Rename package and redesign types

This creates an abstract `AbstractColorChannels` type and two types,
`ColorChannels` and `ColorMixture`. `ColorChannels` is a "bare"
multichannel color that lacks conversion to other color types;
it is intended to be used in conjunction with MappedArrays if one
wishes to visualize these as RGB images. `ColorMixture` is the
weighted-RGB color type.

.github/workflows/CI.yml

@@ -55,6 +55,6 @@ jobs:
       - run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
-            using FluorophoreColors
-            DocMeta.setdocmeta!(FluorophoreColors, :DocTestSetup, :(using FluorophoreColors); recursive=true)
-            doctest(FluorophoreColors)'
+            using MultichannelColors
+            DocMeta.setdocmeta!(MultichannelColors, :DocTestSetup, :(using MultichannelColors); recursive=true)
+            doctest(MultichannelColors)'

Project.toml

@@ -1,4 +1,4 @@
-name = "FluorophoreColors"
+name = "MultichannelColors"
 uuid = "d4071afc-4203-49ee-90bc-13ebeb18d604"
 authors = ["Tim Holy <[email protected]> and contributors"]
 version = "0.1.0"
@@ -13,7 +13,7 @@ Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 
 [compat]
-ColorTypes = "0.11.1"
+ColorTypes = "0.11.2"
 ColorVectorSpace = "0.9"
 Colors = "0.12"
 FixedPointNumbers = "0.8"

README.md

@@ -1,7 +1,7 @@
-# FluorophoreColors
+# MultichannelColors
 
-[![Build Status](https://github.com/JuliaImages/FluorophoreColors.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaImages/FluorophoreColors.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/JuliaImages/FluorophoreColors.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaImages/FluorophoreColors.jl)
+[![Build Status](https://github.com/JuliaImages/MultichannelColors.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaImages/MultichannelColors.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/JuliaImages/MultichannelColors.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaImages/MultichannelColors.jl)
 
 This package defines [color types](https://github.com/JuliaGraphics/ColorTypes.jl) for use with multichannel fluorescence imaging. Briefly, you can specify the intensity of each color channel plus an RGB value associated with the peak emission
 wavelength of each fluorophore.
@@ -11,7 +11,7 @@ wavelength of each fluorophore.
 Perhaps the easiest way to learn the package is by example. Suppose we are imaging two fluorophores, EGFP and tdTomato.
 
 ```julia
-julia> using FluorophoreColors
+julia> using MultichannelColors
 
 julia> channels = (fluorophore_rgb["EGFP"], fluorophore_rgb["tdTomato"])
 (RGB{N0f8}(0.0,0.925,0.365), RGB{N0f8}(1.0,0.859,0.0))

docs/Project.toml

@@ -1,3 +1,3 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-FluorophoreColors = "d4071afc-4203-49ee-90bc-13ebeb18d604"
+MultichannelColors = "d4071afc-4203-49ee-90bc-13ebeb18d604"

docs/make.jl

@@ -1,16 +1,16 @@
-using FluorophoreColors
+using MultichannelColors
 using Documenter
 
-DocMeta.setdocmeta!(FluorophoreColors, :DocTestSetup, :(using FluorophoreColors); recursive=true)
+DocMeta.setdocmeta!(MultichannelColors, :DocTestSetup, :(using MultichannelColors); recursive=true)
 
 makedocs(;
-    modules=[FluorophoreColors],
+    modules=[MultichannelColors],
     authors="Tim Holy <[email protected]> and contributors",
-    repo="https://github.com/JuliaImages/FluorophoreColors.jl/blob/{commit}{path}#{line}",
-    sitename="FluorophoreColors.jl",
+    repo="https://github.com/JuliaImages/MultichannelColors.jl/blob/{commit}{path}#{line}",
+    sitename="MultichannelColors.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://JuliaImages.github.io/FluorophoreColors.jl",
+        canonical="https://JuliaImages.github.io/MultichannelColors.jl",
         assets=String[],
     ),
     pages=[
@@ -19,6 +19,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/JuliaImages/FluorophoreColors.jl",
+    repo="github.com/JuliaImages/MultichannelColors.jl",
     devbranch="main",
 )

docs/src/index.md

@@ -1,14 +1,14 @@
 ```@meta
-CurrentModule = FluorophoreColors
+CurrentModule = MultichannelColors
 ```
 
-# FluorophoreColors
+# MultichannelColors
 
-Documentation for [FluorophoreColors](https://github.com/JuliaImages/FluorophoreColors.jl).
+Documentation for [MultichannelColors](https://github.com/JuliaImages/MultichannelColors.jl).
 
