DFS2 - Export to NetCDF

# pip install mikeio xarray netcdf4

import mikeio
import xarray as xr
import numpy as np

ds = mikeio.read("../tests/testdata/gebco_sound.dfs2")

ds.Elevation.plot();

The simplest approach is to use the Dataset.to_xarray() or DataArray.to_xarray() method, if no custom information is neeeded.

xr_ds = ds.to_xarray()
xr_ds

<xarray.Dataset>
Dimensions:    (time: 1, y: 264, x: 216)
Coordinates:
  * time       (time) datetime64[ns] 2020-05-15T11:04:52
  * y          (y) float64 55.2 55.21 55.21 55.21 ... 56.29 56.29 56.29 56.3
  * x          (x) float64 12.2 12.21 12.21 12.21 ... 13.09 13.09 13.09 13.1
Data variables:
    Elevation  (time, y, x) float32 -8.0 -8.0 -8.0 -8.0 -9.0 ... nan nan nan nan

xarray.Dataset

• Dimensions:
  • time: 1
  • y: 264
  • x: 216
• Coordinates: (3)
  • time
    (time)
    datetime64[ns]
    2020-05-15T11:04:52

    array(['2020-05-15T11:04:52.000000000'], dtype='datetime64[ns]')

  • y
    (y)
    float64
    55.2 55.21 55.21 ... 56.29 56.3

    array([55.202083, 55.20625 , 55.210417, ..., 56.289583, 56.29375 , 56.297917])

  • x
    (x)
    float64
    12.2 12.21 12.21 ... 13.09 13.1

    array([12.202083, 12.20625 , 12.210417, ..., 13.089583, 13.09375 , 13.097917])

• Data variables: (1)
  • Elevation
    (time, y, x)
    float32
    -8.0 -8.0 -8.0 -8.0 ... nan nan nan

    name :

    Elevation

    units :

    meter

    eumType :

    EUMType.Total_Water_Depth

    eumUnit :

    EUMUnit.meter

    array([[[ -8.,  -8.,  -8., ..., -37., -38., -38.],
            [ -7.,  -7.,  -7., ..., -38., -38., -38.],
            [ -5.,  -6.,  -6., ..., -37., -38., -38.],
            ...,
            [-30., -30., -30., ...,  nan,  nan,  nan],
            [-30., -30., -30., ...,  nan,  nan,  nan],
            [-31., -30., -31., ...,  nan,  nan,  nan]]], dtype=float32)

• Attributes: (0)

xr_da = ds.Elevation.to_xarray()
xr_da

<xarray.DataArray 'Elevation' (time: 1, y: 264, x: 216)>
array([[[ -8.,  -8.,  -8., ..., -37., -38., -38.],
        [ -7.,  -7.,  -7., ..., -38., -38., -38.],
        [ -5.,  -6.,  -6., ..., -37., -38., -38.],
        ...,
        [-30., -30., -30., ...,  nan,  nan,  nan],
        [-30., -30., -30., ...,  nan,  nan,  nan],
        [-31., -30., -31., ...,  nan,  nan,  nan]]], dtype=float32)
Coordinates:
  * time     (time) datetime64[ns] 2020-05-15T11:04:52
  * y        (y) float64 55.2 55.21 55.21 55.21 55.22 ... 56.29 56.29 56.29 56.3
  * x        (x) float64 12.2 12.21 12.21 12.21 12.22 ... 13.09 13.09 13.09 13.1
Attributes:
    name:     Elevation
    units:    meter
    eumType:  EUMType.Total_Water_Depth
    eumUnit:  EUMUnit.meter

xarray.DataArray

'Elevation'

• time: 1
• y: 264
• x: 216

• -8.0 -8.0 -8.0 -8.0 -9.0 -9.0 -9.0 ... nan nan nan nan nan nan nan

  array([[[ -8.,  -8.,  -8., ..., -37., -38., -38.],
          [ -7.,  -7.,  -7., ..., -38., -38., -38.],
          [ -5.,  -6.,  -6., ..., -37., -38., -38.],
          ...,
          [-30., -30., -30., ...,  nan,  nan,  nan],
          [-30., -30., -30., ...,  nan,  nan,  nan],
          [-31., -30., -31., ...,  nan,  nan,  nan]]], dtype=float32)

