Merge pull request #36 from timholy/teh/inference

Improve inferrabililty

src/TiffImages.jl

@@ -25,4 +25,6 @@ include(joinpath("types", "dense.jl"))
 include(joinpath("types", "mmap.jl"))
 include("load.jl")
 
+@deprecate TiffFile(::Type{O}) where O<:Unsigned TiffFile{O}()
+
 end # module

src/files.jl

@@ -5,12 +5,12 @@ Wrap `io` with helper parameters to keep track of file attributes.
 
 $(FIELDS)
 """
-mutable struct TiffFile{O <: Unsigned}
+mutable struct TiffFile{O <: Unsigned, S <: Stream}
     """The relative path to this file"""
     filepath::String
 
     """The file stream"""
-    io::Stream
+    io::S
 
     """Location of the first IFD in the file stream"""
     first_offset::Int
@@ -19,18 +19,18 @@ mutable struct TiffFile{O <: Unsigned}
     need_bswap::Bool
 end
 
-function TiffFile(offset_size::Type{O}) where O <: Unsigned
-    TiffFile{offset_size}("", Stream(format"TIFF", IOBuffer()), -1, false)
-end
+TiffFile{O}(s::Stream) where O <: Unsigned = TiffFile{O, typeof(s)}("", s, -1, false)
+TiffFile{O}(io::IO) where O <: Unsigned    = TiffFile{O}(Stream(format"TIFF", io))
+TiffFile{O}() where O <: Unsigned          = TiffFile{O}(IOBuffer())
 
 function Base.read(io::Stream, ::Type{TiffFile})
     seekstart(io)
-    filepath = extract_filename(io)
+    filepath = String(extract_filename(io))::String
     bs = need_bswap(io)
     offset_size = offsetsize(io)
     first_offset_raw = read(io, offset_size)
     first_offset = Int(bs ? bswap(first_offset_raw) : first_offset_raw)
-    TiffFile{offset_size}(filepath, io, first_offset, bs)
+    TiffFile{offset_size, typeof(io)}(filepath, io, first_offset, bs)
 end
 
 Base.read(io::IOStream, t::Type{TiffFile}) = read(Stream(format"TIFF", io, extract_filename(io)), t)
@@ -103,8 +103,8 @@ function Base.read!(file::TiffFile, arr::BitArray)
     arr
 end
 
-Base.write(file::TiffFile, t) = write(file.io.io, t)
-Base.write(file::TiffFile, arr::AbstractVector{Any}) = write(file.io.io, Array{UInt8}(arr))
+Base.write(file::TiffFile, t) = write(file.io.io, t)::Int
+Base.write(file::TiffFile, arr::AbstractVector{Any}) = write(file.io.io, Array{UInt8}(arr))::Int
 
 Base.seek(file::TiffFile, n::Integer) = seek(file.io, n)
 

src/ifds.jl

@@ -24,8 +24,8 @@ IFD(o::Type{O}) where {O <: Unsigned} = IFD{O}(OrderedDict{UInt16, Tag}())
 
 Base.length(ifd::IFD) = length(ifd.tags)
 Base.keys(ifd::IFD) = keys(ifd.tags)
-Base.iterate(ifd::IFD) = iterate(ifd.tags)
-Base.iterate(ifd::IFD, n::Integer) = iterate(ifd.tags, n)
+Base.iterate(ifd::IFD) = iterate(ifd.tags)::Union{Nothing,Tuple{Pair{UInt16,<:Tag},Int}}
+Base.iterate(ifd::IFD, n::Int) = iterate(ifd.tags, n)::Union{Nothing,Tuple{Pair{UInt16,<:Tag},Int}}
 Base.getindex(ifd::IFD, key::TiffTag) = getindex(ifd, UInt16(key))
 Base.getindex(ifd::IFD{O}, key::UInt16) where {O} = getindex(ifd.tags, key)
 Base.in(key::TiffTag, v::IFD) = in(UInt16(key), v)
@@ -110,22 +110,22 @@ struct IFDLayout
 end
 
 function output(ifd::IFD)
-    nrows = Int(ifd[IMAGELENGTH].data)
-    ncols = Int(ifd[IMAGEWIDTH].data)
+    nrows = Int(ifd[IMAGELENGTH].data)::Int
+    ncols = Int(ifd[IMAGEWIDTH].data)::Int
 
