Problem in reading TIFF floats file

mkitti · November 23, 2023, 7:43am

TiffImages.jl and ImageMagic.jl both seem to have be having some trouble accessing your tiff file. So I decided to create a new wrapper around libtiff via Clang.jl.

LibTIFF.jl

https://github.com/mkitti/LibTIFF.jl

julia> using Pkg

julia> Pkg.add("https://github.com/mkitti/LibTIFF.jl")

julia> using LibTIFF

julia> function read_float32_tiff(filepath)
           tif = TIFFOpen(filepath, "r")
           _length = TIFFGetField(tif, TIFFTAG_IMAGELENGTH, Int32)
           _width = TIFFGetField(tif, TIFFTAG_IMAGEWIDTH, Int32)
           _rowsperstrip = TIFFGetField(tif, TIFFTAG_ROWSPERSTRIP, Int32)
           _bitspersample = TIFFGetField(tif, TIFFTAG_BITSPERSAMPLE, Int32)
           _samplesformat = TIFFGetField(tif, TIFFTAG_SAMPLEFORMAT, Int8)
           @info "Image fields" _length _width _rowsperstrip _bitspersample _samplesformat
           image = Matrix{Float32}(undef, _width, _length)
           for (i,col) in zip(0:_length÷_rowsperstrip, eachcol(image))
               TIFFReadEncodedStrip(tif, i, pointer(col), -1)
           end
           TIFFClose(tif)
           image = permutedims(image, (2,1))
           return image
       end
read_float32_tiff (generic function with 1 method)

The result looks like it matches the MATLAB example.

julia> read_float32_tiff("001.tif")[1:10, 1:10]
TIFFFetchNormalTag: Warning, ASCII value for tag "ImageDescription" does not end in null byte.
┌ Info: Image fields
│   _length = 360
│   _width = 2304
│   _rowsperstrip = 1
│   _bitspersample = 32
└   _samplesformat = 3
10×10 Matrix{Float32}:
 0.0  0.0    0.0      0.0      0.0      0.0      0.0      0.0      0.0    949.15
 0.0  0.0    0.0      0.0      0.0    872.994  864.982  862.223  911.128  940.604
 0.0  0.0    0.0    906.0    905.209  876.51   866.097  862.072  910.672  940.604
 0.0  0.0  869.0    887.646  905.209  876.51   866.097  862.072  910.672  940.604
 0.0  0.0  869.0    887.351  905.209  876.51   866.097  862.072  910.672  940.604
 0.0  0.0  869.0    887.351  905.209  876.51   866.097  862.072  910.672  940.604
 0.0  0.0  869.0    887.351  905.209  876.51   866.097  862.072  910.672  940.604
 0.0  0.0  871.225  887.351  905.209  876.51   866.097  862.072  910.672  940.604
 0.0  0.0  877.187  887.351  905.209  876.51   866.097  862.072  910.672  940.604
 0.0  0.0  877.187  887.351  905.209  876.51   866.097  862.072  910.672  931.802

TiffImages.jl

TiffImages.jl does not seem to recognize the file and errors with the following.

ERROR: MethodError: no method matching interpretation(::Val{TiffImages.PHOTOMETRIC_MINISWHITE})

Stack trace for TiffImages.jl

ERROR: MethodError: no method matching interpretation(::Val{TiffImages.PHOTOMETRIC_MINISWHITE})

Closest candidates are:
  interpretation(::TiffImages.PhotometricInterpretations, ::Val{TiffImages.EXTRASAMPLE_UNSPECIFIED}, ::Val{4})
   @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/layout.jl:63
  interpretation(::TiffImages.PhotometricInterpretations, ::TiffImages.ExtraSamples, ::Int64)
   @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/layout.jl:45
  interpretation(::TiffImages.PhotometricInterpretations)
   @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/layout.jl:38
  ...

