Using readg() with set_time & conformed to IMASDD

Using set_time for sample files where description is not in the
standard format.

Changes were made in the code to use ismissing in places to conform to
requirements of IMASDD.

In record_regular_mesh!(), the deepcopy of each element was replaced
with deepcopy of the entire grid subset to improve speed.

The test runtests.jl was updated to reflect the changes.

All tests pass now with following versions:

JuliaFusion/EFIT.jl@8580ca8
ProjectTorreyPines/IMASdd.jl@6a6968a
ProjectTorreyPines/IMASggd.jl@b11ad15
ProjectTorreyPines/SOLPS2imas.jl@f843e6a

Note that EFIT version that was used has not been merged with its
master branch yet at the time of this test.

In conclusion, in future, OMAS can be removed now.

sample/geqdsk_iter_small_sample

@@ -1,4 +1,4 @@
-  EFITD    00/00/2008    #002296  0200ms Convert   0  65  65
+  EFITD    00/00/2008    #002296  0200   0  65  65
  0.624390220E+01 0.124878049E+02 0.619999981E+01 0.307804870E+01 0.200000050E+00
  0.635000000E+01 0.580000000E+00 0.118000000E+02 0.000000000E+00 0.530000019E+01
  0.150229038E+08 0.118000000E+02 0.000000000E+00 0.635000000E+01 0.000000000E+00

src/SD4SOLPS.jl

@@ -68,13 +68,20 @@ end
 Transfers the equilibrium reconstruction in an EFIT-style gEQDSK file into
 the IMAS DD structure.
 """
-function geqdsk_to_imas!(eqdsk_file, dd; time_index=1)
+function geqdsk_to_imas!(eqdsk_file, dd; set_time=nothing, time_index=1)
     # https://github.com/JuliaFusion/EFIT.jl/blob/master/src/io.jl
-    g = EFIT.readg(eqdsk_file)
+    g = EFIT.readg(eqdsk_file; set_time=set_time)
     # Copying ideas from OMFIT: omfit/omfit_classes/omfit_eqdsk.py / to_omas()
     eq = dd.equilibrium
-    resize!(eq.time_slice, 1)
+    if IMASDD.ismissing(eq, :time)
+        eq.time = Array{Float64}(undef, time_index)
+    end
+    eq.time[time_index] = g.time
+    if length(eq.time_slice) < time_index
+        resize!(eq.time_slice, time_index)
+    end
     eqt = eq.time_slice[time_index]
+    eqt.time = g.time
 
     # 0D
     gq = eqt.global_quantities

src/repair_eq.jl

@@ -71,8 +71,14 @@ function add_rho_to_equilibrium!(dd::IMASDD.dd)
                 continue
             end
         end
-        if length(eqt.profiles_1d.phi) == 0
-            resize!(eqt.profiles_1d.phi, n)
+        if (
+            if IMASDD.ismissing(eqt.profiles_1d, :phi)
+                true
+            else
+                IMASDD.isempty(eqt.profiles_1d.phi)
+            end
+        )
+            eqt.profiles_1d.phi = Array{Float64}(undef, n)
             psi2 = eqt.profiles_2d[1].psi
             req = collect(eqt.profiles_2d[1].grid.dim1)
             zeq = collect(eqt.profiles_2d[1].grid.dim2)

src/supersize_profile.jl

@@ -231,10 +231,9 @@ function fill_in_extrapolated_core_profile!(
             ).(psi_for_quantity[in_bounds])
 
         # Make sure the output 1D rho grid exists; create it if needed
-        if length(dd.core_profiles.profiles_1d[it].grid.rho_tor_norm) == 0
-            resize!(dd.core_profiles.profiles_1d[it].grid.rho_tor_norm, 201)
-            # If you don't like this default, then you should write grid.rho_tor_norm before
-            # calling this function.
+        if IMASDD.ismissing(dd.core_profiles.profiles_1d[it].grid, :rho_tor_norm)
+            # If you don't like this default, then you should write grid.rho_tor_norm
+            # before calling this function.
             dd.core_profiles.profiles_1d[it].grid.rho_tor_norm =
                 collect(LinRange(0, 1, 201))
         end
@@ -750,15 +749,9 @@ function record_regular_mesh!(
 
