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- [deps.Zygote.extensions] - ZygoteColorsExt = "Colors" - ZygoteDistancesExt = "Distances" - ZygoteTrackerExt = "Tracker" - - [deps.Zygote.weakdeps] - Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" - Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - -[[deps.ZygoteRules]] -deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.3" - -[[deps.cuDNN]] -deps = ["CEnum", "CUDA", "CUDNN_jll"] -git-tree-sha1 = "f65490d187861d6222cb38bcbbff3fd949a7ec3e" -uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" -version = "1.0.4" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+0" - -[[deps.nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" diff --git a/previousVersion/0.0.1/Project.toml b/previousVersion/0.0.1/Project.toml deleted file mode 100644 index d09189f..0000000 --- a/previousVersion/0.0.1/Project.toml +++ /dev/null @@ -1,11 +0,0 @@ -name = "GeneralUtils" -uuid = "c6c72f09-b708-4ac8-ac7c-2084d70108fe" -authors = ["tonaerospace "] -version = "0.1.0" - -[deps] -CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" -DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" -Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" -JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" diff --git a/previousVersion/0.0.1/src/GeneralUtils.jl b/previousVersion/0.0.1/src/GeneralUtils.jl deleted file mode 100644 index a62eb89..0000000 --- a/previousVersion/0.0.1/src/GeneralUtils.jl +++ /dev/null @@ -1,81 +0,0 @@ -module GeneralUtils - - -export noNegative!, randomWithProb, randomChoiceWithProb, findIndex, limitvalue - - -include("interface.jl") -using .interface - - -#------------------------------------------------------------------------------------------------100 - -""" version 0.0.1 - Todo: - - [] - - Change from version: - - - - All features - -""" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -end # generalUtils \ No newline at end of file diff --git a/previousVersion/0.0.1/src/interface.jl b/previousVersion/0.0.1/src/interface.jl deleted file mode 100644 index 6bf67e1..0000000 --- a/previousVersion/0.0.1/src/interface.jl +++ /dev/null @@ -1,813 +0,0 @@ -module interface - - -export noNegative!, randomWithProb, randomChoiceWithProb, findIndex, limitvalue, replaceMoreThan, - replaceLessThan, cartesianAssign!, sumAlongDim3, matMul_3Dto3D_manyTo1batch, - matMul_3Dto4D_batchwise - -using JSON3, DataStructures, Distributions, Flux, CUDA - -#------------------------------------------------------------------------------------------------100 - -noNegative!(a::AbstractVector) = replace!(x -> x < 0 ? 0 : x, a) -findNotZero(x::AbstractVector) = findall( (!iszero).(x) ) -replaceMoreThan(i, target) = i > target ? target : i -replaceLessThan(i, target) = i < target ? target : i -precision(x::Array{<:Array}) = ( std(mean.(x)) / mean(mean.(x)) ) * 100 -precision(x::Array) = std(x) / mean(x) * 100 -replaceAt!(x::AbstractVector, ind::Number, value::Number) = x[ind] = value -notZero(x::AbstractVector) = (!iszero).(x) -Zero(x::AbstractVector) = iszero.(x) -isNan(x::AbstractVector) = isnan.(x) -isInf(x::Number) = abs(x) === Inf -isInf(x::AbstractVector) = isinf.(x) -isLess(x::AbstractVector, target::Number) = isless.(x, target) -isMore(x::Number, target::Number) = x > target -isMore(x::AbstractVector, target::Number) = isMore.(x, target) -absolute(x::AbstractVector) = abs.(x) -vecEleMul(x::AbstractVector, y::AbstractVector) = x .* y -vecEleMul(x::Number, y::AbstractVector) = x .* y -expDecay(initialValue::Number, decayFactor::Number, timePass::Number) = - initialValue * (1 - decayFactor)^timePass -mul!(x::AbstractVector, y::AbstractVector) = x .*= y -mul(x::AbstractVector, y::AbstractVector) = x .* y - -ReLu(x::Number) = max(0, x) - -updateVector!(x::AbstractVector, target::Number) = x .= target -updateVector!(x::AbstractVector, target::AbstractArray) = x .= target - -function selectAdd!(x::AbstractVector, ind::AbstractVector, value::AbstractVector) - @. x = x + (ind * value) -end - - -""" findIndex(input::String, target::Char) - - Find target index inside a collection. - Return 1) Bool array of matched target - 2) CartesianIndex of every matched target -""" -function findIndex(input::String, target::Char) - match_position = [] - for i in input - if i == target - append!(match_position, 1) - else - append!(match_position, 0) - end - end - match_index = findall(isequal.(match_position, 1)) - - return match_position, match_index -end - -function findIndex(input::Array, target::Number) - match_position = isequal.(input, target) - match_index = findall(match_position) - return match_position, match_index -end - -# function findIndex(input::Array, target::Array) -# match_position = isone.(zeros(length(input))) -# for i in target -# match_position = match_position + isequal.(input, i) -# end - -# match_position = replaceMoreThan.(match_position, 1) -# match_index = findall(isone.(match_position)) # Findall donot work with Int64 vector [1, 0, 0, 1]. -# # It only works with BitVector. isone() converts Int64 vector [1, 0, 0, 1] into -# # BitVector [1, 0, 0, 1] - -# return match_position, match_index -# end - -function findIndex(input::Array, target::Symbol) - match_position = isequal.(input, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findIndex(collection::Array{String}, target::String) - match_position = isequal.(collection, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findIndex(collection::Array{String}, target::Array{String}) - match_position = nothing - match_index = nothing - - for i in target - match_pos = isequal.(collection, i) - match_ind = findall(match_pos) - - if match_position === nothing - match_position = match_pos - - else - match_position = hcat(match_position, match_pos) - end - - if match_index === nothing - match_index = match_ind - else - match_index = hcat(match_index, match_ind) - end - end - - return match_position, match_index -end - -function findIndex(collection::OrderedDict, target::Symbol) - collection_keys = keys(collection) - collection_keys_array = [i for i in collection_keys] - match_position = isequal.(collection_keys_array, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findMax(collection::AbstractVector) - maxValue, maxIndex = findmax(collection) - matchPosition = isequal.(collection, maxValue) - return maxValue, maxIndex, matchPosition -end - - - -""" read_textfile_by_index(folder_path::String, read_file_number::Integer=1) - - with multiple text file in a folder, - this function read x_th text file in a folder (filename is sorted by OS) - - # Example - utils.read_textfile_by_index(cleaned_data_path, 2) - read 2nd txt file in a folder -""" -function read_textfile_by_index(folder_path::String, read_file_number::Integer=1) - if isdir(folder_path) - filenumber = length(readdir(folder_path)) - - if read_file_number > filenumber - error("you specified read_file_number = $read_file_number which is out - of range, the cleaned data folder has only $filenumber files") - return nothing, nothing, nothing - else - content = 0 - # open each file in the directory and read - filename = readdir(folder_path, join=true, sort=false)[read_file_number] - f = open(filename) - content = readlines(f) - # content = read(f) - close(f) - end - - return read_file_number, filename, content - else - error("ERROR no file or folder at $folder_path") - return nothing, nothing, nothing - end - -end - -#------------------------------------------------------------------------------------------------100 - -""" Array_to_JSON3_str(data::AbstractArray) - - encode Array to JSON3 String - - # Example - - a = [1.23 4.7889; 9987.1 -123.07; -0.0027 -6.75] - json3_str = Array_to_JSON3_str(a) - - json3_str = {"Array":[1.23,9987.1,-0.0027,4.7889,-123.07,-6.75],"size":[3,2]} -""" -function Array_to_JSON3_str(data::AbstractArray) - d = Dict("Array"=> data, "size"=>size(data)) - json3_str = JSON3.write(d) - return json3_str -end - -#------------------------------------------------------------------------------------------------100 - -""" JSON3_str_to_Array(json3_str::String) - - decode JSON3 String to Array - - # Example - - json3_str = {"Array":[1.23,9987.1,-0.0027,4.7889,-123.07,-6.75],"size":[3,2]} - a = JSON3_str_to_Array(json3_str) - - a = [1.23 4.7889; 9987.1 -123.07; -0.0027 -6.75] -""" -function JSON3_str_to_Array(json3_str::String) - d = JSON3.read(json3_str) - array = reshape(Array(d.Array), (d.size[1], d.size[2])) - return array -end - -#------------------------------------------------------------------------------------------------100 - -""" Convert JSON3.read object to OrderedDict - - # Example - dict = dictionary(["a"=>4, "b"=>6]) - OrDict = OrderedDict(dict) - jsonString = JSON3.write(OrDict) # use jsonString to exchange. One can save it to file or send it thru pub/sub - jsonObject = JSON3.read(jsonString) - OrDict2 = JSON3read_to_OrDict(jsonObject) # example here - Adict2 = dictionary(OrDict2) - - Andyferris's github https://github.com/andyferris/Dictionaries.jl -""" -function JSON3read_to_OrDict(x) - dict = OrderedDict() - for (k, v) in x - k = string(k) - dict[k] = v - end - return dict -end - -#------------------------------------------------------------------------------------------------100 - -""" - print time of cpu executtion at the line inwhich this macro is used -""" -macro timeline(expr) - quote - print("line ", $(__source__.line), ": ") - @time $(esc(expr)) - end -end - - -batchindex(batch_counter::Number, batch_size::Number; offset=0) = - (offset + (batch_counter-1) * batch_size + 1) : offset + (batch_counter * batch_size) - -function flip_true_false(x::Bool) - if x == true - x = false - elseif x == false - x = true - else - error("undefined condition line $(@__LINE__)") - end - - return x -end - -function flip_true_false(x::Int) - if x == 1 - x = 0 - elseif x == 0 - x = 1 - else - throw("not define input of type $(typeof(x)) yet") - end - - return x -end - -""" - Return drawed index - # Example - drawed_index = randomWithProb([0.5, 0.2, 0.3]) - -""" -randomWithProb(probability::AbstractVector) = rand(Distributions.Categorical(probability)) # return drawed index - -""" - Draw from choices according to its probability. - Probability range is 0.0 to 1.0 and all probability must summed up to 1 - (may get probability from NNlib's softmax function) - - # Example - - draw = draw_choices([true, false, nothing], [0.5, 0.2, 0.3]) -""" -function randomChoiceWithProb(choices::Array, probability::Array) - if length(choices) != length(probability) - error("random is not possible, choices array length != probability array length") - elseif sum(probability) != 1.0 - error("probability does not sum to 1.0") - end - - return choices[randomWithProb(probability)] -end - -function randomChoiceOnTarget(target::Number, targetMatch::Number, choices::AbstractVector, - probability::AbstractVector) - if length(choices) != length(probability) - throw("random is not possible, choices array length != probability array length") - end - return target == targetMatch ? randomChoiceWithProb(choices, probability) : target - # dist = Distributions.Categorical(probability) - # draw_result = choices[rand(dist)] -end - -function randomChoiceOnTarget(target::AbstractVector, choiceList::AbstractVector, - probability::AbstractVector) - return randomChoiceOnTarget.