Julia: Expose crystals and reflection lists from image

The memory management isn't quite right here yet.

3 files changed, 23 insertions, 10 deletions

diff --git a/julia/CrystFEL/src/crystal.jl b/julia/CrystFEL/src/crystal.jl
index 129c028c..eba7a615 100644
--- a/julia/CrystFEL/src/crystal.jl
+++ b/julia/CrystFEL/src/crystal.jl
@@ -10,7 +10,6 @@ mutable struct InternalCrystal end
 
 mutable struct Crystal
     internalptr::Ptr{InternalCrystal}
-    in_image   # if true, this PeakList belongs to an Image struct
 end
 
 
@@ -40,13 +39,11 @@ function Crystal(cell::UnitCell; profileradius=2e6, mosaicity=0)
           Cvoid, (Ptr{InternalCrystal},Cdouble),
           out, mosaicity)
 
-    cr = Crystal(out, false)
+    cr = Crystal(out)
 
     finalizer(cr) do x
-        if !x.in_image
-            ccall((:crystal_free, libcrystfel), Cvoid, (Ptr{InternalCrystal},),
-                  x.internalptr)
-        end
+        ccall((:crystal_free, libcrystfel), Cvoid, (Ptr{InternalCrystal},),
+              x.internalptr)
     end
 
     return cr
diff --git a/julia/CrystFEL/src/image.jl b/julia/CrystFEL/src/image.jl
index de79a556..a9d9c28f 100644
--- a/julia/CrystFEL/src/image.jl
+++ b/julia/CrystFEL/src/image.jl
@@ -5,16 +5,23 @@ import ..CrystFEL.DataTemplates: DataTemplate, InternalDataTemplate
 import ..CrystFEL.DetGeoms: DetGeom
 import ..CrystFEL.PeakLists: PeakList, InternalPeakList
 import ..CrystFEL.Crystals: Crystal, InternalCrystal
+import ..CrystFEL.RefLists: RefList, InternalRefList, UnmergedReflection
+import ..CrystFEL.Symmetry: SymOpList
 export Image
 
 const HEADER_CACHE_SIZE = 128
 
+mutable struct CrystalRefListPair
+    crystal::Ptr{InternalCrystal}
+    reflist::Ptr{InternalRefList}
+end
+
 mutable struct InternalImage
     dp::Ptr{Ptr{Cfloat}}
     bad::Ptr{Ptr{Cint}}
     sat::Ptr{Ptr{Cfloat}}
     hit::Cint
-    crystals::Ptr{Ptr{Cvoid}}
+    crystals::Ptr{CrystalRefListPair}
     n_crystals::Cint
     indexed_by::Cint
     n_indexing_tries::Cint
@@ -43,20 +50,28 @@ end
 mutable struct Image
     internalptr::Ptr{InternalImage}
     peaklist::Union{Nothing,PeakList}
+    crystals
+    reflists
 end
 
 
 function makecrystallist(listptr, n)
 
-    crystals = Crystal[]
+    crystals = []
 
     if listptr == C_NULL
         return crystals
     end
 
     for i in 1:n
-        crystalptr = unsafe_load(listptr, i)
-        push!(crystals, Crystal(crystalptr, true))
+        pairptr = unsafe_load(listptr, i)
+        cr = Crystal(pairptr.crystal)
+        if pairptr.reflist == C_NULL
+            reflist = nothing
+        else
+            reflist = RefList{UnmergedReflection}(pairptr.reflist, SymOpList("1"))
+        end
+        push!(crystals, (crystal=cr, reflections=reflist))
     end
 
     crystals
diff --git a/julia/CrystFEL/src/reflists.jl b/julia/CrystFEL/src/reflists.jl
index 007f0f07..d6b3a951 100644
--- a/julia/CrystFEL/src/reflists.jl
+++ b/julia/CrystFEL/src/reflists.jl
@@ -5,6 +5,7 @@ import ..CrystFEL: libcrystfel
 import ..CrystFEL.Symmetry: SymOpList, InternalSymOpList, symmetry_name
 export RefList, loadreflist
 export Reflection, UnmergedReflection, MergedReflection
+export InternalRefList
 
 
 # The internal libcrystfel structures, not exposed directly