diff --git a/REQUIRE b/REQUIRE new file mode 100644 index 00000000..3b0ee32f --- /dev/null +++ b/REQUIRE @@ -0,0 +1,14 @@ +julia 1 +LightGraphs +MetaGraphs +DataFrames +CSV +BigArrays +DataStructures +LsqFit +OffsetArrays +ImageFiltering +Query +JSON +NearestNeighbors +ProgressMeter diff --git a/src/Utils/SynapseTables.jl b/src/Utils/SynapseTables.jl index ea8891fd..31b9c2d0 100755 --- a/src/Utils/SynapseTables.jl +++ b/src/Utils/SynapseTables.jl @@ -18,7 +18,7 @@ function preprocess(self::SynapseTable, voxelSize::Tuple) # this is not working due to a DataFrames bug # https://github.com/JuliaData/DataFrames.jl/issues/1862 # we need to add true to make it work as old ways... - @showprogress 1 "transform datatype to Float32..." for (key, value) in DataFrames.eachcol(self, true) + @showprogress 1 "transform datatype to Float32..." for (key, value) in DataFrames.eachcol(self) #if key!=:presyn_wt && key!=:postsyn_wt # self[key] = round.(Int, value) #end diff --git a/test/Neurons.jl b/test/Neurons.jl index 0d8cfac9..baf23fdd 100755 --- a/test/Neurons.jl +++ b/test/Neurons.jl @@ -142,7 +142,7 @@ end println("\nattaching presynapses in DataFrame...") # the default reading of CSV is immutable and the dropmissing will fail! # https://github.com/JuliaData/DataFrames.jl/issues/1393#issuecomment-500019773 - preSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).pre.synapses.csv"); copycols=true) + preSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).pre.synapses.csv"), DataFrame; copycols=true) @time preSynapses = SynapseTables.preprocess(preSynapses, (5,5,45)) println("get ", DataFrames.nrow(preSynapses), " synapses.") @time Neurons.attach_pre_synapses!(neuron, preSynapses) @@ -152,7 +152,7 @@ end @test numPreSynapses > 2 println("\nattaching postsynapses in DataFrame...") - postSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).post.synapses.csv"); copycols=true) + postSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).post.synapses.csv"), DataFrame; copycols=true) @time postSynapses = SynapseTables.preprocess(postSynapses, (5,5,45)) println("get ", DataFrames.nrow(postSynapses), " synapses.") @time Neurons.attach_post_synapses!(neuron, postSynapses) diff --git a/test/Synapses.jl b/test/Synapses.jl index 9d0e726a..668d40f4 100755 --- a/test/Synapses.jl +++ b/test/Synapses.jl @@ -5,7 +5,7 @@ using RealNeuralNetworks.Neurons.Segments.Synapses @testset "test Synapses module" begin df = CSV.read(joinpath(Base.@__DIR__, - "../asset/77625.pre.synapses.csv")) + "../asset/77625.pre.synapses.csv"), DataFrame) synapseList = Vector{Synapse{Float32}}() for row in DataFrames.eachrow(df) push!(synapseList, Synapse(row))