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tlnagy / TiffImages.jl

💎 Pure-Julia TIFF I/O with a focus on correctness 🧐
http://tamasnagy.com/TiffImages.jl/
MIT License
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TiffImages fails to open a `bfconvert` converted OME-TIFF #151

Open adityanprasad opened 6 months ago

adityanprasad commented 6 months ago

I used the bftools command-line tool bfconvert to convert a Zeiss CZI mosaic into an OME-TIFF. I'm having trouble reading into Julia using either OMETIFF.jl or TiffImages.jl. The error message is attached below (same error for OMETIFF and TiffImages.jl). I am using Julia 1.10.1 on MacOS. The image I used is available here: https://drive.google.com/file/d/1PD7BthTuj-UgJhltqyp64oqmv2MwF1Es/view?usp=sharing. pyometiff seems to be able to read the image.

Thanks for all your work on these packages!

In [3]: img = TiffImages.load("/Users/adityaprasad/Downloads/output1.ome.tiff")
ERROR: BoundsError: attempt to access 0-element Vector{TiffImages.Tag} at index [1]
Stacktrace:
  [1] getindex
    @ ./essentials.jl:13 [inlined]
  [2] first
    @ ./abstractarray.jl:452 [inlined]
  [3] getindex
    @ ~/.julia/packages/TiffImages/yETMK/src/ifds.jl:69 [inlined]
  [4] getindex
    @ ~/.julia/packages/TiffImages/yETMK/src/ifds.jl:68 [inlined]
  [5] read!(target::Matrix{TiffImages.Palette{…}}, tf::TiffFile{UInt32, FileIO.Stream{…}}, ifd::TiffImages.IFD{UInt32})
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/ifds.jl:207
  [6] macro expansion
    @ ~/.julia/packages/TiffImages/yETMK/src/load.jl:85 [inlined]
  [7] macro expansion
    @ ~/.julia/packages/ProgressMeter/vnCY0/src/ProgressMeter.jl:957 [inlined]
  [8] load(tf::TiffFile{UInt32, FileIO.Stream{…}}, ifds::Vector{TiffImages.IFD{…}}, N::Int64; verbose::Bool)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:84
  [9] load
    @ ~/.julia/packages/TiffImages/yETMK/src/load.jl:77 [inlined]
 [10] load(tf::TiffFile{UInt32, FileIO.Stream{…}}; verbose::Bool, mmap::Bool, lazyio::Bool)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:38
 [11] load(tf::TiffFile{UInt32, FileIO.Stream{FileIO.DataFormat{:TIFF}, IOStream, String}})
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:18
 [12] load(io::IOStream; kwargs::@Kwargs{})
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:17
 [13] load
    @ ~/.julia/packages/TiffImages/yETMK/src/load.jl:17 [inlined]
 [14] tlnagy/OMETIFF.jl#13
    @ ~/.julia/packages/TiffImages/yETMK/src/load.jl:13 [inlined]
 [15] open(::TiffImages.var"#13#14"{@Kwargs{}}, ::String, ::Vararg{String}; kwargs::@Kwargs{})
    @ Base ./io.jl:396
 [16] open
    @ ./io.jl:393 [inlined]
 [17] #load#12
    @ ~/.julia/packages/TiffImages/yETMK/src/load.jl:12 [inlined]
 [18] load(filepath::String)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:11
 [19] top-level scope
    @ REPL[5]:1
 [20] top-level scope
    @ ~/.julia/juliaup/julia-1.10.1+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/REPL/src/REPL.jl:1428
Some type information was truncated. Use `show(err)` to see complete types.
tlnagy commented 6 months ago

I get a slightly different error on TiffImages master:

