Merge pull request #31 from JuliaIO/teh/helix

Switch to Project.toml and fixes for multichannel images

.travis.yml

@@ -2,9 +2,10 @@ language: julia
 os:
   - linux
   - osx
+  - windows
 julia:
-  - 0.7
   - 1.0
+  - 1
   - nightly
 notifications:
   email: false

Project.toml

@@ -0,0 +1,40 @@
+name = "NRRD"
+uuid = "9bb6cfbd-7763-5393-b1b5-1c8e09872146"
+authors = ["Tim Holy <tim.holy@gmail.com>"]
+version = "0.6.0"
+
+[deps]
+AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
+ColorVectorSpace = "c3611d14-8923-5661-9e6a-0046d554d3a4"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+ImageAxes = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac"
+ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
+Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7"
+MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900"
+Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Quaternions = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
+[compat]
+AxisArrays = "0.3, 0.4"
+ColorVectorSpace = "0.7, 0.8"
+FileIO = "1"
+ImageAxes = "0.6"
+ImageCore = "0.8.1"
+Libz = "1"
+MappedArrays = "0.2"
+Quaternions = "0.4"
+StaticArrays = "0.11, 0.12"
+Unitful = "0.14, 0.15, 0.16, 0.17, 0.18"
+julia = "1"
+
+[extras]
+ImageMetadata = "bc367c6b-8a6b-528e-b4bd-a4b897500b49"
+SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Statistics", "Test", "SimpleTraits", "ImageMetadata"]

README.md

@@ -1,8 +1,7 @@
 # NRRD
-[![NRRD](http://pkg.julialang.org/badges/NRRD_0.4.svg)](http://pkg.julialang.org/?pkg=NRRD)
-[![NRRD](http://pkg.julialang.org/badges/NRRD_0.5.svg)](http://pkg.julialang.org/?pkg=NRRD)
 [![Build Status](https://travis-ci.org/JuliaIO/NRRD.jl.svg?branch=master)](https://travis-ci.org/JuliaIO/NRRD.jl)
 [![codecov.io](http://codecov.io/github/JuliaIO/NRRD.jl/coverage.svg?branch=master)](http://codecov.io/github/JuliaIO/NRRD.jl?branch=master)
+[![PkgEval][pkgeval-img]][pkgeval-url]
 
 Package for reading NRRD files.
 Implements the  [FileIO](https://github.com/JuliaIO/FileIO.jl) interface.
@@ -25,7 +24,7 @@ just the header. Assuming you want to save "rich" axis information, a
 low-level approach using AxisArrays is the following:
 
 ```julia
-using NRRD, FileIO, FixedPointNumbers, AxisArrays, Unitful
+using NRRD, FileIO, ImageCore, AxisArrays, Unitful
 using Unitful: μm, s
 
 # For a 480x640x200 image with time as the third axis,
@@ -42,3 +41,6 @@ open("mydata.nhdr", "w") do io
     NRRD.write_header(io, "0004", header)
 end
 ```
+
+[pkgeval-img]: https://juliaci.github.io/NanosoldierReports/pkgeval_badges/N/NRRD.svg
+[pkgeval-url]: https://juliaci.github.io/NanosoldierReports/pkgeval_badges/report.html

src/NRRD.jl

@@ -2,17 +2,15 @@ module NRRD
 
 using Mmap, Printf
 # Packages needed to return the possible range of element types
-using FixedPointNumbers, Colors, ColorVectorSpace, StaticArrays, Quaternions
+using ImageCore, ColorVectorSpace, StaticArrays, Quaternions
 # Other packages
 using AxisArrays, ImageAxes, Unitful, MappedArrays
 using FileIO
 import Libz
-import FixedPointNumbers
 
-using Colors: AbstractGray
 using AxisArrays: HasAxes
 
-string2type = Dict(
+const string2type = Dict(
     "signed char" => Int8,
     "int8" => Int8,
     "int8_t" => Int8,
@@ -66,7 +64,7 @@ type2string(::Type{T}) where {T} = type2string(eltype(T), T)
 type2string(::Type{T}, ::Type{T}) where {T} = error("type $T unrecognized")
 type2string(::Type{T1}, ::Type{T2}) where {T1,T2} = type2string(T1)
 
