Fix multiple docs warnings

KomaMRICore/src/KomaMRICore.jl

@@ -48,8 +48,6 @@ export Grad, RF, ADC, Delay
 export Mag, dur
 #Phantom
 export brain_phantom2D, brain_phantom3D
-#Spinors
-export Spinor, Rx, Ry, Rz, Q, Un
 #Secondary
 export get_kspace, rotx, roty, rotz
 #ISMRMRD

KomaMRICore/src/simulation/GPUFunctions.jl

@@ -12,11 +12,11 @@ function print_gpus()
     check_use_cuda()
     if use_cuda[]
 	    cuda_devices = [Symbol("($(i-1)$(i == 1 ? "*" : " "))") => name(d) for (i,d) = enumerate(devices())]
-		@info "$(length(devices())) CUDA capable device(s)." cuda_devices... 
+		@info "$(length(devices())) CUDA capable device(s)." cuda_devices...
     else
         @info "0 CUDA capable devices(s)."
     end
-	return 
+	return
 end
 
 """
@@ -47,7 +47,11 @@ adapt_storage(to::KomaCUDAAdaptor, x) = CUDA.cu(x)
 
 Tries to move `x` to the current GPU device. Inspired by Flux's `gpu` function.
 
-This works for functions, and any struct marked with [`@functor`](@ref).
+This works for functions, and any struct marked with `@functor`.
+
+Use [`cpu`](@ref) to copy back to ordinary `Array`s.
+
+See also [`f32`](@ref) and [`f64`](@ref) to change element type only.
 
 # Examples
 ```julia
@@ -70,7 +74,9 @@ adapt_storage(to::KomaCPUAdaptor, x::AbstractRange) = x
 
 Tries to move object to CPU. Inspired by Flux's `cpu` function.
 
-This works for functions, and any struct marked with [`@functor`](@ref).
+This works for functions, and any struct marked with `@functor`.
+
+See also [`gpu`](@ref).
 
 # Examples
 ```julia
@@ -88,15 +94,21 @@ adapt_storage(T::Type{<:Real}, xs::AbstractArray{<:Bool}) = xs #Type piracy
 
 """
     f32(m)
+
 Converts the `eltype` of model's parameters to `Float32`
-Recurses into structs marked with [`@functor`](@ref).
+Recurses into structs marked with `@functor`.
+
+See also [`f64`](@ref).
 """
 f32(m) = paramtype(Float32, m)
 
 """
     f64(m)
+
 Converts the `eltype` of model's parameters to `Float64` (which is Koma's default)..
-Recurses into structs marked with [`@functor`](@ref).
+Recurses into structs marked with `@functor`.
+
+See also [`f32`](@ref).
 """
 f64(m) = paramtype(Float64, m)
 

KomaMRICore/src/simulation/SimulatorCore.jl

@@ -6,7 +6,40 @@ include("Bloch/BlochSimulationMethod.jl") #Defines Bloch simulation method
 include("Bloch/BlochDictSimulationMethod.jl") #Defines BlochDict simulation method
 
 """
-Returns a dictionary with default simulation parameters.
+    sim_params = default_sim_params(sim_params=Dict{String,Any}())
+
+This function returns a dictionary containing default simulation parameters while also
+allowing the user to define some of them.
+
+# Arguments
+- `sim_params`: (`::Dict{String,Any}`, `=Dict{String,Any}()`) user-defined dictionary with
+    simulation parameters. The following lists its keys along with their possible values:
+    * "return_type": defines the output of the [`simulate`](@ref) function. Possible values
+        are `"raw"`, `"mat"`, and `"state"`, corresponding to outputting a MRIReco
+        `RawAcquisitionData`, the signal values, and the last magnetization state of the
+        simulation, respectively
+    * "sim_method": defines the type of simulation. The default value is `Bloch()`, but you
+        can alternatively use the `BlochDict()` simulation method. Moreover, you have the
+        flexibility to create your own methods without altering the KomaMRI source code
+    * "Δt": raster time for gradients
+    * "Δt_rf": raster time for RFs
+    * "precision": defines the floating-point simulation precision. You can choose between
+        `"f32"` and `"f64"` to use `Float32` and `Float64` primitive types, respectively.
+        It's important to note that, especially for GPU operations, using `"f32"` is
+        generally much faster
+    * "Nblocks": divides the simulation into a specified number of time blocks. This parameter
+        is designed to conserve RAM resources, as **KomaMRI** computes a series of
+        simulations consecutively, each with the specified number of blocks determined by
+        the value of `"Nblocks"`
+    * "Nthreads": divides the **Phantom** into a specified number of threads. Because spins
+        are modeled independently of each other, **KomaMRI** can solve simulations in
+        parallel threads, speeding up the execution time
+    * "gpu": is a boolean that determines whether to use GPU or CPU hardware resources, as
+        long as they are available on the host computer
+    * "gpu_device": sets the index ID of the available GPU in the host computer
+
+# Returns
+- `sim_params`: (`::Dict{String,Any}`) dictionary with simulation parameters
 """
 function default_sim_params(sim_params=Dict{String,Any}())
     get!(sim_params, "gpu", true); if sim_params["gpu"] check_use_cuda(); sim_params["gpu"] &= use_cuda[] end

