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Commit 7523bd96 authored by Hilb, Stephan's avatar Hilb, Stephan
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code: split off FD project

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uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
name = "FD"
uuid = "edd53c04-b66a-11e8-3f8d-297d8a5291a5"
authors = ["Stephan Hilb <stephan.hilb@mathematik.uni-stuttgart.de>"]
version = "0.1.0"
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module FD
using StaticArrays
#using SparseArrays
using OffsetArrays
#using LinearMaps
#using IterativeSolvers
include("filtering.jl")
"Finite Differences"
module FDiff
using OffsetArrays
const forward = OffsetVector([-1, 1], -1)
const backward = OffsetVector([-1, 1], -2)
const central = OffsetVector([-1, 0, 1], -2)
function dirfd(fd, ndims, dir)
dir <= ndims || throw(ArgumentError("need dir <= ndims!"))
dfd = OffsetArray(zeros(ntuple(i -> i == dir ? length(fd) : 1, ndims)), ntuple(i -> i == dir ? fd.offsets[1] : -1, ndims))
# Workaround: LinearIndices(::OffsetVector) are not 1-based, so copyto! chockes
copyto!(dfd, fd.parent)
end
end
using .Filtering
using .FDiff
"""
_fdkern(fd, ndims, dir)
Create from `fd` a finite difference kernel usable in `ndims` dimension
oriented in dimension `dir`.
"""
# TODO: make it typestable on ndims
function _fdkern(fd::OffsetArray{T,1,Array{T,1}}, ndims::Integer, dir::Integer) where T
1 <= dir <= ndims || throw(ArgumentError("dimesion $(dir) out of range 1:$(ndims)"))
dfd = OffsetArray{T}(undef, Tuple(i == dir ? axes(fd, 1) : (0:0) for i in 1:ndims))
# copyto! from OffsetArray fails, broadcasting for differing axes fails too
# workaround: copyto! from parent
copyto!(dfd, fd.parent)
end
# Grid
abstract type AbstractGrid{d} <: AbstractArray{Float64, d} end
Base.ndims(grid::AbstractGrid{d}) where d = d
Base.axes(grid::AbstractGrid) = Base.OneTo.(size(grid))
Base.length(grid::AbstractGrid) = prod(size(grid))
Base.IndexStyle(::Type{<:AbstractGrid}) = IndexCartesian()
# aka `StepRangeLen{Float64,Base.TwicePrecision{Float64},Base.TwicePrecision{Float64}}`
const FDStepRange = typeof(0:0.1:1)
struct Grid{d} <: AbstractGrid{d}
domain::NTuple{d, FDStepRange}
end
Grid(domain::FDStepRange...) = Grid(domain)
Base.show(io::IO, grid::Grid) =
print("Grid from $(first.(grid.domain)) to $(last.(grid.domain)) ",
"with spacing $(step.(grid.domain))")
Base.size(grid::Grid) = ntuple(i -> grid.domain[i].len, ndims(grid))
Base.iterate(grid::Grid) = iterate(Iterators.product(grid.domain...))
Base.iterate(grid::Grid, state) = iterate(Iterators.product(grid.domain...), state)
Base.getindex(grid::Grid, idx...) = SVector(getindex.(grid.domain, idx))
Base.getindex(grid::Grid, I::CartesianIndex) = SVector(getindex.(grid.domain, Tuple(I)))
# GridView
struct GridView{d} <: AbstractGrid{d}
grid::AbstractGrid{d}
indices::NTuple{d, UnitRange{Int}}
end
GridView(grid, indices::UnitRange{Int}...) = GridView(grid, indices)
Base.size(grid::GridView) = length.(grid.indices)
# FIXME: this is terrible!
Base.iterate(grid::GridView) = iterate(grid.grid[I] for I in CartesianIndices(grid.indices))
Base.iterate(grid::GridView, state) = iterate([grid.grid[I] for I in CartesianIndices(grid.indices)], state)
Base.getindex(grid::GridView, idx...) = getindex(grid.grid, (first.(grid.indices) .- 1 .+ Base.to_indices(grid, idx))...)
# MetaGrid
struct MetaGrid{d} <: AbstractGrid{d}
grid::Grid{d}
indices::Array{NTuple{d, UnitRange{Int}}, d}
overlap::Int
end
"""
MetaGrid(domain::NTuple{d, FDStepRange}, pnum::NTuple{d, Int}, overlap::Int)
Create a grid on `domain`, partitioned along dimensions according to `pnum`
respecting `overlap`.
