Merge pull request #32 from JoshuaBillson/mnf

Made CairoMakie an Extension

Project.toml

@@ -1,11 +1,10 @@
 name = "RemoteSensingToolbox"
 uuid = "c88070b3-ddf6-46c7-b699-196056389566"
 authors = ["Joshua Billson"]
-version = "0.1.0"
+version = "0.2.0"
 
 [deps]
 ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -19,6 +18,13 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 TableOperations = "ab02a1b2-a7df-11e8-156e-fb1833f50b87"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
+[weakdeps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+
+[extensions]
+RemoteSensingToolboxMakieExt = "CairoMakie"
+
 [compat]
 ArchGDAL = "0.10"
 CairoMakie = "0.10"

ext/RemoteSensingToolboxMakieExt.jl

@@ -0,0 +1,54 @@
+module RemoteSensingToolboxMakieExt
+
+using RemoteSensingToolbox, CairoMakie, Rasters, Statistics
+using Pipe: @pipe
+import Tables
+
+function RemoteSensingToolbox.plot_signatures(bandset::Type{<:AbstractBandset}, raster::AbstractRasterStack, shp, label::Symbol; colors=Makie.wong_colors())
+    # Create Figure
+    fig = Figure(resolution=(1000,500))
+
+    # Create Axis
+    ax = Axis(
+        fig[1,1], 
+        xlabel="Wavelength (nm)", 
+        ylabel="Reflectance", 
+        xlabelfont=:bold, 
+        ylabelfont=:bold, 
+        xlabelpadding=10.0, 
+        ylabelpadding=10.0, 
+    )
+
+    # Plot Signatures
+    RemoteSensingToolbox.plot_signatures!(ax, bandset, raster, shp, label; colors=colors)
+
+    # Add Legend
+    Legend(fig[1,2], ax, "Classification")
+
+    # Return Figure
+    return fig
+end
+
+function RemoteSensingToolbox.plot_signatures!(ax, bandset::Type{<:AbstractBandset}, raster::AbstractRasterStack, shp, label::Symbol; colors=Makie.wong_colors())
+    # Extract Signatures
+    extracted = @pipe RemoteSensingToolbox.extract_signatures(raster, shp, label) |> RemoteSensingToolbox.fold_rows(mean, _, :label)
+
+    # Plot Signatures
+    RemoteSensingToolbox.plot_signatures!(ax, bandset, extracted, :label, colors)
+end
+
+function RemoteSensingToolbox.plot_signatures!(ax, bandset::Type{<:AbstractBandset}, sigs, labelcolumn::Symbol, colors)
+    # Extract Signatures
+    cols = Tables.columnnames(sigs)
+    bs = filter(x -> x in cols, bands(bandset))
+    sig_matrix = hcat([Tables.getcolumn(sigs, b) for b in bs]...)
+
+    # Plot Signatures
+    xs = [wavelength(bandset, b) for b in bs]
+    labels = Tables.getcolumn(sigs, labelcolumn)
+    for i in 1:size(sig_matrix,1)
+        lines!(ax, xs, sig_matrix[i,:], label=labels[i]; color=colors[i])
+    end
+end
+
+end

src/Bandsets/interface.jl

@@ -89,7 +89,7 @@ Read and decode the quality assurance mask for the given `AbstractBandset`.
 - `src`: Either a directory containing the quality assurance mask named according to standard conventions or the file itself.
 
 # Returns
-The decoded quality assurance mask as a `RasterStack`. Masked values are encoded as 1, non-masked values as 0, and missing values as 255.
+The decoded quality assurance mask as a `RasterStack`. Encodes masked values as 1 and non-masked values as 0.
 
