handle multiple positions breaking unevenly across files (#105)

fix #104

Author: tlnagy

Project.toml

@@ -1,7 +1,7 @@
 name = "OMETIFF"
 uuid = "2d0ec36b-e807-5756-994b-45af29551fcf"
 authors = ["Tamas Nagy <[email protected]>"]
-version = "0.4.3"
+version = "0.4.4"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"

src/parsing.jl

@@ -56,6 +56,7 @@ function ifdindex!(ifd_index::OrderedDict{Int, NTuple{4, Int}},
     #
     # TODO: This assumes a dense numbering of the indices, is this always true?
     prev_ifd = length(ifd_index) > 0 ? maximum(keys(ifd_index)) : 0
+    prev_filepath = ""
     for tiffdata in tiffdatas
         try # if this tiffdata specifies the corresponding IFD
             ifd = parse(Int, tiffdata["IFD"]) + 1
@@ -73,8 +74,22 @@ function ifdindex!(ifd_index::OrderedDict{Int, NTuple{4, Int}},
             # if this file isn't one we've observed before, increment the offset
             if !in(filepath, keys(obs_filepaths))
                 obs_filepaths[filepath] = prev_ifd
+            # if this isn't the first file and we're switching files and we've
+            # found an even bigger prev_ifd in the earlier file then
+            # bump the offset, see https://github.com/tlnagy/OMETIFF.jl/issues/104
+            elseif prev_filepath != "" && prev_filepath != filepath && obs_filepaths[filepath] < prev_ifd
+                old_offset = obs_filepaths[filepath]
+                δ = prev_ifd - old_offset
+                # update the offset associated with this file to this new larger value
+                obs_filepaths[filepath] = prev_ifd
+
+                # shift all the previously detected IFDs by δ 
+                shift!(ifd_files, δ, prev_ifd+1)
+                shift!(ifd_index, δ, prev_ifd+1)
             end
 
+            prev_filepath = filepath
+
             ifd += obs_filepaths[filepath]
 
             ifd_files[ifd] = (make_uuid(uuid), filepath)

src/utils.jl

@@ -10,3 +10,47 @@ function to_symbol(input::String)
     Symbol(replace(fixed, r"^[\d]"=>s"_\g<0>"))
 end
 
+"""
+    shift!(d, δ, o)
+
+Given an `OrderedDict` d, shifts all keys greater than or equal to `o` by `δ`.
+Preserves original order.
+
+```jldoctest
+julia> d = OrderedDict(vcat(6 => 'F', 1:5 .=> 'A':'E'))
+OrderedDict{Int64, Char} with 6 entries:
+  6 => 'F'
+  1 => 'A'
+  2 => 'B'
+  3 => 'C'
+  4 => 'D'
+  5 => 'E'
+
+julia> shift!(d, 1, 3)
+
+julia> d
+OrderedDict{Int64, Char} with 6 entries:
+  7 => 'F'
+  1 => 'A'
+  2 => 'B'
+  4 => 'C'
+  5 => 'D'
+  6 => 'E'
+```
+"""
+function shift!(d::OrderedDict{Int, S}, δ::Int, o::Int) where S
+    ks = Int[]
+    vs = S[]
+    shift = Bool[]
+
+    for k in keys(d)
+        push!(ks, k)
+        push!(vs, pop!(d, k))
+        push!(shift, k >= o) # if shifting is needed for this item
+    end
+
+    for (k,v,s) in zip(ks, vs, shift)
+        # if shift needed, update key
+        d[s ? k + δ : k] = v
+    end
+end