"""
function MetaGrid(domain::NTuple{d, FDStepRange}, pnum::NTuple{d, Int}, overlap::Int) where d
grid = Grid(domain)
tsize = size(grid) .+ (pnum .- 1) .* overlap
psize = tsize pnum
osize = tsize .- pnum .* psize
overhang(I, j) = I[j] == pnum[j] ? osize[j] : 0
indices = Array{NTuple{d, UnitRange{Int}}, d}(undef, pnum)
for I in CartesianIndices(pnum)
indices[I] = ntuple(j -> ((I[j] - 1) * psize[j] - (I[j] - 1) * overlap + 1) :
( I[j] * psize[j] - (I[j] - 1) * overlap + overhang(I, j)), d)
end
MetaGrid{d}(grid, indices, overlap)
end
Base.size(grid::MetaGrid) = size(grid.grid)
Base.iterate(grid::MetaGrid) = iterate(grid.grid)
Base.iterate(grid::MetaGrid, state) = iterate(grid.grid, state)
Base.getindex(grid::MetaGrid, idx...) = getindex(grid.grid, idx...)
indices(grid::MetaGrid, idx...) = getindex(grid.indices, idx...)
Base.view(grid::MetaGrid, idx...) = GridView(grid, indices(grid, idx...))
parts(grid::MetaGrid) = CartesianIndices(grid.indices)
## GridFunction
abstract type AbstractGridFunction{G,T,d,n} <: AbstractArray{T,1} end
rangedim(f::AbstractGridFunction{G,T,d,n}) where {G,T,d,n} = n
domaindim(f::AbstractGridFunction{G,T,d}) where {G,T,d} = d
Base.similar(f::F, ::Type{S}, dims::Int...) where {F<:AbstractGridFunction, S} =
GridFunction(f.grid, Array{S}(undef, length(f)))
"""
GridFunction{G<:AbstractGrid,T,d,n,D}
`n`-dimensional function values of type `T` on a Grid `G` of dimension `d`.
`D == d + 1`
"""
struct GridFunction{G<:AbstractGrid,T,d,n,A,D} <: AbstractGridFunction{G,T,d,n}
grid::G
data::A
function GridFunction{G,T,d,n,A,D}(grid::G, data::A) where {G,T,d,n,D,A<:AbstractArray{T,D}}
D == d + 1 || throw(ArgumentError)
d == ndims(grid) || throw(ArgumentError)
(size(grid)..., n) == size(data) || throw(ArgumentError("data does not match given size"))
new(grid, data)
end
end
# TODO: check size(data)
#GridFunction(grid::G, data::AbstractArray{T,D}) where {d,G<:AbstractGrid{d},T,D} =
# GridFunction{G,T,d,size(data, d+1),typeof(data),d+1}(grid, data)
function GridFunction(grid::G, data::AbstractArray, ::Val{n}) where {d,G<:AbstractGrid{d}, n}
if length(data) ÷ length(grid) == 1 && n > 1
data = repeat(data, inner=ntuple(i -> i == d+1 ? n : 1, d+1))
else
# TODO: check size(data)
data = reshape(data, size(grid)..., n)
end
length(data) ÷ length(grid) == n || throw(ArgumentError("dimensions don't match"))
GridFunction{G,eltype(data),d,n,typeof(data),d+1}(grid, data)
end
function GridFunction(grid::G, data::AbstractArray) where {d,G<:AbstractGrid{d}}
GridFunction(grid, data, Val(length(data) ÷ length(grid)))
end
function GridFunction(f::Function, n::Int, grid::G) where {G<:AbstractGrid}
data = Array{Float64,ndims(grid)+1}(undef, size(grid)..., n)
for I in CartesianIndices(grid)
data[Tuple(I)..., :] .= f(grid[I])
end
GridFunction(grid, data)
end
function GridFunction(grid::AbstractGrid, ::UndefInitializer, ::Val{n} = Val(1)) where n
data = Array{Float64}(undef, size(grid)..., 1)
GridFunction{typeof(grid), eltype(data), ndims(grid), n, typeof(data), ndims(grid) + 1}(grid, data)
end
#Base.show(io::IO, grid::GridFunction) =
# print("GridFunction on $(length(grid)) grid points")
Base.size(f::GridFunction) = (length(f.data),)
#Base.axes(f::GridFunction) = (Base.OneTo(length(f.data)),)
Base.getindex(f::GridFunction, idx::Int) = getindex(f.data, idx)
Base.setindex!(f::GridFunction, v, idx::Int) = setindex!(f.data, v, idx)
## TODO: using this prints #undef for display(f)
#Base.getindex(f::GridFunction, idx...) = getindex(f.data, idx...)
#Base.setindex!(f::GridFunction, v, idx...) = setindex!(f.data, v, idx...)