 ```@index
 ```
 
 ```@autodocs
-Modules = [FluorophoreColors]
+Modules = [MultichannelColors]
 ```

src/FluorophoreColors.jl → src/MultichannelColors.jl

@@ -1,4 +1,4 @@
-module FluorophoreColors
+module MultichannelColors
 
 using Compat
 
@@ -9,7 +9,8 @@ using Colors
 using ColorVectorSpace
 using Requires
 
-export fluorophore_rgb, @fluorophore_rgb_str, ColorMixture
+export AbstractColorChannels, ColorChannels, ColorMixture
+export fluorophore_rgb, @fluorophore_rgb_str
 
 include("types.jl")
 include("fluorophores.jl")

src/types.jl

@@ -1,53 +1,118 @@
-# For custom colortypes, the main things we need are
-# - utitlies for extracting channels
-# - conversion to RGB for display
-# Making the main representation by RGB means we can do the latter efficiently without requiring
-# world-age violations.
+"""
+    AbstractColorChannels{T<:Number,N}
 
+An abstract type for multichannel/multiband/hyperspectral colors. Concrete derived types should have
+a field, `channels`, which is a `NTuple{N,T}`. The channels can be returned with `Tuple(c::AbstractColorChannels)`.
 """
-    ColorMixture((rgb₁, rgb₂), (i₁, i₂))          # store intensities
-    ColorMixture{T}((rgb₁, rgb₂), (i₁, i₂))       # same, but coerce to element type T for colors and intensities
+abstract type AbstractColorChannels{T<:Number,N} <: Color{T,N} end
 
-Represent the multichannel fluorescence intensity at a point. `rgbⱼ` is an RGB color corresponding
-to fluorophore `j` (e.g., see [`fluorophore_rgb`](@ref)) whose emission intensity is `iⱼ`.
+ColorTypes.comp1(c::AbstractColorChannels) = c.channels[1]
+ColorTypes.comp2(c::AbstractColorChannels) = c.channels[2]
+ColorTypes.comp3(c::AbstractColorChannels) = c.channels[3]
+ColorTypes.comp4(c::AbstractColorChannels) = c.channels[4]
+ColorTypes.comp5(c::AbstractColorChannels) = c.channels[5]
 
-While the example shows two fluorophores, any number may be used, as long as the number of `rgb` colors
-matches the number of intensities `i`.
+Base.Tuple(c::AbstractColorChannels) = c.channels
 
-If you're constructing such colors in a high-performance loop, there may be other methods that may
-yield better performance due to challenges with type-inference, unless the color is known
-at compile time.
+function Base.show(io::IO, c::AbstractColorChannels)
+    print(io, '(')
+    chans = Tuple(c)
+    for (j, intensity) in enumerate(chans)
+        j > 1 && print(io, ", ")
+        print(io, intensity)
+        print_subscript(io, length(chans), j)
+    end
+    print(io, ')')
+end
 
-# Examples
+"""
+    ColorChannels(i₁, i₂, ...)
+    ColorChannels((i₁, i₂, ...))
+    ColorChannels{T}(...)                # coerce to element type T
 
-To construct a 16-bit "pixel" from a dual-channel EGFP (peak emission 507nm)/tdTomato (peak emission 581nm) image,
-you might do the following:
+Represent multichannel "raw" colors, which lack `convert` methods to standard color spaces.
+If `c` is a `ColorChannels` object, then `Tuple(c)` is a tuple of intensities (one per channel).
 
-```jldoctest
-julia> using FluorophoreColors
+[`ColorMixture`](@ref) is an alternative with a built-in conversion to RGB.
 
-julia> channelcolors = (fluorophore_rgb["EGFP"], fluorophore_rgb["tdTomato"]);
+# Examples
 
-julia> c = ColorMixture{N0f16}(channelcolors, #= GFP intensity =# 0.2, #= tdTomato intensity =# 0.85)
-(0.2N0f16₁, 0.85N0f16₂)
+## Hyperspectral/multiband colors
 
-julia> convert(RGB, c)
-RGB{N0f16}(0.85, 0.9151, 0.07294)
+Images from the [Operational Land Imager](https://en.wikipedia.org/wiki/Operational_Land_Imager) have
+[11 wavelength bands](https://landsat.gsfc.nasa.gov/satellites/landsat-8/landsat-8-bands/). A single pixel
+could be represented as
+
+```julia
+julia> using MultichannelColors
+
+julia> c = ColorChannels{N0f16}(0.25, 0.15, ...)   # 11 entries in all
 ```
 
