Move ImageView into package

This is in preparation for the GUI-centric workflow.

Author: timholy

Project.toml

@@ -10,15 +10,10 @@ ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
 ImageIO = "82e4d734-157c-48bb-816b-45c225c6df19"
 ImageMorphology = "787d08f9-d448-5407-9aad-5290dd7ab264"
 ImageSegmentation = "80713f31-8817-5129-9cf8-209ff8fb23e1"
+ImageView = "86fae568-95e7-573e-a6b2-d8a6b900c9ef"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
 
-[weakdeps]
-ImageView = "86fae568-95e7-573e-a6b2-d8a6b900c9ef"
-
-[extensions]
-CounterMarkingImageViewExt = "ImageView"
-
 [compat]
 FileIO = "1"
 Glob = "1"
@@ -31,8 +26,7 @@ XLSX = "0.10"
 julia = "1.10"
 
 [extras]
-ImageView = "86fae568-95e7-573e-a6b2-d8a6b900c9ef"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["ImageView", "Test"]
+test = ["Test"]

ext/CounterMarkingImageViewExt.jl

@@ -6,13 +6,15 @@ using ImageMorphology: label_components
 using FileIO
 using XLSX
 using Glob
+using ImageView
+using Random
 
 export segment_image, stimulus_index, spots, Spot, upperleft
 export writexlsx, process_images
 export randshow, meanshow
 
 include("segment.jl")
-include("stubs.jl")
 include("xlxs.jl")
+include("gui.jl")
 
 end

src/CounterMarking.jl

@@ -0,0 +1,48 @@
+
+
+
+function linkpair(img, imgc)
+    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
+function get_random_color(seed)
+    Random.seed!(seed)
+    rand(RGB{N0f8})
+end
+
+"""
+    randshow(seg; kwargs...)
+    randshow(img, seg; kwargs...)
+
+Display a segmented image using random colors for each segment. The version with
+`img` displays the original image and the segmented image one atop the other,
+and zooming on one will zoom on the other.
+
+!!! note You must load the `ImageView` package to use this function.
+"""
+function randshow end
+
+"""
+    meanshow(seg; kwargs...)
+    meanshow(img, seg; kwargs...)
+
+Display a segmented image using the mean color of each segment. The version with
+`img` displays the original image and the segmented image one atop the other,
+and zooming on one will zoom on the other.
+
+!!! note
+    You must load the `ImageView` package to use this function.
+"""
+function meanshow end
+
+
+randshow(seg; kwargs...) = imshow(map(i->get_random_color(i), labels_map(seg)); kwargs...)
+meanshow(seg; kwargs...) = imshow(map(i->segment_mean(seg, i), labels_map(seg)); kwargs...)
+
+randshow(img, seg; kwargs...) = linkpair(img, map(i->get_random_color(i), labels_map(seg)); kwargs...)
+meanshow(img, seg; kwargs...) = linkpair(img, map(i->segment_mean(seg, i), labels_map(seg)); kwargs...)

src/gui.jl

@@ -13,8 +13,6 @@ function segment_image(
         min_size::Int = 50,         # minimum size of segments to keep
     )
     seg = unseeded_region_growing(img, threshold)
-    L = label_components(labels_map(seg))   # insist on contiguous regions
-    seg = SegmentedImage(img, L)
     if prune
         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)))
@@ -36,6 +34,19 @@ 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...)
+
 struct Spot
     npixels::Int
     centroid::Tuple{Int, Int}
@@ -54,7 +65,7 @@ stimulus segment and the second element is the `Spot` object for that segment.
 Spots larger than `max_size_frac * npixels` (default: 10% of the image) are ignored.
 """
 function spots(
-        seg;
+        seg::SegmentedImage;
         max_size_frac=0.1,            # no spot is bigger than max_size_frac * npixels
     )
     keypair(i, j) = i < j ? (i, j) : (j, i)
@@ -128,3 +139,12 @@ function upperleft(spotdict::AbstractDict{Int, Spot}, stimulus, imgsize)
     end
     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

src/segment.jl

@@ -1,18 +1,14 @@
 using CounterMarking
 using FileIO
 using XLSX
+using ImageView
+using Glob
 using Test
 
 @testset "CounterMarking.jl" begin
     testdir = joinpath(@__DIR__, "..", "docs", "src", "assets")
     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)