Modify ui

yufongpeng · Apr 11, 2024 · 339b5a3 · 339b5a3
1 parent eeb4a86
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diff --git a/README.md b/README.md
@@ -131,6 +131,17 @@ To calculate relative signal, concentration or accuracy and save the result, cal
 ## User Interface
 Use the function `ui_init` which activates an environment for ui and run `interactive_calibrate!` on the batch.
 
+Two windows will pop out. 
+One is the main GUI.
+![image1](ui/main.png "Main GUI")
+Calibration curve settings, and the apearance can be modified through the interface. There are also widgets for saving figure, calibration settings.
+
+![image2](ui/point.png "Select or delete calibration points")
+Calibration points can be deleted or added back by left click.
+
+Another window is a table containing data for each points.
+![image3](ui/table.png "Detailed data")
+
 ## Reading and writting data to disk
 To use data on disk, user should create a directory in the following structure:
 ```

diff --git a/ui/Manifest.toml b/ui/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.10.2"
 manifest_format = "2.0"
-project_hash = "c6f3f7dc7675b3f4eb668a776a9e77869dd8fab4"
+project_hash = "95b05fb44ba88b6ef0b9957a153ae34e2e2095d2"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -192,9 +192,9 @@ version = "3.24.0"
 
 [[deps.ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
-git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4"
+git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d"
 uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
-version = "0.11.4"
+version = "0.11.5"
 
 [[deps.ColorVectorSpace]]
 deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"]
@@ -250,9 +250,9 @@ weakdeps = ["IntervalSets", "StaticArrays"]
     ConstructionBaseStaticArraysExt = "StaticArrays"
 
 [[deps.Contour]]
-git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781"
+git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8"
 uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
-version = "0.6.2"
+version = "0.6.3"
 
 [[deps.Crayons]]
 git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
@@ -382,9 +382,9 @@ version = "0.1.2"
 
 [[deps.FFMPEG_jll]]
 deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
-git-tree-sha1 = "ab3f7e1819dba9434a3a5126510c8fda3a4e7000"
+git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "6.1.1+0"
+version = "4.4.4+1"
 
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
@@ -414,10 +414,10 @@ version = "0.9.21"
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 
 [[deps.FillArrays]]
-deps = ["LinearAlgebra", "Random"]
-git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1"
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "bfe82a708416cf00b73a3198db0859c82f741558"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "1.9.3"
+version = "1.10.0"
 weakdeps = ["PDMats", "SparseArrays", "Statistics"]
 
     [deps.FillArrays.extensions]
@@ -483,9 +483,9 @@ version = "2.13.1+0"
 
 [[deps.FreeTypeAbstraction]]
 deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"]
-git-tree-sha1 = "055626e1a35f6771fe99060e835b72ca61a52621"
+git-tree-sha1 = "2493cdfd0740015955a8e46de4ef28f49460d8bc"
 uuid = "663a7486-cb36-511b-a19d-713bb74d65c9"
-version = "0.10.1"
+version = "0.10.3"
 
 [[deps.FriBidi_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -706,10 +706,10 @@ version = "0.15.1"
     Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [[deps.IntervalArithmetic]]
-deps = ["CRlibm_jll", "RoundingEmulator"]
-git-tree-sha1 = "552505ed27d2a90ff04c15b0ecf4634e0ab5547b"
+deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"]
+git-tree-sha1 = "a066535c05e21f8e18b18e759a5d790b7a706399"
 uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