#Base.IndexStyle(::Type{<:GridFunction}) = IndexLinear()
#component(f::GridFunction, k::Integer) = view(reshape(f.data,
Base.view(f::AbstractGridFunction{G}, idx...) where G<:MetaGrid =
GridFunction(GridView(f.grid, indices(f.grid, idx...)), view(f.data, indices(f.grid, idx...)..., :))
grid(f::GridFunction) = f.grid
Base.:*(a::Number, b::GridFunction) = GridFunction(b.grid, a * b.data, Val(rangedim(b)))
## Operations
function fdfilter(f::GridFunction{G,T,d,n}, kern) where {G,T,d,n}
A = zeros(axes(f.data))
for k = 1:n
vidx = ntuple(i -> i <= d ? Colon() : k, d + 1)
imfilter!(view(A, vidx...), f.data[vidx...], kern)
end
GridFunction(f.grid, A)
end
derivate(f::GridFunction, dir::Integer; fd = FDiff.forward) = fdfilter(f, _fdkern(fd, ndims(f.grid), dir))
# currently gradient and divergence are specific implementations (as needed for
# chambolles algorithm), other choices may be reasonable
function gradient(f::GridFunction{G,T,d,1}; fd=FDiff.forward) where {G,T,d}
#A = Array{T,d+1}(undef, (size(f.grid)..., d))
A = zeros(size(f.grid)..., d)
for k = 1:d
vidx = ntuple(i -> i <= d ? Colon() : k, d + 1)
vidx2 = ntuple(i -> i <= d ? Colon() : 1, d + 1)
imfilter!(view(A, vidx...), f.data[vidx2...], bidx -> trim_kernel(_fdkern(fd, ndims(f.grid), k), bidx))
# FIXME: hackish, only for forward fd
selectdim(selectdim(A, d+1, k), k, size(f.grid, k)) .= 0
end
GridFunction(f.grid, A)
end
function divergence(f::GridFunction{G,T,d}; fd=FDiff.backward) where {d,G<:AbstractGrid{d},T}
A = zeros(size(f.grid)..., 1)
for k = 1:d
vidx = ntuple(i -> i <= d ? Colon() : 1, d + 1)
vidx2 = ntuple(i -> i <= d ? Colon() : k, d + 1)
imfilter!(view(A, vidx...), f.data[vidx2...], bidx -> trim_kernel(_fdkern(fd, ndims(f.grid), k), bidx))
end
GridFunction(f.grid, A)
end
function pw_norm(f::GridFunction)
d = domaindim(f)
GridFunction(f.grid, sqrt.(sum(f.data.^2, dims=d+1)), Val(1))
end
function my_norm(f::GridFunction)
d = domaindim(f)
GridFunction(f.grid, sqrt.(sum(f.data.^2, dims=d+1)), Val(rangedim(f)))
end
function pwmul(f::GridFunction{G,T,d,1}, g::GridFunction{G,T,d}) where {G,T,d}
# TODO: maybe comprehension?
data = similar(g.data)
for I in CartesianIndices(f.grid)
data[Tuple(I)..., :] = f.data[Tuple(I)..., 1] * g.data[Tuple(I)..., :]
end
GridFunction(f.grid, data, Val(rangedim(g)))
end
"""
neuman_kernel(kernel, bidx)
Modify `kernel` to be usable on a boundary `bixd` in a neumannn boundary setting.
Ghost nodes are eliminated through central finite differences. Currently only
the basic 5-star Laplace is supported.
"""
function neumann_kernel(kernel, bidx)
out = copy(kernel)
for (i, bi) in enumerate(bidx)
colrange = (i == j ? Colon() : 0 for j in 1:ndims(kernel))
out[colrange...] .+= bi * FDiff.forward
end
out /= 2 ^ count(!iszero, bidx)
trim_kernel(out, bidx)
end
function divergence(grid::Grid{d}, field) where d
field = reshape(field, (size(grid)..., ndims(grid)))
size(field, d+1) == d || throw(ArgumentError("need a d-vectorfield on a d-grid"))
dst = zeros(size(field))
for k in 1:d
kern = FDiff.dirfd(FDiff.backward, d, k)
imfilter!(selectdim(dst, d+1, k), selectdim(field, d+1, k), bidx -> trim_kernel(kern, bidx))
end
out = dropdims(sum(dst, dims=d+1), dims=d+1)
out[:]
end
function gradient(grid::Grid, img::AbstractArray)
img = reshape(img, size(grid))
d = ndims(img)
dst = zeros(size(img)..., d)
for k in 1:d
kern = FDiff.dirfd(FDiff.forward, d, k)
imfilter!(selectdim(dst, d+1, k), img, bidx -> trim_kernel(kern, bidx))
# FIXME: hack
selectdim(selectdim(dst, d+1, k), k, size(grid, k)) .= 0
end
reshape(dst, length(grid) * ndims(grid))
end
function my_norm(grid::Grid, img::AbstractArray)
img = reshape(img, (size(grid)..., ndims(grid)))
d = ndims(grid)
out = sqrt.(sum(img.^2, dims=d+1))
out = repeat(out, inner=ntuple(i -> i == d+1 ? size(img, d+1) : 1, d+1))
out[:]
end
function apply(kern, flatimg, size)
img = reshape(flatimg, size)
out = imfilter(kern, img)
reshape(out, prod(size))
end
function solve(pde, shape::NTuple{d, Integer}) where d
ndims(pde.stencil) == d || throw("dimension mismatch")
length(pde.f) == prod(shape) || throw("bounds mismatch")
A = LinearMap{Float64}(u -> apply(pde.stencil, u, shape), prod(shape), issymmetric=true, isposdef=true)