     # Preserve record of standard (non extended) mesh
     for i ∈ 1:5
-        std_sub = get_grid_subset(grid_ggd, -i)
         orig_sub = get_grid_subset(grid_ggd, i)
-        resize!(std_sub.element, length(orig_sub.element))
-        for j ∈ 1:length(orig_sub.element)
-            std_sub.element[j] = deepcopy(orig_sub.element[j])
-        end
-        std_sub.identifier.index = -i
-        std_sub.dimension = deepcopy(orig_sub.dimension)
-        std_sub.metric = deepcopy(orig_sub.metric)
+        grid_ggd.grid_subset[n_existing_subsets+i] = deepcopy(orig_sub)
+        grid_ggd.grid_subset[n_existing_subsets+i].identifier.index = -i
     end
     all_nodes_sub = get_grid_subset(grid_ggd, 1)
     all_edges_sub = get_grid_subset(grid_ggd, 2)

test/runtests.jl

@@ -183,8 +183,9 @@ if args["core_profile_extension"]
         @test isfile(b2time)
         @test isfile(b2mn)
         @test isfile(eqdsk)
+        eqdsk_time = parse(Float64, split(eqdsk, ".")[end]) / 1000.0
         dd = SOLPS2IMAS.solps2imas(b2fgmtry, b2time; b2mn=b2mn)
-        SD4SOLPS.geqdsk_to_imas!(eqdsk, dd)
+        SD4SOLPS.geqdsk_to_imas!(eqdsk, dd; set_time=eqdsk_time)
         rho = dd.equilibrium.time_slice[1].profiles_1d.rho_tor_norm
 
         if !SD4SOLPS.check_rho_1d(dd; time_slice=1)
@@ -219,8 +220,9 @@ if args["edge_profile_extension"]
     @testset "edge_profile_extension" begin
         # Test for getting mesh spacing
         b2fgmtry, b2time, b2mn, eqdsk = define_default_sample_set()
+        eqdsk_time = parse(Float64, split(eqdsk, ".")[end]) / 1000.0
         dd = SOLPS2IMAS.solps2imas(b2fgmtry, b2time; b2mn=b2mn)
-        SD4SOLPS.geqdsk_to_imas!(eqdsk, dd)
+        SD4SOLPS.geqdsk_to_imas!(eqdsk, dd; set_time=eqdsk_time)
         dpsin = SD4SOLPS.mesh_psi_spacing(dd)
         @test dpsin > 0.0
 
@@ -298,8 +300,6 @@ if args["heavy_utilities"]
         resize!(dd.core_profiles.profiles_1d, prof_time_idx)
         n = 101
         rho_n = Array(LinRange(0, 1.0, n))
-        resize!(dd.core_profiles.profiles_1d[prof_time_idx].grid.rho_tor_norm, n)
-        resize!(dd.core_profiles.profiles_1d[prof_time_idx].electrons.density, n)
         dd.core_profiles.profiles_1d[prof_time_idx].grid.rho_tor_norm = rho_n
         dd.core_profiles.profiles_1d[prof_time_idx].electrons.density =
             make_test_profile(rho_n)
@@ -356,7 +356,17 @@ if args["geqdsk_to_imas"]
         for sample_file ∈ sample_files
             println(sample_file)
             dd = IMASDD.dd()
-            SD4SOLPS.geqdsk_to_imas!(sample_file, dd; time_index=tslice)
+            if endswith(sample_file, "00")
+                eqdsk_time = parse(Float64, split(sample_file, ".")[end]) / 1000.0
+            else
+                eqdsk_time = nothing
+            end
+            SD4SOLPS.geqdsk_to_imas!(
+                sample_file,
+                dd;
+                set_time=eqdsk_time,
+                time_index=tslice,
+            )
             eqt = dd.equilibrium.time_slice[tslice]
 
             # global