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refactor: Rework parametric types for more flexibility
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First step for GenericMappingTools#806.

Example use case: `mat2grid(transpose([1 2 3; 4 5 6]))`

Also added docstrings to the types which can later be automatically included
into the documentation[1].

[1]: https://juliadocs.github.io/Documenter.jl/stable/man/syntax/#@docs-block
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@adigitoleo
adigitoleo committed Jan 17, 2022
1 parent fc138de commit 0164606
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2 changes: 1 addition & 1 deletion src/blendimg.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ Blend two 2D UInt8 or 2 RGB images using transparency.
### Returns
A GMT intensity Image
"""
function blendimg!(color::GMTimage{UInt8, 3}, shade::GMTimage{UInt8, 2}; new=false)
function blendimg!(color::GMTimage{AbstractArray{UInt8, 3}}, shade::GMTimage{AbstractArray{UInt8, 2}}; new=false)

blend = (new) ? Array{UInt8,3}(undef, size(shade,1), size(shade,2), 3) : color.image

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211 changes: 160 additions & 51 deletions src/gmt_main.jl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,36 @@
Base.@kwdef mutable struct GMTgrid{T<:Real,N} <: AbstractArray{T,N}
"""
GMTgrid(fields...)
Construct a GMT grid from data using optional header information.
# Fields
- `proj4::String` Projection string in PROJ4 syntax (Optional)
- `wkt::String` Projection string in WKT syntax (Optional)
- `epsg::Int` EPSG code
- `range::Array{Float64,1}` 1x6[8] vector with [x_min, x_max, y_min, y_max, z_min, z_max [, v_min, v_max]]
- `inc::Array{Float64,1}` 1x2[3] vector with [x_inc, y_inc [,v_inc]]
- `registration::Int` Registration type: 0 -> Grid registration; 1 -> Pixel registration
- `nodata::Float64` The value of nodata
- `title::String` Title (Optional)
- `comment::String` Remark (Optional)
- `command::String` Command used to create the grid (Optional)
- `names::Vector{String}` To use whith multi-layered and when layers have names (Optional)
- `x::Array{Float64,1}` [1 x n_columns] vector with XX coordinates
- `y::Array{Float64,1}` [1 x n_rows] vector with YY coordinates
- `v::Array{Float64,1}` [v x n_bands] vector with VV (vertical for 3D grids) coordinates
- `z::Array{Float32,2}` [n_rows x n_columns] grid array
- `x_units::String` Units of XX axis (Optional)
- `y_units::String` Units of YY axis (Optional)
- `v_units::String` Units of Vertical axis (Optional)
- `z_units::String` Units of z vlues (Optional)
- `layout::String` A three character string describing the grid memory layout
- `scale::Union{Float64,Float32}` When saving in file apply `z = z * scale + offset`
- `offset::Union{Float64,Float32}`
- `pad::Int` When != 0 means that the array is placed in a padded array of PAD rows/cols
"""
Base.@kwdef mutable struct GMTgrid{T<:AbstractArray}
proj4::String
wkt::String
epsg::Int
Expand All @@ -13,7 +45,7 @@ Base.@kwdef mutable struct GMTgrid{T<:Real,N} <: AbstractArray{T,N}
x::Array{Float64,1}
y::Array{Float64,1}
v::Union{Vector{<:Real}, Vector{String}}
z::Array{T,N}
z::T
x_unit::String
y_unit::String
v_unit::String
Expand All @@ -24,14 +56,14 @@ Base.@kwdef mutable struct GMTgrid{T<:Real,N} <: AbstractArray{T,N}
pad::Int=0
end
Base.size(G::GMTgrid) = size(G.z)
Base.getindex(G::GMTgrid{T,N}, inds::Vararg{Int,N}) where {T,N} = G.z[inds...]
Base.setindex!(G::GMTgrid{T,N}, val, inds::Vararg{Int,N}) where {T,N} = G.z[inds...] = val
Base.getindex(G::GMTgrid, inds::Vararg{Int,N}) where N = G.z[inds...]
Base.setindex!(G::GMTgrid, val, inds::Vararg{Int,N}) where N = G.z[inds...] = val

