diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 663f8d2..4c2ee4d 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -73,6 +73,6 @@ jobs: shell: julia --project=docs --color=yes {0} run: | using Documenter: DocMeta, doctest - using QMRIColors - DocMeta.setdocmeta!(QMRIColors, :DocTestSetup, :(using QMRIColors); recursive=true) - doctest(QMRIColors) + using QuantitativeMRIColors + DocMeta.setdocmeta!(QuantitativeMRIColors, :DocTestSetup, :(using QuantitativeMRIColors); recursive=true) + doctest(QuantitativeMRIColors) diff --git a/Project.toml b/Project.toml index d0e1b8f..a98fd6e 100644 --- a/Project.toml +++ b/Project.toml @@ -1,4 +1,4 @@ -name = "QMRIColors" +name = "QuantitativeMRIColors" uuid = "2bec176e-9e8c-4764-a62f-295118d1ec05" authors = ["aTrotier and contributors"] version = "1.0.0" diff --git a/README.md b/README.md index 14be601..2e67d40 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ -# QMRIColors +# QuantitativeMRIColors -[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://magneticresonanceimaging.github.io/QMRIColors.jl/stable/) -[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://magneticresonanceimaging.github.io/QMRIColors.jl/dev/) -[![Build Status](https://github.com/magneticresonanceimaging/QMRIColors.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/magneticresonanceimaging/QMRIColors.jl/actions/workflows/CI.yml?query=branch%3Amain) -[![Coverage](https://codecov.io/gh/magneticresonanceimaging/QMRIColors.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/magneticresonanceimaging/QMRIColors.jl) +[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://magneticresonanceimaging.github.io/QuantitativeMRIColors.jl/stable/) +[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://magneticresonanceimaging.github.io/QuantitativeMRIColors.jl/dev/) +[![Build Status](https://github.com/magneticresonanceimaging/QuantitativeMRIColors.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/magneticresonanceimaging/QuantitativeMRIColors.jl/actions/workflows/CI.yml?query=branch%3Amain) +[![Coverage](https://codecov.io/gh/magneticresonanceimaging/QuantitativeMRIColors.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/magneticresonanceimaging/QuantitativeMRIColors.jl) Julia package of https://github.com/mfuderer/colorResources @@ -20,19 +20,19 @@ Julia package of https://github.com/mfuderer/colorResources ```@example 1 # x is the image to be displayed, (loLev,upLev) is the relevant range of the values # we take T1 as an example -using QMRIColors +using QuantitativeMRIColors cmap,imClip = relaxationColorMap("T1",x,loLev,upLev) VIEW(imClip,c=cmap,clim=(loLev,upLev)) ``` > [!IMPORTANT] ->

In the above, "VIEW" refers to your favorite viewing software (CairoMakie, Plots, PyPlot, ...) : [see example](https://magneticresonanceimaging.github.io/QMRIColors.jl/dev/example/)

+>

In the above, "VIEW" refers to your favorite viewing software (CairoMakie, Plots, PyPlot, ...) : [see example](https://magneticresonanceimaging.github.io/QuantitativeMRIColors.jl/dev/example/)

The relaxationColorMap() function selects the appropriate color-map (in this case, Lipari for T1) and applies logarithm-processing on that color map. The resulting colormap is returned.

The "imclip" image should retain the distinction between the "invalid" value of 0 (which is to be displayed as black) and "valid" values that are below loLev (these should be shown in a dark shade of blue). Depending on the calibration of your screen, you may or may not see that distinction.


