Changing SynthDiag -> FusionSyntheticDiagnostics

Also, falling back to using IMASdd since IMAS is not registered yet.

When IMAS gets registered, following changes will revert using IMAS.

src/FusionSyntheticDiagnostics.jl:3 using IMAS: IMAS
src/gas_injection.jl:30 Delete
src/gas_injection.jl:31 Uncomment
src/interferometer.jl:26 Delete
src/interferometer.jl:27 Uncomment
src/langmuir_probes.jl:23 Delete
src/langmuir_probes.jl:24 Uncomment
Some minor changes in runtests might be required.

NOTICE.md

@@ -1,9 +1,9 @@
-GGDUtils.jl
+FusionSyntheticDiagnostics.jl
 =========
 
-The purpose of this NOTICE file is to provide legal notices and acknowledgments that must be displayed to users in any derivative works or distributions. This file does not alter the terms of the Apache 2.0 license that governs the use and distribution of the SynthDiag.jl package.
+The purpose of this NOTICE file is to provide legal notices and acknowledgments that must be displayed to users in any derivative works or distributions. This file does not alter the terms of the Apache 2.0 license that governs the use and distribution of the FusionSyntheticDiagnostics.jl package.
 
-GGDUtils.jl was originally developed under the ProjectTorreyPines by the Magnetic Fusion Energy group at General Atomics.
+FusionSyntheticDiagnostics.jl was originally developed under the ProjectTorreyPines by the Magnetic Fusion Energy group at General Atomics.
 
 If this software contributes to an academic publication, please cite it as follows:
 A. Gupta, D. Eldon, H. Anand, A. Dautt-Silva, S. De Pascuale, J. Lore, O. Meneghini, and J.S. Park, "Plasma boundary control development using a time-dependent scrape-off layer model in closed-loop simulations", Nucl. Mater. Energy, manuscript in preparation for PSI conference (2024).

Project.toml

@@ -1,4 +1,4 @@
-name = "SynthDiag"
+name = "FusionSyntheticDiagnostics"
 uuid = "c6e34158-aa22-49e4-bb12-15cbcb518ce6"
 authors = ["Anchal Gupta <guptaa@fusion.gat.com>"]
 version = "1.0.3"
@@ -7,8 +7,8 @@ version = "1.0.3"
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-GGDUtils = "b7b5e640-9b39-4803-84eb-376048795def"
-IMAS = "13ead8c1-b7d1-41bb-a6d0-5b8b65ed587a"
+IMASdd = "c5a45a97-b3f9-491c-b9a7-aa88c3bc0067"
+IMASggd = "b7b5e640-9b39-4803-84eb-376048795def"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
 PhysicalConstants = "5ad8b20f-a522-5ce9-bfc9-ddf1d5bda6ab"
@@ -23,13 +23,13 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 ArgParse = "1"
 DSP = "0.7.9"
 DelimitedFiles = "1.9.1"
-GGDUtils = "1.0.3"
-IMAS = "1.2.2"
+IMASdd = "2"
+IMASggd = "2"
 Interpolations = "0.15.1"
 LsqFit = "0.15.0"
 PhysicalConstants = "0.2.3"
 Plots = "1.40.3"
 QuadGK = "2.9.4"
 StaticArrays = "1.9.2"
 Statistics = "1.9.0"
-julia = ">= 1.10"
+julia = "1.10"

README.md

@@ -1,18 +1,16 @@
-# SynthDiag.jl
+# FusionSyntheticDiagnostics.jl
 
-![Format Check](https://github.com/ProjectTorreyPines/SynthDiag.jl/actions/workflows/format_check.yml/badge.svg)
-![Docs](https://github.com/ProjectTorreyPines/SynthDiag.jl/actions/workflows/make_docs.yml/badge.svg)
-![Tests](https://github.com/ProjectTorreyPines/SynthDiag.jl/actions/workflows/test.yml/badge.svg)
+![Format Check](https://github.com/ProjectTorreyPines/FusionSyntheticDiagnostics.jl/actions/workflows/format_check.yml/badge.svg)
+![Docs](https://github.com/ProjectTorreyPines/FusionSyntheticDiagnostics.jl/actions/workflows/make_docs.yml/badge.svg)
+![Tests](https://github.com/ProjectTorreyPines/FusionSyntheticDiagnostics.jl/actions/workflows/test.yml/badge.svg)
 
