file Character, path to output netCDF file (*.nc)
#'
#' @param n_timestep Integer, the number of unique timesteps for which there is
#' temperature data
#'
#' @param n_depth Integer, the largest number of depth measurements in any
#'  profile
#'
#' @param n_stations  Integer, how many sites are to be added to the file
#'
#' @param close_file Logical, whether or not to close the connection to the file
#'  after creation. Leaving the file open allows for the immediate addition of
#'  data. Defaults to FALSE.
#' 
#' @param time_units netcdf4-style string description of time units 
#'
#' @export
#'
#' @author Nick Brown <nick.brown@@carleton.ca>
# =============================================================================
createOrthogonalThermistorNCF <- function(file, n_stations, n_timestep,
                                          n_depth, close_file=F,
                                          time_units="days since 1970-01-01 00:00:00"){
  missval <- -999
  ## Create Dimensions
  dummyDimTime <- c(1:n_timestep)
  dimTime <- ncdim_def("time",
                       units=time_units, unlim = F,
                       vals = dummyDimTime,
                       create_dimvar = T)

  dummyDimStation <- c(1:n_stations)
  dimStation <- ncdim_def("station",
                          unlim = F, vals = dummyDimStation, units = '',
                          create_dimvar = F)

  dummyDimDepth <- c(1:n_depth)*0.1 # so that the coordinate var is float not int
  dimDepth <- ncdim_def('depth',
                        unlim = F, vals = dummyDimDepth, units = '',
                        create_dimvar = T)

  dummyDimNameStrlen <- c(1:25)
  dimNameStrlen <- ncdim_def("name_strlen",
                             unlim = F, vals = dummyDimNameStrlen, units = '',
                             create_dimvar = F)

  ## Create Variables

  varLon <- ncvar_def(name = 'longitude', prec='float',
                      units = "degrees_E",
                      dim = list(dimStation),
                      longname = "Longitude")

  varLat <- ncvar_def(name = 'latitude', prec='float',
                      units = "degrees_N",
                      dim = list(dimStation),
                      longname = "Latitude")

  varElev <- ncvar_def(name= 'elevation', prec='float',
                       units = 'm',
                       dim=list(dimStation),
                       longname = "Station surface elevation")

  varStnName <- ncvar_def(name = 'platform_id', prec='char',
                          units = '',
                          dim = list(dimNameStrlen, dimStation),
                          longname = "Station Name")

  varTemp <- ncvar_def(name = 'soil_temperature', prec='float',
                       units = "degrees_C",
                       dim = list(dimDepth, dimTime, dimStation),
                       longname = "Ground temperature")


  ## Create File
  ncnew <- nc_create(file, vars = list(varLon, varLat, varElev, varStnName,
                                       varTemp))

  ## Create Attributes from templates in '/PermafrostDB/extdata' or
  ##                                    '/PermafrostDB/inst/extdata' (unbuilt)
  f <- 'extdata'
  p <- 'PermafrostDB'
  nc_attributes_from_template(ncnew, system.file(f, 'depth.csv', package=p))
  nc_attributes_from_template(ncnew, system.file(f, 'latitude.csv', package=p))
  nc_attributes_from_template(ncnew, system.file(f, 'longitude.csv', package=p))
  nc_attributes_from_template(ncnew, system.file(f, 'platform_id.csv', package=p))
  nc_attributes_from_template(ncnew, system.file(f, 'soil_temperature.csv', package=p))
  nc_attributes_from_template(ncnew, system.file(f, 'time.csv', package=p))
  nc_attributes_from_template(ncnew, system.file(f, '_global_CU_database.csv', package=p))

  ## Close File or Return
  if (close_file){
    nc_close(ncnew)
    return(file)
  }else{
    return(ncnew)
  }
}