========================== Using libCrystFEL in Julia ========================== CrystFEL's shared library component, *libcrystfel*, can be accessed from `Julia `_. This way, you can carry out almost any process available in the CrystFEL tools, and much more besides. The Julia package for CrystFEL is found in the ``julia`` directory of the CrystFEL source code package. The easiest way to get started is to use ``Pkg.develop``. Start Julia, press ``]``, then run the following command, substituting the correct location of the CrystFEL package on your system:: (@v1.9) pkg> dev /home/twhite/crystfel/julia/CrystFEL Afterwards, import the CrystFEL package as follows:: julia> using CrystFEL It's imperative that the same version of the Julia package is used as CrystFEL itself, otherwise you are likely to experience spontaneous crashes of the whole Julia session. You only need to perform the ``pkg dev`` process once, not every session. Should you ever need to, you can remove the CrystFEL package in the usual way:: (@v1.9) pkg> rm CrystFEL The Julia package for CrystFEL is a fairly thin wrapper around the `libcrystfel C API `_, so you can read the API documentation for some idea of the possibilities. Below is a brief overview. Unit cells ========== Create a ``UnitCell`` object as follows:: cell = UnitCell(MonoclinicLattice, PrimitiveCell, UniqueAxisB, 123, 45, 80, 90, 97, 90) The arguments are, in order: * Lattice type, one of ``TriclinicLattice``, ``MonoclinicLattice``, ``OrthorhombicLattice``, ``TetragonalLattice``, ``HexagonalLattice``, ``RhombohedralLattice`` or ``CubicLattice``. * Centering, one of ``PrimitiveCell`` (P), ``ACenteredCell``, ``BCenteredCell``, ``CCenteredCell``, ``BodyCenteredCell`` (I), ``FaceCenteredCell`` (F), ``RhombohedralCell`` (R) or ``RhombohedralCellOnHexagonalAxes`` ("H"). * Unique axis, one of ``UniqueAxisA``, ``UniqueAxisB``, ``UniqueAxisC``, ``NoUniqueAxis`` (for lattice types that do not have a unique axis, e.g. cubic), or ``UnknownUniqueAxis`` (which should be avoided, but is sometimes necessary). * Cell axis lengths a,b,c, in Angstroms. * Cell angles α,β,γ, in degrees. For many cases, you don't need to specify every parameter. Where possible, the unique axis will be determined from the cell parameters, and can be omitted:: cell = UnitCell(MonoclinicLattice, PrimitiveCell, 123, 45, 80, 90, 97, 90) Cell axis lengths, angles and centering types can be omitted if they are fixed by the lattice type. For example:: julia> UnitCell(CubicLattice, FaceCenteredCell, 40) UnitCell(CubicLattice, FaceCenteredCell, NoUniqueAxis, 40.0 Å, 40.0 Å, 40.0 Å, 90.0°, 90.0°, 90.0°) or:: julia> UnitCell(RhombohedralLattice, 23, 75) UnitCell(RhombohedralLattice, RhombohedralCell, NoUniqueAxis, 23.0 Å, 23.0 Å, 23.0 Å, 75.0°, 75.0°, 75.0°) Reflection lists ================ A ``RefList`` is a container for reflection data. In Julia, a distinction is made between merged and unmerged reflections. Merged reflections have multiplicities (number of contributing measurements), whereas unmerged reflections have detector locations, background levels and parameters related to diffraction geometry such as excitation errors and Lorentz factors. No such distinction exists in CrystFEL's C API, and in "reality", both types of reflection have all fields. The distinction controls how the objects are printed, and may help in writing clearer programs. Load a reflection list from a data file (".hkl file") using ``loadreflist``:: julia> q = loadreflist("example.hkl") Merged reflection list in point group mmm h k l intensity σ(intens) nmeas 0 0 5 23.45 124.51 11 0 0 6 32302.69 10091.34 8 0 0 7 -87.37 167.23 5 0 0 8 8051.75 3828.24 6 0 0 9 94.13 128.59 3 0 0 10 3703.07 1118.85 5 0 0 11 4.81 31.46 5 0 0 12 27287.94 14143.77 6 0 0 13 148.50 32.46 2 0 0 14 818.33 447.23 3 ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ This produces a merged reflection list:: julia> typeof(q) RefList{MergedReflection} Unmerged