Base.BroadcastStyle(::Type{<:GMTgrid}) = Broadcast.ArrayStyle{GMTgrid}()
function Base.similar(bc::Broadcast.Broadcasted{Broadcast.ArrayStyle{GMTgrid}}, ::Type{ElType}) where ElType
G = find4similar(bc.args) # Scan the inputs for the GMTgrid:
GMTgrid(G.proj4, G.wkt, G.epsg, G.range, G.inc, G.registration, G.nodata, G.title, G.remark, G.command, G.names, G.x, G.y, G.v, similar(Array{ElType}, axes(bc)), G.x_unit, G.y_unit, G.v_unit, G.z_unit, G.layout, 1f0, 0f0, G.pad)
end
#Base.BroadcastStyle(::Type{<:GMTgrid}) = Broadcast.ArrayStyle{GMTgrid}()
#function Base.similar(bc::Broadcast.Broadcasted{Broadcast.ArrayStyle{GMTgrid}}, ::Type{ElType}) where ElType
# G = find4similar(bc.args) # Scan the inputs for the GMTgrid:
# GMTgrid(G.proj4, G.wkt, G.epsg, G.range, G.inc, G.registration, G.nodata, G.title, G.remark, G.command, G.names, G.x, G.y, G.v, similar(Array{ElType}, axes(bc)), G.x_unit, G.y_unit, G.v_unit, G.z_unit, G.layout, 1f0, 0f0, G.pad)
#end

find4similar(bc::Base.Broadcast.Broadcasted) = find4similar(bc.args)
find4similar(args::Tuple) = find4similar(find4similar(args[1]), Base.tail(args))
Expand All @@ -40,7 +72,35 @@ find4similar(::Tuple{}) = nothing
find4similar(G::GMTgrid, rest) = G
find4similar(::Any, rest) = find4similar(rest)

mutable struct GMTimage{T<:Unsigned, N} <: AbstractArray{T,N}
"""
GMTimage(fields...)
Construct a GMT image from data using optional header information.
# Fields
- `proj4::String` Projection string in PROJ4 syntax (Optional)
- `wkt::String` Projection string in WKT syntax (Optional)
- `epsg::Int` EPSG code
- `range::Array{Float64,1}` 1x6 vector with [x_min x_max y_min y_max z_min z_max]
- `inc::Array{Float64,1}` 1x2 vector with [x_inc y_inc]
- `registration::Int` Registration type: 0 -> Grid registration; 1 -> Pixel registration
- `nodata::Unsigned` The value of nodata
- `color_interp::String` If equal to "Gray" an indexed image with no cmap will get a gray cmap
- `metadata::Vector{String}` To store any metadata that can eventually be passed to GDAL (Optional)
- `names::Vector{String}` To use whith multi-band and when bands have names (Optional)
- `x::Array{Float64,1}` [1 x n_columns] vector with XX coordinates
- `y::Array{Float64,1}` [1 x n_rows] vector with YY coordinates
- `v::Array{Float64,1}` [v x n_bands] vector with vertical coords or wavelengths in hypercubes (Optional)
- `image::Array{T,N}` [n_rows x n_columns x n_bands] image array
- `colormap::Array{Int32,1}`
- `alpha::Array{UInt8,2}` A [n_rows x n_columns] alpha array
- `layout::String` A four character string describing the image memory layout
- `pad::Int` When != 0 means that the array is placed in a padded array of PAD rows/cols
"""
mutable struct GMTimage{T<:AbstractArray{T1} where T1 <: Unsigned}
proj4::String
wkt::String
epsg::Int
Expand All @@ -54,54 +114,103 @@ mutable struct GMTimage{T<:Unsigned, N} <: AbstractArray{T,N}
x::Array{Float64,1}
y::Array{Float64,1}
v::Array{Float64,1}
image::Array{T,N}
image::T
colormap::Array{Int32,1}
n_colors::Int
alpha::Array{UInt8,2}
layout::String
pad::Int
end
Base.size(I::GMTimage) = size(I.image)
Base.getindex(I::GMTimage{T,N}, inds::Vararg{Int,N}) where {T,N} = I.image[inds...]
Base.setindex!(I::GMTimage{T,N}, val, inds::Vararg{Int,N}) where {T,N} = I.image[inds...] = val

