From f2829b1abb24be08a9f7214ec2d54ad9d142d7e7 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Mon, 22 Jan 2024 14:14:55 +0100
Subject: Julia: Finish implementing partial_sim.jl

---
 julia/partial_sim.jl | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

(limited to 'julia')

diff --git a/julia/partial_sim.jl b/julia/partial_sim.jl
index 11384f47..efc621f9 100644
--- a/julia/partial_sim.jl
+++ b/julia/partial_sim.jl
@@ -1,7 +1,8 @@
 using CrystFEL
 
-dtempl = loaddatatemplate("julia/alignment-test.geom")
-cell = UnitCell(MonoclinicLattice, PrimitiveCell, 123, 45, 80, 90, 97, 90)
+dtempl = loaddatatemplate("input.geom")
+cell = UnitCell(OrthorhombicLattice, PrimitiveCell, 40.0, 50.0, 60.0)
+full = loadreflist("input.hkl")
 let st = Stream("partials.stream", "w", dtempl)
     for i in 1:10
         println("Writing image ", i)
@@ -11,6 +12,18 @@ let st = Stream("partials.stream", "w", dtempl)
         image.ev = "//"
         cr = Crystal(rotatecell(cell))
         reflections = predictreflections(cr, image)
+        calculatepartialities!(reflections, cr, image, model=XSphereModel)
+        for refl in reflections
+            f = full[asymmetricindices(full.symmetry, refl.indices...)...]
+            if f !== nothing
+                refl.intensity = f.intensity * refl.partiality * refl.lorentzfactor
+            else
+                # No matching "full" intensity - can't do anything
+                # Reflections with zero measurements won't be written to file
+                refl.nmeasurements = 0
+                println("Not found: ", refl.indices)
+            end
+        end
         push!(image, cr, reflections)
         chunkwrite(st, image)
     end
-- 
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