-If you must construct colors inferrably inside a function body, use
+See the [FixedPointNumbers](https://github.com/JuliaMath/FixedPointNumbers.jl) package for information about `N0f16`.
+
+## Visualizing Images
+
+You can create a custom function mapping a `ColorChannel` to a numeric or RGB value and apply it to the image using
+broadcasting, or use [MappedArrays](https://github.com/JuliaArrays/MappedArrays.jl) to apply it "lazily"
+(useful for large data sets).
+
+Let's compute the [Enhanced Vegetation Index](https://www.usgs.gov/landsat-missions/landsat-enhanced-vegetation-index)
+and render positive values in green and negative values in magenta:
 
-```jldoctest; setup=:(using FluorophoreColors)
-julia> channelcolors = (fluorophore_rgb"EGFP", fluorophore_rgb"tdTomato");
+```julia
+julia> function evi(c::ColorChannels{T,11}) where T<:FixedPoint
+           # Valid for Landsat 8 with 11 spectral bands
+           b = Tuple(c)                      # extract the bands
+           evi = 2.5 * (b[5] - b[4]) / (b[5] + 6*b[4] - 7.5*b[2] + eps(T))
+           return evi > zero(evi) ? RGB(0, evi, 0) : RGB(-evi, 0, -evi)
+       end;
 
