compute tail and head radius ratio, which could be an important metri…

…c to identify spine

src/BranchNets.jl

@@ -149,11 +149,20 @@ end
 function load_swc( fileName::AbstractString )
     swcString = readstring( fileName )
     BranchNet( swcString )
+end
+
+function load_gzip_swc( fileName::AbstractString )
+    swc = SWCs.load_gzip_swc( fileName )
+    BranchNet( swc )
 end 
 
-function save(self::BranchNet, fileName)
+function save(self::BranchNet, fileName::AbstractString)
     swc = SWC(self)
     SWCs.save( swc, fileName )
+end
+
+function save_gzip_swc( self::BranchNet, fileName::AbstractString )
+    SWCs.save_gzip_swc( SWCs.SWC(self), fileName )
 end 
 
 ####################### properties ##############
@@ -435,6 +444,9 @@ end
 
 
 ############################### Base functions ###################################
+function Base.getindex(self::BranchNet, index::Integer)
+    get_branch_list(self)[index]
+end 
 """
 merge two nets at a specific branch location.
 the root node of second net will be connected to the first net

src/Branches.jl

@@ -49,9 +49,28 @@ function get_path_length(self::Branch)
         ret += norm( [map((x,y)-> x-y, self[i][1:3], self[i-1][1:3] )...] )
     end
     ret
+end
+
+function get_radius_list( self::Branch ) map(n->n[4], self) end 
+
+"""
+    get_tail_head_radius_ratio( self::Branch )
+the spine is normally thick in tail, and thin in the head. 
+The head should point to dendrite. This is a very good feature to identify spine.
+"""
+function get_tail_head_radius_ratio( self::Branch )
+    radiusList = get_radius_list( self )
+    N = length(self)
+    headRadiusList = radiusList[1:cld(N,2)]
+    tailRadiusList = radiusList[cld(N,2):N]
+    maximum(tailRadiusList) / minimum(headRadiusList)
 end 
 
 ###################### Base functions ################
+function Base.start( self::Branch ) 1 end 
+function Base.next( self::Branch, state::Integer ) get_node_list(self)[state], state+1 end 
+function Base.done( self::Branch, state::Integer ) state > length(self) end 
+
 function Base.endof(self::Branch) length(self) end
 function Base.isempty(self::Branch) isempty(self.nodeList) end 
 

test/Branches.jl

@@ -0,0 +1,15 @@
+using RealNeuralNetworks
+using RealNeuralNetworks.BranchNets
+using RealNeuralNetworks.BranchNets.Branches
+using Base.Test
+
+
+@testset "test Branches" begin
+    # construct a branch
+    branchNet = BranchNets.load_gzip_swc("../assert/76869.swc.gz")
+    # get a random branch
+    branch = branchNet[5]
+
+    println("get tail head radius ratio ...")
+    @time Branches.get_tail_head_radius_ratio( branch )
+end