• Coordinates: (3)
  • time
    (time)
    datetime64[ns]
    2020-05-15T11:04:52

    array(['2020-05-15T11:04:52.000000000'], dtype='datetime64[ns]')

  • y
    (y)
    float64
    55.2 55.21 55.21 ... 56.29 56.3

    array([55.202083, 55.20625 , 55.210417, ..., 56.289583, 56.29375 , 56.297917])

  • x
    (x)
    float64
    12.2 12.21 12.21 ... 13.09 13.1

    array([12.202083, 12.20625 , 12.210417, ..., 13.089583, 13.09375 , 13.097917])

• Attributes: (4)

  name :

  Elevation

  units :

  meter

  eumType :

  EUMType.Total_Water_Depth

  eumUnit :

  EUMUnit.meter

Save it as a NetCDF file:

xr_da.to_netcdf("gebco_std.nc")

Customized NetCDF

1. Time-invariant file -> remove time dimension
2. Rename y, x to lat, lon
3. Lowercase names
4. Add other metadata

x = ds.geometry.x
y = ds.geometry.y

res = {}

spdims = ["lat", "lon"]

if len(ds.time) > 1:
    dims = ["t"] + spdims
    coords = {"t": ds.time}
else:
    dims = spdims
    coords = {}
    
coords["lon"] = xr.DataArray(x, dims="lon", attrs={"standard_name" : "longitude", "units" : "degrees_east"})
coords["lat"] = xr.DataArray(y, dims="lat", attrs={"standard_name" : "latitude", "units" : "degrees_north"})

for da in ds:
    name = da.name.lower()
    res[name] = xr.DataArray(np.squeeze(da.to_numpy()), dims=dims, 
    attrs={'name': name,
            # TODO add standard name from https://cfconventions.org/standard-names.html
            'units': da.unit.name,
            'eumType' : da.type,
            'eumUnit' : da.unit})        

xr_ds = xr.Dataset(res, coords=coords, attrs={'title': 'Converted from Dfs2 by MIKE IO'})

xr_ds

<xarray.Dataset>
Dimensions:    (lon: 216, lat: 264)
Coordinates:
  * lon        (lon) float64 12.2 12.21 12.21 12.21 ... 13.09 13.09 13.09 13.1
  * lat        (lat) float64 55.2 55.21 55.21 55.21 ... 56.29 56.29 56.29 56.3
Data variables:
    elevation  (lat, lon) float32 -8.0 -8.0 -8.0 -8.0 -9.0 ... nan nan nan nan
Attributes:
    title:    Converted from Dfs2 by MIKE IO

xarray.Dataset

• Dimensions:
  • lon: 216
  • lat: 264
• Coordinates: (2)
  • lon
    (lon)
    float64
    12.2 12.21 12.21 ... 13.09 13.1

    standard_name :

    longitude

    units :

    degrees_east

    array([12.202083, 12.20625 , 12.210417, ..., 13.089583, 13.09375 , 13.097917])

  • lat
    (lat)
    float64
    55.2 55.21 55.21 ... 56.29 56.3

    standard_name :

    latitude

    units :

    degrees_north

    array([55.202083, 55.20625 , 55.210417, ..., 56.289583, 56.29375 , 56.297917])

• Data variables: (1)
  • elevation
    (lat, lon)
    float32
    -8.0 -8.0 -8.0 -8.0 ... nan nan nan

    name :

    elevation

    units :

    meter

    eumType :

    EUMType.Total_Water_Depth

    eumUnit :

    EUMUnit.meter

    array([[ -8.,  -8.,  -8., ..., -37., -38., -38.],
           [ -7.,  -7.,  -7., ..., -38., -38., -38.],
           [ -5.,  -6.,  -6., ..., -37., -38., -38.],
           ...,
           [-30., -30., -30., ...,  nan,  nan,  nan],
           [-30., -30., -30., ...,  nan,  nan,  nan],
           [-31., -30., -31., ...,  nan,  nan,  nan]], dtype=float32)

• Attributes: (1)

  title :

  Converted from Dfs2 by MIKE IO

xr_ds.elevation.plot();

xr_ds.to_netcdf("gebco.nc")

Clean up

import os
os.remove("gebco_std.nc")
os.remove("gebco.nc")