-Package that defines synthetic diagnostics to generate sensor data based on plasma profile and syntehtic actuators. For installation and usage instructions, see the [online documentation](https://projecttorreypines.github.io/SynthDiag.jl/stable). For documentation on under development branch, see [dev online documentation](https://projecttorreypines.github.io/SynthDiag.jl/dev).
+Package that defines synthetic diagnostics to generate sensor data based on plasma profile and synthetic actuators for fusion devices. For installation and usage instructions, see the [online documentation](https://projecttorreypines.github.io/FusionSyntheticDiagnostics.jl/stable). For documentation on under development branch, see [dev online documentation](https://projecttorreypines.github.io/FusionSyntheticDiagnostics.jl/dev).
 
 ## Installation
 
-SynthDiag is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). First [install Julia](https://github.com/JuliaLang/juliaup?tab=readme-ov-file#juliaup---julia-version-manager), then:
+First [install Julia](https://github.com/JuliaLang/juliaup?tab=readme-ov-file#juliaup---julia-version-manager), then:
 
 ```julia
 using Pkg
-Pkg.Registry.add(RegistrySpec(url="https://github.com/ProjectTorreyPines/FuseRegistry.jl.git"))
-Pkg.Registry.add("General")
-Pkg.add("SynthDiag")
+Pkg.add("FusionSyntheticDiagnostics")
 ```

docs/make.jl

@@ -1,15 +1,15 @@
 using Documenter
-using SynthDiag
+using FusionSyntheticDiagnostics
 
 makedocs(;
-    modules=[SynthDiag],
+    modules=[FusionSyntheticDiagnostics],
     format=Documenter.HTML(),
-    sitename="SynthDiag",
+    sitename="FusionSyntheticDiagnostics",
     checkdocs=:none,
 )
 
 deploydocs(;
-    repo="github.com/ProjectTorreyPines/SynthDiag.jl.git",
+    repo="github.com/ProjectTorreyPines/FusionSyntheticDiagnostics.jl.git",
     target="build",
     branch="gh-pages",
     devbranch="master",

docs/src/index.md

@@ -1,5 +1,5 @@
 
-# SynthDiag.jl 
+# FusionSyntheticDiagnostics.jl 
 
 ```@contents
 Pages = ["index.md"]
@@ -8,13 +8,11 @@ Depth = 5
 
 ## Installation
 
-SynthDiag is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). First [install Julia](https://github.com/JuliaLang/juliaup?tab=readme-ov-file#juliaup---julia-version-manager), then:
+First [install Julia](https://github.com/JuliaLang/juliaup?tab=readme-ov-file#juliaup---julia-version-manager), then:
 
 ```julia
 using Pkg
-Pkg.Registry.add(RegistrySpec(url="https://github.com/ProjectTorreyPines/FuseRegistry.jl.git"))
-Pkg.Registry.add("General")
-Pkg.add("SynthDiag")
+Pkg.add("FusionSyntheticDiagnostics")
 ```
 
 ## Synthetic Diagnostics
@@ -48,13 +46,13 @@ Gas valves can be added using IMAS compatible `JSON` file that describes the met
 add_gas_injection!
 compute_gas_injection
 compute_gas_injection!
-SynthDiag.get_lpf
-SynthDiag.dribble
-SynthDiag.downsample_smooth
-SynthDiag.find_delay
+FusionSyntheticDiagnostics.get_lpf
+FusionSyntheticDiagnostics.dribble
+FusionSyntheticDiagnostics.downsample_smooth
+FusionSyntheticDiagnostics.find_delay
 get_gas_injection_response
-SynthDiag.gi_model
-SynthDiag.int_gi_model
+FusionSyntheticDiagnostics.gi_model
+FusionSyntheticDiagnostics.int_gi_model
 get_required_gas_cmd
 ```
 

