Merge pull request #1 from HolyLab/cjg/updates

Cjg/updates

Author: Cody-G

.travis.yml

@@ -4,8 +4,8 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
-  - nightly
+  - 1.0
+  - 1.1
 notifications:
   email: false
 git:
@@ -18,18 +18,22 @@ git:
 #  - julia: nightly
 
 ## uncomment and modify the following lines to manually install system packages
-#addons:
-#  apt: # apt-get for linux
-#    packages:
-#    - gfortran
-#before_script: # homebrew for mac
-#  - if [ $TRAVIS_OS_NAME = osx ]; then brew install gcc; fi
+addons:
+  apt:
+    packages:
+      - build-essential
+      - gfortran
+      - pkg-config
+      - hdf5-tools
 
 ## uncomment the following lines to override the default test script
-#script:
-#  - julia -e 'Pkg.clone(pwd()); Pkg.build("ImageInterpLast"); Pkg.test("ImageInterpLast"; coverage=true)'
+script:
+  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+  - julia ci_prep.jl
+  - julia -e 'using Pkg; Pkg.build(); Pkg.test("ImageInterpLast"; coverage=true)'
 after_success:
-  # push coverage results to Coveralls
-  - julia -e 'cd(Pkg.dir("ImageInterpLast")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
   # push coverage results to Codecov
-  - julia -e 'cd(Pkg.dir("ImageInterpLast")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+  - julia -e 'import Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+  # update the documentation
+  #   - julia -e 'using Pkg; Pkg.add("Documenter")'
+    #  - julia -e 'using CachedCalls; cd(dirname(dirname(pathof(CachedCalls)))); ENV["DOCUMENTER_DEBUG"] = "true"; include(joinpath("docs", "make.jl"))'

Project.toml

@@ -0,0 +1,14 @@
+name = "ImageInterpLast"
+uuid = "2857f282-5c94-11e9-0b5d-cb5f26255b42"
+version = "0.1.0"
+
+[deps]
+AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
+CachedArrays = "d8fd01e4-1764-11e9-0a01-8f76bebf08d8"
+Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.6
-CachedSeries
+julia 1.0
+CachedArrays
 Images
 AxisArrays

appveyor.yml

@@ -1,16 +1,18 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.6-latest-win32.exe"
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 1
+  - julia_version: 1.1
+  #- julia_version: nightly
 
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
+
+# # Uncomment the following lines to allow failures on nightly julia
+# # (tests will run but not make your overall status red)
+# matrix:
+#   allow_failures:
+#   - julia_version: nightly
 
 branches:
   only:
@@ -24,24 +26,12 @@ notifications:
     on_build_status_changed: false
 
 install:
-  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
-# If there's a newer build queued for the same PR, cancel this one
-  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
-        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
-        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
-        throw "There are newer queued builds for this pull request, failing early." }
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $env:JULIA_URL,
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 build_script:
-# Need to convert from shallow to complete for Pkg.clone to work
-  - IF EXIST .git\shallow (git fetch --unshallow)
-  - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"ImageInterpLast\"); Pkg.build(\"ImageInterpLast\")"
-
+  - C:\julia\bin\julia ci_prep.jl
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 test_script:
-  - C:\projects\julia\bin\julia -e "Pkg.test(\"ImageInterpLast\")"
+  - echo "%JL_TEST_SCRIPT%
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"

ci_prep.jl

@@ -0,0 +1,11 @@
+using Pkg, LibGit2;
+user_regs = joinpath(DEPOT_PATH[1],"registries");
+mkpath(user_regs);
+all_registries = Dict("General" => "https://github.com/JuliaRegistries/General.git",
+	      "HolyLabRegistry" => "https://github.com/HolyLab/HolyLabRegistry.git");
+Base.shred!(LibGit2.CachedCredentials()) do creds
+  for (reg, url) in all_registries
+    path = joinpath(user_regs, reg);
+    LibGit2.with(Pkg.GitTools.clone(url, path; header = "registry $reg from $(repr(url))", credentials = creds)) do repo end
+  end
+end

src/ImageInterpLast.jl

@@ -1,17 +1,14 @@
-__precompile__()
-
 module ImageInterpLast
 
-using CachedSeries, Images, AxisArrays
+using CachedArrays, Images, AxisArrays
+const axes = Base.axes
 
