Updated docs

grizzuti · Mar 7, 2023 · 9f351c7 · 9f351c7
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diff --git a/Manifest.toml b/Manifest.toml
@@ -20,7 +20,7 @@ version = "1.0.0"
 
 [[deps.AbstractProximableFunctions]]
 deps = ["AbstractLinearOperators", "LinearAlgebra", "Roots"]
-git-tree-sha1 = "f6aff955ee16ca57db3d95d7267f05304814dcba"
+git-tree-sha1 = "84aa8fc140e1930dea273c261b0b7a0d4aa9a3b8"
 repo-rev = "main"
 repo-url = "https://github.com/grizzuti/AbstractProximableFunctions.git"
 uuid = "9ed10759-246d-4065-822b-90d32585fe69"
@@ -214,9 +214,9 @@ version = "0.3.0"
 
 [[deps.Compat]]
 deps = ["Dates", "LinearAlgebra", "UUIDs"]
-git-tree-sha1 = "61fdd77467a5c3ad071ef8277ac6bd6af7dd4c04"
+git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.6.0"
+version = "4.6.1"
 
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -355,9 +355,9 @@ version = "0.3.2"
 
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
-git-tree-sha1 = "90630efff0894f8142308e334473eba54c433549"
+git-tree-sha1 = "f9818144ce7c8c41edf5c4c179c684d92aa4d9fe"
 uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-version = "1.5.0"
+version = "1.6.0"
 
 [[deps.FFTW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -810,9 +810,9 @@ version = "0.12.3"
 
 [[deps.Parsers]]
 deps = ["Dates", "SnoopPrecompile"]
-git-tree-sha1 = "6f4fbcd1ad45905a5dee3f4256fabb49aa2110c6"
+git-tree-sha1 = "478ac6c952fddd4399e71d4779797c538d0ff2bf"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.5.7"
+version = "2.5.8"
 
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "RetrospectiveMotionCorrectionMRI"
 uuid = "24772341-69a6-4cfa-a9d8-04aed0acc5f5"
 authors = ["Gabrio Rizzuti <rizzuti.gabrio@gmail.com>"]
-version = "0.1.0"
+version = "1.0.0"
 
 [deps]
 AbstractLinearOperators = "bb902dec-a34b-4f3c-9707-4856bea60ee0"

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,23 +1,19 @@
-using Documenter, AbstractProximableFunctions, FastSolversForWeightedTV, RetrospectiveMotionCorrectionMRI
+using Documenter, AbstractLinearOperators, AbstractProximableFunctions, FastSolversForWeightedTV, RetrospectiveMotionCorrectionMRI
 
 const RealOrComplex{T<:Real} = Union{T, Complex{T}}
 
 format = Documenter.HTML()
 
 Introduction = "Introduction" => "index.md"
 Installation = "Installation" => "installation.md"
+Theory = "Rigid motion correction for MRI" => "theory.md"
 GettingStarted = "Getting started" => "examples.md"
-Fourier = "Motion-perturbed Fourier transform" => "Fourier.md"
-ParameterEstimation = "Rigid motion parameter estimation" => "parameter_estimation.md"
-ImageReconstruction = "Image reconstruction" => "image_reconstruction.md"
 MainFunctions = "Main functions" => "functions.md"
 
 PAGES = [
     Introduction,
     Installation,
-    Fourier,
-    ImageReconstruction,
-    ParameterEstimation,
+    Theory,
     GettingStarted,
     MainFunctions
     ]

diff --git a/docs/src/Fourier.md b/docs/src/Fourier.md
diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -1,3 +1,3 @@
-# Getting started
+# [Getting started](@id examples)
 
 aaa
diff --git a/docs/src/functions.md b/docs/src/functions.md
@@ -1,5 +1,30 @@
 # Main functions
 
+## Motion correction
+
+```@docs
+motion_corrected_reconstruction(F::RetrospectiveMotionCorrectionMRI.StructuredNFFTtype2LinOp{T}, d::AbstractArray{CT,2}, u::AbstractArray{CT,3}, θ::AbstractArray{T,2}, options::RetrospectiveMotionCorrectionMRI.MotionCorrectionOptionsAlternatingFISTADiff) where {T<:Real,CT<:RealOrComplex{T}}
+```
+
+```@docs
+motion_correction_options(; image_reconstruction_options::ImageReconstructionOptionsFISTA, parameter_estimation_options::ParameterEstimationOptionsDiff, niter::Integer, niter_estimate_Lipschitz::Union{Nothing,Integer}=nothing, verbose::Bool=false, fun_history::Bool=false)
+```
+
+## Image reconstruction
+
+```@docs
+image_reconstruction(F::AbstractLinearOperator{CT,3,2}, d::AbstractArray{CT,2}, initial_estimate::AbstractArray{CT,3}, options::RetrospectiveMotionCorrectionMRI.ImageReconstructionOptionsFISTA) where {CT<:RealOrComplex}
+```
+
+```@docs
+image_reconstruction_options(; prox::AbstractProximableFunction,
+                               Lipschitz_constant::Union{Nothing,Real}=nothing,
+                               Nesterov::Bool=true,
+                               reset_counter::Union{Nothing,Integer}=nothing,
+                               niter::Union{Nothing,Integer}=nothing,
+                               verbose::Bool=false,
+                               fun_history::Bool=false)
+```
 
 ## Rigid motion parameter estimation
 

diff --git a/docs/src/image_reconstruction.md b/docs/src/image_reconstruction.md
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,10 +1,11 @@
 # [Introduction](@id intro)
 
-This package implements the algorithmic tools to perform retrospective motion correction for MRI based on a reference-guided TV regularization (see `[2]`). It combines several custom packages, the most important building blocks are:
+This package implements the algorithmic tools to perform retrospective motion correction for MRI based on a reference-guided TV regularization (see [[2]](@ref references)). It combines several custom packages, the most important building blocks are:
 - `FastSolversForWeightedTV`: for the computation of proximal/projection operators 
 - `UtilitiesForMRI`: for the computation and differentiation of the non-uniform Fourier transform with respect to rigid-body motion perturbation.
 
 ## [Related publications](@id references)
 
 1. Ehrhardt, M. J., and Betcke, M. M., (2015). Multi-Contrast MRI Reconstruction with Structure-Guided Total Variation (https://arxiv.org/abs/1511.06631), _SIAM J. IMAGING SCIENCES_, **9(3)**, 1084-1106, doi:[10.1137/15M1047325](https://doi.org/10.1137/15M1047325)
-2. Rizzuti, G., Sbrizzi, A., and van Leeuwen, T., (2022). Joint Retrospective Motion Correction and Reconstruction for Brain MRI With a Reference Contrast, _IEEE Transaction on Computational Imaging_, **8**, 490-504, doi:[10.1109/TCI.2022.3183383](hhtps://doi.org/10.1109/TCI.2022.3183383)
+2. Rizzuti, G., Sbrizzi, A., and van Leeuwen, T., (2022). Joint Retrospective Motion Correction and Reconstruction for Brain MRI With a Reference Contrast, _IEEE Transaction on Computational Imaging_, **8**, 490-504, doi:[10.1109/TCI.2022.3183383](hhtps://doi.org/10.1109/TCI.2022.3183383)
+3. Beck, A., and Teboulle, M., (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems, _SIAM Journal on Imaging Sciences_, **2(1)**, 183-202, doi:[10.1137/080716542](https://doi.org/10.1137/080716542)
diff --git a/docs/src/parameter_estimation.md b/docs/src/parameter_estimation.md