Merge pull request #18 from tlnagy/tn/update-for-1.0

Update for Julia 1.0 and EzXML 0.8

Author: tlnagy

.travis.yml

@@ -4,8 +4,7 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
-  - 0.7
+  - 1.0 
   - nightly
 notifications:
   email: false
@@ -31,4 +30,4 @@ matrix:
 #  - julia -e 'Pkg.clone(pwd()); Pkg.build("OMETIFF"); Pkg.test("OMETIFF"; coverage=true)'
 after_success:
   # push coverage results to Codecov
-  - julia -e 'cd(Pkg.dir("OMETIFF")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+  - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())' 

REQUIRE

@@ -1,5 +1,5 @@
-julia 0.6
-EzXML 0.4.2
+julia 0.7
+EzXML 0.8
 Unitful
 FixedPointNumbers
 FileIO

src/files.jl

@@ -53,15 +53,21 @@ function loadxml(file::TiffFile)
     rawxml = ""
 
     for i in 1:number_of_entries
-        tag_bytes = Unsigned[]
-        append!(tag_bytes, read(file.io, UInt16, 2))
-        append!(tag_bytes, read(file.io, UInt32, 2))
-        tag_id, tag_type, data_count, data_offset = Int.(do_bswap(file, tag_bytes))
+        combined = Unsigned[]
+        tag_info = Array{UInt16}(undef, 2)
+        data_info = Array{UInt32}(undef, 2)
+        read!(file.io, tag_info)
+        read!(file.io, data_info)
+        append!(combined, tag_info)
+        append!(combined, data_info)
+        tag_id, tag_type, data_count, data_offset = Int.(do_bswap(file, combined))
 
         if tag_id == 270 # Image Description tag
             seek(file.io, data_offset)
             # strip null values from string
-            raw_str = replace(String(read(file.io, UInt8, data_count)), "\0", "")
+            _data = Array{UInt8}(undef, data_count)
+            read!(file.io, _data)
+            raw_str = replace(String(_data), "\0"=>"")
             # check if is xml since ImageJ display settings are also stored in
             # ImageDescription tags
             # TODO: This should be replaced with some proper validation
@@ -87,7 +93,8 @@ function load_master_xml(file::TiffFile)
     omexml = loadxml(file)
     try
         # Check if the full OME-XML metadata is stored in another file
-        metadata_file = findfirst(omexml, "/ns:OME/ns:BinaryOnly", ["ns"=>namespace(omexml)])
+        metadata_file = findfirst("/ns:OME/ns:BinaryOnly", omexml, ["ns"=>namespace(omexml)])
+        (metadata_file == nothing) && return omexml
         uuid, filepath = metadata_file["UUID"], joinpath(dirname(file.filepath), metadata_file["MetadataFile"])
 
         # we have a companion metadata file
@@ -108,12 +115,12 @@ end
 
 
 """
-    Base.next(file::TiffFile)
+    next(file::TiffFile)
 
 Loads the next IFD in `file` and returns a list of the strip offsets to load the
 data stored in this IFD.
 """
-function Base.next(file::TiffFile)
+function next(file::TiffFile)
     next_ifd, strip_offset_list = _next(file, file.offsets[end])
     (next_ifd > 0) && push!(file.offsets, next_ifd)
     strip_offset_list
@@ -131,11 +138,15 @@ function _next(file::TiffFile, offset::Int)
     height = 0
 
     for i in 1:number_of_entries
-        tag_bytes = Unsigned[]
-        append!(tag_bytes, read(file.io, UInt16, 2))
-        append!(tag_bytes, read(file.io, UInt32, 2))
-        tag_id, tag_type, data_count, data_offset = Int.(do_bswap(file, tag_bytes))
-
+        combined = Unsigned[]
+        tag_info = Array{UInt16}(undef, 2)
+        data_info = Array{UInt32}(undef, 2)
+        read!(file.io, tag_info)
+        read!(file.io, data_info)
+        append!(combined, tag_info)
+        append!(combined, data_info)
+        tag_id, tag_type, data_count, data_offset = Int.(do_bswap(file, combined))
+        
         curr_pos = position(file.io)
         if tag_id == 256
             width = data_offset
@@ -152,7 +163,9 @@ function _next(file::TiffFile, offset::Int)
             # if the data is spread across multiple strips
             if strip_num > 1
                 seek(file.io, strip_offset)
-                strip_offsets = do_bswap(file, read(file.io, UInt32, strip_num))
+                strip_info = Array{UInt32}(undef, strip_num)
+                read!(file.io, strip_info)
+                strip_offsets = do_bswap(file, strip_info)
                 strip_offset_list = Int.(strip_offsets)
             else
                 strip_offset_list = [strip_offset]
@@ -177,7 +190,9 @@ function load_comments(file)
     seek(file.io, comment_offset)
     comment_header = read(file.io, UInt32)
     comment_length = Int(do_bswap(file, read(file.io, UInt32)))
-    metadata = JSON.parse(String(read(file.io, UInt8, comment_length)))
+    metadata_bytes = Array{UInt8}(undef, comment_length)
+    read!(file.io, metadata_bytes)
+    metadata = JSON.parse(String(metadata_bytes))
     if !haskey(metadata, "Summary")
         return ""
     end

