Merge pull request #39 from ProjectTorreyPines/OMAS_IMAS

Replace OMAS with IMASDD in GGDUtils

Project.toml

@@ -6,6 +6,7 @@ version = "0.2.1"
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
+IMASDD = "06b86afa-9f21-11ec-2ef8-e51b8960cfc5"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"

examples/plotting.ipynb

@@ -24,7 +24,7 @@
    "source": [
     "using Pkg\n",
     "Pkg.activate(\"./\")\n",
-    "Pkg.add(url=\"git@github.com:ProjectTorreyPines/OMAS.jl.git\")\n",
+    "Pkg.add(url=\"git@github.com:ProjectTorreyPines/IMASDD.jl.git\")\n",
     "Pkg.develop(path=\"../\")\n",
     "Pkg.add(\"Plots\")\n",
     "Pkg.add(\"LaTeXStrings\")"
@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using OMAS\n",
+    "using IMASDD\n",
     "using GGDUtils\n",
     "using Plots\n",
     "using LaTeXStrings"
@@ -48,7 +48,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dd = OMAS.json2imas(\"../samples/time_dep_edge_profiles_last_step_only.json\")\n",
+    "dd = IMASDD.json2imas(\"../samples/time_dep_edge_profiles_last_step_only.json\")\n",
     "grid_ggd = dd.edge_profiles.grid_ggd[1]\n",
     "space = grid_ggd.space[1]"
    ]
@@ -146,15 +146,15 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Julia 1.9.2",
+   "display_name": "Julia 1.9.4",
    "language": "julia",
    "name": "julia-1.9"
   },
   "language_info": {
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.9.2"
+   "version": "1.9.4"
   },
   "orig_nbformat": 4
  },

examples/plotting_interferometer.ipynb

@@ -24,7 +24,7 @@
    "source": [
     "using Pkg\n",
     "Pkg.activate(\"./\")\n",
-    "Pkg.add(url=\"git@github.com:ProjectTorreyPines/OMAS.jl.git\")\n",
+    "Pkg.add(url=\"git@github.com:ProjectTorreyPines/IMASDD.jl.git\")\n",
     "Pkg.develop(path=\"../\")\n",
     "Pkg.add(\"Plots\")"
    ]
@@ -35,7 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using OMAS\n",
+    "using IMASDD\n",
     "using GGDUtils\n",
     "using Plots"
    ]
@@ -53,7 +53,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ids = OMAS.json2imas(\"$(@__DIR__)/../samples/time_dep_edge_profiles_with_interferometer.json\")\n",
+    "ids = IMASDD.json2imas(\"$(@__DIR__)/../samples/time_dep_edge_profiles_with_interferometer.json\")\n",
     "grid_ggd = ids.edge_profiles.grid_ggd[1]\n",
     "space = grid_ggd.space[1]"
    ]
@@ -226,15 +226,15 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Julia 1.9.2",
+   "display_name": "Julia 1.9.4",
    "language": "julia",
    "name": "julia-1.9"
   },
   "language_info": {
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.9.2"
+   "version": "1.9.4"
   },
   "orig_nbformat": 4
  },

makefile

@@ -13,16 +13,17 @@ env_with_cloned_repo r:
 	@echo "Creating Julia environment by creating local clones of dependent repositories"
 	@echo "Cloning the repositories and generating Manifest.toml"
 	-dn=$(shell dirname $(shell pwd)); \
-	if [[ "$${dn:(-10)}" == ".julia/dev" ]]; then rn="OMAS" ; else rn="OMAS.jl"; fi; \
-	git clone "git@github.com:ProjectTorreyPines/OMAS.jl.git" ../$${rn}; \
-	julia --project=. -e 'using Pkg; Pkg.rm("OMAS"); Pkg.develop(path="../'$${rn}'"); Pkg.instantiate()'
+	if [[ "$${dn:(-10)}" == ".julia/dev" ]]; then ext="" ; else ext=".jl";fi; \
+	git clone "git@github.com:ProjectTorreyPines/OMAS.jl.git" ../OMAS$${ext}; \
+	git clone "git@github.com:ProjectTorreyPines/IMASDD.jl.git" ../IMASDD$${ext}; \
+	julia --project=. -e 'using Pkg; Pkg.rm(["OMAS", "IMASDD"]); Pkg.develop(path="../OMAS'$${ext}'"); Pkg.develop(path="../IMASDD'$${ext}'"); Pkg.instantiate()'
 