-import CachedSeries: update_cache!, cache, cache_idxs
+import CachedArrays: update_cache!, cache, AbstractCachedArray
 import Base: size, getindex, show
 
-export interplast, ImageInterpLast2, ImageInterpLast3
+export interp_last, ImgItpLast
 
 include("util.jl")
-include("interp_last2.jl")
-include("interp_last3.jl")
 include("interp_last.jl")
 
 end

src/interp_last.jl

@@ -1,14 +1,65 @@
-#user interface
+mutable struct ImgItpLast{TO,N,TI,NC,A<:AbstractArray{TI,N}} <: AbstractCachedArray{TO,N,TI,NC,A}
+    parent::A
+    coefs::Vector{Float64}
+    cached::Array{TO,NC}
+    current_I::Tuple
+end
+
+function ImgItpLast(img::Array34{T}, coefs, nd_cache=ndims(img)-1, out_type=Float64) where {T}
+    nd = ndims(img)
+    map(check01, coefs)
+    if size(img,3) !== length(coefs)
+        error("Input image size in the Z-slice dimension (3) should equal the number of interpolation coefficients provided")
+    end
+    if nd_cache > nd
+        error("nd_cache must be less than or equal to ndims(img)")
+    end
+    ncache_rngs = axes(img)[nd_cache+1:nd]
+    ci = map(first, ncache_rngs)
+    za = ImgItpLast{out_type,nd,T,nd_cache,typeof(img)}(img, coefs, zeros(out_type, size(img)[1:nd_cache]...), ci)
+    update_cache!(za, ci)
+    return za
+end
 
-interplast(A::AbstractArray, coef::Float64; kwargs...) = interplast(A, fill(coef, size(A,3)); kwargs...)
+ImgItpLast(img::Array34{T}, coef::Float64, nd_cache=ndims(img)-1, out_type=Float64) where {T} =
+    ImgItpLast(img, fill(coef, size(img, 3)), nd_cache, out_type)
+
+function update_cache!(A::ImgItpLast{TO,N,TI,2}, inds::NTuple{NQ, Int}) where {TO,N,TI,NQ}
+    #sometimes indexing works better than views with memory-mapped arrays
+    pslice = A.parent[:, :, inds...]
+    pslice_next = A.parent[:, :, Base.front(inds)...,last(inds)+1]
+    coef = A.coefs[first(inds)] #get coef for this slice
+    interp!(A.cached, pslice, pslice_next, coef)
+    A.current_I = inds
+end
+
+function update_cache!(A::ImgItpLast{TO,N,TI,3}, inds::NTuple{NQ,Int}) where {TO,N,TI,NQ}
+    #sometimes indexing works better than views with memory-mapped arrays
+    pslice = A.parent[:, :, :, inds...]
+    pslice_next = A.parent[:, :, :, Base.front(inds)...,last(inds)+1]
+    interp!(A.cached, pslice, pslice_next, A.coefs)
+    A.current_I = inds
+end
+
+size(A::ImgItpLast) = (Base.front(size(A.parent))...,last(size(A.parent))-1,)
+Base.axes(A::ImgItpLast) = (Base.front(axes(parent(A)))..., first(last(axes(parent(A)))):(last(last(axes(parent(A))))-1),)
+show(io::IO, A::ImgItpLast{TO}) where {TO} = print(io, "ImgItpLast of size $(size(A)) mapped to element type $TO\n")
+show(io::IO, ::MIME"text/plain", A::ImgItpLast{TO}) where {TO} = show(io, A)
+
+ImgItpLast(img::ImageMeta, coefs, out_type=Float64; kwargs...) = ImageMeta(ImgItpLast(data(img), coefs, out_type; kwargs...), properties(img))
+ImgItpLast(img::AxisArray, coefs, out_type=Float64; kwargs...) = match_axisspacing(ImgItpLast(data(img),coefs,out_type; kwargs...), img)
+
+
+#user interface
+interp_last(A::AbstractArray, coef::Float64; kwargs...) = interp_last(A, fill(coef, size(A,3)); kwargs...)
 
