Merge pull request #186 from WilhelmusLab/feat-fill-holes

feat: add function to fill interior holes

Author: tdivoll

src/IceFloeTracker.jl

@@ -79,7 +79,7 @@ end
 
 Module for morphological operations with structuring element functionality adapted from ImageMorphology v0.4.3.
 
-This module is temporary until v0.5 of ImageMorphology is relaeased.
+This module is temporary until v0.5 of ImageMorphology is released.
 
 Main functionality is `dilate(img, se)` for landmask computations.
 
@@ -136,5 +136,6 @@ module MorphSE
     include("morphSE/closing.jl")
     include("morphSE/bothat.jl")
     include("morphSE/mreconstruct.jl")
+    include("morphSE/fill_holes.jl")
 end
 end

src/morphSE/fill_holes.jl

@@ -0,0 +1,57 @@
+# From https://github.com/JuliaImages/ImageMorphology.jl/pull/119
+
+"""
+    fill_holes(img; [dims])
+    fill_holes(img; se)
+Fill the holes in image 'img'. Could be binary or grascale
+The `dims` keyword is used to specify the dimension to process by constructing the box shape
+structuring element [`strel_box(img; dims)`](@ref strel_box). For generic structuring
+element, the half-size is expected to be either `0` or `1` along each dimension.
+The output has the same type as input image
+"""
+
+function fill_holes(img; dims=coords_spatial(img))
+    return fill_holes(img, strel_box(img, dims))
+end
+
+function fill_holes(img, se)
+    return fill_holes!(similar(img), img, se)
+end
+
+function fill_holes!(out, img; dims=coords_spatial(img))
+    return fill_holes!(out, img, strel_box(img, dims))
+end
+
+function fill_holes!(out, img, se)
+    return _fill_holes!(out, img, se)
+end
+
+function _fill_holes!(out, img, se)
+    N = ndims(img)
+
+    axes(out) == axes(img) || throw(DimensionMismatch("images should have the same axes"))
+
+    se_size = strel_size(se)
+    if length(se_size) != N
+        msg = "the input structuring element is not for $N dimensional array, instead it is for $(length(se_size)) dimensional array"
+        throw(DimensionMismatch(msg))
+    end
+    if !all(x -> in(x, (1, 3)), strel_size(se))
+        msg = "structuring element with half-size larger than 1 is invalid"
+        throw(DimensionMismatch(msg))
+    end
+
+    tmp = similar(img)
+
+    # fill marker image with max
+    fill!(tmp, typemax(eltype(img)))
+    # fill borders with 0
+    dimensions = size(tmp)
+    outerrange = CartesianIndices(map(i -> 1:i, dimensions))
+    innerrange = CartesianIndices(map(i -> (1 + 1):(i - 1), dimensions))
+    for i in EdgeIterator(outerrange, innerrange)
+        tmp[i] = 0
+    end
+
+    return mreconstruct!(erode, out, tmp, img, se)
+end

test/runtests.jl

@@ -17,7 +17,7 @@ testnames = [n[6:(end - 3)] for n in alltests]
 
 ## Put the filenames to test below
 
-to_test = #alltests # uncomment this line to run all tests or add individual files below 
+to_test = alltests # uncomment this line to run all tests or add individual files below 
 [
     # "test-create-landmask.jl",
     # "test-create-cloudmask.jl",
@@ -30,7 +30,7 @@ to_test = #alltests # uncomment this line to run all tests or add individual fil
     # "test-segmentation-b.jl",
     # "test-segmentation-c.jl",
     # "test-segmentation-d-e.jl",
-     "test-segmentation-f.jl",
+    # "test-segmentation-f.jl",
     # "test-bwtraceboundary.jl",
     # "test-resample-boundary.jl",
     # "test-regionprops.jl",

test/test-morphSE.jl

@@ -9,21 +9,31 @@
     se = IceFloeTracker.MorphSE.strel_box((n, n))
     @test IceFloeTracker.MorphSE.dilate(a, se) == ones(Int, n, n)
 