 env_with_git_url u:
 	@echo "Pulling sample files using dvc"
 	-dvc pull
 	@echo "Creating Julia environment with the git urls without creating local clones"
 	@echo "Generating Project.toml and Manifest.toml"
-	julia --project=. -e 'using Pkg; Pkg.rm("OMAS"); Pkg.add(url="git@github.com:ProjectTorreyPines/OMAS.jl.git", rev="master"); Pkg.instantiate()'
+	julia --project=. -e 'using Pkg; Pkg.rm(["OMAS", "IMASDD"]); Pkg.add(url="git@github.com:ProjectTorreyPines/OMAS.jl.git", rev="master"); Pkg.add(url="git@github.com:ProjectTorreyPines/IMASDD.jl.git", rev="master"); Pkg.instantiate()'
 
 clean:
 	@echo "Deleting Manifest.toml"

src/GGDUtils.jl

@@ -1,6 +1,6 @@
 module GGDUtils
 
-using OMAS: OMAS
+import OMAS as IMASDD
 
 const inv_16pi = 1.0 / (16π)
 

src/interpolations.jl

@@ -7,7 +7,7 @@ export interp
 export get_kdtree
 export get_TPS_mats
 
-function get_kdtree(space::OMAS.edge_profiles__grid_ggd___space)
+function get_kdtree(space::IMASDD.edge_profiles__grid_ggd___space)
     grid_nodes = space.objects_per_dimension[1].object
     grid_faces = space.objects_per_dimension[3].object
     grid_faces = [cell for cell ∈ grid_faces if length(cell.nodes) == 4]
@@ -19,8 +19,8 @@ function get_kdtree(space::OMAS.edge_profiles__grid_ggd___space)
 end
 
 function get_kdtree(
-    space::OMAS.edge_profiles__grid_ggd___space,
-    subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    space::IMASDD.edge_profiles__grid_ggd___space,
+    subset::IMASDD.edge_profiles__grid_ggd___grid_subset,
 )
     subset_centers = get_subset_centers(space, subset)
     return KDTree([SVector{2}(sc) for sc ∈ subset_centers]; leafsize=10)
@@ -167,15 +167,15 @@ function interp(y::Vector{T}, x::Vector{Tuple{U, U}}) where {T <: Real, U <: Rea
     return interp(y, get_TPS_mats(x))
 end
 
-function get_TPS_mats(space::OMAS.edge_profiles__grid_ggd___space)
+function get_TPS_mats(space::IMASDD.edge_profiles__grid_ggd___space)
     nodes = [Tuple(node.geometry) for node ∈ space.objects_per_dimension[1].object]
     return get_TPS_mats(nodes)
 end
 
 """
     interp(
     prop_values::Vector{T},
-    space::OMAS.edge_profiles__grid_ggd___space
+    space::IMASDD.edge_profiles__grid_ggd___space
 
 ) where {T <: Real}
 
@@ -185,23 +185,23 @@ of the space.
 """
 function interp(
     prop_values::Vector{T},
-    space::OMAS.edge_profiles__grid_ggd___space,
+    space::IMASDD.edge_profiles__grid_ggd___space,
 ) where {T <: Real}
     return interp(prop_values, get_TPS_mats(space))
 end
 
 function get_TPS_mats(
-    space::OMAS.edge_profiles__grid_ggd___space,
-    subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    space::IMASDD.edge_profiles__grid_ggd___space,
+    subset::IMASDD.edge_profiles__grid_ggd___grid_subset,
 )
     return get_TPS_mats(get_subset_centers(space, subset))
 end
 