-    samplesperpixel = Int(ifd[SAMPLESPERPIXEL].data)
+    samplesperpixel = Int(ifd[SAMPLESPERPIXEL].data)::Int
     sampleformats = fill(UInt16(0x01), samplesperpixel)
     if SAMPLEFORMAT in ifd
-        sampleformats = ifd[SAMPLEFORMAT].data
+        sampleformats = ifd[SAMPLEFORMAT].data  # can a type be specified for this?
     end
 
-    interpretation = Int(ifd[PHOTOMETRIC].data)
+    interpretation = Int(ifd[PHOTOMETRIC].data)::Int
 
     strip_nbytes = ifd[STRIPBYTECOUNTS].data
-    nbytes = Int(sum(strip_nbytes))
-    bitsperpixel = ifd[BITSPERSAMPLE].data
-    rawtypes = Set{DataType}()
-    mappedtypes = Set{DataType}()
+    nbytes = Int(sum(strip_nbytes))::Int
+    bitsperpixel = ifd[BITSPERSAMPLE].data::Union{Int,UInt16,Vector{UInt16}}
+    rawtypes = Base.IdSet{Any}()
+    mappedtypes = Base.IdSet{Any}()
     for i in 1:samplesperpixel
         rawtype = rawtype_mapping[(SampleFormats(sampleformats[i]), bitsperpixel[i])]
         push!(rawtypes, rawtype)
@@ -138,7 +138,7 @@ function output(ifd::IFD)
         end
     end
     (length(rawtypes) > 1) && error("Variable per-pixel storage types are not yet supported")
-    rawtype = first(rawtypes)
+    rawtype = first(rawtypes)::DataType
     readtype = rawtype
 
     compression = COMPRESSION_NONE
@@ -158,7 +158,7 @@ function output(ifd::IFD)
         nbytes,
         readtype,
         rawtype,
-        first(mappedtypes),
+        first(mappedtypes)::DataType,
         compression,
         PhotometricInterpretations(interpretation))
 end
@@ -175,7 +175,7 @@ function Base.read!(target::AbstractArray{T, N}, tf::TiffFile, ifd::IFD) where {
     if layout.compression != COMPRESSION_NONE
         # strip_nbytes is the number of bytes pre-inflation so we need to
         # calculate the expected size once decompressed and update the values
-        strip_nbytes = fill(rowsperstrip*layout.ncols, length(strip_nbytes))
+        strip_nbytes = fill(rowsperstrip*layout.ncols, length(strip_nbytes)::Int)
         strip_nbytes[end] = (layout.nrows - (rowsperstrip * (nstrips-1))) * layout.ncols
     end
 
@@ -189,13 +189,13 @@ function Base.read!(target::AbstractArray{T, N}, tf::TiffFile, ifd::IFD) where {
     if nstrips > 1
         startbyte = 1
         for i in 1:nstrips
-            seek(tf, strip_offsets[i])
-            nbytes = Int(strip_nbytes[i] / sizeof(T))
+            seek(tf, strip_offsets[i]::Core.BuiltinInts)
+            nbytes = Int(strip_nbytes[i]::Core.BuiltinInts / sizeof(T))
             read!(tf, view(target, startbyte:(startbyte+nbytes-1)), layout.compression)
             startbyte += nbytes
         end
     else
-        seek(tf, strip_offsets[1])
+        seek(tf, strip_offsets[1]::Core.BuiltinInts)
         read!(tf, target, layout.compression)
     end
 end
@@ -222,14 +222,24 @@ function Base.write(tf::TiffFile{O}, ifd::IFD{O}) where {O <: Unsigned}
     write(tf, O(0))
 
