Separate KomaMRI into simpler subpackages

[cncastillo]

This needs to be done to remove a lot of the dependencies of the UI like Blink, PlotlyJS, etc.

The idea of doing this is to reduce the number of dependencies to the minimum if someone just wants to simulate data.

To replace MRIReco, the KomaMRIBase package should use instead:
MRIBase
-> RawAcquisitionData
-> AcquisitionData
MRIFiles
-> ISMRMRD

Then, the KomaMRI package can have other dependencies.

Not sure if the plots for our datatypes should be included in KomaMRIBase. Maybe also have KomaMRIPlots?

In summary:
├── KomaMRI.jl (depends on Base and UI)
│ ├── KomaMRIBase.jl (least dependencies)
│ └── KomaMRIPlots.jl (separated to include plots only if needed)

We will need to think about the best way to do this.

---

Subpackages:

• KomaMRIBase #265
• KomaMRICore
• KomaMRIFiles #232
• KomaMRIPlots

[cncastillo]

We need to think what goes where: KomaMRI (UI, All the rest); KomaMRIBase (simulation); KomaMRIPlots (Plots)

• ArgCheck = "2" <---Used, but not neccessary
• AssetRegistry = "0.1" <---UI
• Blink = "0.12" <---UI
• CUDA = "3" <---Base
• Distributions = "0.25" <---Base
• FFTW = "1" <---(?)
• FileIO = "1" <---IO
• HDF5 = "0.16" <---IO
• Hwloc = "2" <---N threads
• Images = "0.24, 0.25" <---(?)
• Interact = "0.10" <---UI
• Interpolations = "0.13, 0.14" <--Base
• Ipopt = "0.7, 1" <---Example DiffPrepMCMRF
• JLD2 = "0.4" <---IO
• JuMP = "0.21, 1" <---Example DiffPrepMCMRF
• LinearOperators = "2" <---(?)
• MAT = "0.10" <---IO
• MRIReco = "0.4.2" <---Recon
• MathOptInterface = "0.9, 0.10, 1" <---Example DiffPrepMCMRF
• Mux = "0.7" <---UI
• PackageCompiler = "1, 2" <---Not used
• Parameters = "0.12" <---Base
• PlotlyJS = "0.18" <---Plots/UI
• ProgressMeter = "1" <---Base
• Reexport = "1" <---MRIReco/Blink
• Scanf = "0.5" <---Example DiffPrepMCMRF
• Suppressor = "0.2" <--Not used

[beorostica]

(needed) CUDA = "3" <---Base
(needed) Hwloc = "2" <---Base
(needed) Interpolations = "0.13, 0.14" <-- Base, (por sacar)
(added) MRIFiles <---Base
(needed) Parameters = "0.12" <---Base
(needed) ProgressMeter = "1" <---Base
(needed) Reexport = "1" <---Base
(added) ThreadsX <--- Base
(needed) PlotlyJS = "0.18" <---Base (Plots), UI

(needed) FileIO = "1" <---Base, IO
(needed) HDF5 = "0.16" <---Base, IO
(needed) JLD2 = "0.4" <---Base, IO
(needed) MAT = "0.10" <---Base, IO
(needed) Scanf = "0.5" <---Base, IO

(needed) AssetRegistry = "0.1" <---UI
(needed) Blink = "0.12" <---UI
(needed) Interact = "0.10" <---UI
(needed) MRIReco = "0.4.2" <---Reco, UI

[cncastillo]

For the moment, it was decided to separate the package in:

├── KomaMRI.jl: includes the KomaUI and Reconstruction (dependencies: Blink, Mux, MRIReco, KomaMRICore, KomaMRIPlots, etc).

• (needed) AssetRegistry = "0.1" <---UI
• (needed) Blink = "0.12" <---UI
• (needed) Interact = "0.10" <---UI
• (needed) MRIReco = "0.4.2" <---Reco, UI

│ ├── KomaMRICore.jl: least amount of dependencies, just simulation, and IO: Pulseq, ISMRMRD, etc.

• (needed) CUDA = "3" <---Base
• (needed) Hwloc = "2" <---Base
• (needed) Interpolations = "0.13, 0.14" <-- Base, (por sacar)
• (added) MRIFiles <---Base
• (needed) Parameters = "0.12" <---Base
• (needed) ProgressMeter = "1" <---Base
• (needed) Reexport = "1" <---Base
• (added) ThreadsX <--- Base
• (needed) FileIO = "1" <---Base, IO
• (needed) HDF5 = "0.16" <---Base, IO
• (needed) JLD2 = "0.4" <---Base, IO
• (needed) MAT = "0.10" <---Base, IO
• (needed) Scanf = "0.5" <---Base, IO

│ └── KomaMRIPlots.jl: just the Plots, mainly to remove PlotlyJS as a dependency as it could be a heavy package.

• (needed) PlotlyJS = "0.18" <---Base (Plots), UI

@beorostica Please use these names. All the KomaUI.jl stuff is part of KomaMRI.jl, not KomaMRIPlots. KomaMRIPlots should include the functions defined in DisplayFunctions.jl. For the time being, I would focus on KomaMRICore.

[cncastillo]

This issue should not be closed as separating the IO part is necessary @beorostica. Also we will remove CUDA.jl as a strong dependancy with package extensions and allow the use of more backends:

• Move KomaCore to use KernelAbstractions.jl (to support CUDA, AMD, Metal, etc) #179

│ ├── KomaMRICore.jl: least amount of dependencies, just simulation
(needed) CUDA = "3" <---Base
(needed) Hwloc = "2" <---Base
(needed) Interpolations = "0.13, 0.14" <-- Base, (Do we need this dependancy???)
(added) MRIFiles <---Base
(needed) Parameters = "0.12" <---Base
(needed) ProgressMeter = "1" <---Base
(needed) Reexport = "1" <---Base
(added) ThreadsX <--- Base
│ ├── KomaMRIIO.jl: IO helper functions: read/write Pulseq, read JEMRIS/MRiLab etc.
(needed) FileIO = "1" <---Base, IO
(needed) HDF5 = "0.16" <---Base, IO
(needed) JLD2 = "0.4" <---Base, IO
(needed) MAT = "0.10" <---Base, IO
(needed) Scanf = "0.5" <---Base, IO

There are some questions that are important:

• Do we want the phantom examples to be part of the core? (like bran_phantom_2d) We could separate to a package KomaMRIPhantoms.jl for examples. as they could be quite heavy specialy if we want to add phantoms with realistic data. They also should be stored in the HDF5 phantom file Motion Phantom #183.
• Do we want the MRD export to be part of the core? The default could always be a matrix and as a package extension when importing using MRIFiles automatically export to MRD.

We need to reevaluate the dependancies given the changes that are being done to the internal interpolation.