 """
     interp(
     prop_values::Vector{Real},
-    space::OMAS.edge_profiles__grid_ggd___space,
-    subset::OMAS.edge_profiles__grid_ggd___grid_subset
+    space::IMASDD.edge_profiles__grid_ggd___space,
+    subset::IMASDD.edge_profiles__grid_ggd___grid_subset
 
 )
 
@@ -210,16 +210,16 @@ it is assumed that the property values are provided for each element of the subs
 """
 function interp(
     prop_values::Vector{T},
-    space::OMAS.edge_profiles__grid_ggd___space,
-    subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    space::IMASDD.edge_profiles__grid_ggd___space,
+    subset::IMASDD.edge_profiles__grid_ggd___grid_subset,
 ) where {T <: Real}
     return interp(prop_values, get_TPS_mats(space, subset))
 end
 
 """
     interp(
     prop::edge_profiles__prop_on_subset,
-    grid_ggd::OMAS.edge_profiles__grid_ggd,
+    grid_ggd::IMASDD.edge_profiles__grid_ggd,
     value_field::Symbol=:values
 
 )
@@ -231,7 +231,7 @@ get_e_field_par = interp(dd.edge_profiles.ggd[1].e_field[1], grid_ggd, :parallel
 """
 function interp(
     prop::edge_profiles__prop_on_subset,
-    grid_ggd::OMAS.edge_profiles__grid_ggd,
+    grid_ggd::IMASDD.edge_profiles__grid_ggd,
     value_field::Symbol=:values,
 )
     subset = get_grid_subset_with_index(grid_ggd, prop.grid_subset_index)
@@ -241,9 +241,9 @@ end
 
 """
     interp(
-    prop_arr::Vector{T},
-    space::OMAS.edge_profiles__grid_ggd___space,
-    subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    prop_arr::AbstractVector{T},
+    space::IMASDD.edge_profiles__grid_ggd___space,
+    subset::IMASDD.edge_profiles__grid_ggd___grid_subset,
     value_field::Symbol=:values
 
 ) where {T <: edge_profiles__prop_on_subset}
@@ -253,9 +253,9 @@ sol = get_grid_subset_with_index(dd.edge_profiles.grid_ggd[1], 23)
 get_electron_density = interp(dd.edge_profiles.ggd[1].electrons.density, space, sol)
 """
 function interp(
-    prop_arr::Vector{T},
-    space::OMAS.edge_profiles__grid_ggd___space,
-    subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    prop_arr::AbstractVector{T},
+    space::IMASDD.edge_profiles__grid_ggd___space,
+    subset::IMASDD.edge_profiles__grid_ggd___grid_subset,
     value_field::Symbol=:values,
 ) where {T <: edge_profiles__prop_on_subset}
     prop = get_prop_with_grid_subset_index(prop_arr, subset.identifier.index)
@@ -264,8 +264,8 @@ end
 
 """
     interp(
-    prop_arr::Vector{T},
-    grid_ggd::OMAS.edge_profiles__grid_ggd,
+    prop_arr::AbstractVector{T},
+    grid_ggd::IMASDD.edge_profiles__grid_ggd,
     grid_subset_index::Int,
     value_field::Symbol=:values
 
@@ -275,8 +275,8 @@ Example:
 get_n_e_sep = interp(dd.edge_profiles.ggd[1].electrons.density, grid_ggd, 16)
 """
 function interp(
-    prop_arr::Vector{T},
-    grid_ggd::OMAS.edge_profiles__grid_ggd,
+    prop_arr::AbstractVector{T},
+    grid_ggd::IMASDD.edge_profiles__grid_ggd,
     grid_subset_index::Int,
     value_field::Symbol=:values,
 ) where {T <: edge_profiles__prop_on_subset}
@@ -286,7 +286,7 @@ function interp(
     return interp(getfield(prop, value_field), space, subset)
 end
 
