Process completed with exit code 1.

failed to run `@example` block in src/generated/examples/subspace_julia_epg.md:46-52 ```@example subspace_julia_epg b = BrukerFile(path_raw) raw = RawAcquisitionData_MESE(b) acq = AcquisitionData(raw,OffsetBruker = true); nothing #hide ``` exception = SystemError: opening file "/workspace_QMRI/PROJECTS_DATA/2021_RECH_mcT2_Bruker/PROJ_JULIA_MSME_CS/data/exp_raw/mouse_patho/20230317_085834_AT_MSME_CS_44_1_1/10/acqp": No such file or directory Stacktrace: [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) @ Base ./error.jl:176 [2] systemerror @ Base ./error.jl:175 [inlined] [3] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) @ Base ./iostream.jl:293 [4] open @ ./iostream.jl:275 [inlined] [5] open(f::MRIFiles.var"#40#41"{Int64, MRIFiles.JcampdxFile, Vector{String}}, args::String; kwargs::@kwargs{}) @ Base ./io.jl:394 [6] open(f::Function, args::String) @ Base ./io.jl:393 [7] #read#39 @ ~/.julia/packages/MRIFiles/63O1w/src/Bruker/Jcampdx.jl:197 [inlined] [8] read (repeats 2 times) @ ~/.julia/packages/MRIFiles/63O1w/src/Bruker/Jcampdx.jl:195 [inlined] [9] getindex(b::MRIFiles.BrukerFile, parameter::String) @ MRIFiles ~/.julia/packages/MRIFiles/63O1w/src/Bruker/Bruker.jl:47 [10] acqDataType(b::MRIFiles.BrukerFile) @ MRIFiles ~/.julia/packages/MRIFiles/63O1w/src/Bruker/Bruker.jl:230 [11] RawAcquisitionData_MESE(b::MRIFiles.BrukerFile) @ Subspace_MESE ~/work/PAPER_subspace_MESE/PAPER_subspace_MESE/src/bruker_sequence.jl:16 [12] top-level scope @ subspace_julia_epg.md:49 [13] eval @ ./boot.jl:385 [inlined] [14] #58 @ ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:754 [inlined] [15] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [16] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:753 [17] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [18] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [19] with_logger @ ./logging.jl:627 [inlined] [20] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [21] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752

failed to run `@example` block in src/generated/examples/subspace_julia_epg.md:56-59 ```@example subspace_julia_epg coilsens = espirit(acq,eigThresh_2=0.0); nothing #hide ``` exception = UndefVarError: `acq` not defined Stacktrace: [1] top-level scope @ subspace_julia_epg.md:57 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752

failed to run `@example` block in src/generated/examples/subspace_julia_epg.md:63-72 ```@example subspace_julia_epg params = Dict{Symbol,Any}() params[:reconSize] = acq.encodingSize params[:reco] = "direct" im_u = reconstruction(acq, params); im_u_sos = mergeChannels(im_u) heatmap(im_u_sos[:,:,55,15,1,1],colormap=:grays) ``` exception = UndefVarError: `acq` not defined Stacktrace: [1] top-level scope @ subspace_julia_epg.md:65 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752

failed to run `@example` block in src/generated/examples/subspace_julia_epg.md:91-109 ```@example subspace_julia_epg params = Dict{Symbol,Any}() params[:reconSize] = acq.encodingSize params[:reco] = "multiCoilMultiEchoSubspace" params[:regularization] = "L1" params[:sparseTrafo] = "Wavelet" #sparse trafo params[:λ] = Float32(0.03) params[:solver] = "fista" params[:iterations] = 60 #params[:iterationsInner] = 5 params[:senseMaps] = coilsens params[:normalizeReg] = true params[:basis] = basis_epg α_epg = reconstruction(acq, params) im_TE_julia = abs.(applySubspace(α_epg, params[:basis])); nothing #hide ``` exception = UndefVarError: `acq` not defined Stacktrace: [1] top-level scope @ subspace_julia_epg.md:93 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752

failed to run `@example` block in src/generated/examples/subspace_julia_epg.md:131-140 ```@example subspace_julia_epg TE_vec = Float32.(LinRange(TE,TE*ETL,ETL)) fit_und= Subspace_MESE.T2Fit_exp_noise(abs.(im_u_sos[:,:,slice_to_show,:,1,1]),TE_vec;removePoint=true,L=4) fit_julia = Subspace_MESE.T2Fit_exp_noise(abs.(im_TE_julia[:,:,slice_to_show,:,1,1]),TE_vec;removePoint=true,L=4) if isfile(path_bart) fit_bart = Subspace_MESE.T2Fit_exp_noise(abs.(im_TE_bart[:,:,slice_to_show,1,1,:]),TE_vec;removePoint=true,L=4) end; nothing #hide ``` exception = UndefVarError: `im_u_sos` not defined Stacktrace: [1] top-level scope @ subspace_julia_epg.md:134 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752

failed to run `@example` block in src/generated/examples/subspace_julia_epg.md:144-207 ```@example subspace_julia_epg using CairoMakie.Makie.MakieCore titlesize=20 ylabelsize=20 aspect = DataAspect() f=Figure(size=(1200,1000)) #plot echo 1 colorrange=MakieCore.Automatic() colormap=:grays ax = Axis(f[1,1];title="FFT\n ",ylabel = "Echo n°1\nTE = 7 ms",titlesize,ylabelsize) heatmap!(ax,im_u_sos[:,:,slice_to_show,1,1,1];colorrange,colormap) hidedecorations!(ax,label=false) ax = Axis(f[1,2];title="MRIReco\nW=0.03",titlesize) heatmap!(ax,im_TE_julia[:,:,slice_to_show,1,1,1];colorrange,colormap) hidedecorations!(ax) if(isfile(path_bart)) ax = Axis(f[1,3];title="BART\nW=0.0025",titlesize) heatmap!(ax,abs.(im_TE_bart[:,:,slice_to_show,1,1,1]);colorrange,colormap) hidedecorations!(ax) end #plot echo 10 ax = Axis(f[2,1];ylabel = "Echo n°10\nTE = 70 ms",titlesize,ylabelsize) heatmap!(ax,im_u_sos[:,:,slice_to_show,10,1,1];colorrange,colormap) hidedecorations!(ax,label=false) ax = Axis(f[2,2];titlesize) heatmap!(ax,im_TE_julia[:,:,slice_to_show,10,1,1];colorrange,colormap) hidedecorations!(ax) if(isfile(path_bart)) ax = Axis(f[2,3];titlesize) heatmap!(ax,abs.(im_TE_bart[:,:,slice_to_show,1,1,10]);colorrange,colormap) hidedecorations!(ax) end #plot T2 map colorrange=(0,150) colormap=:magma ax = Axis(f[3,1];ylabel = "T₂ map",titlesize,ylabelsize) heatmap!(ax,fit_und[:,:,2];colorrange,colormap) hidedecorations!(ax,label=false) ax = Axis(f[3,2]) h=heatmap!(ax,fit_julia[:,:,2];colorrange,colormap) hidedecorations!(ax) if(isfile(path_bart)) ax = Axis(f[3,3]) heatmap!(ax,fit_bart[:,:,2];colorrange,colormap) hidedecorations!(ax) end Colorbar(f[3,end+1],h,label = "T₂ [ms]",labelrotation=-pi/2,labelsize=20) f #save("fig_bart_julia.png",f) #save("fig_bart_julia.eps",f) #save("fig_bart_julia.pdf",f) ``` exception = UndefVarError: `im_u_sos` not defined Stacktrace: [1] top-level scope @ subspace_julia_epg.md:157 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752