A simplified processing can be done by

```@example 2 -using QMRIColors +using QuantitativeMRIColors cmap = relaxationColorMap("T1") VIEW(x,c=cmap) # Do not use range limits here! ``` diff --git a/docs/Project.toml b/docs/Project.toml index 8a0e5f1..7458a2f 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -6,4 +6,4 @@ FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" JLD = "4138dd39-2aa7-5051-a626-17a0bb65d9c8" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9" -QMRIColors = "2bec176e-9e8c-4764-a62f-295118d1ec05" +QuantitativeMRIColors = "2bec176e-9e8c-4764-a62f-295118d1ec05" diff --git a/docs/make.jl b/docs/make.jl index f3ef8d9..c4ec5ab 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,14 +1,14 @@ -using QMRIColors +using QuantitativeMRIColors using Documenter -DocMeta.setdocmeta!(QMRIColors, :DocTestSetup, :(using QMRIColors); recursive=true) +DocMeta.setdocmeta!(QuantitativeMRIColors, :DocTestSetup, :(using QuantitativeMRIColors); recursive=true) makedocs(; - modules=[QMRIColors], + modules=[QuantitativeMRIColors], authors="aTrotier and contributors", - sitename="QMRIColors.jl", + sitename="QuantitativeMRIColors.jl", format=Documenter.HTML(; - canonical="https://magneticresonanceimaging.github.io/QMRIColors.jl", + canonical="https://magneticresonanceimaging.github.io/QuantitativeMRIColors.jl", edit_link="main", assets=String[], ), @@ -22,6 +22,6 @@ makedocs(; ) deploydocs(; - repo="github.com/MagneticResonanceImaging/QMRIColors.jl", + repo="github.com/MagneticResonanceImaging/QuantitativeMRIColors.jl", devbranch="main", ) diff --git a/docs/src/api.md b/docs/src/api.md index 1da5c3f..8d7ff11 100644 --- a/docs/src/api.md +++ b/docs/src/api.md @@ -2,5 +2,5 @@ ``` ```@autodocs -Modules = [QMRIColors] +Modules = [QuantitativeMRIColors] ``` diff --git a/docs/src/clip.md b/docs/src/clip.md index 6bc394a..16e358a 100644 --- a/docs/src/clip.md +++ b/docs/src/clip.md @@ -6,7 +6,7 @@ The "imclip" image should retain the distinction between the "invalid" value of A simplified processing can be done by ```julia -using QMRIColors +using QuantitativeMRIColors cmap = relaxationColorMap("T1") VIEW(x,c=cmap) # Do not use range limits here! ``` @@ -23,7 +23,7 @@ Let's build an example to see the effect. ## Create a Synthetic phantom ```@example clip -using QMRIColors +using QuantitativeMRIColors using CairoMakie # ----- Make test object: gradually increasing T1, but invalid outside a circle diff --git a/docs/src/colormaps.md b/docs/src/colormaps.md index 899077e..0d6a806 100644 --- a/docs/src/colormaps.md +++ b/docs/src/colormaps.md @@ -1,7 +1,7 @@ # qMRI colormaps ```@example 1 -using QMRIColors +using QuantitativeMRIColors using CairoMakie ``` diff --git a/docs/src/example.md b/docs/src/example.md index 7061a6b..3b44ef5 100644 --- a/docs/src/example.md +++ b/docs/src/example.md @@ -9,7 +9,7 @@ Download sample used in the following example ```@example 3 using FileIO using Downloads -using QMRIColors +using QuantitativeMRIColors using CairoMakie url = "https://github.com/mfuderer/colorResources/raw/refs/heads/main/sampleT1map.jld" @@ -25,7 +25,7 @@ nothing # hide For `Makie.jl` the colormap can be directly used like `heatmap(x,colormap=cmap,colorrange=(loLev,upLev))` ```@example 3 -using QMRIColors +using QuantitativeMRIColors using CairoMakie # ----- Make test object: gradually increasing T1, but invalid outside a circle @@ -69,7 +69,7 @@ end Using GR backend ```@example 3 -using QMRIColors +using QuantitativeMRIColors using Plots #GR backend loLev = 700 @@ -90,7 +90,7 @@ The colormap needs to be converted to a usable format with the following command ```@example 4 using FileIO -using QMRIColors +using QuantitativeMRIColors x = FileIO.load("sampleT1map.jld")["sampleT1map"] diff --git a/docs/src/index.md b/docs/src/index.md index ebda43d..f7d6838 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,8 +1,8 @@ ```@meta -CurrentModule = QMRIColors +CurrentModule = QuantitativeMRIColors ``` -Documentation for [QMRIColors](https://github.com/magneticresonanceimaging/QMRIColors.jl). +Documentation for [QuantitativeMRIColors](https://github.com/magneticresonanceimaging/QuantitativeMRIColors.jl). # Introduction diff --git a/src/qMRIColors.jl b/src/qMRIColors.jl index 7a5eb81..d81eda0 100644 --- a/src/qMRIColors.jl +++ b/src/qMRIColors.jl @@ -1,4 +1,4 @@ -module QMRIColors +module QuantitativeMRIColors export relaxationColorMap, colorLogRemap, read_map_csv using Colors diff --git a/test/runtests.jl b/test/runtests.jl index df74bd7..901acea 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,8 +1,8 @@ -using QMRIColors +using QuantitativeMRIColors using Colors using Test -@testset "QMRIColors.jl" begin +@testset "QuantitativeMRIColors.jl" begin @testset "colormap" begin # T1 test