Add mask_outline & bump LazyGrids compat (#29)

* Add mask_outline

* Show outline in docs

* LazyGrids compat and v0.10

Project.toml

@@ -1,7 +1,7 @@
 name = "ImageGeoms"
 uuid = "9ee76f2b-840d-4475-b6d6-e485c9297852"
 authors = ["Jeff Fessler <[email protected]> and contributors"]
-version = "0.9"
+version = "0.10"
 
 [deps]
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
@@ -10,6 +10,6 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 
 [compat]
 FillArrays = "0.12, 0.13"
-LazyGrids = "0.4"
+LazyGrids = "0.4, 0.5"
 Requires = "1.3"
 julia = "1.6"

docs/lit/examples/2-mask.jl

@@ -16,9 +16,9 @@ This page was generated from a single Julia file:
 
 #md # The corresponding notebook can be viewed in
 #md # [nbviewer](http://nbviewer.jupyter.org/) here:
-#md # [`1-overview.ipynb`](@__NBVIEWER_ROOT_URL__/1-overview.ipynb),
+#md # [`2-mask.ipynb`](@__NBVIEWER_ROOT_URL__/2-mask.ipynb),
 #md # and opened in [binder](https://mybinder.org/) here:
-#md # [`1-overview.ipynb`](@__BINDER_ROOT_URL__/1-overview.ipynb).
+#md # [`2-mask.ipynb`](@__BINDER_ROOT_URL__/2-mask.ipynb).
 
 
 # ### Setup
@@ -28,8 +28,8 @@ This page was generated from a single Julia file:
 using MIRTjim: jim, prompt # must be first!
 using ImageGeoms: ImageGeom, MaskCircle, MaskAllButEdge
 using ImageGeoms: maskit, embed, embed!, getindex!, jim #, size
+using ImageGeoms: mask_outline
 using Unitful: mm
-using InteractiveUtils: versioninfo
 
 
 # The following line is helpful when running this file as a script;
@@ -38,9 +38,9 @@ using InteractiveUtils: versioninfo
 isinteractive() ? jim(:prompt, true) : prompt(:draw);
 
 
-# ### Mask overview
-
 #=
+## Mask overview
+
 In tomographic image reconstruction, patients are usually more "round"
 than "square" so often we only want to estimate the pixels inside some
 support `mask`: a `Bool` array indicating which pixels are to be estimated.
@@ -79,7 +79,7 @@ ig = ImageGeom(MaskAllButEdge() ; dims=(32,32,16))
 jim(ig)
 
 
-# ### Mask operations
+# ## Mask operations
 
 # Often we need to extract the pixel values within a mask:
 
@@ -95,7 +95,7 @@ core = ramp[ig.mask]
 # Or equivalently:
 maskit(ramp, ig.mask)
 
-# Conversely, we can embed that list of pixels back into an array:
+# Conversely, we can `embed` that list of pixels back into an array:
 array = embed(core, ig.mask)
 
 
@@ -108,13 +108,13 @@ array = collect(zeros(Float16, ig))
 embed!(array, core, ig.mask)
 
 
-# ### Reproducibility
-
-# This page was generated with the following version of Julia:
-
-io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
-
-
-# And with the following package versions
-
-import Pkg; Pkg.status()
+#=
+## Mask outline
+Sometimes we need the outline of the mask.
+=#
+ig = ImageGeom(MaskCircle() ; dims=(40,32))
+outline = mask_outline(ig.mask)
+jim(
+ jim(ig.mask, "Mask"; prompt=false),
+ jim(outline, "Outline"; prompt=false),
+)

src/mask.jl

@@ -46,20 +46,20 @@ mask_or(mask::AbstractArray{Bool,3}) =
 mask_or(mask::AbstractArray{Bool}) = throw("ndims(mask) = $(ndims(mask))")
 
 
-
-#=
 """
     mask_outline(mask)
-return outer boundary of 2D mask (or mask_or for 3D)
+Return outer boundary of 2D `mask` (or `mask_or` for 3D).
 """
 function mask_outline(mask::AbstractMatrix{Bool})
-    tmp = imfilter(mask, centered(ones(Int32,3,3))) # dilate
-#    tmp = tmp[2:end-1,2:end-1] # 'same'
-    return (tmp .> 1) .& (.! mask)
+#   out = imfilter(mask, centered(ones(Int32,3,3))) # dilate
+#   out = out[2:end-1,2:end-1] # 'same'
+    out = copy(mask)
+    for s1 in -1:1, s2 in -1:1
+        out .|= circshift(mask, (s1,s2))
+    end
+    return @. (out > 0) & !mask
 end
 mask_outline(mask::AbstractArray{Bool,3}) = mask_outline(mask_or(mask))
-=#
-
 
 
 """
@@ -99,7 +99,7 @@ Out:
 function embed(x::AbstractMatrix{<:Number}, mask::AbstractArray{Bool})
     L = size(x,2)
     out = zeros(eltype(x), prod(size(mask)), L)
-    for l=1:L
+    for l in 1:L
         out[:,l] = vec(embed(x[:,l], mask))
     end
     reshape(out, size(mask)..., L)

test/mask.jl

@@ -1,7 +1,7 @@
 # mask.jl
 
 using ImageGeoms: embed, embed!, mask_or, maskit, getindex!
-#using ImageGeoms: mask_outline
+using ImageGeoms: mask_outline
 
 using Test: @test, @testset, @test_throws, @inferred
 #using SparseArrays: sparse
@@ -44,15 +44,21 @@ function mask_or_test()
 end
 
 
-#=
-function mask_outline_test() # todo
+function mask_outline_test()
     mask2 = trues(3,4)
-    @test (@inferred mask_outline(mask2)) == falses(3,4)
+    out2 = @inferred mask_outline(mask2)
+    @test out2 == falses(3,4)
     mask3 = trues(3,4,5)
-    @test (@inferred mask_outline(mask3)) == falses(3,4)
+    out3 = @inferred mask_outline(mask3)
+    @test out3 == falses(3,4)
+    mask4 = trues(5,6)
+    f = (a,b) -> [a, a+1, b-1, b]
+    mask4[f(begin, end), begin:end] .= 0
+    mask4[begin:end, f(begin,end)] .= 0
+    out4 = @inferred mask_outline(mask4)
+    @test count(out4) == 10
     true
 end
-=#
 
 function maskit_test()
     mask = [false true true; true false false]
@@ -75,11 +81,9 @@ end
 @testset "mask_or" begin
     @test mask_or_test()
 end
-#=
 @testset "mask_outline" begin
    @test mask_outline_test()
 end
-=#
 @testset "maskit" begin
     @test maskit_test()
 end