     for (tag, poses) in remotedata
+        tag = tag::Tag
         data_pos = position(tf.io)
+        data = tag.data
         # add NUL terminator to the end of Strings that don't have it already
-        data = (eltype(tag) == String && !endswith(tag.data, '\0')) ? tag.data * "\0" : tag.data
-        write(tf, data)
+        if eltype(tag) === String
+            data = data::SubString{String}
+            if !endswith(data, '\0')
+                data *= "\0"
+            end
+            write(tf, data)  # compile-time dispatch
+        else
+            write(tf, data)  # run-time dispatch
+        end
         push!(poses, data_pos)
     end
 
     for (tag, poses) in remotedata
+        tag = tag::Tag
         orig_pos, data_pos = poses
         seek(tf, orig_pos)
         write(tf, tag, data_pos)

src/layout.jl

@@ -1,6 +1,6 @@
-nrows(ifd::IFD) = Int(ifd[IMAGELENGTH].data)
-ncols(ifd::IFD) = Int(ifd[IMAGEWIDTH].data)
-nsamples(ifd::IFD) = Int(ifd[SAMPLESPERPIXEL].data)
+nrows(ifd::IFD) = Int(ifd[IMAGELENGTH].data)::Int
+ncols(ifd::IFD) = Int(ifd[IMAGEWIDTH].data)::Int
+nsamples(ifd::IFD) = Int(ifd[SAMPLESPERPIXEL].data)::Int
 
 """
     interpretation(ifd)
@@ -36,25 +36,25 @@ interpretation(::Val{PHOTOMETRIC_YCBCR}) = YCbCr
 interpretation(::Val{PHOTOMETRIC_CIELAB}) = Lab
 
 function interpretation(p::PhotometricInterpretations, extrasamples::ExtraSamples, samplesperpixel::Int)
-    interp = interpretation(p)
-    len = length(interp)
+    interp = interpretation(p)::Type{<:Colorant}
+    len = length(interp)::Int
     if len + 1 == samplesperpixel
         return interpretation(p, extrasamples, Val(samplesperpixel))
     elseif len == samplesperpixel
         return interp, false
     elseif len < samplesperpixel
         return interp, true
     else
-        error("TIFF file says it contains $interp values, but only has $samplesperpixel samples per pixel instead of the minimum required $(length(interp))")
+        error("TIFF file says it contains $interp values, but only has $samplesperpixel samples per pixel instead of the minimum required $len")
     end
 end
 _pad(::Type{RGB}) = RGBX
 _pad(::Type{T}) where {T} = T
 
 interpretation(p::PhotometricInterpretations, extrasamples::ExtraSamples, nsamples::Val) = interpretation(p, Val(extrasamples), nsamples)
-interpretation(p::PhotometricInterpretations, ::Val{EXTRASAMPLE_UNSPECIFIED}, ::Val) = interpretation(p), true
+interpretation(p::PhotometricInterpretations, ::Val{EXTRASAMPLE_UNSPECIFIED}, @nospecialize(::Val)) = interpretation(p), true
 interpretation(p::PhotometricInterpretations, ::Val{EXTRASAMPLE_UNSPECIFIED}, ::Val{4}) = _pad(interpretation(p)), false
-interpretation(p::PhotometricInterpretations, ::Val{EXTRASAMPLE_ASSOCALPHA}, ::Val) = coloralpha(interpretation(p)), false
+interpretation(p::PhotometricInterpretations, ::Val{EXTRASAMPLE_ASSOCALPHA}, @nospecialize(::Val)) = coloralpha(interpretation(p)), false
 interpretation(p::PhotometricInterpretations, ::Val{EXTRASAMPLE_UNASSALPHA}, nsamples::Val) = interpretation(p, Val(EXTRASAMPLE_ASSOCALPHA), nsamples)
 
