[WIP] Add support for writing to mmapped TIFFs

Project.toml

@@ -7,6 +7,7 @@ version = "0.2.2"
 ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+FileWatching = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 FixedPointNumbers = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 IndirectArrays = "9b13fd28-a010-5f03-acff-a1bbcff69959"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"

src/TiffImages.jl

@@ -7,6 +7,7 @@ end
 using ColorTypes
 using DocStringExtensions
 using FileIO
+using FileWatching
 using FixedPointNumbers
 using IndirectArrays
 using OffsetArrays
@@ -29,6 +30,8 @@ include(joinpath("types", "dense.jl"))
 include(joinpath("types", "mmap.jl"))
 include("load.jl")
 
+export convert!
+
 @deprecate TiffFile(::Type{O}) where O<:Unsigned TiffFile{O}()
 
 end # module

src/types/mmap.jl

@@ -6,12 +6,12 @@ images too large to store in memory.
 
 $(FIELDS)
 """
-mutable struct DiskTaggedImage{T <: Colorant, O <: Unsigned, AA <: AbstractArray} <: AbstractDenseTIFF{T, 3}
+mutable struct DiskTaggedImage{T <: Colorant, O <: Unsigned, S <: Stream, AA <: AbstractArray} <: AbstractDenseTIFF{T, 3}
 
     """
     Pointer to keep track of the backing file
     """
-    file::TiffFile{O}
+    file::TiffFile{O, S}
     """
     The associated tags for each slice in this array
     """
@@ -29,22 +29,53 @@ mutable struct DiskTaggedImage{T <: Colorant, O <: Unsigned, AA <: AbstractArray
     """
     cache_index::Int
 
+    microcache::Vector{T}
+
     """
     A flag tracking whether this file is editable
     """
     readonly::Bool
+end
 
-    function DiskTaggedImage(file::TiffFile{O}, ifds::Vector{IFD{O}}) where {O}
-        ifd = ifds[1]
-        dims = (nrows(ifd), ncols(ifd), length(ifds))
-        cache = getcache(ifd)
-        new{eltype(cache), O, typeof(cache)}(file, ifds, dims, cache, -1, false)
-    end
+function DiskTaggedImage(file::TiffFile{O, S}, ifds::Vector{IFD{O}}) where {O, S}
+    ifd = ifds[1]
+    dims = (nrows(ifd), ncols(ifd), length(ifds))
+    cache = getcache(ifd)
+    microcache = Vector{eltype(cache)}(undef, 1)
+    img = DiskTaggedImage{eltype(cache), O, S, typeof(cache)}(file, ifds, dims, cache, -1, microcache, true)
+    @async watch(img)
+    img
 end
 
 Base.size(A::DiskTaggedImage) = A.dims
 
-function Base.getindex(A::DiskTaggedImage{T, O, AA}, i1::Int, i2::Int, i::Int) where {T, O, AA}
+function convert!(A::DiskTaggedImage; writeable=false) 
+    if writeable
+        A.readonly = false
+        try
+            close(A.file.io)
+        catch
+        end
+        path = A.file.filepath
+        A.file.io = Stream(format"TIFF", open(path, append=true, read=true), path)
+    end
+    return nothing
+end
+
+function watch(A::DiskTaggedImage)
+    @info "Watching $(A.file.filepath) for changes"
+    while true
+        ev = watch_file(A.file.filepath)
+        if ev.renamed
+            error("Watched file $(A.file.filepath) has been moved.")
+        elseif ev.changed
+            A.cache_index = -1 #invalidate cache
+            convert!(A; writeable=!A.readonly)
+        end
+    end
+end
+
+function Base.getindex(A::DiskTaggedImage, i1::Int, i2::Int, i::Int)
     # check the loaded cache is already the correct slice
     if A.cache_index == i
         return A.cache[i2, i1]
@@ -65,8 +96,32 @@ function Base.getindex(A::DiskTaggedImage{T, O, AA}, i1::Int, i2::Int, i::Int) w
     return A.cache[i2, i1]
 end
 
-function Base.setindex!(A::DiskTaggedImage, I...)
-    error("This array is on disk and is read only. Convert to a mutable in-memory version by running "*
-          "`copy(arr)`. \n\n𝗡𝗼𝘁𝗲: For large files this can be quite expensive. A future PR will add "*
-          "support for reading and writing to/from disk.")
+function Base.setindex!(A::DiskTaggedImage{T, O, S, AA}, value, i1::Int, i2::Int, i3::Int) where {T, O, S, AA}
+    if A.readonly
+        error("This is a read only memory-mapped file. Make sure to run convert!(img, writeable=true) first.")
+    end
+
+    linear = LinearIndices((1:size(A, 2), 1:size(A, 1)))
+    linidx = O(linear[i2, i1] * sizeof(T))::O
+
+    ifd = A.ifds[i3]
+
+    bytecounts = ifd[STRIPBYTECOUNTS].data::Vector{O}
+
+    stripidx = 1
+    counts = O(0)
+    for i in 1:length(bytecounts)
+        stripidx = i
+        counts = bytecounts[stripidx]::O
+        (linidx < counts) && break
+        linidx -= counts
+    end
+
+    A.cache_index = -1
+
+    offsets = ifd[STRIPOFFSETS].data::Vector{O}
+    offset = offsets[stripidx]::O
+    seek(A.file, Int(offset+linidx))
+    A.microcache[1] = value
+    write(A.file.io, A.microcache)
 end