GUI and jump options are now extensions

Project.toml

@@ -5,26 +5,24 @@ version = "1.0.0-DEV"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
-HiGHS = "87dc4568-4c63-4d18-b0c0-bb2238e4078b"
-JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NativeFileDialog = "e1fe445b-aa65-4df4-81c1-2041507f0fd4"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-PolygonOps = "647866c9-e3ac-4575-94e7-e3d426903924"
-RipQP = "1e40b3f8-35eb-4cd8-8edd-3e515bb9de08"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+PolygonOps = "647866c9-e3ac-4575-94e7-e3d426903924"
 
 [weakdeps]
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 QuadraticModels = "f468eda6-eac5-11e8-05a5-ff9e497bcd19"
 RipQP = "1e40b3f8-35eb-4cd8-8edd-3e515bb9de08"
-Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
 
 [extensions]
+gui_ext = "GLMakie"
 tikhonov_ripqp_ext = ["RipQP", "QuadraticModels"]
+tikhonov_jump_ext = "JuMP"
 
 [compat]
 julia = "1.9.0"

src/gui.jl → ext/gui_ext.jl

@@ -1,6 +1,10 @@
-function select_peaks(file::String = pick_file(pwd()))
+module gui_ext
 
-    invres = readresults(file)
+using NMRInversions, GLMakie, PolygonOps, LinearAlgebra
+
+function NMRInversions.select_peaks(file::String=pick_file(pwd()))
+
+    invres = NMRInversions.readresults(file)
     dir = invres.dir
     indir = invres.indir
     f = invres.f
@@ -34,7 +38,7 @@ function select_peaks(file::String = pick_file(pwd()))
     m = GridLayout(f[1, 1:2])
     n = GridLayout(f[2:3, 2])
     b = GridLayout(f[2, 1])
-    # ax3d = Axis3(n[1, 1])
+    ax3d = Axis3(n[1, 1])
 
     # Title textbox
     tb = Textbox(f[3, 1], placeholder="Insert a title for the plot, then press enter.",
@@ -72,7 +76,7 @@ function select_peaks(file::String = pick_file(pwd()))
     hidedecorations!(axtop)
     hidedecorations!(axright)
     hidedecorations!(axmain)
-    # hidedecorations!(ax3d)
+    hidedecorations!(ax3d)
 
     colgap!(m, 0)
     rowgap!(m, 0)
@@ -82,7 +86,7 @@ function select_peaks(file::String = pick_file(pwd()))
         empty!(axmain)
         empty!(axtop)
         empty!(axright)
-        # empty!(ax3d)
+        empty!(ax3d)
 
         # Static plots
         contourf!(axmain, z, colormap=:tempo, levels=50)
@@ -91,16 +95,16 @@ function select_peaks(file::String = pick_file(pwd()))
         # Plot diagonal line
         lines!(axmain, [(0, 0), (length(indir), length(dir))], color=:black, linewidth=1)
 
-        # surface!(ax3d, x, y, z, colormap=:tempo)
+        surface!(ax3d, x, y, z, colormap=:tempo)
 
         # Dynamic plots
         contourf!(axmain, spo, mode=:relative, levels=range(0.01, 1, 20), extendlow=:transparent, extendhigh=:transparent, colormap=:blues)
         lines!(axtop, indir_dist, colormap=:tab10, colorrange=(1, 10), color=8)
         lines!(axright, dir_dist, 1:length(dir), colormap=:tab10, colorrange=(1, 10), color=8)
 
-        # surface!(ax3d, x, y, spo, colormap=:blues,
-            # colorrange=(minimum(filter(x -> x != 0, vec(z))), maximum(z)),
-            # lowclip=:transparent)
+        surface!(ax3d, x, y, spo, colormap=:blues,
+        colorrange=(minimum(filter(x -> x != 0, vec(z))), maximum(z)),
+        lowclip=:transparent)
 
         # Plot the points in the selection vector
         scatter!(axmain, selection, colormap=:tab10, colorrange=(1, 10), color=8)
@@ -119,7 +123,7 @@ function select_peaks(file::String = pick_file(pwd()))
 
         if size(selection[], 1) > 2
             polygon[] = vcat(selection[], [selection[][1]])
-            mask[] = [inpolygon(p, polygon[]; in=1, on=1, out=0) for p in points]
+            mask[] = [PolygonOps.inpolygon(p, polygon[]; in=1, on=1, out=0) for p in points]
         end
 
     end
@@ -275,23 +279,21 @@ function select_peaks(file::String = pick_file(pwd()))
 
     on(exportb.clicks) do _
         if isnothing(tb.stored_string[])
-            pubfig(title="")
+            NMRInversions.pubfig(title="")
         else
-            pubfig(title=tb.stored_string[])
+            NMRInversions.pubfig(title=tb.stored_string[])
         end
     end
 
-
-
     reset_limits!(axmain)
     f
 
 end
 
 
-function pubfig(file="inversion_results.txt"; title="", ppu=2)
+function NMRInversions.pubfig(file="inversion_results.txt"; title="", ppu=2)
 
-    invres = readresults(file)
+    invres = NMRInversions.readresults(file)
     dir = invres.dir
     indir = invres.indir
     f = invres.f
@@ -398,4 +400,7 @@ function pubfig(file="inversion_results.txt"; title="", ppu=2)
 
     Makie.save("Results.png", m, px_per_unit=ppu)
 