-julia> c = ColorMixture{N0f8}(channelcolors, #= GFP intensity =# 0.2, #= tdTomato intensity =# 0.85)
-(0.2N0f8₁, 0.851N0f8₂)
+julia> evi.(img)     # img is an array of ColorChannels{T,11} values
 ```
 
-This allows the RGB *values* to be visible to the compiler. However, the fluorophore names must be hard-coded,
-and you must preserve the `N0f8` element type of fluorophore_rgb"NAME".
+If the images are too dark, you may wish to apply some additional scaling to the `evi` value.
 """
-struct ColorMixture{T,N,Cs} <: Color{T,N}
+struct ColorChannels{T<:Number,N} <: AbstractColorChannels{T,N}
+    channels::NTuple{N,T}
+end
+
+ColorChannels{T}(channels::NTuple{N,Any}) where {T<:Number,N} = ColorChannels{T,N}(channels)
+ColorChannels{T}(channels::Vararg{Any,N}) where {T<:Number,N} = ColorChannels{T}(channels)
+
+ColorChannels(channels::NTuple{N,Number}) where {N} = ColorChannels(promote(channels...))
+ColorChannels(channels::Vararg{Number,N}) where {N} = ColorChannels(channels)
+
+
+"""
+    ColorMixture((rgb₁, rgb₂, ...), (i₁, i₂, ...))
+    ColorMixture((rgb₁, rgb₂, ...), i₁, i₂, ...)
+    ColorMixture{T}(...)                       # coerce intensities to element type
+
+Represent multichannel colors with a defined conversion to RGB. `rgbⱼ` is an RGB color corresponding
+to channel `j`, and its intensity is `iⱼ`.
+
+Colors are converted to RGB with intensity-weighting,
+``
+c_{rgb} = \\sum_j i_j \\mathrm{rgb}_j
+``
+Depending on the the `rgbⱼ` and `iⱼ`, values may exceed the 0-to-1 colorscale of RGBs.
+Conversion to `RGB{Float32}` may be safer than ones limited to 0-to-1.
+
+# Examples
+
+Let's create a two-channel value where channel 1 is rendered in cyan and channel 2 is rendered in red:
+
+```jldoctest
+julia> using MultichannelColors
+
+julia> channels = (RGB(0, 0.5, 0.5), RGB(1, 0, 0));
+
+julia> c = ColorMixture(channels, (0.8, 0.2))
+(0.8₁, 0.2₂)
+```
+"""
+struct ColorMixture{T<:Number,N,Cs} <: AbstractColorChannels{T,N}
     channels::NTuple{N,T}
 
     Compat.@constprop :aggressive function ColorMixture{T,N,Cs}(channels::NTuple{N}) where {T,N,Cs}
@@ -60,6 +125,7 @@ Compat.@constprop :aggressive ColorMixture{T}(Cs::NTuple{N,RGB{N0f8}}, channels:
 Compat.@constprop :aggressive ColorMixture{T}(Cs::NTuple{N,AbstractRGB}, channels::NTuple{N,Real}) where {T,N} = ColorMixture{T,N,RGB{N0f8}.(Cs)}(channels)
 Compat.@constprop :aggressive ColorMixture{T}(Cs::NTuple{N,AbstractRGB}, channels::Vararg{Real,N}) where {T,N} = ColorMixture{T}(Cs, channels)
 
+Compat.@constprop :aggressive ColorMixture(Cs::NTuple{N,AbstractRGB}, channels::NTuple{N,Integer}) where {N} = ColorMixture{N0f8}(Cs, channels)
 Compat.@constprop :aggressive ColorMixture(Cs::NTuple{N,AbstractRGB}, channels::NTuple{N,Real}) where {N} = ColorMixture{eltype(map(z -> zero(N0f8)*z, channels))}(Cs, channels)
 Compat.@constprop :aggressive ColorMixture(Cs::NTuple{N,AbstractRGB}, channels::Vararg{Real,N}) where {N} = ColorMixture(Cs, channels)
 
@@ -74,37 +140,27 @@ Create a ColorMixture `c` from a "template" `cobj`. `c` will be the same type as
 is known. In conjunction with a [function barrier](https://docs.julialang.org/en/v1/manual/performance-tips/#kernel-functions),
 this form can be used to circumvent performance problems due to poor inferrability.
 """
-ColorMixture{T}(Cs::NTuple{N,AbstractRGB}) where {T,N} = ColorMixture{T}(Cs, ntuple(_ -> zero(T), N))
+ColorMixture{T}(Cs::NTuple{N,AbstractRGB}) where {T<:Number,N} = ColorMixture{T}(Cs, ntuple(_ -> zero(T), N))
 ColorMixture(Cs::NTuple{N,RGB{N0f8}}) where {N} = ColorMixture{N0f8}(Cs)
 
 (::ColorMixture{T,N,Cs})(channels::NTuple{N,Real}) where {T,N,Cs} = ColorMixture{T,N,Cs}(channels)
 (::ColorMixture{T,N,Cs})(channels::Vararg{Real,N}) where {T,N,Cs} = ColorMixture{T,N,Cs}(channels)
 
 
-Base.:(==)(a::ColorMixture{Ta,N,Cs}, b::ColorMixture{Tb,N,Cs}) where {Ta,Tb,N,Cs} = a.channels == b.channels
+Base.:(==)(a::ColorMixture{Ta,N,Cs}, b::ColorMixture{Tb,N,Cs}) where {Ta<:Number,Tb<:Number,N,Cs} = a.channels == b.channels
 Base.:(==)(a::ColorMixture, b::ColorMixture) = false
 
-function Base.show(io::IO, c::ColorMixture)
-    print(io, '(')
-    for (j, intensity) in enumerate(c.channels)
