Merge pull request #235 from MIT-AI-Accelerator/gnadt

Gnadt

.gitignore

@@ -7,6 +7,7 @@ Overrides.toml
 data/
 dev/
 docs/build/
+docs/src/examples/
 examples/*.html
 examples/*.md
 maps/

docs/make.jl

@@ -1,34 +1,49 @@
 using Documenter, MagNav, PlutoStaticHTML
 
-# cd(pkgdir(MagNav)) # for local development
+# define directory paths
+package_dir  = pkgdir(MagNav)
+docs_src_dir = joinpath(package_dir,"docs","src")
+folder       = "examples"
 
-# run Pluto notebooks in notebooks_dir & create Markdown files
+# run Pluto notebooks in src_dir & create Markdown files
 # done sequentially to avoid recompiling multiple times
-println("building example notebooks")
-notebooks_dir = joinpath(pkgdir(MagNav),"examples")
-build_options = BuildOptions(notebooks_dir;
-                             output_format   = documenter_output,
-                             use_distributed = false)
-build_notebooks(build_options)
+println("building example Pluto notebooks")
+src_dir = joinpath(package_dir,folder)
+bopts   = BuildOptions(src_dir;
+                       output_format   = documenter_output,
+                       use_distributed = false)
+build_notebooks(bopts)
 
+# map sidebar names to Markdown files
 notebooks = [
-    "Feature Importance"    => "../../examples/pluto_fi.md",
-    "Linear Models"         => "../../examples/pluto_linear.md",
-    "Magnetic Anomaly Maps" => "../../examples/pluto_maps.md",
-    "Model 3"               => "../../examples/pluto_model3.md",
-    "Using SGL Data"        => "../../examples/pluto_sgl.md",
-    "Using Simulated Data"  => "../../examples/pluto_sim.md",
+    "Feature Importance"    => "$folder/pluto_fi.md",
+    "Linear Models"         => "$folder/pluto_linear.md",
+    "Magnetic Anomaly Maps" => "$folder/pluto_maps.md",
+    "Model 3"               => "$folder/pluto_model3.md",
+    "Using SGL Data"        => "$folder/pluto_sgl.md",
+    "Using Simulated Data"  => "$folder/pluto_sim.md",
 ]
 
+# create folder in docs/src if it doesn't exist
+dst_dir = joinpath(docs_src_dir,folder)
+isdir(dst_dir) || mkdir(dst_dir)
+
+# move Markdown files into folder in docs/src
+for notebook in notebooks
+    src = joinpath(package_dir ,notebook[2])
+    dst = joinpath(docs_src_dir,notebook[2])
+    mv(src,dst;force=true)
+end
+
 makedocs(
-    modules = [MagNav],
-    format  = Documenter.HTML(
-        assets     = ["assets/favicon.ico"],
-        mathengine = Documenter.MathJax3(),
+    modules  = [MagNav],
+    sitename = "MagNav.jl",
+    format   = Documenter.HTML(
+        assets              = ["assets/favicon.ico"],
+        mathengine          = Documenter.MathJax3(),
+        size_threshold      = nothing,
+        size_threshold_warn = nothing,
     ),
-    checkdocs = :exports,
-    warnonly  = true,
-    sitename  = "MagNav.jl",
     pages = [
         "Home"                      => "index.md",
         "Custom Structs"            => "structs.md",
@@ -37,8 +52,11 @@ makedocs(
         "Aeromagnetic Compensation" => "comp.md",
         "NN-Based Model Diagrams"   => "nncomp.md",
         "Navigation Algorithms"     => "nav.md",
-        "Example Notebooks"         => notebooks,
+        "Example Pluto Notebooks"   => notebooks,
     ],
+    checkdocs = :exports,
+    warnonly  = true,
+    # remotes   = nothing, #* uncomment for local development
 )
 
 deploydocs(

examples/pluto_maps.jl

@@ -54,7 +54,7 @@ This is the Perth map (at 800 m) as provided by Sander Geophysics Ltd.
 begin
 	map_gxf = MagNav.ottawa_area_maps_gxf()*"/Perth_Mag.gxf"
 	p_mapS_plot = map_gxf2h5(map_gxf,800;fill_map=false)
-	p1 = plot_map(p_mapS_plot;legend=false)
+	p1 = plot_map(p_mapS_plot)
 end
 
