xarray ODIM backend

In this example, we read ODIM_H5 (HDF5) data files using the xarray odim backend.

[1]:
import glob
import os
import wradlib as wrl
import warnings
warnings.filterwarnings('ignore')
import matplotlib.pyplot as pl
import numpy as np
import xarray as xr
try:
    get_ipython().magic("matplotlib inline")
except:
    pl.ion()
from wradlib.io import open_odim_dataset

Load ODIM_H5 Volume Data

[2]:
fpath = 'hdf5/knmi_polar_volume.h5'
f = wrl.util.get_wradlib_data_file(fpath)
vol = wrl.io.open_odim_dataset(f)

Inspect RadarVolume

[3]:
display(vol)
<wradlib.RadarVolume>
Dimension(s): (sweep: 14)
Elevation(s): (0.3, 0.4, 0.8, 1.1, 2.0, 3.0, 4.5, 6.0, 8.0, 10.0, 12.0, 15.0, 20.0, 25.0)

Inspect root group

The sweep dimension contains the number of scans in this radar volume. Further the dataset consists of variables (location coordinates, time_coverage) and attributes (Conventions, metadata).

[4]:
vol.root
[4]:
<xarray.Dataset>
Dimensions:              (sweep: 14)
Coordinates:
    time                 datetime64[ns] 2011-06-10T11:40:02
    sweep_mode           <U20 'azimuth_surveillance'
    longitude            float64 4.79
    altitude             float64 50.0
    latitude             float64 52.95
Dimensions without coordinates: sweep
Data variables:
    volume_number        int64 0
    platform_type        <U5 'fixed'
    instrument_type      <U5 'radar'
    primary_axis         <U6 'axis_z'
    time_coverage_start  <U20 '2011-06-10T11:40:02Z'
    time_coverage_end    <U20 '2011-06-10T11:43:54Z'
    sweep_group_name     (sweep) <U8 'sweep_0' 'sweep_1' ... 'sweep_13'
    sweep_fixed_angle    (sweep) float64 0.3 0.4 0.8 1.1 ... 12.0 15.0 20.0 25.0
Attributes:
    version:          None
    title:            None
    institution:      None
    references:       None
    source:           None
    history:          None
    comment:          im/exported using wradlib
    instrument_name:  None
    fixed_angle:      0.30000001192092896

Inspect sweep group(s)

The sweep-groups can be accessed via their respective keys. The dimensions consist of range and time with added coordinates azimuth, elevation, range and time. There will be variables like radar moments (DBZH etc.) and sweep-dependend metadata (like fixed_angle, sweep_mode etc.).

[5]:
display(vol[0])
<xarray.Dataset>
Dimensions:     (azimuth: 360, range: 320)
Coordinates:
  * azimuth     (azimuth) float32 0.5 1.5 2.5 3.5 ... 356.5 357.5 358.5 359.5
    elevation   (azimuth) float32 0.3 0.3 0.3 0.3 0.3 ... 0.3 0.3 0.3 0.3 0.3
    rtime       (azimuth) datetime64[ns] 2011-06-10T11:40:17.361118208 ... 20...
  * range       (range) float32 500.0 1.5e+03 2.5e+03 ... 3.185e+05 3.195e+05
    time        datetime64[ns] 2011-06-10T11:40:02
    sweep_mode  <U20 'azimuth_surveillance'
    longitude   float64 4.79
    latitude    float64 52.95
    altitude    float64 50.0
Data variables:
    DBZH        (azimuth, range) float32 ...
Attributes:
    fixed_angle:  0.30000001192092896

Goereferencing

[6]:
swp = vol[0].copy().pipe(wrl.georef.georeference_dataset)

Plotting

[7]:
swp.DBZH.plot.pcolormesh(x='x', y='y')
pl.gca().set_aspect('equal')
../../_images/notebooks_fileio_wradlib_odim_backend_14_0.png
[8]:
fig = pl.figure(figsize=(10,10))
swp.DBZH.wradlib.plot_ppi(proj='cg', fig=fig)
[8]:
<matplotlib.collections.QuadMesh at 0x7f2fe8a8a340>
../../_images/notebooks_fileio_wradlib_odim_backend_15_1.png
[9]:
import cartopy
import cartopy.crs as ccrs
import cartopy.feature as cfeature

