replaced images with ImageTransform

Author: behinger

Project.toml

@@ -4,13 +4,13 @@ authors = ["Benedikt V. Ehinger", "Maanik Marathe"]
 version = "0.2.0"
 
 [deps]
-Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+ImageMorphology = "787d08f9-d448-5407-9aad-5290dd7ab264"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [compat]
-Images = "0.25"
+ImageMorphology = "0.4"
 Random = "1"
 SparseArrays = "1"
 StatsBase = "0.33, 0.34"

src/ClusterDepth.jl

@@ -1,7 +1,7 @@
 module ClusterDepth
 
 using Random
-using Images
+using ImageMorphology
 using SparseArrays
 #using ExtendableSparse
 using StatsBase

src/cluster.jl

@@ -24,14 +24,14 @@ clusterdepth(data::AbstractArray, args...; kwargs...) =
 function clusterdepth(
     rng,
     data::AbstractArray;
-    τ = 2.3,
-    stat_type = :onesample_ttest,
-    perm_type = :sign,
-    side_type = :abs,
-    nperm = 5000,
-    pval_type = :troendle,
-    (statfun!) = nothing,
-    statfun = nothing,
+    τ=2.3,
+    stat_type=:onesample_ttest,
+    perm_type=:sign,
+    side_type=:abs,
+    nperm=5000,
+    pval_type=:troendle,
+    (statfun!)=nothing,
+    statfun=nothing,
 )
     if stat_type == :onesample_ttest
         statfun! = studentt!
@@ -57,13 +57,13 @@ function clusterdepth(
         data,
         permfun,
         τ;
-        nₚ = nperm,
-        (statfun!) = statfun!,
-        statfun = statfun,
-        sidefun = sidefun,
+        nₚ=nperm,
+        (statfun!)=statfun!,
+        statfun=statfun,
+        sidefun=sidefun,
     )
 
-    return pvals(statfun(data), cdmTuple, τ; type = pval_type)
+    return pvals(statfun(data), cdmTuple, τ; type=pval_type)
 end
 
 
@@ -74,10 +74,10 @@ function perm_clusterdepths_both(
     data,
     permfun,
     τ;
-    statfun = nothing,
-    (statfun!) = nothing,
-    nₚ = 1000,
-    sidefun = nothing,
+    statfun=nothing,
+    (statfun!)=nothing,
+    nₚ=1000,
+    sidefun=nothing,
 )
     @assert !(isnothing(statfun) && isnothing(statfun!)) "either statfun or statfun! has to be defined"
 
@@ -218,7 +218,7 @@ if the first and last cluster start on the first/last sample, we dont know their
 	Input is assumed to be a thresholded Array with only 0/1
 """
 function cluster(data)
-    label = label_components(data)
+    label = label_components(Matrix(data))
     K = maximum(label)
     start = fill(0, K)
     stop = fill(0, K)

test/cluster.jl

@@ -1,11 +1,11 @@
 @testset "cluster" begin
     s, l = ClusterDepth.cluster(
-        [4.0, 0.0, 10.0, 0.0, 3.0, 4.0, 0, 4.0, 4.0, 0.0, 0.0, 5.0] .> 0.9,
+        [4.0 0.0 10.0 0.0 3.0 4.0 0 4.0 4.0 0.0 0.0 5.0] .> 0.9,
     )
     @test s == [3, 5, 8]
     @test l == [0, 1, 1]
 
-    s, l = ClusterDepth.cluster([0.0, 0.0, 0.0, 0.0] .> 0.9)
+    s, l = ClusterDepth.cluster([0.0 0.0 0.0 0.0] .> 0.9)
     @test s == []
     @test l == []
 end
@@ -17,5 +17,5 @@ end
 
 @testset "Tests for 3D data" begin
     data = randn(StableRNG(1), 3, 20, 5)
-    @show ClusterDepth.clusterdepth(data; τ = 0.4, nperm = 5)
+    @show ClusterDepth.clusterdepth(data; τ=0.4, nperm=5)
 end