From 533a3ac24ac4b919fb6c6fb38a54f6f1393b9f6e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Tue, 26 Nov 2024 13:54:57 -0500
Subject: [PATCH] doc(sdt): vsup draft

---
 docs/src/tutorials/bivariate-vsup.jl | 68 +++++++++++++++++-----------
 1 file changed, 42 insertions(+), 26 deletions(-)

diff --git a/docs/src/tutorials/bivariate-vsup.jl b/docs/src/tutorials/bivariate-vsup.jl
index 7db741ae4..aeb83fe6e 100644
--- a/docs/src/tutorials/bivariate-vsup.jl
+++ b/docs/src/tutorials/bivariate-vsup.jl
@@ -9,39 +9,53 @@ CairoMakie.activate!(; type = "png", px_per_unit = 2) #hide
 # get some data
 
 POL = SpeciesDistributionToolkit.gadm("BEL");
-spatialextent = SpeciesDistributionToolkit.boundingbox(POL; padding=1.0)
+spatialextent = SpeciesDistributionToolkit.boundingbox(POL; padding = 0.1)
 
 # some layers
 
 provider = RasterData(CHELSA2, BioClim)
-val = SDMLayer(
+layers = [mask!(SDMLayer(
         provider;
-        layer = 1,
-        spatialextent...
-    )
-val = convert(SDMLayer{Float16}, val)
-val = trim(mask!(val, POL))
+        layer = i,
+        spatialextent...,
+    ), POL) for i in [1, 3]]
+
+layers = [convert(SDMLayer{Float16}, l) for l in layers]
+
+# unpack
+
+val, unc = layers
+
+# temperature layer
 
 # fig-hm
-heatmap(val; axis=(aspect=DataAspect(), ))
+heatmap(val; axis = (aspect = DataAspect(),))
+lines!(POL[1].geometry, color=:black)
 current_figure() #hide
 
-# fake uncertainty with randomness
-# TODO: add randomness
-
-unc = (val - rand(values(val))).^2.0
+# now see the seasonality layer
 
 # fig-hm-unc
-heatmap(unc; axis=(aspect=DataAspect(), ))
+heatmap(unc; axis = (aspect = DataAspect(),))
+lines!(POL[1].geometry, color=:black)
 current_figure() #hide
 
+# ## Value-suppressing uncertainty palette
+
 # function for VSUP
 
-function _vsup_grid(vbins, ubins, vpal, upal=colorant"#e3e3e3", shrinkage=0.5, exponent=1.0)
+function _vsup_grid(
+    vbins,
+    ubins,
+    vpal;
+    upal = colorant"#f3f3f344",
+    s = 0.5,
+    k = 1.0,
+)
     pal = fill(upal, (vbins, ubins))
     for i in 1:ubins
-        shrkfac = ((i - 1) / (ubins - 1))^exponent
-        subst = 0.5 - shrkfac * shrinkage / 2
+        shrkfac = ((i - 1) / (ubins - 1))^k
+        subst = 0.5 - shrkfac * s / 2
         pal[:, i] .= CairoMakie.cgrad(vpal)[LinRange(0.5 - subst, 0.5 + subst, vbins)]
         # Apply the mix to the uncertain color
         for j in 1:vbins
@@ -62,21 +76,23 @@ end
 
 # VSUP test - what are the parameters
 
-ubins = 50
-vbins = 50
-vbin = quantize(val, vbins)
-ubin = quantize(unc, ubins)
+ubins = 31
+vbins = 31
+vbin = discretize(quantize(val, vbins), vbins)
+ubin = discretize(quantize(unc, ubins), ubins)
 
-pal = _vsup_grid(ubins, vbins, :isoluminant_cgo_70_c39_n256)
+pal = _vsup_grid(vbins, ubins, :diverging_isoluminant_cjm_75_c23_n256)
 
 # fig-vsup-colorpalette
-f = Figure(; size=(800,400))
+f = Figure(; size = (800, 400))
 ax = Axis(f[1, 1]; aspect = DataAspect())
 heatmap!(ax, vbin + (ubin - 1) * maximum(vbin); colormap = vcat(pal...))
 hidespines!(ax)
 hidedecorations!(ax)
+lines!(POL[1].geometry, color=:black)
 current_figure() #hide
 
+# fig-vsup-legend
 p = PolarAxis(
     f[1, 2];
     theta_0 = -pi / 2.5,
@@ -86,14 +102,14 @@ p = PolarAxis(
 )
 surface!(
     p,
-    0 .. π/5,
+    0 .. π / 5,
     0 .. 1,
     zeros(size(pal));
     color = reverse(pal),
     shading = NoShading,
 )
-thetalims!(p, 0, pi/5)
+thetalims!(p, 0, pi / 5)
 colsize!(f.layout, 1, Relative(0.7))
-current_figure()
+current_figure() #hide
 
-# Bivariate palette test
+# ## Bivariate palette