 _mappedtype(::Type{T}) where {T} = T
@@ -76,10 +76,11 @@ end
 
 Allocate a cache for this IFD with correct type and size.
 """
-getcache(ifd::IFD) = getcache(ifd, Val(rawtype(ifd)))
-getcache(ifd::IFD, ::Val{Bool}) = BitArray(undef, ncols(ifd), nrows(ifd))
-function getcache(ifd::IFD, ::Val{T}) where {T}
+function getcache(ifd::IFD)
+    T = rawtype(ifd)
+    if T === Bool
+        return BitArray(undef, ncols(ifd), nrows(ifd))
+    end
     colortype, extras = interpretation(ifd)
-
-    Array{colortype{_mappedtype(T)}}(undef, ncols(ifd), nrows(ifd))
+    return Array{colortype{_mappedtype(T)}}(undef, ncols(ifd), nrows(ifd))
 end

src/load.jl

@@ -4,9 +4,8 @@ function load(filepath::String; verbose=true, mmap = false)
     end
 end
 
-function load(io::IOStream; verbose=true, mmap = false)
-    tf = read(io, TiffFile)
-
+load(io::IOStream; verbose=true, mmap = false) = load(read(io, TiffFile); verbose=verbose, mmap=mmap)
+function load(tf::TiffFile; verbose=true, mmap = false)
     isdense = true
     ifds = IFD{offset(tf)}[]
 
@@ -33,7 +32,11 @@ function load(io::IOStream; verbose=true, mmap = false)
     if mmap
         loaded = DiskTaggedImage(tf, ifds)
     else
-        loaded = load(tf, ifds, Val(nplanes); verbose=verbose)
+        if nplanes == 1
+            loaded = load(tf, ifds, nothing; verbose=verbose)
+        else
+            loaded = load(tf, ifds, nplanes; verbose=verbose)
+        end
     end
 
     if eltype(loaded) <: Palette
@@ -54,15 +57,15 @@ function load(io::IOStream; verbose=true, mmap = false)
     return DenseTaggedImage(data, ifds)
 end
 
-function load(tf::TiffFile, ifds, ::Val{1}; verbose = true)
+function load(tf::TiffFile, ifds::AbstractVector{<:IFD}, ::Nothing; verbose = true)
     ifd = ifds[1]
     cache = getcache(ifd)
     read!(cache, tf, ifd)
 
-    return Array(cache')
+    return Matrix(cache')
 end
 
-function load(tf::TiffFile, ifds, ::Val{N}; verbose = true) where {N}
+function load(tf::TiffFile, ifds::AbstractVector{<:IFD}, N; verbose = true)
     ifd = ifds[1]
 
     cache = getcache(ifd)

src/tags.jl

@@ -45,7 +45,8 @@ load(tf::TiffFile, t::Tag) = t
 function load(tf::TiffFile{O}, t::Tag{RemoteData{O}}) where {O <: Unsigned}
     T = t.data.datatype
     N = t.data.count
-    rawdata = Vector{UInt8}(undef, bytes(T)*N)
+    nb = bytes(T)::Int
+    rawdata = Vector{UInt8}(undef, nb*N)
 
     pos = position(tf.io)
     seek(tf, t.data.position)
@@ -54,7 +55,7 @@ function load(tf::TiffFile{O}, t::Tag{RemoteData{O}}) where {O <: Unsigned}
     # if this datatype is comprised of multiple bytes and this file needs to be
     # bitswapped then we'll need to reverse the byte order inside each datatype
     # unit
-    if tf.need_bswap && bytes(T) >= 2
+    if tf.need_bswap && nb >= 2
         reverse!(rawdata)
         data = Array{T}(reverse(reinterpret(T, rawdata)))
     elseif T == String
@@ -70,7 +71,7 @@ function load(tf::TiffFile{O}, t::Tag{RemoteData{O}}) where {O <: Unsigned}
     end
     seek(tf, pos)
 
