Merge pull request #63 from GenericMappingTools/fixes-band-names

Fix things that broke after the default band names ("Band1" instead of "Band 1"

Project.toml

@@ -1,7 +1,7 @@
 name = "RemoteS"
 uuid = "26020ff4-e92a-488e-a723-09c28e89e04a"
 authors = ["Joaquim Luis <jmfluis@gmail.com>"]
-version = "1.1.0"
+version = "1.1.1"
 
 [deps]
 GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
@@ -21,7 +21,7 @@ test = ["Test"]
 
 [compat]
 julia = "1.6"
-GMT = "1"
+GMT = "1.9"
 PrecompileTools = "1.0"
 SatelliteToolboxTle = "1"
 SatelliteToolboxPropagators = "0.3"

src/spectral_indices.jl

@@ -3,8 +3,8 @@ const generic_docs = "
 - The second form is more versatile but also more complex to describe.
   - `cube`: Is the file name of a 'cube', a multi-layered file normally created with the [`cutcube`](@ref) function.
      If this file was created with band descriptions one can use the `bands` or the `bandnames` options.
-  - `bands`: _cubes_ created with [`cutcube`](@ref) assign descriptions starting with \"Band 1 ...\" an so on
-    the other bands. So when `bands` is used we search for bands named \"Band band[k]\", where band[k] loops
+  - `bands`: _cubes_ created with [`cutcube`](@ref) assign descriptions starting with \"Band1 ...\" an so on
+    the other bands. So when `bands` is used we search for bands named \"Band'band[k]'\", where band[k] loops
     over all elements of the `bands` vector. WARNING: the elements order in the vector must be sorted in increasing
     wavelength numbers, _i.e._ like the example for the first form.
   - `layers`: Use this option when you are certain of the bands order in the cube or the it doesn't have a bands
@@ -130,7 +130,7 @@ $(generic_docs)
 mndwi(green, swir2; kw...) = sp_indices(swir2, green; index="MNDWI", kw...)
 mndwi(cube::GMT.GMTimage{UInt16, 3}, bnds; kw...) = sp_indices(cube, find_layers(cube, bnds, 2); index="MNDWI", kw...)
 mndwi(cube::String; bands::Vector{Int}=Int[], layers::Vector{Int}=Int[], bandnames::Vector{String}=String[], kw...) =
-	helper_si_method(cube, "MNDWI"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["green", "swir 2"], kw...)
+	helper_si_method(cube, "MNDWI"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["green", "swir2"], kw...)
 
 # ----------------------------------------------------------------------------------------------------------
 """
@@ -238,7 +238,7 @@ $(generic_docs)
 ndwi2(nir, swir2; kw...) = sp_indices(swir2, nir; index="NDWI2", kw...)
 ndwi2(cube::GMT.GMTimage{UInt16, 3}, bnds; kw...) = sp_indices(cube, find_layers(cube, bnds, 2); index="NDWI2", kw...)
 ndwi2(cube::String; bands::Vector{Int}=Int[], layers::Vector{Int}=Int[], bandnames::Vector{String}=String[], kw...) =
-	helper_si_method(cube, "NDWI2"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["nir", "swir 2"], kw...)
+	helper_si_method(cube, "NDWI2"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["nir", "swir2"], kw...)
 
 # ----------------------------------------------------------------------------------------------------------
 """
@@ -273,7 +273,7 @@ SATVI = ((swir1 - red) / (swir1 + red + L)) * (1.0 + L) - (swir2 / 2.0)
 satvi(red, swir2, swir3; kw...) = sp_indices(red, swir2, swir3; index="SATVI", kw...)
 satvi(cube::GMT.GMTimage{UInt16, 3}, bnds; kw...) = sp_indices(cube, find_layers(cube, bnds, 3); index="SATVI", kw...)
 satvi(cube::String; bands::Vector{Int}=Int[], layers::Vector{Int}=Int[], bandnames::Vector{String}=String[], kw...) =
-	helper_si_method(cube, "SATVI"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["red", "swir 1", "swir 2"], kw...)
+	helper_si_method(cube, "SATVI"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["red", "swir1", "swir2"], kw...)
 
 # ----------------------------------------------------------------------------------------------------------
 """
@@ -309,7 +309,7 @@ $(generic_docs)
 slavi(red, nir, swir2; kw...) = sp_indices(red, nir, swir2; index="SLAVI", kw...)
 slavi(cube::GMT.GMTimage{UInt16, 3}, bnds; kw...) = sp_indices(cube, find_layers(cube, bnds, 3); index="SLAVI", kw...)
 slavi(cube::String; bands::Vector{Int}=Int[], layers::Vector{Int}=Int[], bandnames::Vector{String}=String[], kw...) =
-	helper_si_method(cube, "SLAVI"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["red", "nir", "swir 2"], kw...)
+	helper_si_method(cube, "SLAVI"; bands=bands, layers=layers, bandnames=bandnames, defbandnames=["red", "nir", "swir2"], kw...)
 