Stacktrace:
  [1] interpretation(p::TiffImages.PhotometricInterpretations)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/layout.jl:38
  [2] interpretation(p::TiffImages.PhotometricInterpretations, extrasamples::TiffImages.ExtraSamples, samplesperpixel::Int64)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/layout.jl:46
  [3] interpretation(ifd::TiffImages.IFD{UInt32})
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/layout.jl:29
  [4] getcache(ifd::TiffImages.IFD{UInt32})
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/layout.jl:91
  [5] load(tf::TiffImages.TiffFile{UInt32, Stream{DataFormat{:TIFF}, IOStream, String}}, ifds::Vector{TiffImages.IFD{UInt32}}, ::Nothing; verbose::Bool)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:71
  [6] load
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:69 [inlined]
  [7] load(tf::TiffImages.TiffFile{UInt32, Stream{DataFormat{:TIFF}, IOStream, String}}; verbose::Bool, mmap::Bool, lazyio::Bool)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:36
  [8] load(tf::TiffImages.TiffFile{UInt32, Stream{DataFormat{:TIFF}, IOStream, String}})
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:18
  [9] load(io::IOStream; kwargs::@Kwargs{})
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:17
 [10] load
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:17 [inlined]
 [11] #13
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:13 [inlined]
 [12] open(::TiffImages.var"#13#14"{@Kwargs{}}, ::String, ::Vararg{String}; kwargs::@Kwargs{})
    @ Base ./io.jl:396
 [13] open
    @ Base ./io.jl:393 [inlined]
 [14] #load#12
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:12 [inlined]
 [15] load(filepath::String)
    @ TiffImages ~/.julia/packages/TiffImages/yETMK/src/load.jl:11
 [16] #invokelatest#2
    @ Base ./essentials.jl:950 [inlined]
 [17] invokelatest
    @ Base ./essentials.jl:947 [inlined]
 [18] #_#1
    @ LazyModules ~/.julia/packages/LazyModules/d9Be6/src/LazyModules.jl:29 [inlined]
 [19] (::LazyModules.LazyFunction)(args::String)
    @ LazyModules ~/.julia/packages/LazyModules/d9Be6/src/LazyModules.jl:27
 [20] load(f::File{DataFormat{:TIFF}, String}; canonicalize::Nothing, kwargs::@Kwargs{})
    @ ImageIO ~/.julia/packages/ImageIO/XthUV/src/ImageIO.jl:111
 [21] load(f::File{DataFormat{:TIFF}, String})
    @ ImageIO ~/.julia/packages/ImageIO/XthUV/src/ImageIO.jl:109
 [22] #invokelatest#2
    @ Base ./essentials.jl:950 [inlined]
 [23] invokelatest
    @ Base ./essentials.jl:947 [inlined]
 [24] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:219
 [25] action
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:196 [inlined]
 [26] action
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 [inlined]
 [27] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:113
 [28] load(::String)
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:109
 [29] top-level scope
    @ REPL[13]:1
Stacktrace:
 [1] handle_error(e::MethodError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/error_handling.jl:61
 [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/error_handling.jl:56
 [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Formatted; options::@Kwargs{})
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:228
 [4] action
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:196 [inlined]
 [5] action
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 [inlined]
 [6] load(::String; options::@Kwargs{})
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:113
 [7] load(::String)
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:109
 [8] top-level scope
   @ REPL[13]:1

ImageMagick.jl

ImageMagick.jl seems to read the file as a 32-bit Int TIFF as the original poster displayed.

julia> load("/home/mkitti/Downloads/001.tif")
[ Info: Precompiling ImageMagick [6218d12a-5da1-5696-b52f-db25d2ecc6d1]
┌ Warning: some versions of ImageMagick give spurious low-order bits for 32-bit TIFFs
└ @ ImageMagick ~/.julia/packages/ImageMagick/KDZC2/src/ImageMagick.jl:99

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Problem in reading TIFF floats file

LibTIFF.jl

TiffImages.jl

ImageMagick.jl

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