u = zeros(prod(shape))
cg!(u, A, pde.f)
return u
end
end
#module FD
#
#using OffsetArrays
#include("filtering.jl")
#
#
#"FD-Kernels"
#module Kernels
#
#using OffsetArrays
#
#const forward = OffsetVector([-1, 1], 0:1)
#const backward = OffsetVector([-1, 1], -1:0)
#const central = OffsetVector([-1, 0, 1], -1:1)
#
#end
#
#using .Filtering
#using .Kernels
#
#
#
### Implementation
#
#
### Grid
#
## aka `StepRangeLen{Float64,Base.TwicePrecision{Float64},Base.TwicePrecision{Float64}}`
#const FDStepRange = typeof(0:0.1:1)
#
#struct Grid{d}
# domain::NTuple{d, FDStepRange}
#end
#
#Grid(domain::FDStepRange...) = Grid(domain)
#Grid(ndims::Integer, range::FDStepRange) = Grid(ntuple(i -> range, ndims))
#
#Base.show(io::IO, grid::Grid) =
# print("FDGrid from $(first.(grid.domain)) to $(last.(grid.domain)) ",
# "with spacing $(step.(grid.domain))")
#
## this is not type-stable?
##Base.size(grid::Grid) = getproperty.(grid.domain, :len)
#Base.size(grid::Grid) = ntuple(i -> grid.domain[i].len, ndims(grid))
#Base.getindex(grid::Grid, idx...) = SVector(getindex.(grid.domain, idx))
#
#Base.ndims(grid::Grid{d}) where d = d
#Base.axes(grid::Grid) = Base.OneTo.(size(grid))
#Base.length(grid::Grid) = prod(size(grid))
#
## TODO: there might be a better way to wrap that product iterator
#Base.iterate(grid::Grid) = iterate(Iterators.product(grid.domain...))
#Base.iterate(grid::Grid, state) = iterate(Iterators.product(grid.domain...), state)
#
#
### GridFunction
#
#struct GridFunction{T,d} <: AbstractArray{T,1}
# grid::Grid{d}
# data::Array{T,1}
#end
#
#Base.show(io::IO, grid::GridFunction) =
# print("GridFunction on $(length(grid)) grid points")
#
#Base.size(f::GridFunction) = size(f.data)
#Base.getindex(f::GridFunction, idx...) = getindex(f.data, idx...)
#Base.setindex!(f::GridFunction, v, idx...) = setindex!(f.data, v, idx...)
#
#Base.IndexStyle(::Type{<:GridFunction}) = IndexLinear()
#Base.similar(f::GridFunction, ::Type{S}, size::Int...) where S =
# GridFunction(f.grid, Array{S}(undef, size))
#
### Operations
#
#function fdfilter(f::GridFunction, kern)
# A = imfilter(reshape(f.data, size(f.grid)), kern)
# GridFunction(f.grid, A[:])
#end
#
#derivate(f::GridFunction, dir::Integer; fd = FDiff.forward) = fdfilter(f, _fdkern(fd, ndims(f.grid), dir))
#
##gradient(f::GridFunction) = GridFunction(f.grid,
#
#
#"""
# neuman_kernel(kernel, bidx)
#
#Modify `kernel` to be usable on a boundary `bixd` in a neumannn boundary setting.
#
#Ghost nodes are eliminated through central finite differences. Currently only
#the basic 5-star Laplace is supported.
#"""
#function neumann_kernel(kernel, bidx)
# out = copy(kernel)
# for (i, bi) in enumerate(bidx)
# colrange = (i == j ? Colon() : 0 for j in 1:ndims(kernel))
# out[colrange...] .+= bi * FDiff.forward
# end
# out /= 2 ^ count(!iszero, bidx)
# trim_kernel(out, bidx)
#end
#
#function divergence(grid::Grid{d}, field) where d
# field = reshape(field, (size(grid)..., ndims(grid)))
# size(field, d+1) == d || throw(ArgumentError("need a d-vectorfield on a d-grid"))
# dst = zeros(size(field))
# for k in 1:d
# kern = FDiff.dirfd(FDiff.backward, d, k)
# imfilter!(selectdim(dst, d+1, k), selectdim(field, d+1, k), kern)
# end
# out = dropdims(sum(dst, dims=d+1), dims=d+1)
# reshape(out, length(grid))
#end
#
#function gradient(grid::Grid, img::AbstractArray)
# img = reshape(img, size(grid))
# d = ndims(img)
# dst = zeros(size(img)..., d)
# for k in 1:d
# kern = FDiff.dirfd(FDiff.forward, d, k)
# imfilter!(selectdim(dst, d+1, k), img, kern)
# end
# reshape(dst, length(grid) * ndims(grid))
#end
#
#end
module Filtering
export imfilter, imfilter!, trim_kernel
@inline function _shift_range(range, shift::Integer)
Base.UnitRange(first(range)+shift : last(range)+shift)
end
## TODO: allow border to be tuple
#function _innershift_indices(a::Array{T, d}, shift::NTuple{d, Integer}, border = abs(maximum(shift))) where {T, d}
# abs(maximum(shift)) <= border || throw("cannot shift by $shift with border $border")
# range(i) = (1 + shift[i] + border):(lastindex(a, i) + shift[i] - border)
# ntuple(range, Val(ndims(a)))
#end
#
#function innershift_view(a::Array{T, d}, shift::NTuple{d, Integer} = ntuple(i -> 0, d), border = abs(maximum(shift))) where {T, d}