(target, 1, (choiceList,), (probability,)) -end - -function linearly_weighted_avg(a::Array) - total = 0.0 - for (i, v) in enumerate(a) - total = total + (i * v) - end - - return total / sum(a) -end - - -""" Convert String that is holded inside a variable to Symbol -# Example -x = "hello" # x is a variable holding String "hello" \n -y = variable_to_symbol(x) # y holds :hello -""" -function variable_str_to_symbol(variable) - semi = :($variable) - symbol = Symbol(semi) - - return symbol -end - - -""" get useable type of specified fieldname inside a composite struct - - # Example - julia> @Base.kwdef mutable struct some_struct - a::Union{Bool, Nothing} = nothing - b::Union{Float64, Nothing} = nothing - c::Union{Int64, AbstractFloat} = 3.5 - d::Union{String, Nothing} = nothing - end - - julia> a = some_struct() - julia> fieldname_useable_type(some_struct, :c) =result=> [Int64, Float64] -""" -function fieldname_useable_type(somestruct, fieldname::Symbol; - test_types=[2.0, 2, true, :h, "str", 'c', missing, nothing])::Vector{DataType} - new_instance = somestruct() - useable_type = [] - - for i in test_types - try - new_instance.:($fieldname) = i - type = typeof(new_instance.:($fieldname)) - if type ∉ useable_type - push!(useable_type, type) - end - catch - - end - end - - return useable_type -end - - -function randomNoRepeat(drawOptions::Array, draw_number::Integer; - exclude_list::Union{AbstractArray,Nothing}=nothing) - draw_option = copy(drawOptions) - draw_option = isnothing(exclude_list) ? draw_option : - filter!(x -> x ∉ exclude_list, draw_option) - shuffle!(draw_option) - drawed_items = [] - while length(drawed_items) < draw_number - push!(drawed_items, pop!(draw_option)) - end - return drawed_items -end - -""" using cron to schedule backup job by - 1. sudo nano /etc/crontab <<< this is a system-wide cron file - 2. to execute julia file @ 2.00am everyday add the following line at the buttom of the file - 0 2 * * * root julia-1.7 /home/syncthing_backup_script.jl - - Requirements using Dates -""" -function folderBackup(sourceFolderAbsolutePath::String, # absolute path to folder to be backuped - backupFolderAbsolutePath::String; # absolute path to folder used to store backup file - totalBackupFiles::Integer=7, # total backup file, the oldest will be deleted - containerName::Union{Array{String}, Nothing}=nothing) # container using source_folder - - sep = (Sys.iswindows() ? "\\" : '/') - - if sourceFolderAbsolutePath[end] == sep - sourceFolderAbsolutePath = sourceFolderAbsolutePath[1:end-1] - end - if backupFolderAbsolutePath[end] != sl - backupFolderAbsolutePath = backupFolderAbsolutePath * sep - end - - if isdir(backupFolderAbsolutePath) - else - mkpath(backupFolderAbsolutePath) - end - - # stop running docker container service - if containerName !== nothing - println("stop running services") - for i in containerName - try run(`docker stop $i`) catch; end - sleep(10) # wait for services to stop - end - end - - # do backup - println("doing backup now") - timestamp = string(Dates.now()) - name = split(sourceFolderAbsolutePath, sep)[end] * "--" - filename = name * timestamp * ".zip" # resulting compressed filename - run(`chmod -R a+rwx $sourceFolderAbsolutePath`) - # zip -r [destination+filename] [source folder to be zipped] - run(`zip -r $(backupFolderAbsolutePath * filename) $sourceFolderAbsolutePath`) - - # check if total backup file is more than user specified, if yes, delete the oldest backup - backupFiles = readdir(backupFolderAbsolutePath) - - while length(backupFiles) > totalBackupFiles - run(`rm $(backupFolderAbsolutePath * backupFiles[1])`) - backupFiles = readdir(backupFolderAbsolutePath) - end - - # start docker services - if containerName !== nothing - println("start services") - for i in containerName - try run(`docker start $i`) catch; end - sleep(10) # wait for services to stop - end - end -end - -function lowerclip!(data::AbstractVector, lowerbound::Number) - replace!(x -> x < lowerbound ? lowerbound : x, data) -end - -function upperclip!(data::AbstractVector, upperbound::Number) - replace!(x -> x > upperbound ? upperbound : x, data) -end - -function normalise(x::AbstractArray, mu, std) - ϵ = oftype(x[1], 1e-5) - μ = mu - # σ = std(x, dims=dims, mean=μ, corrected=false) # use this when Zygote#478 gets merged - σ = std - return (x .- μ) ./ (σ .+ ϵ) -end - -function minMaxScaler(x::AbstractVector) - min = findmin(x)[1] - max = findmax(x)[1] - - scaler(a::Number, min::Number, max::Number) = (a-min) / (max-min) - return scaler.(x, min, max) -end - -""" a = [-1e200, -1e-200, 1e200, 1e-200] \n - result = vtclamp.(a, 1e-6, 1e6, -1e6, -1e-6) -""" -function customclamp(x::Number, poslo::Number, poshi::Number, - neglo::Number, neghi::Number) - signx = sign(x) - if signx == -1 - if neghi < x < 0 - return neghi - elseif x < neglo - return neglo - else - return x - end - elseif signx == +1 - if poshi < x - return poshi - elseif 0 < x < poslo - return poslo - else - return x - end - end -end - -function unitVec(x::AbstractVector) - y = √(sum(x.^2)) - return x./y -end - -function replaceAt!(x::AbstractVector, ind::AbstractVector, value::Number) - for i in ind - x[i] = value - end -end - -function signbitVec(x::AbstractVector) - sign = signbit.(x) * 1 - signVec = replace(s -> s == 0 ? -1 : s, sign) - return signVec -end - -function deleteall!(x::AbstractVector) - for i in 1:length(x) - deleteat!(x, 1) - end -end - -""" Select specific range of vectors in a dict, return a new dict -# Example -dict = Dict(:a => [1:5...], - :b => [6:10...]) - -call -> selectRange(dict, 1:3) -return -> Dict{Any, Any} with 2 entries: - :a => [1, 2, 3] - :b => [6, 7, 8] -""" -function selectRange(d::Dict{Symbol, <:AbstractVector}, range) - newDict = Dict{Symbol, AbstractVector}() - for (k, v) in d - newDict[k] = v[range] - end - - return newDict -end - -""" Assign value to a given Dict by array of keys - - # Example - d = Dict( - :a1=> Dict(:c=> 5), - :a2=> Dict( - :k=> 10, - :b=> Dict( - :s=> "target", - ) - ) - ) - index = [:a2, :b, :s] \n - assignDict!(d, [:a2, :b, :s], "wow") - - return 1 if no target key in a given dict. -""" -function assignDict!(dict::Dict, accessArray::Array{Symbol}, valueToAssign) - wd = nothing - for i in accessArray - println(i) - if i != accessArray[end] - if wd === nothing && haskey(dict, i) - wd = Ref(dict[i]) - elseif wd.x !== nothing && haskey(wd.x, i) - wd = Ref(wd.x[i]) - else - return 1 # error, no target key in a given dict. - end - else - wd.x[i] = valueToAssign - return 0 - end - end -end - -""" convert hour(0-23), minute(0-59) into julia time object -# Example - time -""" -function iTime(h::Integer, m::Integer) - if h == 0 - h = 12 - ampm = "am" - elseif 1 <= h <= 11 - ampm = "am" - elseif h == 12 - ampm = "pm" - elseif 13 <= h <= 23 - h = h - 12 - ampm = "pm" - else - error("hour out of range") - end - - m = m < 10 ? "0$m" : m - t = "$h:$m$ampm" - - return Time(t, "HH:MMp") -end - -""" replace a number according to the limit - if value is lower than lowerbound return lowerbound replacement value - if value is more than upperbound return upperbound replacement value - - # Example - limitvalue(4, (-5 => 0), (5 => 5)) -""" -function limitvalue(v::Number, lowerbound::Pair, upperbound::Pair) - lwLimit, lwReplace = lowerbound - upLimit, upReplace = upperbound - - if v < lwLimit - v = lwReplace - elseif v > upLimit - v = upReplace - else - end - return v -end - -""" ELEMENT-wise multiply of each slice of 3D input matrix ,a, to all slice of 3D another matrix ,b, and - concatenate at the 4th dimension. - - Example - julia> input = rand(32, 32, 128) # batch at 3rd dim - julia> weight = rand(32, 32, 1024) - julia> r = matMul_3Dto3D_manyTo1batch(input, weight); - julia> size(r) - (32, 32, 1024, 128) -""" -function matMul_3Dto3D_manyTo1batch(a::Array, b::Array; resultStorage::Union{Array, Nothing}=nothing) - asize = [size(a)...] - bsize = [size(b)...] - if resultStorage === nothing - resultStorage = similar(a, eltype(b), bsize[1], bsize[2], bsize[3], asize[3]) - end - - c = [slice .* b for slice in eachslice(a, dims=3)] - resultStorage .= cat(c..., dims=4) - - return resultStorage -end -""" GPU version of batchMatEleMul - - Example - julia> using Flux, CUDA - julia> device = Flux.CUDA.functional() ? gpu : cpu - julia> if device == gpu CUDA.device!(0) end - julia> input = rand(32, 32, 128) |> gpu # 128-batches - julia> weight = rand(32, 32, 1024) |> gpu # 1-batch - julia> r = batchMatEleMul_gpu(input, weight); - julia> size(r) - (32, 32, 1024, 128) -""" -function matMul_3Dto3D_manyTo1batch(a::CuArray, b::CuArray; - resultStorage::Union{CuArray, Nothing}=nothing, threads=128) - asize = [size(a)...] - bsize = [size(b)...] - if resultStorage === nothing - resultStorage = similar(a, eltype(b), bsize[1], bsize[2], bsize[3], asize[3]) |> gpu - end - CUDA.