Revision 27fa41066bf09a3c1ca00fd333f72755e481b16f authored by H.F on 13 April 2021, 10:57:05 UTC, committed by H.F on 13 April 2021, 10:57:05 UTC
1 parent f3455fe
test15.log
ERROR: LoadError: TaskFailedException:
UndefVarError: remove_small_area not defined
Stacktrace:
[1] create3dmask(::Array{Gray{Normed{UInt16,16}},3}) at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/segmentation3d.jl:33
[2] macro expansion at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/segmentation3d.jl:49 [inlined]
[3] (::var"#179#threadsfor_fun#22"{Array{Gray{Normed{UInt16,16}},3},Array{Gray{Normed{UInt16,16}},3},Array{Float64,1},Array{Float64,1},UnitRange{Int64}})(::Bool) at ./threadingconstructs.jl:61
[4] (::var"#179#threadsfor_fun#22"{Array{Gray{Normed{UInt16,16}},3},Array{Gray{Normed{UInt16,16}},3},Array{Float64,1},Array{Float64,1},UnitRange{Int64}})() at ./threadingconstructs.jl:28
Stacktrace:
[1] wait(::Task) at ./task.jl:267
[2] macro expansion at ./threadingconstructs.jl:69 [inlined]
[3] extract3dnucleus at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/segmentation3d.jl:46 [inlined]
[4] macro expansion at ./util.jl:175 [inlined]
[5] playing(::Int64) at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/test15.jl:36
[6] macro expansion at ./util.jl:175 [inlined]
[7] top-level scope at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/test15.jl:49
[8] include(::Module, ::String) at ./Base.jl:377
[9] exec_options(::Base.JLOptions) at ./client.jl:288
[10] _start() at ./client.jl:484
in expression starting at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/test15.jl:48
Loading 11
226.906063 seconds (3.42 M allocations: 34.673 GiB, 0.42% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
125.315130 seconds (348.13 M allocations: 75.175 GiB, 37.48% gc time)
Finding connected component
7.279594 seconds (179.93 k allocations: 4.934 GiB, 0.19% gc time)
Detecting contacted branch
5.923156 seconds (1.38 M allocations: 49.314 GiB, 16.25% gc time)
Found contacted branch: [2, 13, 16]
Splitting branch 2 now
Finding connected component
Reassigning contacted branch 2
Splitting branch 13 now
Finding connected component
Reassigning contacted branch 13
Branch 13 -> 100
Branch 13 -> 101
Splitting branch 16 now
Finding connected component
Reassigning contacted branch 16
36.826227 seconds (3.93 M allocations: 100.044 GiB, 9.67% gc time)
Grant domain for each detected cell by watershed
44.868765 seconds (1.81 M allocations: 28.169 GiB, 29.86% gc time)
Drawing longlived_maps
[2, 3, 4, 8, 9, 15, 16, 23, 31, 100, 101]
50.959920 seconds (1.90 M allocations: 32.778 GiB, 26.32% gc time)
tracking cell 1
4.067262 seconds (12.71 M allocations: 2.708 GiB, 55.32% gc time)
Extracting nucleus
Computing file changes ...