-function get_TPS_mats(grid_ggd::OMAS.edge_profiles__grid_ggd, grid_subset_index::Int)
+function get_TPS_mats(grid_ggd::IMASDD.edge_profiles__grid_ggd, grid_subset_index::Int)
     subset = get_grid_subset_with_index(grid_ggd, grid_subset_index)
     space = grid_ggd.space[subset.element[1].object[1].space]
     return get_TPS_mats(space, subset)
@@ -295,7 +295,7 @@ end
 #! format off
 """
     interp(
-    prop_arr::Vector{T},
+    prop_arr::AbstractVector{T},
     TPS_mats::Tuple{Matrix{U}, Matrix{U}, Matrix{U}, Vector{Tuple{U, U}}},
     grid_subset_index::Int,
     value_field::Symbol=:values,
@@ -316,7 +316,7 @@ This will run faster has heavy matrix calculations will happen only once.
 """
 #! format on
 function interp(
-    prop_arr::Vector{T},
+    prop_arr::AbstractVector{T},
     TPS_mats::Tuple{Matrix{U}, Matrix{U}, Matrix{U}, Vector{Tuple{U, U}}},
     grid_subset_index::Int,
     value_field::Val{V}=Val(:values),
@@ -330,7 +330,7 @@ const RHO_EXT_POS = [1.0001, 1.1, 5]
 const RHO_EXT_NEG = [-5, -0.0001] # I guess this would be at a PF coil or something?
 
 """
-    interp(eqt::OMAS.equilibrium__time_slice)
+    interp(eqt::IMASDD.equilibrium__time_slice)
 
 For a given equilibrium time slice, return a function that can be used to interpolate
 from (r, z) space to rho (normalized toroidal flux coordinate)space.
@@ -339,7 +339,7 @@ Example:
 rz2rho = interp(dd.equilibrium.time_slice[1])
 rho = rz2rho.([(r, z) for r in 3:0.01:9, for z in -5:0.01:5])
 """
-function interp(eqt::OMAS.equilibrium__time_slice)
+function interp(eqt::IMASDD.equilibrium__time_slice)
     p1 = eqt.profiles_1d
     p2 = eqt.profiles_2d[1]
     gq = eqt.global_quantities
@@ -370,7 +370,7 @@ end
 """
     interp(
     prop::Vector{T},
-    prof::OMAS.core_profiles__profiles_1d,
+    prof::IMASDD.core_profiles__profiles_1d,
 
 ) where {T <: Real}
 
@@ -384,7 +384,7 @@ get_n_e(1) # Returns electron density at rho = 1 (separatix)
 """
 function interp(
     prop::Vector{T},
-    prof::OMAS.core_profiles__profiles_1d,
+    prof::IMASDD.core_profiles__profiles_1d,
 ) where {T <: Real}
     rho_prof = copy(prof.grid.rho_tor_norm)
     length(prop) == length(rho_prof) ||
@@ -400,7 +400,7 @@ end
 """
     interp(
     prop::Vector{T},
-    prof::OMAS.core_profiles__profiles_1d,
+    prof::IMASDD.core_profiles__profiles_1d,
     rz2rho::Function,
 
 )
@@ -418,7 +418,7 @@ get_n_e(5.0, 3.5) # Returns electron density at (R, Z) = (5.0, 3.5)
 """
 function interp(
     prop::Vector{T},
-    prof::OMAS.core_profiles__profiles_1d,
+    prof::IMASDD.core_profiles__profiles_1d,
     rz2rho::Function,
 ) where {T <: Real}
     itp = interp(prop, prof)
@@ -431,8 +431,8 @@ end
 """
     interp(
     prop::Vector{T},
-    prof::OMAS.core_profiles__profiles_1d,
-    eqt::OMAS.equilibrium__time_slice,
+    prof::IMASDD.core_profiles__profiles_1d,
+    eqt::IMASDD.equilibrium__time_slice,
 
 ) where {T <: Real}
 
@@ -449,8 +449,8 @@ get_n_e(5.0, 3.5) # Returns electron density at (R, Z) = (5.0, 3.5)
 """
 function interp(
     prop::Vector{T},
-    prof::OMAS.core_profiles__profiles_1d,
-    eqt::OMAS.equilibrium__time_slice,
+    prof::IMASDD.core_profiles__profiles_1d,
+    eqt::IMASDD.equilibrium__time_slice,
 ) where {T <: Real}
     rz2rho = interp(eqt)
     return interp(prop, prof, rz2rho)