Base.BroadcastStyle(::Type{<:GMTimage}) = Broadcast.ArrayStyle{GMTimage}()
function Base.similar(bc::Broadcast.Broadcasted{Broadcast.ArrayStyle{GMTimage}}, ::Type{ElType}) where ElType
I = find4similar(bc.args) # Scan the inputs for the GMTimage:
GMTimage(I.proj4, I.wkt, I.epsg, I.range, I.inc, I.registration, I.nodata, I.color_interp, I.metadata, I.names, I.x, I.y, I.v, similar(Array{ElType}, axes(bc)), I.colormap, I.n_colors, I.alpha, I.layout, I.pad)
end
Base.getindex(I::GMTimage, inds::Vararg{Int,N}) where N = I.image[inds...]
Base.setindex!(I::GMTimage, val, inds::Vararg{Int,N}) where N = I.image[inds...] = val

#Base.BroadcastStyle(::Type{<:GMTimage}) = Broadcast.ArrayStyle{GMTimage}()
#function Base.similar(bc::Broadcast.Broadcasted{Broadcast.ArrayStyle{GMTimage}}, ::Type{ElType}) where ElType
# I = find4similar(bc.args) # Scan the inputs for the GMTimage:
# GMTimage(I.proj4, I.wkt, I.epsg, I.range, I.inc, I.registration, I.nodata, I.color_interp, I.metadata, I.names, I.x, I.y, I.v, similar(Array{ElType}, axes(bc)), I.colormap, I.n_colors, I.alpha, I.layout, I.pad)
#end
find4similar(I::GMTimage, rest) = I

"""
GMTcpt(fields...)
Construct a GMT [CPT] from data using optional header information.
- `colormap::Array{Float64,2}` Mx3 matrix equal to the first three columns of cpt
- `alpha::Array{Float64,1}` Vector of alpha values. One for each color.
- `range::Array{Float64,2}` Mx2 matrix with z range for each slice
- `minmax::Array{Float64,1}` Two elements Vector with zmin,zmax
- `bfn::Array{Float64,2}` A 3x3(4?) matrix with BFN colors (one per row) in [0 1] interval
- `depth::Cint` Color depth 24, 8, 1
- `hinge::Cdouble` Z-value at discontinuous color break, or NaN
- `cpt::Array{Float64,2}` Mx6 matrix with r1 g1 b1 r2 g2 b2 for z1 z2 of each slice
- `label::Vector{String}` Labels of a Categorical CPT
- `key::Vector{String}` Keys of a Categorical CPT
- `model::String` String with color model rgb, hsv, or cmyk [rgb]
- `comment::Array{String,1}` Cell array with any comments
[CPT]: https://docs.generic-mapping-tools.org/latest/cookbook/cpts.html
"""
mutable struct GMTcpt
colormap::Array{Float64,2} # Mx3 matrix equal to the first three columns of cpt
alpha::Array{Float64,1} # Vector of alpha values. One for each color.
range::Array{Float64,2} # Mx2 matrix with z range for each slice
minmax::Array{Float64,1} # Two elements Vector with zmin,zmax
bfn::Array{Float64,2} # A 3x3(4?) matrix with BFN colors (one per row) in [0 1] interval
depth::Cint # Color depth 24, 8, 1
hinge::Cdouble # Z-value at discontinuous color break, or NaN
cpt::Array{Float64,2} # Mx6 matrix with r1 g1 b1 r2 g2 b2 for z1 z2 of each slice
label::Vector{String} # Labels of a Categorical CPT
key::Vector{String} # Keys of a Categorical CPT
model::String # String with color model rgb, hsv, or cmyk [rgb]
comment::Array{String,1} # Cell array with any comments
colormap::Array{Float64,2}
alpha::Array{Float64,1}
range::Array{Float64,2}
minmax::Array{Float64,1}
bfn::Array{Float64,2}
depth::Cint
hinge::Cdouble
cpt::Array{Float64,2}
label::Vector{String}
key::Vector{String}
model::String
comment::Array{String,1}
end
GMTcpt() = GMTcpt(Array{Float64,2}(undef,0,0), Vector{Float64}(undef,0), Array{Float64,2}(undef,0,0), Vector{Float64}(undef,0), Array{Float64,2}(undef,0,0), 0, 0.0, Array{Float64,2}(undef,0,0), String[], String[], string(), String[])
Base.size(C::GMTcpt) = size(C.range, 1)
Base.isempty(C::GMTcpt) = (size(C) == 0)