src/loader.jl

@@ -5,7 +5,7 @@ function load(f::File{format"OMETIFF"})
 end
 
 function load(io::Stream{format"OMETIFF"})
-    if io.filename != nothing && !contains(io.filename, ".ome.tif")
+    if io.filename != nothing && !occursin(".ome.tif", io.filename)
         throw(FileIO.LoaderError("OMETIFF", "Not an OME TIFF file!"))
     end
 
@@ -16,48 +16,48 @@ function load(io::Stream{format"OMETIFF"})
     omexml = load_master_xml(orig_file)
 
     # find all images in this dataset
-    images = find(omexml, "/ns:OME/ns:Image",["ns"=>namespace(omexml)])
-    results = Array{AxisArray}(length(images))
+    images = findall("/ns:OME/ns:Image", omexml, ["ns"=>namespace(omexml)])
+    results = Array{AxisArray}(undef, length(images))
 
-    pos_names = nodecontent.(find(omexml, "/ns:OME/ns:Image/ns:StageLabel[@Name]/@Name",["ns"=>namespace(omexml)]))
+    pos_names = nodecontent.(findall("/ns:OME/ns:Image/ns:StageLabel[@Name]/@Name", omexml, ["ns"=>namespace(omexml)]))
     # if all position names aren't unique then substitute names
     if length(pos_names) == 0 || !allunique(pos_names)
         pos_names = ["Pos$i" for i in 1:length(images)]
     end
 
     pixels = []
-    master_rawtype = Nullable{DataType}()
+    master_rawtype = nothing
     mappedtype = Int64
     master_dims = []
-    axes_dims = Nullable{Vector{AxisArrays.Axis}}()
+    axes_dims = nothing
     for (idx, image) in enumerate(images)
-        pixel = findfirst(image, "./ns:Pixels", ["ns"=>namespace(omexml)])
+        pixel = findfirst("./ns:Pixels", image, ["ns"=>namespace(omexml)])
         dims, axes_info = build_axes(pixel)
         rawtype, mappedtype = type_mapping[pixel["Type"]]
 
-        if isnull(master_rawtype)
-            master_rawtype = Nullable(rawtype)
-        elseif get(master_rawtype) != rawtype
+        if master_rawtype == nothing
+            master_rawtype = rawtype
+        elseif master_rawtype != rawtype
             throw(FileIO.LoaderError("OMETIFF", "Multiple different storage types not supported in a multi position image"))
         end
 
-        if isnull(axes_dims)
-            axes_dims = Nullable(axes_info)
+        if axes_dims == nothing
+            axes_dims = axes_info
             master_dims = dims
-        elseif get(axes_dims) != axes_info
+        elseif axes_dims != axes_info
             throw(FileIO.LoaderError("OMETIFF", "Axes changing between multiple imaging positions is not supported yet"))
         end
         push!(pixels, pixel)
     end
-    push!(get(axes_dims), Axis{:position}(Symbol.(pos_names)))
+    push!(axes_dims, Axis{:position}(Symbol.(pos_names)))
     push!(master_dims, length(pos_names))
 
-    data = Array{get(master_rawtype), length(master_dims)}(master_dims...)
+    data = Array{master_rawtype, length(master_dims)}(undef, master_dims...)
 
     for (pos_idx, pixel) in enumerate(pixels)
         files = Dict{String, TiffFile}()
 
-        tiffdatas = find(pixel, "./ns:TiffData", ["ns"=>namespace(omexml)])
+        tiffdatas = findall("./ns:TiffData", pixel, ["ns"=>namespace(omexml)])
 
