Merge pull request #31 from timholy/teh/stimuli

Allow stimulus-related metadata

src/ImagineFormat.jl

@@ -82,10 +82,10 @@ function load(io::Stream{format"Imagine"}; mode="r")
 end
 
 abstract type Endian end
-mutable struct LittleEndian <: Endian; end
-mutable struct BigEndian <: Endian; end
-const endian_dict = Dict("l"=>LittleEndian, "b"=>BigEndian)
-const nrrd_endian_dict = Dict(LittleEndian=>"little",BigEndian=>"big")
+struct LittleEndian <: Endian; end
+struct BigEndian <: Endian; end
+const endian_dict = Dict("l"=>LittleEndian(), "b"=>BigEndian())
+const nrrd_endian_dict = Dict(LittleEndian()=>"little",BigEndian()=>"big")
 parse_endian(s::AbstractString) = endian_dict[lowercase(s)]
 
 function parse_vector_int(s::AbstractString)
@@ -222,7 +222,12 @@ const field_key_dict = Dict{AbstractString,Function}(
     "angle from horizontal (deg)"  => float64_or_empty,
     "x translation in pixels"      => x->parse(Int,x) != 0,
     "y translation in pixels"      => x->parse(Int,x) != 0,
-    "rotation angle in degree"     => x->parse(Float64,x) != 0)
+    "rotation angle in degree"     => x->parse(Float64,x) != 0,
+    "stimulus scan hi"             => parse_vector_int,
+    "stimulus scan lo"             => parse_vector_int,
+    "stimulus frame hi"            => parse_vector_int,
+    "stimulus frame lo"            => parse_vector_int,
+    "stimulus sequence"            => identity)
 
 
 function parse_header(s::IOStream)
@@ -256,7 +261,7 @@ function parse_header(s::IOStream)
                 end
                 headerdict[k] = thisdict
             else
-                func = field_key_dict[k]
+                func = get(field_key_dict, k, identity)
                 try
                     headerdict[k] = func(v)
                 catch err
@@ -318,34 +323,56 @@ function imagine2nrrd(nrrdname::AbstractString, h::Dict{String, Any}, datafilena
 end
 
 """
-`save_header(filename, header)` writes a header dictionary in Imagine format.
+    save_header(filename, header; section=())
 
-`save_header(destname, srcname, img::AbstractArray, [T::Type =
-eltype(img)])` writes a `.imagine` file with name `destname`, using
-the `.imagine` file `srcname` as a template. Size and element type
-fields are updated from `img` and `T`, respectively.
+Write a `header` dictionary in Imagine format.
+`section` can be one of `general`, `misc`, `ai`, or `camera`, to write additional entries
+in the specified section. For example,
+
+    header["stimulus info"] = "here is some info"
+    Imagine.save_header(filename, header; misc=("stimulus info",))
+
+would allow one to insert "stimulus info" into the "[misc params]" section of the `.imagine`
+file.
 """
-function save_header(filename::AbstractString, h::Dict{String, Any})
+function save_header(filename::AbstractString, h::Dict{String};
+                     general=(),
+                     misc=(),
+                     ai=(),
+                     camera=())
     open(filename, "w") do io
         write(io, magic(format"Imagine"))
         println(io, "\n[general]")
-        writekv(io, h, ("header version", "app version", "date and time", "byte order", "rig"))
+        writekv(io, h, ("header version", "app version", "date and time", "byte order", "rig", general...))
         println(io, "\n[misc params]")
-        writekv(io, h, ("stimulus file content", "comment", "ai data file","image data file", "piezo"))
+        writekv(io, h, ("stimulus file content", "comment", "ai data file","image data file", "piezo", misc...))
         println(io, "\n[ai]")
-        writekv(io, h, ("nscans", "channel list", "label list", "scan rate", "min sample", "max sample", "min input", "max input"))
+        writekv(io, h, ("nscans", "channel list", "label list", "scan rate", "min sample", "max sample", "min input", "max input", ai...))
         println(io, "\n[camera]")
-        writekv(io, h, ("original image depth", "saved image depth", "image width", "image height", "number of frames requested", "nStacks", "idle time between stacks", "pre amp gain", "gain", "exposure time", "vertical shift speed", "vertical clock vol amp", "readout rate", "pixel order", "frame index offset", "frames per stack", "pixel data type", "camera", "um per pixel", "binning", "angle from horizontal (deg)", "bidirectional"))
+        writekv(io, h, ("original image depth", "saved image depth", "image width",
+                        "image height", "number of frames requested", "nStacks",
+                        "idle time between stacks", "pre amp gain", "gain", "exposure time",
+                        "vertical shift speed", "vertical clock vol amp", "readout rate",
+                        "pixel order", "frame index offset", "frames per stack",
+                        "pixel data type", "camera", "um per pixel", "binning",
+                        "angle from horizontal (deg)", "bidirectional", camera...))
     end
     nothing
 end
 