reflection lists (``RefList{UnmergedReflection}``) come from spot prediction - see below. Reflection lists can be iterated over. For example:: julia> for refl in q println(refl) end MergedReflection((0, 0, 5), intensity=23.450000762939453, σ(intensity)=124.51000213623047, nmeasurements=11) MergedReflection((0, 0, 6), intensity=32302.689453125, σ(intensity)=10091.33984375, nmeasurements=8) MergedReflection((0, 0, 7), intensity=-87.37000274658203, σ(intensity)=167.22999572753906, nmeasurements=5) MergedReflection((0, 0, 8), intensity=8051.75, σ(intensity)=3828.239990234375, nmeasurements=6) MergedReflection((0, 0, 9), intensity=94.12999725341797, σ(intensity)=128.58999633789062, nmeasurements=3) MergedReflection((0, 0, 10), intensity=3703.070068359375, σ(intensity)=1118.8499755859375, nmeasurements=5) MergedReflection((0, 0, 11), intensity=4.809999942779541, σ(intensity)=31.459999084472656, nmeasurements=5) MergedReflection((0, 0, 12), intensity=27287.939453125, σ(intensity)=14143.76953125, nmeasurements=6) MergedReflection((0, 0, 13), intensity=148.5, σ(intensity)=32.459999084472656, nmeasurements=2) MergedReflection((0, 0, 14), intensity=818.3300170898438, σ(intensity)=447.2300109863281, nmeasurements=3) ... You can subscript a RefList using Miller indices:: julia> q[1, 13, 43] MergedReflection((1, 13, 43), intensity=-28.18000030517578, σ(intensity)=7.230000019073486, nmeasurements=6) Linear indexing is **not** supported, so you **can't** do things like ``q[10:end]``. Symmetry ======== Symmetry operations are represented by ``SymOp`` objects, which are contained within ``SymOpList`` objects. A point group is therefore represented by a ``SymOpList``, but note that not all ``SymOpList`` objects represent a symmetry group (in the sense of group theory). One counterexample is lists of indexing ambiguity operations. Create a point group from the Herman-Mauguin symbol as follows:: julia> s = SymOpList("2/m") 4-element SymOpList ("2/m") -h,-k,l h,k,-l hkl -h,-k,-l The list can be subscripted linearly:: julia> s[1] SymOp("-h,-k,l") Images and DataTemplates ======================== A ``DataTemplate`` represents the contents of a CrystFEL geometry file, which describes the layout of information in the data, the physical positions of parts of the detector, and the values of various items of metadata (or information about where to get those values). Create a ``DataTemplate`` by loading a geometry file:: dtempl = loaddatatemplate("/path/to/my.geom") An ``Image`` is an overall container structure representing one frame of a serial crystallography dataset. Create one by loading an image from file:: image = Image(dtempl, "/path/to/mydata.cxi", "//32") You can use any kind of file supported by CrystFEL here. In the example, ``//32`` is the frame ID - leave it out if there is only one frame per file. If you're simulating data, you can create an empty image like this:: image = Image(dtempl) However, several caveats apply to doing this. The ``DataTemplate`` must not say that any metadata values (e.g. the wavelength) should be taken from file headers, because there is no file in this case. An error will be thrown if there is any problem. Peak lists ========== A ``PeakList`` represents a list of positions on the detector surface. Create it and add peaks like this:: peaklist = PeakList() push!(peaklist, 10.0, 20.0, 1, 2000.0) The arguments to ``push!(::PeakList, ...)`` are, in order, the fast scan coordinate, slow scan coordinate (both relative to the panel corner), panel number (indexed from zero) and the spot intensity in detector units. You can assign your peaklist to an ``Image`` by setting ``image.peaklist``. Note that any ``PeakList`` can only be assigned to a single ``Image``. An error will be thrown if you try to add the same ``PeakList`` again (even to the same ``Image``). If necessary, you can make a copy using ``deepcopy``. Crystals ======== Indexing ======== Prediction ==========