Release 0.0.4 (#17)

.github/workflows/CI.yml

@@ -3,6 +3,7 @@ on:
   push:
     branches:
       - main
+      - develop
     tags: '*'
   pull_request:
 concurrency:

Project.toml

@@ -1,7 +1,7 @@
 name = "MPIMagneticFields"
 uuid = "f6dda52a-86e9-4b50-afb7-f39836a99446"
 authors = ["Marija Boberg <[email protected]> and contributors"]
-version = "0.0.3"
+version = "0.0.4"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

README.md

@@ -2,6 +2,7 @@
 
 Package for handling the magnetic fields used in [Magnetic Particle Imaging](https://en.wikipedia.org/wiki/Magnetic_particle_imaging).
 
+[![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://magneticparticleimaging.github.io/MPIMagneticFields.jl/main/)
 [![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://magneticparticleimaging.github.io/MPIMagneticFields.jl/dev/)
 [![Build status](https://github.com/MagneticParticleImaging/MPIMagneticFields.jl/workflows/CI/badge.svg)](https://github.com/MagneticParticleImaging/MPIMagneticFields.jl/actions)
 [![codecov.io](https://codecov.io/gh/MagneticParticleImaging/MPIMagneticFields.jl/branch/main/graph/badge.svg)](https://app.codecov.io/github/MagneticParticleImaging/MPIMagneticFields.jl/tree/main)

example/FFLOrientation.jl

@@ -0,0 +1,9 @@
+using MPIMagneticFields
+using PyPlot
+
+field = IdealXYFFL(5.0)
+
+for angle in 0:pi/10:2pi
+  imshow([sign(val[1]) == sign(val[2]) ? sign(val[1]) + sign(val[2]) > 0 : sign(val[1]) - sign(val[2]) > 0 for val in value(field, [-0.02:0.001:0.02, -0.02:0.001:0.02, 0], angle)])
+  sleep(1)
+end

example/NewDefinition.jl

@@ -0,0 +1,36 @@
+using MPIMagneticFields
+using PyPlot
+using LinearAlgebra
+
+mutable struct IdealDipoleField{T, V} <: AbstractMagneticField where {T <: Number, V <: AbstractVector{T}}
+  magneticMoment::V
+
+  function IdealDipoleField(magneticMoment::V) where {T <: Number, V <: AbstractVector{T}}
+    return new{T, V}(magneticMoment)
+  end
+end
+
+MPIMagneticFields.FieldStyle(::IdealDipoleField) = OtherField()
+MPIMagneticFields.FieldDefinitionStyle(::IdealDipoleField) = MethodBasedFieldDefinition()
+MPIMagneticFields.FieldTimeDependencyStyle(::IdealDipoleField) = TimeConstant()
+
+function MPIMagneticFields.value_(field::IdealDipoleField, r)
+  if norm(r) == 0
+    return zeros(eltype(field.magneticMoment), length(field.magneticMoment))
+  else
+    return MPIMagneticFields.μ₀/(4*π) * (3 .* r .* dot(field.magneticMoment, r) ./ norm(r)^5 .- field.magneticMoment*norm(r)^3)
+  end
+end
+
+dipole = IdealDipoleField([0.1, 0.0, 0.0])
+
+xyRange = -0.02:0.0001:0.02
+quiverPoints = [(x, y) for x in xyRange[1:50:end] for y in xyRange[1:50:end]]
+X = [x for (x, y) in quiverPoints]
+Y = [y for (x, y) in quiverPoints]
+U = [dipole[x, y, 0][1] for (x, y) in quiverPoints]
+V = [dipole[x, y, 0][2] for (x, y) in quiverPoints]
+
+figure(1)
+imshow(log.(norm.(dipole[xyRange, xyRange, 0])), extent=(minimum(xyRange), maximum(xyRange), minimum(xyRange), maximum(xyRange)))
+quiver(X, Y, U, V)

example/Superposition.jl

@@ -0,0 +1,13 @@
+using MPIMagneticFields
+using PyPlot
+using LinearAlgebra
+
+gradient = IdealFFP([1, 1, 2])
+focusfield = IdealHomogeneousField([0.01, 0, 0])
+superimposed = gradient + focusfield
+
+figure(1)
+imshow(norm.(gradient[-0.02:0.001:0.02, -0.02:0.001:0.02, 0]))
+
+figure(2)
+imshow(norm.(superimposed[-0.02:0.001:0.02, -0.02:0.001:0.02, 0]))

