From fc587d44ebb595ac2edb98e970346fcc6ae037d7 Mon Sep 17 00:00:00 2001
From: Tim Holy <tim.holy@gmail.com>
Date: Thu, 6 Dec 2018 16:56:10 -0600
Subject: [PATCH 1/2] Add test to ensure pixelspacing gets saved

---
 test/REQUIRE     |  2 +-
 test/runtests.jl | 14 ++++++++++++++
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/test/REQUIRE b/test/REQUIRE
index 4007dfe..194d701 100644
--- a/test/REQUIRE
+++ b/test/REQUIRE
@@ -1,2 +1,2 @@
 SimpleTraits
-ImageMetadata
+ImageMetadata 0.5.2
diff --git a/test/runtests.jl b/test/runtests.jl
index ad7b3d2..22fcf10 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -144,6 +144,20 @@ include("unu-make.jl")
         save(outname, img)
         imgc = load(outname)
         @test img == imgc
+
+        # With units
+        img = AxisArray(rand(N0f16, 5, 7), (:y, :x), (1.0u"mm", 1.2u"mm"))
+        outname = joinpath(writedir, "imagemeta.nhdr")
+        save(outname, img)
+        imgc = load(outname)
+        @test img == imgc
+        @test pixelspacing(imgc) == (1.0u"mm", 1.2u"mm")
+        img = ImageMeta(img, info=false)
+        save(outname, img)
+        imgc = load(outname)
+        @test img == imgc
+        @test AxisArrays.HasAxes(img) isa AxisArrays.HasAxes{true}
+        @test pixelspacing(imgc) == (1.0u"mm", 1.2u"mm")
     end
 
     GC.gc()  # to close any mmapped files

From f3ad657638e05322b50e25dec364418aaec24f41 Mon Sep 17 00:00:00 2001
From: Tim Holy <tim.holy@gmail.com>
Date: Fri, 7 Dec 2018 07:41:06 -0600
Subject: [PATCH 2/2] Be more selective about writing orientation information

ITK applies more exclusivity among fields, for compatibility we should
try to impose the same exclusions.
---
 src/NRRD.jl      | 20 ++++++++++++--------
 test/runtests.jl |  3 +--
 2 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/src/NRRD.jl b/src/NRRD.jl
index 014380d..ccd350a 100644
--- a/src/NRRD.jl
+++ b/src/NRRD.jl
@@ -271,16 +271,16 @@ function load(io::Stream{format"NRRD"}, Tuser::Type=Any; mode="r", mmap=:auto)
     isa(axs, Dims) ? A : AxisArray(A, axs)
 end
 
-function save(f::File{format"NRRD"}, img::AbstractArray; props::Dict = Dict{String,Any}(), keyvals=nothing, comments=nothing)
+function save(f::File{format"NRRD"}, img::AbstractArray; kwargs...)
     open(f, "w") do io
         write(io, magic(format"NRRD"))
-        save(io, img; props=props, keyvals=keyvals, comments=comments)
+        save(io, img; kwargs...)
     end
 end
 
-function save(io::Stream{format"NRRD"}, img::AbstractArray{T}; props::Dict = Dict{String,Any}(), keyvals=nothing, comments=nothing) where T
+function save(io::Stream{format"NRRD"}, img::AbstractArray{T}; props::Dict = Dict{String,Any}(), keyvals=nothing, comments=nothing, kwargs...) where T
     axs = axisinfo(img)
-    header = headerinfo(T, axs)
+    header = headerinfo(T, axs; kwargs...)
     header_eltype!(header, T)
     # copy fields from props to override those in header
     for (k, v) in props
@@ -378,6 +378,7 @@ function headerinfo(T, axs)
     if isa(axs, Base.Indices)
         axs = map(length, axs)
     end
+    specifyorientation = false
     if isa(axs, Dims)
         header["sizes"] = [axs...]
     else
@@ -387,8 +388,7 @@ function headerinfo(T, axs)
         isspace = map(s->!startswith(string(s), "time"), axnames)
         if haskey(axes2space, axnames)
             header["space"] = axes2space[axnames]
-        else
-            header["space dimension"] = sum(isspace)
+            specifyorientation = true
         end
         header["kinds"] = [isspc ? "domain" : "time" for isspc in isspace]
         if !all(isdefaultname, axnames)
@@ -402,10 +402,14 @@ function headerinfo(T, axs)
             header["units"] = [unitstr...]
         end
         if !all(x->x==1, spacing)
-            header["spacings"] = [spacing...]
+            if specifyorientation
+                header["space directions"] = [ntuple(d->d==i ? spacing[i] : 0, length(spacing)) for i = 1:length(spacing)]
+            else
+                header["spacings"] = [Float64.(spacing)...]
+            end
         end
         origin = map(x->isa(x, Quantity) ? ustrip(x) : x, map(first, rng))
-        if any(x->x!=0, origin)
+        if specifyorientation && any(x->x!=0, origin)
             header["space origin"] = [origin[[isspace...]]...]
         end
     end
diff --git a/test/runtests.jl b/test/runtests.jl
index 22fcf10..65dec67 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -146,8 +146,7 @@ include("unu-make.jl")
         @test img == imgc
 
         # With units
-        img = AxisArray(rand(N0f16, 5, 7), (:y, :x), (1.0u"mm", 1.2u"mm"))
-        outname = joinpath(writedir, "imagemeta.nhdr")
+        img = AxisArray(img, (:y, :x), (1.0u"mm", 1.2u"mm"))
         save(outname, img)
         imgc = load(outname)
         @test img == imgc