Concept

The hierarchical IMAS data model is represented in OMAS as a set of nested ODS objects (OMAS Data Structure).

The ODS class extends native Python dictionary and list classes with:

1. On-the-fly check for compliance with IMAS data model

   • enforce consistency with IMAS data structure

   • enforce correct data type

   • enforce correct number of data dimensions (1D, 2D, 3D, …)

   • warn if obsolescent IMAS entries are used

2. Graceful error handling with suggestions for navigating the hierarchical data structure:

   LookupError: `equilibrium.time_slice.:.does_not_exist` is not a valid IMAS location
                                          ^^^^^^^^^^^^^^
   Did you mean: ['coordinate_system', 'profiles_1d', 'profiles_2d', 'ggd', 'time', 'convergence', 'boundary', 'global_quantities', 'constraints']
   

3. Dynamic creation of the tree hierarchy as items they are accessed with support for different syntaxes:

   ods['equilibrium']['time_slice'][0]['profiles_2d'][0]['psi']   # standard Python dictionary syntax
   ods[['equilibrium','time_slice',0,'profiles_2d',0,'psi']]      # list of nodes syntax
   ods['equilibrium.time_slice[0].profiles_2d[0].psi']            # IMAS hierarchical tree syntax
   ods['equilibrium.time_slice.0.profiles_2d.0.psi']              # . separated string syntax
   
   NOTE: Python3.6+ f-strings can be very handy when looping over arrays of structures. For example:
   for time_index in range(len(ods[f'equilibrium.time_slice'])):
       for grid_index in range(len(ods[f'equilibrium.time_slice.{time_index}.profiles_2d'])):
           print(ods[f'equilibrium.time_slice.{time_index}.profiles_2d.{grid_index}.psi'])
   

4. Extract sigle time slice from whole data structure:

   ods.slice_at_time(1000.)
   

5. Simplified handling of array of structures

   ods['wall.description_2d.3.limiter.type.name']       # use `#` to access entries as in a list
   ods['wall.description_2d.-1.limiter.type.name']      # use `-#` to access entries from the end of the list
   ods['equilibrium.time_slice.:.global_quantities.ip'] # use `:` to collect quantities across list of structures
   ods['wall.description_2d.+.limiter.type.name']       # use `+` to append entries to a list of structures
   

6. Automatic handling of XML code.parameters will show them as dictionaries and save them as XML into IMAS:

   ods['equilibrium.code.parameters'] = CodeParameters('./parameters.xml')
   

7. Automatic COCOS transformations [read the COCOS cheatsheet]:

   with omas_environment(ods, cocosio=2):
       ods['equilibrium.time_slice.0.profiles_1d.psi'] = gEQDSK['psi']
   

8. Automatic coordinate interpolations:

   with omas_environment(ods, coordsio={'equilibrium.time_slice[0].profiles_1d.psi': gEQDSK['psi']}):
       ods['equilibrium.time_slice[0].profiles_1d.pressure'] = gEQDSK['pressure']
   

9. Automatic units conversions via pint Python package:

   ods['equilibrium.time_slice[0].constraints.diamagnetic_flux.time_measurement'] = 8.0 * milliseconds
   ods['equilibrium.time_slice[0].constraints.diamagnetic_flux.time_measurement'] # will return 0.008
   

10. Unified interface for querying about time dimension:

    ods.time('equilibrium')                                     # will return an array of times
    ods.time('equilibrium.time_slice')                          # will return an array of times
    ods.time('equilibrium.time_slice.0.global_quantities.ip')   # will return a scalar time
    

11. Seamless handling of uncertain quantities via uncertainties Python package:

    ods['equilibrium.time_slice.0.profiles_1d.q'] = uarray(nom_value, std_dev)
    

12. Evaluate derived physics quantities from more fundamental ones:

    ods.physics_core_profiles_pressures()
    

13. Get data as multidimensional array structures in xarray format:

    ods['core_profiles.profiles_1d.0.electrons.densdensity_thermality'].xarray()
    

14. Conveniently plot individual quantities:

    ods.plot_quantity('core_profiles.profiles_1d.0.electrons.density_thermal')
    

15. Use regular expressions with @ construct for accessing data and plotting:

    ods['@core.*0.elect.*dens.*th']
    ods.plot_quantity('@core.*0.elect.*dens.*th')
    

16. Predefined set of plots available:

    ods.plot_core_profiles_summary()
    

17. On the fly data mapping of experimental data from native database:

    with ods1.open('machine', 'd3d', 168830, options={'EFIT_tree': 'EFIT01'}):
        plot(ods['equilibrium.time_slice.0.global_quantities.ip'])
    

18. Save/load ODSs to/from different backend storage systems:

OMAS format	Description	Storage type	Remote storage	Python Requirements
pickle	Files using native Python serialization tools	Python binary file	no
Json	Using Json format for representing hierarchical data	ASCII file	no
NetCDF	Files using binary NetCDF format (flat data structure)	Binary file	no	netCDF4
HDF5	Files using binary HDF5 format (hierarchical data structure)	Binary file	no	h5py
S3	Cloud storage using Amazon Simple Storage Service	Object Store	yes	boto3
MongoDB	Document-based distributed database	MongoDB Database	yes	pymongo
HDC	Hierarchical Dynamic Containers	Memory	no	pyhdc (optional)
UDA	Universal Data Access	UDA Database	yes	pyuda (optional)
ASCII	Format used by the IMAS AL 4.0.x ASCII backend	ASCII file	no
MACHINE	Access tokamaks experimental data with imas syntax	Native experimental databases	yes	MDSplus
IMAS	ITER data storage system	IMAS Database	no	imas (optional)