TiffImages fails to open a bfconvert converted OME-TIFF #151
Description
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.