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use voxel size to correct radius #6

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use voxel size to correct radius #6

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2 changes: 2 additions & 0 deletions src/DBFs.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@ module DBFs

using Base.Cartesian

typealias DBF Vector{Float32}

"""
use segmentation to get binary image to save memory usage
"""
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11 changes: 4 additions & 7 deletions src/Skeletons.jl
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Expand Up @@ -122,7 +122,6 @@ function skeletonize{T}( points::Array{T,2}; DBF=DBFs.compute_DBF(points),
if farthest_node == root_node break end #this can happen apparently

new_path = LightGraphs.enumerate_paths( dsp_dbf,farthest_node );

push!(paths, new_path)
#can't do this in-place with arrays
#this fn call is getting ridiculous
Expand All @@ -136,6 +135,7 @@ function skeletonize{T}( points::Array{T,2}; DBF=DBFs.compute_DBF(points),

println("Consolidating Paths")
path_nodes, path_edges = consolidate_paths( paths );

node_radii = DBF[path_nodes];

# build a new graph containing only the skeleton nodes and edges
Expand Down Expand Up @@ -215,9 +215,8 @@ function make_neighbor_graph{T}( points::Array{T,2}, ind2node=nothing, max_dims=
#26-connectivity neighborhood
# weights computed by euc_dist to center voxel
nhood = [[i,j,k] for i=1:3,j=1:3,k=1:3];
map!( x-> (x .- [2,2,2]).*[voxel_size ...] , nhood );
nhood_weights = map( norm, nhood );

map!( x-> (x .- [2,2,2]), nhood );
nhood_weights = map( x -> norm(x.*[voxel_size...]), nhood );
#only adding weights for non-duplicate nodes
_,non_duplicates = findnz( ind2node );

Expand Down Expand Up @@ -392,7 +391,7 @@ end
"""
function remove_path_from_rns( reachable_nodes::Vector, path::Vector,
points, ind2node, dbf, max_dims, inspected_nodes,
scale_param::Int=6, const_param::Int=6 );
scale_param::Int=1000, const_param::Int=1000 );

r = dbf[path]*scale_param + const_param;

Expand Down Expand Up @@ -507,8 +506,6 @@ function distill!{T}(point_array::Array{T,2},
path_edges[i] = (id_map[path_edges[i][1]], id_map[path_edges[i][2]])
end
# rebuild the roots and destinations
@show root_nodes
@show id_map
for i in 1:length(root_nodes)
root_nodes[i] = id_map[ root_nodes[i] ]
end
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6 changes: 3 additions & 3 deletions test/runtests.jl
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Expand Up @@ -2,7 +2,7 @@ using TEASAR
using Base.Test
using HDF5

const DEFAULT_VOXEL_SIZE = (UInt32(80), UInt32(80), UInt32(40))
const DEFAULT_VOXEL_SIZE = (UInt32(80), UInt32(80), UInt32(45))

function get_seg_from_h5()
# read seg data
Expand Down Expand Up @@ -31,8 +31,8 @@ seg[47:54, 47:54, 71:78] = 1


@testset "test teasar" begin
# @time swc = TEASAR.skeletonize(seg; voxel_size=DEFAULT_VOXEL_SIZE)
@time swc = TEASAR.skeletonize( seg )
@time swc = TEASAR.skeletonize(seg; voxel_size=DEFAULT_VOXEL_SIZE)
#@time swc = TEASAR.skeletonize( seg )
@test TEASAR.SWCs.get_points_num(swc) > 1
@show swc
TEASAR.SWCs.save(swc, tempname() * ".swc")
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