Reading output in Python

The helita package has a complete python interface to read the output, input, and visualise files from RH 1.5D. The helita tools are described in detail in section helita.

If helita is not available, the easiest and fastest way to read the RH 1.5D output (or input) files in Python is via the xarray package. xarray can load the output files as a dataset directly, but in the case of the output_aux.hdf5 and output_indata.hdf5 one needs to specify which group to read (see above).

Here is a quick example on how to read some output from RH 1.5D with xarray:

>>> import xarray
>>> ray = xarray.open_dataset("output_ray.hdf5")
>>> ray
<xarray.Dataset>
Dimensions:              (height: 82, wavelength: 902, wavelength_selected: 10, x: 1, y: 1)
Coordinates:
  * wavelength           (wavelength) float64 28.0 31.4 32.8 33.7 34.3 35.3 ...
  * wavelength_selected  (wavelength_selected) float64 85.1 276.4 278.5
  * x                    (x) float64 0.0
  * y                    (y) float64 0.0
Dimensions without coordinates: height
Data variables:
    Jlambda              (x, y, height, wavelength_selected) float64 ...
    chi                  (x, y, height, wavelength_selected) float64 ...
    intensity            (x, y, wavelength) float64 ...
    scattering           (x, y, height, wavelength_selected) float64 ...
    source_function      (x, y, height, wavelength_selected) float64 ...
    wavelength_indices   (wavelength_selected) int32 ...
Attributes:
    atmosID:              FALC_82_5x5.hdf5 (Wed Jan 10 15:29:28 2018)
    snapshot_number:      0
    rev_id:               001d537  Tiago Pereira  2018-01-10 12:34:07 +0100
    nx:                   1
    ny:                   1
    nz:                   82
    nwave:                902
    wavelength_selected:  3
    creation_time:        2018-01-10T16:16:42+0100
>>> aux = xarray.open_dataset("output_aux.hdf5", group="atom_MG")
>>> aux
<xarray.Dataset>
Dimensions:          (continuum: 10, height: 82, level: 11, line: 15, x: 1, y: 1)
Coordinates:
  * x                (x) float64 0.0
  * y                (y) float64 0.0
Dimensions without coordinates: continuum, height, level, line
Data variables:
    Rij_continuum    (continuum, x, y, height) float64 ...
    Rij_line         (line, x, y, height) float64 ...
    Rji_continuum    (continuum, x, y, height) float64 ...
    Rji_line         (line, x, y, height) float64 ...
    populations      (level, x, y, height) float64 ...
    populations_LTE  (level, x, y, height) float64 ...
Attributes:
    nlevel:      11
    nline:       15
    ncontinuum:  10