add number of branching point metric

seung-lab · Oct 23, 2017 · c78104a · c78104a
1 parent cadb36d
commit c78104a
Show file tree

Hide file tree

Showing 3 changed files with 34 additions and 9 deletions.
diff --git a/scripts/skeletonize.jl b/scripts/skeletonize.jl
@@ -72,6 +72,7 @@ function main()
         while true 
             handle, body = fetch(sqsChannel) 
             d = JSON.parse( body )
+            println("tracing cell: $(d["id"])")
             try 
                 trace(d["id"]; swcDir=d["swcdir"], mip=d["mip"])
             catch err 

diff --git a/scripts/statistics.jl b/scripts/statistics.jl
@@ -2,28 +2,37 @@
 include("Common.jl")
 using Common
 using RealNeuralNetworks.SWCs 
+using RealNeuralNetworks.BranchNets
 using HDF5
 #using Plots
 # use pyplot backend for vectorized output
 #Plots.pyplot()
 
 function main()
     args = parse_commandline()
-    lengthList = Vector{Float64}()
+    numBranchingPointsList = Vector{Int}()
+    totalPathLengthList = Vector{Float64}()
     @sync begin
         for fileName in readdir( args["swcdir"] )
             if contains(fileName, ".swc")
                 @async begin 
                     @time swc = SWCs.load( joinpath( args["swcdir"], fileName ) )
-                    total_length = SWCs.get_total_length( swc )
-                    println("length of $(fileName): $(total_length/1000) micron")
-                    push!(lengthList, total_length)
+                    totalPathLength = SWCs.get_total_length( swc )
+                    println("total path length of cell $(fileName): " * 
+                            "$(totalPathLength/1000) micron")
+                    push!(totalPathLengthList, totalPathLength)
+
+                    branchNet = BranchNet(swc)
+                    numBranchingPoints = BranchNets.get_num_branching_points(branchNet)
+                    println("number of branching points of cell $(fileName): $numBranchingPoints")
+                    push!(numBranchingPointsList, numBranchingPoints)
                 end
             end 
         end 
     end
     @show lengthList
-    h5write("statistics.h5", "lengthList", lengthList)
+    h5write("statistics.h5",    "totalPathLengthList",      totalPathLengthList,
+                                "numBranchingPointsList",   numBranchingPointsList)
     #p = histogram( lengthList )    
     # display(p)
 end

diff --git a/src/BranchNets.jl b/src/BranchNets.jl
@@ -131,10 +131,18 @@ function BranchNet{T}( seg::Array{T,3}; obj_id::T = convert(T,1),
     BranchNet( nodeNet )
 end
 
-function BranchNet( swcString::AbstractString )
-    swc = SWC(swcString)
+function BranchNet( swc::SWC )
     nodeNet = NodeNet( swc )
     BranchNet( nodeNet )
+end 
+
+"""
+    BranchNet( swcString::AbstractString )
+transform string from swc content to BranchNet 
+"""
+function BranchNet( swcString::AbstractString )
+    swc = SWC(swcString)
+    BranchNet( swc )
 end
 
 ######################### IO ################
@@ -155,10 +163,15 @@ end
 
 get the number of branches  
 """
-function get_num_branches(self::BranchNet) length(self.branchList) end 
+function get_num_branches(self::BranchNet) length(self.branchList) end
+"""
+    get_num_branching_points(self::BranchNet)
+get number of branching points. assume that neuron tree do not have loop, 
+so the number of branching points is num_branches-1.
+"""
+function get_num_branching_points(self::BranchNet) get_num_branches(self)-1 end 
 function get_branch_list(self::BranchNet) self.branchList end 
 function get_connectivity_matrix(self::BranchNet) self.connectivityMatrix end 
-function get_num_node_edges(self::BranchNet) error("unimplemented") end 
 
 """
     get_branch_length_list( self::BranchNet )
@@ -184,6 +197,8 @@ function get_num_nodes( self::BranchNet )
     sum(map(length, branchList))
 end 
 
+
+
 """
     get_children_branch_index_list(self::BranchNet, parentBranchIndex::Integer)
 """