Add functions to access cluster basis to lattices (fixes #298)

src/GlassCat/data/sources.txt

@@ -1,7 +1,7 @@
 NIKON a49714470fa875ad4fd8d11cbc0edbf1adfe877f42926d7612c1649dd9441e75 https://www.nikon.com/products/components/assets/pdf/nikon_zemax_data.zip
 OHARA 0c9021bf11b8d4e660012191818685ad3110d4f9490699cabdc89aae1fd26d2e https://www.oharacorp.com/xls/OHARA_201130_CATALOG.zip
 HOYA b02c203e5a5b7a8918cc786badf0a9db1fe2572372c1c163dc306b0a8a908854 http://www.hoya-opticalworld.com/common/agf/HOYA20210105.agf
-SCHOTT 02c3212e6984a553994caf7533c6c08f284f6ebc9312dbf90e605226577577e8 https://www.schott.com/d/advanced_optics/6959f9a4-0e4f-4ef2-a302-2347468a82f5/1.32/schott-optical-glass-overview-zemax-format.zip
+SCHOTT 02c3212e6984a553994caf7533c6c08f284f6ebc9312dbf90e605226577577e8 https://mss-p-009-delivery.stylelabs.cloud/api/public/content/a79c07aa61da4c05a2c0bbab93d09a7f?v=3b65e351&download=true
 SUMITA fad12bfb1754ee9e33f7a6ec65c784c1dd1b8e87fde1ac2e440d24e85630c758 https://www.sumita-opt.co.jp/en/wp/wp-content/themes/sumita-opt-en/download-files.php files%5B%5D=new_sumita.agf&category=data
 ARCHER 7df8c42fb499720165c86d77dc8065db5126541a71b4e9d6a4849e27b25dd82d https://raw.githubusercontent.com/nzhagen/zemaxglass/master/AGF_files/archer.agf
 ARTON d214e050f7330257c8cfcd517b1f35b64077dac62cf2729f73b3723e00a59263 https://raw.githubusercontent.com/nzhagen/zemaxglass/master/AGF_files/arton.agf

src/RepeatingStructures/Cluster.jl

@@ -37,6 +37,8 @@ clusterelements(a::LatticeCluster) = a.clusterelements
 export clusterelements
 elementbasis(a::LatticeCluster) = a.elementbasis
 clustersize(a::LatticeCluster) = length(a.clusterelements)
+clusterbasis(a::LatticeCluster) = a.clusterbasis
+export clusterbasis
 
 """returns the positions of every element in a cluster given the cluster indices"""
 function Base.getindex(A::LatticeCluster{N1,N,T,B1,B2}, indices::Vararg{Int, N}) where{N1,N,T,B1<:Basis{N,Int},B2<:Basis{N,T}} 
@@ -92,3 +94,5 @@ elementbasis(a::ClusterWithProperties) = elementbasis(cluster(a))
 export elementbasis
 clustersize(a::ClusterWithProperties) = clustersize(a.cluster)
 export clustersize
+clusterbasis(a::ClusterWithProperties) = clusterbasis(a.cluster)
+export clusterbasis

src/RepeatingStructures/HexagonalLattice.jl

@@ -19,7 +19,7 @@ struct HexBasis1{N,T} <: Basis{N,T}
 end
 export HexBasis1
 
-basis(::HexBasis1{2,T}) where{T} = SMatrix{2,2,T}(T(1.5),T(.5)*sqrt(T(3)),T(1.5),T(-.5)*(sqrt(T(3))))
+basismatrix(::HexBasis1{2,T}) where{T} = SMatrix{2,2,T}(T(1.5),T(.5)*sqrt(T(3)),T(1.5),T(-.5)*(sqrt(T(3))))
 
 # SVector{2,SVector{2,T}}(hexe₁(T),hexe₂(T))
 
@@ -180,5 +180,5 @@ function tilevertices(::HexBasis3{2,T}) where{T}
         sin60, cos60)
 end
 
-basis(::HexBasis3{2,T}) where{T} = SMatrix{2,2,T}(T(2*sin60),T(0),T(sin60),T(1.5))
+basismatrix(::HexBasis3{2,T}) where{T} = SMatrix{2,2,T}(T(2*sin60),T(0),T(sin60),T(1.5))
 

src/RepeatingStructures/Lattice.jl

@@ -41,7 +41,7 @@ abstract type Basis{N,T<:Real} end
 export Basis
 
 function Base.getindex(A::B1, indices::Vararg{Int, N}) where{N,T,B1<:Basis{N,T}}
-    return basis(A)*SVector{N,Int}(indices)
+    return basismatrix(A)*SVector{N,Int}(indices)
 end
 
 #     temp::SVector{N,T} = (basis(A)*SVector{N,Int}(indices))::SVector{N,T}
@@ -77,7 +77,7 @@ struct LatticeBasis{N,T<:Real} <: Basis{N,T}
 end
 export LatticeBasis
 
-function basis(a::LatticeBasis{N,T})::SMatrix{N,N,T,N*N} where{N,T} 
+function basismatrix(a::LatticeBasis{N,T})::SMatrix{N,N,T,N*N} where{N,T} 
     return a.basisvectors
 end
 

src/RepeatingStructures/RectangularLattice.jl

@@ -8,7 +8,7 @@ struct RectangularBasis{N,T} <: Basis{N,T}
 end
 export RectangularBasis
 
-basis(::RectangularBasis{2,T}) where{T} = SMatrix{2,2,T}(T(1),T(0),T(0),T(1))
+basismatrix(::RectangularBasis{2,T}) where{T} = SMatrix{2,2,T}(T(1),T(0),T(0),T(1))
 
 # SVector{2,SVector{2,T}}(hexe₁(T),hexe₂(T))
 

src/RepeatingStructures/Repeat.jl

@@ -4,7 +4,7 @@
 
 module Repeat
 
-export basis
+export basismatrix
 
 using Base: offset_if_vec
 using StaticArrays:SVector,MVector,SMatrix,MMatrix

test/runtests.jl

@@ -10,6 +10,7 @@ using Suppressor
 using Random
 using Unitful
 using Plots
+using DataFrames
 
 using OpticSim
 # Geometry Module
@@ -94,6 +95,7 @@ end
 include("Benchmarks/Benchmarks.jl")
 
 alltestsets = [
+    "Repeat",
     "ParaxialAnalysis",
     "Paraxial",
     "JuliaLang",
@@ -109,7 +111,7 @@ alltestsets = [
     "Visualization",
     "Allocations",
     "GlassCat",
-    "Transform",
+    "Transform"
 ]
 
 runtestsets = ALL_TESTS ? alltestsets : intersect(alltestsets, ARGS)

test/testsets/Repeat.jl

@@ -0,0 +1,18 @@
+# MIT license
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# See LICENSE in the project root for full license information.
+
+@testset "Repeat" begin
+    function hex3RGB()
+        clusterelements = SVector((0,0),(-1,0),(-1,1))
+        colors = [colorant"red",colorant"green",colorant"blue"]
+        names = ["R","G","B"]
+        eltlattice = Repeat.HexBasis1()
+        clusterbasis = Repeat.LatticeBasis(( -1,2),(2,-1))
+        lattice = Repeat.LatticeCluster(clusterbasis,eltlattice,clusterelements)
+        properties =  DataFrame(Color = colors, Name = names)
+        return Repeat.ClusterWithProperties(lattice,properties)
+    end
+
+    @test [-1 2;2 -1] == Repeat.basismatrix(Repeat.clusterbasis(hex3RGB()))
+end