 # ----------------------------------------------------------------------------------------------------------
 function helper_sp_indices(kwargs...)

src/utils.jl

@@ -72,6 +72,17 @@ we search for a made up `bandnames=["red", "green", "blue"]`.
 
 Return an auto-stretched UInt8 RGB GMTimage OR a GMTimage{UInt16,3} if the `raw` option is set to `true`.
 
+    Irgb = truecolor(cube::GMTgrid, [bands|layers::Vector{Int}], [bandnames::Vector{String}], [type=UInt8])
+
+Make an RGB composition of 3 bands from the `cube` file holding a Float32 multi-layered array.
+The band selection can be made with `bands` vector, case in which we will search for bands named "Band band[k]"
+or where the bands description contain the contents of `bandnames`. If none of `bands` or `bandnames` is used
+we search for a made up `bandnames=["red", "green", "blue"]`.
+
+By default we scale the bands to 0-255. Use `type=UInt16` to scale the bands to 0-65535`. Note that this
+will matter only for the guessing of the good limits to perform the histogram stretching.
+
+
 ### Example:
 Make an RGB composite from data in the cube file "LC08__cube.tiff"
 ```julia
@@ -102,7 +113,7 @@ function truecolor(bndR, bndG, bndB)
 	end
 	Io = mat2img(img, I);
 	Io.layout = (isa(bndR, GMT.GMTimage)) ? "T" * bndR.layout[2] * "Ba" : "TRBa"	# This is shitty fragile
-	(isa(bndR, GMT.GMTimage) && startswith(bndR.layout, "BC")) && (Io.layout = "BCBa")	# Hoorible patch that needs to know why.
+	(isa(bndR, GMT.GMTimage) && startswith(bndR.layout, "BC")) && (Io.layout = "BCBa")	# Horrible patch that needs to know why.
 	Io
 end
 
@@ -121,14 +132,14 @@ end
 
 truecolor(cube::GMT.GMTgrid{Float32, 3}, layers::Vector{Int}) = truecolor(cube, layers=layers)
 function truecolor(cube::GMT.GMTgrid{Float32, 3}; bands::Vector{Int}=Int[], layers::Vector{Int}=Int[],
-	               bandnames::Vector{String}=String[])
+	               bandnames::Vector{String}=String[], type::DataType=UInt8)
 	(isempty(bands) && isempty(bandnames) && isempty(layers)) && (bandnames = ["red", "green", "blue"])
 	isempty(layers) && (layers = find_layers(cube, bandnames, bands))
 	(length(layers) != 3) && error("For an RGB composition 'bands' must be a 3 elements array and not $(length(layers))")
-	img = Array{UInt8, 3}(undef, size(cube,1), size(cube,2), 3)
-	img[:,:,1] = rescale(@view(cube[:,:,layers[1]]), stretch=true, type=UInt8)
-	img[:,:,2] = rescale(@view(cube[:,:,layers[2]]), stretch=true, type=UInt8)
-	img[:,:,3] = rescale(@view(cube[:,:,layers[3]]), stretch=true, type=UInt8)
+	img = Array{type, 3}(undef, size(cube,1), size(cube,2), 3)
+	img[:,:,1] = rescale(@view(cube[:,:,layers[1]]), stretch=true, type=type)
+	img[:,:,2] = rescale(@view(cube[:,:,layers[2]]), stretch=true, type=type)
+	img[:,:,3] = rescale(@view(cube[:,:,layers[3]]), stretch=true, type=type)
 	Io = mat2img(img, cube);	Io.layout = "TRBa"
 	Io
 end
@@ -223,7 +234,7 @@ function find_layers(fname::String; bands::Vector{Int}=Int[], layers::Vector{Int
 	(all(desc .== "")) && error("This cube file has no band descriptions so cannot use the 'band' or 'bandnames' options.")
 	(alllayers) && return collect(1:nbands), desc	# OK, just return them ALL
 
-	(!isempty(bands)) && (bandnames = ["Band $(bands[k])" for k = 1:length(bands)])		# Create a bandnames vector
+	(!isempty(bands)) && (bandnames = ["Band$(bands[k])" for k = 1:length(bands)])		# Create a bandnames vector
 	_layers = helper_find_layers(lowercase.(desc), bandnames)
 	return _layers, desc