examples/plotting_interferometer.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Plotting interferometer using GGDUtils\n",
+    "# Plotting interferometer using IMASggd\n",
     " \n",
     " For running this notebook, you need to install package IJulia in your home environment (that is messy, but that is the only way I know right now). So in your terminal:\n",
     " ```\n",
@@ -25,8 +25,7 @@
     "using Pkg\n",
     "Pkg.activate(\"./\")\n",
     "Pkg.add(\"IMASdd\")\n",
-    "Pkg.Registry.add(RegistrySpec(url=\"https://github.com/ProjectTorreyPines/FuseRegistry.jl.git\"))\n",
-    "Pkg.add(\"GGDUtils\")\n",
+    "Pkg.add(\"IMASggd\")\n",
     "Pkg.add(\"Plots\")"
    ]
   },
@@ -37,7 +36,7 @@
    "outputs": [],
    "source": [
     "using IMASdd\n",
-    "using GGDUtils\n",
+    "using IMASggd\n",
     "using Plots"
    ]
   },
@@ -218,7 +217,7 @@
    "source": [
     "gr()\n",
     "\n",
-    "n_e = GGDUtils.get_prop_with_grid_subset_index(ids.edge_profiles.ggd[1].electrons.density, -5)\n",
+    "n_e = IMASggd.get_prop_with_grid_subset_index(ids.edge_profiles.ggd[1].electrons.density, -5)\n",
     "plot(ids.edge_profiles.grid_ggd, n_e, colorbar_title=\"Electrons density / m^(-3)\", left_margin=10Plots.pt)\n",
     "plot!(space)\n",
     "plot!(ids.interferometer, legend=true, size=[635, 900]) # Adding a size comment to make plot aspect ratio better"

src/SynthDiag.jl → src/FusionSyntheticDiagnostics.jl

@@ -1,6 +1,6 @@
-module SynthDiag
+module FusionSyntheticDiagnostics
 
-using IMAS: IMAS
+import IMASdd as IMAS
 
 include("$(@__DIR__)/noise.jl")
 
@@ -12,4 +12,4 @@ include("$(@__DIR__)/langmuir_probes.jl")
 
 include("$(@__DIR__)/gas_injection.jl")
 
-end # module SynthDiag
+end # module FusionSyntheticDiagnostics

src/gas_injection.jl

@@ -27,7 +27,8 @@ function add_gas_injection!(
     verbose::Bool=false,
 )::IMAS.dd
     if endswith(config, ".json")
-        config_dict = convert_strings_to_symbols(IMAS.IMASdd.JSON.parsefile(config))
+        config_dict = convert_strings_to_symbols(IMAS.JSON.parsefile(config)) # Use with import IMASdd as IMAS
+        # config_dict = convert_strings_to_symbols(IMAS.IMASdd.JSON.parsefile(config)) # Use with using IMAS: IMAS
         add_gas_injection!(config_dict, ids; overwrite=overwrite, verbose=verbose)
     else
         error("Only JSON files are supported.")
@@ -106,9 +107,9 @@ end
 Compute the gas flow rate based on the command signal in the all gas valves.
 """
 function compute_gas_injection!(
-    ids::IMAS.dd;
+    ids::IMAS.dd{T};
     valves::Dict{String, Dict{Symbol, Any}}=Dict{String, Dict{Symbol, Any}}(),
-)::Array{Vector{Float64}}
+)::Array{Vector{Float64}} where {T}
     if IMAS.ismissing(ids.gas_injection, :latency)
         global_latency = 0.0
     elseif IMAS.isempty(ids.gas_injection.latency)