-version = "0.22.9"
+version = "0.22.10"
 weakdeps = ["DiffRules", "ForwardDiff", "RecipesBase"]
 
     [deps.IntervalArithmetic.extensions]
@@ -912,9 +912,9 @@ version = "2.54.5+0"
 
 [[deps.Libtiff_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "6355fb9a4d22d867318db186fd09b09b35bd2ed7"
+git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a"
 uuid = "89763e89-9b03-5906-acba-b20f662cd828"
-version = "4.6.0+0"
+version = "4.5.1+1"
 
 [[deps.Libuuid_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1021,9 +1021,9 @@ version = "0.4.11"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
-git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272"
+git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
-version = "1.1.0"
+version = "1.2.0"
 
 [[deps.Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
@@ -1143,10 +1143,10 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.5+0"
 
 [[deps.Optim]]
-deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "PackageExtensionCompat", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
-git-tree-sha1 = "d1223e69af90b6d26cea5b6f3b289b3148ba702c"
+deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
+git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89"
 uuid = "429524aa-4258-5aef-a3af-852621145aeb"
-version = "1.9.3"
+version = "1.9.4"
 
     [deps.Optim.extensions]
     OptimMOIExt = "MathOptInterface"
@@ -1182,12 +1182,6 @@ git-tree-sha1 = "67186a2bc9a90f9f85ff3cc8277868961fb57cbd"
 uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883"
 version = "0.4.3"
 
-[[deps.PackageExtensionCompat]]
-git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518"
-uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930"
-version = "1.0.2"
-weakdeps = ["Requires", "TOML"]
-
 [[deps.Packing]]
 deps = ["GeometryBasics"]
 git-tree-sha1 = "ec3edfe723df33528e085e632414499f26650501"
@@ -1604,9 +1598,9 @@ version = "1.7.0"
 
 [[deps.StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf"
+git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.34.2"
+version = "0.34.3"
 
 [[deps.StatsFuns]]
 deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]

diff --git a/ui/Project.toml b/ui/Project.toml
@@ -1,4 +1,5 @@
 [deps]
+Blink = "ad839575-38b3-5650-b840-f874b8c74a25"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
@@ -9,10 +10,11 @@ PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9"
 
 [compat]
+Blink = "0.12"
 CSV = "0.10"
 GLM = "1.9"
 GLMakie = "0.8"
 Plotly = "0.4"
 PrettyTables = "2.2"
 TypedTables = "1.4"
-julia = "1.10"
+julia = "1.10"
diff --git a/ui/main.png b/ui/main.png
diff --git a/ui/point.png b/ui/point.png
diff --git a/ui/src/calplot.jl b/ui/src/calplot.jl
@@ -1,5 +1,6 @@
 """
-    interactive_calibrate!(batch::Batch;
+    interactive_calibrate!(batch::Batch; 
+                root = pwd(), 
                 lloq_multiplier = 4//3, dev_acc = 0.15,
                 fig_attr = Dict{Symbol, Any}(:resolution => (1350, 900)), 
                 axis_attr = cal -> Dict(:title => string(first(cal.analyte)), :xlabel => "Concentration (nM)", :ylabel => "Abundance", :titlesize => 20), 
@@ -14,13 +15,15 @@ Interactively calibrate signal and concentration.
 
 # Arguments
 * `batch`: `Batch`.
+* `root`: root directory for saving objects.
 * `dev_acc`: allowed accuracy deviation.
 * `lloq_multiplier`: multiplier for `dev_acc` at LLOQ level.
-* `fig_attr`: `Dicti` contains attributes of `Figure`.
+* `fig_attr`: `Dict` contains attributes of `Figure`.
 * `axis_attr`: a function map each calibtation curve to a `Dict` containing its attributes of `Axis`.
 * `plot_attr`: a function map each calibtation curve to a `Dict` containing its attributes of plots (`Line` or `Scatter`).