src/Common.jl

@@ -1,6 +1,53 @@
 #Base.size(S::SquaresVector) = (S.count,)
 Base.IndexStyle(::Type{<:AbstractMagneticField}) = IndexCartesian()
-Base.getindex(field::AbstractMagneticField, r...) = value(field, [r...]) # TODO: How to deal with rotation and translation?
+Base.getindex(field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), field, args...)
 
-# TODO: This only works with eachindex() available, which is only the case for fields defining a grid. How shall we solve this? Create a container?
-#LinearAlgebra.norm(field::AbstractMagneticField) = [norm(field[i]) for i ∈ eachindex(field)]
+getindex_(::TimeConstant, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), field, args...)
+
+getindex_(::TimeConstant, ::NoMovement, field::AbstractMagneticField, args...) = value(field, [args...])
+
+getindex_(::TimeConstant, ::RotationalMovement, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), RotationalDimensionalityStyle(field), field, args...)
+getindex_(::TimeConstant, ::RotationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-1]...], [args[end]...])
+getindex_(::TimeConstant, ::RotationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-2]...], [args[end-1:end]...])
+getindex_(::TimeConstant, ::RotationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-3]...], [args[end-2:end]...])
+
+getindex_(::TimeConstant, ::TranslationalMovement, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), TranslationalDimensionalityStyle(field), field, args...)
+getindex_(::TimeConstant, ::TranslationalMovement, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-1]...], [args[end]...])
+getindex_(::TimeConstant, ::TranslationalMovement, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-2]...], [args[end-1:end]...])
+getindex_(::TimeConstant, ::TranslationalMovement, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-3]...], [args[end-2:end]...])
+
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), RotationalDimensionalityStyle(field), TranslationalDimensionalityStyle(field), field, args...)
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-2]...], [args[end-1]...], [args[end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-3]...], [args[end-2]...], [args[end-1:end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-4]...], [args[end-3]...], [args[end-2:end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-3]...], [args[end-2:end-1]...], [args[end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-4]...], [args[end-3:end-2]...], [args[end-1:end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-5]...], [args[end-4:end-3]...], [args[end-2:end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-4]...], [args[end-3:end-1]...], [args[end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-5]...], [args[end-4:end-2]...], [args[end-1:end]...])
+getindex_(::TimeConstant, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, [args[1:end-6]...], [args[end-5:end-3]...], [args[end-2:end]...])
+
+getindex_(::TimeVarying, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), field, args...)
+
+getindex_(::TimeVarying, ::NoMovement, field::AbstractMagneticField, args...) = value(field, args[1], [args[2:end]...])
+
+getindex_(::TimeVarying, ::RotationalMovement, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), RotationalDimensionalityStyle(field), field, args...)
+getindex_(::TimeVarying, ::RotationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[2:end-1]...], [args[end]...])
+getindex_(::TimeVarying, ::RotationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[2:end-2]...], [args[end-1:end]...])
+getindex_(::TimeVarying, ::RotationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[2:end-3]...], [args[end-2:end]...])
+
+getindex_(::TimeVarying, ::TranslationalMovement, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), TranslationalDimensionalityStyle(field), field, args...)
+getindex_(::TimeVarying, ::TranslationalMovement, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[2:end-1]...], [args[end]...])
+getindex_(::TimeVarying, ::TranslationalMovement, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[2:end-2]...], [args[end-1:end]...])
+getindex_(::TimeVarying, ::TranslationalMovement, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[2:end-3]...], [args[end-2:end]...])
+
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, field::AbstractMagneticField, args...) = getindex_(FieldTimeDependencyStyle(field), FieldMovementStyle(field), RotationalDimensionalityStyle(field), TranslationalDimensionalityStyle(field), field, args...)
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-4:end-2]...], [args[end-1]...], [args[end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-5:end-3]...], [args[end-2]...], [args[end-1:end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{OneDimensional}, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-6:end-4]...], [args[end-3]...], [args[end-2:end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-5:end-3]...], [args[end-2:end-1]...], [args[end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-6:end-4]...], [args[end-3:end-2]...], [args[end-1:end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{TwoDimensional}, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-7:end-5]...], [args[end-4:end-3]...], [args[end-2:end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, ::TranslationalDimensionalityStyle{OneDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-6:end-4]...], [args[end-3:end-1]...], [args[end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, ::TranslationalDimensionalityStyle{TwoDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-7:end-5]...], [args[end-4:end-2]...], [args[end-1:end]...])
+getindex_(::TimeVarying, ::RotationalTranslationalMovement, ::RotationalDimensionalityStyle{ThreeDimensional}, ::TranslationalDimensionalityStyle{ThreeDimensional}, field::AbstractMagneticField, args...) = value(field, args[1], [args[end-8:end-6]...], [args[end-5:end-3]...], [args[end-2:end]...])