map_trans = ccrs.AzimuthalEquidistant(central_latitude=swp.latitude.values,
                                      central_longitude=swp.longitude.values)
[10]:
map_proj = ccrs.AzimuthalEquidistant(central_latitude=swp.latitude.values,
                                      central_longitude=swp.longitude.values)
pm = swp.DBZH.wradlib.plot_ppi(proj=map_proj)
ax = pl.gca()
ax.gridlines(crs=map_proj)
print(ax)
< GeoAxes: <cartopy.crs.AzimuthalEquidistant object at 0x7f2fe0710ef0> >
../../_images/notebooks_fileio_wradlib_odim_backend_17_1.png
[11]:
map_proj = ccrs.Mercator(central_longitude=swp.longitude.values)
fig = pl.figure(figsize=(10,8))
ax = fig.add_subplot(111, projection=map_proj)
pm = swp.DBZH.wradlib.plot_ppi(ax=ax)
ax.gridlines(draw_labels=True)
[11]:
<cartopy.mpl.gridliner.Gridliner at 0x7f2fdcf47a60>
../../_images/notebooks_fileio_wradlib_odim_backend_18_1.png
[12]:
import cartopy.feature as cfeature
def plot_borders(ax):
    borders = cfeature.NaturalEarthFeature(category='physical',
                                           name='coastline',
                                           scale='10m',
                                           facecolor='none')
    ax.add_feature(borders, edgecolor='black', lw=2, zorder=4)

map_proj = ccrs.Mercator(central_longitude=swp.longitude.values)
fig = pl.figure(figsize=(10,8))
ax = fig.add_subplot(111, projection=map_proj)

DBZH = swp.DBZH
pm = DBZH.where(DBZH > 0).wradlib.plot_ppi(ax=ax)
plot_borders(ax)
ax.gridlines(draw_labels=True)
[12]:
<cartopy.mpl.gridliner.Gridliner at 0x7f2fdcec2c40>
../../_images/notebooks_fileio_wradlib_odim_backend_19_1.png
[13]:
import matplotlib.path as mpath
theta = np.linspace(0, 2*np.pi, 100)
center, radius = [0.5, 0.5], 0.5
verts = np.vstack([np.sin(theta), np.cos(theta)]).T
circle = mpath.Path(verts * radius + center)

map_proj = ccrs.AzimuthalEquidistant(central_latitude=swp.latitude.values,
                                     central_longitude=swp.longitude.values,
                                    )
fig = pl.figure(figsize=(10,8))
ax = fig.add_subplot(111, projection=map_proj)
ax.set_boundary(circle, transform=ax.transAxes)

pm = swp.DBZH.wradlib.plot_ppi(proj=map_proj, ax=ax)
ax = pl.gca()
ax.gridlines(crs=map_proj)
[13]:
<cartopy.mpl.gridliner.Gridliner at 0x7f2fdcd6db50>
../../_images/notebooks_fileio_wradlib_odim_backend_20_1.png
[14]:
fig = pl.figure(figsize=(10, 8))
proj=ccrs.AzimuthalEquidistant(central_latitude=swp.latitude.values,
                               central_longitude=swp.longitude.values)
ax = fig.add_subplot(111, projection=proj)
pm = swp.DBZH.wradlib.plot_ppi(ax=ax)
ax.gridlines()
[14]:
<cartopy.mpl.gridliner.Gridliner at 0x7f2fdca05220>
../../_images/notebooks_fileio_wradlib_odim_backend_21_1.png
[15]:
swp.DBZH.wradlib.plot_ppi()
[15]:
<matplotlib.collections.QuadMesh at 0x7f2fdcc67f10>
../../_images/notebooks_fileio_wradlib_odim_backend_22_1.png

Inspect radar moments

The DataArrays can be accessed by key or by attribute. Each DataArray has dimensions and coordinates of it’s parent dataset. There are attributes connected which are defined by ODIM_H5 standard.