# view(a, _innershift_indices(a, shift, border)...)
#end
@inline function _bidx_to_range(range::AbstractUnitRange, bidx::Integer)
if bidx > 0
return last(range):last(range)
elseif bidx < 0
return first(range):first(range)
else
return first(range)+1:last(range)-1
end
end
# we return Base.Slice since that is what `OffsetArray` uses for `axes()`
function _trim_kernel_axes(kaxes, bidx)
ntuple(Val(length(kaxes))) do i
if bidx[i] < 0
return Base.Slice(0:last(kaxes[i]))
elseif bidx[i] > 0
return Base.Slice(first(kaxes[i]):0)
else
return Base.Slice(kaxes[i])
end
end
end
"""
trim_kernel(kernel, bidx)
Trim `kernel` so that the resulting kernel is usable on the boundary
indicated by `bidx`
"""
function trim_kernel(kernel, bidx)
dst_axes = _trim_kernel_axes(axes(kernel), bidx)
out = similar(kernel, dst_axes)
range = CartesianIndices(out)
copyto!(out, range, kernel, range)
end
"""
imfilter!(dst, img, kern, slice=:inner)
Filters `img` applying `kern` and write to `dst`. `dst` is added to, so you
should initialize with zeros.
"""
# TODO: weirdly Base.Slice instead of Base.UnitRange leads to axes that are not
# compatible when broadcasting, figure out why!
function imfilter!(dst, img, kern, slice=_bidx_to_range.(axes(img), ntuple(i->0, ndims(img))))
ndims(dst) == ndims(img) == ndims(kern) == length(slice) ||
throw(ArgumentError("dst, image, kernel or slice dimensions disagree ($(ndims(dst)) vs $(ndims(img)) vs $(ndims(kern)) vs $(length(slice)))"))
axes(dst) == axes(img) || throw(ArgumentError("output and input image axes disagree"))
all(size(kern) .<= size(img)) || throw(ArgumentError("kernel bigger than image"))
last.(slice) .+ last.(axes(kern)) <= last.(axes(img)) || first.(slice) .+ first.(axes(kern)) >= first.(axes(img)) ||
throw(ArgumentError("kern and/or slice out of bounds for image"))
dstslice = view(dst, UnitRange.(slice)...)
for i in CartesianIndices(kern)
iszero(kern[i]) && continue
dstslice .+= kern[i] .* view(img, (_shift_range.(slice, Tuple(i)))...)
end
dst
end
function imfilter!(dst, img, kernelf::Function)
for bidx in Iterators.product(ntuple(i -> -1:1, ndims(img))...)
range = _bidx_to_range.(axes(img), bidx)
imfilter!(dst, img, kernelf(bidx), range)
end
dst
end
"""
imfilter(img, kernelf)
Filter `img` using a kernel function `kernelf(bidx) = kernel` specifying a
kernel for each type of node.
"""
# need zeros here, because `imfilter!` acts additively
imfilter(img, kernelf::Function) = imfilter!(zeros(size(img)), img, kernelf)
"""
imfilter(img, kern)
Filter `img` by `kern` using correlation.
Boundary is zeroed out.