 # ╔═╡ 438f2f01-5cbe-4088-b365-571de4f9539a
@@ -116,9 +116,11 @@ md"## Plot all Ottawa area maps
 
 # ╔═╡ 6d4a87c8-41d7-4478-b52a-4dc5a1ae18ea
 begin
-	p2 = plot_map(n_mapS_395;legend=false,clims=(-500,500),map_color=:magma) # 395 m
-	plot_map!(p2,e_mapS_plot;legend=false,clims=(-500,500),map_color=:usgs ) # 395 m
-	plot_map!(p2,p_mapS_plot;legend=false,clims=(-500,500),map_color=:gray2) # 800 m
+	clims = (-500,500)
+	dpi   = 50
+	p2 = plot_map(n_mapS_395;clims=clims,dpi=dpi,legend=false)     # 395 m
+	plot_map!(p2,e_mapS_plot;clims=clims,dpi=dpi,map_color=:magma) # 395 m
+	plot_map!(p2,p_mapS_plot;clims=clims,dpi=dpi,map_color=:gray)  # 800 m
 end
 
 # ╔═╡ 2d18bbeb-ad4e-4c5b-80a3-25bd99f45c73
@@ -136,7 +138,7 @@ begin # the Eastern drape map contains an additional drape (altitude) map
 	alt_val = 200:500
 	alt_cdf = [sum(e_alts .< a) for a in alt_val] / sum(e_mask)
 	p3 = plot(alt_val,alt_cdf,xlab="altitude [m]",ylab="fraction [-]",
-	          title="altitude map CDF",lab=false)
+	          title="altitude map CDF",lab=false,dpi=200)
 end
 
 # ╔═╡ 3f6b725b-f1c7-41fb-9854-c737b9698a40
@@ -147,10 +149,10 @@ Minimal areas have map data collected at 395 m or higher (colored spots), so a l
 
 # ╔═╡ ae1acc31-19db-4e94-85dc-e6274186978e
 begin
-	p4 = plot_map(e_mapS_plot;map_color=:gray,legend=false)
+	p4 = plot_map(e_mapS_plot;dpi=dpi,legend=false,map_color=:gray)
 	e_mapS_plot_ = deepcopy(e_mapS_plot)
 	e_mapS_plot_.map[e_mapS_drp.alt .<= 395] .= 0
-	plot_map!(p4,e_mapS_plot_)
+	plot_map!(p4,e_mapS_plot_;dpi=dpi)
 end
 
 # ╔═╡ 504842a2-61e0-4154-a1e9-5182c97b6090
@@ -169,8 +171,8 @@ begin
 	xx        = [(e_mapS_395.xx[1]-dx*px):dx:(e_mapS_395.xx[end]+dx*px_end);]
 	yy        = [(e_mapS_395.yy[1]-dy*py):dy:(e_mapS_395.yy[end]+dy*py_end);]
 	(lon,lat) = map_border(e_mapS_plot;sort_border=true) # get map border
-	p5 = plot_map(map_map,xx,yy)
-	plot_path!(p5,lat,lon,path_color=:black)
+	p5 = plot_map(map_map,xx,yy;dpi=dpi)
+	plot_path!(p5,lat,lon;path_color=:black)
 end
 
 # ╔═╡ 8b5c030a-e0b9-4a7a-a901-a6967edbe70b
@@ -183,8 +185,8 @@ md"## Plot combined Eastern Ontario & NAMAD maps together
 begin
 	mapS_combined = map_combine(e_mapS_plot,n_mapS_395)
 	mapS_upward   = upward_fft(mapS_combined,395)
-	p6 = plot_map(mapS_upward)
-	plot_path!(p6,lat,lon,path_color=:black)
+	p6 = plot_map(mapS_upward;dpi=dpi)
+	plot_path!(p6,lat,lon;path_color=:black)
 end
 
 # ╔═╡ 1b4d1092-1680-4676-a69d-6acc2549d588
@@ -198,9 +200,9 @@ begin
 	ind_trim   = (rad2deg.(lon) .> -76) .& (rad2deg.(lat) .< 45)
 	lon_trim   = lon[ind_trim]
 	lat_trim   = lat[ind_trim]
-	p7 = plot_map(mapS_combined,map_color=:gray)
-	plot_path!(p7,lat,lon,path_color=:black)
-	plot_path!(p7,lat_trim,lon_trim,path_color=:red)
+	p7 = plot_map(mapS_combined;dpi=dpi,map_color=:gray)
+	plot_path!(p7,lat,lon;path_color=:black)
+	plot_path!(p7,lat_trim,lon_trim;path_color=:red)
 end
 