[16]:
display(swp.DBZH)
<xarray.DataArray 'DBZH' (azimuth: 360, range: 320)>
array([[ 22. ,  17. ,  -8. , ..., -31.5, -31.5, -31.5],
       [ 24. ,  24.5,  -9. , ..., -31.5, -31.5, -31.5],
       [ 35.5,  42. ,  12. , ..., -31.5, -31.5, -31.5],
       ...,
       [ 23. ,  14. , -13. , ..., -31.5, -31.5, -31.5],
       [ 23. ,  14. ,  -9. , ..., -31.5, -31.5, -31.5],
       [ 22. ,  18.5, -11.5, ..., -31.5, -31.5, -31.5]], dtype=float32)
Coordinates: (12/15)
  * azimuth     (azimuth) float32 0.5 1.5 2.5 3.5 ... 356.5 357.5 358.5 359.5
    elevation   (azimuth) float32 0.3 0.3 0.3 0.3 0.3 ... 0.3 0.3 0.3 0.3 0.3
    rtime       (azimuth) datetime64[ns] 2011-06-10T11:40:17.361118208 ... 20...
  * range       (range) float32 500.0 1.5e+03 2.5e+03 ... 3.185e+05 3.195e+05
    time        datetime64[ns] 2011-06-10T11:40:02
    sweep_mode  <U20 'azimuth_surveillance'
    ...          ...
    x           (azimuth, range) float32 4.363 13.09 ... -2.777e+03 -2.786e+03
    y           (azimuth, range) float32 500.0 1.5e+03 ... 3.183e+05 3.193e+05
    z           (azimuth, range) float32 53.0 58.0 64.0 ... 7.691e+03 7.734e+03
    gr          (azimuth, range) float32 500.0 1.5e+03 ... 3.183e+05 3.193e+05
    rays        (azimuth, range) float32 0.5 0.5 0.5 0.5 ... 359.5 359.5 359.5
    bins        (azimuth, range) float32 500.0 1.5e+03 ... 3.185e+05 3.195e+05
Attributes:
    _Undetect:      [0.]
    long_name:      Equivalent reflectivity factor H
    units:          dBZ
    standard_name:  radar_equivalent_reflectivity_factor_h

Create simple plot

Using xarray features a simple plot can be created like this. Note the sortby('rtime') method, which sorts the radials by time.

[17]:
swp.DBZH.sortby('rtime').plot(x="range", y="rtime", add_labels=False)
[17]:
<matplotlib.collections.QuadMesh at 0x7f2fdccf5220>
../../_images/notebooks_fileio_wradlib_odim_backend_26_1.png
[18]:
fig = pl.figure(figsize=(5,5))
pm = swp.DBZH.wradlib.plot_ppi(proj={'latmin': 33e3}, fig=fig)
../../_images/notebooks_fileio_wradlib_odim_backend_27_0.png

Mask some values

[19]:
swp['DBZH'] = swp['DBZH'].where(swp['DBZH'] >= 0)
swp['DBZH'].plot()
[19]:
<matplotlib.collections.QuadMesh at 0x7f2fdca9f760>
../../_images/notebooks_fileio_wradlib_odim_backend_29_1.png

Export to ODIM and CfRadial2

[20]:
vol.to_odim('knmi_odim.h5')
vol.to_cfradial2('knmi_odim_as_cfradial.nc')

Import again

[21]:
vola = wrl.io.open_odim_dataset('knmi_odim.h5')
[22]:
volb = wrl.io.open_cfradial2_dataset('knmi_odim_as_cfradial.nc')

Check equality

[23]:
xr.testing.assert_allclose(vol.root, vola.root)
xr.testing.assert_equal(vol[0], vola[0])
xr.testing.assert_allclose(vol.root, volb.root)
xr.testing.assert_equal(vol[0], volb[0])
xr.testing.assert_allclose(vola.root, volb.root)
xr.testing.assert_equal(vola[0], volb[0])

More ODIM loading mechanisms

Use xr.open_dataset to retrieve explicit group

[24]:
swp = xr.open_dataset(f, engine="odim", group="dataset14")
display(swp)
<xarray.Dataset>
Dimensions:     (azimuth: 360, range: 240)
Coordinates:
  * azimuth     (azimuth) float32 0.5 1.5 2.5 3.5 ... 356.5 357.5 358.5 359.5
    elevation   (azimuth) float32 25.0 25.0 25.0 25.0 ... 25.0 25.0 25.0 25.0
    rtime       (azimuth) datetime64[ns] 2011-06-10T11:43:48.763874560 ... 20...
  * range       (range) float32 250.0 750.0 1.25e+03 ... 1.192e+05 1.198e+05
    time        datetime64[ns] 2011-06-10T11:43:45
    sweep_mode  <U20 'azimuth_surveillance'
    longitude   float64 4.79
    latitude    float64 52.95
    altitude    float64 50.0
Data variables:
    DBZH        (azimuth, range) float32 -31.5 -0.5 0.0 ... -31.5 -31.5 -31.5
Attributes:
    fixed_angle:  25.0