@sync begin - @cuda threads=threads matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage) - end - return resultStorage -end -function matMul_3Dto3D_manyTo1batch_gpu!(a::CuArray, b::CuArray, resultStorage::CuArray) - _, _, _, p = size(resultStorage) - - index = threadIdx().x # this example only requires linear indexing, so just use `x` - stride = blockDim().x - for i in index:stride:p - view(resultStorage, :, :, :, i) .= view(a, :, :, i) .* b - end - return nothing -end - -""" ELEMENT-wise multiply of each slice of 3D input matrix ,a, to all batch of another 4D matrix ,b, and - concatenate at the 4th dimension. - - Example - julia> - julia> a = rand(2,2,3) # 3-batches - julia> b = rand(2,2,4,3) # 3-batches - julia> r = GeneralUtils.matMul_3Dto4D_batchwise(a, b); - julia> size(r) - (2, 2, 4, 3) -""" -function matMul_3Dto4D_batchwise(a::Array, b::Array; resultStorage::Union{Array, Nothing}=nothing) - asize = [size(a)...] - bsize = [size(b)...] - if asize[end] != bsize[end] - error("batch number of a and b must be equal") - end - if resultStorage === nothing - resultStorage = zeros(bsize[1], bsize[2], bsize[3], asize[3]) - end - for i in 1:asize[3] - view(resultStorage, :, :, :, i) .= a[:, :, i] .* b[:, :, :, i] - end - return resultStorage -end - -#TODO -function matMul_4Dto4D_batchwise(a::Array, b::Array; - resultStorage::Union{Array, Nothing}=nothing) - error("this function is under constrution") - asize = [size(a)...] - bsize = [size(b)...] - if asize[end] != bsize[end] - error("batch number of a and b must be equal") - end - if resultStorage === nothing - resultStorage = zeros(bsize[1], bsize[2], bsize[3], asize[3]) - end -end - -""" assign matrix b to matrix a according to matrix b's CartesianIndex -""" -cartesianAssign!(a::CuArray, b::CuArray) = @cuda cartesianAssign!(a, b) - -function cartesianAssign!(a, b) - for (i, v) in enumerate(b) - a[CartesianIndices(b)[i].I...] = v - end - return nothing -end - -function sumAlongDim3(a::Array) - totalDim = length(size(a)) - - if totalDim == 3 - d1, d2, d3 = size(a) - r = zeros(1, 1, d3) - for i in 1:d3 - view(r, 1, 1, i) .= sum(a[:, :, i]) - end - elseif totalDim == 4 - 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- [deps.Zygote.extensions] - ZygoteColorsExt = "Colors" - ZygoteDistancesExt = "Distances" - ZygoteTrackerExt = "Tracker" - - [deps.Zygote.weakdeps] - Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" - Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - -[[deps.ZygoteRules]] -deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.3" - -[[deps.cuDNN]] -deps = ["CEnum", "CUDA", "CUDNN_jll"] -git-tree-sha1 = "f65490d187861d6222cb38bcbbff3fd949a7ec3e" -uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" -version = "1.0.4" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+0" - -[[deps.nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" diff --git a/previousVersion/0.0.2/Project.toml b/previousVersion/0.0.2/Project.toml deleted file mode 100644 index d09189f..0000000 --- a/previousVersion/0.0.2/Project.toml +++ /dev/null @@ -1,11 +0,0 @@ -name = "GeneralUtils" -uuid = "c6c72f09-b708-4ac8-ac7c-2084d70108fe" -authors = ["tonaerospace "] -version = "0.1.0" - -[deps] -CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" -DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" -Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" -JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" diff --git a/previousVersion/0.0.2/src/GeneralUtils.jl b/previousVersion/0.0.2/src/GeneralUtils.jl deleted file mode 100644 index 5cd0f5f..0000000 --- a/previousVersion/0.0.2/src/GeneralUtils.jl +++ /dev/null @@ -1,81 +0,0 @@ -module GeneralUtils - - -export noNegative!, randomWithProb, randomChoiceWithProb, findIndex, limitvalue - - -include("interface.jl") -using .interface - - -#------------------------------------------------------------------------------------------------100 - -""" version 0.0.2 - Todo: - - [] - - Change from version: - - - - All features - -""" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -end # generalUtils \ No newline at end of file diff --git a/previousVersion/0.0.2/src/interface.jl b/previousVersion/0.0.2/src/interface.jl deleted file mode 100644 index 74e7edd..0000000 --- a/previousVersion/0.0.2/src/interface.jl +++ /dev/null @@ -1,841 +0,0 @@ -module interface - - -export noNegative!, randomWithProb, randomChoiceWithProb, findIndex, limitvalue, replaceMoreThan, - replaceLessThan, cartesianAssign!, sumAlongDim3, matMul_3Dto3D_manyTo1batch, - matMul_3Dto4D_batchwise - -using JSON3, DataStructures, Distributions, Flux, CUDA - -#------------------------------------------------------------------------------------------------100 - -noNegative!(a::AbstractVector) = replace!(x -> x < 0 ? 0 : x, a) -findNotZero(x::AbstractVector) = findall( (!iszero).(x) ) -replaceMoreThan(i, target) = i > target ? target : i -replaceLessThan(i, target) = i < target ? target : i -precision(x::Array{<:Array}) = ( std(mean.(x)) / mean(mean.(x)) ) * 100 -precision(x::Array) = std(x) / mean(x) * 100 -replaceAt!(x::AbstractVector, ind::Number, value::Number) = x[ind] = value -notZero(x::AbstractVector) = (!iszero).(x) -Zero(x::AbstractVector) = iszero.(x) -isNan(x::AbstractVector) = isnan.(x) -isInf(x::Number) = abs(x) === Inf -isInf(x::AbstractVector) = isinf.(x) -isLess(x::AbstractVector, target::Number) = isless.(x, target) -isMore(x::Number, target::Number) = x > target -isMore(x::AbstractVector, target::Number) = isMore.(x, target) -absolute(x::AbstractVector) = abs.(x) -vecEleMul(x::AbstractVector, y::AbstractVector) = x .* y -vecEleMul(x::Number, y::AbstractVector) = x .* y -expDecay(initialValue::Number, decayFactor::Number, timePass::Number) = - initialValue * (1 - decayFactor)^timePass -mul!(x::AbstractVector, y::AbstractVector) = x .*= y -mul(x::AbstractVector, y::AbstractVector) = x .* y - -ReLu(x::Number) = max(0, x) - -updateVector!(x::AbstractVector, target::Number) = x .= target -updateVector!(x::AbstractVector, target::AbstractArray) = x .= target - -function selectAdd!(x::AbstractVector, ind::AbstractVector, value::AbstractVector) - @. x = x + (ind * value) -end - - -""" findIndex(input::String, target::Char) - - Find target index inside a collection. - Return 1) Bool array of matched target - 2) CartesianIndex of every matched target -""" -function findIndex(input::String, target::Char) - match_position = [] - for i in input - if i == target - append!(match_position, 1) - else - append!(match_position, 0) - end - end - match_index = findall(isequal.(match_position, 1)) - - return match_position, match_index -end - -function findIndex(input::Array, target::Number) - match_position = isequal.(input, target) - match_index = findall(match_position) - return match_position, match_index -end - -# function findIndex(input::Array, target::Array) -# match_position = isone.(zeros(length(input))) -# for i in target -# match_position = match_position + isequal.(input, i) -# end - -# match_position = replaceMoreThan.(match_position, 1) -# match_index = findall(isone.(match_position)) # Findall donot work with Int64 vector [1, 0, 0, 1]. -# # It only works with BitVector. isone() converts Int64 vector [1, 0, 0, 1] into -# # BitVector [1, 0, 0, 1] - -# return match_position, match_index -# end - -function findIndex(input::Array, target::Symbol) - match_position = isequal.(input, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findIndex(collection::Array{String}, target::String) - match_position = isequal.(collection, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findIndex(collection::Array{String}, target::Array{String}) - match_position = nothing - match_index = nothing - - for i in target - match_pos = isequal.(collection, i) - match_ind = findall(match_pos) - - if match_position === nothing - match_position = match_pos - - else - match_position = hcat(match_position, match_pos) - end - - if match_index === nothing - match_index = match_ind - else - match_index = hcat(match_index, match_ind) - end - end - - return match_position, match_index -end - -function findIndex(collection::OrderedDict, target::Symbol) - collection_keys = keys(collection) - collection_keys_array = [i for i in collection_keys] - match_position = isequal.(collection_keys_array, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findMax(collection::AbstractVector) - maxValue, maxIndex = findmax(collection) - matchPosition = isequal.