+end
+
+
 end

ext/tikhonov_jump_ext.jl

@@ -0,0 +1,43 @@
+module tikhonov_jump_ext
+
+using NMRInversions, JuMP, LinearAlgebra, SparseArrays
+
+# import JuMP: @variable
+# import JuMP: @variables
+# import JuMP: @constraint
+# import JuMP: @constraints
+# import JuMP: @objective
+
+function NMRInversions.solve_regularization(K::AbstractMatrix, g::AbstractVector, α::Real, solver::Symbol, order::Int=0)
+
+    A = sparse([K; √(α) .* NMRInversions.Γ(size(K, 2), order)])
+    b = sparse([g; zeros(size(A, 1) - size(g, 1))])
+
+    @eval model = JuMP.Model($(solver).Optimizer)
+    set_silent(model)
+    @variable(model, f[1:size(K, 2)] >= 0)
+    @variable(model, z[1:size(b, 1)])
+    @constraint(model, z .== A * f - b)
+    @objective(model, Min, sum(z .^ 2))
+
+    JuMP.optimize!(model)
+
+    return JuMP.value.(f), vec(K * JuMP.value.(f) .- g)
+
+end
+
+
+# other qp formulations
+
+
+#     # set_silent(model)
+#     # @variable(model, f[1:size(K, 2)] >= 0)
+#     # @variable(model, r[1:size(K, 1)])
+#     # @constraint(model, r .== g .- K * f)
+#     # @objective(model, Min, LinearAlgebra.dot(r, r) + α * LinearAlgebra.dot(f, f))
+#     # optimize!(model)
+#     # @assert is_solved_and_feasible(model)
+#     # return value.(f), value.(r)
+
+
+end

ext/tikhonov_ripqp_ext.jl

@@ -34,14 +34,6 @@ function NMRInversions.solve_regularization(K::AbstractMatrix, g::AbstractVector
 
 end
 
-function NMRInversions.foo()
-    println("Hello, World, updated!")
-end
-
-function NMRInversions.foo(a::Int)
-    println("sdfasdfa!")
-end
-
 
 
 

src/NMRInversions.jl

@@ -6,103 +6,64 @@ using LinearAlgebra
 using SparseArrays
 using NativeFileDialog
 using PolygonOps
-# using GLMakie
-import JuMP
-import HiGHS
 import Optimization, OptimizationOptimJL
 
 """
 to do list:
-- Move the makie gui to extension
 - add L curve method 
-- add SVD to 1D kernels, implement GCV for 1D inversion
-
+- add gcv for reci method
 """
 
 ## The following are custom types for multiple dispatch purposes
 # Pulse sequences
-customtypes = Dict(
-    :IR => :inversion1D,
-    :CPMG => :inversion1D,
-    :PFG => :inversion1D,
-    :IRCPMG => :inversion2D
-)
 
 abstract type inversion1D end
 abstract type inversion2D end
 export inversion1D, inversion2D
 
-for (a, A) in customtypes
-    eval(
-        quote
-            struct $a <: $A end
-            export $a
-        end
-    )
-end
+struct IR <: inversion1D end
+struct CPMG <: inversion1D end
+struct PFG <: inversion1D end
+struct IRCPMG <: inversion2D end
+export IR, CPMG, PFG, IRCPMG
 
 # Supported solvers 
 abstract type regularization_solver end
 export regularization_solver
 
-for x in [:song, :ripqp, :pdhgm] 
-    eval(
-        quote
-            struct $x <: regularization_solver end
-            export $x
-        end
-    )
-end
+struct song <: regularization_solver end
+struct ripqp <: regularization_solver end
+struct pdhgm <: regularization_solver end
+export song, ripqp, pdhgm
 
 # Supported methods to determine regularization α parameter
 abstract type smoothing_optimizer end
 export smoothing_optimizer
 
-for x in [:gcv, :brd, :lcurve] 
-    eval(
-        quote
-            struct $x <: smoothing_optimizer end
-            export $x
-        end
-    )
-end
-
-
-# The following functions are modified from extension files
-ext_functions = Dict(
-    :select_peaks => :GLMakie,
-    :pubfig => :GLMakie
-)
-
-for (a,b) in ext_functions 
-    eval(
-        quote
-            function $a()
-                @warn("The function $(string($a)) is only available after loading the $(string($b)) extension. \nDo that by typing 'using $(string($b))'")
-            end
-            export $a
-        end
-    )
-end
-
+struct gcv <: smoothing_optimizer end
+struct brd <: smoothing_optimizer end
+struct lcurve <: smoothing_optimizer end
+export gcv, brd, lcurve
 
 ## Include the package files 
 include("inversions_io.jl")
 include("kernels.jl")
 include("misc.jl")
 include("inversions_1D.jl")
 include("inversions_2D.jl")
-# include("gui.jl")
 include("tikhonov_song.jl")
-include("tikhonov_jump.jl")
-
+include("L1_regularization.jl")
 
 
 # Export useful functions
 export invert
 export create_kernel
 export import_1D
 export import_spinsolve, import_geospec
-export select_peaks
+
+# The following functions are modified from extension files
+function select_peaks end
+function pubfig end
+export select_peaks, pubfig
 
 end

src/inversions_2D.jl

@@ -50,8 +50,8 @@ function invert(
         display("Data saved as inversion_results.txt")
     end
 
-    if plot == true
-        return select_peaks(joinpath(pwd(), "inversion_results.txt"))
+    if plot == true && !isnothing(Base.get_extension(NMRInversions, :gui_ext))
+        return NMRInversions.select_peaks(joinpath(pwd(), "inversion_results.txt"))
     end
 
     return f, r