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Merge pull request #34 from henry2004y/simplify_ndim
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Simplify ndim
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@henry2004y
henry2004y authored Nov 30, 2023
2 parents 18f7211 + e6c0d09 commit afa4589
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "Batsrus"
uuid = "e74ebddf-6ac1-4047-a0e5-c32c99e57753"
authors = ["Hongyang Zhou <[email protected]>"]
version = "0.4.2"
version = "0.4.3"

[deps]
FortranFiles = "c58ffaec-ab22-586d-bfc5-781a99fd0b10"
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59 changes: 13 additions & 46 deletions src/io.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -425,60 +425,27 @@ function allocateBuffer(filehead::NamedTuple, T::DataType)
x, w
end

"Read ascii format data."
"Read ascii format coordinates and data values."
function getascii!(x, w, fileID::IOStream, filehead::NamedTuple)
ndim, nx = filehead.ndim, filehead.nx

# Read coordinates & values row by row
if ndim == 1
for ix = 1:nx[1]
temp = parse.(Float64, split(readline(fileID)))
x[ix,:] .= temp[1]
w[ix,:] .= temp[2:end]
end
elseif ndim == 2
for j = 1:nx[2], i = 1:nx[1]
temp = parse.(Float64, split(readline(fileID)))
x[i,j,:] .= temp[1:2]
w[i,j,:] .= temp[3:end]
end
elseif ndim == 3
for k = 1:nx[3], j = 1:nx[2], i = 1:nx[1]
temp = parse.(Float64, split(readline(fileID)))
x[i,j,k,:] .= temp[1:3]
w[i,j,k,:] .= temp[4:end]
end
ndim = filehead.ndim
Ids = CartesianIndices(size(x)[1:ndim])
for ids in Ids
temp = parse.(Float64, split(readline(fileID)))
x[ids,:] = temp[1:ndim]
w[ids,:] = temp[ndim+1:end]
end

return
end

"Read binary format data."
"Read binary format coordinates and data values."
function getbinary!(x, w, fileID::IOStream, filehead::NamedTuple)
ndim, nw = filehead.ndim, filehead.nw

# Read coordinates & values
if ndim == 1
read!(fileID, x)
skip(fileID, 2*TAG)
for iw = 1:nw
read!(fileID, @view w[:,iw])
skip(fileID, 2*TAG)
end
elseif ndim == 2
read!(fileID, x)
skip(fileID, 2*TAG)
for iw = 1:nw
read!(fileID, @view w[:,:,iw])
skip(fileID, 2*TAG)
end
elseif ndim == 3
read!(fileID, x)
dimlast = filehead.ndim + 1
read!(fileID, x)
skip(fileID, 2*TAG)
for iw in axes(w, dimlast)
read!(fileID, selectdim(w, dimlast, iw))
skip(fileID, 2*TAG)
for iw = 1:nw
read!(fileID, @view w[:,:,:,iw])
skip(fileID, 2*TAG)
end
end

return
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175 changes: 69 additions & 106 deletions src/select.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,29 +10,21 @@ function cutdata(data::BATLData, var::AbstractString;
plotrange=[-Inf,Inf,-Inf,Inf], dir::String="x", sequence::Int=1)

x, w = data.x, data.w
VarIndex_ = findfirst(x->x==lowercase(var), lowercase.(data.head.wnames))
isempty(VarIndex_) && error("$(var) not found in header variables!")