(collection, maxValue) - return maxValue, maxIndex, matchPosition -end - - - -""" read_textfile_by_index(folder_path::String, read_file_number::Integer=1) - - with multiple text file in a folder, - this function read x_th text file in a folder (filename is sorted by OS) - - # Example - utils.read_textfile_by_index(cleaned_data_path, 2) - read 2nd txt file in a folder -""" -function read_textfile_by_index(folder_path::String, read_file_number::Integer=1) - if isdir(folder_path) - filenumber = length(readdir(folder_path)) - - if read_file_number > filenumber - error("you specified read_file_number = $read_file_number which is out - of range, the cleaned data folder has only $filenumber files") - return nothing, nothing, nothing - else - content = 0 - # open each file in the directory and read - filename = readdir(folder_path, join=true, sort=false)[read_file_number] - f = open(filename) - content = readlines(f) - # content = read(f) - close(f) - end - - return read_file_number, filename, content - else - error("ERROR no file or folder at $folder_path") - return nothing, nothing, nothing - end - -end - -#------------------------------------------------------------------------------------------------100 - -""" Array_to_JSON3_str(data::AbstractArray) - - encode Array to JSON3 String - - # Example - - a = [1.23 4.7889; 9987.1 -123.07; -0.0027 -6.75] - json3_str = Array_to_JSON3_str(a) - - json3_str = {"Array":[1.23,9987.1,-0.0027,4.7889,-123.07,-6.75],"size":[3,2]} -""" -function Array_to_JSON3_str(data::AbstractArray) - d = Dict("Array"=> data, "size"=>size(data)) - json3_str = JSON3.write(d) - return json3_str -end - -#------------------------------------------------------------------------------------------------100 - -""" JSON3_str_to_Array(json3_str::String) - - decode JSON3 String to Array - - # Example - - json3_str = {"Array":[1.23,9987.1,-0.0027,4.7889,-123.07,-6.75],"size":[3,2]} - a = JSON3_str_to_Array(json3_str) - - a = [1.23 4.7889; 9987.1 -123.07; -0.0027 -6.75] -""" -function JSON3_str_to_Array(json3_str::String) - d = JSON3.read(json3_str) - array = reshape(Array(d.Array), (d.size[1], d.size[2])) - return array -end - -#------------------------------------------------------------------------------------------------100 - -""" Convert JSON3.read object to OrderedDict - - # Example - dict = dictionary(["a"=>4, "b"=>6]) - OrDict = OrderedDict(dict) - jsonString = JSON3.write(OrDict) # use jsonString to exchange. One can save it to file or send it thru pub/sub - jsonObject = JSON3.read(jsonString) - OrDict2 = JSON3read_to_OrDict(jsonObject) # example here - Adict2 = dictionary(OrDict2) - - Andyferris's github https://github.com/andyferris/Dictionaries.jl -""" -function JSON3read_to_OrDict(x) - dict = OrderedDict() - for (k, v) in x - k = string(k) - dict[k] = v - end - return dict -end - -#------------------------------------------------------------------------------------------------100 - -""" - print time of cpu executtion at the line inwhich this macro is used -""" -macro timeline(expr) - quote - print("line ", $(__source__.line), ": ") - @time $(esc(expr)) - end -end - - -batchindex(batch_counter::Number, batch_size::Number; offset=0) = - (offset + (batch_counter-1) * batch_size + 1) : offset + (batch_counter * batch_size) - -function flip_true_false(x::Bool) - if x == true - x = false - elseif x == false - x = true - else - error("undefined condition line $(@__LINE__)") - end - - return x -end - -function flip_true_false(x::Int) - if x == 1 - x = 0 - elseif x == 0 - x = 1 - else - throw("not define input of type $(typeof(x)) yet") - end - - return x -end - -""" - Return drawed index - # Example - drawed_index = randomWithProb([0.5, 0.2, 0.3]) - -""" -randomWithProb(probability::AbstractVector) = rand(Distributions.Categorical(probability)) # return drawed index - -""" - Draw from choices according to its probability. - Probability range is 0.0 to 1.0 and all probability must summed up to 1 - (may get probability from NNlib's softmax function) - - # Example - - draw = draw_choices([true, false, nothing], [0.5, 0.2, 0.3]) -""" -function randomChoiceWithProb(choices::Array, probability::Array) - if length(choices) != length(probability) - error("random is not possible, choices array length != probability array length") - elseif sum(probability) != 1.0 - error("probability does not sum to 1.0") - end - - return choices[randomWithProb(probability)] -end - -function randomChoiceOnTarget(target::Number, targetMatch::Number, choices::AbstractVector, - probability::AbstractVector) - if length(choices) != length(probability) - throw("random is not possible, choices array length != probability array length") - end - return target == targetMatch ? randomChoiceWithProb(choices, probability) : target - # dist = Distributions.Categorical(probability) - # draw_result = choices[rand(dist)] -end - -function randomChoiceOnTarget(target::AbstractVector, choiceList::AbstractVector, - probability::AbstractVector) - return randomChoiceOnTarget.(target, 1, (choiceList,), (probability,)) -end - -function linearly_weighted_avg(a::Array) - total = 0.0 - for (i, v) in enumerate(a) - total = total + (i * v) - end - - return total / sum(a) -end - - -""" Convert String that is holded inside a variable to Symbol -# Example -x = "hello" # x is a variable holding String "hello" \n -y = variable_to_symbol(x) # y holds :hello -""" -function variable_str_to_symbol(variable) - semi = :($variable) - symbol = Symbol(semi) - - return symbol -end - - -""" get useable type of specified fieldname inside a composite struct - - # Example - julia> @Base.kwdef mutable struct some_struct - a::Union{Bool, Nothing} = nothing - b::Union{Float64, Nothing} = nothing - c::Union{Int64, AbstractFloat} = 3.5 - d::Union{String, Nothing} = nothing - end - - julia> a = some_struct() - julia> fieldname_useable_type(some_struct, :c) =result=> [Int64, Float64] -""" -function fieldname_useable_type(somestruct, fieldname::Symbol; - test_types=[2.0, 2, true, :h, "str", 'c', missing, nothing])::Vector{DataType} - new_instance = somestruct() - useable_type = [] - - for i in test_types - try - new_instance.:($fieldname) = i - type = typeof(new_instance.:($fieldname)) - if type ∉ useable_type - push!(useable_type, type) - end - catch - - end - end - - return useable_type -end - - -function randomNoRepeat(drawOptions::Array, draw_number::Integer; - exclude_list::Union{AbstractArray,Nothing}=nothing) - draw_option = copy(drawOptions) - draw_option = isnothing(exclude_list) ? draw_option : - filter!(x -> x ∉ exclude_list, draw_option) - shuffle!(draw_option) - drawed_items = [] - while length(drawed_items) < draw_number - push!(drawed_items, pop!(draw_option)) - end - return drawed_items -end - -""" using cron to schedule backup job by - 1. sudo nano /etc/crontab <<< this is a system-wide cron file - 2. to execute julia file @ 2.00am everyday add the following line at the buttom of the file - 0 2 * * * root julia-1.7 /home/syncthing_backup_script.jl - - Requirements using Dates -""" -function folderBackup(sourceFolderAbsolutePath::String, # absolute path to folder to be backuped - backupFolderAbsolutePath::String; # absolute path to folder used to store backup file - totalBackupFiles::Integer=7, # total backup file, the oldest will be deleted - containerName::Union{Array{String}, Nothing}=nothing) # container using source_folder - - sep = (Sys.iswindows() ? "\\" : '/') - - if sourceFolderAbsolutePath[end] == sep - sourceFolderAbsolutePath = sourceFolderAbsolutePath[1:end-1] - end - if backupFolderAbsolutePath[end] != sl - backupFolderAbsolutePath = backupFolderAbsolutePath * sep - end - - if isdir(backupFolderAbsolutePath) - else - mkpath(backupFolderAbsolutePath) - end - - # stop running docker container service - if containerName !== nothing - println("stop running services") - for i in containerName - try run(`docker stop $i`) catch; end - sleep(10) # wait for services to stop - end - end - - # do backup - println("doing backup now") - timestamp = string(Dates.now()) - name = split(sourceFolderAbsolutePath, sep)[end] * "--" - filename = name * timestamp * ".zip" # resulting compressed filename - run(`chmod -R a+rwx $sourceFolderAbsolutePath`) - # zip -r [destination+filename] [source folder to be zipped] - run(`zip -r $(backupFolderAbsolutePath * filename) $sourceFolderAbsolutePath`) - - # check if total backup file is more than user specified, if yes, delete the oldest backup - backupFiles = readdir(backupFolderAbsolutePath) - - while length(backupFiles) > totalBackupFiles - run(`rm $(backupFolderAbsolutePath * backupFiles[1])`) - backupFiles = readdir(backupFolderAbsolutePath) - end - - # start docker services - if containerName !== nothing - println("start services") - for i in containerName - try run(`docker start $i`) catch; end - sleep(10) # wait for services to stop - end - end -end - -function lowerclip!(data::AbstractVector, lowerbound::Number) - replace!(x -> x < lowerbound ? lowerbound : x, data) -end - -function upperclip!(data::AbstractVector, upperbound::Number) - replace!(x -> x > upperbound ? upperbound : x, data) -end - -function normalise(x::AbstractArray, mu, std) - ϵ = oftype(x[1], 1e-5) - μ = mu - # σ = std(x, dims=dims, mean=μ, corrected=false) # use this when Zygote#478 gets merged - σ = std - return (x .- μ) ./ (σ .+ ϵ) -end - -function minMaxScaler(x::AbstractVector) - min = findmin(x)[1] - max = findmax(x)[1] - - scaler(a::Number, min::Number, max::Number) = (a-min) / (max-min) - return scaler.(x, min, max) -end - -""" a = [-1e200, -1e-200, 1e200, 1e-200] \n - result = vtclamp.(a, 1e-6, 1e6, -1e6, -1e-6) -""" -function customclamp(x::Number, poslo::Number, poshi::Number, - neglo::Number, neghi::Number) - signx = sign(x) - if signx == -1 - if neghi < x < 0 - return neghi - elseif x < neglo - return neglo - else - return x - end - elseif signx == +1 - if poshi < x - return poshi - elseif 0 < x < poslo - return poslo - else - return x - end - end -end - -function unitVec(x::AbstractVector) - y = √(sum(x.^2)) - return x./y -end - -function replaceAt!(x::AbstractVector, ind::AbstractVector, value::Number) - for i in ind - x[i] = value - end -end - -function signbitVec(x::AbstractVector) - sign = signbit.(x) * 1 - signVec = replace(s -> s == 0 ? -1 : s, sign) - return signVec -end - -function deleteall!(x::AbstractVector) - for i in 1:length(x) - deleteat!(x, 1) - end -end - -""" Select specific range of vectors in a dict, return a new dict -# Example -dict = Dict(:a => [1:5...], - :b => [6:10...]) - -call -> selectRange(dict, 1:3) -return -> Dict{Any, Any} with 2 entries: - :a => [1, 2, 3] - :b => [6, 7, 8] -""" -function selectRange(d::Dict{Symbol, <:AbstractVector}, range) - newDict = Dict{Symbol, AbstractVector}() - for (k, v) in d - newDict[k] = v[range] - end - - return newDict -end - -""" Assign value to a given Dict by array of keys - - # Example - d = Dict( - :a1=> Dict(:c=> 5), - :a2=> Dict( - :k=> 10, - :b=> Dict( - :s=> "target", - ) - ) - ) - index = [:a2, :b, :s] \n - assignDict!(d, [:a2, :b, :s], "wow") - - return 1 if no target key in a given dict. -""" -function assignDict!(dict::Dict, accessArray::Array{Symbol}, valueToAssign) - wd = nothing - for i in accessArray - println(i) - if i != accessArray[end] - if wd === nothing && haskey(dict, i) - wd = Ref(dict[i]) - elseif wd.x !