src/interferometer.jl

@@ -1,7 +1,7 @@
 using StaticArrays
 import PhysicalConstants.CODATA2018: c_0, ε_0, m_e, m_u, e
 import QuadGK: quadgk, BatchIntegrand
-import GGDUtils: interp, get_grid_subset, get_subset_boundary, subset_do, get_TPS_mats
+import IMASggd: interp, get_grid_subset, get_subset_boundary, subset_do, get_TPS_mats
 
 export add_interferometer!, compute_interferometer!, compute_interferometer
 
@@ -23,7 +23,8 @@ function add_interferometer!(
     overwrite::Bool=false, verbose::Bool=false, rtol::Float64=1e-3, n_e_gsi::Int=5,
 )::IMAS.dd
     if endswith(config, ".json")
-        config_dict = convert_strings_to_symbols(IMAS.IMASdd.JSON.parsefile(config))
+        config_dict = convert_strings_to_symbols(IMAS.JSON.parsefile(config)) # Use with import IMASdd as IMAS
+        # config_dict = convert_strings_to_symbols(IMAS.IMASdd.JSON.parsefile(config)) # Use with using IMAS as IMAS
         add_interferometer!(
             config_dict,
             ids;

src/langmuir_probes.jl

@@ -1,4 +1,4 @@
-import GGDUtils: interp, get_types_with
+import IMASggd: interp, get_types_with
 import PhysicalConstants.CODATA2018: m_e, m_u, e
 
 export add_langmuir_probes!, compute_langmuir_probes!, langmuir_probe_current
@@ -20,7 +20,8 @@ function add_langmuir_probes!(
     overwrite=false, verbose=false, kwargs...,
 )::IMAS.dd
     if endswith(config, ".json")
-        config_dict = convert_strings_to_symbols(IMAS.IMASdd.JSON.parsefile(config))
+        config_dict = convert_strings_to_symbols(IMAS.JSON.parsefile(config)) # Use with import IMASdd as IMAS
+        # config_dict = convert_strings_to_symbols(IMAS.IMASdd.JSON.parsefile(config)) # Use with using IMAS: IMAS
         add_langmuir_probes!(
             config_dict,
             ids;

test/runtests.jl

@@ -1,7 +1,8 @@
-using SynthDiag: IMAS, add_interferometer!, add_langmuir_probes!, add_gas_injection!,
+using FusionSyntheticDiagnostics: IMAS, add_interferometer!, add_langmuir_probes!,
+    add_gas_injection!,
     compute_gas_injection!, get_gas_injection_response, Noise, OverwriteAttemptError,
     langmuir_probe_current
-using IMAS: json2imas
+using IMASdd: json2imas
 using Test
 using Printf
 using Plots

test/speedtest.jl

@@ -1,7 +1,8 @@
-using SynthDiag: add_interferometer!, add_langmuir_probes!, Noise,
+using FusionSyntheticDiagnostics: IMAS, add_interferometer!, add_langmuir_probes!,
+    Noise,
     OverwriteAttemptError, add_gas_injection!, compute_gas_injection,
     get_gas_injection_response
-using SynthDiag.IMAS: json2imas, dd
+import IMASdd: json2imas
 using DelimitedFiles: readdlm
 
 println("-----------------------------------------------------------------------------")
@@ -45,7 +46,7 @@ print("add_langmuir_probes!() time (true runtime): ")
 println("-----------------------------------------------------------------------------")
 config = "$(@__DIR__)/../src/default_gas_injection.json"
 excitation(t) = 0.6
-ids = dd();
+ids = IMAS.dd();
 add_gas_injection!(config, ids)
 ttotal = 5
 nt = Int(ttotal * 1000) + 1
@@ -89,8 +90,9 @@ ids.gas_injection.valve[1].response_curve = gasd_resp_curve
 gasd_model[:time_constant] = 0.3
 gasd_model[:damping] = 0.8
 
-valves = Dict("GASD" => gasd_model)
-
+valves = Dict{String, Dict{Symbol, Any}}("GASD" => gasd_model)
+println(typeof(ids))
+println(typeof(valves))
 print("compute_gas_injection() time with compilation: ")
 @time compute_gas_injection(ids; valves=valves)