Julia: Add cell rotation

4 files changed, 42 insertions, 7 deletions

diff --git a/julia/CrystFEL/Manifest.toml b/julia/CrystFEL/Manifest.toml
index c59e01e9..e4ee3ce8 100644
--- a/julia/CrystFEL/Manifest.toml
+++ b/julia/CrystFEL/Manifest.toml
@@ -2,11 +2,22 @@
 
 julia_version = "1.9.2"
 manifest_format = "2.0"
-project_hash = "f604830d70fa58877def5710c5d1fa32dcb3f998"
+project_hash = "4cf05e6854a627b02f001d01f38d3c0cbfcf00bd"
 
 [[deps.Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
+[[deps.Random]]
+deps = ["SHA", "Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[deps.SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
+
+[[deps.Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
 [[deps.Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
diff --git a/julia/CrystFEL/Project.toml b/julia/CrystFEL/Project.toml
index 6be52e40..8c81af0f 100644
--- a/julia/CrystFEL/Project.toml
+++ b/julia/CrystFEL/Project.toml
@@ -5,3 +5,4 @@ version = "0.1.0"
 
 [deps]
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
diff --git a/julia/CrystFEL/src/cell.jl b/julia/CrystFEL/src/cell.jl
index 80250221..c098f8ca 100644
--- a/julia/CrystFEL/src/cell.jl
+++ b/julia/CrystFEL/src/cell.jl
@@ -1,5 +1,7 @@
 module UnitCells
 
+using Random
+
 import ..CrystFEL: libcrystfel
 export UnitCell, LatticeType, CenteringType, UniqueAxis
 export TriclinicLattice, MonoclinicLattice, OrthorhombicLattice
@@ -306,6 +308,8 @@ function Base.show(io::IO, uc::UnitCell)
 end
 
 
+# This type is for talking to libcrystfel, and is named to avoid conflicting
+# with other quaternion libraries.
 mutable struct CrystFELQuaternion
     w::Cdouble
     x::Cdouble
@@ -313,6 +317,18 @@ mutable struct CrystFELQuaternion
     z::Cdouble
 end
 
+function randomquat()
+    r = ()->2.0*rand(Float64)-1.0
+    q = [r(), r(), r(), r()]
+    q ./ √(sum(q.^2))
+end
+
+
+"""
+    rotatecell(uc::UnitCell, quaternion)
+
+Rotate a unit cell according to a quaternion (represented as a vector of 4 floats).
+"""
 function rotatecell(uc, quat)
     q = CrystFELQuaternion(quat...)
     out = @ccall libcrystfel.cell_rotate(uc.internalptr::Ptr{InternalUnitCell},
@@ -323,4 +339,16 @@ function rotatecell(uc, quat)
     UnitCell(out)
 end
 
+
+"""
+    rotatecell(uc::UnitCell)
+
+Rotate a unit cell at random in three dimensions.  Use this routine for
+simulating serial crystallography datasets.
+
+Equivalent to CrystFEL routine `cell_rotate(uc, random_quaternion(<rng>))`.
+"""
+rotatecell(uc) = rotatecell(uc, randomquat())
+
+
 end   # of module
diff --git a/julia/alignment-test.jl b/julia/alignment-test.jl
index e6e1ab63..6fec3256 100644
--- a/julia/alignment-test.jl
+++ b/julia/alignment-test.jl
@@ -16,18 +16,13 @@ function sketch_pattern(image, cr)
 end
 
 
-function randomrotation(cell)
-    rotatecell(cell, (1,0,0,0))
-end
-
-
 function simulate_and_index(cell, image_true, dtempl_moved, n)
 
     indexer = Indexer("asdf", dtempl_moved, cell, retry=false, multilattice=false, refine=true)
 
     for _ in 1:n
 
-        cr = Crystal(randomrotation(cell))
+        cr = Crystal(rotatecell(cell))
         peaklist = sketch_pattern(image_true, cr)
         image_moved = Image(dtempl_moved)