== nothing && haskey(wd.x, i) - wd = Ref(wd.x[i]) - else - return 1 # error, no target key in a given dict. - end - else - wd.x[i] = valueToAssign - return 0 - end - end -end - -""" convert hour(0-23), minute(0-59) into julia time object -# Example - time -""" -function iTime(h::Integer, m::Integer) - if h == 0 - h = 12 - ampm = "am" - elseif 1 <= h <= 11 - ampm = "am" - elseif h == 12 - ampm = "pm" - elseif 13 <= h <= 23 - h = h - 12 - ampm = "pm" - else - error("hour out of range") - end - - m = m < 10 ? "0$m" : m - t = "$h:$m$ampm" - - return Time(t, "HH:MMp") -end - -""" replace a number according to the limit - if value is lower than lowerbound return lowerbound replacement value - if value is more than upperbound return upperbound replacement value - - # Example - limitvalue(4, (-5 => 0), (5 => 5)) -""" -function limitvalue(v::Number, lowerbound::Pair, upperbound::Pair) - lwLimit, lwReplace = lowerbound - upLimit, upReplace = upperbound - - if v < lwLimit - v = lwReplace - elseif v > upLimit - v = upReplace - else - end - return v -end - -""" assign matrix b to matrix a according to matrix b's CartesianIndex -""" -cartesianAssign!(a::CuArray, b::CuArray) = @cuda cartesianAssign!(a, b) - -function cartesianAssign!(a, b) - for (i, v) in enumerate(b) - a[CartesianIndices(b)[i].I...] = v - end - return nothing -end - -function sumAlongDim3(a::Array) - totalDim = length(size(a)) - - if totalDim == 3 - d1, d2, d3 = size(a) - r = zeros(1, 1, d3) - for i in 1:d3 - view(r, 1, 1, i) .= sum(a[:, :, i]) - end - elseif totalDim == 4 - d1, d2, d3, d4 = size(a) - r = zeros(1, 1, d3, d4) - for j in 1:d4 - for i in 1:d3 - view(r, 1, 1, i, j) .= sum(a[:, :, i, j]) - end - end - else - error("this condition is not define yet") - end - - return r -end - - -""" ELEMENT-wise multiply of each slice of 3D input matrix ,a, to all slice of 3D another matrix ,b, and - concatenate at the 4th dimension. - - Example - julia> input = rand(32, 32, 128) # batch at 3rd dim - julia> weight = rand(32, 32, 1024) - julia> r = matMul_3Dto3D_manyTo1batch(input, weight); - julia> size(r) - (32, 32, 1024, 128) -""" -function matMul_3Dto3D_manyTo1batch(a::Array, b::Array; resultStorage::Union{Array, Nothing}=nothing) - asize = [size(a)...] - bsize = [size(b)...] - if resultStorage === nothing - resultStorage = similar(a, eltype(b), bsize[1], bsize[2], bsize[3], asize[3]) - end - - c = [slice .* b for slice in eachslice(a, dims=3)] - resultStorage .= cat(c..., dims=4) - - return resultStorage -end - -# function matMul_3Dto3D_manyTo1batch(a::CuArray, b::CuArray; # XXX working code -# resultStorage::Union{CuArray, Nothing}=nothing, threads=256) -# asize = [size(a)...] -# bsize = [size(b)...] -# if resultStorage === nothing -# resultStorage = similar(a, eltype(b), bsize[1], bsize[2], bsize[3], asize[3]) |> gpu -# end -# CUDA.@sync begin -# @cuda threads=threads matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage) -# end -# return resultStorage -# end - -# function matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage) # XXX working code -# _, _, _, p = size(resultStorage) - -# index = threadIdx().x # this example only requires linear indexing, so just use `x` -# stride = blockDim().x -# for i in index:stride:p -# view(resultStorage, :, :, :, i) .= view(a, :, :, i) .* b -# end -# return nothing -# end - -""" GPU kernel -""" -function matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage) - _, _, batch = size(a) # This kernel use 1 thread per batch - i = (blockIdx().x - 1) * blockDim().x + threadIdx().x - if i <= batch # guard against unused threads to accessing memory out of bound - # @cuprintln("thread $i") - view(resultStorage, :, :, :, i) .= view(a, :, :, i) .* b - end - return nothing -end - -""" GPU version of batchMatEleMul - - Example - julia> using Flux, CUDA - julia> device = Flux.CUDA.functional() ? gpu : cpu - julia> if device == gpu CUDA.device!(0) end - julia> input = rand(32, 32, 128) |> gpu; # 128-batches - julia> weight = rand(32, 32, 1024) |> gpu; # 1-batch - julia> r = matMul_3Dto3D_manyTo1batch(input, weight); - julia> size(r) - (32, 32, 1024, 128) -""" -function matMul_3Dto3D_manyTo1batch(a::CuArray, b::CuArray; - resultStorage::Union{CuArray, Nothing}=nothing) - asize = [size(a)...] - bsize = [size(b)...] - if resultStorage === nothing - resultStorage = similar(a, eltype(b), bsize[1], bsize[2], bsize[3], asize[3]) |> gpu - end - - kernel = @cuda launch=false matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage) - config = launch_configuration(kernel.fun) - - # threads to be launched. Since one can't launch exact thread number the kernel needs, - # one just launch threads more than this kernel needs then use a guard inside the kernel - # to prevent unused threads to access memory. - threads = min(1024, config.threads) # most NVIDIA gpu has 1024 threads per block - blocks = cld(asize[3], threads) # This kernel use 1 thread per batch - - CUDA.@sync begin - kernel(a, b, resultStorage; threads, blocks) - end - return resultStorage -end - - - - -""" ELEMENT-wise multiply of each slice of 3D input matrix ,a, to all batch of another 4D matrix ,b, and - concatenate at the 4th dimension. - - Example - julia> - julia> a = rand(2,2,3) # 3-batches - julia> b = rand(2,2,4,3) # 3-batches - julia> r = GeneralUtils.matMul_3Dto4D_batchwise(a, b); - julia> size(r) - (2, 2, 4, 3) -""" -function matMul_3Dto4D_batchwise(a::Array, b::Array; resultStorage::Union{Array, Nothing}=nothing) - asize = [size(a)...] - bsize = [size(b)...] - if asize[end] != bsize[end] - error("batch number of a and b must be equal") - end - if resultStorage === nothing - resultStorage = zeros(bsize[1], bsize[2], bsize[3], asize[3]) - end - for i in 1:asize[3] - view(resultStorage, :, :, :, i) .= a[:, :, i] .* b[:, :, :, i] - end - return resultStorage -end - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -end # module \ No newline at end of file diff --git a/previousVersion/0.0.2/test/etc.jl b/previousVersion/0.0.2/test/etc.jl deleted file mode 100644 index e69de29..0000000 diff --git a/previousVersion/0.0.3/Manifest.toml b/previousVersion/0.0.3/Manifest.toml deleted file mode 100644 index e23be4a..0000000 --- a/previousVersion/0.0.3/Manifest.toml +++ /dev/null @@ -1,911 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.9.2" -manifest_format = "2.0" -project_hash = "168be3100b37ab8a45dff337b2c1caa16b5ecd26" - -[[deps.AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "8bc0aaec0ca548eb6cf5f0d7d16351650c1ee956" -uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.3.2" -weakdeps = ["ChainRulesCore"] - 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-[deps] -CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" -DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" -Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" -JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/previousVersion/0.0.3/src/GeneralUtils.jl b/previousVersion/0.0.3/src/GeneralUtils.jl deleted file mode 100644 index 23c07c9..0000000 --- a/previousVersion/0.0.3/src/GeneralUtils.jl +++ /dev/null @@ -1,81 +0,0 @@ -module GeneralUtils - - -export noNegative!, randomWithProb, randomChoiceWithProb, findIndex, limitvalue - - -include("interface.jl") -using .interface - - -#------------------------------------------------------------------------------------------------100 - -""" version 0.0.3 - Todo: - - [*1] cartesianAssign for different matrix dimension - - Change from version: 0.0.2 - - - - All features - -""" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -end # generalUtils \ No newline at end of file diff --git a/previousVersion/0.0.3/src/interface.jl b/previousVersion/0.0.3/src/interface.jl deleted file mode 100644 index ca3f56b..0000000 --- a/previousVersion/0.0.3/src/interface.jl +++ /dev/null @@ -1,1108 +0,0 @@ -module interface - - -export noNegative!, randomWithProb, randomChoiceWithProb, findIndex, limitvalue, replaceMoreThan, - replaceLessThan, replaceBetween, cartesianAssign!, sumAlongDim3, matMul_3Dto3D_manyTo1batch, - matMul_3Dto4D_batchwise, isNotEqual, linear_to_cartesian, vectorMax, - multiply_last, multiply_random_elements, replaceElements, replaceElements!, isBetween, - isLess, allTrue, getStringBetweenCharacters - -using JSON3, DataStructures, Distributions, Flux, CUDA, Random - -#------------------------------------------------------------------------------------------------100 - -noNegative!(a::AbstractVector) = replace!(x -> x < 0 ? 0 : x, a) -findNotZero(x::AbstractVector) = findall( (!iszero).(x) ) -replaceMoreThan(x, target, replaceValue) = x > target ? replaceValue : x -replaceMoreThan(x, target, a, b) = x > target ? a : b -replaceLessThan(x, target, replaceValue) = x < target ? replaceValue : x -replaceLessThan(x, target, a, b) = x < target ? a : b -replaceBetween(x, lowerbound, upperbound, replaceValue) = lowerbound < x < upperbound ? replaceValue : x -precision(x::Array{<:Array}) = ( std(mean.(x)) / mean(mean.(x)) ) * 100 -precision(x::Array) = std(x) / mean(x) * 100 -replaceAt!(x::AbstractVector, ind::Number, value::Number) = x[ind] = value -notZero(x::AbstractVector) = (!iszero).(x) -Zero(x::AbstractVector) = iszero.(x) -isNan(x::AbstractVector) = isnan.(x) -isInf(x::Number) = abs(x) === Inf -isInf(x::AbstractVector) = isinf.(x) -isNotEqual(x::Number, target::Number) = isequal(isequal(x, target), 0) -isBetween(x, lowerlimit, upperlimit) = lowerlimit < x < upperlimit ? true : false -absolute(x::AbstractVector) = abs.(x) -vecEleMul(x::AbstractVector, y::AbstractVector) = x .* y -vecEleMul(x::Number, y::AbstractVector) = x .* y -expDecay(initialValue::Number, decayFactor::Number, timePass::Number) = - initialValue * (1 - decayFactor)^timePass -mul!(x::AbstractVector, y::AbstractVector) = x .*= y -mul(x::AbstractVector, y::AbstractVector) = x .* y -allTrue(args...) = false ∈ [args...] ? false : true - -ReLu(x::Number) = max(0, x) - -updateVector!