         # TODO: Only the IFDs with a corresponding slice should be loaded.
         slices = DefaultDict{String, Dict{Int, ImageSlice}}(Dict{Int, ImageSlice}())
@@ -79,7 +79,7 @@ function load(io::Stream{format"OMETIFF"})
                 read_dims = n_strips > 1 ? (strip_len) : (width, height)
 
                 # TODO: This shouldn't be allocated for each ifd
-                tmp = Array{get(master_rawtype)}(read_dims...)
+                tmp = Array{master_rawtype}(undef, read_dims...)
                 for j in 1:n_strips
                     seek(file.io, strip_offsets[j])
                     read!(file.io, tmp)
@@ -96,8 +96,8 @@ function load(io::Stream{format"OMETIFF"})
         # drop unnecessary axes
         # TODO: Reduce the number of allocations here
     end
-    squeezed_data = squeeze(Gray.(reinterpret(mappedtype, data)), (find(master_dims .== 1)...))
-    ImageMeta(AxisArray(squeezed_data, get(axes_dims)[master_dims .> 1]...), Summary=summary)
+    squeezed_data = dropdims(Gray.(reinterpret(mappedtype, data)); dims=tuple(findall(master_dims .== 1)...))
+    ImageMeta(AxisArray(squeezed_data, axes_dims[master_dims .> 1]...), Summary=summary)
 end
 
 """Corresponding Julian types for OME-XML types"""

src/parsing.jl

@@ -40,7 +40,7 @@ function read_tiffdata(tiffdata::EzXML.Node, files::Dict{String, TiffFile}, orig
     c = parse(Int, tiffdata["FirstC"])+1
     p = parse(Int, tiffdata["PlaneCount"])
 
-    uuid_node = findfirst(tiffdata, "./ns:UUID", ["ns"=>namespace(tiffdata)])
+    uuid_node = findfirst("./ns:UUID", tiffdata, ["ns"=>namespace(tiffdata)])
     uuid = nodecontent(uuid_node)
     filepath = joinpath(dirname(orig_file.filepath), uuid_node["FileName"])
 
@@ -70,7 +70,7 @@ function build_axes(image::EzXML.Node)
     dims = map(x->parse(Int, image[x]), dim_names)
 
     # extract channel names
-    channel_names = nodecontent.(find(image, "ns:Channel/@Name", ["ns"=>namespace(image)]))
+    channel_names = nodecontent.(findall("ns:Channel/@Name", image, ["ns"=>namespace(image)]))
     if isempty(channel_names)
         channel_names = ["C$x" for x in 1:dims[4]]
     end
@@ -83,6 +83,7 @@ function build_axes(image::EzXML.Node)
         unittype = getfield(Unitful, Symbol(image["TimeIncrementUnit"]))
 
         time_axis = Axis{:time}(Unitful.upreferred.((0:increment:increment*(dims[5]-1))*unittype))
+    catch
     end
 
     axes = [

src/utils.jl

@@ -4,9 +4,9 @@
 Cleans up `input` string and converts it into a symbol
 """
 function to_symbol(input::String)
-    fixed = replace(input, r"[^\w\ \-\_]", "")
-    fixed = replace(fixed, r"[\ \-\_]+", "_")
-    Symbol(replace(fixed, r"^[\d]", s"_\g<0>"))
+    fixed = replace(input, r"[^\w\ \-\_]"=>"")
+    fixed = replace(fixed, r"[\ \-\_]+"=>"_")
+    Symbol(replace(fixed, r"^[\d]"=>s"_\g<0>"))
 end
 
 
@@ -37,7 +37,8 @@ function check_bswap(io::Union{Stream, IOStream})
     # check if we need to swap byte order
     need_bswap = endianness != myendian()
 
-    tiff_version = read(io, UInt8, 2)
+    tiff_version = Array{UInt8}(undef, 2)
+    read!(io, tiff_version)
     (tiff_version != [0x2a, 0x00] && tiff_version != [0x00, 0x2a]) && error("Big-TIFF files aren't supported yet")
 
     return need_bswap

test/runtests.jl

@@ -1,7 +1,7 @@
 using OMETIFF
 using FileIO
 using AxisArrays
-using Base.Test
+using Test
 
 @testset "Single file OME-TIFFs" begin
     @testset "Single Channel OME-TIFF" begin