Add basic tests

.github/workflows/CI.yml

@@ -24,12 +24,14 @@ jobs:
       matrix:
         version:
           - '1.10'
-          - '1.6'
-          - 'pre'
+          - '1'
         os:
           - ubuntu-latest
         arch:
           - x64
+        include:
+          - os: ubuntu-latest
+            prefix: xvfb-run
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
@@ -39,6 +41,8 @@ jobs:
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        with:
+          prefix: ${{ matrix.prefix }}
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v5
         with:

Project.toml

@@ -1,11 +1,12 @@
 name = "CounterMarking"
 uuid = "454fbcff-fa78-4492-9c80-2cfc3f2a4b52"
 authors = ["Tim Holy <[email protected]> and contributors"]
-version = "1.0.0-DEV"
+version = "1.0.0"
 
 [deps]
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
+ImageIO = "82e4d734-157c-48bb-816b-45c225c6df19"
 ImageMorphology = "787d08f9-d448-5407-9aad-5290dd7ab264"
 ImageSegmentation = "80713f31-8817-5129-9cf8-209ff8fb23e1"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -19,13 +20,15 @@ CounterMarkingImageViewExt = "ImageView"
 [compat]
 FileIO = "1"
 ImageCore = "0.10"
+ImageIO = "0.6"
 ImageMorphology = "0.4"
 ImageSegmentation = "1.9"
 ImageView = "0.12"
 julia = "1.10"
 
 [extras]
+ImageView = "86fae568-95e7-573e-a6b2-d8a6b900c9ef"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["ImageView", "Test"]

README.md

@@ -1,6 +1,7 @@
 # CounterMarking
 
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://HolyLab.github.io/CounterMarking.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://HolyLab.github.io/CounterMarking.jl/dev/)
 [![Build Status](https://github.com/HolyLab/CounterMarking.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/HolyLab/CounterMarking.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/HolyLab/CounterMarking.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/HolyLab/CounterMarking.jl)
+
+Utilities for analyzing images from mouse territorial countermarking experiments.

ext/CounterMarkingImageViewExt.jl

@@ -6,23 +6,23 @@ using ImageSegmentation
 using ImageView
 using Random
 
-function colorize(seg, segidxs::AbstractSet{Int}, color::Colorant)
-    label = seg.image_indexmap
-    img = similar(label, promote_type(typeof(color), valtype(seg.segment_means)))
-    fill!(img, zero(eltype(img)))
-    for idx in eachindex(label)
-        label[idx] ∈ segidxs || continue
-        img[idx] = color
-    end
-    return img
-end
+# function colorize(seg, segidxs::AbstractSet{Int}, color::Colorant)
+#     label = seg.image_indexmap
+#     img = similar(label, promote_type(typeof(color), valtype(seg.segment_means)))
+#     fill!(img, zero(eltype(img)))
+#     for idx in eachindex(label)
+#         label[idx] ∈ segidxs || continue
+#         img[idx] = color
+#     end
+#     return img
+# end
 
 function linkpair(img, imgc)
-    gd = imshow(img)
-    zr = gd["roi"]["zoomregion"]
-    slicedata = gd["roi"]["slicedata"]
-    gdc = imshow(imgc, nothing, zr, slicedata)
-    return (gd, gdc)
+    zr, slicedata = roi(img)
+    gd = imshow_gui((800, 800), (2,1); slicedata=slicedata)
+    imshow(gd["frame"][1,1], gd["canvas"][1,1], img, nothing, zr, slicedata)
+    imshow(gd["frame"][2,1], gd["canvas"][2,1], imgc, nothing, zr, slicedata)
+    return gd
 end
 
 # For visualization
@@ -34,4 +34,7 @@ end
 CounterMarking.randshow(seg; kwargs...) = imshow(map(i->get_random_color(i), labels_map(seg)); kwargs...)
 CounterMarking.meanshow(seg; kwargs...) = imshow(map(i->segment_mean(seg, i), labels_map(seg)); kwargs...)
 
+CounterMarking.randshow(img, seg; kwargs...) = linkpair(img, map(i->get_random_color(i), labels_map(seg)); kwargs...)
+CounterMarking.meanshow(img, seg; kwargs...) = linkpair(img, map(i->segment_mean(seg, i), labels_map(seg)); kwargs...)
+
 end

test/runtests.jl

@@ -1,6 +1,36 @@
 using CounterMarking
+using FileIO
 using Test
 
 @testset "CounterMarking.jl" begin
-    # Write your tests here.
+    testdir = "testimages"
+    img = load(joinpath(testdir, "Picture.png"))
+    seg = segment_image(img)
+    # Without ImageView loaded, we can't visualize it, but we get a helpful error
+    if !isdefined(@__MODULE__, :ImageView)
+        @test_throws "using ImageView" randshow(seg)
+        @test_throws "using ImageView" meanshow(seg)
+    end
+    @eval using ImageView
+    dct = meanshow(seg)
+    @test haskey(dct, "gui")
+    dct = randshow(seg)
+    @test haskey(dct, "gui")
+    dct = randshow(img, seg)
+    @test haskey(dct, "window")
+    dct = meanshow(img, seg)
+    @test haskey(dct, "window")
+    ImageView.closeall()
+
+    spotdict, stimulus = spots(seg)
+    _, stimspot = stimulus
+    @test stimspot.npixels > 1000
+    @test stimspot.centroid[1] < size(img, 1) ÷ 2
+    @test stimspot.centroid[2] > size(img, 2) ÷ 2
+
+    stdspotdict, stdstimulus = upperleft(spotdict, stimulus, size(img))
+    _, stimspot = stdstimulus
+    @test stimspot.npixels > 1000
+    @test stimspot.centroid[1] < size(img, 1) ÷ 2
+    @test stimspot.centroid[2] < size(img, 2) ÷ 2
 end