Use xr.open_mfdataset to retrieve timeseries of explicit group

[25]:
fpath = os.path.join(wrl.util.get_wradlib_data_path(), "hdf5/71*.h5")
f = glob.glob(fpath)
ts = xr.open_mfdataset(f, engine="odim", concat_dim="time", combine="nested", group="dataset1")
display(ts)
<xarray.Dataset>
Dimensions:     (time: 2, azimuth: 360, range: 1200)
Coordinates:
  * azimuth     (azimuth) float32 0.5 1.5 2.5 3.5 ... 356.5 357.5 358.5 359.5
    elevation   (azimuth) float32 dask.array<chunksize=(360,), meta=np.ndarray>
    rtime       (time, azimuth) datetime64[ns] 2018-12-20T06:12:41.009703424 ...
  * range       (range) float32 125.0 375.0 625.0 ... 2.996e+05 2.999e+05
  * time        (time) datetime64[ns] 2018-12-20T06:12:28 2018-12-20T06:06:28
    sweep_mode  <U20 'azimuth_surveillance'
    longitude   float64 151.2
    latitude    float64 -33.7
    altitude    float64 195.0
Data variables:
    DBZH        (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    DBZH_CLEAN  (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    VRADDH      (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    VRADH       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    WRADH       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    TH          (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    ZDR         (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    RHOHV       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    PHIDP       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    KDP         (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    SNRH        (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
Attributes:
    fixed_angle:  0.5

Use wrl.io.open_odim_mfdataset to retrieve volume timeseries

[26]:
fpath = os.path.join(wrl.util.get_wradlib_data_path(), "hdf5/71*.h5")
f = glob.glob(fpath)
ts = wrl.io.open_odim_mfdataset(f)
display(ts)
100%|██████████| 14/14 [00:03<00:00,  3.51it/s]
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/micromamba/envs/wradlib-tests/lib/python3.9/site-packages/IPython/core/formatters.py in __call__(self, obj)
    700                 type_pprinters=self.type_printers,
    701                 deferred_pprinters=self.deferred_printers)
--> 702             printer.pretty(obj)
    703             printer.flush()
    704             return stream.getvalue()

~/micromamba/envs/wradlib-tests/lib/python3.9/site-packages/IPython/lib/pretty.py in pretty(self, obj)
    392                         if cls is not object \
    393                                 and callable(cls.__dict__.get('__repr__')):
--> 394                             return _repr_pprint(obj, self, cycle)
    395
    396             return _default_pprint(obj, self, cycle)

~/micromamba/envs/wradlib-tests/lib/python3.9/site-packages/IPython/lib/pretty.py in _repr_pprint(obj, p, cycle)
    698     """A pprint that just redirects to the normal repr function."""
    699     # Find newlines and replace them with p.break_()
--> 700     output = repr(obj)
    701     lines = output.splitlines()
    702     with p.group():

~/micromamba/envs/wradlib-tests/lib/python3.9/site-packages/wradlib/io/xarray.py in __repr__(self)
   2211         summary.append("{} ({})".format(dims, dims_summary))
   2212         dim0 = list(set(self[0].dims) & {"azimuth", "elevation", "time"})[0]
-> 2213         angle = f"{self._dims[dim0].capitalize()}(s):"
   2214         angle_summary = [f"{v.attrs['fixed_angle']:.1f}" for v in self]
   2215         angle_summary = ", ".join(angle_summary)

KeyError: 'time'
[27]:
display(ts[0])
<xarray.Dataset>
Dimensions:     (time: 2, azimuth: 360, range: 1200)
Coordinates:
  * azimuth     (azimuth) float32 0.5 1.5 2.5 3.5 ... 356.5 357.5 358.5 359.5
    elevation   (azimuth) float32 dask.array<chunksize=(360,), meta=np.ndarray>
    rtime       (time, azimuth) datetime64[ns] 2018-12-20T06:12:41.009703424 ...
  * range       (range) float32 125.0 375.0 625.0 ... 2.996e+05 2.999e+05
  * time        (time) datetime64[ns] 2018-12-20T06:12:28 2018-12-20T06:06:28
    sweep_mode  <U20 'azimuth_surveillance'
    longitude   float64 151.2
    latitude    float64 -33.7
    altitude    float64 195.0
Data variables:
    DBZH        (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    DBZH_CLEAN  (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    VRADDH      (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    VRADH       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    WRADH       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    TH          (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    ZDR         (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    RHOHV       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    PHIDP       (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    KDP         (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
    SNRH        (time, azimuth, range) float32 dask.array<chunksize=(1, 360, 1200), meta=np.ndarray>
Attributes:
    fixed_angle:  0.5