"""
GMTps(postscript::String, length::Int, mode::Int, comment::Arrray{String,1})
Construct a GMT postscript plot container.
- `postscript` Actual PS plot (text string)
- `length` Byte length of postscript
- `mode` 1 = Has header, 2 = Has trailer, 3 = Has both
- `comment` Cell array with any comments
"""
mutable struct GMTps
postscript::String # Actual PS plot (text string)
length::Int # Byte length of postscript
mode::Int # 1 = Has header, 2 = Has trailer, 3 = Has both
comment::Array{String,1} # Cell array with any comments
postscript::String
length::Int
mode::Int
comment::Array{String,1}
end
GMTps() = GMTps(string(), 0, 0, String[])
Base.size(P::GMTps) = P.length
Base.isempty(P::GMTps) = (P.length == 0)

mutable struct GMTdataset{T<:Real, N} <: AbstractArray{T,N}
data::Array{T,N}
"""
GMTdataset(fields...)
Construct a GMT dataset from data using optional header information.
- `data::Array{T,N}` Mx2 Matrix with segment data
- `ds_bbox::Vector{Float64}` Global BoundingBox (for when there are many segments)
- `bbox::Vector{Float64}` Segment BoundingBox
- `attrib::Dict{String,String}` Dictionary with attributes/values (optional)
- `colnames::Vector{String}` Column names. Antecipate using this with a future Tables inerface
- `text::Vector{String}` Array with text after data coordinates (mandatory only when plotting Text)
- `header::String` String with segment header (Optional but sometimes very useful)
- `comment::Vector{String}` Array with any dataset comments [empty after first segment]
- `proj4::String` Projection string in PROJ4 syntax (Optional)
- `wkt::String` Projection string in WKT syntax (Optional)
- `geom::Integer` Geometry type. One of the GDAL's enum (wkbPoint, wkbPolygon, etc...)
"""
mutable struct GMTdataset{T<:AbstractArray{T1} where T1 <: Real}
data::T
ds_bbox::Vector{Float64}
bbox::Vector{Float64}
attrib::Dict{String, String}
Expand All @@ -114,22 +223,22 @@ mutable struct GMTdataset{T<:Real, N} <: AbstractArray{T,N}
geom::Int
end
Base.size(D::GMTdataset) = size(D.data)
Base.getindex(D::GMTdataset{T,N}, inds::Vararg{Int,N}) where {T,N} = D.data[inds...]
Base.setindex!(D::GMTdataset{T,N}, val, inds::Vararg{Int,N}) where {T,N} = D.data[inds...] = val

Base.BroadcastStyle(::Type{<:GMTdataset}) = Broadcast.ArrayStyle{GMTdataset}()
function Base.similar(bc::Broadcast.Broadcasted{Broadcast.ArrayStyle{GMTdataset}}, ::Type{ElType}) where ElType
D = find4similar(bc.args) # Scan the inputs for the GMTdataset:
GMTdataset(D.data, D.ds_bbox, D.bbox, D.attrib, D.colnames, D.text, D.header, D.comment, D.proj4, D.wkt, D.geom)
end
Base.getindex(D::GMTdataset, inds::Vararg{Int,N}) where N = D.data[inds...]
Base.setindex!(D::GMTdataset, val, inds::Vararg{Int,N}) where N = D.data[inds...] = val

#Base.BroadcastStyle(::Type{<:GMTdataset}) = Broadcast.ArrayStyle{GMTdataset}()
#function Base.similar(bc::Broadcast.Broadcasted{Broadcast.ArrayStyle{GMTdataset}}, ::Type{ElType}) where ElType
# D = find4similar(bc.args) # Scan the inputs for the GMTdataset:
# GMTdataset(D.data, D.ds_bbox, D.bbox, D.attrib, D.colnames, D.text, D.header, D.comment, D.proj4, D.wkt, D.geom)
#end
find4similar(D::GMTdataset, rest) = D