 end
@@ -484,15 +495,15 @@ function parse_lsat8_file(fname::String; band::Int=0, layer::Int=0, mtl::String=
 
 	if (nbands > 1)
 		if (0 < layer < 12)			# Try to find which Band is at layer 'layer'
-			((_band = tryparse(Int, split(desc[layer])[2])) === nothing) && @warn("Failed to find Band with description in layer $layout")
+			((_band = tryparse(Int, split(desc[layer])[1][5:end])) === nothing) && @warn("Failed to find Band with description in layer $layer")
 			(_band !== nothing) && (band = _band)
 		end
 		(band < 1) && error("The `band` option must contain the wished Landsat 8 band number. Use `band=N` to set it.")
 		(band > 11) && throw(ArgumentError("Bad Landsat 8 band number $band"))
 		MTL = ((ind = findfirst(startswith.(meta, "MTL=GROUP ="))) !== nothing) ? meta[ind][5:end] :
 			error("Data in a cube (> one layer) must contain the MTL info in Metadata and this one does not.")
 
-		((band_layer = findfirst(startswith.(desc, "Band $band"))) === nothing) && error("Band $band not found in this cube")
+		((band_layer = findfirst(startswith.(desc, "Band$band"))) === nothing) && error("Band $band not found in this cube")
 		pars = parse_mtl(split(MTL, "\n"), band)
 	else
 		pars = read_mtl(fname, mtl)		# No 'band' here because it's suposed to be findable in 'fname'

test/runtests.jl

@@ -14,8 +14,8 @@ truecolor(mat2img(rand(UInt16, 16, 16), noconv=1), mat2img(rand(UInt16, 16, 16),
 @test RemoteS.assign_description(["AC08_B2.TIF", "AC08_B5.TIF"], String[])  == ["AC08_B2", "AC08_B5"]
 @test RemoteS.assign_description(["AC08_B2.TIF", "AC08_B5.TIF"], ["B2", "B5"]) == ["B2", "B5"]
 
-@test reportbands(mat2img(rand(UInt16, 4,4,3), names=["Band 1", "Band 2", "Band 3"]), 3)[1] == "Band 3"
-@test reportbands(mat2img(rand(UInt16, 4,4,3), names=["Band 1", "Band 2", "Band 3"]), layers=[1,3]) == ["Band 1", "Band 3"]
+@test reportbands(mat2img(rand(UInt16, 4,4,3), names=["Band1", "Band2", "Band3"]), 3)[1] == "Band3"
+@test reportbands(mat2img(rand(UInt16, 4,4,3), names=["Band1", "Band2", "Band3"]), layers=[1,3]) == ["Band1", "Band3"]
 
 #sat_tracks(position=true);
 #sat_tracks(position=true, tle=["1 27424U 02022A   21245.83760660  .00000135  00000-0  39999-4 0  9997"; "2 27424  98.2123 186.0654 0002229  67.6025 313.3829 14.57107527 28342"]);
@@ -31,7 +31,7 @@ truecolor("LC08_cube.tiff");	println("	truecolor 1")
 truecolor(cube, [3,2,1]);		println("	truecolor 2")
 truecolor(cube, layers=[3,2,1]); println("	truecolor 3")
 	println("	reportbands 1")
-@test reportbands("LC08_cube.tiff", 2)[1] == "Band 3 - Green [0.53-0.59]"
+@test reportbands("LC08_cube.tiff", 2)[1] == "Band3 - Green [0.53-0.59]"
 	println("	reportbands 2")
 reportbands(cube);
 	println("	subcube")
@@ -46,8 +46,8 @@ R = subcube("LC08_cube.tiff", bandnames=["red"]);	println("	subcube R")
 G = subcube("LC08_cube.tiff", bandnames=["green"]);	println("	subcube G")
 B = subcube("LC08_cube.tiff", bandnames=["blue"]);	println("	subcube B")
 NIR = subcube("LC08_cube.tiff", bandnames=["nir"]);	println("	subcube NIR")
-SW1 = subcube("LC08_cube.tiff", bandnames=["swir 1"]);	println("	subcube SW1")
-SW2 = subcube("LC08_cube.tiff", bandnames=["swir 2"]);	println("	subcube SW2")
+SW1 = subcube("LC08_cube.tiff", bandnames=["swir1"]);	println("	subcube SW1")
+SW2 = subcube("LC08_cube.tiff", bandnames=["swir2"]);	println("	subcube SW2")
 G1 = evi("LC08_cube.tiff"); println("	evi 1")
 G2 = evi(B, R, NIR);		println("	evi 2")
 G3 = evi(cube,[1,3,4]);		println("	evi 3")