 # Example
 ```julia-repl

src/RemoteSensingToolbox.jl

@@ -2,7 +2,6 @@ module RemoteSensingToolbox
 
 import ArchGDAL
 import ImageCore
-import CairoMakie
 import Tables
 import TableOperations
 using OrderedCollections

src/Spectral/Spectral.jl

@@ -8,7 +8,6 @@ using Logging
 using LinearAlgebra
 using Pipe: @pipe
 
-import CairoMakie: Figure, Axis, lines!, Legend, save, Makie.wong_colors, cgrad
 import RemoteSensingToolbox: align_rasters, efficient_read, RasterTable, transform_column, dropmissing, fold_rows
 import ..Bandsets: AbstractBandset, wavelength, bands, wavelengths
 

src/Spectral/analysis.jl

@@ -1,13 +1,13 @@
 """
-    extract_signatures(stack::AbstractRasterStack, shp, label::Symbol; drop_missing=false)
+    extract_signatures(stack::AbstractRasterStack, shp, label::Symbol; drop_missing=true)
 
 Extract signatures from the given `RasterStack` within regions specified by a provided shapefile.
 
 # Parameters
 - `stack`: The `RasterStack` from which to extract spectral signatures.
 - `shp`: A `Tables.jl` compatible object containing a :geometry column storing a `GeoInterface.jl` compatible geometry and a label column indicating the land cover type.
 - `label`: The column in `shp` corresponding to the land cover type.
-- 'drop_missing': Drop all rows with at least one missing value in either the bands or labels (default = true).
+- `drop_missing`: Drop all rows with at least one missing value in either the bands or labels (default = true).
 
 # Returns
 A `RasterTable` consisting of rows for each observed signature and columns storing the respective bands and land cover type.
@@ -39,7 +39,7 @@ julia> extract_signatures(landsat, shp, :C_name) |> DataFrame
 """
 function extract_signatures(stack::AbstractRasterStack, shp, label::Symbol; drop_missing=true)
     # Prepare Labels
-    labels = shp[:,label]
+    labels = Tables.getcolumn(shp, label)
     fill_to_label = Set(labels) |> enumerate |> Dict
     label_to_fill = Set(labels) |> enumerate .|> reverse |> Dict
 
@@ -84,29 +84,8 @@ shp = Shapefile.Table("data/landcover/landcover.shp") |> DataFrame
 plot_signatures(Landsat8, landsat, shp, :MC_name)
 ```
 """
-function plot_signatures(bandset::Type{<:AbstractBandset}, raster::AbstractRasterStack, shp, label::Symbol; colors=wong_colors())
-    # Create Figure
-    fig = Figure(resolution=(1000,500))
-
-    # Create Axis
-    ax = Axis(
-        fig[1,1], 
-        xlabel="Wavelength (nm)", 
-        ylabel="Reflectance", 
-        xlabelfont=:bold, 
-        ylabelfont=:bold, 
-        xlabelpadding=10.0, 
-        ylabelpadding=10.0, 
-    )
-
-    # Plot Signatures
-    plot_signatures!(ax, bandset, raster, shp, label; colors=colors)
-
-    # Add Legend
-    Legend(fig[1,2], ax, "Classification")
-
-    # Return Figure
-    return fig
+function plot_signatures(args...; kwargs...)
+    error("`plot_signatures` requires `CairoMakie` to be activated in your environment! Run `import CairoMakie` to fix this problem.")
 end
 
