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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),
norm(v1*v2n + v2*v1n))
end
end
let st = Stream("/home/twhite/experiments/cxidb-193/short.stream", "r"),
merged = mergereflections(allcrystals(st), SymOpList("mmm")) do refl,crystal
polfrac = 1.0
polangle = 0.0
lp = transpose(crystal.cell.reciprocalcartesian) * refl.symmetricindices
tt = anglebetween([0,0,1], lp+[0,0,refl.kpred])
phi = atan(lp[2], lp[1]) - polangle
pol = polfrac*(1.0 - cos(phi)*cos(phi)*sin(tt)*sin(tt)) +
(1.0-polfrac)*(1.0 - sin(phi)*sin(phi)*sin(tt)*sin(tt))
return refl.intensity / pol
end
savereflist!(merged, "merged.hkl")
end
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