-        j > 1 && print(io, ", ")
-        print(io, intensity)
-        print_subscript(io, length(c), j)
-    end
-    print(io, ')')
-end
+Base.isequal(a::ColorMixture{Ta,N,Cs}, b::ColorMixture{Tb,N,Cs}) where {Ta<:Number,Tb<:Number,N,Cs} = isequal(a.channels, b.channels)
+Base.isequal(a::ColorMixture, b::ColorMixture) = false
 
 # These definitions use floats to avoid overflow
-function Base.convert(::Type{RGB{T}}, c::ColorMixture{T,N,Cs}) where {T,N,Cs}
-    convert(RGB{T}, sum(map(*, c.channels, Cs); init=zero(RGB{floattype(T)})))
-end
-function Base.convert(::Type{RGB{T}}, c::ColorMixture{R,N,Cs}) where {T,R,N,Cs}
+function Base.convert(::Type{RGB{T}}, c::ColorMixture{R,N,Cs}) where {T,R<:Number,N,Cs}
     convert(RGB{T}, sum(map((w, rgb) -> convert(RGB{floattype(T)}, w*rgb), c.channels, Cs)))
 end
-Base.convert(::Type{RGB}, c::ColorMixture{T}) where T = convert(RGB{T}, c)
+Base.convert(::Type{RGB}, c::ColorMixture{T}) where T<:Number = convert(RGB{T}, c)
 Base.convert(::Type{RGB24}, c::ColorMixture) = convert(RGB24, convert(RGB, c))
 
 ColorTypes._comp(::Val{N}, c::ColorMixture) where N = c.channels[N]
-Compat.@constprop :aggressive ColorTypes.mapc(f, c::ColorMixture{T,N,Cs}) where {T,N,Cs} = ColorMixture(Cs, map(f, c.channels))
-Compat.@constprop :aggressive ColorTypes.mapreducec(f, op, v0, c::ColorMixture{T,N,Cs}) where {T,N,Cs} = mapreduce(f, op, v0, c.channels)
-Compat.@constprop :aggressive ColorTypes.reducec(op, v0, c::ColorMixture{T,N,Cs}) where {T,N,Cs} = reduce(op, c.channels; init=v0)
+Compat.@constprop :aggressive ColorTypes.mapc(f, c::ColorMixture{T,N,Cs}) where {T<:Number,N,Cs} = ColorMixture(Cs, map(f, c.channels))
+Compat.@constprop :aggressive ColorTypes.mapreducec(f, op, v0, c::ColorMixture{T,N,Cs}) where {T<:Number,N,Cs} = mapreduce(f, op, c.channels; init=v0)
+Compat.@constprop :aggressive ColorTypes.reducec(op, v0, c::ColorMixture{T,N,Cs}) where {T<:Number,N,Cs} = reduce(op, c.channels; init=v0)

test/runtests.jl

@@ -1,12 +1,12 @@
-using FluorophoreColors
+using MultichannelColors
 using Test
 
 # interacts via @require
 using StructArrays
 using ImageCore
 
-@testset "FluorophoreColors.jl" begin
-    @test isempty(detect_ambiguities(FluorophoreColors))
+@testset "MultichannelColors.jl" begin
+    @test isempty(detect_ambiguities(MultichannelColors))
 
     @testset "Fluorophore lookup" begin
         cfp = fluorophore_rgb["ECFP"]
@@ -78,8 +78,8 @@ using ImageCore
         else
             @test_broken @inferred(mapc(x->2x, c)) === ColorMixture{Float32}(channels, (0.8, 0.4))
         end
-        @test @inferred(mapreducec(x->2x, +, c)) === 1.2f0
-        @test @inferred(reducec(+, c)) === reduce(+, (0.4N0f8, 0.2N0f8))
+        @test @inferred(mapreducec(x->2x, +, 0f0, c)) === 1.2f0
+        @test @inferred(reducec(+, 0N0f8, c)) === reduce(+, (0.4N0f8, 0.2N0f8))
     end
 
     @testset "StructArrays" begin
@@ -94,7 +94,7 @@ using ImageCore
         @test red[1] === 0.0N0f8
 
         # Hyperspectral
-        cols = FluorophoreColors.Colors.distinguishable_colors(16, [RGB(0,0,0)]; dropseed=true)
+        cols = MultichannelColors.Colors.distinguishable_colors(16, [RGB(0,0,0)]; dropseed=true)
         ctemplate = ColorMixture{Float32}((cols...,))
         comps = collect(reshape((0:31)/32f0, 16, 2))
         compsr = reinterpret(reshape, typeof(ctemplate), comps)
@@ -123,10 +123,10 @@ using ImageCore
     @testset "IO" begin
         channels = (fluorophore_rgb["EGFP"], fluorophore_rgb["tdTomato"])
         c = ColorMixture(channels, (1, 0))
-        @test sprint(show, c) == "(1.0₁, 0.0₂)"
+        @test sprint(show, c) == "(1.0N0f8₁, 0.0N0f8₂)"
 
         # Hyperspectral
-        cols = FluorophoreColors.Colors.distinguishable_colors(16, [RGB(0,0,0)]; dropseed=true)
+        cols = MultichannelColors.Colors.distinguishable_colors(16, [RGB(0,0,0)]; dropseed=true)
         ctemplate = ColorMixture{Float32}((cols...,))
         c = ctemplate([i/16 for i = 0:15]...)
         @test sprint(show, c) == "(0.0₀₁, 0.0625₀₂, 0.125₀₃, 0.1875₀₄, 0.25₀₅, 0.3125₀₆, 0.375₀₇, 0.4375₀₈, 0.5₀₉, 0.5625₁₀, 0.625₁₁, 0.6875₁₂, 0.75₁₃, 0.8125₁₄, 0.875₁₅, 0.9375₁₆)"