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juliaNotebookTest.ipynb unable to read task 9 spleen files
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"
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