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Merge 3f592e5 into b7b3104
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@jingpengw
jingpengw committed Jul 24, 2019
2 parents b7b3104 + 3f592e5 commit a13adf4
Showing 1 changed file with 37 additions and 37 deletions.
74 changes: 37 additions & 37 deletions src/Utils/SynapseTables.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ function preprocess(self::SynapseTable, voxelSize::Tuple)
#if key!=:presyn_wt && key!=:postsyn_wt
# self[key] = round.(Int, value)
#end
self[key] = Vector{Float32}(value)
self[!, key] = Vector{Float32}(value)
end

println("remove self connections...")
Expand All @@ -44,25 +44,25 @@ function preprocess(self::SynapseTable, voxelSize::Tuple)
end

println("transform to physical coordinate...")
self[:BBOX_bx] = (self[:BBOX_bx] .- one(Float32)) .* voxelSize[1]
self[:BBOX_by] = (self[:BBOX_by] .- one(Float32)) .* voxelSize[2]
self[:BBOX_bz] = (self[:BBOX_bz] .- one(Float32)) .* voxelSize[3]
self[!, :BBOX_bx] = (self[!, :BBOX_bx] .- one(Float32)) .* voxelSize[1]
self[!, :BBOX_by] = (self[!, :BBOX_by] .- one(Float32)) .* voxelSize[2]
self[!, :BBOX_bz] = (self[!, :BBOX_bz] .- one(Float32)) .* voxelSize[3]

self[:BBOX_ex] = (self[:BBOX_ex] .- one(Float32)) .* voxelSize[1]
self[:BBOX_ey] = (self[:BBOX_ey] .- one(Float32)) .* voxelSize[2]
self[:BBOX_ez] = (self[:BBOX_ez] .- one(Float32)) .* voxelSize[3]
self[!, :BBOX_ex] = (self[!, :BBOX_ex] .- one(Float32)) .* voxelSize[1]
self[!, :BBOX_ey] = (self[!, :BBOX_ey] .- one(Float32)) .* voxelSize[2]
self[!, :BBOX_ez] = (self[!, :BBOX_ez] .- one(Float32)) .* voxelSize[3]

self[:psd_x] = (self[:psd_x] .-one(Float32)) .* voxelSize[1]
self[:psd_y] = (self[:psd_y] .-one(Float32)) .* voxelSize[2]
self[:psd_z] = (self[:psd_z] .-one(Float32)) .* voxelSize[3]
self[!, :psd_x] = (self[!, :psd_x] .-one(Float32)) .* voxelSize[1]
self[!, :psd_y] = (self[!, :psd_y] .-one(Float32)) .* voxelSize[2]
self[!, :psd_z] = (self[!, :psd_z] .-one(Float32)) .* voxelSize[3]

self[:presyn_x] = (self[:presyn_x] .- one(Float32)) .* voxelSize[1]
self[:presyn_y] = (self[:presyn_y] .- one(Float32)) .* voxelSize[2]
self[:presyn_z] = (self[:presyn_z] .- one(Float32)) .* voxelSize[3]
self[!, :presyn_x] = (self[!, :presyn_x] .- one(Float32)) .* voxelSize[1]
self[!, :presyn_y] = (self[!, :presyn_y] .- one(Float32)) .* voxelSize[2]
self[!, :presyn_z] = (self[!, :presyn_z] .- one(Float32)) .* voxelSize[3]

self[:postsyn_x] = (self[:postsyn_x] .- one(Float32)) .* voxelSize[1]
self[:postsyn_y] = (self[:postsyn_y] .- one(Float32)) .* voxelSize[2]
self[:postsyn_z] = (self[:postsyn_z] .- one(Float32)) .* voxelSize[3]
self[!, :postsyn_x] = (self[!, :postsyn_x] .- one(Float32)) .* voxelSize[1]
self[!, :postsyn_y] = (self[!, :postsyn_y] .- one(Float32)) .* voxelSize[2]
self[!, :postsyn_z] = (self[!, :postsyn_z] .- one(Float32)) .* voxelSize[3]
return self
end

