Add functions for interacting with IMAS data

[eldond]

New features:

• geqdsk2imas!() writes data from one or more GEQDSKFile instance to the IMAS schema
• imas2geqdsk() reads equilibrium and wall data from an IMAS dd and outputs GEQDSKFile(s)

Updates:

• The path is split from filenames when recording file into GEQDSKFile during io

Close #15

[orso82]

@eldond this looks good, though I have not tested it.

One thing you could try is to use the identify_cocos() method https://github.com/ProjectTorreyPines/CoordinateConventions.jl/blob/290e6b7e062cebcb4b07d422d39718271ad042d0/src/CoordinateConventions.jl#L304 since gEQDSKs can be in COCOS 1,3,5,7

There's an open issue about ProjectTorreyPines/CoordinateConventions.jl#1 but that should not affect you here

The other thing is that I have now made https://github.com/ProjectTorreyPines/IMAS.jl public. I much rather you use the IMAS.flux_surfaces(eqt) function to get the derived quantities in dd. The intention is to register IMAS.jl in the general registry, though we need to wait a couple of days for the packages that it depends on to be registered there.

[eldond]

@orso82 I deleted derived quantities other than X-points, since EFIT.jl has an X-point finding function. If IMAS can do better at finding X-points, then maybe EFIT's X-point finder should be deleted and IMAS should be used for this instead. If EFIT should keep an X-point finding function, then I think it's okay for its results to be loaded into IMASdd.

I will look at identify_cocos

[eldond]

@orso82 Okay, I think this is done. I'm using identify_cocos, I put in a bunch of tests, and I documented the functions.

[orso82]

mostly comments on stile and using IMAS(dd) time handling features

[anchal-physics]

This is not related to this branch's main motive but it would be nice if this small fix can be piggy backed into it. At this line:

EFIT.jl/src/utils.jl

Line 194 in 60b41dc

psi_int = Interpolations.LinearInterpolation((r_eq, z_eq), psi_eq)

Using LinearInterpolationsis deprecated and will be removed in future. This warning is printed every ime we use this function. Please just rename it to linear_interpolations. Thanks.

[orso82]

👍 some more comments, mostly removing unnecessary manual handling of time-dependent quantities. Also some tips about keyword arguments.

@bclyons12 could you please chime in about cocos_clockwise_phi ?

[eldond]

Removing some of the time assignments / setup seems to have been problematic. @orso82 , the way I tried to resolve this previously may not have been well aligned with ideal IMAS usage. How would you recommend addressing this?

julia> include("test/runtests.jl")
Precompiling EFIT
  1 dependency successfully precompiled in 5 seconds. 123 already precompiled.
Test Summary: | Pass  Total  Time
find xpoint   |   20     20  9.7s
Got the expected exception
Test Summary: | Pass  Total  Time
parse header  |    4      4  0.1s
Test files are identified with COCOS = [5, 7]
test file 1 info: filename = g000001.01000, time = 0.001
imas: Error During Test at /home/eldond/.julia/dev/EFIT/test/runtests.jl:156
  Test threw exception
  Expression: eqt.time == (gs[1]).time
  equilibrium.time_slice[1].time is missing
  Stacktrace:
   [1] getproperty(ids::IMASdd.IDS, field::Symbol)
     @ IMASdd ~/.julia/dev/IMASdd/src/data.jl:213
   [2] macro expansion
     @ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined]
   [3] macro expansion
     @ ~/.julia/dev/EFIT/test/runtests.jl:156 [inlined]
   [4] macro expansion
     @ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
   [5] top-level scope
     @ ~/.julia/dev/EFIT/test/runtests.jl:143
test file 2 info: filename = g184833.03600, time = 3.6
imas: Error During Test at /home/eldond/.julia/dev/EFIT/test/runtests.jl:142
  Got exception outside of a @test
  equilibrium.time_slice[1].time is missing
  Stacktrace:
    [1] getproperty
      @ ~/.julia/dev/IMASdd/src/data.jl:213 [inlined]
    [2] time_array_local(ids::IMASdd.IDSvector{T} where T<:IMASdd.IDSvectorTimeElement)
      @ IMASdd ~/.julia/dev/IMASdd/src/time.jl:120
    [3] resize!(ids::IMASdd.IDSvector{IMASdd.equilibrium__time_slice{Float64}}, time0::Float64)
      @ IMASdd ~/.julia/dev/IMASdd/src/data.jl:969
    [4] resize!(ids::IMASdd.IDSvector{IMASdd.equilibrium__time_slice{Float64}})
      @ IMASdd ~/.julia/dev/IMASdd/src/data.jl:965
    [5] geqdsk2imas!(g::GEQDSKFile, eq::IMASdd.equilibrium{Float64}; wall::Nothing, geqdsk_cocos::Int64, dd_cocos::Int64, cocos_clockwise_phi::Bool, add_derived::Bool)
      @ EFIT ~/.julia/dev/EFIT/src/io.jl:427
    [6] macro expansion
      @ ~/.julia/dev/EFIT/test/runtests.jl:161 [inlined]
    [7] macro expansion
      @ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
    [8] top-level scope
      @ ~/.julia/dev/EFIT/test/runtests.jl:143
    [9] include(fname::String)
      @ Base.MainInclude ./client.jl:489
   [10] top-level scope
      @ REPL[2]:1
   [11] eval
      @ ./boot.jl:385 [inlined]
   [12] eval_user_input(ast::Any, backend::REPL.REPLBackend, mod::Module)
      @ REPL ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/REPL/src/REPL.jl:150
   [13] repl_backend_loop(backend::REPL.REPLBackend, get_module::Function)
      @ REPL ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/REPL/src/REPL.jl:246
   [14] start_repl_backend(backend::REPL.REPLBackend, consumer::Any; get_module::Function)
      @ REPL ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/REPL/src/REPL.jl:231
   [15] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool, backend::Any)
      @ REPL ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/REPL/src/REPL.jl:389
   [16] run_repl(repl::REPL.AbstractREPL, consumer::Any)
      @ REPL ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/REPL/src/REPL.jl:375
   [17] (::Base.var"#1013#1015"{Bool, Bool, Bool})(REPL::Module)
      @ Base ./client.jl:432
   [18] #invokelatest#2
      @ ./essentials.jl:892 [inlined]
   [19] invokelatest
      @ ./essentials.jl:889 [inlined]
   [20] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
      @ Base ./client.jl:416
   [21] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:333
   [22] _start()
      @ Base ./client.jl:552
Test Summary: | Pass  Error  Total  Time
imas          |    1      2      3  6.9s
ERROR: LoadError: Some tests did not pass: 1 passed, 0 failed, 2 errored, 0 broken.
in expression starting at /home/eldond/.julia/dev/EFIT/test/runtests.jl:142

[eldond]

@orso82 whoops, this got forgotten. Currently stuck on trying to use IMAS time handling as intended.

[orso82]

let me know if you need help @eldond

[orso82]

@eldong FYI that @mgyoo86 is interested in this