From 4f685045442ce3ce2029d1044ba17ad272f77c5f Mon Sep 17 00:00:00 2001
From: Tamas Nagy <tamas@tamasnagy.com>
Date: Sat, 21 Jan 2023 16:50:28 -0800
Subject: [PATCH] handle multiple positions breaking unevenly across files
 (#105)

fix #104
---
 Project.toml                          |    2 +-
 src/parsing.jl                        |   15 +
 src/utils.jl                          |   44 +
 test/testdata/issues/issue104.ome.xml | 8707 +++++++++++++++++++++++++
 test/tiffdatas.jl                     |   12 +
 5 files changed, 8779 insertions(+), 1 deletion(-)
 create mode 100644 test/testdata/issues/issue104.ome.xml

diff --git a/Project.toml b/Project.toml
index 0a1d413..5ce8c23 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "OMETIFF"
 uuid = "2d0ec36b-e807-5756-994b-45af29551fcf"
 authors = ["Tamas Nagy <tamas@tamasnagy.com>"]
-version = "0.4.3"
+version = "0.4.4"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
diff --git a/src/parsing.jl b/src/parsing.jl
index 07e4cbd..9699404 100644
--- a/src/parsing.jl
+++ b/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)
diff --git a/src/utils.jl b/src/utils.jl
index f28aff5..8a6dcbc 100644
--- a/src/utils.jl
+++ b/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
\ No newline at end of file
diff --git a/test/testdata/issues/issue104.ome.xml b/test/testdata/issues/issue104.ome.xml
new file mode 100644
index 0000000..d2d1745
--- /dev/null
+++ b/test/testdata/issues/issue104.ome.xml
@@ -0,0 +1,8707 @@
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+  <Instrument ID="Instrument:0">
+    <Detector ID="Detector:0"/>
+  </Instrument>
+  <Image ID="Image:0" Name="dish2_ctrl_v_bix_1_MMStack">
+    <Description>
+ Taken using runnable:
+    UV exposed at frame #120 for 30s on COM4/DAC09 at power=1.0
+    At only position 0</Description>
+    <InstrumentRef ID="Instrument:0"/>
+    <StageLabel Name="Lane1_Ctrl" X="488.81" XUnit="µm" Y="-3714.66" YUnit="µm"/>
+    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="0.653" PhysicalSizeXUnit="µm" PhysicalSizeY="0.653" PhysicalSizeYUnit="µm" SizeC="3" SizeT="361" SizeX="1024" SizeY="1024" SizeZ="1" TimeIncrement="7500.0" TimeIncrementUnit="ms" Type="uint16">
+      <Channel ID="Channel:0:0" Name="EPI_mNG" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:1" Name="EPI_BFP" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:2" Name="EPI_RFP" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="6" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="1" FirstZ="0" IFD="7" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="1" FirstZ="0" IFD="8" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="12" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="2" FirstZ="0" IFD="13" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="2" FirstZ="0" IFD="14" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="18" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="3" FirstZ="0" IFD="19" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="3" FirstZ="0" IFD="20" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="24" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="4" FirstZ="0" IFD="25" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="4" FirstZ="0" IFD="26" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="30" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="5" FirstZ="0" IFD="31" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="5" FirstZ="0" IFD="32" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="36" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="6" FirstZ="0" IFD="37" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="6" FirstZ="0" IFD="38" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="7" FirstZ="0" IFD="42" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="7" FirstZ="0" IFD="43" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="7" FirstZ="0" IFD="44" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="8" FirstZ="0" IFD="48" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="8" FirstZ="0" IFD="49" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="8" FirstZ="0" IFD="50" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="9" FirstZ="0" IFD="54" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="9" FirstZ="0" IFD="55" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="9" FirstZ="0" IFD="56" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="10" FirstZ="0" IFD="60" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="10" FirstZ="0" IFD="61" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="10" FirstZ="0" IFD="62" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="11" FirstZ="0" IFD="66" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="11" FirstZ="0" IFD="67" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="11" FirstZ="0" IFD="68" