Merge pull request #26 from ProjectTorreyPines/dep_update

SOLPS2IMAS dependecy removed.

Simple PR, so merging without review.

Project.toml

@@ -10,7 +10,6 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-SOLPS2IMAS = "09becab6-0636-4c23-a92a-2b3723265c31"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

samples/.gitignore

@@ -1,4 +1 @@
-/edge_profiles.h5
-/b2time.nc
-/b2mn.dat
-/b2fgmtry
+/time_dep_edge_profiles_last_step_only.json

samples/time_dep_edge_profiles_last_step_only.json.dvc

@@ -0,0 +1,12 @@
+md5: 3ea764e4095ca2b8a5359cd76259e26a
+frozen: true
+deps:
+- path: ITER_Lore_2296_00000/IMAS/time_dep_edge_profiles_last_step_only.json
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: 88f14955a52cd4d4fd7e86e2274436a34f4203ec
+outs:
+- md5: db47dee590648770a5ce49c0e0706acf
+  size: 4087084
+  hash: md5
+  path: time_dep_edge_profiles_last_step_only.json

test/runtests.jl

@@ -1,7 +1,6 @@
 import GGDUtils: interp, get_kdtree, project_prop_on_subset!, get_grid_subset_with_index
-import OMAS: h5i2imas
+import OMAS: json2imas
 import Statistics: mean
-import SOLPS2IMAS: solps2imas
 using Test
 using ArgParse: ArgParse
 
@@ -34,14 +33,18 @@ function parse_commandline()
 end
 args = parse_commandline()
 
+print("json2imas() time: ")
+@time ids = json2imas(
+    "$(@__DIR__)/../samples/time_dep_edge_profiles_last_step_only.json",
+)
+
 if args["interp"]
     @testset "interp" begin
         # ids = h5i2imas("$(@__DIR__)/../samples/edge_profiles.h5")
         b2gmtry = "$(@__DIR__)/../samples/b2fgmtry"
         b2output = "$(@__DIR__)/../samples/b2time.nc"
         gsdesc = "$(@__DIR__)/../samples/gridspacedesc.yml"
         b2mn = "$(@__DIR__)/../samples/b2mn.dat"
-        ids = solps2imas(b2gmtry, b2output, gsdesc, b2mn)
         n_e = ids.edge_profiles.ggd[1].electrons.density[1]
         grid_ggd = ids.edge_profiles.grid_ggd[1]
         space = grid_ggd.space[1]
@@ -54,7 +57,8 @@ if args["interp"]
         grid_val = ids.edge_profiles.ggd[1].electrons.density[1].values[chosen_index]
 
         # test interp(prop, grid_ggd)
-        get_n_e = interp(n_e, grid_ggd)
+        print("interp(prop, grid_ggd) time: ")
+        @time get_n_e = interp(n_e, grid_ggd)
         searched_val = get_n_e(cell_center...)
         println("Electron density at: ", cell_center)
         println("Grid Value: ", grid_val)
@@ -63,21 +67,26 @@ if args["interp"]
 
         # test interp(prop_arr, space, subset)
         subset = get_grid_subset_with_index(grid_ggd, 5)
-        get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density, space, subset)
+        print("interp(prop_arr, space, subset) time: ")
+        @time get_n_e =
+            interp(ids.edge_profiles.ggd[1].electrons.density, space, subset)
         searched_val = get_n_e(cell_center...)
         @test abs.((grid_val .- searched_val) ./ grid_val) < allowed_rtol
 
         # test interp(prop_arr, grid_ggd, grid_subset_index)
-        get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density, grid_ggd, 5)
+        print("interp(prop_arr, grid_ggd, grid_subset_index) time: ")
+        @time get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density, grid_ggd, 5)
         searched_val = get_n_e(cell_center...)
         @test abs.((grid_val .- searched_val) ./ grid_val) < allowed_rtol
 
         # Use the kdtree to interpolate several quantities using
         # inverse distance weighing
         kdtree = get_kdtree(space)
-        get_T_e =
+        print("interp(prop_arr, kdtree) time: ")
+        @time get_T_e =
             interp(ids.edge_profiles.ggd[1].electrons.temperature[1].values, kdtree)
-        get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density[1].values, kdtree)
+        @time get_n_e =
+            interp(ids.edge_profiles.ggd[1].electrons.density[1].values, kdtree)
 
         grid_val =
             ids.edge_profiles.ggd[1].electrons.temperature[1].values[chosen_index]
@@ -116,27 +125,24 @@ end
 
 if args["projection"]
     @testset "project_prop_on_subset!" begin
-        b2gmtry = "$(@__DIR__)/../samples/b2fgmtry"
-        b2output = "$(@__DIR__)/../samples/b2time.nc"
-        gsdesc = "$(@__DIR__)/../samples/gridspacedesc.yml"
-        b2mn = "$(@__DIR__)/../samples/b2mn.dat"
-        dd = solps2imas(b2gmtry, b2output, gsdesc, b2mn)
-        space = dd.edge_profiles.grid_ggd[1].space[1]
-        prop = dd.edge_profiles.ggd[1].electrons.density
+        space = ids.edge_profiles.grid_ggd[1].space[1]
+        prop = ids.edge_profiles.ggd[1].electrons.density
         # All cells
-        from_subset = get_grid_subset_with_index(dd.edge_profiles.grid_ggd[1], 5)
-        kdtree = get_kdtree(space, from_subset)
+        from_subset = get_grid_subset_with_index(ids.edge_profiles.grid_ggd[1], 5)
         # separatix
-        to_subset = get_grid_subset_with_index(dd.edge_profiles.grid_ggd[1], 16)
-        separatix_centers, values_at_separatix =
+        to_subset = get_grid_subset_with_index(ids.edge_profiles.grid_ggd[1], 16)
+        print("project_prop_on_subset!(prop, from_subset, to_subset, space) time: ")
+        @time separatix_centers, values_at_separatix =
             project_prop_on_subset!(prop, from_subset, to_subset, space)
         # println("Projected to separatix:")
         # for ii ∈ eachindex(separatix_centers)
         #     println(separatix_centers[ii], ": ", values_at_separatix[ii])
         # end
 
-        subset_core = get_grid_subset_with_index(dd.edge_profiles.grid_ggd[1], 22)
-        core_element_inds, values_at_core =
+        subset_core =
+            get_grid_subset_with_index(ids.edge_profiles.grid_ggd[1], 22)
+        print("project_prop_on_subset!(prop, from_subset, subset_core) time: ")
+        @time core_element_inds, values_at_core =
             project_prop_on_subset!(prop, from_subset, subset_core)
         # println("Project to core:")
         # for ii ∈ eachindex(core_element_inds)
@@ -153,12 +159,7 @@ end
 
 if args["in"]
     @testset "test ∈" begin
-        b2gmtry = "$(@__DIR__)/../samples/b2fgmtry"
-        b2output = "$(@__DIR__)/../samples/b2time.nc"
-        gsdesc = "$(@__DIR__)/../samples/gridspacedesc.yml"
-        b2mn = "$(@__DIR__)/../samples/b2mn.dat"
-        dd = solps2imas(b2gmtry, b2output, gsdesc, b2mn)
-        grid_ggd = dd.edge_profiles.grid_ggd[1]
+        grid_ggd = ids.edge_profiles.grid_ggd[1]
         space = grid_ggd.space[1]
         subset_corebnd = get_grid_subset_with_index(grid_ggd, 15)
         subset_sol = get_grid_subset_with_index(grid_ggd, 23)