-    Tag(t.tag, data)
+    Tag(t.tag, data)::Tag
 end
 
 bytes(x::Type) = sizeof(x)
@@ -91,19 +92,19 @@ function Base.read(tf::TiffFile{O}, ::Type{Tag}) where O <: Unsigned
         T = tiff_to_julian[datatype]
     end
 
-    nbytes = bytes(T) * count
+    nbytes = bytes(T)::Int * count
     if nbytes <= sizeof(O)
         if tf.need_bswap
             reverse!(view(data, 1:nbytes))
         end
-        if T == String
+        if T === String
             return Tag(tag, String(data))
-        elseif T == Any
-            return Tag(tag, Array{Any}(data))
+        elseif T === Any
+            return Tag(tag, Vector{Any}(data))
         elseif count == 1
-            return Tag(tag, first(reinterpret(T, data)))
+            return Tag(tag, first(reinterpret(T, data)))::Tag
         else
-            return Tag(tag, Array(reinterpret(T, data)[1:Int(count)]))
+            return Tag(tag, reinterpret(T, data)[1:Int(count)])
         end
     else
         (tf.need_bswap) && reverse!(data)
@@ -145,13 +146,19 @@ function Base.write(tf::TiffFile{O}, t::Tag{T}) where {O <: Unsigned, T}
         return false
     end
 
+    data = t.data
     # add NUL terminator to the end of Strings that don't have it already
-    data = (T == String && !endswith(t.data, '\0')) ? t.data * "\0" : t.data
+    if T === String
+        data = data::SubString{String}
+        if !endswith(data, '\0')
+            data *= "\0"
+        end
+    end
 
     write(tf, t.tag)
     write(tf, julian_to_tiff[eltype(t)])
     write(tf, O(length(t)))
-    nbytes = write(tf.io, data)
+    nbytes = write(tf.io, data)::Int
 
     # write padding
     if nbytes < sizeof(O)

src/types/dense.jl

@@ -83,8 +83,7 @@ Base.write(io::IOStream, img::DenseTaggedImage) = write(Stream(format"TIFF", io,
 
 function Base.write(io::Stream, img::DenseTaggedImage)
     O = offset(img)
-    tf = TiffFile(O)
-    tf.io = io
+    tf = TiffFile{O}(io)
 
     prev_ifd_record = write(tf) # record that will have be updated
 
@@ -104,7 +103,7 @@ function Base.write(io::Stream, img::DenseTaggedImage)
         ifd[COMPRESSION] = COMPRESSION_NONE
         ifd[STRIPOFFSETS] = O(data_pos)
         ifd[STRIPBYTECOUNTS] = O(ifd_pos-data_pos)
-        ifd[SOFTWARE] = "$(parentmodule(IFD)).jl v$PKGVERSION"
+        ifd[SOFTWARE] = "$(parentmodule(IFD)::Module).jl v$PKGVERSION"
         sort!(ifd.tags)
 
         seek(tf.io, ifd_pos)

src/utils.jl

@@ -29,10 +29,11 @@ const fdpattern = r"<fd (.*)>"
 Extract the name of the file backing a stream
 """
 function extract_filename(io::IOStream)
-    filename = match(filepattern, io.name)
+    name = String(io.name)
+    filename = match(filepattern, name)
     if filename !== nothing
-        return filename[1]
-    elseif match(fdpattern, io.name) !== nothing
+        return String(filename[1])
+    elseif match(fdpattern, name) !== nothing
         return ""
     else
         error("Can't extract filename from the given stream")
@@ -156,7 +157,7 @@ const julian_to_tiff = Dict(
 )
 
 # sampleformat, bitspersample => Julian type
-const rawtype_mapping = Dict(
+const rawtype_mapping = Dict{Tuple{TiffImages.SampleFormats, UInt16}, DataType}(
     (SAMPLEFORMAT_UINT, 1) => Bool,
     (SAMPLEFORMAT_UINT, 8) => UInt8,
     (SAMPLEFORMAT_UINT, 16) => UInt16,