KomaMRICore/test/runtests.jl

@@ -415,6 +415,8 @@ end
 end
 
 @testitem "Spinors×Mag" tags=[:core] begin
+    using KomaMRICore: Spinor, Rx, Ry, Rz, Q, Un
+
     # Spinor 2x2 representation should be equivalent to a 3x1 vector rotation
     x = rand(3); x = x./sum(x)
     θ = rand() * π

docs/make.jl

@@ -68,6 +68,7 @@ makedocs(
     modules = [KomaMRI, KomaMRICore, KomaMRIFiles, KomaMRIPlots],
     sitename = "KomaMRI.jl: General MRI simulation framework",
     authors = "Boris Orostica Navarrete and Carlos Castillo Passi",
+    checkdocs = :exports,
     pages = [
         "Home" => "index.md";
         "Getting Started" => "getting-started.md";

docs/src/api.md

@@ -100,33 +100,66 @@ ADC
 Delay
 ```
 
-## Read Data
 
-```@meta
-CurrentModule = KomaMRIFiles
+## Sequence-related Functions
+
+### `dur`
+```@docs
+dur
 ```
 
-### `read_seq`
+### `rotx`
 ```@docs
-read_seq
+rotx
 ```
 
-### `read_phantom_jemris`
+### `roty`
 ```@docs
-read_phantom_jemris
+roty
 ```
 
-### `read_phantom_MRiLab`
+### `rotz`
 ```@docs
-read_phantom_MRiLab
+rotz
 ```
 
-### `signal_to_raw_data`
+### `get_kspace`
 ```@docs
-signal_to_raw_data
+get_kspace
 ```
 
-## Pulse Design
+### `get_M1`
+```@docs
+get_M1
+```
+
+### `get_M2`
+```@docs
+get_M2
+```
+
+### `get_flip_angles`
+```@docs
+get_flip_angles
+```
+
+### `is_RF_on`
+```@docs
+is_RF_on
+```
+
+### `is_GR_on`
+```@docs
+is_GR_on
+```
+
+### `is_ADC_on`
+```@docs
+is_ADC_on
+```
+
+
+## Prebuilt Sequence Building Blocks
 
 ```@meta
 CurrentModule = KomaMRICore
@@ -167,8 +200,63 @@ PulseDesigner.spiral_base
 PulseDesigner.EPI_example
 ```
 
+
+## Input/Output
+
+```@meta
+CurrentModule = KomaMRIFiles
+```
+
+### `read_seq`
+```@docs
+read_seq
+```
+
+### `read_phantom_jemris`
+```@docs
+read_phantom_jemris
+```
+
+### `read_phantom_MRiLab`
+```@docs
+read_phantom_MRiLab
+```
+
+
+## Functor Functions
+
+```@meta
+CurrentModule = KomaMRICore
+```
+
+### `f32`
+```@docs
+f32
+```
+
+### `f64`
+```@docs
+f64
+```
+
+### `cpu`
+```@docs
+cpu
+```
+
+### `gpu`
+```@docs
+gpu
+```
+
+
 ## Simulation
 
+### `default_sim_params`
+```@docs
+default_sim_params
+```
+
 ### `simulate`
 ```@docs
 simulate
@@ -179,6 +267,17 @@ simulate
 simulate_slice_profile
 ```
 
+### `signal_to_raw_data`
+```@docs
+signal_to_raw_data
+```
+
+### `Mag`
+```@docs
+Mag
+```
+
+
 ## Plots
 
 ```@meta
@@ -235,6 +334,16 @@ plot_signal
 plot_image
 ```
 
+### `plot_dict`
+```@docs
+plot_dict
+```
+
+### `plot_seqd`
+```@docs
+plot_seqd
+```
+
 
 ## UI
 

docs/src/create-your-own-phantom.md

@@ -115,7 +115,7 @@ T2 = T2*1e-3
 T2s = T2s*1e-3
 ```
 
-Finally, we can invoke the [`Phantom`](@Ref) constructor. However, before doing so, we choose not to store spins where the proton density is zero to avoid unnecessary data storage. This is achieved by applying the mask `ρ.!=0` to the arrays. Additionally, please note that we set the z-position array filled with zeros.
+Finally, we can invoke the [`Phantom`](@ref) constructor. However, before doing so, we choose not to store spins where the proton density is zero to avoid unnecessary data storage. This is achieved by applying the mask `ρ.!=0` to the arrays. Additionally, please note that we set the z-position array filled with zeros.
 ```julia
 # Define the phantom
 obj = Phantom{Float64}(