juliaNotebookTest.ipynb unable to read task 9 spleen files

[elbert5770]

With the correct paths to the task 9 data on Ubuntu 22.04

patientNum = 2
data_dir = "/home/elbert5770/Documents/julia/MRIimages/Task09_Spleen"
train_labels = map(fileEntry-> joinpath(data_dir,"labelsTr",fileEntry),readdir(joinpath(data_dir,"labelsTr"); sort=true))
train_images = map(fileEntry-> joinpath(data_dir,"imagesTr",fileEntry),readdir(joinpath(data_dir,"imagesTr"); sort=true))
zipped = collect(zip(train_images, train_labels))
tupl = zipped[patientNum]
targetSpacing = (1, 1, 1)
loaded = LoadFromMonai.loadBySitkromImageAndLabelPaths(tupl[1], tupl[2], targetSpacing)

gives the following error with Python 3.10.4 installed:

Python: RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /home/conda/feedstock_root/build_artifacts/libsimpleitk_1627514680097/work/Code/IO/src/sitkImageReaderBase.cxx:105:
sitk::ERROR: Unable to determine ImageIO reader for "/home/elbert5770/Documents/julia/MRIimages/Task09_Spleen/imagesTr/._spleen_12.nii.gz"

Stacktrace:
  [1] pythrow()
    @ PythonCall ~/.julia/packages/PythonCall/XgP8G/src/err.jl:94
  [2] errcheck
    @ ~/.julia/packages/PythonCall/XgP8G/src/err.jl:10 [inlined]
  [3] pycallargs
    @ ~/.julia/packages/PythonCall/XgP8G/src/abstract/object.jl:153 [inlined]
  [4] pycall(f::PythonCall.Py, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ PythonCall ~/.julia/packages/PythonCall/XgP8G/src/abstract/object.jl:171
  [5] pycall
    @ ~/.julia/packages/PythonCall/XgP8G/src/abstract/object.jl:161 [inlined]
  [6] #_#11
    @ ~/.julia/packages/PythonCall/XgP8G/src/Py.jl:360 [inlined]
  [7] Py
    @ ~/.julia/packages/PythonCall/XgP8G/src/Py.jl:360 [inlined]
  [8] loadBySitkromImageAndLabelPaths(imagePath::String, labelPath::String, targetSpacing::Tuple{Int64, Int64, Int64})
    @ MedPipe3D.LoadFromMonai ~/.julia/packages/MedPipe3D/NqvPg/src/fromMonai/LoadFromMonai.jl:123
  [9] top-level scope
    @ ~/Documents/julia/MRIimages/juliaNotebookTest.ipynb:21
 [10] eval
    @ ./boot.jl:373 [inlined]
 [11] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
...
    @ Base ./Base.jl:418
 [21] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:292
 [22] _start()
    @ Base ./client.jl:495