(x::AbstractVector, target::Number) = x .= target -updateVector!(x::AbstractVector, target::AbstractArray) = x .= target - -function selectAdd!(x::AbstractVector, ind::AbstractVector, value::AbstractVector) - @. x = x + (ind * value) -end - - - -""" FindIndex(input::String, target::Char) - - Arguments: - text, input text - target, target character - Return: - (a bool vector of match/not match, position vector of the matched) - - Example: - ```jldoctest - julia> using GeneralUtils - julia> text = "Hello World!" - julia> findIndex(text, 'l') - (Bool[0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0], [3, 4, 10]) - ``` -""" -function findIndex(text::String, target::Char) - charlist = [i for i in text] - match_position = isequal.(charlist, target) - match_index = findall(isequal.(match_position, 1)) - - return match_position, match_index -end - -function findIndex(input::Array, target::Number) - match_position = isequal.(input, target) - match_index = findall(match_position) - return match_position, match_index -end - -# function findIndex(input::Array, target::Array) -# match_position = isone.(zeros(length(input))) -# for i in target -# match_position = match_position + isequal.(input, i) -# end - -# match_position = replaceMoreThan.(match_position, 1) -# match_index = findall(isone.(match_position)) # Findall donot work with Int64 vector [1, 0, 0, 1]. -# # It only works with BitVector. isone() converts Int64 vector [1, 0, 0, 1] into -# # BitVector [1, 0, 0, 1] - -# return match_position, match_index -# end - -function findIndex(input::Array, target::Symbol) - match_position = isequal.(input, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findIndex(collection::Array{String}, target::String) - match_position = isequal.(collection, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findIndex(collection::Array{String}, target::Array{String}) - match_position = nothing - match_index = nothing - - for i in target - match_pos = isequal.(collection, i) - match_ind = findall(match_pos) - - if match_position === nothing - match_position = match_pos - - else - match_position = hcat(match_position, match_pos) - end - - if match_index === nothing - match_index = match_ind - else - match_index = hcat(match_index, match_ind) - end - end - - return match_position, match_index -end - -function findIndex(collection::OrderedDict, target::Symbol) - collection_keys = keys(collection) - collection_keys_array = [i for i in collection_keys] - match_position = isequal.(collection_keys_array, target) - match_index = findall(match_position) - - return match_position, match_index -end - -function findMax(collection::AbstractVector) - maxValue, maxIndex = findmax(collection) - matchPosition = isequal.(collection, maxValue) - return maxValue, maxIndex, matchPosition -end - - - -""" read_textfile_by_index(folder_path::String, read_file_number::Integer=1) - - with multiple text file in a folder, - this function read x_th text file in a folder (filename is sorted by OS) - - # Example - utils.read_textfile_by_index(cleaned_data_path, 2) - read 2nd txt file in a folder -""" -function read_textfile_by_index(folder_path::String, read_file_number::Integer=1) - if isdir(folder_path) - filenumber = length(readdir(folder_path)) - - if read_file_number > filenumber - error("you specified read_file_number = $read_file_number which is out - of range, the cleaned data folder has only $filenumber files") - return nothing, nothing, nothing - else - content = 0 - # open each file in the directory and read - filename = readdir(folder_path, join=true, sort=false)[read_file_number] - f = open(filename) - content = readlines(f) - # content = read(f) - close(f) - end - - return read_file_number, filename, content - else - error("ERROR no file or folder at $folder_path") - return nothing, nothing, nothing - end - -end - -#------------------------------------------------------------------------------------------------100 - -""" Array_to_JSON3_str(data::AbstractArray) - - encode Array to JSON3 String - - # Example - - a = [1.23 4.7889; 9987.1 -123.07; -0.0027 -6.75] - json3_str = Array_to_JSON3_str(a) - - json3_str = {"Array":[1.23,9987.1,-0.0027,4.7889,-123.07,-6.75],"size":[3,2]} -""" -function Array_to_JSON3_str(data::AbstractArray) - d = Dict("Array"=> data, "size"=>size(data)) - json3_str = JSON3.write(d) - return json3_str -end - -#------------------------------------------------------------------------------------------------100 - -""" JSON3_str_to_Array(json3_str::String) - - decode JSON3 String to Array - - # Example - - json3_str = {"Array":[1.23,9987.1,-0.0027,4.7889,-123.07,-6.75],"size":[3,2]} - a = JSON3_str_to_Array(json3_str) - - a = [1.23 4.7889; 9987.1 -123.07; -0.0027 -6.75] -""" -function JSON3_str_to_Array(json3_str::String) - d = JSON3.read(json3_str) - array = reshape(Array(d.Array), (d.size[1], d.size[2])) - return array -end - -#------------------------------------------------------------------------------------------------100 - -""" Convert JSON3.read object to OrderedDict - - # Example - dict = dictionary(["a"=>4, "b"=>6]) - OrDict = OrderedDict(dict) - jsonString = JSON3.write(OrDict) # use jsonString to exchange. One can save it to file or send it thru pub/sub - jsonObject = JSON3.read(jsonString) - OrDict2 = JSON3read_to_OrDict(jsonObject) # example here - Adict2 = dictionary(OrDict2) - - Andyferris's github https://github.com/andyferris/Dictionaries.jl -""" -function JSON3read_to_OrDict(x) - dict = OrderedDict() - for (k, v) in x - k = string(k) - dict[k] = v - end - return dict -end - -#------------------------------------------------------------------------------------------------100 - -""" - print time of cpu executtion at the line inwhich this macro is used -""" -macro timeline(expr) - quote - print("line ", $(__source__.line), ": ") - @time $(esc(expr)) - end -end - - -batchindex(batch_counter::Number, batch_size::Number; offset=0) = - (offset + (batch_counter-1) * batch_size + 1) : offset + (batch_counter * batch_size) - -function flip_true_false(x::Bool) - if x == true - x = false - elseif x == false - x = true - else - error("undefined condition line $(@__LINE__)") - end - - return x -end - -function flip_true_false(x::Int) - if x == 1 - x = 0 - elseif x == 0 - x = 1 - else - throw("not define input of type $(typeof(x)) yet") - end - - return x -end - -""" - Return drawed index - # Example - drawed_index = randomWithProb([0.5, 0.2, 0.3]) - -""" -randomWithProb(probability::AbstractVector) = rand(Distributions.Categorical(probability)) # return drawed index - -""" - Draw from choices according to its probability. - Probability range is 0.0 to 1.0 and all probability must summed up to 1 - (may get probability from NNlib's softmax function) - - # Example - - draw = randomChoiceWithProb([true, false, nothing], [0.5, 0.2, 0.3]) -""" -function randomChoiceWithProb(choices::Array, probability::Array) - if length(choices) != length(probability) - error("random is not possible, choices array length != probability array length") - elseif sum(probability) != 1.0 - error("probability does not sum to 1.0") - end - - return choices[randomWithProb(probability)] -end - -function randomChoiceOnTarget(target::Number, targetMatch::Number, choices::AbstractVector, - probability::AbstractVector) - if length(choices) != length(probability) - throw("random is not possible, choices array length != probability array length") - end - return target == targetMatch ? randomChoiceWithProb(choices, probability) : target - # dist = Distributions.Categorical(probability) - # draw_result = choices[rand(dist)] -end - -function randomChoiceOnTarget(target::AbstractVector, choiceList::AbstractVector, - probability::AbstractVector) - return randomChoiceOnTarget.(target, 1, (choiceList,), (probability,)) -end - -function linearly_weighted_avg(a::Array) - total = 0.0 - for (i, v) in enumerate(a) - total = total + (i * v) - end - - return total / sum(a) -end - - -""" Convert String that is holded inside a variable to Symbol -# Example -x = "hello" # x is a variable holding String "hello" \n -y = variable_to_symbol(x) # y holds :hello -""" -function variable_str_to_symbol(variable) - semi = :($variable) - symbol = Symbol(semi) - - return symbol -end - - -""" get useable type of specified fieldname inside a composite struct - - # Example - julia> @Base.kwdef mutable struct some_struct - a::Union{Bool, Nothing} = nothing - b::Union{Float64, Nothing} = nothing - c::Union{Int64, AbstractFloat} = 3.5 - d::Union{String, Nothing} = nothing - end - - julia> a = some_struct() - julia> fieldname_useable_type(some_struct, :c) =result=> [Int64, Float64] -""" -function fieldname_useable_type(somestruct, fieldname::Symbol; - test_types=[2.0, 2, true, :h, "str", 'c', missing, nothing])::Vector{DataType} - new_instance = somestruct() - useable_type = [] - - for i in test_types - try - new_instance.:($fieldname) = i - type = typeof(new_instance.:($fieldname)) - if type ∉ useable_type - push!(useable_type, type) - end - catch - - end - end - - return useable_type -end - - -function randomNoRepeat(drawOptions::Array, draw_number::Integer; - exclude_list::Union{AbstractArray,Nothing}=nothing) - draw_option = copy(drawOptions) - draw_option = isnothing(exclude_list) ? draw_option : - filter!(x -> x ∉ exclude_list, draw_option) - shuffle!(draw_option) - drawed_items = [] - while length(drawed_items) < draw_number - push!(drawed_items, pop!