From 0ebaf0eb0465be23d8fee4088271cb92154a606d Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 27 Feb 2024 11:35:46 +0100
Subject: Julia: Move merging utils to separate module

---
 julia/CrystFEL/src/CrystFEL.jl   |  4 +++
 julia/CrystFEL/src/mergeutils.jl | 57 ++++++++++++++++++++++++++++++++++++++++
 julia/process_hkl.jl             | 52 ------------------------------------
 3 files changed, 61 insertions(+), 52 deletions(-)
 create mode 100644 julia/CrystFEL/src/mergeutils.jl

diff --git a/julia/CrystFEL/src/CrystFEL.jl b/julia/CrystFEL/src/CrystFEL.jl
index 5ecfab91..897d2614 100644
--- a/julia/CrystFEL/src/CrystFEL.jl
+++ b/julia/CrystFEL/src/CrystFEL.jl
@@ -87,4 +87,8 @@ include("peaksearch.jl")
 using .PeakSearch
 export zaefpeaks, peakfinder8, peakfinder9
 
+include("mergeutils.jl")
+using .MergeUtils
+export @addmeasurement, cstddev, mergereflections
+
 end  # of module
diff --git a/julia/CrystFEL/src/mergeutils.jl b/julia/CrystFEL/src/mergeutils.jl
new file mode 100644
index 00000000..b75bd2e8
--- /dev/null
+++ b/julia/CrystFEL/src/mergeutils.jl
@@ -0,0 +1,57 @@
+module MergeUtils
+
+using ..CrystFEL.RefLists
+using ..CrystFEL.Symmetry
+export @addmeasurement, cstddev, mergereflections
+
+macro addmeasurement(measurement, weight,
+                     mean, sumweight, wksp)
+    return quote
+        delta = $(esc(measurement)) - $(esc(mean))
+        newsumweight = $(esc(sumweight)) + $(esc(weight))
+        R = delta * $(esc(weight)) / newsumweight
+        $(esc(mean)) += R
+        $(esc(wksp)) += $(esc(sumweight)) * delta * R
+        $(esc(sumweight)) = newsumweight
+    end
+end
+
+cstddev(nmeas, work1, work2) = sqrt(work2/work1)/sqrt(nmeas)
+
+
+function mergereflections(correction, crystalrefls, sym)
+
+    merged = RefList{MergedReflection}(sym)
+
+    for (cr,reflections) in crystalrefls
+
+        for refl in reflections
+
+            indices = asymmetricindices(sym, refl.indices)
+            model_version = get!(merged, indices)
+            @addmeasurement(correction(refl, cr), 1.0,
+                            model_version.intensity,
+                            model_version.temp1,
+                            model_version.temp2)
+            model_version.nmeasurements += 1
+
+        end
+    end
+
+    for refl in merged
+        if refl.nmeasurements > 1
+            refl.sigintensity = cstddev(refl.nmeasurements, refl.temp1, refl.temp2)
+        else
+            # Cannot delete a reflection from a list (especially not
+            # while iterating), but setting nmeasurements to zero
+            # prevents it from being written to the output file.
+            refl.nmeasurements = 0
+        end
+    end
+
+    return merged
+
+end
+
+
+end  # of module
diff --git a/julia/process_hkl.jl b/julia/process_hkl.jl
index d2cebc86..80b78e52 100644
--- a/julia/process_hkl.jl
+++ b/julia/process_hkl.jl
@@ -1,57 +1,6 @@
 using CrystFEL
 using LinearAlgebra
 
-
-macro addmeasurement(measurement, weight,
-                     mean, sumweight, wksp)
-    return quote
-        delta = $(esc(measurement)) - $(esc(mean))
-        newsumweight = $(esc(sumweight)) + $(esc(weight))
-        R = delta * $(esc(weight)) / newsumweight
-        $(esc(mean)) += R
-        $(esc(wksp)) += $(esc(sumweight)) * delta * R
-        $(esc(sumweight)) = newsumweight
-    end
-end
-
-cstddev(nmeas, work1, work2) = sqrt(work2/work1)/sqrt(nmeas)
-
-
-function mergereflections(correction, crystalrefls, sym)
-
-    merged = RefList{MergedReflection}(sym)
-
-    for (cr,reflections) in crystalrefls
-
-        for refl in reflections
-
-            indices = asymmetricindices(sym, refl.indices)
-            model_version = get!(merged, indices)
-            @addmeasurement(correction(refl, cr), 1.0,
-                            model_version.intensity,
-                            model_version.temp1,
-                            model_version.temp2)
-            model_version.nmeasurements += 1
-
-        end
-    end
-
-    for refl in merged
-        if refl.nmeasurements > 1
-            refl.sigintensity = cstddev(refl.nmeasurements, refl.temp1, refl.temp2)
-        else
-            # Cannot delete a reflection from a list (especially not
-            # while iterating), but setting nmeasurements to zero
-            # prevents it from being written to the output file.
-            refl.nmeasurements = 0
-        end
-    end
-
-    return merged
-
-end
-
-
 function anglebetween(v1, v2)
     let v1n = norm(v1), v2n = norm(v2)
         return 2*atan(norm(v1*v2n - v2*v1n),
@@ -59,7 +8,6 @@ function anglebetween(v1, v2)
     end
 end
 
-
 let st = Stream("/home/twhite/experiments/cxidb-193/short.stream", "r"),
     merged = mergereflections(allcrystals(st), SymOpList("mmm")) do refl,crystal
 
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