"""
imfilter(img, kern) = imfilter(img, bidx -> trim_kernel(kern, bidx))
# TODO: use keyword arguments
imfilter_inner(img, kern) = imfilter(img, bidx -> all(bidx .== 0) ? kern : zeros(ntuple(i -> 0, ndims(img))))
end
[[Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
[[ColorTypes]]
deps = ["FixedPointNumbers", "Random", "Test"]
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[[Contour]]
deps = ["LinearAlgebra", "StaticArrays", "Test"]
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deps = ["InteractiveUtils", "REPL", "Random", "Serialization", "Test"]
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[[Dates]]
deps = ["Printf"]
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deps = ["Mmap"]
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[[Distributed]]
deps = ["LinearAlgebra", "Random", "Serialization", "Sockets"]
uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
[[FD]]
deps = ["OffsetArrays", "StaticArrays"]
path = "FD"
uuid = "edd53c04-b66a-11e8-3f8d-297d8a5291a5"
version = "0.1.0"
[[FixedPointNumbers]]
deps = ["Pkg", "Test"]
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version = "0.5.3"
[[GR]]
deps = ["Base64", "DelimitedFiles", "Pkg", "Random", "Serialization", "Sockets", "Test"]
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uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
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[[InteractiveUtils]]
deps = ["LinearAlgebra", "Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
[[JSON]]
deps = ["Dates", "Distributed", "Mmap", "Pkg", "Sockets", "Test", "Unicode"]
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[[LibGit2]]
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deps = ["Libdl"]
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uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
[[Markdown]]
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deps = ["Pkg", "Test"]
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[[Mmap]]
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deps = ["Compat"]
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[[OffsetArrays]]
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[[Pkg]]
deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
[[PlotThemes]]
deps = ["PlotUtils", "Requires", "Test"]
git-tree-sha1 = "f3afd2d58e1f6ac9be2cea46e4a9083ccc1d990b"
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[[PlotUtils]]
deps = ["Colors", "Dates", "Printf", "Random", "Reexport", "Test"]
git-tree-sha1 = "78553a920c4869d20742ba66193e3692369086ec"
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[[Plots]]
deps = ["Base64", "Contour", "Dates", "FixedPointNumbers", "GR", "JSON", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "Random", "RecipesBase", "Reexport", "Requires", "Showoff", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "Test", "UUIDs"]
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[[Printf]]
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[[REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets"]
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[[Random]]
deps = ["Serialization"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
[[RecipesBase]]
deps = ["Pkg", "Random", "Test"]
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[[Reexport]]
deps = ["Pkg"]
git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
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[[Requires]]
deps = ["Test"]
git-tree-sha1 = "f6fbf4ba64d295e146e49e021207993b6b48c7d1"
uuid = "ae029012-a4dd-5104-9daa-d747884805df"
version = "0.5.2"
[[SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
[[Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
[[SharedArrays]]
deps = ["Distributed", "Mmap", "Random", "Serialization"]
uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
[[Showoff]]
deps = ["Compat", "Pkg"]
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[[Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
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deps = ["DataStructures", "Random", "Test"]
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[[SparseArrays]]
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[[Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
[[StatsBase]]
deps = ["DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "Test"]
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uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.25.0"
[[Test]]
deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
[[UUIDs]]
deps = ["Random"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
[[Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
[deps]
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
FD = "edd53c04-b66a-11e8-3f8d-297d8a5291a5"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
include("fd.jl")
using StaticArrays
using SparseArrays
using OffsetArrays
......@@ -7,16 +5,18 @@ using LinearAlgebra
using Colors
using Plots
using FD
imf(f, grid) = [f(x) for x in grid]
imshow(grid, img) = plot(Gray.((reshape(float.(img), size(grid)) .- minimum(float.(img))) / (maximum(float.(img)) - minimum(float.(img))) ), show=true)
function _fpiter(grid, p, f, A, α, β, τ)
x = (A'*A + β*I) \ (FDM.divergence(grid, p) .+ A'*f ./ α)
q = FDM.gradient(grid, x)
x = (A'*A + β*I) \ (FD.divergence(grid, p) .+ A'*f ./ α)
q = FD.gradient(grid, x)
p_new = (p .+ τ .* q) ./ (1 .+ τ .* FDM.my_norm(grid, q))
p_new = (p .+ τ .* q) ./ (1 .+ τ .* FD.my_norm(grid, q))
reserr = maximum(sum((p_new .- p).^2, dims=ndims(p)))
(p_new, reserr)
......@@ -32,7 +32,7 @@ function fpalg(grid, f, A; α, β, τ = 1/8, ϵ = 1e-4)
#sleep(0.1 / k)
(p, reserr) = _fpiter(grid, p, f, A, α, β, τ)
uimg = (A'*A + β*I) \ (α * FDM.divergence(grid, p) .+ A'*f)
uimg = (A'*A + β*I) \ (α * FD.divergence(grid, p) .+ A'*f)
imshow(grid, uimg)
println("[$(lpad(k, 4))] res = $(round(reserr, digits=5))")
......@@ -43,8 +43,8 @@ end
#st = OffsetArray([0 -1 0; -1 4 -1; 0 -1 0], (-2, -2))
grid = FDM.Grid(0:0.01:1, 0:0.01:1)
#grid = FDM.Grid(0:0.5:1, 0:0.5:1)
grid = FD.Grid(0:0.01:1, 0:0.01:1)
#grid = FD.Grid(0:0.5:1, 0:0.5:1)
n = 1
#A = spdiagm(collect(k => fill(1/(2n+1), length(grid)-abs(k)) for k in -n:n)...)
