Rename package and redesign types #5
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## main #5 +/- ##
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- Coverage 67.07% 60.00% -7.08%
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- Misses 27 38 +11
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The conceptual changes look good to me. Although I'm not sure if AbstractColorChannels and ColorChannels (plural form) are good names for types -- we usually use plural forms for modules. How about AbstractMultiChannelColor and MultiChannelColor?
We might need to support alias for specific channels -- I'm thinking of something like this:
const MColor2Channels = (RGB(0, 0.5, 0.5), RGB(1, 0, 0))
const MColor2{T} = ColorMixture{T,2,MColor2Channels}
MColor2{Float32}(0.8, 0.2) # equivalent to `ColorMixture(MColor2Channels, (0.8, 0.2))`For ColorMixture, to avoid confusions. we need to clearly document that it is not RGB colorspace:
length(T)is not3mapcapplies to the original channels and not to the RGB channels- etc
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. The package name has been changed to reflect the wider applicability. This also adds Documenter documentation and slims the README.
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Addressed the points above. Now with greatly expanded documentation. The docs talk about arithmetic operations, but those will be implemented in the next PR. |
| The color types in this package support two fundamental categories of operations: | ||
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| - arithmetic operations such as `+` and `-` and multiplying or dividing by a scalar. You can also scale each color channel independently with `⊙` (obtained with `\odotTAB`) or its synonym `hadamard`, e.g., `g ⊙ c` where `c` is a color object defined in this package and `g` is a tuple of real numbers (the "gains"). | ||
| - extracting the independent channel intensities as a tuple with `Tuple(c)`. |
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| Use the package interactively or in code with | ||
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| ```jldoctest demo |
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Just a confirmation: is the jldoctest deliberately used here rather than the @repl block?
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Yes, though there are many ways to solve the same problem. Basically I want doctests to make sure the code keeps working, and I don't want to have to use setup=:(using MultiChannelColors) on each doctest. So I created a named doctest, demo, and am loading the package in the first instance.
| julia> typeof(ctemplate) | ||
| ColorMixture{Float32, 2, (RGB{N0f8}(0.0,1.0,0.0), RGB{N0f8}(1.0,0.0,0.0))} | ||
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| julia> c = ctemplate(0.2, 0.4) |
| ```julia | ||
| A = rand(0x0000:0x0fff, 100, 100, 11); | ||
| img = StructArray{MultiChannelColor{N4f12,11}}(A; dims=3) | ||
| ``` |
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If we provide a better tool in ImageCore in the spirit of JuliaImages/ImageCore.jl#179, then this story might be changed.
Might be worth leaving a note about future improvement.
I was thinking of something like:
module ImageLayouts
const CHW = DenseImageLayout{:CHW}()
const CWH = DenseImageLayout{:CWH}()
const HWC = DenseImageLayout{:HWC}()
endso that users can use a unified interface:
using ImageCore # which exports the ImageLayouts module
colorview(ImageLayouts.CHW, img)we might end up with a new function, though -- pretty much like the strel concept I introduced in ImageMorphology.
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Yes, I really like the idea of these custom layouts!
| If you'll be hard-coding the name of the fluorophore, consider using a slightly different syntax: | ||
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| ```jldoctest demo | ||
| julia> channels = (fluorophore_rgb"EGFP", fluorophore_rgb"tdTomato") |
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Will fluorophore"EGFP" be easier to use? I'm not sure. -- just that I have never seen underscores used in string macros.
Is there non-RGB fluorophore?
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No non-RGB fluorophore currently. I guess I would think that fluorophore"EGFP" might return an entire object that is a complete characterization of the fluorophore, e.g., full spectra, cross section, quantum yield, and so on (this list only scratches the surface). In contrast, fluorophore_rgb makes it clear that what you're getting is an RGB value that represents the fluorophore.
Co-authored-by: Johnny Chen <[email protected]>
This creates an abstract
AbstractColorChannelstype and two types,ColorChannelsandColorMixture.ColorChannelsis 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.
ColorMixtureis theweighted-RGB color type.
Closes #2