 """
@@ -146,15 +125,6 @@ plot_signatures!(ax2, Sentinel2, sentinel, shp, :MC_name; colors=cgrad(:tab10))
 Legend(fig[:,2], ax1)
 ```
 """
-function plot_signatures!(ax, bandset::Type{<:AbstractBandset}, raster::AbstractRasterStack, shp, label::Symbol; colors=wong_colors())
-    # Extract Signatures
-    extracted = @pipe extract_signatures(raster, shp, label) |> fold_rows(mean, _, :label)
-
-    # Prepare Signatures For Plotting
-    sigs = Tables.matrix(extracted)[:,2:end] .|> Float32
-    labels = Tables.matrix(extracted)[:,1] .|> string
-    bands = filter(!=(:label), Tables.columnnames(extracted))
-
-    # Plot Signatures
-    _plot_signatures!(ax, bandset, sigs, bands, labels; colors=colors)
+function plot_signatures!(args...; kwargs...)
+    error("`plot_signatures!` requires `CairoMakie` to be activated in your environment! Run `import CairoMakie` to fix this problem.")
 end

src/Spectral/utils.jl

@@ -1,30 +1,3 @@
 function _rasterize(shp, to, fill)
     Rasters.rasterize(last, shp, to=to, fill=fill, verbose=false, progress=false)
-end
-
-function _sort_signature(bandset::Type{<:AbstractBandset}, reflectances::Vector{<:Number}, bands::Vector{Symbol})
-    sorted = @pipe zip(wavelength.(bandset, bands), reflectances) |> collect |> sort(_, by=first)
-    return (first.(sorted), last.(sorted))
-end
-
-function _plot_signatures!(ax, bandset::Type{<:AbstractBandset}, sigs::Matrix{<:AbstractFloat}, bands::Vector{Symbol}, labels; colors=wong_colors(), kwargs...)
-    # Check Arguments
-    (size(sigs, 2) != length(bands)) && throw(ArgumentError("Length of signatures ($(size(sigs, 2))) must be equal to number of bands ($(length(bands)))!"))
-    (size(sigs, 1) != length(labels)) && throw(ArgumentError("Number of signatures ($(size(sigs, 1))) must be equal to number of labels ($(length(labels)))"))
-
-    # Plot Signatures
-    for i in 1:size(sigs,1)
-        _plot_signature!(ax, bandset, sigs[i,:], bands, label=labels[i]; color=colors[i], kwargs...)
-    end
-end
-
-function _plot_signature!(ax, bandset::Type{<:AbstractBandset}, signature::Vector{<:AbstractFloat}, bands::Vector{Symbol}; kwargs...)
-    # Check Arguments
-    (length(signature) != length(bands)) && throw(ArgumentError("Length of signatures ($(length(sigs))) must be equal to number of bands ($(length(bands)))!"))
-
-    # Sort Bands In Ascending Order
-    x, y = _sort_signature(bandset, signature, bands)
-
-    # Plot Signature
-    lines!(ax, x, y; kwargs...)
 end

src/raster_table.jl

@@ -3,6 +3,13 @@ mutable struct RasterTable <: Tables.AbstractColumns
     cols::Vector{Vector}
 end
 
+function _dim_cols(raster)
+    ds = Iterators.product(dims(raster)...)
+    xs = @pipe map(first, ds) |> reshape(_, :)
+    ys = @pipe map(x -> x[2], ds) |> reshape(_, :)
+    return (xs, ys)
+end
+
 function _replace_missing(raster::AbstractRaster)
     m = missingval(raster)
     r = reshape(raster, :)

src/visualization.jl

@@ -76,6 +76,8 @@ end
 
 function plot_mask(mask, classes, figure=(;), legend=(;))
     # Create Color Gradient
+    return  1
+    """
     colors = CairoMakie.cgrad(:viridis, length(classes), categorical=true)
 
     # Create Plot
@@ -87,12 +89,14 @@ function plot_mask(mask, classes, figure=(;), legend=(;))
     CairoMakie.Legend(fig[1,2], elements, classes, "Legend", legend...)
 
     return fig
+    """
 end
 
 function plot_image(img)
-    fig, ax, plt = @pipe img |> rotr90 |> CairoMakie.image(_, axis=(;aspect=CairoMakie.DataAspect()), figure=(; resolution=reverse(size(img)) .+ 64))
-    CairoMakie.hidedecorations!(ax)
-    return fig, ax, plt
+    return 1
+    #fig, ax, plt = @pipe img |> rotr90 |> CairoMakie.image(_, axis=(;aspect=CairoMakie.DataAspect()), figure=(; resolution=reverse(size(img)) .+ 64))
+    #CairoMakie.hidedecorations!(ax)
+    #return fig, ax, plt
 end
 
 "Adjust image histogram by performing a linear stretch to squeeze all values between the percentiles `lower` and `upper` into the range [0,1]."

test/Project.toml

@@ -1,5 +1,8 @@
 [deps]
 ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 Pipe = "b98c9c47-44ae-5843-9183-064241ee97a0"
+Shapefile = "8e980c4a-a4fe-5da2-b3a7-4b4b0353a2f4"
+Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/data/landcover/landcover.prj

@@ -0,0 +1 @@
+PROJCS["WGS_1984_UTM_Zone_11N",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",-117.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]

test/runtests.jl

@@ -1,7 +1,9 @@
 using RemoteSensingToolbox
 using Test
 using Images
+using Shapefile
 import ArchGDAL
+import Tables
 using Pipe: @pipe
 
 @testset "Landsat" begin
@@ -79,3 +81,20 @@ end
     @test names(sentinel) == names(recovered)
     @test all(isapprox.(tocube(recovered).data, tocube(sentinel).data, atol=0.1))
 end
+
+@testset "makie" begin
+
+    # Load Sentinel
+    sentinel = @pipe read_bands(Sentinel2, "data/sentinel/") |> dn_to_reflectance(Sentinel2, _)
+
+    # Read Shapefile
+    shp = Shapefile.Table("data/landcover/landcover.shp") |> Tables.columntable
+
+    # Should Throw Error Telling Us To Load CairoMakie
+    @test_throws ErrorException plot_signatures(Sentinel2, sentinel, shp, :MC_name)
+
+    using CairoMakie
+
+    # Should Run Now That CairoMakie is Loaded
+    fig = plot_signatures(Sentinel2, sentinel, shp, :MC_name)
+end