-    # Bothat, opening, erode using output from Matlab
+    # Bothat, opening, erode, filling holes, reconstruction using output from Matlab
     A = zeros(Bool, 41, 41)
     A[(21 - 10):(21 + 10), (21 - 10):(21 + 10)] .= 1
+    I = falses(8, 8)
+    I[1:8, 3:6] .= 1
+    I[[CartesianIndex(4, 4), CartesianIndex(5, 5)]] .= 0
+    I
     se = centered(IceFloeTracker.se_disk4())
+
+    #read in expected files from MATLAB
     path = joinpath(test_data_dir, "morphSE")
     erode_withse_exp = readdlm(joinpath(path, "erode_withse1_exp.csv"), ',', Bool)
     bothat_withse_exp = readdlm(joinpath(path, "bothat_withse1_exp.csv"), ',', Bool)
     open_withse_exp = readdlm(joinpath(path, "open_withse1_exp.csv"), ',', Bool)
     reconstruct_exp = readdlm(joinpath(path, "reconstruct_exp.csv"), ',', Int64)
     matrix_A = readdlm(joinpath(path, "mat_a.csv"), ',', Int64)
     matrix_B = readdlm(joinpath(path, "mat_b.csv"), ',', Int64)
+    filled_holes_exp = readdlm(joinpath(path, "filled_holes.csv"), ',', Int64)
+
+    #run tests
     @test open_withse_exp == IceFloeTracker.MorphSE.opening(A, se)
     @test erode_withse_exp == IceFloeTracker.MorphSE.erode(A, se)
     @test bothat_withse_exp == IceFloeTracker.MorphSE.bothat(A, se)
     @test reconstruct_exp == IceFloeTracker.MorphSE.mreconstruct(
         IceFloeTracker.MorphSE.dilate, matrix_B, matrix_A
     )
+    @test filled_holes_exp == IceFloeTracker.MorphSE.fill_holes(I)
 end

test/test-segmentation-f.jl

@@ -4,16 +4,16 @@
 
     ## Load inputs for comparison
     segmentation_B_not_ice_mask = float64.(load("$(test_data_dir)/matlab_not_ice_mask.png"))
-    segmentation_C_ice_mask = load(segmented_c_test_file) .>= 0.5
+    segmentation_C_ice_mask = load(segmented_c_test_file) .> 0
     cloudmask = convert(BitMatrix, load(cloudmask_test_file))
     landmask = convert(BitMatrix, load(current_landmask_file))
-    watershed_intersect = load(watershed_test_file) .>= 0.5
+    watershed_intersect = load(watershed_test_file) .> 0
     ice_labels =
         Int64.(
             vec(DelimitedFiles.readdlm("$(test_data_dir)/ice_labels_floe_region.csv", ','))
         )
     matlab_isolated_floes =
-        float64.(load("$(test_data_dir)/matlab_isolated_floes.png")) .>= 0.5
+        float64.(load("$(test_data_dir)/matlab_isolated_floes.png")) .> 0
 
     ## Run function with Matlab inputs
 
@@ -34,6 +34,6 @@
 
     @test typeof(isolated_floes) == typeof(matlab_isolated_floes)
     @test test_similarity(
-        isolated_floes, matlab_isolated_floes[ice_floe_test_region...], 0.033
+        isolated_floes, matlab_isolated_floes[ice_floe_test_region...], 0.035
     )
 end

test/test_inputs/morphSE/filled_holes.csv

@@ -0,0 +1,8 @@
+0,0,1,1,1,1,0,0
+0,0,1,1,1,1,0,0
+0,0,1,1,1,1,0,0
+0,0,1,1,1,1,0,0
+0,0,1,1,1,1,0,0
+0,0,1,1,1,1,0,0
+0,0,1,1,1,1,0,0
+0,0,1,1,1,1,0,0