-function interplast(A::AbstractArray{T,N}, coefs::Vector{Float64}; cache3d=false, out_type=Float64) where {T,N}
+function interp_last(A::AbstractArray{T,N}, coefs::Vector{Float64}; cache3d=false, out_type=Float64) where {T,N}
     if !in(N, (3,4))
         warn("$N-dimensional input was provided.  Only 3D and 4D inputs are tested; this will probably fail")
     end
     if N ==3 && cache3d
         cache3d = false
         warn("The cache3d kwarg was set for a 3D input matrix. This is only useful for 4D timeseries; ignoring kwarg")
     end
-    return cache3d ? ImageInterpLast3(A, coefs, out_type) : ImageInterpLast2(A, coefs, out_type)
+    return cache3d ? ImgItpLast(A, coefs, 3, out_type) : ImgItpLast(A, coefs, 2, out_type)
 end

src/interp_last2.jl

@@ -1,13 +1,13 @@
 const Array34{T} = Union{AbstractArray{T,3}, AbstractArray{T,4}}
 
-function interp!(ca::AbstractArray{T,3}, img1::AbstractArray{T,3}, img2::AbstractArray{T,3}, coefs::Vector{Float64}) where {T}
+function interp!(ca::AbstractArray{TO,3}, img1::AbstractArray{T,3}, img2::AbstractArray{T,3}, coefs::Vector) where {TO,T}
     for i = 1:size(ca,3)
          interp!(view(ca,:,:,i), view(img1,:,:,i), view(img2,:,:,i), coefs[i])
     end
     return ca
 end
 
-function interp!(ca::AbstractArray{T,2}, img1::AbstractArray{T,2}, img2::AbstractArray{T,2}, coef::Float64) where {T}
+function interp!(ca::AbstractArray{TO,2}, img1::AbstractArray{T,2}, img2::AbstractArray{T,2}, coef) where {TO,T}
     for i in eachindex(ca)
         ca[i] = img1[i]*coef + img2[i]*(1.0-coef)
     end

src/interp_last3.jl

@@ -1,16 +1,18 @@
 using ImageInterpLast
 
-using Base.Test
+using Test
 
 a = zeros(10,10,10,10)
 for t = 1:10
-    a[:,:,:,t] = t
+    a[:,:,:,t] .= t
 end
 
-img2 = ImageInterpLast2(a, 0.5, Float64)
-img3 = ImageInterpLast3(a, 0.5, Float64) 
+img0 = interp_last(a, 0.5; cache3d=false, out_type=Float64)
+img1 = interp_last(a, 0.5; cache3d=false, out_type=Float32)
+img2 = ImgItpLast(a, 0.5, 2, Float64)
+img3 = ImgItpLast(a, 0.5, 3, Float64)
 
-for img in (img2,img3)
+for img in (img0,img1,img2,img3)
     @test all(img[:,:,:,1].==1.5)
     @test all(img[1:2,:,:,1].==1.5)
     @test all(img[1:2,:,2,1].==1.5)
@@ -20,10 +22,10 @@ for img in (img2,img3)
 end
 
 coefs = fill(0.25, 10)
-coefs[6:10] = 1.0
+coefs[6:10] .= 1.0
 
-img2 = ImageInterpLast2(a, coefs, Float64)
-img3 = ImageInterpLast3(a, coefs, Float64) 
+img2 = ImgItpLast(a, coefs, 2, Float64)
+img3 = ImgItpLast(a, coefs, 3, Float64)
 
 for img in (img2,img3)
     @test all(img[:,:,1:5,1].==1.75)
@@ -43,8 +45,8 @@ for img in (img2,img3)
     @test all(img[1:2,:,7,2].==2.0)
 end
 
-img4 = interplast(a, coefs; cache3d=false, out_type=Float64) 
-img5 = interplast(a, coefs; cache3d=true, out_type=Float64)
+img4 = interp_last(a, coefs; cache3d=false, out_type=Float64)
+img5 = interp_last(a, coefs; cache3d=true, out_type=Float64)
 
 @test all(img4[:,:,:,:].==img2[:,:,:,:])
 @test all(img5[:,:,:,:].==img3[:,:,:,:])