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="12" FirstZ="0" IFD="72" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="12" FirstZ="0" IFD="73" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="12" FirstZ="0" IFD="74" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="13" FirstZ="0" IFD="78" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="13" FirstZ="0" IFD="79" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="13" FirstZ="0" IFD="80" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="14" FirstZ="0" IFD="84" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="14" FirstZ="0" IFD="85" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="14" FirstZ="0" IFD="86" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="15" FirstZ="0" IFD="90" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="15" FirstZ="0" IFD="91" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="15" FirstZ="0" IFD="92" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="16" FirstZ="0" IFD="96" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="16" FirstZ="0" IFD="97" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="16" FirstZ="0" IFD="98" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="17" FirstZ="0" IFD="102" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="17" FirstZ="0" IFD="103" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="17" FirstZ="0" IFD="104" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="18" FirstZ="0" IFD="108" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="1" FirstT="18" FirstZ="0" IFD="109" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="2" FirstT="18" FirstZ="0" IFD="110" PlaneCount="1">
+        <UUID FileName="dish2_ctrl_v_bix_1_MMStack.ome.tif">urn:uuid:7ca94c93-4599-4b79-a63b-814a6f24db67</UUID>
+      </TiffData>
+      <TiffData FirstC="0" FirstT="19" FirstZ="0" IFD="114" PlaneCount="1">
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+ Taken using runnable:
+    UV exposed at frame #120 for 30s on COM4/DAC09 at power=1.0
+    At only position 0</Description>
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+      <Plane DeltaT="2683634.0" DeltaTUnit="ms" ExposureTime="45.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="0" TheT="357" TheZ="0"/>
+      <Plane DeltaT="2684651.0" DeltaTUnit="ms" ExposureTime="250.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="1" TheT="357" TheZ="0"/>
+      <Plane DeltaT="2685689.0" DeltaTUnit="ms" ExposureTime="100.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="2" TheT="357" TheZ="0"/>
+      <Plane DeltaT="2691118.0" DeltaTUnit="ms" ExposureTime="45.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="0" TheT="358" TheZ="0"/>
+      <Plane DeltaT="2692135.0" DeltaTUnit="ms" ExposureTime="250.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="1" TheT="358" TheZ="0"/>
+      <Plane DeltaT="2693172.0" DeltaTUnit="ms" ExposureTime="100.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="2" TheT="358" TheZ="0"/>
+      <Plane DeltaT="2698633.0" DeltaTUnit="ms" ExposureTime="45.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="0" TheT="359" TheZ="0"/>
+      <Plane DeltaT="2699650.0" DeltaTUnit="ms" ExposureTime="250.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="1" TheT="359" TheZ="0"/>
+      <Plane DeltaT="2700672.0" DeltaTUnit="ms" ExposureTime="100.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="2" TheT="359" TheZ="0"/>
+      <Plane DeltaT="2706164.0" DeltaTUnit="ms" ExposureTime="45.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="0" TheT="360" TheZ="0"/>
+      <Plane DeltaT="2707213.0" DeltaTUnit="ms" ExposureTime="250.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="1" TheT="360" TheZ="0"/>
+      <Plane DeltaT="2708234.0" DeltaTUnit="ms" ExposureTime="100.0" ExposureTimeUnit="ms" PositionX="-835.97" PositionXUnit="µm" PositionY="-428.96000000000004" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm" TheC="2" TheT="360" TheZ="0"/>
+    </Pixels>
+  </Image>
+</OME>
\ No newline at end of file
diff --git a/test/tiffdatas.jl b/test/tiffdatas.jl
index 700c6e4..26f8598 100644
--- a/test/tiffdatas.jl
+++ b/test/tiffdatas.jl
@@ -251,3 +251,15 @@ end
     # this is the first IFD in the second file
     @test ifd_index[2010] == (1, 3, 190, 3)
 end
+
+@testset "Issue 104" begin
+    filepath = joinpath("testdata", "issues", "issue104.ome.xml")
+    ifd_index, ifd_files, dimlist = get_ifds(root(readxml(filepath)))
+
+    # if this clobbering happens, then the last IFDs in the first file get
+    # overwritten by the first IFDs in the second file so this index will be
+    # missing: 
+    @test ifd_index[2026] == (1, 1, 338, 2)
+    # if any clobbering happens then we won't have enough IFDs
+    @test length(ifd_index) == 2166 
+end
\ No newline at end of file