Julia: MM semantics for Image.crystals

4 files changed, 70 insertions, 10 deletions

diff --git a/julia/CrystFEL/src/image.jl b/julia/CrystFEL/src/image.jl
index a9d9c28f..3384f0c9 100644
--- a/julia/CrystFEL/src/image.jl
+++ b/julia/CrystFEL/src/image.jl
@@ -14,6 +14,8 @@ const HEADER_CACHE_SIZE = 128
 mutable struct CrystalRefListPair
     crystal::Ptr{InternalCrystal}
     reflist::Ptr{InternalRefList}
+    owns_crystal::Cint
+    owns_reflist::Cint
 end
 
 mutable struct InternalImage
@@ -55,7 +57,7 @@ mutable struct Image
 end
 
 
-function makecrystallist(listptr, n)
+function makecrystallist(image, listptr, n)
 
     crystals = []
 
@@ -65,16 +67,33 @@ function makecrystallist(listptr, n)
 
     for i in 1:n
         pairptr = unsafe_load(listptr, i)
-        cr = Crystal(pairptr.crystal)
+
+        # Re-use old Crystal if possible
+        n = findfirst(getfield(image, :crystals)) do x
+            x.internalptr == pairptr.crystal
+        end
+
+        if n !== nothing
+            cr = getfield(image, :crystals)[n]
+        else
+            cr = Crystal(pairptr.crystal)
+        end
+
         if pairptr.reflist == C_NULL
             reflist = nothing
         else
             reflist = RefList{UnmergedReflection}(pairptr.reflist, SymOpList("1"))
+            pairptr.owns_reflist = 0
         end
         push!(crystals, (crystal=cr, reflections=reflist))
+        pairptr.owns_crystal = 0
+        unsafe_store!(listptr, pairptr, i)
+        # We are now responsible for freeing the Crystal and RefList
     end
 
-    crystals
+    image.crystals = map(x->x.crystal, crystals)
+    image.reflists = map(x->x.reflections, crystals)
+    return crystals
 
 end
 
@@ -104,11 +123,12 @@ function Base.getproperty(image::Image, name::Symbol)
         idata = unsafe_load(image.internalptr)
 
         if name === :crystals
-            return makecrystallist(getproperty(idata, :crystals),
-                                   getproperty(idata, :n_crystals))
+            return makecrystallist(image,
+                                   getfield(idata, :crystals),
+                                   getfield(idata, :n_crystals))
 
         else
-            getproperty(idata, name)
+            getfield(idata, name)
         end
     end
 end
@@ -155,6 +175,12 @@ function Base.setproperty!(image::Image, name::Symbol, val)
             assert_type(val, AbstractString)
             val = strdup(val)
 
+        elseif name === :crystals
+            return setfield!(image, :crystals, val)
+
+        elseif name === :reflists
+            return setfield!(image, :reflists, val)
+
         end
 
         idata = unsafe_load(image.internalptr)
@@ -202,7 +228,7 @@ function Image(dtempl::DataTemplate)
         throw(ArgumentError("Failed to create image"))
     end
 
-    image = Image(out, nothing)
+    image = Image(out, nothing, [], [])
 
     finalizer(image) do x
         ccall((:image_free, libcrystfel), Cvoid, (Ptr{InternalImage},), x.internalptr)
@@ -234,7 +260,7 @@ function Image(dtempl::DataTemplate,
         throw(ArgumentError("Failed to load image"))
     end
 
-    image = Image(out, nothing)
+    image = Image(out, nothing, [], [])
 
     finalizer(image) do x
         ccall((:image_free, libcrystfel), Cvoid, (Ptr{InternalImage},), x.internalptr)
diff --git a/julia/make-indexed.jl b/julia/make-indexed.jl
new file mode 100644
index 00000000..7a24f606
--- /dev/null
+++ b/julia/make-indexed.jl
@@ -0,0 +1,26 @@
+using CrystFEL
+using Random
+
+# "Simulate" a diffraction pattern from the reflections
+function sketch_pattern(image, cr)
+    reflist = predictreflections(cr, image)
+    peaklist = PeakList()
+    for refl in reflist
+        if randn() > 0
+            let dpos = refl.detectorposition
+                push!(peaklist, dpos.fs, dpos.ss, dpos.panelnumber, 100.0)
+            end
+        end
+    end
+    return peaklist
+end
+
+
+dtempl = loaddatatemplate("julia/alignment-test.geom")
+cell = UnitCell(MonoclinicLattice, PrimitiveCell, 123, 45, 80, 90, 97, 90)
+indexer = Indexer("asdf", dtempl, cell, retry=false, multilattice=false, refine=true)
+
+image = Image(dtempl)
+cr = Crystal(rotatecell(cell))
+image.peaklist = sketch_pattern(image, cr)
+index(image, indexer)
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index ab4518a9..e91c09d6 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -333,6 +333,8 @@ void image_add_crystal_refls(struct image *image,
 
 	crs[n].cr = cryst;
 	crs[n].refls = reflist;
+	crs[n].image_owns_crystal = 1;
+	crs[n].image_owns_refls = 1;
 	image->crystals = crs;
 	image->n_crystals = n+1;
 }
@@ -373,8 +375,12 @@ void free_all_crystals(struct image *image)
 	int i;
 	if ( image->crystals == NULL ) return;
 	for ( i=0; i<image->n_crystals; i++ ) {
-		crystal_free(image->crystals[i].cr);
-		reflist_free(image->crystals[i].refls);
+		if ( image->crystals[i].image_owns_crystal ) {
+			crystal_free(image->crystals[i].cr);
+		}
+		if ( image->crystals[i].image_owns_refls ) {
+			reflist_free(image->crystals[i].refls);
+		}
 	}
 	cffree(image->crystals);
 	image->crystals = NULL;
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 74ff6eee..3db7de18 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -114,6 +114,8 @@ struct crystal_refls
 {
 	Crystal *cr;
 	RefList *refls;
+	int image_owns_crystal;
+	int image_owns_refls;
 };
 
 struct image