Expand All @@ -71,35 +71,35 @@ function postprocess(self::SynapseTable, voxelSize::Union{Vector, Tuple})
voxelSize = map(Float32, voxelSize)

println("transform to voxel coordinate...")
self[:BBOX_bx] = (self[:BBOX_bx]./voxelSize[1]) .+ one(Float32)
self[:BBOX_by] = (self[:BBOX_by]./voxelSize[2]) .+ one(Float32)
self[:BBOX_bz] = (self[:BBOX_bz]./voxelSize[3]) .+ one(Float32)
self[!, :BBOX_bx] = (self[!, :BBOX_bx]./voxelSize[1]) .+ one(Float32)
self[!, :BBOX_by] = (self[!, :BBOX_by]./voxelSize[2]) .+ one(Float32)
self[!, :BBOX_bz] = (self[!, :BBOX_bz]./voxelSize[3]) .+ one(Float32)

self[:BBOX_ex] = (self[:BBOX_ex]./voxelSize[1]) .+ one(Float32)
self[:BBOX_ey] = (self[:BBOX_ey]./voxelSize[2]) .+ one(Float32)
self[:BBOX_ez] = (self[:BBOX_ez]./voxelSize[3]) .+ one(Float32)
self[!, :BBOX_ex] = (self[!, :BBOX_ex]./voxelSize[1]) .+ one(Float32)
self[!, :BBOX_ey] = (self[!, :BBOX_ey]./voxelSize[2]) .+ one(Float32)
self[!, :BBOX_ez] = (self[!, :BBOX_ez]./voxelSize[3]) .+ one(Float32)


self[:psd_x] = (self[:psd_x]./voxelSize[1]) .+ one(Float32)
self[:psd_y] = (self[:psd_y]./voxelSize[2]) .+ one(Float32)
self[:psd_z] = (self[:psd_z]./voxelSize[3]) .+ one(Float32)
self[!, :psd_x] = (self[!, :psd_x]./voxelSize[1]) .+ one(Float32)
self[!, :psd_y] = (self[!, :psd_y]./voxelSize[2]) .+ one(Float32)
self[!, :psd_z] = (self[!, :psd_z]./voxelSize[3]) .+ one(Float32)

self[:presyn_x] = (self[:presyn_x]./voxelSize[1]) .+ one(Float32)
self[:presyn_y] = (self[:presyn_y]./voxelSize[2]) .+ one(Float32)
self[:presyn_z] = (self[:presyn_z]./voxelSize[3]) .+ one(Float32)
self[!, :presyn_x] = (self[!, :presyn_x]./voxelSize[1]) .+ one(Float32)
self[!, :presyn_y] = (self[!, :presyn_y]./voxelSize[2]) .+ one(Float32)
self[!, :presyn_z] = (self[!, :presyn_z]./voxelSize[3]) .+ one(Float32)

self[:postsyn_x] = (self[:postsyn_x]./voxelSize[1]) .+ one(Float32)
self[:postsyn_y] = (self[:postsyn_y]./voxelSize[2]) .+ one(Float32)
self[:postsyn_z] = (self[:postsyn_z]./voxelSize[3]) .+ one(Float32)
self[!, :postsyn_x] = (self[!, :postsyn_x]./voxelSize[1]) .+ one(Float32)
self[!, :postsyn_y] = (self[!, :postsyn_y]./voxelSize[2]) .+ one(Float32)
self[!, :postsyn_z] = (self[!, :postsyn_z]./voxelSize[3]) .+ one(Float32)

return self
end

function get_coordinate_array(self::SynapseTable, prefix::String)
coordinateNames = get_coordinate_names(prefix)
hcat( self[coordinateNames[1]],
self[coordinateNames[2]],
self[coordinateNames[3]])
hcat( self[!, coordinateNames[1]],
self[!, coordinateNames[2]],
self[!, coordinateNames[3]])
end

function get_coordinate(self::DataFrameRow, prefix::String)
Expand Down Expand Up @@ -160,7 +160,7 @@ function get_mask(self::SynapseTable;
voxelSize = map(Float32, voxelSize)
for coordinatePrefix in coordinatePrefixList
coordinateNames = SynapseTables.get_coordinate_names( coordinatePrefix )
coordinateList = map((c,s)->self[c]/s, coordinateNames, voxelSize)
coordinateList = map((c,s)->self[!, c]/s, coordinateNames, voxelSize)
coordinateList = map(x->round.(Int, x), coordinateList)
for i in 1:length(coordinateList[1])
mask[ coordinateList[1][i],
Expand All @@ -181,8 +181,8 @@ end
@warn("empty synapse table!")
return nothing
else
minCorner = map(x->minimum(self[x]), coordinateNames)
maxCorner = map(x->maximum(self[x]), coordinateNames)
minCorner = map(x->minimum(self[!, x]), coordinateNames)
maxCorner = map(x->maximum(self[!, x]), coordinateNames)
return BoundingBoxes.BoundingBox(minCorner, maxCorner)
end
end
Expand Down

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