 """
-function interactive_calibrate!(batch::Batch;
+function interactive_calibrate!(batch::Batch; 
+                root = pwd(), 
                 lloq_multiplier = 4//3, dev_acc = 0.15,
                 fig_attr = Dict{Symbol, Any}(:resolution => (1350, 900)), 
                 axis_attr = cal -> Dict(:title => string(first(cal.analyte)), :xlabel => "Concentration (nM)", :ylabel => "Abundance", :titlesize => 20), 
@@ -37,6 +40,7 @@ function interactive_calibrate!(batch::Batch;
     axis_attrs = map(axis_attr, batch.calibration)
     plot_attrs = map(plot_attr, batch.calibration)
     i = 1
+    info = Window()
     function draw()
         label_analyte = Label(fig, string(first(batch.calibration[i].analyte)); halign = :left, width = 250)
         button_left = Button(fig, label = "<")
@@ -48,7 +52,7 @@ function interactive_calibrate!(batch::Batch;
         default_w = weight_repr(batch.calibration[i])
         menu_wt = Menu(fig, options = ["none", "1/√x", "1/x", "1/x²"], default = default_w)
         menu_zoom = Menu(fig, options = string.(0:length(unique(batch.calibration[i].table.x))), default = "0", tellwidth = false)
-        menu_show = Menu(fig, options = ["Cal", "Sample"], default = "Cal"; halign = :left, tellwidth = false)
+        # menu_show = Menu(fig, options = ["Cal", "Sample"], default = "Cal"; halign = :left, tellwidth = false)
         menu_export = Menu(fig, options = ["Fig", "Cal", "Fig&Cal"], default = "Cal"; halign = :left, tellwidth = false)
         ax = Axis(fig[1, 1]; axis_attrs[i]...)
         sc = scatter!(ax, batch.calibration[i].table.x, batch.calibration[i].table.y; get_point_attr(plot_attrs[i], batch.calibration[i])...)
@@ -64,17 +68,18 @@ function interactive_calibrate!(batch::Batch;
         button_confirm = Button(fig, label = "confirm", halign = :left)    
         textbox_attr = Textbox(fig, placeholder = "attribute", tellwidth = false, halign = :left)
         textbox_value = Textbox(fig, placeholder = "value (julia expression)", tellwidth = false, halign = :left)
-        button_show = Button(fig, label = "show")
+        button_show = Button(fig, label = "Table")
         button_export = Button(fig, label = "export")
-        button_save = Button(fig, label = "save batch"; halign = :left)
+        button_save = Button(fig, label = "Save batch"; halign = :left)
+        button_saveas = Button(fig, label = "Save batch as")
         lzoom = Label(fig, "Zoom")
         ltype = Label(fig, "Type")
         lzero = Label(fig, "Zero")
         lweight = Label(fig, "Weight")
         lps = Label(fig, "Plot setting", halign = :left, tellwidth = false)
         lc = [label_analyte, button_left, button_right, label_r2, label_formula, lzoom, menu_zoom, 
             ltype, menu_type, lzero, menu_zero, lweight, menu_wt, lps, tall, menu_obj, textbox_attr, button_confirm, textbox_value, 
-            menu_show, menu_export, button_show, button_export, button_save]
+            menu_export, button_show, button_export, button_save, button_saveas]
         fig[1, 2] = vgrid!(
             label_analyte, 
             hgrid!(button_left, button_right),
@@ -87,17 +92,17 @@ function interactive_calibrate!(batch::Batch;
             hgrid!(lps, tall),
             menu_obj, 
             hgrid!(textbox_attr, button_confirm),
-            textbox_value,
-            hgrid!(menu_show, button_show), 
-            hgrid!(menu_export, button_export), 
-            button_save;
+            textbox_value, 
+            hgrid!(button_show, menu_export, button_export), 
+            hgrid!(button_save, button_saveas);
             tellheight = false
         )
         xr = dynamic_range(batch.calibration[i])
         xr = xr .+ (xr[2] - xr[1]) .* (-0.05, 0.05)
         yr = signal_range(batch.calibration[i]) .* ((1 - dev_acc * lloq_multiplier), (1 + dev_acc))
         yr = yr .+ (yr[2] - yr[1]) .* (-0.05, 0.05)
         limits!(ax, xr, yr)
+        body!(info, viewinfo(batch.calibration[i], batch.data, batch.method; lloq_multiplier, dev_acc))
         #display(view_sample(sample; lloq = batch.calibration[i].table.x[findfirst(batch.calibration[i].table.include)], uloq = batch.calibration[i].table.x[findlast(batch.calibration[i].table.include)], lloq_multiplier, dev_acc))
