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module Indexing
import ..CrystFEL: libcrystfel
import ..CrystFEL.UnitCells: UnitCell, InternalUnitCell
import ..CrystFEL.Images: Image, InternalImage
import ..CrystFEL.DataTemplates: wavelength, cameralength
export Indexer, index
mutable struct IndexingPriv end
mutable struct Indexer
indexingpriv::Ptr{IndexingPriv}
end
function indexflags(retry, multilattice, refine, peakcheck, cellcheck)
flags = 0
if retry
flags |= 1
end
if multilattice
flags |= 2
end
if refine
flags |= 4
end
if peakcheck
flags |= 32
end
if cellcheck
flags |= 64
end
return flags
end
"""
Indexer(methods, dtempl, cell;
tolerances=(0.05,0.05,0.05,1.5,1.5,1.5),
retry=true, multilattice=false, refine=true,
peakcheck=true, cellcheck=true,
wavelength_estimate=nothing, clen_estimate=missing,
n_threads=1)
Creates a new CrystFEL indexing engine, which you can later apply to CrystFEL
`Image` structures using `index()`.
"""
function Indexer(methods, dtempl, cell; tolerances=(0.05,0.05,0.05,1.5,1.5,1.5),
retry=true, multilattice=false, refine=true, peakcheck=true, cellcheck=true,
wavelength_estimate=nothing, clen_estimate=missing, n_threads=1)
taketwoopts = Ref{Ptr{Cvoid}}(C_NULL)
xgandalfopts = Ref{Ptr{Cvoid}}(C_NULL)
pinkindexeropts = Ref{Ptr{Cvoid}}(C_NULL)
felixopts = Ref{Ptr{Cvoid}}(C_NULL)
fromfileopts = Ref{Ptr{Cvoid}}(C_NULL)
asdfopts = Ref{Ptr{Cvoid}}(C_NULL)
@ccall libcrystfel.default_method_options(taketwoopts::Ref{Ptr{Cvoid}},
xgandalfopts::Ref{Ptr{Cvoid}},
pinkindexeropts::Ref{Ptr{Cvoid}},
felixopts::Ref{Ptr{Cvoid}},
fromfileopts::Ref{Ptr{Cvoid}},
asdfopts::Ref{Ptr{Cvoid}})::Cvoid
flags = indexflags(retry, multilattice, refine, peakcheck, cellcheck)
let wlfromdtempl = wavelength(dtempl)
if !isnothing(wlfromdtempl)
wavelength_estimate = wlfromdtempl
else
if isnothing(wavelength_estimate)
throw(ArgumentError("Wavelength cannot be determined from data template. "*
"Use Indexer(wavelength_estimate=...)"))
end
end
end
let clenfromdtempl = cameralength(dtempl)
if !isnothing(clenfromdtempl)
clen_estimate = clenfromdtempl
else
if isnothing(clen_estimate)
throw(ArgumentError("Camera length cannot be determined from data template. "*
"Use Indexer(clen_estimate=...)"))
end
end
end
tols = Vector{Cfloat}(undef, 6)
tols[1] = tolerances[1]
tols[2] = tolerances[2]
tols[3] = tolerances[3]
tols[4] = deg2rad(tolerances[4])
tols[5] = deg2rad(tolerances[5])
tols[6] = deg2rad(tolerances[6])
out = @ccall libcrystfel.setup_indexing(methods::Cstring,
cell.internalptr::Ptr{InternalUnitCell},
tols::Ptr{Cfloat},
flags::Cint,
wavelength_estimate::Cdouble,
clen_estimate::Cdouble,
n_threads::Cint,
taketwoopts[]::Ptr{Cvoid},
xgandalfopts[]::Ptr{Cvoid},
pinkindexeropts[]::Ptr{Cvoid},
felixopts[]::Ptr{Cvoid},
fromfileopts[]::Ptr{Cvoid},
asdfopts[]::Ptr{Cvoid})::Ptr{IndexingPriv}
if out == C_NULL
throw(ErrorException("Indexing setup failed"))
end
indexer = Indexer(out)
finalizer(indexer) do x
@ccall libcrystfel.cleanup_indexing(x.indexingpriv::Ptr{IndexingPriv})::Cvoid
end
return indexer
end
"""
index(image::Image, indexer::Indexer; mille=nothing)
Index `image` using `indexer`.
If `mille` is a valid `Mille` object, detector geometry alignment data will
be written.
"""
function index(image::Image, idxr::Indexer; mille=nothing)
if mille === nothing
imille = C_NULL
else
imille = mille.internalptr
end
@ccall libcrystfel.index_pattern_4(image.internalptr::Ptr{InternalImage},
idxr.indexingpriv::Ptr{IndexingPriv},
C_NULL::Ptr{Cvoid},
C_NULL::Ptr{Cvoid},
imille::Ptr{Cvoid})::Cvoid
end
end # of module
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