Improve handling of IFD counts across Image elements (#94)

* Fix multi-image BoundsError

* improve tracking of IFD counts

This improves handling of IFDs where the embedded IFDs are reset
between Images in the OMEXML so we don't accidentally overwrite
the index

* Add test for improved tracking of IFD count

Co-authored-by: Tamas Nagy <[email protected]>

Project.toml

@@ -1,7 +1,7 @@
 name = "OMETIFF"
 uuid = "2d0ec36b-e807-5756-994b-45af29551fcf"
 authors = ["Tamas Nagy <[email protected]>"]
-version = "0.4.0"
+version = "0.4.1"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"

src/parsing.jl

@@ -51,9 +51,11 @@ function ifdindex!(ifd_index::OrderedDict{Int, NTuple{4, Int}},
     tiffdatas = findall(".//ns:TiffData", image, ["ns"=>namespace(image)])
 
     ifd = 1
-    # this is an offset value since multiple ifds can share the same index if
-    # they are split across files, IFD1 (File1), IFD1 (File2), etc
-    prev_ifd = 0
+    # to avoid overwriting previous IFD indices from other images, we make sure
+    # to start counting from the maximum previously observed IFD index. 
+    #
+    # TODO: This assumes a dense numbering of the indices, is this always true?
+    prev_ifd = length(ifd_index) > 0 ? maximum(keys(ifd_index)) : 0
     for tiffdata in tiffdatas
         try # if this tiffdata specifies the corresponding IFD
             ifd = parse(Int, tiffdata["IFD"]) + 1

test/runtests.jl

@@ -141,6 +141,30 @@ end
             @test size(img) == (24, 18, 5)
         end
     end
+    @testset "Multi file T stack with multiple OME image nodes" begin
+        # 3 images, each embedded in one OME image node, each with XYCT = (512, 512, 2, 4)
+        # load master file that contains the full OME-XML
+        @testset "Load master file" begin
+            open(abspath(joinpath(testdata_dir, "multiples/multi_image_node/TSeries-camp-005_Cycle00001_Ch1_000001.ome.tif"))) do f
+                s = getstream(format"OMETIFF", f)
+                img = OMETIFF.load(s)
+                @test size(img) == (128, 128, 2, 4, 3)
+                # check channel indexing
+                @test size(img[Axis{:channel}(:Ch1)]) == (128, 128, 4, 3)
+                # check time indexing
+                @test size(img[Axis{:time}(1)]) == (128, 128, 2, 3)
+                # check image indexing
+                @test size(img[Axis{:position}(:Pos1)]) == (128, 128,  2, 4)
+            end
+        end
+        @testset "Load secondary file" begin
+            open(abspath(joinpath(testdata_dir, "multiples/multi_image_node/TSeries-camp-005_Cycle00002_Ch1_000001.ome.tif"))) do f
+                s = getstream(format"OMETIFF", f)
+                img = OMETIFF.load(s)
+                @test size(img) == (128, 128, 2, 4, 3)
+            end
+        end
+    end
 end
 # let's make sure that the values we return are identical to normal TIFF readers
 @testset "TIFF value verifications" begin