{
"cells": [
{
"cell_type": "code",
"execution_count": 232,
"metadata": {},
"outputs": [],
"source": [
"using MAT\n",
"using Images\n",
"using LinearAlgebra\n"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Skeleton3D (generic function with 1 method)"
]
},
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"include(\"./julia/Skeleton3D.jl\")"
]
},
{
"cell_type": "code",
"execution_count": 267,
"metadata": {},
"outputs": [],
"source": [
"vars = matread(\"./julia/testvol.mat\");\n",
"skel=vars[\"testvol\"]\n",
"skel=padarray(skel,Pad(1, 1,1));\n",
"width = size(skel,1);\n",
"height = size(skel,2);\n",
"depth = size(skel,3);\n",
"\n",
"skel=Int8.(reshape(skel[:],width,height,depth));\n",
"\n",
"# if (nargin==2)\n",
"# spare=padarray(spare,Pad(1, 1,1));\n",
"# end\n",
"\n",
"\n",
"# fill lookup table\n",
"eulerLUT = FillEulerLUT();\n",
"\n",
"unchangedBorders = 0;"
]
},
{
"cell_type": "code",
"execution_count": 269,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"3523-element Array{Int64,1}:\n",
" 9430\n",
" 9431\n",
" 9432\n",
" 9433\n",
" 9434\n",
" 9435\n",
" 9436\n",
" 9497\n",
" 9632\n",
" 10042\n",
" 10085\n",
" 10086\n",
" 10087\n",
" ⋮\n",
" 119864\n",
" 119913\n",
" 119914\n",
" 119990\n",
" 119991\n",
" 119996\n",
" 120055\n",
" 120056\n",
" 120057\n",
" 120060\n",
" 120061\n",
" 120063"
]
},
"execution_count": 269,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"currentBorder=1\n",
"# while (unchangedBorders < 6 ) # loop until no change for all six border types\n",
"# unchangedBorders = 0;\n",
"# for currentBorder=1:6 # loop over all 6 directions\n",
" cands=fill(false,width,height,depth); ##ok<LOGL>\n",
"# cands=false(width,height,depth, \"like\", skel);\n",
" if currentBorder==4\n",
" x=2:size(skel,1); # identify border voxels as candidates\n",
" cands[x,:,:]=((skel[x,:,:] - skel[x.-1,:,:]) .!= 0);\n",
" elseif currentBorder==3\n",
" x=1:size(skel,1)-1;\n",
" cands[x,:,:]=((skel[x,:,:] - skel[x.+1,:,:]) .!= 0);\n",
" elseif currentBorder==1\n",
" y=2:size(skel,2);\n",
" cands[:,y,:]=((skel[:,y,:] - skel[:,y.-1,:]) .!= 0);\n",
" elseif currentBorder==2\n",
" y=1:(size(skel,2)-1);\n",
" cands[:,y,:]=((skel[:,y,:] - skel[:,y.+1,:]) .!= 0);\n",
" elseif currentBorder==6\n",
" z=2:size(skel,3);\n",
" cands[:,:,z]=((skel[:,:,z] - skel[:,:,z.-1]) .!= 0);\n",
" elseif currentBorder==5\n",
" z=1:size(skel,3)-1;\n",
" cands[:,:,z]=((skel[:,:,z] - skel[:,:,z.+1]) .!= 0);\n",
" end\n",
"\n",
" cands[:]=cands[:] .==1 .& skel[:] .==1\n",
" cands1=cands[:] .==1 .& skel[:] .==1\n",
"\n",
" noChange = true;\n",
" if sum(cands1)>0\n",
" cands = findall(n -> n != 0, cands)\n",
" x=map(x->x[1],cands)\n",
" y=map(x->x[2],cands)\n",
" z=map(x->x[3],cands)\n",
" \n",
" cands = findall(n -> n != 0, cands1)\n",
" end"
]
},
{
"cell_type": "code",
"execution_count": 272,
"metadata": {},
"outputs": [
{
"ename": "LoadError",
"evalue": "UndefVarError: ind2sub not defined",
"output_type": "error",
"traceback": [
"UndefVarError: ind2sub not defined",
"",
"Stacktrace:",
" [1] pk_get_nh(::Array{Int8,3}, ::Array{Int64,1}) at C:\\Users\\amira\\Dropbox (MIT)\\CBA\\MetaVoxels\\metavoxels-code\\voxel_designer\\julia\\Skeleton3D.jl:715",
" [2] top-level scope at In[272]:1",
" [3] include_string(::Function, ::Module, ::String, ::String) at .\\loading.jl:1091",
" [4] execute_code(::String, ::String) at C:\\Users\\amira\\.julia\\packages\\IJulia\\rWZ9e\\src\\execute_request.jl:27",
" [5] execute_request(::ZMQ.Socket, ::IJulia.Msg) at C:\\Users\\amira\\.julia\\packages\\IJulia\\rWZ9e\\src\\execute_request.jl:86",
" [6] #invokelatest#1 at .\\essentials.jl:710 [inlined]",
" [7] invokelatest at .\\essentials.jl:709 [inlined]",
" [8] eventloop(::ZMQ.Socket) at C:\\Users\\amira\\.julia\\packages\\IJulia\\rWZ9e\\src\\eventloop.jl:8",
" [9] (::IJulia.var\"#15#18\")() at .\\task.jl:356"
]
}
],
"source": [
"nhood = pk_get_nh(skel,cands);"
]
},
{
"cell_type": "code",
"execution_count": 249,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"3523-element Array{Int64,1}:\n",
" 9430\n",
" 9431\n",
" 9432\n",
" 9433\n",
" 9434\n",
" 9435\n",
" 9436\n",
" 9497\n",
" 9632\n",
" 10042\n",
" 10085\n",
" 10086\n",
" 10087\n",
" ⋮\n",
" 119864\n",
" 119913\n",
" 119914\n",
" 119990\n",
" 119991\n",
" 119996\n",
" 120055\n",
" 120056\n",
" 120057\n",
" 120060\n",
" 120061\n",
" 120063"
]
},
"execution_count": 249,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"x,y,z=Base._sub2ind((width,height,depth),cands)"
]
},
{
"cell_type": "code",
"execution_count": 250,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"9430"
]
},
"execution_count": 250,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"x"
]
},
{
"cell_type": "code",
"execution_count": 251,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"9431"
]
},
"execution_count": 251,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"y"
]
},
{
"cell_type": "code",
"execution_count": 252,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"9432"
]
},
"execution_count": 252,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"z"
]
},
{
"cell_type": "code",
"execution_count": 253,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(3523,)"
]
},
"execution_count": 253,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"size(Base._sub2ind((width,height,depth),cands))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Julia 1.5.2",
"language": "julia",
"name": "julia-1.5"
},
"language_info": {
"file_extension": ".jl",
"mimetype": "application/julia",
"name": "julia",
"version": "1.5.2"
}
},
"nbformat": 4,
"nbformat_minor": 4
}