-function save_header(dest::AbstractString, src::AbstractString, img::AbstractArray, T::Type = eltype(img))
+"""
+    save_header(destname, srcname, img::AbstractArray, [T::Type = eltype(img)])
+
+Write an `.imagine` file with name `destname`, using
+the `.imagine` file `srcname` as a template. Size and element type
+fields are updated from `img` and `T`, respectively.
+"""
+function save_header(dest::AbstractString, src::AbstractString, img::AbstractArray, T::Type = eltype(img); kwargs...)
     h = parse_header(src)
     fillsize!(h, img)
     h["pixel data type"] = lowercase(string(T))
     h["byte order"] = ENDIAN_BOM == 0x04030201 ? "l" : "b"
-    save_header(dest, h)
+    save_header(dest, h; kwargs...)
 end
 
 function fillsize!(h, img::AxisArray)
@@ -398,21 +425,22 @@ function writefield(io, fn, dct::Dict)
     end
 end
 
+writefield(io, fn, ::LittleEndian) = println(io, "byte order=l")
+writefield(io, fn, ::BigEndian)    = println(io, "byte order=b")
+
 writeum(io,x) = print(io, x/μm, " um")
 writeus(io,x::Unitful.Time) = print(io, x/μs, " us")
 writeus(io,x) = nothing
 writeMHz(io,x::Unitful.Frequency) = print(io, x/MHz, " MHz")
 writeMHz(io,x) = nothing
+
 const write_dict = Dict{String,Function}(
     "bidirectional"                => (io,x)->x ? print(io, 1) : print(io, 0),
+    "bidirection"                  => (io,x)->x ? print(io, 1) : print(io, 0),
     "start position"               => writeum,
     "stop position"                => writeum,
     "vertical shift speed"         => (io,x)->(writeus(io,x); print(io,'\n')),
     "readout rate"                 => (io,x)->(writeMHz(io,x); print(io,'\n')),
 )
 
-function __init__()
-    Base.rehash!(nrrd_endian_dict)
-end
-
 end

test/runtests.jl

@@ -40,10 +40,12 @@ MHz = u"MHz"
 
 h = ImagineFormat.parse_header("test_noshift.imagine")
 h["byte order"] = ENDIAN_BOM == 0x04030201 ? "l" : "b"
-ImagineFormat.save_header(ifn, h)
+h["stimulus scan hi"] = [3, 5]
+ImagineFormat.save_header(ifn, h; misc=("stimulus scan hi",))
 h2 = ImagineFormat.parse_header(ifn)
 @test isnan(h["readout rate"]) && isnan(h2["readout rate"])
 @test isnan(h["vertical shift speed"]) && isnan(h2["vertical shift speed"])
+@test h2["stimulus scan hi"] == [3, 5]
 rm(ifn)
 img2 = 0
 GC.gc(); GC.gc(); GC.gc()
@@ -83,6 +85,7 @@ img = load("no_z.imagine")
 @test pixelspacing(img) == (-1μm, -1μm)
 
 # Fix deprecations in loading imagine-cam file incompatibility
+@info "Two warnings are expected"
 img = load("test_nocam.imagine")
 @test isempty(img)