X = @view x[:,:,:,1]
Y = @view x[:,:,:,2]
Z = @view x[:,:,:,3]

W = w[:,:,:,VarIndex_]
var_ = findfirst(x->x==lowercase(var), lowercase.(data.head.wnames))
isempty(var_) && error("$(var) not found in header variables!")

if dir == "x"
cut1 = @view X[sequence,:,:]
cut2 = @view Y[sequence,:,:]
W = @view W[sequence,:,:]
dim, d1, d2 = 1, 2, 3
elseif dir == "y"
cut1 = @view X[:,sequence,:]
cut2 = @view Z[:,sequence,:]
W = @view W[:,sequence,:]
elseif dir == "z"
cut1 = @view X[:,:,sequence]
cut2 = @view Y[:,:,sequence]
W = @view W[:,:,sequence]
dim, d1, d2 = 2, 1, 3
else
dim, d1, d2 = 3, 1, 2
end

cut1 = selectdim(view(x,:,:,:,d1), dim, sequence)
cut2 = selectdim(view(x,:,:,:,d2), dim, sequence)
W = selectdim(view(w,:,:,:,var_), dim, sequence)

if !all(isinf.(plotrange))
cut1, cut2, W = subsurface(cut1, cut2, W, plotrange)
end
Expand Down Expand Up @@ -65,32 +57,34 @@ end
hx = @view x[:,1]
hy = @view y[1,:]

if isinf(limits[1]) limits[1] = minimum(hx) end
if isinf(limits[3]) limits[3] = minimum(hy) end
if isinf(limits[2]) limits[2] = maximum(hx) end
if isinf(limits[4]) limits[4] = maximum(hy) end
if isinf(limits[1]) limits[1] = hx[1] end
if isinf(limits[3]) limits[3] = hy[1] end
if isinf(limits[2]) limits[2] = hx[end] end
if isinf(limits[4]) limits[4] = hy[end] end

xind = findall(limits[1] .≤ hx .≤ limits[2])
yind = findall(limits[3] .≤ hy .≤ limits[4])
xind, yind
xind = searchsortedfirst(hx, limits[1]):searchsortedlast(hx, limits[2])
yind = searchsortedfirst(hy, limits[3]):searchsortedlast(hy, limits[4])

CartesianIndices((xind, yind))
end

@inline function findindexes(x, y, z, limits)
hx = @view x[:,1,1]
hy = @view y[1,:,1]
hz = @view z[1,1,:]

if isinf(limits[1]) limits[1] = minimum(hx) end
if isinf(limits[3]) limits[3] = minimum(hy) end
if isinf(limits[5]) limits[5] = minimum(hz) end
if isinf(limits[2]) limits[2] = maximum(hx) end
if isinf(limits[4]) limits[4] = maximum(hy) end
if isinf(limits[6]) limits[6] = maximum(hz) end

xind = findall(limits[1] .≤ hx .≤ limits[2])
yind = findall(limits[3] .≤ hy .≤ limits[4])
zind = findall(limits[5] .≤ hy .≤ limits[6])
xind, yind, zind
if isinf(limits[1]) limits[1] = hx[1] end
if isinf(limits[3]) limits[3] = hy[1] end
if isinf(limits[5]) limits[5] = hz[1] end
if isinf(limits[2]) limits[2] = hx[end] end
if isinf(limits[4]) limits[4] = hy[end] end
if isinf(limits[6]) limits[6] = hz[end] end

xind = searchsortedfirst(hx, limits[1]):searchsortedlast(hx, limits[2])
yind = searchsortedfirst(hy, limits[3]):searchsortedlast(hy, limits[4])
zind = searchsortedfirst(hz, limits[5]):searchsortedlast(hz, limits[6])

CartesianIndices((xind, yind, zind))
end

"""
Expand All @@ -102,29 +96,32 @@ Extract subset of 2D surface dataset in ndgrid format. See also: [`subvolume`](@
function subsurface(x, y, data, limits)
checkvalidlimits(limits)

xind, yind = findindexes(x, y, limits)
ids = findindexes(x, y, limits)

newdata = subdata(data, xind, yind, size(data))
@views begin
subdata = data[ids]

newx = x[xind, yind]
newy = y[xind, yind]
subx = x[ids]
suby = y[ids]
end

newx, newy, newdata
subx, suby, subdata
end

function subsurface(x, y, u, v, limits)
checkvalidlimits(limits)

