Merge pull request #500 from WilhelmusLab/493-get_new23-final

feat: regularize/final

src/IceFloeTracker.jl

@@ -78,13 +78,7 @@ include("morph_fill.jl")
 include("imcomplement.jl")
 include("imadjust.jl")
 include("ice_masks.jl")
-
-const sk_measure = PyNULL()
-const sk_exposure = PyNULL()
-const getlatlon = PyNULL()
-
-
-
+include("regularize-final.jl")
 
 function get_version_from_toml(pth=dirname(dirname(pathof(IceFloeTracker))))::VersionNumber
     toml = TOML.parsefile(joinpath(pth, "Project.toml"))

src/regularize-final.jl

@@ -0,0 +1,113 @@
+using IceFloeTracker: unsharp_mask, to_uint8, hbreak, morph_fill
+
+# TODO: Add tests for regularize_fill_holes, regularize_sharpening, get_final
+
+"""
+    regularize_fill_holes(img, local_maxima_mask, factor, segment_mask, L0mask)
+
+Regularize `img` by:
+    1. increasing the maxima of `img` by a factor of `factor`
+    2. filtering `img` at positions where either `segment_mask` or `L0mask` are true
+    3. filling holes
+
+# Arguments
+- `img`: The morphological residue image.
+- `local_maxima_mask`: The local maxima mask.
+- `factor`: The factor to apply to the local maxima mask.
+- `segment_mask`: The segment mask -- intersection of bw1 and bw2 in first tiled workflow of `master.m`.
+- `L0mask`: zero-labeled pixels from watershed.
+"""
+function regularize_fill_holes(img, local_maxima_mask, segment_mask, L0mask, factor)
+    new2 = to_uint8(img .+ local_maxima_mask .* factor)
+    new2[segment_mask .|| L0mask] .= 0
+    return IceFloeTracker.MorphSE.fill_holes(new2)
+end
+
+"""
+    regularize_sharpening(img, L0mask, radius, amount, local_maxima_mask, factor, segment_mask, se)
+
+Regularize `img` via sharpening, filtering, reconstruction, and maxima elevating.
+
+# Arguments
+- `img`: The input image.
+- `L0mask`: zero-labeled pixels from watershed.
+- `radius`: The radius of the unsharp mask.
+- `amount`: The amount of unsharp mask.
+- `local_maxima_mask`: The local maxima mask.
+- `factor`: The factor to apply to the local maxima mask.
+- `segment_mask`: The segment mask -- intersection of bw1 and bw2 in first tiled workflow of `master.m`.
+"""
+function regularize_sharpening(
+    img, L0mask, local_maxima_mask, segment_mask, se, radius, amount, factor
+)
+    new3 = unsharp_mask(img, radius, amount, 255)
+    new3[L0mask] .= 0
+    new3 = IceFloeTracker.reconstruct(new3, se, "dilation", false)
+    new3[segment_mask] .= 0
+    return to_uint8(new3 + local_maxima_mask .* factor)
+end
+
+function _regularize(
+    morph_residue, local_maxima_mask, segment_mask, L0mask, se; factor, radius, amount
+)
+    reg_fill_holes = regularize_fill_holes(
+        morph_residue, local_maxima_mask, segment_mask, L0mask, factor[1]
+    )
+    reg_sharpened = regularize_sharpening(
+        reg_fill_holes,
+        L0mask,
+        local_maxima_mask,
+        segment_mask,
+        se,
+        radius,
+        amount,
+        factor[end],
+    )
+    return reg_sharpened
+end
+
+"""
+    get_final(img, label, segment_mask, se_erosion, se_dilation)
+
+Final processing following the tiling workflow.
+
+# Arguments
+- `img`: The input image.
+- `label`: Mode of most common label in the find_ice_labels workflow.
+- `segment_mask`: The segment mask.
+- `se_erosion`: structuring element for erosion.
+- `se_dilation`: structuring element for dilation.
+- `apply_segment_mask=true`: Whether to filter `img` the segment mask.
+
+"""
+function get_final(
+    # this function is used in preprocessing_tiling
+    img,
+    segment_mask,
+    se_erosion,
+    se_dilation,
+    apply_segment_mask::Bool=true,
+)
+    _img = hbreak(img)
+
+    # slow for big images
+    _img .= morph_fill(_img)
+
+    # TODO: decide on criteria for applying segment mask
+    apply_segment_mask && (_img[segment_mask] .= false)
+
+    # tends to fill more than matlabs imfill
+    _img .= IceFloeTracker.MorphSE.fill_holes(_img)
+
+    # marker image
+    _img .= branch(_img)
+
+    #= opening to remove noise while preserving shape/size
+    Note the different structuring elements for erosion and dilation =#
+    mask = sk_morphology.erosion(_img, se_erosion)
+    mask .= sk_morphology.dilation(mask, se_dilation)
+
+    # Restore shape of floes based on the cleaned up `mask`
+    final = IceFloeTracker.MorphSE.mreconstruct(IceFloeTracker.MorphSE.dilate, _img, mask)
+    return final
+end