         # Main.vscodedisplay(batch.calibration[i].table[batch.calibration[i].table.include])
         # fig[1, 3] = vgrid!(map(s -> Label(fig, s; halign = :left), split(sprint(showtable, batch.calibration[i].table), "\n"))...; tellheight = false, width = 250)
@@ -108,12 +113,13 @@ function interactive_calibrate!(batch::Batch;
             label_r2.text = "R² = $(round(r2(batch.calibration[i].model); sigdigits = 4))"
             label_formula.text = formula_repr(batch.calibration[i])
             #sample.x̂ .= inv_predict(batch.calibration[i], sample)
+            body!(info, viewinfo(batch.calibration[i], batch.data, batch.method; lloq_multiplier, dev_acc))
         end
         function update_analyte!()
             for x in lc
                 delete!(x)
             end
-            delete!(ax)    
+            delete!(ax)
             draw()
         end
         on(button_left.clicks) do s
@@ -219,21 +225,20 @@ function interactive_calibrate!(batch::Batch;
             end
         end
         on(button_show.clicks) do s
-            if menu_show.selection[] == "Cal"
-                display(view_cal(batch.calibration[i].table; lloq_multiplier, dev_acc))
-            else
-                display(view_sample(batch.data, first(batch.calibration[i].analyte); lloq = batch.calibration[i].table.x[findfirst(batch.calibration[i].table.include)], uloq = batch.calibration[i].table.x[findlast(batch.calibration[i].table.include)], lloq_multiplier, dev_acc))
+            if !active(info) 
+                info = Window()
+                body!(info, viewinfo(batch.calibration[i], batch.data, batch.method; lloq_multiplier, dev_acc))
             end
-            #Main.vscodedisplay(batch.calibration[i].table[batch.calibration[i].table.include])
+                #Main.vscodedisplay(batch.calibration[i].table[batch.calibration[i].table.include])
         end
         on(button_export.clicks) do s
             if menu_export.selection[] == "Fig" || menu_export.selection[] == "Fig&Cal"
-                save_dialog("Save as", nothing, ["*.png"]; start_folder = pwd()) do f
+                save_dialog("Save figure as", nothing, ["*.png"]; start_folder = root) do f
                     f == "" || save(f, fig; update = false)
                 end
             end
             if menu_export.selection[] == "Cal" || menu_export.selection[] == "Fig&Cal"
-                save_dialog("Save as", nothing, ["*.csv"]; start_folder = pwd()) do f
+                save_dialog("Save calibration as", nothing, ["*.csv"]; start_folder = root) do f
                     f == "" || CSV.write(f, Table(; formula = [formula_repr_utf8(batch.calibration[i])], weight = [weight_repr_utf8(batch.calibration[i])], LLOQ = [format_number(lloq(batch.calibration[i]))], ULOQ = [format_number(uloq(batch.calibration[i]))],  r_squared = [format_number(r2(batch.calibration[i].model))]))
                 end
             end
@@ -256,14 +261,24 @@ function interactive_calibrate!(batch::Batch;
             end
             =#
         end
-        on(button_save.clicks) do s
-            save_dialog("Save as", nothing, ["*.batch"]; start_folder = pwd()) do f
+        on(button_saveas.clicks) do s
+            save_dialog("Save as", nothing, ["*.batch"]; start_folder = root) do f
                 f == "" || ChemistryQuantitativeAnalysis.write(f, batch)
             end
         end
+        on(button_save.clicks) do s
+            if endswith(root, ".batch")
+                ask_dialog("Save batch?\n$root") && ChemistryQuantitativeAnalysis.write(root, batch)
+            else
+                save_dialog("Save as", nothing, ["*.batch"]; start_folder = root) do f
+                    f == "" || ChemistryQuantitativeAnalysis.write(f, batch)
+                end
+            end
+        end
     end
     draw()
-    fig
+    wait(display(fig))
+    close(info)
 end
 
 #get_point_attr(plot_attr::Dict, incl::Bool) = NamedTuple(k => incl ? v[1] : v[2] for (k, v) in get!(plot_attr, :scatter, Dict(:color => [:blue, :red])))