xind, yind = findindexes(x, y, limits)
ids = findindexes(x, y, limits)

sz = size(u)
newu = subdata(u, xind, yind, sz)
newv = subdata(v, xind, yind, sz)
@views begin
newu = u[ids]
newv = v[ids]

newx = x[xind, yind]
newy = y[xind, yind]
subx = x[ids]
suby = y[ids]
end

newx, newy, newu, newv
subx, suby, newu, newv
end

"""
Expand All @@ -136,77 +133,43 @@ Extract subset of 3D dataset in ndgrid format. See also: [`subsurface`](@ref).
function subvolume(x, y, z, data, limits)
checkvalidlimits(limits, 3)

xind, yind, zind = findindexes(x, y, z, limits)
ids = findindexes(x, y, z, limits)

newdata = subdata(data, xind, yind, zind, size(data))
@views begin
subdata = data[ids]

newx = x[xind,yind,zind]
newy = y[xind,yind,zind]
newz = z[xind,yind,zind]
subx = x[ids]
suby = y[ids]
subz = z[ids]
end

newx, newy, newz, newdata
subx, suby, subz, subdata
end

function subvolume(x, y, z, u, v, w, limits)
checkvalidlimits(limits, 3)

sz = size(u)

xind, yind, zind = findindexes(x, y, z, limits)

newu = subdata(u, xind, yind, zind, sz)
newv = subdata(v, xind, yind, zind, sz)
neww = subdata(w, xind, yind, zind, sz)

newx = x[xind,yind,zind]
newy = y[xind,yind,zind]
newz = z[xind,yind,zind]
ids = findindexes(x, y, z, limits)

newx, newy, newz, newu, newv, neww
end

"""
subdata(data, xind, yind, sz)
subdata(data, xind, yind, zind, sz)
Return the sliced data based on indexes `xind` and `yind` of size `sz`.
"""
function subdata(data, xind, yind, sz)
newdata = data[xind,yind]
newsz = size(newdata)

if length(sz) > 2
newdata = reshape(newdata, (newsz[1:2]..., sz[3:end]))
end

newdata
end
@views begin
newu = u[ids]
newv = v[ids]
neww = w[ids]

function subdata(data, xind, yind, zind, sz)
newdata = data[xind,yind,zind]
newsz = size(newdata)

if length(sz) > 3
newdata = @views reshape(newdata, (newsz[1:3]..., sz[4:end]))
subx = x[ids]
suby = y[ids]
subz = z[ids]
end

newdata
subx, suby, subz, newu, newv, neww
end

"Return variable data from string `var`."
function getvar(data::BATLData, var::AbstractString)
VarIndex_ = findfirst(x->x==lowercase(var), lowercase.(data.head.wnames))
isnothing(VarIndex_) && error("$var not found in file header variables!")

ndim = data.head.ndim
if ndim == 1
w = @view data.w[:,VarIndex_]
elseif ndim == 2
w = @view data.w[:,:,VarIndex_]
elseif ndim == 3
w = @view data.w[:,:,:,VarIndex_]
end
w
var_ = findfirst(x->x==lowercase(var), lowercase.(data.head.wnames))
isnothing(var_) && error("$var not found in file header variables!")

w = selectdim(data.w, data.head.ndim+1, var_)
end

"""
Expand All @@ -215,10 +178,10 @@ end
Return variables' data as a dictionary from string vector.
See also: [`getvar`](@ref).
"""
function getvars(data::BATLData, Names::Vector{T}) where T<:AbstractString
dict = Dict()
function getvars(bd::BATLData{U}, Names::Vector{T}) where {U, T<:AbstractString}
dict = Dict{T, Array{U}}()
for name in Names
dict[name] = getvar(data, name)
dict[name] = getvar(bd, name)
end

dict
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Registration pull request created: JuliaRegistries/General/96247

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.4.3 -m "<description of version>" afa4589720f4c524051743e784ccadf01456f90d
git push origin v0.4.3

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