julia> TiffImages.load("output1.ome.tiff")
Loading:  25%|██████████████████████████████▌                                                                                           |  ETA: 0:00:05ERROR: EOFError: read end of file
Stacktrace:
  [1] unsafe_read(s::IOStream, p::Ptr{UInt8}, nb::UInt64)
    @ Base ./iostream.jl:428
  [2] unsafe_read
    @ ./io.jl:761 [inlined]
  [3] read!
    @ ./io.jl:779 [inlined]
  [4] read!
    @ ~/.julia/dev/TiffImages/src/files.jl:94 [inlined]
  [5] read!(target::Matrix{TiffImages.Palette{FixedPointNumbers.N0f16}}, tf::TiffFile{UInt32, FileIO.Stream{FileIO.DataFormat{:TIFF}, IOStream, String}}, ifd::TiffImages.IFD{UInt32})
    @ TiffImages ~/.julia/dev/TiffImages/src/ifds.jl:325
  [6] macro expansion
    @ ~/.julia/dev/TiffImages/src/load.jl:92 [inlined]
  [7] macro expansion
    @ ~/.julia/packages/ProgressMeter/dMfiC/src/ProgressMeter.jl:1010 [inlined]
  [8] load(tf::TiffFile{UInt32, FileIO.Stream{FileIO.DataFormat{:TIFF}, IOStream, String}}, ifds::Vector{TiffImages.IFD{UInt32}}, N::Int64; verbose::Bool)
    @ TiffImages ~/.julia/dev/TiffImages/src/load.jl:91
  [9] load
    @ ~/.julia/dev/TiffImages/src/load.jl:84 [inlined]
 [10] load(tf::TiffFile{UInt32, FileIO.Stream{FileIO.DataFormat{:TIFF}, IOStream, String}}; verbose::Bool, mmap::Bool, lazyio::Bool)
    @ TiffImages ~/.julia/dev/TiffImages/src/load.jl:43
 [11] load(tf::TiffFile{UInt32, FileIO.Stream{FileIO.DataFormat{:TIFF}, IOStream, String}})
    @ TiffImages ~/.julia/dev/TiffImages/src/load.jl:23
 [12] load(io::IOStream; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ TiffImages ~/.julia/dev/TiffImages/src/load.jl:22
 [13] load
    @ ~/.julia/dev/TiffImages/src/load.jl:22 [inlined]
 [14] #49
    @ ~/.julia/dev/TiffImages/src/load.jl:18 [inlined]
 [15] open(::TiffImages.var"#49#50"{Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base ./io.jl:395
 [16] open
    @ ./io.jl:392 [inlined]
 [17] #load#48
    @ ~/.julia/dev/TiffImages/src/load.jl:17 [inlined]
 [18] load(filepath::String)
    @ TiffImages ~/.julia/dev/TiffImages/src/load.jl:16
 [19] top-level scope
    @ REPL[9]:1

So I tried to open the file using Fiji/ImageJ and it similarly fails to open so this might not be a TiffImages issue: 

(Fiji Is Just) ImageJ 2.3.0/1.53q; Java 1.8.0_172 [64-bit]; Linux 6.5.0-18-generic; 358MB of 25500MB (1%)

java.lang.NullPointerException
    at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:510)
    at loci.formats.FormatReader.setId(FormatReader.java:1443)
    at loci.formats.in.OMETiffReader.initializeReader(OMETiffReader.java:1476)
    at loci.formats.in.OMETiffReader.openBytes(OMETiffReader.java:368)
    at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:167)
    at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
    at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
    at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:83)
    at loci.plugins.util.ImageProcessorSource.getObject(ImageProcessorSource.java:72)
    at loci.formats.cache.Cache.recache(Cache.java:204)
    at loci.formats.cache.Cache.recache(Cache.java:224)
    at loci.formats.cache.Cache.setCurrentPos(Cache.java:175)
    at loci.plugins.util.BFVirtualStack.getProcessor(BFVirtualStack.java:176)
    at ij.ImagePlus.setSlice(ImagePlus.java:1961)
    at ij.ImagePlus.setPosition(ImagePlus.java:1847)
    at ij.ImagePlus.setPositionWithoutUpdate(ImagePlus.java:1858)
    at loci.plugins.in.Colorizer$1.show(Colorizer.java:186)
    at ij.ImagePlus.show(ImagePlus.java:479)
    at loci.plugins.in.DisplayHandler.displayNormal(DisplayHandler.java:144)
    at loci.plugins.in.DisplayHandler.displayImage(DisplayHandler.java:130)
    at loci.plugins.in.DisplayHandler.displayImages(DisplayHandler.java:122)
    at loci.plugins.in.Importer.run(Importer.java:89)
    at loci.plugins.LociImporter.run(LociImporter.java:78)
    at ij.IJ.runUserPlugIn(IJ.java:243)
    at ij.IJ.runPlugIn(IJ.java:204)
    at ij.IJ.runPlugIn(IJ.java:193)
    at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:524)
    at HandleExtraFileTypes.run(HandleExtraFileTypes.java:97)
    at ij.IJ.runUserPlugIn(IJ.java:243)
    at ij.IJ.runPlugIn(IJ.java:204)
    at ij.IJ.runPlugIn(IJ.java:193)
    at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:555)
    at ij.io.Opener.openUsingHandleExtraFileTypes(Opener.java:407)
    at ij.io.Opener.openTiff(Opener.java:913)
    at ij.io.Opener.openImage(Opener.java:335)
    at ij.io.Opener.openImage(Opener.java:241)
    at ij.io.Opener.open(Opener.java:104)
    at ij.io.Opener.openAndAddToRecent(Opener.java:310)
    at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:194)
    at ij.plugin.DragAndDrop.run(DragAndDrop.java:160)
    at java.lang.Thread.run(Thread.java:748)

Perhaps this is an issue with bfconvert?