......@@ -68,9 +68,9 @@ img = fpalg(grid, f, A, α=1, β=1, τ=1/100, ϵ=1e-7)
#A = Array{Float64}(undef, (length(grid), length(grid)))
#for i in 1:length(grid)
# ei = float.(1:length(grid) .== i)
# #A[:, i] = FDM.divergence(grid, FDM.gradient(grid, ei))
# #A[:, i] = FDM.divergence(grid, append!(ei, zeros(length(grid))))
# A[:, i] = reshape(reshape(FDM.gradient(grid, ei), size(grid)..., 2)[:,:,2], length(grid))
# #A[:, i] = FD.divergence(grid, FD.gradient(grid, ei))
# #A[:, i] = FD.divergence(grid, append!(ei, zeros(length(grid))))
# A[:, i] = reshape(reshape(FD.gradient(grid, ei), size(grid)..., 2)[:,:,2], length(grid))
#end
#A
......
include("fd.jl")
#include("fd.jl")
using LinearAlgebra
using SparseArrays
import .FDM
import FD
import Colors: Gray
import Plots: plot
# TODO: add clamp option
my_plot(img::FD.AbstractGridFunction{G,T,d,1}) where {G,T,d} =
plot(reshape(Gray.((img .- minimum(img)) ./ (maximum(img) - minimum(img))), size(img.grid)), show=true)
"partition of unity function"
function theta(grid, idx...)
vidx = FDM.indices(grid, idx...)
slices = Vector{Vector{Float64}}(undef, length(idx))
for (k, kglobrange) in enumerate(vidx)
krange = Base.OneTo(length(kglobrange))
slices[k] = min.(krange, reverse(krange), grid.overlap) ./ grid.overlap
# FIXME: dirty hack
if first(kglobrange) == 1
slices[k][1:grid.overlap] .= 1.0
end
if last(kglobrange) == size(grid, k)
slices[k][end-grid.overlap:end] .= 1.0
end
function h(r, rp, i)
i <= first(r) + grid.overlap && return 1.0
i >= last(r) - grid.overlap && return 1.0
(min(i - first(rp), last(rp) - i, grid.overlap) + 1) / (grid.overlap + 1)
end
#dst = Array{Float64}(undef, size(grid)...)
vidx = FD.indices(grid, idx...)
ctheta = map(x -> [h(x[1], x[2], i) for i in x[2]], zip(axes(grid), vidx))
dst = zeros(size(grid))
for (I,J) in zip(CartesianIndices(vidx), CartesianIndices(length.(vidx)))
dst[I] = prod(getindex.(slices, Tuple(J)))
dst[I] = prod(getindex.(ctheta, Tuple(J)))
end
dst
FDM.GridFunction(grid, dst)
FD.GridFunction(grid, dst)
end
function p2u(grid, p, A, f; α, β)
FDM.GridFunction(grid, (A'*A + β*I) \ (α * FDM.divergence(p).data[:] .+ A'*f.data[:]))
FD.GridFunction(grid, (A'*A + β*I) \ (α .* FD.divergence(p).data[:] .+ A'*f.data[:]))
end
# TODO: investigate matrix multiplication performance with GridFunctions
function fpiter(grid, p, f, A, α, β, τ)
x = FDM.GridFunction(grid, (A'*A + β*I) \ (FDM.divergence(p).data[:] .+ A'*f.data[:] ./ α))
q = FDM.gradient(x)
function fpiter(grid, p, w, A, α, β, τ)
x = FD.GridFunction(grid, (A'*A + β*I) \ (FD.divergence(p).data[:] .+ w ./ α))
q = FD.gradient(x)
#display(x.data)
#FDM.my_plot(x)
#FD.my_plot(x)
#checknan(q)
p_new = FDM.GridFunction(grid, (p .+ τ .* q) ./ (1 .+ τ .* FDM.my_norm(q)))
p_new = FD.GridFunction(grid, FD.pwmul(FD.GridFunction(grid, 1 ./ (1 .+ τ .* FD.pw_norm(q))), FD.GridFunction(grid, p .+ τ .* q)))
reserr = maximum(sum((p_new .- p).^2, dims=ndims(p)))
(p_new, reserr)
end
function fpalg(grid, f, A; α, β, τ = 1/8, ϵ = 1e-4)
function fpalg(grid, w, A; α, β, τ = 1/8, ϵ = 1e-4)
local uimg
p = FDM.GridFunction(x -> 0, ndims(grid), grid)
p = FD.GridFunction(x -> 0, ndims(grid), grid)
reserr = 1
k = 0
while reserr > ϵ && k < 30e1
k += 1
#sleep(0.1 / k)
(p, reserr) = fpiter(grid, p, f, A, α, β, τ)
(p, reserr) = fpiter(grid, p, w, A, α, β, τ)