(draw_option)) - end - return drawed_items -end - -""" using cron to schedule backup job by - 1. sudo nano /etc/crontab <<< this is a system-wide cron file - 2. to execute julia file @ 2.00am everyday add the following line at the buttom of the file - 0 2 * * * root julia-1.7 /home/syncthing_backup_script.jl - - Requirements using Dates -""" -function folderBackup(sourceFolderAbsolutePath::String, # absolute path to folder to be backuped - backupFolderAbsolutePath::String; # absolute path to folder used to store backup file - totalBackupFiles::Integer=7, # total backup file, the oldest will be deleted - containerName::Union{Array{String}, Nothing}=nothing) # container using source_folder - - sep = (Sys.iswindows() ? "\\" : '/') - - if sourceFolderAbsolutePath[end] == sep - sourceFolderAbsolutePath = sourceFolderAbsolutePath[1:end-1] - end - if backupFolderAbsolutePath[end] != sl - backupFolderAbsolutePath = backupFolderAbsolutePath * sep - end - - if isdir(backupFolderAbsolutePath) - else - mkpath(backupFolderAbsolutePath) - end - - # stop running docker container service - if containerName !== nothing - println("stop running services") - for i in containerName - try run(`docker stop $i`) catch; end - sleep(10) # wait for services to stop - end - end - - # do backup - println("doing backup now") - timestamp = string(Dates.now()) - name = split(sourceFolderAbsolutePath, sep)[end] * "--" - filename = name * timestamp * ".zip" # resulting compressed filename - run(`chmod -R a+rwx $sourceFolderAbsolutePath`) - # zip -r [destination+filename] [source folder to be zipped] - run(`zip -r $(backupFolderAbsolutePath * filename) $sourceFolderAbsolutePath`) - - # check if total backup file is more than user specified, if yes, delete the oldest backup - backupFiles = readdir(backupFolderAbsolutePath) - - while length(backupFiles) > totalBackupFiles - run(`rm $(backupFolderAbsolutePath * backupFiles[1])`) - backupFiles = readdir(backupFolderAbsolutePath) - end - - # start docker services - if containerName !== nothing - println("start services") - for i in containerName - try run(`docker start $i`) catch; end - sleep(10) # wait for services to stop - end - end -end - -function lowerclip!(data::AbstractVector, lowerbound::Number) - replace!(x -> x < lowerbound ? lowerbound : x, data) -end - -function upperclip!(data::AbstractVector, upperbound::Number) - replace!(x -> x > upperbound ? upperbound : x, data) -end - -function normalise(x::AbstractArray, mu, std) - ϵ = oftype(x[1], 1e-5) - μ = mu - # σ = std(x, dims=dims, mean=μ, corrected=false) # use this when Zygote#478 gets merged - σ = std - return (x .- μ) ./ (σ .+ ϵ) -end - -function minMaxScaler(x::AbstractVector) - min = findmin(x)[1] - max = findmax(x)[1] - - scaler(a::Number, min::Number, max::Number) = (a-min) / (max-min) - return scaler.(x, min, max) -end - -""" a = [-1e200, -1e-200, 1e200, 1e-200] \n - result = vtclamp.(a, 1e-6, 1e6, -1e6, -1e-6) -""" -function customclamp(x::Number, poslo::Number, poshi::Number, - neglo::Number, neghi::Number) - signx = sign(x) - if signx == -1 - if neghi < x < 0 - return neghi - elseif x < neglo - return neglo - else - return x - end - elseif signx == +1 - if poshi < x - return poshi - elseif 0 < x < poslo - return poslo - else - return x - end - end -end - -function unitVec(x::AbstractVector) - y = √(sum(x.^2)) - return x./y -end - -function replaceAt!(x::AbstractVector, ind::AbstractVector, value::Number) - for i in ind - x[i] = value - end -end - -function signbitVec(x::AbstractVector) - sign = signbit.(x) * 1 - signVec = replace(s -> s == 0 ? -1 : s, sign) - return signVec -end - -function deleteall!(x::AbstractVector) - for i in 1:length(x) - deleteat!(x, 1) - end -end - -""" Select specific range of vectors in a dict, return a new dict -# Example -dict = Dict(:a => [1:5...], - :b => [6:10...]) - -call -> selectRange(dict, 1:3) -return -> Dict{Any, Any} with 2 entries: - :a => [1, 2, 3] - :b => [6, 7, 8] -""" -function selectRange(d::Dict{Symbol, <:AbstractVector}, range) - newDict = Dict{Symbol, AbstractVector}() - for (k, v) in d - newDict[k] = v[range] - end - - return newDict -end - -""" Assign value to a given Dict by array of keys - - # Example - d = Dict( - :a1=> Dict(:c=> 5), - :a2=> Dict( - :k=> 10, - :b=> Dict( - :s=> "target", - ) - ) - ) - index = [:a2, :b, :s] \n - assignDict!(d, [:a2, :b, :s], "wow") - - return 1 if no target key in a given dict. -""" -function assignDict!(dict::Dict, accessArray::Array{Symbol}, valueToAssign) - wd = nothing - for i in accessArray - println(i) - if i != accessArray[end] - if wd === nothing && haskey(dict, i) - wd = Ref(dict[i]) - elseif wd.x !== nothing && haskey(wd.x, i) - wd = Ref(wd.x[i]) - else - return 1 # error, no target key in a given dict. - end - else - wd.x[i] = valueToAssign - return 0 - end - end -end - -""" convert hour(0-23), minute(0-59) into julia time object -# Example - time -""" -function iTime(h::Integer, m::Integer) - if h == 0 - h = 12 - ampm = "am" - elseif 1 <= h <= 11 - ampm = "am" - elseif h == 12 - ampm = "pm" - elseif 13 <= h <= 23 - h = h - 12 - ampm = "pm" - else - error("hour out of range") - end - - m = m < 10 ? "0$m" : m - t = "$h:$m$ampm" - - return Time(t, "HH:MMp") -end - -""" replace a number according to the limit - if value is lower than lowerbound return lowerbound replacement value - if value is more than upperbound return upperbound replacement value - - # Example - limitvalue(4, (-5 => 0), (5 => 5)) -""" -function limitvalue(v::Number, lowerbound::Pair, upperbound::Pair) - lwLimit, lwReplace = lowerbound - upLimit, upReplace = upperbound - - if v < lwLimit - v = lwReplace - elseif v > upLimit - v = upReplace - else - end - return v -end - -""" assign matrix b to matrix a according to matrix b's CartesianIndex -""" -function cartesianAssign!(a, b) - for (i, v) in enumerate(b) - a[CartesianIndices(b)[i].I...] = v - end - return nothing -end -cartesianAssign!(a::CuArray, b::CuArray) = @cuda cartesianAssign!(a, b) - -function sumAlongDim3(a::Array) - totalDim = length(size(a)) - - if totalDim == 3 - d1, d2, d3 = size(a) - r = zeros(1, 1, d3) - for i in 1:d3 - view(r, 1, 1, i) .= sum(a[:, :, i]) - end - elseif totalDim == 4 - d1, d2, d3, d4 = size(a) - r = zeros(1, 1, d3, d4) - for j in 1:d4 - for i in 1:d3 - view(r, 1, 1, i, j) .= sum(a[:, :, i, j]) - end - end - else - error("this condition is not define yet") - end - - return r -end - - -""" ELEMENT-wise multiply of each slice of 3D input matrix ,a, to all slice of 3D another matrix ,b, and - concatenate at the 4th dimension. - - Example - julia> input = rand(32, 32, 128) # batch at 3rd dim - julia> weight = rand(32, 32, 1024) - julia> r = matMul_3Dto3D_manyTo1batch(input, weight); - julia> size(r) - (32, 32, 1024, 128) -""" -function matMul_3Dto3D_manyTo1batch(a::Array, b::Array; resultStorage::Union{Array, Nothing}=nothing) - asize = [size(a)...] - bsize = [size(b)...] - if resultStorage === nothing - resultStorage = similar(a, eltype(b), bsize[1], bsize[2], bsize[3], asize[3]) - end - - c = [slice .* b for slice in eachslice(a, dims=3)] - resultStorage .= cat(c..., dims=4) - - return resultStorage -end - -# function matMul_3Dto3D_manyTo1batch(a::CuArray, b::CuArray; # XXX working code -# resultStorage::Union{CuArray, Nothing}=nothing, threads=256) -# asize = [size(a)...] -# bsize = [size(b)...] -# if resultStorage === nothing -# resultStorage = similar(a, eltype(b), bsize[1], bsize[2], bsize[3], asize[3]) |> gpu -# end -# CUDA.@sync begin -# @cuda threads=threads matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage) -# end -# return resultStorage -# end - -# function matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage) # XXX working code -# _, _, _, p = size(resultStorage) - -# index = threadIdx().x # this example only requires linear indexing, so just use `x` -# stride = blockDim().x -# for i in index:stride:p -# view(resultStorage, :, :, :, i) .= view(a, :, :, i) .* b -# end -# return nothing -# end - -""" GPU kernel -""" -function matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage, linear_to_cartesian) - i = (blockIdx().x - 1) * blockDim().x + threadIdx().x - if i <= size(a, 3) # guard against unused threads to accessing memory out of bound - cartesianIndex = linear_to_cartesian(i, size(b)) # example for how to send "inner" function to gpu - # @cuprintln("gpu thread $i $cartesianIndex[2]") - - @. @views resultStorage[:, :, :, i] = a[ :, :, i] * b - # view(resultStorage, :, :, :, i) .= view(a, :, :, i) .* b # alternative code - # @view(resultStorage[:, :, :, i]) .= @view(a[ :, :, i]) .* b # alternative code - end - return nothing -end - -""" GPU version of batchMatEleMul - - Example - julia> using Flux, CUDA - julia> device = Flux.CUDA.functional() ? gpu : cpu - julia> if device == gpu CUDA.device!(0) end - julia> input = rand(32, 32, 128) |> gpu; # 128-batches - julia> weight = rand(32, 32, 1024) |> gpu; # 1-batch. this matrix is essentially (32, 32, 1024, 1) - julia> r = matMul_3Dto3D_manyTo1batch(input, weight); - julia> size(r) - (32, 32, 1024, 128) -""" -function matMul_3Dto3D_manyTo1batch(a::CuArray, b::CuArray; - resultStorage::Union{CuArray, Nothing}=nothing) - if resultStorage === nothing - resultStorage = similar(a, eltype(b), size(b, 1), size(b, 2), size(b, 3), size(a, 3)) |> gpu - end - - kernel = @cuda launch=false matMul_3Dto3D_manyTo1batch_gpu!(a, b, resultStorage, GeneralUtils.linear_to_cartesian) - config = launch_configuration(kernel.fun) - - # threads to be launched. Since one can't launch exact thread number the kernel needs, - # one just launch threads more than this kernel needs then use a guard inside the kernel - # to prevent unused threads to access memory. - threads = min(256, config.threads) # threads per block. depend on gpu. Most NVIDIA gpu has 1024 threads per block - - # total desired threads to launch to gpu. Usually 1 thread per 1 matrix element - totalThreads = size(a, 3) # This kernel use 1 thread per batch - - blocks = cld(totalThreads, threads) - - CUDA.@sync begin - kernel(a, b, resultStorage, GeneralUtils.linear_to_cartesian; threads, blocks) - end - return resultStorage -end - -""" ELEMENT-wise multiply of each slice of 3D input matrix ,a, to all batch of another 4D matrix ,b, and - concatenate at the 4th dimension. - - Example - julia> - julia> a = rand(2,2,3) # 3-batches - julia> b = rand(2,2,4,3) # 3-batches - julia> r = GeneralUtils.matMul_3Dto4D_batchwise(a, b); - julia> size(r) - (2, 2, 4, 3) -""" -function matMul_3Dto4D_batchwise(a::Array, b::Array; resultStorage::Union{Array, Nothing}=nothing) - if size(a, 3) != size(b, 4) - error("batch number of a and b must be equal") - end - if resultStorage === nothing - resultStorage = zeros(size(b, 1), size(b, 2), size(b, 3), size(a, 3)) - end - for i in 1:size(a, 3) - view(resultStorage, :, :, :, i) .