-space2axes = Dict(
+const space2axes = Dict(
     "right-anterior-superior" => (3,(:R,:A,:S)),
     "ras" => (3,(:R,:A,:S)),
     "left-anterior-superior" => (3,(:L,:A,:S)),
@@ -104,9 +102,9 @@ const axes2space = Dict(
 # We put these in a dict so that we don't eval untrusted
 # strings. Please submit PRs to add to this list if you need
 # additional unit support.
-unit_string_dict = Dict("" => 1, "m" => u"m", "mm" => u"mm", "s" => u"s",
-                        "um" => u"μm", "μm" => u"μm", "microns" => u"μm",
-                        "pixel" => 1)
+const unit_string_dict = Dict("" => 1, "m" => u"m", "mm" => u"mm", "s" => u"s",
+                              "um" => u"μm", "μm" => u"μm", "microns" => u"μm",
+                              "pixel" => 1)
 
 struct QString end                 # string with quotes around it: "mm"
 VTuple{T} = Tuple{Vararg{T}}  # space-delimited tuple: 80 150
@@ -620,7 +618,7 @@ struct UnknownColor{T,N} <: Color{T,N}
 end
 
 """
-    outer_eltype!(header, Traw) -> T, nd, perm
+    T, nd, perm = outer_eltype!(header, Traw)
 
 Extract the julia array `eltype` `T`, the number of dimensions `nd`
 **excluding** color/complex/vector/matrix element data, and any
@@ -1055,6 +1053,7 @@ nrrd_format(io, ::Type{StringPTuple{T}}, s::AbstractString) where {T} = nrrd_for
 nrrd_format(io, ::Type{StringPTuple{T}}, container) where {T} = nrrd_format(io, PTuple{T}, container)
 
 alloctype(::Type{T}) where {T} = T
+alloctype(::Type{PTuple{T}}) where {T} = Any
 alloctype(::Type{StringPTuple{T}}) where {T} = Any # Union{String,Vector{T}}
 alloctype(::Type{IntFloat}) = Union{Int,Float64}
 

test/make_ufixed.jl

@@ -1,4 +1,4 @@
-using FileIO, NRRD, FixedPointNumbers, Colors
+using FileIO, NRRD, ImageCore
 
 Alast = nothing
 for (A, name) in ((rand(UInt8, 3, 5), "uint8"),

test/readremote.jl

@@ -1,4 +1,4 @@
-using FileIO, FixedPointNumbers, Colors, ImageCore, Test, Statistics
+using FileIO, ImageCore, Test, Statistics
 
 workdir = joinpath(tempdir(), "ImagesNRRD")
 isdir(workdir) || mkdir(workdir)

test/runtests.jl

@@ -1,4 +1,4 @@
-using FileIO, FixedPointNumbers, ColorTypes, Unitful, AxisArrays, ImageAxes, ImageMetadata
+using FileIO, ImageCore, Unitful, AxisArrays, ImageAxes, ImageMetadata
 using Test, Base.CoreLogging
 
 include("unu-make.jl")
@@ -180,6 +180,11 @@ include("unu-make.jl")
         end
     end
 
+    @testset "Extended eltype" begin
+        img = load(joinpath(dirname(@__FILE__), "io", "test_helix.nrrd"))
+        @test axisnames(img)[end-2:end] == (:R, :A, :S)
+    end
+
     GC.gc()  # to close any mmapped files
     try
         rm(workdir, recursive=true)

test/unu-make.jl

@@ -1,5 +1,5 @@
 # Test headers written by `unu make`
-using NRRD, FileIO, Colors, AxisArrays, ImageAxes, Unitful, SimpleTraits
+using NRRD, FileIO, ImageCore, AxisArrays, ImageAxes, Unitful, SimpleTraits
 using Test
 
 headerpath = joinpath(dirname(@__FILE__), "headers")