src/special_strels.jl

@@ -28,4 +28,10 @@ function se_disk20()
     se = [sum(c.I) <= 11 for c in CartesianIndices((39, 39))]
     _generate_se!(se)
     return se
-end
+end
+
+function se_disk2()
+    se = [sum(c.I) <= 3 for c in CartesianIndices((5,5))]
+    _generate_se!(se)
+    return se
+end

test/test-regularize-final.jl

@@ -0,0 +1,63 @@
+using IceFloeTracker:
+    get_tiles,
+    regularize_fill_holes,
+    regularize_sharpening,
+    _regularize,
+    se_disk2,
+    get_final
+using DelimitedFiles: readdlm
+
+se = collect(IceFloeTracker.MorphSE.strel_diamond((3, 3)))
+
+test_files_dir = joinpath(@__DIR__, "test_inputs/regularize")
+
+morph_residue = readdlm(joinpath(test_files_dir, "morph_residue.csv"), ',', Int)
+local_maxima_mask = readdlm(joinpath(test_files_dir, "local_maxima_mask.csv"), ',', Int)
+segment_mask = readdlm(joinpath(test_files_dir, "segment_mask.csv"), ',', Bool)
+L0mask = readdlm(joinpath(test_files_dir, "L0mask.csv"), ',', Bool)
+expected_regularized_holes_filled = readdlm(
+    joinpath(test_files_dir, "reg_holes_filled_expected.csv"), ',', Int
+)
+expected_regularized_sharpened = readdlm(
+    joinpath(test_files_dir, "reg_sharpened.csv"), ',', Int
+)
+
+get_final_input = readdlm(joinpath(test_files_dir, "get_final.csv"), ',', Bool)
+se_erosion = se
+se_dilation = se_disk2()
+get_final_expected = readdlm(joinpath(test_files_dir, "get_final_expected.csv"), ',', Bool)
+
+@testset "regularize/get_final" begin
+    @testset "regularize_fill_holes/sharpening" begin
+        reg_holes_filled = regularize_fill_holes(
+            morph_residue, local_maxima_mask, segment_mask, L0mask, 0.3
+        )
+
+        reg_sharpened = regularize_sharpening(
+            reg_holes_filled, L0mask, local_maxima_mask, segment_mask, se, 10, 2, 0.5
+        )
+
+        reg = _regularize(
+            morph_residue,
+            local_maxima_mask,
+            segment_mask,
+            L0mask,
+            se;
+            factor=(0.3, 0.5),
+            radius=10,
+            amount=2,
+        )
+
+        @test expected_regularized_holes_filled == reg_holes_filled
+        @test expected_regularized_sharpened == reg_sharpened
+        @test expected_regularized_sharpened == reg
+    end
+
+    @testset "get_final" begin
+        get_final_output = get_final(
+            get_final_input, segment_mask, se_erosion, se_dilation, true
+        )
+
+        @test get_final_output == get_final_expected
+    end
+end