= a[:, :, i] .* b[:, :, :, i] - end - return resultStorage -end - -""" GPU-compatible linear index to cartesian index conversion -""" -function linear_to_cartesian(i::Int, arraySize::NTuple{4,Int}) - # Check that the linear coordinate is valid - # prod(arraySize) is the same as *(arraySize...). they multipy all elements in an array. - # but this code use prod() because splat breaks GPU performance - if i < 1 || i > prod(arraySize) - error("Invalid linear coordinate") - end - # Extract the dimensions of the matrix - n1, n2, n3, n4 = arraySize - # Compute the cartesian coordinate using rem and div functions - i1 = ((i-1) % (n1)) + 1 # +1 convert 0-based to 1-based index - i2 = ((i-1) ÷ (n1)) % n2 + 1 - i3 = ((i-1) ÷ (n1*n2)) % n3 + 1 - i4 = (i-1) ÷ (n1*n2*n3) + 1 - # Return the cartesian coordinate as a tuple - return (i1, i2, i3, i4) -end - -""" return a vector with true at max value and false for other value. - if vector is all-zeros, return all-false vector. -""" -function vectorMax(x) - if sum(isNotEqual.(x, 0)) == 0 # guard against all-zeros array - # instead of returning all-zeros original vector, - # return all-false vector to prevent type instability - return isNotEqual.(x, 0) - else - return isequal.(x, maximum(x)) - end -end - -function multiply_last(matrix, x, n) - # X is the scalar to multiply - # matrix is the column-major 2D matrix - # n is the number of elements to be multiplied, starting from the last one - # returns a new matrix with the same shape as the original one - - # get the number of rows and columns of the matrix - rows, cols = size(matrix) - - # create a copy of the matrix to avoid mutating the original one - result = copy(matrix) - - # loop over the last n elements in column-major order - for i in (rows * cols - n + 1):(rows * cols) - # get the row and column indices of the current element - row = (i - 1) % rows + 1 - col = (i - 1) ÷ rows + 1 - - # multiply the element by X and store it in the result matrix - result[row, col] *= x - end - - # return the result matrix - return result -end - -function multiply_random_elements(A, x, n, rng=MersenneTwister(1234)) - # rng is a random number generator object, see https://docs.julialang.org/en/v1/stdlib/Random/ - # x is a scalar value to multiply by - # A is a column-major 2D matrix or a vector - # n is the number of elements to be multiplied - # returns a new array with n randomly chosen distinct elements multiplied by x - B = copy(A) # make a copy of A to avoid mutating it - d = ndims(A) # get the number of dimensions of A - if d == 1 # if A is a vector - m = length(A) # get the length of A - indices = collect(1:m) # create an array of indices from 1 to m - shuffle!(rng, indices) # shuffle the indices in-place using the RNG - for i in 1:n # loop n times - j = indices[i] # get the i-th shuffled index - B[j] *= x # multiply the element at j by x - end - elseif d == 2 # if A is a matrix - m = size(A, 1) # number of rows in A - p = size(A, 2) # number of columns in A - indices = collect(1:m*p) # create an array of linear indices from 1 to m*p - shuffle!(rng, indices) # shuffle the indices in-place using the RNG - for i in 1:n # loop n times - j = indices[i] # get the i-th shuffled index - B[j] *= x # multiply the element at j by x - end - else # if A is neither a vector nor a matrix - error("A must be a vector or a matrix") - end - return B # return the new array -end - -""" Randomly (rng controlled) choose position of elements that has value, markValue, from matrix mask and - replace matrix A's elements of the same position with value, a. - - Example - julia> mask = rand([-1,0,1],4,4,1) - julia> A = rand(4,4,1) - julia> C = replaceElements(mask, A, -1, 5.0, 3) -""" -function replaceElements(mask::AbstractArray{<:Any}, markValue::Number, A::AbstractArray{<:Any}, a::Number, - n::Int=0; rng::AbstractRNG=MersenneTwister(1234)) - """ Prompt - Write a julia function to operate on column-major 3D matrix. The function randomly - choose elements in matrix mask that has value markValue and replace elements in matrix A at - the same position with value a. The choosing randomness is controlled by rng function. - I also want to specify how many elements to be replaced. - """ - - total_x_tobeReplced = sum(isequal.(mask, markValue)) - if n == 0 || n > total_x_tobeReplced - n = total_x_tobeReplced - end - - # check if mask and A have the same size - if size(mask) != size(A) - error("mask and A must have the same size") - end - C = copy(A) - # get the indices of elements in mask that equal markValue - indices = findall(x -> x == markValue, mask) - # shuffle the indices using the rng function - shuffle!(rng, indices) - # select the first n indices - selected = indices[1:n] - # replace the elements in A at the selected positions with a - for i in selected - C[i] = a - end - return C -end - -""" Randomly (rng controlled) choose position of elements that has value, markValue, from matrix mask and - replace matrix A's elements of the same position with value, a. if n == 0, all marked value is replaced - - Example - julia> mask = rand([-1,0,1],4,4,1) - julia> A = rand(4,4,1) - julia> C = replaceElements(mask, A, -1, 5.0, 3) -""" -function replaceElements!(mask::AbstractArray{<:Any}, markValue::Number, A::AbstractArray{<:Any}, a::Number, - n::Int=0; rng::AbstractRNG=MersenneTwister(1234)) - total_x_tobeReplced = sum(isequal.(mask, markValue)) - remaining = 0 - if n == 0 || n > total_x_tobeReplced - remaining = n - total_x_tobeReplced - n = total_x_tobeReplced - end - - # check if mask and A have the same size - if size(mask) != size(A) - error("mask and A must have the same size, mask $(size(mask)) A $(size(A))") - end - # get the indices of elements in mask that equal markValue - indices = findall(x -> x == markValue, mask) - # shuffle the indices using the rng function - shuffle!(rng, indices) - # select the first n indices - selected = indices[1:n] - # replace the elements in A at the selected positions with a - for i in selected - A[i] = a - end - - return remaining -end - -""" Replace n elements that has value x with user specified value a. -""" -function replaceElements(A::AbstractArray{<:Any}, x::Number, a::Number, n::Int=0, rng=MersenneTwister(1234)) - total_x_tobeReplced = sum(isequal.(A, x)) - if n == 0 || n > total_x_tobeReplced - n = total_x_tobeReplced - end - - B = copy(A) - # A is a column-major 3D matrix - # x is the value to be replaced - # a is the new value - # rng is a random number generator function - # n is the number of elements to be replaced - - # find the indices of elements in A that equal x - indices = findall(==(x), B) - - # shuffle the indices using the rng function - shuffle!(rng, indices) - - # select the first n indices - selected = indices[1:n] - - # replace the elements at the selected indices with a - for i in selected - B[i] = a - end - - # return the modified matrix A - return B -end - - -function replaceElements!(A::AbstractArray{<:Any}, x::Number, a::Number, n::Int=0, rng=MersenneTwister(1234)) - total_x_tobeReplced = sum(isequal.(A, x)) - if n == 0 || n > total_x_tobeReplced - n = total_x_tobeReplced - end - - # A is a column-major 3D matrix - # x is the value to be replaced - # a is the new value - # rng is a random number generator function - # n is the number of elements to be replaced - - # find the indices of elements in A that equal x - indices = findall(==(x), A) - - # shuffle the indices using the rng function - shuffle!(rng, indices) - - # select the first n indices - selected = indices[1:n] - - # replace the elements at the selected indices with a - for i in selected - A[i] = a - end -end - - - - - -""" Get characters between specified characters. - - Arguments: - startChar, start character - endChar, end character. - endCharPosition, end character position after startChar. Can be "next" or "end". - "next" means the closed endChar just after startChar. - "end" means the furthest endChar. - includeChar, whether to include the startChar and endChar. Default is true - Return: - the characters between specified characters. - - Example: - ```jldoctest - julia> using GeneralUtils - julia> text = "{\"ask\": {\"text\": \"Could you please tell me about the special event?\"\n }}\n \n " - julia> getStringBetweenCharacters(text, '{', '}', endCharPosition="end") - {\"ask\": {\"text\": \"Could you please tell me about the special event?\"\n }} - ``` -""" -function getStringBetweenCharacters(text::T, startChar::Char, endChar::Char; - endCharLocation::String="next", includeChar::Bool=true) where {T<:AbstractString} - - # get the position of the startChar - startCharPosition = findfirst(startChar, text) - endCharPosition = nothing - - if endCharLocation == "end" - # get the first position of the endChar coming from the end of text - endCharPosition = findlast(endChar, text) - elseif endCharLocation == "next" - # get the first position of the endChar after startCharPosition - endCharPosition = findnext(endChar, text, startCharPosition + 1) - else - error("endCharPositio must be \"end\" or \"next\"") - end - - @show startCharPosition, endCharPosition - - # get characters between startChar and endChar from text - extractedText = text[startCharPosition:endCharPosition] - # convert substring to string - extractedText = string(extractedText) - - extractedText = includeChar == true ? extractedText : extractedText[2:end-1] - - return extractedText -end - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -end # module \ No newline at end of file diff --git a/previousVersion/0.0.3/test/etc.jl b/previousVersion/0.0.3/test/etc.jl deleted file mode 100644 index e69de29..0000000