rm in favor of just fenz

MolloiLab · Sep 20, 2023 · fe48131 · fe48131
1 parent df91282
commit fe48131
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Showing 13 changed files with 131 additions and 2,629 deletions.
diff --git a/Manifest.toml b/Manifest.toml
diff --git a/src/DistanceTransforms.jl b/src/DistanceTransforms.jl
@@ -1,31 +1,21 @@
 module DistanceTransforms
 
-using CUDA
-using FLoops
-# using FoldsCUDA
+abstract type DistanceTransform end
 
-include("./borgefors.jl")
 include("./felzenszwalb.jl")
 include("./maurer.jl")
 include("./utils.jl")
-include("./wenbo.jl")
 
 export DistanceTransform,
     transform,
     transform!,
 
-    # Export chamfer.jl functions
-    Borgefors,
-
     # Export maurer.jl functions
     Maurer,
 
     # Export felzenszwalb.jl functions
     Felzenszwalb,
 
     # Export utils.jl functions
-    boolean_indicator,
-
-    # Export wenbo.jl functions
-    Wenbo
+    boolean_indicator
 end
diff --git a/src/borgefors.jl b/src/borgefors.jl
diff --git a/src/felzenszwalb.jl b/src/felzenszwalb.jl
@@ -1,7 +1,5 @@
-
 using FLoops
 using CUDA
-using FoldsThreads
 
 """
 ## Felzenszwalb
@@ -184,34 +182,3 @@ function transform(vol::CuArray{T, 3}, tfm::Felzenszwalb; output=similar(vol, Fl
     end
     return output
 end
-
-function transform(img::AbstractMatrix, tfm::Felzenszwalb, ex; output=similar(img, Float32), v=ones(size(img)), z=ones(size(img) .+ 1))
-	# 1
-	@floop ex for k in CartesianIndices(@view(img[:, 1]))
-	    @views transform(img[k,:], tfm; output=output[k,:], v=v[k,:], z=z[k,:])
-	end
-	output2 = similar(output)
-	# 2
-	@floop ex for k in CartesianIndices(@view(img[1, :]))
-	    @views transform(output[:,k], tfm; output=output2[:,k], v=fill!(v[:,k], 1), z=fill!(z[:,k], 1))
-	end
-	# end
-	return output2
-end
-
-function transform(vol::AbstractArray, tfm::Felzenszwalb, ex; output=similar(vol, Float32), v=ones(size(vol)), z=ones(size(vol) .+ 1))
-	# 1
-    @floop ex for k in CartesianIndices(@view(vol[1,:,:]))
-        @views transform(vol[:, k], tfm; output=output[:, k], v=v[:, k], z=z[:, k])
-    end
-	output2 = similar(output)
-	# 2
-    @floop ex for k in CartesianIndices(@view(vol[:,1,:]))
-        @views transform(output[k[1], :, k[2]], tfm; output=output2[k[1], :, k[2]], v=fill!(v[k[1], :, k[2]], 1), z=fill!(z[k[1], :, k[2]], 1))
-    end
-	# 3
-    @floop ex for k in CartesianIndices(@view(vol[:,:,1]))
-        @views transform(output2[k, :], tfm; output=output[k, :], v=fill!(v[k, :], 1), z=fill!(z[k, :], 1))
-    end
-    return output
-end
diff --git a/src/maurer.jl b/src/maurer.jl
@@ -6,26 +6,24 @@ using ImageMorphology
 ```julia
 struct Maurer <: DistanceTransform end
 ```
-
 Wrapper function for `ImageMorphology.feature_transform` and `ImageMorphology.distance_transform`. Applies a true Euclidean distance transform to the array elements and returns an array with spatial information embedded in the elements.
 """
 struct Maurer <: DistanceTransform end
 
 """
-## transform (Maurer)
+## transform (Felzenszwalb)
 
 ```julia
 transform(img, tfm::Maurer)
-
 transform(img::BitArray, tfm::Maurer)
 ```
 
 Wrapper function for `ImageMorphology.feature_transform` and `ImageMorphology.distance_transform`. Applies a true Euclidean distance transform to the array elements and returns an array with spatial information embedded in the elements.
 
-Arguments
+#### Arguments
 - img: N-dimensional array to be transformed based on location to the nearest background (0) pixel
 
-Citation
+#### Citation
 - 'A Linear Time Algorithm for Computing Exact Euclidean Distance Transforms of Binary Images in Arbitrary Dimensions' [Maurer et al., 2003] (DOI: 10.1109/TPAMI.2003.1177156)
 """
 transform(img, tfm::Maurer) = distance_transform(feature_transform(Bool.(img)))

diff --git a/src/utils.jl b/src/utils.jl
@@ -1,59 +1,18 @@
-### A Pluto.jl notebook ###
-# v0.19.8
+using LoopVectorization
 
-using Markdown
-using InteractiveUtils
-
-# ╔═╡ 4b4b6c39-e155-462a-b0ad-65688c949577
-# ╠═╡ show_logs = false
-begin
-	using Pkg
-	Pkg.activate("..")
-	using Revise
-	using PlutoUI
-	using Test
-	using CUDA
-	using DistanceTransforms
-	using LoopVectorization
-end
-
-# ╔═╡ 4db00b10-0440-4f28-bf91-01dca21847b0
-TableOfContents()
-
-# ╔═╡ 64661943-81d4-40c5-9479-fcc381544185
-md"""
-## Boolean Indicator
-"""
-
-# ╔═╡ 5f558b4b-d109-45d7-b2f8-fa03c0ff5db6
-begin
 """
-```julia
-boolean_indicator(f)
-```
+	boolean_indicator(f)
+	boolean_indicator(f::BitArray)
 
-If `f` is a boolean indicator where 0's correspond to background and 1s correspond to the foreground, then mark background pixels with a large number `1e10`
+If `f` is a boolean indicator where 0's correspond to background and 1s correspond to the foreground, then mark background pixels with a large number `1e10`.
+Uses LoopVectorization.jl for speed up if array is `BitArray`
 """
 boolean_indicator(f) = @. ifelse(f < 0.5, 1.0f10, 0.0f0)
 
-"""
-```julia
-boolean_indicator(f::BitArray)
-```
-
-If `f` is a boolean indicator where 0's correspond to background and 1s correspond to the foreground, then mark background pixels with a large number `1e10`. Uses LoopVectorization.jl for speed up
-"""
 function boolean_indicator(f::BitArray)
 	f_new = similar(f, Float32)
 	@turbo warn_check_args=false for i in CartesianIndices(f_new)
 		   @inbounds f_new[i] = f[i] ? 0f0 : 1f10
 	end
 	return f_new
 end
-end
-
-# ╔═╡ Cell order:
-# ╠═4b4b6c39-e155-462a-b0ad-65688c949577
-# ╠═4db00b10-0440-4f28-bf91-01dca21847b0
-# ╟─64661943-81d4-40c5-9479-fcc381544185
-# ╠═5f558b4b-d109-45d7-b2f8-fa03c0ff5db6