src/CommonFields/CommonFields.jl

@@ -0,0 +1,4 @@
+
+include("FFL.jl")
+include("FFP.jl")
+include("Homogeneous.jl")

src/CommonFields/FFL.jl

@@ -0,0 +1,12 @@
+export IdealXYFFL
+mutable struct IdealXYFFL{GT} <: AbstractMagneticField where {GT <: Number}
+  gradient::GT
+end
+
+FieldStyle(::IdealXYFFL) = GradientField()
+FieldDefinitionStyle(::IdealXYFFL) = MethodBasedFieldDefinition()
+FieldTimeDependencyStyle(::IdealXYFFL) = TimeConstant()
+GradientFieldStyle(::IdealXYFFL) = FFLGradientField()
+FieldMovementStyle(::IdealXYFFL) = RotationalMovement()
+
+value_(field::IdealXYFFL, r, ϕ) = [-sin(ϕ)^2 -sin(ϕ)*cos(ϕ) 0; -sin(ϕ)*cos(ϕ) -cos(ϕ)^2 0; 0 0 1]*r.*field.gradient

src/CommonFields/FFP.jl

@@ -0,0 +1,11 @@
+export IdealFFP
+mutable struct IdealFFP{GT} <: AbstractMagneticField where {GT <: Number}
+  gradient::Vector{GT}
+end
+
+FieldStyle(::IdealFFP) = GradientField()
+FieldDefinitionStyle(::IdealFFP) = MethodBasedFieldDefinition()
+FieldTimeDependencyStyle(::IdealFFP) = TimeConstant()
+GradientFieldStyle(::IdealFFP) = FFPGradientField()
+
+value_(field::IdealFFP, r) = r.*field.gradient

src/CommonFields/Homogeneous.jl

@@ -0,0 +1,27 @@
+export IdealHomogeneousField
+mutable struct IdealHomogeneousField{U} <: AbstractMagneticField where {T <: Number, U <: AbstractVector{T}}
+  value::U
+
+  function IdealHomogeneousField(value::U) where {T <: Number, U <: AbstractVector{T}}
+    new{U}(value)
+  end
+end
+
+FieldStyle(::IdealHomogeneousField) = HomogeneousField()
+FieldDefinitionStyle(::IdealHomogeneousField) = MethodBasedFieldDefinition()
+FieldTimeDependencyStyle(::IdealHomogeneousField) = TimeConstant()
+
+value_(field::IdealHomogeneousField, r) = field.value
+
+# TODO: Define other combinations
+export IdealXYRotatedHomogeneousField
+mutable struct IdealXYRotatedHomogeneousField{T} <: AbstractMagneticField where {T <: Number}
+  amplitude::T
+end
+
+FieldStyle(::IdealXYRotatedHomogeneousField) = HomogeneousField()
+FieldDefinitionStyle(::IdealXYRotatedHomogeneousField) = MethodBasedFieldDefinition()
+FieldTimeDependencyStyle(::IdealXYRotatedHomogeneousField) = TimeConstant()
+FieldMovementStyle(::IdealXYRotatedHomogeneousField) = RotationalMovement()
+
+value_(field::IdealXYRotatedHomogeneousField, r, ϕ) = [sin(ϕ), cos(ϕ), 0].*field.amplitude