 # ╔═╡ 8dd4196a-692f-4f4f-8f4a-6d8c39c4e3ac
@@ -222,7 +224,8 @@ md" The trend of the map values agree, as expected.
 
 # ╔═╡ 992dce6d-3bed-428c-84ca-2ee9bc9f0167
 begin
-	p8 = plot(e_mapS_val,lab="Eastern",ylab="map value [nT]",dpi=200)
+    p8 = plot(ylab="map value [nT]",dpi=200)
+	plot!(p8,e_mapS_val,lab="Eastern")
 	plot!(p8,n_mapS_val,lab="NAMAD")
 end
 

src/map_functions.jl

@@ -1456,7 +1456,7 @@ Plot map on an existing plot.
 - `clims`:      (optional) color scale limits
 - `dpi`:        (optional) dots per inch (image resolution)
 - `margin`:     (optional) margin around plot [mm]
-- `Nmax`:       (optional) maximum number of data points plotted
+- `Nmax`:       (optional) maximum number of data points plotted (per axis)
 - `legend`:     (optional) if true, show legend
 - `axis`:       (optional) if true, show axes
 - `map_color`:  (optional) filled contour color scheme {`:usgs`,`:gray`,`:gray1`,`:gray2`,`:plasma`,`:magma`}
@@ -1580,7 +1580,7 @@ Plot map on an existing plot.
 - `clims`:      (optional) color scale limits
 - `dpi`:        (optional) dots per inch (image resolution)
 - `margin`:     (optional) margin around plot [mm]
-- `Nmax`:       (optional) maximum number of data points plotted
+- `Nmax`:       (optional) maximum number of data points plotted (per axis)
 - `legend`:     (optional) if true, show legend
 - `axis`:       (optional) if true, show axes
 - `map_color`:  (optional) filled contour color scheme {`:usgs`,`:gray`,`:gray1`,`:gray2`,`:plasma`,`:magma`}
@@ -1643,7 +1643,7 @@ Plot map on an existing plot.
 - `clims`:      (optional) color scale limits
 - `dpi`:        (optional) dots per inch (image resolution)
 - `margin`:     (optional) margin around plot [mm]
-- `Nmax`:       (optional) maximum number of data points plotted
+- `Nmax`:       (optional) maximum number of data points plotted (per axis)
 - `legend`:     (optional) if true, show legend
 - `axis`:       (optional) if true, show axes
 - `map_color`:  (optional) filled contour color scheme {`:usgs`,`:gray`,`:gray1`,`:gray2`,`:plasma`,`:magma`}
@@ -1653,9 +1653,9 @@ Plot map on an existing plot.
 - `b_e`:        (optional) plotting backend
 
 **Returns:**
-- `nothing`: map (if typeof(`map_map`) = `MapV`, `mapX`) is plotted on `p1`
-- `nothing`: map (if typeof(`map_map`) = `MapV`, `mapY`) is plotted on `p2`
-- `nothing`: map (if typeof(`map_map`) = `MapV`, `mapZ`) is plotted on `p3`
+- `nothing`: `mapX` is plotted on `p1`
+- `nothing`: `mapY` is plotted on `p2`
+- `nothing`: `mapZ` is plotted on `p3`
 """
 function plot_map!(p1, p2, p3, mapV::MapV;
                    clims::Tuple       = (-500,500),
@@ -1710,7 +1710,7 @@ Plot map.
 - `clims`:      (optional) color scale limits
 - `dpi`:        (optional) dots per inch (image resolution)
 - `margin`:     (optional) margin around plot [mm]
-- `Nmax`:       (optional) maximum number of data points plotted
+- `Nmax`:       (optional) maximum number of data points plotted (per axis)
 - `legend`:     (optional) if true, show legend
 - `axis`:       (optional) if true, show axes
 - `map_color`:  (optional) filled contour color scheme {`:usgs`,`:gray`,`:gray1`,`:gray2`,`:plasma`,`:magma`}
@@ -1773,7 +1773,7 @@ Plot map.
 - `clims`:      (optional) color scale limits
 - `dpi`:        (optional) dots per inch (image resolution)
 - `margin`:     (optional) margin around plot [mm]
-- `Nmax`:       (optional) maximum number of data points plotted
+- `Nmax`:       (optional) maximum number of data points plotted (per axis)
 - `legend`:     (optional) if true, show legend
 - `axis`:       (optional) if true, show axes
 - `map_color`:  (optional) filled contour color scheme {`:usgs`,`:gray`,`:gray1`,`:gray2`,`:plasma`,`:magma`}