GMTdataset(data::Array{Float64,2}, text::Vector{String}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], text, "", String[], "", "", 0)
GMTdataset(data::Array{Float64,2}, text::String) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], [text], "", String[], "", "", 0)
GMTdataset(data::Array{Float64,2}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], String[], "", String[], "", "", 0)
GMTdataset(data::Array{Float32,2}, text::Vector{String}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], text, "", String[], "", "", 0)
GMTdataset(data::Array{Float32,2}, text::String) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], [text], "", String[], "", "", 0)
GMTdataset(data::Array{Float32,2}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], String[], "", String[], "", "", 0)
GMTdataset(data::AbstractArray{Float64,2}, text::Vector{String}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], text, "", String[], "", "", 0)
GMTdataset(data::AbstractArray{Float64,2}, text::String) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], [text], "", String[], "", "", 0)
GMTdataset(data::AbstractArray{Float64,2}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], String[], "", String[], "", "", 0)
GMTdataset(data::AbstractArray{Float32,2}, text::Vector{String}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], text, "", String[], "", "", 0)
GMTdataset(data::AbstractArray{Float32,2}, text::String) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], [text], "", String[], "", "", 0)
GMTdataset(data::AbstractArray{Float32,2}) = GMTdataset(data, Float64[], Float64[], Dict{String, String}(), String[], String[], "", String[], "", "", 0)
GMTdataset() = GMTdataset(Array{Float64,2}(undef,0,0), Float64[], Float64[], Dict{String, String}(), String[], String[], "", String[], "", "", 0)

struct WrapperPluto fname::String end
Expand Down
10 changes: 5 additions & 5 deletions src/precompile_GMT_i.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@ function _precompile_()
@assert Base.precompile(Tuple{typeof(put_in_legend_bag),Dict{Symbol, Any},Vector{String},Matrix{Float64}}) # time: 0.0101455
@assert Base.precompile(Tuple{typeof(add_opt_module),Dict{Symbol, Any}}) # time: 0.365098

@assert Base.precompile(Tuple{typeof(imshow),GMTgrid{Float32, 2}}) # time: 12.84012
@assert Base.precompile(Tuple{typeof(finish_PS_module),Dict{Symbol, Any},Vector{String},String,Bool,Bool,Bool,GMTgrid{Float32, 2},Vararg{Any, N} where N}) # time: 0.1452611
@assert Base.precompile(Tuple{Core.kwftype(typeof(grdimage)),NamedTuple{(:show,), Tuple{Bool}},typeof(grdimage),String,GMTgrid{Float32, 2}}) # time: 0.043773
@assert Base.precompile(Tuple{typeof(common_get_R_cpt),Dict{Symbol, Any},String,String,String,Int64,GMTgrid{Float32, 2},Nothing,Nothing,String}) # time: 0.0355232
@assert Base.precompile(Tuple{typeof(common_shade),Dict{Symbol, Any},String,GMTgrid{Float32, 2},GMTcpt,Nothing,Nothing,String}) # time: 0.0226077
@assert Base.precompile(Tuple{typeof(imshow),GMTgrid{Array{Float32, 2}}}) # time: 12.84012
@assert Base.precompile(Tuple{typeof(finish_PS_module),Dict{Symbol, Any},Vector{String},String,Bool,Bool,Bool,GMTgrid{Array{Float32, 2}},Vararg{Any, N} where N}) # time: 0.1452611
@assert Base.precompile(Tuple{Core.kwftype(typeof(grdimage)),NamedTuple{(:show,), Tuple{Bool}},typeof(grdimage),String,GMTgrid{Array{Float32, 2}}}) # time: 0.043773
@assert Base.precompile(Tuple{typeof(common_get_R_cpt),Dict{Symbol, Any},String,String,String,Int64,GMTgrid{Array{Float32, 2}},Nothing,Nothing,String}) # time: 0.0355232
@assert Base.precompile(Tuple{typeof(common_shade),Dict{Symbol, Any},String,GMTgrid{Array{Float32, 2}},GMTcpt,Nothing,Nothing,String}) # time: 0.0226077
end

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