1+ """
2+ ReadonlyTiffDiskArray(mappedtype, rawtype, ifds, dims) -> ReadonlyTiffDiskArray
3+
4+ A lazy representation of a OMETIFF file. This custom type is needed since TIFF
5+ files are laid out noncontiguously and nonregularly. It uses an internal index
6+ to determine the mapping from indices to the locations of data slices on disk.
7+ These slices are generally XY slices and are usually loaded in all at once so it
8+ is quickly loaded into an internal cache to speed up the process. Externally,
9+ this type should behave very similarly to an in-memory array, albeit with a
10+ higher cost of accessing an element.
11+
12+ $(FIELDS)
13+ """
14+ mutable struct ReadonlyTiffDiskArray{T <: Gray , R, N1, N2} <: AbstractArray{T, N2}
15+ """
16+ A map of dimensions (sans XY) to the corresponding [`IFD`](@ref)
17+ """
18+ ifds:: OrderedDict{NTuple{N1, Int}, IFD}
19+
20+ """
21+ The full set of dimensions of the TIFF file, including XY
22+ """
23+ dims:: NTuple{N2, Int}
24+
25+ """
26+ An internal cache to fill when reading from disk
27+ """
28+ cache:: Array{R, 2}
29+
30+ """
31+ The dimension indices corresponding to the slice currently in the cache
32+ """
33+ cache_index:: NTuple{N1, Int}
34+
35+ function ReadonlyTiffDiskArray (:: Type{T} , :: Type{R} , ifds:: OrderedDict{NTuple{N1, Int}, IFD} , dims:: NTuple{N2, Int} ) where {T, R, N1, N2}
36+ if N2 - 2 != N1
37+ error (" $N2 dimensions given, but the IFDs are indexed on $N1 dimensions instead of " *
38+ " expected $(N2- 2 ) ."
39+ end
40+ new {T, R, N1, N2} (ifds, dims, Array {R} (undef, dims[1 ], dims[2 ]), (- 1 , - 1 , - 1 , - 1 ))
41+ end
42+ end
43+
44+ Base. size (A:: ReadonlyTiffDiskArray ) = A. dims
45+
46+ function Base. getindex (A:: ReadonlyTiffDiskArray{Gray{T}, R, N1, N2} , i1:: Int , i2:: Int , i:: Vararg{Int, N1} ) where {T, R, N1, N2}
47+ # check the loaded cache is already the correct slice
48+ if A. cache_index == i
49+ return Gray (reinterpret (T, A. cache[i2, i1]))
50+ end
51+
52+ ifd = A. ifds[i]
53+
54+ # if the file isn't open, lets open a handle and update it
55+ if ! isopen (ifd. file. io)
56+ path = ifd. file. filepath
57+ ifd. file. io = Stream (format "" open (path), path)
58+ end
59+
60+ n_strips = length (ifd. strip_offsets)
61+ strip_len = floor (Int, (size (A. cache, 1 ) * size (A. cache, 2 )) / n_strips)
62+
63+ # if the data is striped then we need to change the buffer shape so that we
64+ # can read into it. This should be replaced with a view of cache in Julia
65+ # >1.4, see https://github.com/JuliaLang/julia/pull/33046
66+ if n_strips > 1 && size (tmp) != (strip_len, )
67+ tmp = Array {R} (undef, strip_len)
68+ else
69+ tmp = A. cache
70+ end
71+
72+ _read_ifd_data! (ifd, A. cache, tmp)
73+
74+ A. cache_index = i
75+
76+ return Gray (reinterpret (T, A. cache[i2, i1]))
77+ end
78+
79+ function Base. setindex! (A:: ReadonlyTiffDiskArray{Gray{T}, R, N1, N2} , X, I... ) where {T, R, N1, N2}
80+ error (" This array is on disk and is read only. Convert to a mutable in-memory version by running " *
81+ " `copy(arr)`. \n\n 𝗡𝗼𝘁𝗲: For large files this can be quite expensive. A future PR will add " *
82+ " support for reading and writing to/from disk."
83+ end
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