Open adityanprasad opened 6 months ago
I get a slightly different error on TiffImages master:
julia> TiffImages.load("output1.ome.tiff")
Loading: 25%|βββββββββββββββββββββββββββββββ | 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
?
I used the
bftools
command-line toolbfconvert
to convert a Zeiss CZI mosaic into an OME-TIFF. I'm having trouble reading into Julia using eitherOMETIFF.jl
orTiffImages.jl
. The error message is attached below (same error forOMETIFF
andTiffImages.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!