"name": "PythonCall.PyException",
	"message": "Python: RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /home/conda/feedstock_root/build_artifacts/libsimpleitk_1627514680097/work/Code/IO/src/sitkImageReaderBase.cxx:105:\nsitk::ERROR: Unable to determine ImageIO reader for \"/home/elbert5770/Documents/julia/MRIimages/Task09_Spleen/imagesTr/._spleen_12.nii.gz\"",
	"stack": "Python: RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /home/conda/feedstock_root/build_artifacts/libsimpleitk_1627514680097/work/Code/IO/src/sitkImageReaderBase.cxx:105:\nsitk::ERROR: Unable to determine ImageIO reader for \"/home/elbert5770/Documents/julia/MRIimages/Task09_Spleen/imagesTr/._spleen_12.nii.gz\"\n\nStacktrace:\n  [1] pythrow()\n    @ PythonCall ~/.julia/packages/PythonCall/XgP8G/src/err.jl:94\n  [2] errcheck\n    @ ~/.julia/packages/PythonCall/XgP8G/src/err.jl:10 [inlined]\n  [3] pycallargs\n    @ ~/.julia/packages/PythonCall/XgP8G/src/abstract/object.jl:153 [inlined]\n  [4] pycall(f::PythonCall.Py, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})\n    @ PythonCall ~/.julia/packages/PythonCall/XgP8G/src/abstract/object.jl:171\n  [5] pycall\n    @ ~/.julia/packages/PythonCall/XgP8G/src/abstract/object.jl:161 [inlined]\n  [6] #_#11\n    @ ~/.julia/packages/PythonCall/XgP8G/src/Py.jl:360 [inlined]\n  [7] Py\n    @ ~/.julia/packages/PythonCall/XgP8G/src/Py.jl:360 [inlined]\n  [8] loadBySitkromImageAndLabelPaths(imagePath::String, labelPath::String, targetSpacing::Tuple{Int64, Int64, Int64})\n    @ MedPipe3D.LoadFromMonai ~/.julia/packages/MedPipe3D/NqvPg/src/fromMonai/LoadFromMonai.jl:123\n  [9] top-level scope\n    @ ~/Documents/julia/MRIimages/juliaNotebookTest.ipynb:21\n [10] eval\n    @ ./boot.jl:373 [inlined]\n [11] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)\n    @ Base ./loading.jl:1196\n [12] #invokelatest#2\n    @ ./essentials.jl:716 [inlined]\n [13] invokelatest\n    @ ./essentials.jl:714 [inlined]\n [14] (::VSCodeServer.var\"#164#165\"{VSCodeServer.NotebookRunCellArguments, String})()\n    @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.24/scripts/packages/VSCodeServer/src/serve_notebook.jl:19\n [15] withpath(f::VSCodeServer.var\"#164#165\"{VSCodeServer.NotebookRunCellArguments, String}, path::String)\n    @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.24/scripts/packages/VSCodeServer/src/repl.jl:184\n [16] notebook_runcell_request(conn::VSCodeServer.JSONRPC.JSONRPCEndpoint{Base.PipeEndpoint, Base.PipeEndpoint}, params::VSCodeServer.NotebookRunCellArguments)\n    @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.24/scripts/packages/VSCodeServer/src/serve_notebook.jl:13\n [17] dispatch_msg(x::VSCodeServer.JSONRPC.JSONRPCEndpoint{Base.PipeEndpoint, Base.PipeEndpoint}, dispatcher::VSCodeServer.JSONRPC.MsgDispatcher, msg::Dict{String, Any})\n    @ VSCodeServer.JSONRPC ~/.vscode/extensions/julialang.language-julia-1.6.24/scripts/packages/JSONRPC/src/typed.jl:67\n [18] serve_notebook(pipename::String, outputchannel_logger::Base.CoreLogging.SimpleLogger; crashreporting_pipename::String)\n    @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.24/scripts/packages/VSCodeServer/src/serve_notebook.jl:136\n [19] top-level scope\n    @ ~/.vscode/extensions/julialang.language-julia-1.6.24/scripts/notebook/notebook.jl:32\n [20] include(mod::Module, _path::String)\n    @ Base ./Base.jl:418\n [21] exec_options(opts::Base.JLOptions)\n    @ Base ./client.jl:292\n [22] _start()\n    @ Base ./client.jl:495"

[elbert5770]

CT-Org files work just fine as long as the label files are manually placed in a 'labels' folder and images are placed in a 'images' folder. Assuming you can download the CT-Org files (see issue 2).

[jakubMitura14]

Thanks for interest in my tools

Sometimes julia do not parse paths correctly
Try
zipped=map(tupl -> (replace(tupl[1], "." => ""), replace(tupl[2], "." => "")),zipped)

And generally check some path in array and compare it with true one, for reference, the methods that can be used

https://docs.julialang.org/en/v1/base/file/

[jakubMitura14]

Did it helped @elbert5770 :)?

[elbert5770]

Yes, although the line in the original file is the correct one:
zipped=map(tupl -> (replace(tupl[1], "." => ""), replace(tupl[2], "." => "")),zipped)

It's just confusing because of all the hidden files in the directory. TBH, it would probably be better to ignore the hidden files rather than strip the ._