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seung-lab / RealNeuralNetworks.jl

A unified framework for skeletonization, morphological analysis, and connectivity analysis.
Apache License 2.0
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there exists some point with more than one parent #49

Closed xiuliren closed 5 years ago

xiuliren commented 5 years ago

when I run skeletonization code, the problem was spotted by an assertion:

the closest segment is a terminal segment, merge the root segment of the other net                   
need to break the closest segment and rebuild connectivity matrix                                    
ERROR: LoadError: AssertionError: length(parentSegmentIdList) == 1                                   
Stacktrace:                                                                                          
 [1] get_parent_segment_id(::SparseArrays.SparseMatrixCSC{Bool,Int64}, ::Int64) at /usr/people/jingpe
ng/.julia/dev/RealNeuralNetworks/src/Neurons.jl:589                                                  
 [2] get_parent_segment_id at /usr/people/jingpeng/.julia/dev/RealNeuralNetworks/src/Neurons.jl:579 [
inlined]                                                                                             
 [3] Array{RealNeuralNetworks.SWCs.PointObjs.PointObj,1}(::Neuron) at /usr/people/jingpeng/.julia/dev
/RealNeuralNetworks/src/Neurons.jl:1432                                                              
 [4] #trace#3(::String, ::UInt32, ::String, ::Tuple{Int64,Int64,Int64}, ::String, ::Function, ::Int64
) at /usr/people/jingpeng/.julia/dev/RealNeuralNetworks/scripts/skeletonize.jl:45                    
 [5] (::getfield(Main, Symbol("#kw##trace")))(::NamedTuple{(:swcDir, :mip, :meshName, :voxelSize, :se
gmentationLayer),Tuple{String,UInt32,String,Tuple{Int64,Int64,Int64},String}}, ::typeof(trace), ::Int
64) at ./none:0                                                                                      
 [6] macro expansion at ./logging.jl:314 [inlined]                                                   
 [7] main() at /usr/people/jingpeng/.julia/dev/RealNeuralNetworks/scripts/skeletonize.jl:102         
 [8] top-level scope at none:0                                                                       
 [9] include at ./boot.jl:317 [inlined]                                                              
 [10] include_relative(::Module, ::String) at ./loading.jl:1038                                      
 [11] include(::Module, ::String) at ./sysimg.jl:29                                                  
 [12] exec_options(::Base.JLOptions) at ./client.jl:239                                              
 [13] _start() at ./client.jl:432                                                                    
in expression starting at /usr/people/jingpeng/.julia/dev/RealNeuralNetworks/scripts/skeletonize.jl:1
36

such as neuron 79951

xiuliren commented 5 years ago

this is not really a problem! Because the assertion is testing length(parentSegmentIdList) == 1 but the root segment do not have any parent, the assertion should be: length(parentSegmentIdList) <= 1