u = p2u(grid, p, A, f, α=α, β=β)
#FDM.my_plot(uimg)
println("[$(lpad(k, 4))] res = $(round(reserr, digits=5))")
println("min/max: $(minimum(uimg)) / $(maximum(uimg))")
println("min/max: $(minimum(p)) / $(maximum(p))")
#FD.my_plot(uimg)
#println("[$(lpad(k, 4))] res = $(round(reserr, digits=5))")
#println("min/max: $(minimum(uimg)) / $(maximum(uimg))")
#println("min/max: $(minimum(p)) / $(maximum(p))")
end
p
#uimg
end
grid = FDM.MetaGrid((0:0.01:1, 0:0.01:1), (3, 3), 5)
grid = FD.MetaGrid((0:0.01:1, 0:0.01:1), (3, 3), 5)
A = I
#A = spdiagm(0 => ones(length(grid)), 1 => ones(length(grid)-1) )
#f = A * f
f = FDM.GridFunction(x -> float(norm(x .- [0.5, 0.5]) < 0.4), 1, grid)
g = FDM.GridFunction(x -> norm(x), 2, grid)
f = FD.GridFunction(x -> float(norm(x .- [0.5, 0.5]) < 0.4), 1, grid)
g = FD.GridFunction(x -> norm(x), 2, grid)
α=1
β=1
τ=1/100
ϵ=1e-7
ρ=0.25
p = FD.GridFunction(x -> 0, 2, grid)
function dditer(grid, p, A, f; α, β, τ, ϵ, ρ)
p .= (1-ρ) .* p
for part in FD.parts(grid)
gridv = view(grid, Tuple(part)...)
fv = view(f, Tuple(part)...)
#p.data .= 0
pv = view(p, Tuple(part)...)
for part in parts(grid)
gridv = view(grid, part...)
fv = view(f, part...)
fpalg(gridv, fv, A, α=1, β=1, τ=1/100, ϵ=1e-7)
θ = theta(grid, Tuple(part)...)
θv = view(θ, Tuple(part)...)
w = FD.GridFunction(grid, A' * f.data[:] - FD.divergence(FD.pwmul(FD.GridFunction(grid, 1 .- θ), p)))
wv = view(w, Tuple(part)...)
#wv = A' * fv
pv .+= ρ .* fpalg(gridv, wv, A, α=α*θv, β=β, τ=τ, ϵ=ϵ)
#u = p2u(grid, p, A, f, α=α*θ, β=β)
u = p2u(grid, p, A, f, α=α, β=β)
uv = view(u, Tuple(part)...)
my_plot(θv)
#sleep(1)
#my_plot(FD.pw_norm(pv))
@show maximum(pv), minimum(pv)
#sleep(1)
#my_plot(θv)
return
end
end
dditer(grid, p, A, f, α=α, β=β, τ=τ, ϵ=ϵ, ρ=ρ)
#for n = 1:10
# println("iteration $n")
# dditer(grid, p, A, f, α=α, β=β, τ=τ, ϵ=ϵ, ρ=ρ)
#end
#gridv = view(grid, 1, 1)
#fv = view(f, 1, 1)
#g = view(g, 1, 1)
FDM.my_plot(f)
#FD.my_plot(f)
#FDM.plot(f)
#FD.plot(f)
......
......@@ -210,10 +210,13 @@ Base.setindex!(f::GridFunction, v, idx::Int) = setindex!(f.data, v, idx)
#component(f::GridFunction, k::Integer) = view(reshape(f.data,
Base.view(f::AbstractGridFunction{G}, idx...) where G<:MetaGrid =
GridFunction(GridView(f.grid, indices(f.grid, idx...)), view(f.data, indices(f.grid, idx...)...))
GridFunction(GridView(f.grid, indices(f.grid, idx...)), view(f.data, indices(f.grid, idx...)..., :))
grid(f::GridFunction) = f.grid
Base.:*(a::Number, b::GridFunction) = GridFunction(b.grid, a * b.data, Val(rangedim(b)))
import Colors: Gray
......@@ -263,11 +266,25 @@ function divergence(f::GridFunction{G,T,d}; fd=FD.backward) where {d,G<:Abstract
GridFunction(f.grid, A)
end
function pw_norm(f::GridFunction)
d = domaindim(f)
GridFunction(f.grid, sqrt.(sum(f.data.^2, dims=d+1)), Val(1))
end
function my_norm(f::GridFunction)
d = domaindim(f)
GridFunction(f.grid, sqrt.(sum(f.data.^2, dims=d+1)), Val(rangedim(f)))
end
function pwmul(f::GridFunction{G,T,d,1}, g::GridFunction{G,T,d}) where {G,T,d}
# TODO: maybe comprehension?
data = similar(g.data)
for I in CartesianIndices(f.grid)
data[Tuple(I)..., :] = f.data[Tuple(I)..., 1] * g.data[Tuple(I)..., :]
end
GridFunction(f.grid, data, Val(rangedim(g)))
end
......
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