Add GUI test

Also fixes the doc build

Author: timholy

.github/workflows/CI.yml

@@ -69,14 +69,19 @@ jobs:
           Pkg.develop(PackageSpec(path=pwd()))
           Pkg.instantiate()
       - uses: julia-actions/julia-buildpkg@v1
+        with:
+          prefix: xvfb-run
       - uses: julia-actions/julia-docdeploy@v1
+        with:
+          prefix: xvfb-run
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
       - name: Run doctests
-        shell: julia --project=docs --color=yes {0}
+        shell: xvfb-run julia --project=docs --color=yes {0}
         run: |
           using Documenter: DocMeta, doctest
           using CounterMarking
           DocMeta.setdocmeta!(CounterMarking, :DocTestSetup, :(using CounterMarking); recursive=true)
           doctest(CounterMarking)
+          

docs/src/assets/Picture.png

@@ -1,5 +1,10 @@
 
-function gui(outbase, files; colors=distinguishable_colors(15, [RGB(1, 1, 1)]; dropseed=true))
+function gui(
+        outbase, files;
+        colors=distinguishable_colors(15, [RGB(1, 1, 1)]; dropseed=true),
+        btnclick = Condition(),         # used for testing
+        whichbutton = Ref{Symbol}(),    # used for testing
+    )
     channelpct(x) = string(round(Int, x * 100)) * '%'
 
     outbase, _ = splitext(outbase)
@@ -60,8 +65,6 @@ function gui(outbase, files; colors=distinguishable_colors(15, [RGB(1, 1, 1)]; d
         push!(cbs, cb)
     end
     # Add "Done & Next" and "Skip" buttons
-    btnclick = Condition()
-    whichbutton = Ref{Symbol}()
     donebtn = button("Done & Next")
     skipbtn = button("Skip")
     push!(guibx, donebtn)
@@ -129,6 +132,8 @@ function gui(outbase, files; colors=distinguishable_colors(15, [RGB(1, 1, 1)]; d
         end
     end
     destroy(win)
+    notify(btnclick)   # used in testing
+    return
 end
 gui(outbase, glob::Glob.GlobMatch; kwargs...) = gui(outbase, Glob.glob(glob); kwargs...)
 

docs/src/assets/Picture.png

@@ -14,7 +14,7 @@ function segment_image(
     )
     seg = unseeded_region_growing(img, threshold)
     if prune
-        println("Pruning segments smaller than $min_size pixels")
+        # println("Pruning segments smaller than $min_size pixels")
         seg = prune_segments(seg, label -> segment_pixel_count(seg, label) < min_size, (l1, l2) -> colordiff(segment_mean(seg, l1), segment_mean(seg, l2)))
     end
     return seg
@@ -34,18 +34,18 @@ function stimulus_index(seg::SegmentedImage, colorproj = RGB{Float32}(1, 1, -2))
     return i
 end
 
-function contiguous(seg::SegmentedImage, img::AbstractMatrix{<:Color}; min_size::Int = 50)
-    L = label_components(labels_map(seg))   # insist on contiguous regions
-    newseg = SegmentedImage(img, L)
-    newseg = prune_segments(newseg, label -> segment_pixel_count(newseg, label) < min_size, (l1, l2) -> colordiff(segment_mean(newseg, l1), segment_mean(newseg, l2)))
-    mapping = Dict(k => Set{Int}() for k in segment_labels(seg))
-    for (i, l) in pairs(seg.image_indexmap)
-        push!(mapping[l], newseg.image_indexmap[i])
-    end
-    return mapping
-end
-contiguous(seg::SegmentedImage, img::AbstractMatrix{<:Colorant}; kwargs...) =
-    contiguous(seg, color.(img); kwargs...)
+# function contiguous(seg::SegmentedImage, img::AbstractMatrix{<:Color}; min_size::Int = 50)
+#     L = label_components(labels_map(seg))   # insist on contiguous regions
+#     newseg = SegmentedImage(img, L)
+#     newseg = prune_segments(newseg, label -> segment_pixel_count(newseg, label) < min_size, (l1, l2) -> colordiff(segment_mean(newseg, l1), segment_mean(newseg, l2)))
+#     mapping = Dict(k => Set{Int}() for k in segment_labels(seg))
+#     for (i, l) in pairs(seg.image_indexmap)
+#         push!(mapping[l], newseg.image_indexmap[i])
+#     end
+#     return mapping
+# end
+# contiguous(seg::SegmentedImage, img::AbstractMatrix{<:Colorant}; kwargs...) =
+#     contiguous(seg, color.(img); kwargs...)
 
 struct Spot
     npixels::Int
@@ -75,7 +75,7 @@ function spots(
     label = seg.image_indexmap
     R = CartesianIndices(label)
     Ibegin, Iend = extrema(R)
-    I1 = one(Ibegin)
+    I1 = oneunit(Ibegin)
     centroidsacc = Dict{Int, Tuple{Int, Int, Int}}()   # accumulator for centroids
     nadj = Dict{Tuple{Int, Int}, Int}()             # number of times two segments are adjacent
     for idx in R
@@ -140,11 +140,11 @@ function upperleft(spotdict::AbstractDict{Int, Spot}, stimulus, imgsize)
     return Dict(k => flip(v) for (k, v) in spotdict), sidx => flip(ss)
 end
 
-function colorize(seg::SegmentedImage, coloridx::AbstractDict, colors=distinguishable_colors(length(unique(values(coloridx)))))
-    label = seg.image_indexmap
-    img = similar(label, eltype(colors))
-    for idx in eachindex(label)
-        img[idx] = colors[coloridx[label[idx]]]
-    end
-    return img
-end
+# function colorize(seg::SegmentedImage, coloridx::AbstractDict, colors=distinguishable_colors(length(unique(values(coloridx)))))
+#     label = seg.image_indexmap
+#     img = similar(label, eltype(colors))
+#     for idx in eachindex(label)
+#         img[idx] = colors[coloridx[label[idx]]]
+#     end
+#     return img
+# end

src/gui.jl

@@ -40,4 +40,16 @@ using Test
     process_images(tmpfile, glob"*.png"; dirname=testdir)
     data = XLSX.readtable(tmpfile, "Picture")
     @test isa(data, XLSX.DataTable)
+
+    # Test the gui
+    rm(tmpfile, force=true)
+    btnclick = Condition()
+    whichbutton = Ref{Symbol}()
+    @async gui(tmpfile, [joinpath(testdir, "Picture.png")]; btnclick, whichbutton)
+    sleep(5)
+    whichbutton[] = :done
+    notify(btnclick)
+    wait(btnclick)
+    @test isfile(tmpfile)
+    @test isfile(splitext(tmpfile)[1] * ".jld2")
 end